Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003065.1 Hibiscus syriacus cultivar Beakdansim tig00006389_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: 89459
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:11183 original size:14 final size:14
Alignment explanation
Indices: 11164--11198 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11154 GCATTTTTAT
11164 TTTACATTCACATC
1 TTTACATTCACATC
**
11178 TTTACATTTGCATC
1 TTTACATTCACATC
11192 TTTACAT
1 TTTACAT
11199 AATTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (14 bp):
TTTACATTCACATC
Found at i:13567 original size:15 final size:16
Alignment explanation
Indices: 13536--13574 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
13526 TCATCTATTT
13536 GAAAAAAAGAAAGAAA
1 GAAAAAAAGAAAGAAA
13552 GAAAAAAACG-AA-AAA
1 GAAAAAAA-GAAAGAAA
13567 GAAAAAAA
1 GAAAAAAA
13575 AGGATAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.50
16 10 0.45
17 1 0.05
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
GAAAAAAAGAAAGAAA
Found at i:13585 original size:19 final size:19
Alignment explanation
Indices: 13537--13617 Score: 50
Period size: 19 Copynumber: 4.5 Consensus size: 19
13527 CATCTATTTG
13537 AAAAAAAGAA-AG-AAAGA
1 AAAAAAAGAATAGAAAAGA
*
13554 AAAAAACG---A-AAAAGA
1 AAAAAAAGAATAGAAAAGA
* *
13569 AAAAAAAGGATAGAAAATA
1 AAAAAAAGAATAGAAAAGA
**
13588 TTAAAAAGAATAGAAAA-A
1 AAAAAAAGAATAGAAAAGA
13606 ATAAGAAAAGAA
1 A-AA-AAAAGAA
13618 ATTGAATCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 13 0.27
17 7 0.14
18 2 0.04
19 20 0.41
20 7 0.14
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (19 bp):
AAAAAAAGAATAGAAAAGA
Found at i:16654 original size:42 final size:41
Alignment explanation
Indices: 16597--16683 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 41
16587 TCATTCGGTC
* * * * *
16597 CATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGT
1 CATCTGTAAGCCTTTCGAGCAAGATG-ATAAAGCCTTCAGGT
16639 CATCTGTAAGCCTTTCGAGCAAGATGATAAAGCCTTCAGGT
1 CATCTGTAAGCCTTTCGAGCAAGATGATAAAGCCTTCAGGT
16680 CATC
1 CATC
16684 CATAAGACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 16 0.40
42 24 0.60
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
CATCTGTAAGCCTTTCGAGCAAGATGATAAAGCCTTCAGGT
Found at i:16695 original size:42 final size:42
Alignment explanation
Indices: 16603--16695 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
16593 GGTCCATCTG
* * * * * **
16603 TAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTG
1 TAAGCCTTTCGAGCAAGATGTATAAAGCCTTCAGGTCATCCA
16645 TAAGCCTTTCGAGCAAGATG-ATAAAGCCTTCAGGTCATCCA
1 TAAGCCTTTCGAGCAAGATGTATAAAGCCTTCAGGTCATCCA
16686 TAAGACCTTT
1 TAAG-CCTTT
16696 AGTGCTGGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 20 0.47
42 23 0.53
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (42 bp):
TAAGCCTTTCGAGCAAGATGTATAAAGCCTTCAGGTCATCCA
Found at i:16936 original size:42 final size:42
Alignment explanation
Indices: 16848--16939 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
16838 ATTCGTAAGT
* * * *
16848 CCTTCGGGCCATCTGTAAGTCTTTTGAGCATGATGTTTAAAT
1 CCTTCGGGCCATCTGTAAGGCTTTTGAGCAAGATGTATAAAG
* * *
16890 CCTTCGGGTCATCTGTCAGGCTTTTTGAGTAAGATG-ATAAAG
1 CCTTCGGGCCATCTGTAAGGC-TTTTGAGCAAGATGTATAAAG
16932 CCTTCGGG
1 CCTTCGGG
16940 AAATCCATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 30 0.71
43 12 0.29
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (42 bp):
CCTTCGGGCCATCTGTAAGGCTTTTGAGCAAGATGTATAAAG
Found at i:17094 original size:266 final size:260
Alignment explanation
Indices: 16582--17194 Score: 920
Period size: 266 Copynumber: 2.3 Consensus size: 260
16572 TCCTAAATTT
*
16582 GTAAGTCATTCGGTCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
1 GTAAGTCCTTCGGTCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
** *
16647 AGCCTTTCGAGCAAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTTAGTGCTGGATGCTTTC
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCAGGAAATCCATAAGACCTTCAGTGCTGGATGCTTTC
* *
16712 AAATGCGATTTTAGAAACTAAGCCTTTCAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
131 AAATGAGATTTTAGAAACTAAGCCTTTAAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
* * *
16777 AGCTAAGCCTAATAAAGGGGTTCCTTGACAACTAAGAAACTAAGTTTTCGAGGGTTTCTTGATTC
196 AGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTC
* *
16842 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTTGAGCATGATGTTTAAATCCTTCGGGTCATCTGTC
1 GTAAGTCCTTCGGTCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGT-
* * * * * * *
16907 AGGCTTTTTGAGTAAGATGATAAAGCCTTCGGGAAATCCATAAGACCTTCAGTGTTGGATGTTTT
65 AAGCCTTTCGAGCAAGATGATAAAGCCTTCAGGAAATCCATAAGACCTTCAGTGCTGGATGCTTT
* * *
16972 CAAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTTCTAATTATCTCAAAAGAGTTGTT
130 CAAATGAGATTTTAGAAACTAAGCC----TTTAA-GGATTTCCTAATTATCTAAAAAGAGTTGTT
* * *
17037 AAAGGAAGGTAAGCCAAACAAAGGGGTTCCTTGATAACTAATAAACTAAGCTTTCGAGGGTTTCT
190 AAAGGAAGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCT
17102 TGATTC
255 TGATTC
* * * *
17108 GTAAGTCCTTCAGTCCATCTATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGTCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
17173 AGCCTTTCGAGCAAGATGATAA
66 AGCCTTTCGAGCAAGATGATAA
17195 GTCATTCGGG
Statistics
Matches: 313, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
260 61 0.19
261 79 0.25
265 23 0.07
266 150 0.48
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (260 bp):
GTAAGTCCTTCGGTCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
AGCCTTTCGAGCAAGATGATAAAGCCTTCAGGAAATCCATAAGACCTTCAGTGCTGGATGCTTTC
AAATGAGATTTTAGAAACTAAGCCTTTAAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
AGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTC
Found at i:17221 original size:42 final size:42
Alignment explanation
Indices: 17122--17221 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
17112 GTCCTTCAGT
* * * *
17122 CCATCTATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
1 CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
* *
17164 TCATCTATAAGCCTTTCGAGCAAGATG-ATAAGTCATTCGGG
1 CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
17205 CCAT-TCATAAGACCTTT
1 CCATCT-ATAAG-CCTTT
17222 GGGCAGAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
40 1 0.02
41 19 0.39
42 29 0.59
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (42 bp):
CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
Found at i:17625 original size:3 final size:3
Alignment explanation
Indices: 17610--17654 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
17600 TCTTATACCA
*
17610 TAT TAT T-T T-T TAT TA- TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17655 AAATAAACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17629 original size:15 final size:17
Alignment explanation
Indices: 17609--17654 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
17599 TTCTTATACC
17609 ATATTATT-TT-TTATT
1 ATATTATTATTATTATT
17624 ATATTATTATTATTATT
1 ATATTATTATTATTATT
17641 ATAATTATTATTAT
1 AT-ATTATTATTAT
17655 AAATAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.29
16 2 0.07
17 7 0.25
18 11 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTATTATTATTATT
Found at i:18320 original size:42 final size:41
Alignment explanation
Indices: 18256--18349 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 41
18246 TTGTAAGTCA
* * * * *
18256 TTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATG-ATAAAGCC
18298 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
*
18339 TTCAGGTCATC
1 TTCGGGTCATC
18350 CATAAGACCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 16 0.35
42 30 0.65
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (41 bp):
TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
Found at i:18800 original size:265 final size:260
Alignment explanation
Indices: 18248--18885 Score: 954
Period size: 265 Copynumber: 2.4 Consensus size: 260
18238 TCCTAAATTT
*
18248 GTAAGTCATTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* *
18313 AGCCTTTCGAGCAAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCTGGATGCTTTC
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
* *
18378 AAATGCGATTTTAGAAACTAAGCCTTTCAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
131 AAATGAGATTTTAGAAACTAAGCCTTTAAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
* * *
18443 AGCTAAGCCTAATAAAGGGGTTCCTTGACAACTAAGAAACTAAGTTTTCGAGGGTTTCTTGATTC
196 AGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTC
* *
18508 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTTGAGCATGATGTTTAAATCCTTCGGGTCATCTGTC
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * * * * *
18573 AGGCTTTTGAGTAAGATGATAAAGCCTTCGGGAAATCCATAAGACCTTCAGTGTTGGATGTTTTC
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
* * *
18638 AAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTTCTAATTATCTCAAAAGAGTTGTTA
131 AAATGAGATTTTAGAAACTAAGCC----TTTAA-GGATTTCCTAATTATCTAAAAAGAGTTGTTA
* *
18703 AAGGAAGGTAAGCCAAACAAAGGGGTTCCTTGACAACTAATAAACTAAGCTTTCGAGGGTTTCTT
191 AAGGAAGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTT
18768 GATTC
256 GATTC
* * * * *
18773 GTAAGTCCTTCAGTCCATCTATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * *
18838 AGCCTTTCGAGCAAGATGAT-AAGTCATTCGGGCCATTCATAAGACCTT
66 AGCCTTTCGAGCAAGATGATAAAG-CCTTCGGGACATCCATAAGACCTT
18886 TGGGCAGAAT
Statistics
Matches: 337, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
260 142 0.42
264 7 0.02
265 188 0.56
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (260 bp):
GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
AGCCTTTCGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
AAATGAGATTTTAGAAACTAAGCCTTTAAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
AGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTC
Found at i:18886 original size:42 final size:42
Alignment explanation
Indices: 18787--18886 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
18777 GTCCTTCAGT
* * * *
18787 CCATCTATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
1 CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
* *
18829 TCATCTATAAGCCTTTCGAGCAAGATG-ATAAGTCATTCGGG
1 CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
18870 CCAT-TCATAAGACCTTT
1 CCATCT-ATAAG-CCTTT
18887 GGGCAGAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
40 1 0.02
41 19 0.39
42 29 0.59
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (42 bp):
CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
Found at i:19290 original size:3 final size:3
Alignment explanation
Indices: 19275--19324 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
19265 TCTTATACCA
* *
19275 TAT TAT T-T T-T TAT TA- TAT TAT TAT TAT TAT TAT TA- AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19319 TAT TAT
1 TAT TAT
19325 AAATAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:19304 original size:17 final size:17
Alignment explanation
Indices: 19274--19325 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
19264 TTCTTATACC
19274 ATATTATT-TT-TTATT
1 ATATTATTATTATTATT
19289 ATATTATTATTATTATT
1 ATATTATTATTATTATT
* *
19306 AT-TAAATAATTATTATT
1 ATAT-TATTATTATTATT
19323 ATA
1 ATA
19326 AATAAACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.26
16 3 0.10
17 20 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATTATTATTATT
Found at i:19307 original size:20 final size:20
Alignment explanation
Indices: 19275--19324 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
19265 TCTTATACCA
*
19275 TATTATT-TT-TTATTATAT
1 TATTATTATTATTATTAAAT
19293 TATTATTATTATTATTAAAT
1 TATTATTATTATTATTAAAT
*
19313 AATTATTATTAT
1 TATTATTATTAT
19325 AAATAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.25
19 2 0.07
20 19 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATTATTATTAAAT
Found at i:19331 original size:20 final size:20
Alignment explanation
Indices: 19294--19331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19284 TTATTATATT
* *
19294 ATTATTATTATTATTAAATA
1 ATTATTATTATAAATAAATA
19314 ATTATTATTATAAATAAA
1 ATTATTATTATAAATAAA
19332 CTATAACAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTATTATAAATAAATA
Found at i:19988 original size:42 final size:41
Alignment explanation
Indices: 19924--20017 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 41
19914 TTGTAAGTCA
* * * * *
19924 TTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATG-ATAAAGCC
19966 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
*
20007 TTCAGGTCATC
1 TTCGGGTCATC
20018 CATAAGACCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 16 0.35
42 30 0.65
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (41 bp):
TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
Found at i:20468 original size:265 final size:260
Alignment explanation
Indices: 19916--20553 Score: 954
Period size: 265 Copynumber: 2.4 Consensus size: 260
19906 TCCTAAATTT
*
19916 GTAAGTCATTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* *
19981 AGCCTTTCGAGCAAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTCAGTGCTGGATGCTTTC
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
* *
20046 AAATGCGATTTTAGAAACTAAGCCTTTCAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
131 AAATGAGATTTTAGAAACTAAGCCTTTAAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
* * *
20111 AGCTAAGCCTAATAAAGGGGTTCCTTGACAACTAAGAAACTAAGTTTTCGAGGGTTTCTTGATTC
196 AGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTC
* *
20176 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTTGAGCATGATGTTTAAATCCTTCGGGTCATCTGTC
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * * * * *
20241 AGGCTTTTGAGTAAGATGATAAAGCCTTCGGGAAATCCATAAGACCTTCAGTGTTGGATGTTTTC
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
* * *
20306 AAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTTCTAATTATCTCAAAAGAGTTGTTA
131 AAATGAGATTTTAGAAACTAAGCC----TTTAA-GGATTTCCTAATTATCTAAAAAGAGTTGTTA
* *
20371 AAGGAAGGTAAGCCAAACAAAGGGGTTCCTTGACAACTAATAAACTAAGCTTTCGAGGGTTTCTT
191 AAGGAAGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTT
20436 GATTC
256 GATTC
* * * * *
20441 GTAAGTCCTTCAGTCCATCTATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * *
20506 AGCCTTTCGAGCAAGATGAT-AAGTCATTCGGGCCATTCATAAGACCTT
66 AGCCTTTCGAGCAAGATGATAAAG-CCTTCGGGACATCCATAAGACCTT
20554 TGGGCAGAAT
Statistics
Matches: 337, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
260 142 0.42
264 7 0.02
265 188 0.56
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (260 bp):
GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
AGCCTTTCGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
AAATGAGATTTTAGAAACTAAGCCTTTAAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
AGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTC
Found at i:20554 original size:42 final size:42
Alignment explanation
Indices: 20455--20554 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
20445 GTCCTTCAGT
* * * *
20455 CCATCTATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
1 CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
* *
20497 TCATCTATAAGCCTTTCGAGCAAGATG-ATAAGTCATTCGGG
1 CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
20538 CCAT-TCATAAGACCTTT
1 CCATCT-ATAAG-CCTTT
20555 GGGCAGAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
40 1 0.02
41 19 0.39
42 29 0.59
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (42 bp):
CCATCTATAAGCCTTTCGAGCAAGATGCATAAATCATTCGGG
Found at i:20958 original size:3 final size:3
Alignment explanation
Indices: 20943--20992 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
20933 TCTTATACCA
* *
20943 TAT TAT T-T T-T TAT TA- TAT TAT TAT TAT TAT TAT TA- AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20987 TAT TAT
1 TAT TAT
20993 AAATAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:20972 original size:17 final size:17
Alignment explanation
Indices: 20942--20993 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
20932 TTCTTATACC
20942 ATATTATT-TT-TTATT
1 ATATTATTATTATTATT
20957 ATATTATTATTATTATT
1 ATATTATTATTATTATT
* *
20974 AT-TAAATAATTATTATT
1 ATAT-TATTATTATTATT
20991 ATA
1 ATA
20994 AATAAACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.26
16 3 0.10
17 20 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATTATTATTATT
Found at i:20975 original size:20 final size:20
Alignment explanation
Indices: 20943--20992 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
20933 TCTTATACCA
*
20943 TATTATT-TT-TTATTATAT
1 TATTATTATTATTATTAAAT
20961 TATTATTATTATTATTAAAT
1 TATTATTATTATTATTAAAT
*
20981 AATTATTATTAT
1 TATTATTATTAT
20993 AAATAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.25
19 2 0.07
20 19 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATTATTATTAAAT
Found at i:20999 original size:20 final size:20
Alignment explanation
Indices: 20962--20999 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20952 TTATTATATT
* *
20962 ATTATTATTATTATTAAATA
1 ATTATTATTATAAATAAATA
20982 ATTATTATTATAAATAAA
1 ATTATTATTATAAATAAA
21000 CTATAACAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTATTATAAATAAATA
Found at i:21657 original size:42 final size:41
Alignment explanation
Indices: 21593--21686 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 41
21583 TTGTAAGTCA
* * * * *
21593 TTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATG-ATAAAGCC
21635 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
1 TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
*
21676 TTCAGGTCATC
1 TTCGGGTCATC
21687 CATAAGACCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 16 0.35
42 30 0.65
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (41 bp):
TTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAAGCC
Found at i:22218 original size:265 final size:260
Alignment explanation
Indices: 21585--22222 Score: 936
Period size: 265 Copynumber: 2.4 Consensus size: 260
21575 TCCTAAATTT
*
21585 GTAAGTCATTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * * *
21650 AGCCTTTCGAGCAAGATGATAAAGCCTTCAGGTCATCCATAAGACCTTCATTGCTGGATGCTTTC
66 AGCCTTTTGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
* *
21715 AAATGCGATTTTAGAAACTAAGCCTTTCAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
131 AAATGAGATTTTAGAAACTAAGCCTTTAAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
* * *
21780 AGCTAAGCCTAATAAAGGGGTTCCTTGACAACTAAGAAACTAAGTTTTCGAGGGTTTCTTGATTC
196 AGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTC
* *
21845 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTTGAGCATGATGTTTAAATCCTTCGGGTCATCTGTC
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * * * * *
21910 AGGCTTTTGAGTAAGATGATAAAGCCTTTGGGAAATCCATAAGACCTTCAGTGTTGGATGTTTTC
66 AGCCTTTTGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
* * *
21975 AAATGAGATTTTAGAAACTAAGCCTAATTTTAAGGGGTTTTCTAATTATCTCAAAAGAGTTGTTA
131 AAATGAGATTTTAGAAACTAAGCC----TTTAA-GGATTTCCTAATTATCTAAAAAGAGTTGTTA
* *
22040 AAGGAAGGTAAGCCAAACAAAGGGGTTCCTTGACAACTAATAAACTAAGCTTTCGAGGGTTTCTT
191 AAGGAAGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTT
22105 GATTC
256 GATTC
* * * * *
22110 GTAAGTCCTTCAGTCCATCTATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * *
22175 AGCCTTTTGAGCAAGATGAT-AAGTCATTCGGGCCATTCATAAGACCTT
66 AGCCTTTTGAGCAAGATGATAAAG-CCTTCGGGACATCCATAAGACCTT
22223 TGGGCAGAAT
Statistics
Matches: 335, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
260 140 0.42
264 7 0.02
265 188 0.56
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (260 bp):
GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
AGCCTTTTGAGCAAGATGATAAAGCCTTCGGGACATCCATAAGACCTTCAGTGCTGGATGCTTTC
AAATGAGATTTTAGAAACTAAGCCTTTAAGGATTTCCTAATTATCTAAAAAGAGTTGTTAAAGGA
AGCTAAGCCAAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTC
Found at i:22627 original size:3 final size:3
Alignment explanation
Indices: 22612--22661 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
22602 TCTTATACCA
* *
22612 TAT TAT T-T T-T TAT TA- TAT TAT TAT TAT TAT TAT TA- AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22656 TAT TAT
1 TAT TAT
22662 AAATAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:22641 original size:17 final size:17
Alignment explanation
Indices: 22611--22662 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
22601 TTCTTATACC
22611 ATATTATT-TT-TTATT
1 ATATTATTATTATTATT
22626 ATATTATTATTATTATT
1 ATATTATTATTATTATT
* *
22643 AT-TAAATAATTATTATT
1 ATAT-TATTATTATTATT
22660 ATA
1 ATA
22663 AATAAACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.26
16 3 0.10
17 20 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATTATTATTATT
Found at i:22644 original size:20 final size:20
Alignment explanation
Indices: 22612--22661 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
22602 TCTTATACCA
*
22612 TATTATT-TT-TTATTATAT
1 TATTATTATTATTATTAAAT
22630 TATTATTATTATTATTAAAT
1 TATTATTATTATTATTAAAT
*
22650 AATTATTATTAT
1 TATTATTATTAT
22662 AAATAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.25
19 2 0.07
20 19 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATTATTATTAAAT
Found at i:22668 original size:20 final size:20
Alignment explanation
Indices: 22631--22668 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22621 TTATTATATT
* *
22631 ATTATTATTATTATTAAATA
1 ATTATTATTATAAATAAATA
22651 ATTATTATTATAAATAAA
1 ATTATTATTATAAATAAA
22669 CTATAACAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTATTATAAATAAATA
Found at i:23468 original size:17 final size:17
Alignment explanation
Indices: 23446--23482 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
23436 CTCCATCGAA
23446 GCCTCCAGAAGCACCAC
1 GCCTCCAGAAGCACCAC
23463 GCCTCCAGAAGCACCAC
1 GCCTCCAGAAGCACCAC
23480 GCC
1 GCC
23483 GGCCGAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.49, G:0.19, T:0.05
Consensus pattern (17 bp):
GCCTCCAGAAGCACCAC
Found at i:24067 original size:2 final size:2
Alignment explanation
Indices: 24056--24086 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24046 CTACTGAAAA
24056 AT AT -T 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
24087 TAGTTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:27174 original size:19 final size:19
Alignment explanation
Indices: 27150--27232 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 19
27140 AACTCCTTCG
27150 TTGCATTTGTATTTTCATT
1 TTGCATTTGTATTTTCATT
* *
27169 TTGCATTCGTACTTT-ATT
1 TTGCATTTGTATTTTCATT
* *
27187 TTGCATTTATCTTTTTACATT
1 TTGCATTTGT-ATTTT-CATT
*
27208 TT-CATTTGCATTTTCATT
1 TTGCATTTGTATTTTCATT
*
27226 TTACATT
1 TTGCATT
27233 CACATCTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 17 0.33
19 24 0.47
20 5 0.10
21 5 0.10
ACGTcount: A:0.18, C:0.14, G:0.07, T:0.60
Consensus pattern (19 bp):
TTGCATTTGTATTTTCATT
Found at i:29739 original size:18 final size:17
Alignment explanation
Indices: 29697--29742 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
29687 CATCTATTAG
29697 GAAAAAAAAGAAAGAAA
1 GAAAAAAAAGAAAGAAA
*
29714 GAAGAAAAAGAAAGGAAA
1 GAAAAAAAAGAAA-GAAA
29732 -ATAAAAAAAGA
1 GA-AAAAAAAGA
29743 TATGAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
GAAAAAAAAGAAAGAAA
Found at i:32795 original size:42 final size:41
Alignment explanation
Indices: 32748--32826 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 41
32738 TTAGGCCATT
* * * * *
32748 TGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATC
1 TGTAAGCCTTTCAAGCAAGATG-ATAAAGCCTTCGGGTCATC
32790 TGTAAGCCTTTCAAGCAAGATGATAAAGCCTTCGGGT
1 TGTAAGCCTTTCAAGCAAGATGATAAAGCCTTCGGGT
32827 TATCCATAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 13 0.41
42 19 0.59
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (41 bp):
TGTAAGCCTTTCAAGCAAGATGATAAAGCCTTCGGGTCATC
Found at i:33259 original size:20 final size:20
Alignment explanation
Indices: 33234--33304 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
33224 TTCTTGATTC
33234 GTAAGTCCTTCGGGTCATCT
1 GTAAGTCCTTCGGGTCATCT
* * *
33254 GTAAGTCTTTCGAG-CATGAT
1 GTAAGTCCTTCGGGTCAT-CT
*
33274 GTTTAAATCCTTCGGGTCATCT
1 G--TAAGTCCTTCGGGTCATCT
*
33296 ATAAG-CCTT
1 GTAAGTCCTT
33305 TCTAGCAAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
19 7 0.18
20 17 0.45
22 11 0.29
23 3 0.08
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
GTAAGTCCTTCGGGTCATCT
Found at i:33306 original size:42 final size:41
Alignment explanation
Indices: 33239--33347 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
33229 GATTCGTAAG
* * * *
33239 TCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGTTTAAA
1 TCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATG-ATAAA
* *
33281 TCCTTCGGGTCATCTATAAGCCTTTCTAGCAAGATGATAAG
1 TCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAA
* * *
33322 TCCTTCAGGCCATTTATAAGACCTTT
1 TCCTTCGGGTCATCTATAAG-CCTTT
33348 GGGAAGAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 20 0.35
42 37 0.65
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (41 bp):
TCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAA
Found at i:33751 original size:3 final size:3
Alignment explanation
Indices: 33736--33773 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
33726 TCTTGTCCCA
33736 TAT TAT T-T T-T TAT TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
33774 AATAATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35631 original size:25 final size:25
Alignment explanation
Indices: 35603--35650 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
35593 AGACTGATTT
*
35603 ATCT-TTTAAAATGATATTTTTTAAA
1 ATCTCTTTAAAA-GATAATTTTTAAA
35628 ATCTCTTTAAAAGATAATTTTTA
1 ATCTCTTTAAAAGATAATTTTTA
35651 GGTATTAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (25 bp):
ATCTCTTTAAAAGATAATTTTTAAA
Found at i:39045 original size:55 final size:55
Alignment explanation
Indices: 38979--39283 Score: 270
Period size: 55 Copynumber: 5.5 Consensus size: 55
38969 AATAACAAGC
* **
38979 ATGCTCCCTATTCCTTCAGGAAGTATA-AGACTCGAACAATATTCATAAAATGTAT
1 ATGCTCCCTATTCCTTCAGGAAGTATAGA-ACTCGAACAATCTTCATAAAATGGGT
* * * * * *
39034 ATGCTCCCTATTCGTTCAGGGAGTATA-AGACTTGAATAATCTTCA-ATAAACGAGT
1 ATGCTCCCTATTCCTTCAGGAAGTATAGA-ACTCGAACAATCTTCATA-AAATGGGT
* * *
39089 -TCGCTCCCTATTCGTTCAGGGAGTATTGAACTCGAACAATCTTCATAAAATGGGT
1 AT-GCTCCCTATTCCTTCAGGAAGTATAGAACTCGAACAATCTTCATAAAATGGGT
* * * *
39144 CTGCTCTCTATTCCTTCA-GAGAGTATAGAACTCGAATAATCTTCA-ACAAACGGGT
1 ATGCTCCCTATTCCTTCAGGA-AGTATAGAACTCGAACAATCTTCATA-AAATGGGT
** * *
39199 CCGCTCTCTATTCCTTCA-GAGAGTATAGAACTCAAACAATCTTCATAAAATGGGT
1 ATGCTCCCTATTCCTTCAGGA-AGTATAGAACTCGAACAATCTTCATAAAATGGGT
39254 -TCGCTCCCTATT-CTATCA-GAGAGTATAGAA
1 AT-GCTCCCTATTCCT-TCAGGA-AGTATAGAA
39284 TTCAATCTTC
Statistics
Matches: 215, Mismatches: 25, Indels: 20
0.83 0.10 0.08
Matches are distributed among these distances:
54 6 0.03
55 205 0.95
56 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (55 bp):
ATGCTCCCTATTCCTTCAGGAAGTATAGAACTCGAACAATCTTCATAAAATGGGT
Found at i:39281 original size:110 final size:108
Alignment explanation
Indices: 38981--39283 Score: 371
Period size: 110 Copynumber: 2.8 Consensus size: 108
38971 TAACAAGCAT
* **
38981 GCTCCCTATTCCTTCAGGAAGTATA-AGACTCGAACAATATTCATAAAATGTATAT-GCTCCCTA
1 GCTCCCTATTCCTTCAGG-AGTATAGA-ACTCGAACAATCTTCATAAAATGGGT-TCGCTCCCTA
* * * *
39044 TTCGTTCAGGGAGTATA-AGACTTGAATAATCTTCAATAAACGAGTTC
63 TTC-TTCAGAGAGTATAGA-ACTCGAATAATCTTCAACAAACGAGTCC
* * *
39091 GCTCCCTATTCGTTCAGGGAGTATTGAACTCGAACAATCTTCATAAAATGGG-TCTGCTCTCTAT
1 GCTCCCTATTCCTTCA-GGAGTATAGAACTCGAACAATCTTCATAAAATGGGTTC-GCTCCCTAT
*
39155 TCCTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAACGGGTCC
64 T-CTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAACGAGTCC
* *
39201 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCATAAAATGGGTTCGCTCCCTATT
1 GCTCCCTATTCCTTCAG-GAGTATAGAACTCGAACAATCTTCATAAAATGGGTTCGCTCCCTATT
39266 CTATCAGAGAGTATAGAA
65 CT-TCAGAGAGTATAGAA
39284 TTCAATCTTC
Statistics
Matches: 168, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
108 1 0.01
109 3 0.02
110 157 0.93
111 7 0.04
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (108 bp):
GCTCCCTATTCCTTCAGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTTCGCTCCCTATTC
TTCAGAGAGTATAGAACTCGAATAATCTTCAACAAACGAGTCC
Found at i:39351 original size:36 final size:36
Alignment explanation
Indices: 39299--39442 Score: 198
Period size: 36 Copynumber: 3.9 Consensus size: 36
39289 TCTTCATAAA
39299 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATG
1 ATGA-TTTGCTTCACTACTCTTCCGTGAAGGCTTATG
39336 ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTATG
1 ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTATG
* *
39372 ATGATTTGTTTCACTACTCTTCCGTGAAGGCTTAAG
1 ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTATG
* * * * * *
39408 TTTGAATTGCTTCATTGCTCTTTCATGAAGGCTTA
1 -ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
39443 AGATTGAACT
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 66 0.68
37 31 0.32
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (36 bp):
ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTATG
Found at i:39699 original size:17 final size:17
Alignment explanation
Indices: 39667--39699 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39657 TATCTTCGTC
39667 TCAATGCTTCAATATCT
1 TCAATGCTTCAATATCT
39684 TCAAT-CTTCAACTATC
1 TCAATGCTTCAA-TATC
39700 CCTGTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.39
Consensus pattern (17 bp):
TCAATGCTTCAATATCT
Found at i:40750 original size:7 final size:7
Alignment explanation
Indices: 40734--40888 Score: 72
Period size: 7 Copynumber: 22.7 Consensus size: 7
40724 CTTTTATTTA
40734 TTTTTC-
1 TTTTTCT
40740 TTTTTCT
1 TTTTTCT
*
40747 TTTTTCA
1 TTTTTCT
**
40754 TCATT-T
1 TTTTTCT
*
40760 TTTATCT
1 TTTTTCT
*
40767 TTCTTCT
1 TTTTTCT
*
40774 TTATTCT
1 TTTTTCT
40781 TTTTTCAT
1 TTTTTC-T
*
40789 TTTTTAT
1 TTTTTCT
*
40796 TTTCTCT
1 TTTTTCT
*
40803 TTTCTCT
1 TTTTTCT
40810 TTTCTTC-
1 TTT-TTCT
40817 TTTTTCT
1 TTTTTCT
*** *
40824 TTCACCA
1 TTTTTCT
40831 TTTTTC-
1 TTTTTCT
*
40837 ATTTT-T
1 TTTTTCT
* *
40843 TTTCTCA
1 TTTTTCT
*
40850 TTTTTCA
1 TTTTTCT
40857 TTTTTCAT
1 TTTTTC-T
40865 TTTTT-T
1 TTTTTCT
40871 TTTTT-T
1 TTTTTCT
*
40877 TTTTTAT
1 TTTTTCT
40884 TTTTT
1 TTTTT
40889 TTTATTTTTT
Statistics
Matches: 112, Mismatches: 28, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
6 30 0.27
7 69 0.62
8 13 0.12
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCT
Found at i:40764 original size:30 final size:29
Alignment explanation
Indices: 40730--40812 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 29
40720 CCCCCTTTTA
40730 TTTATTTTTCTTTTTCTTTTTTCATCATTT
1 TTTATTTTTCTTTTTCTTTTTT-ATCATTT
* * *
40760 TTTATCTTTCTTCTTTATTCTTTTTTCATTT
1 TTTATTTTTCTT-TTTCTT-TTTTATCATTT
40791 TTTATTTTCTCTTTTCTCTTTT
1 TTTATTTT-TCTTTT-TCTTTT
40813 CTTCTTTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 11 0.25
31 22 0.50
32 11 0.25
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTATTTTTCTTTTTCTTTTTTATCATTT
Found at i:40815 original size:34 final size:32
Alignment explanation
Indices: 40734--40820 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 32
40724 CTTTTATTTA
40734 TTTTTCTTTTTCTTTTTTCATCATTTTTTATC
1 TTTTTCTTTTTCTTTTTTCATCATTTTTTATC
* *
40766 TTTCTTCTTTATTCTTTTTTCAT-TTTTTATTTTC
1 TTT-TTCTTT-TTCTTTTTTCATCATTTT-TTATC
40800 TCTTTTCTCTTTTCTTCTTTT
1 T-TTTTCT-TTTTCTT-TTTT
40821 TCTTTCACCA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
32 3 0.06
33 10 0.21
34 26 0.55
35 8 0.17
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTTCTTTTTCTTTTTTCATCATTTTTTATC
Found at i:40868 original size:1 final size:1
Alignment explanation
Indices: 40864--40898 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
40854 TCATTTTTCA
* *
40864 TTTTTTTTTTTTTTTTTTATTTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40899 CATCAAGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:40874 original size:20 final size:20
Alignment explanation
Indices: 40733--40861 Score: 61
Period size: 20 Copynumber: 6.3 Consensus size: 20
40723 CCTTTTATTT
* *
40733 ATTTTTCTTTTTCTTTTTTC
1 ATTTTTTTTTTTCATTTTTC
** *
40753 ATCATTTTTTATC-TTTCTTC
1 ATTTTTTTTTTTCATTT-TTC
*
40773 -TTTATTCTTTTTTCATTTTTT
1 ATTT-TT-TTTTTTCATTTTTC
* *
40794 ATTTTCTCTTTTC-TCTTTTC
1 ATTTTTTTTTTTCAT-TTTTC
*
40814 -TTCTTTTTCTTTCACCATTTTTC
1 ATT-TTTTT-TTT--TCATTTTTC
*
40837 A-TTTTTTTTCTCATTTTTC
1 ATTTTTTTTTTTCATTTTTC
40856 ATTTTT
1 ATTTTT
40862 CATTTTTTTT
Statistics
Matches: 80, Mismatches: 16, Indels: 26
0.66 0.13 0.21
Matches are distributed among these distances:
19 16 0.20
20 31 0.39
21 14 0.17
22 11 0.14
23 7 0.09
24 1 0.01
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTTTTTTTTCATTTTTC
Found at i:40896 original size:26 final size:28
Alignment explanation
Indices: 40831--40898 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 28
40821 TCTTTCACCA
*
40831 TTTTTCATTTTTTTTCTCATTTTTCATTT
1 TTTTTTATTTTTTTTCT-ATTTTTCATTT
40860 TTCATTTT-TTTTTTTT-T-TTTTT-ATTT
1 TT--TTTTATTTTTTTTCTATTTTTCATTT
40886 TTTTTTATTTTTT
1 TTTTTTATTTTTT
40899 CATCAAGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
24 4 0.11
25 6 0.17
26 6 0.17
27 5 0.14
29 3 0.09
30 8 0.23
31 3 0.09
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (28 bp):
TTTTTTATTTTTTTTCTATTTTTCATTT
Found at i:54044 original size:22 final size:22
Alignment explanation
Indices: 54016--54062 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
54006 AAAAGGATTT
54016 GGACCCACTAGCTATGATACTA
1 GGACCCACTAGCTATGATACTA
54038 GGACCCACTAGCTATGATACTA
1 GGACCCACTAGCTATGATACTA
54060 GGA
1 GGA
54063 ACCATAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (22 bp):
GGACCCACTAGCTATGATACTA
Found at i:54839 original size:10 final size:10
Alignment explanation
Indices: 54824--54850 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54814 TACAACTTCC
54824 TATATTAAAT
1 TATATTAAAT
54834 TATATTAAAT
1 TATATTAAAT
54844 TATATTA
1 TATATTA
54851 CAAATAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATTAAAT
Found at i:59193 original size:24 final size:24
Alignment explanation
Indices: 59166--59215 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
59156 ACAAAAAATA
*
59166 TAATTAGTTTAAA-AAATAATTAAT
1 TAATTAATTTAAATAAATAA-TAAT
59190 TAATTAATTTAAATAAATAATAAT
1 TAATTAATTTAAATAAATAATAAT
59214 TA
1 TA
59216 TATAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TAATTAATTTAAATAAATAATAAT
Found at i:59242 original size:30 final size:30
Alignment explanation
Indices: 59175--59271 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
59165 ATAATTAGTT
* * *
59175 TAAAAAATAATTA-ATTAAT-TAATTTAAA
1 TAAAAAATAATTATATAAATATTATTTTAA
*
59203 TAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAATAATTATATAAATATTATTTTAA
* * *
59233 TAAAAAATAA-TATTTATATAATTATATTAA
1 TAAAAAATAATTATATAAAT-ATTATTTTAA
*
59263 TATAAAATA
1 TAAAAAATA
59272 TAAAAACTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 12 0.21
29 12 0.21
30 33 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TAAAAAATAATTATATAAATATTATTTTAA
Found at i:59927 original size:52 final size:52
Alignment explanation
Indices: 59849--59962 Score: 228
Period size: 52 Copynumber: 2.2 Consensus size: 52
59839 CTTCTATTTG
59849 ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
1 ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
59901 ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
1 ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
59953 ATACGAAATT
1 ATACGAAATT
59963 ATGGTTTCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (52 bp):
ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
Found at i:75125 original size:22 final size:22
Alignment explanation
Indices: 75097--75143 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
75087 AAAAGGATTT
75097 GGACCCACTAGCTATGATACTA
1 GGACCCACTAGCTATGATACTA
75119 GGACCCACTAGCTATGATACTA
1 GGACCCACTAGCTATGATACTA
75141 GGA
1 GGA
75144 ACCATAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (22 bp):
GGACCCACTAGCTATGATACTA
Found at i:75913 original size:10 final size:10
Alignment explanation
Indices: 75898--75924 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
75888 TACAACTTCC
75898 TATATTAAAT
1 TATATTAAAT
75908 TATATTAAAT
1 TATATTAAAT
75918 TATATTA
1 TATATTA
75925 CAAATAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATTAAAT
Found at i:80259 original size:19 final size:20
Alignment explanation
Indices: 80224--80267 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
80214 TTAGTTTAAA
* *
80224 AAATAATTAATTAATTATTT
1 AAATAAATAATTAATTATAT
80244 AAATAAATAA-TAATTATAT
1 AAATAAATAATTAATTATAT
80263 AAATA
1 AAATA
80268 TTATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAAATAATTAATTATAT
Found at i:80273 original size:30 final size:32
Alignment explanation
Indices: 80237--80312 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 32
80227 TAATTAATTA
*
80237 ATTATTTAAATAAATAAT-A-ATTATATAAAT
1 ATTATTTAAATAAAAAATAATATTATATAAAT
* *
80267 ATTATTTTAATAAAAAATAATATTATATAATT
1 ATTATTTAAATAAAAAATAATATTATATAAAT
80299 A-TA-TTAATATAAAA
1 ATTATTTAA-ATAAAA
80313 TAAAAACTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 19 0.49
31 9 0.23
32 11 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATTATTTAAATAAAAAATAATATTATATAAAT
Found at i:80966 original size:52 final size:52
Alignment explanation
Indices: 80888--81001 Score: 228
Period size: 52 Copynumber: 2.2 Consensus size: 52
80878 TCTTCTATTG
80888 ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
1 ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
80940 ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
1 ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
80992 ATACGAAATT
1 ATACGAAATT
81002 ATGGTTTCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (52 bp):
ATACGAAATTGGACGACTTTGTTGCAGTAAACCATCAGTAGGTGTCCTAGCT
Done.