Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000807.1 Hibiscus syriacus cultivar Beakdansim tig00001565_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: 66092
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:2159 original size:21 final size:20
Alignment explanation
Indices: 2128--2169 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
2118 AAAAATATAA
2128 ATAAAATATTTAAATATCTTAT
1 ATAAAATATTTAAA-AT-TTAT
2150 ATAAAA-ATTTAAAATTTAT
1 ATAAAATATTTAAAATTTAT
2169 A
1 A
2170 CCGCCCCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 7 0.35
22 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAATATTTAAAATTTAT
Found at i:3168 original size:13 final size:14
Alignment explanation
Indices: 3144--3172 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3134 GAAAAATTAT
3144 ATAAAAACTATTTC
1 ATAAAAACTATTTC
3158 ATAAAAA-TATTTC
1 ATAAAAACTATTTC
3171 AT
1 AT
3173 TTCTAGGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAAAAACTATTTC
Found at i:3318 original size:29 final size:28
Alignment explanation
Indices: 3273--3328 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3263 TTTTTTCTAA
*
3273 AAAATTTAGGGTCTAATTAAAATTTTTG
1 AAAATTTAGGGTCTAATGAAAATTTTTG
*
3301 AAAATTTGAGAGGT-TAATGAGAATTTTT
1 AAAATTT-AG-GGTCTAATGAAAATTTTT
3329 AAATATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
29 14 0.58
30 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (28 bp):
AAAATTTAGGGTCTAATGAAAATTTTTG
Found at i:11134 original size:29 final size:29
Alignment explanation
Indices: 11089--11222 Score: 119
Period size: 29 Copynumber: 4.6 Consensus size: 29
11079 TTCGATTTCT
* *
11089 TTTAATTTCTG-TCATTTACATTTTTGATC
1 TTTAATTTATGCT-ATTTACATTTTTGACC
* * * *
11118 TTTAGTTTATGCTATTTATATTTATGCCC
1 TTTAATTTATGCTATTTACATTTTTGACC
* **
11147 TTTAATTTATGTTATTTACA-TTTCCACCC
1 TTTAATTTATGCTATTTACATTTTTGA-CC
* *
11176 TTTAATTTCTGCTATTTACATTTTTGCCC
1 TTTAATTTATGCTATTTACATTTTTGACC
* *
11205 TTTAATTTCTGTTATTTA
1 TTTAATTTATGCTATTTA
11223 TACTTCTACC
Statistics
Matches: 83, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
28 2 0.02
29 77 0.93
30 4 0.05
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.57
Consensus pattern (29 bp):
TTTAATTTATGCTATTTACATTTTTGACC
Found at i:11153 original size:58 final size:58
Alignment explanation
Indices: 11089--11222 Score: 171
Period size: 58 Copynumber: 2.3 Consensus size: 58
11079 TTCGATTTCT
* ** * * *
11089 TTTAATTTCTGTCATTTACATTTTTGA-TCTTTAGTTTATGCTATTTATATTTATGCCC
1 TTTAATTTCTGTTATTTACA-TTTCCACCCTTTAATTTATGCTATTTACATTTATGCCC
* * *
11147 TTTAATTTATGTTATTTACATTTCCACCCTTTAATTTCTGCTATTTACATTTTTGCCC
1 TTTAATTTCTGTTATTTACATTTCCACCCTTTAATTTATGCTATTTACATTTATGCCC
11205 TTTAATTTCTGTTATTTA
1 TTTAATTTCTGTTATTTA
11223 TACTTCTACC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 4 0.06
58 61 0.94
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.57
Consensus pattern (58 bp):
TTTAATTTCTGTTATTTACATTTCCACCCTTTAATTTATGCTATTTACATTTATGCCC
Found at i:11222 original size:14 final size:14
Alignment explanation
Indices: 11089--11222 Score: 54
Period size: 14 Copynumber: 9.3 Consensus size: 14
11079 TTCGATTTCT
11089 TTTAATTTCTG-TCA
1 TTTAATTTCTGCT-A
* * *
11103 TTTACATTTTTGATC
1 TTTA-ATTTCTGCTA
* *
11118 TTTAGTTTATGCTA
1 TTTAATTTCTGCTA
* **
11132 TTTATATTTATGCCC
1 TTTA-ATTTCTGCTA
* *
11147 TTTAATTTATGTTA
1 TTTAATTTCTGCTA
** **
11161 TTTACATTTCCACCC
1 TTTA-ATTTCTGCTA
11176 TTTAATTTCTGCTA
1 TTTAATTTCTGCTA
* **
11190 TTTACATTTTTGCCC
1 TTTA-ATTTCTGCTA
*
11205 TTTAATTTCTGTTA
1 TTTAATTTCTGCTA
11219 TTTA
1 TTTA
11223 TACTTCTACC
Statistics
Matches: 86, Mismatches: 29, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
14 45 0.52
15 40 0.47
16 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTAATTTCTGCTA
Found at i:11750 original size:12 final size:13
Alignment explanation
Indices: 11735--11796 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 13
11725 TTAAAATATA
11735 TATTATAT-TTAT
1 TATTATATATTAT
*
11747 TATTATATACTA-
1 TATTATATATTAT
* *
11759 TAGTAT-GATTAT
1 TATTATATATTAT
11771 TATTAT-TATTAT
1 TATTATATATTAT
11783 TATTAT-TATTAT
1 TATTATATATTAT
11795 TA
1 TA
11797 ATACAAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
11 3 0.07
12 37 0.88
13 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:11751 original size:3 final size:3
Alignment explanation
Indices: 11743--11796 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
11733 TATATTATAT
* * *
11743 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11788 TTA TTA TTA
1 TTA TTA TTA
11797 ATACAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:20892 original size:33 final size:32
Alignment explanation
Indices: 20759--20925 Score: 237
Period size: 32 Copynumber: 5.2 Consensus size: 32
20749 AAGCAATAAA
* *
20759 GGGCATC-TTGGAAGATTCAACATCATATATTG
1 GGGCATCTTTGG-AGATTCAACATCAAATGTTG
*
20791 GGGTATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
20823 GGGTATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
20855 GGGCATCTTTGGAGATTCAACATCAAATTGTTG
1 GGGCATCTTTGGAGATTCAACATCAAA-TGTTG
* ** *
20888 GGGCATCTTTGGAGATTCAATATTGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
20920 GGGCAT
1 GGGCAT
20926 TCAATATCCT
Statistics
Matches: 125, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
32 92 0.74
33 33 0.26
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:21077 original size:34 final size:34
Alignment explanation
Indices: 21034--21119 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
21024 AAAAAAAAAA
* *
21034 TTGTGTCACTTGAGATAATTTCTCAAAACAAATT
1 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
21068 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
1 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
** *
21102 CCGTCTCGCTTGAGACAA
1 TTGTCTCACTTGAGACAA
21120 ATTTTCTCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (34 bp):
TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
Found at i:21495 original size:36 final size:36
Alignment explanation
Indices: 21448--21809 Score: 300
Period size: 36 Copynumber: 10.1 Consensus size: 36
21438 CGAAACAGAA
21448 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * *
21484 AAATTTTGTCTCCCTTGACACAATTTCTCTCGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
21520 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * *
21556 AAATTTTGTCTCCTTTAAGACGGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * *
21592 AAATTTTGTCTCCCTTGAGACAATCTCCCTTGAGAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * *
21628 --A----GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
1 AAATTTTGTCTCCCTTGAGAC--A----GTTTCCCTTGAAAC
* * * *
21664 --A-GTT-TCT--CTCGAAACAAATTTATCTCCCTTGGAAA-
1 AAATTTTGTCTCCCTTGAGAC--A-GT-T-TCCCTT-GAAAC
* * *
21699 ATATTTTGTCTCCCTTGAGACAGTTTCCATTAAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* *
21735 AAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* *
21771 AAATTTTGTCTCCCTTGAGACAATTTCACTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
21807 AAA
1 AAA
21810 AGATTTTATC
Statistics
Matches: 267, Mismatches: 40, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
30 12 0.04
32 1 0.00
33 2 0.01
34 1 0.00
35 9 0.03
36 225 0.84
37 2 0.01
38 5 0.02
39 4 0.01
41 6 0.02
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
Found at i:21499 original size:21 final size:21
Alignment explanation
Indices: 21473--21568 Score: 72
Period size: 21 Copynumber: 5.1 Consensus size: 21
21463 TGAGACAGTT
21473 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
21494 TCCCTTGACAC-AA--TT-TC
1 TCCCTTGAAACAAATTTTGTC
*
21511 T--CTCGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
21530 TCCCTTGAGAC--A----GTT
1 TCCCTTGAAACAAATTTTGTC
21545 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
21566 TCC
1 TCC
21569 TTTAAGACGG
Statistics
Matches: 55, Mismatches: 8, Indels: 24
0.63 0.09 0.28
Matches are distributed among these distances:
15 18 0.33
16 2 0.04
17 4 0.07
18 4 0.07
19 4 0.07
20 2 0.04
21 21 0.38
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.36
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:21620 original size:15 final size:15
Alignment explanation
Indices: 21600--21644 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
21590 ACAAATTTTG
21600 TCTCCCTTGAGACAA
1 TCTCCCTTGAGACAA
*
21615 TCTCCCTTGAGACAG
1 TCTCCCTTGAGACAA
* *
21630 TTTCCCTTGAAACAA
1 TCTCCCTTGAGACAA
21645 ATTTTGTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (15 bp):
TCTCCCTTGAGACAA
Found at i:21633 original size:51 final size:51
Alignment explanation
Indices: 21564--21664 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
21554 ACAAATTTTG
* *
21564 TCTCCTTTAAGACGGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
1 TCTCCCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
*
21615 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 TCTCCCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
21665 GTTTCTCTCG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.35
Consensus pattern (51 bp):
TCTCCCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
Found at i:21658 original size:21 final size:20
Alignment explanation
Indices: 21632--21716 Score: 56
Period size: 21 Copynumber: 4.4 Consensus size: 20
21622 TGAGACAGTT
21632 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAA-TTTGTC
* *
21653 TCCCTTGAGAC--AGTT-TC
1 TCCCTTGAAACAAATTTGTC
* *
21670 T--CTCGAAACAAATTTATC
1 TCCCTTGAAACAAATTTGTC
*
21688 TCCCTTGGAAA-ATATTTTGTC
1 TCCCTT-GAAACA-AATTTGTC
21709 TCCCTTGA
1 TCCCTTGA
21717 GACAGTTTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
15 6 0.12
17 6 0.12
18 5 0.10
19 1 0.02
20 5 0.10
21 26 0.53
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.38
Consensus pattern (20 bp):
TCCCTTGAAACAAATTTGTC
Found at i:21735 original size:56 final size:56
Alignment explanation
Indices: 21581--21740 Score: 163
Period size: 56 Copynumber: 2.9 Consensus size: 56
21571 TAAGACGGTT
* * * ** * *
21581 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATCTCCCTTGAGAC--A-GT-T-
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTCAAAACAAATTTATC
*
21632 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTCGAAACAAATTTATC
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTCAAAACAAATTTATC
* *
21688 TCCCTTGGAAA-ATATTTTGTCTCCCTTGAGACAGTTTC-CATTAAAACAAATTT
1 TCCCTT-GAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC-TCAAAACAAATTT
21741 TGTCTCTCTT
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
51 42 0.45
53 1 0.01
54 1 0.01
55 2 0.02
56 43 0.46
57 4 0.04
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (56 bp):
TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTCAAAACAAATTTATC
Found at i:21937 original size:43 final size:43
Alignment explanation
Indices: 21876--22106 Score: 221
Period size: 43 Copynumber: 5.1 Consensus size: 43
21866 CCTGATTTTC
*
21876 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
** *
21919 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCGTCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
* **
21962 AGGGGTTCCTTGATGAAAAATTTGATGACAAACTTGAAGGACCATCGTGATATGT
1 AGGGGTTTCTTGATG-AAAAGCT--TG----A---GAA--ACCATCGTGATATGT
* * *
22017 AGGGG-TTCTTTGAGGACAAGCTTGAGAAATCATCGTGATATGT
1 AGGGGTTTC-TTGATGAAAAGCTTGAGAAACCATCGTGATATGT
* **
22060 AGGGGTTTCTTGATAAAAAGCTTGAGGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
22103 AGGG
1 AGGG
22107 ATTCCTTGGT
Statistics
Matches: 152, Mismatches: 22, Indels: 28
0.75 0.11 0.14
Matches are distributed among these distances:
43 104 0.68
44 8 0.05
45 3 0.02
46 2 0.01
48 1 0.01
50 1 0.01
52 2 0.01
53 1 0.01
54 6 0.04
55 24 0.16
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (43 bp):
AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
Found at i:22462 original size:90 final size:90
Alignment explanation
Indices: 22135--22714 Score: 966
Period size: 90 Copynumber: 6.4 Consensus size: 90
22125 AGAAACTGAG
*
22135 CTTGATTTTTAAGTCCTTCGGGCCATTCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
1 CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
22200 TAAGAAACTGAGCCTTCGGGGGTTT
66 TAAGAAACTGAGCCTTCGGGGGTTT
* * * * *
22225 CTTGA-TTTTAAGTCATTCGGGTCATCCGTAAGACCTTCAGTGCAGTATGTTTTCAAATGAGATT
1 CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
22289 TAAGAAACTGAGCCTTCGGGGGTTT
66 TAAGAAACTGAGCCTTCGGGGGTTT
22314 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
*
22379 CTAAGAAACTGAGCCTTCAGGGGTTT
65 CTAAGAAACTGAGCCTTCGGGGGTTT
* * *
22405 CTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAGGATATTTTCAAATGAGATT
1 CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
22470 TAAGAAACTGAGCCTTCGGGGGTTT
66 TAAGAAACTGAGCCTTCGGGGGTTT
22495 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
22560 CTAAGAAACTGAGCCTTCGGGGGTTT
65 CTAAGAAACTGAGCCTTCGGGGGTTT
* * *
22586 CTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATT
1 CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
*
22651 TAAGAAACTAAGCCTTCGGGGGTTT
66 TAAGAAACTGAGCCTTCGGGGGTTT
* * *
22676 CTTGATTTTTTAAGTCCTTCAGG-CAACTATAAGACCTTC
1 CTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
22715 GGGCAAAATG
Statistics
Matches: 459, Mismatches: 27, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
89 83 0.18
90 190 0.41
91 186 0.41
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (90 bp):
CTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATC
TAAGAAACTGAGCCTTCGGGGGTTT
Found at i:22514 original size:181 final size:181
Alignment explanation
Indices: 22135--22714 Score: 1040
Period size: 181 Copynumber: 3.2 Consensus size: 181
22125 AGAAACTGAG
*
22135 CTTGA-TTTTTAAGTCCTTCGGGCCATTCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
* *
22199 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGA-TTTTAAGTCATTCGGGTCATCCGTAAGACCTTC
66 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
*
22263 AGTGCAGTATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
131 AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
22314 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
*
22379 CTAAGAAACTGAGCCTTCAGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
66 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
*
22444 AGTGCAGGATATTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
131 AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
22495 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
1 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
22560 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
66 CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
* *
22625 AGTGCAAGATGTTTTCAAATGAGATTTAAGAAACTAAGCCTTCGGGGGTTT
131 AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
* * *
22676 CTTGATTTTTTAAGTCCTTCAGG-CAACTATAAGACCTTC
1 CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
22715 GGGCAAAATG
Statistics
Matches: 386, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
179 5 0.01
180 102 0.26
181 279 0.72
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (181 bp):
CTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGAT
CTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTC
AGTGCAGGATGTTTTCAAATGAGATTTAAGAAACTGAGCCTTCGGGGGTTT
Found at i:22912 original size:3 final size:3
Alignment explanation
Indices: 22904--22951 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
22894 ATATATATAT
* * *
22904 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22949 TTA
1 TTA
22952 ATACAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:25229 original size:14 final size:14
Alignment explanation
Indices: 25210--25240 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
25200 ATTTTCTTTA
25210 TTAATTAAATATAT
1 TTAATTAAATATAT
25224 TTAATTAAATATAT
1 TTAATTAAATATAT
25238 TTA
1 TTA
25241 TGTGAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAATTAAATATAT
Found at i:29390 original size:54 final size:54
Alignment explanation
Indices: 29303--29548 Score: 341
Period size: 54 Copynumber: 4.5 Consensus size: 54
29293 TATGTATTGC
*
29303 ATTTACCGTATTGGCACTATATGTGCAACCTAATAAATTCATAATTACTTTATGA
1 ATTT-CCGTATTGGCACTATGTGTGCAACCTAATAAATTCATAATTACTTTATGA
29358 ATTTCCGTATTGGCACTATGTGTGCAACCTAATAAATTCATAATTACTTTATGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTAATAAATTCATAATTACTTTATGA
* *
29412 ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTAATAAATTCATAATTACTTTATGA
* * * * * * * *
29466 ATTTCCATATTGGAACTATGTGTG-TACCTCATGTAATTCATAATGAGTTTGTGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTAAT-AAATTCATAATTACTTTATGA
* * *
29520 ATTACCGTATCGGCACTAAGTGTGCAACC
1 ATTTCCGTATTGGCACTATGTGTGCAACC
29549 CACAGAATTC
Statistics
Matches: 172, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
53 5 0.03
54 160 0.93
55 7 0.04
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (54 bp):
ATTTCCGTATTGGCACTATGTGTGCAACCTAATAAATTCATAATTACTTTATGA
Found at i:29597 original size:108 final size:108
Alignment explanation
Indices: 29392--29597 Score: 227
Period size: 108 Copynumber: 1.9 Consensus size: 108
29382 CAACCTAATA
* * * * * *
29392 AATTCATAATTACTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATT
1 AATTCATAATGACTTTATGAATTACCGTATCGGCACTAAGTGTGCAACCCAAGAAATTCATAATG
* * ** ** *
29457 AGTTTATGAATTTCCATATTGGAACTATGTGTGTACCTCATGT
66 AGCTTATGAAATGACATATCAGAACTACGTGTGTACCTCATGT
* *
29500 AATTCATAATGAGTTTGTGAATTACCGTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAAT
1 AATTCATAATGACTTTATGAATTACCGTATCGGCACTAAGTGTGCAACCCA-AGAAATTCATAAT
* *
29564 GAGCTTAT-AAATGACAGTATCAGTACTCCGTGTG
65 GAGCTTATGAAATGACA-TATCAGAACTACGTGTG
29598 CGCCCCAAAG
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
107 5 0.06
108 72 0.91
109 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (108 bp):
AATTCATAATGACTTTATGAATTACCGTATCGGCACTAAGTGTGCAACCCAAGAAATTCATAATG
AGCTTATGAAATGACATATCAGAACTACGTGTGTACCTCATGT
Found at i:30387 original size:26 final size:26
Alignment explanation
Indices: 30357--30409 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
30347 AATGTATACG
30357 GGAAATGGGTGTTACAAGAGATATGA
1 GGAAATGGGTGTTACAAGAGATATGA
*
30383 GGAAATGGGTGTTATAAGAGATATGA
1 GGAAATGGGTGTTACAAGAGATATGA
30409 G
1 G
30410 AGAGCAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.36, T:0.25
Consensus pattern (26 bp):
GGAAATGGGTGTTACAAGAGATATGA
Found at i:34449 original size:11 final size:11
Alignment explanation
Indices: 34430--34469 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
34420 TTCATATTCG
34430 GAAAAAATAGA
1 GAAAAAATAGA
*
34441 GATAAAATAGAA
1 GAAAAAATAG-A
34453 GAAAAAATAGA
1 GAAAAAATAGA
*
34464 TAAAAA
1 GAAAAA
34470 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (11 bp):
GAAAAAATAGA
Found at i:34459 original size:12 final size:12
Alignment explanation
Indices: 34430--34463 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
34420 TTCATATTCG
34430 GAAAAAATAG-A
1 GAAAAAATAGAA
*
34441 GATAAAATAGAA
1 GAAAAAATAGAA
34453 GAAAAAATAGA
1 GAAAAAATAGA
34464 TAAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (12 bp):
GAAAAAATAGAA
Found at i:34460 original size:23 final size:20
Alignment explanation
Indices: 34430--34478 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
34420 TTCATATTCG
34430 GAAAAAATAGAGATAAAATAGAA
1 GAAAAAAT--AGATAAAA-AGAA
34453 GAAAAAATAGATAAAAAGAA
1 GAAAAAATAGATAAAAAGAA
34473 -AAAAAA
1 GAAAAAA
34479 ACAACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 8 0.31
23 8 0.31
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (20 bp):
GAAAAAATAGATAAAAAGAA
Found at i:34464 original size:21 final size:21
Alignment explanation
Indices: 34430--34479 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
34420 TTCATATTCG
34430 GAAAAAATAGAGATAAAATAGAA
1 GAAAAAATA-AGATAAAA-AGAA
34453 GAAAAAAT-AGATAAAAAGAA
1 GAAAAAATAAGATAAAAAGAA
*
34473 AAAAAAA
1 GAAAAAA
34480 CAACAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.38
21 8 0.31
23 8 0.31
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (21 bp):
GAAAAAATAAGATAAAAAGAA
Found at i:34505 original size:16 final size:15
Alignment explanation
Indices: 34466--34519 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
34456 AAAATAGATA
* *
34466 AAAAGAAAAAAAAAC
1 AAAAGAAATAAAAAG
34481 AACAA-AAATAAAAAGG
1 AA-AAGAAATAAAAA-G
34497 AAAAGAAATAAAAAG
1 AAAAGAAATAAAAAG
34512 AAAAGAAA
1 AAAAGAAA
34520 AAAGATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 21 0.62
16 13 0.38
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (15 bp):
AAAAGAAATAAAAAG
Found at i:36912 original size:9 final size:9
Alignment explanation
Indices: 36898--36932 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
36888 TCTGCACACA
36898 TATCATTAT
1 TATCATTAT
36907 TATCATTAT
1 TATCATTAT
* *
36916 TAACATTCT
1 TATCATTAT
36925 TATCATTA
1 TATCATTA
36933 ATTCATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (9 bp):
TATCATTAT
Found at i:37224 original size:21 final size:21
Alignment explanation
Indices: 37200--37248 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
37190 TCTAAGGACT
* *
37200 ACATATATGTCCAGAAGAACC
1 ACATAGATATCCAGAAGAACC
* *
37221 ACATAGATATCCCGAAGGACC
1 ACATAGATATCCAGAAGAACC
*
37242 ACGTAGA
1 ACATAGA
37249 ACCCTCGATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.16
Consensus pattern (21 bp):
ACATAGATATCCAGAAGAACC
Found at i:39480 original size:260 final size:258
Alignment explanation
Indices: 39013--40084 Score: 1470
Period size: 259 Copynumber: 4.1 Consensus size: 258
39003 CATTAAGTTG
* * * * * * *
39013 TTTTGA-AAAATGAGAAAGCGATTTCTAAATTTTATCTTTTTAATAATTTT-AGAAAATGAAATC
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTC-ATTTAAT-GTTTTCAGAAAATGAAATT
* * *
39076 TTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTAATTCCAAAATTGGTAAGT
64 TTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGT
* * * *
39141 CCTTAAGG-CTATCAATAAG-CATTTCGAGCATGTTGATTAAATCATTCGGGTCATCTGTCAGTC
129 CCTTCAGGTC-ATCAGTAAGTC-TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTC
* *
39204 TTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCGGGCATGATGTTTTCACATG
192 TTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACATG
39269 ATT
257 A-T
*
39272 TTTTGAGAAAATGAGAAGGAGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAACTTT
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAA-TTT
*
39337 TGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
65 TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
*
39402 CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCCATCTGTCAGTCTTT
130 CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTT
* * * * * * *
39467 CGAGCAAGATGATAAGTCCTTCAGACCATCTGTAAAACCATCAGACATGATTTTTTCACATGAT
195 CGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACATGAT
* **
39531 TTTCGAGAAAATGAGAAGGCGATTTCCAAAACTTCTCATTTAATGTTTTCAGAAAATGAAATTTT
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAA-TTT
* * * * * * *
39596 TGAAACGTAAAAAAGTGATTTCCAGAGTTTTTTACCTAGTAAACTATTTCCAAAATTGGTATGTC
65 TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
* * * *
39661 CTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCC-TCAGGTCATCTGTCAGTCTTT
130 CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTT
* * *
39725 CGAGCAAAGATGATAAGTCCTTCGGGCCATCTGTAATACCTTCAAGCAGGATGTTTCCACATGAT
195 CGAGC-AAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACATGAT
* *
39790 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGCTTCTCATTTAATGTTTTCAAAAAATGAAAATTT
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATG-AAATTT
* **
39855 TGAAAAGTAAGAAAGCGATTTCCAGAGTTTCTTACCCAGTAGCCTATTTCCAAAATTGGTAAGTC
65 TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
* * *
39920 CTTTAGGTCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTT
130 CTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTT
* * * * * * * * *
39985 TGAGCAAGATGTTGAGTCCTTCGAGTCGTCTATAAGACCTTCGGGCAGGATATTTTCACATGAT
195 CGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACATGAT
* *
40049 TTTCGATAAAATGAGAAGGCGATTTCCAAAGTTTCT
1 TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCT
40085 TACCCAGTAA
Statistics
Matches: 725, Mismatches: 80, Indels: 16
0.88 0.10 0.02
Matches are distributed among these distances:
258 28 0.04
259 469 0.65
260 226 0.31
261 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (258 bp):
TTTTGAGAAAATGAGAAGGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTT
GAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCC
TTCAGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTC
GAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAGACCTTCAGGCAGGATGTTTTCACATGAT
Found at i:39499 original size:41 final size:42
Alignment explanation
Indices: 39396--39501 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
39386 CCAAAATTGG
* * *
39396 TAAGTCCTTCAGGTCATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTCAGGCCATCTGTAAGTCTTTCGAGCAAGATGAT
* * *
39438 TAAATCCTTCGGGCCATCTGTCAGTCTTTCGAGCAAGATGA-
1 TAAGTCCTTCAGGCCATCTGTAAGTCTTTCGAGCAAGATGAT
*
39479 TAAGTCCTTCAGACCATCTGTAA
1 TAAGTCCTTCAGGCCATCTGTAA
39502 AACCATCAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 19 0.35
42 35 0.65
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCAGGCCATCTGTAAGTCTTTCGAGCAAGATGAT
Found at i:39756 original size:42 final size:42
Alignment explanation
Indices: 39658--39760 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 42
39648 AAATTGGTAT
*
39658 GTCCTTCGGGCCAT-TAGTAAGTCTTTCGAGCATGATGATTAA
1 GTCCTTCGGGCCATCT-GTAAGTCTTTCGAGCAAGATGATTAA
* * * *
39700 ATCC-TCAGGTCATCTGTCAGTCTTTCGAGCAAAGATGA-TAA
1 GTCCTTCGGGCCATCTGTAAGTCTTTCGAGC-AAGATGATTAA
39741 GTCCTTCGGGCCATCTGTAA
1 GTCCTTCGGGCCATCTGTAA
39761 TACCTTCAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
41 27 0.55
42 22 0.45
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (42 bp):
GTCCTTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGATTAA
Found at i:40213 original size:198 final size:198
Alignment explanation
Indices: 39864--40277 Score: 587
Period size: 198 Copynumber: 2.1 Consensus size: 198
39854 TTGAAAAGTA
* * ** * *
39864 AGAAAGCGATTTCCAGAGTTTCTTACCCAGTAGCCTATTTCCAAAATTGGTAAGTCCTTTAGGTC
1 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
* * *
39929 ATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
* *
39994 TGTTGAGTCCTTCGAGTCGTCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGATAAA
131 TGTTGAGTCATTCGAGTCGTCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGAGAAA
40059 ATG
196 ATG
*
40062 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTTAGTCATTCAGG-C
1 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
* * * * *
40126 TATCAGTTAGTCTTTTGAGCATGATGATTAAATTCTTCGGGTCATCTATCAGTCTTTCGAGTAAG
66 -ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAG
* * * * * *
40191 ATGTTGAGTCATTCGGGTCGTCTATAAGACTTTTGGGCATGATGTTTTCACATGATTTTTGAGAA
130 ATGTTGAGTCATTCGAGTCGTCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGAGAA
40256 AATG
195 AATG
**
40260 AGAAGGTTATTTCCAAAG
1 AGAAGGCGATTTCCAAAG
40278 CTTATCATTT
Statistics
Matches: 190, Mismatches: 25, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
197 1 0.01
198 189 0.99
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (198 bp):
AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCAGGTC
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGA
TGTTGAGTCATTCGAGTCGTCTATAAGACCTTCGGGCAGGATATTTTCACATGATTTTCGAGAAA
ATG
Found at i:40572 original size:258 final size:256
Alignment explanation
Indices: 40062--40949 Score: 1041
Period size: 258 Copynumber: 3.4 Consensus size: 256
40052 CGATAAAATG
* * * *
40062 AGAAGGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTTAGTCATTCAGGCT
1 AGAAAGCGATTTCCAAAGTTTCTTA-CCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCC
* * * * *
40127 ATCAGTTAGTCTTTTGAGCATGATGATTAAATTCTTCGGGTCATCTATCAGTCTTTCGAGTAAGA
65 ATCAGTAAGTCTTTCGAGCATGATGATTAAA-TCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGA
* * * *
40192 TGTTGAGTCATTCGGGTCGTCTATAAGACTTTTGGGCATGATGTTTTCACATGATTTTTGAGAAA
129 TGTTAAGTCATTCGGGTCATCTATAAGAC-ATTGGGCATGATGTTTTCACATGATTTTCGAGAAA
* * * * *
40257 ATGAGAAGGTTATTTCCAAAGCTTATCATTTAATGTTTTCAGAAAATGAATTTTTTGAAAAGTA
193 ATGAGAAAGTGATTTCCAAATCTTCTCATTTAATGTTTTTAGAAAATGAATTTTTTGAAAAGTA
* * * * *
40321 AGAAAGTGATTTCCAATGTTTCTTACTCAGTAAAATATTT-GAAAATTAGTAAGTCATTCGGGCC
1 AGAAAGCGATTTCCAAAGTTTCTTAC-CAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCC
* * * *
40385 ATTAGTAAGTCTTTTGAGCATGATGATTAAATCTTTCGGGTTATCTGTTAGTCTTTCGAGCAAGA
65 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTT-GGGTCATCTGTCAGTCTTTCGAGCAAGA
** * * * *
40450 TGTTAAGTCATTCATGCCATCTATAAGACATTCGGGCATGATGTTTTTACATTACTTTCGAGAAA
129 TGTTAAGTCATTCGGGTCATCTATAAGACATT-GGGCATGATGTTTTCACATGATTTTCGAGAAA
* *
40515 ATGAGAAAGCGATTTCCAAATCTTCTCATTTAATGTTTTTAGAAAATGAAATTTTTGAAAAGTA
193 ATGAGAAAGTGATTTCCAAATCTTCTCATTTAATGTTTTTAGAAAATGAATTTTTTGAAAAGTA
* * * * * *
40579 AGAAAGCGATTTCCAAAATTTCTTACCAGTAGACTATTTCCAAAATTTGTAAGTCTTTTGGGCCT
1 AGAAAGCGATTTCCAAAGTTTCTTACCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCCA
* * * * *
40644 TCAGTAAGCCTTTCAAGCATGATGATTAAGTCCTTTTGGTCATCTGTCAATCTTTCGAGCAAGAT
66 TCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTTGGGTCATCTGTCAGTCTTTCGAGCAAGAT
* * * *
40709 GATAAGTCATTCGGGTAATCTATAAGATCCTTGAGCATGATGTTTTCACATGATTTTC-A-AAAA
130 GTTAAGTCATTCGGGTCATCTATAAGA-CATTGGGCATGATGTTTTCACATGATTTTCGAGAAAA
** * * *
40772 TGAGAAAGTGATTTCCAAAGT-TTCTCGCTTAGTGTTTTTAAAAAATTAATTTTTTGAAAAGTA
194 TGAGAAAGTGATTTCCAAA-TCTTCTCATTTAATGTTTTTAGAAAATGAATTTTTTGAAAAGTA
* * * * * *
40835 A-AAAGCAATTTTCAAAGTTTCTTACCTAGTAAATTATTTCCGAAATTGGTACGTACA-TCGGAC
1 AGAAAGCGATTTCCAAAGTTTCTTACC-AGTAAACTATTTCCAAAATTGGTAAGT-CATTCGGGC
* * * *
40898 CATCAGTAAGTCTTTCGAGTATGATGATTGAATCATTTGGATTATCTGTCAG
64 CATCAGTAAGTCTTTCGAGCATGATGATTAAATC-TTTGGGTCATCTGTCAG
40950 CCTCATTTGA
Statistics
Matches: 529, Mismatches: 90, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
255 23 0.04
256 125 0.24
257 20 0.04
258 320 0.60
259 41 0.08
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (256 bp):
AGAAAGCGATTTCCAAAGTTTCTTACCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCCA
TCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGATG
TTAAGTCATTCGGGTCATCTATAAGACATTGGGCATGATGTTTTCACATGATTTTCGAGAAAATG
AGAAAGTGATTTCCAAATCTTCTCATTTAATGTTTTTAGAAAATGAATTTTTTGAAAAGTA
Found at i:41081 original size:3 final size:3
Alignment explanation
Indices: 41073--41144 Score: 65
Period size: 3 Copynumber: 23.7 Consensus size: 3
41063 TTTTTCTAGG
* * * * *
41073 TTA TTA TTA ATA TTTA ATA TTA ATA ATA TTG TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
41118 TACA TTA TTA TTA TTA TTA TTA TTA TT
1 T-TA TTA TTA TTA TTA TTA TTA TTA TT
41145 TATGTTTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 1 0.02
3 52 0.93
4 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:41398 original size:17 final size:17
Alignment explanation
Indices: 41376--41408 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41366 GCCGCTCGCC
41376 CACAACCATTGGATCAG
1 CACAACCATTGGATCAG
41393 CACAACCATTGGATCA
1 CACAACCATTGGATCA
41409 AATCTGATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.18
Consensus pattern (17 bp):
CACAACCATTGGATCAG
Found at i:41503 original size:22 final size:24
Alignment explanation
Indices: 41471--41519 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
41461 GTACCACCAA
*
41471 CAACACCAAATCC-GCCTCAG-AG
1 CAACACCAAATCCACCCTCAGCAG
*
41493 CAACACTAAATCCACCCTCAGCAG
1 CAACACCAAATCCACCCTCAGCAG
41517 CAA
1 CAA
41520 AGGCATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 6 0.26
24 5 0.22
ACGTcount: A:0.39, C:0.41, G:0.10, T:0.10
Consensus pattern (24 bp):
CAACACCAAATCCACCCTCAGCAG
Found at i:42125 original size:22 final size:22
Alignment explanation
Indices: 42097--42139 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42087 AGTTTTATTA
42097 AAGTTTTCT-CTTTTTACTTTTC
1 AAGTTTTCTCCTTTTT-CTTTTC
*
42119 AAGTTTTTTCCTTTTTCTTTT
1 AAGTTTTCTCCTTTTTCTTTT
42140 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (22 bp):
AAGTTTTCTCCTTTTTCTTTTC
Found at i:44479 original size:22 final size:22
Alignment explanation
Indices: 44451--44493 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44441 AGTTTTATTA
44451 AAGTTTTCT-CTTTTTACTTTTC
1 AAGTTTTCTCCTTTTT-CTTTTC
*
44473 AAGTTTTTTCCTTTTTCTTTT
1 AAGTTTTCTCCTTTTTCTTTT
44494 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (22 bp):
AAGTTTTCTCCTTTTTCTTTTC
Found at i:45150 original size:19 final size:18
Alignment explanation
Indices: 45096--45138 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
45086 TCTTCTTATT
*
45096 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATTGCTTTTA
45115 TTTATTTAATTGCTTTTA
1 TTTATTTAATTGCTTTTA
45133 -TTATTT
1 TTTATTT
45139 TTAATATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTAATTGCTTTTA
Found at i:45760 original size:29 final size:29
Alignment explanation
Indices: 45727--45841 Score: 176
Period size: 29 Copynumber: 4.0 Consensus size: 29
45717 TTCAATTTCT
*
45727 TTTAATTTATGTTATTTACATTTATGCCC
1 TTTAATTTATGTTATTTACATTTCTGCCC
* *
45756 TTTAATTTATGATATTTATATTTCTGCCC
1 TTTAATTTATGTTATTTACATTTCTGCCC
* * *
45785 TTTAATTTCTATTATTTACATTTCTACCC
1 TTTAATTTATGTTATTTACATTTCTGCCC
45814 TTTAATTTATGTTATTTACATTTCTGCC
1 TTTAATTTATGTTATTTACATTTCTGCC
45842 TTATATTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (29 bp):
TTTAATTTATGTTATTTACATTTCTGCCC
Found at i:45763 original size:14 final size:14
Alignment explanation
Indices: 45727--45792 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 14
45717 TTCAATTTCT
**
45727 TTTAATTTATGTTA
1 TTTAATTTATGCCA
*
45741 TTTACATTTATGCCC
1 TTTA-ATTTATGCCA
**
45756 TTTAATTTATGATA
1 TTTAATTTATGCCA
* *
45770 TTTATATTTCTGCCC
1 TTTA-ATTTATGCCA
45785 TTTAATTT
1 TTTAATTT
45793 CTATTATTTA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
14 19 0.47
15 21 0.52
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTAATTTATGCCA
Found at i:45938 original size:95 final size:96
Alignment explanation
Indices: 45828--46014 Score: 322
Period size: 95 Copynumber: 2.0 Consensus size: 96
45818 ATTTATGTTA
* * *
45828 TTTACATTTCTGCCTTATATTTTTAATTCATTTCGTTTTACTTCCTTTATATTTGTTATTTGTTT
1 TTTACATTTCAGCCTTATATTTTTAATTCATTTCGATTTACTTCCTCTATATTTGTTATTTGTTT
*
45893 CTAATTTTGTTCATTTTCAATTTTCTTTTAT
66 CTAATTTTCTTCATTTTCAATTTTCTTTTAT
45924 TTTA-ATTTCAGCCTTATATTTTTAATTCATTTCGATTTACTTCCTCTATATTTGTTATTTGTTT
1 TTTACATTTCAGCCTTATATTTTTAATTCATTTCGATTTACTTCCTCTATATTTGTTATTTGTTT
*
45988 TTAATTTTCTTCATTTTCAATTTTCTT
66 CTAATTTTCTTCATTTTCAATTTTCTT
46015 CATTTTCAAT
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
95 82 0.95
96 4 0.05
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.63
Consensus pattern (96 bp):
TTTACATTTCAGCCTTATATTTTTAATTCATTTCGATTTACTTCCTCTATATTTGTTATTTGTTT
CTAATTTTCTTCATTTTCAATTTTCTTTTAT
Found at i:46009 original size:16 final size:16
Alignment explanation
Indices: 45985--46030 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
45975 TTGTTATTTG
*
45985 TTTTTAATTTTCTTCA
1 TTTTCAATTTTCTTCA
46001 TTTTCAATTTTCTTCA
1 TTTTCAATTTTCTTCA
46017 TTTTCAATTTTCTT
1 TTTTCAATTTTCTT
46031 TAACTTGGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCAATTTTCTTCA
Found at i:46357 original size:13 final size:13
Alignment explanation
Indices: 46339--46363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46329 TTATCTTCTG
46339 TTTTATTTTATTA
1 TTTTATTTTATTA
46352 TTTTATTTTATT
1 TTTTATTTTATT
46364 TTACTTTTAT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:46376 original size:18 final size:18
Alignment explanation
Indices: 46339--46376 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
46329 TTATCTTCTG
*
46339 TTTTATTTTATTATTTTA
1 TTTTATTTTATTATTATA
46357 TTTTATTTTACTT-TTATA
1 TTTTATTTTA-TTATTATA
46375 TT
1 TT
46377 AAATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTATTATA
Found at i:48767 original size:2 final size:2
Alignment explanation
Indices: 48762--48812 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
48752 TTTTTTTTTT
48762 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
48804 TA TA TA TA T
1 TA TA TA TA T
48813 TTCTAATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52979 original size:98 final size:95
Alignment explanation
Indices: 52724--52966 Score: 373
Period size: 95 Copynumber: 2.5 Consensus size: 95
52714 TGTATACCCG
* *
52724 TTAT-ATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTCTATG
1 TTATAATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
*
52788 GAGAAGATTCAACTAGCCTGATAAATGTGA
66 GAGAAGATTCAACTAGCCTGATAAAGGTGA
*
52818 TTATAATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATG
1 TTATAATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
* *
52883 GATAAGATTCAGCTAGCCTGATAAAGGTGA
66 GAGAAGATTCAACTAGCCTGATAAAGGTGA
*
52913 TTATAATATTTGTACAAT-AAGATTGAGATGTCCCTCTAGAGCAATTGGTTAAAC
1 TTATAATA----TACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAAC
52967 ATCTCGGCTT
Statistics
Matches: 137, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
94 4 0.03
95 92 0.67
98 35 0.26
99 6 0.04
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (95 bp):
TTATAATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
GAGAAGATTCAACTAGCCTGATAAAGGTGA
Found at i:54336 original size:85 final size:85
Alignment explanation
Indices: 54192--54955 Score: 1041
Period size: 85 Copynumber: 9.0 Consensus size: 85
54182 ATATTGACAA
* * * *
54192 CATAGCTCAAGACAAGAAGGGATATCTGTCAACCAAGACCTTCGATTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
54257 AAGGCACATCAAATTTACAG
66 AAGGCATATCAAATTTACAG
* * * *
54277 TATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAGACCTTCGAGTTCGATTACACTCACCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
54342 AAGGCATATCAAATTTACAG
66 AAGGCATATCAAATTTACAG
* * * * *
54362 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGTGTTCGATTACATTCAGCTCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
54427 AAGGCATATCAAATTCACAG
66 AAGGCATATCAAATTTACAG
* * *
54447 CATAGCTCAAGTCGAGAAGGGCTATCTGTCAACCAAGACATTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
54512 AAGGCATATCAAATTTGCAG
66 AAGGCATATCAAATTTACAG
* * * * *
54532 CATAGCTTAAGGTGAGAA-GGCTATCTGTCAACCAAGACCTTCGAGTTTGATTACAATCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
54596 AAGGCATATCAAATTTACAT
66 AAGGCATATCAAATTTACAG
* * * *
54616 CATAACGCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCAAATTACACTCAACTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTC-GATTACACTCAGCTC
*
54681 AAAGGCATATCAAATTTGCAG
65 AAAGGCATATCAAATTTACAG
* **
54702 CATAGCTTAAGGCGAGAAGGGCGATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
54767 AAGGAATATCAAATTTACAG
66 AAGGCATATCAAATTTACAG
* * * *
54787 CATAACTCAAGACGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTTGATTACATTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
54852 AAGGCATATCAAATTTGCAG
66 AAGGCATATCAAATTTACAG
* * * * * * * * *
54872 GATAGCTCAAGGAGAGAAGGGGTATCTGGCAA-TAA-ACCTTTGAGTTTGATTCCATTCAGCTC-
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
54934 AAGGACATGTCAAATTTACAG
66 AAGG-CATATCAAATTTACAG
54955 C
1 C
54956 TTAACTTGAG
Statistics
Matches: 598, Mismatches: 78, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
82 4 0.01
83 39 0.07
84 77 0.13
85 403 0.67
86 75 0.13
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (85 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
AAGGCATATCAAATTTACAG
Found at i:56651 original size:2 final size:2
Alignment explanation
Indices: 56644--56678 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56634 TATATTTTAT
56644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56679 TTTTTCTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56792 original size:2 final size:2
Alignment explanation
Indices: 56785--56814 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56775 TCTTAAACAT
56785 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
56815 ATTTATTTTT
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):
TA
Found at i:56953 original size:15 final size:16
Alignment explanation
Indices: 56935--56964 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56925 GTTTTTTTGT
56935 TTATTTTTT-ATTTAG
1 TTATTTTTTAATTTAG
56950 TTATTTTTTAATTTA
1 TTATTTTTTAATTTA
56965 ATTTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTATTTTTTAATTTAG
Found at i:56966 original size:5 final size:5
Alignment explanation
Indices: 56956--56983 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
56946 TTAGTTATTT
56956 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
56984 TTTTCATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:62230 original size:20 final size:19
Alignment explanation
Indices: 62184--62230 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
62174 GTACATTATG
62184 ATATAT-ACATGCATCATA
1 ATATATAACATGCATCATA
* *
62202 TTATCATAACATTCATCATAA
1 ATAT-ATAACATGCATCAT-A
62223 ATATATAA
1 ATATATAA
62231 TATATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 2 0.09
20 14 0.61
21 4 0.17
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATATAACATGCATCATA
Done.