Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014780.1 Kokia drynarioides strain JFW-HI SEQ_129822, 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: 136343
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 210 characters in sequence are not A, C, G, or T
Found at i:132 original size:20 final size:20
Alignment explanation
Indices: 100--159 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
90 TACATTTCTT
*
100 TCATTCTTTTTTCTTTCCTC
1 TCATTCTTCTTTCTTTCCTC
*
120 TCCTTCTTCTTTCTTTCCTC
1 TCATTCTTCTTTCTTTCCTC
*
140 TCATTCTTCCTTTATTTCCT
1 TCATTCTT-CTTTCTTTCCT
160 TTCTTGCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 25 0.71
21 10 0.29
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (20 bp):
TCATTCTTCTTTCTTTCCTC
Found at i:18979 original size:6 final size:6
Alignment explanation
Indices: 18970--18996 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18960 TTTGACTTTG
18970 GGTTCA GGTTCA GGTTCA GGTTCA GGT
1 GGTTCA GGTTCA GGTTCA GGTTCA GGT
18997 ACGGGTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.37, T:0.33
Consensus pattern (6 bp):
GGTTCA
Found at i:19003 original size:18 final size:18
Alignment explanation
Indices: 18970--19004 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18960 TTTGACTTTG
*
18970 GGTTCAGGTTCAGGTTCA
1 GGTTCAGGTACAGGTTCA
*
18988 GGTTCAGGTACGGGTTC
1 GGTTCAGGTACAGGTTC
19005 GATTTTATCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.17, G:0.37, T:0.31
Consensus pattern (18 bp):
GGTTCAGGTACAGGTTCA
Found at i:27711 original size:26 final size:28
Alignment explanation
Indices: 27675--27732 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
27665 TACATGGACC
* * *
27675 GATTGTTTAACTA-GTAGACAATATAA-
1 GATTATTTAACTACATAAACAATATAAT
27701 GATTATTTAACTACATAAACAATATAAT
1 GATTATTTAACTACATAAACAATATAAT
27729 GATT
1 GATT
27733 TTGCCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 12 0.44
27 11 0.41
28 4 0.15
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (28 bp):
GATTATTTAACTACATAAACAATATAAT
Found at i:27797 original size:21 final size:21
Alignment explanation
Indices: 27773--27812 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27763 TAAAACGACG
**
27773 TAGTTTTGCCTTTTAACTTAA
1 TAGTTTTAACTTTTAACTTAA
27794 TAGTTTTAACTTTTAACTT
1 TAGTTTTAACTTTTAACTT
27813 TAAAAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (21 bp):
TAGTTTTAACTTTTAACTTAA
Found at i:28703 original size:23 final size:23
Alignment explanation
Indices: 28677--28758 Score: 139
Period size: 23 Copynumber: 3.6 Consensus size: 23
28667 GAAAATGTTT
*
28677 ATATAAATATTTTATAGTATA-AA
1 ATATAAATATTTTA-ATTATATAA
28700 ATATAAATATTTTAATTATATAA
1 ATATAAATATTTTAATTATATAA
28723 ATATAAATATTTTAATTATATAA
1 ATATAAATATTTTAATTATATAA
28746 ATATAAATATTTT
1 ATATAAATATTTT
28759 TTAAATCATC
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
22 5 0.09
23 52 0.91
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
ATATAAATATTTTAATTATATAA
Found at i:29129 original size:17 final size:18
Alignment explanation
Indices: 29097--29134 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29087 AATCAAAATT
*
29097 TATTTTATAATAAAATGA
1 TATTTTATAATAAAATAA
29115 TATTTTATAAT-AAATAA
1 TATTTTATAATAAAATAA
29132 TAT
1 TAT
29135 CTTTTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TATTTTATAATAAAATAA
Found at i:29442 original size:22 final size:20
Alignment explanation
Indices: 29416--29456 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
29406 AATAATTGTT
29416 TTATAGTAATACATTATATTAA
1 TTATAGTAATA-ATT-TATTAA
*
29438 TTATATTAATAATTTATTA
1 TTATAGTAATAATTTATTA
29457 TAAGATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTATAGTAATAATTTATTAA
Found at i:29516 original size:18 final size:18
Alignment explanation
Indices: 29491--29540 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
29481 TTTAATAATA
29491 TTAAAAATTAT-AATATT
1 TTAAAAATTATAAATATT
29508 TTAATAAATT-TAAATATT
1 TTAA-AAATTATAAATATT
29526 TTCAAAAATTA-AAAT
1 TT-AAAAATTATAAAT
29541 CAATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.17
18 22 0.76
19 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAAATTATAAATATT
Found at i:29844 original size:28 final size:28
Alignment explanation
Indices: 29813--29870 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
29803 ATTGACAAAC
29813 AAACATGATATATCTATT-TTGTAAAAAA
1 AAACATGATATATCTATTCTT-TAAAAAA
29841 AAACATGATATATCTATTCTTTAAAAAA
1 AAACATGATATATCTATTCTTTAAAAAA
29869 AA
1 AA
29871 CTTAATCCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (28 bp):
AAACATGATATATCTATTCTTTAAAAAA
Found at i:30430 original size:28 final size:28
Alignment explanation
Indices: 30354--30445 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
30344 AGGCCCACCC
*
30354 ATAT-TTTTTTATTCTATTAAAAATATTTAT
1 ATATATTTTTTATT-TATTAAATA-ATTT-T
* *
30384 ATTATATTATTTTA-ATATTTAATAATTTT
1 A-TATATT-TTTTATTTATTAAATAATTTT
**
30413 ATATATTTTTTATTTATTAAATTTTTTT
1 ATATATTTTTTATTTATTAAATAATTTT
30441 ATATA
1 ATATA
30446 GTCATCTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
27 5 0.10
28 22 0.43
29 2 0.04
30 5 0.10
31 10 0.20
32 2 0.04
33 5 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (28 bp):
ATATATTTTTTATTTATTAAATAATTTT
Found at i:31074 original size:18 final size:17
Alignment explanation
Indices: 31048--31090 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
31038 TTAAATTTTT
*
31048 TTTAAAAAATTCAATAAA
1 TTTATAAAATTCAA-AAA
*
31066 TTTATAAAATTCTAAAA
1 TTTATAAAATTCAAAAA
*
31083 TATATAAA
1 TTTATAAA
31091 TATAAATGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
TTTATAAAATTCAAAAA
Found at i:31088 original size:17 final size:18
Alignment explanation
Indices: 31053--31090 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
31043 TTTTTTTTAA
*
31053 AAAATTCAATAAATTTAT
1 AAAATTCAATAAATATAT
*
31071 AAAATTCTA-AAATATAT
1 AAAATTCAATAAATATAT
31088 AAA
1 AAA
31091 TATAAATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTCAATAAATATAT
Found at i:45190 original size:31 final size:32
Alignment explanation
Indices: 45147--45211 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
45137 AATTTATATT
45147 TTATGTATTATTATA-TT-AAATTATTAAAATA
1 TTATGTATTATTATATTTAAAATT-TTAAAATA
*
45178 TTATTTATTATTATATTTAAAATTTTAAAATA
1 TTATGTATTATTATATTTAAAATTTTAAAATA
45210 TT
1 TT
45212 TCGTGTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 14 0.45
32 12 0.39
33 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (32 bp):
TTATGTATTATTATATTTAAAATTTTAAAATA
Found at i:47119 original size:10 final size:11
Alignment explanation
Indices: 47104--47132 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
47094 ATCACATGGG
47104 TTTCTTTTC-T
1 TTTCTTTTCTT
47114 TTTCTTTTCTT
1 TTTCTTTTCTT
47125 TTTCTTTT
1 TTTCTTTT
47133 ACAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:47996 original size:41 final size:41
Alignment explanation
Indices: 47941--48024 Score: 136
Period size: 41 Copynumber: 2.0 Consensus size: 41
47931 TTATATGGGT
47941 AGAAGAGGAAAAATTCA-TCAATGTTAAAAAACGAATGATAA
1 AGAAGAGGAAAAATTCACT-AATGTTAAAAAACGAATGATAA
47982 AGAAGA-GAATAAATTCACTAATGTTAAAAAACGAATGATAA
1 AGAAGAGGAA-AAATTCACTAATGTTAAAAAACGAATGATAA
48023 AG
1 AG
48025 TGGAGTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
40 3 0.07
41 37 0.90
42 1 0.02
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.20
Consensus pattern (41 bp):
AGAAGAGGAAAAATTCACTAATGTTAAAAAACGAATGATAA
Found at i:49297 original size:3 final size:3
Alignment explanation
Indices: 49289--49314 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49279 TATTTATTCA
49289 AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AG
49315 GTCTTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:49882 original size:18 final size:19
Alignment explanation
Indices: 49861--49898 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
49851 TTTTTAAAAA
*
49861 TATAAAT-TTTTTAATTTT
1 TATAAATGTTTTGAATTTT
49879 TATAAATGTTTTGAATTTT
1 TATAAATGTTTTGAATTTT
49898 T
1 T
49899 TTGTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TATAAATGTTTTGAATTTT
Found at i:57139 original size:30 final size:31
Alignment explanation
Indices: 57098--57156 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
57088 GAGGTCCCTA
*
57098 AACTATCTAAAAATTACATTTTTAACCCTTT
1 AACTATCTAAAAATTACATTTTAAACCCTTT
*
57129 AACT-TCTAAAAATTCCATTTTAAACCCT
1 AACTATCTAAAAATTACATTTTAAACCCT
57157 AAATTTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (31 bp):
AACTATCTAAAAATTACATTTTAAACCCTTT
Found at i:64710 original size:206 final size:206
Alignment explanation
Indices: 64340--65713 Score: 1944
Period size: 206 Copynumber: 6.7 Consensus size: 206
64330 AACTCAGGGG
* * * *
64340 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACATTGGGAAACAGGTCGAAGCAAT
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
* * * *
64405 AAAATGGTTAGCTTTCTGATGAGATACTAAGAAGAGGACCAAATTCGTCTTCCTGATAAGATACA
66 AAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
* * * * * *
64470 GAGAAGCAGATTGAAATAAATGACGCGATCATCTTCCTAATGAGACACAGAGAAGAAGACCAAAT
131 GAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAAT
64535 CAAACCCACGC
196 CAAACCCACGC
* * * *
64546 TCGATGTGAGTAAATCTTCGAATCCCAGCTTCCAGATAAGATACTGAGAAGCAGGTCGAAGCATT
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
*
64611 AAAATGGTTAGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATGAGATACA
66 AAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
* *
64676 GAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGGAGAAGACCAAAT
131 GAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAAT
*
64741 CAAACCCATGC
196 CAAACCCACGC
* *
64752 TCGATGTGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATACTGAGAAGTAGGGTCGAAGCAA
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCA-GGTCGAAGCAA
* * * * *
64817 TAAAATGGTTAACTTACTGATGAGATATTGAGAAGTGGTCCAAATTCGTCTTCCTGATGTGATAC
65 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * * * *
64882 AGAGAAGAGGATTGGAACAAATGACGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAA
130 AGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAA
*
64947 TCAAACTCACGC
195 TCAAACCCACGC
* * * * * * **
64959 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGACATTGGGAAACAGGTTAAAGCAAT
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
* *
65024 AAAATGGTTAGCTTTCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAGATACA
66 AAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
* * * * *
65089 GAGAAGCGGATTAAAACAAATGACGCGATCATCTTCCTAATGAGACACAGAGAAGAAGACCAAAT
131 GAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAAT
* *
65154 AAAACTCACGC
196 CAAACCCACGC
* * * * *
65165 TCGATGTGAGCAAATCTTCAAATCTCAGCTTCCAGATGAGATACTGAGAAGC-GGATTGAAGCAT
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGG-TCGAAGCAA
* *
65229 TAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATAC
65 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* *
65294 AGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGGAGAAGACCAAA
130 AGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAA
*
65359 TCAAACCCATGC
195 TCAAACCCACGC
* * * *
65371 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATAAGTTACTGAGAAGCAGGGTCGAAGAAA
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCA-GGTCGAAGCAA
* * * *
65436 TAAAATGGTTAACTTCCTAATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGTA-AAA
65 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATG-AGATA
* *
65500 CAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCTTAATGAGATACTGAGAAGAAGACCAA
129 CAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAA
65565 ATCAAACCCACGC
194 ATCAAACCCACGC
* * *
65578 TCGATGTGAGCAAATCTTC-AAACCCTAGCTTCTTGATGAGATACTGAGAAGCAGGTTGAAGCAA
1 TCGATGTGAGCAAATCTTCGAATCCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
* * * * * * *
65642 TAAAGTGGTTAGCTCCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACAC
65 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
65707 AGAGAAG
130 AGAGAAG
65714 TAGTGAACCA
Statistics
Matches: 1036, Mismatches: 125, Indels: 14
0.88 0.11 0.01
Matches are distributed among these distances:
205 3 0.00
206 667 0.64
207 363 0.35
208 3 0.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (206 bp):
TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
AAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
GAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAAT
CAAACCCACGC
Found at i:65169 original size:413 final size:412
Alignment explanation
Indices: 64340--65713 Score: 1975
Period size: 413 Copynumber: 3.3 Consensus size: 412
64330 AACTCAGGGG
* * * *
64340 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACATTGGGAAACAGGTCGAAGCAAT
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
* * *
64405 AAAATGGTTAGCTTTCTGATGAGATACTAAGAAGAGGACCAAATTCGTCTTCCTGATAAGATACA
66 AAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
* * * * *
64470 GAGAAGCA-GATTGAAATAAATGACGCGATCATCTTCCTAATGAGACACAGAGAAGAAGACCAAA
131 GAGAAG-AGGATTGAAACAAATGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
* *
64534 TCAAACCCACGCTCGATGTGAGTAAATCTTCGAATCCCAGCTTCCAGATAAGATACTGAGAAGCA
195 TCAAACCCACGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATAAGATACTGAGAAGCA
*
64599 GGTCGAAGCATTAAAATGGTTAGCTTCCTGATGAGATACTGAGAA-ATGGACCAAATTCGTCTTC
260 GGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGA-GGACCAAATTCGTCTTC
*
64663 CTGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAG
324 CTGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAG
* *
64728 GAGAAGACCAAATCAAACCCATGC
389 AAGAAGACCAAATCAAACCCACGC
* *
64752 TCGATGTGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATACTGAGAAGTAGGGTCGAAGCAA
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCA-GGTCGAAGCAA
* * * * * *
64817 TAAAATGGTTAACTTACTGATGAGATATTGAGAAGTGGTCCAAATTCGTCTTCCTGATGTGATAC
65 TAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* *
64882 AGAGAAGAGGATTGGAACAAATGACGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAA
130 AGAGAAGAGGATTGAAACAAATGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
* * * * * *
64947 TCAAACTCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGACATTGGGAAACA
195 TCAAACCCACGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATAAGATACTGAGAAGCA
** *
65012 GGTTAAAGCAATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCC
260 GGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCC
* * * * *
65077 TGATGAGATACAGAGAAGCGGATTAAAACAAATGACGCGATCATCTTCCTAATGAGACACAGAGA
325 TGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGA
* *
65142 AGAAGACCAAATAAAACTCACGC
390 AGAAGACCAAATCAAACCCACGC
* * * * *
65165 TCGATGTGAGCAAATCTTCAAATCTCAGCTTCCAGATGAGATACTGAGAAGC-GGATTGAAGCAT
1 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGG-TCGAAGCAA
*
65229 TAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATAC
65 TAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* * *
65294 AGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGGAGAAGACCAAA
130 AGAGAAGAGGATTGAAACAAATGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
* * *
65359 TCAAACCCATGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATAAGTTACTGAGAAGCA
195 TCAAACCCACGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATAAGATACTGAGAAGCA
* * * * *
65424 GGGTCGAAGAAATAAAATGGTTAACTTCCTAATGAGATATTGAGAAGTGGACCAAATTCGTCTTC
260 -GGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTC
* * *
65489 CTGATGTA-AAACAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCTTAATGAGATACTGA
324 CTGATG-AGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGA
65553 GAAGAAGACCAAATCAAACCCACGC
388 GAAGAAGACCAAATCAAACCCACGC
* * *
65578 TCGATGTGAGCAAATCTTC-AAACCCTAGCTTCTTGATGAGATACTGAGAAGCAGGTTGAAGCAA
1 TCGATGTGAGCAAATCTTCGAATCCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
* * ** * * * *
65642 TAAAGTGGTTAGCTCCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACAC
65 TAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
65707 AGAGAAG
130 AGAGAAG
65714 TAGTGAACCA
Statistics
Matches: 851, Mismatches: 103, Indels: 15
0.88 0.11 0.02
Matches are distributed among these distances:
411 2 0.00
412 233 0.27
413 612 0.72
414 4 0.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (412 bp):
TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
AAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA
GAGAAGAGGATTGAAACAAATGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT
CAAACCCACGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATAAGATACTGAGAAGCAG
GTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCT
GATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTAATGAGATACTGAGAA
GAAGACCAAATCAAACCCACGC
Found at i:65529 original size:619 final size:619
Alignment explanation
Indices: 64340--65713 Score: 2282
Period size: 619 Copynumber: 2.2 Consensus size: 619
64330 AACTCAGGGG
* *
64340 TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACATTGGGAAACAGGTCGAAGCAAT
1 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGGGAAACAGGTTGAAGCAAT
* *
64405 AAAATGGTTAGCTTTCTGATGAGATACTAAGAAGAGGACCAAATTCGTCTTCCTGATAAGATACA
66 AAAATGGTTAGCTTTCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAGATACA
* *
64470 GAGAAGCAGATTGAAATAAATGACGCGATCATCTTCCTAATGAGACACAGAGAAGAAGACCAAAT
131 GAGAAGCAGATTAAAACAAATGACGCGATCATCTTCCTAATGAGACACAGAGAAGAAGACCAAAT
* * *
64535 CAAACCCACGCTCGATGTGAGTAAATCTTCGAATCCCAGCTTCCAGATAAGATACTGAGAAGCAG
196 AAAACCCACGCTCGATGTGAGCAAATCTTCAAATCCCAGCTTCCAGATAAGATACTGAGAAGCAG
* *
64600 GTCGAAGCATTAAAATGGTTAGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCT
261 GTCGAAGCATTAAAATGGTTAGCTTCCTGATGAGATACTAAGAAATAGACCAAATTCGTCTTCCT
64665 GATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGGA
326 GATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGGA
*
64730 GAAGACCAAATCAAACCCATGCTCGATGTGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATA
391 GAAGACCAAATCAAACCCATGCTCGATGTGAGCAAATCTTCGAATCCCAACTTCCTGATAAGATA
* * * *
64795 CTGAGAAGTAGGGTCGAAGCAATAAAATGGTTAACTTACTGATGAGATATTGAGAAGTGGTCCAA
456 CTGAGAAGCAGGGTCGAAGAAATAAAATGGTTAACTTACTAATGAGATATTGAGAAGTGGACCAA
* * * * *
64860 ATTCGTCTTCCTGATGTGATACAGAGAAGAGGATTGGAACAAATGACGCGGTCATCTTCTTGATG
521 ATTCGTCTTCCTGATGTAAAACAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCTTAATG
*
64925 AGATACTGAGAAGAAGACCAAATCAAACTCACGC
586 AGATACTGAGAAGAAGACCAAATCAAACCCACGC
* *
64959 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATAAGACATTGGGAAACAGGTTAAAGCAAT
1 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGGGAAACAGGTTGAAGCAAT
65024 AAAATGGTTAGCTTTCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAGATACA
66 AAAATGGTTAGCTTTCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAGATACA
*
65089 GAGAAGCGGATTAAAACAAATGACGCGATCATCTTCCTAATGAGACACAGAGAAGAAGACCAAAT
131 GAGAAGCAGATTAAAACAAATGACGCGATCATCTTCCTAATGAGACACAGAGAAGAAGACCAAAT
* * *
65154 AAAACTCACGCTCGATGTGAGCAAATCTTCAAATCTCAGCTTCCAGATGAGATACTGAGAAGC-G
196 AAAACCCACGCTCGATGTGAGCAAATCTTCAAATCCCAGCTTCCAGATAAGATACTGAGAAGCAG
* *
65218 GATTGAAGCATTAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTAGACCAAATTCGTCTTCC
261 G-TCGAAGCATTAAAATGGTTAGCTTCCTGATGAGATACTAAGAAATAGACCAAATTCGTCTTCC
65283 TGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGG
325 TGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGG
* * *
65348 AGAAGACCAAATCAAACCCATGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATAAGTT
390 AGAAGACCAAATCAAACCCATGCTCGATGTGAGCAAATCTTCGAATCCCAACTTCCTGATAAGAT
*
65413 ACTGAGAAGCAGGGTCGAAGAAATAAAATGGTTAACTTCCTAATGAGATATTGAGAAGTGGACCA
455 ACTGAGAAGCAGGGTCGAAGAAATAAAATGGTTAACTTACTAATGAGATATTGAGAAGTGGACCA
65478 AATTCGTCTTCCTGATGTAAAACAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCTTAAT
520 AATTCGTCTTCCTGATGTAAAACAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCTTAAT
65543 GAGATACTGAGAAGAAGACCAAATCAAACCCACGC
585 GAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * * * * * *
65578 TCGATGTGAGCAAATCTTCAAACCCTAGCTTCTTGATGAGATACTGAGAAGCAGGTTGAAGCAAT
1 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGGGAAACAGGTTGAAGCAAT
* ** * * * * * *
65643 AAAGTGGTTAGCTCCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACA
66 AAAATGGTTAGCTTTCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAGATACA
65708 GAGAAG
131 GAGAAG
65714 TAGTGAACCA
Statistics
Matches: 702, Mismatches: 52, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
618 2 0.00
619 700 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (619 bp):
TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGGGAAACAGGTTGAAGCAAT
AAAATGGTTAGCTTTCTGATGAGATACTGAGAAGAGGACCAAATTCGTCTTCCTGATGAGATACA
GAGAAGCAGATTAAAACAAATGACGCGATCATCTTCCTAATGAGACACAGAGAAGAAGACCAAAT
AAAACCCACGCTCGATGTGAGCAAATCTTCAAATCCCAGCTTCCAGATAAGATACTGAGAAGCAG
GTCGAAGCATTAAAATGGTTAGCTTCCTGATGAGATACTAAGAAATAGACCAAATTCGTCTTCCT
GATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGGA
GAAGACCAAATCAAACCCATGCTCGATGTGAGCAAATCTTCGAATCCCAACTTCCTGATAAGATA
CTGAGAAGCAGGGTCGAAGAAATAAAATGGTTAACTTACTAATGAGATATTGAGAAGTGGACCAA
ATTCGTCTTCCTGATGTAAAACAGAGAAGAGGATTGAAACAAACGACGCGGTCATCTTCTTAATG
AGATACTGAGAAGAAGACCAAATCAAACCCACGC
Found at i:66099 original size:6 final size:6
Alignment explanation
Indices: 66088--66143 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
66078 GGCCTAACAG
* * * *
66088 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGTTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
66134 AATTTA AATT
1 AATTTA AATT
66144 AATGTCCAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 8 0.20
6 33 0.80
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:66113 original size:17 final size:17
Alignment explanation
Indices: 66091--66133 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
66081 CTAACAGAAT
66091 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
66108 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
66125 TTAAATTTA
1 TTAAATTTA
66134 AATTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:66145 original size:17 final size:16
Alignment explanation
Indices: 66091--66145 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
66081 CTAACAGAAT
66091 TTAAATTTATTTTAAAA
1 TTAAATTTATTTT-AAA
*
66108 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAA-A
*
66125 TTAAATTTAAATTTAAA
1 TTAAATTT-ATTTTAAA
66142 TTAA
1 TTAA
66146 TGTCCAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 2 0.06
17 25 0.76
18 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:66145 original size:23 final size:23
Alignment explanation
Indices: 66088--66145 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
66078 GGCCTAACAG
* *
66088 AATTTAAATTTATTTTAAAATTA
1 AATTTAAATTAAGTTTAAAATTA
** *
66111 AATTTATTTTAAGTTTAAATTTA
1 AATTTAAATTAAGTTTAAAATTA
66134 AATTTAAATTAA
1 AATTTAAATTAA
66146 TGTCCAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AATTTAAATTAAGTTTAAAATTA
Found at i:67361 original size:168 final size:168
Alignment explanation
Indices: 67083--67409 Score: 627
Period size: 168 Copynumber: 1.9 Consensus size: 168
67073 AGAAAACGGA
*
67083 CGTTTTGCTTACCGAATGAAGGGGACCGGCGGTGCTTGGCGCGTGACAGTGACGGACGACAGGCG
1 CGTTTTGCTTACCGAATGAAGGGGACCGGCGGTGCTTGGCGCATGACAGTGACGGACGACAGGCG
67148 TGTAGACGGGCGGGGGTACGCGACAACCACACACGACGGTCGACAAGGCGCGTGCGGTGGTGCAC
66 TGTAGACGGGCGGGGGTACGCGACAACCACACACGACGGTCGACAAGGCGCGTGCGGTGGTGCAC
67213 AACGGTGACCGGACGTGAGGCCATGGCCGTCAACAGGG
131 AACGGTGACCGGACGTGAGGCCATGGCCGTCAACAGGG
*
67251 CGTTTTGCTTACCGAATGAAGGGGACCGGCGGTGCTTGGCGCATGACAGTGACGGACGACAGGTG
1 CGTTTTGCTTACCGAATGAAGGGGACCGGCGGTGCTTGGCGCATGACAGTGACGGACGACAGGCG
*
67316 TGTAGACGGGCGGGGGTACGCGACGACCACACACGACGGTCGACAAGGCGCGTGCGGTGGTGCAC
66 TGTAGACGGGCGGGGGTACGCGACAACCACACACGACGGTCGACAAGGCGCGTGCGGTGGTGCAC
67381 AACGGTGACCGGACGTGAGGCCATGGCCG
131 AACGGTGACCGGACGTGAGGCCATGGCCG
67410 GCCATGAGAG
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 156 1.00
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.14
Consensus pattern (168 bp):
CGTTTTGCTTACCGAATGAAGGGGACCGGCGGTGCTTGGCGCATGACAGTGACGGACGACAGGCG
TGTAGACGGGCGGGGGTACGCGACAACCACACACGACGGTCGACAAGGCGCGTGCGGTGGTGCAC
AACGGTGACCGGACGTGAGGCCATGGCCGTCAACAGGG
Found at i:68038 original size:29 final size:29
Alignment explanation
Indices: 67992--68172 Score: 135
Period size: 29 Copynumber: 6.2 Consensus size: 29
67982 AAACTGTTCG
* *
67992 AAAATTACA-TTTGTACCCTCGAACTTCTA
1 AAAATTCCATTTTG-ACCCTCGAACTTCCA
**
68021 AAAATTCCATTTTGACCCTAAAACTTCCA
1 AAAATTCCATTTTGACCCTCGAACTTCCA
68050 AAAATTCCATTTTGA-CCTCGAAACTTCCA
1 AAAATTCCATTTTGACCCTCG-AACTTCCA
** * * *
68079 AAAATTATATTTTTACCC-CTAAATGTCCA
1 AAAATTCCATTTTGACCCTCGAACT-TCCA
* *
68108 AAAACTCCATTTT-AACCTCGAAAC-TCTCA
1 AAAATTCCATTTTGACCCTCG-AACTTC-CA
68137 AAAATTACCATTTT-ACCC-CTGAA-TATCCA
1 AAAATT-CCATTTTGACCCTC-GAACT-TCCA
68166 AAAATTC
1 AAAATTC
68173 AGTTTTATAT
Statistics
Matches: 122, Mismatches: 19, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
28 12 0.10
29 89 0.73
30 21 0.17
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATTCCATTTTGACCCTCGAACTTCCA
Found at i:68179 original size:58 final size:57
Alignment explanation
Indices: 67992--68179 Score: 179
Period size: 58 Copynumber: 3.2 Consensus size: 57
67982 AAACTGTTCG
* * * *
67992 AAAATTACATTTGTACCCTCG-AACTTCTAAAAATTCCATTTTGA-CCCTAAA-ACTTCCA
1 AAAATT-CATTT-TAACCTCGAAACTTCCAAAAATTACATTTTTACCCCTAAATA--TCCA
* * *
68050 AAAATTCCATTTTGACCTCGAAACTTCCAAAAATTATATTTTTACCCCTAAATGTCCA
1 AAAATT-CATTTTAACCTCGAAACTTCCAAAAATTACATTTTTACCCCTAAATATCCA
* *
68108 AAAACTCCATTTTAACCTCGAAAC-TCTCAAAAATTACCA-TTTTACCCCTGAATATCCA
1 AAAA-TTCATTTTAACCTCGAAACTTC-CAAAAATTA-CATTTTTACCCCTAAATATCCA
68166 AAAATTCAGTTTTA
1 AAAATTCA-TTTTA
68180 TATCCCGCTT
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
57 11 0.10
58 89 0.82
59 9 0.08
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (57 bp):
AAAATTCATTTTAACCTCGAAACTTCCAAAAATTACATTTTTACCCCTAAATATCCA
Found at i:72815 original size:18 final size:18
Alignment explanation
Indices: 72794--72832 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
72784 TATTTAATTT
*
72794 AAAT-TTTTATAATGTAAA
1 AAATATTTTAT-ATATAAA
72812 AAATATTTTATATATAAA
1 AAATATTTTATATATAAA
72830 AAA
1 AAA
72833 GAAAATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATATTTTATATATAAA
Found at i:76592 original size:13 final size:13
Alignment explanation
Indices: 76574--76598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76564 TTATGATTAT
76574 TTTTTTAATAATA
1 TTTTTTAATAATA
76587 TTTTTTAATAAT
1 TTTTTTAATAAT
76599 TTAAATCTGA
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:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAATAATA
Found at i:77367 original size:15 final size:15
Alignment explanation
Indices: 77347--77397 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
77337 TTGTCTTAGA
77347 TTATGTTTTAATCAC
1 TTATGTTTTAATCAC
*
77362 TTATGTTTGAAAT-A-
1 TTATGTTT-TAATCAC
* *
77376 TTACGTTTTAGTCAC
1 TTATGTTTTAATCAC
77391 TTATGTT
1 TTATGTT
77398 ATCGTTTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 15 0.54
16 3 0.11
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (15 bp):
TTATGTTTTAATCAC
Found at i:80087 original size:12 final size:12
Alignment explanation
Indices: 80072--80097 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
80062 ATACATCTAA
80072 AAATATTAAAAC
1 AAATATTAAAAC
80084 AAATATTAAAAC
1 AAATATTAAAAC
80096 AA
1 AA
80098 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:80135 original size:41 final size:41
Alignment explanation
Indices: 80074--80154 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
80064 ACATCTAAAA
*
80074 ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAATG
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAATG
* * *
80115 ATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAAT
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAAT
80155 ACAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.22
Consensus pattern (41 bp):
ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAATG
Found at i:81257 original size:21 final size:22
Alignment explanation
Indices: 81213--81263 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
81203 TAATTGAATT
* * *
81213 TATTTTAATTTTAATATTATAA
1 TATTTAAAATTTAATATGATAA
81235 TATTTAAAATTTAATATGA-AA
1 TATTTAAAATTTAATATGATAA
*
81256 TAATTAAA
1 TATTTAAA
81264 TAAGATACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTAAAATTTAATATGATAA
Found at i:83837 original size:25 final size:23
Alignment explanation
Indices: 83796--83842 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
83786 CTAATTAGGG
83796 AATTATTGTTTAGATTTAATTTT
1 AATTATTGTTTAGATTTAATTTT
*
83819 AATTATCTTTTTAGAATTTAATTT
1 AATTAT-TGTTTAG-ATTTAATTT
83843 GGATCCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTTT
Found at i:84258 original size:15 final size:15
Alignment explanation
Indices: 84221--84259 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
84211 TTATGTGTGC
*
84221 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
84236 AT-ATTCTTGATATA
1 TTAATTCTTGATATA
84250 TTAATTCTTG
1 TTAATTCTTG
84260 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:89196 original size:23 final size:23
Alignment explanation
Indices: 89170--89332 Score: 110
Period size: 23 Copynumber: 7.4 Consensus size: 23
89160 AGTGTTGGGT
89170 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
89193 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
* *
89212 -AC--TGAGCACATAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
89232 ATCAAAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * * *
89255 ATCAGAGAGCATGA-GACGTGCTA
1 AACAGAGAGCA-CACAAAGTGCTA
* *
89278 AACA-ACGAACACACACAGTGCTA
1 AACAGA-GAGCACACAAAGTGCTA
* *
89301 ATCAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
89324 ATCAGAGAG
1 AACAGAGAG
89333 AGCGCTAGTG
Statistics
Matches: 110, Mismatches: 19, Indels: 22
0.73 0.13 0.15
Matches are distributed among these distances:
16 9 0.08
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 2 0.02
23 90 0.82
24 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:89220 original size:39 final size:39
Alignment explanation
Indices: 89176--89250 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
89166 GGGTAACAGA
* *
89176 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACT
* * *
89215 GAGCACATAAAGTGCTAATCAAAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGT
89251 GCTAATCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACT
Found at i:89322 original size:46 final size:46
Alignment explanation
Indices: 89215--89324 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 46
89205 ACAAAGTACT
* * * *
89215 GAGCACATAAAGTGCTAATCAAAGAGCACACGAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAAACAAAGAACACACGAAGTGCTAATCAGA
* * *
89261 GAGCATGAGAC-GTGCTAAACAACGAACACAC-ACAGTGCTAATCAGA
1 GAGCA-CACACAGTGCTAAACAAAGAACACACGA-AGTGCTAATCAGA
89307 GAGCACACACAGTGCTAA
1 GAGCACACACAGTGCTAA
89325 TCAGAGAGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
45 4 0.08
46 47 0.89
47 2 0.04
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.14
Consensus pattern (46 bp):
GAGCACACACAGTGCTAAACAAAGAACACACGAAGTGCTAATCAGA
Found at i:91667 original size:24 final size:25
Alignment explanation
Indices: 91640--91690 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
91630 ACCCGACTGT
91640 TAAGTGGTA-TTTTTTTATTTGGTA
1 TAAGTGGTATTTTTTTTATTTGGTA
91664 TAAGTGGTATTTTTTTTATTTGGTA
1 TAAGTGGTATTTTTTTTATTTGGTA
91689 TA
1 TA
91691 GTAATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (25 bp):
TAAGTGGTATTTTTTTTATTTGGTA
Found at i:91701 original size:24 final size:25
Alignment explanation
Indices: 91648--91701 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
91638 GTTAAGTGGT
**
91648 ATTTTTTTATTTGGTATAAGTGGTA
1 ATTTTTTTATTTGGTATAAGTAATA
*
91673 TTTTTTTTATTTGGTAT-AGTAATA
1 ATTTTTTTATTTGGTATAAGTAATA
91697 ATTTT
1 ATTTT
91702 AGTCCTCTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (25 bp):
ATTTTTTTATTTGGTATAAGTAATA
Found at i:95068 original size:22 final size:21
Alignment explanation
Indices: 95005--95070 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
94995 TTTTTGGGGA
*
95005 TAAAAATTAAATTGTAATTTT
1 TAAAAATTAAATTATAATTTT
* *
95026 TAAAATAATAAAAATATAATTTT
1 T-AAA-AATTAAATTATAATTTT
*
95049 TAAAAGATTAAATTAAAATTTT
1 TAAAA-ATTAAATTATAATTTT
95071 ATCATTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
21 2 0.06
22 19 0.53
23 15 0.42
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAAATTAAATTATAATTTT
Found at i:104385 original size:25 final size:25
Alignment explanation
Indices: 104367--104425 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
104357 AACAAAAGTG
* *
104367 CATAAGTGCTGGGGAAACAGAAGCA
1 CATAAGTGCTGCGAAAACAGAAGCA
104392 CATAAGTGCTGCGAAAACAGAAGCA
1 CATAAGTGCTGCGAAAACAGAAGCA
104417 CATAAGTGC
1 CATAAGTGC
104426 AGCAGAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (25 bp):
CATAAGTGCTGCGAAAACAGAAGCA
Found at i:104444 original size:26 final size:25
Alignment explanation
Indices: 104367--104433 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
104357 AACAAAAGTG
* * *
104367 CATAAGTGCTGGGGAAACAGAAGCA
1 CATAAGTGCAGCGAAAACAGAAGCA
*
104392 CATAAGTGCTGCGAAAACAGAAGCA
1 CATAAGTGCAGCGAAAACAGAAGCA
104417 CATAAGTGCAGCAGAAA
1 CATAAGTGCAGC-GAAA
104434 TAGTAGGCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
25 34 0.89
26 4 0.11
ACGTcount: A:0.43, C:0.18, G:0.27, T:0.12
Consensus pattern (25 bp):
CATAAGTGCAGCGAAAACAGAAGCA
Found at i:104468 original size:22 final size:23
Alignment explanation
Indices: 104435--104486 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
104425 CAGCAGAAAT
* *
104435 AGTAGGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCTAAAC
104458 AG-AAGCACACACAGTGCTAAAC
1 AGTAAGCACACACAGTGCTAAAC
104480 AGTAAGC
1 AGTAAGC
104487 GCGCTAGCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (23 bp):
AGTAAGCACACACAGTGCTAAAC
Found at i:124959 original size:29 final size:29
Alignment explanation
Indices: 124926--124983 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
124916 TTGACATGGT
*
124926 CGTTAATTGACTAACAATGCTGATGTGAC
1 CGTTAATTGACTAACAATGCTGACGTGAC
**
124955 CGTTAATTGACTAACGGTGCTGACGTGAC
1 CGTTAATTGACTAACAATGCTGACGTGAC
124984 AAATTTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (29 bp):
CGTTAATTGACTAACAATGCTGACGTGAC
Found at i:131568 original size:43 final size:42
Alignment explanation
Indices: 131373--131579 Score: 175
Period size: 43 Copynumber: 4.8 Consensus size: 42
131363 TTCACTTGGC
*
131373 GTATAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTAT
1 GTATAAAAGGAAGACTCATGTCTCG-GATGAGCATGAGATTAT
* * * * * *
131416 GTATAAAATGGAATACTCGTGACTCGGGATAAGCATAAGTTTAT
1 GTATAAAA-GGAAGACTCATGTCTC-GGATGAGCATGAGATTAT
* * * * * *
131460 GTGTAAATGGAAGACTCATGACTCAGAATGAACATGAGATTAC
1 GTATAAAAGGAAGACTCATGTCTC-GGATGAGCATGAGATTAT
*
131503 GTA-AGAAAGGAAGACACATGTCTCTGGATGAGCATGAGATTAT
1 GTATA-AAAGGAAGACTCATGTCTC-GGATGAGCATGAGATTAT
** * *
131546 G-ATTAAAAGGAAGACTTTTGTCTCAGTTGAGCAT
1 GTA-TAAAAGGAAGACTCATGTCTCGGATGAGCAT
131580 AAGGTGGTTT
Statistics
Matches: 128, Mismatches: 31, Indels: 11
0.75 0.18 0.06
Matches are distributed among these distances:
42 10 0.08
43 83 0.65
44 34 0.27
45 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (42 bp):
GTATAAAAGGAAGACTCATGTCTCGGATGAGCATGAGATTAT
Found at i:133960 original size:33 final size:33
Alignment explanation
Indices: 133912--133978 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
133902 GAGGTAAACC
*
133912 TTGGACAATGGCACACCATGCAATATAACAATA
1 TTGGACAATGACACACCATGCAATATAACAATA
* *
133945 TTGGACAGTGACACACCTTGCAATATAACAATA
1 TTGGACAATGACACACCATGCAATATAACAATA
133978 T
1 T
133979 CAGAGATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (33 bp):
TTGGACAATGACACACCATGCAATATAACAATA
Found at i:135184 original size:17 final size:17
Alignment explanation
Indices: 135162--135224 Score: 92
Period size: 17 Copynumber: 3.7 Consensus size: 17
135152 TTGGAAATTG
*
135162 AATTTAAGTTTATTTGA
1 AATTTAAATTTATTTGA
135179 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTGA
135196 AATTTAAATTTATTAT-A
1 AATTTAAATTTATT-TGA
*
135213 AAATTAAATTTA
1 AATTTAAATTTA
135225 GAAAAGTTCG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
17 42 0.98
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:135280 original size:15 final size:15
Alignment explanation
Indices: 135260--135311 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
135250 TCCAAAACAA
135260 ATGGCCCAGTTACAG
1 ATGGCCCAGTTACAG
** *
135275 ATGGCCCAAATACAA
1 ATGGCCCAGTTACAG
135290 ATGGCCCAGTTACAG
1 ATGGCCCAGTTACAG
135305 ATGGCCC
1 ATGGCCC
135312 GAATACAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (15 bp):
ATGGCCCAGTTACAG
Found at i:135290 original size:30 final size:30
Alignment explanation
Indices: 135251--135323 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
135241 AAAAAAAAAT
135251 CCAAA-ACAAATGGCCCAGTTACAGATGGC
1 CCAAATACAAATGGCCCAGTTACAGATGGC
135280 CCAAATACAAATGGCCCAGTTACAGATGGC
1 CCAAATACAAATGGCCCAGTTACAGATGGC
*
135310 CCGAATACAAATGG
1 CCAAATACAAATGG
135324 TCCAATTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 5 0.12
30 37 0.88
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (30 bp):
CCAAATACAAATGGCCCAGTTACAGATGGC
Found at i:135318 original size:15 final size:14
Alignment explanation
Indices: 135251--135329 Score: 68
Period size: 15 Copynumber: 5.4 Consensus size: 14
135241 AAAAAAAAAT
*
135251 CCAAAACAAATGGC
1 CCAATACAAATGGC
* *
135265 CCAGTTACAGATGGC
1 CCA-ATACAAATGGC
135280 CCAAATACAAATGGC
1 CC-AATACAAATGGC
* *
135295 CCAGTTACAGATGGC
1 CCA-ATACAAATGGC
*
135310 CCGAATACAAATGGT
1 CC-AATACAAATGGC
135325 CCAAT
1 CCAAT
135330 TATAAAGTGC
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
14 7 0.14
15 42 0.82
16 2 0.04
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (14 bp):
CCAATACAAATGGC
Found at i:135955 original size:28 final size:29
Alignment explanation
Indices: 135885--135955 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
135875 CTAATGACCC
*
135885 CATTAATATTAAATAAATTTTTTTAAAAAT
1 CATTAATATT-AATAAATTGTTTTAAAAAT
* *
135915 CATTAATAGTAATAAA-TGTTTTAATAAT
1 CATTAATATTAATAAATTGTTTTAAAAAT
* *
135943 TATTATTATTAAT
1 CATTAATATTAAT
135956 TAATAATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 20 0.57
29 6 0.17
30 9 0.26
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
CATTAATATTAATAAATTGTTTTAAAAAT
Done.