Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005589.1 Hibiscus syriacus cultivar Beakdansim tig00012982_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: 57923
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:188 original size:44 final size:44
Alignment explanation
Indices: 126--223 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
116 CACTTATATG
* * *
126 CATTTCAATTATGTCATCCTTACATGTCTTTTATACACTATTATA
1 CATTTC-ATTATGGCATCCTTACATGCCTTTGATACACTATTATA
* * *
171 CCTTTCATTATGGCATCCTTTCATGCCTTTGATACACTGTTATA
1 CATTTCATTATGGCATCCTTACATGCCTTTGATACACTATTATA
215 CATTTCATT
1 CATTTCATT
224 TATAACATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 41 0.89
45 5 0.11
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (44 bp):
CATTTCATTATGGCATCCTTACATGCCTTTGATACACTATTATA
Found at i:550 original size:81 final size:79
Alignment explanation
Indices: 348--554 Score: 252
Period size: 79 Copynumber: 2.6 Consensus size: 79
338 TTAACGTTCG
* *
348 TCTAACTGGCATAATTGACAACTTTCTGCCAAATGCACAGCTAGGCCATTATTCTTTACTCAATG
1 TCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTATTCTTTACTCAACG
* * * *
413 GTACTTACCGTTCA
66 ATACTAACCATTAA
* * * ** * *
427 TCTAACTGACATAATTTACACTTTTCTATCAAATTCATAGCTAGGCCATTATTCTTTTACTCAAC
1 TCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTATTC-TTTACTCAAC
*
492 GATACATAACTATTAA
65 GATAC-TAACCATTAA
* *
508 TTTAACTGGCATAATTGACACCTTTCTGCCAAAAGCACAGCTAGGCC
1 TCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCC
555 TCAAAGACAC
Statistics
Matches: 103, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
79 46 0.45
80 13 0.13
81 44 0.43
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (79 bp):
TCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTATTCTTTACTCAACG
ATACTAACCATTAA
Found at i:787 original size:67 final size:68
Alignment explanation
Indices: 510--1017 Score: 605
Period size: 66 Copynumber: 7.7 Consensus size: 68
500 ACTATTAATT
* * * * * * **
510 TAACTGGCATAATTGACACCTTTCTGCCAAAAGCACAGCTAGGCCTCAAAGACACTTAGTTTTTC
1 TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
575 A--
66 ATC
* * *
576 TAACTAGCATAAATGACACCTTTCTATCATATGAACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
1 TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
641 ATC
66 ATC
* * * * *
644 TAACAGACATAAATGACACATTTCTGTCAAATG--CAGTTA-GTCTCAAAGGCA-TTAGCCTTTC
1 TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
*
705 ATT
66 ATC
** * *
708 TAACTGAAATAAATGACACCTTTCTGTCATGTGCACAGTTA-GCCTCAAAGGCACTTAGCCGTTC
1 TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
772 ATC
66 ATC
* * * * * *
775 TAACTGGCATAAA-GACACATTTCTATCAAATGCATAATTAGGCCTCAAAGGCACTTAGTCTTTC
1 TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
839 ATC
66 ATC
* *
842 TAACTGGC--AAATGACATCTTTCTGTCATATACACAGTTAGGCCTC-AAGGCACTTAGCCTTTC
1 TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
904 ATC
66 ATC
* * *
907 TAACTGGCATAAATGATACCTTTTTGTCATATGAACAGTTAGGCCTCAAAGGCA-TTAGCCTTTC
1 TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
971 ATC
66 ATC
*
974 TAACTGGCATAAATG-CACCTTTATGT-ATATGCACA-TTAAGGCCT
1 TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTT-AGGCCT
1018 ATTGATCTTT
Statistics
Matches: 378, Mismatches: 53, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
64 42 0.11
65 55 0.15
66 134 0.35
67 114 0.30
68 33 0.09
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (68 bp):
TAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTC
ATC
Found at i:1541 original size:57 final size:59
Alignment explanation
Indices: 1384--1606 Score: 257
Period size: 57 Copynumber: 3.9 Consensus size: 59
1374 TTCCCATACG
* * *
1384 GAAATTCATACA--TAGTATGA-ATTCTTGTCCT-TTAGCACAC-AAGGTGCCCA-ATAC-A
1 GAAATTCATACACTTAGTATGATTTTCTTATCATGTTAGCACACGAA-GTG-CCATAT-CTA
* * *
1439 GAAATTTATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCATATCTG
1 GAAATTCATACACTTAGTATGATTTTCTTATCATGTTAGCACACGAAGTGCCATATCTA
* *
1498 GAAATTCATACACATAGT-TGATTTTC-TATCATGTTAGCACACGAAGTGCCCTATCTA
1 GAAATTCATACACTTAGTATGATTTTCTTATCATGTTAGCACACGAAGTGCCATATCTA
* * *
1555 GAAATTCATACACTTACTATGATTTCCTTATCATTTTAGCACACGAAGTGCC
1 GAAATTCATACACTTAGTATGATTTTCTTATCATGTTAGCACACGAAGTGCC
1607 CTATTTGGTA
Statistics
Matches: 145, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
55 11 0.08
57 53 0.37
58 26 0.18
59 53 0.37
60 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGATTTTCTTATCATGTTAGCACACGAAGTGCCATATCTA
Found at i:1608 original size:59 final size:58
Alignment explanation
Indices: 1384--1610 Score: 270
Period size: 59 Copynumber: 3.9 Consensus size: 58
1374 TTCCCATACG
* * * *
1384 GAAATTCATACA--TAGTATGAATTCTTGTCCT-TTAGCACAC-AAGGTGCCCAATAC-A
1 GAAATTCATACACTTAGTATGATTTCTTATCATGTTAGCACACGAA-GTGCCCTAT-CTA
* * *
1439 GAAATTTATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCATATCTG
1 GAAATTCATACACTTAGTATG-ATTTCTTATCATGTTAGCACACGAAGTGCCCTATCTA
*
1498 GAAATTCATACACATAGT-TGATTT-TCTATCATGTTAGCACACGAAGTGCCCTATCTA
1 GAAATTCATACACTTAGTATGATTTCT-TATCATGTTAGCACACGAAGTGCCCTATCTA
* *
1555 GAAATTCATACACTTACTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTAT
1 GAAATTCATACACTTAGTATGATTT-CTTATCATGTTAGCACACGAAGTGCCCTAT
1611 TTGGTAATCA
Statistics
Matches: 148, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
55 11 0.07
56 1 0.01
57 56 0.38
58 18 0.12
59 59 0.40
60 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (58 bp):
GAAATTCATACACTTAGTATGATTTCTTATCATGTTAGCACACGAAGTGCCCTATCTA
Found at i:2621 original size:3 final size:3
Alignment explanation
Indices: 2613--2643 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2603 GCACCCACGT
2613 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2644 TATAGAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2832 original size:24 final size:24
Alignment explanation
Indices: 2805--2856 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2795 TTTACCAATT
2805 ATTCAATTCAATCATCAAATTTTA
1 ATTCAATTCAATCATCAAATTTTA
** *
2829 ATTCTTTTCAATTATCAAATTTTA
1 ATTCAATTCAATCATCAAATTTTA
2853 ATTC
1 ATTC
2857 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTCAATTCAATCATCAAATTTTA
Found at i:2857 original size:24 final size:24
Alignment explanation
Indices: 2811--2865 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
2801 AATTATTCAA
*
2811 TTCAATCATCAAATTTTAATTCTT
1 TTCAATTATCAAATTTTAATTCTT
2835 TTCAATTATCAAATTTTAATTCTT
1 TTCAATTATCAAATTTTAATTCTT
2859 TTCAATT
1 TTCAATT
2866 TAGTCCTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (24 bp):
TTCAATTATCAAATTTTAATTCTT
Found at i:5243 original size:45 final size:45
Alignment explanation
Indices: 5162--5263 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 45
5152 CACCTATATG
* * * *
5162 CATTTCAATTATGTCATCTTTACATGTCTTTTATACACTATTATA
1 CATTTCATTTATGGCATCTTTACATGCCTTTGATACACTATTATA
* *
5207 CCTTTTATTTATGGCATCCTTT-CATGCCTTTGATACACTATTATA
1 CATTTCATTTATGGCAT-CTTTACATGCCTTTGATACACTATTATA
5252 CATTTCATTTAT
1 CATTTCATTTAT
5264 AACATCCATT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 44 0.92
46 4 0.08
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (45 bp):
CATTTCATTTATGGCATCTTTACATGCCTTTGATACACTATTATA
Found at i:5270 original size:45 final size:45
Alignment explanation
Indices: 5162--5276 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 45
5152 CACCTATATG
* * * *
5162 CATTTCAATTATGTCAT-CTTTACATGTCTTTTATACACTATTATA
1 CATTTCATTTATGACATCCTTT-CATGCCTTTGATACACTATTATA
* * *
5207 CCTTTTATTTATGGCATCCTTTCATGCCTTTGATACACTATTATA
1 CATTTCATTTATGACATCCTTTCATGCCTTTGATACACTATTATA
* *
5252 CATTTCATTTATAACATCCATTCAT
1 CATTTCATTTATGACATCCTTTCAT
5277 ACAATTATGC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 54 0.93
46 4 0.07
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (45 bp):
CATTTCATTTATGACATCCTTTCATGCCTTTGATACACTATTATA
Found at i:5502 original size:68 final size:68
Alignment explanation
Indices: 5393--5868 Score: 551
Period size: 68 Copynumber: 7.0 Consensus size: 68
5383 TATTCTTTTA
* * * * * * * *
5393 CTCAACGGTACTTAACCGTTCATCTAACTGACATAATTGACACATTT-TTTCCAAATGCACAGCT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGT-CAAATGCACAGTT
5457 AGGC
65 AGGC
* * * *
5461 CTCAAAGACACTTAGTCTTTCATCTAATTGGCATAAATGACATC-TTTCTGTCATATGCACAGTT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACA-CATTTCTGTCAAATGCACAGTT
5525 AGGC
65 AGGC
* * * * *
5529 CTCAAAGGTACTTAGCCTTTCATCTAATTGGCATAAATGACACCTTTTTGTAAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTA
5594 GGC
66 GGC
* * * * * *
5597 CTCAAAGACACTTAGCCTTTCATATAATTGGCATAAATGACACCTTTCTGTCATATGTACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTA
5662 GGC
66 GGC
* * * * * * * *
5665 CTTAAAGGTACCTAGTCTTTCATGTAACTGGCATAAATGACTCATTTATGTCAAATGCACTGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTA
5730 GGC
66 GGC
* *
5733 CTCAAAGGCAATTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTA
*
5798 GGT
66 GGC
* * * * * * *
5801 CTTAAAGGCATTTAGCCTTTCATCGAACTGGCATAAATGACACCTTTCTATCATATGCACGGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTA
5866 GGC
66 GGC
5869 TTCTTGATCT
Statistics
Matches: 349, Mismatches: 56, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
67 1 0.00
68 345 0.99
69 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTA
GGC
Found at i:5637 original size:136 final size:135
Alignment explanation
Indices: 5393--5868 Score: 621
Period size: 136 Copynumber: 3.5 Consensus size: 135
5383 TATTCTTTTA
* * * * * *
5393 CTCAACGGTACTTAACCGTTCATCTAACTGACATAATTGACACATTTTT-TCCAAATGCACAGCT
1 CTCAAAGGTACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTTTGT-CAAATGCACAGTT
*
5457 AGGCCTCAAAGACACTTAGTCTTTCATCTAATTGGCATAAATGACATCTTTCTGTCATATGCACA
65 AGGCCTCAAAGACACTTAGCCTTTCATCTAATTGGCATAAATGACA-CTTTCTGTCATATGCACA
5522 GTTAGGC
129 GTTAGGC
* * *
5529 CTCAAAGGTACTTAGCCTTTCATCTAATTGGCATAAATGACACCTTTTTGTAAAATGCACAGTTA
1 CTCAAAGGTACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTTTGTCAAATGCACAGTTA
* *
5594 GGCCTCAAAGACACTTAGCCTTTCATATAATTGGCATAAATGACACCTTTCTGTCATATGTACAG
66 GGCCTCAAAGACACTTAGCCTTTCATCTAATTGGCATAAATGACA-CTTTCTGTCATATGCACAG
5659 TTAGGC
130 TTAGGC
* * * * * * *
5665 CTTAAAGGTACCTAGTCTTTCATGTAACTGGCATAAATGACTCATTTATGTCAAATGCACTGTTA
1 CTCAAAGGTACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTTTGTCAAATGCACAGTTA
* * *
5730 GGCCTCAAAGGCAATTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAG
66 GGCCTCAAAGACACTTAGCCTTTCATCTAATTGGCATAAATGACAC-TTTCTGTCATATGCACAG
*
5795 TTAGGT
130 TTAGGC
* * * * * * * * *
5801 CTTAAAGGCATTTAGCCTTTCATCGAACTGGCATAAATGACACCTTTCTATCATATGCACGGTTA
1 CTCAAAGGTACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTTTGTCAAATGCACAGTTA
5866 GGC
66 GGC
5869 TTCTTGATCT
Statistics
Matches: 297, Mismatches: 41, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
135 1 0.00
136 295 0.99
137 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (135 bp):
CTCAAAGGTACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTTTGTCAAATGCACAGTTA
GGCCTCAAAGACACTTAGCCTTTCATCTAATTGGCATAAATGACACTTTCTGTCATATGCACAGT
TAGGC
Found at i:6374 original size:59 final size:59
Alignment explanation
Indices: 6241--6477 Score: 327
Period size: 59 Copynumber: 4.0 Consensus size: 59
6231 TATGTTTCCC
* * * *
6241 ATATGGAAATTCATACACTTAGTATGAATTTCTTGTCCT-TTAGCACAC-AAGGTGCCCA
1 ATATAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAA-GTGCCCT
* *
6299 ATACAGAAATTTATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCT
1 ATATAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCT
* * *
6358 ATATGGAAATTCATACACTTAGTATGATTTTCTTTTCATGTTAGCACACGAAGTGCCCT
1 ATATAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCT
* * *
6417 ATATAGAAATTCATACACTTAGTATG-CTTTACTTATCATTTTAGCACACAAAGTGCCCT
1 ATATAGAAATTCATACACTTAGTATGAATTT-CTTATCATGTTAGCACACGAAGTGCCCT
6476 AT
1 AT
6478 CTGGTAATCA
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
58 37 0.23
59 121 0.76
60 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (59 bp):
ATATAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCT
Found at i:9971 original size:20 final size:20
Alignment explanation
Indices: 9942--9980 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9932 TTTCCACCAC
*
9942 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
9962 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
9981 TGTGGACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:18768 original size:21 final size:21
Alignment explanation
Indices: 18742--18798 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
18732 TTGAGGGTCT
18742 TATGTGGTCCTTCGGGAAAAA
1 TATGTGGTCCTTCGGGAAAAA
* *
18763 TATGTGGTCCTTCGAGACAAA
1 TATGTGGTCCTTCGGGAAAAA
18784 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
18799 TGCAAACCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGAAAAA
Found at i:18814 original size:23 final size:23
Alignment explanation
Indices: 18784--18836 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
18774 TCGAGACAAA
18784 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
* *
18807 TATGTGGCACTTCGGTGTACACC
1 TATGTGGCACTTCGGTGCAAACC
18830 TATGTGG
1 TATGTGG
18837 TCCTTTGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:28047 original size:31 final size:31
Alignment explanation
Indices: 28009--28164 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
27999 AGGGTCGAGG
28009 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
28040 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
28071 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
28102 ATTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
28133 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
28164 G
1 G
28165 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:31097 original size:31 final size:31
Alignment explanation
Indices: 31059--31214 Score: 278
Period size: 31 Copynumber: 5.0 Consensus size: 31
31049 AGGGTCGAGG
31059 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31090 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31121 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
31152 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
31183 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
31214 G
1 G
31215 GTCCTTCGGG
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 120 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:34135 original size:31 final size:31
Alignment explanation
Indices: 34097--34252 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
34087 AGGGTCGAGG
34097 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
34128 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
34159 GTTTACCTATGTTCTTCGGGACATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
34190 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
34221 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
34252 G
1 G
34253 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:37182 original size:31 final size:31
Alignment explanation
Indices: 37144--37299 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
37134 AGGGTCGAGG
37144 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
37175 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
37206 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
37237 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
37268 GTTTACCTAGGTTCTTCAGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
37299 G
1 G
37300 GTCCTTCGGG
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:39476 original size:64 final size:64
Alignment explanation
Indices: 39407--39561 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 64
39397 TTGAAGGTGT
** *** *
39407 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACATCGAATACAATTCATG
39470 C
64 C
* * * *
39471 ATCGATGCATAAGTAGTGCATCGTTGCATACCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATACAATTCATGC
*
39535 ATCGATGCATCAGTAGTGCATCGATGC
1 ATCGATGCATAAGTAGTGCATCGATGC
39562 TTACTTTAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 1 0.01
64 73 0.95
65 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATACAATTCATGC
Found at i:40256 original size:31 final size:31
Alignment explanation
Indices: 40218--40342 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
40208 AGGGTCGAGG
*
40218 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
40249 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
40280 GTTTACCTATGTTCTTCGGGACATTTGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
40311 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
40342 G
1 G
40343 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:42348 original size:31 final size:31
Alignment explanation
Indices: 42310--42402 Score: 107
Period size: 35 Copynumber: 2.9 Consensus size: 31
42300 TGACTAGTCG
42310 GTGCTGAACCTATACAAGGAATTACCAAT-A
1 GTGCTGAACCTATACAAGGAATTACCAATCA
* * *
42340 GTGACTGAACCTGCCAGAGATAGGAATTACCAGTCA
1 GTG-CTGAACCT---ATACA-AGGAATTACCAATCA
42376 GTGCTGAACCTATACAAGGAATTACCA
1 GTGCTGAACCTATACAAGGAATTACCA
42403 GCAGCTACTG
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
30 3 0.06
31 19 0.37
32 3 0.06
34 3 0.06
35 20 0.38
36 4 0.08
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
GTGCTGAACCTATACAAGGAATTACCAATCA
Found at i:42386 original size:66 final size:66
Alignment explanation
Indices: 42295--42424 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 66
42285 TAAGTCTATA
* * * *
42295 AGGAATGACTAGTCGGTGCTGAACCTATACAAGGAATTACCAATAG-TGACTGAACCTGCCAGAG
1 AGGAATGACCAGTCAGTGCTGAACCTATACAAGGAATTACCAACAGCT-ACTGAACATGCCAGAG
42359 AT
65 AT
* *
42361 AGGAATTACCAGTCAGTGCTGAACCTATACAAGGAATTACCAGCAGCTACTGAACATGCCAGAG
1 AGGAATGACCAGTCAGTGCTGAACCTATACAAGGAATTACCAACAGCTACTGAACATGCCAGAG
42425 TCTTCTTACC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 56 0.98
67 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (66 bp):
AGGAATGACCAGTCAGTGCTGAACCTATACAAGGAATTACCAACAGCTACTGAACATGCCAGAGA
T
Found at i:42403 original size:31 final size:31
Alignment explanation
Indices: 42294--42403 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 31
42284 TTAAGTCTAT
* * *
42294 AAGGAATGACTAGTCGGTGCTGAACCTATAC
1 AAGGAATTACCAGTCAGTGCTGAACCTATAC
* * *
42325 AAGGAATTACCAAT-AGTGACTGAACCTGCCAGAG
1 AAGGAATTACCAGTCAGTG-CTGAACCT---ATAC
42359 ATAGGAATTACCAGTCAGTGCTGAACCTATAC
1 A-AGGAATTACCAGTCAGTGCTGAACCTATAC
42391 AAGGAATTACCAG
1 AAGGAATTACCAG
42404 CAGCTACTGA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
30 3 0.05
31 31 0.48
32 3 0.05
34 3 0.05
35 20 0.31
36 4 0.06
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGTGCTGAACCTATAC
Found at i:42414 original size:31 final size:30
Alignment explanation
Indices: 42313--42415 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 30
42303 CTAGTCGGTG
**
42313 CTGAACCTATACAAGGAATTACCAATAGTGA
1 CTGAACCTATACAAGGAATTACCAGCAGT-A
* * *
42344 CTGAACCTGCCAGAGATAGGAATTACCAGTCAGTG
1 CTGAACCT---ATACA-AGGAATTACCAG-CAGTA
42379 CTGAACCTATACAAGGAATTACCAGCAGCTA
1 CTGAACCTATACAAGGAATTACCAGCAG-TA
42410 CTGAAC
1 CTGAAC
42416 ATGCCAGAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
30 3 0.05
31 27 0.47
32 3 0.05
34 3 0.05
35 19 0.33
36 3 0.05
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (30 bp):
CTGAACCTATACAAGGAATTACCAGCAGTA
Found at i:42504 original size:12 final size:12
Alignment explanation
Indices: 42487--42511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42477 AAGCAGAGAT
42487 ATCAGAAATCAG
1 ATCAGAAATCAG
42499 ATCAGAAATCAG
1 ATCAGAAATCAG
42511 A
1 A
42512 AATCAGGACA
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:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (12 bp):
ATCAGAAATCAG
Found at i:42511 original size:19 final size:19
Alignment explanation
Indices: 42487--42530 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
42477 AAGCAGAGAT
42487 ATCAGAAATCA-GATCAGAA
1 ATCAGAAATCAGGA-CAGAA
*
42506 ATCAGAAATCAGGACATAA
1 ATCAGAAATCAGGACAGAA
42525 ATCAGA
1 ATCAGA
42531 GAAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (19 bp):
ATCAGAAATCAGGACAGAA
Found at i:44562 original size:10 final size:10
Alignment explanation
Indices: 44547--44594 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
44537 CAATGGCTGA
*
44547 TCAACGACGG
1 TCAACGATGG
*
44557 TCAACGGTTGG
1 TCAAC-GATGG
44568 TCAACGATGG
1 TCAACGATGG
*
44578 TCAACGGTTGG
1 TCAAC-GATGG
44589 TCAACG
1 TCAACG
44595 GTCAGCGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 15 0.47
11 17 0.53
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (10 bp):
TCAACGATGG
Found at i:44569 original size:11 final size:11
Alignment explanation
Indices: 44555--44596 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
44545 GATCAACGAC
44555 GGTCAACGGTT
1 GGTCAACGGTT
*
44566 GGTCAAC-GAT
1 GGTCAACGGTT
44576 GGTCAACGGTT
1 GGTCAACGGTT
44587 GGTCAACGGT
1 GGTCAACGGT
44597 CAGCGGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (11 bp):
GGTCAACGGTT
Found at i:44571 original size:21 final size:21
Alignment explanation
Indices: 44547--44594 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
44537 CAATGGCTGA
44547 TCAACGACGGTCAACGGTTGG
1 TCAACGACGGTCAACGGTTGG
*
44568 TCAACGATGGTCAACGGTTGG
1 TCAACGACGGTCAACGGTTGG
44589 TCAACG
1 TCAACG
44595 GTCAGCGGGT
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:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (21 bp):
TCAACGACGGTCAACGGTTGG
Found at i:48250 original size:19 final size:18
Alignment explanation
Indices: 48222--48258 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
48212 GTTTTAGGTG
*
48222 TATATTTTACTTATATTAT
1 TATATATTACTT-TATTAT
48241 TATATATTACTTTATTAT
1 TATATATTACTTTATTAT
48259 ATACATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATTACTTTATTAT
Found at i:52099 original size:7 final size:7
Alignment explanation
Indices: 52089--52143 Score: 58
Period size: 7 Copynumber: 7.6 Consensus size: 7
52079 AAAAAAGGGA
52089 AAAAAAG
1 AAAAAAG
52096 AAAAAGAG
1 AAAAA-AG
*
52104 AAAAGAG
1 AAAAAAG
52111 AAAAAAG
1 AAAAAAG
52118 -AAAAAG
1 AAAAAAG
*
52124 AAAAAAT
1 AAAAAAG
52131 AAGAAGAAG
1 AA-AA-AAG
52140 AAAA
1 AAAA
52144 TAGTCACATC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 6 0.15
7 20 0.50
8 10 0.25
9 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:52134 original size:16 final size:15
Alignment explanation
Indices: 52087--52143 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
52077 GGAAAAAAGG
*
52087 GAAAAA-AAGAAAAA
1 GAAAAAGAAAAAAAA
*
52101 GAGAAAAGAGAAAAAA
1 GA-AAAAGAAAAAAAA
52117 GAAAAAGAAAAAATAA
1 GAAAAAGAAAAAA-AA
*
52133 GAAGAAGAAAA
1 GAAAAAGAAAA
52144 TAGTCACATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.06
15 14 0.39
16 20 0.56
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAAAAA
Found at i:54082 original size:42 final size:40
Alignment explanation
Indices: 54007--54113 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 40
53997 AAGGGTTTCT
54007 TGATGAGTAAGTCCTTCGGCCATCAGTAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGCCATCAGTAAGTCTTTCGAGCA
*
54048 TGATGCGTAAGTCCTCCGAGCCATCTA-TAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCG-GCCATC-AGTAAGTCTTTCGAGCA
* *
54090 AGATGATAAGTCCTTCGGGCCATC
1 TGATGGTAAGTCCTTC-GGCCATC
54114 CATGAGACCC
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
41 31 0.53
42 26 0.45
43 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (40 bp):
TGATGGTAAGTCCTTCGGCCATCAGTAAGTCTTTCGAGCA
Found at i:54100 original size:21 final size:21
Alignment explanation
Indices: 54033--54106 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 21
54023 CGGCCATCAG
* * *
54033 TAAGTCTTTCGAGCATGATGCG
1 TAAGTCCTTCGAGCAAGATG-A
* * **
54055 TAAGTCCTCCGAGCCATCT-A
1 TAAGTCCTTCGAGCAAGATGA
*
54075 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCCTTCGAGCAAGATGA
54096 TAAGTCCTTCG
1 TAAGTCCTTCG
54107 GGCCATCCAT
Statistics
Matches: 38, Mismatches: 13, Indels: 3
0.70 0.24 0.06
Matches are distributed among these distances:
20 14 0.37
21 11 0.29
22 13 0.34
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (21 bp):
TAAGTCCTTCGAGCAAGATGA
Found at i:54349 original size:21 final size:20
Alignment explanation
Indices: 54324--54388 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
54314 TGAGACAGTT
54324 TCTCTTGAAACGAATTTTATC
1 TCTCTTGAAACGAATTTT-TC
*
54345 TCTCTTGAGAC-AA--TTTC
1 TCTCTTGAAACGAATTTTTC
*
54362 -C-CTTGAAACGAGTTTTGTC
1 TCTCTTGAAACGAATTTT-TC
54381 TCTCTTGA
1 TCTCTTGA
54389 GACAGTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
15 7 0.20
16 2 0.06
17 2 0.06
18 4 0.11
19 2 0.06
20 3 0.09
21 15 0.43
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (20 bp):
TCTCTTGAAACGAATTTTTC
Found at i:54353 original size:36 final size:36
Alignment explanation
Indices: 54286--54441 Score: 206
Period size: 36 Copynumber: 4.4 Consensus size: 36
54276 GCATAAGTCT
* * * *
54286 GTTTCT-TTAAAACAAAGTTTGTCTCTTTTGAGACA
1 GTTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACA
*
54321 GTTTCTCTTGAAACGAATTTTATCTCTCTTGAGACA
1 GTTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACA
* * *
54357 ATTTCCCTTGAAACGAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACA
* * *
54393 GTTTCTCTTGAAACAAATTTTGTCTCCCTTGAAACA
1 GTTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACA
54429 GTTTCTCTTGAAA
1 GTTTCTCTTGAAA
54442 TAAAAAAAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 6 0.06
36 99 0.94
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
GTTTCTCTTGAAACGAATTTTGTCTCTCTTGAGACA
Found at i:54440 original size:15 final size:15
Alignment explanation
Indices: 54381--54441 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
54371 GAGTTTTGTC
*
54381 TCTCTTGAGACAGTT
1 TCTCTTGAAACAGTT
*
54396 TCTCTTGAAACAAATTTT
1 TCTCTTGAAAC--A-GTT
54414 GTCTCCCTTGAAACAGTT
1 -TCT--CTTGAAACAGTT
54432 TCTCTTGAAA
1 TCTCTTGAAA
54442 TAAAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
15 17 0.46
17 4 0.11
18 4 0.11
19 4 0.11
21 8 0.22
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (15 bp):
TCTCTTGAAACAGTT
Found at i:55220 original size:91 final size:91
Alignment explanation
Indices: 55115--55369 Score: 325
Period size: 91 Copynumber: 2.8 Consensus size: 91
55105 TAACAATTCA
* * * * * *
55115 AATGGAGAGTTCATAATGAGAATAACTCATCCACCAAGGAAGAATAAATTCATTATGAGAAGAAC
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * * *** *
55180 ATGTTCGACCCTT-CCTTGGCGTTACC
66 TTGTTC-AACCTTGCATCAACATTACC
*
55206 AATGGAGAGTTCATAATGAAAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
55271 TTGTTCAACCTTGGATCAACATTTCC
66 TTGTTCAACCTTGCATCAACATTACC
* *
55297 AGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGG-AGAAGAAGTTCATAATAAGAAGAAC
1 AATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAAC
55361 TTGTTCAAC
66 TTGTTCAAC
55370 TTAGCTCGAT
Statistics
Matches: 144, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
90 38 0.26
91 106 0.74
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (91 bp):
AATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTGCATCAACATTACC
Found at i:55610 original size:118 final size:117
Alignment explanation
Indices: 55282--55628 Score: 510
Period size: 115 Copynumber: 3.0 Consensus size: 117
55272 TGTTCAACCT
*
55282 TGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCC-AACGA-GGAGAAGAAGT
1 TGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAA-GAGGGAGAAGAAGT
* * * * *
55345 TCATAATAAGAAGAACTTGTTCAA-CTTAGCTCGATTCCATCACAGAATGAGG
65 TCATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTTCATCACAGAAGGAGG
* * *
55397 TGGAACAACATTTCCAATGGGAGAGTTTATAATGAGAAGAACTC-T--GAAGAGGGAGAAAAAGT
1 TGGATCAACATTTCCAAT-GGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGT
55459 TCATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTTCATCACAGAAGGAGG
65 TCATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTTCATCACAGAAGGAGG
* *
55512 TGGATCAATATTTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAGGAGGGAGAAGAAGT
1 TGGATCAACA-TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGT
55577 TCATAATGAGAAGAACTTGTTCAACCTTGGTTCGA-TTCTATCACAGAAGGAG
65 TCATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTTC-ATCACAGAAGGAG
55629 TATATCAACA
Statistics
Matches: 209, Mismatches: 14, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
113 2 0.01
114 35 0.17
115 73 0.35
116 33 0.16
117 3 0.01
118 63 0.30
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (117 bp):
TGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTTCATCACAGAAGGAGG
Done.