Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004662.1 Hibiscus syriacus cultivar Beakdansim tig00010454_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: 83381
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1045 original size:22 final size:20
Alignment explanation
Indices: 1016--1061 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1006 GTTTTACCTG
* *
1016 TTTTCTTTCTTCTTTTTTTCT
1 TTTTCTTTCTT-TTTCTCTCT
1037 TTTTGCTTTCTTTTTCTCTCT
1 TTTT-CTTTCTTTTTCTCTCT
1058 TTTT
1 TTTT
1062 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTTCTTTTTCTCTCT
Found at i:1049 original size:11 final size:10
Alignment explanation
Indices: 1016--1061 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
1006 GTTTTACCTG
1016 TTTTCTTTCT
1 TTTTCTTTCT
*
1026 TCTTTTTTTCT
1 T-TTTCTTTCT
1037 TTTTGCTTTCT
1 TTTT-CTTTCT
*
1048 TTTTCTCTCT
1 TTTTCTTTCT
1058 TTTT
1 TTTT
1062 ATTTTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 13 0.42
11 18 0.58
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:1074 original size:7 final size:8
Alignment explanation
Indices: 1057--1082 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1047 TTTTTCTCTC
1057 TTTTTATT
1 TTTTTATT
1065 TTTTTATT
1 TTTTTATT
1073 TTTTTATT
1 TTTTTATT
1081 TT
1 TT
1083 ATCTCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:1077 original size:27 final size:27
Alignment explanation
Indices: 1016--1077 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 27
1006 GTTTTACCTG
* *
1016 TTTTCTTTCTTCTTTTTTTCTTTTTGC
1 TTTTTTTTCTTCTTTTTTTCTTTTTGA
1043 TTTCTTTTTCTCTCTTTTTATT-TTTTT-A
1 TTT-TTTTTCT-TCTTTTT-TTCTTTTTGA
1071 TTTTTTT
1 TTTTTTT
1078 ATTTTATCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 7 0.23
28 9 0.30
29 12 0.40
30 2 0.07
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTTTTTTCTTCTTTTTTTCTTTTTGA
Found at i:1111 original size:15 final size:15
Alignment explanation
Indices: 1016--1112 Score: 51
Period size: 15 Copynumber: 6.3 Consensus size: 15
1006 GTTTTACCTG
1016 TTTTCT-TTCTTCTTT
1 TTTTCTCTTCTT-TTT
*
1031 TTTTCTTTTTGCTTTCTT
1 TTTTC-TCTT-CTTT-TT
1049 TTTCTCTCTT-TTTATT
1 TTT-TCTCTTCTTT-TT
*
1065 TTTT-TATT-TTTTT
1 TTTTCTCTTCTTTTT
* *
1078 ATTTTATC-TCTATTAT
1 -TTTTCTCTTCT-TTTT
1094 TTTTCTCTTCTTTTT
1 TTTTCTCTTCTTTTT
1109 TTTT
1 TTTT
1113 TGTTATATCT
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
13 2 0.03
14 11 0.17
15 21 0.32
16 15 0.23
17 3 0.05
18 11 0.17
19 2 0.03
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.78
Consensus pattern (15 bp):
TTTTCTCTTCTTTTT
Found at i:1129 original size:46 final size:46
Alignment explanation
Indices: 1047--1134 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
1037 TTTTGCTTTC
* * *
1047 TTTTTCTCTCTTTTTATTTTTTTATTTTTTTATTTTATCTCTATTA
1 TTTTTCTCTCTTTTTATTTTTTTATATCTCTATTTTATCTCTATTA
1093 TTTTTCTCTTCTTTTT-TTTTTGTTATATCTCT-TTTTATCTCT
1 TTTTTCTC-TCTTTTTATTTTT-TTATATCTCTATTTTATCTCT
1135 GTGTTGTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 23 0.62
47 14 0.38
ACGTcount: A:0.10, C:0.14, G:0.01, T:0.75
Consensus pattern (46 bp):
TTTTTCTCTCTTTTTATTTTTTTATATCTCTATTTTATCTCTATTA
Found at i:2543 original size:49 final size:50
Alignment explanation
Indices: 2467--2601 Score: 175
Period size: 49 Copynumber: 2.7 Consensus size: 50
2457 GGTGTTTGAT
* *
2467 AATTTATGCATCTTAGTCAATGGTTATTTCTGATTTGGC-CACTGTTCTTT-
1 AATTTATGCAT-TTAGTCACTGTTTATTTCTGATTTGGCTCA-TGTTCTTTC
* *
2517 TATTTATGCATTTAGTCACTATTTATTTCTGATTTGGCTCATGTTCTTTC
1 AATTTATGCATTTAGTCACTGTTTATTTCTGATTTGGCTCATGTTCTTTC
* *
2567 AATTTATGCATTTTGGTCACTGTTTATTTATGATT
1 AATTTATGCA-TTTAGTCACTGTTTATTTCTGATT
2602 AAATCAACTA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 32 0.43
50 21 0.28
51 21 0.28
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (50 bp):
AATTTATGCATTTAGTCACTGTTTATTTCTGATTTGGCTCATGTTCTTTC
Found at i:4930 original size:32 final size:32
Alignment explanation
Indices: 4868--4930 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
4858 AAGGTAACCC
* * *
4868 TTGGGTAGGCTCTTAGGCCCCAAAGTACTCCA
1 TTGGGTAGGCGCTAAGGCCCCAAAGCACTCCA
* *
4900 TTGGGTAGGCGCTAAGGCCCTAAGGCACTCC
1 TTGGGTAGGCGCTAAGGCCCCAAAGCACTCC
4931 TTTAGGTTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.22
Consensus pattern (32 bp):
TTGGGTAGGCGCTAAGGCCCCAAAGCACTCCA
Found at i:7418 original size:65 final size:65
Alignment explanation
Indices: 7301--7482 Score: 199
Period size: 65 Copynumber: 2.8 Consensus size: 65
7291 GTGCACTAAC
* ** * * * **
7301 AGAGTGCATCGATACACTAG-GGGTGCATCGGTACACTAATTACATTCGATGTTTCAAAATAGCC
1 AGAGTGCATCGATGCA-TAGCTTGTGCATCGGTACACAAAATGCATTTAATGTTTCAAAATAGCC
7365 A
65 A
* **
7366 TA-AGTGCATCGATGCAT-GGTCTGTGCATCGGTACACAAAATGCATTTAATGTTTCAAAATATT
1 -AGAGTGCATCGATGCATAGCT-TGTGCATCGGTACACAAAATGCATTTAATGTTTCAAAATAGC
7429 CA
64 CA
*
7431 AGAGTGCATCGATGCATAGCTTATGCATCGGTACACAAAATGCATTTGAATG
1 AGAGTGCATCGATGCATAGCTTGTGCATCGGTACACAAAATGCATTT-AATG
7483 GGTGTGCATC
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 2 0.02
65 89 0.90
66 7 0.07
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (65 bp):
AGAGTGCATCGATGCATAGCTTGTGCATCGGTACACAAAATGCATTTAATGTTTCAAAATAGCCA
Found at i:10028 original size:23 final size:22
Alignment explanation
Indices: 9934--10031 Score: 64
Period size: 23 Copynumber: 4.5 Consensus size: 22
9924 AAACCCGACG
* *
9934 GATGTATCGATGCACA-ACAGA
1 GATGCATCGATGCACATTCAGA
*
9955 G-TGCAT-TATGCACATTCA-A
1 GATGCATCGATGCACATTCAGA
* *
9974 GGAATGCATCGGTGCATC-TTCA-T
1 -G-ATGCATCGATGCA-CATTCAGA
*
9997 GATGTATCGATGCACATTCAAGA
1 GATGCATCGATGCACATTC-AGA
10020 GATGCATCGATG
1 GATGCATCGATG
10032 TACTGTTTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
19 8 0.14
20 8 0.14
21 15 0.26
22 7 0.12
23 19 0.33
24 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (22 bp):
GATGCATCGATGCACATTCAGA
Found at i:12848 original size:16 final size:16
Alignment explanation
Indices: 12827--12857 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12817 ACATGTATCA
*
12827 CAAATTTTATCTTTGT
1 CAAATTTTAGCTTTGT
12843 CAAATTTTAGCTTTG
1 CAAATTTTAGCTTTG
12858 GCAACCCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (16 bp):
CAAATTTTAGCTTTGT
Found at i:15085 original size:19 final size:19
Alignment explanation
Indices: 15061--15114 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
15051 ATAAGACTTA
*
15061 GTGCATCGATACACTAGGG
1 GTGCATCGGTACACTAGGG
15080 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
15099 GTGCATCGGTACACTA
1 GTGCATCGGTACACTA
15115 ATTACGTTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (19 bp):
GTGCATCGGTACACTAGGG
Found at i:15234 original size:65 final size:65
Alignment explanation
Indices: 15100--15255 Score: 179
Period size: 65 Copynumber: 2.4 Consensus size: 65
15090 ACACTAGGGG
* * * * * *
15100 TGCATCGGTACACTAATTACGTTCGATGTTTCAAAATAGCCATGAGTGCATCGATGCACGGTCTA
1 TGCATCAGTACACAAAATACATTCGATGTTTCAAAATAGCCAAGAGTGCATCGATGCACGCTCTA
** * ** *
15165 TGCATTGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGACT-T
1 TGCATCAGTACACAAAATACATTCGATGTTTCAAAATAGCCAAGAGTGCATCGATGCACG-CTCT
*
15229 G
65 A
15230 TGCATCAGTACACAAAATACATTCGA
1 TGCATCAGTACACAAAATACATTCGA
15256 AATGGGTGTG
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 75 0.99
66 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (65 bp):
TGCATCAGTACACAAAATACATTCGATGTTTCAAAATAGCCAAGAGTGCATCGATGCACGCTCTA
Found at i:16431 original size:30 final size:33
Alignment explanation
Indices: 16391--16461 Score: 114
Period size: 30 Copynumber: 2.3 Consensus size: 33
16381 ATTTAAAAAA
16391 ATAA-TTTTTTGTATAATTT-AA-ATTTT-TTT
1 ATAATTTTTTTGTATAATTTAAATATTTTCTTT
16420 ATAATTTTTTTGTATAATTTAAATATTTTCTTT
1 ATAATTTTTTTGTATAATTTAAATATTTTCTTT
16453 ATAATTTTT
1 ATAATTTTT
16462 GGAAATGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 4 0.11
30 15 0.39
31 2 0.05
32 5 0.13
33 12 0.32
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (33 bp):
ATAATTTTTTTGTATAATTTAAATATTTTCTTT
Found at i:18721 original size:27 final size:27
Alignment explanation
Indices: 18683--18745 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
18673 GCTAAGTGAG
*
18683 AATACCATGGTTATGTCATGGTTCATC
1 AATACCATGGTTATGTCATGGCTCATC
18710 AATACCATGGTTATGTCATGGCTCATC
1 AATACCATGGTTATGTCATGGCTCATC
*
18737 AATTCCATG
1 AATACCATG
18746 ATTCCTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (27 bp):
AATACCATGGTTATGTCATGGCTCATC
Found at i:24694 original size:187 final size:186
Alignment explanation
Indices: 24372--24766 Score: 607
Period size: 187 Copynumber: 2.1 Consensus size: 186
24362 ATTAAATTTT
* *
24372 AAATATTAAATATATTATATATATAACATATGGACTTAGCCCAAACCATTTAAAACTCAATTAAT
1 AAATATTAAATATA-T-TATATATAACATATGGACTAAGCCCAAACCATTTAAAACCCAATTAAT
*
24437 AATTTAAGATTCAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAAT
64 AATTTAAGATTCAATAAATTTTAAACCTAAATCAATATTAATTAAATAAAAAATTTATATAAAAT
* *
24502 TTTTATTATATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTTAATTAAAA
129 TTTTATTATATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATT-AAA
*
24561 AAATATTAAATATATTATATATAACATAT-GAGCTAAGTCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGA-CTAAGCCCAAACCATTTAAAACCCAATTAATA
* * *
24625 ATTTAAGA-TCTAATAACTTTTAAACTTAAATCAATATTAATTAAATAAAAAATTTATATAAATT
65 ATTTAAGATTC-AATAAATTTTAAACCTAAATCAATATTAATTAAATAAAAAATTTATATAAAAT
* *
24689 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTTTGAATTAAA
129 TTTTATTATATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
* *
24747 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
24767 AATTCGAAAT
Statistics
Matches: 191, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
185 8 0.04
186 17 0.09
187 151 0.79
188 1 0.01
189 14 0.07
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (186 bp):
AAATATTAAATATATTATATATAACATATGGACTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATTCAATAAATTTTAAACCTAAATCAATATTAATTAAATAAAAAATTTATATAAAATTT
TTATTATATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
Found at i:27534 original size:19 final size:20
Alignment explanation
Indices: 27510--27553 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27500 AAAAAAGTTT
*
27510 TTTTTAAT-AATATATTTAA
1 TTTTTAATAAAAATATTTAA
*
27529 TTTTTAATAAAAATATTTTA
1 TTTTTAATAAAAATATTTAA
27549 TTTTT
1 TTTTT
27554 TAAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTAATAAAAATATTTAA
Found at i:27554 original size:21 final size:19
Alignment explanation
Indices: 27509--27556 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
27499 TAAAAAAGTT
*
27509 TTTTTTAATAATATATTTA
1 TTTTTTAATAAAATATTTA
*
27528 ATTTTTAATAAAAATATTTTA
1 TTTTTTAAT-AAAATA-TTTA
27549 TTTTTTAA
1 TTTTTTAA
27557 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTAATAAAATATTTA
Found at i:28184 original size:17 final size:18
Alignment explanation
Indices: 28145--28191 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
28135 TGTTTCTGAG
28145 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
28163 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
28180 GGAATTGGAATC
1 GGAATTGGAATC
28192 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:28869 original size:273 final size:266
Alignment explanation
Indices: 28584--29161 Score: 807
Period size: 273 Copynumber: 2.2 Consensus size: 266
28574 TTTCACCCCG
*
28584 ACCCGACCCGAAATAATAAAAAAATTATCTTTATTCAATAAAAACAATGACTTAATTGGAAAAAA
1 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAA
* * *
28649 ATATATATAGAGAGGGGTTTTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATTTTT
66 AT-TATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TATT
* *
28714 TGGGTCAGGTCGGGTCGGGTATTTTTCA-CCGAAACCCGAAC-CGACACGACCTGAATATCACAC
129 T---T----T-GGGTCGGGTATTTTTCACCCGAAACCAGAACTCGACACGACCCGAATATCACAC
*
28777 TTAAAAAAA-ACCGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCG-GATATATGA
186 TTAAAAAAATACCGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGCAATATATGA
28840 ATTAGAAATCC-GACCC
251 ATTAGAAA-CCTGACCC
*
28856 AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAA
1 -ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAA
*
28921 AATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
65 AATTATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
* *
28986 TTGGGTCGGGTATTTTTCACCCTAAACCAGAACTCGACCCGACCCGAATATCACACTTAAAAAAA
130 TTGGGTCGGGTATTTTTCACCCGAAACCAGAACTCGACACGACCCGAATATCACACTTAAAAAAA
* * * *
29051 TATCGATCTGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGACCCAAATATATGAATTAG
195 TACCGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCG---C-AATATATGAATTAG
29116 AAACCTGACCC
256 AAACCTGACCC
29127 A----ACCCGAAATAATAAAAAAA-TATTTTTATTCAATA
1 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATA
29162 TATGAATAAA
Statistics
Matches: 281, Mismatches: 15, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
263 17 0.06
264 12 0.04
265 44 0.16
266 60 0.21
268 1 0.00
270 3 0.01
271 25 0.09
272 54 0.19
273 65 0.23
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (266 bp):
ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAA
ATTATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTT
TGGGTCGGGTATTTTTCACCCGAAACCAGAACTCGACACGACCCGAATATCACACTTAAAAAAAT
ACCGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGCAATATATGAATTAGAAACC
TGACCC
Found at i:31490 original size:20 final size:20
Alignment explanation
Indices: 31465--31502 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31455 ACTCTTAAAC
*
31465 TTAAAATATTTTCAAAATAA
1 TTAAAAGATTTTCAAAATAA
*
31485 TTAAAAGATTTTTAAAAT
1 TTAAAAGATTTTCAAAAT
31503 TATTGGAAAC
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:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
TTAAAAGATTTTCAAAATAA
Found at i:35342 original size:35 final size:35
Alignment explanation
Indices: 35296--35390 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
35286 GCTGCCTAAT
*
35296 TTTGACC-AAATCAGCCACCCCATTTTCTGCCATC
1 TTTGACCAAAATCAGCCACCCCATTTTCTGCCACC
35330 TTTGACCAAAATCAGCCACCCCATTTTCTGCCACC
1 TTTGACCAAAATCAGCCACCCCATTTTCTGCCACC
* *
35365 TTGGACCAAAATCAGCCACCTCATTT
1 TTTGACCAAAATCAGCCACCCCATTT
35391 GCCATTTTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 7 0.12
35 50 0.88
ACGTcount: A:0.26, C:0.37, G:0.09, T:0.27
Consensus pattern (35 bp):
TTTGACCAAAATCAGCCACCCCATTTTCTGCCACC
Found at i:42284 original size:21 final size:22
Alignment explanation
Indices: 42243--42301 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
42233 AAAAAATGTT
*
42243 ATATAAAA-AAACAATAGACAA
1 ATATAAAATAAACAATAAACAA
*
42264 ATATAAAATAAATAA-AAACAA
1 ATATAAAATAAACAATAAACAA
42285 A-ATAATAAT-AACAATAA
1 ATATAA-AATAAACAATAA
42302 TAAATCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 8 0.25
21 19 0.59
22 5 0.16
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.19
Consensus pattern (22 bp):
ATATAAAATAAACAATAAACAA
Found at i:42362 original size:15 final size:15
Alignment explanation
Indices: 42268--42355 Score: 65
Period size: 15 Copynumber: 5.6 Consensus size: 15
42258 AGACAAATAT
42268 AAAATAAATAA-AAA
1 AAAATAAATAATAAA
42282 CAAAAT-AATAATAACA
1 -AAAATAAATAATAA-A
* *
42298 ATAATAAATCAAAAGAA
1 AAAATAAAT-AATA-AA
42315 TGAAAGATAAA-AATAAA
1 --AAA-ATAAATAATAAA
*
42332 TAAATAAATAATAAA
1 AAAATAAATAATAAA
42347 AAAATAAAT
1 AAAATAAAT
42356 CAAAAAACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.17
15 27 0.47
16 4 0.07
17 6 0.10
18 4 0.07
19 2 0.03
20 5 0.09
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAATAAATAATAAA
Found at i:42374 original size:49 final size:48
Alignment explanation
Indices: 42284--42398 Score: 119
Period size: 49 Copynumber: 2.4 Consensus size: 48
42274 AATAAAAACA
* *
42284 AAAT-AATAATAACAATAATAAATCAAAAGAATGAAAGATAAAAATAAAT
1 AAATAAATAATAA-AAAAATAAATCAAAAAAATGAAAGATAAAAA-AAAT
** *
42333 AAATAAATAATAAAAAAATAAATCAAAAAACATGTGA-ATAAAAAAATT
1 AAATAAATAATAAAAAAATAAATCAAAAAA-ATGAAAGATAAAAAAAAT
* *
42381 AAA-AAATATTAAATAAAT
1 AAATAAATAATAAAAAAAT
42399 CCAAGAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
47 13 0.23
48 6 0.11
49 26 0.46
50 12 0.21
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.22
Consensus pattern (48 bp):
AAATAAATAATAAAAAAATAAATCAAAAAAATGAAAGATAAAAAAAAT
Found at i:42395 original size:23 final size:23
Alignment explanation
Indices: 42321--42397 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 23
42311 AGAATGAAAG
* *
42321 ATAAAAATAAATAAATAAATAATAA
1 ATAAAAA-AATTAAA-AAATATTAA
* * *
42346 A-AAAATAAATCAAAAAACATGTGA
1 ATAAAA-AAATTAAAAAATAT-TAA
42370 ATAAAAAAATTAAAAAATATTAA
1 ATAAAAAAATTAAAAAATATTAA
42393 ATAAA
1 ATAAA
42398 TCCAAGAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
23 11 0.27
24 24 0.59
25 6 0.15
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (23 bp):
ATAAAAAAATTAAAAAATATTAA
Found at i:42927 original size:24 final size:25
Alignment explanation
Indices: 42897--42951 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
42887 TCACAAATGA
*
42897 AGAGAGATGGCGTGAGAGTGAGA-G
1 AGAGAGATGGCGTGAGAGAGAGATG
*
42921 AGAGAGATGGTGTGAGAGAGAGATG
1 AGAGAGATGGCGTGAGAGAGAGATG
42946 -GAGAGA
1 AGAGAGA
42952 ATTCTCTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.49, T:0.13
Consensus pattern (25 bp):
AGAGAGATGGCGTGAGAGAGAGATG
Found at i:43799 original size:36 final size:35
Alignment explanation
Indices: 43725--43840 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 35
43715 AACATGTTTC
* * * *
43725 AAAAACTATATAATATATATTTTCAATTTTTTTAAA
1 AAAAAATATATAATATATATTTTAAAATGTTTT-AA
43761 AAAAAATATATAATATATATTTTAAAAATGTTTTAA
1 AAAAAATATATAATATATATTTT-AAAATGTTTTAA
** * *
43797 AAACTATATATTATATA-AGTTTTCAAAATCGTTTTTA
1 AAAAAATATATAATATATA-TTTT-AAAAT-GTTTTAA
43834 AAAAAAT
1 AAAAAAT
43841 GTTTTAAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
35 1 0.02
36 47 0.71
37 18 0.27
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (35 bp):
AAAAAATATATAATATATATTTTAAAATGTTTTAA
Found at i:43878 original size:39 final size:38
Alignment explanation
Indices: 43830--43941 Score: 147
Period size: 39 Copynumber: 3.0 Consensus size: 38
43820 CAAAATCGTT
*
43830 TTTAAAAAAATGTTTTAAAAACTATATATTATATATAA
1 TTTACAAAAATGTTTTAAAAACTATATATTATATATAA
* * * *
43868 GTTTTCAAAAATATTTTAAAAGCTATATATTAGATAT-A
1 -TTTACAAAAATGTTTTAAAAACTATATATTATATATAA
*
43906 TTTAC-AAAATGTTTTAAAAACTATATAATATATATA
1 TTTACAAAAATGTTTTAAAAACTATATATTATATATA
43942 TATATATATA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
36 26 0.42
37 4 0.06
38 1 0.02
39 31 0.50
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (38 bp):
TTTACAAAAATGTTTTAAAAACTATATATTATATATAA
Found at i:43887 original size:90 final size:85
Alignment explanation
Indices: 43766--43925 Score: 214
Period size: 90 Copynumber: 1.8 Consensus size: 85
43756 TTAAAAAAAA
* * *
43766 ATATATAATATATATTTTAAAAATGTTTTAAAAACTATATATTATATA-AGTTTTCAAAATCGTT
1 ATATATAATATATATTTTAAAAATATTTTAAAAACTATATATTAGATATA-TTTACAAAAT-G-T
43830 TTTAAAAAAATGTTTTAAAAACT
63 TTTAAAAAAATGTTTTAAAAACT
* *
43853 ATATATTATATATAAGTTTTCAAAAATATTTTAAAAGCTATATATTAGATATATTTACAAAATGT
1 ATATATAATATAT-A-TTTT-AAAAATATTTTAAAAACTATATATTAGATATATTTACAAAATGT
43918 TTTAAAAA
63 TTTAAAAA
43926 CTATATAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
87 12 0.19
88 10 0.16
89 5 0.08
90 36 0.56
91 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (85 bp):
ATATATAATATATATTTTAAAAATATTTTAAAAACTATATATTAGATATATTTACAAAATGTTTT
AAAAAAATGTTTTAAAAACT
Found at i:43983 original size:44 final size:46
Alignment explanation
Indices: 43891--43988 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
43881 TTTTAAAAGC
* *
43891 TATATAT-TAGATATATTTACAAAATGTTTTAAAAACTATATAATA
1 TATATATATAGATATATTCACAAAATATTTTAAAAACTATATAATA
* * *
43936 TATATATATATATATATTCA-AAAATCATTTTCAAAGCTATATAATA
1 TATATATATAGATATATTCACAAAAT-ATTTTAAAAACTATATAATA
43982 TATATAT
1 TATATAT
43989 TTTAAAAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 12 0.26
46 34 0.74
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (46 bp):
TATATATATAGATATATTCACAAAATATTTTAAAAACTATATAATA
Found at i:44106 original size:2 final size:2
Alignment explanation
Indices: 44099--44131 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44089 CACTATATTA
44099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44132 ATAAAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45034 original size:86 final size:86
Alignment explanation
Indices: 44794--45966 Score: 1397
Period size: 86 Copynumber: 13.8 Consensus size: 86
44784 ATATGTCATC
* * * * ** ** *
44794 GAGCTGAATGGAATCGAACTCGACA-GT-TTTTGTTGACAGATAGCTTTTCTCAACTTAAGCTAT
1 GAGCTGAGTGTAATCAAACTCGA-AGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
* ** *
44857 GCTGTGAATTTGACATGCCCTT
65 GCTGTAAATTTGATGTGCCTTT
* * * * * * * *
44879 AAGCTGAATGGAATCAAACTCGAAGGTATTTT-TTGATAGATAACCCTTCTCGTCTTGAGTTATA
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
44943 CTGTAAATTTGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* *
44964 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCTCCTTGAGTTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
45029 TTGTAAATTTAATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * *
45050 GAGTTGAGTGTAATCAAACTCGAAGGTC-TTGGTTGACAAATAACCCTTCTCACCTTGAGTTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
45114 CTG---A--TG-TGT--CTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * * *
45127 GAGCTGGGTGTAATCAAACTTGAAGGTCTTTTGTTGACAGATAGCCCTTCTAGGCTTGAGCTATT
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
45192 CTGTAAATTTGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * *
45213 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACATATAACCCTTCTTGCCTTGAGTTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * *
45277 TTGTAAATTGGATGTGTCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * *
45298 GAGCTGAGTGTAATCTAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTTAGTTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
45363 CTGTAAATTTGATATGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * *
45384 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCTCCTTGAGTTATA
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
45448 CTGTAAATTGGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * *
45469 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTCATAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
45534 CTATAAATTGGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * * * *
45555 GAGTTGAGTGTAGTCGAACTCGAAAGTCTTTTGTTGATAGATAGCCCTTATCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
45620 CTATAAATTTGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * *
45641 GAGCTGAGTCTAATCGAACTCAAAGGTCTTTTTTTGACAGATAACCTTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
45706 CTGTAAATTTGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * * *
45727 GAGCTGAGTGCAA-CTGAACTCGAAGTTC-TTGGTTAACAGATAACCCTTCTCGCCTTGAGTTAT
1 GAGCTGAGTGTAATC-AAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
* * * *
45790 GCTATAAATTGGATATACCTTT
65 GCTGTAAATTTGATGTGCCTTT
* * * ** *
45812 GAGTTGAGTGTAATCAAACTCAAAGGTCTTTTGTTAACAGATAGTCCTTCTCTCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
45877 CTGTAAATTTGATGTGCGTTT
66 CTGTAAATTTGATGTGCCTTT
*
45898 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
45963 CTGT
66 CTGT
45967 CAATATTTCC
Statistics
Matches: 938, Mismatches: 133, Indels: 33
0.85 0.12 0.03
Matches are distributed among these distances:
77 29 0.03
78 31 0.03
79 3 0.00
80 1 0.00
81 1 0.00
82 1 0.00
83 2 0.00
84 4 0.00
85 347 0.37
86 519 0.55
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (86 bp):
GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
CTGTAAATTTGATGTGCCTTT
Found at i:45095 original size:171 final size:171
Alignment explanation
Indices: 44821--45966 Score: 1455
Period size: 171 Copynumber: 6.7 Consensus size: 171
44811 ACTCGACAGT
* ** ** * * ** * *
44821 TTTTGTTGACAGATAGCTTTTCTCAACTTAAGCTATGCTGTGAATTTGACATGCCCTTAAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
* * * * ** * * *
44886 ATGGAATCAAACTCGAAGGTATTTTTTGATAGATAACCCTTCTCGTCTTGAGTTATACTGTAAAT
66 GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
* *
44951 TTGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
131 TGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC
* * * * *
44992 TTTTGTTGACAGATAACCCTTCTCTCCTTGAGTTATGTTGTAAATTTAATGTGCCTTTGAGTTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
* * *
45057 GTGTAATCAAACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCACCTTGAGTTATGCTG---A-
66 GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
* **
45118 T-G-TGT--CTTTGAGCTGGGTGTAATCAAACTTGAAGGTC
131 TGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC
* * * *
45155 TTTTGTTGACAGATAGCCCTTCTAGGCTTGAGCTATTCTGTAAATTTGATGTGCCTTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
* * *
45220 GTGTAATCGAACTCGAAGGTCTTGGTTGACATATAACCCTTCTTGCCTTGAGTTATGTTGTAAAT
66 GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
* *
45285 TGGATGTGTCTTTGAGCTGAGTGTAATCTAACTCAAAGGTC
131 TGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC
* * *
45326 TTTTGTTGACAGATAACCCTTCTCGCCTTTAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
* *
45391 GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCTCCTTGAGTTATACTGTAAAT
66 GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
*
45456 TGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC
131 TGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC
* * * * * *
45497 TTTTGTTCATAGATAGCCCTTCTCGCCTTGAGCTATGCTATAAATTGGATGTGCCTTTGAGTTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
* * * * * * * *
45562 GTGTAGTCGAACTCGAAAGTCTTTTGTTGATAGATAGCCCTTATCGCCTTGAGCTATGCTATAAA
66 GTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
* * *
45627 TTTGATGTGCCTTTGAGCTGAGTCTAATCGAACTCAAAGGTC
130 TTGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC
* *
45669 TTTTTTTGACAGATAACCTTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
* * * *
45734 GTGCAA-CTGAACTCGAAGTTCTTGGTTAACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAA
66 GTGTAATC-GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
* * *
45798 TTGGATATACCTTTGAGTTGAGTGTAATCAAACTCAAAGGTC
130 TTGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC
* ** * *
45840 TTTTGTTAACAGATAGTCCTTCTCTCCTTGAGCTATGCTGTAAATTTGATGTGCGTTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
* * * *
45905 GTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
66 GTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
45967 CAATATTTCC
Statistics
Matches: 841, Mismatches: 122, Indels: 23
0.85 0.12 0.02
Matches are distributed among these distances:
163 141 0.17
165 3 0.00
166 2 0.00
167 2 0.00
168 2 0.00
169 3 0.00
171 507 0.60
172 181 0.22
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (171 bp):
TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
TGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC
Found at i:45565 original size:257 final size:257
Alignment explanation
Indices: 44821--45966 Score: 1445
Period size: 257 Copynumber: 4.5 Consensus size: 257
44811 ACTCGACAGT
** * * * * * *
44821 TTTTGTTGACAGATAGCTTTTCTCAACTTAAGCTATGCTGTGAATTTGACATGCCCTTAAGCTGA
1 TTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGA
* * * * * *
44886 ATGGAATCAAACTCGAAGGTATTTT-TTGATAGATAACCCTTCTCGTCTTGAGTTATACTGTAAA
66 GTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGTAAA
*
44950 TTTGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCT
131 TTTGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCT
* * * ** *
45015 CTCCTTGAGTTATGTTGTAAATTTAATGTGCCTTTGAGTTGAGTGTAATCAAACTCGAAGGTC
195 CGCCTTGAGTTATGCTATAAATTGGATGTGCCTTTGAGTTGAGTGTAATCAAACTCAAAGGTC
* * * * * *
45078 -TTGGTTGACAAATAACCCTTCTCACCTTGAGTTATGCTG---A--TG---TGTCTTTGAGCTGG
1 TTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGA
* * * * *
45134 GTGTAATCAAACTTGAAGGTCTTTTGTTGACAGATAGCCCTTCTAGGCTTGAGCTATTCTGTAAA
66 GTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGTAAA
* * *
45199 TTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACATATAACCCTTCTT
131 TTTGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTC
* * * * *
45264 GCCTTGAGTTATGTTGTAAATTGGATGTGTCTTTGAGCTGAGTGTAATCTAACTCAAAGGTC
196 GCCTTGAGTTATGCTATAAATTGGATGTGCCTTTGAGTTGAGTGTAATCAAACTCAAAGGTC
* * * *
45326 TTTTGTTGACAGATAACCCTTCTCGCCTTTAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGA
1 TTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGA
* * * *
45391 GTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCTCCTTGAGTTATACTGTAAA
66 GTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGTAAA
* * * * *
45455 TTGGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTCATAGATAGCCCTTCT
131 TTTGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCT
* * *
45520 CGCCTTGAGCTATGCTATAAATTGGATGTGCCTTTGAGTTGAGTGTAGTCGAACTCGAAA-GTC
195 CGCCTTGAGTTATGCTATAAATTGGATGTGCCTTTGAGTTGAGTGTAATCAAACTC-AAAGGTC
* * * * *
45583 TTTTGTTGATAGATAGCCCTTATCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTTGAGCTGA
1 TTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGA
* * * * * *
45648 GTCTAATCGAACTCAAAGGTCTTTTTTTGACAGATAACCTTTCTCGCCTTGAGCTATGCTGTAAA
66 GTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGTAAA
* * * *
45713 TTTGATGTGCCTTTGAGCTGAGTGCAA-CTGAACTCGAAGTTCTTGGTTAACAGATAACCCTTCT
131 TTTGATGTGCCTTTGAGCTGAGTGTAATC-AAACTCGAAGGTCTTGGTTGACAGATAACCCTTCT
* *
45777 CGCCTTGAGTTATGCTATAAATTGGATATACCTTTGAGTTGAGTGTAATCAAACTCAAAGGTC
195 CGCCTTGAGTTATGCTATAAATTGGATGTGCCTTTGAGTTGAGTGTAATCAAACTCAAAGGTC
* * * * *
45840 TTTTGTTAACAGATAGTCCTTCTCTCCTTGAGCTATGCTGTAAATTTGATGTGCGTTTGAGCTGA
1 TTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGA
* *
45905 GTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
66 GTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGT
45967 CAATATTTCC
Statistics
Matches: 770, Mismatches: 104, Indels: 30
0.85 0.12 0.03
Matches are distributed among these distances:
248 106 0.14
249 109 0.14
251 2 0.00
252 1 0.00
253 1 0.00
254 2 0.00
256 110 0.14
257 363 0.47
258 76 0.10
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (257 bp):
TTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGA
GTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGTAAA
TTTGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTC
GCCTTGAGTTATGCTATAAATTGGATGTGCCTTTGAGTTGAGTGTAATCAAACTCAAAGGTC
Found at i:47377 original size:96 final size:96
Alignment explanation
Indices: 47205--47406 Score: 293
Period size: 96 Copynumber: 2.1 Consensus size: 96
47195 TGACAGCTCA
*
47205 ATAT-TATAATCACCTTTATCAGGCTAGCTGACTCTTATCCATAAAGCTGGGGCGTTTAACCAAT
1 ATATATATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAAT
* *
47269 TGCATTAGAGGGACAGCTCAAGCTTTATTGT
66 TGCATTAGAGGGACAGATCAAGCTTTATTAT
*
47300 AT-TATAATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGTGTTTAACCAA
1 ATATAT-ATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAA
* * **
47364 TTTC-TCTATAGGGATGGATCAAGCTTTATTAT
65 TTGCAT-TAGAGGGACAGATCAAGCTTTATTAT
47396 ATATATATAAT
1 ATATATATAAT
47407 TATAATTTGG
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
94 1 0.01
95 4 0.04
96 87 0.92
97 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (96 bp):
ATATATATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAAT
TGCATTAGAGGGACAGATCAAGCTTTATTAT
Found at i:49982 original size:34 final size:35
Alignment explanation
Indices: 49942--50009 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
49932 TAATAACAAT
*
49942 AATAAATCAAAAGA-ATGAAAGATA-AAAATAAATA
1 AATAAATCAAAA-ATATGAAAAATATAAAATAAATA
* *
49976 AATAAATGAAAAATATGAAAAATATTAAATAAAT
1 AATAAATCAAAAATATGAAAAATATAAAATAAAT
50010 CCAATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.03
34 20 0.69
35 8 0.28
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.22
Consensus pattern (35 bp):
AATAAATCAAAAATATGAAAAATATAAAATAAATA
Found at i:51407 original size:36 final size:36
Alignment explanation
Indices: 51314--51504 Score: 217
Period size: 36 Copynumber: 5.2 Consensus size: 36
51304 AATAATAAAA
*
51314 TTAAAAATGTTTCAAAAACTATATAATAT-T-TATT
1 TTAAAAATGTTTTAAAAACTATATAATATATATATT
*
51348 TTCAAAAAATATTTTTAAAAACTATATAATATATATATT
1 TT--AAAAAT-GTTTTAAAAACTATATAATATATATATT
*
51387 TTAAAAATGTTTTAAAAACTATATATTATATATATT
1 TTAAAAATGTTTTAAAAACTATATAATATATATATT
* *
51423 TTCAAAATGTTTTAAAAACTTTATAATATATATATTTT
1 TTAAAAATGTTTTAAAAACTATATAATATATATA--TT
* * * *
51461 TTCAAAAATCATTTTCAAAGCTATATATTATATAT-TT
1 TT-AAAAAT-GTTTTAAAAACTATATAATATATATATT
51498 TTAAAAA
1 TTAAAAA
51505 AAAACCGATT
Statistics
Matches: 135, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
34 2 0.01
36 68 0.50
37 29 0.21
38 5 0.04
39 11 0.08
40 20 0.15
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.46
Consensus pattern (36 bp):
TTAAAAATGTTTTAAAAACTATATAATATATATATT
Found at i:51615 original size:10 final size:11
Alignment explanation
Indices: 51602--51644 Score: 65
Period size: 10 Copynumber: 4.2 Consensus size: 11
51592 AAAATTACAC
51602 TATAT-TAATA
1 TATATATAATA
51612 TATATAT-ATA
1 TATATATAATA
51622 TATATATAATA
1 TATATATAATA
51633 TA-ATATAATA
1 TATATATAATA
51643 TA
1 TA
51645 ATAAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 25 0.81
11 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATATAATA
Found at i:51616 original size:2 final size:2
Alignment explanation
Indices: 51609--51644 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
51599 CACTATATTA
51609 AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51645 ATAAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:51648 original size:8 final size:9
Alignment explanation
Indices: 51602--51647 Score: 53
Period size: 8 Copynumber: 5.2 Consensus size: 9
51592 AAAATTACAC
51602 TATAT-TAA
1 TATATATAA
51610 TATATAT-A
1 TATATATAA
51618 TATATAT-A
1 TATATATAA
51626 TATAATATAA
1 TAT-ATATAA
51636 TATAATATAA
1 TAT-ATATAA
51646 TA
1 TA
51648 AAAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 17 0.49
9 5 0.14
10 13 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TATATATAA
Found at i:53929 original size:34 final size:30
Alignment explanation
Indices: 53851--53931 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 30
53841 GATTTTCATA
53851 AAATAAATAAATATTATTTATATATATTTAT
1 AAAT-AATAAATATTATTTATATATATTTAT
53882 AAGACTTAGATAAATATTATTTATATATATATTGACAT
1 AA-A--TA-ATAAATATTATTTATATATAT-TT---AT
53920 AAATAATAAATA
1 AAATAATAAATA
53932 ATAATAGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
31 2 0.05
32 1 0.02
33 1 0.02
34 29 0.69
35 4 0.10
37 1 0.02
38 4 0.10
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (30 bp):
AAATAATAAATATTATTTATATATATTTAT
Found at i:53969 original size:16 final size:16
Alignment explanation
Indices: 53945--53975 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53935 ATAGTAATAC
*
53945 TAATGATAAATATATA
1 TAATCATAAATATATA
53961 TAATCATAAATATAT
1 TAATCATAAATATAT
53976 GAAAGTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TAATCATAAATATATA
Found at i:55427 original size:25 final size:26
Alignment explanation
Indices: 55381--55430 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
55371 CATTTGGGCT
* *
55381 CTGTTGGGCTATTTGAAGTTGGGTCA
1 CTGTTGGGCCATCTGAAGTTGGGTCA
55407 CTGTTGGGCCATCTGAA-TTGGGTC
1 CTGTTGGGCCATCTGAAGTTGGGTC
55431 TGGAACTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.14, C:0.16, G:0.34, T:0.36
Consensus pattern (26 bp):
CTGTTGGGCCATCTGAAGTTGGGTCA
Found at i:55475 original size:3 final size:3
Alignment explanation
Indices: 55467--55530 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
55457 GGCCTGTTTG
**
55467 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
55513 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
55531 CAAATAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:56066 original size:2 final size:2
Alignment explanation
Indices: 56059--56087 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56049 TTGACCGAAG
56059 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
56088 TGACGGTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58539 original size:3 final size:3
Alignment explanation
Indices: 58525--58554 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
58515 ATATAATGGA
58525 AAT AATT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
58555 CTATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60458 original size:2 final size:2
Alignment explanation
Indices: 60453--60505 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
60443 AAAAACATAA
60453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60495 AT AT AT AT AT A
1 AT AT AT AT AT A
60506 ATGTATAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60546 original size:39 final size:37
Alignment explanation
Indices: 60497--60814 Score: 319
Period size: 37 Copynumber: 8.6 Consensus size: 37
60487 ATATATATAT
*
60497 ATATATATAATGTATAGTTTTTGAAAATATTTTGAAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTG-AAA
* *
60535 CATATATATAATGTATAGTTTTTGAAAACATTTTGAAA
1 -ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
*
60573 ACT-TATATATTATATAG-TTTTGAAAATATTTTTGAAA
1 A-TATATATAATATATAGTTTTTGAAAATA-TTTTGAAA
** *
60610 ATATATATAATATATAGTTTTTTTAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
* *
60647 ATGTATATAATATATAGTTTTTAAAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
*
60684 ATATATATAATATACA-TTTTTGAAAATATTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATA-TTTTGAAA
* * *
60721 ATATATAT--TATATAG-TTTTAAAAACAATTTTTAAA
1 ATATATATAATATATAGTTTTTGAAAA-TATTTTGAAA
** * * *
60756 A-ATATATTTTATAT-GGTTTTGAAAACATTTATAAAAAA
1 ATATATATAATATATAGTTTTTGAAAATATTT-T--GAAA
* *
60794 ACATATATGATATATAGTTTT
1 ATATATATAATATATAGTTTT
60815 AAAAAGGATT
Statistics
Matches: 239, Mismatches: 25, Indels: 29
0.82 0.09 0.10
Matches are distributed among these distances:
34 6 0.03
35 26 0.11
36 37 0.15
37 106 0.44
38 16 0.07
39 44 0.18
40 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
Found at i:62151 original size:7 final size:7
Alignment explanation
Indices: 62139--62250 Score: 55
Period size: 7 Copynumber: 14.4 Consensus size: 7
62129 ATTTATTTTC
62139 TTTTATT
1 TTTTATT
62146 TTTTATT
1 TTTTATT
62153 TAAACTTTATT
1 T----TTTATT
*
62164 TTGTATT
1 TTTTATT
62171 TTTTAAATT
1 TTTT--ATT
*
62180 TTTAAATT
1 TTT-TATT
62188 TTTGTATT
1 TTT-TATT
**
62196 TTTTAAA
1 TTTTATT
62203 TTTTA-T
1 TTTTATT
62209 TTTTATT
1 TTTTATT
**
62216 TCATATT
1 TTTTATT
62223 TATTTATT
1 T-TTTATT
62231 TATTTATTT
1 T-TTTA-TT
62240 ATTTTATT
1 -TTTTATT
62248 TTT
1 TTT
62251 GCAATCTTAC
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
6 5 0.06
7 33 0.40
8 24 0.29
9 12 0.15
10 1 0.01
11 7 0.09
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (7 bp):
TTTTATT
Found at i:62228 original size:4 final size:4
Alignment explanation
Indices: 62219--62248 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
62209 TTTTATTTCA
62219 TATT TATT TATT TATT TATT TATTT TATT T
1 TATT TATT TATT TATT TATT TA-TT TATT T
62249 TTGCAATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:62236 original size:12 final size:13
Alignment explanation
Indices: 62202--62248 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
62192 TATTTTTTAA
62202 ATTTTA-TT-TTT
1 ATTTTATTTATTT
62213 ATTTCATATTTATTT
1 ATTT--TATTTATTT
62228 A-TTTATTTATTT
1 ATTTTATTTATTT
62240 ATTTTATTT
1 ATTTTATTT
62249 TTGCAATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 4 0.13
12 10 0.32
13 9 0.29
14 4 0.13
15 4 0.13
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:65043 original size:13 final size:13
Alignment explanation
Indices: 65011--65044 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
65001 TAAGATTTTC
65011 TTTGAAAATCATT
1 TTTGAAAATCATT
65024 TTT-AAAATCATT
1 TTTGAAAATCATT
65036 TTTGAAAAT
1 TTTGAAAAT
65045 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:68097 original size:64 final size:64
Alignment explanation
Indices: 68018--68162 Score: 177
Period size: 64 Copynumber: 2.3 Consensus size: 64
68008 AAATGAGCCT
* * * * **
68018 GGAGTGCATCAATGCATG-GTCTGTGTATCGGTACATAAAATGCATTCGATGTTCAAAATATTCA
1 GGAGTGCATCGATGCATGCCT-TGTGCATCGGTACACAAAATGCATTCGAAATTCAAAATATTCA
**
68082 GGAGTGCATCGATGCATGCCTTGTGCATCGGTACACAAAATGCATTCGAAATTCAATTTATTCA
1 GGAGTGCATCGATGCATGCCTTGTGCATCGGTACACAAAATGCATTCGAAATTCAAAATATTCA
*
68146 -AAGGTGCATCGATGCAT
1 GGA-GTGCATCGATGCAT
68163 TAGATGGTGC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 1 0.01
64 68 0.97
65 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (64 bp):
GGAGTGCATCGATGCATGCCTTGTGCATCGGTACACAAAATGCATTCGAAATTCAAAATATTCA
Found at i:75519 original size:316 final size:318
Alignment explanation
Indices: 74917--75873 Score: 1580
Period size: 316 Copynumber: 3.0 Consensus size: 318
74907 TCTGATACCA
* *
74917 CTAAATGTAACCCCCTCAAATCGATACGGATAGCCCGATCCGATCTGGAGTGTCACATTAGGGCC
1 CTAAATGTAACCCCCTCAAACCGATGCGGATAGCCCGATCCGATCTGGAGTGTCACATTAGGGCC
* *
74982 ACCGGAGTGACCCACCGTAAAAATAGCGAAAAATTTAAAACTTTTCTT-AAACTTGTAAACTCAT
66 ACTGGAGCGACCCACCGTAAAAATAGC-AAAAATTTAAAACTTTTCTTAAAACTTGTAAACTCAT
75046 AAAATTATTTATGAGTACAAAATAAAAGTTATTAGTATTCGAAATAAACCAGATTTTCAGACTCA
130 AAAATTATTTATGAGTACAAAATAAAAGTTATTAGTATTCGAAATAAACCAGATTTTCAGACTCA
*
75111 TATATAAAACAAAATATAATTACATTCCCCCTAATCATATGTACCATACTCTAGAAACTACGCCG
195 -ATATAAAACAAAATATAATTACATGCCCCCTAATCATATGTACCATACTCT-GAAACTACGCCG
* * *
75176 GAAGAGCTCCCTTACTAAATTCGATAGATGCACTGGTATAATTCTTTTAACCTCCAATGGT
258 GAAGAGCTCCCTTACTGAATTCGATAGATGCACTGGTACAATTCTTTTAACCTACAATGGT
*
75237 CTAAATGTAACCCCCTCAAACCGATGCAGATAGCCCGATCCGATCTGGAGTGTCACATTA-GGCC
1 CTAAATGTAACCCCCTCAAACCGATGCGGATAGCCCGATCCGATCTGGAGTGTCACATTAGGGCC
*
75301 ACTGGAGCGACCCACCGT-AAAATAGCAAAAATTTAAAACTTTTCTTAAAACCTGTAAACTCATA
66 ACTGGAGCGACCCACCGTAAAAATAGCAAAAATTTAAAACTTTTCTTAAAACTTGTAAACTCATA
75365 AAATTATTTATGAGTACAAAATAAAAGTTATTAGTATTCGAAATAAACCAGATTTTCAGACTC-A
131 AAATTATTTATGAGTACAAAATAAAAGTTATTAGTATTCGAAATAAACCAGATTTTCAGACTCAA
75429 TATAAAACAAAATATAATTACATGCCCCCTAATCATATGTACCATACTCTGCAAACTACGCCGGA
196 TATAAAACAAAATATAATTACATGCCCCCTAATCATATGTACCATACTCTG-AAACTACGCCGGA
* *
75494 AGAGCTCCCTTACTGAATTCGATAGATGCACTAGTACAATTCTTTTAACCTATAATGGT
260 AGAGCTCCCTTACTGAATTCGATAGATGCACTGGTACAATTCTTTTAACCTACAATGGT
* * * * *
75553 CTAAATATAACCCCCTCAAACTGATGCGGATAGCCTGATCTGATCTGGAGTGTCATATTAGGGCC
1 CTAAATGTAACCCCCTCAAACCGATGCGGATAGCCCGATCCGATCTGGAGTGTCACATTAGGGCC
**
75618 ACTGGAGCGACCCACCGTAAAAATAGCAGAAAATTTAAATTTTTTCTTAAAACTTGTAAACTCAT
66 ACTGGAGCGACCCACCGTAAAAATAGCA-AAAATTTAAAACTTTTCTTAAAACTTGTAAACTCAT
*
75683 AATATTATTTATGAGTACAAAATAAAAGTTATTAGTATTCGAAATAAACCAGATTTTCAGACTCA
130 AAAATTATTTATGAGTACAAAATAAAAGTTATTAGTATTCGAAATAAACCAGATTTTCAGACTCA
* * * * *
75748 TATATAAAACAAAATATAATTACATGACCCCTAATCACATATATCATACACTGTAAACTACGCCG
195 -ATATAAAACAAAATATAATTACATGCCCCCTAATCATATGTACCATACTCTG-AAACTACGCCG
* *
75813 GAAGAGCTCCCTTACTGAATTCGATAGATGCACTGGTACAATTCTTTTAGCCTGCAATGGT
258 GAAGAGCTCCCTTACTGAATTCGATAGATGCACTGGTACAATTCTTTTAACCTACAATGGT
75874 GAGTAATAGA
Statistics
Matches: 598, Mismatches: 32, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
315 1 0.00
316 171 0.29
317 42 0.07
318 96 0.16
319 116 0.19
320 57 0.10
321 115 0.19
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (318 bp):
CTAAATGTAACCCCCTCAAACCGATGCGGATAGCCCGATCCGATCTGGAGTGTCACATTAGGGCC
ACTGGAGCGACCCACCGTAAAAATAGCAAAAATTTAAAACTTTTCTTAAAACTTGTAAACTCATA
AAATTATTTATGAGTACAAAATAAAAGTTATTAGTATTCGAAATAAACCAGATTTTCAGACTCAA
TATAAAACAAAATATAATTACATGCCCCCTAATCATATGTACCATACTCTGAAACTACGCCGGAA
GAGCTCCCTTACTGAATTCGATAGATGCACTGGTACAATTCTTTTAACCTACAATGGT
Found at i:80340 original size:83 final size:84
Alignment explanation
Indices: 80201--80599 Score: 497
Period size: 84 Copynumber: 4.7 Consensus size: 84
80191 GTATTACAGT
* *
80201 ATAGCTCAA-GAGAGAAGGGCTATCTGTCAAAAACAACCTTCGAGTTCGATTCCATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCACAAA-AACCTTCGAGTTCGATTCCATTCAGCTCAA
80265 GGCCATATC-AATTTAAAGC
65 GGCCATATCAAATTTAAAGC
*
80284 ATAGCTCAAGGCGAGAAGGGCTATTTGTCACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAAG
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAAG
80349 GCCATATCAAATTTATAA-C
66 GCCATATCAAATTTA-AAGC
* * * *
80368 ATAGCTCAAGGCGAGAAGGGCTATTTTTGTCAACAAAAATCTTCGAGTTCAATTCCATTCAGCTA
1 ATAGCTCAAGGCGAGAAGGGCTA--TCTGTC-ACAAAAACCTTCGAGTTCGATTCCATTCAGCTC
* * *
80433 AAGGGCTTATCAAAATTTACAGC
63 AAGGCCATATC-AAATTTAAAGC
* * *
80456 ATAGCTTAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTTGAGTTCGATTCCATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTC-ACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAA
*
80521 GG-CA-ATCAAA-TTACAGC
65 GGCCATATCAAATTTAAAGC
* * ** * *
80538 ATAGCACAAGGCGACAATTGCTATCTGTC-CACAAAACCTTCAAGTTCAATTCCATTCAGCTC
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCACA-AAAACCTTCGAGTTCGATTCCATTCAGCTC
80600 TATGACAGCG
Statistics
Matches: 281, Mismatches: 26, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
80 2 0.01
81 27 0.10
82 30 0.11
83 51 0.18
84 54 0.19
85 3 0.01
86 45 0.16
87 40 0.14
88 29 0.10
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (84 bp):
ATAGCTCAAGGCGAGAAGGGCTATCTGTCACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAAG
GCCATATCAAATTTAAAGC
Found at i:81269 original size:35 final size:34
Alignment explanation
Indices: 81217--81520 Score: 191
Period size: 34 Copynumber: 8.8 Consensus size: 34
81207 ATCGGTTTTG
81217 AAATATATATAATATATAGTTTTTGAAAACATTTTAA
1 AAATATATAT-A-ATATAG-TTTTGAAAACATTTTAA
*
81254 AAACATATATAATATATAGTTTTTGAAAACATTTTGAA
1 AAATATATAT-A-ATATAG-TTTTGAAAACATTTT-AA
* * * *
81292 AACT-TATATTATATAGTTTTGAAAATATTTTTGA
1 AAATATATATAATATAGTTTTGAAAACA-TTTTAA
* *
81326 AAATATATATAATATATAGTTTT--AAA-ATCTT-G
1 AAATATATAT-A-ATATAGTTTTGAAAACATTTTAA
* *
81358 AAATATATAT-ATATAGTTTTGAAAATATTTT-G
1 AAATATATATAATATAGTTTTGAAAACATTTTAA
* * *
81390 AAATATATAAAATTATAGTTTT-AAAATATTTTTGA
1 AAATATATATAA-TATAGTTTTGAAAACA-TTTTAA
*
81425 AAATATAT-T-ATAT-GTTTTAAAAACAGTTTTTTAA
1 AAATATATATAATATAGTTTTGAAAACA---TTTTAA
* * *
81459 AAATATATATTTTATATGGTTTTG-AAACATTTAAA
1 AAATATATA--TAATATAGTTTTGAAAACATTTTAA
* * *
81494 AAACATATGATGATATAGTTTTTAAAA
1 AAATATAT-ATAATATAGTTTTGAAAA
81521 ATGCTTTTTA
Statistics
Matches: 223, Mismatches: 22, Indels: 46
0.77 0.08 0.16
Matches are distributed among these distances:
29 10 0.04
31 8 0.04
32 32 0.14
33 11 0.05
34 52 0.23
35 41 0.18
36 1 0.00
37 50 0.22
38 13 0.06
39 5 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (34 bp):
AAATATATATAATATAGTTTTGAAAACATTTTAA
Found at i:81270 original size:37 final size:34
Alignment explanation
Indices: 81212--81520 Score: 219
Period size: 37 Copynumber: 8.9 Consensus size: 34
81202 GAAACATCGG
*
81212 TTTTGAAATATATATAATATATAGTTTTTGAAAACA
1 TTTT-AAAAATATATAATATATAG-TTTTGAAAACA
81248 TTTTAAAAACATATATAATATATAGTTTTTGAAAACA
1 TTTT-AAAA-ATATATAATATATAG-TTTTGAAAACA
* * *
81285 TTTTGAAAACT-TATATTATATAGTTTTGAAAATA
1 TTTT-AAAAATATATAATATATAGTTTTGAAAACA
81319 TTTTTGAAAATATATATAATATATAGTTTT--AAA-A
1 -TTTT-AAAA-ATATATAATATATAGTTTTGAAAACA
* * *
81353 TCTT-GAAATATAT-ATATATAGTTTTGAAAATA
1 TTTTAAAAATATATAATATATAGTTTTGAAAACA
* * *
81385 TTTT-GAAATATATAAAATTATAGTTTT-AAAATA
1 TTTTAAAAATATATAATA-TATAGTTTTGAAAACA
* *
81418 TTTTTGAAAATATAT--TATAT-GTTTTAAAAACA
1 -TTTTAAAAATATATAATATATAGTTTTGAAAACA
* *
81450 GTTTTTTAAAAATATATATTTTATATGGTTTTG-AAACA
1 ---TTTTAAAAATATATA--ATATATAGTTTTGAAAACA
* * * *
81488 TTTAAAAAACATATGATGATATAGTTTTTAAAA
1 TTTTAAAAATATATAAT-ATATAGTTTTGAAAA
81521 ATGCTTTTTA
Statistics
Matches: 229, Mismatches: 23, Indels: 43
0.78 0.08 0.15
Matches are distributed among these distances:
29 12 0.05
30 6 0.03
31 10 0.04
32 21 0.09
33 13 0.06
34 47 0.21
35 46 0.20
36 9 0.04
37 50 0.22
38 10 0.04
39 5 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (34 bp):
TTTTAAAAATATATAATATATAGTTTTGAAAACA
Found at i:81556 original size:15 final size:15
Alignment explanation
Indices: 81536--81579 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
81526 TTTTATTTTA
81536 TTTTATATTAATATT
1 TTTTATATTAATATT
81551 TTTTATATT--TATT
1 TTTTATATTAATATT
*
81564 ATTT-TATTAATATT
1 TTTTATATTAATATT
81578 TT
1 TT
81580 CCCTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 5 0.20
15 9 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATATTAATATT
Found at i:81571 original size:27 final size:25
Alignment explanation
Indices: 81525--81579 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
81515 TTAAAAATGC
81525 TTTTTATTTTATTTTATATTAATAT
1 TTTTTATTTTATTTTATATTAATAT
*
81550 TTTTTATATTTATTATTTTATTAATAT
1 TTTTTAT-TTTATT-TTATATTAATAT
81577 TTT
1 TTT
81580 CCCTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 7 0.26
26 6 0.22
27 14 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTTATTTTATTTTATATTAATAT
Found at i:82903 original size:18 final size:17
Alignment explanation
Indices: 82863--82913 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
82853 TTAAAAAAAA
82863 GTTTTATTTTTTATTT-T
1 GTTTTATTTTTT-TTTAT
82880 GTTTTATTTTTTTTTAT
1 GTTTTATTTTTTTTTAT
* *
82897 TTATTTATTTATTTTTA
1 GT-TTTATTTTTTTTTA
82914 CAATCTGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 14 0.47
18 13 0.43
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (17 bp):
GTTTTATTTTTTTTTAT
Found at i:82913 original size:10 final size:10
Alignment explanation
Indices: 82865--82913 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
82855 AAAAAAAAGT
82865 TTTATTTTTTA
1 TTTA-TTTTTA
82876 TTT-TGTTTTA
1 TTTAT-TTTTA
*
82886 TTTTTTTTTA
1 TTTATTTTTA
82896 TTTA--TTTA
1 TTTATTTTTA
82904 TTTATTTTTA
1 TTTATTTTTA
82914 CAATCTGACA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
8 8 0.24
9 1 0.03
10 20 0.61
11 4 0.12
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (10 bp):
TTTATTTTTA
Done.