Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015119.1 Kokia drynarioides strain JFW-HI SEQ_130163, 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: 310394
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 528 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1078 original size:21 final size:21
Alignment explanation
Indices: 1052--1095 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1042 TAGTATTTTG
1052 ATCCGTAGAAATCCCTAAATT
1 ATCCGTAGAAATCCCTAAATT
1073 ATCCGTAGAAATCCCTAAATT
1 ATCCGTAGAAATCCCTAAATT
1094 AT
1 AT
1096 GCTAATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (21 bp):
ATCCGTAGAAATCCCTAAATT
Found at i:1881 original size:13 final size:13
Alignment explanation
Indices: 1860--1893 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1850 TAAACAATAT
1860 AATAATAATCCTA
1 AATAATAATCCTA
*
1873 AATATTAATCCTA
1 AATAATAATCCTA
*
1886 AAAAATAA
1 AATAATAA
1894 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:2441 original size:37 final size:37
Alignment explanation
Indices: 2391--2477 Score: 138
Period size: 37 Copynumber: 2.4 Consensus size: 37
2381 GGGTGAATGA
*
2391 CTGCTTTAAACAAATAACAGAGAATGCATCACTGTGG
1 CTGCTTTAAACAAATAACAGAGAATGAATCACTGTGG
* *
2428 CTGCTTTAAACAAATAACAGAGAATGAATGATTGTGG
1 CTGCTTTAAACAAATAACAGAGAATGAATCACTGTGG
*
2465 CTGCTTAAAACAA
1 CTGCTTTAAACAA
2478 TTAAAAACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (37 bp):
CTGCTTTAAACAAATAACAGAGAATGAATCACTGTGG
Found at i:3604 original size:22 final size:21
Alignment explanation
Indices: 3569--3610 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3559 TATTTAAAAT
3569 ATATATTTATATTAATATTTAC
1 ATATATTTATATTAA-ATTTAC
3591 ATAT-TTTATAATTAAATTTA
1 ATATATTTAT-ATTAAATTTA
3611 AATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATATTTATATTAAATTTAC
Found at i:11102 original size:18 final size:18
Alignment explanation
Indices: 11056--11103 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
11046 CTTTTTTTTT
11056 CTTCTT-TTTCTTTC--C
1 CTTCTTCTTTCTTTCTTC
*
11071 CTTCTTC--TCCTTCTTC
1 CTTCTTCTTTCTTTCTTC
11087 CTTCTTCTTTCTTTCTT
1 CTTCTTCTTTCTTTCTT
11104 TATTTCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 8 0.31
18 7 0.27
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
CTTCTTCTTTCTTTCTTC
Found at i:11118 original size:21 final size:20
Alignment explanation
Indices: 11089--11133 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
11079 CCTTCTTCCT
11089 TCTTCTTTCTTTCTTTATTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
11110 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
11130 -CTTC
1 TCTTC
11134 AATTTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:22554 original size:29 final size:28
Alignment explanation
Indices: 22501--22556 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
22491 ATTAAAAATC
* *
22501 AATAAAAGTTAAAAAATTATTAAATTTT
1 AATAAAAATTAAAAAATTATAAAATTTT
22529 AATAAAAATATAAAAATATT-TAAAATTT
1 AATAAAAAT-TAAAAA-ATTATAAAATTT
22557 ATCAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.33
29 13 0.54
30 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
AATAAAAATTAAAAAATTATAAAATTTT
Found at i:22872 original size:19 final size:19
Alignment explanation
Indices: 22830--22872 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
22820 ATTTCTATAT
** *
22830 ATTTTATAATTTTTTACGA
1 ATTTTATAAAATTTTACAA
*
22849 CTTTTATAAAATTTTACAA
1 ATTTTATAAAATTTTACAA
22868 ATTTT
1 ATTTT
22873 TTTATGATTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTATAAAATTTTACAA
Found at i:22910 original size:28 final size:27
Alignment explanation
Indices: 22870--22943 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 27
22860 TTTTACAAAT
* * *
22870 TTTTTTATGATTTTTAACAATTTTTATA
1 TTTTTTATAATTTTAAACAAATTTTA-A
* *
22898 TTTTTTCTAATTTTAAATAAATTTTAA
1 TTTTTTATAATTTTAAACAAATTTTAA
*
22925 -TTTTTATATTTTTACAACA
1 TTTTTTATAATTTTA-AACA
22944 TTATATAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
26 12 0.32
27 4 0.11
28 21 0.57
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (27 bp):
TTTTTTATAATTTTAAACAAATTTTAA
Found at i:23212 original size:24 final size:24
Alignment explanation
Indices: 23176--23222 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
23166 GAGTGTAAAA
*
23176 AAAAAAAACTTAATTACTTATTTTT
1 AAAAAAAACTTAATAACTT-TTTTT
23201 AAAAAAAA-TTAATAACTTTTTT
1 AAAAAAAACTTAATAACTTTTTT
23223 CACCCTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 9 0.43
25 8 0.38
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAAAACTTAATAACTTTTTTT
Found at i:28913 original size:35 final size:35
Alignment explanation
Indices: 28867--28941 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
28857 AACTGTCTTG
28867 GGGTTAGCAATCATGACTGCCACATTCGCTTGAAT
1 GGGTTAGCAATCATGACTGCCACATTCGCTTGAAT
28902 GGGTTAGCAATCATGACTGCCACATTCGCTTGAAT
1 GGGTTAGCAATCATGACTGCCACATTCGCTTGAAT
*
28937 AGGTT
1 GGGTT
28942 GACCACCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (35 bp):
GGGTTAGCAATCATGACTGCCACATTCGCTTGAAT
Found at i:33856 original size:96 final size:96
Alignment explanation
Indices: 33677--33864 Score: 229
Period size: 96 Copynumber: 2.0 Consensus size: 96
33667 GCGAAAAAGA
* ** * *
33677 TATTTGATTATCTCAATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATC
1 TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACC
*
33742 GAAGATAAGGAAACATTGCCTCGATTTAGGG
66 GAAGATAAAGAAACATTGCCTCGATTTAGGG
* * *
33773 TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAAC
1 TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAA-
* *
33837 CCGAA-ATGAAAG-AATATTGCCTTGATTT
64 CCGAAGAT-AAAGAAACATTGCCTCGATTT
33865 TAAAGTTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 1 0.01
96 70 0.90
97 7 0.09
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (96 bp):
TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACC
GAAGATAAAGAAACATTGCCTCGATTTAGGG
Found at i:34143 original size:28 final size:29
Alignment explanation
Indices: 34092--34147 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
34082 AGACTTTGCG
*
34092 GATTCCCGGGGGCAAAAATGATAATTTTA
1 GATTCCCGGGGGCAAAAACGATAATTTTA
* *
34121 GATTCTCGGGGGC-GAAACGATAATTTT
1 GATTCCCGGGGGCAAAAACGATAATTTT
34148 GGGAAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (29 bp):
GATTCCCGGGGGCAAAAACGATAATTTTA
Found at i:34206 original size:59 final size:58
Alignment explanation
Indices: 34155--34475 Score: 412
Period size: 59 Copynumber: 5.4 Consensus size: 58
34145 TTTGGGAAAA
* *
34155 TTCGAGGTCAAAAATGGGATTTTTGAAAGTTTGGTGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTTGG-GGTAAAAATAGAATTTTTGAAAGT
* * * * * *
34214 TTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGGGTGTAAAAATTGAATTTTTGAAATT
1 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTTGGG-GTAAAAATAGAATTTTTGAAAGT
* * * *
34273 TTTGGTGTTTAAAATGGGATTTTTTG-AAGTTCGAGGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGA-TTTTTGAAAGTTTG-GGGTAAAAATAGAATTTTTGAAAGT
*
34332 TTCGGGGTTAAAAATGGGATTTTT-AGAAGTTTAGGGGTAAAAATAGAAATTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGA-AAGTTT-GGGGTAAAAATAGAATTTTTGAAAGT
* *
34391 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGTTAAAAATTGAAATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTTGGGG-TAAAAATAG-AATTTTTGAAAGT
*
34451 TTCGGGGTTAAAAATGGAATTTTTG
1 TTCGGGGTTAAAAATGGGATTTTTG
34476 GACAATTTAG
Statistics
Matches: 231, Mismatches: 22, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
58 10 0.04
59 176 0.76
60 45 0.19
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.38
Consensus pattern (58 bp):
TTCGGGGTTAAAAATGGGATTTTTGAAAGTTTGGGGTAAAAATAGAATTTTTGAAAGT
Found at i:34226 original size:30 final size:30
Alignment explanation
Indices: 34164--34475 Score: 295
Period size: 30 Copynumber: 10.5 Consensus size: 30
34154 ATTCGAGGTC
*
34164 AAAAATGGGATTTTTGAAAG-TTTGGTGG-T
1 AAAAATGGAATTTTTGAAAGTTTTGG-GGTT
*
34193 AAAAATAGAATTTTTGAAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGAAAGTTTTGGGGTT
* *
34223 AAAAAT-GAGATTTTTGGAAG--TTCGGGTGT
1 AAAAATGGA-ATTTTTGAAAGTTTTGGGGT-T
* * *
34252 AAAAATTGAATTTTTGAAATTTTTGGTGTT
1 AAAAATGGAATTTTTGAAAGTTTTGGGGTT
* * *
34282 TAAAATGGGATTTTTTG-AAG-TTCGAGGG-T
1 AAAAAT-GGAATTTTTGAAAGTTTTG-GGGTT
* *
34311 AAAAATAGAATTTTTGAAAGTTTCGGGGTT
1 AAAAATGGAATTTTTGAAAGTTTTGGGGTT
* *
34341 AAAAATGGGATTTTT-AGAAGTTTAGGGG-T
1 AAAAATGGAATTTTTGA-AAGTTTTGGGGTT
* * *
34370 AAAAATAGAAATTTTGAAAGTTTCGGGGTT
1 AAAAATGGAATTTTTGAAAGTTTTGGGGTT
* *
34400 AAAAATGGGATTTTTGGAAG-TTTGGGGTT
1 AAAAATGGAATTTTTGAAAGTTTTGGGGTT
* *
34429 AAAAATTGAAATTTTTGAAAGTTTCGGGGTT
1 AAAAA-TGGAATTTTTGAAAGTTTTGGGGTT
34460 AAAAATGGAATTTTTG
1 AAAAATGGAATTTTTG
34476 GACAATTTAG
Statistics
Matches: 232, Mismatches: 34, Indels: 33
0.78 0.11 0.11
Matches are distributed among these distances:
28 14 0.06
29 90 0.39
30 102 0.44
31 26 0.11
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (30 bp):
AAAAATGGAATTTTTGAAAGTTTTGGGGTT
Found at i:35488 original size:3 final size:3
Alignment explanation
Indices: 35475--35542 Score: 82
Period size: 3 Copynumber: 21.0 Consensus size: 3
35465 ACTTTTCGAT
35475 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTGCA GTTA TTA TTTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT--A -TTA TTA -TTA TTA
*
35522 TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA
35543 ATGCTATCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
3 48 0.83
4 7 0.12
5 1 0.02
6 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:41985 original size:5 final size:5
Alignment explanation
Indices: 41975--42007 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
41965 TTTATAGAGT
41975 TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG TGG
1 TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG TGG
42008 GAATGGCCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (5 bp):
TGGAG
Found at i:47847 original size:16 final size:17
Alignment explanation
Indices: 47826--47858 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
47816 ACTTCATGCT
*
47826 ATTTTTTTAATT-TTTA
1 ATTTTTATAATTATTTA
47842 ATTTTTATAATTATTTA
1 ATTTTTATAATTATTTA
47859 GTGATGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTATAATTATTTA
Found at i:49659 original size:2 final size:2
Alignment explanation
Indices: 49652--49680 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49642 GTAAAAATGC
49652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49681 ATAACTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50835 original size:26 final size:26
Alignment explanation
Indices: 50774--50822 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
50764 GTTTGAGATG
*
50774 TAATATAATATTTTTATTTAAAATAA
1 TAATATAGTATTTTTATTTAAAATAA
50800 TAATATAGTATTTTTA-TTAAAAT
1 TAATATAGTATTTTTATTTAAAAT
50823 TTTAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TAATATAGTATTTTTATTTAAAATAA
Found at i:53123 original size:4 final size:4
Alignment explanation
Indices: 53114--53140 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53104 GGTTGTCCTA
53114 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
53141 TATTATGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:53260 original size:75 final size:75
Alignment explanation
Indices: 53130--53284 Score: 213
Period size: 75 Copynumber: 2.1 Consensus size: 75
53120 ACATACATAC
* * *
53130 ATACATACATATATTATGCTACATCACTACCTAAAAGCTCCACTAACAACCCTTCATGGCGGATT
1 ATACATACATATATAATGCTACATCACTACCTAAAAGCTCCACTAACAACCCTTCACGGAGGATT
53195 TTCCTAATAT
66 TTCCTAATAT
* * * * * *
53205 GTACATACATATATAATGCTACATCACTACC-AGAAAGCTTCGCTGATAACTCTTCACGGAGGAT
1 ATACATACATATATAATGCTACATCACTACCTA-AAAGCTCCACTAACAACCCTTCACGGAGGAT
53269 TTTCCTAATAT
65 TTTCCTAATAT
53280 ATACA
1 ATACA
53285 AATCTATTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
74 1 0.01
75 68 0.99
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (75 bp):
ATACATACATATATAATGCTACATCACTACCTAAAAGCTCCACTAACAACCCTTCACGGAGGATT
TTCCTAATAT
Found at i:59825 original size:17 final size:17
Alignment explanation
Indices: 59790--59831 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
59780 GTAAAAAATA
*
59790 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
59808 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
59825 GTTAAAG
1 GTTAAAG
59832 GTCAAGAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:59853 original size:34 final size:34
Alignment explanation
Indices: 59806--59881 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
59796 AGAATATGAA
* *
59806 AGGTTAAAGAAGATGGAAGGTTAAAGGTCAAGAG
1 AGGTTAAAAAAGATGGAAGGTTAAAAGTCAAGAG
* *
59840 ATGTTAAAAAAGATGGAAGGTTAAAAGTCAAGGG
1 AGGTTAAAAAAGATGGAAGGTTAAAAGTCAAGAG
59874 AGGTTAAA
1 AGGTTAAA
59882 GGTTGAACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.46, C:0.03, G:0.32, T:0.20
Consensus pattern (34 bp):
AGGTTAAAAAAGATGGAAGGTTAAAAGTCAAGAG
Found at i:61357 original size:17 final size:17
Alignment explanation
Indices: 61329--61369 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
61319 TCTCAATGCT
61329 TTCAAG-TATATTTTCA
1 TTCAAGATATATTTTCA
61345 TTCAAGATATATTTTCA
1 TTCAAGATATATTTTCA
61362 TTCAAGAT
1 TTCAAGAT
61370 CCTCACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (17 bp):
TTCAAGATATATTTTCA
Found at i:67263 original size:126 final size:126
Alignment explanation
Indices: 67038--67289 Score: 450
Period size: 126 Copynumber: 2.0 Consensus size: 126
67028 GGTTATTACA
*
67038 ATTAACACCTCGATAACCCACTAACAATATGCACAAAGATCACGTGCTTCATGTTGGTAATGCAA
1 ATTAACACCTCAATAACCCACTAACAATATGCACAAAGATCACGTGCTTCATGTTGGTAATGCAA
*
67103 AGTGGGCAATCCCATATTTGGTTTAGAAAAGGTTTCTAAGAGGGTTTAAATATAACCTTGC
66 AGTGGACAATCCCATATTTGGTTTAGAAAAGGTTTCTAAGAGGGTTTAAATATAACCTTGC
* * *
67164 ATTAACACCTCAATAACCCACTGACAATGTGCACAAAGATCATGTGCTTCATGTTGGTAATGCAA
1 ATTAACACCTCAATAACCCACTAACAATATGCACAAAGATCACGTGCTTCATGTTGGTAATGCAA
*
67229 AGTGGACAATCCCATATTTGGTTTAGAAAAGGTTTTTAAGAGGGTTTAAATATAACCTTGC
66 AGTGGACAATCCCATATTTGGTTTAGAAAAGGTTTCTAAGAGGGTTTAAATATAACCTTGC
67290 CTCTTGTATT
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 120 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (126 bp):
ATTAACACCTCAATAACCCACTAACAATATGCACAAAGATCACGTGCTTCATGTTGGTAATGCAA
AGTGGACAATCCCATATTTGGTTTAGAAAAGGTTTCTAAGAGGGTTTAAATATAACCTTGC
Found at i:91594 original size:24 final size:24
Alignment explanation
Indices: 91550--91604 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
91540 TTGTTAATTT
* *
91550 TTTTTAATTTTATGAAGTTTTTTTA
1 TTTTT-ATTTTATGAAATTTTTGTA
*
91575 TTTTTATTTT-TGAATATTTTTGTG
1 TTTTTATTTTATGAA-ATTTTTGTA
91599 TTTTTA
1 TTTTTA
91605 AATATTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 17 0.65
25 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (24 bp):
TTTTTATTTTATGAAATTTTTGTA
Found at i:96496 original size:22 final size:20
Alignment explanation
Indices: 96470--96533 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 20
96460 TTTGGTGCTT
96470 TTTTTTTATTGTTTTGATTG
1 TTTTTTTATTGTTTTGATTG
**
96490 ATATTTTTTGCTGTTTTTGAGTTG
1 -T-TTTTTTATTG-TTTTGA-TTG
96514 TTTTTTTATTGTTTTGATTG
1 TTTTTTTATTGTTTTGATTG
96534 CAATTTTCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 3 0.08
21 7 0.19
22 16 0.44
23 7 0.19
24 3 0.08
ACGTcount: A:0.11, C:0.02, G:0.17, T:0.70
Consensus pattern (20 bp):
TTTTTTTATTGTTTTGATTG
Found at i:96540 original size:21 final size:20
Alignment explanation
Indices: 96472--96540 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
96462 TGGTGCTTTT
96472 TTTTTATTGTTTTGATTGATA
1 TTTTTATTGTTTTGATTGA-A
**
96493 TTTTT-TGCTGTTTTTGAGTTGTT
1 TTTTTAT--TG-TTTTGA-TTGAA
96516 TTTTTATTGTTTTGATTGCAA
1 TTTTTATTGTTTTGATTG-AA
96537 TTTT
1 TTTT
96541 CGTGTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 4 0.11
21 15 0.39
22 4 0.11
23 11 0.29
24 4 0.11
ACGTcount: A:0.13, C:0.03, G:0.16, T:0.68
Consensus pattern (20 bp):
TTTTTATTGTTTTGATTGAA
Found at i:96596 original size:12 final size:12
Alignment explanation
Indices: 96543--96626 Score: 50
Period size: 12 Copynumber: 7.3 Consensus size: 12
96533 GCAATTTTCG
*
96543 TGTTATTTTTTT
1 TGTTATTTTTAT
*
96555 TGCTA--TTT-T
1 TGTTATTTTTAT
* *
96564 TGTTGTTTTTAA
1 TGTTATTTTTAT
*
96576 TGTT-GTTTTAT
1 TGTTATTTTTAT
*
96587 TGTTATTTTTGT
1 TGTTATTTTTAT
* * *
96599 TGCTGTTTTGAT
1 TGTTATTTTTAT
*
96611 TGTTATTTTTGT
1 TGTTATTTTTAT
96623 TGTT
1 TGTT
96627 TGGATATTAT
Statistics
Matches: 52, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 12 0.23
12 33 0.63
ACGTcount: A:0.10, C:0.02, G:0.17, T:0.71
Consensus pattern (12 bp):
TGTTATTTTTAT
Found at i:96612 original size:24 final size:23
Alignment explanation
Indices: 96543--96624 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
96533 GCAATTTTCG
* *
96543 TGTTATTTTTTTTGCT-ATTT-T
1 TGTTATTTTTGTTGCTGTTTTAT
* ** *
96564 TGTTGTTTTTAATGTTGTTTTAT
1 TGTTATTTTTGTTGCTGTTTTAT
96587 TGTTATTTTTGTTGCTGTTTTGAT
1 TGTTATTTTTGTTGCTGTTTT-AT
96611 TGTTATTTTTGTTG
1 TGTTATTTTTGTTG
96625 TTTGGATATT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 12 0.24
22 3 0.06
23 18 0.37
24 16 0.33
ACGTcount: A:0.10, C:0.02, G:0.17, T:0.71
Consensus pattern (23 bp):
TGTTATTTTTGTTGCTGTTTTAT
Found at i:96614 original size:44 final size:44
Alignment explanation
Indices: 96543--96627 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
96533 GCAATTTTCG
* *
96543 TGTTATTTTTTTTGCTATTTTTGTTGTT-TTTAATGTTGTTTTAT
1 TGTTATTTTTGTTGCTAGTTTTGTTGTTATTT-ATGTTGTTTTAT
*
96587 TGTTATTTTTGTTGCT-GTTTTGATTGTTATTTTTGTTGTTT
1 TGTTATTTTTGTTGCTAGTTTTG-TTGTTATTTATGTTGTTT
96628 GGATATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 5 0.14
44 28 0.78
45 3 0.08
ACGTcount: A:0.09, C:0.02, G:0.16, T:0.72
Consensus pattern (44 bp):
TGTTATTTTTGTTGCTAGTTTTGTTGTTATTTATGTTGTTTTAT
Found at i:96833 original size:49 final size:48
Alignment explanation
Indices: 96739--96834 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 48
96729 TATCTTAATA
* * * * *
96739 TAATTTTTTTAATGTATTTTAAATTTATTTATTTTTTAATGTTTGTTT
1 TAATGTTTTTAATGTATTTGAAATTTATATATTTTTCAATATTTGTTT
*
96787 TAATGTTTTTAAGTGTATTTGATATATTATATATTTTTCAA-ATTTGTT
1 TAATGTTTTTAA-TGTATTTGAAAT-TTATATATTTTTCAATATTTGTT
96835 ATATGTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 11 0.28
49 16 0.40
50 13 0.32
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.64
Consensus pattern (48 bp):
TAATGTTTTTAATGTATTTGAAATTTATATATTTTTCAATATTTGTTT
Found at i:106063 original size:23 final size:24
Alignment explanation
Indices: 106028--106077 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
106018 GCCTATTTTT
* *
106028 CTTTTTATCTTTTTTAAT-TATTA
1 CTTTTTATATTTTCTAATATATTA
*
106051 CTTTTTCTATTTTCTAATAATATTA
1 CTTTTTATATTTTCTAAT-ATATTA
106076 CT
1 CT
106078 AGTCAACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
25 7 0.32
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (24 bp):
CTTTTTATATTTTCTAATATATTA
Found at i:111495 original size:8 final size:8
Alignment explanation
Indices: 111475--111506 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
111465 TAAATAAGTT
111475 TTTTAATAA
1 TTTTAA-AA
111484 TTTTAAAA
1 TTTTAAAA
111492 TTTTAAAA
1 TTTTAAAA
111500 TTTTAAA
1 TTTTAAA
111507 TTAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.74
9 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTTAAAA
Found at i:112761 original size:24 final size:24
Alignment explanation
Indices: 112734--112780 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
112724 TTATTAAATA
* *
112734 TTAAAATAA-TAAAATATAAATATT
1 TTAAAAAAATTAAAA-AAAAATATT
112758 TTAAAAAAATTAAAAAAAAATAT
1 TTAAAAAAATTAAAAAAAAATAT
112781 GGGCGGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
TTAAAAAAATTAAAAAAAAATATT
Found at i:113452 original size:41 final size:41
Alignment explanation
Indices: 113395--113490 Score: 192
Period size: 41 Copynumber: 2.3 Consensus size: 41
113385 GCAAAGTAAA
113395 ATGAAGCAGAAAAGCTTTTCCCATGCCCCTAACGTCCACCC
1 ATGAAGCAGAAAAGCTTTTCCCATGCCCCTAACGTCCACCC
113436 ATGAAGCAGAAAAGCTTTTCCCATGCCCCTAACGTCCACCC
1 ATGAAGCAGAAAAGCTTTTCCCATGCCCCTAACGTCCACCC
113477 ATGAAGCAGAAAAG
1 ATGAAGCAGAAAAG
113491 GGAAAGCCGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.33, C:0.32, G:0.17, T:0.18
Consensus pattern (41 bp):
ATGAAGCAGAAAAGCTTTTCCCATGCCCCTAACGTCCACCC
Found at i:150997 original size:19 final size:19
Alignment explanation
Indices: 150970--151007 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
150960 AACTTTATCT
*
150970 TATCTTCTT-CCAATATTTC
1 TATCCTCTTACCAA-ATTTC
150989 TATCCTCTTACCAAATTTC
1 TATCCTCTTACCAAATTTC
151008 AAGCTCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (19 bp):
TATCCTCTTACCAAATTTC
Found at i:154132 original size:59 final size:58
Alignment explanation
Indices: 154061--154207 Score: 188
Period size: 59 Copynumber: 2.5 Consensus size: 58
154051 TTTTGGATAC
* * *
154061 TCGAGGG-CAAAATGGTAATTTTGTAAGTTTTAGGATCAAAAATGGAATTTTTGGAAGT
1 TCGAGGGTAAAAAT-GTAATTTTGGAAGTTTTAGGATCAAAAATGGAATTTTTAGAAGT
* * * * *
154119 TCGGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGATTTTTTAGAAGT
1 TCGAGGGTAAAAATGTAA-TTTTGGAAGTTTTAGGATCAAAAATGGAATTTTTAGAAGT
154178 TCGAGGGTAAAAATGTAATTTTTGGAAGTT
1 TCGAGGGTAAAAATGTAA-TTTTGGAAGTT
154208 CGTGGGTAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
58 10 0.13
59 68 0.87
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (58 bp):
TCGAGGGTAAAAATGTAATTTTGGAAGTTTTAGGATCAAAAATGGAATTTTTAGAAGT
Found at i:154222 original size:29 final size:29
Alignment explanation
Indices: 154098--154229 Score: 167
Period size: 29 Copynumber: 4.5 Consensus size: 29
154088 TTTTAGGATC
* *
154098 AAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGTAATTTTTGGAAGTTCGTGGGT
*
154127 AAAAATGTAATTTTTGGAAGTT-TTGGGGTT
1 AAAAATGTAATTTTTGGAAGTTCGT-GGG-T
* * * *
154157 AAAAATGGATTTTTTAGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGTGGGT
154186 AAAAATGTAATTTTTGGAAGTTCGTGGGT
1 AAAAATGTAATTTTTGGAAGTTCGTGGGT
*
154215 AAAAATGTACTTTTT
1 AAAAATGTAATTTTT
154230 AGACAGTTTA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
29 64 0.74
30 23 0.26
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.38
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTCGTGGGT
Found at i:154229 original size:59 final size:58
Alignment explanation
Indices: 154098--154237 Score: 185
Period size: 59 Copynumber: 2.4 Consensus size: 58
154088 TTTTAGGATC
* * *
154098 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGG-ATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTGTGGGGTT
154157 AAAAATGGATTTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTCGT-GGG-T
1 AAAAATGGA-TTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTT-GTGGGGTT
*
154215 AAAAATGTACTTTTTAGACAGTT
1 AAAAATGGA-TTTTTAGA-AGTT
154238 TAGGGACCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
58 18 0.25
59 54 0.74
60 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (58 bp):
AAAAATGGATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTGTGGGGTT
Found at i:155226 original size:12 final size:12
Alignment explanation
Indices: 155206--155253 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
155196 TTTTTTATTA
155206 TTATTATTAATG
1 TTATTATTAATG
* *
155218 TTTTTATTAATA
1 TTATTATTAATG
155230 TTATTATTAATG
1 TTATTATTAATG
*
155242 CTATTATTAATG
1 TTATTATTAATG
155254 ATGGGATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.58
Consensus pattern (12 bp):
TTATTATTAATG
Found at i:155236 original size:24 final size:24
Alignment explanation
Indices: 155195--155252 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
155185 CTTTCAATTT
*
155195 CTTTT-TTATTATTATTATTAATG
1 CTTTTATTAATATTATTATTAATG
*
155218 TTTTTATTAATATTATTATTAATG
1 CTTTTATTAATATTATTATTAATG
*
155242 CTATTATTAAT
1 CTTTTATTAAT
155253 GATGGGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (24 bp):
CTTTTATTAATATTATTATTAATG
Found at i:156014 original size:17 final size:18
Alignment explanation
Indices: 155989--156069 Score: 98
Period size: 17 Copynumber: 4.7 Consensus size: 18
155979 TAAATAGATT
*
155989 TAAACTTAAATTTATAA-
1 TAAATTTAAATTTATAAG
156006 TAAATTTAAATTT-TAAG
1 TAAATTTAAATTTATAAG
*
156023 TAAATTTAAACTTA-AAG
1 TAAATTTAAATTTATAAG
* *
156040 TAAATTTAATTTTA-AAA
1 TAAATTTAAATTTATAAG
156057 TAAATTTAAATTT
1 TAAATTTAAATTT
156070 TGTTGGGCCC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
16 3 0.05
17 53 0.95
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAATTTAAATTTATAAG
Found at i:156015 original size:6 final size:6
Alignment explanation
Indices: 155986--156069 Score: 61
Period size: 6 Copynumber: 14.7 Consensus size: 6
155976 ATTTAAATAG
* * *
155986 ATTTAA ACTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
156032 ACTTAA A-GTAA ATTTAA TTTTAA A-ATAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
156070 TGTTGGGCCC
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 42 0.71
7 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:156066 original size:23 final size:23
Alignment explanation
Indices: 155980--156069 Score: 65
Period size: 23 Copynumber: 3.7 Consensus size: 23
155970 ACTTTGATTT
* * *
155980 AAATAGATTTAAACTTAAATTTA
1 AAATAAATTTAAATTTAATTTTA
*
156003 TAATAAATTTAAATTTTAAGTAAATTTA
1 AAATAAATTTAAA-TTTAA-T---TTTA
* *
156031 AACTTAAA-GTAAATTTAATTTTA
1 AA-ATAAATTTAAATTTAATTTTA
156054 AAATAAATTTAAATTT
1 AAATAAATTTAAATTT
156070 TGTTGGGCCC
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
22 4 0.08
23 24 0.47
24 4 0.08
26 1 0.02
27 5 0.10
28 9 0.18
29 4 0.08
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (23 bp):
AAATAAATTTAAATTTAATTTTA
Found at i:158902 original size:15 final size:15
Alignment explanation
Indices: 158868--158901 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
158858 ATTCTTTTCA
158868 CTTTTGAAATTTATT
1 CTTTTGAAATTTATT
*
158883 CTTTTGAACTTTATT
1 CTTTTGAAATTTATT
158898 -TTTT
1 CTTTT
158902 TATTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (15 bp):
CTTTTGAAATTTATT
Found at i:164816 original size:18 final size:17
Alignment explanation
Indices: 164780--164814 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
164770 TAAAAGATGA
**
164780 TATTTTTTAAATTAATT
1 TATTTTTTAAAAGAATT
164797 TATTTTTTAAAAGAATT
1 TATTTTTTAAAAGAATT
164814 T
1 T
164815 TAATTTATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TATTTTTTAAAAGAATT
Found at i:165604 original size:16 final size:16
Alignment explanation
Indices: 165545--165608 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
165535 TATCGCTAAT
*
165545 ATTTTTGTTATTATT-
1 ATTTTTATTATTATTA
* *
165560 A-TTTGAATATTATATA
1 ATTTTTATTATTAT-TA
*
165576 ATTTTTGTTTTATTATTA
1 A-TTTT-TATTATTATTA
165594 ATTTTTATTATTATT
1 ATTTTTATTATTATT
165609 TTAGATGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
14 9 0.24
15 2 0.05
16 10 0.27
17 4 0.11
18 6 0.16
19 6 0.16
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (16 bp):
ATTTTTATTATTATTA
Found at i:165607 original size:19 final size:19
Alignment explanation
Indices: 165567--165608 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
165557 ATTATTTGAA
*
165567 TATTATATAATTTTTGTTT
1 TATTATATAATTTTTATTT
165586 TATTAT-TAATTTTTATTAT
1 TATTATATAATTTTTATT-T
165605 TATT
1 TATT
165609 TTAGATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TATTATATAATTTTTATTT
Found at i:166508 original size:25 final size:26
Alignment explanation
Indices: 166455--166508 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
166445 AATTTTCATC
* * *
166455 AAATGAAAAAGTGAGAATTACATTTA
1 AAATGAAAAAGTGAGAATCAAATTAA
*
166481 AAAT-AAAAAGTGTGAATCAAATTAA
1 AAATGAAAAAGTGAGAATCAAATTAA
166506 AAA
1 AAA
166509 AATTAAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (26 bp):
AAATGAAAAAGTGAGAATCAAATTAA
Found at i:167423 original size:29 final size:30
Alignment explanation
Indices: 167389--167512 Score: 98
Period size: 29 Copynumber: 4.2 Consensus size: 30
167379 AAAAAATATC
*
167389 AAGTTTAAGTACCAAATTGGGT-TAAAAAA
1 AAGTTTAAGTACCAAATTGAGTCTAAAAAA
* * *
167418 AAGTTTAGGTATCAAATTGAATCT-AAAAA
1 AAGTTTAAGTACCAAATTGAGTCTAAAAAA
* * *
167447 AAGCTTAGGTACCAAATT-AG--GAAAAATA
1 AAGTTTAAGTACCAAATTGAGTCTAAAAA-A
* *
167475 TCAAATTTAAGTACCAAATTGAGTCCAAAAAA
1 --AAGTTTAAGTACCAAATTGAGTCTAAAAAA
167507 AA-TTTA
1 AAGTTTA
167513 GTTATCAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
27 4 0.05
28 2 0.03
29 43 0.57
30 18 0.24
31 2 0.03
32 1 0.01
33 5 0.07
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTGAGTCTAAAAAA
Found at i:167505 original size:58 final size:58
Alignment explanation
Indices: 167430--167613 Score: 206
Period size: 59 Copynumber: 3.1 Consensus size: 58
167420 GTTTAGGTAT
* * * * *
167430 CAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAATATCAAATTTAAGTAC
1 CAAATTGAGTCCAAAAAAAGTTTAGGTATCAAATTAGAAAAAATATCAAA-TTAAGTAC
* * * *
167489 CAAATTGAGTCCAAAAAAAATTTAGTTATCAAATTAGAAAAAATATCAAGTCAAGTAC
1 CAAATTGAGTCCAAAAAAAGTTTAGGTATCAAATTAGAAAAAATATCAAATTAAGTAC
* * * *
167547 TAAATTGTGTCCAAAAAGAAGTTTAGGCATCAAATTAGTAAAAAATTAGCAAATTAAGATAC
1 CAAATTGAGTCCAAAAA-AAGTTTAGGTATCAAATTAG-AAAAAA-TATCAAATTAAG-TAC
167609 CAAAT
1 CAAAT
167614 ATTATATTAA
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
58 22 0.21
59 59 0.57
60 6 0.06
61 9 0.09
62 7 0.07
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (58 bp):
CAAATTGAGTCCAAAAAAAGTTTAGGTATCAAATTAGAAAAAATATCAAATTAAGTAC
Found at i:167505 original size:88 final size:89
Alignment explanation
Indices: 167329--167523 Score: 284
Period size: 88 Copynumber: 2.2 Consensus size: 89
167319 AATATTTAAT
* * ** * *
167329 AAATTTAGGTATAAAATTGAATTTAAAAAAATTTTAGGTATCAAATTAGGAAAAAATATCAAGTT
1 AAATTTAGGTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATATCAAATT
* *
167394 TAAGTACCAAATTGGGTTAAAAAA
66 TAAGTACCAAATTGAGTCAAAAAA
*
167418 AAGTTTAGGTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGG-AAAAATATCAAATT
1 AAATTTAGGTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATATCAAATT
*
167482 TAAGTACCAAATTGAGTCCAAAAA
66 TAAGTACCAAATTGAGTCAAAAAA
*
167506 AAATTTAGTTATCAAATT
1 AAATTTAGGTATCAAATT
167524 AGAAAAAATA
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
88 50 0.53
89 44 0.47
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (89 bp):
AAATTTAGGTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATATCAAATT
TAAGTACCAAATTGAGTCAAAAAA
Found at i:167505 original size:89 final size:88
Alignment explanation
Indices: 167329--167523 Score: 284
Period size: 89 Copynumber: 2.2 Consensus size: 88
167319 AATATTTAAT
* * ** * *
167329 AAATTTAGGTATAAAATTGAATTTAAAAAAATTTTAGGTATCAAATTAGGAAAAAATATCAAGTT
1 AAATTTAGGTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATATCAAATT
* *
167394 TAAGTACCAAATTGGGTTAAAAA
66 TAAGTACCAAATTGAGTCAAAAA
167417 AAAGTTTAGGTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGG-AAAAATATCAAAT
1 AAA-TTTAGGTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATATCAAAT
167481 TTAAGTACCAAATTGAGTCCAAAAA
65 TTAAGTACCAAATTGAGT-CAAAAA
*
167506 AAATTTAGTTATCAAATT
1 AAATTTAGGTATCAAATT
167524 AGAAAAAATA
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
88 46 0.48
89 50 0.52
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (88 bp):
AAATTTAGGTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAATATCAAATT
TAAGTACCAAATTGAGTCAAAAA
Found at i:170795 original size:39 final size:39
Alignment explanation
Indices: 170748--170825 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
170738 TTTATGTGAA
*
170748 AATAATCACATATATTTGCTCTCCATTTCTACTTATGAT
1 AATAATCACATATATTTGCTCACCATTTCTACTTATGAT
*
170787 AATAATCACGTATATTTGCTCACCATTTCTACTTATGAT
1 AATAATCACATATATTTGCTCACCATTTCTACTTATGAT
170826 GGCATATGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (39 bp):
AATAATCACATATATTTGCTCACCATTTCTACTTATGAT
Found at i:175483 original size:10 final size:9
Alignment explanation
Indices: 175442--175483 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
175432 TTTTCTATTA
175442 AAAAATCAT
1 AAAAATCAT
*
175451 AAAAATTAT
1 AAAAATCAT
175460 ATAAAATCAT
1 A-AAAATCAT
175470 -AAAATCTAT
1 AAAAATC-AT
175479 AAAAA
1 AAAAA
175484 AATATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 6 0.21
9 11 0.39
10 11 0.39
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAATCAT
Found at i:175484 original size:19 final size:20
Alignment explanation
Indices: 175435--175484 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
175425 ATTCATATTT
175435 TCTATTAAAAAATCATAAAAA
1 TCTA-TAAAAAATCATAAAAA
*
175456 T-TATATAAAATCAT-AAAA
1 TCTATAAAAAATCATAAAAA
175474 TCTATAAAAAA
1 TCTATAAAAAA
175485 ATATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 18 0.69
20 2 0.08
21 1 0.04
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (20 bp):
TCTATAAAAAATCATAAAAA
Found at i:175596 original size:27 final size:27
Alignment explanation
Indices: 175566--175624 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
175556 AAGATTTCTC
* *
175566 AAAAAGATAGAAAATTACAGAAATATA
1 AAAAAGATAGAAAATTACACAAAAATA
** *
175593 AAAATTATATAAAATTACACAAAAATA
1 AAAAAGATAGAAAATTACACAAAAATA
175620 AAAAA
1 AAAAA
175625 ATATTTACAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.20
Consensus pattern (27 bp):
AAAAAGATAGAAAATTACACAAAAATA
Found at i:175626 original size:46 final size:46
Alignment explanation
Indices: 175503--175619 Score: 130
Period size: 46 Copynumber: 2.6 Consensus size: 46
175493 AAAAATTGCG
* * *
175503 AAAATTATGAAAATTA-TC-AAAATATAGAAAATTACAGAAAAATT
1 AAAATTATTAAAATTACACAAAAATATAGAAAATTACAGAAAAATA
* * * * * *
175547 CAAATTATTAAGATTTCTCAAAAAGATAGAAAATTACAGAAATATA
1 AAAATTATTAAAATTACACAAAAATATAGAAAATTACAGAAAAATA
175593 AAAATTATATAAAATTACACAAAAATA
1 AAAATTAT-TAAAATTACACAAAAATA
175620 AAAAAATATT
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
44 12 0.21
45 2 0.03
46 30 0.52
47 14 0.24
ACGTcount: A:0.60, C:0.07, G:0.06, T:0.27
Consensus pattern (46 bp):
AAAATTATTAAAATTACACAAAAATATAGAAAATTACAGAAAAATA
Found at i:176132 original size:11 final size:11
Alignment explanation
Indices: 176105--176159 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
176095 TCTATAATTT
176105 TATAGTTTTTT-
1 TATA-TTTTTTA
176116 TA-ATTTTTTA
1 TATATTTTTTA
* *
176126 AATATTTCTTTG
1 TATATTT-TTTA
*
176138 TATAATTTTTA
1 TATATTTTTTA
176149 TATATTTTTTA
1 TATATTTTTTA
176160 CAATTTGTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 19 0.54
12 8 0.23
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (11 bp):
TATATTTTTTA
Found at i:176498 original size:25 final size:24
Alignment explanation
Indices: 176465--176511 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
176455 GGGGGAATTT
* *
176465 TTATTTTATTTGATATTAATATCA
1 TTATTTTATTTAATATAAATATCA
176489 TTATATTTATTTAATATAAATAT
1 TTAT-TTTATTTAATATAAATAT
176512 AAAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATTTTATTTAATATAAATATCA
Found at i:182197 original size:32 final size:31
Alignment explanation
Indices: 182145--182205 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
182135 ATAAAAAATG
*
182145 TATAAATTTATTAAATATTAAAACAATATAA
1 TATAAATTTATTAAAAATTAAAACAATATAA
* *
182176 TATAAATATTTTTAAAAATTAAAATAATAT
1 TATAAAT-TTATTAAAAATTAAAACAATAT
182206 GGACGAGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
TATAAATTTATTAAAAATTAAAACAATATAA
Found at i:183687 original size:28 final size:30
Alignment explanation
Indices: 183619--183688 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 30
183609 TTGCAATTTA
* *
183619 GACTTATTTGATTCTTTTTAATAGTACAGG
1 GACTAATTTGATTCTTTTTAATAATACAGG
* *
183649 GACTAAATTGATTC-TTTTAATAATA-GGG
1 GACTAATTTGATTCTTTTTAATAATACAGG
183677 GACTAATTTGAT
1 GACTAATTTGAT
183689 ACAATCCCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 13 0.37
29 10 0.29
30 12 0.34
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (30 bp):
GACTAATTTGATTCTTTTTAATAATACAGG
Found at i:184456 original size:18 final size:18
Alignment explanation
Indices: 184435--184481 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
184425 TTATAAAACA
184435 ATATTATATTAATTATAT
1 ATATTATATTAATTATAT
*
184453 ATATTAAATAATAATTATAT
1 ATATT--ATATTAATTATAT
184473 AT-TTATATT
1 ATATTATATT
184482 GTATTAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 5 0.20
19 2 0.08
20 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATATTAATTATAT
Found at i:184659 original size:26 final size:28
Alignment explanation
Indices: 184610--184661 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
184600 AATATTTATT
* *
184610 ATATTTACTTATGTTTTATTATAATAAA
1 ATATTTACTTATGATTTATGATAATAAA
184638 ATATTTA-TTAT-ATTTATGATAATA
1 ATATTTACTTATGATTTATGATAATA
184662 TTTTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 4 0.18
28 7 0.32
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (28 bp):
ATATTTACTTATGATTTATGATAATAAA
Found at i:186300 original size:27 final size:29
Alignment explanation
Indices: 186223--186301 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 29
186213 AGATAAAGCT
186223 AATTATAATTTTAATGTATTAA-AATTACAC
1 AATTAT-ATTTTAATGTATTAATAA-TACAC
*
186253 AATTATATTTTTAT-TATTTAATAA-A-AC
1 AATTATATTTTAATGTA-TTAATAATACAC
*
186280 ATTTATATTTTAATGTATTAAT
1 AATTATATTTTAATGTATTAAT
186302 GTTAAAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
27 19 0.44
28 5 0.12
29 11 0.26
30 8 0.19
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (29 bp):
AATTATATTTTAATGTATTAATAATACAC
Found at i:191124 original size:29 final size:29
Alignment explanation
Indices: 191092--191152 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
191082 TTTTTTAATA
191092 TTTTAATATTTAATATT-ATAGTTTTCTATT
1 TTTTAA-ATTTAATATTAAT-GTTTTCTATT
* *
191122 TTTTAAATTTAATTTTAATGTTTTTTATT
1 TTTTAAATTTAATATTAATGTTTTCTATT
191151 TT
1 TT
191153 AATTGTCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTAAATTTAATATTAATGTTTTCTATT
Found at i:194966 original size:15 final size:15
Alignment explanation
Indices: 194942--194973 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
194932 AATAAATAGC
*
194942 AAAAAGAGAAAAAAG
1 AAAAAAAGAAAAAAG
194957 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
194972 AA
1 AA
194974 TATTTACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:201008 original size:29 final size:31
Alignment explanation
Indices: 200932--201013 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 31
200922 TTTGAACCAC
*
200932 AATTAAAATTTCACAT-TCATAATT--ATATCA
1 AATTAAAA-TTCATATAT-ATAATTACATATCA
* *
200962 AATTAAAATTCATGTATATAATTACATATTA
1 AATTAAAATTCATATATATAATTACATATCA
200993 AATTAAAATT-A-ATATATAATT
1 AATTAAAATTCATATATATAATT
201014 TTAAAATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 20 0.44
30 10 0.22
31 15 0.33
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.41
Consensus pattern (31 bp):
AATTAAAATTCATATATATAATTACATATCA
Found at i:202756 original size:24 final size:24
Alignment explanation
Indices: 202711--202757 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
202701 ATTTATTACT
*
202711 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
202735 ATAATATATTT-GACATTGATTAG
1 ATAATATATTTAG-CATTGATTAG
202758 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:206593 original size:9 final size:9
Alignment explanation
Indices: 206575--206614 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
206565 CATCATCCAA
*
206575 AAAATCTTT
1 AAAATATTT
206584 AAAATATTT
1 AAAATATTT
* *
206593 AAAACATTA
1 AAAATATTT
206602 AAAATATTT
1 AAAATATTT
206611 AAAA
1 AAAA
206615 AAATCCAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATATTT
Found at i:207587 original size:18 final size:18
Alignment explanation
Indices: 207550--207587 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
207540 TCTGTATTTT
*
207550 AAAATAAATTGAAAATAG
1 AAAATAAATAGAAAATAG
207568 AAAATAAATAAGAAAA-AG
1 AAAATAAAT-AGAAAATAG
207586 AA
1 AA
207588 TATTTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAATAAATAGAAAATAG
Found at i:208741 original size:28 final size:27
Alignment explanation
Indices: 208700--208752 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
208690 TATTATTAGG
*
208700 TGGTGCTTACCTGACAGGCGAGCACCAA
1 TGGTGCCTACCTGACAGGCGA-CACCAA
*
208728 TGGTGCCTATCTGACAGGCGACACC
1 TGGTGCCTACCTGACAGGCGACACC
208753 TGATGCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (27 bp):
TGGTGCCTACCTGACAGGCGACACCAA
Found at i:212193 original size:19 final size:19
Alignment explanation
Indices: 212169--212220 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 19
212159 CTTTGAAATT
212169 TATTTTTCATTTGTATATA
1 TATTTTTCATTTGTATATA
212188 TATTTTTTTCATTTGTATATA
1 TA--TTTTTCATTTGTATATA
*
212209 TTTTTTTCATTT
1 TATTTTTCATTT
212221 AGAATTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.40
21 18 0.60
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (19 bp):
TATTTTTCATTTGTATATA
Found at i:212197 original size:21 final size:19
Alignment explanation
Indices: 212171--212220 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 19
212161 TTGAAATTTA
212171 TTTTTCATTTGTATATATATT
1 TTTTTCATTTG--TATATATT
212192 TTTTTCATTTGTATATATT
1 TTTTTCATTTGTATATATT
212211 TTTTTCATTT
1 TTTTTCATTT
212221 AGAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 18 0.62
21 11 0.38
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTTCATTTGTATATATT
Found at i:212588 original size:6 final size:7
Alignment explanation
Indices: 212532--212675 Score: 57
Period size: 7 Copynumber: 20.4 Consensus size: 7
212522 AATCACTTAA
*
212532 AAACCGT
1 AAACCTT
*
212539 AAACCCT
1 AAACCTT
* *
212546 AAATCAT
1 AAACCTT
*
212553 AAACCATA
1 AAACC-TT
212561 AAACCTTT
1 AAACC-TT
*
212569 AAATC-T
1 AAACCTT
212575 AAACCTT
1 AAACCTT
212582 AAA-CTT
1 AAACCTT
*
212588 AATATCC-A
1 AA-A-CCTT
*
212596 AAACCCT
1 AAACCTT
*
212603 AAACATT
1 AAACCTT
212610 AAACCTT
1 AAACCTT
*
212617 AAATC-T
1 AAACCTT
* *
212623 ACTACC-A
1 A-AACCTT
212630 AAACCTT
1 AAACCTT
**
212637 -AACCCC
1 AAACCTT
212643 ATAACCTT
1 A-AACCTT
212651 AAACCTT
1 AAACCTT
212658 AAACCTT
1 AAACCTT
212665 AAACCATT
1 AAACC-TT
212673 AAA
1 AAA
212676 AACCCTGAAC
Statistics
Matches: 101, Mismatches: 25, Indels: 21
0.69 0.17 0.14
Matches are distributed among these distances:
6 21 0.21
7 57 0.56
8 22 0.22
9 1 0.01
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (7 bp):
AAACCTT
Found at i:212600 original size:35 final size:34
Alignment explanation
Indices: 212538--212638 Score: 91
Period size: 35 Copynumber: 2.9 Consensus size: 34
212528 TTAAAAACCG
* *
212538 TAAACCCTAAATCATAA-ACCATAAAACCTTTAA-AT
1 TAAACCTTAAATC-TAATACC--AAAACCTTAAACAT
*
212573 CTAAACCTTAAA-CTTAATATCCAAAACCCTAAACAT
1 -TAAACCTTAAATC-TAATA-CCAAAACCTTAAACAT
*
212609 TAAACCTTAAATCTACTACCAAAACCTTAA
1 TAAACCTTAAATCTAATACCAAAACCTTAA
212639 CCCCATAACC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
34 11 0.20
35 28 0.51
36 14 0.25
37 2 0.04
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (34 bp):
TAAACCTTAAATCTAATACCAAAACCTTAAACAT
Found at i:212869 original size:26 final size:26
Alignment explanation
Indices: 212814--212889 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
212804 CTTAAACCTC
**
212814 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
212840 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
212866 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
212890 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:215549 original size:17 final size:18
Alignment explanation
Indices: 215526--215636 Score: 97
Period size: 17 Copynumber: 6.4 Consensus size: 18
215516 CTAAACCCAT
* *
215526 TTTAAATTTATTTTGAGA
1 TTTAAATTTATTTTAAAA
*
215544 -TTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAAA
* *
215561 TTTAAATTT-GTTTCAAA
1 TTTAAATTTATTTTAAAA
* *
215578 TTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAA
215595 TTTAAATTTATATTT-AAA
1 TTTAAATTTAT-TTTAAAA
* *
215613 TTTAAAATTATTCT-AAA
1 TTTAAATTTATTTTAAAA
215630 TTTAAAT
1 TTTAAAT
215637 AAATAAAAGT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
17 53 0.67
18 26 0.33
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:215564 original size:6 final size:6
Alignment explanation
Indices: 215544--215636 Score: 79
Period size: 6 Copynumber: 16.0 Consensus size: 6
215534 TATTTTGAGA
** *
215544 TTAAAT TTATTT TTAAAT TTAAAT TT--GT TTCAAAT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT
* * *
215590 TTAAGT TTAAAT TTATAT TTAAAT TTAAAA TT--AT TCTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT
215637 AAATAAAAGT
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
4 5 0.07
5 6 0.09
6 51 0.75
7 6 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:215583 original size:52 final size:52
Alignment explanation
Indices: 215526--215636 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 52
215516 CTAAACCCAT
* * * * *
215526 TTTAAATTTATTTTGAGATTAAATTTATTTTTAAATTTAAATTTGTT-TCAAA
1 TTTAAATTTAATTTAAGATTAAATTTATATTTAAATTTAAAATTATTCT-AAA
*
215578 TTTAAATTTAATTTAAGTTTAAATTTATATTTAAATTTAAAATTATTCTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATATTTAAATTTAAAATTATTCTAAA
215630 TTTAAAT
1 TTTAAAT
215637 AAATAAAAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 51 0.98
53 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATATTTAAATTTAAAATTATTCTAAA
Found at i:215585 original size:23 final size:23
Alignment explanation
Indices: 215555--215616 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
215545 TAAATTTATT
215555 TTTAAATTTAAATTT-GTTTCAAA
1 TTTAAATTTAAATTTAGTTT-AAA
215578 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAATTTAAATTT-AGTTTAAA
*
215601 TTTATATTTAAATTTA
1 TTTAAATTTAAATTTA
215617 AAATTATTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 5 0.14
23 21 0.60
24 9 0.26
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTAAA
Found at i:215654 original size:52 final size:52
Alignment explanation
Indices: 215546--215654 Score: 114
Period size: 52 Copynumber: 2.1 Consensus size: 52
215536 TTTTGAGATT
* * * * ** **
215546 AAATTTATTTTTAAATTTAAATTTGTTTCAAATTTAAATTTAATTTAAGTTT
1 AAATTTATATTTAAATTTAAAATTATTTCAAATTTAAATTAAATAAAAGTCA
215598 AAATTTATATTTAAATTTAAAATTA-TTCTAAATTTAAA-TAAATAAAAGTCCA
1 AAATTTATATTTAAATTTAAAATTATTTC-AAATTTAAATTAAATAAAAGT-CA
215650 AAATT
1 AAATT
215655 ACAGACCCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
51 11 0.23
52 36 0.77
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (52 bp):
AAATTTATATTTAAATTTAAAATTATTTCAAATTTAAATTAAATAAAAGTCA
Found at i:216291 original size:3 final size:3
Alignment explanation
Indices: 216273--216323 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
216263 AAATGCATTA
*
216273 AAT AATT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
216319 AAT AA
1 AAT AA
216324 AGAAAGTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:217481 original size:29 final size:29
Alignment explanation
Indices: 217449--217693 Score: 164
Period size: 29 Copynumber: 8.4 Consensus size: 29
217439 AACTATCTAG
*
217449 AAATTACATTTTTACCCTTAAACTTTCCA
1 AAATTACATTTTTACCCTCAAACTTTCCA
* * *
217478 AAATTCCATTTTGA-CCTCAAACTTTCTAA
1 AAATTACATTTTTACCCTCAAACTTTC-CA
* * *
217507 AAATTATATTTTTTCCC-CGAACTTT-CA
1 AAATTACATTTTTACCCTCAAACTTTCCA
* * * **
217534 AAATTCCATTTTTGACCAT-GAACTTTTTGA
1 AAATTACATTTTT-ACCCTCAAAC-TTTCCA
217564 AAATTACATTTTTACCCTCAAAC-TTCTCA
1 AAATTACATTTTTACCCTCAAACTTTC-CA
* *
217593 AAATTCCATTTTTGA-CCTCAAACTTTCTAA
1 AAATTACATTTTT-ACCCTCAAACTTTC-CA
* *
217623 AAATTACA-TTTTACCCCCGAACTTTCCA
1 AAATTACATTTTTACCCTCAAACTTTCCA
* * * * *
217651 GAATTCCA-TTTTAGACCTCGAACCTTCCAA
1 AAATTACATTTTTA-CCCTCAAACTTTCC-A
217681 AAATTACCATTTT
1 AAATTA-CATTTT
217694 ATTTCCGAAT
Statistics
Matches: 168, Mismatches: 33, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
27 12 0.07
28 32 0.19
29 83 0.49
30 36 0.21
31 2 0.01
32 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (29 bp):
AAATTACATTTTTACCCTCAAACTTTCCA
Found at i:217668 original size:58 final size:58
Alignment explanation
Indices: 217438--217876 Score: 319
Period size: 58 Copynumber: 7.5 Consensus size: 58
217428 AAAGGTCCCT
* * ***
217438 AAACTATCTAGAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCATTTT-GACCTC
1 AAACTTTCTAAAAATTACA-TTTTACCCCCGAACTTTCCAAAATTCCATTTTAGACCTC
* ** *
217496 AAACTTTCTAAAAATTATATTTTTTCCCCGAACTTT-CAAAATTCCATTTTTGACCAT-
1 AAACTTTCTAAAAATTACATTTTACCCCCGAACTTTCCAAAATTCCATTTTAGACC-TC
* * * * * *
217553 GAACTTTTTGAAAATTACATTTTTACCCTCAAAC-TTCTCAAAATTCCATTTTTGACCTC
1 AAACTTTCTAAAAATTACA-TTTTACCCCCGAACTTTC-CAAAATTCCATTTTAGACCTC
*
217612 AAACTTTCTAAAAATTACATTTTACCCCCGAACTTTCCAGAATTCCATTTTAGACCTC
1 AAACTTTCTAAAAATTACATTTTACCCCCGAACTTTCCAAAATTCCATTTTAGACCTC
* * * *** * * * *
217670 GAACCTTCCAAAAATTACCATTTTATTTCCGAA-TGTCTAAAAATTTCATTTTTA-ACCAC
1 AAACTTTCTAAAAATTA-CATTTTACCCCCGAACTTTC-CAAAATTCCA-TTTTAGACCTC
* * * * *
217729 GAACCTTTC-AAAAATTATCATTTTACCCCTGGA-TGTCTAGAAATTCCATTTTA-ACC-C
1 -AAACTTTCTAAAAATTA-CATTTTACCCCCGAACTTTCCA-AAATTCCATTTTAGACCTC
* * ** *
217786 TAAACGTTCCAAAAATTACCATTTTACCCCCAGATGTTT-AAAAATTCCATTTTA-ACCTC
1 -AAACTTTCTAAAAATTA-CATTTTACCCCC-GAACTTTCCAAAATTCCATTTTAGACCTC
*
217845 AAACCTTC-AGAAAATTACGATTTTACCCCCGA
1 AAACTTTCTA-AAAATTAC-ATTTTACCCCCGA
217877 TTGTCTAAAG
Statistics
Matches: 308, Mismatches: 55, Indels: 37
0.77 0.14 0.09
Matches are distributed among these distances:
56 14 0.05
57 44 0.14
58 145 0.47
59 93 0.30
60 12 0.04
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.36
Consensus pattern (58 bp):
AAACTTTCTAAAAATTACATTTTACCCCCGAACTTTCCAAAATTCCATTTTAGACCTC
Found at i:217720 original size:59 final size:57
Alignment explanation
Indices: 217592--217927 Score: 286
Period size: 58 Copynumber: 5.8 Consensus size: 57
217582 CAAACTTCTC
* * * * * *
217592 AAAATTCCATTTTTGACCTCAAACTTTCTAAAAATTA-CATTTTACCCCCGAACTTTC-C
1 AAAATTCCA-TTTTAACCTCGAACCTTCCAAAAATTACCATTTTA-CCCCGAA-TGTCTA
* **
217650 AGAATTCCATTTTAGACCTCGAACCTTCCAAAAATTACCATTTTATTTCCGAATGTCTA
1 AAAATTCCATTTTA-ACCTCGAACCTTCCAAAAATTACCATTTTA-CCCCGAATGTCTA
* * * * *
217709 AAAATTTCATTTTTAACCACGAACCTTTCAAAAATTATCATTTTACCCCTGGATGTCTA
1 AAAATTCCA-TTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCC-GAATGTCTA
* * * * *
217768 GAAATTCCATTTTAACC-CTAAACGTTCCAAAAATTACCATTTTACCCCCAGATGTTTA
1 AAAATTCCATTTTAACCTC-GAACCTTCCAAAAATTACCATTTTACCCCGA-ATGTCTA
* * *
217826 AAAATTCCATTTTAACCTCAAACCTT-CAGAAAATTACGATTTTACCCCCGATTGTCTA
1 AAAATTCCATTTTAACCTCGAACCTTCCA-AAAATTACCATTTTA-CCCCGAATGTCTA
* * * *
217884 AAGATTTCATTTTTAA-CTCCGAACATTCCGAAAATTACCATTTT
1 AAAATTCCA-TTTTAACCT-CGAACCTTCCAAAAATTACCATTTT
217928 GTTCTCGAAG
Statistics
Matches: 226, Mismatches: 39, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
57 7 0.03
58 121 0.54
59 92 0.41
60 6 0.03
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.35
Consensus pattern (57 bp):
AAAATTCCATTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCGAATGTCTA
Found at i:217744 original size:117 final size:115
Alignment explanation
Indices: 217477--217927 Score: 332
Period size: 117 Copynumber: 3.9 Consensus size: 115
217467 TAAACTTTCC
* * * ** *
217477 AAAATTCCA-TTTTGACCTCAAACTTTCTAAAAATTATATTTTTTCCCCGAACT-TTCA-AAATT
1 AAAATTCCATTTTTAACCTCAACCTTTC-AAAAATTACATTTTACCCCCGAA-TGTCCAGAAATT
* * * * *** * * *
217539 CCATTTTTGACCATGAACTTTTTGAAAATTA-CATTTTTACCCTCAAACT-TCTC
64 CCA-TTTTAACCCTAAACCTTCCAAAAATTACCA-TTTTACCCCCAGA-TGTCTA
* * *
217592 AAAATTCCATTTTTGACCTCAAACTTTCTAAAAATTACATTTTACCCCCGAACTTTCCAG-AATT
1 AAAATTCCATTTTTAACCTCAACCTTTC-AAAAATTACATTTTACCCCCGAA-TGTCCAGAAATT
* ***
217656 CCATTTTAGA-CCTCGAACCTTCCAAAAATTACCATTTTATTTCC-GAATGTCTA
64 CCATTTTA-ACCCT-AAACCTTCCAAAAATTACCATTTTACCCCCAG-ATGTCTA
* * * * *
217709 AAAATTTCATTTTTAACCACGAACCTTTCAAAAATTATCATTTTACCCCTGGATGTCTAGAAATT
1 AAAATTCCATTTTTAACCTC-AACCTTTCAAAAATTA-CATTTTACCCCCGAATGTCCAGAAATT
* *
217774 CCATTTTAACCCTAAACGTTCCAAAAATTACCATTTTACCCCCAGATGTTTA
64 CCATTTTAACCCTAAACCTTCCAAAAATTACCATTTTACCCCCAGATGTCTA
* *
217826 AAAATTCCA-TTTTAACCTCAAACC-TTCAGAAAATTACGATTTTACCCCCGATTGTCTA-AAGA
1 AAAATTCCATTTTTAACCTC-AACCTTTCA-AAAATTAC-ATTTTACCCCCGAATGTCCAGAA-A
* * * *
217888 TTTCATTTTTAACTCC-GAACATTCCGAAAATTACCATTTT
62 TTCCA-TTTTAAC-CCTAAACCTTCCAAAAATTACCATTTT
217928 GTTCTCGAAG
Statistics
Matches: 278, Mismatches: 40, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
115 16 0.06
116 90 0.32
117 132 0.47
118 40 0.14
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (115 bp):
AAAATTCCATTTTTAACCTCAACCTTTCAAAAATTACATTTTACCCCCGAATGTCCAGAAATTCC
ATTTTAACCCTAAACCTTCCAAAAATTACCATTTTACCCCCAGATGTCTA
Found at i:217753 original size:30 final size:29
Alignment explanation
Indices: 217469--217869 Score: 115
Period size: 29 Copynumber: 13.8 Consensus size: 29
217459 TTTACCCTTA
* *
217469 AACTTTCCAAAATT-CCATTTT-GACCTCA
1 AACTTTCAAAAATTACCATTTTAGACC-CG
* ***
217497 AACTTTCTAAAAATTA-TATTTTTTCCCCG
1 AACTTTC-AAAAATTACCATTTTAGACCCG
* *
217526 AACTTTC-AAAATT-CCATTTTTGACCATG
1 AACTTTCAAAAATTACCATTTTAGACC-CG
** * *
217554 AACTTTTTGAAAATTA-CATTTTTA-CCCTCA
1 AAC-TTTCAAAAATTACCA-TTTTAGACC-CG
* *
217584 AACTTCTC-AAAATT-CCATTTTTGACCTCA
1 AACTT-TCAAAAATTACCATTTTAGACC-CG
**
217613 AACTTTCTAAAAATTA-CATTTTACCCCCG
1 AACTTTC-AAAAATTACCATTTTAGACCCG
* *
217642 AACTTTCCAGAATT-CCATTTTAGACCTCG
1 AACTTTCAAAAATTACCATTTTAGACC-CG
* ***
217671 AACCTTCCAAAAATTACCATTTTATTTCCG
1 AA-CTTTCAAAAATTACCATTTTAGACCCG
* *
217701 AA-TGTCTAAAAATT-TCATTTTTA-ACCACG
1 AACTTTC-AAAAATTACCA-TTTTAGACC-CG
* *
217730 AACCTTTCAAAAATTATCATTTTA-CCCCTG
1 AA-CTTTCAAAAATTACCATTTTAGACCC-G
* * * *
217760 GA-TGTCTAGAAATT-CCATTTTA-ACCCTA
1 AACTTTC-AAAAATTACCATTTTAGACCC-G
* **
217788 AACGTTCCAAAAATTACCATTTTACCCCCAG
1 AAC-TTTCAAAAATTACCATTTTAGACCC-G
** *
217819 ATGTTT-AAAAATT-CCATTTTA-ACCTCA
1 AACTTTCAAAAATTACCATTTTAGACC-CG
* *
217846 AACCTTCAGAAAATTACGATTTTA
1 AACTTTCA-AAAATTACCATTTTA
217870 CCCCCGATTG
Statistics
Matches: 277, Mismatches: 61, Indels: 68
0.68 0.15 0.17
Matches are distributed among these distances:
27 19 0.07
28 61 0.22
29 96 0.35
30 78 0.28
31 23 0.08
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (29 bp):
AACTTTCAAAAATTACCATTTTAGACCCG
Found at i:217858 original size:29 final size:28
Alignment explanation
Indices: 217769--217869 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 28
217759 GGATGTCTAG
217769 AAATT-CCATTTTAACCCTAAACGTTCCAA
1 AAATTACCATTTTAACCC-AAACGTT-CAA
* * * *
217798 AAATTACCATTTTACCCCCAGATGTTTAA
1 AAATTACCATTTTA-ACCCAAACGTTCAA
*
217827 AAATT-CCATTTTAACCTCAAACCTTCAGA
1 AAATTACCATTTTAACC-CAAACGTTCA-A
*
217856 AAATTACGATTTTA
1 AAATTACCATTTTA
217870 CCCCCGATTG
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
27 2 0.04
28 14 0.25
29 18 0.32
30 20 0.35
31 3 0.05
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (28 bp):
AAATTACCATTTTAACCCAAACGTTCAA
Found at i:219897 original size:27 final size:27
Alignment explanation
Indices: 219858--219909 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
219848 CAATGTGAGG
*
219858 TTGGTGCAACCTGCCAGGTATGCACTT
1 TTGGTGCAACCTGCCAGGTAGGCACTT
** *
219885 TTGGTGCCGCCTGTCAGGTAGGCAC
1 TTGGTGCAACCTGCCAGGTAGGCAC
219910 CACCCCACTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.27
Consensus pattern (27 bp):
TTGGTGCAACCTGCCAGGTAGGCACTT
Found at i:219986 original size:9 final size:9
Alignment explanation
Indices: 219963--220030 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
219953 TTTTATTGAT
219963 ATATTTTTA
1 ATATTTTTA
*
219972 AAATTTTTA
1 ATATTTTTA
* *
219981 TTA-TTTAA
1 ATATTTTTA
*
219989 ATATTTTTT
1 ATATTTTTA
219998 AT-TTTTTA
1 ATATTTTTA
**
220006 ATATTAATA
1 ATATTTTTA
220015 ATATTTGTTTA
1 ATA-TT-TTTA
220026 ATATT
1 ATATT
220031 AAATAAATAA
Statistics
Matches: 43, Mismatches: 12, Indels: 7
0.69 0.19 0.11
Matches are distributed among these distances:
8 13 0.30
9 21 0.49
10 4 0.09
11 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (9 bp):
ATATTTTTA
Found at i:219996 original size:17 final size:16
Alignment explanation
Indices: 219964--220010 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
219954 TTTATTGATA
219964 TATTTTTAAA-ATTTT
1 TATTTTTAAATATTTT
219979 TATTATTTAAATATTTTT
1 TATT-TTTAAATA-TTTT
*
219997 TATTTTTTAATATT
1 TATTTTTAAATATT
220011 AATAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.14
16 8 0.29
17 8 0.29
18 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTAAATATTTT
Found at i:219996 original size:18 final size:17
Alignment explanation
Indices: 219964--220010 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
219954 TTTATTGATA
219964 TATTTTTAAA-A-TTTT
1 TATTTTTAAATATTTTT
219979 TATTATTTAAATATTTTT
1 TATT-TTTAAATATTTTT
*
219997 TATTTTTTAATATT
1 TATTTTTAAATATT
220011 AATAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 4 0.14
16 6 0.21
17 10 0.36
18 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTTAAATATTTTT
Found at i:220017 original size:26 final size:26
Alignment explanation
Indices: 219975--220025 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
219965 ATTTTTAAAA
* *
219975 TTTTTATTATTTAAATATTT-TTTAT
1 TTTTTAATATTAAAATATTTGTTTAT
220000 TTTTTAATATTAATAATATTTGTTTA
1 TTTTTAATATTAA-AATATTTGTTTA
220026 ATATTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 7 0.32
27 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTTAATATTAAAATATTTGTTTAT
Found at i:223454 original size:17 final size:15
Alignment explanation
Indices: 223417--223460 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
223407 ATATATTTTA
*
223417 AAAATAAAAGAAATT
1 AAAATAAAAAAAATT
223432 AAAATAAAAAAAATAT
1 AAAATAAAAAAAAT-T
223448 AAGAATACAAAAA
1 AA-AATA-AAAAA
223461 GTTCATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 13 0.52
16 3 0.12
17 4 0.16
18 5 0.20
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (15 bp):
AAAATAAAAAAAATT
Found at i:229844 original size:20 final size:19
Alignment explanation
Indices: 229804--229841 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
229794 ATAGATGAGA
229804 CTGGCGAAGAGCCAAAGAAG
1 CTGGCGAAGAG-CAAAGAAG
229824 CTGGCGAAGGAG-AAAGAA
1 CTGGCGAA-GAGCAAAGAA
229842 AGCGACAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 8 0.47
21 3 0.18
ACGTcount: A:0.42, C:0.16, G:0.37, T:0.05
Consensus pattern (19 bp):
CTGGCGAAGAGCAAAGAAG
Found at i:230606 original size:14 final size:14
Alignment explanation
Indices: 230583--230612 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
230573 ATTAGTACAA
230583 ATATAAATATAAAT
1 ATATAAATATAAAT
*
230597 ATATATATATAAAT
1 ATATAAATATAAAT
230611 AT
1 AT
230613 GTAGATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAAATATAAAT
Found at i:231224 original size:4 final size:4
Alignment explanation
Indices: 231193--231270 Score: 51
Period size: 4 Copynumber: 21.0 Consensus size: 4
231183 CCAACGTGAG
* * *
231193 AAGA AGGA AA-A AATA AAGA AA-A AA-A AAGA AAGA AAGA AAGT AAG-
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* * * *
231237 AAGG AAGA ATG- AA-A AAGG AAGA AAGA AAAA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
231271 TAATGTATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
3 15 0.26
4 43 0.74
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (4 bp):
AAGA
Found at i:231256 original size:14 final size:14
Alignment explanation
Indices: 231221--231266 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
231211 AAAAAAAAAG
*
231221 AAAGAAAGAAAGTAA
1 AAAGGAAGAAAG-AA
* *
231236 GAAGGAAGAATGAA
1 AAAGGAAGAAAGAA
231250 AAAGGAAGAAAGAA
1 AAAGGAAGAAAGAA
231264 AAA
1 AAA
231267 AAGATAATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (14 bp):
AAAGGAAGAAAGAA
Found at i:231637 original size:21 final size:20
Alignment explanation
Indices: 231607--231645 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
231597 AATTTACTTT
231607 AATTTAATTTTGTTAGTTAGC
1 AATTTAATTTTGTT-GTTAGC
*
231628 AATTTTATTTTGTTGTTA
1 AATTTAATTTTGTTGTTA
231646 ATAGTAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.59
Consensus pattern (20 bp):
AATTTAATTTTGTTGTTAGC
Found at i:232447 original size:16 final size:16
Alignment explanation
Indices: 232401--232449 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
232391 TAAACATAGT
*
232401 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
232417 T-A-TAA-TATAAAAA
1 TAATTAATTATCAAAA
232430 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
232446 TAAT
1 TAAT
232450 ATCCCATCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:233845 original size:43 final size:43
Alignment explanation
Indices: 233763--233847 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
233753 ATTAACATGT
* * *
233763 TAAATTATATTAGTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGATTGCATGTTAC
* *
233806 TAAATTATATTACTTTACTCTTATTAATAT-ATTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGATTG-CATGTTA
233848 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGATTGCATGTTAC
Found at i:234483 original size:45 final size:46
Alignment explanation
Indices: 234415--234519 Score: 151
Period size: 45 Copynumber: 2.3 Consensus size: 46
234405 CCATAGCTCA
* **
234415 TCAAGCCAAGGATA-CCAGTCTCAGTTTGACGACCCACTTCAATAC
1 TCAAGCCAAGGATATCAAGTCTCAGTTTGACGACCCACCACAATAC
* *
234460 TCAAGCCGAGGATATCAAG-CTCAGTTTGACGAGCCACCACAATAC
1 TCAAGCCAAGGATATCAAGTCTCAGTTTGACGACCCACCACAATAC
234505 TCAAGCCAAGGATAT
1 TCAAGCCAAGGATAT
234520 TAGGCTTAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 50 0.94
46 3 0.06
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (46 bp):
TCAAGCCAAGGATATCAAGTCTCAGTTTGACGACCCACCACAATAC
Found at i:234829 original size:28 final size:28
Alignment explanation
Indices: 234797--234850 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
234787 ATCATTTATT
*
234797 TAAATTTCATAAC-CTTAAACCCTAAACC
1 TAAATTTCAAAACAC-TAAACCCTAAACC
*
234825 TAAATTTTAAAACACTAAACCCTAAA
1 TAAATTTCAAAACACTAAACCCTAAA
234851 TGTAAACCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (28 bp):
TAAATTTCAAAACACTAAACCCTAAACC
Found at i:234842 original size:21 final size:22
Alignment explanation
Indices: 234813--234873 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
234803 TCATAACCTT
*
234813 AAACCCTAAA-CCTAAATTTTA
1 AAACACTAAACCCTAAATTTTA
*
234834 AAACACTAAACCCTAAA-TGTA
1 AAACACTAAACCCTAAATTTTA
*
234855 AACCA-TAAACCCTAAATTT
1 AAACACTAAACCCTAAATTT
234874 GATACCCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.32
21 17 0.50
22 6 0.18
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.25
Consensus pattern (22 bp):
AAACACTAAACCCTAAATTTTA
Found at i:234863 original size:20 final size:20
Alignment explanation
Indices: 234812--234871 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
234802 TTCATAACCT
* *
234812 TAAACCCTAAA-CCTAAATTT
1 TAAACCATAAACCCTAAA-TG
*
234832 TAAAACACTAAACCCTAAATG
1 TAAACCA-TAAACCCTAAATG
234853 TAAACCATAAACCCTAAAT
1 TAAACCATAAACCCTAAAT
234872 TTGATACCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 11 0.32
22 6 0.18
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAACCATAAACCCTAAATG
Found at i:237883 original size:17 final size:15
Alignment explanation
Indices: 237848--237886 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
237838 AACACATTAC
*
237848 CTTTCTCTCCTTCTT
1 CTTTCTTTCCTTCTT
237863 CTTTCTTTCCTCTCATT
1 CTTTCTTTCCT-TC-TT
237880 CTTTCTT
1 CTTTCTT
237887 CTTTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 9 0.43
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTTCTTTCCTTCTT
Found at i:238040 original size:19 final size:19
Alignment explanation
Indices: 238016--238054 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
238006 TTTACAATCA
*
238016 AAATAAAATTAACACACAC
1 AAATAAAATAAACACACAC
238035 AAATAAAATAAACACACAC
1 AAATAAAATAAACACACAC
238054 A
1 A
238055 CGACACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.13
Consensus pattern (19 bp):
AAATAAAATAAACACACAC
Found at i:239213 original size:4 final size:4
Alignment explanation
Indices: 239199--239276 Score: 79
Period size: 4 Copynumber: 19.8 Consensus size: 4
239189 AATAAATGAA
* * *
239199 AAAG AACG AAAG AAAG AAAG AAAG AAAG AAAG AAAT AAAT AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* * *
239247 -AAG GAAG AAGG AGAGG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAA
239277 AAGAGAAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
3 6 0.09
4 54 0.84
5 4 0.06
ACGTcount: A:0.69, C:0.01, G:0.27, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:239281 original size:20 final size:20
Alignment explanation
Indices: 239242--239281 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
239232 AATAAATAAA
* **
239242 GAAAGAAGGAAGAAGGAGAG
1 GAAAGAAAGAAGAAAAAGAG
239262 GAAAGAAAGAAGAAAAAGAG
1 GAAAGAAAGAAGAAAAAGAG
239282 AAATGTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAGAAAAAGAG
Found at i:242446 original size:546 final size:546
Alignment explanation
Indices: 241414--242513 Score: 2092
Period size: 546 Copynumber: 2.0 Consensus size: 546
241404 CGCTACGTTC
*
241414 TATAGGCTGGCTACTTCGATGCCAGTAATGGGGATGCGACAAATCGATCAGATAAACGTCGGACA
1 TATAGGCTGGCTACTTCGATGCCAGTAATGGGGATGCGACAAATCGATCAGATAAACGTCAGACA
*
241479 TGTGTTTGTCGAAGCTATCAGGAATGCAATGGATGCAAATCGTCAGAGTGCGAGGACGATGAACA
66 CGTGTTTGTCGAAGCTATCAGGAATGCAATGGATGCAAATCGTCAGAGTGCGAGGACGATGAACA
*
241544 TTGAAATATATTCACAACAGTTTTAACGATTTCAAATTACTGAGACCATTGGGCGTCGACCTGGT
131 TTGAAATATATTCACAACAGTTTCAACGATTTCAAATTACTGAGACCATTGGGCGTCGACCTGGT
241609 ATCCCAACTAGGTCATACAGGGTTGATCTCCAAAACAAACACTACGATTGCAGGAGGTTCGATAC
196 ATCCCAACTAGGTCATACAGGGTTGATCTCCAAAACAAACACTACGATTGCAGGAGGTTCGATAC
*
241674 ACTTCGTTATCCCTGTGCACATGTCATTGTAGCTTGTGCTAAAGTGTCGCTCAATGTTGAATAGT
261 ACTTCGTTATCCCTCTGCACATGTCATTGTAGCTTGTGCTAAAGTGTCGCTCAATGTTGAATAGT
* *
241739 TCATCGACCCCGTTTACACTCTCCAGCGTACATTACGTATTTGGGAAAATGAGTTCCCCGTCCTG
326 TCATCGACCCCGTTTACACTCTCAAGCGTACATTACGTATTTGGGAAAACGAGTTCCCCGTCCTG
241804 CCTGACTTGTCCACATGAGAGGTGCTTCTAACAACTTTCGAGGTTATCCCGAACAAAGGTTTGCA
391 CCTGACTTGTCCACATGAGAGGTGCTTCTAACAACTTTCGAGGTTATCCCGAACAAAGGTTTGCA
*
241869 AAGGAATCTGAAAGATCATCCCCATATCACCAGAATCCGCAACGAAATGGACATTATGGAGAAAA
456 AAGGAATATGAAAGATCATCCCCATATCACCAGAATCCGCAACGAAATGGACATTATGGAGAAAA
*
241934 TAGACGGCAGCAAGCTGTGTGGATTA
521 CAGACGGCAGCAAGCTGTGTGGATTA
241960 TATAGGCTGGCTACTTCGATGCCAGTAATGGGGATGCGACAAATCGATCAGATAAACGTCAGACA
1 TATAGGCTGGCTACTTCGATGCCAGTAATGGGGATGCGACAAATCGATCAGATAAACGTCAGACA
242025 CGTGTTTGTCGAAGCTATCAGGAATGCAATGGATGCAAATCGTCAGAGTGCGAGGACGATGAACA
66 CGTGTTTGTCGAAGCTATCAGGAATGCAATGGATGCAAATCGTCAGAGTGCGAGGACGATGAACA
*
242090 TTGAAATATATTCACGACAGTTTCAACGATTTCAAATTACTGAGACCATTGGGCGTCGACCTGGT
131 TTGAAATATATTCACAACAGTTTCAACGATTTCAAATTACTGAGACCATTGGGCGTCGACCTGGT
*
242155 ATCCTAACTAGGTCATACAGGGTTGATCTCCAAAACAAACACTACGATTGCAGGAGGTTCGATAC
196 ATCCCAACTAGGTCATACAGGGTTGATCTCCAAAACAAACACTACGATTGCAGGAGGTTCGATAC
242220 ACTTCGTTATCCCTCTGCACATGTCATTGTAGCTTGTGCTAAAGTGTCGCTCAATGTTGAATAGT
261 ACTTCGTTATCCCTCTGCACATGTCATTGTAGCTTGTGCTAAAGTGTCGCTCAATGTTGAATAGT
242285 TCATCGACCCCGTTTACACTCTCAAGCGTACATTACGTATTTGGGAAAACGAGTTCCCCGTCCTG
326 TCATCGACCCCGTTTACACTCTCAAGCGTACATTACGTATTTGGGAAAACGAGTTCCCCGTCCTG
242350 CCTGACTTGTCCACATGAGAGGTGCTTCTAACAACTTTCGAGGTTATCCCGAACAAAGGTTTGCA
391 CCTGACTTGTCCACATGAGAGGTGCTTCTAACAACTTTCGAGGTTATCCCGAACAAAGGTTTGCA
*
242415 AAGGAATATGAAAGGTCATCCCCATATCACCAGAATCCGCAACGAAATGGACATTATGGAGAAAA
456 AAGGAATATGAAAGATCATCCCCATATCACCAGAATCCGCAACGAAATGGACATTATGGAGAAAA
242480 CAGACGGCAGCAAGCTGTGTGGATTA
521 CAGACGGCAGCAAGCTGTGTGGATTA
*
242506 TGTAGGCT
1 TATAGGCT
242514 AGTTGGGCAT
Statistics
Matches: 542, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
546 542 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (546 bp):
TATAGGCTGGCTACTTCGATGCCAGTAATGGGGATGCGACAAATCGATCAGATAAACGTCAGACA
CGTGTTTGTCGAAGCTATCAGGAATGCAATGGATGCAAATCGTCAGAGTGCGAGGACGATGAACA
TTGAAATATATTCACAACAGTTTCAACGATTTCAAATTACTGAGACCATTGGGCGTCGACCTGGT
ATCCCAACTAGGTCATACAGGGTTGATCTCCAAAACAAACACTACGATTGCAGGAGGTTCGATAC
ACTTCGTTATCCCTCTGCACATGTCATTGTAGCTTGTGCTAAAGTGTCGCTCAATGTTGAATAGT
TCATCGACCCCGTTTACACTCTCAAGCGTACATTACGTATTTGGGAAAACGAGTTCCCCGTCCTG
CCTGACTTGTCCACATGAGAGGTGCTTCTAACAACTTTCGAGGTTATCCCGAACAAAGGTTTGCA
AAGGAATATGAAAGATCATCCCCATATCACCAGAATCCGCAACGAAATGGACATTATGGAGAAAA
CAGACGGCAGCAAGCTGTGTGGATTA
Found at i:243272 original size:45 final size:45
Alignment explanation
Indices: 243204--243294 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
243194 GGAGGAGTAC
* * *
243204 AGTATTGTGGTGGCTCGTTAAACTGAGCTTGATATCCTTGGCTTG
1 AGTATTGCGGTGGCTCGTCAAACTGAGATTGATATCCTTGGCTTG
243249 AGTATTGCGGTGGCTCGTCAAACTGAGATTGATATCCTTGGCTTG
1 AGTATTGCGGTGGCTCGTCAAACTGAGATTGATATCCTTGGCTTG
243294 A
1 A
243295 TAAGCTAGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (45 bp):
AGTATTGCGGTGGCTCGTCAAACTGAGATTGATATCCTTGGCTTG
Found at i:245278 original size:16 final size:16
Alignment explanation
Indices: 245259--245308 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
245249 ATGATGAGAT
245259 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
245275 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
245290 A-TATTTTGACAATTA
1 ATTATTTTGATAATTA
245305 ATTA
1 ATTA
245309 GCTAGGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.33
15 5 0.19
16 13 0.48
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:246204 original size:23 final size:22
Alignment explanation
Indices: 246178--246255 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
246168 CTATAACAAC
246178 ATTAAATAACAAATCAATTAAAA
1 ATTAAATAACAAATCAA-TAAAA
*
246201 ATTAAATTAAACAAAACAA-AAAA
1 ATTAAA-T-AACAAATCAATAAAA
* *
246224 CTTAAAATAATCAAATTAACTAACAA
1 ATT-AAATAA-CAAATCAA-TAA-AA
246250 ATTAAA
1 ATTAAA
246256 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.05
23 19 0.44
24 4 0.09
25 14 0.33
26 4 0.09
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (22 bp):
ATTAAATAACAAATCAATAAAA
Found at i:246457 original size:4 final size:4
Alignment explanation
Indices: 246448--246519 Score: 55
Period size: 4 Copynumber: 19.0 Consensus size: 4
246438 TACATTTTTC
* * * *
246448 TCTT TCTT TC-T TCCT TC-T TCCT TCTT CCTT TCTT TCTT TTTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
*
246494 T-TT T-TT TCCTT TCTT T-TT TCCT TCTT
1 TCTT TCTT T-CTT TCTT TCTT TCTT TCTT
246520 CTCAAGTTGG
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
3 15 0.27
4 38 0.68
5 3 0.05
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TCTT
Found at i:247445 original size:21 final size:19
Alignment explanation
Indices: 247393--247447 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
247383 CAATTGAATT
247393 AATATTATAAAATATAATATA
1 AATA-TATAAAATA-AATATA
*
247414 AAT-TTTAAAATAAATACATA
1 AATATATAAAATAAAT--ATA
247434 AATATATAAAATAA
1 AATATATAAAATAA
247448 TATCATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 3 0.10
19 8 0.28
20 6 0.21
21 12 0.41
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATATAAAATAAATATA
Found at i:248670 original size:28 final size:28
Alignment explanation
Indices: 248613--248680 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
248603 AGCTTTGGAA
**
248613 AAAAGACATTAATACATTAAATGTAGGG
1 AAAAGACATTAATACATTAAATACAGGG
* *
248641 AAAAGGCATTACA-ACATTAAATACATGG
1 AAAAGACATTA-ATACATTAAATACAGGG
248669 AAAA-ACCATTAA
1 AAAAGA-CATTAA
248681 GTATTAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 1 0.03
28 31 0.94
29 1 0.03
ACGTcount: A:0.53, C:0.12, G:0.13, T:0.22
Consensus pattern (28 bp):
AAAAGACATTAATACATTAAATACAGGG
Found at i:254847 original size:2 final size:2
Alignment explanation
Indices: 254826--254883 Score: 61
Period size: 2 Copynumber: 30.0 Consensus size: 2
254816 ATGTTGTATC
*
254826 AT AT CAT AT A- AT AT AT -T AT AT AT -T A- AT AGT TT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
254866 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
254884 TAGGTATTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
1 4 0.08
2 41 0.85
3 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Done.