Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005176.1 Hibiscus syriacus cultivar Beakdansim tig00011677_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: 252380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1709 original size:90 final size:90
Alignment explanation
Indices: 1596--1773 Score: 304
Period size: 90 Copynumber: 2.0 Consensus size: 90
1586 TAATCCCGAA
* * *
1596 TATTTAATTTTAATTAATTAAATATAGATTTAATTCATTTGAAATAATAAAATA-CCTAATATGA
1 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-ACCCTAATATGA
1660 TTAGGGTAACTTGGATATAAAAGGAT
65 TTAGGGTAACTTGGATATAAAAGGAT
1686 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
1751 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
1774 GTGTGTTAGT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
89 1 0.01
90 82 0.99
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:8419 original size:90 final size:89
Alignment explanation
Indices: 8296--8472 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
8286 TAATCCTCAA
* *
8296 TATTTAATTTCAATTAAATAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAAATAAATATAGATTTAATTAATTTAAAATAATAAAA-ACCTAATATGAT
8361 TAGGGTAACCTGGATATAAAAGGAT
65 TAGGGTAACCTGGATATAAAAGGAT
*
8386 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCTAATATGATT
1 TATTAAATTTCAATTAAATAAATATAGATTTAATTAATTTAAAATAATAAAAACCTAATATGATT
* *
8451 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACCTGGATATAAAAGG
8473 GTGTGTTAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 32 0.39
90 50 0.61
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (89 bp):
TATTAAATTTCAATTAAATAAATATAGATTTAATTAATTTAAAATAATAAAAACCTAATATGATT
AGGGTAACCTGGATATAAAAGGAT
Found at i:8981 original size:31 final size:31
Alignment explanation
Indices: 8943--9053 Score: 195
Period size: 31 Copynumber: 3.5 Consensus size: 31
8933 AGGTTCGAGG
*
8943 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
8974 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
9005 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
9036 GATTTACCTAGGTTCTTC
1 G-TTTACCTATGTTCTTC
9054 AGAATCTATG
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 62 0.81
32 15 0.19
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:11557 original size:3 final size:3
Alignment explanation
Indices: 11549--11595 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
11539 AATTTTTTCA
* * *
11549 TAT TAT TAT TTT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
11596 AATATATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:11604 original size:2 final size:2
Alignment explanation
Indices: 11597--11634 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
11587 TTATTATTAA
*
11597 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11635 CAAGGCCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12080 original size:14 final size:15
Alignment explanation
Indices: 12061--12089 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12051 CTTAGTGGGG
12061 TAATAATAT-AATAA
1 TAATAATATCAATAA
12075 TAATAATATCAATAA
1 TAATAATATCAATAA
12090 ATATAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATAATATCAATAA
Found at i:12328 original size:23 final size:23
Alignment explanation
Indices: 12302--12365 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
12292 CAGCTCATAT
12302 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
*
12325 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCTA-AGTGCCACGTAG
12348 AATTGCACCGT-AGTGCCA
1 AATTGCACC-TAAGTGCCA
12366 TATAATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:12667 original size:103 final size:103
Alignment explanation
Indices: 12381--12703 Score: 565
Period size: 103 Copynumber: 3.1 Consensus size: 103
12371 TAATGTCCAT
*
12381 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
12446 GACTTCACACATATTCCAAAGAATACTTATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
12484 AAGTACCACATATCATTCCTTAAGAATTATATATACATATACCAAGGATCAAGTATGTGTCTCAC
1 AAGGACCACATATCATTCCTTAAGAA-T-CATATACATATACCAAGGATCAAGTATGTGTCTCAC
12549 CAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
64 CAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
12589 AAGGACCATATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
12654 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
12692 AAGGACCACATA
1 AAGGACCACATA
12704 GACCCTCTAC
Statistics
Matches: 208, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
103 110 0.53
104 2 0.01
105 96 0.46
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:13222 original size:19 final size:20
Alignment explanation
Indices: 13185--13222 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13175 TTTTTTATTA
*
13185 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
13205 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
13223 TATAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:13274 original size:21 final size:21
Alignment explanation
Indices: 13250--13292 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13240 TCATATTCGT
*
13250 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
13271 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
13292 T
1 T
13293 AGCCCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:19352 original size:23 final size:23
Alignment explanation
Indices: 19326--19389 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
19316 CAGCTCATAT
*
19326 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
19349 AATTGCATCGGAGTGCCATGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
19372 AATTGCATCGGAGTGCCA
1 AATTGCACCGAAGTGCCA
19390 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:19390 original size:23 final size:23
Alignment explanation
Indices: 19337--19390 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
19327 ATTGCACCTA
*
19337 AGTGCCACGTAGAATTGCATCGG
1 AGTGCCATGTAGAATTGCATCGG
19360 AGTGCCATGTAGAATTGCATCGG
1 AGTGCCATGTAGAATTGCATCGG
19383 AGTGCCAT
1 AGTGCCAT
19391 ATAATAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (23 bp):
AGTGCCATGTAGAATTGCATCGG
Found at i:19754 original size:103 final size:103
Alignment explanation
Indices: 19405--19723 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
19395 TAATGTCCAT
*
19405 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
19470 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
19508 AAGAACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
19573 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
19611 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
19676 GACCTCACACATGTTCC-AA-AATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
19712 AAGGACCACATA
1 AAGGACCACATA
19724 GACCCTCTAC
Statistics
Matches: 212, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
101 29 0.14
102 2 0.01
103 181 0.85
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:20240 original size:18 final size:19
Alignment explanation
Indices: 20203--20239 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20193 TTTATTATTA
20203 TGGGGGAATCGATTCCCCC
1 TGGGGGAATCGATTCCCCC
*
20222 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
20240 TCTAGCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.30, G:0.32, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:20314 original size:70 final size:70
Alignment explanation
Indices: 20223--20357 Score: 261
Period size: 70 Copynumber: 1.9 Consensus size: 70
20213 GATTCCCCCT
*
20223 GGGGGTATCGATTCCCCTCTAGCGTTCTGGAAATTCATATTCGTTTGAGGGGGTATCGATTCCCC
1 GGGGGAATCGATTCCCCTCTAGCGTTCTGGAAATTCATATTCGTTTGAGGGGGTATCGATTCCCC
20288 ATTCA
66 ATTCA
20293 GGGGGAATCGATTCCCCTCTAGCGTTCTGGAAATTCATATTCGTTTGAGGGGGTATCGATTCCCC
1 GGGGGAATCGATTCCCCTCTAGCGTTCTGGAAATTCATATTCGTTTGAGGGGGTATCGATTCCCC
20358 TTGAATGGGT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.32
Consensus pattern (70 bp):
GGGGGAATCGATTCCCCTCTAGCGTTCTGGAAATTCATATTCGTTTGAGGGGGTATCGATTCCCC
ATTCA
Found at i:20361 original size:21 final size:21
Alignment explanation
Indices: 20337--20376 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20327 TCATATTCGT
*
20337 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
20358 TTGAATGGGTATCGATTCC
1 TTGAAGGGGTATCGATTCC
20377 TCTAGCCCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:23595 original size:2 final size:2
Alignment explanation
Indices: 23588--23627 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
23578 AAAAATAAGA
23588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23628 TTGTATCGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26048 original size:26 final size:26
Alignment explanation
Indices: 25977--26049 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
25967 TTAAAACGAT
*
25977 ATAATAAAAAAATTAAAAAAC-AGTAA
1 ATAAT-AAAAAATTAACAAACAAGTAA
* *
26003 ATAATAAAAACATT--CGAACAATTAA
1 ATAATAAAAA-ATTAACAAACAAGTAA
*
26028 GTAATAAAAAATTAACAAACAA
1 ATAATAAAAAATTAACAAACAA
26050 AATAAATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
24 6 0.16
25 18 0.47
26 14 0.37
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (26 bp):
ATAATAAAAAATTAACAAACAAGTAA
Found at i:26068 original size:17 final size:16
Alignment explanation
Indices: 26022--26069 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
26012 ACATTCGAAC
26022 AATTAAGTAAT-AAAA
1 AATTAAGTAATAAAAA
** *
26037 AATTAACAAACAAAATA
1 AATTAAGTAATAAAA-A
26054 AATTAAGTAATAAAAA
1 AATTAAGTAATAAAAA
26070 GTAAATAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
15 8 0.32
16 4 0.16
17 13 0.52
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (16 bp):
AATTAAGTAATAAAAA
Found at i:28040 original size:22 final size:23
Alignment explanation
Indices: 28006--28048 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
27996 ATATAATAAA
28006 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
28029 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
28049 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:28404 original size:53 final size:53
Alignment explanation
Indices: 28347--28466 Score: 124
Period size: 53 Copynumber: 2.3 Consensus size: 53
28337 AATATAACTT
28347 TTATTAAAAATATATT-A-TATATTATTAAAATAAGAATATAATAGTATCA-TATA
1 TTATTAAAAATATATTGAGTATATTATTAAAATAA-AAT-TAATAGTAT-ATTATA
* ** * * *
28400 TTATT-AATATA-ATTGAGTATATTATTGTAATAATATTATTATTATATTATA
1 TTATTAAAAATATATTGAGTATATTATTAAAATAAAATTAATAGTATATTATA
28451 TTATTAAAAATATATT
1 TTATTAAAAATATATT
28467 TTAACTAGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
50 1 0.02
51 19 0.35
52 13 0.24
53 22 0.40
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (53 bp):
TTATTAAAAATATATTGAGTATATTATTAAAATAAAATTAATAGTATATTATA
Found at i:33805 original size:3 final size:3
Alignment explanation
Indices: 33797--33893 Score: 112
Period size: 3 Copynumber: 33.0 Consensus size: 3
33787 TCGTTTTTGT
*
33797 TTA TTA TTA TTA TTA TT- TTA TT- TGT- TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * *
33840 TTA -TA TTA TTA TTA TTTA TTT TTA TTA CTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
33885 TTA TTA TTA
1 TTA TTA TTA
33894 CAAACAAGTC
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
2 6 0.07
3 72 0.89
4 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:34933 original size:2 final size:2
Alignment explanation
Indices: 34926--34955 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34916 AGTCCTTAGC
34926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34956 TTTTAGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35266 original size:28 final size:26
Alignment explanation
Indices: 35235--35297 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
35225 TTTAATACTA
35235 TAGTTTTAATTTT-ATTTTAGTTAATGTT
1 TAGTTTTAATTTTAATTTTA--T-ATGTT
*
35263 TAGTTAT-ATTTTAATTTTATATGTT
1 TAGTTTTAATTTTAATTTTATATGTT
*
35288 TATTTTTAAT
1 TAGTTTTAAT
35298 ATATTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 10 0.33
26 3 0.10
27 5 0.17
28 12 0.40
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (26 bp):
TAGTTTTAATTTTAATTTTATATGTT
Found at i:35275 original size:11 final size:11
Alignment explanation
Indices: 35219--35278 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
35209 TTATTACTTT
35219 TTATATTTTAA
1 TTATATTTTAA
35230 TACTATAGTTTTAA
1 T--TATA-TTTTAA
* *
35244 TTTTATTTTAG
1 TTATATTTTAA
*
35255 TTA-ATGTTTAG
1 TTATAT-TTTAA
35266 TTATATTTTAA
1 TTATATTTTAA
35277 TT
1 TT
35279 TTATATGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 2 0.05
11 22 0.55
12 5 0.12
13 4 0.10
14 7 0.17
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.62
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:35304 original size:15 final size:14
Alignment explanation
Indices: 35217--35316 Score: 53
Period size: 14 Copynumber: 6.8 Consensus size: 14
35207 TTTTATTACT
35217 TTTTATAT-TTTAA
1 TTTTATATATTTAA
**
35230 TACTATAGT-TTTAA
1 TTTTATA-TATTTAA
* *
35244 TTTTATTTTAGTTAA
1 TTTTA-TATATTTAA
35259 TGTTTAGTTATATTTTAA
1 T-TTTA--TATA-TTTAA
* *
35277 TTTTATATGTTTAT
1 TTTTATATATTTAA
35291 TTTTAATATATTTAA
1 TTTT-ATATATTTAA
35306 TTATTAT-TATT
1 TT-TTATATATT
35317 ATTATGTAGT
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
13 5 0.07
14 22 0.33
15 21 0.31
16 6 0.09
17 8 0.12
18 5 0.07
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (14 bp):
TTTTATATATTTAA
Found at i:35396 original size:39 final size:35
Alignment explanation
Indices: 35323--35392 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
35313 TATTATTATG
35323 TAGTCATATAAATATATATATAATAAATAATATTT
1 TAGTCATATAAATATATATATAATAAATAATATTT
35358 TAGTCATATAAATATATATATAATAAATAATATTT
1 TAGTCATATAAATATATATATAATAAATAATATTT
35393 ATTTAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (35 bp):
TAGTCATATAAATATATATATAATAAATAATATTT
Found at i:40754 original size:15 final size:15
Alignment explanation
Indices: 40734--40765 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40724 GATCAATACC
40734 TTTTGCATACATTCA
1 TTTTGCATACATTCA
40749 TTTTGCATACATTCA
1 TTTTGCATACATTCA
40764 TT
1 TT
40766 GCATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:51845 original size:18 final size:18
Alignment explanation
Indices: 51801--51860 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
51791 ATAATACTAC
51801 TAATAATAATTATAATTTTA
1 TAATAATAATTATAA--TTA
** *
51821 TTGTAATAATTATGATTA
1 TAATAATAATTATAATTA
*
51839 TAATAATAATTATTATTA
1 TAATAATAATTATAATTA
51857 TAAT
1 TAAT
51861 GTAATATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 22 0.65
20 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATAATAATTATAATTA
Found at i:52120 original size:55 final size:55
Alignment explanation
Indices: 52055--52268 Score: 218
Period size: 55 Copynumber: 3.9 Consensus size: 55
52045 TTTTGGAAAA
* * * *
52055 CATGTATGCTCCCTATTCTTTCAGAGAGTATAGGATTTGATCAATCTTCAACAAT
1 CATGTATGCTCCCTATTCGTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAT
* *
52110 CATGTATGCTCCATATTTC-TTCAGAGAGTAT-GAGACTCGAACAATCTTCAATAAT
1 CATGTATGCTCCCTA-TTCGTTCAGAGAGTATAG-GACTCGAACAATCTTCAACAAT
* ** ** * *
52165 CGTGTCCGCTCTTTATTCGTTCCGAGAGTATAAGACTCGAACAATCTTCAACAAT
1 CATGTATGCTCCCTATTCGTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAT
* * * * *
52220 CGTGTCCT-CTCTCTATTCGTTCAGAGAGTATAAGACTCGAACAGTCTTC
1 CATGT-ATGCTCCCTATTCGTTCAGAGAGTATAGGACTCGAACAATCTTC
52269 TTCTTATGGG
Statistics
Matches: 137, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
54 4 0.03
55 129 0.94
56 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (55 bp):
CATGTATGCTCCCTATTCGTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAT
Found at i:52243 original size:110 final size:110
Alignment explanation
Indices: 52068--52268 Score: 264
Period size: 110 Copynumber: 1.8 Consensus size: 110
52058 GTATGCTCCC
* * * * *
52068 TATTCTTTCAGAGAGTATAGGATTTGATCAATCTTCAACAATCATGTATGCTCCATATTTCTTCA
1 TATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTATGCTCCATATTTCTTCA
*
52133 GAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCCGCTCTT
66 GAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCCGCTCTT
* * *
52178 TATTCGTTCCGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCCT-CTCTC-TA-TTCGT
1 TATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGT-ATGCTC-CATATTTC-T
*
52240 TCAGAGAGTATAAGACTCGAACAGTCTTC
63 TCAGAGAGTATAAGACTCGAACAATCTTC
52269 TTCTTATGGG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
109 3 0.04
110 73 0.94
111 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (110 bp):
TATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTATGCTCCATATTTCTTCA
GAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCCGCTCTT
Found at i:52323 original size:54 final size:54
Alignment explanation
Indices: 52276--53814 Score: 1857
Period size: 54 Copynumber: 28.9 Consensus size: 54
52266 TTCTTCTTAT
* **
52276 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAAAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * **
52330 GGGTTCGCTCCTTCTTTCTCTAGGGAGTATGAAACTC-AAACATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAA-ATCTTCTTCAAAC
* * *
52384 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATATTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* *
52438 GGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGAACTCG--AA-CATCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
*
52489 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCG--AA-CATCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
**
52540 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* **
52594 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTC-AAACATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAA-ATCTTCTTCAAAC
* * *
52648 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATATTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* *
52702 GGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGAACTCG--AA-CATCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* *
52753 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * *
52807 GGGTTCGCTCCCTCTTTCTCCAGGGAGTATGAAACTC-AAACATCTTCTTCTAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAA-ATCTTCTTCAAAC
52861 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-AAACATC-TCATT---AC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAA-ATCTTC-TTCAAAC
* * * *
52912 GGGTTCTCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATATTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * * * * *
52966 GGATTCGTTCCCTCTTGCTCTAGGGAGTATGGAACTCGAACATCTTATT---AT
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * *
53017 GGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * *
53071 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTTTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * * **
53125 GGGTTCGCTCCCTCTTTCTCCAGGGAGTATGGATCTCGAACATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * * *
53179 TGGTTCGCTCCCTCTTTCTCTAGGGATTATGGAACTCGAACATATTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
*
53233 GGGTTCGCTCCCTCTTTCTCTAGGGAGTAAT-GAACTCG--AA-CATCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGT-ATGGAACTCGAAAATCTTCTTCAAAC
* ** * *
53284 GGGTTCGCTCCCTCTTTCTTTACAGAGTGTGGAACTCG--AA-CATCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
** * * *
53335 GGGTTTACTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATATTCTCCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
*
53389 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCG--AA-CATCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * * * *
53440 GAGTTTGCTCCCTCTTTCTCTAAGGAGTATGGAACTCGGACATCTTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * **
53494 GGGTTCGCTCCCTCTTGCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * * *
53548 GGGTTCGCTCCCTCTTTCTCTAGAGAGTATGAAACTCTG-ACATCCTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GAAAATCTTCTTCAAAC
* * * * **
53602 GGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACTCGAACATCCTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* * * * * **
53656 GAGTTTGCTCCCTCTTTCTTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
* *
53711 GGGTTCGCTCCCTCTTTCT-TCAGGGAGTATAGAACTCGAACGA-CTTCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAA-AATCTTCTTCAAAC
* * * * * *
53765 AGGATCGCTCCTTCTTTTTTTAAGGAGTATGGAACTCGAATAATCTTCTT
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAA-AATCTTCTT
53815 TTATTTCACT
Statistics
Matches: 1313, Mismatches: 138, Indels: 67
0.86 0.09 0.04
Matches are distributed among these distances:
50 1 0.00
51 360 0.27
52 7 0.01
53 16 0.01
54 868 0.66
55 61 0.05
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (54 bp):
GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCAAAC
Found at i:52556 original size:264 final size:264
Alignment explanation
Indices: 52276--53804 Score: 2121
Period size: 264 Copynumber: 5.8 Consensus size: 264
52266 TTCTTCTTAT
* *
52276 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAAAATCTTCTTCTTACGGGTTCGCTCC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCTAACGGGTTCGCTCC
*
52341 TTCTTTCTCTAGGGAGTATGAAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTA
66 CTCTTTCTCTAGGGAGTATGAAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTA
*
52406 GGGAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGA
131 GGGAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
52471 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTC
196 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTC
52536 AAAC
261 AAAC
*
52540 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCTAACGGGTTCGCTCC
52605 CTCTTTCTCTAGGGAGTATGAAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTA
66 CTCTTTCTCTAGGGAGTATGAAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTA
*
52670 GGGAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGA
131 GGGAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
52735 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTC
196 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACA---TC
*
52800 TTCTAAC
258 TTCAAAC
* *
52807 GGGTTCGCTCCCTCTTTCTCCAGGGAGTATGAAACTC-AAACATCTTCTTCTAACGGGTTCGCTC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAA-ATCTTCTTCTAACGGGTTCGCTC
* * *
52871 CCTCTTTCTCTAGGGAGTATGGAACTCAAACATC-TC--ATTACGGGTTCTCTCCCTCTTTCTCT
65 CCTCTTTCTCTAGGGAGTATGAAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCT
* * * * *
52933 AGGGAGTATGGAACTCGGACATATTCTTCAAACGGATTCGTTCCCTCTTGCTCTAGGGAGTATGG
130 AGGGAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGG
* * * *
52998 AACTCGAACATCTT-ATTATGGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCT
195 AACTCGAACATCTTCA-AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GA-A-CA
53062 TCTTCAAAC
256 TCTTCAAAC
* * * *
53071 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTTTTCAAACGGGTTCGCTCC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCTAACGGGTTCGCTCC
* * * * *
53136 CTCTTTCTCCAGGGAGTATGGATCTCGAACATCTTCTTCTTACTGGTTCGCTCCCTCTTTCTCTA
66 CTCTTTCTCTAGGGAGTATGAAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTA
* *
53201 GGGATTATGGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAAT-G
131 GGGAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT-ATGG
* ** *
53265 AACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTACAGAGTGTGGAACTCGAACATCTT
195 AACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
53330 CAAAC
260 CAAAC
** * * * *
53335 GGGTTTACTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATATTCTCCAAACGGGTTCGCTCC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCTAACGGGTTCGCTCC
* * ** * *
53400 CTCTTTCTCTAGGGAGTATGGAACTCGAACA---TCTTCAAACGAGTTTGCTCCCTCTTTCTCTA
66 CTCTTTCTCTAGGGAGTATGAAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTA
* * * * *
53462 AGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTGCTCTAGGGAGTATGGA
131 GGGAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
** * *
53527 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGAGAGTATGAAACTCTGACATC
196 ACTCGAACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GA-A-C
*
53592 CTCTTCAAAC
255 ATCTTCAAAC
* * * * * * *
53602 GGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACTCGAACATCCTCTTCTTACGAGTTTGCTCC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCTAACGGGTTCGCTCC
* *
53667 CTCTTTCTTTCAGGGAGTAT-AGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCT-
66 CTCTTTCTCT-AGGGAGTATGA-AACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTC
* * * * * * *
53730 TCAGGGAGTAT-AGAACTCGAACGA-CTTCTTCAAACAGGATCGCTCCTTCTTTTTTTAAGGAGT
129 T-AGGGAGTATGA-AACTCGAAC-ATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
53793 ATGGAACTCGAA
191 ATGGAACTCGAA
53805 TAATCTTCTT
Statistics
Matches: 1139, Mismatches: 97, Indels: 51
0.89 0.08 0.04
Matches are distributed among these distances:
260 2 0.00
261 92 0.08
263 1 0.00
264 622 0.55
265 8 0.01
266 9 0.01
267 299 0.26
268 20 0.02
270 1 0.00
271 84 0.07
272 1 0.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (264 bp):
GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTCTTCTAACGGGTTCGCTCC
CTCTTTCTCTAGGGAGTATGAAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTA
GGGAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTC
AAAC
Found at i:53065 original size:423 final size:424
Alignment explanation
Indices: 52245--53802 Score: 2082
Period size: 423 Copynumber: 3.7 Consensus size: 424
52235 TTCGTTCAGA
** *
52245 GAGTAT-AAGACTCGAACAGTCTTCTTCTTATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 GAGTATGAA-ACTCGAACA-TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * ** * * *
52309 ACTTGAAAATCTTCTTCTTACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATGAAACTCAAACATC
64 ACTCG--AATCATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATC
* * * *
52374 TTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATATTCTTCAAACG
127 TTCTTCTAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATGAAACTCAAACATCTTCTTCAAACG
* *
52439 GGTTCGTTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCT
192 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCTCTCCCTCT
*
52504 TTCTCTAGGGAGTATGGAACTC-GA-ACA-TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGA
257 TTCTCTAGGGAGTATGGAACTCGGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGA
* * *
52566 GTATGGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTC
322 GTATGGAACTCG--AA-CATCTTATTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
** **
52631 AAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
384 GGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
52672 GAGTATGAAACTCGAACATATTCTTCAAACGGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGAAC
1 GAGTATGAAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
52737 TCGAA-CATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCT
66 TCGAATCATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCT
*
52801 TCTAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATGAAACTCAAACATCTTCTTCTAACGGGTT
131 TCTAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATGAAACTCAAACATCTTCTTCAAACGGGTT
* *
52866 CGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAACATC-TCATTACGGGTTCTCTCCCTCTTTC
196 CGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCA-AACGGGTTCTCTCCCTCTTTC
* * *
52930 TCTAGGGAGTATGGAACTCGGACATATTCTTCAAACGGATTCGTTCCCTCTTGCTCTAGGGAGTA
260 TCTAGGGAGTATGGAACTCGGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTA
* *
52995 TGGAACTCGAACATCTTATTATGGGTTCGTTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACAT
325 TGGAACTCGAACATCTTATTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACAT
53060 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
390 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * * * *
53095 GAGTATGGAACTCGGACATCTTTTTCAAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATGGATC
1 GAGTATGAAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
* ** * * *
53160 TCGAACATCTTCTTCTTACTGGTTCGCTCCCTCTTTCTCTAGGGATTATGGAACTCGAACATATT
66 TCG-A-ATCATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
* * *
53225 CTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAATG-AACTCGAACA---TCTTCAAACGG
129 CTTCTAACGGGTTCGCTCCCTCTTTCTCCAGGGAGT-ATGAAACTCAAACATCTTCTTCAAACGG
* ** *
53286 GTTCGCTCCCTCTTTCTTTACAGAGTGTGGAACTCGAACATCTTCAAACGGGTT-TACTCCCTCT
193 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCT-CTCCCTCT
* *
53350 TTCTCTAGGGAGTATGGAACTCGAACATATTCTCCAAACGGGTTCGCTCCCTCTTTCTCTAGGGA
257 TTCTCTAGGGAGTATGGAACTCGGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGA
* * * *
53415 GTATGGAACTCGAACATCTTCA-AACGAGTTTGCTCCCTCTTTCTCTAAGGAGTATGGAACTCGG
322 GTATGGAACTCGAACATCTT-ATTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGG
*
53479 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTGCTCTAGG
386 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* ** * *
53518 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGAGAGTATGAAAC
1 GAGTATGAAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
* * * *
53583 TCTGACATCCTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACTCGAACATCCT
66 TC-GA-ATCATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
* * * * * **
53648 CTTCTTACGAGTTTGCTCCCTCTTTCTTTCAGGGAGTAT-AGAACTCAAAAATCTTCTTCTTACG
129 CTTCTAACGGGTTCGCTCCCTCTTTC-TCCAGGGAGTATGA-AACTCAAACATCTTCTTCAAACG
* * * *
53712 GGTTCGCTCCCTCTTTCT-TCAGGGAGTATAGAACTCGAACGACTTCTTCAAACAGGATCGCTCC
192 GGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAAC-A--TCTTCAAACGGGTTCTCTCC
* * * *
53776 TTCTTTTTTTAAGGAGTATGGAACTCG
253 CTCTTTCTCTAGGGAGTATGGAACTCG
53803 AATAATCTTC
Statistics
Matches: 1000, Mismatches: 107, Indels: 45
0.87 0.09 0.04
Matches are distributed among these distances:
422 4 0.00
423 680 0.68
424 28 0.03
425 3 0.00
426 183 0.18
427 60 0.06
428 3 0.00
430 39 0.04
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (424 bp):
GAGTATGAAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
TCGAATCATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCT
TCTAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATGAAACTCAAACATCTTCTTCAAACGGGTT
CGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCTCTCCCTCTTTCT
CTAGGGAGTATGGAACTCGGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
GGAACTCGAACATCTTATTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATC
TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:54182 original size:37 final size:36
Alignment explanation
Indices: 54100--54208 Score: 130
Period size: 37 Copynumber: 3.0 Consensus size: 36
54090 CATAAAACAT
**
54100 ATCTGCTTCACTACTCTTCGGCAAAGGCTTAAGACTG
1 ATCTGCTTCACTACTCTTCGGTGAAGGCTTAAGA-TG
* *
54137 ATCGGCTTCACCACTCTTCGGTGAAGGCTTAAGATGG
1 ATCTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT-G
* *
54174 AGT-TGCTTCACTAATCTTCGTTGAAGGCTTAAGAT
1 A-TCTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
54209 TGACTTTGCC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.02
37 60 0.97
38 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (36 bp):
ATCTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
Found at i:55568 original size:124 final size:125
Alignment explanation
Indices: 55334--55588 Score: 381
Period size: 124 Copynumber: 2.0 Consensus size: 125
55324 ATTAGTGCTG
*
55334 CAACATCATCTTATACTGGTACGGGCCTCCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATT
1 CAACATCATCTTATACTGGTACAGGCCTCCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATT
* * *
55399 CTCAAGGCGTTCTTGGTCTGTATCTTGTCATCTCAACATGATGTGGGT-TCAGTCATGCCC
66 CTCAAGGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTAT-AGTCATGCCC
* * * *
55459 TAACATTATCTTA-ACTGGTACAGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
1 CAACATCATCTTATACTGGTACAGGCCTCCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATT
* *
55523 CTTC-ATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTATAGTCGTGCCC
66 C-TCAAGGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTATAGTCATGCCC
55583 CAACAT
1 CAACAT
55589 ATTATAACTT
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
124 103 0.88
125 14 0.12
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (125 bp):
CAACATCATCTTATACTGGTACAGGCCTCCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATT
CTCAAGGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTATAGTCATGCCC
Found at i:62046 original size:15 final size:15
Alignment explanation
Indices: 62026--62062 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
62016 AATTTTATTG
62026 TAATAATTATGATTA
1 TAATAATTATGATTA
*
62041 TAATAATTATTATTA
1 TAATAATTATGATTA
*
62056 TTATAAT
1 TAATAAT
62063 GTAATATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TAATAATTATGATTA
Found at i:63107 original size:15 final size:15
Alignment explanation
Indices: 63087--63118 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
63077 AAAATAATGC
63087 AATGAATGTATACAA
1 AATGAATGTATACAA
*
63102 AATGAATGTATGCAA
1 AATGAATGTATACAA
63117 AA
1 AA
63119 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AATGAATGTATACAA
Found at i:68007 original size:3 final size:3
Alignment explanation
Indices: 67999--68030 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
67989 TATTATACTT
67999 GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
68031 AACAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:68428 original size:18 final size:18
Alignment explanation
Indices: 68401--68437 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
68391 CAAGTTTATC
*
68401 TTTTCGAAATTCAATTTA
1 TTTTCAAAATTCAATTTA
68419 TTTTCAAAATTCAATTTA
1 TTTTCAAAATTCAATTTA
68437 T
1 T
68438 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTCAAAATTCAATTTA
Found at i:68442 original size:20 final size:20
Alignment explanation
Indices: 68395--68442 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
68385 AGATTCCAAG
* *
68395 TTTATCTTTTCGAAATTCAA
1 TTTATATTTTCAAAATTCAA
68415 -TT-TATTTTCAAAATTCAA
1 TTTATATTTTCAAAATTCAA
68433 TTTATATTTT
1 TTTATATTTT
68443 TATATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 14 0.58
19 4 0.17
20 6 0.25
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTATATTTTCAAAATTCAA
Found at i:68993 original size:18 final size:18
Alignment explanation
Indices: 68966--69002 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
68956 CAAGTTTATC
*
68966 TTTTCGAAATTCAATTTA
1 TTTTCAAAATTCAATTTA
68984 TTTTCAAAATTCAATTTA
1 TTTTCAAAATTCAATTTA
69002 T
1 T
69003 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTCAAAATTCAATTTA
Found at i:69007 original size:20 final size:20
Alignment explanation
Indices: 68960--69007 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
68950 AGATTCCAAG
* *
68960 TTTATCTTTTCGAAATTCAA
1 TTTATATTTTCAAAATTCAA
68980 -TT-TATTTTCAAAATTCAA
1 TTTATATTTTCAAAATTCAA
68998 TTTATATTTT
1 TTTATATTTT
69008 TATATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 14 0.58
19 4 0.17
20 6 0.25
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTATATTTTCAAAATTCAA
Found at i:69349 original size:565 final size:565
Alignment explanation
Indices: 68280--69413 Score: 2268
Period size: 565 Copynumber: 2.0 Consensus size: 565
68270 AAATTATATC
68280 AAGTTGATTAGTTTAGAAATACTTATGCTAATAATTTGTTGAGTCATTTGAATTTTTATCATTCT
1 AAGTTGATTAGTTTAGAAATACTTATGCTAATAATTTGTTGAGTCATTTGAATTTTTATCATTCT
68345 TATGTTTGTCATGACTTTGAATACATTTCTATATATTAATAGATTCCAAGTTTATCTTTTCGAAA
66 TATGTTTGTCATGACTTTGAATACATTTCTATATATTAATAGATTCCAAGTTTATCTTTTCGAAA
68410 TTCAATTTATTTTCAAAATTCAATTTATATTTTTATATAAACATCATGCAAATGGATTAACATAA
131 TTCAATTTATTTTCAAAATTCAATTTATATTTTTATATAAACATCATGCAAATGGATTAACATAA
68475 TTTTGAAATAAGCAAAAGATTTCTGGCTATTACTTTATGTTAATACTTTTAAATACCTAGAATCC
196 TTTTGAAATAAGCAAAAGATTTCTGGCTATTACTTTATGTTAATACTTTTAAATACCTAGAATCC
68540 AAAGTAAGTCTTATCAACATTTACAAATATTATTGAAAAGCAAACAAGTTATTATCATCATAGAG
261 AAAGTAAGTCTTATCAACATTTACAAATATTATTGAAAAGCAAACAAGTTATTATCATCATAGAG
68605 CCATTTGGAAGCAAGTAAAATAAAAAAGAAAAAAAGAAATTCTGAGCCGAAACTACAGGAAATGA
326 CCATTTGGAAGCAAGTAAAATAAAAAAGAAAAAAAGAAATTCTGAGCCGAAACTACAGGAAATGA
68670 TGAATGTATTGTCAAATATTTTACGAAAATCTGGGCAGAAGCCATAGGAAATGATGAATGTGTTG
391 TGAATGTATTGTCAAATATTTTACGAAAATCTGGGCAGAAGCCATAGGAAATGATGAATGTGTTG
68735 TCAAATATTTTACGAACCAGTAATTATGGTGCTGAACCAACGTTGCGATCATATGGTGTTTCCAT
456 TCAAATATTTTACGAACCAGTAATTATGGTGCTGAACCAACGTTGCGATCATATGGTGTTTCCAT
68800 TTATTGATCCAAAATGAAGTTTATCTTCTTCAACCCCAAGGTTAG
521 TTATTGATCCAAAATGAAGTTTATCTTCTTCAACCCCAAGGTTAG
68845 AAGTTGATTAGTTTAGAAATACTTATGCTAATAATTTGTTGAGTCATTTGAATTTTTATCATTCT
1 AAGTTGATTAGTTTAGAAATACTTATGCTAATAATTTGTTGAGTCATTTGAATTTTTATCATTCT
68910 TATGTTTGTCATGACTTTGAATACATTTCTATATATTAATAGATTCCAAGTTTATCTTTTCGAAA
66 TATGTTTGTCATGACTTTGAATACATTTCTATATATTAATAGATTCCAAGTTTATCTTTTCGAAA
68975 TTCAATTTATTTTCAAAATTCAATTTATATTTTTATATAAACATCATGCAAATGGATTAACATAA
131 TTCAATTTATTTTCAAAATTCAATTTATATTTTTATATAAACATCATGCAAATGGATTAACATAA
69040 TTTTGAAATAAGCAAAAGATTTCTGGCTATTACTTTATGTTAATACTTTTAAATACCTAGAATCC
196 TTTTGAAATAAGCAAAAGATTTCTGGCTATTACTTTATGTTAATACTTTTAAATACCTAGAATCC
69105 AAAGTAAGTCTTATCAACATTTACAAATATTATTGAAAAGCAAACAAGTTATTATCATCATAGAG
261 AAAGTAAGTCTTATCAACATTTACAAATATTATTGAAAAGCAAACAAGTTATTATCATCATAGAG
69170 CCATTTGGAAGCAAGTAAAATAAAAAAGAAAAAAAGAAATTCTGAGCCGAAACTACAGGAAATGA
326 CCATTTGGAAGCAAGTAAAATAAAAAAGAAAAAAAGAAATTCTGAGCCGAAACTACAGGAAATGA
69235 TGAATGTATTGTCAAATATTTTACGAAAATCTGGGCAGAAGCCATAGGAAATGATGAATGTGTTG
391 TGAATGTATTGTCAAATATTTTACGAAAATCTGGGCAGAAGCCATAGGAAATGATGAATGTGTTG
69300 TCAAATATTTTACGAACCAGTAATTATGGTGCTGAACCAACGTTGCGATCATATGGTGTTTCCAT
456 TCAAATATTTTACGAACCAGTAATTATGGTGCTGAACCAACGTTGCGATCATATGGTGTTTCCAT
69365 TTATTGATCCAAAATGAAGTTTATCTTCTTCAACCCCAAGGTTAG
521 TTATTGATCCAAAATGAAGTTTATCTTCTTCAACCCCAAGGTTAG
69410 AAGT
1 AAGT
69414 GAGATATGAT
Statistics
Matches: 569, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
565 569 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (565 bp):
AAGTTGATTAGTTTAGAAATACTTATGCTAATAATTTGTTGAGTCATTTGAATTTTTATCATTCT
TATGTTTGTCATGACTTTGAATACATTTCTATATATTAATAGATTCCAAGTTTATCTTTTCGAAA
TTCAATTTATTTTCAAAATTCAATTTATATTTTTATATAAACATCATGCAAATGGATTAACATAA
TTTTGAAATAAGCAAAAGATTTCTGGCTATTACTTTATGTTAATACTTTTAAATACCTAGAATCC
AAAGTAAGTCTTATCAACATTTACAAATATTATTGAAAAGCAAACAAGTTATTATCATCATAGAG
CCATTTGGAAGCAAGTAAAATAAAAAAGAAAAAAAGAAATTCTGAGCCGAAACTACAGGAAATGA
TGAATGTATTGTCAAATATTTTACGAAAATCTGGGCAGAAGCCATAGGAAATGATGAATGTGTTG
TCAAATATTTTACGAACCAGTAATTATGGTGCTGAACCAACGTTGCGATCATATGGTGTTTCCAT
TTATTGATCCAAAATGAAGTTTATCTTCTTCAACCCCAAGGTTAG
Found at i:70236 original size:123 final size:123
Alignment explanation
Indices: 70017--70564 Score: 872
Period size: 123 Copynumber: 4.5 Consensus size: 123
70007 CACTCGATGG
* *
70017 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGACGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
70082 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* *
70140 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTGTCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* *
70205 ATGAGAATAGCTTGTTCAACTTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* * *
70263 ATCAACTTTTCCAGAGAATGTTCATAATGAGAAGAACTTATCTGTAGAGGAACAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
70328 ATGAAAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* *
70386 ATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * *
70451 ATGATAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAAATAGATCATC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* *
70509 ATCAA-TATTTCC-G-GAAGAGTTCATAATGATAAGAACTCATCT-AAGAAGG-AGAAGAA
1 ATCAACT-TTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAA
70565 TTTGTTCAAC
Statistics
Matches: 395, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
121 12 0.03
122 28 0.07
123 355 0.90
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:70952 original size:3 final size:3
Alignment explanation
Indices: 70944--71035 Score: 102
Period size: 3 Copynumber: 31.0 Consensus size: 3
70934 CTTTTGTTTT
*
70944 TTA TTA TTA TTA TT- TTA TT- TGT- TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* *
70987 -TA TTA TTA TTA TTTA TTT TTA TCTA TTA TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
71033 TTA
1 TTA
71036 CAAACAGGTC
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
2 6 0.08
3 65 0.84
4 6 0.08
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:70966 original size:25 final size:26
Alignment explanation
Indices: 70936--71035 Score: 95
Period size: 25 Copynumber: 4.0 Consensus size: 26
70926 TTATTTCGCT
* *
70936 TTTGTTTTTTATTATTATTATT-TTA
1 TTTGTTTATTACTATTATTATTATTA
70961 TTTGTTTATTACTATTATTATTATTA
1 TTTGTTTATTACTATTATTATTATTA
* *
70987 TATT-ATTATTA-T-TTATTTTTATCTA
1 T-TTGTTTATTACTATTATTATTAT-TA
*
71012 -TT-ATTATTACTATTATTATTATTA
1 TTTGTTTATTACTATTATTATTATTA
71036 CAAACAGGTC
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
23 9 0.14
24 12 0.18
25 32 0.49
26 10 0.15
27 2 0.03
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTGTTTATTACTATTATTATTATTA
Found at i:71019 original size:49 final size:45
Alignment explanation
Indices: 70944--71035 Score: 132
Period size: 49 Copynumber: 2.0 Consensus size: 45
70934 CTTTTGTTTT
70944 TTATTATTATTATTTTATTTGTTTATTACTATTATTATTATTATA
1 TTATTATTATTATTTTATTTGTTTATTACTATTATTATTATTATA
70989 TTATTATTATTTATTTTTATCTAT-TATTATTACTATTATTATTATTA
1 TTATTATTA-TTA-TTTTAT-T-TGT-TTATTACTATTATTATTATTA
71036 CAAACAGGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
45 9 0.21
46 3 0.07
47 6 0.14
48 2 0.05
49 22 0.52
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (45 bp):
TTATTATTATTATTTTATTTGTTTATTACTATTATTATTATTATA
Found at i:72090 original size:2 final size:2
Alignment explanation
Indices: 72083--72110 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
72073 AGTCCTTAGC
72083 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
72111 GGTAAAATAA
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:72462 original size:15 final size:14
Alignment explanation
Indices: 72424--72474 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
72414 CACTGTTTAG
72424 TTATAT-TTTAATT
1 TTATATATTTAATT
* *
72437 TTATATGTTTATTT
1 TTATATATTTAATT
72451 TTAATATATTTAATT
1 TT-ATATATTTAATT
72466 ATTAT-TATT
1 -TTATATATT
72475 ATTATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 6 0.19
14 12 0.38
15 12 0.38
16 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:72471 original size:3 final size:3
Alignment explanation
Indices: 72463--72515 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
72453 AATATATTTA
72463 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
72511 ATT AT
1 ATT AT
72516 GTAGTCATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:72590 original size:39 final size:35
Alignment explanation
Indices: 72517--72584 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
72507 TATTATTATG
*
72517 TAGTCATATAAATATATATATAATAAATAATATTT
1 TAGTCATATAAATACATATATAATAAATAATATTT
*
72552 TAGTCATATAAATACATATATAATATATAATAT
1 TAGTCATATAAATACATATATAATAAATAATAT
72585 CTATTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (35 bp):
TAGTCATATAAATACATATATAATAAATAATATTT
Found at i:73779 original size:17 final size:17
Alignment explanation
Indices: 73701--73783 Score: 53
Period size: 17 Copynumber: 4.9 Consensus size: 17
73691 CATTTAAAAT
*
73701 CATCTAGTTCATTTAGG
1 CATCTAGTTCATTTATG
* ** *
73718 GAAGTTGTTCATTTATG
1 CATCTAGTTCATTTATG
*
73735 CATTTAGATT-ATTTA-G
1 CATCTAG-TTCATTTATG
* * *
73751 TAAGCTACTTCATTTATG
1 -CATCTAGTTCATTTATG
73769 CATCTAGTTCATTTA
1 CATCTAGTTCATTTA
73784 ATAAAGTTAG
Statistics
Matches: 46, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
16 3 0.07
17 40 0.87
18 3 0.07
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (17 bp):
CATCTAGTTCATTTATG
Found at i:73783 original size:34 final size:34
Alignment explanation
Indices: 73701--73783 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
73691 CATTTAAAAT
**
73701 CATCTAGTTCATTTAGGGAAGTTGTTCATTTATG
1 CATCTAGTTCATTTAGGGAAGTACTTCATTTATG
* *
73735 CATTTAGATT-ATTTA-GTAAGCTACTTCATTTATG
1 CATCTAG-TTCATTTAGGGAAG-TACTTCATTTATG
73769 CATCTAGTTCATTTA
1 CATCTAGTTCATTTA
73784 ATAAAGTTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
33 6 0.15
34 33 0.80
35 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (34 bp):
CATCTAGTTCATTTAGGGAAGTACTTCATTTATG
Found at i:73815 original size:17 final size:17
Alignment explanation
Indices: 73772--73843 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
73762 ATTTATGCAT
73772 CTAGTTCATTTAA-TAAA
1 CTAGTTCA-TTAATTAAA
* *
73789 GTTAGCTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
73807 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
73824 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
73841 CTA
1 CTA
73844 ACTCTTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
17 35 0.78
18 10 0.22
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:89057 original size:60 final size:59
Alignment explanation
Indices: 88962--89138 Score: 178
Period size: 60 Copynumber: 3.0 Consensus size: 59
88952 ACATGTTTAG
** ** * *
88962 ATGAAATTGGAATATTCAAAAGTTT-GGGAACTAATTTAGAAAGAGGGTTATAGTTTAGGG
1 ATGAAATTAAAATATTCAAAAGTTTAAAG-ACTAATTTA-AAAGAGAGTTATAGTTTAGGA
* * * * * *
89022 ATGAAATTAGAATGTTCAAAATTTTAAAGATTAATTTAAAATGTGAGTCA-AGGTTTAGGA
1 ATGAAATTAAAATATTCAAAAGTTTAAAGACTAATTTAAAA-GAGAGTTATA-GTTTAGGA
* *
89082 ATGAAATTAAAATATTCAAAAGTTTAAAGACTAATTTAAATGAAAGTTATAGTTTAG
1 ATGAAATTAAAATATTCAAAAGTTTAAAGACTAATTTAAAAGAGAGTTATAGTTTAG
89139 AGACATATTA
Statistics
Matches: 95, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
59 15 0.16
60 79 0.83
61 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (59 bp):
ATGAAATTAAAATATTCAAAAGTTTAAAGACTAATTTAAAAGAGAGTTATAGTTTAGGA
Found at i:90647 original size:15 final size:15
Alignment explanation
Indices: 90627--90656 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
90617 ACCAGTTTAG
*
90627 AGCAAAGGGCAAGCT
1 AGCAAAGAGCAAGCT
90642 AGCAAAGAGCAAGCT
1 AGCAAAGAGCAAGCT
90657 TACAGTTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.30, T:0.07
Consensus pattern (15 bp):
AGCAAAGAGCAAGCT
Found at i:102087 original size:3 final size:3
Alignment explanation
Indices: 102079--102131 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
102069 TTTTTATCCA
102079 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
102127 TAT TA
1 TAT TA
102132 AATATATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:102158 original size:14 final size:13
Alignment explanation
Indices: 102130--102166 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
102120 TTATTATTAT
102130 TAAATATATTAAA
1 TAAATATATTAAA
102143 TAAATATATATAAA
1 TAAATATAT-TAAA
102157 TAAATA-ATTA
1 TAAATATATTA
102167 CAGACCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 11 0.48
14 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATATTAAA
Found at i:103525 original size:20 final size:21
Alignment explanation
Indices: 103488--103528 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
103478 GGTATTTTTA
**
103488 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
103509 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
103529 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:106147 original size:14 final size:14
Alignment explanation
Indices: 106128--106156 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
106118 GGAAATGTCC
106128 ATGCTGCGGTCGAG
1 ATGCTGCGGTCGAG
106142 ATGCTGCGGTCGAG
1 ATGCTGCGGTCGAG
106156 A
1 A
106157 GACTTCGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.21, G:0.41, T:0.21
Consensus pattern (14 bp):
ATGCTGCGGTCGAG
Found at i:107333 original size:20 final size:21
Alignment explanation
Indices: 107272--107344 Score: 85
Period size: 23 Copynumber: 3.4 Consensus size: 21
107262 ATATAGAATT
* *
107272 TGTCCCGAAGGACCACGTAGAAA
1 TGTCCCGACGGACCACATAG--A
* *
107295 TGTCCCGAAGGACCACATATA
1 TGTCCCGACGGACCACATAGA
107316 TGTCCCGACGGA-CACATAGA
1 TGTCCCGACGGACCACATAGA
107336 TGTCCCGAC
1 TGTCCCGAC
107345 TCTCAAACAG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
20 16 0.35
21 12 0.26
23 18 0.39
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
TGTCCCGACGGACCACATAGA
Found at i:108958 original size:61 final size:61
Alignment explanation
Indices: 108887--109009 Score: 174
Period size: 61 Copynumber: 2.0 Consensus size: 61
108877 CACTAAGTAC
* * * * * *
108887 AGGTGGTGGGCATGACCTTATGTGTCATATCCGGATTAGAACTAGAGTGTAAACCTAGTGT
1 AGGTGGTGGGCACGACCCTACGTATCATATCCGGATTAAAACTAGAGCGTAAACCTAGTGT
* *
108948 AGGTGGTGGGCACGACCCTACGTATCATATCCGGATTAAAACTAGAGCGTAAGCTTAGTGT
1 AGGTGGTGGGCACGACCCTACGTATCATATCCGGATTAAAACTAGAGCGTAAACCTAGTGT
109009 A
1 A
109010 TGTTTAGCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (61 bp):
AGGTGGTGGGCACGACCCTACGTATCATATCCGGATTAAAACTAGAGCGTAAACCTAGTGT
Found at i:117396 original size:19 final size:19
Alignment explanation
Indices: 117357--117396 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
117347 ACGTGACCTT
*
117357 CACACTAGCATAAAATTTC
1 CACACTAGCATAAAATGTC
* *
117376 CACAGTAGCATAAACTGTC
1 CACACTAGCATAAAATGTC
117395 CA
1 CA
117397 TATAACTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.23
Consensus pattern (19 bp):
CACACTAGCATAAAATGTC
Found at i:118686 original size:127 final size:130
Alignment explanation
Indices: 118530--118804 Score: 378
Period size: 137 Copynumber: 2.1 Consensus size: 130
118520 AGTGAAAAAT
* *
118530 AAAATAAAAATTGAAGTTACACAGGTATTCTACAGTGGCATATGAGCAAGTGGTTCAAA-T-T-T
1 AAAATAAAAACTGAAGTTACACAGGTATTCTACAGTGGCATATGAGCAACTGGTTCAAATTATAT
* * * *
118592 G-ACTTGAAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAATTGAAGAACTAAATTGA
66 GAACTTGAAATAAAGGATGAATTGAAAAAATAAGAAAATTATGAAAAATTGAAGAACTAAAGTGA
* *
118656 AAAATAGAAAACTGAAGTTACATAGGTATTCTATAGTGGCATATGAGCAACTGGTTCAAATTTGA
1 AAAATA-AAAACTGAAGTTACACAGGTATTCTACAGTGGCATATGAGCAACTGGTTCAAA-TT-A
*
118721 TAAAAATGAACTTGAAATAAAGGATGAATTGAAAAAATAAGAAAATTATGAAAAATTGAAGGACT
63 T----ATGAACTTGAAATAAAGGATGAATTGAAAAAATAAGAAAATTATGAAAAATTGAAGAACT
118786 AAAGTGA
124 AAAGTGA
118793 AAAATAAAAACT
1 AAAATAAAAACT
118805 TGTTATCGAA
Statistics
Matches: 129, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
126 6 0.05
127 49 0.38
129 1 0.01
131 1 0.01
136 8 0.06
137 64 0.50
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (130 bp):
AAAATAAAAACTGAAGTTACACAGGTATTCTACAGTGGCATATGAGCAACTGGTTCAAATTATAT
GAACTTGAAATAAAGGATGAATTGAAAAAATAAGAAAATTATGAAAAATTGAAGAACTAAAGTGA
Found at i:118957 original size:21 final size:21
Alignment explanation
Indices: 118933--118972 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
118923 AATTAGAGAC
*
118933 TAAATCATAAAATTGTCGGAA
1 TAAATAATAAAATTGTCGGAA
* *
118954 TAAATAATCAAATTTTCGG
1 TAAATAATAAAATTGTCGG
118973 TTTTTTGAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (21 bp):
TAAATAATAAAATTGTCGGAA
Found at i:119207 original size:2 final size:2
Alignment explanation
Indices: 119200--119239 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
119190 ACATATTACA
119200 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
119240 TAATTTAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121917 original size:23 final size:20
Alignment explanation
Indices: 121880--121932 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
121870 CGGTTCAACC
121880 TAAATTTTTT-GATTTTTTAT
1 TAAATTTTTTAGA-TTTTTAT
121900 TAAATGTTTTTAGTATTTTTAT
1 TAAAT-TTTTTAG-ATTTTTAT
*
121922 TTAATTTTTTA
1 TAAATTTTTTA
121933 AATAATTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 11 0.38
22 12 0.41
23 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (20 bp):
TAAATTTTTTAGATTTTTAT
Found at i:124117 original size:3 final size:3
Alignment explanation
Indices: 124111--124138 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
124101 TTTTCATTTG
124111 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
124139 CTAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:125544 original size:11 final size:11
Alignment explanation
Indices: 125517--125549 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
125507 TTTATAATCC
125517 TATTTATAAA-
1 TATTTATAAAT
125527 T-TTTATAAAT
1 TATTTATAAAT
125537 TATTTATAAAT
1 TATTTATAAAT
125548 TA
1 TA
125550 ATATGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.38
10 2 0.10
11 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTTATAAAT
Found at i:135768 original size:12 final size:11
Alignment explanation
Indices: 135749--135808 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
135739 AAAACAAAAT
135749 AAAAAATAATA
1 AAAAAATAATA
135760 AAAATAATAATAA
1 AAAA-AATAAT-A
*
135773 AAAAAATTATGA
1 AAAAAATAAT-A
*
135785 TGAAAAAT-A-A
1 -AAAAAATAATA
135795 AAAAAATAATA
1 AAAAAATAATA
135806 AAA
1 AAA
135809 TAGAAAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 6 0.15
10 2 0.05
11 8 0.20
12 13 0.32
13 11 0.28
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:136185 original size:18 final size:18
Alignment explanation
Indices: 136162--136201 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
136152 CAAGTTTATC
136162 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
*
136180 TTTTTGAAATTCAATTTG
1 TTTTTGAAATTCAATTTA
136198 TTTT
1 TTTT
136202 ATATAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:137641 original size:114 final size:113
Alignment explanation
Indices: 137388--138164 Score: 691
Period size: 114 Copynumber: 6.7 Consensus size: 113
137378 TTTTCGGAAG
* * * * * * *
137388 AGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAAAAGAAGTTCATAATGTGAAGAACTTGTTT
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* ** ** * ** *** * *
137453 AACCTTTTACTCAAATTCATCACTT-TATG-GATCAACATTGATAGATAG
66 AACCTCTTGTTTGAATTCATCA-TTCGA-GAGATCAATTTTTCCAGAGAA
* *
137501 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
137566 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAATTTTTCCAGAGAA
66 -AACCTCTTGTTTGAATTCATCATTCGAGAGATCAATTTTTCCAGAGAA
* **
137615 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* ** * *** *
137680 AACCTTTTGCATG-ACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCTAGAGAA
66 AACCTCTTGTTTGAATTC-AT--CA-TTCGAG--AGATC-A-AT----TTTTCCAGAGAA
* * *
137739 AGTTTATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * *
137804 AAACCTCTTGTTTGAATTCATCATTTGAGAGATCAACTTTTCCAGAGGA
66 -AACCTCTTGTTTGAATTCATCATTCGAGAGATCAATTTTTCCAGAGAA
* * **
137853 AGTTCATAATAAGAAGAACTCATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* ** * ***
137918 AACCTTTTGCATG-ACTCTATCACAGAAGGAGATAGATCATCATCAACTTTTCCAGAGAA
66 AACCTCTTGTTTGAATTC-AT--CA-TTCGAG--AGATCA--AT----TTTTCCAGAGAA
*
137977 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
138042 AAACCTCTTGTTTGAATTCATCATTCGAGGGATTAACTTTTCTAGAGAA
66 -AACCTCTTGTTTGAATTCATCATTCGAGAGATCAATTTTTCCAGAGAA
* * * * * * *
138091 AATTTATAATAAGAAGAAATCATCTGAAGAA-GAACAAGAAGTTCATAACGAGAAGAGTTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
*
138155 AACCTTTTGT
66 AACCTCTTGT
138165 ATGATCTATC
Statistics
Matches: 543, Mismatches: 90, Indels: 63
0.78 0.13 0.09
Matches are distributed among these distances:
112 15 0.03
113 114 0.21
114 196 0.36
115 4 0.01
116 6 0.01
118 13 0.02
119 2 0.00
120 12 0.02
122 6 0.01
123 4 0.01
124 141 0.26
125 24 0.04
126 6 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (113 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AACCTCTTGTTTGAATTCATCATTCGAGAGATCAATTTTTCCAGAGAA
Found at i:137748 original size:124 final size:121
Alignment explanation
Indices: 137501--138243 Score: 700
Period size: 114 Copynumber: 6.3 Consensus size: 121
137491 TGATAGATAG
* * * *
137501 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
* * * ***
137566 AAACCTCTTGTTTGA-AT-TCATCA-TTCGAG--AGATCAAT----TTTTCCAGAGAA
66 -AACCTTTTGTATGATCTATCA-CAGAAGGAGATAGATCAATCAACTTTTCCAGAGAA
*
137615 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
* *
137680 AACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCTAGAGAA
66 AACCTTTTGTATGA-TCTATCACAGAAGGAGATAGATC-A-ATCAACTTTTCCAGAGAA
* * * * *
137739 AGTTTATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
* * * *** *
137804 AAACCTCTTGTTTGA-AT-TCATCA-TTTGAG--AG----ATCAACTTTTCCAGAGGA
66 -AACCTTTTGTATGATCTATCA-CAGAAGGAGATAGATCAATCAACTTTTCCAGAGAA
* *
137853 AGTTCATAATAAGAAGAACTCATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
*
137918 AACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATCATCAACTTTTCCAGAGAA
66 AACCTTTTGTATGA-TCTATCACAGAAGGAGATAGATCA--ATCAACTTTTCCAGAGAA
* * *
137977 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
* * * *** * *
138042 AAACCTCTTGTTTGA-AT-TCATCA-TTCGAG--GGAT---T-AACTTTTCTAGAGAA
66 -AACCTTTTGTATGATCTATCA-CAGAAGGAGATAGATCAATCAACTTTTCCAGAGAA
* * * * *
138091 AATTTATAATAAGAAGAAATCATCTGAAGAA-GAACAAGAAGTTCATAACGAGAAGAGTTTGTTC
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
* * *
138155 AACCTTTTGTATGATCTATCACAAAAGGATATAGATCAGTATCAACATTTT-CAGA-AG
66 AACCTTTTGTATGATCTATCACAGAAGGAGATAGATCA--ATCAAC-TTTTCCAGAGAA
* *
138212 TGTTCATAATTAGAAGAACTCATCTGAAGAAG
1 AGTTCATAATAAGAAGAACTCATCTGAAGAAG
138244 AAGGAGCAAA
Statistics
Matches: 508, Mismatches: 80, Indels: 74
0.77 0.12 0.11
Matches are distributed among these distances:
112 12 0.02
113 54 0.11
114 180 0.35
115 7 0.01
116 15 0.03
118 7 0.01
119 1 0.00
120 7 0.01
121 28 0.06
122 18 0.04
123 10 0.02
124 147 0.29
125 22 0.04
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (121 bp):
AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTC
AACCTTTTGTATGATCTATCACAGAAGGAGATAGATCAATCAACTTTTCCAGAGAA
Found at i:137795 original size:238 final size:237
Alignment explanation
Indices: 137501--138243 Score: 1213
Period size: 238 Copynumber: 3.1 Consensus size: 237
137491 TGATAGATAG
*
137501 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
*
137566 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAATTTTTCCAGAGAAAGTTCATAATAAGAAG
66 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAG
137631 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACT
131 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACT
137696 CTATCACAGAAGGAGATAGATCAACATCAACTTTTCTAGAGAA
196 CTATCACAGAAGGAGATAGATCAACATCAACTTTTC-AGAGAA
* *
137739 AGTTTATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* *
137804 AAACCTCTTGTTTGAATTCATCATTTGAGAGATCAACTTTTCCAGAGGAAGTTCATAATAAGAAG
66 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAG
*
137869 AACTCATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACT
131 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACT
*
137934 CTATCACAGAAGGAGATAGATCATCATCAACTTTTCCAGAGAA
196 CTATCACAGAAGGAGATAGATCAACATCAACTTTT-CAGAGAA
137977 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * *
138042 AAACCTCTTGTTTGAATTCATCATTCGAGGGATTAACTTTTCTAGAGAAAATTTATAATAAGAAG
66 AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAG
* * * * *
138107 AAATCATCTGAAGAA-GAACAAGAAGTTCATAACGAGAAGAGTTTGTTCAACCTTTTGTATGA-T
131 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACT
* * ** *
138170 CTATCACAAAAGGATATAGATCAGTATCAACATTTTCAGA-AG
196 CTATCACAGAAGGAGATAGATCAACATCAAC-TTTTCAGAGAA
* *
138212 TGTTCATAATTAGAAGAACTCATCTGAAGAAG
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAG
138244 AAGGAGCAAA
Statistics
Matches: 473, Mismatches: 30, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
235 31 0.07
236 32 0.07
237 47 0.10
238 362 0.77
239 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (237 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AAACCTCTTGTTTGAATTCATCATTCGAGAGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAG
AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACT
CTATCACAGAAGGAGATAGATCAACATCAACTTTTCAGAGAA
Found at i:138476 original size:3 final size:3
Alignment explanation
Indices: 138470--138521 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
138460 TTTTTATTTG
*
138470 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
138518 ATT A
1 ATT A
138522 CTAAATAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:139927 original size:11 final size:12
Alignment explanation
Indices: 139905--139933 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
139895 GTATTTATAA
139905 ATTTTATAAATT
1 ATTTTATAAATT
139917 ATTTT-TAAATT
1 ATTTTATAAATT
139928 ATTTTA
1 ATTTTA
139934 ATTATGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTATAAATT
Found at i:141071 original size:24 final size:24
Alignment explanation
Indices: 141044--141128 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
141034 TAAATCAAAA
* *
141044 ATCAAAACATAGTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
141068 ATCAGATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* ** * *
141092 ATCCATTCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
141116 ATTATAACAAAAT
1 ATCAAAACAAAAT
141129 TCATGTCGAA
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:145812 original size:24 final size:24
Alignment explanation
Indices: 145785--145841 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
145775 CATAGTCCAT
*
145785 GTCAAGTATCAGATCAAAATTCAG
1 GTCAAGTATCAGATCAAAATTCAA
* * *
145809 GTCAAGTATCCGTTCAGAATTCAA
1 GTCAAGTATCAGATCAAAATTCAA
*
145833 GTCAGGTAT
1 GTCAAGTAT
145842 TATAACAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATTCAA
Found at i:151857 original size:17 final size:16
Alignment explanation
Indices: 151817--151889 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 16
151807 TCATTCAAAT
* *
151817 CATGTACTTCATTTAG
1 CATGTAGTTCATTAAG
*
151833 CATTTAGTTCATTAAAG
1 CATGTAGTTCATT-AAG
151850 CATGTAGTTCATCTAAG
1 CATGTAGTTCAT-TAAG
* *
151867 CAAGCTATTTCATTTAAG
1 CATG-TAGTTCA-TTAAG
151885 CATGT
1 CATGT
151890 TGAATCATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
16 11 0.24
17 20 0.43
18 14 0.30
19 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (16 bp):
CATGTAGTTCATTAAG
Found at i:151916 original size:18 final size:18
Alignment explanation
Indices: 151895--151941 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
151885 CATGTTGAAT
151895 CATTCAA-TAAAGCTAGTC
1 CATTCAATTAAA-CTAGTC
151913 CATT-AATTAAACTAGTC
1 CATTCAATTAAACTAGTC
*
151930 CATTCATTTAAA
1 CATTCAATTAAA
151942 TTGATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.34
Consensus pattern (18 bp):
CATTCAATTAAACTAGTC
Found at i:155195 original size:16 final size:16
Alignment explanation
Indices: 155162--155194 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
155152 TTGGAGTGAA
*
155162 TTGGCGAGGTTTTGTT
1 TTGGAGAGGTTTTGTT
155178 TTGGAGAGGTTTT-TT
1 TTGGAGAGGTTTTGTT
155193 TT
1 TT
155195 TATTACTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.09, C:0.03, G:0.33, T:0.55
Consensus pattern (16 bp):
TTGGAGAGGTTTTGTT
Found at i:158639 original size:20 final size:20
Alignment explanation
Indices: 158623--158675 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
158613 TTAATGTTAT
*
158623 AATGTTAAATTTGATGTCAG
1 AATGTGAAATTTGATGTCAG
158643 AATGTGAAATTTGATGTCAG
1 AATGTGAAATTTGATGTCAG
158663 AATGTGAAATTTG
1 AATGTGAAATTTG
158676 GACTATTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (20 bp):
AATGTGAAATTTGATGTCAG
Found at i:160248 original size:50 final size:49
Alignment explanation
Indices: 160179--160329 Score: 203
Period size: 50 Copynumber: 3.0 Consensus size: 49
160169 ATAGTGTATA
**
160179 TAAAGGACACTTAACGCATATGGTGGGCACATCCTTATATGTATTAGCAC
1 TAAAGGACACTTAGTGCATATGGTGGGCACA-CCTTATATGTATTAGCAC
* *
160229 TAAAGGACACTTAGTGCATATGGTGGGCATGACCTTATGTGTATTAGCAC
1 TAAAGGACACTTAGTGCATATGGTGGGCA-CACCTTATATGTATTAGCAC
* * * *
160279 TAAAGGACACTTAGTGTATATGGTAGGCACGACCTTATCTGTATTGGCAC
1 TAAAGGACACTTAGTGCATATGGTGGGCAC-ACCTTATATGTATTAGCAC
160329 T
1 T
160330 TCAGTGAATA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
50 89 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (49 bp):
TAAAGGACACTTAGTGCATATGGTGGGCACACCTTATATGTATTAGCAC
Found at i:160860 original size:22 final size:24
Alignment explanation
Indices: 160818--160864 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
160808 AAATGAATAC
160818 TATTATATTAAATTATGTTTTAAA
1 TATTATATTAAATTATGTTTTAAA
160842 TATTA-ATT-AATTA-GATTTTAAA
1 TATTATATTAAATTATG-TTTTAAA
160864 T
1 T
160865 TAGAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.05
22 13 0.59
23 3 0.14
24 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TATTATATTAAATTATGTTTTAAA
Found at i:163565 original size:13 final size:13
Alignment explanation
Indices: 163547--163580 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
163537 AAGATTTTTC
*
163547 TTTGAAAATCATT
1 TTTGAAAATCAAT
163560 TTTG-AAATCAAT
1 TTTGAAAATCAAT
163572 TTTGAAAAT
1 TTTGAAAAT
163581 TATGAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:165963 original size:21 final size:21
Alignment explanation
Indices: 165939--166004 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
165929 CAAGGAATGC
165939 ATCGGTGCACTTTCATAGTGT
1 ATCGGTGCACTTTCATAGTGT
* * *
165960 ATCGATGCACATTCA-AGGAATGC
1 ATCGGTGCACTTTCATA-G--TGT
*
165983 ATCGGTACACTTTCATAGTGT
1 ATCGGTGCACTTTCATAGTGT
166004 A
1 A
166005 ATGATGCACT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 1 0.03
21 17 0.50
23 15 0.44
24 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (21 bp):
ATCGGTGCACTTTCATAGTGT
Found at i:165997 original size:23 final size:23
Alignment explanation
Indices: 165921--165997 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
165911 AGTGTATTGA
165921 TACACATTCAAGGAATGCATCGG
1 TACACATTCAAGGAATGCATCGG
* * * *
165944 TGCACTTTCATA-G--TGTATCGA
1 TACACATTCA-AGGAATGCATCGG
*
165965 TGCACATTCAAGGAATGCATCGG
1 TACACATTCAAGGAATGCATCGG
*
165988 TACACTTTCA
1 TACACATTCA
165998 TAGTGTAATG
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
20 1 0.02
21 16 0.39
23 23 0.56
24 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (23 bp):
TACACATTCAAGGAATGCATCGG
Found at i:166011 original size:44 final size:44
Alignment explanation
Indices: 165911--166013 Score: 163
Period size: 44 Copynumber: 2.3 Consensus size: 44
165901 TACACTCTTG
* * *
165911 AGTGTATTGATACACATTCAAGGAATGCATCGGTGCACTTTCAT
1 AGTGTAATGATGCACATTCAAGGAATGCATCGGTACACTTTCAT
165955 AGTGT-ATCGATGCACATTCAAGGAATGCATCGGTACACTTTCAT
1 AGTGTAAT-GATGCACATTCAAGGAATGCATCGGTACACTTTCAT
165999 AGTGTAATGATGCAC
1 AGTGTAATGATGCAC
166014 TTTGCACAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
43 1 0.02
44 51 0.94
45 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
AGTGTAATGATGCACATTCAAGGAATGCATCGGTACACTTTCAT
Found at i:166014 original size:21 final size:21
Alignment explanation
Indices: 165944--166016 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 21
165934 AATGCATCGG
165944 TGCACTTTCATAGTGT-ATCGA
1 TGCACTTTCATAGTGTAAT-GA
*
165965 TGCACATTCA-AG-G-AATGCA
1 TGCACTTTCATAGTGTAATG-A
165984 TCGGTACACTTTCATAGTGTAATGA
1 T--G--CACTTTCATAGTGTAATGA
166009 TGCACTTT
1 TGCACTTT
166017 GCACAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
18 1 0.02
19 5 0.12
20 2 0.05
21 16 0.39
23 8 0.20
24 2 0.05
25 3 0.07
26 4 0.10
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (21 bp):
TGCACTTTCATAGTGTAATGA
Found at i:172555 original size:13 final size:13
Alignment explanation
Indices: 172534--172575 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
172524 TATTTTTTAT
172534 TATTTTTTAAAAA
1 TATTTTTTAAAAA
*
172547 TATTATTT-AAAA
1 TATTTTTTAAAAA
172559 TATTTTTTTAAAAA
1 TA-TTTTTTAAAAA
172573 TAT
1 TAT
172576 GAACGTGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 6 0.24
13 13 0.52
14 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTTTAAAAA
Found at i:174135 original size:27 final size:30
Alignment explanation
Indices: 174068--174135 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
174058 ATGTCATTAA
*
174068 TAATTTAT-AAAATGTTTTTATATTTATTG
1 TAATTTATAAAAAAGTTTTTATATTTATTG
*
174097 TAATTTATAAAAAAG-TTTTCT-TTTATT-
1 TAATTTATAAAAAAGTTTTTATATTTATTG
174124 TAATTTATAAAA
1 TAATTTATAAAA
174136 GTATGTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 12 0.33
28 6 0.17
29 13 0.36
30 5 0.14
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (30 bp):
TAATTTATAAAAAAGTTTTTATATTTATTG
Found at i:174199 original size:80 final size:80
Alignment explanation
Indices: 174058--174213 Score: 217
Period size: 80 Copynumber: 1.9 Consensus size: 80
174048 CTCACCCCTA
** * *
174058 ATGTCATTAATAATTTATAAAATGTTTTTATATTTATTGTAATTTATAAAAAAGTTTTCTTTTAT
1 ATGTCATTAATAATTTATAAAATGTTTAAACATTTATTGAAATTTATAAAAAAGTTTTCTTTTAT
*
174123 TTAATTTATAAAAGT
66 ATAATTTATAAAAGT
* *
174138 ATGTCATTAATAATTTATGAGATGTTTAAACATTTATT-AAATTTAT-AAAAAGATTTGTCTTTT
1 ATGTCATTAATAATTTATAAAATGTTTAAACATTTATTGAAATTTATAAAAAAG-TTT-TCTTTT
174201 ATATAATTTATAA
64 ATATAATTTATAA
174214 GTGTTATCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 6 0.09
79 10 0.15
80 51 0.76
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (80 bp):
ATGTCATTAATAATTTATAAAATGTTTAAACATTTATTGAAATTTATAAAAAAGTTTTCTTTTAT
ATAATTTATAAAAGT
Found at i:175072 original size:42 final size:41
Alignment explanation
Indices: 174982--175082 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 41
174972 ATGCTCAAAG
* *
174982 CCTAATTTTTTAAATCTTACTTTTTATATTTATAATTGATGT
1 CCTAATTTTTTAAAT-TTACTTTTTACATTTATAATTGATGC
** * *
175024 TGTAATTTTTTAAATTTCATTTTTTACCTTTATAATTG-TGCC
1 CCTAATTTTTTAAATTT-ACTTTTTACATTTATAATTGATG-C
175066 CCTAA-TTTTTAAATTTA
1 CCTAATTTTTTAAATTTA
175083 TAATTGAAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
40 1 0.02
41 15 0.31
42 33 0.67
ACGTcount: A:0.28, C:0.11, G:0.05, T:0.56
Consensus pattern (41 bp):
CCTAATTTTTTAAATTTACTTTTTACATTTATAATTGATGC
Found at i:175174 original size:43 final size:43
Alignment explanation
Indices: 175103--175239 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 43
175093 CCATACACTT
* * *
175103 TTTTTTTCAATTTTACTTGCTACCTTTATAATTGAGTCCCCTAA
1 TTTTTTT-AATCTCACTTTCTACCTTTATAATTGAGTCCCCTAA
* ** * *
175147 TTTTTTTAATCTCACTTTTTATTTTTATAATTGAGGCTCCT-A
1 TTTTTTTAATCTCACTTTCTACCTTTATAATTGAGTCCCCTAA
* *
175189 TGTTTCTTTAATCTCACTTTCTACCATCATAATTGAGGT-CCCTAA
1 T-TTT-TTTAATCTCACTTTCTACCTTTATAATTGA-GTCCCCTAA
175234 TTTTTT
1 TTTTTT
175240 AAATTTTATA
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
42 2 0.03
43 31 0.42
44 38 0.51
45 3 0.04
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (43 bp):
TTTTTTTAATCTCACTTTCTACCTTTATAATTGAGTCCCCTAA
Found at i:178823 original size:29 final size:29
Alignment explanation
Indices: 178780--178862 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
178770 CTCACCTAAC
*
178780 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
178810 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
178839 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
178863 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:182250 original size:15 final size:15
Alignment explanation
Indices: 182230--182259 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
182220 CTTTCTTATA
182230 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
182245 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
182260 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:183589 original size:29 final size:29
Alignment explanation
Indices: 183546--183628 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
183536 CTCACCTAAC
*
183546 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
183576 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
183605 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
183629 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:186625 original size:21 final size:20
Alignment explanation
Indices: 186601--186665 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
186591 AACTTTGAAA
186601 AAATGGCTTTCAAAGTTTGGT
1 AAATGG-TTTCAAAGTTTGGT
*
186622 AAAT-GTTTC----TTT-GA
1 AAATGGTTTCAAAGTTTGGT
186636 AAATGGTTTTCAAAGTTTGGT
1 AAATGG-TTTCAAAGTTTGGT
186657 AAAT-GTTTC
1 AAATGGTTTC
186666 TTTGAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 16
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 8 0.23
20 5 0.14
21 9 0.26
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (20 bp):
AAATGGTTTCAAAGTTTGGT
Found at i:186693 original size:38 final size:36
Alignment explanation
Indices: 186593--186713 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 36
186583 TGGTAACCAA
*
186593 CTTTGAAAAAATGGCTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
186630 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
186665 CTTTGAAAAATAGTTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-G-GTTTTCAAAGTTTGGTAAATGTTT
*
186703 -GTTGAAAAATG
1 CTTTGAAAAATG
186714 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
35 34 0.44
36 6 0.08
37 15 0.19
38 22 0.29
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:191247 original size:21 final size:21
Alignment explanation
Indices: 191223--191283 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
191213 AACTTTGAAA
191223 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
191244 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
191258 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
191279 AAATG
1 AAATG
191284 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:191315 original size:38 final size:36
Alignment explanation
Indices: 191215--191335 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 36
191205 TGGTAACCAA
191215 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
191252 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
191287 CTTTGAAAAATAGTTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-G-GTTTTCAAAGTTTGGTAAATGTTT
*
191325 -GTTGAAAAATG
1 CTTTGAAAAATG
191336 ATAATGGGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
35 35 0.45
36 6 0.08
37 15 0.19
38 22 0.28
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:197436 original size:13 final size:13
Alignment explanation
Indices: 197420--197467 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
197410 TCAATGCATT
*
197420 TCATAAATGAGCG
1 TCATAAATGAGTG
*
197433 TCATAAATGTGTG
1 TCATAAATGAGTG
197446 TCATAAAT-ACGTG
1 TCATAAATGA-GTG
197459 TCATAAATG
1 TCATAAATG
197468 CACGTTATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (13 bp):
TCATAAATGAGTG
Found at i:223970 original size:16 final size:17
Alignment explanation
Indices: 223949--223981 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
223939 CTCAAATAAA
223949 ATTATTTTATTA-CTTT
1 ATTATTTTATTATCTTT
223965 ATTATTTTATTATCTTT
1 ATTATTTTATTATCTTT
223982 CATTTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTATTTTATTATCTTT
Found at i:224152 original size:75 final size:76
Alignment explanation
Indices: 224014--224157 Score: 184
Period size: 75 Copynumber: 1.9 Consensus size: 76
224004 AGGATTGTTC
* * * *
224014 ATAAATAATATCATTTTAATTTTTATTTGATTGATAGTAAATGTTAAATTCATTATTAATAAAT-
1 ATAAAGAATATCATTTTAATTTTTATTTGATTGACAGTAAATGTTAAATCCAATATTAATAAATC
224078 TCAAATAATTG
66 TCAAATAATTG
* * * * *
224089 ATAAAGAATATCATTTTAATTTTTATTTGGTTGACATTAAAT-TTGAAGTCCAATCTTAGTAAAT
1 ATAAAGAATATCATTTTAATTTTTATTTGATTGACAGTAAATGTT-AAATCCAATATTAATAAAT
224153 CTCAA
65 CTCAA
224158 TCGAAACTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
74 2 0.03
75 52 0.90
76 4 0.07
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (76 bp):
ATAAAGAATATCATTTTAATTTTTATTTGATTGACAGTAAATGTTAAATCCAATATTAATAAATC
TCAAATAATTG
Found at i:227298 original size:13 final size:13
Alignment explanation
Indices: 227280--227305 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
227270 AGCCCAACTT
227280 GTCATAAATTTGA
1 GTCATAAATTTGA
227293 GTCATAAATTTGA
1 GTCATAAATTTGA
227306 CTCGAAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
GTCATAAATTTGA
Found at i:232851 original size:23 final size:23
Alignment explanation
Indices: 232820--232875 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
232810 GTGCCGATGT
*
232820 AAGCAGTTAGTTGTGTAGTTAGG
1 AAGCTGTTAGTTGTGTAGTTAGG
*
232843 AAGTTGTTAGTTGTGTAGTTAGG
1 AAGCTGTTAGTTGTGTAGTTAGG
232866 AAGCTGTTAG
1 AAGCTGTTAG
232876 GAGTAGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.04, G:0.34, T:0.38
Consensus pattern (23 bp):
AAGCTGTTAGTTGTGTAGTTAGG
Done.