Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007936.1 Hibiscus syriacus cultivar Beakdansim tig00110346_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: 2869312
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:518084 original size:22 final size:19
Alignment explanation
Indices: 518059--518122 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 19
518049 ATGGAACTTG
518059 GAGAATAAGAAGAGAGGAAAAT
1 GAGAATAA-AAGA-A-GAAAAT
518081 GAGAATAAAAGAAGAAAAT
1 GAGAATAAAAGAAGAAAAT
*
518100 GA-AGA-AAATGAAGAAAAT
1 GAGA-ATAAAAGAAGAAAAT
*
518118 AAGAA
1 GAGAA
518123 GATGAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 15 0.39
19 10 0.26
20 1 0.03
21 4 0.11
22 8 0.21
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.09
Consensus pattern (19 bp):
GAGAATAAAAGAAGAAAAT
Found at i:518105 original size:9 final size:9
Alignment explanation
Indices: 518087--518128 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
518077 AAATGAGAAT
518087 AAAA-GAAG
1 AAAATGAAG
518095 AAAATGAAG
1 AAAATGAAG
518104 AAAATGAAG
1 AAAATGAAG
518113 AAAAT-AAG
1 AAAATGAAG
*
518121 AAGATGAA
1 AAAATGAA
518129 AAGAAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
8 11 0.35
9 20 0.65
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (9 bp):
AAAATGAAG
Found at i:518121 original size:17 final size:18
Alignment explanation
Indices: 518087--518128 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
518077 AAATGAGAAT
518087 AAAA-GAAGAAAATGAAG
1 AAAATGAAGAAAATGAAG
518104 AAAATGAAGAAAAT-AAG
1 AAAATGAAGAAAATGAAG
*
518121 AAGATGAA
1 AAAATGAA
518129 AAGAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (18 bp):
AAAATGAAGAAAATGAAG
Found at i:522037 original size:33 final size:34
Alignment explanation
Indices: 522000--522072 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
521990 AAAATATTAC
* * * *
522000 AATTATAATATTTAAATTATTATAA-ATTTTATT
1 AATTATAATATTAAAATCAGTATAATATATTATT
*
522033 AATTAT-TTATTAAAATCAGTATAATATATTATT
1 AATTATAATATTAAAATCAGTATAATATATTATT
522066 AATTATA
1 AATTATA
522073 TTAATTACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (34 bp):
AATTATAATATTAAAATCAGTATAATATATTATT
Found at i:527070 original size:20 final size:20
Alignment explanation
Indices: 527041--527083 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
527031 ATTCCACCAC
*
527041 ATGCAACTACATGCTTCTAA
1 ATGCAACTACATGCTCCTAA
* *
527061 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
527081 ATG
1 ATG
527084 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:527185 original size:24 final size:24
Alignment explanation
Indices: 527153--527202 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
527143 GTTATCACAC
527153 CCCCAAACTTAAGCTATTGCTTGT
1 CCCCAAACTTAAGCTATTGCTTGT
527177 CCCCAAACTTAAGCTATTGCTTGT
1 CCCCAAACTTAAGCTATTGCTTGT
527201 CC
1 CC
527203 TCAAGCAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (24 bp):
CCCCAAACTTAAGCTATTGCTTGT
Found at i:538769 original size:23 final size:23
Alignment explanation
Indices: 538743--538791 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
538733 ATAAAGAACC
*
538743 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
538766 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
538789 AAA
1 AAA
538792 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:542095 original size:26 final size:26
Alignment explanation
Indices: 542066--542126 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
542056 ATTGAAATAG
542066 AAAAGTTAAGGATGAAAGAGAAAAGA
1 AAAAGTTAAGGATGAAAGAGAAAAGA
542092 AAAAGTTAAGGATGAAAGAGAAAAGA
1 AAAAGTTAAGGATGAAAGAGAAAAGA
542118 AAAAGTTAA
1 AAAAGTTAA
542127 AAATTTGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.13
Consensus pattern (26 bp):
AAAAGTTAAGGATGAAAGAGAAAAGA
Found at i:542420 original size:5 final size:5
Alignment explanation
Indices: 542410--542459 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
542400 AATTAATTAC
* * * *
542410 AAAAT AAAAT AAAAT AAAAT AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
542460 CTTAAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (5 bp):
AAAAG
Found at i:542430 original size:15 final size:15
Alignment explanation
Indices: 542410--542458 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
542400 AATTAATTAC
* *
542410 AAAATAAAATAAAAT
1 AAAATAAAAGAAAAG
542425 AAAATAAAAGAAAAG
1 AAAATAAAAGAAAAG
*
542440 AAAAGAAAAGAAAAG
1 AAAATAAAAGAAAAG
542455 AAAA
1 AAAA
542459 GCTTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (15 bp):
AAAATAAAAGAAAAG
Found at i:546651 original size:21 final size:21
Alignment explanation
Indices: 546625--546666 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
546615 CGAGCTATGG
*
546625 CTTTGAAGTAAGGCGCCTTGA
1 CTTTGAAGTAAAGCGCCTTGA
*
546646 CTTTGAAGTAAAGCTCCTTGA
1 CTTTGAAGTAAAGCGCCTTGA
546667 TTCTTAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
CTTTGAAGTAAAGCGCCTTGA
Found at i:548895 original size:23 final size:23
Alignment explanation
Indices: 548869--548917 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
548859 ATAAATAACC
* *
548869 AAAATAAACT-TAAATATACCATT
1 AAAAGAAACTCTAAACAT-CCATT
*
548892 AAAAGAAAGTCTAAACATCCATT
1 AAAAGAAACTCTAAACATCCATT
548915 AAA
1 AAA
548918 CCAACCACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAAGAAACTCTAAACATCCATT
Found at i:554003 original size:272 final size:273
Alignment explanation
Indices: 553505--554011 Score: 770
Period size: 272 Copynumber: 1.9 Consensus size: 273
553495 GAGTGGAAAT
* * *
553505 TATTTTTGAAAATTTTTATTGTAATCCGCTATATCAGGCCATAACGCATATGTTGAGTCTAGGGA
1 TATTTTTGAAAATTTTTATTGTAATCCGCTAGATCAGGCCATAACGCATAGGTAGAGTCTAGGGA
* * *
553570 GTTACAATTTAGTTGGTATCAGAGCTTTTAATTTTTAAACCCTTGGACTATGAATAGTTTCGAGA
66 GTTACAATTTAGTTAGTATAAGAGCTTTTAATTTTTAAACCCTTGGACTATGAATAGCTTCGAGA
* * *
553635 AAAAAACCTAATTTTGAAATATTTTACAAAACAAGTTCTAAAAGTCATGTCACCAAGTTTTCATA
131 AAAAAACATAATTTTGAAATATTTTACAAAACAAGTTCTAAAAGTCATGTCACCAAATTTTCACA
553700 AGTTTTATTGTGTACGGGACTTCAAGTGCCGATTCTAAGCCTATGTTTCATCTTATGTAGTGAAC
196 AGTTTTATTGTGTACGGGACTTCAAGTGCCGATTCTAAGCCTATGTTTCATCTTATGTAGTGAAC
553765 CTTTAGATGATAC
261 CTTTAGATGATAC
* * * *
553778 TATTTTTTAAATTTTTTATTGTAATCTGCTAGATCAGGTCATAACGCATAGGATAG-GTCTAGGG
1 TATTTTTGAAAATTTTTATTGTAATCCGCTAGATCAGGCCATAACGCATAGG-TAGAGTCTAGGG
* * * *
553842 -GTTATAATTTAGTTAGTATAAGAGCTTTTGATTTTTAAACCCTTGGACTGT-AGTTAGGCTT-G
65 AGTTACAATTTAGTTAGTATAAGAGCTTTTAATTTTTAAACCCTTGGACTATGA-ATA-GCTTCG
*
553904 AGAAAAAAACATAATTTTGAAATATTTTACAAAACAAGTTCTAAAAGTCATGTCACCAAATTTTT
128 AGAAAAAAACATAATTTTGAAATATTTTACAAAACAAGTTCTAAAAGTCATGTCACCAAATTTTC
* * *
553969 ACAAGTTTTATTGTGTACGTGAGTTCAGGTGCCGATTCTAAGC
193 ACAAGTTTTATTGTGTACGGGACTTCAAGTGCCGATTCTAAGC
554012 ACTAGACAAG
Statistics
Matches: 210, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
271 1 0.00
272 150 0.71
273 57 0.27
274 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (273 bp):
TATTTTTGAAAATTTTTATTGTAATCCGCTAGATCAGGCCATAACGCATAGGTAGAGTCTAGGGA
GTTACAATTTAGTTAGTATAAGAGCTTTTAATTTTTAAACCCTTGGACTATGAATAGCTTCGAGA
AAAAAACATAATTTTGAAATATTTTACAAAACAAGTTCTAAAAGTCATGTCACCAAATTTTCACA
AGTTTTATTGTGTACGGGACTTCAAGTGCCGATTCTAAGCCTATGTTTCATCTTATGTAGTGAAC
CTTTAGATGATAC
Found at i:559265 original size:21 final size:21
Alignment explanation
Indices: 559239--559280 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
559229 TATACAACGA
559239 TCCTCACACATGTTGTGCTGG
1 TCCTCACACATGTTGTGCTGG
559260 TCCTCACACATGTTGTGCTGG
1 TCCTCACACATGTTGTGCTGG
559281 AGGGGTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.24, T:0.33
Consensus pattern (21 bp):
TCCTCACACATGTTGTGCTGG
Found at i:561162 original size:35 final size:34
Alignment explanation
Indices: 561077--561163 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
561067 AAATGGTATT
*
561077 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
561111 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
561149 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
561164 GCTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:561333 original size:3 final size:3
Alignment explanation
Indices: 561325--561349 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
561315 GGGCGGTGGC
561325 CGT CGT CGT CGT CGT CGT CGT CGT C
1 CGT CGT CGT CGT CGT CGT CGT CGT C
561350 CTAAGCTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CGT
Found at i:561727 original size:21 final size:18
Alignment explanation
Indices: 561687--561721 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
561677 AGGCGATGGC
561687 GGCATCATATATGGCTGT
1 GGCATCATATATGGCTGT
561705 GGCATCATATATGGCTG
1 GGCATCATATATGGCTG
561722 CGGTGGCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (18 bp):
GGCATCATATATGGCTGT
Found at i:563445 original size:17 final size:18
Alignment explanation
Indices: 563402--563442 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
563392 GAATTATATT
563402 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
563419 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
563437 ATTAAA
1 AGTAAA
563443 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:567356 original size:2 final size:2
Alignment explanation
Indices: 567349--567376 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
567339 TGTGAAAATA
567349 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
567377 CTTATATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:568732 original size:190 final size:189
Alignment explanation
Indices: 568410--568788 Score: 740
Period size: 190 Copynumber: 2.0 Consensus size: 189
568400 GGCACATTCT
568410 ATCTTCTTGCTCTAGCATTCCTGTTAATTTGGACTCCCTCATCAGTTTGGTGATTGGTTACGGGG
1 ATCTTCTTGCTCTAGCATTCCTGTTAATTTGGACTCCCTCATCAGTTTGGTGATTGGTTACGGGG
568475 TCCCCCACCATCTGGTTCACTGCCACAAGCTCACAATCGACCTGGTATTGTGTTGTTAAATTCTA
66 TCCCCCACCATCTGGTTCACTGCCACAAGCTCACAATCGACCTGGTATTGTGTTGTTAAATTCTA
*
568540 AGGGTCCTTCAAGCGTCGATGCGAAGTTGGGTAAACACTTTGTCAACTAAAACGTTTGG
131 AGGGTCCTTCAAGCGTCGATGCGAAGTTGGGTAAACACTTTGTCAACCAAAACGTTTGG
568599 ATCTTCTTGCTCTAGCATTCCTGTTAATTTGGACTCCCCTCATCAGTTTGGTGATTGGTTACGGG
1 ATCTTCTTGCTCTAGCATTCCTGTTAATTTGGACT-CCCTCATCAGTTTGGTGATTGGTTACGGG
568664 GTCCCCCACCATCTGGTTCACTGCCACAAGCTCACAATCGACCTGGTATTGTGTTGTTAAATTCT
65 GTCCCCCACCATCTGGTTCACTGCCACAAGCTCACAATCGACCTGGTATTGTGTTGTTAAATTCT
568729 AAGGGTCCTTCAAGCGTCGATGCGAAGTTGGGTAAACACTTTGTCAACCAAAACGTTTGG
130 AAGGGTCCTTCAAGCGTCGATGCGAAGTTGGGTAAACACTTTGTCAACCAAAACGTTTGG
568789 GGGAATTGGT
Statistics
Matches: 188, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
189 35 0.19
190 153 0.81
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (189 bp):
ATCTTCTTGCTCTAGCATTCCTGTTAATTTGGACTCCCTCATCAGTTTGGTGATTGGTTACGGGG
TCCCCCACCATCTGGTTCACTGCCACAAGCTCACAATCGACCTGGTATTGTGTTGTTAAATTCTA
AGGGTCCTTCAAGCGTCGATGCGAAGTTGGGTAAACACTTTGTCAACCAAAACGTTTGG
Found at i:568872 original size:2 final size:2
Alignment explanation
Indices: 568867--568905 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
568857 ATATATTCTT
568867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
568906 GTTGGCAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:568972 original size:37 final size:36
Alignment explanation
Indices: 568931--569108 Score: 250
Period size: 37 Copynumber: 4.8 Consensus size: 36
568921 TTGAAAATAC
568931 ATATATAATATATAGTTTTTAAAATCATTTTTTAAAA
1 ATATATAATATATAGTTTTTAAAA-CATTTTTTAAAA
* *
568968 ATATATATATTATATAGTTTTTAAAACAATTTTGAAAA
1 ATATATA-A-TATATAGTTTTTAAAACATTTTTTAAAA
*
569006 TTATATAATATATAGTTTTTAAAACATTTTTTGAAAA
1 ATATATAATATATAGTTTTTAAAACATTTTTT-AAAA
*
569043 TTATATAATATATAGTTTTTGAAAACA-TTTTTAAAA
1 ATATATAATATATAGTTTTT-AAAACATTTTTTAAAA
*
569079 TATATATAATATATAGTTTTGAAAACATTT
1 -ATATATAATATATAGTTTTTAAAACATTT
569109 CTATATTATA
Statistics
Matches: 128, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
36 32 0.25
37 57 0.45
38 23 0.18
39 16 0.12
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (36 bp):
ATATATAATATATAGTTTTTAAAACATTTTTTAAAA
Found at i:569103 original size:25 final size:25
Alignment explanation
Indices: 569070--569184 Score: 72
Period size: 27 Copynumber: 4.4 Consensus size: 25
569060 TTTGAAAACA
569070 TTTTTAAAATATATATAATATATAG
1 TTTTTAAAATATATATAATATATAG
* * * *
569095 TTTTGAAAACATTTCTATATTATATAG
1 TTTT-TAAA-ATATATATAATATATAG
*
569122 TTTTTAAAA-ATCATTTTGAATATATA-
1 TTTTTAAAATAT-A-TAT-AATATATAG
* * *
569148 TATATATATATATATATATATATATAG
1 TTTTTA-AAATATATATA-ATATATAG
569175 TTTTTTAAAA
1 -TTTTTAAAA
569185 CATTTTGAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 18
0.65 0.16 0.18
Matches are distributed among these distances:
24 1 0.02
25 6 0.09
26 21 0.33
27 30 0.47
28 6 0.09
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTTTAAAATATATATAATATATAG
Found at i:569136 original size:29 final size:27
Alignment explanation
Indices: 569083--569137 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
569073 TTAAAATATA
*
569083 TATAATATATAGTTTTGAAAACATTTC
1 TATAATATATAGTTTTAAAAACATTTC
*
569110 TATATTATATAGTTTTTAAAAATCATTT
1 TATAATATATAG-TTTTAAAAA-CATTT
569138 TGAATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (27 bp):
TATAATATATAGTTTTAAAAACATTTC
Found at i:569148 original size:2 final size:2
Alignment explanation
Indices: 569141--569173 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
569131 ATCATTTTGA
569141 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 A
569174 GTTTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:569240 original size:37 final size:37
Alignment explanation
Indices: 568926--569159 Score: 109
Period size: 37 Copynumber: 6.5 Consensus size: 37
568916 GGTTTTTGAA
* ** * *
568926 AATACATATATAATATATAGTTTTTAAAATCATTTTTTA
1 AATATATATATAATATATAGTTTAAAAAAACA--TTTTG
* * **
568965 AAAATATATATATTATATAGTTT-TTAAAACAATTTTG
1 AATATATATATAATATATAGTTTAAAAAAAC-ATTTTG
* **
569002 AAAAT-TATATAATATATAGTTT-TTAAAACATTTTTTG
1 AATATATATATAATATATAGTTTAAAAAAACA--TTTTG
* *** *
569039 AAAAT-TATATAATATATAGTTTTTGAAAACATTTTT
1 AATATATATATAATATATAGTTTAAAAAAACATTTTG
* **
569075 AAAATATATATAATATATAGTTT-TGAAAACATTTCT-
1 AATATATATATAATATATAGTTTAAAAAAACATTT-TG
* *
569111 -ATAT-TATAT-A-GT-T--TTT-AAAAATCATTTTG
1 AATATATATATAATATATAGTTTAAAAAAACATTTTG
569140 AATATATATATATATATATA
1 AATATATATATA-ATATATA
569160 TATATATATA
Statistics
Matches: 166, Mismatches: 15, Indels: 31
0.78 0.07 0.15
Matches are distributed among these distances:
28 1 0.01
29 11 0.07
30 4 0.02
31 6 0.04
32 1 0.01
33 2 0.01
34 6 0.04
35 5 0.03
36 43 0.26
37 54 0.33
38 12 0.07
39 21 0.13
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (37 bp):
AATATATATATAATATATAGTTTAAAAAAACATTTTG
Found at i:569247 original size:37 final size:37
Alignment explanation
Indices: 569155--569253 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 37
569145 ATATATATAT
***
569155 ATATATATATATATATATAGTTTTTTAAAACATTTTGA
1 ATATATATATAT-TATATAGTTTAAAAAAACATTTTGA
* * *
569193 AAATTATATATAATATATAGTTTAAAAAAATATTTTTG-
1 ATA-TATATATATTATATAGTTTAAAAAAACA-TTTTGA
569231 ATATATATATATTATATAGTTTA
1 ATATATATATATTATATAGTTTA
569254 TATCATATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
37 19 0.37
38 19 0.37
39 13 0.25
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (37 bp):
ATATATATATATTATATAGTTTAAAAAAACATTTTGA
Found at i:569278 original size:5 final size:5
Alignment explanation
Indices: 569261--569318 Score: 84
Period size: 5 Copynumber: 11.8 Consensus size: 5
569251 TTATATCATA
569261 TTATT ATTA-T TTATT TTATT TTATT TTATT TTATT TTATT TTA-T TTATT
1 TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
*
569310 TTGTT TTAT
1 TTATT TTAT
569319 GGTCCAGGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
4 7 0.15
5 38 0.79
6 3 0.06
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:570477 original size:2 final size:2
Alignment explanation
Indices: 570470--570527 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
570460 TTATTATTGT
*
570470 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT 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 TA TA TA
570511 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
570528 TTATTTATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:570596 original size:2 final size:2
Alignment explanation
Indices: 570589--570620 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
570579 CCTTGTGTTT
570589 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
570621 CCTTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:570644 original size:12 final size:12
Alignment explanation
Indices: 570627--570687 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
570617 TATACCTTTA
570627 TTTTATTTTTGT
1 TTTTATTTTTGT
570639 TTTTATTTTT-T
1 TTTTATTTTTGT
*
570650 TATTTATAATTTTTT
1 T-TTTAT--TTTTGT
570665 ATTTTATTTTTTGT
1 -TTTTA-TTTTTGT
*
570679 CTTTATTTT
1 TTTTATTTT
570688 ACTTTCTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
11 2 0.05
12 19 0.46
13 4 0.10
14 9 0.22
15 5 0.12
16 2 0.05
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTGT
Found at i:570675 original size:13 final size:13
Alignment explanation
Indices: 570623--570737 Score: 83
Period size: 13 Copynumber: 8.6 Consensus size: 13
570613 TATATATACC
570623 TTTATTTTATTTT
1 TTTATTTTATTTT
*
570636 TGT-TTTTATTTT
1 TTTATTTTATTTT
*
570648 TTTATTTATAATTT
1 TTTATTT-TATTTT
570662 TTTATTTTATTTT
1 TTTATTTTATTTT
*
570675 TTGT-CTTTATTTT
1 TT-TATTTTATTTT
* *
570688 ACTTT-CTTTATCTTA
1 --TTTATTTTAT-TTT
*
570703 TTTATTCTCATTTT
1 TTTATT-TTATTTT
*
570717 CTTATTTTATTTT
1 TTTATTTTATTTT
*
570730 CTTATTTT
1 TTTATTTT
570738 TTTCTTCCTT
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
12 11 0.13
13 37 0.45
14 28 0.34
15 7 0.08
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:570684 original size:28 final size:27
Alignment explanation
Indices: 570623--570676 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
570613 TATATATACC
570623 TTTATTT-T-ATTTTTGTTTTTATTTT
1 TTTATTTATAATTTTTGTTTTTATTTT
570648 TTTATTTATAATTTTT-TATTTTATTTT
1 TTTATTTATAATTTTTGT-TTTTATTTT
570675 TT
1 TT
570677 GTCTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 7 0.27
26 2 0.08
27 17 0.65
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTATTTATAATTTTTGTTTTTATTTT
Found at i:570738 original size:14 final size:13
Alignment explanation
Indices: 570623--570738 Score: 62
Period size: 14 Copynumber: 8.7 Consensus size: 13
570613 TATATATACC
570623 TTTA-TTTTA-TT
1 TTTATTTTTATTT
*
570634 TTTGTTTTTATTTT
1 TTTATTTTTA-TTT
*
570648 TTTATTTATAATTT
1 TTTATTT-TTATTT
570662 TTTA-TTTTATTT
1 TTTATTTTTATTT
* *
570674 TTTGTCTTTATTT
1 TTTATTTTTATTT
*
570687 TACTT-TCTTTATCTT
1 T--TTATTTTTAT-TT
* *
570702 ATTTATTCTCATTT
1 -TTTATTTTTATTT
570716 TCTTA-TTTTATTT
1 T-TTATTTTTATTT
570729 TCTTATTTTT
1 T-TTATTTTT
570739 TTCTTCCTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
11 3 0.04
12 13 0.16
13 22 0.27
14 33 0.40
15 10 0.12
16 1 0.01
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:573483 original size:100 final size:99
Alignment explanation
Indices: 573371--573589 Score: 323
Period size: 100 Copynumber: 2.2 Consensus size: 99
573361 AGATTATAAT
*
573371 ATTATATATATATATATAATCAAA-CTTGAGCTATCCCTCTAAAGAAATTGGTTAAACGCCCCGA
1 ATTATA-ATATATATACAAT-AAAGCTTGAGCTATCCCTCTAAAGAAATTGGTTAAACGCCCCGA
*
573435 CTTTATGGATAAGATTCAGCTAAGCCTTATAAAGGTG
64 CTTTATGGATAAGATTCAGCTAA-CCTGATAAAGGTG
* * * * *
573472 ATTATAATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGTCT
1 ATTATAATATATATACAATAAAGCTTGAGCTATCCCTCTAAAGAAATTGGTTAAACGCCCCGACT
*
573537 TTATGGATAATATTCAGCTAACCTGATAAAGGTG
66 TTATGGATAAGATTCAGCTAACCTGATAAAGGTG
*
573571 ATTATAATATCTATACAAT
1 ATTATAATATATATACAAT
573590 GATATTAAGA
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
99 33 0.31
100 69 0.64
101 6 0.06
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (99 bp):
ATTATAATATATATACAATAAAGCTTGAGCTATCCCTCTAAAGAAATTGGTTAAACGCCCCGACT
TTATGGATAAGATTCAGCTAACCTGATAAAGGTG
Found at i:573637 original size:98 final size:99
Alignment explanation
Indices: 573371--573642 Score: 316
Period size: 100 Copynumber: 2.7 Consensus size: 99
573361 AGATTATAAT
* * * ** *
573371 ATTATATATATATATATAATCAAACTTGAGCTATCCCTCTA-AAGAAATTGGTTAAACGCCCCGA
1 ATTATA-ATATATATACAAT-AAACTTAAGATGCCCCTCTAGAA-CAATTGGTTAAACGCCCCGA
*
573435 CTTTATGGATAAGATTCAGCTAAGCCTTATAAAGGTG
63 CTTTATGGATAAGATTCAGCTAAGCCTGATAAAGGTG
* * * * *
573472 ATTATAATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGTCT
1 ATTATAATATATATACAATAAA-CTTAAGATGCCCCTCTAGAACAATTGGTTAAACGCCCCGACT
*
573537 TTATGGATAATATTCAGCTAA-CCTGATAAAGGTG
65 TTATGGATAAGATTCAGCTAAGCCTGATAAAGGTG
* * * * *
573571 ATTATAATATCTATACAATGATA-TTAAGATGCCCCTCTAGAACAATTAGTTAAACTCCCCGGCT
1 ATTATAATATATATACAAT-AAACTTAAGATGCCCCTCTAGAACAATTGGTTAAACGCCCCGACT
573635 TTATGGAT
65 TTATGGAT
573643 CCAGCTAGCC
Statistics
Matches: 151, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
98 42 0.28
99 33 0.22
100 69 0.46
101 7 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (99 bp):
ATTATAATATATATACAATAAACTTAAGATGCCCCTCTAGAACAATTGGTTAAACGCCCCGACTT
TATGGATAAGATTCAGCTAAGCCTGATAAAGGTG
Found at i:574924 original size:84 final size:83
Alignment explanation
Indices: 574731--575673 Score: 923
Period size: 84 Copynumber: 11.3 Consensus size: 83
574721 CTATCGACAA
* * * * *
574731 CATAACTCAAGGCGAGAAGGGTTGTCTGTCAGC-CAAGACCTTCGAGTTTGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCA-CAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
** *
574795 CAAGATACATCATTTGCAG
65 CAAGGCACATCATTTACAG
* * * * * *
574814 TATATCCCAAGGCTAGAAAGGCTATCTACCACTAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAC-AAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
574879 CAAGGCATATCATTTACAG
65 CAAGGCACATCATTTACAG
* * * * * * *
574898 CATAAATTAAGTCGAGAATGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
574963 CAAGGCACATCATTTACAA
65 CAAGGCACATCATTTACAG
* * * * * * * *
574982 CATAACTTAAGTCGAGAAAGGCTATCTG-C-C-AAAGACCCTCGAGTTCGATTACACTCAGCTTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TC
* * * *
575044 GAGGGCATATCATTTACAA
65 CAAGGCACATCATTTACAG
* * * * **
575063 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAATACCTTTGAGTTCGACTATACTCAGCTCC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
* * *
575128 AAGGCATATCTTTTGCAG
66 AAGGCACATCATTTACAG
* * * * *
575146 CATATCTCAAGGTTAGAAGGGTTATCTGCCACCAAAAGACCTTCAAGTTCGACTATGCCCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCA-CAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * *
575211 CAAGGTATATCCTTTACAA
65 CAAGGCACATCATTTACAG
* * * * *
575230 CATAAATCAAGGCTAGAAGGGTTATTTACCAACTAAAGACCTTCGAGTTCGACTACGCTTAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* **
575295 CAAGGTACATCATTTGTAG
65 CAAGGCACATCATTTACAG
* * * * * * * **
575314 CATAGCTTAAGTCGAGAAGGGTTATATG-C-C-AAAGACCCTCGAGTTCGATTACATTCAGCTTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TC
* *
575376 GATGGCACATCATTTACAG
65 CAAGGCACATCATTTACAG
* * * *
575395 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGGCCTTCGAGTTTGACTACACTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTG-CCACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
575460 CAAGGCACATCATTTACAG
65 CAAGGCACATCATTTACAG
* * * * * * *
575479 CTTAACTTAAGTCGAGAAGGGTTATCTGCCA-ACAAAGACCTTTGAGTTCGAATACACTCAGCT-
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCACA-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
575542 CAATGACACATCATTTGCAG
65 CAA-GGCACATCATTTACAG
* *
575562 TATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
575627 CAAGGCACATCATTTACAG
65 CAAGGCACATCATTTACAG
* *
575646 CATAGCTCAAGGCAAGAAGGGTTATCTG
1 CATAACTCAAGGCTAGAAGGGTTATCTG
575674 TCAATAAAAT
Statistics
Matches: 704, Mismatches: 137, Indels: 37
0.80 0.16 0.04
Matches are distributed among these distances:
80 49 0.07
81 82 0.12
82 6 0.01
83 136 0.19
84 401 0.57
85 30 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (83 bp):
CATAACTCAAGGCTAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
AAGGCACATCATTTACAG
Found at i:575346 original size:332 final size:331
Alignment explanation
Indices: 574727--575670 Score: 1246
Period size: 332 Copynumber: 2.8 Consensus size: 331
574717 GAAACTATCG
* * * *
574727 ACAACATAACTCAAGGCGAGAAGGGTTGTCTGTCAGCCAAGACCTTCGAGTTTGACTACGCTCAG
1 ACAACATAACTCAAGGCTAGAAGGGTTATCTGTCA-CCAAAACCTTCGAGTTTGACTACACTCAG
** * * * * * * *
574792 CTCCAAGATACATCATTTGCAGTATATCCCAAGGCTAGAAAGGCTATCTACCACTAAAAGACCTT
65 CTCCAAGGCACATCATTTGCAGCATATCTCAAGGTTAGAAGGGTTATCTGCCACCAAAAGACCTT
* * * *
574857 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAAATTAAGTCGAGAATGGTTA
130 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAAATCAAGGCTAGAAGGGTTA
* * *
574922 TCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTACAACATAA
195 TCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAG
* * * *
574987 CTTAAGTCGAGAAAGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAT
260 CTTAAGTCGAGAAGGGTTATATGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
575052 ATCATTT
325 ATCATTT
* * *
575059 ACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAATACCTTTGAGTTCGACTATACTCAG
1 ACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA-ACCTTCGAGTTTGACTACACTCAG
* *
575124 CTCCAAGGCATATCTTTTGCAGCATATCTCAAGGTTAGAAGGGTTATCTGCCACCAAAAGACCTT
65 CTCCAAGGCACATCATTTGCAGCATATCTCAAGGTTAGAAGGGTTATCTGCCACCAAAAGACCTT
* * * * * *
575189 CAAGTTCGACTATGCCCAGCTCCAAGGTATATCCTTTACAACATAAATCAAGGCTAGAAGGGTTA
130 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAAATCAAGGCTAGAAGGGTTA
* * * * * **
575254 TTTACCAACTAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGGTACATCATTTGTAGCATAG
195 TCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAG
* *
575319 CTTAAGTCGAGAAGGGTTATATGCCAAAGACCCTCGAGTTCGATTACATTCAGCTTCGATGGCAC
260 CTTAAGTCGAGAAGGGTTATATGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
575384 ATCATTT
325 ATCATTT
* *
575391 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGGCCTTCGAGTTTGACTACACTCA
1 ACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAA--CCTTCGAGTTTGACTACACTCA
* * * * * *
575456 GCTCCAAGGCACATCATTTACAGCTTAACTTAA-GTCGAGAAGGGTTATCTGCCAAC-AAAGACC
64 GCTCCAAGGCACATCATTTGCAGCATATCTCAAGGT-TAGAAGGGTTATCTGCCACCAAAAGACC
* * * * * * * *
575519 TTTGAGTTCGAATACACTCAGCT-CAATGACACATCATTTGCAGTATAACTCAAGGCTAGAAGGG
128 TTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTACAGCATAAATCAAGGCTAGAAGGG
575583 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCA
192 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCA
* * *
575648 TAGCTCAAGGCAAGAAGGGTTAT
257 TAGCTTAAGTCGAGAAGGGTTAT
575671 CTGTCAATAA
Statistics
Matches: 526, Mismatches: 81, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
331 8 0.02
332 454 0.86
333 64 0.12
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (331 bp):
ACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAACCTTCGAGTTTGACTACACTCAGC
TCCAAGGCACATCATTTGCAGCATATCTCAAGGTTAGAAGGGTTATCTGCCACCAAAAGACCTTC
GAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAAATCAAGGCTAGAAGGGTTAT
CTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGC
TTAAGTCGAGAAGGGTTATATGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
TCATTT
Found at i:575540 original size:416 final size:413
Alignment explanation
Indices: 574731--575672 Score: 1086
Period size: 416 Copynumber: 2.3 Consensus size: 413
574721 CTATCGACAA
* * * * * * *
574731 CATAACTCAAGGCGAGAAGGGTTGTCTGTCAGCC-AAGACCTTCGAGTTTGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCCCAGCTC
** * ** *** * *
574795 CAAGATACATCATTTGCAGTATATCCCAAGGCTAGAAAGGCTATCTACCACTAAAAGACCTTCGA
66 CAAGGCACATCATTTACAACATAAATCAAGGCTAGAAGGGTTATCTACCACTAAAAGACCTTCGA
* * *
574860 GTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAAATTAAGTCGAGAATGGTTATCT
131 GTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAAATTAAGTCGAGAAGGGTTATAT
* ** *
574925 GCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTACAACATAACTT
196 G---ACCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTC
* * * * *
574990 AAGTCGAGAAAGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
258 AAGGCGAGAAAGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATC
* * * * * *
575055 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAATACCTTTGAGTTCGACTATAC
323 ATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGAATACAC
* * *
575120 TCAGCTCCAA-GGCATATCTTTTGCAG
388 TCAGCT-CAATGACACATCATTTGCAG
* * *
575146 CATATCTCAAGGTTAGAAGGGTTATCTGCC-ACCAAAAGACCTTCAAGTTCGACTATGCCCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCAAGTTCGACTACGCCCAGCT
* * * *
575210 CCAAGGTATATCCTTTACAACATAAATCAAGGCTAGAAGGGTTATTTACCAACT-AAAGACCTTC
65 CCAAGGCACATCATTTACAACATAAATCAAGGCTAGAAGGGTTATCTACC-ACTAAAAGACCTTC
* * ** **
575274 GAGTTCGACTACGCTTAGCTCCAAGGTACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGTTAT
129 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAAATTAAGTCGAGAAGGGTTAT
* * * * *
575339 ATG-CCAAAGACCCTCGAGTTCGATTACATTCAGCTTCGATGGCACATCATTTACAGCATAACTC
194 ATGACCAAAGACCCTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAACATAACTC
* * * * * *
575403 AAGGCTAGAAGGGTTATCTGTCAACAAAAGGCCTTCGAGTTTGACTACACTCAGC-TCCAAGGCA
258 AAGGCGAGAAAGGCTATCTG-C--C-AAAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCA
* * * *
575467 CATCATTTACAGCTTAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGAAT
319 CATCATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGAAT
575532 ACACTCAGCTCAATGACACATCATTTGCAG
384 ACACTCAGCTCAATGACACATCATTTGCAG
* * *
575562 TATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCCCAGCTC
* ** *
575627 CAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATCT
66 CAAGGCACATCATTTACAACATAAATCAAGGCTAGAAGGGTTATCT
575673 GTCAATAAAA
Statistics
Matches: 439, Mismatches: 78, Indels: 19
0.82 0.15 0.04
Matches are distributed among these distances:
412 26 0.06
413 41 0.09
414 3 0.01
415 28 0.06
416 310 0.71
417 31 0.07
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (413 bp):
CATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCCCAGCTC
CAAGGCACATCATTTACAACATAAATCAAGGCTAGAAGGGTTATCTACCACTAAAAGACCTTCGA
GTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAAATTAAGTCGAGAAGGGTTATAT
GACCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAG
GCGAGAAAGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATT
TACAACATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGAATACACTCA
GCTCAATGACACATCATTTGCAG
Found at i:576445 original size:37 final size:37
Alignment explanation
Indices: 576363--576685 Score: 352
Period size: 37 Copynumber: 8.8 Consensus size: 37
576353 TGAAAAATGG
*
576363 TTTTTGAAAATACGTATATAATATATAGTTTTTTAAAATA
1 TTTTTGAAAATA--TATATAATATATAG-TTTTTAAAACA
*
576403 TTTTTTGAAAATATATATATTATATAGTTTTTAAAACA
1 -TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
576441 TTTTTGAAAAT-TATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
576477 TTTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACA
1 -TTTTTGAAAATATATATAATATATAGTTTTT-AAAACA
*
576515 TTTTTAAAATATATATAATAATATATAGTTTTTGAAAACA
1 TTTTTGAAA-ATATAT-ATAATATATAGTTTTT-AAAACA
576555 ---TT-----TATATAT--TATATAGTTTTTAAAA-A
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
*
576581 TCATTTTGAAAATATATATAATATATAGCTTCTTAAAACA
1 T--TTTTGAAAATATATATAATATATAG-TTTTTAAAACA
** *
576621 -TTTTGAAAATTATATATAATATATAGTTTAAAAAATA
1 TTTTTGAAAA-TATATATAATATATAGTTTTTAAAACA
*
576658 TTTTTG-AAATATATATATTATATAGTTT
1 TTTTTGAAAATATATATAATATATAGTTT
576686 ATATCATATT
Statistics
Matches: 251, Mismatches: 10, Indels: 47
0.81 0.03 0.15
Matches are distributed among these distances:
26 1 0.00
27 4 0.02
28 12 0.05
30 2 0.01
31 7 0.03
36 49 0.20
37 70 0.28
38 46 0.18
39 24 0.10
40 24 0.10
41 12 0.05
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:576585 original size:29 final size:29
Alignment explanation
Indices: 576515--576598 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 29
576505 TTTGAAAACA
*
576515 TTTTTAAAAT-ATATATAATAATATATAG
1 TTTTTAAAATCATTTATAATAATATATAG
*
576543 TTTTTGAAAA-CATTTAT-ATATTATATAG
1 TTTTT-AAAATCATTTATAATAATATATAG
576571 TTTTTAAAAATCATTT-TGAA-AATATATA
1 TTTTT-AAAATCATTTAT-AATAATATATA
576599 TAATATATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 25 0.53
29 21 0.45
30 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (29 bp):
TTTTTAAAATCATTTATAATAATATATAG
Found at i:576686 original size:36 final size:37
Alignment explanation
Indices: 576557--576686 Score: 142
Period size: 38 Copynumber: 3.5 Consensus size: 37
576547 TGAAAACATT
* * *
576557 TATATATTATATAGTTTTTAAAAATCATTTTGAAAATA
1 TATATAATATATAGCTTTAAAAAAT-ATTTTGAAAATA
* *
576595 TATATAATATATAGCTTCT-TAAAACATTTTGAAAATTA
1 TATATAATATATAGCTT-TAAAAAATATTTTGAAAA-TA
576633 TATATAATATATAG-TTTAAAAAATATTTTTG-AAATA
1 TATATAATATATAGCTTTAAAAAATA-TTTTGAAAATA
*
576669 TATATATTATATAG-TTTA
1 TATATAATATATAGCTTTA
576687 TATCATATTA
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
36 20 0.25
37 20 0.25
38 40 0.49
39 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATAATATATAGCTTTAAAAAATATTTTGAAAATA
Found at i:576737 original size:33 final size:30
Alignment explanation
Indices: 576683--576747 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
576673 TATTATATAG
* *
576683 TTTATATCATATTATTATTATTTATTTTAT
1 TTTATATCATATTATTATTATTAATTTAAT
*
576713 TTTATTTCATATTATTAATTTTATTAATTTAAT
1 TTTATATCATATTATT-A--TTATTAATTTAAT
576746 TT
1 TT
576748 AATTAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 15 0.52
31 1 0.03
33 13 0.45
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTATATCATATTATTATTATTAATTTAAT
Found at i:576744 original size:14 final size:14
Alignment explanation
Indices: 576727--576756 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
576717 TTTCATATTA
*
576727 TTAATTTTATTAAT
1 TTAATTTAATTAAT
576741 TTAATTTAATTAAT
1 TTAATTTAATTAAT
576755 TT
1 TT
576757 TTTTTTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTAATTTAATTAAT
Found at i:578106 original size:23 final size:21
Alignment explanation
Indices: 578065--578196 Score: 99
Period size: 22 Copynumber: 5.9 Consensus size: 21
578055 TATATATACC
*
578065 TTTATTTTATTTTAATTTTTAAT
1 TTTA-TTTATTTT-ATTTTTTAT
578088 TTTATTTATTTATATTTTTTAT
1 TTTATTTATTT-TATTTTTTAT
* * *
578110 TTCATTT-TTTGTCTTTATTTTAC
1 TTTATTTATTT-T-ATT-TTTTAT
*
578133 TTTATTTATCTTATTTATTATCAT
1 TTTATTTATTTTATTT-TT-T-AT
578157 TTTATTT-TTTTATTTTTTAT
1 TTTATTTATTTTATTTTTTAT
578177 TTT-TTTATTTTTTATTTTTT
1 TTTATTTA--TTTTATTTTTT
578197 TCTTCCTTTG
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
19 3 0.03
20 5 0.06
21 6 0.07
22 40 0.45
23 25 0.28
24 10 0.11
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.77
Consensus pattern (21 bp):
TTTATTTATTTTATTTTTTAT
Found at i:578166 original size:7 final size:7
Alignment explanation
Indices: 578133--578196 Score: 65
Period size: 7 Copynumber: 8.4 Consensus size: 7
578123 TTTATTTTAC
578133 TTTATTT
1 TTTATTT
578140 ATCTTATTT
1 -T-TTATTT
* *
578149 ATTATCAT
1 TTTAT-TT
578157 TTTATTTT
1 TTTA-TTT
578165 TTTATTT
1 TTTATTT
578172 TTTATTTT
1 TTTA-TTT
578180 TTTATTT
1 TTTATTT
578187 TTTATTT
1 TTTATTT
578194 TTT
1 TTT
578197 TCTTCCTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
7 24 0.50
8 17 0.35
9 7 0.15
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTATTT
Found at i:578167 original size:8 final size:8
Alignment explanation
Indices: 578087--578197 Score: 77
Period size: 8 Copynumber: 13.5 Consensus size: 8
578077 TAATTTTTAA
578087 TTTTATTT
1 TTTTATTT
*
578095 ATTTATATT
1 TTTTAT-TT
578104 TTTTATTT
1 TTTTATTT
578112 CATTTT-TTGT
1 --TTTTATT-T
*
578122 CTTTATTT
1 TTTTATTT
578130 TACTTTATTT
1 T--TTTATTT
*
578140 ATCTTA-TT
1 -TTTTATTT
* **
578148 TATTATCA
1 TTTTATTT
578156 TTTTATTT
1 TTTTATTT
578164 TTTTA-TT
1 TTTTATTT
578171 TTTTATTT
1 TTTTATTT
578179 TTTTA-TT
1 TTTTATTT
578186 TTTTATTT
1 TTTTATTT
578194 TTTT
1 TTTT
578198 CTTCCTTTGA
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
7 18 0.22
8 36 0.44
9 14 0.17
10 12 0.15
11 1 0.01
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTATTT
Found at i:578174 original size:15 final size:15
Alignment explanation
Indices: 578087--578197 Score: 91
Period size: 15 Copynumber: 6.8 Consensus size: 15
578077 TAATTTTTAA
578087 TTTTATTTATTTATATT
1 TTTTATTT-TTT-TATT
578104 TTTTATTTCATTTT-TT
1 TTTTATTT--TTTTATT
578120 GTCTTTATTTTACTTTATT
1 -T-TTTATTTT--TTTATT
* *
578139 TATCTTA-TTTATTATCA
1 T-T-TTATTTTTTTAT-T
578156 TTTTATTTTTTTATT
1 TTTTATTTTTTTATT
578171 TTTTATTTTTTTATT
1 TTTTATTTTTTTATT
578186 TTTTATTTTTTT
1 TTTTATTTTTTT
578198 CTTCCTTTGA
Statistics
Matches: 80, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
15 30 0.38
16 15 0.19
17 11 0.14
18 19 0.24
19 5 0.06
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTTTATT
Found at i:578197 original size:23 final size:23
Alignment explanation
Indices: 578087--578197 Score: 75
Period size: 23 Copynumber: 4.5 Consensus size: 23
578077 TAATTTTTAA
*
578087 TTTTATTTATTTATATTTTTTATT
1 TTTTATTTTTTTAT-TTTTTTATT
578111 TCATTT-TTTGTCTTTATTTTACTTTATT
1 T--TTTATTT-T-TTTATTTT--TTTATT
* **
578139 TATCTTA-TTTATTATCATTTTATT
1 T-T-TTATTTTTTTATTTTTTTATT
578163 TTTT-TATTTTTTATTTTTTTATT
1 TTTTAT-TTTTTTATTTTTTTATT
578186 TTTTATTTTTTT
1 TTTTATTTTTTT
578198 CTTCCTTTGA
Statistics
Matches: 69, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
22 2 0.03
23 25 0.36
24 9 0.13
25 3 0.04
26 11 0.16
27 8 0.12
28 11 0.16
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (23 bp):
TTTTATTTTTTTATTTTTTTATT
Found at i:578254 original size:11 final size:11
Alignment explanation
Indices: 578240--578269 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
578230 TTTTTGTTTT
578240 TTTATTTAATA
1 TTTATTTAATA
578251 TTTATTTAATA
1 TTTATTTAATA
*
578262 TTTTTTTA
1 TTTATTTA
578270 TTTGACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATTTAATA
Found at i:582077 original size:17 final size:17
Alignment explanation
Indices: 582036--582081 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
582026 ATTTAAAATA
582036 ATATTTTACTATCATAAT
1 ATATTTTA-TATCATAAT
* * *
582054 ATTTTTTATATTATATT
1 ATATTTTATATCATAAT
582071 ATATTTTATAT
1 ATATTTTATAT
582082 AAATAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTTTATATCATAAT
Found at i:584514 original size:14 final size:14
Alignment explanation
Indices: 584492--584534 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
584482 TTCAACACTA
584492 TGTTCGTTTATGTT
1 TGTTCGTTTATGTT
*
584506 TGTTTGTTTATGTT
1 TGTTCGTTTATGTT
*
584520 AT-TTCATTTATGTT
1 -TGTTCGTTTATGTT
584534 T
1 T
584535 AGCCCAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 23 0.92
15 1 0.04
ACGTcount: A:0.12, C:0.05, G:0.16, T:0.67
Consensus pattern (14 bp):
TGTTCGTTTATGTT
Found at i:584987 original size:10 final size:10
Alignment explanation
Indices: 584971--585058 Score: 95
Period size: 10 Copynumber: 8.5 Consensus size: 10
584961 TTGTTGTGTG
584971 GTTTATGTTC
1 GTTTATGTTC
*
584981 ATTTATGTTC
1 GTTTATGTTC
*
584991 GTTTGTTTTGTTC
1 G--T-TTATGTTC
*
585004 ATTTATGTTC
1 GTTTATGTTC
* *
585014 GTTTACGTTT
1 GTTTATGTTC
585024 GTTTATGTTC
1 GTTTATGTTC
*
585034 ATTTATGTTC
1 GTTTATGTTC
585044 GTTTATGTTC
1 GTTTATGTTC
585054 GTTTA
1 GTTTA
585059 CAGCCTTGCG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
10 54 0.86
11 1 0.02
12 1 0.02
13 7 0.11
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.61
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:585006 original size:23 final size:24
Alignment explanation
Indices: 584971--585047 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 24
584961 TTGTTGTGTG
584971 GTTTATGTTCATTTATGTTCGTTT
1 GTTTATGTTCATTTATGTTCGTTT
584995 GTTT-TGTTCATTTATGTTCGTTTACGTTT
1 GTTTATGTTCATTTA---T-G-TT-CGTTT
585024 GTTTATGTTCATTTATGTTCGTTT
1 GTTTATGTTCATTTATGTTCGTTT
585048 ATGTTCGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
23 10 0.22
24 9 0.20
25 2 0.04
26 2 0.04
27 2 0.04
28 2 0.04
29 9 0.20
30 10 0.22
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.62
Consensus pattern (24 bp):
GTTTATGTTCATTTATGTTCGTTT
Found at i:585035 original size:30 final size:30
Alignment explanation
Indices: 584990--585058 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
584980 CATTTATGTT
584990 CGTTTGTTT-TGTTCATTTATGTTCGTTTA
1 CGTTTGTTTATGTTCATTTATGTTCGTTTA
585019 CGTTTGTTTATGTTCATTTATGTTCGTTTA
1 CGTTTGTTTATGTTCATTTATGTTCGTTTA
* *
585049 TGTTCGTTTA
1 CGTTTGTTTA
585059 CAGCCTTGCG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 9 0.24
30 28 0.76
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (30 bp):
CGTTTGTTTATGTTCATTTATGTTCGTTTA
Found at i:588621 original size:21 final size:21
Alignment explanation
Indices: 588595--588661 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
588585 GATGAAGTGG
* * *
588595 AAGTAGATGAATTACATTGGC
1 AAGTAGATGAAGTACCTTGGT
*
588616 AAGTAGATTAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
*
588637 AAATAGATGAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
588658 AAGT
1 AAGT
588662 GTATCTGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (21 bp):
AAGTAGATGAAGTACCTTGGT
Found at i:589728 original size:97 final size:96
Alignment explanation
Indices: 589561--589753 Score: 305
Period size: 97 Copynumber: 2.0 Consensus size: 96
589551 AAGAGGCCAA
* * *
589561 AGAAAGATAGGACTCCGAGTGAACGAGAATGCAAGGAATAAGAAGTATGCAAACTCTTTAATCCT
1 AGAAAGATAGGACTCCAAGTAAACGAGAATGCAAGGAAGAAGAAGTATGCAAACTCTTTAATCCT
* *
589626 ACTAACACAAGGAAGAGAGTGTGTTAGATGAT
66 ACTAACACAAGG-AGAGAATGTATTAGATGAT
* *
589658 AGAAAGATAGGACTCCAAGTAAACGAGAATGCAAGGAAGATGAATTATGCAAACTCTTTAATCCT
1 AGAAAGATAGGACTCCAAGTAAACGAGAATGCAAGGAAGAAGAAGTATGCAAACTCTTTAATCCT
*
589723 CCTAACACAAGGAGAGAATGTATTAGATGAT
66 ACTAACACAAGGAGAGAATGTATTAGATGAT
589754 GTAGAGGAAC
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
96 17 0.19
97 71 0.81
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (96 bp):
AGAAAGATAGGACTCCAAGTAAACGAGAATGCAAGGAAGAAGAAGTATGCAAACTCTTTAATCCT
ACTAACACAAGGAGAGAATGTATTAGATGAT
Found at i:592913 original size:31 final size:31
Alignment explanation
Indices: 592841--592913 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
592831 TAAAACTTAT
* *
592841 AATACGGTCCCCTAACATTTAGTCCATTTGC
1 AATACGGTCCCCCAACATTTAGTCCATTTAC
* * *
592872 AATACAGTCCCCCAACATTTAGTTCGTTTAC
1 AATACGGTCCCCCAACATTTAGTCCATTTAC
*
592903 AATATGGTCCC
1 AATACGGTCCC
592914 TTATGTAACC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (31 bp):
AATACGGTCCCCCAACATTTAGTCCATTTAC
Found at i:597509 original size:30 final size:30
Alignment explanation
Indices: 597466--597698 Score: 231
Period size: 30 Copynumber: 7.8 Consensus size: 30
597456 ACCACAACAG
* *
597466 AAAAACTAGAAACTTATGGGACTAAAATAGC
1 AAAAA-TAAAAACTTAAGGGACTAAAATAGC
*
597497 AAAAATAAAAACTGAAGGGACTAAAATAGC
1 AAAAATAAAAACTTAAGGGACTAAAATAGC
* * *
597527 AAAAACAAAAACTAAAGGGACTAAAATATC
1 AAAAATAAAAACTTAAGGGACTAAAATAGC
* * * *
597557 AAGAATATAAA-TTAAAGGATTAAAATAGC
1 AAAAATAAAAACTTAAGGGACTAAAATAGC
* * *
597586 AAAAACATAAACTTCAA-GGACTAAAATAAC
1 AAAAATAAAAACTT-AAGGGACTAAAATAGC
* *
597616 AAAAATAAAAACTTAAGAGACTAAAATAGA
1 AAAAATAAAAACTTAAGGGACTAAAATAGC
* * *
597646 AAAAACAAAAACTTAAGAGACAAAAATAG-
1 AAAAATAAAAACTTAAGGGACTAAAATAGC
* * *
597675 -TAAATAGAAACTTAAGGGGCTAAA
1 AAAAATAAAAACTTAAGGGACTAAA
597699 TAGTAAATAA
Statistics
Matches: 169, Mismatches: 30, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
28 18 0.11
29 25 0.15
30 119 0.70
31 7 0.04
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.17
Consensus pattern (30 bp):
AAAAATAAAAACTTAAGGGACTAAAATAGC
Found at i:599154 original size:12 final size:12
Alignment explanation
Indices: 599139--599163 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
599129 ATAATAATAA
599139 TAATAATATTTT
1 TAATAATATTTT
599151 TAATAATATTTT
1 TAATAATATTTT
599163 T
1 T
599164 GTAGACCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATAATATTTT
Found at i:599158 original size:3 final size:3
Alignment explanation
Indices: 599121--599146 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
599111 ATAAATTTGT
599121 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
599147 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:599622 original size:131 final size:131
Alignment explanation
Indices: 599352--599833 Score: 626
Period size: 131 Copynumber: 3.6 Consensus size: 131
599342 GGTCATCTAA
* * * * * * * * * *
599352 GGGTGACACAACTCCTACATGATGAGGAGATCTGGTCGGGGGATAATACTGTTCCTACGTGATAA
1 GGGTGACATAGCTCTTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGTGATGA
* * ** * *
599417 GGATGTCTTGGCCATCCTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGACGACTAATTA
66 GGATG-GTAGGCCATATTTAGCGA---TGATAACACGGTTCCTACGCGATGAGGACGACTAGTTA
599482 TCAAG
127 TCAAG
599487 GGGTGACATAGCTCTTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGTGATGA
1 GGGTGACATAGCTCTTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGTGATGA
*
599552 GGATGGTAGGCCATATTTAGCGATGATAACACGGTTCCTACGCGATGAGGATGACTAGTTATCAA
66 GGATGGTAGGCCATATTTAGCGATGATAACACGGTTCCTACGCGATGAGGACGACTAGTTATCAA
599617 G
131 G
*
599618 GGGTGACATAGCTCTTACGTGATGAGGAGGTCTGGTCGGTGGATGACAAGGTTCCTACGTGATGA
1 GGGTGACATAGCTCTTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGTGATGA
* * * * *
599683 GGATGGTAGGCCATATTTAGCGATGATAACACGGTTCCTACGTGATAAGGACAACTGGTTATCTA
66 GGATGGTAGGCCATATTTAGCGATGATAACACGGTTCCTACGCGATGAGGACGACTAGTTATCAA
599748 G
131 G
* * * *
599749 GGTTGACATGGCTAC-TACGTGATGAGGAGGTCTGGTCAGG-GGATGACACGATTCCTACGCGAT
1 GGGTGACATAGCT-CTTACGTGATGAGGAGGTCTGGTC-GGTGGATGACACGGTTCCTACGTGAT
* * *
599812 GAGGATGGCATGCCATCTTTAG
64 GAGGATGGTAGGCCATATTTAG
599834 GGATAATGAT
Statistics
Matches: 313, Mismatches: 32, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
131 237 0.76
132 3 0.01
134 13 0.04
135 60 0.19
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (131 bp):
GGGTGACATAGCTCTTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGTGATGA
GGATGGTAGGCCATATTTAGCGATGATAACACGGTTCCTACGCGATGAGGACGACTAGTTATCAA
G
Found at i:600004 original size:66 final size:65
Alignment explanation
Indices: 599874--600042 Score: 194
Period size: 66 Copynumber: 2.6 Consensus size: 65
599864 AAATGATGCT
* * **
599874 TCAAGAGAAGCTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAACTATGGGTGT
1 TCAAAAGAAACTATCTCAAGAGAGACAAAATT-GTTTCAAGGGAAACAATCTCAAAGATGGGTGT
599939 C
65 C
* * * * * *
599940 TCAAAAGAAATTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAATAATCTCAAAGGTTGGTGT
1 TCAAAAGAAACTATCTCAAGAGAGACAAAA-TTGTTTCAAGGGAAACAATCTCAAAGATGGGTGT
*
600005 T
65 C
**
600006 TCATGAGAAACTATCTCAAGAGAGACAAAATTTGTTT
1 TCAAAAGAAACTATCTCAAGAGAGACAAAA-TTGTTT
600043 TTAGAAAACT
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
66 83 0.98
67 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (65 bp):
TCAAAAGAAACTATCTCAAGAGAGACAAAATTGTTTCAAGGGAAACAATCTCAAAGATGGGTGTC
Found at i:600052 original size:35 final size:35
Alignment explanation
Indices: 600013--600079 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
600003 GTTTCATGAG
600013 AAACTATCTCAAGAGAGACAAAATTTGTTTTTAGA
1 AAACTATCTCAAGAGAGACAAAATTTGTTTTTAGA
* * * * * *
600048 AAACTGTTTCAAGCGATACAAATTTTTTTTTT
1 AAACTATCTCAAGAGAGACAAAATTTGTTTTT
600080 CAAGAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (35 bp):
AAACTATCTCAAGAGAGACAAAATTTGTTTTTAGA
Found at i:601300 original size:15 final size:15
Alignment explanation
Indices: 601277--601335 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
601267 TTTTTCTTTG
*
601277 TTTTTTCTTTGTTTC
1 TTTTCTCTTTGTTTC
*
601292 TTTTCTCTTTTTTTC
1 TTTTCTCTTTGTTTC
*
601307 TTTTTTCTTTGCTTT-
1 TTTTCTCTTTG-TTTC
601322 TTTTCTCTTTGTTT
1 TTTTCTCTTTGTTT
601336 TGATTTGATC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
14 3 0.08
15 32 0.84
16 3 0.08
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (15 bp):
TTTTCTCTTTGTTTC
Found at i:601313 original size:22 final size:22
Alignment explanation
Indices: 601268--601335 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
601258 ATCTTGTCAT
601268 TTTTCTTTGTTTTTTCTTTGTTTC
1 TTTTC-TT-TTTTTTCTTTGTTTC
601292 TTTTCTCTTTTTTTCTTT-TTTC
1 TTTTCT-TTTTTTTCTTTGTTTC
*
601314 TTTGCTTTTTTTCTCTTTGTTT
1 TTTTCTTTTTTT-TCTTTGTTT
601336 TGATTTGATC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 6 0.15
22 14 0.35
23 14 0.35
24 6 0.15
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTTTTTCTTTGTTTC
Found at i:601337 original size:20 final size:20
Alignment explanation
Indices: 601298--601337 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
601288 TTTCTTTTCT
*
601298 CTTTTTTTCTTTTTTCTTTG
1 CTTTTTTTCTTTTGTCTTTG
601318 CTTTTTTTCTCTTTGT-TTTG
1 CTTTTTTTCT-TTTGTCTTTG
601338 ATTTGATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (20 bp):
CTTTTTTTCTTTTGTCTTTG
Found at i:603198 original size:30 final size:30
Alignment explanation
Indices: 603164--603225 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
603154 TGATGAAATA
*
603164 TAACACAAACAAAAG-AGAAAAACGAGTTAG
1 TAACACAAAAAAAAGTA-AAAAACGAGTTAG
*
603194 TAACACAAAAAAAAGTAAAAAATGAGTTAG
1 TAACACAAAAAAAAGTAAAAAACGAGTTAG
603224 TA
1 TA
603226 CAAGAAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (30 bp):
TAACACAAAAAAAAGTAAAAAACGAGTTAG
Found at i:605136 original size:31 final size:30
Alignment explanation
Indices: 605075--605246 Score: 281
Period size: 30 Copynumber: 5.7 Consensus size: 30
605065 CATATTCGAT
* * *
605075 TTAAAGGACCAAAATATCAAAAATAGAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGAAAC
** *
605105 TTAAGGGACTAAAATAAAAAAAAATATAAAC
1 TTAAGGGACTAAAAT-AGCAAAAATAGAAAC
605136 TTAAGGGACTAAAATAGCAAAAATAGAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGAAAC
605166 TTAAGGGACTAAAATAGCAAAAATAGAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGAAAC
605196 TTAAGGGACTAAAATAGCAAAAATAGAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGAAAC
605226 TTAAGGGACTAAAATAGCAAA
1 TTAAGGGACTAAAATAGCAAA
605247 TAGAAAATTA
Statistics
Matches: 133, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
30 106 0.80
31 27 0.20
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGCAAAAATAGAAAC
Found at i:605713 original size:16 final size:16
Alignment explanation
Indices: 605688--605719 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
605678 GTTGCTTCCT
*
605688 TCATTTCCCTTATTTC
1 TCATTACCCTTATTTC
605704 TCATTACCCTTATTTC
1 TCATTACCCTTATTTC
605720 CCCCATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTACCCTTATTTC
Found at i:606116 original size:26 final size:29
Alignment explanation
Indices: 606086--606152 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
606076 CTAATTTTTA
606086 ATAAATTATATA-GAT-TAA-ATAAATAT
1 ATAAATTATATAGGATGTAATATAAATAT
* *
606112 ATAAATCAT-TAGGATGTAATATATATAT
1 ATAAATTATATAGGATGTAATATAAATAT
*
606140 ATATATATATATA
1 ATAAAT-TATATA
606153 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 2 0.06
26 11 0.34
27 3 0.09
28 12 0.38
29 2 0.06
30 2 0.06
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
ATAAATTATATAGGATGTAATATAAATAT
Found at i:606137 original size:2 final size:2
Alignment explanation
Indices: 606130--606163 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
606120 TTAGGATGTA
606130 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
606164 TTTATATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:606328 original size:63 final size:63
Alignment explanation
Indices: 606259--606383 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
606249 CATTTAAAAA
*
606259 AAACAAAAAGGTGCTTGATGTCATGCAATGCTTGATAATATATTATATAATTATATATGTATG
1 AAACAAAAAGGTGCTTGATGTCAAGCAATGCTTGATAATATATTATATAATTATATATGTATG
*
606322 AAACAAAAAGGTGTTTGATGTCAAGCAATGCTTGATAATATATTATATAATTATATATGTAT
1 AAACAAAAAGGTGCTTGATGTCAAGCAATGCTTGATAATATATTATATAATTATATATGTAT
606384 ACATGCATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (63 bp):
AAACAAAAAGGTGCTTGATGTCAAGCAATGCTTGATAATATATTATATAATTATATATGTATG
Found at i:608021 original size:3 final size:3
Alignment explanation
Indices: 608013--608068 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
608003 TGTAAAAGCA
* * * *
608013 AAT AAT AAT AAT ATT AAT -AT AAT AAT GAT ATT AAT AAT ATT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
608061 AAT AAT AA
1 AAT AAT AA
608069 AAAGGGTCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:610130 original size:134 final size:134
Alignment explanation
Indices: 609883--610208 Score: 440
Period size: 134 Copynumber: 2.4 Consensus size: 134
609873 TGAGTTATAA
* * * * * *
609883 AATATCAAATCTTAAAAGAGAGGGATTTATTCCACTTCTTCTTGAAGGAAAATCAGATATGGGGA
1 AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAAATATGAGGA
* * *
609948 CTTTTATTCATTCCATTGCTCTTCAGGGAAGATTGAATCGAGGAAGACTTATTCCACTATCACTC
66 CTTTGATTCATTCCATTGCTCCTCAGGGAAGATTGAATCAAGGAAGACTTATTCCACTATCACTC
610013 AAGG
131 AAGG
* *
610017 AATATCAAATCTTGAAATAGAGGGATTTGTTCTGCTTCTTCTTGAGGGAAAATCAAATCA-GAGG
1 AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAAAT-ATGAGG
* * * *
610081 ACTTTGATTTATTCCATTGCTCCTCAAGGG-AGATTGAATCAAGGTAGACTTGTTCCACTGTCAC
65 ACTTTGATTCATTCCATTGCTCCTC-AGGGAAGATTGAATCAAGGAAGACTTATTCCACTATCAC
*
610145 TCAGGG
129 TCAAGG
* * * *
610151 AATATCAATTCTTGAAAGGGATGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAAAT
1 AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAAAT
610209 TTGGATCCAC
Statistics
Matches: 168, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
134 163 0.97
135 5 0.03
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (134 bp):
AATATCAAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAAATATGAGGA
CTTTGATTCATTCCATTGCTCCTCAGGGAAGATTGAATCAAGGAAGACTTATTCCACTATCACTC
AAGG
Found at i:611050 original size:233 final size:224
Alignment explanation
Indices: 610645--611057 Score: 501
Period size: 233 Copynumber: 1.8 Consensus size: 224
610635 TTGGAAATCA
610645 TTTTCTTACTTTTCAAAAATCTCAATTTTCAGATTTAAATGAGATTTTTTTCGAAAAAAACGTGA
1 TTTTCTTACTTTTCAAAAATCTCAATTTTCAGATTTAAATGAGATTTTTTTCGAAAAAAACGTGA
* * * * * * *
610710 AAACATCCTGTTCGAAGGTCTTATGGATGGCCTGAAAGACTTATCATTTTTCTCGAAAGGCTTAT
66 AAACATCCTGTCCAAAGGTCTTATGGATGGCCTCAAAGACTTATCATCTTGCTCGAAAGACTTAC
* * * * *
610775 ATATGACCCGAAAGATTTAATCATCTTGCTTTAAAAACTTACTGATGGCCTGAAGAACTTACAAA
131 AGATGACCCGAAAGATTTAAACATCATGCTTCAAAAACTTACTAATGGCCTGAAGAACTTACAAA
610840 TTTTGGAAATAGTTTACTATGTAAGAAAT
196 TTTTGGAAATAGTTTACTATGTAAGAAAT
* *
610869 TTTTCTTACTTTTCAAAAGAT-TCAATTTTTAGATTTAAATGAGAAAATTTTCTCATTTTTTGAA
1 TTTTCTTACTTTTCAAAA-ATCTCAATTTTCAGATTTAAATGAG---A---T-T--TTTTTCGAA
* * * *
610933 AAACATGTGAAAACATCCTG-CCAAAAGGTGTTGTGGATGGCC-CAAAGGACTTATCATCTTGCT
56 AAAAACGTGAAAACATCCTGTCC-AAAGGTCTTATGGATGGCCTCAAA-GACTTATCATCTTGCT
* *
610996 TGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGC-TCAAAAGACTTACTAATGGCC
119 CGAAAGACTTACAGATGACCCGAAAGATTTAAACATCATGCTTCAAAA-ACTTACTAATGGCC
611058 CAAAGGAATT
Statistics
Matches: 156, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
224 39 0.25
225 2 0.01
227 1 0.01
230 1 0.01
231 1 0.01
232 9 0.06
233 103 0.66
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (224 bp):
TTTTCTTACTTTTCAAAAATCTCAATTTTCAGATTTAAATGAGATTTTTTTCGAAAAAAACGTGA
AAACATCCTGTCCAAAGGTCTTATGGATGGCCTCAAAGACTTATCATCTTGCTCGAAAGACTTAC
AGATGACCCGAAAGATTTAAACATCATGCTTCAAAAACTTACTAATGGCCTGAAGAACTTACAAA
TTTTGGAAATAGTTTACTATGTAAGAAAT
Found at i:611064 original size:42 final size:41
Alignment explanation
Indices: 610968--611064 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
610958 AGGTGTTGTG
* * **
610968 GATGGCCCAAAGGACTTATCATCTTGCTTGAAAGACTTACA
1 GATGGCCCAAAGGACTTAACATCATGCTCAAAAGACTTACA
* * *
611009 GATGACCCGAAGGATTTAAACATCATGCTCAAAAGACTTACTA
1 GATGGCCCAAAGGACTT-AACATCATGCTCAAAAGACTTAC-A
611052 -ATGGCCCAAAGGA
1 GATGGCCCAAAGGA
611065 ATTATCTTGG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 14 0.31
42 30 0.67
43 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (41 bp):
GATGGCCCAAAGGACTTAACATCATGCTCAAAAGACTTACA
Found at i:613207 original size:21 final size:21
Alignment explanation
Indices: 613183--613222 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
613173 TTCAAATTTC
613183 TTTATGTATTTTTATCTATCT
1 TTTATGTATTTTTATCTATCT
* * *
613204 TTTATTTCTTTTTTTCTAT
1 TTTATGTATTTTTATCTAT
613223 TATTTTTCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTATGTATTTTTATCTATCT
Found at i:613241 original size:25 final size:27
Alignment explanation
Indices: 613208--613258 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
613198 CTATCTTTTA
613208 TTTC-TTTTT-TTCTATTATTTTTCTC
1 TTTCTTTTTTCTTCTATTATTTTTCTC
*
613233 TTTCTTTTTTCTTCTTTTATTTTTCT
1 TTTCTTTTTTCTTCTATTATTTTTCT
613259 TTTTTCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 5 0.22
27 14 0.61
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTCTTTTTTCTTCTATTATTTTTCTC
Found at i:613250 original size:21 final size:21
Alignment explanation
Indices: 613191--613314 Score: 94
Period size: 21 Copynumber: 5.7 Consensus size: 21
613181 TCTTTATGTA
* *
613191 TTTTTATCTATCTTTT-ATTTC
1 TTTTT-TCTTTCTTTTCTTTTC
*
613212 TTTTTTTCTATTATTTTTCTCTTTC
1 -TTTTTTCT-TT-CTTTTCT-TTTC
*
613237 TTTTTTC-TTCTTTTATTTTTC
1 TTTTTTCTTTCTTTT-CTTTTC
*
613258 TTTTTTCCTTTCTTTT-TTTCC
1 TTTTTT-CTTTCTTTTCTTTTC
613279 TTTTTTCTTTTCTTTTCTTTTC
1 TTTTTTC-TTTCTTTTCTTTTC
*
613301 TTTCTT-TTTCTTTT
1 TTTTTTCTTTCTTTT
613315 TTCGAGTGCG
Statistics
Matches: 85, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
20 9 0.11
21 35 0.41
22 19 0.22
23 11 0.13
24 7 0.08
25 4 0.05
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTCTTTCTTTTCTTTTC
Found at i:613257 original size:14 final size:14
Alignment explanation
Indices: 613212--613263 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
613202 CTTTTATTTC
*
613212 TTTTT-TTCTATTA
1 TTTTTCTTCTTTTA
613225 TTTTTC-TCTTTCT-
1 TTTTTCTTCTTT-TA
613238 TTTTTCTTCTTTTA
1 TTTTTCTTCTTTTA
613252 TTTTTCTT-TTTT
1 TTTTTCTTCTTTT
613264 CCTTTCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 20 0.59
14 14 0.41
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTCTTTTA
Found at i:613269 original size:33 final size:35
Alignment explanation
Indices: 613225--613316 Score: 104
Period size: 34 Copynumber: 2.7 Consensus size: 35
613215 TTTTCTATTA
613225 TTTTTCTCTTTCTTTTTTCTTCTTTTAT-TTTTC-T
1 TTTTTC-CTTTCTTTTTTCTTCTTTTATCTTTTCTT
* *
613259 TTTTTCCTTTCTTTTTT-TCCTTTTTTCTTTTCTT
1 TTTTTCCTTTCTTTTTTCTTCTTTTATCTTTTCTT
*
613293 TTCTTTTCTTTC-TTTTTCTT-TTTT
1 TT-TTTCCTTTCTTTTTTCTTCTTTT
613317 CGAGTGCGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
32 7 0.14
33 16 0.32
34 18 0.36
35 9 0.18
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (35 bp):
TTTTTCCTTTCTTTTTTCTTCTTTTATCTTTTCTT
Found at i:614786 original size:19 final size:19
Alignment explanation
Indices: 614762--614808 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
614752 ATAATAGGAG
*
614762 TGTAAAAATTGATAAAGAA
1 TGTAAAAATTGAAAAAGAA
614781 TGTAAAGAA-TGAAAAAGAA
1 TGTAAA-AATTGAAAAAGAA
*
614800 TGTGAAAAT
1 TGTAAAAAT
614809 GTATAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.23
Consensus pattern (19 bp):
TGTAAAAATTGAAAAAGAA
Found at i:619307 original size:45 final size:45
Alignment explanation
Indices: 619257--619722 Score: 675
Period size: 45 Copynumber: 10.4 Consensus size: 45
619247 ATTTCAACTA
* *
619257 TGGCATCCTTTCATGTCAATAATGCACTCATATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
* * **
619302 TGGCATCTTTTCGTACCGATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
**
619347 TGGCATCCTTTCATACCGATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
* * *
619392 TGGCATTCTTTCATGCCGATAATGCACACATATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
619437 TGGCAT-CTTCTCATGTCGATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTT-TCATGTCGATAATGCACCCATATGCATTATTATTT
*
619482 TTGCATCCTTTCATGTCGAT-ATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
* * * * *
619526 TTGCATCATTCCATGCCGATAATGTACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
* ** *
619571 TGGCATTCTTTCATACCGATAATGAACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
* *
619616 TGGCATCTTTTCATGTCGATAATGCACCCGTATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
*
619661 TTGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
* *
619706 TGTCACCCTTTCATGTC
1 TGGCATCCTTTCATGTC
619723 TTTTATACTC
Statistics
Matches: 382, Mismatches: 36, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
44 44 0.12
45 335 0.88
46 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (45 bp):
TGGCATCCTTTCATGTCGATAATGCACCCATATGCATTATTATTT
Found at i:619677 original size:224 final size:224
Alignment explanation
Indices: 619259--619722 Score: 736
Period size: 224 Copynumber: 2.1 Consensus size: 224
619249 TTCAACTATG
* * * *
619259 GCATCCTTTCATGTCAATAATGCACTCATATGCATTATTATTTTGGCATCTTTTCGTACCGATAA
1 GCATCCTTTCATGTCAATAATGCACCCATATGCATTATTATTTTGGCATCATTCCATACCGATAA
*
619324 TGCACCCATATGCATTATTATTTTGGCATCCTTTCATACCGATAATGCACCCATATGCATTATTA
66 TGCACCCATATGCATTATTATTTTGGCATCCTTTCATACCGATAATGAACCCATATGCATTATTA
619389 TTTTGGCATTCTTTCATGCCGATAATGCACACATATGCATTATTATTTTGGCATCTTCTCATGTC
131 TTTTGGCATTCTTTCATGCCGATAATGCACACATATGCATTATTATTTTGGCATCTTCTCATGTC
619454 GATAATGCACCCATATGCATTATTATTTTT
196 GATAATGCACCCATATGCATTATTA-TTTT
* * *
619484 GCATCCTTTCATGTCGAT-ATGCACCCATATGCATTATTATTTTTGCATCATTCCATGCCGATAA
1 GCATCCTTTCATGTCAATAATGCACCCATATGCATTATTATTTTGGCATCATTCCATACCGATAA
* *
619548 TGTACCCATATGCATTATTATTTTGGCATTCTTTCATACCGATAATGAACCCATATGCATTATTA
66 TGCACCCATATGCATTATTATTTTGGCATCCTTTCATACCGATAATGAACCCATATGCATTATTA
* * * *
619613 TTTTGGCA-TCTTTTCATGTCGATAATGCACCCGTATGCATTATTATTTTTGCATCCTT-TCATG
131 TTTTGGCATTC-TTTCATGCCGATAATGCACACATATGCATTATTATTTTGGCAT-CTTCTCATG
619676 TCGATAATGCACCCATATGCATTATTATTTT
194 TCGATAATGCACCCATATGCATTATTATTTT
*
619707 GTCACCCTTTCATGTC
1 G-CATCCTTTCATGTC
619723 TTTTATACTC
Statistics
Matches: 221, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
223 7 0.03
224 194 0.88
225 20 0.09
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (224 bp):
GCATCCTTTCATGTCAATAATGCACCCATATGCATTATTATTTTGGCATCATTCCATACCGATAA
TGCACCCATATGCATTATTATTTTGGCATCCTTTCATACCGATAATGAACCCATATGCATTATTA
TTTTGGCATTCTTTCATGCCGATAATGCACACATATGCATTATTATTTTGGCATCTTCTCATGTC
GATAATGCACCCATATGCATTATTATTTT
Found at i:619782 original size:46 final size:45
Alignment explanation
Indices: 619714--619821 Score: 146
Period size: 46 Copynumber: 2.4 Consensus size: 45
619704 TTTGTCACCC
* * *
619714 TTTCATGTCTTTTATACTCTATTATACA-TATCATTTATGGCATCA
1 TTTCATGCCTTTTATACGCTATTATACAGT-TCATTTATGGAATCA
* *
619759 TTTCATGCCCTTTTATACGCTATTATATAGTTCATTTATGGAATCC
1 TTTCATG-CCTTTTATACGCTATTATACAGTTCATTTATGGAATCA
619805 TTTCATGCCTTTTATAC
1 TTTCATGCCTTTTATAC
619822 AACGTTATGC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 17 0.30
46 38 0.68
47 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.48
Consensus pattern (45 bp):
TTTCATGCCTTTTATACGCTATTATACAGTTCATTTATGGAATCA
Found at i:620279 original size:57 final size:57
Alignment explanation
Indices: 620202--620363 Score: 166
Period size: 57 Copynumber: 2.9 Consensus size: 57
620192 AAATTCATAT
* * ** * * **
620202 AATTTCTT-AGTTTTTACACATAAAGTTCTTATATATAAATTCATAAACATTTTAAG
1 AATTTCTTAACTTTTTACACATAAAGTGCCCATACAGAAATTCATAAACAAATTAAG
* ** *
620258 AATTTCTTAACTTTTTGCACATTCAGTGCCCATACAGAAATTCATAAACAAATTATG
1 AATTTCTTAACTTTTTACACATAAAGTGCCCATACAGAAATTCATAAACAAATTAAG
* * * *
620315 AATTTCTTATCTTTTGA-ACACAAAGTGCCCATACGGAAATTCATAAACA
1 AATTTCTTAACTTTTTACACATAAAGTGCCCATACAGAAATTCATAAACA
620364 TATATCTTTT
Statistics
Matches: 86, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
56 36 0.42
57 50 0.58
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (57 bp):
AATTTCTTAACTTTTTACACATAAAGTGCCCATACAGAAATTCATAAACAAATTAAG
Found at i:620356 original size:56 final size:57
Alignment explanation
Indices: 620238--620363 Score: 164
Period size: 56 Copynumber: 2.2 Consensus size: 57
620228 TCTTATATAT
** * ***
620238 AAATTCATAAACATTTTAAGAATTTCTTAACTTTTTGCACATTCAGTGCCCATACAG
1 AAATTCATAAACAAATTAAGAATTTCTTAACTTTTTGAACACAAAGTGCCCATACAG
* * *
620295 AAATTCATAAACAAATTATGAATTTCTTATC-TTTTGAACACAAAGTGCCCATACGG
1 AAATTCATAAACAAATTAAGAATTTCTTAACTTTTTGAACACAAAGTGCCCATACAG
620351 AAATTCATAAACA
1 AAATTCATAAACA
620364 TATATCTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
56 33 0.55
57 27 0.45
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (57 bp):
AAATTCATAAACAAATTAAGAATTTCTTAACTTTTTGAACACAAAGTGCCCATACAG
Found at i:621996 original size:2 final size:2
Alignment explanation
Indices: 621989--622065 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
621979 CCATAAAATT
621989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
622031 TA 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 T
622066 CTTTCTAACA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:623925 original size:45 final size:45
Alignment explanation
Indices: 623829--623926 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
623819 AATATGACAT
** * * *
623829 CCTTTCATGTCGATAATGCATCCATGAGCATTATTATTTTGGTAT
1 CCTTTCATACCGATAATGCACCCATGAGCATTATTATTTTGGCAC
*
623874 CTTTTCATACCGATAATGCACCCAT-ATGCATTATTATTTTGGCAC
1 CCTTTCATACCGATAATGCACCCATGA-GCATTATTATTTTGGCAC
623919 CCTTTCAT
1 CCTTTCAT
623927 GCCTTTTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 44 0.98
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (45 bp):
CCTTTCATACCGATAATGCACCCATGAGCATTATTATTTTGGCAC
Found at i:623990 original size:46 final size:45
Alignment explanation
Indices: 623921--624027 Score: 126
Period size: 46 Copynumber: 2.4 Consensus size: 45
623911 TTTGGCACCC
* * * *
623921 TTTCATGCCTTTTATACT-CTATTATACATTTCTTTTATGGAATCA
1 TTTCATCCCTTTTATA-TGTTATTATACAATTCATTTATGGAATCA
* *
623966 TTTCATTCCCTTTTATATGTTATTATACAATTCATTTATGGCATCC
1 TTTCA-TCCCTTTTATATGTTATTATACAATTCATTTATGGAATCA
*
624012 TTTCATGCCTTTTATA
1 TTTCATCCCTTTTATA
624028 CAACGTTATG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 16 0.30
46 37 0.70
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (45 bp):
TTTCATCCCTTTTATATGTTATTATACAATTCATTTATGGAATCA
Found at i:624138 original size:68 final size:67
Alignment explanation
Indices: 624062--624263 Score: 307
Period size: 67 Copynumber: 3.0 Consensus size: 67
624052 TAGTCTTTTA
* * ** * *
624062 CTCAAAGGCATTTAACCTTTCATAAAACTGGCATAATTGACA-CTTATCTGTCAAATGCACAGCT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTT-TCTGTC-AATGCACAGTT
*
624126 AGGT
64 AGGC
*
624130 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAATGCACAGTTAA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAATGCACAGTTAG
624195 GC
66 GC
624197 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAATGCACAGTTAG
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAATGCACAGTTAG
624262 GC
66 GC
624264 TATTAATATT
Statistics
Matches: 124, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
67 78 0.63
68 43 0.35
69 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (67 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAATGCACAGTTAG
GC
Found at i:624460 original size:23 final size:23
Alignment explanation
Indices: 624419--624462 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
624409 TAAAGAAATT
*
624419 CATATAATTTCTTAGTTTTTGCA
1 CATATAATTTCTTACTTTTTGCA
624442 CATA-AATTTCTTAACTTTTTG
1 CATATAATTTCTT-ACTTTTTG
624463 AACACTCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (23 bp):
CATATAATTTCTTACTTTTTGCA
Found at i:624598 original size:56 final size:55
Alignment explanation
Indices: 624443--624590 Score: 156
Period size: 56 Copynumber: 2.6 Consensus size: 55
624433 GTTTTTGCAC
* * * *
624443 ATAAATTTCTTAACTTTTTGAACACTCAGTGCCCGTACGTAAATTCATAAACAAATT
1 ATAAATTTCTTATCTTTTTGAACACTCAGTG-CCATAAG-AAATTCATAAACAAATG
* * **
624500 ATGAATTTCTTATC-TTTTGCACACAAAGTGCCCATACAGAAATTCATAAA-AAATG
1 ATAAATTTCTTATCTTTTTGAACACTCAGTG-CCATA-AGAAATTCATAAACAAATG
*
624555 ATAAATTTTCTTATCTTTTTGTACACTCAGTGCCAT
1 ATAAA-TTTCTTATCTTTTTGAACACTCAGTGCCAT
624591 TATGAAATCA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
55 8 0.11
56 42 0.55
57 26 0.34
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (55 bp):
ATAAATTTCTTATCTTTTTGAACACTCAGTGCCATAAGAAATTCATAAACAAATG
Found at i:627605 original size:3 final size:3
Alignment explanation
Indices: 627597--627680 Score: 141
Period size: 3 Copynumber: 27.7 Consensus size: 3
627587 TGTAAAAATA
* *
627597 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
627645 AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
627681 ATAAATAAGG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 73 0.96
4 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:629351 original size:59 final size:60
Alignment explanation
Indices: 629275--629457 Score: 201
Period size: 59 Copynumber: 3.1 Consensus size: 60
629265 CATATGTCCT
629275 CAAACTATAACCCTCATTCTAAATTGGTTCTTAAACTTTTGAATATTCTAATTTCAT-CC
1 CAAACTATAACCCTCATTCTAAATTGGTTCTTAAACTTTTGAATATTCTAATTTCATCCC
** * * * * *
629334 CAAACTATAACTGTCATTTTAAATT-ATTCTTTAAACTTTTGAACATTCCAATTACATCCC
1 CAAACTATAACCCTCATTCTAAATTGGTTC-TTAAACTTTTGAATATTCTAATTTCATCCC
* * * ** * *
629394 CAAACTGTGACCCTCATTCTAAATTGGTCCCCAAACTTTTGAAT-CTCTCAATTTCATGCC
1 CAAACTATAACCCTCATTCTAAATTGGTTCTTAAACTTTTGAATATTCT-AATTTCATCCC
629454 CAAA
1 CAAA
629458 GTCATCCAAA
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
58 3 0.03
59 48 0.48
60 46 0.46
61 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (60 bp):
CAAACTATAACCCTCATTCTAAATTGGTTCTTAAACTTTTGAATATTCTAATTTCATCCC
Found at i:629446 original size:60 final size:58
Alignment explanation
Indices: 629275--629457 Score: 188
Period size: 60 Copynumber: 3.1 Consensus size: 58
629265 CATATGTCCT
* *
629275 CAAACTATAACCCTCATTCTAAATTGGTTCTTAAACTTTTGAATATTCTAATTTCATCC
1 CAAACTATAACCCTCATTCTAAATTGGTCCTTAAACTTTTGAATCTTC-AATTTCATCC
** * ** * *
629334 CAAACTATAACTGTCATTTTAAATTATTCTTTAAACTTTTGAA-CATTCCAATTACATCCC
1 CAAACTATAACCCTCATTCTAAATTGGTCCTTAAACTTTTGAATC-TT-CAATTTCAT-CC
* * **
629394 CAAACTGTGACCCTCATTCTAAATTGGTCCCCAAACTTTTGAATCTCTCAATTTCATGCC
1 CAAACTATAACCCTCATTCTAAATTGGTCCTTAAACTTTTGAATCT-TCAATTTCAT-CC
629454 CAAA
1 CAAA
629458 GTCATCCAAA
Statistics
Matches: 98, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
59 45 0.46
60 51 0.52
61 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (58 bp):
CAAACTATAACCCTCATTCTAAATTGGTCCTTAAACTTTTGAATCTTCAATTTCATCC
Found at i:630224 original size:12 final size:14
Alignment explanation
Indices: 630198--630228 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
630188 TTATCATATA
630198 TTATATATTTATTT
1 TTATATATTTATTT
630212 TTATATATTT-TTT
1 TTATATATTTATTT
630225 TTAT
1 TTAT
630229 TAATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATATATTTATTT
Found at i:630309 original size:38 final size:38
Alignment explanation
Indices: 630255--630328 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
630245 TTAAAATTTT
* *
630255 ATAATATCATCATTTCTAGATATTTTAAAAATTTACTC
1 ATAAGATCATCATTTCTAGAAATTTTAAAAATTTACTC
630293 ATAAGATCATCATTTCTAGAAATTTTAAAAATTTAC
1 ATAAGATCATCATTTCTAGAAATTTTAAAAATTTAC
630329 CTATAAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (38 bp):
ATAAGATCATCATTTCTAGAAATTTTAAAAATTTACTC
Found at i:631477 original size:12 final size:12
Alignment explanation
Indices: 631450--631481 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
631440 TCATCAAAAA
631450 ATATTTTTAAAT
1 ATATTTTTAAAT
631462 -TATTTTTAAAT
1 ATATTTTTAAAT
631473 ATATTTTTA
1 ATATTTTTA
631482 TAAATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTTTTAAAT
Found at i:642657 original size:19 final size:20
Alignment explanation
Indices: 642620--642659 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
642610 CTTTCAAGTT
642620 GGTTGTTTCTTTAATTTTTG
1 GGTTGTTTCTTTAATTTTTG
642640 GGTTGTTTCTTTAATTTTTG
1 GGTTGTTTCTTTAATTTTTG
642660 TTTTGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.05, G:0.20, T:0.65
Consensus pattern (20 bp):
GGTTGTTTCTTTAATTTTTG
Found at i:642667 original size:24 final size:22
Alignment explanation
Indices: 642617--642661 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
642607 TTACTTTCAA
642617 GTTGGTTGTTTCTTTAATTTTT
1 GTTGGTTGTTTCTTTAATTTTT
642639 G--GGTTGTTTCTTTAATTTTT
1 GTTGGTTGTTTCTTTAATTTTT
642659 GTT
1 GTT
642662 TTGGTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 20 0.95
22 1 0.05
ACGTcount: A:0.09, C:0.04, G:0.20, T:0.67
Consensus pattern (22 bp):
GTTGGTTGTTTCTTTAATTTTT
Found at i:643149 original size:52 final size:52
Alignment explanation
Indices: 643078--643190 Score: 181
Period size: 52 Copynumber: 2.2 Consensus size: 52
643068 GGTACTGGAA
*
643078 GAACAATATCGAGACTATAAGGTTAAATTGAAAGGAATGGTATGAATCGGAT
1 GAACAATATCAAGACTATAAGGTTAAATTGAAAGGAATGGTATGAATCGGAT
* * * *
643130 GAACAATATCAATATTATAATGTTAAATTGAAAGGAATTGTATGAATCGGAT
1 GAACAATATCAAGACTATAAGGTTAAATTGAAAGGAATGGTATGAATCGGAT
643182 GAACAATAT
1 GAACAATAT
643191 TGATACTGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.28
Consensus pattern (52 bp):
GAACAATATCAAGACTATAAGGTTAAATTGAAAGGAATGGTATGAATCGGAT
Found at i:643732 original size:15 final size:15
Alignment explanation
Indices: 643714--643765 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
643704 ATGTTTTCTA
* *
643714 TGAAAAGGTTCTATG
1 TGAAAATGTTCTAAG
*
643729 TGAAAATGTGCTAAG
1 TGAAAATGTTCTAAG
*
643744 TGAAAATGTTCTACG
1 TGAAAATGTTCTAAG
643759 TGAAAAT
1 TGAAAAT
643766 ACCCTATGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (15 bp):
TGAAAATGTTCTAAG
Found at i:651218 original size:54 final size:51
Alignment explanation
Indices: 651158--651261 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
651148 GCTCATAAGC
*
651158 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCATATTA
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCATATTA
** * * * *
651212 TTATTTTTTTCAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCATATT
651262 TGCATCGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
51 21 0.49
53 2 0.05
54 20 0.47
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (51 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCATATTA
Found at i:653925 original size:15 final size:15
Alignment explanation
Indices: 653907--653958 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
653897 ATGTTTTCTA
* *
653907 TGAAAAGGTTCTATG
1 TGAAAATGTTCTAAG
*
653922 TGAAAATGTGCTAAG
1 TGAAAATGTTCTAAG
*
653937 TGAAAATGTTCTACG
1 TGAAAATGTTCTAAG
653952 TGAAAAT
1 TGAAAAT
653959 ACCCTATGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (15 bp):
TGAAAATGTTCTAAG
Found at i:653970 original size:30 final size:30
Alignment explanation
Indices: 653907--653970 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
653897 ATGTTTTCTA
* ***
653907 TGAAAAGGTTCTATGTGAAAATGTGCTAAG
1 TGAAAAGGTTCTACGTGAAAATACCCTAAG
* *
653937 TGAAAATGTTCTACGTGAAAATACCCTATG
1 TGAAAAGGTTCTACGTGAAAATACCCTAAG
653967 TGAA
1 TGAA
653971 TGTGCTCTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (30 bp):
TGAAAAGGTTCTACGTGAAAATACCCTAAG
Found at i:654157 original size:24 final size:25
Alignment explanation
Indices: 654105--654164 Score: 95
Period size: 24 Copynumber: 2.4 Consensus size: 25
654095 ATGCGATCAT
* *
654105 TCGGGACAAATTTCTACGTGGTCCT
1 TCGGGACAAATTTCTACGCGGTCCG
654130 TCGGGACAAATTTC-ACGCGGTCCG
1 TCGGGACAAATTTCTACGCGGTCCG
654154 TCGGGACAAAT
1 TCGGGACAAAT
654165 CTATGTGGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
24 19 0.58
25 14 0.42
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (25 bp):
TCGGGACAAATTTCTACGCGGTCCG
Found at i:654191 original size:24 final size:24
Alignment explanation
Indices: 654160--654217 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
654150 TCCGTCGGGA
*
654160 CAAA-TCTATGTGGCACTTCGGTG
1 CAAATTCTATGTGGAACTTCGGTG
* *
654183 CATATTCTATGTGGAATTTCGGTG
1 CAAATTCTATGTGGAACTTCGGTG
*
654207 CAAATTATATG
1 CAAATTCTATG
654218 AGAAGTGGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (24 bp):
CAAATTCTATGTGGAACTTCGGTG
Found at i:660863 original size:15 final size:15
Alignment explanation
Indices: 660845--660896 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
660835 ATGTTTTCTA
*
660845 TGAAAATGTTCTATG
1 TGAAAATGTTCTAAG
*
660860 TGAAAATGTGCTAAG
1 TGAAAATGTTCTAAG
*
660875 TGAAAATGTTCTACG
1 TGAAAATGTTCTAAG
660890 TGAAAAT
1 TGAAAAT
660897 ACCCTATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (15 bp):
TGAAAATGTTCTAAG
Found at i:660908 original size:30 final size:30
Alignment explanation
Indices: 660845--660921 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
660835 ATGTTTTCTA
* ***
660845 TGAAAATGTTCTATGTGAAAATGTGCTAAG
1 TGAAAATGTTCTACGTGAAAATACCCTAAG
*
660875 TGAAAATGTTCTACGTGAAAATACCCTATG
1 TGAAAATGTTCTACGTGAAAATACCCTAAG
* *
660905 TGAATATGCTCTACGTG
1 TGAAAATGTTCTACGTG
660922 GATAAAACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (30 bp):
TGAAAATGTTCTACGTGAAAATACCCTAAG
Found at i:661070 original size:25 final size:25
Alignment explanation
Indices: 661042--661102 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 25
661032 TATACAGTCA
* *
661042 TTCGGGACAAATTTCTACGTGGTCC
1 TTCGGGACAAATTTCCACGCGGTCC
661067 TTCGGGACAAA-TTCCACGCGGTCC
1 TTCGGGACAAATTTCCACGCGGTCC
*
661091 TTCAGGACAAAT
1 TTCGGGACAAAT
661103 CTATGTGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
TTCGGGACAAATTTCCACGCGGTCC
Found at i:661155 original size:24 final size:24
Alignment explanation
Indices: 661104--661155 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
661094 AGGACAAATC
* * * *
661104 TATGTGGCACTTCGGTGCATATTC
1 TATGTGGAACTTCGGTACAAATTA
*
661128 TATGTGGAATTTCGGTACAAATTA
1 TATGTGGAACTTCGGTACAAATTA
661152 TATG
1 TATG
661156 AGAAGTGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (24 bp):
TATGTGGAACTTCGGTACAAATTA
Found at i:662151 original size:27 final size:27
Alignment explanation
Indices: 662112--662167 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
662102 AATCATCATA
* *
662112 ATAATAAGGTAAACTACATGAATGATC
1 ATAATAAGATAAACTACATAAATGATC
*
662139 ATAATAAGATAAATTACATAAATGATC
1 ATAATAAGATAAACTACATAAATGATC
662166 AT
1 AT
662168 TTAATTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.29
Consensus pattern (27 bp):
ATAATAAGATAAACTACATAAATGATC
Found at i:663251 original size:74 final size:72
Alignment explanation
Indices: 663173--663344 Score: 256
Period size: 74 Copynumber: 2.4 Consensus size: 72
663163 AGTTGAAAAC
*
663173 TTGAAATGTAAAATATATTTTCAAATTATCAAAAAAAATAT-TTTAAATATATATATATATATTG
1 TTGAAATGTAAAATATATTTTCAAATAATCAAAAAAAATATATTTAAA-ATATATAT-T-TATTG
663237 AAAGATAAAG
63 AAAGATAAAG
* * * *
663247 TTGAAATGTAAAACATATTTTCGAATAATCATAAAAAATATATTTAAAATATATATTTTTTGAAA
1 TTGAAATGTAAAATATATTTTCAAATAATCAAAAAAAATATATTTAAAATATATATTTATTGAAA
663312 GATAAAG
66 GATAAAG
*
663319 TTGAAATGTAAAATATATCTTCAAAT
1 TTGAAATGTAAAATATATTTTCAAAT
663345 CTAACCATCG
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
72 37 0.42
73 1 0.01
74 45 0.51
75 6 0.07
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (72 bp):
TTGAAATGTAAAATATATTTTCAAATAATCAAAAAAAATATATTTAAAATATATATTTATTGAAA
GATAAAG
Found at i:664087 original size:6 final size:6
Alignment explanation
Indices: 664076--664106 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
664066 TATAGGGGAC
664076 GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA G
1 GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA G
664107 TGATTACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAGCA
Found at i:673295 original size:20 final size:20
Alignment explanation
Indices: 673270--673316 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
673260 TATTGTTCAG
673270 AAGACT-GACATATGACTCAA
1 AAGACTAGACATATGA-TCAA
*
673290 AAGACTTAGACATATGATCGA
1 AAGAC-TAGACATATGATCAA
673311 AAGACT
1 AAGACT
673317 TATAGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
22 9 0.38
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (20 bp):
AAGACTAGACATATGATCAA
Found at i:673315 original size:21 final size:22
Alignment explanation
Indices: 673276--673318 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
673266 TCAGAAGACT
673276 GACATATGACTCAAAAGACTTA
1 GACATATGACTCAAAAGACTTA
*
673298 GACATATGA-TCGAAAGACTTA
1 GACATATGACTCAAAAGACTTA
673319 TAGATGACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (22 bp):
GACATATGACTCAAAAGACTTA
Found at i:677661 original size:12 final size:12
Alignment explanation
Indices: 677644--677668 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
677634 AAAAATATAC
677644 ATATATACATAT
1 ATATATACATAT
677656 ATATATACATAT
1 ATATATACATAT
677668 A
1 A
677669 GCATTAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATACATAT
Found at i:677729 original size:16 final size:17
Alignment explanation
Indices: 677708--677762 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 17
677698 GAAAAAAATA
677708 ATAAT-AATATATGTAT
1 ATAATAAATATATGTAT
*
677724 ATAATAAAATAAATGTAAAT
1 ATAAT-AAATATATGT--AT
677744 ATATATAAATATATGTAT
1 ATA-ATAAATATATGTAT
677762 A
1 A
677763 AATGAGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 5 0.16
18 11 0.34
20 14 0.44
21 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
ATAATAAATATATGTAT
Done.