Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002352.1 Hibiscus syriacus cultivar Beakdansim tig00004797_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: 2012169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:312137 original size:15 final size:15
Alignment explanation
Indices: 312114--312146 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
312104 CGTAGGACTC
312114 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
312129 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
312144 CTA
1 CTA
312147 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:312308 original size:12 final size:12
Alignment explanation
Indices: 312291--312336 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
312281 TATCATGTTC
*
312291 TCATATCACAGG
1 TCATATCACAGA
*
312303 TCATATCACATA
1 TCATATCACAGA
*
312315 TCATATCACATA
1 TCATATCACAGA
*
312327 GCATATCACA
1 TCATATCACA
312337 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:312322 original size:24 final size:24
Alignment explanation
Indices: 312291--312337 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
312281 TATCATGTTC
*
312291 TCATATCACA-GGTCATATCACATA
1 TCATATCACATAG-CATATCACATA
312315 TCATATCACATAGCATATCACAT
1 TCATATCACATAGCATATCACAT
312338 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
TCATATCACATAGCATATCACATA
Found at i:312337 original size:12 final size:12
Alignment explanation
Indices: 312304--312337 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
312294 TATCACAGGT
*
312304 CATATCACATAT
1 CATATCACATAG
312316 CATATCACATAG
1 CATATCACATAG
312328 CATATCACAT
1 CATATCACAT
312338 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCACATAG
Found at i:312823 original size:64 final size:63
Alignment explanation
Indices: 312646--312824 Score: 216
Period size: 64 Copynumber: 2.8 Consensus size: 63
312636 TAATGAAGAT
* * * ** * * * **
312646 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT-TTACTATTAATGGG
* *
312710 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-TGAATTGCATTCGATGTTT-ACTATTAATGGG
312774 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT
312825 TTATTTTAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
63 2 0.02
64 96 0.98
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTACTATTAATGGG
Found at i:312843 original size:64 final size:64
Alignment explanation
Indices: 312709--312870 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 64
312699 TTATTGCTGG
* * *
312709 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAAAGA
* * *
312773 GATGCATCGATGCACTACTTATGCATCGATGCA-TGAATTGCATTCGATGTTTTTA-TTTTAAA-
1 GATGCATCGATGCACTACTTATGCATCGATGCACCG-ATTGCATTCGATG-TTTCACTATTAAAG
312835 A
64 A
** *
312836 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
312871 ATTCAAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 3 0.04
64 78 0.92
65 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:317384 original size:10 final size:12
Alignment explanation
Indices: 317361--317401 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
317351 ATAAAATTCG
317361 AATATCATATTAA
1 AATAT-ATATTAA
317374 AATA-A-ATTAAA
1 AATATATATT-AA
317385 AATATATATTAA
1 AATATATATTAA
317397 AATAT
1 AATAT
317402 TAATTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 3 0.12
11 7 0.28
12 8 0.32
13 7 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
AATATATATTAA
Found at i:318428 original size:3 final size:3
Alignment explanation
Indices: 318399--318480 Score: 83
Period size: 3 Copynumber: 26.7 Consensus size: 3
318389 TTGGGTTTTG
* * * * *
318399 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TTA TTA TAA TTA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
318446 TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
318481 TAAATAACAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
3 61 0.91
4 6 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:318454 original size:24 final size:24
Alignment explanation
Indices: 318399--318480 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
318389 TTGGGTTTTG
* * * *
318399 TAATATTAATAAATAATAT-ATAT
1 TAATAATAATAATTATTATAATAA
*
318422 TAATAATAATAATTATTATAATTA
1 TAATAATAATAATTATTATAATAA
318446 TAATAATAATAATTATTATAATAA
1 TAATAATAATAATTATTATAATAA
318470 TAATAATAATA
1 TAATAATAATA
318481 TAAATAACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 16 0.31
24 36 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATAATAATTATTATAATAA
Found at i:318888 original size:113 final size:113
Alignment explanation
Indices: 318711--319232 Score: 664
Period size: 113 Copynumber: 4.7 Consensus size: 113
318701 TAGAGTCATT
* **
318711 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * * *
318772 TTATGAACTTTCTCTGTAAAAGTTGATCCATTAAGTGATGAATTTGAA
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAA
* * * *
318820 CAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * **
318885 TTATGAACTCAAACTGGAAAAGCTGGTCCATCAAGTGATGGATTTGGG
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAA
*
318933 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
318998 TTATGAACTCGAACTGGAAAAGATGATCCATTGAA-TGATGGATTTGAG
66 TTATGAACTCTAACTGGAAAAGCTGATCCA-TCAAGTGATGAATTTGAA
* *
319046 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * * *
319111 TTATGAACTTTCTCTGGCAAAGCTGATCCATCAAATGATGAA-TTCAA
66 TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAA
*
319158 GCAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTT-CTCTCTTCAGATGAGTTCTTCT
1 -CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCT-TCTTCAGATGAGTTCTTCT
319221 CATTATGAACTC
64 CATTATGAACTC
319233 GACCTAGCAA
Statistics
Matches: 364, Mismatches: 41, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
109 28 0.08
110 1 0.00
111 5 0.01
112 69 0.19
113 258 0.71
114 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGAATTTGAA
Found at i:319068 original size:226 final size:225
Alignment explanation
Indices: 318711--319267 Score: 746
Period size: 226 Copynumber: 2.5 Consensus size: 225
318701 TAGAGTCATT
* *
318711 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-TCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
**** * * * * *
318773 TATGAACTTTCTCTGTAAAAGTTGATCCATT-AAGTGATGAATTTGAACAAAGGGTTAAACAAGT
66 TATGAACTCGAACTGGAAAAGATGATCCATTGAA-TGATGGATTTGAACAAAAGGTTAAACAAAT
318837 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGG
* * * ***
318902 AAAAGCTGGTCCATCAAGTGATGGATTTGGG
195 AAAAGCTGATCCATCAAATGATGAATTCAAG
* *
318933 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
* *
318998 TTATGAACTCGAACTGGAAAAGATGATCCATTGAATGATGGATTTGAGCAAAAGGTTGAACAAAT
65 TTATGAACTCGAACTGGAAAAGATGATCCATTGAATGATGGATTTGAACAAAAGGTTAAACAAAT
* * * ****
319063 TCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGG
*
319128 CAAAGCTGATCCATCAAATGATGAATTCAAG
195 AAAAGCTGATCCATCAAATGATGAATTCAAG
319159 CAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTCTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCT-TCTTCAGATGAGTTCTTCTCA
* * * * *
319223 TTATGAACTCGACCTAGCAATGCTGATCCATTGAATGATGGATTT
65 TTATGAACTCGAACTGGAAAAGATGATCCATTGAATGATGGATTT
319268 AAATCTTTGC
Statistics
Matches: 293, Mismatches: 36, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
222 29 0.10
223 1 0.00
224 5 0.02
225 95 0.32
226 161 0.55
227 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (225 bp):
CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGAACTGGAAAAGATGATCCATTGAATGATGGATTTGAACAAAAGGTTAAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGA
AAAGCTGATCCATCAAATGATGAATTCAAG
Found at i:320220 original size:92 final size:91
Alignment explanation
Indices: 319954--320225 Score: 411
Period size: 94 Copynumber: 2.9 Consensus size: 91
319944 CGATCATGCA
* * * *
319954 ATTCATCTTTTAATTCCAATGATTGGTTCTGGGTTTTATATCAAACCAGATCAGATAACTCAAAG
1 ATTCATCTTTCAAATCCAATGATTGGTTCTGGG-TTCATACCAAACCAGATCAGATAACTCAAAG
320019 AACACTTCCAGAAGATGCTATGAGCAC
65 AACACTTCCAGAAGATGCTATGAGCAC
**
320046 ATTCATC-TTCTAAATTTAATGATTGGTTTTTCTGGGTTCATACCAAACCAGATCAGATAACTCA
1 ATTCATCTTTC-AAATCCAATGATTGG---TTCTGGGTTCATACCAAACCAGATCAGATAACTCA
*
320110 AAGAACACTTCCAAAAGATGCTATGAGCAC
62 AAGAACACTTCCAGAAGATGCTATGAGCAC
*
320140 ATTCATCTTTCAAGTCCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 ATTCATCTTTCAAATCCAATGATTGGTTCTG-GGTTCATACCAAACCAGATCAGATAACTCAAAG
320205 AACACTTCCAGAAGATGCTAT
65 AACACTTCCAGAAGATGCTAT
320226 TGGGTCTATG
Statistics
Matches: 163, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
91 7 0.04
92 72 0.44
94 74 0.45
95 10 0.06
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (91 bp):
ATTCATCTTTCAAATCCAATGATTGGTTCTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATGAGCAC
Found at i:321107 original size:17 final size:16
Alignment explanation
Indices: 321087--321136 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
321077 TCTTAACCCC
321087 TTTTTTTCTTTTTTCTT
1 TTTTTTTCTTTTTT-TT
321104 TTTTTTTCTTTTTTTT
1 TTTTTTTCTTTTTTTT
* *
321120 TTACTTTCCTTTTTTTT
1 TT-TTTTTCTTTTTTTT
321137 ATCAAGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTTCTTTTTTTT
Found at i:321108 original size:10 final size:10
Alignment explanation
Indices: 321095--321120 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
321085 CCTTTTTTTC
321095 TTTTTTCTTT
1 TTTTTTCTTT
321105 TTTTTTCTTT
1 TTTTTTCTTT
321115 TTTTTT
1 TTTTTT
321121 TACTTTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:328474 original size:15 final size:15
Alignment explanation
Indices: 328451--328482 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
328441 TGAAATGAAT
328451 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
328466 AATGCATGTATGCAA
1 AATGAATGTATGCAA
328481 AA
1 AA
328483 AAAAAGGTAT
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:333096 original size:14 final size:16
Alignment explanation
Indices: 333079--333116 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
333069 AGCGTTTCAT
333079 TTCTCT-TCTT-TCTC
1 TTCTCTCTCTTCTCTC
333093 TTCTCTCTCTTCTCTC
1 TTCTCTCTCTTCTCTC
333109 TTCTCTCT
1 TTCTCTCT
333117 GAGAGAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 6 0.27
15 4 0.18
16 12 0.55
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCTCTCTCTTCTCTC
Found at i:333116 original size:9 final size:9
Alignment explanation
Indices: 333080--333109 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
333070 GCGTTTCATT
*
333080 TCTCTTCTT
1 TCTCTTCTC
333089 TCTCTTCTC
1 TCTCTTCTC
333098 TCTCTTCTC
1 TCTCTTCTC
333107 TCT
1 TCT
333110 TCTCTCTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (9 bp):
TCTCTTCTC
Found at i:333784 original size:3 final size:3
Alignment explanation
Indices: 333754--333830 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
333744 TTTGGGTTTT
* * * * *
333754 ATA ATA TTA ATAA ATA ATA TATA TTA ATA ATA ATT ATA ATT ATA ATT
1 ATA ATA ATA AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
333801 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
333831 TAAATATAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:333798 original size:12 final size:12
Alignment explanation
Indices: 333752--333839 Score: 85
Period size: 12 Copynumber: 7.5 Consensus size: 12
333742 AATTTGGGTT
*
333752 TTATAATATTAA
1 TTATAATAATAA
333764 -TA-AATAAT-A
1 TTATAATAATAA
333773 TATATTAATAATAA
1 T-TA-TAATAATAA
*
333787 TTATAATTATAA
1 TTATAATAATAA
333799 TTATAATAATAA
1 TTATAATAATAA
*
333811 TAATAATAATAA
1 TTATAATAATAA
*
333823 TAATAAT-ATAA
1 TTATAATAATAA
*
333834 ATATAA
1 TTATAA
333840 ATAACATTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
9 1 0.02
10 5 0.08
11 12 0.18
12 37 0.57
13 8 0.12
14 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTATAATAATAA
Found at i:338378 original size:14 final size:14
Alignment explanation
Indices: 338361--338390 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
338351 GTTAAATAGG
*
338361 AAAATAAATAAATA
1 AAAAGAAATAAATA
338375 AAAAGAAATAAATA
1 AAAAGAAATAAATA
338389 AA
1 AA
338391 TTAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (14 bp):
AAAAGAAATAAATA
Found at i:340402 original size:67 final size:67
Alignment explanation
Indices: 340324--340454 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 67
340314 AAAGCGTCGT
* * *
340324 TGTTCCTGCTACACCAAAATAAGGAGAAATAGTAAGCTATAATGGTTCAAAGAATTCAAGCAAAG
1 TGTTCCCGCTACACCAAAACAAGGAGAAATAGTAAGCCATAATGGTTCAAAGAATTCAAGCAAAG
340389 TA
66 TA
* *
340391 TGTTCCCGCTACACTAAAACAAGGAGAAATAGTAAGCCATGATGGTTCAAAGAATTCAAGCAAA
1 TGTTCCCGCTACACCAAAACAAGGAGAAATAGTAAGCCATAATGGTTCAAAGAATTCAAGCAAA
340455 ACATTATTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (67 bp):
TGTTCCCGCTACACCAAAACAAGGAGAAATAGTAAGCCATAATGGTTCAAAGAATTCAAGCAAAG
TA
Found at i:350096 original size:17 final size:17
Alignment explanation
Indices: 350074--350108 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
350064 AAGTAGAGAG
350074 TGGAAACAAAATAAAAC
1 TGGAAACAAAATAAAAC
350091 TGGAAACAAAATAAAAC
1 TGGAAACAAAATAAAAC
350108 T
1 T
350109 CTTGCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.14
Consensus pattern (17 bp):
TGGAAACAAAATAAAAC
Found at i:355487 original size:2 final size:2
Alignment explanation
Indices: 355482--355510 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
355472 TATTAATAAA
355482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
355511 AAATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:355858 original size:51 final size:51
Alignment explanation
Indices: 355778--355996 Score: 230
Period size: 51 Copynumber: 4.3 Consensus size: 51
355768 TTCATACTAC
* * * *
355778 AAAAAAATGTAGCA-TTAACACATATTTACACCGGTGTAAG-ACAATAAAAT
1 AAAAAAGTGTAACACTTAACACATACTTACACAGGTGTAAGTA-AATAAAAT
* * ** *
355828 AAACAAGTGTAACACTTAATACATACTTACACATTTGTAAGTAAATAAAAC
1 AAAAAAGTGTAACACTTAACACATACTTACACAGGTGTAAGTAAATAAAAT
* * * *
355879 AAAAAAATGTAACACTTAACACATA-ATACACAAGTGTAAGTGAATAAAAT
1 AAAAAAGTGTAACACTTAACACATACTTACACAGGTGTAAGTAAATAAAAT
* *
355929 AAAAAAAAGTGTAGCACTTAATACATACTTACA-ACGGTGTAAGTAAATAAAAT
1 --AAAAAAGTGTAACACTTAACACATACTTACACA-GGTGTAAGTAAATAAAAT
*
355982 AAAAAAGTGCAACAC
1 AAAAAAGTGTAACAC
355997 GTTGAAGACA
Statistics
Matches: 138, Mismatches: 25, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
50 31 0.22
51 63 0.46
52 24 0.17
53 20 0.14
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (51 bp):
AAAAAAGTGTAACACTTAACACATACTTACACAGGTGTAAGTAAATAAAAT
Found at i:355970 original size:103 final size:102
Alignment explanation
Indices: 355776--355996 Score: 277
Period size: 103 Copynumber: 2.2 Consensus size: 102
355766 AATTCATACT
* * ** *
355776 ACAAAAAAATGTAGCA-TTAACACATATTTACACCGGTGTAAGACAATAAAATAAACAAGTGTAA
1 ACAAAAAAATGTAACACTTAACACATATATACACAAGTGTAAGACAATAAAATAAAAAAGTGTAA
**
355840 CACTTAATACATACTTACACATTTGTAAGTAAATAAA
66 CACTTAATACATACTTACACAGGTGTAAGTAAATAAA
**
355877 ACAAAAAAATGTAACACTTAACACATA-ATACACAAGTGTAAGTGAATAAAATAAAAAAAAGTGT
1 ACAAAAAAATGTAACACTTAACACATATATACACAAGTGTAAGACAATAAAAT--AAAAAAGTGT
*
355941 AGCACTTAATACATACTTACA-ACGGTGTAAGTAAATAAA
64 AACACTTAATACATACTTACACA-GGTGTAAGTAAATAAA
* * *
355980 ATAAAAAAGTGCAACAC
1 ACAAAAAAATGTAACAC
355997 GTTGAAGACA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
101 35 0.34
102 11 0.11
103 57 0.55
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (102 bp):
ACAAAAAAATGTAACACTTAACACATATATACACAAGTGTAAGACAATAAAATAAAAAAGTGTAA
CACTTAATACATACTTACACAGGTGTAAGTAAATAAA
Found at i:356047 original size:2 final size:2
Alignment explanation
Indices: 356035--356089 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
356025 AATCACAAAT
* * *
356035 TA TA CA TA TA TA TA -A TG T- TA TA AA T- TA TA -A 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
356073 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
356090 GAGTTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:357132 original size:2 final size:2
Alignment explanation
Indices: 357125--357157 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
357115 TTCATCAATT
357125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
357158 TATTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:357341 original size:30 final size:32
Alignment explanation
Indices: 357290--357348 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
357280 TACTTTTTTA
*
357290 TTTTCTCTTATGTTATTTTCATT-TTTATTCC
1 TTTTCTCTTATCTTATTTTCATTCTTTATTCC
*
357321 TTTTCT-TTATCTTTTTTTCATTCTTTAT
1 TTTTCTCTTATCTTATTTTCATTCTTTAT
357349 ATTTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (32 bp):
TTTTCTCTTATCTTATTTTCATTCTTTATTCC
Found at i:358189 original size:20 final size:20
Alignment explanation
Indices: 358164--358201 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
358154 GGACTAAGGG
358164 TCTGGCAGGCCCAAGGGGTC
1 TCTGGCAGGCCCAAGGGGTC
358184 TCTGGCAGGCCCAAGGGG
1 TCTGGCAGGCCCAAGGGG
358202 GCACCGGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.29, G:0.42, T:0.13
Consensus pattern (20 bp):
TCTGGCAGGCCCAAGGGGTC
Found at i:358210 original size:20 final size:20
Alignment explanation
Indices: 358167--358210 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
358157 CTAAGGGTCT
* * *
358167 GGCAGGCCCAAGGGGTCTCT
1 GGCAGGCCCAAGGGGGCACC
358187 GGCAGGCCCAAGGGGGCACC
1 GGCAGGCCCAAGGGGGCACC
358207 GGCA
1 GGCA
358211 AGGAGAACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.43, T:0.07
Consensus pattern (20 bp):
GGCAGGCCCAAGGGGGCACC
Found at i:367579 original size:68 final size:72
Alignment explanation
Indices: 367507--367659 Score: 215
Period size: 73 Copynumber: 2.2 Consensus size: 72
367497 AATACTTCGC
* *
367507 TTAGGATGAAAACCTGAGAGAGCGTCTTAAGTC-A-AAAAA-AGAGAAA-AAAAAACAAAAAAGA
1 TTAGGGTGAAAACCTGAGAGAGCGTCTTAAGTCGAGAAAAAGAGAAAAATAAAAAACAAAAAAGA
367568 AGAACGT
66 AGAACGT
* * *
367575 TTAGGGTGAAAACCTGAGAGGGTGTCTTAAGTCGAGAAAAAGAGAAAAATTAAAAAACGAAAAAG
1 TTAGGGTGAAAACCTGAGAGAGCGTCTTAAGTCGAGAAAAAGAGAAAAA-TAAAAAACAAAAAAG
*
367640 AAGAATGT
65 AAGAACGT
367648 TTAGGGTGAAAA
1 TTAGGGTGAAAA
367660 TCCGAAAGGG
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
68 30 0.41
69 1 0.01
70 5 0.07
71 6 0.08
73 32 0.43
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (72 bp):
TTAGGGTGAAAACCTGAGAGAGCGTCTTAAGTCGAGAAAAAGAGAAAAATAAAAAACAAAAAAGA
AGAACGT
Found at i:367695 original size:8 final size:8
Alignment explanation
Indices: 367682--367750 Score: 59
Period size: 8 Copynumber: 8.2 Consensus size: 8
367672 CCCTAAATTG
367682 GAAAAAAA
1 GAAAAAAA
367690 GAAAAAAA
1 GAAAAAAA
367698 GAGAAAAAGGA
1 GA-AAAAA--A
*
367709 AAAAAAAA
1 GAAAAAAA
*
367717 GAACAAAA
1 GAAAAAAA
*
367725 GAAAAATA
1 GAAAAAAA
367733 GAAAAGAAA
1 GAAAA-AAA
*
367742 -AAATAAA
1 GAAAAAAA
367749 GA
1 GA
367751 GGGTTCAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
7 3 0.06
8 32 0.65
9 7 0.14
10 5 0.10
11 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (8 bp):
GAAAAAAA
Found at i:367696 original size:73 final size:73
Alignment explanation
Indices: 367507--367697 Score: 187
Period size: 73 Copynumber: 2.7 Consensus size: 73
367497 AATACTTCGC
* * * * *
367507 TTAGGATGAAAACCTGAGAGAGCGTCTTAAGTC-AAAAAAAGAG--AAA--AAAAAACAAAAAAG
1 TTAGGGTGAAAACCTGAAAGGGCGCCTAAAGTCGAAAAAAAGAGAAAAATTAAAAAACAAAAAAG
367567 AAGAACGT
66 AAGAACGT
* * * * * *
367575 TTAGGGTGAAAACCTGAGAGGGTGTCTTAAGTCGAGAAAAAGAGAAAAATTAAAAAACGAAAAAG
1 TTAGGGTGAAAACCTGAAAGGGCGCCTAAAGTCGAAAAAAAGAGAAAAATTAAAAAACAAAAAAG
*
367640 AAGAATGT
66 AAGAACGT
* * *
367648 TTAGGGTGAAAATCC-GAAAGGGCGCCCTAAATTGGAAAAAAAGAAAAAAA
1 TTAGGGTGAAAA-CCTGAAAGGGCG-CCTAAAGTCGAAAAAAAGAGAAAAA
367698 GAGAAAAAGG
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
68 30 0.29
69 9 0.09
71 3 0.03
73 39 0.38
74 21 0.21
ACGTcount: A:0.52, C:0.09, G:0.24, T:0.15
Consensus pattern (73 bp):
TTAGGGTGAAAACCTGAAAGGGCGCCTAAAGTCGAAAAAAAGAGAAAAATTAAAAAACAAAAAAG
AAGAACGT
Found at i:367710 original size:17 final size:17
Alignment explanation
Indices: 367684--367744 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
367674 CTAAATTGGA
*
367684 AAAAAAGAAAAAAAGAG
1 AAAAAAGAAAAAAAAAG
*
367701 AAAAAGGAAAAAAAAAG
1 AAAAAAGAAAAAAAAAG
367718 AACAAAAGAAAAATAGAAAAG
1 AA-AAAAG-AAAA-A-AAAAG
367739 AAAAAA
1 AAAAAA
367745 TAAAGAGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 17 0.46
18 4 0.11
19 4 0.11
20 5 0.14
21 7 0.19
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAG
Found at i:367713 original size:19 final size:18
Alignment explanation
Indices: 367682--367743 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
367672 CCCTAAATTG
367682 GAAAAA-AAGAAAAAAAGA
1 GAAAAAGAA-AAAAAAAGA
367700 GAAAAAGGAAAAAAAAAGA
1 GAAAAA-GAAAAAAAAAGA
367719 -ACAAAAGAAAAATAGAAA-A
1 GA-AAAAGAAAAA-A-AAAGA
367738 GAAAAA
1 GAAAAA
367744 ATAAAGAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
18 13 0.34
19 19 0.50
20 6 0.16
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAAAAAAAAGA
Found at i:367713 original size:27 final size:27
Alignment explanation
Indices: 367683--367744 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
367673 CCTAAATTGG
*
367683 AAAAAAAGAAAAAAAGAGAAAA-AGGAA
1 AAAAAAAGAAAAAAAGA-AAAATAGAAA
*
367710 AAAAAAAGAACAAAAGAAAAATAGAAA
1 AAAAAAAGAAAAAAAGAAAAATAGAAA
367737 AGAAAAAA
1 A-AAAAAA
367745 TAAAGAGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 4 0.13
27 21 0.68
28 6 0.19
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (27 bp):
AAAAAAAGAAAAAAAGAAAAATAGAAA
Found at i:369099 original size:106 final size:106
Alignment explanation
Indices: 368834--369110 Score: 319
Period size: 109 Copynumber: 2.6 Consensus size: 106
368824 GACGAAGGGG
* * * *
368834 TTTCCTAGTTTCAGAGCCAATCTCAATTTCACAGCAAAGGATATTGGACTCAAGACAACACAAGC
1 TTTCCTAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGC
*
368899 TCAACTTCACAACGAAGGGGCGACTGATTACAACAAACAAC
66 TCAACTTCACAACGAAGGGGAGACTGATTACAACAAACAAC
* * * *
368940 TTT-TTAGCTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACATCAC
1 TTTCCTAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACAC
* * * *
369004 AAGCTCAACTTCACAACGAATGGGAGGCTGGCTGT-CAACAAATAA-
62 AAGCTCAACTTCACAACGAAGGGGAGACT-GAT-TACAACAAACAAC
* * * *
369049 TTTCCCAGTTTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGAAACAA-ACAA
1 TTTCCTAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
369111 CTTACTTAGA
Statistics
Matches: 143, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
105 7 0.05
106 46 0.32
107 1 0.01
108 1 0.01
109 74 0.52
110 13 0.09
111 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
TTTCCTAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGC
TCAACTTCACAACGAAGGGGAGACTGATTACAACAAACAAC
Found at i:372056 original size:12 final size:10
Alignment explanation
Indices: 372032--372070 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
372022 TGTATTTTTA
372032 ATTTTTAATT
1 ATTTTTAATT
372042 ATTATTTACATT
1 ATT-TTTA-ATT
372054 ATTTTTAATT
1 ATTTTTAATT
*
372064 AATTTTA
1 ATTTTTA
372071 TTTAACAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 12 0.46
11 8 0.31
12 6 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTAATT
Found at i:373167 original size:19 final size:19
Alignment explanation
Indices: 373143--373195 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
373133 AATAACCAAC
373143 AAAATCGCAATGCGAAATA
1 AAAATCGCAATGCGAAATA
373162 AAAATCGCAATGCGAAATA
1 AAAATCGCAATGCGAAATA
*
373181 AAAATCGCAACGCGA
1 AAAATCGCAATGCGA
373196 TCTCCGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATA
Found at i:373274 original size:21 final size:21
Alignment explanation
Indices: 373245--373291 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
373235 ATTCTGACTA
373245 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
373266 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
373287 TCGCA
1 TCGCA
373292 AGGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:373312 original size:20 final size:20
Alignment explanation
Indices: 373287--373354 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
373277 TTTTCCTAAT
*
373287 TCGCAAGGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
373307 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
*
373327 TCGCAATGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
373347 TCGCAACG
1 TCGCAACG
373355 AGATTCTGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.02
20 41 0.98
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:373362 original size:20 final size:20
Alignment explanation
Indices: 373302--373362 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
373292 AGGCGAATAC
373302 GTAAATCGCAACGCGATTAC-
1 GTAAATCGCAACGCGATT-CT
* *
373322 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGCGATTCT
*
373342 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGCGATTCT
373362 G
1 G
373363 ACTATCGCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
GTAAATCGCAACGCGATTCT
Found at i:374081 original size:24 final size:24
Alignment explanation
Indices: 374030--374083 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
374020 GTATTCGAAA
*
374030 TTTGATCTTGGTCAATACCCTGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
374054 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
374078 TTTGAT
1 TTTGAT
374084 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:376540 original size:20 final size:21
Alignment explanation
Indices: 376515--376623 Score: 156
Period size: 20 Copynumber: 5.4 Consensus size: 21
376505 CAACGCGGAA
376515 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAATATGACT
*
376535 ATCGCAACACGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
*
376555 ATCGCAATGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
376575 ATCGCAACGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
*
376595 ATCGCAACACGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
376615 ATCGCAACG
1 ATCGCAACG
376624 AGAGAATCAC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
20 77 0.96
21 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:376661 original size:19 final size:19
Alignment explanation
Indices: 376628--376740 Score: 84
Period size: 19 Copynumber: 6.4 Consensus size: 19
376618 GCAACGAGAG
* *
376628 AATCACAATGCGAAATGAA
1 AATCGCAATGAGAAATGAA
*
376647 ATTCGCAATGAGAAATGAA
1 AATCGCAATGAGAAATGAA
*
376666 AATCGCAACGAG---TG--
1 AATCGCAATGAGAAATGAA
*
376680 AATCGCAATGCGAAATGAA
1 AATCGCAATGAGAAATGAA
*
376699 AATCGCAACGAG---TG--
1 AATCGCAATGAGAAATGAA
*
376713 AATCGCAATGCGAAAATGAA
1 AATCGCAATGAG-AAATGAA
376733 AATCGCAA
1 AATCGCAA
376741 CGCGAAATTA
Statistics
Matches: 72, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
14 20 0.28
16 4 0.06
17 2 0.03
18 2 0.03
19 36 0.50
20 8 0.11
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGAGAAATGAA
Found at i:376675 original size:52 final size:52
Alignment explanation
Indices: 376606--376706 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
376596 TCGCAACACG
** *
376606 GAAATGACTATCGCAACGAGAGAATCACAATGCGAAATGAAATTCGCAATGA
1 GAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAATGA
* *
376658 GAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAATGAAAATCGCAA
1 GAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAA
376707 CGAGTGAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.16
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAATGA
Found at i:376685 original size:14 final size:14
Alignment explanation
Indices: 376666--376720 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
376656 GAGAAATGAA
376666 AATCGCAACGAGTG
1 AATCGCAACGAGTG
*
376680 AATCGCAATGCGAAATG
1 AATCGCAA--CG-AGTG
376697 AAAATCGCAACGAGTG
1 --AATCGCAACGAGTG
376713 AATCGCAA
1 AATCGCAA
376721 TGCGAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
16 5 0.15
17 5 0.15
19 8 0.24
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (14 bp):
AATCGCAACGAGTG
Found at i:376735 original size:34 final size:33
Alignment explanation
Indices: 376649--376742 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
376639 GAAATGAAAT
*
376649 TCGCAATGAGAAATGAAAATCGCAACGAGTGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGTGAA
376682 TCGCAATGCGAAATGAAAATCGCAACGAGTGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGTGAA
376715 TCGCAATGCGAAAATGAAAATCGCAACG
1 TCGCAATGCG-AAATGAAAATCGCAACG
376743 CGAAATTAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
33 42 0.71
34 17 0.29
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGTGAA
Found at i:376800 original size:34 final size:34
Alignment explanation
Indices: 376757--376852 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
376747 ATTAGTTTCG
376757 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
376791 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** *
376824 CGTTGCGATAGTCATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
376853 AATCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:376973 original size:14 final size:14
Alignment explanation
Indices: 376954--376990 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
376944 CATCAATTAA
376954 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
376968 ACAAATCATCTTTT
1 ACAAATCAACATTT
376982 ACAAATCAA
1 ACAAATCAA
376991 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:378432 original size:42 final size:42
Alignment explanation
Indices: 378353--378443 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
378343 CCTCTTCAAC
* * *
378353 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
378395 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
378437 GATGACA
1 GATGACA
378444 TGCGAGTCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:378948 original size:20 final size:20
Alignment explanation
Indices: 378925--378993 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
378915 GAAACTTAAA
378925 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
378945 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
378965 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
378985 ATCGCAACG
1 ATCGCAACG
378994 AGAGAATCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:379347 original size:94 final size:94
Alignment explanation
Indices: 379201--379580 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
379191 ATGGATTGCA
* * * *
379201 TTAC-TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCAGAATATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
379265 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
379294 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
379359 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
379388 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
379453 TTAGCAGAATTAGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
379482 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAA
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
379546 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
379576 TTACT
1 TTACT
379581 AAGCAATCTA
Statistics
Matches: 274, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
93 23 0.08
94 251 0.92
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:381276 original size:20 final size:20
Alignment explanation
Indices: 381253--381308 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
381243 TGAAATGAAA
381253 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
381273 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
381293 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
381309 CGCAACGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:381381 original size:33 final size:33
Alignment explanation
Indices: 381344--381413 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
381334 GCGATTTTGG
381344 TTTCGCGTTGCGATTATCTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCAATTTTCA
* **
381377 TTTCGCGTTGCGATTCTCTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCAATTTTCA
381410 TTTC
1 TTTC
381414 TCTCGTTGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCAATTTTCA
Found at i:381416 original size:21 final size:21
Alignment explanation
Indices: 381390--381466 Score: 81
Period size: 20 Copynumber: 3.8 Consensus size: 21
381380 CGCGTTGCGA
*
381390 TTCTCTCGTTGTGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
381411 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
381432 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
381452 TT-TCAT-GTTGCGATT
1 TTCTC-TCGTTGCGATT
381467 ATAAATTTAG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
20 28 0.57
21 21 0.43
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:381990 original size:20 final size:20
Alignment explanation
Indices: 381961--382172 Score: 171
Period size: 20 Copynumber: 10.6 Consensus size: 20
381951 CTTTAAAAAT
381961 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
381981 CGCATTGCGATTTTACGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
382003 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
382022 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
382042 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
382062 CGCGTTGCGATTTA--TATT
1 CGCGTTGCGATTTACGGATA
** * *
382080 CTTGTTACGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
* * *
382100 CGCATTGTGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
382120 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
382141 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
382162 CTCGTTGCGAT
1 CGCGTTGCGAT
382173 AGTCAGAATC
Statistics
Matches: 148, Mismatches: 35, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
18 13 0.09
19 2 0.01
20 83 0.56
21 48 0.32
22 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:382020 original size:41 final size:41
Alignment explanation
Indices: 381963--382172 Score: 268
Period size: 41 Copynumber: 5.2 Consensus size: 41
381953 TTAAAAATCG
381963 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTAT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTAT
*
382004 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTAT
* * *
382044 CGTTGCGATTTACAGATACGCGTTGCGA-TTTA--TATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTAT
* * * * *
382082 TGTTACGATTTATGGATACGCATTGTGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTAT
* * *
382123 CATTGCGATTTACGGATACGCGTTGCGATTTTACGGA-TACT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTA-T
382164 CGTTGCGAT
1 CGTTGCGAT
382173 AGTCAGAATC
Statistics
Matches: 146, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
38 28 0.19
39 4 0.03
40 42 0.29
41 72 0.49
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTAT
Found at i:382114 original size:21 final size:21
Alignment explanation
Indices: 382090--382172 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
382080 CTTGTTACGA
* *
382090 TTTATGGATACGCATTGTGAT
1 TTTACGGATACGCATTGCGAT
* *
382111 TTTACGTAT-TGTCATTGCGA-
1 TTTACGGATACG-CATTGCGAT
*
382131 TTTACGGATACGCGTTGCGAT
1 TTTACGGATACGCATTGCGAT
* *
382152 TTTACGGATACTCGTTGCGAT
1 TTTACGGATACGCATTGCGAT
382173 AGTCAGAATC
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (21 bp):
TTTACGGATACGCATTGCGAT
Found at i:382204 original size:20 final size:20
Alignment explanation
Indices: 382181--382233 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
382171 ATAGTCAGAA
*
382181 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
382201 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
382221 TCGCGTTGCGATT
1 TCGCGTTGCGATT
382234 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:382294 original size:42 final size:42
Alignment explanation
Indices: 382201--382294 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
382191 ATTTATATGT
* *
382201 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
382242 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
382284 TCGCGTTGCGA
1 TCGCGTTGCGA
382295 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:382332 original size:20 final size:19
Alignment explanation
Indices: 382283--382336 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
382273 ATTCTTCATA
382283 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
382302 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
382323 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
382337 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:383259 original size:20 final size:20
Alignment explanation
Indices: 383234--383327 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
383224 AATTGGAAAA
383234 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
** *
383254 ATCGCAATGTTATACTTACT
1 ATCGCAATGCGATACTGACT
* * *
383274 ATCGCAATACGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
383295 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
383315 TTCGCAACGCGAT
1 ATCGCAATGCGAT
383328 TTACATAGCG
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.04
20 40 0.71
21 12 0.21
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:383930 original size:19 final size:19
Alignment explanation
Indices: 383908--384086 Score: 144
Period size: 19 Copynumber: 9.8 Consensus size: 19
383898 CAAAATTGCA
*
383908 TTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCGCG
383927 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
383946 TTGCGATTTTTATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
383965 TTGCAATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
383984 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
* **
383998 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
384017 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
** *
384031 TTGCGATAGTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCG
* * *
384051 TTGCAATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
384071 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
384087 AACCAAAAGA
Statistics
Matches: 126, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
14 19 0.15
16 4 0.03
17 5 0.04
19 70 0.56
20 27 0.21
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:384016 original size:33 final size:33
Alignment explanation
Indices: 383974--384061 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
383964 GTTGCAATTT
383974 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
384007 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
384040 TCATTTCCGCATTGCAATTCTC
1 TCATTT-CGCGTTGCGATTCTC
384062 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 38 0.75
34 13 0.25
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:387671 original size:14 final size:14
Alignment explanation
Indices: 387652--387678 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
387642 ATTGTTTAAT
387652 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
387666 TGATTTGTAAAAG
1 TGATTTGTAAAAG
387679 TTTTTGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:387865 original size:19 final size:19
Alignment explanation
Indices: 387843--387993 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
387833 CGAAATTAAA
387843 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
387862 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
387877 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
387895 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
* *
387909 TTAGAGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
387928 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
387943 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
387961 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
387980 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
387994 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:387889 original size:33 final size:32
Alignment explanation
Indices: 387847--387973 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
387837 ATTAAATTCG
387847 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
387880 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
387913 AGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
387946 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
387974 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:387932 original size:66 final size:66
Alignment explanation
Indices: 387848--387972 Score: 241
Period size: 66 Copynumber: 1.9 Consensus size: 66
387838 TTAAATTCGC
387848 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
387913 A
66 A
*
387914 GTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
387973 TAGTAATTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
A
Found at i:390496 original size:24 final size:24
Alignment explanation
Indices: 390462--390514 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
390452 CTGAAACATC
*
390462 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
390486 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
390510 ATCAA
1 ATCAA
390515 TTTTTGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:391535 original size:19 final size:20
Alignment explanation
Indices: 391497--391546 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
391487 ATTCATTTGA
391497 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
391517 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
391536 CTATCGCAACG
1 CTATCGCAACG
391547 ACAAAATCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:391634 original size:20 final size:20
Alignment explanation
Indices: 391609--391647 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
391599 CGATTCTCTC
391609 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
391629 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
391648 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:391749 original size:14 final size:14
Alignment explanation
Indices: 391730--391780 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
391720 CATCAATTAA
*
391730 ACAAATCAACATTT
1 ACAAATCAACTTTT
*
391744 ACAAATCATCTTTT
1 ACAAATCAACTTTT
*
391758 ACAAATCATCTTTT
1 ACAAATCAACTTTT
391772 ACAAATCAA
1 ACAAATCAA
391781 TTAAACAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:393663 original size:19 final size:19
Alignment explanation
Indices: 393631--393696 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
393621 CGAAACTTAA
393631 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
393650 A-CGCAACGCAGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
393669 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
393688 ATCGCAACG
1 ATCGCAACG
393697 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 8 0.21
19 24 0.62
20 7 0.18
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:393704 original size:14 final size:14
Alignment explanation
Indices: 393685--393742 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
393675 ATGCGAAATG
393685 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
393699 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
393715 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
393731 AAAATCGCAACG
1 AAAATCGCAACG
393743 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:393727 original size:32 final size:33
Alignment explanation
Indices: 393669--393747 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
393659 AGAAATGGCT
393669 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
393702 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
393734 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
393748 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:393794 original size:14 final size:14
Alignment explanation
Indices: 393775--393831 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
393765 TTTCATTTCG
393775 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
393789 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
393805 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
393821 CG-TGCGATTTT
1 CGTTGCGATTTT
393832 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 9 0.24
14 11 0.30
16 8 0.22
18 9 0.24
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:393804 original size:32 final size:32
Alignment explanation
Indices: 393759--393847 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
393749 ACAAATCGCA
*
393759 TGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCG
393791 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 -TGCGATTTTCATTTCGCATTGCGATTTTGTCG
393823 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
393848 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 5 0.09
32 44 0.81
33 5 0.09
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.46
Consensus pattern (32 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:393866 original size:20 final size:19
Alignment explanation
Indices: 393832--393886 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
393822 GTGCGATTTT
*
393832 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
393851 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
393871 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
393887 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:394194 original size:18 final size:18
Alignment explanation
Indices: 394168--394212 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
394158 GTCGATCAGA
*
394168 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
394186 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
394204 TGATGGCTC
1 TGATGGCTC
394213 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:395684 original size:20 final size:20
Alignment explanation
Indices: 395636--395694 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
395626 AATAGTTTCT
** *
395636 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
395656 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
395676 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
395695 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:395976 original size:20 final size:21
Alignment explanation
Indices: 395951--395997 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
395941 CTGAGAGATT
395951 GAGATA-GACGGATTTCGCCG
1 GAGATAGGACGGATTTCGCCG
*
395971 GAGATAGGGACGGATTTCGTCG
1 GAGATA-GGACGGATTTCGCCG
395993 GAGAT
1 GAGAT
395998 GGGTGAGAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.25
22 18 0.75
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (21 bp):
GAGATAGGACGGATTTCGCCG
Found at i:396214 original size:20 final size:20
Alignment explanation
Indices: 396188--396297 Score: 127
Period size: 20 Copynumber: 5.7 Consensus size: 20
396178 GATTATGTAT
*
396188 TATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGAAAGTCAG
* *
396208 AATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGAAAGTCAG
* *
396228 AATCGCGTTGCGAAAGT---
1 TATCGCATTGCGAAAGTCAG
* *
396245 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGAAAGTCAG
*
396265 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGAAAGTCAG
396285 TATCGCATTGCGA
1 TATCGCATTGCGA
396298 TTTTCCCAAT
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
17 14 0.17
20 68 0.83
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (20 bp):
TATCGCATTGCGAAAGTCAG
Found at i:396240 original size:40 final size:40
Alignment explanation
Indices: 396189--396297 Score: 134
Period size: 37 Copynumber: 2.8 Consensus size: 40
396179 ATTATGTATT
* * *
396189 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGA
* *
396229 ATCGCGTTGCGAAAGT---TATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGA
* *
396266 ATCGCATTGCGATAGTCAGTATCGCATTGCGA
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGA
396298 TTTTCCCAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
37 30 0.51
40 29 0.49
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (40 bp):
ATCGCGTTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGA
Found at i:396270 original size:57 final size:57
Alignment explanation
Indices: 396187--396297 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
396177 CGATTATGTA
* * * *
396187 TTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAG
1 TTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAG
* * * *
396244 TTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGA
1 TTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGAATCGCATTGCGA
396298 TTTTCCCAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (57 bp):
TTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAG
Found at i:396298 original size:20 final size:20
Alignment explanation
Indices: 396168--396298 Score: 126
Period size: 20 Copynumber: 6.7 Consensus size: 20
396158 CGCTTTGAAA
*
396168 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
396189 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* * *
396209 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
396229 ATCGCGTTGCGAAAGT---T
1 ATCGCATTGCGATAGTCAGT
*
396246 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
396266 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
396286 ATCGCATTGCGAT
1 ATCGCATTGCGAT
396299 TTTCCCAATT
Statistics
Matches: 98, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
17 14 0.14
19 2 0.02
20 71 0.72
21 11 0.11
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:396298 original size:40 final size:39
Alignment explanation
Indices: 396168--396298 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 39
396158 CGCTTTGAAA
* *
396168 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGA-TA-GTAGTATCGCGTTGCGAAAGTCAGT
* * *
396209 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGT---T
1 ATCGCATTGCGATAGT-AGTATCGCGTTGCGAAAGTCAGT
* *
396246 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGTATCGCGTTGCGAAAGTCAGT
396286 ATCGCATTGCGAT
1 ATCGCATTGCGAT
396299 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
37 30 0.40
39 2 0.03
40 32 0.43
41 11 0.15
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (39 bp):
ATCGCATTGCGATAGTAGTATCGCGTTGCGAAAGTCAGT
Found at i:412416 original size:18 final size:18
Alignment explanation
Indices: 412378--412451 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 18
412368 ATAATAATCT
* *
412378 TTTTAAGTTG-CACCCCA
1 TTTTAAGTTGTAACCCAA
* * *
412395 TTTTAAGTTGTAATCTAT
1 TTTTAAGTTGTAACCCAA
*
412413 TTTTAAGTTGCAACCCAA
1 TTTTAAGTTGTAACCCAA
412431 TTTTAAGTTGTAACCC-A
1 TTTTAAGTTGTAACCCAA
412448 TTTT
1 TTTT
412452 CTGGTGATGG
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
17 15 0.33
18 31 0.67
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTTAAGTTGTAACCCAA
Found at i:412451 original size:36 final size:35
Alignment explanation
Indices: 412377--412451 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 35
412367 AATAATAATC
* * *
412377 TTTTTAAGTTGCACCCCATTTTAAGTTGTAATCTA
1 TTTTTAAGTTGCACCCAATTTTAAGTTGTAACCCA
412412 TTTTTAAGTTGCAACCCAATTTTAAGTTGTAACCCA
1 TTTTTAAGTTGC-ACCCAATTTTAAGTTGTAACCCA
412448 TTTT
1 TTTT
412452 CTGGTGATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 12 0.33
36 24 0.67
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (35 bp):
TTTTTAAGTTGCACCCAATTTTAAGTTGTAACCCA
Found at i:416510 original size:21 final size:19
Alignment explanation
Indices: 416470--416526 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 19
416460 CAACAATTGG
416470 TAACAATTGATA--TTTTT
1 TAACAATTGATATCTTTTT
416487 TAACAATTGATATCCTTTTGT
1 TAACAATTGATAT-CTTTT-T
416508 TAACAATTGATATCTTTTT
1 TAACAATTGATATCTTTTT
416527 CATTAAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.33
19 1 0.03
20 9 0.25
21 14 0.39
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:416764 original size:20 final size:18
Alignment explanation
Indices: 416739--416813 Score: 55
Period size: 20 Copynumber: 4.0 Consensus size: 18
416729 AAAATGCTAA
416739 AGTGTATCGATACCCCTATG
1 AGTGTATCGATACCCC--TG
* *
416759 AGTGTATCCATA-CACTG
1 AGTGTATCGATACCCCTG
416776 -GTGTATCGATACCCCCTG
1 AGTGTATCGATA-CCCCTG
* *
416794 CAGGTGTATCCATACACCTG
1 -A-GTGTATCGATACCCCTG
416814 TGACTGCTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 10 0.23
17 2 0.05
18 4 0.09
19 2 0.05
20 16 0.36
21 10 0.23
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (18 bp):
AGTGTATCGATACCCCTG
Found at i:416787 original size:36 final size:37
Alignment explanation
Indices: 416740--416810 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 37
416730 AAATGCTAAA
416740 GTGTATCGATACCCCTATG-A-GTGTATCCATACACTG
1 GTGTATCGATACCCC-ATGCAGGTGTATCCATACACTG
*
416776 GTGTATCGATACCCCCTGCAGGTGTATCCATACAC
1 GTGTATCGATACCCCATGCAGGTGTATCCATACAC
416811 CTGTGACTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 2 0.06
36 16 0.50
37 14 0.44
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (37 bp):
GTGTATCGATACCCCATGCAGGTGTATCCATACACTG
Found at i:416883 original size:20 final size:21
Alignment explanation
Indices: 416840--416895 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
416830 GAATGTAAAT
*
416840 AGTGTACCGATACA-CCTATG
1 AGTGTACCGATACACCCTATC
416860 AGTGTACCGATACACCCTA-C
1 AGTGTACCGATACACCCTATC
416880 AGTGTATCC-ATACACC
1 AGTGTA-CCGATACACC
416896 ATGGCTGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 27 0.82
21 6 0.18
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (21 bp):
AGTGTACCGATACACCCTATC
Found at i:418513 original size:18 final size:18
Alignment explanation
Indices: 418486--418619 Score: 123
Period size: 18 Copynumber: 7.6 Consensus size: 18
418476 TGCACGGAAT
*
418486 AACCTTTTTTTAAGTTGC
1 AACCTATTTTTAAGTTGC
418504 AACCTATTTTTAAGTTGC
1 AACCTATTTTTAAGTTGC
* * **
418522 ACCCCA-TTTTAAGTTAT
1 AACCTATTTTTAAGTTGC
* *
418539 AATCTATTTTTAAGTTGT
1 AACCTATTTTTAAGTTGC
* *
418557 ACCCTA-TTTTAAGTTAC
1 AACCTATTTTTAAGTTGC
*
418574 AACCTATTTTT-AGATGC
1 AACCTATTTTTAAGTTGC
*
418591 AATAC-ATTTTTAAGTTGC
1 AA-CCTATTTTTAAGTTGC
*
418609 AACCCATTTTT
1 AACCTATTTTT
418620 TGGTGATGGG
Statistics
Matches: 92, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
17 39 0.42
18 53 0.58
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (18 bp):
AACCTATTTTTAAGTTGC
Found at i:418531 original size:17 final size:17
Alignment explanation
Indices: 418493--418618 Score: 101
Period size: 17 Copynumber: 7.2 Consensus size: 17
418483 AATAACCTTT
418493 TTTTAAGTTGCAACCTA
1 TTTTAAGTTGCAACCTA
* *
418510 TTTTTAAGTTGCACCCCA
1 -TTTTAAGTTGCAACCTA
** *
418528 TTTTAAGTTATAATCTA
1 TTTTAAGTTGCAACCTA
* *
418545 TTTTTAAGTTGTACCCTA
1 -TTTTAAGTTGCAACCTA
*
418563 TTTTAAGTTACAACCTA
1 TTTTAAGTTGCAACCTA
* * *
418580 TTTTTAGATGCAATAC-A
1 TTTTAAGTTGCAA-CCTA
*
418597 TTTTTAAGTTGCAACCCA
1 -TTTTAAGTTGCAACCTA
418615 TTTT
1 TTTT
418619 TTGGTGATGG
Statistics
Matches: 84, Mismatches: 20, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
17 42 0.50
18 42 0.50
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (17 bp):
TTTTAAGTTGCAACCTA
Found at i:418546 original size:35 final size:35
Alignment explanation
Indices: 418493--418585 Score: 141
Period size: 35 Copynumber: 2.7 Consensus size: 35
418483 AATAACCTTT
*
418493 TTTTAAGTTGCAACCTATTTTTAAGTTGCACCCCA
1 TTTTAAGTTACAACCTATTTTTAAGTTGCACCCCA
* * * *
418528 TTTTAAGTTATAATCTATTTTTAAGTTGTACCCTA
1 TTTTAAGTTACAACCTATTTTTAAGTTGCACCCCA
418563 TTTTAAGTTACAACCTATTTTTA
1 TTTTAAGTTACAACCTATTTTTA
418586 GATGCAATAC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (35 bp):
TTTTAAGTTACAACCTATTTTTAAGTTGCACCCCA
Found at i:419309 original size:42 final size:41
Alignment explanation
Indices: 419117--419320 Score: 182
Period size: 42 Copynumber: 4.8 Consensus size: 41
419107 TACATTTACT
* **
419117 CTAAGTTTTTCAATCCCA-TTTTGTACATTTATAATTAA-GCTT
1 CTAA-TTTTTCAATCTCACTTTT-TAC-TTTATAATTAAGGCAC
* * *
419159 CTAATTTTTTTCAATCTCAC-TTTTACCTTTATAATGAAGACTC
1 CTAA--TTTTTCAATCTCACTTTTTA-CTTTATAATTAAGGCAC
*
419202 CTAATTATTT-AATCTCACTTTTTACTTATATAATTAAGGCCC
1 CTAATT-TTTCAATCTCACTTTTTACTT-TATAATTAAGGCAC
* *
419244 CTAATTTTTTCAATCCCACTTTTTACTTGTATAATTTAGGCAC
1 CTAA-TTTTTCAATCTCACTTTTTACTT-TATAATTAAGGCAC
* * *
419287 TTAATTTTTCAATCTCACTTTTTAATATATAATT
1 CTAATTTTTCAATCTCACTTTTTACTTTATAATT
419321 TCACTTTTCA
Statistics
Matches: 137, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
41 20 0.15
42 62 0.45
43 55 0.40
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (41 bp):
CTAATTTTTCAATCTCACTTTTTACTTTATAATTAAGGCAC
Found at i:419316 original size:84 final size:84
Alignment explanation
Indices: 419117--419320 Score: 220
Period size: 85 Copynumber: 2.4 Consensus size: 84
419107 TACATTTACT
* * ** *
419117 CTAAGTTTTTCAATCCCA-TTTTGTACATTTATAATTAAGCTTCTAATTTTTTTCAATCTCACTT
1 CTAA-TTTTTCAATCTCACTTTT-TACATATATAATTAAGCCCCTAATTTTTTTCAATCCCACTT
*
419181 TTACCTTTATAATGAAGACTC
64 TTACCTTTATAATGAAGACAC
*
419202 CTAATTATTT-AATCTCACTTTTTACTTATATAATTAAGGCCCCTAA-TTTTTTCAATCCCACTT
1 CTAATT-TTTCAATCTCACTTTTTACATATATAATTAA-GCCCCTAATTTTTTTCAATCCCAC-T
** *
419265 TTTA-CTTGTATAATTTAGGCAC
63 TTTACCTT-TATAATGAAGACAC
*
419287 TTAATTTTTCAATCTCACTTTTTA-ATATATAATT
1 CTAATTTTTCAATCTCACTTTTTACATATATAATT
419321 TCACTTTTCA
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
84 50 0.50
85 51 0.50
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (84 bp):
CTAATTTTTCAATCTCACTTTTTACATATATAATTAAGCCCCTAATTTTTTTCAATCCCACTTTT
ACCTTTATAATGAAGACAC
Found at i:419912 original size:2 final size:2
Alignment explanation
Indices: 419849--419894 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
419839 TATAGAATGG
* *
419849 TA TA TA TA CA AA 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
419891 TA TA
1 TA TA
419895 GTTTTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:420031 original size:3 final size:3
Alignment explanation
Indices: 420023--420049 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
420013 TTTTCATCTT
420023 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
420050 ATTTGGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:430795 original size:24 final size:20
Alignment explanation
Indices: 430768--430825 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
430758 GCATAAGGAG
*
430768 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TG-T-A-GAA
*
430792 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
430812 TGCATCGATGCACT
1 TGCATCGATGCACT
430826 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:432343 original size:22 final size:21
Alignment explanation
Indices: 432314--432377 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
432304 GGATATCTTA
432314 TATGGCACTTCGGTGCATTTC
1 TATGGCACTTCGGTGCATTTC
* * *
432335 TATGCGCACTAC-GTGTAATTC
1 TATG-GCACTTCGGTGCATTTC
432356 TACGTGGCACTTCGGTGCATTT
1 TA--TGGCACTTCGGTGCATTT
432378 ATACGAGCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 13 0.39
22 12 0.36
23 8 0.24
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (21 bp):
TATGGCACTTCGGTGCATTTC
Found at i:437330 original size:23 final size:23
Alignment explanation
Indices: 437303--437370 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
437293 AATATTATAT
*
437303 GGCACTTCGGTGTATTTATACGC
1 GGCACTTCGGTGCATTTATACGC
* * * *
437326 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTATACGC
437349 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTATACG
437371 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTATACGC
Found at i:437670 original size:66 final size:66
Alignment explanation
Indices: 437564--437798 Score: 278
Period size: 66 Copynumber: 3.6 Consensus size: 66
437554 ATGTTGGTTA
* *
437564 AAACAAAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTTGCTTGAGACAGTTTCTCTT
1 AAACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTT
437629 G
66 G
* * * * *
437630 AAACATAAACATTTTAGATTGATTCTCTTGAAACAAATTTTGTCTCGCTTAAGACAATTTCTCTT
1 AAACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTT
437695 G
66 G
** * * * *
437696 AAACATAAACCTTTGAGATTGTTTCTCTCAAAAAAAAGTTTTATCTCACTTGAGACAGTTTCCCT
1 AAACATAAACCTTTGAGATTGTTTCTCTTGAAACAAA-TTTTGTCTCGCTTGAGACAGTTTCTCT
437761 TG
65 TG
* * *
437763 AAGC-TCAAA-TTTTGA-AGTTGTTTCACTTGAAACAAA
1 AAACAT-AAACCTTTGAGA-TTGTTTCTCTTGAAACAAA
437799 ATTGATATCA
Statistics
Matches: 142, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
65 1 0.01
66 111 0.78
67 30 0.21
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (66 bp):
AAACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTT
G
Found at i:437986 original size:103 final size:102
Alignment explanation
Indices: 437708--438043 Score: 374
Period size: 102 Copynumber: 3.3 Consensus size: 102
437698 ACATAAACCT
* * * ** * * * *
437708 TTGAGATTGTTTCTCTCAAAAAAAAGTTTTATCTCACTTGAGAC-AGTTTCCCTTGAAGCTCAAA
1 TTGAGATTATTTCTCTTAAAACAAA-TTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACACAAA
* *
437772 TTTTGAAGTTGTTTCACTTGAAACAAAATTGATATCAC
65 TTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCAC
* * * * ** *
437810 TTGAGATTGTTT-TCCTAAAAACATATTTCGTCTCGCTTGAGACAATTTTGCCTCAAAACATAAA
1 TTGAGATTATTTCT-CTTAAAACAAATTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACACAAA
437874 TTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCAC
65 TTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCAC
*
437912 TTGAGATTATTTCTCTTGAAACAAAGTTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACACAAA
1 TTGAGATTATTTCTCTTAAAACAAA-TTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACACAAA
* * *
437977 TTTTGAAATTGTTTCACTCGAAA-AAAATTTTATCTCGC
65 TTTTGAAATTGTTTCACTTGAAACAAAA-TTGATCTCAC
* * *
438015 ATGAGA-TAGCTTCTCTTGAAACAAATTTC
1 TTGAGATTA-TTTCTCTTAAAACAAATTTC
438044 TTTCCATTAA
Statistics
Matches: 200, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
101 16 0.08
102 98 0.49
103 86 0.43
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (102 bp):
TTGAGATTATTTCTCTTAAAACAAATTTCGTCTCGCTTGAGACAATTTTCCCTTGAAACACAAAT
TTTGAAATTGTTTCACTTGAAACAAAATTGATCTCAC
Found at i:442115 original size:18 final size:18
Alignment explanation
Indices: 442083--442130 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
442073 AAATGCACCA
* *
442083 AAGTGCCATAGTGCATCTG
1 AAGTGCCACAATGCA-CTG
442102 -AGTGCCACAATGCACTG
1 AAGTGCCACAATGCACTG
*
442119 AAGTGTCACAAT
1 AAGTGCCACAAT
442131 ATACTCGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (18 bp):
AAGTGCCACAATGCACTG
Found at i:446206 original size:5 final size:5
Alignment explanation
Indices: 446196--446238 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
446186 TCTTGGATGC
446196 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
446239 GTGATACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:448059 original size:86 final size:86
Alignment explanation
Indices: 447914--448086 Score: 247
Period size: 86 Copynumber: 2.0 Consensus size: 86
447904 GTTTGGTTTC
* *
447914 TATGCACATCCCTAAACACTCACTTATAGTCTAGATGGCTATCCTAAATAGATTATCTACTGCAG
1 TATGCACATCCCTAAACACTCACTCATAGTCTAGATGGCTATCCTAAACAGATTATCTACTGCAG
*
447979 ATAAACTTGCGTGAATAGGGA
66 ATAAACTTGCGCGAATAGGGA
* * * * * *
448000 TATGCACATCCCTAAATACTCACTCATAGTCTGGATGGCTATTCTAGACAGATTGTCTACTGCTG
1 TATGCACATCCCTAAACACTCACTCATAGTCTAGATGGCTATCCTAAACAGATTATCTACTGCAG
* *
448065 ATAGACTTGCGCGAATGGGGA
66 ATAAACTTGCGCGAATAGGGA
448086 T
1 T
448087 CTGGGTGGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (86 bp):
TATGCACATCCCTAAACACTCACTCATAGTCTAGATGGCTATCCTAAACAGATTATCTACTGCAG
ATAAACTTGCGCGAATAGGGA
Found at i:452609 original size:18 final size:19
Alignment explanation
Indices: 452583--452632 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
452573 AATAGCTAAG
* *
452583 GTATTGATACTCATGG-GA
1 GTATCGATACTCAGGGAGA
*
452601 GTATCGATACTTAGGGTAGA
1 GTATCGATACTCAGGG-AGA
452621 GTATCGATACTC
1 GTATCGATACTC
452633 CTAGTATGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (19 bp):
GTATCGATACTCAGGGAGA
Found at i:453936 original size:26 final size:26
Alignment explanation
Indices: 453898--453979 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
453888 TCTTTAAGTT
*
453898 TCAATGAATTACATGACTCTAGAGTG
1 TCAATGAAGTACATGACTCTAGAGTG
453924 TCAATGAAGTACATGACTCTAGAGTG
1 TCAATGAAGTACATGACTCTAGAGTG
* *
453950 TCAACGAAGTGCATGACTCTAGAGTG
1 TCAATGAAGTACATGACTCTAGAGTG
453976 TCAA
1 TCAA
453980 GCTTACTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (26 bp):
TCAATGAAGTACATGACTCTAGAGTG
Found at i:460385 original size:12 final size:12
Alignment explanation
Indices: 460368--460396 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
460358 TGTGTTTTGT
460368 ATATTTTTCTTC
1 ATATTTTTCTTC
460380 ATA-TTTTCTTC
1 ATATTTTTCTTC
460391 ATATTT
1 ATATTT
460397 ATTTAATTAA
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:0.21, C:0.14, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTTTTCTTC
Found at i:464692 original size:51 final size:51
Alignment explanation
Indices: 464627--464746 Score: 125
Period size: 51 Copynumber: 2.4 Consensus size: 51
464617 CACCCGTAGC
* ** * * *
464627 AGTAAAGCGCGCCCCCTGAACCTCGCTATATGCTGATTTGG-CACCACGTGG
1 AGTATAGCGCGCCCCCTGAACCGAGCTATACGCTGACTGGGTCA-CACGTGG
* * * *
464678 AGTATAGCGCGCCCCTTGTATCGAGCTATACGCTGACTGGGTTACACGTGG
1 AGTATAGCGCGCCCCCTGAACCGAGCTATACGCTGACTGGGTCACACGTGG
*
464729 GGTATAGCGCGCCCCCTG
1 AGTATAGCGCGCCCCCTG
464747 CTTCGCACTA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (51 bp):
AGTATAGCGCGCCCCCTGAACCGAGCTATACGCTGACTGGGTCACACGTGG
Found at i:468423 original size:35 final size:34
Alignment explanation
Indices: 468339--468424 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 34
468329 TTTGGTATTT
*
468339 AAATACAACAAACTTACAATAAGAATTAAATGGA
1 AAATACAACAAAATTACAATAAGAATTAAATGGA
* *
468373 AAATGATAACCAAATTACAATAACTGATATTAAATGG-
1 AAAT-ACAACAAAATTACAATAA--GA-ATTAAATGGA
*
468410 TAATA-AACAAAATTA
1 AAATACAACAAAATTA
468425 ACTAAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
34 4 0.09
35 24 0.56
36 1 0.02
37 5 0.12
38 9 0.21
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.24
Consensus pattern (34 bp):
AAATACAACAAAATTACAATAAGAATTAAATGGA
Found at i:468649 original size:3 final size:3
Alignment explanation
Indices: 468643--468698 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
468633 GCTGTCATCA
* * * * *
468643 TCG TCG TCG TCG TCG TCG TCA CCA TCG TCG TCA TCG TCA TCG TCG TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
468691 TCG TCG TC
1 TCG TCG TC
468699 CTGAGCAGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.07, C:0.36, G:0.25, T:0.32
Consensus pattern (3 bp):
TCG
Found at i:471177 original size:22 final size:22
Alignment explanation
Indices: 471143--471184 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
471133 GAAAAATTTG
*
471143 AATAAATGAAAATTTTTATACT
1 AATAAATGAAAATTTATATACT
**
471165 AATAAATTTAAATTTATATA
1 AATAAATGAAAATTTATATA
471185 TTTGAACTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AATAAATGAAAATTTATATACT
Found at i:473553 original size:84 final size:84
Alignment explanation
Indices: 473412--473580 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
473402 AAATAAACTA
473412 TGATCAAATCATGTCAAATCATCAAGAACAAGAAATACTATATTTGCGGAAGCGTACCTAGATTA
1 TGATCAAATCATGTCAAATCATCAAGAACAAGAAATACTATATTTGCGGAAGCGTACCTAGATTA
473477 ATTGAAATGTTGAAATTTT
66 ATTGAAATGTTGAAATTTT
473496 TGATCAAATCATGTCAAATCATCAAGAACAAGAAATACTATATTTGCGGAAGCGTACCTAGATTA
1 TGATCAAATCATGTCAAATCATCAAGAACAAGAAATACTATATTTGCGGAAGCGTACCTAGATTA
473561 ATTGAAATGTTGAAATTTT
66 ATTGAAATGTTGAAATTTT
473580 T
1 T
473581 AAGTCTTTCT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (84 bp):
TGATCAAATCATGTCAAATCATCAAGAACAAGAAATACTATATTTGCGGAAGCGTACCTAGATTA
ATTGAAATGTTGAAATTTT
Found at i:476502 original size:15 final size:17
Alignment explanation
Indices: 476471--476502 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
476461 ATGTATTTTT
476471 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
476488 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
476503 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:479932 original size:80 final size:80
Alignment explanation
Indices: 479790--479994 Score: 256
Period size: 80 Copynumber: 2.5 Consensus size: 80
479780 AAAGTGGAAA
* * * *
479790 AAATATT-TAATGATTCCATATATTATAATCAATAAAAAAACTAAACCTCTATCGCTTAAATTAA
1 AAATATTATAATGATTTCATATA-TATTAT-AAT-TAAAAACTAAACCTCTATAGCTTAAATTAA
*
479854 GAAAATAAGTGGAAAAAC
63 GAAAACAAGTGGAAAAAC
* *
479872 AAATATTATAATGATTTCATATATATTATAATTAAAAGCTAAACCAT-TATAGTTTAAATTAAGA
1 AAATATTATAATGATTTCATATATATTATAATTAAAAACTAAACC-TCTATAGCTTAAATTAAGA
* *
479936 AAACAAGTGGACAAAT
65 AAACAAGTGGAAAAAC
479952 AAATATTATAATGA-TTCTATATATATTATAATTAAAAAC-AAAC
1 AAATATTATAATGATTTC-ATATATATTATAATTAAAAACTAAAC
479995 AAACTACTAT
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
79 7 0.06
80 73 0.66
81 4 0.04
82 12 0.11
83 14 0.13
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (80 bp):
AAATATTATAATGATTTCATATATATTATAATTAAAAACTAAACCTCTATAGCTTAAATTAAGAA
AACAAGTGGAAAAAC
Found at i:480024 original size:80 final size:80
Alignment explanation
Indices: 479790--480025 Score: 189
Period size: 80 Copynumber: 2.9 Consensus size: 80
479780 AAAGTGGAAA
* * * * *
479790 AAATATT-TAATGATTCCATATATTATAATCAATAAAAAAACTAAACC-TCTATCGCT-TAAATT
1 AAATATTATAATGATTTCATATA-TATTAT-AAT-TAAAAACTAAACCAT-AAT-ACTATAAATT
* *
479852 AAGAAAATAAGTGGAAAAAC
61 AACAAAAAAAGTGGAAAAAC
* * * * *
479872 AAATATTATAATGATTTCATATATATTATAATTAAAAGCTAAACCATTATAGTTTAAATTAAGAA
1 AAATATTATAATGATTTCATATATATTATAATTAAAAACTAAACCATAATACTATAAATTAACAA
* * *
479937 AACAAGTGGACAAAT
66 AAAAAGTGGAAAAAC
**
479952 AAATATTATAATGA-TTCTATATATATTATAATTAAAAAC-AAA-CA-AACTACTATATCTTCAA
1 AAATATTATAATGATTTC-ATATATATTATAATTAAAAACTAAACCATAA-TACTATAAATT-AA
480013 CAAACAAAAGTGG
63 CAAA-AAAAGTGG
480026 TGATTTTGTA
Statistics
Matches: 130, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
77 1 0.01
78 9 0.07
79 12 0.09
80 78 0.60
81 4 0.03
82 12 0.09
83 14 0.11
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (80 bp):
AAATATTATAATGATTTCATATATATTATAATTAAAAACTAAACCATAATACTATAAATTAACAA
AAAAAGTGGAAAAAC
Found at i:480725 original size:20 final size:20
Alignment explanation
Indices: 480705--480810 Score: 106
Period size: 20 Copynumber: 5.2 Consensus size: 20
480695 AAATCGTAAT
*
480705 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
480725 GCGATACTTACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
480745 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* *
480766 GAGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
480786 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
480806 GCGAT
1 GCGAT
480811 TTACATAGCG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Done.