Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002680.1 Hibiscus syriacus cultivar Beakdansim tig00005543_pilon, 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: 157021
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:16133 original size:13 final size:13
Alignment explanation
Indices: 16115--16174 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
16105 TTTGGTAATC
16115 CCCGCCCCGATTA
1 CCCGCCCCGATTA
16128 CCCGCCCCGATTA
1 CCCGCCCCGATTA
*
16141 CCCGCCCTGATTA
1 CCCGCCCCGATTA
16154 -CC-CCCCGA-TA
1 CCCGCCCCGATTA
*
16164 CCCGACCCGAT
1 CCCGCCCCGAT
16175 AAATATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 2 0.05
11 7 0.17
12 7 0.17
13 25 0.61
ACGTcount: A:0.17, C:0.53, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:16307 original size:12 final size:12
Alignment explanation
Indices: 16292--16326 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
16282 CGATTCTCGG
16292 CCCAATACCCGA
1 CCCAATACCCGA
*
16304 CCCAATACCCGG
1 CCCAATACCCGA
16316 CCCAATACCCG
1 CCCAATACCCG
16327 TTTATGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:19747 original size:67 final size:67
Alignment explanation
Indices: 19669--19797 Score: 249
Period size: 67 Copynumber: 1.9 Consensus size: 67
19659 GGTGTAGTGC
19669 TAATATGAAACAAAAATTAAACTTTAGGTATGATTTTTAAAAATTAAAAGTTTAGGTACTAAGGT
1 TAATATGAAACAAAAATTAAACTTTAGGTATGATTTTTAAAAATTAAAAGTTTAGGTACTAAGGT
19734 GT
66 GT
*
19736 TAATATGAAACAAAAATTGAACTTTAGGTATGATTTTTAAAAATTAAAAGTTTAGGTACTAA
1 TAATATGAAACAAAAATTAAACTTTAGGTATGATTTTTAAAAATTAAAAGTTTAGGTACTAA
19798 AATGAATCAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.36
Consensus pattern (67 bp):
TAATATGAAACAAAAATTAAACTTTAGGTATGATTTTTAAAAATTAAAAGTTTAGGTACTAAGGT
GT
Found at i:20321 original size:47 final size:46
Alignment explanation
Indices: 20251--20352 Score: 177
Period size: 47 Copynumber: 2.2 Consensus size: 46
20241 GGTTCAAATC
20251 CGGGTACCTGGGTTTTTGCTACTCGAAGTTTTGGGTACCCAGATTTT
1 CGGGTA-CTGGGTTTTTGCTACTCGAAGTTTTGGGTACCCAGATTTT
*
20298 CGGGTACTGGGTTTGTTGTTACTCGAAGTTTTGGGTACCCAGATTTT
1 CGGGTACTGGGTTT-TTGCTACTCGAAGTTTTGGGTACCCAGATTTT
20345 CGGGTACT
1 CGGGTACT
20353 TGATTGGTCG
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
46 8 0.15
47 45 0.85
ACGTcount: A:0.15, C:0.18, G:0.29, T:0.38
Consensus pattern (46 bp):
CGGGTACTGGGTTTTTGCTACTCGAAGTTTTGGGTACCCAGATTTT
Found at i:26768 original size:31 final size:30
Alignment explanation
Indices: 26733--26802 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
26723 AGTTTCAAAA
*
26733 GTAACAAATTACTCACTAACGTTATCAAATT
1 GTAACAAATT-CTCACTAACATTATCAAATT
* * *
26764 GTAACAAAATTGTCACTAACATTATCTATTT
1 GTAAC-AAATTCTCACTAACATTATCAAATT
26795 GTAACAAA
1 GTAACAAA
26803 ATGATCACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.09
31 26 0.76
32 5 0.15
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
GTAACAAATTCTCACTAACATTATCAAATT
Found at i:26811 original size:31 final size:31
Alignment explanation
Indices: 26745--26804 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
26735 AACAAATTAC
*
26745 TCACTAACGTTATCAAATTGTAACAAAATTG
1 TCACTAACATTATCAAATTGTAACAAAATTG
* *
26776 TCACTAACATTATCTATTTGTAACAAAAT
1 TCACTAACATTATCAAATTGTAACAAAAT
26805 GATCACTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TCACTAACATTATCAAATTGTAACAAAATTG
Found at i:36425 original size:22 final size:22
Alignment explanation
Indices: 36381--36441 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
36371 AGTATTATAT
*
36381 TATATTTTAAAAAGTATTAATTAA
1 TATATTTTAAATA-T-TTAATTAA
*
36405 TATATTTTAAATATTTTATTAA
1 TATATTTTAAATATTTAATTAA
*
36427 AATATTATT-AATATT
1 TATATT-TTAAATATT
36442 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 18 0.55
23 3 0.09
24 12 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATTTTAAATATTTAATTAA
Found at i:36443 original size:17 final size:17
Alignment explanation
Indices: 36421--36459 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
36411 TTAAATATTT
* * *
36421 TATTAAAATATTATTAA
1 TATTAAAAAATAAATAA
36438 TATTAAAAAATAAATAA
1 TATTAAAAAATAAATAA
36455 TATTA
1 TATTA
36460 TTGATTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATTAAAAAATAAATAA
Found at i:36606 original size:22 final size:23
Alignment explanation
Indices: 36578--36624 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
36568 TTGAGTATTT
36578 TATTATAATATTA-AAATAATAA
1 TATTATAATATTAGAAATAATAA
* *
36600 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAGAAATAATAA
36623 TA
1 TA
36625 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAGAAATAATAA
Found at i:36629 original size:22 final size:22
Alignment explanation
Indices: 36586--36629 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
36576 TTTATTATAA
*
36586 TATTAAAATAATAATATTATAT
1 TATTAAAATAATAATATAATAT
*
36608 TATTAGAAATATTAATA-AATAT
1 TATTA-AAATAATAATATAATAT
36630 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAATAATAATATAATAT
Found at i:37763 original size:27 final size:27
Alignment explanation
Indices: 37733--37821 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
37723 TGAATTAATA
37733 AATTTATATTTTTTAAAAAATAATTAT
1 AATTTATATTTTTTAAAAAATAATTAT
*** *
37760 AATTT-TATGAATTAAAAGATTAATTAT
1 AATTTATATTTTTTAAAA-AATAATTAT
* *
37787 AAAGTTATAATTTTTAAAAAATACATTTAT
1 -AATTTATATTTTTTAAAAAATA-A-TTAT
37817 AATTT
1 AATTT
37822 TAAAAATGAA
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
26 9 0.20
27 13 0.28
28 7 0.15
29 13 0.28
30 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (27 bp):
AATTTATATTTTTTAAAAAATAATTAT
Found at i:37848 original size:2 final size:2
Alignment explanation
Indices: 37841--37866 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37831 ATCATGAATT
37841 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
37867 CTTTATTTTT
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):
TA
Found at i:39334 original size:3 final size:3
Alignment explanation
Indices: 39321--39371 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
39311 TTTTCTATCG
** *
39321 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39366 TTA TTA
1 TTA TTA
39372 GTATATTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.13
3 34 0.87
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39349 original size:29 final size:28
Alignment explanation
Indices: 39316--39371 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
39306 CGGGTTTTTC
*
39316 TATCGTTATTTTATTATTATTATTATTAT
1 TATCGTTATCTTATTATT-TTATTATTAT
39345 TATCGTTATCTTATTATTTTATTATTA
1 TATCGTTATCTTATTATTTTATTATTA
39372 GTATATTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (28 bp):
TATCGTTATCTTATTATTTTATTATTAT
Found at i:42972 original size:31 final size:32
Alignment explanation
Indices: 42936--42999 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
42926 TTATTTTACA
42936 TATACTAACTTATTT-TTCTCTTTTGTTTGTG
1 TATACTAACTTATTTCTTCTCTTTTGTTTGTG
42967 TATACTAACTTATTTCTTCTCTTTTGTTTGTG
1 TATACTAACTTATTTCTTCTCTTTTGTTTGTG
42999 T
1 T
43000 CATTTTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (32 bp):
TATACTAACTTATTTCTTCTCTTTTGTTTGTG
Found at i:44920 original size:24 final size:21
Alignment explanation
Indices: 44872--44926 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 21
44862 AAGATCAAAC
*
44872 CAAAGAAAAAAAAACAAAGAG
1 CAAAGAAAAAAAAACAAAAAG
*
44893 CAAAGAAAAAATCAAAGCAAAAAT
1 CAAAGAAAAAA--AAA-CAAAAAG
44917 CAAAGAAAAA
1 CAAAGAAAAA
44927 GCAAAGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
23 3 0.10
24 15 0.52
ACGTcount: A:0.75, C:0.11, G:0.11, T:0.04
Consensus pattern (21 bp):
CAAAGAAAAAAAAACAAAAAG
Found at i:44925 original size:11 final size:12
Alignment explanation
Indices: 44893--44939 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
44883 AAACAAAGAG
44893 CAAAGAAAAAAT
1 CAAAGAAAAAAT
*
44905 CAAAGCAAAAAT
1 CAAAGAAAAAAT
*
44917 CAAAG-AAAAAG
1 CAAAGAAAAAAT
44928 CAAAGAACAAAA
1 CAAAGAA-AAAA
44940 AAGAGGACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 10 0.32
12 17 0.55
13 4 0.13
ACGTcount: A:0.72, C:0.13, G:0.11, T:0.04
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:44939 original size:24 final size:25
Alignment explanation
Indices: 44884--44939 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
44874 AAGAAAAAAA
*
44884 AACAAAGAGCAAAGAAAAAATCAAAG
1 AACAAA-AGCAAAGAAAAAAGCAAAG
* *
44910 CA-AAAATCAAAG-AAAAAGCAAAG
1 AACAAAAGCAAAGAAAAAAGCAAAG
44933 AACAAAA
1 AACAAAA
44940 AAGAGGACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 11 0.44
24 10 0.40
25 3 0.12
26 1 0.04
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.04
Consensus pattern (25 bp):
AACAAAAGCAAAGAAAAAAGCAAAG
Found at i:46116 original size:4 final size:4
Alignment explanation
Indices: 46107--46152 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
46097 AGAAAAGTAT
* *
46107 ATAC ATAC ATAC ACAC ACAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
46153 CCATGATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:46865 original size:36 final size:36
Alignment explanation
Indices: 46818--46922 Score: 117
Period size: 36 Copynumber: 3.0 Consensus size: 36
46808 TTGAGATCGT
*
46818 TTTCTCAAAAAAC-AATCTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAAT-TTTGTCTCGCTTGAGACAA
** *
46854 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
46890 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
46923 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
34 22 0.38
35 1 0.02
36 32 0.55
37 3 0.05
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:47198 original size:28 final size:29
Alignment explanation
Indices: 47167--47268 Score: 142
Period size: 29 Copynumber: 3.7 Consensus size: 29
47157 ACAGTTTCTC
47167 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
47195 TTGAATAAAAATCTTTGAGTTTGTTCCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
* * *
47224 TTGAATAAATATCTTTGAG-TCGTTTCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
47252 TTG---AAAAATCTTTGAGT
1 TTGAATAAAAATCTTTGAGT
47269 CTATTTATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
25 12 0.18
28 15 0.22
29 41 0.60
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (29 bp):
TTGAATAAAAATCTTTGAGTTTGTTCCTT
Found at i:47355 original size:52 final size:53
Alignment explanation
Indices: 47277--47382 Score: 187
Period size: 52 Copynumber: 2.0 Consensus size: 53
47267 GTCTATTTAT
47277 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAG
1 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAG
*
47329 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
47383 ATTGTTTCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 38 0.75
54 13 0.25
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (53 bp):
TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAG
Found at i:47382 original size:26 final size:28
Alignment explanation
Indices: 47352--47410 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
47342 TTTGTCTCTC
47352 TTGAGA-CAATT-TTGTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
*** *
47378 TTGAGATTGTTTCTTTTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
47406 TTGAG
1 TTGAG
47411 TTTGTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.22
27 2 0.07
28 19 0.70
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (28 bp):
TTGAGATCAATTCTTGTGAAAAAAATCT
Found at i:47422 original size:27 final size:28
Alignment explanation
Indices: 47366--47503 Score: 116
Period size: 28 Copynumber: 4.5 Consensus size: 28
47356 GACAATTTTG
47366 TGAAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCTTT
*
47394 TGAAAAAAATCTTTGAGTTTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCTTT
* * *
47422 GGAAACAAAATTTTTTCTCTCTTAAGATAGTTTCTTT
1 TGAAA-AAAA-------TCT-TTGAGATTGTTTCTTT
*
47459 TGAAACAAAAATCTTTGAGTTTGTTTCTTT
1 TG-AA-AAAAATCTTTGAGATTGTTTCTTT
47489 TGAAACAAAAT-TTTG
1 TGAAA-AAAATCTTTG
47504 TCTCTCTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
28 36 0.40
29 11 0.12
30 15 0.17
31 3 0.03
36 3 0.03
37 14 0.16
38 6 0.07
39 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGATTGTTTCTTT
Found at i:47464 original size:37 final size:36
Alignment explanation
Indices: 47414--47535 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
47404 CTTTGAGTTT
*
47414 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAA-TTTTTCTCTCTTAAGATA
* * * *
47451 GTTTCTTTTGAAACAAAA-----ATCT-TTGAGTTT
1 GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
47481 GTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATTTT-TCTCTCTTAAGATA
*
47518 ATTTCTTTTGAAACAAAA
1 GTTTCTTTTGAAACAAAA
47536 ATCTTTGAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 23 0.34
31 3 0.04
36 3 0.04
37 39 0.57
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (36 bp):
GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
Found at i:47477 original size:67 final size:67
Alignment explanation
Indices: 47381--47595 Score: 278
Period size: 67 Copynumber: 3.3 Consensus size: 67
47371 AAAATCTTTG
* *
47381 AGATTGTTTCTTTTG-AA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
47444 TA
66 TA
*
47446 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
47511 TA
66 TA
* * * * *
47513 AGATAATTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCT
*
47575 CTTG
64 CTTA
**
47579 AGACCGTTTCTTTTGAA
1 AGATAGTTTCTTTTGAA
47596 GTAAATCTTT
Statistics
Matches: 134, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
65 15 0.11
66 33 0.25
67 84 0.63
68 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (67 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
TA
Found at i:47829 original size:121 final size:119
Alignment explanation
Indices: 47654--47878 Score: 258
Period size: 121 Copynumber: 1.9 Consensus size: 119
47644 TTAACAAAAT
* * **
47654 CATCTTTGAGTCAATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACGGTTTCTAATGAAAAAA
1 CATCTTTGAGTCAATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAAA
47719 CTAACTTTTGAGAGTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGAGATC
66 --AAC-TTTGAGAGTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGAGATC
* ** **
47775 CATCTTTGAGTCAGTTTCTTTTGAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTTTTGAAAA
1 CATCTTTGAGTCAATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTAATGAAAA
* ** * *
47838 AAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
64 AAAACTTTGAGAGTGTTTCATTTGAAACAAAATTTGGTCTC
47879 TCGAGACAAC
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
118 20 0.23
119 13 0.15
120 7 0.08
121 43 0.49
122 4 0.05
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (119 bp):
CATCTTTGAGTCAATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAAA
AACTTTGAGAGTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGAGATC
Found at i:47856 original size:64 final size:63
Alignment explanation
Indices: 47776--47900 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 63
47766 GATGAGATCC
* *
47776 ATCTTTGAGTCAGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCAGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
** * **
47840 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCAGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
47901 TACCCACCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
63 19 0.35
64 35 0.65
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (63 bp):
ATCTTTGAGTCAGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:47937 original size:40 final size:40
Alignment explanation
Indices: 47882--47961 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
47872 TTGTCTCTCG
47882 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
*
47922 AGACAACTTCTTTTGAAAATACCCACCTTTGATATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
47962 CTATTAAAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
Found at i:48580 original size:28 final size:28
Alignment explanation
Indices: 48509--48590 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
48499 TAAAAATATC
* * *
48509 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
** *
48537 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
48565 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
48591 CATAACTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:48946 original size:130 final size:129
Alignment explanation
Indices: 48694--48955 Score: 398
Period size: 130 Copynumber: 2.0 Consensus size: 129
48684 ATAGATAACC
48694 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
** * * * * *
48759 TCACGTATGAGTCGTGTCATCCCTTGACCAGATTTCCTCATCACGTAGGAGCCGTGTCACCCTT
66 TCACGTATGAGTAATGTCATCCATCGACCAGATTTCCTCATCACGGAGGAACAGTGTCACCCTT
* *
48823 AGATAACCAGTCGTCCTCATCATGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTC
* * * *
48888 ATCATGTATGAGTAATGTCATCCATCGACCAGATTTCTTCATCACGGGGGAATAGTGTCACCCTT
65 ATCACGTATGAGTAATGTCATCCATCGACCAGATTTCCTCATCACGGAGGAACAGTGTCACCCTT
48953 AGA
1 AGA
48956 CGACCCGAAC
Statistics
Matches: 119, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
129 52 0.44
130 67 0.56
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGTAATGTCATCCATCGACCAGATTTCCTCATCACGGAGGAACAGTGTCACCCTT
Found at i:49161 original size:3 final size:3
Alignment explanation
Indices: 49148--49198 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
49138 TTTTCTATCG
** *
49148 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49193 TTA TTA
1 TTA TTA
49199 GTATATTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.13
3 34 0.87
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:49176 original size:29 final size:28
Alignment explanation
Indices: 49143--49198 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
49133 CGGGTTTTTC
*
49143 TATCGTTATTTTATTATTATTATTATTAT
1 TATCGTTATCTTATTATT-TTATTATTAT
49172 TATCGTTATCTTATTATTTTATTATTA
1 TATCGTTATCTTATTATTTTATTATTA
49199 GTATATTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (28 bp):
TATCGTTATCTTATTATTTTATTATTAT
Found at i:91064 original size:11 final size:11
Alignment explanation
Indices: 91050--91075 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
91040 TATATAAATT
91050 AATTATAGTAA
1 AATTATAGTAA
91061 AATTATAGTAA
1 AATTATAGTAA
91072 AATT
1 AATT
91076 TAACTTGTTA
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AATTATAGTAA
Found at i:91674 original size:14 final size:15
Alignment explanation
Indices: 91657--91685 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
91647 AATATATATT
91657 TTATAAAAT-TTTAA
1 TTATAAAATATTTAA
91671 TTATAAAATATTTAA
1 TTATAAAATATTTAA
91686 AATAATCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATAAAATATTTAA
Found at i:91813 original size:19 final size:19
Alignment explanation
Indices: 91789--91825 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
91779 ATAACCAATA
*
91789 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
91808 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
91826 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:91922 original size:21 final size:21
Alignment explanation
Indices: 91896--92019 Score: 239
Period size: 21 Copynumber: 5.9 Consensus size: 21
91886 TGACTAATCA
91896 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
91917 TTGCGATATCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
91938 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
91959 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
91980 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
92001 TTGCGATAGCACTGTTCAC
1 TTGCGATAGCACTGTTCAC
92020 ATTTTATAAT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 101 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:92738 original size:20 final size:20
Alignment explanation
Indices: 92715--92766 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
92705 AACGCGATCC
92715 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
92735 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
92755 CCAAAATCGCAA
1 CCAGAATCGCAA
92767 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:92847 original size:20 final size:20
Alignment explanation
Indices: 92822--93015 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
92812 GATTTTCCAT
* *
92822 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
92842 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
92862 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
92882 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
92902 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
92922 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
92942 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
92962 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
92983 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
93003 AATCGCAACGCGA
1 AATCGCAACGCGA
93016 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:92867 original size:40 final size:39
Alignment explanation
Indices: 92818--93015 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
92808 TTGCGATTTT
* ** *
92818 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
92856 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
92897 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
92937 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
92976 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
93016 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:92905 original size:60 final size:60
Alignment explanation
Indices: 92822--93014 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
92812 GATTTTCCAT
* ** * *
92822 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
92882 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
92942 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
93003 AATCGCAACGCG
1 AATCGCAACGCG
93015 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:93438 original size:33 final size:33
Alignment explanation
Indices: 93396--93466 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
93386 TTCACTTAGA
*
93396 TTTCATTTCGCGTTACGATTATGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
* * *
93429 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
93462 TTTCA
1 TTTCA
93467 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
Found at i:93606 original size:14 final size:14
Alignment explanation
Indices: 93587--93641 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
93577 AGAATGACTG
93587 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
93601 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
93620 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
93634 TCGCAACG
1 TCGCAACG
93642 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:93624 original size:33 final size:33
Alignment explanation
Indices: 93587--93657 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
93577 AGAATGACTG
**
93587 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
93620 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
93653 TCGCA
1 TCGCA
93658 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:93675 original size:19 final size:19
Alignment explanation
Indices: 93653--93750 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
93643 GAAACCAAAA
*
93653 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
93672 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
93686 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
93705 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
93719 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
93738 TCGCGTTGCGATT
1 TCGCGTTGCGATT
93751 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:93694 original size:14 final size:14
Alignment explanation
Indices: 93675--93764 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
93665 TTTCATTTCG
93675 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
93689 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
93708 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
93722 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
93739 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
93755 CGTTGCGATT
1 CGTTGCGATT
93765 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:93700 original size:33 final size:33
Alignment explanation
Indices: 93658--93772 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
93648 CAAAATCGCA
93658 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
93691 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
93724 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
93757 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
93773 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:95699 original size:185 final size:186
Alignment explanation
Indices: 95469--95935 Score: 918
Period size: 185 Copynumber: 2.5 Consensus size: 186
95459 TAGATTGCTT
*
95469 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
95534 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
95599 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
95654 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
95719 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
95784 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
95840 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
95905 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
95936 TTCAATTTGC
Statistics
Matches: 280, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.55
186 126 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:95783 original size:93 final size:93
Alignment explanation
Indices: 95469--95935 Score: 918
Period size: 93 Copynumber: 5.0 Consensus size: 93
95459 TAGATTGCTT
*
95469 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
95534 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
95562 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
95626 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
95654 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
95719 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
95747 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
95812 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
95840 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
95905 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
95933 AGT
1 AGT
95936 TTCAATTTGC
Statistics
Matches: 372, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.25
93 280 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:96007 original size:19 final size:19
Alignment explanation
Indices: 95967--96095 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
95957 TAGTTTACTT
* *
95967 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
95987 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
96006 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
96025 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
96039 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
96058 TTGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
96072 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
96091 TCGCA
1 TCGCA
96096 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:96046 original size:33 final size:32
Alignment explanation
Indices: 96003--96095 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
95993 CGCGAAACCA
**
96003 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
96035 AGAATCGCAACGCGAAACCAAAATTGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
96068 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
96096 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:96093 original size:52 final size:52
Alignment explanation
Indices: 95967--96095 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
95957 TAGTTTACTT
**
95967 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * * *
96019 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATTGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
96072 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
96096 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:96113 original size:19 final size:19
Alignment explanation
Indices: 96091--96225 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
96081 GAAACCAAAA
*
96091 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
96110 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
96126 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
96143 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
96159 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
96176 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
96195 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
96215 TCGTGTTGCGA
1 TCGCGTTGCGA
96226 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:96132 original size:14 final size:14
Alignment explanation
Indices: 96113--96169 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
96103 TTTCATTTCG
96113 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
96127 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
96144 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
96160 CGTTGCGATT
1 CGTTGCGATT
96170 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:96138 original size:33 final size:33
Alignment explanation
Indices: 96096--96188 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
96086 CAAAATCGCA
*
96096 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
96129 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
96162 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
96189 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:98164 original size:14 final size:14
Alignment explanation
Indices: 98145--98180 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
98135 ATTGTTTAAT
98145 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
98159 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
98173 TGATTTGT
1 TGATTTGT
98181 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:98303 original size:19 final size:19
Alignment explanation
Indices: 98287--98388 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
98277 AAAAATGACT
98287 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
98306 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
98325 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
98339 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
98358 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
98378 ATCGCAATGCG
1 ATCGCAATGCG
98389 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:98437 original size:33 final size:33
Alignment explanation
Indices: 98395--98718 Score: 181
Period size: 33 Copynumber: 9.5 Consensus size: 33
98385 TGCGTTTATA
98395 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
98428 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
98464 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
98497 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
98532 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
98565 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
98605 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
98636 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
98669 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
98703 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
98719 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 21, Indels: 46
0.79 0.07 0.15
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 133 0.54
34 29 0.12
35 18 0.07
36 19 0.08
37 2 0.01
38 20 0.08
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:98457 original size:52 final size:52
Alignment explanation
Indices: 98395--98690 Score: 255
Period size: 52 Copynumber: 5.6 Consensus size: 52
98385 TGCGTTTATA
98395 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
1 ATTTCG-ATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* *
98447 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTTTC
1 ATTTCG-ATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * * * *
98501 GTTGCGATTTTC-ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * *
98553 GTTGCGATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * *
98605 GTTGCGATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * *
98657 GTTGCGATTTTC-ATTTC-CGCATTGCGATTTTCAT
1 ATTTCGA-TTGCGATTTCTCG--TTGCGATTTTCAT
98691 GTTGGGATTT
Statistics
Matches: 226, Mismatches: 13, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
51 1 0.00
52 198 0.88
53 18 0.08
54 9 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:98503 original size:85 final size:85
Alignment explanation
Indices: 98395--98632 Score: 351
Period size: 85 Copynumber: 2.8 Consensus size: 85
98385 TGCGTTTATA
* *
98395 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
98460 ATTCTTTCGTTGCGATTTTC
66 ATTCTGTCGTTGCGATTTTC
*
98480 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
98545 ATTCTGTCGTTGCGATTTTC
66 ATTCTGTCGTTGCGATTTTC
*
98565 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
98625 TTGCGATT
61 TTGCGATT
98633 TTCATTTCGC
Statistics
Matches: 142, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
85 121 0.85
87 7 0.05
88 8 0.06
90 6 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (85 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTGTCGTTGCGATTTTC
Found at i:101228 original size:24 final size:24
Alignment explanation
Indices: 101194--101240 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
101184 CTGAAACATC
101194 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
101218 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
101241 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:101950 original size:20 final size:20
Alignment explanation
Indices: 101922--102290 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
101912 AAATTTCAGT
* * * *
101922 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
101942 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
101962 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
101982 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
102002 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
102022 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
102042 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
102062 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
102082 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
102102 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
102122 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
102142 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
102162 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
102182 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
102202 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
102222 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
102242 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
102262 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
102282 GTTGCGATT
1 GTTGCGATT
102291 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:102582 original size:16 final size:17
Alignment explanation
Indices: 102553--102604 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
102543 ATCATAAATA
*
102553 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
102570 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
102585 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
102603 AT
1 AT
102605 CATAAATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:103933 original size:23 final size:22
Alignment explanation
Indices: 103884--103926 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
103874 TAACTCGTAT
103884 GAAAAAACTTTATGAAAAAAAA
1 GAAAAAACTTTATGAAAAAAAA
*
103906 GAAAAATACTTTCT-AAAAAAA
1 GAAAAA-ACTTTATGAAAAAAA
103927 TATAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
GAAAAAACTTTATGAAAAAAAA
Found at i:105160 original size:18 final size:18
Alignment explanation
Indices: 105116--105162 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
105106 TAAGTGAACA
*
105116 AATTAAAATATTAATATT
1 AATTAAATTATTAATATT
105134 AATTGAAATTATTAA-ATT
1 AATT-AAATTATTAATATT
105152 ATATTAAATTA
1 A-ATTAAATTA
105163 ATATAAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTAAATTATTAATATT
Found at i:109465 original size:2 final size:2
Alignment explanation
Indices: 109458--109483 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
109448 TACGTGCAAA
109458 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
109484 TTTTAATTTT
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:118363 original size:16 final size:16
Alignment explanation
Indices: 118344--118437 Score: 80
Period size: 16 Copynumber: 5.8 Consensus size: 16
118334 TTTGGTTAAA
118344 TTCGGTTCGGGTTGCT
1 TTCGGTTCGGGTTGCT
* ***
118360 TTCGGATCGGGTTAAAA
1 TTCGGTTCGGGTT-GCT
* * *
118377 TTCGATTCAGGTTTCT
1 TTCGGTTCGGGTTGCT
*
118393 TTCGGTTCGAGTTGCT
1 TTCGGTTCGGGTTGCT
*
118409 TTCGGTTCGTGTTGCT
1 TTCGGTTCGGGTTGCT
* *
118425 TTTGGTTCAGGTT
1 TTCGGTTCGGGTT
118438 AATTTCGATT
Statistics
Matches: 59, Mismatches: 18, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
16 49 0.83
17 10 0.17
ACGTcount: A:0.10, C:0.16, G:0.30, T:0.45
Consensus pattern (16 bp):
TTCGGTTCGGGTTGCT
Found at i:118470 original size:38 final size:38
Alignment explanation
Indices: 118408--118487 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
118398 TTCGAGTTGC
* * *
118408 TTTCGGTTCGTGTTGCTTTTGGTTCAGGTTAATTTCGA
1 TTTCGGTTCGGGTTGATTTCGGTTCAGGTTAATTTCGA
* * *
118446 TTTCGGTTCGGGTTGATTTCGGTTCTGTTTTATTTCGA
1 TTTCGGTTCGGGTTGATTTCGGTTCAGGTTAATTTCGA
118484 TTTC
1 TTTC
118488 ACTAAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.53
Consensus pattern (38 bp):
TTTCGGTTCGGGTTGATTTCGGTTCAGGTTAATTTCGA
Found at i:118482 original size:16 final size:16
Alignment explanation
Indices: 118344--118470 Score: 65
Period size: 16 Copynumber: 7.5 Consensus size: 16
118334 TTTGGTTAAA
*
118344 TTCGGTTCGGGTTGCT
1 TTCGGTTCGGGTTGAT
* * *
118360 TTCGGATCGGGTTAAAA
1 TTCGGTTCGGGTT-GAT
* * **
118377 TTCGATTCAGGTTTCT
1 TTCGGTTCGGGTTGAT
* *
118393 TTCGGTTCGAGTTGCT
1 TTCGGTTCGGGTTGAT
* *
118409 TTCGGTTCGTGTTGCT
1 TTCGGTTCGGGTTGAT
* *
118425 TTTGGTTCAGGTTAATTTCGAT
1 TTCGGTTC-GG----GTT-GAT
118447 TTCGGTTCGGGTTGAT
1 TTCGGTTCGGGTTGAT
118463 TTCGGTTC
1 TTCGGTTC
118471 TGTTTTATTT
Statistics
Matches: 83, Mismatches: 21, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
16 57 0.69
17 13 0.16
21 4 0.05
22 9 0.11
ACGTcount: A:0.10, C:0.16, G:0.29, T:0.45
Consensus pattern (16 bp):
TTCGGTTCGGGTTGAT
Found at i:119729 original size:10 final size:11
Alignment explanation
Indices: 119709--119775 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
119699 ACAAAATGTT
119709 AAATAATAAAA
1 AAATAATAAAA
119720 AAAT-AT-AAA
1 AAATAATAAAA
119729 AAATAATAATAA
1 AAATAATAA-AA
*
119741 TAATGAA-AGAAA
1 AAAT-AATA-AAA
119753 GAAATAATAAAA
1 -AAATAATAAAA
*
119765 TAATAATAAAA
1 AAATAATAAAA
119776 GGTTAAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
9 7 0.15
10 4 0.09
11 15 0.33
12 13 0.28
13 7 0.15
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (11 bp):
AAATAATAAAA
Found at i:121186 original size:29 final size:29
Alignment explanation
Indices: 121140--121200 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
121130 AAAATTATAT
**
121140 ATTATATATATTTAAAATGTTTTTCAAAA
1 ATTATATATATTTAAAATGTTTTAAAAAA
121169 ATTATATAATATTT-AAATGTTTTAAAAAA
1 ATTATAT-ATATTTAAAATGTTTTAAAAAA
121198 ATT
1 ATT
121201 CAAAACAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (29 bp):
ATTATATATATTTAAAATGTTTTAAAAAA
Found at i:121244 original size:38 final size:38
Alignment explanation
Indices: 121106--121307 Score: 118
Period size: 38 Copynumber: 5.4 Consensus size: 38
121096 AAATTTTATA
* * * **
121106 ATATATATTTTCAGAAACGGTTT-AAAAATTATATATT
1 ATATATATTTTCAAAAATGTTTTCAAAAACAATATATT
** *
121143 ATATATA-TTT--AAAATGTTTTTCAAAAATTATATAAT
1 ATATATATTTTCAAAAATG-TTTTCAAAAACAATATATT
* * * **
121179 ATTTAAATGTTTTAAAAA--AATTC-AAAACAATATATT
1 ATATATAT-TTTCAAAAATGTTTTCAAAAACAATATATT
*
121215 ATATACT-TTTTCAAAAATGATTTT-AAAAACTATATATT
1 ATATA-TATTTTCAAAAATG-TTTTCAAAAACAATATATT
* * *
121253 ATATATATTTTCTAAAATGTTTTCAAAAATTATGTATATT
1 ATATATATTTTCAAAAATGTTTTCAAAAA-CA-ATATATT
121293 ATA-AGTATTTTCAAA
1 ATATA-TATTTTCAAA
121308 GATCGTTTGC
Statistics
Matches: 127, Mismatches: 22, Indels: 29
0.71 0.12 0.16
Matches are distributed among these distances:
34 4 0.03
35 11 0.09
36 36 0.28
37 15 0.12
38 38 0.30
39 1 0.01
40 22 0.17
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (38 bp):
ATATATATTTTCAAAAATGTTTTCAAAAACAATATATT
Found at i:121291 original size:40 final size:39
Alignment explanation
Indices: 121202--121307 Score: 121
Period size: 38 Copynumber: 2.7 Consensus size: 39
121192 AAAAAAATTC
*
121202 AAAACAATATATTATATACT-TTTTCAAAAATGATTTTA
1 AAAACTATATATTATATACTATTTTCAAAAATGATTTTA
*
121240 AAAACTATATATTATATA-TATTTTCTAAAATG-TTTTCA
1 AAAACTATATATTATATACTATTTTCAAAAATGATTTT-A
* *
121278 AAAATTATGTATATTATA-AGTATTTTCAAA
1 AAAACTA--TATATTATATACTATTTTCAAA
121308 GATCGTTTGC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
37 5 0.08
38 35 0.59
39 1 0.02
40 18 0.31
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (39 bp):
AAAACTATATATTATATACTATTTTCAAAAATGATTTTA
Found at i:133497 original size:68 final size:68
Alignment explanation
Indices: 133388--133534 Score: 285
Period size: 68 Copynumber: 2.2 Consensus size: 68
133378 ATCATTAACG
133388 GCATCAGTTCTTTCAAATGAAACATTCATTACCAGCCAAGATATACAGCGACAGATAAACCATCA
1 GCATCAGTTCTTTCAAATGAAACATTCATTACCAGCCAAGATATACAGCGACAGATAAACCATCA
133453 ACA
66 ACA
133456 GCATCAGTTCTTTCAAATGAAACATTCATTACCAGCCAAGATATACAGCGACAGATAAACCATCA
1 GCATCAGTTCTTTCAAATGAAACATTCATTACCAGCCAAGATATACAGCGACAGATAAACCATCA
*
133521 ACG
66 ACA
133524 GCATCAGTTCT
1 GCATCAGTTCT
133535 CGACAACAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 78 1.00
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (68 bp):
GCATCAGTTCTTTCAAATGAAACATTCATTACCAGCCAAGATATACAGCGACAGATAAACCATCA
ACA
Found at i:136640 original size:25 final size:25
Alignment explanation
Indices: 136594--136643 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
136584 ACCTCCTTAA
136594 AAATATATTTATCCAAAATAAATTT
1 AAATATATTTATCCAAAATAAATTT
**
136619 AAATA-ATTTATTTAAAATTAAATTT
1 AAATATATTTATCCAAAA-TAAATTT
136644 CATGCGCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATATATTTATCCAAAATAAATTT
Found at i:138949 original size:2 final size:2
Alignment explanation
Indices: 138942--138969 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
138932 GAGAAATCAA
138942 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
138970 TAAAACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:141162 original size:13 final size:13
Alignment explanation
Indices: 141144--141172 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
141134 AACGATAATA
141144 GGGTTCTTGATTT
1 GGGTTCTTGATTT
141157 GGGTTCTTGATTT
1 GGGTTCTTGATTT
141170 GGG
1 GGG
141173 GGACGGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.38, T:0.48
Consensus pattern (13 bp):
GGGTTCTTGATTT
Found at i:146823 original size:4 final size:4
Alignment explanation
Indices: 146814--146852 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
146804 TGTATTTTAA
* * *
146814 ATAC ATAC ATAC ATAC ATGC ATAC ATGC ATAC ATGC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
146853 AAGAACACAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:146827 original size:8 final size:8
Alignment explanation
Indices: 146817--146852 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
146807 ATTTTAAATA
*
146817 CATACATA
1 CATACATG
146825 CATACATG
1 CATACATG
146833 CATACATG
1 CATACATG
146841 CATACATG
1 CATACATG
146849 CATA
1 CATA
146853 AAGAACACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (8 bp):
CATACATG
Found at i:154174 original size:195 final size:199
Alignment explanation
Indices: 153797--154181 Score: 511
Period size: 195 Copynumber: 1.9 Consensus size: 199
153787 CGTTAGAACT
153797 GGGGGAGAAGAGAGGCATTTCAAGCACCAGTCACCTTAAATAACAACTTGCTACATAAAAAATGC
1 GGGGGAGAAGAGAGGCATTTCAAGCACCAGTCACCTTAAATAACAACTTGCTACATAAAAAATGC
* * * * *
153862 ACCGAATGCAGTAGCACATTGCAAAAAAAATATTAATATTAATTATATGATTTTTTTTATATTTT
66 ACCGAAAGCAGTAGCACATTGCAAAAAAAATA-TAATATTAATTATATGAATTATATGATATTTT
*
153927 TTTAGGAATGATTAATTTATATATTTACCAGGACCTAAAGAAATATAATAAATTTATTATTTGGG
130 TTTAGGAATGATTAATTTATATATTTACCAGGACCTAAAGAAATATAATAAATGTATTATTTGGG
153992 GGGGG
195 GGGGG
* **
153997 GGGGGAG-AGAAGCGGCATTTCAAGCACCAGTCACCTTAAATAACTGCTTGCTACAACATAAAAA
1 GGGGGAGAAG-AGAGGCATTTCAAGCACCAGTCACCTTAAATAACAACTTGCT---ACATAAAAA
* *
154061 ATGCACTGAAAGCAGTTGCACATTGCAAAAAGAAA-A-AA-A-T-ATTA-AT-AATTATATGAT-
62 ATGCACCGAAAGCAGTAGCACATTGCAAAAA-AAATATAATATTAATTATATGAATTATATGATA
** *
154118 TTTTTTTAGGAATTTTTAATTTATATATTTGCCAGGACCTAAAGAAA-ATAAATAAATGTATTAT
126 TTTTTTTAGGAATGATTAATTTATATATTTACCAGGACCTAAAGAAATAT-AATAAATGTATTAT
154182 CTTATGCATT
Statistics
Matches: 165, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
194 2 0.01
195 57 0.35
196 7 0.04
197 2 0.01
198 4 0.02
199 3 0.02
200 47 0.28
201 2 0.01
203 38 0.23
204 3 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (199 bp):
GGGGGAGAAGAGAGGCATTTCAAGCACCAGTCACCTTAAATAACAACTTGCTACATAAAAAATGC
ACCGAAAGCAGTAGCACATTGCAAAAAAAATATAATATTAATTATATGAATTATATGATATTTTT
TTAGGAATGATTAATTTATATATTTACCAGGACCTAAAGAAATATAATAAATGTATTATTTGGGG
GGGG
Done.