Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 2 of 147
Found at i:229887 original size:11 final size:11
Alignment explanation
Indices: 229852--229905 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
229842 TGTAATCAAT
229852 ATAACTTAATA
1 ATAACTTAATA
* *
229863 TTAA-TTATTA
1 ATAACTTAATA
229873 ATAACTTAATA
1 ATAACTTAATA
* *
229884 ATAAATTAGTA
1 ATAACTTAATA
*
229895 ATAATTTAATA
1 ATAACTTAATA
229906 GTAAATAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
10 8 0.24
11 26 0.76
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (11 bp):
ATAACTTAATA
Found at i:229982 original size:22 final size:22
Alignment explanation
Indices: 229957--230026 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
229947 AGTAAATTAG
*
229957 TAATAATACAATAATAAATGCA
1 TAATAATATAATAATAAATGCA
* * *
229979 TAATACTTTTATAATAAAT-CAA
1 TAATAATATAATAATAAATGC-A
* *
230001 TTATAATATAATTATAAATGCA
1 TAATAATATAATAATAAATGCA
230023 TAAT
1 TAAT
230027 CGCACAGTAT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (22 bp):
TAATAATATAATAATAAATGCA
Found at i:230204 original size:22 final size:22
Alignment explanation
Indices: 230154--230254 Score: 98
Period size: 21 Copynumber: 4.7 Consensus size: 22
230144 ATTCATTGAA
*
230154 AACTTAAAAGTAAATCAAT-AT
1 AACTTAATAGTAAATCAATAAT
*
230175 AACTTAATAGTAAATCATTAAT
1 AACTTAATAGTAAATCAATAAT
* ** *
230197 AACATAATAGTTCATCAATGAT
1 AACTTAATAGTAAATCAATAAT
* *
230219 AATTTAATA-TAAATCAGTAAT
1 AACTTAATAGTAAATCAATAAT
* *
230240 AACTTGATAATAAAT
1 AACTTAATAGTAAAT
230255 TATAGATAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 3
0.78 0.19 0.04
Matches are distributed among these distances:
21 32 0.51
22 31 0.49
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (22 bp):
AACTTAATAGTAAATCAATAAT
Found at i:230274 original size:22 final size:22
Alignment explanation
Indices: 230215--230298 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
230205 AGTTCATCAA
* *
230215 TGATAATTTAAT-ATAAATCAG
1 TGATAATTTAGTAATAAATTAG
* *
230236 TAATAACTT-GATAATAAATTA-
1 TGATAATTTAG-TAATAAATTAG
*
230257 TAGATAATTTAGTGATAAATTAG
1 T-GATAATTTAGTAATAAATTAG
*
230280 TGATAATTTTGTAATAAAT
1 TGATAATTTAGTAATAAAT
230299 AATTAAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
21 9 0.18
22 38 0.78
23 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.40
Consensus pattern (22 bp):
TGATAATTTAGTAATAAATTAG
Found at i:230295 original size:44 final size:43
Alignment explanation
Indices: 230216--230298 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
230206 GTTCATCAAT
230216 GATAATTTAATATAAATCAGTAATAACTTGATAATAAATTATA
1 GATAATTTAATATAAATCAGTAATAACTTGATAATAAATTATA
* * * *
230259 GATAATTTAGTGATAAATTAGTGATAATTTTG-TAATAAAT
1 GATAATTTAAT-ATAAATCAGTAATAA-CTTGATAATAAAT
230299 AATTAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 10 0.29
44 21 0.62
45 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (43 bp):
GATAATTTAATATAAATCAGTAATAACTTGATAATAAATTATA
Found at i:230382 original size:22 final size:21
Alignment explanation
Indices: 230327--230386 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
230317 TAAGTTAATG
* *
230327 AAAATGTAATAATAAATATAT
1 AAAATATAATAGTAAATATAT
230348 AAAATATAATAGTAAATA-ATT
1 AAAATATAATAGTAAATATA-T
*
230369 AAAATTTTAATAGTAAAT
1 AAAA-TATAATAGTAAAT
230387 TAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 21 0.62
22 12 0.35
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAATATAATAGTAAATATAT
Found at i:230389 original size:19 final size:19
Alignment explanation
Indices: 230365--230412 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
230355 AATAGTAAAT
230365 AATTAA-AATTTTAATAGTA
1 AATTAATAA-TTTAATAGTA
*
230384 AATTAATAATTTAGTAGTA
1 AATTAATAATTTAATAGTA
*
230403 AATTATTAAT
1 AATTAATAAT
230413 AATGCAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
AATTAATAATTTAATAGTA
Found at i:230413 original size:22 final size:21
Alignment explanation
Indices: 230333--230415 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 21
230323 AATGAAAATG
* *
230333 TAATAATAAATATATAA-AATA
1 TAATAGTAAATAT-TAATAATT
230354 TAATAGTAAATAATTAA-AATTT
1 TAATAGTAAAT-ATTAATAA-TT
230376 TAATAGT-AA-ATTAATAATT
1 TAATAGTAAATATTAATAATT
*
230395 TAGTAGTAAATTATTAATAAT
1 TAATAGTAAA-TATTAATAAT
230416 GCAATTCTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
19 13 0.25
20 4 0.08
21 17 0.32
22 19 0.36
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TAATAGTAAATATTAATAATT
Found at i:230567 original size:22 final size:22
Alignment explanation
Indices: 230541--230605 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
230531 TAACTTTATA
*
230541 TAAATCTTCAATAATTTAGTGG
1 TAAATCTTCAATAATTTAATGG
**
230563 TAAATCACCAATAATTTAATGG
1 TAAATCTTCAATAATTTAATGG
*
230585 TAAATCATTC-ATAACTTAATG
1 TAAATC-TTCAATAATTTAATG
230606 ACAAATCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (22 bp):
TAAATCTTCAATAATTTAATGG
Found at i:231092 original size:22 final size:22
Alignment explanation
Indices: 231000--231198 Score: 106
Period size: 22 Copynumber: 8.9 Consensus size: 22
230990 TAAATTAGTG
*
231000 ATAACTTAATAGAAAATCAATT
1 ATAACTTAATAGTAAATCAATT
* *
231022 -TCAATTTAATAGT-AATTAATT
1 AT-AACTTAATAGTAAATCAATT
*
231043 GATAAACTTAATAGTAAATC-ATAA
1 -AT-AACTTAATAGTAAATCAAT-T
231067 ATAACTT-ATAGTAAAATCAATT
1 ATAACTTAATAGT-AAATCAATT
* * * *
231089 ATAATTTAGTAGTTAATC-GTT
1 ATAACTTAATAGTAAATCAATT
* *
231110 GAAAACTTAAAAGTAAATCAA-T
1 -ATAACTTAATAGTAAATCAATT
* * *
231132 AAAAATTAGTAGTAATTAATC-ATT
1 ATAACTTAATAGT-A--AATCAATT
* * *
231156 AATAATTTAATAGTTAATCAATA
1 -ATAACTTAATAGTAAATCAATT
231179 ATAACTTAAATAGTAAATCA
1 ATAACTT-AATAGTAAATCA
231199 TGAATAATTT
Statistics
Matches: 132, Mismatches: 28, Indels: 33
0.68 0.15 0.17
Matches are distributed among these distances:
21 25 0.19
22 54 0.41
23 35 0.27
24 8 0.06
25 10 0.08
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCAATT
Found at i:231185 original size:68 final size:67
Alignment explanation
Indices: 231000--231198 Score: 198
Period size: 67 Copynumber: 2.9 Consensus size: 67
230990 TAAATTAGTG
* * *
231000 ATAACTTAATAG-AAAATCAATT-TCAATTTAATAG-TAATTAATTGATAAACTTAATAGTAAAT
1 ATAACTT-ATAGTAAAATCAATTAT-AATTTAATAGTTAATCAA-TAAT-AACTTAAAAGTAAAT
231062 C-ATAA
62 CAATAA
* **
231067 ATAACTTATAGTAAAATCAATTATAATTTAGTAGTTAATCGTTGAA-AACTTAAAAGTAAATCAA
1 ATAACTTATAGTAAAATCAATTATAATTTAATAGTTAATCAAT-AATAACTTAAAAGTAAATCAA
231131 TAA
65 TAA
231134 A-AA-TTAGTAGTAATTAATC-ATTAATAATTTAATAGTTAATCAATAATAACTTAAATAGTAAA
1 ATAACTTA-TAGTAA--AATCAATT-ATAATTTAATAGTTAATCAATAATAACTTAAA-AGTAAA
231196 TCA
61 TCA
231199 TGAATAATTT
Statistics
Matches: 112, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
65 3 0.03
66 27 0.24
67 37 0.33
68 36 0.32
69 9 0.08
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (67 bp):
ATAACTTATAGTAAAATCAATTATAATTTAATAGTTAATCAATAATAACTTAAAAGTAAATCAAT
AA
Found at i:231371 original size:44 final size:44
Alignment explanation
Indices: 231317--231423 Score: 121
Period size: 44 Copynumber: 2.4 Consensus size: 44
231307 AATGATAACA
* *
231317 TAGTAATAAA-TATATAATAAT-ATAATAGTAAATTATTAATAATT
1 TAGTAGTAAATTAT-TAAT-ATCATAATAGTAAATTACTAATAATT
* *
231361 TAG-ATGTAAATTATTGATATCTTAATAGTAAATTACTAATAATT
1 TAGTA-GTAAATTATTAATATCATAATAGTAAATTACTAATAATT
231405 TAGTAGTAAATTAGTTAAT
1 TAGTAGTAAATTA-TTAAT
231424 CATTGATAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
43 3 0.06
44 42 0.79
45 8 0.15
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (44 bp):
TAGTAGTAAATTATTAATATCATAATAGTAAATTACTAATAATT
Found at i:231411 original size:22 final size:22
Alignment explanation
Indices: 231317--231423 Score: 103
Period size: 22 Copynumber: 4.8 Consensus size: 22
231307 AATGATAACA
* *
231317 TAGTAATAAA-TATATAATAATA
1 TAGTAGTAAATTAT-TAATAATT
*
231339 TAATAGTAAATTATTAATAATT
1 TAGTAGTAAATTATTAATAATT
*
231361 TAG-ATGTAAATTATTGAT-ATCT
1 TAGTA-GTAAATTATTAATAAT-T
* *
231383 TAATAGTAAATTACTAATAATT
1 TAGTAGTAAATTATTAATAATT
231405 TAGTAGTAAATTAGTTAAT
1 TAGTAGTAAATTA-TTAAT
231424 CATTGATAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
21 3 0.04
22 56 0.81
23 10 0.14
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (22 bp):
TAGTAGTAAATTATTAATAATT
Found at i:231465 original size:22 final size:22
Alignment explanation
Indices: 231416--231620 Score: 125
Period size: 22 Copynumber: 9.4 Consensus size: 22
231406 AGTAGTAAAT
* *
231416 TAGTTAATCATTGATAATTT-A
1 TAGTAAATCATCGATAATTTAA
* *
231437 TAATAAATCATCGATAAATTAA
1 TAGTAAATCATCGATAATTTAA
* *
231459 TAGTAAATCAGT-TATAATTTTA
1 TAGTAAATCA-TCGATAATTTAA
** * * *
231481 TAACAAATTATCGATAACTTAG
1 TAGTAAATCATCGATAATTTAA
*
231503 TAGTAAATCATCAATAATTTAA
1 TAGTAAATCATCGATAATTTAA
*
231525 TAGTAAATCAATC-ATAACTTAGA
1 TAGTAAATC-ATCGATAATTTA-A
* *
231548 -AGTAAATTAAT--ACTAATTTAG
1 TAGTAAA-TCATCGA-TAATTTAA
* *
231569 TAGTAAATCATTGATAATTTAG
1 TAGTAAATCATCGATAATTTAA
* * * **
231591 CAGTATATCATTGATAGCTTAA
1 TAGTAAATCATCGATAATTTAA
231613 TAGTAAAT
1 TAGTAAAT
231621 TGTTAATAAC
Statistics
Matches: 141, Mismatches: 33, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
21 21 0.15
22 113 0.80
23 7 0.05
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (22 bp):
TAGTAAATCATCGATAATTTAA
Found at i:231542 original size:44 final size:44
Alignment explanation
Indices: 231429--231620 Score: 142
Period size: 44 Copynumber: 4.4 Consensus size: 44
231419 TTAATCATTG
* * * *
231429 ATAATTT-ATAATAAATC-ATCGATAAATTAATAGTAAATCAGTT
1 ATAATTTAATAGTAAATCAATCGATAACTTAGTAGTAAATCA-TA
* ** *
231472 ATAATTTTATAACAAAT-TATCGATAACTTAGTAGTAAATCATCA
1 ATAATTTAATAGTAAATCAATCGATAACTTAGTAGTAAATCAT-A
* *
231516 ATAATTTAATAGTAAATCAATC-ATAACTTAGAAGTAAATTAATA
1 ATAATTTAATAGTAAATCAATCGATAACTTAGTAGTAAA-TCATA
* * * * * * *
231560 CTAATTTAGTAGTAAATC-ATTGATAATTTAGCAGTATATCATTG
1 ATAATTTAATAGTAAATCAATCGATAACTTAGTAGTAAATCA-TA
**
231604 ATAGCTTAATAGTAAAT
1 ATAATTTAATAGTAAAT
231621 TGTTAATAAC
Statistics
Matches: 120, Mismatches: 22, Indels: 13
0.77 0.14 0.08
Matches are distributed among these distances:
43 12 0.10
44 102 0.85
45 6 0.05
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (44 bp):
ATAATTTAATAGTAAATCAATCGATAACTTAGTAGTAAATCATA
Found at i:231555 original size:66 final size:66
Alignment explanation
Indices: 231440--231589 Score: 171
Period size: 66 Copynumber: 2.3 Consensus size: 66
231430 TAATTTATAA
* * * * *
231440 TAAATCATCGATAAATTAATAGTAAATCAGTTATAATTTTATAACAAATT-AT-CGATAACTTAG
1 TAAATCATCGATAATTTAATAGTAAATCAATCATAATCTTAGAACAAATTAATAC--TAACTTAG
231503 TAG
64 TAG
* * *
231506 TAAATCATCAATAATTTAATAGTAAATCAATCATAA-CTTAGAAGTAAATTAATACTAATTTAGT
1 TAAATCATCGATAATTTAATAGTAAATCAATCATAATCTTAGAA-CAAATTAATACTAACTTAGT
231570 AG
65 AG
*
231572 TAAATCATTGATAATTTA
1 TAAATCATCGATAATTTA
231590 GCAGTATATC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 5 0.07
66 63 0.89
67 2 0.03
68 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (66 bp):
TAAATCATCGATAATTTAATAGTAAATCAATCATAATCTTAGAACAAATTAATACTAACTTAGTA
G
Found at i:231651 original size:22 final size:22
Alignment explanation
Indices: 231610--231657 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
231600 ATTGATAGCT
**
231610 TAATAGTAAATTGTTAATAACA
1 TAATAGTAAATTAATAATAACA
* *
231632 TAATAGTAAATTAATGATAACT
1 TAATAGTAAATTAATAATAACA
231654 TAAT
1 TAAT
231658 CGTCAATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (22 bp):
TAATAGTAAATTAATAATAACA
Found at i:231969 original size:31 final size:31
Alignment explanation
Indices: 231920--232001 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
231910 AACATAAATT
*
231920 TTATTAATAATTATCAAAAGTATATCATA-AG-
1 TTATTAAAAATTA-CAAAAGTATATCA-AGAGA
*
231951 TTATTAAAAAATTACAAAAATTATATCAAGAGA
1 TTATT-AAAAATTAC-AAAAGTATATCAAGAGA
*
231984 TTATTAAAATTTACAAAA
1 TTATTAAAAATTACAAAA
232002 AATTATTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
31 11 0.25
32 28 0.64
33 5 0.11
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (31 bp):
TTATTAAAAATTACAAAAGTATATCAAGAGA
Found at i:231976 original size:32 final size:33
Alignment explanation
Indices: 231935--232007 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 33
231925 AATAATTATC
*
231935 AAAAGTATATCATA-AG-TTATTAAAAAATTAC-A
1 AAAATTATATCA-AGAGATTATT-AAAAATTACAA
*
231967 AAAATTATATCAAGAGATTATTAAAATTTACAA
1 AAAATTATATCAAGAGATTATTAAAAATTACAA
232000 AAAATTAT
1 AAAATTAT
232008 TAAAATTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 1 0.03
32 21 0.58
33 14 0.39
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (33 bp):
AAAATTATATCAAGAGATTATTAAAAATTACAA
Found at i:232065 original size:15 final size:17
Alignment explanation
Indices: 232038--232070 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
232028 CAAAAATTTT
232038 ATCAAACATTATA-AAA
1 ATCAAACATTATATAAA
232054 ATCAAA-ATTATATAAA
1 ATCAAACATTATATAAA
232070 A
1 A
232071 AGTTATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
ATCAAACATTATATAAA
Found at i:233023 original size:2 final size:2
Alignment explanation
Indices: 233018--233048 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
233008 TTTTATAAAC
*
233018 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
233049 CACACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:236284 original size:43 final size:43
Alignment explanation
Indices: 236153--236384 Score: 249
Period size: 43 Copynumber: 5.4 Consensus size: 43
236143 GCAAAGGCTC
* *
236153 ACAACTTTTGAAAAAAAAATAAAGCTC-TCATAATCAGAGACTAA
1 ACAAC-TTTGAAAAATAAATAAAGCTCATC-TAATCAGAGGCTAA
* * * *
236197 A-ACACTTTTGAAAAAT--A-AAGGCTCCTCTAAACAGAGGCTTA
1 ACA-AC-TTTGAAAAATAAATAAAGCTCATCTAATCAGAGGCTAA
*
236238 ACAACTTTGAAAAATAAATAAAGCTCATCTAATTAGAGGCTAA
1 ACAACTTTGAAAAATAAATAAAGCTCATCTAATCAGAGGCTAA
* *
236281 ACAACTTTGAAAAATAAATAAAGCTCCTCTAATCAGAGGCTTA
1 ACAACTTTGAAAAATAAATAAAGCTCATCTAATCAGAGGCTAA
* * * * *
236324 ACAACTTTAAAAAATAAATAAAGCTTATCTAAACAGAGACTCA
1 ACAACTTTGAAAAATAAATAAAGCTCATCTAATCAGAGGCTAA
* *
236367 ACAACTTTTAAGAATAAA
1 ACAACTTTGAAAAATAAA
236385 AGCTCCTCTA
Statistics
Matches: 161, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
40 10 0.06
41 20 0.12
42 5 0.03
43 113 0.70
44 13 0.08
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (43 bp):
ACAACTTTGAAAAATAAATAAAGCTCATCTAATCAGAGGCTAA
Found at i:236337 original size:86 final size:83
Alignment explanation
Indices: 236153--236419 Score: 326
Period size: 86 Copynumber: 3.2 Consensus size: 83
236143 GCAAAGGCTC
236153 ACAACTTTTGAAAAAA-AAATAAAGCTC-TCATAATCAGAGACTAAA-ACACTTTTGAAAAATAA
1 ACAAC-TTT-AAAAAATAAATAAAGCTCATC-TAATCAGAGACTAAACA-AC-TTTGAAAAATAA
*
236215 AGGCTCCTCTAAACAGAGGCTTA
61 AAGCTCCTCTAAACAGAGGCTTA
* * *
236238 ACAACTTTGAAAAATAAATAAAGCTCATCTAATTAGAGGCTAAACAACTTTGAAAAATAAATAAA
1 ACAACTTTAAAAAATAAATAAAGCTCATCTAATCAGAGACTAAACAACTTTGAAAAAT--A-AAA
*
236303 GCTCCTCTAATCAGAGGCTTA
63 GCTCCTCTAAACAGAGGCTTA
* * * * *
236324 ACAACTTTAAAAAATAAATAAAGCTTATCTAAACAGAGACTCAACAACTTTTAAGAATAAAAGCT
1 ACAACTTTAAAAAATAAATAAAGCTCATCTAATCAGAGACTAAACAACTTTGAAAAATAAAAGCT
236389 CCTCTAAACAGAGG-TTCA
66 CCTCTAAACAGAGGCTT-A
*
236407 ATAACTTTAAAAA
1 ACAACTTTAAAAA
236420 TTTAAAACTC
Statistics
Matches: 160, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
82 2 0.01
83 47 0.29
84 30 0.19
85 9 0.06
86 72 0.45
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (83 bp):
ACAACTTTAAAAAATAAATAAAGCTCATCTAATCAGAGACTAAACAACTTTGAAAAATAAAAGCT
CCTCTAAACAGAGGCTTA
Found at i:236431 original size:40 final size:41
Alignment explanation
Indices: 236153--236420 Score: 206
Period size: 43 Copynumber: 6.4 Consensus size: 41
236143 GCAAAGGCTC
* * **
236153 ACAACTTTTGAAAAAAAAATAAAGCT-CTCATAATCAGAGACTA
1 ACAAC-TTTG-AAAAATAATAAAGCTCCTC-TAAACAGAGGTTA
* *
236196 AAACACTTTTGAAAAAT-A-AAGGCTCCTCTAAACAGAGGCTTA
1 ACA-AC-TTTGAAAAATAATAAAGCTCCTCTAAACAGAGG-TTA
* ** *
236238 ACAACTTTGAAAAATAAATAAAGCTCATCTAATTAGAGGCTAA
1 ACAACTTTGAAAAAT-AATAAAGCTCCTCTAAACAGAGG-TTA
*
236281 ACAACTTTGAAAAATAAATAAAGCTCCTCTAATCAGAGGCTTA
1 ACAACTTTGAAAAAT-AATAAAGCTCCTCTAAACAGAGG-TTA
* ** * *
236324 ACAACTTTAAAAAATAAATAAAGCTTATCTAAACAGAGACTCA
1 ACAACTTTGAAAAAT-AATAAAGCTCCTCTAAACAGAG-GTTA
* *
236367 ACAACTTTTAAGAAT-A-AAAGCTCCTCTAAACAGAGGTTCA
1 ACAACTTTGAAAAATAATAAAGCTCCTCTAAACAGAGGTT-A
*
236407 ATAACTTT-AAAAAT
1 ACAACTTTGAAAAAT
236421 TTAAAACTCC
Statistics
Matches: 188, Mismatches: 29, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
39 6 0.03
40 35 0.19
41 16 0.09
42 9 0.05
43 115 0.61
44 7 0.04
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (41 bp):
ACAACTTTGAAAAATAATAAAGCTCCTCTAAACAGAGGTTA
Found at i:236951 original size:21 final size:21
Alignment explanation
Indices: 236923--237305 Score: 444
Period size: 21 Copynumber: 17.9 Consensus size: 21
236913 GTTTCCAATA
236923 TCAAAGATTCTCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAC
*
236944 TTAAAGATTCTCATTTGCAAAC
1 TCAAAGATTCTCATTTG-AAAC
*
236966 -CGTAAAGATTCTCATTTAAAAAC
1 TC--AAAGATTCTCATTT-GAAAC
*
236989 TCAAAGATTCTCATTTAAAAAC
1 TCAAAGATTCTCATTT-GAAAC
*
237011 TCAATGATTCTCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAC
* *
237032 TTAAAGATTATCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAC
* * *
237053 TCAATGATTCTCACTTAAAAC
1 TCAAAGATTCTCATTTGAAAC
* * **
237074 TCAAATATTTTCATTAAAAAAC
1 TCAAAGATTCTCATT-TGAAAC
237096 TCAAAGATTCTCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAC
237117 TCAAAGATTCTCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAC
* * *
237138 TTAAATATTTTCATTTGAAAAC
1 TCAAAGATTCTCATTTG-AAAC
*
237160 TCAAAGGTTCTCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAC
* *
237181 TCAAAGATTTTCATTTGAAAT
1 TCAAAGATTCTCATTTGAAAC
** * *
237202 TTTAAGATTCTTATTTGAACC
1 TCAAAGATTCTCATTTGAAAC
* *
237223 TCAAAGATTCTTATTTGAACC
1 TCAAAGATTCTCATTTGAAAC
237244 TCAAAGATTCTCATTTGAAAAC
1 TCAAAGATTCTCATTTG-AAAC
*
237266 TCAAAGATTCTTATTTGAAAAC
1 TCAAAGATTCTCATTTG-AAAC
237288 TCAAAGATTCTCATTTGA
1 TCAAAGATTCTCATTTGA
237306 GGATTCACAA
Statistics
Matches: 310, Mismatches: 44, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
21 177 0.57
22 114 0.37
23 18 0.06
24 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (21 bp):
TCAAAGATTCTCATTTGAAAC
Found at i:237071 original size:64 final size:65
Alignment explanation
Indices: 236923--237305 Score: 433
Period size: 64 Copynumber: 6.0 Consensus size: 65
236913 GTTTCCAATA
* * * *
236923 TCAAAGATTCTCATTTG-AAACTTAAAGATTCTCATTTGCAAAC-CGTAAAGATTCTCATTTAAA
1 TCAAAGATTCTCATTTGAAAACTCAATGATTCTCATTTGAAAACTC--AAAGATTCTCATTT-GA
236986 AAC
63 AAC
* * *
236989 TCAAAGATTCTCATTTAAAAACTCAATGATTCTCATTTG-AAACTTAAAGATTATCATTTGAAAC
1 TCAAAGATTCTCATTTGAAAACTCAATGATTCTCATTTGAAAACTCAAAGATTCTCATTTGAAAC
* * * **
237053 TCAATGATTCTCACTT-AAAACTCAAAT-ATTTTCATTAAAAAACTCAAAGATTCTCATTTGAAA
1 TCAAAGATTCTCATTTGAAAACTC-AATGATTCTCATTTGAAAACTCAAAGATTCTCATTTGAAA
237116 C
65 C
* * *
237117 TCAAAGATTCTCATTTG-AAACTTAAAT-ATTTTCATTTGAAAACTCAAAGGTTCTCATTTGAAA
1 TCAAAGATTCTCATTTGAAAAC-TCAATGATTCTCATTTGAAAACTCAAAGATTCTCATTTGAAA
237180 C
65 C
* ** * * * * *
237181 TCAAAGATTTTCATTTGAAATTTTAA-GATTCTTATTTG-AACCTCAAAGATTCTTATTTGAACC
1 TCAAAGATTCTCATTTGAAAACTCAATGATTCTCATTTGAAAACTCAAAGATTCTCATTTGAAAC
* *
237244 TCAAAGATTCTCATTTGAAAACTCAAAGATTCTTATTTGAAAACTCAAAGATTCTCATTTGA
1 TCAAAGATTCTCATTTGAAAACTCAATGATTCTCATTTGAAAACTCAAAGATTCTCATTTGA
237306 GGATTCACAA
Statistics
Matches: 272, Mismatches: 35, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
63 58 0.21
64 139 0.51
65 36 0.13
66 20 0.07
67 19 0.07
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (65 bp):
TCAAAGATTCTCATTTGAAAACTCAATGATTCTCATTTGAAAACTCAAAGATTCTCATTTGAAAC
Found at i:237107 original size:85 final size:86
Alignment explanation
Indices: 236923--237305 Score: 477
Period size: 85 Copynumber: 4.5 Consensus size: 86
236913 GTTTCCAATA
236923 TCAAAGATTCTCATTTGAAACTTAAAGATTCTCATTTGCAAAC-CGTAAAGATTCTCATTTAAAA
1 TCAAAGATTCTCATTTGAAACTTAAAGATTCTCATTTG-AAACTC--AAAGATTCTCATTTAAAA
236987 ACTCAAAGATTCTCATTTAAAAAC
63 ACTCAAAGATTCTCATTTAAAAAC
* * * *
237011 TCAATGATTCTCATTTGAAACTTAAAGATTATCATTTGAAACTCAATGATTCTCACTT-AAAACT
1 TCAAAGATTCTCATTTGAAACTTAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAAAACT
* * *
237075 CAAATATTTTCATTAAAAAAC
66 CAAAGATTCTCATTTAAAAAC
* * * * *
237096 TCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAAACTTAAATATTTTCATTTGAAAACT
1 TCAAAGATTCTCATTTGAAACTTAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAAAACT
* *
237161 CAAAGGTTCTCATTT-GAAAC
66 CAAAGATTCTCATTTAAAAAC
* * * * * * * *
237181 TCAAAGATTTTCATTTGAAATTTTAAGATTCTTATTTGAACCTCAAAGATTCTTATTT-GAACCT
1 TCAAAGATTCTCATTTGAAACTTAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAAAACT
*
237245 CAAAGATTCTCATTTGAAAAC
66 CAAAGATTCTCATTTAAAAAC
* *
237266 TCAAAGATTCTTATTTGAAAACTCAAAGATTCTCATTTGA
1 TCAAAGATTCTCATTTG-AAACTTAAAGATTCTCATTTGA
237306 GGATTCACAA
Statistics
Matches: 251, Mismatches: 40, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
84 18 0.07
85 145 0.58
86 47 0.19
87 4 0.02
88 37 0.15
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (86 bp):
TCAAAGATTCTCATTTGAAACTTAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAAAACT
CAAAGATTCTCATTTAAAAAC
Found at i:238393 original size:15 final size:16
Alignment explanation
Indices: 238375--238404 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
238365 TTCTTTTCTC
238375 TTATTTTCA-TCTTTT
1 TTATTTTCATTCTTTT
238390 TTATTTTCATTCTTT
1 TTATTTTCATTCTTT
238405 CATTTTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTCATTCTTTT
Found at i:238421 original size:17 final size:16
Alignment explanation
Indices: 238399--238479 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 16
238389 TTTATTTTCA
238399 TTCTTTCATTTTCTATT
1 TTCTTTCATTTT-TATT
*
238416 TTCTTT--TTTTTCTT
1 TTCTTTCATTTTTATT
238430 TT-TTTCATTTTT-TT
1 TTCTTTCATTTTTATT
* * *
238444 CTCTTTCCTTTTTTCCTT
1 TTCTTT-CATTTTT-ATT
* *
238462 TTTTTTTATTTTTATT
1 TTCTTTCATTTTTATT
238478 TT
1 TT
238480 TTCATCCATT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
13 3 0.06
14 8 0.16
15 12 0.24
16 10 0.20
17 11 0.22
18 6 0.12
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTCATTTTTATT
Found at i:238425 original size:8 final size:8
Alignment explanation
Indices: 238414--238481 Score: 59
Period size: 8 Copynumber: 8.4 Consensus size: 8
238404 TCATTTTCTA
238414 TTTTCTTTT
1 TTTTC-TTT
238423 TTTTCTTT
1 TTTTCTTT
238431 TTTTCATTT
1 TTTTC-TTT
*
238440 TTTTC-TC
1 TTTTCTTT
*
238447 TTTCCTTT
1 TTTTCTTT
*
238455 TTTCCTTT
1 TTTTCTTT
238463 TTTT-TTAT
1 TTTTCTT-T
*
238471 TTTTATTT
1 TTTTCTTT
238479 TTT
1 TTT
238482 CATCCATTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
7 7 0.14
8 29 0.57
9 15 0.29
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTT
Found at i:238428 original size:9 final size:9
Alignment explanation
Indices: 238414--238481 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
238404 TCATTTTCTA
238414 TTTTCTTTT
1 TTTTCTTTT
238423 TTTTC-TTT
1 TTTTCTTTT
238431 TTTTCATTTT
1 TTTTC-TTTT
238441 TTTCTCTTTCCTT
1 TTT-TC-TT--TT
*
238454 TTTTCCTTT
1 TTTTCTTTT
*
238463 TTTT-TTAT
1 TTTTCTTTT
*
238471 TTTTATTTT
1 TTTTCTTTT
238480 TT
1 TT
238482 CATCCATTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
8 14 0.29
9 16 0.33
10 6 0.12
11 5 0.10
12 2 0.04
13 5 0.10
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:238436 original size:30 final size:29
Alignment explanation
Indices: 238362--238440 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
238352 TCAATTTGAG
238362 TTTTTCTTTTCTCTT-ATTTTCATCTTTTTT
1 TTTTTCTTTT-T-TTCATTTTCATCTTTTTT
* * *
238392 ATTTTCATTCTTTCATTTTCTAT-TTTCTTT
1 TTTTTCTTTTTTTCATTTTC-ATCTTT-TTT
238422 TTTTTCTTTTTTTCATTTT
1 TTTTTCTTTTTTTCATTTT
238441 TTTCTCTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
28 2 0.05
29 10 0.25
30 28 0.70
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTTTCTTTTTTTCATTTTCATCTTTTTT
Found at i:238444 original size:33 final size:32
Alignment explanation
Indices: 238407--238474 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
238397 CATTCTTTCA
*
238407 TTTTCTATTTTCTTTTTT-TTCTTTTTTTCATTT
1 TTTTCTATTTCCTTTTTTCTT-TTTTTTT-ATTT
*
238440 TTTTCTCTTTCCTTTTTTCCTTTTTTTTTATTT
1 TTTTCTATTTCCTTTTTT-CTTTTTTTTTATTT
238473 TT
1 TT
238475 ATTTTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 22 0.71
34 7 0.23
35 2 0.06
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (32 bp):
TTTTCTATTTCCTTTTTTCTTTTTTTTTATTT
Found at i:242705 original size:9 final size:9
Alignment explanation
Indices: 242691--242719 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
242681 TCAACCAAAA
242691 TTTTATTTT
1 TTTTATTTT
242700 TTTTA-TTT
1 TTTTATTTT
242708 TTTTATTTT
1 TTTTATTTT
242717 TTT
1 TTT
242720 GATTGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTATTTT
Found at i:249219 original size:2 final size:2
Alignment explanation
Indices: 249212--249238 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
249202 TACAATCTAC
249212 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 T
249239 TAATAAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:251309 original size:27 final size:27
Alignment explanation
Indices: 251277--251328 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
251267 AATGATGATC
251277 CATTTTATCACATCAATGAAAAAGAGT
1 CATTTTATCACATCAATGAAAAAGAGT
*
251304 CATTTTATCATATCAATGAAAAAGA
1 CATTTTATCACATCAATGAAAAAGA
251329 AAATTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (27 bp):
CATTTTATCACATCAATGAAAAAGAGT
Found at i:255806 original size:14 final size:14
Alignment explanation
Indices: 255763--255805 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
255753 TTGATATTTC
255763 AATTTTTTCTTAAA
1 AATTTTTTCTTAAA
*
255777 TATTTTTTCTTAAA
1 AATTTTTTCTTAAA
*
255791 AATTTATTC-TAAA
1 AATTTTTTCTTAAA
255804 AA
1 AA
255806 AATTGATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTTTTCTTAAA
Found at i:256077 original size:21 final size:22
Alignment explanation
Indices: 256051--256092 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
256041 AAATTTGATA
*
256051 TTTCAATATTT-TCTTAAATAT
1 TTTCAACATTTATCTTAAATAT
256072 TTTCAACATTTATCTTAAATA
1 TTTCAACATTTATCTTAAATA
256093 AAATTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTCAACATTTATCTTAAATAT
Found at i:256200 original size:22 final size:21
Alignment explanation
Indices: 256166--256206 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
256156 AAAATTCACC
*
256166 CAAAAATAAAATAGAGAATTG
1 CAAAAATAAAATAAAGAATTG
*
256187 CAAAAATAGTAATAAAGAAT
1 CAAAAATA-AAATAAAGAAT
256207 ATAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20
Consensus pattern (21 bp):
CAAAAATAAAATAAAGAATTG
Found at i:258011 original size:67 final size:68
Alignment explanation
Indices: 257925--258053 Score: 174
Period size: 67 Copynumber: 1.9 Consensus size: 68
257915 GTAATTAAAC
* *
257925 TTTAAAAAGCTCCTCTAACTAAAGGCT-ATAATAC-TTGAAAAAAT-CTTCAAACCAGAAGCTAC
1 TTTAAAAAACTCCTATAACTAAAGG-TAATAATACTTTGAAAAAATCCTT-AAACCAGAAGCTAC
257987 AGTAT
64 AGTAT
* * *
257992 TTTAAAAAACTCCTATAACTAAAGGTAATAATACTTTTAAAAACTCCTTTAACCAGAAGCTA
1 TTTAAAAAACTCCTATAACTAAAGGTAATAATACTTTGAAAAAATCCTTAAACCAGAAGCTA
258054 TGATATTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
66 1 0.02
67 30 0.56
68 20 0.37
69 3 0.06
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.29
Consensus pattern (68 bp):
TTTAAAAAACTCCTATAACTAAAGGTAATAATACTTTGAAAAAATCCTTAAACCAGAAGCTACAG
TAT
Found at i:258067 original size:68 final size:67
Alignment explanation
Indices: 257928--258068 Score: 153
Period size: 68 Copynumber: 2.1 Consensus size: 67
257918 ATTAAACTTT
* *
257928 AAAAAGCTCCTCTAACTAAAGGCTATAATACTTGAAAAAATCTTCAAACCAGAAGCTACAGTATT
1 AAAAAACTCCTATAACTAAAGGCTATAATACTTGAAAAAATCTTCAAACCAGAAGCTACAGTATT
**
257993 TT
66 AA
* * * *
257995 AAAAAACTCCTATAACTAAAGG-TAATAATACTTTTAAAAACTCCTT-TAACCAGAAGCTA-TGA
1 AAAAAACTCCTATAACTAAAGGCT-ATAATAC-TTGAAAAAAT-CTTCAAACCAGAAGCTACAG-
258057 TATTAA
62 TATTAA
258063 AAAAAA
1 AAAAAA
258069 AAATCCTCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
66 1 0.02
67 28 0.45
68 30 0.48
69 3 0.05
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.27
Consensus pattern (67 bp):
AAAAAACTCCTATAACTAAAGGCTATAATACTTGAAAAAATCTTCAAACCAGAAGCTACAGTATT
AA
Found at i:258134 original size:31 final size:33
Alignment explanation
Indices: 258083--258162 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 33
258073 CCTCTAACGA
* * * *
258083 AAGGCTATGCCATTTTAAAAA-CTCATTTAACT
1 AAGGCTATGACACTTGAAAAATCTCATTCAACT
* *
258115 -AGGCTATGGCACTTGAAAAATCTCCTTCAACT
1 AAGGCTATGACACTTGAAAAATCTCATTCAACT
258147 AAAGGCTATGACACTT
1 -AAGGCTATGACACTT
258163 TAAATAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 17 0.44
32 9 0.23
34 13 0.33
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (33 bp):
AAGGCTATGACACTTGAAAAATCTCATTCAACT
Found at i:258322 original size:30 final size:31
Alignment explanation
Indices: 258252--258324 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
258242 TAGAGCTCTT
258252 AAACTTAAAAAACTCCTAACCAGAGGCAATG
1 AAACTTAAAAAACTCCTAACCAGAGGCAATG
* * *
258283 AAACTTAAAAAACTCTTAACTAGAGGCTATG
1 AAACTTAAAAAACTCCTAACCAGAGGCAATG
*
258314 ACAC-TAAAAAA
1 AAACTTAAAAAA
258325 TAAAAACTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 7 0.18
31 31 0.82
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (31 bp):
AAACTTAAAAAACTCCTAACCAGAGGCAATG
Found at i:258481 original size:43 final size:43
Alignment explanation
Indices: 258413--258495 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
258403 AGTTTTCATC
*
258413 TTTGAGATTCTCATCGAAAGCTCGAGATTCACACTAAAAGGTT
1 TTTGAGATTCACATCGAAAGCTCGAGATTCACACTAAAAGGTT
** * * *
258456 TTTGAGATTCACATCGAGGGTTCGAGATTTACATTAAAAG
1 TTTGAGATTCACATCGAAAGCTCGAGATTCACACTAAAAG
258496 TTTAAGATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (43 bp):
TTTGAGATTCACATCGAAAGCTCGAGATTCACACTAAAAGGTT
Found at i:258592 original size:65 final size:63
Alignment explanation
Indices: 258413--258593 Score: 161
Period size: 65 Copynumber: 2.8 Consensus size: 63
258403 AGTTTTCATC
* * * *
258413 TTTGAGATTCT-CATCGAAAGCTCGAGATTCACACTAAAAGGTTTTTGAGATTCACATCGAGGG
1 TTTGAGATT-TACATCGAAAGTTCAAGATTCACACCAAAAAGTTTTTGAGATTCACATCGAGGG
* ** * * * *
258476 TTCGAGATTTACATTAAAAGTTTAAGATTCACACC--AAAGTATTCTTAAGATTTATATCAAGAG
1 TTTGAGATTTACATCGAAAGTTCAAGATTCACACCAAAAAGT-TT-TTGAGATTCACATC--GAG
**
258539 TT
62 GG
* *
258541 TTTGAGATTTACATCGAAGGTTCAAAATTCACACCAAAAAGTTTTTGAGATTC
1 TTTGAGATTTACATCGAAAGTTCAAGATTCACACCAAAAAGTTTTTGAGATTC
258594 CCATTGAAGG
Statistics
Matches: 90, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
61 4 0.04
62 3 0.03
63 37 0.41
65 39 0.43
66 2 0.02
67 5 0.06
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (63 bp):
TTTGAGATTTACATCGAAAGTTCAAGATTCACACCAAAAAGTTTTTGAGATTCACATCGAGGG
Found at i:258736 original size:20 final size:21
Alignment explanation
Indices: 258711--258752 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
258701 ATTAAAGGTC
258711 TTTGATATTCATATC-AAAAG
1 TTTGATATTCATATCGAAAAG
*
258731 TTTGATCTTCATATCGAAAAG
1 TTTGATATTCATATCGAAAAG
258752 T
1 T
258753 CCTCAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTGATATTCATATCGAAAAG
Found at i:258894 original size:43 final size:43
Alignment explanation
Indices: 258845--258959 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
258835 AGTTCTGGAG
* * *
258845 ATTCACATTAAAGGTTAGGGATTCACACTAAAAGGTCATTGAA
1 ATTCACAATAAGGGTTAGGGATTCTCACTAAAAGGTCATTGAA
* *
258888 ATTCACAATAAGGGTTTA-GGATTCTCACCAAAAGGTCTTTGAA
1 ATTCACAATAAGGG-TTAGGGATTCTCACTAAAAGGTCATTGAA
* * *
258931 ATTCATAGTAAGGGTTTGGGATTCTCACT
1 ATTCACAATAAGGGTTAGGGATTCTCACT
258960 GAAGTTCAAG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 2 0.03
43 56 0.92
44 3 0.05
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (43 bp):
ATTCACAATAAGGGTTAGGGATTCTCACTAAAAGGTCATTGAA
Found at i:259048 original size:42 final size:44
Alignment explanation
Indices: 258991--259083 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 44
258981 AAAGTTCTTA
* * *
258991 AGATTCACATAAAAAG-TTATCTAGATTCACATC-AAAG-GTTCG
1 AGATTCACACAAAAAGATT-TCGAGATTCACATCGAAAGTCTTCG
* **
259033 AGATTCACACCAAAAGATTTCGAGATTTGCATCGAAAGTCTTCG
1 AGATTCACACAAAAAGATTTCGAGATTCACATCGAAAGTCTTCG
259077 AGATTCA
1 AGATTCA
259084 AATCAAAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 25 0.60
43 6 0.14
44 11 0.26
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (44 bp):
AGATTCACACAAAAAGATTTCGAGATTCACATCGAAAGTCTTCG
Found at i:259057 original size:22 final size:21
Alignment explanation
Indices: 258968--259090 Score: 95
Period size: 22 Copynumber: 5.7 Consensus size: 21
258958 CTGAAGTTCA
* **
258968 AGATTCACACTAAAAAGTTCTTA
1 AGATTCACA-TCAAAAGTT-TCG
* *
258991 AGATTCACATAAAAAGTTATCT
1 AGATTCACATCAAAAGTT-TCG
*
259013 AGATTCACATC-AAAGGTTCG
1 AGATTCACATCAAAAGTTTCG
*
259033 AGATTCACACCAAAAGATTTCG
1 AGATTCACATCAAAAG-TTTCG
** *
259055 AGATTTGCATCGAAAGTCTTCG
1 AGATTCACATCAAAAGT-TTCG
*
259077 AGATTCAAATCAAA
1 AGATTCACATCAAA
259091 GGTTCAAAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
20 12 0.15
21 10 0.12
22 50 0.62
23 9 0.11
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (21 bp):
AGATTCACATCAAAAGTTTCG
Found at i:259847 original size:6 final size:6
Alignment explanation
Indices: 259836--259871 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
259826 CTTTTTCTCT
259836 AATGCA AATGCA AATGCA ATTATGCA AATGCA AATG
1 AATGCA AATGCA AATGCA A--ATGCA AATGCA AATG
259872 TTTTTCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 22 0.79
8 6 0.21
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (6 bp):
AATGCA
Found at i:264163 original size:17 final size:17
Alignment explanation
Indices: 264143--264180 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
264133 TTCTTAAAGA
264143 ATTTAGAAAATGTTGAT
1 ATTTAGAAAATGTTGAT
* *
264160 ATTTAGGAAATTTTGAT
1 ATTTAGAAAATGTTGAT
264177 ATTT
1 ATTT
264181 CAACATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (17 bp):
ATTTAGAAAATGTTGAT
Found at i:264418 original size:21 final size:21
Alignment explanation
Indices: 264397--264462 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
264387 AAAATACAAT
264397 AAAAATCATAAAAATAGGAATA
1 AAAAAT-ATAAAAATAGGAATA
*
264419 AAAAATATAAAAATA--CATA
1 AAAAATATAAAAATAGGAATA
264438 AAAAATAAGTAAAAAT--GAATA
1 AAAAAT-A-TAAAAATAGGAATA
264459 AAAA
1 AAAA
264463 GAAAATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.23
20 1 0.03
21 23 0.59
22 6 0.15
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (21 bp):
AAAAATATAAAAATAGGAATA
Found at i:265719 original size:15 final size:15
Alignment explanation
Indices: 265699--265744 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
265689 TGCTGAAAAA
265699 TTTTTTACTTTCTTC
1 TTTTTTACTTTCTTC
*
265714 TTTTTTTCTTTCATT-
1 TTTTTTACTTTC-TTC
*
265729 TTTTTTA-TTTTTTC
1 TTTTTTACTTTCTTC
265743 TT
1 TT
265745 AATTTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 2 0.08
14 5 0.19
15 17 0.65
16 2 0.08
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTACTTTCTTC
Found at i:276023 original size:59 final size:58
Alignment explanation
Indices: 275950--276179 Score: 214
Period size: 59 Copynumber: 3.9 Consensus size: 58
275940 TTATTCAATG
* **
275950 AAAATTGATACTTTCAACCTTTTCTCAAAAAAACTCTTTCAAAATTTTTATTTTCAAGA
1 AAAATTGATACTTTCAACCTTTTCTCAAAAAAA-TATTTTTAAATTTTTATTTTCAAGA
* ** * *
276009 AAAATTGATACTTTCAA-CTTTTCCTTAAAATATTTTTTTTTGAATTTTTAATTTT-AATG-
1 AAAATTGATACTTTCAACCTTTT-CTCAAAA-AAATATTTTTAAATTTTT-ATTTTCAA-GA
* * * * *
276068 AAAATTGATACTTTCAACTTTTTCTTAAAATATATATTTTTTAATTTTTATTTTCGAGA
1 AAAATTGATACTTTCAACCTTTTCTCAAAA-AAATATTTTTAAATTTTTATTTTCAAGA
* * * *
276127 AAAATTGAAACTTTCAACTTTTTCTCAAAAATATTCTTTTTGAAATTTTTATT
1 AAAATTGATACTTTCAACCTTTTCTCAAAAA-AATATTTTT-AAATTTTTATT
276180 CTTTAAGGAA
Statistics
Matches: 144, Mismatches: 18, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
58 12 0.08
59 111 0.77
60 21 0.15
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.49
Consensus pattern (58 bp):
AAAATTGATACTTTCAACCTTTTCTCAAAAAAATATTTTTAAATTTTTATTTTCAAGA
Found at i:276070 original size:118 final size:120
Alignment explanation
Indices: 275946--276218 Score: 322
Period size: 118 Copynumber: 2.3 Consensus size: 120
275936 GCATTTATTC
*
275946 AATGAAAATTGATACTTTCAACCTTTTCTCAAAA-AAACTCTTTCAAAATTTTTATTTTCAAGAA
1 AATGAAAATTGATACTTTCAACCTTTTCTCAAAATAAA-TATTTCAAAATTTTTATTTTCAAGAA
* * *
276010 AAATTGATACTTTCAACTTTTCCT-TAAAATATTTTTTTTTG-AATTTTTAAT-TTT
65 AAATTGAAACTTTCAACTTTTCCTCAAAAATA-TTCTTTTTGAAATTTTTAATCTTT
* * * *** *
276064 AATGAAAATTGATACTTTCAACTTTTTCTTAAAATATATATTTTTTAATTTTTATTTTCGAGAAA
1 AATGAAAATTGATACTTTCAACCTTTTCTCAAAATAAATATTTCAAAATTTTTATTTTCAAGAAA
* *
276129 AATTGAAACTTTCAACTTTTTCTCAAAAATATTCTTTTTGAAATTTTTATTCTTT
66 AATTGAAACTTTCAACTTTTCCTCAAAAATATTCTTTTTGAAATTTTTAATCTTT
* * ** *
276184 AAGGAAAATCT-ATACTCTCAATTTTTTCTTAAAAT
1 AATGAAAAT-TGATACTTTCAACCTTTTCTCAAAAT
276219 GTTTTTTGAA
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
118 83 0.62
119 17 0.13
120 33 0.25
121 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (120 bp):
AATGAAAATTGATACTTTCAACCTTTTCTCAAAATAAATATTTCAAAATTTTTATTTTCAAGAAA
AATTGAAACTTTCAACTTTTCCTCAAAAATATTCTTTTTGAAATTTTTAATCTTT
Found at i:276341 original size:17 final size:17
Alignment explanation
Indices: 276300--276376 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
276290 TTTAAATGAT
* *
276300 TTTCAGATTCGCAAGGA
1 TTTCAGATTCACAAGAA
** *
276317 TTGGAGATTCATAAGAA
1 TTTCAGATTCACAAGAA
*
276334 TTTCAGATTCACAAAAA
1 TTTCAGATTCACAAGAA
** * *
276351 TTAGAGATTCGCAAGAT
1 TTTCAGATTCACAAGAA
276368 TTTCAGATT
1 TTTCAGATT
276377 TGCAAAATTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (17 bp):
TTTCAGATTCACAAGAA
Found at i:276343 original size:34 final size:34
Alignment explanation
Indices: 276260--276383 Score: 108
Period size: 34 Copynumber: 3.7 Consensus size: 34
276250 TTTTTGGTTA
* * * *
276260 ACAA-AATTTCAAATTTGCAAAAATTAGAGCTTT
1 ACAAGAATTTCAGATTCGCAAAAATTAGAGATTC
* ** *
276293 A-AATGATTTTCAGATTCGCAAGGATTGGAGATTC
1 ACAA-GAATTTCAGATTCGCAAAAATTAGAGATTC
* *
276327 ATAAGAATTTCAGATTCACAAAAATTAGAGATTC
1 ACAAGAATTTCAGATTCGCAAAAATTAGAGATTC
* * *
276361 GCAAGATTTTCAGATTTGCAAAA
1 ACAAGAATTTCAGATTCGCAAAA
276384 TTTGAAGATT
Statistics
Matches: 70, Mismatches: 18, Indels: 5
0.75 0.19 0.05
Matches are distributed among these distances:
32 2 0.03
33 1 0.01
34 65 0.93
35 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (34 bp):
ACAAGAATTTCAGATTCGCAAAAATTAGAGATTC
Found at i:276393 original size:34 final size:33
Alignment explanation
Indices: 276297--276398 Score: 98
Period size: 34 Copynumber: 3.0 Consensus size: 33
276287 AGCTTTAAAT
* * **
276297 GATTTTCAGATTCGCAAGGATTGGAGATTCATAA
1 GATTTTCAGATTCGCAA-AATTGAAGATTCGCAA
* *
276331 GAATTTCAGATTCACAAAAATT-AGAGATTCGCAA
1 GATTTTCAGATTCGC-AAAATTGA-AGATTCGCAA
*
276365 GATTTTCAGATTTGCAAAATTTGAAGATTCGCAA
1 GATTTTCAGATTCGCAAAA-TTGAAGATTCGCAA
276399 AAATTTTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
33 4 0.07
34 48 0.87
35 3 0.05
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (33 bp):
GATTTTCAGATTCGCAAAATTGAAGATTCGCAA
Found at i:276404 original size:68 final size:68
Alignment explanation
Indices: 276262--276404 Score: 146
Period size: 68 Copynumber: 2.1 Consensus size: 68
276252 TTTGGTTAAC
** * * * *
276262 AAAATTTCAAATTTGCAAAAATTAGAGCTTTAAATGATTTTCAGATTCGCAAGGATTGGAGATTC
1 AAAATTTCAAATTCACAAAAATTAGAGATTGAAATGATTTTCAGATTCGCAAGAATTGAAGATTC
*
276327 ATA
66 ACA
* * * *
276330 AGAATTTCAGATTCACAAAAATTAGAGATTCGCAA-GATTTTCAGATTTGCAA-AATTTGAAGAT
1 AAAATTTCAAATTCACAAAAATTAGAGATT-GAAATGATTTTCAGATTCGCAAGAA-TTGAAGAT
*
276393 TCGCA
64 TCACA
276398 AAAATTT
1 AAAATTT
276405 TTTGTTCACA
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
67 1 0.02
68 57 0.95
69 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (68 bp):
AAAATTTCAAATTCACAAAAATTAGAGATTGAAATGATTTTCAGATTCGCAAGAATTGAAGATTC
ACA
Found at i:276536 original size:22 final size:22
Alignment explanation
Indices: 276511--276580 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 22
276501 GATTCACAAC
*
276511 CAAAATTTCAGAGG-TTCTCATT
1 CAAAATTTCA-AGGATTCTAATT
* *
276533 CAAAAATT-ATAGGATT-TTATT
1 CAAAATTTCA-AGGATTCTAATT
276554 CAAAATTTCAAGGATTCTAATT
1 CAAAATTTCAAGGATTCTAATT
276576 CAAAA
1 CAAAA
276581 ACACTGGGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 21 0.52
22 19 0.47
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (22 bp):
CAAAATTTCAAGGATTCTAATT
Found at i:277811 original size:9 final size:9
Alignment explanation
Indices: 277796--277836 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
277786 GAGTCTTCTT
277796 TTTTTTTTCA
1 TTTTTTTT-A
277806 TTTTTTTTA
1 TTTTTTTTA
277815 --TTTTTTA
1 TTTTTTTTA
277822 TTTTTTTTA
1 TTTTTTTTA
277831 TTTTTT
1 TTTTTT
277837 CGTTTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.10, C:0.02, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:277836 original size:16 final size:16
Alignment explanation
Indices: 277794--277836 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
277784 TTGAGTCTTC
*
277794 TTTTT-TTTTTCATTT
1 TTTTTATTTTTTATTT
277809 TTTTTATTTTTTATTT
1 TTTTTATTTTTTATTT
277825 TTTTTATTTTTT
1 TTTTTATTTTTT
277837 CGTTTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.09, C:0.02, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTATTTTTTATTT
Found at i:277842 original size:16 final size:16
Alignment explanation
Indices: 277794--277844 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
277784 TTGAGTCTTC
277794 TTTT-TTTTTTCATTTT
1 TTTTATTTTTTC-TTTT
*
277810 TTTTATTTTTTATTTT
1 TTTTATTTTTTCTTTT
277826 TTTTATTTTTTCGTTTT
1 TTTTATTTTTTC-TTTT
277843 TT
1 TT
277845 CTACTTCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.08, C:0.04, G:0.02, T:0.86
Consensus pattern (16 bp):
TTTTATTTTTTCTTTT
Found at i:278232 original size:211 final size:211
Alignment explanation
Indices: 277864--278283 Score: 759
Period size: 211 Copynumber: 2.0 Consensus size: 211
277854 CCATTATTAG
277864 TATCTTCTACACATCAATCTTTAAAACATAAGAACAAAGCATGATTACCTTACTCCATCACGACC
1 TATCTTCTACACATCAATCTTTAAAACATAAGAACAAAGCATGATTACCTTACTCCATCACGACC
*
277929 ATACCTTAGTCCAACATATGATAATTTAATTTGAGCATTCACATTCAATCAAAATAGACTTTTAA
66 ATACCTTAGTCCAACATATGATAATTCAATTTGAGCATTCACATTCAATCAAAATAGACTTTTAA
*
277994 AGATTGCAATGTAGGATATAATGAGGCGTCATGAAAGAAATGGATAAAATAGGCCCAAAACATAT
131 AGATTGCAATGTAAGATATAATGAGGCGTCATGAAAGAAATGGATAAAATAGGCCCAAAACATAT
278059 GTTTAAAGGGTTCACA
196 GTTTAAAGGGTTCACA
* *
278075 TATCTTCTATACATCAATCTTTAAAACATAAGAACAAAGCATGATTACCTTACTCCATCATGACC
1 TATCTTCTACACATCAATCTTTAAAACATAAGAACAAAGCATGATTACCTTACTCCATCACGACC
278140 ATACCTTAGTCCAACATATGATAATTCAATTTGAGCATTCACATTCAATCAAAATAGACTTTTAA
66 ATACCTTAGTCCAACATATGATAATTCAATTTGAGCATTCACATTCAATCAAAATAGACTTTTAA
* * * * *
278205 AGGTTGTAATGTAAGCTATAGTGAGGCGTCATGAAAGAAATGGATAAAATAGGCTCAAAACATAT
131 AGATTGCAATGTAAGATATAATGAGGCGTCATGAAAGAAATGGATAAAATAGGCCCAAAACATAT
278270 GTTTAAAGGGTTCA
196 GTTTAAAGGGTTCA
278284 AACCAAATGA
Statistics
Matches: 200, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
211 200 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (211 bp):
TATCTTCTACACATCAATCTTTAAAACATAAGAACAAAGCATGATTACCTTACTCCATCACGACC
ATACCTTAGTCCAACATATGATAATTCAATTTGAGCATTCACATTCAATCAAAATAGACTTTTAA
AGATTGCAATGTAAGATATAATGAGGCGTCATGAAAGAAATGGATAAAATAGGCCCAAAACATAT
GTTTAAAGGGTTCACA
Found at i:281948 original size:58 final size:58
Alignment explanation
Indices: 281878--282254 Score: 303
Period size: 58 Copynumber: 6.2 Consensus size: 58
281868 GCCTTTATTC
* * *
281878 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATCTTTCGAAATTTTCATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTGAAATTTTTATTTTT
* * * * * *
281936 AAGAAAAATTGATACTTTCAA-TTTT-TTGAAAAATATTTTTTGAAAATTTCATCTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTGAAATTTTTATTTTT
* * *
281992 AAGGAAAATTGATACTTTCAACTTTTCCTTAAAATATATTTTTT-AAATTTTTATTTTCAAAAAA
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAA-AAATTTTTTGAAATTTTTA-TTT-------
282056 AAATT
57 ---TT
* * *
282061 GATAGAAAAATTGATACTGTCAACTTTTCCTCAAAAATACTTTTTTTTTGAAATTTTTATTCTTT
1 A--AGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-A---ATTTTTTGAAATTTTTATT-TTT
* * * *
282126 ATA-AAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTAAAATTTTTATTTTT
1 A-AGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTGAAATTTTTATTTTT
* * * *
282184 AAGAAAAATTAACACTTTCAACTTTTTCTCAAAAATATTCTTTTTGAAATTTTTATTCTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-AAT-TTTTTGAAATTTTTATT-TTT
*
282245 AAGGAAAATT
1 AAGAAAAATT
282255 TAACTATATG
Statistics
Matches: 262, Mismatches: 31, Indels: 49
0.77 0.09 0.14
Matches are distributed among these distances:
56 44 0.17
57 9 0.03
58 64 0.24
59 32 0.12
60 16 0.06
61 12 0.05
62 1 0.00
63 29 0.11
64 2 0.01
65 2 0.01
69 2 0.01
70 1 0.00
71 30 0.11
74 8 0.03
75 10 0.04
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (58 bp):
AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTGAAATTTTTATTTTT
Found at i:282077 original size:71 final size:74
Alignment explanation
Indices: 281996--282139 Score: 197
Period size: 71 Copynumber: 2.0 Consensus size: 74
281986 ATCTTTAAGG
* *
281996 AAAATTGATACTTTCAACTTTTCCT-TAAAATA-TATTTTTT-AAATTTTTATT-TTCAAAAAAA
1 AAAATTGATACTGTCAACTTTTCCTCAAAAATACTATTTTTTGAAATTTTTATTCTT-AAAAAAA
282057 AATTGATAGA
65 AATTGATAGA
* * *
282067 AAAATTGATACTGTCAACTTTTCCTCAAAAATACTTTTTTTTTGAAATTTTTATTCTTTATAAAA
1 AAAATTGATACTGTCAACTTTTCCTCAAAAATAC-TATTTTTTGAAATTTTTATTCTTAAAAAAA
282132 AATTGATA
65 AATTGATA
282140 CTTTCAACTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
71 24 0.38
72 6 0.10
74 7 0.11
75 24 0.38
76 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (74 bp):
AAAATTGATACTGTCAACTTTTCCTCAAAAATACTATTTTTTGAAATTTTTATTCTTAAAAAAAA
ATTGATAGA
Found at i:289574 original size:25 final size:26
Alignment explanation
Indices: 289516--289575 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
289506 TAATAAAATG
289516 ATATAATTTAATTTATCTCATTAATA
1 ATATAATTTAATTTATCTCATTAATA
* *
289542 A-ATTATTTAATTTA-CTGA-TAATA
1 ATATAATTTAATTTATCTCATTAATA
289565 TATATAATTTA
1 -ATATAATTTA
289576 TATATGGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 5 0.17
24 4 0.14
25 19 0.66
26 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (26 bp):
ATATAATTTAATTTATCTCATTAATA
Found at i:293828 original size:2 final size:2
Alignment explanation
Indices: 293821--293852 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
293811 CTTTGTTTTG
293821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
293853 TCACACACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:297324 original size:106 final size:106
Alignment explanation
Indices: 297139--297345 Score: 333
Period size: 106 Copynumber: 2.0 Consensus size: 106
297129 CAACTTGGCG
* * * * *
297139 AAATTTTGGTGAAGGTCTTAATTTGTTCATATCACAGTCTTAATCTATTCTAATTGCTCACAAGT
1 AAATTTTGGTAAAGGTCTTAATTTGTTCACATCACAGTCTTAATCTATTATAAATGCTCACAAGC
297204 AAACGTGTAAATCAATAATAAATAAATAAATTAATTATTTT
66 AAACGTGTAAATCAATAATAAATAAATAAATTAATTATTTT
* *
297245 AAATTTTGGTAAATGTCTTAATTTGTTCACATCACTGTCTTAATCTATTATAAATGCTCACAAGC
1 AAATTTTGGTAAAGGTCTTAATTTGTTCACATCACAGTCTTAATCTATTATAAATGCTCACAAGC
* *
297310 AAACGTGTAAATCAATAATAAATTAATTAATTAATT
66 AAACGTGTAAATCAATAATAAATAAATAAATTAATT
297346 GTTTAAAAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (106 bp):
AAATTTTGGTAAAGGTCTTAATTTGTTCACATCACAGTCTTAATCTATTATAAATGCTCACAAGC
AAACGTGTAAATCAATAATAAATAAATAAATTAATTATTTT
Found at i:300200 original size:17 final size:18
Alignment explanation
Indices: 300174--300207 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
300164 TTTAGCCTCA
300174 AGGCCAAAA-TTTATGTG
1 AGGCCAAAATTTTATGTG
*
300191 AGGCCTAAATTTTATGT
1 AGGCCAAAATTTTATGT
300208 CAATTGGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (18 bp):
AGGCCAAAATTTTATGTG
Found at i:300206 original size:18 final size:17
Alignment explanation
Indices: 300174--300207 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
300164 TTTAGCCTCA
300174 AGGCCAAAATTTATGTG
1 AGGCCAAAATTTATGTG
*
300191 AGGCCTAAATTTTATGT
1 AGGCC-AAAATTTATGT
300208 CAATTGGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (17 bp):
AGGCCAAAATTTATGTG
Found at i:300261 original size:5 final size:5
Alignment explanation
Indices: 300253--300314 Score: 54
Period size: 5 Copynumber: 11.6 Consensus size: 5
300243 AATATTTTGT
* *
300253 TTTTA TTTTA CTCTTTTA TTTTA TTTTA TTTT- CTTCA TCTTTA TTTTA
1 TTTTA TTTTA -T--TTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA
300301 TTTTA TTTTTA TTT
1 TTTTA -TTTTA TTT
300315 ATTATTTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.04
5 30 0.64
6 10 0.21
7 1 0.02
8 4 0.09
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:300315 original size:10 final size:11
Alignment explanation
Indices: 300245--300322 Score: 59
Period size: 13 Copynumber: 6.5 Consensus size: 11
300235 ATTCAAATAA
*
300245 TATTTTGTTTT
1 TATTTTATTTT
300256 TATTTTACTCTTT
1 TATTTTA-T-TTT
300269 TATTTTATTTT
1 TATTTTATTTT
* *
300280 ATTTTCTTCATCTT
1 -TATT-TT-ATTTT
300294 TATTTTA-TTT
1 TATTTTATTTT
300304 TATTTTTATTTAT
1 TA-TTTTATTT-T
300317 TATTTT
1 TATTTT
300323 TCTCTTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.07
11 15 0.28
12 13 0.24
13 18 0.33
14 4 0.07
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:300315 original size:20 final size:20
Alignment explanation
Indices: 300253--300317 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
300243 AATATTTTGT
300253 TTTTATTTTACTCTTTTATTTTA
1 TTTTATTTTA-T-TTTTA-TTTA
* ** *
300276 TTTTATTTTCTTCATCTTTA
1 TTTTATTTTATTTTTATTTA
300296 TTTTATTTTATTTTTATTTA
1 TTTTATTTTATTTTTATTTA
300316 TT
1 TT
300318 ATTTTTCTCT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 22 0.65
21 2 0.06
22 1 0.03
23 9 0.26
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTATTTTATTTTTATTTA
Found at i:300330 original size:20 final size:20
Alignment explanation
Indices: 300255--300330 Score: 52
Period size: 20 Copynumber: 3.8 Consensus size: 20
300245 TATTTTGTTT
*
300255 TTATTTTACTCTTTTATTTTA
1 TTATTTTTCTCTTTTA-TTTA
*
300276 TTTTATTTTCTTCATCTTTA-TT-
1 TTAT-TTTTC-TC-T-TTTATTTA
*
300298 TTA-TTTTAT-TTTTATTTA
1 TTATTTTTCTCTTTTATTTA
300316 TTATTTTTCTCTTTT
1 TTATTTTTCTCTTTT
300331 TTTTGCTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 17
0.66 0.08 0.27
Matches are distributed among these distances:
16 4 0.10
17 3 0.07
18 3 0.07
19 6 0.14
20 8 0.19
21 3 0.07
22 6 0.14
23 4 0.10
24 1 0.02
25 4 0.10
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (20 bp):
TTATTTTTCTCTTTTATTTA
Found at i:301792 original size:5 final size:5
Alignment explanation
Indices: 301784--301838 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 5
301774 TTTTATTTTG
* *
301784 ATAAA ATAAA A-AAA GTAAA A-CAA ATAAA AT-AA AT-AA AT-AA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
301829 AT-AA ATAAA A
1 ATAAA ATAAA A
301839 AATACCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 22 0.52
5 20 0.48
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
ATAAA
Found at i:301811 original size:9 final size:9
Alignment explanation
Indices: 301787--301838 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
301777 TATTTTGATA
301787 AAATAAAA-
1 AAATAAAAT
*
301795 AAAGTAAAAC
1 AAA-TAAAAT
301805 AAATAAAAT
1 AAATAAAAT
301814 AAAT-AAAT
1 AAATAAAAT
301822 AAATAAAAT
1 AAATAAAAT
301831 AAATAAAA
1 AAATAAAA
301839 AATACCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
8 11 0.28
9 26 0.65
10 3 0.08
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:301819 original size:4 final size:4
Alignment explanation
Indices: 301805--301842 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
301795 AAAGTAAAAC
301805 AAAT AAAAT AAAT AAAT AAAT AAAAT AAAT AAA- AAAT A
1 AAAT -AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A
301843 CCAAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.10
4 20 0.65
5 8 0.26
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:301823 original size:13 final size:13
Alignment explanation
Indices: 301784--301837 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
301774 TTTTATTTTG
*
301784 ATAAAATAAAAAA
1 ATAAAATAAATAA
*
301797 AGTAAAACAAATAA
1 A-TAAAATAAATAA
301811 A-ATAAATAAATAA
1 ATA-AAATAAATAA
301824 ATAAAATAAATAA
1 ATAAAATAAATAA
301837 A
1 A
301838 AAATACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 1 0.03
13 22 0.63
14 12 0.34
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
ATAAAATAAATAA
Found at i:302482 original size:13 final size:13
Alignment explanation
Indices: 302464--302489 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
302454 CCTTCTGGGG
302464 TTTGAATTCAATC
1 TTTGAATTCAATC
302477 TTTGAATTCAATC
1 TTTGAATTCAATC
302490 CAAACTCTGT
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:0.08, T:0.46
Consensus pattern (13 bp):
TTTGAATTCAATC
Found at i:302665 original size:16 final size:15
Alignment explanation
Indices: 302572--302756 Score: 99
Period size: 16 Copynumber: 12.7 Consensus size: 15
302562 AAATTAATCA
302572 AAATAA-AAA-AGAT
1 AAATAATAAATAGAT
*
302585 AAATATATTAATAGAT
1 AAATA-ATAAATAGAT
* *
302601 AACAAAAATAATTAGAT
1 -A-AATAATAAATAGAT
*
302618 AAATTAAAGAAATAGAT
1 AAA-T-AATAAATAGAT
*
302635 AAATAAT-AAT-TAT
1 AAATAATAAATAGAT
302648 AAATAATAAAGTAGAT
1 AAATAATAAA-TAGAT
*
302664 AAATAATAAA-ATAT
1 AAATAATAAATAGAT
* *
302678 TAATAGATAAA-AAAT
1 AAATA-ATAAATAGAT
* *
302693 AAA-AATAAAAATAT
1 AAATAATAAATAGAT
* *
302707 ATATTAATAAATAGAC
1 A-AATAATAAATAGAT
302723 AAATAATAAA-A-AT
1 AAATAATAAATAGAT
302736 AAA-AATAAA-A-AT
1 AAATAATAAATAGAT
302748 AAA-AATAAA
1 AAATAATAAA
302757 AGCCAATTGA
Statistics
Matches: 137, Mismatches: 21, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
12 18 0.13
13 23 0.17
14 19 0.14
15 26 0.19
16 27 0.20
17 21 0.15
18 3 0.02
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (15 bp):
AAATAATAAATAGAT
Found at i:302694 original size:29 final size:29
Alignment explanation
Indices: 302583--302757 Score: 81
Period size: 29 Copynumber: 6.2 Consensus size: 29
302573 AATAAAAAAG
*
302583 ATAAATATATTAATAGAT-AACAA-AAATA
1 ATAAA-ATATTAATAGATAAAAAATAAATA
* *
302611 ATTAGATAA-ATTAA-AGA-AATAGATAAATA
1 A-TA-A-AATATTAATAGATAAAAAATAAATA
* * *
302640 AT-AATTATAAATA-ATAAAGTAGATAAATA
1 ATAAAATATTAATAGATAAA--AAATAAATA
302669 ATAAAATATTAATAGATAAAAAATAAA-A
1 ATAAAATATTAATAGATAAAAAATAAATA
* * *
302697 ATAAAAATATATATTA-ATAAATAGACAAATA
1 AT-AAAATAT-TAATAGATAAA-AAATAAATA
*
302728 ATAAAA-A-TAA-AAAT-AAAAATAAA-A
1 ATAAAATATTAATAGATAAAAAATAAATA
302752 ATAAAA
1 ATAAAA
302758 GCCAATTGAG
Statistics
Matches: 115, Mismatches: 15, Indels: 38
0.68 0.09 0.23
Matches are distributed among these distances:
24 7 0.06
25 6 0.05
26 9 0.08
27 7 0.06
28 10 0.09
29 43 0.37
30 24 0.21
31 9 0.08
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (29 bp):
ATAAAATATTAATAGATAAAAAATAAATA
Found at i:302701 original size:51 final size:49
Alignment explanation
Indices: 302628--302756 Score: 129
Period size: 51 Copynumber: 2.6 Consensus size: 49
302618 AAATTAAAGA
* ** *
302628 AATAGATAAATAATAATTATAAATAATAAAGTAGATAAATA-ATAAAATATT
1 AATAGATAAAAAATAAAAATAAA-AATAAAGTA-ATAAATAGA-AAAATAAT
* *
302679 AATAGATAAAAAATAAAAATAAAAATATATATTAATAAATAGACAAATAAT
1 AATAGATAAAAAATAAAAATAAAAATA-A-AGTAATAAATAGAAAAATAAT
*
302730 AA-AAAT-AAAAATAAAAATAAAAATAAA
1 AATAGATAAAAAATAAAAATAAAAATAAA
302757 AGCCAATTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 19 0.28
50 7 0.10
51 36 0.53
52 4 0.06
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.26
Consensus pattern (49 bp):
AATAGATAAAAAATAAAAATAAAAATAAAGTAATAAATAGAAAAATAAT
Found at i:302702 original size:5 final size:6
Alignment explanation
Indices: 302687--302757 Score: 72
Period size: 6 Copynumber: 11.7 Consensus size: 6
302677 TTAATAGATA
* * * * *
302687 AAAAAT AAAAAT AAAAAT ATATATT AATAAAT AGACA- AATAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT A-AAAAT AA-AAAT AAAAAT AAAAAT AAAAAT
302736 AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAA
302758 GCCAATTGAG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
5 2 0.04
6 43 0.83
7 7 0.13
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:302705 original size:37 final size:36
Alignment explanation
Indices: 302664--302743 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
302654 TAAAGTAGAT
*
302664 AAATAATA-AAATATTAATAGATAAAAAATAAAAATAA
1 AAATAATATAAATA--AATAGACAAAAAATAAAAATAA
* *
302701 AAATATATATTAATAAATAGACAAATAATAAAAATAA
1 AAATA-ATATAAATAAATAGACAAAAAATAAAAATAA
302738 AAATAA
1 AAATAA
302744 AAATAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
36 1 0.03
37 30 0.79
38 3 0.08
39 4 0.11
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (36 bp):
AAATAATATAAATAAATAGACAAAAAATAAAAATAA
Found at i:308350 original size:155 final size:155
Alignment explanation
Indices: 308078--308397 Score: 468
Period size: 155 Copynumber: 2.0 Consensus size: 155
308068 TACTCACTTT
*
308078 TATGGATGATATATAAATTTATATATAGTATAACTGTCATAAGAAAGGAGTTCAACTGTATATGT
1 TATGGATGATATATAAA-TTATATATAGTATAACTGTCAT---AAAGGAGTTCAACTATATATGT
** * * *
308143 ATATATATATAGGTAAAATGGCGTTTTCTAAGTTTGGAATTTTAAGATTTAAATGTGGCTTTCAG
62 ATATATATATAGGTAAAATGGCAATTCCTAAGTTTGGAATTTTAAGATTTAAATATGGCTTTCAA
308208 GCTCAAGGACTTTGTCTTTTAAGCTTAAA
127 GCTCAAGGACTTTGTCTTTTAAGCTTAAA
*
308237 TATGGATGATATATAAA-TATATA-ACGTATAACTGTCAT-AAGGAGTTCAATTATATATGTATA
1 TATGGATGATATATAAATTATATATA-GTATAACTGTCATAAAGGAGTTCAACTATATATG--TA
308299 TATATATATAGGTAAAATGGCAATTCCTAAG-TTGGAAATTTTAAGATTTAAATATGGCTTTCAA
63 TATATATATAGGTAAAATGGCAATTCCTAAGTTTGG-AATTTTAAGATTTAAATATGGCTTTCAA
*
308363 GTTCAAGGACTTTGTCTTTTAAGCTTAAA
127 GCTCAAGGACTTTGTCTTTTAAGCTTAAA
308392 TATGGA
1 TATGGA
308398 GAGGTTGAAC
Statistics
Matches: 149, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
153 18 0.12
154 4 0.03
155 90 0.60
156 1 0.01
157 19 0.13
159 17 0.11
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.38
Consensus pattern (155 bp):
TATGGATGATATATAAATTATATATAGTATAACTGTCATAAAGGAGTTCAACTATATATGTATAT
ATATATAGGTAAAATGGCAATTCCTAAGTTTGGAATTTTAAGATTTAAATATGGCTTTCAAGCTC
AAGGACTTTGTCTTTTAAGCTTAAA
Found at i:309297 original size:24 final size:22
Alignment explanation
Indices: 309270--309325 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
309260 TAATAGTGCC
309270 AAAAAAAAACAAAATAAATACATG
1 AAAAAAAAACAAAATAAA-A-ATG
* * *
309294 AAAACAAACCAAAATACAAATG
1 AAAAAAAAACAAAATAAAAATG
309316 AAGAAAAAAA
1 AA-AAAAAAA
309326 AGTCTTGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 5 0.19
23 6 0.23
24 15 0.58
ACGTcount: A:0.75, C:0.11, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAAAAAACAAAATAAAAATG
Found at i:310047 original size:21 final size:20
Alignment explanation
Indices: 310022--310087 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
310012 ATATATTTTC
310022 TTTTTATTCATTTTTACTTAT
1 TTTTTATTCATTTTTA-TTAT
310043 TTTTTATGT-ATTTTTA-TAT
1 TTTTTAT-TCATTTTTATTAT
*
310062 TTTTTATTCCTATTTTTATGAT
1 TTTTTATT-C-ATTTTTATTAT
310084 TTTT
1 TTTT
310088 ATTGTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 1 0.03
19 10 0.26
21 21 0.54
22 7 0.18
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (20 bp):
TTTTTATTCATTTTTATTAT
Found at i:311161 original size:22 final size:22
Alignment explanation
Indices: 311105--311164 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
311095 TTTTTTTTGA
*
311105 ATTTCAATATTTTGATTTCTTTT
1 ATTTTAATATTTT-ATTTCTTTT
*
311128 A-TTTATTGATTTTATTT-TTGTT
1 ATTTTAAT-ATTTTATTTCTT-TT
311150 ATTTTAATATTTTAT
1 ATTTTAATATTTTAT
311165 CGTTCATGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 2 0.06
22 18 0.58
23 11 0.35
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.68
Consensus pattern (22 bp):
ATTTTAATATTTTATTTCTTTT
Found at i:311630 original size:14 final size:15
Alignment explanation
Indices: 311603--311631 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
311593 TTTTTATTTC
311603 AATAAAATCAATAAA
1 AATAAAATCAATAAA
311618 AATAAAA-CAATAAA
1 AATAAAATCAATAAA
311632 TTACATCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AATAAAATCAATAAA
Found at i:311748 original size:7 final size:7
Alignment explanation
Indices: 311707--311749 Score: 54
Period size: 6 Copynumber: 6.1 Consensus size: 7
311697 AAATTTCTTT
311707 TAAAAAA
1 TAAAAAA
311714 TACAAAAA
1 TA-AAAAA
311722 GTAAAAAA
1 -TAAAAAA
311730 T-AAAAA
1 TAAAAAA
311736 T-AAAAA
1 TAAAAAA
311742 TAAAAAA
1 TAAAAAA
311749 T
1 T
311750 TTGATCTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.36
7 9 0.27
8 10 0.30
9 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:314599 original size:6 final size:6
Alignment explanation
Indices: 314588--314623 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
314578 ATAAGAAAAA
314588 CATTTG CATTTG CATAATTG CATTTG CATTTG CATT
1 CATTTG CATTTG CAT--TTG CATTTG CATTTG CATT
314624 AGAGAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 22 0.79
8 6 0.21
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (6 bp):
CATTTG
Found at i:315432 original size:22 final size:21
Alignment explanation
Indices: 315376--315498 Score: 86
Period size: 22 Copynumber: 5.7 Consensus size: 21
315366 ATTTTGAACC
*
315376 TTTGATTTGAATCTCGAAGACT
1 TTTGATGTGAATCTCGAA-ACT
** **
315398 TTCAATGCAAATCTCGAAATCT
1 TTTGATGTGAATCTCGAAA-CT
* *
315420 TTTGGTGTGAATCTCG-AACC
1 TTTGATGTGAATCTCGAAACT
*
315440 TTTGATGTGAATCTAGATAACT
1 TTTGATGTGAATCTCGA-AACT
* **
315462 TTTTATGTGAATCTTAAGAACT
1 TTTGATGTGAATCTCGA-AACT
*
315484 TTTTAGTGTGAATCT
1 TTTGA-TGTGAATCT
315499 TGAACTTCAG
Statistics
Matches: 79, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
20 15 0.19
21 3 0.04
22 52 0.66
23 9 0.11
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (21 bp):
TTTGATGTGAATCTCGAAACT
Found at i:315598 original size:23 final size:23
Alignment explanation
Indices: 315531--315601 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
315521 ACCCTTACTA
*
315531 TGAATTTCAAGGACCTTTTGGTG
1 TGAATTTCAAGGACCTTTTAGTG
* ** * *
315554 AGAATCCCAA--ACC-CTTATTG
1 TGAATTTCAAGGACCTTTTAGTG
315574 TGAATTTCAAGGACCTTTTAGTG
1 TGAATTTCAAGGACCTTTTAGTG
315597 TGAAT
1 TGAAT
315602 CCCTAACCTT
Statistics
Matches: 34, Mismatches: 11, Indels: 6
0.67 0.22 0.12
Matches are distributed among these distances:
20 11 0.32
21 3 0.09
22 3 0.09
23 17 0.50
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (23 bp):
TGAATTTCAAGGACCTTTTAGTG
Found at i:315619 original size:43 final size:43
Alignment explanation
Indices: 315507--315621 Score: 167
Period size: 43 Copynumber: 2.7 Consensus size: 43
315497 CTTGAACTTC
* *
315507 AGTGAGAATCCCAAACCCTTACTATGAATTTCAAGGACCTTTT
1 AGTGAGAATCCCAAACCCTTAATGTGAATTTCAAGGACCTTTT
* *
315550 GGTGAGAATCCCAAACCCTTATTGTGAATTTCAAGGACCTTTT
1 AGTGAGAATCCCAAACCCTTAATGTGAATTTCAAGGACCTTTT
* * *
315593 AGTGTGAATCCCTAACCTTTAATGTGAAT
1 AGTGAGAATCCCAAACCCTTAATGTGAAT
315622 CTCTAGAACT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (43 bp):
AGTGAGAATCCCAAACCCTTAATGTGAATTTCAAGGACCTTTT
Found at i:315753 original size:20 final size:21
Alignment explanation
Indices: 315714--315755 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
315704 AATTTTGAGG
315714 ACTTTTCGATATGAAGATCAA
1 ACTTTTCGATATGAAGATCAA
* *
315735 ACTTTT-GATGTGAATATCAA
1 ACTTTTCGATATGAAGATCAA
315755 A
1 A
315756 GACCTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (21 bp):
ACTTTTCGATATGAAGATCAA
Found at i:316041 original size:43 final size:43
Alignment explanation
Indices: 315971--316053 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
315961 GAATCTTAAA
* *
315971 CTTTTAATGTAAATCTCGAACCCTCGATGTGAATCTCAAAAAC
1 CTTTTAATGTAAATCTCGAACCCTCGATGAGAATATCAAAAAC
* * * **
316014 CTTTTAGTGTGAATCTCGAGCTTTCGATGAGAATATCAAA
1 CTTTTAATGTAAATCTCGAACCCTCGATGAGAATATCAAA
316054 GATGAAAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (43 bp):
CTTTTAATGTAAATCTCGAACCCTCGATGAGAATATCAAAAAC
Found at i:316192 original size:31 final size:31
Alignment explanation
Indices: 316142--316229 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
316132 TAAGTTTTTA
*
316142 TTTTTT-AGTGTCATAGCCTCTAGTTAAGAG
1 TTTTTTAAGTTTCATAGCCTCTAGTTAAGAG
* * *
316172 TTTTTTAAGTTTCATTGCCTCTGGTTAGGAG
1 TTTTTTAAGTTTCATAGCCTCTAGTTAAGAG
* *
316203 TTTTTTAAGTTTAAGAG-CTCTAGTTAA
1 TTTTTTAAGTTTCATAGCCTCTAGTTAA
316230 AAGACTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
30 14 0.29
31 34 0.71
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (31 bp):
TTTTTTAAGTTTCATAGCCTCTAGTTAAGAG
Found at i:316526 original size:67 final size:68
Alignment explanation
Indices: 316414--316542 Score: 165
Period size: 67 Copynumber: 1.9 Consensus size: 68
316404 TTTAATATCA
* * *
316414 TAGCTTCTGGTTCAAGGAGTTTTTAAAAGTATTATTACCTTTAGTTATAGGAGTTTTTTAAAATA
1 TAGCTTCTGGTTCAAGGAGTTTTTAAAAGTATTATTACCTCTAGTTAGAGGAGCTTTTTAAAATA
316479 CTG
66 CTG
* **
316482 TAGCTTCTGGTTTGAA-GA-TTTTTTCAAGTATTA-TAGCCTCTAGTTAGAGGAGCTTTTTAAA
1 TAGCTTCTGG-TTCAAGGAGTTTTTAAAAGTATTATTA-CCTCTAGTTAGAGGAGCTTTTTAAA
316543 GTTTAATTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
66 2 0.04
67 35 0.66
68 12 0.23
69 4 0.08
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (68 bp):
TAGCTTCTGGTTCAAGGAGTTTTTAAAAGTATTATTACCTCTAGTTAGAGGAGCTTTTTAAAATA
CTG
Found at i:317417 original size:20 final size:19
Alignment explanation
Indices: 317392--317429 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
317382 TGGTAGCTCT
317392 ACAAAAAAAAAAGCCTATAA
1 ACAAAAAAAAAA-CCTATAA
317412 ACAAAAAAAAAACCTATA
1 ACAAAAAAAAAACCTATA
317430 GACCCGAGAC
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:0.71, C:0.16, G:0.03, T:0.11
Consensus pattern (19 bp):
ACAAAAAAAAAACCTATAA
Found at i:318294 original size:22 final size:21
Alignment explanation
Indices: 318269--318309 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
318259 TATTTTTTAT
*
318269 ATTCTTTATTACTATTTTTGCA
1 ATTCTCTATT-CTATTTTTGCA
*
318291 ATTCTCTATTTTATTTTTG
1 ATTCTCTATTCTATTTTTG
318310 GGTGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.63
Consensus pattern (21 bp):
ATTCTCTATTCTATTTTTGCA
Found at i:318422 original size:21 final size:22
Alignment explanation
Indices: 318383--318424 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
318373 ACTTAAATTT
*
318383 TATTTAAGATAAATGTTGAAAA
1 TATTTAAGATAAATATTGAAAA
318405 TATTTAAGA-AAATATTGAAA
1 TATTTAAGATAAATATTGAAA
318425 TATCAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (22 bp):
TATTTAAGATAAATATTGAAAA
Found at i:318690 original size:14 final size:14
Alignment explanation
Indices: 318667--318710 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
318657 AAATATCAAT
* *
318667 TTTTTTAGAATAAA
1 TTTTTAAGAAAAAA
318681 TTTTTAAGAAAAAA
1 TTTTTAAGAAAAAA
*
318695 TATTTAAGAAAAAA
1 TTTTTAAGAAAAAA
318709 TT
1 TT
318711 GAAATATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTTTAAGAAAAAA
Found at i:321809 original size:2 final size:2
Alignment explanation
Indices: 321802--321837 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
321792 GTGCATGATT
321802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
321838 AAGAATAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:322328 original size:106 final size:106
Alignment explanation
Indices: 322143--322349 Score: 351
Period size: 106 Copynumber: 2.0 Consensus size: 106
322133 CAACTTGGCG
* * * *
322143 AAATTTTGGTGAAGGTCTTAATTTGTTCATATCACTGTCTTAATCTATTATAATTGCTCACAGGT
1 AAATTTTGGTAAAGGTCTTAATTTGTTCACATCACTGTCTTAATCTATTATAATTGCTCACAAGC
*
322208 AAACGTGTAAATCAATAATAAATAAATTAATTAATTATTTT
66 AAACGTGTAAATCAATAATAAATAAATAAATTAATTATTTT
* *
322249 AAATTTTGGTAAATGTCTTAATTTGTTCACATCACTGTCTTAATCTATTCTAATTGCTCACAAGC
1 AAATTTTGGTAAAGGTCTTAATTTGTTCACATCACTGTCTTAATCTATTATAATTGCTCACAAGC
322314 AAACGTGTAAATCAATAATAAATAAATAAATTAATT
66 AAACGTGTAAATCAATAATAAATAAATAAATTAATT
322350 GTTTCAAAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (106 bp):
AAATTTTGGTAAAGGTCTTAATTTGTTCACATCACTGTCTTAATCTATTATAATTGCTCACAAGC
AAACGTGTAAATCAATAATAAATAAATAAATTAATTATTTT
Found at i:328889 original size:5 final size:5
Alignment explanation
Indices: 328881--328942 Score: 54
Period size: 5 Copynumber: 11.6 Consensus size: 5
328871 AATATTTTGT
* *
328881 TTTTA TTTTA CTCTATTA TTTTA TTTTA TTTT- CTTCA TCTTTA TTTTA
1 TTTTA TTTTA -T-T-TTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA
328929 TTTTA TTTTTA TTT
1 TTTTA -TTTTA TTT
328943 ATTATTTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.04
5 29 0.62
6 11 0.23
7 2 0.04
8 3 0.06
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:328943 original size:10 final size:11
Alignment explanation
Indices: 328873--328950 Score: 50
Period size: 13 Copynumber: 6.5 Consensus size: 11
328863 ATTCAAATAA
*
328873 TATTTTGTTTT
1 TATTTTATTTT
*
328884 TATTTTACTCTAT
1 TATTTTA-T-TTT
328897 TATTTTATTTT
1 TATTTTATTTT
* *
328908 ATTTTCTTCATCTT
1 -TATT-TT-ATTTT
328922 TATTTTA-TTT
1 TATTTTATTTT
328932 TATTTTTATTTAT
1 TA-TTTTATTT-T
328945 TATTTT
1 TATTTT
328951 TCTCTTTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
10 4 0.08
11 14 0.27
12 13 0.25
13 17 0.33
14 4 0.08
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.74
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:328943 original size:20 final size:20
Alignment explanation
Indices: 328881--328945 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
328871 AATATTTTGT
328881 TTTTATTTTACTCTATTATTTTA
1 TTTTATTTTA-T-TATTA-TTTA
* *
328904 TTTTATTTTCTTCA-TCTTTA
1 TTTTATTTTATT-ATTATTTA
*
328924 TTTTATTTTATTTTTATTTA
1 TTTTATTTTATTATTATTTA
328944 TT
1 TT
328946 ATTTTTCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 22 0.63
21 2 0.06
22 2 0.06
23 9 0.26
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTTATTATTATTTA
Found at i:330439 original size:18 final size:17
Alignment explanation
Indices: 330416--330464 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
330406 TATTTTGATA
330416 AAATAAAAAAAGTAAAAC
1 AAATAAAAAAA-TAAAAC
*
330434 AAATAAATAAAATAAAAT
1 AAATAAA-AAAATAAAAC
330452 AAATAAAAAAATA
1 AAATAAAAAAATA
330465 CCAAAAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 19 0.66
19 4 0.14
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (17 bp):
AAATAAAAAAATAAAAC
Found at i:330440 original size:9 final size:8
Alignment explanation
Indices: 330415--330464 Score: 64
Period size: 9 Copynumber: 5.8 Consensus size: 8
330405 TTATTTTGAT
330415 AAAATAAA
1 AAAATAAA
330423 AAAAGTAAA
1 AAAA-TAAA
330432 ACAAATAAA
1 A-AAATAAA
330441 TAAAATAAA
1 -AAAATAAA
330450 ATAAATAAA
1 A-AAATAAA
330459 AAAATA
1 AAAATA
330465 CCAAAAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 10 0.26
9 24 0.63
10 4 0.11
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (8 bp):
AAAATAAA
Found at i:330451 original size:14 final size:14
Alignment explanation
Indices: 330413--330459 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
330403 TTTTATTTTG
330413 ATAAAATAAAA-AA
1 ATAAAATAAAATAA
*
330426 AGTAAAA-CAAATAA
1 A-TAAAATAAAATAA
330440 ATAAAATAAAATAA
1 ATAAAATAAAATAA
330454 ATAAAA
1 ATAAAA
330460 AAATACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 9 0.31
14 20 0.69
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (14 bp):
ATAAAATAAAATAA
Found at i:330928 original size:21 final size:22
Alignment explanation
Indices: 330902--330942 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
330892 AAGTTTTCCA
*
330902 GAAAAAGAAC-TCCAAAAATTT
1 GAAAAAAAACTTCCAAAAATTT
*
330923 GAAAAAAAACTTCTAAAAAT
1 GAAAAAAAACTTCCAAAAAT
330943 CCTATACTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.61, C:0.12, G:0.07, T:0.20
Consensus pattern (22 bp):
GAAAAAAAACTTCCAAAAATTT
Found at i:331102 original size:13 final size:13
Alignment explanation
Indices: 331084--331108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331074 CCTTTTGGGG
331084 TTTGAATTCAATA
1 TTTGAATTCAATA
331097 TTTGAATTCAAT
1 TTTGAATTCAAT
331109 CCAAACTCTG
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:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTGAATTCAATA
Found at i:331294 original size:24 final size:23
Alignment explanation
Indices: 331270--331326 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
331260 AATAATTATA
*
331270 AAAAATAAAAGTAGA-TAAATAAT
1 AAAAATAAAA-TAGATTAAAAAAT
*
331293 AAAAATATTAATAGATTAAAAAAT
1 AAAAATA-AAATAGATTAAAAAAT
331317 AAAAATAAAA
1 AAAAATAAAA
331327 ATATATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAAATAAAATAGATTAAAAAAT
Found at i:331299 original size:47 final size:52
Alignment explanation
Indices: 331193--331299 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 52
331183 AACTAATCAA
*
331193 AATAAAAA-AGATAAATATATTAATAGATAACAAAAAATAATTAGATAAATT
1 AATAAAAATAGATAAATATATTAATAGATAACAAAAAATAAGTAGATAAATT
* *
331244 AA-AGAAATAGATAAATA-A-TAAT-TATAA-AAAATAA-AAGTAGATAAA-T
1 AATAAAAATAGATAAATATATTAATAGATAACAAAA-AATAAGTAGATAAATT
331290 AATAAAAATA
1 AATAAAAATA
331300 TTAATAGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
46 3 0.06
47 20 0.41
48 6 0.12
49 4 0.08
50 5 0.10
51 11 0.22
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (52 bp):
AATAAAAATAGATAAATATATTAATAGATAACAAAAAATAAGTAGATAAATT
Found at i:331325 original size:37 final size:39
Alignment explanation
Indices: 331284--331372 Score: 107
Period size: 37 Copynumber: 2.4 Consensus size: 39
331274 ATAAAAGTAG
* *
331284 ATAAATAATAAAAATATTAATAGAT-TA-AAA-AATAAAA
1 ATAAA-AATAAAAATATTAATAAATAGACAAATAATAAAA
*
331321 ATAAAAAT--ATATATTAATAAATAGACAAATAATAAAA
1 ATAAAAATAAAAATATTAATAAATAGACAAATAATAAAA
331358 ATAAAAATAAAAATA
1 ATAAAAATAAAAATA
331373 AAAATAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
34 12 0.28
35 1 0.02
36 6 0.14
37 20 0.47
39 4 0.09
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (39 bp):
ATAAAAATAAAAATATTAATAAATAGACAAATAATAAAA
Found at i:331326 original size:5 final size:6
Alignment explanation
Indices: 331311--331381 Score: 72
Period size: 6 Copynumber: 11.7 Consensus size: 6
331301 TAATAGATTA
* * * * *
331311 AAAAAT AAAAAT AAAAAT ATATATT AATAAAT AGACA- AATAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT A-AAAAT AA-AAAT AAAAAT AAAAAT AAAAAT
331360 AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAA
331382 GCCAATTGAG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
5 2 0.04
6 43 0.83
7 7 0.13
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:332282 original size:18 final size:19
Alignment explanation
Indices: 332261--332297 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
332251 ACCATTTCTT
332261 TAAAATAAT-AAAAATGAA
1 TAAAATAATAAAAAATGAA
332279 TAAAATAATAAAAAATGAA
1 TAAAATAATAAAAAATGAA
332298 AGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (19 bp):
TAAAATAATAAAAAATGAA
Found at i:336973 original size:151 final size:155
Alignment explanation
Indices: 336762--337083 Score: 438
Period size: 159 Copynumber: 2.0 Consensus size: 155
336752 TACTCACTTT
336762 TATGGATGATATATAAATATATATATAGTATAACTGTCATAAGAAAGGAGTTCAACTATATATG-
1 TATGGATGATATATAAATATATATATAGTATAACTGTCAT---AAAGGAGTTCAACTATATATGA
** * * *
336826 TATATATATAGGTAAAATGGCGTTTTCTAAGTTTGG-AATTTTAAGATTTAAATGTGGCTTTCAG
63 TATATATATAGGTAAAATGGCAATTCCTAAG-TTGGAAATTTTAAGATTTAAATATGGCTTTCAA
336890 GCTCAAGGACTTTGTCTTTTAAGCTTAAA
127 GCTCAAGGACTTTGTCTTTTAAGCTTAAA
* *
336919 TATGGATGATATATAAATATATA-A-CGTATAACTGTCAT-AAGGAGTTCAATTATATATGTATA
1 TATGGATGATATATAAATATATATATAGTATAACTGTCATAAAGGAGTTCAACTATATATG----
336981 TATATATATATATAGGTAAAATGGCAATTCCTAAGTTGGAAATTTTAAGATTTAAATATGGCTTT
62 ---ATATATATATAGGTAAAATGGCAATTCCTAAGTTGGAAATTTTAAGATTTAAATATGGCTTT
*
337046 CAAGTTCAAGGACTTTGTCTTTTAAGCTTAAA
124 CAAGCTCAAGGACTTTGTCTTTTAAGCTTAAA
337078 TATGGA
1 TATGGA
337084 GAGGTTGAAC
Statistics
Matches: 148, Mismatches: 8, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
151 19 0.13
155 13 0.09
156 1 0.01
157 23 0.16
158 4 0.03
159 88 0.59
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (155 bp):
TATGGATGATATATAAATATATATATAGTATAACTGTCATAAAGGAGTTCAACTATATATGATAT
ATATATAGGTAAAATGGCAATTCCTAAGTTGGAAATTTTAAGATTTAAATATGGCTTTCAAGCTC
AAGGACTTTGTCTTTTAAGCTTAAA
Found at i:337441 original size:15 final size:16
Alignment explanation
Indices: 337411--337456 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
337401 AATAAAAATT
*
337411 AAGAA-AAAATAAAAA
1 AAGAAGAAAGTAAAAA
*
337426 AA-ATGAAAG-AAAAA
1 AAGAAGAAAGTAAAAA
337440 AAGAAGAAAGTAAAAA
1 AAGAAGAAAGTAAAAA
337456 A
1 A
337457 TTTTTCAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 8 0.32
15 11 0.44
16 6 0.24
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AAGAAGAAAGTAAAAA
Done.