Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005277.1 Hibiscus syriacus cultivar Beakdansim tig00011934_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: 81200
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:624 original size:21 final size:21
Alignment explanation
Indices: 598--646 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
588 AGTTTGTATC
*
598 TTCTCTGTTTTTTTTTTCTGT
1 TTCTCTGTCTTTTTTTTCTGT
619 TTCTC--TCTTTTTTTTCTGT
1 TTCTCTGTCTTTTTTTTCTGT
*
638 CTCTCTGTC
1 TTCTCTGTC
647 CCGTTCTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 17 0.71
21 7 0.29
ACGTcount: A:0.00, C:0.22, G:0.08, T:0.69
Consensus pattern (21 bp):
TTCTCTGTCTTTTTTTTCTGT
Found at i:1107 original size:11 final size:11
Alignment explanation
Indices: 1073--1109 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1063 AATTGGTCTG
1073 TAATAT-TATT
1 TAATATATATT
1083 T-ATATATATTT
1 TAATATATA-TT
1094 TAATATATATT
1 TAATATATATT
1105 TAATA
1 TAATA
1110 ATAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.17
10 3 0.12
11 10 0.42
12 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATATATATT
Found at i:1113 original size:3 final size:3
Alignment explanation
Indices: 1105--1167 Score: 94
Period size: 3 Copynumber: 21.7 Consensus size: 3
1095 AATATATATT
*
1105 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA T-A TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1151 TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1168 TGGATAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1466 original size:3 final size:3
Alignment explanation
Indices: 1458--1483 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1448 GCAATATCCT
1458 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1484 TTTCTCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2380 original size:22 final size:22
Alignment explanation
Indices: 2352--2396 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2342 GGAGGCGAAC
2352 ATGTTCTGTTCTATTGGCATTG
1 ATGTTCTGTTCTATTGGCATTG
2374 ATGTTCTGTTCTATTGGCATTG
1 ATGTTCTGTTCTATTGGCATTG
2396 A
1 A
2397 AGTAAAGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.13, G:0.22, T:0.49
Consensus pattern (22 bp):
ATGTTCTGTTCTATTGGCATTG
Found at i:4610 original size:23 final size:23
Alignment explanation
Indices: 4584--4631 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
4574 ATAAAGTACA
* *
4584 ATAACATACTAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
4607 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
4630 AT
1 AT
4632 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:4742 original size:22 final size:22
Alignment explanation
Indices: 4708--4752 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4698 TATTATATTG
*
4708 AAAGTATCCATACTT-TTTATAA
1 AAAGGATCCATACTTCTTT-TAA
*
4730 AAAGGATCGATACTTCTTTTAA
1 AAAGGATCCATACTTCTTTTAA
4752 A
1 A
4753 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (22 bp):
AAAGGATCCATACTTCTTTTAA
Found at i:5084 original size:23 final size:23
Alignment explanation
Indices: 5057--5115 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
5047 TACCACTACC
5057 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
5080 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
5103 TATTACATCATAT
1 TATTACATTATAT
5116 GTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:5569 original size:39 final size:39
Alignment explanation
Indices: 5515--5601 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
5505 TCAAGTTGTA
*
5515 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
5554 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
5593 GATTTTGAT
1 GATTTTGAT
5602 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:5884 original size:18 final size:18
Alignment explanation
Indices: 5861--5897 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5851 CGAAATATAT
5861 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
5879 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
5897 A
1 A
5898 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:6309 original size:25 final size:25
Alignment explanation
Indices: 6281--6331 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
6271 ATTTTCCAAA
*
6281 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
6306 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
6331 T
1 T
6332 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:6625 original size:21 final size:21
Alignment explanation
Indices: 6595--6665 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
6585 GATAGACACT
*
6595 TTACAATATAACCACTACCTA
1 TTACATTATAACCACTACCTA
*
6616 TTACATTATAAACGA-TACCTA
1 TTACATTAT-AACCACTACCTA
* *
6637 TTACATTATATAAGCGCTACCTA
1 TTACA-T-TATAACCACTACCTA
6660 TTACAT
1 TTACAT
6666 CATATGTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 19 0.46
22 8 0.20
23 14 0.34
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (21 bp):
TTACATTATAACCACTACCTA
Found at i:6657 original size:23 final size:22
Alignment explanation
Indices: 6600--6670 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
6590 ACACTTTACA
*
6600 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
6623 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
6644 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
6667 ATAT
1 ATAT
6671 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.40
22 4 0.10
23 21 0.50
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:7122 original size:23 final size:23
Alignment explanation
Indices: 7093--7148 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
7083 CAATAACCAC
7093 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
7116 TATCTATTACATTATATAAGCGT
1 TACCTATTACATTATATAAACGA
7139 TACCTATTAC
1 TACCTATTAC
7149 TCATATGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:7197 original size:22 final size:22
Alignment explanation
Indices: 7172--7219 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
7162 TATTATATTG
7172 AAAGTG-TCCATACTTTGTATAA
1 AAAGTGATCCATACTTT-TATAA
* *
7194 AAAG-GATCGATACTTTTTTAA
1 AAAGTGATCCATACTTTTATAA
7215 AAAGT
1 AAAGT
7220 TATGTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
AAAGTGATCCATACTTTTATAA
Found at i:7548 original size:25 final size:25
Alignment explanation
Indices: 7491--7556 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
7481 CACTCAAAAG
*
7491 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
7516 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
7541 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
7557 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:10719 original size:23 final size:23
Alignment explanation
Indices: 10689--10753 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
10679 AAAAATGATA
10689 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
*
10712 GATACCTATTACATTATATAAGC
1 GATACCTATTACATTATATAAAC
* *
10735 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
10754 TTTTACCTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:12353 original size:9 final size:9
Alignment explanation
Indices: 12339--12418 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
12329 CTTGTTTGGA
12339 TCATCATCT
1 TCATCATCT
12348 TCATCATCAT
1 TCATCATC-T
*
12358 CATCATCATCG
1 --TCATCATCT
12369 TCATCATCT
1 TCATCATCT
* *
12378 TCATCGTCA
1 TCATCATCT
* * *
12387 GCTTCATCG
1 TCATCATCT
*
12396 TCATCATCA
1 TCATCATCT
*
12405 TCGTCATCT
1 TCATCATCT
12414 TCATC
1 TCATC
12419 GTCAGCTTCA
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
9 45 0.83
10 1 0.02
12 8 0.15
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.38
Consensus pattern (9 bp):
TCATCATCT
Found at i:12355 original size:12 final size:12
Alignment explanation
Indices: 12342--12430 Score: 97
Period size: 12 Copynumber: 7.4 Consensus size: 12
12332 GTTTGGATCA
* *
12342 TCATCTTCATCA
1 TCATCGTCATCT
* *
12354 TCATCATCATCA
1 TCATCGTCATCT
* *
12366 TCGTCATCATCT
1 TCATCGTCATCT
*
12378 TCATCGTCAGCT
1 TCATCGTCATCT
*
12390 TCATCGTCATCA
1 TCATCGTCATCT
12402 TCATCGTCATCT
1 TCATCGTCATCT
*
12414 TCATCGTCAGCT
1 TCATCGTCATCT
12426 TCATC
1 TCATC
12431 TTCTGCGACC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 67 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.37
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:12357 original size:6 final size:6
Alignment explanation
Indices: 12338--12418 Score: 81
Period size: 6 Copynumber: 13.5 Consensus size: 6
12328 ACTTGTTTGG
* * * *
12338 ATCATC ATCTTC ATCATC ATCATC ATCATC GTCATC ATCTTC ATCGTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * * *
12386 AGCTTC ATCGTC ATCATC ATCGTC ATCTTC ATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATC
12419 GTCAGCTTCA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (6 bp):
ATCATC
Found at i:12394 original size:36 final size:36
Alignment explanation
Indices: 12354--12430 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
12344 ATCTTCATCA
*
12354 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
12390 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
12426 TCATC
1 TCATC
12431 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.21, C:0.34, G:0.09, T:0.36
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:12433 original size:6 final size:6
Alignment explanation
Indices: 12342--12433 Score: 76
Period size: 6 Copynumber: 15.3 Consensus size: 6
12332 GTTTGGATCA
* * * * * * *
12342 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
12390 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
12434 TGCGACCGCT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:14254 original size:199 final size:199
Alignment explanation
Indices: 13896--15251 Score: 2538
Period size: 199 Copynumber: 6.8 Consensus size: 199
13886 TTTAAATTAG
*
13896 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTCGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
13960 CTTATACCGGTTAGATTGAAAAATTACATATTATATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
14025 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
14090 AAAA
196 AAAA
14094 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
14159 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
14224 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
14289 AAAA
196 AAAA
* *
14293 TATCGACACAAACTAAAATAGTATCTACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
14358 CTTGTACCGATTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
14423 CGACAC-TTTT-TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
14486 AAAA
196 AAAA
*
14490 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
14555 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
14620 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
14685 AAAA
196 AAAA
14689 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
14754 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
14819 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
14884 AAAA
196 AAAA
*
14888 TATCGACACAAACTAAAATAGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
14953 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
15018 CGACACTTTTTATATACGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
15083 AAAA
196 AAAA
15087 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
15152 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGGA
* *
15217 TCGATAGTTTTTATATATGGATCGACACTTTATGG
130 TCGACACTTTTTATATATGGATCGACACTTTATGG
15252 CCATATTGTA
Statistics
Matches: 1130, Mismatches: 24, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
197 189 0.17
198 26 0.02
199 867 0.77
200 48 0.04
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
AAAA
Found at i:15414 original size:19 final size:19
Alignment explanation
Indices: 15368--15416 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
15358 TTATATTCAC
*
15368 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
15387 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
15406 ATACAAAATTA
1 ATACAAAATTA
15417 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:17242 original size:32 final size:33
Alignment explanation
Indices: 17206--17270 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
17196 CATCTTAATA
* *
17206 TCACCCCTTAACACC-CAACTTCTTTCTCCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
17238 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
17271 CCATCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.22, C:0.48, G:0.00, T:0.31
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:17328 original size:21 final size:21
Alignment explanation
Indices: 17303--17346 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
17293 CCCCTTATGC
17303 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
17324 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
17345 CT
1 CT
17347 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:19733 original size:20 final size:20
Alignment explanation
Indices: 19706--19752 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
19696 TCCGGTAACG
19706 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
19725 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
19746 TTTTACC
1 TTTTACC
19753 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:20327 original size:229 final size:228
Alignment explanation
Indices: 19801--20521 Score: 1345
Period size: 228 Copynumber: 3.1 Consensus size: 228
19791 ACTTTTATAC
19801 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
*
19866 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAA
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-ACAAAA
19931 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
130 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
19996 GATAATAATAAATATGTTTTCCACAGTGAAATAA
195 GATAATAATAAATATGTTTTCCACAGTGAAATAA
*
20030 GTATGAACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
20095 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAAT
20160 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
131 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
20225 ATAATAATAAATATGTTTTCCACAGTGAAATAA
196 ATAATAATAAATATGTTTTCCACAGTGAAATAA
20258 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TT
20323 TTTTTAATAGTGTTTCATGTTTTCCACCTACAAATATTAATTTAATAATTTCATTTACACACAAA
65 TTTTTAATAGTGTTTCATGTTTTCCACCTAC-AATATTAATTTAATAATTTCATTTACACACAAA
*
20388 ATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCA
129 ATTATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCA
*
20453 AAGATAATAATAAATATATTTT-CACAGTGAAATAA
193 AAGATAATAATAAATATGTTTTCCACAGTGAAATAA
* *
20488 GTATGGACACTTTTATAAAAAAGATAGATACTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTT
20522 ACAATATAAT
Statistics
Matches: 482, Mismatches: 7, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
228 165 0.34
229 155 0.32
230 89 0.18
231 73 0.15
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (228 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAAT
TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
ATAATAATAAATATGTTTTCCACAGTGAAATAA
Found at i:20782 original size:11 final size:11
Alignment explanation
Indices: 20766--20790 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20756 ATTCAGTACT
20766 ACCGTATATTA
1 ACCGTATATTA
20777 ACCGTATATTA
1 ACCGTATATTA
20788 ACC
1 ACC
20791 CACCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:21403 original size:35 final size:35
Alignment explanation
Indices: 21357--21443 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
21347 TAGTATTTTT
*
21357 TAAATAGTTATTATATTTTATATT-AAT-ATATTTATG
1 TAAATA-TTATT-TATTTT-TATTAAATAATATTTATA
21393 TAAATATTATTT-TTTTTATTAAAATAATATTTATA
1 TAAATATTATTTATTTTTATT-AAATAATATTTATA
*
21428 TAATTATTATTTATTT
1 TAAATATTATTTATTT
21444 AGAATTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 4 0.09
33 4 0.09
34 4 0.09
35 24 0.53
36 9 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (35 bp):
TAAATATTATTTATTTTTATTAAATAATATTTATA
Found at i:21607 original size:17 final size:17
Alignment explanation
Indices: 21585--21638 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
21575 AATGTTAATA
21585 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * *
21602 TTTAAATTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
21619 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
21636 TTT
1 TTT
21639 TTTATAATGT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:32875 original size:23 final size:23
Alignment explanation
Indices: 32849--32897 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
32839 ATAATTATAC
* *
32849 TTTTATGACATATTTTTTTTTAT
1 TTTTATGACACATTTTTCTTTAT
*
32872 TTTTATGATACATTTTTCTTTAT
1 TTTTATGACACATTTTTCTTTAT
32895 TTT
1 TTT
32898 GTCATGTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTATGACACATTTTTCTTTAT
Found at i:32910 original size:23 final size:22
Alignment explanation
Indices: 32849--32922 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 22
32839 ATAATTATAC
32849 TTTTATGACATATTTTTT-TTTAT
1 TTTTATG--ATATTTTTTCTTTAT
*
32872 TTTTATGATACATTTTTCTTTAT
1 TTTTATGATA-TTTTTTCTTTAT
*
32895 TTTGTCATG-TATTTTTGTCGTTAT
1 TTT-T-ATGATATTTTT-TCTTTAT
32919 TTTT
1 TTTT
32923 GTTTATTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.07
22 5 0.12
23 20 0.47
24 12 0.28
25 3 0.07
ACGTcount: A:0.18, C:0.07, G:0.08, T:0.68
Consensus pattern (22 bp):
TTTTATGATATTTTTTCTTTAT
Found at i:41799 original size:30 final size:32
Alignment explanation
Indices: 41764--41839 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 32
41754 ATAGTTATTA
*
41764 TATTTTATATT-AAT-ATATTTATGTAAATAT
1 TATTTTATATTAAATAATATTTATATAAATAT
* *
41794 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATATTTATATAAATAT
41827 TA-TTTAT-TTAAAT
1 TATTTTATATTAAAT
41840 TTATTAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 14 0.36
31 2 0.05
32 7 0.18
33 16 0.41
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (32 bp):
TATTTTATATTAAATAATATTTATATAAATAT
Found at i:43581 original size:21 final size:21
Alignment explanation
Indices: 43551--43598 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
43541 GCAGGGGTAC
* *
43551 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
43572 ATGCCAAGCCCACTAGTTCAT
1 ATGCCAAGCCCACCACTTCAT
43593 ATGCCA
1 ATGCCA
43599 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:43628 original size:21 final size:21
Alignment explanation
Indices: 43602--43674 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
43592 TATGCCATCT
*
43602 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
43623 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
43644 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
43665 CCGCAGGGTT
1 CCGCAGGGTT
43675 TCATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:44300 original size:34 final size:34
Alignment explanation
Indices: 44195--44301 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
44185 ATAAATGTTT
*
44195 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
44229 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
44263 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
44297 TTAAA
1 TTAAA
44302 TTTCAACTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:44924 original size:128 final size:128
Alignment explanation
Indices: 44696--45686 Score: 1775
Period size: 128 Copynumber: 7.7 Consensus size: 128
44686 AGAATCCATC
* *
44696 TAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTATGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
44761 AGAAGGCGCGCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
** * *
44824 TAGTGTCATCGACGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
44889 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
*
44952 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
45017 GGAAGACGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
45080 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
45145 GGAAGGCGCGCCCTCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
* *
45208 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTAAAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
45273 GGAAGGCACGCCCCCGGGAACGCGCCTTTAAGTCCCATGAGAAATAATAGGTAATGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
45336 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
45401 GGAAGGCGCGCCCCCGGGAACACGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
45464 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
45529 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATAAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
* *
45592 TAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAGAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
45657 GGAAGGCGCGCCTCCGGGAACGCGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
45687 TATGAATAGT
Statistics
Matches: 826, Mismatches: 37, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 826 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTAATGATATGAA
Found at i:45780 original size:8 final size:8
Alignment explanation
Indices: 45767--45804 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
45757 TCACAAGCTT
45767 TCAAATTC
1 TCAAATTC
45775 TCAAATTC
1 TCAAATTC
* *
45783 CCAAACTC
1 TCAAATTC
45791 T-AAATTC
1 TCAAATTC
45798 TCAAATT
1 TCAAATT
45805 ATCTGAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:50260 original size:37 final size:37
Alignment explanation
Indices: 50186--50260 Score: 84
Period size: 37 Copynumber: 2.0 Consensus size: 37
50176 TACTATTTTT
**
50186 AATTTATATATTTTCTTTAAAAATTTTAAATTTATAA
1 AATTTATATATTTTCTTTAAAAATTTTAAATAGATAA
50223 AATTTATATAATATTT-TTTACAAAA-TTTAAA-AGATAA
1 AATTTATAT-AT-TTTCTTTA-AAAATTTTAAATAGATAA
50260 A
1 A
50261 TAGGTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
37 14 0.42
38 12 0.36
39 7 0.21
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAATTTTAAATAGATAA
Found at i:51155 original size:16 final size:16
Alignment explanation
Indices: 51134--51164 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
51124 ATAAACACAT
51134 AATTAGAAATATAATA
1 AATTAGAAATATAATA
51150 AATTAGAAATATAAT
1 AATTAGAAATATAAT
51165 TATAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
AATTAGAAATATAATA
Found at i:54643 original size:21 final size:20
Alignment explanation
Indices: 54557--54714 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
54547 AAATGACCAA
**
54557 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
54576 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
54596 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
54616 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
54637 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* ** *
54658 CAAATTCGCATTGCGGTTTT
1 CAAAATCGCAACGCGATTTT
* *
54678 ACAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
54699 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
54715 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:54743 original size:20 final size:20
Alignment explanation
Indices: 54681--54910 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
54671 CGGTTTTACA
* ** *
54681 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
54701 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
54721 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
54741 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
54761 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
54781 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
54801 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
54821 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
54841 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
54861 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
54881 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
54901 AAATCACAAC
1 AAATCGCAAC
54911 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:58143 original size:19 final size:19
Alignment explanation
Indices: 58121--58356 Score: 198
Period size: 19 Copynumber: 13.7 Consensus size: 19
58111 CGGAAATTAC
*
58121 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
58140 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
58154 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
58174 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
58188 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58207 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
58226 AATCACAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
58240 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58259 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
58278 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
58292 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
58311 AATCGCAA----AGA-GAG
1 AATCGCAATGCGAAATGAA
58325 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
58344 AAACGCATTGCGA
1 AATCGCAATGCGA
58357 TTCTCTCGTT
Statistics
Matches: 175, Mismatches: 16, Indels: 52
0.72 0.07 0.21
Matches are distributed among these distances:
14 51 0.29
15 5 0.03
16 7 0.04
17 6 0.03
18 6 0.03
19 87 0.50
20 13 0.07
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:58208 original size:33 final size:33
Alignment explanation
Indices: 58121--58350 Score: 236
Period size: 33 Copynumber: 6.8 Consensus size: 33
58111 CGGAAATTAC
* * *
58121 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
58154 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* *
58188 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * *
58220 AAT-GAAAAT-C-ACAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGA-AATGA-A-AATCGCAA--CG--A-GAG
58259 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
58292 AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
58325 AATCGCAATGCGAAATGAAAAACGCA
1 AATCGCAATGCGAAATGAAAATCGCA
58351 TTGCGATTCT
Statistics
Matches: 168, Mismatches: 14, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.01
31 6 0.04
32 7 0.04
33 96 0.57
34 30 0.18
35 2 0.01
36 2 0.01
38 10 0.06
39 7 0.04
40 6 0.04
41 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:58236 original size:52 final size:52
Alignment explanation
Indices: 58149--58318 Score: 322
Period size: 52 Copynumber: 3.2 Consensus size: 52
58139 AAATCCCAAC
58149 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
58202 ATGAAAATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
58254 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
58306 ATGAAAATCGCAA
1 ATGAAAATCGCAA
58319 AGAGAGAATC
Statistics
Matches: 115, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 99 0.86
53 16 0.14
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:58393 original size:20 final size:19
Alignment explanation
Indices: 58365--58440 Score: 72
Period size: 20 Copynumber: 4.2 Consensus size: 19
58355 GATTCTCTCG
*
58365 TTGCGATTTTCATTTCCGCA
1 TTGCAATTTTCATTT-CGCA
58385 TTGCAATTTTCATTTCGCA
1 TTGCAATTTTCATTTCGCA
* *
58404 TTGCGA--TTC-TCTCG--
1 TTGCAATTTTCATTTCGCA
*
58418 TTGCGATTTTCATTTCGCA
1 TTGCAATTTTCATTTCGCA
58437 TTGC
1 TTGC
58441 GATAGTCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.13
16 7 0.15
17 7 0.15
19 13 0.28
20 14 0.30
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCAATTTTCATTTCGCA
Found at i:58451 original size:19 final size:19
Alignment explanation
Indices: 58365--58443 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 19
58355 GATTCTCTCG
58365 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
58385 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
58404 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
58418 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
58437 TTGCGAT
1 TTGCGAT
58444 AGTCATTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.14
17 7 0.14
19 16 0.32
20 14 0.28
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:58569 original size:14 final size:14
Alignment explanation
Indices: 58550--58586 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
58540 CATCAATTAC
58550 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
58564 ACAAATCATCTTTT
1 ACAAATCAACTTTT
58578 ACAAATCAA
1 ACAAATCAA
58587 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:60580 original size:14 final size:14
Alignment explanation
Indices: 60561--60617 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
60551 GCGAAATGAA
*
60561 AATCGCAACGACAG
1 AATCGCAACGAAAG
60575 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
60592 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
60608 AATCGCAACG
1 AATCGCAACG
60618 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:60588 original size:33 final size:33
Alignment explanation
Indices: 60542--60634 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
60532 GCGAAACCAA
*
60542 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
60575 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
60608 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
60635 TGCGATTTTG
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:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:60599 original size:19 final size:19
Alignment explanation
Indices: 60507--60639 Score: 124
Period size: 19 Copynumber: 7.5 Consensus size: 19
60497 GTTTACTTTT
* *
60507 GCAACACGAAACTTAAAATC
1 GCAACGCGAAA-TGAAAATC
**
60527 GCAACGCGAAACCAAAATC
1 GCAACGCGAAATGAAAATC
60546 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
60565 GCAA--CGACA-G--AATC
1 GCAACGCGAAATGAAAATC
*
60579 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
60598 GCAA--CGAAA-G--AATC
1 GCAACGCGAAATGAAAATC
60612 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
60631 GCAATGCGA
1 GCAACGCGA
60640 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 47 0.49
20 10 0.11
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:60657 original size:19 final size:18
Alignment explanation
Indices: 60635--60744 Score: 83
Period size: 19 Copynumber: 6.3 Consensus size: 18
60625 AAAATCGCAA
60635 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
60654 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
60668 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
60687 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
60701 TGCGATTTTTATTTCGCGT
1 TGCGA-TTTTGTTTCGCGT
*
60720 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
60740 TGCGA
1 TGCGA
60745 AAGTAAACTA
Statistics
Matches: 72, Mismatches: 7, Indels: 23
0.71 0.07 0.23
Matches are distributed among these distances:
14 19 0.26
15 4 0.06
16 2 0.03
17 2 0.03
18 6 0.08
19 27 0.38
20 12 0.17
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:60677 original size:33 final size:33
Alignment explanation
Indices: 60635--60726 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
60625 AAAATCGCAA
60635 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
60668 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
60701 TGCGATTTTTATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
60727 TTAAGTTTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:60908 original size:93 final size:93
Alignment explanation
Indices: 60792--61353 Score: 1108
Period size: 93 Copynumber: 6.1 Consensus size: 93
60782 ATGGATTGCA
60792 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
60856 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
60884 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
60949 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
60977 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
61042 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
61070 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
61135 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
61163 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
61228 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
61256 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
61321 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
61349 TTACT
1 TTACT
61354 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 464 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:63097 original size:19 final size:19
Alignment explanation
Indices: 63073--63156 Score: 88
Period size: 19 Copynumber: 4.7 Consensus size: 19
63063 ACAACGAGAG
*
63073 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
* *
63092 AATCGCAACGAGAAATAAA
1 AATCGCAACGCGAAATGAA
*
63111 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
63125 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
63144 AATCGCAATGCGA
1 AATCGCAACGCGA
63157 TTTTGGTTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 2 0.04
17 1 0.02
18 1 0.02
19 38 0.73
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:63114 original size:52 final size:52
Alignment explanation
Indices: 63051--63151 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
63041 TCTTTTGGTT
* *
63051 GAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGACAATCGCAACGA
1 GAAATAAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
63103 GAAATAAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAAATAAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAA
63152 TGCGATTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.50, C:0.20, G:0.21, T:0.10
Consensus pattern (52 bp):
GAAATAAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:63187 original size:14 final size:14
Alignment explanation
Indices: 63168--63224 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
63158 TTTGGTTTCG
63168 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
63182 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
63201 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
63215 CGTTGCGATT
1 CGTTGCGATT
63225 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:63202 original size:33 final size:33
Alignment explanation
Indices: 63165--63229 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
63155 GATTTTGGTT
63165 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
63198 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
63230 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:63265 original size:41 final size:41
Alignment explanation
Indices: 63208--63285 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
63198 TCGCGTTGCG
*
63208 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
63249 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
63286 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:63270 original size:20 final size:21
Alignment explanation
Indices: 63209--63284 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
63199 CGCGTTGCGA
63209 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
63230 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
63250 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
63271 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
63285 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:63406 original size:33 final size:33
Alignment explanation
Indices: 63364--63434 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
63354 AATACTAACT
*
63364 TGAAAATCGCAACGAGAAAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAAAATAGCAACGCGAAA
* * *
63397 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAAAATAGCAACGCGAAA
63430 TGAAA
1 TGAAA
63435 TCTAAGTGAA
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:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAAAATAGCAACGCGAAA
Found at i:63668 original size:22 final size:22
Alignment explanation
Indices: 63616--63670 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
63606 TGGTTGTGAG
**
63616 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
63638 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
63660 GGATTTCTTCG
1 GGATTTCTTCG
63671 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:63842 original size:20 final size:20
Alignment explanation
Indices: 63817--64010 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
63807 CTTTAAATAT
63817 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
63837 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
63859 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
63878 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
63898 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
63918 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
63938 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
63958 CGAGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
63978 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
63998 CGCGTTGCGATTT
1 CGCGTTGCGATTT
64011 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:64004 original size:60 final size:60
Alignment explanation
Indices: 63817--64010 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
63807 CTTTAAATAT
* **
63817 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGAGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* *** *
63878 CGCGTTGCGATATACGGATACGCA-TTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACG-AGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
63938 CACGTTGCGATTTACGGATACGAGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGAGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
63998 CGCGTTGCGATTT
1 CGCGTTGCGATTT
64011 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 83 0.75
61 27 0.24
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGAGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:64027 original size:21 final size:21
Alignment explanation
Indices: 63997--64079 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
63987 ATTTTCATAT
*
63997 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
64018 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
64039 TCACATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
64060 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
64080 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:64490 original size:42 final size:44
Alignment explanation
Indices: 64389--64492 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 44
64379 AAGGAGCCAA
* * * *
64389 CTATAGATCT-GACCTTTTGCGGCGTTTTTTTACAAAAATGCCG
1 CTATAGATCTCGACCTTTTACGGCATTTGTTTACAAAAACGCCG
* *
64432 CTATATATCTCAACCTTTTACGGCATTTGTTT-C-AAAACGCCG
1 CTATAGATCTCGACCTTTTACGGCATTTGTTTACAAAAACGCCG
*
64474 CTATAGATATCGACCTTTT
1 CTATAGATCTCGACCTTTT
64493 GTGATGTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 24 0.47
43 10 0.20
44 17 0.33
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (44 bp):
CTATAGATCTCGACCTTTTACGGCATTTGTTTACAAAAACGCCG
Found at i:66761 original size:5 final size:5
Alignment explanation
Indices: 66753--66793 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
66743 ATTATTATAT
*
66753 ATAAT ATAATA ATAAA ATAAA AT-AA ATAAA ATAAA ATAAA A
1 ATAAA ATAA-A ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
66794 AAGACAACTC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
4 4 0.12
5 25 0.76
6 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
ATAAA
Found at i:66782 original size:14 final size:14
Alignment explanation
Indices: 66763--66792 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
66753 ATAATATAAT
66763 AATAAAATAAAATA
1 AATAAAATAAAATA
66777 AATAAAATAAAATA
1 AATAAAATAAAATA
66791 AA
1 AA
66793 AAAGACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AATAAAATAAAATA
Found at i:66787 original size:19 final size:21
Alignment explanation
Indices: 66753--66793 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
66743 ATTATTATAT
66753 ATAATATAATAATAAAATAAA
1 ATAATATAATAATAAAATAAA
66774 ATAA-ATAA-AATAAAATAAA
1 ATAATATAATAATAAAATAAA
66793 A
1 A
66794 AAGACAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
ATAATATAATAATAAAATAAA
Found at i:68302 original size:30 final size:30
Alignment explanation
Indices: 68226--68302 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
68216 AGATGGCCTT
* *
68226 AGTCCATGTACCATTTAACATTGGTGGCTA
1 AGTCCATGTATCATTTAACATTAGTGGCTA
* * * * *
68256 ATTCCCTATATTATTTAACCTTAGTGGCTA
1 AGTCCATGTATCATTTAACATTAGTGGCTA
68286 AGTCCATGTATCATTTA
1 AGTCCATGTATCATTTA
68303 GTGCTTAGCT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (30 bp):
AGTCCATGTATCATTTAACATTAGTGGCTA
Found at i:68730 original size:22 final size:23
Alignment explanation
Indices: 68673--68745 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 23
68663 AAAGAATTTC
*
68673 GAAAAATGTTTGATGAAAGAATTTT
1 GAAAAATGTTTGATG-AA-ATTTTT
*
68698 G-AAAATGTTTGAT-AAGTTTTT
1 GAAAAATGTTTGATGAAATTTTT
*
68719 GAAAAATTTTTGATGAAATTTTT
1 GAAAAATGTTTGATGAAATTTTT
68742 GAAA
1 GAAA
68746 TTGATGTCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
21 5 0.12
22 13 0.31
23 11 0.26
24 12 0.29
25 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (23 bp):
GAAAAATGTTTGATGAAATTTTT
Found at i:68737 original size:12 final size:11
Alignment explanation
Indices: 68694--68743 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
68684 GATGAAAGAA
68694 TTTTGA-AAAT
1 TTTTGATAAAT
* *
68704 GTTTGATAAGT
1 TTTTGATAAAT
*
68715 TTTTGAAAAAT
1 TTTTGATAAAT
68726 TTTTGATGAAAT
1 TTTTGAT-AAAT
68738 TTTTGA
1 TTTTGA
68744 AATTGATGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 5 0.16
11 17 0.53
12 10 0.31
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (11 bp):
TTTTGATAAAT
Found at i:69423 original size:19 final size:21
Alignment explanation
Indices: 69399--69446 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
69389 ATATACATTT
**
69399 TATGAACAGT-AA-AATATGG
1 TATGAACAGTGAACAATACCG
*
69418 TATGAATAGTGAACAATACCG
1 TATGAACAGTGAACAATACCG
69439 TATGAACA
1 TATGAACA
69447 ATGCCATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 12 0.52
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (21 bp):
TATGAACAGTGAACAATACCG
Found at i:70036 original size:17 final size:19
Alignment explanation
Indices: 69994--70038 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
69984 TATTTATCAG
69994 TAATCATATTATTATCACT
1 TAATCATATTATTATCACT
*
70013 TATTCAT-TT-TTATCA-T
1 TAATCATATTATTATCACT
70029 ATAATCATAT
1 -TAATCATAT
70039 GTTGAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 1 0.05
17 12 0.55
18 3 0.14
19 6 0.27
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATCATATTATTATCACT
Found at i:70312 original size:22 final size:22
Alignment explanation
Indices: 70287--70347 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
70277 GGCATATGAA
*
70287 ATTTGTCCCGAATGACCTA-TGT
1 ATTTGTCCCGAAGGACC-ACTGT
*
70309 ATTTATCCCGAAGGACCACTGT
1 ATTTGTCCCGAAGGACCACTGT
*
70331 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
70348 GCGTAAACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCACTGT
Found at i:70859 original size:2 final size:2
Alignment explanation
Indices: 70815--70846 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
70805 ATAAGAATAA
70815 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
70847 CCATTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72298 original size:2 final size:2
Alignment explanation
Indices: 72291--72326 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
72281 CAACTTATTG
72291 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
72327 ATTACAGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75960 original size:21 final size:21
Alignment explanation
Indices: 75936--75995 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
75926 ACTTTGAAAG
75936 AATGGTTTTCAAAGTTTGGTA
1 AATGGTTTTCAAAGTTTGGTA
*
75957 AAT-G-TTTC----TTT-GAA
1 AATGGTTTTCAAAGTTTGGTA
75971 AATGGTTTTCAAAGTTTGGTA
1 AATGGTTTTCAAAGTTTGGTA
75992 AATG
1 AATG
75996 TTTCTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (21 bp):
AATGGTTTTCAAAGTTTGGTA
Found at i:75975 original size:35 final size:35
Alignment explanation
Indices: 75927--76043 Score: 155
Period size: 35 Copynumber: 3.3 Consensus size: 35
75917 TGGTAACCAA
75927 CTTTGAAAGAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AA-AATGGTTTTCAAAGTTTGGTAAATGTTT
75964 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
75999 CTTTAAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTT-GAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
76036 -GTTGAAAA
1 CTTTGAAAA
76044 ATGATAATGG
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 36 0.49
36 9 0.12
37 28 0.38
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:76026 original size:37 final size:36
Alignment explanation
Indices: 75927--76044 Score: 157
Period size: 37 Copynumber: 3.2 Consensus size: 36
75917 TGGTAACCAA
*
75927 CTTTGAAAGAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTT-AAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
75964 CTTT-GAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
75999 CTTTAAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTAAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
* *
76036 GTTGAAAAA
1 CTTTAAAAA
76045 TGATAATGGG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 33 0.46
36 5 0.07
37 34 0.47
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:80464 original size:34 final size:35
Alignment explanation
Indices: 80423--80566 Score: 222
Period size: 34 Copynumber: 4.2 Consensus size: 35
80413 TGAAAGTATT
80423 AAAATGGTTTTCAAAGTTTGGTAAATGTTTC-TTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
*
80457 AAAATGGTTTTCAAAATTTGGTAAATG-TTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
80491 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
80526 AAAAATAGTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
80561 AAAATG
1 AAAATG
80567 ATAATGGGAT
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
33 3 0.03
34 60 0.59
35 10 0.10
36 28 0.28
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:80503 original size:68 final size:70
Alignment explanation
Indices: 80423--80566 Score: 231
Period size: 70 Copynumber: 2.1 Consensus size: 70
80413 TGAAAGTATT
*
80423 AAAATGGTTTTCAAAGTTTGGTAAATGTTTC-TTG-AAAATGGTTTTCAAAATTTGGTAAATGTT
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATAGTTTTCAAAATTTGGTAAATGTT
80486 CT-TTG
66 -TGTTG
* *
80491 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATAGTTTTCAAAGTTTGGTAGATGTT
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATAGTTTTCAAAATTTGGTAAATGTT
80556 TGTTG
66 TGTTG
80561 AAAATG
1 AAAATG
80567 ATAATGGGAT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
68 31 0.44
69 4 0.06
70 35 0.50
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (70 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATAGTTTTCAAAATTTGGTAAATGTT
TGTTG
Done.