Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015202.1 Kokia drynarioides strain JFW-HI SEQ_130246, 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: 539317
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 763 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:6468 original size:12 final size:13
Alignment explanation
Indices: 6451--6479 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6441 ATGTGGGTGA
6451 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
6463 AAAAATAAAAAAT
1 AAAAATAAAAAAT
6476 AAAA
1 AAAA
6480 TTACTTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:11066 original size:33 final size:33
Alignment explanation
Indices: 11029--11112 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
11019 AAGCACAAGT
* * *
11029 AGAAGTCCTGCAAGATCTCGGAGAAGCATTAGC
1 AGAAGTCCTGTAAGATCTAGGAGAAGCAATAGC
* **
11062 AGAAGCCCCATAAGATCTAGGAGAAGCAATAGC
1 AGAAGTCCTGTAAGATCTAGGAGAAGCAATAGC
11095 AGAAGTCCTGTAAGATCT
1 AGAAGTCCTGTAAGATCT
11113 TCTAAGAGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (33 bp):
AGAAGTCCTGTAAGATCTAGGAGAAGCAATAGC
Found at i:22037 original size:12 final size:13
Alignment explanation
Indices: 21991--22032 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
21981 AATTCTAAGA
21991 TTATTGAAAAGTATT
1 TTATT-AAAA-TATT
22006 ATTATT-AAATATT
1 -TTATTAAAATATT
22019 TTATTAAAATATT
1 TTATTAAAATATT
22032 T
1 T
22033 GTTAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 12 0.48
14 3 0.12
16 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (13 bp):
TTATTAAAATATT
Found at i:26755 original size:4 final size:4
Alignment explanation
Indices: 26746--26773 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
26736 AACCATTGAT
26746 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
26774 ATGTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:35778 original size:6 final size:6
Alignment explanation
Indices: 35767--35808 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
35757 AATATTCTGT
* *
35767 CCATGC CCATGC CCATGC CCATGC CCGTGC CCGTGC CCATGC
1 CCATGC CCATGC CCATGC CCATGC CCATGC CCATGC CCATGC
35809 ATGGCATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.12, C:0.50, G:0.21, T:0.17
Consensus pattern (6 bp):
CCATGC
Found at i:46404 original size:29 final size:30
Alignment explanation
Indices: 46358--46430 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
46348 AACTATATAT
* *
46358 AAATTATGATTTAGTGTGGAATTGTATACGTG
1 AAATTTTGATTT--TGTGGAATTGTATACATG
* * *
46390 -CATTTTGATTTTGTGTAATTTTATACATG
1 AAATTTTGATTTTGTGGAATTGTATACATG
46419 AAATTTTGATTT
1 AAATTTTGATTT
46431 GATCCAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 15 0.44
30 10 0.29
31 9 0.26
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (30 bp):
AAATTTTGATTTTGTGGAATTGTATACATG
Found at i:46669 original size:31 final size:29
Alignment explanation
Indices: 46611--46669 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
46601 AGAGTTTCAT
* *
46611 AATTACACCAAATCGAAGTTTACATATAC
1 AATTACACCAAATCAAAATTTACATATAC
*
46640 AATTACACATCAAATCAAAATTTATATATA
1 AATTACAC--CAAATCAAAATTTACATATA
46670 ATTTTGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
31 17 0.68
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (29 bp):
AATTACACCAAATCAAAATTTACATATAC
Found at i:65868 original size:6 final size:6
Alignment explanation
Indices: 65857--65896 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
65847 AGCTAAGCCC
65857 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCA
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTCA
65897 TCTACTCGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.17
Consensus pattern (6 bp):
CTCAGG
Found at i:87351 original size:24 final size:24
Alignment explanation
Indices: 87323--87382 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
87313 CTAGACTAAT
87323 AAGAGTTTAACTCAAACAAATAAA
1 AAGAGTTTAACTCAAACAAATAAA
* * * *
87347 AAGAGTTTAATTGAAACTATTAAA
1 AAGAGTTTAACTCAAACAAATAAA
*
87371 CAGAGTTTAACT
1 AAGAGTTTAACT
87383 AAAAGATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (24 bp):
AAGAGTTTAACTCAAACAAATAAA
Found at i:93514 original size:17 final size:18
Alignment explanation
Indices: 93484--93517 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
93474 TCATACTCAA
93484 TCTATATTTAGCTTATGC
1 TCTATATTTAGCTTATGC
*
93502 TCTA-ATTTTGCTTATG
1 TCTATATTTAGCTTATG
93518 TTTTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.53
Consensus pattern (18 bp):
TCTATATTTAGCTTATGC
Found at i:94937 original size:60 final size:60
Alignment explanation
Indices: 94844--94998 Score: 274
Period size: 60 Copynumber: 2.6 Consensus size: 60
94834 AAAAAAATTG
*
94844 GTGTTGGCCATGCAATGGTTGACACCCCCTTTTTTATCTGATAGAAAATTCAATTTTTTA
1 GTGTTGGCCATGCAATGGTTGACACCCCCTTTTTTATCTGACAGAAAATTCAATTTTTTA
94904 GTGTTGGCCATGCAATGGTTGACACCCCCTTTTTTATCTGACAGAAAATTCAATTTTTTA
1 GTGTTGGCCATGCAATGGTTGACACCCCCTTTTTTATCTGACAGAAAATTCAATTTTTTA
** *
94964 GTGTTGGCCATGCAATGGCCGACACCCCTTTTTTT
1 GTGTTGGCCATGCAATGGTTGACACCCCCTTTTTT
94999 CAGATAATTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (60 bp):
GTGTTGGCCATGCAATGGTTGACACCCCCTTTTTTATCTGACAGAAAATTCAATTTTTTA
Found at i:95793 original size:61 final size:60
Alignment explanation
Indices: 95528--95830 Score: 287
Period size: 60 Copynumber: 5.0 Consensus size: 60
95518 AGAGGAAGTT
* * * * **
95528 GGTGTCGGCCATTATATGGCCAACACCAAAAAAATTTAA-TTTTTTACCAAATAAAAAAGG
1 GGTGTCGGCCATTACATGACCAACACC-AAAAAATTGAATTTTTTTATCTGATAAAAAAGG
** * *
95588 GGTGTCGGCCATGGCATGACCAACACAAAAAAAATCGAA-TTTTTTATCTGA-AAAAAAGG
1 GGTGTCGGCCATTACATGACCAACAC-CAAAAAATTGAATTTTTTTATCTGATAAAAAAGG
* * *
95647 AGGTGTCGACTA-TAGCATGACCAACACCAAAATATTTTGAAATTTTTTTATCTG---AAAAAGG
1 -GGTGTCGGCCATTA-CATGACCAACACCAAAA-A-ATTG-AATTTTTTTATCTGATAAAAAAGG
* * * *
95708 GGTGTCGGCTATTGCATGGCCAACACCAAAAAATTGAATTTTTTTATCTGATAAAAAAAAG
1 GGTGTCGGCCATTACATGACCAACACCAAAAAATTGAATTTTTTTATCTGAT-AAAAAAGG
* * * *
95769 GGTGTTGGCCATTACATGACCAACACCTAAAAATTTAATTTTTTTATCAGATTAAAAAAGG
1 GGTGTCGGCCATTACATGACCAACACCAAAAAATTGAATTTTTTTATCTGA-TAAAAAAGG
95830 G
1 G
95831 CGTCAGTCAT
Statistics
Matches: 200, Mismatches: 30, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
57 14 0.07
58 3 0.01
59 13 0.06
60 88 0.44
61 68 0.34
62 3 0.01
63 11 0.05
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (60 bp):
GGTGTCGGCCATTACATGACCAACACCAAAAAATTGAATTTTTTTATCTGATAAAAAAGG
Found at i:95853 original size:60 final size:60
Alignment explanation
Indices: 95723--95859 Score: 150
Period size: 61 Copynumber: 2.3 Consensus size: 60
95713 CGGCTATTGC
* * ** * *
95723 ATGGCCAACACCAAAAAATTGAATTTTTTTATCTGATAAAAAAAAGGGTGTTGGCCATTAC
1 ATGGCCAACACC-AAAAATTGAATTTTTTTATCAGATAAAAAAAAGGGCGTCAGCCATGAA
* * * *
95784 ATGACCAACACCTAAAAATTTAATTTTTTTATCAGAT-TAAAAAAGGGCGTCAGTCATGAA
1 ATGGCCAACACC-AAAAATTGAATTTTTTTATCAGATAAAAAAAAGGGCGTCAGCCATGAA
*
95844 ATGGTCAACACCAAAA
1 ATGGCCAACACCAAAA
95860 TTTTTTTTCT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
59 4 0.06
60 26 0.41
61 33 0.52
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (60 bp):
ATGGCCAACACCAAAAATTGAATTTTTTTATCAGATAAAAAAAAGGGCGTCAGCCATGAA
Found at i:102432 original size:3 final size:3
Alignment explanation
Indices: 102418--102448 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
102408 AAATTTGGAA
102418 ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
102449 GTTGTTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:130788 original size:14 final size:14
Alignment explanation
Indices: 130771--130815 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
130761 CAGGAAAAAT
130771 ATTTAATCGTATCA
1 ATTTAATCGTATCA
*
130785 ATTTATAT-GAAT--
1 ATTTA-ATCGTATCA
130797 ATTTAATCGTATCA
1 ATTTAATCGTATCA
130811 ATTTA
1 ATTTA
130816 TATGAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
11 2 0.08
12 8 0.32
14 13 0.52
15 2 0.08
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (14 bp):
ATTTAATCGTATCA
Found at i:130804 original size:26 final size:26
Alignment explanation
Indices: 130768--130824 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
130758 TTGCAGGAAA
130768 AATATTTAATCGTATCAATTTATATG
1 AATATTTAATCGTATCAATTTATATG
130794 AATATTTAATCGTATCAATTTATATG
1 AATATTTAATCGTATCAATTTATATG
130820 AATAT
1 AATAT
130825 ATCATTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (26 bp):
AATATTTAATCGTATCAATTTATATG
Found at i:132603 original size:54 final size:54
Alignment explanation
Indices: 132521--132641 Score: 224
Period size: 54 Copynumber: 2.2 Consensus size: 54
132511 TGAGAAGTAC
*
132521 ATAAAAATTTGAGAAATGAAGGTGACTGGACATAGCATAAAAATCAAGCTAGGA
1 ATAAAAATTTGAGAAATGAAAGTGACTGGACATAGCATAAAAATCAAGCTAGGA
132575 ATAAAAATTTGAGAAATGAAAGTGACTGGACATAGCATAAAAATCAAGCTAGGA
1 ATAAAAATTTGAGAAATGAAAGTGACTGGACATAGCATAAAAATCAAGCTAGGA
132629 ATAAAAATATTGA
1 ATAAAAAT-TTGA
132642 ATTAGACATG
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
54 61 0.94
55 4 0.06
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.21
Consensus pattern (54 bp):
ATAAAAATTTGAGAAATGAAAGTGACTGGACATAGCATAAAAATCAAGCTAGGA
Found at i:142215 original size:22 final size:22
Alignment explanation
Indices: 142179--142232 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
142169 AAATATTGAG
* *
142179 AAAACAACAAGAAAATAGAAGC
1 AAAACAACAAAAAAAAAGAAGC
* *
142201 AAAACAATAAAAAAAAAGGAGC
1 AAAACAACAAAAAAAAAGAAGC
142223 AAGAA-AACAA
1 AA-AACAACAA
142233 CAGTTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (22 bp):
AAAACAACAAAAAAAAAGAAGC
Found at i:142814 original size:26 final size:25
Alignment explanation
Indices: 142784--142837 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
142774 TTCTTCTATT
*
142784 TTAATAACAATTTATATGTAAATAAA
1 TTAATAACAATTTACATGT-AATAAA
*
142810 TTAATGACAATTTACATGTAATAAA
1 TTAATAACAATTTACATGTAATAAA
142835 TTA
1 TTA
142838 GTAAACTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (25 bp):
TTAATAACAATTTACATGTAATAAA
Found at i:143582 original size:65 final size:65
Alignment explanation
Indices: 143499--143703 Score: 292
Period size: 65 Copynumber: 3.2 Consensus size: 65
143489 TCTTTTTTTT
* **
143499 TTTTCATCTTCTTCGATTCTCTCTTTTGAGAAACAAAAACTCTAGAGATCCTTAGAGAAATAAT-
1 TTTTCTTCTTCTTCGATTCTCTCTTTTGAGAAACAAAAACTCTAGAGATTTTTAGAGAAATAATC
* *
143563 TGTTTCTTCTTCTTTGATTCTCTCTTTTGAAAAACAAAAAACTC--GAGATTTTTAGAGAAATAA
1 T-TTTCTTCTTCTTCGATTCTCTCTTTTGAGAAAC-AAAAACTCTAGAGATTTTTAGAGAAATAA
143626 TC
64 TC
*
143628 TCTTCTTCTTCTTCGATTC-CTTCTTTTGAGAAACAAAAACTCTAGAGATTTTTAGAGAAATAAT
1 TTTTCTTCTTCTTCGATTCTC-TCTTTTGAGAAACAAAAACTCTAGAGATTTTTAGAGAAATAAT
143692 C
65 C
*
143693 TCTTCTTCTTC
1 TTTTCTTCTTC
143704 AATATTGTCC
Statistics
Matches: 127, Mismatches: 8, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
63 9 0.07
64 47 0.37
65 63 0.50
66 8 0.06
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (65 bp):
TTTTCTTCTTCTTCGATTCTCTCTTTTGAGAAACAAAAACTCTAGAGATTTTTAGAGAAATAATC
Found at i:153662 original size:24 final size:24
Alignment explanation
Indices: 153611--153665 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
153601 TCTTTTAGTT
* * *
153611 AAACTTTGTTTATTTGTTTCAATT
1 AAACTCTGTTTAGTTGTTTCAATC
* *
153635 AAACTCTGTTTAGTTGTTTGAGTC
1 AAACTCTGTTTAGTTGTTTCAATC
153659 AAACTCT
1 AAACTCT
153666 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTAGTTGTTTCAATC
Found at i:154692 original size:17 final size:17
Alignment explanation
Indices: 154670--154704 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
154660 GTATATATAT
154670 ACACAGCAACAAGAAGC
1 ACACAGCAACAAGAAGC
154687 ACACAGCAACAAGAAGC
1 ACACAGCAACAAGAAGC
154704 A
1 A
154705 AGCTAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.29, G:0.17, T:0.00
Consensus pattern (17 bp):
ACACAGCAACAAGAAGC
Found at i:155751 original size:2 final size:2
Alignment explanation
Indices: 155744--155775 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
155734 CACTTGTGGT
155744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
155776 TTTTAGAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:158693 original size:2 final size:2
Alignment explanation
Indices: 158686--158710 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
158676 GACCATCCAC
158686 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
158711 AACCAAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:160041 original size:2 final size:2
Alignment explanation
Indices: 160034--160065 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
160024 TAACAGAATA
160034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160066 TTCTCTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160473 original size:7 final size:7
Alignment explanation
Indices: 160461--160488 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
160451 CACTGCTACT
160461 GCCCACC
1 GCCCACC
160468 GCCCACC
1 GCCCACC
160475 GCCCACC
1 GCCCACC
160482 GCCCACC
1 GCCCACC
160489 CTTTCATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.71, G:0.14, T:0.00
Consensus pattern (7 bp):
GCCCACC
Found at i:165858 original size:18 final size:18
Alignment explanation
Indices: 165832--165872 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
165822 TGCCATTATA
*
165832 ATTTTAAATAATAATACT
1 ATTTAAAATAATAATACT
* *
165850 ATTTAAAATATTAATATT
1 ATTTAAAATAATAATACT
165868 ATTTA
1 ATTTA
165873 TTCGTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTAAAATAATAATACT
Found at i:165899 original size:10 final size:10
Alignment explanation
Indices: 165886--165928 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
165876 GTATTATTTT
165886 AATATATAAA
1 AATATATAAA
165896 AATATTATAAA
1 AATA-TATAAA
* *
165907 AACATAAAAA
1 AATATATAAA
*
165917 AATATACAAA
1 AATATATAAA
165927 AA
1 AA
165929 AACATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (10 bp):
AATATATAAA
Found at i:170355 original size:2 final size:2
Alignment explanation
Indices: 170348--170385 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
170338 TTTTCCCCTT
170348 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
170386 GAATAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:173289 original size:2 final size:2
Alignment explanation
Indices: 173282--173315 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
173272 CCTTCAGGAA
*
173282 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173316 GTAAAATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:176644 original size:14 final size:15
Alignment explanation
Indices: 176615--176649 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
176605 AGTCAAATAT
176615 AATAAAAAAAACAAA
1 AATAAAAAAAACAAA
*
176630 AATAAAATAAA-AAA
1 AATAAAAAAAACAAA
176644 AATAAA
1 AATAAA
176650 GGTAAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (15 bp):
AATAAAAAAAACAAA
Found at i:183849 original size:26 final size:24
Alignment explanation
Indices: 183809--183856 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
183799 TCTACATGGG
183809 CATAATTTCTCATATTCATCATTTCT
1 CATAATTTCTCATA-TCA-CATTTCT
183835 CATAATTTCAT-ATATCACATTT
1 CATAATTTC-TCATATCACATTT
183857 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 12 0.57
27 1 0.05
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (24 bp):
CATAATTTCTCATATCACATTTCT
Found at i:184469 original size:20 final size:20
Alignment explanation
Indices: 184444--184485 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
184434 CTAGTATATC
184444 TCGAAATATGCAGTTCCTTT
1 TCGAAATATGCAGTTCCTTT
184464 TCGAAATATGCAGTTCCTTT
1 TCGAAATATGCAGTTCCTTT
184484 TC
1 TC
184486 TTTCATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (20 bp):
TCGAAATATGCAGTTCCTTT
Found at i:193419 original size:19 final size:19
Alignment explanation
Indices: 193361--193409 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
193351 AATTTAGGAG
*
193361 GGTTTGAGTAAAAAAATTA
1 GGTTTGAATAAAAAAATTA
193380 GGTTTGAATAAAAAAATTA
1 GGTTTGAATAAAAAAATTA
193399 GGTTTGAATAA
1 GGTTTGAATAA
193410 TAGATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (19 bp):
GGTTTGAATAAAAAAATTA
Found at i:194322 original size:13 final size:13
Alignment explanation
Indices: 194304--194337 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
194294 TTTGACAAAA
194304 CACACACACATTG
1 CACACACACATTG
194317 CACACACACATTG
1 CACACACACATTG
194330 CACACACA
1 CACACACA
194338 AGTGCTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.41, G:0.06, T:0.12
Consensus pattern (13 bp):
CACACACACATTG
Found at i:195416 original size:28 final size:28
Alignment explanation
Indices: 195381--195442 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
195371 CAATGAAACT
* **
195381 TTTTGGATACTCGGGGGCAAAATGGTAA
1 TTTTGGATACTCGGGAGCAAAATAATAA
*
195409 TTTTGGATTCTCGGGAGCAAAATAATAA
1 TTTTGGATACTCGGGAGCAAAATAATAA
195437 TTTTGG
1 TTTTGG
195443 GGAAATTCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (28 bp):
TTTTGGATACTCGGGAGCAAAATAATAA
Found at i:195555 original size:29 final size:29
Alignment explanation
Indices: 195480--195585 Score: 87
Period size: 29 Copynumber: 3.7 Consensus size: 29
195470 TTAGACATTG
*
195480 GGGGTAAAAGGGTAA-TTTTGAGAGT-TTC-
1 GGGGTAAAATGGTAATTTTTGA-A-TATTCA
* *
195508 GAGGTCAAAATGG-AGTTTTTGAATATTCA
1 GGGGT-AAAATGGTAATTTTTGAATATTCA
*
195537 GGGGTAAAATGGTAATTTTTGAA-ACTTTA
1 GGGGTAAAATGGTAATTTTTGAATA-TTCA
*
195566 GGGGTTAAAATGGAAATTTT
1 GGGG-TAAAATGGTAATTTT
195586 AGAGGTTTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
27 1 0.02
28 17 0.27
29 32 0.50
30 14 0.22
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGAATATTCA
Found at i:195615 original size:21 final size:21
Alignment explanation
Indices: 195591--195637 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
195581 ATTTTAGAGG
195591 TTTGAGGG-TAAAAATGGAATT
1 TTTG-GGGTTAAAAATGGAATT
195612 TTTGGGGTTAAAAATGGAATT
1 TTTGGGGTTAAAAATGGAATT
195633 TTTGG
1 TTTGG
195638 AAATTTCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.32, C:0.00, G:0.30, T:0.38
Consensus pattern (21 bp):
TTTGGGGTTAAAAATGGAATT
Found at i:195649 original size:79 final size:80
Alignment explanation
Indices: 195542--195695 Score: 197
Period size: 79 Copynumber: 1.9 Consensus size: 80
195532 ATTCAGGGGT
* *
195542 AAAATGGTAATTTTTGAAACTTTAGGGGTT-AAAATGGAAATTTTAGAGGTTTGAGGGTAAAAAT
1 AAAATGGTAATTTTTGAAACTTTAGGGGTTGAAAATGG-AATTTTAGAAGTTCGAGGGTAAAAAT
195606 GGAATTTTTGGGGTTA
65 GGAATTTTTGGGGTTA
* * * * *
195622 AAAATGG-AATTTTTGGAAA-TTTCGGGGTTGAAAATGGGATTTTGGAAGTTCGGGGGTAGAAAT
1 AAAATGGTAATTTTT-GAAACTTTAGGGGTTGAAAATGGAATTTTAGAAGTTCGAGGGTAAAAAT
*
195685 GGGATTTTTGG
65 GGAATTTTTGG
195696 AAGTTTCGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
79 46 0.72
80 18 0.28
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (80 bp):
AAAATGGTAATTTTTGAAACTTTAGGGGTTGAAAATGGAATTTTAGAAGTTCGAGGGTAAAAATG
GAATTTTTGGGGTTA
Found at i:195668 original size:59 final size:59
Alignment explanation
Indices: 195615--195850 Score: 332
Period size: 59 Copynumber: 4.0 Consensus size: 59
195605 TGGAATTTTT
* * * ** *
195615 GGGGTTAAAAATGGAATTTTTGGAAATTTCGGGGTTGAAAATGGGA-TTTTGGAAGTTC
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* * *
195673 GGGGGTAGAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTTGAAGTTC
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC
*
195732 GAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC
* **
195791 GGGGGTAAAAATGGAATTTTTGGAAG-TTCTAGGGTTTAAAATGGAATTTTTGGAAGTTC
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAATGGAATTTTTGGAAGTTC
195850 G
1 G
195851 AGGGACCTCC
Statistics
Matches: 159, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
58 42 0.26
59 117 0.74
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (59 bp):
GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC
Found at i:195677 original size:29 final size:30
Alignment explanation
Indices: 195615--195850 Score: 270
Period size: 30 Copynumber: 8.0 Consensus size: 30
195605 TGGAATTTTT
*
195615 GGGGTTAAAAATGGAATTTTTGGAAATTTC-
1 GGGGTTAAAAATGGAATTTTTGG-AAGTTCG
* *
195645 GGGGTTGAAAATGGGA-TTTTGGAAGTTCG
1 GGGGTTAAAAATGGAATTTTTGGAAGTTCG
* *
195674 GGGG-TAGAAATGGGATTTTTGGAAGTTTC-
1 GGGGTTAAAAATGGAATTTTTGGAAG-TTCG
* * *
195703 GAGGTCAAAAATGGAATTTTTTGAAGTTCG
1 GGGGTTAAAAATGGAATTTTTGGAAGTTCG
*
195733 AGGG-TAAAAATGGAATTTTTGGAAGTTTC-
1 GGGGTTAAAAATGGAATTTTTGGAAG-TTCG
* *
195762 GAGGTCAAAAATGGAATTTTTGGAAGTTCG
1 GGGGTTAAAAATGGAATTTTTGGAAGTTCG
*
195792 GGGG-TAAAAATGGAATTTTTGGAAGTTCT
1 GGGGTTAAAAATGGAATTTTTGGAAGTTCG
* *
195821 AGGGTTTAAAATGGAATTTTTGGAAGTTCG
1 GGGGTTAAAAATGGAATTTTTGGAAGTTCG
195851 AGGGACCTCC
Statistics
Matches: 174, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
28 14 0.08
29 75 0.43
30 85 0.49
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (30 bp):
GGGGTTAAAAATGGAATTTTTGGAAGTTCG
Found at i:197575 original size:17 final size:16
Alignment explanation
Indices: 197567--197629 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 16
197557 TAAATATATT
197567 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTA-AA
197585 TAAATTTAAATTTTAAA
1 TAAATTTAAA-TTTAAA
*
197602 TAAATTTAAACTTAAAA
1 TAAATTTAAA-TTTAAA
197619 TAAATTTAAAT
1 TAAATTTAAAT
197630 CTTGTTGGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.02
17 33 0.79
18 8 0.19
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:197591 original size:24 final size:23
Alignment explanation
Indices: 197554--197602 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
197544 ATTGAACTTG
*
197554 ATTTAAATATATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
197577 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAACTTTAA
197601 AT
1 AT
197603 AAATTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:197592 original size:34 final size:33
Alignment explanation
Indices: 197554--197629 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
197544 ATTGAACTTG
** * *
197554 ATTTAAATATATTTAAACTTTAAATTTATAATAA
1 ATTTAAATATAAATAAA-TTTAAACTTAAAATAA
*
197588 ATTTAAATTTTAAATAAATTTAAACTTAAAATAA
1 ATTTAAA-TATAAATAAATTTAAACTTAAAATAA
197622 ATTTAAAT
1 ATTTAAAT
197630 CTTGTTGGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 1 0.03
34 28 0.78
35 7 0.19
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (33 bp):
ATTTAAATATAAATAAATTTAAACTTAAAATAA
Found at i:197594 original size:6 final size:6
Alignment explanation
Indices: 197564--197629 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
197554 ATTTAAATAT
197564 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTAA A--TAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA
* *
197611 ACTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
197630 CTTGTTGGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
4 6 0.12
5 6 0.12
6 23 0.47
7 14 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:204359 original size:30 final size:28
Alignment explanation
Indices: 204325--204632 Score: 230
Period size: 29 Copynumber: 10.5 Consensus size: 28
204315 CCCAGGGGGC
204325 AAAATGGTAA-TTTTGGAAAGTTTGGGGTTA
1 AAAATGG-AATTTTTGG-AAGTTTGGGG-TA
* **
204355 AAAATGGAATTTTTAGACA-TCCGAGGGT-
1 AAAATGGAATTTTTGGA-AGTTTG-GGGTA
* * *
204383 AAAATGGTACTTTTGAAAGTTTTGGGGGTCAA
1 AAAATGGAATTTTTGGAAG-TTT-GGGGT--A
* * * *
204415 AAAAGGGAA-TTTTAGAGGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTA
* *
204443 AAAATTGAATTTTTGGAAGTCTCGGGGTCA
1 AAAATGGAATTTTTGGAAGT-TTGGGGT-A
204473 AAAATGGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-GGGGTA
*
204502 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTT-TGGGGTA
204531 AAAATGG-ATTTTTGGAAGTTTGGTGGTA
1 AAAATGGAATTTTTGGAAGTTTGG-GGTA
* * *
204559 AAAATGTAATTTTTAGAAGTTTCGGGGTTT
1 AAAATGGAATTTTTGGAAGTTT-GGGG-TA
* * *
204589 AAAATGTAATTTTTGGAAGTTCGAAGGTA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTA
**
204618 AAAATATAATTTTTG
1 AAAATGGAATTTTTG
204633 AATAGTTTAG
Statistics
Matches: 227, Mismatches: 31, Indels: 41
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.01
28 44 0.19
29 91 0.40
30 76 0.33
31 6 0.03
32 7 0.03
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTA
Found at i:204397 original size:58 final size:59
Alignment explanation
Indices: 204325--204543 Score: 163
Period size: 59 Copynumber: 3.7 Consensus size: 59
204315 CCCAGGGGGC
*
204325 AAAATGGTAATTTTGGAAAGTTTGGGGTTAAAAATGGAATTTTTAGACATCCGAGGGT-
1 AAAATGGTAATTTTGGAAAGTTTGGGGTAAAAAATGGAATTTTTAGACATCCGAGGGTA
* * ** *
204383 AAAATGGTACTTTT-GAAAGTTTTGGGGGTCAAAAAAGGGAA-TTTTAGAGGTTCGAGGGTA
1 AAAATGGTAATTTTGGAAAG-TTT-GGGGT-AAAAAATGGAATTTTTAGACATCCGAGGGTA
* * * * **
204443 AAAATTG-AATTTTTGG-AAGTCTCGGGGTCAAAAATGGAATTTTTGGA-AGT-TTAGGGGTA
1 AAAATGGTAA-TTTTGGAAAGT-TTGGGGTAAAAAATGGAATTTTTAGACA-TCCGA-GGGTA
*
204502 AAAATGG-AATTTTTGG-AAGTTCGGGGGT-AAAAATGG-ATTTTT
1 AAAATGGTAA-TTTTGGAAAGTT-TGGGGTAAAAAATGGAATTTTT
204544 GGAAGTTTGG
Statistics
Matches: 133, Mismatches: 17, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
57 11 0.08
58 35 0.26
59 63 0.47
60 23 0.17
61 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTGGAAAGTTTGGGGTAAAAAATGGAATTTTTAGACATCCGAGGGTA
Found at i:204501 original size:59 final size:56
Alignment explanation
Indices: 204438--204632 Score: 225
Period size: 59 Copynumber: 3.4 Consensus size: 56
204428 AGAGGTTCGA
204438 GGGTAAAAATTGAATTTTTGGAAGTCTCGGGGTCAAAAATGGAATTTTTGGAAGTTTAG
1 GGGTAAAAATTGAATTTTTGGAAGT-TCGGGGT-AAAAATGGAATTTTTGGAAGTTT-G
*
204497 GGGTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGG-ATTTTTGGAAGTTTG
1 GGGTAAAAATTGAATTTTTGGAAGTTC-GGGGTAAAAATGGAATTTTTGGAAGTTTG
* * * *
204553 GTGGTAAAAA-TGTAATTTTTAGAAGTTTCGGGGTTTAAAATGTAATTTTTGGAAGTTCG
1 G-GGTAAAAATTG-AATTTTTGGAAG-TTCGGGG-TAAAAATGGAATTTTTGGAAGTTTG
*
204612 AAGGTAAAAATAT-AATTTTTG
1 -GGGTAAAAAT-TGAATTTTTG
204633 AATAGTTTAG
Statistics
Matches: 119, Mismatches: 8, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
56 3 0.03
57 37 0.31
58 20 0.17
59 58 0.49
61 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (56 bp):
GGGTAAAAATTGAATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTGGAAGTTTG
Found at i:212759 original size:75 final size:75
Alignment explanation
Indices: 212673--212833 Score: 304
Period size: 75 Copynumber: 2.1 Consensus size: 75
212663 ATACCAATAA
212673 TTTAATTTTCTAAATCAATTATTTATTCAAACAAAACAATTATAAAATATTAACATTTTAAAAAT
1 TTTAATTTTCTAAATCAATTATTTATTCAAACAAAACAATTATAAAATATTAACATTTTAAAAAT
212738 CTCAAAAATT
66 CTCAAAAATT
212748 TTTAATTTTCTAAATCAATTATTTATTCAAACAAAACAATTATAAAATATTAACATTTTAAAAAT
1 TTTAATTTTCTAAATCAATTATTTATTCAAACAAAACAATTATAAAATATTAACATTTTAAAAAT
212813 CTCAAAAATT
66 CTCAAAAATT
* *
212823 TTAAAATTTCT
1 TTTAATTTTCT
212834 CATCTTAATA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (75 bp):
TTTAATTTTCTAAATCAATTATTTATTCAAACAAAACAATTATAAAATATTAACATTTTAAAAAT
CTCAAAAATT
Found at i:217514 original size:19 final size:19
Alignment explanation
Indices: 217451--217517 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
217441 CAACCATGTA
* * *
217451 TGACAAAAATTACCTTTTT
1 TGACAAAAATTGCCATTTC
* *
217470 TGACAAAACTTGGTCATTTC
1 TGACAAAAATT-GCCATTTC
* *
217490 TCACAAAAATTGCCATTCC
1 TGACAAAAATTGCCATTTC
217509 TGACAAAAA
1 TGACAAAAA
217518 CTATTTTGGT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 24 0.65
20 13 0.35
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (19 bp):
TGACAAAAATTGCCATTTC
Found at i:220139 original size:8 final size:8
Alignment explanation
Indices: 220126--220158 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
220116 TAAACTACTT
220126 GGGCAAAG
1 GGGCAAAG
220134 GGGCAAAG
1 GGGCAAAG
220142 GGGCAAAG
1 GGGCAAAG
220150 GGGCAAAG
1 GGGCAAAG
220158 G
1 G
220159 AATAGAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.52, T:0.00
Consensus pattern (8 bp):
GGGCAAAG
Found at i:222417 original size:2 final size:2
Alignment explanation
Indices: 222404--222435 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
222394 TAATTTTTAT
*
222404 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222436 ATAGTCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:223679 original size:60 final size:58
Alignment explanation
Indices: 223602--223713 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 58
223592 TCAAGAAGTG
*
223602 AAGTTCAGGTACCTAATTGGATCAAAATAAACTTTAGATACCAAATTGAACCTTAAAGCT
1 AAGTTCAGGTACCTAATTGGACCAAAA-AAAC-TTAGATACCAAATTGAACCTTAAAGCT
* * *
223662 AAGTTC-GAGTACCTAATTGGACCAAAAAAACTTAGGTATCAATTTGAACCTT
1 AAGTTCAG-GTACCTAATTGGACCAAAAAAACTTAGATACCAAATTGAACCTT
223714 GAAAACGAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 18 0.38
59 5 0.11
60 24 0.51
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (58 bp):
AAGTTCAGGTACCTAATTGGACCAAAAAAACTTAGATACCAAATTGAACCTTAAAGCT
Found at i:225883 original size:15 final size:16
Alignment explanation
Indices: 225863--225896 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
225853 TCCGTTATAT
*
225863 TCCCCCTCTCCCA-CC
1 TCCCCCGCTCCCATCC
225878 TCCCCCGCTCCCATCC
1 TCCCCCGCTCCCATCC
225894 TCC
1 TCC
225897 TTCCCACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.06, C:0.71, G:0.03, T:0.21
Consensus pattern (16 bp):
TCCCCCGCTCCCATCC
Found at i:239941 original size:19 final size:19
Alignment explanation
Indices: 239914--239964 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
239904 TCAATTTAAC
*
239914 TAAAAAAAAGTAAA-TAAAA
1 TAAATAAAA-TAAAGTAAAA
239933 TAAATAAAATGAAAGTAAAA
1 TAAATAAAAT-AAAGTAAAA
239953 T-AATAAAATAAA
1 TAAATAAAATAAA
239965 ATAATGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 19 0.66
20 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (19 bp):
TAAATAAAATAAAGTAAAA
Found at i:239948 original size:24 final size:24
Alignment explanation
Indices: 239920--239966 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
239910 TAACTAAAAA
239920 AAAGTAAATAAAAT-AAATAAAATG
1 AAAGTAAA-AAAATAAAATAAAATG
*
239944 AAAGTAAAATAATAAAATAAAAT
1 AAAGTAAAAAAATAAAATAAAAT
239967 AATGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.21
Consensus pattern (24 bp):
AAAGTAAAAAAATAAAATAAAATG
Found at i:239951 original size:11 final size:9
Alignment explanation
Indices: 239914--239964 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
239904 TCAATTTAAC
*
239914 TAAAAAAAA
1 TAAATAAAA
239923 GTAAATAAAA
1 -TAAATAAAA
239933 TAAATAAAA
1 TAAATAAAA
239942 TGAAAGTAAAA
1 T-AAA-TAAAA
239953 T-AATAAAA
1 TAAATAAAA
239961 TAAA
1 TAAA
239965 ATAATGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 6 0.16
9 14 0.38
10 11 0.30
11 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (9 bp):
TAAATAAAA
Found at i:248287 original size:177 final size:176
Alignment explanation
Indices: 247991--248346 Score: 658
Period size: 177 Copynumber: 2.0 Consensus size: 176
247981 AGATTATAAA
247991 AATTAAACAAAAATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
1 AATTAAACAAAAATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
248056 AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTACAAATCTGAAGAGTACTAAAAAAAAT
66 AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTACAAATCTGAAGAGTACT-AAAAAAAT
*
248121 TTGAAATCAAAACAAAAAATCCAACAAATTAGTACATGGGATGGAAC
130 GTGAAATCAAAACAAAAAATCCAACAAATTAGTACATGGGATGGAAC
*
248168 AATTAAACAAACATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
1 AATTAAACAAAAATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
* *
248233 AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTATAAATCTGGAGAGTACTAAAAAAATG
66 AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTACAAATCTGAAGAGTACTAAAAAAATG
*
248298 TGAAATCAAACCAAAAAATCCAACAAATTAGTACATGGGATGGAAC
131 TGAAATCAAAACAAAAAATCCAACAAATTAGTACATGGGATGGAAC
248344 AAT
1 AAT
248347 ATCTAAAGAA
Statistics
Matches: 174, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
176 56 0.32
177 118 0.68
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (176 bp):
AATTAAACAAAAATTTATGATGTGTTCTGCAGTGACATCTTCTATAGGAAAGGTCAAGAAATCAA
AATCAAGGGAGAAACCATTTCTGAATTAGACATTCTTTACAAATCTGAAGAGTACTAAAAAAATG
TGAAATCAAAACAAAAAATCCAACAAATTAGTACATGGGATGGAAC
Found at i:254867 original size:50 final size:50
Alignment explanation
Indices: 254804--254954 Score: 266
Period size: 50 Copynumber: 3.0 Consensus size: 50
254794 AGAACAACAA
* *
254804 TGATGGATAAGCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTC
1 TGATGGTTGAGCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTC
254854 TGATGGTTGAGCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTC
1 TGATGGTTGAGCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTC
* *
254904 TGATGGTTGGGCAGATTAAGGACAATTGCAAATCAATGAGCTATCAATTC
1 TGATGGTTGAGCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTC
254954 T
1 T
254955 CTCACAACTG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 97 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (50 bp):
TGATGGTTGAGCAGATTATGGACAATTGCAAATCAATGAGCTATCAATTC
Found at i:268007 original size:18 final size:17
Alignment explanation
Indices: 267984--268026 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
267974 AAATAAATTT
267984 TTAATTAAATAAATTGAA
1 TTAATTAAAT-AATTGAA
**
268002 TTAATTGAAATTTTTGAA
1 TTAATT-AAATAATTGAA
268020 TTAATTA
1 TTAATTA
268027 CAACTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TTAATTAAATAATTGAA
Found at i:272275 original size:18 final size:18
Alignment explanation
Indices: 272241--272275 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
272231 TTTATAATAA
* *
272241 TATATATTTTGTTATTTT
1 TATATATTATGTAATTTT
272259 TATATATTATGTAATTT
1 TATATATTATGTAATTT
272276 AGAATACATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
TATATATTATGTAATTTT
Found at i:273442 original size:12 final size:12
Alignment explanation
Indices: 273422--273468 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
273412 TAATATTATT
*
273422 TTAATATAAATA
1 TTAAAATAAATA
273434 TTAAAAT-AATA
1 TTAAAATAAATA
* *
273445 TTAAAATGACTA
1 TTAAAATAAATA
273457 TATAAAATAAAT
1 T-TAAAATAAAT
273469 TCAATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 11 0.38
12 10 0.34
13 8 0.28
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (12 bp):
TTAAAATAAATA
Found at i:284712 original size:26 final size:27
Alignment explanation
Indices: 284676--284727 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
284666 AATGAAACCG
284676 ATATAATTAA-TTTTCATATCATGTTC
1 ATATAATTAATTTTTCATATCATGTTC
*
284702 ATATAATTAATTTTTTATATCATGTT
1 ATATAATTAATTTTTCATATCATGTT
284728 TTTAGAGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (27 bp):
ATATAATTAATTTTTCATATCATGTTC
Found at i:286181 original size:30 final size:29
Alignment explanation
Indices: 286116--286432 Score: 286
Period size: 29 Copynumber: 10.8 Consensus size: 29
286106 ATTCGAGGTT
* * ** **
286116 AAAAATAGAACTTTTGGAAGTTCGGGGGA
1 AAAAATGGAATTTTTGGAAGTTTTGGGTC
286145 AAAAATGGAATTTTTGGAAGTTTTGGTGTC
1 AAAAATGGAATTTTTGGAAGTTTTGG-GTC
* **
286175 AAAAAT-GAGATTTTTGGAAGTTCTGGGGA
1 AAAAATGGA-ATTTTTGGAAGTTTTGGGTC
286204 AAAAATGGAATTTTTGGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGAAGTTTTG-GGTC
* *
286234 -AAAATGGGATTTTTGGAAGTTTAGGGGT-
1 AAAAATGGAATTTTTGGAAGTTT-TGGGTC
286262 AAAAATGGAATTTTTGGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGAAGTTTTG-GGTC
* * **
286292 AAAAATGGGATTTTTTGAAGTTCGGGGGT-
1 AAAAATGGAATTTTTGGAAGTT-TTGGGTC
* * *
286321 -AAAATGAAATTTTTGGAAGTTTCAGAGTC
1 AAAAATGGAATTTTTGGAAGTTT-TGGGTC
*
286350 AAAAATGGAATTTTTTGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTT-GGGTC
* **
286380 AAAAATGGGATTTTTGGAAGTTCGGGGAT-
1 AAAAATGGAATTTTTGGAAGTTTTGGG-TC
* *
286409 AAAAATAGAATTTTTAGACAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
286433 AGGGACCTCC
Statistics
Matches: 235, Mismatches: 38, Indels: 29
0.78 0.13 0.10
Matches are distributed among these distances:
28 22 0.09
29 112 0.48
30 100 0.43
31 1 0.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTTGGGTC
Found at i:286190 original size:59 final size:59
Alignment explanation
Indices: 286086--286401 Score: 361
Period size: 59 Copynumber: 5.4 Consensus size: 59
286076 ACACGGGGGT
* ** * * * * *
286086 AAAATGGTAATTTTGGGAAAATTCGAGGTTAAAAATAGAACTTTTGGAAGTTCGGGGGAA
1 AAAATGG-AATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGAA
* *
286146 AAAATGGAATTTTTGGAAGTTTTG-GTGTCAAAAATGAGATTTTTGGAAGTTCTGGGGAA
1 AAAATGGAATTTTTGGAAGTTTTGAG-GTCAAAAATGGGATTTTTGGAAGTTCGGGGGAA
** *
286205 AAAATGGAATTTTTGGAAGTTTTGAGGTC-AAAATGGGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGAA
* *
286263 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTTGAAGTTCGGGGG-T
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGAA
* * * * * **
286321 AAAATGAAATTTTTGGAAG-TTTCAGAGTCAAAAATGGAATTTTTTGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGAG-GTCAAAAATGGGATTTTTGGAAG-TTCGGGGGAA
*
286381 AAAATGGGATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
286402 CGGGGATAAA
Statistics
Matches: 223, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
57 5 0.02
58 95 0.43
59 97 0.43
60 25 0.11
61 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGAA
Found at i:286238 original size:88 final size:87
Alignment explanation
Indices: 286127--286435 Score: 347
Period size: 88 Copynumber: 3.5 Consensus size: 87
286117 AAAATAGAAC
* * * *
286127 TTTTGGAAGTTCGGGGGAAAAAATGGAATTTTTGGAAGTTTTGGTGTCAAAAAT-GAGATTTTTG
1 TTTTGGAAGTTCGGAGG-TAAAATGGAATTTTTGGAAGTTTAGGAGTCAAAAATGGA-ATTTTTG
* * *
286191 GAAGTTCTGGGGAAAAAATGGAAT
64 GAAGTTTTGGGGCAAAAATGGGAT
** * *
286215 TTTTGGAAGTTTTGAGGTCAAAATGGGATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTGG
1 TTTTGGAAGTTCGGAGGT-AAAATGGAATTTTTGGAAGTTTAGGAGTCAAAAATGGAATTTTTGG
*
286279 AAGTTTTGAGGTCAAAAATGGGAT
65 AAGTTTTG-GGGCAAAAATGGGAT
* * * *
286303 TTTTTGAAGTTCGGGGGTAAAATGAAATTTTTGGAAGTTTCA-GAGTCAAAAATGGAATTTTTTG
1 TTTTGGAAGTTCGGAGGTAAAATGGAATTTTTGGAAGTTT-AGGAGTCAAAAATGGAATTTTTGG
286367 AAGTTTTGGGGTCAAAAATGGGAT
65 AAGTTTTGGGG-CAAAAATGGGAT
* *
286391 TTTTGGAAGTTCGG-GGATAAAAATAGAATTTTTAGACAGTTTAGG
1 TTTTGGAAGTTCGGAGG-T-AAAATGGAATTTTTGGA-AGTTTAGG
286436 GACCTCCGGG
Statistics
Matches: 187, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
87 48 0.26
88 118 0.63
89 15 0.08
90 6 0.03
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (87 bp):
TTTTGGAAGTTCGGAGGTAAAATGGAATTTTTGGAAGTTTAGGAGTCAAAAATGGAATTTTTGGA
AGTTTTGGGGCAAAAATGGGAT
Found at i:286247 original size:58 final size:60
Alignment explanation
Indices: 286127--286401 Score: 357
Period size: 58 Copynumber: 4.7 Consensus size: 60
286117 AAAATAGAAC
* * *
286127 TTTTGGAAGTTCGGGGGAAAAAATGGAATTTTTGGAAGTTTTG-GTGTCAAAAATGAGAT
1 TTTTGGAAGTTCTGGGGAAAAAATGGAATTTTTGGAAGTTTTGAGAGTCAAAAATGGGAT
286186 TTTTGGAAGTTCTGGGGAAAAAATGGAATTTTTGGAAGTTTTGAG-GTC-AAAATGGGAT
1 TTTTGGAAGTTCTGGGGAAAAAATGGAATTTTTGGAAGTTTTGAGAGTCAAAAATGGGAT
*
286244 TTTTGGAAGTT-TAGGGGTAAAAATGGAATTTTTGGAAGTTTTGAG-GTCAAAAATGGGAT
1 TTTTGGAAGTTCT-GGGGAAAAAATGGAATTTTTGGAAGTTTTGAGAGTCAAAAATGGGAT
* ** * * *
286303 TTTTTGAAGTTC-GGGGGTAAAATGAAATTTTTGGAAG-TTTCAGAGTCAAAAATGGAAT
1 TTTTGGAAGTTCTGGGGAAAAAATGGAATTTTTGGAAGTTTTGAGAGTCAAAAATGGGAT
* * * *
286361 TTTTTGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
1 TTTTGGAAGTTCTGGGG-AAAAAATGGAATTTTTGGAAGTT
286402 CGGGGATAAA
Statistics
Matches: 194, Mismatches: 14, Indels: 14
0.87 0.06 0.06
Matches are distributed among these distances:
57 6 0.03
58 100 0.52
59 69 0.36
60 18 0.09
61 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.36
Consensus pattern (60 bp):
TTTTGGAAGTTCTGGGGAAAAAATGGAATTTTTGGAAGTTTTGAGAGTCAAAAATGGGAT
Found at i:286423 original size:59 final size:59
Alignment explanation
Indices: 286081--286432 Score: 338
Period size: 59 Copynumber: 6.0 Consensus size: 59
286071 CGGATACACG
* ** * * * * * **
286081 GGGGT-AAAATGGTAATTTTGGGAAAATTCGAGGTTAAAAATAGAACTTTTGGAAGTTCG
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTT
* * *
286140 GGGGAAAAAATGGAATTTTTGGAAGTTTTGGTGTCAAAAAT-GAGATTTTTGGAAGTTCT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGA-ATTTTTGGAAGTTTT
* * * *
286199 GGGGAAAAAATGGAATTTTTGGAAGTTTTGAGGTC-AAAATGGGATTTTTGGAAGTTTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTT
* * * **
286257 GGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTTGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTT
* ** * *
286316 GGGGT-AAAATGAAATTTTTGGAAGTTTCAGAGTCAAAAATGGAATTTTTTGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTT
* * * *
286374 GGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGAT-AAAAATAGAATTTTTAGACAGTTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTTGGGG-TCAAAAATGGAATTTTTGGA-AGTTT
286433 AGGGACCTCC
Statistics
Matches: 252, Mismatches: 33, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
58 104 0.41
59 118 0.47
60 30 0.12
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTT
Found at i:287494 original size:15 final size:16
Alignment explanation
Indices: 287474--287530 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
287464 TTAATTATTA
287474 TTATTAATAA-AACAT
1 TTATTAATAATAACAT
* **
287489 TTATTATTAATGTC-T
1 TTATTAATAATAACAT
287504 TTATTAATAATAACAATT
1 TTATTAATAATAAC-A-T
287522 TTATTAATA
1 TTATTAATA
287531 CCTATTAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 21 0.66
16 1 0.03
18 10 0.31
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (16 bp):
TTATTAATAATAACAT
Found at i:288278 original size:17 final size:16
Alignment explanation
Indices: 288256--288299 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
288246 ACATTTAAAA
288256 TAAATTTATAAAAAATT
1 TAAATTTA-AAAAAATT
**
288273 TAAATTTCAACCAAATT
1 TAAATTT-AAAAAAATT
288290 TAAATTTAAA
1 TAAATTTAAA
288300 TTTAGAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 20 0.87
18 1 0.04
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATTTAAAAAAATT
Found at i:288310 original size:17 final size:17
Alignment explanation
Indices: 288290--288337 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
288280 CAACCAAATT
*
288290 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
288307 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
288324 TAAATTTAAGTTTA
1 TAAATTTAAATTTA
288338 TTGGGCCCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:289678 original size:21 final size:24
Alignment explanation
Indices: 289621--289682 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 24
289611 AAAAATATTT
289621 AAAGAATAAATAAATTTAAATTTAG
1 AAAGAATAAAT-AATTTAAATTTAG
289646 AAA-AAT-AA-AATTT-AA-TT-G
1 AAAGAATAAATAATTTAAATTTAG
289664 AAAGAATAAATAA-TTAAAT
1 AAAGAATAAATAATTTAAAT
289683 GATAAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
18 4 0.12
19 5 0.16
20 6 0.19
21 9 0.28
23 2 0.06
24 3 0.09
25 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (24 bp):
AAAGAATAAATAATTTAAATTTAG
Found at i:289680 original size:20 final size:22
Alignment explanation
Indices: 289621--289680 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 22
289611 AAAAATATTT
289621 AAAGAATAAATAAATTTAAATTTAG
1 AAAGAATAAAT-AA-TT-AATTTAG
*
289646 AAA-AATAAA-ATTTAA-TT-G
1 AAAGAATAAATAATTAATTTAG
289664 AAAGAATAAATAATTAA
1 AAAGAATAAATAATTAA
289681 ATGATAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 4 0.13
19 8 0.26
20 7 0.23
21 2 0.06
22 1 0.03
24 6 0.19
25 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
AAAGAATAAATAATTAATTTAG
Found at i:296378 original size:15 final size:16
Alignment explanation
Indices: 296340--296372 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
296330 AACTCCATCC
*
296340 AAACTAATTTCTAGAA
1 AAACAAATTTCTAGAA
296356 AAACAAATTTCT-GAA
1 AAACAAATTTCTAGAA
296371 AA
1 AA
296373 TGAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (16 bp):
AAACAAATTTCTAGAA
Found at i:302808 original size:7 final size:7
Alignment explanation
Indices: 302796--302826 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
302786 CAAAGCTAAA
302796 AAATATT
1 AAATATT
302803 AAATATT
1 AAATATT
302810 AAATATT
1 AAATATT
302817 AAATATT
1 AAATATT
302824 AAA
1 AAA
302827 AACTTAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATATT
Found at i:319489 original size:14 final size:13
Alignment explanation
Indices: 319472--319510 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
319462 TTTTTATAAG
319472 ATATAAGTTATATA
1 ATATAAGTT-TATA
*
319486 ATATATGTTTATA
1 ATATAAGTTTATA
319499 ATTATAAGTTTA
1 A-TATAAGTTTA
319511 AATCTCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (13 bp):
ATATAAGTTTATA
Found at i:319491 original size:16 final size:15
Alignment explanation
Indices: 319464--319510 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
319454 CTCAATTTTT
*
319464 TTTATAAGATATAAG
1 TTTATAATATATAAG
319479 TTATATAATATAT--G
1 TT-TATAATATATAAG
319493 TTTATAAT-TATAAG
1 TTTATAATATATAAG
319507 TTTA
1 TTTA
319511 AATCTCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 3 0.11
13 6 0.21
14 8 0.29
15 2 0.07
16 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (15 bp):
TTTATAATATATAAG
Found at i:321403 original size:34 final size:35
Alignment explanation
Indices: 321337--321405 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
321327 TAGCATTCAT
*
321337 TTCACTGGATTCCAGTGTGATAGAACACAATTTTC
1 TTCACTGGATTCCAGTGTCATAGAACACAATTTTC
*
321372 TTCATTGGATTCCAGTG-CAT-GAAACACAATTTTC
1 TTCACTGGATTCCAGTGTCATAG-AACACAATTTTC
321406 AAAATCTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 1 0.03
34 14 0.45
35 16 0.52
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (35 bp):
TTCACTGGATTCCAGTGTCATAGAACACAATTTTC
Found at i:324958 original size:21 final size:22
Alignment explanation
Indices: 324922--324967 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
324912 TTAATTCGAA
*
324922 AAATAATTTAAA-TTTTGAGTT
1 AAATAATTCAAATTTTTGAGTT
*
324943 AAATAATTCAAGTTTTTTGAGTT
1 AAATAATTCAA-ATTTTTGAGTT
324966 AA
1 AA
324968 TCAAGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
23 11 0.52
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (22 bp):
AAATAATTCAAATTTTTGAGTT
Found at i:331200 original size:31 final size:31
Alignment explanation
Indices: 331142--331200 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
331132 CTAGTAACTC
* * *
331142 AAATAAAAACTTTTGAATATTTCAATGACTT
1 AAATAAAAACTTTTAAATAGTTAAATGACTT
* *
331173 AAATGAAAATTTTTAAATAGTTAAATGA
1 AAATAAAAACTTTTAAATAGTTAAATGA
331201 TCATTTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.37
Consensus pattern (31 bp):
AAATAAAAACTTTTAAATAGTTAAATGACTT
Found at i:339574 original size:2 final size:2
Alignment explanation
Indices: 339567--339601 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
339557 TAGAATGGAA
*
339567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
339602 ATTAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:340142 original size:1 final size:1
Alignment explanation
Indices: 340136--340169 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
340126 GCATATAAGC
* *
340136 AAAAAAAAAAAAGAAAAAAAAGAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
340170 GGGAAATCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:344266 original size:4 final size:4
Alignment explanation
Indices: 344257--344287 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
344247 TACTAAAATG
344257 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
344288 TATATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:346470 original size:18 final size:17
Alignment explanation
Indices: 346444--346478 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
346434 TGGTTCAACC
346444 ATTGAATTTATCAATACA
1 ATTGAATTTATC-ATACA
*
346462 ATTGTATTTATCATACA
1 ATTGAATTTATCATACA
346479 TATAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
ATTGAATTTATCATACA
Found at i:363263 original size:596 final size:596
Alignment explanation
Indices: 362121--363318 Score: 2263
Period size: 596 Copynumber: 2.0 Consensus size: 596
362111 TTGGTCCCAG
* * *
362121 CTTT-ATTGTTTTCATCGCGGGTTTCTCCATTAAGTCCGATGACAAACTCACCTTTTCTTTAGGT
1 CTTTCATTGTTTTCATCGCGGGTTTCTCCATTAAGTCCGATGACAAACTCACATCTTCCTTAGGT
362185 GGAAGCCCCTTTGATGACTCATCAAGCTCCGATGTTACCTTTTCATTGACCCTCACGGATTGCTG
66 GGAAGCCCCTTTGATGACTCATCAAGCTCCGATGTTACCTTTTCATTGACCCTCACGGATTGCTG
*
362250 CTTTGGACAGTTTCGCAACTCATGCGGACCACGGCACAAGAAGCACTTGACTCGCTTCTTTTTGC
131 CTTTGGACAGTTCCGCAACTCATGCGGACCACGGCACAAGAAGCACTTGACTCGCTTCTTTTTGC
362315 TCCTCTTTGCCCCCTTGGCTTCGCTCGAACCAAGCTTCATGGGCACCTTGTCTATCTCATCGATG
196 TCCTCTTTGCCCCCTTGGCTTCGCTCGAACCAAGCTTCATGGGCACCTTGTCTATCTCATCGATG
*
362380 ACAGACTTTTTCGGACATTTTCGCAACCTATACGGACCATGACACAAGAAGCACTCCACTGGCTT
261 ACAGACTTTTTCAGACATTTTCGCAACCTATACGGACCATGACACAAGAAGCACTCCACTGGCTT
362445 CTTCTCGCTTTTGGCCTTCTTGGCTTCGACACCTTTTGCGCTCGAACCAAGTCTCGTGGCCTTAC
326 CTTCTCGCTTTTGGCCTTCTTGGCTTCGACACCTTTTGCGCTCGAACCAAGTCTCGTGGCCTTAC
362510 CTTTCGGCTTGCCCCTCTTAGACAACTCGGATTTCCTTGGACATTTCTTCAGCAAATGTGGACCG
391 CTTTCGGCTTGCCCCTCTTAGACAACTCGGATTTCCTTGGACATTTCTTCAGCAAATGTGGACCG
*
362575 TTGCAAAGAAAACATTTCAACTTGTCTCTCTTTTCGTTGGGTTTCTTCATCCCAACTCGTGGTTT
456 TTGCAAAGAAAACATTTCAACTTGCCTCTCTTTTCGTTGGGTTTCTTCATCCCAACTCGTGGTTT
*
362640 CCCATTACCACAATTGTTACTGTTGCCATCACCATCGCCATCATCATCTTCCTTGTGATTCTCTT
521 CCCATTACCACAATTGTTACCGTTGCCATCACCATCGCCATCATCATCTTCCTTGTGATTCTCTT
*
362705 CACATACGCCC
586 CACATACACCC
362716 CTTTCATTGTTTTCATCGCGGGTTTCTCCATTAAGTCCGATGACAAACTCACATCTTCCTTAGGT
1 CTTTCATTGTTTTCATCGCGGGTTTCTCCATTAAGTCCGATGACAAACTCACATCTTCCTTAGGT
362781 GGAAGCCCCTTTGATGACTCATCAAGCTCCGATGTTACCTTTTCATTGACCCTCACGGATTGCTG
66 GGAAGCCCCTTTGATGACTCATCAAGCTCCGATGTTACCTTTTCATTGACCCTCACGGATTGCTG
362846 CTTTGGACAGTTCCGCAACTCATGCGGACCACGGCACAAGAAGCACTTGACTCGCTTCTTTTTGC
131 CTTTGGACAGTTCCGCAACTCATGCGGACCACGGCACAAGAAGCACTTGACTCGCTTCTTTTTGC
*
362911 TCCTCTTTGCCCCCTTGGCTTCGCTCGAACCAAGCTTCATGGGCACCTTGTCTATTTCATCGATG
196 TCCTCTTTGCCCCCTTGGCTTCGCTCGAACCAAGCTTCATGGGCACCTTGTCTATCTCATCGATG
* *
362976 ATAGACTTTTTCAGACATTTTCGCAACCTATGCGGACCATGACACAAGAAGCACTCCACTGGCTT
261 ACAGACTTTTTCAGACATTTTCGCAACCTATACGGACCATGACACAAGAAGCACTCCACTGGCTT
363041 CTTCTCGCTTTTGGCCTTCTTGGCTTCGACACCTTTTGCGCTCGAACCAAGTCTCGTGGCCTTAC
326 CTTCTCGCTTTTGGCCTTCTTGGCTTCGACACCTTTTGCGCTCGAACCAAGTCTCGTGGCCTTAC
363106 CTTTCGGCTTGCCCCTCTTAGACAACTCGGATTTCCTTGGACATTTCTTCAGCAAATGTGGACCG
391 CTTTCGGCTTGCCCCTCTTAGACAACTCGGATTTCCTTGGACATTTCTTCAGCAAATGTGGACCG
363171 TTGCAAAGAAAACATTTCAACTTGCCTCTCTTTTCGTTGGGTTTCTTCATCCCAACTCGTGGTTT
456 TTGCAAAGAAAACATTTCAACTTGCCTCTCTTTTCGTTGGGTTTCTTCATCCCAACTCGTGGTTT
* *
363236 CCCATTACCACAATTGTTGCCGTTGCCATCGCCATCGCCATCATCATCTTCCTTGTGATTCTCTT
521 CCCATTACCACAATTGTTACCGTTGCCATCACCATCGCCATCATCATCTTCCTTGTGATTCTCTT
*
363301 CACATGCACCC
586 CACATACACCC
363312 CTTTCAT
1 CTTTCAT
363319 CGGACTTGGA
Statistics
Matches: 588, Mismatches: 14, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
595 4 0.01
596 584 0.99
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.33
Consensus pattern (596 bp):
CTTTCATTGTTTTCATCGCGGGTTTCTCCATTAAGTCCGATGACAAACTCACATCTTCCTTAGGT
GGAAGCCCCTTTGATGACTCATCAAGCTCCGATGTTACCTTTTCATTGACCCTCACGGATTGCTG
CTTTGGACAGTTCCGCAACTCATGCGGACCACGGCACAAGAAGCACTTGACTCGCTTCTTTTTGC
TCCTCTTTGCCCCCTTGGCTTCGCTCGAACCAAGCTTCATGGGCACCTTGTCTATCTCATCGATG
ACAGACTTTTTCAGACATTTTCGCAACCTATACGGACCATGACACAAGAAGCACTCCACTGGCTT
CTTCTCGCTTTTGGCCTTCTTGGCTTCGACACCTTTTGCGCTCGAACCAAGTCTCGTGGCCTTAC
CTTTCGGCTTGCCCCTCTTAGACAACTCGGATTTCCTTGGACATTTCTTCAGCAAATGTGGACCG
TTGCAAAGAAAACATTTCAACTTGCCTCTCTTTTCGTTGGGTTTCTTCATCCCAACTCGTGGTTT
CCCATTACCACAATTGTTACCGTTGCCATCACCATCGCCATCATCATCTTCCTTGTGATTCTCTT
CACATACACCC
Found at i:365045 original size:12 final size:12
Alignment explanation
Indices: 365028--365052 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
365018 GCTTTCACTT
365028 CCACTTCCGCTA
1 CCACTTCCGCTA
365040 CCACTTCCGCTA
1 CCACTTCCGCTA
365052 C
1 C
365053 TTTCACTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.52, G:0.08, T:0.24
Consensus pattern (12 bp):
CCACTTCCGCTA
Found at i:365054 original size:27 final size:27
Alignment explanation
Indices: 365024--365094 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
365014 CACTGCTTTC
* *
365024 ACTTCCACTTCCGCTACCACTTCCGCT
1 ACTTCCACTTCCACTACCACTTCCACT
* * *
365051 ACTTTCACTACCACTACCGCTTCCACT
1 ACTTCCACTTCCACTACCACTTCCACT
365078 AC-TCTCACTTCCACTAC
1 ACTTC-CACTTCCACTAC
365095 TACTACTCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.20, C:0.46, G:0.04, T:0.30
Consensus pattern (27 bp):
ACTTCCACTTCCACTACCACTTCCACT
Found at i:365090 original size:15 final size:15
Alignment explanation
Indices: 365041--365095 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
365031 CTTCCGCTAC
* *
365041 CACTTCCGCTACTTT
1 CACTTCCACTACTCT
*
365056 CACTACCACTA--C-
1 CACTTCCACTACTCT
*
365068 CGCTTCCACTACTCT
1 CACTTCCACTACTCT
365083 CACTTCCACTACT
1 CACTTCCACTACT
365096 ACTACTCGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
12 9 0.29
14 1 0.03
15 21 0.68
ACGTcount: A:0.20, C:0.45, G:0.04, T:0.31
Consensus pattern (15 bp):
CACTTCCACTACTCT
Found at i:369258 original size:6 final size:6
Alignment explanation
Indices: 369247--369298 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
369237 ATGGAAGGTA
* * *
369247 ATGTAT ATGTAT ATGTAT ATGTAT ATCTAT ATGTAT ATCTAC ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
369295 ATGT
1 ATGT
369299 TGGCCATAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (6 bp):
ATGTAT
Found at i:371611 original size:42 final size:42
Alignment explanation
Indices: 371552--371635 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
371542 AGTGTTCATG
371552 GTTTGAGCATATTTTGAACCTTTTTGCAATTGTTTCAGCTTC
1 GTTTGAGCATATTTTGAACCTTTTTGCAATTGTTTCAGCTTC
371594 GTTTGAGCATATTTTGAACCTTTTTGCAATTGTTTCAGCTTC
1 GTTTGAGCATATTTTGAACCTTTTTGCAATTGTTTCAGCTTC
371636 CAATATATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (42 bp):
GTTTGAGCATATTTTGAACCTTTTTGCAATTGTTTCAGCTTC
Found at i:376517 original size:30 final size:29
Alignment explanation
Indices: 376477--376767 Score: 195
Period size: 29 Copynumber: 9.9 Consensus size: 29
376467 CCCTGAAGGT
376477 CCCC-AAACTTCCCAAAATTCCATTTTTGA
1 CCCCGAAACTTCCCAAAATTCCATTTTT-A
* **
376506 CCTCGAAACTTCAAAAAATTCCATTTTTA
1 CCCCGAAACTTCCCAAAATTCCATTTTTA
*
376535 CCCTCG-AACTTCCC-AATTTCCCATTTTTGA
1 CCC-CGAAACTTCCCAAAATT-CCATTTTT-A
* * ***
376565 -CCCAAAACTTCCAAAAAATTTTGTTTTTA
1 CCCCGAAACTTCC-CAAAATTCCATTTTTA
*
376594 CCCCCG-AACTTCCCCAAAATCCCATTTTTGA
1 -CCCCGAAACTT-CCCAAAATTCCATTTTT-A
* * * **
376625 CCCCAAAAGTTCCAAAAATTTTATTTTTA
1 CCCCGAAACTTCCCAAAATTCCATTTTTA
* *
376654 CCCTCG-AACTTCCCAAAATCCCATTTTAA
1 CCC-CGAAACTTCCCAAAATTCCATTTTTA
* * *
376683 CCCCGAAACTTCCAAAAATTTCA-TTGTA
1 CCCCGAAACTTCCCAAAATTCCATTTTTA
* *
376711 CCCTTG-AACTTCCCAAAATCCCATTTTTGA
1 CCC-CGAAACTTCCCAAAATTCCATTTTT-A
*
376741 CCCCAAAACTT-CCAAAGATTACCATTT
1 CCCCGAAACTTCCCAAA-ATT-CCATTT
376768 CACCCTCGAG
Statistics
Matches: 197, Mismatches: 45, Indels: 38
0.70 0.16 0.14
Matches are distributed among these distances:
28 27 0.14
29 77 0.39
30 73 0.37
31 20 0.10
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (29 bp):
CCCCGAAACTTCCCAAAATTCCATTTTTA
Found at i:376544 original size:29 final size:29
Alignment explanation
Indices: 376482--376776 Score: 183
Period size: 30 Copynumber: 10.0 Consensus size: 29
376472 AAGGTCCCCA
*
376482 AACTTCCCAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
376511 AAACTTCAAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * **
376541 AACTTCC-CAATTTCCCATTTTTGACCC-AA
1 AACTTCCAAAAATT-CCATTTTT-ACCCTCG
*** *
376570 AACTTCCAAAAAATTTTGTTTTTACCCCCG
1 AACTTCC-AAAAATTCCATTTTTACCCTCG
* * *
376600 AACTTCCCCAAAATCCCATTTTTGACCC-CAA
1 AACTT-CCAAAAATTCCATTTTT-ACCCTC-G
* **
376631 AAGTTCCAAAAATTTTATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
376660 AACTTCCCAAAATCCCATTTTAACCC-CG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
376688 AAACTTCCAAAAATTTCA-TTGTACCCTTG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
376717 AACTTCCCAAAATCCCATTTTTGACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
* *
376747 AACTTCCAAAGATTACCA-TTTCACCCTCG
1 AACTTCCAAAAATT-CCATTTTTACCCTCG
376776 A
1 A
376777 GAATCCAAAA
Statistics
Matches: 199, Mismatches: 49, Indels: 35
0.70 0.17 0.12
Matches are distributed among these distances:
28 26 0.13
29 73 0.37
30 83 0.42
31 17 0.09
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:376580 original size:59 final size:60
Alignment explanation
Indices: 376482--376756 Score: 364
Period size: 59 Copynumber: 4.7 Consensus size: 60
376472 AAGGTCCCCA
* * * *
376482 AACTTCCCAAAATTCCATTTTTGACCTCGAAACTT-CAAAAAATTCCATTTTTACCCTCG
1 AACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAATTTCATTTTTACCCTCG
** ** *
376541 AACTTCCCAATTTCCCATTTTTGA-CCCAAAACTTCCAAAAAATTTTGTTTTTACCCCCG
1 AACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAATTTCATTTTTACCCTCG
* *
376600 AACTTCCCCAAAATCCCATTTTTGACCCCAAAAGTTCC-AAAAATTTTATTTTTACCCTCG
1 AACTT-CCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAATTTCATTTTTACCCTCG
* * * *
376660 AACTTCCCAAAATCCCA-TTTTAACCCCGAAACTTCC-AAAAATTTCA-TTGTACCCTTG
1 AACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAATTTCATTTTTACCCTCG
376717 AACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAA
1 AACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAA
376757 GATTACCATT
Statistics
Matches: 189, Mismatches: 22, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
57 26 0.14
58 50 0.26
59 60 0.32
60 42 0.22
61 11 0.06
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.32
Consensus pattern (60 bp):
AACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAATTTCATTTTTACCCTCG
Found at i:376823 original size:116 final size:116
Alignment explanation
Indices: 376482--376796 Score: 291
Period size: 119 Copynumber: 2.7 Consensus size: 116
376472 AAGGTCCCCA
* * * * * *
376482 AACTT-CCCAAAATTCCATTTTTGACCTCGAAACTTCAAAAAATTCCATTTTTACCCTCGAACTT
1 AACTTCCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCACCCTCGAACAT
** * * * * ** * **
376546 CCCAATTTCCCATTTTTGA-CCCAAAACTTCCAAAAAATTTTGTTTTTACCCCCG
66 CCCAAAATACCA-TTTTAACCCCGAAAC-TCC-AAAAA-TCTCATTGTACCCTTG
* ** * *
376600 AACTTCCCCAAAATCCCATTTTTGACCCCAAAAGTTCCAAAAATTTTATTTTTACCCTCGAACTT
1 AACTTCCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCACCCTCGAACAT
* *
376665 CCCAAAATCCCATTTTAACCCCGAAACTTCCAAAAATTTCATTGTACCCTTG
66 CCCAAAATACCATTTTAACCCCGAAAC-TCCAAAAATCTCATTGTACCCTTG
*
376717 AACTT-CCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAGATTACCA-TTTCACCCTCGAGA-
1 AACTTCCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATT-CCATTTTCACCCTCGA-AC
376779 AT-CCAAAATTACCATTTT
64 ATCCCAAAA-TACCATTTT
376797 CTCCCCGGGT
Statistics
Matches: 169, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
115 6 0.04
116 57 0.34
117 18 0.11
118 15 0.09
119 73 0.43
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.32
Consensus pattern (116 bp):
AACTTCCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCACCCTCGAACAT
CCCAAAATACCATTTTAACCCCGAAACTCCAAAAATCTCATTGTACCCTTG
Found at i:380409 original size:32 final size:29
Alignment explanation
Indices: 380373--380435 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
380363 AAAAAATATT
380373 AAAATAATAAAATTAATAATTTAATTCTCATA
1 AAAAT-ATAAAATT--TAATTTAATTCTCATA
* * *
380405 AAAATATATAATTTAATTTTATTCTCCTA
1 AAAATATAAAATTTAATTTAATTCTCATA
380434 AA
1 AA
380436 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.57
31 7 0.25
32 5 0.18
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATATAAAATTTAATTTAATTCTCATA
Found at i:382101 original size:28 final size:28
Alignment explanation
Indices: 382038--382129 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 28
382028 AATAAAAAAA
* * *
382038 TGGGGTTAAAAATGTAAATTTGGAAAGTT
1 TGGGGTT-AAAATGCAATTTTAGAAAGTT
382067 TGAGGGTTAAAATGCAATTTTAGAAAGTT
1 TG-GGGTTAAAATGCAATTTTAGAAAGTT
* * *
382096 TGGGGTTAAAATGTGATTTTTAGGAAGTT
1 TGGGGTTAAAATG-CAATTTTAGAAAGTT
382125 TGGGG
1 TGGGG
382130 GCTAAAATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 11 0.20
29 39 0.71
30 5 0.09
ACGTcount: A:0.33, C:0.01, G:0.30, T:0.36
Consensus pattern (28 bp):
TGGGGTTAAAATGCAATTTTAGAAAGTT
Found at i:386879 original size:16 final size:17
Alignment explanation
Indices: 386860--386912 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
386850 TAAAAATAAT
386860 TATATAAAA-AATAAAA
1 TATATAAAATAATAAAA
* *
386876 TATATAAAATTATTAAA
1 TATATAAAATAATAAAA
*
386893 TAT-TAAAATAATATAA
1 TATATAAAATAATAAAA
386909 TATA
1 TATA
386913 AATATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TATATAAAATAATAAAA
Found at i:386885 original size:29 final size:27
Alignment explanation
Indices: 386852--386931 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 27
386842 AATAATGTTA
386852 AAAATAATTATATAAAAAATAAAATATAT
1 AAAAT-ATTATATAAAAAATAAAATA-AT
* * *
386881 AAAATTATTAAATATTAAAATAATATAAT
1 AAAA-TATTATATA-AAAAATAAAATAAT
* *
386910 ATAAATATTTTTTAAAAAATAA
1 A-AAATATTATATAAAAAATAA
386932 TATAGGTGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
28 7 0.17
29 20 0.49
30 14 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
AAAATATTATATAAAAAATAAAATAAT
Found at i:386886 original size:26 final size:26
Alignment explanation
Indices: 386857--386908 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
386847 TGTTAAAAAT
386857 AATTATATAAAAAATAAAAT-ATATAA
1 AATTAT-TAAAAAATAAAATAATATAA
* *
386883 AATTATTAAATATTAAAATAATATAA
1 AATTATTAAAAAATAAAATAATATAA
386909 TATAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AATTATTAAAAAATAAAATAATATAA
Found at i:386895 original size:15 final size:15
Alignment explanation
Indices: 386852--386914 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
386842 AATAATGTTA
*
386852 AAAATAAT-TATATAA
1 AAAATAATATA-ATAT
*
386867 AAAATAAAAT-ATAT
1 AAAATAATATAATAT
*
386881 AAAATTAT-TAAATATT
1 AAAATAATAT-AATA-T
386897 AAAATAATATAATAT
1 AAAATAATATAATAT
386912 AAA
1 AAA
386915 TATTTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
13 1 0.03
14 9 0.24
15 14 0.37
16 13 0.34
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAATATAATAT
Found at i:388229 original size:91 final size:89
Alignment explanation
Indices: 388117--388287 Score: 218
Period size: 91 Copynumber: 1.9 Consensus size: 89
388107 ATACAATCGA
*** *
388117 TCCTCATATTTTTCATTTTGAGTAATTT-TTTTTCTTTTATGACCTTTTAACTTTCATTTGTTTT
1 TCCTCATATTTTTCATTTTGAGTAATTTAAAATT-TTTTATAACCTTTTAACTTT-ATTTGTTTT
*
388181 TTCATTCTCTTTTGCTTCTCCATTGG
64 TTCATTCTCTTCTGCTTCTCCATTGG
* * * * *
388207 TCCTCATATTTTTTCGTTTTGAGTAATTTAAAATTTTTTATAATCTTTTAGCTTTTTTTTTTTTT
1 TCCTCATA-TTTTTCATTTTGAGTAATTTAAAATTTTTTATAACCTTTTAACTTTATTTGTTTTT
388272 TCATTCTCTTCTGCTT
65 TCATTCTCTTCTGCTT
388288 TTCCCTCTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
90 31 0.45
91 36 0.52
92 2 0.03
ACGTcount: A:0.16, C:0.16, G:0.07, T:0.61
Consensus pattern (89 bp):
TCCTCATATTTTTCATTTTGAGTAATTTAAAATTTTTTATAACCTTTTAACTTTATTTGTTTTTT
CATTCTCTTCTGCTTCTCCATTGG
Found at i:389047 original size:29 final size:28
Alignment explanation
Indices: 388993--389049 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
388983 TTAGTTCCGA
** *
388993 TTATATTTTTAGAACTGGATTTTTTTAT
1 TTATATTTTTAGAACTAAATTCTTTTAT
*
389021 TTATATTGTTTAGATCTAAATTCTTTTAT
1 TTATATT-TTTAGAACTAAATTCTTTTAT
389050 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (28 bp):
TTATATTTTTAGAACTAAATTCTTTTAT
Found at i:392223 original size:4 final size:4
Alignment explanation
Indices: 392214--392244 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
392204 TTCATTGATT
392214 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
392245 TTGTGTGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:393459 original size:21 final size:22
Alignment explanation
Indices: 393423--393464 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
393413 AATTTTAAAA
*
393423 TTTAAAAATAATTATAAATTTT
1 TTTAAAAATAACTATAAATTTT
393445 TTTAAAAA-AACTATAAATTT
1 TTTAAAAATAACTATAAATTT
393465 ATACAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAAAATAACTATAAATTTT
Found at i:397840 original size:29 final size:28
Alignment explanation
Indices: 397798--397863 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
397788 ACAAAATCGA
* *
397798 ATAGTTAGGTAACCATTTTGTATCTTTTC
1 ATAGTT-GGTAACCATGTTATATCTTTTC
*
397827 ATAGTTGGTTAACCATGTTATGTCTTTTC
1 ATAGTTGG-TAACCATGTTATATCTTTTC
*
397856 ATAATTGG
1 ATAGTTGG
397864 GTGGTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (28 bp):
ATAGTTGGTAACCATGTTATATCTTTTC
Found at i:408080 original size:2 final size:2
Alignment explanation
Indices: 408073--408099 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
408063 AAATTCATGC
408073 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
408100 AGTAGGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:416533 original size:8 final size:8
Alignment explanation
Indices: 416522--416546 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
416512 TTCTTAGCCA
416522 TTAAAATT
1 TTAAAATT
416530 TTAAAATT
1 TTAAAATT
416538 TTAAAATT
1 TTAAAATT
416546 T
1 T
416547 CAATCCCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAAAATT
Found at i:418178 original size:41 final size:41
Alignment explanation
Indices: 418089--418178 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 41
418079 TTGCTATTTG
418089 ATCTAATTTACTCATTTTTTAAATAAAAATAATAAAAACAT
1 ATCTAATTTACTCATTTTTTAAATAAAAATAATAAAAACAT
* *
418130 AGACTAATTTACTTATTTTTTAAATAAAAATAATAAAATACA-
1 A-TCTAATTTACTCATTTTTTAAATAAAAATAATAAAA-ACAT
418172 ATCTAAT
1 ATCTAAT
418179 AAAATACAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 6 0.14
42 35 0.80
43 3 0.07
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (41 bp):
ATCTAATTTACTCATTTTTTAAATAAAAATAATAAAAACAT
Found at i:418180 original size:15 final size:15
Alignment explanation
Indices: 418160--418192 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
418150 TAAATAAAAA
418160 TAATAAAATACAATC
1 TAATAAAATACAATC
418175 TAATAAAATACAATC
1 TAATAAAATACAATC
418190 TAA
1 TAA
418193 CTCCTAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATAAAATACAATC
Found at i:432234 original size:11 final size:11
Alignment explanation
Indices: 432218--432263 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
432208 GGGGACCAAC
* *
432218 GAAAAATGAAG
1 GAAAAAAGAAA
432229 GAAAAAAGAAA
1 GAAAAAAGAAA
432240 G-AAAAA-AAA
1 GAAAAAAGAAA
432249 GAAAGAAAGAAA
1 GAAA-AAAGAAA
432261 GAA
1 GAA
432264 GAAGGAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 4 0.13
10 7 0.23
11 13 0.43
12 6 0.20
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:432246 original size:13 final size:13
Alignment explanation
Indices: 432230--432266 Score: 56
Period size: 13 Copynumber: 2.7 Consensus size: 13
432220 AAAATGAAGG
432230 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
432243 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
432256 AGAAAGAAGAA
1 A-AAA-AAGAA
432267 GGAAGAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.64
14 3 0.14
15 5 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:433426 original size:61 final size:58
Alignment explanation
Indices: 433143--433404 Score: 237
Period size: 61 Copynumber: 4.4 Consensus size: 58
433133 AGGGGAAGTT
* * * *
433143 GGTGTCGGCCATT-ACATGGCCAACACCAAAAAATTTTGCAATCTTTTTATCCGAGAAAAGGG
1 GGTGTCGGCCATTCA-ATGGCCAACACCCAAAAA---TGCAAT-TTTTTTTTCGAGAAAAAGG
* **
433205 GGTGTCGACCATTTGATGGCC-A-ACCCAAAAATGCAA-TTTTTTTTCGAG-AAAAGG
1 GGTGTCGGCCATTCAATGGCCAACACCCAAAAATGCAATTTTTTTTTCGAGAAAAAGG
* ** * * *
433259 GGATGTCGGCCATCCAATGATCAACACCCAAAAATGTAATTTTTTTTTCAAGAAAAGGGG
1 GG-TGTCGGCCATTCAATGGCCAACACCCAAAAATGCAATTTTTTTTTCGAGAAAA-AGG
* **
433319 GTGTCGTCGGCCATGCAATAACCAACACCCAAAAATGCAATTTTTTTTTCGAGAAAAAGG
1 G-GT-GTCGGCCATTCAATGGCCAACACCCAAAAATGCAATTTTTTTTTCGAGAAAAAGG
* **
433379 AGTGTCGGCCATTTGATGGCCAACAC
1 GGTGTCGGCCATTCAATGGCCAACAC
433405 AAAAAAATTT
Statistics
Matches: 164, Mismatches: 27, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
54 7 0.04
55 23 0.14
56 1 0.01
57 18 0.11
58 29 0.18
59 5 0.03
60 14 0.09
61 49 0.30
62 18 0.11
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (58 bp):
GGTGTCGGCCATTCAATGGCCAACACCCAAAAATGCAATTTTTTTTTCGAGAAAAAGG
Found at i:442598 original size:49 final size:49
Alignment explanation
Indices: 442545--442717 Score: 177
Period size: 49 Copynumber: 3.5 Consensus size: 49
442535 GGTTATTGAT
* * *
442545 ATAGTGAAAATCATCGTTGTTGGGCCATTCGGGATGGTAGAATATGTAA
1 ATAGTGAAAATCATCGTTGTCGGGCCATTCGAGATGGTAGAATATGCAA
* * * * * *
442594 ATAGTGAAGACCATTGTTGTCGGGCCACTT-GTGAGGGTAGAATATACAA
1 ATAGTGAAAATCATCGTTGTCGGGCCA-TTCGAGATGGTAGAATATGCAA
* * * *
442643 ATAGTGAAAATCATCATTGTCGGGTCACTCGAGATTGTAGAATATGCAA
1 ATAGTGAAAATCATCGTTGTCGGGCCATTCGAGATGGTAGAATATGCAA
* * * *
442692 ATATTGAAAGTCATTGTTGTCAGGCC
1 ATAGTGAAAATCATCGTTGTCGGGCC
442718 GCCCGGGATG
Statistics
Matches: 98, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
48 1 0.01
49 95 0.97
50 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (49 bp):
ATAGTGAAAATCATCGTTGTCGGGCCATTCGAGATGGTAGAATATGCAA
Found at i:442740 original size:98 final size:98
Alignment explanation
Indices: 442545--442740 Score: 223
Period size: 98 Copynumber: 2.0 Consensus size: 98
442535 GGTTATTGAT
* * * * *
442545 ATAGTGAAAATCATCGTTGTTGGGCCATTCGGGATGGTAGAATATGTAAATAGTGAAGACCATTG
1 ATAGTGAAAATCATCATTGTCGGGCCACTCGAGATGGTAGAATATGCAAATAGTGAAGACCATTG
* ** *
442610 TTGTCGGGCCACTTGTGAGGGTAGAATATACAA
66 TTGTCAGGCCACCCGGGAGGGTAGAATATACAA
* * * *
442643 ATAGTGAAAATCATCATTGTCGGGTCACTCGAGATTGTAGAATATGCAAATATTGAA-AGTCATT
1 ATAGTGAAAATCATCATTGTCGGGCCACTCGAGATGGTAGAATATGCAAATAGTGAAGA-CCATT
* * * *
442707 GTTGTCAGGCCGCCCGGGATGGTTGAATGTACAA
65 GTTGTCAGGCCACCCGGGAGGGTAGAATATACAA
442741 GTTCTACATG
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
97 1 0.01
98 79 0.99
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (98 bp):
ATAGTGAAAATCATCATTGTCGGGCCACTCGAGATGGTAGAATATGCAAATAGTGAAGACCATTG
TTGTCAGGCCACCCGGGAGGGTAGAATATACAA
Found at i:443430 original size:18 final size:18
Alignment explanation
Indices: 443403--443439 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
443393 TAAGTATTGG
443403 TTTGGGTGGCAATTAGGT
1 TTTGGGTGGCAATTAGGT
*
443421 TTTGGTTGGCAATTAGGT
1 TTTGGGTGGCAATTAGGT
443439 T
1 T
443440 AATATAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.05, G:0.35, T:0.43
Consensus pattern (18 bp):
TTTGGGTGGCAATTAGGT
Found at i:444027 original size:21 final size:20
Alignment explanation
Indices: 444002--444044 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
443992 AATGGAAAAT
444002 AAAGAA-AAAAAAAGAAAGTTA
1 AAAGAACAAAAAAA-AAA-TTA
*
444023 AAAGAACATAAAAAAAATTA
1 AAAGAACAAAAAAAAAATTA
444043 AA
1 AA
444045 TTACTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (20 bp):
AAAGAACAAAAAAAAAATTA
Found at i:457005 original size:21 final size:22
Alignment explanation
Indices: 456960--457011 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
456950 AAAAACAACG
*
456960 AATAAGAGATTTTAGAGGGAGA
1 AATAAGAGATTTTAGAGGAAGA
456982 AATAAGAGATTTTAGA-GAAGA
1 AATAAGAGATTTTAGAGGAAGA
*
457003 AATTAGAGA
1 AATAAGAGA
457012 GAAAGCAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (22 bp):
AATAAGAGATTTTAGAGGAAGA
Found at i:461145 original size:3 final size:3
Alignment explanation
Indices: 461137--461175 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
461127 GTAAATAGTG
461137 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
461176 ATGGTGCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:466109 original size:17 final size:16
Alignment explanation
Indices: 466069--466110 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
466059 AAAGAAATGA
466069 AGAAT-AAAAGAAAAC
1 AGAATGAAAAGAAAAC
* *
466084 AAAAAGAAAAGCAAAAC
1 AGAATGAAAAG-AAAAC
466101 AGAATGAAAA
1 AGAATGAAAA
466111 ATAAAGAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 3 0.14
16 5 0.24
17 13 0.62
ACGTcount: A:0.74, C:0.07, G:0.14, T:0.05
Consensus pattern (16 bp):
AGAATGAAAAGAAAAC
Found at i:481805 original size:16 final size:18
Alignment explanation
Indices: 481766--481799 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
481756 TAAATTTATA
481766 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
481783 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
481800 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Done.