Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003190.1 Kokia drynarioides strain JFW-HI SEQ_115802, 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: 575368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 121 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:270064 original size:20 final size:21
Alignment explanation
Indices: 270041--270089 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
270031 TACTATTTTT
* * *
270041 ATTTTTTTAAT-CTTTTACCG
1 ATTTTTTTAATAATTTTAACA
270061 A-TTTTTTAATAATTTTAACA
1 ATTTTTTTAATAATTTTAACA
270081 ATTTTTTTA
1 ATTTTTTTA
270090 TATCAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.38
20 8 0.33
21 7 0.29
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTTTAATAATTTTAACA
Found at i:271977 original size:12 final size:12
Alignment explanation
Indices: 271960--271985 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
271950 TACGAGATAT
271960 ATATGCAAAATG
1 ATATGCAAAATG
271972 ATATGCAAAATG
1 ATATGCAAAATG
271984 AT
1 AT
271986 CATGGGAATG
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:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
ATATGCAAAATG
Found at i:272965 original size:18 final size:17
Alignment explanation
Indices: 272916--272971 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
272906 GATTTTTATA
272916 TAATTTATTAATAA-TTT
1 TAATTT-TTAATAATTTT
*
272933 TATATTTTCATATAATTTCT
1 TA-ATTTTTA-ATAATTT-T
272953 TAATTTTTAATAATTTT
1 TAATTTTTAATAATTTT
272970 TA
1 TA
272972 TTCTATCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 7 0.21
18 15 0.45
19 8 0.24
20 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTTTAATAATTTT
Found at i:272966 original size:10 final size:10
Alignment explanation
Indices: 272907--272971 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
272897 AATCATTCTG
272907 ATTTTTATATA
1 ATTTTTA-ATA
272918 ATTTATTAATA
1 ATTT-TTAATA
272929 A-TTTT-AT-
1 ATTTTTAATA
*
272936 ATTTTCATATA
1 ATTTTTA-ATA
*
272947 ATTTCT--TA
1 ATTTTTAATA
272955 ATTTTTAATA
1 ATTTTTAATA
272965 ATTTTTA
1 ATTTTTA
272972 TTCTATCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
7 1 0.02
8 12 0.28
9 2 0.05
10 13 0.30
11 12 0.28
12 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:272969 original size:29 final size:28
Alignment explanation
Indices: 272907--272961 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
272897 AATCATTCTG
*
272907 ATTTTTATATAATTTATTAATAATTTTAT
1 ATTTTCATATAATTTATTAAT-ATTTTAT
*
272936 ATTTTCATATAATTTCTTAAT-TTTTA
1 ATTTTCATATAATTTATTAATATTTTA
272962 ATAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
29 19 0.79
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTTCATATAATTTATTAATATTTTAT
Found at i:278156 original size:20 final size:21
Alignment explanation
Indices: 278131--278169 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
278121 ACAAGAAACA
*
278131 TAAAAT-CGTAATTTAGACCC
1 TAAAATCCATAATTTAGACCC
278151 TAAAATCCATAATTTAGAC
1 TAAAATCCATAATTTAGAC
278170 TATATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (21 bp):
TAAAATCCATAATTTAGACCC
Found at i:281587 original size:17 final size:17
Alignment explanation
Indices: 281550--281587 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
281540 ATTTGATAGA
*
281550 TCAATTATCTAATATGT
1 TCAATTATCTAATATGC
281567 TCAATTATCATAATAT-C
1 TCAATTATC-TAATATGC
281584 TCAA
1 TCAA
281588 GAAGCTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (17 bp):
TCAATTATCTAATATGC
Found at i:283784 original size:18 final size:19
Alignment explanation
Indices: 283750--283785 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
283740 AATCGAGTCA
*
283750 CAAATTAATAGTATTAATC
1 CAAATTAATAATATTAATC
283769 CAAATTAA-AATATTAAT
1 CAAATTAATAATATTAAT
283786 TAAACTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (19 bp):
CAAATTAATAATATTAATC
Found at i:285990 original size:18 final size:18
Alignment explanation
Indices: 285967--286003 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
285957 TTACAAAGAA
285967 AAACTAAACATCCAATAT
1 AAACTAAACATCCAATAT
285985 AAACTAAACATCCAATAT
1 AAACTAAACATCCAATAT
286003 A
1 A
286004 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (18 bp):
AAACTAAACATCCAATAT
Found at i:310280 original size:36 final size:36
Alignment explanation
Indices: 310240--310311 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
310230 GAATTACTTA
310240 GGCTGCCATCTGAGCAAGAGGTTGAATTTGCTATTG
1 GGCTGCCATCTGAGCAAGAGGTTGAATTTGCTATTG
310276 GGCTGCCATCTGAGCAAGAGGTTGAATTTGCTATTG
1 GGCTGCCATCTGAGCAAGAGGTTGAATTTGCTATTG
310312 CTTTAACATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (36 bp):
GGCTGCCATCTGAGCAAGAGGTTGAATTTGCTATTG
Found at i:326293 original size:37 final size:37
Alignment explanation
Indices: 326252--326427 Score: 289
Period size: 37 Copynumber: 4.8 Consensus size: 37
326242 TGCATTTAAA
*
326252 TATTCAGGCTATGTGCCTAGTAAGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
326289 TATTCAGGCTATGTGCCTAATAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
326326 TATTTAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTT
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
326363 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
326400 TATTCGGGCTATATGCCTAGTAGGCTTT
1 TATTCAGGCTATGTGCCTAGTAGGCTTT
326428 AGGCCGATGA
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 129 1.00
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.38
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:326305 original size:21 final size:19
Alignment explanation
Indices: 326279--326379 Score: 70
Period size: 21 Copynumber: 5.3 Consensus size: 19
326269 TAGTAAGCTT
326279 TGTGCCGGTGTATTCAGGCTA
1 TGTGCCGGT-TATT-AGGCTA
* *
326300 TGTGCC---TAATAGGCTT
1 TGTGCCGGTTATTAGGCTA
326316 TGTGCCGGTGTATTTAGGCTA
1 TGTGCCGGT-TA-TTAGGCTA
* *
326337 TGTGCC---TAGTAGGCTT
1 TGTGCCGGTTATTAGGCTA
326353 TGTGCCGGTTTATTCAGGCTA
1 TGTGCCGG-TTATT-AGGCTA
326374 TGTGCC
1 TGTGCC
326380 TAGTAGGCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
16 23 0.37
17 5 0.08
20 5 0.08
21 29 0.47
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.37
Consensus pattern (19 bp):
TGTGCCGGTTATTAGGCTA
Found at i:326393 original size:16 final size:16
Alignment explanation
Indices: 326257--326394 Score: 60
Period size: 16 Copynumber: 7.7 Consensus size: 16
326247 TTAAATATTC
326257 AGGCTATGTGCCTAGT
1 AGGCTATGTGCCTAGT
* * *
326273 AAGCTTTGTGCCGGTGTATT
1 AGGCTATGTGCC----TAGT
*
326293 CAGGCTATGTGCCTAAT
1 -AGGCTATGTGCCTAGT
* *
326310 AGGCTTTGTGCCGGTGTATTT
1 AGGCTATGTGCC----TA-GT
326331 AGGCTATGTGCCTAGT
1 AGGCTATGTGCCTAGT
* *
326347 AGGCTTTGTGCCGGTTTATT
1 AGGCTATGTGCC----TAGT
326367 CAGGCTATGTGCCTAGT
1 -AGGCTATGTGCCTAGT
*
326384 AGGCTTTGTGC
1 AGGCTATGTGC
326395 TGGTGTATTC
Statistics
Matches: 92, Mismatches: 15, Indels: 30
0.67 0.11 0.22
Matches are distributed among these distances:
16 43 0.47
17 8 0.09
20 8 0.09
21 33 0.36
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.36
Consensus pattern (16 bp):
AGGCTATGTGCCTAGT
Found at i:329670 original size:16 final size:16
Alignment explanation
Indices: 329645--329709 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
329635 CTAAATATTC
329645 AGGCTATGTGCCTAGT
1 AGGCTATGTGCCTAGT
*
329661 AGGCTTTGTGCCGGT-GTTTT
1 AGGCTATGTGCC--TAG---T
329681 CAGGCTATGTGCCTAGT
1 -AGGCTATGTGCCTAGT
*
329698 AGGCTTTGTGCC
1 AGGCTATGTGCC
329710 GGTGTTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
16 22 0.56
17 2 0.05
18 1 0.03
19 1 0.03
20 2 0.05
21 11 0.28
ACGTcount: A:0.12, C:0.20, G:0.32, T:0.35
Consensus pattern (16 bp):
AGGCTATGTGCCTAGT
Found at i:329683 original size:37 final size:37
Alignment explanation
Indices: 329642--329751 Score: 202
Period size: 37 Copynumber: 3.0 Consensus size: 37
329632 CATCTAAATA
329642 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
329679 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
* *
329716 TTCAGGCTATGTGTCTGGTAGGCTTTGTGCCGGTGT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGT
329752 ATTTGGGTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.10, C:0.18, G:0.34, T:0.38
Consensus pattern (37 bp):
TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
Found at i:329691 original size:21 final size:21
Alignment explanation
Indices: 329661--329728 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
329651 TGTGCCTAGT
*
329661 AGGCTTTGTGCCGGTGTTTTC
1 AGGCTATGTGCCGGTGTTTTC
329682 AGGCTATGTGCC--TAG---T-
1 AGGCTATGTGCCGGT-GTTTTC
*
329698 AGGCTTTGTGCCGGTGTTTTC
1 AGGCTATGTGCCGGTGTTTTC
329719 AGGCTATGTG
1 AGGCTATGTG
329729 TCTGGTAGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
16 11 0.30
17 2 0.05
18 1 0.03
19 1 0.03
20 2 0.05
21 20 0.54
ACGTcount: A:0.10, C:0.18, G:0.34, T:0.38
Consensus pattern (21 bp):
AGGCTATGTGCCGGTGTTTTC
Found at i:329766 original size:74 final size:74
Alignment explanation
Indices: 329642--329787 Score: 197
Period size: 74 Copynumber: 2.0 Consensus size: 74
329632 CATCTAAATA
329642 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAGGCTTT-G
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAGGCTTTAG
329706 TGCCGGTGTT
66 T-CCGGTGTT
* * * * * * *
329716 TTCAGGCTATGTGTCTGGTAGGCTTTGTGCCGGTGTATTT-GGGTTGTGTGCCTATTAGTCTTTA
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGT-TTTCAGGCTATGTGCCTAGTAGGCTTTA
329780 GTCCGGTG
65 GTCCGGTG
329788 AATCAAGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
74 58 0.92
75 5 0.08
ACGTcount: A:0.10, C:0.17, G:0.33, T:0.40
Consensus pattern (74 bp):
TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAGGCTTTAG
TCCGGTGTT
Found at i:333446 original size:16 final size:16
Alignment explanation
Indices: 333421--333521 Score: 58
Period size: 16 Copynumber: 5.7 Consensus size: 16
333411 CTAAATATTC
333421 AGGCTATGTGCCTAGT
1 AGGCTATGTGCCTAGT
* *
333437 AGGCTTTGTGCCAGCGTATT
1 AGGCTATGTG-C--C-TAGT
*
333457 CAGGCTATGTGCGTAGT
1 -AGGCTATGTGCCTAGT
* *
333474 AGGCTTTGTGCCAGTGTATT
1 AGGCTATGTGCC----TAGT
333494 CAGGCTATGTGCCTAGT
1 -AGGCTATGTGCCTAGT
*
333511 AGGCTTTGTGC
1 AGGCTATGTGC
333522 TGGTGTGTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
16 29 0.45
17 7 0.11
19 1 0.02
20 7 0.11
21 20 0.31
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.34
Consensus pattern (16 bp):
AGGCTATGTGCCTAGT
Found at i:333467 original size:21 final size:21
Alignment explanation
Indices: 333437--333506 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
333427 TGTGCCTAGT
*
333437 AGGCTTTGTGCCAGCGTATTC
1 AGGCTATGTGCCAGCGTATTC
*
333458 AGGCTATGT----GCGTAGT-
1 AGGCTATGTGCCAGCGTATTC
* *
333474 AGGCTTTGTGCCAGTGTATTC
1 AGGCTATGTGCCAGCGTATTC
333495 AGGCTATGTGCC
1 AGGCTATGTGCC
333507 TAGTAGGCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
16 8 0.21
17 6 0.16
20 5 0.13
21 19 0.50
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (21 bp):
AGGCTATGTGCCAGCGTATTC
Found at i:333537 original size:37 final size:37
Alignment explanation
Indices: 333416--333547 Score: 201
Period size: 37 Copynumber: 3.6 Consensus size: 37
333406 TGCATCTAAA
*
333416 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGCG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
*
333453 TATTCAGGCTATGTGCGTAGTAGGCTTTGTGCCAGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
**
333490 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
* * *
333527 TGTTCGGGCTATGTGTCTAGT
1 TATTCAGGCTATGTGCCTAGT
333548 TGTCTTTAGG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 87 1.00
ACGTcount: A:0.14, C:0.17, G:0.32, T:0.36
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
Found at i:337274 original size:72 final size:73
Alignment explanation
Indices: 337188--337362 Score: 280
Period size: 72 Copynumber: 2.4 Consensus size: 73
337178 TGCATCCAAA
*
337188 TATTCAGGCCATGTGCCTAGTAGGCTTTGTGCCGGTGTATTCAGGCTATGTGCCTAGTAGGC-TG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTG
337252 TGCCGGTG
66 TGCCGGTG
*
337260 TATTCAGGCTATGTGTCTAGTAGGCTTTGTGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTT
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTATTCAGGCTATGTGCCTAGTAGGC-TT
337325 GTGCCGGTG
65 GTGCCGGTG
* * * *
337334 TATTCGGGTTGTGTGCCTAGTAGCCTTTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTG
337363 GGTCGGTGAA
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 60 0.64
74 34 0.36
ACGTcount: A:0.13, C:0.19, G:0.33, T:0.35
Consensus pattern (73 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTG
TGCCGGTG
Found at i:337370 original size:37 final size:37
Alignment explanation
Indices: 337188--337362 Score: 282
Period size: 37 Copynumber: 4.8 Consensus size: 37
337178 TGCATCCAAA
*
337188 TATTCAGGCCATGTGCCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
337225 TATTCAGGCTATGTGCCTAGTAGGC--TGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
337260 TATTCAGGCTATGTGTCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
337297 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* * * *
337334 TATTCGGGTTGTGTGCCTAGTAGCCTTTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTG
337363 GGTCGGTGAA
Statistics
Matches: 129, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
35 34 0.26
37 95 0.74
ACGTcount: A:0.13, C:0.19, G:0.33, T:0.35
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:344273 original size:31 final size:31
Alignment explanation
Indices: 344232--344295 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
344222 TTATAACTAT
*
344232 ATACATAGCTGCATATGGCAAGTTATCCAAG
1 ATACAAAGCTGCATATGGCAAGTTATCCAAG
344263 ATACAAAGCTGCATATGGCAAGTTATCCAAG
1 ATACAAAGCTGCATATGGCAAGTTATCCAAG
344294 AT
1 AT
344296 TCAACTAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (31 bp):
ATACAAAGCTGCATATGGCAAGTTATCCAAG
Found at i:346102 original size:71 final size:71
Alignment explanation
Indices: 345985--346131 Score: 249
Period size: 71 Copynumber: 2.1 Consensus size: 71
345975 ATTGTTAGGA
* * *
345985 TTGTTTCCGGTCTAGACATCACTACCGATGCACAATTCATTCAGTACTAAGTCATCACCTTCCTA
1 TTGTTTCCGGTCTAGACAGCACTACCGATGCACAAATCATTCAGTACCAAGTCATCACCTTCCTA
346050 TGTTAG
66 TGTTAG
* *
346056 TTGTTTCCGGTCTAGACAGCACTACCGATGCACAAATCATTTAGTACCAAGTCATCACCTTCCTC
1 TTGTTTCCGGTCTAGACAGCACTACCGATGCACAAATCATTCAGTACCAAGTCATCACCTTCCTA
346121 TGTTAG
66 TGTTAG
346127 TTGTT
1 TTGTT
346132 CTAGGAAAGC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (71 bp):
TTGTTTCCGGTCTAGACAGCACTACCGATGCACAAATCATTCAGTACCAAGTCATCACCTTCCTA
TGTTAG
Found at i:350359 original size:13 final size:13
Alignment explanation
Indices: 350341--350367 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
350331 TCATGTTCTT
350341 TCTCCTTGAATCG
1 TCTCCTTGAATCG
350354 TCTCCTTGAATCG
1 TCTCCTTGAATCG
350367 T
1 T
350368 TGTGGAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.41
Consensus pattern (13 bp):
TCTCCTTGAATCG
Found at i:357021 original size:34 final size:34
Alignment explanation
Indices: 356936--357064 Score: 109
Period size: 35 Copynumber: 3.7 Consensus size: 34
356926 TATTTAAATT
* * *
356936 GTCGGTTTATCCGACTAGTGATGGGCGCAACATTC
1 GTCGG-TTATCCAACTAGTGCTGGGCACAACATTC
* * *
356971 GTCAGTTTATCTAACTAATGCTGGGCAC-ACTATTC
1 GTC-GGTTATCCAACTAGTGCTGGGCACAAC-ATTC
*
357006 GTCGGTTATCCAACTAGTGCTGGGTGCAAAACATT-
1 GTCGGTTATCCAACTAGTGCT-GG-GCACAACATTC
* *
357041 GTTGGTATATCCAACTAGAGCTGG
1 GTCGGT-TATCCAACTAGTGCTGG
357065 TCTCATTATT
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
34 17 0.22
35 36 0.47
36 21 0.28
37 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (34 bp):
GTCGGTTATCCAACTAGTGCTGGGCACAACATTC
Found at i:357060 original size:145 final size:145
Alignment explanation
Indices: 356797--357074 Score: 333
Period size: 145 Copynumber: 1.9 Consensus size: 145
356787 TATTCGTCAG
* * * * * *
356797 TTATCTGACTAGTGTTGGGCGCAACCTTCATGAGTTTATCTAACTAGTGTTGGGCACACAAATCA
1 TTATCCGACTAGTGATGGGCGCAACATTCATCAGTTTATCTAACTAATGCTGGGCACACAAATCA
* *** * * * * *
356862 TTGATTATTTGACTAGCGCTGGGCGCAAAACATCTTTGGTTTATCCGATTAGAGTTGGGCTTATT
66 TCGATTATCCAACTAGCGCTGGGCGCAAAACATCTTTGGTATATCCAACTAGAGCTGGGCTCATT
356927 ATTTAAATTGTCGGT
131 ATTTAAATTGTCGGT
* * * *
356942 TTATCCGACTAGTGATGGGCGCAACATTCGTCAGTTTATCTAACTAATGCTGGGCACACTATTCG
1 TTATCCGACTAGTGATGGGCGCAACATTCATCAGTTTATCTAACTAATGCTGGGCACACAAATCA
* * * *
357007 TCGGTTATCCAACTAGTGCTGGGTGCAAAACAT-TGTTGGTATATCCAACTAGAGCTGGTCTCAT
66 TCGATTATCCAACTAGCGCTGGGCGCAAAACATCT-TTGGTATATCCAACTAGAGCTGGGCTCAT
357071 TATT
130 TATT
357075 AATATCATGA
Statistics
Matches: 109, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
144 1 0.01
145 108 0.99
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (145 bp):
TTATCCGACTAGTGATGGGCGCAACATTCATCAGTTTATCTAACTAATGCTGGGCACACAAATCA
TCGATTATCCAACTAGCGCTGGGCGCAAAACATCTTTGGTATATCCAACTAGAGCTGGGCTCATT
ATTTAAATTGTCGGT
Found at i:366160 original size:23 final size:24
Alignment explanation
Indices: 366111--366156 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
366101 TCAGTCACCT
366111 GAAAAAGGAAAATGAGAAAAGAAA
1 GAAAAAGGAAAATGAGAAAAGAAA
*
366135 GAAAAA-GAAAA-GTGAAAAGAAA
1 GAAAAAGGAAAATGAGAAAAGAAA
366157 AGAAGAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 5 0.24
24 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (24 bp):
GAAAAAGGAAAATGAGAAAAGAAA
Found at i:370585 original size:125 final size:125
Alignment explanation
Indices: 370363--370613 Score: 502
Period size: 125 Copynumber: 2.0 Consensus size: 125
370353 AATATGAAAT
370363 TAGGACATAGAAATTATTAAAATGTGATTTTATGCTTTATTATATAGTTTTCATGCATAAAATGG
1 TAGGACATAGAAATTATTAAAATGTGATTTTATGCTTTATTATATAGTTTTCATGCATAAAATGG
370428 TTTATTTTATAACTATTTAAACATATTATATTTTTAAGACATAAAGTGGACCAAGCATGA
66 TTTATTTTATAACTATTTAAACATATTATATTTTTAAGACATAAAGTGGACCAAGCATGA
370488 TAGGACATAGAAATTATTAAAATGTGATTTTATGCTTTATTATATAGTTTTCATGCATAAAATGG
1 TAGGACATAGAAATTATTAAAATGTGATTTTATGCTTTATTATATAGTTTTCATGCATAAAATGG
370553 TTTATTTTATAACTATTTAAACATATTATATTTTTAAGACATAAAGTGGACCAAGCATGA
66 TTTATTTTATAACTATTTAAACATATTATATTTTTAAGACATAAAGTGGACCAAGCATGA
370613 T
1 T
370614 TAAATTAAAT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (125 bp):
TAGGACATAGAAATTATTAAAATGTGATTTTATGCTTTATTATATAGTTTTCATGCATAAAATGG
TTTATTTTATAACTATTTAAACATATTATATTTTTAAGACATAAAGTGGACCAAGCATGA
Found at i:376314 original size:37 final size:37
Alignment explanation
Indices: 376260--376523 Score: 314
Period size: 37 Copynumber: 7.2 Consensus size: 37
376250 TATTCATTCT
* *
376260 TGAAT-CACCGGCCCAAAGCCTACTAGGCACACAGCC
1 TGAATACACCGGCACAAAGCCTACTAGGCACATAGCC
* * * *
376296 TGAATACACTGGCACAAAGCCTACTAGGAACATAACT
1 TGAATACACCGGCACAAAGCCTACTAGGCACATAGCC
* * *
376333 TGAATACACTGGCACAAAGCCTACTAGGTACATAGCT
1 TGAATACACCGGCACAAAGCCTACTAGGCACATAGCC
** *
376370 TGAATACACCAACACAAAGCCTACTAAGCACATAGCC
1 TGAATACACCGGCACAAAGCCTACTAGGCACATAGCC
* *
376407 TAAATACACCGACACAAAGCCTACTAGGCACATAGCC
1 TGAATACACCGGCACAAAGCCTACTAGGCACATAGCC
** *
376444 TGAATACACCAACACAAAGCTTACTAGGCACATAGCC
1 TGAATACACCGGCACAAAGCCTACTAGGCACATAGCC
* * * * * *
376481 TGACTACACCGGCAAAAAGCTTCCTAAGAACATAGCC
1 TGAATACACCGGCACAAAGCCTACTAGGCACATAGCC
376518 TGAATA
1 TGAATA
376524 TTTAGATGCA
Statistics
Matches: 199, Mismatches: 28, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
36 5 0.03
37 194 0.97
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.16
Consensus pattern (37 bp):
TGAATACACCGGCACAAAGCCTACTAGGCACATAGCC
Found at i:385358 original size:17 final size:16
Alignment explanation
Indices: 385338--385378 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
385328 ACTACAATGC
*
385338 AAATGAACTAACAAGTA
1 AAATGAAC-AACAACTA
385355 AAATGCAACAACAACTA
1 AAATG-AACAACAACTA
385372 AAATGAA
1 AAATGAA
385379 ATGACAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 17 0.77
18 3 0.14
ACGTcount: A:0.61, C:0.15, G:0.10, T:0.15
Consensus pattern (16 bp):
AAATGAACAACAACTA
Found at i:399915 original size:24 final size:24
Alignment explanation
Indices: 399887--399958 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
399877 TATTGGTTAT
399887 CCTTTTTAGGCTCGTAAGAGCTAA
1 CCTTTTTAGGCTCGTAAGAGCTAA
* * *
399911 CCTTTTTGGGCTTGAAAGAGCTAA
1 CCTTTTTAGGCTCGTAAGAGCTAA
*
399935 CCTTTCTAGGCTCGTAAGAGCTAA
1 CCTTTTTAGGCTCGTAAGAGCTAA
399959 TTTTGTCTGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (24 bp):
CCTTTTTAGGCTCGTAAGAGCTAA
Found at i:407997 original size:10 final size:10
Alignment explanation
Indices: 407977--408010 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
407967 GATTTTTTTA
407977 TAAAAAT-TT
1 TAAAAATATT
407986 TAAAAATATT
1 TAAAAATATT
407996 TAAAAATATT
1 TAAAAATATT
408006 TAAAA
1 TAAAA
408011 GTATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAAATATT
Found at i:408907 original size:14 final size:14
Alignment explanation
Indices: 408888--408918 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
408878 TTGCTACAAT
408888 TTACTATTATGTTG
1 TTACTATTATGTTG
*
408902 TTACTATTTTGTTG
1 TTACTATTATGTTG
408916 TTA
1 TTA
408919 TTGTTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:408983 original size:30 final size:30
Alignment explanation
Indices: 408949--409013 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
408939 ACTTATTTTA
* *
408949 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
408979 TTGTTAAATTTGTTATTATTTTAAAGACAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
409009 TTGTT
1 TTGTT
409014 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (30 bp):
TTGTTAAATTTGTTATTATTTTAAAGACAT
Found at i:423673 original size:20 final size:21
Alignment explanation
Indices: 423639--423677 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
423629 CATTTTTCTA
423639 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTATTTGTTTCACT
423660 TTTACTTTTA-TTGTTTCA
1 TTTACTTTTATTTGTTTCA
423678 AAATCCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTACTTTTATTTGTTTCACT
Found at i:423770 original size:35 final size:35
Alignment explanation
Indices: 423731--423802 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
423721 GAAGCATGGA
*
423731 TTGTCGGCGCATTCTGTGGTGAGTCAGCATAGTTT
1 TTGTCGGCGCATTCTGTGATGAGTCAGCATAGTTT
*
423766 TTGTCGGTGCATTCTGTGATGAGTCAGCATAGTTT
1 TTGTCGGCGCATTCTGTGATGAGTCAGCATAGTTT
423801 TT
1 TT
423803 CAGCAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.40
Consensus pattern (35 bp):
TTGTCGGCGCATTCTGTGATGAGTCAGCATAGTTT
Found at i:424964 original size:21 final size:21
Alignment explanation
Indices: 424938--424984 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
424928 ATGGCCAACT
*
424938 GAAGGAAAAGGAAGAA-AAAGA
1 GAAGGAAAAAG-AGAATAAAGA
424959 GAAGGAAAAAGAGAATAAAGA
1 GAAGGAAAAAGAGAATAAAGA
424980 GAAGG
1 GAAGG
424985 GCCTTAACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (21 bp):
GAAGGAAAAAGAGAATAAAGA
Found at i:424968 original size:12 final size:12
Alignment explanation
Indices: 424938--424973 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
424928 ATGGCCAACT
424938 GAAGG-AAAAG-
1 GAAGGAAAAAGA
424948 GAA-GAAAAAGA
1 GAAGGAAAAAGA
424959 GAAGGAAAAAGA
1 GAAGGAAAAAGA
424971 GAA
1 GAA
424974 TAAAGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.04
10 8 0.35
11 3 0.13
12 11 0.48
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
GAAGGAAAAAGA
Found at i:425308 original size:24 final size:24
Alignment explanation
Indices: 425273--425319 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
425263 TAAGACGGAT
* * *
425273 AAAAAGAGGAAGAGGCATAAAGAC
1 AAAAAGAAGAAGAAGCACAAAGAC
425297 AAAAAGAAGAAGAAGCACAAAGA
1 AAAAAGAAGAAGAAGCACAAAGA
425320 AGAGGGTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.64, C:0.09, G:0.26, T:0.02
Consensus pattern (24 bp):
AAAAAGAAGAAGAAGCACAAAGAC
Found at i:431147 original size:31 final size:31
Alignment explanation
Indices: 431109--431170 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
431099 AGCCGATTGA
431109 GTTAGTTTTATTTCAGTTTTTCATGCATACC
1 GTTAGTTTTATTTCAGTTTTTCATGCATACC
431140 GTTAGTTTTATTTCAGTTTTTCATGCATACC
1 GTTAGTTTTATTTCAGTTTTTCATGCATACC
431171 ATGTAGATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (31 bp):
GTTAGTTTTATTTCAGTTTTTCATGCATACC
Found at i:432183 original size:13 final size:13
Alignment explanation
Indices: 432165--432189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
432155 CCCATTTGGT
432165 CATTTTTAGCATA
1 CATTTTTAGCATA
432178 CATTTTTAGCAT
1 CATTTTTAGCAT
432190 TTTTAATTTA
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATA
Found at i:432334 original size:26 final size:26
Alignment explanation
Indices: 432305--432363 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
432295 TTGCGTCCAA
* * *
432305 AATTATTACTGCAGGAACCTGTTAAG
1 AATTATCACTACAAGAACCTGTTAAG
* *
432331 AATTATCACTACAAGAACTTGTTCAG
1 AATTATCACTACAAGAACCTGTTAAG
432357 AATTATC
1 AATTATC
432364 GCTATGTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (26 bp):
AATTATCACTACAAGAACCTGTTAAG
Found at i:434833 original size:21 final size:22
Alignment explanation
Indices: 434807--434850 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
434797 AAAAATGTTT
*
434807 CAAAA-GAATCTTGTCTTGAGA
1 CAAAAGGAATATTGTCTTGAGA
*
434828 CAAAAGGCATATTGTCTTGAGA
1 CAAAAGGAATATTGTCTTGAGA
434850 C
1 C
434851 CAACCAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (22 bp):
CAAAAGGAATATTGTCTTGAGA
Found at i:439798 original size:7 final size:7
Alignment explanation
Indices: 439780--439838 Score: 63
Period size: 6 Copynumber: 8.6 Consensus size: 7
439770 CAATATATAG
439780 TTTTCTTC
1 TTTTC-TC
439788 TTTTCTC
1 TTTTCTC
439795 TTTTCTC
1 TTTTCTC
439802 TTTTCCTC
1 TTTT-CTC
439810 TTCTTC-C
1 TT-TTCTC
439817 TTTT-TC
1 TTTTCTC
439823 TTTTCT-
1 TTTTCTC
439829 TTTTCT-
1 TTTTCTC
439835 TTTT
1 TTTT
439839 TTTAAGTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
6 17 0.36
7 17 0.36
8 11 0.23
9 2 0.04
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCTC
Found at i:439800 original size:15 final size:15
Alignment explanation
Indices: 439780--439829 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
439770 CAATATATAG
439780 TTTTCTTCTTTTCTC
1 TTTTCTTCTTTTCTC
439795 TTTTC-TCTTTTC-C
1 TTTTCTTCTTTTCTC
*
439808 TCTTCTTCCTTTT-TC
1 TTTTCTT-CTTTTCTC
439823 TTTTCTT
1 TTTTCTT
439830 TTTCTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.17
14 8 0.27
15 17 0.57
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTCTTCTTTTCTC
Found at i:442609 original size:23 final size:22
Alignment explanation
Indices: 442583--442626 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
442573 AAAATATTTC
*
442583 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
442606 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
442627 TTATTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:444036 original size:16 final size:17
Alignment explanation
Indices: 444009--444041 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
443999 TACCAAGTTG
*
444009 TTAATATAATTTTACAA
1 TTAATATAATTTAACAA
444026 TTAAT-TAATTTAACAA
1 TTAATATAATTTAACAA
444042 AAATACAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATATAATTTAACAA
Found at i:454136 original size:17 final size:18
Alignment explanation
Indices: 454110--454156 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
454100 ATACTTATAA
454110 GAATGGAAATGCAACT-AC
1 GAAT-GAAATGCAACTAAC
454128 -AATGCAAATGC-ACTAAC
1 GAATG-AAATGCAACTAAC
454145 GAATGAAATGCA
1 GAATGAAATGCA
454157 GTGACAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 4 0.16
17 17 0.68
18 4 0.16
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (18 bp):
GAATGAAATGCAACTAAC
Found at i:458901 original size:24 final size:24
Alignment explanation
Indices: 458868--458914 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
458858 GTTAAGAGTA
*
458868 AAAACTGTCAGTGCAAATGTAATAT
1 AAAACTGTCAGAGCAAAT-TAATAT
458893 AAAA-TGTCAGAGCAAATTAATA
1 AAAACTGTCAGAGCAAATTAATA
458915 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAACTGTCAGAGCAAATTAATAT
Found at i:467055 original size:24 final size:24
Alignment explanation
Indices: 467022--467068 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
467012 GTTAAGAGTA
*
467022 AAAACTGTCAGTGCAAATGTAATAT
1 AAAACTGTCAGAGCAAAT-TAATAT
467047 AAAA-TGTCAGAGCAAATTAATA
1 AAAACTGTCAGAGCAAATTAATA
467069 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAACTGTCAGAGCAAATTAATAT
Found at i:472913 original size:6 final size:6
Alignment explanation
Indices: 472902--472952 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
472892 TATAGCAATA
* *
472902 TTTCTT TTTCTT TTCTCTT TTTC-T CTT-TT TCTCTT TTTC-T TTTCTT
1 TTTCTT TTTCTT TT-TCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
472948 TTTCT
1 TTTCT
472953 CATTTACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 10 0.27
6 21 0.57
7 6 0.16
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:472925 original size:8 final size:8
Alignment explanation
Indices: 472912--472941 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
472902 TTTCTTTTTC
472912 TTTTCTCT
1 TTTTCTCT
472920 TTTTCTCT
1 TTTTCTCT
472928 TTTTCTCT
1 TTTTCTCT
472936 TTTTCT
1 TTTTCT
472942 TTTCTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCTCT
Found at i:472965 original size:27 final size:29
Alignment explanation
Indices: 472906--472966 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 29
472896 GCAATATTTC
* * **
472906 TTTTTCTTTTCTCTTTTTCTCTTTTTCTC
1 TTTTTCTTTTCTCTTTTTCTCATTTACAA
472935 TTTTTC-TTT-TCTTTTTCTCATTTACAA
1 TTTTTCTTTTCTCTTTTTCTCATTTACAA
472962 TTTTT
1 TTTTT
472967 ATAAGTGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 19 0.68
28 3 0.11
29 6 0.21
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTTCTTTTCTCTTTTTCTCATTTACAA
Found at i:484417 original size:77 final size:75
Alignment explanation
Indices: 484336--484509 Score: 197
Period size: 75 Copynumber: 2.3 Consensus size: 75
484326 GTTTTGCATC
* * * * * *
484336 ATTATGTGTTTTGTTCTTGTTAAATGCATCTTTGTTTAATGTTTTGCATTAATACATTTGCATAT
1 ATTATGTGTTTTG-T-TTATTAAATGCATCTCTATTTAATGTTTTGCAGTAATACATTAGCATAC
484401 TTTAAAACTTGA
64 TTTAAAACTTGA
** * *
484413 ATTATGTGTCGTGTTTATTAAATGCATCTCTATTTAATGTTTTGTAGTAATACATTAGCATCCTT
1 ATTATGTGTTTTGTTTATTAAATGCATCTCTATTTAATGTTTTGCAGTAATACATTAGCATACTT
* *
484478 TAATACTTGC
66 TAAAACTTGA
* *
484488 ATTGTGTGTTTT-TATATTAAAT
1 ATTATGTGTTTTGTTTATTAAAT
484510 AAGTTGTGCA
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
74 9 0.11
75 60 0.74
76 1 0.01
77 11 0.14
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (75 bp):
ATTATGTGTTTTGTTTATTAAATGCATCTCTATTTAATGTTTTGCAGTAATACATTAGCATACTT
TAAAACTTGA
Found at i:485511 original size:24 final size:24
Alignment explanation
Indices: 485455--485511 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
485445 GTATTAAAAG
* *
485455 TTTCCAAATATTGAAAAAAGGAAA
1 TTTCAAAATAGTGAAAAAAGGAAA
485479 -TTCAAAAATAGTGAAAAAAGGAAA
1 TTTC-AAAATAGTGAAAAAAGGAAA
*
485503 TTTCGAAAT
1 TTTCAAAAT
485512 TAAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.11
24 22 0.79
25 3 0.11
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (24 bp):
TTTCAAAATAGTGAAAAAAGGAAA
Found at i:485520 original size:25 final size:24
Alignment explanation
Indices: 485492--485543 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
485482 AAAAATAGTG
* *
485492 AAAAAAGGAAATTTCGAAATTAAAA
1 AAAAAAAGAAAATTCG-AATTAAAA
485517 AAAAAAAGAAAATTCGAATTAAAA
1 AAAAAAAGAAAATTCGAATTAAAA
485541 AAA
1 AAA
485544 TATTCTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (24 bp):
AAAAAAAGAAAATTCGAATTAAAA
Found at i:487963 original size:32 final size:32
Alignment explanation
Indices: 487913--488262 Score: 362
Period size: 32 Copynumber: 10.8 Consensus size: 32
487903 CCTAGTATAT
* * *
487913 TCGTATGAGCTATTAATCTATGAGA-AATATGC
1 TCGTAAGAGCTATCAATCTATGA-ACAATAAGC
* * **
487945 TCGTAAGAGATATCAATCTATGAACAGTGTGC
1 TCGTAAGAGCTATCAATCTATGAACAATAAGC
* * * * * *
487977 TCATAAAAGCTATCAATATGTGAATAGTAAGC
1 TCGTAAGAGCTATCAATCTATGAACAATAAGC
* *
488009 TTGT-AGAAGCTATCAATCTATGAATAATAAGC
1 TCGTAAG-AGCTATCAATCTATGAACAATAAGC
488041 TCGTAAGAGCTATCAATCTATGAACAATAAGC
1 TCGTAAGAGCTATCAATCTATGAACAATAAGC
*
488073 TCGTAAAAGCTATCAATCTATGAACAATAAGCTCAC
1 TCGTAAGAGCTATCAATCTATGAACAATAAG----C
* * *
488109 TCGTAAGAGTTGTTAATCTATGAACAATAAGC
1 TCGTAAGAGCTATCAATCTATGAACAATAAGC
* * *
488141 TCGTAAGAGCTGTCGATCTATGAATAATAAGC
1 TCGTAAGAGCTATCAATCTATGAACAATAAGC
* * * *
488173 TCGTAAGAGCTTTCGATCTACGAATAATAAGC
1 TCGTAAGAGCTATCAATCTATGAACAATAAGC
** * *
488205 TCGTAAGTTCTTTCAATCTATGAACAATAATC
1 TCGTAAGAGCTATCAATCTATGAACAATAAGC
488237 TCGTAAGAGCTATCAATCTATGAACA
1 TCGTAAGAGCTATCAATCTATGAACA
488263 TTGATTCATC
Statistics
Matches: 270, Mismatches: 41, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
31 2 0.01
32 238 0.88
33 2 0.01
36 28 0.10
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (32 bp):
TCGTAAGAGCTATCAATCTATGAACAATAAGC
Found at i:488192 original size:132 final size:128
Alignment explanation
Indices: 487913--488262 Score: 364
Period size: 132 Copynumber: 2.7 Consensus size: 128
487903 CCTAGTATAT
* * * * * * * *
487913 TCGTATGAGCTATTAATCTATGAGA-AATATGCTCGTAAGAGATATCAATCTATGAACAGT-GTG
1 TCGTAAGAGCTATCAATCTACGA-ACAATAAGCTCGTAAAAGCTATCAATCTATGAACAATAAT-
* * * * * * * * *
487976 CTCATAAAAGCTATCAATATGTGAATAGTAAGCTTGT-AGAAGCTATCAATCTATGAATAATAAG
64 CTCGTAAGAGCTATCAATCTATGAACAATAAGCTCGTAAG-AGCTGTCGATCTATGAATAATAAG
488040 C
128 C
*
488041 TCGTAAGAGCTATCAATCTATGAACAATAAGCTCGTAAAAGCTATCAATCTATGAACAATAAGCT
1 TCGTAAGAGCTATCAATCTACGAACAATAAGCTCGTAAAAGCTATCAATCTATGAACAATAA--T
* * *
488106 CACTCGTAAGAGTTGTTAATCTATGAACAATAAGCTCGTAAGAGCTGTCGATCTATGAATAATAA
64 --CTCGTAAGAGCTATCAATCTATGAACAATAAGCTCGTAAGAGCTGTCGATCTATGAATAATAA
488171 GC
127 GC
* * * *** *
488173 TCGTAAGAGCTTTCGATCTACGAATAATAAGCTCGTAAGTTCTTTCAATCTATGAACAATAATCT
1 TCGTAAGAGCTATCAATCTACGAACAATAAGCTCGTAAAAGCTATCAATCTATGAACAATAATCT
488238 CGTAAGAGCTATCAATCTATGAACA
66 CGTAAGAGCTATCAATCTATGAACA
488263 TTGATTCATC
Statistics
Matches: 185, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
127 1 0.01
128 76 0.41
130 1 0.01
131 1 0.01
132 104 0.56
133 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (128 bp):
TCGTAAGAGCTATCAATCTACGAACAATAAGCTCGTAAAAGCTATCAATCTATGAACAATAATCT
CGTAAGAGCTATCAATCTATGAACAATAAGCTCGTAAGAGCTGTCGATCTATGAATAATAAGC
Found at i:510483 original size:50 final size:51
Alignment explanation
Indices: 510425--510622 Score: 267
Period size: 50 Copynumber: 3.9 Consensus size: 51
510415 TTAATAAAGT
* * * *
510425 CATGCATTATGTAACTCTCGTGATAGTTAAGTTTTCATCA-TAAATATTGA
1 CATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCATCATTAAATATTGA
* *
510475 CATGCATTAAGTAACTCTCAAGTTAGTTAAGTTTGCATCA-TAAATAATGA
1 CATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCATCATTAAATATTGA
* *
510525 CATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCATCATTAAAT-TATGT
1 CATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCATCATTAAATAT-TGA
* *
510576 CATGCATTAAGTAACTCCCATGGTAGTTAAAGTTTGCATCATTAAAT
1 CATGCATTAAGTAACTCTCATGTTAGTT-AAGTTTGCATCATTAAAT
510623 TAAGCTATGC
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
50 82 0.62
51 32 0.24
52 18 0.14
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (51 bp):
CATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCATCATTAAATATTGA
Found at i:510633 original size:52 final size:50
Alignment explanation
Indices: 510411--510644 Score: 258
Period size: 50 Copynumber: 4.6 Consensus size: 50
510401 TATGTGTTCT
* * * * * *
510411 TCATTTAATAAAGTCATGCATTATGTAACTCTCGTGATAGTTAAGTTTTCA
1 TCATTAAATTAAG-CATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCA
* * *
510462 TCATAAATATTGA-CATGCATTAAGTAACTCTCAAGTTAGTTAAGTTTGCA
1 TCATTAA-ATTAAGCATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCA
*
510512 TCA-TAAA-TAATGACATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCA
1 TCATTAAATTAA-G-CATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCA
* * *
510562 TCATTAAATTATGTCATGCATTAAGTAACTCCCATGGTAGTTAAAGTTTGCA
1 TCATTAAATTAAG-CATGCATTAAGTAACTCTCATGTTAGTT-AAGTTTGCA
*
510614 TCATTAAATTAAGCTATGCATTAAGAAACTC
1 TCATTAAATTAAGC-ATGCATTAAGTAACTC
510645 ATTTGTTCAT
Statistics
Matches: 155, Mismatches: 20, Indels: 15
0.82 0.11 0.08
Matches are distributed among these distances:
47 2 0.01
48 1 0.01
49 2 0.01
50 73 0.47
51 36 0.23
52 41 0.26
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (50 bp):
TCATTAAATTAAGCATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCA
Found at i:512212 original size:30 final size:30
Alignment explanation
Indices: 512176--512235 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
512166 AGAAGAAAGG
512176 CTACAAACGTTCATACCAATGATGGAAGTT
1 CTACAAACGTTCATACCAATGATGGAAGTT
512206 CTACAAACGTTCATACCAATGATGGAAGTT
1 CTACAAACGTTCATACCAATGATGGAAGTT
512236 TTCAACGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (30 bp):
CTACAAACGTTCATACCAATGATGGAAGTT
Found at i:514561 original size:52 final size:52
Alignment explanation
Indices: 514400--514623 Score: 337
Period size: 52 Copynumber: 4.4 Consensus size: 52
514390 ATTTAATAAA
* * *
514400 GTCATGCATTATGTAACTCTCATGATAGTT-AAGTTTGCATCA-TAAATAAT
1 GTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAT
* * *
514450 GGCATGCATCAAGTAACTCTCATGTTAGTTAAA-TTTGCATCATTAAATTGT
1 GTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAT
514501 GTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAT
1 GTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAT
* * * *
514553 GTCGTGCATTAACTAACTCTCATGTTAGTTAAATTTTGCATCATTAAATTAA
1 GTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAT
514605 GTCATGCATTAAGTAACTC
1 GTCATGCATTAAGTAACTC
514624 ATTTGTTCAT
Statistics
Matches: 156, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
50 35 0.22
51 39 0.25
52 82 0.53
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (52 bp):
GTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAT
Found at i:514645 original size:103 final size:103
Alignment explanation
Indices: 514389--514623 Score: 348
Period size: 103 Copynumber: 2.3 Consensus size: 103
514379 ATGTGTTCTG
* * * *
514389 CATTTAATAAAGTCATGCATTATGTAACTCTCATGATAGTT-AAGTTTGCATCA-TAAATAATGG
1 CATTAAATTAAGTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATAATGG
*
514452 CATGCATCAAGTAACTCTCATGTTAGTTAAATTTGCAT
66 CATGCATCAACTAACTCTCATGTTAGTTAAATTTGCAT
** * *
514490 CATTAAATTGTGTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTATGT
1 CATTAAATTAAGTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATAATGG
* *
514555 CGTGCATTAACTAACTCTCATGTTAGTTAAATTTTGCAT
66 CATGCATCAACTAACTCTCATGTTAGTTAAA-TTTGCAT
514594 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTAAGTAACTC
514624 ATTTGTTCAT
Statistics
Matches: 118, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
101 35 0.30
102 12 0.10
103 36 0.31
104 35 0.30
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (103 bp):
CATTAAATTAAGTCATGCATTAAGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATAATGG
CATGCATCAACTAACTCTCATGTTAGTTAAATTTGCAT
Found at i:518818 original size:75 final size:75
Alignment explanation
Indices: 518664--518803 Score: 199
Period size: 75 Copynumber: 1.9 Consensus size: 75
518654 TATATTTGAA
* * * * * * *
518664 AAATGCATCTTTGTTTAATGTTTTACATTAATACATTTGCATCTTTTAAAACTTGCATTATGTGT
1 AAATACATCTTTATTTAATGTTCTACATTAATACATTAGCATCCTTTAAAACATGCATTATGTAT
518729 CTTGTTTATT
66 CTTGTTTATT
* *
518739 AAATACATCTTTATTTGATGTTCTACATTAATACATTAGCATCCTTTAATACATGCATTATGTAT
1 AAATACATCTTTATTTAATGTTCTACATTAATACATTAGCATCCTTTAAAACATGCATTATGTAT
518804 TTTTCATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 56 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (75 bp):
AAATACATCTTTATTTAATGTTCTACATTAATACATTAGCATCCTTTAAAACATGCATTATGTAT
CTTGTTTATT
Found at i:520264 original size:42 final size:44
Alignment explanation
Indices: 520218--520315 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 44
520208 AGTGGATGCC
* *
520218 TTCCACGTAGCTTTCTT-TTTTTTCATTTCATGAAAGTGG-TTT
1 TTCCACGTAGCTTTCTTCCTTTGTCATTTCATGAAAGTGGCTTT
* * * *
520260 TTCCATGTAGC-TTCTTCCTTTGTCGTTTCTTGAATGTGGCTTT
1 TTCCACGTAGCTTTCTTCCTTTGTCATTTCATGAAAGTGGCTTT
520303 TTCCACGTAGCTT
1 TTCCACGTAGCTT
520316 CGTCTATCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 5 0.11
42 27 0.59
43 13 0.28
44 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.16, T:0.50
Consensus pattern (44 bp):
TTCCACGTAGCTTTCTTCCTTTGTCATTTCATGAAAGTGGCTTT
Found at i:525452 original size:21 final size:20
Alignment explanation
Indices: 525415--525454 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
525405 TCCTCAAGTA
*
525415 AAACAAAAACTAGCAAGGAT
1 AAACAAAAACTACCAAGGAT
*
525435 AAACAAAAATTTACCAAGGA
1 AAACAAAAA-CTACCAAGGA
525455 AAATGATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.15, G:0.12, T:0.12
Consensus pattern (20 bp):
AAACAAAAACTACCAAGGAT
Found at i:528410 original size:34 final size:34
Alignment explanation
Indices: 528367--528434 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
528357 TACATCGACA
*
528367 ATAAAGTCCAAGTGTGTCAACAATGGTACCTACT
1 ATAAAGTCCAAGTGCGTCAACAATGGTACCTACT
528401 ATAAAGTCCAAGTGCGTCAACAATGGTACCTACT
1 ATAAAGTCCAAGTGCGTCAACAATGGTACCTACT
528435 TATTCTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (34 bp):
ATAAAGTCCAAGTGCGTCAACAATGGTACCTACT
Found at i:537873 original size:37 final size:37
Alignment explanation
Indices: 537832--537907 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
537822 GTTTCGAGCC
537832 CTAACTATTTGGCATGTTAACAAAGTTACTAATTTGA
1 CTAACTATTTGGCATGTTAACAAAGTTACTAATTTGA
537869 CTAACTATTTGGCATGTTAACAAAGTTACTAATTTGA
1 CTAACTATTTGGCATGTTAACAAAGTTACTAATTTGA
537906 CT
1 CT
537908 GAATGATTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (37 bp):
CTAACTATTTGGCATGTTAACAAAGTTACTAATTTGA
Found at i:540792 original size:29 final size:28
Alignment explanation
Indices: 540740--541056 Score: 223
Period size: 29 Copynumber: 11.1 Consensus size: 28
540730 AGTTCCAGAG
* *
540740 AGTTTGGGGTTAAAATGT-ATTTTTAGAA
1 AGTTTAGGGTAAAAATGTAATTTTT-GAA
540768 AGTTTAGGGATAAAAATGTAATTTTTGAGA
1 AGTTTAGGG-TAAAAATGTAATTTTTGA-A
* *
540798 AGTTGAGGTTAAAAATGTAATTTTTGAA
1 AGTTTAGGGTAAAAATGTAATTTTTGAA
** *
540826 AGTTTAGGGGGAAAATGCAATTTTTGAGA
1 AGTTTAGGGTAAAAATGTAATTTTTGA-A
* * *
540855 AGTTCGAGGGT-AAAATGTGATTTTTGGA
1 AGTT-TAGGGTAAAAATGTAATTTTTGAA
* * *
540883 AGTTCAAGGGTAAAAATGTGATTTTTGGA
1 AGTT-TAGGGTAAAAATGTAATTTTTGAA
* * *
540912 AGTTTGAGGGCAAAAATGCAATTTTTGGA
1 AGTTT-AGGGTAAAAATGTAATTTTTGAA
* * *
540941 AGTTTTGGGGCAAAAATGTGATTTTTGAA
1 AG-TTTAGGGTAAAAATGTAATTTTTGAA
** * *
540970 AGTTCGGGGGCAATAATGTAATTTTTGAGA
1 AGTT-TAGGGTAAAAATGTAATTTTTGA-A
* * * *
541000 AGTTT-GAAGTAAAAAGGTGA-TTTTCAGA
1 AGTTTAG-GGTAAAAATGTAATTTTTGA-A
*
541028 AGTTCAAGGGT-AAAATGTAATTTTT-AA
1 AGTT-TAGGGTAAAAATGTAATTTTTGAA
541055 AG
1 AG
541057 AAAATAATAG
Statistics
Matches: 238, Mismatches: 37, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.01
28 64 0.27
29 144 0.61
30 27 0.11
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
AGTTTAGGGTAAAAATGTAATTTTTGAA
Found at i:540828 original size:58 final size:58
Alignment explanation
Indices: 540746--541056 Score: 289
Period size: 58 Copynumber: 5.4 Consensus size: 58
540736 AGAGAGTTTG
*
540746 GGGTTAAAATGT-ATTTTTAGAAAGTTTAGGGATAAAAATGTAATTTTTGAGAAGTT-GA
1 GGGTAAAAATGTAATTTTT-GAAAGTTTAGGG-TAAAAATGTAATTTTTGAGAAGTTCGA
* ** *
540804 GGTTAAAAATGTAATTTTTGAAAGTTTAGGGGGAAAATGCAATTTTTGAGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAAAGTTTAGGGTAAAAATGTAATTTTTGAGAAGTTCGA
* * * * *
540862 GGGT-AAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTGATTTTTG-GAAGTTTGA
1 GGGTAAAAATGTAATTTTTGAAAGTT-TAGGGTAAAAATGTAATTTTTGAGAAGTTCGA
* * * * * * *
540919 GGGCAAAAATGCAATTTTTGGAAGTTTTGGGGCAAAAATGTGATTTTTGA-AAGTTCGG
1 GGGTAAAAATGTAATTTTTGAAAG-TTTAGGGTAAAAATGTAATTTTTGAGAAGTTCGA
* * * * * * *
540977 GGGCAATAATGTAATTTTTGAGAAGTTT-GAAGTAAAAAGGTGA-TTTTCAGAAGTTCAA
1 GGGTAAAAATGTAATTTTTGA-AAGTTTAG-GGTAAAAATGTAATTTTTGAGAAGTTCGA
541035 GGGT-AAAATGTAATTTTT-AAAG
1 GGGTAAAAATGTAATTTTTGAAAG
541057 AAAATAATAG
Statistics
Matches: 211, Mismatches: 33, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
55 3 0.01
56 1 0.00
57 70 0.33
58 126 0.60
59 11 0.05
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTAGGGTAAAAATGTAATTTTTGAGAAGTTCGA
Found at i:543385 original size:39 final size:39
Alignment explanation
Indices: 543265--544382 Score: 630
Period size: 39 Copynumber: 28.7 Consensus size: 39
543255 GTTGGCTGCA
* *
543265 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * *
543304 ATCTG-CCCAGGTTCGGGGTAAAAGA-T--C-GAATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTG-ATGG-TG
** * *
543340 CAATCTGCCTTAGGCTCGAGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * **
543381 ATCTGCCTCAAGCTCGGGATAAGAGATCGGATGACTGCAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGA-TGGTG
* * *** * * *
543421 -TCTGCCCTAGGCTTAAGGTAAGAGATTGACTAATAGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * *
543459 ATTTGCCCCAAGCTCGGGGTAAGAGATCGGATGGCT-GTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCT-GATGGTG
* * *
543498 ATCTGCCCCAAGCTCGGGGTAAGAGACTAGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * ** * * *
543537 ATCTGACCCAAGCTCGGGTTAAAAGATCGAATGGTTGTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * *
543576 ATTTGCCTCAAGCTCGGGGTAAGAGATTGGTTGATGGTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * *
543615 ATCTACCCTAGGCTCGAGGTAAGAGATT---AGATGGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG-T--G
* * *
543654 ATCTACCCCAAGCTCAGGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * **
543693 ATCTGCCCCAAGCTCGGGGTAAGAAATCGGATGACT-GCA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGA-TGGTG
* *
543732 ATCTACCCCAAGCTCGGGATAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** *
543771 ATTTGCCCCAAGCTCTAGGTAAGAGATT-G--GATGGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG-T--G
* *
543810 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
** *
543849 ATCTATCCCAAGCTCAGGGTAAGAGATT-G--GATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG-TG
* * *
543886 CAATCTGCCTCAGGCTCGGGGTAAGAGATTAGCTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * ** *
543927 ATCTGCCCCGAGCTCGAGACAAAAGA-T--C-GAATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTG-ATGG-TG
* * * *
543964 CAATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTA
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * ** * * *
544005 ATCTACCTCAGGCTCGGGGTAAGAGATCAGATAGCT-GTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCT-GATGGTG
* *
544044 ATCTGCCCTAAGCTCGGGGTAAGAGA-T--CAGATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG-TG
* * *
544081 TAATCTGCCCTAAGCTCGAGGTAAGAGACTGGCTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * *
544122 ATCTGCCCCAGGCTTGGGGTAAGAGA-T--CGGATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG-TG
* * *
544159 CAATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * *
544200 ATTTGCCTCAGGCTCAGGGTAAAAGA-T--C-GAATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTG-ATGG-TG
* *
544237 CAATCTGCCCCAAGCTCGAGGTAAGAGAGTGGCTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * *
544278 ATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGGCTGCT-
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCT-GATGGTG
* *
544317 ATCTTCCCC-AGACTCGGGGTAAGAGATTGGCTGATGGTA
1 ATCTGCCCCAAG-CTCGGGGTAAGAGATTGGCTGATGGTG
* * * *
544356 ATCTACCCCAAGGTCTGGGTAAAAGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT
544383 CGAATGGCTA
Statistics
Matches: 823, Mismatches: 189, Indels: 134
0.72 0.16 0.12
Matches are distributed among these distances:
35 9 0.01
36 34 0.04
37 12 0.01
38 39 0.05
39 652 0.79
40 20 0.02
41 13 0.02
42 41 0.05
43 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:543440 original size:78 final size:77
Alignment explanation
Indices: 543257--544148 Score: 846
Period size: 78 Copynumber: 11.5 Consensus size: 77
543247 TTTAAGATGT
* * * *
543257 TGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCAGGTTCGGGG
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGCTCGGGG
* *
543322 TAAAAGATCGAA
66 TAAGAGATCGGA
* *
543334 TGGCTGCAATCTGCCTTAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCGGG
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCC-CAAGCTCGGG
*
543399 ATAAGAGATCGGA
65 GTAAGAGATCGGA
* * *** * * * *
543412 TGACTGCAGTCTGCCCTAGGCTTAAGGTAAGAGATTGACTAATAGTGATTTGCCCCAAGCTCGGG
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCGGG
543477 GTAAGAGATCGGA
65 GTAAGAGATCGGA
* * * * * *
543490 TGGCTGTAATCTGCCCCAAGCTCGGGGTAAGAGACTAGTTGATGGTGATCTGACCCAAGCTCGGG
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCGGG
* * *
543555 TTAAAAGATCGAA
65 GTAAGAGATCGGA
* * * * * * * * *
543568 TGGTTGTAATTTG-CCTCAAGCTCGGGGTAAGAGATTGGTTGATGGTAATCTACCCTAGGCTCGA
1 TGGCTGCAATCTGCCCT-AGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGCTCGG
**
543632 GGTAAGAGATTAGA
64 GGTAAGAGATCGGA
* * * * * *
543646 TGGCTACAATCTACCCCAAGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGG
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCGGG
*
543711 GTAAGAAATCGGA
65 GTAAGAGATCGGA
* * * * * * **
543724 TGACTGCAATCTACCCCAAGCTCGGGATAAGAGATTGGCTGATGGTGATTTGCCCCAAGCTCTAG
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCGGG
*
543789 GTAAGAGATTGGA
65 GTAAGAGATCGGA
* * *
543802 TGGCTACAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTATCCCAAGCTCAGG
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCT-GCCCAAGCTCGGG
*
543867 GTAAGAGATTGGA
65 GTAAGAGATCGGA
* * *
543880 TGGCTGCAATCTG-CCTCAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCGAGCTCGA
1 TGGCTGCAATCTGCCCT-AGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCGG
** * *
543944 GACAAAAGATCGAA
64 GGTAAGAGATCGGA
* * * * * *
543958 TGGCTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTAATCTACCTCAGGCTCGGG
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCC-CAAGCTCGGG
*
544023 GTAAGAGATCAGA
65 GTAAGAGATCGGA
* * * *
544036 TAGCTGTAATCTGCCCTAAGCTCGGGGTAAGAGA-T--CAGATGGCTGTAATCTGCCCTAAGCTC
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCC-AAGCTC
* *
544098 GAGGTAAGAGACTGGCTGA
62 GGGGTAAGAGA-T--CGGA
* *
544117 TGG-TG--ATCTGCCCCAGGCTTGGGGTAAGAGAT
1 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGAT
544149 CGGATGGCTG
Statistics
Matches: 669, Mismatches: 127, Indels: 36
0.80 0.15 0.04
Matches are distributed among these distances:
75 5 0.01
76 1 0.00
77 62 0.09
78 584 0.87
79 10 0.01
80 2 0.00
81 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (77 bp):
TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGCTCGGGG
TAAGAGATCGGA
Found at i:544149 original size:78 final size:78
Alignment explanation
Indices: 544044--544421 Score: 443
Period size: 78 Copynumber: 4.8 Consensus size: 78
544034 GATAGCTGTA
* * * *
544044 ATCTGCCCTAAGCTCGGGGTAAGAGATCAGATGGCTGTAATCTGCCCTAAGCTCGAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
*
544109 CTGGCTGATGGTG
66 TTGGCTGATGGTG
* * * * * *
544122 ATCTGCCCCAGGCTTGGGGTAAGAGATCGGATGGCTGCAATCTACCCTAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
544187 TTGGCTGATGGTG
66 TTGGCTGATGGTG
* * * * * *
544200 ATTTGCCTCAGGCTCAGGGTAAAAGATCGAATGGCTGCAATCTGCCCCAAGCTCGAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
*
544265 GTGGCTGATGGTG
66 TTGGCTGATGGTG
* * * * *
544278 ATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGGCTGCTATCTTCCC-CAGACTCGGGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAG-CTCGAGGTAAGAG
*
544342 ATTGGCTGATGGTA
65 ATTGGCTGATGGTG
* * * * * * * * *
544356 ATCTACCCCAAGGTCTGGGTAAAAGATCGAATGGCTACAATCTGCCTTAGGCTTGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
544421 T
66 T
544422 CGGATGGCTG
Statistics
Matches: 254, Mismatches: 44, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
77 2 0.01
78 251 0.99
79 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (78 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
TTGGCTGATGGTG
Found at i:544439 original size:78 final size:77
Alignment explanation
Indices: 544004--544437 Score: 310
Period size: 78 Copynumber: 5.6 Consensus size: 77
543994 GGTTGATGGT
* * * * * * * *
544004 AATCTACCTCAGGCTCGGGGTAAGAGATCAGATAGCTGTAATCTGCCCTAAGCTCGGGGTAAGAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATCGGAT-GGTGTAATCTGCCCCAAGGTCTGGGTAAAAG
*
544069 ATC-AGATGGCTGT
65 ATCGA-ATGGCTGC
* * * *
544082 AATCTGCCCTAAGCTCGAGGTAAGAGACTGGCTGATGGTG--ATCTGCCCC-AGG-CTTGGGGTA
1 AATCTGCCCCAGGCTCGGGGTAAGAGA-T--CGGATGGTGTAATCTGCCCCAAGGTC-T-GGGTA
* *
544143 AGAGATCGGATGGCTGC
61 AAAGATCGAATGGCTGC
* * * * * * * * *
544160 AATCTACCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCTC-AGGCTCAGGGTAAAA
1 AATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGGT-GTAATCTGCCCCAAGG-TCTGGGTAAAA
544224 GATCGAATGGCTGC
64 GATCGAATGGCTGC
* * * *
544238 AATCTGCCCCAAGCTCGAGGTAAGAGAGTGGCTGATGGTG--ATCTGCCCCAAGCTC-GAGGTAA
1 AATCTGCCCCAGGCTCGGGGTAAGAGA-T--CGGATGGTGTAATCTGCCCCAAGGTCTG-GGTAA
*
544300 AAGATCGGATGGCTGC
62 AAGATCGAATGGCTGC
* * * * * * *
544316 TATCTTCCCCAGACTCGGGGTAAGAGATTGGCTGATGGTAATCTACCCCAAGGTCTGGGTAAAAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGGT-GTAATCTGCCCCAAGGTCTGGGTAAAAG
*
544381 ATCGAATGGCTAC
65 ATCGAATGGCTGC
** *
544394 AATCTGCCTTAGGCTTGGGGTAAGAGATCGGATGGCTGTAATCT
1 AATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGG-TGTAATCT
544438 ACTGCTCCTC
Statistics
Matches: 277, Mismatches: 58, Indels: 42
0.73 0.15 0.11
Matches are distributed among these distances:
75 8 0.03
76 3 0.01
77 5 0.02
78 242 0.87
79 6 0.02
80 5 0.02
81 8 0.03
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (77 bp):
AATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGGTGTAATCTGCCCCAAGGTCTGGGTAAAAGA
TCGAATGGCTGC
Found at i:555899 original size:14 final size:14
Alignment explanation
Indices: 555880--555921 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
555870 TATACAAATG
555880 AATAAATATACGAA
1 AATAAATATACGAA
*
555894 AATAAATATAAGAAA
1 AATAAATATACG-AA
555909 AATAAA-ATACGAA
1 AATAAATATACGAA
555922 TCATGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 15 0.60
15 8 0.32
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:556254 original size:57 final size:57
Alignment explanation
Indices: 556076--556406 Score: 344
Period size: 57 Copynumber: 5.7 Consensus size: 57
556066 AGTTTAGGGT
* *** *
556076 AAAATGTAATATTTGAGAAGTTTGAGGCAAAAAATGTAATTTCTGGAAGTTTG-GGAGCA
1 AAAATGTAATTTTTG-GAAGTTT-AGGGGTAAAATGTAATTTTTGGAAGTTTGAGG-GCA
* * * *
556135 AAAATGTAATTTTTGAGAAGTTTAAGGGTAAAAATGTGATTTTTGGAAGTTCGAGGACA
1 AAAATGTAATTTTTG-GAAGTTTAGGGGT-AAAATGTAATTTTTGGAAGTTTGAGGGCA
* * * *
556194 AAAATGTAATTTTTGTAAGTTTAGGGGTAAAATGTAGTTTTTAGAAGTTTGAGGGTA
1 AAAATGTAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGGAAGTTTGAGGGCA
* * * * *
556251 AAAATATAATTTTTGGAAGTTTGGGGGAAAAATGCAATTTTTGGAAGTTCGAGGG-A
1 AAAATGTAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGGAAGTTTGAGGGCA
* * * *
556307 AAAATATAATTTTTGGAAGTTTGGGGGCAAAATGTAATTTTTGGAAG-TTCAGGGGCA
1 AAAATGTAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGGAAGTTTGA-GGGCA
* * * *
556364 AAATTGCAATTTTTGGAAGTTTGGGGGTAAAATTTTAATTTTT
1 AAAATGTAATTTTTGGAAGTTTAGGGGTAAAA-TGTAATTTTT
556407 AAAAAAAGGA
Statistics
Matches: 233, Mismatches: 34, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
55 2 0.01
56 49 0.21
57 99 0.42
58 22 0.09
59 59 0.25
60 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGGAAGTTTGAGGGCA
Found at i:556389 original size:28 final size:28
Alignment explanation
Indices: 556076--556389 Score: 319
Period size: 28 Copynumber: 10.9 Consensus size: 28
556066 AGTTTAGGGT
* *
556076 AAAATGTAATATTTGAGAAGTTTGAGGCAA
1 AAAATGTAATTTTTG-GAAGTTTGGGGC-A
*
556106 AAAATGTAATTTCTGGAAGTTTGGGAGCA
1 AAAATGTAATTTTTGGAAGTTTGGG-GCA
* *
556135 AAAATGTAATTTTTGAGAAGTTTAAGGGTA
1 AAAATGTAATTTTTG-GAAGTTT-GGGGCA
* * *
556165 AAAATGTGATTTTTGGAAGTTCGAGGACA
1 AAAATGTAATTTTTGGAAGTTTG-GGGCA
* *
556194 AAAATGTAATTTTTGTAAGTTTAGGGG-T
1 AAAATGTAATTTTTGGAAGTTT-GGGGCA
* * *
556222 AAAATGTAGTTTTTAGAAGTTTGAGGGTA
1 AAAATGTAATTTTTGGAAGTTTG-GGGCA
* *
556251 AAAATATAATTTTTGGAAGTTTGGGGGA
1 AAAATGTAATTTTTGGAAGTTTGGGGCA
* *
556279 AAAATGCAATTTTTGGAAGTTCGAGGG-A
1 AAAATGTAATTTTTGGAAGTTTG-GGGCA
*
556307 AAAATATAATTTTTGGAAGTTTGGGGGC-
1 AAAATGTAATTTTTGGAAGTTT-GGGGCA
*
556335 AAAATGTAATTTTTGGAAGTTCAGGGGCA
1 AAAATGTAATTTTTGGAAGTT-TGGGGCA
* *
556364 AAATTGCAATTTTTGGAAGTTTGGGG
1 AAAATGTAATTTTTGGAAGTTTGGGG
556390 GTAAAATTTT
Statistics
Matches: 237, Mismatches: 35, Indels: 26
0.80 0.12 0.09
Matches are distributed among these distances:
27 1 0.00
28 98 0.41
29 97 0.41
30 39 0.16
31 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTGGGGCA
Found at i:556390 original size:29 final size:29
Alignment explanation
Indices: 556076--556406 Score: 330
Period size: 29 Copynumber: 11.5 Consensus size: 29
556066 AGTTTAGGGT
* *
556076 AAAATGTAATATTTGAGAAGTTT-GAGGCAA
1 AAAATGTAATTTTTG-GAAGTTTGGGGGC-A
* *
556106 AAAATGTAATTTCTGGAAGTTTGGGAGCA
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
** *
556135 AAAATGTAATTTTTGAGAAGTTTAAGGGTA
1 AAAATGTAATTTTTG-GAAGTTTGGGGGCA
* * * *
556165 AAAATGTGATTTTTGGAAGTTCGAGGACA
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
* * *
556194 AAAATGTAATTTTTGTAAGTTTAGGGG-T
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
* * * *
556222 AAAATGTAGTTTTTAGAAGTTTGAGGGTA
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
*
556251 AAAATATAATTTTTGGAAGTTTGGGGG-A
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
* * *
556279 AAAATGCAATTTTTGGAAGTTCGAGGG-A
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
*
556307 AAAATATAATTTTTGGAAGTTTGGGGGC-
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
**
556335 AAAATGTAATTTTTGGAAGTTCAGGGGCA
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
* * *
556364 AAATTGCAATTTTTGGAAGTTTGGGGGTA
1 AAAATGTAATTTTTGGAAGTTTGGGGGCA
* *
556393 AAATTTTAATTTTT
1 AAAATGTAATTTTT
556407 AAAAAAAGGA
Statistics
Matches: 247, Mismatches: 49, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
28 95 0.38
29 112 0.45
30 40 0.16
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTGGGGGCA
Found at i:558860 original size:25 final size:22
Alignment explanation
Indices: 558832--558876 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 22
558822 GAATAAGCAA
558832 TACACAATAATATAACAATAGTAGG
1 TACA-AATAA-ATAA-AATAGTAGG
558857 TACAAATAAATAAAATAGTA
1 TACAAATAAATAAAATAGTA
558877 CTAATGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 5 0.25
25 4 0.20
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.24
Consensus pattern (22 bp):
TACAAATAAATAAAATAGTAGG
Found at i:558895 original size:2 final size:2
Alignment explanation
Indices: 558883--558916 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
558873 AGTACTAATG
*
558883 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
558917 ATTAGCAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:563077 original size:10 final size:9
Alignment explanation
Indices: 563062--563105 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
563052 ATTCAATAAT
563062 TTAATTTCGG
1 TTAATTT-GG
*
563072 TTAATTTAG
1 TTAATTTGG
563081 TTAATTTCGG
1 TTAATTT-GG
*
563091 TTCATTTGG
1 TTAATTTGG
563100 TTAATT
1 TTAATT
563106 CAATTAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (9 bp):
TTAATTTGG
Found at i:563086 original size:19 final size:19
Alignment explanation
Indices: 563062--563105 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
563052 ATTCAATAAT
563062 TTAATTTCGGTTAATTTAG
1 TTAATTTCGGTTAATTTAG
* *
563081 TTAATTTCGGTTCATTTGG
1 TTAATTTCGGTTAATTTAG
563100 TTAATT
1 TTAATT
563106 CAATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (19 bp):
TTAATTTCGGTTAATTTAG
Found at i:563782 original size:57 final size:55
Alignment explanation
Indices: 563651--563821 Score: 188
Period size: 57 Copynumber: 3.1 Consensus size: 55
563641 TATTTTGTAC
* * * **
563651 TTTGATATTTTTTTTAATAT-AGTATATAAATTTTTT-ATTTAATTTGATAAATAAA
1 TTTGATATATTTTTTAATTTGA-TATTTAAATTTTTTAATTTAATTTG-TATTTAAA
*
563706 TTT-A-ATATTTTTTAATTTGATATTTGAATTTTTTAGATTTAATTTAGTATTTAAA
1 TTTGATATATTTTTTAATTTGATATTTAAATTTTTTA-ATTTAATTT-GTATTTAAA
*
563761 TTTGATATATTTTTTAATTTGATATTTAAATTATTTTATATTCAATTTTGTATTTAAA
1 TTTGATATATTTTTTAATTTGATATTTAAATT-TTTTA-ATTTAA-TTTGTATTTAAA
563819 TTT
1 TTT
563822 ATTAAATATT
Statistics
Matches: 99, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
53 24 0.24
54 2 0.02
55 21 0.21
56 2 0.02
57 25 0.25
58 22 0.22
59 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.60
Consensus pattern (55 bp):
TTTGATATATTTTTTAATTTGATATTTAAATTTTTTAATTTAATTTGTATTTAAA
Found at i:564090 original size:30 final size:27
Alignment explanation
Indices: 564054--564150 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 27
564044 TCAAACTTAG
564054 ATACCAAATTAGAAAAAAAATCAAGTTTGA
1 ATACCAAATTA-AAAAAAAATCAA-TTT-A
564084 ATACCAAATTACACAAAAAAAT--ATTTA
1 ATACCAAATTA-A-AAAAAAATCAATTTA
* *
564111 GGTACTAAATTAAAAAAAATATCAAATTTAA
1 -ATACCAAATTAAAAAAAA-ATC-AATTT-A
564142 ATACCAAAT
1 ATACCAAAT
564151 ATTATATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
26 6 0.11
27 4 0.07
28 12 0.22
29 1 0.02
30 23 0.42
31 9 0.16
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (27 bp):
ATACCAAATTAAAAAAAAATCAATTTA
Found at i:568148 original size:1 final size:1
Alignment explanation
Indices: 568142--568166 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
568132 GAAATTTCTA
568142 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
568167 AAATTTCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:568501 original size:21 final size:21
Alignment explanation
Indices: 568475--568518 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
568465 TTTTTTTAGC
568475 TTTTAATGTAAAAAAAATAAA
1 TTTTAATGTAAAAAAAATAAA
* * *
568496 TTTTAATTTAAAATAAATTAA
1 TTTTAATGTAAAAAAAATAAA
568517 TT
1 TT
568519 AAATGTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTAATGTAAAAAAAATAAA
Found at i:570096 original size:21 final size:21
Alignment explanation
Indices: 570071--570113 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
570061 CAGTAAAAAT
570071 ATAACTTACCAATTTCTAGAA
1 ATAACTTACCAATTTCTAGAA
570092 ATAACTTACCAATTTCTAGAA
1 ATAACTTACCAATTTCTAGAA
570113 A
1 A
570114 ACACAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
ATAACTTACCAATTTCTAGAA
Found at i:570793 original size:20 final size:20
Alignment explanation
Indices: 570768--570814 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
570758 ATTCCCCTAT
570768 TAGATTTGACACTAATCTGG
1 TAGATTTGACACTAATCTGG
*
570788 TAGATTTGACACTAATTTGG
1 TAGATTTGACACTAATCTGG
570808 TAGATTT
1 TAGATTT
570815 ATGTCGTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (20 bp):
TAGATTTGACACTAATCTGG
Found at i:571354 original size:25 final size:23
Alignment explanation
Indices: 571326--571371 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
571316 GTTGGATCCA
571326 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
571351 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
571372 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:572450 original size:19 final size:20
Alignment explanation
Indices: 572403--572460 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
572393 TTTTCTTCTC
* *
572403 TTTTTTTCCCAATTTTTTTCC
1 TTTTTTT-CAAATTTTTTTCA
*
572424 TTTCTTTCAAATTTTTTT-A
1 TTTTTTTCAAATTTTTTTCA
* *
572443 TTTTTTTCGACTTTTTTT
1 TTTTTTTCAAATTTTTTT
572461 TTCATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
20 10 0.32
21 6 0.19
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTTTCAAATTTTTTTCA
Found at i:574866 original size:3 final size:3
Alignment explanation
Indices: 574858--574902 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
574848 AAATAACAAC
574858 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
574903 AAGCTAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.