Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015173.1 Kokia drynarioides strain JFW-HI SEQ_130217, 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: 270794
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:2366 original size:21 final size:21
Alignment explanation
Indices: 2341--2380 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2331 TAATATCATA
2341 TTAATATTTTTATCTTAAATT
1 TTAATATTTTTATCTTAAATT
2362 TTAATATTTTTATCTTAAA
1 TTAATATTTTTATCTTAAA
2381 AAAATCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAATATTTTTATCTTAAATT
Found at i:12150 original size:29 final size:31
Alignment explanation
Indices: 12118--12183 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
12108 GCCAAGTCGA
* *
12118 GTGTTTATATT-G-ACTTGGGCCACATGCCC
1 GTGTGTATATTCGAACTTGGGCCACACGCCC
* *
12147 GTGTGTCTATTCGAATTTGGGCCACACGCCC
1 GTGTGTATATTCGAACTTGGGCCACACGCCC
12178 GTGTGT
1 GTGTGT
12184 CTCTCCGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 9 0.29
30 1 0.03
31 21 0.68
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.33
Consensus pattern (31 bp):
GTGTGTATATTCGAACTTGGGCCACACGCCC
Found at i:12886 original size:27 final size:28
Alignment explanation
Indices: 12847--12991 Score: 97
Period size: 27 Copynumber: 5.4 Consensus size: 28
12837 TCTCTCTATA
*
12847 ATATCATTACGGATAATCATTTTCAATG
1 ATATCATTACGGATAATCCTTTTCAATG
* *
12875 ATATCATT-CGGAT-GTCCCTTTTC-ATA
1 ATATCATTACGGATAAT-CCTTTTCAATG
* **
12901 ATATCCTTATAGATAATCCTTTTCAATG
1 ATATCATTACGGATAATCCTTTTCAATG
** * * *
12929 ATATC-TTTTGGAT-ATCTTTTTCTATA
1 ATATCATTACGGATAATCCTTTTCAATG
* *
12955 ATATCTTTACGGAT-ATTCTTTATCAATG
1 ATATCATTACGGATAATCCTTT-TCAATG
*
12983 -TATCTTTAC
1 ATATCATTAC
12992 AGGTATGAAG
Statistics
Matches: 92, Mismatches: 19, Indels: 13
0.74 0.15 0.10
Matches are distributed among these distances:
26 25 0.27
27 47 0.51
28 20 0.22
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (28 bp):
ATATCATTACGGATAATCCTTTTCAATG
Found at i:12902 original size:54 final size:53
Alignment explanation
Indices: 12841--12986 Score: 161
Period size: 54 Copynumber: 2.7 Consensus size: 53
12831 AATAATTCTC
*
12841 TCTATAATATCATTACGGATAATCATTTTCAATGATATCATTCGGATGTCCCTTT
1 TCTATAATATCATTACGGATAATC-TTTTCAATGATATCATTCGGATAT-CCTTT
* ** * * *
12896 TC-ATAATATCCTTATAGATAATCCTTTTCAATGATATCTTTTGGATATCTTTT
1 TCTATAATATCATTACGGATAAT-CTTTTCAATGATATCATTCGGATATCCTTT
* *
12949 TCTATAATATCTTTACGGATATTCTTTATCAATG-TATC
1 TCTATAATATCATTACGGATAATCTTT-TCAATGATATC
12987 TTTACAGGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
53 14 0.18
54 60 0.78
55 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (53 bp):
TCTATAATATCATTACGGATAATCTTTTCAATGATATCATTCGGATATCCTTT
Found at i:12958 original size:26 final size:26
Alignment explanation
Indices: 12891--12962 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
12881 TTCGGATGTC
*
12891 CCTTTTCATAATATCCTTATAGATAAT
1 CCTTTTCATAATAT-CTTTTAGATAAT
* *
12918 CCTTTTCAATGATATCTTTTGGAT-AT
1 CCTTTTC-ATAATATCTTTTAGATAAT
*
12944 CTTTTTCTATAATATCTTT
1 CCTTTTC-ATAATATCTTT
12963 ACGGATATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 18 0.47
27 14 0.37
28 6 0.16
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (26 bp):
CCTTTTCATAATATCTTTTAGATAAT
Found at i:14951 original size:19 final size:20
Alignment explanation
Indices: 14929--14973 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
14919 AATTTAACAC
* *
14929 TTAATTTTTTTTTGTT-AAT
1 TTAATTCTTTTTAGTTAAAT
14948 TTAATTCTTTTTAGTTAAAT
1 TTAATTCTTTTTAGTTAAAT
14968 TTAATT
1 TTAATT
14974 ATTAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TTAATTCTTTTTAGTTAAAT
Found at i:17141 original size:2 final size:2
Alignment explanation
Indices: 17136--17161 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17126 TTTATAAGAG
17136 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
17162 TAAACTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28142 original size:55 final size:55
Alignment explanation
Indices: 27996--28142 Score: 213
Period size: 55 Copynumber: 2.7 Consensus size: 55
27986 ACTCGTTTAG
* * * * *
27996 TGAAATTAAAATAATTTTTTAAACTTAATTCTGAAGACTCGTTTACAATTAAAAT
1 TGAAATTAAAATGATTTTTTAAACTTAGTTCTAAATACTCGTTTACAATCAAAAT
* * *
28051 TGAAATTAAAATGATTCTTTAAACTTAGTTCGAAATACTTGTTTACAATCAAAAT
1 TGAAATTAAAATGATTTTTTAAACTTAGTTCTAAATACTCGTTTACAATCAAAAT
*
28106 TGAAATTAAAATGATTTTTTAAACTTAGTTTTAAATA
1 TGAAATTAAAATGATTTTTTAAACTTAGTTCTAAATA
28143 TGAATACTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (55 bp):
TGAAATTAAAATGATTTTTTAAACTTAGTTCTAAATACTCGTTTACAATCAAAAT
Found at i:28289 original size:15 final size:17
Alignment explanation
Indices: 28268--28308 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
28258 TTAATATTTA
28268 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
28284 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
28300 AAAATTATA
1 AAAATTATA
28309 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:30612 original size:135 final size:135
Alignment explanation
Indices: 30370--30650 Score: 519
Period size: 135 Copynumber: 2.1 Consensus size: 135
30360 GAGATGCCTG
* *
30370 AGAAGGTCGCCCAGAAATTCAGCGTTGGTCGTGGGGGAGAGCGCAAATGTGAGGCTCAAGGCCAT
1 AGAAGGTCGCCCAGAAATTCAGCGTTGGTAGTGGGGGAGAGCGCAAATGTGAGGCCCAAGGCCAT
30435 TGTGAGTTTAGAAACTGAAGGTTATAAAAGGAAAATGAAGGAAAGTACAACTGTAGAGGGTAAGA
66 TGTGAGTTTAGAAACTGAAGGTTATAAAAGGAAAATGAAGGAAAGTACAACTGTAGAGGGTAAGA
30500 ATCTT
131 ATCTT
30505 AGAAGGTCGCCCAGAAATTCAGCGTTGGTAGTGGGGGAGAGCGCAAATGTGAGGCCCAA-GCTCA
1 AGAAGGTCGCCCAGAAATTCAGCGTTGGTAGTGGGGGAGAGCGCAAATGTGAGGCCCAAGGC-CA
*
30569 TTGTGAGTTTAGAAACTGAAGGTTATAAAAGGAAAATTAAGGAAAGTACAACTGTAGAGGGTAAG
65 TTGTGAGTTTAGAAACTGAAGGTTATAAAAGGAAAATGAAGGAAAGTACAACTGTAGAGGGTAAG
30634 AATCTT
130 AATCTT
30640 AGAAGGTCGCC
1 AGAAGGTCGCC
30651 AAGATTTACT
Statistics
Matches: 142, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
134 2 0.01
135 140 0.99
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (135 bp):
AGAAGGTCGCCCAGAAATTCAGCGTTGGTAGTGGGGGAGAGCGCAAATGTGAGGCCCAAGGCCAT
TGTGAGTTTAGAAACTGAAGGTTATAAAAGGAAAATGAAGGAAAGTACAACTGTAGAGGGTAAGA
ATCTT
Found at i:37116 original size:19 final size:19
Alignment explanation
Indices: 37092--37129 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
37082 TAAGGAAATG
*
37092 ATATCTCTTAATTAGAATA
1 ATATCTCCTAATTAGAATA
37111 ATATCTCCTAATTAGAATA
1 ATATCTCCTAATTAGAATA
37130 TTTAAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (19 bp):
ATATCTCCTAATTAGAATA
Found at i:38874 original size:27 final size:27
Alignment explanation
Indices: 38819--38874 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
38809 CAACTTTCTC
*
38819 TTTTATTTCTATTCAATTTCTTTCTTT
1 TTTTATTTCTATTCAATTTCTTTCCTT
*
38846 TTTTATTT-T-TTCATTATTCTTCTCCTT
1 TTTTATTTCTATTCAAT-TTCTT-TCCTT
38873 TT
1 TT
38875 GACTAACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 5 0.20
26 6 0.24
27 14 0.56
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTATTTCTATTCAATTTCTTTCCTT
Found at i:42791 original size:16 final size:16
Alignment explanation
Indices: 42770--42809 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
42760 TCAGTTCCGT
42770 CTATAACAGCCA-TCTG
1 CTATAACAG-CATTCTG
*
42786 CTATAACAGCATTTTG
1 CTATAACAGCATTCTG
42802 CTATAACA
1 CTATAACA
42810 ACCAAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (16 bp):
CTATAACAGCATTCTG
Found at i:43407 original size:26 final size:27
Alignment explanation
Indices: 43353--43408 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
43343 TGATTTGATC
*
43353 CTCACTTTCTTTATTTTTTGATCATAATT
1 CTCACTTTCTTTA--TTTTGATCAAAATT
*
43382 CTCACTTTCTTTA-TTTGATGAAAATT
1 CTCACTTTCTTTATTTTGATCAAAATT
43408 C
1 C
43409 ACGATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.48
29 13 0.52
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.54
Consensus pattern (27 bp):
CTCACTTTCTTTATTTTGATCAAAATT
Found at i:44896 original size:24 final size:25
Alignment explanation
Indices: 44869--44917 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
44859 TAAGTACTTT
44869 AATTT-TTTCTTTTATAT-TTTTTTA
1 AATTTCTTT-TTTTATATATTTTTTA
*
44893 AATTTCTTTTTTTATTTATTTTTTA
1 AATTTCTTTTTTTATATATTTTTTA
44918 TTCTCTTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (25 bp):
AATTTCTTTTTTTATATATTTTTTA
Found at i:52572 original size:71 final size:67
Alignment explanation
Indices: 52436--52580 Score: 191
Period size: 71 Copynumber: 2.1 Consensus size: 67
52426 ACATAATAAC
* * *
52436 TTAAGATGTGTGGAGATAGAAGAAATTAAATACCTATAATGAGTCTCAAAATATTGAAAATTGAT
1 TTAAGACGTGTGGAGATAGAAGAAATTAAATACCTATAATGAGCCTCAAAATATTGAAAACTGAT
52501 TG
66 TG
* ** *
52503 TTAAGACGTGTGGAGATTGAAGAAATTACATATCTATTTATAATGAGCCTCGAAATATTGAAAAC
1 TTAAGACGTGTGGAGATAGAAGAAATTA-A-A--TACCTATAATGAGCCTCAAAATATTGAAAAC
52568 TGATTG
62 TGATTG
52574 TTAAGAC
1 TTAAGAC
52581 AACTGTCTCG
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
67 26 0.39
68 1 0.01
69 1 0.01
71 39 0.58
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (67 bp):
TTAAGACGTGTGGAGATAGAAGAAATTAAATACCTATAATGAGCCTCAAAATATTGAAAACTGAT
TG
Found at i:60708 original size:5 final size:5
Alignment explanation
Indices: 60695--60731 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
60685 GAAATTATGG
* *
60695 TGTTG TGTTT TGTTT TGTTT TGTTT TGTTT TATTT TG
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TG
60732 ATTGCAATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.22, T:0.76
Consensus pattern (5 bp):
TGTTT
Found at i:63653 original size:12 final size:12
Alignment explanation
Indices: 63636--63721 Score: 88
Period size: 12 Copynumber: 7.3 Consensus size: 12
63626 ATAATATCCA
*
63636 AACAACCAAAAT
1 AACAACAAAAAT
*
63648 AACAACAAAAAC
1 AACAACAAAAAT
*
63660 AACAGCAAAAAT
1 AACAACAAAAAT
**
63672 AAC-AGGAAAAT
1 AACAACAAAAAT
63683 AACAACAAAAAT
1 AACAACAAAAAT
63695 AACATA-AAAAA-
1 AACA-ACAAAAAT
*
63706 AACAACAAAGAT
1 AACAACAAAAAT
63718 AACA
1 AACA
63722 GTAAAAACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
10 1 0.02
11 16 0.27
12 42 0.70
13 1 0.02
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:63681 original size:23 final size:23
Alignment explanation
Indices: 63636--63739 Score: 109
Period size: 23 Copynumber: 4.4 Consensus size: 23
63626 ATAATATCCA
* *
63636 AACAACCAAAATAACAACAAAAAC
1 AACAACAAAAATAAC-AGAAAAAC
* * *
63660 AACAGCAAAAATAACAGGAAAAT
1 AACAACAAAAATAACAGAAAAAC
* *
63683 AACAACAAAAATAACATAAAAAA
1 AACAACAAAAATAACAGAAAAAC
*
63706 AACAACAAAGATAACAGTAAAAAC
1 AACAACAAAAATAACAG-AAAAAC
*
63730 AACATCAAAA
1 AACAACAAAA
63740 CAGTAAAAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
23 39 0.60
24 26 0.40
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (23 bp):
AACAACAAAAATAACAGAAAAAC
Found at i:63682 original size:35 final size:34
Alignment explanation
Indices: 63635--63739 Score: 111
Period size: 35 Copynumber: 3.0 Consensus size: 34
63625 AATAATATCC
63635 AAACAACCAAAATAACAACAAAAACAACAGCAAAAA
1 AAACAA-CAAAATAACAACAAAAACAACA-CAAAAA
* ** * *
63671 TAACAGGAAAATAACAACAAAAATAACATAAAAA
1 AAACAACAAAATAACAACAAAAACAACACAAAAA
**
63705 AAACAACAAAGATAACAGTAAAAACAACATCAAAA
1 AAACAACAAA-ATAACAACAAAAACAACA-CAAAA
63740 CAGTAAAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
34 12 0.22
35 35 0.64
36 8 0.15
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (34 bp):
AAACAACAAAATAACAACAAAAACAACACAAAAA
Found at i:63733 original size:12 final size:12
Alignment explanation
Indices: 63643--63739 Score: 81
Period size: 12 Copynumber: 8.2 Consensus size: 12
63633 CCAAACAACC
*
63643 AAAATAACAACA
1 AAAATAACAGCA
*
63655 AAAACAACAGCA
1 AAAATAACAGCA
*
63667 AAAATAACAG-G
1 AAAATAACAGCA
*
63678 AAAATAACAACA
1 AAAATAACAGCA
*
63690 AAAATAACA-TA
1 AAAATAACAGCA
* *
63701 AAAAAAACAACA
1 AAAATAACAGCA
* *
63713 AAGATAACAGTA
1 AAAATAACAGCA
* *
63725 AAAACAACATCA
1 AAAATAACAGCA
63737 AAA
1 AAA
63740 CAGTAAAAAA
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
11 18 0.27
12 48 0.73
ACGTcount: A:0.71, C:0.15, G:0.05, T:0.08
Consensus pattern (12 bp):
AAAATAACAGCA
Found at i:63741 original size:20 final size:19
Alignment explanation
Indices: 63718--63832 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 19
63708 CAACAAAGAT
*
63718 AACAGTAAAAACAACATCAA
1 AACAGTAAAAA-AACAACAA
63738 AACAGTAAAAAATAGCAACTAA
1 AACAGTAAAAAA-A-CAAC-AA
* *
63760 AACAGTAAAAAAGCACCAA
1 AACAGTAAAAAAACAACAA
* *
63779 AATAGTAAAAAAAAATAACACCAA
1 AACAGT----AAAAA-AACAACAA
* *
63803 AACAATAAAAAAGCAATCAA
1 AACAGTAAAAAAACAA-CAA
63823 AACAGTAAAA
1 AACAGTAAAA
63833 GAAAACCGCA
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
19 11 0.14
20 32 0.42
21 3 0.04
22 14 0.18
23 5 0.07
24 11 0.14
ACGTcount: A:0.67, C:0.16, G:0.07, T:0.10
Consensus pattern (19 bp):
AACAGTAAAAAAACAACAA
Found at i:63791 original size:43 final size:42
Alignment explanation
Indices: 63718--63850 Score: 135
Period size: 44 Copynumber: 3.1 Consensus size: 42
63708 CAACAAAGAT
*
63718 AACAGTAAAAACAACATCAAAACAGT--AAAAAATAGCAACTAA
1 AACAGTAAAAA-AGCATCAAAACAGTAAAAAAAATAGC-ACTAA
* * * *
63760 AACAGTAAAAAAGCACCAAAATAGTAAAAAAAAATAACACCAA
1 AACAGTAAAAAAGCATCAAAACAGT-AAAAAAAATAGCACTAA
* **
63803 AACAATAAAAAAGCAATCAAAACAGTAAAAGAAAACCGCACTAA
1 AACAGTAAAAAAGC-ATCAAAACAGTAAAA-AAAATAGCACTAA
63847 AACA
1 AACA
63851 ACAATATAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
41 11 0.15
42 11 0.15
43 21 0.28
44 31 0.42
ACGTcount: A:0.65, C:0.17, G:0.08, T:0.10
Consensus pattern (42 bp):
AACAGTAAAAAAGCATCAAAACAGTAAAAAAAATAGCACTAA
Found at i:63849 original size:44 final size:40
Alignment explanation
Indices: 63718--63851 Score: 115
Period size: 43 Copynumber: 3.1 Consensus size: 40
63708 CAACAAAGAT
* * *
63718 AACAGTAAAAACAACATCAAAACAGTAAAAAATAGCAACTAA
1 AACAATAAAAA-AGCATCAAAACAGTAAAAAAAAGC-ACTAA
* * * * *
63760 AACAGTAAAAAAGCACCAAAATAGTAAAAAAAAATAACACCAA
1 AACAATAAAAAAGCATCAAAACAGT--AAAAAAA-AGCACTAA
63803 AACAATAAAAAAGCAATCAAAACAGTAAAAGAAAACCGCACTAA
1 AACAATAAAAAAGC-ATCAAAACAGTAAAA-AAAA--GCACTAA
63847 AACAA
1 AACAA
63852 CAATATAATT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
41 11 0.15
42 16 0.22
43 26 0.35
44 21 0.28
ACGTcount: A:0.66, C:0.17, G:0.07, T:0.10
Consensus pattern (40 bp):
AACAATAAAAAAGCATCAAAACAGTAAAAAAAAGCACTAA
Found at i:68755 original size:23 final size:22
Alignment explanation
Indices: 68722--68784 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
68712 TATTAAATTT
68722 TAATAAAAAAATATTTAAAAAAA
1 TAATAAAAAAAT-TTTAAAAAAA
* *
68745 TAATAATAAAATTTTATAAAAA
1 TAATAAAAAAATTTTAAAAAAA
** *
68767 TCGT-AAAAAATTATAAAA
1 TAATAAAAAAATTTTAAAA
68785 TATATAGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 11 0.33
22 11 0.33
23 11 0.33
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
TAATAAAAAAATTTTAAAAAAA
Found at i:68795 original size:28 final size:28
Alignment explanation
Indices: 68741--68843 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 28
68731 AATATTTAAA
* *
68741 AAAATAATAATAAAATTTTATAAAAATCGT
1 AAAA-AATTATAAAATTTTAT-AAAATCAT
*
68771 AAAAAATTATAAAA-TATATAGAAAT-AT
1 AAAAAATTATAAAATTTTATA-AAATCAT
* *
68798 AAAAAATTACAAAATTTTATAAAGTCAT
1 AAAAAATTATAAAATTTTATAAAATCAT
68826 AAGAAAATTATATAAATT
1 AA-AAAATTATA-AAATT
68844 ATAAGGAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
27 18 0.30
28 17 0.28
29 17 0.28
30 9 0.15
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAAATTATAAAATTTTATAAAATCAT
Found at i:68812 original size:56 final size:58
Alignment explanation
Indices: 68752--68859 Score: 152
Period size: 56 Copynumber: 1.9 Consensus size: 58
68742 AAATAATAAT
*
68752 AAAATTTTATAAAAATCGTAA-AAAATTATA-AAA-TATATA-GAAATATAAAAAATTAC
1 AAAATTTTAT-AAAATCATAAGAAAATTATATAAATTATA-AGGAAATATAAAAAATTAC
*
68808 AAAATTTTATAAAGTCATAAGAAAATTATATAAATTATAAGGAAATATAAAA
1 AAAATTTTATAAAATCATAAGAAAATTATATAAATTATAAGGAAATATAAAA
68860 TTCGTACAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
55 8 0.17
56 19 0.41
57 4 0.09
58 15 0.33
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (58 bp):
AAAATTTTATAAAATCATAAGAAAATTATATAAATTATAAGGAAATATAAAAAATTAC
Found at i:68853 original size:20 final size:20
Alignment explanation
Indices: 68808--68861 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
68798 AAAAAATTAC
* *
68808 AAAATTTTATAAAGTCATAAG
1 AAAATTATATAAA-TTATAAG
68829 AAAATTATATAAATTATAAG
1 AAAATTATATAAATTATAAG
*
68849 GAAA-TATA-AAATT
1 AAAATTATATAAATT
68862 CGTACAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.17
19 4 0.13
20 9 0.30
21 12 0.40
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (20 bp):
AAAATTATATAAATTATAAG
Found at i:69137 original size:20 final size:20
Alignment explanation
Indices: 69102--69152 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
69092 ATGTATGAAT
* *
69102 TTTTAATAAATTTTA--AAG
1 TTTTAATAATTTTTATTAAA
*
69120 TTTTTAT-ATTTTTATTAAA
1 TTTTAATAATTTTTATTAAA
69139 TTTTAATAATTTTT
1 TTTTAATAATTTTT
69153 CTAAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.23
18 6 0.23
19 8 0.31
20 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAATAATTTTTATTAAA
Found at i:69152 original size:10 final size:10
Alignment explanation
Indices: 69099--69152 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
69089 AAAATGTATG
69099 AATTTTTAAT
1 AATTTTTAAT
*
69109 AAATTTTAA-
1 AATTTTTAAT
*
69118 AGTTTTT-AT
1 AATTTTTAAT
*
69127 -ATTTTTATT
1 AATTTTTAAT
*
69136 AAATTTTAAT
1 AATTTTTAAT
69146 AATTTTT
1 AATTTTT
69153 CTAAAAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
8 6 0.18
9 6 0.18
10 21 0.64
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:70271 original size:23 final size:23
Alignment explanation
Indices: 70240--70288 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
70230 AATTAATTTT
*
70240 TTAACAATTAAAAATTAAAAAAA
1 TTAAAAATTAAAAATTAAAAAAA
**
70263 TTAAAAATTAAAAATTATTAAAA
1 TTAAAAATTAAAAATTAAAAAAA
70286 TTA
1 TTA
70289 TTGAAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TTAAAAATTAAAAATTAAAAAAA
Found at i:70288 original size:6 final size:7
Alignment explanation
Indices: 70240--70279 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
70230 AATTAATTTT
*
70240 TTAACAA
1 TTAAAAA
70247 TTAAAAA
1 TTAAAAA
70254 TTAAAAAAA
1 TT--AAAAA
70263 TTAAAAA
1 TTAAAAA
70270 TTAAAAA
1 TTAAAAA
70277 TTA
1 TTA
70280 TTAAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 23 0.77
9 7 0.23
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:70288 original size:16 final size:16
Alignment explanation
Indices: 70245--70276 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
70235 ATTTTTTAAC
70245 AATTAAAAATTAAAAA
1 AATTAAAAATTAAAAA
70261 AATTAAAAATTAAAAA
1 AATTAAAAATTAAAAA
70277 TTATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AATTAAAAATTAAAAA
Found at i:72622 original size:43 final size:43
Alignment explanation
Indices: 72512--72699 Score: 227
Period size: 43 Copynumber: 4.4 Consensus size: 43
72502 TTATGAGAAA
* * ** *
72512 AAACGCCGCTATAGAACATGGTCTTTAGCGGTGCTTAACT-AT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCCTCAC
*
72554 AAACGCCTCTAAAGAACATGGTCTTTAGCGGCGCTTCCCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCCTCAC
* *
72597 AAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTCCCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCCTCAC
* * * **
72640 AAACACCGCTAAAGAACATGGTCTTTAGTGGCGTTTTTGCT-AC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCG-CTTCCCTCAC
*
72683 AAACACCGCTAAAGAAC
1 AAACGCCGCTAAAGAAC
72700 CGCTAAAGAA
Statistics
Matches: 128, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 35 0.27
43 89 0.70
44 4 0.03
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCCCTCAC
Found at i:72727 original size:54 final size:55
Alignment explanation
Indices: 72644--72748 Score: 176
Period size: 54 Copynumber: 1.9 Consensus size: 55
72634 CCTCACAAAC
* *
72644 ACCGCTAAAGAACATGGTCTTTAGTGGCGTTTTTG-CTACAAACACCGCTAAAGA
1 ACCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTGCCCACAAACACCGCTAAAGA
*
72698 ACCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTGCCCACAAACGCCGCTA
1 ACCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTGCCCACAAACACCGCTA
72749 TAGATAATGT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 34 0.72
55 13 0.28
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (55 bp):
ACCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTGCCCACAAACACCGCTAAAGA
Found at i:72774 original size:98 final size:97
Alignment explanation
Indices: 72602--72793 Score: 244
Period size: 98 Copynumber: 2.0 Consensus size: 97
72592 CTCACAAACG
*
72602 CCGCTAAAGACCATGATCTTTAGCGGCGCTTCCCTCACAAACACCGCTAAAGAACATGGTCTTTA
1 CCGCTAAAGAACATGATCTTTAGCGGCGCTTCCCTCACAAACACCGCTAAAGAACATGGTCTTTA
* * *
72667 GTGGCGTTTTTGCTACAAACACCGCTAAAGAA
66 GTGGAGTTTTTCCCACAAACACCGCTAAAGAA
* * * * * *
72699 CCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTGCC-CACAAACGCCGCTATAGATA-ATGTTCT
1 CCGCTAAAGAACATGATCTTTAGCGGCG--CTTCCCTCACAAACACCGCTAAAGA-ACATGGTCT
*
72762 TTAGTGGAGTTTTTCCCACAAACGCCGCTAAA
63 TTAGTGGAGTTTTTCCCACAAACACCGCTAAA
72794 ATTAACAGAT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
97 26 0.32
98 50 0.62
99 5 0.06
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (97 bp):
CCGCTAAAGAACATGATCTTTAGCGGCGCTTCCCTCACAAACACCGCTAAAGAACATGGTCTTTA
GTGGAGTTTTTCCCACAAACACCGCTAAAGAA
Found at i:73140 original size:21 final size:21
Alignment explanation
Indices: 73111--73155 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
73101 ACTTTCTTCA
* *
73111 CTTCTCTCGTTGCTGCCTCCG
1 CTTCCCTCGCTGCTGCCTCCG
*
73132 CTTCCCTCGCTGCTGCCTCTG
1 CTTCCCTCGCTGCTGCCTCCG
73153 CTT
1 CTT
73156 TAAATTGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.44, G:0.18, T:0.38
Consensus pattern (21 bp):
CTTCCCTCGCTGCTGCCTCCG
Found at i:73998 original size:40 final size:41
Alignment explanation
Indices: 73918--74066 Score: 151
Period size: 41 Copynumber: 3.7 Consensus size: 41
73908 AAAAAACGCT
* * * * *
73918 GCAAAAGGT-AAAGTAATAGCAGCGTTTTTCCATAAA-CGCC
1 GCAAAAGGTCAAAGCAATAGCGGCGTTTAT-GAGAAAGCGCC
73958 GCAAAAGGT-AAAGCAATAGCGGCGTTTATGAGAAAGCGCC
1 GCAAAAGGTCAAAGCAATAGCGGCGTTTATGAGAAAGCGCC
* * * * *
73998 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAATGCGCT
1 GCAAAAGGTCAAAGCAATAGCGGCGTTTATGAGAAAGCGCC
* * *
74039 GCTAAAGGTCAGAGCATTAGCGGCGTTT
1 GCAAAAGGTCAAAGCAATAGCGGCGTTT
74067 TCTCATAAGC
Statistics
Matches: 97, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.04
40 38 0.39
41 55 0.57
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.21
Consensus pattern (41 bp):
GCAAAAGGTCAAAGCAATAGCGGCGTTTATGAGAAAGCGCC
Found at i:74026 original size:41 final size:41
Alignment explanation
Indices: 73954--74066 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
73944 TTTCCATAAA
* * *
73954 CGCCGCAAAAGGT-AAAGCAATAGCGGCGTTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
*
73994 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAATG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
*
74035 CGCTGCTAAAGGTCAGAGCATTAGCGGCGTTT
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTT
74067 TCTCATAAGC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 12 0.18
41 55 0.82
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.20
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAG
Found at i:76361 original size:43 final size:43
Alignment explanation
Indices: 76304--76517 Score: 259
Period size: 43 Copynumber: 5.0 Consensus size: 43
76294 GCAGAGTTTA
* * *
76304 TGGGCAAAGTGCCGTTAAAGACCATGTTCTTTAGAGGGGTTTGT
1 TGGG-AAAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTTGT
* * *
76348 TGGGAAAGAGCCGTTAAAGACCATGTTCTTTAGCTGCGTTCGT
1 TGGGAAAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTTGT
* * * *
76391 GGGGAAAGCGCCGNTAAAGATCATGCTCTTTAGCGGCGTTTG-
1 TGGGAAAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTTGT
* * *
76433 TGGGTAAGGCGCAGCTAAAGACCATGTTCTTTAGCGGCGTTTGT
1 TGGG-AAAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTTGT
* * *
76477 TGAGAAAGCGCCGTTAAAGACCATGCTCTATAGCGGCGTTT
1 TGGGAAAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTT
76518 TTTCTTATAA
Statistics
Matches: 144, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
42 3 0.02
43 134 0.93
44 7 0.05
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (43 bp):
TGGGAAAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTTGT
Found at i:77752 original size:41 final size:41
Alignment explanation
Indices: 77682--77985 Score: 320
Period size: 41 Copynumber: 7.4 Consensus size: 41
77672 CGTTTGCTTA
*
77682 ACCTTTAGCGGCGTTTTCCCTATAAACGCCGCTAATGCTCTG
1 ACCTTTAGCGGCGCTTTCCC-ATAAACGCCGCTAATGCTCTG
* * * * *
77724 ACCTTTAGCTGTGCTCTCCCATAAACGCCACTAATGCTTTG
1 ACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTG
* * *
77765 TCCTTTAGCGGCGCTTTGCCAGAAACGCCGCTAATGCTCTG
1 ACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTG
* * * * *
77806 ATCTTTAGTGGCGCTTTACCATAAACGCCGCAAATTCTCTG
1 ACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTG
** *
77847 ACCTTTAGCGGCGCTTTCCCATAAGTGTCGCTAATGCTCTG
1 ACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTG
* * ** ** *
77888 ACATTTAGCGACATTTTCCCATAAGTGCCGCTAATGCTCTA
1 ACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTG
* * ** * *
77929 ACCTTTAACGGTGCTTTTTCATAAGCGCCGCTAATGCTATG
1 ACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTG
*
77970 ACCTTTAGCGACGCTT
1 ACCTTTAGCGGCGCTT
77986 GATGCTCTGA
Statistics
Matches: 213, Mismatches: 49, Indels: 1
0.81 0.19 0.00
Matches are distributed among these distances:
41 197 0.92
42 16 0.08
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (41 bp):
ACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTG
Found at i:77979 original size:24 final size:25
Alignment explanation
Indices: 77952--78007 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
77942 CTTTTTCATA
*
77952 AGCGCCGC-TAATGCTATGACCTTT
1 AGCGACGCTTAATGCTATGACCTTT
* * *
77976 AGCGACGCTTGATGCTCTGACTTTT
1 AGCGACGCTTAATGCTATGACCTTT
78001 AGCGACG
1 AGCGACG
78008 TTTTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (25 bp):
AGCGACGCTTAATGCTATGACCTTT
Found at i:78052 original size:17 final size:17
Alignment explanation
Indices: 78027--78061 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
78017 AAACGCCGCT
*
78027 ATTGTTTTACCTTTTGC
1 ATTGCTTTACCTTTTGC
78044 ATTGCTTTACCTTTTGC
1 ATTGCTTTACCTTTTGC
78061 A
1 A
78062 GCATTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.20, G:0.11, T:0.54
Consensus pattern (17 bp):
ATTGCTTTACCTTTTGC
Found at i:81745 original size:6 final size:6
Alignment explanation
Indices: 81734--81764 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
81724 TAAATTTCTG
81734 TATTTC TATTTC TATTTC TATTTC TATTTC T
1 TATTTC TATTTC TATTTC TATTTC TATTTC T
81765 TTTTGTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTC
Found at i:83020 original size:26 final size:26
Alignment explanation
Indices: 82991--83040 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
82981 GTCAAATTTA
**
82991 ATTAAAATTAACTGTTAAATTTGTTT
1 ATTAAAAAAAACTGTTAAATTTGTTT
*
83017 ATTAAAAAAAATTGTTAAATTTGT
1 ATTAAAAAAAACTGTTAAATTTGT
83041 GTCATATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (26 bp):
ATTAAAAAAAACTGTTAAATTTGTTT
Found at i:83443 original size:32 final size:30
Alignment explanation
Indices: 83407--83480 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
83397 TACACTCAAA
* ***
83407 GTCACTAAACTAATTAATAAATTTACATTTTG
1 GTCACTAAACT-ATCAA-AAATTTACAAAATG
*
83439 GTCACTCAACT-TCAAAAATTTACAAAATG
1 GTCACTAAACTATCAAAAATTTACAAAATG
83468 GTCACTAAACTAT
1 GTCACTAAACTAT
83481 TGAAAAGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 21 0.60
30 4 0.11
32 10 0.29
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (30 bp):
GTCACTAAACTATCAAAAATTTACAAAATG
Found at i:83839 original size:31 final size:31
Alignment explanation
Indices: 83804--83863 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
83794 GCTTAACAGC
83804 TTAATGACTTAAACAAAAACTTCCAAATAGT
1 TTAATGACTTAAACAAAAACTTCCAAATAGT
* ** *
83835 TTAATGGCTTAAATGAAAACTTTCAAATA
1 TTAATGACTTAAACAAAAACTTCCAAATA
83864 ATCCAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (31 bp):
TTAATGACTTAAACAAAAACTTCCAAATAGT
Found at i:97936 original size:20 final size:20
Alignment explanation
Indices: 97910--97956 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
97900 AATTTTATAA
*
97910 TAAATTTT-TATATTTGTTTT
1 TAAATTTTGTATAATT-TTTT
*
97930 TAGATTTTGTATAATTTTTT
1 TAAATTTTGTATAATTTTTT
97950 TAAATTT
1 TAAATTT
97957 GCATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (20 bp):
TAAATTTTGTATAATTTTTT
Found at i:99652 original size:25 final size:25
Alignment explanation
Indices: 99624--99714 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 25
99614 TTTATATCAA
99624 TTTGTTTTGTTTTATATTGCATTAT
1 TTTGTTTTGTTTTATATTGCATTAT
* *
99649 TTTGCTTTGTTTTATATTGCTTTAGATTAC
1 TTTGTTTTGTTTTATATTGC-----ATTAT
* * *
99679 TTTGTTTTGCTTTATATTACTTTAT
1 TTTGTTTTGTTTTATATTGCATTAT
*
99704 ATTGTTTTGTT
1 TTTGTTTTGTT
99715 ATACCTTGTA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
25 31 0.60
30 21 0.40
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.66
Consensus pattern (25 bp):
TTTGTTTTGTTTTATATTGCATTAT
Found at i:99672 original size:10 final size:10
Alignment explanation
Indices: 99659--99707 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
99649 TTTGCTTTGT
99659 TTTATATTGC
1 TTTATATTGC
* *
99669 TTTAGATTAC
1 TTTATATTGC
* *
99679 TTTGTTTTGC
1 TTTATATTGC
*
99689 TTTATATTAC
1 TTTATATTGC
99699 TTTATATTG
1 TTTATATTG
99708 TTTTGTTATA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.20, C:0.08, G:0.10, T:0.61
Consensus pattern (10 bp):
TTTATATTGC
Found at i:99713 original size:30 final size:30
Alignment explanation
Indices: 99644--99714 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
99634 TTTATATTGC
* * *
99644 ATTATTTTGCTTTGTTTTATATTGCTTTAG
1 ATTATTTTGTTTTGCTTTATATTACTTTAG
* *
99674 ATTACTTTGTTTTGCTTTATATTACTTTAT
1 ATTATTTTGTTTTGCTTTATATTACTTTAG
*
99704 ATTGTTTTGTT
1 ATTATTTTGTT
99715 ATACCTTGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.17, C:0.07, G:0.11, T:0.65
Consensus pattern (30 bp):
ATTATTTTGTTTTGCTTTATATTACTTTAG
Found at i:99728 original size:50 final size:50
Alignment explanation
Indices: 99674--99786 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 50
99664 ATTGCTTTAG
* * *
99674 ATTACTTTGTTTTGCT-TTATATTACTTTATATTGTTTTGTTATACCTTGT
1 ATTACTTTGCTTTG-TATTATATTACTTTATATTGCTTTGCTATACCTTGT
* * * *
99724 ATTACTTTGCTTTGTATTATTTTATTTTATATTGCTTTGCTATGCCTTTT
1 ATTACTTTGCTTTGTATTATATTACTTTATATTGCTTTGCTATACCTTGT
99774 ATTACTTTGCTTT
1 ATTACTTTGCTTT
99787 ATCTTGTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 1 0.02
50 54 0.98
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.62
Consensus pattern (50 bp):
ATTACTTTGCTTTGTATTATATTACTTTATATTGCTTTGCTATACCTTGT
Found at i:99738 original size:25 final size:24
Alignment explanation
Indices: 99709--99786 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 24
99699 TTTATATTGT
*
99709 TTTGTTATACCTTGTATTACTTTGC
1 TTTG-TATACCTTATATTACTTTGC
** *
99734 TTTGTATTATTTTATTTTA-TATTGC
1 TTTGTA-TACCTTATATTACT-TTGC
* *
99759 TTTGCTATGCCTTTTATTACTTTGC
1 TTTG-TATACCTTATATTACTTTGC
99784 TTT
1 TTT
99787 ATCTTGTTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
24 3 0.08
25 34 0.85
26 3 0.08
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.62
Consensus pattern (24 bp):
TTTGTATACCTTATATTACTTTGC
Found at i:99849 original size:10 final size:10
Alignment explanation
Indices: 99836--99894 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
99826 TTTATATTTT
99836 TTTGTTTTAC
1 TTTGTTTTAC
99846 TTTGTTTTA-
1 TTTGTTTTAC
99855 TATTGTTTTAC
1 T-TTGTTTTAC
* *
99866 TTTATATTAC
1 TTTGTTTTAC
* **
99876 TTTGCTTTGT
1 TTTGTTTTAC
99886 TTTGTTTTA
1 TTTGTTTTA
99895 GTTTATATTG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
9 1 0.03
10 36 0.95
11 1 0.03
ACGTcount: A:0.14, C:0.07, G:0.10, T:0.69
Consensus pattern (10 bp):
TTTGTTTTAC
Found at i:99869 original size:15 final size:15
Alignment explanation
Indices: 99851--99912 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
99841 TTTACTTTGT
99851 TTTATATTGTTTTAC
1 TTTATATTGTTTTAC
** *
99866 TTTATATTACTTTGC
1 TTTATATTGTTTTAC
* * *
99881 TTTGTTTTGTTTTAG
1 TTTATATTGTTTTAC
99896 TTTATATTGTTTT-C
1 TTTATATTGTTTTAC
99910 TTT
1 TTT
99913 TGTTCTATAT
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
14 3 0.09
15 32 0.91
ACGTcount: A:0.15, C:0.06, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTATATTGTTTTAC
Found at i:99884 original size:35 final size:35
Alignment explanation
Indices: 99845--100201 Score: 207
Period size: 35 Copynumber: 10.2 Consensus size: 35
99835 TTTTGTTTTA
*
99845 CTTTGTTTTATATTGTTTTACTTTATATTACTTTG
1 CTTTGTTTTATATTGTTTTGCTTTATATTACTTTG
* *
99880 CTTTG---T-T-TTGTTTTAG-TTTATATT-GTTTT
1 CTTTGTTTTATATTGTTTT-GCTTTATATTACTTTG
* ** * * *
99909 CTTTTGTTCTATATTGCGTTGTTTTGTATTACTTTTA
1 C-TTTGTTTTATATTGTTTTGCTTTATATTAC-TTTG
*** * * * * *
99946 CTTTACATTACT-TTGCTTT-ATATCATTTTATTTTG
1 CTTTGTTTTA-TATTGTTTTGCT-TTATATTACTTTG
* *
99981 CTTTGTTTTATATTCTTTTGTTTTATATTACTTTG
1 CTTTGTTTTATATTGTTTTGCTTTATATTACTTTG
* *
100016 CTTTGTTTTATATTGCTTTGCTTTTTATTA-TTTGG
1 CTTTGTTTTATATTGTTTTGCTTTATATTACTTT-G
100051 CTTTGTTTTATATTGTTTTGCTATGTTTTATATTACTTTG
1 CTTTGTTTTATATTGTTTTGC-----TTTATATTACTTTG
* ** ***
100091 TTTTGTTTTATATTACTTTGCTTTATATCGTTTTG
1 CTTTGTTTTATATTGTTTTGCTTTATATTACTTTG
* * *
100126 CTTTGCTTTATATCGTTTTGCTTTGCT-TTA-TATTG
1 CTTTGTTTTATATTGTTTTGCTTT-ATATTACT-TTG
* * * *
100161 CTTTGCTTTGTATTATTTTGCTTTATATTGCTTTG
1 CTTTGTTTTATATTGTTTTGCTTTATATTACTTTG
100196 CTTTGT
1 CTTTGT
100202 ATTACTTTAT
Statistics
Matches: 243, Mismatches: 54, Indels: 50
0.70 0.16 0.14
Matches are distributed among these distances:
29 4 0.02
30 19 0.08
31 1 0.00
32 1 0.00
33 1 0.00
34 8 0.03
35 155 0.64
36 19 0.08
37 5 0.02
40 27 0.11
41 3 0.01
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.65
Consensus pattern (35 bp):
CTTTGTTTTATATTGTTTTGCTTTATATTACTTTG
Found at i:99907 original size:20 final size:20
Alignment explanation
Indices: 99882--99924 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
99872 TTACTTTGCT
*
99882 TTGTTTTGTTTTAGTT-TATA
1 TTGTTTTCTTTT-GTTCTATA
99902 TTGTTTTCTTTTGTTCTATA
1 TTGTTTTCTTTTGTTCTATA
99922 TTG
1 TTG
99925 CGTTGTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.70
Consensus pattern (20 bp):
TTGTTTTCTTTTGTTCTATA
Found at i:99916 original size:30 final size:30
Alignment explanation
Indices: 99679--99903 Score: 126
Period size: 30 Copynumber: 7.6 Consensus size: 30
99669 TTTAGATTAC
* *
99679 TTTGTTTTGCTTTATATTACTTT-ATATTGT
1 TTTGTTTTACTTTATATTACTTTGCT-TTGT
* * *
99709 TTTGTTATACCTTGTATTACTTTGCTTTGT
1 TTTGTTTTACTTTATATTACTTTGCTTTGT
* * * * * *
99739 ATTATTTTATTTTATATTGCTTTGCTATGCC
1 TTTGTTTTACTTTATATTACTTTGCTTTG-T
* * *
99770 TTT-TATTACTTTGCT-TTA-TCTTGTTTTGT
1 TTTGTTTTACTTT-ATATTACT-TTGCTTTGT
*
99799 TTTGTTTTA-TGTTATTTTACTTT--TTT-T
1 TTTGTTTTACT-TTATATTACTTTGCTTTGT
* * * * * *
99826 TTTATATTT-TTTTGTTTTACTTTGTTTTAT
1 TTTGT-TTTACTTTATATTACTTTGCTTTGT
*
99856 ATTGTTTTACTTTATATTACTTTGCTTTGT
1 TTTGTTTTACTTTATATTACTTTGCTTTGT
*
99886 TTTGTTTTAGTTTATATT
1 TTTGTTTTACTTTATATT
99904 GTTTTCTTTT
Statistics
Matches: 146, Mismatches: 35, Indels: 28
0.70 0.17 0.13
Matches are distributed among these distances:
27 16 0.11
28 7 0.05
29 12 0.08
30 106 0.73
31 5 0.03
ACGTcount: A:0.15, C:0.08, G:0.10, T:0.68
Consensus pattern (30 bp):
TTTGTTTTACTTTATATTACTTTGCTTTGT
Found at i:99933 original size:20 final size:19
Alignment explanation
Indices: 99887--99935 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
99877 TTGCTTTGTT
**
99887 TTGTTTTAGTTTATATTGTT
1 TTGTTTT-GTTTATATTGCG
*
99907 TTCTTTTGTTCTATATTGCG
1 TTGTTTTGTT-TATATTGCG
99927 TTGTTTTGT
1 TTGTTTTGT
99936 ATTACTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.67
Consensus pattern (19 bp):
TTGTTTTGTTTATATTGCG
Found at i:99999 original size:20 final size:19
Alignment explanation
Indices: 99977--100176 Score: 138
Period size: 20 Copynumber: 10.8 Consensus size: 19
99967 ATCATTTTAT
99977 TTTGCTTTGTTTTATATTC
1 TTTGCTTTGTTTTATATTC
99996 --T--TTTGTTTTATATTAC
1 TTTGCTTTGTTTTATATT-C
100012 TTTGCTTTGTTTTATATTGC
1 TTTGCTTTGTTTTATATT-C
*
100032 TTTGCTTT-TTAT-TA-T-
1 TTTGCTTTGTTTTATATTC
* *
100047 TTGGCTTTGTTTTATATTGT
1 TTTGCTTTGTTTTATATT-C
*
100067 TTTGCTATGTTTTATATTAC
1 TTTGCTTTGTTTTATATT-C
*
100087 TTTGTTTTGTTTTATATTAC
1 TTTGCTTTGTTTTATATT-C
* **
100107 TTTGC--T-TTATATCGT-
1 TTTGCTTTGTTTTATATTC
*
100122 TTTGCTTTGCTTTATA-TC
1 TTTGCTTTGTTTTATATTC
*
100140 GTTTTGCTTTGCTTTATATTGC
1 --TTTGCTTTGTTTTATATT-C
*
100162 TTTGCTTTGTATTAT
1 TTTGCTTTGTTTTAT
100177 TTTGCTTTAT
Statistics
Matches: 144, Mismatches: 19, Indels: 35
0.73 0.10 0.18
Matches are distributed among these distances:
15 25 0.17
16 4 0.03
17 12 0.08
18 9 0.06
19 3 0.02
20 89 0.62
21 1 0.01
22 1 0.01
ACGTcount: A:0.13, C:0.10, G:0.12, T:0.65
Consensus pattern (19 bp):
TTTGCTTTGTTTTATATTC
Found at i:100036 original size:55 final size:55
Alignment explanation
Indices: 99922--100249 Score: 216
Period size: 55 Copynumber: 6.1 Consensus size: 55
99912 TTGTTCTATA
* * * * * * * * *
99922 TTGCGTTGTTTTGTATTACTTTTACTTTACATTACTTTGCTTT-ATATCATTTTATT
1 TTGCTTTGTTTTATATTGC-TTTGCTTTATATTACTTTGCTTTGCT-TTATATTACT
* * *
99978 TTGCTTTGTTTTATATT-CTTTTGTTTTATATTACTTTGCTTTGTTTTATATTGCT
1 TTGCTTTGTTTTATATTGC-TTTGCTTTATATTACTTTGCTTTGCTTTATATTACT
* ** * *
100033 TTGCTTT-TTATTAT-TTGGCTTTGTTTTATATTGTTTTGCTATGTTTTATATTACT
1 TTGCTTTGTT-TTATATT-GCTTTGCTTTATATTACTTTGCTTTGCTTTATATTACT
* * *** ***
100088 TTGTTTTGTTTTATATTACTTTGCTTTATATCGTTTTGCTTTGCTTTATATCGTT
1 TTGCTTTGTTTTATATTGCTTTGCTTTATATTACTTTGCTTTGCTTTATATTACT
* * *
100143 TTGCTTTGCTTTATATTGCTTTGCTTTGTATTA---T--TTTGCTTTATATTGCT
1 TTGCTTTGTTTTATATTGCTTTGCTTTATATTACTTTGCTTTGCTTTATATTACT
* ** * *
100193 TTGCTTTG-----TATTACTTTATTTTATATTACTTTGTTTTGCTTTATATTACC
1 TTGCTTTGTTTTATATTGCTTTGCTTTATATTACTTTGCTTTGCTTTATATTACT
100243 TTGCTTT
1 TTGCTTT
100250 ACGTTATATT
Statistics
Matches: 224, Mismatches: 37, Indels: 28
0.78 0.13 0.10
Matches are distributed among these distances:
45 16 0.07
48 1 0.00
50 43 0.19
52 1 0.00
54 4 0.02
55 138 0.62
56 21 0.09
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (55 bp):
TTGCTTTGTTTTATATTGCTTTGCTTTATATTACTTTGCTTTGCTTTATATTACT
Found at i:100070 original size:15 final size:15
Alignment explanation
Indices: 99971--100229 Score: 82
Period size: 15 Copynumber: 16.3 Consensus size: 15
99961 CTTTATATCA
*
99971 TTTTATTTTGCTTTG
1 TTTTATATTGCTTTG
99986 TTTTATATT-CTTTTG
1 TTTTATATTGC-TTTG
100001 TTTTATATTACTTTGCTTTG
1 -TTT-TA-TA--TTGCTTTG
100021 TTTTATATTGCTTTG
1 TTTTATATTGCTTTG
100036 CTTTTTATTATTTGGCTTTG
1 --TTTTA-TA-TT-GCTTTG
100056 TTTTATATTG---T-
1 TTTTATATTGCTTTG
** * *
100067 TTTGCTA-TGTTTTA
1 TTTTATATTGCTTTG
* *
100081 TATTACT-TTGTTTTG
1 TTTTA-TATTGCTTTG
*
100096 TTTTATATTACTTTG
1 TTTTATATTGCTTTG
*
100111 CTTTATATCGTTTTGCTTTG
1 -TTT-TA---TATTGCTTTG
*
100131 CTTTATATCGTTTTGCTTTG
1 -TTT-TA---TATTGCTTTG
*
100151 CTTTATATTGCTTTG
1 TTTTATATTGCTTTG
* * **
100166 CTTTGTATTATTTTG
1 TTTTATATTGCTTTG
*
100181 CTTTATATTGCTTTG
1 TTTTATATTGCTTTG
* * * *
100196 CTTTGTATTACTTTA
1 TTTTATATTGCTTTG
*
100211 TTTTATATTACTTTG
1 TTTTATATTGCTTTG
100226 TTTT
1 TTTT
100230 GCTTTATATT
Statistics
Matches: 194, Mismatches: 26, Indels: 48
0.72 0.10 0.18
Matches are distributed among these distances:
10 2 0.01
11 5 0.03
12 1 0.01
13 1 0.01
14 4 0.02
15 99 0.51
16 8 0.04
17 13 0.07
18 13 0.07
19 7 0.04
20 40 0.21
21 1 0.01
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.66
Consensus pattern (15 bp):
TTTTATATTGCTTTG
Found at i:100181 original size:30 final size:30
Alignment explanation
Indices: 100146--100230 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
100136 TATCGTTTTG
100146 CTTTGCTTTATATTGCTTTGCTTTGTATTA
1 CTTTGCTTTATATTGCTTTGCTTTGTATTA
*
100176 TTTTGCTTTATATTGCTTTGCTTTGTATTA
1 CTTTGCTTTATATTGCTTTGCTTTGTATTA
** * *
100206 CTTTATTTTATATTACTTTGTTTTG
1 CTTTGCTTTATATTGCTTTGCTTTG
100231 CTTTATATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.14, C:0.11, G:0.12, T:0.64
Consensus pattern (30 bp):
CTTTGCTTTATATTGCTTTGCTTTGTATTA
Found at i:100200 original size:20 final size:20
Alignment explanation
Indices: 99997--100260 Score: 126
Period size: 20 Copynumber: 13.7 Consensus size: 20
99987 TTTATATTCT
* *
99997 TTTGTTTTATATTACTTTGC
1 TTTGCTTTATATTGCTTTGC
*
100017 TTTGTTTTATATTGCTTTGC
1 TTTGCTTTATATTGCTTTGC
*
100037 -TT--TTTAT-TAT--TTGGC
1 TTTGCTTTATAT-TGCTTTGC
* *
100052 TTTGTTTTATATTGTTTTGC
1 TTTGCTTTATATTGCTTTGC
* * * *
100072 TATGTTTTATATTACTTTGT
1 TTTGCTTTATATTGCTTTGC
* *
100092 TTTG-TTT-TA-T--ATTAC
1 TTTGCTTTATATTGCTTTGC
* *
100107 TTTGCTTTATATCGTTTTGC
1 TTTGCTTTATATTGCTTTGC
* *
100127 TTTGCTTTATATCGTTTTGC
1 TTTGCTTTATATTGCTTTGC
100147 TTTGCTTTATATTGCTTTGC
1 TTTGCTTTATATTGCTTTGC
* *
100167 TTTG-TATTATTTTGCTTT-A
1 TTTGCT-TTATATTGCTTTGC
* *
100186 TATTGCTTTGCT-TTG-TATTAC
1 T-TTGCTTT-ATATTGCT-TTGC
** * *
100207 TTTATTTTATATTACTTTGT
1 TTTGCTTTATATTGCTTTGC
* *
100227 TTTGCTTTATATTACCTTGC
1 TTTGCTTTATATTGCTTTGC
* *
100247 TTTACGTTATATTG
1 TTTGCTTTATATTG
100261 TTTTATTTTG
Statistics
Matches: 191, Mismatches: 33, Indels: 40
0.72 0.12 0.15
Matches are distributed among these distances:
15 10 0.05
16 6 0.03
17 9 0.05
18 8 0.04
19 10 0.05
20 144 0.75
21 4 0.02
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.63
Consensus pattern (20 bp):
TTTGCTTTATATTGCTTTGC
Found at i:100262 original size:35 final size:35
Alignment explanation
Indices: 100183--100264 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
100173 TTATTTTGCT
* * * * *
100183 TTATATTGCTTTGCTTTGTATTACTTTATTTTATA
1 TTATATTGTTTTGCTTTATATTACCTTACTTTACA
* *
100218 TTACT-TTGTTTTGCTTTATATTACCTTGCTTTACG
1 TTA-TATTGTTTTGCTTTATATTACCTTACTTTACA
100253 TTATATTGTTTT
1 TTATATTGTTTT
100265 ATTTTGCATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
34 1 0.03
35 36 0.95
36 1 0.03
ACGTcount: A:0.17, C:0.11, G:0.10, T:0.62
Consensus pattern (35 bp):
TTATATTGTTTTGCTTTATATTACCTTACTTTACA
Found at i:106697 original size:22 final size:22
Alignment explanation
Indices: 106641--106705 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
106631 CATGAACATT
* *
106641 GAACTCTAAACTCTAA-ATCTTA
1 GAACCCTAAACCCTAAGAT-TTA
* *
106663 GAACCTTAGACCCTAAGATTTA
1 GAACCCTAAACCCTAAGATTTA
* *
106685 GACCCCTAAACCC-AAGGTTTA
1 GAACCCTAAACCCTAAGATTTA
106706 AGGTTTAGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 7 0.21
22 25 0.74
23 2 0.06
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (22 bp):
GAACCCTAAACCCTAAGATTTA
Found at i:107518 original size:21 final size:20
Alignment explanation
Indices: 107494--107551 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
107484 TTCATTTATT
* **
107494 TAATTTCAATAAATTAAATGC
1 TAATTTGAA-AAATTAAATAA
*
107515 TAATTTGAACAATTAAATAA
1 TAATTTGAAAAATTAAATAA
107535 TAATTTGAAGAAATTAA
1 TAATTTGAA-AAATTAA
107552 TTTAATCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (20 bp):
TAATTTGAAAAATTAAATAA
Found at i:116216 original size:25 final size:25
Alignment explanation
Indices: 116186--116238 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
116176 CGAAGTACTA
*
116186 AACAGAGAGCATATAAGTGCTGGGC
1 AACAGAGAGCACATAAGTGCTGGGC
116211 AACAGAGAGCACATAAGTGCTGGGC
1 AACAGAGAGCACATAAGTGCTGGGC
116236 AAC
1 AAC
116239 TCAAAGTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.13
Consensus pattern (25 bp):
AACAGAGAGCACATAAGTGCTGGGC
Found at i:116272 original size:23 final size:23
Alignment explanation
Indices: 116242--116351 Score: 168
Period size: 23 Copynumber: 4.8 Consensus size: 23
116232 GGGCAACTCA
*
116242 AAGTGCTAATCAGAGAGCACACG
1 AAGTGCTAAACAGAGAGCACACG
*
116265 AAGTGCTAAACAAAGAGCACACG
1 AAGTGCTAAACAGAGAGCACACG
*
116288 AAGTGCTAAACAGAGAGAACAC-
1 AAGTGCTAAACAGAGAGCACACG
*
116310 ACAGTGCTAATCAGAGAGCACACG
1 A-AGTGCTAAACAGAGAGCACACG
116334 AAGTGCTAAACAGAGAGC
1 AAGTGCTAAACAGAGAGC
116352 GCGCTAGTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
22 1 0.01
23 76 0.97
24 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (23 bp):
AAGTGCTAAACAGAGAGCACACG
Found at i:116452 original size:24 final size:26
Alignment explanation
Indices: 116414--116461 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
116404 TCTACATGGG
116414 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
116440 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
116462 ACATTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:122381 original size:18 final size:19
Alignment explanation
Indices: 122348--122387 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
122338 TATAAGAGAT
*
122348 ATTTATAATAATATTTGAA
1 ATTTATAATAATATTTAAA
*
122367 ATTTA-AATTATATTTAAA
1 ATTTATAATAATATTTAAA
122385 ATT
1 ATT
122388 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTTATAATAATATTTAAA
Found at i:152269 original size:2 final size:2
Alignment explanation
Indices: 152262--152291 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
152252 GACAAAAATA
152262 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
152292 GCATGAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153340 original size:19 final size:18
Alignment explanation
Indices: 153328--153368 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
153318 AAAAATTTCC
153328 CTCTGAATAAAAAAATCTT
1 CTCTGAAT-AAAAAATCTT
*
153347 CTCTGAATAAAATAATCCT
1 CTCTGAATAAAA-AATCTT
153366 CTC
1 CTC
153369 AATCTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (18 bp):
CTCTGAATAAAAAATCTT
Found at i:158449 original size:31 final size:31
Alignment explanation
Indices: 158388--158459 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
158378 TTTATATATC
* *
158388 TTTATA-T-TTTTTAATAAATTAAATTAAAT
1 TTTATATTATTTTTAAAAAATTAAATGAAAT
*
158417 TTT-TATTATTTTTAAAAAATTGAAATGCAAT
1 TTTATATTATTTTTAAAAAATT-AAATGAAAT
158448 TTTACTATTATT
1 TTTA-TATTATT
158460 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 2 0.06
29 4 0.11
30 12 0.34
31 10 0.29
33 7 0.20
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTATATTATTTTTAAAAAATTAAATGAAAT
Found at i:160624 original size:36 final size:35
Alignment explanation
Indices: 160571--160642 Score: 81
Period size: 36 Copynumber: 2.0 Consensus size: 35
160561 TTTACTGCTG
* * *
160571 TTTTTTTATTGTCTTGTTGTCATTTTATTATTATA
1 TTTTTTTATTGTCTTGTTATCATTTTAATAATATA
* * *
160606 TTTTTATTATTTTGTTGTTATTATTTTAATAATATA
1 TTTTT-TTATTGTCTTGTTATCATTTTAATAATATA
160642 T
1 T
160643 AATTTTTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
35 5 0.17
36 25 0.83
ACGTcount: A:0.22, C:0.03, G:0.07, T:0.68
Consensus pattern (35 bp):
TTTTTTTATTGTCTTGTTATCATTTTAATAATATA
Found at i:160631 original size:14 final size:14
Alignment explanation
Indices: 160595--160633 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
160585 TGTTGTCATT
* *
160595 TTATTATTATATTT
1 TTATTATTTTATTG
*
160609 TTATTATTTTGTTG
1 TTATTATTTTATTG
160623 TTATTATTTTA
1 TTATTATTTTA
160634 ATAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (14 bp):
TTATTATTTTATTG
Found at i:164328 original size:14 final size:14
Alignment explanation
Indices: 164309--164336 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
164299 GTAAAACAAT
164309 GAAAATATTTTACA
1 GAAAATATTTTACA
164323 GAAAATATTTTACA
1 GAAAATATTTTACA
164337 TGCAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
GAAAATATTTTACA
Found at i:166271 original size:54 final size:54
Alignment explanation
Indices: 166198--166306 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
166188 TATTGATTAA
166198 TAAGTTTCTGGTAATATAAATAATAGTATGTAGGAAGGCAACAATATTAAGTAC
1 TAAGTTTCTGGTAATATAAATAATAGTATGTAGGAAGGCAACAATATTAAGTAC
166252 TAAGTTTCTGGTAATATAAATAATAGTATGTAGGAAGGCAACAATATTAAGTAC
1 TAAGTTTCTGGTAATATAAATAATAGTATGTAGGAAGGCAACAATATTAAGTAC
166306 T
1 T
166307 CTAAAATATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.32
Consensus pattern (54 bp):
TAAGTTTCTGGTAATATAAATAATAGTATGTAGGAAGGCAACAATATTAAGTAC
Found at i:170167 original size:30 final size:27
Alignment explanation
Indices: 170091--170169 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 27
170081 TTTTATATTC
*
170091 TTTTAAAATTTAAAATTTAATCTTTTA
1 TTTTAAATTTTAAAATTTAATCTTTTA
* *
170118 TTTTTATTTTTAATGAATTTAATGCTTTTA
1 TTTTAAATTTTAA--AATTTAAT-CTTTTA
170148 TATTTCAAATTTTAAAATTTAA
1 T-TTT-AAATTTTAAAATTTAA
170170 ATTTAATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 10 0.24
29 8 0.19
30 14 0.33
31 3 0.07
32 7 0.17
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTTAAATTTTAAAATTTAATCTTTTA
Found at i:171594 original size:15 final size:16
Alignment explanation
Indices: 171576--171605 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
171566 AAGTTTTATT
171576 TTTTTTTAT-TTTTTA
1 TTTTTTTATCTTTTTA
171591 TTTTTTTATCTTTTT
1 TTTTTTTATCTTTTT
171606 GTATAGGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTATCTTTTTA
Found at i:171604 original size:17 final size:17
Alignment explanation
Indices: 171569--171605 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
171559 AAGTTGGAAG
*
171569 TTTTATTTTTTTTTATT
1 TTTTATTTTTTTATATT
*
171586 TTTTATTTTTTTATCTT
1 TTTTATTTTTTTATATT
171603 TTT
1 TTT
171606 GTATAGGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTATTTTTTTATATT
Found at i:177709 original size:12 final size:12
Alignment explanation
Indices: 177668--177703 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
177658 ACTTAGCTTG
177668 GTTCCTTTTCAC
1 GTTCCTTTTCAC
177680 GTTCCTTTTCAC
1 GTTCCTTTTCAC
177692 GTTCCTTTTCAC
1 GTTCCTTTTCAC
177704 TCTCCTGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.33, G:0.08, T:0.50
Consensus pattern (12 bp):
GTTCCTTTTCAC
Found at i:197918 original size:18 final size:18
Alignment explanation
Indices: 197895--197929 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
197885 TAAAGAAATG
197895 TAAGTTTAATTAATTTTT
1 TAAGTTTAATTAATTTTT
**
197913 TAAGTTTGGTTAATTTT
1 TAAGTTTAATTAATTTT
197930 AAATTTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (18 bp):
TAAGTTTAATTAATTTTT
Found at i:197989 original size:20 final size:19
Alignment explanation
Indices: 197966--198004 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
197956 TGTTAGTTAA
*
197966 TTTGATTATTTTAAATTTTT
1 TTTGATTAATTT-AATTTTT
*
197986 TTTGTTTAATTTAATTTTT
1 TTTGATTAATTTAATTTTT
198005 AATTGATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTGATTAATTTAATTTTT
Found at i:198139 original size:20 final size:21
Alignment explanation
Indices: 198098--198140 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
198088 TAATTTACTT
198098 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
198119 TAATTTTATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
198139 TA
1 TA
198141 GTAGTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:198634 original size:21 final size:21
Alignment explanation
Indices: 198608--198652 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
198598 AGTATATTTA
*
198608 TAAAATAGTTATATAATACAAG
1 TAAATTAGTTATATAATA-AAG
198630 TAAATTTAGTTATATAATAAAG
1 TAAA-TTAGTTATATAATAAAG
198652 T
1 T
198653 TATAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (21 bp):
TAAATTAGTTATATAATAAAG
Found at i:198886 original size:16 final size:16
Alignment explanation
Indices: 198841--198890 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
198831 AAAAAAAGTT
*
198841 TAATTAATTACTAAAA
1 TAATTAATTACAAAAA
198857 T-A-TAATATA-AAAAA
1 TAATTAAT-TACAAAAA
*
198871 TAATTAATTACCAAAA
1 TAATTAATTACAAAAA
198887 TAAT
1 TAAT
198891 ATCCCCGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTACAAAAA
Found at i:199291 original size:15 final size:15
Alignment explanation
Indices: 199267--199304 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
199257 GAGCTCGCGT
*
199267 ATCGTTCATTGAGGG
1 ATCGTGCATTGAGGG
199282 ATCGTGCATTGAGGG
1 ATCGTGCATTGAGGG
199297 ATCGTGCA
1 ATCGTGCA
199305 CAGGGTCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (15 bp):
ATCGTGCATTGAGGG
Found at i:203193 original size:12 final size:12
Alignment explanation
Indices: 203176--203201 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
203166 AATATGTGTA
203176 ACTGGATTTTCG
1 ACTGGATTTTCG
203188 ACTGGATTTTCG
1 ACTGGATTTTCG
203200 AC
1 AC
203202 GTCATTCGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (12 bp):
ACTGGATTTTCG
Found at i:203935 original size:4 final size:4
Alignment explanation
Indices: 203913--203987 Score: 114
Period size: 4 Copynumber: 18.2 Consensus size: 4
203903 TTTTTTACTC
* *
203913 CTTT CTTT CCTCT CCTT CTTT CTTT CTTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT
203963 CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT C
203988 CCGTTTATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
4 58 0.89
5 7 0.11
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:204675 original size:19 final size:20
Alignment explanation
Indices: 204614--204694 Score: 71
Period size: 19 Copynumber: 4.2 Consensus size: 20
204604 AATATTTTAA
204614 TTAAAATATAAT--ATTATT
1 TTAAAATATAATACATTATT
* **
204632 TAAAAATATAATACA-TAAA
1 TTAAAATATAATACATTATT
* *
204651 TAAAAATCTAATA-ATTATT
1 TTAAAATATAATACATTATT
* *
204670 TTAAAATATAAAATATTATT
1 TTAAAATATAATACATTATT
204690 TTAAA
1 TTAAA
204695 TTCTAAAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
18 12 0.24
19 26 0.52
20 12 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAATATAATACATTATT
Found at i:204701 original size:20 final size:20
Alignment explanation
Indices: 204664--204705 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
204654 AAATCTAATA
204664 ATTATTTTAAAATATAAAAT
1 ATTATTTTAAAATATAAAAT
* *
204684 ATTATTTTAAATTCTAAAAT
1 ATTATTTTAAAATATAAAAT
204704 AT
1 AT
204706 ATGATACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTATTTTAAAATATAAAAT
Found at i:207314 original size:18 final size:16
Alignment explanation
Indices: 207283--207326 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
207273 GGTTTGGGGT
*
207283 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
207300 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
207314 TTAAAAATTTATT
1 TTAAAAATTTATT
207327 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:208590 original size:25 final size:25
Alignment explanation
Indices: 208553--208602 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
208543 TGCTTGCTGG
208553 TTCAGTGCAAGAGCAGCCACAACAA
1 TTCAGTGCAAGAGCAGCCACAACAA
*
208578 TTCAGTGCGAGAGCAGCCACAACAA
1 TTCAGTGCAAGAGCAGCCACAACAA
208603 AGAAGAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.28, G:0.22, T:0.12
Consensus pattern (25 bp):
TTCAGTGCAAGAGCAGCCACAACAA
Found at i:216053 original size:145 final size:143
Alignment explanation
Indices: 215887--216159 Score: 440
Period size: 145 Copynumber: 1.9 Consensus size: 143
215877 TTCATTAGGT
*
215887 AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGACATCCTTGTATTTTTTTTCAACTCG
1 AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGACACCCTTGTA-TTTTTTTCAACTCG
* **
215952 TATCATATTAATATACGTTTATA-TCAGTACTTGAAAAAAAATTTGAAGGTGATGGCACACTGAT
65 TATCATATTAATATACGTTTATACT-AATACTTG-AAAAAAATTTGAAGGTGATAACACACTGAT
216016 GGCCAACACCCCTTTA
128 GGCCAACACCCCTTTA
*
216032 AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGGCACCCTTGTATTTTTTTCAACTCGT
1 AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGACACCCTTGTATTTTTTTCAACTCGT
* * *
216097 ATCATATTGATATACGTTTATACTAATACTTGAAAAAATTTTGAGGGTGATAACACACTGATG
66 ATCATATTAATATACGTTTATACTAATACTTGAAAAAAATTTGAAGGTGATAACACACTGATG
216160 ATCGACACCC
Statistics
Matches: 119, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
143 27 0.23
144 43 0.36
145 49 0.41
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (143 bp):
AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGACACCCTTGTATTTTTTTCAACTCGT
ATCATATTAATATACGTTTATACTAATACTTGAAAAAAATTTGAAGGTGATAACACACTGATGGC
CAACACCCCTTTA
Found at i:216172 original size:144 final size:145
Alignment explanation
Indices: 215887--216175 Score: 440
Period size: 144 Copynumber: 2.0 Consensus size: 145
215877 TTCATTAGGT
*
215887 AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGACATCCTTGTATTTTTTTTCAACTCG
1 AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGACACCCTTGTATTTTTTTTCAACTCG
* **
215952 TATCATATTAATATACGTTTATATCAGTACTTGAAAAAAAATTTGAAGGTGATGGCACACTGATG
66 TATCATATTAATATACGTTTATATCAATACTTGAAAAAAAATTTGAAGGTGATAACACACTGATG
*
216017 GCCAACACCCCTTTA
131 ACCAACACCCCTTTA
*
216032 AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGGCACCCTTGTA-TTTTTTTCAACTCG
1 AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGACACCCTTGTATTTTTTTTCAACTCG
* * *
216096 TATCATATTGATATACGTTTATA-CTAATACTTG-AAAAAATTTTGAGGGTGATAACACACTGAT
66 TATCATATTAATATACGTTTATATC-AATACTTGAAAAAAAATTTGAAGGTGATAACACACTGAT
* *
216159 GATCGACACCCCCTTTA
130 GACCAACA-CCCCTTTA
216176 TCAAATTAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
143 32 0.24
144 51 0.39
145 48 0.37
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (145 bp):
AAAAAAATAATTTTTTGGGTGCTGGGGACTAAATAGTCGACACCCTTGTATTTTTTTTCAACTCG
TATCATATTAATATACGTTTATATCAATACTTGAAAAAAAATTTGAAGGTGATAACACACTGATG
ACCAACACCCCTTTA
Found at i:216282 original size:18 final size:18
Alignment explanation
Indices: 216259--216298 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
216249 AATGTCAAGT
* *
216259 TTTTTTAATTTTAATTTA
1 TTTTTTAATATAAATTTA
*
216277 TTTTTTTATATAAATTTA
1 TTTTTTAATATAAATTTA
216295 TTTT
1 TTTT
216299 AAACTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTAATATAAATTTA
Found at i:216328 original size:66 final size:68
Alignment explanation
Indices: 216258--216392 Score: 154
Period size: 66 Copynumber: 2.0 Consensus size: 68
216248 CAATGTCAAG
* ** *
216258 TTTTTTTAATTTTAA-TTTATTTTT-TTATATAAATTTATTTTAAACTTTAATTAACTTATTTC-
1 TTTTTTTAAATTTAATTTTATTTTTAAAAT-TAAATTTATTTTAAACTGTAATTAACTTATTTCT
216320 TTAA
65 TTAA
* * *
216324 --TTTTTAAATTTAATTTTGATTTTTAAAATTAATTTTATTTTAAACTGTAATTCATTTATTTCT
1 TTTTTTTAAATTTAATTTT-ATTTTTAAAATTAAATTTATTTTAAACTGTAATTAACTTATTTCT
216387 TTAA
65 TTAA
216391 TT
1 TT
216393 AATTTTGATT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
64 12 0.21
65 3 0.05
66 35 0.62
67 6 0.11
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (68 bp):
TTTTTTTAAATTTAATTTTATTTTTAAAATTAAATTTATTTTAAACTGTAATTAACTTATTTCTT
TAA
Found at i:216345 original size:19 final size:19
Alignment explanation
Indices: 216323--216416 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
216313 TTATTTCTTA
*
216323 ATTTTTAAATTTAATTTTG
1 ATTTTTAAAATTAATTTTG
216342 ATTTTTAAAATTAATTTT-
1 ATTTTTAAAATTAATTTTG
* *
216360 A-TTTTAAACTGTAATTCATTT
1 ATTTTTAAAAT-TAATT--TTG
*
216381 ATTTCTT-TAATTAATTTTG
1 ATTT-TTAAAATTAATTTTG
216400 ATTTTTAAAATTAATTT
1 ATTTTTAAAATTAATTT
216417 CATTTTAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
17 8 0.13
18 8 0.13
19 32 0.52
20 2 0.03
21 6 0.10
22 4 0.06
23 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTTTAAAATTAATTTTG
Found at i:216398 original size:39 final size:43
Alignment explanation
Indices: 216350--216435 Score: 110
Period size: 41 Copynumber: 2.1 Consensus size: 43
216340 TGATTTTTAA
* *
216350 AATTAATTTT-A-TTTTAAACTGTAA-TTCA-TTT-ATTTCTTT
1 AATTAATTTTGATTTTTAAAAT-TAATTTCATTTTAATTTATTT
216389 AATTAATTTTGATTTTTAAAATTAATTTCATTTTAATTTATTT
1 AATTAATTTTGATTTTTAAAATTAATTTCATTTTAATTTATTT
216432 AATT
1 AATT
216436 TTACAATCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
39 10 0.25
40 4 0.10
41 12 0.30
42 3 0.08
43 11 0.28
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (43 bp):
AATTAATTTTGATTTTTAAAATTAATTTCATTTTAATTTATTT
Found at i:216666 original size:40 final size:41
Alignment explanation
Indices: 216614--216696 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 41
216604 TGTACCAGAC
*
216614 ATAATTTTTATAAAATTTT-ATG-GTTTTTAATTAA-TTTATA
1 ATAATTATTAT-AAATTTTCATGAGTTTTTAA-TAATTTTATA
*
216654 ATAATTATTATAAATTTTCATGATTTTTTAATAATTTTATA
1 ATAATTATTATAAATTTTCATGAGTTTTTAATAATTTTATA
216695 AT
1 AT
216697 TTTTTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
39 7 0.18
40 16 0.42
41 15 0.39
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (41 bp):
ATAATTATTATAAATTTTCATGAGTTTTTAATAATTTTATA
Found at i:216709 original size:29 final size:30
Alignment explanation
Indices: 216648--216714 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
216638 TTTTAATTAA
216648 TTTATAATAATTATTATAAATTTTCATGAT
1 TTTATAATAATTATTATAAATTTTCATGAT
* * * **
216678 TTTTTAATAATT-TTATAATTTTTTATTTT
1 TTTATAATAATTATTATAAATTTTCATGAT
216707 TTTATAAT
1 TTTATAAT
216715 TCCAGAATGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (30 bp):
TTTATAATAATTATTATAAATTTTCATGAT
Found at i:219582 original size:15 final size:15
Alignment explanation
Indices: 219571--219600 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
219561 GAGAAGAAGT
219571 CAAAGAAGAAGAAAA
1 CAAAGAAGAAGAAAA
*
219586 CCAAGAAGAAGAAAA
1 CAAAGAAGAAGAAAA
219601 GGCGGAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (15 bp):
CAAAGAAGAAGAAAA
Found at i:227039 original size:12 final size:14
Alignment explanation
Indices: 227022--227054 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
227012 GAAAAGGCGG
227022 TAAAAATAAAA-A-
1 TAAAAATAAAATAT
227034 TAAAAATAAAATAT
1 TAAAAATAAAATAT
227048 TAAAAAT
1 TAAAAAT
227055 TTATCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 1 0.05
14 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAAATAAAATAT
Found at i:230482 original size:33 final size:30
Alignment explanation
Indices: 230436--230497 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
230426 TCCAGGCGGA
*
230436 TATCCACCGGCTGGAGCGTACCCCCCTCAAGGC
1 TATCCACCAGCT-G-GC-TACCCCCCTCAAGGC
* *
230469 TATCCTCCAGCTGGCTACCCTCCTCAAGG
1 TATCCACCAGCTGGCTACCCCCCTCAAGG
230498 AGGATACCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 13 0.50
31 2 0.08
32 1 0.04
33 10 0.38
ACGTcount: A:0.18, C:0.42, G:0.21, T:0.19
Consensus pattern (30 bp):
TATCCACCAGCTGGCTACCCCCCTCAAGGC
Found at i:230758 original size:9 final size:9
Alignment explanation
Indices: 230730--230790 Score: 68
Period size: 9 Copynumber: 6.8 Consensus size: 9
230720 CACCATTTGT
*
230730 CTCATGGTT
1 CTCATGGTG
* *
230739 CCCACGGTG
1 CTCATGGTG
230748 CTCATGGTG
1 CTCATGGTG
*
230757 CTTATGGTG
1 CTCATGGTG
*
230766 GTCATGGTG
1 CTCATGGTG
*
230775 CTTATGGTG
1 CTCATGGTG
230784 CTCATGG
1 CTCATGG
230791 ATTTGGTCAC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.11, C:0.21, G:0.33, T:0.34
Consensus pattern (9 bp):
CTCATGGTG
Found at i:230765 original size:18 final size:18
Alignment explanation
Indices: 230744--230790 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
230734 TGGTTCCCAC
230744 GGTGCTCATGGTGCTTAT
1 GGTGCTCATGGTGCTTAT
*
230762 GGTGGTCATGGTGCTTAT
1 GGTGCTCATGGTGCTTAT
230780 GGTGCTCATGG
1 GGTGCTCATGG
230791 ATTTGGTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.38, T:0.36
Consensus pattern (18 bp):
GGTGCTCATGGTGCTTAT
Found at i:230878 original size:24 final size:24
Alignment explanation
Indices: 230849--230898 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
230839 GCATCATGGG
*
230849 GGGAAATTCAAGCACGGGAAGCAT
1 GGGAAATTCAAGCACGGAAAGCAT
*
230873 GGGAAATTTAAGCACGGAAAGCAT
1 GGGAAATTCAAGCACGGAAAGCAT
230897 GG
1 GG
230899 AGGAGGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.34, T:0.14
Consensus pattern (24 bp):
GGGAAATTCAAGCACGGAAAGCAT
Found at i:239292 original size:18 final size:18
Alignment explanation
Indices: 239269--239311 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
239259 TATGTTTTCA
*
239269 AATAATA-TATTAATTAAT
1 AATAATATTA-TAATAAAT
*
239287 AATAATGTTATAATAAAT
1 AATAATATTATAATAAAT
239305 AATAATA
1 AATAATA
239312 ATTTATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AATAATATTATAATAAAT
Found at i:252164 original size:18 final size:19
Alignment explanation
Indices: 252130--252170 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
252120 ACCTCAATTT
*
252130 TTTTTCTTCTTCTTTCCA-
1 TTTTCCTTCTTCTTTCCAC
252148 TTTTCCTTCTT-TATTCCAC
1 TTTTCCTTCTTCT-TTCCAC
252167 TTTT
1 TTTT
252171 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 15 0.75
19 4 0.20
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTCCTTCTTCTTTCCAC
Found at i:253219 original size:30 final size:29
Alignment explanation
Indices: 253185--253248 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
253175 AATTTACAAG
*
253185 AATTGGATC-AAATCAAAATTTCATGTATAC
1 AATTGGA-CAAAATC-AAAGTTCATGTATAC
*
253215 AATTGTACAAAATCAAAGTTCATGTATAC
1 AATTGGACAAAATCAAAGTTCATGTATAC
253244 AATTG
1 AATTG
253249 CACGTTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (29 bp):
AATTGGACAAAATCAAAGTTCATGTATAC
Found at i:255674 original size:29 final size:29
Alignment explanation
Indices: 255607--255662 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
255597 TCAATCTTTA
* *
255607 AGAACAATTTATTCAATTTAAATTCAAAC
1 AGAATAATTTATTCAATTTAAAATCAAAC
255636 AGAATAATTTATTCAATTTAAAATCAA
1 AGAATAATTTATTCAATTTAAAATCAA
255663 TCAACTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.36
Consensus pattern (29 bp):
AGAATAATTTATTCAATTTAAAATCAAAC
Found at i:256384 original size:17 final size:18
Alignment explanation
Indices: 256346--256386 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
256336 TAAAAATATT
*
256346 GAATATAATAAATAAATA
1 GAATAAAATAAATAAATA
*
256364 -AATAAAATAATTAAA-A
1 GAATAAAATAAATAAATA
256380 GAATAAA
1 GAATAAA
256387 GTTATTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
GAATAAAATAAATAAATA
Found at i:262778 original size:24 final size:24
Alignment explanation
Indices: 262750--262800 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
262740 AGAAATAATC
* *
262750 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
* *
262774 TTTCAATTAAGCTTTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
262798 TTT
1 TTT
262801 AAGTCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:270411 original size:20 final size:20
Alignment explanation
Indices: 270386--270426 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
270376 GATTAGAATG
270386 AGTAACTTAGGGAGGTATTT
1 AGTAACTTAGGGAGGTATTT
270406 AGTAACTTAGGGAGGTATTT
1 AGTAACTTAGGGAGGTATTT
270426 A
1 A
270427 TAGGTGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (20 bp):
AGTAACTTAGGGAGGTATTT
Found at i:270738 original size:63 final size:66
Alignment explanation
Indices: 270656--270794 Score: 221
Period size: 67 Copynumber: 2.1 Consensus size: 66
270646 TTGGTTTGTT
270656 ATTTATTTATTTATATTCAT-AA-AAT-AATAAATAAATAATAAAACAAAATTAATACTATTTTA
1 ATTTATTTATTTATATTCATAAATAATAAATAAATAAATAATAAAACAAAATTAATACTATTTTA
270718 C
66 C
* *
270719 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTT
1 ATTTATTTATTTATATTCATA-AATAATAAATAAATAAATAATAAAACAAAATTAATACTATTTT
*
270784 AT
65 AC
270786 ATTTATTTA
1 ATTTATTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
63 20 0.29
65 2 0.03
66 3 0.04
67 44 0.64
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (66 bp):
ATTTATTTATTTATATTCATAAATAATAAATAAATAAATAATAAAACAAAATTAATACTATTTTA
C
Done.