Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004709.1 Kokia drynarioides strain JFW-HI SEQ_118278, 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: 185400
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Warning! 234 characters in sequence are not A, C, G, or T
Found at i:16278 original size:2 final size:2
Alignment explanation
Indices: 16271--16301 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16261 TTGCACTATT
16271 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16302 TAGCTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28679 original size:13 final size:13
Alignment explanation
Indices: 28647--28684 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
28637 AATTGAGAAG
*
28647 AAAAAAA-AGAAA
1 AAAAAAACAAAAA
28659 AAAAAAACAAAAA
1 AAAAAAACAAAAA
*
28672 CAAAAAACAAAAA
1 AAAAAAACAAAAA
28685 TAACAGCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:28920 original size:42 final size:43
Alignment explanation
Indices: 28842--28929 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 43
28832 AATGGAATTA
*
28842 AATGGGAATTTTAAGATTAGTGATAACTTTT-AAAAAATATTT
1 AATGGGAATTTTAAGATTAGTGACAACTTTTAAAAAAATATTT
* *
28884 AATGGGAATTTTAA-AGTTGGTGACAATTTTTTAAAAAAATATTT
1 AATGGGAATTTTAAGA-TTAGTGACAA-CTTTTAAAAAAATATTT
28928 AA
1 AA
28930 AGGAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
41 1 0.03
42 22 0.55
43 4 0.10
44 13 0.32
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.40
Consensus pattern (43 bp):
AATGGGAATTTTAAGATTAGTGACAACTTTTAAAAAAATATTT
Found at i:29702 original size:16 final size:17
Alignment explanation
Indices: 29681--29714 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29671 CTGTCCTATC
29681 TTTCA-CTCATTTATTT
1 TTTCACCTCATTTATTT
29697 TTTCACTCTCATTTATTT
1 TTTCAC-CTCATTTATTT
29715 AAGATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
18 11 0.69
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTCACCTCATTTATTT
Found at i:32590 original size:29 final size:30
Alignment explanation
Indices: 32548--32604 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
32538 TTCTTTTAAA
* *
32548 TTTTATAATTATATTTTTCATTTGATAAGT
1 TTTTATAATCATATTTTTAATTTGATAAGT
*
32578 TTTTATAA-CATATTTTTAATTTTATAA
1 TTTTATAATCATATTTTTAATTTGATAA
32605 ATATTTTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTTATAATCATATTTTTAATTTGATAAGT
Found at i:37597 original size:2 final size:2
Alignment explanation
Indices: 37590--37619 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
37580 TGACACTTTA
37590 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
37620 TAAAACATAT
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:38927 original size:21 final size:20
Alignment explanation
Indices: 38889--38947 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
38879 AACATCATTT
*
38889 TTAAAAATAAATATAAATTA
1 TTAAAAATAAATAAAAATTA
*
38909 TTAAAAATTATATAAAAA-TA
1 TTAAAAA-TAAATAAAAATTA
*
38929 TTTATAAA-AAA-AAAAATTA
1 -TTAAAAATAAATAAAAATTA
38948 CAACTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
18 5 0.16
19 4 0.12
20 9 0.28
21 14 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAAAATAAATAAAAATTA
Found at i:38930 original size:20 final size:20
Alignment explanation
Indices: 38889--38930 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
38879 AACATCATTT
*
38889 TTAAAAATAAATATAAATTA
1 TTAAAAATAAATATAAAATA
*
38909 TTAAAAAT-TATATAAAAATA
1 TTAAAAATAAATAT-AAAATA
38929 TT
1 TT
38931 TATAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAATAAATATAAAATA
Found at i:42246 original size:30 final size:29
Alignment explanation
Indices: 42212--42268 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
42202 GCATTGGCTC
*
42212 AAATCTAAATTTCATATATAAAATTACACA
1 AAATC-AAAATTCATATATAAAATTACACA
* *
42242 AAATCAAAATTCTTGTATAAAATTACA
1 AAATCAAAATTCATATATAAAATTACA
42269 TATTAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (29 bp):
AAATCAAAATTCATATATAAAATTACACA
Found at i:44190 original size:17 final size:17
Alignment explanation
Indices: 44168--44201 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44158 CAAAATCATT
*
44168 TTTTGTTTTTTATTTCA
1 TTTTGTTTTTAATTTCA
44185 TTTTGTTTTTAATTTCA
1 TTTTGTTTTTAATTTCA
44202 GTCCACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTGTTTTTAATTTCA
Found at i:44448 original size:2 final size:2
Alignment explanation
Indices: 44443--44475 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44433 ATTTTTTGAG
44443 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
44476 TTCAGACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:44684 original size:180 final size:181
Alignment explanation
Indices: 44461--44797 Score: 595
Period size: 180 Copynumber: 1.9 Consensus size: 181
44451 TCTCTCTCTC
44461 TCTCTCTCTCTCTCTTTCAGACATACAATTCATTCACAATTTATTTAATTACAAACTTACAACTC
1 TCTCTCTCTCTCTCTTTCAGACATACAATTCATTCACAATTTATTTAATTACAAACTTACAACTC
*
44526 AAAATACTAACTCCATTTAATTTTACACATTCATTTACTACCTTTCAATCAATCAAGAATCAAAT
66 AAAATACTAACTCCATTTAATCTTACACATTCATTTACTACCTTTCAATCAATCAAGAATCAAAT
44591 TCAATCACGCAAGAACTTAGGAATCACATAGGGTTTACAGAACTTTTCGAG
131 TCAATCACGCAAGAACTTAGGAATCACATAGGGTTTACAGAACTTTTCGAG
* * * * * *
44642 TCTCTCTCTCT-TTTTTTATACATACAATTCATTCATAATTTATTTAATTATAAACTTGCAACTC
1 TCTCTCTCTCTCTCTTTCAGACATACAATTCATTCACAATTTATTTAATTACAAACTTACAACTC
44706 AAAATACTAACTCCATTTAATCTTACACATTCATTTACTACCTTTCAATCAATCAAGAATCAAAT
66 AAAATACTAACTCCATTTAATCTTACACATTCATTTACTACCTTTCAATCAATCAAGAATCAAAT
*
44771 TCAATCACGCAAGAATTTAGGAATCAC
131 TCAATCACGCAAGAACTTAGGAATCAC
44798 GTATGAATAT
Statistics
Matches: 148, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
180 137 0.93
181 11 0.07
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (181 bp):
TCTCTCTCTCTCTCTTTCAGACATACAATTCATTCACAATTTATTTAATTACAAACTTACAACTC
AAAATACTAACTCCATTTAATCTTACACATTCATTTACTACCTTTCAATCAATCAAGAATCAAAT
TCAATCACGCAAGAACTTAGGAATCACATAGGGTTTACAGAACTTTTCGAG
Found at i:46414 original size:194 final size:193
Alignment explanation
Indices: 46086--46435 Score: 513
Period size: 194 Copynumber: 1.8 Consensus size: 193
46076 CCGATATTGT
* * * * * * *
46086 TCACACGAGCTGTCAAGGACTCGTAACGTATGCGGTACCCCAGCCATCGGTACGGTGTCTGTCTG
1 TCACACGAGATGTCAAGAACTCGCAACATATGCGGTACCCCAGCCATCGATACGGTATCTGTCTA
46151 TAAACTGTCCCCTAACGATGCTGCTCACACGAGCTGTCGAAAATATGCATTTAAGCATAAATCTC
66 TAAACTGTCCCCTAACGATGCTGCTCACACGAGCTGTCGAAAATATGCATTTAAGCATAAATCTC
46216 AGCCATCGTAGGGCCTATAATCCATTAAGGATTCATATCTCCTTTTCCGACCCACGATGCAGC
131 AGCCATCGTAGGGCCTATAATCCATTAAGGATTCATATCTCCTTTTCCGACCCACGATGCAGC
* * *
46279 TCACACGAGATGTCGAGAACTCGCAACATATGCGGTACCTCAGCCATCGATACTGTATCTGTGC-
1 TCACACGAGATGTCAAGAACTCGCAACATATGCGGTACCCCAGCCATCGATACGGTATCTGT-CT
* * * * * * *
46343 ATATAATTGTTCCCTAATGATGTTGCTCACACGAGCTGTCGAGAATATGTATTTATGCATAAATC
65 ATA-AACTGTCCCCTAACGATGCTGCTCACACGAGCTGTCGAAAATATGCATTTAAGCATAAATC
*
46408 TCAGCCATTGTAGGGCCTATAATCCATT
129 TCAGCCATCGTAGGGCCTATAATCCATT
46436 CAAATGACCC
Statistics
Matches: 137, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
193 55 0.40
194 82 0.60
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (193 bp):
TCACACGAGATGTCAAGAACTCGCAACATATGCGGTACCCCAGCCATCGATACGGTATCTGTCTA
TAAACTGTCCCCTAACGATGCTGCTCACACGAGCTGTCGAAAATATGCATTTAAGCATAAATCTC
AGCCATCGTAGGGCCTATAATCCATTAAGGATTCATATCTCCTTTTCCGACCCACGATGCAGC
Found at i:52647 original size:2 final size:2
Alignment explanation
Indices: 52642--52670 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52632 AAAAAAAATC
52642 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
52671 AATTAAGGAA
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:54752 original size:40 final size:40
Alignment explanation
Indices: 54701--54831 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 40
54691 ATTTAGTTGT
54701 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTC
**** * * *
54741 TTCAATCTGCCCTC-TGATTAAAGTAAAAGATTGGATAGTT
1 TTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGGTC
* *
54781 TTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTC
54821 TTCAATCTGCC
1 TTCAATCTGCC
54832 TTCTGGTTAG
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
39 1 0.01
40 71 0.97
41 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (40 bp):
TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTC
Found at i:54793 original size:80 final size:80
Alignment explanation
Indices: 54700--54855 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 80
54690 GATTTAGTTG
* *
54700 TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGATTAAAGT
1 TTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATCTTCAATCTGCCCTCTGATTAAAGT
54765 AAAAGATTGGATAGT
66 AAAAGATTGGATAGT
* * **
54780 TTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATCTTCAATCTGCCTTCTGGTTAGGGT
1 TTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATCTTCAATCTGCCCTCTGATTAAAGT
*
54845 AAGAGATTGGA
66 AAAAGATTGGA
54856 GGTTGTAACT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (80 bp):
TTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATCTTCAATCTGCCCTCTGATTAAAGT
AAAAGATTGGATAGT
Found at i:54845 original size:40 final size:39
Alignment explanation
Indices: 54701--54855 Score: 141
Period size: 40 Copynumber: 3.9 Consensus size: 39
54691 ATTTAGTTGT
* ** *
54701 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTC
1 TTCAATCTGCCTC-TGATTAGGGTAAGAGATTGGATGATC
** * *
54741 TTCAATCTGCCCTCTGATTAAAGTAAAAGATTGGAT-AGTT
1 TTCAATCTG-CCTCTGATTAGGGTAAGAGATTGGATGA-TC
* ** *
54781 TTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATC
1 TTCAATCTGCCTC-TGATTAGGGTAAGAGATTGGATGATC
*
54821 TTCAATCTGCCTTCTGGTTAGGGTAAGAGATTGGA
1 TTCAATCTGCC-TCTGATTAGGGTAAGAGATTGGA
54856 GGTTGTAACT
Statistics
Matches: 89, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
39 3 0.03
40 81 0.91
41 5 0.06
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (39 bp):
TTCAATCTGCCTCTGATTAGGGTAAGAGATTGGATGATC
Found at i:73421 original size:3 final size:3
Alignment explanation
Indices: 73413--73449 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
73403 AAGAGTATCC
73413 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
73450 TATATACCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:84955 original size:11 final size:11
Alignment explanation
Indices: 84939--84964 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
84929 TGCCTTTGAA
84939 CTTCCCAAAAC
1 CTTCCCAAAAC
84950 CTTCCCAAAAC
1 CTTCCCAAAAC
84961 CTTC
1 CTTC
84965 ATCTATCGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.23
Consensus pattern (11 bp):
CTTCCCAAAAC
Found at i:86765 original size:19 final size:19
Alignment explanation
Indices: 86722--86787 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
86712 CAAAAAGAAT
86722 ATTCAAAATAATCTTTAAA
1 ATTCAAAATAATCTTTAAA
* * *
86741 AATCAAGATAATTTTTAAA
1 ATTCAAAATAATCTTTAAA
*
86760 TTTCAAAAT-AT-TTATAAAA
1 ATTCAAAATAATCTT-T-AAA
86779 ATTCAAAAT
1 ATTCAAAAT
86788 TTATAGTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 2 0.05
18 3 0.08
19 33 0.87
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTCAAAATAATCTTTAAA
Found at i:87097 original size:31 final size:31
Alignment explanation
Indices: 87035--87094 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
87025 AACTCGAAAA
* **
87035 ATTTCACTCGATTCGATTCAACTCTAATTTC
1 ATTTCACTCGACTCGATTCAACTAAAATTTC
*
87066 ATTTCACTCGACTCGATTTAA-TAAAATTT
1 ATTTCACTCGACTCGATTCAACTAAAATTT
87095 TCAAATTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTTCACTCGACTCGATTCAACTAAAATTTC
Found at i:117481 original size:30 final size:29
Alignment explanation
Indices: 117447--117652 Score: 118
Period size: 30 Copynumber: 6.9 Consensus size: 29
117437 ATTCTATTTC
117447 AAAATTATATTTTAACCCCAAATTTTCCCA
1 AAAATTATATTTTAACCCCAAATTTT-CCA
* *** *
117477 AAAATTATATTTTGACTCCTTTACTTTCCA
1 AAAATTATATTTTAAC-CCCAAATTTTCCA
* ** * *
117507 AAATTTATATTTTAACATTCTAACTTTCC-
1 AAAATTATATTTTAAC-CCCAAATTTTCCA
* *
117536 AAAACTATATTTTAACCCCTAAACTTTT-TA
1 AAAATTATATTTTAACCCC-AAA-TTTTCCA
* * *
117566 AAATTTATATTTTAACCTCCAAACTTTCTA
1 AAAATTATATTTTAACC-CCAAATTTTCCA
*
117596 AAAATT-TCATTTTGACCCCCAAACCTTTT--A
1 AAAATTAT-ATTTT-AACCCCAAA--TTTTCCA
117626 AAAATT-TCATTTTAACCCCTAAATTTT
1 AAAATTAT-ATTTTAACCCC-AAATTTT
117653 ATAAAATTTT
Statistics
Matches: 139, Mismatches: 26, Indels: 24
0.74 0.14 0.13
Matches are distributed among these distances:
28 5 0.04
29 25 0.18
30 95 0.68
31 11 0.08
32 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.42
Consensus pattern (29 bp):
AAAATTATATTTTAACCCCAAATTTTCCA
Found at i:117591 original size:59 final size:59
Alignment explanation
Indices: 117447--117642 Score: 191
Period size: 59 Copynumber: 3.3 Consensus size: 59
117437 ATTCTATTTC
* * ** **
117447 AAAA-TTATATTTTAACC-CCAAATTTTCCCAAAAATTATATTTTGACTCCTTTACTTTCC
1 AAAATTTATATTTTAACCTCCAAACTTT-CCAAAAA-TATATTTTGACCCCTAAACTTTTA
* * * * * *
117506 AAAATTTATATTTTAACATTCTAACTTTCCAAAACTATATTTTAACCCCTAAACTTTTT
1 AAAATTTATATTTTAACCTCCAAACTTTCCAAAAATATATTTTGACCCCTAAACTTTTA
* * *
117565 AAAATTTATATTTTAACCTCCAAACTTTCTAAAAATTTCATTTTGACCCCCAAACCTTTTA
1 AAAATTTATATTTTAACCTCCAAACTTTCCAAAAATAT-ATTTTGACCCCTAAA-CTTTTA
*
117626 AAAATTT-CATTTTAACC
1 AAAATTTATATTTTAACC
117643 CCTAAATTTT
Statistics
Matches: 112, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
59 54 0.48
60 40 0.36
61 18 0.16
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.42
Consensus pattern (59 bp):
AAAATTTATATTTTAACCTCCAAACTTTCCAAAAATATATTTTGACCCCTAAACTTTTA
Found at i:117638 original size:60 final size:60
Alignment explanation
Indices: 117544--117672 Score: 163
Period size: 60 Copynumber: 2.1 Consensus size: 60
117534 CCAAAACTAT
* * * *
117544 ATTTTAACCCCTAAACTTTTTAAAATTTATATTTTAACCTCC-AAACTTTCTAAAAATTTC
1 ATTTTAACCCCCAAACTTTTAAAAATTTACATTTTAACC-CCTAAACTTTATAAAAATTTC
* * *
117604 ATTTTGACCCCCAAACCTTTTAAAAATTT-CATTTTAACCCCTAAATTTTATAAAATTTTC
1 ATTTTAACCCCCAAA-CTTTTAAAAATTTACATTTTAACCCCTAAACTTTATAAAAATTTC
117664 ATTTTAACC
1 ATTTTAACC
117673 TCGAACTTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.03
60 45 0.76
61 12 0.20
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.43
Consensus pattern (60 bp):
ATTTTAACCCCCAAACTTTTAAAAATTTACATTTTAACCCCTAAACTTTATAAAAATTTC
Found at i:117658 original size:30 final size:30
Alignment explanation
Indices: 117544--117672 Score: 142
Period size: 30 Copynumber: 4.3 Consensus size: 30
117534 CCAAAACTAT
* *
117544 ATTTTAACCCCTAAA-CTTTTTAAAATTTAT
1 ATTTTAACCCCTAAACCTTTTAAAAATTT-C
117574 ATTTTAACCTCC-AAA-CTTTCTAAAAATTTC
1 ATTTTAACC-CCTAAACCTTT-TAAAAATTTC
* *
117604 ATTTTGACCCCCAAACCTTTTAAAAATTTC
1 ATTTTAACCCCTAAACCTTTTAAAAATTTC
117634 ATTTTAACCCCTAAA--TTTTATAAAATTTTC
1 ATTTTAACCCCTAAACCTTTTA-AAAA-TTTC
117664 ATTTTAACC
1 ATTTTAACC
117673 TCGAACTTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.06
29 6 0.07
30 63 0.72
31 14 0.16
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.43
Consensus pattern (30 bp):
ATTTTAACCCCTAAACCTTTTAAAAATTTC
Found at i:117720 original size:90 final size:89
Alignment explanation
Indices: 117528--117721 Score: 223
Period size: 90 Copynumber: 2.2 Consensus size: 89
117518 TTAACATTCT
*
117528 AACTTTCCAAAACTATATTTTAACCCCTAAACTTTTTAAAATTTATATTTTAACCTCCAAACTTT
1 AACTTTCCAAAA-TTTATTTTAACCCCTAAACTTTTTAAAATTTATATTTTAACCTCCAAACTTT
** *
117593 CTAAAAATTTCATTTTGACCCCCAA
65 CTAAAAATAGCATTTTGACCCACAA
* ** *
117618 ACCTTTTAAAAATTTCATTTTAACCCCTAAA-TTTTATAAAATTT-TCATTTTAACCT-CGAACT
1 AACTTTCCAAAATTT-ATTTTAACCCCTAAACTTTT-TAAAATTTAT-ATTTTAACCTCCAAACT
* * *
117680 TTCTGGAGAATAGCATTTTGACCCATAA
63 TTCT-AAAAATAGCATTTTGACCCACAA
117708 AACTTTCCAAAATT
1 AACTTTCCAAAATT
117722 GTGATTTTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
89 16 0.19
90 70 0.81
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (89 bp):
AACTTTCCAAAATTTATTTTAACCCCTAAACTTTTTAAAATTTATATTTTAACCTCCAAACTTTC
TAAAAATAGCATTTTGACCCACAA
Found at i:121397 original size:22 final size:22
Alignment explanation
Indices: 121372--121414 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
121362 TAATTTCAAG
121372 TTTAAAAT-TATACTAACTATTC
1 TTTAAAATATAT-CTAACTATTC
**
121394 TTTATTATATATCTAACTATT
1 TTTAAAATATATCTAACTATT
121415 ATGAATCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAAATATATCTAACTATTC
Found at i:126334 original size:81 final size:81
Alignment explanation
Indices: 125972--126308 Score: 550
Period size: 81 Copynumber: 4.2 Consensus size: 81
125962 GCCTGAAGAT
* *
125972 AAGTTTCCTTGGAGCAGAGTCCTCAACTCTACTATTTTGATTATCAGAATTTCTGTTGTCAAGAG
1 AAGTTTCCTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
126037 TTCTTTGGCAGGACTC
66 TTCTTTGGCAGGACTC
126053 AAGTTTCGC-TGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGA
1 AAGTTTC-CTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGA
126117 GTTCTTTGGCAGGACTC
65 GTTCTTTGGCAGGACTC
* * *
126134 AAGTTTCGTTGGAGCAGAGTCCACACCTCTATTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
1 AAGTTTCCTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
*
126199 TTTTTTGGCAGGACTC
66 TTCTTTGGCAGGACTC
* * * * *
126215 AAGTTTCGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCACCGGAATTTCTGTTGTCAACAT
1 AAGTTTCCTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
*
126280 TTCTTTGGCGGGACTC
66 TTCTTTGGCAGGACTC
126296 AAGTTTCCTTGGA
1 AAGTTTCCTTGGA
126309 CTAAACTCCT
Statistics
Matches: 239, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
81 238 1.00
82 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (81 bp):
AAGTTTCCTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
TTCTTTGGCAGGACTC
Found at i:126423 original size:84 final size:83
Alignment explanation
Indices: 126330--126647 Score: 322
Period size: 84 Copynumber: 3.8 Consensus size: 83
126320 GACTTTGGCA
* * * * *
126330 TTTTGGTTATGATCATCTACGTTGTCAACAATTAATTTTCGCCTGAACTTGAGTATCCTTGGAGT
1 TTTTGGTTATCACCATTTACGTTGTCAACAATTACTTTTCG-CTGAACTTGAGTCTCCTTGGAGT
** *
126395 AAGTTCCTCGATTCTACTG
65 AAACTCCTTGATTCTACTG
* ** *
126414 TTTTTGTTATCACCATTTTGGTTGTCAACAATTACTCTTT-GCTGAAACTTCAGTCTCCTTGGAG
1 TTTTGGTTATCACCATTTACGTTGTCAACAATTACT-TTTCGCTG-AACTTGAGTCTCCTTGGAG
126478 TAAACTCCTTGACTT-TACTG
64 TAAACTCCTTGA-TTCTACTG
* * * *
126498 TTTTGGTTATCACCATTTCCGTTGTCAACAATTTCTCTTCGTCTGAACTTGAGTCT-CTTCGGGG
1 TTTTGGTTATCACCATTTACGTTGTCAACAATTACTTTTCG-CTGAACTTGAGTCTCCTT-GGAG
*
126562 TAAACTCCTTGACTCTACTG
64 TAAACTCCTTGATTCTACTG
* * * * *
126582 TTTTGGTTATCATCATTTATGTTATTAAC-ATATACCCTTT-GCTTGAACTTGAGTCTCCTTGGA
1 TTTTGGTTATCACCATTTACGTTGTCAACAAT-TA-CTTTTCGC-TGAACTTGAGTCTCCTTGGA
126645 GTA
63 GTA
126648 CAGTCCTCAA
Statistics
Matches: 194, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
83 12 0.06
84 168 0.87
85 14 0.07
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (83 bp):
TTTTGGTTATCACCATTTACGTTGTCAACAATTACTTTTCGCTGAACTTGAGTCTCCTTGGAGTA
AACTCCTTGATTCTACTG
Found at i:126489 original size:168 final size:168
Alignment explanation
Indices: 126301--126647 Score: 407
Period size: 168 Copynumber: 2.1 Consensus size: 168
126291 GACTCAAGTT
* * * *
126301 TCCTTGGACTAAACTCCTTGACTTTGGC-ATTTTGGTTATGATCATCTACGTTGTCAACAATTAA
1 TCCTTGGAGTAAACTCCTTGACTTT-ACTATTTTGGTTATCACCATCTACGTTGTCAACAATTAA
* ** * *
126365 TTTTCGCCTGAACTTGAGTATCCTT-GGAGTAAGTTCCTCGATTCTACTGTTTTTGTTATCACCA
65 TCTTCGCCTGAACTTGAGTAT-CTTCGGAGTAAACTCCTCGACTCTACTGTTTTGGTTATCACCA
* *
126429 TTT-TGGTTGTCAACA-ATTACTCTTTGC-TGAAACTTCAGTC
129 TTTAT-GTTATCAACATA-TACCCTTTGCTTG-AACTTCAGTC
* * * **
126469 TCCTTGGAGTAAACTCCTTGACTTTACTGTTTTGGTTATCACCATTTCCGTTGTCAACAATTTCT
1 TCCTTGGAGTAAACTCCTTGACTTTACTATTTTGGTTATCACCATCTACGTTGTCAACAATTAAT
* * * * *
126534 CTTCGTCTGAACTTGAGTCTCTTCGGGGTAAACTCCTTGACTCTACTGTTTTGGTTATCATCATT
66 CTTCGCCTGAACTTGAGTATCTTCGGAGTAAACTCCTCGACTCTACTGTTTTGGTTATCACCATT
* *
126599 TATGTTATTAACATATACCCTTTGCTTGAACTTGAGTC
131 TATGTTATCAACATATACCCTTTGCTTGAACTTCAGTC
126637 TCCTTGGAGTA
1 TCCTTGGAGTA
126648 CAGTCCTCAA
Statistics
Matches: 151, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
167 4 0.03
168 143 0.95
169 4 0.03
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (168 bp):
TCCTTGGAGTAAACTCCTTGACTTTACTATTTTGGTTATCACCATCTACGTTGTCAACAATTAAT
CTTCGCCTGAACTTGAGTATCTTCGGAGTAAACTCCTCGACTCTACTGTTTTGGTTATCACCATT
TATGTTATCAACATATACCCTTTGCTTGAACTTCAGTC
Found at i:126692 original size:168 final size:168
Alignment explanation
Indices: 126349--126693 Score: 356
Period size: 168 Copynumber: 2.1 Consensus size: 168
126339 TGATCATCTA
* ** *
126349 CGTTGTCAACAATTAATTTTCGCCTGAACTTGAGTATCCTTGGAGTAAGTTCCTCGATTCTACTG
1 CGTTGTCAACAATTAATCTTCGCCTGAACTTGAGTATCCTTGGAGTAAACTCCTCGACTCTACTG
* * *
126414 TTTTTGTTATCACCATTTTGGTTGTCAACAATTACTCTTTGCTGAAACTTCAGTCTCCTTGGAGT
66 TTTTGGTTATCACCATTTTGGTTATCAACAATTACCCTTTGCTGAAACTTCAGTCTCCTTGGAGT
** ** ***
126479 AAACTCCTTGACTTTACTGTTTTGGTTATCACCATTTC
131 AAACTCCTCAACTTTACCATTCCAGTTATCACCATTTC
** * * * *
126517 CGTTGTCAACAATTTCTCTTCGTCTGAACTTGAGTCT-CTTCGGGGTAAACTCCTTGACTCTACT
1 CGTTGTCAACAATTAATCTTCGCCTGAACTTGAGTATCCTT-GGAGTAAACTCCTCGACTCTACT
* * *
126581 GTTTTGGTTATCATCATTTAT-GTTATTAAC-ATATACCCTTTGCTTG-AACTTGAGTCTCCTTG
65 GTTTTGGTTATCACCATTT-TGGTTATCAACAAT-TACCCTTTGC-TGAAACTTCAGTCTCCTTG
* * * * * *
126643 GAGTACAGTCCTCAACTTTGCCATTCCAGTTGTCATCGTTTC
127 GAGTAAACTCCTCAACTTTACCATTCCAGTTATCACCATTTC
*
126685 TGTTGTCAA
1 CGTTGTCAA
126694 TGAGCTCTCT
Statistics
Matches: 143, Mismatches: 30, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
167 5 0.03
168 135 0.94
169 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (168 bp):
CGTTGTCAACAATTAATCTTCGCCTGAACTTGAGTATCCTTGGAGTAAACTCCTCGACTCTACTG
TTTTGGTTATCACCATTTTGGTTATCAACAATTACCCTTTGCTGAAACTTCAGTCTCCTTGGAGT
AAACTCCTCAACTTTACCATTCCAGTTATCACCATTTC
Found at i:130125 original size:26 final size:27
Alignment explanation
Indices: 130075--130125 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
130065 AAATGTTGAT
* *
130075 TAAAACATTAATATTTTTTTGACAAAA
1 TAAAACATTAATATTTTTGTAACAAAA
130102 TAAAACATTAATA-TTTTGTAACAA
1 TAAAACATTAATATTTTTGTAACAA
130126 TGTTGGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (27 bp):
TAAAACATTAATATTTTTGTAACAAAA
Found at i:130234 original size:15 final size:16
Alignment explanation
Indices: 130214--130243 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
130204 AAATTTTAAA
130214 AAAAT-ATTCAAAAAT
1 AAAATAATTCAAAAAT
130229 AAAATAATTCAAAAA
1 AAAATAATTCAAAAA
130244 ATTATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAATTCAAAAAT
Found at i:130402 original size:31 final size:31
Alignment explanation
Indices: 130366--130432 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
130356 AGAAAAAAAA
* *
130366 AAATTCGATTTTTTTCAAAAAGTTGATGATC
1 AAATTCGATTCTTTTCAAAAAGTTGAAGATC
* *
130397 AAATTCGATTCTTTTGAAAAGGTTGAAGATC
1 AAATTCGATTCTTTTCAAAAAGTTGAAGATC
130428 AAATT
1 AAATT
130433 TAACTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (31 bp):
AAATTCGATTCTTTTCAAAAAGTTGAAGATC
Found at i:130885 original size:15 final size:17
Alignment explanation
Indices: 130865--130908 Score: 74
Period size: 15 Copynumber: 2.7 Consensus size: 17
130855 TATTTGAGAG
130865 TATTTTAATTTTTT-T-
1 TATTTTAATTTTTTATA
130880 TATTTTAATTTTTTATA
1 TATTTTAATTTTTTATA
130897 TATTTTAATTTT
1 TATTTTAATTTT
130909 ATTGTGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 14 0.52
16 1 0.04
17 12 0.44
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTTAATTTTTTATA
Found at i:131754 original size:58 final size:60
Alignment explanation
Indices: 131643--131814 Score: 212
Period size: 58 Copynumber: 3.0 Consensus size: 60
131633 TAATATTTAA
* * *
131643 TAAGTTTAAATACTAAATTGAATCTAAAAAAA-ATAGATATCAAATT-AGAAAAAATATC
1 TAAGTTTAAATACCAAATTGAATCCAAAAAAATTTAGATATCAAATTAAGAAAAAATATC
* *
131701 -AAGTTCAAATACCAAATTGAGTCCAAAAAAATTTAGATATCAAATTAAGAAAAAATATC
1 TAAGTTTAAATACCAAATTGAATCCAAAAAAATTTAGATATCAAATTAAGAAAAAATATC
* * * *
131760 TAA-TTTAAGTATCAAATTGAAT-CAAAAAAATTTA-AGTACCAAATTATGAAAAAAT
1 TAAGTTTAAATACCAAATTGAATCCAAAAAAATTTAGA-TATCAAATTAAGAAAAAAT
131815 GTCAAACCTA
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
57 28 0.28
58 42 0.42
59 27 0.27
60 2 0.02
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (60 bp):
TAAGTTTAAATACCAAATTGAATCCAAAAAAATTTAGATATCAAATTAAGAAAAAATATC
Found at i:131813 original size:27 final size:27
Alignment explanation
Indices: 131725--131813 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
131715 AATTGAGTCC
*
131725 AAAAAAATTT-AGATATCAAATTAAGAA
1 AAAAAAATTTAAG-TATCAAATTATGAA
131752 AAAATATCTAATTTAAGTATCAAA-T-TGAA
1 AAAA-A---AATTTAAGTATCAAATTATGAA
*
131781 TCAAAAAAATTTAAGTACCAAATTATGAA
1 --AAAAAAATTTAAGTATCAAATTATGAA
131810 AAAA
1 AAAA
131814 TGTCAAACCT
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
27 22 0.43
28 2 0.04
29 7 0.14
30 2 0.04
31 16 0.31
32 2 0.04
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (27 bp):
AAAAAAATTTAAGTATCAAATTATGAA
Found at i:141880 original size:16 final size:16
Alignment explanation
Indices: 141861--141904 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
141851 TATATCATAA
141861 TTATATTTAAAATATT
1 TTATATTTAAAATATT
* *
141877 TTATATTTATAATTTT
1 TTATATTTAAAATATT
141893 TTCATATATTAA
1 TT-ATAT-TTAA
141905 TCTGTCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 16 0.70
17 4 0.17
18 3 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:143477 original size:17 final size:17
Alignment explanation
Indices: 143455--143488 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
143445 TATGATTATA
143455 TTATAATATAATATAAT
1 TTATAATATAATATAAT
* *
143472 TTATAATTTAATTTAAT
1 TTATAATATAATATAAT
143489 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATATAATATAAT
Found at i:150564 original size:24 final size:25
Alignment explanation
Indices: 150524--150573 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
150514 GTTTGTTTAT
**
150524 TATTCATTAATATTGTTTGTGAACA
1 TATTCATTAATATTGTTCATGAACA
150549 TATTCAATTAA-A-TGTTCATGAACA
1 TATTC-ATTAATATTGTTCATGAACA
150573 T
1 T
150574 GTACGTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 11 0.50
25 6 0.27
26 5 0.23
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (25 bp):
TATTCATTAATATTGTTCATGAACA
Found at i:150606 original size:23 final size:23
Alignment explanation
Indices: 150543--150606 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
150533 ATATTGTTTG
* * *
150543 TGAACATATTCAATTAAATGTTCA
1 TGAACATGTTCGATT-AATGATCA
* *
150567 TGAACATGTACGTTTAATGATCA
1 TGAACATGTTCGATTAATGATCA
150590 TGAACATGTTCGATTAA
1 TGAACATGTTCGATTAA
150607 GTTAAATGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGATCA
Found at i:153643 original size:10 final size:10
Alignment explanation
Indices: 153606--153649 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
153596 AAACCCCTTG
*
153606 TTTTCTTTTC
1 TTTTCTTTTT
* *
153616 TTTTGTTTCT
1 TTTTCTTTTT
*
153626 TCTTCTTTTT
1 TTTTCTTTTT
153636 TTTTCTTTTT
1 TTTTCTTTTT
153646 TTTT
1 TTTT
153650 TTTCTTCAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:156384 original size:29 final size:28
Alignment explanation
Indices: 156341--156560 Score: 160
Period size: 30 Copynumber: 7.5 Consensus size: 28
156331 GCTCAAGGTT
* *
156341 AAAAGATGAAATTTTTAGACATTCGGGGT-
1 AAAA-ATGGAATTTTTGGA-ATTCGGGGTC
* *
156370 AAAAATGGAATTTTTGGAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGA-ATTCGGGGTC
* *
156399 AAAAATGGAATTTTTGGAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGA-ATTCGGGGTC
* *
156428 AAAAAATGAAAATTTTGGAAGTTCAGGGGT-
1 -AAAAATGGAATTTTTGGAA-TTC-GGGGTC
*
156458 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAA--TTCGGGGTC
* *
156488 AAAAATGGAATTTTTTGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAA--TTCGGGGTC
* *
156518 AAAAAT-GAGGTTTTTGGAAGTTCAAGGGT-
1 AAAAATGGA-ATTTTTGGAA-TTC-GGGGTC
*
156547 AAAAATGAAATTTT
1 AAAAATGGAATTTT
156561 CGAACAGTTT
Statistics
Matches: 157, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
28 19 0.12
29 66 0.42
30 67 0.43
31 5 0.03
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAATTCGGGGTC
Found at i:156435 original size:30 final size:29
Alignment explanation
Indices: 156362--156524 Score: 197
Period size: 29 Copynumber: 5.6 Consensus size: 29
156352 TTTTTAGACA
156362 TTCGGGGT-AAAAATGGAATTTTTGGAGT
1 TTCGGGGTCAAAAATGGAATTTTTGGAGT
*
156390 TTCGAGGTCAAAAATGGAATTTTTGGAGT
1 TTCGGGGTCAAAAATGGAATTTTTGGAGT
* * *
156419 TTTGGGGTCAAAAAATGAAAATTTTGGAAG-
1 TTCGGGGTC-AAAAATGGAATTTTTGG-AGT
156449 TTCAGGGGT-AAAAATGGAATTTTTGGAAGT
1 TTC-GGGGTCAAAAATGGAATTTTTGG-AGT
* *
156479 TTCGAGGTCAAAAATGGAATTTTTTGAAGT
1 TTCGGGGTCAAAAATGGAA-TTTTTGGAGT
*
156509 TTTGGGGTCAAAAATG
1 TTCGGGGTCAAAAATG
156525 AGGTTTTTGG
Statistics
Matches: 116, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.06
29 49 0.42
30 47 0.41
31 13 0.11
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (29 bp):
TTCGGGGTCAAAAATGGAATTTTTGGAGT
Found at i:156435 original size:59 final size:59
Alignment explanation
Indices: 156362--156560 Score: 196
Period size: 59 Copynumber: 3.4 Consensus size: 59
156352 TTTTTAGACA
* *
156362 TTCGGGGT-AAAAATGGAATTTTTGGAGTTTCGAGGTCAAAAATGGAATTTTTGG-AGT
1 TTCGAGGTCAAAAATGGAATTTTTGGAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGT
* * * *
156419 TTTGGGGTCAAAAAATGAAAATTTTGGAAG-TTCAGGGGT-AAAAATGGAATTTTTGGAAGT
1 TTCGAGGTC-AAAAATGGAATTTTTGG-AGTTTC-GGGGTCAAAAATGGAATTTTTGGAAGT
* * *
156479 TTCGAGGTCAAAAATGGAATTTTTTGAAGTTTTGGGGTCAAAAAT-GAGGTTTTTGGAAG-
1 TTCGAGGTCAAAAATGGAA-TTTTTGGAGTTTCGGGGTCAAAAATGGA-ATTTTTGGAAGT
* *
156538 TTCAAGGGT-AAAAATGAAATTTT
1 TTCGA-GGTCAAAAATGGAATTTT
156561 CGAACAGTTT
Statistics
Matches: 119, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
57 7 0.06
58 4 0.03
59 66 0.55
60 42 0.35
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.34
Consensus pattern (59 bp):
TTCGAGGTCAAAAATGGAATTTTTGGAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGT
Found at i:156532 original size:30 final size:29
Alignment explanation
Indices: 156362--156539 Score: 177
Period size: 30 Copynumber: 6.0 Consensus size: 29
156352 TTTTTAGACA
156362 TTCGGGGT-AAAAATGGAATTTTTGG-AGT
1 TTCGGGGTCAAAAATGG-ATTTTTGGAAGT
*
156390 TTCGAGGTCAAAAATGGAATTTTTGG-AGT
1 TTCGGGGTCAAAAATGG-ATTTTTGGAAGT
* * *
156419 TTTGGGGTCAAAAAATGAAAATTTTGGAAG-
1 TTCGGGGTC-AAAAATG-GATTTTTGGAAGT
156449 TTCAGGGGT-AAAAATGGAATTTTTGGAAGT
1 TTC-GGGGTCAAAAATGG-ATTTTTGGAAGT
* *
156479 TTCGAGGTCAAAAATGGAATTTTTTGAAGT
1 TTCGGGGTCAAAAATGG-ATTTTTGGAAGT
* *
156509 TTTGGGGTCAAAAATGAGGTTTTTGGAAGT
1 TTCGGGGTCAAAAATG-GATTTTTGGAAGT
156539 T
1 T
156540 CAAGGGTAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
28 7 0.06
29 48 0.38
30 64 0.50
31 8 0.06
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
TTCGGGGTCAAAAATGGATTTTTGGAAGT
Found at i:157680 original size:3 final size:3
Alignment explanation
Indices: 157674--157758 Score: 50
Period size: 3 Copynumber: 28.3 Consensus size: 3
157664 TTTTTTTCAT
* * * * *
157674 TTA TTA -TA ATA TTTA TTA TTA TTA ATA -AA TTCA TTA CTG TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* * *
157719 TTA ATA TTA TCA -TA TTCG TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T
157759 GAATAATTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
2 4 0.06
3 50 0.81
4 8 0.13
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:157731 original size:24 final size:25
Alignment explanation
Indices: 157689--157757 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
157679 ATAATATTTA
*
157689 TTATTATTAATA-AATTCATTACT-G
1 TTATTATTAATATTA-TCATTACTCG
*
157713 TTATTATTAATATTATCA-TATTCG
1 TTATTATTAATATTATCATTACTCG
* *
157737 TTATTATTATTATTATTATTA
1 TTATTATTAATATTATCATTA
157758 TGAATAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 3 0.08
24 32 0.84
25 3 0.08
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.57
Consensus pattern (25 bp):
TTATTATTAATATTATCATTACTCG
Found at i:159915 original size:2 final size:2
Alignment explanation
Indices: 159910--159966 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
159900 AAAAATAATA
159910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159952 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
159967 AAGCAAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:161133 original size:13 final size:13
Alignment explanation
Indices: 161093--161133 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
161083 AATGAACTTA
161093 AATTTAATAAAAT
1 AATTTAATAAAAT
* *
161106 -AGTTATTAAAA-
1 AATTTAATAAAAT
161117 AATTTAATAAAAT
1 AATTTAATAAAAT
161130 AATT
1 AATT
161134 GAAATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
AATTTAATAAAAT
Found at i:164090 original size:41 final size:41
Alignment explanation
Indices: 164003--164189 Score: 171
Period size: 41 Copynumber: 4.5 Consensus size: 41
163993 TTACGCTCTA
* * * *
164003 TCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCC-TTAATCATAATCTCATTCTCATC
* * * *
164045 TCGAGACGTTAGTCTTCCTTAATCAAAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
* * *
164086 TCGAGACATGAGTCTTCCTTATTCATAGTCTCATTCTTATC
1 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
* * * * *
164127 TCGAGATATGAGTCTTCCATTTATACA-ATTTCTCATGCTCAAC
1 TCGAGACATGAGTCTTCC-TTAAT-CATA-ATCTCATTCTCATC
164170 -CTGAGACATGAGTCTTCCTT
1 TC-GAGACATGAGTCTTCCTT
164190 TTTATACACC
Statistics
Matches: 119, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
41 70 0.59
42 22 0.18
43 27 0.23
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATC
Found at i:164141 original size:82 final size:83
Alignment explanation
Indices: 163997--164189 Score: 201
Period size: 82 Copynumber: 2.3 Consensus size: 83
163987 ATAACCTTAC
* * * * * *
163997 GCTCTATCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCATCTCGAGACGTTAGTCTTC
1 GCTCAATCGAGACATGAGTCTTCC-TTAACCATAGTCTCATTCTCATCTCGAGACATGAGTCTTC
164062 C-TTAAT-CAAAATCTCAT
65 CATTAATACAAAATCTCAT
* * ** * *
164079 TCTCATTTCGAGACATGAGTCTTCCTTATTCATAGTCTCATTCTTATCTCGAGATATGAGTCTTC
1 GCTCA-ATCGAGACATGAGTCTTCCTTAACCATAGTCTCATTCTCATCTCGAGACATGAGTCTTC
* **
164144 CATTTATACAATTTCTCAT
65 CATTAATACAAAATCTCAT
*
164163 GCTCAACCTGAGACATGAGTCTTCCTT
1 GCTCAATC-GAGACATGAGTCTTCCTT
164190 TTTATACACC
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
82 37 0.42
83 21 0.24
84 31 0.35
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.39
Consensus pattern (83 bp):
GCTCAATCGAGACATGAGTCTTCCTTAACCATAGTCTCATTCTCATCTCGAGACATGAGTCTTCC
ATTAATACAAAATCTCAT
Found at i:165036 original size:22 final size:21
Alignment explanation
Indices: 164989--165036 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
164979 TACTTTCATA
*
164989 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
165010 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
165032 ATTAA
1 ATTAA
165037 TCAATATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:177482 original size:24 final size:24
Alignment explanation
Indices: 177455--177507 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
177445 TCAGAGAATG
* * *
177455 TACGTTTATGCTTGTCAGTCACTA
1 TACGTTTATACTCGTCAGCCACTA
177479 TACGTTTATACTCGTCAGCCACTA
1 TACGTTTATACTCGTCAGCCACTA
177503 TACGT
1 TACGT
177508 ACTATACGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (24 bp):
TACGTTTATACTCGTCAGCCACTA
Done.