Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009163.1 Hibiscus syriacus cultivar Beakdansim tig00112698_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: 103450
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:12339 original size:9 final size:9
Alignment explanation
Indices: 12336--12380 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
12326 TAAAAAGATG
12336 AAAATGAAA
1 AAAATGAAA
12345 AAAATGAAA
1 AAAATGAAA
12354 AAGAA--AAA
1 AA-AATGAAA
12362 AAAATG--A
1 AAAATGAAA
12369 AAAATGAAA
1 AAAATGAAA
12378 AAA
1 AAA
12381 GAAATGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
7 9 0.29
8 5 0.16
9 15 0.48
10 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (9 bp):
AAAATGAAA
Found at i:12362 original size:17 final size:18
Alignment explanation
Indices: 12342--12391 Score: 84
Period size: 17 Copynumber: 2.8 Consensus size: 18
12332 GATGAAAATG
12342 AAAAAAATGAAAAA-GAA
1 AAAAAAATGAAAAATGAA
12359 AAAAAAATGAAAAATGAA
1 AAAAAAATGAAAAATGAA
12377 AAAAGAAATGAAAAA
1 AAAA-AAATGAAAAA
12392 ATAAAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 14 0.45
18 7 0.23
19 10 0.32
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (18 bp):
AAAAAAATGAAAAATGAA
Found at i:12363 original size:24 final size:22
Alignment explanation
Indices: 12313--12404 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 22
12303 ATGCTTGAAG
*
12313 AAAAAAAAACAAAT-AAAAAGA
1 AAAAAAAAAAAAATGAAAAAGA
**
12334 TGAAAATGAAAAAAATGAAAAAGA
1 --AAAAAAAAAAAAATGAAAAAGA
12358 AAAAAAAATGAAAAATGAAAAAAGA
1 AAAAAAAA--AAAAATG-AAAAAGA
*
12383 AATGAAAAAATAAAA-GAAAAAG
1 AA--AAAAAAAAAAATGAAAAAG
12405 GAGGGTTTGA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
22 6 0.11
23 17 0.30
24 15 0.26
25 13 0.23
27 6 0.11
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (22 bp):
AAAAAAAAAAAAATGAAAAAGA
Found at i:12365 original size:26 final size:28
Alignment explanation
Indices: 12336--12397 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 28
12326 TAAAAAGATG
12336 AAAATGAAAAAAATG-AAAAAGAAA-AA
1 AAAATGAAAAAAATGAAAAAAGAAAGAA
12362 AAAATG--AAAAATGAAAAAAGAAATGAA
1 AAAATGAAAAAAATGAAAAAAGAAA-GAA
12389 AAAAT-AAAA
1 AAAATGAAAA
12398 GAAAAAGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
24 7 0.23
25 9 0.29
26 6 0.19
27 7 0.23
28 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (28 bp):
AAAATGAAAAAAATGAAAAAAGAAAGAA
Found at i:12372 original size:12 final size:12
Alignment explanation
Indices: 12345--12403 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
12335 GAAAATGAAA
12345 AAAATGAAAAAGA
1 AAAATGAAAAA-A
*
12358 AAAA--AAAATGA
1 AAAATGAAAA-AA
12369 AAAATGAAAAAA
1 AAAATGAAAAAA
*
12381 GAAATGAAAAAA
1 AAAATGAAAAAA
12393 TAAAA-GAAAAA
1 -AAAATGAAAAA
12404 GGAGGGTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 9 0.24
12 18 0.47
13 11 0.29
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (12 bp):
AAAATGAAAAAA
Found at i:12373 original size:33 final size:34
Alignment explanation
Indices: 12317--12380 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
12307 TTGAAGAAAA
12317 AAAAACAAATAAAAAGATGAAAATGAAAAAAATG
1 AAAAACAAATAAAAAGATGAAAATGAAAAAAATG
*
12351 AAAAAGAAA-AAAAA-ATGAAAAATGAAAAAA
1 AAAAACAAATAAAAAGATG-AAAATGAAAAAA
12381 GAAATGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 3 0.11
33 17 0.61
34 8 0.29
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (34 bp):
AAAAACAAATAAAAAGATGAAAATGAAAAAAATG
Found at i:12397 original size:19 final size:17
Alignment explanation
Indices: 12342--12403 Score: 79
Period size: 17 Copynumber: 3.4 Consensus size: 17
12332 GATGAAAATG
*
12342 AAAAAAATGAAAAAGAA
1 AAAAAAATGAAAAATAA
12359 AAAAAAATGAAAAATGAA
1 AAAAAAATGAAAAAT-AA
12377 AAAAGAAATGAAAAAATAA
1 AAAA-AAATG-AAAAATAA
12396 AAGAAAAA
1 AA-AAAAA
12404 GGAGGGTTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
17 14 0.35
18 6 0.15
19 12 0.30
20 8 0.20
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (17 bp):
AAAAAAATGAAAAATAA
Found at i:13451 original size:18 final size:18
Alignment explanation
Indices: 13402--13452 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
13392 TTTTCAGGAG
13402 AGTTCATAATGAG-AAGA
1 AGTTCATAATGAGAAAGA
* *
13419 A-CTCATCCAACGAGAAAGA
1 AGTTCAT--AATGAGAAAGA
13438 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
13453 GAACTTGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
16 4 0.15
17 1 0.04
18 12 0.46
19 5 0.19
20 4 0.15
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.20
Consensus pattern (18 bp):
AGTTCATAATGAGAAAGA
Found at i:13664 original size:221 final size:220
Alignment explanation
Indices: 13253--13683 Score: 629
Period size: 221 Copynumber: 2.0 Consensus size: 220
13243 GGAGGTGAAC
*
13253 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAATCATTCGACAGAGGAGAAGAAGTTCATAAT
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAATCATCCGACAGAGGAGAAGAAGTTCATAAT
* * *
13318 GAGAAGAGCTTGTTCGACTTATCACTCGATTTATGACATTTTGAATCAGTGACACCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACTTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAG
* * * * *
13383 GGATTGATATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAAAGAAGTTCATAAT
131 GGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGAAAGAAGTTCATAAT
13448 GAGAAGAACTTGTTCAAATTCGCAT
196 GAGAAGAACTTGTTCAAATTCGCAT
* *
13473 CAACATTTTCAATGGAGAGTTCATAATGA-AAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAA-TCATCCGACAGA-GGAGAAGAAGTTCATA
* * *
13537 ATGAGAAGAGCTT-TTTGAAC-TATCACTTGATTCACGAACATTTCGAATCAGTGACGCCTCGCT
64 ATGAGAAGAGCTTGTTCG-ACTTATCACTCGATTCACG-ACATTTCGAATCAGTGACACCTCGCT
* *
13600 TGAGGGATCGACATTTCCATGAAGAGTTCATAATGAGAAGAACTCATCATAAAG-GAGA-AAGTT
127 TGAGGGATCGACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATC-CAAAGAGAAAGAAGTT
13663 CATAATGAGAAGAACTTGTTC
190 CATAATGAGAAGAACTTGTTC
13684 CTTTCAAATT
Statistics
Matches: 189, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
219 5 0.03
220 54 0.29
221 97 0.51
222 30 0.16
223 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (220 bp):
CAACATTTCCAATGGAGAGTTCATAATGAGAAGAATCATCCGACAGAGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACTTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAG
GGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGAAAGAAGTTCATAAT
GAGAAGAACTTGTTCAAATTCGCAT
Found at i:15531 original size:18 final size:19
Alignment explanation
Indices: 15508--15592 Score: 63
Period size: 20 Copynumber: 4.5 Consensus size: 19
15498 TTTTGATATC
15508 TTTTATTTTAATCCTTTAT
1 TTTTATTTTAATCCTTTAT
15527 TTTATATTTTAAT--TTTA-
1 TTT-TATTTTAATCCTTTAT
15544 TTTTA-TTTAATTCCTTTAAT
1 TTTTATTTTAA-TCCTTT-AT
* * *
15564 TTCAGTAATTTAAT-TTTTAT
1 TT--TTATTTTAATCCTTTAT
15584 TTTTATTTT
1 TTTTATTTT
15593 TGCTTTACGT
Statistics
Matches: 53, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
15 5 0.09
16 3 0.06
17 3 0.06
18 12 0.23
19 4 0.08
20 15 0.28
21 3 0.06
22 3 0.06
23 5 0.09
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTTATTTTAATCCTTTAT
Found at i:15553 original size:35 final size:37
Alignment explanation
Indices: 15491--15591 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 37
15481 TTATTTTGAG
* * *
15491 TTTTATATTTTGA-TATCTTTTATTTTAA-TCCTTT-A
1 TTTTATATTTTAATTTTATTTTA-TTTAATTCCTTTAA
15526 TTTTATATTTTAATTTTATTTTATTTAATTCCTTTAA
1 TTTTATATTTTAATTTTATTTTATTTAATTCCTTTAA
* *
15563 TTTCAGTAATTTAATTTTTATTTTTATTT
1 TTTTA-TATTTTAA-TTTTA-TTTTATTT
15592 TTGCTTTACG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
35 17 0.31
36 13 0.24
37 5 0.09
38 7 0.13
39 5 0.09
40 8 0.15
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (37 bp):
TTTTATATTTTAATTTTATTTTATTTAATTCCTTTAA
Found at i:15651 original size:22 final size:22
Alignment explanation
Indices: 15626--15672 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
15616 AATTTAATCA
15626 TTTAACTA-TTATATTATTTTAT
1 TTTAACTATTTAT-TTATTTTAT
* *
15648 TTTAAGTGTTTATTTATTTTAT
1 TTTAACTATTTATTTATTTTAT
15670 TTT
1 TTT
15673 TAGTCACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTAACTATTTATTTATTTTAT
Found at i:16663 original size:2 final size:2
Alignment explanation
Indices: 16658--16770 Score: 226
Period size: 2 Copynumber: 56.5 Consensus size: 2
16648 TTTGTACGTG
16658 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
16700 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
16742 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16771 TACAAATGAT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 111 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32990 original size:45 final size:45
Alignment explanation
Indices: 32930--33119 Score: 274
Period size: 45 Copynumber: 4.2 Consensus size: 45
32920 ACTGGTGGTA
* * * * * * *
32930 GTGGGGGTGGGGACTTGTATTTATAATGGTGCTTGGGCGGTGATG
1 GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
*
32975 GTGGAGGTGGAGACTTGTACTTGT-ATGGGTGCTTGGGTGGTGATG
1 GTGGCGGTGGAGACTTGTACTTGTGA-GGGTGCTTGGGTGGTGATG
*
33020 GTGGTGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
1 GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
33065 GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
1 GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
*
33110 ATGGCGGTGG
1 GTGGCGGTGG
33120 GGGAGACTTA
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.01
45 132 0.99
46 1 0.01
ACGTcount: A:0.12, C:0.07, G:0.48, T:0.32
Consensus pattern (45 bp):
GTGGCGGTGGAGACTTGTACTTGTGAGGGTGCTTGGGTGGTGATG
Found at i:33346 original size:27 final size:27
Alignment explanation
Indices: 33308--33362 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
33298 TGATAATGAC
33308 CTGGTGGAGGAGGTGGAGACTTATAAA
1 CTGGTGGAGGAGGTGGAGACTTATAAA
33335 CTGGTGGAGGAGGTGGAGACTTATAAA
1 CTGGTGGAGGAGGTGGAGACTTATAAA
33362 C
1 C
33363 AGGAGTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.09, G:0.40, T:0.22
Consensus pattern (27 bp):
CTGGTGGAGGAGGTGGAGACTTATAAA
Found at i:35955 original size:2 final size:2
Alignment explanation
Indices: 35918--35943 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35908 TATATTCAAT
35918 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
35944 ATTTCAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37759 original size:21 final size:22
Alignment explanation
Indices: 37738--37779 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37728 TAGATTGCTC
*
37738 AGAGGGAATTGATTCCCCCTCA
1 AGAGGGAATCGATTCCCCCTCA
* *
37760 AGGGGGTATCGATTCCCCCT
1 AGAGGGAATCGATTCCCCCT
37780 GAATGGTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (22 bp):
AGAGGGAATCGATTCCCCCTCA
Found at i:37850 original size:22 final size:22
Alignment explanation
Indices: 37820--37874 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
37810 CTCGGAGGGA
37820 ACCGA-TCCCCCCCAAGGAGGT
1 ACCGATTCCCCCCCAAGGAGGT
* *
37841 ATCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGAGGT
37863 ACCGATTCCCCC
1 ACCGATTCCCCC
37875 TGTTTAACAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.15
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGAGGT
Found at i:47402 original size:14 final size:16
Alignment explanation
Indices: 47371--47402 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47361 CAAGCTAACT
47371 AAGATTGGATTGCTTG
1 AAGATTGGATTGCTTG
47387 AAGATTGG-TT-CTTG
1 AAGATTGGATTGCTTG
47401 AA
1 AA
47403 AAGAAGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (16 bp):
AAGATTGGATTGCTTG
Found at i:52791 original size:3 final size:3
Alignment explanation
Indices: 52783--52844 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
52773 ACAAATAAAT
* *
52783 ATA ATA ATA ATA ATA ATA ATA ATTA ATT ATT A-A AT- ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA AT-A ATA
52828 ATTA A-A ATA A-A ATA ATA
1 A-TA ATA ATA ATA ATA ATA
52845 TAAATATAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 7 0.14
3 34 0.68
4 9 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:52800 original size:17 final size:16
Alignment explanation
Indices: 52779--52857 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 16
52769 TATAACAAAT
52779 AAATATAATAATAATA
1 AAATATAATAATAATA
* *
52795 ATAATAATAATTAATTATT
1 A-AAT-ATAA-TAATAATA
*
52814 AAATATAATAAATAATT
1 AAATATAAT-AATAATA
52831 AAA-ATAA-AATAATA
1 AAATATAATAATAATA
*
52845 TAAATATAGTAAT
1 -AAATATAATAAT
52858 TTAAATAGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 9 0.18
17 19 0.37
18 7 0.14
19 7 0.14
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (16 bp):
AAATATAATAATAATA
Found at i:52858 original size:48 final size:48
Alignment explanation
Indices: 52767--52858 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
52757 AAGTTAAATG
* *
52767 AATATAACAAATAAATATAATAATAATAATAATAATAATTAATTATTA
1 AATATAACAAATAAATAAAATAATAATAATAATAATAAGTAATTATTA
* *
52815 AATATAATAAATAATTAAAATAA-AATAAT-ATAAATATAGTAATT
1 AATATAACAAATAAATAAAATAATAATAATAAT-AATA-AGTAATT
52859 TAAATAGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 2 0.05
47 10 0.26
48 26 0.68
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (48 bp):
AATATAACAAATAAATAAAATAATAATAATAATAATAAGTAATTATTA
Found at i:65595 original size:13 final size:13
Alignment explanation
Indices: 65577--65605 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
65567 TACTTGATCT
65577 AATTATTATTAAA
1 AATTATTATTAAA
65590 AATTATTATTAAA
1 AATTATTATTAAA
65603 AAT
1 AAT
65606 AAGATTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATTATTAAA
Found at i:73585 original size:2 final size:2
Alignment explanation
Indices: 73578--73618 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
73568 GAAAGTAAGA
*
73578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73619 CGCATTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:74065 original size:43 final size:43
Alignment explanation
Indices: 74004--74089 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
73994 TTAAATATTA
74004 ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
1 ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
74047 ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
1 ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
74090 CTGAATGACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (43 bp):
ATGACAAGTGGCTTAATTAAATGTATTTAAATAGTTGAGTGGC
Found at i:87365 original size:15 final size:15
Alignment explanation
Indices: 87345--87374 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
87335 ATTAATGATA
87345 TTAAAAATATATAAT
1 TTAAAAATATATAAT
87360 TTAAAAATATATAAT
1 TTAAAAATATATAAT
87375 AAGTTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAATATATAAT
Found at i:95867 original size:22 final size:23
Alignment explanation
Indices: 95836--95878 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
95826 AATCCTAAAC
*
95836 TTCTAGATTTGAAATTTAAATAT
1 TTCTAGATTTGAAATATAAATAT
*
95859 TTCTA-ATTTTAAATATAAAT
1 TTCTAGATTTGAAATATAAAT
95879 TTTTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (23 bp):
TTCTAGATTTGAAATATAAATAT
Found at i:98403 original size:23 final size:23
Alignment explanation
Indices: 98377--98435 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
98367 AACCACTACC
98377 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
98400 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
98423 TATTACATCATAT
1 TATTACATTATAT
98436 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:98815 original size:21 final size:21
Alignment explanation
Indices: 98785--98853 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
98775 GATAGATACT
*
98785 TTACAATATAACCACTACCTA
1 TTACATTATAACCACTACCTA
*
98806 TTACATTATAAACGA-TACCTA
1 TTACATTAT-AACCACTACCTA
* *
98827 TTACATTATAAGCGCTACCTA
1 TTACATTATAACCACTACCTA
98848 TTACAT
1 TTACAT
98854 CATATTTTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.85
22 4 0.10
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.33
Consensus pattern (21 bp):
TTACATTATAACCACTACCTA
Found at i:99257 original size:23 final size:23
Alignment explanation
Indices: 99231--99287 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
99221 CCACTACTTG
99231 TTACATTATATAAACGATACCTA
1 TTACATTATATAAACGATACCTA
** *
99254 TTACATTATATAAGTGCTACCTA
1 TTACATTATATAAACGATACCTA
*
99277 TTACATCATAT
1 TTACATTATAT
99288 TTTTACCTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (23 bp):
TTACATTATATAAACGATACCTA
Found at i:99671 original size:21 final size:21
Alignment explanation
Indices: 99632--99696 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
99622 GATAGATACT
* *
99632 TTACAATAT-AACCATACCTA
1 TTACATTATAAACGATACCTA
99652 TTACATTATAAACGATACCTA
1 TTACATTATAAACGATACCTA
* *
99673 TT--ATTATAAGCGCTA-CTA
1 TTACATTATAAACGATACCTA
99691 TTACAT
1 TTACAT
99697 CATATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 5 0.13
19 11 0.29
20 10 0.26
21 12 0.32
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (21 bp):
TTACATTATAAACGATACCTA
Found at i:100107 original size:20 final size:21
Alignment explanation
Indices: 100047--100115 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 21
100037 GATAGATACT
*
100047 TTACA-ATATAACCACTACCT-
1 TTACATATATAA-CGCTACCTA
*
100067 TTACATTATATAAACGATACCTA
1 TTACA-TATAT-AACGCTACCTA
100090 TTACATATAT-ACGCTACCTA
1 TTACATATATAACGCTACCTA
100110 TTACAT
1 TTACAT
100116 CATTTTTTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 20 0.48
22 15 0.36
23 7 0.17
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (21 bp):
TTACATATATAACGCTACCTA
Found at i:100496 original size:23 final size:23
Alignment explanation
Indices: 100468--100532 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
100458 GATACTTTAC
100468 ATATAACCACTACCTATTACATT
1 ATATAACCACTACCTATTACATT
*
100491 ATATAAACGA-TACCTATTACATT
1 ATAT-AACCACTACCTATTACATT
* *
100514 ATATAAGCGCTACCTATTA
1 ATATAACCACTACCTATTA
100533 TCATATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.06
23 30 0.83
24 4 0.11
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:100786 original size:419 final size:425
Alignment explanation
Indices: 98200--101164 Score: 4966
Period size: 419 Copynumber: 7.0 Consensus size: 425
98190 TATGTTATTG
98200 TTTTTAATTTAATATAATATATATCGTAACGTAAAAAAG-AATCA-TAGACGCCTATAATTACTA
1 TTTTTAATTT-A-ATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTA
*
98263 AATTAATATCTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAGT
64 AATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGT
98328 ATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAA
129 ATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAA
*
98393 CGATACATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGT
194 CGATACCTATTACATTATATAAGCGCTACCTATTA-ATCATATTTTTACCTATTATATTGAAAGT
*
98458 GTCCATACATTTTATAAAAAAGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
258 GTCCATAC-TTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
* *
98523 TTTAAGTA-TGTTTCATGTTTTCCACCTAAAATATTAATTTAATAATTTCATTTGCAC-AAAAAT
322 TTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
*
98586 TATTTGATTGTTTTGATATTTTATAAAATAATATTTATAA
386 TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
98626 TTTTTAATTTAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTAAA
1 TTTTTAATTTAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTAAA
98691 TTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAAGTA
66 TTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAAGTA
98756 TAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACA-T-TATAAAC
130 TAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAAC
98819 GATACCTATTACA-T-TATAAGCGCTACCTATTACATCATA-TTTTACCTATTATATTGAAAGTG
195 GATACCTATTACATTATATAAGCGCTACCTATTA-ATCATATTTTTACCTATTATATTGAAAGTG
* *
98881 TCCATACTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTTAATTTTTT
259 TCCATACTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTT
*
98946 TAAATGGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTA
324 T-AATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTA
99011 TTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
388 TTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
99049 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAA-TT--TAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
*
99114 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTAAAAAAAG
63 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* *
99179 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACTTGTTACATTATATAA
128 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
*
99244 ACGATACCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
193 ACGATACCTATTACATTATATAAGCGCTACCTATTA-ATCATATTTTTACCTATTATATTGAAAG
* *
99309 TGTACATACTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTTAATTTT
257 TGTCCATACTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTT
99374 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA-TTACACAAAAAA-
321 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
*
99437 TA-TTGATTATTTTGATATTTTATAAAATAATATTTAGAA
386 TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
99476 --TTTAATTTAATAATAATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTAA
1 TTTTTAATTTAATAAT-ATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTAA
*
99539 ATTAATATCTTAAATCTCACTCAAAAGATAACCTTAAATTAATG-TTTCCACAGTGAAAAAAGTA
65 ATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTA
99603 TAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCA-TACCTATTACA-T-TATAAAC
130 TAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAAC
99665 GATACCTATT--A-T-TATAAGCGCTA-CTATTACATCATATTTTTACCTATTATATTGAAAGTG
195 GATACCTATTACATTATATAAGCGCTACCTATTA-ATCATATTTTTACCTATTATATTGAAAGTG
*
99725 TCCATACTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTTAATTTTTT
259 TCCATACTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTT
99790 TTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-AAAAATTA
323 TTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTA
99854 TTT-ATTGTTTTGATATTTTATAAAATAATA-TTAGAA
388 TTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
99890 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAA-TACT
1 TTTTTAA-TT--TAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
*
99954 AAATTAATATCTTAAATCTCACTC-AAAGATAACCTTAAATTAATGTTTT-CACAGTG-AAAAAG
63 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
100016 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCT-TTACATTATATAA
128 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
100080 ACGATACCTATTACA-TATAT-A-CGCTACCTATTACATCAT-TTTTTACCTATTATATTGAAAG
193 ACGATACCTATTACATTATATAAGCGCTACCTATTA-ATCATATTTTTACCTATTATATTGAAAG
* *
100141 TGTCCATACTTTTTATAAAAATGATCGATACTT-TGTTAAAGTTATGTAATTTATGTTTCAATTT
257 TGTCCATAC-TTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
100205 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
321 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
100270 TATTTGATTGTTTTGATA-TTT-T-AAATAATATTTAGAA
386 TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
100307 TTTTTAATTTAATAATATATATATCGTAACGTAAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAAT-A-ATATATATCGTAACGT-AAAAAAGAAATCATTAGACGCCTATAATTACT
*
100372 AAATTAATATCTTAAAACTCACTCAAAAGATAACC-TAAATTAATATTTTCCACAGTG-AAAAAG
63 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
100435 TA-A-ACACTTTTATAAAAAGGATAGATACTTTAC-ATATAACCACTACCTATTACATTATATAA
128 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
100497 ACGATACCTATTACATTATATAAGCGCTACCTATT-ATCATATTTTTACCTATTATATTGAAAGT
193 ACGATACCTATTACATTATATAAGCGCTACCTATTAATCATATTTTTACCTATTATATTGAAAGT
*
100561 GTCCATACTTTTTATAAAAATGATCGATACTT-TGTTTAAAGTTATGTAATTTATGTTTCAATTT
258 GTCCATAC-TTTTATAAAAAGGATCGATACTTCT-TTTAAAGTTATGTAATTTATGTTTCAATTT
*
100625 TTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTACACAAAAAAA
321 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-AAAAAA
100690 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
385 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
* *
100731 -TTTTAATTTAATAATATATAT-GTAATGTAAAAAAGAAATCATTAGACGTCTATAATTACTAAA
1 TTTTTAATTTAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTAAA
100794 TTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTAT
66 TTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTAT
*
100859 AGACAGTTTTAT-AAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACG
131 AGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACG
*
100923 --A--TA-TACATTATATAAGCGCTACCTATTACATCATATTTTTAGCTATTATATTGAAAGTGT
196 ATACCTATTACATTATATAAGCGCTACCTATTA-ATCATATTTTTACCTATTATATTGAAAGTGT
*
100983 CCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATCTTTCAATTTTTT
260 CCATAC-TTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTT
*
101048 TAATAGTGTTTTCATGTTTTCCACCTACAATATTATTTTAATAATTT-ATTTACACAAAAAATTA
324 TAATAGTG-TTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTA
101112 TTTGATTGTTTTGATATTTTAT--AATAATATTTAGAA
388 TTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
* *
101148 -TTTAAATTTAACAATAT
1 TTTTTAATTTAATAATAT
101165 TAACCAAAGA
Statistics
Matches: 2437, Mismatches: 41, Indels: 131
0.93 0.02 0.05
Matches are distributed among these distances:
414 165 0.07
415 101 0.04
416 83 0.03
417 240 0.10
418 192 0.08
419 254 0.10
420 235 0.10
421 146 0.06
422 172 0.07
423 222 0.09
424 46 0.02
425 92 0.04
426 197 0.08
427 120 0.05
428 3 0.00
429 36 0.01
430 126 0.05
431 7 0.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (425 bp):
TTTTTAATTTAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTAAA
TTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTAT
AGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACG
ATACCTATTACATTATATAAGCGCTACCTATTAATCATATTTTTACCTATTATATTGAAAGTGTC
CATACTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTA
ATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTT
GATTGTTTTGATATTTTATAAAATAATATTTAGAA
Found at i:100952 original size:23 final size:23
Alignment explanation
Indices: 100891--100958 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
100881 ATACTTTACA
* *
100891 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
100914 ATATAAACG--A--TA-TACATT
1 ATATAAACGCTACCTATTACATT
* *
100932 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
100955 ATAT
1 ATAT
100959 TTTTAGCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 14 0.39
19 2 0.06
20 1 0.03
21 1 0.03
22 2 0.06
23 16 0.44
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:101346 original size:15 final size:16
Alignment explanation
Indices: 101313--101346 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
101303 TTATCTTACA
*
101313 TTTTTCAATCGACACT
1 TTTTTAAATCGACACT
101329 TTTTTAAATCGACA-T
1 TTTTTAAATCGACACT
101344 TTT
1 TTT
101347 GTTGTGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTTTAAATCGACACT
Found at i:102546 original size:12 final size:13
Alignment explanation
Indices: 102523--102613 Score: 86
Period size: 12 Copynumber: 7.3 Consensus size: 13
102513 CTTGTTTGGA
*
102523 TCATCATCATCAT
1 TCATCGTCATCAT
102536 TC-TCGTCATCATCT
1 TCATCGTCATCA--T
*
102550 TCATCGTCAGC-T
1 TCATCGTCATCAT
102562 TCATCGTCATCA-
1 TCATCGTCATCAT
102574 TCATCGTCATC-T
1 TCATCGTCATCAT
*
102586 TCATCGTCAGC-T
1 TCATCGTCATCAT
*
102598 TCATCTTCATC-T
1 TCATCGTCATCAT
102610 TCAT
1 TCAT
102614 TGACCGCTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
12 55 0.82
13 2 0.03
14 3 0.04
15 7 0.10
ACGTcount: A:0.20, C:0.33, G:0.08, T:0.40
Consensus pattern (13 bp):
TCATCGTCATCAT
Found at i:102546 original size:15 final size:15
Alignment explanation
Indices: 102526--102575 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
102516 GTTTGGATCA
102526 TCATCATCATTC-TCG
1 TCATCATC-TTCATCG
102541 TCATCATCTTCATCG
1 TCATCATCTTCATCG
*
102556 ---TCAGCTTCATCG
1 TCATCATCTTCATCG
102568 TCATCATC
1 TCATCATC
102576 ATCGTCATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 11 0.38
14 3 0.10
15 15 0.52
ACGTcount: A:0.20, C:0.34, G:0.08, T:0.38
Consensus pattern (15 bp):
TCATCATCTTCATCG
Found at i:102553 original size:6 final size:6
Alignment explanation
Indices: 102544--102613 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
102534 ATTCTCGTCA
* * * * * *
102544 TCATCT TCATCG TCAGCT TCATCG TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
102592 TCAGCT TCATCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCAT
102614 TGACCGCTTG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.40
Consensus pattern (6 bp):
TCATCT
Found at i:102571 original size:24 final size:24
Alignment explanation
Indices: 102544--102613 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
102534 ATTCTCGTCA
*
102544 TCATCTTCATCGTCAGCTTCATCG
1 TCATCTTCATCGTCATCTTCATCG
*
102568 TCATCATCATCGTCATCTTCATCG
1 TCATCTTCATCGTCATCTTCATCG
* *
102592 TCAGCTTCATCTTCATCTTCAT
1 TCATCTTCATCGTCATCTTCAT
102614 TGACCGCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.40
Consensus pattern (24 bp):
TCATCTTCATCGTCATCTTCATCG
Found at i:102622 original size:24 final size:24
Alignment explanation
Indices: 102548--102622 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
102538 TCGTCATCAT
* * *
102548 CTTCATCGTCAGCTTCATCGTCAT
1 CTTCATCGTCATCTTCATCGACAG
* *
102572 CATCATCGTCATCTTCATCGTCAG
1 CTTCATCGTCATCTTCATCGACAG
* * *
102596 CTTCATCTTCATCTTCATTGACCG
1 CTTCATCGTCATCTTCATCGACAG
102620 CTT
1 CTT
102623 GGTTGTCCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.17, C:0.33, G:0.11, T:0.39
Consensus pattern (24 bp):
CTTCATCGTCATCTTCATCGACAG
Done.