Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005728.1 Hibiscus syriacus cultivar Beakdansim tig00013386_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 971753
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 6
Found at i:556204 original size:16 final size:16
Alignment explanation
Indices: 556183--556216 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
556173 TTACTATTCA
*
556183 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
556199 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
556215 CG
1 CG
556217 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:558082 original size:22 final size:22
Alignment explanation
Indices: 558041--558129 Score: 151
Period size: 22 Copynumber: 4.0 Consensus size: 22
558031 CTCGTATAAA
558041 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
558064 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
558086 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
558108 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
558130 GATGTCCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 53 0.82
23 12 0.18
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:558095 original size:13 final size:13
Alignment explanation
Indices: 558055--558117 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
558045 CCGAAGTGCC
558055 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
558068 CC---GAAGTGC-
1 CCGTAGAATTGCA
558077 CCGTAGAATTGCA
1 CCGTAGAATTGCA
558090 CCGTAG---TGC-
1 CCGTAGAATTGCA
558099 CCGTAGAATTGCA
1 CCGTAGAATTGCA
558112 CCGTAG
1 CCGTAG
558118 TGCCCGTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 8 0.20
10 9 0.22
12 9 0.22
13 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:559845 original size:21 final size:21
Alignment explanation
Indices: 559821--559865 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
559811 TCTTGTTCGT
* *
559821 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
559842 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
559863 TTG
1 TTG
559866 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:563040 original size:22 final size:22
Alignment explanation
Indices: 562999--563087 Score: 151
Period size: 22 Copynumber: 4.0 Consensus size: 22
562989 CTCGTATAAA
562999 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
563022 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
563044 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
563066 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
563088 GATGTCCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 53 0.82
23 12 0.18
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:563053 original size:13 final size:13
Alignment explanation
Indices: 563013--563075 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
563003 CCGAAGTGCC
563013 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
563026 CC---GAAGTGC-
1 CCGTAGAATTGCA
563035 CCGTAGAATTGCA
1 CCGTAGAATTGCA
563048 CCGTAG---TGC-
1 CCGTAGAATTGCA
563057 CCGTAGAATTGCA
1 CCGTAGAATTGCA
563070 CCGTAG
1 CCGTAG
563076 TGCCCGTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 8 0.20
10 9 0.22
12 9 0.22
13 14 0.35
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:564801 original size:21 final size:21
Alignment explanation
Indices: 564777--564821 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
564767 TCTTGTTCGT
* *
564777 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
564798 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
564819 TTG
1 TTG
564822 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:568460 original size:21 final size:21
Alignment explanation
Indices: 568436--568531 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 21
568426 AACTTTGAAA
568436 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
568457 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
568471 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
568492 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
568506 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
568527 AAATG
1 AAATG
568532 TTTCTTTGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 28
0.64 0.04 0.31
Matches are distributed among these distances:
14 10 0.18
15 8 0.14
16 8 0.14
19 8 0.14
20 8 0.14
21 15 0.26
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:568491 original size:70 final size:70
Alignment explanation
Indices: 568401--568564 Score: 226
Period size: 70 Copynumber: 2.3 Consensus size: 70
568391 TGAAAGTATT
568401 AAAATGGTTTTC-AAGTTTGGTAA-CCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTT
1 AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG--AAAATGGTTTTCAAAGTTTGGTAAATGTT
568464 TCTTTG-
64 TCTTTGA
****
568470 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
568535 CTTTGA
65 CTTTGA
*
568541 AAAATAGTTTTTCAAAGTTTGGTA
1 AAAAT-GGTTTTCAAAGTTTGGTA
568565 GATGTTTGTT
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
69 12 0.14
70 44 0.52
71 8 0.09
72 21 0.25
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.43
Consensus pattern (70 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
TTTGA
Found at i:568577 original size:36 final size:36
Alignment explanation
Indices: 568428--568582 Score: 244
Period size: 35 Copynumber: 4.3 Consensus size: 36
568418 TGGTAACCAA
568428 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
568465 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
568500 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
568535 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
568572 -GTTGAAAAATG
1 CTTTGAAAAATG
568583 ATAATGAGAT
Statistics
Matches: 113, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
35 71 0.63
36 14 0.12
37 28 0.25
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:572346 original size:19 final size:19
Alignment explanation
Indices: 572322--572359 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
572312 TCGTGGGGAG
572322 GGGGATGGAATATGCTGTC
1 GGGGATGGAATATGCTGTC
572341 GGGGATGGAATATGCTGTC
1 GGGGATGGAATATGCTGTC
572360 TTTGATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.42, T:0.26
Consensus pattern (19 bp):
GGGGATGGAATATGCTGTC
Found at i:582408 original size:15 final size:15
Alignment explanation
Indices: 582377--582406 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
582367 GTAGATGATG
582377 ATAAAACTAAACTAA
1 ATAAAACTAAACTAA
582392 ATAAAA-TAAACTAA
1 ATAAAACTAAACTAA
582406 A
1 A
582407 ATGGTTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAAACTAAACTAA
Found at i:585395 original size:19 final size:18
Alignment explanation
Indices: 585371--585440 Score: 95
Period size: 19 Copynumber: 3.8 Consensus size: 18
585361 GGCCACTGAT
585371 TAAGATCTAAGACTAAAAA
1 TAAGATCTAA-ACTAAAAA
** *
585390 TAAGATCTAAACTATGAT
1 TAAGATCTAAACTAAAAA
585408 TAAGATCTAAGACTAAAAA
1 TAAGATCTAA-ACTAAAAA
585427 TAAGATCTAAACTA
1 TAAGATCTAAACTA
585441 TAATCTACCT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 19 0.43
19 25 0.57
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.26
Consensus pattern (18 bp):
TAAGATCTAAACTAAAAA
Found at i:585408 original size:37 final size:37
Alignment explanation
Indices: 585367--585441 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
585357 TTCTGGCCAC
585367 TGATTAAGATCTAAGACTAAAAATAAGATCTAAACTA
1 TGATTAAGATCTAAGACTAAAAATAAGATCTAAACTA
585404 TGATTAAGATCTAAGACTAAAAATAAGATCTAAACTA
1 TGATTAAGATCTAAGACTAAAAATAAGATCTAAACTA
585441 T
1 T
585442 AATCTACCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (37 bp):
TGATTAAGATCTAAGACTAAAAATAAGATCTAAACTA
Found at i:589448 original size:21 final size:21
Alignment explanation
Indices: 589422--589474 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
589412 TAATGTGGTT
589422 AAATGCAAAACTATTACAAAC
1 AAATGCAAAACTATTACAAAC
589443 AAATGCAAAACTATTACAAAC
1 AAATGCAAAACTATTACAAAC
**
589464 AGCTGCAAAAC
1 AAATGCAAAAC
589475 CAAATGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.55, C:0.21, G:0.08, T:0.17
Consensus pattern (21 bp):
AAATGCAAAACTATTACAAAC
Found at i:601439 original size:23 final size:23
Alignment explanation
Indices: 601411--601469 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
601401 AAATTAATAA
601411 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
601434 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
601457 TATA--ATGTAAAAT
1 TATATTATGTAAAAT
601470 TATAACTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.25
23 27 0.75
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:601510 original size:13 final size:13
Alignment explanation
Indices: 601481--601515 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
601471 ATAACTAATA
*
601481 ATATTAAAT-ATT
1 ATATTAAATAAAT
601493 ATATTAAATAAAT
1 ATATTAAATAAAT
601506 ATATTAAATA
1 ATATTAAATA
601516 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:604524 original size:8 final size:8
Alignment explanation
Indices: 604511--604551 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
604501 CTCATTTTCA
604511 GAGAATTT
1 GAGAATTT
604519 GAGAATTT
1 GAGAATTT
*
604527 -AGAGTTT
1 GAGAATTT
*
604534 GGGAATTT
1 GAGAATTT
604542 GAGAATTT
1 GAGAATTT
604550 GA
1 GA
604552 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:604844 original size:126 final size:126
Alignment explanation
Indices: 604619--605223 Score: 1165
Period size: 126 Copynumber: 4.8 Consensus size: 126
604609 CTATAATCGG
604619 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
604684 TCATTGCCCTATTATGTCATTCATGTACCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
604745 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
604810 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
604871 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
604936 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
604997 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
605062 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGTCACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
*
605123 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
605188 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
605224 ATAACTTAAA
Statistics
Matches: 473, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 473 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:605672 original size:33 final size:34
Alignment explanation
Indices: 605611--605710 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
605601 AAATTTAATG
*
605611 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
605645 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
605678 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
605711 AAAAATTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:605718 original size:33 final size:33
Alignment explanation
Indices: 605611--605710 Score: 121
Period size: 34 Copynumber: 3.0 Consensus size: 33
605601 AAATTTAATG
*
605611 TTAAATTTCGAATACTATAATTTATATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
* * **
605644 TTTAAATTT-GAATAATATTATTTTTATTTTTATT
1 -TTAAATTTCGAATAATATAATTTATA-TTTTAAA
*
605678 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
605711 AAAAATTTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 27 0.49
34 28 0.51
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAA
Found at i:606320 original size:21 final size:21
Alignment explanation
Indices: 606232--606325 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
606222 TATGGTATAA
*
606232 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
606253 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
606274 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
606295 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
606316 AACCCTGCGG
1 AACCCTGCGG
606326 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:606355 original size:21 final size:21
Alignment explanation
Indices: 606329--606376 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
606319 CCTGCGGAGA
*
606329 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
606350 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
606371 GGGCAT
1 TGGCAT
606377 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:608165 original size:14 final size:15
Alignment explanation
Indices: 608099--608166 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 15
608089 ATAATTCTAA
608099 ATAAATAATAATT-AT
1 ATAAATAAT-ATTAAT
*
608114 ATAAATATTATTTTAAT
1 ATAAATA--ATATTAAT
* *
608131 AATAAAATAATATTTAC
1 -AT-AAATAATATTAAT
608148 ATAAAT-ATATTAAT
1 ATAAATAATATTAAT
608162 ATAAA
1 ATAAA
608167 AAACAATAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 11 0.26
15 11 0.26
16 4 0.10
17 9 0.21
18 2 0.05
19 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAATAATATTAAT
Found at i:608883 original size:16 final size:16
Alignment explanation
Indices: 608858--608890 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
608848 GAATATTTGA
*
608858 GAGTTCATTATCAAAT
1 GAGTTAATTATCAAAT
608874 GAGTTAATTATCAAAT
1 GAGTTAATTATCAAAT
608890 G
1 G
608891 GTTGATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (16 bp):
GAGTTAATTATCAAAT
Found at i:609222 original size:16 final size:16
Alignment explanation
Indices: 609186--609224 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
609176 AATGTTGATC
609186 CAAAATAAAAAAGTTT
1 CAAAATAAAAAAGTTT
*
609202 TAAAATAAAAATA-TTT
1 CAAAATAAAAA-AGTTT
609218 CAAAATA
1 CAAAATA
609225 TATAAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (16 bp):
CAAAATAAAAAAGTTT
Found at i:612478 original size:31 final size:31
Alignment explanation
Indices: 612443--612528 Score: 120
Period size: 30 Copynumber: 2.8 Consensus size: 31
612433 AAACGGCCGG
* *
612443 TAAATGTTGGGGGACTGTATTGCAAACTGAC
1 TAAATGTTGGGGAACTGTATTGCAAACAGAC
*
612474 TAAATGTT-GGGTACTGTATTGCAAACAGAC
1 TAAATGTTGGGGAACTGTATTGCAAACAGAC
**
612504 TAAATAATGGGGAACTGTATTGCAA
1 TAAATGTTGGGGAACTGTATTGCAA
612529 GTTTTAAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 26 0.53
31 23 0.47
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (31 bp):
TAAATGTTGGGGAACTGTATTGCAAACAGAC
Found at i:613496 original size:18 final size:18
Alignment explanation
Indices: 613454--613496 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
613444 TAACTGAAAT
* *
613454 TATTAAATATTAAATATA
1 TATTATATATTAAATACA
613472 T-TATATATATTAAATACA
1 TAT-TATATATTAAATACA
613490 TATTATA
1 TATTATA
613497 AGCTCAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATATATTAAATACA
Found at i:614641 original size:5 final size:5
Alignment explanation
Indices: 614631--614702 Score: 90
Period size: 5 Copynumber: 14.4 Consensus size: 5
614621 ATGGCAAAGA
* * * *
614631 GTCGG GTCGG GCCGG GTCGG TTCGG GTCGG GTCGG GCCGG GTCGG GCCGG
1 GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG
* *
614681 GTCGG GCCGG GTTGG GTCGG GT
1 GTCGG GTCGG GTCGG GTCGG GT
614703 TTTTGGGCCA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.00, C:0.24, G:0.58, T:0.18
Consensus pattern (5 bp):
GTCGG
Found at i:616381 original size:74 final size:74
Alignment explanation
Indices: 616260--616404 Score: 281
Period size: 74 Copynumber: 2.0 Consensus size: 74
616250 AGACAAAATT
*
616260 TGTTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAATCGTCTCAATGGAGACAAAAT
1 TGTTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAAT
616325 TTGTTCTTG
66 TTGTTCTTG
616334 TGTTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAAT
1 TGTTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAAT
616399 TTGTTC
66 TTGTTC
616405 CAAGGGAAAC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (74 bp):
TGTTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAAT
TTGTTCTTG
Found at i:616466 original size:101 final size:102
Alignment explanation
Indices: 616336--616532 Score: 290
Period size: 101 Copynumber: 1.9 Consensus size: 102
616326 TGTTCTTGTG
*
616336 TTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAA-ATCGTCTCAAGGGAGACAAAATT
1 TTTCAAGGAAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAGAT-GTCTCAAGGGAGACAAAATT
*
616400 TGTTCCAAGGGAAACTATCTCAAAAGAGACAAAATTCA
65 TATTCCAAGGGAAACTATCTCAAAAGAGACAAAATTCA
* * *
616438 TTTCAAGGAAAATGTTTTCAATG-TTTATGTTTCAAGAGAAGGTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGAAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAGATGTCTCAAGGGAGACAAAATTT
* * * *
616502 ATTTCAAGGGAAATTGTCTCAAGAGAGACAA
66 ATTCCAAGGGAAACTATCTCAAAAGAGACAA
616533 TAGTGAGCAC
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 64 0.75
102 21 0.25
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (102 bp):
TTTCAAGGAAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAGATGTCTCAAGGGAGACAAAATTT
ATTCCAAGGGAAACTATCTCAAAAGAGACAAAATTCA
Found at i:616845 original size:110 final size:110
Alignment explanation
Indices: 616708--616906 Score: 317
Period size: 110 Copynumber: 1.8 Consensus size: 110
616698 AACTGGGAAA
* * *
616708 TTGTTTGTTGACAGCCAGTCGCCCCTTCGTAGTGAAGTTGAGCTTGTGTTGTCTCAAGTTCAATA
1 TTGTTTGCTGACAACCAGTCGCCCCTTCGTAGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAATA
*
616773 TCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG
66 TCCTTCGCTATGAAGTTAAAATTGACTCTGAATGAAACTGAAAAG
* **
616818 TTGTTTGCTGACAACCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATA
1 TTGTTTGCTGACAACCAGTCGCCCCTTCGTAGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAATA
* *
616883 TCTTTCGCTGTGAAGTTAAAATTG
66 TCCTTCGCTATGAAGTTAAAATTG
616907 GCTTTGAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 80 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (110 bp):
TTGTTTGCTGACAACCAGTCGCCCCTTCGTAGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAATA
TCCTTCGCTATGAAGTTAAAATTGACTCTGAATGAAACTGAAAAG
Found at i:618029 original size:16 final size:16
Alignment explanation
Indices: 617995--618029 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
617985 AAGAGTTTCG
617995 AAAAATGTTTAATCAA
1 AAAAATGTTTAATCAA
618011 AAAAACTGTTTAATCAA
1 AAAAA-TGTTTAATCAA
618028 AA
1 AA
618030 GTTTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAAATGTTTAATCAA
Found at i:619417 original size:21 final size:21
Alignment explanation
Indices: 619302--619417 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
619292 GCGAAATAAA
**
619302 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
619322 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
619342 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
619363 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
619383 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
619405 AATCGCAACGCGA
1 AATCGCAACGCGA
619418 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:619430 original size:20 final size:20
Alignment explanation
Indices: 619405--619597 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
619395 GATTTTCCAG
* ** *
619405 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
619425 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
619445 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
619465 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
619485 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
619505 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
619525 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
619545 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
619566 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
619586 AATCGCAACGCG
1 AATCGCAACGCG
619598 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:620016 original size:33 final size:33
Alignment explanation
Indices: 619977--620047 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
619967 TTAACTTAGA
*
619977 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTATCGTTGCGAT
* *
620010 TTTCATTTCGCGTTGCTATTCTATCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTATCGTTGCGAT
620043 TTTCA
1 TTTCA
620048 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTATCGTTGCGAT
Found at i:620153 original size:21 final size:20
Alignment explanation
Indices: 620127--620233 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
620117 TGCAGAAGAG
620127 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
620148 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
620168 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
620190 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
620204 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
620223 TCGCAACGAGA
1 TCGCAACGAGA
620234 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:620207 original size:14 final size:14
Alignment explanation
Indices: 620188--620244 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
620178 GAAAAATGAA
620188 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
620202 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
620221 AATCGCAACGAGAG
1 AATCGCAACGAGAG
620235 AATCGCAACG
1 AATCGCAACG
620245 CAAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:620219 original size:33 final size:33
Alignment explanation
Indices: 620180--620260 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
620170 TGCAACGAGA
620180 AAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 AAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
620213 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 AAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
620246 AAAACCAAAATCGCA
1 AAAATGAAAATCGCA
620261 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.09
Consensus pattern (33 bp):
AAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:620278 original size:19 final size:19
Alignment explanation
Indices: 620256--620320 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
620246 AAAACCAAAA
620256 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
620275 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
620291 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
620308 TCGCGTTGCGATT
1 TCGCATTGCGATT
620321 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 7 0.18
19 19 0.49
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:620299 original size:14 final size:14
Alignment explanation
Indices: 620280--620334 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
620270 TCATTTCGCA
620280 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
620294 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
620313 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
620327 TTGCGATT
1 TTGCGATT
620335 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:620303 original size:33 final size:33
Alignment explanation
Indices: 620261--620342 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
620251 CAAAATCGCA
620261 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
620294 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
620327 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
620343 TCTCGTTGCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:620345 original size:21 final size:21
Alignment explanation
Indices: 620319--620383 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
620309 CGCGTTGCGA
620319 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
620340 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
620360 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
620381 TTC
1 TTC
620384 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:622227 original size:93 final size:93
Alignment explanation
Indices: 622068--622383 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
622058 TAGATTGCTT
*
622068 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
622133 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
622161 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
622226 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
622254 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
622319 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
622347 AGTAAATTTGTTCGGTTGCTACCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
622384 AATACCCTAA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:622518 original size:14 final size:14
Alignment explanation
Indices: 622499--622555 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
622489 CGAAACTTAA
622499 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
622513 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
622532 AATCGCAACGACAG
1 AATCGCAACGAGAG
622546 AATCGCAACG
1 AATCGCAACG
622556 CGAAACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:622537 original size:19 final size:18
Alignment explanation
Indices: 622513--622604 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
622503 GCAACGAGAG
622513 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
622532 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
622546 AATCGCAACGCGAAACAAA
1 AATCGCAACGCGAAA-GAA
*
622565 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
622579 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
622598 AATCGCA
1 AATCGCA
622605 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 18 0.31
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.44
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:622539 original size:33 final size:33
Alignment explanation
Indices: 622481--622604 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
622471 TAGTTTACTT
* * *
622481 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-AAAAATCGCAACGACAGAA
**
622515 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACAAAAATCGCAACGACAGAA
*
622548 TCGCAACGCGAAACAAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACAAAAATCGCAACGACAGAA
*
622581 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACAAAAATCGCA
622605 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.85
34 12 0.15
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACAAAAATCGCAACGACAGAA
Found at i:622582 original size:14 final size:14
Alignment explanation
Indices: 622530--622588 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
622520 ACGCGAAATG
622530 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
622544 AGAATCGCAACGCGAAAC
1 AAAATCGCAA--CG--AC
622562 AAAAATCGCAACGAC
1 -AAAATCGCAACGAC
622577 AAAATCGCAACG
1 AAAATCGCAACG
622589 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.55
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 9 0.24
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:622622 original size:19 final size:19
Alignment explanation
Indices: 622600--622739 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
622590 GAAACCAAAA
* *
622600 TCGCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
622619 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * *
622638 TCGCATTGAGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
622654 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
622671 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
622690 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
622709 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
622729 TCGTGTTGCGA
1 TCGCGTTGCGA
622740 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
14 6 0.06
16 5 0.05
17 5 0.05
19 69 0.71
20 12 0.12
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:624680 original size:14 final size:14
Alignment explanation
Indices: 624661--624696 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
624651 ATTGTTTAAT
624661 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
624675 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
624689 TGATTTGT
1 TGATTTGT
624697 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:624879 original size:20 final size:19
Alignment explanation
Indices: 624803--624901 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
624793 AAAAATGACT
624803 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
624822 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
624841 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
624855 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
624875 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
624895 ATCGCAA
1 ATCGCAA
624902 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 3 0.04
19 25 0.36
20 30 0.43
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:624904 original size:54 final size:53
Alignment explanation
Indices: 624803--624919 Score: 209
Period size: 54 Copynumber: 2.2 Consensus size: 53
624793 AAAAATGACT
624803 ATCGCAATGC-GAAATGAAAATCACAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAAAATCGCAACGAGAGA
*
624855 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCACAATGC-GAAATGAAAATCGCAACGAGAGA
624909 ATCGCAATGCG
1 ATCGCAATGCG
624920 ATTTTCATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 10 0.16
53 18 0.29
54 34 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:624938 original size:19 final size:19
Alignment explanation
Indices: 624910--625190 Score: 350
Period size: 19 Copynumber: 15.7 Consensus size: 19
624900 AACGAGAGAA
*
624910 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
624929 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
624948 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
624965 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
624982 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
625001 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
625020 TCGCATTGCGA--TTC-TA
1 TCGCATTGCGATTTTCATT
625036 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
625053 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
625072 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
625089 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
625106 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
625125 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
625144 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
625162 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
625178 TCGCATTGCGATT
1 TCGCATTGCGATT
625191 CTCTCGTTGC
Statistics
Matches: 230, Mismatches: 9, Indels: 46
0.81 0.03 0.16
Matches are distributed among these distances:
14 29 0.13
16 19 0.08
17 20 0.09
18 7 0.03
19 119 0.52
20 36 0.16
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:624992 original size:33 final size:33
Alignment explanation
Indices: 624934--625065 Score: 192
Period size: 33 Copynumber: 3.8 Consensus size: 33
624924 TCATTTCGCA
*
624934 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTATCG
*
624968 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TATCG
625004 CATTGCGATTTTCATTTCGCATTGCGATTCTATCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTATCG
625039 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
625066 TTCATTTCCG
Statistics
Matches: 91, Mismatches: 2, Indels: 11
0.88 0.02 0.11
Matches are distributed among these distances:
33 37 0.41
34 15 0.16
35 7 0.08
36 7 0.08
38 25 0.27
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTATCG
Found at i:625078 original size:72 final size:71
Alignment explanation
Indices: 624910--625162 Score: 363
Period size: 72 Copynumber: 3.5 Consensus size: 71
624900 AACGAGAGAA
* *
624910 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTATCGTTGCGAT
624975 TTTCATT
65 TTTCATT
624982 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATT
625047 TTCATT
66 TTCATT
* *
625053 TCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TATCG--TT
625113 GCGATTTTCATT
60 GCGATTTTCATT
625125 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCAT
625163 GTTGGGATTT
Statistics
Matches: 168, Mismatches: 4, Indels: 15
0.90 0.02 0.08
Matches are distributed among these distances:
67 6 0.04
69 7 0.04
70 7 0.04
71 51 0.30
72 93 0.55
74 3 0.02
75 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (71 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATT
TTCATT
Found at i:625172 original size:53 final size:55
Alignment explanation
Indices: 624910--625190 Score: 292
Period size: 53 Copynumber: 5.2 Consensus size: 55
624900 AACGAGAGAA
* *
624910 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA-TT-CG-ATTGCGATTTTCATT
624965 TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA-TTCG-ATTGCGATTTTCATT
*
625020 TCGCATTGCGA--TTC-TATCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA-TTCG-ATTGCGATTTTCATT
*
625072 TCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCA-TTCG-ATTGCGATTTTCATT
*
625125 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA-T-G-TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTCGATTGCGATTTTCATT
625178 TCGCATTGCGATT
1 TCGCATTGCGATT
625191 CTCTCGTTGC
Statistics
Matches: 208, Mismatches: 6, Indels: 26
0.87 0.03 0.11
Matches are distributed among these distances:
52 54 0.26
53 110 0.53
54 10 0.05
55 13 0.06
56 3 0.01
57 6 0.03
58 12 0.06
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (55 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTCGATTGCGATTTTCATT
Found at i:625212 original size:33 final size:33
Alignment explanation
Indices: 625058--625204 Score: 188
Period size: 33 Copynumber: 4.2 Consensus size: 33
625048 TCATTTCGCA
625058 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
625092 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
625128 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
625164 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
625197 TTGCGATT
1 TTGCGATT
625205 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 32 0.32
34 29 0.29
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:625212 original size:105 final size:103
Alignment explanation
Indices: 624987--625204 Score: 318
Period size: 105 Copynumber: 2.1 Consensus size: 103
624977 TCATTTCGCA
624987 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCA-
625052 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
65 TTCG-ATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
*
625092 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TAT-CG--TTGCGAT
*
625157 TTTCA-T-G-TTGGGATTTTCATTT-CGCATTGCGATTCTCTCG
60 TTTCATTCGATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
625197 TTGCGATT
1 TTGCGATT
625205 GTAATTTCCG
Statistics
Matches: 105, Mismatches: 2, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
105 70 0.67
106 14 0.13
107 3 0.03
108 3 0.03
109 3 0.03
111 12 0.11
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (103 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCAT
TCGATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
Found at i:627503 original size:12 final size:12
Alignment explanation
Indices: 627486--627510 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
627476 TCTTCGGGGA
627486 CTTTTTCTTCTT
1 CTTTTTCTTCTT
627498 CTTTTTCTTCTT
1 CTTTTTCTTCTT
627510 C
1 C
627511 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:627738 original size:24 final size:24
Alignment explanation
Indices: 627698--627752 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
627688 AAAATCCGTG
* * *
627698 TATTGACCAATATCAAAGTTCGGA
1 TATTGACCAAGACCAAAGTTCGAA
*
627722 TATTGACCAAGACCAAATTTCGAA
1 TATTGACCAAGACCAAAGTTCGAA
*
627746 TACTGAC
1 TATTGAC
627753 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGACCAAAGTTCGAA
Found at i:628452 original size:20 final size:20
Alignment explanation
Indices: 628424--628652 Score: 226
Period size: 20 Copynumber: 11.4 Consensus size: 20
628414 AAATTTCAGT
* * *
628424 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
628444 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
628464 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
628484 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
628504 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
628524 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
628544 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
628564 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
628584 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
628604 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
628624 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
628644 GTTGCGATT
1 GTTGCGATT
628653 CTTGAAAATC
Statistics
Matches: 180, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:628625 original size:60 final size:60
Alignment explanation
Indices: 628424--628633 Score: 253
Period size: 60 Copynumber: 3.5 Consensus size: 60
628414 AAATTTCAGT
* * * * * * *
628424 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGA-TACACGTTGCGATTTACGGATACGC
** *
628484 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACACGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
* * * *
628544 ATTGCGATTTACGGATACGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
*
628604 GTTGCGATTTATGTG-TTCGCGTTGCGATTT
1 GTTGCGATTTACG-GATTCGCGTTGCGATTT
628634 TCATATTCGC
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.02
60 126 0.98
61 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (60 bp):
GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
Found at i:629546 original size:18 final size:16
Alignment explanation
Indices: 629523--629562 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
629513 AAAAATGTAA
629523 ATAATATATACATATTAT
1 ATAATATATAC--ATTAT
*
629541 ATAATATATGCATTAT
1 ATAATATATACATTAT
629557 ATAATA
1 ATAATA
629563 AGGGCGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
ATAATATATACATTAT
Found at i:630398 original size:19 final size:19
Alignment explanation
Indices: 630376--630462 Score: 156
Period size: 19 Copynumber: 4.6 Consensus size: 19
630366 TTTAAACCCC
630376 AAATTCCTTTTCGATCTCA
1 AAATTCCTTTTCGATCTCA
630395 AAATTCCTTTTCGATCTCA
1 AAATTCCTTTTCGATCTCA
630414 AAATTCCTTTTCGATCTCA
1 AAATTCCTTTTCGATCTCA
*
630433 AAATTCCTTTTCGATCTCG
1 AAATTCCTTTTCGATCTCA
*
630452 AATTTCCTTTT
1 AAATTCCTTTT
630463 TCGCTTCTCT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.24, C:0.25, G:0.06, T:0.45
Consensus pattern (19 bp):
AAATTCCTTTTCGATCTCA
Found at i:632314 original size:20 final size:19
Alignment explanation
Indices: 632290--632348 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
632280 CGATACACAA
632290 GTAAGTGCATCGATGCACC
1 GTAAGTGCATCGATGCACC
* *
632309 GTTAAGGATGCATCGATACACT
1 G-TAA-G-TGCATCGATGCACC
632331 GTATAGTGCATCGATGCA
1 GTA-AGTGCATCGATGCA
632349 TACCTTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 14 0.42
21 4 0.12
22 14 0.42
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (19 bp):
GTAAGTGCATCGATGCACC
Found at i:633212 original size:23 final size:23
Alignment explanation
Indices: 633177--633242 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
633167 TATTATATGA
* *
633177 CACTACGGTGCAATTTTACGCGG
1 CACTCCGGTGCAATTATACGCGG
* * *
633200 TACTCCGGTGCAATTCTACGTGG
1 CACTCCGGTGCAATTATACGCGG
*
633223 CACTTCGGTGCAATTATACG
1 CACTCCGGTGCAATTATACG
633243 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
CACTCCGGTGCAATTATACGCGG
Found at i:637934 original size:64 final size:64
Alignment explanation
Indices: 637814--637958 Score: 168
Period size: 64 Copynumber: 2.3 Consensus size: 64
637804 TGCACATTCA
* * *
637814 AAGTGCATCGATGCACCCCTTAAAGAAGAAACATCGAATGCAATTAGTGCATCGATGCATAAG-
1 AAGTGCATCGATGCACCCCTTAAAGAAGAAACATCGAATGCAATTAGCGCACCGATGCACAAGT
** * * * * *
637877 GCGTGCATCGATGCACTCCCTTGATATAA-AAACATCGAATGTATTTTGCGCACCGATGCACAAG
1 AAGTGCATCGATGCAC-CCCTT-AAAGAAGAAACATCGAATGCAATTAGCGCACCGATGCACAAG
637941 T
64 T
637942 AAGTGCATCGATGCACC
1 AAGTGCATCGATGCACC
637959 GTTAAGGATG
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
63 14 0.21
64 35 0.52
65 18 0.27
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (64 bp):
AAGTGCATCGATGCACCCCTTAAAGAAGAAACATCGAATGCAATTAGCGCACCGATGCACAAGT
Found at i:637992 original size:20 final size:20
Alignment explanation
Indices: 637967--638019 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
637957 CCGTTAAGGA
637967 TGCATCGATGCATTGTATAG
1 TGCATCGATGCATTGTATAG
637987 TGCATCGATGCATTGTATAG
1 TGCATCGATGCATTGTATAG
638007 TGCATCGATGCAT
1 TGCATCGATGCAT
638020 ACCTTCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
TGCATCGATGCATTGTATAG
Found at i:641570 original size:20 final size:21
Alignment explanation
Indices: 641516--641578 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
641506 GATTCCCCTG
641516 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
641540 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
641560 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
641579 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:645426 original size:22 final size:21
Alignment explanation
Indices: 645384--645423 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
645374 GAGTTTGTTT
*
645384 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
645405 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
645424 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:648464 original size:23 final size:23
Alignment explanation
Indices: 648426--648493 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
648416 ATTATTATAT
* *
648426 GGCACTACAGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
648449 GGCACTCCGGTTCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* *
648472 GGCACTTCGGTGCAATTATACG
1 GGCACTCCGGTGCAATTCTACG
648494 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:658000 original size:28 final size:28
Alignment explanation
Indices: 657969--658023 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
657959 ATTTATGTTA
657969 AAAATA-TTTTTAAATTAAGAATAAAAAC
1 AAAATATTTTTTAAATTAAG-ATAAAAAC
*
657997 AAAATATTTTTTAATTTAAGATAAAAA
1 AAAATATTTTTTAAATTAAGATAAAAA
658024 TAATACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATATTTTTTAAATTAAGATAAAAAC
Found at i:658060 original size:25 final size:24
Alignment explanation
Indices: 658032--658190 Score: 82
Period size: 25 Copynumber: 6.5 Consensus size: 24
658022 AATAATACAT
658032 ATATATATATTAAGTTAAGAATAAA
1 ATATATATATTAAGTTAA-AATAAA
* *
658057 ATATATGTTTTTAAGTTAAAATAAA
1 ATATAT-ATATTAAGTTAAAATAAA
* * *
658082 A-AT-TTTAAGTTATGATAAGAATAAA
1 ATATATAT-A-TTAAGTTAA-AATAAA
658107 ATAT-T-T-TTAAGTTAAAATAAGA
1 ATATATATATTAAGTTAAAATAA-A
*
658129 ATA-AT-TAAGTTAAGATTAAAACAAA
1 ATATATAT-A-TTAAG-TTAAAATAAA
* *
658154 ATATATTAAATT-ATTTAAAATAATA
1 ATATA-TATATTAAGTTAAAATAA-A
658179 ATATAATATATT
1 ATAT-ATATATT
658191 TAAGAAATTC
Statistics
Matches: 106, Mismatches: 12, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
21 5 0.05
22 15 0.14
23 1 0.01
24 17 0.16
25 41 0.39
26 25 0.24
27 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (24 bp):
ATATATATATTAAGTTAAAATAAA
Found at i:658117 original size:27 final size:25
Alignment explanation
Indices: 658076--658132 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
658066 TTTAAGTTAA
**
658076 AATAAAAATTTTAAGTTATGATAAG
1 AATAAAAATTTTAAGTTAAAATAAG
658101 AATAAAATATTTTTAAGTTAAAATAAG
1 AATAAAA-A-TTTTAAGTTAAAATAAG
658128 AATAA
1 AATAA
658133 TTAAGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.25
26 1 0.04
27 20 0.71
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (25 bp):
AATAAAAATTTTAAGTTAAAATAAG
Found at i:658123 original size:46 final size:47
Alignment explanation
Indices: 658040--658157 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 47
658030 ATATATATAT
* * * *
658040 ATTAAGTTAAGAATAAAA-TATATGTTTTTAAGTTAAAATAAAAAT-
1 ATTAAGTTAAGATTAAAACAAAATATTTTTAAGTTAAAATAAAAATA
* * * *
658085 TTTAAGTTATGA-TAAGAATAAAATATTTTTAAGTTAAAATAAGAATA
1 ATTAAGTTAAGATTAA-AACAAAATATTTTTAAGTTAAAATAAAAATA
658132 ATTAAGTTAAGATTAAAACAAAATAT
1 ATTAAGTTAAGATTAAAACAAAATAT
658158 ATTAAATTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
44 3 0.05
45 12 0.20
46 23 0.38
47 19 0.32
48 3 0.05
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.36
Consensus pattern (47 bp):
ATTAAGTTAAGATTAAAACAAAATATTTTTAAGTTAAAATAAAAATA
Found at i:658161 original size:26 final size:25
Alignment explanation
Indices: 658113--658162 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
658103 TAAAATATTT
*
658113 TTAAGTTAAAATAAGAATAATTAAG
1 TTAAGTTAAAACAAGAATAATTAAG
658138 TTAAGATTAAAACAA-AATATATTAA
1 TTAAG-TTAAAACAAGAATA-ATTAA
658163 ATTATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (25 bp):
TTAAGTTAAAACAAGAATAATTAAG
Found at i:658793 original size:17 final size:17
Alignment explanation
Indices: 658762--658797 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
658752 AATCTCCAAT
658762 ATTTGATTTAATTATTA
1 ATTTGATTTAATTATTA
658779 ATTT-ATTTAATTTATTA
1 ATTTGATTTAA-TTATTA
658796 AT
1 AT
658798 AGTATGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTGATTTAATTATTA
Found at i:661556 original size:3 final size:3
Alignment explanation
Indices: 661550--661626 Score: 104
Period size: 3 Copynumber: 26.3 Consensus size: 3
661540 AATAATTATT
* *
661550 TAA TAA TAA T-A TAA TAA TAA TAA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
661596 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
661627 TTAAGTAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 4 0.06
3 60 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:661882 original size:76 final size:76
Alignment explanation
Indices: 661780--662570 Score: 1447
Period size: 76 Copynumber: 10.4 Consensus size: 76
661770 GAGGTCTTAA
* *
661780 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
661845 AGGCTTTTTGG
66 AGGCTTTTTGG
661856 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
661921 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
661932 AAACATCACGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
661997 AGGCTTTTTGG
66 AGGCTTTTTGG
*
662008 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
662073 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
662084 AAACATCATGCACTGAATGGCTTACAGATGACCCGAAGGCTTTGACAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
662149 AGGCTTTTTGG
66 AGGCTTTTTGG
*
662160 AAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
662225 AGGCTTTTTGG
66 AGGCTTTTTGG
*
662236 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
662301 AGGCTTTTTGG
66 AGGCTTTTTGG
662312 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
662377 AGGCTTTTTGG
66 AGGCTTTTTGG
*
662388 AAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
662453 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
662464 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAAGCTCCCG
662529 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
662541 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
662571 TGGGAAATAG
Statistics
Matches: 694, Mismatches: 20, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
76 640 0.92
77 54 0.08
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:663719 original size:54 final size:52
Alignment explanation
Indices: 663637--663755 Score: 168
Period size: 54 Copynumber: 2.3 Consensus size: 52
663627 AGAATAACAG
***
663637 GTTCGTAAAACATTTGACAGTGCATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-TTTT-CTGTGGCTTCTGCTCAGAT
*
663691 GTTCGTAAAACATTTGACAACACATTCATTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTGCTCAGAT
*
663743 GTTC-TCAAACATT
1 GTTCGTAAAACATT
663756 GAAGCTCTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
51 8 0.13
52 22 0.37
53 4 0.07
54 26 0.43
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTGCTCAGAT
Found at i:665995 original size:116 final size:116
Alignment explanation
Indices: 665786--666009 Score: 349
Period size: 116 Copynumber: 1.9 Consensus size: 116
665776 ATGCAGTTCA
* * * * *
665786 TCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGAACAC
1 TCTTTCAAATCCAATGATCGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
* *
665851 TTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCATC
66 TTCCAGAAGATACTATTAGGTCTCCTTATTTCTACTATGAGCAAATTCATC
* * *
665902 TCTTTTAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
1 TCTTTCAAATCCAATGATCGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
*
665967 TTCCAGAAGATACTATTAGGTCTTCTTATTTCTACTATGAGCA
66 TTCCAGAAGATACTATTAGGTCTCCTTATTTCTACTATGAGCA
666010 CATGGCACTT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
116 97 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (116 bp):
TCTTTCAAATCCAATGATCGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATACTATTAGGTCTCCTTATTTCTACTATGAGCAAATTCATC
Found at i:674717 original size:3 final size:3
Alignment explanation
Indices: 674711--674784 Score: 98
Period size: 3 Copynumber: 25.3 Consensus size: 3
674701 AATAATTATT
* *
674711 TAA TAA TAA T-A TAA TAA TAA TAA T-A TAA TAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
674757 TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
674785 TTAAGTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:674719 original size:14 final size:13
Alignment explanation
Indices: 674700--674788 Score: 98
Period size: 12 Copynumber: 7.0 Consensus size: 13
674690 TTTGGATTTG
674700 TAATAATTATTTAA
1 TAATAA-TATTTAA
674714 TAATAATA--TAA
1 TAATAATATTTAA
*
674725 TAATAATAATATAA
1 TAATAAT-ATTTAA
674739 TAATAATATTT-A
1 TAATAATATTTAA
*
674751 TAATAATA-ATAA
1 TAATAATATTTAA
674763 TAATAAT-TTTAA
1 TAATAATATTTAA
674775 TAATAATAATTTAA
1 TAATAAT-ATTTAA
674789 GTAAAATGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
11 11 0.17
12 28 0.43
13 5 0.08
14 21 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:681592 original size:45 final size:48
Alignment explanation
Indices: 681517--681615 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 48
681507 ATTTATTTTC
* *
681517 ATTTTTCGAATAAATGCTTGCGAACTAGATATCATGCGGTTAGG-TTT
1 ATTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
* *
681564 ATTTTTTGAAT-AA-GCATGCGAATTAGATATCATGAGGTTAGGATTT
1 ATTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
*
681610 CTTTTT
1 ATTTTT
681616 GTGGATAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 26 0.57
46 10 0.22
47 10 0.22
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (48 bp):
ATTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
Found at i:687656 original size:2 final size:2
Alignment explanation
Indices: 687649--687673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
687639 TTCATTATTG
687649 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
687674 GTATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:691244 original size:16 final size:16
Alignment explanation
Indices: 691223--691311 Score: 81
Period size: 16 Copynumber: 5.4 Consensus size: 16
691213 ATAAAAGAGA
691223 AAAAATGAGAAAAAAG
1 AAAAATGAGAAAAAAG
**
691239 AAAAATGATGGAAAAGGG
1 AAAAATGA--GAAAAAAG
**
691257 AAAAGGGAAGAAAAAATG
1 AAAAATG-AGAAAAAA-G
*
691275 AAAAATGAAAAAAAAG
1 AAAAATGAGAAAAAAG
691291 AAAAATGA-AAAAAAG
1 AAAAATGAGAAAAAAG
*
691306 AGAAAT
1 AAAAAT
691312 AAAAGGAGGG
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
15 12 0.20
16 17 0.29
17 12 0.20
18 17 0.29
19 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:691304 original size:15 final size:15
Alignment explanation
Indices: 691266--691315 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
691256 GAAAAGGGAA
*
691266 GAAAAAATGAAAAAT
1 GAAAAAAAGAAAAAT
691281 GAAAAAAAAGAAAAAT
1 G-AAAAAAAGAAAAAT
*
691297 GAAAAAAAGAGAAAT
1 GAAAAAAAGAAAAAT
691312 -AAAA
1 GAAAA
691316 GGAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 4 0.12
15 14 0.44
16 14 0.44
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:692712 original size:55 final size:55
Alignment explanation
Indices: 692641--693108 Score: 511
Period size: 55 Copynumber: 8.6 Consensus size: 55
692631 ATTGAAGATT
* * * **
692641 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTTTGAAGATTGTTC
* * **
692696 GAGTTCTATACTCTCTGAAAGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTTTGAAGATTGTTC
* *
692751 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACATGTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTTTGAAGATTGTTC
* * *
692806 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGCTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTTTGAAGATTGTTC
* * *
692861 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTTTTAAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTTTGAAGATTGTTC
* * * * * *
692912 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-CTGTTTATTGAAGATTTTTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACAC-GTTTTTTGAAGATTGTTC
* * * *
692967 GAGTTCTATACTCTCTGAAGAAATAGTGAGCGGACCCGTTTTATTGGAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTT-TTGAAGATTGTTC
* * ** * * * *
693023 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAAACACATTTTATAAAGATTGTTT
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTTTGAAGATTGTTC
*
693078 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
693109 AGACTTATCA
Statistics
Matches: 352, Mismatches: 52, Indels: 18
0.83 0.12 0.04
Matches are distributed among these distances:
50 1 0.00
51 42 0.12
52 1 0.00
54 3 0.01
55 263 0.75
56 42 0.12
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTTTGAAGATTGTTC
Found at i:692786 original size:110 final size:110
Alignment explanation
Indices: 692641--693108 Score: 574
Period size: 110 Copynumber: 4.3 Consensus size: 110
692631 ATTGAAGATT
* * *
692641 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATA
*
692706 CTCTCTGAAAGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
66 CTCTCTGAAAGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
* *
692751 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACATGTTTGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATA
* *
692816 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGCTC
66 CTCTCTGAAAGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
* * * *
692861 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTTTTAAAGA---TT-GAGTCCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATA
* * * *
692922 CTCTCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAAGATTTTTA
66 CTCTCTGAAAGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGTTC
* * * * * *
692967 GAGTTCTATACTCTCTGAAGAAATAGTGAGCGGACCCGTTTTATTGGAGATTGTTCAAG-TCTTA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACG-TTTGTTGAAGATTGTTCGAGTTC-TA
* ** * * * *
693031 TACTCTCTGAATGAATAGAGAGCAAACACATTTTATAAAGATTGTTT
64 TACTCTCTGAAAGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
693078 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
693109 AGACTTATCA
Statistics
Matches: 308, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
105 4 0.01
106 77 0.25
107 10 0.03
110 153 0.50
111 60 0.19
112 4 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (110 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATA
CTCTCTGAAAGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
Found at i:693000 original size:161 final size:161
Alignment explanation
Indices: 692641--693074 Score: 548
Period size: 161 Copynumber: 2.7 Consensus size: 161
692631 ATTGAAGATT
* * ** *
692641 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTATGAAGATTGTTCGAGTTCTAT
* * * * *
692705 ACTCTCTGAAAGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCGAGTTCTATACTCTCTGAA
65 ACTCTCTGAAAGAATAGAGAGCGAACACGTTTTATAAAGA---TT-GAGTCCTATACTCTCTGAA
* * *
692770 GGAATAGAGAGCGGACATGTTTGTTGAAGATTGTTC
126 AGAATAGAGAGCGGACATGTTTATTGAAGATTGTTA
*
692806 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGCTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATA
* * *
692871 CTCTCTGAAGGAATAGGGAGCGAACACGTTTTTTAAAGATTGAGTCCTATACTCTCTGAAAGAAT
66 CTCTCTGAAAGAATAGAGAGCGAACACGTTTTATAAAGATTGAGTCCTATACTCTCTGAAAGAAT
* * *
692936 AGGGAGCGGACCTGTTTATTGAAGATTTTTA
131 AGAGAGCGGACATGTTTATTGAAGATTGTTA
* * * *
692967 GAGTTCTATACTCTCTGAAGAAATAGTGAGCGGACCCGTTTTATTGGAGATTGTTCAAG-TCTTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGTTCGAGTTC-TA
* * *
693031 TACTCTCTGAATGAATAGAGAGCAAACACATTTTATAAAGATTG
64 TACTCTCTGAAAGAATAGAGAGCGAACACGTTTTATAAAGATTG
693075 TTTGAGTCTT
Statistics
Matches: 236, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
161 91 0.39
162 55 0.23
164 1 0.00
165 89 0.38
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (161 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATA
CTCTCTGAAAGAATAGAGAGCGAACACGTTTTATAAAGATTGAGTCCTATACTCTCTGAAAGAAT
AGAGAGCGGACATGTTTATTGAAGATTGTTA
Found at i:696543 original size:18 final size:18
Alignment explanation
Indices: 696520--696555 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
696510 TGTGTTCTAT
696520 GTGGTCCT-TCGGGACATA
1 GTGGTCCTAT-GGGACATA
696538 GTGGTCCTATGGGACATA
1 GTGGTCCTATGGGACATA
696556 TGTGTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.28
Consensus pattern (18 bp):
GTGGTCCTATGGGACATA
Found at i:696567 original size:46 final size:46
Alignment explanation
Indices: 696496--696599 Score: 154
Period size: 46 Copynumber: 2.3 Consensus size: 46
696486 TTCTACGTGA
*
696496 TCCTACGGGACATATGTGTTCTATGTGGTCCTTCGGGACATAGTGG
1 TCCTACGGGACATATGTGTTCTATGTGGTCATTCGGGACATAGTGG
* * *
696542 TCCTATGGGACATATGTGTTGTATGTGGTCATTTGGGACATAGTGG
1 TCCTACGGGACATATGTGTTCTATGTGGTCATTCGGGACATAGTGG
* *
696588 TCTTACGAGACA
1 TCCTACGGGACA
696600 AATTTCTATG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (46 bp):
TCCTACGGGACATATGTGTTCTATGTGGTCATTCGGGACATAGTGG
Found at i:700653 original size:46 final size:46
Alignment explanation
Indices: 700585--700679 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
700575 TACGTGGTCT
*
700585 TACGAGACATATGTGTTTTATGTGGTCCTTCAGGACATAGTAGTCC
1 TACGAGACATATGTGTTCTATGTGGTCCTTCAGGACATAGTAGTCC
* *
700631 TACGAGACATATGTGTTCTATGTGGTCCTTCGGGACATAGTGGTCC
1 TACGAGACATATGTGTTCTATGTGGTCCTTCAGGACATAGTAGTCC
700677 TAC
1 TAC
700680 AGGACAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (46 bp):
TACGAGACATATGTGTTCTATGTGGTCCTTCAGGACATAGTAGTCC
Found at i:701418 original size:16 final size:16
Alignment explanation
Indices: 701371--701412 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
701361 TATTTAGTGT
701371 TTTGTAAAAGCAAATGG
1 TTTG-AAAAGCAAATGG
701388 TTTGAAAAGCAAATGG
1 TTTGAAAAGCAAATGG
701404 TTTGAAAAG
1 TTTGAAAAG
701413 TCAATGTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (16 bp):
TTTGAAAAGCAAATGG
Found at i:702111 original size:32 final size:32
Alignment explanation
Indices: 702071--702139 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
702061 TATATATACT
* * *
702071 TATATATATTAGTGGGTTTTATTTAATAAATA
1 TATATATATGAGTAGGTTTTATTTAATAAACA
*
702103 TATATATATGATTAGGTTTTATTTAATAAACA
1 TATATATATGAGTAGGTTTTATTTAATAAACA
702135 TATAT
1 TATAT
702140 TAATTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.49
Consensus pattern (32 bp):
TATATATATGAGTAGGTTTTATTTAATAAACA
Found at i:702430 original size:22 final size:21
Alignment explanation
Indices: 702403--702468 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
702393 AATACCCATT
702403 TATATATTATTTTTTAATTAAA
1 TATATATTATTTTTTAA-TAAA
* *
702425 TATATATT-TTTATTGAGTAAA
1 TATATATTATTT-TTTAATAAA
*
702446 -A-ATAATA-TTTTTAATAAA
1 TATATATTATTTTTTAATAAA
702464 TATAT
1 TATAT
702469 TATTTAGGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
18 7 0.20
19 7 0.20
20 3 0.09
21 7 0.20
22 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TATATATTATTTTTTAATAAA
Found at i:702436 original size:18 final size:17
Alignment explanation
Indices: 702413--702473 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 17
702403 TATATATTAT
702413 TTTTTAATTAAATATATA
1 TTTTTAA-TAAATATATA
*
702431 TTTTTATTGAGTAAAAATAATA
1 TTTTTA---A-TAAATAT-ATA
702453 TTTTTAATAAATATATTA
1 TTTTTAATAAATATA-TA
702471 TTT
1 TTT
702474 AGGGTCGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 1 0.03
18 17 0.49
19 1 0.03
21 7 0.20
22 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTTTAATAAATATATA
Found at i:713901 original size:17 final size:18
Alignment explanation
Indices: 713860--713906 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
713850 TGTTTCTGAG
*
713860 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTCAA
713878 GGAATTGGAATCTGTCAA
1 GGAATTGGAATCTGTCAA
713896 -GAATTGGAATC
1 GGAATTGGAATC
713907 CAATTTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTCAA
Found at i:714673 original size:261 final size:248
Alignment explanation
Indices: 714211--714816 Score: 789
Period size: 261 Copynumber: 2.4 Consensus size: 248
714201 CCGAGACCTG
714211 ACCCGACCAAAATAAAGTTTCACCTGACCCGAACCGAATATATGAATTAG-AA--ACCCGACCCG
1 ACCCGACCAAAATAAAGTTTCACC-GACCCGAACCGAATATATGAATTAGAAACGACCCGACCCG
* *
714273 AAACAATAAAAAAATTATTTTTATTCAATAAAAATAGACTTAATTGAAAAAATATATATAGAGAG
65 AAATAATAAAAAAATTATTTTTATTCAATAAAAACAGACTTAATTGAAAAAATATATATAGAGAG
* *
714338 GGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGGTCGGGTCGGGT
130 GGTATTACTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTT--GTCGGGTCGGGT
*
714403 ATTTTTCACCCTAAACCCGAACCCGACTGACCCGAATATCACACTTTAAAAAACCGATCCGACCC
193 ATTTTTCACCCTAAACCCG-A-CC--C-GACCCGAATATCACAC-TTAAAAAA---A-CAGACCC
714468 A
248 A
*
714469 A-CCGACCAAAATAAAGTTTCACCGACCCGAACCGAATATATGATTTAGAAATTCGACCCGACCC
1 ACCCGACCAAAATAAAGTTTCACCGACCCGAACCGAATATATGAATTAGAAA--CGACCCGACCC
714533 GAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTAACTTAATTGAAAAAAAATTATATAT
64 GAAATAATAAAAAAATTATTTTTATTCAATAAAAACAG--ACTTAATTG--AAAAAA-TATATAT
*
714598 AGAG-GGGTATTACTGTAATTATTTCTAAATATATAAGGTAAAATTATATA-TATTT-TCGGGTC
124 AGAGAGGGTATTACTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTGTCGGGTC
* * *
714660 GGGTATTTTTCACCCTAAATCCGACCCGACCCGAATATCATACTTAAAAAAACAGACTCA
189 GGGTATTTTTCACCCTAAACCCGACCCGACCCGAATATCACACTTAAAAAAACAGACCCA
* * * *
714720 ACCCGACCAAAATAAAGTTTCACCCGAACC-AACCCGAATATATAAATTAAAAACCTGACCCGAA
1 ACCCGACCAAAATAAAGTTTCA-CCGACCCGAA-CCGAATATATGAATTAGAAA-C-GACCCGAC
*
714784 CTGAAATAATAATAAAAA-TATTTTTATTCAATA
62 CCGAAATAATAA-AAAAATTATTTTTATTCAATA
714817 TATAAACAAA
Statistics
Matches: 316, Mismatches: 17, Indels: 35
0.86 0.05 0.10
Matches are distributed among these distances:
251 7 0.02
252 24 0.08
253 56 0.18
254 5 0.02
255 8 0.03
256 39 0.12
257 25 0.08
258 1 0.00
259 2 0.01
260 1 0.00
261 74 0.23
263 9 0.03
264 4 0.01
265 50 0.16
266 11 0.03
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (248 bp):
ACCCGACCAAAATAAAGTTTCACCGACCCGAACCGAATATATGAATTAGAAACGACCCGACCCGA
AATAATAAAAAAATTATTTTTATTCAATAAAAACAGACTTAATTGAAAAAATATATATAGAGAGG
GTATTACTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTGTCGGGTCGGGTATT
TTTCACCCTAAACCCGACCCGACCCGAATATCACACTTAAAAAAACAGACCCA
Found at i:714937 original size:16 final size:16
Alignment explanation
Indices: 714916--714948 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
714906 TAATAAAAAA
714916 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
714932 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
714948 A
1 A
714949 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:715031 original size:16 final size:16
Alignment explanation
Indices: 715010--715064 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
715000 CGTTCATTTA
715010 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
715026 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
715042 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
715058 ATAAACG
1 ATAAACG
715065 TTGGAGACCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:716118 original size:14 final size:14
Alignment explanation
Indices: 716101--716156 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
716091 AATGAACATA
716101 AACGAACATAACCG
1 AACGAACATAACCG
716115 AACGAACAT-A---
1 AACGAACATAACCG
716125 AACGAACATAACCG
1 AACGAACATAACCG
716139 AACGAACATAACCG
1 AACGAACATAACCG
716153 AACG
1 AACG
716157 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.27, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:716155 original size:10 final size:10
Alignment explanation
Indices: 716094--716141 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
716084 ATAAATGAAT
716094 GAACATAAAC
1 GAACATAAAC
716104 GAACATAACCGAAC
1 GAACAT-A---AAC
716118 GAACATAAAC
1 GAACATAAAC
*
716128 GAACATAACC
1 GAACATAAAC
716138 GAAC
1 GAAC
716142 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:716166 original size:24 final size:24
Alignment explanation
Indices: 716094--716155 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
716084 ATAAATGAAT
716094 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
716118 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
716142 GAACATAACCGAAC
1 GAACATAAACGAAC
716156 GTTCACGAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:719947 original size:3 final size:3
Alignment explanation
Indices: 719939--719980 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
719929 ATATTAATAC
*
719939 TAT TAT TAT CAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
719981 TTAATACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:725341 original size:2 final size:2
Alignment explanation
Indices: 725334--725367 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
725324 ACTTGATAAC
* *
725334 TA TA TA TA TA TA TA TA TG TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
725368 AACATGTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:726279 original size:2 final size:2
Alignment explanation
Indices: 726274--726319 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
726264 TTAAAAAATA
* * *
726274 AT AT AT AC AT AT AA AT AT AC 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
726316 AT AT
1 AT AT
726320 TGAAATTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:726904 original size:39 final size:40
Alignment explanation
Indices: 726819--726905 Score: 92
Period size: 39 Copynumber: 2.2 Consensus size: 40
726809 CCCCTAAATA
* *
726819 TAAAAAAATAATATATATATGAAATTATTAAGTTTTTTTT
1 TAAAAAAATAATATATATATGAAATTATTAAGTTTATTGT
726859 TCAAAAAAA-AAT-TATATAAT-AAATTATT-AGATTTGATTGT
1 T-AAAAAAATAATATATAT-ATGAAATTATTAAG-TTT-ATTGT
726899 TAAAAAA
1 TAAAAAA
726906 CATTTTTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
38 2 0.05
39 22 0.54
40 10 0.24
41 7 0.17
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (40 bp):
TAAAAAAATAATATATATATGAAATTATTAAGTTTATTGT
Found at i:727029 original size:3 final size:3
Alignment explanation
Indices: 727021--727047 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
727011 ATTTTTCCTC
727021 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
727048 TTAAGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:727245 original size:20 final size:20
Alignment explanation
Indices: 727222--727332 Score: 195
Period size: 20 Copynumber: 5.5 Consensus size: 20
727212 CTCAGTTTCC
*
727222 AAAATCGCAGCGTGAATAGT
1 AAAATCGCAACGTGAATAGT
*
727242 AAAAATCGCAACATGAATAGT
1 -AAAATCGCAACGTGAATAGT
727263 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
727283 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
727303 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
727323 AAAATCGCAA
1 AAAATCGCAA
727333 AACCGCGTTG
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
20 69 0.79
21 18 0.21
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:727709 original size:20 final size:20
Alignment explanation
Indices: 727681--727739 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
727671 CATATAGATT
727681 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
* *
727701 CGTTACGATTTTTATTATTCA
1 CGTTGCGA-TTTTACTATTCA
*
727722 CGTTGCGAATTTGACTAT
1 CGTTGCG-ATTTTACTAT
727740 CGAGTTGCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 7 0.22
21 24 0.75
22 1 0.03
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:727770 original size:40 final size:40
Alignment explanation
Indices: 727723--727809 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
727713 TATTATTCAC
*
727723 GTTGCGAATTTGACTATCGAGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGAGTTGCGAATTTGACTTCTGT
*
727763 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATCGAGTTGCGAATTTGACTTCTGT
727803 GTTGCGA
1 GTTGCGA
727810 TTTACAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGAGTTGCGAATTTGACTTCTGT
Found at i:727806 original size:20 final size:20
Alignment explanation
Indices: 727723--727809 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
727713 TATTATTCAC
*
727723 GTTGCGAATTTGACTATCGA
1 GTTGCGAATTTGACTATCGT
* *
727743 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGT
*
727763 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGT
727783 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GT
727803 GTTGCGA
1 GTTGCGA
727810 TTTACAAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 2 0.03
20 57 0.97
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGT
Found at i:727828 original size:40 final size:40
Alignment explanation
Indices: 727723--727829 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
727713 TATTATTCAC
* *
727723 GTTGCGAATTTGACTATCG-AGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAATCGCA-TTGCGAATTTGACTTCTGT
* *
727763 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACAATCGCATTGCGAATTTGACTTCTGT
727803 GTTGCG-ATTT-ACAAAATCGCATTGCGA
1 GTTGCGAATTTGAC--AATCGCATTGCGA
727830 TTTACAGATT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
38 2 0.03
39 4 0.07
40 54 0.90
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.38
Consensus pattern (40 bp):
GTTGCGAATTTGACAATCGCATTGCGAATTTGACTTCTGT
Found at i:727847 original size:20 final size:20
Alignment explanation
Indices: 727803--727847 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
727793 TGACTTCTGT
727803 GTTGCGATTTACAAAATCGC
1 GTTGCGATTTACAAAATCGC
* * *
727823 ATTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAAATCGC
727843 GTTGC
1 GTTGC
727848 AAAATTGGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
GTTGCGATTTACAAAATCGC
Found at i:730856 original size:4 final size:4
Alignment explanation
Indices: 730839--730868 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
730829 CCTTAAAACT
730839 ATAA ATACA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATA-A ATAA ATAA ATAA ATAA ATAA A
730869 GCTATACCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:733658 original size:21 final size:21
Alignment explanation
Indices: 733632--733672 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
733622 GGATGTCTTT
733632 TTCCTTCTATAGCCCATTGGA
1 TTCCTTCTATAGCCCATTGGA
*
733653 TTCCTTCTATAGCCCTTTGG
1 TTCCTTCTATAGCCCATTGG
733673 GCGTAATGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (21 bp):
TTCCTTCTATAGCCCATTGGA
Found at i:743131 original size:37 final size:37
Alignment explanation
Indices: 743055--743131 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
743045 TTTTATATTT
*
743055 TTTAATTTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTTGTAAAAAAATTATATAAATATTATCAA
*
743092 TTTAATTTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTTGTAAA-AAAATTATATAAATATTAT-CAA
743129 TTT
1 TTT
743132 GTAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 17 0.47
37 19 0.53
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:746280 original size:30 final size:30
Alignment explanation
Indices: 746240--746302 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
746230 TTTTGTTAAG
*
746240 TTCAATTTACCTGACAGCGAATTCTTTTTC
1 TTCAACTTACCTGACAGCGAATTCTTTTTC
746270 TTCAACTTACCTGACAGCGAATTCTTTTTC
1 TTCAACTTACCTGACAGCGAATTCTTTTTC
746300 TTC
1 TTC
746303 TTGTCTATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (30 bp):
TTCAACTTACCTGACAGCGAATTCTTTTTC
Found at i:753030 original size:12 final size:12
Alignment explanation
Indices: 753010--753116 Score: 70
Period size: 12 Copynumber: 9.2 Consensus size: 12
753000 ATAAATCGTA
753010 AAAAT-AAAAAT
1 AAAATAAAAAAT
753021 AAAATAAAAAAT
1 AAAATAAAAAAT
*
753033 AAATTGAAGAAAAT
1 AAAAT-AA-AAAAT
*
753047 --AAT--TAAAT
1 AAAATAAAAAAT
753055 AAAATAAAAAGAT
1 AAAATAAAAA-AT
753068 -AAAT-AAAAAT
1 AAAATAAAAAAT
753078 AGAAATAAATAAAT
1 A-AAATAAA-AAAT
753092 -AAAT-AAAAAT
1 AAAATAAAAAAT
*
753102 AAACCTAAAAAAT
1 AAA-ATAAAAAAT
753115 AA
1 AA
753117 TAAAAATTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 28
0.70 0.05 0.26
Matches are distributed among these distances:
8 4 0.05
10 9 0.12
11 13 0.17
12 27 0.36
13 14 0.18
14 9 0.12
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (12 bp):
AAAATAAAAAAT
Done.