Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012864.1 Kokia drynarioides strain JFW-HI SEQ_127878, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 275618
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 12 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5981 original size:7 final size:7
Alignment explanation
Indices: 5969--6009 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
5959 AAAAGTGGAG
5969 AAGTAAA
1 AAGTAAA
5976 AAGTAAA
1 AAGTAAA
5983 AAGTAAA
1 AAGTAAA
5990 AAGTAAA
1 AAGTAAA
5997 AAGTAAA
1 AAGTAAA
6004 AAGTAA
1 AAGTAA
6010 TTAAAACCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AAGTAAA
Found at i:6901 original size:76 final size:75
Alignment explanation
Indices: 6776--6927 Score: 243
Period size: 76 Copynumber: 2.0 Consensus size: 75
6766 GGAAAGTTAT
* *
6776 AATGAAGTGATTAAATTTTTAAAAATTTGACTGAAAATGGAATGGAATTGGGTACGTGCGGTGTA
1 AATGAAGTGATTAAATTTTTAAAAAATTGACTGAAAATGAAATGGAATTGGGTACGTGCGGTGTA
6841 TAATAATGTG
66 TAATAATGTG
*
6851 AATGAAGTG-TTAAATTTTTAAAAAAAATTGACTGAAAATGAAATGGAATTGGGTACGTGTGGTG
1 AATGAAGTGATTAAATTTTT--AAAAAATTGACTGAAAATGAAATGGAATTGGGTACGTGCGGTG
*
6915 TATTATAATGTG
64 TATAATAATGTG
6927 A
1 A
6928 TTAGCTGTGG
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
74 10 0.14
75 9 0.13
76 52 0.73
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (75 bp):
AATGAAGTGATTAAATTTTTAAAAAATTGACTGAAAATGAAATGGAATTGGGTACGTGCGGTGTA
TAATAATGTG
Found at i:7118 original size:3 final size:3
Alignment explanation
Indices: 7110--7144 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7100 GTCAATCTGC
7110 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
7145 GGCAGGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:12578 original size:76 final size:76
Alignment explanation
Indices: 12495--12645 Score: 196
Period size: 76 Copynumber: 2.0 Consensus size: 76
12485 TTTTCTATTA
* ** * * *
12495 CTGTACTTTT-TTGGGTTAAATGTCGGGATGACAATTCGGATAGCGGATTTGGATATATCTGATC
1 CTGTACTTTTGTTAGGCCAAATGTAGGGATGACAATTCGGATAGCGGA-TTGAATATATCTGATA
12559 CAAATTTACTGT
65 CAAATTTACTGT
* * * *
12571 CTGTACTTTTGTTAGGCCAAATGTAGGGATGATAATTCGGATTGCGGATTGAATATATTTGATAT
1 CTGTACTTTTGTTAGGCCAAATGTAGGGATGACAATTCGGATAGCGGATTGAATATATCTGATAC
12636 AAATTTACTG
66 AAATTTACTG
12646 GTTGCAAACT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
76 33 0.52
77 31 0.48
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.38
Consensus pattern (76 bp):
CTGTACTTTTGTTAGGCCAAATGTAGGGATGACAATTCGGATAGCGGATTGAATATATCTGATAC
AAATTTACTGT
Found at i:17886 original size:217 final size:217
Alignment explanation
Indices: 17500--17934 Score: 789
Period size: 217 Copynumber: 2.0 Consensus size: 217
17490 TATAGACCAG
* *
17500 TTCCATGAGGAGGACACAACGAGGGCGTCGCTAGAATGGATGGGGGAGAATGTCATGGGTTGTGT
1 TTCCATAAGGAGGACACAACGAGGGCGTCGCTAGAACGGATGGGGGAGAATGTCATGGGTTGTGT
*
17565 ATTTGAGCTTACAACCATGACTCATTTGAGTGACCCGTCATGTTCAAAAGGAGGCATTTGGCCCA
66 ATTTGAGCCTACAACCATGACTCATTTGAGTGACCCGTCATGTTCAAAAGGAGGCATTTGGCCCA
17630 ATCAAACTAGTCCACTGCTTGGAATGAGTGAAAGCTTATCTACAAAGCTTGGCAAACATGAAAGG
131 ATCAAACTAGTCCACTGCTTGGAATGAGTGAAAGCTTATCTACAAAGCTTGGCAAACATGAAAGG
*
17695 TGATCTTGAAAGATTGACAATA
196 TGATCTTAAAAGATTGACAATA
* *
17717 TTCCATAAGGAGGACATAACGAGGGTGTCGCTAGAACGGATGGGGGAGAATGTCATGGGTTGTGT
1 TTCCATAAGGAGGACACAACGAGGGCGTCGCTAGAACGGATGGGGGAGAATGTCATGGGTTGTGT
*
17782 ATTTGAGCCTACAACCATGACTCATTTGAGTGACCCGTCATGTTCAAAAGGAGGCATTTGGCTCA
66 ATTTGAGCCTACAACCATGACTCATTTGAGTGACCCGTCATGTTCAAAAGGAGGCATTTGGCCCA
*
17847 ATCAAACTAGTCCACTGCTTGGAATGAGTGAAGGCTTATCTACAAAGCTTGGCAAACATGAAAGG
131 ATCAAACTAGTCCACTGCTTGGAATGAGTGAAAGCTTATCTACAAAGCTTGGCAAACATGAAAGG
*
17912 TGATCTTAAAAGATTGACGATA
196 TGATCTTAAAAGATTGACAATA
17934 T
1 T
17935 CAGATTTTAT
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 209 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (217 bp):
TTCCATAAGGAGGACACAACGAGGGCGTCGCTAGAACGGATGGGGGAGAATGTCATGGGTTGTGT
ATTTGAGCCTACAACCATGACTCATTTGAGTGACCCGTCATGTTCAAAAGGAGGCATTTGGCCCA
ATCAAACTAGTCCACTGCTTGGAATGAGTGAAAGCTTATCTACAAAGCTTGGCAAACATGAAAGG
TGATCTTAAAAGATTGACAATA
Found at i:21517 original size:17 final size:18
Alignment explanation
Indices: 21495--21528 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21485 TACCGTAAAT
21495 TAAAATTTAT-AATATTG
1 TAAAATTTATCAATATTG
21512 TAAAATTTATCAATATT
1 TAAAATTTATCAATATT
21529 AAATCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TAAAATTTATCAATATTG
Found at i:21762 original size:17 final size:19
Alignment explanation
Indices: 21730--21764 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
21720 ATTATAATAA
21730 AAAGAAGAATTCAAAAGAT
1 AAAGAAGAATTCAAAAGAT
21749 AAAG-AGAA-TCAAAAGA
1 AAAGAAGAATTCAAAAGA
21765 AAACCCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.66, C:0.06, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAGAAGAATTCAAAAGAT
Found at i:30608 original size:13 final size:13
Alignment explanation
Indices: 30582--30618 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
30572 AAAGAAAAAA
30582 GAAAAGAA-AGAG
1 GAAAAGAAGAGAG
30594 GAAAAGAAGAGAG
1 GAAAAGAAGAGAG
30607 GAACAAG-AGAGA
1 GAA-AAGAAGAGA
30619 TGCGAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 12 0.52
14 3 0.13
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (13 bp):
GAAAAGAAGAGAG
Found at i:38466 original size:36 final size:36
Alignment explanation
Indices: 38357--38470 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 36
38347 CCTTATGTTT
* **
38357 TAACCGAGACATAAGTTCTTCCTTAGCATTACGCTC
1 TAACCGAGACGTAAGCACTTCCTTAGCATTACGCTC
**
38393 TAATAGAGACGTAAGCACTTCCTTAGCATTACGCTC
1 TAACCGAGACGTAAGCACTTCCTTAGCATTACGCTC
* * **
38429 TAACCGAGACGTAAGCACTTCCATAGCAATATTCTC
1 TAACCGAGACGTAAGCACTTCCTTAGCATTACGCTC
38465 TAACCG
1 TAACCG
38471 TGACATATGC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (36 bp):
TAACCGAGACGTAAGCACTTCCTTAGCATTACGCTC
Found at i:38503 original size:36 final size:36
Alignment explanation
Indices: 38463--38552 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
38453 AGCAATATTC
* * *
38463 TCTAACCGTGACATATGCAATCACGCAACATTACAG
1 TCTAACCGAGACATAAGCAATCACACAACATTACAG
* **
38499 TCTAATCGAGATGTAAGCAATCACACAACATTAC-G
1 TCTAACCGAGACATAAGCAATCACACAACATTACAG
* *
38534 CTCTAATCGAGACGTAAGC
1 -TCTAACCGAGACATAAGC
38553 TTTTTCATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
35 1 0.02
36 45 0.98
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.22
Consensus pattern (36 bp):
TCTAACCGAGACATAAGCAATCACACAACATTACAG
Found at i:41830 original size:14 final size:14
Alignment explanation
Indices: 41811--41841 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41801 TTATTTGTTC
41811 ATTCTAATTAAACA
1 ATTCTAATTAAACA
*
41825 ATTCTAATTAAATA
1 ATTCTAATTAAACA
41839 ATT
1 ATT
41842 TTACTTTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTCTAATTAAACA
Found at i:52692 original size:21 final size:23
Alignment explanation
Indices: 52668--52710 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52658 AAAAAAATTT
52668 AAATT-TT-GAGTTAATCAAATC
1 AAATTATTAGAGTTAATCAAATC
*
52689 AAATTATTAGAGTTATTCAAAT
1 AAATTATTAGAGTTAATCAAAT
52711 TATTTGAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (23 bp):
AAATTATTAGAGTTAATCAAATC
Found at i:52905 original size:18 final size:18
Alignment explanation
Indices: 52883--52939 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
52873 AAATTACAAA
* *
52883 AAAAATTAAAATAATTTTT
1 AAAATTTAAAAT-ATTTAT
52902 AAAATTTAAAATATTTAT
1 AAAATTTAAAATATTTAT
*
52920 AAAAATTCTAAAATTTTTAT
1 -AAAATT-TAAAATATTTAT
52940 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.15
19 17 0.52
20 11 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTTAAAATATTTAT
Found at i:52905 original size:19 final size:18
Alignment explanation
Indices: 52883--52926 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
52873 AAATTACAAA
*
52883 AAAAATTAAAATAATTTTT
1 AAAAATTAAAAT-ATTTAT
*
52902 AAAATTTAAAATATTTAT
1 AAAAATTAAAATATTTAT
52920 AAAAATT
1 AAAAATT
52927 CTAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:52969 original size:21 final size:21
Alignment explanation
Indices: 52939--52988 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
52929 AAAATTTTTA
* *
52939 TTTTTAAAAAAATTTATAATT
1 TTTTTAAAAAAATATATAAAT
*
52960 TTTTTTAAAAAATATATAAAT
1 TTTTTAAAAAAATATATAAAT
52981 TTTTTAAA
1 TTTTTAAA
52989 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTAAAAAAATATATAAAT
Found at i:52980 original size:29 final size:28
Alignment explanation
Indices: 52948--53017 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
52938 ATTTTTAAAA
52948 AAATTTATAATTTTTTTTAAAAAATATAT
1 AAATTTATAATTTTTTTTAAAAAATA-AT
* * *
52977 AAATTTTTTAA-ATTTTTTATAAAATAAT
1 AAA-TTTATAATTTTTTTTAAAAAATAAT
* *
53005 AATTTTAGAATTT
1 AAATTTATAATTT
53018 AAATAATTGA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
27 5 0.16
28 5 0.16
29 16 0.50
30 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
AAATTTATAATTTTTTTTAAAAAATAAT
Found at i:55421 original size:29 final size:29
Alignment explanation
Indices: 55374--55431 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
55364 AGACTTTTCG
*
55374 GATTCTCAGGGGGGCGAAAATGGTAATTTTA
1 GATTCTCA-GGGGGCG-AAACGGTAATTTTA
*
55405 GATTCTC-GGGGGTGAAACGGTAATTTT
1 GATTCTCAGGGGGCGAAACGGTAATTTT
55432 GGGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.48
29 6 0.24
31 7 0.28
ACGTcount: A:0.26, C:0.10, G:0.33, T:0.31
Consensus pattern (29 bp):
GATTCTCAGGGGGCGAAACGGTAATTTTA
Found at i:55525 original size:30 final size:29
Alignment explanation
Indices: 55477--55942 Score: 338
Period size: 29 Copynumber: 15.7 Consensus size: 29
55467 TTCGGGGGTG
* *
55477 AAATGGTAATTTTAGGAAGTTTTGGAGTCAA
1 AAATGG-AATTTTTGGAAGTTTTGGGGT-AA
* * **
55508 AAATGGAATTTTGGGAAG-TTCGAGGCCAA
1 AAATGGAATTTTTGGAAGTTTTG-GGGTAA
* * *
55537 AAATAGAATTTTTTAGAAGTTTTGGTGTTAA
1 AAATGGAA-TTTTTGGAAGTTTTGG-GGTAA
*
55568 AAATGTAA-TTTTGGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTTGGGGT-AA
* * *
55597 AAATGGGATTTTTAGAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
* *
55626 AATTGGGATTTTTGGAAGTTTTGGGGTTAA
1 AAATGGAATTTTTGGAAGTTTTGGGG-TAA
* *
55656 AAATAGG-ATTTTTAGAAGTTTGGGGGTAA
1 AAAT-GGAATTTTTGGAAGTTTTGGGGTAA
* *
55685 AAATGGGATTTTTTGGAAG-TTCGAGGGTAA
1 AAAT-GGAATTTTTGGAAGTTTTG-GGGTAA
* * *
55715 AAATTGAATTTTTGGAAGTTTGGGGGTGA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
* *** *
55744 AAATGGGATTTTTGGAAGTTCAAGGGTGA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
** *
55773 AAAT-GAGATTTTTAAAAG-TTCGAGGGTAA
1 AAATGGA-ATTTTTGGAAGTTTTG-GGGTAA
* *
55802 AAATGAGATTTTTTGGGAG-TTTGAGGGTAA
1 AAATG-GAATTTTTGGAAGTTTTG-GGGTAA
* **
55832 AAATGGGATTTTTTGGAAGTTCGGGGGTAAA
1 AAAT-GGAATTTTTGGAAGTTTTGGGGT-AA
* * *
55863 AAATGGGATTTTTAGAAGTTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
*
55892 AAATGGAATTTTTGGAAG-TTCGGGCGTAA
1 AAATGGAATTTTTGGAAGTTTTGGG-GTAA
*
55921 AAAT-GATATTTTTAGACAGTTT
1 AAATGGA-ATTTTTGGA-AGTTT
55943 AGGGACCCTC
Statistics
Matches: 351, Mismatches: 62, Indels: 44
0.77 0.14 0.10
Matches are distributed among these distances:
28 11 0.03
29 168 0.48
30 139 0.40
31 33 0.09
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTTGGGGTAA
Found at i:55616 original size:59 final size:58
Alignment explanation
Indices: 55486--55925 Score: 313
Period size: 59 Copynumber: 7.4 Consensus size: 58
55476 GAAATGGTAA
* * * * * *
55486 TTTTAGGAAGTTTTGGAGTCAAAAATGGAATTTTGGGAAG-TTCGAGGCCAAAAATAGAATT
1 TTTTA-GAAGTTTGGGGGT-AAAAATGGAATTTT-GGAAGTTTTGGGGTCAAAAATAGGA-T
* * * *
55547 TTTTAGAAGTTTTGGTGTTAAAAATGTAATTTTGGAAGTTTTGGGGTCAAAAATGGGAT
1 TTTTAGAAG-TTTGGGGGTAAAAATGGAATTTTGGAAGTTTTGGGGTCAAAAATAGGAT
* * *
55606 TTTTAGAAGTTTGGGGGTAAAATTGGGATTTTTGGAAGTTTTGGGGTTAAAAATAGGAT
1 TTTTAGAAGTTTGGGGGTAAAAAT-GGAATTTTGGAAGTTTTGGGGTCAAAAATAGGAT
* * * *
55665 TTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTTGGAAG-TTCGAGGGT-AAAAATTGAAT
1 TTTTAGAAGTTTGGGGGTAAAAAT-GGA-ATTTTGGAAGTTTTG-GGGTCAAAAATAGGAT
* * * *** *
55724 TTTTGGAAGTTTGGGGGTGAAAATGGGATTTTTGGAAGTTCAAGGGT-GAAAAT-GAGAT
1 TTTTAGAAGTTTGGGGGTAAAAAT-GGAATTTTGGAAGTTTTGGGGTCAAAAATAG-GAT
* * * * * *
55782 TTTTAAAAGTTCGAGGGTAAAAATGAGATTTTTTGGGAG-TTTGAGGGT-AAAAATGGGATT
1 TTTTAGAAGTTTGGGGGTAAAAATG-GA-ATTTTGGAAGTTTTG-GGGTCAAAAATAGGA-T
* * * * *
55842 TTTTGGAAGTTCGGGGGTAAAAAATGGGATTTTTAGAAGTTTAGGGGT-AAAAAT-GGAAT
1 TTTTAGAAGTTTGGGGGT-AAAAAT-GGAATTTTGGAAGTTTTGGGGTCAAAAATAGG-AT
* * *
55901 TTTTGGAAGTTCGGGCGTAAAAATG
1 TTTTAGAAGTTTGGGGGTAAAAATG
55926 ATATTTTTAG
Statistics
Matches: 318, Mismatches: 45, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.01
58 61 0.19
59 151 0.47
60 81 0.25
61 21 0.07
62 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.35
Consensus pattern (58 bp):
TTTTAGAAGTTTGGGGGTAAAAATGGAATTTTGGAAGTTTTGGGGTCAAAAATAGGAT
Found at i:55942 original size:59 final size:58
Alignment explanation
Indices: 55535--55946 Score: 368
Period size: 59 Copynumber: 7.0 Consensus size: 58
55525 GTTCGAGGCC
* * * * *
55535 AAAAATAGAATTTTTTAGAAGTTTTGGTGTTAAAAATGTA-A-TTTTGGAAGTTTTGGGGT
1 AAAAATGGAA-TTTTTAGAAG-TTCGGGGGTAAAAATG-AGATTTTTGGAAGTTTAGGGGT
* * * * *
55594 CAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAATTGGGATTTTTGGAAGTTTTGGGGTT
1 -AAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGAGATTTTTGGAAGTTTAGGGG-T
* * *
55654 AAAAATAGG-ATTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTTGGAAG-TTCGAGGGT
1 AAAAAT-GGAATTTTTAGAAGTTCGGGGGTAAAAATGAGA-TTTTTGGAAGTTTAG-GGGT
* * * * * * *
55713 AAAAATTGAATTTTTGGAAGTTTGGGGGTGAAAATGGGATTTTTGGAAGTTCAAGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGAGATTTTTGGAAGTTTAGGGGT
* * * *
55771 GAAAAT-GAGATTTTTAAAAGTTCGAGGGTAAAAATGAGATTTTTTGGGAGTTT-GAGGGT
1 AAAAATGGA-ATTTTTAGAAGTTCGGGGGTAAAAATGAGA-TTTTTGGAAGTTTAG-GGGT
* * * *
55830 AAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAAAATGGGATTTTTAGAAGTTTAGGGGT
1 AAAAAT-GGAATTTTTAGAAGTTCGGGGGT-AAAAATGAGATTTTTGGAAGTTTAGGGGT
* * * *
55890 AAAAATGGAATTTTTGGAAGTTCGGGCGTAAAAATGATATTTTTAGACAGTTTAGGG
1 AAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGAGATTTTTGGA-AGTTTAGGG
55947 ACCCTCGGGA
Statistics
Matches: 300, Mismatches: 36, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
57 2 0.01
58 74 0.25
59 151 0.50
60 61 0.20
61 12 0.04
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (58 bp):
AAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGAGATTTTTGGAAGTTTAGGGGT
Found at i:58125 original size:17 final size:17
Alignment explanation
Indices: 58089--58137 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
58079 TTTAAATTAT
*
58089 TTTATATTTATTTCTAAA
1 TTTAAATTTATTT-TAAA
58107 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
58124 TTTAAATTTATTTT
1 TTTAAATTTATTTT
58138 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:58138 original size:18 final size:18
Alignment explanation
Indices: 58089--58149 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
58079 TTTAAATTAT
* *
58089 TTTATATTTATTTCTAAA
1 TTTAAATTTATTTTTAAA
58107 TTTAAATTTA-TTTTAAA
1 TTTAAATTTATTTTTAAA
**
58124 TTTAAATTTATTTTTATT
1 TTTAAATTTATTTTTAAA
58142 TTTAAATT
1 TTTAAATT
58150 CAATTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 16 0.42
18 22 0.58
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:58160 original size:23 final size:23
Alignment explanation
Indices: 58064--58149 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 23
58054 CCTTGGGTAA
* *
58064 ATTTTTACTTTTGAGTTTAAA-TT
1 ATTTTTA-TTTTAAATTTAAATTT
*
58087 A-TTTTATATTT-ATTTCTAAATTT
1 ATTTTTAT-TTTAAATT-TAAATTT
**
58110 AAATTTATTTTAAATTTAAATTT
1 ATTTTTATTTTAAATTTAAATTT
58133 ATTTTTATTTTTAAATT
1 ATTTTTA-TTTTAAATT
58150 CAATTTGTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
21 4 0.08
22 12 0.23
23 19 0.37
24 17 0.33
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
ATTTTTATTTTAAATTTAAATTT
Found at i:58166 original size:24 final size:24
Alignment explanation
Indices: 58117--58162 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
58107 TTTAAATTTA
*
58117 TTTTAAATTTAAATTTATTTTTAT
1 TTTTAAATTTAAATTTATTTTAAT
* *
58141 TTTTAAA-TTCAATTTGTTTTAA
1 TTTTAAATTTAAATTTATTTTAA
58163 ATTTCAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTAAATTTAAATTTATTTTAAT
Found at i:58168 original size:17 final size:18
Alignment explanation
Indices: 58136--58183 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
58126 TAAATTTATT
*
58136 TTTATTTTTAAA-TTCAA
1 TTTAGTTTTAAATTTCAA
58153 TTT-GTTTTAAATTTCAA
1 TTTAGTTTTAAATTTCAA
58170 TTTAG-TTTAAATTT
1 TTTAGTTTTAAATTT
58184 GAAATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 7 0.25
17 20 0.71
18 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTAGTTTTAAATTTCAA
Found at i:60157 original size:29 final size:29
Alignment explanation
Indices: 60126--60356 Score: 189
Period size: 30 Copynumber: 7.9 Consensus size: 29
60116 AAAAATAATA
* *
60126 TTTTGACCCCAAACTTCTCTAAAATTCCA-
1 TTTTGACCCCGAACTT-TCCAAAATTCCAT
** * * *
60155 TTTTGACCTTGATCTTTTCATAAATTACAT
1 TTTTGACCCCGAACTTTCCA-AAATTCCAT
*
60185 TTTTG-CCCTCTAACTTTCCAAAATTCCAT
1 TTTTGACCC-CGAACTTTCCAAAATTCCAT
* * * *
60214 TTTTGACCTCGATCTTTTCATAAATTACAT
1 TTTTGACCCCGAACTTTCCA-AAATTCCAT
*
60244 TTTTGCCCCCGAACTTTCCAAAATTCCAT
1 TTTTGACCCCGAACTTTCCAAAATTCCAT
* * ** * *
60273 TTTTAACCTCGATTTTTTCAAAAATTACAT
1 TTTTGACCCCGA-ACTTTCCAAAATTCCAT
* *
60303 TTTT-ATCCCAAACTTTCCAAAATTCCAT
1 TTTTGACCCCGAACTTTCCAAAATTCCAT
*
60331 TTTTGACCCCGAAACTTTCAAAAATT
1 TTTTGACCCCG-AACTTTCCAAAATT
60357 ATCATTTTAT
Statistics
Matches: 154, Mismatches: 40, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
28 19 0.12
29 67 0.44
30 68 0.44
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.41
Consensus pattern (29 bp):
TTTTGACCCCGAACTTTCCAAAATTCCAT
Found at i:60221 original size:59 final size:58
Alignment explanation
Indices: 60126--60364 Score: 302
Period size: 59 Copynumber: 4.1 Consensus size: 58
60116 AAAAATAATA
* *
60126 TTTTGACCCCAAACTTCTCTAAAATTCCA-TTTTGACCTTGATCTTTTCATAAATTACAT
1 TTTTG-CCCCAAACTT-TCCAAAATTCCATTTTTGACCTCGATCTTTTCATAAATTACAT
*
60185 TTTTGCCCTCTAACTTTCCAAAATTCCATTTTTGACCTCGATCTTTTCATAAATTACAT
1 TTTTGCCC-CAAACTTTCCAAAATTCCATTTTTGACCTCGATCTTTTCATAAATTACAT
* * * *
60244 TTTTGCCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTTTTCAAAAATTACAT
1 TTTTG-CCCCAAACTTTCCAAAATTCCATTTTTGACCTCGATCTTTTCATAAATTACAT
** * * *
60303 TTTTATCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAAAC-TTTCAAAAATTATCAT
1 TTTTGCCCCAAACTTTCCAAAATTCCATTTTTGACCTCG-ATCTTTTCATAAATTA-CAT
60362 TTT
1 TTT
60365 ATCCCTGTAT
Statistics
Matches: 161, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
58 56 0.35
59 102 0.63
60 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.42
Consensus pattern (58 bp):
TTTTGCCCCAAACTTTCCAAAATTCCATTTTTGACCTCGATCTTTTCATAAATTACAT
Found at i:60245 original size:30 final size:29
Alignment explanation
Indices: 60146--60364 Score: 167
Period size: 29 Copynumber: 7.4 Consensus size: 29
60136 AAACTTCTCT
* *
60146 AAAATTCCA-TTTTGACCTTGATCTTTTC
1 AAAATTACATTTTTGACCTCGATCTTTTC
* * * *
60174 ATAAATTACATTTTTGCCCTCTAACTTTCC
1 A-AAATTACATTTTTGACCTCGATCTTTTC
*
60204 AAAATTCCATTTTTGACCTCGATCTTTTC
1 AAAATTACATTTTTGACCTCGATCTTTTC
* * * *
60233 ATAAATTACATTTTTGCCCCCGAACTTTCC
1 A-AAATTACATTTTTGACCTCGATCTTTTC
* * *
60263 AAAATTCCATTTTTAACCTCGATTTTTTC
1 AAAATTACATTTTTGACCTCGATCTTTTC
* * *
60292 AAAAATTACATTTTT-ATCC-CAAACTTTCC
1 -AAAATTACATTTTTGA-CCTCGATCTTTTC
* * *
60321 AAAATTCCATTTTTGACCCCGAAAC-TTTC
1 AAAATTACATTTTTGACCTCG-ATCTTTTC
60350 AAAAATTATCATTTT
1 -AAAATTA-CATTTT
60365 ATCCCTGTAT
Statistics
Matches: 149, Mismatches: 32, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
28 16 0.11
29 64 0.43
30 63 0.42
31 6 0.04
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTTGACCTCGATCTTTTC
Found at i:60401 original size:58 final size:60
Alignment explanation
Indices: 60204--60509 Score: 178
Period size: 59 Copynumber: 5.2 Consensus size: 60
60194 CTAACTTTCC
* * * * *
60204 AAAATTCCATTTTTG-ACCTCG--ATCTTTTCATAAATTA-CATTTTTGCCCCCGAACTTTCC-
1 AAAATTCCATTTTTGAACC-CGAAATC-TTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCCA
* * * * * *
60263 AAAATTCCATTTTT-AACCTCG-ATTTTTTCAAAAATTA-CATTTTTATCC-CAAACTTTCC-
1 AAAATTCCATTTTTGAACC-CGAAATCTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCCA
* * * * *
60321 AAAATTCCATTTTTGACCCCGAAA-CTTTCAAAAATTATCATTTTATCCCT-GTATGTCTA
1 AAAATTCCATTTTTGAACCCGAAATCTTCCAAAAATTACCATTTTA-CCCTCGAATGTCCA
* * *
60380 AAAAATCCATTTTT-AATCCGAAATCTTCCAAAATTTACCATTTTACCCTCGAATGTCCA
1 AAAATTCCATTTTTGAACCCGAAATCTTCCAAAAATTACCATTTTACCCTCGAATGTCCA
* ** * **
60439 AAAATTTCATTTTTG-ACCTCG-AGCCTTCCAAAAATTACCATTTCACCC-CGAGCGTCC-
1 AAAATTCCATTTTTGAACC-CGAAATCTTCCAAAAATTACCATTTTACCCTCGAATGTCCA
60496 AAAATTACCATTTT
1 AAAATT-CCATTTT
60510 ACCCCCGTAT
Statistics
Matches: 202, Mismatches: 32, Indels: 27
0.77 0.12 0.10
Matches are distributed among these distances:
57 6 0.03
58 69 0.34
59 124 0.61
60 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (60 bp):
AAAATTCCATTTTTGAACCCGAAATCTTCCAAAAATTACCATTTTACCCTCGAATGTCCA
Found at i:60412 original size:59 final size:59
Alignment explanation
Indices: 60321--60509 Score: 181
Period size: 59 Copynumber: 3.2 Consensus size: 59
60311 CAAACTTTCC
* * * * *
60321 AAAATTCCATTTTTGACCCCGAAACTTTCAAAAATTATCATTTTATCCCT-GTATGTCTA
1 AAAATTCCATTTTTGAACCCGAAACTTCCAAAAATTACCATTTTA-CCCTCGAATGTCCA
* * *
60380 AAAAATCCATTTTT-AATCCGAAATCTTCCAAAATTTACCATTTTACCCTCGAATGTCCA
1 AAAATTCCATTTTTGAACCCGAAA-CTTCCAAAAATTACCATTTTACCCTCGAATGTCCA
* ** * **
60439 AAAATTTCATTTTTG-ACCTCGAGCCTTCCAAAAATTACCATTTCACCC-CGAGCGTCC-
1 AAAATTCCATTTTTGAACC-CGAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCA
60496 AAAATTACCATTTT
1 AAAATT-CCATTTT
60510 ACCCCCGTAT
Statistics
Matches: 107, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
57 6 0.06
58 24 0.22
59 74 0.69
60 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTGAACCCGAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCA
Found at i:60443 original size:30 final size:29
Alignment explanation
Indices: 60406--60513 Score: 91
Period size: 29 Copynumber: 3.8 Consensus size: 29
60396 TCCGAAATCT
*
60406 TCCAAAATTTACCATTTTACCCTCGAATG
1 TCCAAAAATTACCATTTTACCCTCGAATG
* *
60435 TCCAAAAATT-TCATTTTTGA-CCTCGAGCCT-
1 TCCAAAAATTACCA-TTTT-ACCCTCGA--ATG
* **
60465 TCCAAAAATTACCATTTCACCC-CGAGCG
1 TCCAAAAATTACCATTTTACCCTCGAATG
60493 TCC-AAAATTACCATTTTACCC
1 TCCAAAAATTACCATTTTACCC
60514 CCGTATCCAA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
27 17 0.27
28 5 0.08
29 23 0.36
30 16 0.25
31 3 0.05
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCGAATG
Found at i:63046 original size:23 final size:23
Alignment explanation
Indices: 63020--63080 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
63010 TAAAATATTA
*
63020 CAATAAATATGATTTAAATGTAT
1 CAATTAATATGATTTAAATGTAT
* *
63043 CAATTCATATGGTTTAAATGTAT
1 CAATTAATATGATTTAAATGTAT
*
63066 CAATTAGTATGATTT
1 CAATTAATATGATTT
63081 TAATTATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (23 bp):
CAATTAATATGATTTAAATGTAT
Found at i:63088 original size:127 final size:127
Alignment explanation
Indices: 62904--63136 Score: 387
Period size: 127 Copynumber: 1.8 Consensus size: 127
62894 ATAATTTAAT
* * *
62904 ATTTAAATGTATCAATTAATATTGTTTAAAATCATCAATTAATATGCTTTTAGTTATTATTAATA
1 ATTTAAATGTATCAATTAATATGGTTTAAAATCATCAATTAATATGATTTTAATTATTATTAATA
*
62969 ATAATTAATATTACAATAAATATATCATAGATTATAATAAATAAAATATTACAATAAATATG
66 ATAATTAATATTACAATAAATATATCATAGATTACAATAAATAAAATATTACAATAAATATG
* * *
63031 ATTTAAATGTATCAATTCATATGGTTT-AAATGTATCAATTAGTATGATTTTAATTATTATTAAT
1 ATTTAAATGTATCAATTAATATGGTTTAAAAT-CATCAATTAATATGATTTTAATTATTATTAAT
63095 AATAATTAATATTACAATAAATATATCATAGATTACAATAAA
65 AATAATTAATATTACAATAAATATATCATAGATTACAATAAA
63137 AATATCATAG
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
126 4 0.04
127 94 0.96
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (127 bp):
ATTTAAATGTATCAATTAATATGGTTTAAAATCATCAATTAATATGATTTTAATTATTATTAATA
ATAATTAATATTACAATAAATATATCATAGATTACAATAAATAAAATATTACAATAAATATG
Found at i:63130 original size:21 final size:21
Alignment explanation
Indices: 63105--63163 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
63095 AATAATTAAT
63105 ATTACAATAAATATATCATAG
1 ATTACAATAAATATATCATAG
*
63126 ATTACAATAAAAATATCATAG
1 ATTACAATAAATATATCATAG
*
63147 ATTATAATAAATTATAT
1 ATTACAATAAA-TATAT
63164 TATGTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 30 0.88
22 4 0.12
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (21 bp):
ATTACAATAAATATATCATAG
Found at i:63452 original size:20 final size:20
Alignment explanation
Indices: 63407--63453 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
63397 AAAAAAAAAA
* *
63407 TCAAAATAATTTTCAAAAGT
1 TCAAAATAATTTTAAAAACT
*
63427 TTAAAAT-ATTTATAAAAACT
1 TCAAAATAATTT-TAAAAACT
63447 TCAAAAT
1 TCAAAAT
63454 TTATATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (20 bp):
TCAAAATAATTTTAAAAACT
Found at i:63477 original size:25 final size:24
Alignment explanation
Indices: 63432--63480 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
63422 AAAGTTTAAA
*
63432 ATATTTATAAAAACTTCAAAATTT
1 ATATTTATAAAAAATTCAAAATTT
* *
63456 ATATTTTTAAAAAATTATAAAATTT
1 ATATTTATAAAAAATT-CAAAATTT
63481 CTAAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATTTATAAAAAATTCAAAATTT
Found at i:63509 original size:32 final size:32
Alignment explanation
Indices: 63464--63526 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
63454 TTATATTTTT
*
63464 AAAAAATTATAAAA-TTTCTAAAAATATATAATA
1 AAAAAAGTATAAAATTTTCT-AAAATA-ATAATA
63497 AAAAAAGT-TAAAATTTTCTAAAATAATAAT
1 AAAAAAGTATAAAATTTTCTAAAATAATAAT
63527 TTTGGAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.18
32 11 0.39
33 12 0.43
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (32 bp):
AAAAAAGTATAAAATTTTCTAAAATAATAATA
Found at i:63827 original size:22 final size:23
Alignment explanation
Indices: 63800--63869 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 23
63790 CTACAATGGT
* *
63800 ATTATTTTATTGTAATATTATTA
1 ATTATTTTAATGCAATATTATTA
*
63823 A-TA-TTTAATGCAATATTTTTA
1 ATTATTTTAATGCAATATTATTA
63844 ATTA-TTT-AT-CAATA-TATTA
1 ATTATTTTAATGCAATATTATTA
*
63863 ATCATTT
1 ATTATTT
63870 AAAATGTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.17
20 7 0.17
21 18 0.45
22 7 0.17
23 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (23 bp):
ATTATTTTAATGCAATATTATTA
Found at i:65025 original size:93 final size:94
Alignment explanation
Indices: 64913--65088 Score: 223
Period size: 94 Copynumber: 1.9 Consensus size: 94
64903 AAACTTTTTC
* **** *
64913 AAAAAAATAATTAAGCCCCTCCTTT-TTTTTTCACTGAATTACG-CACTTGAACTTTCAAAATGC
1 AAAAAAACAATTAAGCCCCTCCTTTATCCCCTCACTCAATT-CGACACTTGAACTTTCAAAATGC
*
64976 AT-AAAAAATGCCCTCAAACTTCTTCTTAA
65 ATAAAAAAATACCCTCAAACTTCTTCTTAA
* * *
65005 AAAAAAAGCAATTAAGCCCCTGCTTTATCCCCTCACTCAATTGGATACTTGAACTTTCAAAATGC
1 AAAAAAA-CAATTAAGCCCCTCCTTTATCCCCTCACTCAATTCGACACTTGAACTTTCAAAATGC
65070 ATAAAAAAATACCCTCAAA
65 ATAAAAAAATACCCTCAAA
65089 ATTTTTCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
92 7 0.10
93 17 0.24
94 31 0.44
95 15 0.21
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (94 bp):
AAAAAAACAATTAAGCCCCTCCTTTATCCCCTCACTCAATTCGACACTTGAACTTTCAAAATGCA
TAAAAAAATACCCTCAAACTTCTTCTTAA
Found at i:65272 original size:31 final size:32
Alignment explanation
Indices: 65220--65284 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
65210 AATTCAAATT
* *
65220 ATTTTATAAAAATCGTAAAAAAAAATTGTAAA
1 ATTTTATAAAAATCATAAAAAAAAATTATAAA
65252 ATTTTATAAAAATCAT-AAAAAAAATTATAAA
1 ATTTTATAAAAATCATAAAAAAAAATTATAAA
65283 AT
1 AT
65285 ATATCGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 16 0.52
32 15 0.48
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (32 bp):
ATTTTATAAAAATCATAAAAAAAAATTATAAA
Found at i:65432 original size:10 final size:11
Alignment explanation
Indices: 65398--65432 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
65388 GACATGTGGC
*
65398 AAAAAATATAA
1 AAAAAAAATAA
65409 AAAAAAAATAA
1 AAAAAAAATAA
*
65420 AAAAACAATAA
1 AAAAAAAATAA
65431 AA
1 AA
65433 GTTATAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:65553 original size:56 final size:53
Alignment explanation
Indices: 65486--65616 Score: 140
Period size: 56 Copynumber: 2.3 Consensus size: 53
65476 TTATAATTTT
* *
65486 TTTTACGAATTTTATATTTCTTTATATTCTTTATGATTTTCTTACGA-CTTTATAAAA
1 TTTTAC-AATTTTATATTTCTATATA-T-TTTATAATTTT-TTACGATC-TTATAAAA
*
65543 TTTTATAATTTTTTATATTTCTATATATTTTATAATTTTTTACGATGCTTATAAAA
1 TTTTACAA--TTTTATATTTCTATATATTTTATAATTTTTTACGAT-CTTATAAAA
65599 TTTTACATATTTT-TATTT
1 TTTTACA-ATTTTATATTT
65617 TTATTAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
54 5 0.08
55 10 0.15
56 26 0.40
57 8 0.12
58 16 0.25
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.60
Consensus pattern (53 bp):
TTTTACAATTTTATATTTCTATATATTTTATAATTTTTTACGATCTTATAAAA
Found at i:67750 original size:30 final size:30
Alignment explanation
Indices: 67714--67777 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
67704 ACTTAATTAA
*
67714 AAAAGTTATAATTT-GGTCTTTGAGCTATT
1 AAAAGTTATAATTTAAGTCTTTGAGCTATT
* * *
67743 CAAAAGTTTTCATTTAAGTTTTTGAGCTATT
1 -AAAAGTTATAATTTAAGTCTTTGAGCTATT
67774 AAAA
1 AAAA
67778 CCAACGTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
AAAAGTTATAATTTAAGTCTTTGAGCTATT
Found at i:76585 original size:12 final size:11
Alignment explanation
Indices: 76565--76604 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
76555 TTTAATTAAC
76565 ATTTTAAAAAA
1 ATTTTAAAAAA
76576 ATTTTAAAAAA
1 ATTTTAAAAAA
*
76587 ATAATTAAAAAA
1 AT-TTTAAAAAA
*
76599 TTTTTA
1 ATTTTA
76605 GATTTGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:80228 original size:6 final size:6
Alignment explanation
Indices: 80219--80247 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
80209 TCTTTTCACA
80219 ATCTCC ATCTCC ATCTCC ATCTCC ATCTC
1 ATCTCC ATCTCC ATCTCC ATCTCC ATCTC
80248 TGTCTCAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.34
Consensus pattern (6 bp):
ATCTCC
Found at i:84858 original size:3 final size:3
Alignment explanation
Indices: 84850--84884 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
84840 CAGGGTATTC
*
84850 GGA GGA GGA GGA GGA -GA GGA GGA GGA GGA AGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
84885 AGAGAAGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:84870 original size:14 final size:15
Alignment explanation
Indices: 84851--84884 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
84841 AGGGTATTCG
84851 GAGGAGGAGGAGG-A
1 GAGGAGGAGGAGGAA
84865 GAGGAGGAGGAGGAA
1 GAGGAGGAGGAGGAA
84880 GAGGA
1 GAGGA
84885 AGAGAAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (15 bp):
GAGGAGGAGGAGGAA
Found at i:84897 original size:15 final size:15
Alignment explanation
Indices: 84862--84915 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
84852 AGGAGGAGGA
* *
84862 GGAGAGGAGGAGGAG
1 GGAGAGGAAGAGAAG
*
84877 GAAGAGGAAGAGAAG
1 GGAGAGGAAGAGAAG
84892 GGAGAGAGAAGA-AAG
1 GGAGAG-GAAGAGAAG
*
84907 GGAAAGGAA
1 GGAGAGGAA
84916 AAGGAGGAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 3 0.09
15 25 0.76
16 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (15 bp):
GGAGAGGAAGAGAAG
Found at i:84953 original size:39 final size:44
Alignment explanation
Indices: 84872--84955 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
84862 GGAGAGGAGG
* *
84872 AGGAGGAAGAGGAAGAGAAGGGAGAGAGAAGAAAGGGAAAGGAAA
1 AGGAGGAAGA-GAAGAGAAGGGAGAAAGAAGAAAGAGAAAGGAAA
84917 AGGAGGAAGA-AAGAGAA-GGA-AAAGAA-AAAGAG-AAGGAAA
1 AGGAGGAAGAGAAGAGAAGGGAGAAAGAAGAAAGAGAAAGGAAA
84956 GAAAAAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
39 7 0.19
40 5 0.14
41 5 0.14
42 3 0.08
43 7 0.19
45 10 0.27
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (44 bp):
AGGAGGAAGAGAAGAGAAGGGAGAAAGAAGAAAGAGAAAGGAAA
Found at i:84958 original size:16 final size:17
Alignment explanation
Indices: 84926--84965 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
84916 AAGGAGGAAG
84926 AAAGAGAAGGAAAAGAA
1 AAAGAGAAGGAAAAGAA
84943 AAAGAGAAGG-AAAGAA
1 AAAGAGAAGGAAAAGAA
84959 AAAGAGA
1 AAAGAGA
84966 GAGACGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAAGAGAAGGAAAAGAA
Found at i:85004 original size:16 final size:17
Alignment explanation
Indices: 84926--85006 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 17
84916 AAGGAGGAAG
* *
84926 AAAGAGAAGGAAAAGAA
1 AAAGAGAAAGAAGAGAA
*
84943 AAAGAGAAGGAA-AGAA
1 AAAGAGAAAGAAGAGAA
*
84959 AAAGAGAGAGACGAAGAGAGG
1 AAAGAGA-A-A-GAAGAGA-A
84980 AAA-AGAAAGAAGA-AA
1 AAAGAGAAAGAAGAGAA
84995 AAAGAGAAAGAA
1 AAAGAGAAAGAA
85007 AGGAAAGCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
15 3 0.05
16 20 0.36
17 18 0.33
18 1 0.02
19 4 0.07
20 6 0.11
21 3 0.05
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGAGAAAGAAGAGAA
Found at i:89862 original size:15 final size:15
Alignment explanation
Indices: 89844--89879 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
89834 TAAAATATTG
89844 AAACCTTAAACC-CTA
1 AAACCTTAAACCTC-A
89859 AAACCTTAAACCTCA
1 AAACCTTAAACCTCA
89874 AAACCT
1 AAACCT
89880 AATATCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
AAACCTTAAACCTCA
Found at i:93450 original size:19 final size:17
Alignment explanation
Indices: 93421--93468 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
93411 TAAAATGTAT
93421 AATATAATTAAATAATATA
1 AATA-AATTAAATAA-ATA
93440 AATTAAATTAAAATAAATA
1 AA-TAAATT-AAATAAATA
93459 AATAAATTAA
1 AATAAATTAA
93469 TTATTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.07
18 6 0.22
19 11 0.41
20 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAATTAAATAAATA
Found at i:98142 original size:36 final size:35
Alignment explanation
Indices: 98101--98180 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
98091 ATGAAATTAT
*
98101 TTTTTGTTTAT-ATAAATGTACTAACGT-TTAAATACC
1 TTTTTGTTTATGAT--ATGTACTAACATCTT-AATACC
* *
98137 TTTTTGTTTATGATATGTAGTAATATCTTAATACC
1 TTTTTGTTTATGATATGTACTAACATCTTAATACC
98172 TTTTTGTTT
1 TTTTTGTTT
98181 CATGCATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 24 0.62
36 13 0.33
37 2 0.05
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.54
Consensus pattern (35 bp):
TTTTTGTTTATGATATGTACTAACATCTTAATACC
Found at i:101105 original size:21 final size:21
Alignment explanation
Indices: 101080--101129 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
101070 CAACTTTTAC
101080 CGATACAAG-AATACAAACTAT
1 CGATACAAGCAAT-CAAACTAT
** *
101101 CGATACTTGCAATTAAACTAT
1 CGATACAAGCAATCAAACTAT
101122 CGATACAA
1 CGATACAA
101130 CCCAAGCCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (21 bp):
CGATACAAGCAATCAAACTAT
Found at i:109263 original size:17 final size:17
Alignment explanation
Indices: 109241--109276 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
109231 CAAGTTAGTG
109241 AAAATTAGAGGGTAAGT
1 AAAATTAGAGGGTAAGT
109258 AAAATTAGAGGGTAAGT
1 AAAATTAGAGGGTAAGT
109275 AA
1 AA
109277 GAAAGAATAA
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:0.50, C:0.00, G:0.28, T:0.22
Consensus pattern (17 bp):
AAAATTAGAGGGTAAGT
Found at i:116718 original size:69 final size:68
Alignment explanation
Indices: 116603--116730 Score: 177
Period size: 69 Copynumber: 1.9 Consensus size: 68
116593 CTATAAACTC
* * *
116603 CTCCTTCGACTTATCCAAACTTGTTTGGGAGTCTTACAGGGGTGAGTTGTTGCTGCCTTACCTTG
1 CTCCTTCGACTTATCCAAACTTGTTTGGGAGTCTCACAGAGGTGAGTTGTTACTGCCTTACCTTG
116668 GAA
66 GAA
* * *
116671 CTCCTTC-AGCTTATCCCAAGCTTGTTTGGGAGTCTCATAGAGTTGAGTTGTTACTGCCTT
1 CTCCTTCGA-CTTAT-CCAAACTTGTTTGGGAGTCTCACAGAGGTGAGTTGTTACTGCCTT
116731 CTCGACAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
67 1 0.02
68 12 0.23
69 39 0.75
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (68 bp):
CTCCTTCGACTTATCCAAACTTGTTTGGGAGTCTCACAGAGGTGAGTTGTTACTGCCTTACCTTG
GAA
Found at i:121340 original size:37 final size:37
Alignment explanation
Indices: 121275--121351 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
121265 CAAATTGTTT
* * *
121275 ACCGTTATAATTTAACAATTCTCCGAAACTTAAC-GCA
1 ACCGCTATAATTCAACAATTCTCAGAAACTT-ACTGCA
* *
121312 ACCGCTATAATTCAACAGTTCTTAGAAACTTACTGCA
1 ACCGCTATAATTCAACAATTCTCAGAAACTTACTGCA
121349 ACC
1 ACC
121352 AAGATAATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 2 0.06
37 32 0.94
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29
Consensus pattern (37 bp):
ACCGCTATAATTCAACAATTCTCAGAAACTTACTGCA
Found at i:124941 original size:30 final size:29
Alignment explanation
Indices: 124906--125016 Score: 74
Period size: 30 Copynumber: 3.9 Consensus size: 29
124896 CGTTGGATAT
124906 GGCATTGAAGATGGGAACCAGTTAGGCACA
1 GGCATTGAAGATGGGAACCAGTTAGG-ACA
* * *
124936 GGCATTGGATAT-GG---C-GTT-GGATA
1 GGCATTGAAGATGGGAACCAGTTAGGACA
* * *
124959 TGGCATTGGAGAAGGGAACCAGGTAGGTACA
1 -GGCATTGAAGATGGGAACCAGTTAGG-ACA
*
124990 GGCATGGGAA-ATGGGAACCAGTTAGGA
1 GGCAT-TGAAGATGGGAACCAGTTAGGA
125017 ATGGGCATTG
Statistics
Matches: 61, Mismatches: 11, Indels: 19
0.67 0.12 0.21
Matches are distributed among these distances:
23 2 0.03
24 12 0.20
25 5 0.08
26 1 0.02
28 1 0.02
29 5 0.08
30 31 0.51
31 4 0.07
ACGTcount: A:0.31, C:0.13, G:0.38, T:0.19
Consensus pattern (29 bp):
GGCATTGAAGATGGGAACCAGTTAGGACA
Found at i:124957 original size:12 final size:12
Alignment explanation
Indices: 124936--124968 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
124926 GTTAGGCACA
124936 GGCATTGGATAT
1 GGCATTGGATAT
*
124948 GGCGTTGGATAT
1 GGCATTGGATAT
124960 GGCATTGGA
1 GGCATTGGA
124969 GAAGGGAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.21, C:0.09, G:0.39, T:0.30
Consensus pattern (12 bp):
GGCATTGGATAT
Found at i:124964 original size:54 final size:54
Alignment explanation
Indices: 124882--125003 Score: 190
Period size: 54 Copynumber: 2.3 Consensus size: 54
124872 CTCAGGAAAT
* *
124882 GGCATGGGATATGGCGTTGGATATGGCATTGAAGATGGGAACCAGTTAGGCACA
1 GGCATGGGATATGGCGTTGGATATGGCATTGAAGAAGGGAACCAGGTAGGCACA
* * *
124936 GGCATTGGATATGGCGTTGGATATGGCATTGGAGAAGGGAACCAGGTAGGTACA
1 GGCATGGGATATGGCGTTGGATATGGCATTGAAGAAGGGAACCAGGTAGGCACA
*
124990 GGCATGGGAAATGG
1 GGCATGGGATATGG
125004 GAACCAGTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.28, C:0.11, G:0.39, T:0.21
Consensus pattern (54 bp):
GGCATGGGATATGGCGTTGGATATGGCATTGAAGAAGGGAACCAGGTAGGCACA
Found at i:124968 original size:24 final size:24
Alignment explanation
Indices: 124880--124968 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 24
124870 GGCTCAGGAA
*
124880 ATGGCATGGGATATGGCGTTGGAT
1 ATGGCATTGGATATGGCGTTGGAT
* * *
124904 ATGGCATTGAAGATGGGAACCAGTTAGGCAC
1 ATGGCATTGGATAT-GG---C-GTT-GG-AT
124935 A-GGCATTGGATATGGCGTTGGAT
1 ATGGCATTGGATATGGCGTTGGAT
124958 ATGGCATTGGA
1 ATGGCATTGGA
124969 GAAGGGAACC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
23 2 0.04
24 22 0.44
25 5 0.10
26 1 0.02
28 1 0.02
29 5 0.10
30 12 0.24
31 2 0.04
ACGTcount: A:0.26, C:0.11, G:0.37, T:0.26
Consensus pattern (24 bp):
ATGGCATTGGATATGGCGTTGGAT
Found at i:125084 original size:84 final size:84
Alignment explanation
Indices: 124996--125154 Score: 237
Period size: 84 Copynumber: 1.9 Consensus size: 84
124986 TACAGGCATG
* * *
124996 GGAAATGGGAACCAGTTAGGAATGGGCATTGGGTACGGCATTGGAAATGGGGGTCAATCAGGAAA
1 GGAAATGGGAACCAGATAGGAATGGGCATCGGGTACGGCATTGGAAATGGGGGTCAAGCAGGAAA
125061 TAACATGGGACTTGGTAAT
66 TAACATGGGACTTGGTAAT
* * * * *
125080 GGAAATGGGAACCAGATGGGAATGGGTATCGGGTATGGCATTGGAAATGGGGGTCAGGCCGGAAA
1 GGAAATGGGAACCAGATAGGAATGGGCATCGGGTACGGCATTGGAAATGGGGGTCAAGCAGGAAA
*
125145 TAGCATGGGA
66 TAACATGGGA
125155 TATGGCATTG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.31, C:0.11, G:0.39, T:0.19
Consensus pattern (84 bp):
GGAAATGGGAACCAGATAGGAATGGGCATCGGGTACGGCATTGGAAATGGGGGTCAAGCAGGAAA
TAACATGGGACTTGGTAAT
Found at i:125238 original size:42 final size:42
Alignment explanation
Indices: 125179--125265 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
125169 TGGCAGTGGG
* *
125179 AATGGGAACCAGTTAGGAACTGGTTTTGGATATGGTATTGGA
1 AATGGGAACCAGTTAGGAACCGGTATTGGATATGGTATTGGA
*
125221 AATGGGAACCAGTTAGGAACCGGTATTGGATTTGGTATTGGA
1 AATGGGAACCAGTTAGGAACCGGTATTGGATATGGTATTGGA
125263 AAT
1 AAT
125266 AGAGGTCAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (42 bp):
AATGGGAACCAGTTAGGAACCGGTATTGGATATGGTATTGGA
Found at i:129280 original size:18 final size:18
Alignment explanation
Indices: 129259--129307 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
129249 CGAGCTCAGT
* *
129259 AAAAGGTGTGTGCGCTGC
1 AAAAGGTGCGAGCGCTGC
* *
129277 AAAAAGTGCGAGCTCTGC
1 AAAAGGTGCGAGCGCTGC
*
129295 AAAAGGTGAGAGC
1 AAAAGGTGCGAGC
129308 CATTAAATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.35, T:0.16
Consensus pattern (18 bp):
AAAAGGTGCGAGCGCTGC
Found at i:129415 original size:33 final size:33
Alignment explanation
Indices: 129375--129452 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
129365 GACAATAAGC
*
129375 AAAGGTGCAAGCCATCAAAGTGCG-AGCTTTGCA
1 AAAGGTGCAAGCCATCAAAGTGCGCA-CTCTGCA
* * *
129408 AAAGGTGCGAGCCATTAAAGTGCGCACTCTGTA
1 AAAGGTGCAAGCCATCAAAGTGCGCACTCTGCA
129441 AAAGGTGCAAGC
1 AAAGGTGCAAGC
129453 TCGCCAAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 38 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (33 bp):
AAAGGTGCAAGCCATCAAAGTGCGCACTCTGCA
Found at i:129515 original size:46 final size:47
Alignment explanation
Indices: 129459--129550 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 47
129449 AAGCTCGCCA
* *
129459 AAAGTTTGAGCCTGTCAAAGACAGTTAGTC-AAAGTGCGAGCCTGTC
1 AAAGTGTGAGCCTGTCAAAGACAGTCAGTCAAAAGTGCGAGCCTGTC
* *** *
129505 AAAGTGTGAGCTTGTTGCAGACAGTCAGTCAAAAGTGTGAGCCTGT
1 AAAGTGTGAGCCTGTCAAAGACAGTCAGTCAAAAGTGCGAGCCTGT
129551 TGAAGACAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 24 0.63
47 14 0.37
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (47 bp):
AAAGTGTGAGCCTGTCAAAGACAGTCAGTCAAAAGTGCGAGCCTGTC
Found at i:129536 original size:30 final size:30
Alignment explanation
Indices: 129502--129581 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
129492 GTGCGAGCCT
* * *
129502 GTCAAAGTGTGAGCTTGTTGCAGACAGTCA
1 GTCAAAGTGTGAGCCTGTTGAAGACAGTAA
129532 GTCAAAAGTGTGAGCCTGTTGAAGACAGTAA
1 GTC-AAAGTGTGAGCCTGTTGAAGACAGTAA
* *
129563 GCCAAAGTTATGAGCCTGT
1 GTCAAAG-TGTGAGCCTGT
129582 CAAAGTGCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 7 0.16
31 36 0.84
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (30 bp):
GTCAAAGTGTGAGCCTGTTGAAGACAGTAA
Found at i:129605 original size:78 final size:77
Alignment explanation
Indices: 129457--129605 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 77
129447 GCAAGCTCGC
* * * * *
129457 CAAAAGTTTGAGCCTGTCAAAGACAGTTAGTCAAAGTGCGAGCCTGTCAAAGTGTGAGCTTGTTG
1 CAAAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTACGAGCCTGTCAAAGTGCGAGCTTGTTG
*
129522 CAGACAGTCAGT
66 AAGACAGTCAGT
** *
129534 CAAAAGTGTGAGCCTGTTGAAGACAGTAAGCCAAAGTTATGAGCCTGTCAAAGTGCGAGCTTGTT
1 CAAAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAG-TACGAGCCTGTCAAAGTGCGAGCTTGTT
129599 GAAGACA
65 GAAGACA
129606 ATAAGCAAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
77 31 0.50
78 31 0.50
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (77 bp):
CAAAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTACGAGCCTGTCAAAGTGCGAGCTTGTTG
AAGACAGTCAGT
Found at i:129694 original size:34 final size:33
Alignment explanation
Indices: 129631--129696 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
129621 GCTCAACAAT
129631 GTGCAAGCTGCAAAACTGCGAGCTTAACAAAAAA
1 GTGCAAGCTGCAAAACTGCGAGC-TAACAAAAAA
* *
129665 GTGCAAGCTCGGCAAAAGTGGGAGC-AACAAAA
1 GTGCAAGCT--GCAAAACTGCGAGCTAACAAAA
129697 GAGCAAGCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 16 0.57
36 12 0.43
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (33 bp):
GTGCAAGCTGCAAAACTGCGAGCTAACAAAAAA
Found at i:131505 original size:19 final size:19
Alignment explanation
Indices: 131450--131505 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
131440 GAGTATTTGC
* *
131450 AAGAGCTCGCAGTTCGCAG
1 AAGAGCTCGCAGCTCGCAA
* * *
131469 AAGAGCTTGCAACCCGCAA
1 AAGAGCTCGCAGCTCGCAA
*
131488 AAGAGCTCGTAGCTCGCA
1 AAGAGCTCGCAGCTCGCA
131506 GTTTGCAGTT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.14
Consensus pattern (19 bp):
AAGAGCTCGCAGCTCGCAA
Found at i:132861 original size:14 final size:14
Alignment explanation
Indices: 132825--132865 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
132815 TATATTTTAA
*
132825 ATATTTAAATA-TA
1 ATATTTAAATATTT
132838 ATCA-TTAAATATTT
1 AT-ATTTAAATATTT
132852 ATATTTAAATATTT
1 ATATTTAAATATTT
132866 GTATAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTTAAATATTT
Found at i:135875 original size:6 final size:7
Alignment explanation
Indices: 135850--135874 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
135840 ATCTTCCCCA
135850 TTTTTAT
1 TTTTTAT
135857 TTTTTAT
1 TTTTTAT
135864 TTTTTAT
1 TTTTTAT
135871 TTTT
1 TTTT
135875 AAAGCTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:141590 original size:27 final size:28
Alignment explanation
Indices: 141526--141588 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
141516 AGCTCGGACC
* *
141526 AAATTCAATTTGAATAATAAAAAATTTA
1 AAATTAAATTTGAATAATAAAAAATATA
* *
141554 AATTTAAATTT-AATTATAAAAATATATA
1 AAATTAAATTTGAATAATAAAAA-ATATA
141582 AAATTAA
1 AAATTAA
141589 TTAAATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
AAATTAAATTTGAATAATAAAAAATATA
Found at i:141945 original size:15 final size:15
Alignment explanation
Indices: 141925--141954 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
141915 ATCTTGAATC
*
141925 TTAAAATTTTAAAAT
1 TTAAAATTTAAAAAT
141940 TTAAAATTTAAAAAT
1 TTAAAATTTAAAAAT
141955 AAAGATTATT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAAATTTAAAAAT
Found at i:144831 original size:30 final size:30
Alignment explanation
Indices: 144797--144862 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
144787 ACAAAGTCAG
*
144797 CTTGTGTGAGCAATTCTATAATAAAATCAA
1 CTTGTGTGAGAAATTCTATAATAAAATCAA
* **
144827 CTTGTGTGAGAAATTCTATTATAATGTCAA
1 CTTGTGTGAGAAATTCTATAATAAAATCAA
144857 CTTGTG
1 CTTGTG
144863 CCTGTGTCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (30 bp):
CTTGTGTGAGAAATTCTATAATAAAATCAA
Found at i:150235 original size:14 final size:13
Alignment explanation
Indices: 150208--150245 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
150198 GGGTAAATAG
*
150208 TTAATTAAATTAT
1 TTAATTATATTAT
150221 TTAATTTATATTAT
1 TTAA-TTATATTAT
150235 TTAATTATATT
1 TTAATTATATT
150246 GTACATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:157696 original size:35 final size:34
Alignment explanation
Indices: 157645--157719 Score: 105
Period size: 35 Copynumber: 2.2 Consensus size: 34
157635 GCTTTGTTGA
* * * *
157645 ATGAGCTCAGGTGAGTTTTAATCTGTCTTGGTATG
1 ATGAACTCAGGTGAGTTCTAATCTG-CTCGGCATG
157680 ATGAACTCAGGTGAGTTCTAATCTGCTCGGCATG
1 ATGAACTCAGGTGAGTTCTAATCTGCTCGGCATG
157714 ATGAAC
1 ATGAAC
157720 CAAGCTCATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 13 0.36
35 23 0.64
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (34 bp):
ATGAACTCAGGTGAGTTCTAATCTGCTCGGCATG
Found at i:168959 original size:23 final size:25
Alignment explanation
Indices: 168933--168978 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
168923 ATATATAAAA
168933 ATTTCTC-AAAATAAT-ATTTTTTT
1 ATTTCTCAAAAATAATGATTTTTTT
*
168956 ATTTTTCAAAAATAATGATTTTT
1 ATTTCTCAAAAATAATGATTTTT
168979 ATAATTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 8 0.40
25 6 0.30
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTTCTCAAAAATAATGATTTTTTT
Found at i:169371 original size:28 final size:27
Alignment explanation
Indices: 169339--169399 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
169329 TCATATTTTA
*
169339 AAATAAAGTGTTTAAATAATCATAGTTC
1 AAATAAAGTGTTTAAATAATAATA-TTC
* * *
169367 AAATAATGTGTTTTAATAATAATATTT
1 AAATAAAGTGTTTAAATAATAATATTC
169394 AAATAA
1 AAATAA
169400 TTTAATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.39
Consensus pattern (27 bp):
AAATAAAGTGTTTAAATAATAATATTC
Found at i:173086 original size:14 final size:13
Alignment explanation
Indices: 173063--173114 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
173053 TTTTTTTTCA
*
173063 ATATTATTATATAT
1 ATATTTTTAT-TAT
173077 ATATTTTTATTAT
1 ATATTTTTATTAT
* *
173090 AAATTTTGATTAT
1 ATATTTTTATTAT
*
173103 ATCTTATTTATT
1 ATATT-TTTATT
173115 TTTTTGACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
13 17 0.55
14 14 0.45
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
ATATTTTTATTAT
Found at i:173527 original size:125 final size:125
Alignment explanation
Indices: 173391--173624 Score: 362
Period size: 125 Copynumber: 1.9 Consensus size: 125
173381 TAATTTTTTT
* * *
173391 TCAACTTATAAGTAAGAAAATAATGTATTTCAACGCACTCGAATTCATGTTCT-TCTATATTAAC
1 TCAACTTATAAGTAAAAAAATAATGTATTTCAACGCACTCGAACTCATGTTCTCTC-ACATTAAC
*
173455 AACAATATTCATACCAATCAAACTAAAACTCAATCGATATAATAAAATTCATAGTTTCTCC
65 AACAATAATCATACCAATCAAACTAAAACTCAATCGATATAATAAAATTCATAGTTTCTCC
** *
173516 TCAACTTATAAGTAAAAAAATAATGTATTTCAGTGCACTTGAACTCATGTTCTCTCACATTAACA
1 TCAACTTATAAGTAAAAAAATAATGTATTTCAACGCACTCGAACTCATGTTCTCTCACATTAACA
* * *
173581 ATAATAATCATACCAATCAAACTAAGATTCAATCGATATAATAA
66 ACAATAATCATACCAATCAAACTAAAACTCAATCGATATAATAA
173625 TACTAAATTT
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
125 96 0.98
126 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (125 bp):
TCAACTTATAAGTAAAAAAATAATGTATTTCAACGCACTCGAACTCATGTTCTCTCACATTAACA
ACAATAATCATACCAATCAAACTAAAACTCAATCGATATAATAAAATTCATAGTTTCTCC
Found at i:178324 original size:55 final size:55
Alignment explanation
Indices: 178264--178371 Score: 153
Period size: 55 Copynumber: 2.0 Consensus size: 55
178254 CAAGATTATG
* * * *
178264 TTATGTGGAAGTCCTTAAGGACTATTTGATATGTGGTAAGTCCACCATGACTACC
1 TTATGTGGAAGTCCATAAGGACTATCTGATATGTGGAAAGTCCACCAGGACTACC
* * *
178319 TTATGTGGAGGTTCATAAGGACTATCTGATATGTGGAAAGTCCATCAGGACTA
1 TTATGTGGAAGTCCATAAGGACTATCTGATATGTGGAAAGTCCACCAGGACTA
178372 TCGTTGTGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (55 bp):
TTATGTGGAAGTCCATAAGGACTATCTGATATGTGGAAAGTCCACCAGGACTACC
Found at i:178372 original size:29 final size:28
Alignment explanation
Indices: 178265--178373 Score: 105
Period size: 29 Copynumber: 3.9 Consensus size: 28
178255 AAGATTATGT
* *
178265 TATGTGGAAGTCCTTAAGGACTATTTGA
1 TATGTGGAAGTCCATAAGGACTATCTGA
** * *
178293 TATGTGGTAAGTCCACCATGACTACCT--
1 TATGTGG-AAGTCCATAAGGACTATCTGA
* *
178320 TATGTGGAGGTTCATAAGGACTATCTGA
1 TATGTGGAAGTCCATAAGGACTATCTGA
*
178348 TATGTGGAAAGTCCATCAGGACTATC
1 TATGTGG-AAGTCCATAAGGACTATC
178374 GTTGTGAAGA
Statistics
Matches: 62, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
26 13 0.21
27 7 0.11
28 14 0.23
29 28 0.45
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (28 bp):
TATGTGGAAGTCCATAAGGACTATCTGA
Found at i:186679 original size:29 final size:29
Alignment explanation
Indices: 186620--187008 Score: 342
Period size: 29 Copynumber: 13.3 Consensus size: 29
186610 AATTGAGTCA
* *
186620 AAAATG-TAA-TTTTGGAT-GTCGAGGGC
1 AAAATGATAATTTTTGGATATTCGAGGGT
** *
186646 AAAATGATAATTTTTGGATGGTCAAGGGT
1 AAAATGATAATTTTTGGATATTCGAGGGT
* * * *
186675 AAAATGGTAATTTTTTGACA-CCTGAGGGT
1 AAAATGATAATTTTTGGATATTC-GAGGGT
* * * * *
186704 AAAACGCTAATTTTTGGACACTCAAGGGT
1 AAAATGATAATTTTTGGATATTCGAGGGT
*
186733 AAAATGATAATTTTTGGATATTCGGGGGT
1 AAAATGATAATTTTTGGATATTCGAGGGT
186762 AAAATGATAATTTTTGGATATTCGAGGGT
1 AAAATGATAATTTTTGGATATTCGAGGGT
*
186791 AAAATGATAATTTTTGGAAAGTTCGAGGGT
1 AAAATGATAATTTTTGGATA-TTCGAGGGT
*
186821 AAAATGATAATTTTTGGAAAGTTCG-GGGTT
1 AAAATGATAATTTTTGGATA-TTCGAGGG-T
* * *
186851 AAAATTG-TGATTTTTGGACATTTG-GTGGT
1 AAAA-TGATAATTTTTGGATATTCGAG-GGT
* *
186880 AAAATGGTAATTTTTGGATGTTCGAGGGT
1 AAAATGATAATTTTTGGATATTCGAGGGT
* * * *
186909 GAAATGGTAATTTTTGGAAAGTTCGGGGGT
1 AAAATGATAATTTTTGGATA-TTCGAGGGT
* * * *
186939 AAAAAATGGTAAATTTTGGACACTCGAGGGT
1 --AAAATGATAATTTTTGGATATTCGAGGGT
* * * *
186970 AAAACGGTAATTTTTGGACACTCGAGGGT
1 AAAATGATAATTTTTGGATATTCGAGGGT
186999 AAAATGATAA
1 AAAATGATAA
187009 ATGTTGAGAA
Statistics
Matches: 308, Mismatches: 41, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.02
27 3 0.01
28 11 0.04
29 200 0.65
30 62 0.20
31 9 0.03
32 17 0.06
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGATAATTTTTGGATATTCGAGGGT
Found at i:186818 original size:30 final size:30
Alignment explanation
Indices: 186638--187073 Score: 337
Period size: 29 Copynumber: 14.8 Consensus size: 30
186628 ATTTTGGATG
* * *
186638 TCGAGGGCAAAATGATAATTTTTGG-ATGG
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
* * * * **
186667 TCAAGGGTAAAATGGTAATTTTTTGACACC
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
* * * *
186697 T-GAGGGTAAAACGCTAATTTTTGGACA-C
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
* *
186725 TCAAGGGTAAAATGATAATTTTTGGATA-T
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
* *
186754 TCGGGGGTAAAATGATAATTTTTGGATA-T
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
186783 TCGAGGGTAAAATGATAATTTTTGGAAAGT
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
186813 TCGAGGGTAAAATGATAATTTTTGGAAAGT
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
* *
186843 TCG-GGGTTAAAATTG-TGATTTTTGGACA-T
1 TCGAGGG-TAAAA-TGATAATTTTTGGAAAGT
* * *
186872 TTG-GTGGTAAAATGGTAATTTTTGG-ATGT
1 TCGAG-GGTAAAATGATAATTTTTGGAAAGT
* *
186901 TCGAGGGTGAAATGGTAATTTTTGGAAAGT
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
* * * * *
186931 TCGGGGGTAAAAAATGGTAAATTTTGGACA-C
1 TCGAGGGT--AAAATGATAATTTTTGGAAAGT
* * * *
186962 TCGAGGGTAAAACGGTAATTTTTGGACA-C
1 TCGAGGGTAAAATGATAATTTTTGGAAAGT
* *
186991 TCGAGGGTAAAATGATAAATGTT-GAGAAGT
1 TCGAGGGTAAAATGATAATTTTTGGA-AAGT
**
187021 TCGACCGTCAAAATG-TAATTTTTGGAAAGT
1 TCGAGGGT-AAAATGATAATTTTTGGAAAGT
* *
187051 TC-AGGGCCAAAAT-ATGATTTTTG
1 TCGAGGG-TAAAATGATAATTTTTG
187074 TAGAGTTCAG
Statistics
Matches: 337, Mismatches: 52, Indels: 36
0.79 0.12 0.08
Matches are distributed among these distances:
28 6 0.02
29 215 0.64
30 82 0.24
31 17 0.05
32 17 0.05
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (30 bp):
TCGAGGGTAAAATGATAATTTTTGGAAAGT
Found at i:187071 original size:29 final size:29
Alignment explanation
Indices: 187029--187085 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
187019 GTTCGACCGT
*
187029 CAAAATGTAATTTTTGGAAAGTTCAGGGC
1 CAAAATATAATTTTTGGAAAGTTCAGGGC
* * *
187058 CAAAATATGATTTTTGTAGAGTTCAGGG
1 CAAAATATAATTTTTGGAAAGTTCAGGG
187086 ACCTTCTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (29 bp):
CAAAATATAATTTTTGGAAAGTTCAGGGC
Found at i:187636 original size:20 final size:20
Alignment explanation
Indices: 187611--187654 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
187601 CCGGTTCGCT
*
187611 GTCCGTCGCCACGCCCCGTC
1 GTCCGTCACCACGCCCCGTC
*
187631 GTCCGTCACCACGCGCCGTC
1 GTCCGTCACCACGCCCCGTC
187651 GTCC
1 GTCC
187655 ACGGTGGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.07, C:0.52, G:0.25, T:0.16
Consensus pattern (20 bp):
GTCCGTCACCACGCCCCGTC
Found at i:188048 original size:3 final size:3
Alignment explanation
Indices: 188040--188097 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
188030 TTCGGGTCCC
** *
188040 TTA TTA TTA TTA TTA TTA AGA TTA TTA ATA TTA -TA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
188085 TGTA GTTA TTA TT
1 T-TA -TTA TTA TT
188098 TAATGAAACC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 2 0.04
3 36 0.80
4 6 0.13
5 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:188320 original size:25 final size:24
Alignment explanation
Indices: 188290--188339 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
188280 ACTTTGCTTC
*
188290 GAATGCTATCTGTTGTATTGCTTTT
1 GAATGC-ATCTGTTGTATTGATTTT
* *
188315 GAATGCCTCTTTTGTATTGATTTT
1 GAATGCATCTGTTGTATTGATTTT
188339 G
1 G
188340 GATCATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (24 bp):
GAATGCATCTGTTGTATTGATTTT
Found at i:188729 original size:15 final size:15
Alignment explanation
Indices: 188709--188739 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
188699 AATGTATTGG
188709 ACATTTTGAAATTTA
1 ACATTTTGAAATTTA
188724 ACATTTTGAAATTTA
1 ACATTTTGAAATTTA
188739 A
1 A
188740 AGTAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (15 bp):
ACATTTTGAAATTTA
Found at i:189497 original size:209 final size:209
Alignment explanation
Indices: 189137--190047 Score: 1340
Period size: 209 Copynumber: 4.4 Consensus size: 209
189127 TCTCTCGATC
* * * * **
189137 TACTTCTCTATATCTCATTAGGAAGATGACTGCATCACTTGTTTTAATCCGTTTCTCTGTATCTC
1 TACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTC
* * ** *
189202 ATCAAGAAGATGGATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCTTC
66 ATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAACCACTTTATTGCTTC
* * * * * *
189267 AACCCGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGTTTTGCTCACAGTGAGCTTTGTT
131 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGTTTCGCTCACATTGAGCTTTGTT
*
189332 TCCTTGATTTGGTA
196 TCCTTGATTTGGCA
* * * *
189346 TACTTCT-TAGTATCTCATCAAGAAGATGATCACATCACTTGTTTTAATCCGCTTCTCTATATCT
1 TACTTCTCT-GTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCT
* *
189410 CATCAGGAAGATGAATTTGATCCACTTCTCTGTATCTCATCAGGAAGACAACCACTTTATTGCTT
65 CATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAACCACTTTATTGCTT
* * * *
189475 CGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGATTCAAAGTTTTGCTCACATTAAGCTTTGT
130 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGTTTCGCTCACATTGAGCTTTGT
*
189540 TTCATTGATTTGGCA
195 TTCCTTGATTTGGCA
189555 TACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTC
1 TACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTC
* *
189620 ATCAGGAAGCTGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAACCACTTTAATGCTTC
66 ATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAACCACTTTATTGCTTC
* * *
189685 GACTTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTTGAAGTTTCGCTCACTTTGAGCTTTGTT
131 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGTTTCGCTCACATTGAGCTTTGTT
*
189750 TCTTTGATTTGGCA
196 TCCTTGATTTGGCA
* * *
189764 TACTTCTCTGTATCTCATCAAGAAGAAGACCACATCACTTGTTTTAATCCACTTCTCTATATCTC
1 TACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTC
* * *
189829 ATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACAACTC-TTTTATTGCTT
66 ATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAAC-CACTTTATTGCTT
* ** * * *
189893 TGACCTGCTTCTCAGTATCTTTTTAGGAAGTTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGT
130 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGTTTCGCTCACATTGAGCTTTGT
*
189958 TTCCTTGATTTGGTA
195 TTCCTTGATTTGGCA
* *
189973 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCACTTCTCTGTATCTC
1 TACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTC
190038 ATCAGGAAGA
66 ATCAGGAAGA
190048 CAACCATTTT
Statistics
Matches: 634, Mismatches: 65, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
208 1 0.00
209 631 1.00
210 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (209 bp):
TACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTC
ATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACAACCACTTTATTGCTTC
GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGTTTCGCTCACATTGAGCTTTGTT
TCCTTGATTTGGCA
Found at i:190134 original size:172 final size:172
Alignment explanation
Indices: 189848--190219 Score: 620
Period size: 172 Copynumber: 2.2 Consensus size: 172
189838 ACGGATTTGG
* *
189848 TCCACTTCTCTGTATCTCATCAAGAAGACAACTCTTTTATTGCTTTGACCTGCTTCTCAGTATCT
1 TCCACTTCTCTGTATCTCATCAGGAAGACAACTCTTTTATTGCTTCGACCTGCTTCTCAGTATCT
** * * *
189913 TTTTAGGAAGTTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCCTTGATTTGGTATACTT
66 CATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCCTTAATTTGGTATACTT
*
189978 CTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAA
131 CTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTAAA
190020 TCCACTTCTCTGTATCTCATCAGGAAGACAAC-CATTTTATTGCTTCGACCTGCTTCTCAGTATC
1 TCCACTTCTCTGTATCTCATCAGGAAGACAACTC-TTTTATTGCTTCGACCTGCTTCTCAGTATC
190084 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCCTTAATTTGGTATACT
65 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCCTTAATTTGGTATACT
* *
190149 TCTCTGTATCTTATTAGGAAGATGACCGCCTCACTTGTTTAAA
130 TCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTAAA
* *
190192 TCCTCTTCTCTATATCTCATCAGGAAGA
1 TCCACTTCTCTGTATCTCATCAGGAAGA
190220 TGAATTTGGT
Statistics
Matches: 187, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
171 1 0.01
172 186 0.99
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (172 bp):
TCCACTTCTCTGTATCTCATCAGGAAGACAACTCTTTTATTGCTTCGACCTGCTTCTCAGTATCT
CATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCCTTAATTTGGTATACTT
CTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTAAA
Found at i:190345 original size:39 final size:39
Alignment explanation
Indices: 190286--190429 Score: 144
Period size: 39 Copynumber: 3.7 Consensus size: 39
190276 AATGATCATC
* * *
190286 ATCTGCCCCATGATCGGGGTAAGAGATTGGCTGATTATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATTATA
* * * ** * **
190325 ATCTTCCCCAGGCTCGGGGTAAGAGATCGAATGACTGCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATTATA
* * * *
190364 ATCTGCCCCAAGCTTGGGGTAAGAGATTTGCTGATAATT
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATTATA
*
190403 ATCTGCCCCAAGCTCAGGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT
190430 CAGATGACTG
Statistics
Matches: 81, Mismatches: 24, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATTATA
Found at i:190463 original size:78 final size:78
Alignment explanation
Indices: 190286--190448 Score: 220
Period size: 78 Copynumber: 2.1 Consensus size: 78
190276 AATGATCATC
* * * * * *
190286 ATCTGCCCCATGATCGGGGTAAGAGATTGGCTGATTATGATCTTCCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATAATGATCTGCCCCAAGCTCAGGGTAAGAGA
190351 TCGAATGACTGCA
66 TCGAATGACTGCA
* * *
190364 ATCTGCCCCAAGCTTGGGGTAAGAGATTTGCTGATAATTATCTGCCCCAAGCTCAGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATAATGATCTGCCCCAAGCTCAGGGTAAGAGA
190429 TC-AGATGACTGCA
66 TCGA-ATGACTGCA
*
190442 ATTTGCC
1 ATCTGCC
190449 TCGCGGTCGG
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 1 0.01
78 73 0.99
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATAATGATCTGCCCCAAGCTCAGGGTAAGAGA
TCGAATGACTGCA
Found at i:196873 original size:21 final size:22
Alignment explanation
Indices: 196827--196887 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
196817 CGATCTAAGA
196827 AAAAATAAAAGAAACA-A-AATT
1 AAAAATAAAAGAAA-ATAGAATT
196848 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
196870 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
196888 GAAAGTCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 1 0.03
21 15 0.42
22 19 0.53
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:196880 original size:15 final size:16
Alignment explanation
Indices: 196853--196882 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
196843 AAATTAAAAA
196853 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
196869 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
196883 AATAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:200252 original size:13 final size:12
Alignment explanation
Indices: 200234--200284 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
200224 GGACAAAAGT
200234 AAATAAATAAATA
1 AAATAAATAAA-A
*
200247 AAATAAGATAGAA
1 AAATAA-ATAAAA
200260 AAATAAA-AAAA
1 AAATAAATAAAA
*
200271 AATAAAAATAAAA
1 AA-ATAAATAAAA
200284 A
1 A
200285 TACTTGGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 5 0.16
12 5 0.16
13 18 0.56
14 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (12 bp):
AAATAAATAAAA
Found at i:200277 original size:8 final size:8
Alignment explanation
Indices: 200234--200284 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
200224 GGACAAAAGT
*
200234 AAATAAAT
1 AAATAAAA
200242 AAATAAAA
1 AAATAAAA
*
200250 TAAGATAGAA
1 -AA-ATAAAA
200260 AAATAAAA
1 AAATAAAA
200268 AAA-AATAA
1 AAATAA-AA
200276 AAATAAAA
1 AAATAAAA
200284 A
1 A
200285 TACTTGGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
7 2 0.06
8 23 0.64
9 6 0.17
10 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (8 bp):
AAATAAAA
Found at i:202859 original size:22 final size:22
Alignment explanation
Indices: 202819--202879 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
202809 CGATCTAAGG
202819 AAAAATAAAAGAAAA-AGAATT
1 AAAAATAAAAGAAAATAGAATT
202840 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
202862 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
202880 GAAAGTCGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 15 0.41
22 21 0.57
23 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:202870 original size:15 final size:15
Alignment explanation
Indices: 202831--202875 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
202821 AAATAAAAGA
* *
202831 AAAAGAATTAAAAAT
1 AAAAGAAATAGAAAT
*
202846 AAAAGAAAATAGAATT
1 AAAAG-AAATAGAAAT
202862 AAAAGAAATAGAAA
1 AAAAGAAATAGAAA
202876 ATAGGAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (15 bp):
AAAAGAAATAGAAAT
Found at i:203701 original size:19 final size:19
Alignment explanation
Indices: 203677--203719 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
203667 AAACATAAAT
203677 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
203696 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
203715 TAAAT
1 TAAAT
203720 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:209974 original size:87 final size:87
Alignment explanation
Indices: 209881--210048 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 87
209871 TGGTTGTCTA
* * *
209881 AGGGTAAAACGATAATTTTTGGACAG-TCGGGGGTAAAATGGTAA-TTTTTGGACACCCG-GAGG
1 AGGGTAAAACGATAA-TTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTTGAAAACCCGAG-GG
209943 TAAAATGGTAATTTTTAGACACTCG
63 TAAAATGGTAATTTTTAGACACTCG
* * **
209968 AGGGTAAAATGATAATTTTGGATGTTCGAGGGTAAAATGGTAATTTTTTGAAAATTCGAGGGTAA
1 AGGGTAAAACGATAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTTGAAAACCCGAGGGTAA
210033 AATGGTAATTTTTAGA
66 AATGGTAATTTTTAGA
210049 AAGTTTGGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
85 1 0.01
86 24 0.34
87 45 0.63
88 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (87 bp):
AGGGTAAAACGATAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTTGAAAACCCGAGGGTAA
AATGGTAATTTTTAGACACTCG
Found at i:209996 original size:28 final size:29
Alignment explanation
Indices: 209830--210253 Score: 187
Period size: 29 Copynumber: 14.6 Consensus size: 29
209820 AATGAAGTCA
* *
209830 AAAAT-GTAATTTTTGGATGTT-GGGGGG
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* * * *
209857 AAAACGATAATTTTTGGTTG-TCTAAGGGT
1 AAAATGGTAATTTTTGGATGTTC-GAGGGT
* * * *
209886 AAAACGATAATTTTTGGACAG-TCGGGGGT
1 AAAATGGTAATTTTTGGA-TGTTCGAGGGT
****
209915 AAAATGGTAATTTTTGGACACCCG-GAGGT
1 AAAATGGTAATTTTTGGATGTTCGAG-GGT
* ***
209944 AAAATGGTAATTTTTAGACACTCGAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
*
209973 AAAATGATAA-TTTTGGATGTTCGAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* **
210001 AAAATGGTAATTTTTTGAAAATTCGAGGGT
1 AAAATGGTAA-TTTTTGGATGTTCGAGGGT
* * *
210031 AAAATGGTAATTTTTAGAAAGTTTG-GGGT
1 AAAATGGTAATTTTT-GGATGTTCGAGGGT
* ** *
210060 CAAAAAT-GTGATTTTTGGACATCCG-GTGGT
1 --AAAATGGTAATTTTTGGATGTTCGAG-GGT
* *
210090 AAAATGGTAA-TTTTGTATGTT-TAGGGGT
1 AAAATGGTAATTTTTGGATGTTCGA-GGGT
* * *
210118 GAATTGGTAA-TTTTGGAAAGTTC-AGGGT
1 AAAATGGTAATTTTTGG-ATGTTCGAGGGT
* ****
210146 AAAAAATGGTAATGTTTGGACACCCGAGGGT
1 --AAAATGGTAATTTTTGGATGTTCGAGGGT
* **
210177 AAAACGGTAATTTTTGGACACTT-GAGGGT
1 AAAATGGTAATTTTTGGA-TGTTCGAGGGT
* * *
210206 AAAATTGTAATTTTTGAGAAGTTTG-GGAGT
1 AAAATGGTAATTTTTG-GATGTTCGAGG-GT
210236 CAAAAT-GTAATTTTTGGA
1 -AAAATGGTAATTTTTGGA
210254 AAGTTTGATG
Statistics
Matches: 310, Mismatches: 60, Indels: 52
0.73 0.14 0.12
Matches are distributed among these distances:
27 5 0.02
28 68 0.22
29 145 0.47
30 72 0.23
31 20 0.06
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATGTTCGAGGGT
Found at i:210210 original size:58 final size:58
Alignment explanation
Indices: 209881--210221 Score: 225
Period size: 58 Copynumber: 5.9 Consensus size: 58
209871 TGGTTGTCTA
* * * * *
209881 AGGGTAAAACGATAATTTTTGGACAGTCGGGGGTAAAATGGTAATTTTTGGACACCCG
1 AGGGTAAAATGGTAATTTTTGGACACTCGAGGGTAAAATGGTAATTTTTGGACACTCG
* * ***
209939 -GAGGTAAAATGGTAATTTTTAGACACTCGAGGGTAAAATGATAA-TTTTGGATGTTCG
1 AG-GGTAAAATGGTAATTTTTGGACACTCGAGGGTAAAATGGTAATTTTTGGACACTCG
* * * * * * *
209996 AGGGTAAAATGGTAATTTTTTGAAAATTCGAGGGTAAAATGGTAATTTTTAGAAAGTTTG
1 AGGGTAAAATGGTAA-TTTTTGGACACTCGAGGGTAAAATGGTAATTTTTGGACA-CTCG
* * ** **
210056 -GGGTCAAAAAT-GTGATTTTTGGACA-TCCG-GTGGTAAAATGGTAA-TTTTGTA-TGTTT
1 AGGGT--AAAATGGTAATTTTTGGACACT-CGAG-GGTAAAATGGTAATTTTTGGACACTCG
* * * * * *
210112 AGGGGTGAATTGGTAA-TTTTGGAAAGTTC-AGGGTAAAAAATGGTAATGTTTGGACACCCG
1 A-GGGTAAAATGGTAATTTTTGGACA-CTCGAGGGT--AAAATGGTAATTTTTGGACACTCG
* * *
210172 AGGGTAAAACGGTAATTTTTGGACACTTGAGGGTAAAATTGTAATTTTTG
1 AGGGTAAAATGGTAATTTTTGGACACTCGAGGGTAAAATGGTAATTTTTG
210222 AGAAGTTTGG
Statistics
Matches: 216, Mismatches: 46, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
56 16 0.07
57 28 0.13
58 97 0.45
59 50 0.23
60 20 0.09
61 5 0.02
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTTGGACACTCGAGGGTAAAATGGTAATTTTTGGACACTCG
Found at i:210221 original size:117 final size:115
Alignment explanation
Indices: 209868--210255 Score: 328
Period size: 117 Copynumber: 3.3 Consensus size: 115
209858 AAACGATAAT
* * * * * *
209868 TTTTGGTTGTCTA-AGGGTAAAACGATAATTTTTGG-ACAGTCGGGGGTAAAATGGTAATTTTTG
1 TTTTGGATGT-TAGAGGGTAAAATGGTAATTTTTGGAAAATTCGAGGGTAAAATGGTAATTTTTG
* *
209931 GACACCCGGAGGTAAAATGGTAATTTTTAGACACTCGAGGGTAAAA-TGATAA
65 GACACCCGG-GGTAAAAAGGTAATTTTTGGACACTCGAGGGTAAAATTG-TAA
* * *
209983 TTTTGGATGTTCGAGGGTAAAATGGTAATTTTTTGAAAATTCGAGGGTAAAATGGTAATTTTTAG
1 TTTTGGATGTTAGAGGGTAAAATGGTAATTTTTGGAAAATTCGAGGGTAAAATGGTAATTTTTGG
* *** * * *
210048 AAAGTTTGGGGTCAAAAATGTGATTTTTGGACA-TCCG-GTGGTAAAATGGTAA
66 ACA-CCCGGGGT-AAAAAGGTAATTTTTGGACACT-CGAG-GGTAAAATTGTAA
* * * * *
210100 TTTTGTATGTTTAG-GGGTGAATTGGTAA-TTTTGGAAAGTTC-AGGGTAAAAAATGGTAATGTT
1 TTTTGGATG-TTAGAGGGTAAAATGGTAATTTTTGGAAAATTCGAGGGT--AAAATGGTAATTTT
* *
210162 TGGACACCCGAGGGTAAAACGGTAATTTTTGGACACTTGAGGGTAAAATTGTAA
63 TGGACACCCG-GGGTAAAAAGGTAATTTTTGGACACTCGAGGGTAAAATTGTAA
* *
210216 TTTTTGAGAAGTTTG-GGAGTCAAAAT-GTAATTTTTGGAAA
1 -TTTTG-GATGTTAGAGG-GT-AAAATGGTAATTTTTGGAAA
210256 GTTTGATGCC
Statistics
Matches: 215, Mismatches: 40, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
114 1 0.00
115 33 0.15
116 74 0.34
117 83 0.39
118 12 0.06
119 12 0.06
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (115 bp):
TTTTGGATGTTAGAGGGTAAAATGGTAATTTTTGGAAAATTCGAGGGTAAAATGGTAATTTTTGG
ACACCCGGGGTAAAAAGGTAATTTTTGGACACTCGAGGGTAAAATTGTAA
Found at i:210269 original size:29 final size:29
Alignment explanation
Indices: 210206--210270 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
210196 ACTTGAGGGT
*
210206 AAAATTGTAATTTTTGAGAAGTTTGGGAGTC
1 AAAA-TGTAATTTTTGAGAAGTTT-GGAGCC
210237 AAAATGTAATTTTTG-GAAAGTTT-GATGCC
1 AAAATGTAATTTTTGAG-AAGTTTGGA-GCC
210266 AAAAT
1 AAAAT
210271 ACGATTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 2 0.06
29 8 0.26
30 17 0.55
31 4 0.13
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTTTGGAGCC
Found at i:210815 original size:20 final size:21
Alignment explanation
Indices: 210790--210830 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
210780 ATCATTTTAA
210790 CTTCCTTTC-TAAAAAAAAGC
1 CTTCCTTTCTTAAAAAAAAGC
*
210810 CTTCCTTTCTTCAAAAAAAGC
1 CTTCCTTTCTTAAAAAAAAGC
210831 TCTCAAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (21 bp):
CTTCCTTTCTTAAAAAAAAGC
Found at i:211759 original size:33 final size:33
Alignment explanation
Indices: 211721--211795 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
211711 TTGCAACGGC
*
211721 GGTGGCAGTAGATGGGCGATGATGCAACTTGGT
1 GGTGGCAGCAGATGGGCGATGATGCAACTTGGT
* *
211754 GGTGGCAGCAGATGGGCGGTGGTGCAACTTGGT
1 GGTGGCAGCAGATGGGCGATGATGCAACTTGGT
211787 GGTGGCAGC
1 GGTGGCAGC
211796 TGGTGACGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.17, C:0.15, G:0.47, T:0.21
Consensus pattern (33 bp):
GGTGGCAGCAGATGGGCGATGATGCAACTTGGT
Found at i:213990 original size:19 final size:19
Alignment explanation
Indices: 213954--213991 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
213944 ATTATTGTCA
213954 AAAAATATTATTGATTAAAT
1 AAAAATATTATT-ATTAAAT
213974 AAAAATATATATT-TTAAA
1 AAAAATAT-TATTATTAAA
213992 CATAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAATATTATTATTAAAT
Found at i:216023 original size:22 final size:21
Alignment explanation
Indices: 215988--216032 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
215978 TTTTTATTTA
*
215988 TTAATCAAGTTCTCTTGAGAGTC
1 TTAATCAAATTCTCTT-AG-GTC
216011 TTAAT-AAATTCTCTTAGGTC
1 TTAATCAAATTCTCTTAGGTC
216031 TT
1 TT
216033 GTTTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 2 0.10
22 9 0.43
23 5 0.24
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (21 bp):
TTAATCAAATTCTCTTAGGTC
Found at i:216111 original size:50 final size:50
Alignment explanation
Indices: 215994--216104 Score: 206
Period size: 50 Copynumber: 2.2 Consensus size: 50
215984 TTTATTAATC
215994 AAGTT-CTCTTGAGAGTCTTAATAAATTCTCTTAGGTCTTGTTTATTTTAG
1 AAGTTGCT-TTGAGAGTCTTAATAAATTCTCTTAGGTCTTGTTTATTTTAG
216044 AAGTTGCTTTGAGAGTCTTAATAAATTCTCTTAGGTCTTGTTTATTTTAG
1 AAGTTGCTTTGAGAGTCTTAATAAATTCTCTTAGGTCTTGTTTATTTTAG
216094 AAGTTGCTTTG
1 AAGTTGCTTTG
216105 GTAGTCTCTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
50 58 0.97
51 2 0.03
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (50 bp):
AAGTTGCTTTGAGAGTCTTAATAAATTCTCTTAGGTCTTGTTTATTTTAG
Found at i:230587 original size:15 final size:16
Alignment explanation
Indices: 230567--230607 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
230557 GTGTAAAGTA
230567 AGAATCAAAATGATC-
1 AGAATCAAAATGATCT
230582 AGAATCAAAATGATCT
1 AGAATCAAAATGATCT
*
230598 AGCATCAAAA
1 AGAATCAAAA
230608 GATACTCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (16 bp):
AGAATCAAAATGATCT
Found at i:233225 original size:18 final size:19
Alignment explanation
Indices: 233190--233228 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
233180 AATAAATATA
233190 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
233209 AATA-AATTATAAA-TTAAT
1 AATACAATT-TAAATTTAAT
233227 AA
1 AA
233229 AAAGAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Found at i:234120 original size:11 final size:11
Alignment explanation
Indices: 234106--234165 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
234096 TTTTGTAGGT
234106 TTTTGGTGCTG
1 TTTTGGTGCTG
*
234117 TTTTAGTGCTG
1 TTTTGGTGCTG
*
234128 TTGTTGGTGCTA
1 TT-TTGGTGCTG
* *
234140 TTTTTGTGTTG
1 TTTTGGTGCTG
*
234151 TTTTGGTGCTA
1 TTTTGGTGCTG
234162 TTTT
1 TTTT
234166 ATTGTTGTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
11 30 0.77
12 9 0.23
ACGTcount: A:0.05, C:0.07, G:0.28, T:0.60
Consensus pattern (11 bp):
TTTTGGTGCTG
Found at i:234159 original size:22 final size:22
Alignment explanation
Indices: 234106--234175 Score: 88
Period size: 22 Copynumber: 3.1 Consensus size: 22
234096 TTTTGTAGGT
* * *
234106 TTTTGGTGCTGTTTTAGTGCTG
1 TTTTGGTGCTATTTTTGTGTTG
234128 TTGTTGGTGCTATTTTTGTGTTG
1 TT-TTGGTGCTATTTTTGTGTTG
234151 TTTTGGTGCTATTTTAT-TGTTG
1 TTTTGGTGCTATTTT-TGTGTTG
234173 TTT
1 TTT
234176 CATAGCTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 23 0.53
23 20 0.47
ACGTcount: A:0.06, C:0.06, G:0.27, T:0.61
Consensus pattern (22 bp):
TTTTGGTGCTATTTTTGTGTTG
Found at i:235311 original size:13 final size:13
Alignment explanation
Indices: 235293--235320 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
235283 TATTTTTCCT
235293 ATTGTTATTTTAA
1 ATTGTTATTTTAA
235306 ATTGTTATTTTAA
1 ATTGTTATTTTAA
235319 AT
1 AT
235321 ATTTGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
ATTGTTATTTTAA
Found at i:244802 original size:22 final size:23
Alignment explanation
Indices: 244754--244802 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
244744 TAAAAACTTT
244754 TAAAAAAACTAAATAAAAATAAC
1 TAAAAAAACTAAATAAAAATAAC
* * *
244777 -AAAAACACTAAA-ACAAATTAC
1 TAAAAAAACTAAATAAAAATAAC
244798 TAAAA
1 TAAAA
244803 TAAAAACAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.16
Consensus pattern (23 bp):
TAAAAAAACTAAATAAAAATAAC
Found at i:245117 original size:27 final size:29
Alignment explanation
Indices: 245082--245136 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
245072 TTACATATCT
* *
245082 GAAATTTAATTTTTTA-T-TTTTAATTTC
1 GAAAATTAATTTTCTATTATTTTAATTTC
245109 GAAAATTAATTTTCTATTATTTTAATTT
1 GAAAATTAATTTTCTATTATTTTAATTT
245137 AATAATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 14 0.58
28 1 0.04
29 9 0.38
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (29 bp):
GAAAATTAATTTTCTATTATTTTAATTTC
Found at i:245904 original size:4 final size:4
Alignment explanation
Indices: 245895--245920 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
245885 TACAACAATA
245895 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
245921 CTGATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Done.