Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 38
Found at i:5028217 original size:20 final size:20
Alignment explanation
Indices: 5028139--5028208 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
5028129 TTTCCAGATG
5028139 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
5028159 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
5028179 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
5028199 TTTTCCAGAA
1 TTTTCCAGAA
5028209 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:5028217 original size:40 final size:40
Alignment explanation
Indices: 5028139--5028217 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
5028129 TTTCCAGATG
* **
5028139 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
5028179 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
5028218 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:5028233 original size:29 final size:30
Alignment explanation
Indices: 5028191--5028262 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
5028181 TTACAGAAAT
5028191 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
5028220 GTAATTCATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
5028250 GTAATTCATTTTC
1 GTAATTCATTTTC
5028263 TGGAAAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:5028263 original size:15 final size:15
Alignment explanation
Indices: 5028191--5028262 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
5028181 TTACAGAAAT
5028191 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
5028206 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
5028220 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
5028235 GTAATTCAAATTCTA
1 GTAATTCATTTTCCA
5028250 GTAATTCATTTTC
1 GTAATTCATTTTC
5028263 TGGAAAACCA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
14 12 0.26
15 35 0.74
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:5029123 original size:10 final size:11
Alignment explanation
Indices: 5029103--5029133 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
5029093 ATATACAACA
5029103 TTTCTTTTTTT
1 TTTCTTTTTTT
5029114 TTTCTTTTTTT
1 TTTCTTTTTTT
5029125 TTTCATTTT
1 TTTC-TTTT
5029134 AACGTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:5030030 original size:3 final size:3
Alignment explanation
Indices: 5030022--5030067 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
5030012 TTGGTTTGTA
*
5030022 AAT AAT AAT AAT ATTT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5030067 A
1 A
5030068 TAGGGTAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:5035607 original size:24 final size:24
Alignment explanation
Indices: 5035562--5035655 Score: 129
Period size: 24 Copynumber: 4.0 Consensus size: 24
5035552 ACCTATGTGA
* *
5035562 TCCTTCGGGAT-ATTTCTACGTGG
1 TCCTTAGGGATAAATTCTACGTGG
5035585 TCCTTAGGGATAAATTCTACGTGG
1 TCCTTAGGGATAAATTCTACGTGG
*
5035609 TCCTTAGGGA-AAATTCTACGTAG
1 TCCTTAGGGATAAATTCTACGTGG
* *
5035632 TCCTTTGGGACAAATTCTACGTGG
1 TCCTTAGGGATAAATTCTACGTGG
5035656 CACTTCAGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
23 31 0.48
24 33 0.52
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (24 bp):
TCCTTAGGGATAAATTCTACGTGG
Found at i:5042179 original size:24 final size:24
Alignment explanation
Indices: 5042061--5042163 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
5042051 GAGTCGAGGG
* *
5042061 TTCTACGCGGTCTTTCGGGAC-AA
1 TTCTACGTGGTCCTTCGGGACAAA
* * * * *
5042084 -CCTATGTGATCCTTCGGGA-TAT
1 TTCTACGTGGTCCTTCGGGACAAA
*
5042106 TTCTACGTGGTCCTTAGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
5042130 TTCTACGTGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
5042154 TTCTACGTGG
1 TTCTACGTGG
5042164 CACTTCAGTG
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
22 15 0.23
23 15 0.23
24 34 0.53
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.32
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:5042714 original size:20 final size:21
Alignment explanation
Indices: 5042672--5042711 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5042662 TATCTTTTAT
5042672 AAAAAAAATGTTCTATTGTTC
1 AAAAAAAATGTTCTATTGTTC
*
5042693 AAAAGAAAAT-TTTTATTGT
1 AAAA-AAAATGTTCTATTGT
5042712 CAACTGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAAAAAATGTTCTATTGTTC
Found at i:5043019 original size:18 final size:18
Alignment explanation
Indices: 5042992--5043033 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5042982 GAAAAAGAGG
5042992 AGAAGAAGAAGAAAAATA
1 AGAAGAAGAAGAAAAATA
* *
5043010 AGAAGTAGAAGAAGAATA
1 AGAAGAAGAAGAAAAATA
*
5043028 GGAAGA
1 AGAAGA
5043034 CACGTGGGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (18 bp):
AGAAGAAGAAGAAAAATA
Found at i:5044543 original size:388 final size:390
Alignment explanation
Indices: 5043825--5044550 Score: 962
Period size: 388 Copynumber: 1.9 Consensus size: 390
5043815 GATTGAAACG
* * * * *
5043825 TCGTACCGATAGTAGATGCTAAATGTAACGATGAAATAAGCCCCTAAATATTTGACTAAATAATC
1 TCGTACCAATAGTAGATGCTAAATGCAACGATGAAAGAAGCCCCTAAATATTTAAATAAATAATC
*
5043890 ACTCTAATTCTTATTTATTTTTAAATACAAATTAAAACTTATCTAAACTTATCAGAGCCAAGTTT
66 ACTCTAAATCTTATTTATTTTTAAATACAAATTAAAACTTATCTAAACTTATCAGAGCCAAGTTT
* ** * * * *
5043955 CAATCCTGAGAACTGTGGGTCATGGAGCCATGACACTTCCACTACGCCACTCTGATTAGTCGATC
131 CAATCCTGAGAACTATGGGTCATGGAGCCACCACACTTCCACTACACCACTCTAATGAATCGATC
* * * *
5044020 AAATTTTACCAACAATTATAATTGTATTTTGTAAAAGCATAATATGGTATAATTCTGTAATTTAT
196 AAATATTACCAACAATTATAATTGTATTTTATAAAAACATAATATGGTATAATTCTGAAATTTAT
* * *
5044085 CATTGTACTAATGAAGTTGAGAAGTTGGTCTTCTACTCTAATTTGCAATAATAAATTGTTCATTA
261 CACTGTACTAATGAAGTTGAGAAGTTGCTCTTCTACTCTAATTTGCAATAATAAATTGTACATTA
5044150 TAAAAACTAAAATGTAACTCACAAATGTGCATGCAACCCGATGTCGGAATGATAACCCTCTAACA
326 TAAAAACTAAAATGTAACTCACAAATGTGCATGCAACCCGATGTCGGAATGATAACCCTCTAACA
* * * *
5044215 TCGTACCAATGGTGGATGCTAAATGCATCGATGAAAGAAGTCCCC-AAATATTTAAATAAATAGT
1 TCGTACCAATAGTAGATGCTAAATGCAACGATGAAAGAAG-CCCCTAAATATTTAAATAAATAAT
* * * **
5044279 CACTTTAAATCTTATTTATTTTTAAATACAAATTAAAATTTATC-AGAATTTATTTGA-CC-AGA
65 CACTCTAAATCTTATTTATTTTTAAATACAAATTAAAACTTATCTA-AACTTATCAGAGCCAAG-
* * * ** ** *
5044341 TTTCGATCCTG-GACCTATGGGTTAT-GAGTCCACCATGCTTCCGTTACACCACTCTAATGAATT
128 TTTCAATCCTGAGAACTATGGGTCATGGAG-CCACCACACTTCCACTACACCACTCTAATGAATC
* * * * *
5044404 GTTTAGAA-ATTACCAACAATTTTTATTGTATTTTATAAAAACATAATATGGTCTAATTCTGAAA
192 GATCA-AATATTACCAACAATTATAATTGTATTTTATAAAAACATAATATGGTATAATTCTGAAA
*
5044468 TTTATCACTGTACTAATGAAGTTGAGAAGTTGCTCTTCTACTTTAATTTGCAATAATAAATTGTA
256 TTTATCACTGTACTAATGAAGTTGAGAAGTTGCTCTTCTACTCTAATTTGCAATAATAAATTGTA
*
5044533 GATTATAAAAACTAAAAT
321 CATTATAAAAACTAAAAT
5044551 ATTTCTGTAA
Statistics
Matches: 287, Mismatches: 44, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
387 3 0.01
388 166 0.58
389 15 0.05
390 99 0.34
391 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (390 bp):
TCGTACCAATAGTAGATGCTAAATGCAACGATGAAAGAAGCCCCTAAATATTTAAATAAATAATC
ACTCTAAATCTTATTTATTTTTAAATACAAATTAAAACTTATCTAAACTTATCAGAGCCAAGTTT
CAATCCTGAGAACTATGGGTCATGGAGCCACCACACTTCCACTACACCACTCTAATGAATCGATC
AAATATTACCAACAATTATAATTGTATTTTATAAAAACATAATATGGTATAATTCTGAAATTTAT
CACTGTACTAATGAAGTTGAGAAGTTGCTCTTCTACTCTAATTTGCAATAATAAATTGTACATTA
TAAAAACTAAAATGTAACTCACAAATGTGCATGCAACCCGATGTCGGAATGATAACCCTCTAACA
Found at i:5050407 original size:11 final size:11
Alignment explanation
Indices: 5050376--5050409 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5050366 TAGCCTTGAA
*
5050376 TTCTTAACAAC
1 TTCTTAACAGC
*
5050387 TTCTCAACAGC
1 TTCTTAACAGC
5050398 TTCTTAACAGC
1 TTCTTAACAGC
5050409 T
1 T
5050410 AGGTTGTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (11 bp):
TTCTTAACAGC
Found at i:5050539 original size:21 final size:21
Alignment explanation
Indices: 5050513--5050552 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5050503 GAATAAAGAA
* *
5050513 TATATTTTTTTCGTTCTTTAT
1 TATATTTTCTTCATTCTTTAT
5050534 TATATTTTCTTCATTCTTT
1 TATATTTTCTTCATTCTTT
5050553 CTACATTATT
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:0.15, C:0.12, G:0.03, T:0.70
Consensus pattern (21 bp):
TATATTTTCTTCATTCTTTAT
Found at i:5051962 original size:18 final size:17
Alignment explanation
Indices: 5051939--5051975 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
5051929 CTTTATACAT
5051939 TTGCTATGGATTCTAAGG
1 TTGCTATGGATTCT-AGG
5051957 TTGCTATGGATTCTAGG
1 TTGCTATGGATTCTAGG
5051974 TT
1 TT
5051976 TTCTTCTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.43
Consensus pattern (17 bp):
TTGCTATGGATTCTAGG
Found at i:5059005 original size:45 final size:45
Alignment explanation
Indices: 5058955--5059138 Score: 298
Period size: 45 Copynumber: 4.1 Consensus size: 45
5058945 TCTTTATTGA
*
5058955 TGTACATGTTCGACATGTAATGTGATATGAAATGTGGATATGTAT
1 TGTACATGTTTGACATGTAATGTGATATGAAATGTGGATATGTAT
* *
5059000 TGTACATGTTTAACATGTAATGTGATATGAAATATGGATATGTAT
1 TGTACATGTTTGACATGTAATGTGATATGAAATGTGGATATGTAT
*
5059045 TGTACATGTTTGACAAT-TATTGTGATATGAAATGTGGATATGTAT
1 TGTACATGTTTGAC-ATGTAATGTGATATGAAATGTGGATATGTAT
* *
5059090 TGTACATGTTTGACATGTAATGTGATATGAAATGTGGATCTGCAT
1 TGTACATGTTTGACATGTAATGTGATATGAAATGTGGATATGTAT
5059135 TGTA
1 TGTA
5059139 AATTGTGTAT
Statistics
Matches: 128, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
44 2 0.02
45 124 0.97
46 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.40
Consensus pattern (45 bp):
TGTACATGTTTGACATGTAATGTGATATGAAATGTGGATATGTAT
Found at i:5061276 original size:21 final size:20
Alignment explanation
Indices: 5061250--5061347 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
5061240 ATCAGTTTCC
5061250 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
5061271 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
5061290 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
5061311 ACAGAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
5061333 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
5061348 ACACATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.27
21 42 0.67
22 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:5061340 original size:20 final size:20
Alignment explanation
Indices: 5061315--5061507 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
5061305 GATTTTACAG
* ** *
5061315 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
5061335 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
5061355 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
5061375 AATCGCAACGTGTATCTGTA
1 AATCGCAACGCGTATCCGTA
5061395 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5061415 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5061435 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
5061455 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
5061476 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5061496 AATCGCAACGCG
1 AATCGCAACGCG
5061508 ATTTTTAAAG
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 127 0.86
21 19 0.13
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:5061398 original size:60 final size:60
Alignment explanation
Indices: 5061315--5061507 Score: 255
Period size: 60 Copynumber: 3.2 Consensus size: 60
5061305 GATTTTACAG
* * * *
5061315 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACACGTAAATCGCAATGCGTATCCGTA
* *
5061375 AATCGCAACGTGTATCTGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGCG-AACACGTAAATCGCAATGCGTATCCGTA
* * * *
5061435 TATCGCAACGCGTATCCGTAAATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACG-CGAACACGT-AAATCGCAATGCGTATCCGTA
5061496 AATCGCAACGCG
1 AATCGCAACGCG
5061508 ATTTTTAAAG
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
59 1 0.01
60 81 0.70
61 34 0.29
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGCGAACACGTAAATCGCAATGCGTATCCGTA
Found at i:5061926 original size:33 final size:33
Alignment explanation
Indices: 5061887--5061957 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
5061877 TTCACTTAGA
*
5061887 TTTCATTTCGCGTTACGATTCTCTTGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
5061920 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGTT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
5061953 TTTCA
1 TTTCA
5061958 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.10, C:0.23, G:0.17, T:0.51
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:5062063 original size:21 final size:20
Alignment explanation
Indices: 5062037--5062143 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
5062027 TGCAGAAGAG
5062037 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
5062058 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
5062078 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
5062100 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
5062114 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
5062133 TCGCAACGAGA
1 TCGCAACGAGA
5062144 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:5062117 original size:14 final size:14
Alignment explanation
Indices: 5062098--5062154 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5062088 GAAAAATGAA
5062098 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5062112 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5062131 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5062145 AATCGCAACG
1 AATCGCAACG
5062155 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5062129 original size:33 final size:33
Alignment explanation
Indices: 5062091--5062170 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
5062081 GCAACGAGAA
5062091 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
5062124 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
5062157 AAACCAAAATCGCA
1 AAATGAAAATCGCA
5062171 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:5062188 original size:19 final size:19
Alignment explanation
Indices: 5062166--5062293 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
5062156 GAAACCAAAA
*
5062166 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5062185 TCGCGGTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5062199 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5062218 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5062232 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
5062252 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
5062272 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5062292 TC
1 TC
5062294 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 19 0.22
16 6 0.07
17 6 0.07
19 21 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5062210 original size:14 final size:14
Alignment explanation
Indices: 5062191--5062244 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
5062181 CATTTCGCGG
5062191 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
*
5062205 TGCGATTTTCATTTCGCGT
1 TGCGA--TTC---TCTCGT
5062224 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
5062238 TGCGATT
1 TGCGATT
5062245 TTCATTTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
TGCGATTCTCTCGT
Found at i:5062213 original size:33 final size:33
Alignment explanation
Indices: 5062171--5062252 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
5062161 CAAAATCGCA
5062171 TTGCGATTTTCATTTCGCGGTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGGTGCGATTCTCTCG
*
5062204 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGGTGCGATTCTCTCG
5062237 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
5062253 TCTCGTTGCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGGTGCGATTCTCTCG
Found at i:5062255 original size:21 final size:21
Alignment explanation
Indices: 5062229--5062293 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
5062219 CGCGTTGCGA
5062229 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
5062250 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
5062270 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
5062291 TTC
1 TTC
5062294 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:5064135 original size:93 final size:93
Alignment explanation
Indices: 5063976--5064444 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
5063966 TAGATTGCTT
*
5063976 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5064041 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5064069 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5064134 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5064162 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
5064227 TTTGTCTTTGTTTTTTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
5064255 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5064320 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5064348 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5064413 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5064440 AGTAA
1 AGTAA
5064445 TGCAATCCAT
Statistics
Matches: 371, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 365 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5064548 original size:19 final size:17
Alignment explanation
Indices: 5064524--5064615 Score: 70
Period size: 19 Copynumber: 5.4 Consensus size: 17
5064514 GCAACGAGAG
5064524 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA--AA
*
5064543 AATCGCAA--C-AAAAG
1 AATCGCAACGCGAAAAA
5064557 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA--AA
*
5064576 AATCGCAA--CG-ACAA
1 AATCGCAACGCGAAAAA
5064590 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA--AA
5064609 AATCGCA
1 AATCGCA
5064616 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 19 0.32
16 7 0.12
17 7 0.12
19 26 0.44
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.08
Consensus pattern (17 bp):
AATCGCAACGCGAAAAA
Found at i:5064550 original size:33 final size:33
Alignment explanation
Indices: 5064492--5064615 Score: 169
Period size: 33 Copynumber: 3.7 Consensus size: 33
5064482 TAGTTTACTT
* * *
5064492 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGAAAGAA
** *
5064526 TCGCAACGCGAAATGAAAATCGCAACAAAAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGAAAGAA
5064559 TCGCAACGCGAAACCAAAATCGCAACGACAA-AA
1 TCGCAACGCGAAACCAAAATCGCAACGA-AAGAA
5064592 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
5064616 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
33 67 0.83
34 14 0.17
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGAAAGAA
Found at i:5064592 original size:14 final size:14
Alignment explanation
Indices: 5064573--5064599 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5064563 AACGCGAAAC
5064573 CAAAATCGCAACGA
1 CAAAATCGCAACGA
5064587 CAAAATCGCAACG
1 CAAAATCGCAACG
5064600 CGAAACCAAA
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:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:5064633 original size:19 final size:19
Alignment explanation
Indices: 5064611--5064783 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
5064601 GAAACCAAAA
*
5064611 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5064630 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5064644 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
5064663 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
5064679 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
5064696 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
5064715 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
5064734 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
5064753 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
5064773 TCGTGTTGCGA
1 TCGCGTTGCGA
5064784 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5064652 original size:14 final size:14
Alignment explanation
Indices: 5064633--5064689 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
5064623 TTTCATTTCG
5064633 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5064647 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
5064664 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
5064680 CGTTGCGATT
1 CGTTGCGATT
5064690 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5064741 original size:38 final size:38
Alignment explanation
Indices: 5064611--5064783 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
5064601 GAAACCAAAA
*
5064611 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
5064646 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
5064679 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
5064715 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
5064753 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
5064784 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:5066725 original size:14 final size:14
Alignment explanation
Indices: 5066706--5066741 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5066696 ATTGTTTAAT
5066706 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5066720 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5066734 TGATTTGT
1 TGATTTGT
5066742 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5066865 original size:20 final size:19
Alignment explanation
Indices: 5066848--5066946 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
5066838 AAAAATGACT
5066848 ATCGCAATGTGGAAATGAAA
1 ATCGCAATGT-GAAATGAAA
*
5066868 ATCGCAATGTGAAATAAAA
1 ATCGCAATGTGAAATGAAA
* *
5066887 ATCGCAA--CG--A-GAGA
1 ATCGCAATGTGAAATGAAA
*
5066901 ATCGCAATGCGAAATGAAA
1 ATCGCAATGTGAAATGAAA
*
5066920 ATCGCAATGCGGAAATGAAA
1 ATCGCAATG-TGAAATGAAA
5066940 ATCGCAA
1 ATCGCAA
5066947 CGAGAGAATC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 27 0.40
20 26 0.39
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGTGAAATGAAA
Found at i:5066978 original size:53 final size:53
Alignment explanation
Indices: 5066848--5066965 Score: 193
Period size: 53 Copynumber: 2.2 Consensus size: 53
5066838 AAAAATGACT
* *
5066848 ATCGCAATGTGGAAATGAAAATCGCAATG-TGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATG-CGAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
*
5066901 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
5066954 ATCGCAATGCGA
1 ATCGCAATGCGA
5066966 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 18 0.30
53 43 0.70
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGA
Found at i:5066983 original size:19 final size:19
Alignment explanation
Indices: 5066955--5067177 Score: 216
Period size: 19 Copynumber: 12.7 Consensus size: 19
5066945 AACGAGAGAA
* *
5066955 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
5066974 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
5066990 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5067007 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5067026 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
5067042 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5067059 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
5067078 TCCACATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
5067095 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5067112 TCACATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5067131 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
5067149 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
5067165 TCGCATTGCGATT
1 TCGCATTGCGATT
5067178 CTCTCGTTGC
Statistics
Matches: 168, Mismatches: 14, Indels: 44
0.74 0.06 0.19
Matches are distributed among these distances:
14 29 0.17
16 20 0.12
17 19 0.11
18 4 0.02
19 72 0.43
20 24 0.14
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5066998 original size:33 final size:33
Alignment explanation
Indices: 5066961--5067124 Score: 145
Period size: 33 Copynumber: 4.8 Consensus size: 33
5066951 AGAATCGCAA
* *
5066961 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCACATTGCGATTCTCTCGT
* *
5066994 TGCGATTTTCATTTCGCATTGCGATT-T-TCAT
1 TGCGATTTTCATTTCACATTGCGATTCTCTCGT
* * * * *
5067025 TTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCACATTGCGA--TTC-TCTCG--T
5067065 TGCGATTTTCATTTCCACATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CACATTGCGATTCTCTCGT
5067099 TGCGATTTTCATTTCACATTGCGATT
1 TGCGATTTTCATTTCACATTGCGATT
5067125 TTCATTTCCG
Statistics
Matches: 107, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
31 9 0.08
32 5 0.05
33 46 0.43
34 15 0.14
35 2 0.02
36 4 0.04
37 4 0.04
38 3 0.03
39 12 0.11
40 7 0.07
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCACATTGCGATTCTCTCGT
Found at i:5067109 original size:53 final size:52
Alignment explanation
Indices: 5066955--5067177 Score: 358
Period size: 53 Copynumber: 4.2 Consensus size: 52
5066945 AACGAGAGAA
* *
5066955 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
5067007 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
5067059 TCGCATTGCGATTTTCATTTCCACATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
* * *
5067112 TCACATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
5067165 TCGCATTGCGATT
1 TCGCATTGCGATT
5067178 CTCTCGTTGC
Statistics
Matches: 161, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
52 70 0.43
53 90 0.56
54 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:5067123 original size:86 final size:84
Alignment explanation
Indices: 5067012--5067191 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 84
5067002 TCATTTCGCA
*
5067012 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCACATTGCGATTTCATCTCCGATTGCGATTTTCA--T-G--TTGCGATTT
5067073 TCATTTCCACATTGCGATTCTCTCG
61 TCATTT-CACATTGCGATTCTCTCG
* *
5067098 TTGCGATTTTCATTTCACATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCACATTGCGA-TTTCATCTCCG-ATTGCGATTTTCATGTTGCGATTTTCA
*
5067163 TTTCGCATTGCGATTCTCTCG
64 TTTCACATTGCGATTCTCTCG
5067184 TTGCGATT
1 TTGCGATT
5067192 GTAATTTCCG
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
86 49 0.58
87 14 0.17
88 3 0.04
89 3 0.04
90 3 0.04
92 12 0.14
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCACATTGCGATTTCATCTCCGATTGCGATTTTCATGTTGCGATTTTCATT
TCACATTGCGATTCTCTCG
Found at i:5067175 original size:33 final size:34
Alignment explanation
Indices: 5066993--5067191 Score: 167
Period size: 33 Copynumber: 5.7 Consensus size: 34
5066983 GATTCTCTCG
5066993 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTTCGCA
*
5067031 TTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
* * * * *
5067064 TTGCGATTTTCAT--TT-CCACATTGCGATTCTCTCG
1 TTGCGATTTTCATCGTTGCGA-TTTTC-ATT-TCGCA
*
5067098 TTGCGATTTTCATTTCACATTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCA--T--CGTTGCGATTTTCATTT-CGCA
*
5067137 TTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
*
5067170 TTGCGATTCTC-TCGTTGCGATT
1 TTGCGATTTTCATCGTTGCGATT
5067192 GTAATTTCCG
Statistics
Matches: 132, Mismatches: 16, Indels: 31
0.74 0.09 0.17
Matches are distributed among these distances:
31 2 0.02
32 6 0.05
33 54 0.41
34 30 0.23
35 3 0.02
36 1 0.01
37 1 0.01
38 11 0.08
39 17 0.13
40 5 0.04
41 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
Found at i:5067206 original size:53 final size:53
Alignment explanation
Indices: 5066992--5067210 Score: 200
Period size: 53 Copynumber: 4.2 Consensus size: 53
5066982 CGATTCTCTC
* * *
5066992 GTTGCGATTTTCATTTCGCATTGCGATTTTCA-TTTCGCATTGCGA-TTCTC-T
1 GTTGCGATTTTCATTTCACATTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT
* * * *
5067043 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTGCGA-TTCTC-T
1 -GTTGCGATTTTCATTTCACATTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT
* * *
5067096 CGTTGCGATTTTCATTTCACATTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 -GTTGCGATTTTCATTTCACATTGCGATTTTCAGTTCCGCATTGCAATTTCCAT
* * * * *
5067150 GTTGGGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGT
1 GTTGCGATTTTCATTTCACATTGCGATT-T-TCAGTTCCGCATTGCAATTTCCAT
5067203 GTTGCGAT
1 GTTGCGAT
5067211 AGTCAAATGC
Statistics
Matches: 148, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
52 32 0.22
53 106 0.72
54 8 0.05
55 2 0.01
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (53 bp):
GTTGCGATTTTCATTTCACATTGCGATTTTCAGTTCCGCATTGCAATTTCCAT
Found at i:5069493 original size:12 final size:12
Alignment explanation
Indices: 5069476--5069500 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5069466 TCTTCGGGGA
5069476 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5069488 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5069500 C
1 C
5069501 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5069709 original size:24 final size:24
Alignment explanation
Indices: 5069675--5069721 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5069665 CTGAAACATC
5069675 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5069699 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5069722 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:5070442 original size:20 final size:20
Alignment explanation
Indices: 5070414--5070642 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
5070404 AAATTTCAGT
* * *
5070414 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
5070434 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
5070454 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
5070474 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
5070494 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
5070514 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
5070534 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
5070554 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
5070574 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
5070594 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
5070614 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
5070634 GTTGCGATT
1 GTTGCGATT
5070643 CTGTAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:5070660 original size:21 final size:20
Alignment explanation
Indices: 5070636--5070685 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
5070626 ATATTCGCGT
5070636 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
5070657 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
5070678 TGCGATTT
1 TGCGATTT
5070686 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:5072881 original size:47 final size:47
Alignment explanation
Indices: 5072789--5072877 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 47
5072779 TTTATTTTCG
5072789 TTTTTTCAAAAAATGCATGCGAACTAGAGATCATGTGGTTAGGTTTA
1 TTTTTTCAAAAAATGCATGCGAACTAGAGATCATGTGGTTAGGTTTA
* * * *
5072836 TTTTTTCAAACAA-GTATGCGAATTAGATATCATGTGGTTAGG
1 TTTTTTCAAAAAATGCATGCGAACTAGAGATCATGTGGTTAGG
5072878 GTTTTGATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 26 0.68
47 12 0.32
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.37
Consensus pattern (47 bp):
TTTTTTCAAAAAATGCATGCGAACTAGAGATCATGTGGTTAGGTTTA
Found at i:5075701 original size:17 final size:18
Alignment explanation
Indices: 5075669--5075709 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
5075659 TTTACTGGTT
*
5075669 TTGACCCGACCCGACCCG
1 TTGACCCGACCCGACCCA
*
5075687 TTGACCTGA-CCGACCCA
1 TTGACCCGACCCGACCCA
5075704 TTGACC
1 TTGACC
5075710 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.17
Consensus pattern (18 bp):
TTGACCCGACCCGACCCA
Found at i:5075764 original size:29 final size:29
Alignment explanation
Indices: 5075731--5075898 Score: 182
Period size: 29 Copynumber: 5.9 Consensus size: 29
5075721 AAATTTTAGT
* *
5075731 AATTAATTTGAAATGGGTGTTACTTTGGG
1 AATTAATTTGAAAAGGGTGTTATTTTGGG
*
5075760 AATTAATTTGAAAAAGGTGTTATTTTGGG
1 AATTAATTTGAAAAGGGTGTTATTTTGGG
* * * *
5075789 AATTTAA-TTCAAAA-AGTGCTATTTTGCG
1 AA-TTAATTTGAAAAGGGTGTTATTTTGGG
* *
5075817 AATTTAATTTGTAAA--GTGCTATTTTGGG
1 AA-TTAATTTGAAAAGGGTGTTATTTTGGG
*
5075845 AATTAATTTGAAAAGGGTGTTATTTTGGT
1 AATTAATTTGAAAAGGGTGTTATTTTGGG
* *
5075874 AATTATTTTAAAAAGGGTGTTATTT
1 AATTAATTTGAAAAGGGTGTTATTT
5075899 CTGTAAAATA
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
27 11 0.09
28 32 0.27
29 73 0.61
30 4 0.03
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.43
Consensus pattern (29 bp):
AATTAATTTGAAAAGGGTGTTATTTTGGG
Found at i:5075812 original size:28 final size:27
Alignment explanation
Indices: 5075754--5075888 Score: 108
Period size: 28 Copynumber: 4.8 Consensus size: 27
5075744 TGGGTGTTAC
* *
5075754 TTTGGGAATTAATTTGAAAAAGGTGTTAT
1 TTTGGGAATTAA-TTCAAAAA-GTGCTAT
5075783 TTTGGGAATTTAATTCAAAAAGTGCTAT
1 TTTGGGAA-TTAATTCAAAAAGTGCTAT
* ***
5075811 TTTGCGAATTTAATTTGTAAAGTGCTAT
1 TTTGGGAA-TTAATTCAAAAAGTGCTAT
* * *
5075839 TTTGGGAATTAATTTGAAAAGGGTGTTAT
1 TTTGGGAATTAA-TTCAAAA-AGTGCTAT
* * *
5075868 TTTGGTAATTATTTTAAAAAG
1 TTTGGGAATTAATTCAAAAAG
5075889 GGTGTTATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
27 5 0.06
28 47 0.54
29 31 0.36
30 4 0.05
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (27 bp):
TTTGGGAATTAATTCAAAAAGTGCTAT
Found at i:5076627 original size:24 final size:24
Alignment explanation
Indices: 5076592--5076710 Score: 103
Period size: 24 Copynumber: 5.0 Consensus size: 24
5076582 AATAGTTATA
* *
5076592 TGATATGATACTTGACCTGAATTT
1 TGATATGATACCTGACCTGAATTC
* * * * *
5076616 TTATATGCTACTTGACATGGATTC
1 TGATATGATACCTGACCTGAATTC
* * *
5076640 TGATCTGTTACCTGACCTGAATTT
1 TGATATGATACCTGACCTGAATTC
* * * *
5076664 TTATATGATACATGACATGGATTC
1 TGATATGATACCTGACCTGAATTC
*
5076688 TGATATGTTACCTGACCTGAATT
1 TGATATGATACCTGACCTGAATT
5076711 ATGTTTTAAT
Statistics
Matches: 71, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (24 bp):
TGATATGATACCTGACCTGAATTC
Found at i:5076660 original size:48 final size:48
Alignment explanation
Indices: 5076592--5076710 Score: 193
Period size: 48 Copynumber: 2.5 Consensus size: 48
5076582 AATAGTTATA
* * * *
5076592 TGATATGATACTTGACCTGAATTTTTATATGCTACTTGACATGGATTC
1 TGATATGTTACCTGACCTGAATTTTTATATGATACATGACATGGATTC
*
5076640 TGATCTGTTACCTGACCTGAATTTTTATATGATACATGACATGGATTC
1 TGATATGTTACCTGACCTGAATTTTTATATGATACATGACATGGATTC
5076688 TGATATGTTACCTGACCTGAATT
1 TGATATGTTACCTGACCTGAATT
5076711 ATGTTTTAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (48 bp):
TGATATGTTACCTGACCTGAATTTTTATATGATACATGACATGGATTC
Found at i:5081458 original size:21 final size:21
Alignment explanation
Indices: 5081434--5081475 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5081424 GAATAAATAA
**
5081434 TATATTTTCTTTGTTCTTTCT
1 TATATTTTCTTCATTCTTTCT
5081455 TATATTTTCTTCATTCTTTCT
1 TATATTTTCTTCATTCTTTCT
5081476 GCATTATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.69
Consensus pattern (21 bp):
TATATTTTCTTCATTCTTTCT
Found at i:5082194 original size:13 final size:13
Alignment explanation
Indices: 5082140--5082194 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
5082130 TGTGTCATAA
* *
5082140 ATTTATGATGCGC
1 ATTTATGACGCAC
5082153 ATTTATGACAG-AC
1 ATTTATGAC-GCAC
*
5082166 ATTTATGACGCGC
1 ATTTATGACGCAC
5082179 ATTTATGACGCAC
1 ATTTATGACGCAC
5082192 ATT
1 ATT
5082195 GAGCATCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
12 1 0.03
13 34 0.94
14 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:5087705 original size:31 final size:30
Alignment explanation
Indices: 5087669--5087728 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
5087659 TTATATGAGC
5087669 TATGTGATAAAGGTATGGAAAATAATATGTT
1 TATGTGATAAAGGTATGG-AAATAATATGTT
*
5087700 TATGTGATAAAGGTATGGAAATGATATGT
1 TATGTGATAAAGGTATGGAAATAATATGT
5087729 CTACGCGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATAATATGTT
Found at i:5088621 original size:11 final size:11
Alignment explanation
Indices: 5088560--5088623 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
5088550 TTTACGAAAA
5088560 TACTGTAGCAG
1 TACTGTAGCAG
*
5088571 TACTCTAGCAG
1 TACTGTAGCAG
* *
5088582 TACTGTATCAA
1 TACTGTAGCAG
* **
5088593 TATTGTAGCTT
1 TACTGTAGCAG
*
5088604 TAATGTAGCAG
1 TACTGTAGCAG
*
5088615 TATTGTAGC
1 TACTGTAGC
5088624 GAGGGTATCG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (11 bp):
TACTGTAGCAG
Found at i:5094728 original size:54 final size:54
Alignment explanation
Indices: 5094646--5094766 Score: 206
Period size: 54 Copynumber: 2.2 Consensus size: 54
5094636 CTCTCAAGGA
* *
5094646 TGCATCGGTACACTATATGTAAAATTCAAATATTTCGACTGTTATAAGACCTAG
1 TGCATCGGTACACAATATGTAAAATTCAAATATTTCGACCGTTATAAGACCTAG
* *
5094700 TGCATCGGTACACAATGTGTAAAATTCAAATATTTCGACCGTTATAAGACCTAT
1 TGCATCGGTACACAATATGTAAAATTCAAATATTTCGACCGTTATAAGACCTAG
5094754 TGCATCGGTACAC
1 TGCATCGGTACAC
5094767 TTGGGGTGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (54 bp):
TGCATCGGTACACAATATGTAAAATTCAAATATTTCGACCGTTATAAGACCTAG
Found at i:5096423 original size:13 final size:13
Alignment explanation
Indices: 5096388--5096425 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
5096378 TCCTAATGGG
5096388 CAATGTTTGAAAA
1 CAATGTTTGAAAA
*
5096401 TAAT-TTTGAAAA
1 CAATGTTTGAAAA
5096413 CAATGTTTGAAAA
1 CAATGTTTGAAAA
5096426 ATTATGATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:5096474 original size:17 final size:17
Alignment explanation
Indices: 5096452--5096493 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
5096442 TTTTCATGAA
5096452 AACAACATAATTAAATC
1 AACAACATAATTAAATC
*
5096469 AACAACAACAATTAAATC
1 AACAAC-ATAATTAAATC
5096487 AA-AACAT
1 AACAACAT
5096494 TTTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 9 0.41
18 12 0.55
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (17 bp):
AACAACATAATTAAATC
Found at i:5096960 original size:44 final size:44
Alignment explanation
Indices: 5096898--5097015 Score: 175
Period size: 44 Copynumber: 2.7 Consensus size: 44
5096888 CGACAAGTGT
* *
5096898 ATCGGTACA-CTACATAGTGTATCGATGCACATTCAAGGAATGC
1 ATCGGTACACCTCCATAGTGTATCGATGCACATTCAAGGAATAC
* *
5096941 ATCGGTGCACCTCCATAGTGTATCGATGCATATTCAAGGAATAC
1 ATCGGTACACCTCCATAGTGTATCGATGCACATTCAAGGAATAC
* *
5096985 ATCGGTACACTTTCATAGTGTATCGATGCAC
1 ATCGGTACACCTCCATAGTGTATCGATGCAC
5097016 TACGCATAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
43 8 0.12
44 58 0.88
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
ATCGGTACACCTCCATAGTGTATCGATGCACATTCAAGGAATAC
Found at i:5100713 original size:20 final size:21
Alignment explanation
Indices: 5100674--5100713 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5100664 GAAGCTTTAA
* *
5100674 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
5100695 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
5100714 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:5102911 original size:64 final size:65
Alignment explanation
Indices: 5102758--5102913 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
5102748 ATAAGACCTA
* * * * * * * *
5102758 GTGCATCGGTACACTAATTACATTCGATGTTTTAAAAGAGTCATGAGTGTATCGATGCATGGTAT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAATCAGGAGTGCATCAATGCATGGTAT
* *
5102823 GTGTATCGGTACATAAAATGCATTCGATGTTTCAATAA-AATCAGGAGTGCATCAATGCATGG-A
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAA-AAGAATCAGGAGTGCATCAATGCATGGTA
5102886 T
65 T
5102887 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
5102914 ATTAGGGTGT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 27 0.35
65 49 0.63
66 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAATCAGGAGTGCATCAATGCATGGTAT
Found at i:5105210 original size:3 final size:3
Alignment explanation
Indices: 5105202--5105239 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5105192 CTACACAAAA
5105202 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5105240 CAGTGGGACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5107955 original size:23 final size:23
Alignment explanation
Indices: 5107925--5107969 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5107915 AAAAGATACA
5107925 CAATCAGCATTAAACGGAGGGCC
1 CAATCAGCATTAAACGGAGGGCC
5107948 CAATCAGCATTAAACGGAGGGC
1 CAATCAGCATTAAACGGAGGGC
5107970 GCTGACCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.27, T:0.13
Consensus pattern (23 bp):
CAATCAGCATTAAACGGAGGGCC
Found at i:5109079 original size:103 final size:98
Alignment explanation
Indices: 5108911--5109164 Score: 302
Period size: 103 Copynumber: 2.6 Consensus size: 98
5108901 TTATTGTTTC
* ** * *
5108911 ATTTTTTTATTTTACGTATAAATTAATTAGATTATTTATTTTGATTTTACATATTAAACTGTATT
1 ATTTATTTATTTTAAATATAAATTAATTAGACTATTTATTTT-ATTTTACATATTAAACTATATT
5108976 TGAGTAGTTTGGTAAGTTTAGTTTAAATTATATT
65 TGAGTAGTTTGGTAAGTTTAGTTTAAATTATATT
*
5109010 TTTTACTTT-TTAATTGAGTAATATAAATT-ATTAGACTATTTATTTTAATTTTACATATTAAA-
1 ATTTA-TTTATT--TT-A--AATATAAATTAATTAGACTATTTATTTT-ATTTTACATATTAAAC
* * *
5109072 TCATATTTGAGTGGTTTGGTAATTTTAGTTTAAATTTTATT
59 T-ATATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTATATT
*
5109113 ATTTATTTATTTTAAATATAAATTAATTAGACTA-TT-TTTTATTTAACATATT
1 ATTTATTTATTTTAAATATAAATTAATTAGACTATTTATTTTATTTTACATATT
5109165 TTTTGTTTAA
Statistics
Matches: 134, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
96 11 0.08
97 4 0.03
98 12 0.09
99 14 0.10
100 4 0.03
101 4 0.03
102 5 0.04
103 72 0.54
104 8 0.06
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.55
Consensus pattern (98 bp):
ATTTATTTATTTTAAATATAAATTAATTAGACTATTTATTTTATTTTACATATTAAACTATATTT
GAGTAGTTTGGTAAGTTTAGTTTAAATTATATT
Found at i:5112871 original size:84 final size:84
Alignment explanation
Indices: 5112522--5113891 Score: 1748
Period size: 84 Copynumber: 16.3 Consensus size: 84
5112512 CATCGAATGG
* * * * * **
5112522 AATCAAACTCGAAAGT-TTTGGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTATAAATTTG
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TG
* * * *
5112586 ATGTGTCTCTAAGCTGAATGT
64 ATGTGCCTTTGAGCTGAGTGT
* * * * * * *
5112607 AATCAAACTCGAAGGTCTTTTGTCGACAGATAGCCCTTGTCGCATTGAGCTATGCTGTAAATTTG
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TG
* * * * *
5112672 ATGTTCCTTTTAACTAAATGT
64 ATGTGCCTTTGAGCTGAGTGT
* ** * * * *
5112693 AATCGAACTCTAAGGTC-TTTACTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTTG
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TG
*
5112757 ATGTACCTTTGAGCTGAGTGT
64 ATGTGCCTTTGAGCTGAGTGT
* * *
5112778 AATCGAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGCCTTGAGCTACGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
5112843 GTGCCTTTGAGCTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
* * *
5112862 AATCAAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCT-CCTTGAGCTATGCTGCAAATGG
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCT-TGCCTTGAGCTATGCTGCAAATGA
* *
5112926 TGTGCCTTTAACCTGAGTGT
65 TGTGCCTTTGAGCTGAGTGT
* * *
5112946 AATTGAACTCGAAGGTCTTTGGTT-GCATATAGCCCTTCTTGCCTTGAGCTATG-TGTCAAATGA
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG-CAAATGA
*
5113009 TGTGCCTTTGAGCTGAGTAT
65 TGTGCCTTTGAGCTGAGTGT
* * * * *
5113029 AATTGAACTCGAAGGTCTTTTTTTGGCAGATATCCCTTCTTGCCTTGAGCTATACTGCAAATAAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
*
5113094 ATGCCTTTGAGCTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
* * * * *
5113113 AATCGAACTCAAAGGTCTTTTGTTGGCAGATAGTCCTTCTTGCCTGGAGCTATGTTGCAACTGAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
5113178 GTGCCTTTGAGCTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
* ** * * * *
5113197 AATCGAAATCGAAGGTCTTTTACTGGAAAATAGCCCTTCTTGCCTTGAGCTATGCTACAAATGAC
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
5113262 GTGCCTTTGAGCTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
*
5113281 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
**
5113346 GTGCCTTTGATTTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
* * * *
5113365 AATCGAAATCGAAGGTCTTTTATTGGTAGATAGCCCTTCTTGCCTTGAGCTATGCTACAAATGAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
5113430 GTGCCTTTGAGCTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
*
5113449 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCCTGCCTTGAGCTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
*
5113514 GTTCCTTTGAGCTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
* * * * * *
5113533 AATCGAACTCAAATGTATTTTGTTGGTAGATAGCCCTTTTTACCTTGAGCTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
5113598 GTGCCTTTGAGCTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
* * * * * ** *
5113617 AATCGAACTCGGAGGTCTATTGTTGGTAGATAACCCTTCTTGCCTTGAGTTATGCTATAAATGGT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
* * *
5113682 GTGTCTTTGAGCTAATTGT
66 GTGCCTTTGAGCTGAGTGT
* * *
5113701 AATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
5113766 GTGCCTTTGAGCTGAGTGT
66 GTGCCTTTGAGCTGAGTGT
* * * *
5113785 AATTGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGACTTGAGCTATGTTGTAAATGAT
1 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
*
5113850 ATGCCTTTGAGCTGAGTG-
66 GTGCCTTTGAGCTGAGTGT
5113868 -ATCGAACAT-GAAGGTCTTTTGTTG
1 AATCGAAC-TCGAAGGTCTTTTGTTG
5113892 AATGTGTTTT
Statistics
Matches: 1127, Mismatches: 150, Indels: 19
0.87 0.12 0.01
Matches are distributed among these distances:
82 24 0.02
83 72 0.06
84 835 0.74
85 88 0.08
86 108 0.10
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (84 bp):
AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
GTGCCTTTGAGCTGAGTGT
Found at i:5118528 original size:4 final size:4
Alignment explanation
Indices: 5118521--5118546 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5118511 AAGAAAAATA
5118521 AATC AATC AATC AATC AATC AATC AA
1 AATC AATC AATC AATC AATC AATC AA
5118547 AGGAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
AATC
Found at i:5120679 original size:104 final size:103
Alignment explanation
Indices: 5120569--5120878 Score: 302
Period size: 112 Copynumber: 2.9 Consensus size: 103
5120559 TAAAAACAAT
* ** * *
5120569 AAATAAAACAATAAAATTTTGACTAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAAT
1 AAATAAAAAAATAAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAATATGTAAAA-
*
5120634 TAAAAATAAATATTCTAATAATTTATATTACTCAATAAA
65 TAAAAATAAATAGTCTAATAATTTATATTACTCAATAAA
* *
5120673 AAATAAAAAAATATAATTTAAACTAAACTTACCAAACTACTCAAATACAACTTAATATGTAAAAT
1 AAATAAAAAAATAAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAATATGTAAAAT
* * *
5120738 CAATATAAATAGTCTAATAA-TTATAATT--TAAATTAAA
66 AAAAATAAATAGTCTAATAATTTAT-ATTACTCAA-TAAA
* * * **
5120775 AAATTACACTAAAAATTACAAGAAAATTTAAATTAAACTTACCAAACCACACGAATACAGTTTAA
1 AAA-TA-A--AAAAA-T-----AAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAA
* * *
5120840 TCTGTAAAATCAAAATAAATAATCTAATTAATTTATATT
56 TATGTAAAATAAAAATAAATAGTCTAA-TAATTTATATT
5120879 TAAAATAAGA
Statistics
Matches: 171, Mismatches: 21, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
101 3 0.02
102 11 0.06
103 23 0.13
104 58 0.34
106 5 0.03
107 1 0.01
112 60 0.35
113 6 0.04
114 4 0.02
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (103 bp):
AAATAAAAAAATAAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAATATGTAAAAT
AAAAATAAATAGTCTAATAATTTATATTACTCAATAAA
Found at i:5121760 original size:17 final size:17
Alignment explanation
Indices: 5121740--5121776 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5121730 CATTTTTCAT
5121740 ATATTAATATTTGTATG
1 ATATTAATATTTGTATG
5121757 ATATTAATATTTGTATG
1 ATATTAATATTTGTATG
5121774 ATA
1 ATA
5121777 AAGTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (17 bp):
ATATTAATATTTGTATG
Found at i:5121864 original size:60 final size:59
Alignment explanation
Indices: 5121807--5121921 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 59
5121797 AATTATAGGA
* * * * *
5121807 TATTGTTTTATTAAGTTCATTGACTATTAAAAGTTATAAAATGGTCTTCTGACTATAGAG
1 TATTGCTTTATTAAGTCCATTAACTATTAAAAGTTACAAAATGGTC-ACTGACTATAGAG
* * * * *
5121867 TGTTGCTTTGTTGAGTCCCTTAATTATTAAAAGTTACAAAATGGTCACTGACTAT
1 TATTGCTTTATTAAGTCCATTAACTATTAAAAGTTACAAAATGGTCACTGACTAT
5121922 TCATTATGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
59 8 0.18
60 37 0.82
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (59 bp):
TATTGCTTTATTAAGTCCATTAACTATTAAAAGTTACAAAATGGTCACTGACTATAGAG
Found at i:5125318 original size:40 final size:40
Alignment explanation
Indices: 5125263--5125342 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
5125253 ATTATTGATC
5125263 AATGATGAAAGACTTTGGTAAAAAGAGGCTATATTAAACT
1 AATGATGAAAGACTTTGGTAAAAAGAGGCTATATTAAACT
*
5125303 AATGATGGAAGACTTTGGTAAAAAGAGGCTATATTAAACT
1 AATGATGAAAGACTTTGGTAAAAAGAGGCTATATTAAACT
5125343 CTTTTTGATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (40 bp):
AATGATGAAAGACTTTGGTAAAAAGAGGCTATATTAAACT
Found at i:5130376 original size:10 final size:10
Alignment explanation
Indices: 5130363--5130396 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5130353 ATAAACATGA
5130363 ATATGTATAT
1 ATATGTATAT
*
5130373 ATATGAATAT
1 ATATGTATAT
*
5130383 ATATATATAT
1 ATATGTATAT
5130393 ATAT
1 ATAT
5130397 ATAATTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (10 bp):
ATATGTATAT
Found at i:5130378 original size:16 final size:16
Alignment explanation
Indices: 5130359--5130392 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5130349 ATGAATAAAC
*
5130359 ATGAATATGTATATAT
1 ATGAATATATATATAT
5130375 ATGAATATATATATAT
1 ATGAATATATATATAT
5130391 AT
1 AT
5130393 ATATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
ATGAATATATATATAT
Found at i:5131011 original size:66 final size:66
Alignment explanation
Indices: 5130930--5131063 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
5130920 CGAACGCATA
5130930 TAGAAGAGATTCGATCGATGAAATCATGGGGTTGTTTTCAGGTGAAAATGAAACAACTTTTTGGA
1 TAGAAGAGATTCGATCGATGAAATCATGGGGTTGTTTTCAGGTGAAAATGAAACAACTTTTTGGA
5130995 G
66 G
5130996 TAGAAGAGATTCGATCGATGAAATCATGGGGTTGTTTTCAGGTGAAAATGAAACAACTTTTTGGA
1 TAGAAGAGATTCGATCGATGAAATCATGGGGTTGTTTTCAGGTGAAAATGAAACAACTTTTTGGA
5131061 G
66 G
5131062 TA
1 TA
5131064 AATACGAACC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.31
Consensus pattern (66 bp):
TAGAAGAGATTCGATCGATGAAATCATGGGGTTGTTTTCAGGTGAAAATGAAACAACTTTTTGGA
G
Found at i:5134662 original size:17 final size:18
Alignment explanation
Indices: 5134629--5134662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5134619 CCGCTATTAG
5134629 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
5134647 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
5134663 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:5137557 original size:12 final size:12
Alignment explanation
Indices: 5137540--5137564 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5137530 ACAATAACAG
5137540 TTTAAAACATAT
1 TTTAAAACATAT
5137552 TTTAAAACATAT
1 TTTAAAACATAT
5137564 T
1 T
5137565 CTTATTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAAACATAT
Found at i:5139078 original size:2 final size:2
Alignment explanation
Indices: 5139071--5139183 Score: 80
Period size: 2 Copynumber: 60.5 Consensus size: 2
5139061 TAAAAATAAT
*
5139071 TA TA TA TA TA TA TA TA TA TA TA -A TA TA AA TA TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
5139110 -A TA AA TT TA -A TT TA AA T- TA AA 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
* * * *
5139149 TA TA -A TA TT TA TA TA TT TA -A TT TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5139184 CCGACCCGAT
Statistics
Matches: 83, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
1 8 0.10
2 75 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5140792 original size:10 final size:10
Alignment explanation
Indices: 5140777--5140819 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
5140767 CAGTTCAATG
5140777 GCCGGTCAAC
1 GCCGGTCAAC
*
5140787 GCCGGTCAAA
1 GCCGGTCAAC
*
5140797 GTTCTGGTCAAC
1 G--CCGGTCAAC
5140809 GCCGGTCAAC
1 GCCGGTCAAC
5140819 G
1 G
5140820 ATTAACGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 19 0.70
12 8 0.30
ACGTcount: A:0.21, C:0.33, G:0.30, T:0.16
Consensus pattern (10 bp):
GCCGGTCAAC
Found at i:5143319 original size:2 final size:2
Alignment explanation
Indices: 5143312--5143367 Score: 103
Period size: 2 Copynumber: 27.5 Consensus size: 2
5143302 CCAAACATAA
5143312 AT 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 AT
5143354 AT AT AT AT CAT AT A
1 AT AT AT AT -AT AT A
5143368 CATGCATATT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5143683 original size:17 final size:17
Alignment explanation
Indices: 5143645--5143676 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5143635 CCATGTACAC
5143645 ATGTGAGTACTATAGAT
1 ATGTGAGTACTATAGAT
5143662 ATGTGAGT-CTATAGA
1 ATGTGAGTACTATAGA
5143677 GGTTGTGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (17 bp):
ATGTGAGTACTATAGAT
Found at i:5143740 original size:23 final size:23
Alignment explanation
Indices: 5143706--5143774 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
5143696 CACCACAACT
*
5143706 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* ** * **
5143729 CGTAGAATTGCACTTAAGTACTG
1 CGTAGAAATGCACCGAAGTGCCA
*
5143752 CGTAGAAATACACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
5143775 TAAAAGACGT
Statistics
Matches: 32, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:5148791 original size:17 final size:17
Alignment explanation
Indices: 5148753--5148784 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5148743 CCATGTACAC
5148753 ATGTGAGTACTATAGAT
1 ATGTGAGTACTATAGAT
5148770 ATGTGAGT-CTATAGA
1 ATGTGAGTACTATAGA
5148785 GGTTGTGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (17 bp):
ATGTGAGTACTATAGAT
Found at i:5148848 original size:23 final size:23
Alignment explanation
Indices: 5148814--5148880 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
5148804 CACCACAGCT
* *
5148814 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* * * *
5148837 CGTAGAATTGCACCTAAGTGTCG
1 CGTAGAAATGCACCAAAGTGCCA
5148860 CGTAGAAATGCACCAAAGTGC
1 CGTAGAAATGCACCAAAGTGC
5148881 TATATAAGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:5149148 original size:30 final size:29
Alignment explanation
Indices: 5149112--5149170 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
5149102 TGTAAACATA
*
5149112 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATTCATATAAACACGTAG-TTCAT
* *
5149142 TCACATATTCATTTAATCACGTAGTTCAT
1 TCACATATTCATATAAACACGTAGTTCAT
5149171 GTAAATTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (29 bp):
TCACATATTCATATAAACACGTAGTTCAT
Found at i:5150339 original size:20 final size:20
Alignment explanation
Indices: 5150314--5150351 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5150304 TTCCCCTTGA
5150314 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
5150334 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
5150352 TTAACATGTG
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:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:5150367 original size:24 final size:24
Alignment explanation
Indices: 5150315--5150392 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
5150305 TCCCCTTGAA
*
5150315 GTGCATCGATGCATTC--T-ATA-
1 GTGCATCGATGCATTCTTTAACAT
5150335 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
*
5150359 GTGCATCGACGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
5150383 GTGCATCGAT
1 GTGCATCGAT
5150393 ACACTACCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 16 0.31
22 1 0.02
23 2 0.04
24 32 0.63
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (24 bp):
GTGCATCGATGCATTCTTTAACAT
Found at i:5151986 original size:194 final size:194
Alignment explanation
Indices: 5151657--5152046 Score: 744
Period size: 194 Copynumber: 2.0 Consensus size: 194
5151647 ATCAATACTT
5151657 TCGTTAAAACTCATTTCAAACATATAAAACTGTCATGTAATACATATGGAACACATTAGAGGATC
1 TCGTTAAAACTCATTTCAAACATATAAAACTGTCATGTAATACATATGGAACACATTAGAGGATC
* *
5151722 AAAGTATTTATCAGATATTATTCAGAGATACTTGATAATCTTATTGGGTAGAGAAACATGAATCT
66 AAAGTATTTATAAGATATTATTCAGAGATACTTGATAATCTTATTGGGTAGAGAAACACGAATCT
*
5151787 TTAGTATACCGGTACAATGCTAGAATTTAGAATCACTATTGGAAGAGTTCATTAACTAACGAAA
131 TTAGTATACCGGTACAATGCTAGAATTTAGAATCACTATTAGAAGAGTTCATTAACTAACGAAA
*
5151851 TCGTTAAAACTCATTTCAAACATATAAAACTGTCATGTAGTACATATGGAACACATTAGAGGATC
1 TCGTTAAAACTCATTTCAAACATATAAAACTGTCATGTAATACATATGGAACACATTAGAGGATC
5151916 AAAGTATTTATAAGATATTATTCAGAGATACTTGATAATCTTATTGGGTAGAGAAACACGAATCT
66 AAAGTATTTATAAGATATTATTCAGAGATACTTGATAATCTTATTGGGTAGAGAAACACGAATCT
5151981 TTAGTATACCGGTACAATGCTAGAATTTAGAATCACTATTAGAAGAGTTCATTAACTAACGAAA
131 TTAGTATACCGGTACAATGCTAGAATTTAGAATCACTATTAGAAGAGTTCATTAACTAACGAAA
5152045 TC
1 TC
5152047 ATCAGTTATT
Statistics
Matches: 192, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
194 192 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (194 bp):
TCGTTAAAACTCATTTCAAACATATAAAACTGTCATGTAATACATATGGAACACATTAGAGGATC
AAAGTATTTATAAGATATTATTCAGAGATACTTGATAATCTTATTGGGTAGAGAAACACGAATCT
TTAGTATACCGGTACAATGCTAGAATTTAGAATCACTATTAGAAGAGTTCATTAACTAACGAAA
Found at i:5155724 original size:2 final size:2
Alignment explanation
Indices: 5155717--5155770 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
5155707 TATGTGTCTT
5155717 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5155759 TA TA TA TA -A TA T
1 TA TA TA TA TA TA T
5155771 TTTAATAGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5158530 original size:20 final size:20
Alignment explanation
Indices: 5158507--5158558 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5158497 AACGCGATCC
5158507 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
5158527 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
5158547 CCAAAATCGCAA
1 CCAGAATCGCAA
5158559 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:5158639 original size:20 final size:20
Alignment explanation
Indices: 5158614--5158807 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
5158604 GATTTTCCAT
* *
5158614 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
5158634 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
5158654 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
5158674 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
5158694 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
5158714 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
5158734 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
5158754 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
5158775 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
5158795 AATCGCAACGCGA
1 AATCGCAACGCGA
5158808 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:5158659 original size:40 final size:39
Alignment explanation
Indices: 5158610--5158807 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
5158600 TTGCGATTTT
* ** *
5158610 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
5158648 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
5158689 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
5158729 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
5158768 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
5158808 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:5158697 original size:60 final size:60
Alignment explanation
Indices: 5158614--5158806 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
5158604 GATTTTCCAT
* ** * *
5158614 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
5158674 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
5158734 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
5158795 AATCGCAACGCG
1 AATCGCAACGCG
5158807 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:5159227 original size:33 final size:33
Alignment explanation
Indices: 5159188--5159258 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5159178 TTCACTTAGA
*
5159188 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
5159221 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
5159254 TTTCA
1 TTTCA
5159259 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:5159398 original size:14 final size:14
Alignment explanation
Indices: 5159379--5159433 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5159369 AGAATGACTG
5159379 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
5159393 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
5159412 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
5159426 TCGCAACG
1 TCGCAACG
5159434 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:5159416 original size:33 final size:33
Alignment explanation
Indices: 5159379--5159449 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
5159369 AGAATGACTG
**
5159379 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
5159412 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
5159445 TCGCA
1 TCGCA
5159450 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:5159467 original size:19 final size:19
Alignment explanation
Indices: 5159445--5159542 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
5159435 GAAACCAAAA
*
5159445 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5159464 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5159478 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5159497 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
5159511 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
5159530 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5159543 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5159486 original size:14 final size:14
Alignment explanation
Indices: 5159467--5159556 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5159457 TTTCATTTCG
5159467 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5159481 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5159500 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5159514 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
5159531 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
5159547 CGTTGCGATT
1 CGTTGCGATT
5159557 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5159492 original size:33 final size:33
Alignment explanation
Indices: 5159450--5159564 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5159440 CAAAATCGCA
5159450 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5159483 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
5159516 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5159549 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
5159565 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:5161493 original size:185 final size:185
Alignment explanation
Indices: 5161263--5161734 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
5161253 TAGATTGCTT
*
5161263 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5161328 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
5161393 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
5161448 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5161513 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
5161578 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
5161633 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5161698 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
5161735 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5161577 original size:93 final size:93
Alignment explanation
Indices: 5161263--5161734 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
5161253 TAGATTGCTT
*
5161263 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5161328 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
5161356 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5161420 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5161448 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5161513 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5161541 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5161605 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5161633 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5161698 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5161726 AGTAAATTT
1 AGTAAATTT
5161735 ATCCATTCAA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5161818 original size:19 final size:19
Alignment explanation
Indices: 5161778--5161906 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5161768 TAGTTTACTT
* *
5161778 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
5161798 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
5161817 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
5161836 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
5161850 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
5161869 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
5161883 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
5161902 TCGCA
1 TCGCA
5161907 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:5161857 original size:33 final size:32
Alignment explanation
Indices: 5161814--5161906 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
5161804 CGCGAAACCA
**
5161814 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
5161846 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
5161879 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
5161907 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:5161904 original size:52 final size:52
Alignment explanation
Indices: 5161778--5161906 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
5161768 TAGTTTACTT
**
5161778 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
5161830 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
5161883 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
5161907 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:5161924 original size:19 final size:19
Alignment explanation
Indices: 5161902--5162036 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
5161892 GAAACCAAAA
*
5161902 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5161921 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
5161937 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
5161954 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
5161970 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
5161987 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
5162006 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
5162026 TCGTGTTGCGA
1 TCGCGTTGCGA
5162037 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5161943 original size:14 final size:14
Alignment explanation
Indices: 5161924--5161980 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5161914 TTTCATTTCG
5161924 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
5161938 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
5161955 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
5161971 CGTTGCGATT
1 CGTTGCGATT
5161981 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:5161949 original size:33 final size:33
Alignment explanation
Indices: 5161907--5161999 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5161897 CAAAATCGCA
*
5161907 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
5161940 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
5161973 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
5162000 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:5163957 original size:14 final size:14
Alignment explanation
Indices: 5163938--5163973 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5163928 ATTGTTTAAT
5163938 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5163952 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5163966 TGATTTGT
1 TGATTTGT
5163974 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5164096 original size:19 final size:19
Alignment explanation
Indices: 5164080--5164181 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
5164070 AAAAATGACT
5164080 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5164099 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5164118 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5164132 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5164151 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5164171 ATCGCAATGCG
1 ATCGCAATGCG
5164182 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5164234 original size:19 final size:19
Alignment explanation
Indices: 5164210--5164474 Score: 389
Period size: 19 Copynumber: 14.7 Consensus size: 19
5164200 GATTATCTCG
5164210 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5164229 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5164248 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
5164262 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5164281 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5164300 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5164319 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5164338 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5164357 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5164376 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
5164390 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5164409 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5164428 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5164442 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5164462 TTGCGATTTTCAT
1 TTGCGATTTTCAT
5164475 GTTGGGATTT
Statistics
Matches: 224, Mismatches: 6, Indels: 31
0.86 0.02 0.12
Matches are distributed among these distances:
14 18 0.08
16 22 0.10
17 19 0.08
18 2 0.01
19 150 0.67
20 13 0.06
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5164250 original size:52 final size:51
Alignment explanation
Indices: 5164188--5164500 Score: 306
Period size: 52 Copynumber: 5.9 Consensus size: 51
5164178 TGCGTTTATA
*
5164188 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
*
5164240 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
5164292 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGA-TTTCATTTCGCATTGCGATTTTC
*
5164349 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
*
5164401 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
* *
5164453 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTCA-TTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTCATTTCGCATTGCGATT
5164501 GTATTTTCCG
Statistics
Matches: 240, Mismatches: 9, Indels: 25
0.88 0.03 0.09
Matches are distributed among these distances:
48 9 0.04
49 6 0.03
50 2 0.01
51 8 0.03
52 129 0.54
53 10 0.04
54 6 0.03
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (51 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTCATTTCGCATTGCGATTTTC
Found at i:5164358 original size:128 final size:122
Alignment explanation
Indices: 5164210--5164471 Score: 170
Period size: 128 Copynumber: 2.1 Consensus size: 122
5164200 GATTATCTCG
* *
5164210 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
5164272 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
5164336 CA
121 CA
* * * *
5164338 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTAATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
5164400 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
5164460 CA
121 CA
5164462 TTGCGATTTT
1 TTGCGATTTT
5164472 CATGTTGGGA
Statistics
Matches: 122, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.15
124 15 0.12
125 2 0.02
126 2 0.02
128 74 0.61
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:5167009 original size:24 final size:24
Alignment explanation
Indices: 5166975--5167021 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5166965 CTGAAACATC
5166975 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5166999 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5167022 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:5167731 original size:20 final size:20
Alignment explanation
Indices: 5167703--5168071 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
5167693 AAATTTAAGT
* * * *
5167703 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5167723 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
5167743 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5167763 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5167783 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5167803 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5167823 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
5167843 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5167863 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5167883 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
5167903 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
5167923 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5167943 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
5167963 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
5167983 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
5168003 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
5168023 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
5168043 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
5168063 GTTGCGATT
1 GTTGCGATT
5168072 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:5169150 original size:30 final size:30
Alignment explanation
Indices: 5169114--5169219 Score: 128
Period size: 30 Copynumber: 3.6 Consensus size: 30
5169104 TTTTTTCATT
*
5169114 TAAGTATCTAAAGTATTTTTTTTATCAAAA
1 TAAGTATCTAAAGTATTTTTTTTGTCAAAA
*
5169144 TAAGTATCTGAAGT-TATTTTTTTGTCAAAA
1 TAAGTATCTAAAGTAT-TTTTTTTGTCAAAA
*
5169174 T-AGATAACTAAAGTA-TTTTTTTGTCAAAA
1 TAAG-TATCTAAAGTATTTTTTTTGTCAAAA
* *
5169203 TAGGTACCTAAAGTATT
1 TAAGTATCTAAAGTATT
5169220 CAATTTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
29 28 0.43
30 37 0.57
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (30 bp):
TAAGTATCTAAAGTATTTTTTTTGTCAAAA
Found at i:5169190 original size:29 final size:29
Alignment explanation
Indices: 5169121--5169219 Score: 119
Period size: 29 Copynumber: 3.3 Consensus size: 29
5169111 ATTTAAGTAT
* *
5169121 CTAAAGTATTTTTTTTATCAAAATA-AGTAT
1 CTAAAGTA-TTTTTTTGTCAAAATAGA-TAA
*
5169151 CTGAAGTTATTTTTTTGTCAAAATAGATAA
1 CTAAAG-TATTTTTTTGTCAAAATAGATAA
* *
5169181 CTAAAGTATTTTTTTGTCAAAATAGGTAC
1 CTAAAGTATTTTTTTGTCAAAATAGATAA
5169210 CTAAAGTATT
1 CTAAAGTATT
5169220 CAATTTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
29 31 0.51
30 27 0.44
31 3 0.05
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.43
Consensus pattern (29 bp):
CTAAAGTATTTTTTTGTCAAAATAGATAA
Found at i:5169335 original size:28 final size:28
Alignment explanation
Indices: 5169303--5169402 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
5169293 GAAAATGTTT
*
5169303 AAATAATTTAGGTACATATTTTGACATA
1 AAATAATTTAGGTACATATTTTGACAAA
* *
5169331 AAATACTTTAGGTACCTATTTTGACAAA
1 AAATAATTTAGGTACATATTTTGACAAA
* * ** **
5169359 AAAAAAGTTAAAATATTTATTTTGACAAA
1 AAATAA-TTTAGGTACATATTTTGACAAA
* *
5169388 AAATACTTTAAGTAC
1 AAATAATTTAGGTAC
5169403 TTAAATGAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
28 35 0.62
29 21 0.38
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (28 bp):
AAATAATTTAGGTACATATTTTGACAAA
Found at i:5169398 original size:29 final size:29
Alignment explanation
Indices: 5169319--5169398 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
5169309 TTTAGGTACA
* **
5169319 TATTTTGACATAAAATACTTT-AGGTACC
1 TATTTTGACAAAAAATACTTTAAAATACC
* ** **
5169347 TATTTTGACAAAAAAAAAGTTAAAATATT
1 TATTTTGACAAAAAATACTTTAAAATACC
5169376 TATTTTGACAAAAAATACTTTAA
1 TATTTTGACAAAAAATACTTTAA
5169399 GTACTTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
28 17 0.43
29 23 0.57
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (29 bp):
TATTTTGACAAAAAATACTTTAAAATACC
Found at i:5170567 original size:56 final size:56
Alignment explanation
Indices: 5170481--5170594 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
5170471 GACACCAAGT
*
5170481 AAGGTTTCTTTAGGTGTCCATGATGGTGCATTTGACACTACTACTGTTGAAACCAC
1 AAGGTTACTTTAGGTGTCCATGATGGTGCATTTGACACTACTACTGTTGAAACCAC
5170537 AAGGTTACTTTAGGTGTCCATGATGGTGCATTTGACACTACTACTGTTGAAACCAC
1 AAGGTTACTTTAGGTGTCCATGATGGTGCATTTGACACTACTACTGTTGAAACCAC
5170593 AA
1 AA
5170595 ATCCTGCTGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (56 bp):
AAGGTTACTTTAGGTGTCCATGATGGTGCATTTGACACTACTACTGTTGAAACCAC
Found at i:5178106 original size:30 final size:29
Alignment explanation
Indices: 5178071--5178133 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
5178061 ACAAAAAATC
5178071 TGCCAACCCATTGAACA-ATGCACCATTCGG
1 TGCCAA-CCATTGAA-ATATGCACCATTCGG
*
5178101 TGCCAACCTTTGAAATTATGCACCATTCGG
1 TGCCAACCATTGAAA-TATGCACCATTCGG
5178131 TGC
1 TGC
5178134 ATCTTTGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 1 0.03
29 7 0.23
30 22 0.73
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (29 bp):
TGCCAACCATTGAAATATGCACCATTCGG
Found at i:5178935 original size:437 final size:437
Alignment explanation
Indices: 5178121--5178984 Score: 1428
Period size: 437 Copynumber: 2.0 Consensus size: 437
5178111 TGAAATTATG
*
5178121 CACCATTCGGTGCATCTTTGACTTTTAACAATCTCCCACTTGAAGACTGATTTTAATATGTCTTC
1 CACCATTCGGTGCATCATTGACTTTTAACAATCTCCCACTTGAAGACTGATTTTAATATGTCTTC
* * * * **
5178186 ACACCTTGATCAATGTAGCAGCATTTATGGTCGTGTTACTCTAGGATGCCAACTGAATCTGAACA
66 ACACATTGATCAATGCAGCAACATTTATGGTCGTGTTACTCTAGCATGCCAACTGAAGATGAACA
* **
5178251 CAACTTCAATTTTTCCGTAGTCACCGTCTTTGTTAACATGTCTGCTGGATTTTGAGCTCCACTAG
131 CAACTTCAATTTGTCCGTAGTCACCGTCTTTGTTAACATGTCTGCCAGATTTTGAGCTCCACTAG
*
5178316 TCTTTGAAGGATTGTTCCTCACTTGAACATCCTTGGCAAGACCCTGCTTCGACCCTTCTCTTAAG
196 TCTTTGAAGGATTGTTCCTCACTTGAACATCCTTCGCAAGACCCTGCTTCGACCCTTCTCTTAAG
*
5178381 ATGGTCTCTGAAGCCATGTTCTCTACACGAACATGCTCGACAAACTCCTTGGACACATACAACTA
261 ATGGTCTCTGAAGCCATGTTCTCTACACGAACATGCTCGACAAACTCCTTGGACACAGACAACTA
*
5178446 TTCTTGCACTTGGCTTCTACTTGGTTTGGTAGAAATGAACCTTATTGAGCCAACTCTCAACGCCT
326 TTCTTGCACTTGGCTTCTACTTGATTTGGTAGAAATGAACCTTATTGAGCCAACTCTCAACGCCT
*
5178511 CTTCGATCTTGGGTTCAT-TCTCTTCTCTAGAAAACTTTTAAAATATA
391 CTTCGATCTTGGGTTCGTCT-TCTTCTCTAGAAAACTTTTAAAATATA
*
5178558 CACCATTCGGTGCATCATTGACTTTTAACAATCTCCCACTTGAAGACTGATTTTAATCTGTCTTC
1 CACCATTCGGTGCATCATTGACTTTTAACAATCTCCCACTTGAAGACTGATTTTAATATGTCTTC
* * * *
5178623 ACACATTGATCAATGCATCAATATTTCTGGTTGTGTTACTCTAGCATGCCAACTGAAGATGAACA
66 ACACATTGATCAATGCAGCAACATTTATGGTCGTGTTACTCTAGCATGCCAACTGAAGATGAACA
* * *
5178688 CAACTTCAGTTTGTCCGTAGTCACCGTCTTTTTTAACATGTCTGCCATATTTTGAGCTCCACTAG
131 CAACTTCAATTTGTCCGTAGTCACCGTCTTTGTTAACATGTCTGCCAGATTTTGAGCTCCACTAG
* * *
5178753 TCTTTGAAGGATTGTTCCTCACTTGAACATTC-TCGCTAAG-CCCTTGTTTTGACCCTTCTCTTA
196 TCTTTGAAGGATTGTTCCTCACTTGAACATCCTTCGC-AAGACCC-TGCTTCGACCCTTCTCTTA
*
5178816 AGATGGTCTCTGAAGCCATGTTCTCTACACGAACATGCTCGACAAACTCCTTGGACACGGACAAC
259 AGATGGTCTCTGAAGCCATGTTCTCTACACGAACATGCTCGACAAACTCCTTGGACACAGACAAC
*
5178881 TATTCTTGCACTTGGCTTCTACTTGATTTGGTAGAAATGAACCTTATTGAGCCAACTCTCAATGC
324 TATTCTTGCACTTGGCTTCTACTTGATTTGGTAGAAATGAACCTTATTGAGCCAACTCTCAACGC
*
5178946 CTCTTCGATCTTGGGTTCGTCTTCTTCTCTGGAAAACTT
389 CTCTTCGATCTTGGGTTCGTCTTCTTCTCTAGAAAACTT
5178985 GATCTTGGGC
Statistics
Matches: 396, Mismatches: 28, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
436 6 0.02
437 389 0.98
438 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (437 bp):
CACCATTCGGTGCATCATTGACTTTTAACAATCTCCCACTTGAAGACTGATTTTAATATGTCTTC
ACACATTGATCAATGCAGCAACATTTATGGTCGTGTTACTCTAGCATGCCAACTGAAGATGAACA
CAACTTCAATTTGTCCGTAGTCACCGTCTTTGTTAACATGTCTGCCAGATTTTGAGCTCCACTAG
TCTTTGAAGGATTGTTCCTCACTTGAACATCCTTCGCAAGACCCTGCTTCGACCCTTCTCTTAAG
ATGGTCTCTGAAGCCATGTTCTCTACACGAACATGCTCGACAAACTCCTTGGACACAGACAACTA
TTCTTGCACTTGGCTTCTACTTGATTTGGTAGAAATGAACCTTATTGAGCCAACTCTCAACGCCT
CTTCGATCTTGGGTTCGTCTTCTTCTCTAGAAAACTTTTAAAATATA
Done.