Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009149.1 Hibiscus syriacus cultivar Beakdansim tig00112673_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: 1143513
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 4 of 6
Found at i:566216 original size:18 final size:18
Alignment explanation
Indices: 566190--566233 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
566180 GTGAAGTATG
*
566190 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGTCGTGGCA
*
566208 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGCA
*
566226 AGTGTTGT
1 AATGTTGT
566234 AAGGTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGCA
Found at i:566840 original size:12 final size:12
Alignment explanation
Indices: 566823--566847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
566813 CTTTAATGGT
566823 TTGTCACTTGGC
1 TTGTCACTTGGC
566835 TTGTCACTTGGC
1 TTGTCACTTGGC
566847 T
1 T
566848 GAAGTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TTGTCACTTGGC
Found at i:567103 original size:12 final size:12
Alignment explanation
Indices: 567071--567104 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
567061 GAATTGGAAG
*
567071 ACATTCTTACTA
1 ACATTCTTGCTA
567083 ACATTCTTGCTA
1 ACATTCTTGCTA
567095 ACATTCTTGC
1 ACATTCTTGC
567105 ATATGATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (12 bp):
ACATTCTTGCTA
Found at i:572666 original size:18 final size:18
Alignment explanation
Indices: 572640--572683 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
572630 GTGAAGTATG
* *
572640 AATGGTGTTGTCGTGGAA
1 AATGTTGTTGTCCTGGAA
*
572658 AATGTTGTTGTCCTGGTA
1 AATGTTGTTGTCCTGGAA
*
572676 AGTGTTGT
1 AATGTTGT
572684 AAGGTTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.07, G:0.34, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCCTGGAA
Found at i:573676 original size:17 final size:17
Alignment explanation
Indices: 573651--573686 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
573641 AATTAAGATT
573651 TAATCTAATAAATGAAC
1 TAATCTAATAAATGAAC
* *
573668 TAATTTAATGAATGAAC
1 TAATCTAATAAATGAAC
573685 TA
1 TA
573687 GATGATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (17 bp):
TAATCTAATAAATGAAC
Found at i:580973 original size:18 final size:18
Alignment explanation
Indices: 580950--580989 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
580940 ATTCTAAATC
580950 TTTTGCTAATGTAAGTTA
1 TTTTGCTAATGTAAGTTA
580968 TTTTGCTAATGTAAGTTA
1 TTTTGCTAATGTAAGTTA
580986 TTTT
1 TTTT
580990 ACATAGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.55
Consensus pattern (18 bp):
TTTTGCTAATGTAAGTTA
Found at i:582174 original size:14 final size:15
Alignment explanation
Indices: 582142--582173 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
582132 GCACCAGGGC
582142 TTTAACTCTTTGTTT
1 TTTAACTCTTTGTTT
582157 TTTAACTCTTTGTTT
1 TTTAACTCTTTGTTT
582172 TT
1 TT
582174 AGGACAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTAACTCTTTGTTT
Found at i:582570 original size:36 final size:36
Alignment explanation
Indices: 582528--582603 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
582518 TTATAGCTAA
*
582528 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
582564 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
582600 AAAA
1 AAAA
582604 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:588210 original size:19 final size:19
Alignment explanation
Indices: 588173--588211 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
588163 ACTCAACCTG
588173 TAAATGATCTGACATATTGT
1 TAAATGATCTGA-ATATTGT
588193 TAAAGTGATCTG-ATATTGT
1 TAAA-TGATCTGAATATTGT
588212 CCCAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (19 bp):
TAAATGATCTGAATATTGT
Found at i:588929 original size:23 final size:23
Alignment explanation
Indices: 588899--588952 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
588889 CAACAACCGA
*
588899 CAAGCATCAATGTACCAATTCAG
1 CAAGCATCAATGCACCAATTCAG
* * *
588922 CAAGCATCATTGCATCAATTTAG
1 CAAGCATCAATGCACCAATTCAG
588945 CAAGCATC
1 CAAGCATC
588953 CTCAATTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (23 bp):
CAAGCATCAATGCACCAATTCAG
Found at i:589070 original size:20 final size:20
Alignment explanation
Indices: 589045--589105 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
589035 AACACTTACA
*
589045 AATATCAAGTAGAAGCAAGC
1 AATATCAAGCAGAAGCAAGC
* * *
589065 AATATCAAACAAAAGCAAAC
1 AATATCAAGCAGAAGCAAGC
* *
589085 AATATAAAGCAGAATCAAGC
1 AATATCAAGCAGAAGCAAGC
589105 A
1 A
589106 CCAAGTATTG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.13, T:0.13
Consensus pattern (20 bp):
AATATCAAGCAGAAGCAAGC
Found at i:591661 original size:21 final size:21
Alignment explanation
Indices: 591636--591675 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
591626 AAGACTTTAT
591636 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
591657 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
591676 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:598311 original size:64 final size:65
Alignment explanation
Indices: 598187--598342 Score: 167
Period size: 64 Copynumber: 2.4 Consensus size: 65
598177 CACACCCATT
* *
598187 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGAATCGATGCACTCTTAAATATTTTG-AACA
1 TCGAATGCATTTTGTGTACCGATGCACAAGCCAAGAATCGATGCACTCTCAAATATTTTGAAACA
* * *
598251 TCGAATGCATTTTGTGTACCGATGCA-TAGACCAAGCATCGATGCACTC-CAGACTCA-TTTGAA
1 TCGAATGCATTTTGTGTACCGATGCACAAG-CCAAGAATCGATGCACTCTCA-AAT-ATTTTGAA
598313 ACA
63 ACA
* * * * *
598316 TTGAATGTAATTAGTGCACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
598343 CCCTAGTGTA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 3 0.04
64 48 0.62
65 26 0.34
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAGCCAAGAATCGATGCACTCTCAAATATTTTGAAACA
Found at i:600523 original size:2 final size:2
Alignment explanation
Indices: 600516--600547 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
600506 TTTATACCAG
600516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
600548 AAGAATATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:600804 original size:6 final size:6
Alignment explanation
Indices: 600795--600869 Score: 53
Period size: 6 Copynumber: 12.5 Consensus size: 6
600785 TCGAGTTCGA
*** ** *
600795 GTTTGG GTTTGG GTTTGG GTTCCA GTTTCA GTTTGG GTTTGG GTTTTG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * *
600843 GTTAGG GTCCT-G GTTTGG GTTTTG GTT
1 GTTTGG GT-TTGG GTTTGG GTTTGG GTT
600870 AGGGAAGATG
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
5 1 0.02
6 53 0.98
ACGTcount: A:0.04, C:0.07, G:0.40, T:0.49
Consensus pattern (6 bp):
GTTTGG
Found at i:601574 original size:61 final size:61
Alignment explanation
Indices: 601498--601633 Score: 227
Period size: 61 Copynumber: 2.2 Consensus size: 61
601488 TCCTAGTTTT
* *
601498 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATATATTAATTTAAGCTTCATATTTC
1 AAATTTGTTCAATTTAGTCCAAATTTAATGATACAATATATTAATTTAAGCTTCATATTTA
* * *
601559 AAATTTCTTCAATTTAGTCCAAATTTAATGTTACAATTTATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATGATACAATATATTAATTTAAGCTTCATATTTA
601620 AAATTTGTTCAATT
1 AAATTTGTTCAATT
601634 CCTTATATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (61 bp):
AAATTTGTTCAATTTAGTCCAAATTTAATGATACAATATATTAATTTAAGCTTCATATTTA
Found at i:601735 original size:9 final size:9
Alignment explanation
Indices: 601723--601755 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
601713 AACTATATAA
601723 TATATAGTT
1 TATATAGTT
601732 TATATA-TGT
1 TATATAGT-T
601741 TATATAGTT
1 TATATAGTT
601750 TATATA
1 TATATA
601756 TACTAATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (9 bp):
TATATAGTT
Found at i:601787 original size:18 final size:18
Alignment explanation
Indices: 601716--601807 Score: 77
Period size: 18 Copynumber: 5.3 Consensus size: 18
601706 ACTAATGAAC
601716 TATATAATATATAGTTTA
1 TATATAATATATAGTTTA
**
601734 TATATGTTATATAGTTTA
1 TATATAATATATAGTTTA
*
601752 TATATACTA-ATA----A
1 TATATAATATATAGTTTA
*
601765 CTATATAATATATAGTTTG
1 -TATATAATATATAGTTTA
** *
601784 TATATACCATATACTTTA
1 TATATAATATATAGTTTA
601802 TATATA
1 TATATA
601808 TAGTTTTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.02
14 8 0.14
15 3 0.05
17 3 0.05
18 43 0.74
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (18 bp):
TATATAATATATAGTTTA
Found at i:601788 original size:50 final size:51
Alignment explanation
Indices: 601690--601807 Score: 175
Period size: 50 Copynumber: 2.3 Consensus size: 51
601680 AATAAATTAA
* **
601690 TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATGT
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
*
601741 TATATAGTTTATATATACTAAT-AACTATATAATATATAGTTTGTATATAC
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
* *
601791 CATATACTTTATATATA
1 TATATAGTTTATATATA
601808 TAGTTTTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 40 0.66
51 21 0.34
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (51 bp):
TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
Found at i:601821 original size:32 final size:32
Alignment explanation
Indices: 601741--601813 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
601731 TTATATATGT
*
601741 TATATAGTTTATATATACTAATAACTATATAA
1 TATATAGTTTATATATACCAATAACTATATAA
* *
601773 TATATAGTTTGTATATACC-ATATACTTTAT-A
1 TATATAGTTTATATATACCAATA-ACTATATAA
601804 TATATAGTTT
1 TATATAGTTT
601814 TTTATATAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (32 bp):
TATATAGTTTATATATACCAATAACTATATAA
Found at i:601847 original size:18 final size:18
Alignment explanation
Indices: 601816--601877 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
601806 TATAGTTTTT
*
601816 TATATAGTTCATATGTAAAC
1 TATATAG-T-ATATATAAAC
601836 TATATAGTATATATAAAC
1 TATATAGTATATATAAAC
*
601854 TATATATGTA-ATATATAC
1 TATATA-GTATATATAAAC
601872 TATATA
1 TATATA
601878 AATCATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 28 0.72
19 4 0.10
20 7 0.18
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (18 bp):
TATATAGTATATATAAAC
Found at i:602045 original size:7 final size:7
Alignment explanation
Indices: 602030--602143 Score: 51
Period size: 7 Copynumber: 16.6 Consensus size: 7
602020 ATATGTAAAT
*
602030 TATACTA
1 TATAGTA
602037 TATAGTATA
1 TATAG--TA
*
602046 TATAGTT
1 TATAGTA
602053 TATA-TA
1 TATAGTA
*
602059 TATAATA
1 TATAGTA
602066 TATAGTA
1 TATAGTA
*
602073 TATA-AA
1 TATAGTA
*
602079 TATA-AA
1 TATAGTA
602085 CTATAGTA
1 -TATAGTA
*
602093 TGTAGTA
1 TATAGTA
*
602100 TATA-AA
1 TATAGTA
*
602106 TATA-AA
1 TATAGTA
*
602112 CTATAGTT
1 -TATAGTA
*
602120 TTTA-TA
1 TATAGTA
602126 TATAGTA
1 TATAGTA
*
602133 TATACTA
1 TATAGTA
602140 TATA
1 TATA
602144 AATAGTTTAT
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
6 23 0.27
7 53 0.63
8 1 0.01
9 7 0.08
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (7 bp):
TATAGTA
Found at i:602049 original size:9 final size:9
Alignment explanation
Indices: 602035--602076 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
602025 TAAATTATAC
602035 TATATAGTA
1 TATATAGTA
602044 TATATAGTTTA
1 TATATAG--TA
602055 TATATA-TAA
1 TATATAGT-A
602064 TATATAGTA
1 TATATAGTA
602073 TATA
1 TATA
602077 AATATAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.03
9 19 0.66
10 1 0.03
11 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (9 bp):
TATATAGTA
Found at i:602060 original size:20 final size:20
Alignment explanation
Indices: 602030--602144 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
602020 ATATGTAAAT
602030 TATACTATATAGT-ATATATAG
1 TATA-TATATA-TAATATATAG
*
602051 TTTATATATATAATATATAG
1 TATATATATATAATATATAG
*
602071 TATATAAATATAA-ACTATAG
1 TATATATATATAATA-TATAG
*
602091 TATGTAGTATATAA-ATATA-
1 TATATA-TATATAATATATAG
* * *
602110 AACTATAGT-TTTTATATATAG
1 TA-TATA-TATATAATATATAG
602131 TATATACTATATAA
1 TATATA-TATATAA
602145 ATAGTTTATA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
19 6 0.08
20 54 0.73
21 14 0.19
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (20 bp):
TATATATATATAATATATAG
Found at i:602136 original size:27 final size:27
Alignment explanation
Indices: 602059--602118 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
602049 AGTTTATATA
* *
602059 TATAATATATAGTATATAAATATAAAC
1 TATAGTATGTAGTATATAAATATAAAC
602086 TATAGTATGTAGTATATAAATATAAAC
1 TATAGTATGTAGTATATAAATATAAAC
602113 TATAGT
1 TATAGT
602119 TTTTATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.38
Consensus pattern (27 bp):
TATAGTATGTAGTATATAAATATAAAC
Found at i:602193 original size:24 final size:24
Alignment explanation
Indices: 602151--602198 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
602141 ATAAATAGTT
*
602151 TATATAGTTCACTAATAAATTATA
1 TATATAGTTCACTAATAAACTATA
*
602175 TATATAGTTCA-TATGTAAACTATA
1 TATATAGTTCACTA-ATAAACTATA
602199 GTTTATATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (24 bp):
TATATAGTTCACTAATAAACTATA
Found at i:602214 original size:17 final size:17
Alignment explanation
Indices: 602177--602250 Score: 87
Period size: 17 Copynumber: 4.2 Consensus size: 17
602167 AAATTATATA
*
602177 TATAGTTCATATGTAAAC
1 TATAGTTTATATG-AAAC
*
602195 TATAGTTTATATGCAAC
1 TATAGTTTATATGAAAC
*
602212 TATAGTTTATATGTAAC
1 TATAGTTTATATGAAAC
602229 TATAGTTAGTATAT-AAAC
1 TATAGTT--TATATGAAAC
602247 TATA
1 TATA
602251 TAGTTTAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
17 26 0.52
18 19 0.38
19 5 0.10
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (17 bp):
TATAGTTTATATGAAAC
Found at i:602248 original size:35 final size:35
Alignment explanation
Indices: 602177--602250 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
602167 AAATTATATA
*
602177 TATAGTTCATATGTAAACTATAGTTTATATGCAAC
1 TATAGTTCATATGTAAACTATAGTTTATATGAAAC
*
602212 TATAGTTTATATGT-AACTATAGTTAGTATAT-AAAC
1 TATAGTTCATATGTAAACTATAGTT--TATATGAAAC
602247 TATA
1 TATA
602251 TAGTTTAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 10 0.29
35 20 0.57
36 5 0.14
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (35 bp):
TATAGTTCATATGTAAACTATAGTTTATATGAAAC
Found at i:602286 original size:54 final size:51
Alignment explanation
Indices: 602220--602323 Score: 138
Period size: 54 Copynumber: 2.0 Consensus size: 51
602210 ACTATAGTTT
*
602220 ATATGTAACTATAGTT-AGTATATAAACTATATAGTTTAACTATAGTTCATATC
1 ATATGTAACTATAGTTCA-TATATAAACTATATAATTT-A-TATAGTTCATATC
* *
602273 ATATGTAAACTATAGTTCATATATCAACTATATAATTTATATAGTTTATAT
1 ATATGT-AACTATAGTTCATATATAAACTATATAATTTATATAGTTCATAT
602324 ATAAATATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
52 11 0.24
53 7 0.15
54 27 0.59
55 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (51 bp):
ATATGTAACTATAGTTCATATATAAACTATATAATTTATATAGTTCATATC
Found at i:602362 original size:25 final size:27
Alignment explanation
Indices: 602328--602384 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
602318 TTATATATAA
*
602328 ATATCAACTAT-A-GTATATAGTTTAT
1 ATATAAACTATAATGTATATAGTTTAT
* *
602353 ATATAAACTATAATTTATATAGTTTTT
1 ATATAAACTATAATGTATATAGTTTAT
602380 ATATA
1 ATATA
602385 TAGTTCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 10 0.37
26 1 0.04
27 16 0.59
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (27 bp):
ATATAAACTATAATGTATATAGTTTAT
Found at i:602385 original size:31 final size:31
Alignment explanation
Indices: 602303--602386 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 31
602293 ATATCAACTA
* *
602303 TATAATTTATATAGTTTATATATAAATATCAAC
1 TATAATTTATATAGTTT-T-TATATATATAAAC
*
602336 TAT-A-GTATATAG---TT-TATATATAAAC
1 TATAATTTATATAGTTTTTATATATATAAAC
602361 TATAATTTATATAGTTTTTATATATA
1 TATAATTTATATAGTTTTTATATATA
602387 GTTCATATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
25 12 0.29
26 2 0.05
27 8 0.20
30 2 0.05
31 13 0.32
32 1 0.02
33 3 0.07
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.49
Consensus pattern (31 bp):
TATAATTTATATAGTTTTTATATATATAAAC
Found at i:602405 original size:60 final size:60
Alignment explanation
Indices: 602268--602414 Score: 148
Period size: 58 Copynumber: 2.5 Consensus size: 60
602258 ACTATAGTTC
* *
602268 ATATCATATGTAAA-CTATAGTTCATATATCAACTATATAATTTATATAGTTTATATATAA
1 ATATCATATGTAAATATATAGTTCATATATAAAC-ATATAATTTATATAGTTTATATATAA
* * * *
602328 ATATCA-A-CTATAGTATATAGTTTATATATAAAC-TATAATTTATATAGTTTTTATATATA
1 ATATCATATGTA-AATATATAGTTCATATATAAACATATAATTTATATAGTTTATATATA-A
*
602387 GT-TCATATGTAAAT-TATA-TT-ATATATAA
1 ATATCATATGTAAATATATAGTTCATATATAA
602415 CTTTTTAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
56 8 0.11
57 2 0.03
58 32 0.44
59 7 0.10
60 24 0.33
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (60 bp):
ATATCATATGTAAATATATAGTTCATATATAAACATATAATTTATATAGTTTATATATAA
Found at i:602736 original size:179 final size:181
Alignment explanation
Indices: 602411--602753 Score: 557
Period size: 179 Copynumber: 1.9 Consensus size: 181
602401 TATATTATAT
* *
602411 ATAACTTTTTAAATGGGTATAATTTTGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAAT
1 ATAACTTTTTAAATGGGAATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAAT
* * *
602476 TATTTTGATTTGATCCCTCATCAATATGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTT
66 TATTTCGATTTGATCCCTCATCAATATGTGTTGTTTAATTTATTAAAATTTTTATTTGTAATTTC
602541 ATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATCTAAAATTGGCCC
131 ATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATCTAAAATTGGCCC
*
602592 ATAACTTTTTAAATGTGAATAATTTAGTA-TTTTTTGTATTAATTTCAACCTCACAATTTAAAAT
1 ATAACTTTTTAAATGGGAATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAAT
* *
602656 TATTTCGATTTGATCCCTTAT-AATGTGTGTTGTTTAATTTATTAAAA-TTTTATTTTGTAATTT
66 TATTTCGATTTGATCCCTCATCAATATGTGTTGTTTAATTTATTAAAATTTTTA-TTTGTAATTT
* * *
602719 CATATTTGTTCAATTTAGTTCTTAAATTTGTATTT
130 CATATTTGTTCAATTTAGTCCTTAAAATTATATTT
602754 TTCATAAAAT
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
178 5 0.03
179 65 0.43
180 54 0.36
181 26 0.17
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.52
Consensus pattern (181 bp):
ATAACTTTTTAAATGGGAATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAAT
TATTTCGATTTGATCCCTCATCAATATGTGTTGTTTAATTTATTAAAATTTTTATTTGTAATTTC
ATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATCTAAAATTGGCCC
Found at i:606664 original size:29 final size:30
Alignment explanation
Indices: 606630--606705 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 30
606620 TTTTCTTACC
606630 TAAGTATCTAAAGTA-CTTTT-TGGTCAAAA
1 TAAGTATCTAAAGTATCTTTTCT-GTCAAAA
606659 TAAGTATCTAAAGTTATCTTTTCTGTCAAAA
1 TAAGTATCTAAAG-TATCTTTTCTGTCAAAA
*
606690 TAGGTATCTAAAGTAT
1 TAAGTATCTAAAGTAT
606706 TCAATTTGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 13 0.30
30 5 0.12
31 24 0.56
32 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (30 bp):
TAAGTATCTAAAGTATCTTTTCTGTCAAAA
Found at i:606733 original size:30 final size:30
Alignment explanation
Indices: 606697--606767 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
606687 AAATAGGTAT
* *
606697 CTAAAGTATTCAATTTGTTCATCTAAGTAC
1 CTAAAGTATTCAATTCGTACATCTAAGTAC
606727 CTAAAGTATTCAATTCGTACATCTAAGTAC
1 CTAAAGTATTCAATTCGTACATCTAAGTAC
*
606757 CTAAATTATTC
1 CTAAAGTATTC
606768 TTTAATTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
CTAAAGTATTCAATTCGTACATCTAAGTAC
Found at i:615322 original size:15 final size:14
Alignment explanation
Indices: 615298--615327 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
615288 TCACTTTTTA
615298 TCTTTTAAAATTAT
1 TCTTTTAAAATTAT
615312 TCTTCTTAAAATTAT
1 TCTT-TTAAAATTAT
615327 T
1 T
615328 TTAAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (14 bp):
TCTTTTAAAATTAT
Found at i:621591 original size:24 final size:24
Alignment explanation
Indices: 621556--621603 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
621546 AAGCCCTTAT
*
621556 GCACCCTGTTTCAACAAAATCGAC
1 GCACCCTATTTCAACAAAATCGAC
*
621580 GCACCCTATTTCAATAAAATCGAC
1 GCACCCTATTTCAACAAAATCGAC
621604 ACTTTGTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.23
Consensus pattern (24 bp):
GCACCCTATTTCAACAAAATCGAC
Found at i:625664 original size:26 final size:25
Alignment explanation
Indices: 625630--625679 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
625620 GCCTTAGCAT
625630 AAAAATTTGATAATGAATGATGAAA
1 AAAAATTTGATAATGAATGATGAAA
*
625655 AAAAACTTTGATAATGAATTATGAA
1 AAAAA-TTTGATAATGAATGATGAA
625680 GACCCCGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30
Consensus pattern (25 bp):
AAAAATTTGATAATGAATGATGAAA
Found at i:626350 original size:20 final size:20
Alignment explanation
Indices: 626313--626351 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
626303 AAAGCTCATA
* *
626313 TAGGATCATATAGATGCATT
1 TAGGAGCATACAGATGCATT
*
626333 TAGGAGCATACAGTTGCAT
1 TAGGAGCATACAGATGCAT
626352 GTGGTGGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (20 bp):
TAGGAGCATACAGATGCATT
Found at i:628358 original size:20 final size:20
Alignment explanation
Indices: 628329--628380 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
628319 TATGCTGGAT
*
628329 AGTATCGATACCGTTGAAGC
1 AGTATTGATACCGTTGAAGC
* *
628349 AGTATTGATACCGTTGCAGT
1 AGTATTGATACCGTTGAAGC
*
628369 AATATTGATACC
1 AGTATTGATACC
628381 ATTGTAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTATTGATACCGTTGAAGC
Found at i:628491 original size:20 final size:20
Alignment explanation
Indices: 628442--628497 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
628432 TACCGTAAGG
* *
628442 GGGTATCGATAACATAGTAT
1 GGGTATCGATACCATAGTAA
*
628462 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
628484 GGGTATCGATACCA
1 GGGTATCGATACCA
628498 GGAAGCATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:628564 original size:95 final size:96
Alignment explanation
Indices: 628375--628590 Score: 240
Period size: 95 Copynumber: 2.3 Consensus size: 96
628365 CAGTAATATT
* * * *
628375 GATACCATTGTAAGGGTATCGATACCAAGAAAACATCTAATCTAATTTTAGTATCGATACCGTAA
1 GATACCATGGTAAGGGTATCGATACCAAGAAAACATCAAACCTAATTTTAGTATCGATACCGGAA
** *
628440 GGGGGTATCGATAACATAGTATGGTAGTATC
66 GGAAGTATCGATAACATAGTATGGAAGTATC
* * *
628471 GATACCATGGTAAGGGTATCGATACC-AGGAAGCATCAAACCTAATTTTGGTATCGATACCCGGA
1 GATACCATGGTAAGGGTATCGATACCAAGAAAACATCAAACCTAATTTTAGTATCGATA-CCGGA
* * * * *
628535 A-GAAGTATTGGTACCATAGTGTTGAAGTATC
65 AGGAAGTATCGATAACATAGTATGGAAGTATC
* *
628566 GATACTATGGT-AGTAGTATCGATAC
1 GATACCATGGTAAG-GGTATCGATAC
628591 TACTAAGCTT
Statistics
Matches: 101, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
94 2 0.02
95 69 0.68
96 30 0.30
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (96 bp):
GATACCATGGTAAGGGTATCGATACCAAGAAAACATCAAACCTAATTTTAGTATCGATACCGGAA
GGAAGTATCGATAACATAGTATGGAAGTATC
Found at i:629681 original size:21 final size:21
Alignment explanation
Indices: 629655--629703 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
629645 GGGAGCGTCA
629655 GTGCATCGATACATATACAAG
1 GTGCATCGATACATATACAAG
* **
629676 GTGCATCGGTGGATATACAAG
1 GTGCATCGATACATATACAAG
629697 GTGCATC
1 GTGCATC
629704 AAGGCATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (21 bp):
GTGCATCGATACATATACAAG
Found at i:629873 original size:65 final size:65
Alignment explanation
Indices: 629770--629911 Score: 182
Period size: 65 Copynumber: 2.2 Consensus size: 65
629760 GCACTAAGAG
* * * * * *
629770 TGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCAT-GTCTTGTGCATCGATGCATCAA
1 TGCATTCGATGTTTTCAAAATACCCTAAGTGCATCGATGCATGGT-ATGAGCATCAATGCATAAA
629833 A
65 A
629834 TGCATTCGATGTTTTCATAAA-ACCCTAAGTGCATCGATGCATGGTATGAGCATCAATGCATAAA
1 TGCATTCGATGTTTTCA-AAATACCCTAAGTGCATCGATGCATGGTATGAGCATCAATGCATAAA
629898 A
65 A
*
629899 TGCATTTGATGTT
1 TGCATTCGATGTT
629912 CAATTTATTC
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 11 0.16
65 52 0.76
66 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (65 bp):
TGCATTCGATGTTTTCAAAATACCCTAAGTGCATCGATGCATGGTATGAGCATCAATGCATAAAA
Found at i:629958 original size:20 final size:20
Alignment explanation
Indices: 629922--629959 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
629912 CAATTTATTC
*
629922 ATTGGTGCATTGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
629942 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
629960 TCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:632654 original size:21 final size:23
Alignment explanation
Indices: 632602--632679 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
632592 GGCTTTGTGC
* *
632602 ATCGATGCACATTTAA-GGAGTGC
1 ATCGATGCACATTCAAGGGA-TGT
* * *
632625 ATCGGTGCACCTTC-ATGG-TGT
1 ATCGATGCACATTCAAGGGATGT
632646 ATCGATGCACATTCAAAGGGATGT
1 ATCGATGCACATTC-AAGGGATGT
632670 ATCGATGCAC
1 ATCGATGCAC
632680 TGTTAAGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.32
22 1 0.02
23 16 0.36
24 13 0.30
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (23 bp):
ATCGATGCACATTCAAGGGATGT
Found at i:638563 original size:19 final size:19
Alignment explanation
Indices: 638535--638586 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
638525 AATAGCCTGA
* *
638535 GTGCAACGATGCATGTCTT
1 GTGCATCGATGCATGTATT
638554 GTGCATCGATGCATGTATT
1 GTGCATCGATGCATGTATT
638573 GTGCATCGATGCAT
1 GTGCATCGATGCAT
638587 CAAATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCATGTATT
Found at i:639169 original size:46 final size:45
Alignment explanation
Indices: 638967--639175 Score: 240
Period size: 45 Copynumber: 4.6 Consensus size: 45
638957 ATGCCATTGC
* ** * * **
638967 TGAAATGCATATGTGTGCATGGTCAACTGAAAAGTGTGTTATAGT
1 TGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGGCATAGT
* *
639012 TGAAATGCATATGGGTGCATTGTCAACAGAAAATTATGGCATAGT
1 TGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGGCATAGT
* *
639057 TGAAATGCATATGGGTGCATTATCAATAGAAAATTATGGCATAGT
1 TGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGGCATAGT
* **
639102 TGAAATGCATATGGGTGCATTATTAACAGAAAAGTATGTTATAGT
1 TGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGGCATAGT
* * *
639147 TAAAAAAGCATAAT-GGTGCATTATAAACA
1 T-GAAATGCAT-ATGGGTGCATTATCAACA
639176 TGAATGGAGG
Statistics
Matches: 145, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
45 122 0.84
46 21 0.14
47 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (45 bp):
TGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGGCATAGT
Found at i:646928 original size:13 final size:14
Alignment explanation
Indices: 646912--646940 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
646902 CATATGGAAC
646912 TTAAGTAA-TTTAA
1 TTAAGTAATTTTAA
646925 TTAAGTAATTTTAA
1 TTAAGTAATTTTAA
646939 TT
1 TT
646941 TAACGGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTAAGTAATTTTAA
Found at i:648865 original size:47 final size:47
Alignment explanation
Indices: 648808--648945 Score: 239
Period size: 43 Copynumber: 3.0 Consensus size: 47
648798 TAATACCTAG
648808 GAAGTATGTTTTGATAAATTAATGTCAATAACATAAATACCTGAAAT
1 GAAGTATGTTTTGATAAATTAATGTCAATAACATAAATACCTGAAAT
648855 GAAGTATGTTTTGATAAATTAATGTCAATAAC----ATACCTGAAAT
1 GAAGTATGTTTTGATAAATTAATGTCAATAACATAAATACCTGAAAT
*
648898 GAAGTATGTTTTGATAAATTAATGTCAATAACATAAATACCTAAAAT
1 GAAGTATGTTTTGATAAATTAATGTCAATAACATAAATACCTGAAAT
648945 G
1 G
648946 GATGCTCTAT
Statistics
Matches: 86, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
43 43 0.50
47 43 0.50
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (47 bp):
GAAGTATGTTTTGATAAATTAATGTCAATAACATAAATACCTGAAAT
Found at i:649923 original size:13 final size:13
Alignment explanation
Indices: 649871--649927 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
649861 AGATTTTTAA
649871 AATA-TTTAAATTT
1 AATATTTTAAA-TT
*
649884 AATATTTTAACTT
1 AATATTTTAAATT
* * *
649897 ACCTAATGTAAATT
1 A-ATATTTTAAATT
649911 AATATTTTAAATT
1 AATATTTTAAATT
649924 AATA
1 AATA
649928 GGAAGATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 20 0.59
14 14 0.41
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (13 bp):
AATATTTTAAATT
Found at i:651898 original size:79 final size:79
Alignment explanation
Indices: 651796--651954 Score: 223
Period size: 79 Copynumber: 2.0 Consensus size: 79
651786 AAAAAACAAT
**
651796 ATTATAGGTGGTGCTCAATATTAACATTTCTGGTAGAAAAAATAATATTTTAGGTAACACTTTAC
1 ATTATAGGTGGTGCTCAATATTAACATTTCTAATAGAAAAAATAATATTTTAGGTAACACTTTAC
*
651861 CGGAAACGTTAAAA
66 CGAAAACGTTAAAA
* * *
651875 ATTATAGGTAGCGT-CT-AATATTAATATTTTTAATAGAAAAAATAATGTTTTAGGTAACACTTT
1 ATTATAGGT-G-GTGCTCAATATTAACATTTCTAATAGAAAAAATAATATTTTAGGTAACACTTT
*
651938 ACCGAAAATGTTAAAA
64 ACCGAAAACGTTAAAA
651954 A
1 A
651955 AATATAAACA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
79 66 0.93
80 3 0.04
81 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (79 bp):
ATTATAGGTGGTGCTCAATATTAACATTTCTAATAGAAAAAATAATATTTTAGGTAACACTTTAC
CGAAAACGTTAAAA
Found at i:652114 original size:20 final size:20
Alignment explanation
Indices: 652089--652137 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
652079 ATTTAATGGG
652089 CACCAAATTGTTTACCATTC
1 CACCAAATTGTTTACCATTC
652109 CACCAAATTGTTTACCATTC
1 CACCAAATTGTTTACCATTC
652129 CACCAAATT
1 CACCAAATT
652138 ATGTATCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.33
Consensus pattern (20 bp):
CACCAAATTGTTTACCATTC
Found at i:654596 original size:15 final size:15
Alignment explanation
Indices: 654576--654613 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
654566 ACCTTAACTG
654576 GTTCAGCTGCTTTCA
1 GTTCAGCTGCTTTCA
654591 GTTCAGCTGCTTTCA
1 GTTCAGCTGCTTTCA
654606 GTTCAGCT
1 GTTCAGCT
654614 TCCATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.39
Consensus pattern (15 bp):
GTTCAGCTGCTTTCA
Found at i:658365 original size:31 final size:31
Alignment explanation
Indices: 658316--658402 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 31
658306 ATTAATGTAG
*
658316 TAAATTGATATTTTATATAAAATTTAGAGGAT
1 TAAATTAATATTTTATATAAAATTTA-AGGAT
658348 TAAATTAATA-TTTATAT-AAATTTAA-GAT
1 TAAATTAATATTTTATATAAAATTTAAGGAT
* * * *
658376 CAAATTAGTATTTTGTTTAAAATTTAA
1 TAAATTAATATTTTATATAAAATTTAA
658403 AGGTTACATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
28 11 0.23
29 6 0.12
30 15 0.31
31 7 0.15
32 9 0.19
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (31 bp):
TAAATTAATATTTTATATAAAATTTAAGGAT
Found at i:658387 original size:28 final size:31
Alignment explanation
Indices: 658317--658388 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 31
658307 TTAATGTAGT
* *
658317 AAATTGATATTTTATATAAAATTTAGAGGATT
1 AAATTAATA-TTTATATAAAATTTAGAGGATC
658349 AAATTAATATTTATAT-AAATTTA-A-GATC
1 AAATTAATATTTATATAAAATTTAGAGGATC
*
658377 AAATTAGTATTT
1 AAATTAATATTT
658389 TGTTTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 14 0.38
29 1 0.03
30 7 0.19
31 7 0.19
32 8 0.22
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (31 bp):
AAATTAATATTTATATAAAATTTAGAGGATC
Found at i:658806 original size:21 final size:20
Alignment explanation
Indices: 658780--658888 Score: 128
Period size: 20 Copynumber: 5.3 Consensus size: 20
658770 GATTCTGACT
658780 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
** *
658801 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
658822 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
658842 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* *
658862 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
658882 ATCGCAA
1 ATCGCAA
658889 TCATTCAGAA
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
20 42 0.57
21 32 0.43
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:658875 original size:40 final size:41
Alignment explanation
Indices: 658780--658888 Score: 175
Period size: 40 Copynumber: 2.7 Consensus size: 41
658770 GATTCTGACT
*
658780 ATCGCAACGAGTATCCGTAAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGACAATACGTAAA
*
658822 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-AA
1 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
*
658862 ATCGCAACGCGTATCTGTAAATCGCAA
1 ATCGCAACGCGTATCCGTAAATCGCAA
658889 TCATTCAGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 28 0.44
41 19 0.30
42 17 0.27
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
Found at i:658881 original size:20 final size:20
Alignment explanation
Indices: 658723--658888 Score: 126
Period size: 20 Copynumber: 8.2 Consensus size: 20
658713 TTCCATAATT
* *
658723 GCAACGCGAATATGAAAATC
1 GCAACGCGAATCTGTAAATC
*
658743 GCAACGCGAA-CATATAAATC
1 GCAACGCGAATC-TGTAAATC
* *
658763 GCAACGCGATTCTG-ACTATC
1 GCAACGCGAATCTGTA-AATC
* * *
658783 GCAACGAGTATCCGTAAAATC
1 GCAACGCGAATCTGT-AAATC
658804 GCAACGAC-AATAC-GTAAAATC
1 GCAACG-CGAAT-CTGT-AAATC
* *
658825 GCAACGCGTATCCGTAAATC
1 GCAACGCGAATCTGTAAATC
*
658845 GCAACGAGAATAC-GTAAATC
1 GCAACGCGAAT-CTGTAAATC
*
658865 GCAACGCGTATCTGTAAATC
1 GCAACGCGAATCTGTAAATC
658885 GCAA
1 GCAA
658889 TCATTCAGAA
Statistics
Matches: 117, Mismatches: 18, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.02
20 82 0.70
21 31 0.26
22 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
GCAACGCGAATCTGTAAATC
Found at i:659237 original size:20 final size:20
Alignment explanation
Indices: 659212--659262 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
659202 TTCTAAACTT
*
659212 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
659232 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
659252 AATATCGCAAC
1 AAAATCGCAAC
659263 GAGAGAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.53, C:0.20, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:659307 original size:19 final size:19
Alignment explanation
Indices: 659272--659308 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
659262 CGAGAGAATC
**
659272 GCAACGCGAAATGAAAATT
1 GCAACGCGAAACCAAAATT
659291 GCAACGCGAAACCAAAAT
1 GCAACGCGAAACCAAAAT
659309 CGCATTGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.11
Consensus pattern (19 bp):
GCAACGCGAAACCAAAATT
Found at i:659330 original size:19 final size:19
Alignment explanation
Indices: 659308--659372 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
659298 GAAACCAAAA
*
659308 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
659327 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
659341 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
659360 TCGCGTTGCGATT
1 TCGCGTTGCGATT
659373 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:659349 original size:14 final size:14
Alignment explanation
Indices: 659330--659386 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
659320 TTTCATTTCG
659330 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
659344 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
659363 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
659377 CGTTGCGATT
1 CGTTGCGATT
659387 TTTATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:659355 original size:33 final size:33
Alignment explanation
Indices: 659313--659394 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
659303 CAAAATCGCA
659313 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
659346 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
659379 TTGCGATTTTTATTTC
1 TTGCGATTTTCATTTC
659395 AACCAAAAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:661252 original size:94 final size:94
Alignment explanation
Indices: 661091--661470 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
661081 TAGATTGCTT
* * *
661091 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
661156 ATTTGTCTTTTGTTTTGTCTTTTGGTT-AA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
661185 AGTAAATTTATTCGGTTGCTGCCAGTTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
661250 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
661279 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
661344 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
661373 AGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
661438 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
661466 AGTAA
1 AGTAA
661471 TGCAATCCAT
Statistics
Matches: 276, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 25 0.09
94 251 0.91
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:661577 original size:14 final size:14
Alignment explanation
Indices: 661558--661641 Score: 96
Period size: 14 Copynumber: 5.6 Consensus size: 14
661548 AAAAATGACT
661558 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
661572 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
661586 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
661605 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
661619 ATCGCAACGACAAA
1 ATCGCAACGAGAGA
661633 ATCGCAACG
1 ATCGCAACG
661642 CGAAACCAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
14 43 0.70
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 8 0.13
ACGTcount: A:0.45, C:0.24, G:0.23, T:0.08
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:661609 original size:47 final size:47
Alignment explanation
Indices: 661558--661660 Score: 161
Period size: 47 Copynumber: 2.2 Consensus size: 47
661548 AAAAATGACT
* * **
661558 ATCGCAACGAGAGAATCGCAACGAGAGAATCGCAACACGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGACAAAATCGCAACACGAAACCAAA
*
661605 ATCGCAACGAGAGAATCGCAACGACAAAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAGAATCGCAACGACAAAATCGCAACACGAAACCAAA
661652 ATCGCAACG
1 ATCGCAACG
661661 CGAAACTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.08
Consensus pattern (47 bp):
ATCGCAACGAGAGAATCGCAACGACAAAATCGCAACACGAAACCAAA
Found at i:661675 original size:19 final size:19
Alignment explanation
Indices: 661629--661666 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
661619 ATCGCAACGA
661629 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
661648 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
661667 TATAATCGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.32, G:0.16, T:0.05
Consensus pattern (19 bp):
CAAAATCGCAACGCGAAAC
Found at i:661694 original size:19 final size:19
Alignment explanation
Indices: 661672--661792 Score: 100
Period size: 19 Copynumber: 6.8 Consensus size: 19
661662 GAAACTATAA
*
661672 TCGCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
661691 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
661705 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
661724 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
661738 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
661757 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
661778 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
661793 AAGTTCCAGA
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.25
16 6 0.08
17 6 0.08
19 34 0.43
21 14 0.17
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:661713 original size:14 final size:14
Alignment explanation
Indices: 661694--661750 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
661684 TTTCATTTCG
661694 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
661708 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
661727 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
661741 CGTTGCGATT
1 CGTTGCGATT
661751 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:661722 original size:33 final size:33
Alignment explanation
Indices: 661675--661768 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
661665 ACTATAATCG
*
661675 CGTTACGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
661708 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
661741 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
661769 AGTCATTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:662269 original size:21 final size:21
Alignment explanation
Indices: 662245--662311 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
662235 TCATTCCTCG
662245 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
662266 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
662287 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
662308 AGAG
1 AGAG
662312 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:662269 original size:42 final size:42
Alignment explanation
Indices: 662218--662311 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
662208 CCACTCCTAT
* *
662218 CATTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CATTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * * *
662260 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
662302 CATTCAAGAG
1 CATTCAAGAG
662312 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.09
42 37 0.86
43 2 0.05
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (42 bp):
CATTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:663681 original size:14 final size:14
Alignment explanation
Indices: 663662--663697 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
663652 ATTGTTTAAT
663662 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
663676 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
663690 TGATTTGT
1 TGATTTGT
663698 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:663826 original size:19 final size:18
Alignment explanation
Indices: 663804--663862 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
663794 AAAAATGACT
663804 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
*
663823 ATCGCAA-CG--A-GAGA
1 ATCGCAATCGAAATGAAA
663837 ATCGCAATACGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
663856 ATCGCAA
1 ATCGCAA
663863 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (18 bp):
ATCGCAATCGAAATGAAA
Found at i:663883 original size:33 final size:33
Alignment explanation
Indices: 663804--663883 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
663794 AAAAATGACT
* *
663804 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
663837 ATCGCAATACGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
663870 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
663884 CTAAATTCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:663935 original size:33 final size:33
Alignment explanation
Indices: 663893--664053 Score: 197
Period size: 33 Copynumber: 4.8 Consensus size: 33
663883 ACTAAATTCA
*
663893 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
663926 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* *
663965 CGTTGCGATTTTCA---CG--TTGCGATTTTCA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
663993 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
664026 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
664054 AGACATTAAG
Statistics
Matches: 111, Mismatches: 6, Indels: 22
0.80 0.04 0.16
Matches are distributed among these distances:
28 15 0.14
29 1 0.01
31 2 0.02
32 1 0.01
33 65 0.59
34 7 0.06
35 2 0.02
36 2 0.02
38 1 0.01
39 15 0.14
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:663972 original size:20 final size:19
Alignment explanation
Indices: 663926--663973 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
663916 GCGATTCTCT
**
663926 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
663945 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
663965 CGTTGCGAT
1 CGTTGCGAT
663974 TTTCACGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:663982 original size:14 final size:14
Alignment explanation
Indices: 663965--664039 Score: 87
Period size: 14 Copynumber: 5.0 Consensus size: 14
663955 GTCATTTCCG
663965 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
663979 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
663993 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
* *
664007 TTTCGCATTGCGATTCTCT
1 ---CG--TTGCGATTTTCA
664026 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
664040 TTTCGCATTG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 38 0.73
16 2 0.04
17 2 0.04
19 10 0.19
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:666484 original size:24 final size:24
Alignment explanation
Indices: 666450--666503 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
666440 CTGAAAAATC
666450 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
666474 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
666498 ATCAAA
1 ATCAAA
666504 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:666517 original size:24 final size:24
Alignment explanation
Indices: 666450--666517 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
666440 CTGAAAAATC
* * *
666450 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
666474 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
666498 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
666518 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:667379 original size:20 final size:21
Alignment explanation
Indices: 667346--667454 Score: 86
Period size: 20 Copynumber: 5.5 Consensus size: 21
667336 AGAATCTCGT
*
667346 TGCGATTTAC-TAAATCGCAA
1 TGCGAATTACGTAAATCGCAA
667366 TGC-AATTACGTAAATCGCAA
1 TGCGAATTACGTAAATCGCAA
* *
667386 TGCGAA-TACGT-ATTCGCAT
1 TGCGAATTACGTAAATCGCAA
* * *
667405 TGCGATTTACAT-AATCGCAT
1 TGCGAATTACGTAAATCGCAA
* * *
667425 TGCGATTTACGT-ATTCGCAT
1 TGCGAATTACGTAAATCGCAA
*
667445 TGCGATTTAC
1 TGCGAATTAC
667455 AGATACGCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
19 16 0.21
20 60 0.77
21 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
TGCGAATTACGTAAATCGCAA
Found at i:667403 original size:39 final size:40
Alignment explanation
Indices: 667360--667455 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
667350 ATTTACTAAA
*
667360 TCGCAATGC-AATTACGTAAATCGCAATGCGA-ATACGTAT
1 TCGCAATGCGAATTACAT-AATCGCAATGCGATATACGTAT
* * * *
667399 TCGCATTGCGATTTACATAATCGCATTGCGATTTACGTAT
1 TCGCAATGCGAATTACATAATCGCAATGCGATATACGTAT
* *
667439 TCGCATTGCGATTTACA
1 TCGCAATGCGAATTACA
667456 GATACGCATT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 20 0.40
40 30 0.60
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (40 bp):
TCGCAATGCGAATTACATAATCGCAATGCGATATACGTAT
Found at i:667421 original size:59 final size:60
Alignment explanation
Indices: 667345--667474 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 60
667335 CAGAATCTCG
*
667345 TTGCGATTTACTAAATCGCAATGC-AATTACGTAAATCGCAATGCGA-ATAC-GTATTCGCA
1 TTGCGATTTACTAAATCGCAATGCGAATTACGT-AATCGCAATGCGATATACAG-ATACGCA
* * * * *
667404 TTGCGATTTAC-ATAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACAGATACGCA
1 TTGCGATTTACTA-AATCGCAATGCGAATTACGTAATCGCAATGCGATATACAGATACGCA
667464 TTGCGATTTAC
1 TTGCGATTTAC
667475 GGATACGCGT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
58 1 0.02
59 32 0.52
60 27 0.44
61 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (60 bp):
TTGCGATTTACTAAATCGCAATGCGAATTACGTAATCGCAATGCGATATACAGATACGCA
Found at i:667443 original size:40 final size:40
Alignment explanation
Indices: 667378--667533 Score: 156
Period size: 40 Copynumber: 3.9 Consensus size: 40
667368 CAATTACGTA
* * *
667378 AATCGCAATGCGA-ATACGTATTCGCATTGCGATTTACAT
1 AATCGCATTGCGATTTACGTATACGCATTGCGATTTACAT
*
667417 AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACA-
1 AATCGCATTGCGATTTACGTATACGCATTGCGATTTACAT
* * * *
667456 GATACGCATTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 AAT-CGCATTGCGATTTACGTATACGCATTGCGA-TTTACAT
* * * *
667498 -ATTGTCGTTGCGATTTACGAATACGCGTTGCGATTT
1 AATCG-CATTGCGATTTACGTATACGCATTGCGATTT
667534 TACGGATACT
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
39 14 0.14
40 55 0.54
41 33 0.32
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (40 bp):
AATCGCATTGCGATTTACGTATACGCATTGCGATTTACAT
Found at i:667463 original size:20 final size:19
Alignment explanation
Indices: 667400--667551 Score: 137
Period size: 20 Copynumber: 7.5 Consensus size: 19
667390 AATACGTATT
667400 CGCATTGCGATTTAC-ATAA
1 CGCATTGCGATTTACGAT-A
*
667419 TCGCATTGCGATTTACGTATT
1 -CGCATTGCGATTTACG-ATA
667440 CGCATTGCGATTTACAGATA
1 CGCATTGCGATTTAC-GATA
667460 CGCATTGCGATTTACGGATA
1 CGCATTGCGATTTAC-GATA
*
667480 CGCGTTGCGATTTTACG-TA
1 CGCATTGCGA-TTTACGATA
* *
667499 TTGTCGTTGCGATTTACGAATA
1 -CG-CATTGCGATTTACG-ATA
*
667521 CGCGTTGCGATTTTACGGATA
1 CGCATTGCGA-TTTAC-GATA
*
667542 CTCATTGCGA
1 CGCATTGCGA
667552 CAGTCAGAAT
Statistics
Matches: 114, Mismatches: 8, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.02
20 76 0.67
21 31 0.27
22 5 0.04
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (19 bp):
CGCATTGCGATTTACGATA
Found at i:667471 original size:60 final size:60
Alignment explanation
Indices: 667345--667533 Score: 176
Period size: 60 Copynumber: 3.1 Consensus size: 60
667335 CAGAATCTCG
* * * * * * *
667345 TTGCGATTTAC-TAAATCGCAATGC-AATTACGTAAATCGCAATGCGA-ATACGTATTCGCA
1 TTGCGATTTACAT-AATCGCATTGCGATTTACGT-ATTCGCATTGCGATTTACGAATACGCA
667404 TTGCGATTTACATAATCGCATTGCGATTTACGTATTCGCATTGCGATTTAC-AGATACGCA
1 TTGCGATTTACATAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGA-ATACGCA
* * *
667464 TTGCGATTTACGGAT-A-CGCGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGAATACGCG
1 TTGCGATTTAC--ATAATCGCATTGCGA-TTTACGTATTCG-CATTGCGATTTACGAATACGCA
667525 TTGCGATTT
1 TTGCGATTT
667534 TACGGATACT
Statistics
Matches: 111, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
59 32 0.29
60 38 0.34
61 38 0.34
62 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (60 bp):
TTGCGATTTACATAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGAATACGCA
Found at i:667550 original size:41 final size:41
Alignment explanation
Indices: 667422--667551 Score: 163
Period size: 41 Copynumber: 3.2 Consensus size: 41
667412 TACATAATCG
* * * * *
667422 CATTGCGATTTACGTATTCGCATTGCGA-TTTACAGATACG
1 CATTGCGATTTACGAATACGCGTTGCGATTTTACGGATACT
* * **
667462 CATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CATTGCGATTTACGAATACGCGTTGCGATTTTACGGATACT
*
667503 CGTTGCGATTTACGAATACGCGTTGCGATTTTACGGATACT
1 CATTGCGATTTACGAATACGCGTTGCGATTTTACGGATACT
667544 CATTGCGA
1 CATTGCGA
667552 CAGTCAGAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 25 0.33
41 50 0.67
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (41 bp):
CATTGCGATTTACGAATACGCGTTGCGATTTTACGGATACT
Found at i:667591 original size:20 final size:20
Alignment explanation
Indices: 667566--667633 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
667556 CAGAATCACA
*
667566 TTGTGATTTAT-ATGTTCGCG
1 TTGTGATTT-TCATATTCGCG
667586 TTGTGATTTTCATATTCGCG
1 TTGTGATTTTCATATTCGCG
667606 TTGTGATTTTCATATTCGCG
1 TTGTGATTTTCATATTCGCG
*
667626 TTGCGATT
1 TTGTGATT
667634 CTGGAAAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.15, C:0.13, G:0.22, T:0.50
Consensus pattern (20 bp):
TTGTGATTTTCATATTCGCG
Found at i:667732 original size:20 final size:19
Alignment explanation
Indices: 667683--667736 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
667673 ATTCTTCATA
667683 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
667702 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
667723 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
667737 TTTATTTCGT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:672838 original size:470 final size:471
Alignment explanation
Indices: 671756--673641 Score: 3695
Period size: 472 Copynumber: 4.0 Consensus size: 471
671746 TTTATCATCA
671756 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
1 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
671821 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
66 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
671886 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
131 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
671951 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
196 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
672016 ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTTGAACAGTCTGAAGTAGTT
261 ACATGCATACAACCTTAATTCAAAGCTGGATAATC-TTTTTTTTTTTGAACAGTCTGAAGTAGTT
672081 ATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCA
325 ATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCA
672146 GCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAG
390 GCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAG
672211 TTCAAAGTTGGATAATC
455 TTCAAAGTTGGATAATC
672228 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
1 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
672293 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
66 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
672358 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
131 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
672423 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
196 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
*
672488 ACATGCATACAACCTTAATTCAAAGCTGGATAATC-TTTTTTTTTTGAACACTCTGAAGTAGTTA
261 ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTGAACAGTCTGAAGTAGTTA
*
672552 TAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCGCACACCCTACAATCGCAG
326 TAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCAG
672617 CCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAGT
391 CCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAGT
672682 TCAAAGTTGGATAATC
456 TCAAAGTTGGATAATC
672698 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
1 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
672763 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
66 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
672828 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
131 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
672893 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
196 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
672958 ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTGAACAGTCTGAAGTAGTTA
261 ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTGAACAGTCTGAAGTAGTTA
* *
673023 TAAGATACTATCTGTTTAAAGTCTTTCTAAGCCATTGACAACGCGCGCACACCCTACAATCGCAG
326 TAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCAG
673088 CCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAGT
391 CCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAGT
673153 TCAAAGTTGGATAATC
456 TCAAAGTTGGATAATC
673169 TTATAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAG
1 -T-TAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAG
673234 CATTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAAC
64 CATTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAAC
673299 AACGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAA
129 AACGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAA
673364 AAGTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCT
194 AAGTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCT
673429 TAACATGCATACAACCTTAATTCAAAGCTGGATAATC-TTTTTTTTTTGAACAGTCTGAAGTAGT
259 TAACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTGAACAGTCTGAAGTAGT
673493 TATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGC
324 TATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGC
673558 AGCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGA
389 AGCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGA
673623 GTTCAAAGTTGGATAATC
454 GTTCAAAGTTGGATAATC
673641 T
1 T
673642 CTAAATACCT
Statistics
Matches: 1405, Mismatches: 6, Indels: 7
0.99 0.00 0.00
Matches are distributed among these distances:
470 468 0.33
471 174 0.12
472 469 0.33
473 294 0.21
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (471 bp):
TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTGAACAGTCTGAAGTAGTTA
TAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCAG
CCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAGT
TCAAAGTTGGATAATC
Found at i:673580 original size:943 final size:942
Alignment explanation
Indices: 671756--673641 Score: 3711
Period size: 943 Copynumber: 2.0 Consensus size: 942
671746 TTTATCATCA
671756 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
1 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
671821 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
66 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
671886 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
131 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
671951 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
196 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
672016 ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTTGAACAGTCTGAAGTAGTT
261 ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTTGAACAGTCTGAAGTAGTT
672081 ATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCA
326 ATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCA
672146 GCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAG
391 GCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAG
672211 TTCAAAGTTGGATAATCTTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATA
456 TTCAAAGTTGGATAATCTTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATA
672276 AAAGTGAACCATAAGCATTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAA
521 AAAGTGAACCATAAGCATTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAA
672341 CTCCAAATGCCAAACAACGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAA
586 CTCCAAATGCCAAACAACGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAA
672406 CTAAAATTACTTGAAAAGTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAA
651 CTAAAATTACTTGAAAAGTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAA
672471 TTTTGCTGCATGGCTTAACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTGAA
716 TTTTGCTGCATGGCTTAACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTGAA
*
672536 CACTCTGAAGTAGTTATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCGCA
781 CACTCTGAAGTAGTTATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACA
672601 CACCCTACAATCGCAGCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTG
846 CACCCTACAATCGCAGCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTG
672666 AGGCCACTCAATGAGTTCAAAGTTGGATAATC
911 AGGCCACTCAATGAGTTCAAAGTTGGATAATC
672698 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
1 TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
672763 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
66 TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
672828 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
131 CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
672893 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
196 GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
672958 ACATGCATACAACCTTAATTCAAAGCTGGATAATC-TTTTTTTTTTTGAACAGTCTGAAGTAGTT
261 ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTTGAACAGTCTGAAGTAGTT
* *
673022 ATAAGATACTATCTGTTTAAAGTCTTTCTAAGCCATTGACAACGCGCGCACACCCTACAATCGCA
326 ATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCA
673087 GCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAG
391 GCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAG
673152 TTCAAAGTTGGATAATCTTATAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAA
456 TTCAAAGTTGGATAATC-T-TAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAA
673217 TAAAAGTGAACCATAAGCATTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTA
519 TAAAAGTGAACCATAAGCATTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTA
673282 AACTCCAAATGCCAAACAACGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACA
584 AACTCCAAATGCCAAACAACGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACA
673347 AACTAAAATTACTTGAAAAGTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGC
649 AACTAAAATTACTTGAAAAGTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGC
673412 AATTTTGCTGCATGGCTTAACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTG
714 AATTTTGCTGCATGGCTTAACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTG
*
673477 AACAGTCTGAAGTAGTTATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCA
779 AACACTCTGAAGTAGTTATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCA
673542 CACACCCTACAATCGCAGCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAAC
844 CACACCCTACAATCGCAGCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAAC
673607 TGAGGCCACTCAATGAGTTCAAAGTTGGATAATC
909 TGAGGCCACTCAATGAGTTCAAAGTTGGATAATC
673641 T
1 T
673642 CTAAATACCT
Statistics
Matches: 938, Mismatches: 4, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
941 174 0.19
942 296 0.32
943 468 0.50
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (942 bp):
TTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATAAAAGTGAACCATAAGCA
TTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAACTCCAAATGCCAAACAA
CGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAACTAAAATTACTTGAAAA
GTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAATTTTGCTGCATGGCTTA
ACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTTTGAACAGTCTGAAGTAGTT
ATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACACACCCTACAATCGCA
GCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTGAGGCCACTCAATGAG
TTCAAAGTTGGATAATCTTAGATCAAATTAAGCCAGGAGCTGGTAAGTTCCCAAAATGGAAAATA
AAAGTGAACCATAAGCATTCAGGGGATGAAATAACATTCGGAGTTTCCAACATGATTTCTTTAAA
CTCCAAATGCCAAACAACGACCAGACGACATGCAGTTAGAGAAGCAAGCAAAGATGGAACACAAA
CTAAAATTACTTGAAAAGTTAAGAATTGGGAAGCAGCAGGAAAATATCATCAAGCAAAATGGCAA
TTTTGCTGCATGGCTTAACATGCATACAACCTTAATTCAAAGCTGGATAATCTTTTTTTTTTGAA
CACTCTGAAGTAGTTATAAGATACTATCTGTTCAAAGTCTTTCTAAGCCATTGACAACGCGCACA
CACCCTACAATCGCAGCCGCTTGAACCCAGATCCTCTAAGGAGAATAACACTCCCTTTACAACTG
AGGCCACTCAATGAGTTCAAAGTTGGATAATC
Found at i:674497 original size:13 final size:13
Alignment explanation
Indices: 674479--674514 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
674469 ACTTGAAAAT
674479 AAAAAAAAAACAG
1 AAAAAAAAAACAG
*
674492 AAAAAAGAAACAG
1 AAAAAAAAAACAG
674505 AAAAGAAAAA
1 AAAA-AAAAA
674515 GATTTATCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAG
Found at i:702188 original size:21 final size:20
Alignment explanation
Indices: 702159--702198 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
702149 TAAGGCATTA
*
702159 AACATCATAAACAAAACAAAT
1 AACAACATAAA-AAAACAAAT
*
702180 AACAACATACAAAAACAAA
1 AACAACATAAAAAAACAAA
702199 CGTTCATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.70, C:0.20, G:0.00, T:0.10
Consensus pattern (20 bp):
AACAACATAAAAAAACAAAT
Found at i:709836 original size:20 final size:20
Alignment explanation
Indices: 709811--709848 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
709801 ATTCGACCCT
709811 GAAGTTAAGCAATCGTTCCC
1 GAAGTTAAGCAATCGTTCCC
709831 GAAGTTAAGCAATCGTTC
1 GAAGTTAAGCAATCGTTC
709849 AGACTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
GAAGTTAAGCAATCGTTCCC
Found at i:712484 original size:64 final size:64
Alignment explanation
Indices: 712416--712537 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
712406 ATTGTTCAAG
* * * *
712416 GTGTATCGATGCACATGAAGTGTATCGATGCACTCC-TTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATGCACAGGAAGTGCATAGATGCAC-CCACTTAAAATAAAAACATCGAATGTCATCA
* * *
712480 GTGTATCGATGCACAGGTAGTGCATAGATGCACCCACTTAAAGTACAAACATCGAATG
1 GTGTATCGATGCACAGGAAGTGCATAGATGCACCCACTTAAAATAAAAACATCGAATG
712538 GGATTTATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 2 0.04
64 48 0.96
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAGGAAGTGCATAGATGCACCCACTTAAAATAAAAACATCGAATGTCATCA
Found at i:716545 original size:13 final size:13
Alignment explanation
Indices: 716527--716553 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
716517 AAATATTAAA
716527 GAAGGACAAAATG
1 GAAGGACAAAATG
716540 GAAGGACAAAATG
1 GAAGGACAAAATG
716553 G
1 G
716554 TCATTTGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.33, T:0.07
Consensus pattern (13 bp):
GAAGGACAAAATG
Found at i:717252 original size:64 final size:64
Alignment explanation
Indices: 717184--717347 Score: 190
Period size: 64 Copynumber: 2.6 Consensus size: 64
717174 ATTGTTCAAG
* * *
717184 GTGTATCGATGCACATGAAGTGTATCGATGCACTCC-TTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATGCACAGGAAGTGCATCGATGCAC-CCGCTTAAAATAAAAACATCGAATGTCATCA
* * * * *
717248 GTGTATCGATGCACAGGTAGTGCATCGATGCACCCGCTTAAAGTACAAACATCGAATGTGATTTA
1 GTGTATCGATGCACAGGAAGTGCATCGATGCACCCGCTTAAAATAAAAACATCGAATGTCA-TCA
* *
717313 -TGTACCGATGCATA-GATAGTGCATCGATGCACCCG
1 GTGTATCGATGCACAGGA-AGTGCATCGATGCACCCG
717348 TCAAGGGATG
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 3 0.03
64 81 0.94
65 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAGGAAGTGCATCGATGCACCCGCTTAAAATAAAAACATCGAATGTCATCA
Found at i:718067 original size:18 final size:18
Alignment explanation
Indices: 718044--718079 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
718034 AGGGATTATC
*
718044 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
718062 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
718080 TTCATAGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:728229 original size:24 final size:24
Alignment explanation
Indices: 728183--728292 Score: 125
Period size: 24 Copynumber: 4.7 Consensus size: 24
728173 CGGTCCTTTG
* *
728183 GGACAAA-TCTATGTGGTTCTTCA
1 GGACAAATTCTATGTGATCCTTCA
* * *
728206 AGACAAATTCTACGTGATCATTCA
1 GGACAAATTCTATGTGATCCTTCA
* * *
728230 GGACAACTTTTATGTGGTCCTTCA
1 GGACAAATTCTATGTGATCCTTCA
728254 GGACAAATTCTATGTGATCCTTCA
1 GGACAAATTCTATGTGATCCTTCA
*
728278 TGACAAA-TCTATGTG
1 GGACAAATTCTATGTG
728293 GCACTTCGGT
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 14 0.20
24 57 0.80
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (24 bp):
GGACAAATTCTATGTGATCCTTCA
Found at i:728253 original size:48 final size:48
Alignment explanation
Indices: 728192--728283 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
728182 GGGACAAATC
*
728192 TATGTGGTTCTTCAAGACAAATTCTACGTGATCATTCAGGACAACTTT
1 TATGTGGTCCTTCAAGACAAATTCTACGTGATCATTCAGGACAACTTT
* * * *
728240 TATGTGGTCCTTCAGGACAAATTCTATGTGATCCTTCATGACAA
1 TATGTGGTCCTTCAAGACAAATTCTACGTGATCATTCAGGACAA
728284 ATCTATGTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (48 bp):
TATGTGGTCCTTCAAGACAAATTCTACGTGATCATTCAGGACAACTTT
Found at i:734463 original size:21 final size:21
Alignment explanation
Indices: 734439--734489 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
734429 CGGATGAACC
734439 GTATCGATACTGAT-TGAAGT
1 GTATCGATACTGATGTGAAGT
* *
734459 AGTATTGATACTGATGTGGAGT
1 -GTATCGATACTGATGTGAAGT
734481 -TATCGATAC
1 GTATCGATAC
734490 CAGGAGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 13 0.50
22 5 0.19
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (21 bp):
GTATCGATACTGATGTGAAGT
Found at i:735381 original size:25 final size:24
Alignment explanation
Indices: 735300--735426 Score: 150
Period size: 24 Copynumber: 5.3 Consensus size: 24
735290 GAGTAGAGTG
* *
735300 TTCTACGCGGTCATTCGGGA-AAA
1 TTCTACGTGGTCCTTCGGGACAAA
* * *
735323 ATCTATGTAGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
735347 TTCTACGTGGTCCTTCTGGAAAAA
1 TTCTACGTGGTCCTTCGGGACAAA
*
735371 TTTCTACGTGGTCTTTCGGGACAAA
1 -TTCTACGTGGTCCTTCGGGACAAA
*
735396 TTCTACGTGGTCCTTCAGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
735420 -TCTACGT
1 TTCTACGT
735427 AGAACTTCGG
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
23 22 0.25
24 44 0.51
25 21 0.24
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:735399 original size:49 final size:48
Alignment explanation
Indices: 735300--735428 Score: 163
Period size: 49 Copynumber: 2.7 Consensus size: 48
735290 GAGTAGAGTG
* * * *
735300 TTCTACGCGGTCATTCGGGAAAAA-TCTATGTAGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCAGGAAAAATTCTACGTAGTCCTTCGGGACAAA
* * *
735347 TTCTACGTGGTCCTTCTGGAAAAATTTCTACGTGGTCTTTCGGGACAAA
1 TTCTACGTGGTCCTTCAGGAAAAA-TTCTACGTAGTCCTTCGGGACAAA
*
735396 TTCTACGTGGTCCTTCAGGACAAA-TCTACGTAG
1 TTCTACGTGGTCCTTCAGGAAAAATTCTACGTAG
735429 AACTTCGGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
47 29 0.41
49 42 0.59
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (48 bp):
TTCTACGTGGTCCTTCAGGAAAAATTCTACGTAGTCCTTCGGGACAAA
Found at i:738401 original size:21 final size:22
Alignment explanation
Indices: 738375--738417 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
738365 ATATTTTTAT
738375 AAAATA-TTAGTAATAAT-TAAA
1 AAAATATTTA-TAATAATCTAAA
738396 AAAATATTTATAATAATCTAAA
1 AAAATATTTATAATAATCTAAA
738418 TAGAAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAATATTTATAATAATCTAAA
Found at i:739116 original size:14 final size:14
Alignment explanation
Indices: 739078--739113 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
739068 TATTATATTA
739078 TATTAAAAATAAAT
1 TATTAAAAATAAAT
*
739092 TATTTAAAATAAAT
1 TATTAAAAATAAAT
739106 T-TTAAAAA
1 TATTAAAAA
739114 ATATACTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAAAAATAAAT
Found at i:739495 original size:3 final size:3
Alignment explanation
Indices: 739437--739476 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
739427 ATATTTTCCC
* *
739437 CTT CTT CTT CCTT CTT CTT CTT CAT CTT CTT CAT CTT CTT
1 CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
739477 TTACTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.05, C:0.35, G:0.00, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:739609 original size:21 final size:22
Alignment explanation
Indices: 739576--739619 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
739566 TTAAAAACAA
739576 AATTAACAATATAACAT-TACTT
1 AATTAACAATAT-ACATCTACTT
739598 AATTAA-AATATACATCTACTT
1 AATTAACAATATACATCTACTT
739619 A
1 A
739620 CTAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAACAATATACATCTACTT
Found at i:739626 original size:196 final size:195
Alignment explanation
Indices: 739287--739955 Score: 722
Period size: 196 Copynumber: 3.4 Consensus size: 195
739277 TTGCTCCAAA
* *
739287 TCTTCTCAAACTACATGCATAATATTAAAATTTTATTAACATTCATCAACAATCAAATTAACTAT
1 TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACATTCATCAACAATC--A--AA-T-T
739352 AATATATAATTTAAAAATTAAAAA-ATATAATTAACGATATAATATTACTT--TTAATTAATATA
60 AATATATAATTTAAAAATTAAAAACA-A-AATTAACGATATAATATTACTTAATTAA--AATATA
* * *
739414 CATCTACTTGCTAATATTTTCCCCTTCTTCTTCCTTCTTCTTCTTCATCTTCTTCATCTTCTTTT
121 CATCTACTTACTAATATTTTCTCATTCTTCTTCCTTC-TCTTCTTC-TCTTCTTC-TCTTCTTTT
*
739479 ACTA-TTTTTCCT
183 ACAATTTTTTCCT
* * * * *
739491 TCTTCCCAAATTGCATGCATAATATTAAAAGTTTAGTAATATTCGTCAACAATCAAATT-ATATA
1 TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACATTCATCAACAATCAAATTAATATA
* *
739555 TAATTTAAAAATTAAAAACAAAATTAACAATATAACATTACTTAATTAAAATATACATCTACTTA
66 TAATTTAAAAATTAAAAACAAAATTAACGATATAATATTACTTAATTAAAATATACATCTACTTA
*
739620 CTAATATTTTCTCTTTCATT-TTCCTTCT-TT-TTCTGCTTC-T-TCTTCTTTTACAATTTTTTC
131 CTAATATTTTCTCATTC-TTCTTCCTTCTCTTCTTCT-CTTCTTCTCTTCTTTTACAATTTTTTC
739680 CT
194 CT
* * *
739682 TCATCTCAAATTACATGCATAATATTAAAATTATATTAACATTTC-TCAACAATCAAATTAACTA
1 TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACA-TTCATCAACAATCAAATTAA-TA
* * *
739746 TAATATATCTTTTAAAAAATGAAAACAAAATTAATGATATAATATTACTTAATTAAAAAACTAAA
64 T-ATA-A---TTTAAAAATTAAAAACAAAATTAACGATATAATATTACTTAATT--AAAA-T--A
* *
739811 TTTACATCTACTTACTAATATTTTCTCATTCTTCTT-CTTC-CTTC--CCCTCCTTCTTCTTCTT
119 --TACATCTACTTACTAATATTTTCTCATTCTTCTTCCTTCTCTTCTTCTCTTCTTC-TCTTCTT
739872 TTACAATTTTCTTCCT
181 TTACAATTTT-TTCCT
* * *
739888 TCTTCTCAAATTACATGCATAATATTAAATTTTTAGTAACATTTATCAACAATTAAATTAA-ATA
1 TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACATTCATCAACAATCAAATTAATATA
739952 TAAT
66 TAAT
739956 ATATTATTTA
Statistics
Matches: 402, Mismatches: 34, Indels: 63
0.81 0.07 0.13
Matches are distributed among these distances:
190 12 0.03
191 56 0.14
192 6 0.01
193 10 0.02
194 5 0.01
195 2 0.00
196 57 0.14
197 26 0.06
198 45 0.11
199 2 0.00
200 6 0.01
201 1 0.00
202 5 0.01
203 6 0.01
204 57 0.14
205 49 0.12
206 57 0.14
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.43
Consensus pattern (195 bp):
TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACATTCATCAACAATCAAATTAATATA
TAATTTAAAAATTAAAAACAAAATTAACGATATAATATTACTTAATTAAAATATACATCTACTTA
CTAATATTTTCTCATTCTTCTTCCTTCTCTTCTTCTCTTCTTCTCTTCTTTTACAATTTTTTCCT
Found at i:739939 original size:206 final size:200
Alignment explanation
Indices: 739287--739971 Score: 783
Period size: 206 Copynumber: 3.4 Consensus size: 200
739277 TTGCTCCAAA
* *
739287 TCTTCTCAAACTACATGCATAATATTAAAATTTTATTAACATTCATCAACAATCAAATTAACTAT
1 TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACATTCATCAACAATCAAATTAACTAT
* * *
739352 AATATATAATTTAAAAATTAAAAA-ATATAATTAACGATATAATATTACTT--TT-AATTAATAT
66 AATATAT-TTTTAAAAAATAAAAACA-A-AATTAACGATATAATATTACTTAATTAAAATAAT-T
* * * * *
739413 ACATCTACTTGCTAATATTTTCCCCTTCTTCTTCCTTCTTCTTCTTCATCTTCTTCATCTTCTTT
127 ACATCTACTTACTAATATTTTCTCATTCTTCTTCCTTC--CTTC--C-TCTCCTTCTTCTTCTTT
*
739478 TACTA-TTTTTCCT
187 TACAATTTTTTCCT
* * * * *
739491 TCTTCCCAAATTGCATGCATAATATTAAAAGTTTAGTAATATTCGTCAACAATCAAATT-A-TAT
1 TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACATTCATCAACAATCAAATTAACTAT
* * *
739554 -ATA-A--TTTAAAAATTAAAAACAAAATTAACAATATAACATTACTTAATTAAAAT-A-TACAT
66 AATATATTTTTAAAAAATAAAAACAAAATTAACGATATAATATTACTTAATTAAAATAATTACAT
* ** *
739613 CTACTTACTAATATTTTCTCTTTCATT-TTCCTT-CTTTTTCTGCTTCTTCTTCTTTTACAATTT
131 CTACTTACTAATATTTTCTCATTC-TTCTTCCTTCCTTCCTCTCCTTCTTCTTCTTTTACAATTT
739676 TTTCCT
195 TTTCCT
* * *
739682 TCATCTCAAATTACATGCATAATATTAAAATTATATTAACATTTC-TCAACAATCAAATTAACTA
1 TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACA-TTCATCAACAATCAAATTAACTA
* *
739746 TAATATATCTTTTAAAAAATGAAAACAAAATTAATGATATAATATTACTTAATTAAAAAACTAAA
65 TAATATAT-TTTTAAAAAATAAAAACAAAATTAACGATATAATATTACTTAATT--AAAA-T-AA
*
739811 TTTACATCTACTTACTAATATTTTCTCATTCTTCTT-CTTCCTTCCCCTCCTTCTTCTTCTTTTA
125 -TTACATCTACTTACTAATATTTTCTCATTCTTCTTCCTTCCTTCCTCTCCTTCTTCTTCTTTTA
739875 CAATTTTCTTCCT
189 CAATTTT-TTCCT
* * * *
739888 TCTTCTCAAATTACATGCATAATATTAAATTTTTAGTAACATTTATCAACAATTAAATTAAATAT
1 TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACATTCATCAACAATCAAATTAACTAT
739953 AATATATTATTTAAAAAAT
66 AATATATT-TTTAAAAAAT
739972 TCTTCTTACT
Statistics
Matches: 413, Mismatches: 42, Indels: 50
0.82 0.08 0.10
Matches are distributed among these distances:
190 19 0.05
191 56 0.14
192 4 0.01
193 6 0.01
194 3 0.01
195 1 0.00
196 52 0.13
197 18 0.04
198 43 0.10
199 3 0.01
200 5 0.01
201 4 0.01
202 3 0.01
203 2 0.00
204 57 0.14
205 60 0.15
206 77 0.19
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (200 bp):
TCTTCTCAAATTACATGCATAATATTAAAATTTTAGTAACATTCATCAACAATCAAATTAACTAT
AATATATTTTTAAAAAATAAAAACAAAATTAACGATATAATATTACTTAATTAAAATAATTACAT
CTACTTACTAATATTTTCTCATTCTTCTTCCTTCCTTCCTCTCCTTCTTCTTCTTTTACAATTTT
TTCCT
Found at i:740006 original size:26 final size:29
Alignment explanation
Indices: 739950--740014 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 29
739940 TTAAATTAAA
739950 TATAATATATTATTTAAAAAATTCTTCTTAC
1 TATAATATATTATTTAAAAAA-T-TTCTTAC
739981 TATAATATATTATTT-AAAAA-TT-TTAC
1 TATAATATATTATTTAAAAAATTTCTTAC
740007 TATAATAT
1 TATAATAT
740015 TACTTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 12 0.35
27 2 0.06
30 5 0.15
31 15 0.44
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (29 bp):
TATAATATATTATTTAAAAAATTTCTTAC
Found at i:740553 original size:49 final size:50
Alignment explanation
Indices: 740487--740602 Score: 146
Period size: 49 Copynumber: 2.3 Consensus size: 50
740477 GGAAGTTTTC
* * * *
740487 TTTTTAACAGTGGAGACGGGTTGTA-TCCCA-TCGTTTACACTGTAGCTTT
1 TTTTTAATAGTGAAGACGGGTTGTATTCCCACT-GTCTACACTGTAACTTT
*
740536 TTTTTAATAGTGAAGACGGGTTGTATTCCCACTGTCTACATTGTAACTTT
1 TTTTTAATAGTGAAGACGGGTTGTATTCCCACTGTCTACACTGTAACTTT
*
740586 TTTGTGAATAGTGAAGA
1 TTT-TTAATAGTGAAGA
740603 TGTTTTGTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 23 0.40
50 22 0.38
51 13 0.22
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (50 bp):
TTTTTAATAGTGAAGACGGGTTGTATTCCCACTGTCTACACTGTAACTTT
Found at i:740623 original size:51 final size:50
Alignment explanation
Indices: 740487--740623 Score: 125
Period size: 51 Copynumber: 2.8 Consensus size: 50
740477 GGAAGTTTTC
* * * * * *
740487 TTTTT-AACAGTGGAGACGGGTTGTATCCCATC-GTTTACACTGTAGCTT
1 TTTTTGAATAGTGAAGACGGGTTGTATACCAACTGTCTACACTGTAACTT
* * * *
740535 TTTTTTAATAGTGAAGACGGGTTGTATTCCCACTGTCTACATTGTAACTT
1 TTTTTGAATAGTGAAGACGGGTTGTATACCAACTGTCTACACTGTAACTT
* ** *
740585 TTTTGTGAATAGTGAAGATGTTTTGTATACCAATTGTCT
1 TTTT-TGAATAGTGAAGACGGGTTGTATACCAACTGTCT
740624 TTAATTTTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
48 5 0.07
49 22 0.31
50 17 0.24
51 27 0.38
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (50 bp):
TTTTTGAATAGTGAAGACGGGTTGTATACCAACTGTCTACACTGTAACTT
Found at i:742786 original size:21 final size:21
Alignment explanation
Indices: 742760--742827 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
742750 TACATTCTGT
742760 AGCCATTTCAGATGGCACCGC
1 AGCCATTTCAGATGGCACCGC
* * *
742781 AGCCATATCAGATAGCACCAC
1 AGCCATTTCAGATGGCACCGC
* * * * *
742802 AACCATTTTATATGCCACTGC
1 AGCCATTTCAGATGGCACCGC
742823 AGCCA
1 AGCCA
742828 GGTCATATGT
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.21
Consensus pattern (21 bp):
AGCCATTTCAGATGGCACCGC
Found at i:743153 original size:3 final size:3
Alignment explanation
Indices: 743145--743177 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
743135 TATATGCTCC
*
743145 TGA TGA TGA TGA TGA TGA TGA TGG TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
743178 GAGTGAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:758654 original size:21 final size:20
Alignment explanation
Indices: 758630--758694 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
758620 TTTAGCTTTA
*
758630 TATTCTATTTTTATTGAATTT
1 TATTC-ATTTTTATTGATTTT
* **
758651 TATTCACTTTTAATTCTTTTT
1 TATTCA-TTTTTATTGATTTT
758672 TATTGCATTTTTATTGATTTT
1 TATT-CATTTTTATTGATTTT
758693 TA
1 TA
758695 AAAATAGTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.91
22 2 0.06
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTCATTTTTATTGATTTT
Found at i:758661 original size:10 final size:10
Alignment explanation
Indices: 758630--758694 Score: 58
Period size: 10 Copynumber: 6.2 Consensus size: 10
758620 TTTAGCTTTA
758630 TATTCTATTTT
1 TATTC-ATTTT
* *
758641 TATTGAATTT
1 TATTCATTTT
758651 TATTCACTTTT
1 TATTCA-TTTT
* *
758662 AATTCTTTTT
1 TATTCATTTT
758672 TATTGCATTTT
1 TATT-CATTTT
*
758683 TATTGATTTT
1 TATTCATTTT
758693 TA
1 TA
758695 AAAATAGTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
10 23 0.53
11 20 0.47
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.66
Consensus pattern (10 bp):
TATTCATTTT
Found at i:759862 original size:26 final size:27
Alignment explanation
Indices: 759810--759889 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 27
759800 AATTTAGAAT
759810 TTTTTAAAAAATATATGAAAA-TA-ATTTA
1 TTTTT-AAAAAT-TAT-AAAATTATATTTA
759838 TTTTTAAAAATTA-AAAATTATATTT-
1 TTTTTAAAAATTATAAAATTATATTTA
* *
759863 TTTTTAAAATTTATCAAATTAT-TTTA
1 TTTTTAAAAATTATAAAATTATATTTA
759889 T
1 T
759890 AACTAATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
24 4 0.09
25 17 0.37
26 14 0.30
27 6 0.13
28 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TTTTTAAAAATTATAAAATTATATTTA
Found at i:765616 original size:19 final size:19
Alignment explanation
Indices: 765592--765648 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
765582 ATACTATCTT
765592 AAGAAACTCAGAAGGGCAG
1 AAGAAACTCAGAAGGGCAG
*
765611 AAGAAACTCAGAAGGGTAG
1 AAGAAACTCAGAAGGGCAG
765630 AAGAAACTCAGAAGGGCAG
1 AAGAAACTCAGAAGGGCAG
765649 CAATAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.47, C:0.14, G:0.32, T:0.07
Consensus pattern (19 bp):
AAGAAACTCAGAAGGGCAG
Found at i:766954 original size:17 final size:16
Alignment explanation
Indices: 766907--766957 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
766897 AATCAATTTA
*
766907 ATTTAAATTAAAAATAT
1 ATTT-AATTAAATATAT
**
766924 ATTTAA-TATCTATAT
1 ATTTAATTAAATATAT
766939 ATTTAATTTAAATATAT
1 ATTTAA-TTAAATATAT
766956 AT
1 AT
766958 ACCCGGCCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 12 0.44
16 2 0.07
17 13 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAATTAAATATAT
Done.