Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005461.1 Kokia drynarioides strain JFW-HI SEQ_119506, 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: 187920
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:239 original size:59 final size:58
Alignment explanation
Indices: 120--369 Score: 188
Period size: 59 Copynumber: 4.3 Consensus size: 58
110 ACCCGGGGAC
* * ** * **
120 AAAATGGTAA-TTTTGGAC-TCTCGAGGGTAAAACGGTAATTTTGGGAAAGTTCAGAGTTA
1 AAAATGG-AATTTTTGGACATC-CGAGGGTAAAATGATAATTTTGAAAAAATTGGGA-TTA
* * *
179 AAAATGGAATTTTTAGACACCCGAGGGTAAAATGATAACTTTTGAAAAGATTGGGATTA
1 AAAATGGAATTTTTGGACATCCGAGGGTAAAATGATAA-TTTTGAAAAAATTGGGATTA
* * * * * *
238 AAAACGAAATTTTTGGACATCCGAGGGTAAAGTGGTAATTTT-AAGGAAAATCGGGATAA
1 AAAATGGAATTTTTGGACATCCGAGGGTAAAATGATAATTTTGAA--AAAATTGGGATTA
* * ***
297 AAAATGGAATTTTTGGACATTCG-GGGTGAAAT-AGTAATTTTTGAAATCTTTGAGG-TTA
1 AAAATGGAATTTTTGGACATCCGAGGGTAAAATGA-TAA-TTTTGAAAAAATTG-GGATTA
355 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
370 TAGGTTCGAG
Statistics
Matches: 152, Mismatches: 30, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
57 2 0.01
58 36 0.24
59 100 0.66
60 14 0.09
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (58 bp):
AAAATGGAATTTTTGGACATCCGAGGGTAAAATGATAATTTTGAAAAAATTGGGATTA
Found at i:380 original size:29 final size:29
Alignment explanation
Indices: 332--779 Score: 301
Period size: 29 Copynumber: 15.3 Consensus size: 29
322 GTGAAATAGT
* * *
332 AATTTTTGAAATCTTTGAGGTTAAAAATGG
1 AATTTTTGAAA-GTTTGGGGGTAAAAATGG
* * * * * *
362 AATTTTTGTAGGTTCGAGGGCAAAAATGT
1 AATTTTTGAAAGTTTGGGGGTAAAAATGG
* * * *
391 ATTTTTTGGAAGTTTCGGGGTCAAAAATCG
1 AATTTTTGAAAGTTTGGGGGT-AAAAATGG
**
421 AATTTTTGAAAGTTTGGGGGTAAAAATAT
1 AATTTTTGAAAGTTTGGGGGTAAAAATGG
* *
450 ATTTTTTGGAAA-TTTTGGGGTCAAAAATGG
1 AATTTTT-GAAAGTTTGGGGGT-AAAAATGG
* **
480 AATTTTTGGAAGTTTGGGGGTAAAAATAT
1 AATTTTTGAAAGTTTGGGGGTAAAAATGG
* * ** * *
509 AATTTTTGGAAGTTTCGATGTCAAAATGA
1 AATTTTTGAAAGTTTGGGGGTAAAAATGG
* * **
538 AATTTTTGGAAGTTTGAGGGTAAAAATAT
1 AATTTTTGAAAGTTTGGGGGTAAAAATGG
* *
567 AATTTTTGATAGTTTTGGGGTTAAAAATGG
1 AATTTTTGAAAG-TTTGGGGGTAAAAATGG
* * **
597 AATTTTTGGAAGTTTAGGGGTAAAAATAT
1 AATTTTTGAAAGTTTGGGGGTAAAAATGG
* * *
626 AATTTTTGGAAGTTT-AGGGTCAAAATGG
1 AATTTTTGAAAGTTTGGGGGTAAAAATGG
* * **
654 AATTTTTTG-AAGTTTAGGGGTAAATATAT
1 AA-TTTTTGAAAGTTTGGGGGTAAAAATGG
* **
683 AATTTTTGGAAGTTTCAGGGTCAAAAATGG
1 AATTTTTGAAAGTTTGGGGGT-AAAAATGG
* * * * **
713 AATTTTTGGAAGTTCGAGTGTAAAAATAT
1 AATTTTTGAAAGTTTGGGGGTAAAAATGG
*
742 AATTTTTGGAAA-TTTTGGGGTCAAAAATGG
1 AATTTTT-GAAAGTTTGGGGGT-AAAAATGG
*
772 AAATTTTG
1 AATTTTTG
780 GATAGTTTAG
Statistics
Matches: 325, Mismatches: 82, Indels: 23
0.76 0.19 0.05
Matches are distributed among these distances:
28 23 0.07
29 184 0.57
30 118 0.36
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (29 bp):
AATTTTTGAAAGTTTGGGGGTAAAAATGG
Found at i:409 original size:117 final size:116
Alignment explanation
Indices: 288--792 Score: 529
Period size: 117 Copynumber: 4.3 Consensus size: 116
278 TTAAGGAAAA
* * *
288 TCGGGATAAAAAATGGAATTTTTGGACA-TTCGGGGT-GAAATAGTAATTTTTGAAATCTTTGAG
1 TCGGGATCAAAAATGGAATTTTTGGA-AGTTAGGGGTAAAAATA-TAATTTTTGAAAT-TTTGAG
* * * * * *
351 GTTAAAAATGGAATTTTTGTAGGTTCGAGGGCAAAAATGTATTTTTTGGAAGTT
63 GTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTT
* * * * * *
405 TCGGGGTCAAAAATCGAATTTTTGAAAGTTTGGGGGTAAAAATATATTTTTTGGAAATTTTGGGG
1 TCGGGATCAAAAATGGAATTTTTGGAAG-TTAGGGGTAAAAATATAATTTTT-GAAATTTTGAGG
* *
470 TCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATATAATTTTTGGAAGTT
64 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTT
* * * * *
523 TCGATG-TC-AAAATGAAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGATAGTTTTGGG
1 TCG-GGATCAAAAATGGAATTTTTGGAAGTTAG-GGGTAAAAATATAATTTTTGA-AATTTTGAG
* *
586 GTTAAAAATGGAATTTTTGGAAGTT-TAGGGGTAAAAATATAATTTTTGGAAGTT
63 GTCAAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATATAATTTTTGGAAGTT
* * * * * *
640 TAGGG-TC-AAAATGGAATTTTTTGAAGTTTAGGGGTAAATATATAATTTTTGGAAGTTTCAGGG
1 TCGGGATCAAAAATGGAATTTTTGGAAG-TTAGGGGTAAAAATATAATTTTTGAAATTTTGA-GG
* *
703 TCAAAAATGGAATTTTTGGAAGTTCGAGTGTAAAAATATAATTTTTGGAAATT
64 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTT
* * *
756 TTGGGGTCAAAAATGGAAATTTTGGATAGTTTAGGGG
1 TCGGGATCAAAAATGGAATTTTTGGA-AG-TTAGGGG
793 ACTTCACGGC
Statistics
Matches: 330, Mismatches: 44, Indels: 26
0.82 0.11 0.06
Matches are distributed among these distances:
115 4 0.01
116 98 0.30
117 122 0.37
118 85 0.26
119 21 0.06
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (116 bp):
TCGGGATCAAAAATGGAATTTTTGGAAGTTAGGGGTAAAAATATAATTTTTGAAATTTTGAGGTC
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTT
Found at i:426 original size:59 final size:59
Alignment explanation
Indices: 296--791 Score: 555
Period size: 59 Copynumber: 8.5 Consensus size: 59
286 AATCGGGATA
* * * * * *
296 AAAAATGGAATTTTTGGACA-TTCG-GGGT-GAAATAGTAATTTTT-GAAATCTTTGAGGTT
1 AAAAATGGAATTTTTGGA-AGTTTGAGGGTAAAAATA-TAATTTTTGGAAGT-TTCGGGGTC
* * * * * *
354 AAAAATGGAATTTTTGTAGGTTCGAGGGCAAAAATGTATTTTTTGGAAGTTTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTCGGGGTC
* * * * * *
413 AAAAATCGAATTTTTGAAAGTTTGGGGGTAAAAATATATTTTTTGGAAATTTTGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTCGGGGTC
* **
472 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATATAATTTTTGGAAGTTTCGATGTC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTCGGGGTC
* * *
531 -AAAATGAAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTT-GATAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGA-AGTTTCGGGGTC
*
589 AAAAATGGAATTTTTGGAAGTTT-AGGGGTAAAAATATAATTTTTGGAAGTTT-AGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGA-GGGTAAAAATATAATTTTTGGAAGTTTCGGGGTC
* * *
647 -AAAATGGAATTTTTTGAAGTTT-AGGGGTAAATATATAATTTTTGGAAGTTTCAGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGA-GGGTAAAAATATAATTTTTGGAAGTTTCGGGGTC
* * * *
705 AAAAATGGAATTTTTGGAAGTTCGAGTGTAAAAATATAATTTTTGGAAATTTTGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTCGGGGTC
*
764 AAAAATGGAAATTTTGGATAGTTT-AGGG
1 AAAAATGGAATTTTTGGA-AGTTTGAGGG
792 GACTTCACGG
Statistics
Matches: 379, Mismatches: 47, Indels: 23
0.84 0.10 0.05
Matches are distributed among these distances:
57 51 0.13
58 81 0.21
59 232 0.61
60 15 0.04
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTCGGGGTC
Found at i:7250 original size:53 final size:52
Alignment explanation
Indices: 7186--7305 Score: 195
Period size: 53 Copynumber: 2.3 Consensus size: 52
7176 ATAACAACTT
* *
7186 TAACTCCCAATATTTATACATTTTATCAATTTAGTCTTGATTCTAAAAAAATA
1 TAACTCTCAATATTTATACATTTTATCAATTTAGACTTGATTCT-AAAAAATA
*
7239 TAACTCTCAATATTTATACATTTTGTCAATTTAGACTTGATTCTAAAAAATA
1 TAACTCTCAATATTTATACATTTTATCAATTTAGACTTGATTCTAAAAAATA
*
7291 TAACTCTCAACATTT
1 TAACTCTCAATATTT
7306 GCATTCTGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 22 0.35
53 41 0.65
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (52 bp):
TAACTCTCAATATTTATACATTTTATCAATTTAGACTTGATTCTAAAAAATA
Found at i:8047 original size:11 final size:11
Alignment explanation
Indices: 8031--8055 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8021 TACGACTTAA
8031 ACTCGTGTCAC
1 ACTCGTGTCAC
8042 ACTCGTGTCAC
1 ACTCGTGTCAC
8053 ACT
1 ACT
8056 TAAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.36, G:0.16, T:0.28
Consensus pattern (11 bp):
ACTCGTGTCAC
Found at i:12031 original size:31 final size:30
Alignment explanation
Indices: 11971--12031 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
11961 GTTGGCAATC
* *
11971 ATTTTCATTTTAATCCTTTAATTTTAATAA
1 ATTTTCATTTTAATACGTTAATTTTAATAA
12001 ATTTTCATTTTATATTACGTTAA-TTTAATAA
1 ATTTTCATTTTA-A-TACGTTAATTTTAATAA
12032 TATTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 12 0.44
31 9 0.33
32 6 0.22
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (30 bp):
ATTTTCATTTTAATACGTTAATTTTAATAA
Found at i:12085 original size:21 final size:21
Alignment explanation
Indices: 12060--12105 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12050 TTAGTCTCTC
*
12060 TTTTATATTTTTAAAAA-TTAA
1 TTTTAT-TTTTTAAAAACTAAA
12081 TTTTATTTTTTAAAAACTAAA
1 TTTTATTTTTTAAAAACTAAA
12102 TTTT
1 TTTT
12106 TACAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTATTTTTTAAAAACTAAA
Found at i:14062 original size:17 final size:18
Alignment explanation
Indices: 14030--14064 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14020 TACTGAATTT
14030 TATCGATACCAAAATTTTA
1 TATCGATACC-AAATTTTA
14049 TATCGATACC-AATTTT
1 TATCGATACCAAATTTT
14065 GCATCATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (18 bp):
TATCGATACCAAATTTTA
Found at i:16812 original size:30 final size:30
Alignment explanation
Indices: 16752--16828 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
16742 CACGATCTGG
**
16752 CACATGGTTGTGTG-CCAGCCCGTATGGCT
1 CACATGGCCGTGTGCCCAGCCCGTATGGCT
* * *
16781 CACATGGCCGTTTGCCCAGTCCGTGTGGCT
1 CACATGGCCGTGTGCCCAGCCCGTATGGCT
16811 CACATGGCCGTGTGCCCA
1 CACATGGCCGTGTGCCCA
16829 CCCTGTGGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 11 0.27
30 30 0.73
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (30 bp):
CACATGGCCGTGTGCCCAGCCCGTATGGCT
Found at i:16823 original size:17 final size:17
Alignment explanation
Indices: 16771--16824 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
16761 GTGTGCCAGC
*
16771 CCGTATGGCTCACATGG
1 CCGTGTGGCTCACATGG
* *
16788 CCGT-TTGC-C-CA-GT
1 CCGTGTGGCTCACATGG
16801 CCGTGTGGCTCACATGG
1 CCGTGTGGCTCACATGG
16818 CCGTGTG
1 CCGTGTG
16825 CCCACCCTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 5 0.17
14 5 0.17
15 2 0.07
16 5 0.17
17 12 0.41
ACGTcount: A:0.11, C:0.31, G:0.31, T:0.26
Consensus pattern (17 bp):
CCGTGTGGCTCACATGG
Found at i:20313 original size:23 final size:23
Alignment explanation
Indices: 20286--20362 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
20276 ATTTAAAACA
*
20286 AAACATTATGGCAGGAGAGTTAC
1 AAACATAATGGCAGGAGAGTTAC
* *
20309 AAACATAATGACAGAAGAGTTAC
1 AAACATAATGGCAGGAGAGTTAC
20332 AAACATAATGGCAGGAGAGTTAC
1 AAACATAATGGCAGGAGAGTTAC
20355 AAA-ATAAT
1 AAACATAAT
20363 AATAATTGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 5 0.10
23 44 0.90
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (23 bp):
AAACATAATGGCAGGAGAGTTAC
Found at i:21573 original size:29 final size:30
Alignment explanation
Indices: 21532--21602 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
21522 ACGTTAACAA
21532 GACA-CCCTCACATTT-CAAGTGGTTCTAG
1 GACACCCCTCACATTTCCAAGTGGTTCTAG
21560 GACACCCCTCACATTTCCAAGTGGTTCTAG
1 GACACCCCTCACATTTCCAAGTGGTTCTAG
21590 GACACCCC-CACAT
1 GACACCCCTCACAT
21603 GTTCTGTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 4 0.10
29 16 0.39
30 21 0.51
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.24
Consensus pattern (30 bp):
GACACCCCTCACATTTCCAAGTGGTTCTAG
Found at i:39884 original size:20 final size:22
Alignment explanation
Indices: 39850--39889 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39840 GAAGAGAAGG
39850 TGTATCGGCTGAAAA-AGGCTC
1 TGTATCGGCTGAAAACAGGCTC
*
39871 TGTAT-GGCTTAAAACAGGC
1 TGTATCGGCTGAAAACAGGC
39890 ACCAAGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
TGTATCGGCTGAAAACAGGCTC
Found at i:40306 original size:43 final size:43
Alignment explanation
Indices: 40271--40613 Score: 376
Period size: 43 Copynumber: 8.0 Consensus size: 43
40261 ATGCCATTAT
* * * *
40271 AGAACATGGTCTTTAGCGACACTTTTCCTACAAATGCCACTAA
1 AGAACATGGTCTTTAGCGACGCTTTCCCCACAAACGCCACTAA
* * * * * * *
40314 AGAACATGGTCTTTAACGGCACTTT-TCCATAAATGCCGC-AA
1 AGAACATGGTCTTTAGCGACGCTTTCCCCACAAACGCCACTAA
* * * *
40355 ATATCATGTTCTTTAGCGACGCTTTCCCCACAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGACGCTTTCCCCACAAACGCCACTAA
* * * *
40398 AGAACATGGTCTTTAGTGACGCTTTACCCACAAATGCCGCTAA
1 AGAACATGGTCTTTAGCGACGCTTTCCCCACAAACGCCACTAA
*
40441 AGAACATGGTCTTTAGCAACGCTTTCCCCA-AAAGCGCCACTAA
1 AGAACATGGTCTTTAGCGACGCTTTCCCCACAAA-CGCCACTAA
* * *
40484 AGAACATGGTCTTTAGTGACGC-TTCCCTCACAAACGTCGCTAA
1 AGAACATGGTCTTTAGCGACGCTTTCCC-CACAAACGCCACTAA
40527 AGAACATGGTCTTTAGC-AGCGC-TTCCCTCACAAACGCCACTAA
1 AGAACATGGTCTTTAGCGA-CGCTTTCCC-CACAAACGCCACTAA
*
40570 AGAACATGGTCTTTAGCGACGC-TTCCCTCACAAACGCTACTAA
1 AGAACATGGTCTTTAGCGACGCTTTCCC-CACAAACGCCACTAA
40613 A
1 A
40614 ATTAATAGAA
Statistics
Matches: 259, Mismatches: 34, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
41 21 0.08
42 30 0.12
43 204 0.79
44 4 0.02
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCGACGCTTTCCCCACAAACGCCACTAA
Found at i:45096 original size:22 final size:23
Alignment explanation
Indices: 45062--45116 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
45052 GAACGCTAGC
45062 GTGCTTACTGTTCAACACTGTGT
1 GTGCTTACTGTTCAACACTGTGT
*
45085 GTGCTT-CTGTTCAGCACTGTGT
1 GTGCTTACTGTTCAACACTGTGT
*
45107 GTGCCTACTG
1 GTGCTTACTG
45117 AATTGCACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.13, C:0.24, G:0.25, T:0.38
Consensus pattern (23 bp):
GTGCTTACTGTTCAACACTGTGT
Found at i:51262 original size:17 final size:17
Alignment explanation
Indices: 51242--51285 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
51232 ATTGGAGTTG
51242 AGAATGAAATCGAGTGA
1 AGAATGAAATCGAGTGA
* *
51259 AGAATGAAATGGAGTGG
1 AGAATGAAATCGAGTGA
51276 AGAATGAAAT
1 AGAATGAAAT
51286 TAGGGATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.32, T:0.18
Consensus pattern (17 bp):
AGAATGAAATCGAGTGA
Found at i:51508 original size:41 final size:41
Alignment explanation
Indices: 51440--51522 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
51430 CGTTTTTCAA
* * * *
51440 ATAAACGCTGCTATTGCTTGACCTTTAGTGGTATTTTTACC
1 ATAAACGCTACTATTACTTGACCTTTAGCGGCATTTTTACC
* ** *
51481 ATAAACGTTACTATTACTTGATTTTTAGCGGCGTTTTTACC
1 ATAAACGCTACTATTACTTGACCTTTAGCGGCATTTTTACC
51522 A
1 A
51523 CAAATGTCGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (41 bp):
ATAAACGCTACTATTACTTGACCTTTAGCGGCATTTTTACC
Found at i:53545 original size:41 final size:41
Alignment explanation
Indices: 53473--53768 Score: 328
Period size: 41 Copynumber: 7.2 Consensus size: 41
53463 TGTAAATAAA
* ** * *
53473 TTAGCAGCGCTT-TCCCAAAAACATCGTTAATGCTCTGACCT
1 TTAGCGGCGCTTCT-CCAAAAACGCCGCTAATGCTTTGACCT
* *
53514 TTAGCGGCGCTT-TCACATAAACGCCGCTAATGCTTTGACAT
1 TTAGCGGCGCTTCTC-CAAAAACGCCGCTAATGCTTTGACCT
* * * * * *
53555 TTAACAGCGCTTCTCCAAAAACCCCGCTATTGCTCTGACTT
1 TTAGCGGCGCTTCTCCAAAAACGCCGCTAATGCTTTGACCT
* *
53596 TTAGCGGCGCTTCTCCAAAAATGCCACTAATGCTTTGACCT
1 TTAGCGGCGCTTCTCCAAAAACGCCGCTAATGCTTTGACCT
* *
53637 TTAGCGGCGCTT-TCCCAAAAACGCAGCTAATGCTTTGAACT
1 TTAGCGGCGCTTCT-CCAAAAACGCCGCTAATGCTTTGACCT
53678 TTAGCGGCGCTTCTCCAAAAACGCCGCTAATGCTTTGACCT
1 TTAGCGGCGCTTCTCCAAAAACGCCGCTAATGCTTTGACCT
* * * * * *
53719 TTGGCAGTGCTTCTCCAAAAACGCCGTTAATGCTCTAACCT
1 TTAGCGGCGCTTCTCCAAAAACGCCGCTAATGCTTTGACCT
*
53760 TTAGTGGCG
1 TTAGCGGCG
53769 TTTTTTCTAT
Statistics
Matches: 213, Mismatches: 38, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
40 2 0.01
41 208 0.98
42 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGCTTCTCCAAAAACGCCGCTAATGCTTTGACCT
Found at i:53626 original size:82 final size:82
Alignment explanation
Indices: 53473--53768 Score: 364
Period size: 82 Copynumber: 3.6 Consensus size: 82
53463 TGTAAATAAA
** * *
53473 TTAGCAGCGCTTTCCCAAAAACATCGTTAATGCTCTGACCTTTAGCGGCGCTT-TCACATAAACG
1 TTAGCAGCGCTTTCCCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCTC-CAAAAACG
*
53537 CCGCTAATGCTTTGACAT
65 CCGCTAATGCTTTGACCT
* * * * *
53555 TTAACAGCGC-TTCTCCAAAAACCCCGCTATTGCTCTGACTTTTAGCGGCGCTTCTCCAAAAATG
1 TTAGCAGCGCTTTC-CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCTCCAAAAACG
*
53619 CCACTAATGCTTTGACCT
65 CCGCTAATGCTTTGACCT
* * * *
53637 TTAGCGGCGCTTTCCCAAAAACGCAGCTAATGCTTTGAACTTTAGCGGCGCTTCTCCAAAAACGC
1 TTAGCAGCGCTTTCCCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCTCCAAAAACGC
53702 CGCTAATGCTTTGACCT
66 CGCTAATGCTTTGACCT
* * * * *
53719 TTGGCAGTGC-TTCTCCAAAAACGCCGTTAATGCTCTAACCTTTAGTGGCG
1 TTAGCAGCGCTTTC-CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
53769 TTTTTTCTAT
Statistics
Matches: 181, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
81 6 0.03
82 170 0.94
83 5 0.03
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (82 bp):
TTAGCAGCGCTTTCCCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCTCCAAAAACGC
CGCTAATGCTTTGACCT
Found at i:53649 original size:123 final size:123
Alignment explanation
Indices: 53473--53768 Score: 362
Period size: 123 Copynumber: 2.4 Consensus size: 123
53463 TGTAAATAAA
** ** *
53473 TTAGCAGCGCTT-TCCCAAAAACATCGTTAATGCTCTGACCTTTAGCGGCGCTTTCACATAAACG
1 TTAGCAGCGCTTCT-CCAAAAACGCCACTAATGCTCTGACCTTTAGCGGCGCTTTCACAAAAACG
* * *
53537 CCGCTAATGCTTTG-ACATTTAACAGCGCTTCTCCAAAAACCCCGCTATTGCTCTGACTT
65 CAGCTAATGCTTTGAAC-TTTAACAGCGCTTCTCCAAAAACCCCGCTAATGCTCTGACCT
* * * *
53596 TTAGCGGCGCTTCTCCAAAAATGCCACTAATGCTTTGACCTTTAGCGGCGCTTTCCCAAAAACGC
1 TTAGCAGCGCTTCTCCAAAAACGCCACTAATGCTCTGACCTTTAGCGGCGCTTTCACAAAAACGC
* * * *
53661 AGCTAATGCTTTGAACTTTAGCGGCGCTTCTCCAAAAACGCCGCTAATGCTTTGACCT
66 AGCTAATGCTTTGAACTTTAACAGCGCTTCTCCAAAAACCCCGCTAATGCTCTGACCT
* * ** * *
53719 TTGGCAGTGCTTCTCCAAAAACGCCGTTAATGCTCTAACCTTTAGTGGCG
1 TTAGCAGCGCTTCTCCAAAAACGCCACTAATGCTCTGACCTTTAGCGGCG
53769 TTTTTTCTAT
Statistics
Matches: 146, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
123 143 0.98
124 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (123 bp):
TTAGCAGCGCTTCTCCAAAAACGCCACTAATGCTCTGACCTTTAGCGGCGCTTTCACAAAAACGC
AGCTAATGCTTTGAACTTTAACAGCGCTTCTCCAAAAACCCCGCTAATGCTCTGACCT
Found at i:55857 original size:41 final size:42
Alignment explanation
Indices: 55809--55992 Score: 180
Period size: 42 Copynumber: 4.4 Consensus size: 42
55799 TTATATGAAT
* * * * * *
55809 GGAAGACTCGTGACTCGAAACGAGCATGAGGATAT-ATTTAA
1 GGAAGACTCATGACTCGAGATGAGAATGAGAATATGATTAAA
*
55850 GGAAGACTCATGTCTC-ATGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGACTCGA-GATGAGAATGAGAATATGATTAAA
* *
55892 GGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGACTCGAGATGAGAATGAGAATATGATTAAA
* * * *
55934 GGAAGACTCATGACTC-AGAATGAGCATAAGATTATGTTTAAAAA
1 GGAAGACTCATGACTCGAG-ATGAGAATGAGAATATGATT--AAA
55978 GGAAGA--CATGACTCG
1 GGAAGACTCATGACTCG
55993 GTAGAGCATA
Statistics
Matches: 122, Mismatches: 14, Indels: 12
0.82 0.09 0.08
Matches are distributed among these distances:
40 1 0.01
41 28 0.23
42 84 0.69
44 9 0.07
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (42 bp):
GGAAGACTCATGACTCGAGATGAGAATGAGAATATGATTAAA
Found at i:55899 original size:42 final size:42
Alignment explanation
Indices: 55834--55984 Score: 187
Period size: 42 Copynumber: 3.6 Consensus size: 42
55824 CGAAACGAGC
* * *
55834 ATGAGGATAT-ATTTAAGGAAGACTCATGTCTCATGATGAGA
1 ATGAGAATATGATTAAAGGAAGACTCATGTCTCAGGATGAGA
*
55875 ATGAGAATATGATTAAAGGAAGACTCATGTCTCGGGATGAGA
1 ATGAGAATATGATTAAAGGAAGACTCATGTCTCAGGATGAGA
* * *
55917 ATGAGAATATGATTAAAGGAAGACTCATGACTCAGAATGAGC
1 ATGAGAATATGATTAAAGGAAGACTCATGTCTCAGGATGAGA
* * *
55959 ATAAGATTATGTTTAAAAAGGAAGAC
1 ATGAGAATATGATT--AAAGGAAGAC
55985 ATGACTCGGT
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 9 0.09
42 77 0.80
44 10 0.10
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (42 bp):
ATGAGAATATGATTAAAGGAAGACTCATGTCTCAGGATGAGA
Found at i:65000 original size:17 final size:17
Alignment explanation
Indices: 64978--65026 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
64968 TATTAAAATT
64978 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
64995 ATTTTTT-AAAT-T---
1 ATTTTTTAAAATATAAA
65007 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
65024 ATT
1 ATT
65027 ATTAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 1 0.04
15 1 0.04
16 4 0.15
17 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTTAAAATATAAA
Found at i:65057 original size:31 final size:29
Alignment explanation
Indices: 64962--65063 Score: 159
Period size: 29 Copynumber: 3.4 Consensus size: 29
64952 CAAATGATTT
64962 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
* *
64991 TAAAATTTTTTAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
*
65020 TAAAATTATTAAAATTATTGTTTTGAAATAA
1 TAAAATTATTAAAATTATT-TTTTAAAAT-A
65051 TAAAATTATTAAA
1 TAAAATTATTAAA
65064 TAATTTTAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 44 0.67
30 8 0.12
31 14 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:65537 original size:190 final size:193
Alignment explanation
Indices: 65119--65543 Score: 651
Period size: 193 Copynumber: 2.2 Consensus size: 193
65109 TCATCATTTT
65119 AATTTCTAGATTTTCTTACATTTTCCCATCAACCAAACACCCAAAAAAATTTGTTTTTCTTGCAT
1 AATTTCTAGATTTTCTTACATTTTCCCATCAACCAAACACCC--AAAAATTTGTTTTTCTTGCAT
* * *
65184 TCGATTGAGATTCTTGCATAGATAGAAAATGGGTTATCTTAGTTCAAATTTCAAACACAAACCCA
64 ACGATTGAGATTCTTGCATAGATAGAAAATGGATTATCATAGTTCAAATTTCAAACACAAACCCA
* * * *
65249 TCAATCTTTTCTTCCCCAAGACCCAATCACATTTCAAAACCAAGTGCAAATTCTTTAGCAACAAT
129 TCAATCTTTCCTTCCCC-AGACCCAATCACAGTTCAAAACCAAGTGCAAATTCTTGAGCAACAAG
65314 A
193 A
* * *
65315 AATTTCTAGATTTTCCTACATTTTCCCATCAACCAAACACCC-TAAATTTTTTTTTCTTGCATAC
1 AATTTCTAGATTTTCTTACATTTTCCCATCAACCAAACACCCAAAAATTTGTTTTTCTTGCATAC
* *
65379 GATTGAGATTCTTGCATAGATA-ACAAATGGATTATCATAGTTTAAATTTCAAACACAAATCCAT
66 GATTGAGATTCTTGCATAGATAGA-AAATGGATTATCATAGTTCAAATTTCAAACACAAACCCAT
* *
65443 CAATCTTTCCTT-CCC-GACCCAATTACAGTTCAAAACCAAGTGCAAATTCTTGAGGAACAAGA
130 CAATCTTTCCTTCCCCAGACCCAATCACAGTTCAAAACCAAGTGCAAATTCTTGAGCAACAAGA
*
65505 AATTTCCAGATTTTCTTACATTTTCCCATCAACCAAACA
1 AATTTCTAGATTTTCTTACATTTTCCCATCAACCAAACA
65544 GGACTGGTAA
Statistics
Matches: 212, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
190 79 0.37
192 4 0.02
193 88 0.42
196 41 0.19
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (193 bp):
AATTTCTAGATTTTCTTACATTTTCCCATCAACCAAACACCCAAAAATTTGTTTTTCTTGCATAC
GATTGAGATTCTTGCATAGATAGAAAATGGATTATCATAGTTCAAATTTCAAACACAAACCCATC
AATCTTTCCTTCCCCAGACCCAATCACAGTTCAAAACCAAGTGCAAATTCTTGAGCAACAAGA
Found at i:66126 original size:20 final size:20
Alignment explanation
Indices: 66101--66214 Score: 98
Period size: 20 Copynumber: 5.9 Consensus size: 20
66091 GATGATGATT
66101 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
66121 ATAATTTT---AT-ATTTTA
1 ATAATTTTAAAATAATTTTA
* * *
66137 AAAAATTTAAATTAATTTTAAA
1 ATAATTTTAAAATAATTTT--A
*
66159 ATAAATTT-AAA-AATTTT-
1 ATAATTTTAAAATAATTTTA
*
66176 ATATTTTTAAAAATAATTTTA
1 ATAATTTT-AAAATAATTTTA
*
66197 ATAATTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
66215 GCTGACATGG
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
16 12 0.16
17 8 0.11
19 4 0.05
20 34 0.45
21 9 0.12
22 8 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:66174 original size:47 final size:49
Alignment explanation
Indices: 66101--66209 Score: 161
Period size: 47 Copynumber: 2.3 Consensus size: 49
66091 GATGATGATT
* *
66101 ATAATTTTAAAATAATTTTAATAATTTTATA-TTTT-AAAA-AATTTAA
1 ATAATTTTAAAATAAATTTAAAAATTTTATATTTTTAAAAATAATTTAA
*
66147 ATTAATTTTAAAATAAATTTAAAAATTTTATATTTTTAAAAATAATTTTA
1 A-TAATTTTAAAATAAATTTAAAAATTTTATATTTTTAAAAATAATTTAA
66197 ATAATTTTAAAAT
1 ATAATTTTAAAAT
66210 CATTTGCTGA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
46 1 0.02
47 28 0.50
48 4 0.07
49 16 0.29
50 7 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (49 bp):
ATAATTTTAAAATAAATTTAAAAATTTTATATTTTTAAAAATAATTTAA
Found at i:66188 original size:29 final size:30
Alignment explanation
Indices: 66133--66207 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
66123 AATTTTATAT
* *
66133 TTTAAAAAATTTAAATTAATTTTAAAATAAA
1 TTTAAAAATTTTAAATT-ATTTAAAAATAAA
* *
66164 TTTAAAAATTTTATATT-TTTAAAAATAAT
1 TTTAAAAATTTTAAATTATTTAAAAATAAA
*
66193 TTTAATAATTTTAAA
1 TTTAAAAATTTTAAA
66208 ATCATTTGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 23 0.61
31 15 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTTAAAAATTTTAAATTATTTAAAAATAAA
Found at i:67222 original size:42 final size:42
Alignment explanation
Indices: 67155--67272 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
67145 GAGCATGTGG
* * *
67155 ATAT-ATTTAAGGAAAACTCATGTCTCAGGATGAGAATGAGA
1 ATATGATTAAAGGAAGACTCATGTCTCAGAATGAGAATGAGA
67196 ATATGATTAAAGGAAGACTCATGTCTCAGAATGAGAATGAGA
1 ATATGATTAAAGGAAGACTCATGTCTCAGAATGAGAATGAGA
* *
67238 ATATGATTCAAGGAAGACTCATGACTCAGAATGAG
1 ATATGATTAAAGGAAGACTCATGTCTCAGAATGAG
67273 CTTGGGATTA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
41 4 0.06
42 67 0.94
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (42 bp):
ATATGATTAAAGGAAGACTCATGTCTCAGAATGAGAATGAGA
Found at i:67306 original size:44 final size:42
Alignment explanation
Indices: 67119--67308 Score: 177
Period size: 42 Copynumber: 4.5 Consensus size: 42
67109 ACTTGATGTA
* * * * *
67119 TAAATGGAAGACTCGTGACTC-GAAACGAGCATGTGGATAT-AT
1 TAAA-GGAAGACTCATGACTCAG-AATGAGAATGAGAATATGAT
* * * *
67161 TTAAGGAAAACTCATGTCTCAGGATGAGAATGAGAATATGAT
1 TAAAGGAAGACTCATGACTCAGAATGAGAATGAGAATATGAT
*
67203 TAAAGGAAGACTCATGTCTCAGAATGAGAATGAGAATATGAT
1 TAAAGGAAGACTCATGACTCAGAATGAGAATGAGAATATGAT
* ** * * *
67245 TCAAGGAAGACTCATGACTCAGAATGAGCTTGGGATTATGTT
1 TAAAGGAAGACTCATGACTCAGAATGAGAATGAGAATATGAT
*
67287 TAAAAAGGAAGACTTATGACTC
1 T--AAAGGAAGACTCATGACTC
67309 GGTAGAGCAT
Statistics
Matches: 123, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
41 25 0.20
42 81 0.66
44 17 0.14
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.25
Consensus pattern (42 bp):
TAAAGGAAGACTCATGACTCAGAATGAGAATGAGAATATGAT
Found at i:89090 original size:33 final size:32
Alignment explanation
Indices: 89010--89095 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 32
89000 CCAAGGCTAA
* *
89010 AAGGGTCTAAAATTATGTTTTTACTTTTATTTTT
1 AAGGGTCCAAAATT-TTTTTTTA-TTTTATTTTT
89044 AAGGTGTCC--AATTTTATTTTT-TTTTAGTTTTT
1 AAGG-GTCCAAAATTTT-TTTTTATTTTA-TTTTT
89076 AAGGGTCCAAAATTTTTTTT
1 AAGGGTCCAAAATTTTTTTT
89096 ACCAACTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
31 9 0.20
32 14 0.31
33 15 0.33
34 4 0.09
35 3 0.07
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.56
Consensus pattern (32 bp):
AAGGGTCCAAAATTTTTTTTTATTTTATTTTT
Found at i:89137 original size:31 final size:30
Alignment explanation
Indices: 89060--89138 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
89050 TCCAATTTTA
* * *
89060 TTTTTTTTT-AGTTTTTAAGGGTCCAAAAT
1 TTTTTTTTTCAATTTTTAAGAGACCAAAAT
** * *
89089 TTTTTTTACCAACTTTTAAGAGACCTAAATT
1 TTTTTTTTTCAATTTTTAAGAGACC-AAAAT
89120 TTTTTTTTTCAATTTTTAA
1 TTTTTTTTTCAATTTTTAA
89139 TGAATTTAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 7 0.18
30 11 0.29
31 20 0.53
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.56
Consensus pattern (30 bp):
TTTTTTTTTCAATTTTTAAGAGACCAAAAT
Found at i:95115 original size:13 final size:13
Alignment explanation
Indices: 95099--95130 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
95089 CTACTTAACT
95099 AAAAAAATTAATA
1 AAAAAAATTAATA
*
95112 AAAACAATTAATA
1 AAAAAAATTAATA
95125 AAAAAA
1 AAAAAA
95131 CTAAATCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAAAATTAATA
Found at i:95477 original size:20 final size:21
Alignment explanation
Indices: 95440--95479 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
95430 GAATGTTGGC
**
95440 AACAATGCAGCATTAGCATGA
1 AACAATGCAGCAGCAGCATGA
95461 AACAA-GCAGCAGCAGCATG
1 AACAATGCAGCAGCAGCATG
95480 GAGCAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (21 bp):
AACAATGCAGCAGCAGCATGA
Found at i:103793 original size:25 final size:24
Alignment explanation
Indices: 103736--103795 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
103726 TTCATTTAAC
103736 TTAATCGAATATGTTAACGAACATA
1 TTAAT-GAATATGTTAACGAACATA
* *
103761 -TAATTGAATATGTTCACGAGCAATA
1 TTAA-TGAATATGTTAACGAAC-ATA
103786 TTAATGAATA
1 TTAATGAATA
103796 ATAAACAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 17 0.57
25 10 0.33
26 3 0.10
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (24 bp):
TTAATGAATATGTTAACGAACATA
Found at i:103897 original size:12 final size:12
Alignment explanation
Indices: 103880--103913 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
103870 TAAATGAATC
103880 ATAAACGAGTCA
1 ATAAACGAGTCA
*
103892 ATAAACGAGCCA
1 ATAAACGAGTCA
103904 ATAAACGAGT
1 ATAAACGAGT
103914 TTATTCGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.15
Consensus pattern (12 bp):
ATAAACGAGTCA
Found at i:112636 original size:42 final size:42
Alignment explanation
Indices: 112589--112673 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
112579 ATCATAGCAA
*
112589 TGCCGATTCCATTGTTGATACTAGCTTAATTTGGATTGATAG
1 TGCCGATTCCATTGTTGATACTAGCTTAATTTGGACTGATAG
*
112631 TGCCGATTCCATTGTTGCTACTAGCTTAATTTGGACTGATAG
1 TGCCGATTCCATTGTTGATACTAGCTTAATTTGGACTGATAG
112673 T
1 T
112674 CTTGCGTCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (42 bp):
TGCCGATTCCATTGTTGATACTAGCTTAATTTGGACTGATAG
Found at i:113843 original size:3 final size:3
Alignment explanation
Indices: 113829--113879 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
113819 ACATCCAAAT
* * *
113829 AAC AAA AAC AAC AACC AA- AAC AAC AAC AAA AAT AAC AAC AA- AAC
1 AAC AAC AAC AAC AA-C AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
113873 AAC AAC A
1 AAC AAC A
113880 GAAATAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.73, C:0.25, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:113850 original size:12 final size:12
Alignment explanation
Indices: 113833--113878 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
113823 CCAAATAACA
113833 AAAACAACAACC
1 AAAACAACAACC
*
113845 AAAACAACAACA
1 AAAACAACAACC
*
113857 AAAATAACAA-C
1 AAAACAACAACC
113868 AAAACAACAAC
1 AAAACAACAAC
113879 AGAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.72, C:0.26, G:0.00, T:0.02
Consensus pattern (12 bp):
AAAACAACAACC
Found at i:113870 original size:23 final size:23
Alignment explanation
Indices: 113829--113918 Score: 99
Period size: 24 Copynumber: 3.8 Consensus size: 23
113819 ACATCCAAAT
*
113829 AACAAAAACAACAACCAAAACAAC
1 AACAAAAATAACAA-CAAAACAAC
113853 AACAAAAATAACAACAAAACAAC
1 AACAAAAATAACAACAAAACAAC
* * *
113876 AACAGAAATAATAACAAAAGCAGC
1 AACAAAAATAACAACAAAA-CAAC
* * *
113900 AACCAAAATAGCAAAAAAA
1 AACAAAAATAACAACAAAA
113919 AAAAATACCA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 26 0.46
24 30 0.54
ACGTcount: A:0.70, C:0.21, G:0.04, T:0.04
Consensus pattern (23 bp):
AACAAAAATAACAACAAAACAAC
Found at i:113875 original size:20 final size:20
Alignment explanation
Indices: 113812--113877 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
113802 TAAAAACACA
* * *
113812 AAAAATAACATCCAAATAAC
1 AAAAATAACAACAAAACAAC
*
113832 AAAAACAACAACCAAAACAACAAC
1 AAAAATAACAA-C--AA-AACAAC
113856 AAAAATAACAACAAAACAAC
1 AAAAATAACAACAAAACAAC
113876 AA
1 AA
113878 CAGAAATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 17 0.46
21 3 0.08
23 2 0.05
24 15 0.41
ACGTcount: A:0.71, C:0.23, G:0.00, T:0.06
Consensus pattern (20 bp):
AAAAATAACAACAAAACAAC
Found at i:115233 original size:16 final size:15
Alignment explanation
Indices: 115214--115261 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
115204 TTCATTTTTT
115214 TTTAATTTTTATAAAA
1 TTTAATTTTTA-AAAA
**
115230 TTTATATTTTTAAATT
1 TTTA-ATTTTTAAAAA
115246 TTGTAATTTTTAAAAA
1 TT-TAATTTTTAAAAA
115262 ATTACATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTAATTTTTAAAAA
Found at i:125833 original size:18 final size:18
Alignment explanation
Indices: 125810--125845 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
125800 TCAAAATGAT
125810 GTAATTTTACCTTTTAAC
1 GTAATTTTACCTTTTAAC
125828 GTAATTTTACCTTTTAAC
1 GTAATTTTACCTTTTAAC
125846 TTTATGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (18 bp):
GTAATTTTACCTTTTAAC
Found at i:136610 original size:29 final size:32
Alignment explanation
Indices: 136559--136647 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 32
136549 TTTTTTAAAA
136559 TTTTAAAAATTTAAGAAATTATAAAAAAATA-T
1 TTTTAAAAA-TTAAGAAATTATAAAAAAATATT
*
136591 TTTTAAAAATTAA-AAA-TATAAAAATATATT
1 TTTTAAAAATTAAGAAATTATAAAAAAATATT
* * *
136621 TTTTAAATATTAATAAAGTTTTAAAAA
1 TTTTAAAAATTAAGAAA-TTATAAAAA
136648 TATAATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 11 0.22
30 16 0.32
31 7 0.14
32 9 0.18
33 7 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (32 bp):
TTTTAAAAATTAAGAAATTATAAAAAAATATT
Found at i:136635 original size:27 final size:27
Alignment explanation
Indices: 136578--136633 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
136568 TTTAAGAAAT
136578 TATAAAAAAATATTTTTAAAAATTAAAAA
1 TATAAAAAAATATTTTTAAAAATT--AAA
* *
136607 TATAAAAATATATTTTTTAAATATTAA
1 TATAAAAAAATA-TTTTTAAAAATTAA
136634 TAAAGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 11 0.46
30 11 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TATAAAAAAATATTTTTAAAAATTAAA
Found at i:139353 original size:16 final size:16
Alignment explanation
Indices: 139307--139353 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
139297 TTTAAATATT
139307 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
139324 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
139340 TATATTTTTTATTT
1 TATATTTTTTATTT
139354 ATTGAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:142842 original size:9 final size:9
Alignment explanation
Indices: 142800--142979 Score: 105
Period size: 9 Copynumber: 18.8 Consensus size: 9
142790 AATGATTTTT
142800 TTTTTATAA
1 TTTTTATAA
* *
142809 ATTTGATAA
1 TTTTTATAA
*
142818 TTTATTAGAA
1 TTT-TTATAA
142828 -TTTTATAA
1 TTTTTATAA
*
142836 GTTTTATGAA
1 TTTTTAT-AA
142846 TTTTTTATAA
1 -TTTTTATAA
142856 TTTTTATAA
1 TTTTTATAA
*
142865 GTTTATATAAA
1 -TTTTTAT-AA
** *
142876 AATTTAAATA
1 TTTTTATA-A
142886 TTTTTA-ATA
1 TTTTTATA-A
142895 TGTTTTAT-A
1 T-TTTTATAA
*
142904 TGTTTATATA
1 TTTTTATA-A
*
142914 TTTATTATGA
1 TTT-TTATAA
*
142924 TTTTTATAGG
1 TTTTTATA-A
142934 TTTTTATAA
1 TTTTTATAA
142943 TTTTTATAA
1 TTTTTATAA
142952 TTTTTATAAAA
1 TTTTTAT--AA
*
142963 TTTTTAATAT
1 TTTTT-ATAA
142973 TTTTTAT
1 TTTTTAT
142980 TTGAAAAATG
Statistics
Matches: 134, Mismatches: 21, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
8 10 0.07
9 55 0.41
10 48 0.36
11 19 0.14
12 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:142869 original size:28 final size:27
Alignment explanation
Indices: 142800--142871 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
142790 AATGATTTTT
*
142800 TTTTTATAAATTTGATAATTTATTAGAA
1 TTTTTATAAGTTT-ATAATTTATTAGAA
* *
142828 -TTTTATAAGTTTTATGAATTTTTTATAA
1 TTTTTATAAG-TTTAT-AATTTATTAGAA
142856 TTTTTATAAGTTTATA
1 TTTTTATAAGTTTATA
142872 TAAAAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 11 0.29
28 18 0.47
29 9 0.24
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTTTATAAGTTTATAATTTATTAGAA
Found at i:142946 original size:18 final size:18
Alignment explanation
Indices: 142800--142979 Score: 105
Period size: 20 Copynumber: 9.4 Consensus size: 18
142790 AATGATTTTT
* *
142800 TTTTTATAAATTTGATAA
1 TTTTTATAATTTTTATAA
*
142818 TTTATTAGAA-TTTTATAA
1 TTT-TTATAATTTTTATAA
*
142836 GTTTTATGAATTTTTTATAA
1 TTTTTAT-AA-TTTTTATAA
*
142856 TTTTTATAAGTTTATATAAA
1 TTTTTATAA-TTTTTAT-AA
** *
142876 AATTTAAATATTTTTA-ATA
1 TTTTTATA-ATTTTTATA-A
*
142895 TGTTTTAT-ATGTTTATATA
1 T-TTTTATAATTTTTATA-A
* *
142914 TTTATTATGATTTTTATAGG
1 TTT-TTATAATTTTTATA-A
142934 TTTTTATAATTTTTATAA
1 TTTTTATAATTTTTATAA
*
142952 TTTTTATAAAATTTTTAATAT
1 TTTTTAT--AATTTTT-ATAA
142973 TTTTTAT
1 TTTTTAT
142980 TTGAAAAATG
Statistics
Matches: 127, Mismatches: 21, Indels: 25
0.73 0.12 0.14
Matches are distributed among these distances:
17 3 0.02
18 30 0.24
19 35 0.28
20 48 0.38
21 11 0.09
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTTATAATTTTTATAA
Found at i:142966 original size:28 final size:28
Alignment explanation
Indices: 142828--142975 Score: 90
Period size: 28 Copynumber: 5.1 Consensus size: 28
142818 TTTATTAGAA
* **
142828 TTTTATAAGTTTTATGAATTTTTTATAAT
1 TTTTATAATTTTTAT-AAAATTTTATAAT
* *
142857 TTTTATAAGTTTATATAAAAATTTA-AAT
1 TTTTATAA-TTTTTATAAAATTTTATAAT
*
142885 ATTTT-TAATATGTTT-T-ATATGTTTATATAT
1 -TTTTATAAT-T-TTTATAAAAT-TTTATA-AT
* ***
142915 TTATTATGATTTTTATAGGTTTTTATAAT
1 TT-TTATAATTTTTATAAAATTTTATAAT
142944 TTTTATAATTTTTATAAAATTTT-TAAT
1 TTTTATAATTTTTATAAAATTTTATAAT
142971 ATTTT
1 -TTTT
142976 TTATTTGAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 25
0.69 0.12 0.19
Matches are distributed among these distances:
27 7 0.08
28 33 0.36
29 30 0.33
30 17 0.19
31 4 0.04
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTATAATTTTTATAAAATTTTATAAT
Found at i:149824 original size:11 final size:12
Alignment explanation
Indices: 149806--149859 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
149796 CAACCCAATA
149806 TTATTTTTATAT
1 TTATTTTTATAT
149818 TTATTTTTTATAT
1 TTA-TTTTTATAT
*
149831 TTATTTTTCTAT
1 TTATTTTTATAT
*
149843 TGATTTGTT-TAT
1 TTATTT-TTATAT
149855 TTATT
1 TTATT
149860 ATATGTCCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 23 0.62
13 14 0.38
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (12 bp):
TTATTTTTATAT
Found at i:149830 original size:24 final size:25
Alignment explanation
Indices: 149803--149859 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
149793 AGACAACCCA
*
149803 ATATTATTTTTATATTTATTT-TTT
1 ATATTATTTTTATATTGATTTGTTT
*
149827 ATATTTATTTTTCTATTGATTTGTTT
1 ATA-TTATTTTTATATTGATTTGTTT
149853 AT-TTATT
1 ATATTATT
149860 ATATGTCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 8 0.28
25 16 0.55
26 5 0.17
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (25 bp):
ATATTATTTTTATATTGATTTGTTT
Found at i:150607 original size:10 final size:10
Alignment explanation
Indices: 150592--150616 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
150582 CTAATCGGAT
150592 AAAAAAAGAA
1 AAAAAAAGAA
150602 AAAAAAAGAA
1 AAAAAAAGAA
150612 AAAAA
1 AAAAA
150617 TAAGTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:161072 original size:124 final size:125
Alignment explanation
Indices: 160851--161101 Score: 416
Period size: 124 Copynumber: 2.0 Consensus size: 125
160841 ATGATAATAT
*
160851 TTAATTAAACAAAATATTCAGGGCTTATAACAACATAAACATGGATTAAATATAAACAAGCAATT
1 TTAATTAAACAAAATATTCAGGGCCTATAACAACATAAACATGGATTAAATATAAACAAGCAATT
* * * * *
160916 ATACACAATCAACCTAACACTTGAAAAATTTCAGCCATTTTAATTAAAGAAATAATAGCA
66 AAACACAACCAACCCAAAACTTGAAAAATTTCAGCCATCTTAATTAAAGAAATAATAGCA
*
160976 TTAATTAAACAAAATATTCAGGGCCTATAACAACATAAAC-TTGATTAAATATAAACAAGCAATT
1 TTAATTAAACAAAATATTCAGGGCCTATAACAACATAAACATGGATTAAATATAAACAAGCAATT
161040 AAACACAACCAACCCAAAACTT-AAAGAATTTCAGCCATCTTAATTAAAGAAATAATAGCA
66 AAACACAACCAACCCAAAACTTGAAA-AATTTCAGCCATCTTAATTAAAGAAATAATAGCA
161100 TT
1 TT
161102 CATCATGATA
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
123 3 0.03
124 76 0.64
125 39 0.33
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (125 bp):
TTAATTAAACAAAATATTCAGGGCCTATAACAACATAAACATGGATTAAATATAAACAAGCAATT
AAACACAACCAACCCAAAACTTGAAAAATTTCAGCCATCTTAATTAAAGAAATAATAGCA
Found at i:171254 original size:12 final size:12
Alignment explanation
Indices: 171215--171256 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
171205 GTTATTCATT
171215 AACATTGTTCGTG
1 AACA-TGTTCGTG
171228 AACATGTTCAG-G
1 AACATGTTC-GTG
171240 AACATGTTCGTG
1 AACATGTTCGTG
171252 AACAT
1 AACAT
171257 TAAACAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.04
12 21 0.78
13 5 0.19
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:171521 original size:7 final size:7
Alignment explanation
Indices: 171509--171543 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
171499 ATCTTGTCTT
171509 CCATCCC
1 CCATCCC
171516 CCATCCC
1 CCATCCC
171523 CCATCCC
1 CCATCCC
171530 CCATCCC
1 CCATCCC
171537 CCATCCC
1 CCATCCC
171544 GTCCCCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.71, G:0.00, T:0.14
Consensus pattern (7 bp):
CCATCCC
Found at i:174354 original size:22 final size:22
Alignment explanation
Indices: 174329--174384 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
174319 AGTTAACATC
174329 TCTCGAAACAAATAAGTGTATG
1 TCTCGAAACAAATAAGTGTATG
*
174351 TCTCGAAACAAATGAGTGTATG
1 TCTCGAAACAAATAAGTGTATG
* *
174373 TTTCGAGACAAA
1 TCTCGAAACAAA
174385 AGGAATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (22 bp):
TCTCGAAACAAATAAGTGTATG
Found at i:175135 original size:34 final size:34
Alignment explanation
Indices: 175091--175171 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
175081 AAGAACATCG
*
175091 ACACCGAAGTGCAATATCAAAACAAAATAGAGTA
1 ACACCAAAGTGCAATATCAAAACAAAATAGAGTA
* *
175125 ACACCAAAGTGCAATATCAAAATAGAATAGAGTA
1 ACACCAAAGTGCAATATCAAAACAAAATAGAGTA
*
175159 GCACCAAAGTGCA
1 ACACCAAAGTGCA
175172 TGTTACAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.15
Consensus pattern (34 bp):
ACACCAAAGTGCAATATCAAAACAAAATAGAGTA
Found at i:176330 original size:11 final size:11
Alignment explanation
Indices: 176314--176359 Score: 83
Period size: 11 Copynumber: 4.2 Consensus size: 11
176304 GATTTTACTA
176314 GAAATTTTAAT
1 GAAATTTTAAT
176325 GAAATTTTAAT
1 GAAATTTTAAT
176336 GAAATTTTAAT
1 GAAATTTTAAT
*
176347 GAAATTTCAAT
1 GAAATTTTAAT
176358 GA
1 GA
176360 TTTCTCTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (11 bp):
GAAATTTTAAT
Found at i:176341 original size:22 final size:22
Alignment explanation
Indices: 176305--176359 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
176295 TGGAGGCTTG
*
176305 ATTTTACTAGAAATTTTAATGAA
1 ATTTTAAT-GAAATTTTAATGAA
176328 ATTTTAATGAAATTTTAATGAA
1 ATTTTAATGAAATTTTAATGAA
*
176350 ATTTCAATGA
1 ATTTTAATGA
176360 TTTCTCTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (22 bp):
ATTTTAATGAAATTTTAATGAA
Found at i:177633 original size:28 final size:28
Alignment explanation
Indices: 177596--177689 Score: 136
Period size: 28 Copynumber: 3.3 Consensus size: 28
177586 TTTTTTATAG
177596 AGATAGCCACAAAGGCGTCCATTTACAA
1 AGATAGCCACAAAGGCGTCCATTTACAA
* *
177624 AGATAACCACACAGGCGTCCATTTACAA
1 AGATAGCCACAAAGGCGTCCATTTACAA
*
177652 AGATAGCCACAAAGGCATCCATTTA-ATA
1 AGATAGCCACAAAGGCGTCCATTTACA-A
177680 GAGATAGCCA
1 -AGATAGCCA
177690 TAAAAGCTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
27 1 0.02
28 49 0.83
29 9 0.15
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.18
Consensus pattern (28 bp):
AGATAGCCACAAAGGCGTCCATTTACAA
Found at i:181090 original size:30 final size:30
Alignment explanation
Indices: 181056--181117 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
181046 ATTATTAAGT
181056 CCTTAAAAGTTT-T-AAAAGTTTTAATTAAAC
1 CCTTAAAA-TTTATGAAAA-TTTTAATTAAAC
181086 CCTTAAAATTTATGAAAATTTTAATTAAAC
1 CCTTAAAATTTATGAAAATTTTAATTAAAC
181116 CC
1 CC
181118 CCTAAAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 3 0.10
30 23 0.77
31 4 0.13
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.39
Consensus pattern (30 bp):
CCTTAAAATTTATGAAAATTTTAATTAAAC
Found at i:184101 original size:22 final size:20
Alignment explanation
Indices: 184076--184131 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
184066 ACAGGAAAGT
184076 AATTAAATATTTAATTTCGAAA
1 AATTAAATATTTAATTT--AAA
*
184098 AATTAAATAATTAAATTTAAA
1 AATTAAAT-ATTTAATTTAAA
184119 AATTTAAA-ATTTA
1 AA-TTAAATATTTA
184132 GTGGTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 4 0.13
21 5 0.17
22 13 0.43
23 8 0.27
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTAAATATTTAATTTAAA
Found at i:185654 original size:15 final size:15
Alignment explanation
Indices: 185614--185663 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 15
185604 GTTTATTTTA
185614 TTTTATTT-TAATATT
1 TTTTATTTAT-ATATT
*
185629 TATTACTTTTATATATT
1 TTTTA--TTTATATATT
185646 TTTTATTTATA-ATT
1 TTTTATTTATATATT
185660 TTTT
1 TTTT
185664 TATATAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 7 0.23
15 10 0.33
17 12 0.40
18 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTATATATT
Found at i:185664 original size:15 final size:15
Alignment explanation
Indices: 185614--185666 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
185604 GTTTATTTTA
185614 TTTTATTTTAATATT
1 TTTTATTTTAATATT
*
185629 TATTACTTTTATATATT
1 TTTTA-TTTTA-ATATT
185646 TTTTATTTATAAT-TT
1 TTTTATTT-TAATATT
185661 TTTTAT
1 TTTTAT
185667 ATAATCATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 12 0.36
16 10 0.30
17 11 0.33
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTTAATATT
Found at i:186619 original size:2 final size:2
Alignment explanation
Indices: 186612--186636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
186602 AAAATTTAAA
186612 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 A
186637 ACAGTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:187407 original size:207 final size:207
Alignment explanation
Indices: 187052--187467 Score: 787
Period size: 207 Copynumber: 2.0 Consensus size: 207
187042 CTTATTAATA
*
187052 TTATTTTAATAAATTTAAATATTATATTAGATAGATAATAATTTATTTTTATTATATTCAATAAA
1 TTATTTTAATAAATTTAAATATTATATTAGATAGATAATAATTTATTTTTATTATATTCAAGAAA
187117 AATTCATCATAATTCCCATTTCCTACCCTTAAAGAAATACCAAATCATTCAACTCTCCATCTAAT
66 AATTCATCATAATTCCCATTTCCTACCCTTAAAGAAATACCAAATCATTCAACTCTCCATCTAAT
187182 CAACCCACCTTAAAACCAAGTAAAAAAAAAAAGTTAAACAATAAAAAAGGGTCCTTGAATTTTTA
131 CAACCCACCTTAAAACCAAGTAAAAAAAAAAAGTTAAACAATAAAAAAGGGTCCTTGAATTTTTA
187247 TAGTTTAACTTG
196 TAGTTTAACTTG
*
187259 TTATTTTGATAAATTTAAATATTATATTAGATAGATAATAATTTATTTTTATTATATTCAAGAAA
1 TTATTTTAATAAATTTAAATATTATATTAGATAGATAATAATTTATTTTTATTATATTCAAGAAA
187324 AATTCATCATAATTCCCATTTCCTACCCTTAAAGAAATACCAAATCATTCAACTCTCCATCTAAT
66 AATTCATCATAATTCCCATTTCCTACCCTTAAAGAAATACCAAATCATTCAACTCTCCATCTAAT
* * *
187389 CAACCCACCTTAAAACCAAGTAAAAAAAAAAAGTTAAATAATAAAAAAGGGTCCTTGATTTTTTG
131 CAACCCACCTTAAAACCAAGTAAAAAAAAAAAGTTAAACAATAAAAAAGGGTCCTTGAATTTTTA
187454 TAGTTTAACTTG
196 TAGTTTAACTTG
187466 TT
1 TT
187468 TACATATAAG
Statistics
Matches: 204, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 204 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (207 bp):
TTATTTTAATAAATTTAAATATTATATTAGATAGATAATAATTTATTTTTATTATATTCAAGAAA
AATTCATCATAATTCCCATTTCCTACCCTTAAAGAAATACCAAATCATTCAACTCTCCATCTAAT
CAACCCACCTTAAAACCAAGTAAAAAAAAAAAGTTAAACAATAAAAAAGGGTCCTTGAATTTTTA
TAGTTTAACTTG
Done.