Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 725 of 770
Found at i:229356428 original size:30 final size:30
Alignment explanation
Indices: 229356394--229356491 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
229356384 AGCTCACTCC
229356394 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
229356424 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
229356454 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
229356484 TAGCTCAT
1 TAGCTCAT
229356492 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:229357963 original size:19 final size:19
Alignment explanation
Indices: 229357939--229357978 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
229357929 AGCTCCCATG
*
229357939 TAGCTCCACACCAGCTCAT
1 TAGCTCCAAACCAGCTCAT
*
229357958 TAGCTCGAAACCAGCTCAT
1 TAGCTCCAAACCAGCTCAT
229357977 TA
1 TA
229357979 TCAGCTCGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.35, G:0.12, T:0.23
Consensus pattern (19 bp):
TAGCTCCAAACCAGCTCAT
Found at i:229359227 original size:14 final size:13
Alignment explanation
Indices: 229359188--229359230 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
229359178 AAACTGACCA
229359188 ATTTGTTCATACC
1 ATTTGTTCATACC
*
229359201 ATTTGTTCCTACC
1 ATTTGTTCATACC
* *
229359214 CTTTCGTTCTTACC
1 ATTT-GTTCATACC
229359228 ATT
1 ATT
229359231 CCATTCGTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.16, C:0.28, G:0.07, T:0.49
Consensus pattern (13 bp):
ATTTGTTCATACC
Found at i:229362465 original size:79 final size:80
Alignment explanation
Indices: 229362333--229362587 Score: 367
Period size: 79 Copynumber: 3.2 Consensus size: 80
229362323 TGGATGATAA
* * * *
229362333 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTCG
229362397 TGCGAGTTACTATATC
65 TGCGAGTTACTATATC
229362413 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGT
*
229362477 ACGAGTTACTATATC
66 GCGAGTTACTATATC
* * *
229362492 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT-CGGGCTATGTCCCGAAGGCATTCGA
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGT
229362556 GCGAG-TAGCTATATC
66 GCGAGTTA-CTATATC
* *
229362571 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
229362588 TACTTGGCTT
Statistics
Matches: 161, Mismatches: 11, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
78 17 0.11
79 107 0.66
80 37 0.23
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGT
GCGAGTTACTATATC
Found at i:229362546 original size:119 final size:119
Alignment explanation
Indices: 229362333--229362587 Score: 356
Period size: 119 Copynumber: 2.2 Consensus size: 119
229362323 TGGATGATAA
* * * *
229362333 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTCGCACGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTCGT
* *
229362398 GCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTA-CTATATC
66 GCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTCGAGCGAG-TAGCTATATC
* *
229362452 CGGGCTAAGTCCCGAAGGCATTCGTACGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTCG
1 CGGGCTAAGTCCCGAAGGCATTCGCACGAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTCG
*
229362516 TGCGAGTTACTATAT-CGGGCTATGTCCCGAAGGCATTCGAGCGAGTAGCTATATC
65 TGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCATTCGAGCGAGTAGCTATATC
* *
229362571 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
229362588 TACTTGGCTT
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
118 26 0.21
119 96 0.79
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (119 bp):
CGGGCTAAGTCCCGAAGGCATTCGCACGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTCGT
GCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTCGAGCGAGTAGCTATATC
Found at i:229362583 original size:39 final size:40
Alignment explanation
Indices: 229362333--229362587 Score: 358
Period size: 40 Copynumber: 6.5 Consensus size: 40
229362323 TGGATGATAA
* * * *
229362333 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TC
1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTA-TATC
*
229362373 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATATC
*
229362413 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATATC
*
229362452 CGGGCTAAGTCCCGAAGGCATTCGTACGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATATC
229362492 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT-
1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATATC
* *
229362531 CGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTA-CTATATC
* *
229362571 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
229362588 TACTTGGCTT
Statistics
Matches: 200, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
38 2 0.01
39 87 0.44
40 111 0.56
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATATC
Found at i:229367603 original size:58 final size:58
Alignment explanation
Indices: 229367529--229367751 Score: 179
Period size: 58 Copynumber: 3.9 Consensus size: 58
229367519 TACGGTGACG
* *
229367529 AGAT-TGGCACTAAGTGTGCATGCTGAAAATATATGGCACTAAGTGTGC-ATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGAAAATATACGGCACTAAGTGTGCGA-GCTCGAA
* * **
229367586 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGAGCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGAAAATATACGGCACTAAGTGTGCGAGCTCGAA
* * ** * * * * * *
229367644 GGGTATGGCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-A
1 AGATATGGCACTAAGTGTGCATGCTGAAAA-TATACGGCACTAAGTGTGCGAGCTCGAA
** * *
229367702 TTATATAGCACTAAGTGTGCGA-GTTGAATACATATA--GCACTAAGTGTGCG
1 AGATATGGCACTAAGTGTGC-ATGCTGAA-A-ATATACGGCACTAAGTGTGCG
229367752 GATTCACTAT
Statistics
Matches: 133, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
57 17 0.13
58 90 0.68
59 25 0.19
60 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGAAAATATACGGCACTAAGTGTGCGAGCTCGAA
Found at i:229367664 original size:29 final size:29
Alignment explanation
Indices: 229367533--229367663 Score: 174
Period size: 29 Copynumber: 4.5 Consensus size: 29
229367523 GTGACGAGAT
*
229367533 TGGCACTAAGTGTGCATGCTGAAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
229367562 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
229367591 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
229367620 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
229367649 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
229367664 GGGTTTAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 89 0.99
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:229367720 original size:28 final size:28
Alignment explanation
Indices: 229367651--229367751 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
229367641 GAAGGGTATG
* * * *
229367651 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
229367681 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
229367709 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
229367738 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
229367752 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:229375520 original size:58 final size:58
Alignment explanation
Indices: 229375446--229375668 Score: 179
Period size: 58 Copynumber: 3.9 Consensus size: 58
229375436 TACGGTGACG
* *
229375446 AGAT-TGGCACTAAGTGTGCATGCTGAAAATATATGGCACTAAGTGTGC-ATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGAAAATATACGGCACTAAGTGTGCGA-GCTCGAA
* * **
229375503 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGAGCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGAAAATATACGGCACTAAGTGTGCGAGCTCGAA
* * ** * * * * * *
229375561 GGGTATGGCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-A
1 AGATATGGCACTAAGTGTGCATGCTGAAAA-TATACGGCACTAAGTGTGCGAGCTCGAA
** * *
229375619 TTATATAGCACTAAGTGTGCGA-GTTGAATACATATA--GCACTAAGTGTGCG
1 AGATATGGCACTAAGTGTGC-ATGCTGAA-A-ATATACGGCACTAAGTGTGCG
229375669 GATTCACTAT
Statistics
Matches: 133, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
57 17 0.13
58 90 0.68
59 25 0.19
60 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGAAAATATACGGCACTAAGTGTGCGAGCTCGAA
Found at i:229375581 original size:29 final size:29
Alignment explanation
Indices: 229375450--229375580 Score: 174
Period size: 29 Copynumber: 4.5 Consensus size: 29
229375440 GTGACGAGAT
*
229375450 TGGCACTAAGTGTGCATGCTGAAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
229375479 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
229375508 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
229375537 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
229375566 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
229375581 GGGTTTAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 89 0.99
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:229375637 original size:28 final size:28
Alignment explanation
Indices: 229375568--229375668 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
229375558 GAAGGGTATG
* * * *
229375568 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
229375598 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
229375626 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
229375655 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
229375669 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:229385935 original size:15 final size:15
Alignment explanation
Indices: 229385912--229385941 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
229385902 TCCGCCTCTT
229385912 TGGTCTTCCGCCTGC
1 TGGTCTTCCGCCTGC
*
229385927 TGGTTTTCCGCCTGC
1 TGGTCTTCCGCCTGC
229385942 GTGCTTGCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.37, G:0.27, T:0.37
Consensus pattern (15 bp):
TGGTCTTCCGCCTGC
Found at i:229389283 original size:18 final size:17
Alignment explanation
Indices: 229389256--229389289 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
229389246 CCTTGCCTGT
229389256 GTTCCGCCTGCCGCCCGC
1 GTTCCGCCTG-CGCCCGC
*
229389274 GTTCCTCCTGCGCCCG
1 GTTCCGCCTGCGCCCG
229389290 GCTCGCCCTC
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:0.00, C:0.53, G:0.26, T:0.21
Consensus pattern (17 bp):
GTTCCGCCTGCGCCCGC
Found at i:229389857 original size:16 final size:16
Alignment explanation
Indices: 229389832--229389863 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
229389822 TCTCCCGCTC
229389832 TCCCTCCCGCCGGTTT
1 TCCCTCCCGCCGGTTT
*
229389848 TCCCTGCCGCCGGTTT
1 TCCCTCCCGCCGGTTT
229389864 GCCTCCGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.47, G:0.22, T:0.31
Consensus pattern (16 bp):
TCCCTCCCGCCGGTTT
Found at i:229390475 original size:3 final size:3
Alignment explanation
Indices: 229390463--229390543 Score: 79
Period size: 3 Copynumber: 29.3 Consensus size: 3
229390453 CGCCGGGCTC
229390463 CCT CCT -CT CCT CCT CCT -CT CCT -CT CCCT CCT CCT CCT -CT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT -CCT CCT CCT CCT CCT CCT
* *
229390505 CCT -CG CCT -CG CCT CCT CCT -CT CCT CCT -CT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
229390544 GCCTCGCCCC
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
2 14 0.22
3 49 0.75
4 2 0.03
ACGTcount: A:0.00, C:0.64, G:0.02, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:229390476 original size:8 final size:8
Alignment explanation
Indices: 229390463--229390540 Score: 92
Period size: 8 Copynumber: 9.9 Consensus size: 8
229390453 CGCCGGGCTC
229390463 CCTCCTCT
1 CCTCCTCT
229390471 CCTCCTC-
1 CCTCCTCT
229390478 CTCTCCTCT
1 C-CTCCTCT
229390487 -C-CCTCCT
1 CCTCCT-CT
229390494 CCTCCTCT
1 CCTCCTCT
*
229390502 CCTCCTCG
1 CCTCCTCT
229390510 CCTCGC-CT
1 CCTC-CTCT
229390518 CCTCCTCT
1 CCTCCTCT
229390526 CCTCCTCT
1 CCTCCTCT
229390534 CCTCCTC
1 CCTCCTC
229390541 CTCGCCTCGC
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
6 3 0.05
7 5 0.08
8 49 0.80
9 4 0.07
ACGTcount: A:0.00, C:0.64, G:0.03, T:0.33
Consensus pattern (8 bp):
CCTCCTCT
Found at i:229390548 original size:11 final size:11
Alignment explanation
Indices: 229390463--229390543 Score: 105
Period size: 11 Copynumber: 7.4 Consensus size: 11
229390453 CGCCGGGCTC
229390463 CCTCCTCTCCT
1 CCTCCTCTCCT
229390474 CCTCCTCTCCT
1 CCTCCTCTCCT
229390485 -CTCC-CTCCT
1 CCTCCTCTCCT
229390494 CCTCCTCTCCT
1 CCTCCTCTCCT
*
229390505 CCTCGCCTCGCCT
1 CCT--CCTCTCCT
229390518 CCTCCTCTCCT
1 CCTCCTCTCCT
229390529 CCT-CTCCTCCT
1 CCTCCT-CTCCT
229390540 CCTC
1 CCTC
229390544 GCCTCGCCCC
Statistics
Matches: 62, Mismatches: 2, Indels: 11
0.83 0.03 0.15
Matches are distributed among these distances:
9 5 0.08
10 10 0.16
11 37 0.60
13 10 0.16
ACGTcount: A:0.00, C:0.64, G:0.02, T:0.33
Consensus pattern (11 bp):
CCTCCTCTCCT
Found at i:229390585 original size:27 final size:29
Alignment explanation
Indices: 229390534--229390591 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
229390524 CTCCTCCTCT
*
229390534 CCTCCTCCTCGCCTCGCCCCTCGCCTCGCC
1 CCTCCTCCTCGCCTCG-CCCTCGCCCCGCC
*
229390564 CCTCCTCCTCTCCTCG-CC-CGCCCCGCC
1 CCTCCTCCTCGCCTCGCCCTCGCCCCGCC
229390591 C
1 C
229390592 TGTCTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.35
28 2 0.08
30 15 0.58
ACGTcount: A:0.00, C:0.69, G:0.12, T:0.19
Consensus pattern (29 bp):
CCTCCTCCTCGCCTCGCCCTCGCCCCGCC
Found at i:229391155 original size:14 final size:15
Alignment explanation
Indices: 229391131--229391164 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
229391121 CCGTCGCCGC
229391131 CCCCGCTTCCCCCTG
1 CCCCGCTTCCCCCTG
*
229391146 CCCC-CTTCCCCTTG
1 CCCCGCTTCCCCCTG
229391160 CCCCG
1 CCCCG
229391165 GCTCTTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.68, G:0.12, T:0.21
Consensus pattern (15 bp):
CCCCGCTTCCCCCTG
Found at i:229393366 original size:13 final size:13
Alignment explanation
Indices: 229393348--229393382 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
229393338 GCTTTTCCGG
229393348 CCCTTTCCCCCGC
1 CCCTTTCCCCCGC
229393361 CCCTTT-CCCCGC
1 CCCTTTCCCCCGC
229393373 CCTCTTTCCC
1 CC-CTTTCCC
229393383 TTTCTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 10 0.50
14 2 0.10
ACGTcount: A:0.00, C:0.66, G:0.06, T:0.29
Consensus pattern (13 bp):
CCCTTTCCCCCGC
Found at i:229395696 original size:20 final size:20
Alignment explanation
Indices: 229395668--229395705 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
229395658 TTGCTTGTCC
*
229395668 CTCTTTTTCCTCTCCTCTCT
1 CTCTCTTTCCTCTCCTCTCT
229395688 CTCTCTTTCCTCTCCTCT
1 CTCTCTTTCCTCTCCTCT
229395706 TCCTCTCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (20 bp):
CTCTCTTTCCTCTCCTCTCT
Found at i:229395711 original size:20 final size:19
Alignment explanation
Indices: 229395667--229395712 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
229395657 TTTGCTTGTC
*
229395667 CCTCTTTTTCCTCTCCTCT
1 CCTCTCTTTCCTCTCCTCT
229395686 CTCTCTCTTTCCTCTCCTCTT
1 C-CTCTCTTTCCTCTCCTC-T
229395707 CCTCTC
1 CCTCTC
229395713 GCCCTCCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.88
21 2 0.08
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (19 bp):
CCTCTCTTTCCTCTCCTCT
Found at i:229397926 original size:20 final size:22
Alignment explanation
Indices: 229397878--229397926 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
229397868 TTCTTCCTGC
229397878 TCGTTCCCCGCTCGCCGTCCCT
1 TCGTTCCCCGCTCGCCGTCCCT
* *
229397900 TTG-TCCCCTC-CGCC-TCCCT
1 TCGTTCCCCGCTCGCCGTCCCT
229397919 TCGTTCCC
1 TCGTTCCC
229397927 TGCTTTCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 8 0.35
21 6 0.26
22 2 0.09
ACGTcount: A:0.00, C:0.55, G:0.14, T:0.31
Consensus pattern (22 bp):
TCGTTCCCCGCTCGCCGTCCCT
Found at i:229397927 original size:19 final size:20
Alignment explanation
Indices: 229397890--229397927 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
229397880 GTTCCCCGCT
*
229397890 CGCCGTCCCTTTGTCCCCTC
1 CGCCGTCCCTTCGTCCCCTC
*
229397910 CGCC-TCCCTTCGTTCCCT
1 CGCCGTCCCTTCGTCCCCT
229397928 GCTTTCTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.00, C:0.55, G:0.13, T:0.32
Consensus pattern (20 bp):
CGCCGTCCCTTCGTCCCCTC
Found at i:229398673 original size:27 final size:27
Alignment explanation
Indices: 229398615--229398692 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
229398605 CCCGGTCCCG
229398615 CTCCCTCGCGTCCCTCTCCT-CCTCGC
1 CTCCCTCGCGTCCCTCTCCTCCCTCGC
* * *
229398641 GTCCCTCGCCTCCCTCTCGTCCCTCGC
1 CTCCCTCGCGTCCCTCTCCTCCCTCGC
*
229398668 CTCCCTCTCGTCCCTCTCCTCCCTC
1 CTCCCTCGCGTCCCTCTCCTCCCTC
229398693 TCGCTCTCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 17 0.39
27 27 0.61
ACGTcount: A:0.00, C:0.62, G:0.10, T:0.28
Consensus pattern (27 bp):
CTCCCTCGCGTCCCTCTCCTCCCTCGC
Found at i:229398684 original size:9 final size:9
Alignment explanation
Indices: 229398616--229398695 Score: 81
Period size: 9 Copynumber: 9.0 Consensus size: 9
229398606 CCGGTCCCGC
*
229398616 TCCCTCGCG
1 TCCCTCTCG
*
229398625 TCCCTCTCC
1 TCCCTCTCG
*
229398634 T-CCTCGCG
1 TCCCTCTCG
* *
229398642 TCCCTCGCC
1 TCCCTCTCG
229398651 TCCCTCTCG
1 TCCCTCTCG
* *
229398660 TCCCTCGCC
1 TCCCTCTCG
229398669 TCCCTCTCG
1 TCCCTCTCG
*
229398678 TCCCTCTCC
1 TCCCTCTCG
229398687 TCCCTCTCG
1 TCCCTCTCG
229398696 CTCTCCTCCC
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
8 6 0.11
9 51 0.89
ACGTcount: A:0.00, C:0.60, G:0.11, T:0.29
Consensus pattern (9 bp):
TCCCTCTCG
Found at i:229398693 original size:18 final size:18
Alignment explanation
Indices: 229398615--229398707 Score: 122
Period size: 18 Copynumber: 5.4 Consensus size: 18
229398605 CCCGGTCCCG
*
229398615 CTCCCTCGCGTCCCTCTC
1 CTCCCTCTCGTCCCTCTC
* *
229398633 CT-CCTCGCGTCCCTCGC
1 CTCCCTCTCGTCCCTCTC
*
229398650 CTCCCTCTCGTCCCTCGC
1 CTCCCTCTCGTCCCTCTC
229398668 CTCCCTCTCGTCCCTCTC
1 CTCCCTCTCGTCCCTCTC
229398686 CTCCCTCTCG---CTCTC
1 CTCCCTCTCGTCCCTCTC
229398701 CTCCCTC
1 CTCCCTC
229398708 CGCCCTTTCC
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
15 12 0.17
17 16 0.23
18 43 0.61
ACGTcount: A:0.00, C:0.61, G:0.10, T:0.29
Consensus pattern (18 bp):
CTCCCTCTCGTCCCTCTC
Found at i:229399888 original size:18 final size:20
Alignment explanation
Indices: 229399856--229399894 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
229399846 CTTCGCCCTG
229399856 CTCTCTCTGCTCCCTGCCTC
1 CTCTCTCTGCTCCCTGCCTC
*
229399876 CTCTC-CTGC-CCCTGGCTC
1 CTCTCTCTGCTCCCTGCCTC
229399894 C
1 C
229399895 CCCTTTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.00, C:0.56, G:0.13, T:0.31
Consensus pattern (20 bp):
CTCTCTCTGCTCCCTGCCTC
Found at i:229401052 original size:18 final size:18
Alignment explanation
Indices: 229401031--229401077 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
229401021 GTGCGTTCGC
229401031 CCCCCGCGCCGCCCTTGG
1 CCCCCGCGCCGCCCTTGG
*
229401049 -CCCCGCGCCGTCCTTGG
1 CCCCCGCGCCGCCCTTGG
229401066 CCCCCGC-CCGCC
1 CCCCCGCGCCGCC
229401078 GTGCCTTCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.00, C:0.64, G:0.26, T:0.11
Consensus pattern (18 bp):
CCCCCGCGCCGCCCTTGG
Found at i:229402567 original size:16 final size:16
Alignment explanation
Indices: 229402530--229402589 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
229402520 CTCCCTTCCG
229402530 TCCCTTG-CTCCCCTCGC
1 TCCCTTGTCTCCCC-C-C
*
229402547 TCCC-TGTTTCCCCCCC
1 TCCCTTGTCT-CCCCCC
229402563 TCCCTTGTCTCCCCCC
1 TCCCTTGTCTCCCCCC
*
229402579 TCCCTTCTCTC
1 TCCCTTGTCTC
229402590 TCGCTCTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 23 0.62
17 10 0.27
18 4 0.11
ACGTcount: A:0.00, C:0.60, G:0.07, T:0.33
Consensus pattern (16 bp):
TCCCTTGTCTCCCCCC
Found at i:229403596 original size:20 final size:20
Alignment explanation
Indices: 229403568--229403609 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
229403558 GCCTTGCTGT
*
229403568 CCTTTCCTTGCTTCCTCCTC
1 CCTTGCCTTGCTTCCTCCTC
*
229403588 CCTTGCCTTGCTTTCTCCTC
1 CCTTGCCTTGCTTCCTCCTC
229403608 CC
1 CC
229403610 GCTTTCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.07, T:0.43
Consensus pattern (20 bp):
CCTTGCCTTGCTTCCTCCTC
Found at i:229407277 original size:40 final size:40
Alignment explanation
Indices: 229407184--229407362 Score: 192
Period size: 39 Copynumber: 4.6 Consensus size: 40
229407174 AAATTGAATG
* * ****
229407184 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGTGGCT
*
229407223 ATATCCGGGTTAAGACCCGAAGGCAATTATGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGTGGCT
* *
229407263 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGTGGCT
* *
229407303 A-ATCCGGGCTAAGACCCGAAGGC-ATTCGTGC--G-AG-T
1 ATATCCGGGCTAAGACCCGAAGGCAATT-ATGCTAGTGGCT
*
229407338 AAATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
229407363 TTTGTGCAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 2 0.02
36 23 0.18
37 1 0.01
38 3 0.02
39 55 0.44
40 42 0.33
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGTGGCT
Found at i:229407350 original size:36 final size:36
Alignment explanation
Indices: 229407225--229407369 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 36
229407215 CTGAAATTAT
* * * *
229407225 ATCCGGGTTAAGACCCGAAGGCAATTATGCTAGTGGCTAT
1 ATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGT-G--AA
* * *
229407265 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTA
1 ATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGT-G-AA
229407304 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGT-AA
1 ATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAA
229407340 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCA-TTGTGC
229407370 AAATCGTGAT
Statistics
Matches: 96, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
36 28 0.29
37 2 0.02
38 3 0.03
39 28 0.29
40 35 0.36
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (36 bp):
ATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAA
Found at i:229409587 original size:51 final size:51
Alignment explanation
Indices: 229409511--229409613 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
229409501 TACACGCGAG
*
229409511 AATGCATTTCGTCCGAAGCTATTATGTGTAAATGCTTCGAGGATGGGCTGA
1 AATGCATTTCGTCCGAAGCTATTATGTGTAAACGCTTCGAGGATGGGCTGA
229409562 AATGCATTTCGTCCGAAGCTATTATGTGTAAACGCTTCGAGGATGGGCTGA
1 AATGCATTTCGTCCGAAGCTATTATGTGTAAACGCTTCGAGGATGGGCTGA
229409613 A
1 A
229409614 TGATGATATA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (51 bp):
AATGCATTTCGTCCGAAGCTATTATGTGTAAACGCTTCGAGGATGGGCTGA
Found at i:229415417 original size:40 final size:39
Alignment explanation
Indices: 229415252--229415435 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
229415242 AAATTGAATG
* * *
229415252 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
229415292 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
229415332 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
229415372 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
229415411 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
229415436 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:229415460 original size:80 final size:81
Alignment explanation
Indices: 229415292--229415480 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
229415282 GCTGGAAATT
* * * *
229415292 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
229415357 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
229415373 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
229415436 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
229415452 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
229415481 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:229418169 original size:40 final size:40
Alignment explanation
Indices: 229418080--229418346 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
229418070 TGAATGATAC
* * * *
229418080 CCGGGCTAAGCCCCGAAGGCATTT-AGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
*
229418119 CCGGGATAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
229418159 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
229418199 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGCTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * *
229418239 CCGGGTTAAGACCCAAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
229418279 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATA-
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * *
229418318 CCGGGGTTAAGACCCAAAGGCAATTGTGC
1 CC-GGGCTAAGACCCGAAGGCATTTGTGC
229418347 TTGTGGTTAT
Statistics
Matches: 203, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 24 0.12
40 177 0.87
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:229418212 original size:80 final size:80
Alignment explanation
Indices: 229418113--229418366 Score: 413
Period size: 80 Copynumber: 3.2 Consensus size: 80
229418103 TAGCTAGTGA
* *
229418113 TTATATCCGGGATAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGTTAAGACCCGAAGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGTTAAGACCCAAAGG
229418178 CATTTGTGCGAGTTG
66 CATTTGTGCGAGTTG
*
229418193 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGCTGCTATATCCGGGTTAAGACCCAAAGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGTTAAGACCCAAAGG
229418258 CATTTGTGCGAGTTG
66 CATTTGTGCGAGTTG
*
229418273 TTATATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATA-CCGGGGTTAAGACCCAAAG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC-GGGTTAAGACCCAAAG
* ** *
229418337 GCAATTGTGCTTGTGG
65 GCATTTGTGCGAGTTG
229418353 TTATATCC-GGCTAA
1 TTATATCCGGGCTAA
229418367 ATTCTGAAGA
Statistics
Matches: 164, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
79 8 0.05
80 156 0.95
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (80 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGTTAAGACCCAAAGG
CATTTGTGCGAGTTG
Found at i:229420150 original size:46 final size:46
Alignment explanation
Indices: 229420083--229420244 Score: 197
Period size: 46 Copynumber: 3.5 Consensus size: 46
229420073 TGTAACCCGC
*
229420083 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
229420129 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
229420179 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
229420222 CCATAAGTGAACTCGGACTCAAC
1 CCATAAGTGAACTCGGACTCAAC
229420245 GAGTTCGGAT
Statistics
Matches: 98, Mismatches: 9, Indels: 18
0.78 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 50 0.51
47 28 0.29
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:229422670 original size:30 final size:30
Alignment explanation
Indices: 229422626--229422714 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
229422616 CAAAGATAAC
229422626 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
229422655 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
229422685 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
229422715 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:229422674 original size:15 final size:15
Alignment explanation
Indices: 229422626--229422705 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
229422616 CAAAGATAAC
*
229422626 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
229422640 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
229422655 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
229422670 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
229422685 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
229422700 AAGAAA
1 AAGAAA
229422706 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:229422714 original size:15 final size:15
Alignment explanation
Indices: 229422637--229422714 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
229422627 AGAAAACCGA
229422637 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
229422652 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
229422666 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
229422681 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
229422697 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
229422712 ATA
1 ATA
229422715 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:229425770 original size:93 final size:93
Alignment explanation
Indices: 229425658--229425829 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
229425648 GCCCATAAGT
* *
229425658 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
229425723 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
229425751 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
229425816 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
229425830 AACCATCCTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:229425825 original size:46 final size:46
Alignment explanation
Indices: 229425650--229425825 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
229425640 TGTAACCCGC
* * *
229425650 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
229425696 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
229425746 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
229425789 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
229425826 TGCCAACCAT
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:229429482 original size:29 final size:29
Alignment explanation
Indices: 229429448--229429522 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
229429438 TACTCGATTT
*
229429448 CGCACACTTAGTGCCATGCGATTTAG-GCC
1 CGCACACTTAGTGCCATGC-ACTTAGAGCC
** * * *
229429477 CGCACACACAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCACTTAGAGCC
229429506 CGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
229429523 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 3 0.08
29 34 0.92
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTAGAGCC
Found at i:229437330 original size:29 final size:29
Alignment explanation
Indices: 229437296--229437370 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
229437286 TACTCGATTT
*
229437296 CGCACACTTAGTGCCATGCGATTTAG-GCC
1 CGCACACTTAGTGCCATGC-ACTTAGAGCC
** * * *
229437325 CGCACACACAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCACTTAGAGCC
229437354 CGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
229437371 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 3 0.08
29 34 0.92
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTAGAGCC
Found at i:229442810 original size:40 final size:40
Alignment explanation
Indices: 229442716--229442900 Score: 182
Period size: 40 Copynumber: 4.6 Consensus size: 40
229442706 TATTCGAATG
* *
229442716 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTCGTGCTA-GTGACT
* * *
229442757 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTCGTGCTAG-TGACT
* *
229442797 ATATCCGGGCTAAGA-CTCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATC-CGAAGGCATTCGTGCTAGTGACT
* *
229442837 ATATCCGGGCTAAG-TCCCGAAGGCA-TCTGTTCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTC-GTGCTAGTGACT
* *
229442877 ATATCTGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
229442901 CTTGTGCAAG
Statistics
Matches: 120, Mismatches: 16, Indels: 17
0.78 0.10 0.11
Matches are distributed among these distances:
39 3 0.03
40 86 0.72
41 30 0.25
42 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTCGTGCTAGTGACT
Found at i:229442887 original size:80 final size:81
Alignment explanation
Indices: 229442716--229442900 Score: 225
Period size: 80 Copynumber: 2.3 Consensus size: 81
229442706 TATTCGAATG
* * *
229442716 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
*
229442781 ATTCGTGCGAGTTGCT
66 ATTCGTGCGAGTTGCC
* * *
229442797 ATATCCGGGCTAAGACTCGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTAAG-TCCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGAT-CCGAAGG
* *
229442860 CA-TCTGTTCTAG-TGACC
65 CATTC-GTGCGAGTTG-CC
*
229442877 ATATCTGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
229442901 CTTGTGCAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
79 5 0.06
80 54 0.60
81 31 0.34
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (81 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCGTGCGAGTTGCC
Found at i:229451475 original size:38 final size:38
Alignment explanation
Indices: 229451428--229451567 Score: 196
Period size: 38 Copynumber: 3.7 Consensus size: 38
229451418 GCTACTCGCT
*
229451428 CGAATGCCTTCGGGACATAGCCCGGATATAGTAACTCA
1 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCA
229451466 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCA
1 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCA
* *
229451504 CAAATGCCTTCGGGACTTAGCCC-GA-ACTAGTCACT-A
1 CGAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCA
229451540 GCGCAAATGCCTTCGGGACTTAGCCCGG
1 -CG--AATGCCTTCGGGACTTAGCCCGG
229451568 TTATCATCCA
Statistics
Matches: 93, Mismatches: 4, Indels: 8
0.89 0.04 0.08
Matches are distributed among these distances:
36 2 0.02
37 10 0.11
38 59 0.63
39 21 0.23
40 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (38 bp):
CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCA
Found at i:229458617 original size:29 final size:29
Alignment explanation
Indices: 229458581--229458743 Score: 202
Period size: 29 Copynumber: 5.6 Consensus size: 29
229458571 AATAAACGAT
***
229458581 CTCGCACACTTAGTGCCATGCGATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
*
229458610 CTCGCACACATAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
* *
229458639 TTTGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
*
229458668 TTCGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
* ** *
229458697 TTCGCACACTTAGTGCCATA-CCTTCCAAG
1 CTCGCACACTTAGTGCCATATAATT-TAAG
*
229458726 CCCGCACACTTAGTGCCA
1 CTCGCACACTTAGTGCCA
229458744 ATCTTGTCAC
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
28 2 0.02
29 118 0.98
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CTCGCACACTTAGTGCCATATAATTTAAG
Found at i:229464167 original size:17 final size:17
Alignment explanation
Indices: 229464145--229464180 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
229464135 TCCTTGGAAT
229464145 AAGCAATCATTTTCGTC
1 AAGCAATCATTTTCGTC
229464162 AAGCAATCATTTTCGTC
1 AAGCAATCATTTTCGTC
229464179 AA
1 AA
229464181 TCTGAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (17 bp):
AAGCAATCATTTTCGTC
Found at i:229469088 original size:29 final size:29
Alignment explanation
Indices: 229469052--229469214 Score: 202
Period size: 29 Copynumber: 5.6 Consensus size: 29
229469042 AATAAACGAT
***
229469052 CTCGCACACTTAGTGCCATGCGATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
*
229469081 CTCGCACACATAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
* *
229469110 TTTGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
*
229469139 TTCGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
* ** *
229469168 TTCGCACACTTAGTGCCATA-CCTTCCAAG
1 CTCGCACACTTAGTGCCATATAATT-TAAG
*
229469197 CCCGCACACTTAGTGCCA
1 CTCGCACACTTAGTGCCA
229469215 ATCTTGTCAC
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
28 2 0.02
29 118 0.98
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CTCGCACACTTAGTGCCATATAATTTAAG
Found at i:229474285 original size:25 final size:26
Alignment explanation
Indices: 229474248--229474299 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
229474238 TCAAACATGC
229474248 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
229474274 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
229474299 A
1 A
229474300 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:229475768 original size:26 final size:25
Alignment explanation
Indices: 229475732--229475859 Score: 178
Period size: 26 Copynumber: 5.2 Consensus size: 25
229475722 CATGAAATTC
229475732 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCCA
229475758 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCCA
229475784 TTATCATGGAACATTTACCTAA-CCA
1 TTATCAT-GAACATTTACCTAACCCA
229475809 TTATCATGAACATTTACCTAA-CC-
1 TTATCATGAACATTTACCTAACCCA
*
229475832 TTATCAT--A-ATTTACCTAACCTA
1 TTATCATGAACATTTACCTAACCCA
229475854 TTATCA
1 TTATCA
229475860 ATTTGTACCA
Statistics
Matches: 98, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
20 10 0.10
21 2 0.02
22 6 0.06
23 7 0.07
24 16 0.16
25 10 0.10
26 46 0.47
27 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCCA
Found at i:229475868 original size:22 final size:20
Alignment explanation
Indices: 229475796--229475852 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 20
229475786 ATCATGGAAC
229475796 ATTTACCTAACCATTATCATGAA
1 ATTTACCTAACC-TTATCAT--A
229475819 CATTTACCTAACCTTATCATA
1 -ATTTACCTAACCTTATCATA
229475840 ATTTACCTAACCT
1 ATTTACCTAACCT
229475853 ATTATCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.39
21 1 0.03
23 7 0.21
24 12 0.36
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (20 bp):
ATTTACCTAACCTTATCATA
Found at i:229481532 original size:25 final size:25
Alignment explanation
Indices: 229481474--229481606 Score: 225
Period size: 25 Copynumber: 5.3 Consensus size: 25
229481464 ACATGAAATT
229481474 ATTATCATGAAACATTTACCTAACCC
1 ATTATCATGAAACATTTACCTAA-CC
229481500 ATTATCATGAAACATTTACCTAACC
1 ATTATCATGAAACATTTACCTAACC
229481525 ATTATCATG-AACATTTACCTAACCC
1 ATTATCATGAAACATTTACCTAA-CC
229481550 ATTATCATG-AACATTTACCTAACC
1 ATTATCATGAAACATTTACCTAACC
229481574 ATTATCATGAAACATTTACCTAACC
1 ATTATCATGAAACATTTACCTAACC
229481599 TATTATCA
1 -ATTATCA
229481607 ATTTGTACCA
Statistics
Matches: 104, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
24 24 0.23
25 50 0.48
26 30 0.29
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (25 bp):
ATTATCATGAAACATTTACCTAACC
Found at i:229482454 original size:33 final size:33
Alignment explanation
Indices: 229482412--229482478 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
229482402 TTTGGATGAC
*
229482412 CCAGCGGAAATAGCCAGGTTGAGAACAGACGAT
1 CCAGCGGAAATAGCCAGGTCGAGAACAGACGAT
229482445 CCAGCGGAAATAGCCAGGTCGAGAACAGACGAT
1 CCAGCGGAAATAGCCAGGTCGAGAACAGACGAT
229482478 C
1 C
229482479 ATGAGGCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.30, T:0.10
Consensus pattern (33 bp):
CCAGCGGAAATAGCCAGGTCGAGAACAGACGAT
Found at i:229489977 original size:14 final size:14
Alignment explanation
Indices: 229489958--229489986 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
229489948 CGCTGAGGTA
229489958 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
229489972 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
229489986 T
1 T
229489987 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:229490167 original size:72 final size:72
Alignment explanation
Indices: 229489973--229490319 Score: 436
Period size: 72 Copynumber: 4.7 Consensus size: 72
229489963 AATTTCTGTT
*
229489973 TTTCAATTTCTGTTCGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-A-ACACGT
1 TTTCAATTTCTGTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGT
229490035 TGAGGTAA
65 TGAGGTAA
229490043 TTTCAATTTCT-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
229490107 GAGGTAA
66 GAGGTAA
* * **
229490114 TTTCAATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
*
229490179 GAGGTAT
66 GAGGTAA
* *
229490186 TTTCAATTTCTGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACA
1 TTTCAATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACA
* *
229490250 TGCTGAGGT-A
62 CGTTGAGGTAA
*
229490260 TTCTCAATTTCTGTCTTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGC
1 TT-TCAATTTCTGT-TTTC------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
229490320 TTCAGATCAC
Statistics
Matches: 246, Mismatches: 16, Indels: 19
0.88 0.06 0.07
Matches are distributed among these distances:
68 2 0.01
69 39 0.16
70 12 0.05
71 25 0.10
72 73 0.30
73 34 0.14
74 2 0.01
75 21 0.09
76 4 0.02
81 34 0.14
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (72 bp):
TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTT
GAGGTAA
Found at i:229490717 original size:44 final size:45
Alignment explanation
Indices: 229490634--229490732 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 45
229490624 TGAAGCTGTT
* *
229490634 AATCTTATAT-TTCTGAAGTCACAGTAAAGCAGATCGAAGCTACA
1 AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
* * ** *
229490678 AATCTTATATCCT-TGAAGTTACATTAAAGTGGATTGAAGCCACA
1 AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
* *
229490722 AAGCATATATC
1 AATCTTATATC
229490733 AGAAGATGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (45 bp):
AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
Found at i:229491480 original size:12 final size:12
Alignment explanation
Indices: 229491463--229491503 Score: 73
Period size: 12 Copynumber: 3.3 Consensus size: 12
229491453 TTAAAACATA
229491463 AAAAAAATATAC
1 AAAAAAATATAC
229491475 AAAAAAGATATAC
1 AAAAAA-ATATAC
229491488 AAAAAAATATAC
1 AAAAAAATATAC
229491500 AAAA
1 AAAA
229491504 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 16 0.57
13 12 0.43
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (12 bp):
AAAAAAATATAC
Found at i:229491480 original size:13 final size:13
Alignment explanation
Indices: 229491462--229491503 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
229491452 ATTAAAACAT
229491462 AAAAAAAATATAC
1 AAAAAAAATATAC
*
229491475 AAAAAAGATATAC
1 AAAAAAAATATAC
229491488 -AAAAAAATATAC
1 AAAAAAAATATAC
229491500 AAAA
1 AAAA
229491504 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (13 bp):
AAAAAAAATATAC
Found at i:229492112 original size:3 final size:3
Alignment explanation
Indices: 229492104--229492146 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
229492094 TGCATTTCAA
229492104 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
229492147 GAAATACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:229492255 original size:3 final size:3
Alignment explanation
Indices: 229492247--229492291 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
229492237 TGTGTTTCAA
229492247 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
229492292 ATATCCTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:229492565 original size:33 final size:30
Alignment explanation
Indices: 229492507--229492579 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 30
229492497 TAATATTATG
*
229492507 TATATATTTTAATATTATCAGTTATATATA
1 TATATATTTTAATACTATCAGTTATATATA
* *
229492537 CTATATGATTTCTAATACTATTATTTATATATA
1 -TATAT-ATTT-TAATACTATCAGTTATATATA
229492570 TATATATTTT
1 TATATATTTT
229492580 CTTAGTACCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 9 0.24
32 9 0.24
33 18 0.49
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (30 bp):
TATATATTTTAATACTATCAGTTATATATA
Found at i:229496820 original size:40 final size:39
Alignment explanation
Indices: 229496776--229497034 Score: 342
Period size: 39 Copynumber: 6.6 Consensus size: 39
229496766 AGTGGCTAAT
229496776 TCCGGGCTAAGTCCAGAAGGCATTCGTGCGAGCTACTATA
1 TCCGGGCTAAGTCC-GAAGGCATTCGTGCGAGCTACTATA
*
229496816 TCCGGGCTAAGTCCCAAGGCATTCGTGCGAGCTACTATA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGCTACTATA
* * *
229496855 TCTGGGCAAAGTCCGAAGGCGTTCGTGCGAGCTACTATA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGCTACTATA
*
229496894 TCCGGGCTAAGTCCCGAAGGCGTTCGTGCGAGCTACTATA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGCTACTATA
* * * *
229496934 TCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATTATA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGCTACTATA
* * * *
229496974 -CCGGGCTAAGTCCGAAGGCATTTGTGCAAGTTACCATA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGCTACTATA
*
229497012 ACCGGGCTAAGTCCCG-AGGCATT
1 TCCGGGCTAAGT-CCGAAGGCATT
229497035 TGAGCTAGTG
Statistics
Matches: 202, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
38 23 0.11
39 98 0.49
40 81 0.40
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGCTACTATA
Found at i:229496985 original size:118 final size:118
Alignment explanation
Indices: 229496776--229497034 Score: 369
Period size: 118 Copynumber: 2.2 Consensus size: 118
229496766 AGTGGCTAAT
*
229496776 TCCGGGCTAAGTCCAGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCAAGGCATTCG
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCAAGGCATTCG
* * * *
229496841 TGCGAGCTACTATATCTGGGCAAAGTCCGAAGGCGTTCGTGCGAGCTACTATA
66 TGCGAGCTACTATATCCGGGCAAAGTCCGAAGGCATTCGTGCAAGCTACCATA
* * *
229496894 TCCGGGCTAAGTCCCGAAGGCGTTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCC-AAGGCATTC
* * * * *
229496959 GTGCGAGTTATTATA-CCGGGCTAAGTCCGAAGGCATTTGTGCAAGTTACCATA
65 GTGCGAGCTACTATATCCGGGCAAAGTCCGAAGGCATTCGTGCAAGCTACCATA
*
229497012 ACCGGGCTAAGTCCCG-AGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
229497035 TGAGCTAGTG
Statistics
Matches: 125, Mismatches: 15, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
117 6 0.05
118 99 0.79
119 20 0.16
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.24
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCAAGGCATTCG
TGCGAGCTACTATATCCGGGCAAAGTCCGAAGGCATTCGTGCAAGCTACCATA
Found at i:229497067 original size:78 final size:80
Alignment explanation
Indices: 229496777--229497069 Score: 251
Period size: 78 Copynumber: 3.7 Consensus size: 80
229496767 GTGGCTAATT
* * * **
229496777 CCGGGCTAAGTCCAGAAGGCATTCGTGCGAGCT-ACTATATCCGGGCTAAGTCCC-AAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TGACTATATCCGGGCTAAACCCCGAAGGCATTC
* * *
229496840 GTGCGAGCTACTATAT
65 GTGCAAGCTACCATAA
* * * * * ** *
229496856 CTGGGCAAAGT-CCGAAGGCGTTCGTGCGAGCT-ACTATATCCGGGCTAAGTCCCGAAGGCGTTC
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TGACTATATCCGGGCTAAACCCCGAAGGCATTC
* * *
229496919 GTGCGAGCTACTATAT
65 GTGCAAGCTACCATAA
* * * * ** *
229496935 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATTATA-CCGGGCT-AAGTCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATATCCGGGCTAAACCCCGAAGGCATTCG
*
229496998 TGCAAGTTACCATAA
66 TGCAAGCTACCATAA
* *
229497013 CCGGGCTAAGTCCCG-AGGCATTTGAGCTAGTGGCTATATCC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATATCCGGGCTAAACCCCGAAGG
229497070 TACTTGGTTT
Statistics
Matches: 183, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
77 21 0.11
78 89 0.49
79 50 0.27
80 23 0.13
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATATCCGGGCTAAACCCCGAAGGCATTCG
TGCAAGCTACCATAA
Found at i:229501766 original size:66 final size:68
Alignment explanation
Indices: 229501690--229501876 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
229501680 TAGTACCACT
*
229501690 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
229501752 CACG
65 CACG
229501756 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
229501821 ATCACG
63 ATCACG
229501827 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
229501877 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:229501801 original size:71 final size:71
Alignment explanation
Indices: 229501713--229501876 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
229501703 CGATTTGTCT
229501713 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
229501778 CTTTCA
66 CTTTCA
229501784 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
229501849 CTTTCA
66 CTTTCA
229501855 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
229501877 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:229501914 original size:71 final size:70
Alignment explanation
Indices: 229501713--229501910 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
229501703 CGATTTGTCT
* * *
229501713 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
229501778 CTTTCA
65 CTTTCA
* * *
229501784 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
229501849 CTTTCA
65 CTTTCA
* *
229501855 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
229501911 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:229509331 original size:66 final size:68
Alignment explanation
Indices: 229509255--229509441 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
229509245 TAGTACCACT
*
229509255 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
229509317 CACG
65 CACG
229509321 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
229509386 ATCACG
63 ATCACG
229509392 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
229509442 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:229509366 original size:71 final size:71
Alignment explanation
Indices: 229509278--229509441 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
229509268 CGATTTGTCT
229509278 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
229509343 CTTTCA
66 CTTTCA
229509349 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
229509414 CTTTCA
66 CTTTCA
229509420 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
229509442 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:229509479 original size:71 final size:70
Alignment explanation
Indices: 229509278--229509475 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
229509268 CGATTTGTCT
* * *
229509278 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
229509343 CTTTCA
65 CTTTCA
* * *
229509349 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
229509414 CTTTCA
65 CTTTCA
* *
229509420 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
229509476 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:229515358 original size:40 final size:39
Alignment explanation
Indices: 229515293--229515498 Score: 244
Period size: 40 Copynumber: 5.6 Consensus size: 39
229515283 AGTGGCTAAT
229515293 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGCTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTA-TATA
229515332 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTA-TATA
* *
229515372 TCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAG-TATATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTATATA
229515410 TCCGGGCTAAGTCCCGAAGGC-TT-GT----GCTATAT-
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTATATA
* *
229515442 T---GGCTAAGTCCCGAAGGC-TTTGTGC-AGTTA-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTATATA
*
229515475 ACCGGGCTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
229515499 TGAGCTAGTG
Statistics
Matches: 152, Mismatches: 4, Indels: 24
0.84 0.02 0.13
Matches are distributed among these distances:
29 19 0.12
30 2 0.01
32 4 0.03
33 8 0.05
36 19 0.12
37 4 0.03
38 25 0.16
39 14 0.09
40 57 0.38
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTATATA
Found at i:229515427 original size:78 final size:70
Alignment explanation
Indices: 229515367--229515498 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 70
229515357 GTGCGAGCTA
229515367 CTATA-TCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTATATATCCGGGCTAAGTCCCGAAGGC
1 CTATATTCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTATATATCCGGGCTAAGTCCCGAAGGC
229515431 -TTGTG
65 ATTGTG
*
229515436 CTATATT---GGCTAAGTCCCGAAGGCTTTGTGC-AGT-TAATAACCGGGCTAAGTCCCGAAGGC
1 CTATATTCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTAT-ATATCCGGGCTAAGTCCCGAAGGC
229515496 ATT
65 ATT
229515499 TGAGCTAGTG
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
64 1 0.02
65 26 0.44
66 9 0.15
67 17 0.29
69 5 0.08
70 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (70 bp):
CTATATTCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTATATATCCGGGCTAAGTCCCGAAGGCA
TTGTG
Found at i:229515511 original size:65 final size:66
Alignment explanation
Indices: 229515376--229515512 Score: 183
Period size: 65 Copynumber: 2.1 Consensus size: 66
229515366 ACTATATCCG
* *
229515376 GGCTAAGTCCCGAAGGCGTTTGTGCGAGTATATATCCGGGCTAAGTCCCGAAGGCTTGTGCTATA
1 GGCTAAGTCCCGAAGGCGTTTGTGCGAGTATATAACCGGGCTAAGTCCCGAAGGCTTGAGC-ATA
*
229515441 TT
65 GT
229515443 GGCTAAGTCCCGAAGGC-TTTGTGC-AGT-TAATAACCGGGCTAAGTCCCGAAGGCATTTGAGC-
1 GGCTAAGTCCCGAAGGCGTTTGTGCGAGTAT-ATAACCGGGCTAAGTCCCGAAGGC--TTGAGCA
229515504 TAGT
63 TAGT
229515508 GGCTA
1 GGCTA
229515513 TATCCGGCTA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
64 1 0.02
65 34 0.53
66 7 0.11
67 22 0.34
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (66 bp):
GGCTAAGTCCCGAAGGCGTTTGTGCGAGTATATAACCGGGCTAAGTCCCGAAGGCTTGAGCATAG
T
Found at i:229519024 original size:42 final size:42
Alignment explanation
Indices: 229518929--229519009 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
229518919 AAACATGGCC
229518929 ACACAACACGCCCATGGGGCTGACCATGTGTCACACACGACA
1 ACACAACACGCCCATGGGGCTGACCATGTGTCACACACGACA
*
229518971 ACACAACACGCCCATGGGGCTGACCGTGTGTCACACACG
1 ACACAACACGCCCATGGGGCTGACCATGTGTCACACACG
229519010 GCCTAGACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.36, G:0.23, T:0.12
Consensus pattern (42 bp):
ACACAACACGCCCATGGGGCTGACCATGTGTCACACACGACA
Found at i:229519977 original size:95 final size:96
Alignment explanation
Indices: 229519812--229520033 Score: 239
Period size: 95 Copynumber: 2.3 Consensus size: 96
229519802 AAATGCCAAC
* *
229519812 GCCATGTCCCAGACATGGTCTTACACT-AGCTAGCACATCAAAGTCGATGCCATGTCCCAGATAG
1 GCCATGTCCCAGACA-GGTCTTACACTGAGCTAGCACATAAAAGTCGATGCCATGTCCCAGATAA
* *
229519876 GTCTTACAC-AGGCTATGATCTAT-CG-GTGTCGAT
65 GTCTTACACTA-GCT-TG-TATATCCGAG-GCCGAT
* *
229519909 GCCATGTCCCAGACAGGTCTTACACTGA-C-A-CACTTAACAAG-CTGTTGCCATGTCCCAGATA
1 GCCATGTCCCAGACAGGTCTTACACTGAGCTAGCACATAA-AAGTC-GATGCCATGTCCCAGATA
229519970 AGTCTTACACTAGCTTGTATATCCCGAGGCCGAT
64 AGTCTTACACTAGCTTGTATAT-CCGAGGCCGAT
*
229520004 G-CATGTCCCAGACATGTCTTACACTG-GCTA
1 GCCATGTCCCAGACAGGTCTTACACTGAGCTA
229520034 TCATAATATG
Statistics
Matches: 109, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
93 4 0.04
94 33 0.30
95 42 0.39
96 14 0.13
97 16 0.15
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (96 bp):
GCCATGTCCCAGACAGGTCTTACACTGAGCTAGCACATAAAAGTCGATGCCATGTCCCAGATAAG
TCTTACACTAGCTTGTATATCCGAGGCCGAT
Found at i:229522563 original size:40 final size:40
Alignment explanation
Indices: 229522455--229522664 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
229522445 CGGGATTTAA
* * * * *
229522455 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
229522495 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
229522535 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
229522575 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
229522615 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
229522655 CCGGATATAT
1 CCGGATATAT
229522665 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:229530698 original size:40 final size:40
Alignment explanation
Indices: 229530590--229530799 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
229530580 CGGGATTTAA
* * * * *
229530590 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
229530630 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
229530670 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
229530710 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
229530750 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
229530790 CCGGATATAT
1 CCGGATATAT
229530800 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:229533205 original size:40 final size:40
Alignment explanation
Indices: 229533146--229533353 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
229533136 CAATTGAATG
* * * *
229533146 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
229533186 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
229533226 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
229533266 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
229533306 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
229533346 ATATCCGG
1 ATATCCGG
229533354 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:229533284 original size:80 final size:80
Alignment explanation
Indices: 229533147--229533353 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
229533137 AATTGAATGA
* * ** * * *
229533147 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
229533212 TTGTGCTAGT-G-AC
66 TTGTGCAAGTCGTAC
* * *
229533225 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
229533290 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
229533307 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
229533354 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 105 0.96
81 1 0.01
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:229537803 original size:47 final size:47
Alignment explanation
Indices: 229537752--229538229 Score: 678
Period size: 47 Copynumber: 10.1 Consensus size: 47
229537742 TTAGGATTTT
*
229537752 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
229537799 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
229537846 ATGTGATG-ATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
229537892 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
229537943 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
229537990 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C-----ATGCGTATGTGTGATAAGGCCGAATGGCCA
229538043 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
229538090 ATGTAATG-A--TGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
229538134 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** * * *
229538181 ATGTGATGAATGTGAACATGAATATATGTGGTAA-GCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
229538227 ATG
1 ATG
229538230 CGAAACGTGT
Statistics
Matches: 393, Mismatches: 24, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
44 42 0.11
45 1 0.00
46 61 0.16
47 200 0.51
48 1 0.00
49 2 0.01
51 43 0.11
52 1 0.00
53 42 0.11
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:229537943 original size:144 final size:143
Alignment explanation
Indices: 229537774--229538229 Score: 653
Period size: 144 Copynumber: 3.2 Consensus size: 143
229537764 TGAACATGCG
229537774 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
1 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
*
229537839 ATGGCCAATGTGATG-ATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
66 ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
229537903 GTGAACCCGTATATA
131 GTGAA-CCG-ATATA
229537918 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
1 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
** *
229537983 ATGGCCAATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCAATGTG
66 ATGGCCAATGTGATGAATGTGAA-C-----ATGCATATGTGTGATAAGGCCGAATGGCCAATGTG
***
229538048 ATGAATGTGAA-C-ATGCG
125 ATGAATGTGAACCGATATA
*
229538065 TATGTGTGATAAGGCCGAATGGCCAATGTAATG-A--TGAACATGCGTATGTGTGATAAGGCCGA
1 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
* *
229538127 ATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAAT
66 ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
*
229538192 GTGAACATGA-ATA
131 GTGAAC-CGATATA
*
229538205 TATGTG-G-TAA-GCCGAATGGCTAATG
1 TATGTGTGATAAGGCCGAATGGCCAATG
229538230 CGAAACGTGT
Statistics
Matches: 284, Mismatches: 18, Indels: 27
0.86 0.05 0.08
Matches are distributed among these distances:
137 14 0.05
138 44 0.15
139 1 0.00
140 6 0.02
141 1 0.00
143 1 0.00
144 131 0.46
145 7 0.02
146 2 0.01
147 34 0.12
149 1 0.00
151 42 0.15
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (143 bp):
TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
GTGAACCGATATA
Found at i:229537947 original size:24 final size:24
Alignment explanation
Indices: 229537919--229537994 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
229537909 CCGTATATAT
229537919 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
229537943 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
229537966 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
229537990 ATGTG
1 ATGTG
229537995 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:229538115 original size:191 final size:193
Alignment explanation
Indices: 229537752--229538207 Score: 680
Period size: 191 Copynumber: 2.4 Consensus size: 193
229537742 TTAGGATTTT
*
229537752 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*** *
229537816 ----ATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGATGTGAACATGCGTATGTGTGAT
66 TGATATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGATGTGAACATGCGTATGTGTGAT
* *
229537877 AAGGCCGAATGGCCAATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCC
131 AAGGCCGAATGGCCAATGTAATGAA-GTGAA-CCG-ATACATATGTGTGATAAGGCCGAATGGCC
229537942 A
193 A
229537943 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
229538008 TGTATATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTG
66 TG-ATATATATATGCGTGATAAGGCCGAATGGCCAATGTGATG-ATGTGAACATGCGTATGTGTG
* *
229538073 ATAAGGCCGAATGGCCAATGTAATG-A-TGAA-C-ATGCGTATGTGTGATAAGGCCGAATGGCCA
129 ATAAGGCCGAATGGCCAATGTAATGAAGTGAACCGATACATATGTGTGATAAGGCCGAATGGCCA
* * * *
229538134 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
229538199 TGA-ATATAT
66 TGATATATAT
229538208 GTGGTAAGCC
Statistics
Matches: 245, Mismatches: 13, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
189 6 0.02
190 1 0.00
191 152 0.62
192 1 0.00
193 1 0.00
195 4 0.02
197 35 0.14
198 45 0.18
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.26
Consensus pattern (193 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
TGATATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGATGTGAACATGCGTATGTGTGAT
AAGGCCGAATGGCCAATGTAATGAAGTGAACCGATACATATGTGTGATAAGGCCGAATGGCCA
Found at i:229538124 original size:91 final size:93
Alignment explanation
Indices: 229537752--229538229 Score: 552
Period size: 100 Copynumber: 5.0 Consensus size: 93
229537742 TTAGGATTTT
* * * * *
229537752 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTAATGAA-GTGAACA
**
229537817 TGCGTATGTGTGATAAGGCCGAATGGCCA
65 TGAATATGTGTGATAAGGCCGAATGGCCA
* * * *
229537846 ATGTGATG-ATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTAATGAA-GTGAA--
229537910 CGTAT-ATATATGTGTGATAAGGCCGAATGGCCA
63 C--ATGA-ATATGTGTGATAAGGCCGAATGGCCA
* * * *
229537943 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTAATGAA-GTGAA-C
* *
229538008 TGTATATATATATGCGTGATAAGGCCGAATGGCCA
64 ---AT-GA-ATATGTGTGATAAGGCCGAATGGCCA
* * *
229538043 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTAATG-A-TGAACAT
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTAATGAAGTGAACAT
**
229538106 GCGTATGTGTGATAAGGCCGAATGGCCA
66 GAATATGTGTGATAAGGCCGAATGGCCA
*
229538134 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTAATGAA-GTGAACA
* * *
229538199 TGAATATATGTGGTAA-GCCGAATGGCTA
65 TGAATATGTGTGATAAGGCCGAATGGCCA
229538227 ATG
1 ATG
229538230 CGAAACGTGT
Statistics
Matches: 355, Mismatches: 17, Indels: 25
0.89 0.04 0.06
Matches are distributed among these distances:
91 75 0.21
92 1 0.00
93 70 0.20
94 26 0.07
95 1 0.00
96 1 0.00
97 41 0.12
98 58 0.16
99 1 0.00
100 81 0.23
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (93 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTAATGAAGTGAACAT
GAATATGTGTGATAAGGCCGAATGGCCA
Found at i:229538263 original size:46 final size:45
Alignment explanation
Indices: 229538204--229538293 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
229538194 GAACATGAAT
* *
229538204 ATATGTGGTAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
229538249 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGT-AAGCCAAATGGCTAATGCGAAACATGTATGAGATG
229538294 TGTAATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 9 0.23
46 30 0.77
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (45 bp):
ATATGTGGTAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:229538533 original size:36 final size:37
Alignment explanation
Indices: 229538437--229538617 Score: 303
Period size: 37 Copynumber: 4.9 Consensus size: 37
229538427 GGAAATATAT
*
229538437 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
229538474 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
229538511 TCCGGGTAAGA-CCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
229538547 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
229538584 T-CGGGTAAGACCCGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
229538618 CGTCTGAGCT
Statistics
Matches: 137, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
36 65 0.47
37 72 0.53
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:229538557 original size:73 final size:74
Alignment explanation
Indices: 229538437--229538616 Score: 319
Period size: 73 Copynumber: 2.5 Consensus size: 74
229538427 GGAAATATAT
229538437 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACGTGTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACGTGTG
229538502 GAGATTTTG
66 GAGATTTTG
229538511 TCCGGGTAAGA-CCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACGTGTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACGTGTG
229538575 GAGATTTTG
66 GAGATTTTG
* * *
229538584 T-CGGGTAAGACCCGATAACTTCATGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
229538617 TCGTCTGAGC
Statistics
Matches: 102, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
72 9 0.09
73 82 0.80
74 11 0.11
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (74 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACGTGTG
GAGATTTTG
Found at i:229544235 original size:46 final size:47
Alignment explanation
Indices: 229544134--229544251 Score: 148
Period size: 46 Copynumber: 2.5 Consensus size: 47
229544124 CTTCGACATA
** * *
229544134 GACTTACATGAATTATTCCTGTCCCCAATGCCATATATATATAATATG
1 GACTTACATGGCTCATTCCTGTCCCCAAAGCCA-ATATATATAATATG
* * *
229544182 GGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTAATATG
1 GACTTACATGGCTCATTCCTGTCCCCAAAGCCAATATATATAATATG
*
229544228 GACTTACATGGCTCATTTCTGTCC
1 GACTTACATGGCTCATTCCTGTCC
229544252 TGTCCTGTCC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 34 0.57
48 26 0.43
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (47 bp):
GACTTACATGGCTCATTCCTGTCCCCAAAGCCAATATATATAATATG
Found at i:229547959 original size:18 final size:19
Alignment explanation
Indices: 229547936--229547976 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
229547926 TTGTAAAGTG
229547936 AATTTTGG-TAAAAATGTC
1 AATTTTGGATAAAAATGTC
* *
229547954 AATTTTGGATTAAAATGTG
1 AATTTTGGATAAAAATGTC
229547973 AATT
1 AATT
229547977 ATTGAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.41
Consensus pattern (19 bp):
AATTTTGGATAAAAATGTC
Found at i:229548619 original size:28 final size:28
Alignment explanation
Indices: 229548583--229548657 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
229548573 TCAAATATGG
* *
229548583 CACTCAGTGTATGAAATATTGAGAATGA
1 CACTTAGTGTACGAAATATTGAGAATGA
* *
229548611 CACTTAGTGTGCGAGATATTGAGAATGA
1 CACTTAGTGTACGAAATATTGAGAATGA
* *
229548639 CACTTAGTGTGCAAAATAT
1 CACTTAGTGTACGAAATAT
229548658 CGAATGATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (28 bp):
CACTTAGTGTACGAAATATTGAGAATGA
Found at i:229552214 original size:30 final size:30
Alignment explanation
Indices: 229552159--229552289 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
229552149 ATAGTGAATC
*
229552159 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
229552188 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
229552218 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
229552246 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
229552276 CGCACACTTAGTGC
1 CGCACACTTAGTGC
229552290 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:229552269 original size:58 final size:58
Alignment explanation
Indices: 229552158--229552289 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
229552148 TATAGTGAAT
* * * * *
229552158 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
229552217 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
229552275 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
229552290 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:229560143 original size:29 final size:29
Alignment explanation
Indices: 229560111--229560240 Score: 156
Period size: 29 Copynumber: 4.5 Consensus size: 29
229560101 ATAGTGAATC
*
229560111 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
* *
229560140 CGCACACTTAGTGCTATATAATTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
229560169 CGCACACTTAGTGCTATATA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AACT
* * * *
229560197 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATA-TATTTTCAACT
229560227 CGCACACTTAGTGC
1 CGCACACTTAGTGC
229560241 CAATCTTGTC
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
27 2 0.02
28 20 0.22
29 49 0.55
30 17 0.19
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAACT
Found at i:229564836 original size:40 final size:40
Alignment explanation
Indices: 229564667--229564873 Score: 184
Period size: 40 Copynumber: 5.2 Consensus size: 40
229564657 CGGGATTTAA
** * * * * *
229564667 CCGGATATAGCGACTCGCTCGATTGTCTTCGGGACCTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * *
229564707 CCGGTTATAGTGATTCGCACGATTGCCTTCGGGTCTTAAC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * *
229564747 CCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
**
229564787 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * *
229564827 CCGGATATAATTACTAGCA-TAATTGCCTTCGGGACTTAG-
1 CCGGATATAGTAACTCGCACGAA-TGCCTTCGGGTCTTAGC
229564866 CCGGATAT
1 CCGGATAT
229564874 CATTCCAATG
Statistics
Matches: 138, Mismatches: 28, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
39 10 0.07
40 128 0.93
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:229564854 original size:80 final size:79
Alignment explanation
Indices: 229564721--229564873 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 79
229564711 TTATAGTGAT
* * ** * *
229564721 TCGCACGATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAG
1 TCGCACGAATGCCTTCGGGTCTTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAG
229564786 CCCGGATATAACAAC
66 -CCGGATATAACAAC
* * * *
229564801 TCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAATTACTAGCATAATTGCCTTCGGGACTTAG
1 TCGCACGAATGCCTTCGGGTCTTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAG
229564866 CCGGATAT
66 CCGGATAT
229564874 CATTCCAATG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 8 0.13
80 55 0.87
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (79 bp):
TCGCACGAATGCCTTCGGGTCTTAACCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAG
CCGGATATAACAAC
Found at i:229566878 original size:39 final size:39
Alignment explanation
Indices: 229566719--229566880 Score: 168
Period size: 39 Copynumber: 4.2 Consensus size: 39
229566709 TCTTTGGAAT
* * *
229566719 TTAGCC-GATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
** * * *
229566757 TTAAAACGG-TATAGCAACTCGCACAAATGCCTTCGAGTC
1 TT-AGCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
229566796 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTC
1 TTAG-CCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
229566836 TTAGCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC
229566875 TTAGCC
1 TTAGCC
229566881 CGGGTATCAT
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
38 3 0.03
39 66 0.65
40 33 0.32
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (39 bp):
TTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
Found at i:229568937 original size:40 final size:40
Alignment explanation
Indices: 229568872--229569039 Score: 223
Period size: 40 Copynumber: 4.2 Consensus size: 40
229568862 TCTTCGGAAT
* ** *
229568872 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
229568911 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
229568951 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
229568991 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTC
229569031 TTAGCCCGG
1 TTAGCCCGG
229569040 GTATCATTCA
Statistics
Matches: 114, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 3 0.03
40 110 0.96
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:229573265 original size:40 final size:40
Alignment explanation
Indices: 229573191--229573333 Score: 160
Period size: 40 Copynumber: 3.6 Consensus size: 40
229573181 CCGCACCAAG
* * * * * * *
229573191 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAC
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
229573231 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
229573271 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
229573311 GCCTTCGGGTCTTAACCCGGATA
1 GCCTTCGGGTCTTAGCCCGGATA
229573334 AATTTCAGCA
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:229573368 original size:38 final size:40
Alignment explanation
Indices: 229573231--229573372 Score: 164
Period size: 40 Copynumber: 3.6 Consensus size: 40
229573221 TTGCACAAAC
* * *
229573231 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT
*
229573271 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * * *
229573311 GCCTTCGGGTCTTAACCCGGATA-AATTTC-AGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* *
229573349 GTCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
229573373 CATTCAATTT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
38 28 0.32
39 5 0.06
40 55 0.62
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
Found at i:229578336 original size:40 final size:40
Alignment explanation
Indices: 229578281--229578490 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
229578271 AACATTGGAA
229578281 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
229578321 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
229578361 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
229578401 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
229578440 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
229578481 CTATATCCGG
1 ATATATCCGG
229578491 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:229585688 original size:112 final size:110
Alignment explanation
Indices: 229585483--229585702 Score: 239
Period size: 112 Copynumber: 2.0 Consensus size: 110
229585473 TTTTGTAGGA
* *** * *
229585483 TTTATTAGTGGCGTTTTTGTGAAACGCCGCAATAGGTTTGGATTTAGCGGCGCTAGTGTATAAAC
1 TTTATTAGTGGCGTTTTTGTGAAACGCCGCAATAGCTTCCCATTTAGCGGCGCTAGTGCAAAAAC
* * ** *
229585548 GCCGCTAATATTATTTTGTTCAGATCAAAGTGTCGTCGTTTTGTTAG
66 GCCGCAAATATAATTAAGTTCAGATCAAA--ATCGTCGTTTTGTTAG
* *
229585595 TTTATTAGTGGCGTTTATT-TGAAACGCCGCAATAGCTTACCCTTTTAGCGGCGCTATTGCAAAA
1 TTTATTAGTGGCGTTT-TTGTGAAACGCCGCAATAGCTT-CCCATTTAGCGGCGCTAGTGCAAAA
* *
229585659 ACGCCGCAAATGTAAATTAAGTT-TG-TCAAAATCGTCGTTTTGTT
64 ACGCCGCAAATAT-AATTAAGTTCAGATCAAAATCGTCGTTTTGTT
229585703 GTCTTCATTT
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
110 13 0.14
112 39 0.43
113 32 0.36
114 6 0.07
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (110 bp):
TTTATTAGTGGCGTTTTTGTGAAACGCCGCAATAGCTTCCCATTTAGCGGCGCTAGTGCAAAAAC
GCCGCAAATATAATTAAGTTCAGATCAAAATCGTCGTTTTGTTAG
Found at i:229586363 original size:2 final size:2
Alignment explanation
Indices: 229586356--229586386 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
229586346 TAATAGGAGT
229586356 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
229586387 TTATCCGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:229586491 original size:14 final size:15
Alignment explanation
Indices: 229586472--229586501 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
229586462 TGTGTTTATA
229586472 TAAATACAT-AATTC
1 TAAATACATAAATTC
229586486 TAAATACATAAATTC
1 TAAATACATAAATTC
229586501 T
1 T
229586502 GAAGTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATACATAAATTC
Found at i:229589758 original size:23 final size:23
Alignment explanation
Indices: 229589728--229589777 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
229589718 AACATTAATC
229589728 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
229589751 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
229589774 AAAT
1 AAAT
229589778 AAACTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:229590675 original size:26 final size:26
Alignment explanation
Indices: 229590646--229590755 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
229590636 TGATACAAAT
229590646 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
229590672 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
229590698 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
229590724 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
229590750 TGATAA
1 TGATAA
229590756 GAATTCATGT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:229592260 original size:25 final size:25
Alignment explanation
Indices: 229592231--229592279 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
229592221 ATAGTTTTAC
229592231 CCCTAGGAGATAAATT-ACCGAAATA
1 CCCTAGG-GATAAATTGACCGAAATA
* *
229592256 CCCTAGGGTTAAATTGACCTAAAT
1 CCCTAGGGATAAATTGACCGAAAT
229592280 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGGATAAATTGACCGAAATA
Found at i:229594063 original size:12 final size:12
Alignment explanation
Indices: 229594046--229594088 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
229594036 ACTCGGGGAA
229594046 GAGGCCGTGGTC
1 GAGGCCGTGGTC
229594058 GAGGCCGTGGTC
1 GAGGCCGTGGTC
229594070 GAGGCCGTGGTC
1 GAGGCCGTGGTC
229594082 GAGGCCG
1 GAGGCCG
229594089 AGGTAGTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.09, C:0.26, G:0.51, T:0.14
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:229599049 original size:25 final size:25
Alignment explanation
Indices: 229599018--229599074 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
229599008 TCCATTCATA
229599018 ATGATAATGGTTAGGTAAATGTTTC
1 ATGATAATGGTTAGGTAAATGTTTC
229599043 ATGATAATGGTTAGGTAAATGTTTC
1 ATGATAATGGTTAGGTAAATGTTTC
229599068 ATGATAA
1 ATGATAA
229599075 GAATTCATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.39
Consensus pattern (25 bp):
ATGATAATGGTTAGGTAAATGTTTC
Found at i:229601094 original size:135 final size:135
Alignment explanation
Indices: 229600851--229601133 Score: 507
Period size: 135 Copynumber: 2.1 Consensus size: 135
229600841 GAGTAGTCTC
*
229600851 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
229600916 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAA-GGCTCTGGCCCAGTACCA
229600981 CTGTTA
130 CTGTTA
229600987 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTA-TTT-AAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
229601050 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGCTCTGGCCCAGTACCA
65 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGCTCTGGCCCAGTACCA
229601115 CTGTTA
130 CTGTTA
**
229601121 CCTGAATGGGCTT
1 CCCAAATGGGCTT
229601134 AGGCCCAATG
Statistics
Matches: 143, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
134 35 0.24
135 68 0.48
136 23 0.16
137 17 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (135 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGCTCTGGCCCAGTACCAC
TGTTA
Found at i:229601996 original size:17 final size:17
Alignment explanation
Indices: 229601974--229602009 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
229601964 GATGTGGACA
229601974 ATTAATGATTTCCCGGC
1 ATTAATGATTTCCCGGC
229601991 ATTAATGATTTCCCGGC
1 ATTAATGATTTCCCGGC
229602008 AT
1 AT
229602010 ATGCGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (17 bp):
ATTAATGATTTCCCGGC
Found at i:229606418 original size:42 final size:43
Alignment explanation
Indices: 229606367--229606492 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 43
229606357 CTTTTTTTGC
229606367 AAAAGCGCCGCTAAAAGTACAGGT-TATAGCGGCGTTTTTCT-A
1 AAAAGCGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTT-TAA
229606409 AAAAGCGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTAA
1 AAAAGCGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTAA
* * * * *
229606452 AAAAGCGCCACT-AAAGTTCTTGGCCTATAGCGACGTTTTTT
1 AAAAGCGCCGCTAAAAGTAC-AGGTCTATAGCGGCGTTTTTT
229606493 TAGAAAAACG
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
42 31 0.41
43 45 0.59
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTAA
Found at i:229606526 original size:43 final size:43
Alignment explanation
Indices: 229606393--229606581 Score: 125
Period size: 43 Copynumber: 4.4 Consensus size: 43
229606383 GTACAGGTTA
* * * * * * *
229606393 TAGCGGCGTTTTTCTAAAAAGCGCCGCTAAAAGTA-CAGGTCTA
1 TAGCGACGTTTTTTTAAAAAACGCCGCT-ATAGGACCTGGTCTT
* * * ** * * *
229606436 TAGCGGCG-TTTTTTAAAAAAGCGCCACTAAAGTTCTTGGCCTA
1 TAGCGACGTTTTTTTAAAAAA-CGCCGCTATAGGACCTGGTCTT
*
229606479 TAGCGACGTTTTTTTAGAAAAACGCTGCTATA-GACCT-GTACTT
1 TAGCGACGTTTTTTTA-AAAAACGCCGCTATAGGACCTGGT-CTT
* * *
229606522 TAGCGACGCTTTTTTAAAAAATGCCGCTATAGGTCCTGGTCTT
1 TAGCGACGTTTTTTTAAAAAACGCCGCTATAGGACCTGGTCTT
* *
229606565 TGGCGGCGTTTTTTTAA
1 TAGCGACGTTTTTTTAA
229606582 GAGCGCGCTG
Statistics
Matches: 116, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
42 29 0.25
43 66 0.57
44 16 0.14
45 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (43 bp):
TAGCGACGTTTTTTTAAAAAACGCCGCTATAGGACCTGGTCTT
Found at i:229606577 original size:41 final size:41
Alignment explanation
Indices: 229606523--229606634 Score: 95
Period size: 41 Copynumber: 2.7 Consensus size: 41
229606513 CCTGTACTTT
* *
229606523 AGCGACGCTTTTTTAAAAAATGCCGCT-ATAGGTCCTGGTCTTT
1 AGCGGCGC-TTTTTAAAAAA-GCCGCTGA-AGGTCCTGGTCTTC
* ** *
229606566 GGCGGCG-TTTTTTTAAGAGCGCGCTGAAGGTCCTGGTCTTC
1 AGCGGCGCTTTTTAAAAAAGC-CGCTGAAGGTCCTGGTCTTC
*
229606607 AGCGGCGCTTTATAAAAAACGCCG-TGAA
1 AGCGGCGCTTTTTAAAAAA-GCCGCTGAA
229606635 CTTTTGTGGC
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
40 2 0.04
41 35 0.65
42 10 0.19
43 7 0.13
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29
Consensus pattern (41 bp):
AGCGGCGCTTTTTAAAAAAGCCGCTGAAGGTCCTGGTCTTC
Found at i:229609293 original size:28 final size:28
Alignment explanation
Indices: 229609228--229609328 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
229609218 ATAGTGAATC
*
229609228 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
229609257 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
229609285 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
229609315 CGCACACTTAGTGC
1 CGCACACTTAGTGC
229609329 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:229617998 original size:40 final size:39
Alignment explanation
Indices: 229617954--229618134 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
229617944 GTTCAAAACA
* * ** * *
229617954 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
229617994 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
229618034 CCTTCGGGCTTAGCCCGG-TATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
*
229618072 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
229618111 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
229618135 CTCGAACATT
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 36 0.28
39 53 0.41
40 40 0.31
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Done.