Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011263.1 Kokia drynarioides strain JFW-HI SEQ_126242, 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: 232945
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 283 characters in sequence are not A, C, G, or T
Found at i:19915 original size:31 final size:31
Alignment explanation
Indices: 19880--19948 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
19870 TTTTTTTATC
*
19880 TATTTTAGTATATGAACTTGACAAT-TAGATT
1 TATTTTAGTATATGAACTTGAAAATATA-ATT
* * *
19911 TATTTTGGTATTTGAATTTGAAAATATAATT
1 TATTTTAGTATATGAACTTGAAAATATAATT
*
19942 TTTTTTA
1 TATTTTA
19949 TTACGTGACT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (31 bp):
TATTTTAGTATATGAACTTGAAAATATAATT
Found at i:21257 original size:20 final size:18
Alignment explanation
Indices: 21229--21271 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
21219 AATTTTTAGT
*
21229 TTTTAATAAATTATATATTA
1 TTTTAATAAA-AATAT-TTA
*
21249 TTTTGATAAAAATATTTA
1 TTTTAATAAAAATATTTA
21267 TTTTA
1 TTTTA
21272 TATACATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTAATAAAAATATTTA
Found at i:28596 original size:2 final size:2
Alignment explanation
Indices: 28589--28614 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28579 ATGCAGACCT
28589 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
28615 TTATGATTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:35871 original size:34 final size:34
Alignment explanation
Indices: 35827--35970 Score: 225
Period size: 34 Copynumber: 4.2 Consensus size: 34
35817 CTAAGAAAAG
* *
35827 ACCAGTTAGTAACATATTGAGTATTAACTAAGAA
1 ACCAGATAGTAACATATTGAGCATTAACTAAGAA
35861 ACCAGATAGTAACATATTGAGCATTAACTAAGAA
1 ACCAGATAGTAACATATTGAGCATTAACTAAGAA
*
35895 ACCAGCTAGTAACATATTGAGCATTAACTAAGAA
1 ACCAGATAGTAACATATTGAGCATTAACTAAGAA
* * *
35929 ACCAGTTAGTAATATATTGAGCATTAACTAAGAG
1 ACCAGATAGTAACATATTGAGCATTAACTAAGAA
*
35963 ACAAGATA
1 ACCAGATA
35971 ATAGTTTTAA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 102 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (34 bp):
ACCAGATAGTAACATATTGAGCATTAACTAAGAA
Found at i:40744 original size:307 final size:308
Alignment explanation
Indices: 40189--40745 Score: 748
Period size: 307 Copynumber: 1.8 Consensus size: 308
40179 AGTTTTAGAA
* *
40189 AATTAACATGATAATATTTAAGCCATTGCAAAGTATGAGAGTAGAGATCTAGGAAGAGTTTGTTG
1 AATTAACATGATAATATTTAAGCAATTGCAAAGTATGAGAGTAGAGATCTAGGAAGAGTTAGTTG
* *
40254 GCAGATGTCATCTTTTACATGGGGACAAGAGAGGTGTATACAAGTGTTCTTCAAGTGGATCTCAT
66 GCAGATATCATCTTTTACATGGGGACAAGAGAGGTGTATACAAGTGTTCTTCAAGTGAATCTCAT
* * **
40319 GCTGCCAACTATCTTTTTGGACAATAAACTTAGTGAATACTGGTGGAGTTTTCAACACGTGCCAC
131 GCTGCCAACTATCTTTTTAGACAATAAACATAACGAATACTGGTGGAGTTTTCAACACGTGCCAC
*
40384 TAATAGCTATAGGTCGTCATTGCTACTATTAAGAGGAGCGAACCTCATTAGTTTTATGTCCACTG
196 TAATAGCTATAGGTCGTCATTGCTAATATTAAGAGGAGCGAACCTCATTAGTTTTATGTCCACTG
40449 TGTCACCTATCTGAATACAGACTGAGATCTTAATATGATATTGCTTAG
261 TGTCACCTATCTGAATACAGACTGAGATCTTAATATGATATTGCTTAG
* * * *
40497 AATTAACATGGTGATGTTTAAGCAATTGTAAAGTATGAGAGT-GAAGATCTAGGAAGAGTTAGTT
1 AATTAACATGATAATATTTAAGCAATTGCAAAGTATGAGAGTAG-AGATCTAGGAAGAGTTAGTT
* * * *
40561 GGGCAGATATCTTCTTTTACATGGGGATAAGAGAGGTGTGTA-TAG-GTTCTTCAAGTGAATCTC
65 -GGCAGATATCATCTTTTACATGGGGACAAGAGAGGTGTATACAAGTGTTCTTCAAGTGAATCTC
*** * * *** *
40624 ATGCTGCTGTCTGTCTTTTTAGACAATAAACATAACGAGT-CATGGTGGAG-TTTGGGCGCGTGC
129 ATGCTGCCAACTATCTTTTTAGACAATAAACATAACGAATAC-TGGTGGAGTTTTCAACACGTGC
* * * * *
40687 CTCTAATAGCTATA-GTCCGTTATTGCTAATATTAAGGGGGAGCGAATCTTATTAGTTTT
193 CACTAATAGCTATAGGT-CGTCATTGCTAATATTAA-GAGGAGCGAACCTCATTAGTTTT
40746 TTTGACTACG
Statistics
Matches: 213, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
305 2 0.01
306 39 0.18
307 77 0.36
308 58 0.27
309 37 0.17
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (308 bp):
AATTAACATGATAATATTTAAGCAATTGCAAAGTATGAGAGTAGAGATCTAGGAAGAGTTAGTTG
GCAGATATCATCTTTTACATGGGGACAAGAGAGGTGTATACAAGTGTTCTTCAAGTGAATCTCAT
GCTGCCAACTATCTTTTTAGACAATAAACATAACGAATACTGGTGGAGTTTTCAACACGTGCCAC
TAATAGCTATAGGTCGTCATTGCTAATATTAAGAGGAGCGAACCTCATTAGTTTTATGTCCACTG
TGTCACCTATCTGAATACAGACTGAGATCTTAATATGATATTGCTTAG
Found at i:54905 original size:9 final size:9
Alignment explanation
Indices: 54886--54924 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
54876 TTAATGAACG
54886 TTTTA-TAT
1 TTTTATTAT
54894 TTTTATTAT
1 TTTTATTAT
*
54903 TTTTATAAT
1 TTTTATTAT
54912 TTTTAATTAT
1 TTTT-ATTAT
54922 TTT
1 TTT
54925 ATTGATGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 5 0.19
9 15 0.56
10 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATTAT
Found at i:54926 original size:18 final size:17
Alignment explanation
Indices: 54886--54924 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
54876 TTAATGAACG
54886 TTTTATATTTTTATTAT
1 TTTTATATTTTTATTAT
54903 TTTTATAATTTTTAATTAT
1 TTTTAT-ATTTTT-ATTAT
54922 TTT
1 TTT
54925 ATTGATGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 6 0.30
19 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATATTTTTATTAT
Found at i:69947 original size:4 final size:4
Alignment explanation
Indices: 69938--69962 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
69928 GGAAAGTGGG
69938 AGCC AGCC AGCC AGCC AGCC AGCC A
1 AGCC AGCC AGCC AGCC AGCC AGCC A
69963 ATTCACTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.48, G:0.24, T:0.00
Consensus pattern (4 bp):
AGCC
Found at i:74988 original size:23 final size:23
Alignment explanation
Indices: 74936--74989 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
74926 ATCATCCTAG
*
74936 AAAAAAAAAATCCAACAAAAAAT
1 AAAAAAAAAATCAAACAAAAAAT
* *
74959 TAAAAAAAAATCAAAC-TAAAAT
1 AAAAAAAAAATCAAACAAAAAAT
*
74981 AAAGAAAAA
1 AAAAAAAAA
74990 GATTTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.78, C:0.09, G:0.02, T:0.11
Consensus pattern (23 bp):
AAAAAAAAAATCAAACAAAAAAT
Found at i:77994 original size:42 final size:42
Alignment explanation
Indices: 77935--78018 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
77925 TTGCACTGCT
77935 TCATCGCTCTTACTGCTATGAATTCCTTGAGCAGCTGAAGGA
1 TCATCGCTCTTACTGCTATGAATTCCTTGAGCAGCTGAAGGA
77977 TCATCGCTCTTACTGCTATGAATTCCTTGAGCAGCTGAAGGA
1 TCATCGCTCTTACTGCTATGAATTCCTTGAGCAGCTGAAGGA
78019 GTTAGAGGAT
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:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (42 bp):
TCATCGCTCTTACTGCTATGAATTCCTTGAGCAGCTGAAGGA
Found at i:86660 original size:21 final size:21
Alignment explanation
Indices: 86622--86663 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
86612 TGGATAAGTG
*
86622 ATTTAATTTATTATTTATTTT
1 ATTTAATTTATTAATTATTTT
86643 ATTTAATTT-TATAATTATTTT
1 ATTTAATTTAT-TAATTATTTT
86664 TACATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTAATTTATTAATTATTTT
Found at i:89445 original size:16 final size:17
Alignment explanation
Indices: 89421--89452 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
89411 TAAGTTCGCT
89421 AAATAATTTAAAAAATA
1 AAATAATTTAAAAAATA
89438 AAAT-ATTTAAAAAAT
1 AAATAATTTAAAAAAT
89453 TTATCATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAATTTAAAAAATA
Found at i:89554 original size:9 final size:9
Alignment explanation
Indices: 89540--89592 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
89530 AAATATATTT
89540 TATTTTTTA
1 TATTTTTTA
89549 TA-TTTTTA
1 TATTTTTTA
*
89557 TATTTTTTC
1 TATTTTTTA
*
89566 TATTGTTTAA
1 TATT-TTTTA
89576 TATTTTTT-
1 TATTTTTTA
89584 TAATTTTTT
1 T-ATTTTTT
89593 TTTGCATTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 9 0.24
9 21 0.57
10 7 0.19
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (9 bp):
TATTTTTTA
Found at i:89556 original size:8 final size:8
Alignment explanation
Indices: 89532--89582 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
89522 GCTCTAGTAA
89532 ATATATTTT
1 ATAT-TTTT
89541 AT-TTTTT
1 ATATTTTT
89548 ATATTTTT
1 ATATTTTT
89556 ATATTTTTT
1 ATA-TTTTT
*
89565 CTATTGTTT
1 ATATT-TTT
89574 AATATTTTT
1 -ATATTTTT
89583 TTAATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 6 0.17
8 11 0.31
9 15 0.42
10 4 0.11
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (8 bp):
ATATTTTT
Found at i:89562 original size:17 final size:19
Alignment explanation
Indices: 89540--89583 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
89530 AAATATATTT
89540 TATTTTTTATATT-TTT-A
1 TATTTTTTATATTGTTTAA
*
89557 TATTTTTTCTATTGTTTAA
1 TATTTTTTATATTGTTTAA
89576 TATTTTTT
1 TATTTTTT
89584 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.50
18 3 0.12
19 9 0.38
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (19 bp):
TATTTTTTATATTGTTTAA
Found at i:102988 original size:24 final size:24
Alignment explanation
Indices: 102961--103008 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
102951 TTAAAGATAA
*
102961 AAAAATTAAAAAAAATAAAAAATT
1 AAAAATCAAAAAAAATAAAAAATT
* *
102985 AAAAGTCAAAAGAAATAAAAAATT
1 AAAAATCAAAAAAAATAAAAAATT
103009 GAACACCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAAATCAAAAAAAATAAAAAATT
Found at i:103005 original size:41 final size:42
Alignment explanation
Indices: 102915--103008 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 42
102905 CATAAATAAT
* * * *
102915 AAAAAATAATTATAAAAATATGAAAAATTAAAGAAGTTAAAG
1 AAAAAAAAATTATAAAAAAATAAAAAATTAAAGAAGTAAAAG
*
102957 ATAAAAAAATTA-AAAAAAATAAAAAATT-AA-AAGTCAAAAG
1 AAAAAAAAATTATAAAAAAATAAAAAATTAAAGAAGT-AAAAG
102997 AAATAAAAAATT
1 AAA-AAAAAATT
103009 GAACACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
39 4 0.09
40 8 0.18
41 22 0.50
42 10 0.23
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (42 bp):
AAAAAAAAATTATAAAAAAATAAAAAATTAAAGAAGTAAAAG
Found at i:106638 original size:59 final size:59
Alignment explanation
Indices: 106573--106685 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
106563 TGTTACATAA
**
106573 AATATTATGAGAT-TTGTAATTGTTTGCT-TAATT-AGGCAATATTTTCTGTAATTATACAT
1 AATATTATGA-ATGTTGTAATAATTTG-TGTAATTGA-GCAATATTTTCTGTAATTATACAT
* *
106632 AATATTATGAATGTTGTAATAATTTGTGTAATTGAGTAATATTTTGTGTAATTA
1 AATATTATGAATGTTGTAATAATTTGTGTAATTGAGCAATATTTTCTGTAATTA
106686 GCCAATGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
58 3 0.06
59 43 0.91
60 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.48
Consensus pattern (59 bp):
AATATTATGAATGTTGTAATAATTTGTGTAATTGAGCAATATTTTCTGTAATTATACAT
Found at i:106670 original size:20 final size:20
Alignment explanation
Indices: 106647--106684 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
106637 TATGAATGTT
106647 GTAATAATTTGTGTAATTGA
1 GTAATAATTTGTGTAATTGA
*
106667 GTAATATTTTGTGTAATT
1 GTAATAATTTGTGTAATT
106685 AGCCAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
GTAATAATTTGTGTAATTGA
Found at i:106696 original size:20 final size:20
Alignment explanation
Indices: 106649--106705 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
106639 TGAATGTTGT
* *
106649 AATAATTTGTGTAATTGAGT
1 AATATTTTGTGTAATTGAGC
106669 AATATTTTGTGTAATT-AGCC
1 AATATTTTGTGTAATTGAG-C
* *
106689 AATGTTTTGTATAATTG
1 AATATTTTGTGTAATTG
106706 TGTCGCACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.47
Consensus pattern (20 bp):
AATATTTTGTGTAATTGAGC
Found at i:107410 original size:62 final size:62
Alignment explanation
Indices: 107313--107436 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
107303 GTTTTTTATG
107313 TTTTTATTCTGTTTCTTCCAAAATGCATGTTTTTTTGTGGGCGATTAGCTTAAGTTTGACCA
1 TTTTTATTCTGTTTCTTCCAAAATGCATGTTTTTTTGTGGGCGATTAGCTTAAGTTTGACCA
107375 TTTTTATTCTGTTTCTTCCAAAATGCATGTTTTTTTGTGGGCGATTAGCTTAAGTTTGACCA
1 TTTTTATTCTGTTTCTTCCAAAATGCATGTTTTTTTGTGGGCGATTAGCTTAAGTTTGACCA
107437 ATAAACCGGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (62 bp):
TTTTTATTCTGTTTCTTCCAAAATGCATGTTTTTTTGTGGGCGATTAGCTTAAGTTTGACCA
Found at i:108825 original size:19 final size:20
Alignment explanation
Indices: 108801--108851 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
108791 CATAATTCAT
108801 AATAATATTACACC-TTGAG
1 AATAATATTACACCATTGAG
108820 AATAAT-TTGACACCATTTGAG
1 AATAATATT-ACACCA-TTGAG
*
108841 AATGATATTAC
1 AATAATATTAC
108852 GAGATAGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
21 12 0.44
22 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (20 bp):
AATAATATTACACCATTGAG
Found at i:112165 original size:14 final size:14
Alignment explanation
Indices: 112146--112175 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
112136 CCATAAGTAG
112146 AATCAAATCATTAT
1 AATCAAATCATTAT
112160 AATCAAATCATTAT
1 AATCAAATCATTAT
112174 AA
1 AA
112176 CAACCGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (14 bp):
AATCAAATCATTAT
Found at i:117029 original size:2 final size:2
Alignment explanation
Indices: 117022--117068 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
117012 TGAAAGTACC
* * * *
117022 AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT TT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117063 AT AT AT
1 AT AT AT
117069 TCTTTGCCGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:118415 original size:6 final size:6
Alignment explanation
Indices: 118407--118452 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
118397 GCTTGCACTT
* *
118407 GTGTGT GTGTGG GTGTGG GTGTGG GTGTGG GTGTGG GTGTGT GTGT
1 GTGTGG GTGTGG GTGTGG GTGTGG GTGTGG GTGTGG GTGTGG GTGT
118453 CCATTTTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (6 bp):
GTGTGG
Found at i:118434 original size:18 final size:18
Alignment explanation
Indices: 118407--118452 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
118397 GCTTGCACTT
118407 GTGTGTGTGTGGGTGTGG
1 GTGTGTGTGTGGGTGTGG
*
118425 GTGTGGGTGTGGGTGTGG
1 GTGTGTGTGTGGGTGTGG
118443 GTGTGTGTGT
1 GTGTGTGTGT
118453 CCATTTTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (18 bp):
GTGTGTGTGTGGGTGTGG
Found at i:122363 original size:4 final size:4
Alignment explanation
Indices: 122354--122378 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
122344 AATTTATTAC
122354 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
122379 TTTCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:125275 original size:3 final size:3
Alignment explanation
Indices: 125267--125291 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
125257 CCAATTTTAC
125267 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
125292 TCTTTTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:127134 original size:5 final size:5
Alignment explanation
Indices: 127124--127158 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
127114 TAATTTGGAG
127124 GAATT GAATT GAATT GAATT GAATT GAATT GAATT
1 GAATT GAATT GAATT GAATT GAATT GAATT GAATT
127159 TTATTTTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GAATT
Found at i:128847 original size:26 final size:26
Alignment explanation
Indices: 128807--128857 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
128797 CCATTTTTTT
*
128807 TTTTTTTTTACATATTAAAA-ATTAAC
1 TTTTTTTTAACATA-TAAAAGATTAAC
*
128833 TTTTTTTTAATATATAAAAGATTAA
1 TTTTTTTTAACATATAAAAGATTAA
128858 AAATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTTTTTTAACATATAAAAGATTAAC
Found at i:128850 original size:25 final size:26
Alignment explanation
Indices: 128808--128857 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
128798 CATTTTTTTT
128808 TTTTTTTTACATATTAAAA-ATTAAC
1 TTTTTTTTACATATTAAAAGATTAAC
128833 TTTTTTTTA-ATATATAAAAGATTAA
1 TTTTTTTTACATAT-TAAAAGATTAA
128858 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.17
25 14 0.61
26 5 0.22
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTTTTTTACATATTAAAAGATTAAC
Found at i:128864 original size:26 final size:25
Alignment explanation
Indices: 128810--128864 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
128800 TTTTTTTTTT
***
128810 TTTTTTACATATTAAAAATTAACTT
1 TTTTTTACATATTAAAAATTAAAAA
128835 TTTTTTA-ATATATAAAAGATTAAAAA
1 TTTTTTACATAT-TAAAA-ATTAAAAA
128861 TTTT
1 TTTT
128865 AATCAAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 4 0.16
25 12 0.48
26 9 0.36
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTTTACATATTAAAAATTAAAAA
Found at i:132968 original size:2 final size:2
Alignment explanation
Indices: 132963--132998 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
132953 ACTGAAATAC
*
132963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132999 TGCTACACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:137696 original size:27 final size:26
Alignment explanation
Indices: 137655--137706 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
137645 ATGTACCCAA
* **
137655 TTTTTTTTTTTTTTTTTGAAATTTAG
1 TTTTTTTTTTATTTTTAAAAATTTAG
137681 TTTTTATTTTTATTTTTAAAAATTTA
1 TTTTT-TTTTTATTTTTAAAAATTTA
137707 ATCTCTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTTTTTTTATTTTTAAAAATTTAG
Found at i:148052 original size:36 final size:36
Alignment explanation
Indices: 148012--148083 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
148002 AAAGATGAAG
*
148012 ATGAAGAAGAGAGGTGTGTGAAAATAAGTTTAGGGT
1 ATGAAGAAGAGAGGCGTGTGAAAATAAGTTTAGGGT
148048 ATGAAGAAGAGAGGCGTGTGAAAATAAGTTTAGGGT
1 ATGAAGAAGAGAGGCGTGTGAAAATAAGTTTAGGGT
148084 TTTTTCAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.01, G:0.36, T:0.24
Consensus pattern (36 bp):
ATGAAGAAGAGAGGCGTGTGAAAATAAGTTTAGGGT
Found at i:158186 original size:22 final size:22
Alignment explanation
Indices: 158161--158234 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
158151 AGTGTTTATT
158161 GATTTTTAGTTCTACCTACTTG
1 GATTTTTAGTTCTACCTACTTG
* **
158183 GATTTAATTATGTTTTGTATTTA-TT-
1 GATTT--TTA-G--TTCTACCTACTTG
158208 GATTTTTAGTTCTACCTACTTG
1 GATTTTTAGTTCTACCTACTTG
158230 GATTT
1 GATTT
158235 AATTATGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 6 0.15
21 2 0.05
22 11 0.28
23 3 0.08
24 3 0.08
25 6 0.15
26 2 0.05
27 6 0.15
ACGTcount: A:0.20, C:0.11, G:0.14, T:0.55
Consensus pattern (22 bp):
GATTTTTAGTTCTACCTACTTG
Found at i:158210 original size:47 final size:47
Alignment explanation
Indices: 158155--158261 Score: 214
Period size: 47 Copynumber: 2.3 Consensus size: 47
158145 TTAAAGAGTG
158155 TTTATTGATTTTTAGTTCTACCTACTTGGATTTAATTATGTTTTGTA
1 TTTATTGATTTTTAGTTCTACCTACTTGGATTTAATTATGTTTTGTA
158202 TTTATTGATTTTTAGTTCTACCTACTTGGATTTAATTATGTTTTGTA
1 TTTATTGATTTTTAGTTCTACCTACTTGGATTTAATTATGTTTTGTA
158249 TTTATTGATTTTT
1 TTTATTGATTTTT
158262 TAAAAAATGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (47 bp):
TTTATTGATTTTTAGTTCTACCTACTTGGATTTAATTATGTTTTGTA
Found at i:167321 original size:2 final size:2
Alignment explanation
Indices: 167314--167356 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
167304 AAGTAAGTGC
*
167314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
167356 T
1 T
167357 CTTTTCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:169081 original size:20 final size:20
Alignment explanation
Indices: 169056--169093 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
169046 AGTTGAAACT
169056 CCATAACTGGAAAGCAAATA
1 CCATAACTGGAAAGCAAATA
*
169076 CCATAATTGGAAAGCAAA
1 CCATAACTGGAAAGCAAA
169094 GATCGGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (20 bp):
CCATAACTGGAAAGCAAATA
Found at i:171261 original size:13 final size:13
Alignment explanation
Indices: 171243--171267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171233 TCAGCTGCAA
171243 AATAATAATAAAT
1 AATAATAATAAAT
171256 AATAATAATAAA
1 AATAATAATAAA
171268 ACAGATGCAA
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):
AATAATAATAAAT
Found at i:175070 original size:19 final size:19
Alignment explanation
Indices: 175033--175070 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
175023 TTCAAAAAAA
*
175033 TTTAAATTATTTTTATTAT
1 TTTAAATTAATTTTATTAT
175052 TTTAAATATAATTTT-TTAT
1 TTTAAAT-TAATTTTATTAT
175071 ATAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTAAATTAATTTTATTAT
Found at i:177905 original size:30 final size:29
Alignment explanation
Indices: 177871--177927 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
177861 TAATTGAACT
*
177871 AAATCAAAATTTAATATATAAAATTATACA
1 AAATCAAAA-TCAATATATAAAATTATACA
* *
177901 AAATCAAAATCCATGTATAAAATTATA
1 AAATCAAAATCAATATATAAAATTATA
177928 AATCATACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.32
Consensus pattern (29 bp):
AAATCAAAATCAATATATAAAATTATACA
Found at i:191411 original size:11 final size:10
Alignment explanation
Indices: 191395--191435 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
191385 TTATTTTAGG
191395 TTTAAATTTA
1 TTTAAATTTA
191405 TTATAAATTTAA
1 TT-TAAATTT-A
191417 CTTTAAATTTA
1 -TTTAAATTTA
191428 TTTAAATT
1 TTTAAATT
191436 AATAATATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.36
11 8 0.29
12 8 0.29
13 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:191415 original size:17 final size:17
Alignment explanation
Indices: 191375--191421 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
191365 GAGCTCAACA
*
191375 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTAT
**
191392 AGGTTTAAATTTATTAT
1 AAATTTAAATTTATTAT
*
191409 AAATTTAACTTTA
1 AAATTTAAATTTA
191422 AATTTATTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTAT
Found at i:192070 original size:22 final size:23
Alignment explanation
Indices: 192040--192100 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
192030 TTTACTTTGC
* *
192040 AATATTTAATAGTAATAAAT-AT
1 AATAATTAATAATAATAAATAAT
192062 AATAATTAATAATAA-AAATAAT
1 AATAATTAATAATAATAAATAAT
* *
192084 AATAATAAATATTAATA
1 AATAATTAATAATAATA
192101 TTAATAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 4 0.12
22 28 0.85
23 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AATAATTAATAATAATAAATAAT
Found at i:192076 original size:19 final size:19
Alignment explanation
Indices: 192052--192107 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
192042 TATTTAATAG
192052 TAATAAATATAATAATTAA
1 TAATAAATATAATAATTAA
192071 TAAT-AA-A-AATAA-TAA
1 TAATAAATATAATAATTAA
192086 TAATAAATATTAAT-ATTAA
1 TAATAAATA-TAATAATTAA
192105 TAA
1 TAA
192108 CTTAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 7 0.22
16 7 0.22
17 2 0.06
18 3 0.09
19 13 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATAAATATAATAATTAA
Found at i:193414 original size:30 final size:29
Alignment explanation
Indices: 193324--193488 Score: 203
Period size: 30 Copynumber: 5.6 Consensus size: 29
193314 ACCTCTGAAC
* *
193324 TTCCAAAAATTCCATTTTGACCCTGAACT
1 TTCCAAAAATTCCATTTTAACCCTAAACT
193353 TTCC-AAAATTACCATTTT-ACCCTCAAA-T
1 TTCCAAAAATT-CCATTTTAACCCT-AAACT
193381 TTCCAAAAATTCCATGTTTAACCCTAAACT
1 TTCCAAAAATTCCAT-TTTAACCCTAAACT
*
193411 TTCCAAAATTTCCATTTTAAACCCTAAACT
1 TTCCAAAAATTCCATTTT-AACCCTAAACT
*
193441 TTCCAAAAATTCTATTTTTAACCCTAAACT
1 TTCCAAAAATTCCA-TTTTAACCCTAAACT
*
193471 TTTCAAAAATAT-CATTTT
1 TTCCAAAAAT-TCCATTTT
193489 TGACCCATTT
Statistics
Matches: 121, Mismatches: 6, Indels: 18
0.83 0.04 0.12
Matches are distributed among these distances:
28 20 0.17
29 32 0.26
30 64 0.53
31 5 0.04
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTAACCCTAAACT
Found at i:193534 original size:30 final size:29
Alignment explanation
Indices: 193499--193608 Score: 75
Period size: 30 Copynumber: 3.8 Consensus size: 29
193489 TGACCCATTT
193499 TCCAAAAATTACCGTTTTGCCCCCGAAGTG
1 TCCAAAAATTACCGTTTTGCCCCCG-AGTG
* * **
193529 TCC--AAATTACTGTTTTACCCCCGCA-CA
1 TCCAAAAATTACCGTTTTGCCCCCG-AGTG
* * *
193556 TACAAAAATTACCATTTT-CATCCTCGAGTG
1 TCCAAAAATTACCGTTTTGC--CCCCGAGTG
*
193586 TCCAAAAATTATCGTTTTAGCCC
1 TCCAAAAATTACCGTTTT-GCCC
193609 TGAACCTCCA
Statistics
Matches: 59, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
27 2 0.03
28 20 0.34
29 12 0.20
30 24 0.41
32 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (29 bp):
TCCAAAAATTACCGTTTTGCCCCCGAGTG
Found at i:202175 original size:96 final size:96
Alignment explanation
Indices: 201996--202178 Score: 212
Period size: 96 Copynumber: 1.9 Consensus size: 96
201986 ATGAAGAGGA
* * ** *
201996 TATTTGATTATCTTGATTTGTAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAAAATC
1 TATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAAAATC
* *
202061 GAGGATAAGGAAACATTGCCTCGATTAAGGG
66 GAGAATAAAGAAACATTGCCTCGATTAAGGG
*
202092 TATTCGATTAT-TTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTCGAAA
1 TATTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC-AAA
* *
202155 CTCGA-AATAAA-AGAATATTGCCTC
63 ATCGAGAATAAAGA-AACATTGCCTC
202179 AATTTTTAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
95 4 0.05
96 62 0.85
97 7 0.10
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (96 bp):
TATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAAAATC
GAGAATAAAGAAACATTGCCTCGATTAAGGG
Found at i:202621 original size:59 final size:58
Alignment explanation
Indices: 202558--202827 Score: 234
Period size: 59 Copynumber: 4.6 Consensus size: 58
202548 ATCCGGGGGT
* * *
202558 AAAATGGTAGTTTTTGAAAGTTTCAGTGTCAAAAAT-GGAATTTTGGAAGTTCAGGGCTA
1 AAAATGG-AATTTTTGGAAGTTTCAGGGT-AAAAATGGGAATTTTGGAAGTTCAGGGCTA
* * * * * *
202617 AAAATGAAACTTTTGGACGTTTC-GAGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCAG-GGT-AAAAATGGGAATTTTGGAAGTTCAGGGCTA
** *
202676 AAAATGGAATTTTTGGAAGTTTGGGGGT-AAAAT-GGAATTTTTGGAAGTTTCGAGGTC-A
1 AAAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGGAA-TTTTGGAAG-TTC-AGGGCTA
* *
202734 AAAATGGGATTTTTGGAAG-TTCAGGGGTAAAAATGGGATTTTTGGAAGTTTC-GGAG-TCA
1 AAAATGGAATTTTTGGAAGTTTCA-GGGTAAAAATGGGAATTTTGGAAG-TTCAGG-GCT-A
*
202793 AAAATGGGATTTTTGGAAG-TTCAAGGGTAAAAATG
1 AAAATGGAATTTTTGGAAGTTTC-AGGGTAAAAATG
202828 AAATTTTTGG
Statistics
Matches: 176, Mismatches: 22, Indels: 26
0.79 0.10 0.12
Matches are distributed among these distances:
56 3 0.02
57 19 0.11
58 46 0.26
59 103 0.59
60 5 0.03
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGGAATTTTGGAAGTTCAGGGCTA
Found at i:202689 original size:146 final size:147
Alignment explanation
Indices: 202530--202842 Score: 438
Period size: 146 Copynumber: 2.1 Consensus size: 147
202520 TTCGAGGTCG
* *
202530 AAAATGGAGTTTTTGGACA-TCCGGGGGTAAAATGGTAGTTTTTGAAAGTTTC-AGTGTCAAAAA
1 AAAATGGAATTTTTGGACAGTCCGGGGGTAAAATGG-AATTTTTGAAAGTTTCGAG-GTCAAAAA
*
202593 T-GGAATTTTGGAAGTTCAGGGCTAAAAATGAAACTTTTGGACGTTTC-GAGGTCAAAAATGGGA
64 TGGGAATTTTGGAAGTTCAGGGCTAAAAATGAAACTTTTGGAAGTTTCGGA-GTCAAAAATGGGA
* *
202656 TTTTTGGAAGTTTAGGGGTA
128 TTTTTGGAAGTTCAAGGGTA
** *
202676 AAAATGGAATTTTTGGA-AGTTTGGGGGTAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATG
1 AAAATGGAATTTTTGGACAGTCCGGGGGTAAAATGGAATTTTTGAAAGTTTCGAGGTCAAAAATG
* * ** *
202740 GGATTTTTGGAAGTTCAGGGGTAAAAATGGGATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTT
66 GGAATTTTGGAAGTTCAGGGCTAAAAATGAAACTTTTGGAAGTTTCGGAGTCAAAAATGGGATTT
202805 TTGGAAGTTCAAGGGTA
131 TTGGAAGTTCAAGGGTA
*
202822 AAAATGAAATTTTTGGACAGT
1 AAAATGGAATTTTTGGACAGT
202843 TTAGGGACCC
Statistics
Matches: 148, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
145 24 0.16
146 119 0.80
147 5 0.03
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (147 bp):
AAAATGGAATTTTTGGACAGTCCGGGGGTAAAATGGAATTTTTGAAAGTTTCGAGGTCAAAAATG
GGAATTTTGGAAGTTCAGGGCTAAAAATGAAACTTTTGGAAGTTTCGGAGTCAAAAATGGGATTT
TTGGAAGTTCAAGGGTA
Found at i:202784 original size:87 final size:88
Alignment explanation
Indices: 202588--202848 Score: 332
Period size: 87 Copynumber: 3.0 Consensus size: 88
202578 TTTCAGTGTC
* * * * * *
202588 AAAAAT-GGAATTTTGGAAGTTCAGGGCTAAAAATGAAACTTTTGGACGTTTCGAGGTCAAAAAT
1 AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAAT
202652 GGGATTTTTGGAAGTTTAGGGGT
66 GGGATTTTTGGAAGTTTAGGGGT
* *
202675 AAAAATGGAATTTTTGGAAGTTTGGGGGT-AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAAT
1 AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAAT
*
202739 GGGATTTTTGGAAGTTCAGGGGT
66 GGGATTTTTGGAAGTTTAGGGGT
* * * *
202762 AAAAATGGGATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAG-TTCAAGGGT-AAAA
1 AAAAATGGGATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAA
**
202825 ATGAAATTTTTGGACAGTTTAGGG
64 ATGGGATTTTTGGA-AGTTTAGGG
202849 ACCCTCAAGG
Statistics
Matches: 152, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
87 86 0.57
88 37 0.24
89 29 0.19
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (88 bp):
AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAAT
GGGATTTTTGGAAGTTTAGGGGT
Found at i:202834 original size:59 final size:59
Alignment explanation
Indices: 202588--202844 Score: 278
Period size: 59 Copynumber: 4.4 Consensus size: 59
202578 TTTCAGTGTC
** * * *
202588 AAAAATGGAA-TTTTGGAAG-TTCAGG-G-CTAAAAATGAAACTTTTGGACGTTTC-GAGGT
1 AAAAATGGAATTTTTGGAAGTTTC-GGAGTC-AAAAATGGGATTTTTGGAAG-TTCAGGGGT
* * * * **
202645 CAAAAATGGGATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTGGAAGTTTGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCAGGGGT
202704 -AAAATGGAATTTTTGGAAGTTTC-GAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGA-GTCAAAAATGGGATTTTTGGAAGTTCAGGGGT
* *
202762 AAAAATGGGATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCAAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCAGGGGT
*
202821 AAAAATGAAATTTTTGGACAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
202845 AGGGACCCTC
Statistics
Matches: 172, Mismatches: 17, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
56 1 0.01
57 23 0.13
58 37 0.22
59 101 0.59
60 10 0.06
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCAGGGGT
Found at i:202848 original size:29 final size:28
Alignment explanation
Indices: 202554--202848 Score: 272
Period size: 29 Copynumber: 10.1 Consensus size: 28
202544 GGACATCCGG
* *
202554 GGGT-AAAATGGTAGTTTTTGAAAGTTTCA
1 GGGTAAAAATGG-AATTTTTGGAAGTTT-A
* *
202583 GTGTCAAAAATGGAA-TTTTGGAAGTTCA
1 GGGT-AAAAATGGAATTTTTGGAAGTTTA
* * * *
202611 GGGCTAAAAATGAAACTTTTGGACGTTTC
1 GGG-TAAAAATGGAATTTTTGGAAGTTTA
*
202640 GAGGTCAAAAATGGGATTTTTGGAAGTTTA
1 G-GGT-AAAAATGGAATTTTTGGAAGTTTA
*
202670 GGGGTAAAAATGGAATTTTTGGAAGTTTGG
1 -GGGTAAAAATGGAATTTTTGGAAGTTT-A
*
202700 GGGT-AAAATGGAATTTTTGGAAGTTTC
1 GGGTAAAAATGGAATTTTTGGAAGTTTA
* *
202727 GAGGTCAAAAATGGGATTTTTGGAAGTTCA
1 G-GGT-AAAAATGGAATTTTTGGAAGTTTA
* *
202757 GGGGTAAAAATGGGATTTTTGGAAGTTTC
1 -GGGTAAAAATGGAATTTTTGGAAGTTTA
* *
202786 GGAGTCAAAAATGGGATTTTTGGAAGTTCAA
1 GG-GT-AAAAATGGAATTTTTGGAAGTT-TA
*
202817 GGGTAAAAATGAAATTTTTGGACAGTTTA
1 GGGTAAAAATGGAATTTTTGGA-AGTTTA
202846 GGG
1 GGG
202849 ACCCTCAAGG
Statistics
Matches: 223, Mismatches: 27, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
27 1 0.00
28 39 0.17
29 96 0.43
30 76 0.34
31 11 0.05
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:203916 original size:16 final size:16
Alignment explanation
Indices: 203895--203948 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
203885 ACGTTATTTA
203895 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
203911 TTATTATT---ATTA-
1 TTATTATTAAAAATAT
*
203923 ATATTATTAAAAATAT
1 TTATTATTAAAAATAT
203939 TTATTATTAA
1 TTATTATTAA
203949 TAGTCATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
15 3 0.10
16 17 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:203930 original size:19 final size:19
Alignment explanation
Indices: 203874--203930 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
203864 ATTTCCCTTT
203874 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAA--TTATTTA
*
203895 TTATTATTAAAAATATTTA
1 TTATTATTAAAATTATTTA
*
203914 TTATTATTAATATTATT
1 TTATTATTAAAATTATT
203931 AAAAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 21 0.64
21 12 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTATTAAAATTATTTA
Found at i:203963 original size:28 final size:27
Alignment explanation
Indices: 203896--203950 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
203886 CGTTATTTAT
*
203896 TATTATTAAAAATATTTATTATTATTAA
1 TATTA-TAAAAATATTTATTATTAATAA
203924 TATTATTAAAAATATTTATTATTAATA
1 TATTA-TAAAAATATTTATTATTAATA
203951 GTCATTAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TATTATAAAAATATTTATTATTAATAA
Found at i:204590 original size:15 final size:15
Alignment explanation
Indices: 204568--204609 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
204558 GCCATTAGGT
204568 CATTTGTAATTGGGC
1 CATTTGTAATTGGGC
* *
204583 CGTTTGTATTTGGGC
1 CATTTGTAATTGGGC
204598 CATTTGTAATTG
1 CATTTGTAATTG
204610 AACTTTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.17, C:0.12, G:0.26, T:0.45
Consensus pattern (15 bp):
CATTTGTAATTGGGC
Found at i:204664 original size:17 final size:16
Alignment explanation
Indices: 204642--204726 Score: 91
Period size: 17 Copynumber: 5.1 Consensus size: 16
204632 TTGGACTTTC
*
204642 TAAATTTAATTTTATAA
1 TAAATTTAATTTCA-AA
204659 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTCAAA
204676 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTCAAA
*
204693 TAAACTTAAATTT-AAA
1 TAAA-TTTAATTTCAAA
* *
204709 TAAATTCAATTTCCAA
1 TAAATTTAATTTCAAA
204725 TA
1 TA
204727 GGTTCAGACA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
15 7 0.11
16 11 0.18
17 35 0.57
18 8 0.13
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAATTTCAAA
Found at i:204680 original size:34 final size:32
Alignment explanation
Indices: 204642--204726 Score: 107
Period size: 34 Copynumber: 2.6 Consensus size: 32
204632 TTGGACTTTC
* *
204642 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAATTTCA-AATAAACTTAAATTT-AAA
204676 TAAATTTAAATTTCAAATAAACTTAAATTTAAA
1 TAAATTT-AATTTCAAATAAACTTAAATTTAAA
* *
204709 TAAATTCAATTTCCAATA
1 TAAATTTAATTTCAAATA
204727 GGTTCAGACA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 10 0.22
33 9 0.20
34 21 0.46
35 6 0.13
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (32 bp):
TAAATTTAATTTCAAATAAACTTAAATTTAAA
Found at i:204726 original size:16 final size:17
Alignment explanation
Indices: 204642--204714 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
204632 TTGGACTTTC
*
204642 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
204659 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
204676 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
204693 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
204709 TAAATT
1 TAAATT
204715 CAATTTCCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.15
17 38 0.73
18 6 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:204934 original size:24 final size:26
Alignment explanation
Indices: 204898--204945 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
204888 AGAGAAATGT
204898 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
204922 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
204946 CCCATGTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:205046 original size:23 final size:23
Alignment explanation
Indices: 205027--205074 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
205017 TCAGCACTAT
205027 GTGTGCTTATTGTTTCGCACTTC
1 GTGTGCTTATTGTTTCGCACTTC
*
205050 GTGTGCTTATTGTTTCGCACCTC
1 GTGTGCTTATTGTTTCGCACTTC
205073 GT
1 GT
205075 ATGCCTACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.08, C:0.23, G:0.23, T:0.46
Consensus pattern (23 bp):
GTGTGCTTATTGTTTCGCACTTC
Found at i:205126 original size:22 final size:23
Alignment explanation
Indices: 205076--205152 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 23
205066 GCACCTCGTA
* **
205076 TGCCTACTGATTTGCGTTATGTG
1 TGCCTACTGAATTGCACTATGTG
**
205099 CACCTACT-AATTGCACTATGTG
1 TGCCTACTGAATTGCACTATGTG
* * *
205121 TGCCTACTGGATTGCATTGTGTG
1 TGCCTACTGAATTGCACTATGTG
*
205144 TGCTTACTG
1 TGCCTACTG
205153 TTTCCCCAGC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 17 0.40
23 25 0.60
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (23 bp):
TGCCTACTGAATTGCACTATGTG
Found at i:213858 original size:21 final size:20
Alignment explanation
Indices: 213835--213887 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
213825 AAGAAATTCT
*
213835 TTTTACTTATTTTGAAAAGA
1 TTTTATTTATTTTGAAAAGA
* *
213855 TTTTATTTTTTTTGCAAAGA
1 TTTTATTTATTTTGAAAAGA
213875 GTTTTATTTATTT
1 -TTTTATTTATTT
213888 ATTGTTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.60
Consensus pattern (20 bp):
TTTTATTTATTTTGAAAAGA
Found at i:219156 original size:33 final size:32
Alignment explanation
Indices: 219093--219166 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
219083 GTCAAAGTTG
* *
219093 TTTATTTTATTAATTTTGTTTTCATTAAATT-
1 TTTATTTTATTAATTTTATTTTCATAAAATTA
*
219124 TGTTATTTT-TCTAATTTTATTTTGACTAAAATTA
1 T-TTATTTTAT-TAATTTTATTTTCA-TAAAATTA
219158 TTTATTTTA
1 TTTATTTTA
219167 AGTAAATAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
31 2 0.06
32 19 0.54
33 13 0.37
34 1 0.03
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (32 bp):
TTTATTTTATTAATTTTATTTTCATAAAATTA
Found at i:221535 original size:16 final size:16
Alignment explanation
Indices: 221514--221569 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
221504 ATATATATAT
* *
221514 AAGAAATAAAAGAATG
1 AAGAAACAAAAGAAAG
* *
221530 AAGAAAGAAAA-AAAA
1 AAGAAACAAAAGAAAG
*
221545 AAGAAACAAAAGAAGG
1 AAGAAACAAAAGAAAG
221561 AAG-AACAAA
1 AAGAAACAAA
221570 GGCTCAAACG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 18 0.55
16 15 0.45
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (16 bp):
AAGAAACAAAAGAAAG
Found at i:225347 original size:3 final size:3
Alignment explanation
Indices: 225339--225366 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
225329 GCTCAATTTT
225339 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
225367 AAGTACCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Done.