Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000733.1 Hibiscus syriacus cultivar Beakdansim tig00001423_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: 159352
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3995 original size:21 final size:21
Alignment explanation
Indices: 3969--4013 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3959 CCCTAAATTA
*
3969 TAAATCATAATCCCAT-AATCC
1 TAAATCATAA-ACCATAAATCC
*
3990 TAAATCTTAAACCATAAATCC
1 TAAATCATAAACCATAAATCC
4011 TAA
1 TAA
4014 GCCCTGACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATCATAAACCATAAATCC
Found at i:5103 original size:2 final size:2
Alignment explanation
Indices: 5096--5132 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5086 CATGATGTGT
5096 TA TA TA TA 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 TA TA TA TA T
5133 TAAGAGTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5256 original size:29 final size:29
Alignment explanation
Indices: 5223--5283 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
5213 ATTATTTTTG
5223 TAGTTAATTTATAAATTTCAATTAAATCT
1 TAGTTAATTTATAAATTTCAATTAAATCT
5252 TAGTTAATTTATAAATTTCAATTAAATCT
1 TAGTTAATTTATAAATTTCAATTAAATCT
5281 TAG
1 TAG
5284 ATGTATCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (29 bp):
TAGTTAATTTATAAATTTCAATTAAATCT
Found at i:6184 original size:22 final size:21
Alignment explanation
Indices: 6159--6199 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
6149 TATAAAAAAT
6159 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
6181 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
6200 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:7216 original size:21 final size:21
Alignment explanation
Indices: 7174--7218 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
7164 TGATAAAAAA
* *
7174 TTATTTAAAATATTATTATTT
1 TTATTTAAAACATAATTATTT
7195 TTATTTAAAACATCAATT-TTT
1 TTATTTAAAACAT-AATTATTT
7216 TTA
1 TTA
7219 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTTAAAACATAATTATTT
Found at i:7787 original size:17 final size:16
Alignment explanation
Indices: 7755--7792 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
7745 AATTTACAAT
7755 TAATT-TAAATATATC
1 TAATTATAAATATATC
7770 TAATTATAAATAATATC
1 TAATTATAAAT-ATATC
7787 TAATTA
1 TAATTA
7793 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTATAAATATATC
Found at i:9063 original size:82 final size:82
Alignment explanation
Indices: 8931--9081 Score: 248
Period size: 82 Copynumber: 1.8 Consensus size: 82
8921 GCCCCCAATT
* *
8931 TTTTTTATCATTAAATAATATTGGGATAATTACCTATTGATGCCTTTAAATTTTGATTTATTTTA
1 TTTTTTATCATTAAATAATATTGGGATAATTACCTATTGAGGCCTTTAAATTTTAATTTATTTTA
8996 ATTTTTCCCACTCCCAA
66 ATTTTTCCCACTCCCAA
* * * *
9013 TTTTTTATCATTAAATAATATTGGGATAATTATCTATTTAGGTCTTTAAATTTTAATTTATTTTG
1 TTTTTTATCATTAAATAATATTGGGATAATTACCTATTGAGGCCTTTAAATTTTAATTTATTTTA
9078 ATTT
66 ATTT
9082 AACCCCCTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (82 bp):
TTTTTTATCATTAAATAATATTGGGATAATTACCTATTGAGGCCTTTAAATTTTAATTTATTTTA
ATTTTTCCCACTCCCAA
Found at i:10445 original size:31 final size:31
Alignment explanation
Indices: 10353--10463 Score: 102
Period size: 31 Copynumber: 3.5 Consensus size: 31
10343 GTTACTAAAT
*
10353 TCATTAAACTTAGT-GAACT-GTTACAAAATGAG
1 TCATTAAACTTA-TCAAACTAG-TACAAAATG-G
*
10385 -CATTAAACTTTTGCAAACTAGTACAAAATGG
1 TCATTAAACTTAT-CAAACTAGTACAAAATGG
* * * *
10416 TCATTGAACTTATCAAACTATTACGAAATGT
1 TCATTAAACTTATCAAACTAGTACAAAATGG
*
10447 TCCTTAAACTTATCAAA
1 TCATTAAACTTATCAAA
10464 TTTTATCACT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
30 1 0.02
31 41 0.62
32 23 0.35
33 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (31 bp):
TCATTAAACTTATCAAACTAGTACAAAATGG
Found at i:10602 original size:23 final size:23
Alignment explanation
Indices: 10572--10619 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
10562 TCGTTTCAAC
10572 ATAGTTTAATAATCATTTTGTAT
1 ATAGTTTAATAATCATTTTGTAT
10595 ATAGTTTAATAATCATTTTGTAT
1 ATAGTTTAATAATCATTTTGTAT
10618 AT
1 AT
10620 TTACCCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (23 bp):
ATAGTTTAATAATCATTTTGTAT
Found at i:11974 original size:21 final size:19
Alignment explanation
Indices: 11950--12088 Score: 116
Period size: 21 Copynumber: 6.7 Consensus size: 19
11940 TAAATCGCAA
11950 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTT--CGT
* *
11971 TGCGATTTATTCCAAGTTCGT
1 TGCGA--TAGTCGAAGTTCGT
11992 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTT--CGT
* *
12013 TGCGATTTATTCCAAGTTCGT
1 TGCGA--TAGTCGAAGTTCGT
12034 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTT--CGT
* *
12055 TGCGATTTATTCCAAGTTCGT
1 TGCGA--TAGTCGAAGTTCGT
12076 TGCGATAGTCGAA
1 TGCGATAGTCGAA
12089 CGAGACGAGA
Statistics
Matches: 96, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
19 24 0.25
21 45 0.47
23 27 0.28
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (19 bp):
TGCGATAGTCGAAGTTCGT
Found at i:11997 original size:42 final size:42
Alignment explanation
Indices: 11950--12088 Score: 278
Period size: 42 Copynumber: 3.3 Consensus size: 42
11940 TAAATCGCAA
11950 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
11992 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
12034 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1 TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
12076 TGCGATAGTCGAA
1 TGCGATAGTCGAA
12089 CGAGACGAGA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (42 bp):
TGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
Found at i:14321 original size:126 final size:126
Alignment explanation
Indices: 14096--14349 Score: 400
Period size: 126 Copynumber: 2.0 Consensus size: 126
14086 AGAACGAGCT
* * *
14096 TTCAATCTAAGCTAACGTTGAATGAGTTTCTAAAGAACACCGATATTCACTGGTGCATAACCGAT
1 TTCAACCTAAGCTAAAGTTGAATGAGTTTCTAAAGAACACCGATATTCACTAGTGCATAACCGAT
** *
14161 CACCACGTGTGATAAAAAAGTTGTTAGATCTGTAAATAAGGCTTATATCACAAATAAGTAC
66 CACCACAAGTGATAAAAAAGTTGTTAGATCTGTAAATAAGGCTTATATAACAAATAAGTAC
* * * *
14222 TTCAACCTAAGCTAAAGTTGAATGGGTTTCTAATGAACATCGATATTCACTAGTGCATAACTGAT
1 TTCAACCTAAGCTAAAGTTGAATGAGTTTCTAAAGAACACCGATATTCACTAGTGCATAACCGAT
* *
14287 CACCACAAGTGATAAAAAAGTTGTTTGGTCTGTAAATAAGGCTTATATAACAAATAAGTAC
66 CACCACAAGTGATAAAAAAGTTGTTAGATCTGTAAATAAGGCTTATATAACAAATAAGTAC
14348 TT
1 TT
14350 AAAGTATGCC
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 116 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (126 bp):
TTCAACCTAAGCTAAAGTTGAATGAGTTTCTAAAGAACACCGATATTCACTAGTGCATAACCGAT
CACCACAAGTGATAAAAAAGTTGTTAGATCTGTAAATAAGGCTTATATAACAAATAAGTAC
Found at i:14435 original size:31 final size:29
Alignment explanation
Indices: 14375--14436 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
14365 TTCATCTAAG
* *
14375 TACCTAAAGTACTTTTTGGTCAAAGTAGA
1 TACCTAAAGTACATTTTGATCAAAGTAGA
14404 TACCTAAAGTTATCATTTTGATC-AAGATAGA
1 TACCTAAAG-TA-CATTTTGATCAAAG-TAGA
14435 TA
1 TA
14437 GTATTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.32
30 5 0.18
31 14 0.50
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (29 bp):
TACCTAAAGTACATTTTGATCAAAGTAGA
Found at i:24130 original size:15 final size:15
Alignment explanation
Indices: 24110--24139 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24100 AAGATAATTT
*
24110 TTTAAATACTAAAAC
1 TTTAAAAACTAAAAC
24125 TTTAAAAACTAAAAC
1 TTTAAAAACTAAAAC
24140 ATATTCATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (15 bp):
TTTAAAAACTAAAAC
Found at i:28196 original size:20 final size:20
Alignment explanation
Indices: 28167--28205 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28157 ACGACGGTTA
28167 AAAAGATAAAAAAAAACGTT
1 AAAAGATAAAAAAAAACGTT
* *
28187 AAAAGCTAAATAAAAACGT
1 AAAAGATAAAAAAAAACGT
28206 GTCATAAAAG
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:0.67, C:0.08, G:0.10, T:0.15
Consensus pattern (20 bp):
AAAAGATAAAAAAAAACGTT
Found at i:29770 original size:21 final size:21
Alignment explanation
Indices: 29691--29763 Score: 137
Period size: 21 Copynumber: 3.5 Consensus size: 21
29681 TTTTGTTTGT
29691 TTCGCTGTTTAATCCTTTTCA
1 TTCGCTGTTTAATCCTTTTCA
29712 TTCGCTGTTTAATCCTTTTCA
1 TTCGCTGTTTAATCCTTTTCA
29733 TTCGCTGTTTAATCCTTTTCA
1 TTCGCTGTTTAATCCTTTTCA
*
29754 TTCACTGTTT
1 TTCGCTGTTT
29764 GGACCTTGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.14, C:0.23, G:0.10, T:0.53
Consensus pattern (21 bp):
TTCGCTGTTTAATCCTTTTCA
Found at i:31192 original size:14 final size:14
Alignment explanation
Indices: 31154--31195 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
31144 AAGTCAATGT
*
31154 CGATCAACGGTCTA
1 CGATCAACGGTCAA
* *
31168 CAAT-GACGGTCAA
1 CGATCAACGGTCAA
31181 CGATCAACGGTCAA
1 CGATCAACGGTCAA
31195 C
1 C
31196 AGCTTAGCTC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (14 bp):
CGATCAACGGTCAA
Found at i:33440 original size:16 final size:18
Alignment explanation
Indices: 33419--33456 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
33409 AACGTCTTTT
33419 AAAACA-ATTTTAAGA-A
1 AAAACATATTTTAAGACA
*
33435 AAAACATTTTTTAAGACA
1 AAAACATATTTTAAGACA
33453 AAAA
1 AAAA
33457 TGGTATGCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAACATATTTTAAGACA
Found at i:41766 original size:2 final size:2
Alignment explanation
Indices: 41761--41796 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41751 AAAGACAAAT
41761 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
41797 AAGATCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44983 original size:13 final size:13
Alignment explanation
Indices: 44965--44989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44955 GTTCATGTAT
44965 TCGGTAAGTTAAA
1 TCGGTAAGTTAAA
44978 TCGGTAAGTTAA
1 TCGGTAAGTTAA
44990 GTTAGATCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
TCGGTAAGTTAAA
Found at i:45638 original size:22 final size:22
Alignment explanation
Indices: 45608--45650 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
45598 TATATTCATG
* *
45608 TTTGGTTTTTTTTTTTTAATAA
1 TTTGGTTTTGTTTATTTAATAA
*
45630 TTTGTTTTTGTTTATTTAATA
1 TTTGGTTTTGTTTATTTAATA
45651 TATATATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (22 bp):
TTTGGTTTTGTTTATTTAATAA
Found at i:47245 original size:24 final size:24
Alignment explanation
Indices: 47217--47264 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
47207 TGCATTTCAG
47217 TCGTTCGTCCTGTGGTTTCATTTA
1 TCGTTCGTCCTGTGGTTTCATTTA
47241 TCGTTCGTCCTGTGGTTTCATTTA
1 TCGTTCGTCCTGTGGTTTCATTTA
47265 GAGAAACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.21, G:0.21, T:0.50
Consensus pattern (24 bp):
TCGTTCGTCCTGTGGTTTCATTTA
Found at i:47589 original size:12 final size:11
Alignment explanation
Indices: 47546--47587 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
47536 TCAGTTCAAC
47546 TTAAATTTT-T
1 TTAAATTTTAT
*
47556 TTATATTTTTAT
1 TTA-AATTTTAT
47568 TTAAATTTTAT
1 TTAAATTTTAT
47579 TTAAATTTT
1 TTAAATTTT
47588 TAAATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 3 0.11
11 21 0.75
12 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTAAATTTTAT
Found at i:51099 original size:18 final size:19
Alignment explanation
Indices: 51068--51112 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
51058 AATATGTAAA
*
51068 TCGCAACTGAATTTCAAAT
1 TCGCAACAGAATTTCAAAT
* *
51087 TCGCAACAG-ATTTTAATT
1 TCGCAACAGAATTTCAAAT
51105 TCGCAACA
1 TCGCAACA
51113 CAAATGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (19 bp):
TCGCAACAGAATTTCAAAT
Found at i:51262 original size:14 final size:15
Alignment explanation
Indices: 51243--51280 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
51233 TCCCCATCTC
51243 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
51257 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
51273 TAATTTTT
1 TAATTTTT
51281 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:51854 original size:12 final size:12
Alignment explanation
Indices: 51833--51866 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
51823 ACCACATTTC
*
51833 CAATACCAAACA
1 CAATATCAAACA
51845 CAATATCAAACA
1 CAATATCAAACA
*
51857 CAATCTCAAA
1 CAATATCAAA
51867 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:52043 original size:24 final size:24
Alignment explanation
Indices: 51992--52045 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
51982 GTATTCGAAA
*
51992 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
52016 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
52040 TTTGAT
1 TTTGAT
52046 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:54341 original size:18 final size:18
Alignment explanation
Indices: 54318--54353 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54308 AAGCAAAAGG
*
54318 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
54336 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
54354 CAACCAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:54697 original size:20 final size:20
Alignment explanation
Indices: 54672--54711 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
54662 CGAAATAAGG
54672 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
54692 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
54712 AACGCTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:54840 original size:25 final size:25
Alignment explanation
Indices: 54802--54851 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
54792 AAATCAATTA
*
54802 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
*
54827 AACATTGTTATGGGTATATTATTTG
1 AACATTGTTATGGGTACATTATTTG
54852 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:55258 original size:18 final size:18
Alignment explanation
Indices: 55237--55273 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55227 GTAATTGGAG
55237 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
55255 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
55273 T
1 T
55274 ATAAATTTCG
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:55280 original size:24 final size:24
Alignment explanation
Indices: 55229--55281 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
55219 TTTCATATGT
* * *
55229 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
55253 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
55277 AATTT
1 AATTT
55282 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:55625 original size:39 final size:39
Alignment explanation
Indices: 55582--55668 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
55572 TCCGATGCTC
55582 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
* *
55621 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
55660 ATCAAAATC
1 ATCAAAATC
55669 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
Found at i:57464 original size:21 final size:21
Alignment explanation
Indices: 57407--57481 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
57397 GGCGGGACCA
* * *
57407 CTTGAACGATGACAGGGGCCT
1 CTTGAATGATGAGAGGAGCCT
* * *
57428 CTTGAACGGT-AGGAGGAGCTT
1 CTTGAATGATGA-GAGGAGCCT
*
57449 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAATGATGAGAGGAGCCT
57470 CTTGAATGATGA
1 CTTGAATGATGA
57482 TAGGTGCATC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (21 bp):
CTTGAATGATGAGAGGAGCCT
Found at i:61568 original size:30 final size:30
Alignment explanation
Indices: 61524--61660 Score: 172
Period size: 30 Copynumber: 4.6 Consensus size: 30
61514 CCAAGAAGTG
* *
61524 ATTTTCGGTTATTTTTTAGCG-CTTAATAAT
1 ATTTTCAGTCATTTTTTAGCGTC-TAATAAT
* *
61554 ATTTTCAGTCA-TTTTTAACGCCTAATAAT
1 ATTTTCAGTCATTTTTTAGCGTCTAATAAT
61583 ATTTTCAGTCATTTTTTAGCGTCTAATAAT
1 ATTTTCAGTCATTTTTTAGCGTCTAATAAT
* * *
61613 GTTTTCAATCATTTTTTAGCGTCTGATAAT
1 ATTTTCAGTCATTTTTTAGCGTCTAATAAT
61643 ATTTTC-GATCATTTTTTA
1 ATTTTCAG-TCATTTTTTA
61661 CCGATTTTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
29 26 0.28
30 68 0.72
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (30 bp):
ATTTTCAGTCATTTTTTAGCGTCTAATAAT
Found at i:61618 original size:59 final size:59
Alignment explanation
Indices: 61524--61660 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 59
61514 CCAAGAAGTG
* *
61524 ATTTTCGGTTATTTTTTAGCGCTTAATAATATTTTCAGTCA-TTTTTAACGCCTAATAAT
1 ATTTTC-GTCATTTTTTAGCGCTTAATAATATTTTCAATCATTTTTTAACGCCTAATAAT
* * * *
61583 ATTTTCAGTCATTTTTTAGCG-TCTAATAATGTTTTCAATCATTTTTTAGCGTCTGATAAT
1 ATTTTC-GTCATTTTTTAGCGCT-TAATAATATTTTCAATCATTTTTTAACGCCTAATAAT
61643 ATTTTCGATCATTTTTTA
1 ATTTTCG-TCATTTTTTA
61661 CCGATTTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.01
59 36 0.53
60 31 0.46
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (59 bp):
ATTTTCGTCATTTTTTAGCGCTTAATAATATTTTCAATCATTTTTTAACGCCTAATAAT
Found at i:63921 original size:25 final size:25
Alignment explanation
Indices: 63892--63943 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
63882 TTCAAAGAAT
63892 TATTTT-TATAAATATATATTT-ATAA
1 TATTTTATATAAAT-TA-ATTTAATAA
*
63917 TATTTTATTTAAATTAATTTAATAA
1 TATTTTATATAAATTAATTTAATAA
63942 TA
1 TA
63944 AATGAGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.17
25 14 0.58
26 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTTATATAAATTAATTTAATAA
Found at i:70897 original size:32 final size:32
Alignment explanation
Indices: 70861--70934 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
70851 AATATTAAAA
*
70861 ATTAAAATATTTAAAAT-ATTTTTTTAATATT-T
1 ATTAAAATA--TAAAATAATATTTTTAATATTAT
*
70893 ATTAATAATATAATATAATATTTTTAATATTAT
1 ATTAA-AATATAAAATAATATTTTTAATATTAT
*
70926 AATAAAATA
1 ATTAAAATA
70935 ATCAATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 5 0.14
32 22 0.61
33 9 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
ATTAAAATATAAAATAATATTTTTAATATTAT
Found at i:70926 original size:22 final size:23
Alignment explanation
Indices: 70885--70934 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
70875 AATATTTTTT
70885 TAATATTTATTAATAATATAATA
1 TAATATTTATTAATAATATAATA
*
70908 TAATATTT-TTAATATTATAATA
1 TAATATTTATTAATAATATAATA
*
70930 AAATA
1 TAATA
70935 ATCAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATTTATTAATAATATAATA
Found at i:71127 original size:23 final size:23
Alignment explanation
Indices: 71101--71154 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
71091 TATTAATATA
**
71101 AAAATATTTTAATAAAGATATTT
1 AAAATATACTAATAAAGATATTT
* * *
71124 AAAATATACTAATTAATATTTTT
1 AAAATATACTAATAAAGATATTT
71147 AAAATATA
1 AAAATATA
71155 ATATGACACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AAAATATACTAATAAAGATATTT
Found at i:71269 original size:17 final size:20
Alignment explanation
Indices: 71249--71288 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
71239 TAATAAAATT
71249 ATAA-AAATA-AT-ATTTTA
1 ATAATAAATATATAATTTTA
71266 ATAATAAATATATAATTTTA
1 ATAATAAATATATAATTTTA
71286 ATA
1 ATA
71289 TTTTAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 5 0.25
19 2 0.10
20 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATAAATATATAATTTTA
Found at i:71306 original size:28 final size:30
Alignment explanation
Indices: 71256--71315 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
71246 ATTATAAAAA
71256 TAATATTTTAATAATAAATATA-TAA-TTT
1 TAATATTTTAATAATAAATATATTAAGTTT
71284 TAATATTTTAA-AA-ACAATAATATTAAGTTT
1 TAATATTTTAATAATA-AAT-ATATTAAGTTT
71314 TA
1 TA
71316 TGATAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 1 0.04
27 5 0.18
28 14 0.50
29 3 0.11
30 5 0.18
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
TAATATTTTAATAATAAATATATTAAGTTT
Found at i:78695 original size:20 final size:20
Alignment explanation
Indices: 78670--78707 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
78660 GTTAAGGTTG
*
78670 GTTAAAGCTGTTAGCAGGAT
1 GTTAAAGCTATTAGCAGGAT
*
78690 GTTAAATCTATTAGCAGG
1 GTTAAAGCTATTAGCAGG
78708 GAGTTGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTAAAGCTATTAGCAGGAT
Found at i:83915 original size:21 final size:21
Alignment explanation
Indices: 83886--83928 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
83876 ATTCTGACTA
83886 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
83907 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
83928 T
1 T
83929 AATCGCAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:83961 original size:20 final size:20
Alignment explanation
Indices: 83929--84003 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
83919 TTTCCTAATT
*
83929 AATCGCAACGCGAATACGTA
1 AATCGCAATGCGAATACGTA
* *
83949 AATCACAATGCGAATACATA
1 AATCGCAATGCGAATACGTA
83969 AATCGCAATGCGAATACGTA
1 AATCGCAATGCGAATACGTA
*
83989 AATCGCAACGCGAAT
1 AATCGCAATGCGAAT
84004 CTGACTATTG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
AATCGCAATGCGAATACGTA
Found at i:84016 original size:20 final size:20
Alignment explanation
Indices: 83990--84056 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
83980 GAATACGTAA
* *
83990 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
*
84010 ATTGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
84030 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
84050 ATCGCAA
1 ATCGCAA
84057 TACTGAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:85159 original size:12 final size:13
Alignment explanation
Indices: 85144--85176 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
85134 AAAAGAAAAA
85144 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
85156 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
85170 GAAGAAA
1 GAAGAAA
85177 ATGCCACGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 6 0.32
14 9 0.47
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:85170 original size:14 final size:14
Alignment explanation
Indices: 85151--85177 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
85141 AAAGAAGAAA
85151 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
85165 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
85178 TGCCACGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:87377 original size:20 final size:20
Alignment explanation
Indices: 87351--87443 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
87341 AGACATTCAT
87351 TTGACTATCGCAACAC-GAA
1 TTGACTATCGCAACACGGAA
*
87370 TATGACTATTGCAACACGGAA
1 T-TGACTATCGCAACACGGAA
* **
87391 ATGACTATCGCAAGGCGGAA
1 TTGACTATCGCAACACGGAA
* *
87411 TTAACTATCGCAACGCGGAA
1 TTGACTATCGCAACACGGAA
87431 TTGACTATCGCAA
1 TTGACTATCGCAA
87444 TGAGAGAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.02
20 59 0.94
21 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACACGGAA
Found at i:87494 original size:33 final size:33
Alignment explanation
Indices: 87452--87519 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
87442 AATGAGAGAA
**
87452 TCGCATTGCGATTCA-CTCGTTGCGATTTTCATT
1 TCGCATTGCGATT-ATCTCGTTGCGATAGTCATT
87485 TCGCATTGCGATTATCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTATCTCGTTGCGATAGTCATT
87518 TC
1 TC
87520 TACGTTGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (33 bp):
TCGCATTGCGATTATCTCGTTGCGATAGTCATT
Found at i:89141 original size:21 final size:21
Alignment explanation
Indices: 89060--89146 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
89050 GAATGTTGGG
* *
89060 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
89081 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
89102 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
89123 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
89144 AGG
1 AGG
89147 TGAGTCGGGT
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:89730 original size:20 final size:19
Alignment explanation
Indices: 89654--89734 Score: 64
Period size: 20 Copynumber: 4.4 Consensus size: 19
89644 CTATCGCAAC
*
89654 GCGATAGTCATTTTCGCGTT
1 GCGATAGTCA-TTTCGCATT
* **
89674 GCAATTTTCATTTCGCATT
1 GCGATAGTCATTTCGCATT
*
89693 GCGAT--TC-TCTCG--TT
1 GCGATAGTCATTTCGCATT
89707 GCGATAGTCATTTTCGCATT
1 GCGATAGTCA-TTTCGCATT
89727 GCGATAGT
1 GCGATAGT
89735 AAACTATTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
14 7 0.15
16 6 0.12
17 2 0.04
18 4 0.08
19 12 0.25
20 17 0.35
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
GCGATAGTCATTTCGCATT
Found at i:91508 original size:20 final size:20
Alignment explanation
Indices: 91485--91539 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
91475 CTGAAACTTT
91485 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
91505 AAATTGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
91525 TTATCGCAACGCGAA
1 AAATCGCAACACGAA
91540 TTTGACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.15
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:91595 original size:33 final size:34
Alignment explanation
Indices: 91527--91599 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
91517 GAAAATGATT
* **
91527 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
91561 ATCGCAACGCGAA-ATGAAAATCGCAACG-ACAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCA-AGA
91594 ATCGCA
1 ATCGCA
91600 TTGCGATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 21 0.60
34 13 0.37
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:91958 original size:22 final size:22
Alignment explanation
Indices: 91924--91985 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
91914 TGACCGTGAA
*
91924 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
* *
91946 TGATATCGTCGGAGATGGTGAC
1 TGATTTCGTCGGAGATGGAGAC
91968 TGATTTCGTCGGAGATGG
1 TGATTTCGTCGGAGATGG
91986 GGACGGATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.21, C:0.15, G:0.37, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:92239 original size:21 final size:21
Alignment explanation
Indices: 92215--92254 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
92205 ATTCGCATTG
92215 CGAATTAGGAAAATCGCAAAT
1 CGAATTAGGAAAATCGCAAAT
*
92236 CGAATTTGGAAAATCGCAA
1 CGAATTAGGAAAATCGCAA
92255 TGCGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAAAT
Found at i:92736 original size:2 final size:2
Alignment explanation
Indices: 92729--92803 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
92719 AATCATAAGA
92729 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
92771 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
92804 AACGGGGTAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:99324 original size:16 final size:15
Alignment explanation
Indices: 99299--99399 Score: 55
Period size: 16 Copynumber: 6.5 Consensus size: 15
99289 TTTCAAATTG
99299 AAAT-TAATAACAAAT
1 AAATATAATAA-AAAT
99314 AAATATAAT--AAAT
1 AAATATAATAAAAAT
*
99327 AAATATAATAATAAT
1 AAATATAATAAAAAT
* * * *
99342 TAATAATATTAATTATT
1 AAAT-ATAATAA-AAAT
*
99359 AAATATATTAAATAATT
1 AAATATAATAAA-AA-T
*
99376 AAAATATCATAATAAAT
1 -AAATATAATAA-AAAT
99393 AAATATA
1 AAATATA
99400 GTAATTAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
13 13 0.19
15 10 0.15
16 24 0.36
17 8 0.12
18 11 0.16
19 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATAATAAAAAT
Found at i:99326 original size:13 final size:13
Alignment explanation
Indices: 99305--99337 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
99295 ATTGAAATTA
*
99305 ATAACAAATAAAT
1 ATAATAAATAAAT
99318 ATAATAAATAAAT
1 ATAATAAATAAAT
99331 ATAATAA
1 ATAATAA
99338 TAATTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
ATAATAAATAAAT
Found at i:99404 original size:16 final size:16
Alignment explanation
Indices: 99301--99427 Score: 73
Period size: 17 Copynumber: 7.8 Consensus size: 16
99291 TCAAATTGAA
* *
99301 ATTAAT-AACAAATAA
1 ATTAATAAATAAATAT
99316 ATATAATAAATAAATAT
1 AT-TAATAAATAAATAT
* *
99333 AATAAT-AATTAATAAT
1 ATTAATAAATAAAT-AT
* *
99349 ATTAATTATTAAATAT
1 ATTAATAAATAAATAT
*
99365 ATTAAATAATTAAA-AT
1 ATT-AATAAATAAATAT
99381 ATCATAATAAATAAATAT
1 AT--TAATAAATAAATAT
* *
99399 AGTAATTAAA-ATATAT
1 ATTAA-TAAATAAATAT
*
99415 ATTTTATAAATAA
1 A-TTAATAAATAA
99428 TAATTATAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 20
0.72 0.12 0.17
Matches are distributed among these distances:
15 8 0.09
16 37 0.43
17 38 0.44
18 4 0.05
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.38
Consensus pattern (16 bp):
ATTAATAAATAAATAT
Found at i:99436 original size:13 final size:14
Alignment explanation
Indices: 99312--99436 Score: 60
Period size: 16 Copynumber: 8.3 Consensus size: 14
99302 TTAATAACAA
99312 ATAAATATAATAA--
1 ATAAATAT-ATAATT
*
99325 ATAAATATAATAATA
1 ATAAATAT-ATAATT
*
99340 ATTAATAATATTAATT
1 ATAAAT-ATA-TAATT
*
99356 ATTAAATATATTAAATA
1 A-TAAATATA-T-AATT
*
99373 ATTAAAATATCATAATAA
1 A-T-AAATAT-ATAAT-T
99391 ATAAATATAGTAATT
1 ATAAATATA-TAATT
*
99406 A-AAATATATATTTT
1 ATAAATATATA-ATT
99420 ATAAATA-ATAATT
1 ATAAATATATAATT
99433 ATAA
1 ATAA
99437 TCTATTTTGT
Statistics
Matches: 93, Mismatches: 7, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
13 21 0.23
14 13 0.14
15 13 0.14
16 22 0.24
17 14 0.15
18 9 0.10
19 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (14 bp):
ATAAATATATAATT
Found at i:99499 original size:21 final size:21
Alignment explanation
Indices: 99475--99515 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
99465 AACTATACAC
99475 ATAATA-TAGTAAATATAATAA
1 ATAATATTA-TAAATATAATAA
*
99496 ATAATATTATAATTATAATA
1 ATAATATTATAAATATAATA
99516 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATATTATAAATATAATAA
Found at i:105926 original size:18 final size:16
Alignment explanation
Indices: 105905--105963 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 16
105895 TATTTATAAA
105905 ATATTTATTTTAATTACT
1 ATATTTA-TTT-ATTACT
*
105923 ATATTTATTTATTATT
1 ATATTTATTTATTACT
* *
105939 ATATTTTAATTATTTATT
1 ATA-TTTATTTA-TTACT
105957 ATATTTA
1 ATATTTA
105964 ATACTTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 8 0.22
17 14 0.38
18 15 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATTTATTTATTACT
Found at i:105941 original size:16 final size:16
Alignment explanation
Indices: 105905--106023 Score: 79
Period size: 16 Copynumber: 7.4 Consensus size: 16
105895 TATTTATAAA
*
105905 ATATTTATTTTAATTACT
1 ATATTTA-TTT-ATTATT
105923 ATATTTATTTATTATT
1 ATATTTATTTATTATT
*
105939 ATA-TT-TTAATTATT
1 ATATTTATTTATTATT
*
105953 -TATTATATTTAATACTT
1 ATATT-TATTTATTA-TT
*
105970 A-ATATTATTAATTATT
1 ATAT-TTATTTATTATT
*
105986 -TATTATACTTATTTATT
1 ATATT-TATTTA-TTATT
*
106003 ATATTTATTTGTTATT
1 ATATTTATTTATTATT
106019 A-ATTT
1 ATATTT
106024 CAATTTGAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
13 2 0.02
14 9 0.11
15 8 0.10
16 27 0.33
17 23 0.28
18 12 0.15
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (16 bp):
ATATTTATTTATTATT
Found at i:105999 original size:13 final size:13
Alignment explanation
Indices: 105964--106017 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
105954 ATTATATTTA
105964 ATACTTAATATTATT
1 ATACTT-AT-TTATT
105979 A-A-TTATTTATT
1 ATACTTATTTATT
105990 ATACTTATTTATT
1 ATACTTATTTATT
* *
106003 ATATTTATTTGTT
1 ATACTTATTTATT
106016 AT
1 AT
106018 TAATTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 6 0.17
12 3 0.09
13 24 0.69
14 1 0.03
15 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (13 bp):
ATACTTATTTATT
Found at i:106017 original size:26 final size:26
Alignment explanation
Indices: 105934--106011 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
105924 TATTTATTTA
* * *
105934 TTATTATATTTTA-ATTATTTATTAT
1 TTATTATACTTAATATTATTAATTAT
*
105959 ATT-TAATACTTAATATTATTAATTAT
1 -TTATTATACTTAATATTATTAATTAT
105985 TTATTATACTT-AT-TTATT-A-TAT
1 TTATTATACTTAATATTATTAATTAT
106007 TTATT
1 TTATT
106012 TGTTATTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
22 8 0.18
23 1 0.02
24 5 0.11
25 11 0.24
26 20 0.44
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (26 bp):
TTATTATACTTAATATTATTAATTAT
Found at i:112415 original size:2 final size:2
Alignment explanation
Indices: 112408--112448 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
112398 GCATCAAAGC
112408 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
112449 GTTTTGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:120904 original size:21 final size:21
Alignment explanation
Indices: 120880--121039 Score: 193
Period size: 21 Copynumber: 7.7 Consensus size: 21
120870 TCGTACCAAG
*
120880 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
120901 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
120922 GATGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
120943 GACGAGAAGACCATTCATCAA
1 GACGAGAAGACCATTCATCAA
120964 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
* * *
120985 GACGAGAAAACCCTTCATAAA
1 GACGAGAAGACCATTCATCAA
* *
121006 GACGAGAAGACC-TTCGTAAA
1 GACGAGAAGACCATTCATCAA
121026 GACGAGAAGACCAT
1 GACGAGAAGACCAT
121040 ATCGCATGGA
Statistics
Matches: 125, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
20 20 0.16
21 103 0.82
22 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:120959 original size:63 final size:63
Alignment explanation
Indices: 120880--121033 Score: 220
Period size: 63 Copynumber: 2.5 Consensus size: 63
120870 TCGTACCAAG
* * * ** *
120880 GACGAGAAGAGCATTCATCAAGACGAGAATGTCATTCATCAAGATGAGAATGCCATTCATCAA
1 GACGAGAAGACCATTCATCAAGACGAGAATGCCATTCATCAAGACGAGAAAACCATTCATAAA
*
120943 GACGAGAAGACCATTCATCAAGACGAGAATGCCATTCATCAAGACGAGAAAACCCTTCATAAA
1 GACGAGAAGACCATTCATCAAGACGAGAATGCCATTCATCAAGACGAGAAAACCATTCATAAA
* *
121006 GACGAGAAGACC-TTCGTAAAGACGAGAA
1 GACGAGAAGACCATTCATCAAGACGAGAA
121034 GACCATATCG
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
62 14 0.17
63 68 0.83
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.17
Consensus pattern (63 bp):
GACGAGAAGACCATTCATCAAGACGAGAATGCCATTCATCAAGACGAGAAAACCATTCATAAA
Found at i:123640 original size:17 final size:17
Alignment explanation
Indices: 123622--123659 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
123612 AGAAATGTAG
*
123622 AAAGAGAAAAGGAAAAGA
1 AAAGA-AAAAAGAAAAGA
123640 AAAGAAAAAAGAAAAGA
1 AAAGAAAAAAGAAAAGA
123657 AAA
1 AAA
123660 AATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAGA
Found at i:123649 original size:12 final size:12
Alignment explanation
Indices: 123634--123661 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
123624 AGAGAAAAGG
123634 AAAAGAAAAGAA
1 AAAAGAAAAGAA
123646 AAAAGAAAAGAA
1 AAAAGAAAAGAA
123658 AAAA
1 AAAA
123662 TTAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:126451 original size:36 final size:36
Alignment explanation
Indices: 126404--126574 Score: 211
Period size: 36 Copynumber: 4.7 Consensus size: 36
126394 ACTGAAGAGG
* **
126404 AGTGAAGCAAACCATCTGAATCCTTCACTGGAGAAT
1 AGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAAT
126440 AGTGAAGCAAACCATCCT-AAGCCTTCACCAGAGAAT
1 AGTGAAGCAAACCAT-CTGAAGCCTTCACCAGAGAAT
*
126476 AGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAGT
1 AGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAAT
* * *
126512 AGTGAAGCAAACCATCTTAAGTCTTCACCA-AAAAGT
1 AGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAA-T
* * *
126548 AGTGAAGCAGATCCATTTTAAGCCTTC
1 AGTGAAGCA-AACCATCTGAAGCCTTC
126575 TCAGAAGAGT
Statistics
Matches: 120, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
35 4 0.03
36 100 0.83
37 16 0.13
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (36 bp):
AGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAAT
Found at i:127340 original size:212 final size:211
Alignment explanation
Indices: 126896--128123 Score: 1526
Period size: 212 Copynumber: 5.8 Consensus size: 211
126886 AGGTTCGACA
* * * * **
126896 TTTGAAGAAGATATCCGAGTTCCATACTCC-TATAGAAAG-AGAGAGCGAACCC--ATTTGAAGA
1 TTTGAAG-AGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAG-GAGAGAACCCGTATAAGAAGA
** *
126957 TTGTTCGAGTTCCATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAG-A-TTGTTCGAGT
64 -TGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGT
* * ** * *
127019 TCTATACTTCCTGAAAGAAAGAGGAAGCGAAAACGTTTGAAGATTATTCGAGTTCCATACTCCCT
127 TCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTTTGAAGA-TGTTCGAGTTCCATACTCCTT
* *
127084 AGAGAAAGAGGGAGCGAACCCG
190 AAAGAAAGAAGGAGCGAACCCG
** * * * * * *
127106 TAAGAAGAAGATGTTTGAGTTCTATACTTCC-TGAAGAAAGAGGGAGCGAACCCGT-T-TGAAGA
1 TTTGAAG-AGATGTTCGAGTTCCATAC-TCCTTAAAGAAAGAAGGAGAGAACCCGTATAAGAAGA
* * * ** *
127168 TGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATATGTTCGAGTTC
64 TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTC
* * * ** * * * *
127232 CATACTCCTTAAAGAAAGAATGAGAGAACCCGTAATAAGAAGATTTTCGAGTTCCATACTCCCTA
129 TATACTCCCTGAAGAAAGAGGGAGCGAACCCGT--T-TGAAGATGTTCGAGTTCCATACTCCTTA
* * *
127297 GAGAAAGAGGGAGCGAACCTG
191 AAGAAAGAAGGAGCGAACCCG
** * * * * * ** * *
127318 TAAGAAGAAGATTTTCGAGTTCTATACTTCC-TAGAGAAAGAGGGAGCGAACCTATTTGAAGAAT
1 TTTGAAG-AGATGTTCGAGTTCCATAC-TCCTTAAAGAAAGAAGGAGAGAACCCGTAT-AAGAAG
*
127382 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTTGAGTT
63 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTT
127447 CTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAAA
128 CTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAAA
127512 GAAAGAAGGAGCGAACCCG
193 GAAAGAAGGAGCGAACCCG
* *
127531 TTTGAAGATATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCGTAATAAGAAGAT
1 TTTGAAGAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGAGAACCCGT-ATAAGAAGAT
* * * *
127596 TTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCTGTAAGAAGAAGATTTTCGAGTTCT
65 GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCT
127661 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAAAGA
130 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAAAGA
127726 AAGAAGGAGCGAACCCG
195 AAGAAGGAGCGAACCCG
* * *
127743 TTTGAAGATATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCTGTAATAAGAAGAT
1 TTTGAAGAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGAGAACCCGT-ATAAGAAGAT
* * * *
127808 TTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAATATTTTCGAGTTCT
65 GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCT
*
127873 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTTCATACTCCTTAAAGA
130 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAAAGA
127938 AAGAAGGAGCGAACCCG
195 AAGAAGGAGCGAACCCG
* *
127955 TTTGAAGATATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGAGAACCCGTAATAAGAAGAT
1 TTTGAAGAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGAGAACCCGT-ATAAGAAGAT
* *
128020 TTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTTT
65 GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCT
** * *
128085 ATACTCCCTGAAGAGGGAGAGAGCGAACCTGTTTGAAGA
130 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGA
128124 AGATGTTCGA
Statistics
Matches: 917, Mismatches: 86, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
210 84 0.09
211 47 0.05
212 642 0.70
213 55 0.06
214 1 0.00
215 49 0.05
216 39 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (211 bp):
TTTGAAGAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGAGAACCCGTATAAGAAGATG
TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCTA
TACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAAAGAA
AGAAGGAGCGAACCCG
Found at i:127539 original size:320 final size:318
Alignment explanation
Indices: 126911--128123 Score: 1528
Period size: 320 Copynumber: 3.8 Consensus size: 318
126901 AGAAGATATC
* * **
126911 CGAGTTCCATACTCC-TATAGAAAGAGA-GAGCGAACCC--ATTTGAAGATTGTTCGAGTTCCAT
1 CGAGTTCCATACTCCTTAAAGAAAGA-ATGAGAGAACCCGTATAAGAAGATT-TTCGAGTTCCAT
**
126972 ACTCCCT-GAAGAAAGAGGGAGCGAACCCGT---TTGAAGATTGTTCGAGTTCTATACTTCCTGA
64 ACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAGAAGAAGATT-TTCGAGTTCTATACTTCCT-A
* * * *
127033 AAGAAAGAGGAAGCGAAAAC-GTTTGAAGAT-TATTCGAGTTCCATACTCCCTAGAGAAAGAGGG
126 AAGAAAGAGGGAGCG-AACCTATTTGAAGATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGG
* *
127096 AGCGAACCCGTAAGAAGAAGATGTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGT
190 AGCGAACCCGTAAGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGT
127161 TTGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATGTT
255 TTGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATGTT
127225 CGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCGTAATAAGAAGATTTTCGAGTTCCATA
1 CGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCGT-ATAAGAAGATTTTCGAGTTCCATA
* *
127290 CTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAAGATTTTCGAGTTCTATACTTCCTAGAGA
65 CTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTTCCTAAAGA
127355 AAGAGGGAGCGAACCTATTTGAAGAATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCG
130 AAGAGGGAGCGAACCTATTTGAAG-ATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCG
*
127420 AACCCGTAAGAAGAAGATGTTTGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGA
194 AACCCGTAAGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGA
127485 AGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATGTT
259 AGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATGTT
127545 CGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCGTAATAAGAAGATTTTCGAGTTCCATA
1 CGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCGT-ATAAGAAGATTTTCGAGTTCCATA
* * * *
127610 CTCCCTAGAGAAAGAGGGAGTGAACCTGTAAGAAGAAGATTTTCGAGTTCTATACTCCCTGAAGA
65 CTCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTTCCTAAAGA
** * * *
127675 AAGAGGGAGCGAACCCGTTTGAAG--ATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGA
130 AAGAGGGAGCGAACCTATTTGAAGATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGA
** * * * * ** * * *
127738 ACCCGTTTGAAG-ATATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCTGTAATAA
195 ACCCGTAAGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGT--T-T
* * * * * ** *
127802 GAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTAAGAAGAATATTTT
257 GAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATATGTT
* * * ** * * * *
127865 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGT-T-TGAAGATGTTCGAGTTTCATAC
1 CGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCGTATAAGAAGATTTTCGAGTTCCATAC
* * * ** * *
127928 TCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATATGTTCGAGTTCTATAC-TCCTTAAAGA
66 TCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTTCC-TAAAGA
* * **
127991 AAGAAGGAGAGAACCCGTAATAAGAAGAT-T-TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
130 AAGAGGGAGCGAA-CC-T-ATTTGAAGATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
* ** * *
128054 CGAACCCGTAAGAAGAAGATGTTCGAGTTTTATACTCCCTGAAGAGGGAGAGAGCGAACCTGTTT
192 CGAACCCGTAAGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTT
128119 GAAGA
257 GAAGA
128124 AGATGTTCGA
Statistics
Matches: 792, Mismatches: 84, Indels: 43
0.86 0.09 0.05
Matches are distributed among these distances:
314 16 0.02
315 20 0.03
316 71 0.09
317 141 0.18
318 34 0.04
319 117 0.15
320 393 0.50
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (318 bp):
CGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCGTATAAGAAGATTTTCGAGTTCCATAC
TCCCTAGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTTTCGAGTTCTATACTTCCTAAAGAA
AGAGGGAGCGAACCTATTTGAAGATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA
CCCGTAAGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAG
ATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATGTT
Found at i:128144 original size:54 final size:54
Alignment explanation
Indices: 126896--128135 Score: 1319
Period size: 54 Copynumber: 23.4 Consensus size: 54
126886 AGGTTCGACA
* * * * *
126896 TTTGAAGAAGATATCCGAGTTCCATACT-CCTATAGAAAGAGAGAGCGAACCCA
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* *
126949 TTTGAAG-A-TTGTTCGAGTTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * * * **
127001 TTTGAAG-A-TTGTTCGAGTTCTATACTTCCTGAAAGAAAGAGGAAGCGAAAACG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCG
* * *
127054 TTTGAAG-A-TTATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
** * * * *
127106 TAAGAAGAAGATGTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* *
127160 TTT---GAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * ** *
127211 TTTGAAG-ATATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * * *
127264 TAAT-AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTG
1 T-TTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
** * * * * **
127318 TAAGAAGAAGATTTTCGAGTTCTATACTTCCTAGAGAAAGAGGGAGCGAACCTA
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* *
127372 TTTGAAGAATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
** * * *
127426 TAAGAAGAAGATGTTTGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* *
127480 TTT---GAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * ** *
127531 TTTGAAG-ATATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * * * *
127584 TAAT-AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCTG
1 T-TTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
** * * *
127638 TAAGAAGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* *
127692 TTT---GAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * ** * *
127743 TTTGAAG-ATATGTTCGAGTTCCATACTCCTTAAAGAAAGAATGAGAGAACCTG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * * *
127796 TAAT-AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTG
1 T-TTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
** * * * *
127850 TAAGAAGAATATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * *
127904 TTT---GAAGATGTTCGAGTTTCATACTCCTTAAAGAAAGAAGGAGCGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * * * *
127955 TTTGAAG-ATATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGAGAACCCG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
* * *
128008 TAAT-AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG
1 T-TTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
** ** * ** * *
128062 TAAGAAGAAGATGTTCGAGTTTTATACTCCCTGAAGAGGGAGAGAGCGAACCTG
1 TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
128116 TTTGAAGAAGATGTTCGAGT
1 TTTGAAGAAGATGTTCGAGT
128136 CTTATACTCT
Statistics
Matches: 1008, Mismatches: 151, Indels: 55
0.83 0.12 0.05
Matches are distributed among these distances:
51 196 0.19
52 73 0.07
53 243 0.24
54 496 0.49
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (54 bp):
TTTGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG
Found at i:128204 original size:55 final size:55
Alignment explanation
Indices: 128122--128282 Score: 252
Period size: 55 Copynumber: 2.9 Consensus size: 55
128112 CCTGTTTGAA
* * *
128122 GAAGA-TGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCATACAAGATTATT
1 GAAGATTGTTCGTGTCTCATACTCTCTGAACAAATAGAGAGCATACACGATTATT
* *
128176 GAAGATTGTTCGTGTCTCATACTCTCTGAACGAATAGAGAGCAGACACGATTATT
1 GAAGATTGTTCGTGTCTCATACTCTCTGAACAAATAGAGAGCATACACGATTATT
* *
128231 AAAGATTGTTCGTGTCTCATACTCTCTGAAGAAATAGAGAGCATACACGATT
1 GAAGATTGTTCGTGTCTCATACTCTCTGAACAAATAGAGAGCATACACGATT
128283 CTTAGAGATT
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 5 0.05
55 92 0.95
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGTGTCTCATACTCTCTGAACAAATAGAGAGCATACACGATTATT
Found at i:128292 original size:55 final size:55
Alignment explanation
Indices: 128127--128315 Score: 238
Period size: 55 Copynumber: 3.4 Consensus size: 55
128117 TTGAAGAAGA
* * *
128127 TGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCATACAAGATTATT-GAAGAT
1 TGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCATACACGATTATTAG-AGAT
* * *
128182 TGTTCGTGTCTCATACTCTCTGAACG-AATAGAGAGCAGACACGATTATTAAAGAT
1 TGTTCGAGTCTCATACTCTCTGAA-GAAATAGAGAGCATACACGATTATTAGAGAT
* *
128237 TGTTCGTGTCTCATACTCTCTGAAGAAATAGAGAGCATACACGATTCTTAGAGAT
1 TGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCATACACGATTATTAGAGAT
* * * *
128292 TATTCGAGTTTCATATTCCCTGAA
1 TGTTCGAGTCTCATACTCTCTGAA
128316 AGCAATAGGG
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
54 1 0.01
55 116 0.99
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (55 bp):
TGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCATACACGATTATTAGAGAT
Found at i:138932 original size:28 final size:28
Alignment explanation
Indices: 138875--138934 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
138865 GAAAAAATTT
138875 AAATAATTTATGTACCTATTTTAATAAA
1 AAATAATTTATGTACCTATTTTAATAAA
** *
138903 AAATAACTTTATGTATTTATTTTGATAAA
1 AAATAA-TTTATGTACCTATTTTAATAAA
138932 AAA
1 AAA
138935 AAACATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (28 bp):
AAATAATTTATGTACCTATTTTAATAAA
Found at i:149257 original size:60 final size:60
Alignment explanation
Indices: 149114--149293 Score: 179
Period size: 60 Copynumber: 3.0 Consensus size: 60
149104 AATATACATT
* * * * *
149114 TAGTTTGGGATGAAATTGGAATGTTCAAAAGCTTTGGGGATTAATTTAGAATGAAGATCAA
1 TAGTTTGGGATGAAATTGAAATATTCAAAAG-TTTGAGGACTAATTTAAAATGAAGATCAA
* *
149175 TA-TTCGGGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAGTTTAAAATGATA-ATC-A
1 TAGTT-TGGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAAAATGA-AGATCAA
* * * * *
149234 TAGTTTAGGGATGAAATTAAAATATTTAAAAGTTTAAGGA-TCAATCTAAAATAAAGATCA
1 TAGTTT-GGGATGAAATTGAAATATTCAAAAGTTTGAGGACT-AATTTAAAATGAAGATCA
149294 TACTTTGAGG
Statistics
Matches: 98, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
59 5 0.05
60 67 0.68
61 26 0.27
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (60 bp):
TAGTTTGGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAAAATGAAGATCAA
Found at i:149274 original size:29 final size:29
Alignment explanation
Indices: 149182--149274 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
149172 CAATATTCGG
* * *
149182 GGATGAAATTGAAATATTCAAAAGTTTGA
1 GGATGAAATTAAAATATTTAAAAGTTTAA
** * * * *
149211 GGACT-AGTTTAAAATGATAATCATAGTTTAG
1 GGA-TGAAATTAAAAT-AT-TTAAAAGTTTAA
149242 GGATGAAATTAAAATATTTAAAAGTTTAA
1 GGATGAAATTAAAATATTTAAAAGTTTAA
149271 GGAT
1 GGAT
149275 CAATCTAAAA
Statistics
Matches: 45, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
29 22 0.49
30 6 0.13
31 17 0.38
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (29 bp):
GGATGAAATTAAAATATTTAAAAGTTTAA
Found at i:151113 original size:20 final size:21
Alignment explanation
Indices: 151080--151119 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
151070 CTACTTGGGG
151080 TAAACTATGCA-TTTAATACT
1 TAAACTATGCATTTTAATACT
151100 TAAACTAT-CAATTTTAATAC
1 TAAACTATGC-ATTTTAATAC
151120 ATTTTAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 9 0.50
21 8 0.44
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (21 bp):
TAAACTATGCATTTTAATACT
Found at i:151131 original size:31 final size:31
Alignment explanation
Indices: 151091--151161 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
151081 AAACTATGCA
*
151091 TTTAATACTTAAACTATCAATTTTAATACAT
1 TTTAGTACTTAAACTATCAATTTTAATACAT
* *
151122 TTTAGTACTTAAACTATCAATTTTATTTCAT
1 TTTAGTACTTAAACTATCAATTTTAATACAT
151153 TTTAGTACT
1 TTTAGTACT
151162 CAACCATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTAGTACTTAAACTATCAATTTTAATACAT
Found at i:153212 original size:14 final size:14
Alignment explanation
Indices: 153195--153224 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
153185 TCTTTTCCCT
*
153195 TTTAAATTTTGCTA
1 TTTAAATTTAGCTA
153209 TTTAAATTTAGCTA
1 TTTAAATTTAGCTA
153223 TT
1 TT
153225 ATCAATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTAAATTTAGCTA
Done.