Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 52 of 208
Found at i:14634328 original size:7 final size:7
Alignment explanation
Indices: 14634313--14634346 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
14634303 TCAAGTAATT
*
14634313 CATTAAA
1 CATTTAA
14634320 CATTTAA
1 CATTTAA
14634327 CATTTAA
1 CATTTAA
14634334 CATTTAA
1 CATTTAA
14634341 CATTTA
1 CATTTA
14634347 CTAATGTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
CATTTAA
Found at i:14634876 original size:2 final size:2
Alignment explanation
Indices: 14634871--14634899 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14634861 ATTAAACATC
14634871 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 A
14634900 CATTAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14637259 original size:26 final size:25
Alignment explanation
Indices: 14637209--14637284 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 25
14637199 ACACCAATAT
* * *
14637209 CGCAGTAAAGTTGCCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGT-ACAGTAA
* *
14637235 CGCAGCAAAGCTGCCATTATCAGTAT
1 CGCAGCAAAGCTGCCAGTA-CAGTAA
*
14637261 CGCATCAAAGCTGCCAGTACAGTA
1 CGCAGCAAAGCTGCCAGTACAGTA
14637285 TACTTCCTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 6 0.14
26 36 0.86
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (25 bp):
CGCAGCAAAGCTGCCAGTACAGTAA
Found at i:14641043 original size:14 final size:14
Alignment explanation
Indices: 14641024--14641053 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
14641014 ACTTGTGAGT
14641024 TATTAAAGCACGTA
1 TATTAAAGCACGTA
14641038 TATTAAAGCACGTA
1 TATTAAAGCACGTA
14641052 TA
1 TA
14641054 CGATGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
TATTAAAGCACGTA
Found at i:14644221 original size:9 final size:9
Alignment explanation
Indices: 14644207--14644237 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
14644197 GTCAAACGAA
14644207 TCGAGTTAT
1 TCGAGTTAT
*
14644216 TCGAGTTAA
1 TCGAGTTAT
14644225 TCGAGTTAT
1 TCGAGTTAT
14644234 TCGA
1 TCGA
14644238 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:14645891 original size:22 final size:24
Alignment explanation
Indices: 14645865--14645920 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
14645855 TTAAATTATC
14645865 ATTTTTATTTTCT-TATATA-TTT-
1 ATTTTTATTTT-TATATATACTTTA
*
14645887 ATTTTCATTTTTATATATACTTTA
1 ATTTTTATTTTTATATATACTTTA
*
14645911 ATATTTATTT
1 ATTTTTATTT
14645921 ATATTTGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 16 0.57
23 3 0.11
24 8 0.29
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTATTTTTATATATACTTTA
Found at i:14646255 original size:9 final size:9
Alignment explanation
Indices: 14646241--14646283 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
14646231 CCTTTCTAAC
14646241 CTCTCAATT
1 CTCTCAATT
*
14646250 CTCTCAACT
1 CTCTCAATT
*
14646259 CTCTTAATT
1 CTCTCAATT
*
14646268 TTCTCAATT
1 CTCTCAATT
*
14646277 TTCTCAA
1 CTCTCAA
14646284 GTTTTGTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (9 bp):
CTCTCAATT
Found at i:14646262 original size:18 final size:18
Alignment explanation
Indices: 14646218--14646274 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
14646208 TACTCAAGTC
* *
14646218 CAACTCTCTCAATCCTTT
1 CAACTCTCTCAATTCTCT
14646236 CTAAC-CTCTCAATTCTCT
1 C-AACTCTCTCAATTCTCT
* *
14646254 CAACTCTCTTAATTTTCT
1 CAACTCTCTCAATTCTCT
14646272 CAA
1 CAA
14646275 TTTTCTCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.09
18 27 0.82
19 3 0.09
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (18 bp):
CAACTCTCTCAATTCTCT
Found at i:14649060 original size:43 final size:43
Alignment explanation
Indices: 14649012--14649136 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 43
14649002 AGCTTGTACA
* * *
14649012 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
14649055 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
* *
14649098 ATGCCAATGTCCCAGACGTGGTCTTACACGAAAAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-TAAACACA
14649137 TATCAGAGGT
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
42 4 0.06
43 58 0.82
44 9 0.13
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:14658367 original size:19 final size:20
Alignment explanation
Indices: 14658339--14658385 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
14658329 TGATTATTGG
* *
14658339 TTTTGATTATGTGATGG-CT
1 TTTTGTTTATGTGATGGCCA
14658358 TTTTGTTTATGTGATGGCCA
1 TTTTGTTTATGTGATGGCCA
14658378 TTTTGTTT
1 TTTTGTTT
14658386 GTATCTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.13, C:0.06, G:0.23, T:0.57
Consensus pattern (20 bp):
TTTTGTTTATGTGATGGCCA
Found at i:14662348 original size:185 final size:184
Alignment explanation
Indices: 14662032--14662380 Score: 556
Period size: 185 Copynumber: 1.9 Consensus size: 184
14662022 ATGCCATAGC
14662032 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
1 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
* * *
14662097 GTTCAACTTAATTCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATTACTGCAGTCCTTTTG
66 GTTCAACTAAATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTTG
14662162 TCTTGTGTAATATTTGCACTCAAACTCTTATTGTGTAATATTTTTCTGTTTTAGT
131 TCTTGTGTAATATTTGCACTCAAACT-TTATTGTGTAATATTTTTCTGTTTTAGT
* * * * **
14662217 ACATGAGAACACTAAAAAACTTTGTAGCTGGTGTTGGTATGGCTTTTCTGAAAATGTAGCTTAAT
1 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
* * *
14662282 GTTCAAC-AACATGCATGTTTATCTCAGGAAGGCAGTGTGCGGTTTGCATGACTGCAGTCTTTTT
66 GTTCAACTAA-ATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTT
*
14662346 GTCTTGTGTGATATTTGCACTCAAACTTTATTGTG
130 GTCTTGTGTAATATTTGCACTCAAACTTTATTGTG
14662381 AAATTAATAT
Statistics
Matches: 150, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
184 9 0.06
185 141 0.94
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (184 bp):
ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
GTTCAACTAAATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTTG
TCTTGTGTAATATTTGCACTCAAACTTTATTGTGTAATATTTTTCTGTTTTAGT
Found at i:14685734 original size:167 final size:167
Alignment explanation
Indices: 14685458--14685792 Score: 670
Period size: 167 Copynumber: 2.0 Consensus size: 167
14685448 TATTTTTCAA
14685458 CCCATTTGGTATTACCAAGTTTAATAATTAATTTCTTGGTGCTTGTGACTGACCTTAGCATATTT
1 CCCATTTGGTATTACCAAGTTTAATAATTAATTTCTTGGTGCTTGTGACTGACCTTAGCATATTT
14685523 CATTTTGCTACAAAATTATCAATTCAAGCAGAAAAATGTGATAGAGCATAATATTCACAGGGAAT
66 CATTTTGCTACAAAATTATCAATTCAAGCAGAAAAATGTGATAGAGCATAATATTCACAGGGAAT
14685588 AACCGAATAAGCATTGATCTGGCATGTCTAATCATGT
131 AACCGAATAAGCATTGATCTGGCATGTCTAATCATGT
14685625 CCCATTTGGTATTACCAAGTTTAATAATTAATTTCTTGGTGCTTGTGACTGACCTTAGCATATTT
1 CCCATTTGGTATTACCAAGTTTAATAATTAATTTCTTGGTGCTTGTGACTGACCTTAGCATATTT
14685690 CATTTTGCTACAAAATTATCAATTCAAGCAGAAAAATGTGATAGAGCATAATATTCACAGGGAAT
66 CATTTTGCTACAAAATTATCAATTCAAGCAGAAAAATGTGATAGAGCATAATATTCACAGGGAAT
14685755 AACCGAATAAGCATTGATCTGGCATGTCTAATCATGT
131 AACCGAATAAGCATTGATCTGGCATGTCTAATCATGT
14685792 C
1 C
14685793 ACTTTTTTTA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 168 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (167 bp):
CCCATTTGGTATTACCAAGTTTAATAATTAATTTCTTGGTGCTTGTGACTGACCTTAGCATATTT
CATTTTGCTACAAAATTATCAATTCAAGCAGAAAAATGTGATAGAGCATAATATTCACAGGGAAT
AACCGAATAAGCATTGATCTGGCATGTCTAATCATGT
Found at i:14690358 original size:20 final size:21
Alignment explanation
Indices: 14690321--14690377 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
14690311 TTTTTTATAA
*
14690321 TTTAAAAAAA-AATTTGAAAT
1 TTTAAAAAAATATTTTGAAAT
* *
14690341 TTT-TATAAATATTTTG-AAT
1 TTTAAAAAAATATTTTGAAAT
14690360 TTTAAAAAAATATTTTGA
1 TTTAAAAAAATATTTTGA
14690378 TTTTTTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTAAAAAAATATTTTGAAAT
Found at i:14693543 original size:2 final size:2
Alignment explanation
Indices: 14693538--14693578 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
14693528 TTGGTGTGTT
14693538 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
14693579 TATGAGTTTG
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:14698447 original size:2 final size:2
Alignment explanation
Indices: 14698434--14698468 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
14698424 AGCCAGGCTT
*
14698434 TA TA TG 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 T
14698469 TGAAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14704857 original size:30 final size:30
Alignment explanation
Indices: 14704804--14704862 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
14704794 AAACCTTTTA
*
14704804 TTTTCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCCAC
*
14704833 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCC-AAAACTTTTACTCCCTTCCCA
14704863 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.20, C:0.39, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:14710074 original size:23 final size:23
Alignment explanation
Indices: 14710047--14710098 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
14710037 ACTAAATATT
14710047 AAATAAAAATAATTACATTTTCA
1 AAATAAAAATAATTACATTTTCA
14710070 AAATAAAAATAATTACATTTTCA
1 AAATAAAAATAATTACATTTTCA
14710093 AAATAA
1 AAATAA
14710099 TAATTTGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAAAAATAATTACATTTTCA
Found at i:14721874 original size:34 final size:34
Alignment explanation
Indices: 14721836--14721906 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
14721826 TTTATGTTTC
14721836 CAAATCAAAATCAACTCAAATAAATAATCTTTAA
1 CAAATCAAAATCAACTCAAATAAATAATCTTTAA
*
14721870 CAAATCAAAATCAACTCAAATAAGTAATCTTTAA
1 CAAATCAAAATCAACTCAAATAAATAATCTTTAA
14721904 CAA
1 CAA
14721907 TTATACATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.55, C:0.18, G:0.01, T:0.25
Consensus pattern (34 bp):
CAAATCAAAATCAACTCAAATAAATAATCTTTAA
Found at i:14724675 original size:2 final size:2
Alignment explanation
Indices: 14724657--14724703 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
14724647 CAAATCTAAA
14724657 AT AT AT -T AT -T AT CAT AT AT AT AT AT AT AT AT AT AT -T A- AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14724696 -T AT AT AT A
1 AT AT AT AT A
14724704 ATTATAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
1 5 0.13
2 32 0.82
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14730065 original size:45 final size:44
Alignment explanation
Indices: 14730015--14730107 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
14730005 GGTTCGCTGT
*
14730015 AATGGAATAGAGAC-GTAATAGTAATT-TAAT-TGTTTGGTTGAATGG
1 AATGGAATAGA-ACTGTAATAGT-ATTCT--TGTGTTTGGTTGAATGA
14730060 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGA
1 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGA
14730104 AATG
1 AATG
14730108 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGA
Found at i:14730384 original size:120 final size:120
Alignment explanation
Indices: 14730254--14730725 Score: 876
Period size: 120 Copynumber: 3.9 Consensus size: 120
14730244 ATTTTAACAG
*
14730254 AATTATTATTAAATATAATTTAA-AAAATATATATAATTTAATAAAATTCTTAATATTAAATATT
1 AATTATTATTAAACATAATTTAATAAAA-ATATATAATTTAATAAAATTCTTAATATTAAATATT
14730318 CTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAAT
65 CTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAAT
* *
14730374 AATTATTATTAAATATAATTTAATAAACATATATAATTTAATAAAATTCTTAATATTAAATATTC
1 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
14730439 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAAT
66 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAAT
*
14730494 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATTAAATATTC
1 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
14730559 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAAT
66 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAAT
14730614 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
1 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
*
14730679 TTATATGAATTTATTAAAATCATAATATATAATACTATAAAA-ATAAT
66 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAT
14730726 ATTTTTATTT
Statistics
Matches: 345, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
119 5 0.01
120 337 0.98
121 3 0.01
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (120 bp):
AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
TTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAAT
Found at i:14731440 original size:30 final size:30
Alignment explanation
Indices: 14731406--14731465 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
14731396 TTCAGTTTTA
14731406 AGCCAAGATAAAGTAGGCAATACCAGAATT
1 AGCCAAGATAAAGTAGGCAATACCAGAATT
14731436 AGCCAAGATAAAGTAGGCAATACCAGAATT
1 AGCCAAGATAAAGTAGGCAATACCAGAATT
14731466 GTGATGAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (30 bp):
AGCCAAGATAAAGTAGGCAATACCAGAATT
Found at i:14733272 original size:29 final size:29
Alignment explanation
Indices: 14733239--14733326 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 29
14733229 AAAGAAACAG
14733239 AAGTTAAATAGCAGACGATGAAGATTAGA
1 AAGTTAAATAGCAGACGATGAAGATTAGA
14733268 AAG-T---TAG-A-A--ATGAAGATTAGA
1 AAGTTAAATAGCAGACGATGAAGATTAGA
* * *
14733289 AAGTTGAATAGCAGACGATGGAGATTAAA
1 AAGTTAAATAGCAGACGATGAAGATTAGA
*
14733318 AAGTAAAAT
1 AAGTTAAAT
14733327 GAACGCTGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
21 15 0.32
22 1 0.02
23 1 0.02
24 1 0.02
25 6 0.13
26 1 0.02
27 1 0.02
28 1 0.02
29 20 0.43
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.22
Consensus pattern (29 bp):
AAGTTAAATAGCAGACGATGAAGATTAGA
Found at i:14733531 original size:18 final size:18
Alignment explanation
Indices: 14733508--14733547 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
14733498 AGATTTGGAA
*
14733508 AAGAAGGAAATGTAGGAG
1 AAGAAGGAAACGTAGGAG
14733526 AAGAAGGAAACGTAGGAG
1 AAGAAGGAAACGTAGGAG
14733544 AAGA
1 AAGA
14733548 TGCTGAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.38, T:0.07
Consensus pattern (18 bp):
AAGAAGGAAACGTAGGAG
Found at i:14741312 original size:13 final size:13
Alignment explanation
Indices: 14741294--14741320 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14741284 AAGTCTCTGC
14741294 AGTTAATAAAAAA
1 AGTTAATAAAAAA
14741307 AGTTAATAAAAAA
1 AGTTAATAAAAAA
14741320 A
1 A
14741321 TTTATTAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
AGTTAATAAAAAA
Found at i:14741506 original size:26 final size:27
Alignment explanation
Indices: 14741471--14741529 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
14741461 AAAATTATAA
* *
14741471 AAAAATATAATATTTAT-TAAACAT-T
1 AAAAATATAAAATTCATATAAACATAT
*
14741496 AAAAATAATAAAATTCATATAAACTTAT
1 AAAAAT-ATAAAATTCATATAAACATAT
14741524 AAAAAT
1 AAAAAT
14741530 TTTAAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.21
26 9 0.32
27 6 0.21
28 7 0.25
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAAATATAAAATTCATATAAACATAT
Found at i:14741526 original size:28 final size:29
Alignment explanation
Indices: 14741465--14741529 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 29
14741455 AATTAAAAAA
*
14741465 TTATAAAAA-AATATAATATTTATTAAAC
1 TTATAAAAATAATATAATATTCATTAAAC
*
14741493 AT-TAAAAATAATA-AA-ATTCATATAAAC
1 TTATAAAAATAATATAATATTCAT-TAAAC
14741520 TTATAAAAAT
1 TTATAAAAAT
14741530 TTTAAAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 5 0.16
27 14 0.45
28 12 0.39
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (29 bp):
TTATAAAAATAATATAATATTCATTAAAC
Found at i:14741539 original size:20 final size:20
Alignment explanation
Indices: 14741516--14741570 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
14741506 AAATTCATAT
* *
14741516 AAACTTATAAAAATTTTAAA
1 AAACATATAAAAATTATAAA
* *
14741536 AAACCTATAAATATTATAAA
1 AAACATATAAAAATTATAAA
14741556 AAACATATAATAAAT
1 AAACATATAA-AAAT
14741571 CTAATAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
AAACATATAAAAATTATAAA
Found at i:14741585 original size:19 final size:18
Alignment explanation
Indices: 14741563--14741615 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
14741553 AAAAAACATA
14741563 TAATAAATCTAATAAATTT
1 TAATAAAT-TAATAAATTT
*
14741582 TAATAAATTATACAAATTT
1 TAATAAATTA-ATAAATTT
14741601 T-ATAAAATTAATAAA
1 TAAT-AAATTAATAAA
14741616 ACACATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAAATTAATAAATTT
Found at i:14742259 original size:10 final size:10
Alignment explanation
Indices: 14742244--14742348 Score: 74
Period size: 10 Copynumber: 10.7 Consensus size: 10
14742234 TAATTCAAGG
*
14742244 TTTTATGATT
1 TTTTATAATT
14742254 TTTTATAA-T
1 TTTTATAATT
*
14742263 TTTTATAAGT
1 TTTTATAATT
* *
14742273 ATATATCAA-T
1 TTTTAT-AATT
* *
14742283 TTTAAT-ATA
1 TTTTATAATT
*
14742292 TTTAATAATT
1 TTTTATAATT
14742302 TTTT-TAATT
1 TTTTATAATT
14742311 TTTTATAATT
1 TTTTATAATT
*
14742321 TTTCATAAGTT
1 TTTTATAA-TT
* *
14742332 TTTAAGAATT
1 TTTTATAATT
14742342 TTTTATA
1 TTTTATA
14742349 TGTTTTTCCT
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
8 1 0.01
9 24 0.32
10 40 0.53
11 10 0.13
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTATAATT
Found at i:14742265 original size:9 final size:9
Alignment explanation
Indices: 14742253--14742335 Score: 60
Period size: 9 Copynumber: 8.7 Consensus size: 9
14742243 GTTTTATGAT
14742253 TTTTTATAA
1 TTTTTATAA
14742262 TTTTTATAA
1 TTTTTATAA
* *
14742271 GTATATATCAA
1 -TTTTTAT-AA
*
14742282 TTTTAAT-A
1 TTTTTATAA
*
14742290 TATTTAATAA
1 T-TTTTATAA
*
14742300 TTTTTTTAA
1 TTTTTATAA
14742309 TTTTTTATAA
1 -TTTTTATAA
14742319 TTTTTCATAA
1 TTTTT-ATAA
14742329 GTTTTTA
1 -TTTTTA
14742336 AGAATTTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
8 2 0.03
9 26 0.44
10 24 0.41
11 7 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:14742341 original size:21 final size:20
Alignment explanation
Indices: 14742252--14742355 Score: 72
Period size: 19 Copynumber: 5.2 Consensus size: 20
14742242 GGTTTTATGA
*
14742252 TTTTTTATAATTTTTATAAG
1 TTTTTAATAATTTTTATAAG
* * *
14742272 TATAT-ATCAATTTTAAT-A-
1 TTTTTAAT-AATTTTTATAAG
* *
14742290 TATTTAATAATTTTTTTAA-
1 TTTTTAATAATTTTTATAAG
*
14742309 TTTTTTATAATTTTTCATAAG
1 TTTTTAATAATTTTT-ATAAG
* *
14742330 TTTTTAAGAATTTTTTATATG
1 TTTTTAATAA-TTTTTATAAG
14742351 TTTTT
1 TTTTT
14742356 CCTAAAATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
18 11 0.17
19 19 0.29
20 14 0.21
21 17 0.26
22 5 0.08
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTAATAATTTTTATAAG
Found at i:14742479 original size:30 final size:31
Alignment explanation
Indices: 14742419--14742492 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
14742409 ACTATTAGAA
*
14742419 TTTATTAGATTTTTTGATGATATTTATAAGTT
1 TTTATTA-ATTTTTTGATAATATTTATAAGTT
*
14742451 TTTATTAATTTTTT-ATAA-ATTTTGTAAGTT
1 TTTATTAATTTTTTGATAATA-TTTATAAGTT
*
14742481 TATATTAATTTT
1 TTTATTAATTTT
14742493 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 1 0.03
30 23 0.61
31 7 0.18
32 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (31 bp):
TTTATTAATTTTTTGATAATATTTATAAGTT
Found at i:14742528 original size:20 final size:19
Alignment explanation
Indices: 14742503--14742549 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
14742493 AATAAAAAAT
14742503 TAATTTCTTTCCTATTTTTA
1 TAATTT-TTTCCTATTTTTA
*
14742523 TAATTTTTTTCTATTTTT-
1 TAATTTTTTCCTATTTTTA
*
14742541 TTATTTTTT
1 TAATTTTTT
14742550 ATCATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TAATTTTTTCCTATTTTTA
Found at i:14742538 original size:19 final size:19
Alignment explanation
Indices: 14742503--14742560 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
14742493 AATAAAAAAT
*
14742503 TAATTTCTTTCCTATTTTTA
1 TAATTT-TTTTCTATTTTTA
14742523 TAATTTTTTTCTATTTTT-
1 TAATTTTTTTCTATTTTTA
*
14742541 TTATTTTTTATC-ATTTTTA
1 TAATTTTTT-TCTATTTTTA
14742560 T
1 T
14742561 GGGAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 14 0.41
19 14 0.41
20 6 0.18
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (19 bp):
TAATTTTTTTCTATTTTTA
Found at i:14755243 original size:17 final size:17
Alignment explanation
Indices: 14755200--14755243 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
14755190 AAAATTGTCA
*
14755200 AATAAATAAAATTACATT
1 AATAAA-AAATTTACATT
14755218 -ATAAAAAATTTACATT
1 AATAAAAAATTTACATT
14755234 AATAAAAAAT
1 AATAAAAAAT
14755244 CACAAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAAAAAATTTACATT
Found at i:14755559 original size:98 final size:98
Alignment explanation
Indices: 14755205--14755598 Score: 448
Period size: 98 Copynumber: 4.0 Consensus size: 98
14755195 TGTCAAATAA
** * * *
14755205 ATAAAATTACATTATAAAAAATTTACATTAATAAAAAATCACAAAATACTAAACTGAACACTAAC
1 ATAAAATTATTTTA-AAAAAAATTACATTACTAAAAAATCACAAAACACT-AA---AACACTAAC
14755270 AATTTATATAACCTAATCATAAATTACT-A-AAAA-AACT
61 AA-TT-TATAACCTAATCATAAATTACTAACAAAATAACT
* *
14755307 ATAAAATTATCTTTAAAAAAAATTACATTACTAAAAAATCACAAAACCCTAAACTAAACGGTAAC
1 ATAAAATTAT-TTTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAA--ACAC--TAAC
* * *
14755372 AAATTATAAACTAATCACAAATTACTAACAAAATAACT
61 AATTTATAACCTAATCATAAATTACTAACAAAATAACT
* * *
14755410 ATAACATTA----AAAAAAATTTACATTACTAATAAAA-CACAAAATAC-AAAACACTAACAATT
1 ATAAAATTATTTTAAAAAAAATTACATTACTAA-AAAATCACAAAACACTAAAACACTAACAATT
* *
14755469 TACAACCTAATCATAAATTACTAATAAAATAACT
65 TATAACCTAATCATAAATTACTAACAAAATAACT
*
14755503 ATAAAATTATTTTTAAAAAAAATTACATTACTAAAATATCACAAAACAC-AAAACACTAACAATT
1 ATAAAATTA-TTTTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAAACACTAACAATT
14755567 TATAACCTAATCATAAATTACTAACAAAATAA
65 TATAACCTAATCATAAATTACTAACAAAATAA
14755599 TTCACAAAAT
Statistics
Matches: 251, Mismatches: 26, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
93 45 0.18
95 3 0.01
97 6 0.02
98 101 0.40
99 4 0.02
100 23 0.09
101 4 0.02
102 50 0.20
103 15 0.06
ACGTcount: A:0.57, C:0.15, G:0.01, T:0.27
Consensus pattern (98 bp):
ATAAAATTATTTTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAAACACTAACAATTT
ATAACCTAATCATAAATTACTAACAAAATAACT
Found at i:14755617 original size:88 final size:90
Alignment explanation
Indices: 14755525--14755692 Score: 236
Period size: 92 Copynumber: 1.9 Consensus size: 90
14755515 TTAAAAAAAA
* *
14755525 TTACATTACTAA-AATATCAC-AAA-AC-ACAAAACACTAACAATTTATAACCTAATCATAAATT
1 TTACATTAATAAGAA-ATCACAAAATACAACAAAACAC-AACAATTTATAACATAATCATAAATT
14755586 ACTAACAAAATAATTCACAAAATAATT
64 ACTAACAAAATAATTCACAAAATAATT
* *
14755613 TTACATTAATAAGAAATCACAAAATACTAAACTAAACACAACAATTTATAACATAATCCTAAATT
1 TTACATTAATAAGAAATCACAAAATAC--AACAAAACACAACAATTTATAACATAATCATAAATT
14755678 ACTAACAAAATAATT
64 ACTAACAAAATAATT
14755693 ATAAAAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
88 16 0.23
89 5 0.07
90 2 0.03
92 39 0.56
93 8 0.11
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.27
Consensus pattern (90 bp):
TTACATTAATAAGAAATCACAAAATACAACAAAACACAACAATTTATAACATAATCATAAATTAC
TAACAAAATAATTCACAAAATAATT
Found at i:14755637 original size:98 final size:95
Alignment explanation
Indices: 14755439--14755698 Score: 273
Period size: 98 Copynumber: 2.7 Consensus size: 95
14755429 ACATTACTAA
* * *
14755439 TAAAA-CACAAAATACAAAACACTAACAATTTACAACCTAATCATAAATTACTAATAAAATAACT
1 TAAAATCACAAAA-ACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAATT
* * * * *
14755503 ATAAAATTATTTTTAAAAAAAATTACATTAC
65 ACAAAATTAATTTTAAAAAAAATGAAATCAC
14755534 TAAAATATCACAAAACACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAA
1 T-AAA-ATCACAAAA-ACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAA
* *
14755599 TTCACAAAA-TAATTTTACATTAATAA-GAAATCAC
63 TT-ACAAAATTAATTTTA-A-AAAAAATGAAATCAC
* * * *
14755633 -AAAAT-AC-TAAACTAAACAC-AACAATTTATAACATAATCCTAAATTACTAACAAAATAATTA
1 TAAAATCACAAAAACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAATTA
*
14755694 TAAAA
66 CAAAA
14755699 AAAACTGCAT
Statistics
Matches: 143, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
91 5 0.03
92 39 0.27
93 8 0.06
94 2 0.01
95 3 0.02
96 5 0.03
97 4 0.03
98 62 0.43
99 11 0.08
100 4 0.03
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (95 bp):
TAAAATCACAAAAACAAAACACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAATTA
CAAAATTAATTTTAAAAAAAATGAAATCAC
Found at i:14756110 original size:28 final size:28
Alignment explanation
Indices: 14756068--14756143 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
14756058 ATGGGACTAG
* *
14756068 TGTAATTTTATAAAATTAAATTCTTTGA
1 TGTAATTTAATAAAATTAAATGCTTTGA
*
14756096 TGTAATTTAACAAAATTAAATGCTTTGA
1 TGTAATTTAATAAAATTAAATGCTTTGA
14756124 TGTAATTTAATAAAATTAAA
1 TGTAATTTAATAAAATTAAA
14756144 AGCATGGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (28 bp):
TGTAATTTAATAAAATTAAATGCTTTGA
Found at i:14762097 original size:48 final size:48
Alignment explanation
Indices: 14762006--14762097 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
14761996 GTGAAAAATC
* * * ** *
14762006 TTTGAGTTAGTTAAGTTGATAAGTTTTATTTTATTGTCTTAACTTAGT
1 TTTGAGTTAGTCAAGTTGACAAGTCTTATTTTATCATCCTAACTTAGT
14762054 TTTGAGTTAGTCAAGTTGACAAGTCTTATTTTATCATCCTAACT
1 TTTGAGTTAGTCAAGTTGACAAGTCTTATTTTATCATCCTAACT
14762098 CGATGTGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (48 bp):
TTTGAGTTAGTCAAGTTGACAAGTCTTATTTTATCATCCTAACTTAGT
Found at i:14765143 original size:44 final size:44
Alignment explanation
Indices: 14765073--14765191 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 44
14765063 CTGCAAACCA
*
14765073 CTGTGAATCCACAACCAGAAGCAGATTCCATCTACAGGGTA-TTG
1 CTGTGAATCCACAGCCAGAAGCAGATTCCATCTAC-GGGTACTTG
* * * *
14765117 CTGTGAATCCACAGCCA-ATGGTAGATTCCATTTGCGGGTACTTG
1 CTGTGAATCCACAGCCAGA-AGCAGATTCCATCTACGGGTACTTG
* * *
14765161 TTGTGTATCCACAGCC-GAAAGCAAATTCCAT
1 CTGTGAATCCACAGCCAG-AAGCAGATTCCAT
14765192 TTGCAAGATT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.10
44 54 0.89
45 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (44 bp):
CTGTGAATCCACAGCCAGAAGCAGATTCCATCTACGGGTACTTG
Found at i:14769238 original size:60 final size:60
Alignment explanation
Indices: 14769166--14769348 Score: 185
Period size: 60 Copynumber: 3.1 Consensus size: 60
14769156 AGATAAGCCC
* ** *
14769166 TGAACTTGGCAATTGTTTTCACATTGAGG-CTTGAACTTTTTTTTGGTCTAAGTTAGGTCT
1 TGAACTTAGCAATTGTTCCCACATTG-GGTCTTGAACTTTTTTTTGGTCCAAGTTAGGTCT
* **
14769226 TGAACTTAGCAATTGTTCCCACATTGGGTCTTGAACTTTTTTTTTGTCCAAGTTAGACCT
1 TGAACTTAGCAATTGTTCCCACATTGGGTCTTGAACTTTTTTTTGGTCCAAGTTAGGTCT
* * * * ** *
14769286 TGAA-TTTGACAATTCTTCACGCATTATGACTTGAACTTTTTTTT-GTCCAAGTTA-GTCAT
1 TGAACTTAG-CAATTGTTCCCACATTGGGTCTTGAACTTTTTTTTGGTCCAAGTTAGGTC-T
14769345 TGAA
1 TGAA
14769349 AACCTGAAAG
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 20 0.19
60 83 0.80
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.43
Consensus pattern (60 bp):
TGAACTTAGCAATTGTTCCCACATTGGGTCTTGAACTTTTTTTTGGTCCAAGTTAGGTCT
Found at i:14769976 original size:6 final size:6
Alignment explanation
Indices: 14769960--14769990 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
14769950 GGAGAGAAAT
*
14769960 GAGAAG AAGAAG GAGAAG GAGAAG GAGAAG G
1 GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG G
14769991 TATGTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAGAAG
Found at i:14770356 original size:95 final size:95
Alignment explanation
Indices: 14770236--14770612 Score: 463
Period size: 95 Copynumber: 3.9 Consensus size: 95
14770226 TAATGTAAAA
* * *
14770236 TTATTTTGTTTGTAATTTATGATTAGGTTATAAATTGTTAGTGTTCAGTGTTTTGTGATTTTTTA
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTATTTTGTGATTTTTTA
14770301 GTAATGTAATTTTTTTTTAAAAAATTATAG
66 GTAATGTAATTTTTTTTTAAAAAATTATAG
* *
14770331 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTAGTGTTTTA-TATTTTGTGATTTATT
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTG-TTTAGTATTTTGTGATTTTTT
** *
14770395 AGTAATGTAATTTTTTTTTAAAATGTTATAT
65 AGTAATGTAATTTTTTTTTAAAAAATTATAG
* * * *
14770426 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTACTGTTTAGTTTAGGATTCTGTGAGT
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTA--G--T-GTTTAGTATTTTGTGATT
*
14770491 TTTTAGTAATGTAA--TTTTTTTAAAATATTTATAG
61 TTTTAGTAATGTAATTTTTTTTTAAAA-AATTATAG
*
14770525 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTATTGTTTAGTTTAATATTTTGTGA
1 TTATTTTGTTAGTAATTTATGATTAGG-T-TATAAATTGTTA--G--T-GTTTAGTATTTTGTGA
* *
14770590 TTTTTTATTAATGTAAATTTTTT
59 TTTTTTAGTAATGTAATTTTTTT
14770613 ATAATGTAAT
Statistics
Matches: 246, Mismatches: 24, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
95 121 0.49
96 3 0.01
97 1 0.00
98 11 0.04
99 36 0.15
100 24 0.10
101 45 0.18
103 5 0.02
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (95 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTATTTTGTGATTTTTTA
GTAATGTAATTTTTTTTTAAAAAATTATAG
Found at i:14770443 original size:190 final size:197
Alignment explanation
Indices: 14770236--14770612 Score: 529
Period size: 190 Copynumber: 1.9 Consensus size: 197
14770226 TAATGTAAAA
* * * *
14770236 TTATTTTGTTTGTAATTTATGATTAGGTTATAAATTGTTAGTGTTCAG-T-G-TTTTGTGATTTT
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTACTGTTCAGTTAGATTCTGTGAGTTT
14770298 TTAGTAATGTAATTTTTTTTTAAAA-AATTATAGTTATTTTGTTAGTAATTTATGATTAGG-T-T
66 TTAGTAATGTAA--TTTTTTTAAAATAATTATAGTTATTTTGTTAGTAATTTATGATTAGGTTAT
* *
14770360 ATAAATTATTA-G-T-GTTTTATATTTTGTGATTTATTAGTAATGTAATTTTTTTTTAAAATGTT
129 ATAAATTATTATGTTAGTTTAATATTTTGTGATTTATTAGTAATGTAAATTTTTTTTAAAATGTT
14770422 ATAT
194 ATAT
* *
14770426 TTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTACTGTTTAGTTTAGGATTCTGTGAGT
1 TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTACTGTTCAG-TTA-GATTCTGTGAGT
*
14770491 TTTTAGTAATGTAATTTTTTTAAAATATTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTAT
64 TTTTAGTAATGTAATTTTTTTAAAATAATTATAGTTATTTTGTTAGTAATTTATGATTAGGTTAT
* * *
14770556 ATAAATTGTTATTGTTTAGTTTAATATTTTGTGATTTTTTATTAATGTAAATTTTTT
129 ATAAATTATTA-TG-TTAGTTTAATATTTTGTGATTTATTAGTAATGTAAATTTTTT
14770613 ATAATGTAAT
Statistics
Matches: 162, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
190 44 0.27
192 1 0.01
193 11 0.07
194 35 0.22
195 23 0.14
196 11 0.07
198 1 0.01
200 1 0.01
201 35 0.22
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (197 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTACTGTTCAGTTAGATTCTGTGAGTTT
TTAGTAATGTAATTTTTTTAAAATAATTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAT
AAATTATTATGTTAGTTTAATATTTTGTGATTTATTAGTAATGTAAATTTTTTTTAAAATGTTAT
AT
Found at i:14770617 original size:16 final size:17
Alignment explanation
Indices: 14770589--14770621 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
14770579 ATATTTTGTG
14770589 ATTTTTTATTAATGTAA
1 ATTTTTTATTAATGTAA
14770606 ATTTTTTA-TAATGTAA
1 ATTTTTTATTAATGTAA
14770622 TTTCATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTTTATTAATGTAA
Found at i:14773029 original size:75 final size:76
Alignment explanation
Indices: 14772937--14773099 Score: 247
Period size: 75 Copynumber: 2.2 Consensus size: 76
14772927 GTAATTTAAA
* * * * *
14772937 TAACTTTATATTTATGTAATGACTTTTTTGCCATTTTAGTTATTAATTTTAGGG-GTTTTTTGCA
1 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGTGTTTTTTACA
*
14773001 ATTTAAATAGT
66 ATTTAAATAAT
*
14773012 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGTTTTTTTTACA
1 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGTGTTTTTTACA
14773077 ATTTAAATAAT
66 ATTTAAATAAT
*
14773088 AAACTTTGTATT
1 TAACTTTGTATT
14773100 ATTTAATTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 50 0.63
76 29 0.37
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (76 bp):
TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGTGTTTTTTACA
ATTTAAATAAT
Found at i:14774352 original size:23 final size:23
Alignment explanation
Indices: 14774326--14774379 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
14774316 TACTAAATAA
* *
14774326 ATTAATAACAAT-AAAATAATAT
1 ATTAATAAAAATCAAAATAAAAT
*
14774348 CATTAA-AAAAATCAAATTAAAAT
1 -ATTAATAAAAATCAAAATAAAAT
14774371 ATTAATAAA
1 ATTAATAAA
14774380 CTAATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTAATAAAAATCAAAATAAAAT
Found at i:14777980 original size:27 final size:27
Alignment explanation
Indices: 14777894--14777981 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 27
14777884 GCCGCTTATG
* * *
14777894 AGATAGGTGTCACCAGTGGTGCCTACT
1 AGATAGGAGTCACCAGTGGCGCCTACC
* * *
14777921 AGATAAGAGTCACCAGTGGCACCTAGC
1 AGATAGGAGTCACCAGTGGCGCCTACC
*
14777948 AGATAGGAGTCACCAGTGACGCCTACC
1 AGATAGGAGTCACCAGTGGCGCCTACC
14777975 AGATAGG
1 AGATAGG
14777982 CACCACCTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (27 bp):
AGATAGGAGTCACCAGTGGCGCCTACC
Found at i:14781200 original size:9 final size:9
Alignment explanation
Indices: 14781186--14781243 Score: 62
Period size: 9 Copynumber: 6.0 Consensus size: 9
14781176 TTGTAAATAT
14781186 ATATTAAAA
1 ATATTAAAA
14781195 ATATTAAAA
1 ATATTAAAA
14781204 ATATTAAAA
1 ATATTAAAA
*
14781213 ATTACTAAAAA
1 A-TA-TTAAAA
*
14781224 ATCTTTAAAA
1 AT-ATTAAAA
14781234 ATATATAAAA
1 ATAT-TAAAA
14781244 TGCTAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 20 0.49
10 15 0.37
11 6 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATTAAAA
Found at i:14781213 original size:10 final size:10
Alignment explanation
Indices: 14781186--14781243 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
14781176 TTGTAAATAT
14781186 ATATT-AAAA
1 ATATTAAAAA
14781195 ATATT-AAAA
1 ATATTAAAAA
14781204 ATATTAAAAA
1 ATATTAAAAA
* *
14781214 TTACTAAAAA
1 ATATTAAAAA
* *
14781224 ATCTTTAAAA
1 ATATTAAAAA
14781234 ATATATAAAA
1 ATAT-TAAAA
14781244 TGCTAAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
9 14 0.36
10 21 0.54
11 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
ATATTAAAAA
Found at i:14783308 original size:14 final size:15
Alignment explanation
Indices: 14783284--14783312 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14783274 TTTTTCTATG
14783284 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
14783299 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
14783313 AGTTTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:14784510 original size:43 final size:43
Alignment explanation
Indices: 14784460--14784575 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
14784450 TATGTGTTTT
*
14784460 CATGTAAGACCACATCTGGGA-TGTCGGCATCGATATCTGATTA
1 CATGTAAGACCACATCTGGGACAGT-GGCATCGATATCTGATTA
* *** *
14784503 CGTGTAAGACCTTGTCTGGGACAGTGGCATCGATATGTGATTA
1 CATGTAAGACCACATCTGGGACAGTGGCATCGATATCTGATTA
* *
14784546 CATGTAAGACCACGTTTGGGAC-GATGGCAT
1 CATGTAAGACCACATCTGGGACAG-TGGCAT
14784576 TGTACGAGCT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
42 1 0.02
43 58 0.95
44 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCACATCTGGGACAGTGGCATCGATATCTGATTA
Found at i:14799051 original size:34 final size:34
Alignment explanation
Indices: 14799013--14799086 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
14799003 TTTAGTGCTC
* *
14799013 TTTGGTTGTGTGGGATGGATACACTTATGTGCAA
1 TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
* *
14799047 TTTGGTTGTGAGGGATGAATGCACTTATGTTCAA
1 TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
14799081 TTTGGT
1 TTTGGT
14799087 GTATTTAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.08, G:0.31, T:0.41
Consensus pattern (34 bp):
TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
Found at i:14801034 original size:41 final size:41
Alignment explanation
Indices: 14800964--14801092 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 41
14800954 GCACATATCT
* * * * *
14800964 TGAAATGATACACCGGCACAAAGCTTGCTAGGCTTAAAGCC
1 TGAAATAATACACCGGCATAAAGCCTGCTAGACATAAAGCC
** * *
14801005 TGATTTAATACACCGGCATGAAGCCTGCTAGACATAAAGTC
1 TGAAATAATACACCGGCATAAAGCCTGCTAGACATAAAGCC
* * * *
14801046 TGAAATATTTCACCGGCATCAAGCCTGCTAGTCACATAGAGCC
1 TGAAATAATACACCGGCATAAAGCCTGCTAG--ACATAAAGCC
14801089 TGAA
1 TGAA
14801093 TATCTTGGAT
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 58 0.83
43 12 0.17
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (41 bp):
TGAAATAATACACCGGCATAAAGCCTGCTAGACATAAAGCC
Found at i:14802918 original size:13 final size:13
Alignment explanation
Indices: 14802900--14802925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14802890 CATTTCCAGG
14802900 TCATTTTCATTTT
1 TCATTTTCATTTT
14802913 TCATTTTCATTTT
1 TCATTTTCATTTT
14802926 GAAGAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:14802977 original size:57 final size:58
Alignment explanation
Indices: 14802910--14803030 Score: 192
Period size: 57 Copynumber: 2.1 Consensus size: 58
14802900 TCATTTTCAT
*
14802910 TTTTCATTTTCATTTTGAAGAAAA-CTACATTCATTTCCAAATATTTCCC-TTTCTCCC
1 TTTTCATTTTCATTTTGAAGAAAACCT-CATTCATTTCCAAATATTTCCCATTTCTCCA
* *
14802967 TTTTCATTTTCATTTTGGAGAAAACCTCATTCATTTCCAAATGTTTCCCATTTCTCCA
1 TTTTCATTTTCATTTTGAAGAAAACCTCATTCATTTCCAAATATTTCCCATTTCTCCA
14803025 TTTTCA
1 TTTTCA
14803031 CCATTTCTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
57 44 0.75
58 15 0.25
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (58 bp):
TTTTCATTTTCATTTTGAAGAAAACCTCATTCATTTCCAAATATTTCCCATTTCTCCA
Found at i:14804445 original size:14 final size:14
Alignment explanation
Indices: 14804399--14804445 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
14804389 TGTATTATTT
*
14804399 TTATAATCTTAAATA
1 TTAT-ATCTAAAATA
*
14804414 TTAAATCTAAAA-A
1 TTATATCTAAAATA
*
14804427 TTATATGTAAAATA
1 TTATATCTAAAATA
14804441 TTATA
1 TTATA
14804446 ATATACAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 11 0.41
14 13 0.48
15 3 0.11
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (14 bp):
TTATATCTAAAATA
Found at i:14813570 original size:69 final size:69
Alignment explanation
Indices: 14813459--14813628 Score: 250
Period size: 69 Copynumber: 2.5 Consensus size: 69
14813449 ATCAGATGTG
* * * * *
14813459 ATCGAGTAGTTTTAGGAGTTACGATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTA
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
14813524 GGTC
66 GGTC
* *
14813528 ATCGAGTTGTTTTATGAGTTGCAATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
14813593 GGTC
66 GGTC
** *
14813597 ATCGAACTATTTTAGGAGTTGCGATCTTAAAT
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAAT
14813629 TACCTAACTC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 89 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (69 bp):
ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
GGTC
Found at i:14813733 original size:106 final size:106
Alignment explanation
Indices: 14813545--14813794 Score: 383
Period size: 106 Copynumber: 2.4 Consensus size: 106
14813535 TGTTTTATGA
* * ** * *
14813545 GTTGCAATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTAGGTCATCGAACTATTTT
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
* * *
14813610 AGGAGTTGCGATCTTAAATTACCTAACTCAAAGAAACTTAG
66 AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
* *
14813651 GTTGCGATCTTAAATCGGCTAACCTTTATAATACCAGTTGTGAACGTAGGTCATCAAACTATTTC
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
* *
14813716 AAGAGTTGCGATATTAAATCAGCTAACTCAAAGAAACTTCG
66 AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
14813757 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGT
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGT
14813795 ACTTGTATAG
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 129 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (106 bp):
GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
Found at i:14825952 original size:15 final size:15
Alignment explanation
Indices: 14825894--14825969 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
14825884 CCGAATAAGC
*
14825894 TTGAACTCAAAAATAC
1 TTGAACTCAAAAA-AT
* *
14825910 TTGAACATGATAAAAT
1 TTGAAC-TCAAAAAAT
**
14825926 TTGAACAAAAAAAAT
1 TTGAACTCAAAAAAT
14825941 TTGAACTCAAAAAAT
1 TTGAACTCAAAAAAT
* * *
14825956 CTGCACTTAAAAAA
1 TTGAACTCAAAAAA
14825970 ATCCAAACCC
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
15 30 0.62
16 13 0.27
17 5 0.10
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.25
Consensus pattern (15 bp):
TTGAACTCAAAAAAT
Found at i:14825954 original size:16 final size:16
Alignment explanation
Indices: 14825894--14825954 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
14825884 CCGAATAAGC
* *
14825894 TTGAACTCAAAAATAC
1 TTGAACTCAAAAAAAT
* *
14825910 TTGAACAT-GATAAAAT
1 TTGAAC-TCAAAAAAAT
*
14825926 TTGAAC-AAAAAAAAT
1 TTGAACTCAAAAAAAT
14825941 TTGAACTCAAAAAA
1 TTGAACTCAAAAAA
14825955 TCTGCACTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 12 0.34
16 22 0.63
17 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (16 bp):
TTGAACTCAAAAAAAT
Found at i:14827594 original size:26 final size:26
Alignment explanation
Indices: 14827562--14827615 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
14827552 CCTCCTCTAC
14827562 CACTAGTTTTTAACAATGAAAACTAT
1 CACTAGTTTTTAACAATGAAAACTAT
14827588 CACTAGTTTTTAACAATGAAAACTAT
1 CACTAGTTTTTAACAATGAAAACTAT
14827614 CA
1 CA
14827616 TATTTGGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (26 bp):
CACTAGTTTTTAACAATGAAAACTAT
Found at i:14830592 original size:26 final size:26
Alignment explanation
Indices: 14830521--14830595 Score: 93
Period size: 25 Copynumber: 2.9 Consensus size: 26
14830511 AAATATTTTC
14830521 TCAAAATTTTACTAGAG-GTAAAATCA
1 TCAAAATTTTACTAG-GTGTAAAATCA
* *
14830547 TCAAAA-TTTACT-GATGGTAAAATCG
1 TCAAAATTTTACTAGGT-GTAAAATCA
14830572 TCAAAATTTTACTAGGTGTAAAAT
1 TCAAAATTTTACTAGGTGTAAAAT
14830596 AGGGTTGAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.02
25 20 0.48
26 19 0.45
27 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACTAGGTGTAAAATCA
Found at i:14832773 original size:25 final size:25
Alignment explanation
Indices: 14832739--14832879 Score: 116
Period size: 25 Copynumber: 5.6 Consensus size: 25
14832729 GTACATGTAT
*
14832739 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTATGAATCGGTAA
* *
14832764 GCTC-TCACGAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
14832789 GCTCATA-GAAGCTGA-GAATCGGTAA
1 GCTCATACG-AGCT-ATGAATCGGTAA
*
14832814 GCTC-TCATGAG-T-TGCAAATCGGTAA
1 GCTCAT-ACGAGCTATG--AATCGGTAA
* *
14832839 GCTC-TCACGAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
14832864 GCTCATACGAGCTATG
1 GCTCATACGAGCTATG
14832880 GTGTGTCCGC
Statistics
Matches: 95, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
23 1 0.01
24 4 0.04
25 85 0.89
26 4 0.04
27 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCGGTAA
Found at i:14832852 original size:50 final size:50
Alignment explanation
Indices: 14832739--14832876 Score: 160
Period size: 50 Copynumber: 2.8 Consensus size: 50
14832729 GTACATGTAT
* *
14832739 GCTCATACGAGCT-ATGAATCGGTATGCTCTCACGAGCTGTAAATCGGTAA
1 GCTCATACGAGCTGA-GAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAA
* *
14832789 GCTCATA-GAAGCTGAGAATCGGTAAGCTCTCATGAGTTGCAAATCGGTAA
1 GCTCATACG-AGCTGAGAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAA
14832839 GCTC-TCACGAGCTGTA-AATCGGTAAGCTCAT-ACGAGCT
1 GCTCAT-ACGAGCTG-AGAATCGGTAAGCTC-TCACGAGCT
14832877 ATGGTGTGTC
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
49 2 0.03
50 70 0.92
51 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (50 bp):
GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAA
Found at i:14837189 original size:25 final size:25
Alignment explanation
Indices: 14837136--14837248 Score: 99
Period size: 25 Copynumber: 4.5 Consensus size: 25
14837126 GTACATGTAT
* *
14837136 GCTCATACGAGCTATGAATTCG-TAT
1 GCTCATACGAGCTAT-AAATCGATAA
14837161 GCTC-TCACGAGCTATAAATCGATAA
1 GCTCAT-ACGAGCTATAAATCGATAA
* * * *
14837186 GCTCATACAAGTCGA-GAATCGGTAA
1 GCTCATACGAG-CTATAAATCGATAA
*
14837211 GCTC-TAGCGAGCTACAAATCGATAA
1 GCTCATA-CGAGCTATAAATCGATAA
14837236 GCTCATACGAGCT
1 GCTCATACGAGCT
14837249 GTGGTGTGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
24 10 0.14
25 56 0.79
26 5 0.07
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTATAAATCGATAA
Found at i:14843609 original size:20 final size:19
Alignment explanation
Indices: 14843583--14843671 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 19
14843573 ATAGATGCGT
14843583 AACAGAGGCACCGAAGTGC
1 AACAGAGGCACCGAAGTGC
14843602 AGACAGAGGCA-CGATTA-TGC
1 A-ACAGAGGCACCGA--AGTGC
* *
14843622 AATCAAAGGCACCAAAGTGC
1 AA-CAGAGGCACCGAAGTGC
* * *
14843642 AAATAGAGACACCGAAGTGT
1 -AACAGAGGCACCGAAGTGC
14843662 AACAGAGGCA
1 AACAGAGGCA
14843672 TTGAACTGCA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
19 14 0.26
20 35 0.65
21 5 0.09
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.10
Consensus pattern (19 bp):
AACAGAGGCACCGAAGTGC
Found at i:14857853 original size:16 final size:16
Alignment explanation
Indices: 14857834--14857866 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
14857824 TCACCTCAAT
14857834 AAATTTTATAAAATTA
1 AAATTTTATAAAATTA
*
14857850 AAATTTTATAATATTA
1 AAATTTTATAAAATTA
14857866 A
1 A
14857867 CTGAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTTATAAAATTA
Found at i:14858772 original size:19 final size:18
Alignment explanation
Indices: 14858750--14858791 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
14858740 AATTCAAAAA
14858750 TAAAAATA-AAAATATTTTT
1 TAAAAATATAAAA-A-TTTT
14858769 TAAAAATATAAAAATTTT
1 TAAAAATATAAAAATTTT
14858787 TAAAA
1 TAAAA
14858792 TTCAATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATATAAAAATTTT
Found at i:14862149 original size:16 final size:16
Alignment explanation
Indices: 14862113--14862159 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
14862103 CTCATCACTT
* *
14862113 TATGGTGTGTTGGGGG
1 TATGGTGTGTTTGGAG
14862129 T-TGGTGTGTTTGGAG
1 TATGGTGTGTTTGGAG
*
14862144 TATGGTTTGTTTGGAG
1 TATGGTGTGTTTGGAG
14862160 GACATGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.45
Consensus pattern (16 bp):
TATGGTGTGTTTGGAG
Found at i:14863815 original size:13 final size:14
Alignment explanation
Indices: 14863781--14863870 Score: 66
Period size: 13 Copynumber: 6.7 Consensus size: 14
14863771 CCAATGTTTC
* *
14863781 ATTTCATAT-ATCT
1 ATTTCATATAACCG
14863794 ATTTCCATATAACCG
1 ATTT-CATATAACCG
**
14863809 A-TTCATATAA-AT
1 ATTTCATATAACCG
* *
14863821 ATTTCATAT-ATCT
1 ATTTCATATAACCG
14863834 ATTTTCATATAACCG
1 A-TTTCATATAACCG
14863849 A-TTCATATAACC-
1 ATTTCATATAACCG
14863861 ATTTCATATA
1 ATTTCATATA
14863871 TCTATATTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
12 3 0.05
13 39 0.62
14 15 0.24
15 6 0.10
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTTCATATAACCG
Found at i:14863826 original size:40 final size:39
Alignment explanation
Indices: 14863780--14863884 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 39
14863770 TCCAATGTTT
14863780 CATTTCATATATCTATTTCCATATAACCGATTCATATAAA
1 CATTTCATATATCTATTT-CATATAACCGATTCATATAAA
* *
14863820 TATTTCATATATCTATTTTCATATAACCGATTCATATAAC
1 CATTTCATATATCTA-TTTCATATAACCGATTCATATAAA
14863860 CATTTCATATATCTATATTCATATA
1 CATTTCATATATCTAT-TTCATATA
14863885 TTCATTTTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
39 1 0.02
40 56 0.93
41 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (39 bp):
CATTTCATATATCTATTTCATATAACCGATTCATATAAA
Found at i:14863879 original size:27 final size:26
Alignment explanation
Indices: 14863780--14863884 Score: 97
Period size: 27 Copynumber: 3.9 Consensus size: 26
14863770 TCCAATGTTT
*
14863780 CATTTCATATATCTATTTCCATATAAC
1 CATTTCATATAACTATTT-CATATAAC
* *
14863807 CGA-TTCATATAAATATTTCATATATC
1 C-ATTTCATATAACTATTTCATATAAC
* *
14863833 TATTTTCATATAACCGA-TTCATATAAC
1 CA-TTTCATATAA-CTATTTCATATAAC
*
14863860 CATTTCATATATCTATATTCATATA
1 CATTTCATATAACTAT-TTCATATA
14863885 TTCATTTTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
25 3 0.05
26 16 0.26
27 41 0.66
28 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (26 bp):
CATTTCATATAACTATTTCATATAAC
Found at i:14863894 original size:14 final size:14
Alignment explanation
Indices: 14863782--14863894 Score: 60
Period size: 13 Copynumber: 8.4 Consensus size: 14
14863772 CAATGTTTCA
14863782 TTTCATATATCTAT
1 TTTCATATATCTAT
* * *
14863796 TTCCATATAACCGA-
1 TTTCATAT-ATCTAT
**
14863810 -TTCATATAAATA-
1 TTTCATATATCTAT
14863822 TTTCATATATCTAT
1 TTTCATATATCTAT
* *
14863836 TTTCATATAACCGA-
1 TTTCATAT-ATCTAT
* *
14863850 -TTCATATAACCA-
1 TTTCATATATCTAT
14863862 TTTCATATATCTAT
1 TTTCATATATCTAT
*
14863876 ATTCATATAT-TCAT
1 TTTCATATATCT-AT
14863890 TTTCA
1 TTTCA
14863895 CACGATGAAC
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
12 5 0.07
13 34 0.45
14 30 0.40
15 6 0.08
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (14 bp):
TTTCATATATCTAT
Found at i:14866325 original size:23 final size:25
Alignment explanation
Indices: 14866298--14866349 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
14866288 TTTTTTTAGC
14866298 TATTTCATTATTTAGTTATT-TT-T
1 TATTTCATTATTTAGTTATTGTTAT
* * *
14866321 TATTTCTTTTTTTTGTTATTGTTAT
1 TATTTCATTATTTAGTTATTGTTAT
14866346 TATT
1 TATT
14866350 ATTATTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 2 0.08
25 5 0.21
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (25 bp):
TATTTCATTATTTAGTTATTGTTAT
Found at i:14866396 original size:26 final size:23
Alignment explanation
Indices: 14866367--14866424 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
14866357 TTATTATTTC
*
14866367 TATATTTATACACGCATTTTTTA
1 TATATATATACACGCATTTTTTA
* *
14866390 TAGTATATATATATGCATTTTTTA
1 TA-TATATATACACGCATTTTTTA
14866414 TATATAATATA
1 TATAT-ATATA
14866425 TATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (23 bp):
TATATATATACACGCATTTTTTA
Found at i:14866407 original size:24 final size:24
Alignment explanation
Indices: 14866380--14866427 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
14866370 ATTTATACAC
14866380 GCATTTTTTATAGTAT-ATATATAT
1 GCATTTTTTATA-TATAATATATAT
14866404 GCATTTTTTATATATAATATATAT
1 GCATTTTTTATATATAATATATAT
14866428 ATTTTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
GCATTTTTTATATATAATATATAT
Found at i:14871444 original size:6 final size:6
Alignment explanation
Indices: 14871433--14871472 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
14871423 TGAAAGTGAT
14871433 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
14871473 TGGAGAGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:14881480 original size:34 final size:35
Alignment explanation
Indices: 14881346--14881499 Score: 93
Period size: 34 Copynumber: 4.5 Consensus size: 35
14881336 TTCAATTATG
* *
14881346 TCCCGCCATAATGCCAGAACTTCATT-TATCAATCA
1 TCCCGCCACAATGCCAGAACTTCATTCAATCAA-CA
* * ** *
14881381 TCCAGCCACAATGCCA-ATAATTTTTTCAATTAACA
1 TCCCGCCACAATGCCAGA-ACTTCATTCAATCAACA
* * * **
14881416 TTCTG-TACAACCCCA-ATACTTCATTCAATCAACA
1 TCCCGCCACAATGCCAGA-ACTTCATTCAATCAACA
* *
14881450 TCCCGCCACAATGCCAGAATTTCATT-AATCAATA
1 TCCCGCCACAATGCCAGAACTTCATTCAATCAACA
* * *
14881484 TCTCTCCACAACGCCA
1 TCCCGCCACAATGCCA
14881500 ATAGATCAAA
Statistics
Matches: 89, Mismatches: 26, Indels: 9
0.72 0.21 0.07
Matches are distributed among these distances:
34 46 0.52
35 38 0.43
36 5 0.06
ACGTcount: A:0.34, C:0.32, G:0.06, T:0.28
Consensus pattern (35 bp):
TCCCGCCACAATGCCAGAACTTCATTCAATCAACA
Found at i:14881742 original size:9 final size:9
Alignment explanation
Indices: 14881728--14881752 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14881718 CACTCAATAG
14881728 AACAACATC
1 AACAACATC
14881737 AACAACATC
1 AACAACATC
14881746 AACAACA
1 AACAACA
14881753 ACAAAGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (9 bp):
AACAACATC
Found at i:14893660 original size:19 final size:19
Alignment explanation
Indices: 14893633--14893673 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
14893623 TAAAATAAGT
14893633 ATGTGATTACAATCATCTC
1 ATGTGATTACAATCATCTC
*
14893652 ATGTTATTACAATCATCTC
1 ATGTGATTACAATCATCTC
14893671 ATG
1 ATG
14893674 ATTAGTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (19 bp):
ATGTGATTACAATCATCTC
Found at i:14902974 original size:35 final size:34
Alignment explanation
Indices: 14902935--14903019 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
14902925 TTAACATTTC
* **
14902935 GCCACAACCCCAATACTTAATTAAATTTACATCCT
1 GCCACAACACCAATACTTAATT-AATCAACATCCT
* *
14902970 GCCACAACACCAGA-ACTTTATTAATCAATATCCT
1 GCCACAACACCA-ATACTTAATTAATCAACATCCT
*
14903004 GCCACAACGCCAATAC
1 GCCACAACACCAATAC
14903020 GTCATAACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
33 1 0.02
34 22 0.52
35 18 0.43
36 1 0.02
ACGTcount: A:0.38, C:0.33, G:0.06, T:0.24
Consensus pattern (34 bp):
GCCACAACACCAATACTTAATTAATCAACATCCT
Found at i:14913591 original size:87 final size:87
Alignment explanation
Indices: 14913439--14913601 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 87
14913429 CATGTATAAC
* * *
14913439 GTTGAGTTCTTACTCTTGATGAATTCATAGCCCCCGAGTTTTGGTGATCACATTGAGACGAACTT
1 GTTGAGTTCTTACTCTTAATGAATTCATAGCCCCAGAGTTTGGGTGATCACATTGAGACGAACTT
14913504 GATGAATTCACCGACATGTGAG
66 GATGAATTCACCGACATGTGAG
* * * *
14913526 GTTGAGTTTCTTACTCTTAATGAGTTCATA-TCCCAGAGTTTGGGTGGTC-CTATTGAGACGTAC
1 GTTGAG-TTCTTACTCTTAATGAATTCATAGCCCCAGAGTTTGGGTGATCAC-ATTGAGACGAAC
14913589 TTGATGAATTCAC
64 TTGATGAATTCAC
14913602 TGAATTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 1 0.01
87 45 0.67
88 21 0.31
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (87 bp):
GTTGAGTTCTTACTCTTAATGAATTCATAGCCCCAGAGTTTGGGTGATCACATTGAGACGAACTT
GATGAATTCACCGACATGTGAG
Found at i:14914491 original size:24 final size:24
Alignment explanation
Indices: 14914463--14914515 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
14914453 CACATGTTTC
14914463 TTTTCAG-TATATTTTTCGATTAGT
1 TTTTCAGCTATATTTTTCGATTA-T
*
14914487 TTTTCAGCTCTATTTTTCGATTAT
1 TTTTCAGCTATATTTTTCGATTAT
14914511 TTTTC
1 TTTTC
14914516 TTTTCTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.17, C:0.13, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTTCAGCTATATTTTTCGATTAT
Found at i:14914513 original size:11 final size:11
Alignment explanation
Indices: 14914472--14914515 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
14914462 CTTTTCAGTA
14914472 TATTTTTCGAT
1 TATTTTTCGAT
*
14914483 TAGTTTTTCAGCT
1 TA-TTTTTC-GAT
14914496 CTATTTTTCGAT
1 -TATTTTTCGAT
14914508 TATTTTTC
1 TATTTTTC
14914516 TTTTCTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 10 0.36
12 8 0.29
13 8 0.29
14 2 0.07
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (11 bp):
TATTTTTCGAT
Found at i:14915052 original size:20 final size:21
Alignment explanation
Indices: 14915014--14915052 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
14915004 AAATCTAAAA
*
14915014 AAAAAGAATAATAGCTAAATT
1 AAAAAGAATAAAAGCTAAATT
*
14915035 AAAAA-AATAAAAGTTAAA
1 AAAAAGAATAAAAGCTAAA
14915053 GGCTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (21 bp):
AAAAAGAATAAAAGCTAAATT
Found at i:14918177 original size:23 final size:23
Alignment explanation
Indices: 14918150--14918194 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
14918140 CGAAAATATT
14918150 AAATATATATA-TTTTTATTTTTA
1 AAATATA-ATAGTTTTTATTTTTA
14918173 AAATATAATAGTTTTTTATTTT
1 AAATATAATAG-TTTTTATTTT
14918195 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 7 0.35
24 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTTA
Found at i:14918324 original size:59 final size:59
Alignment explanation
Indices: 14918261--14918448 Score: 243
Period size: 68 Copynumber: 3.1 Consensus size: 59
14918251 TCAAGTTTGT
*
14918261 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATATAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATATAATTAATAATTTGATAAA
*
14918320 TTTACTAATTAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAA-T--T--AA-T-AT--AATTAATAATTTGAT
14918385 AAA
57 AAA
* * *
14918388 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAA-TTAATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATATAATTAATAATTTGATAAA
14918446 TTT
1 TTT
14918449 GATAATTTTA
Statistics
Matches: 114, Mismatches: 6, Indels: 19
0.82 0.04 0.14
Matches are distributed among these distances:
58 10 0.09
59 40 0.35
60 1 0.01
61 1 0.01
62 2 0.02
63 2 0.02
64 2 0.02
65 2 0.02
66 2 0.02
67 1 0.01
68 51 0.45
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATATAATTAATAATTTGATAAA
Found at i:14918362 original size:9 final size:9
Alignment explanation
Indices: 14918350--14918377 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
14918340 TTTTATTACA
14918350 ACAATTAAT
1 ACAATTAAT
14918359 ACAATTAAT
1 ACAATTAAT
14918368 ACAATTAAT
1 ACAATTAAT
14918377 A
1 A
14918378 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:14918365 original size:68 final size:68
Alignment explanation
Indices: 14918291--14918462 Score: 294
Period size: 68 Copynumber: 2.5 Consensus size: 68
14918281 TTTTGTTACA
* *
14918291 ACAATTAATATAATTAATAATTTGATAAATTTACTAATTAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
14918356 AAT
66 AAT
14918359 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
14918424 AAT
66 AAT
*
14918427 ACAATT-A-ACAATTAATAAATTTGATAATTTTACTAA
1 ACAATTAATACAATTAAT-AATTTGATAAATTTACTAA
14918463 CAATTAATTT
Statistics
Matches: 100, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
66 9 0.09
67 19 0.19
68 72 0.72
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:14918438 original size:16 final size:15
Alignment explanation
Indices: 14918417--14918447 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
14918407 ATTTTATTAC
14918417 AACAATTAATACAATT
1 AACAATTAATA-AATT
14918433 AACAATTAATAAATT
1 AACAATTAATAAATT
14918448 TGATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (15 bp):
AACAATTAATAAATT
Found at i:14918470 original size:16 final size:16
Alignment explanation
Indices: 14918451--14918492 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
14918441 ATAAATTTGA
*
14918451 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
14918467 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
14918483 TAGTTTTAAT
1 TAATTTTAAT
14918493 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:14918491 original size:22 final size:23
Alignment explanation
Indices: 14918466--14918521 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
14918456 TTACTAACAA
* * *
14918466 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAACTAATT
*
14918488 TTAATTTTATTAAAAAACTAATT
1 TTAATTTTAATAAAAAACTAATT
14918511 TTAATTTTAAT
1 TTAATTTTAAT
14918522 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAACTAATT
Found at i:14935541 original size:19 final size:19
Alignment explanation
Indices: 14935517--14935556 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
14935507 GTAAATCGTT
14935517 TGATTGGAATAACGGAATA
1 TGATTGGAATAACGGAATA
14935536 TGATTGGAATAACGGAATA
1 TGATTGGAATAACGGAATA
14935555 TG
1 TG
14935557 TTGCTTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.28
Consensus pattern (19 bp):
TGATTGGAATAACGGAATA
Found at i:14938611 original size:50 final size:50
Alignment explanation
Indices: 14938520--14938739 Score: 194
Period size: 51 Copynumber: 4.4 Consensus size: 50
14938510 CGGGTTGCAA
* * * *
14938520 AGGCTTTCCAGATAACTTCACCACTAAGGCTTCCCAAATAATATGACACGT
1 AGGCTTTTCAGATAAC-TCACCACAAAGGCTTTCCAAATAATATGACACAT
* *
14938571 AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAGATAATATGCCACAT
1 AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAAATAATATGACACAT
* * * * * *
14938621 AGGC-CTTCAGATAACTCGCCATAAAGGCTTTCCAAATGACT-TGTCACAA
1 AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAAAT-AATATGACACAT
* * ** * * *
14938670 AGGCTTTCCAAATAACTTTGCCACTAAGGCTTCCCAAATAATATGTCACAT
1 AGGCTTTTCAGATAAC-TCACCACAAAGGCTTTCCAAATAATATGACACAT
* *
14938721 AGACCTTTT-AAATAACTCA
1 AG-GCTTTTCAGATAACTCA
14938740 ACATTAAGGC
Statistics
Matches: 138, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
49 39 0.28
50 46 0.33
51 49 0.36
52 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (50 bp):
AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAAATAATATGACACAT
Found at i:14938641 original size:24 final size:24
Alignment explanation
Indices: 14938577--14938648 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
14938567 ACGTAGGCTT
* *
14938577 TTCAGATAACTCACCACAAAGGCT
1 TTCAGATAACTCGCCACAAAGGCC
* *
14938601 TTCCAGATAA-TATGCCACATAGGCC
1 TT-CAGATAACT-CGCCACAAAGGCC
*
14938626 TTCAGATAACTCGCCATAAAGGC
1 TTCAGATAACTCGCCACAAAGGC
14938649 TTTCCAAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
24 19 0.50
25 19 0.50
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (24 bp):
TTCAGATAACTCGCCACAAAGGCC
Found at i:14938649 original size:49 final size:50
Alignment explanation
Indices: 14938520--14938722 Score: 166
Period size: 50 Copynumber: 4.0 Consensus size: 50
14938510 CGGGTTGCAA
* *
14938520 AGGCT-TTCCAGATAACTTCACCACT-AAGGCTTCCCAAATAATATGACACGT
1 AGGCTCTT-CAGATAAC-TCACCA-TAAAGGCTTTCCAAATAATATGACACAT
* * * *
14938571 AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAGATAATATGCCACAT
1 AGGCTCTTCAGATAACTCACCATAAAGGCTTTCCAAATAATATGACACAT
* * * *
14938621 AGGC-CTTCAGATAACTCGCCATAAAGGCTTTCCAAATGACT-TGTCACAA
1 AGGCTCTTCAGATAACTCACCATAAAGGCTTTCCAAAT-AATATGACACAT
* ** * *
14938670 AGGCT-TTCCAAATAACTTTGCCACT-AAGGCTTCCCAAATAATATGTCACAT
1 AGGCTCTT-CAGATAAC-TCACCA-TAAAGGCTTTCCAAATAATATGACACAT
14938721 AG
1 AG
14938723 ACCTTTTAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
49 41 0.32
50 43 0.34
51 40 0.31
52 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (50 bp):
AGGCTCTTCAGATAACTCACCATAAAGGCTTTCCAAATAATATGACACAT
Found at i:14938671 original size:25 final size:26
Alignment explanation
Indices: 14938517--14938710 Score: 130
Period size: 25 Copynumber: 7.7 Consensus size: 26
14938507 ACTCGGGTTG
* **
14938517 CAAAGGCTTTCCAGATAACTTCACCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* * * *
14938543 CTAAGGCTTCCCAAATAA-TATGACA
1 CAAAGGCTTTCCAAATAACTTTGCCA
** * * **
14938568 CGTAGGCTTTTCAGATAAC-TCACCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* *
14938593 CAAAGGCTTTCCAGATAA-TATGCCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* * * *
14938618 CATAGGCCTT-CAGATAAC-TCGCCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* * *
14938642 TAAAGGCTTTCCAAATGAC-TTGTCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
14938667 CAAAGGCTTTCCAAATAACTTTGCCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* *
14938693 CTAAGGCTTCCCAAATAA
1 CAAAGGCTTTCCAAATAA
14938711 TATGTCACAT
Statistics
Matches: 125, Mismatches: 38, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
24 18 0.14
25 71 0.57
26 36 0.29
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (26 bp):
CAAAGGCTTTCCAAATAACTTTGCCA
Found at i:14944182 original size:48 final size:48
Alignment explanation
Indices: 14944113--14944311 Score: 254
Period size: 48 Copynumber: 4.1 Consensus size: 48
14944103 TCAGAATAAA
* * *
14944113 AACAGATTTCTCGGTGGCCTGCACACAGTCCATTCCACCTTTGTATAAT
1 AACAGA-TTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
* * *
14944162 AACAGATTCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTT
1 AACAGATTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
* * * * *
14944210 AACAGGTTGTTGGTGGCCTGCACACAGTCCGTGCCACCCTTATATCAT
1 AACAGATTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
* * * *
14944258 AACAGAATATCGGTGGTCTGCACACAGTCCATGCCACCCTTGTGTCAT
1 AACAGATTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
14944306 AACAGA
1 AACAGA
14944312 ATATCGGTAC
Statistics
Matches: 130, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
48 124 0.95
49 6 0.05
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (48 bp):
AACAGATTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
Found at i:14945809 original size:15 final size:16
Alignment explanation
Indices: 14945789--14945823 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
14945779 ATTTAACGGT
14945789 AAATTTTATA-TTTGA
1 AAATTTTATATTTTGA
*
14945804 AAATTTTTTATTTTGA
1 AAATTTTATATTTTGA
14945820 AAAT
1 AAAT
14945824 GCCATTAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (16 bp):
AAATTTTATATTTTGA
Found at i:14945818 original size:16 final size:17
Alignment explanation
Indices: 14945792--14945823 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
14945782 TAACGGTAAA
14945792 TTTTATATTTGAAAATT
1 TTTTATATTTGAAAATT
14945809 TTTTAT-TTTGAAAAT
1 TTTTATATTTGAAAAT
14945824 GCCATTAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTATATTTGAAAATT
Found at i:14953667 original size:23 final size:22
Alignment explanation
Indices: 14953628--14953670 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
14953618 GATTGAATTG
14953628 AATTTTTAATATCTTATTTTAT
1 AATTTTTAATATCTTATTTTAT
14953650 AATTTTATAATAAT-TTATTTT
1 AATTTT-TAAT-ATCTTATTTT
14953671 TATTGAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 11 0.58
24 2 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
AATTTTTAATATCTTATTTTAT
Found at i:14956074 original size:28 final size:28
Alignment explanation
Indices: 14956013--14956074 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
14956003 TCTAAAAAGG
* * *
14956013 TTTTTAAATTTAAAGTTTTTTTTTCAAT
1 TTTTAAAATTTAAAGTTTTTTTTTAAAA
14956041 TATTTAAAATTTAAA-TATTTTTTTTAAAA
1 T-TTTAAAATTTAAAGT-TTTTTTTTAAAA
14956070 TTTTA
1 TTTTA
14956075 TAACAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTAAAATTTAAAGTTTTTTTTTAAAA
Found at i:14956156 original size:23 final size:22
Alignment explanation
Indices: 14956130--14956178 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
14956120 TATAATTATA
14956130 TATTTTAGAA-TTTTATAAAAAAT
1 TATTTTA-AACTTTTA-AAAAAAT
14956153 TATTTTTAAACTTTTAAAAAAAT
1 TA-TTTTAAACTTTTAAAAAAAT
14956176 TAT
1 TAT
14956179 ATTTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 1 0.04
23 13 0.54
24 10 0.42
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTTAAACTTTTAAAAAAAT
Found at i:14956167 original size:24 final size:24
Alignment explanation
Indices: 14956128--14956184 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
14956118 TTTATAATTA
14956128 TATATTTTAGAATTTTATAAAAAAT
1 TATATTTTAGAATTTTA-AAAAAAT
14956153 TAT-TTTTA-AACTTTTAAAAAAAT
1 TATATTTTAGAA-TTTTAAAAAAAT
14956176 TATATTTTA
1 TATATTTTA
14956185 TATATGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 12 0.40
24 15 0.50
25 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATATTTTAGAATTTTAAAAAAAT
Found at i:14956453 original size:32 final size:31
Alignment explanation
Indices: 14956399--14956458 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
14956389 AATTATCACA
14956399 TGGCACATTTTCATCAGCCAAAATATGCCATG
1 TGGCACATTTTCATCAGCCAAAAT-TGCCATG
* ** *
14956431 TGGCACCTTTTCATTTGTCAAAATTGCC
1 TGGCACATTTTCATCAGCCAAAATTGCC
14956459 TAACAATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 4 0.17
32 20 0.83
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (31 bp):
TGGCACATTTTCATCAGCCAAAATTGCCATG
Found at i:14957620 original size:19 final size:19
Alignment explanation
Indices: 14957558--14957626 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
14957548 GACATTTTCC
*
14957558 ATTAAGTGTAATTAATGGTTGG
1 ATTAAGT-TAATTAA--GTTAG
* **
14957580 ATTATGTTAATTAA-CAATG
1 ATTAAGTTAATTAAGTTA-G
14957599 ATTAAGTTAATTAAGTTAG
1 ATTAAGTTAATTAAGTTAG
14957618 ATTAA-TTAA
1 ATTAAGTTAA
14957627 GTCTTAATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.11
19 20 0.53
20 1 0.03
21 7 0.18
22 6 0.16
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTAAGTTAATTAAGTTAG
Found at i:14959480 original size:6 final size:6
Alignment explanation
Indices: 14959441--14959480 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
14959431 CAAGTTTCCA
*
14959441 TTTCTAT TTTCAT TTTCAT TTTCAT TTCCAT TTTCAT TTT
1 TTTC-AT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTT
14959481 TGGAAACCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCAT
Found at i:14963696 original size:30 final size:30
Alignment explanation
Indices: 14963673--14963933 Score: 380
Period size: 30 Copynumber: 8.7 Consensus size: 30
14963663 GTATATGTTT
* *
14963673 TATATATTGCCGAATTGA-TTGTATATGGG
1 TATACATTGCCGAATTGATTTGTATATGGA
*
14963702 TATACATTTCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
14963732 TATACATTGTCAAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
***
14963762 TATACATTGTTAAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
14963792 TATACATTGCCGAATTAATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
14963822 TATACATTGCTGAATTGATTTGTATATCGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
14963852 TATACATTGTCGAATTGATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
14963882 TATACATTGCCGAATTGATTTGTATATGTA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
14963912 TATATATTGCCGAATTGATTTG
1 TATACATTGCCGAATTGATTTG
14963934 AGCATTGGAT
Statistics
Matches: 210, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
29 16 0.08
30 194 0.92
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:14964160 original size:41 final size:42
Alignment explanation
Indices: 14964054--14964176 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 42
14964044 GATGTGTGAT
*
14964054 TTCGTGTAAGACCATGTCTGGGACATTGGCATCAAAGTGAGAAA
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCATA-TGAG-AA
*
14964098 AT-GTGTAAGACCATGTCTGGGACATTGGCATCATAT-ATG-A
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCATATGA-GAA
* * *
14964138 TTCGTATAAGACCCTGTCTGGGACAGTGGCATCGATATG
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATC-ATATG
14964177 CGTTAACATG
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
40 2 0.03
41 28 0.41
42 6 0.09
43 32 0.46
44 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (42 bp):
TTCGTGTAAGACCATGTCTGGGACATTGGCATCATATGAGAA
Found at i:14967879 original size:9 final size:9
Alignment explanation
Indices: 14967862--14967898 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
14967852 TGAGTTTTCG
14967862 AATTCGAAT
1 AATTCGAAT
*
14967871 AACTCGAAT
1 AATTCGAAT
14967880 AATTCGAAT
1 AATTCGAAT
14967889 AATTCGAAT
1 AATTCGAAT
14967898 A
1 A
14967899 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:14967975 original size:21 final size:21
Alignment explanation
Indices: 14967934--14967976 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
14967924 ACCCCAAACT
* *
14967934 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
14967955 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
14967976 C
1 C
14967977 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:14968934 original size:5 final size:5
Alignment explanation
Indices: 14968924--14968949 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
14968914 CTCGAAAATT
14968924 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
14968950 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:14974757 original size:77 final size:77
Alignment explanation
Indices: 14974669--14974812 Score: 227
Period size: 77 Copynumber: 1.9 Consensus size: 77
14974659 TTTTTAAACA
* * * *
14974669 TTTAAATTTTAAATTATTCTAAATACTTTTTGGG-ATATTTGAAATACAGTTTATAAATAAATAA
1 TTTAAAATTTAAATTATTCCAAATACTTTTTGGGAATATTTGAAATACAGTGTATAAAGAAA-AA
14974733 AAATTATATGTAT
65 AAATTATATGTAT
*
14974746 TTTAAAATTTAAATTATTCCAAATACTTTTTGGGAATATTTGAAATACGGTGTATAAAGAAAAAA
1 TTTAAAATTTAAATTATTCCAAATACTTTTTGGGAATATTTGAAATACAGTGTATAAAGAAAAAA
14974811 AA
66 AA
14974813 GTTGAAAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 37 0.61
78 24 0.39
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (77 bp):
TTTAAAATTTAAATTATTCCAAATACTTTTTGGGAATATTTGAAATACAGTGTATAAAGAAAAAA
AATTATATGTAT
Found at i:15018309 original size:3 final size:3
Alignment explanation
Indices: 15018301--15018342 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
15018291 TACTATGATT
15018301 TTA 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 TTA
15018343 CTACTACTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:15020122 original size:19 final size:20
Alignment explanation
Indices: 15020100--15020160 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 20
15020090 TCAAAACAAG
15020100 TTCAAAATAATTTTTAAAA-
1 TTCAAAATAATTTTTAAAAT
* *
15020119 TTCATAAT-ATTTATAAAAAT
1 TTCAAAATAATTT-TTAAAAT
15020139 TTCAAAATTTATATTTTTAAAA
1 TTCAAAA--TA-ATTTTTAAAA
15020161 AATAAAGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 6 0.19
22 1 0.03
23 5 0.16
24 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TTCAAAATAATTTTTAAAAT
Found at i:15023779 original size:21 final size:22
Alignment explanation
Indices: 15023742--15023784 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
15023732 ATTATTTTTA
*
15023742 ATTTTTAAAACTCAAAAAATAT
1 ATTTTTAAAAATCAAAAAATAT
15023764 ATTTTTAAAAAT-AAAAAATAT
1 ATTTTTAAAAATCAAAAAATAT
15023785 TAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTTTTAAAAATCAAAAAATAT
Found at i:15023792 original size:22 final size:22
Alignment explanation
Indices: 15023745--15023792 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
15023735 ATTTTTAATT
* **
15023745 TTTAAAACTCAAAAAATATATT
1 TTTAAAAATCAAAAAATATAAA
15023767 TTTAAAAAT-AAAAAATATTAAA
1 TTTAAAAATCAAAAAATA-TAAA
15023789 TTTA
1 TTTA
15023793 TTAAAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAAATCAAAAAATATAAA
Done.