Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 16
Found at i:858366 original size:33 final size:33
Alignment explanation
Indices: 858324--858410 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 33
858314 ACAAATCGCA
*
858324 TTGCGATTTTCATTTCGCGTTGAGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGAGATTTTGTCG
*
858357 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGAGATTTTGTCG
*
858390 TTGCGATTTT-ATTTCTCATTG
1 TTGCGATTTTCATTTCGCATTG
858411 CGATAGCGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 10 0.20
33 41 0.80
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.51
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGAGATTTTGTCG
Found at i:858431 original size:20 final size:20
Alignment explanation
Indices: 858408--858453 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
858398 TTATTTCTCA
858408 TTGCGATAG-CGATTTTCGCG
1 TTGCGATAGTC-ATTTTCGCG
* *
858428 TTGCAATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
858448 TTGCGA
1 TTGCGA
858454 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:859017 original size:18 final size:18
Alignment explanation
Indices: 858994--859041 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
858984 CGGGTCGATC
858994 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
* *
859012 AGGTGATAGCTTTGGGTG
1 AGGTGATGGCTCTGGGTG
859030 AGGTGATGGCTC
1 AGGTGATGGCTC
859042 CCGAAGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.10, G:0.46, T:0.29
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:860369 original size:20 final size:20
Alignment explanation
Indices: 860336--860392 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
860326 AATAGTTTCT
**
860336 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
* *
860356 GAAAATGACTATCGTAACGC
1 GAAAATGACTATCGCAACAC
**
860376 GAATTTGACTATCGCAA
1 GAAAATGACTATCGCAA
860393 TGAGAGAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:860442 original size:19 final size:19
Alignment explanation
Indices: 860420--860470 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
860410 GAAACTAAAA
860420 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
860439 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
860458 TCGCGTTGCGATT
1 TCGCGTTGCGATT
860471 CTCGGTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:860933 original size:20 final size:20
Alignment explanation
Indices: 860905--860957 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
860895 GATTATGTAT
*
860905 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
860925 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
860945 TATCGCATTGCGA
1 TATCGCGTTGCGA
860958 TTTTCCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:860958 original size:20 final size:20
Alignment explanation
Indices: 860885--860958 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
860875 CGCTTTGAAA
*
860885 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
860906 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
860926 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
860946 ATCGCATTGCGAT
1 ATCGCATTGCGAT
860959 TTTCCCAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.04
20 33 0.73
21 10 0.22
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:861032 original size:20 final size:20
Alignment explanation
Indices: 860884--861039 Score: 59
Period size: 20 Copynumber: 7.7 Consensus size: 20
860874 GCGCTTTGAA
860884 AATCGCATTGCGATTATGT-AT
1 AATCGCATTGCGA-TA-GTCAT
* * * *
860905 TATCTCGTTGCGAAAGTCAGT
1 AATCGCATTGCGATAGTCA-T
*
860926 -ATCGCGTTGCGATAGTCAGT
1 AATCGCATTGCGATAGTCA-T
** **
860946 -ATCGCATTGCGATTTTCCC
1 AATCGCATTGCGATAGTCAT
* * *
860965 AATTCGCGTTGCGAT-TTACTT
1 AA-TCGCATTGCGATAGT-CAT
* * ** *
860986 ATTCGCATTGCGAATTGGGAA
1 AATCGCATTGCG-ATAGTCAT
861007 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAT
*
861027 AATCGCGTTGCGA
1 AATCGCATTGCGA
861040 ATCTGGAAAC
Statistics
Matches: 101, Mismatches: 27, Indels: 15
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.02
20 62 0.61
21 37 0.37
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAT
Found at i:861625 original size:2 final size:2
Alignment explanation
Indices: 861618--861673 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
861608 TTTAAAATTA
861618 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
861659 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
861674 ATAATTTTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:874524 original size:17 final size:17
Alignment explanation
Indices: 874502--874554 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
874492 GTTAAATGTT
874502 TTAAAGAGGAGTAAGTG
1 TTAAAGAGGAGTAAGTG
*
874519 TT--A-A--AGTAAGGGG
1 TTAAAGAGGAGTAA-GTG
874532 TTAAAGAGGAGTAAGTG
1 TTAAAGAGGAGTAAGTG
874549 TTAAAG
1 TTAAAG
874555 TAAGGGGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 5 0.18
13 4 0.14
14 1 0.04
15 2 0.07
16 1 0.04
17 10 0.36
18 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.25
Consensus pattern (17 bp):
TTAAAGAGGAGTAAGTG
Found at i:874538 original size:30 final size:30
Alignment explanation
Indices: 874502--874561 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
874492 GTTAAATGTT
874502 TTAAAGAGGAGTAAGTGTTAAAGTAAGGGG
1 TTAAAGAGGAGTAAGTGTTAAAGTAAGGGG
874532 TTAAAGAGGAGTAAGTGTTAAAGTAAGGGG
1 TTAAAGAGGAGTAAGTGTTAAAGTAAGGGG
874562 GAGTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.37, T:0.23
Consensus pattern (30 bp):
TTAAAGAGGAGTAAGTGTTAAAGTAAGGGG
Found at i:878552 original size:180 final size:181
Alignment explanation
Indices: 878250--878611 Score: 717
Period size: 180 Copynumber: 2.0 Consensus size: 181
878240 AGCAAGTAAA
878250 GAATGGAGAAATTAAAATTTTTGAGGTTAAGGTGGATGAGAATTTGTATTATAAAGGAAGAATCG
1 GAATGGAGAAATTAAAATTTTTGAGGTTAAGGTGGATGAGAATTTGTATTATAAAGGAAGAATCG
878315 TGATACCCGATGATGAGGATTTGAAGAAATTTTTGTTGACAGAGGCTCATTGTAGTCCATTGACA
66 TGATACCCGATGATGAGGATTTGAAGAAATTTTTGTTGACAGAGGCTCATTGTAGTCCATTGACA
878380 TGTATCCGGGTGGAACCAAGATGTATATCGATTTAAAGGA-CGGTATTGGT
131 TGTATCCGGGTGGAACCAAGATGTATATCGATTTAAAGGATCGGTATTGGT
878430 GAATGGAGAAATTAAAATTTTTGAGGTTAAGGTGGATGAGAATTTGTATTATAAAGGAAGAATCG
1 GAATGGAGAAATTAAAATTTTTGAGGTTAAGGTGGATGAGAATTTGTATTATAAAGGAAGAATCG
878495 TGATACCCGATGATGAGGATTTGAAGAAATTTTTGTTGACAGAGGCTCATTGTAGTCCATTGACA
66 TGATACCCGATGATGAGGATTTGAAGAAATTTTTGTTGACAGAGGCTCATTGTAGTCCATTGACA
878560 TGTATCCGGGTGGAACCAAGATGTATATCGATTTAAAGGATCGGTATTGGT
131 TGTATCCGGGTGGAACCAAGATGTATATCGATTTAAAGGATCGGTATTGGT
878611 G
1 G
878612 GTCAAGAATG
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 170 0.94
181 11 0.06
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (181 bp):
GAATGGAGAAATTAAAATTTTTGAGGTTAAGGTGGATGAGAATTTGTATTATAAAGGAAGAATCG
TGATACCCGATGATGAGGATTTGAAGAAATTTTTGTTGACAGAGGCTCATTGTAGTCCATTGACA
TGTATCCGGGTGGAACCAAGATGTATATCGATTTAAAGGATCGGTATTGGT
Found at i:881098 original size:30 final size:30
Alignment explanation
Indices: 881034--881099 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
881024 TATGAGCTAT
* * ** *
881034 GTGATAAAGGTATGGAAATGATGTGTATAT
1 GTGATAAAAGTATGGAAATAATACGTATAC
*
881064 GTGATAAAAGTATGGAAATAATACGTCTAC
1 GTGATAAAAGTATGGAAATAATACGTATAC
881094 GTGATA
1 GTGATA
881100 TGAACTATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (30 bp):
GTGATAAAAGTATGGAAATAATACGTATAC
Found at i:881368 original size:23 final size:23
Alignment explanation
Indices: 881334--881379 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
881324 ACATATTATA
881334 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
881357 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
881380 CGGTCTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:882616 original size:4 final size:4
Alignment explanation
Indices: 882607--882655 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
882597 CTAAAACGAA
* *
882607 AAAT AAAT AAAT AAAT -AA- AAAT AAAC AAAT AAAT ACAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
882653 AAA
1 AAA
882656 GTATATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 4 0.10
4 35 0.90
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:882738 original size:34 final size:36
Alignment explanation
Indices: 882694--882942 Score: 130
Period size: 36 Copynumber: 6.3 Consensus size: 36
882684 TTTCGAAGCC
* * *
882694 TATATGATATATTTTCAAAAACGTTTT-AAGATTATA
1 TATATTATATATTTTC-AAAACGTTTTCAAAACTATA
*
882730 TAT-TATATATATTTTCAAAATGTTTTCAAAACTATATATATTATA
1 TATAT-TATATATTTTCAAAACGTTTTCAAAAC---------TATA
*
882775 TATATTATATATATTTCAAAA-GTTTTCAAAATTATA
1 TATATTATATAT-TTTCAAAACGTTTTCAAAACTATA
* *
882811 TAT-TATATATATTTTCAAAATGTTTTCAAAAATTATA
1 TATAT-TATATATTTTCAAAACGTTTTC-AAAACTATA
882848 TATAATATATATATTTTCAAAAAACGTTTTCTAAAAACTATA
1 TAT-AT-TATATATTTTC--AAAACGTTTTC--AAAACTATA
* * * *
882890 TAT-TATATTTTTTTTCAAAAATCGTTTTAAAAAACTATTT
1 TATAT-TATATATTTTC-AAAA-CGTTTT-CAAAACTA-TA
882930 TATATTAATATAT
1 TATATT-ATATAT
882943 ATATTAAATA
Statistics
Matches: 174, Mismatches: 13, Indels: 47
0.74 0.06 0.20
Matches are distributed among these distances:
35 19 0.11
36 36 0.21
37 12 0.07
39 25 0.14
40 22 0.13
41 15 0.09
42 12 0.07
45 24 0.14
46 9 0.05
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATTATATATTTTCAAAACGTTTTCAAAACTATA
Found at i:882746 original size:36 final size:37
Alignment explanation
Indices: 882700--882922 Score: 202
Period size: 36 Copynumber: 5.7 Consensus size: 37
882690 AGCCTATATG
*
882700 ATATATTTTCAAAAACGTTTT-AAGATTATATATTAT
1 ATATATTTTCAAAAACGTTTTCAAAATTATATATTAT
*
882736 ATATATTTTC-AAAATGTTTTCAAAACTATATATATTAT
1 ATATATTTTCAAAAACGTTTTCAAAA-T-TATATATTAT
*
882774 ATATATTATAT-ATATTTCAAAAGTTTTCAAAATTATATATTAT
1 ATATATT-T-TCA-A----AAACGTTTTCAAAATTATATATTAT
*
882817 ATATATTTTC-AAAATGTTTTCAAAAATTATATATAATAT
1 ATATATTTTCAAAAACGTTTTC-AAAATTATATAT--TAT
*
882856 ATATATTTTCAAAAAACGTTTTCTAAAAACTATATATTAT
1 ATATATTTTC-AAAAACGTTTTC--AAAATTATATATTAT
* * *
882896 ATTTTTTTTCAAAAATCGTTTTAAAAA
1 ATATATTTTCAAAAA-CGTTTTCAAAA
882923 ACTATTTTAT
Statistics
Matches: 159, Mismatches: 9, Indels: 36
0.78 0.04 0.18
Matches are distributed among these distances:
35 9 0.06
36 22 0.14
37 13 0.08
38 21 0.13
39 19 0.12
40 19 0.12
41 12 0.08
42 13 0.08
43 17 0.11
44 1 0.01
45 13 0.08
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
ATATATTTTCAAAAACGTTTTCAAAATTATATATTAT
Found at i:882776 original size:11 final size:9
Alignment explanation
Indices: 882762--882789 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
882752 TTTTCAAAAC
882762 TATATATAT
1 TATATATAT
882771 TATATATAT
1 TATATATAT
882780 TATATATAT
1 TATATATAT
882789 T
1 T
882790 TCAAAAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATATAT
Found at i:882785 original size:81 final size:81
Alignment explanation
Indices: 882694--882944 Score: 284
Period size: 81 Copynumber: 3.1 Consensus size: 81
882684 TTTCGAAGCC
* *
882694 TATATGATATATTTTCAAAAACGTTTT-AAGATTATATATTATATATATTTTCAAAATGTTTTCA
1 TATATTATATATTTTCAAAAACGTTTTAAAAATTATATATTATATATATTTTCAAAATGTTTTCA
882758 AAACTATATATATTATA
66 AAACTAT-TATATTATA
*
882775 TATATTATATATATTTC-AAAA-GTTTTCAAAATTATATATTATATATATTTTCAAAATGTTTTC
1 TATATTATATAT-TTTCAAAAACGTTTTAAAAATTATATATTATATATATTTTCAAAATGTTTTC
882838 AAAA--ATTATA-TATA
65 AAAACTATTATATTATA
* * *
882852 -ATA-TATATATTTTCAAAAAACGTTTTCTAAAAACTATATATTATATTTTTTTTCAAAAATCGT
1 TATATTATATATTTTC-AAAAACG-TTT-TAAAAATTATATATTATATATATTTTC-AAAAT-GT
*
882915 TTTAAAAAACTATTTTATATTAATA
61 TTT-CAAAACTA--TTATATT-ATA
882940 TATAT
1 TATAT
882945 ATTAAATAAG
Statistics
Matches: 145, Mismatches: 7, Indels: 27
0.81 0.04 0.15
Matches are distributed among these distances:
74 4 0.03
75 7 0.05
76 7 0.05
77 5 0.03
78 7 0.05
79 25 0.17
80 10 0.07
81 59 0.41
82 8 0.06
84 1 0.01
86 5 0.03
87 1 0.01
88 3 0.02
89 3 0.02
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (81 bp):
TATATTATATATTTTCAAAAACGTTTTAAAAATTATATATTATATATATTTTCAAAATGTTTTCA
AAACTATTATATTATA
Found at i:882800 original size:45 final size:45
Alignment explanation
Indices: 882726--882823 Score: 164
Period size: 43 Copynumber: 2.2 Consensus size: 45
882716 GTTTTAAGAT
882726 TATATATTATATATATTTTCAAAATGTTTTCAAAACTATATATATTA
1 TATATATTATATATATTTTCAAAATGTTTTCAAAA-T-TATATATTA
882773 TATATATTATATATA-TTTCAAAA-GTTTTCAAAATTATATATTA
1 TATATATTATATATATTTTCAAAATGTTTTCAAAATTATATATTA
882816 TATATATT
1 TATATATT
882824 TTCAAAATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
43 17 0.33
44 1 0.02
45 10 0.20
46 8 0.16
47 15 0.29
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (45 bp):
TATATATTATATATATTTTCAAAATGTTTTCAAAATTATATATTA
Found at i:882850 original size:39 final size:39
Alignment explanation
Indices: 882771--882944 Score: 173
Period size: 39 Copynumber: 4.5 Consensus size: 39
882761 CTATATATAT
882771 TATATATATTATATATA-TTTC-AAAA-GTTTTC-AAAA
1 TATATATATTATATATATTTTCAAAAATGTTTTCAAAAA
882806 T-TATATATTATATATATTTTC-AAAATGTTTTCAAAAA
1 TATATATATTATATATATTTTCAAAAATGTTTTCAAAAA
* *
882843 TTATATATAATATATATATTTTCAAAAAACGTTTTCTAAAAA
1 -TATATATATTATATATATTTTC-AAAAATGTTTTC-AAAAA
* * * *
882885 -CTATATATTATATTTTTTTTCAAAAATCGTTTTAAAAAA
1 TATATATATTATATATATTTTCAAAAAT-GTTTTCAAAAA
*
882924 CTATTTTATATTAATATATAT
1 -TA-TATATATT-ATATATAT
882945 ATTAAATAAG
Statistics
Matches: 114, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
34 15 0.13
35 9 0.08
36 6 0.05
37 4 0.04
38 1 0.01
39 29 0.25
40 22 0.19
41 10 0.09
42 12 0.11
43 6 0.05
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (39 bp):
TATATATATTATATATATTTTCAAAAATGTTTTCAAAAA
Found at i:883402 original size:64 final size:64
Alignment explanation
Indices: 883295--883504 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
883285 TTTTTCAGAG
* * * * *
883295 TGATGCACCGATGCACCAATCCATGCATCGATGCTC-CATGGATTAAATTGAACATCGAATGCAT
1 TGATGCATCGATGCACC-AGCCATGCACCGATGCACTC-TGGATTATATTGAACATCGAATGCAT
883359 T
64 T
* * *
883360 TCATGCATCGATGCACACA-CCATGCACCGATGCACT-TAGGATTTTATGAGAACATCGAATGCA
1 TGATGCATCGATGCAC-CAGCCATGCACCGATGCACTCT-GGATTATAT-TGAACATCGAATGCA
883423 TT
63 TT
* * * *
883425 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGG-CTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAGCCATGCACCGATGCACTCTGGATTATATTG-AACATCGAATGCATT
883489 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
883505 TAAGGGTCCA
Statistics
Matches: 124, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
63 2 0.02
64 56 0.45
65 64 0.52
66 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAGCCATGCACCGATGCACTCTGGATTATATTGAACATCGAATGCATT
Found at i:883413 original size:65 final size:65
Alignment explanation
Indices: 883344--883504 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 65
883334 GGATTAAATT
*
883344 GAACATCGAATGCATTTCATGCATCGATGCACACA-CCATGCACCGATGCACT-TAGGAT-TTTA
1 GAACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCACCGATGCACTCT-GGATATTT-
883406 TGA
63 TGA
* *
883409 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCACCGATGCACTCTGGATATTTTGA
*
883474 -AACATCGAATGCACTTGATGCATCGATGCAC
1 GAACATCGAATGCATTTGATGCATCGATGCAC
883505 TAAGGGTCCA
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
64 32 0.36
65 53 0.60
66 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (65 bp):
GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCACCGATGCACTCTGGATATTTTGA
Found at i:884699 original size:21 final size:21
Alignment explanation
Indices: 884662--884735 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
884652 TACTCTTTAA
884662 AATATAATAATATTTTTAAATTT
1 AATATAAT-A-ATTTTTAAATTT
884685 AATATAATAATTTTTAATATTT
1 AATATAATAATTTTTAA-ATTT
* * *
884707 TA-ATAAT-ATTATT-ATTTT
1 AATATAATAATTTTTAAATTT
884725 AATA-AATAATT
1 AATATAATAATT
884736 AATAAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.16
19 5 0.11
20 5 0.11
21 13 0.30
22 6 0.14
23 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATATAATAATTTTTAAATTT
Found at i:884710 original size:15 final size:15
Alignment explanation
Indices: 884669--884728 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
884659 TAAAATATAA
884669 TAATATTTTTAA-ATT
1 TAATA-TTTTAATATT
** *
884684 TAATATAATAATTTT
1 TAATATTTTAATATT
884699 TAATATTTTAATAATAT
1 TAATATTTTAAT-AT-T
*
884716 TATTATTTTAATA
1 TAATATTTTAATA
884729 AATAATTAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.11
15 17 0.49
16 2 0.06
17 12 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATATTTTAATATT
Found at i:884792 original size:23 final size:22
Alignment explanation
Indices: 884720--884794 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
884710 TAATATTATT
884720 ATTTTAATAAATAATTAATA-A
1 ATTTTAATAAATAATTAATATA
* * * *
884741 A-ATTAAT-AATATATTATTCTC
1 ATTTTAATAAATA-ATTAATATA
*
884762 ATTTTAATAAATAATTAATGTA
1 ATTTTAATAAATAATTAATATA
884784 ATTTATAATAA
1 ATTT-TAATAA
884795 CTTTATTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 4 0.10
20 10 0.24
21 2 0.05
22 15 0.37
23 10 0.24
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (22 bp):
ATTTTAATAAATAATTAATATA
Found at i:884869 original size:14 final size:14
Alignment explanation
Indices: 884850--884907 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
884840 AATTATAGAT
**
884850 ATAATATTTTAATA
1 ATAATATTGAAATA
884864 ATAATATTGAAATAA
1 ATAATATTGAAAT-A
884879 ATAATATT-AAATA
1 ATAATATTGAAATA
*
884892 A-AAGTATTGTAATA
1 ATAA-TATTGAAATA
884906 AT
1 AT
884908 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.05
13 6 0.16
14 20 0.54
15 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
ATAATATTGAAATA
Found at i:884899 original size:28 final size:29
Alignment explanation
Indices: 884850--884906 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
884840 AATTATAGAT
*
884850 ATAATATTTTAATAATAATATTGAAATAA
1 ATAATATTTAAATAATAATATTGAAATAA
*
884879 ATAATA-TTAAATAA-AAGTATTGTAATAA
1 ATAATATTTAAATAATAA-TATTGAAATAA
884907 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 17 0.68
29 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (29 bp):
ATAATATTTAAATAATAATATTGAAATAA
Found at i:885864 original size:2 final size:2
Alignment explanation
Indices: 885857--885908 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
885847 ATAATCAAAT
885857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
885899 TA TA TA TA TA
1 TA TA TA TA TA
885909 GATGTAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:888629 original size:15 final size:15
Alignment explanation
Indices: 888609--888641 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
888599 AGCTTTGAAA
888609 TGAATGGAAAAACAT
1 TGAATGGAAAAACAT
888624 TGAATGGAAAAACAT
1 TGAATGGAAAAACAT
888639 TGA
1 TGA
888642 GCATCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (15 bp):
TGAATGGAAAAACAT
Found at i:890226 original size:44 final size:43
Alignment explanation
Indices: 890130--890416 Score: 439
Period size: 43 Copynumber: 6.6 Consensus size: 43
890120 AGCAAGCTCA
**
890130 TTTGCTGTGTGCAATAGTAAGCCTTACAGTTTCCCCAGGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCC
* *
890173 TTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCCAGGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCC
*
890217 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCC
*
890261 TTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCC
890304 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCC
* * * *
890347 TTTGCTGTGTGCAAGTGTAAGCCTTATAGTTTCCCCAGGCTCT
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCC
* *
890390 TTTGCTATGTGCAAGGATAAGACCTTA
1 TTTGCTGTGTGCAAGGGTAAG-CCTTA
890417 TCATTTTTGC
Statistics
Matches: 225, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
43 137 0.61
44 88 0.39
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (43 bp):
TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCC
Found at i:890297 original size:87 final size:86
Alignment explanation
Indices: 890130--890416 Score: 457
Period size: 87 Copynumber: 3.3 Consensus size: 86
890120 AGCAAGCTCA
**
890130 TTTGCTGTGTGCAATAGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGC
890195 CTTATAGTTTCCCCCAGGTTCC
66 CTTATAGTTT-CCCCAGGTTCC
*
890217 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAG
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAG
*
890282 CCTTACAGTTTCCCCAGGTTCC
65 CCTTATAGTTTCCCCAGGTTCC
* *
890304 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGTGTAAGC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGC
* *
890369 CTTATAGTTTCCCCAGGCTCT
66 CTTATAGTTTCCCCAGGTTCC
* *
890390 TTTGCTATGTGCAAGGATAAGACCTTA
1 TTTGCTGTGTGCAAGGGTAAG-CCTTA
890417 TCATTTTTGC
Statistics
Matches: 186, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
86 67 0.36
87 78 0.42
88 41 0.22
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (86 bp):
TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGC
CTTATAGTTTCCCCAGGTTCC
Found at i:904311 original size:30 final size:30
Alignment explanation
Indices: 904267--904325 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
904257 GGAAGAATCG
*
904267 GCTGAGAACCGGCAAAACCGG-GATGAACCA
1 GCTGAAAACCGGCAAAACCGGTG-TGAACCA
*
904297 GCTGAAAACTGGCAAAACCGGTGTGAACC
1 GCTGAAAACCGGCAAAACCGGTGTGAACC
904326 GCCGATTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.36, C:0.25, G:0.29, T:0.10
Consensus pattern (30 bp):
GCTGAAAACCGGCAAAACCGGTGTGAACCA
Found at i:907099 original size:6 final size:6
Alignment explanation
Indices: 907088--907444 Score: 705
Period size: 6 Copynumber: 59.5 Consensus size: 6
907078 TATTTATCTT
907088 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
1 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
907136 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
1 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
907184 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
1 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
907232 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
1 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
907280 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
1 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
907328 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
1 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
907376 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
1 TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC TTACTC
*
907424 TTACTC TTACTC TTACAC TTA
1 TTACTC TTACTC TTACTC TTA
907445 ACTTATATGA
Statistics
Matches: 350, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 350 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
TTACTC
Found at i:911552 original size:129 final size:127
Alignment explanation
Indices: 911217--912125 Score: 1416
Period size: 127 Copynumber: 7.1 Consensus size: 127
911207 TATTCACGTA
* * *
911217 AAGGCGTGTTCCCCGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
* * *
911282 ATGTCACTTATGTCCCC-TAGGAACTATTCATGTCAATACTTATTATTTCTTAGGGGGCCGTG
66 ATGTCACTTATGTCCCCGGA-GAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
* * * * *
911344 AAGGCACGTTCCCGGGGGCGCACCTTCCAGTATTTTGTCAGATAATATATTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
911409 ATGTCACTTATGTCCCCGGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
66 ATGTCACTTATGTCCCCGGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
*
911471 AAGGCGCGTTCCCGGGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 AAGGCGCGTTCCC--GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
911536 TTATGTCATTTATGTCCCTCGG-GAACTATTCATGTCAATACCTATTATTTCTTAGGGGACTGTG
64 TTATGTCACTTATGTCCC-CGGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
* *
911600 AAGGCGCGTTCCCGGGGGCGTGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
* *
911665 ATGTCACTTATGTCCCCCGG-GAACTATTCATGTCAATACCTATTATTCCTTAGGGTACCGTG
66 ATGTCACTTATGT-CCCCGGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
* * *
911727 AAGGCACGTTCCCGGGGGCGCACCTTCCATTATTTTGTAAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
911792 ATGTCACTTATGTCCCCCGGA-AACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
66 ATGTCACTTATGT-CCCCGGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
* ** *
911854 AAGGCGCATTCCCAAGGG-GCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
911918 ATGTCACTTATGTCCCTTGG-GAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
66 ATGTCACTTATGTCCC-CGGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
* * *
911980 AAGGCGCGTTCCCGGGGGGGTGCGTCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTA
1 AAGGCGCGTTCCC--GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
912045 TTATGTCACTTATGTCCTCAGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
64 TTATGTCACTTATGTCCCCGGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
912109 AAGGCGCGTTCCCGGGG
1 AAGGCGCGTTCCCGGGG
912126 AACTATAGAT
Statistics
Matches: 722, Mismatches: 48, Indels: 24
0.91 0.06 0.03
Matches are distributed among these distances:
125 3 0.00
126 111 0.15
127 368 0.51
128 8 0.01
129 229 0.32
130 3 0.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (127 bp):
AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
ATGTCACTTATGTCCCCGGAGAACTATTCATGTCAATACCTATTATTTCTTAGGGGACCGTG
Found at i:912567 original size:34 final size:34
Alignment explanation
Indices: 912528--912634 Score: 153
Period size: 34 Copynumber: 3.1 Consensus size: 34
912518 TTAAGTTGAG
* * *
912528 TTTAATGTTAAATTTTGAATACTATAATTTAG-AT
1 TTTAATTTTAAATTTCGAATAATATAATTT-GTAT
*
912562 TTTAATTTTAAATTTCGAATAATATTATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
*
912596 TTTAATTTTAAATTTCGAATATTATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
912630 TTTAA
1 TTTAA
912635 AAACATTTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 1 0.02
34 65 0.98
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTGTAT
Found at i:913166 original size:21 final size:20
Alignment explanation
Indices: 913139--913208 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
913129 GGTATAAAAC
*
913139 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
*
913159 CCTGGCGGGCTAGAAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
913180 CCCTGCGGGCTAGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
913201 CCCTGCGG
1 -CCTGCGG
913209 AGATGACATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:913288 original size:42 final size:42
Alignment explanation
Indices: 913186--913288 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 42
913176 GTAACCCTGC
* * * * *
913186 GGGCTAGGAATGTAACCCTGCGGAGATGACATATGAACTGGT
1 GGGCTTGGCATGTACCCCTGAGGAGATGACATATGAACTGGA
* * * * *
913228 GGGCTTGGCATATCCCCCTGAGGAGATGGCATCTGAAGTGGA
1 GGGCTTGGCATGTACCCCTGAGGAGATGACATATGAACTGGA
913270 GGG-TTGGGCATGTACCCCT
1 GGGCTT-GGCATGTACCCCT
913289 ATGGCATCGG
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
41 2 0.04
42 46 0.96
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (42 bp):
GGGCTTGGCATGTACCCCTGAGGAGATGACATATGAACTGGA
Found at i:915012 original size:24 final size:25
Alignment explanation
Indices: 914985--915032 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
914975 ATAATTAGCG
914985 TAAA-AAATAAATAATTA-ATAAATT
1 TAAATAAAT-AATAATTATATAAATT
915009 TAAATAAATAATAATTATATAAAT
1 TAAATAAATAATAATTATATAAAT
915033 ATTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAATAAATAATAATTATATAAATT
Found at i:915053 original size:31 final size:33
Alignment explanation
Indices: 915008--915088 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 33
914998 ATTAATAAAT
* *
915008 TTAA-ATAAATAATAATTATATAAAT-ATTATT
1 TTAATATAAAAAATAATTATATAAATAATTATA
* *
915039 TTAATA-AAAAAATAA-TATTTATATAATTATA
1 TTAATATAAAAAATAATTATATAAATAATTATA
*
915070 TTAATATAAAATATAATTA
1 TTAATATAAAAAATAATTA
915089 CTATTTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
30 7 0.17
31 23 0.56
32 9 0.22
33 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TTAATATAAAAAATAATTATATAAATAATTATA
Found at i:915403 original size:60 final size:61
Alignment explanation
Indices: 915302--915443 Score: 164
Period size: 60 Copynumber: 2.3 Consensus size: 61
915292 TGAAAGGGGT
* * * * * *
915302 GTCCCAGGGTATGCGCCTTTCACACGTGGTAACTGAATCAGC-AAAACCC-CGTGAAGGCGC
1 GTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAATCAGCGAAAACCCAGGT-AAAGCGC
* *
915362 GTCCCCGGGGATGCGCCTTTCACACGTGGCATC-CAACTCAGCGTAAACCCAGGTAAAGCGC
1 GTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAA-TCAGCGAAAACCCAGGTAAAGCGC
*
915423 GTCACCGGGGATGCGCCTTTC
1 GTCCCCGGGGATGCGCCTTTC
915444 GCCACCTCAG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.03
60 34 0.49
61 32 0.46
62 2 0.03
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.18
Consensus pattern (61 bp):
GTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAATCAGCGAAAACCCAGGTAAAGCGC
Found at i:916381 original size:19 final size:18
Alignment explanation
Indices: 916344--916385 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
916334 ATCCTTTAAA
916344 ATTTTAAAATTTCTATAT
1 ATTTTAAAATTTCTATAT
* *
916362 ATTTTAAATATTTTTTTAT
1 ATTTTAAA-ATTTCTATAT
916381 ATTTT
1 ATTTT
916386 TTTAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTAAAATTTCTATAT
Found at i:922042 original size:34 final size:34
Alignment explanation
Indices: 921999--922124 Score: 125
Period size: 34 Copynumber: 3.8 Consensus size: 34
921989 TTCGTCCTAC
921999 TAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATATAATTT
* * *
922033 TAGGATTCAAACTCCTAAAGATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATATAATTT
* * * *
922067 T-GG-CT-AGGA-TTCAAAAAATAGGATATAATTT
1 TAGGATTCA-AACTCCTAAAAATAGGATATAATTT
* * *
922098 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
922125 CCACAAGTAC
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
31 19 0.27
32 3 0.04
33 4 0.06
34 45 0.63
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATATAATTT
Found at i:922520 original size:18 final size:17
Alignment explanation
Indices: 922481--922523 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
922471 ATTATATGGA
922481 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
922497 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
922515 TATTATTAT
1 TATTATTAT
922524 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:926037 original size:22 final size:21
Alignment explanation
Indices: 926002--926052 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
925992 AGATCCAATC
926002 AAGAAGAAA-AAAGAAAAGAAGCA
1 AAGAA-AAACAAAGAAAA-AA-CA
926025 AA-AAAAACAAAGAAAAAACA
1 AAGAAAAACAAAGAAAAAACA
926045 AAGAAAAA
1 AAGAAAAA
926053 AGAGAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 4 0.15
21 10 0.38
22 10 0.38
23 2 0.08
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (21 bp):
AAGAAAAACAAAGAAAAAACA
Found at i:926040 original size:11 final size:11
Alignment explanation
Indices: 926026--926053 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
926016 AAAGAAGCAA
926026 AAAAAACAAAG
1 AAAAAACAAAG
926037 AAAAAACAAAG
1 AAAAAACAAAG
926048 AAAAAA
1 AAAAAA
926054 GAGAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAG
Found at i:926076 original size:24 final size:23
Alignment explanation
Indices: 926049--926101 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
926039 AAAACAAAGA
926049 AAAAAGAGAAACAATAACAA-AATG
1 AAAAAGAGAAA-AA-AACAAGAATG
* *
926073 AAAAA-AGGAAAAAACAAGAATT
1 AAAAAGAGAAAAAAACAAGAATG
926095 AAAAAGA
1 AAAAAGA
926102 AAGAGGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 5 0.20
22 10 0.40
23 5 0.20
24 5 0.20
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.08
Consensus pattern (23 bp):
AAAAAGAGAAAAAAACAAGAATG
Found at i:926766 original size:22 final size:22
Alignment explanation
Indices: 926735--926789 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
926725 GCTATCCCAT
*
926735 CAAACATTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
926757 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
926779 CAAACCTTTGA
1 CAAACCTTTGA
926790 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:927216 original size:18 final size:18
Alignment explanation
Indices: 927193--927228 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
927183 TCAACATCAA
* *
927193 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
927211 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
927229 GGATTCATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:927751 original size:36 final size:36
Alignment explanation
Indices: 927708--927951 Score: 209
Period size: 36 Copynumber: 6.9 Consensus size: 36
927698 ACTAGAAGAG
*
927708 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
927744 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
927780 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
927816 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
927845 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* * *
927882 TTTTGTCTCTATTGAGACAGTTTCTCTTGAATC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
927917 TTTTCGTCTATCTTGAGACAGTTACTCTTGAAACA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACA
927952 CAAAATCTTC
Statistics
Matches: 168, Mismatches: 28, Indels: 23
0.77 0.13 0.11
Matches are distributed among these distances:
28 2 0.01
29 19 0.11
30 3 0.02
35 6 0.04
36 107 0.64
37 31 0.18
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:928845 original size:105 final size:105
Alignment explanation
Indices: 928663--929389 Score: 1086
Period size: 105 Copynumber: 7.0 Consensus size: 105
928653 GCACTTGAGG
* * * * *
928663 CAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
928728 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
928769 CAATGCAAGTTCAACTTCACGACGAAGGGACTGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
928834 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
928874 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
928939 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
928979 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
929044 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * *
929084 CAATGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAATAATAATTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
929149 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
929189 CAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGCTTTTCAATAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
929249 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * * ** *
929289 CAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
929354 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
929390 TGGAATAATG
Statistics
Matches: 570, Mismatches: 45, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
100 79 0.14
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 404 0.71
106 74 0.13
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:929981 original size:34 final size:34
Alignment explanation
Indices: 929938--930063 Score: 134
Period size: 34 Copynumber: 3.8 Consensus size: 34
929928 TTCGTCCTAC
929938 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
929972 TAGGATTCAAACTCCTAAAGATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * * *
930006 T-GG-CT-AGGA-TTCAAAAAATAGGATAGAATTT
1 TAGGATTCA-AACTCCTAAAAATAGGATAGAATTT
* * *
930037 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
930064 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
31 20 0.27
32 3 0.04
33 4 0.05
34 46 0.63
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:930459 original size:18 final size:17
Alignment explanation
Indices: 930420--930462 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
930410 ATTATATGGA
930420 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
930436 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
930454 TATTATTAT
1 TATTATTAT
930463 GTATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:931841 original size:29 final size:28
Alignment explanation
Indices: 931754--931841 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
931744 ATTATATCAT
* *
931754 TTTATTTATTGAA-TTTT-ATTATTTTG
1 TTTATTTATTAAACTTTTAATTATTTTA
* * *
931780 TTTCACTCATTATACTTTTAATT-TTTTAAA
1 TTT-ATTTATTAAACTTTTAATTATTTT--A
931810 TTTATTTATTAAACTTTTAAATTATTTTA
1 TTTATTTATTAAACTTTT-AATTATTTTA
931839 TTT
1 TTT
931842 TAATCACTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
26 3 0.06
27 6 0.13
28 8 0.17
29 19 0.40
30 7 0.15
31 4 0.09
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTATTTATTAAACTTTTAATTATTTTA
Found at i:937591 original size:20 final size:20
Alignment explanation
Indices: 937566--937631 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
937556 CCTTTTAGGA
**
937566 AAAGGACTAATTTCTCCCCT
1 AAAGGACTAATCCCTCCCCT
* *
937586 AAAGGATTGATCCCTCCCCT
1 AAAGGACTAATCCCTCCCCT
*
937606 AAAGGA-TCGATCCCTCCCCT
1 AAAGGACT-AATCCCTCCCCT
937626 AAAGGA
1 AAAGGA
937632 TCGATCCCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (20 bp):
AAAGGACTAATCCCTCCCCT
Found at i:937632 original size:20 final size:20
Alignment explanation
Indices: 937579--937639 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
937569 GGACTAATTT
*
937579 CTCCCCTAAAGGATTGATCC
1 CTCCCCTAAAGGATCGATCC
937599 CTCCCCTAAAGGATCGATCC
1 CTCCCCTAAAGGATCGATCC
937619 CTCCCCTAAAGGATCGATCC
1 CTCCCCTAAAGGATCGATCC
937639 C
1 C
937640 CTAGCTCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.21
Consensus pattern (20 bp):
CTCCCCTAAAGGATCGATCC
Found at i:938413 original size:18 final size:18
Alignment explanation
Indices: 938390--938438 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
938380 GTGGGAATAA
938390 GTGTAAATGAGTTTGAAG
1 GTGTAAATGAGTTTGAAG
938408 GTGTAAATGAGTTTGAAG
1 GTGTAAATGAGTTTGAAG
*
938426 GTATAAATAGAGT
1 GTGTAAAT-GAGT
938439 AAAAGGTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.33
Consensus pattern (18 bp):
GTGTAAATGAGTTTGAAG
Found at i:939420 original size:21 final size:22
Alignment explanation
Indices: 939387--939435 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
939377 TTGAGGGTTC
**
939387 TATGTGGTTCTTCGG-GACAAA-
1 TATGTGGCACTTCGGTG-CAAAT
939408 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
939430 TATGTG
1 TATGTG
939436 AGCTGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAT
Found at i:940292 original size:11 final size:9
Alignment explanation
Indices: 940275--940330 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 9
940265 CAAAAGAAAT
940275 TAAAATAAA
1 TAAAATAAA
940284 GTGAAAATAAA
1 -T-AAAATAAA
940295 TAAAAT-AA
1 TAAAATAAA
*
940303 TCAAATAAAA
1 TAAAAT-AAA
940313 TACAAAT-AA
1 TA-AAATAAA
940322 TAAAATAAA
1 TAAAATAAA
940331 AATGATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 11 0.28
9 11 0.28
10 5 0.13
11 12 0.31
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (9 bp):
TAAAATAAA
Found at i:940321 original size:19 final size:18
Alignment explanation
Indices: 940287--940331 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
940277 AAATAAAGTG
940287 AAAAT-AAATAAAATAAT
1 AAAATAAAATAAAATAAT
*
940304 CAAATAAAATACAAATAAT
1 AAAATAAAATA-AAATAAT
940323 AAAATAAAA
1 AAAATAAAA
940332 ATGATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.21
19 15 0.62
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAATAAAATAAT
Found at i:940342 original size:15 final size:14
Alignment explanation
Indices: 940287--940343 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
940277 AAATAAAGTG
940287 AAAATAAATAAAATA
1 AAAAT-AATAAAATA
**
940302 ATCA-AATAAAATA
1 AAAATAATAAAATA
*
940315 CAAATAATAAAATA
1 AAAATAATAAAATA
*
940329 AAAATGATTAAAATA
1 AAAAT-AATAAAATA
940344 TATACATAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
13 10 0.30
14 13 0.39
15 10 0.30
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (14 bp):
AAAATAATAAAATA
Found at i:941973 original size:81 final size:79
Alignment explanation
Indices: 941812--942044 Score: 295
Period size: 81 Copynumber: 2.9 Consensus size: 79
941802 GTTATCGAGA
* ** * * ** * ***
941812 TGAATGGAATCAAACTCGACAATTCTGTTGACAGATAACCCTTCTTGATTTGAGCTATGCTATGA
1 TGAATGGAATCGAACTCGA-AGGTCT-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAA
941877 ATGATGTGCCTTGAGC
64 ATGATGTGCCTTGAGC
* *
941893 TGAATGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTTTAGCCTTGATTTATGCTGCAAAT
1 TGAATGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
941958 GATAGTGCCTTTGAGC
66 GAT-GTGCC-TTGAGC
* *
941974 TGAGTGGAATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 TGAATGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
942039 GATGTG
66 GATGTG
942045 TACTCGAAGC
Statistics
Matches: 133, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
79 33 0.25
80 12 0.09
81 88 0.66
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (79 bp):
TGAATGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
GATGTGCCTTGAGC
Found at i:942056 original size:81 final size:81
Alignment explanation
Indices: 941806--942082 Score: 274
Period size: 81 Copynumber: 3.4 Consensus size: 81
941796 TGATATGTTA
* * * ** * * ** *
941806 TCGAGATGAATGGAATCAAACTCGACAATTCTGTTGACAGATAACCCTTCTTGATTTGAGCTATG
1 TCGAGCTGAGTGGAATCGAACTCGA-AGGTCT-TTGGCAGATAACCCTTCTAGCCTTGAGTTATG
*** *
941871 CTATGAATGAT-GTGCCT
64 CTGCAAATGATAGTGACT
* * *
941888 T-GAGCTGAATGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTTTAGCCTTGATTTATGCT
1 TCGAGCTGAGTGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
*
941952 GCAAATGATAGTGCCT
66 GCAAATGATAGTGACT
* *
941968 TTGAGCTGAGTGGAATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
1 TCGAGCTGAGTGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
942033 GCAAATGAT-GTGTAC-
66 GCAAATGATAGTG-ACT
** * *
942048 TCGAAGCTGAGTTTAGTCAAACTCGAAGGTCTTTG
1 TCG-AGCTGAGTGGAATCGAACTCGAAGGTCTTTG
942083 TATTTCAAGA
Statistics
Matches: 166, Mismatches: 25, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
79 33 0.20
80 16 0.10
81 116 0.70
82 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (81 bp):
TCGAGCTGAGTGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
GCAAATGATAGTGACT
Found at i:942299 original size:36 final size:36
Alignment explanation
Indices: 942217--942540 Score: 301
Period size: 36 Copynumber: 8.9 Consensus size: 36
942207 CAAAGATTGG
942217 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
942254 TGTTTCAAGGGAAATTATCTCAAAAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
942290 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
942326 TGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAGACAAATTT
1 TGTTTCAAGAGAAACTGTCTCAA--GAG----AGACAAAATT
* *
942368 TGTTTCAAGAGAAACTTTCTCAGGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
942405 AGTTCCAAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
942442 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
*
942471 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
942507 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAA
942541 CTTTATTTTG
Statistics
Matches: 234, Mismatches: 31, Indels: 45
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.01
29 15 0.06
30 3 0.01
31 1 0.00
32 2 0.01
33 2 0.01
35 3 0.01
36 104 0.44
37 44 0.19
38 26 0.11
40 3 0.01
42 29 0.12
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:942363 original size:42 final size:42
Alignment explanation
Indices: 942280--942400 Score: 139
Period size: 42 Copynumber: 3.0 Consensus size: 42
942270 ATCTCAAAAG
* *
942280 AGACAAAATTTGTTTCAAGGGAAACTGTCTCAA--GAG----
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGGGAGACAA
942316 AGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGGGAGACAA
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGGGAGACAA
* * *
942358 AGACAAATTTTGTTTCAAGAGAAACTTTC-TCAGGAGAGACAA
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGG-GAGACAA
942400 A
1 A
942401 ACTTAGTTCC
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
36 31 0.42
38 3 0.04
41 4 0.05
42 35 0.48
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (42 bp):
AGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGGGAGACAA
Found at i:942567 original size:37 final size:36
Alignment explanation
Indices: 942473--942548 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
942463 AAAGATTTTG
* *
942473 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTA
942509 TTTCAAAGGAAACTGTCTCAAGAGAGACAAAACTTTA
1 TTTCAAAGGAAACTGTCTCAAGAGAGACAAAA-TTTA
942546 TTT
1 TTT
942549 TGAGTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (36 bp):
TTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:943930 original size:95 final size:94
Alignment explanation
Indices: 943758--943953 Score: 241
Period size: 95 Copynumber: 2.1 Consensus size: 94
943748 GGACAAATCA
* * ** * * * * *
943758 ATATGTAAACACCTTTATCAGGTTAGTTGAATCTTATCTATAAAGTCAGGGTGTTTAACCAATTA
1 ATATATAATCACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTA
*
943823 CCTTAGAGGGACAGCTCAAGATTTATTGT
66 CCTTAGAGGGACAACTCAAGATTTATTGT
* *
943852 ATAGTATAATCACCTTTATCATACTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATA-TATAATCACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
* *
943917 -GCTCTAGAGGGACAACTCAAGCTTTATTGT
65 ACCT-TAGAGGGACAACTCAAGATTTATTGT
943947 ATATATA
1 ATATATA
943954 TAATATTATA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
94 9 0.10
95 77 0.90
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (94 bp):
ATATATAATCACCTTTATCAGACTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTA
CCTTAGAGGGACAACTCAAGATTTATTGT
Found at i:947763 original size:13 final size:13
Alignment explanation
Indices: 947747--947771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
947737 TTAATTAAGA
947747 AAATTAAAAGTTT
1 AAATTAAAAGTTT
947760 AAATTAAAAGTT
1 AAATTAAAAGTT
947772 AAGATAACGA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAATTAAAAGTTT
Found at i:948074 original size:11 final size:9
Alignment explanation
Indices: 948010--948084 Score: 60
Period size: 9 Copynumber: 7.7 Consensus size: 9
948000 ACCAACGAAT
948010 AAATAAATA
1 AAATAAATA
*
948019 CAATAAATGA
1 AAATAAAT-A
*
948029 AAAAAAATA
1 AAATAAATA
*
948038 AAATGAACATC
1 AAAT-AA-ATA
*
948049 AAAGAAATAA
1 AAATAAAT-A
948059 AAATAAAGTGA
1 AAATAAA-T-A
948070 AAATAAATA
1 AAATAAATA
948079 AAATAA
1 AAATAA
948085 TCAAATACAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
9 20 0.38
10 18 0.35
11 14 0.27
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (9 bp):
AAATAAATA
Found at i:948082 original size:26 final size:26
Alignment explanation
Indices: 948020--948084 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
948010 AAATAAATAC
948020 AATAAATGAAA-AAAAATAAAATGAA
1 AATAAATGAAATAAAAATAAAATGAA
* *
948045 CATCAAA-GAAATAAAAATAAAGTGAA
1 AAT-AAATGAAATAAAAATAAAATGAA
*
948071 AATAAATAAAATAA
1 AATAAATGAAATAA
948085 TCAAATACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
25 9 0.27
26 24 0.73
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (26 bp):
AATAAATGAAATAAAAATAAAATGAA
Found at i:948083 original size:20 final size:19
Alignment explanation
Indices: 948010--948084 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
948000 ACCAACGAAT
*
948010 AAATAAATACAATAAATGA
1 AAATAAATAAAATAAATGA
* *
948029 AAAAAAATAAAATGAACAT-C
1 AAATAAATAAAAT-AA-ATGA
*
948049 AAAGAAATAAAAATAAAGTGA
1 AAATAAAT-AAAATAAA-TGA
948070 AAATAAATAAAATAA
1 AAATAAATAAAATAA
948085 TCAAATACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 12 0.27
20 19 0.42
21 14 0.31
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (19 bp):
AAATAAATAAAATAAATGA
Found at i:948097 original size:40 final size:39
Alignment explanation
Indices: 948020--948098 Score: 90
Period size: 41 Copynumber: 2.0 Consensus size: 39
948010 AAATAAATAC
*
948020 AATAAATGAAAAAAAATAAAATGAACATCAAAGAAATAAA
1 AATAAATGAAAAAAAATAAAATGAACA-CAAACAAATAAA
*
948060 AATAAAGTGAAAATAAATAAAAT-AATCA-AATACAAATAA
1 AATAAA-TGAAAAAAAATAAAATGAA-CACAA-ACAAATAA
948099 TCAAATAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 2 0.06
40 15 0.44
41 17 0.50
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.18
Consensus pattern (39 bp):
AATAAATGAAAAAAAATAAAATGAACACAAACAAATAAA
Found at i:948098 original size:14 final size:13
Alignment explanation
Indices: 948074--948106 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
948064 AAGTGAAAAT
948074 AAATAAAATAATC
1 AAATAAAATAATC
948087 AAATACAAATAATC
1 AAATA-AAATAATC
948101 AAATAA
1 AAATAA
948107 TCAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAAATAATC
Found at i:948103 original size:8 final size:8
Alignment explanation
Indices: 948079--948114 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
948069 AAAATAAATA
948079 AAATAATC
1 AAATAATC
948087 AAAT-A-C
1 AAATAATC
948093 AAATAATC
1 AAATAATC
948101 AAATAATC
1 AAATAATC
948109 AAATAA
1 AAATAA
948115 AAATGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 5 0.19
7 2 0.08
8 19 0.73
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATAATC
Found at i:948106 original size:22 final size:23
Alignment explanation
Indices: 948069--948128 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
948059 AAATAAAGTG
948069 AAAATAAATAAAATAATCAAATA
1 AAAATAAATAAAATAATCAAATA
* *
948092 CAAAT-AATCAAATAATCAAATA
1 AAAATAAATAAAATAATCAAATA
* *
948114 AAAATGATTAAAATA
1 AAAATAAATAAAATA
948129 TATACATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAATAAATAAAATAATCAAATA
Found at i:953861 original size:22 final size:23
Alignment explanation
Indices: 953831--953876 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
953821 TGATTTTTGG
* *
953831 AATATTAAATATGATTTTTAATA
1 AATATTAAAAATGAATTTTAATA
953854 AATA-TAAAAATGAATTTTAATA
1 AATATTAAAAATGAATTTTAATA
953876 A
1 A
953877 GTGGCTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
AATATTAAAAATGAATTTTAATA
Found at i:954907 original size:4 final size:4
Alignment explanation
Indices: 954898--954957 Score: 52
Period size: 4 Copynumber: 14.8 Consensus size: 4
954888 GTTAGTAGAA
* **
954898 AAAT AAAT AAAAGT AAAA AAAT ATAAT -AAT AAAT AAAT AAAT -GTT AAAT
1 AAAT AAAT -AAA-T AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
954947 AAAT AAAT AAA
1 AAAT AAAT AAA
954958 AACAAATGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
3 4 0.09
4 31 0.69
5 9 0.20
6 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:954912 original size:18 final size:19
Alignment explanation
Indices: 954891--954926 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
954881 AAAAAATGTT
*
954891 AGTAGAAAAATA-AATAAA
1 AGTAAAAAAATATAATAAA
954909 AGTAAAAAAATATAATAA
1 AGTAAAAAAATATAATAA
954927 TAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AGTAAAAAAATATAATAAA
Found at i:954932 original size:30 final size:29
Alignment explanation
Indices: 954869--954964 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
954859 AAATTCTTCT
* *
954869 ATAAA-AAAAGTAAAAAAATGTTAGTAGAAAA
1 ATAAATAAAAGTAAAAAAAT-ATA--ATAAAA
954900 ATAAATAAAAGTAAAAAAATATAATAATAA
1 ATAAATAAAAGTAAAAAAATATAATAA-AA
* *
954930 ATAAATAAATGTTAAATAAATA-AATAAAA
1 ATAAATAAAAG-TAAAAAAATATAATAAAA
*
954959 ACAAAT
1 ATAAAT
954965 GGAAACAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
29 10 0.18
30 17 0.30
31 16 0.28
32 14 0.25
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (29 bp):
ATAAATAAAAGTAAAAAAATATAATAAAA
Found at i:954939 original size:34 final size:32
Alignment explanation
Indices: 954869--954938 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
954859 AAATTCTTCT
* *
954869 ATAAA-AAAAGTAAAAAAATGTTAGTAGAAAA
1 ATAAATAAAAGTAAAAAAATATTAATAGAAAA
*
954900 ATAAATAAAAGTAAAAAAATA-TAATA-ATAA
1 ATAAATAAAAGTAAAAAAATATTAATAGAAAA
954930 ATAAATAAA
1 ATAAATAAA
954939 TGTTAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 12 0.34
31 9 0.26
32 14 0.40
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (32 bp):
ATAAATAAAAGTAAAAAAATATTAATAGAAAA
Found at i:954954 original size:15 final size:14
Alignment explanation
Indices: 954898--954954 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
954888 GTTAGTAGAA
*
954898 AAATAAATAAAAGT
1 AAATAAATAAATGT
* *
954912 AAAAAAATATAATAAT
1 AAATAAATA-AAT-GT
954928 AAATAAATAAATGTT
1 AAATAAATAAATG-T
954943 AAATAAATAAAT
1 AAATAAATAAAT
954955 AAAAACAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 8 0.23
15 18 0.51
16 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (14 bp):
AAATAAATAAATGT
Found at i:955784 original size:16 final size:16
Alignment explanation
Indices: 955763--955814 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
955753 TGTTGCTTTG
*
955763 GTTTTTGATTTCTGTT
1 GTTTTTGTTTTCTGTT
*
955779 GTTTTT-TTTGTCTGTG
1 GTTTTTGTTT-TCTGTT
955795 GTTTTTTGTTTTCTG-T
1 G-TTTTTGTTTTCTGTT
955811 GTTT
1 GTTT
955815 GGCTTTGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 5 0.17
16 13 0.43
17 9 0.30
18 3 0.10
ACGTcount: A:0.02, C:0.06, G:0.21, T:0.71
Consensus pattern (16 bp):
GTTTTTGTTTTCTGTT
Found at i:956458 original size:10 final size:9
Alignment explanation
Indices: 956434--956496 Score: 74
Period size: 9 Copynumber: 6.8 Consensus size: 9
956424 TTAAACCTGG
956434 AAAA-AAAT
1 AAAATAAAT
*
956442 GAAATAAATT
1 AAAATAAA-T
956452 AAAATAAAT
1 AAAATAAAT
*
956461 AAAATGAAT
1 AAAATAAAT
956470 AAAATAAAAT
1 AAAAT-AAAT
956480 AAAATAAAT
1 AAAATAAAT
956489 AATAATAA
1 AA-AATAA
956497 TATACTAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
8 3 0.06
9 23 0.49
10 21 0.45
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
AAAATAAAT
Found at i:956475 original size:5 final size:5
Alignment explanation
Indices: 956437--956496 Score: 63
Period size: 5 Copynumber: 12.4 Consensus size: 5
956427 AACCTGGAAA
* * *
956437 AAAAT GAAAT AAATT AAAAT -AAAT AAAAT -GAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
956485 -AAAT AATAAT AA
1 AAAAT AA-AAT AA
956497 TATACTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
4 11 0.24
5 29 0.64
6 5 0.11
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:956505 original size:28 final size:28
Alignment explanation
Indices: 956443--956498 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
956433 GAAAAAAATG
*
956443 AAATAAATTAAAATAAATAAAATGAATA
1 AAATAAAATAAAATAAATAAAATGAATA
956471 AAATAAAATAAAATAAATAATAAT-AATA
1 AAATAAAATAAAATAAATAA-AATGAATA
956499 TACTAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (28 bp):
AAATAAAATAAAATAAATAAAATGAATA
Found at i:956591 original size:67 final size:69
Alignment explanation
Indices: 956513--956830 Score: 275
Period size: 67 Copynumber: 4.6 Consensus size: 69
956503 AAATATAATT
* * *
956513 TATATAATATATATATTTCAAAATAT-TTTTTTAAACTACATATTTTA-TTTT-AAAAA-GTTTT
1 TATATATTATATATATTTCAAAA-ATGTTTTTAAAACTATATATTTTAGTTTTAAAAAATGTTTT
956574 CAAAAC
65 -AAAAC
* * * * *
956580 TATATGTTATATAGT-TTTC-AAAATG-CTTTAAAAATAT-TATATAAGTTTTCAAAAAATGTTT
1 TATATATTATATA-TATTTCAAAAATGTTTTTAAAACTATATATTTTAGTTTT-AAAAAATGTTT
*
956641 TTAAAC
64 TAAAAC
*
956647 TATATATTATAT-TATTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTCAAAAAATA
1 TATATATTATATATA-TTTCAAAAATGTTTTTAAAACTATATATT-T-T-AGTTTT--AAAAA-A
*
956711 TTTTTTAAAAC
59 TGTTTTAAAAC
* *
956722 TATATATTATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATA-TTTT-AAAAATGTTTT
1 TATATATTATAT-ATATTTCAAAAATGTTTTTAAAACTATATATTTTAGTTTTAAAAAATGTTTT
956785 AAAAAC
65 -AAAAC
* *
956791 TATATACTATATA-AGTTTTC-AAAATGTTTTAAAAACTATA
1 TATATATTATATATA--TTTCAAAAATGTTTTTAAAACTATA
956831 CAGTATATAA
Statistics
Matches: 206, Mismatches: 24, Indels: 41
0.76 0.09 0.15
Matches are distributed among these distances:
64 5 0.02
65 15 0.07
66 3 0.01
67 39 0.19
68 38 0.18
69 34 0.17
70 3 0.01
71 1 0.00
72 4 0.02
73 6 0.03
74 6 0.03
75 22 0.11
76 29 0.14
77 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (69 bp):
TATATATTATATATATTTCAAAAATGTTTTTAAAACTATATATTTTAGTTTTAAAAAATGTTTTA
AAAC
Found at i:956815 original size:144 final size:148
Alignment explanation
Indices: 956570--956931 Score: 386
Period size: 144 Copynumber: 2.4 Consensus size: 148
956560 TTTTAAAAAG
* * * *
956570 TTTTCAAAACTATATGTTATAT-AGTTTTCAAAATG-CTTTAAAAATAT-TA-TATAAGTTTTCA
1 TTTTTAAAACTATATATTATATAAATTTTCAAAATGTTTTTAAAAATATATATTAT-A-TTTT--
* * * * * *
956631 AAAAATGTTTTTAAACTATATATTATATTATTTTCAAAAATGTTTTTAAAACTATATATTATAT-
62 AAAAATGTTTTAAAACTATATACTATATAATTTTCAAAAATGTTTTAAAAACTATACAGTATATA
956695 AAT-TTTTCAAAA-A-ATA-T-
127 AATGTTTTCAAAACATATATTA
* *
956712 TTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATATTTTAAA
1 TTTTTAAAACTATATATTATATAAATTTTC-AAAATGTTTTTAAAAATATATATTATATTTTAAA
956777 AATGTTTTAAAAACTATATACTATATAAGTTTTC-AAAATGTTTTAAAAACTATACAGTATATAA
65 AATGTTTT-AAAACTATATACTATATAA-TTTTCAAAAATGTTTTAAAAACTATACAGTATATAA
956841 ATGTTTTCAAAACTATATATTA
128 ATGTTTTCAAAAC-ATATATTA
* *
956863 TATTTTCAAAAACTATATAATATATAAATTTTCGAAAATCGTTTTCTGAAAATTATATATTATAT
1 T-TTTT--AAAACTATATATTATATAAATTTTC-AAAAT-GTTTT-T-AAAAATATATATTATAT
956928 TTTA
59 TTTA
956932 TCAAAAACAT
Statistics
Matches: 185, Mismatches: 15, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
142 20 0.11
143 17 0.09
144 47 0.25
145 22 0.12
146 12 0.06
147 3 0.02
148 1 0.01
149 3 0.02
150 1 0.01
151 1 0.01
152 4 0.02
154 28 0.15
155 5 0.03
156 1 0.01
157 20 0.11
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (148 bp):
TTTTTAAAACTATATATTATATAAATTTTCAAAATGTTTTTAAAAATATATATTATATTTTAAAA
ATGTTTTAAAACTATATACTATATAATTTTCAAAAATGTTTTAAAAACTATACAGTATATAAATG
TTTTCAAAACATATATTA
Found at i:956874 original size:22 final size:21
Alignment explanation
Indices: 956834--956887 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
956824 AACTATACAG
*
956834 TATATAA-ATGTTTTCAAAAC
1 TATATAATATATTTTCAAAAC
*
956854 TATATATTATATTTTCAAAAAC
1 TATATAATATATTTTC-AAAAC
956876 TATATAATATAT
1 TATATAATATAT
956888 AAATTTTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 16 0.55
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (21 bp):
TATATAATATATTTTCAAAAC
Found at i:956972 original size:2 final size:2
Alignment explanation
Indices: 956960--957008 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
956950 ACTATATTAC
* *
956960 TA TA TA CA TA TA TA TA TA -A TA -A AA TGA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
957001 TA TA TA TA
1 TA TA TA TA
957009 ACAAAATAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:961257 original size:19 final size:20
Alignment explanation
Indices: 961225--961272 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
961215 TCTAAATCAT
* *
961225 TTTTTAAAATTTCATTTTGG
1 TTTTCAAAATTTCATTTTAG
961245 TTTTCAAAA-TTCATTTTAG
1 TTTTCAAAATTTCATTTTAG
*
961264 CTTTCAAAA
1 TTTTCAAAA
961273 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTAG
Found at i:961967 original size:20 final size:20
Alignment explanation
Indices: 961942--962016 Score: 141
Period size: 20 Copynumber: 3.8 Consensus size: 20
961932 TTGGGGCCTG
961942 ATGGTATCGATACTATAACT
1 ATGGTATCGATACTATAACT
961962 ATGGTATCGATACTATAACT
1 ATGGTATCGATACTATAACT
*
961982 ATGGTATTGATACTATAACT
1 ATGGTATCGATACTATAACT
962002 ATGGTATCGATACTA
1 ATGGTATCGATACTA
962017 CTATACAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (20 bp):
ATGGTATCGATACTATAACT
Found at i:962873 original size:21 final size:20
Alignment explanation
Indices: 962847--962885 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
962837 AACAATTTGT
962847 CAGTATCAATACTGAGCCTAC
1 CAGTATCAATACT-AGCCTAC
*
962868 CAGTATCGATACTAGCCT
1 CAGTATCAATACTAGCCT
962886 TAGGGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (20 bp):
CAGTATCAATACTAGCCTAC
Found at i:962911 original size:17 final size:19
Alignment explanation
Indices: 962870--962916 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
962860 GAGCCTACCA
*
962870 GTATCGATACTAGCCTTAGG
1 GTATCGATACTAGACTTA-G
962890 GTATCGATACT-GACTT-G
1 GTATCGATACTAGACTTAG
*
962907 GTATCAATAC
1 GTATCGATAC
962917 CACATTTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.40
19 4 0.16
20 11 0.44
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (19 bp):
GTATCGATACTAGACTTAG
Found at i:966077 original size:21 final size:20
Alignment explanation
Indices: 966053--966121 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
966043 GAATGAACAA
966053 TATCGATACTGATTGAAGTA-G
1 TATCGATACTGA-TG-AGTAGG
*
966074 TATCGATACTGATGTGTAGG
1 TATCGATACTGATGAGTAGG
* *
966094 TATCGATAC-CAGGAGTAAGG
1 TATCGATACTGATGAGT-AGG
966114 TATCGATA
1 TATCGATA
966122 GTGTAATTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.17
20 23 0.55
21 12 0.29
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGATACTGATGAGTAGG
Found at i:966098 original size:20 final size:20
Alignment explanation
Indices: 966053--966102 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
966043 GAATGAACAA
966053 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
*
966074 TATCGATACTGATGTGTAG-G
1 TATCGATACTGAT-TGAAGAG
966094 TATCGATAC
1 TATCGATAC
966103 CAGGAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:966996 original size:24 final size:24
Alignment explanation
Indices: 966956--967068 Score: 90
Period size: 24 Copynumber: 4.8 Consensus size: 24
966946 GAGTCGAGGG
* *
966956 TTCTACGTTGTCCTTCGGAACAAA
1 TTCTACGTGGTCATTCGGAACAAA
966980 TTCTACGTGGTCATTC-GAGACAAA
1 TTCTACGTGGTCATTCGGA-ACAAA
* * *
967004 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGTGGTCATTCGGAACAAA
* ** *
967028 -TCTATGTGG-CACTTCGGTGCATA
1 TTCTACGTGGTCA-TTCGGAACAAA
967051 TTCTACGTGG-CACTTCGG
1 TTCTACGTGGTCA-TTCGG
967069 TGCAAATTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.01
23 17 0.23
24 54 0.74
25 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (24 bp):
TTCTACGTGGTCATTCGGAACAAA
Found at i:968726 original size:57 final size:54
Alignment explanation
Indices: 968627--968755 Score: 145
Period size: 57 Copynumber: 2.3 Consensus size: 54
968617 TTTGAGACTT
* * * **
968627 TCAAGAAATAAATTCAACAAATTTTTTTTACAAGATAGAATCATATTTGATTC-
1 TCAAGAAATAAATTCAACAAATTTCTTTTACAAAACAGAATCATATAAGATTCA
968680 TCAAGAAATAAATTCAACAATTTAATTTCTTTTACAAAACAGAATCATATAAGATTCA
1 TCAAGAAATAAATTCAAC-A---AATTTCTTTTACAAAACAGAATCATATAAGATTCA
*
968738 T-AGGAAAATAAATTCAAC
1 TCAAG-AAATAAATTCAAC
968756 TTTTTATTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
53 18 0.28
54 1 0.02
57 31 0.48
58 14 0.22
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (54 bp):
TCAAGAAATAAATTCAACAAATTTCTTTTACAAAACAGAATCATATAAGATTCA
Found at i:968782 original size:58 final size:60
Alignment explanation
Indices: 968685--968831 Score: 151
Period size: 58 Copynumber: 2.5 Consensus size: 60
968675 GATTCTCAAG
* * *
968685 AAATAAATTCAACAATTTAATTT-CTTTTACAAAACAGAATC-ATATAAGATTC-ATAGG-A
1 AAATAAATTCAAC-TTTTTATTTCCTTTTACAAAACAGAATCAATACAAGATTCTA-AGGTA
** *
968743 AAATAAATTCAACTTTTTATTTCCTTTT-CAAAGTTAGAATCAATACAAGATTCTAAGGTG
1 AAATAAATTCAACTTTTTATTTCCTTTTACAAA-ACAGAATCAATACAAGATTCTAAGGTA
* *
968803 AAATATATTCAACTATTTATTTCCCTTTT
1 AAATAAATTCAACTTTTTATTT-CCTTTT
968832 TTCAATTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
57 11 0.15
58 24 0.32
59 13 0.17
60 21 0.28
61 6 0.08
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (60 bp):
AAATAAATTCAACTTTTTATTTCCTTTTACAAAACAGAATCAATACAAGATTCTAAGGTA
Found at i:972410 original size:20 final size:21
Alignment explanation
Indices: 972382--972424 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
972372 TTACCTAAAG
972382 AGAAAGAAA-AGAAAGATTTT
1 AGAAAGAAAGAGAAAGATTTT
* **
972402 AGAAGGAAAGAGAGTGATTTT
1 AGAAAGAAAGAGAAAGATTTT
972423 AG
1 AG
972425 TGTGTGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (21 bp):
AGAAAGAAAGAGAAAGATTTT
Found at i:975166 original size:80 final size:80
Alignment explanation
Indices: 975055--975206 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 80
975045 ATTTTTATAT
* * * * *
975055 AAAATATATTTTGGGAGTCGTCATTGACCTTTTTGGGTTAGGTAGGTCAAATACCTAAAAAAAAA
1 AAAATATATTTTGGGAATCGCCATCGACC-TTTTGGATCAGGTAGGTCAAATACCT-AAAAAAAA
975120 TCTTTTAAATGGTTTTG
64 TCTTTTAAATGGTTTTG
* * *
975137 AAAATA-ATTTT-GGAATCGCCATCGGCCTTTTGGATCAGGTAGGTCGAATACCTAAAAAATATC
1 AAAATATATTTTGGGAATCGCCATCGACCTTTTGGATCAGGTAGGTCAAATACCTAAAAAAAATC
975200 TTTTAAA
66 TTTTAAA
975207 AGAGTTTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 16 0.26
79 23 0.37
80 12 0.19
81 5 0.08
82 6 0.10
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (80 bp):
AAAATATATTTTGGGAATCGCCATCGACCTTTTGGATCAGGTAGGTCAAATACCTAAAAAAAATC
TTTTAAATGGTTTTG
Found at i:977460 original size:46 final size:46
Alignment explanation
Indices: 977213--978119 Score: 1559
Period size: 46 Copynumber: 19.8 Consensus size: 46
977203 GATGGAAATG
* * *
977213 TTTGAAAACATCATGTACTGAAGGTCTTACAGATGACCCGAAGG-C
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
977258 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
977303 TTTGAAAACATCAAGCACTGAAGGGATTACAGATGACCCGAAGG-T
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
977348 TTTGAAAACATCAAGCACTGAAGGGCTTATAGATGACCCGAAGGTTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
* *
977395 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
977441 TTTGATAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
977487 TTTGATAACATCATGCAGTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
977533 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
977579 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
977625 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
977671 TTTGAAAACATCATGCATTGAAGGGCTTACAAATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
977717 TTTGAAAACATCATGCACTGAAGGGCTTACAAATAACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
977763 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
977809 TTTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
977855 TTTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * *
977901 TTTGAAAACACCATGCACTGAAGGGCTTACAAATGACTCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
977947 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
977993 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
978039 TTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
978085 TTTGAAAACATCATGCACTAAAGGGCTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
978120 TGGGAAATAG
Statistics
Matches: 822, Mismatches: 38, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
45 127 0.15
46 654 0.80
47 41 0.05
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (46 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:978839 original size:22 final size:22
Alignment explanation
Indices: 978772--978849 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
978762 AATAAAGCTT
* *
978772 TCATCTTTGAAAAAAAGAATCTA
1 TCATCTTTG-AAGAAAGAGTCTA
* * * *
978795 TCATTTTTAAAG-AGGTAGGCTA
1 TCATCTTTGAAGAAAG-AGTCTA
978817 TCATCTTTGAAGAAAGAGTCTA
1 TCATCTTTGAAGAAAGAGTCTA
978839 TCATCTTTGAA
1 TCATCTTTGAA
978850 AAGTGTAGAT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 2 0.05
22 32 0.74
23 9 0.21
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAAAGAGTCTA
Found at i:990406 original size:3 final size:3
Alignment explanation
Indices: 990398--990428 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
990388 TATTTTTATT
990398 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
990429 TTAAATAATT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:992067 original size:31 final size:30
Alignment explanation
Indices: 992035--992091 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
992025 GCTCGCGAGT
992035 TTTC-AAATCGAGTCGAGCTCCATTTTAGAG
1 TTTCTAAATCGAGTCGA-CTCCATTTTAGAG
* *
992065 TTTCTGAGTCGAGTCGACTCCATTTTA
1 TTTCTAAATCGAGTCGACTCCATTTTA
992092 CAACCAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (30 bp):
TTTCTAAATCGAGTCGACTCCATTTTAGAG
Found at i:992902 original size:5 final size:5
Alignment explanation
Indices: 992894--992919 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
992884 TTTTATTATT
992894 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
992920 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1000449 original size:17 final size:17
Alignment explanation
Indices: 1000429--1000462 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1000419 TCAATAAATT
1000429 AAATTCT-TCATATTTAA
1 AAATTCTATCA-ATTTAA
1000446 AAATTCTATCAATTTAA
1 AAATTCTATCAATTTAA
1000463 TTCTTGTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTCTATCAATTTAA
Found at i:1002216 original size:15 final size:15
Alignment explanation
Indices: 1002196--1002226 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1002186 CAACCAGAGA
1002196 AAAGGAACACAAAAG
1 AAAGGAACACAAAAG
1002211 AAAGGAACACAAAAG
1 AAAGGAACACAAAAG
1002226 A
1 A
1002227 TAACCACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.13, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGGAACACAAAAG
Found at i:1005246 original size:45 final size:47
Alignment explanation
Indices: 1005173--1005278 Score: 162
Period size: 45 Copynumber: 2.3 Consensus size: 47
1005163 TTTATTTTCG
1005173 TTTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTTGAAT-AATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
1005220 TTTTTTGAATAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTT
1 TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
1005266 TTTTTGTGAATAA
1 TTTTT-TGAATAA
1005279 CAAAGCATGG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
45 28 0.51
46 10 0.18
47 17 0.31
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:1016028 original size:55 final size:55
Alignment explanation
Indices: 1015956--1016446 Score: 679
Period size: 55 Copynumber: 8.9 Consensus size: 55
1015946 TTGAAGCATC
1015956 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * * *
1016011 AATATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGAAGGCACG-TTCGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATT-GTTG
* *
1016066 AAGATTGTCCGAGTCTTATATTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
** *
1016121 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGGTACG-TTCATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATT-GTTG
* *
1016176 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * * * *
1016231 AGGATTGTTCGAGTCTCATACTCTCTGGA-AAATAGGGAGTAGACACGATTATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * * *
1016285 AGGATTGCTCGAGTCTCATACTCTCTGGAA-AAATAGGGAGCAGACACGATTATTG
1 AAGATTGTTCGAGTCTTATACTCTCT-GAAGAAATAGGGAGCAGACACGATTGTTG
* * *
1016340 AGGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACG-TTCGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATT-GTTG
*
1016395 AAGATTGTTTGAGTCTTATACTCTCTGGAAG-AATAGGGAGCAGACACGATTG
1 AAGATTGTTCGAGTCTTATACTCTCT-GAAGAAATAGGGAGCAGACACGATTG
1016447 ACGAAGATAT
Statistics
Matches: 396, Mismatches: 31, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
54 59 0.15
55 327 0.83
56 10 0.03
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
Found at i:1016373 original size:219 final size:220
Alignment explanation
Indices: 1015956--1016462 Score: 740
Period size: 219 Copynumber: 2.3 Consensus size: 220
1015946 TTGAAGCATC
* *
1015956 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAATATTATTC
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTATTC
* * * *
1016021 GAGTCTTATACTCTCTGAAGAAATAGGGAGAAGGCACGTTCGTTGAAGATTGTCCGAGTCTTATA
66 GAGTCTCATACTCTCTGAAGAAATAGGGAGAAGACACGTTCATTGAAGATTGTCCGAGTCTCATA
* * *
1016086 TTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
131 CTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAG
*
1016151 AAATAGGGAGCAGGTACGTTCATTG
196 AAATAGGGAGCAGGCACGTTCATTG
* * *
1016176 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTATTGAGGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTATTC
* * *
1016241 GAGTCTCATACTCTCTGGA-AAATAGGGAGTAGACACGATT-ATTGAGGATTG-CTCGAGTCTCA
66 GAGTCTCATACTCTCTGAAGAAATAGGGAGAAGACACG-TTCATTGAAGATTGTC-CGAGTCTCA
*
1016303 TACTCTCTGGAA-AAATAGGGAGCAGACACGATTATTGAGGATTGTTCGAGTCTCATACTCTCTG
129 TACTCTCT-GAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTCGAGTCTCATACTCTCTG
*
1016367 AAGAAATAGGGAGCAGGCACGTTCGTTG
193 AAGAAATAGGGAGCAGGCACGTTCATTG
* *
1016395 AAGATTGTTTGAGTCTTATACTCTCTGGAAG-AATAGGGAGCAGACACGATTGA-CGAAGA-TAT
1 AAGATTGTTCGAGTCTTATACTCTCT-GAAGAAATAGGGAGCAGACACGATT-ATTGAAGATTAT
1016457 TCGAGT
64 TCGAGT
1016463 TTTACCCCCT
Statistics
Matches: 259, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
218 9 0.03
219 163 0.63
220 87 0.34
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (220 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTATTC
GAGTCTCATACTCTCTGAAGAAATAGGGAGAAGACACGTTCATTGAAGATTGTCCGAGTCTCATA
CTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAG
AAATAGGGAGCAGGCACGTTCATTG
Found at i:1017378 original size:15 final size:15
Alignment explanation
Indices: 1017358--1017388 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1017348 CAACCAGAGA
*
1017358 AAAGGAAGACAAAAG
1 AAAGGAACACAAAAG
1017373 AAAGGAACACAAAAG
1 AAAGGAACACAAAAG
1017388 A
1 A
1017389 TAACCACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.10, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGGAACACAAAAG
Found at i:1020430 original size:2 final size:2
Alignment explanation
Indices: 1020425--1020454 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1020415 ATCACACATC
1020425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1020455 TACATAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1024233 original size:12 final size:12
Alignment explanation
Indices: 1024216--1024260 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1024206 ACTATACTGT
1024216 ATGAACAGTACC
1 ATGAACAGTACC
* **
1024228 ATGAACAATATT
1 ATGAACAGTACC
1024240 ATGAACAGTACC
1 ATGAACAGTACC
1024252 ATGAACAGT
1 ATGAACAGT
1024261 GAAAATTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:1025701 original size:205 final size:205
Alignment explanation
Indices: 1025349--1025758 Score: 820
Period size: 205 Copynumber: 2.0 Consensus size: 205
1025339 GATCGTGATC
1025349 CCAAGTTTAGTCTCGAATTCCTTCAAGAAGTTCAGCATTACCTACAAAATCAAGTGCTCAATGGT
1 CCAAGTTTAGTCTCGAATTCCTTCAAGAAGTTCAGCATTACCTACAAAATCAAGTGCTCAATGGT
1025414 CAGCTTACGAACCAGTTAGCCACTAAACTTTTAGTCCGTTGCATTAAAGTTTACACATGAAGGCC
66 CAGCTTACGAACCAGTTAGCCACTAAACTTTTAGTCCGTTGCATTAAAGTTTACACATGAAGGCC
1025479 TCATGTACCTCAGGTTGGTAGTTAATAGCCAATACAACTTCAGTTACTCCAACAGCCTTGAGGGC
131 TCATGTACCTCAGGTTGGTAGTTAATAGCCAATACAACTTCAGTTACTCCAACAGCCTTGAGGGC
1025544 CTCAATCTGA
196 CTCAATCTGA
1025554 CCAAGTTTAGTCTCGAATTCCTTCAAGAAGTTCAGCATTACCTACAAAATCAAGTGCTCAATGGT
1 CCAAGTTTAGTCTCGAATTCCTTCAAGAAGTTCAGCATTACCTACAAAATCAAGTGCTCAATGGT
1025619 CAGCTTACGAACCAGTTAGCCACTAAACTTTTAGTCCGTTGCATTAAAGTTTACACATGAAGGCC
66 CAGCTTACGAACCAGTTAGCCACTAAACTTTTAGTCCGTTGCATTAAAGTTTACACATGAAGGCC
1025684 TCATGTACCTCAGGTTGGTAGTTAATAGCCAATACAACTTCAGTTACTCCAACAGCCTTGAGGGC
131 TCATGTACCTCAGGTTGGTAGTTAATAGCCAATACAACTTCAGTTACTCCAACAGCCTTGAGGGC
1025749 CTCAATCTGA
196 CTCAATCTGA
1025759 AAACATCCAA
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 205 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (205 bp):
CCAAGTTTAGTCTCGAATTCCTTCAAGAAGTTCAGCATTACCTACAAAATCAAGTGCTCAATGGT
CAGCTTACGAACCAGTTAGCCACTAAACTTTTAGTCCGTTGCATTAAAGTTTACACATGAAGGCC
TCATGTACCTCAGGTTGGTAGTTAATAGCCAATACAACTTCAGTTACTCCAACAGCCTTGAGGGC
CTCAATCTGA
Found at i:1028355 original size:17 final size:16
Alignment explanation
Indices: 1028333--1028390 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
1028323 CTTAAATATT
1028333 TTTTATTAATATTTTAA
1 TTTTATT-ATATTTTAA
*
1028350 TTTTA-TATATCTTAA
1 TTTTATTATATTTTAA
1028365 TTTT-TTATACTTTTAAA
1 TTTTATTATA-TTTT-AA
*
1028382 TATTATTAT
1 TTTTATTAT
1028391 CTAACATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 16 0.47
16 4 0.12
17 10 0.29
18 4 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTATTATATTTTAA
Found at i:1033016 original size:21 final size:21
Alignment explanation
Indices: 1032990--1033034 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1032980 GATTTCTGGG
* *
1032990 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1033011 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1033032 CAA
1 CAA
1033035 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1034536 original size:32 final size:31
Alignment explanation
Indices: 1034494--1034621 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
1034484 AGAGTCGAGG
1034494 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
1034525 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
1034557 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
1034588 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
1034619 GTT
1 GTT
1034622 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
31 54 0.66
32 28 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1037484 original size:21 final size:21
Alignment explanation
Indices: 1037458--1037502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1037448 GATTTCTGGG
* *
1037458 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1037479 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1037500 CAA
1 CAA
1037503 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1039001 original size:32 final size:31
Alignment explanation
Indices: 1038959--1039086 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
1038949 AGAGTCGAGG
1038959 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
1038990 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
1039022 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
1039053 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
1039084 GTT
1 GTT
1039087 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
31 54 0.66
32 28 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1039106 original size:30 final size:30
Alignment explanation
Indices: 1039045--1039141 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
1039035 CTAAGGAACA
* * ***
1039045 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
1039076 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
1039106 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
1039136 TCTGGA
1 TATGGA
1039142 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Done.