Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 17
Found at i:1749773 original size:21 final size:21
Alignment explanation
Indices: 1749749--1749792 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1749739 GCCGGAGAGG
* *
1749749 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
1749770 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
1749791 AG
1 AG
1749793 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:1751252 original size:20 final size:20
Alignment explanation
Indices: 1751227--1751278 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1751217 ACCCGACGGA
1751227 TGCATCGATGCATGACCCTG
1 TGCATCGATGCATGACCCTG
*
1751247 TGCATCGATACATGACCCTG
1 TGCATCGATGCATGACCCTG
1751267 TGCATCGATGCA
1 TGCATCGATGCA
1751279 CATTCAAGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (20 bp):
TGCATCGATGCATGACCCTG
Found at i:1751480 original size:23 final size:23
Alignment explanation
Indices: 1751454--1751508 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
1751444 CATATATTAA
1751454 AAATTAATCATGTTTAATCAATC
1 AAATTAATCATGTTTAATCAATC
1751477 AAATTAATCATGTTTAATCAATC
1 AAATTAATCATGTTTAATCAATC
1751500 AAATTAATC
1 AAATTAATC
1751509 TTTAAACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATTAATCATGTTTAATCAATC
Found at i:1753756 original size:13 final size:13
Alignment explanation
Indices: 1753738--1753762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1753728 CGCCCAAAAA
1753738 TATTTTGACAAAT
1 TATTTTGACAAAT
1753751 TATTTTGACAAA
1 TATTTTGACAAA
1753763 GCATGGTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TATTTTGACAAAT
Found at i:1763781 original size:39 final size:40
Alignment explanation
Indices: 1763683--1763790 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
1763673 ACCGTAGTGC
* * * *
1763683 TACACATAAGGTCATGCCCTCCATGTACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACATCGAAATGTAT
* *
1763723 TACATATAAGGTCGTGCCCACCATATACATCTAAATGTA-
1 TACACATAAGGTCGTGCCCACCATATACATCGAAATGTAT
1763762 TACACATAAGGTCGTGCCCACCATATACA
1 TACACATAAGGTCGTGCCCACCATATACA
1763791 CTTAGTGTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
39 28 0.46
40 33 0.54
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACATCGAAATGTAT
Found at i:1767034 original size:25 final size:25
Alignment explanation
Indices: 1767006--1767056 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1766996 ATCATATATT
* *
1767006 ATTATATGATATCTTATGTATTATC
1 ATTAAATGATATATTATGTATTATC
* *
1767031 ATTAAATGATATATTTTTTATTATC
1 ATTAAATGATATATTATGTATTATC
1767056 A
1 A
1767057 CTATGTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (25 bp):
ATTAAATGATATATTATGTATTATC
Found at i:1767368 original size:2 final size:2
Alignment explanation
Indices: 1767361--1767386 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1767351 GAAATATTAC
1767361 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
1767387 TGTTATAATT
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:1770256 original size:47 final size:45
Alignment explanation
Indices: 1770165--1770288 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
1770155 GTATGTATGC
*
1770165 AAATAAGCTTACGAGCTTAT-GAAT-AAT-GCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
* *
1770207 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
* *
1770254 AAATAAGCCTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1770289 AGATTTTATA
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
42 20 0.28
43 3 0.04
45 12 0.17
46 3 0.04
47 34 0.47
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:1770602 original size:32 final size:31
Alignment explanation
Indices: 1770551--1770618 Score: 109
Period size: 32 Copynumber: 2.2 Consensus size: 31
1770541 AGTGGCATGT
*
1770551 AATTTGAAATTTTCAATTTATTTGTTCAATA
1 AATTTGAAATGTTCAATTTATTTGTTCAATA
*
1770582 AATTTGAAAATGTTCAATTTATTTGTTGAATA
1 AATTTG-AAATGTTCAATTTATTTGTTCAATA
1770614 AATTT
1 AATTT
1770619 TGGAAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 6 0.18
32 28 0.82
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (31 bp):
AATTTGAAATGTTCAATTTATTTGTTCAATA
Found at i:1772733 original size:20 final size:20
Alignment explanation
Indices: 1772705--1772759 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1772695 GCGCACTAGG
* **
1772705 GTAGAAAAATTAAGAACCAT
1 GTAGGAAAATTAAGAAAAAT
1772725 GTAGGAAAATT-AGAAAAAT
1 GTAGGAAAATTAAGAAAAAT
1772744 GACTAGGAAAATTAAG
1 G--TAGGAAAATTAAG
1772760 TATTTAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 7 0.24
20 10 0.34
21 10 0.34
22 2 0.07
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (20 bp):
GTAGGAAAATTAAGAAAAAT
Found at i:1774767 original size:35 final size:36
Alignment explanation
Indices: 1774715--1774785 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
1774705 ATTGTTGATA
*
1774715 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAAGTTATCCCACTAGTATTAGAAAT
* *
1774751 ATGCT-AAATTAAGTTATCCCATTAGTATTGGAAAT
1 ATGCTCAAATTAAGTTATCCCACTAGTATTAGAAAT
1774786 GACGATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 27 0.84
36 5 0.16
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (36 bp):
ATGCTCAAATTAAGTTATCCCACTAGTATTAGAAAT
Found at i:1775885 original size:23 final size:22
Alignment explanation
Indices: 1775854--1775898 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1775844 AGGTTGAACG
1775854 ATTTATTAAATAGCTACATAAAT
1 ATTTATT-AATAGCTACATAAAT
* *
1775877 ATTTGTTAATAGCTATATAAAT
1 ATTTATTAATAGCTACATAAAT
1775899 GTTAGTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (22 bp):
ATTTATTAATAGCTACATAAAT
Found at i:1780973 original size:20 final size:20
Alignment explanation
Indices: 1780926--1781043 Score: 96
Period size: 20 Copynumber: 5.9 Consensus size: 20
1780916 GCGATTTTCC
* *
1780926 GACTATCTCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
1780946 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
1780966 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
* * *
1780986 GACTATCGCAACGAGATTCT
1 GACTATCGCAATGCGATTAT
* *
1781006 AACTGTCGCAATGCGATGT-T
1 GACTATCGCAATGCGAT-TAT
* *
1781026 AATTATCGCAATGCGATT
1 GACTATCGCAATGCGATT
1781044 TTCAAAGTGC
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 78 0.95
21 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:1781749 original size:20 final size:20
Alignment explanation
Indices: 1781645--1781751 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
1781635 AGAATCGCAA
1781645 TGCGATTTT-AATTTCGCGT
1 TGCGATTTTCAATTTCGCGT
1781664 TGCGATTTTC-ATTTCGCGT
1 TGCGATTTTCAATTTCGCGT
* ** *
1781683 TGCAATAGTCAAATTCGCGT
1 TGCGATTTTCAATTTCGCGT
** * *
1781703 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCAATTTCGCGT
* *
1781723 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCAATTTCGCGT
1781743 TGCGATTTT
1 TGCGATTTT
1781752 AAGTTTCAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 25 0.33
20 51 0.67
ACGTcount: A:0.16, C:0.17, G:0.21, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCAATTTCGCGT
Found at i:1783482 original size:18 final size:18
Alignment explanation
Indices: 1783459--1783509 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
1783449 TTTACTCGTA
1783459 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1783477 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1783495 ATTTCACTTAGATTA
1 ATTTCACTTAGATTA
1783510 CTTAGTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1783703 original size:20 final size:20
Alignment explanation
Indices: 1783678--1783717 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1783668 CGAAATGAAA
1783678 TTCGCGTTGCCATAGTCATT
1 TTCGCGTTGCCATAGTCATT
*
1783698 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCCATAGTCATT
1783718 CGTGTTGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
TTCGCGTTGCCATAGTCATT
Found at i:1783724 original size:18 final size:18
Alignment explanation
Indices: 1783677--1783728 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 18
1783667 GCGAAATGAA
*
1783677 ATTCGCGTTGCCATAGTC
1 ATTCGCGTTGCGATAGTC
1783695 ATTTTCGCGTTGCGATAGTC
1 A--TTCGCGTTGCGATAGTC
*
1783715 ATTCGTGTTGCGAT
1 ATTCGCGTTGCGAT
1783729 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 13 0.43
20 17 0.57
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.38
Consensus pattern (18 bp):
ATTCGCGTTGCGATAGTC
Found at i:1784320 original size:42 final size:42
Alignment explanation
Indices: 1784213--1784323 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 42
1784203 CCCGACTCAC
*
1784213 CTGTCATCATTCAAGAGG--CCTCCCCTATTGTTCAAGAGGCCC
1 CTGTCATCATTCAAGAGGTCCCT-CCC-ATTGTTCAAGAGGCCA
* ** *
1784255 CTATCATCCCTCAAGA-ATCCCCTCCCATTGTTCAAGAGGCCA
1 CTGTCATCATTCAAGAGGT-CCCTCCCATTGTTCAAGAGGCCA
* *
1784297 CTGTCATCGTTGAAGAGGTCCCTCCCA
1 CTGTCATCATTCAAGAGGTCCCTCCCA
1784324 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
42 48 0.87
43 4 0.07
44 3 0.05
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (42 bp):
CTGTCATCATTCAAGAGGTCCCTCCCATTGTTCAAGAGGCCA
Found at i:1785747 original size:14 final size:14
Alignment explanation
Indices: 1785710--1785771 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1785700 TTGCTTGTTT
*
1785710 AATTGATTTATAAA
1 AATTGATTTGTAAA
1785724 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1785738 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1785753 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1785767 TAATT
1 -AATT
1785772 CTTATTTGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1785908 original size:20 final size:20
Alignment explanation
Indices: 1785885--1785923 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1785875 ACGCTAAACT
*
1785885 CAAAATCGCAATGTGAAAGA
1 CAAAATCGCAATGCGAAAGA
1785905 CAAAATCGCAATGCGAAAG
1 CAAAATCGCAATGCGAAAG
1785924 TCAATTCGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
CAAAATCGCAATGCGAAAGA
Found at i:1785993 original size:20 final size:20
Alignment explanation
Indices: 1785966--1786230 Score: 277
Period size: 20 Copynumber: 13.8 Consensus size: 20
1785956 GCGATTTTCT
* *
1785966 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
1785986 CATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1786006 TGTTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1786026 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1786046 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
1786060 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
*
1786079 CCGTTGCGATAATCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
1786100 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1786120 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1786140 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
1786160 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1786180 CGTTGTGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
1786194 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1786214 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1786231 GAATGTGTAA
Statistics
Matches: 203, Mismatches: 28, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
14 22 0.11
16 2 0.01
18 2 0.01
19 1 0.00
20 174 0.86
21 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1786055 original size:94 final size:94
Alignment explanation
Indices: 1785926--1786148 Score: 365
Period size: 94 Copynumber: 2.4 Consensus size: 94
1785916 TGCGAAAGTC
* * * *
1785926 AATTCGCGTTACGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
*
1785991 CGATAATCAAATTCGTGTTGCGATACTCA
66 CGATAATCAAATTCGCGTTGCGATACTCA
* *
1786020 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAGCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
*
1786085 CGATAATCAAATTCGCGTTGCGATAGTCA
66 CGATAATCAAATTCGCGTTGCGATACTCA
*
1786114 AATTCGCGTTGCGATAGACAAATTCGCGTTGCGAT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1786149 AGTCATATTC
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 120 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (94 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
CGATAATCAAATTCGCGTTGCGATACTCA
Found at i:1786199 original size:114 final size:113
Alignment explanation
Indices: 1785902--1786230 Score: 331
Period size: 114 Copynumber: 2.9 Consensus size: 113
1785892 GCAATGTGAA
* ** * * * * *
1785902 AGACAAAATCGCAATGCGAAAGTCAATTCGCGTTACGATAGTCTAATACGCTTTGCGATTTTCT-
1 AGACAAATTCGCGTTGCGATAGTCAATTCGCGTTGCGATAGTCTAATTCGCGTTGTGATTTT-TG
* * * * *
1785966 CGTTGCGATAGTCAAATACCCATTGCGATAATCAAATTCGTGTTGCGAT
65 CGTTGCGATAATCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGAT
** ** ** * * ** *
1786015 ACTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTT-GCGATAGTCA-AATA
1 AGACAAATTCGCGTTGCGATAGTC-AATTCGCGTTGCGATAGTCTAATTCGCG-TTGTGATTTTT
*
1786078 GCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
64 G-CGTTGCGATAATCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGAT
* *
1786129 AGACAAATTCGCGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGTGATTTTTG
1 AGACAAATTCGCGTTGCGATAGTCA-ATTCGCGTTGCGATAGTCTAATTCGCGTTGTGATTTTTG
* *
1786194 AGTTGCGATAATCAAATTCGCGTTGCGATATTCAAAT
65 CGTTGCGATAATCAAATTCGCGTTGCGATAATCAAAT
1786231 GAATGTGTAA
Statistics
Matches: 169, Mismatches: 40, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
113 22 0.13
114 142 0.84
115 5 0.03
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (113 bp):
AGACAAATTCGCGTTGCGATAGTCAATTCGCGTTGCGATAGTCTAATTCGCGTTGTGATTTTTGC
GTTGCGATAATCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGAT
Found at i:1786457 original size:140 final size:140
Alignment explanation
Indices: 1786205--1786470 Score: 514
Period size: 140 Copynumber: 1.9 Consensus size: 140
1786195 GTTGCGATAA
*
1786205 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
1786270 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
1786335 CACATAAAAG
131 CACATAAAAG
*
1786345 TCAAATTCGCGTTGCGATATTTAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
1786410 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1786471 TACAACGTTT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
CACATAAAAG
Found at i:1786553 original size:18 final size:18
Alignment explanation
Indices: 1786530--1786564 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1786520 AAGCCGGTTG
*
1786530 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1786548 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1786565 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1788851 original size:24 final size:24
Alignment explanation
Indices: 1788824--1788870 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1788814 CAAAATCCGA
1788824 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1788848 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1788871 AATACCGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1789708 original size:20 final size:20
Alignment explanation
Indices: 1789683--1789729 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1789673 GAAATTCAGT
1789683 GTTGCGACAGTCAGAATCAC
1 GTTGCGACAGTCAGAATCAC
*
1789703 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCAC
1789723 GTTGCGA
1 GTTGCGA
1789730 TTTACATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCAC
Found at i:1793383 original size:31 final size:31
Alignment explanation
Indices: 1793325--1793383 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1793315 ATAGAGTGAT
*
1793325 CATTTTGTTATAAATCGATAACGTTAATATC
1 CATTTTGTTATAAATCGATAACATTAATATC
*
1793356 CATTTTGTTATAAATCGATAATATTAAT
1 CATTTTGTTATAAATCGATAACATTAAT
1793384 GACCAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (31 bp):
CATTTTGTTATAAATCGATAACATTAATATC
Found at i:1793394 original size:31 final size:31
Alignment explanation
Indices: 1793328--1793394 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1793318 GAGTGATCAT
* *
1793328 TTTGTTATAAATCGATAACGTTAATATCCAT
1 TTTGTTATAAATCGATAACATTAATATCCAA
*
1793359 TTTGTTATAAATCGATAATATTAATGA-CCAA
1 TTTGTTATAAATCGATAACATTAAT-ATCCAA
1793390 TTTGT
1 TTTGT
1793395 CACTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (31 bp):
TTTGTTATAAATCGATAACATTAATATCCAA
Found at i:1808845 original size:3 final size:3
Alignment explanation
Indices: 1808837--1808867 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1808827 TGTGTTTATC
1808837 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1808868 TAATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1808872 original size:3 final size:3
Alignment explanation
Indices: 1808866--1808890 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1808856 CAACAACAAC
1808866 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1808891 GTGTGAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1808962 original size:43 final size:43
Alignment explanation
Indices: 1808903--1808988 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
1808893 GTGAACATAG
* *
1808903 AAATTAGACTCTCAATAATAAAAATAAAAAAACTTATGGATGA
1 AAATTAGACTCCCAATAATAAAAATAAAAAAACTTAAGGATGA
** *
1808946 AAATTAGACTCCCAATAATAAGTATCAAAAAACTTAAGGATGA
1 AAATTAGACTCCCAATAATAAAAATAAAAAAACTTAAGGATGA
1808989 TTTTTCTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.24
Consensus pattern (43 bp):
AAATTAGACTCCCAATAATAAAAATAAAAAAACTTAAGGATGA
Found at i:1809654 original size:23 final size:24
Alignment explanation
Indices: 1809612--1809661 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1809602 AAATATATGT
* *
1809612 TTTTAAAAAATCAATATTAAACTA
1 TTTTAAAAAATAAATATTAAAATA
1809636 TTTTAAAAAATAAAT-TTAAAATA
1 TTTTAAAAAATAAATATTAAAATA
1809659 TTT
1 TTT
1809662 ATTTATGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTTAAAAAATAAATATTAAAATA
Found at i:1809693 original size:16 final size:16
Alignment explanation
Indices: 1809674--1809707 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1809664 TTATGATCAT
1809674 ATAATATAAAT-TTAAA
1 ATAA-ATAAATATTAAA
1809690 ATAAATAAATATTAAA
1 ATAAATAAATATTAAA
1809706 AT
1 AT
1809708 TATTTTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATAAATATTAAA
Found at i:1809738 original size:28 final size:28
Alignment explanation
Indices: 1809691--1809744 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
1809681 AAATTTAAAA
*
1809691 TAAATAAATATTAAAATTATTTTTATCG
1 TAAATAAATATTAAAATTATATTTATCG
1809719 TAAAT-AAT-TTAAAATTTTATATTTAT
1 TAAATAAATATTAAAA--TTATATTTAT
1809745 TTAATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 6 0.26
27 3 0.13
28 14 0.61
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
TAAATAAATATTAAAATTATATTTATCG
Found at i:1810484 original size:16 final size:16
Alignment explanation
Indices: 1810463--1810495 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1810453 CGTTGAGTAC
*
1810463 TTTATAATTTTAAAAT
1 TTTATAAATTTAAAAT
1810479 TTTATAAATTTAAAAT
1 TTTATAAATTTAAAAT
1810495 T
1 T
1810496 AATGGTGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATAAATTTAAAAT
Found at i:1831348 original size:19 final size:20
Alignment explanation
Indices: 1831319--1831364 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1831309 CGCTCTAAGA
*
1831319 AGTTTTTAATATACATAT-AT
1 AGTTTTAAATAT-CATATGAT
1831339 -GTTTTAAATATCATATGAT
1 AGTTTTAAATATCATATGAT
1831358 AGTTTTA
1 AGTTTTA
1831365 CTTGAGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 12 0.52
20 6 0.26
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (20 bp):
AGTTTTAAATATCATATGAT
Found at i:1833088 original size:21 final size:21
Alignment explanation
Indices: 1833041--1833088 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1833031 GGAAATTCGA
*
1833041 TGAACAATATCGATACTGATG
1 TGAATAATATCGATACTGATG
**
1833062 CAAATAATATCGATACTGATG
1 TGAATAATATCGATACTGATG
1833083 TGAATA
1 TGAATA
1833089 TCGATACTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
TGAATAATATCGATACTGATG
Found at i:1833159 original size:17 final size:18
Alignment explanation
Indices: 1833137--1833170 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1833127 CAGAATGCAA
*
1833137 AAAAGG-GTATCGATACT
1 AAAAGGAGTATCAATACT
1833154 AAAAGGAGTATCAATAC
1 AAAAGGAGTATCAATAC
1833171 CATAGTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21
Consensus pattern (18 bp):
AAAAGGAGTATCAATACT
Found at i:1833606 original size:54 final size:54
Alignment explanation
Indices: 1833519--1834385 Score: 1173
Period size: 54 Copynumber: 16.1 Consensus size: 54
1833509 TGCATTTTTA
* * *
1833519 CGTATCGGCACTAAGTGGGCAACCCAC-GAAATTCATAATAATTTTATGAACGAT
1 CGTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGAC
* ** * *
1833573 TGTATCAACACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAATGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* *
1833627 CGTATCGGTACTAAGTGTTCAACCCACAGAATTCATAATAAGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * *
1833681 CGTATCGACACTAAGTGTGTAACCCACAGAATTCTTAATAAGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * * *
1833735 CGTATCAGCACTAAGTCTGTAACCCAC-GTAATTTATAATAAGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGAC
* *
1833789 CGTAAT-GACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGAC
1 CGT-ATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * *
1833843 TGTATCGGCACTAAATGTGTAACCCACAGAATTCATAATAAGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * * * *
1833897 CGTATCAGTACTAAGTGTACAACCCACATAATTCATAATACGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* *
1833951 CGTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * *
1834005 TGTATCGGCACTAAATGTGTAACCCACAGAATTCATAATAAGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * * * *
1834059 CGTATCAGTACTAAGTGTACAACCCACATAATTCATAATACGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
*
1834113 CGTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * * *
1834167 CGTATCAGCAATAAGTGTGCAACCCACATAATTCATAATAAGTGTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* ** * * * *
1834221 TGTATCGAAACTAAGTGTGTAACCCACGGAATTCATAATAAGTTTATGAATGAT
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * *
1834275 CGTATCGGTACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAATGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
* * * * *
1834329 TGTATCGGCACTAATTGTACAACCCACAAAATTCATAATAAGTTTATGATCGAC
1 CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
1834383 CGT
1 CGT
1834386 TGATAACTCC
Statistics
Matches: 707, Mismatches: 101, Indels: 10
0.86 0.12 0.01
Matches are distributed among these distances:
53 3 0.00
54 701 0.99
55 3 0.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (54 bp):
CGTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGAC
Found at i:1834262 original size:27 final size:27
Alignment explanation
Indices: 1834124--1834263 Score: 74
Period size: 27 Copynumber: 5.2 Consensus size: 27
1834114 GTATCGGCAC
*
1834124 TAAGTGTGCAACCCACGGAATTCATAA
1 TAAGTGTGTAACCCACGGAATTCATAA
* * * * * *
1834151 TAAGTTTATGAA-CGACCGTA-TCAGCAA
1 TAAGTGTGT-AACCCACGGAATTCA-TAA
* **
1834178 TAAGTGTGCAACCCACATAATTCATAA
1 TAAGTGTGTAACCCACGGAATTCATAA
* * * *
1834205 TAAGTGTATGAA-CGACTGTA-TCGA-AA
1 TAAGTGTGT-AACCCACGGAATTC-ATAA
1834231 CTAAGTGTGTAACCCACGGAATTCATAA
1 -TAAGTGTGTAACCCACGGAATTCATAA
1834259 TAAGT
1 TAAGT
1834264 TTATGAATGA
Statistics
Matches: 78, Mismatches: 25, Indels: 20
0.63 0.20 0.16
Matches are distributed among these distances:
26 11 0.14
27 56 0.72
28 11 0.14
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (27 bp):
TAAGTGTGTAACCCACGGAATTCATAA
Found at i:1845055 original size:59 final size:59
Alignment explanation
Indices: 1844960--1845357 Score: 593
Period size: 59 Copynumber: 6.8 Consensus size: 59
1844950 AAATTCAATA
* *
1844960 GGAAATTCATATCA-TTAGTATGATTTCCTTATCATTTTAGCACACGAAGTACCCTATCT
1 GGAAATTCATA-CACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCT
* * * *
1845019 GGAAATTGATACACTTAGTATGATTTCCTTAACATTTTAGAACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCT
* *
1845078 GGAAATTCATACACTTAGTATGATTTCCTTA-CATTTTAGCAGACGAAATGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCT
* * * * * *
1845136 GGAAATTCATACATTTAGTATAATTTCATTACCATTTTAGCACAAGAAGTGTCCTATTT
1 GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCT
* *
1845195 GGAAATTCATACACTTAGTATAATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCT
* *
1845254 GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAATGCTCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCT
* *
1845313 AGAAATTCATACAATTAGTATGATTTCCTTACCATTTTAGCACAC
1 GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACAC
1845358 TTAGTGCCAT
Statistics
Matches: 307, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
58 53 0.17
59 254 0.83
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCT
Found at i:1845713 original size:20 final size:20
Alignment explanation
Indices: 1845688--1845742 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
1845678 TGGCCCTTCA
1845688 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
* * *
1845708 GTATCGATATTACTCTACTATG
1 GTATCGATA--CCCCTACCATG
1845730 GTATCGATACCCC
1 GTATCGATACCCC
1845743 CTTCCGGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:1845833 original size:95 final size:95
Alignment explanation
Indices: 1845688--1845910 Score: 295
Period size: 95 Copynumber: 2.3 Consensus size: 95
1845678 TGGCCCTTCA
* * * * * *
1845688 GTATCGATACCCCTACCATGGTATCGATATTACTCTACTATGGTATCGATACCCCCTTCCGGTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACTATACTAGGGTACCGATACCCCCTTCCGCTAT
* * *
1845753 CAATACCAAAATTA-GTTTCGATGTGGCTTG
66 CAATACCAAAATTAGGTTT-GACGTGACCTG
*
1845783 GTATCGATACCCTTACCATGGTATCGATACTACTATACTAGGGTACCGATACCCCCTTCTGCTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACTATACTAGGGTACCGATACCCCCTTCCGCTAT
* * *
1845848 CGATATCAAAATTAGGTTTGACGTTACCTG
66 CAATACCAAAATTAGGTTTGACGTGACCTG
* *
1845878 GTATCGATACCCTCACCATGTTATCGATACTAC
1 GTATCGATACCCTTACCATGGTATCGATACTAC
1845911 CTCATCAGTA
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
95 108 0.96
96 4 0.04
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACTATACTAGGGTACCGATACCCCCTTCCGCTAT
CAATACCAAAATTAGGTTTGACGTGACCTG
Found at i:1845922 original size:20 final size:20
Alignment explanation
Indices: 1845878--1845928 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1845868 ACGTTACCTG
1845878 GTATCGATAC-CCTCACCAT
1 GTATCGATACTCCTCACCAT
*
1845897 GTTATCGATACTACCTCATCA-
1 G-TATCGATACT-CCTCACCAT
1845918 GTATCGATACT
1 GTATCGATACT
1845929 GATTGAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 19 0.68
21 1 0.04
22 7 0.25
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCGATACTCCTCACCAT
Found at i:1845955 original size:21 final size:21
Alignment explanation
Indices: 1845914--1845957 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1845904 ATACTACCTC
**
1845914 ATCAGTATCGATACTGATTGA
1 ATCAGTATCGATACACATTGA
*
1845935 ATCAGTATCGATACACCTTGA
1 ATCAGTATCGATACACATTGA
1845956 AT
1 AT
1845958 AATTCAAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (21 bp):
ATCAGTATCGATACACATTGA
Found at i:1850400 original size:20 final size:21
Alignment explanation
Indices: 1850361--1850405 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1850351 CCTTCTAGCC
1850361 AAGTAATCGATTCTTTTTTAA
1 AAGTAATCGATTCTTTTTTAA
1850382 AAGTAATCGATTC-TTTTTAA
1 AAGTAATCGATTCTTTTTTAA
1850402 AAGT
1 AAGT
1850406 GATCAATCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (21 bp):
AAGTAATCGATTCTTTTTTAA
Found at i:1855803 original size:47 final size:47
Alignment explanation
Indices: 1855752--1855865 Score: 138
Period size: 47 Copynumber: 2.4 Consensus size: 47
1855742 TATGGCCTCT
* *
1855752 TTTCATGCCTTAATGCATCCGTTGATGCATTTTTAGCTATGGCATAC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAACTATGGCATAC
* * * *** * *
1855799 TTTCATGCTTTAAAGTATATTTTCATGCATTTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAACTATGGCATAC
1855846 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
1855866 TTTTATGCCT
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (47 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAACTATGGCATAC
Found at i:1855806 original size:27 final size:25
Alignment explanation
Indices: 1855776--1855853 Score: 58
Period size: 27 Copynumber: 3.2 Consensus size: 25
1855766 GCATCCGTTG
1855776 ATGCATTTTTAGCTATGGCATACTTTC
1 ATGCATTTTTAG-TATGGCAT-CTTTC
**
1855803 ATGC-TTTAAAGTAT---AT-TTTC
1 ATGCATTTTTAGTATGGCATCTTTC
*
1855823 ATGCATTTTTAATTATGGCATCCTTTC
1 ATGCATTTTT-AGTATGGCAT-CTTTC
1855850 ATGC
1 ATGC
1855854 CTTAATGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
20 8 0.21
21 3 0.08
22 6 0.15
25 5 0.13
26 5 0.13
27 12 0.31
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (25 bp):
ATGCATTTTTAGTATGGCATCTTTC
Found at i:1855865 original size:20 final size:20
Alignment explanation
Indices: 1855840--1855939 Score: 112
Period size: 20 Copynumber: 4.7 Consensus size: 20
1855830 TTTAATTATG
1855840 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
1855860 GCATCCTTTTATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
1855880 GCATCCTTTCATGCATTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
1855906 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
1855927 GCATCC-TTCATGC
1 GCATCCTTTCATGC
1855940 ATTTTTAGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
19 7 0.10
20 38 0.55
21 2 0.03
23 3 0.04
24 3 0.04
26 2 0.03
27 14 0.20
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1855914 original size:47 final size:47
Alignment explanation
Indices: 1855860--1856289 Score: 601
Period size: 47 Copynumber: 9.0 Consensus size: 47
1855850 ATGCCTTAAT
*
1855860 GCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1855907 GCATCCTTTCATGCCTTAATGCATCC-TTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
* * * * *
1855953 GCATCCGTTCGTGCCTTAATGAATTCGTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
* * *
1856000 GCATCATTTCATGCCTTAATGTATCCGTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
* *
1856047 GCATCCTTTCATGCCTTAATGTATCCTTTCATGTATTTTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCA--TTTTTAGTTATG
* * *
1856096 GCATCATTTCATGCCTTAATGCATCCGTTCATGTATTTTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCA--TTTTTAGTTATG
* *
1856145 GCATCCTTACATGCCTTAATGCATCATTTCATGCATTTTTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCA---TTTTTAGTTATG
* *
1856195 GTATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
* * *
1856242 ACATTCTTTCATGCCTTAATGCATCCATTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1856289 G
1 G
1856290 ATTCGGTTTA
Statistics
Matches: 348, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
46 42 0.12
47 172 0.49
49 88 0.25
50 46 0.13
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.46
Consensus pattern (47 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
Found at i:1856222 original size:20 final size:20
Alignment explanation
Indices: 1856197--1856275 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
1856187 TAGTTATGGT
1856197 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
*
1856217 ATCCTTTCATGCATTTTTAATTATGAC
1 ATCCTTTCATGC---CTT-A--ATG-C
*
1856244 ATTCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
*
1856264 ATCCATTCATGC
1 ATCCTTTCATGC
1856276 ATTTTTAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
20 23 0.49
21 3 0.06
23 3 0.06
24 3 0.06
26 3 0.06
27 12 0.26
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:1856806 original size:95 final size:94
Alignment explanation
Indices: 1856694--1856872 Score: 240
Period size: 95 Copynumber: 1.9 Consensus size: 94
1856684 AACTACCCTG
*
1856694 GTATCGATACTTCTATACTATGGTA-CGGATACCCCCTTTCCA-TATCGATACCATTTCT-ATAT
1 GTATCGATACTTCTATACTATGGTATC-GATACCCCCTTT-CAGTATCGATACCATTT-TAACAT
* *
1856756 TCTGTAGTGCATGGTATCGATACCCTTCTCTCA
63 TCTGGA-TCCATGGTATCGATACCCTTCTCTCA
* *
1856789 GTATCGATACTAT-TATACTATGGTATCGATACTCCCTTTCAGTATCGATACTATTTTAACATTC
1 GTATCGATACT-TCTATACTATGGTATCGATACCCCCTTTCAGTATCGATACCATTTTAACATTC
1856853 TGGATCCATGGTATCGATAC
65 TGGATCCATGGTATCGATAC
1856873 GTCCCTTTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
94 18 0.24
95 55 0.73
96 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.37
Consensus pattern (94 bp):
GTATCGATACTTCTATACTATGGTATCGATACCCCCTTTCAGTATCGATACCATTTTAACATTCT
GGATCCATGGTATCGATACCCTTCTCTCA
Found at i:1858176 original size:12 final size:12
Alignment explanation
Indices: 1858161--1858185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1858151 CCGGAAGCTC
1858161 ATTAGGAAAAAT
1 ATTAGGAAAAAT
1858173 ATTAGGAAAAAT
1 ATTAGGAAAAAT
1858185 A
1 A
1858186 CTTAACCATC
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:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
ATTAGGAAAAAT
Found at i:1866259 original size:257 final size:260
Alignment explanation
Indices: 1865778--1866428 Score: 773
Period size: 257 Copynumber: 2.5 Consensus size: 260
1865768 CGATGGGATC
* * * * *
1865778 TTTCATATGATATTTTTAAAAAAATAAGAAAGCAAATTTCAAAGTTTCTCATTTAATATTTTCTA
1 TTTCATATGACATTTAT-GAAAAATAAGAAAGC-GATTTCAAAGTTTCTCATTTAATATTTTCTG
1865843 AAAATGAAATTTTTGAAAAGTAAAAAAGTGATTTCCAAAGTTTCTTACCTAGTAATCTATTTCCA
64 AAAATGAAATTTTTGAAAAGTAAAAAAGTGATTTCCAAAGTTTCTTACCTAGTAATCTATTTCCA
* * *
1865908 AAAACGATTAAATCCTCTAGGTCATCAATAAGTCTTTTGAGCATAATGATTAAATCCTATGGGTC
129 AAAACAATTAAATCCTCTAGGTCATCAATAAGGCTTTTGAGCATAATAATTAAATCCTATGGGTC
* * * * * *
1865973 ATCTATAAGTCTTCTTAGAAAGATGATAAGTCGTTCGGGGGATATATAAGACCTTCGGGTAGGAT
194 ATCTATAAGTCTTCTTAGAAAGATGATAAGTCCTTAGGGGCATATATAAGACATTCGGGCAGAAT
1866038 GT
259 GT
* *
1866040 TTTCATATGACA-TT-TGAAAAATAAGAAAGCGATTTGCAAAGTTTATCATTTAATCTTTTCTGA
1 TTTCATATGACATTTATGAAAAATAAGAAAGCGATTT-CAAAGTTTCTCATTTAATATTTTCTGA
* *
1866103 AAATGAAA-TTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTTTTA-CTAGTAATCTATTTCCAA
65 AAATGAAATTTTTGAAAAGTAAAAAAGTGATTTCCAAAGTTTCTTACCTAGTAATCTATTTCCAA
*
1866166 AAACAATTAAATCCTCT-GAGTCATCAGTAAGGCTTTTGAGCATAATAATTAAATCCTTAT-GGT
130 AAACAATTAAATCCTCTAG-GTCATCAATAAGGCTTTTGAGCATAATAATTAAATCC-TATGGGT
* * * * * * * ** *
1866229 TATCTTTCATTC-T-TTCGAACAGGGTGATAAGTCCTTAGGGTCATATATAAGACATTTTGGCAT
193 CATCTATAAGTCTTCTTAGAA-A-GATGATAAGTCCTTAGGGGCATATATAAGACATTCGGGCAG
*
1866292 AATTT
256 AATGT
* * * * * * *
1866297 TTTTATATGATATTTATGAAAAAT--GAAAGTGATTTTCAAAGCTTCTCATTTTAAAATTCTATG
1 TTTCATATGACATTTATGAAAAATAAGAAAGCGA-TTTCAAAGTTTCTCA-TTTAATATTTTCTG
* * * *
1866360 AAAATGAAATTTTTGAAAAAGTAAAAAAGTGATTTCTAAAGCTTCTTACCTAGTAAACTATTTTC
64 AAAATGAAATTTTTG-AAAAGTAAAAAAGTGATTTCCAAAGTTTCTTACCTAGTAATCTATTTCC
1866425 AAAA
128 AAAA
1866429 CTAGTATGTC
Statistics
Matches: 333, Mismatches: 44, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
255 5 0.02
256 3 0.01
257 140 0.42
258 66 0.20
259 59 0.18
260 29 0.09
261 20 0.06
262 11 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (260 bp):
TTTCATATGACATTTATGAAAAATAAGAAAGCGATTTCAAAGTTTCTCATTTAATATTTTCTGAA
AATGAAATTTTTGAAAAGTAAAAAAGTGATTTCCAAAGTTTCTTACCTAGTAATCTATTTCCAAA
AACAATTAAATCCTCTAGGTCATCAATAAGGCTTTTGAGCATAATAATTAAATCCTATGGGTCAT
CTATAAGTCTTCTTAGAAAGATGATAAGTCCTTAGGGGCATATATAAGACATTCGGGCAGAATGT
Found at i:1867003 original size:44 final size:43
Alignment explanation
Indices: 1866897--1867046 Score: 139
Period size: 44 Copynumber: 3.5 Consensus size: 43
1866887 GATTCTATTG
* *
1866897 CATAAGGAGTTGGATCAGCATCACCATATCGATCAA-T--T-A
1 CATAAGGAGTTAGATCAGCATCACCATATCGCTCAATTCATCA
* * *
1866936 CATTAGGAGTTAGATTAGCATCACCATTTCGCTCAATTCCATCA
1 CATAAGGAGTTAGATCAGCATCACCATATCGCTCAATT-CATCA
* * * *
1866980 CATAAGGAGTTAGATCAACATCACTATCTCGC-AAGATTCTATCA
1 CATAAGGAGTTAGATCAGCATCACCATATCGCTCA-ATTC-ATCA
* *
1867024 TATAAGGAGTTGGATCAGCATCA
1 CATAAGGAGTTAGATCAGCATCA
1867047 TCTCGCTTGA
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
39 31 0.34
40 1 0.01
43 3 0.03
44 55 0.61
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (43 bp):
CATAAGGAGTTAGATCAGCATCACCATATCGCTCAATTCATCA
Found at i:1867146 original size:37 final size:36
Alignment explanation
Indices: 1867096--1867289 Score: 232
Period size: 37 Copynumber: 5.4 Consensus size: 36
1867086 TCACTCAAGA
*
1867096 TTTTATCTCACTTGAGACTGTTTTTCTTAAAAATATG
1 TTTTATCTCACTTGAGATTGTTTTTCTT-AAAATATG
*
1867133 TTTTATCTCACTTGAGATTGTTTTTCTTTAAAACATG
1 TTTTATCTCACTTGAGATTGTTTTTC-TTAAAATATG
*
1867170 TTTTATCTCACTTGAGATTATTTTTCTTAAAAT-TG
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAATATG
* * * *
1867205 ATTTAATCTCACTTAAGATT-TTATTCTTAGAATA-G
1 -TTTTATCTCACTTGAGATTGTTTTTCTTAAAATATG
* * **
1867240 ATGTTATCTCACTTGAGATTGTTTTCCTTAAAATAAA
1 -TTTTATCTCACTTGAGATTGTTTTTCTTAAAATATG
1867277 TTTTATCTCACTT
1 TTTTATCTCACTT
1867290 TAAAGTATTT
Statistics
Matches: 136, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
35 31 0.23
36 46 0.34
37 57 0.42
38 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (36 bp):
TTTTATCTCACTTGAGATTGTTTTTCTTAAAATATG
Found at i:1867156 original size:20 final size:20
Alignment explanation
Indices: 1867131--1867193 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
1867121 CTTAAAAATA
1867131 TGTTTTATCTCACTTGAGAT
1 TGTTTTATCTCACTTGAGAT
* * *
1867151 TGTTTT-TCT---TTAAAACA
1 TGTTTTATCTCACTTGAGA-T
1867168 TGTTTTATCTCACTTGAGAT
1 TGTTTTATCTCACTTGAGAT
*
1867188 TATTTT
1 TGTTTT
1867194 TCTTAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
16 4 0.13
17 6 0.19
18 3 0.10
19 3 0.10
20 11 0.35
21 4 0.13
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (20 bp):
TGTTTTATCTCACTTGAGAT
Found at i:1867272 original size:71 final size:71
Alignment explanation
Indices: 1867092--1867289 Score: 231
Period size: 71 Copynumber: 2.7 Consensus size: 71
1867082 CATTTCACTC
* * * *
1867092 AAGATTTTATCTCACTTGAGACTGTTTTTCTTAAAAATATG-TTTTATCTCACTTGAGATTGTTT
1 AAGATGTTATCTCACTTGAGATTGTTTTTCTT-AAAAT-TGATTTTATCTCACTTAAGATTGTTA
1867156 TTCTTTAA
64 TTCTTTAA
* * *
1867164 AACATGTTTTATCTCACTTGAGATTATTTTTCTTAAAATTGATTTAATCTCACTTAAGATT-TTA
1 AAGATG--TTATCTCACTTGAGATTGTTTTTCTTAAAATTGATTTTATCTCACTTAAGATTGTTA
1867228 TTC-TTAGA
64 TTCTTTA-A
* **
1867236 ATAGATGTTATCTCACTTGAGATTGTTTTCCTTAAAATAAATTTTATCTCACTT
1 A-AGATGTTATCTCACTTGAGATTGTTTTTCTTAAAATTGATTTTATCTCACTT
1867290 TAAAGTATTT
Statistics
Matches: 108, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
71 45 0.42
72 13 0.12
73 26 0.24
74 24 0.22
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (71 bp):
AAGATGTTATCTCACTTGAGATTGTTTTTCTTAAAATTGATTTTATCTCACTTAAGATTGTTATT
CTTTAA
Found at i:1867330 original size:107 final size:108
Alignment explanation
Indices: 1867135--1867330 Score: 234
Period size: 107 Copynumber: 1.8 Consensus size: 108
1867125 AAAATATGTT
* ** * * *
1867135 TTATCTCACTTGAGATTGTTTTTCTTTAAAACATGTTTTATCTCACTTGAGATTATTTTTCTTAA
1 TTATCTCACTTGAGATTGTTTTTCCTTAAAACAAATTTTATCTCACTTGAAAGTATTTCTCTTAA
*** **
1867200 AATTGATTTAATCTCACTTAAGATTTTATTCTTAGAATAGATG
66 AACAAATTTAATCTCACAGAAGATTTTATTCTTAGAATAGATG
* * *
1867243 TTATCTCACTTGAGATTG-TTTTCCTTAAAATAAATTTTATCTCACTTTAAAGTATTTCTCTTGA
1 TTATCTCACTTGAGATTGTTTTTCCTTAAAACAAATTTTATCTCACTTGAAAGTATTTCTCTTAA
*
1867307 AACAAATTT-GTCCTCACAGAAGAT
66 AACAAATTTAAT-CTCACAGAAGAT
1867331 AATTTTTTAG
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
106 1 0.01
107 53 0.74
108 18 0.25
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (108 bp):
TTATCTCACTTGAGATTGTTTTTCCTTAAAACAAATTTTATCTCACTTGAAAGTATTTCTCTTAA
AACAAATTTAATCTCACAGAAGATTTTATTCTTAGAATAGATG
Found at i:1869514 original size:3 final size:3
Alignment explanation
Indices: 1869506--1869544 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
1869496 TTTATTTAAT
1869506 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
1869545 TCCTTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1873765 original size:15 final size:16
Alignment explanation
Indices: 1873735--1873771 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
1873725 CGCAGACCAT
1873735 TTTTGTCTTAAAAATTA
1 TTTT-TCTTAAAAATTA
1873752 TTTTTCTT-AAAATTA
1 TTTTTCTTAAAAATTA
1873767 TTTTT
1 TTTTT
1873772 AAAAGATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.60
16 4 0.20
17 4 0.20
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTTCTTAAAAATTA
Found at i:1881078 original size:16 final size:18
Alignment explanation
Indices: 1881047--1881080 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1881037 CTTAGCAAAT
1881047 ATCTCATTTAATTCTTTA
1 ATCTCATTTAATTCTTTA
1881065 ATCTC-TTT-ATTCTTTA
1 ATCTCATTTAATTCTTTA
1881081 TTAATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (18 bp):
ATCTCATTTAATTCTTTA
Found at i:1884101 original size:12 final size:12
Alignment explanation
Indices: 1884084--1884108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1884074 TGCTTGCTTA
1884084 TCGTACATCTAT
1 TCGTACATCTAT
1884096 TCGTACATCTAT
1 TCGTACATCTAT
1884108 T
1 T
1884109 GGGGCAACAC
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:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TCGTACATCTAT
Found at i:1884579 original size:21 final size:21
Alignment explanation
Indices: 1884549--1884599 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
1884539 AGAAGAATAA
1884549 AAAAAAAAAAAGTGAAAAAGTG
1 AAAAAAAAAAA-TGAAAAAGTG
*
1884571 AAAAGAAAAAATGAAAAA--G
1 AAAAAAAAAAATGAAAAAGTG
1884590 AAAAAAAAAA
1 AAAAAAAAAA
1884600 GGAGGGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 10 0.37
21 7 0.26
22 10 0.37
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (21 bp):
AAAAAAAAAAATGAAAAAGTG
Found at i:1884580 original size:14 final size:14
Alignment explanation
Indices: 1884562--1884595 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1884552 AAAAAAAAGT
*
1884562 GAAAAAGTG-AAAA
1 GAAAAAATGAAAAA
1884575 GAAAAAATGAAAAA
1 GAAAAAATGAAAAA
1884589 GAAAAAA
1 GAAAAAA
1884596 AAAAGGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (14 bp):
GAAAAAATGAAAAA
Found at i:1885721 original size:40 final size:41
Alignment explanation
Indices: 1885656--1885754 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 41
1885646 GATGGTCATC
* *
1885656 CGTCCTCATCATGTAGGAACCGTGTCATCC-AT-TAACCATA
1 CGTCCTCATCACGTAGGAACCGTGTCA-CCTATATAACCAGA
*** * *
1885696 CGTCCTCATCACGTAGGAGTTGTGTCACCTCTGATAACCAGC
1 CGTCCTCATCACGTAGGAACCGTGTCACCTAT-ATAACCAGA
1885738 CGTCCTCATCACGTAGG
1 CGTCCTCATCACGTAGG
1885755 TTTCGCGTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
39 2 0.04
40 24 0.49
42 23 0.47
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (41 bp):
CGTCCTCATCACGTAGGAACCGTGTCACCTATATAACCAGA
Found at i:1886131 original size:3 final size:3
Alignment explanation
Indices: 1886123--1886150 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1886113 AACATTTTAT
1886123 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1886151 CACTTAGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1901169 original size:31 final size:31
Alignment explanation
Indices: 1901111--1901171 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1901101 TGACCAAATT
*
1901111 TTAAATAAATAAAAATAAAATTAATCATATC
1 TTAAATAAATAAAAAGAAAATTAATCATATC
* *
1901142 TTAATTAAATAAAACAGAAAA-TGATCATAT
1 TTAAATAAATAAAA-AGAAAATTAATCATAT
1901172 ATTGTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (31 bp):
TTAAATAAATAAAAAGAAAATTAATCATATC
Found at i:1901446 original size:6 final size:6
Alignment explanation
Indices: 1901435--1901487 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
1901425 ATTTTAACGC
*
1901435 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGA GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
1901483 GAGAG
1 GAGAG
1901488 AGGGAGTGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:1901488 original size:12 final size:12
Alignment explanation
Indices: 1901435--1901501 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
1901425 ATTTTAACGC
*
1901435 GAGAGGGAGAGG
1 GAGAGAGAGAGG
*
1901447 GAGAGGGAGAGG
1 GAGAGAGAGAGG
*
1901459 GAGAGGGAGAGG
1 GAGAGAGAGAGG
1901471 GAGAGAGAGAGG
1 GAGAGAGAGAGG
* *
1901483 GAGAGAGGGAGT
1 GAGAGAGAGAGG
1901495 GAGAGAG
1 GAGAGAG
1901502 CAGTGTTTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.36, C:0.00, G:0.63, T:0.01
Consensus pattern (12 bp):
GAGAGAGAGAGG
Found at i:1901498 original size:18 final size:18
Alignment explanation
Indices: 1901435--1901501 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
1901425 ATTTTAACGC
*
1901435 GAGAGGGAGAGGGAGAGG
1 GAGAGAGAGAGGGAGAGG
*
1901453 GAGAGGGAGAGGGAGAGG
1 GAGAGAGAGAGGGAGAGG
1901471 GAGAGAGAGAGGGAGAGAGG
1 GAGAGAGAGA-GG-GAGAGG
*
1901491 GAGTGAGAGAG
1 GAGAGAGAGAG
1901502 CAGTGTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 27 0.60
19 3 0.07
20 15 0.33
ACGTcount: A:0.36, C:0.00, G:0.63, T:0.01
Consensus pattern (18 bp):
GAGAGAGAGAGGGAGAGG
Found at i:1902466 original size:16 final size:16
Alignment explanation
Indices: 1902445--1902489 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1902435 AAACCATGGG
*
1902445 AGGGAGGGAGAGAGAT
1 AGGGAGAGAGAGAGAT
*
1902461 AGGGAGAGAGAGAGAC
1 AGGGAGAGAGAGAGAT
*
1902477 AGAGAGATGAGAG
1 AGGGAGA-GAGAG
1902490 TGAATGTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.51, T:0.04
Consensus pattern (16 bp):
AGGGAGAGAGAGAGAT
Found at i:1908622 original size:31 final size:29
Alignment explanation
Indices: 1908551--1908624 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
1908541 ATTGAATCGT
* *
1908551 TTATACCACTAAATTTTTAATTTTACTAA
1 TTATATCACTAAACTTTTAATTTTACTAA
* *
1908580 TTATAGT-ACTAAACTTTTATTTTTATTTCAA
1 TTATA-TCACTAAACTTTTAATTTTA-CT-AA
1908611 TTATATCACTAAAC
1 TTATATCACTAAAC
1908625 CGTTAAATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 21 0.57
30 2 0.05
31 14 0.38
ACGTcount: A:0.36, C:0.14, G:0.01, T:0.49
Consensus pattern (29 bp):
TTATATCACTAAACTTTTAATTTTACTAA
Found at i:1909050 original size:3 final size:3
Alignment explanation
Indices: 1909042--1909070 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1909032 GTACTTTTTT
1909042 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1909071 GAAAATGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1909549 original size:2 final size:2
Alignment explanation
Indices: 1909542--1909579 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1909532 AGAAAAGGAA
1909542 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1909580 AAGGCGACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1909976 original size:6 final size:6
Alignment explanation
Indices: 1909965--1910003 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1909955 TTGTCAGCTC
*
1909965 TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTTT TGG
1 TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGG
1910004 GTGAGATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (6 bp):
TGGTGT
Found at i:1915546 original size:28 final size:28
Alignment explanation
Indices: 1915514--1915572 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1915504 ACATATTTAA
1915514 AAGT-AATCAATAAAACAAATATAGTAGC
1 AAGTAAAT-AATAAAACAAATATAGTAGC
* *
1915542 AAGTAAATAATAAAACATATATATTAGC
1 AAGTAAATAATAAAACAAATATAGTAGC
1915570 AAG
1 AAG
1915573 GAAAGTTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (28 bp):
AAGTAAATAATAAAACAAATATAGTAGC
Found at i:1916600 original size:31 final size:31
Alignment explanation
Indices: 1916565--1916632 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1916555 CAAAAAAATA
* * *
1916565 TAAGATTTGATCACATT-CTTTTCGTTTTAAT
1 TAAGATTTGATCAC-TTCCATTTAGTTTTAAC
* *
1916596 TAAGACTTGGTCACTTCCATTTAGTTTTAAC
1 TAAGATTTGATCACTTCCATTTAGTTTTAAC
1916627 TAAGAT
1 TAAGAT
1916633 GTGTTTACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.46
Consensus pattern (31 bp):
TAAGATTTGATCACTTCCATTTAGTTTTAAC
Found at i:1916834 original size:30 final size:32
Alignment explanation
Indices: 1916798--1916868 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 32
1916788 TTCAAAAACA
*
1916798 TAAGTTTTTG-CCACTTACGTTAT-TGTTTTGT
1 TAAGTTTTTGACCACTTACGTTATCT-TTTTAT
*
1916829 T-AG-TTTTGATCACTTACGTTATCTTTTTAT
1 TAAGTTTTTGACCACTTACGTTATCTTTTTAT
1916859 TAAGTTTTTG
1 TAAGTTTTTG
1916869 TCATTTGGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
29 5 0.15
30 20 0.59
31 4 0.12
32 5 0.15
ACGTcount: A:0.18, C:0.11, G:0.14, T:0.56
Consensus pattern (32 bp):
TAAGTTTTTGACCACTTACGTTATCTTTTTAT
Found at i:1917787 original size:15 final size:16
Alignment explanation
Indices: 1917769--1917801 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1917759 TAATATATTT
1917769 TTTC-TTAATAAAATA
1 TTTCATTAATAAAATA
*
1917784 TTTCATTTATAAAATA
1 TTTCATTAATAAAATA
1917800 TT
1 TT
1917802 ATTAATGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTCATTAATAAAATA
Found at i:1919148 original size:35 final size:36
Alignment explanation
Indices: 1919097--1919175 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
1919087 ATCGAATTAA
* * * *
1919097 ACGGGGACGGGGAAAAATTGTTTATGCTAAA-TGGG
1 ACGGGGACAGGAAAAAACTGTTTATGCTAAACGGGG
*
1919132 ACGGGGACAGGAAAAAACTGTTTATGTTAAACGGGG
1 ACGGGGACAGGAAAAAACTGTTTATGCTAAACGGGG
1919168 ACGGGGAC
1 ACGGGGAC
1919176 GGGGACGGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
35 27 0.71
36 11 0.29
ACGTcount: A:0.33, C:0.11, G:0.37, T:0.19
Consensus pattern (36 bp):
ACGGGGACAGGAAAAAACTGTTTATGCTAAACGGGG
Found at i:1919244 original size:2 final size:2
Alignment explanation
Indices: 1919237--1919268 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1919227 AAATAATTAT
1919237 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1919269 TAATAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1919299 original size:35 final size:35
Alignment explanation
Indices: 1919256--1919322 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1919246 ATATATATAT
1919256 ATATATATAATATTAATAAATTTAAATTAAATTAA
1 ATATATATAATATTAATAAATTTAAATTAAATTAA
* * *
1919291 ATATATATAATATTTATATATTTAATTTAAAT
1 ATATATATAATATTAATAAATTTAAATTAAAT
1919323 ATATATACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (35 bp):
ATATATATAATATTAATAAATTTAAATTAAATTAA
Found at i:1920152 original size:39 final size:40
Alignment explanation
Indices: 1920060--1920191 Score: 146
Period size: 39 Copynumber: 3.3 Consensus size: 40
1920050 TTTTTTTTAA
*
1920060 ATATAATATATAATTTTTAGAAAACGGATTTCGAAAATATAT
1 ATATATTATATAA-TTTT-GAAAACGGATTTCGAAAATATAT
* * * *
1920102 ACATATTATATAGTTTTGAAAACGGTTTTTTGAAAA-A-AT
1 ATATATTATATAATTTTGAAAACGG-ATTTCGAAAATATAT
*
1920141 ATATATTATATAATTTTGAAAAC--ATTTCGAATATATAT
1 ATATATTATATAATTTTGAAAACGGATTTCGAAAATATAT
1920179 ATATATATATATA
1 ATATAT-TATATA
1920192 TATATATTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
36 7 0.09
37 1 0.01
38 8 0.11
39 29 0.38
40 9 0.12
41 12 0.16
42 10 0.13
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (40 bp):
ATATATTATATAATTTTGAAAACGGATTTCGAAAATATAT
Found at i:1920178 original size:2 final size:2
Alignment explanation
Indices: 1920171--1920198 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1920161 AACATTTCGA
1920171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1920199 TTTTGAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1920205 original size:45 final size:44
Alignment explanation
Indices: 1920139--1920319 Score: 230
Period size: 45 Copynumber: 4.2 Consensus size: 44
1920129 TTTTGAAAAA
*
1920139 ATATATATTATATA-A-TTTTGAAAACATTTCGAATATATATAT
1 ATATATATTATATATATTTTTGAAAACATTTTGAATATATATAT
1920181 ATATATATATATATATATTTTTGAAAACATTTTGAATATATATAT
1 ATATATAT-TATATATATTTTTGAAAACATTTTGAATATATATAT
* *
1920226 ATATATAGTTATATATAGTTTTTAAAAATATTTTGAATATATATAT
1 ATATATA-TTATATATA-TTTTTGAAAACATTTTGAATATATATAT
* * *
1920272 ATATATA-T-TATATAGTTTTG-AAA-ATTTTGAAAACATATAT
1 ATATATATTATATATATTTTTGAAAACATTTTGAATATATATAT
1920312 AATATATA
1 -ATATATA
1920320 GTTTTTGAAA
Statistics
Matches: 126, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
40 15 0.12
41 10 0.08
42 12 0.10
43 12 0.10
44 2 0.02
45 41 0.33
46 34 0.27
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (44 bp):
ATATATATTATATATATTTTTGAAAACATTTTGAATATATATAT
Found at i:1920220 original size:39 final size:39
Alignment explanation
Indices: 1920060--1920411 Score: 186
Period size: 40 Copynumber: 8.9 Consensus size: 39
1920050 TTTTTTTTAA
* *
1920060 ATATA-ATATATA-ATTTTTAGAAAACGGATTTCGAAAATAT
1 ATATATATATATATATTTTT-GAAAAC--ATTTTGAATATAT
* * * *
1920100 ATACATAT-TATATAGTTTTGAAAACGGTTTTTTGAA-A-AA
1 ATATATATATATATATTTTTGAAAAC---ATTTTGAATATAT
* *
1920139 ATATATAT-TATATAATTTTGAAAACATTTCGAATATATATATAT
1 ATATATATATATATATTTTTGAAAACATTT----T-GA-ATATAT
1920183 ATATATATATATATATTTTTGAAAACATTTTGAATATATATAT
1 ATATATATATATATATTTTTGAAAACATTTTG---A-ATATAT
* *
1920226 ATATATAGTTATATATAGTTTTTAAAAATATTTTGAATATAT
1 ATATATA--TATATATA-TTTTTGAAAACATTTTGAATATAT
*
1920268 ATATATATATATTATATAGTTTTG-AAA-ATTTTGAA-A-AC
1 ATATATATATA-TATAT--TTTTGAAAACATTTTGAATATAT
*
1920306 ATATATA-ATATATAGTTTTTGAAAACGTTTT---TA-A-
1 ATATATATATATATA-TTTTTGAAAACATTTTGAATATAT
* * *
1920340 A-ATATATATATAGT-TTTTT-AAAATATTTTGAAAAAAT
1 ATATATATATATA-TATTTTTGAAAACATTTTGAATATAT
*
1920377 ATATATA-ATATATAGTTTTTGAAAATAGTTTTGAA
1 ATATATATATATATA-TTTTTGAAAACA-TTTTGAA
1920412 AATGTATTTA
Statistics
Matches: 254, Mismatches: 21, Indels: 74
0.73 0.06 0.21
Matches are distributed among these distances:
32 8 0.03
33 10 0.04
34 6 0.02
35 9 0.04
36 12 0.05
37 14 0.06
38 18 0.07
39 31 0.12
40 36 0.14
41 23 0.09
42 18 0.07
43 17 0.07
44 9 0.04
45 28 0.11
46 15 0.06
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (39 bp):
ATATATATATATATATTTTTGAAAACATTTTGAATATAT
Found at i:1920317 original size:32 final size:32
Alignment explanation
Indices: 1920274--1920402 Score: 102
Period size: 35 Copynumber: 3.8 Consensus size: 32
1920264 ATATATATAT
*
1920274 ATATATTATATAG-TTTTGAAAATTTTGAAAA
1 ATATATAATATAGTTTTTGAAAATTTTGAAAA
*
1920305 CATATATAATATATAGTTTTTGAAAACGTTTT-TAAA
1 -ATATAT-A-ATATAGTTTTTGAAAA--TTTTGAAAA
*
1920341 ATATAT-ATATAGTTTTTTAAAATATTTTGAAAAAA
1 ATATATAATATAG-TTTTTGAAA-ATTTTG--AAAA
1920376 TATATATAATATATAGTTTTTGAAAAT
1 -ATATAT-A-ATATAGTTTTTGAAAAT
1920403 AGTTTTGAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 23
0.74 0.05 0.22
Matches are distributed among these distances:
32 16 0.21
33 8 0.10
34 7 0.09
35 18 0.23
36 9 0.12
37 6 0.08
38 8 0.10
39 6 0.08
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (32 bp):
ATATATAATATAGTTTTTGAAAATTTTGAAAA
Found at i:1920344 original size:26 final size:26
Alignment explanation
Indices: 1920296--1920345 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1920286 GTTTTGAAAA
*
1920296 TTTTGAAAACATATATAATATATAGT
1 TTTTGAAAACATATATAAAATATAGT
* * *
1920322 TTTTGAAAACGTTTTTAAAATATA
1 TTTTGAAAACATATATAAAATATA
1920346 TATATAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (26 bp):
TTTTGAAAACATATATAAAATATAGT
Found at i:1920390 original size:71 final size:67
Alignment explanation
Indices: 1920274--1920419 Score: 186
Period size: 71 Copynumber: 2.1 Consensus size: 67
1920264 ATATATATAT
*
1920274 ATATATTATATAGTTTTGAAAATTTTGAAAACATATATAATATATAGTTTTTGAAAACGTTTTTA
1 ATATATTATATAGTTTTAAAAATTTTGAAAACATATATAATATATAGTTTTTGAAAACGTTTTTA
1920339 AA
66 AA
* *
1920341 ATATA-TATATAGTTTTTTAAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAATAG
1 ATATATTATATAG--TTTTAAAA-ATTTTG--AAAACATATATAATATATAGTTTTTGAAAA-CG
*
1920405 TTTTGAAA
60 TTTTTAAA
*
1920413 ATGTATT
1 ATATATT
1920420 TAATGTATGG
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
66 7 0.10
67 5 0.07
68 7 0.10
69 6 0.09
71 29 0.43
72 12 0.18
73 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (67 bp):
ATATATTATATAGTTTTAAAAATTTTGAAAACATATATAATATATAGTTTTTGAAAACGTTTTTA
AA
Found at i:1920446 original size:109 final size:109
Alignment explanation
Indices: 1920235--1920438 Score: 274
Period size: 109 Copynumber: 1.9 Consensus size: 109
1920225 TATATATAGT
*
1920235 TATATATAGTTTTTAAAAATATTTTGAATATATATATATATATATTATATAGTTTTGAAAATTTT
1 TATATATAGTTTTTAAAAATATTTTGAATATATATATATATATAATATATAGTTTTGAAAATTTT
*
1920300 GAAAACATATATAATATATAGTTTTTGAAAACGTTTTTAAAATA
66 GAAAACATATATAATATATAGGTTTTGAAAACGTTTTTAAAATA
*
1920344 TATATATAGTTTTTTAAAATATTTTGAA-A-A-A-ATATATATAATATATAGTTTTTGAAAATAG
1 TATATATAGTTTTTAAAAATATTTTGAATATATATATATATATAATATATAG-TTTTG-AAA-A-
** * *
1920405 TTTTGAAAATGTATTTAATGTAT-GGTTTTGAAAA
62 TTTTGAAAACATATATAATATATAGGTTTTGAAAA
1920439 TGATTTTTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
105 16 0.19
106 6 0.07
107 4 0.05
108 12 0.14
109 46 0.55
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (109 bp):
TATATATAGTTTTTAAAAATATTTTGAATATATATATATATATAATATATAGTTTTGAAAATTTT
GAAAACATATATAATATATAGGTTTTGAAAACGTTTTTAAAATA
Found at i:1920501 original size:14 final size:14
Alignment explanation
Indices: 1920484--1920533 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1920474 TATATATATA
1920484 TATTTATTACTTAT
1 TATTTATTACTTAT
1920498 TATTTATTA-TTAT
1 TATTTATTACTTAT
* * *
1920511 TCATTTTTTCCTTTT
1 T-ATTTATTACTTAT
1920526 TATTTATT
1 TATTTATT
1920534 TTTTTATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 5 0.17
14 21 0.70
15 4 0.13
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTATTACTTAT
Found at i:1921696 original size:22 final size:21
Alignment explanation
Indices: 1921670--1921724 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
1921660 AATTTAACCC
1921670 TTTTTATTATTATTTTTTCATTG
1 TTTTTATT-TTA-TTTTTCATTG
1921693 TTTTTCATTTTATTTTTCATT-
1 TTTTT-ATTTTATTTTTCATTG
1921714 TTCTTTATTTT
1 TT-TTTATTTT
1921725 TCTATTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.23
22 12 0.40
23 8 0.27
24 3 0.10
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTATTTTATTTTTCATTG
Found at i:1921720 original size:16 final size:17
Alignment explanation
Indices: 1921701--1921771 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 17
1921691 TGTTTTTCAT
1921701 TTTATTTTTC-ATTTTC
1 TTTATTTTTCTATTTTC
*
1921717 TTTATTTTTCTATTTAC
1 TTTATTTTTCTATTTTC
*
1921734 TTAATTTTATCTA---TC
1 TTTATTTT-TCTATTTTC
* *
1921749 TTTATTTATCTATTTTA
1 TTTATTTTTCTATTTTC
1921766 TTTATT
1 TTTATT
1921772 ATTATTATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 4 0.09
15 7 0.16
16 10 0.23
17 19 0.43
18 4 0.09
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:1921732 original size:28 final size:29
Alignment explanation
Indices: 1921684--1921768 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 29
1921674 TATTATTATT
* *
1921684 TTTTCATTGTTTTTC-ATTTTATTTTTCA
1 TTTTCTTTATTTTTCTATTTTATTTTTCA
*
1921712 TTTTCTTTATTTTTCTA-TTTACTTAATTTTA
1 TTTTCTTTATTTTTCTATTTTA-TT--TTTCA
* *
1921743 TCTATCTTTATTTATCTATTTTATTT
1 T-TTTCTTTATTTTTCTATTTTATTT
1921769 ATTATTATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
28 17 0.37
29 3 0.07
30 1 0.02
31 5 0.11
32 16 0.35
33 4 0.09
ACGTcount: A:0.18, C:0.11, G:0.01, T:0.71
Consensus pattern (29 bp):
TTTTCTTTATTTTTCTATTTTATTTTTCA
Found at i:1921767 original size:13 final size:13
Alignment explanation
Indices: 1921739--1921780 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
1921729 TTTACTTAAT
1921739 TTTATCTATCTTTA
1 TTTATCTAT-TTTA
1921753 TTTATCTATTTTA
1 TTTATCTATTTTA
1921766 TTTAT-TATTATTA
1 TTTATCTATT-TTA
1921779 TT
1 TT
1921781 ATTATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.15
13 14 0.52
14 9 0.33
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATCTATTTTA
Found at i:1921802 original size:20 final size:19
Alignment explanation
Indices: 1921779--1921822 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1921769 ATTATTATTA
1921779 TTATTATATTAATATTGTTT
1 TTATTATATTAATATT-TTT
* * *
1921799 TTATTTTTTTCATATTTTT
1 TTATTATATTAATATTTTT
1921818 TTATT
1 TTATT
1921823 TTACAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTATTATATTAATATTTTT
Found at i:1926793 original size:21 final size:21
Alignment explanation
Indices: 1926769--1926832 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 21
1926759 TATTAATATT
1926769 AATATATTTTATTAAAATAAA
1 AATATATTTTATTAAAATAAA
* *
1926790 AATAT-TTTTA-TAATTATATA
1 AATATATTTTATTAA-AATAAA
1926810 AA-ATA-TTTATTAAAATAAA
1 AATATATTTTATTAAAATAAA
1926829 AATA
1 AATA
1926833 ATATATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
19 15 0.43
20 15 0.43
21 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATATTTTATTAAAATAAA
Found at i:1926793 original size:27 final size:28
Alignment explanation
Indices: 1926743--1926795 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1926733 ATATTACATC
**
1926743 TATATTTTAAATAAAATATTAATATTAA
1 TATATTTTAAATAAAATAAAAATATTAA
*
1926771 TATATTTT-ATTAAAATAAAAATATT
1 TATATTTTAAATAAAATAAAAATATT
1926796 TTTATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TATATTTTAAATAAAATAAAAATATTAA
Found at i:1926849 original size:21 final size:23
Alignment explanation
Indices: 1926782--1926844 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
1926772 ATATTTTATT
*
1926782 AAAATAAAAATATTT-TTATAAT-
1 AAAAT-AAAATATTTATTAAAATA
* *
1926804 TATATAAAATATTTATTAAAATA
1 AAAATAAAATATTTATTAAAATA
*
1926827 AAAATAATATATTT-TTAA
1 AAAATAAAATATTTATTAA
1926845 GTAAATTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 9 0.27
22 13 0.39
23 11 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATAAAATATTTATTAAAATA
Found at i:1932491 original size:64 final size:63
Alignment explanation
Indices: 1932418--1932537 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 63
1932408 ATTGTCCAAG
** * *
1932418 GTGTATCGATGCACTTGAAGTGCATCGATGCACTACTTTAATATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGAACCACTTTAA-ATAAAAACATCGAATGCCATCA
* * *
1932482 GTGTATCGATGCACAAGTAGTGCATCGATGAACCCCTTTAAATACAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCGATGAACCACTTTAAATAAAAACATCGAAT
1932538 AGGATTTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 14 0.29
64 35 0.71
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGAACCACTTTAAATAAAAACATCGAATGCCATCA
Found at i:1932566 original size:63 final size:64
Alignment explanation
Indices: 1932418--1932579 Score: 172
Period size: 63 Copynumber: 2.5 Consensus size: 64
1932408 ATTGTCCAAG
* **
1932418 GTGTATCGATGCACTTGA-AGTGCATCGATGCACTACTTTAATATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCA-TAGATAGTGCATCGATGCACCCCTTTAATATAAAAACATCGAATGCCATCA
* * * *
1932482 GTGTATCGATGCACA-AGTAGTGCATCGATGAACCCCTTTAA-ATACAAACATCGAATAG-GATT
1 GTGTATCGATGCATAGA-TAGTGCATCGATGCACCCCTTTAATATAAAAACATCGAAT-GCCA-T
*
1932544 TA
63 CA
*
1932546 -TGTATCGATGCATAGATAGTGCATCAATGCACCC
1 GTGTATCGATGCATAGATAGTGCATCGATGCACCC
1932580 GTCAAGGGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
62 1 0.01
63 44 0.54
64 37 0.45
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCATAGATAGTGCATCGATGCACCCCTTTAATATAAAAACATCGAATGCCATCA
Found at i:1934929 original size:22 final size:21
Alignment explanation
Indices: 1934901--1934943 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1934891 TAATTTATTA
1934901 TATATTATTAAAATAAAAATAT
1 TATATTA-TAAAATAAAAATAT
**
1934923 TATATTATATTATAAAAATAT
1 TATATTATAAAATAAAAATAT
1934944 CAATAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATTATAAAATAAAAATAT
Found at i:1939991 original size:18 final size:19
Alignment explanation
Indices: 1939956--1939994 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1939946 TTATTCAAGG
1939956 AGTATCGATACCTAAAGGGT
1 AGTATCGATACC-AAAGGGT
1939976 AGTATCGATACC-AAGGGT
1 AGTATCGATACCAAAGGGT
1939994 A
1 A
1939995 CCGATACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGT
Found at i:1940769 original size:21 final size:21
Alignment explanation
Indices: 1940743--1940879 Score: 157
Period size: 21 Copynumber: 6.4 Consensus size: 21
1940733 TCGAGGGTTC
1940743 TATGTGGTCCTTTGGGACATA
1 TATGTGGTCCTTTGGGACATA
* *
1940764 TATGTGATCCTTTGGAACATA
1 TATGTGGTCCTTTGGGACATA
* * *
1940785 TATGAGGTCATTCGGGACATA
1 TATGTGGTCCTTTGGGACATA
* * * *
1940806 TATTTGATTCTTTGGAACATA
1 TATGTGGTCCTTTGGGACATA
*
1940827 TATGTGGTCCTTCGGGACAATTA
1 TATGTGGTCCTTTGGGAC-A-TA
1940850 TATGTGGTCCTTTGGGACATA
1 TATGTGGTCCTTTGGGACATA
*
1940871 TATGAGGTC
1 TATGTGGTC
1940880 ATTCAGGACA
Statistics
Matches: 93, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
21 72 0.77
22 2 0.02
23 19 0.20
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (21 bp):
TATGTGGTCCTTTGGGACATA
Found at i:1940808 original size:23 final size:22
Alignment explanation
Indices: 1940782--1940891 Score: 84
Period size: 21 Copynumber: 5.1 Consensus size: 22
1940772 CCTTTGGAAC
1940782 ATATATGAGGTCATTCGGGACA
1 ATATATGAGGTCATTCGGGACA
* * * *
1940804 TATATTTGA-TTC-TTTGGAAC-
1 -ATATATGAGGTCATTCGGGACA
* *
1940824 ATATATGTGGTCCTTCGGGACA
1 ATATATGAGGTCATTCGGGACA
* * *
1940846 ATTATATGTGGTCCTTTGGGAC-
1 A-TATATGAGGTCATTCGGGACA
*
1940868 ATATATGAGGTCATTCAGGACA
1 ATATATGAGGTCATTCGGGACA
1940890 AT
1 AT
1940892 TTTATATGGC
Statistics
Matches: 68, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
19 6 0.09
20 2 0.03
21 28 0.41
22 6 0.09
23 26 0.38
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (22 bp):
ATATATGAGGTCATTCGGGACA
Found at i:1940819 original size:42 final size:42
Alignment explanation
Indices: 1940756--1940889 Score: 187
Period size: 42 Copynumber: 3.1 Consensus size: 42
1940746 GTGGTCCTTT
1940756 GGGACATATATGTGATCCTTTGGAACATATATGAGGTCATTC
1 GGGACATATATGTGATCCTTTGGAACATATATGAGGTCATTC
* * * *
1940798 GGGACATATATTTGATTCTTTGGAACATATATGTGGTCCTTC
1 GGGACATATATGTGATCCTTTGGAACATATATGAGGTCATTC
* *
1940840 GGGACAATTATATGTGGTCCTTTGGGACATATATGAGGTCATTC
1 GGGAC-A-TATATGTGATCCTTTGGAACATATATGAGGTCATTC
*
1940884 AGGACA
1 GGGACA
1940890 ATTTTATATG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 43 0.54
43 2 0.03
44 34 0.43
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (42 bp):
GGGACATATATGTGATCCTTTGGAACATATATGAGGTCATTC
Found at i:1942773 original size:20 final size:18
Alignment explanation
Indices: 1942748--1942786 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1942738 CTGACATGGT
*
1942748 AAGAAAAGAGGACTGAGAGA
1 AAGAAAA-AGG-CAGAGAGA
1942768 AAGAAAAAGGCAGAGAGA
1 AAGAAAAAGGCAGAGAGA
1942786 A
1 A
1942787 GAATGTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.59, C:0.05, G:0.33, T:0.03
Consensus pattern (18 bp):
AAGAAAAAGGCAGAGAGA
Found at i:1943690 original size:17 final size:16
Alignment explanation
Indices: 1943659--1943696 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1943649 AATTGAACCA
*
1943659 ATTTTTATAAATATAT
1 ATTTTAATAAATATAT
1943675 ATTTTAATATAATATAT
1 ATTTTAATA-AATATAT
1943692 -TTTTA
1 ATTTTA
1943697 TCTTATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTAATAAATATAT
Found at i:1945328 original size:21 final size:21
Alignment explanation
Indices: 1945302--1945345 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1945292 TATACAAGAT
*
1945302 AGCTTGTGTACCAGACTTAAC
1 AGCTTGTATACCAGACTTAAC
1945323 AGCTTGTATACCAGACTTAAC
1 AGCTTGTATACCAGACTTAAC
1945344 AG
1 AG
1945346 ACTCATAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (21 bp):
AGCTTGTATACCAGACTTAAC
Found at i:1945356 original size:21 final size:21
Alignment explanation
Indices: 1945310--1945356 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1945300 ATAGCTTGTG
**
1945310 TACCAGACTTAACAGCTTGTA
1 TACCAGACTTAACAGCTCATA
1945331 TACCAGACTTAACAGACTCATA
1 TACCAGACTTAACAG-CTCATA
1945353 -ACCA
1 TACCA
1945357 ACCTCTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (21 bp):
TACCAGACTTAACAGCTCATA
Found at i:1950186 original size:21 final size:21
Alignment explanation
Indices: 1950160--1950203 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1950150 TATACAAGAT
*
1950160 AGCTTGTGTACCAGACTTAAC
1 AGCTTGTATACCAGACTTAAC
1950181 AGCTTGTATACCAGACTTAAC
1 AGCTTGTATACCAGACTTAAC
1950202 AG
1 AG
1950204 ACTCACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (21 bp):
AGCTTGTATACCAGACTTAAC
Found at i:1950213 original size:13 final size:13
Alignment explanation
Indices: 1950195--1950221 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1950185 TGTATACCAG
1950195 ACTTAACAGACTC
1 ACTTAACAGACTC
1950208 ACTTAACAGACTC
1 ACTTAACAGACTC
1950221 A
1 A
1950222 TAACCAACCT
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:0.41, C:0.30, G:0.07, T:0.22
Consensus pattern (13 bp):
ACTTAACAGACTC
Found at i:1951106 original size:35 final size:36
Alignment explanation
Indices: 1950993--1951133 Score: 243
Period size: 36 Copynumber: 4.0 Consensus size: 36
1950983 AACATCTACC
* *
1950993 AAAC-TTTACCAAACTTAGAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
1951028 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
1951064 AAACATTTACCAAACTTTGAAAACCATTTTT-AAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
1951099 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
1951134 TTGGTTGCCA
Statistics
Matches: 102, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
34 4 0.04
35 38 0.37
36 60 0.59
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:1951114 original size:71 final size:70
Alignment explanation
Indices: 1950993--1951133 Score: 239
Period size: 71 Copynumber: 2.0 Consensus size: 70
1950983 AACATCTACC
1950993 AAACTTTACCAAACTTAGAAAAACATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTT
1 AAACTTTACCAAACTTAGAAAAACATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-TTT
1951058 TCAAAG
65 TCAAAG
* *
1951064 AAACATTTACCAAACTTTGAAAACCATTTTT-AAAGAAACATTTACCAAACTTTGAAAACCATTT
1 AAAC-TTTACCAAACTTAGAAAAACATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTT
1951128 TCAAAG
65 TCAAAG
1951134 TTGGTTGCCA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
70 9 0.13
71 34 0.51
72 24 0.36
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (70 bp):
AAACTTTACCAAACTTAGAAAAACATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTT
CAAAG
Found at i:1951196 original size:29 final size:29
Alignment explanation
Indices: 1951154--1951219 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
1951144 ACCTTTGGAG
*
1951154 TTTTAA-CAATCTCCCACTTGAAGACTGA
1 TTTTAATCTATCTCCCACTTGAAGACTGA
1951182 TTTTAATCTATCTCCCACTTGAAGACTGA
1 TTTTAATCTATCTCCCACTTGAAGACTGA
1951211 TTTTAATCT
1 TTTTAATCT
1951220 GTCTTCACAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 6 0.17
29 30 0.83
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (29 bp):
TTTTAATCTATCTCCCACTTGAAGACTGA
Found at i:1955728 original size:21 final size:20
Alignment explanation
Indices: 1955665--1955764 Score: 60
Period size: 21 Copynumber: 5.4 Consensus size: 20
1955655 TATTTTCAAC
*
1955665 AAACATCTACCAAACTTTGAA
1 AAACATTTACCAAACTTTG-A
**
1955686 AAACATTTTTCAAA----G-
1 AAACATTTACCAAACTTTGA
1955701 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
1955721 AAATCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
1955736 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
1955756 AAACCATTT
1 AAA-CATTT
1955765 TCAAAGTTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 26
0.64 0.08 0.28
Matches are distributed among these distances:
14 5 0.08
15 19 0.32
16 1 0.02
17 1 0.02
19 2 0.03
20 10 0.17
21 21 0.36
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:1955731 original size:35 final size:35
Alignment explanation
Indices: 1955656--1955770 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
1955646 ACCCATTTCT
* *
1955656 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
*
1955690 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAATC
1 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
*
1955726 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
1955761 ATTTTCAAAG
1 ATTTTCAAAG
1955771 TTGATTGCCC
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 1 0.01
35 48 0.64
36 26 0.35
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
Found at i:1958845 original size:22 final size:21
Alignment explanation
Indices: 1958818--1958882 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1958808 ATAAAACTTA
1958818 ATATTTTTTTAAAATATTAAAAT
1 ATATTTTTTT--AATATTAAAAT
* *
1958841 A-ATTTATTTATTATTAAAAT
1 ATATTTTTTTAATATTAAAAT
* * *
1958861 ATATTTTTATAATTTTATAAT
1 ATATTTTTTTAATATTAAAAT
1958882 A
1 A
1958883 AAAATATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 11 0.32
21 15 0.44
22 7 0.21
23 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTTTTTTAATATTAAAAT
Done.