Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009275.1 Hibiscus syriacus cultivar Beakdansim tig00112958_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: 64125
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:154 original size:35 final size:34
Alignment explanation
Indices: 65--169 Score: 151
Period size: 32 Copynumber: 3.0 Consensus size: 34
55 TATGAGATGG
65 GTTATATGAAAATGGATCTATGAGATCATACAAGAAT
1 GTTATATG--AAT-GATCTATGAGATCATACAAGAAT
*
102 GTTATA--AATGATCTATGATATCATACAAGAAT
1 GTTATATGAATGATCTATGAGATCATACAAGAAT
134 GTTATATGCAATGATCTATGAGATCATACAAGAAT
1 GTTATATG-AATGATCTATGAGATCATACAAGAAT
169 G
1 G
170 ACACAAGTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
32 28 0.44
33 3 0.05
35 26 0.41
37 6 0.10
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (34 bp):
GTTATATGAATGATCTATGAGATCATACAAGAAT
Found at i:405 original size:21 final size:21
Alignment explanation
Indices: 376--416 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
366 CGGGATGATA
376 GGTCATTCGGGATATATATGT
1 GGTCATTCGGGATATATATGT
*
397 GGTCCTTCGGGATATATATG
1 GGTCATTCGGGATATATATG
417 CAATCCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (21 bp):
GGTCATTCGGGATATATATGT
Found at i:423 original size:21 final size:21
Alignment explanation
Indices: 381--424 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
371 TGATAGGTCA
***
381 TTCGGGATATATATGTGGTCC
1 TTCGGGATATATATGCAATCC
402 TTCGGGATATATATGCAATCC
1 TTCGGGATATATATGCAATCC
423 TT
1 TT
425 TGGAACATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (21 bp):
TTCGGGATATATATGCAATCC
Found at i:4264 original size:22 final size:22
Alignment explanation
Indices: 4238--4279 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4228 CTTTGTTTTA
4238 TCAAAG-TCAACAGTCAGACCAG
1 TCAAAGCT-AACAGTCAGACCAG
*
4260 TCAAAGCTAACGGTCAGACC
1 TCAAAGCTAACAGTCAGACC
4280 GGTCGACGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.38, C:0.29, G:0.19, T:0.14
Consensus pattern (22 bp):
TCAAAGCTAACAGTCAGACCAG
Found at i:6280 original size:22 final size:21
Alignment explanation
Indices: 6246--6289 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
6236 GGAGAATACT
*
6246 GGAAAAGCTCCGAAATAGAAGA
1 GGAAAAGCTCCG-AAGAGAAGA
6268 GGAAAAGGC-CCGAAGAGAAGA
1 GGAAAA-GCTCCGAAGAGAAGA
6289 G
1 G
6290 CAAGAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 9 0.45
23 2 0.10
ACGTcount: A:0.48, C:0.14, G:0.34, T:0.05
Consensus pattern (21 bp):
GGAAAAGCTCCGAAGAGAAGA
Found at i:7023 original size:24 final size:24
Alignment explanation
Indices: 6969--7037 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
6959 GGTAATATGT
* * * *
6969 TCGTTTATGTTCATTCATTTATGC
1 TCGTTTATGTTCGTTCGTTTACGA
*
6993 TCATTTATGTTCGTTCGTTTACGA
1 TCGTTTATGTTCGTTCGTTTACGA
* *
7017 TCGTTTATTTTCGTTTGTTTA
1 TCGTTTATGTTCGTTCGTTTA
7038 TGTTCATTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (24 bp):
TCGTTTATGTTCGTTCGTTTACGA
Found at i:7050 original size:24 final size:24
Alignment explanation
Indices: 6986--7074 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
6976 TGTTCATTCA
* * * *
6986 TTTATGCTCATTTATGTTCGTTCG
1 TTTATGTTCATTCATTTTCGTTTG
* * * *
7010 TTTACGATCGTTTATTTTCGTTTG
1 TTTATGTTCATTCATTTTCGTTTG
*
7034 TTTATGTTCATTCATTTTCTTTTG
1 TTTATGTTCATTCATTTTCGTTTG
7058 TTTATGTTCATTCATTT
1 TTTATGTTCATTCATTT
7075 ATGTCTAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.13, C:0.13, G:0.12, T:0.61
Consensus pattern (24 bp):
TTTATGTTCATTCATTTTCGTTTG
Found at i:7629 original size:14 final size:13
Alignment explanation
Indices: 7610--7683 Score: 55
Period size: 14 Copynumber: 5.7 Consensus size: 13
7600 TTCATTTACT
*
7610 TTCGTTTGTTCGTG
1 TTCGTTTATT-GTG
7624 TTCGTTTATTGTG
1 TTCGTTTATTGTG
*
7637 TTTGTTTA---TG
1 TTCGTTTATTGTG
*
7647 TTCGTTTATATCTG
1 TTCGTTTAT-TGTG
*
7661 TTCGTTTATATTTG
1 TTCGTTTAT-TGTG
*
7675 TTTGTTTAT
1 TTCGTTTAT
7684 CATTTAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
10 9 0.18
13 10 0.20
14 32 0.63
ACGTcount: A:0.09, C:0.08, G:0.19, T:0.64
Consensus pattern (13 bp):
TTCGTTTATTGTG
Found at i:7648 original size:23 final size:24
Alignment explanation
Indices: 7613--7669 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
7603 ATTTACTTTC
** *
7613 GTTTGTTCGTGTTCGTTTAT-TGT
1 GTTTGTTTATGTTCGTTTATATCT
7636 GTTTGTTTATGTTCGTTTATATCT
1 GTTTGTTTATGTTCGTTTATATCT
*
7660 GTTCGTTTAT
1 GTTTGTTTAT
7670 ATTTGTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.61
Consensus pattern (24 bp):
GTTTGTTTATGTTCGTTTATATCT
Found at i:7651 original size:37 final size:36
Alignment explanation
Indices: 7585--7683 Score: 110
Period size: 37 Copynumber: 2.7 Consensus size: 36
7575 TTCTGGTTTA
* ** *
7585 TGTTCATTTATTGTGTTCATTTACTTTCGTTTGT-TC
1 TGTTCGTTTATTGTGTTTGTTTA-TTTCGTTTATATC
7621 GTGTTCGTTTATTGTGTTTGTTTATGTTCGTTTATATC
1 -TGTTCGTTTATTGTGTTTGTTTAT-TTCGTTTATATC
*
7659 TGTTCGTTTATATTTGTTTGTTTAT
1 TGTTCGTTTAT-TGTGTTTGTTTAT
7684 CATTTAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 39 0.72
38 14 0.26
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63
Consensus pattern (36 bp):
TGTTCGTTTATTGTGTTTGTTTATTTCGTTTATATC
Found at i:7677 original size:24 final size:23
Alignment explanation
Indices: 7624--7677 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
7614 TTTGTTCGTG
* * *
7624 TTCGTTTATTGTGTTTGTTTATG
1 TTCGTTTATTCTGTTCGTTTATA
7647 TTCGTTTATATCTGTTCGTTTATA
1 TTCGTTTAT-TCTGTTCGTTTATA
*
7671 TTTGTTT
1 TTCGTTT
7678 GTTTATCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.11, C:0.07, G:0.17, T:0.65
Consensus pattern (23 bp):
TTCGTTTATTCTGTTCGTTTATA
Found at i:16270 original size:57 final size:57
Alignment explanation
Indices: 16184--16291 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
16174 GTCAATGATT
*
16184 AAATTGTTGGTTTACTAAAATAAAGTATTAAATTCCTTAAATAAAATTAAGATATTA
1 AAATAGTTGGTTTACTAAAATAAAGTATTAAATTCCTTAAATAAAATTAAGATATTA
* *
16241 AAATAGTTTGTTTACTGAAAT-AAGATATTAAATTCCTTAAATAAAATTAAG
1 AAATAGTTGGTTTACTAAAATAAAG-TATTAAATTCCTTAAATAAAATTAAG
16292 GTGACGTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
56 3 0.06
57 44 0.94
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (57 bp):
AAATAGTTGGTTTACTAAAATAAAGTATTAAATTCCTTAAATAAAATTAAGATATTA
Found at i:16640 original size:29 final size:29
Alignment explanation
Indices: 16509--16650 Score: 77
Period size: 29 Copynumber: 4.6 Consensus size: 29
16499 CTTTTGGCAT
*
16509 TCGGGTCGGATTTTTTTTAAAAAAAATTCGGGT
1 TCGGGTCGGA-TTTTTTT--AAAAAATT-GGGG
* * * *
16542 TCGGGTCGGGTTTTTTTAAGTTTGATATTCGGG
1 TCGGGTCGGATTTTTTTAA----AAAATTGGGG
* * ** * *
16575 TCGGGTCAAGTTATTTTTTAAAATTTTAGGA
1 TCGGGTC-GGAT-TTTTTTAAAAAATTGGGG
*
16606 TAGGGTCGGATTTTTTTAAAAAATTGGGG
1 TCGGGTCGGATTTTTTTAAAAAATTGGGG
*
16635 TCGGGTCGGGTTTTTT
1 TCGGGTCGGATTTTTT
16651 AAGTTTGATA
Statistics
Matches: 83, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
29 28 0.34
30 4 0.05
31 12 0.14
32 7 0.08
33 18 0.22
34 6 0.07
35 8 0.10
ACGTcount: A:0.21, C:0.08, G:0.28, T:0.43
Consensus pattern (29 bp):
TCGGGTCGGATTTTTTTAAAAAATTGGGG
Found at i:16676 original size:28 final size:28
Alignment explanation
Indices: 16635--16701 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
16625 AAAATTGGGG
*
16635 TCGGGTCGGG-TTTTTTAAGTTTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
16662 TCGGGTTGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
16690 TCGGGTCGGGTT
1 TCGGGTCGGGTT
16702 CGGGTTCGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.12, C:0.07, G:0.34, T:0.46
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:17453 original size:104 final size:105
Alignment explanation
Indices: 17333--17521 Score: 281
Period size: 104 Copynumber: 1.8 Consensus size: 105
17323 TAAGAGTTCT
* * * * *
17333 AATTCTGACATTATGAATGAAGTAAATTAAATTGGGAGAATCACTCTTATAAAGA-ATATTGACA
1 AATTCTGACATTATGAATGAAGTAAATTAAATTCGAAGAATCACCCTTATAAAAATATATTAACA
* *
17397 ACAATTAATTTAAATTAATCGACTAATAAAAAAAATATTG
66 ACAAGTAATTTAAACTAATCGACTAATAAAAAAAATATTG
* *
17437 AATTCTGACATTATGAATGAAGTAGATTGAATTCGAAGAATCACCCTTATAAAAATATATTAACA
1 AATTCTGACATTATGAATGAAGTAAATTAAATTCGAAGAATCACCCTTATAAAAATATATTAACA
*
17502 ATAAGTAATTTAAACTAATC
66 ACAAGTAATTTAAACTAATC
17522 AATAAATAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
104 49 0.66
105 25 0.34
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (105 bp):
AATTCTGACATTATGAATGAAGTAAATTAAATTCGAAGAATCACCCTTATAAAAATATATTAACA
ACAAGTAATTTAAACTAATCGACTAATAAAAAAAATATTG
Found at i:20897 original size:32 final size:33
Alignment explanation
Indices: 20861--20945 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
20851 GTCAGGTCAA
* * *
20861 TTTTCGGGTCAGGTGATTATCGAATCAGTTG-T
1 TTTTCGGGTCAGATCAATATCGAATCAGTTGAT
**
20893 TTTTCGATTCAGATCAATATCGAATCAGTTGAT
1 TTTTCGGGTCAGATCAATATCGAATCAGTTGAT
* *
20926 TTTT-GGGTCGGGTCAATATC
1 TTTTCGGGTCAGATCAATATC
20946 TGATTGGTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
32 38 0.88
33 5 0.12
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (33 bp):
TTTTCGGGTCAGATCAATATCGAATCAGTTGAT
Found at i:21756 original size:32 final size:33
Alignment explanation
Indices: 21709--21788 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 33
21699 ATTAATTTTT
* *
21709 GTTCGGGTTGCTTTCGGGTCGGGTT-AAATTCG
1 GTTCGGGTTGCTTTCGAGTCGGATTAAAATTCG
* * * *
21741 GTTCGGTTTGTTTTCGAGTCTGATTAAAATTTG
1 GTTCGGGTTGCTTTCGAGTCGGATTAAAATTCG
*
21774 GTTCGGGTTTCTTTC
1 GTTCGGGTTGCTTTC
21789 AGTTTGGGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
32 20 0.53
33 18 0.47
ACGTcount: A:0.11, C:0.14, G:0.30, T:0.45
Consensus pattern (33 bp):
GTTCGGGTTGCTTTCGAGTCGGATTAAAATTCG
Found at i:21810 original size:22 final size:22
Alignment explanation
Indices: 21785--21831 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
21775 TTCGGGTTTC
*
21785 TTTCAGTTTGGGTTAATTTCAG
1 TTTCAGTTCGGGTTAATTTCAG
* *
21807 TTTCGGTTCGGGTTACTTTCAG
1 TTTCAGTTCGGGTTAATTTCAG
21829 TTT
1 TTT
21832 TGCTAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.51
Consensus pattern (22 bp):
TTTCAGTTCGGGTTAATTTCAG
Found at i:28118 original size:44 final size:43
Alignment explanation
Indices: 28009--28122 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 43
27999 AATAATTATT
* *
28009 AATTAATAATTTAGTATTTTTAATTATTTATTGGAAAATTAATA
1 AATTAATAATTTA-TATTTTTTATTATCTATTGGAAAATTAATA
* *
28053 GATTAACAATTTATCATTTTTTATTATCTATTGGAAAATTAATA
1 AATTAATAATTTAT-ATTTTTTATTATCTATTGGAAAATTAATA
* *
28097 AATTAGTAATTTATAATTTTT-TTATC
1 AATTAATAATTTATATTTTTTATTATC
28123 ATCAAATCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 5 0.08
43 7 0.11
44 49 0.80
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (43 bp):
AATTAATAATTTATATTTTTTATTATCTATTGGAAAATTAATA
Found at i:29420 original size:20 final size:19
Alignment explanation
Indices: 29397--29442 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
29387 CGATATACCA
29397 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
29417 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
29437 GGTAAA
1 GGTAAA
29443 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:29587 original size:20 final size:19
Alignment explanation
Indices: 29564--29610 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
29554 CGATATAACA
29564 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
29584 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
29604 GGTAAAA
1 GGTAAAA
29611 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:29612 original size:17 final size:19
Alignment explanation
Indices: 29573--29615 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
29563 AGGTAAAAAT
29573 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
29593 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
29610 ATGATA
1 ATGATA
29616 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:31954 original size:33 final size:33
Alignment explanation
Indices: 31912--31977 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
31902 AAATAGATGG
*
31912 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
31945 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
31978 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:33789 original size:19 final size:19
Alignment explanation
Indices: 33765--33813 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
33755 AATGTCGAGT
33765 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
33784 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
33803 TATTTTTGTAT
1 TAATTTTGTAT
33814 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:34593 original size:198 final size:199
Alignment explanation
Indices: 33884--35638 Score: 3260
Period size: 199 Copynumber: 8.9 Consensus size: 199
33874 TACACATTAA
* *
33884 GGTGCACACATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
33949 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
**
34014 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
*
34078 ACAA
196 ACAG
34082 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAACCCAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAA
34147 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATA
65 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATA
34212 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAA
130 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAA
34277 AACAG
195 AACAG
*
34282 GGTGCACCCATAAAGTGTTGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
34347 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
34412 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTT-CCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
34475 ACAG
196 ACAG
34479 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAACCCAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAA
34544 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATA
65 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATA
**
34609 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAA
130 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAA
*
34674 AACAC
195 AACAG
34679 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
34744 GTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
34808 GTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATA-TTTTTT-CCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
34870 ACAG
196 ACAG
34874 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
34939 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCCGTTTTATGAGAGGATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
35004 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
35068 ACAG
196 ACAG
35072 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
35136 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
*
35201 GTCTAAATAATGTGTCGACACTAATATAGTTTTTGTCGATATTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
35266 ACAG
196 ACAG
35270 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
* * *
35335 GTATAATGTAATATGTAATTTTTCAATCTAATCGGTATAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
35400 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
*
35465 ACAA
196 ACAG
35469 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
35534 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
35598 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
35639 CTAATTTAAT
Statistics
Matches: 1521, Mismatches: 26, Indels: 20
0.97 0.02 0.01
Matches are distributed among these distances:
195 100 0.07
196 72 0.05
197 256 0.17
198 404 0.27
199 544 0.36
200 145 0.10
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
ACAG
Found at i:34625 original size:397 final size:397
Alignment explanation
Indices: 33884--35638 Score: 3281
Period size: 397 Copynumber: 4.4 Consensus size: 397
33874 TACACATTAA
* *
33884 GGTGCACACATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
33949 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
**
34014 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAA
*
34079 CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAACCC
196 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCC
34144 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGG
260 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGG
34209 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
325 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
34274 GAAAACAG
390 GAAAACAG
*
34282 GGTGCACCCATAAAGTGTTGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
34347 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
34412 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCAGAATGAATGGAAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAA
34476 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAACCC
196 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCC
34541 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGG
260 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGG
*
34606 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT
325 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
* *
34671 AAAAACAC
390 GAAAACAG
34679 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
34744 GTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
34808 GTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATA-TTTTTTCCAGAATGAATGGAAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAA
34871 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
196 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
*
34936 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCCGTTTTATGAGAGGA
261 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGA
35001 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATGG
326 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGG
35065 AAAACAG
391 AAAACAG
35072 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
35136 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
*
35201 GTCTAAATAATGTGTCGACACTAATATAGTTTTTGTCGATATTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATGGAAA
35266 ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
195 ACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
* * *
35331 AAAAGTATAATGTAATATGTAATTTTTCAATCTAATCGGTATAATTATACCGGTTTTATGAGAGA
260 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGG
35396 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
325 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
*
35461 GAAAACAA
390 GAAAACAG
35469 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
35534 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
35598 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
35639 CTAATTTAAT
Statistics
Matches: 1326, Mismatches: 25, Indels: 13
0.97 0.02 0.01
Matches are distributed among these distances:
392 52 0.04
393 114 0.09
394 138 0.10
395 106 0.08
396 261 0.20
397 405 0.31
398 250 0.19
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (397 bp):
GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAA
CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGG
AAAACAG
Found at i:37118 original size:18 final size:18
Alignment explanation
Indices: 37097--37164 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
37087 AGCGGTCGCA
37097 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
37115 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
37136 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
37157 GAAGATGA
1 GAAGATGA
37165 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:37121 original size:6 final size:6
Alignment explanation
Indices: 37097--37194 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
37087 AGCGGTCGCA
* * * * * *
37097 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
37145 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
37193 GA
1 GA
37195 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:37132 original size:3 final size:3
Alignment explanation
Indices: 37112--37198 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
37102 TGAAGCTGAC
* * * * * ** *
37112 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
37160 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
37199 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:37147 original size:42 final size:42
Alignment explanation
Indices: 37100--37190 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
37090 GGTCGCAGAA
*
37100 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
37142 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
37184 GATGAAG
1 GATGAAG
37191 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:37198 original size:18 final size:18
Alignment explanation
Indices: 37097--37194 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
37087 AGCGGTCGCA
* *
37097 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
37115 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
37133 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
37151 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
37169 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
37187 GAAGATGA
1 GAAGATGA
37195 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:38966 original size:184 final size:183
Alignment explanation
Indices: 38657--38999 Score: 578
Period size: 184 Copynumber: 1.9 Consensus size: 183
38647 CTTTCAACAT
* *
38657 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
* *
38722 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
*
38787 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACCATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
** * * *
38841 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
38906 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
38971 AATGTGTCGATACCATTTAAAAAGTGTCG
131 AATGTGTCGATACCATTTAAAAAGTGTCG
39000 GTAATTGAAG
Statistics
Matches: 148, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
183 11 0.07
184 137 0.93
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
AATGTGTCGATACCATTTAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:41586 original size:22 final size:23
Alignment explanation
Indices: 41561--41618 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
41551 AGGTAAACAT
41561 ATGTAATAGGTAGC-CCTATATA
1 ATGTAATAGGTAGCGCCTATATA
* **
41583 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCGCCTATATA
41606 ATGTAATAGGTAG
1 ATGTAATAGGTAG
41619 TGGTTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCCTATATA
Found at i:41625 original size:23 final size:23
Alignment explanation
Indices: 41577--41627 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
41567 TAGGTAGCCC
*
41577 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTATCGGT
41600 TATATAATGTAATAGGTAGT-GGT
1 TATATAATGTAATAGGTA-TCGGT
41623 TATAT
1 TATAT
41628 TGTAAAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (23 bp):
TATATAATGTAATAGGTATCGGT
Found at i:41655 original size:20 final size:20
Alignment explanation
Indices: 41630--41668 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41620 GGTTATATTG
* *
41630 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
41650 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
41669 TCACTGTGGA
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:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:42015 original size:21 final size:22
Alignment explanation
Indices: 41989--42057 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 22
41979 TAAACATATG
41989 ATGTAATAGGTAGTC-CTTATA
1 ATGTAATAGGTAGTCGCTTATA
*
42010 ATGTAATAGGTA-TCGTTTATA
1 ATGTAATAGGTAGTCGCTTATA
*
42031 ATGTAATAGGTAGT-GGTTATA
1 ATGTAATAGGTAGTCGCTTATA
*
42052 TTGTAA
1 ATGTAA
42058 AGTGTCTATC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.93
22 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (22 bp):
ATGTAATAGGTAGTCGCTTATA
Found at i:42348 original size:25 final size:25
Alignment explanation
Indices: 42314--42364 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
42304 ACAACAAATC
*
42314 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
42339 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
42364 A
1 A
42365 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:42631 original size:18 final size:18
Alignment explanation
Indices: 42610--42646 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42600 GTAATTGGAG
42610 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
42628 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
42646 T
1 T
42647 ATATATTTCG
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:42654 original size:24 final size:24
Alignment explanation
Indices: 42602--42648 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42592 ATTCATATGT
* *
42602 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
42626 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
42649 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:42984 original size:38 final size:40
Alignment explanation
Indices: 42900--42986 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
42890 TTCGATGCTC
*
42900 ATCAAAATCCAAAGCTCATATGGTGCCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCCAAGCAAAAGGAA
*
42940 ATCAAAATCCAAATCTCATATGATG-CCAAGC-AAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCCAAGCAAAAGGAA
42978 ATCAAAATC
1 ATCAAAATC
42987 TACAACTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 16 0.36
39 6 0.13
40 23 0.51
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.17
Consensus pattern (40 bp):
ATCAAAATCCAAAGCTCATATGATGCCCAAGCAAAAGGAA
Found at i:43425 original size:22 final size:23
Alignment explanation
Indices: 43381--43438 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 23
43371 AGGTAAACAT
43381 ATGTAATAGGTAGCCCTTATATA
1 ATGTAATAGGTAGCCCTTATATA
**
43404 ATGTAATAGGTA-CGTTTATATA
1 ATGTAATAGGTAGCCCTTATATA
43426 ATGTAATAGGTAG
1 ATGTAATAGGTAG
43439 TGGTTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (23 bp):
ATGTAATAGGTAGCCCTTATATA
Found at i:43451 original size:21 final size:20
Alignment explanation
Indices: 43400--43452 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
43390 GTAGCCCTTA
*
43400 TATAATGTAATAGGTACGTT
1 TATATTGTAATAGGTACGTT
43420 TATATAATGTAATAGGTA-GTGGT
1 TATAT--TGTAATAGGTACGT--T
43443 TATATTGTAA
1 TATATTGTAA
43453 AGTGTCTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 7 0.25
22 11 0.39
23 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.42
Consensus pattern (20 bp):
TATATTGTAATAGGTACGTT
Found at i:50682 original size:23 final size:23
Alignment explanation
Indices: 50647--50705 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
50637 ATCTTATATA
*
50647 GCACTACGGTGCAATTCTAAGCG
1 GCACTTCGGTGCAATTCTAAGCG
* * *
50670 GCACTTCGATGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTAAGCG
50693 GCACTTCGGTGCA
1 GCACTTCGGTGCA
50706 TTTATACGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTAAGCG
Found at i:50713 original size:23 final size:23
Alignment explanation
Indices: 50669--50713 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
50659 AATTCTAAGC
*
50669 GGCACTTCGATGCAATTCTACGT
1 GGCACTTCGATGCAATTATACGT
* *
50692 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGATGCAATTATACG
50714 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCGATGCAATTATACGT
Found at i:55890 original size:23 final size:23
Alignment explanation
Indices: 55851--55909 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
55841 ATCTTATATA
*
55851 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* * * *
55874 GCATTTCTGTGCCATTCTACGTG
1 GCACTTCGGTGCAATTCTACGCG
55897 GCACTTCGGTGCA
1 GCACTTCGGTGCA
55910 TTTATACGAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.25, T:0.29
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:58807 original size:21 final size:20
Alignment explanation
Indices: 58782--58833 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
58772 ATACTCATAG
*
58782 GGGTATCAATACTTGACACTA
1 GGGTATCAATACTTCA-ACTA
* *
58803 GGGTATCGATACTTCAAGTA
1 GGGTATCAATACTTCAACTA
*
58823 GAGTATCAATA
1 GGGTATCAATA
58834 TTACTCACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (20 bp):
GGGTATCAATACTTCAACTA
Done.