Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008621.1 Hibiscus syriacus cultivar Beakdansim tig00111584_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: 1991651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:574680 original size:12 final size:12
Alignment explanation
Indices: 574663--574694 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
574653 AATTTTTCGA
574663 TGCTAACTCTGC
1 TGCTAACTCTGC
574675 TGCTAACTCTGC
1 TGCTAACTCTGC
574687 TGCTAACT
1 TGCTAACT
574695 AAGGTGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (12 bp):
TGCTAACTCTGC
Found at i:577548 original size:20 final size:20
Alignment explanation
Indices: 577523--577694 Score: 274
Period size: 20 Copynumber: 8.6 Consensus size: 20
577513 TGATTCAATC
* *
577523 AGTATCGATATCGAAGGCAG
1 AGTATCGATACCGAAGGGAG
577543 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
*
577563 AGTATCGATACTGAAGGGAG
1 AGTATCGATACCGAAGGGAG
577583 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
577603 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
*
577623 AGTATCGATATCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
577643 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
* *
577663 AGTATTGATACCGAAGAGA-
1 AGTATCGATACCGAAGGGAG
577682 ATGTATCGATACC
1 A-GTATCGATACC
577695 ATTCAAAAGA
Statistics
Matches: 142, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
19 1 0.01
20 141 0.99
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGAG
Found at i:577763 original size:22 final size:22
Alignment explanation
Indices: 577735--577788 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
577725 TACCATAGCA
577735 TAGTATCGATACCATAGTATGG
1 TAGTATCGATACCATAGTATGG
* * *
577757 TAGTATCAATTCCATGGTATGG
1 TAGTATCGATACCATAGTATGG
577779 --GTATCGATAC
1 TAGTATCGATAC
577789 TGAAGAGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 8 0.30
22 19 0.70
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (22 bp):
TAGTATCGATACCATAGTATGG
Found at i:578196 original size:54 final size:54
Alignment explanation
Indices: 578113--578719 Score: 770
Period size: 54 Copynumber: 11.3 Consensus size: 54
578103 TACCAAATAA
* * *
578113 GCACTAAGTGTGCATTTCACGGAATTCATCCTGTGTAGATGAATAATCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * *
578167 ACACTAAGTGTGCACTACACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
** * * * * *
578221 ATAATAAGTGTACATCTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * *
578275 ACACTAAGTGTGCATCTCACAGAATTCATCCTATGTGGATAAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * *
578329 GCACTAAGTATGCATTTCAAGGAATTCATCTTATGTTGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * *
578383 GCACTAAGTATGCATTTCACGGAATTTATCCTATGTAGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
*
578437 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCC
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * *
578491 GCACTAAGTGTGCATTTAATGAAATTCATCCTA--TGGATGAATAACCGTTTTG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
*
578543 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * *
578596 GCACTAAGTGTGCATTTCACGAAATTTATCCTATGTGGATGAATAATCATTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* *** * ** ** * *
578650 GCACTATGTGTGCAAACCACGAAATTCATAATATGTTTATGAATAACCGTATGG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* *
578704 GCACTACGGGTGCATT
1 GCACTAAGTGTGCATT
578720 ATAAAGAAAT
Statistics
Matches: 485, Mismatches: 65, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
52 47 0.10
53 50 0.10
54 388 0.80
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
Found at i:582084 original size:20 final size:20
Alignment explanation
Indices: 582061--582111 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
582051 TGAGTATTGG
*
582061 TACTGGATGAACAGTATCGA
1 TACTAGATGAACAGTATCGA
582081 TACTAGATGAACAGTATCGA
1 TACTAGATGAACAGTATCGA
582101 TACTAGATGAA
1 TACTAGATGAA
582112 TTGGGATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (20 bp):
TACTAGATGAACAGTATCGA
Found at i:582826 original size:30 final size:30
Alignment explanation
Indices: 582792--582850 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
582782 TAATAAACCC
* *
582792 TTGTATAATGTTCTAGATAAGATAACGAGA
1 TTGTATAATGTTATAGATAAGAGAACGAGA
582822 TTGTATAATGTTATAGATAAGAGAACGAG
1 TTGTATAATGTTATAGATAAGAGAACGAG
582851 CGAGATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (30 bp):
TTGTATAATGTTATAGATAAGAGAACGAGA
Found at i:600994 original size:21 final size:20
Alignment explanation
Indices: 600947--600994 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
600937 TTTGCATATG
* *
600947 TATTTTACAAATTTATGTTT
1 TATTTTACAAATCTAGGTTT
**
600967 TGCTTTACAAATCTAGGATTT
1 TATTTTACAAATCTAGG-TTT
600988 TATTTTA
1 TATTTTA
600995 TTGTTAATAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (20 bp):
TATTTTACAAATCTAGGTTT
Found at i:602807 original size:16 final size:16
Alignment explanation
Indices: 602786--602816 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
602776 TTACCAGACC
602786 TGTTTTCAACCTGACA
1 TGTTTTCAACCTGACA
*
602802 TGTTTTTAACCTGAC
1 TGTTTTCAACCTGAC
602817 CTGTAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (16 bp):
TGTTTTCAACCTGACA
Found at i:602861 original size:16 final size:16
Alignment explanation
Indices: 602839--602876 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
602829 CGACTTGTTA
602839 ATTACCTGATCTGATAT
1 ATTACCTGA-CTGATAT
*
602856 -TTACCTGACTTATAT
1 ATTACCTGACTGATAT
602871 ATTACC
1 ATTACC
602877 ATGGACGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (16 bp):
ATTACCTGACTGATAT
Found at i:603088 original size:14 final size:14
Alignment explanation
Indices: 603066--603112 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
603056 TGCAAAGGAA
*
603066 AATTAATATAGTTT
1 AATTTATATAGTTT
603080 AATTTATATA----
1 AATTTATATAGTTT
603090 AA-TTATATAGTTT
1 AATTTATATAGTTT
603103 AATTTATATA
1 AATTTATATA
603113 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:603099 original size:23 final size:24
Alignment explanation
Indices: 603065--603114 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
603055 ATGCAAAGGA
603065 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
603089 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
603112 AAA
1 AAA
603115 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:603608 original size:10 final size:10
Alignment explanation
Indices: 603595--603642 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
603585 CAGTAGGTAG
603595 CAGGCAGCAA
1 CAGGCAGCAA
*
603605 CAGGCAACAA
1 CAGGCAGCAA
*
603615 CAGGCAGCAG
1 CAGGCAGCAA
* *
603625 TAGGCAACAA
1 CAGGCAGCAA
603635 CAGGCAGC
1 CAGGCAGC
603643 TGCAGGCAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.40, C:0.29, G:0.29, T:0.02
Consensus pattern (10 bp):
CAGGCAGCAA
Found at i:603649 original size:20 final size:20
Alignment explanation
Indices: 603595--603650 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
603585 CAGTAGGTAG
*
603595 CAGGCAGCAACAGGCAACAA
1 CAGGCAGCAGCAGGCAACAA
*
603615 CAGGCAGCAGTAGGCAACAA
1 CAGGCAGCAGCAGGCAACAA
*
603635 CAGGCAGCTGCAGGCA
1 CAGGCAGCAGCAGGCA
603651 GAATTTCTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.29, G:0.30, T:0.04
Consensus pattern (20 bp):
CAGGCAGCAGCAGGCAACAA
Found at i:605814 original size:13 final size:13
Alignment explanation
Indices: 605796--605863 Score: 100
Period size: 13 Copynumber: 5.2 Consensus size: 13
605786 TGCGTCATAA
*
605796 ATTTATGACGCGC
1 ATTTATGACACGC
605809 ATTTATGACACGC
1 ATTTATGACACGC
605822 ATTTATGACACGC
1 ATTTATGACACGC
* *
605835 ATTTATGACGCGT
1 ATTTATGACACGC
*
605848 ATTTATGACACTC
1 ATTTATGACACGC
605861 ATT
1 ATT
605864 GCGCATCATT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:605937 original size:85 final size:85
Alignment explanation
Indices: 605835--605999 Score: 201
Period size: 85 Copynumber: 1.9 Consensus size: 85
605825 TATGACACGC
* * * *
605835 ATTTATGACGCGTATTTATGACACT-CATTGCGCATCATTGAAGCCCCCGTCA-TA-AATGAAGA
1 ATTTATGACACGCATTTATGAC-CTACATTGCGCATCATTGAAGCACACGTCATTAGAA--AAGA
*
605897 CGACACACATTTGTGTGTAATAA
63 CGACACACATTCGTGTGTAATAA
* ** *
605920 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAGAAAAGATGA
1 ATTTATGACACGCATTTATGACCTACATTGCGCATCATTGAAGCACACGTCATTAGAAAAGACGA
605985 CACACATTCGTGTGT
66 CACACATTCGTGTGT
606000 CGTGATTGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 63 0.93
86 2 0.03
87 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACCTACATTGCGCATCATTGAAGCACACGTCATTAGAAAAGACGA
CACACATTCGTGTGTAATAA
Found at i:606025 original size:2 final size:2
Alignment explanation
Indices: 606018--606045 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
606008 TATGTCGTAA
606018 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
606046 TGTAGATTGA
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:607952 original size:2 final size:2
Alignment explanation
Indices: 607945--607990 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
607935 AATGAAATCA
607945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
607987 AT AT
1 AT AT
607991 TTCTAATATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:608628 original size:16 final size:15
Alignment explanation
Indices: 608602--608631 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
608592 TATTTTGGAC
608602 AAAGGGAAAAAGGGA
1 AAAGGGAAAAAGGGA
608617 AAAGGTGAAAAAGGG
1 AAAGG-GAAAAAGGG
608632 GAAGCATGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (15 bp):
AAAGGGAAAAAGGGA
Found at i:609564 original size:120 final size:120
Alignment explanation
Indices: 609351--609608 Score: 444
Period size: 120 Copynumber: 2.1 Consensus size: 120
609341 GTAAAAATTA
*
609351 AACAGTAGCTACAAATTAAACAGTTTATTTAAATCTTAAATAAAGGAAACTAACAACCTTATACA
1 AACAGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGAAACTAACAACCTTATACA
*
609416 ACCAATCCGAATAAACAACCAACAACACAAACAATGACTACAGAGGAAACAAATC
66 ACCAATCCGAATAAACAACCAACAACACAAACAAAGACTACAGAGGAAACAAATC
* *
609471 AACAGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGCAGCTAACAACCTTATACA
1 AACAGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGAAACTAACAACCTTATACA
* *
609536 AGCAATCCGAATGAACAACCAACAACACAAACAAAGACTACAGAGGAAACAAATC
66 ACCAATCCGAATAAACAACCAACAACACAAACAAAGACTACAGAGGAAACAAATC
* *
609591 AATAGTAGCTATAAATTA
1 AACAGTAGCTACAAATTA
609609 TAGTATATTT
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 130 1.00
ACGTcount: A:0.51, C:0.20, G:0.10, T:0.19
Consensus pattern (120 bp):
AACAGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGAAACTAACAACCTTATACA
ACCAATCCGAATAAACAACCAACAACACAAACAAAGACTACAGAGGAAACAAATC
Found at i:609890 original size:24 final size:24
Alignment explanation
Indices: 609830--609890 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 24
609820 GTGAAAATGC
609830 TCGG-TTAGGGTTTTAGGTTCGGGT
1 TCGGTTTAGGGTTTTA-GTTCGGGT
* *
609854 TCAGATTCA-GGTTTGTA-TTCGGGT
1 TC-GGTTTAGGGTTT-TAGTTCGGGT
609878 TCGGTTTAGGGTT
1 TCGGTTTAGGGTT
609891 CGGGTTTGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
23 4 0.14
24 15 0.52
25 6 0.21
26 4 0.14
ACGTcount: A:0.11, C:0.10, G:0.36, T:0.43
Consensus pattern (24 bp):
TCGGTTTAGGGTTTTAGTTCGGGT
Found at i:609921 original size:12 final size:12
Alignment explanation
Indices: 609844--609921 Score: 52
Period size: 12 Copynumber: 6.5 Consensus size: 12
609834 TTAGGGTTTT
609844 AGGTTCGGGTTC
1 AGGTTCGGGTTC
* *
609856 AGATTCAGGTT-
1 AGGTTCGGGTTC
* *
609867 TGTATTCGGGTTC
1 AG-GTTCGGGTTC
*
609880 -GGTTTAGGGTTC
1 AGG-TTCGGGTTC
* *
609892 GGGTTTGGGTTC
1 AGGTTCGGGTTC
*
609904 GGGTTCGGGTTC
1 AGGTTCGGGTTC
609916 AGGTTC
1 AGGTTC
609922 AGTTCGGTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
11 1 0.02
12 50 0.94
13 2 0.04
ACGTcount: A:0.09, C:0.13, G:0.40, T:0.38
Consensus pattern (12 bp):
AGGTTCGGGTTC
Found at i:609921 original size:18 final size:18
Alignment explanation
Indices: 609844--609933 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 18
609834 TTAGGGTTTT
* *
609844 AGGTTCGGGTTCAGATTC
1 AGGTTCGGGTTCGGGTTC
* **
609862 AGGTTTGTATTCGGGTTC
1 AGGTTCGGGTTCGGGTTC
* *
609880 -GGTTTAGGGTTCGGGTTT
1 AGG-TTCGGGTTCGGGTTC
*
609898 GGGTTCGGGTTCGGGTTC
1 AGGTTCGGGTTCGGGTTC
*
609916 AGGTTC-AGTTC-GGTTC
1 AGGTTCGGGTTCGGGTTC
609932 AG
1 AG
609934 ATTTAGGTTC
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
16 7 0.12
17 6 0.11
18 42 0.74
19 2 0.04
ACGTcount: A:0.10, C:0.13, G:0.39, T:0.38
Consensus pattern (18 bp):
AGGTTCGGGTTCGGGTTC
Found at i:609931 original size:5 final size:6
Alignment explanation
Indices: 609871--609921 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
609861 CAGGTTTGTA
* * * *
609871 TTCGGG TTCGGT TTAGGG TTCGGG TTTGGG TTCGGG TTCGGG TTCAGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
609919 TTC
1 TTC
609922 AGTTCGGTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.04, C:0.14, G:0.43, T:0.39
Consensus pattern (6 bp):
TTCGGG
Found at i:610403 original size:18 final size:19
Alignment explanation
Indices: 610361--610416 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
610351 GATGAACTTC
610361 TAGAGAGAAGACAGAGAAT
1 TAGAGAGAAGACAGAGAAT
* * *
610380 TTGAGAGAA-ACGGAGAGT
1 TAGAGAGAAGACAGAGAAT
*
610398 TAGAGAGAGAGAGAGAGAA
1 TAGAGAGA-AGACAGAGAA
610417 CAAAATGAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 14 0.50
19 9 0.32
20 5 0.18
ACGTcount: A:0.48, C:0.04, G:0.38, T:0.11
Consensus pattern (19 bp):
TAGAGAGAAGACAGAGAAT
Found at i:610700 original size:6 final size:6
Alignment explanation
Indices: 610691--610737 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
610681 ATAGATTATA
*
610691 ATTAAT ATTAAT ATTAAT ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
610736 AT
1 AT
610738 AGTTTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 1 0.03
5 9 0.25
6 26 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:610706 original size:34 final size:32
Alignment explanation
Indices: 610663--610772 Score: 95
Period size: 34 Copynumber: 3.4 Consensus size: 32
610653 ACTATTTATA
610663 ATTAATATTAAAATAATTATAGATTATAATTAAT
1 ATTAATA-TAAAATAATTATA-ATTATAATTAAT
* *
610697 ATTAATAT-TAAT-ATTA-ATATTA-ACTT-AT
1 ATTAATATAAAATAATTATA-ATTATAATTAAT
* * *
610725 ATTAATATAATATAGTTTATAATTTGTAATTAAT
1 ATTAATATAAAATA-ATTATAA-TTATAATTAAT
610759 ATTAATATAAAATA
1 ATTAATATAAAATA
610773 TAGTCTATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
28 10 0.17
29 5 0.08
30 5 0.08
31 8 0.13
32 6 0.10
33 4 0.07
34 22 0.37
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (32 bp):
ATTAATATAAAATAATTATAATTATAATTAAT
Found at i:610712 original size:18 final size:17
Alignment explanation
Indices: 610685--610737 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
610675 ATAATTATAG
610685 ATTATAATTAATATTAAT
1 ATTAT-ATTAATATTAAT
610703 ATTAATATTAATATTAA-
1 ATT-ATATTAATATTAAT
*
610720 CTTATATTAATA-TAAT
1 ATTATATTAATATTAAT
610736 AT
1 AT
610738 AGTTTATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 3 0.10
16 10 0.32
17 2 0.06
18 14 0.45
19 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATATTAATATTAAT
Found at i:610714 original size:22 final size:22
Alignment explanation
Indices: 610644--610737 Score: 63
Period size: 22 Copynumber: 4.1 Consensus size: 22
610634 ATATAAATTT
*
610644 TATTAATTAACTATTTATAATTAA
1 TATTAATTAA-TATTAAT-ATTAA
*
610668 TATTAA--AATAATTATAGATT-A
1 TATTAATTAAT-ATTA-ATATTAA
610689 TAATTAATATTAATATTAATATTAA
1 T-ATT-A-ATTAATATTAATATTAA
610714 TATTAACTT-ATATTAATA-TAA
1 TATTAA-TTAATATTAATATTAA
610735 TAT
1 TAT
610738 AGTTTATAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 21
0.71 0.04 0.26
Matches are distributed among these distances:
21 9 0.16
22 21 0.36
23 5 0.09
24 14 0.24
25 6 0.10
26 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (22 bp):
TATTAATTAATATTAATATTAA
Found at i:610825 original size:21 final size:20
Alignment explanation
Indices: 610789--610833 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
610779 ATAACATTAA
610789 TATATATATATGTTATAAAC
1 TATATATATATGTTATAAAC
610809 TATATAGTATA-GTTTATAAAC
1 TATATA-TATATG-TTATAAAC
610830 TATA
1 TATA
610834 GTTAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (20 bp):
TATATATATATGTTATAAAC
Found at i:610828 original size:59 final size:61
Alignment explanation
Indices: 610764--610880 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 61
610754 TTAATATTAA
* *
610764 TATAAAATATAGTCT-ATA-ACATTAA-T-ATATA-TATATGTTATAAACTATATAGTATAGTT
1 TATAAAATATAGT-TAATATA-ATTAATTAATATAGTATAT-TTATAAACAATATACTATAGTT
*
610823 TATAAACTATAGTTAATATAATTAATTAATATAGTATATTTATAAACAATATACTATA
1 TATAAAATATAGTTAATATAATTAATTAATATAGTATATTTATAAACAATATACTATA
610881 TAAATTATAG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
58 1 0.02
59 20 0.40
60 2 0.04
61 22 0.44
62 5 0.10
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (61 bp):
TATAAAATATAGTTAATATAATTAATTAATATAGTATATTTATAAACAATATACTATAGTT
Found at i:610873 original size:20 final size:21
Alignment explanation
Indices: 610790--610882 Score: 63
Period size: 20 Copynumber: 4.6 Consensus size: 21
610780 TAACATTAAT
* *
610790 ATATA-TATATGTTATAAACT
1 ATATAGTATATATTATAAACA
610810 ATATAGTATAGT-TTATAAAC-
1 ATATAGTATA-TATTATAAACA
* **
610830 -TATAGT-TAATATAATTAATTA
1 ATATAGTAT-ATATTA-TAAACA
610851 ATATAGTATAT-TTATAAACA
1 ATATAGTATATATTATAAACA
*
610871 ATATACTATATA
1 ATATAGTATATA
610883 AATTATAGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
18 2 0.04
19 9 0.16
20 22 0.39
21 14 0.25
22 9 0.16
23 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (21 bp):
ATATAGTATATATTATAAACA
Found at i:611075 original size:24 final size:20
Alignment explanation
Indices: 611024--611082 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
611014 TATAGGTTAC
611024 ATATATAGTTTATATAACAT
1 ATATATAGTTTATATAACAT
*
611044 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATA-ACAT
*
611067 ATACTATAGGTTATAT
1 ATA-TATAGTTTATAT
611083 GTATATAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 7 0.22
21 2 0.06
22 11 0.34
23 8 0.25
24 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (20 bp):
ATATATAGTTTATATAACAT
Found at i:611112 original size:20 final size:21
Alignment explanation
Indices: 611021--611143 Score: 79
Period size: 20 Copynumber: 6.1 Consensus size: 21
611011 AACTATAGGT
611021 TACATAT--ATAGTTTATATA
1 TACATATACATAGTTTATATA
*
611040 -ACATATAAATAGATTGTATATA
1 TACATATACATAG-TT-TATATA
*
611062 TACATATACTATAG-GT-TATA
1 TACATATAC-ATAGTTTATATA
*
611082 T--GTAT--ATAGTTTATATA
1 TACATATACATAGTTTATATA
611099 TAC-TATACATAGTTTATA-A
1 TACATATACATAGTTTATATA
*
611118 TACATGTACTATAAGTTATATATA
1 TACATATAC-AT-AGTT-TATATA
611142 TA
1 TA
611144 GTTTATGTGT
Statistics
Matches: 82, Mismatches: 5, Indels: 29
0.71 0.04 0.25
Matches are distributed among these distances:
15 4 0.05
16 1 0.01
17 5 0.06
18 12 0.15
19 4 0.05
20 23 0.28
21 5 0.06
22 10 0.12
23 11 0.13
24 7 0.09
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (21 bp):
TACATATACATAGTTTATATA
Found at i:611208 original size:13 final size:13
Alignment explanation
Indices: 611190--611214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
611180 TAACTATTGT
611190 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
611203 TTAGGGTTTAGG
1 TTAGGGTTTAGG
611215 ATTTCTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
TTAGGGTTTAGGG
Found at i:611309 original size:2 final size:2
Alignment explanation
Indices: 611302--611335 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
611292 TTATATGGTT
*
611302 TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T
611336 TGTACATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.97
3 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:611346 original size:20 final size:21
Alignment explanation
Indices: 611306--611350 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
611296 ATGGTTTATA
*
611306 TATATATATATATATATAGTT
1 TATATATATATATACATAGTT
*
611327 TATATATAT-TGTACATAGTT
1 TATATATATATATACATAGTT
611347 TATA
1 TATA
611351 CATACATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TATATATATATATACATAGTT
Found at i:611381 original size:35 final size:36
Alignment explanation
Indices: 611341--611411 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
611331 TATATTGTAC
*
611341 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
611376 ATAGTTTACATGTATACATATACTATAAGTTACATA
1 ATAGTTTA-ATACATACATATACTATAAGTTACATA
611412 AATTAACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 7 0.23
37 24 0.77
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.39
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:611478 original size:16 final size:16
Alignment explanation
Indices: 611457--611500 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
611447 ACATATATAA
611457 TTTATATAAACTGTTG
1 TTTATATAAACTGTTG
*
611473 TTTATATAAACCGTTG
1 TTTATATAAACTGTTG
611489 TTTATATAAACT
1 TTTATATAAACT
611501 ATATATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (16 bp):
TTTATATAAACTGTTG
Found at i:611644 original size:2 final size:2
Alignment explanation
Indices: 611637--611765 Score: 51
Period size: 2 Copynumber: 66.5 Consensus size: 2
611627 TGTTTCTTTA
* * *
611637 AT AT AT AT AT AT AT -T AT AT TT CT -T AT AT -T AGT -T AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
611676 AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AT AT AT AA
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
611715 ACT AT AT AT TT AT AT A- AT TT AT AT AT AGT TT AT AT AC AT AGT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T
*
611757 TT AT AT AT A
1 AT AT AT AT A
611766 GTTCACATAA
Statistics
Matches: 93, Mismatches: 20, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
1 9 0.10
2 78 0.84
3 6 0.06
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:611737 original size:17 final size:17
Alignment explanation
Indices: 611688--611740 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
611678 ATATATATAC
*
611688 TATATTAATATAAATTA
1 TATATTTATATAAATTA
*
611705 TA-A--TATATAAACTA
1 TATATTTATATAAATTA
*
611719 TATATTTATATAATTTA
1 TATATTTATATAAATTA
611736 TATAT
1 TATAT
611741 AGTTTATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 11 0.38
15 1 0.03
16 1 0.03
17 16 0.55
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATTTATATAAATTA
Found at i:611739 original size:11 final size:11
Alignment explanation
Indices: 611717--611768 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
611707 ATATATAAAC
611717 TATATA-TTTA
1 TATATAGTTTA
611727 TATA-A-TTTA
1 TATATAGTTTA
611736 TATATAGTTTA
1 TATATAGTTTA
611747 TATACATAGTTTA
1 TAT--ATAGTTTA
611760 TATATAGTT
1 TATATAGTT
611769 CACATAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.24
10 5 0.13
11 13 0.34
13 11 0.29
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:611741 original size:13 final size:13
Alignment explanation
Indices: 611734--611765 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
611724 TTATATAATT
611734 TATATATAGTTTA
1 TATATATAGTTTA
*
611747 TATACATAGTTTA
1 TATATATAGTTTA
611760 TATATA
1 TATATA
611766 GTTCACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (13 bp):
TATATATAGTTTA
Found at i:611748 original size:26 final size:25
Alignment explanation
Indices: 611719--611791 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
611709 ATATAAACTA
*
611719 TATATTTATATAATTTATATATAGTT
1 TATA-TTACATAATTTATATATAGTT
*
611745 TATA-TACATAGTTTATATATAGTT
1 TATATTACATAATTTATATATAGTT
* * *
611769 CACATAAACATAATTTATATATA
1 TATAT-TACATAATTTATATATA
611792 TAGCTTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 20 0.51
26 19 0.49
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (25 bp):
TATATTACATAATTTATATATAGTT
Found at i:611759 original size:24 final size:25
Alignment explanation
Indices: 611728--611791 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 25
611718 ATATATTTAT
* *
611728 ATAATTTATATATAGTT-TATATAC
1 ATAATTTATATATAGTTACATAAAC
*
611752 ATAGTTTATATATAGTTCACATAAAC
1 ATAATTTATATATAGTT-ACATAAAC
611778 ATAATTTATATATA
1 ATAATTTATATATA
611792 TAGCTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 16 0.47
26 18 0.53
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (25 bp):
ATAATTTATATATAGTTACATAAAC
Found at i:611801 original size:26 final size:26
Alignment explanation
Indices: 611734--611801 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
611724 TTATATAATT
* * *
611734 TATATATAGTTTATATACATAGTTTA
1 TATATATAGCTTATAAACATAATTTA
* **
611760 TATATAGT-TCACATAAACATAATTTA
1 TATATA-TAGCTTATAAACATAATTTA
611786 TATATATAGCTTATAA
1 TATATATAGCTTATAA
611802 TAATTATATA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
25 1 0.03
26 29 0.94
27 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (26 bp):
TATATATAGCTTATAAACATAATTTA
Found at i:611826 original size:17 final size:18
Alignment explanation
Indices: 611787--611826 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
611777 CATAATTTAT
611787 ATATATAGCTTATAATAA
1 ATATATAGCTTATAATAA
* *
611805 TTATATAGTTTA-AATAA
1 ATATATAGCTTATAATAA
611822 ATATA
1 ATATA
611827 GTTTATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (18 bp):
ATATATAGCTTATAATAA
Found at i:611827 original size:15 final size:15
Alignment explanation
Indices: 611807--611837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
611797 TATAATAATT
611807 ATATAGTTTAAATAA
1 ATATAGTTTAAATAA
*
611822 ATATAGTTTATATAA
1 ATATAGTTTAAATAA
611837 A
1 A
611838 CTTATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
ATATAGTTTAAATAA
Found at i:611856 original size:46 final size:47
Alignment explanation
Indices: 611758--611855 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 47
611748 ATACATAGTT
*
611758 TATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAA
1 TATATATAGTTCAAATAAACATAATTTATATATATAGCTTATAATAA
* * * * *
611805 T-TATATAGTTTAAATAAATATAGTTTATATA-A-A-CTTATATTTA
1 TATATATAGTTCAAATAAACATAATTTATATATATAGCTTATAATAA
611848 TATATATA
1 TATATATA
611856 TTATATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 9 0.20
44 7 0.16
45 1 0.02
46 26 0.59
47 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (47 bp):
TATATATAGTTCAAATAAACATAATTTATATATATAGCTTATAATAA
Found at i:617918 original size:19 final size:19
Alignment explanation
Indices: 617888--617934 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
617878 ATTGGAAATC
617888 GACAAAATCGGTTGAAATTT
1 GACAAAA-CGGTTGAAATTT
*
617908 GACAAAACGGTTTAAATTT
1 GACAAAACGGTTGAAATTT
617927 GACAAAAC
1 GACAAAAC
617935 TGGTAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (19 bp):
GACAAAACGGTTGAAATTT
Found at i:618142 original size:199 final size:193
Alignment explanation
Indices: 617897--618416 Score: 543
Period size: 193 Copynumber: 2.7 Consensus size: 193
617887 CGACAAAATC
* * * *
617897 GGTTGAAATTTGACAAAA-CGGTTTAAATTTGACAAAACTGGTAAAGAGCTACCAT-AATTTTTG
1 GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACC-TGAAGTCTTG
* * *
617960 A-AATTTGTATCGATACTTTTATAAGTATATGTAGCAAAGTATCGGTACTG-AGGAATTTAAAAG
65 ACAA----TATCGATACTTTTATAAGTATATGTACCAAAGTATAGGTACTGTAGGAATTGAAAAG
* *
618023 AAATGAA-AAAAG-GAAAATGTCTCGAAAATATCGATACCTTACACACATGTATCGATACATGAT
126 AAATGAATAAAAGCG--AA--TAT--AAAATATCGATACCTTACACACATGTATCGATACATGAC
*
618086 GATATAACA
185 AATATAACA
618095 GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACCTGAAGTCTTGA
1 GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACCTGAAGTCTTGA
* * * * *
618160 CAATATCTATACTTTTATAAGTATGTGTACCAAAGTATATGTACTGTAGTAATTGAAAAGAATTG
66 CAATATCGATACTTTTATAAGTATATGTACCAAAGTATAGGTACTGTAGGAATTGAAAAGAAATG
* * * *
618225 AATAATAGCGCATATAAAGTATCGATACCTTAGACACATGTATCGATACATGACAATATAACA
131 AATAAAAGCGAATATAAAATATCGATACCTTACACACATGTATCGATACATGACAATATAACA
* * * ** * * * *
618288 AGTTAAAATCTGACAAAACAAGTTTCAATTTGAAAAAACCAGTAAAGCGCTA-CTGGATA-TGTT
1 GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACCT-GA-AGTCTT
** * * * * * *
618351 GACGCTATCGATACTTTTAGAAATATATGTACCATAGTATTGGTACTTTAAGAATTGAAAAGAAA
64 GACAATATCGATACTTTTATAAGTATATGTACCAAAGTATAGGTACTGTAGGAATTGAAAAGAAA
618416 T
129 T
618417 AAAAAAATGA
Statistics
Matches: 273, Mismatches: 41, Indels: 21
0.81 0.12 0.06
Matches are distributed among these distances:
192 2 0.01
193 146 0.53
194 1 0.00
195 2 0.01
196 38 0.14
197 18 0.07
198 23 0.08
199 41 0.15
200 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (193 bp):
GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACCTGAAGTCTTGA
CAATATCGATACTTTTATAAGTATATGTACCAAAGTATAGGTACTGTAGGAATTGAAAAGAAATG
AATAAAAGCGAATATAAAATATCGATACCTTACACACATGTATCGATACATGACAATATAACA
Found at i:625614 original size:21 final size:21
Alignment explanation
Indices: 625590--625649 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
625580 CGTAAACATA
625590 AAGTATCGATACTTATTATAT
1 AAGTATCGATACTTATTATAT
625611 AAGTATCGATACTTATTATAT
1 AAGTATCGATACTTATTATAT
625632 AAGTATCGATACTT-TTAT
1 AAGTATCGATACTTATTAT
625650 TCCAGTATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (21 bp):
AAGTATCGATACTTATTATAT
Found at i:625955 original size:200 final size:200
Alignment explanation
Indices: 625611--627376 Score: 1559
Period size: 200 Copynumber: 9.1 Consensus size: 200
625601 CTTATTATAT
* *
625611 AAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGC
1 AAGTATCGATACTTATTATATAGGTATCGATACTGTTATTCCAGTATGCATCTCAAACAATTTGC
* * * * *
625676 AT-GCAAAAAAATATCGATACATATATAACAAGTATCGATACTTAGAATTTCGAAACCTTTTACT
66 -TCGC-AAAAAGTATCGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACT
* * **
625740 TTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTATCAATTTAATGATAATAGGCGT
129 TTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCGT
625805 AAACATA
194 AAACATA
* * * * *
625812 AAGTATCGATACGTT-TAATATAGGTATCAATACTATTATTCCAGTATGCTTCTTAAACAATTTG
1 AAGTATCGATAC-TTATTATATAGGTATCGATACTGTTATTCCAGTATGCATCTCAAACAATTTG
* * *
625876 CTCGTC-AAAAGCATCGATACACATGT-ACAAAGTATTGATACTTGGACTTTCGAAACCTATTAC
65 CTCG-CAAAAAGTATCGATACACATATAAC-AAGTATCGATACTTGGACTTTCGAAACCTATTAC
625939 TTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAAATCTACC-GTTTAATGATAAT-GAG
128 TTTAAAGTAATAGGTAAATTTACAATGTAAACGGT-AAAAATCTACCGGTTTAATGATAATAG-G
*
626002 CGTAAATATA
191 CGTAAACATA
* * * * *
626012 AAGTATCGATACTTATTATATAGGCATCGCTACTGTTATTCCAGTATGTATCTCAAATAATTTGT
1 AAGTATCGATACTTATTATATAGGTATCGATACTGTTATTCCAGTATGCATCTCAAACAATTTGC
** * * * *
626077 TCGCAAAAAGTATCGAT--ACAT-GGAC---TTTCGAAACCTAT-TACTTT--AAA-GTA--A--
66 TCGCAAAAAGTATCGATACACATATAACAAGTATCGATA-CT-TGGACTTTCGAAACCTATTACT
* ** * * *
626128 -T-AGGTAA-ATTTACAATGTA-AA--T----GGTAAAAATCTATCGGGTTAATGATAATAGGCG
129 TTAAAGTAATAGGTA-AATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCG
*
626183 TAAATATA
193 TAAACATA
* * **
626191 AAGTATCGATACTTATTATATATGTATCGATATTGTTATTCCAGTATAAATCTCAAACAATTTGC
1 AAGTATCGATACTTATTATATAGGTATCGATACTGTTATTCCAGTATGCATCTCAAACAATTTGC
*
626256 -AG-AAAAAGTATCGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTTT
66 TCGCAAAAAGTATCGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTTT
* * *** ** *
626319 AAAGTAATAGGTAAATTTACACTATAAATAATAAAAATCTACCTTTTTAATGATAATGGGCGTAA
131 AAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCGTAA
626384 ACATA
196 ACATA
* * * *
626389 AAGTATTGATACTTATTATATACGTATCGATAATGTTATTCTAGTATGCATCTCAAACAATTTGC
1 AAGTATCGATACTTATTATATAGGTATCGATACTGTTATTCCAGTATGCATCTCAAACAATTTGC
* * *
626454 TCGCAAAAAGTATC-ACTACACATATAACAAGTATCAATACTTGGAATTTCAAAACCTATTACTT
66 TCGCAAAAAGTATCGA-TACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTT
* * * *
626518 TAAAGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTACCGGTGTAATGATAATATGCATA
130 TAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCGTA
626583 AACATA
195 AACATA
* * * *
626589 AAATATGGATACTTATTATATAGGTATCGATATTGTTATAAT-CGGTATGCATCTCAAACAATTT
1 AAGTATCGATACTTATTATATAGGTATCGATACTGTTAT--TCCAGTATGCATCTCAAACAATTT
* * * *
626653 GCACGCAAAAAGTCTCGATACACATATAACAAGTATCAATACTTGGACTTTTGAAACCTATTACT
64 GCTCGCAAAAAGTATCGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACT
* * * *
626718 TTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAAT-TACCGATTTAATGATAATAGGCAT
129 TTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCGT
626782 AAACATA
194 AAACATA
* * * *
626789 AAGTATCAATACATT-TAATATAGGTATCGATACTTTTATTCCAGTATGCTTCTCAAACAATTTG
1 AAGTATCGATAC-TTATTATATAGGTATCGATACTGTTATTCCAGTATGCATCTCAAACAATTTG
* * * * * * * * * *
626853 CACGTC-AAAAGCATTGTTACATATGT-ACAAAGTATCGATGCTTGGAATTTTGAAAACTATTAC
65 CTCG-CAAAAAGTATCGATACACATATAAC-AAGTATCGATACTTGGACTTTCGAAACCTATTAC
* * * * * * *
626916 TATAAAGTAATAGGTAAATTAACAATGTAAAGGGTAAAAGTTTTACCGGTATAATGATAATAGGT
128 TTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAA-ATCTACCGGTTTAATGATAATAGGC
*
626981 GTATATACCT-
192 GTA-A-ACATA
* * *
626991 -AGTATCGATACTT-TATATATAGGTATCGATATTGTTAGTCCAGTATGCTTCTC-AACAATTTG
1 AAGTATCGATACTTAT-TATATAGGTATCGATACTGTTATTCCAGTATGCATCTCAAACAATTTG
* * * * * * * *
627053 CGCGCTAAAGGTATCGATAC-C--GT---AA-TTTCGAAAC-TGATTACTTT--AAA-GTA--A-
65 CTCGCAAAAAGTATCGATACACATATAACAAGTATCGATACTTG--GACTTTCGAAACCTATTAC
* ** * * * * *
627104 --T-AGGTAA-ATTTACAATGT--AA---A--CGGTAAAAGTCTACCAGTATATTGATAATAGGC
128 TTTAAAGTAATAGGTA-AATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGC
* **
627158 GTAAATACC
192 GTAAACATA
* * * *
627167 AAGTATCGATACTGT-CTATATAGGTATCGATACT-TTCATTACAGTATGCTTCTCAAGCAATTT
1 AAGTATCGATACT-TATTATATAGGTATCGATACTGTT-ATTCCAGTATGCATCTCAAACAATTT
* * * ** *
627230 ACACGCAAAAGGTATCGATACACATATATA-AAGTATCGATACTTATAATTTCGAAACCTATTAC
64 GCTCGCAAAAAGTATCGATACACATATA-ACAAGTATCGATACTTGGACTTTCGAAACCTATTAC
* * * * * * **
627294 TTTAAAGTAATAAGTTAATTTACAATGAAAATGGTAAAAGTATA-AAGTTATAATGATAATAGGC
128 TTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTT-TAATGATAATAGGC
*
627358 GTAAACATC
192 GTAAACATA
627367 AAGTATCGAT
1 AAGTATCGAT
627377 TCGTGGAATT
Statistics
Matches: 1287, Mismatches: 190, Indels: 177
0.78 0.11 0.11
Matches are distributed among these distances:
175 1 0.00
176 3 0.00
177 80 0.06
178 44 0.03
179 88 0.07
180 4 0.00
181 2 0.00
182 7 0.01
183 9 0.01
184 13 0.01
185 22 0.02
186 15 0.01
187 4 0.00
189 2 0.00
190 2 0.00
191 12 0.01
192 12 0.01
193 18 0.01
194 14 0.01
195 9 0.01
196 1 0.00
197 2 0.00
198 102 0.08
199 117 0.09
200 446 0.35
201 249 0.19
202 6 0.00
203 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (200 bp):
AAGTATCGATACTTATTATATAGGTATCGATACTGTTATTCCAGTATGCATCTCAAACAATTTGC
TCGCAAAAAGTATCGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTTT
AAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCGTAA
ACATA
Found at i:626204 original size:179 final size:176
Alignment explanation
Indices: 625904--626467 Score: 619
Period size: 179 Copynumber: 3.0 Consensus size: 176
625894 ACACATGTAC
* *
625904 AAAGTATTGATACTTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
*
625969 ACGGTAAAAAATCTACCGTTTAATGATAATGAGCGTAAATATAAAGTATCGATACTTATTATATA
66 ATGGT-AAAAATCTACCGTTTAATGATAATG-GCGTAAATATAAAGTATCGATACTTATTATATA
* * * * * *
626034 GGCATCGCTACTGTTATTCCAGTATGTATCTCAAATAATTTGTTCGCAA
129 CGTATCGATAATGTTATTCCAGTATGAATCTCAAACAATTTG-TCGCAA
626083 AAAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
* *
626148 ATGGTAAAAATCTATCGGGTTAATGATAATAGGCGTAAATATAAAGTATCGATACTTATTATATA
66 ATGGTAAAAATCTA-CCGTTTAATGATAAT-GGCGTAAATATAAAGTATCGATACTTATTATATA
* * *
626213 TGTATCGATATTGTTATTCCAGTATAAATCTCAAACAATTTG-CAG-AA
129 CGTATCGATAATGTTATTCCAGTATGAATCTCAAACAATTTGTC-GCAA
* *
626260 AAAGTATCGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTTTAAAGTA
1 AAAGTATCGAT--AC--AT-----GGA-C--T--TTCGA-------AACCTATTACTTTAAAGTA
* * ** * *
626325 ATAGGTAAATTTACACTATAAATAATAAAAATCTACCTTTTTAATGATAATGGGCGTAAACATAA
45 ATAGGTAAATTTACAATGTAAATGGTAAAAATCTACC-GTTTAATGATAAT-GGCGTAAATATAA
* * *
626390 AGTATTGATACTTATTATATACGTATCGATAATGTTATTCTAGTATGCATCTCAAACAATTTGCT
108 AGTATCGATACTTATTATATACGTATCGATAATGTTATTCCAGTATGAATCTCAAACAATTTG-T
626455 CGCAA
172 CGCAA
626460 AAAGTATC
1 AAAGTATC
626468 ACTACACATA
Statistics
Matches: 328, Mismatches: 29, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
177 14 0.04
178 10 0.03
179 150 0.46
180 1 0.00
181 2 0.01
186 2 0.01
187 1 0.00
189 1 0.00
191 4 0.01
197 1 0.00
198 130 0.40
199 1 0.00
200 11 0.03
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (176 bp):
AAAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
ATGGTAAAAATCTACCGTTTAATGATAATGGCGTAAATATAAAGTATCGATACTTATTATATACG
TATCGATAATGTTATTCCAGTATGAATCTCAAACAATTTGTCGCAA
Found at i:626370 original size:577 final size:583
Alignment explanation
Indices: 625606--627053 Score: 1721
Period size: 577 Copynumber: 2.5 Consensus size: 583
625596 CGATACTTAT
625606 TATATAAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAA
1 TATA-AAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAA
* * * *
625671 TTTGCATGCAAAAAAATATCGATACATATATAACAAGTATCGATACTTAGAATTTCGAAACCTTT
65 TTTGCACG-AAAAAAGTATCGATACATATATAACAAGTATCGATACTTGGAATTTCGAAACCTAT
*
625736 TACTTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTATCAATTTAATGATAATAG
129 TACTTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTACCAATTTAATGATAATAG
* * *
625801 GCGTAAACATAAAGTATCGATACGTTTAATATAGGTATCAATACTATTATTCCAGTATGCTTCTT
194 GCGTAAACATAAAGTATCGATAC-TTTAATATAGGTATCGATAATGTTATTCCAGTATGCTTCTT
* ** * *
625866 AAACAATTTGCTCGTC-AAAAGCATCGA-TACACATGT-ACAAAGTATTGATACTTGGACTTTCG
258 AAACAATTTGCTCG-CAAAAAGCATC-ACTACACATATAAC-AAGTATCAATACTTGGAATTTCA
* *
625928 AAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAAATCTACC-GTTTAA
320 AAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACAGT-AAAAATCTACCGGTGTAA
* * * *
625992 TGATAATGA-GCGTAAATATAAAGTATCGATACTTATTATATAGGCATCGCTACTGTTAT-TCCA
384 TGATAAT-ATGCATAAACATAAAATATCGATACTTATTATATAGGCATCGATACTGTTATAT-CA
* * *
626055 GTATGTATCTCAAATAATTT-GT-TCG-C-A-AA-AAGTATCGATACATGGACTTTCGAAACCTA
447 GTATGCATCTCAAACAATTTAGTCTCGACAATAACAAGTATCAATACATGGACTTTCGAAACCTA
* * * * *
626114 TTACTTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTATCGGGTTAATGATAATA
512 TTACTTTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAAT-TACCGAGTTAATGATAATA
*
626179 GGCGTAAA
576 GGCATAAA
* **
626187 TATAAAGTATCGATACTTATTATATATGTATCGATA-TTGTTATTCCAGTATAAATCTCAAACAA
1 TATAAAGTATCGATACTTATTATATAAGTATCGATACTT-TTATTCCAGTATGCATCTCAAACAA
* *
626251 TTTGCA-G-AAAAAGTATCGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATT
65 TTTGCACGAAAAAAGTATCGATACATATATAACAAGTATCGATACTTGGAATTTCGAAACCTATT
* * ** ** *
626314 ACTTTAAAGTAATAGGTAAATTTACACTATAAATAATAAAAATCTACCTTTTTAATGATAATGGG
130 ACTTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTACCAATTTAATGATAATAGG
* * * * * *
626379 CGTAAACATAAAGTATTGATACTTATTATATACGTATCGATAATGTTATTCTAGTATGCATCTCA
195 CGTAAACATAAAGTATCGATACTT-TAATATAGGTATCGATAATGTTATTCCAGTATGCTTCTTA
*
626444 AACAATTTGCTCGCAAAAAGTATCACTACACATATAACAAGTATCAATACTTGGAATTTCAAAAC
259 AACAATTTGCTCGCAAAAAGCATCACTACACATATAACAAGTATCAATACTTGGAATTTCAAAAC
626509 CTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTACCGGTGTAATGATA
324 CTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTACCGGTGTAATGATA
* * * *
626574 ATATGCATAAACATAAAATATGGATACTTATTATATAGGTATCGATATTGTTATAATCGGTATGC
389 ATATGCATAAACATAAAATATCGATACTTATTATATAGGCATCGATACTGTTAT-ATCAGTATGC
*
626639 ATCTCAAACAATTTGCACGCAAAAAGTCTCGATACACATATAACAAGTATCAATACTTGGACTTT
453 ATCTCAAACAATTT----------AGTCTCG----ACA-ATAACAAGTATCAATACATGGACTTT
* *
626704 TGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAATTACCGATTTAA
503 CGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAATTACCGAGTTAA
626769 TGATAATAGGCATAAA
568 TGATAATAGGCATAAA
* * * * *
626785 CATAAAGTATCAATACATT-TAATATAGGTATCGATACTTTTATTCCAGTATGCTTCTCAAACAA
1 TATAAAGTATCGATAC-TTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAA
** * * * * * * *
626849 TTTGCACGTCAAAAGCATTGTTACATATGT-ACAAAGTATCGATGCTTGGAATTTTGAAAACTAT
65 TTTGCACGAAAAAAGTATCGATACATATATAAC-AAGTATCGATACTTGGAATTTCGAAACCTAT
* * * * * ** *
626913 TACTATAAAGTAATAGGTAAATTAACAATGTAAAGGGTAAAAGTTTTACCGGTATAATGATAATA
129 TACTTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAA-ATCTACCAATTTAATGATAATA
* * * *
626978 GGTGTATATACCT--AGTATCGATACTTTATATATAGGTATCGATATTGTTAGTCCAGTATGCTT
193 GGCGTA-A-ACATAAAGTATCGATACTTTA-ATATAGGTATCGATAATGTTATTCCAGTATGCTT
*
627041 C-TCAACAATTTGC
255 CTTAAACAATTTGC
627054 GCGCTAAAGG
Statistics
Matches: 734, Mismatches: 94, Indels: 59
0.83 0.11 0.07
Matches are distributed among these distances:
576 16 0.02
577 309 0.42
578 21 0.03
579 4 0.01
580 60 0.08
581 4 0.01
589 2 0.00
590 3 0.00
595 1 0.00
597 1 0.00
598 82 0.11
599 76 0.10
600 88 0.12
601 63 0.09
602 1 0.00
603 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (583 bp):
TATAAAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAAT
TTGCACGAAAAAAGTATCGATACATATATAACAAGTATCGATACTTGGAATTTCGAAACCTATTA
CTTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTACCAATTTAATGATAATAGGC
GTAAACATAAAGTATCGATACTTTAATATAGGTATCGATAATGTTATTCCAGTATGCTTCTTAAA
CAATTTGCTCGCAAAAAGCATCACTACACATATAACAAGTATCAATACTTGGAATTTCAAAACCT
ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTACCGGTGTAATGATAAT
ATGCATAAACATAAAATATCGATACTTATTATATAGGCATCGATACTGTTATATCAGTATGCATC
TCAAACAATTTAGTCTCGACAATAACAAGTATCAATACATGGACTTTCGAAACCTATTACTTTAA
AGTAATAGGTAAATTAACAATGTAAACGCTAAAAATTACCGAGTTAATGATAATAGGCATAAA
Found at i:627215 original size:177 final size:178
Alignment explanation
Indices: 626906--627250 Score: 498
Period size: 177 Copynumber: 1.9 Consensus size: 178
626896 GGAATTTTGA
* * *
626906 AAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAAGGGTAAAAGTTTTACCGGTATAAT
1 AAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTTCTACCAGTATAAT
* * * * * *
626971 GATAATAGGTGTATATACCTAGTATCGATACTTTATATATAGGTATCGATATTGTTAGTCCAGTA
66 GATAATAGGCGTAAATACCAAGTATCGATACTGTATATATAGGTATCGATATTGTCAGTACAGTA
* * *
627036 TGCTTCTCAA-CAATTTGCGCGCTAAAGGTATCGATACCGTAATTTCG
131 TGCTTCTCAAGCAATTTACACGCAAAAGGTATCGATACCGTAATTTCG
* * *
627083 AAACTGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAG-TCTACCAGTATAT
1 AAACT-ATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTTCTACCAGTATAA
* *
627147 TGATAATAGGCGTAAATACCAAGTATCGATACTGTCTATATAGGTATCGATACTT-TCATTACAG
65 TGATAATAGGCGTAAATACCAAGTATCGATACTGTATATATAGGTATCGATA-TTGTCAGTACAG
627211 TATGCTTCTCAAGCAATTTACACGCAAAAGGTATCGATAC
129 TATGCTTCTCAAGCAATTTACACGCAAAAGGTATCGATAC
627251 ACATATATAA
Statistics
Matches: 148, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
177 80 0.54
178 68 0.46
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (178 bp):
AAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTTCTACCAGTATAAT
GATAATAGGCGTAAATACCAAGTATCGATACTGTATATATAGGTATCGATATTGTCAGTACAGTA
TGCTTCTCAAGCAATTTACACGCAAAAGGTATCGATACCGTAATTTCG
Found at i:627732 original size:14 final size:14
Alignment explanation
Indices: 627713--627744 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
627703 TCTACAAAAA
*
627713 TATTATTAATATAT
1 TATTATTAATACAT
627727 TATTATTAATACAT
1 TATTATTAATACAT
627741 TATT
1 TATT
627745 TAAAATTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTATTAATACAT
Found at i:630663 original size:30 final size:31
Alignment explanation
Indices: 630627--630687 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
630617 ATCTTTCTGG
*
630627 TACTAACTCGTTT-TTCTCTTTTGTTTGTGT
1 TACTAACTCATTTCTTCTCTTTTGTTTGTGT
* *
630657 TACTAACTTATTTCTTTTCTTTTGTTTGTGT
1 TACTAACTCATTTCTTCTCTTTTGTTTGTGT
630688 CATTTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.11, C:0.15, G:0.11, T:0.62
Consensus pattern (31 bp):
TACTAACTCATTTCTTCTCTTTTGTTTGTGT
Found at i:632362 original size:7 final size:7
Alignment explanation
Indices: 632350--632422 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 7
632340 AACAAAGAGA
632350 AAAAAAG
1 AAAAAAG
*
632357 AAAAAAC
1 AAAAAAG
*
632364 AAAGAAAA
1 AAA-AAAG
632372 AGAAAAAG
1 A-AAAAAG
*
632380 AAACAAAT
1 AAA-AAAG
632388 AAAAAAG
1 AAAAAAG
* *
632395 CAAAGAG
1 AAAAAAG
632402 -AAAAA-
1 AAAAAAG
*
632407 ACAAAAG
1 AAAAAAG
632414 AAAAAAG
1 AAAAAAG
632421 AA
1 AA
632423 GACAAGAAGC
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
6 8 0.16
7 27 0.53
8 14 0.27
9 2 0.04
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:632363 original size:21 final size:21
Alignment explanation
Indices: 632338--632419 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 21
632328 TGATCAAATC
632338 AAAACAAAGAGAA-AAAAAGAA
1 AAAACAAA-AGAAGAAAAAGAA
*
632359 AAAACAAAGAAAAAGAAAAAGAA
1 AAAAC-AA-AAGAAGAAAAAGAA
* *
632382 ACAAATAAAA-AAGCAAAGAGAA
1 A-AAACAAAAGAAG-AAAAAGAA
632404 AAAACAAAAGAA-AAAA
1 AAAACAAAAGAAGAAAA
632420 GAAGACAAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
20 3 0.06
21 15 0.30
22 17 0.34
23 12 0.24
24 3 0.06
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.01
Consensus pattern (21 bp):
AAAACAAAAGAAGAAAAAGAA
Found at i:632372 original size:20 final size:19
Alignment explanation
Indices: 632338--632393 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
632328 TGATCAAATC
632338 AAAACAAAGAGAAAAAAAGAA
1 AAAACAAAGA-AAAAAAA-AA
632359 AAAACAAAGAAAAAGAAAAA
1 AAAACAAAGAAAAA-AAAAA
* *
632379 GAAACAAATAAAAAA
1 AAAACAAAGAAAAAA
632394 GCAAAGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 18 0.56
21 13 0.41
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAACAAAGAAAAAAAAAA
Found at i:632373 original size:6 final size:6
Alignment explanation
Indices: 632351--632418 Score: 50
Period size: 6 Copynumber: 10.8 Consensus size: 6
632341 ACAAAGAGAA
* * *
632351 AAAAAG AAAAA- ACAAAG AAAAAG AAAAAG AAACAAATA AAAAAG CAAAGAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AA-AAA-G AAAAAG -AAAAAG
632402 AAAAA- ACAAAAG AAAAA
1 AAAAAG A-AAAAG AAAAA
632419 AGAAGACAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
5 5 0.10
6 28 0.57
7 11 0.22
8 5 0.10
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:632374 original size:27 final size:26
Alignment explanation
Indices: 632343--632422 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 26
632333 AAATCAAAAC
*
632343 AAAGAGAAAAAAAGAAA-AAACAAAGA
1 AAAGAGAAAAAAACAAATAAA-AAAGA
*
632369 AAA-AGAAAAAGAAACAAATAAAAAAGC
1 AAAGAG-AAAA-AAACAAATAAAAAAGA
*
632396 AAAGAG-AAAAAACAAAAGAAAAAAGA
1 AAAGAGAAAAAAAC-AAATAAAAAAGA
632422 A
1 A
632423 GACAAGAAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
25 6 0.13
26 21 0.47
27 13 0.29
28 5 0.11
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.01
Consensus pattern (26 bp):
AAAGAGAAAAAAACAAATAAAAAAGA
Found at i:632399 original size:20 final size:18
Alignment explanation
Indices: 632349--632416 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 18
632339 AAACAAAGAG
632349 AAAAAAAGAAA-AAACAA
1 AAAAAAAGAAAGAAACAA
*
632366 AGAAAAAGAAAAAGAAACAA
1 A-AAAAA-AGAAAGAAACAA
632386 ATAAAAAAGCAAAGAGAA-AA
1 A-AAAAAAG-AAAGA-AACAA
*
632406 AACAAAAGAAA
1 AAAAAAAGAAA
632417 AAAGAAGACA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
17 1 0.02
18 8 0.19
19 11 0.26
20 20 0.48
21 2 0.05
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (18 bp):
AAAAAAAGAAAGAAACAA
Found at i:632420 original size:21 final size:21
Alignment explanation
Indices: 632338--632421 Score: 75
Period size: 21 Copynumber: 3.9 Consensus size: 21
632328 TGATCAAATC
632338 AAAACAAAGAGAAAAAA-AGAA
1 AAAACAAA-AGAAAAAAGAGAA
*
632359 AAAAC-AAAG-AAAAAGAAAA
1 AAAACAAAAGAAAAAAGAGAA
*
632378 AGAAACAAATAAAAAAGCAAAGAGAA
1 A-AAAC-AA-AAGAAA--AAAGAGAA
632404 AAAACAAAAGAAAAAAGA
1 AAAACAAAAGAAAAAAGA
632422 AGACAAGAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
18 5 0.10
19 6 0.12
20 6 0.12
21 10 0.20
22 1 0.02
23 7 0.14
24 4 0.08
25 4 0.08
26 8 0.16
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (21 bp):
AAAACAAAAGAAAAAAGAGAA
Found at i:633518 original size:32 final size:32
Alignment explanation
Indices: 633477--633546 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
633467 TGAAGCAAGA
* *
633477 AACATCGAATGTTGGGGCATCTTTGGAGATTC
1 AACATCGAATATTGGAGCATCTTTGGAGATTC
*
633509 AACATCGAATATTGGAGCATCTTTGGGGATTC
1 AACATCGAATATTGGAGCATCTTTGGAGATTC
633541 AACATC
1 AACATC
633547 CTGATGCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (32 bp):
AACATCGAATATTGGAGCATCTTTGGAGATTC
Found at i:633711 original size:60 final size:62
Alignment explanation
Indices: 633619--633782 Score: 201
Period size: 60 Copynumber: 2.6 Consensus size: 62
633609 CAGTATTCTT
* *
633619 TGAGTTGTTTCTCTAGAAAAAAAATTTGTCTCTTGAGACAATTTCTTTT-A-AAAAAA-ATA
1 TGAGTTGTTTCTCTAGAAACAAATTTTGTCTCTTGAGACAATTTCTTTTGAGAAAAAATATA
* * *
633678 TGAGTCTGTTTCTCTGGAAACAAATTTTGTCTCTTCAGACAATTTCTTTTGAGAAAAAATATT
1 TGAGT-TGTTTCTCTAGAAACAAATTTTGTCTCTTGAGACAATTTCTTTTGAGAAAAAATATA
* *
633741 TGAGATTGTTTC-CTTTGAAACAAAATTTTGTCTCTCGAGACA
1 TGAG-TTGTTTCTC-TAGAAAC-AAATTTTGTCTCTTGAGACA
633783 GCTTTTCTTG
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
59 5 0.06
60 40 0.44
61 1 0.01
62 7 0.08
63 18 0.20
64 19 0.21
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (62 bp):
TGAGTTGTTTCTCTAGAAACAAATTTTGTCTCTTGAGACAATTTCTTTTGAGAAAAAATATA
Found at i:634393 original size:3 final size:3
Alignment explanation
Indices: 634376--634409 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
634366 TCTACAAAAA
*
634376 TAT TAT TAA TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
634410 ATACATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:637377 original size:224 final size:226
Alignment explanation
Indices: 636903--637398 Score: 723
Period size: 224 Copynumber: 2.2 Consensus size: 226
636893 ATGACAAACT
* *
636903 CTACTTGTTTTGTTATTATGGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCAGAT
1 CTACTTGTTATGTTATTATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCAGAT
*
636968 TTCTAAGGCTTCATCAGCTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTTATAATAT
66 TTCTAAGGCTTCATCAGCTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATAT
* *
637033 TGGTAACAAATCAAGTAATTAACCTATTTTATTATCGTCGGATTTCTAAGGCTACATAAACTTTA
131 TGATAACAAATCAAGTAATTAACCTATTTTATTATCGTCAGATTTCTAAGGCTACATAAACTTTA
* * *
637098 AACAGTCACTACCTATTACATTAAATAAGCG
196 AAAAGGCACTACCTATTACATTAAATAAGCA
* * **
637129 CTACTTGTTATATTATTATGGTTGATAATGTTTCCAGTAATTAACTTATTTTGTTATCGTGGGAT
1 CTACTTGTTATGTTATTATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCAGAT
* *
637194 TTCTGAGGC-TCTATCAG-TTCAAACTTTGTTAACA-TTTAGGCGCTACCTAATATGTTGATAAT
66 TTCTAAGGCTTC-ATCAGCTT-AAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAAT
* * * *
637256 ATTGATAACAAATCAAGTAGTTAA-CTATTTTGTTATCGTCAGATTTCTAAGG-TTCAATCAACT
129 ATTGATAACAAATCAAGTAATTAACCTATTTTATTATCGTCAGATTTCTAAGGCTAC-ATAAACT
** *
637319 TTAAAAAGGCACTACCTATTATGTTACATAAGCA
193 TTAAAAAGGCACTACCTATTACATTAAATAAGCA
* *
637353 CTACTTGTTGTGTTATTATGGTTGATAATATTTCCAGTAATTAACC
1 CTACTTGTTATGTTATTATGGTTGATAATGTTTCCAGTAATTAACC
637399 GGTTATGTTA
Statistics
Matches: 242, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
223 2 0.01
224 102 0.42
225 53 0.22
226 85 0.35
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (226 bp):
CTACTTGTTATGTTATTATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCAGAT
TTCTAAGGCTTCATCAGCTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGATAATAT
TGATAACAAATCAAGTAATTAACCTATTTTATTATCGTCAGATTTCTAAGGCTACATAAACTTTA
AAAAGGCACTACCTATTACATTAAATAAGCA
Found at i:640040 original size:44 final size:44
Alignment explanation
Indices: 639884--640159 Score: 217
Period size: 45 Copynumber: 6.3 Consensus size: 44
639874 AGTTGAGAAT
* * *
639884 CCTAATTTTTGT-AATCTCA--TTTTATCTTTA-AATTGAGGTC
1 CCTAATTTTTTTCAATCTCACTTTTTATCATTATAATTGAGGCC
** * * ****
639924 TTTAATATTTTTCAATCCCACTTTTTTAT-ATTTATAATTGATAAT
1 CCTAATTTTTTTCAATCTCAC-TTTTTATCA-TTATAATTGAGGCC
639969 CCTAATTTTTTTCCAATCTCACTTTTTATCATTATAATTGAGGCC
1 CCTAATTTTTTT-CAATCTCACTTTTTATCATTATAATTGAGGCC
* * * * *
640014 CCTAATTTTTTTCAATCCCACATTTTA-CTTATATAATTTAAGCC
1 CCTAATTTTTTTCAATCTCACTTTTTATCAT-TATAATTGAGGCC
* * *
640058 CCTAATTTTTTTTCAATCTCACTTTTTACCTTTAAAATTGAGGCC
1 CCTAA-TTTTTTTCAATCTCACTTTTTATCATTATAATTGAGGCC
* * * * **
640103 TCTAATTTTTTT-ATTCTAACCTTTTA-CATTTATAATTGAGATC
1 CCTAATTTTTTTCAATCTCACTTTTTATCA-TTATAATTGAGGCC
640146 CCTAATTTTTTTCA
1 CCTAATTTTTTTCA
640160 GGCATATTTT
Statistics
Matches: 186, Mismatches: 37, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
40 8 0.04
41 6 0.03
42 1 0.01
43 35 0.19
44 46 0.25
45 78 0.42
46 12 0.06
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (44 bp):
CCTAATTTTTTTCAATCTCACTTTTTATCATTATAATTGAGGCC
Found at i:640049 original size:89 final size:88
Alignment explanation
Indices: 639861--640158 Score: 290
Period size: 89 Copynumber: 3.4 Consensus size: 88
639851 ATTTTCTTCA
* * * *
639861 ATTTTATTTTTATAGTTGAGAATCCTAATTTTTGT--AATCTCA--TTTTATCTTTAAATTGAGG
1 ATTTTACTTTTATAATTGATAATCCTAATTTTTTTCCAATCTCACTTTTTATCTTTAAATTGAGG
* * *
639922 TCTTTAATATTTTTCAATCCCAC
66 CCTCTAATTTTTTTCAATCCCAC
* *
639945 TTTTTTA-TATTTATAATTGATAATCCTAATTTTTTTCCAATCTCACTTTTTATCATTATAATTG
1 -ATTTTACT-TTTATAATTGATAATCCTAATTTTTTTCCAATCTCACTTTTTATCTTTA-AATTG
*
640009 AGGCCCCTAATTTTTTTCAATCCCAC
63 AGGCCTCTAATTTTTTTCAATCCCAC
* * * *
640035 ATTTTACTTATATAATT--TAAGCCCCTAATTTTTTTTCAATCTCACTTTTTACCTTTAAAATTG
1 ATTTTACTTTTATAATTGATAA--TCCTAATTTTTTTCCAATCTCACTTTTTATCTTT-AAATTG
* **
640098 AGGCCTCTAATTTTTTT-ATTCTAAC
63 AGGCCTCTAATTTTTTTCAATCCCAC
* * *
640123 CTTTTACATTTATAATTGA-GATCCCTAATTTTTTTC
1 ATTTTACTTTTATAATTGATAAT-CCTAATTTTTTTC
640159 AGGCATATTT
Statistics
Matches: 175, Mismatches: 25, Indels: 23
0.78 0.11 0.10
Matches are distributed among these distances:
84 1 0.01
85 29 0.17
87 10 0.06
88 31 0.18
89 75 0.43
90 29 0.17
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.51
Consensus pattern (88 bp):
ATTTTACTTTTATAATTGATAATCCTAATTTTTTTCCAATCTCACTTTTTATCTTTAAATTGAGG
CCTCTAATTTTTTTCAATCCCAC
Found at i:641723 original size:24 final size:27
Alignment explanation
Indices: 641696--641746 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 27
641686 AAGATGCTTA
*
641696 TTTCATATGT-TATA-ATATA-ATTAT
1 TTTCATATATATATATATATATATTAT
641720 TTTCATATATATATATATATATATTAT
1 TTTCATATATATATATATATATATTAT
641747 ATCTATAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 4 0.17
26 5 0.22
27 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTCATATATATATATATATATATTAT
Found at i:643018 original size:22 final size:21
Alignment explanation
Indices: 642981--643022 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
642971 CCATCTCCAT
*
642981 TTCATCATCAACACCATCAAC
1 TTCATCATCAAAACCATCAAC
643002 TTCATCCATCAAAACCATCAA
1 TTCAT-CATCAAAACCATCAA
643023 TTCTATAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (21 bp):
TTCATCATCAAAACCATCAAC
Found at i:643362 original size:30 final size:30
Alignment explanation
Indices: 643317--643388 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
643307 AATTGGAGTA
* *
643317 CAAAA-AAAGAAAAAAAGAAGAA-AAATTC
1 CAAAAGAAATAAAAAAAAAAGAAGAAATTC
*
643345 AGAAAAG-AATAAAAAAAAAAGAAGAAATTC
1 -CAAAAGAAATAAAAAAAAAAGAAGAAATTC
643375 CAAAAGAAATAAAA
1 CAAAAGAAATAAAA
643389 GCCAAGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.75, C:0.06, G:0.11, T:0.08
Consensus pattern (30 bp):
CAAAAGAAATAAAAAAAAAAGAAGAAATTC
Found at i:644541 original size:23 final size:23
Alignment explanation
Indices: 644515--644562 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
644505 GCAATGATCC
644515 GAGTCAATATTGAGGAGGATCGT
1 GAGTCAATATTGAGGAGGATCGT
* *
644538 GAGTCAATATTTAGGAGGATTGT
1 GAGTCAATATTGAGGAGGATCGT
644561 GA
1 GA
644563 AGCAACCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.29
Consensus pattern (23 bp):
GAGTCAATATTGAGGAGGATCGT
Found at i:646258 original size:24 final size:26
Alignment explanation
Indices: 646214--646262 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
646204 CTTTCTAACT
646214 TTATATATATATGCTTATTTCATATG
1 TTATATATATATGCTTATTTCATATG
646240 TTATA-ATATA-G-TTATTTTCATAT
1 TTATATATATATGCTTA-TTTCATAT
646263 ATATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.14
24 9 0.41
25 5 0.23
26 5 0.23
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (26 bp):
TTATATATATATGCTTATTTCATATG
Found at i:646267 original size:23 final size:22
Alignment explanation
Indices: 646215--646267 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
646205 TTTCTAACTT
646215 TATATAT-ATATGCTTATTTCA
1 TATATATAATATGCTTATTTCA
*
646236 TATGTTATAATATAG-TTATTTTCA
1 TAT-ATATAATAT-GCTTA-TTTCA
646260 TATATATA
1 TATATATA
646268 TTTATAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 3 0.12
23 11 0.42
24 9 0.35
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (22 bp):
TATATATAATATGCTTATTTCA
Found at i:647498 original size:22 final size:21
Alignment explanation
Indices: 647461--647502 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
647451 CCATCTCCAT
647461 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
647482 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
647503 TTCTATAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:649019 original size:23 final size:23
Alignment explanation
Indices: 648993--649040 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
648983 GCAATGATCC
648993 GAGTCAATATTGAGGAGGATCGT
1 GAGTCAATATTGAGGAGGATCGT
* *
649016 GAGTCAATATTTAGGAGGATTGT
1 GAGTCAATATTGAGGAGGATCGT
649039 GA
1 GA
649041 AGCAACCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.29
Consensus pattern (23 bp):
GAGTCAATATTGAGGAGGATCGT
Found at i:651974 original size:22 final size:21
Alignment explanation
Indices: 651942--651983 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
651932 CCATTTCCAT
651942 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
651963 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
651984 TTTCGCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:652554 original size:23 final size:24
Alignment explanation
Indices: 652528--652583 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
652518 CATCACAGCT
*
652528 CGTATAAATTGCA-CCAAGTGCCG
1 CGTAGAAATTGCATCCAAGTGCCG
* *
652551 CGTAGAAATTGCATCGAAGTGCCA
1 CGTAGAAATTGCATCCAAGTGCCG
*
652575 CATAGAAAT
1 CGTAGAAAT
652584 GTCCCGAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
CGTAGAAATTGCATCCAAGTGCCG
Found at i:652598 original size:23 final size:23
Alignment explanation
Indices: 652572--652672 Score: 80
Period size: 23 Copynumber: 4.4 Consensus size: 23
652562 CATCGAAGTG
*
652572 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATATCCCGAAGGA
* * * **
652595 CCACATAGTATTGTCTTGAAGGA
1 CCACATAGAAATATCCCGAAGGA
* * *
652618 CCGCAAAGAAATACCCCGAAGG-
1 CCACATAGAAATATCCCGAAGGA
* *
652640 CCACGTAGAATTATCCCGAAGGA
1 CCACATAGAAATATCCCGAAGGA
652663 CTC-CATAGAA
1 C-CACATAGAA
652673 CCCTCGATTC
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
22 17 0.29
23 40 0.69
24 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.17
Consensus pattern (23 bp):
CCACATAGAAATATCCCGAAGGA
Found at i:659525 original size:24 final size:24
Alignment explanation
Indices: 659493--659543 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
659483 AACTCGTATG
*
659493 AATTGCACTAAAGTGCCGCATAAA
1 AATTGCACTAAAGTGCCACATAAA
* *
659517 AATTGCACTGAAGTGCCACATAGA
1 AATTGCACTAAAGTGCCACATAAA
659541 AAT
1 AAT
659544 GTCCCGAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (24 bp):
AATTGCACTAAAGTGCCACATAAA
Found at i:659697 original size:16 final size:15
Alignment explanation
Indices: 659673--659714 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
659663 TTCACATAGG
659673 TTATCACATAGAT-A
1 TTATCACATAGATCA
659687 TGTATTCACATAGATCA
1 T-TA-TCACATAGATCA
659704 TTATCACATAG
1 TTATCACATAG
659715 CTTATATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.40
16 12 0.48
17 2 0.08
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (15 bp):
TTATCACATAGATCA
Found at i:660843 original size:25 final size:23
Alignment explanation
Indices: 660815--660867 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
660805 AATTTCTTTC
660815 TTTTCTTCTATTTTCAAGTTTTCAT
1 TTTTCTTCTATTTT-AAGTTTT-AT
* *
660840 TTTTATTTTATTTTAAGTTTTAT
1 TTTTCTTCTATTTTAAGTTTTAT
660863 TTTTC
1 TTTTC
660868 AAAATGCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 7 0.28
25 12 0.48
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTCTTCTATTTTAAGTTTTAT
Found at i:660860 original size:12 final size:12
Alignment explanation
Indices: 660823--660865 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
660813 TCTTTTCTTC
660823 TATTTTCAAGTTT
1 TATTTT-AAGTTT
*
660836 TCATTTTTA-TTT
1 T-ATTTTAAGTTT
660848 TATTTTAAGTTT
1 TATTTTAAGTTT
660860 TATTTT
1 TATTTT
660866 TCAAAATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.23
12 13 0.50
13 2 0.08
14 5 0.19
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (12 bp):
TATTTTAAGTTT
Found at i:671645 original size:2 final size:2
Alignment explanation
Indices: 671638--671664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
671628 CGGATGGGAG
671638 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
671665 TTGGTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:673217 original size:27 final size:26
Alignment explanation
Indices: 673178--673229 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
673168 TCTGATATGT
* *
673178 CAGTTTCTGGAAGGTCCAGTCAGCAG
1 CAGTTTCTAGAAGATCCAGTCAGCAG
*
673204 CAGTCTTCTAGAAGATCTAGTCAGCA
1 CAGT-TTCTAGAAGATCCAGTCAGCA
673230 CCTTCTAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (26 bp):
CAGTTTCTAGAAGATCCAGTCAGCAG
Found at i:681881 original size:43 final size:43
Alignment explanation
Indices: 681827--682050 Score: 154
Period size: 43 Copynumber: 5.1 Consensus size: 43
681817 TTTGATCTTA
***
681827 TTTTTAACCTTTATAATTGAGCTCTTAATTTTTTTCAATTTTAC
1 TTTTT-ACCTTTATAATTGAGCTCTTAATTTTTTTCAATCACAC
* * *
681871 TTTTTACCTTTATAATTAAAGC-CTCTAA-TTCTTTCAATCCCA-
1 TTTTTACCTTTATAATT-GAGCTCT-TAATTTTTTTCAATCACAC
* * *
681913 TTTTTA-CTTATATAATTTAGGCACCTAATTTTTTTTTCAATCACAC
1 TTTTTACCTT-TATAATTGA-GCTCTTAA--TTTTTTTCAATCACAC
* * *
681959 TTTTTACCTTTAAAATTGAGGCGTC-TAATTTTTGT-AATCTCAC
1 TTTTTACCTTTATAATTGA-GC-TCTTAATTTTTTTCAATCACAC
* * * * *
682002 ATTTTATCTTTGTAATTGAGGTCTCTAATTTTTTTTCAATCATAC
1 TTTTTACCTTTATAATTGAGCTCT-TAA-TTTTTTTCAATCACAC
682047 TTTT
1 TTTT
682051 ATTTTTATAA
Statistics
Matches: 142, Mismatches: 23, Indels: 29
0.73 0.12 0.15
Matches are distributed among these distances:
41 6 0.04
42 19 0.13
43 50 0.35
44 23 0.16
45 21 0.15
46 19 0.13
47 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (43 bp):
TTTTTACCTTTATAATTGAGCTCTTAATTTTTTTCAATCACAC
Found at i:681964 original size:88 final size:88
Alignment explanation
Indices: 681835--682076 Score: 223
Period size: 88 Copynumber: 2.8 Consensus size: 88
681825 TATTTTTAAC
* * **
681835 CTTTATAATTGAGCT-CTTAA-TTTTTTTCAATTTTACTTTTTACCTTTATAATTAAAGCCTCTA
1 CTTTATAATTGAGGTCCCTAATTTTTTTTCAATCATACTTTTTACCTTTATAATTAAAGCCTCTA
681898 ATTCTTT-CAATC-C-CATTTT-T
66 ATT-TTTGCAATCTCACATTTTAT
* * * * * *
681918 ACTTATATAATTTAGG-CACCTAATTTTTTTTTCAATCACACTTTTTACCTTTAAAATTGAGGCG
1 -CTT-TATAATTGAGGTC-CCTAA-TTTTTTTTCAATCATACTTTTTACCTTTATAATTAAAGCC
*
681982 TCTAATTTTTGTAATCTCACATTTTAT
62 TCTAATTTTTGCAATCTCACATTTTAT
* * ** *
682009 CTTTGTAATTGAGGTCTCTAATTTTTTTTCAATCATAC-TTTTATTTTTATAATTTAAGCCAT-T
1 CTTTATAATTGAGGTCCCTAATTTTTTTTCAATCATACTTTTTACCTTTATAATTAAAGCC-TCT
682072 AATTT
65 AATTT
682077 AATCATTTCC
Statistics
Matches: 126, Mismatches: 21, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
84 3 0.02
85 9 0.07
86 4 0.03
87 25 0.20
88 60 0.48
89 14 0.11
90 10 0.08
91 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (88 bp):
CTTTATAATTGAGGTCCCTAATTTTTTTTCAATCATACTTTTTACCTTTATAATTAAAGCCTCTA
ATTTTTGCAATCTCACATTTTAT
Found at i:682820 original size:30 final size:31
Alignment explanation
Indices: 682764--682836 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
682754 AAAACAAAAT
* * *
682764 TTTGGTGAGTAAAATAGAAAAGTGATAATGA
1 TTTGGTGACTAAAATAGAAAAATGATAATAA
*
682795 TTTGGTGACTAAAA-GGAAAAATGATAATAA
1 TTTGGTGACTAAAATAGAAAAATGATAATAA
*
682825 TTGGGTGACTAA
1 TTTGGTGACTAA
682837 TTATATAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.29
Consensus pattern (31 bp):
TTTGGTGACTAAAATAGAAAAATGATAATAA
Found at i:688043 original size:33 final size:33
Alignment explanation
Indices: 688001--688069 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
687991 CCTTCCCTCC
688001 CCCAACCTTTGATATGTGTTTGTGTGTCAGCAA
1 CCCAACCTTTGATATGTGTTTGTGTGTCAGCAA
688034 CCCAACCTTTGATATGTGTTTGTGTGTCAGCAA
1 CCCAACCTTTGATATGTGTTTGTGTGTCAGCAA
688067 CCC
1 CCC
688070 TATTTAGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (33 bp):
CCCAACCTTTGATATGTGTTTGTGTGTCAGCAA
Found at i:689171 original size:113 final size:113
Alignment explanation
Indices: 688973--689199 Score: 454
Period size: 113 Copynumber: 2.0 Consensus size: 113
688963 GCATCAGAAG
688973 TGGAAACTGGTTGGCAGTCACGAATTCTTGAGGTTGGTTTGATTTTGATAGCATTATTCAAGTTG
1 TGGAAACTGGTTGGCAGTCACGAATTCTTGAGGTTGGTTTGATTTTGATAGCATTATTCAAGTTG
689038 ATTATATTGCTTAGTTTTTCTCGTTTTAACAGATGTCACTGCTTGACT
66 ATTATATTGCTTAGTTTTTCTCGTTTTAACAGATGTCACTGCTTGACT
689086 TGGAAACTGGTTGGCAGTCACGAATTCTTGAGGTTGGTTTGATTTTGATAGCATTATTCAAGTTG
1 TGGAAACTGGTTGGCAGTCACGAATTCTTGAGGTTGGTTTGATTTTGATAGCATTATTCAAGTTG
689151 ATTATATTGCTTAGTTTTTCTCGTTTTAACAGATGTCACTGCTTGACT
66 ATTATATTGCTTAGTTTTTCTCGTTTTAACAGATGTCACTGCTTGACT
689199 T
1 T
689200 TTCTTTCTTC
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (113 bp):
TGGAAACTGGTTGGCAGTCACGAATTCTTGAGGTTGGTTTGATTTTGATAGCATTATTCAAGTTG
ATTATATTGCTTAGTTTTTCTCGTTTTAACAGATGTCACTGCTTGACT
Found at i:690585 original size:146 final size:147
Alignment explanation
Indices: 690321--690605 Score: 439
Period size: 146 Copynumber: 1.9 Consensus size: 147
690311 ACGGTACTAT
*
690321 TTTTATTTAGTGAAAGACATATGGACTTATATTTCCCAATTTCTTTCCCCATAAAAGAAGTAAAT
1 TTTTATTTAGTGAAAGACATATGGACTTATATTTCCAAATTTCTTTCCCCATAAAAGAAGTAAAT
* **
690386 TGTATATTTGGACATTTGTGGTTCTGGATGATACTAGCATCTTCCGTTTTCTTTGAT-GGGTCAT
66 TGTACATTTGGACATTTGTGGTTCCAGATGATACTAGCATCTTCCGTTTTCTTTGATGGGGTCAT
690450 CATAACTTAGGACAGTA
131 CATAACTTAGGACAGTA
* * * *
690467 TTTTGTTTGGTGAAAGACATATGTACTTATATTTCCAAATTTCTTTCCCCATAATAGAAGT-AAT
1 TTTTATTTAGTGAAAGACATATGGACTTATATTTCCAAATTTCTTTCCCCATAAAAGAAGTAAAT
* * *
690531 TGTGCATTTGGACATTTGTGGTTCCAGATGTTACTAGCATCTTCTGTTTCTCTTTGATGGGGTCA
66 TGTACATTTGGACATTTGTGGTTCCAGATGATACTAGCATCTTCCGTTT-TCTTTGATGGGGTCA
*
690596 TCGTAACTTA
130 TCATAACTTA
690606 AATTTGGTGA
Statistics
Matches: 125, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
145 46 0.37
146 64 0.51
147 15 0.12
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (147 bp):
TTTTATTTAGTGAAAGACATATGGACTTATATTTCCAAATTTCTTTCCCCATAAAAGAAGTAAAT
TGTACATTTGGACATTTGTGGTTCCAGATGATACTAGCATCTTCCGTTTTCTTTGATGGGGTCAT
CATAACTTAGGACAGTA
Found at i:700950 original size:28 final size:28
Alignment explanation
Indices: 700919--700999 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
700909 GGATTTTGTG
700919 AGTGACCAAATTATAAATTTTAAAGTTT
1 AGTGACCAAATTATAAATTTTAAAGTTT
* *
700947 AGTGATCAAAGTATAAATTTTGGAAAAGTTT
1 AGTGACCAAATTATAAATTTT---AAAGTTT
* *
700978 AGGGACC-AATTGT-AATTTTAAA
1 AGTGACCAAATTATAAATTTTAAA
701000 AAATTACAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
26 3 0.07
28 19 0.43
29 6 0.14
30 4 0.09
31 12 0.27
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (28 bp):
AGTGACCAAATTATAAATTTTAAAGTTT
Found at i:701980 original size:29 final size:31
Alignment explanation
Indices: 701948--702007 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
701938 GAAAAATTTA
*
701948 GGGACCATTTTG-TAATTTT-GAAAAGTTGG
1 GGGACCAATTTGATAATTTTGGAAAAGTTGG
701977 GGGACCAATTTGATAATTTTGGAAAAGTTGG
1 GGGACCAATTTGATAATTTTGGAAAAGTTGG
702008 ATGGTTGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 7 0.25
31 10 0.36
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (31 bp):
GGGACCAATTTGATAATTTTGGAAAAGTTGG
Found at i:705783 original size:10 final size:10
Alignment explanation
Indices: 705768--705843 Score: 66
Period size: 11 Copynumber: 7.3 Consensus size: 10
705758 TAAAAAAGTT
705768 AAATAAGAAA
1 AAATAAGAAA
705778 AAATAAG-AA
1 AAATAAGAAA
*
705787 AAATAAAAAAA
1 AAAT-AAGAAA
*
705798 AAGAAAAGAATA
1 AA-ATAAGAA-A
705810 AGAATAAGAAA
1 A-AATAAGAAA
*
705821 AAAAACAGAAA
1 AAATA-AGAAA
705832 AAA-AAGAAA
1 AAATAAGAAA
705841 AAA
1 AAA
705844 AAACAAGAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
9 14 0.25
10 13 0.24
11 18 0.33
12 9 0.16
13 1 0.02
ACGTcount: A:0.82, C:0.01, G:0.11, T:0.07
Consensus pattern (10 bp):
AAATAAGAAA
Found at i:705804 original size:24 final size:24
Alignment explanation
Indices: 705776--705857 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 24
705766 TTAAATAAGA
705776 AAAAATAAGAAAAATAAAAAAAAAG
1 AAAAATAAGAAAAA-AAAAAAAAAG
*
705801 AAAAGAATAAGAATAAGAAAAAAAACAG
1 -AAA-AATAAGAA-AA-AAAAAAAAAAG
* * *
705829 AAAAAAAAGAAAAAAAAACAAGAG
1 AAAAATAAGAAAAAAAAAAAAAAG
705853 AAAAA
1 AAAAA
705858 AGATGAGAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 14 0.29
25 2 0.04
26 10 0.20
27 11 0.22
28 11 0.22
29 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (24 bp):
AAAAATAAGAAAAAAAAAAAAAAG
Found at i:705812 original size:37 final size:37
Alignment explanation
Indices: 705769--705841 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
705759 AAAAAAGTTA
*
705769 AATAAGAA-AAAATAAGAAAAATA-AAAAAAAAGAAAAG
1 AATAAGAATAAAA-AA-AAAAACAGAAAAAAAAGAAAAG
*
705806 AATAAGAATAAGAAAAAAAACAGAAAAAAAAGAAAA
1 AATAAGAATAAAAAAAAAAACAGAAAAAAAAGAAAA
705842 AAAAACAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 6 0.19
37 23 0.72
38 3 0.09
ACGTcount: A:0.81, C:0.01, G:0.11, T:0.07
Consensus pattern (37 bp):
AATAAGAATAAAAAAAAAAACAGAAAAAAAAGAAAAG
Found at i:705843 original size:9 final size:9
Alignment explanation
Indices: 705772--705845 Score: 64
Period size: 9 Copynumber: 8.2 Consensus size: 9
705762 AAAGTTAAAT
705772 AAGAAAAAA
1 AAGAAAAAA
705781 TAAG-AAAAA
1 -AAGAAAAAA
*
705790 TA-AAAAAA
1 AAGAAAAAA
705798 AAGAAAAGAA
1 AAGAAAA-AA
* *
705808 TAAGAATAAG
1 -AAGAAAAAA
705818 AA-AAAAAA
1 AAGAAAAAA
*
705826 CAGAAAAAA
1 AAGAAAAAA
705835 AAGAAAAAA
1 AAGAAAAAA
705844 AA
1 AA
705846 ACAAGAGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
8 12 0.24
9 27 0.53
10 6 0.12
11 6 0.12
ACGTcount: A:0.82, C:0.01, G:0.11, T:0.05
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:706344 original size:187 final size:186
Alignment explanation
Indices: 706030--706402 Score: 728
Period size: 187 Copynumber: 2.0 Consensus size: 186
706020 CTATGATCCA
*
706030 GGTGGAAACATTATTGAGTTTGTTGCTACATGTTTAACATGTCAACAAGTAAAGATGAGCATCAA
1 GGTGGAAACATTATTGAGTTTGTTGCTACATGTTTAACATATCAACAAGTAAAGATGAGCATCAA
706095 GTGCTTTCGGAATTGTTGCAACTTATTTCTATTCCAGAGTGGAAGTGGTAAAGAGTCACTATGGA
66 GTGCTTTCGGAATTGTTGCAACTTATTTCTATTCCAGAGTGGAAGTGGTAAAGAGTCACTATGGA
706160 TTTTGTTACTGGACTACCTTTAACATCAAATAAAAAGGATTTCATTTGGGTGATAG
131 TTTTGTTACTGGACTACCTTTAACATCAAATAAAAAGGATTTCATTTGGGTGATAG
706216 GGTGGAAACATTATTGAGTTTGTTGCTACATGTTTAACATATCAACAAGTAAAAGATGAGCATCA
1 GGTGGAAACATTATTGAGTTTGTTGCTACATGTTTAACATATCAACAAGT-AAAGATGAGCATCA
706281 AGTGCTTTCGGAATTGTTGCAACTTATTTCTATTCCAGAGTGGAAGTGGTAAAGAGTCACTATGG
65 AGTGCTTTCGGAATTGTTGCAACTTATTTCTATTCCAGAGTGGAAGTGGTAAAGAGTCACTATGG
706346 ATTTTGTTACTGGACTACCTTTAACATCAAATAAAAAGGATTTCATTTGGGTGATAG
130 ATTTTGTTACTGGACTACCTTTAACATCAAATAAAAAGGATTTCATTTGGGTGATAG
706403 TGACCAGTTA
Statistics
Matches: 185, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
186 49 0.26
187 136 0.74
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.34
Consensus pattern (186 bp):
GGTGGAAACATTATTGAGTTTGTTGCTACATGTTTAACATATCAACAAGTAAAGATGAGCATCAA
GTGCTTTCGGAATTGTTGCAACTTATTTCTATTCCAGAGTGGAAGTGGTAAAGAGTCACTATGGA
TTTTGTTACTGGACTACCTTTAACATCAAATAAAAAGGATTTCATTTGGGTGATAG
Found at i:710290 original size:18 final size:18
Alignment explanation
Indices: 710262--710304 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
710252 ACTCTATTGA
710262 TTATCTTGTTTGTACTAAC
1 TTAT-TTGTTTGTACTAAC
710281 TTATTTGTTTGTACTAAC
1 TTATTTGTTTGTACTAAC
*
710299 TCATTT
1 TTATTT
710305 CTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (18 bp):
TTATTTGTTTGTACTAAC
Found at i:714495 original size:64 final size:64
Alignment explanation
Indices: 714412--714569 Score: 243
Period size: 61 Copynumber: 2.5 Consensus size: 64
714402 TTAAAACAAA
**
714412 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCCATCTTGAG-ACGTTTCCCTTGAAACGAAT
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAACAT-TTGAGAACGTTTCCCTTGAAACGAAT
* *
714476 TTTGTCTCTCTTGAGACAG-TT-TC-TAAAACAAATATTTGAGAACGTTTCCCTTGAAACGAAT
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAACATTTGAGAACGTTTCCCTTGAAACGAAT
714537 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
714570 TCATATTTGA
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
60 5 0.06
61 47 0.55
62 4 0.05
63 4 0.05
64 25 0.29
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (64 bp):
TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAACATTTGAGAACGTTTCCCTTGAAACGAAT
Found at i:715035 original size:8 final size:8
Alignment explanation
Indices: 715024--715055 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
715014 ATATTTATTA
715024 TATTATAT
1 TATTATAT
715032 TA-T-TAT
1 TATTATAT
715038 TATTATAT
1 TATTATAT
715046 TATTATAT
1 TATTATAT
715054 TA
1 TA
715056 AATATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.23
7 2 0.09
8 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATAT
Found at i:719682 original size:120 final size:117
Alignment explanation
Indices: 719457--719694 Score: 415
Period size: 120 Copynumber: 2.0 Consensus size: 117
719447 CTAAAATTAG
719457 CTGGCGGCCAGCTAATTACCCCCAATAAAGGCTTCAAGTTGTGGTGATGTGTGATGTGTTGCACA
1 CTGGCGGCCAGCTAATTACCCCCAATAAAGGCTTCAAGTTGTGGTGATGTGTGATGTGTTGCACA
719522 GGGTATACATTTCCTTTTCAATTCTTGACATCTGGTTGGTTCCAATTAAACTT
66 GGGTATA-ATTTCCTTTTCAATTCTTGACATCTGGTTGGTTCCAATTAAACTT
*
719575 CTGGCGGCACAGCATAATTACCCCCAATAAAGGCTTCAAGTTTTGGTGATGTGTGATTGTGTTGC
1 CTGGCGGC-CAGC-TAATTACCCCCAATAAAGGCTTCAAGTTGTGGTGATGTGTGA-TGTGTTGC
719640 ACAGGGTAT-ATTTCTCTTTTCAATTCTTGACATCTGGTTGGTTCCAATTAAACTT
63 ACAGGGTATAATTTC-CTTTTCAATTCTTGACATCTGGTTGGTTCCAATTAAACTT
719695 TGTAACGAAG
Statistics
Matches: 115, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
118 8 0.07
119 9 0.08
120 81 0.70
121 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (117 bp):
CTGGCGGCCAGCTAATTACCCCCAATAAAGGCTTCAAGTTGTGGTGATGTGTGATGTGTTGCACA
GGGTATAATTTCCTTTTCAATTCTTGACATCTGGTTGGTTCCAATTAAACTT
Found at i:721548 original size:92 final size:92
Alignment explanation
Indices: 721219--721564 Score: 299
Period size: 92 Copynumber: 3.8 Consensus size: 92
721209 TCATGCATCT
* * * * * *
721219 AAGTTATTAAATTAATGGATGAAAGTTTGAATAGCGTTGAAATATCTAAATTAAACATTTTGATG
1 AAGTTGTTACATTAATAGATGAAAGTTTGAATAGCGTTGAAATGTCTAAACTAAACACTTTGATG
* * * * *
721284 TTCACG-GATAGAGAGGTTAATTTATTC
66 TTTACGACAAAG-GAAGTTAACTTATTC
* * * * * *
721311 AAATTGTTACATTAAT-GAATGAAAATTTGAATAACGTTAAAATGTGTTAACTAAACACTTTGAT
1 AAGTTGTTACATTAATAG-ATGAAAGTTTGAATAGCGTTGAAATGTCTAAACTAAACACTTTGAT
* * *
721375 GTTTACCTACTAAA-GAAGTTATCTTATCC
65 GTTTA-CGAC-AAAGGAAGTTAACTTATTC
* * * * * * * * * *
721404 AAGTTGTT---TCAATATATAAAAGTTTAAATAGTGTTGGAATTTCTTAACTAAACACTTTAATA
1 AAGTTGTTACATTAATAGATGAAAGTTTGAATAGCGTTGAAATGTCTAAACTAAACACTTTGATG
* *
721466 TTTACGACAAAGGAATTTAACTTATTG
66 TTTACGACAAAGGAAGTTAACTTATTC
*
721493 AAGTTGTTACATTAATAGATGAAAGTTTGAATAGCGTTGAAATGTCTAAACTAAACACACTTTTA
1 AAGTTGTTACATTAATAGATGAAAGTTTGAATAGCGTTGAAATGTCTAAACT-AA-ACACTTTGA
721558 TGTTTAC
64 TGTTTAC
721565 AAATTAAAAG
Statistics
Matches: 195, Mismatches: 48, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
88 3 0.02
89 22 0.11
90 44 0.23
91 1 0.01
92 88 0.45
93 21 0.11
94 14 0.07
95 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (92 bp):
AAGTTGTTACATTAATAGATGAAAGTTTGAATAGCGTTGAAATGTCTAAACTAAACACTTTGATG
TTTACGACAAAGGAAGTTAACTTATTC
Found at i:725324 original size:134 final size:138
Alignment explanation
Indices: 725164--725466 Score: 392
Period size: 133 Copynumber: 2.2 Consensus size: 138
725154 AATCGTAATC
* * * *
725164 ATTTTTATCAAATTATTGAATCGAATAATTGAAATGAAACCTCATA-CATTAAGGCGAGGATCAC
1 ATTTTAATC-AATTATTGAATCGAATAATTGAAATGAAACCTCA-AGCATTAAGGC-AAGAACAA
* *
725228 TCCAAA-ATCC-CCTAATTTAAGGGAC-TAAAGTGAAATTAATCT-AAGT-GAAGACTCTAATTA
63 T-CAAATATCCACCTAAGTTAAGGCACTTAAAGTGAAATTAATCTAAAGTGGAAGA-TCTAATTA
*
725288 TTAATCCTAATTG
126 TTAATCATAATTG
*
725301 A-TTTAATC-ATTATTGAATCGAATAA-TCAAATGAAACCTCAAGCATTAAGGCAAGAACAATCA
1 ATTTTAATCAATTATTGAATCGAATAATTGAAATGAAACCTCAAGCATTAAGGCAAGAACAATCA
*
725363 AATATCCACCTAAGTTACGGCACTTAAAGTGAAATTAATCTAAAGTGGAAGATCTAATTATTAAT
66 AATATCCACCTAAGTTAAGGCACTTAAAGTGAAATTAATCTAAAGTGGAAGATCTAATTATTAAT
*
725428 CATACTTG
131 CATAATTG
*
725436 ATTTTAATCAATTATTGAATC-AATTATTGAA
1 ATTTTAATCAATTATTGAATCGAATAATTGAA
725467 TCAAATAATT
Statistics
Matches: 145, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
131 4 0.03
132 11 0.08
133 35 0.24
134 34 0.23
135 24 0.17
136 22 0.15
137 15 0.10
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (138 bp):
ATTTTAATCAATTATTGAATCGAATAATTGAAATGAAACCTCAAGCATTAAGGCAAGAACAATCA
AATATCCACCTAAGTTAAGGCACTTAAAGTGAAATTAATCTAAAGTGGAAGATCTAATTATTAAT
CATAATTG
Found at i:725458 original size:12 final size:12
Alignment explanation
Indices: 725441--725480 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
725431 ACTTGATTTT
725441 AATCAATTATTG
1 AATCAATTATTG
725453 AATCAATTATTG
1 AATCAATTATTG
*
725465 AATCAAATAATTG
1 AATC-AATTATTG
725478 AAT
1 AAT
725481 GAAACCCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (12 bp):
AATCAATTATTG
Found at i:729484 original size:17 final size:17
Alignment explanation
Indices: 729464--729496 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
729454 TATATAATTA
*
729464 TATTTTATAAAAATATG
1 TATTTTAAAAAAATATG
729481 TATTTTAAAAAAATAT
1 TATTTTAAAAAAATAT
729497 TAATAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TATTTTAAAAAAATATG
Found at i:730860 original size:17 final size:17
Alignment explanation
Indices: 730838--730877 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
730828 GGAAGTCTAA
*
730838 ATCATTTTCTTGTTTTG
1 ATCATTTTCTTGTTTCG
730855 ATCATTTTCTTGTTTCG
1 ATCATTTTCTTGTTTCG
730872 ATCATT
1 ATCATT
730878 GGGTTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.60
Consensus pattern (17 bp):
ATCATTTTCTTGTTTCG
Found at i:735355 original size:15 final size:14
Alignment explanation
Indices: 735335--735368 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
735325 AACTATTCGG
735335 AGAAAACATGAGAAA
1 AGAAAACATGA-AAA
*
735350 AGAAAACATTAAAA
1 AGAAAACATGAAAA
735364 AGAAA
1 AGAAA
735369 GCAAGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.06, G:0.15, T:0.09
Consensus pattern (14 bp):
AGAAAACATGAAAA
Found at i:736898 original size:321 final size:322
Alignment explanation
Indices: 736239--736917 Score: 1197
Period size: 324 Copynumber: 2.1 Consensus size: 322
736229 TATTCACGCA
*
736239 TATTTTA-TATATAAATTTTTATGTCTCAAACGATTTTAGTATTATTTATTATACCTTAGAAGTA
1 TATTTTATTA-ATTAATTTTTAT-T-T-AAACGATTTTAGTATTATTTATTATACCTTAGAAGTA
* *
736303 AAGATTGCATTATATTACCATATGAATGTTTCTGGTTGATGTTTATAACTCTTATGTATTTATGT
62 AAGATTACATTATATTACCATATGAATGTTTCTGGTTGATGTTTATAACTCTTACGTATTTATGT
736368 ATGTATTTTATTCTTTTAGAATCAATGTTATGAAGGATGGTGAAATACTTATTTTACTTGTTAAT
127 ATGTATTTTATTCTTTTAGAATCAATGTTATGAAGGATGGTGAAATACTTATTTTACTTGTTAAT
736433 CTTTTATATATTGCTTGAATGTTTTTCAAGAACATCGATTTGTAAAATAAGCGTGGAAAACATCA
192 CTTTTATATATTGCTTGAATGTTTTTCAAGAACATCGATTTGTAAAATAAGCGTGGAAAACATCA
736498 CTTGGTTGAAGTGATGCGATCCGATACGACATTTTAATGAAATGGAAACTTGAAATAAATATAGT
257 CTTGGTTGAAGTGATGCGATCCGATACGACATTTTAATGAAATGGAAACTTGAAATAAATATAGT
736563 T
322 T
736564 TATTTTATTAATTAATTTTTATTTAAACGATTTTAGTATTATTTTATTATACCTTAGAAGTAAAG
1 TATTTTATTAATTAATTTTTATTTAAACGATTTTAGTATTA-TTTATTATACCTTAGAAGTAAAG
* *
736629 ATTACATTATATTACCATATGAATGTTTTTGGTTGATGTTTTATGACTCTTACGTATTTATGTAT
65 ATTACATTATATTACCATATGAATGTTTCTGGTTGATG-TTTATAACTCTTACGTATTTATGTAT
736694 GTATTTTATTCTTTTAGAATCAATGTTATGAAGGATGGTGAAATACTTATTTTACTTGTTAATC-
129 GTATTTTATTCTTTTAGAATCAATGTTATGAAGGATGGTGAAATACTTATTTTACTTGTTAATCT
736758 TTTATATATTGCTTGAATG-TTTTCAAGAACATCGATTTGTAAAATAAGCGTGG-AAACATCACT
194 TTTATATATTGCTTGAATGTTTTTCAAGAACATCGATTTGTAAAATAAGCGTGGAAAACATCACT
736821 TGGTTGAAGTGATGCGATCCGATACGACATTTTAATGAAAT-GAGAACTTGAAATAAATATAGTT
259 TGGTTGAAGTGATGCGATCCGATACGACATTTTAATGAAATGGA-AACTTGAAATAAATATAGTT
*
736885 TATTTTATTAATTAATTTTTTATTTAAATGATT
1 TATTTTATTAATTAA-TTTTTATTTAAACGATT
736918 CAATGTTTTT
Statistics
Matches: 343, Mismatches: 6, Indels: 13
0.95 0.02 0.04
Matches are distributed among these distances:
320 2 0.01
321 86 0.25
322 67 0.20
323 79 0.23
324 89 0.26
325 18 0.05
326 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (322 bp):
TATTTTATTAATTAATTTTTATTTAAACGATTTTAGTATTATTTATTATACCTTAGAAGTAAAGA
TTACATTATATTACCATATGAATGTTTCTGGTTGATGTTTATAACTCTTACGTATTTATGTATGT
ATTTTATTCTTTTAGAATCAATGTTATGAAGGATGGTGAAATACTTATTTTACTTGTTAATCTTT
TATATATTGCTTGAATGTTTTTCAAGAACATCGATTTGTAAAATAAGCGTGGAAAACATCACTTG
GTTGAAGTGATGCGATCCGATACGACATTTTAATGAAATGGAAACTTGAAATAAATATAGTT
Found at i:737998 original size:14 final size:13
Alignment explanation
Indices: 737973--737997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
737963 AATAAAAGAA
737973 ATAAACAAAAAAC
1 ATAAACAAAAAAC
737986 ATAAACAAAAAA
1 ATAAACAAAAAA
737998 AAGAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.12, G:0.00, T:0.08
Consensus pattern (13 bp):
ATAAACAAAAAAC
Found at i:738007 original size:10 final size:10
Alignment explanation
Indices: 737992--738021 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
737982 AAACATAAAC
737992 AAAAAAAAGA
1 AAAAAAAAGA
738002 AAAAAAAAGA
1 AAAAAAAAGA
738012 AACAAAAAAG
1 AA-AAAAAAG
738022 GGGAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:738008 original size:13 final size:13
Alignment explanation
Indices: 737960--738020 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 13
737950 AAATAAAAAT
* *
737960 AAAAATAAAAGAA
1 AAAAAAAAAACAA
737973 ATAAACAAAAAACATA
1 A-AAA-AAAAAACA-A
*
737989 AACAAAAAAAAGAA
1 AA-AAAAAAAACAA
738003 AAAAAAAGAAACAA
1 AAAAAAA-AAACAA
738017 AAAA
1 AAAA
738021 GGGGAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.15
14 15 0.38
15 14 0.36
16 4 0.10
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.05
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:741393 original size:80 final size:80
Alignment explanation
Indices: 741260--741421 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
741250 ATACCGACAT
741260 ATGATTTCTTTCTTCAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTC
1 ATGATTTCTTTCTTCAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTC
741325 TACCCATGTTGTGAA
66 TACCCATGTTGTGAA
741340 ATGATTTCTTTCTTCAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTC
1 ATGATTTCTTTCTTCAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTC
*
741405 TACCCATGTTTTGAA
66 TACCCATGTTGTGAA
741420 AT
1 AT
741422 AGTCGATTGC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (80 bp):
ATGATTTCTTTCTTCAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTC
TACCCATGTTGTGAA
Found at i:741438 original size:80 final size:80
Alignment explanation
Indices: 741274--741439 Score: 255
Period size: 80 Copynumber: 2.1 Consensus size: 80
741264 TTTCTTTCTT
741274 CAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTCTACCCATGTTGTGA
1 CAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTCTACCCATGTTGTGA
* * **
741339 AATGATTTCTTTCTT
66 AATGATGTCTTGCCA
*
741354 CAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTCTACCCATGTTTTGA
1 CAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTCTACCCATGTTGTGA
741419 AAT-A-GTCGATTGCCA
66 AATGATGTC--TTGCCA
741434 CAAGAA
1 CAAGAA
741440 TGAACCGGTG
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
78 2 0.03
79 1 0.01
80 76 0.96
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (80 bp):
CAAGAACTTACAAATAGTGGACTGAGTGACACTGGCATATGATGCAGCCTCTACCCATGTTGTGA
AATGATGTCTTGCCA
Found at i:750988 original size:17 final size:17
Alignment explanation
Indices: 750968--751022 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
750958 ACAGAAACAA
750968 AAAAAGAAAAAAATAAT
1 AAAAAGAAAAAAATAAT
750985 AAAAAGAACAAAACATAA-
1 AAAAAGAA-AAAA-ATAAT
*
751003 AAAAAG-GAAAAATAAT
1 AAAAAGAAAAAAATAAT
751019 AAAA
1 AAAA
751023 TATATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 4 0.12
16 8 0.24
17 8 0.24
18 10 0.29
19 4 0.12
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAAAAATAAT
Found at i:751005 original size:28 final size:30
Alignment explanation
Indices: 750937--751007 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
750927 ATATAAAAAG
750937 AAAATAAAAAAAATTAAAATAACAGAAACA
1 AAAATAAAAAAAATTAAAATAACAGAAACA
*
750967 AAAA-AAGAAAAAAATAATAA-AA-AG-AACA
1 AAAATAA-AAAAAATTAA-AATAACAGAAACA
750995 AAACATAAAAAAA
1 AAA-ATAAAAAAA
751008 GGAAAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
28 7 0.19
29 10 0.28
30 17 0.47
31 2 0.06
ACGTcount: A:0.80, C:0.06, G:0.04, T:0.10
Consensus pattern (30 bp):
AAAATAAAAAAAATTAAAATAACAGAAACA
Found at i:751005 original size:34 final size:34
Alignment explanation
Indices: 750932--751022 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
750922 AAATAATATA
* * *
750932 AAAAGAAAATAAAAAA-AATTAAAATAACAGAAAC
1 AAAA-AAAAGAAAAAATAATAAAAAGAACAGAAAC
750966 -AAAAAAAGAAAAAAATAATAAAAAGAACA-AAAC
1 AAAAAAAAG-AAAAAATAATAAAAAGAACAGAAAC
*
750999 ATAAAAAAAGGAAAAATAATAAAA
1 A-AAAAAAAGAAAAAATAATAAAA
751023 TATATAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
32 4 0.08
33 13 0.27
34 24 0.49
35 8 0.16
ACGTcount: A:0.79, C:0.04, G:0.07, T:0.10
Consensus pattern (34 bp):
AAAAAAAAGAAAAAATAATAAAAAGAACAGAAAC
Found at i:751081 original size:2 final size:2
Alignment explanation
Indices: 751076--751108 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
751066 AAAAGAAAAA
751076 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
751109 AACGTTAGGT
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
Done.