Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 27
Found at i:6536434 original size:19 final size:19
Alignment explanation
Indices: 6536412--6536498 Score: 94
Period size: 19 Copynumber: 4.8 Consensus size: 19
6536402 CGCAATTATA
*
6536412 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTC
6536431 GTTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
6536450 ATTTCGCGTTGCGA--TTC
1 GTTTCGCGTTGCGATTTTC
*
6536467 ---TCTCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
* *
6536483 ATTTCTCGTTGCGATT
1 GTTTCGCGTTGCGATT
6536499 CTCTCGTTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.17
16 3 0.05
17 3 0.05
19 44 0.73
ACGTcount: A:0.08, C:0.21, G:0.24, T:0.47
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTC
Found at i:6536475 original size:14 final size:14
Alignment explanation
Indices: 6536456--6536513 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
6536446 TTTCATTTCG
6536456 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6536470 CGTTGCGATTTTCATTTCT
1 CGTTGCGA--TTC---TCT
6536489 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6536503 CGTTGAGATTC
1 CGTTGCGATTC
6536514 ATTTCGCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 21 0.55
16 3 0.08
17 3 0.08
19 11 0.29
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6536479 original size:33 final size:33
Alignment explanation
Indices: 6536437--6536528 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
6536427 TTTGGTTTCG
6536437 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
6536470 CGTTGCGATTTTCATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
6536503 CGTTGAGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
6536529 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 17 0.30
33 39 0.70
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:6536536 original size:19 final size:17
Alignment explanation
Indices: 6536413--6536528 Score: 82
Period size: 19 Copynumber: 6.8 Consensus size: 17
6536403 GCAATTATAG
**
6536413 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGA--TTCA
6536432 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA--TTCA
6536451 TTTCGCGTTGCGATTC-
1 TTTCGCGTTGCGATTCA
*
6536467 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGA--TTCA
*
6536484 TTTCTCGTTGCGATTC-
1 TTTCGCGTTGCGATTCA
* *
6536500 --TCTCGTTGAGATTCA
1 TTTCGCGTTGCGATTCA
6536515 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
6536529 AGTCATTTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
14 23 0.28
16 3 0.04
17 16 0.19
19 41 0.49
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (17 bp):
TTTCGCGTTGCGATTCA
Found at i:6536762 original size:94 final size:93
Alignment explanation
Indices: 6536616--6536995 Score: 589
Period size: 94 Copynumber: 4.1 Consensus size: 93
6536606 ATGGATTGCA
* * * *
6536616 TTACTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACGCAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
* *
6536681 TAGCAAAATTGGCAGCAACCAAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
6536709 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
6536774 TTAGCAGAATTGGCAGCAATCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
6536803 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
6536868 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* **
6536897 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATTGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * * *
6536962 TTAGCAGTATTGTCAGCTACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
6536991 TTACT
1 TTACT
6536996 AAGTAATCTA
Statistics
Matches: 268, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
93 23 0.09
94 245 0.91
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:6538723 original size:20 final size:20
Alignment explanation
Indices: 6538700--6538755 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
6538690 TGAAATGAAA
6538700 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
6538720 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
6538740 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
6538756 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:6538814 original size:33 final size:33
Alignment explanation
Indices: 6538691--6538812 Score: 136
Period size: 33 Copynumber: 3.5 Consensus size: 33
6538681 TCTTTTGGTT
6538691 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAAT--C-A---CAACGC
** *
6538730 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCACAACGC
* *
6538764 GAAATTAAAATCGCAATGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
6538797 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
6538813 TGCGATTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
33 43 0.59
34 6 0.08
38 1 0.01
40 23 0.32
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAACGC
Found at i:6538817 original size:19 final size:19
Alignment explanation
Indices: 6538691--6538817 Score: 67
Period size: 20 Copynumber: 7.1 Consensus size: 19
6538681 TCTTTTGGTT
*
6538691 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
6538710 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
6538730 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
6538748 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
6538764 GAAATTAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
* *
6538781 G--A-GAGAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
6538797 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
6538816 GA
1 GA
6538818 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
14 17 0.21
15 2 0.02
16 3 0.04
17 2 0.02
18 3 0.04
19 24 0.30
20 28 0.35
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:6538863 original size:21 final size:20
Alignment explanation
Indices: 6538844--6538915 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
6538834 CGATTCTCTC
6538844 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
6538864 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
6538885 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
6538905 GTTGCGATTTT
1 GTTGCGATTTT
6538916 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:6539477 original size:20 final size:20
Alignment explanation
Indices: 6539452--6539646 Score: 196
Period size: 20 Copynumber: 9.7 Consensus size: 20
6539442 CTTTAAAAAT
6539452 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6539472 CGCGTTACGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
6539492 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
6539513 CGCATTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
6539533 CTCGTTGCGATTTATAGATA
1 CGCGTTGCGATTTACGGATA
* *
6539553 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
6539573 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6539593 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
6539613 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
6539634 CGCGTTGCGATTT
1 CGCGTTGCGATTT
6539647 TATAGATACT
Statistics
Matches: 137, Mismatches: 32, Indels: 12
0.76 0.18 0.07
Matches are distributed among these distances:
20 105 0.77
21 32 0.23
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:6539511 original size:41 final size:41
Alignment explanation
Indices: 6539454--6539648 Score: 304
Period size: 40 Copynumber: 4.8 Consensus size: 41
6539444 TTAAAAATCG
* *
6539454 CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
6539495 CGTTGCGATTTACGGATACGCATTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
6539535 CGTTGCGATTTATAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
6539575 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
6539616 CATTGCGATTTACGGATACGCGTTGCGATTTTA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTA
6539649 TAGATACTCG
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 73 0.51
41 70 0.49
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:6539699 original size:20 final size:20
Alignment explanation
Indices: 6539674--6539726 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
6539664 ATAGTCAGAA
*
6539674 TCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTATATAT
* * *
6539694 TTGCGTTGTGATTTTTATAT
1 TCGCGTTGCGATTTATATAT
6539714 TCGCGTTGCGATT
1 TCGCGTTGCGATT
6539727 CTGAAAAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.13, G:0.25, T:0.49
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATAT
Found at i:6539825 original size:20 final size:19
Alignment explanation
Indices: 6539776--6539829 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
6539766 ATTCTTCATA
6539776 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
6539795 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
6539816 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
6539830 TTTATTTCGC
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:6539844 original size:19 final size:19
Alignment explanation
Indices: 6539817--6539870 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
6539807 ATTCTGGAGA
*
6539817 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTTATT
6539836 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTTATT
*
6539855 TCGCATTACGATTTTT
1 TCGCATTGCGATTTTT
6539871 TGGGTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.52
Consensus pattern (19 bp):
TCGCATTGCGATTTTTATT
Found at i:6544731 original size:14 final size:14
Alignment explanation
Indices: 6544712--6544740 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6544702 AGTTGTAGGT
6544712 ACATTTGACATGCC
1 ACATTTGACATGCC
6544726 ACATTTGACATGCC
1 ACATTTGACATGCC
6544740 A
1 A
6544741 TTAAGTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (14 bp):
ACATTTGACATGCC
Found at i:6546608 original size:20 final size:20
Alignment explanation
Indices: 6546572--6546609 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6546562 ATCCTATTCC
**
6546572 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
6546592 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
6546610 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:6547324 original size:21 final size:21
Alignment explanation
Indices: 6547298--6547340 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6547288 GGATATGGTT
6547298 TTTGGTGGTCAAACCACACTA
1 TTTGGTGGTCAAACCACACTA
6547319 TTTGGTGGTCAAACCACACTA
1 TTTGGTGGTCAAACCACACTA
6547340 T
1 T
6547341 AAACATGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (21 bp):
TTTGGTGGTCAAACCACACTA
Found at i:6564894 original size:19 final size:20
Alignment explanation
Indices: 6564856--6564903 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
6564846 CAGCTGATGT
*
6564856 TAATTGATATATGGTTGTAA
1 TAATTGATATATGATTGTAA
*
6564876 TAATTGA-ATCTGATTGTAA
1 TAATTGATATATGATTGTAA
*
6564895 TAGTTGATA
1 TAATTGATA
6564904 CGACAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (20 bp):
TAATTGATATATGATTGTAA
Found at i:6565045 original size:38 final size:38
Alignment explanation
Indices: 6564988--6565101 Score: 183
Period size: 38 Copynumber: 3.0 Consensus size: 38
6564978 TCATATGGCG
* *
6564988 ATAATAGTAGCCAGCTTCTGTCAACCAACCTCTAGGTT
1 ATAACAGTAGCCAGATTCTGTCAACCAACCTCTAGGTT
6565026 ATAACAGTAGCCAGATTCTGTCAACCAACCTCTAGGTT
1 ATAACAGTAGCCAGATTCTGTCAACCAACCTCTAGGTT
* **
6565064 ATAACAGTAGCCAGATTTTGTCAACCGGCCTCTAGGTT
1 ATAACAGTAGCCAGATTCTGTCAACCAACCTCTAGGTT
6565102 CATTGTCTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 71 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (38 bp):
ATAACAGTAGCCAGATTCTGTCAACCAACCTCTAGGTT
Found at i:6581104 original size:15 final size:15
Alignment explanation
Indices: 6581084--6581133 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
6581074 AGCAAGGCTC
6581084 TTCGAGTGATGCTTG
1 TTCGAGTGATGCTTG
6581099 TTCGAGTGATGCTTG
1 TTCGAGTGATGCTTG
* *
6581114 TTCGAGTGAAGTTTG
1 TTCGAGTGATGCTTG
6581129 TTCGA
1 TTCGA
6581134 ATGGTGAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (15 bp):
TTCGAGTGATGCTTG
Found at i:6582878 original size:8 final size:8
Alignment explanation
Indices: 6582865--6582895 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
6582855 TGAGTTCATT
6582865 CTTTCTAG
1 CTTTCTAG
6582873 CTTTCTAG
1 CTTTCTAG
*
6582881 CTTGCTAG
1 CTTTCTAG
6582889 CTTTCTA
1 CTTTCTA
6582896 ACCTTGTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (8 bp):
CTTTCTAG
Found at i:6586178 original size:23 final size:23
Alignment explanation
Indices: 6586144--6586204 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
6586134 CATAATTGTC
6586144 CCGAAG-GACCACATAGGCCTGCA
1 CCGAAGTG-CCACATAGGCCTGCA
* **
6586167 TCGAAGTGCCACATAGGTTTGCA
1 CCGAAGTGCCACATAGGCCTGCA
*
6586190 CCGAAGTGTCACATA
1 CCGAAGTGCCACATA
6586205 TTTGTCCCCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
CCGAAGTGCCACATAGGCCTGCA
Found at i:6586244 original size:21 final size:22
Alignment explanation
Indices: 6586199--6586248 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
6586189 ACCGAAGTGT
*
6586199 CACATATTTGTCCCCGAAAGAC
1 CACATAATTGTCCCCGAAAGAC
6586221 CACATAATTGT-CCC-AAATGAC
1 CACATAATTGTCCCCGAAA-GAC
6586242 CACATAA
1 CACATAA
6586249 ACCCTCAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 13 0.50
22 10 0.38
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.22
Consensus pattern (22 bp):
CACATAATTGTCCCCGAAAGAC
Found at i:6589853 original size:29 final size:29
Alignment explanation
Indices: 6589811--6589866 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
6589801 TATTTCTGAA
6589811 CTAACCCTAACGTTAATATATCAACAAAT
1 CTAACCCTAACGTTAATATATCAACAAAT
6589840 CTAACCCTAACGTTAATATATCAACAA
1 CTAACCCTAACGTTAATATATCAACAA
6589867 TCCTTAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.27
Consensus pattern (29 bp):
CTAACCCTAACGTTAATATATCAACAAAT
Found at i:6591994 original size:38 final size:38
Alignment explanation
Indices: 6591952--6592037 Score: 95
Period size: 38 Copynumber: 2.2 Consensus size: 38
6591942 GTGTAAATTC
*
6591952 TTAATATTTATACATACTAAATTAAATTTA-TCTTAAC-A
1 TTAATATATATACATA-TAAATT-AATTTATTCTTAACTA
* * *
6591990 TTAATATATATATATATATATTATTTTATTCTTAACTA
1 TTAATATATATACATATAAATTAATTTATTCTTAACTA
6592028 TTAAGTATAT
1 TTAA-TATAT
6592038 CTTATTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 5 0.12
37 12 0.29
38 19 0.46
39 5 0.12
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (38 bp):
TTAATATATATACATATAAATTAATTTATTCTTAACTA
Found at i:6592109 original size:29 final size:28
Alignment explanation
Indices: 6592003--6592128 Score: 78
Period size: 29 Copynumber: 4.4 Consensus size: 28
6591993 ATATATATAT
* *
6592003 ATATATATTATT-TTATTCTTAACTATTAA
1 ATATATTTTATTCTTA-TCTTAACT-TAAA
* * * *
6592032 GTATATCTTATTTTTATTTTAACTTACAA
1 ATATATTTTATTCTTATCTTAACTTA-AA
* * *
6592061 A-A-ATTTTAGTCCTATTTTAACTTAAA
1 ATATATTTTATTCTTATCTTAACTTAAA
*
6592087 TATATATTTTATTCTTATCTTAATTTTTAAA
1 -ATATATTTTATTCTTATCTTAA--CTTAAA
6592118 CATATATTTTA
1 -ATATATTTTA
6592129 AATTAAAATA
Statistics
Matches: 76, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
26 2 0.03
27 19 0.25
28 3 0.04
29 34 0.45
30 3 0.04
31 15 0.20
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATATTTTATTCTTATCTTAACTTAAA
Found at i:6592172 original size:27 final size:27
Alignment explanation
Indices: 6592114--6592174 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
6592104 TCTTAATTTT
*
6592114 TAAACATATATTTTAAATTAAAATAAAG
1 TAAA-ATATATTATAAATTAAAATAAAG
* *
6592142 TAAAATATATTCATAAGTTAAGATAAA-
1 TAAAATATATT-ATAAATTAAAATAAAG
6592169 TAAAAT
1 TAAAAT
6592175 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (27 bp):
TAAAATATATTATAAATTAAAATAAAG
Found at i:6592267 original size:30 final size:30
Alignment explanation
Indices: 6592202--6592344 Score: 107
Period size: 30 Copynumber: 4.8 Consensus size: 30
6592192 GAATTTAATT
* * **
6592202 TAAAATACATTTTTAAAATT-AAGGTAATAA
1 TAAAATATATTTTTTAAATTAAAATTAA-AA
* * *
6592232 TAAAATATATTTTTTAAGTTGAAA-TAAGA
1 TAAAATATATTTTTTAAATTAAAATTAAAA
*
6592261 TGAAAATATTTTTTTTAAATTAAAATTAAAA
1 T-AAAATATATTTTTTAAATTAAAATTAAAA
** * **
6592292 TAAAATATATTTAATAAGTT-AAGGTAAAA
1 TAAAATATATTTTTTAAATTAAAATTAAAA
6592321 T-AAATATA-TTTTTAATATTAAAAT
1 TAAAATATATTTTTTAA-ATTAAAAT
6592345 GTGAATTTAA
Statistics
Matches: 88, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
27 5 0.06
28 9 0.10
29 12 0.14
30 55 0.62
31 7 0.08
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (30 bp):
TAAAATATATTTTTTAAATTAAAATTAAAA
Found at i:6592576 original size:18 final size:18
Alignment explanation
Indices: 6592553--6592593 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
6592543 TGAATTAAAA
6592553 TAAATATAATCATCTAAT
1 TAAATATAATCATCTAAT
*
6592571 TAAATATAATCTTCTAAT
1 TAAATATAATCATCTAAT
6592589 TAAAT
1 TAAAT
6592594 GATGATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATATAATCATCTAAT
Found at i:6592777 original size:37 final size:37
Alignment explanation
Indices: 6592727--6592852 Score: 162
Period size: 37 Copynumber: 3.2 Consensus size: 37
6592717 AATAAATTAA
*
6592727 ATAGTTATGTGATCTTATTAATAAAATTAAAAGATCG
1 ATAGTAATGTGATCTTATTAATAAAATTAAAAGATCG
6592764 ATAGTAATGTGATCTTATTAATAAAATTAAAAGATCG
1 ATAGTAATGTGATCTTATTAATAAAATTAAAAGATCG
*
6592801 ATAGTAAAATAGTTATGTGATCTTATTGATAAAATTAAAAGATCG
1 ATAG-----TA---ATGTGATCTTATTAATAAAATTAAAAGATCG
6592846 ATAGTAA
1 ATAGTAA
6592853 AATAAAAACT
Statistics
Matches: 79, Mismatches: 2, Indels: 16
0.81 0.02 0.16
Matches are distributed among these distances:
37 41 0.52
40 2 0.03
42 2 0.03
45 34 0.43
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (37 bp):
ATAGTAATGTGATCTTATTAATAAAATTAAAAGATCG
Found at i:6592813 original size:45 final size:45
Alignment explanation
Indices: 6592764--6592856 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
6592754 TAAAAGATCG
6592764 ATAGTAATGTGATCTTATTAATAAAATTAAAAGATCGATAGTAAA
1 ATAGTAATGTGATCTTATTAATAAAATTAAAAGATCGATAGTAAA
* *
6592809 ATAGTTATGTGATCTTATTGATAAAATTAAAAGATCGATAGTAAA
1 ATAGTAATGTGATCTTATTAATAAAATTAAAAGATCGATAGTAAA
6592854 ATA
1 ATA
6592857 AAAACTAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.34
Consensus pattern (45 bp):
ATAGTAATGTGATCTTATTAATAAAATTAAAAGATCGATAGTAAA
Found at i:6593424 original size:89 final size:92
Alignment explanation
Indices: 6593268--6593448 Score: 296
Period size: 89 Copynumber: 2.0 Consensus size: 92
6593258 CTTGAACTGC
* *
6593268 CCTTTCGATACCATTTAATTTGCTAATTGTCTTAGTTGCGAAAATTAAAATTGAAATTGAAATTT
1 CCTTTCGATACCATTTAATTTGCTAATTGTCTTAGTTGCGAAAATTAAAATTAAAATTAAAATTT
6593333 AAAACATTCAATTCAAAA-ACTTACCT
66 AAAACATTCAATTCAAAATACTTACCT
* *
6593359 CCTTTCGGTACCATTT-ATTTGCTGATTGTCTTAGTTGCG-AAATTAAAATTAAAATTAAAATTT
1 CCTTTCGATACCATTTAATTTGCTAATTGTCTTAGTTGCGAAAATTAAAATTAAAATTAAAATTT
*
6593422 AAAACATTCGATTCAAAATACTTACCT
66 AAAACATTCAATTCAAAATACTTACCT
6593449 TTGATTGGTT
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
89 39 0.46
90 30 0.36
91 15 0.18
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (92 bp):
CCTTTCGATACCATTTAATTTGCTAATTGTCTTAGTTGCGAAAATTAAAATTAAAATTAAAATTT
AAAACATTCAATTCAAAATACTTACCT
Found at i:6594776 original size:3 final size:3
Alignment explanation
Indices: 6594768--6594800 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
6594758 AACACATATT
6594768 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
6594801 TTTTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:6595733 original size:73 final size:73
Alignment explanation
Indices: 6595615--6595760 Score: 276
Period size: 73 Copynumber: 2.0 Consensus size: 73
6595605 ACTACTGTAC
6595615 GTTATTTATCATCCACAATGGAAATTGGGATCATCCCCCCTTCTTCCCTGTTAACAAAC-GCTAA
1 GTTATTTATCATCCACAATGGAAATTGGGATCATCCCCCCTTCTTCCCTGTTAACAAACGGCTAA
6595679 TCAATTTG
66 TCAATTTG
6595687 GTTATTTATCATCCACAAATGGAAATTGGGATCATCCCCCCTTCTTCCCTGTTAACAAACGGCTA
1 GTTATTTATCATCCAC-AATGGAAATTGGGATCATCCCCCCTTCTTCCCTGTTAACAAACGGCTA
6595752 ATCAATTTG
65 ATCAATTTG
6595761 TGCAGGGATG
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
72 16 0.22
73 43 0.60
74 13 0.18
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (73 bp):
GTTATTTATCATCCACAATGGAAATTGGGATCATCCCCCCTTCTTCCCTGTTAACAAACGGCTAA
TCAATTTG
Found at i:6595919 original size:17 final size:18
Alignment explanation
Indices: 6595897--6595930 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6595887 GCTGGGATTT
6595897 AAATAA-TTAATTATAAA
1 AAATAATTTAATTATAAA
6595914 AAATAATTTAATTATAA
1 AAATAATTTAATTATAA
6595931 CGATCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATTTAATTATAAA
Found at i:6596829 original size:19 final size:20
Alignment explanation
Indices: 6596801--6596840 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6596791 TATTATTAAC
*
6596801 TAATT-AAAAATATTAAATT
1 TAATTAAAAAATAATAAATT
*
6596820 TAATTTAAAAATAATAAATT
1 TAATTAAAAAATAATAAATT
6596840 T
1 T
6596841 GTTTTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTAAAAAATAATAAATT
Found at i:6597055 original size:19 final size:19
Alignment explanation
Indices: 6597017--6597055 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6597007 TTTTTTTTAG
* * *
6597017 TAAAATTAAAATTATTAAT
1 TAAAATAAAAAGTATAAAT
6597036 TAAAATAAAAAGTATAAAT
1 TAAAATAAAAAGTATAAAT
6597055 T
1 T
6597056 TATAGATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TAAAATAAAAAGTATAAAT
Found at i:6599880 original size:27 final size:27
Alignment explanation
Indices: 6599850--6599911 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
6599840 ACACCCGTAT
6599850 TTGGGCTGTCTGATATGTTCACATTAG
1 TTGGGCTGTCTGATATGTTCACATTAG
6599877 TTGGGCTGTCTGATATGTTCACATTAG
1 TTGGGCTGTCTGATATGTTCACATTAG
6599904 TTGGGCTG
1 TTGGGCTG
6599912 CTACACTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.40
Consensus pattern (27 bp):
TTGGGCTGTCTGATATGTTCACATTAG
Found at i:6600833 original size:30 final size:30
Alignment explanation
Indices: 6600799--6600855 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
6600789 CATGAAGTAC
* *
6600799 TAGAATTTAAATCTAATTTAAATTTTTAAT
1 TAGAATTCAAATCAAATTTAAATTTTTAAT
*
6600829 TAGAATTCAAATCAAATTTAATTTTTT
1 TAGAATTCAAATCAAATTTAAATTTTT
6600856 TAACTGATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (30 bp):
TAGAATTCAAATCAAATTTAAATTTTTAAT
Found at i:6601141 original size:23 final size:24
Alignment explanation
Indices: 6601115--6601161 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
6601105 ACCATCCACA
6601115 AACAACTAATTAGAGTC-ATCTAT
1 AACAACTAATTAGAGTCAATCTAT
6601138 AACAACTAATTAGAGTCAATCTAT
1 AACAACTAATTAGAGTCAATCTAT
6601162 GTAAAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.30
Consensus pattern (24 bp):
AACAACTAATTAGAGTCAATCTAT
Found at i:6604806 original size:19 final size:19
Alignment explanation
Indices: 6604769--6604807 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6604759 ATCGTGTTTC
* *
6604769 ATTTTAATGAGTATAAAAT
1 ATTTTAAAGAATATAAAAT
*
6604788 ATTTTAAAGAATATCAAAT
1 ATTTTAAAGAATATAAAAT
6604807 A
1 A
6604808 CAGTATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (19 bp):
ATTTTAAAGAATATAAAAT
Found at i:6606213 original size:39 final size:43
Alignment explanation
Indices: 6606154--6606245 Score: 113
Period size: 39 Copynumber: 2.3 Consensus size: 43
6606144 TTTAAGTATG
*
6606154 TAGCGGCG-TTTACAATACAAACGCCACAA-A-A-TGATACTT
1 TAGCGGCGTTTTACAATACAAACGCCACAATAGAGTGATAATT
* * *
6606193 TAGCGGCGTTTTTCAA-ACAAACGCCGCAATAGAGTGGTAATT
1 TAGCGGCGTTTTACAATACAAACGCCACAATAGAGTGATAATT
6606235 TAGCGGCGTTT
1 TAGCGGCGTTT
6606246 ATAGCTCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 20 0.44
40 7 0.16
41 1 0.02
42 17 0.38
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTTACAATACAAACGCCACAATAGAGTGATAATT
Found at i:6606242 original size:42 final size:41
Alignment explanation
Indices: 6606191--6606428 Score: 124
Period size: 41 Copynumber: 5.8 Consensus size: 41
6606181 AAAATGATAC
6606191 TTTAGCGGCGTTTTTCAAACAAACGCCGCAATAGAGTGGTAA
1 TTTAGCGGCGTTTTT-AAACAAACGCCGCAATAGAGTGGTAA
* ** ** * *
6606233 TTTAGCGGCGTTTATAGCTCAAACGATGCAATAGAATTGT--
1 TTTAGCGGCGTTTTTA-AACAAACGCCGCAATAGAGTGGTAA
* * ** * * *
6606273 TATAGTGGCGTTTTTTTTCATAAATGCCGCAATAGAGTTGTAA
1 TTTAGCGGCG--TTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * * **
6606316 TTTAGCGGCGTTTTTATACAAACGCCGCGATAGCGT-TTTT
1 TTTAGCGGCGTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * * * * * * **
6606356 TTTAGAGTCATTTGTTCAACAAACGACGCTATTGAGAAGTAA
1 TTTAGCGGCGTTT-TTAAACAAACGCCGCAATAGAGTGGTAA
* *
6606398 TTTAGCGGCGTTTTT-TACAAACGCCGTAATA
1 TTTAGCGGCGTTTTTAAACAAACGCCGCAATA
6606429 TCCATGATCT
Statistics
Matches: 140, Mismatches: 49, Indels: 16
0.68 0.24 0.08
Matches are distributed among these distances:
40 30 0.21
41 56 0.40
42 46 0.33
43 8 0.06
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAACAAACGCCGCAATAGAGTGGTAA
Found at i:6606329 original size:43 final size:43
Alignment explanation
Indices: 6606191--6606330 Score: 119
Period size: 42 Copynumber: 3.3 Consensus size: 43
6606181 AAAATGATAC
* ** *
6606191 TTTAGCGGCGTTTTTCA-AACAAACGCCGCAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTTAGCTCAAACGCCGCAATAGAGTTGTAA
* ** *
6606233 TTTAGCGGCG-TTTATAGCTCAAACGATGCAATAGAATTGT--
1 TTTAGCGGCGTTTTTTAGCTCAAACGCCGCAATAGAGTTGTAA
* * ** *
6606273 TATAGTGGCGTTTTTTTTCAT-AAATGCCGCAATAGAGTTGTAA
1 TTTAGCGGCGTTTTTTAGC-TCAAACGCCGCAATAGAGTTGTAA
6606316 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
6606331 ATACAAACGC
Statistics
Matches: 74, Mismatches: 19, Indels: 9
0.73 0.19 0.09
Matches are distributed among these distances:
40 8 0.11
41 25 0.34
42 28 0.38
43 13 0.18
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTTAGCTCAAACGCCGCAATAGAGTTGTAA
Found at i:6606556 original size:43 final size:41
Alignment explanation
Indices: 6606470--6606556 Score: 102
Period size: 43 Copynumber: 2.1 Consensus size: 41
6606460 CTGCAATAGT
* *
6606470 TTTTGTCATTTATGGCGTTTCTTTAATAAACGCCGCAGTAG
1 TTTTGTCATTTAGGGCGTTTCTTTAATAAACGCCGCAGAAG
* * * *
6606511 TTTTGTCCTTTAGGGGCGTTTTTTGTAATAAACGTCGTAGAAG
1 TTTTGTCATTTA-GGGCGTTTCTT-TAATAAACGCCGCAGAAG
6606554 TTT
1 TTT
6606557 CATTAATCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 11 0.29
42 9 0.24
43 18 0.47
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.44
Consensus pattern (41 bp):
TTTTGTCATTTAGGGCGTTTCTTTAATAAACGCCGCAGAAG
Found at i:6609062 original size:2 final size:2
Alignment explanation
Indices: 6609055--6609080 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6609045 TTAATTTTTA
6609055 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
6609081 TTTATTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6610281 original size:21 final size:21
Alignment explanation
Indices: 6610255--6610313 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
6610245 TGATTTATTA
*
6610255 TTATGGATTTCAATTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
6610276 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
6610297 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
6610314 ATTGAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.54
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:6610510 original size:43 final size:43
Alignment explanation
Indices: 6610461--6610734 Score: 313
Period size: 43 Copynumber: 6.4 Consensus size: 43
6610451 TATAGATATG
* ** *
6610461 ACCTTTTGCGGCGTTTGTTCTAAAAAACGCCGCTATATACCAA-
1 ACCTATTGCGGCGTTTGTT-GGAAAAACGCCGCTAAATACCAAC
* *
6610504 ATCTTTTGCGGCGTTTG-TGGAAAAAACGCCGCTAAAT-CTCAAC
1 ACCTATTGCGGCGTTTGTTGG-AAAAACGCCGCTAAATAC-CAAC
* *
6610547 ACCTATTACGGCGTTTGTGGGAAAAACGCCGCTAAAT-CTCAAC
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATAC-CAAC
* *
6610590 ACCTATTGCGGCGTTTGTTGGAAAAACGCAGCTAAATATCAAC
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATACCAAC
* *
6610633 ACCTATTGCGGCGCTTGTTGGAAAAACGCCGCTAAATATCAAC
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATACCAAC
* * * * ***
6610676 ACCTATTGCGGCATTTGTTGGACAAACGCCGCTATATATCGTT
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATACCAAC
6610719 ACCTATTGCGGCGTTT
1 ACCTATTGCGGCGTTT
6610735 TTTTGTTACC
Statistics
Matches: 204, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
41 1 0.00
42 19 0.09
43 182 0.89
44 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATACCAAC
Found at i:6610658 original size:129 final size:129
Alignment explanation
Indices: 6610461--6610734 Score: 345
Period size: 129 Copynumber: 2.1 Consensus size: 129
6610451 TATAGATATG
* * * * * * *
6610461 ACCTTTTGCGGCGTTTGTTCTAAAAAACGCCGCTATATACCAAATCTTTTGCGGCGTTTGTGGAA
1 ACCTATTGCGGCGTTTGTTCGAAAAAACGCAGCTAAATACCAAACCTATTGCGGCGCTTGTGGAA
* * *
6610526 AAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAC
66 AAAACGCCGCTAAATATCAACACCTATTACGGCATTTGTGGGAAAAACGCCGCTAAATATCAAC
* *
6610590 ACCTATTGCGGCGTTTGTT-GGAAAAACGCAGCTAAATATCAACACCTATTGCGGCGCTTGTTGG
1 ACCTATTGCGGCGTTTGTTCGAAAAAACGCAGCTAAATACCAA-ACCTATTGCGGCGCTTG-TGG
* * * * **
6610654 -AAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTGTTGGACAAACGCCGCTATATATCGT
64 AAAAAACGCCGCTAAATATCAACACCTATTACGGCATTTGTGGGAAAAACGCCGCTAAATATCAA
*
6610718 T
129 C
6610719 ACCTATTGCGGCGTTT
1 ACCTATTGCGGCGTTT
6610735 TTTTGTTACC
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
128 18 0.15
129 103 0.83
130 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (129 bp):
ACCTATTGCGGCGTTTGTTCGAAAAAACGCAGCTAAATACCAAACCTATTGCGGCGCTTGTGGAA
AAAACGCCGCTAAATATCAACACCTATTACGGCATTTGTGGGAAAAACGCCGCTAAATATCAAC
Found at i:6611177 original size:28 final size:29
Alignment explanation
Indices: 6611145--6611210 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
6611135 ATTGATGTTG
6611145 GAAAATTAGGTAATGCTCT-TTGAATATT-
1 GAAAATTAGGTAATGCT-TATTGAATATTA
* *
6611173 GAAAAATAGGTAATGCTTATTTAATATTA
1 GAAAATTAGGTAATGCTTATTGAATATTA
6611202 GAAAATTAG
1 GAAAATTAG
6611211 ATATTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.73
29 8 0.24
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (29 bp):
GAAAATTAGGTAATGCTTATTGAATATTA
Found at i:6615140 original size:31 final size:31
Alignment explanation
Indices: 6615100--6615158 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
6615090 AAACCCAAGA
6615100 AGTTCCTAGTGAGAATGACATATTGAATAGG
1 AGTTCCTAGTGAGAATGACATATTGAATAGG
*
6615131 AGTTTCTAGTGAGAATGACATATTGAAT
1 AGTTCCTAGTGAGAATGACATATTGAAT
6615159 TCACCGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (31 bp):
AGTTCCTAGTGAGAATGACATATTGAATAGG
Found at i:6616076 original size:23 final size:24
Alignment explanation
Indices: 6616046--6616100 Score: 103
Period size: 23 Copynumber: 2.3 Consensus size: 24
6616036 CTATTCTTTC
6616046 GCTTCAATTGAGCTCAAA-TTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
6616069 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
6616093 GCTTCAAT
1 GCTTCAAT
6616101 CAAACTTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:6616799 original size:29 final size:29
Alignment explanation
Indices: 6616766--6616875 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
6616756 CTCATTGAAT
6616766 ATTG-ATATTGGAAAATTAGGTAAATGCTC
1 ATTGAATATTGGAAAATTAGGT-AATGCTC
6616795 ATTGAATATTGGAAAATTAGGTAATGCTC
1 ATTGAATATTGGAAAATTAGGTAATGCTC
6616824 ATTGAATATTGGAAAATTAGGTAATGCTC
1 ATTGAATATTGGAAAATTAGGTAATGCTC
*
6616853 ATTTAATATTGGAAAATTAGGTA
1 ATTGAATATTGGAAAATTAGGTA
6616876 TTTCCACTAG
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
29 62 0.78
30 17 0.22
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.35
Consensus pattern (29 bp):
ATTGAATATTGGAAAATTAGGTAATGCTC
Found at i:6621785 original size:42 final size:42
Alignment explanation
Indices: 6621734--6621852 Score: 159
Period size: 42 Copynumber: 2.9 Consensus size: 42
6621724 TTTTCCCGAA
6621734 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATATT
* * * * *
6621776 TTCCCGTGTTTGTTTTATGTAATTCGTTTTTGGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATATT
* * *
6621818 TTCTCATGTTTGTTTCACGTAATT-GTTTTCCGAAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGAAA
6621853 TGTAATTCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
41 8 0.12
42 57 0.88
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATATT
Found at i:6622232 original size:23 final size:23
Alignment explanation
Indices: 6622206--6622250 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6622196 AATAATATTT
6622206 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
6622229 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
6622251 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:6622356 original size:29 final size:32
Alignment explanation
Indices: 6622290--6622359 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 32
6622280 AATATAATTT
*
6622290 ATAATA-TTTTATTTCATTAAAATATACAAAA
1 ATAATATTTTTATTTCAATAAAATATACAAAA
*
6622321 ATTAATATTTTTA-TT-AATAAAAT-TATAAAA
1 A-TAATATTTTTATTTCAATAAAATATACAAAA
6622351 ATAATATTT
1 ATAATATTT
6622360 AATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 8 0.23
30 7 0.20
31 8 0.23
32 7 0.20
33 5 0.14
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATTTTTATTTCAATAAAATATACAAAA
Found at i:6622367 original size:90 final size:86
Alignment explanation
Indices: 6622218--6622388 Score: 202
Period size: 90 Copynumber: 1.9 Consensus size: 86
6622208 ATAAAGATAT
* * * * * *
6622218 TTAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAAT
1 TTAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAA-
6622283 ATAATTTATAATATTTTATTTCA
65 ATAATTT-TAATATTTTATTTCA
*
6622306 TTAAAATATACAAAAATTAATATTTTTATTAATAAAATTATAAAAATAATA-TTTAAT-AATAAA
1 TTAAAATATAC--AAATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAA
*
6622369 TAAATTATTTTAATATTTTA
62 TAAATAATTTTAATATTTTA
6622389 AAATAATAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
88 21 0.30
89 6 0.08
90 22 0.31
91 12 0.17
92 10 0.14
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (86 bp):
TTAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAAA
TAATTTTAATATTTTATTTCA
Found at i:6622379 original size:48 final size:47
Alignment explanation
Indices: 6622326--6622432 Score: 108
Period size: 48 Copynumber: 2.2 Consensus size: 47
6622316 CAAAAATTAA
*
6622326 TATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA-AT
1 TATTTTTATT-ATAAAATAATAAAAATAA-ATTTAATAATAAATAATAT
* * * * *
6622374 TATTTTAATATTTTAAAATAATAATATTAAATTTTATGATAAATAATAT
1 TATTTT--TATTATAAAATAATAAAAATAAATTTAATAATAAATAATAT
6622423 TATTTATTAT
1 TATTT-TTAT
6622433 ATTTTATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
48 23 0.47
49 21 0.43
50 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (47 bp):
TATTTTTATTATAAAATAATAAAAATAAATTTAATAATAAATAATAT
Found at i:6622938 original size:26 final size:26
Alignment explanation
Indices: 6622899--6622955 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
6622889 GATTTGATTT
* *
6622899 GAAAACTTTAAAATTGAGCTAGACTC
1 GAAAACTCTAAAATGGAGCTAGACTC
* *
6622925 GAAAACTCTGAAATGGAGCTCGACTC
1 GAAAACTCTAAAATGGAGCTAGACTC
*
6622951 AAAAA
1 GAAAA
6622956 TTCGCGAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (26 bp):
GAAAACTCTAAAATGGAGCTAGACTC
Found at i:6623625 original size:8 final size:8
Alignment explanation
Indices: 6623614--6623650 Score: 60
Period size: 7 Copynumber: 4.9 Consensus size: 8
6623604 AATATATGTT
6623614 AATATAAA
1 AATATAAA
6623622 AATAT-AA
1 AATATAAA
6623629 AATATAAA
1 AATATAAA
6623637 AATAT-AA
1 AATATAAA
6623644 AATATAA
1 AATATAA
6623651 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 14 0.52
8 13 0.48
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AATATAAA
Found at i:6623632 original size:7 final size:7
Alignment explanation
Indices: 6623614--6623656 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
6623604 AATATATGTT
6623614 AATATAAA
1 AATAT-AA
6623622 AATATAA
1 AATATAA
6623629 AATATAAA
1 AATAT-AA
6623637 AATATAA
1 AATATAA
6623644 AATATAA
1 AATATAA
*
6623651 TATATA
1 AATATA
6623657 TATATATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
7 21 0.64
8 12 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATATAA
Found at i:6623632 original size:15 final size:15
Alignment explanation
Indices: 6623614--6623650 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
6623604 AATATATGTT
6623614 AATATAAAAATATAA
1 AATATAAAAATATAA
6623629 AATATAAAAATATAA
1 AATATAAAAATATAA
6623644 AATATAA
1 AATATAA
6623651 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATAAAAATATAA
Found at i:6623798 original size:2 final size:2
Alignment explanation
Indices: 6623791--6623821 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6623781 TCCAAAATTA
6623791 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 A
6623822 ATCAGACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6624404 original size:185 final size:182
Alignment explanation
Indices: 6624086--6624472 Score: 582
Period size: 185 Copynumber: 2.1 Consensus size: 182
6624076 ATTAAATTTT
* * *
6624086 AAATATTAAATATATTATATATAACATATGGGCTCAGCCTAAACTATTTGAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCTAAACCATTTAAAACCCAATTAATAA
*
6624151 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATCAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATCAAAAAAATTATATAAATTTT
*
6624216 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAAC---TTTTTTAATTAAA
* **
6624271 AAATATTAAATATATTATATATAACATATGGGCTAAATCC-AAACCATTTAAAATTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCTAAACCATTTAAAACCCAATTAATA
* * *
6624335 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-T
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATCAAAAAAATTATAT-AAATT
6624399 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAATTAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAATTAAA
* * *
6624453 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
6624473 AATTAGCAAA
Statistics
Matches: 186, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
181 8 0.04
182 22 0.12
185 150 0.81
186 6 0.03
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (182 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCTAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATCAAAAAAATTATATAAATTTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAATTAAA
Found at i:6632013 original size:31 final size:31
Alignment explanation
Indices: 6631952--6632064 Score: 106
Period size: 31 Copynumber: 3.6 Consensus size: 31
6631942 CATGAACTTT
* * * *
6631952 TAAAATGTCCAATGTAGTA-CTTTTCATTTGA
1 TAAAATGTCCAATATGGTACCTATAC-TTTGA
6631983 TAAAATGTCCAATATGGTACAC-ATACTTTGA
1 TAAAATGTCCAATATGGTAC-CTATACTTTGA
* **
6632014 TAAAATGTCCATTGGGGTACCTATACTTTG-
1 TAAAATGTCCAATATGGTACCTATACTTTGA
*
6632044 TCAAAATGTCTAATATGGTAC
1 T-AAAATGTCCAATATGGTAC
6632065 TTGAACTATT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
30 2 0.03
31 62 0.93
32 2 0.03
33 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (31 bp):
TAAAATGTCCAATATGGTACCTATACTTTGA
Found at i:6641307 original size:7 final size:6
Alignment explanation
Indices: 6641281--6641310 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
6641271 TTAATTGCGA
6641281 AAAATT AAAATT AAAATT AAAATTT AAAAT
1 AAAATT AAAATT AAAATT AAAA-TT AAAAT
6641311 ATTCAATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:6642666 original size:25 final size:23
Alignment explanation
Indices: 6642621--6642668 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
6642611 TTTTTAGGGA
*
6642621 CTGTTGCTTTGGTTTTTTGGTTT
1 CTGTTGCTTTGGTTTTGTGGTTT
*
6642644 CTGTTGTCTTTTGTGTTTGTGGTTT
1 CTGTTG-CTTTGGT-TTTGTGGTTT
6642669 TTGGTTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.00, C:0.08, G:0.27, T:0.65
Consensus pattern (23 bp):
CTGTTGCTTTGGTTTTGTGGTTT
Found at i:6643373 original size:37 final size:36
Alignment explanation
Indices: 6643183--6643612 Score: 306
Period size: 37 Copynumber: 12.3 Consensus size: 36
6643173 AAATATAATT
*
6643183 TATATAATATAT-ATATTTCAAAATAT-TTTTT-AAAC
1 TATATATTATATAAT-TTTCAAAA-ATGTTTTTAAAAC
*
6643218 TATATATTAT-T--TTTT-AAAAA-GTTTTCAAAAC
1 TATATATTATATAATTTTCAAAAATGTTTTTAAAAC
* *
6643249 TATATGTTATATAGTTTTC-AAAATG-TTTT-AAA-
1 TATATATTATATAATTTTCAAAAATGTTTTTAAAAC
*
6643281 -A-ATATTATATAAGTTTTCAAAAAATGTTTTTAAAAT
1 TATATATTATATAA-TTTTC-AAAAATGTTTTTAAAAC
6643317 TATATATTATATAATTTTCAAAAATGTTTTTAAAAC
1 TATATATTATATAATTTTCAAAAATGTTTTTAAAAC
** *
6643353 TATATATTATATAATCTTTCAAAAACATTTTTTAAAC
1 TATATATTATATAAT-TTTCAAAAATGTTTTTAAAAC
6643390 TATATATTATATAATTTTTCAAAAATGTTTTTAAAAC
1 TATATATTATATAA-TTTTCAAAAATGTTTTTAAAAC
* *
6643427 -------CATAT-ATTTT-AAAAATGTTTTAAAAAC
1 TATATATTATATAATTTTCAAAAATGTTTTTAAAAC
* * *
6643454 TATATACTATAAAAGTTTTC-AAAATGTTTTAAAAAC
1 TATATATTATATAA-TTTTCAAAAATGTTTTTAAAAC
* * * *
6643490 TATACAATATATAAATGTTTTC-AAAATGTTTTCAAAAT
1 TATATATTATAT-AA--TTTTCAAAAATGTTTTTAAAAC
* * *
6643528 TATACA-T-TAT-ATTTT-AAAAATATTTTCAAAAAC
1 TATATATTATATAATTTTCAAAAATGTTTT-TAAAAC
* * * *
6643561 TATATAATATATAAATTTTCGAAAATCGTTTTCCGAAAAT
1 TATATATTATAT-AATTTTCAAAAAT-GTTTT--TAAAAC
6643601 TATATATTATAT
1 TATATATTATAT
6643613 TTTGTCAAAA
Statistics
Matches: 326, Mismatches: 31, Indels: 71
0.76 0.07 0.17
Matches are distributed among these distances:
27 16 0.05
28 4 0.01
29 1 0.00
30 18 0.06
31 23 0.07
32 17 0.05
33 19 0.06
34 21 0.06
35 17 0.05
36 63 0.19
37 64 0.20
38 43 0.13
39 4 0.01
40 16 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATTATATAATTTTCAAAAATGTTTTTAAAAC
Found at i:6643444 original size:27 final size:28
Alignment explanation
Indices: 6643405--6643459 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
6643395 ATTATATAAT
*
6643405 TTTTCAAAAATGTTTTTAAAACCATATA
1 TTTTCAAAAATGTTTTAAAAACCATATA
*
6643433 TTTT-AAAAATGTTTTAAAAACTATATA
1 TTTTCAAAAATGTTTTAAAAACCATATA
6643460 CTATAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (28 bp):
TTTTCAAAAATGTTTTAAAAACCATATA
Found at i:6643477 original size:25 final size:27
Alignment explanation
Indices: 6643410--6643467 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
6643400 ATAATTTTTC
* * *
6643410 AAAAATGTTTTTAAAACCATATATTTT
1 AAAAATGTTTTAAAAACCATATACTAT
*
6643437 AAAAATGTTTTAAAAACTATATACTAT
1 AAAAATGTTTTAAAAACCATATACTAT
6643464 AAAA
1 AAAA
6643468 GTTTTCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (27 bp):
AAAAATGTTTTAAAAACCATATACTAT
Found at i:6643503 original size:38 final size:35
Alignment explanation
Indices: 6643432--6643592 Score: 150
Period size: 36 Copynumber: 4.5 Consensus size: 35
6643422 AAAACCATAT
* *
6643432 ATTTTAAAAATGTTTTAAAAACTATATACTATA-AA
1 ATTTTCAAAATGTTTTAAAAACTATACA-TATATAA
6643467 AGTTTTCAAAATGTTTTAAAAACTATACAATATATAA
1 A-TTTTCAAAATGTTTTAAAAACTATAC-ATATATAA
* *
6643504 ATGTTTTCAAAATGTTTTCAAAATTATACAT-TAT--
1 A--TTTTCAAAATGTTTTAAAAACTATACATATATAA
* * *
6643538 ATTTTAAAAATATTTTCAAAAACTATATAATATATAA
1 ATTTTCAAAATGTTTT-AAAAACTATA-CATATATAA
6643575 ATTTTCGAAAATCGTTTT
1 ATTTTC-AAAAT-GTTTT
6643593 CCGAAAATTA
Statistics
Matches: 104, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
32 13 0.12
33 8 0.08
34 3 0.03
35 4 0.04
36 31 0.30
37 11 0.11
38 30 0.29
39 4 0.04
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (35 bp):
ATTTTCAAAATGTTTTAAAAACTATACATATATAA
Found at i:6643510 original size:63 final size:64
Alignment explanation
Indices: 6643386--6643515 Score: 163
Period size: 63 Copynumber: 2.0 Consensus size: 64
6643376 AACATTTTTT
* * * * * * *
6643386 AAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAACCATATATTTTAAAAATGTTTTAA
1 AAACTATATACTATAAAAGTTTTCAAAAATGTTTTAAAAACCATACAATATAAAAATGTTTTAA
* * *
6643450 AAACTATATACTATAAAAGTTTTC-AAAATGTTTTAAAAACTATACAATATATAAATGTTTTCA
1 AAACTATATACTATAAAAGTTTTCAAAAATGTTTTAAAAACCATACAATATAAAAATGTTTTAA
6643513 AAA
1 AAA
6643516 TGTTTTCAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
63 35 0.62
64 21 0.38
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (64 bp):
AAACTATATACTATAAAAGTTTTCAAAAATGTTTTAAAAACCATACAATATAAAAATGTTTTAA
Found at i:6643518 original size:11 final size:11
Alignment explanation
Indices: 6643502--6643527 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6643492 TACAATATAT
6643502 AAATGTTTTCA
1 AAATGTTTTCA
6643513 AAATGTTTTCA
1 AAATGTTTTCA
6643524 AAAT
1 AAAT
6643528 TATACATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:6644387 original size:84 final size:83
Alignment explanation
Indices: 6644299--6645275 Score: 960
Period size: 84 Copynumber: 11.8 Consensus size: 83
6644289 TGCCTCTGAC
* * * * *
6644299 CTGAGTGTAATCGAACTCGAAGATCTTTGGTTGGCAGATAGCCCTTATCGACTTAAGTTATGCTA
1 CTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTG
* *
6644364 CAAATGATGTGTCTTGGAG
65 CAAATGATATGCCTTGGAG
* * *
6644383 CTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTG
1 CTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTG
*
6644448 CAAATGATATGCCTTAGAG
65 CAAATGATATGCCTTGGAG
* * * * *
6644467 CTGAGCGTAGTCGAACTTGAAGGTC--T-TTAGCAGATAGCCCTTATTGACTTAAGCTATGCTGC
1 CTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
6644529 AAATGATATGCCTTGGAG
66 AAATGATATGCCTTGGAG
* *
6644547 CTGAGAGTAGTCGAACTCGAAGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
1 CTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
6644609 AAATGATATGCCTTGGAG
66 AAATGATATGCCTTGGAG
* * * * * ** * *
6644627 CTGAGCGTAGTCGAACTC-AAAGT-TTTTTTGTCACAGATAACTCTTCAAGCCTTGAGTTATGCT
1 CTGAGCGTAGTCGAACTCGAAGGTCTTTGTTG--GCAGATAGCCCTTCTCGACTTAAGTTATGCT
* * *
6644690 GTAAATGATGTGCCTTAGAG
64 GCAAATGATATGCCTTGGAG
*
6644710 CTGAACGTAGTCGAACTCGAAGGTC--T-TTGGCAGATA-CCCTTCTCGACTTAAGTTATGCTGC
1 CTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
*
6644771 AAATGATGTGCCTTGGAG
66 AAATGATATGCCTTGGAG
* * * * * * * * *
6644789 CTAAGCGTAGTCGAACTTGAATGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
1 CTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTG
* * * *
6644854 TAAATGATGTGTCCTCGAAG
65 CAAATGATATG-CCTTGGAG
* ** * * * * * * **
6644874 TTGAATGTAATCGAACTTGAGGGTC-TTG--GGCAGATAGTCCTTCTTGACTTAAGCTATTATGC
1 CTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
* *
6644936 AAATGATGTGCCTTAGAG
66 AAATGATATGCCTTGGAG
* * *
6644954 CTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTG
1 CTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTG
6645019 CAAATGATATGCCTTGGAG
65 CAAATGATATGCCTTGGAG
* * * * * *** * * *
6645038 CTGAACGTAGTCGAACTCGAAGGTCTTTTGTTGACAAATAGCCATTTTTTCCTTGAGCTATGTTG
1 CTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTG
*
6645103 CAAATGATATGCCTTAGAG
65 CAAATGATATGCCTTGGAG
* * * * * *
6645122 CTGAACGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGA-TCTATGTT
1 CTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAGCCCTTCTCGACTTAAGT-TATGCT
* *
6645186 GTAAATGATATGCCCTGGAG
64 GCAAATGATATGCCTTGGAG
* * * * * * *
6645206 CTGAGCGTAGTCGAACTTGAAGGTCATTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGC
1 CTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
6645271 AAATG
66 AAATG
6645276 TTGTCTTAAA
Statistics
Matches: 751, Mismatches: 122, Indels: 41
0.82 0.13 0.04
Matches are distributed among these distances:
79 61 0.08
80 171 0.23
81 39 0.05
82 6 0.01
83 107 0.14
84 340 0.45
85 27 0.04
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (83 bp):
CTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
AAATGATATGCCTTGGAG
Found at i:6644957 original size:327 final size:326
Alignment explanation
Indices: 6644299--6645275 Score: 1036
Period size: 327 Copynumber: 3.0 Consensus size: 326
6644289 TGCCTCTGAC
* * * * ** * *
6644299 CTGAGTGTAATCGAACTCGAAGATCTTTGGTTGGCAGATAGCCCTT-ATCGACTTAAGTTATGCT
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCACAGATAACCCTTCA-AGACTTAAGTTATGCT
* * * *
6644363 ACAAATGATGTGTCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCT
65 GCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTC-TT--TTGGCAGAT-ACCCT
*
6644428 TCTCGACTTAAGTTATGTTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTTGAAGGTC-
126 TCTCGACTTAAGTTATGTTGCAAATGATATGCCTTAGAGCTAAGCGTAGTCGAACTTGAAGGTCT
* * * * * * * *
6644492 TTT-AGCAGATAGCCCTTATTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGAGTA
191 TTTGTGCAGATAGCCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCTCGAAGCTGAGAGTA
* * *
6644556 GTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCC
256 ATCGAACTCGAAGGTCTTGGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATATGCC
*
6644621 TTGGAG
321 TTAGAG
* * * * * *
6644627 CTGAGCGTAGTCGAACTCAAAGTTTTTTTG-TCACAGATAACTCTTCAAGCCTTGAGTTATGCTG
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCACAGATAACCCTTCAAGACTTAAGTTATGCTG
* *
6644691 TAAATGATGTGCCTTAGAGCTGAACGTAGTCGAACTCGAAGGTC-TTTGGCAGATACCCTTCTCG
66 CAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGCAGATACCCTTCTCG
* * * *
6644755 ACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTTGAATGTCTTTTGG
131 ACTTAAGTTATGTTGCAAATGATATGCCTTAGAGCTAAGCGTAGTCGAACTTGAAGGTCTTTT-G
* * * *
6644820 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCCTCGAAGTTGA-ATGTAA
195 TG-CAGATAGCCCTTCTTGCCTTGAGTTATGCTGTAAATGATATG-CCTCGAAGCTGAGA-GTAA
* * * * * *
6644884 TCGAACTTGAGGGTCTTGGGCAGATAGTCCTTCTTGACTTAAGCTATTATGCAAATGATGTGCCT
257 TCGAACTCGAAGGTCTTGGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATATGCCT
6644949 TAGAG
322 TAGAG
* * * **
6644954 CTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTG
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCACAGATAACCCTTCAAGACTTAAGTTATGCTG
* * *
6645019 CAAATGATATGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGTTGACAAATAGCCATT
66 CAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTG--G-CAGATA-CCCTT
* *** * * *
6645084 TTTTCCTTGAGCTATGTTGCAAATGATATGCCTTAGAGCTGAA-CGTAGTCGAACTCGAAGGTCT
127 CTCGACTTAAGTTATGTTGCAAATGATATGCCTTAGAGCT-AAGCGTAGTCGAACTTGAAGGTCT
* * *
6645148 TTTGTTGGCAAATAGCCCTTCTTGCCTTGA-TCTATGTTGTAAATGATATGCC-CTGGAGCTGAG
191 TTTG-T-GCAGATAGCCCTTCTTGCCTTGAGT-TATGCTGTAAATGATATGCCTC-GAAGCTGAG
* * * * * * * * *
6645211 CGTAGTCGAACTTGAAGGTCATTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATG
252 AGTAATCGAACTCGAAGGTC-TTG--GGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATG
6645276 TTGTCTTAAA
Statistics
Matches: 536, Mismatches: 91, Indels: 37
0.81 0.14 0.06
Matches are distributed among these distances:
322 64 0.12
323 12 0.02
325 2 0.00
326 35 0.07
327 161 0.30
328 94 0.18
329 4 0.01
331 2 0.00
332 32 0.06
333 96 0.18
334 3 0.01
335 31 0.06
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (326 bp):
CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCACAGATAACCCTTCAAGACTTAAGTTATGCTG
CAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGCAGATACCCTTCTCG
ACTTAAGTTATGTTGCAAATGATATGCCTTAGAGCTAAGCGTAGTCGAACTTGAAGGTCTTTTGT
GCAGATAGCCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCTCGAAGCTGAGAGTAATCGA
ACTCGAAGGTCTTGGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATATGCCTTAGA
G
Found at i:6646622 original size:95 final size:94
Alignment explanation
Indices: 6646468--6646651 Score: 314
Period size: 95 Copynumber: 1.9 Consensus size: 94
6646458 ATATAAACAC
* * *
6646468 CTTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGAC
1 CTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGAC
6646533 AACTCAAGCTTTATTGTATAGTATAATTAT
66 AACTCAAGCTTTATTGTATA-TATAATTAT
* *
6646563 CTTTATTAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGAC
1 CTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGAC
6646628 AACTCAAGCTTTATTGTATATATA
66 AACTCAAGCTTTATTGTATATATA
6646652 TAATATTATA
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 4 0.05
95 80 0.95
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (94 bp):
CTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGAC
AACTCAAGCTTTATTGTATATATAATTAT
Found at i:6650183 original size:19 final size:20
Alignment explanation
Indices: 6650161--6650206 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
6650151 AAAGATAATG
*
6650161 AAAATAAATAAAAA-AAAGT
1 AAAATAAATAAAAATAAAGC
6650180 AAAATAAA-AAAAATAAAGC
1 AAAATAAATAAAAATAAAGC
6650199 AAAA-AAAT
1 AAAATAAAT
6650207 GAAAGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAATAAATAAAAATAAAGC
Found at i:6650202 original size:14 final size:13
Alignment explanation
Indices: 6650161--6650220 Score: 57
Period size: 15 Copynumber: 4.3 Consensus size: 13
6650151 AAAGATAATG
6650161 AAAATAAATAAAA
1 AAAATAAATAAAA
6650174 AAAAGTAAAATAAAA
1 AAAA-T-AAATAAAA
**
6650189 AAAATAAAGCAAA
1 AAAATAAATAAAA
*
6650202 AAAATGAAAGAGAAA
1 AAAAT-AAATA-AAA
6650217 AAAA
1 AAAA
6650221 GTCAAAGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 15 0.38
14 6 0.15
15 19 0.47
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (13 bp):
AAAATAAATAAAA
Found at i:6650231 original size:15 final size:14
Alignment explanation
Indices: 6650171--6650232 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
6650161 AAAATAAATA
**
6650171 AAAAAAAGTAAAAT
1 AAAAAAAGTAAAGG
* *
6650185 AAAAAAAATAAAGC
1 AAAAAAAGTAAAGG
6650199 AAAAAAA-TGAAAGAG
1 AAAAAAAGT-AAAG-G
6650214 AAAAAAAGTCAAAGG
1 AAAAAAAGT-AAAGG
6650229 AAAA
1 AAAA
6650233 TAATAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 1 0.03
14 22 0.55
15 12 0.30
16 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (14 bp):
AAAAAAAGTAAAGG
Found at i:6650268 original size:14 final size:13
Alignment explanation
Indices: 6650161--6650289 Score: 68
Period size: 13 Copynumber: 9.6 Consensus size: 13
6650151 AAAGATAATG
*
6650161 AAAATAAATAAAA
1 AAAATAAAGAAAA
*
6650174 AAAAGTAAAATAAAA
1 AAAA-T-AAAGAAAA
*
6650189 AAAATAAAGCAAA
1 AAAATAAAGAAAA
6650202 AAAATGAAAGAGAAA
1 AAAAT-AAAGA-AAA
*
6650217 AAAAGTCAAAGGAAA
1 AAAA-T-AAAGAAAA
* *
6650232 ATAAT--A-AAAT
1 AAAATAAAGAAAA
* *
6650242 AGAATAAACAAAA
1 AAAATAAAGAAAA
6650255 AAAATCAAAGAAAA
1 AAAAT-AAAGAAAA
* *
6650269 CGAAA-AAAGAAGA
1 -AAAATAAAGAAAA
6650282 AAAATAAA
1 AAAATAAA
6650290 ATAAAATGAA
Statistics
Matches: 90, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
10 6 0.07
11 1 0.01
12 4 0.04
13 32 0.36
14 14 0.16
15 28 0.31
16 5 0.06
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (13 bp):
AAAATAAAGAAAA
Found at i:6651550 original size:22 final size:22
Alignment explanation
Indices: 6651512--6651563 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
6651502 CCTGGAAAAG
*
6651512 AAAAATAAAATGAAATAAATTTA
1 AAAAATAAAATGAAATAAA-ATA
6651535 AAAAATAAAATG-AATAAAATA
1 AAAAATAAAATGAAATAAAATA
6651556 AAAAATAA
1 AAAAATAA
6651564 TAATATACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 10 0.36
22 6 0.21
23 12 0.43
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (22 bp):
AAAAATAAAATGAAATAAAATA
Found at i:6651714 original size:34 final size:37
Alignment explanation
Indices: 6651636--6651745 Score: 110
Period size: 34 Copynumber: 3.1 Consensus size: 37
6651626 ATTATATTTT
* * *
6651636 AAAAA-GTTTTCAAAACTATATGTTATATAGTTTTC--
1 AAAAATGTTTTTAAAAC-ATATATTATATAATTTTCAA
6651671 -AAAATG-TTTT-AAA-A-ATATTATATAAGTTTTCAA
1 AAAAATGTTTTTAAAACATATATTATATAA-TTTTCAA
6651704 AAAAATGTTTTTAAAACTATATATTATATAATTTTCAA
1 AAAAATGTTTTTAAAAC-ATATATTATATAATTTTCAA
6651742 AAAA
1 AAAA
6651746 TTTCAAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
30 9 0.15
31 6 0.10
33 3 0.05
34 13 0.21
35 5 0.08
36 3 0.05
38 12 0.19
39 11 0.18
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (37 bp):
AAAAATGTTTTTAAAACATATATTATATAATTTTCAA
Found at i:6651786 original size:32 final size:31
Alignment explanation
Indices: 6651745--6651809 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
6651735 TTTTCAAAAA
* *
6651745 ATTTCAAAAATATTTTTAAAACCATATATTAT
1 ATTTCAAAAATA-TTTAAAAACCATATACTAT
* *
6651777 ATTTTAAAAATATTTAAAAACTATATACTAT
1 ATTTCAAAAATATTTAAAAACCATATACTAT
6651808 AT
1 AT
6651810 AAGTTTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (31 bp):
ATTTCAAAAATATTTAAAAACCATATACTAT
Found at i:6651831 original size:36 final size:37
Alignment explanation
Indices: 6651778--6651860 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 37
6651768 ATATATTATA
* * *
6651778 TTTTAAAAATATTTAAAAACTATATACTATAT-AA-G
1 TTTTCAAAATATTTAAAAACTATACAATATATAAATG
*
6651813 TTTTCAAAATGTTCTAAAAACTATACAATATATAAATG
1 TTTTCAAAATATT-TAAAAACTATACAATATATAAATG
6651851 TTTTCAAAAT
1 TTTTCAAAAT
6651861 TATACATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 11 0.27
36 17 0.41
37 2 0.05
38 11 0.27
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (37 bp):
TTTTCAAAATATTTAAAAACTATACAATATATAAATG
Found at i:6651844 original size:34 final size:34
Alignment explanation
Indices: 6651778--6651844 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
6651768 ATATATTATA
*
6651778 TTTTAAAAATATTTAAAAACTATATACTATATAAG
1 TTTTAAAAATATTTAAAAAC-ATATACAATATAAG
* *
6651813 TTTTCAAAATGTTCTAAAAAC-TATACAATATA
1 TTTTAAAAATATT-TAAAAACATATACAATATA
6651845 TAAATGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.36
35 11 0.39
36 7 0.25
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (34 bp):
TTTTAAAAATATTTAAAAACATATACAATATAAG
Found at i:6651849 original size:27 final size:27
Alignment explanation
Indices: 6651819--6651872 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
6651809 TAAGTTTTCA
6651819 AAATGTTCTAAAAACTATACAATATAT
1 AAATGTTCTAAAAACTATACAATATAT
* * * *
6651846 AAATGTTTTCAAAATTATACATTATAT
1 AAATGTTCTAAAAACTATACAATATAT
6651873 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (27 bp):
AAATGTTCTAAAAACTATACAATATAT
Found at i:6651918 original size:38 final size:37
Alignment explanation
Indices: 6651871--6651982 Score: 122
Period size: 37 Copynumber: 3.0 Consensus size: 37
6651861 TATACATTAT
6651871 ATTTT-AAAAATATTTTCAAAAACTATATAATATATAA
1 ATTTTCAAAAATATTTTCAAAAACTATAT-ATATATAA
* *
6651908 ATTTTCAAAAATTATTTTCCGAAAATTATATAT-TAT-A
1 ATTTTCAAAAA-TATTTT-CAAAAACTATATATATATAA
* * *
6651945 TTTTGTCAAAAACATTTTCACAAACTATATATATATAA
1 ATTT-TCAAAAATATTTTCAAAAACTATATATATATAA
6651983 TAAAATGATA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
36 11 0.18
37 17 0.27
38 16 0.26
39 8 0.13
40 10 0.16
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (37 bp):
ATTTTCAAAAATATTTTCAAAAACTATATATATATAA
Found at i:6651995 original size:19 final size:19
Alignment explanation
Indices: 6651971--6652007 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6651961 TTCACAAACT
*
6651971 ATATATATATAATAAAATG
1 ATATATATATAACAAAATG
6651990 ATATATATATAACAAAAT
1 ATATATATATAACAAAAT
6652008 AACTCCAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATATATATAACAAAATG
Found at i:6656752 original size:6 final size:6
Alignment explanation
Indices: 6656743--6656767 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6656733 TAAGGTTCAT
6656743 GTTCGA GTTCGA GTTCGA GTTCGA G
1 GTTCGA GTTCGA GTTCGA GTTCGA G
6656768 GCTTTAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.36, T:0.32
Consensus pattern (6 bp):
GTTCGA
Found at i:6658947 original size:21 final size:21
Alignment explanation
Indices: 6658903--6658947 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6658893 ATTTGTCATC
* * *
6658903 ATTGATCATCAATGTTGACTA
1 ATTGACCATCAATATTGACAA
*
6658924 ATTGACCATCAATATTGAGAA
1 ATTGACCATCAATATTGACAA
6658945 ATT
1 ATT
6658948 AATATAATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (21 bp):
ATTGACCATCAATATTGACAA
Found at i:6659904 original size:29 final size:29
Alignment explanation
Indices: 6659836--6659906 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
6659826 GATGGCCTCG
**
6659836 CGTTTTACAAAAAGCGAAGTCAGATCTCA
1 CGTTTTATGAAAAGCGAAGTCAGATCTCA
* *
6659865 CGTTTTATGAAAAGCGAGGTCTGATCTCA
1 CGTTTTATGAAAAGCGAAGTCAGATCTCA
*
6659894 CGTTTTTTGAAAA
1 CGTTTTATGAAAA
6659907 TTGAGTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (29 bp):
CGTTTTATGAAAAGCGAAGTCAGATCTCA
Found at i:6661885 original size:15 final size:15
Alignment explanation
Indices: 6661854--6661906 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
6661844 TCAAATATAT
6661854 AAATCCAAACAAATCCA
1 AAAT-CAAAC-AATCCA
* *
6661871 AAGTCTAACAATCCACA
1 AAATCAAACAAT-C-CA
6661888 AAATCAAACAATCCA
1 AAATCAAACAATCCA
6661903 AAAT
1 AAAT
6661907 ATTCAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 9 0.30
16 6 0.20
17 15 0.50
ACGTcount: A:0.57, C:0.26, G:0.02, T:0.15
Consensus pattern (15 bp):
AAATCAAACAATCCA
Found at i:6671520 original size:21 final size:21
Alignment explanation
Indices: 6671491--6671560 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
6671481 TAAATTTACA
*
6671491 AAATTTAAATATTAAAAAAAT
1 AAATATAAATATTAAAAAAAT
*
6671512 AAATATAAA-AATAATAAAAATT
1 AAATATAAATATTAA-AAAAA-T
6671534 GAAATAAGTAAATATATATAAAAAAT
1 -AAAT-A-TAAATAT-TA-AAAAAAT
6671560 A
1 A
6671561 TTAAAATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
20 4 0.11
21 13 0.34
22 1 0.03
23 4 0.11
24 1 0.03
25 5 0.13
26 2 0.05
27 7 0.18
28 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (21 bp):
AAATATAAATATTAAAAAAAT
Found at i:6671527 original size:15 final size:15
Alignment explanation
Indices: 6671496--6671549 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
6671486 TTACAAAATT
6671496 TAAATATTAAAAA-AA
1 TAAATA-TAAAAATAA
6671511 TAAATATAAAAATAA
1 TAAATATAAAAATAA
* **
6671526 TAAAAATTGAAATAA
1 TAAATATAAAAATAA
6671541 GTAAATATA
1 -TAAATATA
6671550 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 6 0.19
15 20 0.62
16 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (15 bp):
TAAATATAAAAATAA
Done.