Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007804.1 Hibiscus syriacus cultivar Beakdansim tig00110122_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: 1697051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:7161 original size:19 final size:20
Alignment explanation
Indices: 7129--7166 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
7119 TGATGGTTGT
*
7129 TTTTGTATGTTG-TTAATTG
1 TTTTGTATGATGTTTAATTG
*
7148 TTTTGTTTGATGTTTAATT
1 TTTTGTATGATGTTTAATT
7167 CCTTGAGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.66
Consensus pattern (20 bp):
TTTTGTATGATGTTTAATTG
Found at i:10218 original size:2 final size:2
Alignment explanation
Indices: 10211--10297 Score: 153
Period size: 2 Copynumber: 45.0 Consensus size: 2
10201 GTTCGTTCTT
10211 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
10253 TA TA TA -A TA TA TA TA TA TA -A TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10292 TA TA TA
1 TA TA TA
10298 CACACACCCC
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 79 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18158 original size:6 final size:6
Alignment explanation
Indices: 18147--18178 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
18137 AATCAACATT
18147 TTTGCA TTTGCA TTTAGCA TTTGCA TTTGCA T
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA T
18179 GTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
TTTGCA
Found at i:18168 original size:13 final size:12
Alignment explanation
Indices: 18147--18178 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
18137 AATCAACATT
18147 TTTGCATTTGCA
1 TTTGCATTTGCA
18159 TTTAGCATTTGCA
1 TTT-GCATTTGCA
18172 TTTGCAT
1 TTTGCAT
18179 GTATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:20714 original size:18 final size:18
Alignment explanation
Indices: 20693--20733 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20683 AAGAGATATG
20693 GAAAAACACAAAAAGAAA
1 GAAAAACACAAAAAGAAA
* *
20711 GAAAAAGAGAAAAAGAAA
1 GAAAAACACAAAAAGAAA
20729 -AAAAA
1 GAAAAA
20734 GAAAACGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (18 bp):
GAAAAACACAAAAAGAAA
Found at i:20721 original size:8 final size:8
Alignment explanation
Indices: 20710--20792 Score: 63
Period size: 8 Copynumber: 10.8 Consensus size: 8
20700 ACAAAAAGAA
20710 AGAAAAAG
1 AGAAAAAG
20718 AGAAAAAG
1 AGAAAAAG
*
20726 A-AAAAAA
1 AGAAAAAG
*
20733 AGAAAACG
1 AGAAAAAG
20741 AG-AAAA-
1 AGAAAAAG
20747 AG-AAAAG
1 AGAAAAAG
20754 A-AAAGAAG
1 AGAAA-AAG
20762 AGAAAAA-
1 AGAAAAAG
20769 AGGAAAAAG
1 A-GAAAAAG
20778 A-AAGAAAG
1 AGAA-AAAG
20786 AAGAAAA
1 -AGAAAA
20793 TAGACAGATC
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
6 6 0.10
7 15 0.25
8 31 0.51
9 7 0.11
10 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.22, T:0.00
Consensus pattern (8 bp):
AGAAAAAG
Found at i:20753 original size:28 final size:29
Alignment explanation
Indices: 20721--20784 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
20711 GAAAAAGAGA
*
20721 AAAAGAAAA-AAAAG-AAAACGAGAAAAAG
1 AAAAGAAAAGAAAAGAAAAAAG-GAAAAAG
*
20749 AAAAGAAAAGAAGAGAAAAAAGGAAAAAG
1 AAAAGAAAAGAAAAGAAAAAAGGAAAAAG
20778 -AAAGAAA
1 AAAAGAAA
20785 GAAGAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 16 0.50
29 11 0.34
30 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAAGAAAAGAAAAGAAAAAAGGAAAAAG
Found at i:20792 original size:23 final size:24
Alignment explanation
Indices: 20702--20792 Score: 104
Period size: 23 Copynumber: 3.9 Consensus size: 24
20692 GGAAAAACAC
*
20702 AAAAAGAAAGAAAAAGAGAAAAAG
1 AAAAAGAAAGAAAGAGAGAAAAAG
20726 AAAAA-AAAGAAA-ACGAGAAAAAG
1 AAAAAGAAAGAAAGA-GAGAAAAAG
20749 -AAAAGAAA-AGAAGAGA-AAAAAGG
1 AAAAAGAAAGA-AAGAGAGAAAAA-G
20772 AAAAAGAAAGAAAGA-AGAAAA
1 AAAAAGAAAGAAAGAGAGAAAA
20793 TAGACAGATC
Statistics
Matches: 59, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
22 11 0.19
23 25 0.42
24 22 0.37
25 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAGAAAGAGAGAAAAAG
Found at i:21469 original size:28 final size:28
Alignment explanation
Indices: 21429--21491 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
21419 GCAAGAAGCC
*
21429 AACCTGAAACACATTACCTCCCCAAATT
1 AACCTGAAACACACTACCTCCCCAAATT
* *
21457 AACCTGAAACACACTACCTTCCCAAGTT
1 AACCTGAAACACACTACCTCCCCAAATT
*
21485 AGCCTGA
1 AACCTGA
21492 GCCTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.35, G:0.08, T:0.21
Consensus pattern (28 bp):
AACCTGAAACACACTACCTCCCCAAATT
Found at i:23246 original size:20 final size:19
Alignment explanation
Indices: 23221--23281 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 19
23211 TTCTTGATTT
23221 GTAAGTCCTCCGGGCCATC
1 GTAAGTCCTCCGGGCCATC
* *
23240 GGTAAGTCTTCCGAGCATCATAC
1 -GTAAGTCCTCCGGGC--CAT-C
23263 GTAAGTCCTCCGGGCCATC
1 GTAAGTCCTCCGGGCCATC
23282 CATAAGACCT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 1 0.03
20 16 0.47
22 16 0.47
23 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (19 bp):
GTAAGTCCTCCGGGCCATC
Found at i:23305 original size:132 final size:132
Alignment explanation
Indices: 22869--23553 Score: 1065
Period size: 132 Copynumber: 5.2 Consensus size: 132
22859 TTTCTTAATG
* * *
22869 CGTAAGTCATCCGGGCCATCCATAAGACCTTTAGTGCAGGATTTTTTCAAATGAGATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* * *
22934 CTAAGCCTTCGGGAGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAACTCTTCCGAGCAAT-
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCAGGCCATCAGTAAGTCTTCCGAGC-ATC
*
22998 ATT
130 ATA
*
23001 CGTAAGTCCTCTGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* *
23066 CTAAGCCTT-TGGGGTTTCTTGATTTGTAAGTCCT-C-GGCCATCAGTAAGTCTTCCGAGCATGA
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCAGGCCATCAGTAAGTCTTCCGAGCATCA
23128 TGA
131 T-A
** **
23131 -GTAAGTTTTCTTGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* * *
23195 CTAAGACTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCGGTAAGTCTTCCGAGCATCA
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCAGGCCATCAGTAAGTCTTCCGAGCATCA
23260 TA
131 TA
* *
23262 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAAATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* *
23327 CTAAGCCTTTGGGGGTTTCTTGATTTGTAAGTCCTCCAAGCCATCAGTAAGTCTTCCGAGCATCA
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCAGGCCATCAGTAAGTCTTCCGAGCATCA
*
23392 TG
131 TA
23394 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
1 CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* *
23459 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCAGGCCATCAGTAAGTCTTCCGAGCATGA
66 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCAGGCCATCAGTAAGTCTTCCGAGCATCA
*
23524 TG
131 TA
* * *
23526 CGTAAGTCCTTCAGGCCATCTATAAGAC
1 CGTAAGTCCTCCGGGCCATCCATAAGAC
23554 ATTGGGCAGG
Statistics
Matches: 511, Mismatches: 36, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
128 2 0.00
129 93 0.18
130 25 0.05
131 25 0.05
132 366 0.72
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (132 bp):
CGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCAGGCCATCAGTAAGTCTTCCGAGCATCA
TA
Found at i:25502 original size:26 final size:29
Alignment explanation
Indices: 25473--25541 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
25463 TAATGTTCAT
*
25473 TTTA-GTAAT-TATAT-TTTGTTTGCTTA
1 TTTACGTAATATATATGCTTGTTTGCTTA
*
25499 TTTAACGTAATATTTATGCTTGTTTGCTTA
1 TTT-ACGTAATATATATGCTTGTTTGCTTA
25529 TTTAACGTAATAT
1 TTT-ACGTAATAT
25542 TTATTCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 3 0.08
27 1 0.03
28 5 0.14
29 4 0.11
30 24 0.65
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (29 bp):
TTTACGTAATATATATGCTTGTTTGCTTA
Found at i:25522 original size:30 final size:30
Alignment explanation
Indices: 25488--25545 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
25478 TAATTATATT
25488 TTGTTTGCTTATTTAACGTAATATTTATGC
1 TTGTTTGCTTATTTAACGTAATATTTATGC
25518 TTGTTTGCTTATTTAACGTAATATTTAT
1 TTGTTTGCTTATTTAACGTAATATTTAT
25546 TCTTAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (30 bp):
TTGTTTGCTTATTTAACGTAATATTTATGC
Found at i:29258 original size:3 final size:3
Alignment explanation
Indices: 29252--29283 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29242 ATTATCGTTA
*
29252 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29284 ATTTACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:30495 original size:19 final size:19
Alignment explanation
Indices: 30449--30495 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
30439 CATTAATTTG
*
30449 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
30469 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
30489 TATATTT
1 TATATTT
30496 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:33001 original size:32 final size:32
Alignment explanation
Indices: 32952--33013 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
32942 TCTTACCTGT
*
32952 ACTAACTAATTTCTTTTCTGTTCTTTGTGTGC
1 ACTAACTAATTTATTTTCTGTTCTTTGTGTGC
* *
32984 ACTAACTTATTTATTTTCTGTTGTTTGTGT
1 ACTAACTAATTTATTTTCTGTTCTTTGTGT
33014 CTTTTTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.15, G:0.13, T:0.56
Consensus pattern (32 bp):
ACTAACTAATTTATTTTCTGTTCTTTGTGTGC
Found at i:37338 original size:103 final size:102
Alignment explanation
Indices: 37153--37457 Score: 373
Period size: 103 Copynumber: 2.9 Consensus size: 102
37143 TTTTGAGAAA
37153 TTTAAAACAAATTGCGTCTCGCTTGAGACATTTTTTCCTTTGATATACAAATTTCGAATTTGCTT
1 TTTAAAACAAATT-CGTCTCGCTTGAGACA-TTTTTCCTTTGA-ATACAAATTTCGAATTTGCTT
*
37218 CACTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
63 CACTTAAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
* * *
37258 -TTAAAACAAACTTCATCTCGCTTTAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTC
1 TTTAAAACAAA-TTCGTCTCGCTTGAGACATTTTTCCTTTGA-ATACAAATTTCGAATTTGCTTC
* *
37322 ACTTAAAACAATATTAATCTCAATTGAGATTGTTGTTTC
64 ACTTAAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
* * * * *
37361 TTTCAAAAAAAAAATTCGTCTCGCTTGAGACATTTTCCCTCAT-AATACAAATTTCAAAGTTG-T
1 TTT---AAAACAAATTCGTCTCGCTTGAGACATTTTTCCT-TTGAATACAAATTTCGAATTTGCT
* * *
37424 TGTATTTAAAACAAAATTAATATCACTTGAGATT
62 T-CACTTAAAACAAAATTAATCTCACTTGAGATT
37458 TTCAAAGATG
Statistics
Matches: 173, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
103 69 0.40
104 28 0.16
105 44 0.25
106 24 0.14
107 8 0.05
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.40
Consensus pattern (102 bp):
TTTAAAACAAATTCGTCTCGCTTGAGACATTTTTCCTTTGAATACAAATTTCGAATTTGCTTCAC
TTAAAACAAAATTAATCTCACTTGAGATTGTTGTTTC
Found at i:37683 original size:29 final size:30
Alignment explanation
Indices: 37629--37713 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 30
37619 TTTCTCTTGA
*
37629 AACAAATCTTTGAGTT-TGTTCCTTTTAAAT-
1 AACAAATCTTTGAGTTAT-TT-CTTTTTAATG
**
37659 AA-AAATCTTTGAGTTATTTCTTTTTTTTG
1 AACAAATCTTTGAGTTATTTCTTTTTAATG
37688 AACAAATCTTTGAGTCTATTTCTTTT
1 AACAAATCTTTGAGT-TATTTCTTTT
37714 GAAACAAAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 6 0.12
29 17 0.35
30 15 0.31
31 10 0.21
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (30 bp):
AACAAATCTTTGAGTTATTTCTTTTTAATG
Found at i:37787 original size:29 final size:30
Alignment explanation
Indices: 37751--37812 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
37741 AATTTCGTGA
*
37751 AAAAATCTTTGAGTC-GTTTCTTTTGAAAC
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
37780 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
37810 AAA
1 AAA
37813 TTTTTGTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (30 bp):
AAAAATCTTTGAGTCTGTTTCTTTGGAAAC
Found at i:37801 original size:91 final size:93
Alignment explanation
Indices: 37691--37867 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 93
37681 TTTTTTGAAC
* *
37691 AAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC-GTGAAAAA
1 AAATCTTTGAGTCTATTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTGAGAAAAA
37755 ATCTTTGAGTC-GTTTCTTTTGAAACAA
66 ATCTTTGAGTCTGTTTCTTTTGAAACAA
* *
37782 AAATCTTTGAGTCTGTTTCTTTGGAAACAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAA
1 AAATCTTTGAGTCTATTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC---TGAGAA
37847 AAAATCTTTGAGTCTGTTTCT
63 AAAATCTTTGAGTCTGTTTCT
37868 CTTAAAATGA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
91 53 0.69
95 18 0.23
96 6 0.08
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (93 bp):
AAATCTTTGAGTCTATTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTGAGAAAAA
ATCTTTGAGTCTGTTTCTTTTGAAACAA
Found at i:37881 original size:66 final size:66
Alignment explanation
Indices: 37767--37891 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
37757 CTTTGAGTCG
*
37767 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAATTTTTGTCTCTCTTGAGAC
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGAAAACAAA-TTTTGTCTCTCTTGAGAC
37832 AA
65 AA
* **
37834 TTTCTTTTGAGA-AAAAATCTTTGAGTCTGTTTCTCTT-AAAATGAATTTTGTCTCTCTT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT-TTGAAAACAAATTTTGTCTCTCTT
37892 AAAACAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
65 13 0.25
66 27 0.51
67 13 0.25
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.46
Consensus pattern (66 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGAAAACAAATTTTGTCTCTCTTGAGACA
A
Found at i:37954 original size:28 final size:26
Alignment explanation
Indices: 37845--37966 Score: 87
Period size: 28 Copynumber: 4.6 Consensus size: 26
37835 TTCTTTTGAG
37845 AAAAAATCTTTGAGTCTGTTTCTCTTA
1 AAAAAATCTTTGAGTCTG-TTCTCTTA
*
37872 AAATGAAT-TTT--GTC---TCTCTTA
1 AAA-AAATCTTTGAGTCTGTTCTCTTA
*
37893 AAACAAATTTTTGAGTCTGTTCAT-TTAAA
1 AAA-AAATCTTTGAGTCTGTTC-TCTT--A
37922 AAAAAATCTTTGAGTCTGTTTCTCTTA
1 AAAAAATCTTTGAGTCTG-TTCTCTTA
37949 ACAAAATCATCTTTGAGT
1 A-AAAA--ATCTTTGAGT
37967 TTATTTCTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 27
0.71 0.04 0.25
Matches are distributed among these distances:
21 13 0.17
22 3 0.04
24 3 0.04
25 3 0.04
27 12 0.16
28 23 0.30
29 9 0.12
30 10 0.13
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (26 bp):
AAAAAATCTTTGAGTCTGTTCTCTTA
Found at i:38147 original size:118 final size:118
Alignment explanation
Indices: 37956--38172 Score: 294
Period size: 118 Copynumber: 1.8 Consensus size: 118
37946 TTAACAAAAT
* * *
37956 CATCTTTGAGTTTATTTCTTTAAAAACAAATTGTGTCTCTCTTGAGACAGTTTCTAATGAAAAAC
1 CATCTTTGAGTATATTTATTTAAAAACAAATTGTGTCTCTCTTGAGACAATTTCTAATGAAAAA-
38021 CAACCTTTGAGATTGTCTCCTTTGAAA-AAAATTGTCTCACTTAAGATGTAATC
65 CAACCTTTGAGATTGTCTCCTTTGAAACAAAATTGTCTCACTTAAGATGTAATC
** * **
38074 CATCTTTGAGTATATTTATTTGGAAACAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAA
1 CATCTTTGAGTATATTTATTTAAAAACAAA-TTGTGTCTCTCTTGAGACAATTTCTAATGA-AAA
* * *
38139 A-AATCTTTGAGTTTGTTTCCTTTGAAACAAAATT
64 ACAACCTTTGAGATTGTCTCCTTTGAAACAAAATT
38173 TTGTCTCTCG
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
118 49 0.58
119 32 0.38
120 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (118 bp):
CATCTTTGAGTATATTTATTTAAAAACAAATTGTGTCTCTCTTGAGACAATTTCTAATGAAAAAC
AACCTTTGAGATTGTCTCCTTTGAAACAAAATTGTCTCACTTAAGATGTAATC
Found at i:38290 original size:31 final size:30
Alignment explanation
Indices: 38255--38321 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
38245 CCTTGAGGCA
38255 GTTTCTCTAGAAATACAAA-ATCTTTGAGTTT
1 GTTTCTCTAGAAATA-AAACATCTTTGAG-TT
* *
38286 GTTTCTCTTGAAATAAAACCATTTTTGAGTT
1 GTTTCTCTAGAAATAAAA-CATCTTTGAGTT
38317 GTTTC
1 GTTTC
38322 ACTTGAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.09
31 21 0.66
32 8 0.25
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (30 bp):
GTTTCTCTAGAAATAAAACATCTTTGAGTT
Found at i:38341 original size:15 final size:15
Alignment explanation
Indices: 38318--38376 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
38308 TTTTGAGTTG
*
38318 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
38333 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
38348 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
38363 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
38377 AGATCATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:38858 original size:63 final size:65
Alignment explanation
Indices: 38682--38859 Score: 166
Period size: 66 Copynumber: 2.7 Consensus size: 65
38672 CAAAACAAAC
* * *
38682 ATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAATTTCCCATGAAACACC
1 ATCTTTGAGAACGTTTCCTTTGAAACGAATTTTGTCTC-TTTGAGACAATTTCCCATGAAACACC
38747 G
65 G
** * * * **
38748 ATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCT-TGCTTGAGACAA-TTCCCTTTAAATG
1 ATCTTTGAGAACGTTT-CCTTTGAAACGAATTTTGTCTCT--TTGAGACAATTTCCCATGAAACA
38811 CC-
63 CCG
***
38813 ATCTTTG-GGTTGTTTCCTTTGAAACGAATTTTGTCTCTTTCGAGACA
1 ATCTTTGAGAACGTTTCCTTTGAAACGAATTTTGTCTCTTT-GAGACA
38860 GTTGCTTTTG
Statistics
Matches: 91, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
62 2 0.02
63 24 0.26
64 6 0.07
65 8 0.09
66 26 0.29
67 25 0.27
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (65 bp):
ATCTTTGAGAACGTTTCCTTTGAAACGAATTTTGTCTCTTTGAGACAATTTCCCATGAAACACCG
Found at i:39279 original size:43 final size:40
Alignment explanation
Indices: 39181--39279 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 40
39171 CCCTAGATGG
* * *
39181 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGA
1 CCAGAACTCTTCATCACGTAGGAACCGTGTCATCCCACGA
** *
39221 CCAGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAAACGA
1 CCAGAACTCTTCATCACGTAGGAACCGTGTCATCCC----ACGA
39264 CCAGAACTCTTCATCA
1 CCAGAACTCTTCATCA
39280 TGTATAAGCA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
39 3 0.07
40 27 0.59
43 16 0.35
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.23
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTAGGAACCGTGTCATCCCACGA
Found at i:39460 original size:3 final size:3
Alignment explanation
Indices: 39454--39497 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
39444 TATTTAATAT
** *
39454 TTA TTA TTA TCG TTA -TA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39498 ATTTACATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:40708 original size:19 final size:19
Alignment explanation
Indices: 40662--40708 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
40652 CATTAATTTG
*
40662 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
40682 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
40702 TATATTT
1 TATATTT
40709 ATTTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:41124 original size:7 final size:8
Alignment explanation
Indices: 41099--41126 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41089 TGAATATAAC
41099 TTTGAATT
1 TTTGAATT
41107 TTTGAATT
1 TTTGAATT
41115 TTTGAATT
1 TTTGAATT
41123 TTTG
1 TTTG
41127 GCTTCAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (8 bp):
TTTGAATT
Found at i:43497 original size:10 final size:10
Alignment explanation
Indices: 43482--43522 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
43472 CATTTAAATA
*
43482 ATAAACGAAT
1 ATAAACGAAC
43492 ATAAACGAAC
1 ATAAACGAAC
**
43502 ACGAACGAAC
1 ATAAACGAAC
43512 ATAAACGAAC
1 ATAAACGAAC
43522 A
1 A
43523 ACACAAACAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:43510 original size:20 final size:20
Alignment explanation
Indices: 43485--43522 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43475 TTAAATAATA
*
43485 AACGAATATAAACGAACACG
1 AACGAACATAAACGAACACG
43505 AACGAACATAAACGAACA
1 AACGAACATAAACGAACA
43523 ACACAAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.21, G:0.13, T:0.08
Consensus pattern (20 bp):
AACGAACATAAACGAACACG
Found at i:49864 original size:20 final size:20
Alignment explanation
Indices: 49839--49886 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
49829 TTCGTCTGTT
*
49839 GCCCGCTGGCCGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
* *
49859 GCCCGCCGTCTGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
*
49879 GTCCGCCG
1 GCCCGCCG
49887 CCACACTCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.00, C:0.54, G:0.33, T:0.12
Consensus pattern (20 bp):
GCCCGCCGGCCGCTGCCGCC
Found at i:56709 original size:15 final size:16
Alignment explanation
Indices: 56680--56710 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56670 TGTTGGTATC
56680 TTAATTTTGAATTAAT
1 TTAATTTTGAATTAAT
56696 TTAATTTT-AATTAAT
1 TTAATTTTGAATTAAT
56711 GATTTTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTAATTTTGAATTAAT
Found at i:60735 original size:65 final size:63
Alignment explanation
Indices: 60589--60737 Score: 169
Period size: 65 Copynumber: 2.3 Consensus size: 63
60579 ATGCATGGTT
* *
60589 GATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATC
1 GATGCATGGTTGGTGCATCGATGCATCAAATGCATTCAATG-TTTCATAAAAT-CTCAGTGCATC
* **
60654 GATGCATGGTAT-GTGCATCGATGCATGAAATGCATTCAATG-TTCAATTTAAT-TCATGGTGCA
1 GATGCATGGT-TGGTGCATCGATGCATCAAATGCATTCAATGTTTC-ATAAAATCTCA--GTGCA
60716 TC
62 TC
60718 GATGCATGGATTGGTGCATC
1 GATGCATGG-TTGGTGCATC
60738 ACTCTAAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 22 0.30
65 44 0.60
66 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GATGCATGGTTGGTGCATCGATGCATCAAATGCATTCAATGTTTCATAAAATCTCAGTGCATC
Found at i:63390 original size:23 final size:22
Alignment explanation
Indices: 63358--63434 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
63348 TGGCCTTGTG
63358 CATCGATGCACATTCAAGGTGT
1 CATCGATGCACATTCAAGGTGT
* * *
63380 ACATCGGTGCACCTTCATGGTGT
1 -CATCGATGCACATTCAAGGTGT
*
63403 -ATCGATGCACATTTAAGGATG-
1 CATCGATGCACATTCAAGG-TGT
*
63424 AATCGATGCAC
1 CATCGATGCAC
63435 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.31
22 12 0.27
23 19 0.42
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGTGT
Found at i:63450 original size:20 final size:21
Alignment explanation
Indices: 63359--63453 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
63349 GGCCTTGTGC
*
63359 ATCGATGCACATTCAAGGTGT
1 ATCGATGCACATTTAAGGTGT
* * * *
63380 ACATCGGTGCACCTTCATGGTGT
1 --ATCGATGCACATTTAAGGTGT
*
63403 ATCGATGCACATTTAAGGATGA
1 ATCGATGCACATTTAAGG-TGT
63425 ATCGATGCAC-TGTT-AGGTGT
1 ATCGATGCACAT-TTAAGGTGT
63445 ATCGATGCA
1 ATCGATGCA
63454 TGAAGCACAA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.18
21 18 0.30
22 14 0.23
23 18 0.30
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (21 bp):
ATCGATGCACATTTAAGGTGT
Found at i:63452 original size:42 final size:44
Alignment explanation
Indices: 63359--63453 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
63349 GGCCTTGTGC
*
63359 ATCGATGCACATTCAAGGTGTACATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGTACATCGATGCACCTTCATGGTGT
* *
63403 ATCGATGCACATTTAAGGATG-A-ATCGATGCA-CTGTTA-GGTGT
1 ATCGATGCACATTCAAGG-TGTACATCGATGCACCT-TCATGGTGT
63445 ATCGATGCA
1 ATCGATGCA
63454 TGAAGCACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 16 0.35
43 10 0.22
44 18 0.39
45 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGTGTACATCGATGCACCTTCATGGTGT
Found at i:67927 original size:18 final size:17
Alignment explanation
Indices: 67873--67921 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
67863 TTGGACCCTT
* *
67873 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
67891 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
67909 AGTGCATTCGATG
1 AGTGCA-TCGATG
67922 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:69060 original size:21 final size:21
Alignment explanation
Indices: 69036--69079 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
69026 ACGGTGCCGG
* *
69036 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
69057 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
69078 AG
1 AG
69080 TTCCCGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:74156 original size:29 final size:30
Alignment explanation
Indices: 74123--74191 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
74113 AAAACATTTT
74123 AAAAC-TTTGAATAAATTCAATT-AAGTCCA
1 AAAACATTT-AATAAATTCAATTCAAGTCCA
*
74152 AAAACATTTTATAAATTCAATTCAAGTCCA
1 AAAACATTTAATAAATTCAATTCAAGTCCA
74182 AAAACCATTT
1 AAAA-CATTT
74192 TGCCTTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 17 0.47
30 14 0.39
31 5 0.14
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAACATTTAATAAATTCAATTCAAGTCCA
Found at i:74181 original size:30 final size:30
Alignment explanation
Indices: 74133--74192 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
74123 AAAACTTTGA
74133 ATAAATTCAATTAAGTCCAAAAA-CATTTT
1 ATAAATTCAATTAAGTCCAAAAACCATTTT
74162 ATAAATTCAATTCAAGTCCAAAAACCATTTT
1 ATAAATTCAATT-AAGTCCAAAAACCATTTT
74193 GCCTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 12 0.41
30 11 0.38
31 6 0.21
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (30 bp):
ATAAATTCAATTAAGTCCAAAAACCATTTT
Found at i:77312 original size:34 final size:30
Alignment explanation
Indices: 77274--77342 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
77264 TTGATATAAC
77274 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
77308 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
77337 AATTTA
1 AATTTA
77343 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:77353 original size:29 final size:30
Alignment explanation
Indices: 77283--77342 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
77273 CAATTTAAGG
77283 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
77314 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
77343 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:77503 original size:20 final size:19
Alignment explanation
Indices: 77451--77512 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 19
77441 GCAATGCATC
77451 CCTGCAGTGCATCCATGCA
1 CCTGCAGTGCATCCATGCA
*
77470 CCTGCACTAGTGCATCGATGCA
1 CCTG--C-AGTGCATCCATGCA
77492 CCATGCAGTGCATCCATGCA
1 CC-TGCAGTGCATCCATGCA
77512 C
1 C
77513 TCAAACACCG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 4 0.11
20 14 0.38
21 2 0.05
22 15 0.41
23 2 0.05
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (19 bp):
CCTGCAGTGCATCCATGCA
Found at i:77578 original size:21 final size:21
Alignment explanation
Indices: 77552--77630 Score: 131
Period size: 21 Copynumber: 3.8 Consensus size: 21
77542 TGCATCCTTA
77552 TGTGCATCGATGCATCAAGGC
1 TGTGCATCGATGCATCAAGGC
77573 TGTGCATCGATGCATCAAGGC
1 TGTGCATCGATGCATCAAGGC
*
77594 TTTGCATCGATGCATCAAGGC
1 TGTGCATCGATGCATCAAGGC
* *
77615 TTTGCATTGATGCATC
1 TGTGCATCGATGCATC
77631 TTGTTGTGTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (21 bp):
TGTGCATCGATGCATCAAGGC
Found at i:79774 original size:65 final size:63
Alignment explanation
Indices: 79575--79785 Score: 207
Period size: 65 Copynumber: 3.3 Consensus size: 63
79565 TGCACTAAGA
* * * *
79575 GTGCATCGATGCATCAAGTGCATTCAATGTTTCA-AAAATAGC-CATAGTGCATCAATGCATGGC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAT--CTC--AGTGCATCGATGCATGGT
79638 TG
62 TG
*
79640 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
79705 -
63 G
* **
79705 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
79768 TG
62 TG
*
79770 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
79786 CTCTGAAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 22 0.18
65 84 0.67
66 7 0.06
67 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:80420 original size:15 final size:15
Alignment explanation
Indices: 80398--80437 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
80388 GAACAAAAAT
80398 CAAA-AGAAAAGAAA
1 CAAAGAGAAAAGAAA
*
80412 CAAAGAGAAAATAAA
1 CAAAGAGAAAAGAAA
80427 CAAAGA-AAAAG
1 CAAAGAGAAAAG
80438 GGACAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (15 bp):
CAAAGAGAAAAGAAA
Found at i:80422 original size:20 final size:19
Alignment explanation
Indices: 80372--80422 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
80362 CAAATCAAAG
*
80372 CAAAAAGAAAAGCAAAGAA
1 CAAAAAGAAAAGAAAAGAA
*
80391 CAAAAATCAAAAGAAAAGAAA
1 CAAAAA-GAAAAGAAAAG-AA
*
80412 CAAAGAGAAAA
1 CAAAAAGAAAA
80423 TAAACAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.23
20 13 0.50
21 7 0.27
ACGTcount: A:0.75, C:0.10, G:0.14, T:0.02
Consensus pattern (19 bp):
CAAAAAGAAAAGAAAAGAA
Found at i:81530 original size:32 final size:32
Alignment explanation
Indices: 81493--81580 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 32
81483 GAACAATGGA
* * *
81493 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATTTTTGGAGATTCAACATCAAATATTG
*
81525 GGGCATTTTTGGAGATTCAACATCGAATATTG
1 GGGCATTTTTGGAGATTCAACATCAAATATTG
*
81557 GGGCATTTTTGGGGATTCAACATC
1 GGGCATTTTTGGAGATTCAACATC
81581 CTGATGCGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (32 bp):
GGGCATTTTTGGAGATTCAACATCAAATATTG
Found at i:82401 original size:65 final size:64
Alignment explanation
Indices: 82299--82468 Score: 217
Period size: 65 Copynumber: 2.7 Consensus size: 64
82289 CAAACAATAT
* **
82299 TCAAGA-TGGA-TTTAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTTGTGAAATTTAC
1 TCAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAA-CAAC
** *
82362 TCAAGATTGGATTTTAACTTCATGACGAAGGATATCCAACTCAAAACCAATTTGGTGAAACAAC
1 TCAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAAC
* *
82426 -C---CTTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGC
1 TCAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGC
82469 TCAACTTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
60 37 0.39
63 7 0.07
64 6 0.06
65 44 0.47
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (64 bp):
TCAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAACAAC
Found at i:82593 original size:124 final size:124
Alignment explanation
Indices: 82428--82654 Score: 395
Period size: 124 Copynumber: 1.8 Consensus size: 124
82418 GAAACAACCC
*
82428 TTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
* *
82493 CCACGATTTCAACTTC-GTGACGAA-GAATATCGTGCCCACAAGCAGTATCCATCTCTAGA
66 CCACAATTTCAACTTCACT-ACGAAGGAA-ATCGTGCCCACAAGCAGTATCCATCTCTAGA
82552 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
82617 CCACAATTTCAACTTCACTACGAAGGAAATCGTGCCCA
66 CCACAATTTCAACTTCACTACGAAGGAAATCGTGCCCA
82655 ACGGATCGAC
Statistics
Matches: 98, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
124 94 0.96
125 4 0.04
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.23
Consensus pattern (124 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
CCACAATTTCAACTTCACTACGAAGGAAATCGTGCCCACAAGCAGTATCCATCTCTAGA
Found at i:82634 original size:32 final size:32
Alignment explanation
Indices: 82556--82643 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 32
82546 TCTAGATTGG
* *
82556 ATTTCAACTTCACAACGAAGGATATCCAATTCAA
1 ATTTCAACTTCACAACGAAGG--AGCCAATCCAA
**
82590 AGCTCAACTTCACAACGAAGGAGCC-ATCCACA
1 ATTTCAACTTCACAACGAAGGAGCCAATCCA-A
*
82622 ATTTCAACTTCACTACGAAGGA
1 ATTTCAACTTCACAACGAAGGA
82644 AATCGTGCCC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 4 0.09
32 23 0.50
34 19 0.41
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (32 bp):
ATTTCAACTTCACAACGAAGGAGCCAATCCAA
Found at i:82896 original size:82 final size:85
Alignment explanation
Indices: 82709--82897 Score: 204
Period size: 85 Copynumber: 2.3 Consensus size: 85
82699 CAGCCCAGTG
* * * *
82709 CAGCATAGCTCAAGATGAGAAGAGCTATATTTCAACAATAATTTTAAAGTTTGATTCCATCCAGC
1 CAGCATAGCTCAAGATGAGAAGAGCTATATGTCAACAATAACTTTAAAGTTCGATTACATCCAGC
* * * *
82774 TTAGGGGCTTATCAAATTTA
66 TCAAGGGCTAACCAAATTTA
* * ** * * * *
82794 TAGCATAGCTTAAGGCGAGAAGAGCTATATGTCAGCAA-ACCTTT-GAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGATGAGAAGAGCTATATGTCAACAATAACTTTAAAGTTCGATTACATCCAGC
82857 TCAAGGGC-AACCAAATTTA
66 TCAAGGGCTAACCAAATTTA
*
82876 CAGCATAACTCAAGATGAGAAG
1 CAGCATAGCTCAAGATGAGAAG
82898 GGTTATCTGT
Statistics
Matches: 83, Mismatches: 21, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
82 26 0.31
83 21 0.25
84 4 0.05
85 32 0.39
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (85 bp):
CAGCATAGCTCAAGATGAGAAGAGCTATATGTCAACAATAACTTTAAAGTTCGATTACATCCAGC
TCAAGGGCTAACCAAATTTA
Found at i:83699 original size:16 final size:17
Alignment explanation
Indices: 83678--83710 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
83668 AGTGACCAGC
83678 GGTGGT-GAATAGTGAT
1 GGTGGTCGAATAGTGAT
83694 GGTGGTCGGAATAGTGA
1 GGTGGTC-GAATAGTGA
83711 CCAACGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.03, G:0.45, T:0.27
Consensus pattern (17 bp):
GGTGGTCGAATAGTGAT
Found at i:84261 original size:27 final size:28
Alignment explanation
Indices: 84231--84286 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
84221 CTTTTAGACA
*
84231 TTAATA-TTTTCTTAATTATTGTTTATT
1 TTAATATTTTTCTTAATTATTATTTATT
*
84258 TTAATATTTTTCTTAATTTTTATTTATT
1 TTAATATTTTTCTTAATTATTATTTATT
84286 T
1 T
84287 CTCTTGTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (28 bp):
TTAATATTTTTCTTAATTATTATTTATT
Found at i:84313 original size:3 final size:3
Alignment explanation
Indices: 84307--84331 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
84297 ATTTTTTTCA
84307 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
84332 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:87166 original size:15 final size:14
Alignment explanation
Indices: 87138--87177 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
87128 AAAGAAAAGA
87138 AATAATAAAAAAAT
1 AATAATAAAAAAAT
87152 AATAATAAAACAAAT
1 AATAATAAAA-AAAT
*
87167 ATTAATAAAAA
1 AATAATAAAAA
87178 TGATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAATAAAAAAAT
Found at i:88804 original size:34 final size:33
Alignment explanation
Indices: 88728--88805 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 33
88718 TACTTACTGT
*
88728 TATAATATATATATATTAAAAACTATATATATT
1 TATAATATATATATATTAAAAACTATATATATA
* * *
88761 TTTAGATATATATATTTTCAAAA-TATATCATATA
1 TATA-ATATATATATATTAAAAACTATAT-ATATA
88795 TAT-ATATATAT
1 TATAATATATAT
88806 TCAAAATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
32 8 0.21
33 8 0.21
34 22 0.58
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (33 bp):
TATAATATATATATATTAAAAACTATATATATA
Found at i:88822 original size:28 final size:28
Alignment explanation
Indices: 88766--88823 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
88756 ATATTTTTAG
* *
88766 ATATATATATTTTCAAAATATATCATAT
1 ATATATATATATTCAAAATATAACATAT
88794 ATATATATATATTCAAAATATGAAC-TAT
1 ATATATATATATTCAAAATAT-AACATAT
88822 AT
1 AT
88824 TGCATGACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (28 bp):
ATATATATATATTCAAAATATAACATAT
Found at i:90189 original size:12 final size:12
Alignment explanation
Indices: 90174--90198 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90164 TAACCTCGAA
90174 GATTGTAATAAT
1 GATTGTAATAAT
90186 GATTGTAATAAT
1 GATTGTAATAAT
90198 G
1 G
90199 CCTGAAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (12 bp):
GATTGTAATAAT
Found at i:93999 original size:13 final size:13
Alignment explanation
Indices: 93981--94005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93971 GCTGTCTCAC
93981 ATAAATAATATAA
1 ATAAATAATATAA
93994 ATAAATAATATA
1 ATAAATAATATA
94006 TATGTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAATAATATAA
Found at i:97036 original size:32 final size:32
Alignment explanation
Indices: 96985--97063 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
96975 CCCCTCCAAG
* * *
96985 GCAGTTGGGCGTGGACCAGACATGATCAACTT
1 GCAGCTGGGCGTGGTCCAGACAGGATCAACTT
* * **
97017 GTAGCTTGGCGTGGTCCAGACAGGATCAGTTT
1 GCAGCTGGGCGTGGTCCAGACAGGATCAACTT
97049 GCAGCTGGGCGTGGT
1 GCAGCTGGGCGTGGT
97064 GTCGATGGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.19, C:0.20, G:0.37, T:0.24
Consensus pattern (32 bp):
GCAGCTGGGCGTGGTCCAGACAGGATCAACTT
Found at i:100879 original size:69 final size:69
Alignment explanation
Indices: 100797--100934 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
100787 TAACTTCTCA
*
100797 TTGAAATCTGAGGGTGTTTTGTGCTTTCGAGGTAAGTTGTGTGTGCCGAGGGATGAGGGTCTGAG
1 TTGAAATCTGAGGGTGTTTTGTGCTTTCGAGGTAAGTTATGTGTGCCGAGGGATGAGGGTCTGAG
100862 GCAT
66 GCAT
100866 TTGAAATCTGAGGGTGTTTTGTGCTTTCGAGGTAAGTTATGTGTGCCGAGGGATGAGGGTCTGAG
1 TTGAAATCTGAGGGTGTTTTGTGCTTTCGAGGTAAGTTATGTGTGCCGAGGGATGAGGGTCTGAG
100931 GCAT
66 GCAT
100935 GAGATTCTCG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.18, C:0.10, G:0.38, T:0.33
Consensus pattern (69 bp):
TTGAAATCTGAGGGTGTTTTGTGCTTTCGAGGTAAGTTATGTGTGCCGAGGGATGAGGGTCTGAG
GCAT
Found at i:111365 original size:48 final size:48
Alignment explanation
Indices: 111273--111365 Score: 107
Period size: 49 Copynumber: 1.9 Consensus size: 48
111263 TTCACTCCAA
* * * * *
111273 TTTGCCTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATTTATCGTG
1 TTTGCCTTTCATCGCGACTAGGAGGGCTCGATAGAGACACTTATCGTG
* *
111321 TTTGCCTTTTTATTGCGACTAGGAGGGCTCGATAG-GACACTTATC
1 TTTGCC-TTTCATCGCGACTAGGAGGGCTCGATAGAGACACTTATC
111366 CATCTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
48 14 0.38
49 23 0.62
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (48 bp):
TTTGCCTTTCATCGCGACTAGGAGGGCTCGATAGAGACACTTATCGTG
Found at i:111856 original size:12 final size:13
Alignment explanation
Indices: 111841--111874 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
111831 ATTTTTTTTT
111841 CAAAAAAAAAA-A
1 CAAAAAAAAAAGA
*
111853 CAAAAAAAAAAGG
1 CAAAAAAAAAAGA
111866 CAAAAAAAA
1 CAAAAAAAA
111875 GGCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAGA
Found at i:111857 original size:11 final size:11
Alignment explanation
Indices: 111843--111894 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
111833 TTTTTTTTCA
111843 AAAAAAAAAAC
1 AAAAAAAAAAC
111854 AAAAAAAAAAGGC
1 AAAAAAAAAA--C
**
111867 AAAAAAAAGGC
1 AAAAAAAAAAC
111878 AAAAAAACAAA-
1 AAAAAAA-AAAC
111889 AAAAAA
1 AAAAAA
111895 GCCAAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 24 0.71
12 1 0.03
13 9 0.26
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:111881 original size:20 final size:20
Alignment explanation
Indices: 111858--111910 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
111848 AAAAACAAAA
* *
111858 AAAAAAGGCAAAAAAAAGGC
1 AAAAAAGACAAAAAAAAGCC
111878 AAAAAA-ACAAAAAAAAAGCC
1 AAAAAAGAC-AAAAAAAAGCC
*
111898 AAAAAAGCCAAAA
1 AAAAAAGACAAAA
111911 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.75, C:0.13, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAGACAAAAAAAAGCC
Found at i:111882 original size:12 final size:12
Alignment explanation
Indices: 111841--111903 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 12
111831 ATTTTTTTTT
**
111841 CAAAAAAAAAAA
1 CAAAAAAAAAGG
111853 CAAAAAAAAAAGG
1 C-AAAAAAAAAGG
111866 C-AAAAAAAAGG
1 CAAAAAAAAAGG
111877 C--AAAAAAA--
1 CAAAAAAAAAGG
*
111885 CAAAAAAAAAGC
1 CAAAAAAAAAGG
111897 CAAAAAA
1 CAAAAAA
111904 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
8 1 0.02
10 14 0.32
11 11 0.25
12 8 0.18
13 10 0.23
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAGG
Found at i:111901 original size:11 final size:11
Alignment explanation
Indices: 111856--111903 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
111846 AAAAAAACAA
*
111856 AAAAAAAAGGC
1 AAAAAAAAGCC
*
111867 AAAAAAAAGGC
1 AAAAAAAAGCC
*
111878 -AAAAAAA-CA
1 AAAAAAAAGCC
111887 AAAAAAAAGCC
1 AAAAAAAAGCC
111898 AAAAAA
1 AAAAAA
111904 GCCAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 14 0.44
11 18 0.56
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGCC
Found at i:111901 original size:19 final size:19
Alignment explanation
Indices: 111841--111903 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
111831 ATTTTTTTTT
111841 CAAAAAAA-AAAACAAAAA-
1 CAAAAAAACAAAA-AAAAAG
** *
111859 -AAAAAGGCAAAAAAAAGG
1 CAAAAAAACAAAAAAAAAG
111877 CAAAAAAACAAAAAAAAAG
1 CAAAAAAACAAAAAAAAAG
111896 CCAAAAAA
1 -CAAAAAA
111904 GCCAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 9 0.26
18 4 0.11
19 15 0.43
20 7 0.20
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (19 bp):
CAAAAAAACAAAAAAAAAG
Found at i:114521 original size:9 final size:9
Alignment explanation
Indices: 114507--114533 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
114497 TAATAACTCG
114507 GATATTTCT
1 GATATTTCT
114516 GATATTTCT
1 GATATTTCT
114525 GATATTTCT
1 GATATTTCT
114534 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:119823 original size:17 final size:15
Alignment explanation
Indices: 119794--119844 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 15
119784 TCAACATTTT
*
119794 AAAA-GAAAATAAAG
1 AAAACGAAATTAAAG
119808 AAAACTTGAAATTAAAAG
1 AAAAC--GAAATT-AAAG
*
119826 AAAACGAAATTTAAG
1 AAAACGAAATTAAAG
119841 AAAA
1 AAAA
119845 AAAAAGAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
16 6 0.19
17 5 0.16
18 9 0.29
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.16
Consensus pattern (15 bp):
AAAACGAAATTAAAG
Found at i:127200 original size:20 final size:20
Alignment explanation
Indices: 127175--127258 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 20
127165 TTTTGGTGCA
127175 GAGGGAATCGATCCCCCCTT
1 GAGGGAATCGATCCCCCCTT
*
127195 GAGGGAA-CTGATTCCCCCTTT
1 GAGGGAATC-GA-TCCCCCCTT
* * *
127216 GAAGAGGAACCGATTCCCCCTA
1 G-AG-GGAATCGATCCCCCCTT
*
127238 CAGGGGAATCGATACCCCCCT
1 GA-GGGAATCGAT-CCCCCCT
127259 GGGGTTCTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
19 1 0.02
20 9 0.18
21 18 0.36
22 15 0.30
23 6 0.12
24 1 0.02
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCTT
Found at i:127230 original size:23 final size:21
Alignment explanation
Indices: 127175--127236 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
127165 TTTTGGTGCA
* *
127175 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCTTT
*
127195 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTTT
127216 GAAGAGGAACCGATTCCCCCT
1 G-AG-GGAACCGATTCCCCCT
127237 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 2 0.06
23 15 0.43
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:134861 original size:18 final size:17
Alignment explanation
Indices: 134838--134876 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
134828 ATTAAAATCA
* *
134838 TTATTATTTTTATTGATT
1 TTATTATTATTAAT-ATT
134856 TTATTATTATTAATATT
1 TTATTATTATTAATATT
134873 TTAT
1 TTAT
134877 CAATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTATTATTATTAATATT
Found at i:135004 original size:17 final size:17
Alignment explanation
Indices: 134961--135008 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
134951 ATTTATAGAA
* *
134961 AATA-TTAAAAAATATT
1 AATATTTAAATAATAAT
134977 AATATTTTAAATAATAAT
1 AATA-TTTAAATAATAAT
134995 AATATTTAAATAAT
1 AATATTTAAATAAT
135009 TTTTATCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
18 14 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATTTAAATAATAAT
Found at i:135220 original size:20 final size:20
Alignment explanation
Indices: 135197--135243 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
135187 GTTTCCAAAT
*
135197 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTATAAA
*
135217 TCGCAACGCGAATTTATAAA
1 TCGCAACGCGAATCTATAAA
135237 TCGCAAC
1 TCGCAAC
135244 ACAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATCTATAAA
Found at i:135256 original size:60 final size:61
Alignment explanation
Indices: 135192--135344 Score: 172
Period size: 60 Copynumber: 2.5 Consensus size: 61
135182 ACCCAGTTTC
* * * *
135192 CAAATTCGCAACGCGAATCTGT-AAA-TCGCAACGCGA-ATTTATAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAAT-AGTCAAATTCGCAACGCGATAGTCA-AAATCGCAACACAAAAGT
* * *
135252 CAAATTTGCAATGC-AATAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATAGTCAAATTCGCAACGCGATAGTCAAAATCGCAACACAAAAGT
*
135312 CAAATTCGCAACGCGGAAT-TTCAAATTCGCAAC
1 CAAATTCGCAACGC-GAATAGTCAAATTCGCAAC
135345 TGAATTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
58 2 0.03
59 6 0.08
60 51 0.65
61 16 0.21
62 3 0.04
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.21
Consensus pattern (61 bp):
CAAATTCGCAACGCGAATAGTCAAATTCGCAACGCGATAGTCAAAATCGCAACACAAAAGT
Found at i:135262 original size:20 final size:21
Alignment explanation
Indices: 135237--135323 Score: 101
Period size: 20 Copynumber: 4.3 Consensus size: 21
135227 AATTTATAAA
135237 TCGCAACACAGA-AGTCAAAT
1 TCGCAACACAGATAGTCAAAT
* **
135257 TTGCAATGCA-ATAGTCAAAT
1 TCGCAACACAGATAGTCAAAT
*
135277 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGATAGTCAAAT
*
135297 TCGCAACACA-AAAGTCAAAT
1 TCGCAACACAGATAGTCAAAT
135317 TCGCAAC
1 TCGCAAC
135324 GCGGAATTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
19 1 0.02
20 56 0.98
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (21 bp):
TCGCAACACAGATAGTCAAAT
Found at i:135281 original size:40 final size:39
Alignment explanation
Indices: 135237--135363 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 39
135227 AATTTATAAA
* *
135237 TCGCAACACAGAAGTCAAATTTGCAATGCAATAGTCAAAT
1 TCGCAACGC-GAAGTCAAATTCGCAATGCAATAGTCAAAT
** *
135277 TCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGA-AGTCAAATTCGCAATGCAATAGTCAAAT
* *
135317 TCGCAACGCGGAATTTCAAATTCGCAACTG-AAT-TTCAAAT
1 TCGCAACGC-GAA-GTCAAATTCGCAA-TGCAATAGTCAAAT
135357 TCGCAAC
1 TCGCAAC
135364 TGAATTTCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
39 2 0.03
40 55 0.75
41 16 0.22
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (39 bp):
TCGCAACGCGAAGTCAAATTCGCAATGCAATAGTCAAAT
Found at i:135351 original size:19 final size:19
Alignment explanation
Indices: 135311--135420 Score: 123
Period size: 19 Copynumber: 5.6 Consensus size: 19
135301 AACACAAAAG
*
135311 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
135332 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
135351 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
135370 TCAAATTTGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
135390 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
135410 T-AATTTCGCAA
1 TCAAATTCGCAA
135421 TAGGTTTTAG
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 46 0.59
20 20 0.26
21 12 0.15
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:135355 original size:60 final size:59
Alignment explanation
Indices: 135192--135363 Score: 165
Period size: 60 Copynumber: 2.9 Consensus size: 59
135182 ACCCAGTTTC
* * *
135192 CAAATTCGCAACGCGAATCTGT-AAA-TCGCAACGCGAATTT-ATAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATAT-TCAAATTCGCAA--CGAATTTCA-AATTCGCAACACAAAAGT
* * * * *
135252 CAAATTTGCAATGC-AATAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATATTCAAATTCGCAACG-AAT-TTCAAATTCGCAACACAAAAGT
135312 CAAATTCGCAACGCGGAAT-TTCAAATTCGCAACTGAATTTCAAATTCGCAAC
1 CAAATTCGCAACGC-GAATATTCAAATTCGCAAC-GAATTTCAAATTCGCAAC
135364 TGAATTTCAA
Statistics
Matches: 91, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
58 3 0.03
59 8 0.09
60 60 0.66
61 16 0.18
62 4 0.04
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (59 bp):
CAAATTCGCAACGCGAATATTCAAATTCGCAACGAATTTCAAATTCGCAACACAAAAGT
Found at i:135382 original size:38 final size:39
Alignment explanation
Indices: 135271--135420 Score: 128
Period size: 40 Copynumber: 3.8 Consensus size: 39
135261 AATGCAATAG
* * **
135271 TCAAATTCGCAACGCG-ATAGTCAAATTCGCAAC-ACAAAAG
1 TCAAATTCGCAACG-GAAT-TTCAAATTCGCAACTA-GAATT
135311 TCAAATTCGCAACGCGGAATTTCAAATTCGCAACT-GAATT
1 TCAAATTCGCAA--CGGAATTTCAAATTCGCAACTAGAATT
* * *
135351 TCAAATTCGCAACTGAATTTCAAATTTGCAACTAGATTT
1 TCAAATTCGCAACGGAATTTCAAATTCGCAACTAGAATT
* * *
135390 TCGAATTCGCAACACGAATTT-AATTTCGCAA
1 TCAAATTCGCAAC-GGAATTTCAAATTCGCAA
135421 TAGGTTTTAG
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
38 19 0.20
39 24 0.26
40 32 0.34
41 14 0.15
42 4 0.04
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (39 bp):
TCAAATTCGCAACGGAATTTCAAATTCGCAACTAGAATT
Found at i:136702 original size:18 final size:18
Alignment explanation
Indices: 136679--136714 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
136669 AAGCAAAAGG
*
136679 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
136697 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
136715 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:137206 original size:64 final size:65
Alignment explanation
Indices: 137082--137210 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 65
137072 ATTTGACTTT
*
137082 CAAATAAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAATAAATCAACTTTTA
1 CAAATAAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAACAAATCAACTTTTA
* * * *
137147 CAAATCAATTATACAAGCAAAAAATAATTCTTATTTCCTCATC-AATTAAACAAATCAACTTTTA
1 CAAATAAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAACAAATCAACTTTTA
137211 ATGTAAAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
64 20 0.34
65 39 0.66
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (65 bp):
CAAATAAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAACAAATCAACTTTTA
Found at i:138610 original size:21 final size:21
Alignment explanation
Indices: 138586--138657 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
138576 GCGGGCGGGA
138586 CCTCTTGAATGATGACAGGGG
1 CCTCTTGAATGATGACAGGGG
* * **
138607 CCTCTTAAACGATGGGAGGGG
1 CCTCTTGAATGATGACAGGGG
* *
138628 CTTCTTCG-ATGATGAGTA-GGG
1 CCTCTT-GAATGATGA-CAGGGG
138649 CCTCTTGAA
1 CCTCTTGAA
138658 CGATAGGAGA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.26
Consensus pattern (21 bp):
CCTCTTGAATGATGACAGGGG
Found at i:138847 original size:12 final size:12
Alignment explanation
Indices: 138830--138868 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
138820 CCGCTGAAAT
*
138830 TAAATTAATACA
1 TAAATTAATAAA
*
138842 TAAATTAGTAAA
1 TAAATTAATAAA
*
138854 TAAATAAATAAA
1 TAAATTAATAAA
138866 TAA
1 TAA
138869 TGTCGAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (12 bp):
TAAATTAATAAA
Found at i:138992 original size:21 final size:21
Alignment explanation
Indices: 138968--139014 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
138958 AACAATCTCG
138968 CGTAGAGT-GACAACCTCACCA
1 CGTAGAGTAGA-AACCTCACCA
* *
138989 CGTAAAGTAGATACCTCACCA
1 CGTAGAGTAGAAACCTCACCA
139010 CGTAG
1 CGTAG
139015 CGCACCATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (21 bp):
CGTAGAGTAGAAACCTCACCA
Found at i:140879 original size:20 final size:20
Alignment explanation
Indices: 140856--140896 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
140846 CTTAAATTCA
140856 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
* *
140876 CAACGTGAAAATTAAAATCG
1 CAACGCGAAAATGAAAATCG
140896 C
1 C
140897 GTTGCGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAATGAAAATCG
Found at i:141485 original size:20 final size:20
Alignment explanation
Indices: 141459--141648 Score: 146
Period size: 20 Copynumber: 9.2 Consensus size: 20
141449 TTCCGCGTTA
141459 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* * * * *
141479 TGAATTTGGCTATCGCGTTG
1 CGAATTTGACTTTTGTGTTG
141499 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
*
141519 CGAATTTGACTTTTCTGTTG
1 CGAATTTGACTTTTGTGTTG
* * * *
141539 CAAATTTGACTATCGCGTTG
1 CGAATTTGACTTTTGTGTTG
* *
141559 CGAATTTGAATTCTGTGTTACGATTTA
1 CGAATTTGACTT-T-TG-T--G--TTG
* *
141586 CAAATTCGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* * * *
141606 CGAATTTGACTATCGCGTTA
1 CGAATTTGACTTTTGTGTTG
*
141626 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTTTGTGTTG
141646 CGA
1 CGA
141649 TTTACAGATT
Statistics
Matches: 126, Mismatches: 37, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
20 107 0.85
21 1 0.01
22 2 0.02
24 1 0.01
25 3 0.02
26 1 0.01
27 11 0.09
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (20 bp):
CGAATTTGACTTTTGTGTTG
Found at i:141525 original size:60 final size:60
Alignment explanation
Indices: 141459--141648 Score: 227
Period size: 60 Copynumber: 3.0 Consensus size: 60
141449 TTCCGCGTTA
* *
141459 CGAATTTGACTTTTGTGTTGTGAATTTGGCTATCGCGTTGCGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTG
* * *
141519 CGAATTTGACTTTTCTGTTGCAAATTTGACTATCGCGTTGCGAATTTGAATTCTGTGTTACGATT
1 CGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-T-TG-T--G--T
*
141584 TA
59 TG
* * * *
141586 CAAATTCGACTTTTGTGTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTG
141646 CGA
1 CGA
141649 TTTACAGATT
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
60 51 0.47
61 1 0.01
62 3 0.03
63 1 0.01
64 1 0.01
65 3 0.03
67 48 0.44
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (60 bp):
CGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTG
Found at i:141539 original size:40 final size:40
Alignment explanation
Indices: 141435--141648 Score: 173
Period size: 40 Copynumber: 5.2 Consensus size: 40
141425 GTGTTTCGCA
*
141435 TTGCGAATTTGA-AATTCCGCGTTACGAATTTGACTTTTGTG
1 TTGCGAATTTGACTA-T-CGCGTTACGAATTTGACTTTTGTG
* * *
141476 TTGTGAATTTGGCTATCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGCGTTACGAATTTGACTTTTGTG
* * * * * * *
141516 TTGCGAATTTGACTTTTC-TGTTGCAAATTTGACTATCGCG
1 TTGCGAATTTGAC-TATCGCGTTACGAATTTGACTTTTGTG
* * *
141556 TTGCGAATTTGAAT-TCTGTGTTACGATTTACAAATTCGACTTTTGTG
1 TTGCGAATTTGACTATC---G---CG--TTACGAATTTGACTTTTGTG
*
141603 TTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGTG
1 TTGCGAATTTGACTATCGCGTTACGAATTTGACTTTTGTG
141643 TTGCGA
1 TTGCGA
141649 TTTACAGATT
Statistics
Matches: 138, Mismatches: 23, Indels: 25
0.74 0.12 0.13
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 86 0.62
41 14 0.10
42 3 0.02
45 2 0.01
47 28 0.20
48 2 0.01
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (40 bp):
TTGCGAATTTGACTATCGCGTTACGAATTTGACTTTTGTG
Found at i:141634 original size:67 final size:67
Alignment explanation
Indices: 141521--141660 Score: 217
Period size: 67 Copynumber: 2.1 Consensus size: 67
141511 TTGTGTTGCG
* *
141521 AATTTGACTTTTCTGTTGCAAATTTGACTATCGCGTTGCGAATTTGAATTCTGTGTTACGATTTA
1 AATTCGACTTTTCTGTTGCAAATTTGACTATCGCGTTACGAATTTGAATTCTGTGTTACGATTTA
141586 CA
66 CA
* * * *
141588 AATTCGACTTTTGTGTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGATTTA
1 AATTCGACTTTTCTGTTGCAAATTTGACTATCGCGTTACGAATTTGAATTCTGTGTTACGATTTA
141653 CA
66 CA
*
141655 GATTCG
1 AATTCG
141661 CGTTGCGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (67 bp):
AATTCGACTTTTCTGTTGCAAATTTGACTATCGCGTTACGAATTTGAATTCTGTGTTACGATTTA
CA
Found at i:141662 original size:40 final size:40
Alignment explanation
Indices: 141583--141670 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
141573 GTGTTACGAT
* * *
141583 TTACAAATTCGACTTTTGTGTTGCGAATTTGACTATCGCG
1 TTACGAATTCGACTTCTGTGTTGCGAATTTGACGATCGCG
*
141623 TTACGAATTTGACTTCTGTGTTGCG-ATTT-ACAGATTCGCG
1 TTACGAATTCGACTTCTGTGTTGCGAATTTGAC-GA-TCGCG
*
141663 TTGCGAAT
1 TTACGAAT
141671 CTGGAAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.05
39 5 0.12
40 34 0.83
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (40 bp):
TTACGAATTCGACTTCTGTGTTGCGAATTTGACGATCGCG
Found at i:141747 original size:20 final size:20
Alignment explanation
Indices: 141722--141771 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
141712 TTACATATTC
141722 GCGTTGCGAAATTGGAAATT
1 GCGTTGCGAAATTGGAAATT
* **
141742 GGGTTGCGAAATTGGAGTTT
1 GCGTTGCGAAATTGGAAATT
141762 GCGTTGCGAA
1 GCGTTGCGAA
141772 TTTGTTGGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.30
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAAATT
Found at i:143221 original size:38 final size:38
Alignment explanation
Indices: 143194--143584 Score: 562
Period size: 38 Copynumber: 10.3 Consensus size: 38
143184 TTTTAATTTT
*
143194 TTTTTTGAAAATGTATATAATATATAGTTTTGAAAACA
1 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
* * *
143232 TTTTTGGAAAGCGTATATAAAATATAGTTTTGAAAACA
1 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
143270 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
1 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
*
143308 TTTTTAGAAAACGTATATAATATATAGTTTTGAAAACA
1 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
143346 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
1 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
*
143384 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAATA
1 TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
143422 TTTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
1 -TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
* * *
143461 -TTTTTGAAAACATATATAATATATAGCTTTTTAAAAAA
1 TTTTTTGAAAACGTATATAATATATAG-TTTTGAAAACA
* *
143499 TATCTTTTGAAAACG--TATAATATATAGTTTTAAAAAAA
1 T-T-TTTTGAAAACGTATATAATATATAGTTTTGAAAACA
*
143537 TGATTTTTG-AAAC--ATATAATATA-ATTTTTGAAAACA
1 T--TTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
143573 TGTTTTTGAAAA
1 T-TTTTTGAAAA
143585 TATATTATAT
Statistics
Matches: 325, Mismatches: 20, Indels: 18
0.90 0.06 0.05
Matches are distributed among these distances:
35 6 0.02
36 14 0.04
37 38 0.12
38 205 0.63
39 51 0.16
40 1 0.00
41 10 0.03
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (38 bp):
TTTTTTGAAAACGTATATAATATATAGTTTTGAAAACA
Found at i:160551 original size:43 final size:43
Alignment explanation
Indices: 160503--160588 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
160493 CTCTAGGGTT
160503 TAATAAAATATTATAAAATCAATAATCTCCAAAAAGCAGTCCA
1 TAATAAAATATTATAAAATCAATAATCTCCAAAAAGCAGTCCA
160546 TAATAAAATATTATAAAATCAATAATCTCCAAAAAGCAGTCCA
1 TAATAAAATATTATAAAATCAATAATCTCCAAAAAGCAGTCCA
160589 CAAGCCGGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (43 bp):
TAATAAAATATTATAAAATCAATAATCTCCAAAAAGCAGTCCA
Found at i:163058 original size:184 final size:184
Alignment explanation
Indices: 162749--163116 Score: 700
Period size: 184 Copynumber: 2.0 Consensus size: 184
162739 TCGGCTGTCA
*
162749 ACACACATACGCCAAGAACCATCTTTCTTTGGCACTAATAGAGCAGGGACTGCACATGGGCTCAT
1 ACACACATACACCAAGAACCATCTTTCTTTGGCACTAATAGAGCAGGGACTGCACATGGGCTCAT
*
162814 ACTCTCTCGGATATAGCCCCTCTCCAATAACTCTTCCACCTGTCGCTGCAACTCTTCGGCCTCCT
66 ACTCTCTCGGATATAGCCCCTCTCCAACAACTCTTCCACCTGTCGCTGCAACTCTTCGGCCTCCT
* *
162879 TGGGACTGAGGCGATATGCTGGTCGATTTTGCAAACTTGACCCAGGAACAAGGT
131 TGGGACTGAGGCGATATGCTGGTCGATTTGGCAAACTTAACCCAGGAACAAGGT
162933 ACACACATACACCAAGAACCATCTTTCTTTGGCACTAATAGAGCAGGGACTGCACATGGGCTCAT
1 ACACACATACACCAAGAACCATCTTTCTTTGGCACTAATAGAGCAGGGACTGCACATGGGCTCAT
162998 ACTCTCTCGGATATAGCCCCTCTCCAACAACTCTTCCACCTGTCGCTGCAACTCTTCGGCCTCCT
66 ACTCTCTCGGATATAGCCCCTCTCCAACAACTCTTCCACCTGTCGCTGCAACTCTTCGGCCTCCT
163063 TGGGACTGAGGCGATATGCTGGTCGATTTGGCAAACTTAACCCAGGAACAAGGT
131 TGGGACTGAGGCGATATGCTGGTCGATTTGGCAAACTTAACCCAGGAACAAGGT
163117 CAATTTGATG
Statistics
Matches: 180, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 180 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.24
Consensus pattern (184 bp):
ACACACATACACCAAGAACCATCTTTCTTTGGCACTAATAGAGCAGGGACTGCACATGGGCTCAT
ACTCTCTCGGATATAGCCCCTCTCCAACAACTCTTCCACCTGTCGCTGCAACTCTTCGGCCTCCT
TGGGACTGAGGCGATATGCTGGTCGATTTGGCAAACTTAACCCAGGAACAAGGT
Found at i:173280 original size:20 final size:21
Alignment explanation
Indices: 173255--173300 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
173245 AATTAATCCT
173255 ACTAATTATTAA-AGCTAAGA
1 ACTAATTATTAAGAGCTAAGA
173275 ACTAA-TATTAAGGAGCTAAGA
1 ACTAATTATTAA-GAGCTAAGA
173296 A-TAAT
1 ACTAAT
173301 GATTCAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.26
20 8 0.35
21 9 0.39
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (21 bp):
ACTAATTATTAAGAGCTAAGA
Found at i:173293 original size:21 final size:19
Alignment explanation
Indices: 173255--173300 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
173245 AATTAATCCT
173255 ACTAATTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
173275 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
173296 A-TAAT
1 ACTAAT
173301 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:180416 original size:607 final size:607
Alignment explanation
Indices: 179264--180474 Score: 2127
Period size: 607 Copynumber: 2.0 Consensus size: 607
179254 GTTTGGCTTG
* * *
179264 CATAGTAGATAACATGAAAAATTTTACTTTTTCGTCGCCCTAGAACTACTTCGAATGCATAGTCA
1 CATAGTAGATAACATGAAAAATTTTACTTTTTCGTCACCCTAGAACTACTCCCAATGCATAGTCA
*
179329 CTAGCATCACACATAAGCTCAAATGGTTCGTTCCAGTCTGGCGGGATAACTATTGGTGCTGCTGA
66 CTAGCATCACACATAAGCTCAAATGGTTCGTTCCACTCTGGCGGGATAACTATTGGTGCTGCTGA
* *
179394 AAGATTTTTCTTCAAATCTGTGAAGGCATTTAAATAATCATTAGTAAACTCAAATGGATGATTTT
131 AAGATTTTTCTTCAAATCTGTGAAGGCATTCAAATAATCATTAGTAAACTCAAATAGATGATTTT
*
179459 GTTGAAGCAAAATACATAAGGGTTTAAAGATTTGAGAAAAGTCTTTTATGAACCGCCTATAGAAT
196 GTTGAAGCAAAAGACATAAGGGTTTAAAGATTTGAGAAAAGTCTTTTATGAACCGCCTATAGAAT
* * * * *
179524 CCTGCATGTCCTAGGAAACTGTGTACACCTCGCACATTTGTAGGTGGGGGAAGATTTGTAATTGT
261 CCTGCATGTCCAAGGAAACTGCGTACACCTCGCACATTAGTAGGTGGGGGAAGATTTGCAATTGC
179589 ATCCACCTTGGCTTTGTCGACTTCGATGCCATGTCATGAAATTTTGTGTCCCAACACTACTCATT
326 ATCCACCTTGGCTTTGTCGACTTCGATGCCATGTCATGAAATTTTGTGTCCCAACACTACTCATT
179654 CAGTTACCATAAAATGGCATTTTTCCCATTTCAGCATTAGGTTGGCTTCTTCACAACGTTTCAAC
391 CAGTTACCATAAAATGGCATTTTTCCCATTTCAGCATTAGGTTGGCTTCTTCACAACGTTTCAAC
* *
179719 ATCTTGGATAAATTACCGAGGCATTGGTCAAAGTCATCACCTGAAACGGAGAAGTCGTCCATAAA
456 ATCTTGGATAAATTACCGAGGCATCGGTCAAAGTCATCACCCGAAACGGAGAAGTCGTCCATAAA
* * *
179784 TATTTCCATGAACTCTTCCACCATATCTGAAAAGATTTCCATTATGCATCCTTGGAATGTAGCTA
521 TATTTCCATGAACTCTTCCACCATATCTGAAAAGATTGCCATCATGCATCATTGGAATGTAGCTA
*
179849 GAGTGTTACACAGTCCAAATGA
586 GAGCGTTACACAGTCCAAATGA
* *
179871 CATAGTAGATAACATGAAAAATTTTACTTTTTCGTCACCCTAGCACTGCTCCCAATGCATAGTCA
1 CATAGTAGATAACATGAAAAATTTTACTTTTTCGTCACCCTAGAACTACTCCCAATGCATAGTCA
* *
179936 CTAGCGTCGCACATAAGCTCAAATGGTTCGTTCCACTCTGGCGGGATAACTATTGGTGCTGCTGA
66 CTAGCATCACACATAAGCTCAAATGGTTCGTTCCACTCTGGCGGGATAACTATTGGTGCTGCTGA
* *
180001 AAGCTTTTTCTTCAAATCTGTGAAGGCATTCAAATAATCTTTAGTAAACTCAAATAGATGATTTT
131 AAGATTTTTCTTCAAATCTGTGAAGGCATTCAAATAATCATTAGTAAACTCAAATAGATGATTTT
* *
180066 GTTGAAGCAAAAGACATAAGGGTTTAGAGATTTGAGAAAAGTCTTTTATGAACCGCCTATATAAT
196 GTTGAAGCAAAAGACATAAGGGTTTAAAGATTTGAGAAAAGTCTTTTATGAACCGCCTATAGAAT
180131 CCTGCATGTCCAAGGAAACTGCGTACACCTCGCACATTAGTAGGTGGGGGAAGATTTGCAATTGC
261 CCTGCATGTCCAAGGAAACTGCGTACACCTCGCACATTAGTAGGTGGGGGAAGATTTGCAATTGC
* *
180196 ATCCACCTTGGCTTTGTCGACTTCGATGCCATGTCATGAAATTTTGTGTCCCAACACTATTCCTT
326 ATCCACCTTGGCTTTGTCGACTTCGATGCCATGTCATGAAATTTTGTGTCCCAACACTACTCATT
*
180261 CAGTTACCATAAAATGGCATTTTTCCCATTTCAGTATTAGGTTGGCTTCTTCACAACGTTTCAAC
391 CAGTTACCATAAAATGGCATTTTTCCCATTTCAGCATTAGGTTGGCTTCTTCACAACGTTTCAAC
*
180326 ATCTTGGATAAATTACTGAGGCATCGGTCAAAGTCATCACCCGAAACGGAGAAGTCGTCCATAAA
456 ATCTTGGATAAATTACCGAGGCATCGGTCAAAGTCATCACCCGAAACGGAGAAGTCGTCCATAAA
180391 TATTTCCATGAACAT-TTCCACCATATCTGAAAAGATTGCCATCATGCATCATTGGAATGTAGCT
521 TATTTCCATGAAC-TCTTCCACCATATCTGAAAAGATTGCCATCATGCATCATTGGAATGTAGCT
*
180455 GGAGCGTTACACAGTCCAAA
585 AGAGCGTTACACAGTCCAAA
180475 CGGCATTCGC
Statistics
Matches: 572, Mismatches: 31, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
607 571 1.00
608 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (607 bp):
CATAGTAGATAACATGAAAAATTTTACTTTTTCGTCACCCTAGAACTACTCCCAATGCATAGTCA
CTAGCATCACACATAAGCTCAAATGGTTCGTTCCACTCTGGCGGGATAACTATTGGTGCTGCTGA
AAGATTTTTCTTCAAATCTGTGAAGGCATTCAAATAATCATTAGTAAACTCAAATAGATGATTTT
GTTGAAGCAAAAGACATAAGGGTTTAAAGATTTGAGAAAAGTCTTTTATGAACCGCCTATAGAAT
CCTGCATGTCCAAGGAAACTGCGTACACCTCGCACATTAGTAGGTGGGGGAAGATTTGCAATTGC
ATCCACCTTGGCTTTGTCGACTTCGATGCCATGTCATGAAATTTTGTGTCCCAACACTACTCATT
CAGTTACCATAAAATGGCATTTTTCCCATTTCAGCATTAGGTTGGCTTCTTCACAACGTTTCAAC
ATCTTGGATAAATTACCGAGGCATCGGTCAAAGTCATCACCCGAAACGGAGAAGTCGTCCATAAA
TATTTCCATGAACTCTTCCACCATATCTGAAAAGATTGCCATCATGCATCATTGGAATGTAGCTA
GAGCGTTACACAGTCCAAATGA
Found at i:184181 original size:21 final size:19
Alignment explanation
Indices: 184143--184188 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
184133 AATTAATCCT
184143 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
184163 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
184184 A-TAAT
1 ACTAAT
184189 GATTTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:191283 original size:26 final size:26
Alignment explanation
Indices: 191253--191332 Score: 151
Period size: 26 Copynumber: 3.1 Consensus size: 26
191243 GACAAAAAAG
191253 TTAAAAGAAATTATACGATAGTGGAA
1 TTAAAAGAAATTATACGATAGTGGAA
*
191279 TTAAAAGAAATTATACGATAGTTGAA
1 TTAAAAGAAATTATACGATAGTGGAA
191305 TTAAAAGAAATTATACGATAGTGGAA
1 TTAAAAGAAATTATACGATAGTGGAA
191331 TT
1 TT
191333 CTTTTGTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.30
Consensus pattern (26 bp):
TTAAAAGAAATTATACGATAGTGGAA
Found at i:196429 original size:15 final size:16
Alignment explanation
Indices: 196411--196449 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
196401 ATAATAAAAA
196411 TGAAAATAAAATATT-
1 TGAAAATAAAATATTG
196426 TGAAAAT-AAATATTG
1 TGAAAATAAAATATTG
*
196441 AGAAAATAA
1 TGAAAATAA
196450 TATCAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 13 0.62
16 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (16 bp):
TGAAAATAAAATATTG
Found at i:207739 original size:114 final size:114
Alignment explanation
Indices: 207533--207760 Score: 395
Period size: 114 Copynumber: 2.0 Consensus size: 114
207523 GTGCACTATA
207533 CTTCTCTAACGAGACTCAATCGATGCGACAACGACGTTCAGACAATGGCAAGGGAGATAACACAA
1 CTTCTCTAACGAGACTCAATCGATGCGACAACGACGTTCAGACAATGGCAAGGGAGATAACACAA
*
207598 ATAGTAGATAAGGACTATGTCATCATAGCAACATGTGGCATTATATATC
66 ATAGTAGATAAGGACTACGTCATCATAGCAACATGTGGCATTATATATC
* * **
207647 CTTCTCTAATGAGACTCAATCGATGCGACAACGACGTTCAGACAATGGCAAGGGAGATATCATGA
1 CTTCTCTAACGAGACTCAATCGATGCGACAACGACGTTCAGACAATGGCAAGGGAGATAACACAA
207712 ATAGTAGATAAGGACTACGTCGA-CATAGCAACATGTGGCATTATATATC
66 ATAGTAGATAAGGACTACGTC-ATCATAGCAACATGTGGCATTATATATC
207761 GACCGCCTCG
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 107 0.99
115 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (114 bp):
CTTCTCTAACGAGACTCAATCGATGCGACAACGACGTTCAGACAATGGCAAGGGAGATAACACAA
ATAGTAGATAAGGACTACGTCATCATAGCAACATGTGGCATTATATATC
Found at i:211552 original size:27 final size:27
Alignment explanation
Indices: 211522--211591 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 27
211512 AACAACAACG
*
211522 ACTCTGTTAACAACTCCAATAATAGTA
1 ACTCTGTTAACAACTCCAATAATAGCA
211549 ACTCTGTTAACAACAACTCCAATAATAGCA
1 ACTCTGTT---AACAACTCCAATAATAGCA
* *
211579 ACTCCGATAACAA
1 ACTCTGTTAACAA
211592 AATACAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 13 0.35
30 24 0.65
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (27 bp):
ACTCTGTTAACAACTCCAATAATAGCA
Found at i:211566 original size:30 final size:30
Alignment explanation
Indices: 211530--211591 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
211520 CGACTCTGTT
* * *
211530 AACAACTCCAATAATAGTAACTCTGTTAAC
1 AACAACTCCAATAATAGCAACTCCGATAAC
211560 AACAACTCCAATAATAGCAACTCCGATAAC
1 AACAACTCCAATAATAGCAACTCCGATAAC
211590 AA
1 AA
211592 AATACAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.47, C:0.26, G:0.06, T:0.21
Consensus pattern (30 bp):
AACAACTCCAATAATAGCAACTCCGATAAC
Found at i:211580 original size:15 final size:15
Alignment explanation
Indices: 211532--211588 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
211522 ACTCTGTTAA
211532 CAACTCCAATAATAG
1 CAACTCCAATAATAG
* *** * *
211547 TAACTCTGTTAACAA
1 CAACTCCAATAATAG
211562 CAACTCCAATAATAG
1 CAACTCCAATAATAG
*
211577 CAACTCCGATAA
1 CAACTCCAATAA
211589 CAAAATACAA
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (15 bp):
CAACTCCAATAATAG
Found at i:218167 original size:16 final size:17
Alignment explanation
Indices: 218146--218180 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
218136 TTTTACCGGA
*
218146 TTAAAAA-CTGATTTTT
1 TTAAAAATCTAATTTTT
218162 TTAAAAATCTAATTTTT
1 TTAAAAATCTAATTTTT
218179 TT
1 TT
218181 CAAACCGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAAAATCTAATTTTT
Found at i:235685 original size:23 final size:23
Alignment explanation
Indices: 235628--235685 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
235618 AAAGATGATG
235628 TTGTTGTGCTTTTAGAACCCTTC
1 TTGTTGTGCTTTTAGAACCCTTC
* *
235651 TTGTTATACTTTTAGAACCCTTC
1 TTGTTGTGCTTTTAGAACCCTTC
235674 TTGTTGTGCTTT
1 TTGTTGTGCTTT
235686 CCCCTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.14, C:0.19, G:0.16, T:0.52
Consensus pattern (23 bp):
TTGTTGTGCTTTTAGAACCCTTC
Found at i:236875 original size:246 final size:246
Alignment explanation
Indices: 236441--236906 Score: 905
Period size: 246 Copynumber: 1.9 Consensus size: 246
236431 AAAGGTTTGC
236441 TTCCCCCTCAGGCCAAATGATGATGTTGTTTAGTCTTTAATTCATTCAAATGAGGGGTGCTTGAT
1 TTCCCCCTCAGGCCAAATGATGATGTTGTTTAGTCTTTAATTCATTCAAATGAGGGGTGCTTGAT
236506 GCCTTGGTTGAATGGTCTTGTAACTCTTCATGCTTGGAGCCTAAACTTGTGGTGTAGGATGCATG
66 GCCTTGGTTGAATGGTCTTGTAACTCTTCATGCTTGGAGCCTAAACTTGTGGTGTAGGATGCATG
236571 GTTGAATGGTTATACCCTCTACCAAAGGTGATGTGAGGTTTGACTATGGTGCTTGTTTGATGTCC
131 GTTGAATGGTTATACCCTCTACCAAAGGTGATGTGAGGTTTGACTATGGTGCTTGTTTGATGTCC
236636 AAGGCATCCACTTAGATAGGTAGGTAGCTTGTTTGTGGTGTTAGCTACATG
196 AAGGCATCCACTTAGATAGGTAGGTAGCTTGTTTGTGGTGTTAGCTACATG
*
236687 TTCCCCCTCAGGCCAAATGATGATGTTGTTTAGTCTTTAATTCATTCAAATGAGTGGTGCTTGAT
1 TTCCCCCTCAGGCCAAATGATGATGTTGTTTAGTCTTTAATTCATTCAAATGAGGGGTGCTTGAT
236752 GCCTTGGTTGAATGGTCTTGTAACTCTTCATGCTTGGAGCCTAAACTTGTGGTGTAGGATGCATG
66 GCCTTGGTTGAATGGTCTTGTAACTCTTCATGCTTGGAGCCTAAACTTGTGGTGTAGGATGCATG
236817 GTTGAATGGTTATACCCTCTACCAAAGGTGATGTGAGGTTTGACTATGGTGCTTGTTTGATGTCC
131 GTTGAATGGTTATACCCTCTACCAAAGGTGATGTGAGGTTTGACTATGGTGCTTGTTTGATGTCC
* *
236882 AAGGCATCCACTTAGGTAGTTAGGT
196 AAGGCATCCACTTAGATAGGTAGGT
236907 GAGTGTAAGC
Statistics
Matches: 217, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
246 217 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (246 bp):
TTCCCCCTCAGGCCAAATGATGATGTTGTTTAGTCTTTAATTCATTCAAATGAGGGGTGCTTGAT
GCCTTGGTTGAATGGTCTTGTAACTCTTCATGCTTGGAGCCTAAACTTGTGGTGTAGGATGCATG
GTTGAATGGTTATACCCTCTACCAAAGGTGATGTGAGGTTTGACTATGGTGCTTGTTTGATGTCC
AAGGCATCCACTTAGATAGGTAGGTAGCTTGTTTGTGGTGTTAGCTACATG
Found at i:237567 original size:108 final size:108
Alignment explanation
Indices: 237378--237574 Score: 324
Period size: 108 Copynumber: 1.8 Consensus size: 108
237368 AACTATAATT
* * *
237378 ATCTACATCACCATTAAATTATACGATGAAAGTTTGATCAGTATTGGAGTTTCAAATGTTATAAA
1 ATCTACATCACCAGTAAATTATACGATGAAAATTAGATCAGTATTGGAGTTTCAAATGTTATAAA
237443 AAATTGCGGCATTTAGATTTTTTTTAAAGTTGTGTGCGTGTGA
66 AAATTGCGGCATTTAGATTTTTTTTAAAGTTGTGTGCGTGTGA
* *
237486 ATCTACATCACTAGTAAATTATACGAAT-AAAATTAGATCGGTATTGGAGTTTCAAATGTTATAA
1 ATCTACATCACCAGTAAATTATACG-ATGAAAATTAGATCAGTATTGGAGTTTCAAATGTTATAA
*
237550 AAAATTGTGGCATTTAGATTTTTTT
65 AAAATTGCGGCATTTAGATTTTTTT
237575 AGAAGTAGTG
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 80 0.98
109 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (108 bp):
ATCTACATCACCAGTAAATTATACGATGAAAATTAGATCAGTATTGGAGTTTCAAATGTTATAAA
AAATTGCGGCATTTAGATTTTTTTTAAAGTTGTGTGCGTGTGA
Found at i:246049 original size:19 final size:20
Alignment explanation
Indices: 246009--246049 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
245999 AATATCAATA
*
246009 CAAATGCTTGATATTGATAT
1 CAAATGCTTGATAGTGATAT
*
246029 CAAATGCTTGGTAGT-ATAT
1 CAAATGCTTGATAGTGATAT
246048 CA
1 CA
246050 TTGATATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (20 bp):
CAAATGCTTGATAGTGATAT
Found at i:248212 original size:23 final size:21
Alignment explanation
Indices: 248185--248224 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
248175 CGGGAATGCA
248185 CATATATATGGTTTAAGGATG
1 CATATATATGGTTTAAGGATG
*
248206 CATATATCTGGTTTAAGGA
1 CATATATATGGTTTAAGGA
248225 AATCACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (21 bp):
CATATATATGGTTTAAGGATG
Found at i:250848 original size:24 final size:25
Alignment explanation
Indices: 250821--250870 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
250811 ATAAATGTAG
250821 TAATTAAAAT-AGATATTTTGTAAA
1 TAATTAAAATAAGATATTTTGTAAA
** *
250845 TAATTATTATAATATATTTTGTAAA
1 TAATTAAAATAAGATATTTTGTAAA
250870 T
1 T
250871 TTTGAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (25 bp):
TAATTAAAATAAGATATTTTGTAAA
Found at i:252713 original size:7 final size:7
Alignment explanation
Indices: 252701--252730 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
252691 TATTAAATTT
252701 AAGGGAA
1 AAGGGAA
252708 AAGGGAA
1 AAGGGAA
252715 AAGGGAA
1 AAGGGAA
252722 AAGGGAA
1 AAGGGAA
252729 AA
1 AA
252731 TAAGCATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (7 bp):
AAGGGAA
Found at i:253313 original size:42 final size:42
Alignment explanation
Indices: 253254--253350 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
253244 CTACTGAGAA
253254 TAGTACCGATACTATAGGCTAAAATGAGATAAATTAGATGAG
1 TAGTACCGATACTATAGGCTAAAATGAGATAAATTAGATGAG
*
253296 TAGTACCGATACTATAGGCTAAAATGAGATAAATTATATGAG
1 TAGTACCGATACTATAGGCTAAAATGAGATAAATTAGATGAG
*
253338 TAGTATCGATACT
1 TAGTACCGATACT
253351 GATTCAATCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (42 bp):
TAGTACCGATACTATAGGCTAAAATGAGATAAATTAGATGAG
Found at i:253915 original size:55 final size:55
Alignment explanation
Indices: 253824--254008 Score: 255
Period size: 55 Copynumber: 3.4 Consensus size: 55
253814 TCAGTAATAT
253824 GTACAGGCACTTTGTGTGCATATTCACGGAAATCATCATGGGTTGATGAATCACC
1 GTACAGGCACTTTGTGTGCATATTCACGGAAATCATCATGGGTTGATGAATCACC
* * * * *
253879 GTACATGCACTTTTTTTGCATATTCAAGGAATTCATCATGGGTTGATGAATCACC
1 GTACAGGCACTTTGTGTGCATATTCACGGAAATCATCATGGGTTGATGAATCACC
* * * **
253934 GTACATGCACTTTGTGTGCGA-ATCCACGGAAATCATCATGAGTTGATGAATCGTC
1 GTACAGGCACTTTGTGTGC-ATATTCACGGAAATCATCATGGGTTGATGAATCACC
*
253989 GTACAGGCACTATGTGTGCA
1 GTACAGGCACTTTGTGTGCA
254009 ACCCACGAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
54 1 0.01
55 112 0.98
56 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (55 bp):
GTACAGGCACTTTGTGTGCATATTCACGGAAATCATCATGGGTTGATGAATCACC
Found at i:260385 original size:55 final size:55
Alignment explanation
Indices: 260322--260583 Score: 321
Period size: 55 Copynumber: 4.8 Consensus size: 55
260312 TGTGTACTAT
* *** *
260322 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGGGTTGATAAATCATTGTAT
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGGGTTGATGAATCACCATAC
260377 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGGGTTGATGAATCACCATAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGGGTTGATGAATCACCATAC
* *
260432 AGGCACTTTGTGTGCATATTCACGAAATTCATCATGGGTTGATGAATCATCATAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGGGTTGATGAATCACCATAC
* * * * * *
260487 AGGCACTTTGTGTGTGA-ATCCATGAAATTCATCATGAGTTGATGAATCACCGTAC
1 AGGCACTTTGTGTG-CATATTCACGGAATTCATCATGGGTTGATGAATCACCATAC
* * * ** * *
260542 ATGCACTATGTATGCA-ACCCACGGAATTTATCATGAGTTGAT
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGGGTTGAT
260584 AAATTTCCGT
Statistics
Matches: 185, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
54 23 0.12
55 161 0.87
56 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (55 bp):
AGGCACTTTGTGTGCATATTCACGGAATTCATCATGGGTTGATGAATCACCATAC
Done.