Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014546.1 Kokia drynarioides strain JFW-HI SEQ_129585, 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: 267279
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:3660 original size:17 final size:17
Alignment explanation
Indices: 3638--3670 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3628 CACTAACACT
*
3638 AAAATGCAATGACAATG
1 AAAATGCAACGACAATG
3655 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
3671 TCTTACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATG
Found at i:18676 original size:19 final size:19
Alignment explanation
Indices: 18654--18692 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
18644 GCGTGTATCC
18654 CAACCACACGAGAGTGTCT
1 CAACCACACGAGAGTGTCT
* *
18673 CAACCACACGGGTGTGTCT
1 CAACCACACGAGAGTGTCT
18692 C
1 C
18693 TTTTGCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.18
Consensus pattern (19 bp):
CAACCACACGAGAGTGTCT
Found at i:23832 original size:22 final size:22
Alignment explanation
Indices: 23807--23848 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
23797 TGCTTAGTAT
*
23807 CTATACCTGTTATGCTCTACAA
1 CTATACCTGGTATGCTCTACAA
*
23829 CTATATCTGGTATGCTCTAC
1 CTATACCTGGTATGCTCTAC
23849 TTTTGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (22 bp):
CTATACCTGGTATGCTCTACAA
Found at i:25872 original size:189 final size:189
Alignment explanation
Indices: 25470--25905 Score: 624
Period size: 189 Copynumber: 2.3 Consensus size: 189
25460 AGTAATTTTT
* * * *
25470 ATGGTTGGGATCCTGCATATGTTGTAATTTCTTAACAGCTTGTGTGAGCAGCATCGTGAGTCGAC
1 ATGGCTGGGAT-CTGCATATGTTGCAATTTCCTGACAGCTTGTGTGAGCAGCATCGTGAGTCGAC
** * * *
25535 GACTTTTGATTGTCTACTGGATTATGACTGTAAGGATCCCTAAGATGATTGAGATTTTGCATACG
65 GACTTTTGATTGAATACTGGATTATGACTATAAGGATCCCTAAGATGACTGAGATTTTGCATACA
* * * * ** *
25600 TTGTAGTTTCTTGACAGCTTGTGTGAGCAACATCGTGAGTGGGTAACATGGATTGTATCG
130 TTGCAATTTCTTGACAGCTTGTGTGAGCAACATCATGAGTCGGTAACATGGACCGTATCA
25660 ATGGCTGGGATCTTGCATATGTTGCAATTTCCTGACAGCTTGTGTGAGCAGCATCGTGAGTCGAC
1 ATGGCTGGGATC-TGCATATGTTGCAATTTCCTGACAGCTTGTGTGAGCAGCATCGTGAGTCGAC
* *
25725 GACTTTTGATTGAATACTGGATTATGACTATAAGGA-CCCTACTG-TGGCTGAGATTTTGCATAC
65 GACTTTTGATTGAATACTGGATTATGACTATAAGGATCCCTA-AGATGACTGAGATTTTGCATAC
*
25788 ATTGCAATTTCTTGACAGCTTGTGTGAGCAGCATCATGAGTCGGTAACATGGACCGTATCA
129 ATTGCAATTTCTTGACAGCTTGTGTGAGCAACATCATGAGTCGGTAACATGGACCGTATCA
* * *
25849 ATGGCTGGGATGCTACATATGTTGCAGTTTCCTGACAGCTTGTGTGAACAGCATCGT
1 ATGGCTGGGAT-CTGCATATGTTGCAATTTCCTGACAGCTTGTGTGAGCAGCATCGT
25906 ATACTGGTTA
Statistics
Matches: 221, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
189 127 0.57
190 94 0.43
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (189 bp):
ATGGCTGGGATCTGCATATGTTGCAATTTCCTGACAGCTTGTGTGAGCAGCATCGTGAGTCGACG
ACTTTTGATTGAATACTGGATTATGACTATAAGGATCCCTAAGATGACTGAGATTTTGCATACAT
TGCAATTTCTTGACAGCTTGTGTGAGCAACATCATGAGTCGGTAACATGGACCGTATCA
Found at i:29167 original size:18 final size:18
Alignment explanation
Indices: 29144--29178 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29134 TTCAAAAATA
*
29144 TAAATTTAATTAATAATT
1 TAAATTCAATTAATAATT
*
29162 TAAATTCACTTAATAAT
1 TAAATTCAATTAATAAT
29179 AATTAAAATT
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:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATTCAATTAATAATT
Found at i:30283 original size:17 final size:17
Alignment explanation
Indices: 30263--30296 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30253 TTCATATATT
*
30263 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
30280 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
30297 GTGAGTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:54699 original size:29 final size:31
Alignment explanation
Indices: 54646--54705 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
54636 GAATTTTGAA
54646 ATTTTTTTATATTTTAAAAAATTATT-TTTT
1 ATTTTTTTATATTTTAAAAAATTATTATTTT
* *
54676 ATTTTTTTA-ATTTTAAAGAGTTATTATTTT
1 ATTTTTTTATATTTTAAAAAATTATTATTTT
54706 TTTACATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (31 bp):
ATTTTTTTATATTTTAAAAAATTATTATTTT
Found at i:55516 original size:30 final size:28
Alignment explanation
Indices: 55480--55537 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
55470 ACCAATTATT
55480 ATAAATTTAAT-TTATATAATTAAAAATTTA
1 ATAAA-TTAATATTATATAA-T-AAAATTTA
*
55510 ATAAATTATTATTATATAATAAAATTTA
1 ATAAATTAATATTATATAATAAAATTTA
55538 GTTGGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 8 0.31
29 5 0.19
30 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATAAATTAATATTATATAATAAAATTTA
Found at i:60517 original size:2 final size:2
Alignment explanation
Indices: 60512--60546 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60502 TTTTTTTTAA
60512 AT AT AT AT 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 AT AT AT AT A
60547 ATAGTTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61759 original size:30 final size:29
Alignment explanation
Indices: 61598--61826 Score: 212
Period size: 29 Copynumber: 7.7 Consensus size: 29
61588 CATTAAAACC
* * *
61598 GGGTCAAATATGAATTTTTGGAAAG-TTCA
1 GGGTCAAACAT-AATTTTTAGAAAGTTTGA
* *
61627 GGGTCAAATCAAAATTTTTAGAAAGTTCGA
1 GGGTCAAA-CATAATTTTTAGAAAGTTTGA
* **
61657 GGGTTAAATTTGAATTTTTAGAAAGTTTGA
1 GGGTCAAACAT-AATTTTTAGAAAGTTTGA
** **
61687 -GGTCAAATTTGAATTTTTAGAAAGTTCAA
1 GGGTCAAACAT-AATTTTTAGAAAGTTTGA
*
61716 GGGTCAAACATAATTTTTAGAAAGTTTTA
1 GGGTCAAACATAATTTTTAGAAAGTTTGA
61745 GGGTCAAGACATAATTTTTAGAAAGTTT-A
1 GGGTCAA-ACATAATTTTTAGAAAGTTTGA
* * * *
61774 GGGGTTAAAAATAATTTTTGGATAGTTTGA
1 -GGGTCAAACATAATTTTTAGAAAGTTTGA
61804 GGGGTCAAAACATAATTTTTAGA
1 -GGGTC-AAACATAATTTTTAGA
61827 TTATTTGGGG
Statistics
Matches: 168, Mismatches: 24, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
29 87 0.52
30 67 0.40
31 14 0.08
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.36
Consensus pattern (29 bp):
GGGTCAAACATAATTTTTAGAAAGTTTGA
Found at i:61837 original size:59 final size:59
Alignment explanation
Indices: 61610--61850 Score: 233
Period size: 59 Copynumber: 4.1 Consensus size: 59
61600 GTCAAATATG
* * * * * **
61610 AATTTTTGGAAAG-TTCAGGGTCAAATCAAAATTTTTAGAAAG-TTCGAGGGTTAAATTT
1 AATTTTTAGAAAGTTTGAGGGTCAAAACATAATTTTTAGAAAGTTTAG-GGGTTAAAAAT
** * * * *
61668 GAATTTTTAGAAAGTTTGA-GGTC-AAATTTGAATTTTTAGAAAGTTCAAGGGTCAAACAT
1 -AATTTTTAGAAAGTTTGAGGGTCAAAACAT-AATTTTTAGAAAGTTTAGGGGTTAAAAAT
* *
61727 AATTTTTAGAAAGTTTTAGGGTCAAGACATAATTTTTAGAAAGTTTAGGGGTTAAAAAT
1 AATTTTTAGAAAGTTTGAGGGTCAAAACATAATTTTTAGAAAGTTTAGGGGTTAAAAAT
* * *
61786 AATTTTTGGATAGTTTGAGGGGTCAAAACATAATTTTTAGATTA-TTT-GGGGTTAAAAAT
1 AATTTTTAGAAAGTTTGA-GGGTCAAAACATAATTTTTAGA-AAGTTTAGGGGTTAAAAAT
61845 AATTTT
1 AATTTT
61851 AAAATAAAGT
Statistics
Matches: 150, Mismatches: 25, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
58 19 0.13
59 99 0.66
60 31 0.21
61 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (59 bp):
AATTTTTAGAAAGTTTGAGGGTCAAAACATAATTTTTAGAAAGTTTAGGGGTTAAAAAT
Found at i:63716 original size:50 final size:50
Alignment explanation
Indices: 63662--63793 Score: 185
Period size: 50 Copynumber: 2.6 Consensus size: 50
63652 GCTTCTGTAT
* *
63662 CTTCAATTTGCCCCTCTATAGCTTTAGGTGTATGAGATTTGCCATTGC-A
1 CTTCAATTTGCACCTCTAAAGCTTTAGGTGTATGAGATTTGCCATTGCGA
* * * *
63711 GCTTCAATCTGCACCTTTACAGCTTTAGGTGTATGAGATTTGTCATTGCGA
1 -CTTCAATTTGCACCTCTAAAGCTTTAGGTGTATGAGATTTGCCATTGCGA
*
63762 CTTCAATTTGCACCTCTAAAGCTTTGGGTGTA
1 CTTCAATTTGCACCTCTAAAGCTTTAGGTGTA
63794 AAAAATTGGA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 71 0.99
51 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (50 bp):
CTTCAATTTGCACCTCTAAAGCTTTAGGTGTATGAGATTTGCCATTGCGA
Found at i:74120 original size:88 final size:89
Alignment explanation
Indices: 73958--74191 Score: 255
Period size: 88 Copynumber: 2.7 Consensus size: 89
73948 CATTAAAACC
* * * * * **
73958 GGGTCAAATTTGAATTTTTTGAAAGTTT-AGGGGTCAAACAAAATTTTTAAAAAG-TTTGGGGTC
1 GGGTCAAATTTGAATTTTTAGAAAGTTTGAGGGTTAAAACATAATTTTTAGAAAGTTTTAAGGTC
74021 AAATTTGAATTTTTGGAAAGTTT-A
66 AAA-TTGAATTTTTGGAAAGTTTAA
* *
74045 GGATTCAAATTTGAATTTTTGGAAAGTTTGAGGGTTAAAACATAATTTTTAGAAAGTTTTAAGGT
1 GG-GTCAAATTTGAATTTTTAGAAAGTTTGAGGGTTAAAACATAATTTTTAGAAAGTTTTAAGGT
74110 CAAGA-T-AATTTTTGGAAAGTTTAA
65 CAA-ATTGAATTTTTGGAAAGTTTAA
** * * * *
74134 GGGTCAAAACAT-AATTTTTAGATAGTTTGAGGGTCAAAACATAATTTTTGGATAGTTT
1 GGGTC-AAATTTGAATTTTTAGAAAGTTTGAGGGTTAAAACATAATTTTTAGAAAGTTT
74192 AGGGGTCAAA
Statistics
Matches: 125, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
87 2 0.02
88 83 0.66
89 30 0.24
90 9 0.07
91 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (89 bp):
GGGTCAAATTTGAATTTTTAGAAAGTTTGAGGGTTAAAACATAATTTTTAGAAAGTTTTAAGGTC
AAATTGAATTTTTGGAAAGTTTAA
Found at i:74130 original size:58 final size:58
Alignment explanation
Indices: 73970--74202 Score: 197
Period size: 58 Copynumber: 3.9 Consensus size: 58
73960 GTCAAATTTG
* * * ** * **
73970 AATTTTTTGAAAGTTT-AGGGGTCAAACAAAATTTTTAAAAAGTTTGGGGTC-AAATTT
1 AATTTTTAGAAAGTTTGA-AGGTCAAACATAATTTTTGGAAAGTTTAGGGTCAAAACAT
* ** *
74027 GAATTTTTGGAAAGTTT--AGGATTCAAATTTGAATTTTTGGAAAGTTTGAGGGTTAAAACAT
1 -AATTTTTAGAAAGTTTGAAGG--TCAAACAT-AATTTTTGGAAAGTTT-AGGGTCAAAACAT
* *
74088 AATTTTTAGAAAGTTTTAAGGTC-AAGATAATTTTTGGAAAGTTTAAGGGTCAAAACAT
1 AATTTTTAGAAAGTTTGAAGGTCAAACATAATTTTTGGAAAGTTT-AGGGTCAAAACAT
* * *
74146 AATTTTTAGATAGTTTGAGGGTCAAAACATAATTTTTGGATAGTTTAGGGGTCAAAA
1 AATTTTTAGAAAGTTTGAAGGTC-AAACATAATTTTTGGAAAGTTTA-GGGTCAAAA
74203 ACAAGTTTAA
Statistics
Matches: 144, Mismatches: 21, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
56 2 0.01
58 68 0.47
59 18 0.12
60 49 0.34
61 4 0.03
62 3 0.02
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (58 bp):
AATTTTTAGAAAGTTTGAAGGTCAAACATAATTTTTGGAAAGTTTAGGGTCAAAACAT
Found at i:74202 original size:30 final size:29
Alignment explanation
Indices: 73970--74201 Score: 202
Period size: 30 Copynumber: 7.9 Consensus size: 29
73960 GTCAAATTTG
* *
73970 AATTTTTTGAAAGTTTAGGGGTCAAACAA
1 AATTTTTGGAAAGTTTAGGGGTCAAACAT
** **
73999 AATTTTTAAAAAGTTT-GGGGTCAAATTT
1 AATTTTTGGAAAGTTTAGGGGTCAAACAT
** **
74027 GAATTTTTGGAAAGTTTAGGATTCAAATTT
1 -AATTTTTGGAAAGTTTAGGGGTCAAACAT
* *
74057 GAATTTTTGGAAAGTTTGAGGGTTAAAACAT
1 -AATTTTTGGAAAGTTT-AGGGGTCAAACAT
* * *
74088 AATTTTTAGAAAGTTTTA-AGGTC-AAGAT
1 AATTTTTGGAAAG-TTTAGGGGTCAAACAT
*
74116 AATTTTTGGAAAGTTTAAGGGTCAAAACAT
1 AATTTTTGGAAAGTTTAGGGGTC-AAACAT
* *
74146 AATTTTTAGATAGTTT-GAGGGTCAAAACAT
1 AATTTTTGGAAAGTTTAG-GGGTC-AAACAT
*
74176 AATTTTTGGATAGTTTAGGGGTCAAA
1 AATTTTTGGAAAGTTTAGGGGTCAAA
74202 AACAAGTTTA
Statistics
Matches: 169, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
27 4 0.02
28 29 0.17
29 33 0.20
30 90 0.53
31 13 0.08
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (29 bp):
AATTTTTGGAAAGTTTAGGGGTCAAACAT
Found at i:76371 original size:24 final size:24
Alignment explanation
Indices: 76327--76373 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
76317 AAAATTCAAA
*
76327 ATATTTATAAAAATTTCAAAATTT
1 ATATTTATAAAAATTTAAAAATTT
*
76351 ATATTTA-AAAACTTATAAAAATT
1 ATATTTATAAAAATT-TAAAAATT
76374 AGAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATTTATAAAAATTTAAAAATTT
Found at i:76790 original size:29 final size:29
Alignment explanation
Indices: 76758--76814 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
76748 TATAAATTTA
76758 ATAAATTTAAAAAATTGAATAATTAAATG
1 ATAAATTTAAAAAATTGAATAATTAAATG
* * * **
76787 ATAATTTTATAAATTTTCATAATTAAAT
1 ATAAATTTAAAAAATTGAATAATTAAAT
76815 CATCAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (29 bp):
ATAAATTTAAAAAATTGAATAATTAAATG
Found at i:80858 original size:3 final size:3
Alignment explanation
Indices: 80844--80878 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
80834 TTGCCATTGT
*
80844 TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
80879 TATAGTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:81363 original size:12 final size:12
Alignment explanation
Indices: 81346--81380 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
81336 GTCTGGTTAT
81346 TATATAATAAAA
1 TATATAATAAAA
81358 TATATAATATAAA
1 TATATAATA-AAA
81371 TATAT-ATAAA
1 TATATAATAAA
81381 TTATTACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.09
12 12 0.55
13 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TATATAATAAAA
Found at i:82903 original size:26 final size:26
Alignment explanation
Indices: 82822--82905 Score: 125
Period size: 26 Copynumber: 3.3 Consensus size: 26
82812 ATCGATGACT
*
82822 TTTAGCAGGCTTCGAGCCGGTGAATG
1 TTTAGCAGGCTTCGAGCCTGTGAATG
* *
82848 -TTAGCAGGCTTTGAGCCTGTGAATC
1 TTTAGCAGGCTTCGAGCCTGTGAATG
*
82873 ATTAGCAGGCTTCGAGCCTGTGAATG
1 TTTAGCAGGCTTCGAGCCTGTGAATG
82899 TTTAGCA
1 TTTAGCA
82906 AGTACTATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
25 22 0.43
26 29 0.57
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (26 bp):
TTTAGCAGGCTTCGAGCCTGTGAATG
Found at i:94971 original size:34 final size:34
Alignment explanation
Indices: 94928--94995 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
94918 CAAGAATTTT
94928 CGTTAATATAGAAAAATGAGATTATAAAACAATC
1 CGTTAATATAGAAAAATGAGATTATAAAACAATC
94962 CGTTAATATAGAAAAATGAGATTATAAAACAATC
1 CGTTAATATAGAAAAATGAGATTATAAAACAATC
94996 TCTGTACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (34 bp):
CGTTAATATAGAAAAATGAGATTATAAAACAATC
Found at i:95429 original size:31 final size:32
Alignment explanation
Indices: 95393--95464 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
95383 TTTGAGTTAA
* *
95393 GACTAAAATTTTA-AAATTTGAAAAATATAGG
1 GACTAAAATTTTACAAATTCGAAAAATATAAG
* *
95424 GACTAAAA-TTTACCAATTCGAAAAGTATAAG
1 GACTAAAATTTTACAAATTCGAAAAATATAAG
95455 GACTAAAATT
1 GACTAAAATT
95465 AATCGAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.11
31 30 0.86
32 1 0.03
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (32 bp):
GACTAAAATTTTACAAATTCGAAAAATATAAG
Found at i:99639 original size:28 final size:28
Alignment explanation
Indices: 99601--99666 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
99591 AAACCTACTC
*
99601 ATTA-TTTTTTTAATTTTTTAA-AAA-TT
1 ATTATTTTTTTTAA-TATTTAATAAATTT
99627 ATTATTTTATTTTAATATTTAATAAATTT
1 ATTATTTT-TTTTAATATTTAATAAATTT
99656 ATATATTTTTT
1 AT-TATTTTTT
99667 ATTTATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 4 0.12
27 9 0.26
28 9 0.26
29 6 0.18
30 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTATTTTTTTTAATATTTAATAAATTT
Found at i:99673 original size:28 final size:25
Alignment explanation
Indices: 99601--99673 Score: 62
Period size: 30 Copynumber: 2.8 Consensus size: 25
99591 AAACCTACTC
*
99601 ATTATT-TTTTTAATTT-TTTAAAA
1 ATTATTATTTTTTATTTATTTAAAA
99624 ATTATTATTTTATT-TTAATATTTAATAA
1 ATTATTATTTT-TTATT--TATTTAA-AA
99652 ATTTATATATTTTTTATTTATT
1 A-TTAT-TATTTTTTATTTATT
99674 AAATTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
23 6 0.15
24 6 0.15
25 1 0.03
26 1 0.03
27 5 0.12
28 7 0.17
29 6 0.15
30 8 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
ATTATTATTTTTTATTTATTTAAAA
Found at i:100531 original size:13 final size:13
Alignment explanation
Indices: 100513--100537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100503 GGTATCGTAA
100513 AATATTAAAAAAT
1 AATATTAAAAAAT
100526 AATATTAAAAAA
1 AATATTAAAAAA
100538 ACAAAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATATTAAAAAAT
Found at i:109774 original size:24 final size:21
Alignment explanation
Indices: 109747--109794 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
109737 ATTTAAAAGA
109747 AAAAAATATGGCATATAAATAAAT
1 AAAAAATAT--CA-ATAAATAAAT
*
109771 -AAAAATATCAATGAATAAAT
1 AAAAAATATCAATAAATAAAT
109791 AAAA
1 AAAA
109795 TTAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
23 8 0.36
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (21 bp):
AAAAAATATCAATAAATAAAT
Found at i:109862 original size:22 final size:23
Alignment explanation
Indices: 109784--109872 Score: 65
Period size: 22 Copynumber: 3.9 Consensus size: 23
109774 AATATCAATG
* * *
109784 AATAAATAAAATTAAATGAAAGC
1 AATAAATAAAAATAAATAAAAAC
* * *
109807 AA-AAATATAAATAGCATAAAAAA
1 AATAAATAAAAATA-AATAAAAAC
* * *
109830 AAAAAAAAAAAATACAT-AAAAC
1 AATAAATAAAAATAAATAAAAAC
*
109852 AATAAATAAAATTAAATAAAA
1 AATAAATAAAAATAAATAAAA
109873 GTGAGAATGT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
22 26 0.52
23 15 0.30
24 9 0.18
ACGTcount: A:0.74, C:0.04, G:0.03, T:0.18
Consensus pattern (23 bp):
AATAAATAAAAATAAATAAAAAC
Found at i:111180 original size:50 final size:50
Alignment explanation
Indices: 111105--111764 Score: 623
Period size: 50 Copynumber: 13.3 Consensus size: 50
111095 TCTTCAATCT
** * * *
111105 GCTTCTGTAGCTTCAATCTATCCCTCTATAACTTTAGGGGTATAAGATTT
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * * * *
111155 GCTTCTGTAGCTTCATTCTGCCCCTCTATAACTTTAAGGGTATAAGATTT
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * * *** *
111205 GCTTTTGTAGTTTCAATTTGTATCTCTACAACTTTAGGGGTATAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * *
111255 GCTTATGTAGCTTCAGTCTGCCTCTCTACAGCTTTAGGGGTATAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * * * * * * * * *
111305 ACTTTTATAGCTTTAATTTTCCCCTTTATAGTTTTAGGGGTACAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * * * *
111355 GCTTTTGTAGCTTTAATTTGCTCCTCTACAACTTTAGGGGTATAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * * *
111405 GCTTCTATAGCTTCAATCCGCCCCTCTACAACTTTAGGAGTATAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * * * * *
111455 GCTTATGTAGCTTTATTTTTCCCCTCTACAGCTTTAAGGGTATAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * * * *
111505 GCTTCTGTAGCTTTAATATGCCCTTTTACAGCTTTTA-TGGTATAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGC-TTTAGGGGTATAAGATTC
* * * * *
111555 GCTTCTATAGCTTTAATCTGCCCCTCTAGAGCTTTAAGGGTATATGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
** *
111605 GCTTCTGTAGCTTCAATCT-ATCC-CT----CTTTAGGGGTATATGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* ** * *
111649 GCTTTTGTAGCTTCAATCTATCCCTCTATAGCTTTAGGGATATAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* * * * * *
111699 GCTTTTATAGCTTTAATTTGCCCCTTTATAGCTTTAGGGGTATAAGATTC
1 GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
* *
111749 CCTTTTGTAGCTTCAA
1 GCTTCTGTAGCTTCAA
111765 GCTACCCCAG
Statistics
Matches: 509, Mismatches: 93, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
44 36 0.07
45 2 0.00
46 2 0.00
48 2 0.00
49 6 0.01
50 457 0.90
51 4 0.01
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (50 bp):
GCTTCTGTAGCTTCAATCTGCCCCTCTACAGCTTTAGGGGTATAAGATTC
Found at i:111649 original size:44 final size:44
Alignment explanation
Indices: 111586--111675 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
111576 CCCTCTAGAG
111586 CTTTAAGGGTATATGATTCGCTTCTGTAGCTTCAATCTATCCCT
1 CTTTAAGGGTATATGATTCGCTTCTGTAGCTTCAATCTATCCCT
* *
111630 CTTTAGGGGTATATGATTCGCTTTTGTAGCTTCAATCTATCCCT
1 CTTTAAGGGTATATGATTCGCTTCTGTAGCTTCAATCTATCCCT
111674 CT
1 CT
111676 ATAGCTTTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (44 bp):
CTTTAAGGGTATATGATTCGCTTCTGTAGCTTCAATCTATCCCT
Found at i:111833 original size:144 final size:144
Alignment explanation
Indices: 111230--111839 Score: 351
Period size: 150 Copynumber: 4.2 Consensus size: 144
111220 ATTTGTATCT
* * * * * * * *
111230 CTACAACTTTAGGGGTATAAGATTCGCTTATGTAGCTTCAGTCTGCCTCTCTACAGCTTTAGGGG
1 CTACAACTTTAGGGATATAAGATTCGCTTCTATAGCTTTAATCTGCCCCTCTAGAGCTTTAAGGG
* * * * ** * * * * * *
111295 TATAAGATTCACTTTTATAGCTTTAATTTTCCCCTTTATAGTTTTAGGGGTACAAGATTCGCTTT
66 TATAAGATTCCCTTCTGTAGCTTCAAGCTACCCC------GATTTAGGCGTATAAGATTCGCGTG
* * *
111360 TGTAGCTTTAAT--TTGCTCCT
125 TGTAGCTTCAATCCAT-C-CCA
* * * * *
111380 CTACAACTTTAGGGGTATAAGATTCGCTTCTATAGCTTCAATCCGCCCCTCTACAACTTT-AGGA
1 CTACAACTTTAGGGATATAAGATTCGCTTCTATAGCTTTAATCTGCCCCTCTAGAGCTTTAAGG-
* * * *** * * *
111444 GTATAAGATTCGCTTATGTAGCTTTATTTTTCCCCTCTACAGCTTTAAGG-GTATAAGATTCGCT
65 GTATAAGATTCCCTTCTGTAGCTTCA-AGCT-ACC-C--C-GATTT-AGGCGTATAAGATTCGCG
* * *
111508 TCTGTAGCTTTAAT--ATGCCCTT
123 TGTGTAGCTTCAATCCAT-CCC-A
* * *
111530 TTACAGCTTTTATGG-TATAAGATTCGCTTCTATAGCTTTAATCTGCCCCTCTAGAGCTTTAAGG
1 CTACAAC-TTTAGGGATATAAGATTCGCTTCTATAGCTTTAATCTGCCCCTCTAGAGCTTTAAGG
* * * * ** * * * *
111594 GTATATGATTCGCTTCTGTAGCTTCAATCTATCCCTCTTTAGGGGTATATGATTCGCTTTTGTAG
65 GTATAAGATTCCCTTCTGTAGCTTCAAGCTACCCCGATTTAGGCGTATAAGATTCGCGTGTGTAG
* *
111659 CTTCAATCTATCCCT
130 CTTCAATCCATCCCA
* * * * * * *
111674 CTATAGCTTTAGGGATATAAGATTCGCTTTTATAGCTTTAATTTGCCCCTTTATAGCTTTAGGGG
1 CTACAACTTTAGGGATATAAGATTCGCTTCTATAGCTTTAATCTGCCCCTCTAGAGCTTTAAGGG
* *
111739 TATAAGATTCCCTTTTGTAGCTTCAAGCTACCCCAGATTTAGGCGTATAAGATTTG-GTGTG-A-
66 TATAAGATTCCCTTCTGTAGCTTCAAGCTACCCC-GATTTAGGCGTATAAGATTCGCGTGTGTAG
* *
111801 CTTCACTCCATTCCA
130 CTTCAATCCATCCCA
111816 CTACAACTTTAATGGGAT-TAAGAT
1 CTACAACTTT-A-GGGATATAAGAT
111840 CTGCTACTTG
Statistics
Matches: 383, Mismatches: 60, Indels: 41
0.79 0.12 0.08
Matches are distributed among these distances:
142 19 0.05
143 17 0.04
144 117 0.31
145 20 0.05
146 2 0.01
147 1 0.00
148 1 0.00
149 6 0.02
150 181 0.47
151 15 0.04
152 2 0.01
153 1 0.00
155 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (144 bp):
CTACAACTTTAGGGATATAAGATTCGCTTCTATAGCTTTAATCTGCCCCTCTAGAGCTTTAAGGG
TATAAGATTCCCTTCTGTAGCTTCAAGCTACCCCGATTTAGGCGTATAAGATTCGCGTGTGTAGC
TTCAATCCATCCCA
Found at i:115074 original size:19 final size:19
Alignment explanation
Indices: 115043--115090 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
115033 TTGATTGTTA
115043 ACTTTTTCTGTTGGCCATTG
1 ACTTTTTC-GTTGGCCATTG
* *
115063 ACTTTTTCGTTGGTCGTTG
1 ACTTTTTCGTTGGCCATTG
*
115082 AATTTTTCG
1 ACTTTTTCG
115091 AGAAACTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.10, C:0.17, G:0.21, T:0.52
Consensus pattern (19 bp):
ACTTTTTCGTTGGCCATTG
Found at i:118267 original size:18 final size:18
Alignment explanation
Indices: 118246--118304 Score: 109
Period size: 18 Copynumber: 3.3 Consensus size: 18
118236 ATCTTGAGCA
118246 TCTTCAAAATCCTAAGAT
1 TCTTCAAAATCCTAAGAT
*
118264 TCTTCAAAATCCTACGAT
1 TCTTCAAAATCCTAAGAT
118282 TCTTCAAAATCCTAAGAT
1 TCTTCAAAATCCTAAGAT
118300 TCTTC
1 TCTTC
118305 TAAACACACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (18 bp):
TCTTCAAAATCCTAAGAT
Found at i:120049 original size:10 final size:10
Alignment explanation
Indices: 120036--120068 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
120026 AATTAAGTAA
120036 GGAGCTGAAT
1 GGAGCTGAAT
120046 GGAGCTGAAT
1 GGAGCTGAAT
*
120056 GGAGTTGAAT
1 GGAGCTGAAT
120066 GGA
1 GGA
120069 CTAGGCTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.30, C:0.06, G:0.42, T:0.21
Consensus pattern (10 bp):
GGAGCTGAAT
Found at i:120497 original size:39 final size:39
Alignment explanation
Indices: 120454--120535 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
120444 AACACCTTAA
120454 AAAAACAACTATTAAATATGTATCAAAATAAGACACATT
1 AAAAACAACTATTAAATATGTATCAAAATAAGACACATT
*
120493 AAAAACAACTATTAAATATGTATCAAACTAAGACACATT
1 AAAAACAACTATTAAATATGTATCAAAATAAGACACATT
120532 AAAA
1 AAAA
120536 CCCTATTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.24
Consensus pattern (39 bp):
AAAAACAACTATTAAATATGTATCAAAATAAGACACATT
Found at i:121612 original size:21 final size:21
Alignment explanation
Indices: 121586--121637 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
121576 CCTGTAACTT
121586 CTACCGATACAAGTATTCAGA
1 CTACCGATACAAGTATTCAGA
121607 CTACCGATACAAGTATTCAGA
1 CTACCGATACAAGTATTCAGA
*
121628 GTACCGATAC
1 CTACCGATAC
121638 TACTATGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (21 bp):
CTACCGATACAAGTATTCAGA
Found at i:122274 original size:26 final size:26
Alignment explanation
Indices: 122231--122287 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
122221 TCTTCCAGAT
*
122231 GTTTAGCTCATAAAAGCCTAAATAGA
1 GTTTAGCTCATAAAAGCCCAAATAGA
* **
122257 GTTTAGCTCTTATGAGCCCAAATAGA
1 GTTTAGCTCATAAAAGCCCAAATAGA
122283 GTTTA
1 GTTTA
122288 ACCATTATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (26 bp):
GTTTAGCTCATAAAAGCCCAAATAGA
Found at i:123815 original size:52 final size:51
Alignment explanation
Indices: 123734--123920 Score: 268
Period size: 52 Copynumber: 3.6 Consensus size: 51
123724 CATTCATTTA
* *
123734 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCATAAAGAAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAG-ATTCAT
* * * *
123786 ATACTCACGATGACACATAGTTATTGGACCTCATAATCCGTAAAGGATTGAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAA-GATTCAT
*
123838 ATACTCATGATGACACATAGTCATCGGACCTCATAAT-CAGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCA-TAAA-GATTCAT
123890 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
123921 TTTTCATTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
51 1 0.01
52 118 0.98
53 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGATTCAT
Found at i:124422 original size:33 final size:33
Alignment explanation
Indices: 124380--124446 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
124370 CACATAAAAC
124380 ACACAATTTCATTATTTTAACATTTTAGTCCTT
1 ACACAATTTCATTATTTTAACATTTTAGTCCTT
124413 ACACAATTTCATTATTTTAACATTTTAGTCCTT
1 ACACAATTTCATTATTTTAACATTTTAGTCCTT
124446 A
1 A
124447 AACCCTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.48
Consensus pattern (33 bp):
ACACAATTTCATTATTTTAACATTTTAGTCCTT
Found at i:130184 original size:21 final size:21
Alignment explanation
Indices: 130136--130184 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
130126 AATAGTGCAG
**
130136 ACTTCTACCGATACAAGTGAC
1 ACTTCTACAAATACAAGTGAC
**
130157 AAATCTACAAATACAAGTGAC
1 ACTTCTACAAATACAAGTGAC
*
130178 TCTTCTA
1 ACTTCTA
130185 TCGAAACAAG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (21 bp):
ACTTCTACAAATACAAGTGAC
Found at i:132400 original size:20 final size:22
Alignment explanation
Indices: 132375--132416 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
132365 TATAATTAGG
132375 CTTAATTAAT-CTTTC-TTAAA
1 CTTAATTAATCCTTTCATTAAA
132395 CTTAATTAATCCTTTCATTAAA
1 CTTAATTAATCCTTTCATTAAA
132417 GCATCAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTAATTAATCCTTTCATTAAA
Found at i:134488 original size:2 final size:2
Alignment explanation
Indices: 134481--134518 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
134471 TTTATAAATG
134481 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
134519 AAAGCTTGGT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:137570 original size:18 final size:17
Alignment explanation
Indices: 137549--137615 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 17
137539 AAATGAAGAC
*
137549 AAAAATATAAATAACATA
1 AAAAATAAAAATAA-ATA
137567 AAAAATAAAAATAAATA
1 AAAAATAAAAATAAATA
137584 AAATACATAAAAATAAATTA
1 AAA-A-ATAAAAATAAA-TA
137604 AATTAAATAAAA
1 AA--AAATAAAA
137616 GCGAGAATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
17 6 0.14
18 14 0.33
19 11 0.26
20 10 0.23
21 1 0.02
22 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAATAAAAATAAATA
Found at i:137584 original size:10 final size:10
Alignment explanation
Indices: 137505--137615 Score: 65
Period size: 10 Copynumber: 11.2 Consensus size: 10
137495 TATGACATAT
137505 AAATAAATAA
1 AAATAAATAA
137515 AAAT--ATCAA
1 AAATAAAT-AA
*
137524 TGAATAAATAA
1 -AAATAAATAA
*
137535 AATTAAATGAA
1 AAATAAAT-AA
*
137546 GACAA-AAATAT
1 -A-AATAAATAA
137557 AAATAACAT--
1 AAATAA-ATAA
137566 AAA-AAATAA
1 AAATAAATAA
137575 AAATAAAT-A
1 AAATAAATAA
*
137584 AAATACATAA
1 AAATAAATAA
*
137594 AAATAAATTA
1 AAATAAATAA
*
137604 AATTAAATAA
1 AAATAAATAA
137614 AA
1 AA
137616 GCGAGAATGT
Statistics
Matches: 78, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
7 2 0.03
8 4 0.05
9 18 0.23
10 39 0.50
11 7 0.09
12 7 0.09
13 1 0.01
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.23
Consensus pattern (10 bp):
AAATAAATAA
Found at i:137595 original size:19 final size:18
Alignment explanation
Indices: 137552--137606 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
137542 TGAAGACAAA
*
137552 AATATAAATAACATAAAA-
1 AATAAAAATAA-ATAAAAT
137570 AATAAAAATAAATAAAAT
1 AATAAAAATAAATAAAAT
*
137588 ACATAAAAATAAATTAAAT
1 A-ATAAAAATAAATAAAAT
137607 TAAATAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 6 0.18
18 11 0.33
19 16 0.48
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAAAAATAAATAAAAT
Found at i:137600 original size:69 final size:70
Alignment explanation
Indices: 137526--137675 Score: 171
Period size: 69 Copynumber: 2.1 Consensus size: 70
137516 AATATCAATG
* *
137526 AATAAATAAAATTAAAT-GAAGACAAAAATATAAATAACATAAAA-AATAA-AAATAAATAAAAT
1 AATAAATAAAATTAAATAAAAG-CAAAAATATAAATAACAAAAAATAATAACAAATAAAT-AAAT
*
137588 ACATAAA
64 AAATAAA
* * * * *
137595 AATAAATTAAATTAAATAAAAGCGAGAATGTAAATAACAAAAAATAATAACCAATAAATAAATAA
1 AATAAATAAAATTAAATAAAAGCAAAAATATAAATAACAAAAAATAATAACAAATAAATAAATAA
*
137660 ATAAT
66 ATAAA
137665 AATAAAGTAAA
1 AATAAA-TAAA
137676 TATATAAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
69 34 0.51
70 23 0.34
71 10 0.15
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (70 bp):
AATAAATAAAATTAAATAAAAGCAAAAATATAAATAACAAAAAATAATAACAAATAAATAAATAA
ATAAA
Found at i:137615 original size:19 final size:19
Alignment explanation
Indices: 137505--137615 Score: 84
Period size: 20 Copynumber: 5.6 Consensus size: 19
137495 TATGACATAT
137505 AAATAAATAAAAATATCAAT-
1 AAATAAATAAAAATA--AATA
* *
137525 GAATAAATAAAATTAAATGA
1 AAATAAATAAAAATAAAT-A
* *
137545 AGACAAAAATATAAATAACAT-
1 A-A-ATAAATAAAAATAA-ATA
137566 AAA-AAATAAAAATAAATA
1 AAATAAATAAAAATAAATA
*
137584 AAATACATAAAAATAAATTA
1 AAATAAATAAAAATAAA-TA
*
137604 AATTAAATAAAA
1 AAATAAATAAAA
137616 GCGAGAATGT
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
17 2 0.03
18 17 0.23
19 13 0.18
20 26 0.36
21 2 0.03
22 11 0.15
23 2 0.03
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.23
Consensus pattern (19 bp):
AAATAAATAAAAATAAATA
Found at i:137700 original size:70 final size:69
Alignment explanation
Indices: 137526--137700 Score: 151
Period size: 69 Copynumber: 2.5 Consensus size: 69
137516 AATATCAATG
* * * *
137526 AATAAA-TAAAATTAAAT-GAAGACAAAAATATAAATAACATAAAAAATAAAAATAAATAAAATA
1 AATAAAGT-AAATTAAATAAAAG-CAAGAATAAAAATAACAAAAAAAATAAAAATAAATAAAATA
*
137589 CATAAA
64 AATAAA
* * ** *
137595 AATAAATTAAATTAAATAAAAGCGAGAATGTAAATAACAAAAAATAATAACCAATAAAT-AAATA
1 AATAAAGTAAATTAAATAAAAGCAAGAATAAAAATAACAAAAAA-AATAA-AAATAAATAAAATA
*
137659 AATAAT
64 AATAAA
* **
137665 AATAAAGTAAA-TATATAAAATGCAATCATAAAAATA
1 AATAAAGTAAATTAAATAAAA-GCAAGAATAAAAATA
137701 TTTAACATAA
Statistics
Matches: 86, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
69 41 0.48
70 38 0.44
71 7 0.08
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (69 bp):
AATAAAGTAAATTAAATAAAAGCAAGAATAAAAATAACAAAAAAAATAAAAATAAATAAAATAAA
TAAA
Found at i:137865 original size:26 final size:25
Alignment explanation
Indices: 137826--137875 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
137816 AATTAAATAA
*
137826 AAAATAAAATAAAAGACATAACAAT
1 AAAATAAAATAAAAGAAATAACAAT
* *
137851 AAAATAATATGAAAATAAATAACAA
1 AAAATAAAAT-AAAAGAAATAACAA
137876 GTAGATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.18
Consensus pattern (25 bp):
AAAATAAAATAAAAGAAATAACAAT
Found at i:137950 original size:13 final size:14
Alignment explanation
Indices: 137917--137950 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
137907 ATTAAATGCT
137917 AAAATAAACAAATA
1 AAAATAAACAAATA
*
137931 AATATAAAC-AATA
1 AAAATAAACAAATA
137944 AAAATAA
1 AAAATAA
137951 TTAAGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAACAAATA
Found at i:138033 original size:25 final size:25
Alignment explanation
Indices: 137993--138040 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
137983 AATAAATAAA
137993 CAAAAAAATCAATAAAT-TAAATGT
1 CAAAAAAATCAATAAATATAAATGT
138017 CAAAATAAA-CAAGTAAATATAAAT
1 CAAAA-AAATCAA-TAAATATAAAT
138041 AATAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (25 bp):
CAAAAAAATCAATAAATATAAATGT
Found at i:138037 original size:101 final size:100
Alignment explanation
Indices: 137855--138046 Score: 253
Period size: 101 Copynumber: 1.9 Consensus size: 100
137845 AACAATAAAA
* *
137855 TAATATGAAAATAAATAACAAGTAGATAAATAAACAAAAAAACAAAAAAAAAATTAAATGCTAAA
1 TAATATGAAAATAAATAACAAATAAATAAATAAACAAAAAAAC---AAAAAAATTAAATGCTAAA
137920 ATAAACAAATAAATATAAACAATAAAAATAATTAAGAT
63 ATAAACAAATAAATATAAACAATAAAAATAATTAAGAT
** *
137958 TAATCATGAAAATAAATGGCAAATAAATAAATAAACAAAAAAATC-AATAAATTAAATG-TCAAA
1 TAAT-ATGAAAATAAATAACAAATAAATAAATAAACAAAAAAA-CAAAAAAATTAAATGCT-AAA
* *
138021 ATAAACAAGTAAATATAAATAATAAA
63 ATAAACAAATAAATATAAACAATAAA
138047 TTTTAAGTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
100 1 0.01
101 39 0.49
103 4 0.05
104 34 0.43
105 1 0.01
ACGTcount: A:0.67, C:0.06, G:0.05, T:0.21
Consensus pattern (100 bp):
TAATATGAAAATAAATAACAAATAAATAAATAAACAAAAAAACAAAAAAATTAAATGCTAAAATA
AACAAATAAATATAAACAATAAAAATAATTAAGAT
Found at i:139029 original size:31 final size:32
Alignment explanation
Indices: 138988--139061 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 32
138978 TGTTTGGATC
*
138988 AGGACAAAAATTTTA-AAATTTCAAAAGTATA
1 AGGACTAAAATTTTACAAATTTCAAAAGTATA
* * *
139019 GGGACTAAAA-TTTACCAATTTGAAAAGTATA
1 AGGACTAAAATTTTACAAATTTCAAAAGTATA
*
139050 AGGATTAAAATT
1 AGGACTAAAATT
139062 AATCAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
30 4 0.11
31 30 0.86
32 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.30
Consensus pattern (32 bp):
AGGACTAAAATTTTACAAATTTCAAAAGTATA
Found at i:151090 original size:22 final size:22
Alignment explanation
Indices: 151063--151108 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
151053 ATGAATTGTG
151063 ATATATGCCAACTATTATGATT
1 ATATATGCCAACTATTATGATT
151085 ATATATGCCAACTATTATGATT
1 ATATATGCCAACTATTATGATT
151107 AT
1 AT
151109 GTTTTTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
ATATATGCCAACTATTATGATT
Found at i:166301 original size:40 final size:40
Alignment explanation
Indices: 166205--166473 Score: 261
Period size: 40 Copynumber: 6.7 Consensus size: 40
166195 CCAAATTGTA
* * * * * *
166205 TGAACTGGAAGTGACATTGTAAACACTGGGATATTTCAAT
1 TGAACTGGCAGTGACACTGTAAACACTGCGATACTACAAC
* * * *
166245 TAAACTAGCAGGGACACTGTAGACACTGCGATACTACAAC
1 TGAACTGGCAGTGACACTGTAAACACTGCGATACTACAAC
*
166285 TGAACTGGCAGTGACACTGTAAACATTGCGATACTACAAC
1 TGAACTGGCAGTGACACTGTAAACACTGCGATACTACAAC
* * * *
166325 TGAACTGGCAATGACACTGTAAACACTACAATGCTATC-AC
1 TGAACTGGCAGTGACACTGTAAACACTGCGATACTA-CAAC
* * * *
166365 TAAACTAGCAATGACACTGTAAACACTGCGATATTACAAC
1 TGAACTGGCAGTGACACTGTAAACACTGCGATACTACAAC
* * * * ** * *
166405 AGAACTGGCGGTGACATTGTAACCACCCCTATACTACAAT
1 TGAACTGGCAGTGACACTGTAAACACTGCGATACTACAAC
* *
166445 TGAACTAGCAGTGACATTGTAAACACTGC
1 TGAACTGGCAGTGACACTGTAAACACTGC
166474 TAGATTCTGT
Statistics
Matches: 183, Mismatches: 44, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 181 0.99
41 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (40 bp):
TGAACTGGCAGTGACACTGTAAACACTGCGATACTACAAC
Found at i:166419 original size:120 final size:120
Alignment explanation
Indices: 166245--166471 Score: 310
Period size: 120 Copynumber: 1.9 Consensus size: 120
166235 ATATTTCAAT
* * *
166245 TAAACTAGCAGGGACACTGTAGACACTGCGATACTACAACTGAACTGGCAGTGACACTGTAAACA
1 TAAACTAGCAAGGACACTGTAAACACTGCGATACTACAACAGAACTGGCAGTGACACTGTAAACA
*** *
166310 TTGCGATACTACAACTGAACTGGCAATGACACTGTAAACACTACAATGCTATCAC
66 CCCCGATACTACAACTGAACTAGCAATGACACTGTAAACACTACAATGCTATCAC
* * * * *
166365 TAAACTAGCAATGACACTGTAAACACTGCGATATTACAACAGAACTGGCGGTGACATTGTAACCA
1 TAAACTAGCAAGGACACTGTAAACACTGCGATACTACAACAGAACTGGCAGTGACACTGTAAACA
* * * *
166430 CCCCTATACTACAATTGAACTAGCAGTGACATTGTAAACACT
66 CCCCGATACTACAACTGAACTAGCAATGACACTGTAAACACT
166472 GCTAGATTCT
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
120 91 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (120 bp):
TAAACTAGCAAGGACACTGTAAACACTGCGATACTACAACAGAACTGGCAGTGACACTGTAAACA
CCCCGATACTACAACTGAACTAGCAATGACACTGTAAACACTACAATGCTATCAC
Found at i:168416 original size:21 final size:21
Alignment explanation
Indices: 168389--168439 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
168379 CGATTATGTA
168389 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
168410 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
168431 ATTTGGATT
1 ATTTGGATT
168440 ATGCTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:169298 original size:47 final size:48
Alignment explanation
Indices: 169234--169328 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 48
169224 GAAATCCCTA
169234 TCAATAATTTTCCTGATTTCCAGTAAGGCATGATCTCATTTCAATAAT
1 TCAATAATTTTCCTGATTTCCAGTAAGGCATGATCTCATTTCAATAAT
*
169282 TCAA-AATTTTCTTGATTTCCAGTAAGGCATGATCTCATTTCAATAAT
1 TCAATAATTTTCCTGATTTCCAGTAAGGCATGATCTCATTTCAATAAT
169329 AATAGAGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 42 0.91
48 4 0.09
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (48 bp):
TCAATAATTTTCCTGATTTCCAGTAAGGCATGATCTCATTTCAATAAT
Found at i:174768 original size:17 final size:17
Alignment explanation
Indices: 174733--174779 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
174723 AACTAAAAGG
*
174733 AATTAAAATGCATTGAC
1 AATTAAAATGCATAGAC
174750 AATTAAAATGCA-AGCAC
1 AATTAAAATGCATAG-AC
174767 AA-TAATAATGCAT
1 AATTAA-AATGCAT
174780 GAAAACTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.26
Consensus pattern (17 bp):
AATTAAAATGCATAGAC
Found at i:175228 original size:3 final size:3
Alignment explanation
Indices: 175193--175239 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
175183 CCTCGGCAGA
*
175193 TTC TTT TTC TTC TT- TCTC TTC ATTC TT- TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC T-TC TTC -TTC TTC TTC TTC TTC TTC TTC TTC
175238 TT
1 TT
175240 GATCCTTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 3 0.08
3 31 0.82
4 4 0.11
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:183582 original size:21 final size:21
Alignment explanation
Indices: 183535--183611 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
183525 AATAGTGTAG
183535 ACTTCTACCAATACAAGTGAC
1 ACTTCTACCAATACAAGTGAC
* **
183556 AGTTCTACTGATACAAGTGAC
1 ACTTCTACCAATACAAGTGAC
* * ***
183577 TCTTCTATCGAA-ACAAGTCTT
1 ACTTCTA-CCAATACAAGTGAC
183598 ACTTCTACCAATAC
1 ACTTCTACCAATAC
183612 TAAAAACTCT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 3 0.07
21 37 0.88
22 2 0.05
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (21 bp):
ACTTCTACCAATACAAGTGAC
Found at i:186323 original size:18 final size:18
Alignment explanation
Indices: 186296--186334 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
186286 ATTACAAGAG
*
186296 GAGGTGGAGGCCTTACGA
1 GAGGTAGAGGCCTTACGA
* *
186314 GAGGTAGAGGTCTTACTA
1 GAGGTAGAGGCCTTACGA
186332 GAG
1 GAG
186335 ATGCCATAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.41, T:0.21
Consensus pattern (18 bp):
GAGGTAGAGGCCTTACGA
Found at i:189637 original size:36 final size:36
Alignment explanation
Indices: 189541--189678 Score: 132
Period size: 36 Copynumber: 3.8 Consensus size: 36
189531 TAGTAACAGG
* * *
189541 CATGAACTTTGGGTTAATAGGGAGAAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
* * * * * * *
189577 AATGACCTTCGAGTTAACAAGGTGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
* * ** *
189613 CATGACCTTTAGGTCAATAGGGTGTAAAACAAGTAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
189649 CATGACCTTTGGGGTCAATAGGGAGTAAAA
1 CATGACCTTT-GGGTCAATAGGGAGTAAAA
189679 CGAATAACGA
Statistics
Matches: 81, Mismatches: 20, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
36 64 0.79
37 17 0.21
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
Found at i:194103 original size:37 final size:36
Alignment explanation
Indices: 194006--194106 Score: 121
Period size: 36 Copynumber: 2.8 Consensus size: 36
193996 TGTAAAAGGC
* * * * *
194006 ATGACCTTTGAGTCAACAAGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTTAACAGGGAGTAAAACGAGCATA
* *
194042 ATGACCTTTGGGTTAACAGTGAGTAAAACGAGCATC
1 ATGACCTTTGGGTTAACAGGGAGTAAAACGAGCATA
*
194078 ATGACCTTTGGGGTTAATAGGGAGTAAAA
1 ATGACCTTT-GGGTTAACAGGGAGTAAAA
194107 TGAATAATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
36 38 0.69
37 17 0.31
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (36 bp):
ATGACCTTTGGGTTAACAGGGAGTAAAACGAGCATA
Found at i:194794 original size:116 final size:116
Alignment explanation
Indices: 194580--194831 Score: 336
Period size: 116 Copynumber: 2.2 Consensus size: 116
194570 AGTAGAACTC
*
194580 ATACTTGTA-CTGGTAGAAGTACAGGGTAAGAGAGAGGTTGTTCTCTGACTTGAATTGTTTCGAT
1 ATACTTGTATC-GGTAGAAGTACAGGGTAAGAGAGAGGTTGATCTCTGACTTGAATTGTTTCGAT
* * *
194644 AGTTGTATAATAGGTATCGGTAGTTCTGTGCATTGAGGTTTC-GAAAGTTTAA
65 AGTTGTATAATAGGTATAGGTAGTTCTGTACATTGAGGTATCAG-AAGTTTAA
*
194696 ATGA-TTGTATCGGTAGAAGTACAGGGT-AGTAGAGAGGTTGATCTCTGACTTGAGTTGTTTCCG
1 AT-ACTTGTATCGGTAGAAGTACAGGGTAAG-AGAGAGGTTGATCTCTGACTTGAATTGTTT-CG
* *
194759 -TAGTTGTATAACT-GGTATAGGTAGTTTTGTACATTGAGGTATCAGTAGTTTAA
63 ATAGTTGTATAA-TAGGTATAGGTAGTTCTGTACATTGAGGTATCAGAAGTTTAA
*
194812 ATACTTGTATCGATAGAAGT
1 ATACTTGTATCGGTAGAAGT
194832 TGTAAGGTAA
Statistics
Matches: 121, Mismatches: 8, Indels: 14
0.85 0.06 0.10
Matches are distributed among these distances:
115 3 0.02
116 112 0.93
117 6 0.05
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.37
Consensus pattern (116 bp):
ATACTTGTATCGGTAGAAGTACAGGGTAAGAGAGAGGTTGATCTCTGACTTGAATTGTTTCGATA
GTTGTATAATAGGTATAGGTAGTTCTGTACATTGAGGTATCAGAAGTTTAA
Found at i:195868 original size:101 final size:100
Alignment explanation
Indices: 195692--195893 Score: 386
Period size: 101 Copynumber: 2.0 Consensus size: 100
195682 TCCAATGTCA
*
195692 TCTCCGCTTTTGTAGTCGAGAAAATTGTAAAGAACAGGTGTGAAGCGTGTCTCACCTTCATCACT
1 TCTCCGCTTTTGTAGTCGAGAAAATTGTAAAGAACAGGTGTGAAGCGTGTCTCACCGTCATCACT
195757 GATTCTACACCTACTAAGTTAACTGAGAATGATTT
66 GATTCTACACCTACTAAGTTAACTGAGAATGATTT
195792 TNCTCCGCTTTTGTAGTCGAGAAAATTGTAAAGAACAGGTGTGAAGCGTGTCTCACCGTCATCAC
1 T-CTCCGCTTTTGTAGTCGAGAAAATTGTAAAGAACAGGTGTGAAGCGTGTCTCACCGTCATCAC
195857 TGATTCTACACCTACTAAGTTAACTGAGAATGATTT
65 TGATTCTACACCTACTAAGTTAACTGAGAATGATTT
195893 T
1 T
195894 TAGACAATAA
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
100 1 0.01
101 99 0.99
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (100 bp):
TCTCCGCTTTTGTAGTCGAGAAAATTGTAAAGAACAGGTGTGAAGCGTGTCTCACCGTCATCACT
GATTCTACACCTACTAAGTTAACTGAGAATGATTT
Found at i:198815 original size:18 final size:18
Alignment explanation
Indices: 198781--198815 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
198771 TGAATATATC
* *
198781 TTTTTATTTTTATTTTTA
1 TTTTTATTTTCACTTTTA
198799 TTTTTATTTTCACTTTT
1 TTTTTATTTTCACTTTT
198816 TCTTTCATAA
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:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTATTTTCACTTTTA
Found at i:198820 original size:6 final size:6
Alignment explanation
Indices: 198781--198808 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
198771 TGAATATATC
198781 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
198809 CACTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:200758 original size:22 final size:22
Alignment explanation
Indices: 200668--200760 Score: 123
Period size: 22 Copynumber: 4.2 Consensus size: 22
200658 CTCTCCATTA
* *
200668 TTTAGCATGTGTTGTGCTCTCCA
1 TTTAGCACGT-TTGTGCTCTCCG
*
200691 TTTAGCACGTTTGTGTTCTCCG
1 TTTAGCACGTTTGTGCTCTCCG
200713 TTTAGCACGTTTGTGCTCTCCG
1 TTTAGCACGTTTGTGCTCTCCG
* * *
200735 TTTAGCACCTTGGTGCTCTTCG
1 TTTAGCACGTTTGTGCTCTCCG
200757 TTTA
1 TTTA
200761 TCGATACAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
22 54 0.86
23 9 0.14
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.44
Consensus pattern (22 bp):
TTTAGCACGTTTGTGCTCTCCG
Found at i:208949 original size:21 final size:21
Alignment explanation
Indices: 208900--208955 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
208890 TAGCACAAAT
* * *
208900 TTCTACCAATAAAAGTGACAG
1 TTCTACCGATACAAGTGACAC
*
208921 TTCTACCGATACAAGTGACTC
1 TTCTACCGATACAAGTGACAC
208942 TTCTACCGATACAA
1 TTCTACCGATACAA
208956 AAAACTCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (21 bp):
TTCTACCGATACAAGTGACAC
Found at i:208962 original size:21 final size:21
Alignment explanation
Indices: 208921--208963 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
208911 AAAGTGACAG
***
208921 TTCTACCGATACAAGTGACTC
1 TTCTACCGATACAAAAAACTC
208942 TTCTACCGATACAAAAAACTC
1 TTCTACCGATACAAAAAACTC
208963 T
1 T
208964 AGAGAGCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAAAAACTC
Found at i:211620 original size:21 final size:21
Alignment explanation
Indices: 211579--211621 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
211569 CAAGTGATAG
*
211579 TTCTACCGATACAAATGACTC
1 TTCTACCGATACAAATAACTC
*
211600 TTCTACTGATACTAAA-AACTC
1 TTCTACCGATAC-AAATAACTC
211621 T
1 T
211622 AGAGAGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAATAACTC
Found at i:227314 original size:22 final size:22
Alignment explanation
Indices: 227286--227350 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
227276 AAAAGAACAG
* *
227286 AGAGCACCAAGGTGCTAAATGA
1 AGAGCACAAACGTGCTAAATGA
* * *
227308 AGAGCACAAACATGCTAAACGG
1 AGAGCACAAACGTGCTAAATGA
* *
227330 AGAGCACTATATGTGCTAAAT
1 AGAGCAC-AAACGTGCTAAAT
227351 AACATAGAGC
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 24 0.73
23 9 0.27
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (22 bp):
AGAGCACAAACGTGCTAAATGA
Found at i:236505 original size:13 final size:13
Alignment explanation
Indices: 236487--236513 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
236477 TATCCTAAAC
236487 ATATAAAATACAT
1 ATATAAAATACAT
236500 ATATAAAATACAT
1 ATATAAAATACAT
236513 A
1 A
236514 AAATAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATAAAATACAT
Found at i:238437 original size:56 final size:56
Alignment explanation
Indices: 238292--238439 Score: 178
Period size: 56 Copynumber: 2.6 Consensus size: 56
238282 TTCAGACATT
* * * *
238292 TCATA-TATTGCCATG-GTTCTTAACCACATGGTCCTACATACATGTAGTCATTCATA
1 TCATATTA-TGCCATGAG-TCTTAACCTCATGGTCTTACATACATGTAGTCAGTAATA
* *
238348 TCATATTCTGCCAT-AGGTCTTAACCTCATGGTCTTACATACAT-TCATTCAGTAATA
1 TCATATTATGCCATGA-GTCTTAACCTCATGGTCTTACATACATGT-AGTCAGTAATA
238404 TCATATTATGCCATGAGTCTTAACCTCATGGTCTTA
1 TCATATTATGCCATGAGTCTTAACCTCATGGTCTTA
238440 TGCAGAGTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
55 1 0.01
56 76 0.95
57 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (56 bp):
TCATATTATGCCATGAGTCTTAACCTCATGGTCTTACATACATGTAGTCAGTAATA
Found at i:240514 original size:80 final size:80
Alignment explanation
Indices: 240430--240618 Score: 279
Period size: 80 Copynumber: 2.4 Consensus size: 80
240420 ACATTCGGTT
* * *
240430 CCTAGTGGATAAACCGCGATAAGTAAGCCAAACTCTAGTTGGATTAACCAACAAATTTCGTCAAT
1 CCTAGCGGATAAACCACGATAAATAAGCCAAACTCTAGTTGGATTAACCAACAAATTTCGTCAAT
240495 TCATGGCACCCAGTG
66 TCATGGCACCCAGTG
* * * *
240510 CCTAGCGGATAAACCACGATAAATGAGCCTAGCTCTAGTTGGATTAACCAACAAATTTTGTCAAT
1 CCTAGCGGATAAACCACGATAAATAAGCCAAACTCTAGTTGGATTAACCAACAAATTTCGTCAAT
*
240575 TCATGGCACCTAGTG
66 TCATGGCACCCAGTG
* * *
240590 CCGAACGGATAAACCACGATAAATGAGCC
1 CCTAGCGGATAAACCACGATAAATAAGCC
240619 CATTGGATTA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 99 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (80 bp):
CCTAGCGGATAAACCACGATAAATAAGCCAAACTCTAGTTGGATTAACCAACAAATTTCGTCAAT
TCATGGCACCCAGTG
Found at i:244174 original size:18 final size:18
Alignment explanation
Indices: 244151--244188 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
244141 CTCGATAGGG
244151 TCTTTCTCTTTATTC-TCT
1 TCTTTCTCTTT-TTCTTCT
244169 TCTTTCTCTTTTTCTTCT
1 TCTTTCTCTTTTTCTTCT
244187 TC
1 TC
244189 CTTTTTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (18 bp):
TCTTTCTCTTTTTCTTCT
Found at i:244184 original size:15 final size:15
Alignment explanation
Indices: 244151--244196 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 15
244141 CTCGATAGGG
244151 TCTTTCTCTTTATTCTCT
1 TCTTTCTC-TT-TT-TCT
244169 TCTTTCTCTTTTTCT
1 TCTTTCTCTTTTTCT
244184 TC-TTC-CTTTTTCT
1 TCTTTCTCTTTTTCT
244197 ACAGCAGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
15 5 0.18
16 2 0.07
17 2 0.07
18 8 0.29
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (15 bp):
TCTTTCTCTTTTTCT
Found at i:253322 original size:56 final size:56
Alignment explanation
Indices: 253242--253445 Score: 311
Period size: 56 Copynumber: 3.6 Consensus size: 56
253232 TTTAGACATT
*
253242 TCATA-TATTGCCATGGGTCTTAACCACATGGTCTTACATACATGCATTCATTCATA
1 TCATATTA-TGCCATGGGTCTTAACCACATGGTCTTACATACATACATTCATTCATA
253298 TCATATTATGCCATGGGTCTTAACCACATGGTCTTACATACATACATTCATTCATA
1 TCATATTATGCCATGGGTCTTAACCACATGGTCTTACATACATACATTCATTCATA
* * * *
253354 TCATATTATGCCATGGGTCTTAACCTCATGGTCTTACATACATTCATTCAGTAATA
1 TCATATTATGCCATGGGTCTTAACCACATGGTCTTACATACATACATTCATTCATA
* ** *
253410 TCATATTATGCGATAAGTCTTAACCTCATGGTCTTA
1 TCATATTATGCCATGGGTCTTAACCACATGGTCTTA
253446 TACAGAGTTT
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
56 137 0.99
57 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (56 bp):
TCATATTATGCCATGGGTCTTAACCACATGGTCTTACATACATACATTCATTCATA
Found at i:255612 original size:19 final size:19
Alignment explanation
Indices: 255588--255628 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
255578 CTACTAAGGA
*
255588 AATAATATCTCTTAATTAG
1 AATAATATCTCATAATTAG
255607 AATAATATCTCATAATTAG
1 AATAATATCTCATAATTAG
255626 AAT
1 AAT
255629 CTCTAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (19 bp):
AATAATATCTCATAATTAG
Found at i:257990 original size:19 final size:19
Alignment explanation
Indices: 257966--258002 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
257956 TACTAAGTAA
*
257966 ATAATATCTCTTAATTAGG
1 ATAATATCTCCTAATTAGG
257985 ATAATATCTCCTAATTAG
1 ATAATATCTCCTAATTAG
258003 AATCTCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (19 bp):
ATAATATCTCCTAATTAGG
Found at i:262813 original size:3 final size:3
Alignment explanation
Indices: 262807--262836 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
262797 TTGTTCAAAT
262807 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
262837 CAATTTACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:263628 original size:29 final size:29
Alignment explanation
Indices: 263564--263641 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
263554 AAATAAAAAC
*
263564 TATA-ATGAACTTTGATCTAATTTGCAATT
1 TATATATGAACTTTGAT-TAATGTGCAATT
*
263593 TCATATATGAACTTTGATT-GTGTGCAATT
1 T-ATATATGAACTTTGATTAATGTGCAATT
*
263622 ATATATATGAAATTTTGATT
1 -TATATATG-AACTTTGATT
263642 TGATCTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 16 0.38
30 14 0.33
31 12 0.29
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (29 bp):
TATATATGAACTTTGATTAATGTGCAATT
Done.