Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006047.1 Hibiscus syriacus cultivar Beakdansim tig00014304_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: 680228
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 3
Found at i:2480 original size:13 final size:14
Alignment explanation
Indices: 2446--2480 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2436 ACAATGTTGG
2446 CATTGAGGTATGGT
1 CATTGAGGTATGGT
2460 CATTGAGGTATGGT
1 CATTGAGGTATGGT
2474 C-TTGAGG
1 CATTGAGG
2481 GTTTTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.20, C:0.09, G:0.37, T:0.34
Consensus pattern (14 bp):
CATTGAGGTATGGT
Found at i:7288 original size:55 final size:55
Alignment explanation
Indices: 7229--7787 Score: 475
Period size: 55 Copynumber: 10.5 Consensus size: 55
7219 GGGATAAGTG
* * * * * *
7229 AGACTTGAAATATCTTCAA-ATGACGAGTCTGCTCCGTATTCCTTCAGGAAGTATA
1 AGACTCGAAATATCTTCAACA-AACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
* * * *
7284 AGACTCGAACA-ATCTTCGTA-AAATGTGTCTGCTCTCTATTCATTCAGAGAGTATA
1 AGACTCGAA-ATATCTTC-AACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
* * *
7339 AGACTTGAACA-ATCTTTAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA
1 AGACTCGAA-ATATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
* *
7394 AGACTC-AAACAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA
1 AGACTCGAAA-TATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
7449 AGACTCG-AATAATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
1 AGACTCGAAAT-ATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
* * * * *
7504 AGACTCG-AATAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-
1 AGACTCGAAAT-ATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
* * * *
7558 AGAACTCGAACA-ATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AG-ACTCGAA-ATATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
* * * * * *
7614 GGACTC---A-ATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAAATATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
* * * * * *
7665 GGACTC---A-ATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAAATATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
* * * * * *
7716 GGACTC---A-ATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAAATATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
*
7767 GGACTC---A-ATCTTCAACAAACG
1 AGACTCGAAATATCTTCAACAAACG
7788 AATTTGCTTC
Statistics
Matches: 460, Mismatches: 33, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
51 165 0.36
53 1 0.00
54 5 0.01
55 283 0.62
56 5 0.01
57 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (55 bp):
AGACTCGAAATATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
Found at i:7422 original size:110 final size:109
Alignment explanation
Indices: 7255--7787 Score: 612
Period size: 110 Copynumber: 5.0 Consensus size: 109
7245 CAAATGACGA
* * * * * *
7255 GTCTGCTCCGTATTCCTTCAGGAAGTATAAGACTCGAACAATCTTCGTA-AAATGTGTCTGCTCT
1 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTC-AACAATCTTC-AACAAACGTGTCCGCTCC
* * *
7319 CTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAACAAACGT
64 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
* *
7365 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCTGCTCCC
1 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTC-AACAATCTTCAACAAACGTGTCCGCTCCC
* * *
7430 TATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAACGT
65 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
* * * *
7475 GTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAACAAACGGGTCCGCTCTC
1 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTC-AACAATCTTCAACAAACGTGTCCGCTCCC
*
7540 TATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACTT
65 TATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGT
* * * * *
7585 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT---CAATCTTCAACGAACTTGTCCGCTCCCT
1 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCAACAATCTTCAACAAACGTGTCCGCTCCCT
* * *
7647 ATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTT
66 ATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
* * * * *
7687 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT---CAATCTTCAACGAACTTGTCCGCTCCCT
1 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCAACAATCTTCAACAAACGTGTCCGCTCCCT
*
7749 ATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
66 ATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACG
7788 AATTTGCTTC
Statistics
Matches: 385, Mismatches: 35, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
102 115 0.30
106 43 0.11
107 1 0.00
109 3 0.01
110 223 0.58
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (109 bp):
GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCAACAATCTTCAACAAACGTGTCCGCTCCCT
ATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
Found at i:7644 original size:51 final size:51
Alignment explanation
Indices: 7308--7787 Score: 537
Period size: 55 Copynumber: 9.0 Consensus size: 51
7298 TTCGTAAAAT
* * * * *
7308 GTGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAACAAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAACAAAC
* * * *
7363 GTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCAAACAATCTTCAACAAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAAC
* * * *
7418 GTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAAC
* * * *
7473 GTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAACAAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAAC
* * *
7528 GGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAAC
* *
7583 TTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
* *
7634 TTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
* *
7685 TTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
*
7736 TTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
1 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
7787 G
1 G
7788 AATTTGCTTC
Statistics
Matches: 396, Mismatches: 20, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
51 167 0.42
54 1 0.00
55 227 0.57
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (51 bp):
GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
Found at i:9137 original size:16 final size:16
Alignment explanation
Indices: 9116--9171 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 16
9106 TTTATTTCTC
9116 TTTTTTCATTTTCCTT
1 TTTTTTCATTTTCCTT
*
9132 TTTTTTCATTTTTCATT
1 TTTTTTCA-TTTTCCTT
*
9149 TTTTCTTCCCTTTTCCTT
1 TTTT-TT-CATTTTCCTT
9167 TTTTT
1 TTTTT
9172 CTTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 8 0.24
17 12 0.35
18 13 0.38
19 1 0.03
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTCATTTTCCTT
Found at i:9153 original size:25 final size:25
Alignment explanation
Indices: 9102--9150 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
9092 TCTTGAACCC
*
9102 TCCTTTTATTTCTCTTTTTTCATTT
1 TCCTTTTATTTCTCATTTTTCATTT
9127 TCCTTTT-TTT-TCATTTTTCATTT
1 TCCTTTTATTTCTCATTTTTCATTT
9150 T
1 T
9151 TTCTTCCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.57
24 3 0.13
25 7 0.30
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.73
Consensus pattern (25 bp):
TCCTTTTATTTCTCATTTTTCATTT
Found at i:9176 original size:24 final size:24
Alignment explanation
Indices: 9149--9194 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
9139 ATTTTTCATT
9149 TTTTCTTCCCTTTTCCTTTTTTTC
1 TTTTCTTCCCTTTTCCTTTTTTTC
* ** *
9173 TTTTTTTTTCTTTTCGTTTTTT
1 TTTTCTTCCCTTTTCCTTTTTT
9195 CCATCATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTTCTTCCCTTTTCCTTTTTTTC
Found at i:9194 original size:43 final size:41
Alignment explanation
Indices: 9124--9233 Score: 96
Period size: 43 Copynumber: 2.6 Consensus size: 41
9114 TCTTTTTTCA
* * * *
9124 TTTTCCTTTTTTTTCATTTTTCATTTTTTCTTCCCTTTTCCTTT
1 TTTTCATTTTTTTTC--TTTTCATTTTTCCAT-CATTTTCCTTT
* * *
9168 TTTTCTTTTTTTTTCTTTTCGTTTTTTCCATCATTTTTCTTT
1 TTTTCATTTTTTTTCTTTTC-ATTTTTCCATCATTTTCCTTT
*
9210 TTTCTCATTTTTTCTCTTTT-ATTT
1 TTT-TCATTTTTTTTCTTTTCATTT
9234 CTTCTTCAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
41 3 0.05
42 17 0.31
43 21 0.38
44 14 0.25
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (41 bp):
TTTTCATTTTTTTTCTTTTCATTTTTCCATCATTTTCCTTT
Found at i:9210 original size:42 final size:42
Alignment explanation
Indices: 9124--9233 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
9114 TCTTTTTTCA
* * *
9124 TTTTCCTTTTTTTTCATTTTTCATTTTTTCTTCCCTTTTCCTTT
1 TTTTCATTTTTTTTC--TTTTCATTTTTTCATCCATTTTCCTTT
* * *
9168 TTTTCTTTTTTTTTCTTTTCGTTTTTTCCAT-CATTTTTCTTT
1 TTTTCATTTTTTTTCTTTTCATTTTTT-CATCCATTTTCCTTT
*
9210 TTTCTCATTTTTTCTCTTTT-ATTT
1 TTT-TCATTTTTTTTCTTTTCATTT
9234 CTTCTTCAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 26 0.46
43 16 0.29
44 14 0.25
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (42 bp):
TTTTCATTTTTTTTCTTTTCATTTTTTCATCCATTTTCCTTT
Found at i:9223 original size:60 final size:61
Alignment explanation
Indices: 9102--9239 Score: 160
Period size: 60 Copynumber: 2.3 Consensus size: 61
9092 TCTTGAACCC
*
9102 TCCTTTTATTTC-TCTTTTTTCATTTTCCTTTTTTTTCATTTTTCATTTTTTCTTCCCTTT
1 TCCTTTTATTTCTTCTTTTTTCATTTTCCTTTTTTATCATTTTTCATTTTTTCTTCCCTTT
* * **
9162 TCCTTTT-TTTCTTTTTTTTTC-TTTTCGTTTTTTCCATCATTTTTC-TTTTTTC-TCATTTTT
1 TCCTTTTATTTCTTCTTTTTTCATTTTCCTTTTTT--ATCATTTTTCATTTTTTCTTC-CCTTT
9222 TCTCTTTTATTTCTTCTT
1 TC-CTTTTATTTCTTCTT
9240 CAAGCAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
59 17 0.26
60 27 0.41
61 14 0.21
62 8 0.12
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (61 bp):
TCCTTTTATTTCTTCTTTTTTCATTTTCCTTTTTTATCATTTTTCATTTTTTCTTCCCTTT
Found at i:18892 original size:45 final size:47
Alignment explanation
Indices: 18824--18912 Score: 146
Period size: 45 Copynumber: 1.9 Consensus size: 47
18814 TGCTTTGTTA
*
18824 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
1 TTCACAAAAATAAATCCTAACCGCATGATATATAATTCGCATGCTTG
*
18871 TTCA-AAAAATAAA-CCTAACCGCATGATATATAGTTCGCATGC
1 TTCACAAAAATAAATCCTAACCGCATGATATATAATTCGCATGC
18913 ATTTATTCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 27 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.28
Consensus pattern (47 bp):
TTCACAAAAATAAATCCTAACCGCATGATATATAATTCGCATGCTTG
Found at i:23943 original size:21 final size:21
Alignment explanation
Indices: 23919--23980 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
23909 GTTAATGACG
*
23919 TGATAGTTCACAATGCTAACC
1 TGATAGTTCACATTGCTAACC
*
23940 TGATAGTTCACATTGCTAACT
1 TGATAGTTCACATTGCTAACC
*
23961 TGATAATTCACATTGCTAAC
1 TGATAGTTCACATTGCTAAC
23981 GTGACAATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (21 bp):
TGATAGTTCACATTGCTAACC
Found at i:31287 original size:29 final size:33
Alignment explanation
Indices: 31223--31289 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
31213 AAGTTTAGTT
31223 TTTA-TTTTATTTTAGTATGCCATCGTTAAAATA
1 TTTAGTTTTATTTTAGTAT-CCATCGTTAAAATA
*
31256 TTTAGTTTT-TTTTAGTAT-C-TCGTTCAAA-A
1 TTTAGTTTTATTTTAGTATCCATCGTTAAAATA
31285 TTTAG
1 TTTAG
31290 CGTTAAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 6 0.19
30 8 0.25
31 1 0.03
33 13 0.41
34 4 0.12
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.54
Consensus pattern (33 bp):
TTTAGTTTTATTTTAGTATCCATCGTTAAAATA
Found at i:41460 original size:68 final size:68
Alignment explanation
Indices: 41375--41851 Score: 738
Period size: 68 Copynumber: 7.1 Consensus size: 68
41365 CTGTTAGGGA
* * * *
41375 TATTTTTTAGGGTAAACTACATATTTGATCACTTATATATTATCTAATTTATGTTTTGGTCATTC
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
*
41440 GAT
66 AAT
*
41443 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAGTTATGTTTTGGTCACTC
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
41508 AAT
66 AAT
41511 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
41576 AAT
66 AAT
41579 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
*
41644 GAT
66 AAT
* * *
41647 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATCATCTAA-TT-TGTTTTGATCCCTC
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
*
41710 GAT
66 AAT
* **
41713 TATTATTTAGGCTAAACTACCTATTTGGTCACTTATATATTATCTAA--TA--TAAT--TCACAT
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCAC-T
41772 -ATAT
65 CA-AT
*
41776 TTTTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
1 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
41841 AAT
66 AAT
41844 TATTATTT
1 TATTATTT
41852 TTTTCAAAAT
Statistics
Matches: 377, Mismatches: 22, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
62 3 0.01
63 48 0.13
64 2 0.01
65 3 0.01
66 60 0.16
67 4 0.01
68 252 0.67
69 5 0.01
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.47
Consensus pattern (68 bp):
TATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTC
AAT
Found at i:41652 original size:31 final size:31
Alignment explanation
Indices: 41398--41642 Score: 114
Period size: 31 Copynumber: 7.3 Consensus size: 31
41388 AAACTACATA
*
41398 TTTGATCACTTATATATTATCTAATTTATGT
1 TTTGGTCACTTATATATTATCTAATTTATGT
** ** **
41429 TTTGGTCA-TTCGATTATTATTTAGGGTAAACTACCT
1 TTTGGTCACTT--A-TA-TA-TTA-TCTAATTTATGT
*
41465 ATTTGGTCACTTATATATTATCTAAGTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
* ** ** **
41497 TTTGGTCACTCAATTATTATTTAGGGTAAACTACCT
1 TTTGGTCACT-TA-TA-TA-TTA-TCTAATTTATGT
41533 ATTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
* ** ** **
41565 TTTGGTCACTCAATTATTATTTAGGGTAAACTACCT
1 TTTGGTCACT-TA-TA-TA-TTA-TCTAATTTATGT
41601 ATTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
41633 TTTGGTCACT
1 TTTGGTCACT
41643 CGATTATTAT
Statistics
Matches: 153, Mismatches: 41, Indels: 40
0.65 0.18 0.17
Matches are distributed among these distances:
30 2 0.01
31 37 0.24
32 21 0.14
33 15 0.10
34 12 0.08
35 15 0.10
36 21 0.14
37 28 0.18
38 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATCTAATTTATGT
Found at i:44920 original size:29 final size:30
Alignment explanation
Indices: 44859--44934 Score: 127
Period size: 29 Copynumber: 2.5 Consensus size: 30
44849 TAATTCAAAA
44859 TTGAATGAATTAATAAGTTTTTTTTTTAGAT
1 TTGAATGAATTAATAAG-TTTTTTTTTAGAT
*
44890 TTGAATGAATTAATAAG-TTTTTTTTATAT
1 TTGAATGAATTAATAAGTTTTTTTTTAGAT
44919 TTGAATGAATTAATAA
1 TTGAATGAATTAATAA
44935 AAAAAATGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 27 0.61
31 17 0.39
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (30 bp):
TTGAATGAATTAATAAGTTTTTTTTTAGAT
Found at i:45004 original size:30 final size:30
Alignment explanation
Indices: 44970--45036 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
44960 ACTAAATTTT
*
44970 TTATAAAATTATA-AAACTTAGAGG-TCCTAA
1 TTATAAAA-TATAGAAAATT-GAGGATCCTAA
*
45000 TTAT-AAATATAGAAAATTGAGGATCCTAC
1 TTATAAAATATAGAAAATTGAGGATCCTAA
45029 TTATAAAA
1 TTATAAAA
45037 ACAAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 8 0.25
29 17 0.53
30 7 0.22
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (30 bp):
TTATAAAATATAGAAAATTGAGGATCCTAA
Found at i:45044 original size:28 final size:28
Alignment explanation
Indices: 44990--45045 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
44980 ATAAAACTTA
* *
44990 GAGGTCCTAATTATAAATATAGAAAATT
1 GAGGTCCTAATTATAAAAACAGAAAATT
*
45018 GAGGATCCTACTTATAAAAACA-AAAATT
1 GAGG-TCCTAATTATAAAAACAGAAAATT
45046 TTAGGGGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (28 bp):
GAGGTCCTAATTATAAAAACAGAAAATT
Found at i:46252 original size:122 final size:121
Alignment explanation
Indices: 45963--46268 Score: 341
Period size: 122 Copynumber: 2.5 Consensus size: 121
45953 AGGGTAAACT
* ** * *
45963 ACGCAGTTAGTACCTAAACTATCAATTTTAGTTTGTTTTAATACCTAAACTTTCAAATTTTTTAA
1 ACGCATTTAGTACCTAAACTATCAATTTTAGTCCGTTTTAATACCTAAACTTTTAATTTTTTTAA
* * *
46028 AATCATACCCAATGTTTTTTTTTGTTTCAATTTATTACCTTACTGTTAAAAACTTA
66 AATCATACCCAATATTTGTTTTTGTTTCAATTTATTACCCTACTGTTAAAAACTTA
* * * * *
46084 ACGCGTTTAGTACATAAACTAT-AAGTTTTTTGTCGGTTTTATTACCTAAACTTTTAATTTTTTT
1 ACGCATTTAGTACCTAAACTATCAA--TTTTAGTCCGTTTTAATACCTAAACTTTTAATTTTTTT
** * **
46148 AAAAATCATACTTAATATTTAGTTTTTGTTTCATTTTATTACCCTGTTGTTAAAAA-TTA
64 -AAAATCATACCCAATATTT-GTTTTTGTTTCAATTTATTACCCTACTGTTAAAAACTTA
* * * *
46207 ATGCATTTAGTACCTAATA-TATCAATTTTGGTCCATTTTAATACCTAAA-TTTTCATTTTTTT
1 ACGCATTTAGTACCTAA-ACTATCAATTTTAGTCCGTTTTAATACCTAAACTTTTAATTTTTTT
46269 TCCAAAAAGG
Statistics
Matches: 154, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
120 2 0.01
121 31 0.20
122 52 0.34
123 36 0.23
124 33 0.21
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.48
Consensus pattern (121 bp):
ACGCATTTAGTACCTAAACTATCAATTTTAGTCCGTTTTAATACCTAAACTTTTAATTTTTTTAA
AATCATACCCAATATTTGTTTTTGTTTCAATTTATTACCCTACTGTTAAAAACTTA
Found at i:48461 original size:47 final size:46
Alignment explanation
Indices: 48398--48488 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 46
48388 GCTGAATTTT
*
48398 ATTTTAAAGTTCAATTTAATCCTTTAAGTTTTTTTGATT-TAATTATA
1 ATTTTAAAGTTCAATTTAATACTTTAA-TTTTTTTG-TTCTAATTATA
* * * *
48445 ATTTTAAATTTGAATTTAGTACTTTCATTTTTTTGTTCTAATTA
1 ATTTTAAAGTTCAATTTAATACTTTAATTTTTTTGTTCTAATTA
48489 GATTCGATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 2 0.05
46 14 0.37
47 22 0.58
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (46 bp):
ATTTTAAAGTTCAATTTAATACTTTAATTTTTTTGTTCTAATTATA
Found at i:48854 original size:21 final size:21
Alignment explanation
Indices: 48828--48883 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
48818 ATGATTTTAA
*
48828 AAAATTAA-AAGTTTAAGTATT
1 AAAATTAATAA-TTTAAGTACT
48849 AAAATTAATAATTTAAGTACT
1 AAAATTAATAATTTAAGTACT
*
48870 AAAAGT-ATAATTTA
1 AAAATTAATAATTTA
48884 CCCTTAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAATTAATAATTTAAGTACT
Found at i:49005 original size:47 final size:47
Alignment explanation
Indices: 48936--49029 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
48926 CAAAAGGTCC
**
48936 AAAACCTTTAAGACATGCATGATGATGTTGTTGAACATGGGCAGTTA
1 AAAACCTTTAAGACATGCATGATGATGAAGTTGAACATGGGCAGTTA
48983 AAAACCTTTAAGACATGCATGATGATGAAGTTGAACATGGGCAGTTA
1 AAAACCTTTAAGACATGCATGATGATGAAGTTGAACATGGGCAGTTA
49030 TTCTAGATAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (47 bp):
AAAACCTTTAAGACATGCATGATGATGAAGTTGAACATGGGCAGTTA
Found at i:51653 original size:30 final size:31
Alignment explanation
Indices: 51617--51724 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
51607 AGTCCAACGC
*
51617 ATATATACTTTAAAC-TTATATGTATATAAT
1 ATATATACTTTAAACTTTATATATATATAAT
*
51647 ATATATACTTTATACTTTATATATATATACATACT
1 ATATATACTTTAAACTTTATATATATAT--A-A-T
*
51682 AATATTATACTTTAATATTTTATATAT-TAT-AT
1 -ATA-TATACTTTAA-ACTTTATATATATATAAT
51714 ATTATATACTT
1 A-TATATACTT
51725 ATAAGTATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
30 14 0.22
31 19 0.29
32 3 0.05
33 2 0.03
34 1 0.02
35 1 0.02
36 3 0.05
37 12 0.18
38 10 0.15
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (31 bp):
ATATATACTTTAAACTTTATATATATATAAT
Found at i:51673 original size:22 final size:22
Alignment explanation
Indices: 51645--51724 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
51635 TATGTATATA
51645 ATATATATACTTTATACTTTAT
1 ATATATATACTTTATACTTTAT
51667 ATATATATAC---ATAC--TA-
1 ATATATATACTTTATACTTTAT
*
51683 ATAT-TATACTTTAATATTTTAT
1 ATATATATACTTT-ATACTTTAT
51705 ATATTATATA-TTATATACTT
1 ATA-TATATACTT-TATACTT
51725 ATAAGTATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 19
0.69 0.03 0.28
Matches are distributed among these distances:
15 5 0.11
16 4 0.09
17 2 0.04
19 7 0.15
21 2 0.04
22 13 0.28
23 8 0.17
24 5 0.11
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATATATACTTTATACTTTAT
Found at i:51735 original size:19 final size:18
Alignment explanation
Indices: 51687--51760 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 18
51677 ATACTAATAT
51687 TATACTT-TAATAT-TT-
1 TATACTTATAATATATTA
*
51702 TATA--TATTATATATTA
1 TATACTTATAATATATTA
*
51718 TATACTTATAAGTATATTG
1 TATACTTATAA-TATATTA
51737 TATAC-TAT-AT-TA-TA
1 TATACTTATAATATATTA
51751 TATACTTATA
1 TATACTTATA
51761 TGGATGTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
13 1 0.02
14 11 0.23
15 11 0.23
16 5 0.11
17 1 0.02
18 7 0.15
19 11 0.23
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (18 bp):
TATACTTATAATATATTA
Found at i:51753 original size:33 final size:32
Alignment explanation
Indices: 51633--51760 Score: 97
Period size: 33 Copynumber: 4.0 Consensus size: 32
51623 ACTTTAAACT
* *
51633 TATATGTATATAATATATATACTTTATACTT-T-A
1 TATAT-TATATACTATATAT--TATATACTTATAA
*
51666 TATA-TATATAC-ATACTAATATTATACTT-TAA
1 TATATTATATACTATA-TATTA-TATACTTATAA
* *
51697 TATTTTATATATTATATATTATATACTTATAA
1 TATATTATATACTATATATTATATACTTATAA
*
51729 GTATATTGTATACTATAT-TATATATACTTATA
1 -TATATTATATACTATATAT-TATATACTTATA
51761 TGGATGTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 16
0.76 0.09 0.16
Matches are distributed among these distances:
29 1 0.01
30 11 0.14
31 19 0.24
32 14 0.18
33 33 0.42
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (32 bp):
TATATTATATACTATATATTATATACTTATAA
Found at i:51896 original size:2 final size:2
Alignment explanation
Indices: 51889--52200 Score: 140
Period size: 2 Copynumber: 158.0 Consensus size: 2
51879 CCTCAAGGTT
* *
51889 TA TA TA TA TA TA CT- TA TA TA CT- TA TA TG TA TG TA TA TA CT-
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * *
51929 TA TA -A TG TA T- TG TT TA TA TA CT- 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
* * *
51969 CA CA CT- TA TA T- TA TA TA TA -A TA TA TG TA TA TA -A GTA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
52009 TA -A GTT TA CA TA TA TA TA CA -A TA TA T- TT TA TA TA TG TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
52049 TA CT- TA TA -A GTG TA TA T- TA TA TA TG TA TG TA TA TA TA TA T-
1 TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
52089 TA TA TA AA TA TA AA CTA TA T- TA TA TA -A 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
* * * * *
52130 TC TA TA TA TA AA TA TA AA CTA TA GTA TA TA GTT TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA TA
*
52173 GTA TA GTT TA TA TA TA TA TA TA TA TA TA
1 -TA TA -TA TA TA TA TA TA TA TA TA TA TA
52201 GTTCACATGT
Statistics
Matches: 234, Mismatches: 42, Indels: 68
0.68 0.12 0.20
Matches are distributed among these distances:
1 19 0.08
2 202 0.86
3 13 0.06
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:52158 original size:45 final size:44
Alignment explanation
Indices: 51943--52170 Score: 152
Period size: 45 Copynumber: 5.2 Consensus size: 44
51933 ATGTATTGTT
* * *
51943 TATATACT-TATATATA-TATATATATACACACTTATATTATAT-A
1 TATATA-TATATATATATTATATAAATATAAAC-TATATTATATAA
* * * * *
51986 TA-ATATATGTATATAAGTATATATAAGTTTACA-TATA-TATACAA
1 TATATATATATATAT-A-T-TATATAAATATAAACTATATTATATAA
** **
52030 TATAT-T-T-TATATATGTATATACTTATAAGTGTATATTATAT-A
1 TATATATATATATATAT-TATATAAATATAA-ACTATATTATATAA
* *
52072 TGTATGTATATATATATTATATAAATATAAACTATATTATATAA
1 TATATATATATATATATTATATAAATATAAACTATATTATATAA
* * *
52116 TATATATATATATATCTATATATAAATATAAACTATAGTATATAG
1 TATATATATATATATAT-TATATAAATATAAACTATATTATATAA
*
52161 TTTATATATA
1 TATATATATA
52171 AAGTATAGTT
Statistics
Matches: 146, Mismatches: 24, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
40 10 0.07
41 2 0.01
42 23 0.16
43 23 0.16
44 35 0.24
45 43 0.29
46 10 0.07
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (44 bp):
TATATATATATATATATTATATAAATATAAACTATATTATATAA
Found at i:52258 original size:20 final size:20
Alignment explanation
Indices: 52235--52282 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
52225 ATATAATTTA
*
52235 TATATATAGTTTGCATATAG
1 TATATATAGTTTACATATAG
* *
52255 TATATATGGTTTATATATAG
1 TATATATAGTTTACATATAG
*
52275 TTTATATA
1 TATATATA
52283 CTACTATGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (20 bp):
TATATATAGTTTACATATAG
Found at i:52269 original size:11 final size:11
Alignment explanation
Indices: 52215--52282 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
52205 ACATGTAAAC
*
52215 TATATAGTATA
1 TATATAGTTTA
*
52226 TATA-ATTTATA
1 TATATAGTT-TA
*
52237 TATATAGTTTG
1 TATATAGTTTA
*
52248 CATATAG--TA
1 TATATAGTTTA
*
52257 TATATGGTTTA
1 TATATAGTTTA
52268 TATATAGTTTA
1 TATATAGTTTA
52279 TATA
1 TATA
52283 CTACTATGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 6 0.14
10 2 0.05
11 33 0.75
12 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.50
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:52316 original size:22 final size:21
Alignment explanation
Indices: 52285--52326 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52275 TTTATATACT
*
52285 ACTATGTATAAACTATATAAAA
1 ACTATATAT-AACTATATAAAA
*
52307 ACTATATATAATTATATAAA
1 ACTATATATAACTATATAAA
52327 TTAACCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (21 bp):
ACTATATATAACTATATAAAA
Found at i:52395 original size:36 final size:36
Alignment explanation
Indices: 52342--52438 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
52332 CATAAACCTA
*
52342 TATATATATATATACTATATAGTTTATACATAGTAG
1 TATATATATATAAACTATATAGTTTATACATAGTAG
* *
52378 TATATA-AGTATAAACTATATAGTTTATATATAGT-T
1 TATATATA-TATAAACTATATAGTTTATACATAGTAG
* *
52413 TATAT-TA-ATAAACTAAATAATTTATA
1 TATATATATATAAACTATATAGTTTATA
52439 TAATTATTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
33 17 0.31
35 7 0.13
36 30 0.56
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
TATATATATATAAACTATATAGTTTATACATAGTAG
Found at i:52409 original size:11 final size:11
Alignment explanation
Indices: 52344--52417 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
52334 TAAACCTATA
*
52344 TATATATA-TA
1 TATATATAGTT
52354 TACTATATAGTT
1 TA-TATATAGTT
* *
52366 TATACATAGTAG
1 TATATATAGT-T
52378 TATATA-AGTAT
1 TATATATAGT-T
*
52389 AAACTATATAGTT
1 -TA-TATATAGTT
52402 TATATATAGTT
1 TATATATAGTT
52413 TATAT
1 TATAT
52418 TAATAAACTA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
10 2 0.04
11 31 0.61
12 10 0.20
13 5 0.10
14 3 0.06
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (11 bp):
TATATATAGTT
Found at i:52845 original size:126 final size:122
Alignment explanation
Indices: 52688--52933 Score: 359
Period size: 126 Copynumber: 2.0 Consensus size: 122
52678 TTTTTAATTA
* **
52688 TTCTTTATAAATACAAAAACATACTTACACCAATATAATTATGTGTTTATTATTAGGT-GCCAAG
1 TTCTTTATAAATACAAAAACATACTTACACCAATATAATTATGTATTTATTATTAAATAG-CAAG
52752 ATAATGAGAGATATACATATTTACACCGGTATAAGTATGTGTTAAGTGCTACACTTTTTTAT
65 ATAATGAGAGATATACATA--T--ACCGGTATAAGTATGTGTTAAGTGCTACACTTTTTTAT
* *
52814 TTCTTTGTAAATACAAAAACATACTTACACCAATATAATTATGTATTTATTGTTAAATAGCAAGA
1 TTCTTTATAAATACAAAAACATACTTACACCAATATAATTATGTATTTATTATTAAATAGCAAGA
* * * *
52879 TACTGAGAGATATACATATACCGGTGTAAGTATGTGTTAAGTGCTATATTTTTTT
66 TAATGAGAGATATACATATACCGGTATAAGTATGTGTTAAGTGCTACACTTTTTT
52934 GTTATATTCA
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
122 33 0.30
124 1 0.01
126 75 0.68
127 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.39
Consensus pattern (122 bp):
TTCTTTATAAATACAAAAACATACTTACACCAATATAATTATGTATTTATTATTAAATAGCAAGA
TAATGAGAGATATACATATACCGGTATAAGTATGTGTTAAGTGCTACACTTTTTTAT
Found at i:57300 original size:60 final size:60
Alignment explanation
Indices: 57226--57402 Score: 302
Period size: 60 Copynumber: 3.0 Consensus size: 60
57216 GTATAATCAT
* *
57226 CTCGGAGTCGATTGGGAGGGAGTTCCGAGCTCTTGGGTGTATTGCAGTGGGCTCATATGC
1 CTCGGGGTCGATTGGGAGGGAGTTCCAAGCTCTTGGGTGTATTGCAGTGGGCTCATATGC
57286 CTCGGGGTCGATTGGG-GAGGAGTTCCAAGCTCTTGGGTGTATTGCAGTGGGCTCATATGC
1 CTCGGGGTCGATTGGGAG-GGAGTTCCAAGCTCTTGGGTGTATTGCAGTGGGCTCATATGC
* *
57346 CTCGGGGTCGATTGGGAAGGAGTTCCAAGCTCTTGGGAGTATTGCAGTGGGCTCATA
1 CTCGGGGTCGATTGGGAGGGAGTTCCAAGCTCTTGGGTGTATTGCAGTGGGCTCATA
57403 GTTACGATAT
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
59 1 0.01
60 110 0.99
ACGTcount: A:0.16, C:0.18, G:0.38, T:0.28
Consensus pattern (60 bp):
CTCGGGGTCGATTGGGAGGGAGTTCCAAGCTCTTGGGTGTATTGCAGTGGGCTCATATGC
Found at i:69778 original size:236 final size:238
Alignment explanation
Indices: 69321--69787 Score: 692
Period size: 236 Copynumber: 2.0 Consensus size: 238
69311 ATACTTAATG
* **
69321 TTTAGCTTTTATTTCATTTTAGTACTTCACTGTTAGAAGCTTAACACATTTAGTACCTAAACTGA
1 TTTAGCTTTTATTTCATTTTAGTACCTCACCATTAGAAGCTTAACACATTTAGTACCTAAACTGA
* *
69386 CAGTTTTGGTCCGTTTTAGTACCTAAACTTAAAAAAAATCAATAACTTAACGTTAACTTTTGAAC
66 CAATTTTGGTCCGTTTTAGTACCTAAACTTAAAAAAAATCAATAAC-TAACGTTAAATTTTGAAC
* * *
69451 GGGATACTAAAATGAAACAAAAACTAAACTTTAAGTATGATTTTAAAAATTCTGAAAGTTTAGGT
130 GAGATACTAAAATGAAACAAAAACTAAACTTTAAGTATGATATTAAAAATTCTAAAAGTTTAGGT
* * *
69516 ATTAAAATAGGCCAAAGTTAATAGTTTAGATACTAAATGTGTAA
195 AATAAAATAGGCCAAAGCTAATAGTTTAAATACTAAATGTGTAA
* * *
69560 TTTAGTTTTTATTTCATTTTAGTACCTCACCATTATAAGCTTAACACGTTTAGTACCTAAACT-A
1 TTTAGCTTTTATTTCATTTTAGTACCTCACCATTAGAAGCTTAACACATTTAGTACCTAAACTGA
69624 TCAATTTTGGTCCGTTTTAGTACCTAAACTT-AAAAAAATCCAA-AA-TAACGTTAAATTTTGAA
66 -CAATTTTGGTCCGTTTTAGTACCTAAACTTAAAAAAAAT-CAATAACTAACGTTAAATTTTGAA
* * * *
69686 CGAGATACTAAAATGAAACAAAAACTAAAGTTTAAGTATGATATTGAAAATTTTAAAAGTTTATG
129 CGAGATACTAAAATGAAACAAAAACTAAACTTTAAGTATGATATTAAAAATTCTAAAAGTTTAGG
*
69751 TAATAAAATAGGCCAATA-CTGATAGTTTAAATACTAA
194 TAATAAAATAGGCCAA-AGCTAATAGTTTAAATACTAA
69788 TCATGTAGTT
Statistics
Matches: 206, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
236 105 0.51
237 1 0.00
238 11 0.05
239 89 0.43
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (238 bp):
TTTAGCTTTTATTTCATTTTAGTACCTCACCATTAGAAGCTTAACACATTTAGTACCTAAACTGA
CAATTTTGGTCCGTTTTAGTACCTAAACTTAAAAAAAATCAATAACTAACGTTAAATTTTGAACG
AGATACTAAAATGAAACAAAAACTAAACTTTAAGTATGATATTAAAAATTCTAAAAGTTTAGGTA
ATAAAATAGGCCAAAGCTAATAGTTTAAATACTAAATGTGTAA
Found at i:70038 original size:22 final size:21
Alignment explanation
Indices: 70013--70053 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
70003 CATACCCACC
*
70013 CTAAACCATAACCCCATAACAT
1 CTAAACCATAAACCC-TAACAT
*
70035 CTAAACTATAAACCCTAAC
1 CTAAACCATAAACCCTAAC
70054 TCAATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (21 bp):
CTAAACCATAAACCCTAACAT
Found at i:75464 original size:18 final size:18
Alignment explanation
Indices: 75389--75457 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
75379 ACTAGATATA
* **
75389 TGAGCTGAACTAGACGAG
1 TGAGCTGGACTAGGTGAG
*
75407 TGAGCTAGACTAGGTGAG
1 TGAGCTGGACTAGGTGAG
*
75425 TGAGATGGACTAGGTGAG
1 TGAGCTGGACTAGGTGAG
75443 TGAGCTGGACTAGGT
1 TGAGCTGGACTAGGT
75458 TGGTGAGGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.28, C:0.12, G:0.39, T:0.22
Consensus pattern (18 bp):
TGAGCTGGACTAGGTGAG
Found at i:78183 original size:19 final size:18
Alignment explanation
Indices: 78159--78194 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
78149 CTATCTAAAC
78159 CACAAGAGAAGCAACAAAA
1 CACAAGAGAAG-AACAAAA
*
78178 CACAAGCGAAGAACAAA
1 CACAAGAGAAGAACAAA
78195 GACAAATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.22, G:0.17, T:0.00
Consensus pattern (18 bp):
CACAAGAGAAGAACAAAA
Found at i:82667 original size:3 final size:3
Alignment explanation
Indices: 82659--82720 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
82649 TTTTTATCCA
*
82659 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
82707 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
82721 AATATATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:82732 original size:11 final size:11
Alignment explanation
Indices: 82716--82747 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
82706 TTATTATTAT
82716 TATTAAATATA
1 TATTAAATATA
82727 TATTAAATATA
1 TATTAAATATA
82738 TATATAAATA
1 TAT-TAAATA
82748 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:84193 original size:13 final size:13
Alignment explanation
Indices: 84177--84223 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
84167 ATATAATAAA
84177 TAAATATTTATTT
1 TAAATATTTATTT
*
84190 TAAATAAATTATTT
1 TAAAT-ATTTATTT
84204 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
84217 TCAATAT
1 TAAATAT
84224 AGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:86546 original size:14 final size:14
Alignment explanation
Indices: 86508--86561 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
86498 ATTTTAAATA
*
86508 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
86522 TTTTACATTTGCAT
1 ATTTACATTTGCAT
86536 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
86551 CTTTGCATTTG
1 ATTTACATTTG
86562 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:92377 original size:114 final size:114
Alignment explanation
Indices: 92086--92426 Score: 574
Period size: 114 Copynumber: 3.0 Consensus size: 114
92076 AAGTGCCATG
92086 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
92151 TGGTTTGGTATGAACCCCAAAAACCCATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGATTTAAAAGATGAATT
92201 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
92266 TGGTTTGGTATGAACCCCAAAATCAATCATTAGATTTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
* *
92315 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * *
92380 TGGTTTGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
92427 CTGCATGATC
Statistics
Matches: 213, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
114 130 0.61
115 83 0.39
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
Found at i:94674 original size:50 final size:50
Alignment explanation
Indices: 94552--94744 Score: 262
Period size: 50 Copynumber: 3.8 Consensus size: 50
94542 ATCTTGGCAA
* * * *
94552 AAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGAGCAG
1 AAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTAC-ATC-TC-GA-CAG
* * *
94606 AAGCCACA-GAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCTCGACAG
1 AAACCACAGGAAAA-GATGAATGTATTGTCAAATGTTTTACATCTCGACAG
*
94656 AAACCACAGGAAAAGATGAATGTATTGTCAAGTGTTTTACATCTCGACAG
1 AAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTACATCTCGACAG
94706 AAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTA
1 AAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTA
94745 TGAACCAGTG
Statistics
Matches: 130, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
50 83 0.64
51 7 0.05
52 2 0.02
53 6 0.05
54 32 0.25
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (50 bp):
AAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTACATCTCGACAG
Found at i:94736 original size:100 final size:104
Alignment explanation
Indices: 94552--94744 Score: 270
Period size: 104 Copynumber: 1.9 Consensus size: 104
94542 ATCTTGGCAA
* * *
94552 AAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGAGCAGAAGCCACAGAA
1 AAACCACAAGAAAAGATGAATGTATTGTCAAATGTTTTACAAACATCTGAGCAGAAACCACAGAA
* *
94617 AAGGATGAATGTGTTGTCAAGTGTTTTACATCTCGACAG
66 AAGGATGAATGTATTGTCAAATGTTTTACATCTCGACAG
* * *
94656 AAACCACAGGAAAAGATGAATGTATTGTCAAGTGTTTTAC-ATC-TC-GA-CAGAAACCACAGGA
1 AAACCACAAGAAAAGATGAATGTATTGTCAAATGTTTTACAAACATCTGAGCAGAAACCACA-GA
94717 AAA-GATGAATGTATTGTCAAATGTTTTA
65 AAAGGATGAATGTATTGTCAAATGTTTTA
94745 TGAACCAGTG
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
100 33 0.41
101 7 0.09
102 2 0.03
103 2 0.03
104 36 0.45
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (104 bp):
AAACCACAAGAAAAGATGAATGTATTGTCAAATGTTTTACAAACATCTGAGCAGAAACCACAGAA
AAGGATGAATGTATTGTCAAATGTTTTACATCTCGACAG
Found at i:95139 original size:22 final size:22
Alignment explanation
Indices: 95113--95192 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
95103 TACATCTACA
95113 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
95135 CTCTTCAAAAATGATAGATTCC
1 CTCTTCAAAGATGATAGATTCT
* * *
95157 CTTTTTAAAGATGACAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
95179 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
95193 AAGCTTTATC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:96026 original size:228 final size:226
Alignment explanation
Indices: 95600--96386 Score: 1089
Period size: 228 Copynumber: 3.4 Consensus size: 226
95590 GATTCAAATC
** * *
95600 CATCATTCAATGGATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
95664 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTGTTTGAATTCATCATTTGATGAATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTGTTTGAATTCATCATTTGATGGATC
*
95729 AACATTGTCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
131 AACATTGTCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
*
95794 GAGAAGAATTTGTTCAACCTTTTGTCTGAATT
195 GAGAAGAATTTGTTCAACTTTTTGTCTGAATT
* * ***
95826 CATCACTTGATGGATTATTTTTGCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * * * *
95890 AAGAAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTG-CTCAAATCTATTACTTGATGG
65 AAGAAG-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTGTTTGAATTC-ATCATTTGATGG
* * *** * *
95954 GTTATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
128 ATCAACATTGTCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
96019 AATGAGAAGAATTTGTTCAACTTTTTGTTTGAATT
192 AATGAGAAGAATTTGTTCAACTTTTTGTCTGAATT
96054 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTAATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC---ATCTGAAGAA
* *
96119 GGAAGAAGAAGTTCACAATGAGAAGAATTTGTTCAA-CTTTTTGTTTGAATTCATCATTTGATGG
63 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTGTTTGAATTCATCATTTGATGG
*
96183 ATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTT
128 ATCAACATTGTCAGGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTT
*
96248 CATAATGAGAAGAACTTGTTCAACTTTTTG-CTTGAATT
189 CATAATGAGAAGAATTTGTTCAACTTTTTGTC-TGAATT
*
96286 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATAAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* *
96351 TGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
63 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
96387 TAATTCTATC
Statistics
Matches: 490, Mismatches: 53, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
226 17 0.03
227 47 0.10
228 180 0.37
229 43 0.09
230 32 0.07
231 19 0.04
232 149 0.30
234 1 0.00
235 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (226 bp):
CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTGTTTGAATTCATCATTTGATGGATC
AACATTGTCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAATTTGTTCAACTTTTTGTCTGAATT
Found at i:96152 original size:116 final size:113
Alignment explanation
Indices: 95600--96386 Score: 1096
Period size: 116 Copynumber: 6.9 Consensus size: 113
95590 GATTCAAATC
** * *
95600 CATCATTCAATGGATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
95664 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC-TTTTTGTTTGAATT
* * *
95713 CATCATTTGATGAATCAACATTGTCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
95778 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATT
* * ***
95826 CATCACTTGATGGATTATTTTTGCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *
95890 AAGAAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTG-CTCAAAT
65 AAGAAG-AAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTTGTTTGAATT
* * * * *** ** *
95940 CTATTACTTGATGGGTTATTTTTTTCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAA
1 C-ATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
96004 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATT
64 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATT
96054 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTAATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTC---ATCTGAAGAA
*
96119 GGAAGAAGAAGTTCACAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATT
63 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATT
96170 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* *
96235 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
63 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATT
*
96286 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATAAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* * *
96351 TGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
63 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
96387 TAATTCTATC
Statistics
Matches: 615, Mismatches: 46, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
112 3 0.00
113 136 0.22
114 139 0.23
115 70 0.11
116 264 0.43
118 1 0.00
119 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (113 bp):
CATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATT
Found at i:96713 original size:3 final size:3
Alignment explanation
Indices: 96705--96807 Score: 190
Period size: 3 Copynumber: 34.7 Consensus size: 3
96695 TTTTTATCCA
96705 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
96753 TAT TAT TAT TAT TAT TAT TAT TA- TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
96800 TAT TAT TA
1 TAT TAT TA
96808 AATATATATT
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 95 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:96819 original size:11 final size:11
Alignment explanation
Indices: 96803--96834 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
96793 TTATTATTAT
96803 TATTAAATATA
1 TATTAAATATA
96814 TATTAAATATA
1 TATTAAATATA
96825 TATATAAATA
1 TAT-TAAATA
96835 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:98273 original size:13 final size:13
Alignment explanation
Indices: 98257--98303 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
98247 ATATAATAAA
98257 TAAATATTTATTT
1 TAAATATTTATTT
*
98270 TAAATAAATTATTT
1 TAAAT-ATTTATTT
98284 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
98297 TCAATAT
1 TAAATAT
98304 AGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:107456 original size:60 final size:59
Alignment explanation
Indices: 107324--107456 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 59
107314 GAGTCATATG
* * * *
107324 TCCCCAAACATAACCCTCATTTTAAATTATTCCTTAAACTTTTAAAAATTCTTATTTCA
1 TCCCCAAACATGACCCTCACTTTAAATCATTCCTTAAACTTTTAAAAATTCTAATTTCA
* *
107383 T-CCCAGAACCATGACTCTCACTTTAAATCAGTT-CTTAAACTTTTAAACATTCTAATTTCA
1 TCCCCA-AA-CATGACCCTCACTTTAAATCA-TTCCTTAAACTTTTAAAAATTCTAATTTCA
107443 TCCCCAAATCATGA
1 TCCCCAAA-CATGA
107457 ATATCATTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
58 4 0.06
59 3 0.05
60 50 0.79
61 6 0.10
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (59 bp):
TCCCCAAACATGACCCTCACTTTAAATCATTCCTTAAACTTTTAAAAATTCTAATTTCA
Found at i:107482 original size:60 final size:59
Alignment explanation
Indices: 107344--107486 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 59
107334 TAACCCTCAT
* * * *
107344 TTTAAATTATTCCTTAAACTTTTAAAAATTCTTATTTCATCCCAGAACCATGACTCTCA
1 TTTAAATTAGTCCTTAAACTTTTAAAAATTCTAATTTCATCCCAGAACCATGAATATCA
* * * *
107403 CTTTAAATCAGTTCTTAAACTTTTAAACATTCTAATTTCATCCCCA-AATCATGAATATCA
1 -TTTAAATTAGTCCTTAAACTTTTAAAAATTCTAATTTCAT-CCCAGAACCATGAATATCA
* *
107463 TTCTAAATTGGTCCCTAAACTTTT
1 TT-TAAATTAGTCCTTAAACTTTT
107487 GCATATTCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 2 0.03
60 63 0.91
61 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.41
Consensus pattern (59 bp):
TTTAAATTAGTCCTTAAACTTTTAAAAATTCTAATTTCATCCCAGAACCATGAATATCA
Found at i:107733 original size:59 final size:59
Alignment explanation
Indices: 107631--107777 Score: 142
Period size: 59 Copynumber: 2.5 Consensus size: 59
107621 ATATGTATAA
* * * *
107631 TTTA-GGATTAAACTAAAGTGTTCAAAAATTTTGAGGAACAATTTAGAA-TAAAGATCATAG
1 TTTAGGGATGAAATTAAA-TGTT-AAAAATTTTGAAGAACAATTTAGAAGGAAAG-TCATAG
*
107691 TTT-GAGGATGAAAATTAAATGTTAAAAA-TTTGAAG-ACTAATTTAGAAGGATAGTCATAG
1 TTTAG-GGATG-AAATTAAATGTTAAAAATTTTGAAGAAC-AATTTAGAAGGAAAGTCATAG
*
107750 TTTAGGGATGAAATTGAAATGTTTAAAA
1 TTTAGGGATGAAATT-AAATGTTAAAAA
107778 GTTTAGGGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
58 7 0.09
59 40 0.54
60 12 0.16
61 8 0.11
62 7 0.09
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (59 bp):
TTTAGGGATGAAATTAAATGTTAAAAATTTTGAAGAACAATTTAGAAGGAAAGTCATAG
Found at i:108918 original size:18 final size:18
Alignment explanation
Indices: 108895--108929 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
108885 GAAAGATATG
108895 AAATAAAAAATAATAAAC
1 AAATAAAAAATAATAAAC
* *
108913 AAATAAATAATATTAAA
1 AAATAAAAAATAATAAA
108930 AACTTAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAAAAATAATAAAC
Found at i:111914 original size:159 final size:162
Alignment explanation
Indices: 111616--111982 Score: 510
Period size: 159 Copynumber: 2.2 Consensus size: 162
111606 CGTGGATGAA
* * *
111616 AATTTGGAAGAATTG-TCGACTTGGTCTGATTCATGTTTTTTTTTTTTGGTTTTGCTATAAGTTC
1 AATTTGGAGGAATTGCT-GACTTGGTCTGCTTCA----TTGTTTTTTTGGTTTTGCTATAAGTTC
* * * * *
111680 TATTTTATTTTATTTTATTTTCTCATTATGGGAGGATGATGAGAACGAATTAACTTTCAAATGCT
61 TATTTTATTTTA--TTATTTTCTCATCATGGGAGGACGAGGAGAACCAACTAACTTTCAAATGCT
111745 GGAGCAAATGAACAATGGAGCTTGTGGGACACTGCTCAC
124 GGAGCAAATGAACAATGGAGCTTGTGGGACACTGCTCAC
*
111784 AATTTGGAGGAATTGCTTACTTGGTCTGCTTCA-TGTTTTTTTGGTTTTGCTATAAGTTCTATTT
1 AATTTGGAGGAATTGCTGACTTGGTCTGCTTCATTGTTTTTTTGGTTTTGCTATAAGTTCTATTT
* *
111848 TGTTTTA-T-TTTTCTCATCATGGGAGGACGAGGAG-ACCAAGCTAACTTTCAAATGTTGGAGCA
66 TATTTTATTATTTTCTCATCATGGGAGGACGAGGAGAACCAA-CTAACTTTCAAATGCTGGAGCA
*
111910 AATGAGCAATGGAGCTTGTGGGACACTGCTCAC
130 AATGAACAATGGAGCTTGTGGGACACTGCTCAC
*
111943 AATTTGGAGGAATTGCTGACTTGGTTTGCTTCATTGTTTT
1 AATTTGGAGGAATTGCTGACTTGGTCTGCTTCATTGTTTT
111983 CTTTTATCAA
Statistics
Matches: 182, Mismatches: 14, Indels: 14
0.87 0.07 0.07
Matches are distributed among these distances:
158 4 0.02
159 106 0.58
160 7 0.04
163 36 0.20
168 28 0.15
169 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.23, T:0.41
Consensus pattern (162 bp):
AATTTGGAGGAATTGCTGACTTGGTCTGCTTCATTGTTTTTTTGGTTTTGCTATAAGTTCTATTT
TATTTTATTATTTTCTCATCATGGGAGGACGAGGAGAACCAACTAACTTTCAAATGCTGGAGCAA
ATGAACAATGGAGCTTGTGGGACACTGCTCAC
Found at i:127960 original size:60 final size:60
Alignment explanation
Indices: 127838--127964 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
127828 AGTATATACA
* * * * *
127838 CATAGTTTGGGATGAAATTGGAATGTTCAAAAAGTTTGGAGACTAATTTAGAAAGCGGGT
1 CATAGTTGGGGATAAAATTGAAATGTTCAAAAAGTTTGGAGACTAATTTAGAAAGAGAGT
*
127898 CATAGTATGGGGATAAAATTGAAATGTTC-AAAAGTTT-GAGGACTAATTTA-AAATGATAGT
1 CATAGT-TGGGGATAAAATTGAAATGTTCAAAAAGTTTGGA-GACTAATTTAGAAA-GAGAGT
127958 CATAGTT
1 CATAGTT
127965 TAGGATACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
59 6 0.10
60 33 0.57
61 19 0.33
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.31
Consensus pattern (60 bp):
CATAGTTGGGGATAAAATTGAAATGTTCAAAAAGTTTGGAGACTAATTTAGAAAGAGAGT
Found at i:130008 original size:32 final size:32
Alignment explanation
Indices: 129957--130020 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
129947 AATACAACCA
* * * *
129957 ACGATCGGTAACTAGTATCAAAACTGATACCG
1 ACGATCGATAACCAATATCAAAACTAATACCG
*
129989 ACGATCGATAACCAATATCAAAATTAATACCG
1 ACGATCGATAACCAATATCAAAACTAATACCG
130021 CTGTCGGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (32 bp):
ACGATCGATAACCAATATCAAAACTAATACCG
Found at i:131063 original size:11 final size:11
Alignment explanation
Indices: 131047--131078 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
131037 GACACTGAAG
131047 GATTATTCAAT
1 GATTATTCAAT
131058 GATTATTCAAT
1 GATTATTCAAT
*
131069 GATCATTCAA
1 GATTATTCAA
131079 ACAATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (11 bp):
GATTATTCAAT
Found at i:131262 original size:116 final size:116
Alignment explanation
Indices: 131058--131612 Score: 765
Period size: 116 Copynumber: 4.9 Consensus size: 116
131048 ATTATTCAAT
131058 GATTATTCAATGATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGC
1 GATTATTCAATGATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGC
131123 TTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAG
66 TTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAG
*
131174 GATTATTCAATGATCATTCAAATAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGC
1 GATTATTCAATGATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGC
131239 TTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAG
66 TTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAG
* * * *
131290 GATTATTCAATGATCATTC-AACTCATTGTCAAGGCAATGAATTGAACAAAAACTTCATTGTTA-
1 GATTATTCAATGATCATTCAAAC-AATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAG
* * *
131353 CTTTAATTTAGTTCTCTGGGTATTGTTAGTTTCCCGGAAAATTGGCACTGAAG
65 C-TTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAG
* **
131406 GATTGTTCAATGATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAAT
1 GATTATTCAATGATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGC
* * *
131471 TTGATTTAGTTATCTGGGTATTTTTATTTT--C----AATTGACACTG-AG
66 TTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAG
131515 GATTATTC----A--ATT----C-ATTGTAAAGACAATGAATTGAACAAAAACTTCGAAT-TTAG
1 GATTATTCAATGATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTC-AATGTTAG
* * * * *
131568 TTTAATTTAGTTCTCTGGGCAGTATTATCTTCCTGGAAAATTGAC
65 CTTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGAC
131613 TCCTTTTAAA
Statistics
Matches: 399, Mismatches: 29, Indels: 34
0.86 0.06 0.07
Matches are distributed among these distances:
98 60 0.15
99 4 0.01
103 3 0.01
104 7 0.02
105 1 0.00
109 9 0.02
110 10 0.03
114 1 0.00
115 3 0.01
116 298 0.75
117 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (116 bp):
GATTATTCAATGATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGC
TTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAG
Found at i:131408 original size:232 final size:238
Alignment explanation
Indices: 130991--131501 Score: 757
Period size: 232 Copynumber: 2.2 Consensus size: 238
130981 GGCTTCAGAA
* * * *
130991 TTAGCTTAGTTTAGCTCTCTGGGCATTGTTATTTTCCCGGAAAATTGACACTGAAGGATTATTCA
1 TTAGCTTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAGGATTATTCA
*
131056 ATGATTATTCAATGATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTA
66 ATGATCATTCAA-GATCA-T---ACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTA
*
131121 GCTTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAGGATTATTCAATG
126 GCTTAATTTAGTTCTCTGGGTATTATTAGTTTCCCGGAAAATTGACACTGAAGGATTATTCAATG
*
131186 ATCATTCAAATAATTGTAAAGACAATGAATTGAACAAAAACTTCAATG
191 ATCATTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATG
131234 TTAGCTTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAGGATTATTCA
1 TTAGCTTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAGGATTATTCA
* * *
131299 ATGATCATTC-A-A-C-T-C-ATTGTCAAGGCAATGAATTGAACAAAAACTTCATTGTTA-CTTT
66 ATGATCATTCAAGATCATACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGC-TT
* * *
131357 AATTTAGTTCTCTGGGTATTGTTAGTTTCCCGGAAAATTGGCACTGAAGGATTGTTCAATGATCA
130 AATTTAGTTCTCTGGGTATTATTAGTTTCCCGGAAAATTGACACTGAAGGATTATTCAATGATCA
131422 TTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATG
195 TTCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATG
** * * *
131466 TTAATTTGATTTAGTTATCTGGGTATTTTTATTTTC
1 TTAGCTTAATTTAGTTCTCTGGGTATTATTATTTTC
131502 AATTGACACT
Statistics
Matches: 249, Mismatches: 18, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
231 1 0.00
232 173 0.69
233 1 0.00
237 1 0.00
239 1 0.00
240 1 0.00
242 1 0.00
243 70 0.28
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (238 bp):
TTAGCTTAATTTAGTTCTCTGGGTATTATTATTTTCCCGGAAAATTGACACTGAAGGATTATTCA
ATGATCATTCAAGATCATACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGCTTA
ATTTAGTTCTCTGGGTATTATTAGTTTCCCGGAAAATTGACACTGAAGGATTATTCAATGATCAT
TCAAACAATTGTAAAGACAATGAATTGAACAAAAACTTCAATG
Found at i:133424 original size:13 final size:13
Alignment explanation
Indices: 133406--133430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
133396 TAAGATATGA
133406 TCACTTTCATTTG
1 TCACTTTCATTTG
133419 TCACTTTCATTT
1 TCACTTTCATTT
133431 TTATTTAATT
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:0.16, C:0.24, G:0.04, T:0.56
Consensus pattern (13 bp):
TCACTTTCATTTG
Found at i:133915 original size:33 final size:33
Alignment explanation
Indices: 133829--133916 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 33
133819 ATATATTTAG
*
133829 AAAATTAAGATAAAATATA-TACTTTAAAAAGTT
1 AAAATTAAG-TAAAATATATTTCTTTAAAAAGTT
*
133862 AAAATAATAGTAAAATATATTTC-TTAAAAAGTT
1 AAAATTA-AGTAAAATATATTTCTTTAAAAAGTT
* *
133895 TAAATTAAGTTCAAATATATTT
1 AAAATTAAG-TAAAATATATTT
133917 TATTTAATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
32 2 0.04
33 41 0.87
34 4 0.09
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (33 bp):
AAAATTAAGTAAAATATATTTCTTTAAAAAGTT
Found at i:138486 original size:51 final size:51
Alignment explanation
Indices: 138410--138513 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
138400 ATCTCGATTC
*
138410 GTTTCGTATTGGCGTAAAAAAAATTATAAGATGAGAAAAGTAAAATGATCA
1 GTTTCGTATTGGCATAAAAAAAATTATAAGATGAGAAAAGTAAAATGATCA
* * *
138461 GTTTCGTATTGGCATAACAAAAATTATATGTTGAGAAAAGTAAAATGATCA
1 GTTTCGTATTGGCATAAAAAAAATTATAAGATGAGAAAAGTAAAATGATCA
138512 GT
1 GT
138514 GGCATAGCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (51 bp):
GTTTCGTATTGGCATAAAAAAAATTATAAGATGAGAAAAGTAAAATGATCA
Found at i:145841 original size:22 final size:22
Alignment explanation
Indices: 145816--145866 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
145806 CACCACAGCT
*
145816 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
145838 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
145860 CGTAGAA
1 CGTAGAA
145867 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:145867 original size:22 final size:22
Alignment explanation
Indices: 145824--145868 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
145814 CTCGTATAAA
145824 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
145846 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
145868 T
1 T
145869 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:146129 original size:30 final size:31
Alignment explanation
Indices: 146088--146147 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
146078 TAGACATAGT
*
146088 ATTTCCATACCTTTAACACACAG-GCATATC
1 ATTTACATACCTTTAACACACAGTGCATATC
* *
146118 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACACAGTGCATAT
146148 AACTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (31 bp):
ATTTACATACCTTTAACACACAGTGCATATC
Found at i:146204 original size:29 final size:29
Alignment explanation
Indices: 146162--146233 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
146152 TTTTCTGCAT
**
146162 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
146191 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
146220 ATTCATGTCATGTA
1 ATTCATGTCATGTA
146234 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:146570 original size:19 final size:20
Alignment explanation
Indices: 146533--146572 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
146523 CTTTTTCTCA
*
146533 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
146553 TGGGGGTATCGATTCCCCCC
1 TGGGGGAATCGATTCCCCCC
146573 AAGCAATCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.35, G:0.33, T:0.23
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:146669 original size:67 final size:68
Alignment explanation
Indices: 146534--146684 Score: 225
Period size: 68 Copynumber: 2.2 Consensus size: 68
146524 TTTTTCTCAT
* * *
146534 GGGGGAATCGGTT-CCCCCCTGGGGGTATCGATTCCCCCCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCCCAAGCAATCTGGAAATTCATATACGA
146598 TGA
66 TGA
* * * *
146601 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCAATCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCCCAAGCAATCTGGAAATTCATATACGA
146665 TGA
66 TGA
146668 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
146685 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
67 35 0.46
68 41 0.54
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCCCAAGCAATCTGGAAATTCATATACGA
TGA
Found at i:146696 original size:67 final size:67
Alignment explanation
Indices: 146534--146706 Score: 224
Period size: 67 Copynumber: 2.6 Consensus size: 67
146524 TTTTTCTCAT
* * * *
146534 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCCCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
146599 GA
66 GA
* * *
146601 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCAATCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
146665 TGA
65 TGA
* *
146668 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
146707 AACCCAGAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 6 0.06
67 47 0.50
68 41 0.44
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:152764 original size:22 final size:22
Alignment explanation
Indices: 152739--152789 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
152729 CACCACAGCT
*
152739 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
152761 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
152783 CGTAGAA
1 CGTAGAA
152790 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:152790 original size:22 final size:22
Alignment explanation
Indices: 152747--152791 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
152737 CTCGTATAAA
152747 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
152769 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
152791 T
1 T
152792 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:153052 original size:30 final size:31
Alignment explanation
Indices: 153011--153070 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
153001 TAGACATAGT
*
153011 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
153041 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
153071 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:153127 original size:29 final size:29
Alignment explanation
Indices: 153085--153156 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
153075 TTTTCTGCAT
**
153085 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
153114 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
153143 ATTCATGTCATGTA
1 ATTCATGTCATGTA
153157 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:153495 original size:19 final size:20
Alignment explanation
Indices: 153458--153496 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
153448 CTTTTTCTCA
*
153458 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
153478 TGGGGGTATCGATTCCCCC
1 TGGGGGAATCGATTCCCCC
153497 AAGCAATCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.33, G:0.33, T:0.23
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:153619 original size:67 final size:67
Alignment explanation
Indices: 153459--153630 Score: 224
Period size: 67 Copynumber: 2.6 Consensus size: 67
153449 TTTTTCTCAT
* * *
153459 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCC-CAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
153523 GA
66 GA
* * *
153525 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCAATCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
153589 TGA
65 TGA
* *
153592 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
153631 AACCCAGAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
65 6 0.06
66 12 0.13
67 58 0.62
68 18 0.19
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:155542 original size:2 final size:2
Alignment explanation
Indices: 155535--155562 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
155525 TGGCACTTTC
155535 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
155563 TAAATTGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:155914 original size:41 final size:43
Alignment explanation
Indices: 155828--155915 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 43
155818 AATCAAATTA
* * ** *
155828 AAATAATGTTATATATATAATTGAATCAAGTTTAAGAATATAC
1 AAATAATCTTATATATATAATTGAAACAAGGGTAAGAATACAC
* *
155871 AAATAATCTTATATATATAATT-AAACTAGGGTAA-AGTACAC
1 AAATAATCTTATATATATAATTGAAACAAGGGTAAGAATACAC
155912 AAAT
1 AAAT
155916 GGTTTCCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 9 0.24
42 8 0.21
43 21 0.55
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (43 bp):
AAATAATCTTATATATATAATTGAAACAAGGGTAAGAATACAC
Found at i:162409 original size:4 final size:4
Alignment explanation
Indices: 162400--162458 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
162390 ACTAATCTAC
162400 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
162448 TATT TATT TAT
1 TATT TATT TAT
162459 ATTTCAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:163465 original size:38 final size:38
Alignment explanation
Indices: 163421--163495 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
163411 AATCGATTCA
* * *
163421 AAAATTATACACCCTCCATTCGATTTGAACTTGACCCG
1 AAAATTATACACCCTCCATCCGACTCGAACTTGACCCG
* *
163459 AAAATTATATACCCTTCATCCGACTCGAACTTGACCC
1 AAAATTATACACCCTCCATCCGACTCGAACTTGACCC
163496 ATTTTTTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.32, C:0.31, G:0.09, T:0.28
Consensus pattern (38 bp):
AAAATTATACACCCTCCATCCGACTCGAACTTGACCCG
Found at i:181090 original size:31 final size:31
Alignment explanation
Indices: 181050--181110 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
181040 AAATTAAGTA
* *
181050 TTTAGTATTT-AAATTATCATTTTTAGTTTAT
1 TTTAATATTTAAAATT-TAATTTTTAGTTTAT
*
181081 TTTAATATTTAAAATTTAATTTTTATTTTA
1 TTTAATATTTAAAATTTAATTTTTAGTTTA
181111 GGGTCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (31 bp):
TTTAATATTTAAAATTTAATTTTTAGTTTAT
Found at i:182101 original size:2 final size:2
Alignment explanation
Indices: 182094--182153 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
182084 TCGGTTAGTT
182094 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
*
182136 TA TA -A T- TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA
182154 ATCAATTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:182160 original size:18 final size:18
Alignment explanation
Indices: 182094--182162 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 18
182084 TCGGTTAGTT
*
182094 TATATAT-ATATATATATA
1 TATATATAAT-TATATAAA
*
182112 TATATATATATATATATATA
1 TATATATA-AT-TATATAAA
182132 TATATATAATTATATAAA
1 TATATATAATTATATAAA
182150 TATA-ATCAATTAT
1 TATATAT-AATTAT
182163 TTACATTATG
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
17 2 0.04
18 24 0.51
19 2 0.04
20 19 0.40
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATATAATTATATAAA
Found at i:182392 original size:15 final size:15
Alignment explanation
Indices: 182372--182415 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
182362 CCCAGAAGTT
182372 TCGGGTATCCGGAAA
1 TCGGGTATCCGGAAA
* **
182387 TCGGGTACCCAAAAA
1 TCGGGTATCCGGAAA
182402 TCCGGGTATCCGGA
1 T-CGGGTATCCGGA
182416 TTTGCACACT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (15 bp):
TCGGGTATCCGGAAA
Found at i:185731 original size:33 final size:32
Alignment explanation
Indices: 185689--185752 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
185679 AAATTGTCCT
* *
185689 TATTATATATTTATTTTTTTAACAAATTATAAAA
1 TATTATATATATA-TTTTTTAAAAAATT-TAAAA
185723 TATT-TATATATATTTTTTAAAAAATTTAAA
1 TATTATATATATATTTTTTAAAAAATTTAAA
185753 TTAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 4 0.14
32 13 0.46
33 7 0.25
34 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTATATATATATTTTTTAAAAAATTTAAAA
Found at i:185795 original size:35 final size:37
Alignment explanation
Indices: 185724--185796 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
185714 ATTATAAAAT
* *
185724 ATTTATATATATTTTTTAAAAAATTTAAATTAATAAA
1 ATTTATATATATTTTTTAAAAAATTAAAAATAATAAA
* *
185761 ATTTATAT-TTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATATATATTTTTTAAAAAATTAAAAATAATAAA
185796 A
1 A
185797 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 6 0.19
36 18 0.56
37 8 0.25
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTATATATATTTTTTAAAAAATTAAAAATAATAAA
Found at i:189931 original size:2 final size:2
Alignment explanation
Indices: 189924--189954 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
189914 TCTTTTAATT
189924 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 T
189955 GACAAGGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:192225 original size:24 final size:24
Alignment explanation
Indices: 192189--192234 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
192179 GAACCTAAAT
* *
192189 ATTATGAAAAATATAATATTTTCG
1 ATTATGAAAAATAAAACATTTTCG
* *
192213 ATTATTAAGAATAAAACATTTT
1 ATTATGAAAAATAAAACATTTT
192235 AGGTTCAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (24 bp):
ATTATGAAAAATAAAACATTTTCG
Found at i:204182 original size:23 final size:21
Alignment explanation
Indices: 204156--204212 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
204146 TTTACCCATT
204156 TAATTTTAAAACATTATTGCACC
1 TAATTTT--AACATTATTGCACC
* * *
204179 TAATTTTGACATTGTTGTACC
1 TAATTTTAACATTATTGCACC
*
204200 TAATTTTGACATT
1 TAATTTTAACATT
204213 GCAATATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 24 0.77
23 7 0.23
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.46
Consensus pattern (21 bp):
TAATTTTAACATTATTGCACC
Found at i:204200 original size:21 final size:21
Alignment explanation
Indices: 204166--204213 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
204156 TAATTTTAAA
*
204166 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
*
204187 ACATTGTTGTACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
204208 ACATTG
1 ACATTG
204214 CAATATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:205404 original size:16 final size:18
Alignment explanation
Indices: 205372--205405 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
205362 TATTAATGTA
205372 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
205390 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
205406 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:205924 original size:23 final size:21
Alignment explanation
Indices: 205898--205944 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
205888 GTGTCACCAA
*
205898 TAACATATGTCATGATCATGTGT
1 TAACACATGTCA-GATCATG-GT
*
205921 TAACACATGTCAGATCCTGGT
1 TAACACATGTCAGATCATGGT
205942 TAA
1 TAA
205945 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (21 bp):
TAACACATGTCAGATCATGGT
Found at i:206075 original size:130 final size:130
Alignment explanation
Indices: 205871--206118 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
205861 AATTTTCTTC
* *
205871 TAATTAGGTGGTGACATGTGTCACCAATAACATATGTCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATGTCATGATCATGTGCTAACACATGTCAGAT
** *
205936 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
206001 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATGTCATGATCATGTGCTAACACATGTCAGAT
206066 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
206119 TATATAAATA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATGTCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:206565 original size:35 final size:35
Alignment explanation
Indices: 206515--206590 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
206505 AATTGAATTT
* * *
206515 AATTGAATTATTTTGGAATTTAGTGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
206550 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
206585 AATTGA
1 AATTGA
206591 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:218589 original size:33 final size:33
Alignment explanation
Indices: 218537--218621 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
218527 GACCATCCGA
* * * *
218537 CCGAGGTCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
218570 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
* *
218603 CCGAGGGTAACCGTGCGAG
1 CCGAGGGCAACCGAGCGAG
218622 GGTAGGTCGC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.25, C:0.26, G:0.38, T:0.12
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:218668 original size:21 final size:20
Alignment explanation
Indices: 218644--218686 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
218634 GGAGTACATG
218644 GCGACCTACGTAGGTCGCCAT
1 GCGACCT-CGTAGGTCGCCAT
*
218665 GCGACCTTGTAGGTCGCCAT
1 GCGACCTCGTAGGTCGCCAT
218685 GC
1 GC
218687 ACTCCGGGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (20 bp):
GCGACCTCGTAGGTCGCCAT
Found at i:218727 original size:10 final size:10
Alignment explanation
Indices: 218708--218835 Score: 103
Period size: 10 Copynumber: 12.5 Consensus size: 10
218698 CCTACCCTCG
*
218708 CTCGGTTGCC
1 CTCGGATGCC
218718 CTCGGATGCC
1 CTCGGATGCC
*
218728 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
218740 GTTCGGATGGC
1 -CTCGGATGCC
*
218751 CTCGGATGCT
1 CTCGGATGCC
*
218761 CTCGGATGGC
1 CTCGGATGCC
*
218771 CTCGGATGCT
1 CTCGGATGCC
*
218781 CTCGGATGGC
1 CTCGGATGCC
*
218791 CTCGGATGCT
1 CTCGGATGCC
**
218801 CTCGGATGGT
1 CTCGGATGCC
*
218811 CTCGGATGCT
1 CTCGGATGCC
* *
218821 TTCGGATGGC
1 CTCGGATGCC
218831 CTCGG
1 CTCGG
218836 TCGAATGGCC
Statistics
Matches: 93, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
10 83 0.89
11 3 0.03
12 2 0.02
13 5 0.05
ACGTcount: A:0.09, C:0.30, G:0.34, T:0.27
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:218767 original size:20 final size:20
Alignment explanation
Indices: 218708--218835 Score: 175
Period size: 20 Copynumber: 6.2 Consensus size: 20
218698 CCTACCCTCG
* * *
218708 CTCGGTTGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
*
218728 CTCGCATAGCTCGTTCGGATGGC
1 CTCGGAT-GCTC--TCGGATGGC
218751 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
218771 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
*
218791 CTCGGATGCTCTCGGATGGT
1 CTCGGATGCTCTCGGATGGC
*
218811 CTCGGATGCTTTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
218831 CTCGG
1 CTCGG
218836 TCGAATGGCC
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
20 76 0.78
21 3 0.03
22 4 0.04
23 14 0.14
ACGTcount: A:0.09, C:0.30, G:0.34, T:0.27
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:219225 original size:29 final size:29
Alignment explanation
Indices: 219183--219238 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
219173 TGTTTGTCGT
**
219183 AGGTCGCTGGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
219212 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
219239 TGTGTTGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.41, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:219348 original size:10 final size:11
Alignment explanation
Indices: 219335--219397 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 11
219325 ACACGGTGGG
219335 CATCCGAG-GC
1 CATCCGAGAGC
219345 CATCCGAGAAGC
1 CATCCGAG-AGC
* *
219357 TATGCGAGAG-
1 CATCCGAGAGC
219367 CATCCGAG-GC
1 CATCCGAGAGC
219377 CATCCGACCGAGGC
1 CATCCGA--GA-GC
219391 CATCCGA
1 CATCCGA
219398 CCAAGGGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 1 0.02
10 21 0.50
11 2 0.05
12 9 0.21
14 9 0.21
ACGTcount: A:0.25, C:0.35, G:0.29, T:0.11
Consensus pattern (11 bp):
CATCCGAGAGC
Found at i:219389 original size:14 final size:14
Alignment explanation
Indices: 219370--219426 Score: 96
Period size: 14 Copynumber: 4.1 Consensus size: 14
219360 GCGAGAGCAT
219370 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
219384 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
* *
219398 CCAAGGGCATCCGA
1 CCGAGGCCATCCGA
219412 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
219426 C
1 C
219427 TGAATTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.23, C:0.42, G:0.28, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:219540 original size:29 final size:29
Alignment explanation
Indices: 219498--219611 Score: 192
Period size: 29 Copynumber: 3.9 Consensus size: 29
219488 AAGCAAGGGT
*
219498 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
219527 AGGTCGCCAGGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
*
219556 AGGTCGCCAGGATTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
* *
219585 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCAGGAGTGCATGGCGACCTA
219612 TGCTTGGGGA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.22, C:0.29, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCAGGAGTGCATGGCGACCTACA
Found at i:220371 original size:23 final size:21
Alignment explanation
Indices: 220327--220383 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
220317 GAAAAACGTG
*
220327 TCATAAAGATATAGATAAATA
1 TCATAAAGACATAGATAAATA
220348 TACCATAAAGACATAGA-AACATA
1 T--CATAAAGACATAGATAA-ATA
*
220371 TCACAAAGACATA
1 TCATAAAGACATA
220384 ATTATTCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 12 0.39
22 2 0.06
23 17 0.55
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (21 bp):
TCATAAAGACATAGATAAATA
Found at i:220494 original size:18 final size:18
Alignment explanation
Indices: 220473--220525 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
220463 GTTAAATAAA
*
220473 ATTAAAGAAAAAAATTAG
1 ATTAAACAAAAAAATTAG
* *
220491 ATTAATCAATAAAATTAG
1 ATTAAACAAAAAAATTAG
* *
220509 ATTAATCAATAAAATTA
1 ATTAAACAAAAAAATTA
220526 ACACAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (18 bp):
ATTAAACAAAAAAATTAG
Found at i:223748 original size:41 final size:41
Alignment explanation
Indices: 223703--223784 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
223693 AGTAATGAAA
223703 GGGCTGGAGGAGTGTATGTGTAACGGTGTCCTTGCAGGCTT
1 GGGCTGGAGGAGTGTATGTGTAACGGTGTCCTTGCAGGCTT
223744 GGGCTGGAGGAGTGTATGTGTAACGGTGTCCTTGCAGGCTT
1 GGGCTGGAGGAGTGTATGTGTAACGGTGTCCTTGCAGGCTT
223785 TCCTGTTGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.29
Consensus pattern (41 bp):
GGGCTGGAGGAGTGTATGTGTAACGGTGTCCTTGCAGGCTT
Found at i:230236 original size:21 final size:20
Alignment explanation
Indices: 230196--230240 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
230186 TATTCAAAAT
230196 ATAAAATATCTTAAAATATA
1 ATAAAATATCTTAAAATATA
*
230216 ATAAATATAT-TTATAATTATA
1 ATAAA-ATATCTTA-AAATATA
230237 ATAA
1 ATAA
230241 TAAATTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAATATCTTAAAATATA
Found at i:230680 original size:23 final size:23
Alignment explanation
Indices: 230654--230702 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
230644 AGCGTGTCAC
*
230654 AAAAACAGATGAAAATGTGCCAT
1 AAAAACAGATAAAAATGTGCCAT
*
230677 AAAAATAGATAAAAATGTGCCAT
1 AAAAACAGATAAAAATGTGCCAT
230700 AAA
1 AAA
230703 GATGAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.18
Consensus pattern (23 bp):
AAAAACAGATAAAAATGTGCCAT
Found at i:249104 original size:35 final size:35
Alignment explanation
Indices: 248992--249123 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 35
248982 AGAAGAAAAA
248992 AAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGG
1 AAGGAAGCATCAGCACTTTCGATTC-AAGTGAACGG
* * *
249028 AAGGAAGCATCGGCACTTTCGATTCAAGAAGAACGA
1 AAGGAAGCATCAGCACTTTCGATTCAAG-TGAACGG
* *
249064 AAGGAAGCACCGGCACTTTCGATTCAAGTGAACGG
1 AAGGAAGCATCAGCACTTTCGATTCAAGTGAACGG
*
249099 AAGGAAGCGTCAGCACTTTCGATTC
1 AAGGAAGCATCAGCACTTTCGATTC
249124 GGTTGTTCAT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 30 0.35
36 56 0.65
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (35 bp):
AAGGAAGCATCAGCACTTTCGATTCAAGTGAACGG
Found at i:256316 original size:29 final size:28
Alignment explanation
Indices: 256274--256332 Score: 109
Period size: 29 Copynumber: 2.1 Consensus size: 28
256264 AAGCACTGTT
256274 GTGGGATATCAAAATTAAATCAACTTACA
1 GTGGGATATCAAAATTAAAT-AACTTACA
256303 GTGGGATATCAAAATTAAATAACTTACA
1 GTGGGATATCAAAATTAAATAACTTACA
256331 GT
1 GT
256333 CAGTTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (28 bp):
GTGGGATATCAAAATTAAATAACTTACA
Found at i:256460 original size:38 final size:37
Alignment explanation
Indices: 256409--256483 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 37
256399 GGTATCAGGC
256409 GACAACTCAGTTTGCTCGGATCCTAATCTTTTTATTTG
1 GACAACTCAGTTTGCTCGGATCCTAATC-TTTTATTTG
256447 GACAACTCAGTTTGCTCGGATCCTAATCTTTTATTTG
1 GACAACTCAGTTTGCTCGGATCCTAATCTTTTATTTG
256484 ACTAAAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 9 0.24
38 28 0.76
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (37 bp):
GACAACTCAGTTTGCTCGGATCCTAATCTTTTATTTG
Found at i:257182 original size:11 final size:10
Alignment explanation
Indices: 257161--257240 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 10
257151 TAAAATAATC
257161 ATTAAAT-TT
1 ATTAAATGTT
*
257170 ATTGAATAGTT
1 ATTAAAT-GTT
*
257181 ATAAAATGATT
1 ATTAAATG-TT
*
257192 ATTAAATTTT
1 ATTAAATGTT
*
257202 ATTGAATAGTT
1 ATTAAAT-GTT
*
257213 ATAAAATGATT
1 ATTAAATG-TT
*
257224 ATTAAATTTT
1 ATTAAATGTT
*
257234 ATCAAAT
1 ATTAAAT
257241 AATTAATAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
9 6 0.11
10 18 0.33
11 30 0.56
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (10 bp):
ATTAAATGTT
Found at i:257208 original size:32 final size:32
Alignment explanation
Indices: 257149--257235 Score: 149
Period size: 32 Copynumber: 2.8 Consensus size: 32
257139 ATTTTATTAG
* *
257149 TATAAAATAATCATTAAA-TTTATTGAATAGT
1 TATAAAATGATTATTAAATTTTATTGAATAGT
257180 TATAAAATGATTATTAAATTTTATTGAATAGT
1 TATAAAATGATTATTAAATTTTATTGAATAGT
257212 TATAAAATGATTATTAAATTTTAT
1 TATAAAATGATTATTAAATTTTAT
257236 CAAATAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
31 16 0.30
32 37 0.70
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (32 bp):
TATAAAATGATTATTAAATTTTATTGAATAGT
Found at i:257235 original size:21 final size:21
Alignment explanation
Indices: 257211--257251 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
257201 TATTGAATAG
* *
257211 TTATAAAATGATTATTAAATT
1 TTATAAAATAATTAATAAATT
*
257232 TTATCAAATAATTAATAAAT
1 TTATAAAATAATTAATAAAT
257252 AATCATTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATAAAATAATTAATAAATT
Found at i:257285 original size:20 final size:22
Alignment explanation
Indices: 257238--257288 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
257228 AATTTTATCA
257238 AATAATTAATAAATAATCATTAT
1 AATAATTAAT-AATAATCATTAT
*
257261 CATAATTAAT-ATAAT-ATTAT
1 AATAATTAATAATAATCATTAT
257281 AATAATTA
1 AATAATTA
257289 TTTTATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 12 0.46
21 5 0.19
23 9 0.35
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAATTAATAATAATCATTAT
Found at i:258835 original size:84 final size:84
Alignment explanation
Indices: 258694--258860 Score: 307
Period size: 84 Copynumber: 2.0 Consensus size: 84
258684 CAAATTCAAG
258694 CAGAAGAAGAAACAGTCTAACAGAGTTTAACCAGGTTGAGTTGCAACAATAACTAAAACAGCAAT
1 CAGAAGAAGAAACAGTCTAACAGAGTTTAACCAGGTTGAGTTGCAACAATAACTAAAACAGCAAT
*
258759 GGCAAGGAGCAGAAGCAAC
66 GGCAAGGAACAGAAGCAAC
* *
258778 CAGAAGAAGAAACAGTCTAGCAGAGTTTAACCAGGTTGAGTTGCATCAATAACTAAAACAGCAAT
1 CAGAAGAAGAAACAGTCTAACAGAGTTTAACCAGGTTGAGTTGCAACAATAACTAAAACAGCAAT
258843 GGCAAGGAACAGAAGCAA
66 GGCAAGGAACAGAAGCAA
258861 AAGGAGAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (84 bp):
CAGAAGAAGAAACAGTCTAACAGAGTTTAACCAGGTTGAGTTGCAACAATAACTAAAACAGCAAT
GGCAAGGAACAGAAGCAAC
Found at i:263444 original size:20 final size:21
Alignment explanation
Indices: 263413--263454 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
263403 ATTTTCTCGT
263413 ATTTTATTAATTGTATTT-TTA
1 ATTTTATTAATT-TATTTATTA
263434 ATTTT-TTAATTTATTTATTA
1 ATTTTATTAATTTATTTATTA
263454 A
1 A
263455 ACTTTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTATTAATTTATTTATTA
Found at i:263460 original size:20 final size:20
Alignment explanation
Indices: 263419--263465 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
263409 TCGTATTTTA
**
263419 TTAATTGTATTTTTAATTTT
1 TTAATTGTATTTTTAAACTT
263439 TTAATT-TATTTATTAAACTT
1 TTAATTGTATTT-TTAAACTT
263459 TTGAATT
1 TT-AATT
263466 AGTCTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 14 0.61
21 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (20 bp):
TTAATTGTATTTTTAAACTT
Found at i:267757 original size:24 final size:24
Alignment explanation
Indices: 267730--267776 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
267720 TGGACACGGA
*
267730 GGAGGTGGTGGCA-ATGGAGGTGGT
1 GGAGGTAGT-GCAGATGGAGGTGGT
*
267754 GGAGGTAGTGCAGGTGGAGGTGG
1 GGAGGTAGTGCAGATGGAGGTGG
267777 AGCTTCAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.17, C:0.04, G:0.60, T:0.19
Consensus pattern (24 bp):
GGAGGTAGTGCAGATGGAGGTGGT
Done.