Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1946983 original size:20 final size:22
Alignment explanation
Indices: 1946960--1947006 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
1946950 CAGGTAAACA
1946960 ATTTAAATATATA-TAG-TTTT
1 ATTTAAATATATATTAGTTTTT
* * *
1946980 ATTTCATTATTTATTAGTTTTT
1 ATTTAAATATATATTAGTTTTT
1947002 ATTTA
1 ATTTA
1947007 TTATATTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTAAATATATATTAGTTTTT
Found at i:1950253 original size:2 final size:2
Alignment explanation
Indices: 1950246--1950285 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1950236 TGAAACATGC
1950246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1950286 TCATGGGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1955233 original size:953 final size:953
Alignment explanation
Indices: 1953338--1955241 Score: 3263
Period size: 952 Copynumber: 2.0 Consensus size: 953
1953328 GTACGATCCA
*
1953338 AATTTGGGTTAAATTATTGGTTGATGCGATATGTATGAGATGCATGTTCTAGTTTTATCATTTTC
1 AATTTGGGTTAAATTATTAGTTGATGCGATATGTATGAGATGCATGTTCTAGTTTTATCATTTTC
*
1953403 GACAAATATGCATGATATCATTGCTCGAATCGATAACCACAACGATTAATATGTTAATTTGTTAA
66 GACAAATATGCATGATATCATTGCTCGAATCGATAACCACAACAATTAATATGTTAATTTGTTAA
* * * *
1953468 TCTTTTTTTTCAATTGCTTTGTTTCTGCAAGGATTTTACGAAATCCATATTCAATCGTTGAAATG
131 TC-TTTTTTTCAATCGATTTATTACTGCAAGGATTTTACGAAATCCATATTCAATCGTTGAAATG
* **
1953533 ATGATCCATGGGAGTGCGATAGCAGATCGTGTTTGGCAGTGGAACAATGGCTGTTCCGATGCGGA
195 ATGATCCATGAGAGTGCGATAGCAGATCAAGTTTGGCAGTGGAACAATGGCTGTTCCGATGCGGA
* * * * *
1953598 AATTCTTCGAGATTGAAAATCTCAAAAGCACGATTATGTTGATAATTGTTATAAAATCCTGAAGT
260 AATTCCTCGAGATTGAAAATCCCAAAAGCACAATTATATTGATAATTATTATAAAATCCTGAAGT
* *
1953663 TTTTCCATAGAAATAAAACTACTATTGAAGGCCCTTGACCCCTCATCAGTAGTAAAAATTGAAGG
325 TTTTCCATAGAAACAAAACTACTATTGAAGGCCCTTGACCCCTCATCAGCAGTAAAAATTGAAGG
*
1953728 CCCATATTAATAATTTTTAACAAAGGTGTAAGAACGTATATATATATATATATATGATATGTTTG
390 CCCATATTAATAATTTTTAACAAAGGCGTAAGAACGTATATATATATATATATATGATATGTTTG
*
1953793 TTTTGCACGGTGTTTGACATGCATGGTTATAGCCCTTGGTCAATTTATAATGGTTTAATTTGAAA
455 TTTTGCACGGTGTTTGACATGCATGGTTATAGCCCTTGGTCAATTTACAATGGTTTAATTTGAAA
* * *
1953858 TACGGTCTGCGAGTCGTGCCTTTTTATATCTCTATTGTATTTCTCTACTCATATACTCCCTCGTA
520 TACGGTCTGCAAGTCGTGCCTTTCTATATCTCTATTGTAATTCTCTACTCATATACTCCCTCGTA
1953923 TGTAAAATGAGTTTCTTTTAAAATTGTAAACCTATGAAGATTCACAAGGAGCAGAAGAATGGCGA
585 TGTAAAATGAGTTTCTTTTAAAATTGTAAACCTATGAAGATTCACAAGGAGCAGAAGAATGGCGA
* * *
1953988 GAAGAAACCTAGAGAGTAGTCTTAGACTTTAGGGTTTTTGGTTATCTCATTGGCTTGGGATGGGC
650 GAAGAAACCTAGAGAGCAGTCTTAGACTTTAGGGTTTTTGGTTATCTCATTAGCTTGAGATGGGC
1954053 CACCTTAGTCATTGTTTTGGGCTATAACCATTGCATCTTATTTATTGCTATATTTGTTATGTATG
715 CACCTTAGTCATTGTTTTGGGCTATAACCATTGCATCTTATTTATTGCTATATTTGTTATGTATG
*
1954118 CAATGCATCAAATGATAAAATAAGAATGAATATTGATAAGATCAATAAGGGTCTAATATTAAAAC
780 CAATGCATCAAATGATAAAATAAGAATGAATATTGATAAGATCAATAAGGGCCTAATATTAAAAC
** * *
1954183 GAACAATGATGAGATAATTATTCAAATCCTTCTTTATAATCTAAGTTAACTTAACCGTCCAATAT
845 GAACAATGATGAGATAATTACACAAATCCCTCTTTATAATCTAAGTTAACTTAACCATCCAATAT
1954248 TTACCCTCGGTAAGGCTTCGATCGATATTGTGTGGGATTTGATG
910 TTACCCTCGGTAAGGCTTCGATCGATATTGTGTGGGATTTGATG
*
1954292 AATTTGGGTTAAATTCTTAGTTGATGCGATATGTATGAGATGCATGTTCTAGTTTTATCATTTTC
1 AATTTGGGTTAAATTATTAGTTGATGCGATATGTATGAGATGCATGTTCTAGTTTTATCATTTTC
* * * *
1954357 GGCAAATATGCATGATATCATTGTTCTAATCGATAACCGCAACAATTAATATGTTAATTTGTTAA
66 GACAAATATGCATGATATCATTGCTCGAATCGATAACCACAACAATTAATATGTTAATTTGTTAA
* *
1954422 TC-TTTTTTCAATCGATTTATTACTGCAAGGATTTTACGAAATCCATATTTAATCGTTGACATGA
131 TCTTTTTTTCAATCGATTTATTACTGCAAGGATTTTACGAAATCCATATTCAATCGTTGAAATGA
** *
1954486 TGATCTGTGAGAGTGCGATAGCAGATCAAGTTTGGCAGTGGAACAATGGTTGTTCCGATGCGGAA
196 TGATCCATGAGAGTGCGATAGCAGATCAAGTTTGGCAGTGGAACAATGGCTGTTCCGATGCGGAA
* * *
1954551 ATTCCTCGAGATTGAAAATCCCAAAAGCACAATTCTATTGATAATTATTATCAAATCGTGAAGTT
261 ATTCCTCGAGATTGAAAATCCCAAAAGCACAATTATATTGATAATTATTATAAAATCCTGAAGTT
* * ** *
1954616 TTTCCATAGAAACAGAAGTACTATTGAAGGCCCTTGACTTCTCATCAGCAGTAGAAATTGAAGGC
326 TTTCCATAGAAACAAAACTACTATTGAAGGCCCTTGACCCCTCATCAGCAGTAAAAATTGAAGGC
*
1954681 CCATATTAATATTTTTTAACAAAGGCGTAAGAACGTATATATATATATATATATGATATGTTTGT
391 CCATATTAATAATTTTTAACAAAGGCGTAAGAACGTATATATATATATATATATGATATGTTTGT
*
1954746 TTTGCACGGTGTTTGACATGCATGGTTATAGCCCTTGTTCAATTTACAATGGTTTAATTTGAAAT
456 TTTGCACGGTGTTTGACATGCATGGTTATAGCCCTTGGTCAATTTACAATGGTTTAATTTGAAAT
* * *
1954811 ACGGTCTGCAAG-CTGTGCCTTTCTATATCTCTGTTGTAATTCTCTTCTCATCTTACTCCCTCGT
521 ACGGTCTGCAAGTC-GTGCCTTTCTATATCTCTATTGTAATTCTCTACTCAT-ATACTCCCTCGT
1954875 ATGTAAAATGAGTTTCTTTTAAAATTGTAAACCTATGAAGATTCACAAGGAGCAGAAGAATGGCG
584 ATGTAAAATGAGTTTCTTTTAAAATTGTAAACCTATGAAGATTCACAAGGAGCAGAAGAATGGCG
*
1954940 AGAAGAAACCTAGAGAGCAGTCTTAGACTTTAGGGTTTTTGGTTCTCTCATTAGCTTGAGATGGG
649 AGAAGAAACCTAGAGAGCAGTCTTAGACTTTAGGGTTTTTGGTTATCTCATTAGCTTGAGATGGG
*
1955005 CCACCTTAGTCATTGTTTTGGGCTATAACCATTGCATCTTATTTATTTCTATATTTGTTATGTAT
714 CCACCTTAGTCATTGTTTTGGGCTATAACCATTGCATCTTATTTATTGCTATATTTGTTATGTAT
1955070 GCAATGCATCAAATGATAAAATAAGAATGAATATTGATAAGATCAATAAGGGCCTAATATTAAAA
779 GCAATGCATCAAATGATAAAATAAGAATGAATATTGATAAGATCAATAAGGGCCTAATATTAAAA
*
1955135 CGAATAATGATGAGATAATTACACAAATCCCTCTTTATAATCTAAGTTAACTTAACCATCCAATA
844 CGAACAATGATGAGATAATTACACAAATCCCTCTTTATAATCTAAGTTAACTTAACCATCCAATA
*
1955200 TTTACCCTCGGTAAGGCTTCGATCGATATTGTGTGGGCTTTG
909 TTTACCCTCGGTAAGGCTTCGATCGATATTGTGTGGGATTTG
1955242 CCAAAGCATT
Statistics
Matches: 892, Mismatches: 56, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
951 1 0.00
952 400 0.45
953 366 0.41
954 125 0.14
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (953 bp):
AATTTGGGTTAAATTATTAGTTGATGCGATATGTATGAGATGCATGTTCTAGTTTTATCATTTTC
GACAAATATGCATGATATCATTGCTCGAATCGATAACCACAACAATTAATATGTTAATTTGTTAA
TCTTTTTTTCAATCGATTTATTACTGCAAGGATTTTACGAAATCCATATTCAATCGTTGAAATGA
TGATCCATGAGAGTGCGATAGCAGATCAAGTTTGGCAGTGGAACAATGGCTGTTCCGATGCGGAA
ATTCCTCGAGATTGAAAATCCCAAAAGCACAATTATATTGATAATTATTATAAAATCCTGAAGTT
TTTCCATAGAAACAAAACTACTATTGAAGGCCCTTGACCCCTCATCAGCAGTAAAAATTGAAGGC
CCATATTAATAATTTTTAACAAAGGCGTAAGAACGTATATATATATATATATATGATATGTTTGT
TTTGCACGGTGTTTGACATGCATGGTTATAGCCCTTGGTCAATTTACAATGGTTTAATTTGAAAT
ACGGTCTGCAAGTCGTGCCTTTCTATATCTCTATTGTAATTCTCTACTCATATACTCCCTCGTAT
GTAAAATGAGTTTCTTTTAAAATTGTAAACCTATGAAGATTCACAAGGAGCAGAAGAATGGCGAG
AAGAAACCTAGAGAGCAGTCTTAGACTTTAGGGTTTTTGGTTATCTCATTAGCTTGAGATGGGCC
ACCTTAGTCATTGTTTTGGGCTATAACCATTGCATCTTATTTATTGCTATATTTGTTATGTATGC
AATGCATCAAATGATAAAATAAGAATGAATATTGATAAGATCAATAAGGGCCTAATATTAAAACG
AACAATGATGAGATAATTACACAAATCCCTCTTTATAATCTAAGTTAACTTAACCATCCAATATT
TACCCTCGGTAAGGCTTCGATCGATATTGTGTGGGATTTGATG
Found at i:1962031 original size:238 final size:234
Alignment explanation
Indices: 1961590--1962345 Score: 974
Period size: 238 Copynumber: 3.2 Consensus size: 234
1961580 ATTTAGGCAT
* *
1961590 CATGCTCGAGAGACTTACTGACGGCCTGAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTT
1 CATGCTCGAGAGACTTACTGATGGCCTGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTT
* * * * *
1961655 CTTACTTTTCAAGAAAAATCAATTTTCAGAAAAGCTTTAAAAGAGAACTTTTGAAATCGCTTTCT
66 CTTACTTTTC---AAAAATCAATTTTCAGAAAAGATTTAAATGAGAAATTTGGAAATCACTTTCT
* * *
1961720 CATATTTCAAAAAATCATGTGAAAACATCATGCCCAAAGGTTTAGTGGATGGCCCGAAGGACTTA
128 CAT-TTT-ACAAAATCATGTGAAAACATCATGCCCGAAGGTTTA-TGGATGGCCC-AAAGACTTA
*
1961785 TCATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAAGAAC
189 TCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGAAC
* * * *
1961831 CATGCTCGAGAGACTTGCTGATGGCTTGAAGGACTTACTGAGTAAGAAACTTTAGAAATCATTTT
1 CATGCTCGAGAGACTTACTGATGGCCTGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTT
* * *
1961896 CTTACTTTTCAAAAATCAATTTTTAGAAAAGATTTAAATTAGAAATTTGGGAAATTACTTTCTCA
66 CTTACTTTTCAAAAATCAATTTTCAGAAAAGATTTAAATGAGAAATTT-GGAAATCACTTTCTCA
* *
1961961 TTTTACGAAAATCATGTGAAAGCATCATGCCCGAAGGTCTTATGGATGGTCCAAATGACTTATCA
130 TTTTAC-AAAATCATGTGAAAACATCATGCCCGAAGGT-TTATGGATGGCCCAAA-GACTTATCA
* * *
1962026 TCTTGCTCGAAAGACTCATAGATGACCCAAAAGATTTAAGAAC
192 TCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGAAC
* * * *
1962069 CATTCTCGAGTGACTTATTGATGGCCTGAAGGACTTACTAAGTAAGAAATTTTGGAAATCATTTT
1 CATGCTCGAGAGACTTACTGATGGCCTGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTT
* * *
1962134 CTTACTTTTCAAAAATCAATTTTCAAAAAAGATTTAAATGAGAAATATTGCAAATCACTTTCTAA
66 CTTACTTTTCAAAAATCAATTTTCAGAAAAGATTTAAATGAGAAAT-TTGGAAATCACTTTCTCA
* * * *
1962199 TTTTACAAAATTCATATGAAAATATCATGCCCGAAGATGTTATGGGTGGCCCGAAAGACTTATCA
130 TTTTACAAAA-TCATGTGAAAACATCATGCCCGAAGGT-TTATGGATGGCCC-AAAGACTTATCA
* ** * * *
1962264 TCTTGCTCTAAAGACTTATAGATGATTCGAAGGGTTTAAGCAT
192 TCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGAAC
* * *
1962307 CATGATTGAAAGACTTACTGATGG-CTCGAAGGACTTACT
1 CATGCTCGAGAGACTTACTGATGGCCT-GAAGGACTTACT
1962346 CATCAAGAAA
Statistics
Matches: 448, Mismatches: 59, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
237 9 0.02
238 348 0.78
239 22 0.05
241 69 0.15
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (234 bp):
CATGCTCGAGAGACTTACTGATGGCCTGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTT
CTTACTTTTCAAAAATCAATTTTCAGAAAAGATTTAAATGAGAAATTTGGAAATCACTTTCTCAT
TTTACAAAATCATGTGAAAACATCATGCCCGAAGGTTTATGGATGGCCCAAAGACTTATCATCTT
GCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGAAC
Found at i:1962539 original size:55 final size:55
Alignment explanation
Indices: 1962453--1963572 Score: 1265
Period size: 55 Copynumber: 20.6 Consensus size: 55
1962443 ATTCATCATG
* * *
1962453 TCAAGAAACCTCTGAAAATCACACTTAGTTTCTTTGAAAGCTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
** * * * * *
1962508 TCAAGAAACTTAAGAAAATCATATTTTGTTTCTTTAAAATCTCATTTGAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * *
1962563 TCAAGAAACTTCTAAAAACCAGACTTAGTTTCTTTAAACA-CTTATTT-AAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAA-AGCTCATTTAAAAATCA
* * * *
1962617 TCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTCAAAGTCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
*
1962672 TCAAGAAACATT-TGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
1 TCAAGAAAC-TTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* *
1962727 TCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAAT-A
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * *
1962781 GTCAAGAAACTTCTGAAAATCAGACTTAGTTTTTTTTAAAA-CTCATTTGAAAATCG
1 -TCAAGAAACTTCTGAAAATCAGACTTAG-TTTCTTTAAAAGCTCATTTAAAAATCA
* * * *
1962837 TAAAGAAACTTATGAAATTCAGACTTAGTTTATTTAAAAGCTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * * *
1962892 TCAAGAAACTTATGAAAATCAGAATCAATTTTTTTAAAAGCTCATTTAAAAGT-A
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * * *
1962946 GTCAAAAAACTTTTGAAAATCAGAATTAGTTTCTTTAAAAACTCATTTGAAAATCG
1 -TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * *
1963002 TAAAGAAACTTCAGAAAATCAGACTTAG-----TT------T-ATTTAAAGATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * *
1963045 TCAAGAAACTTCGGAAAGTCAGACTTAGTTTCTTTGAAAGATCATTTAAAAAT-A
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * *
1963099 GTCAAGAAACTTTTGAAAATCAGACTTAGTTTATTTTAAAAACTCATTTAAAAATAA
1 -TCAAGAAACTTCTGAAAATCAGACTTAGTTT-CTTTAAAAGCTCATTTAAAAATCA
* * * * *
1963156 TCATGAAACTTCTGAAAATCATACTTAGTTT-TTTAAAAACTCATTTGAAAATCG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * *
1963210 TCAAGAAACTTATGAAAATCAAACTTATTTTCTTTAATAA-CTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAA-AAGCTCATTTAAAAATCA
* * * **
1963265 TCAAGAAACTTCAGAAAACCAGACTTAGTTTCTTTAAAAGCTTATTTAAAAATTT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * *
1963320 TCAAGAAACTTCTTAAAATTAAACTTAGTTTCTTTAAAAACTAATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * * * **
1963375 TCAAGAAATTTATAAAAATCAGATTTAGTTTCTTTGAAAGCTCATTTAAAAATTG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* * * **
1963430 TCAAGAAACTTCTGAAAATTAGACTTAGTTTCTTTAAAAACTCATTTGAAAATTG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* *
1963485 TCAAGAAACTTCTTAAAATCAAACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
* *
1963540 TCAAGAAACTTCTGAAAATCATACTTAATTTCT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
1963573 AAAAACACAT
Statistics
Matches: 904, Mismatches: 132, Indels: 58
0.83 0.12 0.05
Matches are distributed among these distances:
43 34 0.04
44 1 0.00
48 2 0.00
50 2 0.00
53 1 0.00
54 114 0.13
55 689 0.76
56 60 0.07
57 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCA
Found at i:1963052 original size:43 final size:44
Alignment explanation
Indices: 1962990--1963089 Score: 141
Period size: 43 Copynumber: 2.3 Consensus size: 44
1962980 TTAAAAACTC
* *
1962990 ATTTGAAA-ATCGTAAAGAAACTTCAGAAAATCAGACTTAGTTT
1 ATTTGAAAGATCATCAAGAAACTTCAGAAAATCAGACTTAGTTT
* *
1963033 ATTT-AAAGATCATCAAGAAACTTCGGAAAGTCAGACTTAGTTT
1 ATTTGAAAGATCATCAAGAAACTTCAGAAAATCAGACTTAGTTT
*
1963076 CTTTGAAAGATCAT
1 ATTTGAAAGATCAT
1963090 TTAAAAATAG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.06
43 38 0.76
44 9 0.18
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (44 bp):
ATTTGAAAGATCATCAAGAAACTTCAGAAAATCAGACTTAGTTT
Found at i:1971801 original size:4 final size:4
Alignment explanation
Indices: 1971792--1971822 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1971782 TTCAAATATA
*
1971792 AAAT AAAT AAAT AAAT AAAT AAAG AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1971823 AATTAGTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:1973310 original size:17 final size:17
Alignment explanation
Indices: 1973288--1973358 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
1973278 ATTAAAAGAG
1973288 CTAGTTTAATTAATGAA
1 CTAGTTTAATTAATGAA
*
1973305 CTAGTTTAATGAATGAA
1 CTAGTTTAATTAATGAA
* *
1973322 CTAGTTTGATTAGTGAA
1 CTAGTTTAATTAATGAA
*
1973339 CTAGTTTAATCAATGAA
1 CTAGTTTAATTAATGAA
1973356 CTA
1 CTA
1973359 ACTTTATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:1975258 original size:20 final size:20
Alignment explanation
Indices: 1975233--1975276 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1975223 TTTCACTCTC
*
1975233 CTCCTATTCTAATTTGACTG
1 CTCCTATTCCAATTTGACTG
*
1975253 CTCCTATTCCAATTTGACTT
1 CTCCTATTCCAATTTGACTG
1975273 CTCC
1 CTCC
1975277 ATCATCTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.07, T:0.43
Consensus pattern (20 bp):
CTCCTATTCCAATTTGACTG
Found at i:1981679 original size:17 final size:17
Alignment explanation
Indices: 1981657--1981713 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
1981647 ATAATAGAGT
1981657 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
* *
1981674 TAGTTTAATGAATAAAC
1 TAGTTTAATTAATGAAC
*
1981691 TAGTTTGATTAATGAAC
1 TAGTTTAATTAATGAAC
1981708 TAGTTT
1 TAGTTT
1981714 GATCAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:1981702 original size:34 final size:34
Alignment explanation
Indices: 1981657--1981726 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
1981647 ATAATAGAGT
*
1981657 TAGTTTAATTAATGAACTAGTTTAATGAATAAAC
1 TAGTTTAATTAATGAACTAGTTTAATCAATAAAC
* *
1981691 TAGTTTGATTAATGAACTAGTTTGATCAATAAAC
1 TAGTTTAATTAATGAACTAGTTTAATCAATAAAC
1981725 TA
1 TA
1981727 ACTTTATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (34 bp):
TAGTTTAATTAATGAACTAGTTTAATCAATAAAC
Found at i:1981714 original size:17 final size:17
Alignment explanation
Indices: 1981657--1981726 Score: 86
Period size: 17 Copynumber: 4.1 Consensus size: 17
1981647 ATAATAGAGT
*
1981657 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATAAAC
*
1981674 TAGTTTAATGAATAAAC
1 TAGTTTAATTAATAAAC
* *
1981691 TAGTTTGATTAATGAAC
1 TAGTTTAATTAATAAAC
* *
1981708 TAGTTTGATCAATAAAC
1 TAGTTTAATTAATAAAC
1981725 TA
1 TA
1981727 ACTTTATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATAAAC
Found at i:1982789 original size:66 final size:68
Alignment explanation
Indices: 1982661--1982790 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 68
1982651 GTTCGCGTAC
* * * *
1982661 GCTAAACGAACATGTTCACGAACGATATACAAATGCTAAGAGATCATGTTCTCAAATTTTAAACA
1 GCTAAACGAACATGTTCACGAACGATATAAAAATGCTAAGAGAACATGTTCACAAATGTTAAACA
1982726 GAT
66 GAT
* * * *
1982729 GCTAAACGAACTTGTTTATGAACG-TA-AAAAATGCTAA-ATGAACATGTTCACGAATGTTAAAC
1 GCTAAACGAACATGTTCACGAACGATATAAAAATGCTAAGA-GAACATGTTCACAAATGTTAAAC
1982791 GAACACTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 1 0.02
66 29 0.55
67 2 0.04
68 21 0.40
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (68 bp):
GCTAAACGAACATGTTCACGAACGATATAAAAATGCTAAGAGAACATGTTCACAAATGTTAAACA
GAT
Found at i:1987528 original size:6 final size:6
Alignment explanation
Indices: 1987508--1987546 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1987498 TGATAAAGAT
*
1987508 GAGGAA -AGTGAA GAGGAA GAGGAA GAAGAA GAGGAA GAG
1 GAGGAA GAG-GAA GAGGAA GAGGAA GAGGAA GAGGAA GAG
1987547 AAAGTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 2 0.07
6 25 0.86
7 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (6 bp):
GAGGAA
Found at i:1987531 original size:18 final size:18
Alignment explanation
Indices: 1987508--1987551 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1987498 TGATAAAGAT
1987508 GAGGAAAGTGAAGAGGAA
1 GAGGAAAGTGAAGAGGAA
*
1987526 GAGG-AAGAAGAAGAGGAA
1 GAGGAAAG-TGAAGAGGAA
1987544 GA-GAAAGT
1 GAGGAAAGT
1987552 TATATGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.43, T:0.05
Consensus pattern (18 bp):
GAGGAAAGTGAAGAGGAA
Found at i:1987660 original size:14 final size:14
Alignment explanation
Indices: 1987634--1987671 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1987624 CCATAATAAT
1987634 TGTAATG-TTTTTA
1 TGTAATGTTTTTTA
*
1987647 TTTAATGTTTTTTA
1 TGTAATGTTTTTTA
1987661 TGTAATGTTTT
1 TGTAATGTTTT
1987672 AATATTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (14 bp):
TGTAATGTTTTTTA
Found at i:1987663 original size:22 final size:22
Alignment explanation
Indices: 1987638--1987689 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
1987628 AATAATTGTA
*
1987638 ATGTTTTTATTTAATGTTT-TTT
1 ATGTTTTT-TTTAATATTTCTTT
* *
1987660 ATGTAATGTTTTAATATTTCTTT
1 ATGT-TTTTTTTAATATTTCTTT
1987683 ATGTTTT
1 ATGTTTT
1987690 ATGTAAAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (22 bp):
ATGTTTTTTTTAATATTTCTTT
Found at i:1988631 original size:6 final size:6
Alignment explanation
Indices: 1988615--1988668 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
1988605 ATAGATGATC
* * * * *
1988615 AAAAAT AAAATT CAAATG CAAATT AAAATT GAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
1988663 AAAATT
1 AAAATT
1988669 GACATAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:1989983 original size:90 final size:90
Alignment explanation
Indices: 1989826--1990003 Score: 304
Period size: 90 Copynumber: 2.0 Consensus size: 90
1989816 CCCAACATAC
*
1989826 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCCAT
* *
1989891 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
1989916 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGGTTTT-ATTATTTCAAATTTATTAAATCCA
1 CCTTTTATATCCAAGTTACCCTAATCATATTA-GGGTTTTCATTATTTCAAATTAATTAAATCCA
1989980 TATTTAATTAATTGAAATTAAATA
65 TATTTAATTAATTGAAATTAAATA
1990004 TTCGGGATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
90 76 0.92
91 7 0.08
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (90 bp):
CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCCAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:1996397 original size:96 final size:95
Alignment explanation
Indices: 1996233--1996424 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 95
1996223 TACATATCGC
1996233 ATTAACCAAAAATTTAACCCAAAATAAGATCGTACAAGTGGCTCTGATGCCACTATTGGGACCGT
1 ATTAACCAAAAATTTAACCCAAAATAAGATCGTACAAGTGGCTCTGATGCCACTATTGGGACCGT
1996298 CGGCGCACCCCATGGCGCAAGCAGAAACAAA
66 CGGCGCACCCCATGGCGC-AGCAGAAACAAA
1996329 ATTAACCAAAAATTTAACCCAAAATAAGATCGTACAAGTGGCTCTGATGCCACTATTGGGACCGT
1 ATTAACCAAAAATTTAACCCAAAATAAGATCGTACAAGTGGCTCTGATGCCACTATTGGGACCGT
1996394 CGGCGCACCCCATGGCGCAGCAGAAACAAA
66 CGGCGCACCCCATGGCGCAGCAGAAACAAA
1996424 A
1 A
1996425 CTCGACAGTC
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 13 0.14
96 83 0.86
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (95 bp):
ATTAACCAAAAATTTAACCCAAAATAAGATCGTACAAGTGGCTCTGATGCCACTATTGGGACCGT
CGGCGCACCCCATGGCGCAGCAGAAACAAA
Found at i:1996865 original size:90 final size:90
Alignment explanation
Indices: 1996712--1996879 Score: 284
Period size: 90 Copynumber: 1.9 Consensus size: 90
1996702 CCTTTTATAT
* *
1996712 CCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCTATATTTAATTAA
1 CCAAGGTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCCATATTTAATTAA
* *
1996777 TTAGAATTTAATAATCCTTGTATGA
66 TTAAAATTAAATAATCCTTGTATGA
1996802 CCAAGGTACCCTAATCATATTAGGGGTTTT-ATTATTTCAAATTAATTAAATCCATATTTAATTA
1 CCAAGGTACCCTAATCATATTA-GGGTTTTCATTATTTCAAATTAATTAAATCCATATTTAATTA
1996866 ATTAAAATTAAATA
65 ATTAAAATTAAATA
1996880 TTCGAGATTA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
90 66 0.90
91 7 0.10
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (90 bp):
CCAAGGTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCCATATTTAATTAA
TTAAAATTAAATAATCCTTGTATGA
Found at i:1998125 original size:37 final size:37
Alignment explanation
Indices: 1998084--1998163 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
1998074 AATACAGAGA
1998084 CACTTTAAGGAAAACTAAAGGCATGTCCCACAAGAAG
1 CACTTTAAGGAAAACTAAAGGCATGTCCCACAAGAAG
*
1998121 CACTTTAAGGAAAACTGAAGGCATGTCCCACAAGAAG
1 CACTTTAAGGAAAACTAAAGGCATGTCCCACAAGAAG
1998158 CACTTT
1 CACTTT
1998164 TACCTTTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (37 bp):
CACTTTAAGGAAAACTAAAGGCATGTCCCACAAGAAG
Found at i:1999149 original size:169 final size:169
Alignment explanation
Indices: 1998464--2000341 Score: 1211
Period size: 170 Copynumber: 11.1 Consensus size: 169
1998454 ATAGTTACCT
* * * *
1998464 ATTATTAACTGAATAAT-ACAGAGAAACTCT-AAAGAAAAGGGAAGACATGTTCCACAAGAAGCA
1 ATTATTAACTGAAGAATGA-AAAGAAACTCTGACA-AAAAGGGAAGACATGTCCCACAAGAAGCA
* * * * *
1998527 ATTTCCCCTTTTTCAGAGAATCTCTACCATGTCATATTATCTCATCCTATTAAACATATTAGGGT
64 TTTTCACCTTTTT-AGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGG
* * *** **
1998592 TTGATGTGTATAATTTCCC--AATTGGGAACATCATAAATGCTT
128 TTGATGTGAAT-AGTTCCCTGAA-TGGGAACATCATTTCTGCCA
* * * * * * *
1998634 ATTATTAATTGAATAAT-ACAAAGAAACTTTGAAAAAAAGGGAAG--GTGCATCCCAAAAGAAAC
1 ATTATTAACTGAAGAATGA-AAAGAAACTCTGACAAAAAGGGAAGACATG--TCCCACAAGAAGC
* * * *
1998696 AATTTCACCTTTTTTAGAGAATCTCTACCATGTCATAATGTCTCATCCCATCAAACATATTGGGG
63 ATTTTCACC-TTTTTAGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGG
* ** * * * ** * *
1998761 GTTAACATGGATAGTTCCCTGACTAGGAACATCATAGCTACCT
127 GTTGATGTGAATAGTTCCCTGAATGGGAACATCATTTCTGCCA
* * * * * * * **
1998804 ATTATTAATTGGAGGAT-ACAGAGAAACTCTGAGGAAAAA-CGAAGACATGTCCCATAAGAAGTT
1 ATTATTAACTGAAGAATGA-AAAGAAACTCTGA-CAAAAAGGGAAGACATGTCCCACAAGAAGCA
* * * * * * * * *
1998867 TTTTCACCTTTTTTAGAAAATCTTTCCCATGTTATCTTGTCTCATTCCATCAAATATATTAGGGT
64 TTTTCACC-TTTTTAGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGG
* * * * *
1998932 TTGATGTAAATAGTTCCCTAAATGGGAACATCATAGT-TGTCT
128 TTGATGTGAATAGTTCCCTGAATGGGAACATCAT-TTCTGCCA
* * *
1998974 ATTATTAACTGAAGAATGAAAAGAGACTCTGACTAAAAGGGAAGACATGTCCCACAATAAGCATT
1 ATTATTAACTGAAGAATGAAAAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAAGAAGCATT
* *
1999039 TTCACCTTTTTAGAGAATATCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGGTTA
66 TTCACCTTTTTAGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGGTTG
** * *
1999104 ACATTAATAGTTCCTTGAATGGGAACA-CTATTTCTGCCA
131 ATGTGAATAGTTCCCTGAATGGGAACATC-ATTTCTGCCA
* * * * * * * *
1999143 ATTATTAACTAAAGAATGGAGAGAAACTCTGAAAAAAATGGAAGTCCTGTCCCATAAGAAGTGC-
1 ATTATTAACTGAAGAATGAAAAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAAGAA--GCA
* * * * * **
1999207 TTTT-ACCTTTTTCGTAGAATCTCTGCCATGTCACA-TAGTCTCATCACGTCAAACATATTAAAG
64 TTTTCACCTTTTTAG-AGAATCTCTACCATGTCATATTA-TCTCATCCCATCAAACATATTAGGG
* * * * * * * *
1999270 GTTAAAG-GCAATAGTTCCCCGACTAGTAACATTATTTATGCCA
127 GTTGATGTG-AATAGTTCCCTGAATGGGAACATCATTTCTGCCA
* * * * * * * **
1999313 ATTATTAACTTACGAATGCAAAGAAAATCTGACGAAAAGGAGAGGAACA--TCCCACAATAAGTG
1 ATTATTAACTGAAGAATGAAAAGAAACTCTGACAAAAAGG-GAAG-ACATGTCCCACAAGAAGCA
* * * *
1999376 TTTTCATCTTTTATTAGAAAATCTCTACCATGTCAAACTATCTCATCCCATCAAACATATTAGGG
64 TTTTCA-CCTTT-TTAGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGG
* * * * *
1999441 ATTGGAT-TGAATAGTTCCCTGATTGAGAACATAATTTCTTCCA
127 GTT-GATGTGAATAGTTCCCTGAATGGGAACATCATTTCTGCCA
* * * * * * * * * *
1999484 ATTATTAATTGAAGAATGCAGAA-AAACTTTGACAAAAAGGTAAGGCGTGTCTCACAAAAAACAC
1 ATTATTAACTGAAGAATG-AAAAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAAGAAGCAT
* * * * * *
1999548 TTTCAACATTTTAAGGGAATCTCTTCCATGTCATATTATCTCATCCCTTCAAACATATTAAGGGT
65 TTTC-ACCTTTTTAGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGGT
** * *
1999613 TGATGTGAATA-TTTGCTCGACTTGGAACATCA----T----
129 TGATGTGAATAGTTCCCT-GAATGGGAACATCATTTCTGCCA
* * * * * * ** * **
1999646 ATCATTAACTGAAAAATGTAGAGAAACTCTAACGAAAAGGGAAGATGTGTCCCACAAGAAACCCT
1 ATTATTAACTGAAGAATGAAAAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAAGAAGCATT
* * * * * * * * * * **
1999711 TTCACCTTTTTATAGAATCTCTGCAAAGTCATACTATATAATCCCATAAAATATATCAATGGTTG
66 TTCACCTTTTTAGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGGTTG
* ** * **
1999776 ATGTGAATAGTT-CCTCAACTATGAAAATCATTT-TTTCA
131 ATGTGAATAGTTCCCTGAA-TGGGAACATCATTTCTGCCA
* * * * * *
1999814 TATTATTAATTGAAGAATGTAGAGAAACTCTAACAAAAAGGGAATG-CAAGTCTCACAAGAAGC-
1 -ATTATTAACTGAAGAATGAAAAGAAACTCTGACAAAAAGGGAA-GACATGTCCCACAAGAAGCA
* * * ** * *
1999877 TCTTTCACCTTTTTCA-AGAATGTCTGCAATAACATATTGTCTCATCCCATCAAACATAATAGGG
64 T-TTTCACCTTTTT-AGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGG
* * * * *
1999941 GTTGATGTGAATAGTTACCC-GATTTGGAACATTATTTTTGCCC
127 GTTGATGTGAATAGTT-CCCTGAATGGGAACATCATTTCTGCCA
* * * * * * * *
1999984 ATTATTAACTTAAAAATGTAAAGAAACTCTAACAAAAAGGGAAGTCATGTTCCAGAAGAAGCACT
1 ATTATTAACTGAAGAATGAAAAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAAGAAGCATT
* * * * * * *
2000049 TTCACCTTTTTCTGAGAATCTTTATCGTATCATATTGTCTCATCCCATCAAACATAATAGGGGTT
66 TTCACCTTTTT-AGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGGTT
* *
2000114 GATGTGAATAGTT-CCTCGATTGGGAACATCATTTCTGCCC
130 GATGTGAATAGTTCCCT-GAATGGGAACATCATTTCTGCCA
* * * * ** * * **
2000154 ATTGTTAACTGAAGAAT-ATAGAGAAACTCTAACAAAAAGGAAAGTGATATCCCACGAGAAGCGG
1 ATTATTAACTGAAGAATGA-AAAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAAGAAGCAT
* * * * **
2000218 CTTCACCTTTTTCATAGAATCTCTACCATGTCATATTTTCTTATCCCATCAAACATATTATTGGT
65 TTTCACCTTTTT-AGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGGT
* * * **
2000283 TAACGTGAATAGTTCCTCT-ATTGGGAACATCATTTCTGCTT
129 TGATGTGAATAGTTCC-CTGAATGGGAACATCATTTCTGCCA
*
2000324 ATTATTTACTGAAGAATG
1 ATTATTAACTGAAGAATG
2000342 CTCTCAAATT
Statistics
Matches: 1339, Mismatches: 308, Indels: 121
0.76 0.17 0.07
Matches are distributed among these distances:
160 1 0.00
161 67 0.05
162 53 0.04
164 1 0.00
166 1 0.00
168 8 0.01
169 345 0.26
170 709 0.53
171 139 0.10
172 15 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (169 bp):
ATTATTAACTGAAGAATGAAAAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAAGAAGCATT
TTCACCTTTTTAGAGAATCTCTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGGTTG
ATGTGAATAGTTCCCTGAATGGGAACATCATTTCTGCCA
Found at i:1999173 original size:339 final size:334
Alignment explanation
Indices: 1998459--2000341 Score: 1018
Period size: 339 Copynumber: 5.6 Consensus size: 334
1998449 ACATCATAGT
* * * * * *
1998459 TACCTATTATTAACTGAATAATACAGAGAAACTCTAAAGAAAAGGGAAGACATGTTCCACAAGAA
1 TACCAATTATTAACTGAAGAATACAGAGAAACTCT-GAGAAAAAGGAAGACATGTCCCATAAGAA
* * * * * * *
1998524 GCAATTTCCCCTTTTTCAGAGAATCTCTACCATGTCATATTATCTCATCCTATTAAACATATTAG
65 GTATTTTCACCTTTTTTAGA-AATCTCTACCATGTCATCTTGTCTCATCC-ATCAAACATATTAG
** * * * * *
1998589 GGTTTGATGTGTATAATTTCCCAATTGGGAACATCATAAATGCTTATTATTAATTGAATAAT-AC
128 GGTTTGATGTAAAT-AGTTCCCAAATGGGAACATCATAATTGC-TATTATTAACTGAAGAATGA-
* * * * * * *
1998653 AAAGAAACTTTGAAAAAAAGGGAAG--GTGCATCCCAAAAGAAACAATTTCACCTTTTTTAGAGA
190 AAAGAAACTCTGACAAAAAGGGAAGACATG--TCCCACAATAAGCATTTTCACC-TTTTTAGAGA
* * **
1998716 ATCTCTACCATGTCATAATGTCTCATCCCATCAAACATATTGGGGGTTAACATGGATAGTTCCCT
252 ATCTCTACCATGTCATAATATCTCATCCCATCAAACATATTAGGGGTTAACATTAATAGTTCCCT
* * * **
1998781 GACTAGGAACATCATAGC
317 GAATGGGAACATAATTTC
* * * * *
1998799 TACCTATTATTAATTGGAGGATACAGAGAAACTCTGAGGAAAAACGAAGACATGTCCCATAAGAA
1 TACCAATTATTAACTGAAGAATACAGAGAAACTCTGA-GAAAAAGGAAGACATGTCCCATAAGAA
* * * * *
1998864 GTTTTTTCACCTTTTTTAGAAAATCTTTCCCATGTTATCTTGTCTCATTCCATCAAATATATTAG
65 GTATTTTCACCTTTTTTAG-AAATCTCTACCATGTCATCTTGTCTCA-TCCATCAAACATATTAG
*
1998929 GGTTTGATGTAAATAGTTCCCTAAATGGGAACATCATAGTTGTCTATTATTAACTGAAGAATGAA
128 GGTTTGATGTAAATAGTTCCC-AAATGGGAACATCATAATTG-CTATTATTAACTGAAGAATGAA
* * *
1998994 AAGAGACTCTGACTAAAAGGGAAGACATGTCCCACAATAAGCATTTTCACCTTTTTAGAGAATAT
191 AAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAATAAGCATTTTCACCTTTTTAGAGAATCT
* *
1999059 CTACCATGTCATATTATCTCATCCCATCAAACATATTAGGGGTTAACATTAATAGTTCCTTGAAT
256 CTACCATGTCATAATATCTCATCCCATCAAACATATTAGGGGTTAACATTAATAGTTCCCTGAAT
1999124 GGGAACACT-ATTTC
321 GGGAACA-TAATTTC
* * ** * * *
1999138 TGCCAATTATTAACTAAAGAATGGAGAGAAACTCTGAAAAAAATGGAAGTCCTGTCCCATAAGAA
1 TACCAATTATTAACTGAAGAATACAGAGAAACTCTGAGAAAAA-GGAAGACATGTCCCATAAGAA
* * * *
1999203 GTGCTTTT-ACCTTTTTCGTAG-AATCTCTGCCATGTCA-CATAGTCTCATCACGTCAAACATAT
65 GT-ATTTTCACCTTTTT--TAGAAATCTCTACCATGTCATC-TTGTCTCATC-CATCAAACATAT
* * * ** * * * * * * * * *
1999265 TAAAGG-TTAAAGGCAATAGTTCCCCGACTAGTAACATTAT-TTATGCCAATTATTAACTTACGA
125 T-AGGGTTTGATGTAAATAGTT-CCCAAATGGGAACATCATAAT-TG-CTATTATTAACTGAAGA
* * * * ** *
1999328 ATGCAAAGAAAATCTGACGAAAAGGAGAGGAACA--TCCCACAATAAGTGTTTTCATCTTTTATT
186 ATGAAAAGAAACTCTGACAAAAAGG-GAAG-ACATGTCCCACAATAAGCATTTTCA-CCTTT-TT
* * **
1999391 AGAAAATCTCTACCATGTCA-AACTATCTCATCCCATCAAACATATTAGGGATT-GGATTGAATA
247 AGAGAATCTCTACCATGTCATAA-TATCTCATCCCATCAAACATATTAGGGGTTAACATT-AATA
* *
1999454 GTTCCCTGATTGAGAACATAATTTC
310 GTTCCCTGAATGGGAACATAATTTC
* * * * * * * * * * *
1999479 TTCCAATTATTAATTGAAGAATGCAGAAAAACTTTGACAAAAAGGTAAGGCGTGTCTCACAAAAA
1 TACCAATTATTAACTGAAGAATACAGAGAAACTCTGAGAAAAAGG-AAGACATGTCCCATAAGAA
** * * * * * * * * *
1999544 ACACTTTCAACATTTTAAGGGAATCTCTTCCATGTCATATTATCTCATCCCTTCAAACATATTAA
65 GTATTTTCACCTTTTTTA-GAAATCTCTACCATGTCATCTTGTCTCAT-CCATCAAACATATT-A
* * * * * * * *
1999609 GGG-TTGATGTGAATATTTGCTCGACTTGGAACATCAT-A-T-C----ATTAACTGAAAAATGTA
127 GGGTTTGATGTAAATAGTT-CCCAAATGGGAACATCATAATTGCTATTATTAACTGAAGAATGAA
* * * ** * * ** *
1999666 GAGAAACTCTAACGAAAAGGGAAGATGTGTCCCACAAGAAACCCTTTCACCTTTTTATAGAATCT
191 AAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAATAAGCATTTTCACCTTTTTAGAGAATCT
* * * * * * * * * ** * ** * *
1999731 CTGCAAAGTCATACTATATAATCCCATAAAATATATCAATGGTTGATGTGAATAGTT-CCTCAAC
256 CTACCATGTCATAATATCTCATCCCATCAAACATATTAGGGGTTAACATTAATAGTTCCCTGAA-
** * *
1999795 TATGAAAATCATTT-
320 TGGGAACATAATTTC
** * ** * * * * *
1999809 TTTCATATTATTAATTGAAGAATGTAGAGAAACTCTAACAAAAAGGGAATG-CAAGTCTCACAAG
1 TACCA-ATTATTAACTGAAGAATACAGAGAAACTCTGAGAAAAA-GGAA-GACATGTCCCATAAG
* * * * * ** * *
1999873 AAGCT-CTTTCACCTTTTTCA-AGAATGTCTGCAATAACATATTGTCTCATCCCATCAAACATAA
63 AAG-TATTTTCACCTTTTTTAGA-AATCTCTACCATGTCATCTTGTCTCAT-CCATCAAACATAT
* * * * * * ** * * *
1999936 TAGGGGTTGATGTGAATAGTTACCCGATTTGGAACATTATTTTTGCCCATTATTAACTTAAAAAT
125 TAGGGTTTGATGTAAATAGTT-CCCAAATGGGAACATCATAATTG-CTATTATTAACTGAAGAAT
* * * * * * * *
2000001 GTAAAGAAACTCTAACAAAAAGGGAAGTCATGTTCCAGAAGAAGCACTTTCACCTTTTTCTGAGA
188 GAAAAGAAACTCTGACAAAAAGGGAAGACATGTCCCACAATAAGCATTTTCACCTTTTT-AGAGA
* * * * * * * * ** *
2000066 ATCTTTATCGTATCATATTGTCTCATCCCATCAAACATAATAGGGGTTGATGTGAATAGTT-CCT
252 ATCTCTACCATGTCATAATATCTCATCCCATCAAACATATTAGGGGTTAACATTAATAGTTCCCT
* *
2000130 CGATTGGGAACATCATTTC
317 -GAATGGGAACATAATTTC
* * * * * * ** * **
2000149 TGCCCATTGTTAACTGAAGAATATAGAGAAACTCTAACAAAAAGGAAAGTGATATCCCACGAGAA
1 TACCAATTATTAACTGAAGAATACAGAGAAACTCTGAGAAAAAGG-AAGACATGTCCCATAAGAA
**** * * *
2000214 GCGGCTTCACCTTTTTCATAG-AATCTCTACCATGTCATATTTTCTTATCCCATCAAACATATTA
65 GTATTTTCACCTTTTT--TAGAAATCTCTACCATGTCATCTTGTCTCAT-CCATCAAACATATTA
* * * * * * * *
2000278 TTGG-TTAACGTGAATAGTTCCTCTATTGGGAACATCAT-TTCTGCTTATTATTTACTGAAGAAT
127 -GGGTTTGATGTAAATAGTTCC-CAAATGGGAACATCATAAT-TGC-TATTATTAACTGAAGAAT
2000341 G
188 G
2000342 CTCTCAAATT
Statistics
Matches: 1209, Mismatches: 271, Indels: 126
0.75 0.17 0.08
Matches are distributed among these distances:
329 4 0.00
330 71 0.06
331 117 0.10
332 13 0.01
333 45 0.04
334 1 0.00
337 1 0.00
338 75 0.06
339 378 0.31
340 295 0.24
341 206 0.17
342 3 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (334 bp):
TACCAATTATTAACTGAAGAATACAGAGAAACTCTGAGAAAAAGGAAGACATGTCCCATAAGAAG
TATTTTCACCTTTTTTAGAAATCTCTACCATGTCATCTTGTCTCATCCATCAAACATATTAGGGT
TTGATGTAAATAGTTCCCAAATGGGAACATCATAATTGCTATTATTAACTGAAGAATGAAAAGAA
ACTCTGACAAAAAGGGAAGACATGTCCCACAATAAGCATTTTCACCTTTTTAGAGAATCTCTACC
ATGTCATAATATCTCATCCCATCAAACATATTAGGGGTTAACATTAATAGTTCCCTGAATGGGAA
CATAATTTC
Found at i:2003220 original size:88 final size:88
Alignment explanation
Indices: 2003071--2003246 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
2003061 ATACAATGAA
2003071 GCTATGACATATTGGAAAGGATTTCCAATAATGACTATCAATTCCCTAATACGAGAAACATGTTT
1 GCTATGACATATTGGAAAGGATTTCCAATAATGACTATCAATTCCCTAATACGAGAAACATGTTT
2003136 GGCAAATGCAATGCTCCAGCAAC
66 GGCAAATGCAATGCTCCAGCAAC
2003159 GCTATGACATATTGGAAAGGATTTCCAATAATGACTATCAATTCCCTAATACGAGAAACATGTTT
1 GCTATGACATATTGGAAAGGATTTCCAATAATGACTATCAATTCCCTAATACGAGAAACATGTTT
2003224 GGCAAATGCAATGCTCCAGCAAC
66 GGCAAATGCAATGCTCCAGCAAC
2003247 CGACATTGAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (88 bp):
GCTATGACATATTGGAAAGGATTTCCAATAATGACTATCAATTCCCTAATACGAGAAACATGTTT
GGCAAATGCAATGCTCCAGCAAC
Found at i:2018091 original size:21 final size:21
Alignment explanation
Indices: 2018061--2018100 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2018051 ACAAGCATCG
*
2018061 TAATTGTCAAATAAATAAACA
1 TAATTCTCAAATAAATAAACA
2018082 TAATTCTCAAATAAATAAA
1 TAATTCTCAAATAAATAAA
2018101 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (21 bp):
TAATTCTCAAATAAATAAACA
Found at i:2020097 original size:223 final size:226
Alignment explanation
Indices: 2019709--2020159 Score: 863
Period size: 223 Copynumber: 2.0 Consensus size: 226
2019699 TGTGAGGCGT
2019709 CATCACCGATCATTTAAGGTGCGATTAGAGCATCATAAAAAATAGGGCGATTTTAATAAAACATT
1 CATCACCGATCATTTAAGGTGCGATTAGAGCATCATAAAAAATAGGGCGATTTTAATAAAACATT
2019774 TTATTTTTAACAAAATACTGAGTTTTGGGGTATACAAAAATTAAAAAATCAGGTTTAGGAGTCAG
66 TTATTTTTAACAAAATACTGAGTTTTGGGGTATACAAAAATTAAAAAATCAGGTTTAGGAGTCAG
2019839 TTACAAATTGGGAAGGATTAGCACCCTGACAAGTTTCCAAAAATTGGTACCTA-GATTACCTTAT
131 TTACAAATTGGGAAGGATTAGCACCCTGACAAGTTTCCAAAAATTGGTACCTATGATTACCTTAT
2019903 ATTTAAAA-AAGAAA-TTTGAATTCCATCTC
196 ATTTAAAATAAGAAATTTTGAATTCCATCTC
2019932 CATCACCGATCATTTAAGGTGCGATTAGAGCATCATAAAAAATAGGGCGATTTTAATAAAACATT
1 CATCACCGATCATTTAAGGTGCGATTAGAGCATCATAAAAAATAGGGCGATTTTAATAAAACATT
2019997 TTATTTTTAACAAAATACTGAGTTTTGGGGTATACAAAAATTAAAAAATCAGGTTTAGGAGTCAG
66 TTATTTTTAACAAAATACTGAGTTTTGGGGTATACAAAAATTAAAAAATCAGGTTTAGGAGTCAG
2020062 TTACAAATTGGGAAGGATTAGCACCCTGACAAGTTTCCAAAAATTGGTACCTAGTTGATTACCTT
131 TTACAAATTGGGAAGGATTAGCACCCTGACAAGTTTCCAAAAATTGGTACCTA--TGATTACCTT
2020127 ATATTTAAAATAAGAAATTTTGAATTCCATCTC
194 ATATTTAAAATAAGAAATTTTGAATTCCATCTC
2020160 TATTAATTTT
Statistics
Matches: 223, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
223 183 0.82
226 19 0.09
227 6 0.03
228 15 0.07
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (226 bp):
CATCACCGATCATTTAAGGTGCGATTAGAGCATCATAAAAAATAGGGCGATTTTAATAAAACATT
TTATTTTTAACAAAATACTGAGTTTTGGGGTATACAAAAATTAAAAAATCAGGTTTAGGAGTCAG
TTACAAATTGGGAAGGATTAGCACCCTGACAAGTTTCCAAAAATTGGTACCTATGATTACCTTAT
ATTTAAAATAAGAAATTTTGAATTCCATCTC
Found at i:2024970 original size:16 final size:16
Alignment explanation
Indices: 2024945--2024983 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2024935 ACCAATGTGT
*
2024945 ACCTTGAAGAAATTGC
1 ACCTTAAAGAAATTGC
2024961 ACCTTAAAGAAATTGC
1 ACCTTAAAGAAATTGC
2024977 ACCTTAA
1 ACCTTAA
2024984 TTGGCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (16 bp):
ACCTTAAAGAAATTGC
Found at i:2033459 original size:17 final size:17
Alignment explanation
Indices: 2033437--2033469 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2033427 GACCCTTTGG
2033437 CTTTATTTCTATTTTCT
1 CTTTATTTCTATTTTCT
*
2033454 CTTTATTTCTCTTTTC
1 CTTTATTTCTATTTTC
2033470 CTTATGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (17 bp):
CTTTATTTCTATTTTCT
Found at i:2034036 original size:3 final size:3
Alignment explanation
Indices: 2034030--2034114 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
2034020 TATGATGATG
2034030 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2034078 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2034115 ATTTTCGAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2035354 original size:2 final size:2
Alignment explanation
Indices: 2035347--2035430 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
2035337 TGTATCTTTA
2035347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2035389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2035430 A
1 A
2035431 CTATCTATTA
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 80 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2043025 original size:13 final size:13
Alignment explanation
Indices: 2043007--2043034 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2042997 GATGAAAGAG
2043007 AGTAAAAGTGAAA
1 AGTAAAAGTGAAA
2043020 AGTAAAAGTGAAA
1 AGTAAAAGTGAAA
2043033 AG
1 AG
2043035 AATATAGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (13 bp):
AGTAAAAGTGAAA
Found at i:2054540 original size:26 final size:26
Alignment explanation
Indices: 2054501--2054550 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2054491 TTGTGAGTGT
2054501 GAGTTGAACCAAGGGTATACATTCGA
1 GAGTTGAACCAAGGGTATACATTCGA
* *
2054527 GAGTTGAACGAAGGGTATATATTC
1 GAGTTGAACCAAGGGTATACATTC
2054551 TAGTCTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (26 bp):
GAGTTGAACCAAGGGTATACATTCGA
Found at i:2062535 original size:40 final size:40
Alignment explanation
Indices: 2062475--2062554 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
2062465 ATTGGAGGAT
* *
2062475 TAATTTGAATAAATGTTAAAGGACAATAAATGATTTAGAA
1 TAATTTGAATAAATGGTAAAGGACAAGAAATGATTTAGAA
*
2062515 TAATTTGAATAAATGGTAAAGGATAAGAAATGATTTAGAA
1 TAATTTGAATAAATGGTAAAGGACAAGAAATGATTTAGAA
2062555 ATAGTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.50, C:0.01, G:0.17, T:0.31
Consensus pattern (40 bp):
TAATTTGAATAAATGGTAAAGGACAAGAAATGATTTAGAA
Found at i:2063409 original size:20 final size:22
Alignment explanation
Indices: 2063365--2063409 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2063355 GGAGTATCGG
*
2063365 TACCATAGTATAGAAGTATCGA
1 TACCATAGTATAGAAGTACCGA
*
2063387 TACCATAGTA-AG-GGTACCGA
1 TACCATAGTATAGAAGTACCGA
2063407 TAC
1 TAC
2063410 TATTGATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 10 0.48
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (22 bp):
TACCATAGTATAGAAGTACCGA
Found at i:2072348 original size:131 final size:132
Alignment explanation
Indices: 2072101--2072365 Score: 514
Period size: 131 Copynumber: 2.0 Consensus size: 132
2072091 CAATATAATT
2072101 AGAGATTGTCTCACATATCTCAAAGCCATGCAACATATTTATTCATTTCTTTTCAACCTTTAATA
1 AGAGATTGTCT-ACATATCTCAAAGCCATGCAACATATTTATTCATTTCTTTTCAACCTTTAATA
2072166 ATAATCAAATTTCACAATATGTCACATGTGTTAGAGTATGCTCAAAGACCAATCCTATGATGATT
65 ATAATCAAATTTCACAATATGTCACATGTGTTAGAGTATGCTCAAAGACCAATCCTATGATGATT
2072231 TTA
130 TTA
2072234 AGAGATTGTCT-CATATCTCAAAGCCATGCAACATATTTATTCATTTCTTTTCAACCTTTAATAA
1 AGAGATTGTCTACATATCTCAAAGCCATGCAACATATTTATTCATTTCTTTTCAACCTTTAATAA
2072298 TAATCAAATTTCACAATATGTCACATGTGTTAGAGTATGCTCAAAGACCAATCCTATGATGATTT
66 TAATCAAATTTCACAATATGTCACATGTGTTAGAGTATGCTCAAAGACCAATCCTATGATGATTT
2072363 TA
131 TA
2072365 A
1 A
2072366 TATTACATTT
Statistics
Matches: 132, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
131 121 0.92
133 11 0.08
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (132 bp):
AGAGATTGTCTACATATCTCAAAGCCATGCAACATATTTATTCATTTCTTTTCAACCTTTAATAA
TAATCAAATTTCACAATATGTCACATGTGTTAGAGTATGCTCAAAGACCAATCCTATGATGATTT
TA
Found at i:2077426 original size:13 final size:13
Alignment explanation
Indices: 2077408--2077432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2077398 ATGACCTTAA
2077408 AAGAAAAGAAAAG
1 AAGAAAAGAAAAG
2077421 AAGAAAAGAAAA
1 AAGAAAAGAAAA
2077433 AAATCTAAAT
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAAG
Found at i:2080771 original size:83 final size:84
Alignment explanation
Indices: 2080674--2080839 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 84
2080664 ATTGTAAAGT
2080674 TTTCATAATATAGTTAGTATAGTATATTAAACAAGTATAAGCCCACATTTTAAAAATAAATGTTA
1 TTTCATAATATAGTTAGTATAGTATATTAAACAAGTATAAGCCCACATTTTAAAAATAAATGTTA
2080739 GTCCA-TTTTTTAGAATAG
66 GTCCATTTTTTTAGAATAG
2080757 TTTCATAATATAGTTAGTATAGTATATTAAACAAGTATAAGCCCACATTTTAAAAATAAATGTTA
1 TTTCATAATATAGTTAGTATAGTATATTAAACAAGTATAAGCCCACATTTTAAAAATAAATGTTA
2080822 GTCCATTTTTTTAGAATA
66 GTCCATTTTTTTAGAATA
2080840 AAGTCCATGT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 70 0.85
84 12 0.15
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (84 bp):
TTTCATAATATAGTTAGTATAGTATATTAAACAAGTATAAGCCCACATTTTAAAAATAAATGTTA
GTCCATTTTTTTAGAATAG
Found at i:2086942 original size:39 final size:39
Alignment explanation
Indices: 2086841--2086997 Score: 136
Period size: 39 Copynumber: 4.0 Consensus size: 39
2086831 CTTGTACCCC
* * * * * *
2086841 CAGTAAGGACATACCCTGTGCACAAAGAAGAAGAGCCTC
1 CAGTAAAGACTTACCCTGAGCACAAAGCAGAGGAGCCTA
* *** * *
2086880 CAGTAAAGTCTTATATTGTGCACAAAGCAGAGGAGCCTG
1 CAGTAAAGACTTACCCTGAGCACAAAGCAGAGGAGCCTA
* * *
2086919 CAGTAAGGACTTACCCTGAGCACAAAGTC-GAGAAACCTA
1 CAGTAAAGACTTACCCTGAGCACAAAG-CAGAGGAGCCTA
* * *
2086958 CGGTAAAGACTTACCCTAAGCACAAAGCAGAGGATCCTA
1 CAGTAAAGACTTACCCTGAGCACAAAGCAGAGGAGCCTA
2086997 C
1 C
2086998 GATAAGCGGT
Statistics
Matches: 93, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
38 1 0.01
39 91 0.98
40 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (39 bp):
CAGTAAAGACTTACCCTGAGCACAAAGCAGAGGAGCCTA
Found at i:2091831 original size:18 final size:18
Alignment explanation
Indices: 2091808--2091859 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
2091798 ATGGCCACGA
2091808 CCTGGCCTATGACCTCGG
1 CCTGGCCTATGACCTCGG
*
2091826 CCTGGCCTATTACCTCGG
1 CCTGGCCTATGACCTCGG
2091844 CCTGGCCTATGACCTC
1 CCTGGCCTATGACCTC
2091860 TAGTCGCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.12, C:0.40, G:0.23, T:0.25
Consensus pattern (18 bp):
CCTGGCCTATGACCTCGG
Found at i:2092618 original size:39 final size:40
Alignment explanation
Indices: 2092574--2092775 Score: 193
Period size: 39 Copynumber: 5.2 Consensus size: 40
2092564 CTTGTACGCC
2092574 CAGTAAGGACTTACCCT-ATGCACAAAGCAGAGGAGCCTG
1 CAGTAAGGACTTACCCTGATGCACAAAGCAGAGGAGCCTG
* * * * *
2092613 CAGTAATGTCTTATCTTG-TGCACAAATCAGAGGAGCCTG
1 CAGTAAGGACTTACCCTGATGCACAAAGCAGAGGAGCCTG
* * * *
2092652 CAATAAGGACTTACCCTGAT-C-CTAAAGCGGAGGAACATG
1 CAGTAAGGACTTACCCTGATGCAC-AAAGCAGAGGAGCCTG
** * *
2092691 TGGTAAGGACTTACCCTGA-GAACAAAGTC-GAGGAACCTG
1 CAGTAAGGACTTACCCTGATGCACAAAG-CAGAGGAGCCTG
* * *
2092730 CGGTAAGGACTTACCCTGA-GCACAAAGCCGAGGAGCCTA
1 CAGTAAGGACTTACCCTGATGCACAAAGCAGAGGAGCCTG
2092769 CAGTAAG
1 CAGTAAG
2092776 CGGTAAGGTC
Statistics
Matches: 132, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
38 2 0.02
39 127 0.96
40 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (40 bp):
CAGTAAGGACTTACCCTGATGCACAAAGCAGAGGAGCCTG
Found at i:2093571 original size:18 final size:18
Alignment explanation
Indices: 2093548--2093590 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2093538 TTCGATCATA
2093548 GTCAACGGTCAACCGTCG
1 GTCAACGGTCAACCGTCG
*
2093566 GTCAACGGTCAACTGTCG
1 GTCAACGGTCAACCGTCG
2093584 GTCAACG
1 GTCAACG
2093591 TTAGACCGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (18 bp):
GTCAACGGTCAACCGTCG
Found at i:2094166 original size:29 final size:30
Alignment explanation
Indices: 2094108--2094166 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2094098 TGGATATGAA
* *
2094108 TTTAATCAAAATTTCACTTTGGTCCCCGAT
1 TTTAATCAAAATTTCAATTTGATCCCCGAT
* *
2094138 TTTAATCAAAA-TTCAATTTTATCCTCGAT
1 TTTAATCAAAATTTCAATTTGATCCCCGAT
2094167 AAATTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (30 bp):
TTTAATCAAAATTTCAATTTGATCCCCGAT
Found at i:2095104 original size:151 final size:153
Alignment explanation
Indices: 2094935--2095238 Score: 594
Period size: 151 Copynumber: 2.0 Consensus size: 153
2094925 GCCTTTTAGG
2094935 TTTAGTTTCTTTAATAATTCATTAATTAGAAACATATAATTAAATTTATAATATGATTAAAATGC
1 TTTAGTTTCTTTAATAATTCATTAATTAGAAACATATAATTAAATTTATAATATGATTAAAATGC
2095000 TATAGAATTA-CACTCAAGTGTACGATTCAC-TAAGTAATAAAGTGGAAGTCTTTTTGGGACTTC
66 TATAGAATTACCACTCAAGTGTACGATTCACATAAGTAATAAAGTGGAAGTCTTTTTGGGACTTC
2095063 GGATGTCGAACCCAAAAATAGCA
131 GGATGTCGAACCCAAAAATAGCA
2095086 TTTAGTTTCTTTAATAATTCATTAATTAGAAACATATAATTAAATTTATAATATGATTAAAATGC
1 TTTAGTTTCTTTAATAATTCATTAATTAGAAACATATAATTAAATTTATAATATGATTAAAATGC
2095151 TATAGAATTACCACTCAAGTGTACGATTCACATAAGTAATAAAGTGGAAGTCTTTTTGGGACTTC
66 TATAGAATTACCACTCAAGTGTACGATTCACATAAGTAATAAAGTGGAAGTCTTTTTGGGACTTC
2095216 GGATGTCGAACCCAAAAATAGCA
131 GGATGTCGAACCCAAAAATAGCA
2095239 GAATATTTAC
Statistics
Matches: 151, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
151 75 0.50
152 20 0.13
153 56 0.37
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (153 bp):
TTTAGTTTCTTTAATAATTCATTAATTAGAAACATATAATTAAATTTATAATATGATTAAAATGC
TATAGAATTACCACTCAAGTGTACGATTCACATAAGTAATAAAGTGGAAGTCTTTTTGGGACTTC
GGATGTCGAACCCAAAAATAGCA
Found at i:2114852 original size:93 final size:93
Alignment explanation
Indices: 2114693--2114879 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
2114683 TTCATAATGG
2114693 TCACCGACTCGATATTTAGATTACTACATACTAATTCATCGCTATCAGACCTACAATATTAGAAA
1 TCACCGACTCGATATTTAGATTACTACATACTAATTCATCGCTATCAGACCTACAATATTAGAAA
2114758 GTAACTACAAAAAAGAAACGAACAAAGT
66 GTAACTACAAAAAAGAAACGAACAAAGT
2114786 TCACCGACTCGATATTTAGATTACTACATACTAATTCATCGCTATCAGACCTACAATATTAGAAA
1 TCACCGACTCGATATTTAGATTACTACATACTAATTCATCGCTATCAGACCTACAATATTAGAAA
2114851 GTAACTACAAAAAAGAAACGAACAAAGT
66 GTAACTACAAAAAAGAAACGAACAAAGT
2114879 T
1 T
2114880 ATTAACTACA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (93 bp):
TCACCGACTCGATATTTAGATTACTACATACTAATTCATCGCTATCAGACCTACAATATTAGAAA
GTAACTACAAAAAAGAAACGAACAAAGT
Found at i:2116584 original size:61 final size:60
Alignment explanation
Indices: 2116486--2116644 Score: 185
Period size: 61 Copynumber: 2.6 Consensus size: 60
2116476 ATCGTAGTGC
* * * *
2116486 TATGACACATAAGGTCGTGCCCACCACCTATAATAAGTTTACACT-ATAGTGATAATTCGGA
1 TATGACACATAA-GTTGTGCCCACCACCTACACTAAGTTTACACTCA-AGTGATAATCCGGA
* **
2116547 TATGACACATAATGTTTTGCCCACCACCTACACTAAGTTTACACTCAAGTTCTAATCCGGA
1 TATGACACATAA-GTTGTGCCCACCACCTACACTAAGTTTACACTCAAGTGATAATCCGGA
* * *
2116608 TATAACACATAAGTTCGTGCCCACCACTTGCACTAAG
1 TATGACACATAAGTT-GTGCCCACCACCTACACTAAG
2116645 AGTTCTTACA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
60 3 0.04
61 80 0.95
62 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (60 bp):
TATGACACATAAGTTGTGCCCACCACCTACACTAAGTTTACACTCAAGTGATAATCCGGA
Found at i:2122122 original size:3 final size:3
Alignment explanation
Indices: 2122114--2122152 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2122104 CACTATTAGC
2122114 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2122153 GAATAAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2124444 original size:12 final size:12
Alignment explanation
Indices: 2124427--2124464 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2124417 CTCATGTATC
2124427 TTTCTATTTTCT
1 TTTCTATTTTCT
2124439 TTTCTA-TTT-T
1 TTTCTATTTTCT
*
2124449 TTTCTTTTTTCT
1 TTTCTATTTTCT
2124461 TTTC
1 TTTC
2124465 GAACTGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 6 0.26
11 6 0.26
12 11 0.48
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTATTTTCT
Found at i:2126150 original size:17 final size:16
Alignment explanation
Indices: 2126125--2126156 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2126115 TCTAACTTAT
2126125 TATTTTCCTTGCATCA
1 TATTTTCCTTGCATCA
2126141 TATTTATCCTTGCATC
1 TATTT-TCCTTGCATC
2126157 TCCAAACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (16 bp):
TATTTTCCTTGCATCA
Found at i:2127475 original size:23 final size:23
Alignment explanation
Indices: 2127459--2127511 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
2127449 ACTTCATCTT
* *
2127459 CATCATCCATTCTACTTTAACAC
1 CATCATCCATTCAACTTCAACAC
2127482 CATCATCCATTCAACTTCAACAC
1 CATCATCCATTCAACTTCAACAC
2127505 CATCATC
1 CATCATC
2127512 AACCTTTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.38, G:0.00, T:0.30
Consensus pattern (23 bp):
CATCATCCATTCAACTTCAACAC
Found at i:2131147 original size:18 final size:18
Alignment explanation
Indices: 2131124--2131169 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 18
2131114 TCAGAAATCT
2131124 TACCTTTTCACAAAGAGG
1 TACCTTTTCACAAAGAGG
2131142 TACC-TTTC-C-AAGAGG
1 TACCTTTTCACAAAGAGG
2131157 TGA-CTTTTCACAA
1 T-ACCTTTTCACAA
2131170 GGACCTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 5 0.21
18 5 0.21
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (18 bp):
TACCTTTTCACAAAGAGG
Found at i:2131784 original size:23 final size:23
Alignment explanation
Indices: 2131754--2131797 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2131744 GTTTGAGATA
*
2131754 CAACTTCATCACCATCATCCATT
1 CAACTTCAACACCATCATCCATT
2131777 CAACTTCAACACCATCATCCA
1 CAACTTCAACACCATCATCCA
2131798 CCTTCCATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (23 bp):
CAACTTCAACACCATCATCCATT
Found at i:2142948 original size:158 final size:159
Alignment explanation
Indices: 2142767--2143085 Score: 615
Period size: 158 Copynumber: 2.0 Consensus size: 159
2142757 TACCATTGAT
2142767 AAGCCTTGATCTAAGGGTCCTTATTTCATGGATCCTTGTCAAACAAACACAAAATAATGTGGACC
1 AAGCCTTGATCTAAGGGTCCTTATTTCATGGATCCTTGTCAAACAAACACAAAATAATGTGGACC
2142832 GTTGATTAAAAGTTAGATCCAAGGGATCCCATAATGTTACGTCATCGATCCCATGCCAACAAACA
66 GTTGATTAAAAGTTAGATCCAAGGGATCCCATAATGTTACGTCATCGAT-CCATGCCAACAAACA
2142897 CAAATG-TTCTCAACCATTGGATC-AGATG
130 CAAATGCTTCTCAACCATTGGATCAAGATG
2142925 AAGCCTTGATCTAAGGGTCCTTATTTCATGGATCCTTGTCAAACAAACACAAAATAATGTGGACC
1 AAGCCTTGATCTAAGGGTCCTTATTTCATGGATCCTTGTCAAACAAACACAAAATAATGTGGACC
2142990 GTTGATTAAAAGTTAGATCCAAGGGATCCCATAATGTTACGTCATCGATCCATGCCAACAAACAC
66 GTTGATTAAAAGTTAGATCCAAGGGATCCCATAATGTTACGTCATCGATCCATGCCAACAAACAC
2143055 AAATGCTTCTCAACCATTGGATCAAGATG
131 AAATGCTTCTCAACCATTGGATCAAGATG
2143084 AA
1 AA
2143086 ATTTGATGGC
Statistics
Matches: 159, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
157 21 0.13
158 131 0.82
159 7 0.04
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (159 bp):
AAGCCTTGATCTAAGGGTCCTTATTTCATGGATCCTTGTCAAACAAACACAAAATAATGTGGACC
GTTGATTAAAAGTTAGATCCAAGGGATCCCATAATGTTACGTCATCGATCCATGCCAACAAACAC
AAATGCTTCTCAACCATTGGATCAAGATG
Found at i:2144483 original size:19 final size:20
Alignment explanation
Indices: 2144446--2144485 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2144436 CGTTAATTAT
*
2144446 TAAAACTTTATATTTTTAAA
1 TAAAACTTTAGATTTTTAAA
2144466 TAAAACTTTAGA-TTTTAAA
1 TAAAACTTTAGATTTTTAAA
2144485 T
1 T
2144486 TCTTTAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAAACTTTAGATTTTTAAA
Found at i:2144786 original size:60 final size:60
Alignment explanation
Indices: 2144720--2144852 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 60
2144710 CAACGCGATC
** * * **
2144720 TCAAATTTGCAACATTAA-CTCCAATTTCGTAACGTGAATATGTAAATCGCAACACAGAAG
1 TCAAATTTGCAACACGAATCTCCAAATT-GCAACGCAAATATGTAAATCGCAACACAGAAG
* ** *
2144780 TCAAATTCT-CAACGCGAATCTGTAAATTGCAACGCAAATTTGTAAATCGCAACACAGAAG
1 TCAAATT-TGCAACACGAATCTCCAAATTGCAACGCAAATATGTAAATCGCAACACAGAAG
*
2144840 TCAAATTCGCAAC
1 TCAAATTTGCAAC
2144853 GCAGAATTTC
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
60 52 0.88
61 7 0.12
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.25
Consensus pattern (60 bp):
TCAAATTTGCAACACGAATCTCCAAATTGCAACGCAAATATGTAAATCGCAACACAGAAG
Found at i:2144849 original size:20 final size:21
Alignment explanation
Indices: 2144759--2144872 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 21
2144749 TAACGTGAAT
2144759 ATGT-AAA-TCGCAACACAGA
1 ATGTCAAATTCGCAACACAGA
* *
2144778 A-GTCAAATTCTCAACGC-GA
1 ATGTCAAATTCGCAACACAGA
*
2144797 ATCTGT-AAATT-GCAACGCA-A
1 A--TGTCAAATTCGCAACACAGA
2144817 ATTTGT-AAA-TCGCAACACAGA
1 A--TGTCAAATTCGCAACACAGA
*
2144838 A-GTCAAATTCGCAACGCAGA
1 ATGTCAAATTCGCAACACAGA
*
2144858 ATTTCAAATTCGCAA
1 ATGTCAAATTCGCAA
2144873 TTGAATTTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
18 4 0.05
19 11 0.14
20 41 0.53
21 19 0.25
22 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (21 bp):
ATGTCAAATTCGCAACACAGA
Found at i:2144880 original size:19 final size:20
Alignment explanation
Indices: 2144840--2144930 Score: 87
Period size: 19 Copynumber: 4.6 Consensus size: 20
2144830 AACACAGAAG
**
2144840 TCAAATTCGCAACGCAGAATT
1 TCAAATTCGCAAC-TTGAATT
2144861 TCAAATTCGCAA-TTGAATT
1 TCAAATTCGCAACTTGAATT
* *
2144880 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACTTGAATT
** *
2144900 TTGAATTCGCAACATGAATT
1 TCAAATTCGCAACTTGAATT
*
2144920 T-AATTTCGCAA
1 TCAAATTCGCAA
2144931 TAGGTTTTAG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
19 25 0.43
20 21 0.36
21 12 0.21
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (20 bp):
TCAAATTCGCAACTTGAATT
Found at i:2144880 original size:60 final size:58
Alignment explanation
Indices: 2144754--2144880 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 58
2144744 TTTCGTAACG
* *
2144754 TGAATATGTAAATCGCAACACAGAAGTCAAATTCTCAACGCGAATCTGTAAATTGCAA
1 TGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGAATCTGTAAATTGCAA
*
2144812 CGCAAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCAGAAT-T-TCAAATTCGCAA
1 TG--AATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGC-GAATCTGT-AAATT-GCAA
2144873 TTGAATTT
1 -TGAATTT
2144881 CAAATTCGCA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
58 1 0.02
59 1 0.02
60 48 0.81
61 8 0.14
62 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (58 bp):
TGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGAATCTGTAAATTGCAA
Found at i:2144918 original size:40 final size:39
Alignment explanation
Indices: 2144840--2144938 Score: 103
Period size: 39 Copynumber: 2.5 Consensus size: 39
2144830 AACACAGAAG
* * *
2144840 TCAAATTCGCAACGCAGAATTTCAAATTCGCAATTGAATT
1 TCAAATTCGCAAC-TAGATTTTCAAATTCGCAAATGAATT
**
2144880 TCAAATTCGCAACTAGATTTTTGAATTCGCAACATGAATT
1 TCAAATTCGCAACTAGATTTTCAAATTCGCAA-ATGAATT
* *
2144920 T-AATTTCGCAA-TAGGTTTT
1 TCAAATTCGCAACTAGATTTT
2144939 AGTTTCGCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
38 7 0.14
39 24 0.47
40 20 0.39
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (39 bp):
TCAAATTCGCAACTAGATTTTCAAATTCGCAAATGAATT
Found at i:2145107 original size:14 final size:15
Alignment explanation
Indices: 2145088--2145125 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2145078 TCCCCATCTC
2145088 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
2145102 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
2145118 TAATTTTT
1 TAATTTTT
2145126 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:2145735 original size:12 final size:12
Alignment explanation
Indices: 2145718--2145757 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
2145708 ACCACATTTC
2145718 CAATACCAAACA
1 CAATACCAAACA
*
2145730 CAATACAAAACA
1 CAATACCAAACA
*
2145742 CAATATCAAACA
1 CAATACCAAACA
2145754 CAAT
1 CAAT
2145758 CACAAAACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (12 bp):
CAATACCAAACA
Found at i:2145745 original size:24 final size:25
Alignment explanation
Indices: 2145718--2145765 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
2145708 ACCACATTTC
2145718 CAATACCAAACACAAT-ACAAAACA
1 CAATACCAAACACAATCACAAAACA
*
2145742 CAATATCAAACACAATCACAAAAC
1 CAATACCAAACACAATCACAAAAC
2145766 CCACAACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.60, C:0.29, G:0.00, T:0.10
Consensus pattern (25 bp):
CAATACCAAACACAATCACAAAACA
Found at i:2145763 original size:12 final size:11
Alignment explanation
Indices: 2145718--2145763 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 11
2145708 ACCACATTTC
2145718 CAATACCAAACA
1 CAATA-CAAACA
2145730 CAATACAAAACA
1 CAATAC-AAACA
2145742 CAATATCAAACA
1 CAATA-CAAACA
2145754 CAATCACAAA
1 CAAT-ACAAA
2145764 ACCCACAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.03
12 28 0.90
13 2 0.06
ACGTcount: A:0.61, C:0.28, G:0.00, T:0.11
Consensus pattern (11 bp):
CAATACAAACA
Found at i:2145917 original size:24 final size:24
Alignment explanation
Indices: 2145890--2145943 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2145880 GTATTCAAAA
2145890 TTTGATCTTGGTCAATACCCAGAG
1 TTTGATCTTGGTCAATACCCAGAG
* *
2145914 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAG
2145938 TTTGAT
1 TTTGAT
2145944 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAG
Found at i:2146128 original size:3 final size:3
Alignment explanation
Indices: 2146120--2146151 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2146110 ATAACCCTGG
2146120 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
2146152 TCCCCGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2148235 original size:18 final size:18
Alignment explanation
Indices: 2148212--2148247 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2148202 AAGCAAAAAG
*
2148212 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
2148230 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
2148248 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2148600 original size:20 final size:20
Alignment explanation
Indices: 2148577--2148622 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2148567 ATCGCAACGT
*
2148577 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCACGTTGC
2148597 GAATTTGACTTTCACGTTGC
1 GAATTTGACTTTCACGTTGC
*
2148617 AAATTT
1 GAATTT
2148623 AACAAAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (20 bp):
GAATTTGACTTTCACGTTGC
Found at i:2148790 original size:66 final size:64
Alignment explanation
Indices: 2148719--2148862 Score: 243
Period size: 66 Copynumber: 2.2 Consensus size: 64
2148709 AATTTAAAAC
*
2148719 AACAAATAAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACTCATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTACTCATC-AATT
2148784 A
64 A
* *
2148785 AACAAATCAACTTTTTCAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACTCATCAATTA
2148849 AACAAATCAACTTT
1 AACAAATCAACTTT
2148863 CAATGTAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
64 19 0.25
65 24 0.32
66 32 0.43
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACTCATCAATTA
Found at i:2150250 original size:21 final size:21
Alignment explanation
Indices: 2150224--2150288 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
2150214 AATTAGGCTT
2150224 TTGAACGG-CGGACGGGACCTC
1 TTGAACGGTCGGA-GGGACCTC
* *
2150245 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGGTCGGAGGGACCTC
* *
2150266 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGGTCGGAGGGACCTC
2150287 TT
1 TT
2150289 CGATGATGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 38 0.93
22 3 0.07
ACGTcount: A:0.15, C:0.22, G:0.43, T:0.20
Consensus pattern (21 bp):
TTGAACGGTCGGAGGGACCTC
Found at i:2150287 original size:42 final size:42
Alignment explanation
Indices: 2150224--2150314 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
2150214 AATTAGGCTT
* *
2150224 TTGAACGGCGGACGGGACCTCTT-GAACGGTGGGAGGGGCCTC
1 TTGAACGGCGGACGGGACCTCTTCG-ACGATGAGAGGGGCCTC
* * * *
2150266 TTGAACGGTGGGA-GGGGCCTCTTCGATGATGAGATGGGCCTC
1 TTGAACGG-CGGACGGGACCTCTTCGACGATGAGAGGGGCCTC
2150308 TTGAACG
1 TTGAACG
2150315 ATAGAATGCG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
42 37 0.90
43 4 0.10
ACGTcount: A:0.18, C:0.21, G:0.41, T:0.21
Consensus pattern (42 bp):
TTGAACGGCGGACGGGACCTCTTCGACGATGAGAGGGGCCTC
Found at i:2150339 original size:42 final size:42
Alignment explanation
Indices: 2150241--2150339 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 42
2150231 GCGGACGGGA
* * * * * *
2150241 CCTCTTGAACGGTGGGAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGGCCTCTTGAACGATAGAAGGCG
* * *
2150283 CCTCTTCG-ATGATGAGATGGGCCTCTTGAACGATAGAATGCG
1 CCTCTT-GAACGATGAGAGGGGCCTCTTGAACGATAGAAGGCG
2150325 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
2150340 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.02
42 43 0.96
43 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.35, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGAGAGGGGCCTCTTGAACGATAGAAGGCG
Found at i:2152509 original size:34 final size:34
Alignment explanation
Indices: 2152463--2152527 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
2152453 ACTTAAATTT
2152463 GCAACGCAAAAATGAAAATCGCAACGAGAAAATC
1 GCAACGCAAAAATGAAAATCGCAACGAGAAAATC
* *
2152497 GCAACGCGAAAATGAAAATCGCAACGCGAAA
1 GCAACGCAAAAATGAAAATCGCAACGAGAAA
2152528 CTAAAATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.51, C:0.22, G:0.20, T:0.08
Consensus pattern (34 bp):
GCAACGCAAAAATGAAAATCGCAACGAGAAAATC
Found at i:2152527 original size:14 final size:14
Alignment explanation
Indices: 2152476--2152509 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2152466 ACGCAAAAAT
2152476 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
2152490 GAAAATCGCAACGC
1 GAAAATCGCAACGA
2152504 GAAAAT
1 GAAAAT
2152510 GAAAATCGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:2152535 original size:19 final size:20
Alignment explanation
Indices: 2152463--2152537 Score: 83
Period size: 20 Copynumber: 4.1 Consensus size: 20
2152453 ACTTAAATTT
*
2152463 GCAACGCAAAAATGAAAATC
1 GCAACGCGAAAATGAAAATC
2152483 GCAA--CG---A-GAAAATC
1 GCAACGCGAAAATGAAAATC
2152497 GCAACGCGAAAATGAAAATC
1 GCAACGCGAAAATGAAAATC
*
2152517 GCAACGCGAAACT-AAAATC
1 GCAACGCGAAAATGAAAATC
2152536 GC
1 GC
2152538 GTTGCGATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
14 11 0.23
15 1 0.02
16 2 0.04
18 1 0.02
19 9 0.19
20 23 0.49
ACGTcount: A:0.49, C:0.23, G:0.19, T:0.09
Consensus pattern (20 bp):
GCAACGCGAAAATGAAAATC
Found at i:2152573 original size:20 final size:21
Alignment explanation
Indices: 2152544--2152582 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2152534 TCGCGTTGCG
*
2152544 ATTTTGGTGTTGC-AATTTTC
1 ATTTTCGTGTTGCGAATTTTC
2152564 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
2152583 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (21 bp):
ATTTTCGTGTTGCGAATTTTC
Found at i:2152952 original size:22 final size:22
Alignment explanation
Indices: 2152925--2152981 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
2152915 ATGGAGATAT
* *
2152925 ACGGATTTTGTCGGAGATGGGG
1 ACGGATTTCGCCGGAGATGGGG
2152947 ACGGATTTCGCCGGAGATGGGG
1 ACGGATTTCGCCGGAGATGGGG
*
2152969 ACGGATGTCGCCG
1 ACGGATTTCGCCG
2152982 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.44, T:0.21
Consensus pattern (22 bp):
ACGGATTTCGCCGGAGATGGGG
Found at i:2153118 original size:20 final size:20
Alignment explanation
Indices: 2153089--2153228 Score: 165
Period size: 20 Copynumber: 7.0 Consensus size: 20
2153079 ATATTGTGTT
2153089 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
2153109 TCGCGCTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
2153129 TTGTGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
2153149 TTGTGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTA
* *
2153168 TTCAGTGTTGCGAATTTGATTA
1 -TC-GCGTTGCGAATTTGACTA
2153190 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
2153210 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
2153229 TCTGTGTTGC
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
20 88 0.83
21 17 0.16
22 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:2153198 original size:41 final size:41
Alignment explanation
Indices: 2153093--2153206 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
2153083 TGTGTTTCGC
* * * **
2153093 GTTGCGAATTTGACTATCGCGCTGCGAATTTG-ACTTTTGT
1 GTTGCGAATTTGATTATCGCGTTGCGAATTTGAAATTCAGT
* *
2153133 GTTGCGAATTTGACTT-TTGTGTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGA-TTATCGCGTTGCGAATTTGAAATTCAGT
2153174 GTTGCGAATTTGATTATCGCGTTGCGAATTTGA
1 GTTGCGAATTTGATTATCGCGTTGCGAATTTGA
2153207 CTATCGCGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
40 28 0.45
41 34 0.55
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.41
Consensus pattern (41 bp):
GTTGCGAATTTGATTATCGCGTTGCGAATTTGAAATTCAGT
Found at i:2153198 original size:61 final size:60
Alignment explanation
Indices: 2153089--2153261 Score: 174
Period size: 61 Copynumber: 2.9 Consensus size: 60
2153079 ATATTGTGTT
* * * * * *
2153089 TCGCGTTGCGAATTTGACTATC-GCGCTGCGAATTTGACTTTTGTGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGAAT-TCAGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
* *
2153149 TTGTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGA-TTATCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTG-AATTCAGTGTTGCGAATTTGACTT-TCGCGTTGCGAATTTGACTA
* * *
2153210 TCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGAA
1 TCGCGTTGCGAATTTGAATTCAGTGTTGCGAATTTGAC--TTTCGCGTTGCGAA
2153262 ATTGGAAACT
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
58 1 0.01
59 4 0.04
60 42 0.45
61 47 0.50
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGAATTCAGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTA
Found at i:2153202 original size:81 final size:80
Alignment explanation
Indices: 2153088--2153261 Score: 251
Period size: 81 Copynumber: 2.2 Consensus size: 80
2153078 AATATTGTGT
* * * *
2153088 TTCGCGTTGCGAATTTGACTATCGCGCTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGT
1 TTCGCGTTGCGAATTTGACTATCGCGCTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
*
2153153 GTTGCGAATTT-GAAA
66 GTTGCG-ATTTACAAA
* * *
2153168 TTCAGTGTTGCGAATTTGATTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTG
1 TTC-GCGTTGCGAATTTGACTATCGCGCTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTG
2153233 TGTTGCGATTTACAAA
65 TGTTGCGATTTACAAA
2153249 TTCGCGTTGCGAA
1 TTCGCGTTGCGAA
2153262 ATTGGAAACT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
80 16 0.19
81 67 0.81
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.40
Consensus pattern (80 bp):
TTCGCGTTGCGAATTTGACTATCGCGCTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
GTTGCGATTTACAAA
Found at i:2153301 original size:20 final size:20
Alignment explanation
Indices: 2153252--2153301 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2153242 TTACAAATTC
2153252 GCGTTGCGAAATTGGAAACT
1 GCGTTGCGAAATTGGAAACT
* * ***
2153272 GGGTTACGAAATTGGAGTTT
1 GCGTTGCGAAATTGGAAACT
2153292 GCGTTGCGAA
1 GCGTTGCGAA
2153302 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.34, T:0.28
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAAACT
Found at i:2156815 original size:16 final size:15
Alignment explanation
Indices: 2156792--2156855 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 15
2156782 AAAATTATTT
*
2156792 AAAAATTTAAGTATA
1 AAAAATTTAAATATA
2156807 AAAATATTTAAATATTCA
1 AAAA-ATTTAAATA-T-A
2156825 AAAAA-TTAAATAT-
1 AAAAATTTAAATATA
*
2156838 AAAAATTCTAAAAATA
1 AAAAATT-TAAATATA
2156854 AA
1 AA
2156856 TATTAAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
13 5 0.12
14 1 0.02
15 11 0.27
16 17 0.41
17 2 0.05
18 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAAATTTAAATATA
Found at i:2156835 original size:24 final size:23
Alignment explanation
Indices: 2156808--2156882 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
2156798 TTAAGTATAA
2156808 AAATATTTAAATATTCAAAAAATT
1 AAATA-TTAAATATTCAAAAAATT
* *
2156832 AAATA-TAAAAATTCTAAAAA-T
1 AAATATTAAATATTCAAAAAATT
*
2156853 AAATATTAAATTAAT-AGAAAAATT
1 AAATATTAAA-TATTCA-AAAAATT
2156877 AAATAT
1 AAATAT
2156883 ATATATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 6 0.14
22 17 0.40
23 7 0.17
24 12 0.29
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (23 bp):
AAATATTAAATATTCAAAAAATT
Found at i:2157512 original size:22 final size:22
Alignment explanation
Indices: 2157487--2157575 Score: 83
Period size: 22 Copynumber: 4.0 Consensus size: 22
2157477 TAGTTTTTCT
*
2157487 TATTTTTAATTGTATTTTTTAA
1 TATTTTTAATTTTATTTTTTAA
* **
2157509 TATTTAT-ATTCAATTTTTTAA
1 TATTTTTAATTTTATTTTTTAA
* *
2157530 TA-ATTCAATTTTTATTTTTTAA
1 TATTTTTAA-TTTTATTTTTTAA
*
2157552 TATTTTTATATTTTAATTTTTAA
1 TATTTTTA-ATTTTATTTTTTAA
2157575 T
1 T
2157576 TTTAAAATAA
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
21 15 0.29
22 19 0.37
23 16 0.31
24 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (22 bp):
TATTTTTAATTTTATTTTTTAA
Found at i:2157557 original size:8 final size:8
Alignment explanation
Indices: 2157503--2157575 Score: 50
Period size: 8 Copynumber: 9.9 Consensus size: 8
2157493 TAATTGTATT
2157503 TTTTAATA
1 TTTTAATA
2157511 -TTT-ATA
1 TTTTAATA
* *
2157517 -TTCAATT
1 TTTTAATA
2157524 TTTTAATA
1 TTTTAATA
* *
2157532 ATTCAAT-
1 TTTTAATA
*
2157539 TTTT-ATT
1 TTTTAATA
2157546 TTTTAATA
1 TTTTAATA
*
2157554 TTTTTATA
1 TTTTAATA
2157562 TTTTAAT-
1 TTTTAATA
2157569 TTTTAAT
1 TTTTAAT
2157576 TTTAAAATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
6 7 0.14
7 18 0.36
8 25 0.50
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTTAATA
Found at i:2157577 original size:13 final size:14
Alignment explanation
Indices: 2157486--2157580 Score: 63
Period size: 14 Copynumber: 6.8 Consensus size: 14
2157476 TTAGTTTTTC
2157486 TTAT-TTTTAA-TT
1 TTATATTTTAATTT
* * *
2157498 GTATTTTTTAATAT
1 TTATATTTTAATTT
*
2157512 TTATA-TTCAATTTT
1 TTATATTTTAA-TTT
* *
2157526 TTAATAATTCAATTT
1 TT-ATATTTTAATTT
*
2157541 TTATTTTTTAATATTT
1 TTATATTTT-A-ATTT
2157557 TTATATTTTAATTT
1 TTATATTTTAATTT
2157571 TTA-ATTTTAA
1 TTATATTTTAA
2157581 AATAAATTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
12 3 0.05
13 17 0.26
14 19 0.29
15 10 0.15
16 17 0.26
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (14 bp):
TTATATTTTAATTT
Found at i:2162572 original size:15 final size:15
Alignment explanation
Indices: 2162550--2162596 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
2162540 TTATATATTT
2162550 ATTC-ATTGTAACAA
1 ATTCTATTGTAACAA
*
2162564 ATTCTATTGTAACGA
1 ATTCTATTGTAACAA
*
2162579 ATTCTATTATAACAA
1 ATTCTATTGTAACAA
2162594 ATT
1 ATT
2162597 ATATATCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 4 0.14
15 25 0.86
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (15 bp):
ATTCTATTGTAACAA
Found at i:2162960 original size:2 final size:2
Alignment explanation
Indices: 2162953--2162993 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2162943 AACGCTGATA
2162953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2162994 ATTTTACTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2163468 original size:31 final size:31
Alignment explanation
Indices: 2163426--2163500 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
2163416 GTAAATGGGT
*
2163426 TAAATTGATTTTGT-TAGTCAAGTTCAAGGAC
1 TAAATTAATTTT-TATAGTCAAGTTCAAGGAC
* * * *
2163457 TCAATTTATTTTTATAGTTAAGTTCGAGGAC
1 TAAATTAATTTTTATAGTCAAGTTCAAGGAC
2163488 TAAATTAATTTTT
1 TAAATTAATTTTT
2163501 TTAAAGTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (31 bp):
TAAATTAATTTTTATAGTCAAGTTCAAGGAC
Found at i:2164020 original size:60 final size:60
Alignment explanation
Indices: 2163949--2164062 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 60
2163939 AATGGTTTCC
2163949 CGACAATAAGATATTATTTTATTGAGTCCCTAGACTATTAAAAGTTACAAAATGCTCATT
1 CGACAATAAGATATTATTTTATTGAGTCCCTAGACTATTAAAAGTTACAAAATGCTCATT
* * **
2164009 CGACTATAAGATATTATTTTGTTGAGTCCCTCTACTATTAAAAGTTACAAAATG
1 CGACAATAAGATATTATTTTATTGAGTCCCTAGACTATTAAAAGTTACAAAATG
2164063 GCCACCAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (60 bp):
CGACAATAAGATATTATTTTATTGAGTCCCTAGACTATTAAAAGTTACAAAATGCTCATT
Found at i:2165896 original size:2 final size:2
Alignment explanation
Indices: 2165885--2165919 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2165875 TAACTATAGG
2165885 TA TA -A 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
2165920 AATAACTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2167792 original size:31 final size:31
Alignment explanation
Indices: 2167736--2167809 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
2167726 CTTGGCTTGC
*
2167736 TTTC-TCTTTT-TGAATTTCTTTTTCTTTTCT
1 TTTCTTCTTTTCTGAATTTCTTATTCTTTT-T
2167766 TTTCTTCTTTTCTGAATTT-TTATTCTTTTT
1 TTTCTTCTTTTCTGAATTTCTTATTCTTTTT
*
2167796 TTATTTTCTTTTCT
1 TT-TCTTCTTTTCT
2167810 TTTTGCACTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 7 0.18
31 25 0.64
32 7 0.18
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.74
Consensus pattern (31 bp):
TTTCTTCTTTTCTGAATTTCTTATTCTTTTT
Found at i:2167811 original size:18 final size:18
Alignment explanation
Indices: 2167754--2167813 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
2167744 TTTGAATTTC
*
2167754 TTTTTCTTTTCTTTTCTT
1 TTTTTATTTTCTTTTCTT
*
2167772 CTTTTCTGAATTTT-TATTCTT
1 -TTTT-T--ATTTTCTTTTCTT
2167793 TTTTTATTTTCTTTTCTT
1 TTTTTATTTTCTTTTCTT
2167811 TTT
1 TTT
2167814 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
17 5 0.15
18 9 0.26
19 5 0.15
20 5 0.15
21 6 0.18
22 4 0.12
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTATTTTCTTTTCTT
Found at i:2171261 original size:18 final size:16
Alignment explanation
Indices: 2171240--2171313 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 16
2171230 GCTTGCTTTC
2171240 TCTTTTTGAATTTCTTTT
1 TCTTTTTG-ATTT-TTTT
*
2171258 TC-TTTTG--TTTTCT
1 TCTTTTTGATTTTTTT
2171271 TCTTTTCTGATTTTTTT
1 TCTTTT-TGATTTTTTT
2171288 TCTTTTTGTATTTTCTTT
1 TCTTTTTG-ATTTT-TTT
2171306 TCTTTTTG
1 TCTTTTTG
2171314 CACTCCAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 2 0.04
16 2 0.04
17 21 0.44
18 13 0.27
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (16 bp):
TCTTTTTGATTTTTTT
Found at i:2171270 original size:30 final size:31
Alignment explanation
Indices: 2171236--2171308 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 31
2171226 CTTAGCTTGC
2171236 TTTCTCTTTT-TGAATTTCTTTTTC-TTTTGT-
1 TTTCTCTTTTCTG-ATTT-TTTTTCTTTTTGTA
2171266 TTTCTTCTTTTCTGATTTTTTTTCTTTTTGTA
1 TTTC-TCTTTTCTGATTTTTTTTCTTTTTGTA
2171298 TTT-TCTTTTCT
1 TTTCTCTTTTCT
2171309 TTTTGCACTC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
30 18 0.46
31 16 0.41
32 5 0.13
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.75
Consensus pattern (31 bp):
TTTCTCTTTTCTGATTTTTTTTCTTTTTGTA
Found at i:2171574 original size:26 final size:28
Alignment explanation
Indices: 2171547--2171597 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
2171537 TAGTAAATGA
*
2171547 AAAT-AAATGGAAT-AATAAA-GATAAG
1 AAATGAAATGAAATAAATAAATGATAAG
2171572 AAATGAAATGAAATAAATAAATGATA
1 AAATGAAATGAAATAAATAAATGATA
2171598 GAGATGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 8 0.36
27 6 0.27
28 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.22
Consensus pattern (28 bp):
AAATGAAATGAAATAAATAAATGATAAG
Found at i:2172900 original size:2 final size:2
Alignment explanation
Indices: 2172889--2172926 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2172879 TAACTATAGG
2172889 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2172927 GAAAATAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2174753 original size:18 final size:17
Alignment explanation
Indices: 2174722--2174755 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2174712 TCTTCTCTGA
2174722 ATTTTTTTTCTTTTTGT
1 ATTTTTTTTCTTTTTGT
2174739 ATTTTCTTTTCTTTTTG
1 ATTTT-TTTTCTTTTTG
2174756 CACTTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (17 bp):
ATTTTTTTTCTTTTTGT
Found at i:2175023 original size:18 final size:18
Alignment explanation
Indices: 2175002--2175037 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2174992 TAAATGGAAT
2175002 AATAAAGAT-AAGAAATGA
1 AATAAA-ATAAAGAAATGA
2175020 AATAAAATAAAGAAATGA
1 AATAAAATAAAGAAATGA
2175038 TAGAGATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (18 bp):
AATAAAATAAAGAAATGA
Found at i:2177833 original size:21 final size:21
Alignment explanation
Indices: 2177809--2177848 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2177799 AACATTTTAC
2177809 TTCTATGATCTTTGTGTGACT
1 TTCTATGATCTTTGTGTGACT
*
2177830 TTCTATGATTTTTGTGTGA
1 TTCTATGATCTTTGTGTGA
2177849 TCTTAACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.20, T:0.55
Consensus pattern (21 bp):
TTCTATGATCTTTGTGTGACT
Found at i:2180256 original size:24 final size:24
Alignment explanation
Indices: 2180229--2180276 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2180219 GTCAAAGATG
2180229 GTGGAGGATGTGGTTAATATGGGC
1 GTGGAGGATGTGGTTAATATGGGC
2180253 GTGGAGGATGTGGTTAATATGGGC
1 GTGGAGGATGTGGTTAATATGGGC
2180277 TTCATAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.46, T:0.29
Consensus pattern (24 bp):
GTGGAGGATGTGGTTAATATGGGC
Found at i:2185526 original size:22 final size:22
Alignment explanation
Indices: 2185501--2185542 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2185491 CAATTCATTT
2185501 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
2185523 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
2185543 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:2185896 original size:18 final size:18
Alignment explanation
Indices: 2185872--2185912 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2185862 AAAAAACAAA
* *
2185872 AAAAAAAGCAAGAAAAGGC
1 AAAAAAA-CAAAAAAAGCC
2185891 AAAAAAACAAAAAAAGCC
1 AAAAAAACAAAAAAAGCC
2185909 AAAA
1 AAAA
2185913 GTTCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAGCC
Found at i:2190104 original size:11 final size:11
Alignment explanation
Indices: 2190090--2190134 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
2190080 TTGCAATTCA
2190090 TTTATCTT-TT
1 TTTATCTTATT
*
2190100 CTTTATCTTGTT
1 -TTTATCTTATT
*
2190112 TTAATCTTATT
1 TTTATCTTATT
2190123 TTTATCTTATT
1 TTTATCTTATT
2190134 T
1 T
2190135 CCAGCACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:2204577 original size:27 final size:28
Alignment explanation
Indices: 2204547--2204604 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
2204537 TATGGGTCTT
2204547 TTTTA-CAGTATAAGTGC-ATT-TTCGTAA
1 TTTTACCA-TATAA-TGCTATTATTCGTAA
*
2204574 TTTTACCATATAATGCTATTATTGGTAA
1 TTTTACCATATAATGCTATTATTCGTAA
2204602 TTT
1 TTT
2204605 CTTATCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.11
27 13 0.48
28 11 0.41
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (28 bp):
TTTTACCATATAATGCTATTATTCGTAA
Found at i:2206508 original size:15 final size:15
Alignment explanation
Indices: 2206477--2206518 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2206467 ATACTATAGG
* *
2206477 ATATA-AATATTATA
1 ATATACAATATAAGA
2206491 ATATACAATATAAGA
1 ATATACAATATAAGA
*
2206506 ATATACTATATAA
1 ATATACAATATAA
2206519 TATTAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (15 bp):
ATATACAATATAAGA
Found at i:2206547 original size:20 final size:20
Alignment explanation
Indices: 2206477--2206645 Score: 94
Period size: 22 Copynumber: 8.0 Consensus size: 20
2206467 ATACTATAGG
*
2206477 ATATAAATATTATAATATACA
1 ATATAAATATTAT-ATATAAA
2206498 ATATAAGA-ATATACTATATAATA
1 ATATAA-ATAT-TA-TATATAA-A
* *
2206521 TTAATAAATATTGTATATAAA
1 AT-ATAAATATTATATATAAA
* *
2206542 ATATAAA-ATATAAATACTATA
1 ATATAAATAT-TATATA-TAAA
* *
2206563 ATATATATATATATATATATAT
1 ATATAAATAT-TATATATA-AA
* *
2206585 ATATATATATATATATATATAT
1 ATATAAATAT-TATATATA-AA
* *
2206607 ATATATATATTATACTATATA
1 ATATAAATATTATA-TATAAA
2206628 ATAT-AATA-TATATATAAA
1 ATATAAATATTATATATAAA
2206646 CATTACTAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 25
0.75 0.09 0.15
Matches are distributed among these distances:
18 5 0.04
19 6 0.05
20 12 0.10
21 29 0.24
22 59 0.48
23 5 0.04
24 6 0.05
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (20 bp):
ATATAAATATTATATATAAA
Found at i:2206570 original size:2 final size:2
Alignment explanation
Indices: 2206549--2206643 Score: 135
Period size: 2 Copynumber: 48.5 Consensus size: 2
2206539 AAAATATAAA
*
2206549 AT AT AA AT ACT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2206591 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
2206632 A- AT AT AT AT AT A
1 AT AT AT AT AT AT A
2206644 AACATTACTA
Statistics
Matches: 85, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
1 4 0.05
2 77 0.91
3 4 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2206639 original size:14 final size:13
Alignment explanation
Indices: 2206435--2206643 Score: 138
Period size: 14 Copynumber: 16.1 Consensus size: 13
2206425 ATATGGAATA
2206435 ATAATATA-ATAT
1 ATAATATATATAT
*
2206447 ATAATTACTACCATAT
1 ATAA-TA-TA-TATAT
*
2206463 ATAA-ATACTATAGG
1 ATAATATA-TATA-T
*
2206477 AT-ATAAATAT-T
1 ATAATATATATAT
*
2206488 ATAATATACA-AT
1 ATAATATATATAT
*
2206500 ATAAGAATATACTAT
1 ATAA-TATATA-TAT
2206515 ATAATAT-TA-AT
1 ATAATATATATAT
*
2206526 A-AATAT-TGTAT
1 ATAATATATATAT
2206537 ATAA-A-ATATA-
1 ATAATATATATAT
*
2206547 A-AATATAAATACT
1 ATAATATATATA-T
2206560 ATAATATATATAT
1 ATAATATATATAT
2206573 ATATATATATATAT
1 ATA-ATATATATAT
2206587 ATATATATATATAT
1 ATA-ATATATATAT
2206601 ATATATATATATAT
1 ATA-ATATATATAT
*
2206615 ATTATACTATATAAT
1 ATAATA-TATAT-AT
2206630 ATAATATATATAT
1 ATAATATATATAT
2206643 A
1 A
2206644 AACATTACTA
Statistics
Matches: 160, Mismatches: 15, Indels: 43
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.01
10 8 0.05
11 16 0.10
12 16 0.10
13 29 0.18
14 68 0.43
15 13 0.08
16 8 0.05
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:2206641 original size:16 final size:16
Alignment explanation
Indices: 2206435--2206644 Score: 139
Period size: 16 Copynumber: 12.9 Consensus size: 16
2206425 ATATGGAATA
2206435 ATAATATAATATATAAT
1 ATAATAT-ATATATAAT
* *
2206452 -TACTACCATATATAA-
1 ATAATA-TATATATAAT
* *
2206467 ATACTATAGGATATAA-
1 ATAATATA-TATATAAT
* *
2206483 ATATTATAATATACAAT
1 ATAATAT-ATATATAAT
*
2206500 ATAAGA-ATATACT-AT
1 ATAATATATATA-TAAT
2206515 ATAATAT-TA-ATAA-
1 ATAATATATATATAAT
* * *
2206528 ATATTGTATATAAAAT
1 ATAATATATATATAAT
* * *
2206544 ATAAAATATAAATACT
1 ATAATATATATATAAT
2206560 ATAATATATATATATAT
1 ATAATATATATATA-AT
2206577 ATATATATATATATATAT
1 ATA-ATATATATATA-AT
2206595 ATATATATATATATATAT
1 ATA-ATATATATATA-AT
*
2206613 ATATTATACTATATAAT
1 ATAATATA-TATATAAT
2206630 ATAATATATATATAA
1 ATAATATATATATAA
2206645 ACATTACTAA
Statistics
Matches: 154, Mismatches: 25, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
13 6 0.04
14 4 0.03
15 18 0.12
16 63 0.41
17 22 0.14
18 41 0.27
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (16 bp):
ATAATATATATATAAT
Found at i:2207428 original size:45 final size:45
Alignment explanation
Indices: 2207342--2207428 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
2207332 CCATTTATTA
* *
2207342 ACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTGT
1 ACCATAAGCTCATAAGCTTATTTTACCAAAACACTTACCATTTGT
* * *
2207387 ACCATAAGTTCATAAGCTTATTTTACCAATACACTTGCCATT
1 ACCATAAGCTCATAAGCTTATTTTACCAAAACACTTACCATT
2207429 ATTCCATAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (45 bp):
ACCATAAGCTCATAAGCTTATTTTACCAAAACACTTACCATTTGT
Found at i:2207553 original size:33 final size:33
Alignment explanation
Indices: 2207516--2207582 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2207506 ACCGTAGTGC
*
2207516 TAATCCGTATTACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
2207549 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
2207582 T
1 T
2207583 CTGTACTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCGTGTCCACCA
Found at i:2212772 original size:13 final size:13
Alignment explanation
Indices: 2212754--2212781 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2212744 TTACGTCATC
2212754 TTAATCGCAACCA
1 TTAATCGCAACCA
2212767 TTAATCGCAACCA
1 TTAATCGCAACCA
2212780 TT
1 TT
2212782 GATGATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (13 bp):
TTAATCGCAACCA
Found at i:2212864 original size:23 final size:23
Alignment explanation
Indices: 2212832--2212901 Score: 115
Period size: 23 Copynumber: 3.0 Consensus size: 23
2212822 TTATTAAACT
2212832 TTTTTGCCCTTAATGAATCTCCA
1 TTTTTGCCCTTAATGAATCTCCA
*
2212855 TTTTTACCCTTAATGAAAT-TCCA
1 TTTTTGCCCTTAATG-AATCTCCA
2212878 TTTTTGCCCTTAATGAATCTCCA
1 TTTTTGCCCTTAATGAATCTCCA
2212901 T
1 T
2212902 AATCACCATA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.07
23 37 0.86
24 3 0.07
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.44
Consensus pattern (23 bp):
TTTTTGCCCTTAATGAATCTCCA
Found at i:2217662 original size:176 final size:179
Alignment explanation
Indices: 2217368--2217724 Score: 675
Period size: 176 Copynumber: 2.0 Consensus size: 179
2217358 TGAAACTTCC
2217368 TTAATCTTTGGAAAAGCTTTCTCAATTCTTGATGTGCTCCTTTTCTATTTGAGCTTTGACAATCA
1 TTAATCTTTGGAAAAGCTTTCTCAATTCTTGATGTGCTCCTTTTCTATTTGAGCTTTGACAATCA
2217433 TGTCATCAACATATACCTCGATCTCCTTATGCATCATGTCATGGAACAAGGTCATAATGGGTCAT
66 TGTCATCAACATATACCTCGATCTCCTTATGCATCATGTCATGGAACAAGGTCATAATGGGTCAT
2217498 TGGTA-TGCCCCGACTTTC-TTACTCTGAAAGGCATCACC-TGTAACAA
131 TGGTATTGCCCCGACTTTCTTTACTCTGAAAGGCATCACCTTGTAACAA
2217544 TTAATCTTTGGAAAAGCTTTCTCAATTCTTGATGTGCTCCTTTTCTATTTGAGCTTTGACAATCA
1 TTAATCTTTGGAAAAGCTTTCTCAATTCTTGATGTGCTCCTTTTCTATTTGAGCTTTGACAATCA
2217609 TGTCATCAACATATACCTCGATCTCCTTATGCATCATGTCATGGAACAAGGTCATAATGGGTCAT
66 TGTCATCAACATATACCTCGATCTCCTTATGCATCATGTCATGGAACAAGGTCATAATGGGTCAT
2217674 TGGTATGTTGCCCCGACTTTCTTTACTCTGAAAGGCATCACCTTGTAACAA
131 TGGTA--TTGCCCCGACTTTCTTTACTCTGAAAGGCATCACCTTGTAACAA
2217725 ATATTCCCTT
Statistics
Matches: 176, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
176 135 0.77
179 13 0.07
180 20 0.11
181 8 0.05
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (179 bp):
TTAATCTTTGGAAAAGCTTTCTCAATTCTTGATGTGCTCCTTTTCTATTTGAGCTTTGACAATCA
TGTCATCAACATATACCTCGATCTCCTTATGCATCATGTCATGGAACAAGGTCATAATGGGTCAT
TGGTATTGCCCCGACTTTCTTTACTCTGAAAGGCATCACCTTGTAACAA
Found at i:2221600 original size:110 final size:112
Alignment explanation
Indices: 2221396--2221620 Score: 436
Period size: 110 Copynumber: 2.0 Consensus size: 112
2221386 CAGAAGTTGG
2221396 TCATATTCGATATATCCTGTCATTTTTTGATAGAACATGGTGATGAGATCTGAAGGGAAGCTGTT
1 TCATATTCGATATATCCTGTCATTTTTTGATAGAACATGGTGATGAGATCTGAAGGGAAGCTGTT
2221461 CCCATCAAACTTCTCAAAATTAGGAAATTTTAACTTTGGGGGAAGAA
66 CCCATCAAACTTCTCAAAATTAGGAAATTTTAACTTTGGGGGAAGAA
2221508 TCATA-TCGA-ATATCCTGTCATTTTTTGATAGAACATGGTGATGAGATCTGAAGGGAAGCTGTT
1 TCATATTCGATATATCCTGTCATTTTTTGATAGAACATGGTGATGAGATCTGAAGGGAAGCTGTT
2221571 CCCATCAAACTTCTCAAAATTAGGAAATTTTAACTTTGGGGGAAGAA
66 CCCATCAAACTTCTCAAAATTAGGAAATTTTAACTTTGGGGGAAGAA
2221618 TCA
1 TCA
2221621 AGTTCGAGAC
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
110 104 0.92
111 4 0.04
112 5 0.04
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (112 bp):
TCATATTCGATATATCCTGTCATTTTTTGATAGAACATGGTGATGAGATCTGAAGGGAAGCTGTT
CCCATCAAACTTCTCAAAATTAGGAAATTTTAACTTTGGGGGAAGAA
Found at i:2226653 original size:7 final size:7
Alignment explanation
Indices: 2226637--2226810 Score: 58
Period size: 7 Copynumber: 24.1 Consensus size: 7
2226627 TAAATATGAA
2226637 ATAATAAT
1 ATAAT-AT
2226645 ATAATAT
1 ATAATAT
2226652 ATAAT-T
1 ATAATAT
2226658 ACTACCATAT
1 A-TA--ATAT
2226668 ATAAATACT
1 AT-AATA-T
*
2226677 ATAAAAT
1 ATAATAT
2226684 ATAAATATT
1 AT-AATA-T
2226693 ATAATAT
1 ATAATAT
*
2226700 A-CA-AT
1 ATAATAT
2226705 ATAATAGT
1 ATAATA-T
***
2226713 ACGCTAT
1 ATAATAT
2226720 ATAATAT
1 ATAATAT
2226727 -TAATA-
1 ATAATAT
*
2226732 AAAAGTAT
1 ATAA-TAT
*
2226740 AT-ATAA
1 ATAATAT
* *
2226746 ATTATAA
1 ATAATAT
*
2226753 ATACTAT
1 ATAATAT
2226760 ATAATAT
1 ATAATAT
2226767 ATAATA-
1 ATAATAT
2226773 AT-ATAT
1 ATAATAT
*
2226779 ATACTAT
1 ATAATAT
*
2226786 ACTTTATAAT
1 A--TAAT-AT
2226796 ATAATAT
1 ATAATAT
*
2226803 ATATTAT
1 ATAATAT
2226810 A
1 A
2226811 AACATTACTA
Statistics
Matches: 124, Mismatches: 22, Indels: 41
0.66 0.12 0.22
Matches are distributed among these distances:
5 6 0.05
6 19 0.15
7 56 0.45
8 26 0.21
9 11 0.09
10 6 0.05
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (7 bp):
ATAATAT
Found at i:2226740 original size:20 final size:20
Alignment explanation
Indices: 2226716--2226773 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2226706 TAATAGTACG
2226716 CTATATAATATTAATAAAAA
1 CTATATAATATTAATAAAAA
* * *
2226736 GTATATATAAATT-ATAAATA
1 CTATATA-ATATTAATAAAAA
2226756 CTATATAATATATAATAA
1 CTATATAATAT-TAATAA
2226774 TATATATACT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 3 0.10
20 19 0.63
21 8 0.27
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (20 bp):
CTATATAATATTAATAAAAA
Found at i:2226769 original size:18 final size:18
Alignment explanation
Indices: 2226621--2226779 Score: 60
Period size: 16 Copynumber: 8.4 Consensus size: 18
2226611 TATTAATAAC
*
2226621 ACTAAATAA-ATATGAAAT
1 ACTATATAATATAT-AAAT
* *
2226639 AATAATATAATATATAATT
1 ACT-ATATAATATATAAAT
**
2226658 AC--TACCATATATAAAT
1 ACTATATAATATATAAAT
2226674 ACTATA-AA-ATATAAAT
1 ACTATATAATATATAAAT
* *
2226690 ATTATAATATACAATATAATAGT
1 ACTAT-ATA-A-TATATAA-A-T
*
2226713 ACGCTATATAATATTAATAAAA
1 A--CTATATAATA-T-ATAAAT
* *
2226735 AGTATATATAAATTATAAAT
1 ACTATATA-ATA-TATAAAT
2226755 ACTATATAATATAT-AAT
1 ACTATATAATATATAAAT
*
2226772 AATATATA
1 ACTATATA
2226780 TACTATACTT
Statistics
Matches: 107, Mismatches: 18, Indels: 33
0.68 0.11 0.21
Matches are distributed among these distances:
16 25 0.23
17 12 0.11
18 8 0.07
19 12 0.11
20 22 0.21
21 10 0.09
22 3 0.03
23 5 0.05
24 7 0.07
25 3 0.03
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (18 bp):
ACTATATAATATATAAAT
Found at i:2226793 original size:26 final size:26
Alignment explanation
Indices: 2226738--2226786 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2226728 AATAAAAAGT
* *
2226738 ATATATAA-ATTATAAATACTATATA
1 ATATATAATAATATATATACTATATA
2226763 ATATATAATAATATATATACTATA
1 ATATATAATAATATATATACTATA
2226787 CTTTATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATATAATAATATATATACTATATA
Done.