Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008011.1 Hibiscus syriacus cultivar Beakdansim tig00110474_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: 1648842
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:149 original size:20 final size:19
Alignment explanation
Indices: 81--162 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
71 AAAAATGACT
81 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
100 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
114 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
133 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
153 ATCGC-ATGCG
1 ATCGCAATGCG
163 TTTATAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 24 0.44
20 14 0.25
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:215 original size:19 final size:19
Alignment explanation
Indices: 191--433 Score: 333
Period size: 19 Copynumber: 13.7 Consensus size: 19
181 GATTATCTCG
191 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
210 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
229 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
243 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
262 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
281 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
300 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
319 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
338 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
350 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
369 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
388 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
402 -TGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
421 TTGCGATTTTCAT
1 TTGCGATTTTCAT
434 GTTGGGATTT
Statistics
Matches: 201, Mismatches: 4, Indels: 37
0.83 0.02 0.15
Matches are distributed among these distances:
12 6 0.03
13 5 0.02
14 12 0.06
15 3 0.01
16 14 0.07
17 19 0.09
19 130 0.65
20 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:230 original size:52 final size:52
Alignment explanation
Indices: 169--433 Score: 419
Period size: 52 Copynumber: 5.0 Consensus size: 52
159 TGCGTTTATA
169 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
221 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
273 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT--ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
330 ATTTCGCATTGCGA-T-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
380 ATTTCGCATTGCGATTCTCTCG-TGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
432 AT
1 AT
434 GTTGGGATTT
Statistics
Matches: 201, Mismatches: 4, Indels: 16
0.91 0.02 0.07
Matches are distributed among these distances:
50 44 0.22
51 15 0.07
52 90 0.45
53 2 0.01
55 6 0.03
57 44 0.22
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2727 original size:12 final size:12
Alignment explanation
Indices: 2710--2734 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2700 TCTTCGGGGA
2710 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2722 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2734 C
1 C
2735 AGGATTATGA
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3650 original size:20 final size:20
Alignment explanation
Indices: 3622--4011 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
3612 AAATTTCAGT
* * * *
3622 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3642 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3662 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3682 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3702 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3722 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3742 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3762 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3782 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3802 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3822 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
3842 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
3863 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3883 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
3903 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
3923 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3943 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3963 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
3983 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
4003 GTTGCGATT
1 GTTGCGATT
4012 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:14987 original size:3 final size:3
Alignment explanation
Indices: 14976--15043 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
14966 TTTTTTTCCG
** *
14976 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
15022 TTT TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA
15044 CAATTTTTGC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15019 original size:20 final size:19
Alignment explanation
Indices: 14981--15043 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
14971 TTCCGTTATT
*
14981 TTATTATTATTATTA-TTA
1 TTATTATTATCATTATTTA
*
14999 TTATTATTATCGTTATCTTA
1 TTATTATTATCATTAT-TTA
* *
15019 TTATTTTTATTATTATTTA
1 TTATTATTATCATTATTTA
15038 TTATTA
1 TTATTA
15044 CAATTTTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 13 0.35
19 8 0.22
20 16 0.43
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTATTATCATTATTTA
Found at i:15131 original size:37 final size:37
Alignment explanation
Indices: 15085--15159 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
15075 TTCAGATTAC
15085 AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
1 AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
15122 AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
1 AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
15159 A
1 A
15160 CTCAGAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.43, G:0.19, T:0.03
Consensus pattern (37 bp):
AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
Found at i:15230 original size:25 final size:25
Alignment explanation
Indices: 15197--15294 Score: 171
Period size: 25 Copynumber: 3.9 Consensus size: 25
15187 AGCAGCCCGT
*
15197 CAGATTAGGGTTTCAAACCCTAAAT
1 CAGATTAGGGTTTCAAACCCTAAAA
15222 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
15247 CA-ATTTAGGGTTTCAAACCCTAAAA
1 CAGA-TTAGGGTTTCAAACCCTAAAA
15272 CAGATTAGGGTTTCAAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
15295 TCCCCTACTC
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
24 1 0.01
25 68 0.97
26 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:29636 original size:43 final size:43
Alignment explanation
Indices: 29588--29742 Score: 177
Period size: 43 Copynumber: 3.5 Consensus size: 43
29578 TGACCGGACT
*
29588 TCCTCATCACGTAGGAGCCATGTCAACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
* * * ** *
29631 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-
1 TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATAACCAG-CCG
* *
29677 TCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
*
29720 TCCTCATCACGTAGGAACCGTGT
1 TCCTCATCACGTAGGAGCCGTGT
29743 TATCACCTTT
Statistics
Matches: 89, Mismatches: 18, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 51 0.57
44 3 0.03
45 3 0.03
46 30 0.34
47 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
Found at i:29687 original size:46 final size:47
Alignment explanation
Indices: 29624--29763 Score: 157
Period size: 46 Copynumber: 3.1 Consensus size: 47
29614 CCATAGATAA
29624 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGACCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
* * * * * * **
29670 CCAGATC-TCTTCATCACGTATGAGCCGTGTCA--ACC-ATAGATAA
1 CCAGACCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
*
29713 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGGTGG
1 CCAGACCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
29759 CCAGA
1 CCAGA
29764 GTTTCATCAG
Statistics
Matches: 71, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
42 1 0.01
43 30 0.42
44 3 0.04
45 3 0.04
46 33 0.46
47 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (47 bp):
CCAGACCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
Found at i:29742 original size:89 final size:87
Alignment explanation
Indices: 29591--29788 Score: 315
Period size: 89 Copynumber: 2.3 Consensus size: 87
29581 CCGGACTTCC
* *
29591 TCATCACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
29656 TCACCTTTAGATGGCCAGATCTCT
66 TCACCTTTAGATGGCCAGA-CT-T
29680 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
* *
29745 TCACCTTTAGGTGGCCAGAGTT
66 TCACCTTTAGATGGCCAGACTT
* **
29767 TCATCAGGTATGAATCGTGTCA
1 TCATCACGTATGAGCCGTGTCA
29789 TCCCCAGACC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 20 0.20
88 1 0.01
89 81 0.79
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (87 bp):
TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
TCACCTTTAGATGGCCAGACTT
Found at i:30133 original size:3 final size:3
Alignment explanation
Indices: 30122--30185 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
30112 TTTTTTTCCG
** *
30122 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30167 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
30186 CAATTTTTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30163 original size:32 final size:32
Alignment explanation
Indices: 30120--30183 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
30110 GTTTTTTTTC
*
30120 CGTTATTTTATTATTATTATTATTA-TTATTAT
1 CGTTATCTTATTATT-TTATTATTATTTATTAT
30152 CGTTATCTTATTATTTTATTATTATTTATTAT
1 CGTTATCTTATTATTTTATTATTATTTATTAT
30184 TACAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (32 bp):
CGTTATCTTATTATTTTATTATTATTTATTAT
Found at i:30273 original size:37 final size:37
Alignment explanation
Indices: 30227--30301 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
30217 TTCAGATTAC
30227 AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
1 AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
30264 AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
1 AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
30301 A
1 A
30302 CTCAGAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.43, G:0.19, T:0.03
Consensus pattern (37 bp):
AAAGGCCCAATCCCGGAGCCCAACAACCCGAAGCCCA
Found at i:30372 original size:25 final size:25
Alignment explanation
Indices: 30339--30436 Score: 171
Period size: 25 Copynumber: 3.9 Consensus size: 25
30329 AGCAGCCCGT
*
30339 CAGATTAGGGTTTCAAACCCTAAAT
1 CAGATTAGGGTTTCAAACCCTAAAA
30364 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
30389 CA-ATTTAGGGTTTCAAACCCTAAAA
1 CAGA-TTAGGGTTTCAAACCCTAAAA
30414 CAGATTAGGGTTTCAAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
30437 TCCCCTACTC
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
24 1 0.01
25 68 0.97
26 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:30829 original size:17 final size:17
Alignment explanation
Indices: 30789--30829 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
30779 ATTTCGAAAC
*
30789 AGAAAAAAAAAAACGAA
1 AGAAAAAAAAAAACCAA
*
30806 AGAAAAAGAAAAAACCAG
1 AGAAAAA-AAAAAACCAA
30824 AGAAAA
1 AGAAAA
30830 TATAGAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAAACCAA
Found at i:34209 original size:29 final size:30
Alignment explanation
Indices: 34166--34229 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
34156 ACAAGTCTTA
* * * *
34166 GAAAAATTGGGGATCATTTCGTAAGTTTT-
1 GAAAAATTGGAGATCAATTCATAAATTTTG
*
34195 GAAAAGTTGGAGATCAATTCATAAATTTTG
1 GAAAAATTGGAGATCAATTCATAAATTTTG
34225 GAAAA
1 GAAAA
34230 TGGAGGGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (30 bp):
GAAAAATTGGAGATCAATTCATAAATTTTG
Found at i:34847 original size:30 final size:31
Alignment explanation
Indices: 34795--34866 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 31
34785 TCTTTAAAGT
34795 TTTTTTAATAATTTCAATTTAAAAGCTTTAA
1 TTTTTTAATAATTTCAATTTAAAAGCTTTAA
* *
34826 TTTTTTAATAATTTCAA-TTAAAAGTTTTAT
1 TTTTTTAATAATTTCAATTTAAAAGCTTTAA
34856 TTTTTTAATAA
1 TTTTTTAATAA
34867 ATTAACTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.56
Consensus pattern (31 bp):
TTTTTTAATAATTTCAATTTAAAAGCTTTAA
Found at i:41151 original size:13 final size:13
Alignment explanation
Indices: 41135--41170 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
41125 ACAATTATTT
*
41135 AAATGAATAATTA
1 AAATAAATAATTA
41148 AAATAAATAATTA
1 AAATAAATAATTA
*
41161 AAGTAAATAA
1 AAATAAATAA
41171 AAAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (13 bp):
AAATAAATAATTA
Found at i:48341 original size:17 final size:16
Alignment explanation
Indices: 48319--48358 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
48309 AATAAGGTAT
48319 AATAATATTAATAAATA
1 AATAATA-TAATAAATA
48336 AATAATA-AATAAATA
1 AATAATATAATAAATA
48351 AA-AATATA
1 AATAATATA
48359 TTATGATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 11 0.50
17 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATATAATAAATA
Found at i:48343 original size:11 final size:11
Alignment explanation
Indices: 48327--48356 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
48317 ATAATAATAT
48327 TAATAAATAAA
1 TAATAAATAAA
48338 TAATAAATAAA
1 TAATAAATAAA
48349 TAA-AAATA
1 TAATAAATA
48357 TATTATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:55283 original size:30 final size:30
Alignment explanation
Indices: 55247--55317 Score: 133
Period size: 30 Copynumber: 2.3 Consensus size: 30
55237 CAAGACACCG
55247 GAGGAGGTCCCACGCGCCGCCACTGCGCGT
1 GAGGAGGTCCCACGCGCCGCCACTGCGCGT
55277 GAGGAGGTCCCACGCGCCGCCACTGCGCGT
1 GAGGAGGTCCCACGCGCCGCCACTGCGCGT
55307 GAGGATGGTCC
1 GAGGA-GGTCC
55318 AAATGGAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 35 0.88
31 5 0.12
ACGTcount: A:0.14, C:0.37, G:0.38, T:0.11
Consensus pattern (30 bp):
GAGGAGGTCCCACGCGCCGCCACTGCGCGT
Found at i:59660 original size:24 final size:24
Alignment explanation
Indices: 59632--59740 Score: 69
Period size: 24 Copynumber: 4.5 Consensus size: 24
59622 GAATATTTTA
*
59632 TTTGATTTCTGATTTGAATTCTGT
1 TTTGATTTCTGATCTGAATTCTGT
** * *
59656 TTTGACATCTTATCTGAAATCTGT
1 TTTGATTTCTGATCTGAATTCTGT
* * *
59680 TATGA-TTCTTAACCT-AGATTCTGT
1 TTTGATTTC-TGATCTGA-ATTCTGT
* * * * *
59704 TCTGATATCTGATTTAAATTATGT
1 TTTGATTTCTGATCTGAATTCTGT
59728 TTTGATTTCTGAT
1 TTTGATTTCTGAT
59741 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
23 3 0.05
24 57 0.90
25 3 0.05
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (24 bp):
TTTGATTTCTGATCTGAATTCTGT
Found at i:62224 original size:33 final size:33
Alignment explanation
Indices: 62178--62244 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
62168 ATGTGACAAA
*
62178 AAGAACAACTAAGGTTTTACTTTT-TATTTCTTT
1 AAGAACAACTAAGG-TTTAATTTTCTATTTCTTT
* * *
62211 AAGAATAATTAAGGTTTAATTTTCTGTTTCTTT
1 AAGAACAACTAAGGTTTAATTTTCTATTTCTTT
62244 A
1 A
62245 TACATTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.49
Consensus pattern (33 bp):
AAGAACAACTAAGGTTTAATTTTCTATTTCTTT
Found at i:63723 original size:20 final size:20
Alignment explanation
Indices: 63698--63753 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
63688 TAAAACTAAT
63698 ATTAAATAAAAATTAATTAA
1 ATTAAATAAAAATTAATTAA
* *
63718 ATTAAAAAAAAAGTAATTAA
1 ATTAAATAAAAATTAATTAA
63738 ATTAAAAATAAAAATT
1 ATT--AAATAAAAATT
63754 TATTGATCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 21 0.70
22 9 0.30
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
ATTAAATAAAAATTAATTAA
Found at i:69132 original size:35 final size:35
Alignment explanation
Indices: 69062--69137 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
69052 AAAACAGTCC
* * *
69062 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
69097 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
69132 TTAATT
1 TCAATT
69138 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:69680 original size:130 final size:130
Alignment explanation
Indices: 69534--69781 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
69524 TATTTATATA
* ** *
69534 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATCTG
* *
69599 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
69664 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATCTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATCTG
* * *
69729 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
69782 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATCTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:69812 original size:130 final size:129
Alignment explanation
Indices: 69548--69812 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
69538 ATTTGGTCCT
* ** * *
69548 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATCTGTTAACACATGATCA
* *** * * **** *
69613 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
69678 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATCTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATCTGTTAACACATGATCA
* * * *
69743 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
69807 -A
128 CA
69808 AAATT
1 AAATT
69813 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATCTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:83305 original size:19 final size:20
Alignment explanation
Indices: 83267--83313 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
83257 AACACAACTA
83267 TTCGCAACGCGAATTTTAGT
1 TTCGCAACGCGAATTTTAGT
*
83287 TTCGTAACGCGAA-TTTAGT
1 TTCGCAACGCGAATTTTAGT
83306 TTCGCAAC
1 TTCGCAAC
83314 TTAATTACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (20 bp):
TTCGCAACGCGAATTTTAGT
Found at i:86807 original size:17 final size:18
Alignment explanation
Indices: 86775--86808 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
86765 TTTAAATATA
86775 AATTATGAAATTAATTTG
1 AATTATGAAATTAATTTG
*
86793 AATTAT-AATTTAATTT
1 AATTATGAAATTAATTT
86809 AAATATCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
AATTATGAAATTAATTTG
Found at i:90569 original size:22 final size:22
Alignment explanation
Indices: 90531--90572 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
90521 ATTAGAGCGC
*
90531 TCAATTTTATAGTGATGTTAAT
1 TCAATTTTATACTGATGTTAAT
90553 TCAATTTTA-ACTCGATGTTA
1 TCAATTTTATACT-GATGTTA
90573 CATCTGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (22 bp):
TCAATTTTATACTGATGTTAAT
Found at i:95888 original size:31 final size:31
Alignment explanation
Indices: 95848--95919 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
95838 TTTATTTATG
* *
95848 TTATTGATTTATAAGGATTT-GATCATTCACT
1 TTATCGATTTATAAGG-TTTCGATCATTCAAT
95879 TTATCGATTTATAAGGTTTCGATCATTCAAT
1 TTATCGATTTATAAGGTTTCGATCATTCAAT
*
95910 TTATCAATTT
1 TTATCGATTT
95920 GTAACATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 3 0.08
31 34 0.92
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (31 bp):
TTATCGATTTATAAGGTTTCGATCATTCAAT
Found at i:96052 original size:31 final size:31
Alignment explanation
Indices: 96006--96087 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
95996 CTGATCTTGC
* * * * * *
96006 ATAAAACACTTATTTATCTTTTAAATTTTAG
1 ATAAAATACTAATTTAACTCTTAAACTTTAA
*
96037 ATAAAATACTAATTTAACTCTTGAACTTTAA
1 ATAAAATACTAATTTAACTCTTAAACTTTAA
*
96068 ATAAAATATTAATTTAACTC
1 ATAAAATACTAATTTAACTC
96088 ATGAATAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (31 bp):
ATAAAATACTAATTTAACTCTTAAACTTTAA
Found at i:105778 original size:22 final size:22
Alignment explanation
Indices: 105752--105793 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
105742 AAAATTATTA
*
105752 TTTCTACTGGTTTTGTTATTTT
1 TTTCTACCGGTTTTGTTATTTT
105774 TTTCTACCGGTTTTGTTATT
1 TTTCTACCGGTTTTGTTATT
105794 GTTGGGCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (22 bp):
TTTCTACCGGTTTTGTTATTTT
Found at i:125363 original size:18 final size:18
Alignment explanation
Indices: 125336--125370 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
125326 TGACATGATA
125336 ATTAAAAAAATTAATATG
1 ATTAAAAAAATTAATATG
*
125354 ATTAACAAAATTAATAT
1 ATTAAAAAAATTAATAT
125371 TATAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
ATTAAAAAAATTAATATG
Found at i:125854 original size:21 final size:21
Alignment explanation
Indices: 125817--125856 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
125807 TAATCTGCAC
125817 TTTTTTTAAATGAATTCAGGA
1 TTTTTTTAAATGAATTCAGGA
*
125838 TTTTTATTGAATG-ATTCAG
1 TTTTT-TTAAATGAATTCAG
125857 TTCGAGATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTTTTTAAATGAATTCAGGA
Found at i:137801 original size:7 final size:6
Alignment explanation
Indices: 137786--137858 Score: 51
Period size: 7 Copynumber: 11.0 Consensus size: 6
137776 ATGACACTTA
137786 AAATTT AAATTCT AAATCTT AAATATT AAATATT ATAATTT --ATTT ATAATTAT
1 AAATTT AAATT-T AAAT-TT AAAT-TT AAAT-TT A-AATTT AAATTT A-AATT-T
137839 AAATGTT AAATCTT AAATTT
1 AAAT-TT AAAT-TT AAATTT
137859 TAAACCCTGC
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.07
6 7 0.12
7 39 0.68
8 7 0.12
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:146652 original size:44 final size:44
Alignment explanation
Indices: 146598--146699 Score: 152
Period size: 44 Copynumber: 2.3 Consensus size: 44
146588 ACGTCGCGCA
*
146598 TGTGACGGTGGTGCGCTAG-TACTTAGCACGTAACCTGACGTCTT
1 TGTGACGGTGGTGCGCT-GTTACTTAGCACGTAACCTGACGTCTG
* * *
146642 TGTGATGGTGGTGCGCTGTTACTTAGCACGTAATCTGATGTCTG
1 TGTGACGGTGGTGCGCTGTTACTTAGCACGTAACCTGACGTCTG
146686 TGTGACGGTGGTGC
1 TGTGACGGTGGTGC
146700 TAAAGTATCG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
43 1 0.02
44 51 0.98
ACGTcount: A:0.16, C:0.19, G:0.33, T:0.32
Consensus pattern (44 bp):
TGTGACGGTGGTGCGCTGTTACTTAGCACGTAACCTGACGTCTG
Found at i:148230 original size:44 final size:45
Alignment explanation
Indices: 148177--148261 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
148167 TTTTTTTAAA
*
148177 AAAAAATGGTAGGT-AATTTTTTATTCTATTATTTAATTTAATTT
1 AAAAAATGGTAGGTAAATTTTTTATGCTATTATTTAATTTAATTT
*
148221 AAAAAATGGTAGTTAAATTTTTTATGCTATTATTTAATTTA
1 AAAAAATGGTAGGTAAATTTTTTATGCTATTATTTAATTTA
148262 GTATATTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 13 0.34
45 25 0.66
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (45 bp):
AAAAAATGGTAGGTAAATTTTTTATGCTATTATTTAATTTAATTT
Found at i:148285 original size:46 final size:45
Alignment explanation
Indices: 148191--148295 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
148181 AATGGTAGGT
* * * * *
148191 AATTTTTTATTCTATTATTTAATTTAATTTAAAAAATGGTAGTTA
1 AATTTTTTATGCTATTATTTAATTTAATATAAAAAATGATACTCA
* ** *
148236 AATTTTTTATGCTATTATTTAATTTAGTATATTGAAATGATTCTCA
1 AATTTTTTATGCTATTATTTAATTTAATATA-AAAAATGATACTCA
148282 AATTTTTTATGCTA
1 AATTTTTTATGCTA
148296 ATTAAGACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 28 0.56
46 22 0.44
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (45 bp):
AATTTTTTATGCTATTATTTAATTTAATATAAAAAATGATACTCA
Found at i:157696 original size:33 final size:34
Alignment explanation
Indices: 157626--157696 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
157616 TTTATATTCT
* * *
157626 ATGACTAACCCATGATTTCTTTTAATACACATGG
1 ATGACTAACCCATGATGTCTTTGAATACAAATGG
* *
157660 ATGACTAGCCCATGATGT-TTTGAATACAAATTG
1 ATGACTAACCCATGATGTCTTTGAATACAAATGG
157693 ATGA
1 ATGA
157697 GTGGTCTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (34 bp):
ATGACTAACCCATGATGTCTTTGAATACAAATGG
Found at i:158743 original size:23 final size:26
Alignment explanation
Indices: 158717--158769 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 26
158707 CTTTGATATA
158717 TTTATC-TATTTA-ATTTTATACT-T
1 TTTATCATATTTAGATTTTATACTAT
* *
158740 TTTA-CATATTTAGGTTTTATATTAT
1 TTTATCATATTTAGATTTTATACTAT
158765 TTTAT
1 TTTAT
158770 TTTAATCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 8 0.33
25 5 0.21
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (26 bp):
TTTATCATATTTAGATTTTATACTAT
Found at i:161079 original size:2 final size:2
Alignment explanation
Indices: 161074--161148 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
161064 TGTGTGTGTC
161074 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
161116 TA TA TA 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 TA TA TA T
161149 TATGACATTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:162222 original size:9 final size:9
Alignment explanation
Indices: 162208--162237 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
162198 TGAATTCATA
162208 TCAATAAAT
1 TCAATAAAT
162217 TCAATAAAT
1 TCAATAAAT
*
162226 TCAATAGAT
1 TCAATAAAT
162235 TCA
1 TCA
162238 TTAGCCCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (9 bp):
TCAATAAAT
Found at i:162348 original size:24 final size:25
Alignment explanation
Indices: 162321--162385 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
162311 AGCTCGTATA
162321 AATTTGCACCGAAGTGA-CACGTAG
1 AATTTGCACCGAAGTGACCACGTAG
* *
162345 AATTTGTC-CCAAAG-GACCGCGTAG
1 AATTTG-CACCGAAGTGACCACGTAG
*
162369 AATTTTGCACCGTAGTG
1 AA-TTTGCACCGAAGTG
162386 CCATATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.06
24 20 0.62
25 9 0.28
26 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (25 bp):
AATTTGCACCGAAGTGACCACGTAG
Found at i:162679 original size:30 final size:30
Alignment explanation
Indices: 162634--162692 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
162624 ATCGTGTAGA
* *
162634 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
162664 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
162693 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:167270 original size:31 final size:31
Alignment explanation
Indices: 167226--167285 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
167216 TTACTGCAGT
**
167226 AGAACTGTGGATAACATTAAATCAAATTAGC
1 AGAACTGCAGATAACATTAAATCAAATTAGC
167257 AGAACTGCAGATAACATTAAATCAAATTA
1 AGAACTGCAGATAACATTAAATCAAATTA
167286 AGGAAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.25
Consensus pattern (31 bp):
AGAACTGCAGATAACATTAAATCAAATTAGC
Found at i:172156 original size:24 final size:24
Alignment explanation
Indices: 172129--172179 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
172119 CTCATTCAAT
* *
172129 TTTAAAATATAAA-TGATATTTTAA
1 TTTAAAATA-AAATTCATATATTAA
172153 TTTAAAATAAAATTCATATATTAA
1 TTTAAAATAAAATTCATATATTAA
172177 TTT
1 TTT
172180 TAATTAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTAAAATAAAATTCATATATTAA
Found at i:176915 original size:12 final size:12
Alignment explanation
Indices: 176898--176922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
176888 TATTAAAATG
176898 GATAAATTGTGT
1 GATAAATTGTGT
176910 GATAAATTGTGT
1 GATAAATTGTGT
176922 G
1 G
176923 TGTGTCTATA
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:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (12 bp):
GATAAATTGTGT
Found at i:178662 original size:9 final size:9
Alignment explanation
Indices: 178648--178699 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
178638 ATATGCAAAA
178648 AAATAAATT
1 AAATAAATT
178657 AAATAAAATATT
1 AAAT--AA-ATT
178669 AAATAAATT
1 AAATAAATT
*
178678 AAAT-ACTT
1 AAATAAATT
178686 AAATAAATT
1 AAATAAATT
178695 AAATA
1 AAATA
178700 CAAAATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 19 0.51
10 2 0.05
11 2 0.05
12 7 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATAAATT
Found at i:178671 original size:17 final size:17
Alignment explanation
Indices: 178651--178700 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
178641 TGCAAAAAAA
*
178651 TAAATTAAATAAAATA-T
1 TAAA-TAAATTAAATACT
178668 TAAATAAATTAAATACT
1 TAAATAAATTAAATACT
178685 TAAATAAATTAAATAC
1 TAAATAAATTAAATAC
178701 AAAATATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 10 0.32
17 21 0.68
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAATAAATTAAATACT
Found at i:178674 original size:21 final size:21
Alignment explanation
Indices: 178648--178711 Score: 73
Period size: 17 Copynumber: 3.1 Consensus size: 21
178638 ATATGCAAAA
178648 AAATAAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
*
178669 AAATAAATTAAAT---A-CTT
1 AAATAAATTAAATAAAATATT
178686 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
178709 AAA
1 AAA
178712 AATATAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 15 0.43
18 1 0.03
21 13 0.37
22 1 0.03
23 5 0.14
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:180287 original size:13 final size:14
Alignment explanation
Indices: 180258--180287 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
180248 AAAAAATCAA
180258 AATCAAATTAGACT
1 AATCAAATTAGACT
180272 AATCAAATTA-ACT
1 AATCAAATTAGACT
180285 AAT
1 AAT
180288 TATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (14 bp):
AATCAAATTAGACT
Found at i:181771 original size:15 final size:15
Alignment explanation
Indices: 181753--181808 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
181743 TAACCGGTTT
181753 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
181768 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
181785 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
181800 CGATTTTAA
1 CGGTTTTAA
181809 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:181781 original size:17 final size:17
Alignment explanation
Indices: 181756--181806 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
181746 CCGGTTTCGG
181756 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
181773 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
181788 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
181805 TT
1 TT
181807 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:182224 original size:13 final size:13
Alignment explanation
Indices: 182203--182257 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
182193 AAGTTCGATA
*
182203 AATTTAAATACTT
1 AATTGAAATACTT
182216 AATTGAAATACTT
1 AATTGAAATACTT
* *
182229 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
182243 AATTGAAATACTT
1 AATTGAAATACTT
182256 AA
1 AA
182258 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:182372 original size:32 final size:33
Alignment explanation
Indices: 182243--182374 Score: 230
Period size: 33 Copynumber: 4.0 Consensus size: 33
182233 AACTCAACAT
* * *
182243 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
182276 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
182309 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
182342 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
182374 A
1 A
182375 TTGAAACAAA
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 12 0.12
33 84 0.88
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:182393 original size:21 final size:21
Alignment explanation
Indices: 182369--182408 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
182359 ACTTCAAGTT
182369 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
182390 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
182409 ATAAAATAAA
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:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:184735 original size:11 final size:12
Alignment explanation
Indices: 184714--184759 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
184704 TCCGGATAAA
184714 AACCGGTTTTTT
1 AACCGGTTTTTT
184726 AACCGGTTTTTTT
1 AACCGG-TTTTTT
184739 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
184753 ATCCGGT
1 AACCGGT
184760 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:184744 original size:15 final size:14
Alignment explanation
Indices: 184713--184752 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
184703 TTCCGGATAA
184713 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
184726 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
184739 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
184753 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:191636 original size:177 final size:174
Alignment explanation
Indices: 191356--191700 Score: 396
Period size: 177 Copynumber: 2.0 Consensus size: 174
191346 AAAACAAAAC
* * *
191356 AAAAAAAATCTAATACGATCAGGAAAACTATTAAAATTTTGACATAAATATTGGATAACGTTTAA
1 AAAAAAAATCAAATACGATCAGGAAAAC-ATTAAAATTTTGACATAAATATTGGATAACATTCAA
*
191421 AATTCAAAAAATTAAAACAAATCAAAATAAACCTTCTTCAAACCGAA-TCCAAAGAAACGGCCGA
65 AATTCAAAAAATCAAAACAAATCAAAATAAACCTTCTTCAAACC-AATTCC-AA-AAA-GGCCGA
* *
191485 TTAATCGTCAAAGGAATA-CAAGATTTAAGATAAAATCAAAACGCATGCA
126 TTAATCGTAAAACGAA-AGCAAGATTTAAGATAAAATCAAAACGCATGCA
* * *
191534 AAAAAAAATCAAATACGATCAGGGAAAA-A-TAATATTTTGACATATATATTGGATCAATATTCA
1 AAAAAAAATCAAATACGATCA-GGAAAACATTAAAATTTTGACATAAATATTGGAT-AACATTCA
** * ** *
191597 AAATTCGGAAAATCAAAGCAAAGT-AAAATCAAA-CTTCTTCGCACCAATTCCAAAAAGGCCTAT
64 AAATTCAAAAAATCAAAACAAA-TCAAAAT-AAACCTTCTTCAAACCAATTCCAAAAAGGCCGAT
* * *
191660 TAATCGTAAAACGAAAGCAATATTTTAGATAAAATTAAAAC
127 TAATCGTAAAACGAAAGCAAGATTTAAGATAAAATCAAAAC
191701 AAATTTTACC
Statistics
Matches: 143, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
173 1 0.01
174 40 0.28
175 3 0.02
176 27 0.19
177 42 0.29
178 24 0.17
179 6 0.04
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (174 bp):
AAAAAAAATCAAATACGATCAGGAAAACATTAAAATTTTGACATAAATATTGGATAACATTCAAA
ATTCAAAAAATCAAAACAAATCAAAATAAACCTTCTTCAAACCAATTCCAAAAAGGCCGATTAAT
CGTAAAACGAAAGCAAGATTTAAGATAAAATCAAAACGCATGCA
Found at i:196046 original size:25 final size:23
Alignment explanation
Indices: 196011--196083 Score: 103
Period size: 25 Copynumber: 3.1 Consensus size: 23
196001 TGATTCGATG
196011 AGAAAGAAGAAAAGTGAAGAGAA
1 AGAAAGAAGAAAAGTGAAGAGAA
196034 AGAAAGTGAAGAAAAGTGAAGAGAA
1 AGAAA--GAAGAAAAGTGAAGAGAA
* *
196059 AG-AAGAAGAAAAATGAAGAAAA
1 AGAAAGAAGAAAAGTGAAGAGAA
196081 AGA
1 AGA
196084 TAGGGAATGG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
22 18 0.40
23 5 0.11
24 2 0.04
25 20 0.44
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (23 bp):
AGAAAGAAGAAAAGTGAAGAGAA
Found at i:196049 original size:10 final size:10
Alignment explanation
Indices: 196036--196080 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
196026 GAAGAGAAAG
196036 AAAGTGAAGA
1 AAAGTGAAGA
196046 AAAGTGAAGA
1 AAAGTGAAGA
*
196056 GAAAGAAGAAGA
1 -AAAG-TGAAGA
*
196068 AAAATGAAGA
1 AAAGTGAAGA
196078 AAA
1 AAA
196081 AGATAGGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 18 0.60
11 7 0.23
12 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (10 bp):
AAAGTGAAGA
Found at i:197500 original size:25 final size:24
Alignment explanation
Indices: 197466--197513 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
197456 CGCTTTTGAA
197466 TTTTACAAAATATGCAGATATCTT
1 TTTTACAAAATATGCAGATATCTT
197490 TTTTATCAAAATATGCAGATATCT
1 TTTTA-CAAAATATGCAGATATCT
197514 GACCAGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (24 bp):
TTTTACAAAATATGCAGATATCTT
Found at i:207766 original size:2 final size:2
Alignment explanation
Indices: 207759--207806 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
207749 AATCTTGGGA
207759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
207801 AT AT AT
1 AT AT AT
207807 TTACGTAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208075 original size:24 final size:24
Alignment explanation
Indices: 208048--208120 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
208038 CGTTCATTTA
208048 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
208072 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
208096 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
208120 C
1 C
208121 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:208077 original size:14 final size:14
Alignment explanation
Indices: 208058--208113 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
208048 CGTTCGTGAA
208058 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
208072 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
208086 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
208096 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
208110 CGTT
1 CGTT
208114 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:208130 original size:24 final size:23
Alignment explanation
Indices: 208059--208133 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
208049 GTTCGTGAAC
* *
208059 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
208083 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
208107 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
208131 GTT
1 GTT
208134 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:208877 original size:10 final size:10
Alignment explanation
Indices: 208862--208936 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
208852 GGGTCTCCAA
208862 CGTTTATGTT
1 CGTTTATGTT
208872 CGTTTATGTT
1 CGTTTATGTT
208882 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
208893 ATGTTCGTGTT
1 -CGTTTATGTT
208904 CGTTTATGTT
1 CGTTTATGTT
208914 CG----TGTT
1 CGTTTATGTT
208920 CGTTTATGTT
1 CGTTTATGTT
208930 CGTTTAT
1 CGTTTAT
208937 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:208893 original size:16 final size:16
Alignment explanation
Indices: 208868--208932 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
208858 CCAACGTTTA
208868 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
208884 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
208900 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
208916 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
208932 T
1 T
208933 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:209023 original size:16 final size:16
Alignment explanation
Indices: 209002--209034 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
208992 AAAAAAATTT
209002 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
209018 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
209034 T
1 T
209035 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:210738 original size:3 final size:3
Alignment explanation
Indices: 210730--210781 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
210720 TAAACACACT
*
210730 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
210777 TAA TA
1 TAA TA
210782 TTTTTTAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 45 0.98
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:211135 original size:105 final size:105
Alignment explanation
Indices: 210907--211138 Score: 238
Period size: 105 Copynumber: 2.2 Consensus size: 105
210897 TCGTTAGATT
* * * * * *
210907 GAACAAATTTTTCTCATTATGAACTTTTTTCTCGTGGATGAGTTCTTCTCATTATGAACTCTTTT
1 GAACAAGTTTTTCTCATTATGAACTTTCTCCTCGTGGACGAGTTCTTCTCATTATAAACTCTTAT
* * *
210972 GGAAATGTTGATCTAAATCCTTTTGCGGTGGACTTAGAAA
66 GGAAATGTTGATCTAAATCCATCTGCGGTGGAATTAGAAA
* * *
211012 GAA-AATGTTTTTCCCATTATGAACTTTCTCCT-TTAGGACGGGTTCTTCTCATTATAAACTCTT
1 GAACAA-GTTTTTCTCATTATGAACTTTCTCCTCGT-GGACGAGTTCTTCTCATTATAAACTCTT
* ** * *
211075 ATGGAAATGTTGGT-TCACCTCCATCTGTGGT-GAATTTGAAA
64 ATGGAAATGTTGATCT-AAATCCATCTGCGGTGGAATTAGAAA
*
211116 GGAACAAGTTCTTCTCATTATGA
1 -GAACAAGTTTTTCTCATTATGA
211139 TGAGTTCTTC
Statistics
Matches: 103, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
104 12 0.12
105 89 0.86
106 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (105 bp):
GAACAAGTTTTTCTCATTATGAACTTTCTCCTCGTGGACGAGTTCTTCTCATTATAAACTCTTAT
GGAAATGTTGATCTAAATCCATCTGCGGTGGAATTAGAAA
Found at i:212426 original size:7 final size:7
Alignment explanation
Indices: 212416--212493 Score: 87
Period size: 7 Copynumber: 11.6 Consensus size: 7
212406 CCTTTTTCTC
212416 TTTTCATT
1 TTTTCA-T
212424 TTTTCAT
1 TTTTCAT
212431 TTCTT--T
1 TT-TTCAT
212437 TTTTCAT
1 TTTTCAT
212444 TTTTCAT
1 TTTTCAT
212451 TTTTCAT
1 TTTTCAT
212458 TTTTCA-
1 TTTTCAT
212464 TTTT--T
1 TTTTCAT
212469 TTTTC-T
1 TTTTCAT
212475 TTTTCATT
1 TTTTCA-T
212483 TTTTCAT
1 TTTTCAT
212490 TTTT
1 TTTT
212494 TTCATCTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 15
0.81 0.00 0.19
Matches are distributed among these distances:
5 6 0.10
6 13 0.21
7 29 0.46
8 15 0.24
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCAT
Found at i:212427 original size:8 final size:8
Alignment explanation
Indices: 212416--212519 Score: 87
Period size: 8 Copynumber: 13.5 Consensus size: 8
212406 CCTTTTTCTC
212416 TTTTCATT
1 TTTTCATT
212424 TTTTCA--
1 TTTTCATT
*
212430 -TTTCTTT
1 TTTTCATT
212437 TTTTCA-T
1 TTTTCATT
212444 TTTTCA-T
1 TTTTCATT
212451 TTTTCA-T
1 TTTTCATT
212458 TTTTCATT
1 TTTTCATT
**
212466 TTTTTTTCT
1 TTTTCAT-T
212475 TTTTCATT
1 TTTTCATT
212483 TTTTCATTT
1 TTTTCA-TT
212492 TTTTCATCT
1 TTTTCAT-T
212501 TTTT-ATT
1 TTTTCATT
* *
212508 TGTTCCTT
1 TTTTCATT
212516 TTTT
1 TTTT
212520 TTTCTTCAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
5 4 0.05
7 25 0.32
8 31 0.39
9 19 0.24
ACGTcount: A:0.10, C:0.13, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:212439 original size:14 final size:13
Alignment explanation
Indices: 212407--212484 Score: 58
Period size: 14 Copynumber: 6.0 Consensus size: 13
212397 TCAAACCCTC
212407 CTTTTTCTC-TTTT
1 CTTTTT-TCATTTT
212420 CATTTTTTCA-TTT
1 C-TTTTTTCATTTT
212433 CTTTTTTTCATTTTT
1 C-TTTTTTCA-TTTT
*
212448 CATTTTTCATTTTT
1 CTTTTTTCA-TTTT
*
212462 CATTTTT--TTTT
1 CTTTTTTCATTTT
212473 C-TTTTTCATTTT
1 CTTTTTTCATTTT
212485 TTCATTTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
10 5 0.09
11 5 0.09
12 4 0.07
13 15 0.26
14 24 0.42
15 4 0.07
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTTTCATTTT
Found at i:212525 original size:24 final size:24
Alignment explanation
Indices: 212443--212525 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 24
212433 CTTTTTTTCA
212443 TTTTTCATTTTTCATTTTTCATTTT
1 TTTTTC-TTTTTCATTTTTCATTTT
212468 TTTTTCTTTTTCATTTTTTCATTTT
1 TTTTTCTTTTTCA-TTTTTCATTTT
* *
212493 TTTCATCTTTTT-ATTTGTTCCTTTT
1 TTT-TTCTTTTTCATTT-TTCATTTT
212518 TTTTTCTT
1 TTTTTCTT
212526 CAAGCATAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
24 14 0.27
25 31 0.60
26 7 0.13
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTTCTTTTTCATTTTTCATTTT
Found at i:223916 original size:30 final size:30
Alignment explanation
Indices: 223882--223947 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
223872 CTTAAGAATC
* *
223882 AAAATAACA-AAATTAAAAAATTAAAGGACT
1 AAAATAACACAAA-CAAAAAATTAAAAGACT
* * *
223912 AAAATGACACAAACAGAAATTTAAAAGACT
1 AAAATAACACAAACAAAAAATTAAAAGACT
223942 AAAATA
1 AAAATA
223948 GTAAAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.65, C:0.09, G:0.08, T:0.18
Consensus pattern (30 bp):
AAAATAACACAAACAAAAAATTAAAAGACT
Found at i:224127 original size:30 final size:30
Alignment explanation
Indices: 224045--224127 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
224035 ACAGTAATTT
* *
224045 CAAAAACTTAAAGGACAAAAATAACAAAAA
1 CAAAAACTCAAAGGACTAAAATAACAAAAA
*
224075 CAGAAACTCAAAGGACCT-AAATAA-AATAAA
1 CAAAAACTCAAAGGA-CTAAAATAACAA-AAA
* *
224105 TAAAAACTCAAATGACTAAAATA
1 CAAAAACTCAAAGGACTAAAATA
224128 TTATTTACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 4 0.09
30 39 0.89
31 1 0.02
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (30 bp):
CAAAAACTCAAAGGACTAAAATAACAAAAA
Found at i:226581 original size:3 final size:3
Alignment explanation
Indices: 226566--226605 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
226556 TAAACACACT
* *
226566 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
226606 TTTTTTAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:229033 original size:38 final size:36
Alignment explanation
Indices: 228962--229207 Score: 133
Period size: 37 Copynumber: 6.6 Consensus size: 36
228952 ACATATATAC
* * * *
228962 ACATATATATTTATATAGTTTGCAAATTGTTTTTGAAAA
1 ACATATATA-ATATATAGTTT-AAAAATATTTTTG-AAA
229001 CACATATATAATATATAGTTTAAAACAT-TTTTTGAAA
1 -ACATATATAATATATAGTTTAAAA-ATATTTTTGAAA
* * * *
229038 ATATGTATATTATATAGTTTTTAAAATATTTTTGAAA
1 ACATATATAATATATAG-TTTAAAAATATTTTTGAAA
* * **
229075 A-TTATATAATATATAGTTTTTGAAAACGTTTTT-AAA
1 ACATATATAATATATAG--TTTAAAAATATTTTTGAAA
* * * ** *
229111 ATATATATAATATATACTTTTGAAAA-CGTTATGAAA
1 ACATATATAATATATA-GTTTAAAAATATTTTTGAAA
* *
229147 ACATTTATATAATATATAATTTTTAAAAA-ACCATTTTGAAA
1 ACA--TATATAATATAT-A-GTTTAAAAATA--TTTTTGAAA
*
229188 ATATATATAATATATAGTTT
1 ACATATATAATATATAGTTT
229208 TTTTAAAAAA
Statistics
Matches: 168, Mismatches: 26, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
35 3 0.02
36 45 0.27
37 48 0.29
38 22 0.13
39 32 0.19
40 9 0.05
41 9 0.05
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
ACATATATAATATATAGTTTAAAAATATTTTTGAAA
Found at i:229088 original size:36 final size:38
Alignment explanation
Indices: 229004--229253 Score: 221
Period size: 36 Copynumber: 6.7 Consensus size: 38
228994 TTGAAAACAC
* *
229004 ATATATAATATATAG--TTTAAAACATTTTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAAAACTTTTTGAAAAT
* * *
229040 ATGTATATTATATAGTTTTTAAAATA-TTTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAAAACTTTTTGAAAAT
*
229077 -TATATAATATATAGTTTTT-GAAAACGTTTTT-AAAAT
1 ATATATAATATATAGTTTTTAAAAAAC-TTTTTGAAAAT
* * * *
229113 ATATATAATATATA-CTTTT-GAAAACGTTATGAAAACAT
1 ATATATAATATATAGTTTTTAAAAAACTTTTTG-AAA-AT
* * *
229151 TTATATAATATATAATTTTTAAAAAACCATTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAAAA-CTTTTTGAAAAT
* *
229190 ATATATAATATATAGTTTTTTTAAAAAACATTTTAAAAAT
1 ATATATAATATATAG--TTTTTAAAAAACTTTTTGAAAAT
* * *
229230 TTATATATTATAT-GTTTTTGAAAA
1 ATATATAATATATAGTTTTTAAAAA
229254 CGTTTATATA
Statistics
Matches: 180, Mismatches: 21, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
35 6 0.03
36 45 0.25
37 41 0.23
38 23 0.13
39 20 0.11
40 29 0.16
41 16 0.09
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (38 bp):
ATATATAATATATAGTTTTTAAAAAACTTTTTGAAAAT
Found at i:229247 original size:39 final size:40
Alignment explanation
Indices: 229144--229248 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 40
229134 AAACGTTATG
**
229144 AAAACATTTATATAATATAT-AATTTTTAAAAAACCATTTT
1 AAAA-ATTTATATAATATATGTTTTTTTAAAAAACCATTTT
* *
229184 GAAAATATATATAATATATAGTTTTTTTAAAAAA-CATTTT
1 AAAAATTTATATAATATAT-GTTTTTTTAAAAAACCATTTT
*
229224 AAAAATTTATATATTATATGTTTTT
1 AAAAATTTATATAATATATGTTTTT
229249 GAAAACGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
39 20 0.36
40 25 0.45
41 11 0.20
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (40 bp):
AAAAATTTATATAATATATGTTTTTTTAAAAAACCATTTT
Found at i:235226 original size:147 final size:147
Alignment explanation
Indices: 235022--235306 Score: 453
Period size: 147 Copynumber: 1.9 Consensus size: 147
235012 CACATGTTGC
* * *
235022 TTCCTCCAGAGATTCGAACTCGCATGTAGTCACTTCCTTCACTTCCAAAAACCCTTTTTCTTCTT
1 TTCCTCCAAAGATTCGAACTCGCATGTAATCACTTCCTCCACTTCCAAAAACCCTTTTTCTTCTT
* *
235087 TACAATCCATCCTTTTAGCTTCATCCAACACCGAGACTGCCCTAACCCGGCCCCAACTCCGTTCA
66 CACAATCCATCCTTTTAGCTTCATCCAACACCGAGACTGCCCTAACCCGGCCACAACTCCGTTCA
235152 ATGTATTCATCGATGCA
131 ATGTATTCATCGATGCA
* *
235169 TTCCTCCAAAGATTCGGACTCGCATGTAATCACTTCCTCCACTTCCAACAACCCTTTTTCTTCTT
1 TTCCTCCAAAGATTCGAACTCGCATGTAATCACTTCCTCCACTTCCAAAAACCCTTTTTCTTCTT
* * * * **
235234 CACAATCCATCCTTTTAGCTTCATTCAACACCGAGACTGCCCTAATCTGGCCACGACTCCGTTTG
66 CACAATCCATCCTTTTAGCTTCATCCAACACCGAGACTGCCCTAACCCGGCCACAACTCCGTTCA
235299 ATGTATTC
131 ATGTATTC
235307 TTTGTAGAGA
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
147 125 1.00
ACGTcount: A:0.23, C:0.34, G:0.11, T:0.32
Consensus pattern (147 bp):
TTCCTCCAAAGATTCGAACTCGCATGTAATCACTTCCTCCACTTCCAAAAACCCTTTTTCTTCTT
CACAATCCATCCTTTTAGCTTCATCCAACACCGAGACTGCCCTAACCCGGCCACAACTCCGTTCA
ATGTATTCATCGATGCA
Found at i:238385 original size:20 final size:20
Alignment explanation
Indices: 238360--238453 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
238350 AATTGGGAAA
*
238360 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
238380 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
238401 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
238421 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
238441 TTCGCAACGCGAT
1 ATCGCAACGCGAT
238454 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:239017 original size:19 final size:19
Alignment explanation
Indices: 238972--239019 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
238962 TTCGAGAATG
*
238972 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
238991 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
239011 AAAATCGCA
1 AAAATCGCA
239020 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:239037 original size:19 final size:19
Alignment explanation
Indices: 239015--239146 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
239005 GAAACCAAAA
*
239015 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
239034 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
239053 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
239067 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
239086 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
239105 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
239125 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
239145 TC
1 TC
239147 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 9 0.09
16 2 0.02
17 3 0.03
19 49 0.51
20 32 0.33
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:241316 original size:42 final size:42
Alignment explanation
Indices: 241269--241441 Score: 188
Period size: 42 Copynumber: 4.1 Consensus size: 42
241259 CCTATTGTTG
*
241269 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
* * * * * * *
241311 AAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTATCGTTG
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
* *
241353 AAGAGGCCCCTATCATTCCTCGAGAGTCCCTTCCCACCGTTC
1 AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
* * * *
241395 AAGAGGCCACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTC
1 AAGAGGCCACTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTC
241437 AAGAG
1 AAGAG
241442 CCCGATTCAC
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 4 0.04
42 100 0.94
43 2 0.02
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (42 bp):
AAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
Found at i:241399 original size:21 final size:21
Alignment explanation
Indices: 241375--241441 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
241365 TCATTCCTCG
241375 AGAGTCCCTTCCCACCGTTCA
1 AGAGTCCCTTCCCACCGTTCA
* * *
241396 AGAGGCCACTGT--CATCGTTGA
1 AGAGTCC-CT-TCCCACCGTTCA
*
241417 AGAGGTCCC-TCCCACCATTCA
1 AGA-GTCCCTTCCCACCGTTCA
241438 AGAG
1 AGAG
241442 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 11
0.65 0.13 0.21
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 26 0.76
22 5 0.15
23 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCTTCCCACCGTTCA
Found at i:241420 original size:84 final size:84
Alignment explanation
Indices: 241237--241411 Score: 323
Period size: 84 Copynumber: 2.1 Consensus size: 84
241227 CCGACTCGCT
* *
241237 TGTCATCCCTCAATAGTCCACTCCTATTGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
1 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
241302 CCACCGTTCAAGAGGCCAC
66 CCACCGTTCAAGAGGCCAC
*
241321 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCTTC
1 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
241386 CCACCGTTCAAGAGGCCAC
66 CCACCGTTCAAGAGGCCAC
241405 TGTCATC
1 TGTCATC
241412 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (84 bp):
TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCAC
Found at i:241441 original size:84 final size:84
Alignment explanation
Indices: 241237--241441 Score: 268
Period size: 84 Copynumber: 2.4 Consensus size: 84
241227 CCGACTCGCT
* * *** *
241237 TGTCATCCCTCAATAGTCCACTCCTATTGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
1 TGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
241302 CCACCGTTCAAGAGGCCAC
66 CCACCGTTCAAGAGGCCAC
* * * * *
241321 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCTTC
1 TGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
241386 CCACCGTTCAAGAGGCCAC
66 CCACCGTTCAAGAGGCCAC
** *
241405 TGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
241442 CCCGATTCAC
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 106 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (84 bp):
TGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCAC
Found at i:242811 original size:14 final size:14
Alignment explanation
Indices: 242792--242827 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
242782 ATTGTTTAAT
242792 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
242806 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
242820 TGATTTGT
1 TGATTTGT
242828 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:242979 original size:33 final size:33
Alignment explanation
Indices: 242934--243023 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
242924 AAAAAGTACT
* *
242934 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
242967 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
243000 ATTGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
243024 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:242990 original size:19 final size:19
Alignment explanation
Indices: 242934--242994 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
242924 AAAAAGTACT
*
242934 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
242953 ATTGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
242967 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
242986 ATCGCAACG
1 ATCGCAACG
242995 AGAGAATTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:243041 original size:19 final size:19
Alignment explanation
Indices: 243019--243169 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
243009 CGAAATTAAA
243019 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
243038 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
243053 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
243071 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
243085 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
243104 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
243119 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
243137 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
243156 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
243170 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:243065 original size:33 final size:32
Alignment explanation
Indices: 243023--243149 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
243013 ATTAAATTCG
243023 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
243056 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
243089 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
243122 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
243150 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:243096 original size:66 final size:66
Alignment explanation
Indices: 243016--243148 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
243006 ACGCGAAATT
*
243016 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
243081 G
66 G
*
243082 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
243147 G
66 G
243148 A
1 A
243149 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:245457 original size:12 final size:12
Alignment explanation
Indices: 245440--245464 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
245430 TCTTCGGGGA
245440 CTTTTTCTTCTT
1 CTTTTTCTTCTT
245452 CTTTTTCTTCTT
1 CTTTTTCTTCTT
245464 C
1 C
245465 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:246707 original size:19 final size:20
Alignment explanation
Indices: 246660--246728 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
246650 ATTCATTTGA
*
246660 CTATCGCAGCGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
246680 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
246700 CT-TCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
246718 CTATCGCAACG
1 CTATCGCAACG
246729 ACAAAATCGC
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
18 8 0.17
19 18 0.38
20 21 0.45
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:246778 original size:14 final size:14
Alignment explanation
Indices: 246759--246812 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
246749 GAAAATCGCA
246759 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
246773 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
246790 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
246806 TTGCGAT
1 TTGCGAT
246813 AGTCTGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:246778 original size:33 final size:33
Alignment explanation
Indices: 246741--246811 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
246731 AAAATCGCAA
*
246741 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
246774 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
246807 TGCGA
1 TGCGA
246812 TAGTCTGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:246830 original size:20 final size:20
Alignment explanation
Indices: 246805--246843 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
246795 CGATTCTCTC
246805 GTTGCGATAGTCTGTTTTGT
1 GTTGCGATAGTCTGTTTTGT
246825 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCTGTTTTG
246844 CCTTCAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.31, T:0.49
Consensus pattern (20 bp):
GTTGCGATAGTCTGTTTTGT
Found at i:246945 original size:14 final size:14
Alignment explanation
Indices: 246926--246962 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
246916 CATCAATTAA
246926 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
246940 ACAAATCATCTTTT
1 ACAAATCAACATTT
246954 ACAAATCAA
1 ACAAATCAA
246963 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:248852 original size:20 final size:20
Alignment explanation
Indices: 248829--248882 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
248819 GAAACTTAAA
248829 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
248849 ATCGCAACGC-AGAAATGGCT
1 ATCGCAACGCGA-AAATGACT
*
248869 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
248883 TTAAAATCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:248904 original size:14 final size:14
Alignment explanation
Indices: 248885--248942 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
248875 ATGCGAAATT
248885 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
248899 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
248915 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
248931 AAAATCGCAACG
1 AAAATCGCAACG
248943 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:248911 original size:33 final size:32
Alignment explanation
Indices: 248869--248958 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
248859 AGAAATGGCT
248869 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACAAA
*
248902 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAATCGCAACGACAAA
* *
248934 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATA-AAATCGCA
248959 TTACGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.58
33 22 0.42
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:248995 original size:14 final size:14
Alignment explanation
Indices: 248976--249033 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
248966 TTTCATTTCG
248976 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
248990 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
249006 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
249022 CGTTGCGATTTT
1 CGTTGCGATTTT
249034 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:249045 original size:33 final size:33
Alignment explanation
Indices: 248962--249049 Score: 151
Period size: 32 Copynumber: 2.7 Consensus size: 33
248952 AATCGCATTA
*
248962 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
*
248995 CGA-TTTCATTTCACATTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
249027 CGATTTTCATTTCGCATTGCGAT
1 CGATTTTCATTTCGCATTGCGAT
249050 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 30 0.59
33 21 0.41
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
Found at i:249068 original size:20 final size:19
Alignment explanation
Indices: 249034--249088 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
249024 TTGCGATTTT
*
249034 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
249053 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
249073 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
249089 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:249593 original size:18 final size:18
Alignment explanation
Indices: 249570--249614 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
249560 GTCGATCAGA
*
249570 TGATAGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
249588 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
*
249606 TGATGGCTC
1 TGATAGCTC
249615 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:250982 original size:20 final size:20
Alignment explanation
Indices: 250934--250992 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
250924 AATAGTTTCT
** *
250934 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
250954 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
250974 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
250993 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:251282 original size:22 final size:22
Alignment explanation
Indices: 251255--251298 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
251245 GATGGAGATA
251255 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
251277 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
251299 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:251512 original size:20 final size:20
Alignment explanation
Indices: 251487--251538 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
251477 ATTATGTATT
*
251487 ATCGCGTTGCGAAATTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
251507 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
251527 ATCTCGTTGCGA
1 ATCGCGTTGCGA
251539 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:251572 original size:20 final size:20
Alignment explanation
Indices: 251547--251600 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
251537 GATTTTGTAT
251547 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
251567 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
251587 TATCGCATTGCGAT
1 TATCGCATTGCGAT
251601 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:251572 original size:61 final size:61
Alignment explanation
Indices: 251466--251603 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
251456 CGCTTTGAAA
* * * * *
251466 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAATTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
251527 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
251588 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
251604 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:251619 original size:61 final size:61
Alignment explanation
Indices: 251466--251621 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
251456 CGCTTTGAAA
* ** * * * * *
251466 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAATTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
251527 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
251588 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
251622 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:268764 original size:81 final size:81
Alignment explanation
Indices: 268636--268791 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
268626 ATAAAAAAAA
* * *
268636 TCACAAATTACTTAAAGGAAACACAGGAAGAGCAAAAGGGTATCAAAA-TTG-TTTCCTCTCATG
1 TCACAAATTACTCAAA-GAAACACAGCAAGAGCAAAAGGGTACCAAAATTTGTTTTCCTCT--TG
268699 CAAATTCCCAGAAATTTTT
63 CAAATTCCCAGAAATTTTT
* * *
268718 TCACAAATTACTCAACA-AAACACAGCTAGAGCTAAAGGGTGCCAAAATTTGTTTTCCTCTTGCA
1 TCACAAATTACTCAA-AGAAACACAGCAAGAGCAAAAGGGTACCAAAATTTGTTTTCCTCTTGCA
268782 AATTCCCAGA
65 AATTCCCAGA
268792 TATATAGCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
81 39 0.60
82 17 0.26
83 9 0.14
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.26
Consensus pattern (81 bp):
TCACAAATTACTCAAAGAAACACAGCAAGAGCAAAAGGGTACCAAAATTTGTTTTCCTCTTGCAA
ATTCCCAGAAATTTTT
Found at i:269001 original size:82 final size:80
Alignment explanation
Indices: 268797--269012 Score: 267
Period size: 82 Copynumber: 2.7 Consensus size: 80
268787 CCAGATATAT
* * *
268797 AGCAAGAGCAAAAGAGTATCAAAATTTGTTTTCCCTCATGCAAATTCCCA-AAAAAAACACAAAT
1 AGCAAGAGCAAAAGGGTATCAAAATTCGTTTTCCCACATGCAAATTCCCAGAAAAAAACACAAAT
*
268861 TACTGAAGGAAATAC
66 TACTGAAAGAAATAC
* * * * * **
268876 AGCAAGACCAAAAGGGTTCATCACAA-CCGTTTTCCTACA-GCAAAATCCCAGAAAGAACTTCAC
1 AGCAAGAGCAAAAGGG-T-ATCAAAATTCGTTTTCCCACATGCAAATTCCCAGAAA-AA-AACAC
268939 AAATTACTGAAAGAAATAC
62 AAATTACTGAAAGAAATAC
*
268958 AGCAAGAGCAAAAGGGTATCAAAATTCGTTTCCCCACATGCAAATTCCCAGAAAA
1 AGCAAGAGCAAAAGGGTATCAAAATTCGTTTTCCCACATGCAAATTCCCAGAAAA
269013 CAAAATTACA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
79 24 0.21
80 19 0.17
81 20 0.18
82 50 0.44
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (80 bp):
AGCAAGAGCAAAAGGGTATCAAAATTCGTTTTCCCACATGCAAATTCCCAGAAAAAAACACAAAT
TACTGAAAGAAATAC
Found at i:277443 original size:2 final size:2
Alignment explanation
Indices: 277436--277487 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
277426 GTTGACATTG
277436 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
277478 TA TA TA TA TA
1 TA TA TA TA TA
277488 ATACTTGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.