Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007931.1 Hibiscus syriacus cultivar Beakdansim tig00110339_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: 2341804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:344537 original size:19 final size:20
Alignment explanation
Indices: 344494--344541 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
344484 TCTAAATCCA
*
344494 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
344514 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
344533 TTTTCAAAA
1 TTTTCAAAA
344542 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:346146 original size:13 final size:13
Alignment explanation
Indices: 346124--346157 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
346114 AAAACAGTTC
346124 GAAAAGAAAAAACA
1 GAAAA-AAAAAACA
346138 GAAAAAAAAAACA
1 GAAAAAAAAAACA
346151 GAAAAAA
1 GAAAAAA
346158 GGAAAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAACA
Found at i:346155 original size:21 final size:20
Alignment explanation
Indices: 346131--346170 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
346121 TTCGAAAAGA
346131 AAAAACAGAAAAAAAAAACAG
1 AAAAA-AGAAAAAAAAAACAG
* *
346152 AAAAAAGGAAAAAACAACA
1 AAAAAAGAAAAAAAAAACA
346171 ACAAAAGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAAACAG
Found at i:355638 original size:2 final size:2
Alignment explanation
Indices: 355631--355674 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
355621 TGATACTTCA
355631 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
355673 AT
1 AT
355675 TTGATGCTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:361066 original size:79 final size:79
Alignment explanation
Indices: 360891--361048 Score: 217
Period size: 79 Copynumber: 2.0 Consensus size: 79
360881 TTGAATTTAT
* *
360891 AATAAACTATGATAATTAATATGATTACTTTTTAAAAGTTAAAACAAAATGTTAGTTATAATAAT
1 AATAAACTATGATAATTAATATGATTACTCTTAAAAAGTTAAAACAAAATGTTAGTTATAATAAT
*** * *
360956 TTGTTTGACAATTA
66 TAAATTAAAAATTA
* * *
360970 AATAAACTATGATAATTAATATGATTACTCTTAAAAAGTTAATATAAATTGTTAGTTATAATAAT
1 AATAAACTATGATAATTAATATGATTACTCTTAAAAAGTTAAAACAAAATGTTAGTTATAATAAT
361035 TAAATTAATAAATT
66 TAAATTAA-AAATT
361049 TACTTTCTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 64 0.94
80 4 0.06
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (79 bp):
AATAAACTATGATAATTAATATGATTACTCTTAAAAAGTTAAAACAAAATGTTAGTTATAATAAT
TAAATTAAAAATTA
Found at i:361843 original size:12 final size:11
Alignment explanation
Indices: 361826--361996 Score: 105
Period size: 12 Copynumber: 14.6 Consensus size: 11
361816 ATGTTTAATG
361826 ATATATATACTT
1 ATATATATA-TT
*
361838 ATATATA-CTT
1 ATATATATATT
*
361848 ATGTATATACTT
1 ATATATATA-TT
*
361860 TTATATATATCT
1 ATATATATAT-T
*
361872 ATATCTATATCT
1 ATATATATAT-T
*
361884 ATATCTATATCT
1 ATATATATAT-T
*
361896 ATATCTATATCT
1 ATATATATAT-T
*
361908 ATATCTATATCT
1 ATATATATAT-T
*
361920 ATATATATACAT
1 ATATATATA-TT
361932 ATACTTATATATT
1 ATA--TATATATT
*
361945 ATACTTTATACTT
1 ATA-TATATA-TT
361958 ATATATATATT
1 ATATATATATT
361969 -TATATAT-TT
1 ATATATATATT
* *
361978 ATATACATACCT
1 ATATATATA-TT
361990 ATATATA
1 ATATATA
361997 GATACTGTTA
Statistics
Matches: 133, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
9 2 0.02
10 21 0.16
11 3 0.02
12 92 0.69
13 9 0.07
14 6 0.05
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (11 bp):
ATATATATATT
Found at i:361876 original size:6 final size:6
Alignment explanation
Indices: 361865--361928 Score: 119
Period size: 6 Copynumber: 10.7 Consensus size: 6
361855 TACTTTTATA
361865 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
*
361913 TATATC TATATA TATA
1 TATATC TATATC TATA
361929 CATATACTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:361934 original size:18 final size:17
Alignment explanation
Indices: 361826--361996 Score: 101
Period size: 16 Copynumber: 10.2 Consensus size: 17
361816 ATGTTTAATG
361826 ATATA-TATA-CT-TAT
1 ATATACTATATCTATAT
*
361840 ATATACT-TATGTATAT
1 ATATACTATATCTATAT
* * *
361856 ACT-T-TTATATATATCT
1 A-TATACTATATCTATAT
361872 ATAT-CTATATCTATAT
1 ATATACTATATCTATAT
*
361888 CTATATCTATATCTATAT
1 ATATA-CTATATCTATAT
*
361906 CTATATCTATATCTATAT
1 ATATA-CTATATCTATAT
361924 ATATAC-ATATACTTATAT
1 ATATACTATAT-C-TATAT
*
361942 ATTATACTTTATACTTATAT
1 A-TATACTATAT-C-TATAT
* * *
361962 ATATA-TTTATATATTT
1 ATATACTATATCTATAT
*
361978 ATATAC-ATACCTATAT
1 ATATACTATATCTATAT
361994 ATA
1 ATA
361997 GATACTGTTA
Statistics
Matches: 128, Mismatches: 16, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 7 0.05
15 4 0.03
16 48 0.38
17 3 0.02
18 45 0.35
19 9 0.07
20 12 0.09
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (17 bp):
ATATACTATATCTATAT
Found at i:361966 original size:6 final size:6
Alignment explanation
Indices: 361826--361996 Score: 84
Period size: 6 Copynumber: 28.5 Consensus size: 6
361816 ATGTTTAATG
* * *
361826 ATATAT ATACT-T ATATAT ACT-TAT GTATAT ACT-TTT ATATAT ATCTAT
1 ATATAT ATA-TAT ATATAT A-TATAT ATATAT A-TATAT ATATAT ATATAT
* * * * * * * *
361874 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
361922 ATATAT ACATAT ACT-TAT ATAT-T ATACTTT ATACT-T ATATAT ATATTT
1 ATATAT ATATAT A-TATAT ATATAT ATA-TAT ATA-TAT ATATAT ATATAT
* * * *
361970 ATATAT TTATAT ACATAC CTATAT ATA
1 ATATAT ATATAT ATATAT ATATAT ATA
361997 GATACTGTTA
Statistics
Matches: 136, Mismatches: 18, Indels: 22
0.77 0.10 0.12
Matches are distributed among these distances:
5 9 0.07
6 118 0.87
7 9 0.07
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:361995 original size:20 final size:19
Alignment explanation
Indices: 361826--361995 Score: 98
Period size: 18 Copynumber: 8.9 Consensus size: 19
361816 ATGTTTAATG
361826 ATATATATACTTATATATACTT
1 ATATATATAC-TATATAT--TT
* * *
361848 ATGTATATACT-TTTATAT
1 ATATATATACTATATATTT
* * *
361866 ATATCTATA-TCTATATCT
1 ATATATATACTATATATTT
* * *
361884 ATATCTATA-TCTATATCT
1 ATATATATACTATATATTT
* * *
361902 ATATCTATA-TCTATATCT
1 ATATATATACTATATATTT
*
361920 ATATATATAC-ATATACTT
1 ATATATATACTATATATTT
* *
361938 ATATATTATACTTTATACTT
1 ATATA-TATACTATATATTT
*
361958 ATATATATATTTATATATTT
1 ATATATATA-CTATATATTT
*
361978 ATATACATACCTATATAT
1 ATATATATA-CTATATAT
361996 AGATACTGTT
Statistics
Matches: 125, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
17 1 0.01
18 67 0.54
19 9 0.07
20 38 0.30
21 1 0.01
22 9 0.07
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.51
Consensus pattern (19 bp):
ATATATATACTATATATTT
Found at i:362545 original size:16 final size:16
Alignment explanation
Indices: 362526--362557 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
362516 ATATATATAG
362526 GTATAAGTATACATAT
1 GTATAAGTATACATAT
*
362542 GTATAAGTATATATAT
1 GTATAAGTATACATAT
362558 ACTTATATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (16 bp):
GTATAAGTATACATAT
Found at i:362558 original size:22 final size:22
Alignment explanation
Indices: 362516--362583 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
362506 GTGTGTAATT
*
362516 ATATATATAGGTATAAGTATAC
1 ATATATATAAGTATAAGTATAC
*
362538 ATATGTATAAGTATATA-TATAC
1 ATATATATAAGTATA-AGTATAC
**
362560 TTATATCATATACTTATAAGTATA
1 --ATAT-ATATAAGTATAAGTATA
362584 ATGTATAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
22 18 0.50
23 1 0.03
24 5 0.14
25 12 0.33
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (22 bp):
ATATATATAAGTATAAGTATAC
Found at i:362652 original size:2 final size:2
Alignment explanation
Indices: 362645--362695 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
362635 TGCATAACAT
362645 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
362687 TA TA TA TA T
1 TA TA TA TA T
362696 TAAAATTGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:365976 original size:18 final size:18
Alignment explanation
Indices: 365933--365978 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
365923 AAATAATAGT
*
365933 ATAGAGGAGGCAAAGAAG
1 ATAGAGGAGGCAAAAAAG
** *
365951 GCATAGGAGGCAAAAAAG
1 ATAGAGGAGGCAAAAAAG
365969 ATAGAGGAGG
1 ATAGAGGAGG
365979 TAGAAGAGAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.39, T:0.07
Consensus pattern (18 bp):
ATAGAGGAGGCAAAAAAG
Found at i:366033 original size:34 final size:34
Alignment explanation
Indices: 365995--366068 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
365985 AGAAGGAAGA
365995 AGAGTGTAATAGCTTATCTTCTTATGAAAGAACC
1 AGAGTGTAATAGCTTATCTTCTTATGAAAGAACC
366029 AGAGTGTAATAGCTTATCTTCTTATGAAAGAACC
1 AGAGTGTAATAGCTTATCTTCTTATGAAAGAACC
366063 AGAGTG
1 AGAGTG
366069 ACACACATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (34 bp):
AGAGTGTAATAGCTTATCTTCTTATGAAAGAACC
Found at i:366237 original size:18 final size:18
Alignment explanation
Indices: 366195--366239 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
366185 GGCTAGGAGG
* *
366195 TAGAGGAGGCAAAGAAGG
1 TAGAGGAGGCAAAAAAGA
* *
366213 CATAGGAGGCAAAAAAGA
1 TAGAGGAGGCAAAAAAGA
366231 TAGAGGAGG
1 TAGAGGAGG
366240 TAGAAGAGAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07
Consensus pattern (18 bp):
TAGAGGAGGCAAAAAAGA
Found at i:377895 original size:23 final size:23
Alignment explanation
Indices: 377877--377937 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
377867 CTCGTATAAA
377877 TACACCGAAGTGCCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
* *
377900 TACACCGAAGTACCGCGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
* *
377923 TACATCGTAGTGCCA
1 TACACCGAAGTGCCA
377938 TATAAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAT
Found at i:385627 original size:63 final size:65
Alignment explanation
Indices: 385518--385679 Score: 154
Period size: 63 Copynumber: 2.5 Consensus size: 65
385508 ATCCCTTGAC
* * * *
385518 GGGTGCATCGATGTACTA-TCTATGCATCGATACA-TAAATCCTATTCGATGTTTGTA-TTTAAG
1 GGGTGCATCGATGCACTACT-TGTGCATCGATACACTAAATCCTATTCGAAGTTTGTATTTTAAA
385580 G
65 G
* * *
385581 GGGTGCATCGATGCACTACTTGTGCATCGATACACT-GATGGC-ATTCGAAGTTTTTATTTTAAA
1 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAAAT-CCTATTCGAAGTTTGTATTTTAAA
*
385644 T
65 G
** * * *
385645 TAGTGCATCGATGCACTTCATGTGCAACGATACAC
1 GGGTGCATCGATGCACTACTTGTGCATCGATACAC
385680 CTTGAACAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
63 44 0.54
64 38 0.46
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (65 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACACTAAATCCTATTCGAAGTTTGTATTTTAAAG
Found at i:386642 original size:30 final size:30
Alignment explanation
Indices: 386607--386665 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
386597 TGATGAAAAA
386607 ATATCAAAAAGGCTCGAGATGACATGAAAC
1 ATATCAAAAAGGCTCGAGATGACATGAAAC
*
386637 ATATCAAAAAGGCTCGAGATGCCATGAAA
1 ATATCAAAAAGGCTCGAGATGACATGAAA
386666 AAATATTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (30 bp):
ATATCAAAAAGGCTCGAGATGACATGAAAC
Found at i:392809 original size:186 final size:193
Alignment explanation
Indices: 392380--393305 Score: 946
Period size: 199 Copynumber: 4.7 Consensus size: 193
392370 CAAACATGTA
* ** * *
392380 TCGACACATTTATTGTAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAAAGTAATAGGT
1 TCGATACATTTATAATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* * * * * **
392445 AAATTTACAATGTAACCGGTAAAAATATATCGATTTTATGACATAATAGAACAACATAATGTATC
66 AAATTTACAATGTAACC---AGAGAT-T-T--AATTTATGAGAGAATAGGTCAACATAATGTATC
* * * * *
392510 GATAC-TTTTAAATTTATATCGATACCTTTGGTCCAGAATTG-ATGTCCAACGAGGTTCACGCAT
124 GATACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAA-TGAATGCCCAACGAGGTGCACGCAT
* *
392573 AAATTA
188 AAAGTG
** * **
392579 TCGATACATTTATTGTAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATAGAA
1 TCGATACATTTATAATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
392644 AAATTTACAATGTAACC-G-G-TTTAA-TTA-GA-A-AATAGGTCAACATAATGTATCGATACTT
66 AAATTTACAATGTAACCAGAGATTTAATTTATGAGAGAATAGGTCAACATAATGTATCGATAC-T
** ** *
392702 TTTTAAA-TTGTGTCGATACTTTTGGTTTAGAATGAATGCCCAACGATATGCACACATAAAGTG
130 TTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTG
** *
392765 TCGATACATTTATTGTAAGTATCGATCCTC-AAAACATCGAAACCGATTAA-TATAAAGTAATAG
1 TCGATACATTTATAATAAGTATCGATCC-CAAAAACATCGAAACCGA-TAATTATAATGTAATAG
* * *
392828 GTAAATTTACAATGTAACCAGTAGAAATATACCGATTTTATGAGAGAATAAGTCAACATAATATA
64 GTAAATTTACAATGTAACCAG-AG--ATTTA---A-TTTATGAGAGAATAGGTCAACATAATGTA
* * *
392893 TCGATACTTTTTTACA-TTGTGTCGATACTTTTGGTCCATAATGAATTCCCAACGAGGTGCACGC
122 TCGATAC-TTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGC
392957 ATAAAGTG
186 ATAAAGTG
* * *
392965 TCGATACATTTATAATAAGTATCGATCCCAATAACATCGAAATCGATAATTATAATATAATAGGT
1 TCGATACATTTATAATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* *
393030 AAA-TTACAATGTAACCAGTCAGAATATACCAATTTTATGAGAGAATAGTTCAACATAATGTATC
66 AAATTTACAATGTAACCAG--AG-AT-T--TAA-TTTATGAGAGAATAGGTCAACATAATGTATC
* **
393094 GACACTTTTTAAATTTGTGTCGATACTTTTGGTCTTGAATGAATGCCCAACGAGGTGCACGCATA
124 GATACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATA
393159 AAGTG
189 AAGTG
* * * *
393164 TCAATACATTTAAAAT-TGTATCGATCCCAAAAACATCGAAACCGATAATTGTAATGTAATAGGT
1 TCGATACATTTATAATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* * * ** * *
393228 AAATTTACAATGTAACAAAAAAATATATTGGTTTTATGAGAGAATAGGTAAACATATTGTATCGA
66 AAATTTACAATGTAAC---CAGAGAT-TT-AATTTATGAGAGAATAGGTCAACATAATGTATCGA
*
393293 CACTTTTTAAATT
126 TACTTTTTAAATT
393306 ATATCGATAT
Statistics
Matches: 624, Mismatches: 72, Indels: 64
0.82 0.09 0.08
Matches are distributed among these distances:
185 26 0.04
186 114 0.18
187 14 0.02
188 3 0.00
189 2 0.00
191 1 0.00
192 4 0.01
193 1 0.00
195 1 0.00
197 46 0.07
198 55 0.09
199 215 0.34
200 140 0.22
202 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (193 bp):
TCGATACATTTATAATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
AAATTTACAATGTAACCAGAGATTTAATTTATGAGAGAATAGGTCAACATAATGTATCGATACTT
TTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTG
Found at i:393636 original size:18 final size:17
Alignment explanation
Indices: 393613--393672 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
393603 GAACCCTAAA
393613 CCTTCTTCTCAACCAAG
1 CCTTCTTCTCAACCAAG
393630 CC--CTTCTCAACGACAA-
1 CCTTCTTCTCAAC--CAAG
*
393646 CCTTCTCCTCAACCAAG
1 CCTTCTTCTCAACCAAG
393663 CGCTTCTTCT
1 C-CTTCTTCT
393673 GAACAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
15 9 0.26
16 5 0.14
17 6 0.17
18 15 0.43
ACGTcount: A:0.22, C:0.43, G:0.07, T:0.28
Consensus pattern (17 bp):
CCTTCTTCTCAACCAAG
Found at i:394676 original size:121 final size:121
Alignment explanation
Indices: 394458--394692 Score: 425
Period size: 121 Copynumber: 1.9 Consensus size: 121
394448 GAGAATGAGA
394458 AAATAGACTCCATTGGCCATGAAGACGACCAACAATTGGGAGACACAATGATGAAAGACGCTCTA
1 AAATAGACTCCATTGGCCATGAAGACGACCAACAATTGGGAGACACAATGATGAAAGACGCTCTA
*
394523 GGTGGAGAGGATGTCACAATTAAGATAATGATGGAATACATGGTCAATTAAGGAGC
66 GGTGGAGAGGATGTCACAATTAAGACAATGATGGAATACATGGTCAATTAAGGAGC
* * *
394579 AAATAGACTCTATTGGCCATGAAGACGACCAACAATTGGGAGACGCAATGATGGAAGACGCTCTA
1 AAATAGACTCCATTGGCCATGAAGACGACCAACAATTGGGAGACACAATGATGAAAGACGCTCTA
*
394644 GGTGGAGAGGATGTCACAATTAAGACAGTGATGGAATACATGGTCAATT
66 GGTGGAGAGGATGTCACAATTAAGACAATGATGGAATACATGGTCAATT
394693 TTCGCGAGCA
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 109 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.20
Consensus pattern (121 bp):
AAATAGACTCCATTGGCCATGAAGACGACCAACAATTGGGAGACACAATGATGAAAGACGCTCTA
GGTGGAGAGGATGTCACAATTAAGACAATGATGGAATACATGGTCAATTAAGGAGC
Found at i:396310 original size:24 final size:23
Alignment explanation
Indices: 396279--396323 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
396269 TTCATTTCAT
396279 ATTTAATTGGAGTTTGAATTTAA
1 ATTTAATTGGAGTTTGAATTTAA
*
396302 ATTTCAATTTGAGTTTGAATTT
1 ATTT-AATTGGAGTTTGAATTT
396324 CAATCTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (23 bp):
ATTTAATTGGAGTTTGAATTTAA
Found at i:396312 original size:18 final size:18
Alignment explanation
Indices: 396291--396327 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
396281 TTAATTGGAG
396291 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
396309 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
396327 T
1 T
396328 CTAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:396334 original size:24 final size:24
Alignment explanation
Indices: 396283--396335 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
396273 TTTCATATTT
* * *
396283 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATCTA
*
396307 AATTTGAGTTTGAATTTCAATCTA
1 AATTTGAGTTTGAATTTAAATCTA
396331 AATTT
1 AATTT
396336 TGGATCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATCTA
Found at i:397356 original size:200 final size:198
Alignment explanation
Indices: 397098--397633 Score: 761
Period size: 200 Copynumber: 2.7 Consensus size: 198
397088 ATAGGTAAAT
*
397098 TATACCAGTTTAATGAGAGAATAGGTCAACATAATGTATCGATAATTTTTAAATTTGTATCGATA
1 TATACCGGTTTAATGAGAGAATAGGTCAACATAATGTATCGATAATTTTTAAATTTGTATCGATA
* * * *
397163 CGCTTTGTCCAGAATAGATACCCAACGAGGTGCATGCATAAAGTGTCGATACATTTATTGTAATT
66 C-TTTTGTCCAGAAT-GATACCCAACGACGTGCACGCATAAAGTGTCGATACATTTATTGTAAGT
397228 ATCGATCCCAAAAACATCGAAA-CTGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCGA
129 ATCGATCCCAAAAACATCGAAATC-GATAATTATAAAGTAATAGGTAAATTTACAATGTAACCGA
397292 AAAAAA
193 AAAAAA
* * * *
397298 TATACCGGTTTCATGAGAGAATATGTCAACATAATGTATCGATACTTTTAAAATTTGTATCGATA
1 TATACCGGTTTAATGAGAGAATAGGTCAACATAATGTATCGATAATTTTTAAATTTGTATCGATA
* * * *
397363 CTTGTTGTCCATAATTGATGCCCAACGATGTGCACACATAAAGTGTCGATACATTTATTGTAAGT
66 CTT-TTGTCCAGAA-TGATACCCAACGACGTGCACGCATAAAGTGTCGATACATTTATTGTAAGT
**
397428 ATCGATCCCAAAAACATCGAAATCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCGGT
129 ATCGATCCCAAAAACATCGAAATCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCGAA
*
397493 AAAAT
194 AAAAA
* * * *
397498 TATACCGGTTTTATGACAGAATAGGTCAACATAATGTATCGATATTTTTTAAATTTGTGTCGATA
1 TATACCGGTTTAATGAGAGAATAGGTCAACATAATGTATCGATAATTTTTAAATTTGTATCGATA
* * * **
397563 CTTTTGGTCCAGAATGA-AGGCCCAACAACGTACACGTATAAAGTGTCGATACATTTATTAAAAG
66 CTTTT-GTCCAGAATGATA--CCCAACGACGTGCACGCATAAAGTGTCGATACATTTATTGTAAG
397627 TATCGAT
128 TATCGAT
397634 ACATAATGAT
Statistics
Matches: 300, Mismatches: 30, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
199 6 0.02
200 292 0.97
201 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (198 bp):
TATACCGGTTTAATGAGAGAATAGGTCAACATAATGTATCGATAATTTTTAAATTTGTATCGATA
CTTTTGTCCAGAATGATACCCAACGACGTGCACGCATAAAGTGTCGATACATTTATTGTAAGTAT
CGATCCCAAAAACATCGAAATCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACCGAAAA
AAA
Found at i:400193 original size:23 final size:23
Alignment explanation
Indices: 400167--400217 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
400157 TAAGTAATTA
** *
400167 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCACT
*
400190 ACCTATTACGTTATATAAGCACT
1 ACCTATTACATTATATAAGCACT
400213 ACCTA
1 ACCTA
400218 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCACT
Found at i:400225 original size:23 final size:23
Alignment explanation
Indices: 400177--400226 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
400167 ACCTATTTTA
* *
400177 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCACTACCTAATACG
*
400200 TTATATAAGCACTACCTAATATG
1 TTATATAAGCACTACCTAATACG
400223 TTAT
1 TTAT
400227 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (23 bp):
TTATATAAGCACTACCTAATACG
Found at i:400323 original size:158 final size:158
Alignment explanation
Indices: 400022--400397 Score: 520
Period size: 158 Copynumber: 2.4 Consensus size: 158
400012 ATCAGCTTTA
* * * ** *
400022 ATAATGCGCAACCTATTACATTACATGAGTGCTACCTAATATGTTATTATGCTTGATAATGTTTC
1 ATAA-GCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTGCTTGATAATGTTTC
* * *
400087 CGGTAATTAACCGGTTATGGTATCCTTGGTAACATTTTAGGCGTTTACCTAATTGGTTGTAATAA
65 CAGTAATTAACCGGTTATGGTATCCTTGGTAACATTTTAGGCGTTCACCTAATTGATTGTAATAA
* *
400152 CAAATTAAGTAATTAACCTATTTTATTAT
130 CAAATTAAATAATTAACATATTTTATTAT
*
400181 ATAAGCGCTACCTATTACGTTATATAAGCACTACCTAATATGTTATTGTGCTTGATAATGTTTCC
1 ATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTGCTTGATAATGTTTCC
* *
400246 AGTAATTAATCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTCACCTAATAT-ATTGTAATAA
66 AGTAATTAACCGGTTATGGTATCCTTGGTAACATTTTAGGCGTTCACCTAAT-TGATTGTAATAA
400310 CAAATTAAATAATTAACATATTTTATTAT
130 CAAATTAAATAATTAACATATTTTATTAT
* * * *** * * *
400339 ATAAGTGCTATCTATTACATTATTTAAGTGTTACCTAATATGCTATTGTGATTAATAAT
1 ATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTGCTTGATAAT
400398 ATTTTCGGTT
Statistics
Matches: 192, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
158 187 0.97
159 5 0.03
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (158 bp):
ATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTGCTTGATAATGTTTCC
AGTAATTAACCGGTTATGGTATCCTTGGTAACATTTTAGGCGTTCACCTAATTGATTGTAATAAC
AAATTAAATAATTAACATATTTTATTAT
Found at i:406936 original size:7 final size:7
Alignment explanation
Indices: 406924--406996 Score: 146
Period size: 7 Copynumber: 10.4 Consensus size: 7
406914 AAGCTACTCT
406924 GCAGAAA
1 GCAGAAA
406931 GCAGAAA
1 GCAGAAA
406938 GCAGAAA
1 GCAGAAA
406945 GCAGAAA
1 GCAGAAA
406952 GCAGAAA
1 GCAGAAA
406959 GCAGAAA
1 GCAGAAA
406966 GCAGAAA
1 GCAGAAA
406973 GCAGAAA
1 GCAGAAA
406980 GCAGAAA
1 GCAGAAA
406987 GCAGAAA
1 GCAGAAA
406994 GCA
1 GCA
406997 TTGATGATCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 66 1.00
ACGTcount: A:0.56, C:0.15, G:0.29, T:0.00
Consensus pattern (7 bp):
GCAGAAA
Found at i:411668 original size:25 final size:25
Alignment explanation
Indices: 411640--411717 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
411630 ATTTTTTAAT
411640 TTTAATTACAGTAAATTAAAATAAA
1 TTTAATTACAGTAAATTAAAATAAA
**** *
411665 TTTAATTATCA--AATATTCTTTTAAT
1 TTTAATTA-CAGTAA-ATTAAAATAAA
*
411690 TTTAATTATAGTAAATTAAAATAAA
1 TTTAATTACAGTAAATTAAAATAAA
411715 TTT
1 TTT
411718 GAGATGCCAA
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
24 3 0.08
25 31 0.82
26 4 0.11
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (25 bp):
TTTAATTACAGTAAATTAAAATAAA
Found at i:411927 original size:43 final size:43
Alignment explanation
Indices: 411876--411985 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 43
411866 TTTACCGTTA
* *
411876 AAATATAAGAATAAAAT-A-ATAGTAAATATATTTTAACTTATT
1 AAATATAAGAATAAAATAAGATA-CAAATATATCTTAACTTATT
411918 AAATAATAAGAATAAAATAAGATACAAATATATCTTAACTTA--
1 AAAT-ATAAGAATAAAATAAGATACAAATATATCTTAACTTATT
411960 AAAGT-TAAGAA-AATAATAAGATACAA
1 AAA-TATAAGAATAA-AATAAGATACAA
411986 TAAAATAAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
40 2 0.03
41 18 0.30
42 7 0.11
43 14 0.23
44 17 0.28
45 3 0.05
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.30
Consensus pattern (43 bp):
AAATATAAGAATAAAATAAGATACAAATATATCTTAACTTATT
Found at i:412111 original size:31 final size:29
Alignment explanation
Indices: 412073--412193 Score: 117
Period size: 29 Copynumber: 4.2 Consensus size: 29
412063 ATTATATTTT
412073 AATATATTTTTAAAAGTTAAGATAATAATAA
1 AATATATTTTT-AAAGTTAA-ATAATAATAA
** *
412104 AATATATTTTTAATTTTAAATAAGAATAA
1 AATATATTTTTAAAGTTAAATAATAATAA
*
412133 AATATATTTTT-AAG-TAAAT-ATAATAGT
1 AATATATTTTTAAAGTTAAATAATAATA-A
*
412160 AATATATATTTATAA--TAAATTAATAATAA
1 AATATATTTTTA-AAGTTAAA-TAATAATAA
412189 AATAT
1 AATAT
412194 TTAAATATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
26 5 0.07
27 15 0.20
28 5 0.07
29 28 0.37
30 12 0.16
31 11 0.14
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (29 bp):
AATATATTTTTAAAGTTAAATAATAATAA
Found at i:412186 original size:88 final size:88
Alignment explanation
Indices: 412026--412193 Score: 195
Period size: 88 Copynumber: 1.9 Consensus size: 88
412016 TATTATATCG
* ** *
412026 TAATTTAAAATAAGAATAAAATATATCTTAACTTCAAATTATATTTTAATATATTTTTAAAAGTT
1 TAATTTAAAATAAGAATAAAATATATCTTAACGTCAAATTATATAGTAATATATTTTTAAAAATT
412091 AAGATAATAATAAAATATATTTT
66 AAGATAATAATAAAATATATTTT
* * * *
412114 TAATTTTAAATAAGAATAAAATATATTTTTAA-GT-AAA-TATAATAGTAATATATATTT-ATAA
1 TAATTTAAAATAAGAATAAAATATA-TCTTAACGTCAAATTAT-ATAGTAATATATTTTTAAAAA
412175 -TAA-ATTAATAATAAAATAT
64 TTAAGA-TAATAATAAAATAT
412194 TTAAATATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
84 1 0.01
85 17 0.25
86 5 0.07
87 16 0.23
88 25 0.36
89 5 0.07
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (88 bp):
TAATTTAAAATAAGAATAAAATATATCTTAACGTCAAATTATATAGTAATATATTTTTAAAAATT
AAGATAATAATAAAATATATTTT
Found at i:413097 original size:59 final size:59
Alignment explanation
Indices: 412942--413124 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 59
412932 ATACATCAAT
* * **
412942 CAAACTATGATCC-TCTTTCTAAATTAGTTTCTAAACTTTTAAATGTTTCAATTTCATCC
1 CAAACTATGATCCTTCATTCTAAATTAG-TCCTAAACTTTTAAACATTTCAATTTCATCC
** * * *
413001 CTAAACTATGATTATT-ATTCTAAATTTGTCCTCAAACTTTTAAACATTTTATTTTCATCC
1 C-AAACTATGATCCTTCATTCTAAATTAGTCCT-AAACTTTTAAACATTTCAATTTCATCC
* *
413061 CAAACTAT-ATCCTTCATTATAAATTAGTCCTAAAACTTTTTCAACATTTCAATTTCATCC
1 CAAACTATGATCCTTCATTCTAAATTAGTCCT-AAAC-TTTTAAACATTTCAATTTCATCC
413121 CAAA
1 CAAA
413125 TTATATGTAT
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
58 4 0.04
59 29 0.28
60 68 0.67
61 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (59 bp):
CAAACTATGATCCTTCATTCTAAATTAGTCCTAAACTTTTAAACATTTCAATTTCATCC
Found at i:413326 original size:60 final size:59
Alignment explanation
Indices: 413258--413437 Score: 186
Period size: 60 Copynumber: 3.0 Consensus size: 59
413248 TAATTTGGGG
* * *
413258 GAAATTGAAAGCTTTAAAAGTTTTGGGGCCAATTTAGAATGAGGT-TTATAGTTTAAGGAT
1 GAAATTGAAAG-TTCAAAAGTTTTGGGACCAATTTAGAATGA-GTATCATAGTTTAAGGAT
** * *
413318 GAAATTGAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGTATCATAGTTTGAGGAT
1 GAAATTGAAA-GTTCAAAAGTTTTGGGACCAATTTAGAATGAGTATCATAGTTTAAGGAT
* * * *
413378 GAAATT-ATAATATTCAAAAG-TTTGGGAACCAATTTAGAATGTGAATCATAGTTTGAGGAT
1 GAAATTGA-AA-GTTCAAAAGTTTTGGG-ACCAATTTAGAATGAGTATCATAGTTTAAGGAT
413438 ATATGATGCA
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
59 7 0.07
60 95 0.92
61 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (59 bp):
GAAATTGAAAGTTCAAAAGTTTTGGGACCAATTTAGAATGAGTATCATAGTTTAAGGAT
Found at i:413401 original size:29 final size:28
Alignment explanation
Indices: 413307--413400 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 28
413297 TGAGGTTTAT
*
413307 AGTTTAAGGATGAAATTGAAATGTTCAAA
1 AGTTTAAGGATGAAATT-AAATATTCAAA
* *
413336 AGTTTAAGGACT-AATTTAGAATGAGTATC-AT
1 AGTTTAAGGA-TGAAATTA-AAT-A-T-TCAAA
*
413367 AGTTTGAGGATGAAATTATAATATTCAAA
1 AGTTTAAGGATGAAATTA-AATATTCAAA
413396 AGTTT
1 AGTTT
413401 GGGAACCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
28 3 0.06
29 24 0.47
30 3 0.06
31 19 0.37
32 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.35
Consensus pattern (28 bp):
AGTTTAAGGATGAAATTAAATATTCAAA
Found at i:417864 original size:17 final size:17
Alignment explanation
Indices: 417842--417913 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
417832 AATTAAGAGT
417842 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
417859 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
417876 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
417893 TAACTTTATTAAATAAAC
1 T-AGTTTAATAAATGAAC
417911 TAG
1 TAG
417914 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 32 0.71
18 13 0.29
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:425067 original size:15 final size:15
Alignment explanation
Indices: 425049--425081 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
425039 ATCAACAAAT
425049 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
425064 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
425079 ATA
1 ATA
425082 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:427757 original size:6 final size:6
Alignment explanation
Indices: 427746--427781 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
427736 TGGGCCTACA
427746 AAAAAT AAAAAT AAAAAT AAAAAT AATATAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-A-AAT AAAA
427782 TATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 21 0.75
7 2 0.07
8 5 0.18
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:428204 original size:84 final size:84
Alignment explanation
Indices: 428024--428738 Score: 907
Period size: 84 Copynumber: 8.5 Consensus size: 84
428014 GAACTCGTCA
* * * * * * **
428024 GTTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATTTGATTTGCCTT-GAGTTTAATGT
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCTTGGAGCTGAGCGT
* *
428088 AATCGAACTCAAAGGTCTTT-
64 AGTCGAACTCGAAGGTCTTTG
* * *
428108 GTTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
*
428173 TCGAACTCGAAGGTCTTTA
66 TCGAACTCGAAGGTCTTTG
* * * *
428192 GTTGGCAGATAACCCCTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTGGAGCTAAGCGTAG
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
428257 TCGAACTCGAAGGTCTTTTG
66 TCGAACTCGAAGGTC-TTTG
* * * *
428277 G-TGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATGTGTCTTGGAGCTGAGCGGAG
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* *
428341 TCGAACTTGAAGGTTTTTG
66 TCGAACTCGAAGGTCTTTG
* * * * * * *
428360 GTTGGAAGATAGCTCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAG
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* *
428425 TCGAACCCGAAGGTCTTTT
66 TCGAACTCGAAGGTCTTTG
* * * * * * *
428444 GTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAAAGATGTGCCTTGGAGCTGAGCATAG
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
**
428509 TCGAACTCGAATATCTTTG
66 TCGAACTCGAAGGTCTTTG
*
428528 GTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
428593 TCGAACTCGAAGGTCTTTTG
66 TCGAACTCGAAGGTC-TTTG
* * * * *
428613 G-TGGCAGATAGCCCTTCTAGCCTTGAGCTATACTGGAAATGATATGCCTTGGAGCTGAGCGGAG
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* *
428677 TCGAACTCAAAGATCTTTG
66 TCGAACTCGAAGGTCTTTG
*
428696 GTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
1 GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGA
428739 ACACGATATC
Statistics
Matches: 548, Mismatches: 77, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
82 10 0.02
83 35 0.06
84 494 0.90
85 9 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (84 bp):
GTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
TCGAACTCGAAGGTCTTTG
Found at i:437814 original size:13 final size:13
Alignment explanation
Indices: 437791--437829 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
437781 AATGACGCGC
*
437791 AATGAGCGTCATA
1 AATGCGCGTCATA
*
437804 AATGCGTGTCATA
1 AATGCGCGTCATA
437817 AATGCGCGTCATA
1 AATGCGCGTCATA
437830 GATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:438242 original size:12 final size:12
Alignment explanation
Indices: 438225--438298 Score: 103
Period size: 12 Copynumber: 6.2 Consensus size: 12
438215 CCCCTGCAAC
438225 CTGTCTGTCTAT
1 CTGTCTGTCTAT
438237 CTGTCTGTCTAT
1 CTGTCTGTCTAT
*
438249 TTGTCTGTCTAT
1 CTGTCTGTCTAT
*
438261 CTGTCTGTCTGT
1 CTGTCTGTCTAT
* *
438273 CTATCTGTCTGT
1 CTGTCTGTCTAT
*
438285 CTATCTGTCTAT
1 CTGTCTGTCTAT
438297 CT
1 CT
438299 AGTTTAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 57 1.00
ACGTcount: A:0.08, C:0.24, G:0.16, T:0.51
Consensus pattern (12 bp):
CTGTCTGTCTAT
Found at i:438299 original size:4 final size:4
Alignment explanation
Indices: 438225--438294 Score: 86
Period size: 4 Copynumber: 17.5 Consensus size: 4
438215 CCCCTGCAAC
* * * *
438225 CTGT CTGT CTAT CTGT CTGT CTAT TTGT CTGT CTAT CTGT CTGT CTGT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT
* *
438273 CTAT CTGT CTGT CTAT CTGT CT
1 CTGT CTGT CTGT CTGT CTGT CT
438295 ATCTAGTTTA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.07, C:0.24, G:0.17, T:0.51
Consensus pattern (4 bp):
CTGT
Found at i:446142 original size:85 final size:85
Alignment explanation
Indices: 446048--446221 Score: 271
Period size: 85 Copynumber: 2.0 Consensus size: 85
446038 TGTCGCGCAA
*
446048 TTGTGTGTCATAAATCTATGACACGTAT-TCATGACGCT-CATTGCGCGTCATTGAAGCCCCCGT
1 TTGTGTGTCATAAATCTATGACACGCATGT-ATGAC-CTACATTGCGCGTCATTGAAGCCCCCGT
446111 CATAAATGAAGATGACACACAT
64 CATAAATGAAGATGACACACAT
* * *
446133 TTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCA
1 TTGTGTGTCATAAATCTATGACACGCATGTATGACCTACATTGCGCGTCATTGAAGCCCCCGTCA
*
446198 TAAATGAAGATGATACACAT
66 TAAATGAAGATGACACACAT
446218 TTGT
1 TTGT
446222 ATGACTTACA
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
84 1 0.01
85 80 0.98
86 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (85 bp):
TTGTGTGTCATAAATCTATGACACGCATGTATGACCTACATTGCGCGTCATTGAAGCCCCCGTCA
TAAATGAAGATGACACACAT
Found at i:455824 original size:14 final size:14
Alignment explanation
Indices: 455805--455832 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
455795 ATCCGGTTCA
455805 CCAAGAAGACTCCT
1 CCAAGAAGACTCCT
455819 CCAAGAAGACTCCT
1 CCAAGAAGACTCCT
455833 TGCGCGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (14 bp):
CCAAGAAGACTCCT
Found at i:459409 original size:58 final size:57
Alignment explanation
Indices: 459197--459411 Score: 219
Period size: 57 Copynumber: 3.8 Consensus size: 57
459187 AATGATGATT
* *
459197 TTTTTAAAGAAACTAAGCTTAATTTTCAAGGGTTTCTTGATGATTATTTCCAATGAAA
1 TTTTTAAAGAAACTAAGCCTAATTTTCAAGGGTTTCTTGATGATTATTT-AAATGAAA
* *
459255 -TTTTAAAGAAGA--AATGCCTGATTTTCAGGGGTTTCTTGATGATTATTTACAATG-AA
1 TTTTTAAAGAA-ACTAA-GCCTAATTTTCAAGGGTTTCTTGATGATTATTTA-AATGAAA
* * *
459311 TTTTTAAAGAAGAC-AAGCCTAATTTTTAGGGGTTTCTTGATGA-TAGTTGTAAACGAAA
1 TTTTTAAAGAA-ACTAAGCCTAATTTTCAAGGGTTTCTTGATGATTA-TT-TAAATGAAA
* * *
459369 GTTTTT-AAGTAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 -TTTTTAAAGAAACTAAGCCTAATTTTCAAGGGTTTCTTGATGA
459412 GTAAGTCCTT
Statistics
Matches: 135, Mismatches: 12, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
56 6 0.04
57 88 0.65
58 36 0.27
59 5 0.04
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (57 bp):
TTTTTAAAGAAACTAAGCCTAATTTTCAAGGGTTTCTTGATGATTATTTAAATGAAA
Found at i:459914 original size:240 final size:240
Alignment explanation
Indices: 459411--460170 Score: 999
Period size: 240 Copynumber: 3.2 Consensus size: 240
459401 TTTCTTGATG
* * ** *
459411 AGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAACCATGATACTTAAATCCTTCGGGTCAGCTAT
1 AGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTAT
* * * *
459476 AATTTTTTCAAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCATGATGTTTTC
66 AAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCATGATGTTTTC
** * *
459541 ACATGATTTTCAAAAAAT-AGGAAAGTGATTTCCAAAGTTTATCATTTAAATCTTTTTTGAAAAT
131 ACATGATTTT-TGAAAATGA-GAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAT
* ** *
459605 TGATTTTTCCTGAAAAGTAAGAAAATAATTCCCAAAGTTTCTTATTT
194 TGATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTATTT
* * *
459652 GGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGTGCATGATGTTTAAATCCTTCGGGTCATCTAT
1 AGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTAT
* * * * *
459717 AAGTCTTTCGACCAAGATGATAAGTCTTTCGGGCCATCCATAAGACATTCGAGTAGGATGTTTTC
66 AAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCATGATGTTTTC
* *
459782 ACATTATTTTTGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAATTTG
131 ACATGATTTTTGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTG
*
459847 ATTTTTCTTGAAAAGTAAGAAAACGATTTTCAAAGTTTCTTATTT
196 ATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTATTT
* * * * * ** *
459892 AGTAATTCATTCGGGGCATCAGTAAGTCTTTTGGGCATGATGTTTAAATGTTTCGGGCCATCTAT
1 AGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTAT
* * * *
459957 AAGTCTTTCGAGCAAGATAATAAGTCATTCGGGCCAT-TATAAGACCTTTGAGCATGATGTTTTT
66 AAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCATGATGTTTTC
* * * *
460021 AAATGA-TTTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAAATG
131 ACATGATTTTTGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTG
* *
460085 ATTTTTCTT-AAAAGGTAAGAAAACGATTTCCAAAGTTTCGTACTT
196 ATTTTTCTTGAAAA-GTAAGAAAACGATTTCCAAAGTTTCTTATTT
* * * * *
460130 AGTAAGT-CTTTGGACTATCAGAAAGTCTTTCGAGCAAGATG
1 AGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
460171 ATAAGTCCTT
Statistics
Matches: 451, Mismatches: 66, Indels: 8
0.86 0.13 0.02
Matches are distributed among these distances:
237 29 0.06
238 97 0.22
239 25 0.06
240 177 0.39
241 123 0.27
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (240 bp):
AGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTAT
AAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCATGATGTTTTC
ACATGATTTTTGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTG
ATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTATTT
Found at i:460310 original size:195 final size:196
Alignment explanation
Indices: 459957--460366 Score: 521
Period size: 195 Copynumber: 2.1 Consensus size: 196
459947 GGCCATCTAT
* * * *
459957 AAGTCTTTCGAGCAAGATAATAAGTCATTCGGGCCATTATAAGACCTTTGAGCATGATGTTTTTA
1 AAGTCTTTCGAGCAAGATGATAAGTCATTCGAGCCATCATAAGACCTTTGAGCATGATGTTTTCA
* * *
460022 AATGATTTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAAATGAT
66 AATAATTTTAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAATGAT
* *
460087 TTTTCTTAAAAGGTAAGAAAACGATTTCCAAAGTTTCGTACTTAGTAAGTC-TT-TGGACTATCA
131 TTTTCTGAAAAGGTAAGAAAACGATTTCCAAAGTTTCGTACTTAGTAAGTCATTCGGGAC-ATCA
460150 GA
195 GA
* *
460152 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTGGGCA-GAATGTTTT
1 AAGTCTTTCGAGCAAGATGATAAGTCATTCGAGCCAT-CATAAGACCTTTGAGCATG-ATGTTTT
* * * *
460216 CACATAATTTTCAAAAAATGAGAAAGCTATTTTCAATGTTGT-TCATTTAAATCTTTTCT-AAAA
64 CAAATAATTTT--AAAAATGAGAAAGCGATTTCCAAAGTT-TCTCATTTAAATCTTTTCTGAAAA
* * *
460279 ATTGA-TTTT-TGAAAA-GTAAGGAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCATTCGGGG
126 A-TGATTTTTCTGAAAAGGTAAGAAAACGATTTCCAAAGTTTCGTACTTAGTAAGTCATTCGGGA
*
460341 CATCAGT
190 CATCAGA
*
460348 AAGTCTTTCGAGCATGATG
1 AAGTCTTTCGAGCAAGATG
460367 TTTAAATCCT
Statistics
Matches: 187, Mismatches: 20, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
195 72 0.39
196 60 0.32
197 12 0.06
198 42 0.22
199 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (196 bp):
AAGTCTTTCGAGCAAGATGATAAGTCATTCGAGCCATCATAAGACCTTTGAGCATGATGTTTTCA
AATAATTTTAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAATGAT
TTTTCTGAAAAGGTAAGAAAACGATTTCCAAAGTTTCGTACTTAGTAAGTCATTCGGGACATCAG
A
Found at i:460540 original size:435 final size:434
Alignment explanation
Indices: 459717--460572 Score: 1170
Period size: 435 Copynumber: 2.0 Consensus size: 434
459707 GGTCATCTAT
* * * *
459717 AAGTCTTTCGACCAAGATGATAAGTCTTTCGGGCCATCCATAAGACATTCGAGTAGGATGTTTTC
1 AAGTCTTTCGACCAAGATGATAAGTCCTTCGAGCCATCCATAAGACATTCGAGCAGAATGTTTTC
* ** * *
459782 ACATTATTTTTGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAATTTG
66 ACATAATTTTAAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTAAAAATTG
* * *
459847 ATTTTTCTTGAAAAGTAAGAAAACGATTTTCAAAGTTTCTTATTTAGTAATTCATTCGGGGCATC
131 A-TTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCATTCGGGGCATC
* * * *
459912 AGTAAGTCTTTTGGGCATGATGTTTAAATGTTTCGGGCCATCTATAAGTCTTTCGAGCAAGATAA
195 AGTAAGTCTTTCGAGCATGATGTTTAAATCTTTCGGGCCATCTAGAAGTCTTTCGAGCAAGATAA
* * * * * *
459977 TAAGTCATTCGGGCCATTATAAGACCTTTGAGCATGATGTTTTTAAATGATTTTGAAAATGAGAA
260 TAAGCCATTCGAGCCATCATAAGACCTTTGAGCATGATGCTTTCAAATGATTTTAAAAATGAGAA
* *
460042 AGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAAATGATTTTTCTTAAAAGGTAAGAAA
325 AGCGATGTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAATGATTTTTCTTAAAAGGTAAGAAA
*
460107 ACGATTTCCAAAGTTTCGTACTTAGTAAGTCTTTGGACTATCAGA
390 ACGATTTCCAAAGTTTCGTACTTAATAAGTCTTTGGACTATCAGA
* * * *
460152 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTGGGCAGAATGTTTTC
1 AAGTCTTTCGACCAAGATGATAAGTCCTTCGAGCCATCCATAAGACATTCGAGCAGAATGTTTTC
* *
460217 ACATAATTTTCAAAAAATGAGAAAGCT-ATTTTCAATGTTGT-TCATTTAAATCTTTTCTAAAAA
66 ACATAATTTT-AAAAAATGAGAAAG-TGATTTCCAAAGTT-TCTCATTTAAATCTTTTCTAAAAA
*
460280 TTGA-TTT-TTGAAAAGTAAGGAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCATTCGGGGCA
128 TTGATTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCATTCGGGGCA
* *
460343 TCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTT-GGGTCATCTAGAAGTCTTTTGAGCAAGA
193 TCAGTAAGTCTTTCGAGCATGATGTTTAAAT-CTTTCGGGCCATCTAGAAGTCTTTCGAGCAAGA
* * * *
460407 TGATAAGCCCTTCGAGTCATCCATAAGACCTTT-AGGCATGAT-CTTTCACATGATTTTCAAAAA
257 TAATAAGCCATTCGAGCCAT-CATAAGACCTTTGA-GCATGATGCTTTCAAATGATTTT--AAAA
* * * *
460470 ATGAGAAAGTGATGTCTAAAGTTTCTCATTTAAATCTTTTCTGAAAATTTATTTTTCTTGAAAA-
318 ATGAGAAAGCGATGTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAATGATTTTTCTT-AAAAG
* *
460534 GTAAGAAAATGATTTCCAAAGTTTCTTACTTAATAAGTC
382 GTAAGAAAACGATTTCCAAAGTTTCGTACTTAATAAGTC
460573 ATTCGAGCCA
Statistics
Matches: 368, Mismatches: 44, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
433 134 0.36
434 24 0.07
435 158 0.43
436 50 0.14
437 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (434 bp):
AAGTCTTTCGACCAAGATGATAAGTCCTTCGAGCCATCCATAAGACATTCGAGCAGAATGTTTTC
ACATAATTTTAAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTAAAAATTG
ATTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCATTCGGGGCATCA
GTAAGTCTTTCGAGCATGATGTTTAAATCTTTCGGGCCATCTAGAAGTCTTTCGAGCAAGATAAT
AAGCCATTCGAGCCATCATAAGACCTTTGAGCATGATGCTTTCAAATGATTTTAAAAATGAGAAA
GCGATGTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAATGATTTTTCTTAAAAGGTAAGAAAA
CGATTTCCAAAGTTTCGTACTTAATAAGTCTTTGGACTATCAGA
Found at i:460593 original size:240 final size:238
Alignment explanation
Indices: 460152--460695 Score: 729
Period size: 240 Copynumber: 2.3 Consensus size: 238
460142 GACTATCAGA
* *
460152 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTGGGCA-GAATGTTTT
1 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTAGGCATG-ATGCTTT
* *
460216 CACATAATTTTCAAAAAATGAGAAAGCTATTTTCAATGTTGTTCATTTAAATCTTTTCTAAAAAT
65 CACATAATTTTCAAAAAATGAGAAAGCTATTCTCAAAGTTGTTCATTTAAATCTTTTCTAAAAAT
* * * *
460281 TGATTTTTGAAAAGTAAGGAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCATTCGGGGCATCA
130 TGATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAATAAGTCATTCGAGCCATCA
* * **
460346 GTAAGTCTTTCGAGCATGATGTTTAAATCCTTTGGGTCATCTAG
195 ATAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTAG
* * *
460390 AAGTCTTTTGAGCAAGATGATAAGCCCTTCGAGTCATCCATAAGACCTTTAGGCATGAT-CTTTC
1 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTAGGCATGATGCTTTC
* *
460454 ACATGATTTTCAAAAAATGAGAAAG-TGATGTCT-AAAGTT-TCTCATTTAAATCTTTTCTGAAA
66 ACATAATTTTCAAAAAATGAGAAAGCT-AT-TCTCAAAGTTGT-TCATTTAAATCTTTTCTAAAA
* *
460516 ATTTATTTTTCTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTAATAAGTCATTCGAGC
128 ATTGA--TTT-TTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAATAAGTCATTCGAGC
* * *
460581 CATCAATAAGTCTTTTGAGCATGATGCTTAAATCCTTCAGGTTATCTAT
190 CATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTAG
* * * ** * *
460630 AAGTCTTTCGAGCAACATGATAAGTCCATCGGGCCATTTATAAGACCTTCAGGCATGATGTTTTC
1 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTAGGCATGATGCTTTC
460695 A
66 A
460696 TATGGTGATA
Statistics
Matches: 266, Mismatches: 32, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
236 2 0.01
237 59 0.22
238 55 0.21
239 4 0.02
240 141 0.53
241 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (238 bp):
AAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTAGGCATGATGCTTTC
ACATAATTTTCAAAAAATGAGAAAGCTATTCTCAAAGTTGTTCATTTAAATCTTTTCTAAAAATT
GATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAATAAGTCATTCGAGCCATCAA
TAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTAG
Found at i:465470 original size:46 final size:45
Alignment explanation
Indices: 465414--465520 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
465404 TGAACTTACC
* * *
465414 ATGCACCGATGCACT-GAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCGA-GATATTT-TG-AAACATCAAATGCACTTG
* *
465460 ATGCATCGATGCACTCTAGCTATTTTGAAACATCAAATGCACTTG
1 ATGCATCGATGCACTCGAGATATTTTGAAACATCAAATGCACTTG
465505 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
465521 TTAGTGCACC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
45 32 0.59
46 18 0.33
47 4 0.07
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACTCGAGATATTTTGAAACATCAAATGCACTTG
Found at i:467675 original size:22 final size:22
Alignment explanation
Indices: 467647--467691 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
467637 ATTGATGATC
467647 TTAAAACTTCTTTTAATAAGGT
1 TTAAAACTTCTTTTAATAAGGT
467669 TTAAAACTTCTTTTAATAAGGT
1 TTAAAACTTCTTTTAATAAGGT
467691 T
1 T
467692 GGAACGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (22 bp):
TTAAAACTTCTTTTAATAAGGT
Found at i:471369 original size:24 final size:22
Alignment explanation
Indices: 471342--471422 Score: 76
Period size: 24 Copynumber: 3.6 Consensus size: 22
471332 ACACTTAATA
471342 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* * *
471366 GTGCATCGATTCAT-CATG-CT
1 GTGCATCGATGCATCCTTGAAT
*
471386 GATGCACCGATGCATGCCTTGAAT
1 G-TGCATCGATGCAT-CCTTGAAT
471410 GTGCATCGATGCA
1 GTGCATCGATGCA
471423 CGAGGTCATG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
20 2 0.04
21 13 0.29
22 1 0.02
23 14 0.31
24 15 0.33
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:474201 original size:21 final size:21
Alignment explanation
Indices: 474160--474201 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
474150 AATGCATTTG
*
474160 ATGCATCGATGCACCATGGGT
1 ATGCATCGATGCACCAAGGGT
*
474181 ATGCATCGATGCACTAAGGGT
1 ATGCATCGATGCACCAAGGGT
474202 CCAACGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (21 bp):
ATGCATCGATGCACCAAGGGT
Found at i:477940 original size:7 final size:7
Alignment explanation
Indices: 477928--477968 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
477918 TTCTCTCTCT
477928 AAAAAGA
1 AAAAAGA
477935 AAAAAG-
1 AAAAAGA
477941 AAAAAGA
1 AAAAAGA
477948 AAAAA-A
1 AAAAAGA
*
477954 TAAAAGA
1 AAAAAGA
*
477961 ATAAAGA
1 AAAAAGA
477968 A
1 A
477969 TAATAAGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (7 bp):
AAAAAGA
Found at i:477946 original size:13 final size:13
Alignment explanation
Indices: 477928--477968 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
477918 TTCTCTCTCT
477928 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
477941 AAAAAGAAAAAA-
1 AAAAAGAAAAAAG
*
477953 ATAAAAGAATAAAG
1 A-AAAAGAAAAAAG
477967 AA
1 AA
477969 TAATAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:477979 original size:18 final size:18
Alignment explanation
Indices: 477949--477999 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
477939 AGAAAAAGAA
*
477949 AAAAATAAAAGAATAAAG
1 AAAAATAAGAGAATAAAG
* *
477967 AATAATAAGAGAATAATG
1 AAAAATAAGAGAATAAAG
*
477985 AAAAATAAGAAAATA
1 AAAAATAAGAGAATA
478000 TAACTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.16
Consensus pattern (18 bp):
AAAAATAAGAGAATAAAG
Found at i:478268 original size:108 final size:109
Alignment explanation
Indices: 478039--478293 Score: 259
Period size: 108 Copynumber: 2.4 Consensus size: 109
478029 TCACGCTTAG
* * * * * *
478039 GTCCCCTTAGGTTT-AAGTGTTTTTACATTCTGGTCACTTGTAGGGACCAAATATGATATTTATC
1 GTCCCTTTAAGTTTAAAGTGTTTTTACATTATGGTCACTTGCAAGGACAAAATATGATATTTATC
* * *
478103 CTTTTTTCGTGCATGTTGTCATTTATTGGGTTATTTTCTGTTCA
66 CTCTTTTCGTGCATGTTATCATTTATTGGATTATTTTCTGTTCA
* * *
478147 GCCCCTCTAAGTTTAAAGTGTTTTTACATTATGGTCA-TCTGCAAGGACTAAAAT-TGTTATTT-
1 GTCCCTTTAAGTTTAAAGTGTTTTTACATTATGGTCACT-TGCAAGGAC-AAAATATGATATTTA
* * * *
478209 TCC-CTTTTCATTGCATGTTATCATTTATTGGATTGTTTTTTGTTTA
64 TCCTCTTTTC-GTGCATGTTATCATTTATTGGATTATTTTCTGTTCA
** * * *
478255 GTCCCTTTAAGTTTAGTGTATTTTTACATTTTAGTCACT
1 GTCCCTTTAAGTTTAAAGTGTTTTTACATTATGGTCACT
478294 AATTAGTTAT
Statistics
Matches: 119, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
107 5 0.04
108 74 0.62
109 36 0.30
110 4 0.03
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.48
Consensus pattern (109 bp):
GTCCCTTTAAGTTTAAAGTGTTTTTACATTATGGTCACTTGCAAGGACAAAATATGATATTTATC
CTCTTTTCGTGCATGTTATCATTTATTGGATTATTTTCTGTTCA
Found at i:480307 original size:20 final size:20
Alignment explanation
Indices: 480284--480323 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
480274 TATTTTAGAT
480284 ACTAAACATGTAGTTTACCC
1 ACTAAACATGTAGTTTACCC
*
480304 ACTAAACATTTAGTTTACCC
1 ACTAAACATGTAGTTTACCC
480324 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (20 bp):
ACTAAACATGTAGTTTACCC
Found at i:489605 original size:39 final size:38
Alignment explanation
Indices: 489562--489636 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
489552 GGGTCTTTGG
*
489562 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTT-TGTGTGT
* *
489601 GTTTCAAGAGAAACAATTTCGAGGGTTTTTTTGTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
489637 TTCAAGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.15
39 28 0.85
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (38 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGTGT
Found at i:489674 original size:36 final size:35
Alignment explanation
Indices: 489634--489841 Score: 155
Period size: 37 Copynumber: 5.9 Consensus size: 35
489624 GGTTTTTTTG
*
489634 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-ATT
* * *
489670 TGTTTCAAAAGAAACTGTATCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-CAAA-TT
* * * *
489707 AG-TTCTAAAAGAAACTATCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGAC-AAATT
* * * *
489743 TGTTTCAAG-GAAAATATATTC-A-A-AG---ATTT
1 TGTTTCAAGAGAAACTGT-CTCAAGAGAGACAAATT
489772 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAA-A-TT
*
489809 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
489842 ACTTGGAAAC
Statistics
Matches: 135, Mismatches: 20, Indels: 34
0.71 0.11 0.18
Matches are distributed among these distances:
29 13 0.10
30 7 0.05
31 1 0.01
32 2 0.01
33 2 0.01
35 9 0.07
36 38 0.28
37 63 0.47
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAATT
Found at i:489849 original size:28 final size:28
Alignment explanation
Indices: 489818--489896 Score: 158
Period size: 28 Copynumber: 2.8 Consensus size: 28
489808 TTGTTTCAAG
489818 GGAAACTGTCTCAAGAGAGACAAAACTT
1 GGAAACTGTCTCAAGAGAGACAAAACTT
489846 GGAAACTGTCTCAAGAGAGACAAAACTT
1 GGAAACTGTCTCAAGAGAGACAAAACTT
489874 GGAAACTGTCTCAAGAGAGACAA
1 GGAAACTGTCTCAAGAGAGACAA
489897 TGGTGAGCAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (28 bp):
GGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:491150 original size:24 final size:22
Alignment explanation
Indices: 491093--491150 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
491083 TTTTATTTTC
491093 AAAGTTTTG-AAAATATCAAAA
1 AAAGTTTTGAAAAATATCAAAA
* * *
491114 AAGAGTTTCGAAAAATATTTAATCA
1 AA-AGTTTTGAAAAATA-TCAA-AA
491139 AAAGTTTTGAAA
1 AAAGTTTTGAAA
491151 GCATTGCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.07
22 6 0.21
23 6 0.21
24 12 0.41
25 3 0.10
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (22 bp):
AAAGTTTTGAAAAATATCAAAA
Found at i:491995 original size:69 final size:69
Alignment explanation
Indices: 491879--492016 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 69
491869 TCTCTCTCTC
* * * * *
491879 TTGATGCTCTATGATCTTCGAGTGGAGTGATTTAGTGATTCGGAAATGATTGTGTTTGATCAATC
1 TTGATGATCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
491944 TCAT
66 TCAT
*
491948 TTGATGATCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
1 TTGATGATCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
492013 TCAT
66 TCAT
492017 AGTTTGAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (69 bp):
TTGATGATCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:492104 original size:24 final size:25
Alignment explanation
Indices: 492077--492129 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
492067 TCTTGTCTTC
492077 TTTTCTCTTCAATTTTC-CTTTGTT
1 TTTTCTCTTCAATTTTCTCTTTGTT
* **
492101 TTTTCTTTTTTATTTTCTCTTTGTT
1 TTTTCTCTTCAATTTTCTCTTTGTT
492126 TTTT
1 TTTT
492130 TTCTCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTTCTCTTCAATTTTCTCTTTGTT
Found at i:492128 original size:25 final size:26
Alignment explanation
Indices: 492077--492147 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 26
492067 TCTTGTCTTC
*
492077 TTTTCTCTTCAATTTTC-CTTTGTTTT
1 TTTTCTCTT-TATTTTCTCTTTGTTTT
492103 TTCTT-T-TTTATTTTCTCTTTGTTTT
1 TT-TTCTCTTTATTTTCTCTTTGTTTT
492128 TTTTCTCTTT-TTTTCTCTTT
1 TTTTCTCTTTATTTTCTCTTT
492148 TTGTTCTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
24 8 0.20
25 24 0.60
26 6 0.15
27 2 0.05
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (26 bp):
TTTTCTCTTTATTTTCTCTTTGTTTT
Found at i:492133 original size:15 final size:14
Alignment explanation
Indices: 492099--492141 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
492089 TTTTCCTTTG
492099 TTTTT-TCTTTTTT
1 TTTTTCTCTTTTTT
*
492112 ATTTTCTCTTTGTTT
1 TTTTTCTCTTT-TTT
492127 TTTTTCTCTTTTTT
1 TTTTTCTCTTTTTT
492141 T
1 T
492142 CTCTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 13 0.50
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (14 bp):
TTTTTCTCTTTTTT
Found at i:492139 original size:12 final size:12
Alignment explanation
Indices: 492089--492149 Score: 63
Period size: 12 Copynumber: 5.0 Consensus size: 12
492079 TTCTCTTCAA
492089 TTTTC-CTTTGTT
1 TTTTCTCTTT-TT
492101 TTTTCT-TTTTT
1 TTTTCTCTTTTT
492112 ATTTTCTCTTTGTT
1 -TTTTCTCTTT-TT
* *
492126 TTTTTTCTCTTT
1 TTTTCTCTTTTT
492138 TTTTCTCTTTTT
1 TTTTCTCTTTTT
492150 GTTCTGATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 2 0.05
12 26 0.63
13 11 0.27
14 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:492140 original size:10 final size:10
Alignment explanation
Indices: 492125--492154 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
492115 TTCTCTTTGT
492125 TTTTTTTCTC
1 TTTTTTTCTC
492135 TTTTTTTCTC
1 TTTTTTTCTC
492145 TTTTTGTTCT
1 TTTTT-TTCT
492155 GATTGAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:492150 original size:27 final size:27
Alignment explanation
Indices: 492099--492152 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
492089 TTTTCCTTTG
*
492099 TTTTTTCTTTTTTATTTTCTCTTTGTT
1 TTTTTTCTTTTTTATTCTCTCTTTGTT
*
492126 TTTTTTCTCTTTTT-TTCTCTTTTTGTT
1 TTTTTTCT-TTTTTATTCTCTCTTTGTT
492153 CTGATTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (27 bp):
TTTTTTCTTTTTTATTCTCTCTTTGTT
Found at i:493386 original size:27 final size:26
Alignment explanation
Indices: 493351--493401 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
493341 GCTTAGTTTC
*
493351 ATGTTTATG-AAAATGCTTAAAAATGAA
1 ATGTATATGCAAAATGC--AAAAATGAA
493378 ATGTATATGCAAAATGCAAAAATG
1 ATGTATATGCAAAATGCAAAAATG
493402 CATGAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (26 bp):
ATGTATATGCAAAATGCAAAAATGAA
Found at i:506148 original size:3 final size:3
Alignment explanation
Indices: 506135--506213 Score: 76
Period size: 3 Copynumber: 26.7 Consensus size: 3
506125 TTTTATATTC
* *
506135 TAT TGT TAT TAT TAT T-T TATT TAT TAC TA- TAT TAT T-T TA- TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
*
506177 ATAT TATT TAT AAT TAT TAT TAT TAT TAT TAT TAT TA
1 -TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
506214 CAATTCAGGC
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
2 8 0.12
3 47 0.73
4 9 0.14
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:511694 original size:15 final size:15
Alignment explanation
Indices: 511671--511717 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
511661 GATCAATACC
* *
511671 TTTTGCATATATTCA
1 TTTTACATACATTCA
511686 TTTTACATACATTCA
1 TTTTACATACATTCA
511701 TTTTACATACATTCA
1 TTTTACATACATTCA
511716 TT
1 TT
511718 ATTCATTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTTACATACATTCA
Found at i:518970 original size:14 final size:15
Alignment explanation
Indices: 518944--519011 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 15
518934 ATGTTTGAAG
518944 AAGAAAAAGAAGAAAA
1 AAGAAAAA-AAGAAAA
518960 AA-AAAAAAAGAAAA
1 AAGAAAAAAAGAAAA
*
518974 AACGAAATAAA-AAAA
1 AA-GAAAAAAAGAAAA
*
518989 ATGAAAAAAA-ATAATA
1 AAGAAAAAAAGA-AA-A
519005 AAGAAAA
1 AAGAAAA
519012 TGAGGGTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
14 17 0.39
15 12 0.27
16 15 0.34
ACGTcount: A:0.82, C:0.01, G:0.10, T:0.06
Consensus pattern (15 bp):
AAGAAAAAAAGAAAA
Found at i:518980 original size:22 final size:22
Alignment explanation
Indices: 518944--518998 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
518934 ATGTTTGAAG
518944 AAGAAAAAGAAGAAAAAAAAAAA
1 AAGAAAAA-AAGAAAAAAAAAAA
* *
518967 AAGAAAAAACGAAATAAAAAAA
1 AAGAAAAAAAGAAAAAAAAAAA
*
518989 ATGAAAAAAA
1 AAGAAAAAAA
518999 ATAATAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.04
Consensus pattern (22 bp):
AAGAAAAAAAGAAAAAAAAAAA
Found at i:519004 original size:22 final size:22
Alignment explanation
Indices: 518956--519014 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
518946 GAAAAAGAAG
*
518956 AAAA-AAAAAAAAAGAAAAAAC
1 AAAATAAAAAAAATGAAAAAAC
*
518977 GAAATAAAAAAAATGAAAAAA-
1 AAAATAAAAAAAATGAAAAAAC
*
518998 AATAATAAAGAAAATGA
1 AA-AATAAAAAAAATGA
519015 GGGTCAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.08
Consensus pattern (22 bp):
AAAATAAAAAAAATGAAAAAAC
Found at i:519382 original size:18 final size:18
Alignment explanation
Indices: 519359--519396 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
519349 CAAGTTTATC
519359 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
519377 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
519395 TT
1 TT
519397 CTTTTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:520087 original size:44 final size:44
Alignment explanation
Indices: 520017--520114 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
520007 ACATCTACAT
* * *
520017 TCTTCAAAGATGATAGATACATTCTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGACAAATACATTCTTCAAAGATGATAGATTCTC
*
520061 TCTTCAAAGATGACAAATTC-TCTCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGACAAATACAT-TCTTCAAAGATGATAGATTCTC
*
520105 TTTTCAAAGA
1 TCTTCAAAGA
520115 AGAAAGATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 47 0.98
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (44 bp):
TCTTCAAAGATGACAAATACATTCTTCAAAGATGATAGATTCTC
Found at i:520122 original size:22 final size:22
Alignment explanation
Indices: 520017--520123 Score: 119
Period size: 22 Copynumber: 4.9 Consensus size: 22
520007 ACATCTACAT
* *
520017 TCTTCAAAGATGATAGATACAT-
1 TCTTCAAAGATGAAAGATTC-TC
* *
520039 TCTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGAAAGATTCTC
520061 TCTTCAAAGATGACAA-ATTCTC
1 TCTTCAAAGATGA-AAGATTCTC
*
520083 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGAAAGATTCTC
* *
520105 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGAAAGATT
520124 TATTGGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
21 2 0.03
22 71 0.96
23 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGAAAGATTCTC
Found at i:520553 original size:20 final size:20
Alignment explanation
Indices: 520491--520554 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
520481 TCCAGAGAAA
520491 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
520511 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
520530 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
520550 GTTCA
1 GTTCA
520555 ACCTTTTGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:520676 original size:20 final size:20
Alignment explanation
Indices: 520614--520677 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
520604 TCCAGAGAAA
520614 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
520634 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
520653 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
520673 GTTCA
1 GTTCA
520678 ACCTTTTGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:520694 original size:123 final size:123
Alignment explanation
Indices: 520471--521166 Score: 1120
Period size: 123 Copynumber: 5.7 Consensus size: 123
520461 ATTAACAAAG
520471 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
1 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
* * *
520536 AATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTTTCACAGAAGGAGATATATCAA
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAA
520594 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
1 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
*
520659 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATAGATCAA
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAA
* *
520717 CATCAACTTTTCCAGAGAAATTTCATAATGAGAATAACTTATCTGAAGAGGAAGAAGAAGTTCAT
1 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
*
520782 AATGAGAAGAACTTGTTCAACCTTTTGCATGAATCTATCACAGAAGGAGATAGATCAA
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAA
* * *
520840 CATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTTATCTGAACAAGAAGAAGAAGTTCAT
1 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
* *
520905 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCAATCACAGAAGGAGATAGATCAG
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAA
520963 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAG----T
1 CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
* * * *
521024 AATGAGAAGAGCTTGTTAAACCTTTTGCATGACTCTATCGCAGAAGGAGATAGATCAT
66 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAA
* * *
521082 CATCAACATTTT-C-GA-AACAGTTCATAATGAGAATAACTCATATGAAGAAGG-AGAAGAAGTT
1 CATCAAC-TTTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTT
* *
521143 CATAGTGAGAAGAATTTGTTCAAC
63 CATAATGAGAAGAACTTGTTCAAC
521167 TTTGCCTTAA
Statistics
Matches: 535, Mismatches: 31, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
117 2 0.00
118 36 0.07
119 65 0.12
120 4 0.01
122 18 0.03
123 410 0.77
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
CATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAA
Found at i:520922 original size:20 final size:20
Alignment explanation
Indices: 520860--520923 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
520850 TCTAGAGAAA
520860 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ** ***
520880 -ATC-TGAACAAGAAGAAGAA
1 GTTCAT-AATGAGAAGAACTT
520899 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
520919 GTTCA
1 GTTCA
520924 ACCTTTTGCA
Statistics
Matches: 29, Mismatches: 12, Indels: 6
0.62 0.26 0.13
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 16 0.55
21 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:521532 original size:3 final size:3
Alignment explanation
Indices: 521524--521611 Score: 110
Period size: 3 Copynumber: 29.7 Consensus size: 3
521514 TTTGTTTTTA
* *
521524 TAT TAT TAT TGA- TAT TAT TAT T-T TATT TAT TAC TAT AAT TAT T-T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
521568 TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
521612 CAATTCAAGC
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
2 5 0.07
3 65 0.88
4 4 0.05
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:522999 original size:41 final size:41
Alignment explanation
Indices: 522919--522999 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
522909 ACTTTTTATA
* *
522919 TTTTAATATTATAGTTTTAATTTCATTTATTTTAGTTATTG
1 TTTTAATATTATAGTTTTAATTTCATATATTTTAATTATTG
* *
522960 TTTTAATTTTATA-TGTTTATTTTCA-ATATATTTAATTATT
1 TTTTAATATTATAGT-TTTAATTTCATATAT-TTTAATTATT
523000 ATTATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.64
Consensus pattern (41 bp):
TTTTAATATTATAGTTTTAATTTCATATATTTTAATTATTG
Found at i:525441 original size:21 final size:21
Alignment explanation
Indices: 525411--525458 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
525401 TAATTTTCAA
*
525411 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
525432 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
525453 ACATTG
1 ACATTG
525459 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:529983 original size:21 final size:21
Alignment explanation
Indices: 529953--530000 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
529943 TAATTTTCAA
*
529953 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
529974 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
529995 ACATTG
1 ACATTG
530001 CATTATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:531820 original size:22 final size:22
Alignment explanation
Indices: 531792--531834 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
531782 TTAATAATAC
531792 TATATAGAAATATAGATTTATT
1 TATATAGAAATATAGATTTATT
531814 TATATAGAAATATAGATTTAT
1 TATATAGAAATATAGATTTAT
531835 AAATCGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (22 bp):
TATATAGAAATATAGATTTATT
Found at i:533892 original size:23 final size:23
Alignment explanation
Indices: 533842--533893 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
533832 ATAAAATCAA
* *
533842 ATGAACGCTAAACGAACATGTTT
1 ATGAACGCTAAACGAACACGTTC
* *
533865 GTGAATGCTAAACGAACACGTTC
1 ATGAACGCTAAACGAACACGTTC
533888 ATGAAC
1 ATGAAC
533894 ATATAAACGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (23 bp):
ATGAACGCTAAACGAACACGTTC
Found at i:538030 original size:45 final size:45
Alignment explanation
Indices: 537978--538067 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
537968 GCCTTTTAGG
537978 GGATTACGAATATTTTAGCCCAATCCGTTTTTTCCTTTCCTCAAA
1 GGATTACGAATATTTTAGCCCAATCCGTTTTTTCCTTTCCTCAAA
538023 GGATTACGAATATTTTAGCCCAATCCGTTTTTTCCTTTCCTCAAA
1 GGATTACGAATATTTTAGCCCAATCCGTTTTTTCCTTTCCTCAAA
538068 TTAGAACGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (45 bp):
GGATTACGAATATTTTAGCCCAATCCGTTTTTTCCTTTCCTCAAA
Found at i:538987 original size:18 final size:17
Alignment explanation
Indices: 538949--538987 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
538939 CGATTGAAGC
* *
538949 TCAAGCTCGAGCTTTGT
1 TCAAGCTCGAACTTAGT
538966 TCAAGCTCGAACTTGAGT
1 TCAAGCTCGAACTT-AGT
538984 TCAA
1 TCAA
538988 ACATGAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (17 bp):
TCAAGCTCGAACTTAGT
Found at i:541205 original size:27 final size:26
Alignment explanation
Indices: 541165--541215 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
541155 CCAGTAGATG
*
541165 CTGACTAGATCTTCTAGAAAACTGCTA
1 CTGACTAGACCTTCTAG-AAACTGCTA
*
541192 CTGACTGGACCTTCTAGAAACTGC
1 CTGACTAGACCTTCTAGAAACTGC
541216 CACTTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (26 bp):
CTGACTAGACCTTCTAGAAACTGCTA
Found at i:542057 original size:18 final size:17
Alignment explanation
Indices: 542023--542055 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
542013 TTCTCATGTT
*
542023 TTTTTTTTCTGTTTTTA
1 TTTTTTTCCTGTTTTTA
542040 TTTTTTTCCTGTTTTT
1 TTTTTTTCCTGTTTTT
542056 TAACTGCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTTCCTGTTTTTA
Found at i:551137 original size:7 final size:7
Alignment explanation
Indices: 551125--551168 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
551115 TAATAAGCTC
551125 AATAAAA
1 AATAAAA
551132 AATAAAA
1 AATAAAA
*
551139 AATAATA
1 AATAAAA
*
551146 AATAAAT
1 AATAAAA
*
551153 AA-AAGA
1 AATAAAA
551159 AATAAAA
1 AATAAAA
551166 AAT
1 AAT
551169 TGTAAAACAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (7 bp):
AATAAAA
Found at i:553241 original size:42 final size:41
Alignment explanation
Indices: 553119--553241 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 41
553109 AAACATCCTA
* * * * * *
553119 CTCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTT
1 CTCGAAAGACTTATAGATGACCCGAAGGACTTATCATCATG
* * * *
553160 CTCTAAAGACTTATAGATGACCCAAAGGATTTAAGCATCATG
1 CTCGAAAGACTTATAGATGACCCGAAGGACTT-ATCATCATG
553202 CTCGAAAGACTTACTA-ATGACCCGAAGGACTTACTCATCA
1 CTCGAAAGACTTA-TAGATGACCCGAAGGACTTA-TCATCA
553242 AGAAACCCTT
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
41 26 0.40
42 37 0.57
43 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (41 bp):
CTCGAAAGACTTATAGATGACCCGAAGGACTTATCATCATG
Found at i:553609 original size:24 final size:24
Alignment explanation
Indices: 553579--553630 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
553569 AGGAACCCCT
*
553579 AAAAATTAGGCTTAGATTTTTTTA
1 AAAAATTAGGCTTAGATTCTTTTA
*
553603 AAAAATTAGGCTTAGCTTCTTTTA
1 AAAAATTAGGCTTAGATTCTTTTA
553627 AAAA
1 AAAA
553631 TTCTTTGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (24 bp):
AAAAATTAGGCTTAGATTCTTTTA
Found at i:553825 original size:301 final size:300
Alignment explanation
Indices: 553105--553910 Score: 943
Period size: 301 Copynumber: 2.7 Consensus size: 300
553095 ATCAGAGATG
* * *
553105 TTGAAAACATCCTACTCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTTCTCTAAAGAC
1 TTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGA-
* *
553170 TTATAGATGACCCA-AAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGACCCGAAGGACTT
65 TTATAGATGA--CAGAA-GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
** * *** **** * *
553234 ACTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTA-AAATCTTTCATTTATAGTTGTCAT
127 ACTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTATC-ATCAAGGA-ACCCCTAAA
* **** **
553298 CA--AGG---A-A--CCCCT-AAAAATTAGGCTTAGCTTCCTTTAAAAAGTCTTTGGAGATGATC
190 AATTAGGCTTAGATTTTTTTAAAAAATTAGGCTTAGCTTCCTTTAAAAAGTCTTTGGAGAAAATC
*
553354 ATAAAAAAACCACCTAAAAATCATGCTTAGTTTCTAAAAACTCATT
255 ATAAAAAAACCACCTAAAAATCAGGCTTAGTTTCTAAAAACTCATT
* * * * *
553400 TTGAAAACATCCTACCCAAAGGTCTTATGGATGGCTCGAAAGACTTATCATCTTGCTCGAAAGAC
1 TTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAT
* *
553465 T-T--AT---AGAAGA-TTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACATACTC
66 TATAGATGACAGAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTC
* * * *
553523 ATCAAGAAACCTTTGACAATCAAGTTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAAATTAG
131 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTATCATCAAGGAACCCCTAAAAATTAG
* * * **
553588 GCTTAGATTTTTTTAAAAAATTAGGCTTAGCTTCTTTTAAAAATTCTTTGGAGAAAATCATCACG
196 GCTTAGATTTTTTTAAAAAATTAGGCTTAGCTTCCTTTAAAAAGTCTTTGGAGAAAATCATAAAA
* *
553653 AAACC-CCTGAAAATCGGGCTTAGTTTCTAAAAACTCATT
261 AAACCACCTAAAAATCAGGCTTAGTTTCTAAAAACTCATT
* * *
553692 TTGAAAA-ATTCTTCCCGAATGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAT
1 TTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGA-
553756 TTATAGATGACATGAACGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
65 TTATAGATGACA-GAA-GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
553821 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTATCATCAAGGAACCCCTAAAAAT
128 CTCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTATCATCAAGGAACCCCTAAAAAT
*
553886 T-GAGCTTAGCTTTCTTTTAAAAAAT
193 TAG-GCTTAGATTT-TTTTAAAAAAT
553911 CTTTGAAAAC
Statistics
Matches: 431, Mismatches: 57, Indels: 39
0.82 0.11 0.07
Matches are distributed among these distances:
284 4 0.01
285 81 0.19
286 8 0.02
287 2 0.00
289 1 0.00
290 1 0.00
291 51 0.12
292 40 0.09
293 50 0.12
294 1 0.00
295 60 0.14
298 1 0.00
299 3 0.01
300 3 0.01
301 114 0.26
302 11 0.03
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (300 bp):
TTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAT
TATAGATGACAGAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTC
ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTATCATCAAGGAACCCCTAAAAATTAG
GCTTAGATTTTTTTAAAAAATTAGGCTTAGCTTCCTTTAAAAAGTCTTTGGAGAAAATCATAAAA
AAACCACCTAAAAATCAGGCTTAGTTTCTAAAAACTCATT
Found at i:553827 original size:42 final size:41
Alignment explanation
Indices: 553714--553827 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
553704 TCCCGAATGT
* *
553714 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
* * ** * * * *
553755 TTTATAGATGACATGAACGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGA
553797 CTTACT-GATGGCCCGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
553828 AGAAACCCTT
Statistics
Matches: 53, Mismatches: 17, Indels: 5
0.71 0.23 0.07
Matches are distributed among these distances:
41 17 0.32
42 35 0.66
43 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:555586 original size:18 final size:17
Alignment explanation
Indices: 555556--555616 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
555546 TTAATAAGCT
555556 TAATAAAAAATAAAAAA
1 TAATAAAAAATAAAAAA
555573 TAATAAATAAATAAAAAA
1 TAATAAA-AAATAAAAAA
* *
555591 TAGTAAAACATAGAATAAA
1 TAATAAAAAATA-AA-AAA
555610 -AATAAAA
1 TAATAAAA
555617 TAAACATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
17 11 0.29
18 24 0.63
19 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (17 bp):
TAATAAAAAATAAAAAA
Found at i:555620 original size:11 final size:11
Alignment explanation
Indices: 555557--555630 Score: 57
Period size: 11 Copynumber: 6.9 Consensus size: 11
555547 TAATAAGCTT
*
555557 AATAAAA-AAT
1 AATAAAATAAA
555567 AA-AAAATAATA
1 AATAAAATAA-A
555578 AAT-AAATAAA
1 AATAAAATAAA
* *
555588 AA-ATAGTAAA
1 AATAAAATAAA
*
555598 ACATAGAATAAA
1 A-ATAAAATAAA
555610 AATAAAATAAA
1 AATAAAATAAA
*
555621 CATAAAATAA
1 AATAAAATAA
555631 GGACATAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
9 4 0.08
10 13 0.25
11 27 0.53
12 7 0.14
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:557117 original size:23 final size:23
Alignment explanation
Indices: 557070--557118 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
557060 GTAGTTGGAC
* * *
557070 TTGAGGTTTGGGTTTGAAGGGTT
1 TTGAGGTTTGGGCTTGAACGATT
*
557093 TTGAGGTTTGGGCTTGACCGATT
1 TTGAGGTTTGGGCTTGAACGATT
557116 TTG
1 TTG
557119 GTTTTTGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.12, C:0.06, G:0.39, T:0.43
Consensus pattern (23 bp):
TTGAGGTTTGGGCTTGAACGATT
Found at i:565578 original size:85 final size:84
Alignment explanation
Indices: 565447--565745 Score: 438
Period size: 85 Copynumber: 3.5 Consensus size: 84
565437 AATGATGTGT
* * * * * * *
565447 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGCCATATATTTATGACACAAAAATATATGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
565512 CAAGC-AGATTTATGACGGGG
66 C-ATCTA-ATTTATGACGGGG
*
565532 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTTTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
565597 CATCTTAATTTATGACGGGG
66 CATC-TAATTTATGACGGGG
* *
565617 GCTTCAATGACGCGCAATGTTAGTCATACATGCTTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
565682 CATCTTAATTTATGACAGGG
66 CATC-TAATTTATGACGGGG
*
565702 GCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAAAT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAAT
565746 GCACGTCATA
Statistics
Matches: 196, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
84 2 0.01
85 193 0.98
86 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (84 bp):
GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
CATCTAATTTATGACGGGG
Found at i:570374 original size:21 final size:21
Alignment explanation
Indices: 570350--570389 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
570340 TTTTATTTTA
*
570350 ATTTAAATCTTGAGATTTGAT
1 ATTTAAATATTGAGATTTGAT
* *
570371 ATTTTAATATTGTGATTTG
1 ATTTAAATATTGAGATTTG
570390 TTTATGAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.53
Consensus pattern (21 bp):
ATTTAAATATTGAGATTTGAT
Found at i:571846 original size:21 final size:21
Alignment explanation
Indices: 571822--571885 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
571812 GCAAATTCGC
571822 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
571843 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
571863 TTTTCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
571884 GT
1 GT
571886 CTACAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:571902 original size:22 final size:22
Alignment explanation
Indices: 571874--571986 Score: 103
Period size: 22 Copynumber: 5.4 Consensus size: 22
571864 TTTCATTTCG
571874 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
571896 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
* ** *
571915 CGTTGTGATTTTCTA-A-AT-T
1 CGTTGCGATAGTCTACAGTTGT
571934 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
571956 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
571978 CGTTGCGAT
1 CGTTGCGAT
571987 TTTCCAAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
19 24 0.33
20 7 0.10
21 3 0.04
22 39 0.53
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.41
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:571919 original size:19 final size:19
Alignment explanation
Indices: 571895--571942 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
571885 TCTACAGTTG
571895 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* *
571914 TCGTTGTGATTTTCTAAAT
1 TCGTTGCGATTTTCCAAAT
571933 TCGTTGCGAT
1 TCGTTGCGAT
571943 AGTCTACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:572779 original size:41 final size:41
Alignment explanation
Indices: 572734--572866 Score: 194
Period size: 41 Copynumber: 3.2 Consensus size: 41
572724 CAACGAATTT
* *
572734 TCGCAATGAATTTGGAAAATCGCAACGACAACTGTAGATTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* * * *
572775 TCGCAACAAATTTGTAAACTATCGCAACAACAACGGTAGACTA
1 TCGCAACGAATTTGGAAA--ATCGCAACGACAACTGTAGACTA
572818 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
572859 TCGCAACG
1 TCGCAACG
572867 CGAACAGGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 44 0.55
43 36 0.45
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:572780 original size:22 final size:22
Alignment explanation
Indices: 572752--572866 Score: 105
Period size: 22 Copynumber: 5.4 Consensus size: 22
572742 AATTTGGAAA
*
572752 ATCGCAACGACAACTGTAGATT
1 ATCGCAACGACAACTGTAGACT
* *
572774 ATCGCAAC-A-AATTTGTAAACT
1 ATCGCAACGACAA-CTGTAGACT
* *
572795 ATCGCAACAACAACGGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
572817 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
572836 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
572858 ATCGCAACG
1 ATCGCAACG
572867 CGAACAGGAA
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
19 12 0.17
20 4 0.06
21 17 0.24
22 36 0.51
23 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:573642 original size:31 final size:31
Alignment explanation
Indices: 573607--573711 Score: 124
Period size: 31 Copynumber: 3.4 Consensus size: 31
573597 AATTAAATTT
* *
573607 TAATTTGACCCTTAAATTTTATACATAATAC
1 TAATTTGACCCTTAAATTTTATATAAAATAC
* *
573638 TAATTTGA-CCTTATATTTTACATAAAATAC
1 TAATTTGACCCTTAAATTTTATATAAAATAC
* * *
573668 TAATTTAACCTTTAAACTTTATATAAAATA-
1 TAATTTGACCCTTAAATTTTATATAAAATAC
573698 TCAATTTGACCCTT
1 T-AATTTGACCCTT
573712 GAATCCAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
30 26 0.43
31 35 0.57
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.43
Consensus pattern (31 bp):
TAATTTGACCCTTAAATTTTATATAAAATAC
Found at i:575855 original size:21 final size:21
Alignment explanation
Indices: 575826--575874 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
575816 TTGTGGTTGC
*
575826 ACCCTATGATGCGCAACTTGA
1 ACCCCATGATGCGCAACTTGA
575847 ACCCCATGATGCGCAACTTGA
1 ACCCCATGATGCGCAACTTGA
575868 ACCCCAT
1 ACCCCAT
575875 CGGAGCTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.20
Consensus pattern (21 bp):
ACCCCATGATGCGCAACTTGA
Found at i:586424 original size:14 final size:14
Alignment explanation
Indices: 586405--586459 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
586395 ACCCTTTGTC
*
586405 CTAAAAAAATAATA
1 CTAAAAAAATAAAA
*
586419 CT-AAAAATTAAAA
1 CTAAAAAAATAAAA
586432 CTAAAAAAATAAAA
1 CTAAAAAAATAAAA
*
586446 CAAATAAAAATAAA
1 CTAA-AAAAATAAA
586460 CAAACAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.31
14 15 0.43
15 9 0.26
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (14 bp):
CTAAAAAAATAAAA
Found at i:586434 original size:13 final size:13
Alignment explanation
Indices: 586408--586446 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
586398 CTTTGTCCTA
*
586408 AAAAAATAATACT
1 AAAAAATAAAACT
*
586421 AAAAATTAAAACT
1 AAAAAATAAAACT
586434 AAAAAAATAAAAC
1 -AAAAAATAAAAC
586447 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAATAAAACT
Found at i:591198 original size:12 final size:12
Alignment explanation
Indices: 591181--591205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
591171 TAGAATTGAC
591181 TTGTCAAATGAG
1 TTGTCAAATGAG
591193 TTGTCAAATGAG
1 TTGTCAAATGAG
591205 T
1 T
591206 GAATAAGAGA
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:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TTGTCAAATGAG
Found at i:592173 original size:44 final size:44
Alignment explanation
Indices: 592110--592508 Score: 587
Period size: 44 Copynumber: 9.2 Consensus size: 44
592100 AATCGAATTA
* * *
592110 ATAACTGAAATACATAATGGTGCATTAAGGCATGAAATGTTGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
592154 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
592198 ATAACTTAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
592242 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
592286 ATAACTGAAATG-GT-A---T--ATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * *
592323 ATAACTGAAATGCATAATGGTACATTAAGGCATGAAAAGATTCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* ** *
592367 ATAATTGAAATGCATAATATTGTATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
592411 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * * * *
592455 ATAAATGAATTGCATAACGGTGCAGTAAGGCATGAAAGGATTCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
592499 ATAAATGAAA
1 ATAACTGAAA
592509 ATAATAAATA
Statistics
Matches: 322, Mismatches: 26, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
37 33 0.10
38 1 0.00
39 2 0.01
42 2 0.01
43 1 0.00
44 283 0.88
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.25
Consensus pattern (44 bp):
ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
Found at i:592412 original size:169 final size:169
Alignment explanation
Indices: 592133--592463 Score: 565
Period size: 169 Copynumber: 2.0 Consensus size: 169
592123 ATAATGGTGC
* * * *
592133 ATTAAGGCATGAAATGTTGCCATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGTACATTAAGGCATGAAAAGATGCC
*
592198 ATAACTTAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGT
66 ATAACTTAAATGCATAATAGTGCATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGT
*
592263 GCATTAAGGCATGAAAGGATGCCATAACTGAAATGGTAT
131 GCATTAAGGCATGAAAGGATGCCATAAATGAAATGGTAT
*
592302 ATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGTACATTAAGGCATGAAAAGATTCC
1 ATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGTACATTAAGGCATGAAAAGATGCC
* *
592367 ATAA-TTGAAATGCATAATATTGTATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGG
66 ATAACTT-AAATGCATAATAGTGCATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGG
592431 TGCATTAAGGCATGAAAGGATGCCATAAATGAA
130 TGCATTAAGGCATGAAAGGATGCCATAAATGAA
592464 TTGCATAACG
Statistics
Matches: 152, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
168 2 0.01
169 150 0.99
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (169 bp):
ATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGTACATTAAGGCATGAAAAGATGCC
ATAACTTAAATGCATAATAGTGCATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGT
GCATTAAGGCATGAAAGGATGCCATAAATGAAATGGTAT
Found at i:592486 original size:213 final size:213
Alignment explanation
Indices: 592110--592508 Score: 656
Period size: 213 Copynumber: 1.9 Consensus size: 213
592100 AATCGAATTA
* * *
592110 ATAACTGAAATACATAATGGTGCATTAAGGCATGAAATGTTGCCATAACTGAAATGCATAATGGT
1 ATAACTGAAATACATAATGGTACATTAAGGCATGAAAAGTTGCCATAACTGAAATGCATAATAGT
*
592175 GCATTAAGGCATGAAAGGATGCCATAACTTAAATGCATAATGGTGCATTAAGGCATGAAAGGATG
66 GCATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATG
* * * *
592240 CCATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCCATAACTGAAATGGTATATT
131 CCATAAATGAAATGCATAACGGTGCAGTAAGGCATGAAAGGATGCCATAAATGAAATGGTATATT
592305 AAGGCATGAAAGGATGCC
196 AAGGCATGAAAGGATGCC
* * *
592323 ATAACTGAAATGCATAATGGTACATTAAGGCATGAAAAGATT-CCATAATTGAAATGCATAATAT
1 ATAACTGAAATACATAATGGTACATTAAGGCATGAAAAG-TTGCCATAACTGAAATGCATAATAG
*
592387 TGTATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGAT
65 TGCATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGAT
* *
592452 GCCATAAATGAATTGCATAACGGTGCAGTAAGGCATGAAAGGATTCCATAAATGAAA
130 GCCATAAATGAAATGCATAACGGTGCAGTAAGGCATGAAAGGATGCCATAAATGAAA
592509 ATAATAAATA
Statistics
Matches: 171, Mismatches: 14, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
213 169 0.99
214 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.25
Consensus pattern (213 bp):
ATAACTGAAATACATAATGGTACATTAAGGCATGAAAAGTTGCCATAACTGAAATGCATAATAGT
GCATTAAGGCATGAAAGGATGCCATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATG
CCATAAATGAAATGCATAACGGTGCAGTAAGGCATGAAAGGATGCCATAAATGAAATGGTATATT
AAGGCATGAAAGGATGCC
Found at i:598794 original size:22 final size:22
Alignment explanation
Indices: 598725--598795 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
598715 ACCGAAAGGG
* * *
598725 AGTATCGGTACCATAGTGTAGT
1 AGTATCGGTACTATAGTATAGA
* *
598747 AGTATCGATACTA-AG-AGA-A
1 AGTATCGGTACTATAGTATAGA
598766 AGGTATCGGTACTATAGTATAGA
1 A-GTATCGGTACTATAGTATAGA
598789 AGTATCG
1 AGTATCG
598796 ATACCATGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.03
20 12 0.32
21 4 0.11
22 19 0.50
23 2 0.05
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (22 bp):
AGTATCGGTACTATAGTATAGA
Found at i:598813 original size:42 final size:42
Alignment explanation
Indices: 598707--598822 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
598697 TGCCAAAATG
* * * *
598707 GTATCGATACCGAA-AG-GGAGTATCGGTACCATAGTGTAGTA
1 GTATCGATACC-AAGAGAGGGGTATCGGTACTATAGTATAGAA
* **
598748 GTATCGATACTAAGAGAAAGGTATCGGTACTATAGTATAGAA
1 GTATCGATACCAAGAGAGGGGTATCGGTACTATAGTATAGAA
* *
598790 GTATCGATACCATG-GTAGGGGTATCGATACTAT
1 GTATCGATACCAAGAG-AGGGGTATCGGTACTAT
598823 TGAGCTTGGA
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
40 2 0.03
41 13 0.22
42 45 0.75
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.27
Consensus pattern (42 bp):
GTATCGATACCAAGAGAGGGGTATCGGTACTATAGTATAGAA
Found at i:599286 original size:44 final size:44
Alignment explanation
Indices: 599223--599540 Score: 496
Period size: 44 Copynumber: 7.2 Consensus size: 44
599213 AACCAAATTA
599223 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
599267 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
599311 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAATGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
599355 ATAACTGAAATGCATAATGGTGCATTAAGGAATGAAATGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
** * *
599399 ATAACTGAAATATATAATGGTGCATTAAGGCATAAAAGGAAGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
599443 ATAACTGAAATGCATATTGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * *
599487 ATAAATGAAATGCATAACT-GTG-TTGTAAGGCATGAAATGATGCC
1 ATAACTGAAATGCATAA-TGGTGCAT-TAAGGCATGAAAGGATGCC
*
599531 ATAAATGAAA
1 ATAACTGAAA
599541 ATAATAAATA
Statistics
Matches: 255, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
43 1 0.00
44 253 0.99
45 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (44 bp):
ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
Done.