Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010868.1 Kokia drynarioides strain JFW-HI SEQ_125836, 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: 624094
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5977 original size:24 final size:25
Alignment explanation
Indices: 5949--5999 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5939 AACAACTATT
5949 AATTTTATCTTA-ATTTAC-TCTGAC
1 AATTTTATCTTATATTTACGT-TGAC
*
5973 AATTTTATTTTATATTTACGTTGAC
1 AATTTTATCTTATATTTACGTTGAC
5998 AA
1 AA
6000 ATTAACTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 11 0.46
25 12 0.50
26 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (25 bp):
AATTTTATCTTATATTTACGTTGAC
Found at i:23305 original size:115 final size:115
Alignment explanation
Indices: 23103--23333 Score: 444
Period size: 115 Copynumber: 2.0 Consensus size: 115
23093 ATACTATAAG
23103 TAAGGAGAAATCAATGGTTCATTCTAATGCTATCATACCCCCAAACTTGAGTTTTTACTTGTCCT
1 TAAGGAGAAATCAATGGTTCATTCTAATGCTATCATACCCCCAAACTTGAGTTTTTACTTGTCCT
23168 CAAGTAAAACAAGAACTAACAAGGTTATAGAAAAAATTTTATCAAAGTAA
66 CAAGTAAAACAAGAACTAACAAGGTTATAGAAAAAATTTTATCAAAGTAA
*
23218 TAAGGAGAAATCAATGGTTCTTTCTAATGCTATCATACCCCCAAACTTGAGTTTTTACTTGTCCT
1 TAAGGAGAAATCAATGGTTCATTCTAATGCTATCATACCCCCAAACTTGAGTTTTTACTTGTCCT
*
23283 CAAGTAAAACAAGAACTAACAAGGTTATAGCAAAAATTTTATCAAAGTAA
66 CAAGTAAAACAAGAACTAACAAGGTTATAGAAAAAATTTTATCAAAGTAA
23333 T
1 T
23334 TATCATTCTA
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (115 bp):
TAAGGAGAAATCAATGGTTCATTCTAATGCTATCATACCCCCAAACTTGAGTTTTTACTTGTCCT
CAAGTAAAACAAGAACTAACAAGGTTATAGAAAAAATTTTATCAAAGTAA
Found at i:24103 original size:17 final size:17
Alignment explanation
Indices: 24075--24128 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
24065 ATATATATGG
24075 AAATGCAATGACAATGA
1 AAATGCAATGACAATGA
* *
24092 AGATGCAGTGACAA-GAA
1 AAATGCAATGACAATG-A
24109 AAATGCAATGACAAATGA
1 AAATGCAATGAC-AATGA
24127 AA
1 AA
24129 TGTGATGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 1 0.03
17 23 0.77
18 5 0.17
19 1 0.03
ACGTcount: A:0.54, C:0.11, G:0.20, T:0.15
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:35453 original size:20 final size:20
Alignment explanation
Indices: 35415--35453 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35405 AATAAAATTG
** *
35415 TAATAAAAAATGAATAAAAC
1 TAATAAAAAACCAAAAAAAC
35435 TAATAAAAAACCAAAAAAA
1 TAATAAAAAACCAAAAAAA
35454 AAACTAATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (20 bp):
TAATAAAAAACCAAAAAAAC
Found at i:39198 original size:17 final size:16
Alignment explanation
Indices: 39176--39212 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
39166 CTGTTCAATC
*
39176 TTTGGGTTTGATTGTT
1 TTTGGGTTTAATTGTT
39192 GTTTGGGTTTAATTGTT
1 -TTTGGGTTTAATTGTT
39209 TTTG
1 TTTG
39213 ACCACGGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.08, C:0.00, G:0.30, T:0.62
Consensus pattern (16 bp):
TTTGGGTTTAATTGTT
Found at i:42969 original size:37 final size:37
Alignment explanation
Indices: 42914--42989 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
42904 TTACTACTAA
*
42914 TGTCGCTGCATGAACACTTCTAGATTGCACCCAAAAC
1 TGTCGCTGCATGAACACTTCCAGATTGCACCCAAAAC
42951 TGTCGCTGCAT-AAGCACTTCCAGATTGCACCCAAAAC
1 TGTCGCTGCATGAA-CACTTCCAGATTGCACCCAAAAC
42988 TG
1 TG
42990 CCCCCGCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (37 bp):
TGTCGCTGCATGAACACTTCCAGATTGCACCCAAAAC
Found at i:43964 original size:16 final size:16
Alignment explanation
Indices: 43943--43973 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43933 TTGTGGATAC
43943 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
43959 CATTTTATCTTTATT
1 CATTTTACCTTTATT
43974 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:56926 original size:18 final size:18
Alignment explanation
Indices: 56905--56941 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
56895 GGAGCAAACA
56905 TAAATTTGATACCAATGT
1 TAAATTTGATACCAATGT
*
56923 TAAATTTGATGCCAATGT
1 TAAATTTGATACCAATGT
56941 T
1 T
56942 TTTTTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (18 bp):
TAAATTTGATACCAATGT
Found at i:61769 original size:18 final size:19
Alignment explanation
Indices: 61686--61772 Score: 56
Period size: 18 Copynumber: 4.6 Consensus size: 19
61676 AGAAAGTACT
* *
61686 ATACTGGCTCATTTGAGC-
1 ATACTAGCTCGTTTGAGCA
61704 ATACT-GTCTCGTTTAGAGCA
1 ATACTAG-CTCGTTT-GAGCA
** * *
61724 ATACTAGCTCG-TAAAACTG
1 ATACTAGCTCGTTTGAGC-A
*
61743 ATACCAGCTCGTTTGAGC-
1 ATACTAGCTCGTTTGAGCA
61761 ATACTAGCTCGT
1 ATACTAGCTCGT
61773 AAGAGCGATA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
17 1 0.02
18 24 0.45
19 15 0.28
20 12 0.23
21 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (19 bp):
ATACTAGCTCGTTTGAGCA
Found at i:61818 original size:19 final size:19
Alignment explanation
Indices: 61686--61818 Score: 83
Period size: 19 Copynumber: 7.1 Consensus size: 19
61676 AGAAAGTACT
* **
61686 ATACTGGCTCATTTGAGC-
1 ATACTGGCTCGTAAGAGCA
* *
61704 ATACTGTCTCGTTTAGAGCA
1 ATACTGGCTCG-TAAGAGCA
* * *
61724 ATACTAGCTCGTAA-AACTG
1 ATACTGGCTCGTAAGAGC-A
** **
61743 ATACCAGCTCGTTTGAGC-
1 ATACTGGCTCGTAAGAGCA
* *
61761 ATACTAGCTCGTAAGAGCG
1 ATACTGGCTCGTAAGAGCA
*
61780 ATACTGGCTCATAAGAGCA
1 ATACTGGCTCGTAAGAGCA
*
61799 ATATTGGCTCGTAAGAGCA
1 ATACTGGCTCGTAAGAGCA
61818 A
1 A
61819 ATTATTGATT
Statistics
Matches: 90, Mismatches: 20, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
18 26 0.29
19 53 0.59
20 11 0.12
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (19 bp):
ATACTGGCTCGTAAGAGCA
Found at i:64368 original size:5 final size:5
Alignment explanation
Indices: 64321--64364 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
64311 CTTCTTACTT
* * *
64321 ATTTC ATCTC ATCTC ATTTC ATTTC ATTTC ATTTC ATTTT ATTT
1 ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTT
64365 TATTGCCTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTC
Found at i:86478 original size:21 final size:21
Alignment explanation
Indices: 86452--86497 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
86442 TCAGTCACTT
86452 GAAAAACAAAAAAAAAAAAGA
1 GAAAAACAAAAAAAAAAAAGA
* * *
86473 GAAAAAGAAGAAAGAAAAAGA
1 GAAAAACAAAAAAAAAAAAGA
86494 -AAAA
1 GAAAA
86498 GAATAAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (21 bp):
GAAAAACAAAAAAAAAAAAGA
Found at i:86481 original size:6 final size:6
Alignment explanation
Indices: 86461--86500 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
86451 TGAAAAACAA
*
86461 AAAAAA AAAAGAG AAAAAG AAGAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAA-AG AAAAAG AA-AAAG AAAAAG AAAAAG AA
86501 TAAATTGCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:91011 original size:50 final size:49
Alignment explanation
Indices: 90944--91401 Score: 188
Period size: 50 Copynumber: 9.1 Consensus size: 49
90934 CGTTACATCG
* * **
90944 TTAGGGAGATAACATTTGCTTCTATAGCTTCAATCTGACCCACTATAACT
1 TTAGGG-GATAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACT
* * * * *
90994 TTAGGGGTATAAGATTTGGTTTTGTAGCTTCATAT-TG-CTCTATTGTAACT
1 TTAGGGG-ATAAGATTTGCTTCTGTAGCTTCA-ATCTGAC-CCACTGCAACT
* * * ** * * *
91044 TCAGAGAGATAAATATTTGCTT-TCGTAGCTTCAATCCAATCCACTACGACT
1 TTAG-GGGAT-AAGATTTGCTTCT-GTAGCTTCAATCTGACCCACTGCAACT
* * * * *
91095 TCA-GGGATATAGGACTTGATGT-TGAAGCTTC-ATCTTG-CTTCACTGCAACT
1 TTAGGGGATA-A-GATTTGCT-TCTGTAGCTTCAATC-TGAC-CCACTGCAACT
* *
91145 TCAGGGAGATAAAGATTTGCTTCTGTAGCTTCAATC-GACCCACTGTAACT
1 TTAGGG-GAT-AAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACT
* * * **
91195 TTA-GGGATATAGGATTCGATGTC-GTAGCTTC-ATCTTG-CTCCATTAAAACT
1 TTAGGGGATA-A-GATTTGCT-TCTGTAGCTTCAATC-TGAC-CCACTGCAACT
* * *
91245 TTAGGGAGATAAAATTTACTTCTGTAGCTTTAATCTGACCCACTGCAACT
1 TTAGGG-GATAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACT
* * * * **
91295 TTAAGGGTATAGGATTTGGTTTTGTAGCTTC-ATCTTG-CTTTACTGCAACT
1 TT-AGGGGATAAGATTTGCTTCTGTAGCTTCAATC-TGAC-CCACTGCAACT
* * * * * *
91345 TCAGAGAGATAAAGATTTGCTTTTGTACCTTCAATCTAATCCACTGCAACT
1 TTAG-GGGAT-AAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACT
*
91396 TCAGGG
1 TTAGGG
91402 ATATAGGATT
Statistics
Matches: 302, Mismatches: 69, Indels: 74
0.68 0.16 0.17
Matches are distributed among these distances:
47 1 0.00
48 8 0.03
49 35 0.12
50 150 0.50
51 93 0.31
52 14 0.05
53 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (49 bp):
TTAGGGGATAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACT
Found at i:91088 original size:101 final size:101
Alignment explanation
Indices: 90949--91417 Score: 500
Period size: 101 Copynumber: 4.7 Consensus size: 101
90939 CATCGTTAGG
* * ** * * *
90949 GAGAT-AACATTTGCTTCTATAGCTTCAATCTGACCCACTATAACTTTAGGGGTATAAGATTTGG
1 GAGATAAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACTTTAGGGATATAGGATTTGA
* * * *
91013 TTTTGTAGCTTCATATTGCTCTATTGTAACTTCAGA
66 TGTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGA
* ** * * * * *
91049 GAGATAAATATTTGCTT-TCGTAGCTTCAATCCAATCCACTACGACTTCAGGGATATAGGACTTG
1 GAGATAAAGATTTGCTTCT-GTAGCTTCAATCTGACCCACTGCAACTTTAGGGATATAGGATTTG
* *
91113 ATGTTGAAGCTTCATCTTGCT-TCACTGCAACTTCAGG
65 ATGTTGTAGCTTCATCTTGCTCT-ACTGCAACTTCAGA
* *
91150 GAGATAAAGATTTGCTTCTGTAGCTTCAATC-GACCCACTGTAACTTTAGGGATATAGGATTCGA
1 GAGATAAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACTTTAGGGATATAGGATTTGA
* * * ** * *
91214 TGTCGTAGCTTCATCTTGCTCCATTAAAACTTTAGG
66 TGTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGA
* *
91250 GAGATAAA-ATTTACTTCTGTAGCTTTAATCTGACCCACTGCAACTTTAAGGG-TATAGGATTTG
1 GAGATAAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACTTT-AGGGATATAGGATTTG
* * *
91313 GTTTTGTAGCTTCATCTTGCTTTACTGCAACTTCAGA
65 ATGTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGA
* * * * * *
91350 GAGATAAAGATTTGCTTTTGTACCTTCAATCTAATCCACTGCAACTTCAGGGATATAGGATTTTA
1 GAGATAAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACTTTAGGGATATAGGATTTGA
91415 TGT
66 TGT
91418 CGTACTGATC
Statistics
Matches: 302, Mismatches: 58, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
99 20 0.07
100 132 0.44
101 149 0.49
102 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (101 bp):
GAGATAAAGATTTGCTTCTGTAGCTTCAATCTGACCCACTGCAACTTTAGGGATATAGGATTTGA
TGTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGA
Found at i:92280 original size:19 final size:17
Alignment explanation
Indices: 92256--92310 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 17
92246 TGACCTCTCC
92256 TTTTTCTTTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
92273 TCTCTTTCGTTCTTT-TTTTT
1 T-T-TTTC-TT-TTTCTTTTT
*
92293 TTTTTC-GTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
92309 TT
1 TT
92311 ATGAAATACT
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
15 3 0.09
16 7 0.22
17 1 0.03
18 5 0.16
19 5 0.16
20 8 0.25
21 3 0.09
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTT
Found at i:92291 original size:18 final size:19
Alignment explanation
Indices: 92264--92310 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
92254 CCTTTTTCTT
92264 TTTC-TTTTTTCTCTTTCG
1 TTTCTTTTTTTCTCTTTCG
* *
92282 -TTCTTTTTTTTTTTTTCG
1 TTTCTTTTTTTCTCTTTCG
92300 TTTCTTTTTTT
1 TTTCTTTTTTT
92311 ATGAAATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 12 0.48
19 10 0.40
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (19 bp):
TTTCTTTTTTTCTCTTTCG
Found at i:92303 original size:23 final size:22
Alignment explanation
Indices: 92255--92310 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
92245 TTGACCTCTC
92255 CTTT-TTCTTTTTCTTTTTTCT
1 CTTTCTTCTTTTTCTTTTTTCT
*
92276 CTTTCGTTCTTTTT-TTTTTTTT
1 CTTTC-TTCTTTTTCTTTTTTCT
92298 CGTTTCTT-TTTTT
1 C-TTTCTTCTTTTT
92311 ATGAAATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 9 0.29
22 10 0.32
23 12 0.39
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (22 bp):
CTTTCTTCTTTTTCTTTTTTCT
Found at i:93630 original size:48 final size:48
Alignment explanation
Indices: 93545--93654 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 48
93535 GCAGCATAAA
* *
93545 ACTTCTTTTTTTGTGTGTTTTAAGATGCCCTTAGTGGGTTTTCATCTCG
1 ACTTCTTTTTTT-TGGGTTTCAAGATGCCCTTAGTGGGTTTTCATCTCG
* * *
93594 GC-TCATTTTTTTTGGGTTTCAAGATGCCTTTTGTGGGTTTTCATCTCG
1 ACTTC-TTTTTTTTGGGTTTCAAGATGCCCTTAGTGGGTTTTCATCTCG
93642 ACTTCTTTTTTTT
1 ACTTCTTTTTTTT
93655 ACCTTTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
48 43 0.81
49 10 0.19
ACGTcount: A:0.11, C:0.16, G:0.19, T:0.54
Consensus pattern (48 bp):
ACTTCTTTTTTTTGGGTTTCAAGATGCCCTTAGTGGGTTTTCATCTCG
Found at i:98376 original size:23 final size:23
Alignment explanation
Indices: 98357--98435 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
98347 AGAAATAAGG
*
98357 ATAAAATAAATCAATAAATAAAA
1 ATAAAATAAATAAATAAATAAAA
* *
98380 ATAAAATCAATAAATAAAAACAAACA
1 ATAAAATAAATAAAT--AAATAAA-A
* * *
98406 ATAAAAGGAACTAAATTAATAAAA
1 ATAAAA-TAAATAAATAAATAAAA
98430 ATAAAA
1 ATAAAA
98436 ACGCATAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
23 13 0.30
24 7 0.16
25 11 0.25
26 7 0.16
27 6 0.14
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (23 bp):
ATAAAATAAATAAATAAATAAAA
Found at i:98386 original size:19 final size:18
Alignment explanation
Indices: 98359--98410 Score: 79
Period size: 19 Copynumber: 2.9 Consensus size: 18
98349 AAATAAGGAT
98359 AAAATAAATCAATAAATA
1 AAAATAAATCAATAAATA
98377 AAAATAAAATCAATAAATA
1 AAAAT-AAATCAATAAATA
*
98396 AAAACAAA-CAATAAA
1 AAAATAAATCAATAAA
98411 AGGAACTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 7 0.22
18 8 0.25
19 17 0.53
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAATAAATCAATAAATA
Found at i:99602 original size:17 final size:18
Alignment explanation
Indices: 99580--99613 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
99570 GGTACGTGCG
99580 GACGTGGCAAG-GCGGTC
1 GACGTGGCAAGAGCGGTC
99597 GACGTGGCAAGAGCGGT
1 GACGTGGCAAGAGCGGT
99614 GTTGACGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.21, C:0.21, G:0.47, T:0.12
Consensus pattern (18 bp):
GACGTGGCAAGAGCGGTC
Found at i:100422 original size:100 final size:99
Alignment explanation
Indices: 100232--100552 Score: 322
Period size: 100 Copynumber: 3.2 Consensus size: 99
100222 CGATCCATCG
* * * ** *
100232 CAACTTCAGGGATCTAGGATTTGATGTCGTAACTTCATCTTGCTCCGTTGCATCTTCAGAGAGAT
1 CAACTTCAGGGGTATAAGATTTGATGTCGTAACTTCATCTTGCTCCACTGCAACTTCAGAGAGAT
* * * * *
100297 AAGATTTGCTTCTATAACTCCAATCTGACCCACTA
66 AAAATTTGCTTATGTAGCTTCAATCTGACCC-CTA
* * * * * *
100332 TAACTTTAGGGGTATAAGATTTGATATGGTATCTTCATCTTGCTCTACTGCAACTTCAGAGAGAT
1 CAACTTCAGGGGTATAAGATTTGATGTCGTAACTTCATCTTGCTCCACTGCAACTTCAGAGAGAT
* * *
100397 AAAATTTGC-TATTGTAGTTTTAATCTGATCCCTA
66 AAAATTTGCTTA-TGTAGCTTCAATCTGACCCCTA
* * * * * *
100431 CAACTTCA-GGGTATAAGATTTTATGTCGTAGCTTCATCCTACTCCACTGTAACTTTAGAGAGAT
1 CAACTTCAGGGGTATAAGATTTGATGTCGTAACTTCATCTTGCTCCACTGCAACTTCAGAGAGAT
* *
100495 AAAGATTTGTTTATGTAGCTTCAATCCGACCCTCTA
66 AAA-ATTTGCTTATGTAGCTTCAATCTGACCC-CTA
* *
100531 CAACTTCAGGTGTATAGGATTT
1 CAACTTCAGGGGTATAAGATTT
100553 TTGTTTTGTA
Statistics
Matches: 178, Mismatches: 38, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
98 50 0.28
99 30 0.17
100 87 0.49
101 11 0.06
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (99 bp):
CAACTTCAGGGGTATAAGATTTGATGTCGTAACTTCATCTTGCTCCACTGCAACTTCAGAGAGAT
AAAATTTGCTTATGTAGCTTCAATCTGACCCCTA
Found at i:100536 original size:51 final size:50
Alignment explanation
Indices: 100428--100603 Score: 153
Period size: 51 Copynumber: 3.5 Consensus size: 50
100418 AATCTGATCC
* * * *
100428 CTACAACTTCAGG-GTATAAGATTTTATGTCGTAGCTTC-ATCCTACTCCA
1 CTACAACTTCAGGAGTATAAGATTTTGTTTTGTAGCTTCAATCCGAC-CCA
** * *
100477 CTGTAACTTTAGAGAG-ATAAAGA-TTTGTTTATGTAGCTTCAATCCGACCCT
1 CTACAACTTCAG-GAGTAT-AAGATTTTGTTT-TGTAGCTTCAATCCGACCCA
* * * *
100528 CTACAACTTCAGGTGTATAGGATTTTTGTTTTGTAGCTTCAATCTGATCCA
1 CTACAACTTCAGGAGTATAAGA-TTTTGTTTTGTAGCTTCAATCCGACCCA
* *
100579 CTACAACTTCAGGAATATAGGATTT
1 CTACAACTTCAGGAGTATAAGATTT
100604 GGTGTGGTAG
Statistics
Matches: 101, Mismatches: 18, Indels: 15
0.75 0.13 0.11
Matches are distributed among these distances:
49 9 0.09
50 16 0.16
51 63 0.62
52 13 0.13
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (50 bp):
CTACAACTTCAGGAGTATAAGATTTTGTTTTGTAGCTTCAATCCGACCCA
Found at i:100587 original size:102 final size:98
Alignment explanation
Indices: 100206--100590 Score: 260
Period size: 100 Copynumber: 3.8 Consensus size: 98
100196 TAGGATTCGA
* * * * * * *
100206 TATTGTAGCCTT-AATCCGATCCATCGCAACTTCAGGGATCTAGGATTTGATGTCGTAACTTCAT
1 TATTGTAG-CTTCAATCCGACCCCT-ACAACTTCAGGG-TATAAGATTTTATGTCGTAGCTTCAT
* * ** * * *
100270 CTTGCTCCGTTGCATCTTCAGAGAGATAAGATTTGC
63 CCTACTCCACTACAACTTCAGAGAGATAAAATTTGC
* * * * * * * * * *
100306 T-TCTATAACTCCAATCTGACCCACTATAACTTTAGGGGTATAAGATTTGATATGGTATCTTCAT
1 TAT-TGTAGCTTCAATCCGACCC-CTACAACTTCA-GGGTATAAGATTTTATGTCGTAGCTTCAT
* * * *
100370 CTTGCTCTACTGCAACTTCAGAGAGATAAAATTTGC
63 CCTACTCCACTACAACTTCAGAGAGATAAAATTTGC
* * * *
100406 TATTGTAGTTTTAATCTGATCCCTACAACTTCAGGGTATAAGATTTTATGTCGTAGCTTCATCCT
1 TATTGTAGCTTCAATCCGACCCCTACAACTTCAGGGTATAAGATTTTATGTCGTAGCTTCATCCT
** *
100471 ACTCCACTGTAACTTTAGAGAGATAAAGATTTG-
66 ACTCCACTACAACTTCAGAGAGATAAA-ATTTGC
* * *
100504 TTTATGTAGCTTCAATCCGACCCTCTACAACTTCAGGTGTATAGGATTTT-TGTTTTGTAGCTTC
1 TAT-TGTAGCTTCAATCCGACCC-CTACAACTTCAGG-GTATAAGATTTTATG--TCGTAGCTTC
100568 AAT-CTGA-TCCACTACAACTTCAG
61 -ATCCT-ACTCCACTACAACTTCAG
100591 GAATATAGGA
Statistics
Matches: 226, Mismatches: 46, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
98 52 0.23
99 32 0.14
100 99 0.44
101 16 0.07
102 24 0.11
103 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (98 bp):
TATTGTAGCTTCAATCCGACCCCTACAACTTCAGGGTATAAGATTTTATGTCGTAGCTTCATCCT
ACTCCACTACAACTTCAGAGAGATAAAATTTGC
Found at i:100890 original size:96 final size:97
Alignment explanation
Indices: 100769--101002 Score: 292
Period size: 96 Copynumber: 2.4 Consensus size: 97
100759 TTCAACTTTA
* * * *
100769 ATCCGACCCACTGCAACTTTAGGGGTATAAGATTTGGTGTTGTAGTTTCATCTTGCTCTACTACA
1 ATCCGACCCACTACAACTTCAGGGGTATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACTACA
*
100834 ACTTCAAAGAGATAAAGAGTTGCTT-CTATAG-
66 ACTTCAAAGAAATAAAGAGTTG-TTACTATAGT
* * * *
100865 ATCCGACCCATTACAACTTCAGGGGTATAGGATTTGATTTTGTAGCTTCATCTTGCTCTATTACA
1 ATCCGACCCACTACAACTTCAGGGGTATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACTACA
* * * *
100930 ACTTCAGAGAAATATAGATTTGTTACTGTAGTTTT
66 ACTTCAAAGAAATAAAGAGTTGTTACTATAG---T
100965 AATCCGACCCACTACAACTTCAGGGGTATAGGATTTGG
1 -ATCCGACCCACTACAACTTCAGGGGTATAGGATTTGG
101003 CATTTCACTG
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
95 2 0.02
96 80 0.68
101 35 0.30
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (97 bp):
ATCCGACCCACTACAACTTCAGGGGTATAGGATTTGGTGTTGTAGCTTCATCTTGCTCTACTACA
ACTTCAAAGAAATAAAGAGTTGTTACTATAGT
Found at i:101769 original size:38 final size:38
Alignment explanation
Indices: 101727--101802 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
101717 CTCGACCTCT
*
101727 CTTTTTTCCTTTTT-TTTTATATTTTTTTTCTTTTTTTC
1 CTTTTTTCCTTTTTCTTTTAT-TTTCTTTTCTTTTTTTC
*
101765 CTTTTTTCCTTTTTCCTTTTCTTTTCTTTTCTTTTTTT
1 CTTTTTTCCTTTTT-CTTTTATTTTCTTTTCTTTTTTT
101803 TTTTTGGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 14 0.41
39 15 0.44
40 5 0.15
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (38 bp):
CTTTTTTCCTTTTTCTTTTATTTTCTTTTCTTTTTTTC
Found at i:101804 original size:10 final size:10
Alignment explanation
Indices: 101728--101804 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
101718 TCGACCTCTC
*
101728 TTTTTTCCTT
1 TTTTTTTCTT
*
101738 TTTTTTTATAT
1 TTTTTTTCT-T
101749 TTTTTTTC--
1 TTTTTTTCTT
*
101757 TTTTTTTC-C
1 TTTTTTTCTT
*
101766 TTTTTTCCTT
1 TTTTTTTCTT
101776 TTTCCTTTTCTT
1 TTT--TTTTCTT
*
101788 TTCTTTTCTT
1 TTTTTTTCTT
101798 TTTTTTT
1 TTTTTTT
101805 TTTGGTGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
8 8 0.15
9 7 0.13
10 23 0.43
11 8 0.15
12 8 0.15
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:117944 original size:7 final size:7
Alignment explanation
Indices: 117932--117962 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
117922 TAAATCAAAT
117932 GTGTTGA
1 GTGTTGA
117939 GTGTTGA
1 GTGTTGA
117946 GTGTTGA
1 GTGTTGA
*
117953 CTGTTGA
1 GTGTTGA
117960 GTG
1 GTG
117963 CTGAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.03, G:0.42, T:0.42
Consensus pattern (7 bp):
GTGTTGA
Found at i:148309 original size:20 final size:20
Alignment explanation
Indices: 148269--148322 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
148259 GTGGATTAGC
148269 ATGATTTATATTAAGTGTAAA
1 ATGATTTA-ATTAAGTGTAAA
148290 TATG-TTTAATTAAGAT-TAAA
1 -ATGATTTAATTAAG-TGTAAA
*
148310 ATGAGTTAATTAA
1 ATGATTTAATTAA
148323 AGCTTAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 3 0.10
20 18 0.62
21 5 0.17
22 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGATTTAATTAAGTGTAAA
Found at i:150133 original size:21 final size:21
Alignment explanation
Indices: 150107--150156 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
150097 GGAGTTTTTA
*
150107 GTATCGGTAGAAGTATGACTT
1 GTATCGGTAGAAGTATCACTT
* * *
150128 GTATCGATAGATGTCTCACTT
1 GTATCGGTAGAAGTATCACTT
150149 GTATCGGT
1 GTATCGGT
150157 GGTATTACCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (21 bp):
GTATCGGTAGAAGTATCACTT
Found at i:170171 original size:17 final size:18
Alignment explanation
Indices: 170151--170188 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
170141 AATTGTCATT
170151 GCATTTTTA-TTGTTTTA
1 GCATTTTTATTTGTTTTA
*
170168 GCA-TTTTATTTGTTTTG
1 GCATTTTTATTTGTTTTA
170185 GCAT
1 GCAT
170189 ATTCATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.61
Consensus pattern (18 bp):
GCATTTTTATTTGTTTTA
Found at i:180822 original size:53 final size:53
Alignment explanation
Indices: 180745--180852 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
180735 TTGGAAAAAT
180745 ATCTGTCGTTAGTAGAGTTTGCTTATAATAACAGCTATCAGTCTAGTATTAAA
1 ATCTGTCGTTAGTAGAGTTTGCTTATAATAACAGCTATCAGTCTAGTATTAAA
*
180798 ATCTGTCGTTAGTAGAGTTTGCTTATAATAATAGCTATCAGTCTAGTATTAAA
1 ATCTGTCGTTAGTAGAGTTTGCTTATAATAACAGCTATCAGTCTAGTATTAAA
180851 AT
1 AT
180853 GGCACCGTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (53 bp):
ATCTGTCGTTAGTAGAGTTTGCTTATAATAACAGCTATCAGTCTAGTATTAAA
Found at i:187467 original size:23 final size:23
Alignment explanation
Indices: 187422--187464 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
187412 TAGGATGCTC
*
187422 CTCGTCAAGAGCAGGGTTGCCTT
1 CTCGTCAAAAGCAGGGTTGCCTT
*
187445 CTCGTCAAAATCA-GGTTGCC
1 CTCGTCAAAAGCAGGGTTGCC
187465 CTTAGGGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
CTCGTCAAAAGCAGGGTTGCCTT
Found at i:197547 original size:626 final size:629
Alignment explanation
Indices: 196345--197606 Score: 2199
Period size: 626 Copynumber: 2.0 Consensus size: 629
196335 GTTACGAAGA
* * *
196345 AATCTTTCTTTCTTATGGCCTATTGTGGCCAAAGGTAACCTACCACATACTAGGTAATTGACCAC
1 AATCTTTCTTTCTTATAGCCTATTGTGCCCAAACGTAACCTACCACATACTAGGTAATTGACCAC
*
196410 ATCCGCATACCATGGGGTTCCGTCGACAGCAAACAGCTTCTCATCAAGAAATGTGTCGACAATTT
66 ATCCGCATACCATGGGGTTCCGTCGACAGCAAACAGCTTCCCATCAAGAAATGTGTCGACAATTT
*
196475 GAAATGTATTTCCATCTTCACTACCCACTTCCAGATGAGACAGGTGATTTGTTGACTTGGTTTTT
131 GAAATGTATTTCCATCTTCACTACACACTTCCAGATGAGACAGGTGATTTGTTGACTTGGTTTTT
*
196540 CGACCCCTTTCGATCCTTTATCTCTATATCAAACTCTTGTAGTAGTAGGATCTATCGTATCAACC
196 CGACCCCTTTCGATCCTTTATCTCTATATCAAACTCTTGTAGTAGTAGGATCCATCGTATCAACC
196605 TTGGTTTAGCGTCCTTCTTTGCAAAAAGGTATCTTAATGTGGAATGATCAGTGAATACAGTAACC
261 TTGGTTTAGCGTCCTTCTTTGCAAAAAGGTATCTTAATGTGGAATGATCAG-G---A-AGTAACC
* * *
196670 TTTGCACCGATAAGATATGAATGAAATTTGTCAAAAGCAAATACTACAGGCAATAACTCTTTTTC
321 TTTACACCGATAAGATATGAATGAAATTTGTCAAAAGCAAATACTACAGCCAACAACTCTTTTTC
* *
196735 TGTGGTTGTGTACTTAATTTAAGCTTCTATGAGAGTCTTGCTAGCATAATATATAGCATGAAATA
386 TGTGATTGTGTACTTAATTTAAGCTTCTATGAGAGTATTGCTAGCATAATATATAGCATGAAATA
* **
196800 CTCTTTCCTTGCATTGTCATAATACTACACCCACTGCAAAATCACTTGCATCACACATTACTTCA
451 CTCTTTCCTTACATTGTCATAATACTACACCCACTAAAAAATCACTTGCATCACACATTACTTCA
* *
196865 ATTGGTTGCGACCAATTTGGTGCAACGACAATGGGTGCCTTCACTAGCTGCTTCTTTATTT-TCA
516 ATTGGTTGCGACCAATTTGGTGCAACGACAATGGGTGCCTTCACCAGCTACTTCTTTATTTGT-A
*
196929 TAAATTTATCCACACATGCATCATCAAACAAGAATATTTTATTTTGCTCC
580 TAAATGTATCCACACATGCATCATCAAACAAGAATATTTTATTTTGCTCC
* *
196979 AATCTTTCTTTCTTATAGCCTGTTGTGCCCAAACGTAACCTACCACATACTAGGTAATTGACCAT
1 AATCTTTCTTTCTTATAGCCTATTGTGCCCAAACGTAACCTACCACATACTAGGTAATTGACCAC
*
197044 ATCCGCATACCATGGGGTTCCGTCGACAGCAAACAGCTTCCCATCAAGAAATGTGTTGACAATTT
66 ATCCGCATACCATGGGGTTCCGTCGACAGCAAACAGCTTCCCATCAAGAAATGTGTCGACAATTT
*
197109 GAAATGTATTTCCGTCTTCACTACACACTTCCAGATGAGACAGGTGATTTG-TGACTTGGTTTTT
131 GAAATGTATTTCCATCTTCACTACACACTTCCAGATGAGACAGGTGATTTGTTGACTTGGTTTTT
*
197173 GGACCCCTTTCGATCCTTTATCTCTATATCAAACTCTTGTAGTAGTAGGATCCATCGTATCAACC
196 CGACCCCTTTCGATCCTTTATCTCTATATCAAACTCTTGTAGTAGTAGGATCCATCGTATCAACC
197238 TTGGTTTAGCGTCCTTCTTTGCAAAAAGGTATCTTAATGTGGAATGATCA-G-AGTAACCTTTAC
261 TTGGTTTAGCGTCCTTCTTTGCAAAAAGGTATCTTAATGTGGAATGATCAGGAAGTAACCTTTAC
*
197301 ACCGATAAGATATGAATGAAATTTGTCGAAAGCAAATACTACAGCCAACAACTCTTTTTCTGTGA
326 ACCGATAAGATATGAATGAAATTTGTCAAAAGCAAATACTACAGCCAACAACTCTTTTTCTGTGA
* *
197366 TTGTGTACTTAATTTGAGCTTCTATGAGAGTATTGCTGGCATAATATATAGCATGAAATACTCTT
391 TTGTGTACTTAATTTAAGCTTCTATGAGAGTATTGCTAGCATAATATATAGCATGAAATACTCTT
*
197431 TCCTTACATTGTCCTAATACTACACCCACTAAAAAATCACTTGCATCACACATTACTTCAATTGG
456 TCCTTACATTGTCATAATACTACACCCACTAAAAAATCACTTGCATCACACATTACTTCAATTGG
197496 TTGCGACCAATTTGGTGCAACGACAATGGGTGCCTTCACCAGCTACTTCTTTATTTGTATAAATG
521 TTGCGACCAATTTGGTGCAACGACAATGGGTGCCTTCACCAGCTACTTCTTTATTTGTATAAATG
*
197561 TATCCACACATGCATCATCAAACAGGAATATTTTATTTTGCTCC
586 TATCCACACATGCATCATCAAACAAGAATATTTTATTTTGCTCC
197605 AA
1 AA
197607 CAAGGAGTAG
Statistics
Matches: 600, Mismatches: 27, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
626 300 0.50
627 1 0.00
631 1 0.00
633 126 0.21
634 172 0.29
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (629 bp):
AATCTTTCTTTCTTATAGCCTATTGTGCCCAAACGTAACCTACCACATACTAGGTAATTGACCAC
ATCCGCATACCATGGGGTTCCGTCGACAGCAAACAGCTTCCCATCAAGAAATGTGTCGACAATTT
GAAATGTATTTCCATCTTCACTACACACTTCCAGATGAGACAGGTGATTTGTTGACTTGGTTTTT
CGACCCCTTTCGATCCTTTATCTCTATATCAAACTCTTGTAGTAGTAGGATCCATCGTATCAACC
TTGGTTTAGCGTCCTTCTTTGCAAAAAGGTATCTTAATGTGGAATGATCAGGAAGTAACCTTTAC
ACCGATAAGATATGAATGAAATTTGTCAAAAGCAAATACTACAGCCAACAACTCTTTTTCTGTGA
TTGTGTACTTAATTTAAGCTTCTATGAGAGTATTGCTAGCATAATATATAGCATGAAATACTCTT
TCCTTACATTGTCATAATACTACACCCACTAAAAAATCACTTGCATCACACATTACTTCAATTGG
TTGCGACCAATTTGGTGCAACGACAATGGGTGCCTTCACCAGCTACTTCTTTATTTGTATAAATG
TATCCACACATGCATCATCAAACAAGAATATTTTATTTTGCTCC
Found at i:204600 original size:21 final size:21
Alignment explanation
Indices: 204570--204620 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
204560 GAGGTTTTAT
* *
204570 TATCAATAGAAGTATGACTTG
1 TATCAGTAGAAGTATCACTTG
* * *
204591 TATCGGTAGATGTCTCACTTG
1 TATCAGTAGAAGTATCACTTG
204612 TATCAGTAG
1 TATCAGTAG
204621 TACTACCTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (21 bp):
TATCAGTAGAAGTATCACTTG
Found at i:212536 original size:19 final size:19
Alignment explanation
Indices: 212514--212558 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
212504 TTATATTAGG
212514 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
212533 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
212552 ATTTAAT
1 ATTTAAT
212559 TCATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:213301 original size:22 final size:21
Alignment explanation
Indices: 213262--213323 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
213252 TTCAACATCC
213262 CTATTTTCTATTTC-TTTTAATT
1 CTATTTTCT-TTTCTTTTTAA-T
213284 CTATTTTCTTTTCTTTTTTAAT
1 CTATTTTCTTTTC-TTTTTAAT
*
213306 -TATGTTTCTTTTATTTTT
1 CTAT-TTTCTTTTCTTTTT
213324 CCTTAGATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 12 0.33
22 18 0.50
23 6 0.17
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.73
Consensus pattern (21 bp):
CTATTTTCTTTTCTTTTTAAT
Found at i:214871 original size:21 final size:21
Alignment explanation
Indices: 214854--214897 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
214844 GAATTTCCAT
* *
214854 AGCAATTTATAGATTTTCAAA
1 AGCAATCTATAAATTTTCAAA
214875 AGCAATCTATAAATTTTCAAA
1 AGCAATCTATAAATTTTCAAA
214896 AG
1 AG
214898 AAAACTGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
AGCAATCTATAAATTTTCAAA
Found at i:216931 original size:108 final size:108
Alignment explanation
Indices: 216819--217013 Score: 236
Period size: 108 Copynumber: 1.8 Consensus size: 108
216809 TAACCCGAAT
* *
216819 AAAAAATA-AAAAAAATAAATTCG-GAATATGTTAGACTGAGTAACC-GGAGTGGAGTGTC-TGG
1 AAAAAAGATAAAAAAA-AAATT-GAGAACATGTTAGACTGAGTAACCGGGA-TGGAGT-TCTTGG
* *
216880 TTGTCATTTCACTTCACGTCAAAAGGGCTAACACATTCTAAATAAAG
62 GTGTCATTTCACTTCACGACAAAAGGGCTAACACATTCTAAATAAAG
* * * *
216927 AAAAAAGATAAGAAAAAAATTGAGAGCATGTTGGGCTGAGTAACCGGGATGGAGTTCTTGGGTGT
1 AAAAAAGATAAAAAAAAAATTGAGAACATGTTAGACTGAGTAACCGGGATGGAGTTCTTGGGTGT
* *
216992 CATTTCATTTCTCGACAAAAGG
66 CATTTCACTTCACGACAAAAGG
217014 TTCAATGTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
107 3 0.04
108 61 0.84
109 9 0.12
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (108 bp):
AAAAAAGATAAAAAAAAAATTGAGAACATGTTAGACTGAGTAACCGGGATGGAGTTCTTGGGTGT
CATTTCACTTCACGACAAAAGGGCTAACACATTCTAAATAAAG
Found at i:217387 original size:2 final size:2
Alignment explanation
Indices: 217376--217404 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
217366 ATACTTTTAG
217376 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
217405 TAGAGTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:217636 original size:19 final size:19
Alignment explanation
Indices: 217614--217658 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
217604 TTATATTAGG
217614 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
217633 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
217652 ATTTAAT
1 ATTTAAT
217659 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:218509 original size:21 final size:22
Alignment explanation
Indices: 218459--218519 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
218449 TTCGACTTCC
*
218459 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTATTTTTAATT
218481 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
218503 CTA-TTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
218520 CCTTAGATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 17 0.46
22 20 0.54
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:218513 original size:15 final size:16
Alignment explanation
Indices: 218464--218493 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
218454 CTTCCCTATT
218464 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
218479 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
218494 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:219553 original size:187 final size:187
Alignment explanation
Indices: 219221--219569 Score: 572
Period size: 187 Copynumber: 1.9 Consensus size: 187
219211 ACAGTTCATG
*
219221 CAAAGAATGATATAGTGGCATTTTCATAATTATGAAACATATAGTGGACTCTATGACCACCTACA
1 CAAAGAATGATATAGTGGCATTTTCATAATTATGAAACATATAGTGGACTCTATCACCACCTACA
* * *
219286 AGTGGACTCTATCACCACACATTGGATAAATGGATCTCCTTATAACACCTCATTTTTTGACTCAA
66 AGTGGACTCTATCACCACACATTGGATAAATGAATCTCCTTATAACACCTCACTTTTGGACTCAA
*
219351 AGAACCTTGTGTTGTCCTTGATATAAGTGTAGTTGTTCCATCATAACTCATATATTT
131 AGAACCTTATGTTGTCCTTGATATAAGTGTAGTTGTTCCATCATAACTCATATATTT
* * * *
219408 CAAATAATGATATATTGGCATTTTCGTAATTATGAAACATATAGTGGACTCTATCACCACCTATA
1 CAAAGAATGATATAGTGGCATTTTCATAATTATGAAACATATAGTGGACTCTATCACCACCTACA
* * *
219473 AGTGGACTTTATCACCATACATTGGATAAATGAATCTCTTTATAACACCTCACTTTTGGACTCAA
66 AGTGGACTCTATCACCACACATTGGATAAATGAATCTCCTTATAACACCTCACTTTTGGACTCAA
* *
219538 AGAGCCTTATGTTGTCTTTGATATAAGTGTAG
131 AGAACCTTATGTTGTCCTTGATATAAGTGTAG
219570 ATGATCTGTT
Statistics
Matches: 148, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
187 148 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (187 bp):
CAAAGAATGATATAGTGGCATTTTCATAATTATGAAACATATAGTGGACTCTATCACCACCTACA
AGTGGACTCTATCACCACACATTGGATAAATGAATCTCCTTATAACACCTCACTTTTGGACTCAA
AGAACCTTATGTTGTCCTTGATATAAGTGTAGTTGTTCCATCATAACTCATATATTT
Found at i:221577 original size:17 final size:17
Alignment explanation
Indices: 221549--221592 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
221539 ACACAAATAT
221549 AATTGA-CTCGCACTAC
1 AATTGAGCTCGCACTAC
221565 AATTGAGCTCGCACTAC
1 AATTGAGCTCGCACTAC
221582 AATTGAGCTCG
1 AATTGAGCTCG
221593 TACCTAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (17 bp):
AATTGAGCTCGCACTAC
Found at i:221816 original size:29 final size:29
Alignment explanation
Indices: 221764--221845 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
221754 CCATCATAAA
221764 ACCCATATACATATATATTATATAAAACAAG
1 ACCCATAT--ATATATATTATATAAAACAAG
*
221795 ACCCATATATATATATTATATATAACAAG
1 ACCCATATATATATATTATATAAAACAAG
* ***
221824 ACTCACGCATATATATTATATA
1 ACCCATATATATATATTATATA
221846 TATAACAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 38 0.83
31 8 0.17
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.33
Consensus pattern (29 bp):
ACCCATATATATATATTATATAAAACAAG
Found at i:221846 original size:29 final size:29
Alignment explanation
Indices: 221773--221878 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
221763 AACCCATATA
* * **
221773 CATATATATTATATAAAACAAGACCCATA
1 CATATATATTATATATAACAAGACTCACG
*
221802 TATATATATTATATATAACAAGACTCACG
1 CATATATATTATATATAACAAGACTCACG
*
221831 CATATATATTATATATATAACAAAACTCACG
1 CATATATA-T-TATATATAACAAGACTCACG
* *
221862 CTTATATATTGTATATA
1 CATATATATTATATATA
221879 CACATACCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 38 0.58
30 2 0.03
31 26 0.39
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (29 bp):
CATATATATTATATATAACAAGACTCACG
Found at i:221846 original size:31 final size:31
Alignment explanation
Indices: 221773--221878 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 31
221763 AACCCATATA
221773 CATATATATTATATA-A-AACAAGA--C-C-
1 CATATATATTATATATATAACAAGACTCACG
221798 CATATATATATATTATATATAACAAGACTCACG
1 CATATATAT-TA-TATATATAACAAGACTCACG
*
221831 CATATATATTATATATATAACAAAACTCACG
1 CATATATATTATATATATAACAAGACTCACG
* *
221862 CTTATATATTGTATATA
1 CATATATATTATATATA
221879 CACATACCTT
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.13
26 2 0.03
27 4 0.06
28 1 0.01
29 7 0.10
31 35 0.50
32 3 0.04
33 9 0.13
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (31 bp):
CATATATATTATATATATAACAAGACTCACG
Found at i:230363 original size:36 final size:34
Alignment explanation
Indices: 230323--230389 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
230313 CCAAACAACT
230323 AAAACAACAGCAAAAATAATAGAAAAAATAACAATA
1 AAAACAACA-CAAAAATAATA-AAAAAATAACAATA
* *
230359 AAAACAACACCAAAATAGTAAAAAAATAACA
1 AAAACAACACAAAAATAATAAAAAAATAACA
230390 CCAAAACAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 11 0.38
35 9 0.31
36 9 0.31
ACGTcount: A:0.72, C:0.13, G:0.04, T:0.10
Consensus pattern (34 bp):
AAAACAACACAAAAATAATAAAAAAATAACAATA
Found at i:230389 original size:22 final size:22
Alignment explanation
Indices: 230358--230480 Score: 116
Period size: 22 Copynumber: 5.8 Consensus size: 22
230348 AAATAACAAT
*
230358 AAAAACAACACCAAAATAGTAA
1 AAAAACAACACCAAAACAGTAA
*
230380 AAAAATAACACCAAAACAGT--
1 AAAAACAACACCAAAACAGTAA
230400 -AAAA-AA-ACCAAAACAGTAA
1 AAAAACAACACCAAAACAGTAA
** *
230419 AAGCACAACACCAAAACAGCAA
1 AAAAACAACACCAAAACAGTAA
*
230441 AAAATAGC-A-ACCAAAACAGCAA
1 AAAA-A-CAACACCAAAACAGTAA
*
230463 AAAAACAGCACCAAAACA
1 AAAAACAACACCAAAACA
230481 ACAATATAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 18
0.76 0.07 0.16
Matches are distributed among these distances:
17 11 0.13
18 2 0.02
19 4 0.05
20 3 0.04
21 3 0.04
22 58 0.69
23 2 0.02
24 1 0.01
ACGTcount: A:0.66, C:0.23, G:0.07, T:0.05
Consensus pattern (22 bp):
AAAAACAACACCAAAACAGTAA
Found at i:230411 original size:39 final size:39
Alignment explanation
Indices: 230367--230480 Score: 120
Period size: 39 Copynumber: 2.8 Consensus size: 39
230357 TAAAAACAAC
* * *
230367 ACCAAAATAGTAAAAAAATAACACCAAAACAGTAAAAAA
1 ACCAAAACAGTAAAAAAACAACACCAAAACAGCAAAAAA
**
230406 ACCAAAACAGTAAAAGCACAACACCAAAACAGCAAAAAATAGCA
1 ACCAAAACAGTAAAAAAACAACACCAAAACAGC--AAAA-A--A
* *
230450 ACCAAAACAGCAAAAAAACAGCACCAAAACA
1 ACCAAAACAGTAAAAAAACAACACCAAAACA
230481 ACAATATAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
39 28 0.46
41 4 0.07
42 1 0.02
44 28 0.46
ACGTcount: A:0.65, C:0.23, G:0.07, T:0.05
Consensus pattern (39 bp):
ACCAAAACAGTAAAAAAACAACACCAAAACAGCAAAAAA
Found at i:230478 original size:11 final size:11
Alignment explanation
Indices: 230427--230480 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
230417 AAAAGCACAA
230427 CACCAAAACAG
1 CACCAAAACAG
* *
230438 CA-AAAAATAG
1 CACCAAAACAG
230448 CAACCAAAACAG
1 C-ACCAAAACAG
**
230460 CAAAAAAACAG
1 CACCAAAACAG
230471 CACCAAAACA
1 CACCAAAACA
230481 ACAATATAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.28, G:0.07, T:0.02
Consensus pattern (11 bp):
CACCAAAACAG
Found at i:236935 original size:28 final size:28
Alignment explanation
Indices: 236884--236937 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
236874 TGTCGATTTC
***
236884 TCCCAGATTGATACTTATGGTTTTTTTG
1 TCCCAGATTGATACTTAAACTTTTTTTG
*
236912 TCCCAGATTGGTACTTAAACTTTTTT
1 TCCCAGATTGATACTTAAACTTTTTT
236938 CCATCAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (28 bp):
TCCCAGATTGATACTTAAACTTTTTTTG
Found at i:237075 original size:20 final size:20
Alignment explanation
Indices: 237052--237119 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
237042 TAAAAAAATT
*
237052 AAAATTAATAAAATTAGAAA
1 AAAATTAATAAAATTACAAA
* *
237072 AAAATAAAATAAAA-TATTAAA
1 AAAAT-TAATAAAATTA-CAAA
*
237093 AAAATTATATATAATT-CAAA
1 AAAATTA-ATAAAATTACAAA
237113 AAAATTA
1 AAAATTA
237120 TGAAAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
20 18 0.46
21 20 0.51
22 1 0.03
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (20 bp):
AAAATTAATAAAATTACAAA
Found at i:237093 original size:21 final size:23
Alignment explanation
Indices: 237042--237097 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 23
237032 TGTTATAATC
237042 TAAAAAAATTAAAATTAATAAAAT
1 TAAAAAAA-TAAAATTAATAAAAT
*
237066 TAGAAAAAAATAAAA-TAA-AATAT
1 T--AAAAAAATAAAATTAATAAAAT
237089 TAAAAAAAT
1 TAAAAAAAT
237098 TATATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 8 0.28
23 5 0.17
24 4 0.14
25 5 0.17
26 7 0.24
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
TAAAAAAATAAAATTAATAAAAT
Found at i:252537 original size:17 final size:17
Alignment explanation
Indices: 252517--252585 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
252507 CATTTGCATC
*
252517 ACATTCCCATTGTCATT
1 ACATTTCCATTGTCATT
** *
252534 ACATTTTAATTGTCACT
1 ACATTTCCATTGTCATT
*
252551 GCATTTCCATTGTCATT
1 ACATTTCCATTGTCATT
*
252568 GCATTTCCATTTGTCATT
1 ACATTTCCA-TTGTCATT
252586 GTAATTTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 35 0.81
18 8 0.19
ACGTcount: A:0.22, C:0.23, G:0.09, T:0.46
Consensus pattern (17 bp):
ACATTTCCATTGTCATT
Found at i:256496 original size:29 final size:30
Alignment explanation
Indices: 256458--256516 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
256448 ATTATGTATC
* *
256458 TGCATTTGATTATG-AAATACATGTGATTT
1 TGCATCTGATTAAGAAAATACATGTGATTT
*
256487 TGCATCTGATTAAGAAAATATATGTGATTT
1 TGCATCTGATTAAGAAAATACATGTGATTT
256517 CGTATTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
TGCATCTGATTAAGAAAATACATGTGATTT
Found at i:258567 original size:19 final size:19
Alignment explanation
Indices: 258540--258577 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
258530 AAGGTAGAAA
258540 AAAG-AAAAAGAAGAAAAAT
1 AAAGAAAAAAGAA-AAAAAT
*
258559 AAAGGAAAAAGAAAAAAAT
1 AAAGAAAAAAGAAAAAAAT
258578 GCAAATAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAGAAAAAAGAAAAAAAT
Found at i:259919 original size:10 final size:9
Alignment explanation
Indices: 259872--259924 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
259862 TTTACATTAA
259872 TTATAATTT
1 TTATAATTT
259881 TTAT-ATTT
1 TTATAATTT
* **
259889 TTCTAAAGT
1 TTATAATTT
259898 TTATAATTT
1 TTATAATTT
259907 TTATAACTTT
1 TTATAA-TTT
259917 TTA-AATTT
1 TTATAATTT
259925 ATTAGATGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
8 10 0.28
9 20 0.56
10 6 0.17
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
TTATAATTT
Found at i:259921 original size:26 final size:25
Alignment explanation
Indices: 259872--259926 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
259862 TTTACATTAA
*
259872 TTATAATTTTTATATTTTTCTAAAGT
1 TTATAATTTTTATACTTTTCTAAA-T
259898 TTATAATTTTTATAACTTTT-TAAAT
1 TTATAATTTTTAT-ACTTTTCTAAAT
259923 TTAT
1 TTAT
259927 TAGATGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.19
26 17 0.63
27 5 0.19
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATAATTTTTATACTTTTCTAAAT
Found at i:260312 original size:2 final size:2
Alignment explanation
Indices: 260305--260349 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
260295 TCTAAAATTA
260305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
260347 AT A
1 AT A
260350 AAAGTTAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:266657 original size:34 final size:34
Alignment explanation
Indices: 266610--266683 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
266600 AAATAACAAC
*
266610 CAAAATAGAAGCAAAAATAACAGCAAAACAATAA
1 CAAAATAGAAGCAAAAATAACACCAAAACAATAA
* *
266644 CAAAATA-ATAGCAAAAATAGCACCAAAACAGTAA
1 CAAAATAGA-AGCAAAAATAACACCAAAACAATAA
*
266678 AAAAAT
1 CAAAAT
266684 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.66, C:0.15, G:0.08, T:0.11
Consensus pattern (34 bp):
CAAAATAGAAGCAAAAATAACACCAAAACAATAA
Found at i:282607 original size:21 final size:21
Alignment explanation
Indices: 282560--282618 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
282550 AATAGTGCAG
* *
282560 ACTTGTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGAGAC
* *
282581 AGTTCTACCGATATAAGAGAC
1 ACTTCTACCGATACAAGAGAC
* * *
282602 TCTTCTATCGAAACAAG
1 ACTTCTACCGATACAAG
282619 TCATACATCT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (21 bp):
ACTTCTACCGATACAAGAGAC
Found at i:282968 original size:31 final size:31
Alignment explanation
Indices: 282926--283044 Score: 197
Period size: 33 Copynumber: 3.8 Consensus size: 31
282916 ACATAGTTTA
*
282926 TATATAAATATATCACATTTAACTAATGTAG
1 TATATATATATATCACATTTAACTAATGTAG
282957 TATATATATATATCACATTTAACTAATGTAG
1 TATATATATATATCACATTTAACTAATGTAG
282988 TATATATATATATATCACATTTAACTAATGTAG
1 --TATATATATATATCACATTTAACTAATGTAG
283021 --TATATATATATCACATTTAACTAA
1 TATATATATATATCACATTTAACTAA
283045 CATACCAACT
Statistics
Matches: 85, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
29 24 0.28
31 30 0.35
33 31 0.36
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
TATATATATATATCACATTTAACTAATGTAG
Found at i:282995 original size:64 final size:62
Alignment explanation
Indices: 282924--283044 Score: 215
Period size: 64 Copynumber: 1.9 Consensus size: 62
282914 GTACATAGTT
282924 TATATATAAATATATCACATTTAACTAATGTAGTATATATATATATCACATTTAACTAATGTAG
1 TATATATAAATATATCACATTTAACTAATGTAG--TATATATATATCACATTTAACTAATGTAG
*
282988 TATATATATATATATCACATTTAACTAATGTAGTATATATATATCACATTTAACTAA
1 TATATATAAATATATCACATTTAACTAATGTAGTATATATATATCACATTTAACTAA
283045 CATACCAACT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 24 0.43
64 32 0.57
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (62 bp):
TATATATAAATATATCACATTTAACTAATGTAGTATATATATATCACATTTAACTAATGTAG
Found at i:284561 original size:22 final size:22
Alignment explanation
Indices: 284519--284561 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
284509 TCATTAAGCT
* *
284519 TTAATTAACCTTTTTTTTATTC
1 TTAATTAACCTTATTTATATTC
284541 TTAATTAAACC-TATTTATATT
1 TTAATT-AACCTTATTTATATT
284562 TAGTTTAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTAACCTTATTTATATTC
Found at i:286967 original size:41 final size:41
Alignment explanation
Indices: 286856--287034 Score: 198
Period size: 41 Copynumber: 4.4 Consensus size: 41
286846 GTATAAATGT
* * * *
286856 AAGACTCATGTCTTGAGATGAGCATGAGATTATTTTAAA-A
1 AAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGG
* * *** * *
286896 AAGACTCGTGACTCAAAATGAACATAAGATTATATTAAAGG
1 AAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGG
* *
286937 AAGACTCATGTCTCGGGGTGAGCATTAGATTATATTAAAGG
1 AAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGG
*
286978 AAGACTCGTGTCTCGGGATGAGCATGAGATTATATTTAAAGG
1 AAGACTCATGTCTCGGGATGAGCATGAGATTATA-TTAAAGG
* *
287020 AAGACTTATGACTCG
1 AAGACTCATGTCTCG
287035 ACATATCATA
Statistics
Matches: 114, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
40 31 0.27
41 64 0.56
42 19 0.17
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (41 bp):
AAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGG
Found at i:287049 original size:82 final size:81
Alignment explanation
Indices: 286856--287062 Score: 193
Period size: 82 Copynumber: 2.5 Consensus size: 81
286846 GTATAAATGT
* * * * *
286856 AAGACTCATGTCTTGAGATGAGCATGAGATTATTTTAAA-AAAGACTCGTGACTCAAAATGAACA
1 AAGACTCATGACTCGACATGAGCATAAGATTA-TTTAAAGGAAGACTCGTGACTCAAAATGAACA
286920 TAAGATTATATTAAAGG
65 TAAGATTATATTAAAGG
* *** * * *** *
286937 AAGACTCATGTCTCGGGGTGAGCATTAGATTATATTAAAGGAAGACTCGTGTCTCGGGATGAGCA
1 AAGACTCATGACTCGACATGAGCATAAGATTAT-TTAAAGGAAGACTCGTGACTCAAAATGAACA
*
287002 TGAGATTATATTTAAAGG
65 TAAGATTATA-TTAAAGG
* * *
287020 AAGACTTATGACTCGACAT-ATCATAAGATTGTTTAAAAGGAAG
1 AAGACTCATGACTCGACATGAGCATAAGATTATTT-AAAGGAAG
287063 GTCTACGACT
Statistics
Matches: 103, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
80 1 0.01
81 35 0.34
82 46 0.45
83 21 0.20
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (81 bp):
AAGACTCATGACTCGACATGAGCATAAGATTATTTAAAGGAAGACTCGTGACTCAAAATGAACAT
AAGATTATATTAAAGG
Found at i:295821 original size:15 final size:15
Alignment explanation
Indices: 295801--295836 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
295791 TTTACATTTT
*
295801 CTTTTATTTGTTTCA
1 CTTTTACTTGTTTCA
295816 CTTTTACTTGTTTCA
1 CTTTTACTTGTTTCA
*
295831 TTTTTA
1 CTTTTA
295837 AATTTTATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.67
Consensus pattern (15 bp):
CTTTTACTTGTTTCA
Found at i:298804 original size:8 final size:7
Alignment explanation
Indices: 298776--298817 Score: 54
Period size: 6 Copynumber: 6.3 Consensus size: 7
298766 AATTGTGAAT
298776 GAGAAAA
1 GAGAAAA
298783 -AGAAAA
1 GAGAAAA
298789 GA-AAAA
1 GAGAAAA
298795 GAGAACAA
1 GAGAA-AA
298803 GAGAAAA
1 GAGAAAA
298810 GA-AAAA
1 GAGAAAA
298816 GA
1 GA
298818 AATATTGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 18 0.56
7 7 0.22
8 7 0.22
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (7 bp):
GAGAAAA
Found at i:298807 original size:21 final size:19
Alignment explanation
Indices: 298776--298817 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
298766 AATTGTGAAT
298776 GAGAAAAAGAAAAGAAAAA
1 GAGAAAAAGAAAAGAAAAA
298795 GAGAACAAGAGAAAAGAAAAA
1 GAGAA-AA-AGAAAAGAAAAA
298816 GA
1 GA
298818 AATATTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 14 0.67
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (19 bp):
GAGAAAAAGAAAAGAAAAA
Found at i:300373 original size:16 final size:16
Alignment explanation
Indices: 300332--300374 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
300322 ATTTACTTTC
* *
300332 TATTGCACTGACAATT
1 TATTGCATTGACAACT
300348 TAACTTGCATTGACAACT
1 T-A-TTGCATTGACAACT
300366 TATTGCATT
1 TATTGCATT
300375 AACAGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (16 bp):
TATTGCATTGACAACT
Found at i:314648 original size:81 final size:82
Alignment explanation
Indices: 314563--314720 Score: 185
Period size: 81 Copynumber: 1.9 Consensus size: 82
314553 ATCCCAGAAA
* * *
314563 AGAGTATTACTCCTCCGAGCCAAAGTCAGAATAAT-ACTATTTCGAGCTA-AAAACAAAGTATTG
1 AGAGTATTACTCCTCCGAGCCAAAATCAGAAT-ATCACTATTTCAAGCTAGAAAACAAAGTAATG
*
314626 CTCTTTCGAGCCAAAGAT
65 CTCTTACGAGCCAAAGAT
** * * * ***
314644 AGAGTATTGGTCTTTCGAGCCAAAATCAGAATATCACTCTTTCAAGCTAGAGTCCAAAGTAATGC
1 AGAGTATTACTCCTCCGAGCCAAAATCAGAATATCACTATTTCAAGCTAGAAAACAAAGTAATGC
314709 TCTTACGAGCCA
66 TCTTACGAGCCA
314721 GAATACCAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
80 2 0.03
81 39 0.62
82 22 0.35
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (82 bp):
AGAGTATTACTCCTCCGAGCCAAAATCAGAATATCACTATTTCAAGCTAGAAAACAAAGTAATGC
TCTTACGAGCCAAAGAT
Found at i:314684 original size:27 final size:27
Alignment explanation
Indices: 314567--314686 Score: 100
Period size: 27 Copynumber: 4.4 Consensus size: 27
314557 CAGAAAAGAG
* * *
314567 TATTACTCCTCCGAGCCAAAGTCAGAA
1 TATTACTCTTTCGAGCCAAAATCAGAA
* * * *
314594 TAATACTATTTCGAGCTAAAAACA-AA
1 TATTACTCTTTCGAGCCAAAATCAGAA
* *
314620 GTATTGCTCTTTCGAGCCAAAGAT-AGAG
1 -TATTACTCTTTCGAGCCAAA-ATCAGAA
**
314648 TATTGGTCTTTCGAGCCAAAATCAGAA
1 TATTACTCTTTCGAGCCAAAATCAGAA
*
314675 TATCACTCTTTC
1 TATTACTCTTTC
314687 AAGCTAGAGT
Statistics
Matches: 71, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
26 4 0.06
27 65 0.92
28 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (27 bp):
TATTACTCTTTCGAGCCAAAATCAGAA
Found at i:325738 original size:52 final size:52
Alignment explanation
Indices: 325580--325765 Score: 250
Period size: 52 Copynumber: 3.6 Consensus size: 52
325570 ATTTCAATTA
* * * *
325580 ATACTCATGATGACACATAGTCATTGGACCTCTTAATTTGTAAAGGAA-TCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAA-GAATTCAT
* * * *
325632 ATACTCAGGATGACACATAGTCATAGG-CTTCATAATCCGTAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGAATTCAT
* *
325683 ATACTCACAATGACACATAGTCACCGGACCTCATAATTCGTAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGAATTCAT
*
325735 ATACTCACGATGACGCATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
325766 TTTACATTTA
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
50 3 0.03
51 39 0.33
52 75 0.64
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGAATTCAT
Found at i:328254 original size:37 final size:37
Alignment explanation
Indices: 328194--328287 Score: 152
Period size: 37 Copynumber: 2.5 Consensus size: 37
328184 ACATGTAAGG
* * *
328194 TTACTAGTCCACGCTAAACCTTTACAATGACAACGGA
1 TTACTAGTCCAAGCTGAATCTTTACAATGACAACGGA
*
328231 TTACTAGTCCAAGATGAATCTTTACAATGACAACGGA
1 TTACTAGTCCAAGCTGAATCTTTACAATGACAACGGA
328268 TTACTAGTCCAAGCTGAATC
1 TTACTAGTCCAAGCTGAATC
328288 CGAGTCACAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (37 bp):
TTACTAGTCCAAGCTGAATCTTTACAATGACAACGGA
Found at i:329169 original size:16 final size:16
Alignment explanation
Indices: 329138--329178 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
329128 TTTCACATCA
*
329138 AGTCCTTTTA-ATTTT
1 AGTCCTTTAACATTTT
329153 A-TCGCTTTAACATTTT
1 AGTC-CTTTAACATTTT
329169 AGTCCTTTAA
1 AGTCCTTTAA
329179 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 2 0.09
15 6 0.27
16 12 0.55
17 2 0.09
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.51
Consensus pattern (16 bp):
AGTCCTTTAACATTTT
Found at i:331925 original size:122 final size:123
Alignment explanation
Indices: 331647--332016 Score: 532
Period size: 122 Copynumber: 3.0 Consensus size: 123
331637 TAATGATTTC
* *
331647 ATTGAATATTAAAAACATGGAAGTTAATATCCTTTTTGGAAAGGATATAATGTTTTAATAAACCT
1 ATTGAATATTAAAAACATGAAAGTTAATATCC-TTTTGGAAAAGATATAATGTTTTAATAAACCT
*
331712 TCCATATATTTCTTTAAAGGAATATTTCCATTTTAATATGACATATTATATAAAAGAAA
65 TCCATATATTTCTTTAAAGGAATATTTCCATTTTAATATGACATATTATATAAAAGGAA
331771 ATTGAATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTT
1 ATTGAATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTT
** * *
331836 TAATATATTTCTTTAAAGGAATA-TTCCATTTTAATATAATATATTATATAAAAGGAA
66 CCATATATTTCTTTAAAGGAATATTTCCATTTTAATATGACATATTATATAAAAGGAA
* * * *
331893 ATTGAATATTTAAAACATGAAAATTAATATCCTTTTGGAAATGATATAATG-TGT--TAAACCTT
1 ATTGAATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTT
* * * * *
331955 CCATATATTTCTCTAAAGATATATATTTTCATTTTAATATGAGATATTAAACTAAAAGGAA
66 CCATATATTTCTTTAAAG-GA-ATATTTCCATTTTAATATGACATATTATA-TAAAAGGAA
332016 A
1 A
332017 GATAGCATAA
Statistics
Matches: 223, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
119 23 0.10
120 1 0.00
121 5 0.02
122 100 0.45
123 63 0.28
124 31 0.14
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (123 bp):
ATTGAATATTAAAAACATGAAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTT
CCATATATTTCTTTAAAGGAATATTTCCATTTTAATATGACATATTATATAAAAGGAA
Found at i:336853 original size:123 final size:123
Alignment explanation
Indices: 336709--337195 Score: 730
Period size: 123 Copynumber: 4.0 Consensus size: 123
336699 AATGATTTCG
* * *
336709 TTGAATATTAAAAGCATGGAAGTTAATATCTTTTTGGAAATGATATAATGTTTTAATAAACCTTC
1 TTGAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
* *
336774 CACATATTTCTTTAAACGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAA
66 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAA
* * *
336832 TTGAATATTAAAAACAGGGAAGCTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTC
1 TTGAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
336897 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAA
66 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAA
* * * * *
336955 TTTAATACTAAAAACATAG-AGTTAATATCCATTTGGAAAGTATATAATGTTTTAATAAACCTTC
1 TTGAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
* *
337019 CATATATTTCTTTAAAGGAATATTTTCATTTTAATATGAGATATTATATAATAGAAAA
66 CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAA
* *
337077 TTGAATATTAAAAACATGAAAGTTAATTTCCTTTTGGAAAGGATATAATGTTTT-A-AAA-CTTC
1 TTGAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
* * * *
337139 CATATATTTCTCTAAAGATATATATTTTCATTTTAATATGAGATATTAAAATAAAAG
66 CATATATTTCTTTAAAG-GA-ATATTTCCATTTTAATATGAGATATT-ATATAAAAG
337196 GAAAGATAGT
Statistics
Matches: 331, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
120 20 0.06
121 4 0.01
122 139 0.42
123 168 0.51
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (123 bp):
TTGAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
CATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAA
Found at i:337195 original size:245 final size:245
Alignment explanation
Indices: 336729--337195 Score: 735
Period size: 245 Copynumber: 1.9 Consensus size: 245
336719 AAAGCATGGA
**
336729 AGTTAATATCTTTTTGGAAATGATATAATGTTTTAATAAACCTTCCACATATTTCTTTAAACGAA
1 AGTTAATATCCATTTGGAAATGATATAATGTTTTAATAAACCTTCCACATATTTCTTTAAACGAA
*
336794 TATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTGAATATTAAAAACAGGGAAGCTAAT
66 TATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTGAATATTAAAAACAGGAAAGCTAAT
*
336859 ATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAAAGGAATATTTCC
131 ATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTCTAAAGGAATATTTCC
*
336924 ATTTTAATATGAGATATTATATAAAAGAAAATTTAATACTAAAAACATAG
196 ATTTTAATATGAGATATTAAATAAAAGAAAATTTAATACTAAAAACATAG
* *
336974 AGTTAATATCCATTTGGAAA-GTATATAATGTTTTAATAAACCTTCCATATATTTCTTTAAAGGA
1 AGTTAATATCCATTTGGAAATG-ATATAATGTTTTAATAAACCTTCCACATATTTCTTTAAACGA
* * * *
337038 ATATTTTCATTTTAATATGAGATATTATATAATAGAAAATTGAATATTAAAAACATGAAAGTTAA
65 ATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTGAATATTAAAAACAGGAAAGCTAA
* * *
337103 TTTCCTTTTGGAAAGGATATAATGTTTT-A-AAA-CTTCCATATATTTCTCTAAAGATATATATT
130 TATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTCTAAAG-GA-ATATT
*
337165 TTCATTTTAATATGAGATATTAAAATAAAAG
193 TCCATTTTAATATGAGATATT-AAATAAAAG
337196 GAAAGATAGT
Statistics
Matches: 203, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
242 20 0.10
243 4 0.02
244 27 0.13
245 152 0.75
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (245 bp):
AGTTAATATCCATTTGGAAATGATATAATGTTTTAATAAACCTTCCACATATTTCTTTAAACGAA
TATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTGAATATTAAAAACAGGAAAGCTAAT
ATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTCTAAAGGAATATTTCC
ATTTTAATATGAGATATTAAATAAAAGAAAATTTAATACTAAAAACATAG
Found at i:339778 original size:21 final size:21
Alignment explanation
Indices: 339730--339788 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
339720 AATAGTGCAG
* *
339730 ACTTCTACCGATATAAGTGAC
1 ACTTCTACCGATACAAGAGAC
**
339751 AAGTCTACCGATACAAGAGAC
1 ACTTCTACCGATACAAGAGAC
* *
339772 TCTTCTACCGAAACAAG
1 ACTTCTACCGATACAAG
339789 TCATACATCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.22
Consensus pattern (21 bp):
ACTTCTACCGATACAAGAGAC
Found at i:340468 original size:36 final size:36
Alignment explanation
Indices: 340415--340518 Score: 113
Period size: 36 Copynumber: 2.9 Consensus size: 36
340405 TGATTGTTAT
* *
340415 TCATTTTACTCCTTGTTGACTCGAA-GGTCATGGTGC
1 TCATTTTACTCCTTGTTGAC-CCAATGGTCATGATGC
340451 TCATTTTACTCAC-TGTTGACCCAATGGTCATGATGC
1 TCATTTTACTC-CTTGTTGACCCAATGGTCATGATGC
* * * * *
340487 TCAATTTACTCCCTATTAACCCAAAGGTCATG
1 TCATTTTACTCCTTGTTGACCCAATGGTCATG
340519 CCTATTACCA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
35 4 0.07
36 54 0.92
37 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (36 bp):
TCATTTTACTCCTTGTTGACCCAATGGTCATGATGC
Found at i:340751 original size:92 final size:91
Alignment explanation
Indices: 340645--340828 Score: 287
Period size: 92 Copynumber: 2.0 Consensus size: 91
340635 TAGGGCTTGT
* *
340645 AATCCATTTTGGATCCTATCCACTTCACAGTGACTCACAATGTCATATAGAATCCGTAACAAATG
1 AATCCATTTTGGATCCTATCCACTTCACAGTGACTCACAATGTCATAGAGAATCCGCAACAAATG
*
340710 CAAGATCTCAGTTATCGGACCATTTA
66 CAAGATCTCAGTCATCGGACCATTTA
* * * *
340736 AATCCATTCTTGGATCCTATTCACTTTACAGTGACTCACGATGTCGTAGAGAATCCGCAACAAAT
1 AATCCATT-TTGGATCCTATCCACTTCACAGTGACTCACAATGTCATAGAGAATCCGCAACAAAT
*
340801 GCAGGATCTCAGTCATCGGACCATTTA
65 GCAAGATCTCAGTCATCGGACCATTTA
340828 A
1 A
340829 CTTTGGCACA
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 8 0.10
92 76 0.90
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (91 bp):
AATCCATTTTGGATCCTATCCACTTCACAGTGACTCACAATGTCATAGAGAATCCGCAACAAATG
CAAGATCTCAGTCATCGGACCATTTA
Found at i:341736 original size:20 final size:21
Alignment explanation
Indices: 341694--341746 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
341684 TCATTAAGCT
* *
341694 TTAATTAACCCCTTTTTAATC
1 TTAATTAACACCTATTTAATC
*
341715 TTAATTAA-ACCTATTTACTC
1 TTAATTAACACCTATTTAATC
341735 TTAATATAACAC
1 TTAAT-TAACAC
341747 ATGTTAATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.52
21 11 0.41
22 2 0.07
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAATTAACACCTATTTAATC
Found at i:347089 original size:21 final size:21
Alignment explanation
Indices: 347039--347096 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
347029 AACAGTGCAA
**
347039 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAAAGAC
* *
347060 AATTTTACCGATACAAAAGAC
1 ACTTCTACCGATACAAAAGAC
* *
347081 TCTTCTACCGAAACAA
1 ACTTCTACCGATACAA
347097 GTCATGCATC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (21 bp):
ACTTCTACCGATACAAAAGAC
Found at i:347843 original size:36 final size:36
Alignment explanation
Indices: 347803--347873 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
347793 TTATCCCGAA
* *
347803 GGTCATGGTGCTCATTTTACTCCCTGTTGACCCAAT
1 GGTCATGATGCTCATTTTACTCCCTATTGACCCAAT
347839 GGTCATGATGCTCATTTTACTCCCTATTGACCCAA
1 GGTCATGATGCTCATTTTACTCCCTATTGACCCAA
347874 AAGTCATGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (36 bp):
GGTCATGATGCTCATTTTACTCCCTATTGACCCAAT
Found at i:347880 original size:36 final size:36
Alignment explanation
Indices: 347804--347881 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
347794 TATCCCGAAG
* * **
347804 GTCATGGTGCTCATTTTACTCCCTGTTGACCCAATG
1 GTCATGATGCTCATTTTACTCCCTATTGACCCAAAA
347840 GTCATGATGCTCATTTTACTCCCTATTGACCCAAAA
1 GTCATGATGCTCATTTTACTCCCTATTGACCCAAAA
347876 GTCATG
1 GTCATG
347882 CCTATTACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.35
Consensus pattern (36 bp):
GTCATGATGCTCATTTTACTCCCTATTGACCCAAAA
Found at i:352974 original size:8 final size:8
Alignment explanation
Indices: 352961--352986 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
352951 ATATCAGCTC
352961 TTATTATT
1 TTATTATT
352969 TTATTATT
1 TTATTATT
352977 TTATTATT
1 TTATTATT
352985 TT
1 TT
352987 GAATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTATT
Found at i:354670 original size:60 final size:60
Alignment explanation
Indices: 354554--354752 Score: 195
Period size: 60 Copynumber: 3.3 Consensus size: 60
354544 AATATTTAAT
* * * * * *
354554 AAATTTAGGTACCAAATTGAATCTAAATAAAAGCTTAGGGTACCAAATCAGGAAAAAATGTC
1 AAATTCAGGTACCAAATTGAGTC-AAAAAAAAGTTTA-GGTACTAAATTAGGAAAAAATGTC
* * * *
354616 AAGTTCAGGTACCAAATTGGGTCCAAAAAAAGTTTAGGTACTAAATTAGGAAAAAGTGTC
1 AAATTCAGGTACCAAATTGAGTCAAAAAAAAGTTTAGGTACTAAATTAGGAAAAAATGTC
* ** * * *
354676 AAATTTAAATATCAAATTGAGTCAAAAAAAAGTTTAGATACTAAATTA--AAAATATATATC
1 AAATTCAGGTACCAAATTGAGTCAAAAAAAAGTTTAGGTACTAAATTAGGAAAA-A-ATGTC
*
354736 AAATTCAGATACCAAAT
1 AAATTCAGGTACCAAAT
354753 ATTGTATTAA
Statistics
Matches: 112, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
58 4 0.04
59 1 0.01
60 78 0.70
61 10 0.09
62 19 0.17
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (60 bp):
AAATTCAGGTACCAAATTGAGTCAAAAAAAAGTTTAGGTACTAAATTAGGAAAAAATGTC
Found at i:355387 original size:14 final size:14
Alignment explanation
Indices: 355370--355396 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
355360 CATTTAGATA
355370 TGCACATTCATTTG
1 TGCACATTCATTTG
355384 TGCACATTCATTT
1 TGCACATTCATTT
355397 TGAAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (14 bp):
TGCACATTCATTTG
Found at i:355417 original size:9 final size:9
Alignment explanation
Indices: 355403--355490 Score: 67
Period size: 9 Copynumber: 10.1 Consensus size: 9
355393 ATTTTGAAAT
355403 TATAAAAAA
1 TATAAAAAA
355412 TATAAAAAA
1 TATAAAAAA
* *
355421 TTTATAAAA
1 TATAAAAAA
355430 TATAAAAAA
1 TATAAAAAA
*
355439 T-T-AAAAT
1 TATAAAAAA
**
355446 TATTTAAAA
1 TATAAAAAA
355455 T-TAAAAAA
1 TATAAAAAA
* *
355463 TTATTAAAAT
1 -TATAAAAAA
355473 TAT-AAAAA
1 TATAAAAAA
*
355481 TATTAAAAA
1 TATAAAAAA
355490 T
1 T
355491 GTTATAAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
7 5 0.08
8 14 0.23
9 38 0.61
10 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TATAAAAAA
Found at i:355426 original size:11 final size:10
Alignment explanation
Indices: 355399--355518 Score: 66
Period size: 9 Copynumber: 13.1 Consensus size: 10
355389 ATTCATTTTG
355399 AAATTATAAA
1 AAATTATAAA
355409 AAA-TATAAA
1 AAATTATAAA
*
355418 AAATT-TATA
1 AAATTATAAA
355427 AAA-TATAAA
1 AAATTATAAA
355436 AAA-T-T--A
1 AAATTATAAA
**
355442 AAATTATTTA
1 AAATTATAAA
355452 AAA-T-TAAA
1 AAATTATAAA
*
355460 AAATTAT-TA
1 AAATTATAAA
355469 AAATTATAAA
1 AAATTATAAA
355479 AATATTA-AAA
1 AA-ATTATAAA
**
355489 ATGTTAT-AA
1 AAATTATAAA
* *
355498 AAATAATTAA
1 AAATTATAAA
*
355508 AACTTATAAA
1 AAATTATAAA
355518 A
1 A
355519 TAAAAAATCA
Statistics
Matches: 84, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
6 4 0.05
7 1 0.01
8 8 0.10
9 41 0.49
10 26 0.31
11 4 0.05
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (10 bp):
AAATTATAAA
Found at i:355427 original size:20 final size:18
Alignment explanation
Indices: 355408--355525 Score: 79
Period size: 18 Copynumber: 6.7 Consensus size: 18
355398 GAAATTATAA
355408 AAAATATAAAAAATTTAT
1 AAAATATAAAAAATTTAT
355426 AAAATATAAAAAA-TTA-
1 AAAATATAAAAAATTTAT
* ** *
355442 AAATTATTTAAAA-TTAA
1 AAAATATAAAAAATTTAT
*
355459 AAAAT-TATTAAAA-TTAT
1 AAAATATA-AAAAATTTAT
*
355476 AAAAATATTAAAAATGTTAT
1 -AAAATATAAAAAAT-TTAT
*
355496 AAAA-ATAATTAAAACTTAT
1 AAAATATAA--AAAATTTAT
355515 AAAATA-AAAAA
1 AAAATATAAAAA
355526 TCATAAAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
16 14 0.17
17 18 0.22
18 25 0.31
19 15 0.19
20 9 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (18 bp):
AAAATATAAAAAATTTAT
Found at i:355431 original size:18 final size:17
Alignment explanation
Indices: 355408--355525 Score: 82
Period size: 17 Copynumber: 6.7 Consensus size: 17
355398 GAAATTATAA
355408 AAAATATAAAAAATTTAT
1 AAAATATAAAAAA-TTAT
355426 AAAATATAAAAAATTA-
1 AAAATATAAAAAATTAT
* ** *
355442 AAATTATTTAAAATTAA
1 AAAATATAAAAAATTAT
*
355459 AAAAT-TATTAAAATTAT
1 AAAATATA-AAAAATTAT
*
355476 AAAAATATTAAAAATGTTAT
1 -AAAATA-TAAAAA-ATTAT
355496 AAAA-ATAATTAAAACTTAT
1 AAAATATAA--AAAA-TTAT
355515 AAAATA-AAAAA
1 AAAATATAAAAA
355526 TCATAAAAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
16 14 0.17
17 21 0.26
18 19 0.23
19 20 0.25
20 7 0.09
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (17 bp):
AAAATATAAAAAATTAT
Found at i:355433 original size:27 final size:25
Alignment explanation
Indices: 355403--355490 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 25
355393 ATTTTGAAAT
355403 TATAAAAAATATAAAAAATTTATAAAA
1 TATAAAAAAT-T-AAAAATTTATAAAA
*
355430 TATAAAAAATT-AAAATTATTTAAAA
1 TATAAAAAATTAAAAATT-TATAAAA
355455 T-TAAAAAATTATTAAAA-TTATAAAAA
1 TATAAAAAATTA--AAAATTTAT-AAAA
*
355481 TATTAAAAAT
1 TATAAAAAAT
355491 GTTATAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
24 15 0.29
25 9 0.17
26 7 0.13
27 21 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
TATAAAAAATTAAAAATTTATAAAA
Found at i:355815 original size:18 final size:18
Alignment explanation
Indices: 355792--355886 Score: 65
Period size: 18 Copynumber: 5.3 Consensus size: 18
355782 CGATTATCTC
355792 TTTTTTAAAATTTTAATA
1 TTTTTTAAAATTTTAATA
*
355810 TTTTTTATAATTTT-ATAA
1 TTTTTTAAAATTTTAAT-A
* *
355828 TTTTCT-AAATATTAATGAA
1 TTTTTTAAAATTTTAAT--A
* *
355847 TTTTTTAAAGTGTTAA-A
1 TTTTTTAAAATTTTAATA
*
355864 TTGTTTTACAATTTT--TA
1 TT-TTTTAAAATTTTAATA
355881 TTTTTT
1 TTTTTT
355887 TTTAATTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
16 4 0.07
17 13 0.21
18 30 0.49
19 7 0.11
20 7 0.11
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (18 bp):
TTTTTTAAAATTTTAATA
Found at i:357274 original size:6 final size:6
Alignment explanation
Indices: 357263--357292 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
357253 CCTAATCTCT
357263 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC
357293 AATCTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCCC
Found at i:358938 original size:27 final size:27
Alignment explanation
Indices: 358887--358940 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
358877 AGGGGATTGA
*
358887 TGATCTTATCGCACTATATGATATTTG
1 TGATCTTATCACACTATATGATATTTG
*
358914 TGATCTCTATCACACTA-ATGTTATTTG
1 TGATCT-TATCACACTATATGATATTTG
358941 GCAGACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (27 bp):
TGATCTTATCACACTATATGATATTTG
Found at i:360617 original size:26 final size:26
Alignment explanation
Indices: 360584--360650 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
360574 AAGTAATAAT
*
360584 AAAATAAATGATAGACTAAATACAGA
1 AAAATAAATGATAAACTAAATACAGA
**
360610 AAAATAAATGATAAACTAAATGTAGA
1 AAAATAAATGATAAACTAAATACAGA
*
360636 AAAATAAATGGTAAA
1 AAAATAAATGATAAA
360651 ATGTAAATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.63, C:0.04, G:0.12, T:0.21
Consensus pattern (26 bp):
AAAATAAATGATAAACTAAATACAGA
Found at i:362140 original size:7 final size:7
Alignment explanation
Indices: 362123--362156 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
362113 CTAAGTTTTA
362123 TTTTA-T
1 TTTTATT
362129 TTTTATT
1 TTTTATT
362136 TTTTATT
1 TTTTATT
362143 TTTATATT
1 TTT-TATT
362151 TTTTAT
1 TTTTAT
362157 ATACTTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 5 0.19
7 14 0.54
8 7 0.27
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTATT
Found at i:362141 original size:13 final size:14
Alignment explanation
Indices: 362123--362153 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
362113 CTAAGTTTTA
362123 TTTTATTTTTAT-T
1 TTTTATTTTTATAT
362136 TTTTATTTTTATAT
1 TTTTATTTTTATAT
362150 TTTT
1 TTTT
362154 TATATACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTATTTTTATAT
Found at i:373576 original size:19 final size:19
Alignment explanation
Indices: 373531--373576 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
373521 AGAACGGTGC
* *
373531 AGACTTCTATCGATACAAG
1 AGACTTTTAACGATACAAG
* *
373550 TGAGTTTTAACGATACAAG
1 AGACTTTTAACGATACAAG
373569 AGACTTTT
1 AGACTTTT
373577 CTATCGAAAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (19 bp):
AGACTTTTAACGATACAAG
Found at i:382554 original size:24 final size:24
Alignment explanation
Indices: 382522--382588 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
382512 ATCGTATACT
*
382522 AGTTAACCATTCTGGGCTCATAAG
1 AGTTAACCATTCTAGGCTCATAAG
*
382546 AGTTAACCATTCTAGGCTCGTAAG
1 AGTTAACCATTCTAGGCTCATAAG
*
382570 AGCTAACCATTCTAGGCTC
1 AGTTAACCATTCTAGGCTC
382589 GTGTAAGCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (24 bp):
AGTTAACCATTCTAGGCTCATAAG
Found at i:386145 original size:13 final size:14
Alignment explanation
Indices: 386127--386156 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
386117 GTCAATGCAA
386127 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
386140 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
386154 TCA
1 TCA
386157 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:386736 original size:31 final size:31
Alignment explanation
Indices: 386698--386760 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
386688 TATCTCTAGA
386698 CTACGAATACTACCCTTCATCATTCCTCTTG
1 CTACGAATACTACCCTTCATCATTCCTCTTG
386729 CTACGAATACTACCCTTCATCATTCCTCTTG
1 CTACGAATACTACCCTTCATCATTCCTCTTG
386760 C
1 C
386761 CCAGCACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.37, G:0.06, T:0.35
Consensus pattern (31 bp):
CTACGAATACTACCCTTCATCATTCCTCTTG
Found at i:398235 original size:16 final size:16
Alignment explanation
Indices: 398214--398245 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
398204 ATAATGTGAA
398214 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
398230 AATAAAGGTAAAATGT
1 AATAAAGATAAAATGT
398246 GATCCACATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:399084 original size:26 final size:26
Alignment explanation
Indices: 399041--399095 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
399031 AATTCTAGGC
399041 ACAATTCTAGACACGTTCATGCAGCG
1 ACAATTCTAGACACGTTCATGCAGCG
*
399067 ACAATTCT-GTACATGTTCATGCAGCG
1 ACAATTCTAG-ACACGTTCATGCAGCG
399093 ACA
1 ACA
399096 TTCCTGGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (26 bp):
ACAATTCTAGACACGTTCATGCAGCG
Found at i:403059 original size:59 final size:59
Alignment explanation
Indices: 402907--403081 Score: 235
Period size: 59 Copynumber: 3.0 Consensus size: 59
402897 TTCAACTGTA
* * * * *
402907 AAATTCATATTTTTGGAAAGTTCAAGGGTTAAATTTGAAATTTGGGAAAATTTAGGGTT
1 AAATTCAAATTTTTGGAAAATTTAAGGGTTAAATTTGAATTTTTGGAAAATTTAGGGTT
*
402966 AAATTCAAATTTTTGGAAAGTTTAAGGGTTAAATTTGAATTTTTGGAAAATTTAGGGTT
1 AAATTCAAATTTTTGGAAAATTTAAGGGTTAAATTTGAATTTTTGGAAAATTTAGGGTT
** * * *
403025 AAATTTGAATTTTTGGAAAAATTT-GGGGTCAAATTTGAATTTTTGAAAAATTTAGGG
1 AAATTCAAATTTTTGG-AAAATTTAAGGGTTAAATTTGAATTTTTGGAAAATTTAGGG
403082 GTCAAAACAT
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
59 99 0.94
60 6 0.06
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (59 bp):
AAATTCAAATTTTTGGAAAATTTAAGGGTTAAATTTGAATTTTTGGAAAATTTAGGGTT
Found at i:403087 original size:30 final size:29
Alignment explanation
Indices: 402915--403081 Score: 217
Period size: 30 Copynumber: 5.7 Consensus size: 29
402905 TAAAATTCAT
* *
402915 ATTTTTGGAAAGTTCAAGGGTTAAATTTGA
1 ATTTTTGGAAAATT-TAGGGTTAAATTTGA
* * **
402945 AATTTGGGAAAATTTAGGGTTAAATTCAA
1 ATTTTTGGAAAATTTAGGGTTAAATTTGA
*
402974 ATTTTTGGAAAGTTTAAGGGTTAAATTTGA
1 ATTTTTGGAAAATTT-AGGGTTAAATTTGA
403004 ATTTTTGGAAAATTTAGGGTTAAATTTGA
1 ATTTTTGGAAAATTTAGGGTTAAATTTGA
* *
403033 ATTTTTGGAAAAATTTGGGGTCAAATTTGA
1 ATTTTTGG-AAAATTTAGGGTTAAATTTGA
*
403063 ATTTTTGAAAAATTTAGGG
1 ATTTTTGGAAAATTTAGGG
403082 GTCAAAACAT
Statistics
Matches: 119, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
29 56 0.47
30 63 0.53
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (29 bp):
ATTTTTGGAAAATTTAGGGTTAAATTTGA
Found at i:404101 original size:13 final size:14
Alignment explanation
Indices: 404085--404132 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
404075 ATATTTGGGC
*
404085 TTTATTTTTGTT-T
1 TTTATTTTTATTAT
*
404098 TTTAATTTTATTAT
1 TTTATTTTTATTAT
404112 TTTATTATTTATTAT
1 TTTATT-TTTATTAT
404127 ATTTAT
1 -TTTAT
404133 AAGATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 10 0.34
14 6 0.21
15 8 0.28
16 5 0.17
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTATTTTTATTAT
Found at i:404840 original size:40 final size:40
Alignment explanation
Indices: 404790--404990 Score: 124
Period size: 39 Copynumber: 5.1 Consensus size: 40
404780 ATTGGATTAT
* * * * *
404790 TTCATTCTGCCCTGTTGTCGGGGTAGGAGATCTGATGGTC
1 TTCAATCTGCCCTATAGTCAGGGTAAGAGATCTGATGGTC
* * * *
404830 TTCAATCTGCCCTCTAGTTAGGGTAAAAGAT-TGTATTG-C
1 TTCAATCTGCCCTATAGTCAGGGTAAGAGATCTG-ATGGTC
* * * *
404869 TTCAATCTGCCCTATGGTCTGGGTAAGAGATCGGATGATC
1 TTCAATCTGCCCTATAGTCAGGGTAAGAGATCTGATGGTC
* * * * * *
404909 TTCAATCTGCCTTTTGGTTAGGGTAAAAGAT-TGGATTG-C
1 TTCAATCTGCCCTATAGTCAGGGTAAGAGATCT-GATGGTC
* * ** *
404948 TTCAATCTGCCCCATGGTTGGGGTAAAAGAT-TGAATGGTC
1 TTCAATCTGCCCTATAGTCAGGGTAAGAGATCTG-ATGGTC
404988 TTC
1 TTC
404991 GCTCCATTTT
Statistics
Matches: 126, Mismatches: 29, Indels: 12
0.75 0.17 0.07
Matches are distributed among these distances:
38 1 0.01
39 63 0.50
40 62 0.49
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (40 bp):
TTCAATCTGCCCTATAGTCAGGGTAAGAGATCTGATGGTC
Found at i:404880 original size:39 final size:39
Alignment explanation
Indices: 404829--404980 Score: 175
Period size: 39 Copynumber: 3.9 Consensus size: 39
404819 ATCTGATGGT
* *
404829 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGTATTG
1 CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTG
* * *
404868 CTTCAATCTGCCCTATGGTCT-GGGTAAGAGATCGGA-TG
1 CTTCAATCTGCCCTCTGGT-TAGGGTAAAAGATTGGATTG
* *
404906 ATCTTCAATCTGCCTTTTGGTTAGGGTAAAAGATTGGATTG
1 --CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTG
*
404947 CTTCAATCTGCCC-CATGGTTGGGGTAAAAGATTG
1 CTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTG
404981 AATGGTCTTC
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
38 2 0.02
39 60 0.63
40 31 0.33
41 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (39 bp):
CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTG
Found at i:404881 original size:79 final size:79
Alignment explanation
Indices: 404771--404978 Score: 263
Period size: 79 Copynumber: 2.6 Consensus size: 79
404761 ATAGCTTTAG
* ** * * * * * *
404771 GGGTAAAATATTGGATTATTTCATTCTGCCCTGTTGTCGGGGTAGGAGATCTGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGGATGATCTTCAAT
404836 CTGCCCTCTAGTTA
66 CTGCCCTCTAGTTA
* *
404850 GGGTAAAAGATTGTATTGCTTCAATCTGCCCTATGGTCTGGGTAAGAGATCGGATGATCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGGATGATCTTCAAT
* * *
404915 CTGCCTTTTGGTTA
66 CTGCCCTCTAGTTA
* * *
404929 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTGGGGTAAAAGAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGAT
404979 TGAATGGTCT
Statistics
Matches: 110, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 110 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.34
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGGATGATCTTCAAT
CTGCCCTCTAGTTA
Found at i:405172 original size:50 final size:50
Alignment explanation
Indices: 405032--405173 Score: 162
Period size: 50 Copynumber: 2.8 Consensus size: 50
405022 GTCCTTGCAA
* * * *
405032 CTTCAATTTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGTCATTACGG
* * *
405082 CTTTAATCTGCCCCTCTATAGCTTTAGGTGTATGACATTTGTCATTACGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGTCATTACGG
** *
405132 CTTCAAT-TCGTTCCTCTACAGCTTTAGGGGTA-GAGGATTTGT
1 CTTCAATCT-GCCCCTCTACAGCTTTAGGTGTATGA-GATTTGT
405174 TGTTCTATCG
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 3 0.04
50 74 0.96
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (50 bp):
CTTCAATCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGTCATTACGG
Found at i:416792 original size:30 final size:31
Alignment explanation
Indices: 416740--416911 Score: 105
Period size: 30 Copynumber: 5.8 Consensus size: 31
416730 CAAATTTGAT
* *
416740 TTTTTG-AAACTTCAGGGTTTAAA-TCAAAAA
1 TTTTTGAAAATTTAAGGG-TTAAATTCAAAAA
*
416770 TTTTTGAAAATTTAAGGGTTAAATT--AGAA
1 TTTTTGAAAATTTAAGGGTTAAATTCAAAAA
* * *
416799 TTTTTGCAAAATTTAGGGGTCAAATTC--GAA
1 TTTTTG-AAAATTTAAGGGTTAAATTCAAAAA
* *
416829 TTTTGGAAAATTTGAGGGTTAAATTC--AAA
1 TTTTTGAAAATTTAAGGGTTAAATTCAAAAA
* * * **
416858 TTTTT-AGAGTTTAGGGGTTAAATT--TGAA
1 TTTTTGAAAATTTAAGGGTTAAATTCAAAAA
* *
416886 TTTTTGGAAAGTTTAGGGGTTAAATT
1 TTTTT-GAAAATTTAAGGGTTAAATT
416912 TGAATTTTTG
Statistics
Matches: 118, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
28 22 0.19
29 32 0.27
30 54 0.46
31 10 0.08
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (31 bp):
TTTTTGAAAATTTAAGGGTTAAATTCAAAAA
Found at i:416912 original size:30 final size:30
Alignment explanation
Indices: 416768--416990 Score: 276
Period size: 30 Copynumber: 7.6 Consensus size: 30
416758 TTAAATCAAA
* *
416768 AATTTTT-GAAAATTTAAGGGTTAAATTAG
1 AATTTTTGGAAAATTTAGGGGTTAAATTTG
* * *
416797 AATTTTTGCAAAATTTAGGGGTCAAATTCG
1 AATTTTTGGAAAATTTAGGGGTTAAATTTG
**
416827 AA-TTTTGGAAAATTT-GAGGGTTAAATTCA
1 AATTTTTGGAAAATTTAG-GGGTTAAATTTG
* *
416856 AATTTTT--AGAGTTTAGGGGTTAAATTTG
1 AATTTTTGGAAAATTTAGGGGTTAAATTTG
*
416884 AATTTTTGGAAAGTTTAGGGGTTAAATTTG
1 AATTTTTGGAAAATTTAGGGGTTAAATTTG
* *
416914 AATTTTTGGAAATTTTAGGGGTTAATTTTG
1 AATTTTTGGAAAATTTAGGGGTTAAATTTG
*
416944 AATTTTTGGAAAATTTGGGGGTTAAATTTG
1 AATTTTTGGAAAATTTAGGGGTTAAATTTG
*
416974 AATTTTTAGAAAATTTA
1 AATTTTTGGAAAATTTA
416991 AAGGTCAAAA
Statistics
Matches: 169, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
28 23 0.14
29 32 0.19
30 114 0.67
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.43
Consensus pattern (30 bp):
AATTTTTGGAAAATTTAGGGGTTAAATTTG
Found at i:417961 original size:13 final size:14
Alignment explanation
Indices: 417945--417986 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
417935 ATATTTGGGC
*
417945 TTTATTTTTGTT-T
1 TTTATTTTTATTAT
*
417958 TTTAATTTTATTAT
1 TTTATTTTTATTAT
417972 TTTATTATTTATTAT
1 TTTATT-TTTATTAT
417987 ACTTATAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 10 0.42
14 6 0.25
15 8 0.33
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTATTTTTATTAT
Found at i:418005 original size:3 final size:3
Alignment explanation
Indices: 417999--418036 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
417989 TTATAAGATA
417999 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
418037 AACAAAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:423603 original size:19 final size:18
Alignment explanation
Indices: 423524--423607 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 18
423514 TCCTTGCGTT
*
423524 CCAATATTGCTCATACGAG
1 CCAATA-TGCTCAAACGAG
* * *
423543 CCAGTATGCTTAAACGAA
1 CCAATATGCTCAAACGAG
* * * *
423561 CTAGTATGCTCAAATGAT
1 CCAATATGCTCAAACGAG
423579 CCAATATGCTCAAAACGAG
1 CCAATATGCTC-AAACGAG
423598 CCAATATGCT
1 CCAATATGCT
423608 ATTCCTTCCG
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
18 32 0.62
19 20 0.38
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (18 bp):
CCAATATGCTCAAACGAG
Done.