Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015683.1 Corchorus olitorius cultivar O-4 contig15716, 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: 112866
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:197 original size:11 final size:11
Alignment explanation
Indices: 183--225 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
173 CATTATTTAT
183 TATTTATAATA
1 TATTTATAATA
* *
194 TATTTATTATT
1 TATTTATAATA
205 TATTTAATAATA
1 TATTT-ATAATA
217 TATATTATA
1 TAT-TTATA
226 TCTAAGATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 14 0.54
12 10 0.38
13 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTTATAATA
Found at i:203 original size:21 final size:24
Alignment explanation
Indices: 174--224 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
164 TTTTGAACTC
174 ATTATT-TATTATTT-ATAATATAT
1 ATTATTAT-TTATTTAATAATATAT
197 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
220 ATTAT
1 ATTAT
225 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.44
23 10 0.40
24 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:561 original size:23 final size:23
Alignment explanation
Indices: 531--576 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
521 TCCACTTAGC
*
531 CCCGTGCTGCTATATGATCCATT
1 CCCGTGCTACTATATGATCCATT
554 CCCGTGCTACTATATGATCCATT
1 CCCGTGCTACTATATGATCCATT
577 TTGGATTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (23 bp):
CCCGTGCTACTATATGATCCATT
Found at i:6022 original size:37 final size:37
Alignment explanation
Indices: 5972--6046 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
5962 CAAAATATCT
* *
5972 TAGTCGAGAAATTATCAGGTGGGATGGACCCACCACA
1 TAGTCGAGAAATTATCAGATGGGACGGACCCACCACA
* *
6009 TAGTCGAGAAATTATTAGATTGGACGGACCCACCACA
1 TAGTCGAGAAATTATCAGATGGGACGGACCCACCACA
6046 T
1 T
6047 TATCAACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (37 bp):
TAGTCGAGAAATTATCAGATGGGACGGACCCACCACA
Found at i:6323 original size:106 final size:108
Alignment explanation
Indices: 6131--6323 Score: 309
Period size: 106 Copynumber: 1.8 Consensus size: 108
6121 TTACCATTTA
* * *
6131 TCCATTATTTAATTTAAAAAGGGACTAAACATCGGGCTAAAATTGTATCTAAATTATAGGATTTG
1 TCCATTATTTAATTTAAAAAGGGACTAAACATCAGACTAAAATTATATCTAAATTATAGGATTTG
*
6196 ACTTGACGTGGTACAATTTTATGGGTTGGTCCCATAGTTGATG
66 ACTTGACGTGGCACAATTTTATGGGTTGGTCCCATAGTTGATG
* * *
6239 TCCATTATTTAATTT-AAAAGGGACTAAATATCAGACTAAAATTATGTCT-AATTTTAGGATTTG
1 TCCATTATTTAATTTAAAAAGGGACTAAACATCAGACTAAAATTATATCTAAATTATAGGATTTG
6302 ACTTGACGTGGCACAATTTTAT
66 ACTTGACGTGGCACAATTTTAT
6324 TGACTGATGT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
106 34 0.44
107 29 0.37
108 15 0.19
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (108 bp):
TCCATTATTTAATTTAAAAAGGGACTAAACATCAGACTAAAATTATATCTAAATTATAGGATTTG
ACTTGACGTGGCACAATTTTATGGGTTGGTCCCATAGTTGATG
Found at i:8043 original size:17 final size:17
Alignment explanation
Indices: 8023--8059 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
8013 TTCTTTATTG
*
8023 AAAAATAGAAAA-AAGA
1 AAAAAAAGAAAAGAAGA
8039 AAAAAAAGAAAAGAAGA
1 AAAAAAAGAAAAGAAGA
8056 AAAA
1 AAAA
8060 TGAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAGAAGA
Found at i:26862 original size:3 final size:3
Alignment explanation
Indices: 26854--26898 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
26844 TAAAGGACTT
* *
26854 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG GGG TGG GGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
26899 CAGCGGTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.71, T:0.29
Consensus pattern (3 bp):
TGG
Found at i:28128 original size:15 final size:16
Alignment explanation
Indices: 28103--28132 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28093 AATAATTATT
28103 TTTAGATTATAATATA
1 TTTAGATTATAATATA
28119 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
28133 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:29247 original size:334 final size:332
Alignment explanation
Indices: 28487--30953 Score: 1748
Period size: 336 Copynumber: 7.5 Consensus size: 332
28477 AAATTTTACA
* *
28487 TCATCTAATCAAATCTCAGACACATTGGATTTTAA-AATT-TGCTTTTACGAGCATCTGAATCTT
1 TCATCTAATCAAATCTCAGTCACATTGGA-TTTAAGGATTAT--TTTTACGAGCATCTGAATCTT
* ** * * *
28550 GTATCGATTTAATTAAAAATTAATTTGGAAAA-ATA-GGAAAACGATAGTACAAA-CGTTAAAAG
63 GTTTCGATTTAATTAAAAATTAATTCAGAAAATATATGAAAAACGATATTA-AAAGCGTGAAAAG
* * * *
28612 TCCTTCAATCTTTTTGGCGTTGAA--A-ATAT-TTTTAAGAGTATTTTAGGCAAAAATTGAGGAA
127 TCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTCAGCCAAAAATTGAGGAA
* * * *** * * * * * * *
28673 ATATCTTTCAAGTCA-AAATTACAAAATTTTAACTGGAATC--GTAA-CAGTC---AT-AGTTTA
192 AAATATTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAAGTAATCAAAATCAGTTTT
** * * * * * *
28730 TAACTAAAAAAGCGTTCCAGAGCCCCGACTCAGTTTTGCATGATTTTAT-GCGCCAAAACTCCTT
257 TTGCTAAAAACGCGTTTC-GGGCCCCGGCTCAGTTTTGCATGATTTT-TGGCACCAAGACTCCTT
*
28794 -AAGATATCCATAT
320 GAA-ATATCTATAT
* * * * * ** * * *
28807 T-ATTATAATCAAATCTTAGTCACATCGGATATAAGAATTTATTTTTAAAACCATCTGAATTTTC
1 TCA-TCTAATCAAATCTCAGTCACATTGGATTTAAGGA-TTATTTTTACGAGCATCTGAATCTTG
* ** * *
28871 TTTCGATTTAGTTGGAAATTAATTCAGAAAA-ATAAGAAAAACGATATTAAAAGTGTGAAAAGTC
64 TTTCGATTTAATTAAAAATTAATTCAGAAAATATATGAAAAACGATATTAAAAGCGTGAAAAGTC
* * * * *
28935 ATCCAATTTTTTTGGCGGTAAATTATATATATTTTATGAGTATTTCATCCAAAAATTGAGGAAAA
129 CTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTCAGCCAAAAATTGAGGAAAA
* *
29000 AT-TCTTCGGGTCATTTTTTGCAAAATTTTA-CCTGAAATCGTGTAAGTTAGTCAAAATCATGAT
194 ATAT-TTCGAGTCATTTTTTGCAAAATTTTAGCC-GAAATCGTGTAAG-TAATCAAAATCA-G-T
*** * * *
29063 TTTTTGCTAAAAATTTGTTTCGTGGCCCCGGCTCAGTTTTGCATAATTTTTGGCATCGAGACTCC
254 TTTTTGCTAAAAACGCGTTTCG-GGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCC
29128 TTGAAATATCTATAT
318 TTGAAATATCTATAT
* *
29143 TCATCTATTCAAATCTCAGTCACATTGCATTTAAGGA-TATTTTTACGAGCATCTGAATCTTGTT
1 TCATCTAATCAAATCTCAGTCACATTGGATTTAAGGATTATTTTTACGAGCATCTGAATCTTGTT
*
29207 TCGATTTAATTAAAAATTAATTCA-AAAATATATGAAAAACGATATTAAAAGCATGAAAAAGTCC
66 TCGATTTAATTAAAAATTAATTCAGAAAATATATGAAAAACGATATTAAAAGCGTG-AAAAGTCC
* ** * * * *
29271 TTCAATCTTTTTGGAATTGAATTATACATATTTTATAAGTATTTTAGACAAAAATTGAGGAAAAA
130 TCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTCAGCCAAAAATTGAGGAAAAA
*** * * * *
29336 TATTTATTGTC-TATTTTTGCAAAATATTAGCCGAAATCGTGTACGTTAGTCAAAATCAAGGTTT
195 TATTTCGAGTCAT-TTTTTGCAAAATTTTAGCCGAAATCGTGTAAG-TAATCAAAATC-AGTTTT
*** * * *
29400 TTGCCTAAAAA-----TT-------CATTTCAG----G-GT-ATTTTTGGC-GCAAGACTCCTTA
257 TTG-CTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTG
29446 AAATATCTATAT
321 AAATATCTATAT
* ** * * * * *
29458 TCATCTAACCAAATCTCAACCACATTGGATTTGAGGA-T-TTGTAAGGCAAGCATCTGAATCATG
1 TCATCTAATCAAATCTCAGTCACATTGGATTTAAGGATTATTTTTA--CGAGCATCTGAATCTTG
* * * * * *
29521 TTTCTATTTAATTAGAAATTAATTCAGCAAATAATAGGAAAAACGATATTAGAAA-CATGAAAAA
64 TTTCGATTTAATTAAAAATTAATTCAGAAAAT-ATATGAAAAACGATATTA-AAAGCGTGAAAAG
* * * * ** *
29585 CCCTTCAATCTTTTTGGCATTGAATTATATA-ATTTTTATGAGTATTGT-GGATAAAAAATTGTG
127 TCCTCCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATT-TCAG-CCAAAAATTGAG
* * * * * ** *
29648 GAAATAA-CTTTCGAATCAATTTTTGCAAAATTGTAGTCGAAATCGTGTAA-TAATCATCA-CGG
189 GAAA-AATATTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAAGTAATCAAAATCAG
* * * * *
29710 TTTTTTTGGATAAAAACGCGTTCCGGAGCCCTGGCTAAGTTTTGCATGATTTTTGGCACCAATAC
253 -TTTTTT-GCTAAAAACGCGTTTCGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGAC
* * *
29775 TCTTTGAGATATCCATAT
315 TCCTTGAAATATCTATAT
* * * * * *
29793 TAATCTAATCAAATCTCAG-CTGCATTTGATTTAAGAATTTATTTTTACCAGCATCTGAATTTTG
1 TCATCTAATCAAATCTCAGTC-ACATTGGATTTAAGGA-TTATTTTTACGAGCATCTGAATCTTG
* * ** * * *
29857 TTTCAATTTAATTAGAAATTAATTCAGATTA-ATATGAAAAATGATATCAAAAGTGTGAAAAGTC
64 TTTCGATTTAATTAAAAATTAATTCAGAAAATATATGAAAAACGATATTAAAAGCGTGAAAAGTC
** * *
29921 CTCCAATCTTTTTTACGTTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGATGGAAA
129 CTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTCAGCCAAAAATTGA-GGAAA
* * * * **
29986 AAT-TTATCGGGTCATTTTTTGCAAAATTTCAGCCGAAATCGTGT-ACTAACCATCA-CAGTTTT
193 AATATT-TCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAAGTAATCAAAATCAGTTTT
* * * * * * *
30048 TGGCTAAAAAAGCGTTTTGGGGCCCTGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTG
257 TTGCTAAAAACGCG-TTTCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTG
*
30113 CAATATCTATAT
321 AAATATCTATAT
* * * * * *
30125 TCATCTAATCAAATATCAG-CAACATTGAATTTAAGCATTTGTTTTTACGAGAATCTGAATCCTG
1 TCATCTAATCAAATCTCAGTC-ACATTGGATTTAAGGA-TTATTTTTACGAGCATCTGAATCTTG
* *
30189 TTTCGCTTTAATTAATTAGAAATTAATTCAGAAAA-ATATGAAAAACGATATTAAAAGCGCGAAA
64 TTTCGATTTAATT-A--A-AAATTAATTCAGAAAATATATGAAAAACGATATTAAAAGCGTGAAA
* * * *
30253 AGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGCGGCTAAAAATTGAGA
125 AGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTCAGCCAAAAATTGAGG
* ** *
30318 AAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ACCAATC---A-CGGTT
190 AAAAATATTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAAGTAATCAAAATCAGTT
* * * *** *
30378 TTTTGGGCTAAAAACACGTTCCGGGCCCCGTG-TTAGTTTTGCATGATTTTTGGTGGCAAAACTC
255 TTTT--GCTAAAAACGCGTTTCGGGCCCCG-GCTCAGTTTTGCATGATTTTTGGCACCAAGACTC
*
30442 ATTGAAATATCTATAT
317 CTTGAAATATCTATAT
* * * *
30458 TCATCTAA-CAAAATCTTAGGCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATT
1 TCATCTAATC-AAATCTCAGTCACATTGGATTTAAGGA-TTATTTTTACGAGCATCTGAATC-TT
* * * * * *
30522 -TTTCGATTTAATTAAAAATTAATTTGAAAAAATATAGGGAAAACGATATTAGAAGCGTGAGAAG
63 GTTTCGATTTAATTAAAAATTAA-TTCAGAAAATATATGAAAAACGATATTAAAAGCGTGAAAAG
* * * * * * *
30586 CCCTTCAATCTTTTTGCCGTTGAATTATATA-CTTTTATGAGTATTGTGA-CTAAAAATT-AAGA
127 TCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATT-TCAGCCAAAAATTGAGGA
* ** *
30648 AAAATATTTC-ACGTACA-TTTTTGCAAAATTTTAGCCGAAATC-T-T--GT-ACCATCAT-GGT
191 AAAATATTTCGA-GT-CATTTTTTGCAAAATTTTAGCCGAAATCGTGTAAGTAATCAAAATCAGT
* * **
30705 TTTTTGGCTAAAAACGCGTTACGGGTCCCTGTG-TCAGTTTTGCATGATTTTT-G-A-CGGGA--
254 TTTTT-GCTAAAAACGCGTTTCGGG-CCCCG-GCTCAGTTTTGCATGATTTTTGGCACCAAGACT
*
30764 -----AATATATTTATAT
316 CCTTGAA-ATATCTATAT
* * * * * * * ** *
30777 TCATGTAACCAAATCTTAGCCACATTGTATTTAAGGATTTGTTTTTACAAGTTTCTAAATCTTGT
1 TCATCTAATCAAATCTCAGTCACATTGGATTTAAGGA-TTATTTTTACGAGCATCTGAATCTTGT
* * * * *
30842 TTCTATTTAATTAAAAATTAATTTAGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAG
65 TTCGATTTAATTAAAAATTAATTCAG-AA-AATATATGAAAAACGATATTAAAAGCGTG-AAAAG
* * * * * *
30907 GCTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGATTATTT
127 TCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTT
30954 TCGTATACCA
Statistics
Matches: 1736, Mismatches: 305, Indels: 211
0.77 0.14 0.09
Matches are distributed among these distances:
314 5 0.00
315 66 0.04
316 56 0.03
317 50 0.03
318 75 0.04
319 93 0.05
320 102 0.06
321 72 0.04
322 18 0.01
323 1 0.00
324 5 0.00
325 43 0.02
326 17 0.01
327 20 0.01
328 42 0.02
329 46 0.03
330 38 0.02
331 54 0.03
332 132 0.08
333 148 0.09
334 204 0.12
335 212 0.12
336 229 0.13
337 4 0.00
338 4 0.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (332 bp):
TCATCTAATCAAATCTCAGTCACATTGGATTTAAGGATTATTTTTACGAGCATCTGAATCTTGTT
TCGATTTAATTAAAAATTAATTCAGAAAATATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
CCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTCAGCCAAAAATTGAGGAAAAAT
ATTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAAGTAATCAAAATCAGTTTTTTGC
TAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATA
TCTATAT
Found at i:37390 original size:2 final size:2
Alignment explanation
Indices: 37383--37409 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37373 GGAGAAAGAA
37383 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 A
37410 ATAGAGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52153 original size:11 final size:12
Alignment explanation
Indices: 52132--52158 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52122 TGGTGCCACA
52132 TTTTGATTTTTT
1 TTTTGATTTTTT
52144 TTTTGATTTTTT
1 TTTTGATTTTTT
52156 TTT
1 TTT
52159 CACTTTTCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (12 bp):
TTTTGATTTTTT
Found at i:53224 original size:80 final size:80
Alignment explanation
Indices: 53091--53250 Score: 257
Period size: 80 Copynumber: 2.0 Consensus size: 80
53081 TTTTCTATGG
* **
53091 CTCCGATAAATTTCATCAACTCTTATCCAACGGTTCGCGGAATTTAACAATTTCCATACAAAAAG
1 CTCCGATAAATTTCATCAACTCTTATCCAACAGTTAACGGAATTTAACAATTTCCATACAAAAAG
*
53156 GCTAATTTATCCCTT
66 ACTAATTTATCCCTT
* * *
53171 CTCCGATAAATTTCATTAACTCTTGTCCAATAGTTAACGGAATTTAACAATTTCCATACAAAAAG
1 CTCCGATAAATTTCATCAACTCTTATCCAACAGTTAACGGAATTTAACAATTTCCATACAAAAAG
53236 ACTAATTTATCCCTT
66 ACTAATTTATCCCTT
53251 TTTTACAAGT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (80 bp):
CTCCGATAAATTTCATCAACTCTTATCCAACAGTTAACGGAATTTAACAATTTCCATACAAAAAG
ACTAATTTATCCCTT
Found at i:53952 original size:12 final size:12
Alignment explanation
Indices: 53935--53966 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
53925 TGACGGTGGA
53935 GGTGGTGGAGGC
1 GGTGGTGGAGGC
*
53947 GGTGGTGGTGGC
1 GGTGGTGGAGGC
53959 GGTGGTGG
1 GGTGGTGG
53967 GGGTTGCGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.06, G:0.69, T:0.22
Consensus pattern (12 bp):
GGTGGTGGAGGC
Found at i:57352 original size:6 final size:6
Alignment explanation
Indices: 57344--57426 Score: 112
Period size: 6 Copynumber: 13.8 Consensus size: 6
57334 CATAGGTGGT
* * * * *
57344 GGCGGT GGCGGT GGCGGC GGTGGC GGCGGT GGCGGC GGTGGC GGCGGC
1 GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC
*
57392 GGCGGC GGCGGC GGCGGC GGCGGT GGCGGC GGCGG
1 GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGG
57427 TGATTGAGGA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.00, C:0.25, G:0.67, T:0.07
Consensus pattern (6 bp):
GGCGGC
Found at i:57362 original size:9 final size:9
Alignment explanation
Indices: 57350--57428 Score: 113
Period size: 9 Copynumber: 8.8 Consensus size: 9
57340 TGGTGGCGGT
57350 GGCGGTGGC
1 GGCGGTGGC
57359 GGCGGTGGC
1 GGCGGTGGC
57368 GGCGGTGGC
1 GGCGGTGGC
57377 GGCGGTGGC
1 GGCGGTGGC
*
57386 GGCGGCGGC
1 GGCGGTGGC
*
57395 GGCGGCGGC
1 GGCGGTGGC
*
57404 GGCGGCGGC
1 GGCGGTGGC
* *
57413 GGTGGCGGC
1 GGCGGTGGC
57422 GGCGGTG
1 GGCGGTG
57429 ATTGAGGAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.00, C:0.25, G:0.67, T:0.08
Consensus pattern (9 bp):
GGCGGTGGC
Found at i:58337 original size:7 final size:7
Alignment explanation
Indices: 58324--58385 Score: 70
Period size: 8 Copynumber: 8.3 Consensus size: 7
58314 TCTTTGACAA
58324 AAAAAAC
1 AAAAAAC
*
58331 CAAAAAC
1 AAAAAAC
58338 AAAAAAAC
1 -AAAAAAC
*
58346 CAAAAAC
1 AAAAAAC
58353 AAAAAGAC
1 AAAAA-AC
58361 AAAAAGAC
1 AAAAA-AC
58369 AAAAAAC
1 AAAAAAC
58376 TAAAAAAC
1 -AAAAAAC
58384 AA
1 AA
58386 CTCTATTCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
7 20 0.42
8 28 0.58
ACGTcount: A:0.79, C:0.16, G:0.03, T:0.02
Consensus pattern (7 bp):
AAAAAAC
Found at i:58343 original size:15 final size:15
Alignment explanation
Indices: 58323--58374 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
58313 TTCTTTGACA
58323 AAAAAAACCAAAAAC
1 AAAAAAACCAAAAAC
58338 AAAAAAACCAAAAAC
1 AAAAAAACCAAAAAC
* *
58353 AAAAAGACAAAAAGAC
1 AAAAAAACCAAAA-AC
58369 AAAAAA
1 AAAAAA
58375 CTAAAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 26 0.79
16 7 0.21
ACGTcount: A:0.81, C:0.15, G:0.04, T:0.00
Consensus pattern (15 bp):
AAAAAAACCAAAAAC
Found at i:58375 original size:23 final size:23
Alignment explanation
Indices: 58332--58385 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
58322 AAAAAAAACC
*
58332 AAAAACAAAAAAACCAAAAAC-A
1 AAAAACAAAAAAACAAAAAACTA
*
58354 AAAAGACAAAAAGACAAAAAACTA
1 AAAA-ACAAAAAAACAAAAAACTA
58378 AAAAACAA
1 AAAAACAA
58386 CTCTATTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 19 0.68
24 5 0.18
ACGTcount: A:0.80, C:0.15, G:0.04, T:0.02
Consensus pattern (23 bp):
AAAAACAAAAAAACAAAAAACTA
Found at i:58380 original size:15 final size:14
Alignment explanation
Indices: 58324--58381 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 14
58314 TCTTTGACAA
58324 AAAAAACCAAAAAC
1 AAAAAACCAAAAAC
58338 AAAAAAACCAAAAAC
1 -AAAAAACCAAAAAC
*
58353 AAAAAGACAAAAAGAC
1 AAAAA-ACCAAAA-AC
*
58369 AAAAAACTAAAAA
1 AAAAAACCAAAAA
58382 ACAACTCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.15
15 26 0.67
16 7 0.18
ACGTcount: A:0.79, C:0.16, G:0.03, T:0.02
Consensus pattern (14 bp):
AAAAAACCAAAAAC
Found at i:63368 original size:16 final size:16
Alignment explanation
Indices: 63339--63395 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 16
63329 AGCGTAACAA
**
63339 AAACAAAATGAAAACG
1 AAACAAAAACAAAACG
63355 AAACAAAAAC-AAA--
1 AAACAAAAACAAAACG
*
63368 AAAC-AGAA-AAAACG
1 AAACAAAAACAAAACG
63382 AAACAAAAACAAAA
1 AAACAAAAACAAAA
63396 AACAGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
12 6 0.19
13 4 0.12
14 4 0.12
15 6 0.19
16 12 0.38
ACGTcount: A:0.77, C:0.14, G:0.07, T:0.02
Consensus pattern (16 bp):
AAACAAAAACAAAACG
Found at i:63389 original size:19 final size:19
Alignment explanation
Indices: 63355--63403 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
63345 AATGAAAACG
*
63355 AAACAAAAACAAAAAACAGAA
1 AAACAGAAAC-AAAAACA-AA
63376 AAA-ACGAAACAAAAACAAA
1 AAACA-GAAACAAAAACAAA
63395 AAACAGAAA
1 AAACAGAAA
63404 AACGAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 9 0.36
20 9 0.36
21 7 0.28
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (19 bp):
AAACAGAAACAAAAACAAA
Found at i:63420 original size:26 final size:27
Alignment explanation
Indices: 63349--63410 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
63339 AAACAAAATG
63349 AAAACGAAACAAAAACAAAAAACAGAA
1 AAAACGAAACAAAAACAAAAAACAGAA
63376 AAAACGAAACAAAAACAAAAAACAG-A
1 AAAACGAAACAAAAACAAAAAACAGAA
63402 AAAACGAAA
1 AAAACGAAA
63411 ACATGCCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 10 0.29
27 25 0.71
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (27 bp):
AAAACGAAACAAAAACAAAAAACAGAA
Found at i:66634 original size:39 final size:39
Alignment explanation
Indices: 66568--66644 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
66558 CATCTTCTAC
*
66568 TTTCCCTTTCATCTCATTCAAATTTCTTAG-AATCCCTAT
1 TTTCCCTTTCATCTCATTCAAAGTTCTT-GCAATCCCTAT
*
66607 TTTCCCTTTCATTTC-TTCAAAAGTTCTTGCAATCCCTA
1 TTTCCCTTTCATCTCATTC-AAAGTTCTTGCAATCCCTA
66645 AAATACTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.22, C:0.29, G:0.04, T:0.45
Consensus pattern (39 bp):
TTTCCCTTTCATCTCATTCAAAGTTCTTGCAATCCCTAT
Found at i:68007 original size:177 final size:177
Alignment explanation
Indices: 67708--68386 Score: 979
Period size: 177 Copynumber: 3.8 Consensus size: 177
67698 AACTACTGCC
*
67708 CATATTAACACTTTTATATCCACAAT-GCCATGTTACGTTCAGGCTCTAACTTTTGGTTCAATTA
1 CATATTAACACTTTTATATCCACAATGGCC-TGTTACGTTCAGGTTCTAACTTTTGGTTCAATTA
* *
67772 TATCAACCCTTAACAATAT-TGATGCCATGTTATGCATTAAACTTACAAACAATTGGGAAAACGT
65 TATCAACCCTTAACAGT-TCTGATACCATGTTATGCATTAAACTTACAAACAATTGGGAAAACGT
* *
67836 GCAGGTAACCAAGTAGAATAAACGTGAACTATGAACTATAAATAAGATT
129 GCAGGTAACCAAGTTGAATAAACGTGAACAATGAACTATAAATAAGATT
*
67885 CAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAGGTTCTAACTTTTGGTTCAATTAT
1 CATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAGGTTCTAACTTTTGGTTCAATTAT
* * * *
67950 ATCAACTCTTAAGC-GTTCTGATACCATGTTATGCATTAAACTTACAAATAGTTGGGAAAACTTG
66 ATCAACCCTTAA-CAGTTCTGATACCATGTTATGCATTAAACTTACAAACAATTGGGAAAACGTG
* * * * * *
68014 CAAGTCACCAACTTGAATAAACGTCAACAATGAAATATAAATAAGACT
130 CAGGTAACCAAGTTGAATAAACGTGAACAATGAACTATAAATAAGATT
* * * * *
68062 CATATTAACACTTTTATATCCACAATGGCCTATTACGTTCAGGTTCGAACTTTTAGTTCAGTTTT
1 CATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAGGTTCTAACTTTTGGTTCAATTAT
* *
68127 ATCAACCCTTAACAGTTCGGATACCATGTTATGCATTAAACTTACAAAAAATTGGGAAAACGTGC
66 ATCAACCCTTAACAGTTCTGATACCATGTTATGCATTAAACTTACAAACAATTGGGAAAACGTGC
* *
68192 AGGTAACC-AGCTTGAATAAACGTGAACAAAGAACTATGAATAAGATT
131 AGGTAACCAAG-TTGAATAAACGTGAACAATGAACTATAAATAAGATT
* * * * *
68239 CATATTAACACTTTCATATCCACAATGGCATGTTACGTACAAGTTCTAACTTTTGGTTCAACTAT
1 CATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAGGTTCTAACTTTTGGTTCAATTAT
* * * *
68304 ATCTACCCTTAGCAGTTCTGATACCATGTTATGCAATAAACTTACAAACAGTTGGGAAAACGTGC
66 ATCAACCCTTAACAGTTCTGATACCATGTTATGCATTAAACTTACAAACAATTGGGAAAACGTGC
*
68369 AGGTAACCAACTTGAATA
131 AGGTAACCAAGTTGAATA
68387 GAAGATCTCA
Statistics
Matches: 444, Mismatches: 52, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
176 3 0.01
177 436 0.98
178 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (177 bp):
CATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAGGTTCTAACTTTTGGTTCAATTAT
ATCAACCCTTAACAGTTCTGATACCATGTTATGCATTAAACTTACAAACAATTGGGAAAACGTGC
AGGTAACCAAGTTGAATAAACGTGAACAATGAACTATAAATAAGATT
Found at i:68973 original size:177 final size:178
Alignment explanation
Indices: 68708--69111 Score: 549
Period size: 177 Copynumber: 2.3 Consensus size: 178
68698 TCTAAAAGTT
* * * *
68708 CAAGTTCTAACATTTGGTTCAATAATATCAACCCTGAACAGCTCTAATAGATACCATGTTATACA
1 CAAGTTCTAACTTTTGGTTCAATTATATCAACCCTTAACAG-T-T-CTAGATACCATGTTATACA
* * * * *
68773 TTAAACTTACAAATAGTTGGGAAAACGTTCAGGTAGCCAACTTGAATAAACGTGAACCATGAACT
63 TTAAACTTACAAACAGTTGGGAAAACATACAAGTAACCAACTTGAATAAACGTGAACCATGAACT
68838 ATAAATAAGATACAAATTAACACTTTTATATCCACAATGGCCTATTACGTC
128 ATAAATAAGATACAAATTAACACTTTTATATCCACAATGGCCTATTACGTC
* * * * * *
68889 CAGGTTCAAACTTTTGATTCAATTATATCAACCCTTAACAGTTCT-GATACTATGTTATGCTTTA
1 CAAGTTCTAACTTTTGGTTCAATTATATCAACCCTTAACAGTTCTAGATACCATGTTATACATTA
*
68953 AACTTACAAACAGTTGGGAAAACATACAAGTAACCAACTTGAATAAACGTGAACTATGAACTATA
66 AACTTACAAACAGTTGGGAAAACATACAAGTAACCAACTTGAATAAACGTGAACCATGAACTATA
* * * * * * *
69018 AATAAGATTCATATTAACACTTTTATATCCATAATGGCTTGTTACTTT
131 AATAAGATACAAATTAACACTTTTATATCCACAATGGCCTATTACGTC
* *
69066 CAAGTTCTAACTTTTGGTTCAAATATATCAATCCTTAACAGTTCTA
1 CAAGTTCTAACTTTTGGTTCAATTATATCAACCCTTAACAGTTCTA
69112 TGAACTATAA
Statistics
Matches: 194, Mismatches: 28, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
177 156 0.80
178 1 0.01
179 1 0.01
180 1 0.01
181 35 0.18
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (178 bp):
CAAGTTCTAACTTTTGGTTCAATTATATCAACCCTTAACAGTTCTAGATACCATGTTATACATTA
AACTTACAAACAGTTGGGAAAACATACAAGTAACCAACTTGAATAAACGTGAACCATGAACTATA
AATAAGATACAAATTAACACTTTTATATCCACAATGGCCTATTACGTC
Found at i:69354 original size:279 final size:280
Alignment explanation
Indices: 68831--69389 Score: 913
Period size: 279 Copynumber: 2.0 Consensus size: 280
68821 AACGTGAACC
68831 ATGAACTATAAATAAGATACAAATTAACACTTTTATATCCACAATGGCCTATTACGTCCAGGTTC
1 ATGAACTATAAATAAGATACAAATTAACACTTTTATATCCACAATGGCCTATTACGTCCAGGTTC
* * * *
68896 AAACTTTTGATTCAATTATATCAACCCTTAACAGTTCTGATACTATGTTATGCTTTAAACTTACA
66 AAACTTTCGATTCAATTATATCAACCCTTAACAGTTATGATACCATGTTATGCATTAAACTTACA
* *
68961 AACAGTTGGGAAAACATACAAGTAACCAACTTGAATAAACGTGAACTATGAACTATAAATAAGAT
131 AACAGTTGGAAAAACATACAAGTAACCAACTTGAATAAACGTCAACTATGAACTATAAATAAGAT
* * *
69026 TCATATTAACACTTTTATATCCATAATGGCTTGTTACTTTCAAGTTCTAACTTTTGGTTCAAATA
196 TCATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAAGTTCTAACTTTTGGTTCAAATA
* *
69091 TATCAATCCTTAACAGTTCT
261 TATCAACCCTTAAAAGTTCT
* * * * *
69111 ATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCTTGTTACGTTCAGG-TC
1 ATGAACTATAAATAAGATACAAATTAACACTTTTATATCCACAATGGCCTATTACGTCCAGGTTC
* * *
69175 TAACTTTCGATTCAATTATATCAAGCCTTAATAGTTATGATACCATGTTATGCATTAAACTTACA
66 AAACTTTCGATTCAATTATATCAACCCTTAACAGTTATGATACCATGTTATGCATTAAACTTACA
*
69240 AACAGTTGGAAAAACATACAAGTAACCAACTTGAATAAACGTCAACTATGAACTATAAATCAGAT
131 AACAGTTGGAAAAACATACAAGTAACCAACTTGAATAAACGTCAACTATGAACTATAAATAAGAT
* *
69305 TCATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAGGTTCTAACTTTTGGTTCAATTA
196 TCATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAAGTTCTAACTTTTGGTTCAAATA
69370 TATCAACCCTTAAAAGTTCT
261 TATCAACCCTTAAAAGTTCT
69390 GAAATCATGT
Statistics
Matches: 257, Mismatches: 22, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
279 200 0.78
280 57 0.22
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (280 bp):
ATGAACTATAAATAAGATACAAATTAACACTTTTATATCCACAATGGCCTATTACGTCCAGGTTC
AAACTTTCGATTCAATTATATCAACCCTTAACAGTTATGATACCATGTTATGCATTAAACTTACA
AACAGTTGGAAAAACATACAAGTAACCAACTTGAATAAACGTCAACTATGAACTATAAATAAGAT
TCATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAAGTTCTAACTTTTGGTTCAAATA
TATCAACCCTTAAAAGTTCT
Found at i:69466 original size:177 final size:176
Alignment explanation
Indices: 69109--69626 Score: 734
Period size: 177 Copynumber: 2.9 Consensus size: 176
69099 CTTAACAGTT
*
69109 CTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCTTGTTACGTTCAGG-
1 CTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGT
* * * * *
69173 TCTAACTTTCGATTCAATTATATCAAGCCTTAATAGTTATGATACCATGTTATGCATTAAACTTA
66 TCTAACTTTTGGTTCAATTATATCAAACCTTAAAAGTTATGATACCATGTTATGCATTAAACTTG
* * *
69238 CAAACAGTTGGAAAAACATACAAGTAACCAACTTGAATAAACGTCAA
131 CAAATAGTTGG-AAAACATGCAAGTAACCAACTTGAATAAACATCAA
* * *
69285 CTATGAACTATAAATCAGATTCATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAGGT
1 CTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGT
* * * *
69350 TCTAACTTTTGGTTCAATTATATCAACCCTTAAAAGTTCTGAAATCATGTTATGCATTAAACTTG
66 TCTAACTTTTGGTTCAATTATATCAAACCTTAAAAGTTATGATACCATGTTATGCATTAAACTTG
* * * *
69415 CAAATAGTTGAGAAAACGTGCAGGTAACCAACTTTAATAAACATGAA
131 CAAATAGTTG-GAAAACATGCAAGTAACCAACTTGAATAAACATCAA
* *
69462 CTATGAACTATAAATGACATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGT
1 CTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGT
* * ** *
69527 TCCAACTTTTGGTTCAATTATTTCAAACCTTAACGGTTATGATACCATGTTATGCATCAAACTTG
66 TCTAACTTTTGGTTCAATTATATCAAACCTTAAAAGTTATGATACCATGTTATGCATTAAACTTG
*
69592 CAAACT-GTTGGGAAAACATGCAAATAACCAACTTG
131 CAAA-TAGTT-GGAAAACATGCAAGTAACCAACTTG
69627 TAAAGAAGGA
Statistics
Matches: 303, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
176 61 0.20
177 239 0.79
178 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (176 bp):
CTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGT
TCTAACTTTTGGTTCAATTATATCAAACCTTAAAAGTTATGATACCATGTTATGCATTAAACTTG
CAAATAGTTGGAAAACATGCAAGTAACCAACTTGAATAAACATCAA
Found at i:70058 original size:626 final size:615
Alignment explanation
Indices: 69283--70567 Score: 1838
Period size: 626 Copynumber: 2.1 Consensus size: 615
69273 AATAAACGTC
* *
69283 AACTATGAACTATAAATCAGATTCATATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAG
1 AACTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAG
* * *
69348 GTTCTAACTTTTGGTTCAATTATATCAACCCTTAAAAGTTCTGAAATCATGTTATGCATTAAACT
66 GTTCTAACTTTTGGTTAAATTATATCAACCCTTAAAAGTTCTGAAACCATGTTATGCATGAAACT
* *
69413 TGCAAATAGTTGAGAAAACGTGCAGGTAACCAACTTTAATAAACATGAACTATGAACTATAAATG
131 TACAAACAGTTGAGAAAACGTGCAGGTAACCAACTTTAATAAACATGAACTATGAACTATAAATG
*
69478 ACATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGTTCCAACTTTTGGTTCA
196 ACATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGTTCCAAATTTTGGTTCA
* * * *
69543 ATTATTTCAAACCTTAACGGTTATGATACCATGTTATGCATCAAACTTGCAAACTGTTGGGAAAA
261 ATTATATCAAACCTTAACAGTTATGATACCATGTTATGCATCAAACTTACAAACAGTTGGGAAAA
*
69608 CATGCAAATAACCAACTTG-TAAAGAAGGA-CTCATGTTATTCAGGATTAAAAATGTGTGATTTT
326 CATGCAAATAACCAACTTGATAAA-AA--ATCTCATGTTATTCAGGATTAAAAATGTGTAATTTT
* * *
69671 ACCACTTTACCCTATGCTTATTAATATAAACATTCGAATTTGAACGAAAATTAGTGCATCTTCGT
388 A-CACTTTACCCTATGCTTATAAATATAAACACTCGAATTTGAACGAAAATTAGTGCACCTTCGT
* * * * *
69736 TAAGCTTTTTATTTTACTTTTATATATCGAAGAAATTGGAGAGACAAAAATAAAGGAAAATACTA
452 TAAGCCTATTATTTTACTTTTATATAACGAAGAAATTGGAGAGAAAAAAACAAAGGAAAATACTA
* *
69801 GTATTATTTATAAGCATTCATCGACAATGAAAGGCACAGGTTTGTTTTATTTCCTTCCTTTTCTC
517 GTATTATATATAAGCATTCATCGACAATGAAAGGCACA----TGTTTGA--T--TT-CTTTTCTC
* *
69866 TGGTTTTCCTTTTACTCCTATTTCTTTGGTTCATTT-AGCTATG
573 TGGTTTTCCTTTTACTCCTATTCCTTTGGTTAATTTGAGC-ATG
69909 AACTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAG
1 AACTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAG
* *
69974 GTTCTAACTTTTGGTTAAATTATATCAACCCTTAATAGTTCTGATACCATGTTATGCATGAAACT
66 GTTCTAACTTTTGGTTAAATTATATCAACCCTTAAAAGTTCTGAAACCATGTTATGCATGAAACT
* *
70039 TACAAACAGTTGGGAAAACGTGCAGGTAACCAACTTTAATAAACGTGAACTATGAACTATAAATG
131 TACAAACAGTTGAGAAAACGTGCAGGTAACCAACTTTAATAAACATGAACTATGAACTATAAATG
* * *
70104 ACATTCAGATTAATACTTTTATATCCACAATGGCCTGTTACGTTCAGGTTCTAAATTTTGGTTCA
196 ACATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGTTCCAAATTTTGGTTCA
* * * *
70169 ATTATATCAACCCTTAACAGTTCTGGTACCATGTTATGCATTAAACTTACAAACAGTTGGGAAAA
261 ATTATATCAAACCTTAACAGTTATGATACCATGTTATGCATCAAACTTACAAACAGTTGGGAAAA
* ** ** **
70234 CGTGCAGGTAACCAACTTGAATAAAAAATCTCATGTTATTTGGGATTGCAAATGTGTAATTTTAC
326 CATGCAAATAACCAACTTG-ATAAAAAATCTCATGTTATTCAGGATTAAAAATGTGTAATTTTAC
* * *
70299 ACTTTACTCTATGCTTATAAATATAAACACTCGAATTTGAACGAAAATTTGTGCACCTTTGTTAA
390 ACTTTACCCTATGCTTATAAATATAAACACTCGAATTTGAACGAAAATTAGTGCACCTTCGTTAA
* * * *
70364 GCCTATTGTTTTACTTTTATATAACGAAGAAATTGTAGAGAAAAAAACAAAGGAAAGTAGTAGTA
455 GCCTATTATTTTACTTTTATATAACGAAGAAATTGGAGAGAAAAAAACAAAGGAAAATACTAGTA
** * * * *
70429 TTATATATAAGTGTTCGTTGAGAATGAGAGGCACATGTTTGATTTCTTTTCTCTGGTTTTCCTTT
520 TTATATATAAGCATTCATCGACAATGAAAGGCACATGTTTGATTTCTTTTCTCTGGTTTTCCTTT
* * * * *
70494 TTCTTCTATTCCTTTTGTTAATTTGGGCGTG
585 TACTCCTATTCCTTTGGTTAATTTGAGCATG
* *
70525 AATTATGAACTATAAATAAGATTTAGGATTAACACTTTTATAT
1 AACTATGAACTATAAATAAGATTCA-GATTAACACTTTTATAT
70568 TCACTATATA
Statistics
Matches: 591, Mismatches: 63, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
616 64 0.11
617 21 0.04
619 1 0.00
621 6 0.01
625 145 0.25
626 348 0.59
627 2 0.00
628 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (615 bp):
AACTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTCAG
GTTCTAACTTTTGGTTAAATTATATCAACCCTTAAAAGTTCTGAAACCATGTTATGCATGAAACT
TACAAACAGTTGAGAAAACGTGCAGGTAACCAACTTTAATAAACATGAACTATGAACTATAAATG
ACATTCAGATTAACACTTTTATATCCACAATGGCATGTTACGTTCAGGTTCCAAATTTTGGTTCA
ATTATATCAAACCTTAACAGTTATGATACCATGTTATGCATCAAACTTACAAACAGTTGGGAAAA
CATGCAAATAACCAACTTGATAAAAAATCTCATGTTATTCAGGATTAAAAATGTGTAATTTTACA
CTTTACCCTATGCTTATAAATATAAACACTCGAATTTGAACGAAAATTAGTGCACCTTCGTTAAG
CCTATTATTTTACTTTTATATAACGAAGAAATTGGAGAGAAAAAAACAAAGGAAAATACTAGTAT
TATATATAAGCATTCATCGACAATGAAAGGCACATGTTTGATTTCTTTTCTCTGGTTTTCCTTTT
ACTCCTATTCCTTTGGTTAATTTGAGCATG
Found at i:70203 original size:177 final size:177
Alignment explanation
Indices: 69907--70258 Score: 623
Period size: 177 Copynumber: 2.0 Consensus size: 177
69897 CATTTAGCTA
*
69907 TGAACTATGAACTATAAATAAGATTCAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTC
1 TGAACTATGAACTATAAATAACATTCAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTC
* *
69972 AGGTTCTAACTTTTGGTTAAATTATATCAACCCTTAATAGTTCTGATACCATGTTATGCATGAAA
66 AGGTTCTAAATTTTGGTTAAATTATATCAACCCTTAACAGTTCTGATACCATGTTATGCATGAAA
*
70037 CTTACAAACAGTTGGGAAAACGTGCAGGTAACCAACTTTAATAAACG
131 CTTACAAACAGTTGGGAAAACGTGCAGGTAACCAACTTGAATAAACG
* *
70084 TGAACTATGAACTATAAATGACATTCAGATTAATACTTTTATATCCACAATGGCCTGTTACGTTC
1 TGAACTATGAACTATAAATAACATTCAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTC
* * *
70149 AGGTTCTAAATTTTGGTTCAATTATATCAACCCTTAACAGTTCTGGTACCATGTTATGCATTAAA
66 AGGTTCTAAATTTTGGTTAAATTATATCAACCCTTAACAGTTCTGATACCATGTTATGCATGAAA
70214 CTTACAAACAGTTGGGAAAACGTGCAGGTAACCAACTTGAATAAA
131 CTTACAAACAGTTGGGAAAACGTGCAGGTAACCAACTTGAATAAA
70259 AAATCTCATG
Statistics
Matches: 166, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
177 166 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (177 bp):
TGAACTATGAACTATAAATAACATTCAGATTAACACTTTTATATCCACAATGGCCTGTTACGTTC
AGGTTCTAAATTTTGGTTAAATTATATCAACCCTTAACAGTTCTGATACCATGTTATGCATGAAA
CTTACAAACAGTTGGGAAAACGTGCAGGTAACCAACTTGAATAAACG
Found at i:73843 original size:2 final size:2
Alignment explanation
Indices: 73838--73881 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
73828 ATAATCATGC
73838 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
73880 AT
1 AT
73882 GACTCGAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75251 original size:17 final size:17
Alignment explanation
Indices: 75229--75262 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
75219 ACATCAAAGA
75229 AAAATAAACTGCTAAGT
1 AAAATAAACTGCTAAGT
75246 AAAATAAACTGCTAAGT
1 AAAATAAACTGCTAAGT
75263 GCTAACCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAATAAACTGCTAAGT
Found at i:80527 original size:42 final size:39
Alignment explanation
Indices: 80481--80587 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 39
80471 TTAAACTTGG
80481 TGGGAACTTTCCCAATTTAAAAACTTTGAAAAAAAAACTAAA
1 TGGGAACTTTCCCAATTTAAAAACTTTG--AAAAAAACT-AA
* ** **
80523 TGGGAACTTTCGCAATTTGGAAAC-TT---AAAAACTGG
1 TGGGAACTTTCCCAATTTAAAAACTTTGAAAAAAACTAA
80558 TGGGAACTTTCCCAATTTAAAAACTTTGAA
1 TGGGAACTTTCCCAATTTAAAAACTTTGAA
80588 CTGATGAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
35 21 0.40
36 9 0.17
41 2 0.04
42 21 0.40
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (39 bp):
TGGGAACTTTCCCAATTTAAAAACTTTGAAAAAAACTAA
Found at i:80582 original size:35 final size:35
Alignment explanation
Indices: 80447--80583 Score: 107
Period size: 35 Copynumber: 3.7 Consensus size: 35
80437 CGAAAATGAC
* * *
80447 GGGAACTTTTCCTAAATTGAAAACTT--AAACTTGGT
1 GGGAAC-TTTCCCAATTTAAAAACTTAAAAAC-TGGT
**
80482 GGGAACTTTCCCAATTTAAAAACTTTGAAAAAAAAACTAAAT
1 GGGAACTTTCCCAATTTAAAAAC-TT-----AAAAACT-GGT
* **
80524 GGGAACTTTCGCAATTTGGAAACTTAAAAACTGGT
1 GGGAACTTTCCCAATTTAAAAACTTAAAAACTGGT
80559 GGGAACTTTCCCAATTTAAAAACTT
1 GGGAACTTTCCCAATTTAAAAACTT
80584 TGAACTGATG
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
34 14 0.17
35 31 0.39
36 7 0.09
41 3 0.04
42 25 0.31
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (35 bp):
GGGAACTTTCCCAATTTAAAAACTTAAAAACTGGT
Found at i:85197 original size:430 final size:435
Alignment explanation
Indices: 84377--85249 Score: 1226
Period size: 430 Copynumber: 2.0 Consensus size: 435
84367 CTCATATTGG
* *
84377 TTAATAAACCATATACACTTTATGCTACGAAAAGCATCTTGGTGGATAATGGTAAGCAAATATAT
1 TTAATAAACCATATACACTTTATGCTACGAAAAGCATCTTGGTGGATAATGGTAAACAAATATAC
* * *
84442 CAAATCCAGATGCCATCGTTGAGCATATTGTATAAAGGGTTTCATACAACACAATTCTACTAGTA
66 CAAATCCAGATGCCATCCTTAAGCATATTGTATAAAGGGTTTCATACAACACAATTATACTAGTA
*
84507 ATTAAGCCTATTATTACAGTAAACAATGCTAAATACACTATCAACAAATTATTAAGCCATCGATT
131 ATTAAACCTATTATTACAGTAAACAATGCTAAATACACTATCAACAAATTATTAAGCCATCGATT
* ** *
84572 AGCAGTGCCCGGGGACTGTTAGGCCTAAATATCGCTTTTAAAAAAGCCACCAAGGACATTATAAA
196 AACAGCACCCGGGGACTGTTAGGCCTAAATATCGCCTTTAAAAAA--CA-CAAGGACA-TATAAA
* *
84637 GAAAAAAAATTATTGTATATGTATTTCTAAGCTTCCCTTATTTCACTGCAGCCTCGCCAAAGTAC
257 GAAAAAAAATTATTGTATATGTAATTCTAAGCTTCCCTTATTTCACTGCAGCCTCCCCAAAGTAC
*
84702 TTCAGCAGCCAGCCATCAGACAGGCGGAACCACCATATCATAAGGCAGGCTGTAATGGAGATCCC
322 TTCAGCAGCCAGCCATCAGACAGACGGAACCACCATATCATAAGGCAGGCTGTAATGGAGATCCC
* *
84767 CAAAAAGCTAAACTGGGTTCTTTCC-CAAAAAAGTATCAATTGCTTTCC
387 CAAAAAGCTAAAATGGGTTCTTTCCAAAAAAAAGTATCAATTGCTTTCC
* **
84815 TTAATAAACCATATACACTTTATGCTATGAAAATTATCTTGGTGGATAATGGTAAAC-AATATAC
1 TTAATAAACCATATACACTTTATGCTACGAAAAGCATCTTGGTGGATAATGGTAAACAAATATAC
* *
84879 CAAATCCAGATGTCATCCTTAAGCATATTGTGTAAAGGGTTTCATACAACACAATTATACTAGTA
66 CAAATCCAGATGCCATCCTTAAGCATATTGTATAAAGGGTTTCATACAACACAATTATACTAGTA
* * * * * * *
84944 CTTAAACCTATTATTACTGTAAACAGTGTTAAATACACTATCAACAAATTATTAAGTCGTCTATT
131 ATTAAACCTATTATTACAGTAAACAATGCTAAATACACTATCAACAAATTATTAAGCCATCGATT
* *
85009 AACAGCCACCTTACGGGGACTGTTAGGCCTAATTATC-CCTTT-AAAAA-A-AA-GACA-CTAAA
196 AACAG-CACC---CGGGGACTGTTAGGCCTAAATATCGCCTTTAAAAAACACAAGGACATATAAA
** *
85068 G-AAAAAAATTATTGTATATGTACATT-TGGGCTTCCCTTATTTCACTGCAGTCTCCCCAAAGTA
257 GAAAAAAAATTATTGTATATGTA-ATTCTAAGCTTCCCTTATTTCACTGCAGCCTCCCCAAAGTA
* * * * *
85131 CTTCAGCAGCCAGGCTTCAGACAGACGGAACCACCATGTCATAATGCAGGCTGTAATGGTGATCC
321 CTTCAGCAGCCAGCCATCAGACAGACGGAACCACCATATCATAAGGCAGGCTGTAATGGAGATCC
* * *
85196 CCAAAAAGGTAAAATGGGTTCTTTCCAAAAAAAAAGTATCCATTGTTTTCC
386 CCAAAAAGCTAAAATGGGTTCTTTCC-AAAAAAAAGTATCAATTGCTTTCC
85247 TTA
1 TTA
85250 TTGGGTCCTT
Statistics
Matches: 388, Mismatches: 40, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
430 137 0.35
431 7 0.02
432 23 0.06
433 4 0.01
434 2 0.01
436 1 0.00
437 127 0.33
438 55 0.14
439 5 0.01
440 4 0.01
441 23 0.06
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (435 bp):
TTAATAAACCATATACACTTTATGCTACGAAAAGCATCTTGGTGGATAATGGTAAACAAATATAC
CAAATCCAGATGCCATCCTTAAGCATATTGTATAAAGGGTTTCATACAACACAATTATACTAGTA
ATTAAACCTATTATTACAGTAAACAATGCTAAATACACTATCAACAAATTATTAAGCCATCGATT
AACAGCACCCGGGGACTGTTAGGCCTAAATATCGCCTTTAAAAAACACAAGGACATATAAAGAAA
AAAAATTATTGTATATGTAATTCTAAGCTTCCCTTATTTCACTGCAGCCTCCCCAAAGTACTTCA
GCAGCCAGCCATCAGACAGACGGAACCACCATATCATAAGGCAGGCTGTAATGGAGATCCCCAAA
AAGCTAAAATGGGTTCTTTCCAAAAAAAAGTATCAATTGCTTTCC
Found at i:87842 original size:439 final size:438
Alignment explanation
Indices: 87024--87905 Score: 1205
Period size: 439 Copynumber: 2.0 Consensus size: 438
87014 CTCATATTGG
* *
87024 TTAATAAACCATATACACTTTATGCTACGAAAAGCATCTTGATGGATAATGGTAAACAATATACC
1 TTAATAAACAATATACACTTTATGCTACGAAAAGCATCTTGATGGATAATGGTAAACAATAGACC
* * * *
87089 AAATCTAGATGCCATCGTTGAGCATATTGTATAAAGGGTTTCATACAACACAATTCTAATAGTAA
66 AAATCCAGATGCCATCCTTAAGCATATTGTATAAAGGGTTTCATACAACACAATTATAATAGTAA
* *
87154 TTAAGCCTATTATTACAGTAAACAGTGCTAAATACACTGTCAACAAATTATTAAGCCATCGATTA
131 TTAAACCTATTATTACAGTAAACAGTGCTAAATACACTATCAACAAATTATTAAGCCATCGATTA
* * * *
87219 GCAGTGCCCGGGGACTGTTAGGCCTAAATATCGCTTTTAAAAAAGCCACCAAGGACATTATAAAG
196 ACAGTACCCGGGGACTGTTAGGCCCAAATATCGCTTTTAAAAAAGACACCAAGGACATTATAAAG
*** * *
87284 AAAAAAAAAATTACTGTATATGTTTTTCAAAACTTCCCTTATTTCACTGCAGCCTCGCCAAAGTA
261 --AAAAAAAATTACTGTATATGTACCTCAAAACTTCCCTTATTTCACTACAGCCTCGCCAAAATA
* *
87349 CTTCAACAGCCAGGCATCAGATAGGCGAAACCACCATATCATAAGGCAGGCTGTAATGGAGATCC
324 CTTCAACAGCCAGGCATCAGACAGGCGAAACCACCATATCATAAGGCAGGCTGTAAAGGAGATCC
* *
87414 CCAAAAAGCTAAACTGGGTTCTTTCC-CAAAAAAGTATCCATTGTTTTAC
389 CCAAAAAGCTAAAATGGGTTCTTTCCAAAAAAAAGTATCCATTGTTTTAC
** * *
87463 TTAATAAACAATATACACTTTATGCTACGAAAATTATTTTGGTGGATAATGGTAAACAATAGACC
1 TTAATAAACAATATACACTTTATGCTACGAAAAGCATCTTGATGGATAATGGTAAACAATAGACC
* * * *
87528 AAATCCAGATGTCATCCTTAAGCATATTGTGTAAAGGGTTTCATACAACACAATTATACTAGTAC
66 AAATCCAGATGCCATCCTTAAGCATATTGTATAAAGGGTTTCATACAACACAATTATAATAGTAA
* * * *
87593 TTAAACCTATTATTACTGTAAACAGTGCTAAATACACTATCAACAAATTATTAAGTCGTCTATTA
131 TTAAACCTATTATTACAGTAAACAGTGCTAAATACACTATCAACAAATTATTAAGCCATCGATTA
* * * *
87658 ACAGTCACCTTACGGGGACTGTTAGGCCCAATTATCTC-TTTAAAAAAGATACCAAGGCCATTAT
196 ACAGT-ACC---CGGGGACTGTTAGGCCCAAATATCGCTTTTAAAAAAGACACCAAGGACATTAT
* ** *
87722 AAAG-AAAAAAATTATTGTATATGTACCTCTGAGCTTCCCTTATTTCACTACAGCCTC-CACAAA
257 AAAGAAAAAAAATTACTGTATATGTACCTCAAAACTTCCCTTATTTCACTACAGCCTCGC-CAAA
** ** * * * * *
87785 ATACTTCAGTAGTTAGGCTTCAGACAGGCGGAACCACCATGTCATAATGCAGGCTGTAAAGGTGA
321 ATACTTCAACAGCCAGGCATCAGACAGGCGAAACCACCATATCATAAGGCAGGCTGTAAAGGAGA
* *
87850 TCCCCAAAAAGCTAAAATGGGTTTTTTCCAAAAAAAAGTATCCATTGTTTTCC
386 TCCCCAAAAAGCTAAAATGGGTTCTTTCCAAAAAAAAGTATCCATTGTTTTAC
87903 TTA
1 TTA
87906 TTGGGTCCTT
Statistics
Matches: 385, Mismatches: 52, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
438 1 0.00
439 308 0.80
440 26 0.07
442 27 0.07
443 23 0.06
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (438 bp):
TTAATAAACAATATACACTTTATGCTACGAAAAGCATCTTGATGGATAATGGTAAACAATAGACC
AAATCCAGATGCCATCCTTAAGCATATTGTATAAAGGGTTTCATACAACACAATTATAATAGTAA
TTAAACCTATTATTACAGTAAACAGTGCTAAATACACTATCAACAAATTATTAAGCCATCGATTA
ACAGTACCCGGGGACTGTTAGGCCCAAATATCGCTTTTAAAAAAGACACCAAGGACATTATAAAG
AAAAAAAATTACTGTATATGTACCTCAAAACTTCCCTTATTTCACTACAGCCTCGCCAAAATACT
TCAACAGCCAGGCATCAGACAGGCGAAACCACCATATCATAAGGCAGGCTGTAAAGGAGATCCCC
AAAAAGCTAAAATGGGTTCTTTCCAAAAAAAAGTATCCATTGTTTTAC
Found at i:89033 original size:789 final size:785
Alignment explanation
Indices: 87515--89072 Score: 2555
Period size: 789 Copynumber: 2.0 Consensus size: 785
87505 TGGATAATGG
*
87515 TAAACAATAGACCAAATCCAGATGTCATCCTTAAGCATATTGTGTAAAGGGTTTCATACAACACA
1 TAAACAATAGACCAAATCCAGATGCCATCCTTAAGCATATTGTGTAAAGGGTTTCATACAACACA
*
87580 ATTATACTAGTACTTAAACCTATTATTACTGTAAACAGTGCTAAATACACTATCAACAAATTATT
66 ATTATACTAGTACTTAAACCTATTATTACTGTAAACAGTGCTAAATAAACTATCAACAAATTATT
* * *
87645 AAGTCGTCTATTAACAGTCACCTTACGGGGACTGTTAGGCCCAATTATCTCTTTAAAAAAGATAC
131 AAGCCATCTATTAACAGTCACCTTACGGGGACTGTTAGGCCCAATTATCTCTTTAAAAAAGACAC
87710 CAAGGCCATTATAAAGAAAAAAATTATTGTATATGTACCTCTGAGCTTCCCTTATTTCACTACAG
196 CAAGGCCATTATAAAGAAAAAAATTATTGTATATGTACCTCTGAGCTTCCCTTATTTCACTACAG
* ** * *
87775 CCTCCACAAAATACTTCAGTAGTTAGGCTTCAGACAGGCGGAACCACCATGTCATAATGCAGGCT
261 CCTCCACAAAATACTTCAGCAGCCAGGCTTCAGACAGGCGGAACCACCATGACATAAGGCAGGCT
*
87840 GTAAAGGTGATCCCCAAAAAGCTAAAATGGGTTTTTTCCAAAAAAAAGTATCCATTGTTTTCCTT
326 GTAAAGGTGATCCCCAAAAAGCTAAAATGGGTTCTTTCC-AAAAAAAGTATCCATTGTTTTCCTT
* *
87905 ATTGGGTCCTTGAATTCGTTCCATCTCTATTTGACAAAAAAAAGCTGTAAATTTCAATGACTTTC
390 ATTGGGTCCTTGAATTCGTTCCATCTCTATTTGACAAAAAAAAGCTGCAAATTTCAAGGACTTTC
* *
87970 CTGTTGTGATGGTTGGTAAGGATAATCGGGTAAAGTGAGATCCTACGCAAGAAAGGAAGATACTG
455 CTATTGTGATGGTTGGTAAGGATAATCAGGTAAAGTGAGATCCTACGCAAGAAAGGAAGATACTG
*
88035 AAATCTGGAAAGTCAATTAGGTTTAGGTTGTTTGCTTAACATGGTATCAGAGCCCAGGTCTGTCC
520 AAATCTGGAAAGTCAATTAGGTTTAGGTTGTTTGCTTAACATGGTATCAGAGCCCAGGTCTGTCA
* * * *
88100 TATTGCCCAAGACTCAGTTGTTCACATCGACTGTTATTTTTCGATTTTTTCTCCTGGTTACACGT
585 TATTGCCAAAGACTCAGTTGTTCACATCGACTGTTATATTTCGATTTTTTCTCCCGGCTACACGT
88165 GAGGGGCGTGTCAAAGTGGTAATATCTCAAATTTATTTAGTTTGATATGACTAAATCCCATATAT
650 GAGGGGCGTGTCAAAGTGGTAATATCTCAAATTTATTTAGTTTGATATGACTAAATCCCATATAT
** * *
88230 ACAAGTTAGCTCTCTCTATCTATTGCCGATTGGTTTT-AGGTTGGATGTACATATAGACCAAATC
715 ACAAGTTAGCTCTCTCTATCTATTAACAATT-GTTTTCAAGTTGGATGTACATATAGACCAAATC
88294 CAGATGA
779 CAGATGA
* * *
88301 TAAACAATAGACCAAATCGAGATGCCATCCTTGAGCATATTGTGTAAAGGGTTTCATACAGCACA
1 TAAACAATAGACCAAATCCAGATGCCATCCTTAAGCATATTGTGTAAAGGGTTTCATACAACACA
88366 ATTATACTAGTACTTAAACCTATTATTACTGTAAACAGTGCTAAATAAACTATCAACAAATTATT
66 ATTATACTAGTACTTAAACCTATTATTACTGTAAACAGTGCTAAATAAACTATCAACAAATTATT
*
88431 AAGCCATCTATTAACAGTCACCTTACGAGGGACTGTTAGGCCTAATTATCTCTTTAAAAAAAAAG
131 AAGCCATCTATTAACAGTCACCTTACG-GGGACTGTTAGGCCCAATTATCTCTTT---AAAAAAG
* * *
88496 ACACTAAGGTCATTATAAAGAAAAAAATTATTGTATATGTACCTCTGAGCTTCCCTTTTTTCACT
192 ACACCAAGGCCATTATAAAGAAAAAAATTATTGTATATGTACCTCTGAGCTTCCCTTATTTCACT
* * ** **
88561 GCAGCCTCCCCAATGTACTTCAGCAGCCAGGCTTCAGATTGGCGGAACCACCATGACATAAGGCA
257 ACAGCCTCCACAAAATACTTCAGCAGCCAGGCTTCAGACAGGCGGAACCACCATGACATAAGGCA
* *
88626 GGCTGTAATGGTGATCCCCAAAAATCTAAAATGGGTTCTTTCC-AAAAAAGTATCCATTGTTTTC
322 GGCTGTAAAGGTGATCCCCAAAAAGCTAAAATGGGTTCTTTCCAAAAAAAGTATCCATTGTTTTC
* *
88690 CTTATTGGGTCCTTGAATTCGTTCCATCTTTATTTGACAAAAAAAAATG-TGCAAATTTCAGGGA
387 CTTATTGGGTCCTTGAATTCGTTCCATCTCTATTTGAC-AAAAAAAA-GCTGCAAATTTCAAGGA
* * *
88754 CTTTCTTATTGTGATGGTTGGTAAGGATAATCAGGTAGAGTGGGATCCTACGCAAGAAAGGAAGA
450 CTTTCCTATTGTGATGGTTGGTAAGGATAATCAGGTAAAGTGAGATCCTACGCAAGAAAGGAAGA
* *
88819 TACTGAAATCTGGAAAGTCAATTAGTTTTAGGTTGTTTGCTTAACATGGTATCAGAGCCTAGGTC
515 TACTGAAATCTGGAAAGTCAATTAGGTTTAGGTTGTTTGCTTAACATGGTATCAGAGCCCAGGTC
88884 TGTCATATTGCCAAAGACTCAGTTGTTCACATCGACTGTTATATTTCGATTTTTTCTCCCGGCTA
580 TGTCATATTGCCAAAGACTCAGTTGTTCACATCGACTGTTATATTTCGATTTTTTCTCCCGGCTA
* ** *
88949 CACGTGAGGGGCGTGTCAAAGTGGTAATATCTCAAATTTATTTTGTTTGATATGACTATGTCCCT
645 CACGTGAGGGGCGTGTCAAAGTGGTAATATCTCAAATTTATTTAGTTTGATATGACTAAATCCCA
* *
89014 TATATACAAGTTGGCTCTCTTTATCTATTAACAATTGTTTTCAAGTTGGATGTACATAT
710 TATATACAAGTTAGCTCTCTCTATCTATTAACAATTGTTTTCAAGTTGGATGTACATAT
89073 TATAAAACAT
Statistics
Matches: 713, Mismatches: 52, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
786 150 0.21
787 26 0.04
788 63 0.09
789 311 0.44
790 163 0.23
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (785 bp):
TAAACAATAGACCAAATCCAGATGCCATCCTTAAGCATATTGTGTAAAGGGTTTCATACAACACA
ATTATACTAGTACTTAAACCTATTATTACTGTAAACAGTGCTAAATAAACTATCAACAAATTATT
AAGCCATCTATTAACAGTCACCTTACGGGGACTGTTAGGCCCAATTATCTCTTTAAAAAAGACAC
CAAGGCCATTATAAAGAAAAAAATTATTGTATATGTACCTCTGAGCTTCCCTTATTTCACTACAG
CCTCCACAAAATACTTCAGCAGCCAGGCTTCAGACAGGCGGAACCACCATGACATAAGGCAGGCT
GTAAAGGTGATCCCCAAAAAGCTAAAATGGGTTCTTTCCAAAAAAAGTATCCATTGTTTTCCTTA
TTGGGTCCTTGAATTCGTTCCATCTCTATTTGACAAAAAAAAGCTGCAAATTTCAAGGACTTTCC
TATTGTGATGGTTGGTAAGGATAATCAGGTAAAGTGAGATCCTACGCAAGAAAGGAAGATACTGA
AATCTGGAAAGTCAATTAGGTTTAGGTTGTTTGCTTAACATGGTATCAGAGCCCAGGTCTGTCAT
ATTGCCAAAGACTCAGTTGTTCACATCGACTGTTATATTTCGATTTTTTCTCCCGGCTACACGTG
AGGGGCGTGTCAAAGTGGTAATATCTCAAATTTATTTAGTTTGATATGACTAAATCCCATATATA
CAAGTTAGCTCTCTCTATCTATTAACAATTGTTTTCAAGTTGGATGTACATATAGACCAAATCCA
GATGA
Found at i:92974 original size:50 final size:50
Alignment explanation
Indices: 92843--92967 Score: 232
Period size: 50 Copynumber: 2.5 Consensus size: 50
92833 GTAGAAGAAA
92843 AAAAAGTTGCTATAGTTGTACTTAAGCAATATATAGATAGAGTAGACGGG
1 AAAAAGTTGCTATAGTTGTACTTAAGCAATATATAGATAGAGTAGACGGG
92893 AAAAAGTTGCTATAGTTGTACTTAAGCAATATATAGATAGAGTAGACGGG
1 AAAAAGTTGCTATAGTTGTACTTAAGCAATATATAGATAGAGTAGACGGG
* *
92943 AAAAAGTTGTTATATTTGTACTTAA
1 AAAAAGTTGCTATAGTTGTACTTAA
92968 TTAATATTAC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (50 bp):
AAAAAGTTGCTATAGTTGTACTTAAGCAATATATAGATAGAGTAGACGGG
Found at i:94226 original size:37 final size:37
Alignment explanation
Indices: 94176--94246 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
94166 AGTGGAGCAA
94176 AAATTCTCATTTCTTCATACCAATTTTACGGGATACC
1 AAATTCTCATTTCTTCATACCAATTTTACGGGATACC
*
94213 AAATTTTCATTTCTTCATACCAATTTTACGGGAT
1 AAATTCTCATTTCTTCATACCAATTTTACGGGAT
94247 GCCGCATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (37 bp):
AAATTCTCATTTCTTCATACCAATTTTACGGGATACC
Found at i:95802 original size:31 final size:31
Alignment explanation
Indices: 95767--95841 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
95757 CTTTATCAAT
*
95767 TGGACTCAATTGACCCAATCTTATGAATACA
1 TGGACTAAATTGACCCAATCTTATGAATACA
* *
95798 TGGACTAAATCGACCCAATCTTATGAGTACA
1 TGGACTAAATTGACCCAATCTTATGAATACA
95829 TGGACTAAATTGA
1 TGGACTAAATTGA
95842 TTACTTTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (31 bp):
TGGACTAAATTGACCCAATCTTATGAATACA
Found at i:95867 original size:29 final size:30
Alignment explanation
Indices: 95818--95893 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
95808 CGACCCAATC
* *
95818 TTATGAGTACATGGACTAAATTGATTACTT
1 TTATGAGTACAAGGACTAAATTGAATACTT
*
95848 TT-TGAGTACAAGGA-TGAAATTGAATATTT
1 TTATGAGTACAAGGACT-AAATTGAATACTT
*
95877 TTATGCAGTACAGGGAC
1 TTATG-AGTACAAGGAC
95894 CTCCCAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 1 0.03
29 24 0.63
30 4 0.11
31 9 0.24
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (30 bp):
TTATGAGTACAAGGACTAAATTGAATACTT
Found at i:100623 original size:19 final size:19
Alignment explanation
Indices: 100599--100635 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
100589 TGTATCTGTA
100599 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
*
100618 ACCGTTTCACCATCGTTT
1 ACCGTTTCACCACCGTTT
100636 TGGGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:100731 original size:19 final size:19
Alignment explanation
Indices: 100707--100743 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
100697 ATACAGTACC
100707 TAATCTAATATGTACAGTG
1 TAATCTAATATGTACAGTG
* *
100726 TAATCTCATCTGTACAGT
1 TAATCTAATATGTACAGT
100744 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATATGTACAGTG
Found at i:107053 original size:233 final size:232
Alignment explanation
Indices: 106616--107053 Score: 682
Period size: 233 Copynumber: 1.9 Consensus size: 232
106606 TTTGATTTAA
** ** * *
106616 GTTTAACTGACTTTTGTCTGTGTGAATACTCATAAGAGCATGCATTAATGATGATACGTGATTTG
1 GTTTAACTGACTTTTGTCTACGAAAATACTCATAAGAGCATCCATTAATGATGATACATGATTTG
*
106681 GTTCTGACATGTAATAATTCCCTTGGCATGGCATGAACATGTTACTGATCAATGATGGTGCCATG
66 CTTCTGACATGTAATAATTCCCTTGGCATGGCATGAACATGTTACTGATCAATGATGGTGCCATG
* *
106746 GTTAAAATATCTACATTACATCTATTTCCCTCTCTTGCTCCTTTTTAAGGGAAACTTACTGCATC
131 GTTAAAATATCTACATTACATATATTTCCCTCTCTTGCTCATTTTTAAGGGAAACTTACTGCATC
106811 TCTGTCAATAGTTTAAATCCATAGGCTTGTGGTTTGT
196 TCTGTCAATAGTTTAAATCCATAGGCTTGTGGTTTGT
** *
106848 GTTTAACTGACTTTTGTCTACGAAAATGTTCATAAGAGCATCCGTTAATGATGATACATGATTTG
1 GTTTAACTGACTTTTGTCTACGAAAATACTCATAAGAGCATCCATTAATGATGATACATGATTTG
* *
106913 CTTCTGATC-TGTGAATAAGTTCCCTTGTCATGGCATGAACATTTTACTGATCAATGATGGTGCC
66 CTTCTGA-CATGT-AATAA-TTCCCTTGGCATGGCATGAACATGTTACTGATCAATGATGGTGCC
* * *
106977 ATGGTT-AAATATCTACATTACATATATTTCCCTCTCTTGTTCATTTTTAAGGTAAACTTGCTGC
128 ATGGTTAAAATATCTACATTACATATATTTCCCTCTCTTGCTCATTTTTAAGGGAAACTTACTGC
107041 ATCTCTGTCAATA
193 ATCTCTGTCAATA
107054 TTTCAAACAT
Statistics
Matches: 186, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
232 65 0.35
233 72 0.39
234 49 0.26
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (232 bp):
GTTTAACTGACTTTTGTCTACGAAAATACTCATAAGAGCATCCATTAATGATGATACATGATTTG
CTTCTGACATGTAATAATTCCCTTGGCATGGCATGAACATGTTACTGATCAATGATGGTGCCATG
GTTAAAATATCTACATTACATATATTTCCCTCTCTTGCTCATTTTTAAGGGAAACTTACTGCATC
TCTGTCAATAGTTTAAATCCATAGGCTTGTGGTTTGT
Found at i:108947 original size:26 final size:26
Alignment explanation
Indices: 108917--108970 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
108907 AAATGATATA
108917 GTACTCATTTTAAAAATT-GAGGTAGG
1 GTACTCATTTTAAAAATTAG-GGTAGG
108943 GTACTCATTTTAAAAATTAGGGTAGG
1 GTACTCATTTTAAAAATTAGGGTAGG
108969 GT
1 GT
108971 TCTCCTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
GTACTCATTTTAAAAATTAGGGTAGG
Found at i:108983 original size:26 final size:26
Alignment explanation
Indices: 108917--108983 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
108907 AAATGATATA
*
108917 GTACTCATTTTAAAAATTGAGGTAGG
1 GTACTCATTTGAAAAATTGAGGTAGG
*
108943 GTACTCATTTTAAAAATT-AGGGTAGG
1 GTACTCATTTGAAAAATTGA-GGTAGG
* *
108969 GTTCTCCTTTGAAAA
1 GTACTCATTTGAAAA
108984 GTCACATGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (26 bp):
GTACTCATTTGAAAAATTGAGGTAGG
Done.