Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000437.1 Hibiscus syriacus cultivar Beakdansim tig00000800_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: 75886
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:395 original size:20 final size:21
Alignment explanation
Indices: 372--428 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
362 CATCCCCCTG
372 GTATCGATACTACCCTC-ACA
1 GTATCGATACTACCCTCAACA
*
392 GTATCGATAC--CCTCTTCAACT
1 GTATCGATACTACC-C-TCAACA
413 GTATCGATACTACCCT
1 GTATCGATACTACCCT
429 TAAGAAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 12 0.39
21 13 0.42
22 1 0.03
23 2 0.06
ACGTcount: A:0.26, C:0.33, G:0.11, T:0.30
Consensus pattern (21 bp):
GTATCGATACTACCCTCAACA
Found at i:400 original size:40 final size:40
Alignment explanation
Indices: 352--428 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
342 CTTAAAAATT
**
352 GTATCGATACCATC-CCCCTGGTATCGATACTACCCTCACA
1 GTATCGATACCATCTCAACT-GTATCGATACTACCCTCACA
*
392 GTATCGATACCCTCTTCAACTGTATCGATACTACCCT
1 GTATCGATACCATC-TCAACTGTATCGATACTACCCT
429 TAAGAAATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 13 0.41
41 16 0.50
42 3 0.09
ACGTcount: A:0.25, C:0.35, G:0.12, T:0.29
Consensus pattern (40 bp):
GTATCGATACCATCTCAACTGTATCGATACTACCCTCACA
Found at i:3468 original size:20 final size:22
Alignment explanation
Indices: 3430--3473 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3420 AATCTTACAT
3430 GGGGGTATCGATACC-CTCTTGG
1 GGGGGTATCGATACCTCTC-TGG
*
3452 GGGGGTATCGGTA-CTCTCTGG
1 GGGGGTATCGATACCTCTCTGG
3473 G
1 G
3474 CAATCTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.11, C:0.20, G:0.41, T:0.27
Consensus pattern (22 bp):
GGGGGTATCGATACCTCTCTGG
Found at i:5633 original size:13 final size:14
Alignment explanation
Indices: 5610--5653 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
5600 TCCTAATGGG
*
5610 CAATTTTTGAAAAT
1 CAATGTTTGAAAAT
*
5624 CGA-GTTTGAAAA-
1 CAATGTTTGAAAAT
5636 CAATGTTTGAAAAT
1 CAATGTTTGAAAAT
5650 CAAT
1 CAAT
5654 ATATGTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 17 0.68
14 6 0.24
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (14 bp):
CAATGTTTGAAAAT
Found at i:10030 original size:21 final size:21
Alignment explanation
Indices: 10006--10045 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9996 AAGACTATTT
10006 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTGAAACA
10027 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
10046 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAACA
Found at i:12744 original size:188 final size:187
Alignment explanation
Indices: 12415--12852 Score: 459
Period size: 188 Copynumber: 2.3 Consensus size: 187
12405 ACTATGTTAT
* * * * * * * *
12415 TTCTTGTTGAGGAAATCTGTTTACTTGTAGATAACTTGATGTTCGTAACGGCACTGCTCATCCAC
1 TTCTTGTTGAGAAAATCTATTTTC-TGGAGATAACTTGATGTTGGGAACGACACTACTCATCCAC
* * * * *
12480 GATGAAGAGAATCTGGCCGCTTATGATTACATTTCTACTTTAATTTGAGGATGTCTAGTCAGTGT
65 GATGAAGAGAATATGGCCGCTTATGATGACATTGCTACTTTAATTTGAGGATGTCTAGTCAATGG
* *** * * *
12545 ACGATATTGTTCCTACTAGATGAGGGTGTCTAAG-AACATCCGAAGATAATATTGTTCA
130 ACGACATTGTTCCTACTAGATGAGGACATCT-AGTAACATACGAAGATAACACTGTTCA
* *
12603 TTCTTGTTGAGAAAATCTAATTTTCTGGAGATAATTTTATGTTGGGAACGACACTACTCATCCAC
1 TTCTTGTTGAGAAAATCT-ATTTTCTGGAGATAACTTGATGTTGGGAACGACACTACTCATCCAC
** * *
12668 GATGAAGAGAATATGGGTGCTTATGATGATATTGCTCCTTT-ATGTTGAGG-TGGTCTAGTCAAT
65 GATGAAGAGAATATGGCCGCTTATGATGACATTGCTACTTTAAT-TTGAGGAT-GTCTAGTCAAT
* * * *
12731 GGACGACATTGTTCCTACTTGATGAGGACATCTAGTAGCATATGAAGATAACACTGTTCC
128 GGACGACATTGTTCCTACTAGATGAGGACATCTAGTAACATACGAAGATAACACTGTTCA
* * ** * * *
12791 TTTTTATAAAGAAAAATCTGATTGTCTGGAGATAAGTTGATGTTGGGAACGACATTACTCAT
1 TTCTTGTTGAG-AAAATCT-ATTTTCTGGAGATAACTTGATGTTGGGAACGACACTACTCAT
12853 AATTTAATGT
Statistics
Matches: 206, Mismatches: 39, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
187 5 0.02
188 152 0.74
189 49 0.24
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (187 bp):
TTCTTGTTGAGAAAATCTATTTTCTGGAGATAACTTGATGTTGGGAACGACACTACTCATCCACG
ATGAAGAGAATATGGCCGCTTATGATGACATTGCTACTTTAATTTGAGGATGTCTAGTCAATGGA
CGACATTGTTCCTACTAGATGAGGACATCTAGTAACATACGAAGATAACACTGTTCA
Found at i:13233 original size:188 final size:188
Alignment explanation
Indices: 12873--13273 Score: 446
Period size: 188 Copynumber: 2.1 Consensus size: 188
12863 TAGGAACGAC
* ** ** *
12873 ACTACTCATCCACAATGAAGAGAATATGGCTTCTTATGATGACATTGCTCATTCATGTTGAGGAG
1 ACTACTCATCCACGATGAAGAGAATATAACCGCTTATGATGACATTGATCATTCATGTTGAGGAG
* * * * * * * * * *
12938 GTCTAATTAGTGGACAATATTGTTCCTACTTGATGAGGACTTCTAGTCGCGTTTGAAGACAACAC
66 GCCTAATCAGGGGACAACATTGTTCCTACTTGATGAAGACGTCTAGTCGCATCTCAAGACAACAA
*
13003 TACTCATTCTTATTAAGGAAATATGATGGCCTAGAGATAATTTGATATTGGAAATGAA
131 TACTCATTCTTATTAAGGAAATATGATGGCCTAGAGATAATTTGATATTGAAAATGAA
* * *
13061 ACTACTCATCCACGATGAAAAGAATCTAACCGCTTATGATGACATTGATCCTTCATGTTGAGGAG
1 ACTACTCATCCACGATGAAGAGAATATAACCGCTTATGATGACATTGATCATTCATGTTGAGGAG
* * *
13126 GCCTAGTCAGGGGACGACATTGTTCCTACTTGATGAAGACGTCTAGTTGCATCTCAAGACAACAA
66 GCCTAATCAGGGGACAACATTGTTCCTACTTGATGAAGACGTCTAGTCGCATCTCAAGACAACAA
** * * * * * * * *
13191 TGTTCCTTCTTGTTGAA-GAAATCTGATTGCATTA-ATATAATTTGATGTTGAAAATGAC
131 TACTCATTCTTATT-AAGGAAATATGATGGC-CTAGAGATAATTTGATATTGAAAATGAA
** *
13249 ACTGTTCATCCATGATGAAGAGAAT
1 ACTACTCATCCACGATGAAGAGAAT
13274 TTGGTCGCCT
Statistics
Matches: 174, Mismatches: 37, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
188 170 0.98
189 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (188 bp):
ACTACTCATCCACGATGAAGAGAATATAACCGCTTATGATGACATTGATCATTCATGTTGAGGAG
GCCTAATCAGGGGACAACATTGTTCCTACTTGATGAAGACGTCTAGTCGCATCTCAAGACAACAA
TACTCATTCTTATTAAGGAAATATGATGGCCTAGAGATAATTTGATATTGAAAATGAA
Found at i:20047 original size:18 final size:19
Alignment explanation
Indices: 20017--20052 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20007 TGTCATAACC
*
20017 ATTTTTAATAAATGATTAA
1 ATTTTTAATAAATAATTAA
20036 ATTTTTAA-AAATAATTA
1 ATTTTTAATAAATAATTA
20053 TGACTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTTTAATAAATAATTAA
Found at i:25355 original size:23 final size:22
Alignment explanation
Indices: 25329--25407 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 22
25319 AAGTTTTTAT
25329 TTTTTATTATAATTTATAAATAG
1 TTTTTATTATAATTTATAAA-AG
25352 TTTTCATATTTATTATAATTTATAAAAAG
1 --TT--T--TTATTATAATTTAT-AAAAG
*
25381 TATTTATTATAATTTATAGAAAG
1 TTTTTATTATAATTTATA-AAAG
25404 TTTT
1 TTTT
25408 GGTATTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
22 1 0.02
23 21 0.46
25 3 0.07
27 2 0.04
29 16 0.35
30 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTTATTATAATTTATAAAAG
Found at i:25387 original size:52 final size:52
Alignment explanation
Indices: 25331--25433 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
25321 GTTTTTATTT
25331 TTTATTATAATTTATA-AATAGTTTTCATATTTATTATAATTTATAAAAAGTA
1 TTTATTATAATTTATAGAA-AGTTTTCATATTTATTATAATTTATAAAAAGTA
** * *
25383 TTTATTATAATTTATAGAAAGTTTTGGTATTTATTGTAATTTATAGAAAGT
1 TTTATTATAATTTATAGAAAGTTTTCATATTTATTATAATTTATAAAAAGT
25434 TTTGATCTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 44 0.96
53 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (52 bp):
TTTATTATAATTTATAGAAAGTTTTCATATTTATTATAATTTATAAAAAGTA
Found at i:25470 original size:29 final size:29
Alignment explanation
Indices: 25272--25542 Score: 152
Period size: 29 Copynumber: 9.6 Consensus size: 29
25262 ATATAGATTT
* * **
25272 TTTAGTGTAATTTATAAAAA-TTATAGGC
1 TTTATTGTAATTTATAAAAAGTTTTAATC
* *** * *
25300 TAATATTGTAATTTATGGGAAGTTTTTATTT
1 T-TTATTGTAATTTATAAAAAG-TTTTAATC
* * * *
25331 TTTATTATAATTTATAAATAGTTTTCATA
1 TTTATTGTAATTTATAAAAAGTTTTAATC
*
25360 TTTATTATAATTTATAAAAAG---T-A--
1 TTTATTGTAATTTATAAAAAGTTTTAATC
* * ** *
25383 TTTATTATAATTTATAGAAAGTTTTGGTA
1 TTTATTGTAATTTATAAAAAGTTTTAATC
* *
25412 TTTATTGTAATTTATAGAAAGTTTTGATC
1 TTTATTGTAATTTATAAAAAGTTTTAATC
25441 TTTATTGTAATTTATAAAAAGTTTTAATC
1 TTTATTGTAATTTATAAAAAGTTTTAATC
* ** *
25470 TATATTGTAATATT-TAAAGAA-TTTTGGTT
1 TTTATTGTAAT-TTATAAA-AAGTTTTAATC
*
25499 TTTATTGTAATATT-T-AAAAGTTTAGAAT-
1 TTTATTGTAAT-TTATAAAAAGTTT-TAATC
*
25527 TTTATTGTAGTTTATA
1 TTTATTGTAATTTATA
25543 TAAATACTTA
Statistics
Matches: 193, Mismatches: 35, Indels: 29
0.75 0.14 0.11
Matches are distributed among these distances:
23 20 0.10
25 1 0.01
26 2 0.01
27 4 0.02
28 17 0.09
29 126 0.65
30 18 0.09
31 5 0.03
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (29 bp):
TTTATTGTAATTTATAAAAAGTTTTAATC
Found at i:25476 original size:58 final size:58
Alignment explanation
Indices: 25270--25521 Score: 177
Period size: 58 Copynumber: 4.4 Consensus size: 58
25260 AAATATAGAT
* * * * * *
25270 TTTTTAGTGTAATTTATAAAAA-TTATAGGCTA-ATATTGTAATTTATGGGAAGTTTTTA
1 TTTTTATTGTAATTTATAAAAAGTTTTA--ATATATATTGTAATTTATAGAAAGTTTTGA
* * * * * *
25328 TTTTTTATTATAATTTATAAATAGTTTTCATATTTATTATAATTTATAAAAAG---T-A
1 -TTTTTATTGTAATTTATAAAAAGTTTTAATATATATTGTAATTTATAGAAAGTTTTGA
* * ** *
25383 --TTTATTATAATTTATAGAAAGTTTTGGTATTTATTGTAATTTATAGAAAGTTTTGA
1 TTTTTATTGTAATTTATAAAAAGTTTTAATATATATTGTAATTTATAGAAAGTTTTGA
* * * *
25439 TCTTTATTGTAATTTATAAAAAGTTTTAATCTATATTGTAATATT-TA-AAGAATTTTGG
1 TTTTTATTGTAATTTATAAAAAGTTTTAATATATATTGTAAT-TTATAGAA-AGTTTTGA
25497 TTTTTATTGTAATATT-T-AAAAGTTT
1 TTTTTATTGTAAT-TTATAAAAAGTTT
25522 AGAATTTTAT
Statistics
Matches: 156, Mismatches: 26, Indels: 24
0.76 0.13 0.12
Matches are distributed among these distances:
52 44 0.28
55 2 0.01
56 2 0.01
57 10 0.06
58 57 0.37
59 38 0.24
60 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.52
Consensus pattern (58 bp):
TTTTTATTGTAATTTATAAAAAGTTTTAATATATATTGTAATTTATAGAAAGTTTTGA
Found at i:27356 original size:32 final size:32
Alignment explanation
Indices: 27315--27378 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
27305 CTAAGGTGAT
* * * *
27315 CCTTGGGTAGGCTCTTAGGCCCCAAGGTACTC
1 CCTTAGGTAGACTCTAAGGCCCCAAGATACTC
27347 CCTTAGGTAGACTCTAAGGCCCCAAGATACTC
1 CCTTAGGTAGACTCTAAGGCCCCAAGATACTC
27379 TCGTATGTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.23
Consensus pattern (32 bp):
CCTTAGGTAGACTCTAAGGCCCCAAGATACTC
Found at i:27889 original size:17 final size:17
Alignment explanation
Indices: 27869--27907 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
27859 ATTTCAAAGT
27869 TATAATTATATAAAAAA
1 TATAATTATATAAAAAA
* *
27886 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
27903 TATAA
1 TATAA
27908 ATAAAATATT
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):
TATAATTATATAAAAAA
Found at i:28025 original size:20 final size:20
Alignment explanation
Indices: 27993--28040 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
27983 AAAAAAATAA
27993 TTAAAATAATT-AATATATGAT
1 TTAAAA-AATTAAATAT-TGAT
*
28014 TTAAAAAATTAAATATTTAT
1 TTAAAAAATTAAATATTGAT
28034 TTAAAAA
1 TTAAAAA
28041 TATCAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAAAAAATTAAATATTGAT
Found at i:29685 original size:3 final size:3
Alignment explanation
Indices: 29677--29728 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
29667 TTATTTTATT
* * *
29677 TAA TAA TAA TAA CAA TAA TAA TAT TTA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
29723 TAA TAA
1 TAA TAA
29729 AAGTAAACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:30009 original size:76 final size:76
Alignment explanation
Indices: 29881--30041 Score: 279
Period size: 76 Copynumber: 2.1 Consensus size: 76
29871 AGAGGTCTTA
*
29881 AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACC
1 AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
29946 CTG-AGGGTTTG
66 C-GAAGGGTTTG
*
29957 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
*
30022 CGAAGGTTTTG
66 CGAAGGGTTTG
30033 AAAACATCA
1 AAAACATCA
30042 TGCACTGAAG
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
75 1 0.01
76 80 0.99
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
CGAAGGGTTTG
Found at i:30039 original size:45 final size:45
Alignment explanation
Indices: 29973--30086 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
29963 TCAAAAAGCT
*
29973 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30020 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30065 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
30087 AAAAGCTCCC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 56 0.88
47 8 0.12
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:30108 original size:76 final size:76
Alignment explanation
Indices: 30020--30922 Score: 1675
Period size: 76 Copynumber: 11.9 Consensus size: 76
30010 TTACAGATGA
* *
30020 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30083 ATCAAAAAGCT
66 ATCAAAAAGCT
30094 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30159 ATCAAAAAGCT
66 ATCAAAAAGCT
30170 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30235 ATCAAAAAGCT
66 ATCAAAAAGCT
*
30246 CCCGAAGGCCTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30311 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
30322 CTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30387 ATCAAAAAGCT
66 ATCAAAAAGCT
*
30398 CCCGAAGGCTTTTTGGAAACATCATTCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30463 ATCAAAAAGCT
66 ATCAAAAAGCT
30474 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
30539 ATCAAAAATCT
66 ATCAAAAAGCT
*
30550 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30615 ATCAAAAAGCT
66 ATCAAAAAGCT
*
30626 CTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30691 ATCAAAAAGCT
66 ATCAAAAAGCT
30702 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30767 ATCAAAAAGCT
66 ATCAAAAAGCT
30778 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30843 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * *
30854 CCCGAAGGCTTTTTGGAAACATTATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30919 ATCA
66 ATCA
30923 TGCACTGAAG
Statistics
Matches: 807, Mismatches: 20, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
74 8 0.01
76 799 0.99
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:30121 original size:121 final size:121
Alignment explanation
Indices: 29907--30162 Score: 451
Period size: 121 Copynumber: 2.1 Consensus size: 121
29897 CCCAAAGGCT
* * *
29907 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGC
29972 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
66 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
30028 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAG
30092 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
65 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
30149 CTTTGAAAACATCA
1 TTTTGAAAACATCA
30163 AAAAGCTCCC
Statistics
Matches: 129, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 1 0.01
121 128 0.99
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (121 bp):
TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
Found at i:30926 original size:45 final size:45
Alignment explanation
Indices: 30854--30967 Score: 165
Period size: 45 Copynumber: 2.5 Consensus size: 45
30844 TCAAAAAGCT
* * * *
30854 CCCGAAGGCTTTTTGGAAACATTATGCATTGAAGGGCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
30901 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30946 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
30968 AAAAGCTCCC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 54 0.87
47 8 0.13
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:30926 original size:121 final size:121
Alignment explanation
Indices: 30778--31043 Score: 469
Period size: 121 Copynumber: 2.2 Consensus size: 121
30768 TCAAAAAGCT
*
30778 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
* * *
30843 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATTATGCATTGAAGGGCTTACAGATGA
64 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
30901 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
30966 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
66 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
*
31022 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
31044 AAAAAGCTCC
Statistics
Matches: 138, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
121 130 0.94
123 8 0.06
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (121 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:30928 original size:197 final size:199
Alignment explanation
Indices: 30702--31097 Score: 742
Period size: 197 Copynumber: 2.0 Consensus size: 199
30692 TCAAAAAGCT
*
30702 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGC-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30767 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
65 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
* *
30832 GCTTTGAAAACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATTATGCATTGAAGGGCTTACA
130 GCTTTGAAAACATCAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACA
30896 GATGA
195 GATGA
30901 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
30965 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
66 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
31030 CTTTGAAAACATCAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
131 CTTTGAAAACATCAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
31095 ATG
196 ATG
31098 TGGGAAATAG
Statistics
Matches: 193, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
197 133 0.69
198 52 0.27
199 8 0.04
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (199 bp):
CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
CTTTGAAAACATCAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
ATGA
Found at i:30989 original size:76 final size:77
Alignment explanation
Indices: 30901--31097 Score: 355
Period size: 76 Copynumber: 2.6 Consensus size: 77
30891 TTACAGATGA
*
30901 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30964 ATC-AAAAAGCT
66 ATCAAAAAAGCT
30975 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
31040 ATCAAAAAAGCT
66 ATCAAAAAAGCT
*
31052 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
31098 TGGGAAATAG
Statistics
Matches: 118, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
74 8 0.07
76 57 0.48
77 53 0.45
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (77 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAAGCT
Found at i:31856 original size:22 final size:22
Alignment explanation
Indices: 31776--31853 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
31766 GATAAAGCTT
*
31776 TCATCTTTGAAAAGAAAATCTG
1 TCATCTTTGAAAAGAAAATCTA
* *
31798 TCATCTTTTAAAAAGAGAATCTA
1 TCATC-TTTGAAAAGAAAATCTA
* *
31821 TCATCTTTGAAGAGATAATCTA
1 TCATCTTTGAAAAGAAAATCTA
31843 TCATCTTTGAA
1 TCATCTTTGAA
31854 GAGTGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 30 0.61
23 19 0.39
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:34558 original size:115 final size:115
Alignment explanation
Indices: 34397--34847 Score: 796
Period size: 115 Copynumber: 3.9 Consensus size: 115
34387 GATCATGCAT
* * * * *
34397 TTCATCTTTTAATTCTAATGATTGG-TTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
34461 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
34511 TTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTTATCCCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
34576 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
34626 TTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
34691 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
34741 TTCATCTTTTAAATCCAATGATTAGTTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
34806 AACGCTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
34848 CGAGAACGTA
Statistics
Matches: 323, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
114 23 0.07
115 300 0.93
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (115 bp):
TTCATCTTTTAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:41083 original size:22 final size:24
Alignment explanation
Indices: 41043--41086 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
41033 AAACCTCTAA
41043 TGAACAAATAAAATAATTAATACC
1 TGAACAAATAAAATAATTAATACC
*
41067 TGAATAAA-AAAAT-ATTAATA
1 TGAACAAATAAAATAATTAATA
41087 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (24 bp):
TGAACAAATAAAATAATTAATACC
Found at i:41097 original size:17 final size:18
Alignment explanation
Indices: 41070--41110 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
41060 TAATACCTGA
*
41070 ATAAAAA-AAT-ATTAAT
1 ATAAAAATAATAAGTAAT
41086 ATAAAAATAATAAGTAAT
1 ATAAAAATAATAAGTAAT
41104 A-AAAAAT
1 ATAAAAAT
41111 TGAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 9 0.41
18 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
ATAAAAATAATAAGTAAT
Found at i:41144 original size:20 final size:21
Alignment explanation
Indices: 41105--41145 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41095 ATAAGTAATA
41105 AAAAATTGAAAGAAAAGAATT
1 AAAAATTGAAAGAAAAGAATT
* *
41126 AAAAATT-AAATAAATGAATT
1 AAAAATTGAAAGAAAAGAATT
41146 TTTAATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
AAAAATTGAAAGAAAAGAATT
Found at i:41615 original size:18 final size:17
Alignment explanation
Indices: 41589--41628 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
41579 ATTTCAAAGT
41589 TATAATTATATAAAAAAA
1 TATAATTATAT-AAAAAA
* *
41607 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
41624 TATAA
1 TATAA
41629 ATAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:41860 original size:112 final size:112
Alignment explanation
Indices: 41627--41847 Score: 263
Period size: 112 Copynumber: 2.0 Consensus size: 112
41617 TATAAAATAT
* * * *
41627 AAATAAAATATTTATTTATATAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACAGCTCTT
1 AAATAAAATATTTATTTATATAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACAGCTCCT
* * * *
41692 TTCTTCGATATAAAAAAATAATTAAAATAATTAATATATGATTTAAA
66 TTCTTCAATATAAAAAAATAAATAAAATAATTAAAACATGATTTAAA
* * ** *
41739 AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTTTAAGACTGC-CC
1 AAATAAAATATTTATTTATATAAAAATATCAGAAAA-GGACATCCAGGTGCCTTAAGACAGCTCC
**
41803 TTTCTT-AATATTGAAAAATAAAT-AAAT-ATTAAAACATGA-TTAAA
65 TTTCTTCAATATAAAAAAATAAATAAAATAATTAAAACATGATTTAAA
41847 A
1 A
41848 TAGGTTAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
108 6 0.06
109 10 0.11
110 4 0.04
111 13 0.14
112 41 0.44
113 19 0.20
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (112 bp):
AAATAAAATATTTATTTATATAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACAGCTCCT
TTCTTCAATATAAAAAAATAAATAAAATAATTAAAACATGATTTAAA
Found at i:41980 original size:27 final size:28
Alignment explanation
Indices: 41925--41983 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
41915 AATTTATGAC
* *
41925 TAAATAATAATAATTAAGAGTAAACATA
1 TAAATAATAATAATTAAAACTAAACATA
* *
41953 TAAATAATAA-AATTAAAACTATATATA
1 TAAATAATAATAATTAAAACTAAACATA
41980 TAAA
1 TAAA
41984 ACTTGTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (28 bp):
TAAATAATAATAATTAAAACTAAACATA
Found at i:43442 original size:3 final size:3
Alignment explanation
Indices: 43434--43489 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
43424 TTATTTTATT
* * *
43434 TAA TAA TAA TAA TAA CAA TAA TAA TAT TTA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43481 TAA TAA TAA
1 TAA TAA TAA
43490 AAGTAAACTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:46754 original size:29 final size:29
Alignment explanation
Indices: 46705--46809 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
46695 GATAAGGATA
*
46705 TAATCCCATGCAGAAAT-AGGACGAGAAAT
1 TAATCCCATGTAG-AATCAGGACGAGAAAT
* *
46734 TAATCCCATATAGAATCAGGACCG-GGAAT
1 TAATCCCATGTAGAATCAGGA-CGAGAAAT
* * *
46763 TAATCTCAGGTAGAATCAGGA-TAGGAAAT
1 TAATCCCATGTAGAATCAGGACGA-GAAAT
46792 TAATCCCATGTAGAATCA
1 TAATCCCATGTAGAATCA
46810 AGAAGGGGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
28 3 0.05
29 57 0.92
30 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (29 bp):
TAATCCCATGTAGAATCAGGACGAGAAAT
Found at i:50263 original size:22 final size:22
Alignment explanation
Indices: 50214--50268 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
50204 TTGTTCTTAT
*
50214 TATTTTATTTTATTTTTCCCTT
1 TATTTTATTTTATTTTTCCCTA
50236 TGATTTT-TTTTATTTTTCCCCTA
1 T-ATTTTATTTTATTTTT-CCCTA
50259 TATTTTATTT
1 TATTTTATTT
50269 CATATTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTTATTTTATTTTTCCCTA
Found at i:56221 original size:85 final size:85
Alignment explanation
Indices: 56117--56283 Score: 253
Period size: 85 Copynumber: 2.0 Consensus size: 85
56107 CTCAATCTAG
* *
56117 TACAACATAACTCAAGGTGAGGAGGGTTAGCTGTCAACAAAAACCTTCGAGTTCAATTTCATTCA
1 TACAACATAACTCAAGGTGAGAAGGGCTAGCTGTCAACAAAAACCTTCGAGTTCAATTTCATTCA
56182 GCTCAAGGGCATATCAAATT
66 GCTCAAGGGCATATCAAATT
* * * * *
56202 TACAGCATAACTCAAGGTGAGAAGGGCTATCTGTCAACGAAAACTTTCGAGTTCATTTTCATTCA
1 TACAACATAACTCAAGGTGAGAAGGGCTAGCTGTCAACAAAAACCTTCGAGTTCAATTTCATTCA
* *
56267 GCTCGAGGGCGTATCAA
66 GCTCAAGGGCATATCAA
56284 CTGTATTGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (85 bp):
TACAACATAACTCAAGGTGAGAAGGGCTAGCTGTCAACAAAAACCTTCGAGTTCAATTTCATTCA
GCTCAAGGGCATATCAAATT
Found at i:56915 original size:17 final size:16
Alignment explanation
Indices: 56893--56936 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
56883 TAGTATAGTT
*
56893 TTTTTTGAAACATACAG
1 TTTTTTGAAAAAT-CAG
* *
56910 TTTTTTTAAAAATCGG
1 TTTTTTGAAAAATCAG
56926 TTTTTTGAAAA
1 TTTTTTGAAAA
56937 TATATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (16 bp):
TTTTTTGAAAAATCAG
Found at i:57025 original size:38 final size:38
Alignment explanation
Indices: 56928--57221 Score: 409
Period size: 38 Copynumber: 7.8 Consensus size: 38
56918 AAAATCGGTT
*
56928 TTTTG-AAAATATATATATTATATAGTTTTTGAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTGAAAACA
56965 TTTTG-AAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTGAAAACA
* *
57002 TTTTGAAAATTATATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAAATATATATAATATATAGTTTTTGAAAACA
*
57040 TTTTGAAAAATATATATAAAATATAGTTTTTGAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTGAAAACA
* *
57078 TTTTGAAAAAATATATATAATTTATAG-TTTTGAAAATA
1 TTTTG-AAAAATATATATAATATATAGTTTTTGAAAACA
*
57116 TTTTGAAAACATATATATAATATATA-TTTTTTAAAACA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTGAAAACA
****
57154 TTTTGAAAACATATATATAATATATAGTTTTTGAATTTTT
1 TTTTGAAAA-ATATATATAATATATAGTTTTTGAA-AACA
*
57194 TTTTG-AAAATGTATATAATATATAGTTT
1 TTTTGAAAAATATATATAATATATAGTTT
57222 CAAAAAAAAT
Statistics
Matches: 233, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
37 45 0.19
38 154 0.66
39 29 0.12
40 5 0.02
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (38 bp):
TTTTGAAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:57266 original size:2 final size:2
Alignment explanation
Indices: 57261--57287 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57251 TATTTTTTAT
57261 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
57288 TATTTACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57901 original size:21 final size:21
Alignment explanation
Indices: 57877--57919 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
57867 AGAAAAATGA
57877 GCATCA-AAAAGGTAAGAAGTC
1 GCATCAGAAAAGGTAA-AAGTC
*
57898 GCATTAGAAAAGGTAAAAGTC
1 GCATCAGAAAAGGTAAAAGTC
57919 G
1 G
57920 AAGCCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.47, C:0.12, G:0.26, T:0.16
Consensus pattern (21 bp):
GCATCAGAAAAGGTAAAAGTC
Found at i:58582 original size:36 final size:36
Alignment explanation
Indices: 58533--58646 Score: 203
Period size: 36 Copynumber: 3.2 Consensus size: 36
58523 TTCTTATTTA
58533 TTTTA-TTTTATTTTTCCCTTTGATTTATTTAATAT
1 TTTTATTTTTATTTTTCCCTTTGATTTATTTAATAT
*
58568 TTTTATTTTTATTTTTCCATTTGATTTATTTAATAT
1 TTTTATTTTTATTTTTCCCTTTGATTTATTTAATAT
58604 TTTTATTTTTATTTTTCCCTTTGATTTATTTAATAT
1 TTTTATTTTTATTTTTCCCTTTGATTTATTTAATAT
58640 TTATTAT
1 TT-TTAT
58647 CTAACATTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
35 5 0.07
36 66 0.88
37 4 0.05
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (36 bp):
TTTTATTTTTATTTTTCCCTTTGATTTATTTAATAT
Found at i:63680 original size:20 final size:21
Alignment explanation
Indices: 63655--63706 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
63645 TTTTCCCAAT
*
63655 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
63675 TCGCAATGCAAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
63696 TCGCAATGCGA
1 TCGCAATGCGA
63707 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:63741 original size:41 final size:40
Alignment explanation
Indices: 63644--63748 Score: 95
Period size: 41 Copynumber: 2.6 Consensus size: 40
63634 TCGCGTTGTG
*
63644 ATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCA
1 ATTTTCCAAATTCGCAATGCG-ATAAGTAAATCGCAATGCA
* ** * * *
63685 AATTTGGAAAATCGCAATGCGAT-ACTGACTATCGCAATGCA
1 ATTTTCCAAATTCGCAATGCGATAAGT-A-AATCGCAATGCA
* *
63726 ATTTTCCTAATTCGCATTGCGAT
1 ATTTTCCAAATTCGCAATGCGAT
63749 TTACGTATTC
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
39 2 0.04
40 3 0.06
41 44 0.90
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (40 bp):
ATTTTCCAAATTCGCAATGCGATAAGTAAATCGCAATGCA
Found at i:63750 original size:21 final size:21
Alignment explanation
Indices: 63716--63777 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
63706 ATACTGACTA
* * *
63716 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
63737 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
63757 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
63778 CGTAATGCGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:63798 original size:20 final size:20
Alignment explanation
Indices: 63775--63888 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
63765 CGATTTTCAT
*
63775 AATCGTAATGCGAATACGTA
1 AATCGCAATGCGAATACGTA
* * *
63795 AATCGCAACGCGATTAAGTA
1 AATCGCAATGCGAATACGTA
* * *
63815 AATCGCAATGCGGATTAGGAA
1 AATCGCAATGC-GAATACGTA
63836 AATCGCAATGCGAATACGTA
1 AATCGCAATGCGAATACGTA
*
63856 AATCGCAATGCGAAT-CTTA
1 AATCGCAATGCGAATACGTA
*
63875 CTATCGCAATGCGA
1 -AATCGCAATGCGA
63889 TTTACATAGC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 59 0.74
21 18 0.22
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGAATACGTA
Found at i:64619 original size:33 final size:35
Alignment explanation
Indices: 64582--64653 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
64572 CCTTACAACT
* *
64582 CCCTAG-TTTTTC-CGAGCTAAACTAGAACTTTTC
1 CCCTAGCTTTTACACGAGCTAAACTAGAACCTTTC
* *
64615 CCCTAGCTTTTACACGGGCTAAGCTAGAACCTTTC
1 CCCTAGCTTTTACACGAGCTAAACTAGAACCTTTC
64650 CCCT
1 CCCT
64654 TTACAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 6 0.18
34 5 0.15
35 22 0.67
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (35 bp):
CCCTAGCTTTTACACGAGCTAAACTAGAACCTTTC
Found at i:65030 original size:8 final size:7
Alignment explanation
Indices: 65016--65155 Score: 51
Period size: 8 Copynumber: 19.0 Consensus size: 7
65006 GTTGCAGCCT
65016 TGATGCA
1 TGATGCA
65023 TGGATGCA
1 T-GATGCA
65031 TG--GCA
1 TGATGCA
65036 TGATGCA
1 TGATGCA
65043 TCGATGCA
1 T-GATGCA
65051 TAGATGCA
1 T-GATGCA
65059 TG--GCAA
1 TGATGC-A
*
65065 GGATGCA
1 TGATGCA
65072 TCGATGCA
1 T-GATGCA
*
65080 CTAATTGCA
1 -TGA-TGCA
**
65089 TTCGATGTT
1 -T-GATGCA
65098 TGGATGCA
1 T-GATGCA
65106 TGGATGCA
1 T-GATGCA
*
65114 T--TGCC
1 TGATGCA
65119 TGATGCA
1 TGATGCA
65126 TCGATGCA
1 T-GATGCA
*
65134 TTAGTGCA
1 TGA-TGCA
65142 -GATGCA
1 TGATGCA
65148 TGGATGCA
1 T-GATGCA
65156 CTGCAGGGAT
Statistics
Matches: 101, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
5 11 0.11
6 6 0.06
7 14 0.14
8 61 0.60
9 8 0.08
10 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (7 bp):
TGATGCA
Found at i:65318 original size:30 final size:30
Alignment explanation
Indices: 65261--65320 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
65251 AACTTTGAAT
65261 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
65291 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
65321 CTTAAGTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:68166 original size:34 final size:32
Alignment explanation
Indices: 68115--68184 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
68105 CCTTACAACT
*
68115 CCCTAGTTTTTCCGGGCTAAACTAGAACCTTC
1 CCCTAGTTTTACCGGGCTAAACTAGAACCTTC
* *
68147 CCCTAGCTTTTACACGGGCTAAGCTAGAACCTTT
1 CCCTAG-TTTTAC-CGGGCTAAACTAGAACCTTC
68181 CCCT
1 CCCT
68185 TTTACAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 6 0.18
33 5 0.15
34 22 0.67
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (32 bp):
CCCTAGTTTTACCGGGCTAAACTAGAACCTTC
Found at i:68562 original size:8 final size:8
Alignment explanation
Indices: 68549--68594 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
68539 TTGCAACCTT
68549 GATGCATG
1 GATGCATG
68557 GATGCAT-
1 GATGCATG
68564 G--GCA-G
1 GATGCATG
*
68569 GATGCATC
1 GATGCATG
68577 GATGCATG
1 GATGCATG
68585 GATGCATG
1 GATGCATG
68593 GA
1 GA
68595 AAGGATGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
5 4 0.12
7 4 0.12
8 24 0.75
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (8 bp):
GATGCATG
Found at i:68589 original size:28 final size:29
Alignment explanation
Indices: 68549--68611 Score: 110
Period size: 28 Copynumber: 2.2 Consensus size: 29
68539 TTGCAACCTT
*
68549 GATGCATGGATGCATGG-CAGGATGCATC
1 GATGCATGGATGCATGGAAAGGATGCATC
68577 GATGCATGGATGCATGGAAAGGATGCATC
1 GATGCATGGATGCATGGAAAGGATGCATC
68606 GATGCA
1 GATGCA
68612 CTAATTGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.21
Consensus pattern (29 bp):
GATGCATGGATGCATGGAAAGGATGCATC
Found at i:68850 original size:30 final size:30
Alignment explanation
Indices: 68792--68851 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
68782 AAACTTTGAA
68792 TAAATTCAATTCAAATCCAAAAACATTTTG
1 TAAATTCAATTCAAATCCAAAAACATTTTG
*
68822 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAATCCAAAAACATTTTG
68852 CCTTAAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTCAAATCCAAAAACATTTTG
Found at i:71636 original size:19 final size:19
Alignment explanation
Indices: 71614--71705 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
71604 AAAAATTACT
71614 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
71633 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
71647 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
71666 ATCACAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
*
71680 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
71699 ATCGCAA
1 ATCGCAA
71706 CTAGAGAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 18 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 25 0.45
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:71656 original size:33 final size:33
Alignment explanation
Indices: 71614--71759 Score: 211
Period size: 33 Copynumber: 4.4 Consensus size: 33
71604 AAAAATTACT
71614 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
*
71647 ATCGCAATGCGAAATGAAAATCACAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
* * *
71680 ATTGCAATGCGAAATGAAAATCGCAACTAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
* * * *
71713 ATTGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
*
71746 ATCGCAAAGCGAAA
1 ATCGCAATGCGAAA
71760 CTAAATTCGC
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 102 1.00
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGATA
Found at i:71811 original size:33 final size:33
Alignment explanation
Indices: 71769--71895 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
71759 ACTAAATTCG
*
71769 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
71802 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* **
71835 CGTTGCGATTTTCATTTCGCATTGTGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
71868 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
71896 AGTAATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:72760 original size:41 final size:42
Alignment explanation
Indices: 72715--72806 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
72705 CCTCTTCAAC
*
72715 GATGACAGTGGCCTCTTGAACG-GTGG-GGGGTACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGG-ACTCTTGAGG
* *
72756 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
72798 GATGACAGG
1 GATGACAGG
72807 TGAGTCGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
41 20 0.44
42 21 0.47
43 4 0.09
ACGTcount: A:0.21, C:0.15, G:0.41, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:72773 original size:21 final size:21
Alignment explanation
Indices: 72741--72802 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
72731 TGAACGGTGG
*
72741 GGGGTACTCTTGAGGGATGATA
1 GGGG-ACTCTTGAGGGATGAGA
* **
72763 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
72784 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
72803 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.06
21 23 0.74
22 6 0.19
ACGTcount: A:0.21, C:0.13, G:0.42, T:0.24
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:73170 original size:20 final size:20
Alignment explanation
Indices: 73145--73212 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
73135 AATAGTTTAA
* *
73145 TTTCGCAACACGAAACTTAC
1 TTTCGCAACACGAAAATGAC
*
73165 TTTCGCAACGCGAAAATGAC
1 TTTCGCAACACGAAAATGAC
* * *
73185 TATCGCAACGCGGAAATGAC
1 TTTCGCAACACGAAAATGAC
*
73205 TATCGCAA
1 TTTCGCAA
73213 ACGTGGAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
TTTCGCAACACGAAAATGAC
Found at i:73215 original size:21 final size:20
Alignment explanation
Indices: 73167--73254 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
73157 AAACTTACTT
*
73167 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
73187 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
73207 TCGCAAACGTGGAAATGGCTA
1 TCGC-AACGCGGAAATGACTA
* **
73228 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
73247 TCGCAACG
1 TCGCAACG
73255 ACAAAATCGC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.24
20 26 0.45
21 18 0.31
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:73249 original size:19 final size:19
Alignment explanation
Indices: 73227--73285 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
73217 GGAAATGGCT
73227 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
73246 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
73260 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
73279 ATCGCAA
1 ATCGCAA
73286 CGCGCAACGC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:73365 original size:19 final size:18
Alignment explanation
Indices: 73341--73398 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
73331 GATTTTGTCG
73341 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
73359 ATTGCGA-TTT--TGTCG-
1 -TTGCGATTTTCATTTCGC
73374 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
73392 GTTGCGA
1 -TTGCGA
73399 AAGTAAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 6 0.19
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 12 0.38
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:73367 original size:33 final size:33
Alignment explanation
Indices: 73310--73398 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 33
73300 CACAATCGCA
*
73310 TTGCGATTTT--TTTCGCGTTTCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
73341 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
73374 TTGCGATTTTCATTTCGCGTTGCGA
1 TTGCGATTTTCATTTCGCGTTGCGA
73399 AAGTAAACTA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
31 10 0.19
33 43 0.81
ACGTcount: A:0.10, C:0.18, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:73379 original size:14 final size:14
Alignment explanation
Indices: 73325--73383 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
73315 ATTTTTTTCG
*
73325 CGTTTCGATTTTGT
1 CGTTGCGATTTTGT
*
73339 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
73356 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
73372 CGTTGCGATTTT
1 CGTTGCGATTTT
73384 CATTTCGCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:73960 original size:18 final size:18
Alignment explanation
Indices: 73937--73984 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
73927 CGGGTCGATC
73937 AGGTGATGGCTCTAGGTG
1 AGGTGATGGCTCTAGGTG
* *
73955 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTAGGTG
73973 AGGTGATGGCTC
1 AGGTGATGGCTC
73985 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTAGGTG
Found at i:75817 original size:20 final size:20
Alignment explanation
Indices: 75792--75854 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
75782 GTATTATCTA
75792 GTTGCGAAAGTCAGTATTGC
1 GTTGCGAAAGTCAGTATTGC
* *
75812 GTTGCGAAATTAAGTA-T-C
1 GTTGCGAAAGTCAGTATTGC
*
75830 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGTATTGC
75850 GTTGC
1 GTTGC
75855 ATTTTGTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 15 0.42
19 1 0.03
20 20 0.56
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATTGC
Found at i:75834 original size:18 final size:18
Alignment explanation
Indices: 75792--75848 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
75782 GTATTATCTA
75792 GTTGCGAAAGTCAGTATTGC
1 GTTGCGAAAGTCAGTA-T-C
* *
75812 GTTGCGAAATTAAGTATC
1 GTTGCGAAAGTCAGTATC
75830 GTTGCGAAAGTCAGTATC
1 GTTGCGAAAGTCAGTATC
75848 G
1 G
75849 CGTTGCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 18 0.55
19 1 0.03
20 14 0.42
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (18 bp):
GTTGCGAAAGTCAGTATC
Found at i:75868 original size:38 final size:39
Alignment explanation
Indices: 75766--75886 Score: 120
Period size: 38 Copynumber: 3.1 Consensus size: 39
75756 CGCTTTGAAA
* *
75766 ATCGCATTGCGATTATGTATTATCTAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATC--GTTGCGAAAGTCAGT
* ** * *
75807 ATTGCGTTGCGAAATT-AAGTATCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGTTGCGAAAGTCAGT
*
75845 ATCGCGTTGC-ATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTAT--CGTTGCGAAAGTCAGT
75885 AT
1 AT
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
37 3 0.05
38 28 0.44
40 22 0.34
41 11 0.17
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (39 bp):
ATCGCGTTGCGATTTTGTATTATCGTTGCGAAAGTCAGT
Done.