Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004507.1 Hibiscus syriacus cultivar Beakdansim tig00009942_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: 1776135
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:800992 original size:14 final size:14
Alignment explanation
Indices: 800973--801000 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
800963 CACTAAAATT
800973 GCGTTGCGAATTTC
1 GCGTTGCGAATTTC
800987 GCGTTGCGAATTTC
1 GCGTTGCGAATTTC
801001 ATTTTCGCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (14 bp):
GCGTTGCGAATTTC
Found at i:801008 original size:20 final size:20
Alignment explanation
Indices: 800983--801053 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
800973 GCGTTGCGAA
800983 TTTCGCGTTGCGAATTTCAT
1 TTTCGCGTTGCGAATTTCAT
801003 TTTCGCGTTGCG------AT
1 TTTCGCGTTGCGAATTTCAT
*
801017 TTTCGTGTTGCGAATTTCAT
1 TTTCGCGTTGCGAATTTCAT
*
801037 TTTCGTGTTGCGAATTT
1 TTTCGCGTTGCGAATTT
801054 AAGTTTCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
14 13 0.30
20 31 0.70
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTCAT
Found at i:801011 original size:34 final size:34
Alignment explanation
Indices: 800973--801053 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
800963 CACTAAAATT
800973 GCGTTGCGAATTTCGCGTTGCGAATTTCATTTTC
1 GCGTTGCGAATTTCGCGTTGCGAATTTCATTTTC
* *
801007 GCGTTGCGATTTTCGTGTTGCGAATTTCATTTTC
1 GCGTTGCGAATTTCGCGTTGCGAATTTCATTTTC
*
801041 GTGTTGCGAATTT
1 GCGTTGCGAATTT
801054 AAGTTTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.14, C:0.17, G:0.25, T:0.44
Consensus pattern (34 bp):
GCGTTGCGAATTTCGCGTTGCGAATTTCATTTTC
Found at i:801018 original size:14 final size:14
Alignment explanation
Indices: 801001--801034 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
800991 TGCGAATTTC
801001 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
801015 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
*
801029 AATTTC
1 ATTTTC
801035 ATTTTCGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:801060 original size:20 final size:20
Alignment explanation
Indices: 801017--801060 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
801007 GCGTTGCGAT
* *
801017 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
801037 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
801057 TTTC
1 TTTC
801061 AAAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:801422 original size:22 final size:22
Alignment explanation
Indices: 801394--801435 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
801384 GGGTCATCGA
801394 ATATGGGGACAGATGTCGTCAG
1 ATATGGGGACAGATGTCGTCAG
*
801416 ATATGGGGACTGATGTCGTC
1 ATATGGGGACAGATGTCGTC
801436 GTAGAGAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (22 bp):
ATATGGGGACAGATGTCGTCAG
Found at i:801570 original size:19 final size:20
Alignment explanation
Indices: 801548--801585 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
801538 AATATTGTGT
801548 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
801567 TTCGCTTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
801586 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:801659 original size:20 final size:19
Alignment explanation
Indices: 801611--801660 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
801601 TGACTTCTGT
801611 GTTGCGAATTACAGATTCAC
1 GTTG-GAATTACAGATTCAC
* *
801631 ATTAGGAATTACAGATTCGC
1 GTT-GGAATTACAGATTCAC
801651 GTTGTGAATT
1 GTTG-GAATT
801661 TAGAAAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (19 bp):
GTTGGAATTACAGATTCAC
Found at i:807995 original size:3 final size:3
Alignment explanation
Indices: 807989--808023 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
807979 ATGGTATTTC
* *
807989 TGA TGA TGA TGA TGA TGA TGA TGA TCA TGA AGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
808024 TAAGTCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:813423 original size:9 final size:9
Alignment explanation
Indices: 813409--813442 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
813399 GTTTAAAAAA
813409 TATTATTGT
1 TATTATTGT
813418 TATTATTGT
1 TATTATTGT
* *
813427 TGTTATTAT
1 TATTATTGT
813436 TATTATT
1 TATTATT
813443 AATAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (9 bp):
TATTATTGT
Found at i:813429 original size:12 final size:12
Alignment explanation
Indices: 813409--813439 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
813399 GTTTAAAAAA
813409 TATTATTGTTAT
1 TATTATTGTTAT
*
813421 TATTGTTGTTAT
1 TATTATTGTTAT
813433 TATTATT
1 TATTATT
813440 ATTAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (12 bp):
TATTATTGTTAT
Found at i:814834 original size:30 final size:30
Alignment explanation
Indices: 814750--814854 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
814740 GGTTTAGTGA
* *
814750 TTTAACTTTCTATTTTAACTATTTTAGTCC
1 TTTAAATTTCTATTTTTACTATTTTAGTCC
* * *
814780 TTTAAATTTCTATTTTTGCCATTTTAGTTC
1 TTTAAATTTCTATTTTTACTATTTTAGTCC
* *
814810 TTT-AATCTTTTGTTTTTACTATTTT-GATCC
1 TTTAAAT-TTCTATTTTTACTATTTTAG-TCC
* *
814840 TTTACATTTTTATTT
1 TTTAAATTTCTATTT
814855 ATTTATTATA
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 4 0.07
30 54 0.90
31 2 0.03
ACGTcount: A:0.20, C:0.13, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTAAATTTCTATTTTTACTATTTTAGTCC
Found at i:817035 original size:30 final size:30
Alignment explanation
Indices: 816997--817059 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
816987 CCAAAATACA
*
816997 TAAATTTT-GAAAATTA-TATTTTTAGTCCC
1 TAAATTTTGGAAAATTACCATTTTT-GTCCC
817026 TAAACTTTTGGAAAATTACCATTTTTGTCCC
1 TAAA-TTTTGGAAAATTACCATTTTTGTCCC
817057 TAA
1 TAA
817060 TGTTTTCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 4 0.13
31 16 0.53
32 6 0.20
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (30 bp):
TAAATTTTGGAAAATTACCATTTTTGTCCC
Found at i:817330 original size:21 final size:21
Alignment explanation
Indices: 817306--817351 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
817296 TTATATATTA
817306 TTAACCTTTAATAATC-TGTTT
1 TTAACCTTTAATAATCAT-TTT
**
817327 TTAATTTTTAATAATCATTTT
1 TTAACCTTTAATAATCATTTT
817348 TTAA
1 TTAA
817352 ATAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAACCTTTAATAATCATTTT
Found at i:817398 original size:26 final size:25
Alignment explanation
Indices: 817345--817414 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
817335 TAATAATCAT
**
817345 TTTTTAAATAATTTAATAATTCTTTA
1 TTTTTAAATAATTTAA-AATTCAATA
817371 TTTTTAAATAATTTAAAATTCAA-A
1 TTTTTAAATAATTTAAAATTCAATA
*
817395 TATTTAAAATAA-TTAAAATT
1 T-TTTTAAATAATTTAAAATT
817415 AGTTAAACCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.25
25 14 0.35
26 16 0.40
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTTAAATAATTTAAAATTCAATA
Found at i:818866 original size:24 final size:22
Alignment explanation
Indices: 818816--818866 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
818806 GTTAACGATA
*
818816 AAAATGTATAAAAACATATTTT
1 AAAATGTATAAAAAAATATTTT
*
818838 AAAATTTATAAATAAAATGATTTT
1 AAAATGTATAAA-AAAAT-ATTTT
*
818862 TAAAT
1 AAAAT
818867 ATATTAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 4 0.17
24 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (22 bp):
AAAATGTATAAAAAAATATTTT
Found at i:823085 original size:18 final size:17
Alignment explanation
Indices: 823044--823104 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 17
823034 TTTTATTAAT
823044 TTATTATTAT-AATA-A
1 TTATTATTATAAATATA
* *
823059 TAATAATTATAAATATTA
1 TTATTATTATAAATA-TA
823077 TTATTATTATAAATAATA
1 TTATTATTATAAAT-ATA
*
823095 ATATTATTAT
1 TTATTATTAT
823105 TATACGCCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
15 8 0.22
16 4 0.11
18 24 0.65
19 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTATTATAAATATA
Found at i:824094 original size:26 final size:26
Alignment explanation
Indices: 824065--824169 Score: 165
Period size: 26 Copynumber: 4.0 Consensus size: 26
824055 TCTATAACTC
824065 CAACGGTGGCCGGCGGTGGCTATCAT
1 CAACGGTGGCCGGCGGTGGCTATCAT
* * *
824091 CAACGGTGGTCGGCGGTGTCTATCGT
1 CAACGGTGGCCGGCGGTGGCTATCAT
*
824117 CAACGGTGGCCGGCAGTGGCTATCAT
1 CAACGGTGGCCGGCGGTGGCTATCAT
*
824143 CAACGGTGGCCGGCGATGGCTATCAT
1 CAACGGTGGCCGGCGGTGGCTATCAT
824169 C
1 C
824170 GTCAGTGCAT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 70 1.00
ACGTcount: A:0.16, C:0.27, G:0.36, T:0.21
Consensus pattern (26 bp):
CAACGGTGGCCGGCGGTGGCTATCAT
Found at i:824490 original size:2 final size:2
Alignment explanation
Indices: 824478--824510 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
824468 TCATTAATTA
*
824478 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
824511 GGATAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:826810 original size:2 final size:2
Alignment explanation
Indices: 826803--826838 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
826793 CCTGTTTAAA
826803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
826839 TTACTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:827011 original size:2 final size:2
Alignment explanation
Indices: 827004--827042 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
826994 AAACCCTAAG
827004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
827043 TATTTCTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:850050 original size:8 final size:8
Alignment explanation
Indices: 850037--850077 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
850027 CTCATTTTCA
850037 GAGAATTT
1 GAGAATTT
850045 GAGAATTT
1 GAGAATTT
*
850053 -AGAGTTT
1 GAGAATTT
*
850060 GGGAATTT
1 GAGAATTT
850068 GAGAATTT
1 GAGAATTT
850076 GA
1 GA
850078 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:850376 original size:128 final size:128
Alignment explanation
Indices: 850148--850648 Score: 896
Period size: 128 Copynumber: 3.9 Consensus size: 128
850138 TAATCGGAGT
850148 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
850213 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
850276 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
850341 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
850404 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
850469 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * * *
850532 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
850596 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
850649 AATCAGGTAA
Statistics
Matches: 360, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
127 1 0.00
128 359 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:850923 original size:14 final size:14
Alignment explanation
Indices: 850904--850933 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
850894 CATAAGTTGA
*
850904 TTTTAATGTATACG
1 TTTTAATATATACG
850918 TTTTAATATATACG
1 TTTTAATATATACG
850932 TT
1 TT
850934 AATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (14 bp):
TTTTAATATATACG
Found at i:851110 original size:33 final size:34
Alignment explanation
Indices: 851049--851148 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
851039 AAATTTAATG
*
851049 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
851083 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
851116 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
851149 AACATTTATC
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:851698 original size:21 final size:20
Alignment explanation
Indices: 851671--851740 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
851661 GGTATAAAAC
*
851671 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
851691 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
851712 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
851733 CCCTGCGG
1 -CCTGCGG
851741 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:851770 original size:21 final size:21
Alignment explanation
Indices: 851744--851791 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
851734 CCTGCGGAGA
*
851744 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
851765 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
851786 GGGCAT
1 TGGCAT
851792 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:853555 original size:32 final size:29
Alignment explanation
Indices: 853500--853575 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 29
853490 TTAATAATTC
*
853500 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAA-AATAATTACATAAATA-TA--TTAA
*
853534 TAAAAAAAATATTTACATAAATATATTAA
1 TAAAAAAAATAATTACATAAATATATTAA
*
853563 TATAAAAAATAAT
1 TAAAAAAAATAAT
853576 AACTATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 15 0.39
31 2 0.05
32 14 0.37
33 3 0.08
34 4 0.11
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAAAAAAATAATTACATAAATATATTAA
Found at i:853569 original size:29 final size:31
Alignment explanation
Indices: 853503--853575 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
853493 ATAATTCTAA
* *
853503 ATAAATAATAATTATATAAATATTATTTTAAT
1 ATAAAAAATAATTACATAAATATTA-TTTAAT
* *
853535 AAAAAAAATATTTACATAAATA-TA-TTAAT
1 ATAAAAAATAATTACATAAATATTATTTAAT
853564 ATAAAAAATAAT
1 ATAAAAAATAAT
853576 AACTATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 15 0.43
31 2 0.06
32 18 0.51
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
ATAAAAAATAATTACATAAATATTATTTAAT
Found at i:860425 original size:30 final size:30
Alignment explanation
Indices: 860391--860475 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
860381 TAATGTGATA
860391 TCTTGTAAATTATGATCAAAATCATAATAT
1 TCTTGTAAATTATGATCAAAATCATAATAT
*
860421 TCTTGTAAATTATGACCAAAATCATAATAT
1 TCTTGTAAATTATGATCAAAATCATAATAT
860451 TCTTGTAAATTATGATCAAAATCAT
1 TCTTGTAAATTATGATCAAAATCAT
860476 GTACACCTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (30 bp):
TCTTGTAAATTATGATCAAAATCATAATAT
Found at i:861115 original size:26 final size:26
Alignment explanation
Indices: 861079--861131 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
861069 TCAAAATAGT
861079 TTCATGCGTAACACAAATATTACATA
1 TTCATGCGTAACACAAATATTACATA
*
861105 TTCATGTGTAACACAAATATTACATA
1 TTCATGCGTAACACAAATATTACATA
861131 T
1 T
861132 ACGATAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.34
Consensus pattern (26 bp):
TTCATGCGTAACACAAATATTACATA
Found at i:866698 original size:22 final size:23
Alignment explanation
Indices: 866673--866719 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
866663 CAAAAAACAG
*
866673 AAAAAA-CGTACTATGAAAGCAA
1 AAAAAATCGTACTATAAAAGCAA
* *
866695 AAAAAATCGTGCTATAAAAGTAA
1 AAAAAATCGTACTATAAAAGCAA
866718 AA
1 AA
866720 TTGTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.60, C:0.11, G:0.13, T:0.17
Consensus pattern (23 bp):
AAAAAATCGTACTATAAAAGCAA
Found at i:868204 original size:15 final size:15
Alignment explanation
Indices: 868181--868232 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
868171 ATATTTAGTT
868181 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTG
* *
868196 GGGCAGGCGGATGCG
1 GGGCGGGCGGATGTG
868211 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTG
*
868226 GGACGGG
1 GGGCGGG
868233 TAATGTCTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.10, C:0.15, G:0.65, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGTG
Found at i:868635 original size:16 final size:17
Alignment explanation
Indices: 868609--868641 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
868599 CATAAAAATC
868609 ATATGAATAAATCAAAA
1 ATATGAATAAATCAAAA
*
868626 ATAT-AATAAATTAAAA
1 ATATGAATAAATCAAAA
868642 TTTTATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (17 bp):
ATATGAATAAATCAAAA
Found at i:876547 original size:20 final size:20
Alignment explanation
Indices: 876460--876553 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
876450 AACATATTGA
876460 AATTTGAC-AAACTCGGTTTC
1 AATTTGACAAAAC-CGGTTTC
* **
876480 AATTTGACAAAACAGGTAAC
1 AATTTGACAAAACCGGTTTC
* * * * **
876500 GAATTTAATAAAATCGATTGG
1 -AATTTGACAAAACCGGTTTC
*
876521 AAATTGACAAAACCGGTTTC
1 AATTTGACAAAACCGGTTTC
876541 AATTTGACAAAAC
1 AATTTGACAAAAC
876554 TGGTAAAGAG
Statistics
Matches: 53, Mismatches: 19, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
20 37 0.70
21 16 0.30
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
AATTTGACAAAACCGGTTTC
Found at i:876863 original size:197 final size:197
Alignment explanation
Indices: 876528--877104 Score: 640
Period size: 197 Copynumber: 3.0 Consensus size: 197
876518 TGGAAATTGA
*
876528 CAAAACCGGTTTCAATTTGACAAAACTGGTAAAGAGCTACCAGAATTGTTGAAATTTGTATCGAT
1 CAAAACCGATTTCAATTTGACAAAACTGGTAAAGAGCTACCAGAATTGTTGAAATTTGTATCGAT
** * *
876593 ACGTTTATAAGTATATGTACCAAAGTATCGGTACTGTAGGAATTTAAAAGAATTATAATAATAGT
66 ACGTTTATAAGTATATGTACCAAAGTATCAATACTGTAGGAATTTAAAAGAATTACAATAATAGC
* *
876658 GGCTATAAAGTATCGATACCTTACACACATGTATTAATACATGACAATATAAAATGTTGAGATTT
131 AGCTATAAAGTATCGATACCTTACACACATGTATCAATACATGACAATATAAAATGTTGAGATTT
876723 GG
196 GG
* * *
876725 CAAAACCGATTTTAATTTGACAAAAAC-GGTAAAGAGCTATCGGAATTGTTGAAATTTGTATCGA
1 CAAAACCGATTTCAATTTGAC-AAAACTGGTAAAGAGCTACCAGAATTGTTGAAATTTGTATCGA
* * *
876789 TACGTTTATAAGTATATGTACCAAAGTATCAATATTTTAGGAATTTAAAAGAATTGCAATAATAG
65 TACGTTTATAAGTATATGTACCAAAGTATCAATACTGTAGGAATTTAAAAGAATTACAATAATAG
* * * * *
876854 CAGCTATAAAGTATCGATACCTTAGACACATGTATCGATACATGACAATATAACATGTTTAAATT
130 CAGCTATAAAGTATCGATACCTTACACACATGTATCAATACATGACAATATAAAATGTTGAGATT
876919 T-G
195 TGG
* ** ** *
876921 ----A-C-A----AA-TT-------C-GGTAAAGAGTTGTCGTAATGGTTGAAATTTGTATCGAT
1 CAAAACCGATTTCAATTTGACAAAACTGGTAAAGAGCTACCAGAATTGTTGAAATTTGTATCGAT
* * ** * *
876967 ACTTTTATAAGTATATGTACTAAAGTATCGGTACTTTAGGAATTTAAAAGAATTGCAATAATAGC
66 ACGTTTATAAGTATATGTACCAAAGTATCAATACTGTAGGAATTTAAAAGAATTACAATAATAGC
* * * * * * *
877032 -GCCTATAAAATATCGATACTTTAGACACATGTATCGATACATGACAATATAACATATTGAAATT
131 AG-CTATAAAGTATCGATACCTTACACACATGTATCAATACATGACAATATAAAATGTTGAGATT
*
877096 TGA
195 TGG
877099 CAAAAC
1 CAAAAC
877105 TAATAAAGTG
Statistics
Matches: 340, Mismatches: 32, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
176 1 0.00
177 154 0.45
182 1 0.00
185 2 0.01
186 2 0.01
190 1 0.00
191 1 0.00
192 1 0.00
196 1 0.00
197 171 0.50
198 5 0.01
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (197 bp):
CAAAACCGATTTCAATTTGACAAAACTGGTAAAGAGCTACCAGAATTGTTGAAATTTGTATCGAT
ACGTTTATAAGTATATGTACCAAAGTATCAATACTGTAGGAATTTAAAAGAATTACAATAATAGC
AGCTATAAAGTATCGATACCTTACACACATGTATCAATACATGACAATATAAAATGTTGAGATTT
GG
Found at i:877040 original size:177 final size:177
Alignment explanation
Indices: 876738--877192 Score: 607
Period size: 177 Copynumber: 2.6 Consensus size: 177
876728 AACCGATTTT
*
876738 AATTTGACAAAAACGGTAAAGAGCTATCGGAATTGTTGAAATTTGTATCGATACGTTTATAAGTA
1 AATTTGACAAAAACGGTAAAGAGCTATCGGAATGGTTGAAATTTGTATCGATACGTTTATAAGTA
* *
876803 TATGTACCAAAGTATCAATATTTTAGGAATTTAAAAGAATTGCAATAATAGCAGCTATAAAGTAT
66 TATGTACCAAAGTATCAATACTTTAGGAATTTAAAAGAATTGCAATAATAGCAGCTATAAAATAT
* *
876868 CGATACCTTAGACACATGTATCGATACATGACAATATAACATGTTTA
131 CGATACCTTAGACACATGTATCGATACATGACAATATAACATATTGA
** * * * *
876915 AATTTGACAAATTCGGTAAAGAGTTGTCGTAATGGTTGAAATTTGTATCGATACTTTTATAAGTA
1 AATTTGACAAAAACGGTAAAGAGCTATCGGAATGGTTGAAATTTGTATCGATACGTTTATAAGTA
* **
876980 TATGTACTAAAGTATCGGTACTTTAGGAATTTAAAAGAATTGCAATAATAGC-GCCTATAAAATA
66 TATGTACCAAAGTATCAATACTTTAGGAATTTAAAAGAATTGCAATAATAGCAG-CTATAAAATA
*
877044 TCGATACTTTAGACACATGTATCGATACATGACAATATAACATATTGA
130 TCGATACCTTAGACACATGTATCGATACATGACAATATAACATATTGA
** * * * *
877092 AATTTGAC-AAAACTAATAAAGTGCTA-CAGGAATTGTTGAAA---GTATCAATACATTTATAAG
1 AATTTGACAAAAAC-GGTAAAGAGCTATC-GGAATGGTTGAAATTTGTATCGATACGTTTATAAG
* * * * *
877152 TATATATACCATAGAATCAGTACTTTAGGAATCTAAAAGAA
64 TATATGTACCAAAGTATCAATACTTTAGGAATTTAAAAGAA
877193 ATGAAAAAAA
Statistics
Matches: 243, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
174 52 0.21
176 5 0.02
177 186 0.77
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (177 bp):
AATTTGACAAAAACGGTAAAGAGCTATCGGAATGGTTGAAATTTGTATCGATACGTTTATAAGTA
TATGTACCAAAGTATCAATACTTTAGGAATTTAAAAGAATTGCAATAATAGCAGCTATAAAATAT
CGATACCTTAGACACATGTATCGATACATGACAATATAACATATTGA
Found at i:877754 original size:25 final size:26
Alignment explanation
Indices: 877698--877754 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
877688 ACATGTAACT
877698 TATAAAATGATTTATCAGTATGCATA
1 TATAAAATGATTTATCAGTATGCATA
*
877724 AATAAAATAGATTT-TCAG-ACT-CATA
1 TATAAAAT-GATTTATCAGTA-TGCATA
877749 TATAAA
1 TATAAA
877755 TCAAAATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 10 0.37
26 12 0.44
27 5 0.19
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (26 bp):
TATAAAATGATTTATCAGTATGCATA
Found at i:878349 original size:24 final size:24
Alignment explanation
Indices: 878322--878390 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
878312 AAACGAAAAT
878322 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
878346 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
878370 ATCAGAAAT-AAGAACAGAATT
1 ATCAGAAATCAA-AACAGAATT
878391 TAGGTCGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:883121 original size:24 final size:24
Alignment explanation
Indices: 883094--883168 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
883084 AAACGGAGAT
* *
883094 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
883118 ATCAGATATCAGAACAGAATCCAA
1 ATCAGAAATCAGAACAGAATTCAG
883142 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
883166 ATC
1 ATC
883169 GATGATCAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:883176 original size:24 final size:24
Alignment explanation
Indices: 883094--883178 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
883084 AAACGGAGAT
* * *
883094 ATCAGAAATCAAAACATAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
* *
883118 ATCAGATATCAGAACAGAATCCAA
1 ATCAGATATCAGAACAGAATTCAG
*
883142 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGATATCAGAACAGAATTCAG
883166 ATC-GATGATCAGA
1 ATCAGAT-ATCAGA
883179 TAAAATATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 2 0.04
24 49 0.96
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATTCAG
Found at i:887974 original size:2 final size:2
Alignment explanation
Indices: 887969--888005 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
887959 TTTCTTCTTC
887969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
888006 CAACCCTCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:895265 original size:21 final size:21
Alignment explanation
Indices: 895235--895281 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
895225 ACTAGAAATA
895235 TTATTATTTCTATTGATTTTG
1 TTATTATTTCTATTGATTTTG
* *
895256 TTATTTTTTCTATTGGTTTTG
1 TTATTATTTCTATTGATTTTG
895277 TTATT
1 TTATT
895282 GTTGGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.04, G:0.11, T:0.70
Consensus pattern (21 bp):
TTATTATTTCTATTGATTTTG
Found at i:895332 original size:21 final size:21
Alignment explanation
Indices: 895307--895346 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
895297 GAAAATGTTA
*
895307 AAAAACATTAATGTTTTAGGT
1 AAAAACAATAATGTTTTAGGT
*
895328 AAAAATAATAATGTTTTAG
1 AAAAACAATAATGTTTTAG
895347 ATACTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (21 bp):
AAAAACAATAATGTTTTAGGT
Found at i:896576 original size:89 final size:87
Alignment explanation
Indices: 896456--896688 Score: 269
Period size: 84 Copynumber: 2.7 Consensus size: 87
896446 CCGCTAAAGT
* *
896456 TAGCGGCGTTTTTTGAACAAACGTCACAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAGAAAA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGG-AG--AA
896521 AAAAAG-TCGCAAAAGATCAGATCTA
63 AAAAAGCT-GCAAAAGATCAGATCTA
* * * * *
896546 TAGCGGTGTTTTTGGAA-AAATGTCGCAAAAGGTTGAGATCTATAGCAACGTTTTT-G-GAATAA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAGAAAAA
* * *
896608 ACGCTGCAAAAGGTCAGATTTA
66 AAGCTGCAAAAGATCAGATCTA
** *
896630 TAGCGGCGTTTTTGGATACAAACACCGCAAAAGGTC-AGATCTATAGCGACATTTTTGGA
1 TAGCGGCGTTTTTGGA-ACAAACGTCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGA
896689 TTCAAACGCC
Statistics
Matches: 121, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
84 36 0.30
85 20 0.17
86 15 0.12
88 1 0.01
89 34 0.28
90 15 0.12
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (87 bp):
TAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAGAAAAA
AAGCTGCAAAAGATCAGATCTA
Found at i:896660 original size:43 final size:42
Alignment explanation
Indices: 896456--896748 Score: 246
Period size: 43 Copynumber: 6.8 Consensus size: 42
896446 CCGCTAAAGT
* * * *
896456 TAGCGGCGTTTTTTGAACAAACGTCACAAAAGGTCGAGATCTA
1 TAGCGACGTTTTTGGAACAAACGCCGCAAAAGGTC-AGATCTA
* * * *
896499 TAGCGACGTTTTTGGAAGAAAAAAAAAGTCGCAAAAGATCAGATCTA
1 TAGCGACGTTTTT-G--G--AACAAACGCCGCAAAAGGTCAGATCTA
** * * *
896546 TAGCGGTGTTTTTGGAA-AAATGTCGCAAAAGGTTGAGATCTA
1 TAGCGACGTTTTTGGAACAAACGCCGCAAAAGG-TCAGATCTA
* * * *
896588 TAGCAACGTTTTTGGAATAAACGCTGCAAAAGGTCAGATTTA
1 TAGCGACGTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTA
* *
896630 TAGCGGCGTTTTTGGATACAAACACCGCAAAAGGTCAGATCTA
1 TAGCGACGTTTTTGGA-ACAAACGCCGCAAAAGGTCAGATCTA
* * * *
896673 TAGCGACATTTTTGGATTCAAACGCCACAAAATGTCAGATCTA
1 TAGCGACGTTTTTGGA-ACAAACGCCGCAAAAGGTCAGATCTA
* * * *
896716 TAACGACATTTTTAGATACAAACTCCGCAAAAG
1 TAGCGACGTTTTTGGA-ACAAACGCCGCAAAAG
896749 AGCTCATGAT
Statistics
Matches: 205, Mismatches: 37, Indels: 16
0.79 0.14 0.06
Matches are distributed among these distances:
41 13 0.06
42 45 0.22
43 110 0.54
44 1 0.00
46 2 0.01
47 18 0.09
48 16 0.08
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (42 bp):
TAGCGACGTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTA
Found at i:898847 original size:32 final size:31
Alignment explanation
Indices: 898775--898886 Score: 103
Period size: 29 Copynumber: 3.8 Consensus size: 31
898765 CAAGATCTCC
* **
898775 TCTTCGAGTC-GTTTCTTTTGAAACA-AAAA
1 TCTTTGAGTCTGTTTCTTTTGAAACATATCA
898804 TC--TGAGT-TGTTTCTTTTGAAACATCATCA
1 TCTTTGAGTCTGTTTCTTTTGAAACAT-ATCA
898833 TCTTTGAGTCTGTTTCTTTTG-AA-ATATCA
1 TCTTTGAGTCTGTTTCTTTTGAAACATATCA
* * **
898862 CCTTTGAGTCGGTTTCCCTTGAAAC
1 TCTTTGAGTCTGTTTCTTTTGAAAC
898887 CATTATCCCT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
27 19 0.28
29 27 0.40
30 4 0.06
31 7 0.10
32 11 0.16
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (31 bp):
TCTTTGAGTCTGTTTCTTTTGAAACATATCA
Found at i:899135 original size:134 final size:133
Alignment explanation
Indices: 898915--899367 Score: 453
Period size: 130 Copynumber: 3.4 Consensus size: 133
898905 TATGTCATCC
* * * ** *
898915 TCATCACGTAGGAACCGTATCATCCACC-GACCAGATCTCCTAATCACGTAGGAGCCGCGTCAAC
1 TCATCACGTAGGAACCGTGTCATCC-CCAGACCAGACCTCCTCATCACGTAGGAGCCATGTCACC
* * * *
898979 CTTAGATAACAAGCTATCCTCATCACGTAGGAACCATGTTATCTACCCTCCCTAAAGATGGCCAA
65 CTTAGATAACCAGC-GT-CTCATCACGTAGGAACCGTGTTATCTACCCTTCCTAAAGATGGCCAA
899044 AACTCT
128 AACTCT
* * *
899050 TCATCACGTATGAGCCGTGGCATCCCC-GACCAGACCTCCTCATCACGTAGGAGCCATGTCACCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCC
* *
899114 TTAGATAACCAGCCGCTCTCATCACGTAGGAACCGTTTTAT-TA---TTCCTAAAGATGGCC-AG
66 TTAGATAACCAG-CG-TCTCATCACGTAGGAACCGTGTTATCTACCCTTCCTAAAGATGGCCAAA
*
899174 CCGT-T
129 AC-TCT
* * ** **
899179 CTCATCACGTAGGAACCGTGTCATCCCCATACTAGACCTCCTCATCATATAGGA-ATAGTGTCAC
1 -TCATCACGTAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGTAGGAGCCA-TGTCAC
* * *
899243 CCCT-GATAACCAGTCGTCATCATTC-CGTAGGAACCGTGTTTTC-GCCCTTCCTAAAGATGGCC
64 CCTTAGATAACCAG-CGTC-TCA-TCACGTAGGAACCGTGTTATCTACCCTTCCTAAAGATGGCC
*
899305 AGAACTCT
126 AAAACTCT
* ** *
899313 TCATCACGTATGAGTCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGTAGGAGC
899368 TGTAACACCC
Statistics
Matches: 261, Mismatches: 42, Indels: 31
0.78 0.13 0.09
Matches are distributed among these distances:
129 5 0.02
130 69 0.26
131 32 0.12
133 63 0.24
134 69 0.26
135 23 0.09
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (133 bp):
TCATCACGTAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCC
TTAGATAACCAGCGTCTCATCACGTAGGAACCGTGTTATCTACCCTTCCTAAAGATGGCCAAAAC
TCT
Found at i:900220 original size:32 final size:32
Alignment explanation
Indices: 900102--900225 Score: 119
Period size: 31 Copynumber: 3.9 Consensus size: 32
900092 ACCTCGACAA
* * * * *
900102 CTGTCCATAGGTTCCGAAGAACCTAGGTAAAT
1 CTGTCCATATGTCCCGTAGAACATAGGTAATT
* * *
900134 -TGTCCATATGTTCCTTAGAACATAGGT-ATA
1 CTGTCCATATGTCCCGTAGAACATAGGTAATT
* * *
900164 CTGTTCATATGTCTCG-AAAGACATAGGTAATT
1 CTGTCCATATGTCCCGTAGA-ACATAGGTAATT
900196 CTGTCCATATGTCCCGTAGAACATAGGTAA
1 CTGTCCATATGTCCCGTAGAACATAGGTAA
900226 ACCCTCGACT
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
30 3 0.04
31 42 0.58
32 26 0.36
33 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (32 bp):
CTGTCCATATGTCCCGTAGAACATAGGTAATT
Found at i:901484 original size:3 final size:3
Alignment explanation
Indices: 901478--901513 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
901468 ACGGAAGGAG
901478 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GA
901514 GTTTGTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:902193 original size:20 final size:21
Alignment explanation
Indices: 902156--902194 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
902146 TTGAAGGCCC
**
902156 ATATTACCAAGTGGACCCAAT
1 ATATTACCAAGTAAACCCAAT
902177 ATATTA-CAAGTAAACCCA
1 ATATTACCAAGTAAACCCA
902195 CCCCAAAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (21 bp):
ATATTACCAAGTAAACCCAAT
Found at i:903478 original size:16 final size:17
Alignment explanation
Indices: 903446--903479 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
903436 TTAGCCCTCT
903446 TAATTACCATGTATTTG
1 TAATTACCATGTATTTG
*
903463 TAATTACC-TTTATTTG
1 TAATTACCATGTATTTG
903479 T
1 T
903480 GGTATCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (17 bp):
TAATTACCATGTATTTG
Found at i:903561 original size:2 final size:2
Alignment explanation
Indices: 903556--903597 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
903546 ATCCATGACT
903556 TA TA TA TA TA TA TA 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 TA TA TA TA
903598 ATTAATGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:906331 original size:15 final size:15
Alignment explanation
Indices: 906311--906345 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
906301 AGCAAGGCTC
*
906311 TTCGAGTGATGCTTG
1 TTCGAGTGAAGCTTG
*
906326 TTCGAGTGAAGTTTG
1 TTCGAGTGAAGCTTG
906341 TTCGA
1 TTCGA
906346 ATTGTAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.40
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:909112 original size:32 final size:32
Alignment explanation
Indices: 909076--909146 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
909066 GTTCTTCATA
909076 ATGTTATTTATGTTCCACATTTTAAACATAAC
1 ATGTTATTTATGTTCCACATTTTAAACATAAC
909108 ATGTTATTTATGTTCCACATTTTAAACATAAC
1 ATGTTATTTATGTTCCACATTTTAAACATAAC
909140 ATGTTAT
1 ATGTTAT
909147 CTGTTTCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (32 bp):
ATGTTATTTATGTTCCACATTTTAAACATAAC
Found at i:929181 original size:36 final size:37
Alignment explanation
Indices: 929092--929195 Score: 113
Period size: 37 Copynumber: 2.8 Consensus size: 37
929082 CCTTTTCGTC
929092 CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
* ** * *
929129 TTGTTAGGATTCAAACTCCTGAAA-TAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
* * *
929165 CTACTATGATTTAAACT-CTTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAG-TAGGAT
929196 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
35 5 0.09
36 23 0.43
37 26 0.48
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
Found at i:929706 original size:20 final size:20
Alignment explanation
Indices: 929681--929718 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
929671 ATTATTATTA
929681 TTTTACTTATATATATATGT
1 TTTTACTTATATATATATGT
* *
929701 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
929719 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTACTTATATATATATGT
Found at i:929748 original size:37 final size:35
Alignment explanation
Indices: 929663--929748 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 35
929653 TTGATTTTCT
* * *
929663 TTTTTATTATTATTATTATTTTACTTATATATATATG
1 TTTTTATT-TT-TTATTATTTTACTCATATATTTATC
*
929700 TTTTTACTTTTTTATATATTTTACTCATTTATTTATC
1 TTTTTA-TTTTTTAT-TATTTTACTCATATATTTATC
929737 TATTTTATTTTT
1 T-TTTTATTTTT
929749 ATCTTTATCC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
36 4 0.10
37 31 0.74
38 7 0.17
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (35 bp):
TTTTTATTTTTTATTATTTTACTCATATATTTATC
Found at i:931053 original size:5 final size:5
Alignment explanation
Indices: 931043--931070 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
931033 TCTTTTAATC
931043 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
931071 CATCACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:932983 original size:17 final size:18
Alignment explanation
Indices: 932961--933004 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
932951 ATCCAATAAA
932961 AAAC-AAAGAAAAAAGAG
1 AAACAAAAGAAAAAAGAG
*
932978 AAACAAAAGAAAAAAGAA
1 AAACAAAAGAAAAAAGAG
932996 AGAACAAAA
1 A-AACAAAA
933005 TCAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (18 bp):
AAACAAAAGAAAAAAGAG
Found at i:933001 original size:19 final size:18
Alignment explanation
Indices: 932959--933017 Score: 75
Period size: 19 Copynumber: 3.3 Consensus size: 18
932949 AGATCCAATA
932959 AAAAAC-AAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
*
932976 AGAAACAAAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
**
932994 AAAGAACAAAATCAAAAAG
1 AAA-AACAAAAGAAAAAAG
933013 AAAAA
1 AAAAA
933018 GGGACAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 5 0.14
18 15 0.42
19 16 0.44
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAACAAAAGAAAAAAG
Found at i:933647 original size:22 final size:22
Alignment explanation
Indices: 933619--933695 Score: 104
Period size: 22 Copynumber: 3.5 Consensus size: 22
933609 GCTACCCCAT
933619 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
933641 CAAACCTTTGTA-CATCAAAT-A
1 CAAACCTTTG-AGCATCAAATGA
* *
933662 CCAAACATTTGAGCATCAAATGC
1 -CAAACCTTTGAGCATCAAATGA
933685 CAAACCTTTGA
1 CAAACCTTTGA
933696 CCAAACACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.04
22 45 0.94
23 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:934780 original size:106 final size:106
Alignment explanation
Indices: 934655--936010 Score: 2164
Period size: 106 Copynumber: 12.9 Consensus size: 106
934645 CGAGATAACA
** * * *
934655 CAAGTTCAACTTCACGACGAAGGGATGGCTGGTTGTCAACAAACAACTTCCCAATTTCAAAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
934720 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
934761 CAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
* *
934826 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAAAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
934867 CAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
934932 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
934973 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCACAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
* *
935038 ATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * * * *
935079 CAAGTTCAACTTCACGATGAAGGGACCGATGGTTGTCAACAAGCAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
** * *
935144 ATTTCAACTTCACAATGAAGGATATTGGACTCAAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
** * *
935185 CAAGTTCAACTTCATAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
*
935249 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
935290 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
*
935355 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
935396 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
935461 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
935502 CAAGTTCAACTTCACGACGAAGGGACCGCTAGTTATCAAT--A-AA-----CAATTTC----CCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
*
935555 ATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
935596 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
*
935661 ATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
935702 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
935767 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
935808 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
* *
935873 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * **** *
935914 CAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCATGGTTCCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
* *
935978 AATTTCAACTTCACAACGGAGGATATTGGACTC
65 AATTTCAACTTCACAGCGAAGGATATTGGACTC
936011 GGAACAATGC
Statistics
Matches: 1165, Mismatches: 71, Indels: 28
0.92 0.06 0.02
Matches are distributed among these distances:
94 81 0.07
96 1 0.00
97 2 0.00
98 7 0.01
102 7 0.01
103 2 0.00
104 1 0.00
105 97 0.08
106 967 0.83
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
Found at i:935524 original size:43 final size:43
Alignment explanation
Indices: 935463--935618 Score: 124
Period size: 43 Copynumber: 3.4 Consensus size: 43
935453 CAGAGCCAAT
*
935463 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAG
* * *
935506 TTCAACTTCAC-GACGAAGGGACCGCTAGTT--A-TCAATAAACAATTTCCCAAT
1 TTCAACTTCACAG-CGAA-GGA----TA-TTGGACTC--TAGACAA---CGCAAG
935557 TTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAG
1 TTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAG
935600 TTCAACTTCAC-GACGAAGG
1 TTCAACTTCACAG-CGAAGG
935619 GACCGCTGGT
Statistics
Matches: 89, Mismatches: 7, Indels: 34
0.68 0.05 0.26
Matches are distributed among these distances:
42 2 0.02
43 36 0.40
44 3 0.03
45 2 0.02
46 10 0.11
47 2 0.02
48 9 0.10
49 2 0.02
50 3 0.03
51 19 0.21
52 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAG
Found at i:936798 original size:36 final size:36
Alignment explanation
Indices: 936709--936812 Score: 127
Period size: 36 Copynumber: 2.8 Consensus size: 36
936699 CCTTTTCGTC
936709 CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAA-TAGGATAGAATT
* ** *
936746 TTGTTAGGATTCAAACTCCTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
* * *
936782 CTACTATGATTTAAACTCATAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAA-ATAGGAT
936813 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 28 0.50
37 28 0.50
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
Found at i:937336 original size:20 final size:20
Alignment explanation
Indices: 937311--937348 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
937301 TTATTATTTA
937311 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
937331 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
937349 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:947584 original size:18 final size:19
Alignment explanation
Indices: 947542--947581 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
947532 TTTGGTTCAC
*
947542 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTACCAG-G
947562 GGAATGTAAGATTACCAGG
1 GGAATGTAAGATTACCAGG
947581 G
1 G
947582 AATAGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.25
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:947807 original size:35 final size:37
Alignment explanation
Indices: 947736--947808 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
947726 GTTGGAAAAT
*
947736 ATTTATATAATTTATTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTATTTAAAAAAATTAAAATCATAAA
*
947773 ATTTATATAATTT-TTT-ACAAAATTAAAAAT-ATAAA
1 ATTTATATAATTTATTTAAAAAAATT-AAAATCATAAA
947808 A
1 A
947809 AGGTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 13 0.39
36 7 0.21
37 13 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (37 bp):
ATTTATATAATTTATTTAAAAAAATTAAAATCATAAA
Found at i:954023 original size:16 final size:16
Alignment explanation
Indices: 954002--954033 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
953992 TTAAATTTAG
954002 ATCCTCAAAAAATTAA
1 ATCCTCAAAAAATTAA
954018 ATCCTCAAAAAATTAA
1 ATCCTCAAAAAATTAA
954034 CAGAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (16 bp):
ATCCTCAAAAAATTAA
Found at i:964693 original size:187 final size:182
Alignment explanation
Indices: 964324--964711 Score: 604
Period size: 187 Copynumber: 2.1 Consensus size: 182
964314 ATTTCGAATT
* *
964324 TATATAA-AAATTAAATA-TTTTTTAATTCAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATAAATTTAATATTTTTTTAATTCAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
964387 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATATTGATTTAAGTTTAAAAGTTATTAA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATATTGATTTAAGTTTAAAAGTTATGAA
964452 ATCTTAAATTATTAATTGAGTTTTAAATAGTTTGAGCTTAGCTCATATGTTA
131 ATCTTAAATTATTAATTGAGTTTTAAATAGTTTGAGCTTAGCTCATATGTTA
*
964504 TATATAATATATTTAATATTTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATAT
1 TATATAATAAATTTAATATTTTTTTAATTC-AAAAAACAGTTTACAATTAATTTAAATAATATAT
*
964569 AATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTT
65 AATTATAAAATAAAAATTTTATATAA--ATTTT--TTAATTAATATTGATTTAAGTTTAAAAGTT
* * * *
964634 ATGGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTG-GGTTAAG-TCCATATGTTA
126 ATGAAATCTTAAATTATTAATTGAGTTTTAAATAGTTTGAGCTT-AGCT-CATATGTTA
964691 TATATAATAAATTTAATATTT
1 TATATAATAAATTTAATATTT
964712 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
180 7 0.04
181 8 0.04
182 11 0.06
183 59 0.31
185 4 0.02
186 4 0.02
187 96 0.51
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (182 bp):
TATATAATAAATTTAATATTTTTTTAATTCAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATATTGATTTAAGTTTAAAAGTTATGAA
ATCTTAAATTATTAATTGAGTTTTAAATAGTTTGAGCTTAGCTCATATGTTA
Found at i:964851 original size:27 final size:28
Alignment explanation
Indices: 964795--964857 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
964785 CCGTTAATCG
964795 ACCGAACTAATTCGGTGATTGATCGAATTA
1 ACCGAACTAATT--GTGATTGATCGAATTA
*
964825 ACCGAACTAATT-TGATTCGGTCG-ATTA
1 ACCGAACTAATTGTGATT-GATCGAATTA
964852 ACCGAA
1 ACCGAA
964858 TTAGTTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 15 0.48
28 4 0.13
30 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (28 bp):
ACCGAACTAATTGTGATTGATCGAATTA
Found at i:967124 original size:23 final size:23
Alignment explanation
Indices: 967082--967198 Score: 99
Period size: 23 Copynumber: 5.0 Consensus size: 23
967072 TATAAATGAG
* *
967082 CATGTTCGCGAACGCCAAACGAA
1 CATGTTCACGAACGCTAAACGAA
* * *
967105 CATATTCACGAACTCTAAACAAA
1 CATGTTCACGAACGCTAAACGAA
* * * *
967128 CATGTTTACGAATGTTTAAATGAA
1 CATGTTCACGAACG-CTAAACGAA
* **
967152 TATGTTCATAAACGCTAAACGAA
1 CATGTTCACGAACGCTAAACGAA
**
967175 CATGTTCGTGAACGCTAAACGAA
1 CATGTTCACGAACGCTAAACGAA
967198 C
1 C
967199 GATAAACGAA
Statistics
Matches: 71, Mismatches: 22, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
23 56 0.79
24 15 0.21
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.24
Consensus pattern (23 bp):
CATGTTCACGAACGCTAAACGAA
Found at i:972397 original size:32 final size:32
Alignment explanation
Indices: 972342--972429 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 32
972332 ATACCACATA
* * **
972342 ATCACTTAAGTACATGTGTCATATGTCAAGAC
1 ATCACTTATGTACACGTAACATATGTCAAGAC
* *
972374 ATCATTTATGTACACGTAACATATGTCACGAC
1 ATCACTTATGTACACGTAACATATGTCAAGAC
* * *
972406 ATTACTTATGTACATGTGACATAT
1 ATCACTTATGTACACGTAACATAT
972430 ATTATGCCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (32 bp):
ATCACTTATGTACACGTAACATATGTCAAGAC
Found at i:978410 original size:2 final size:2
Alignment explanation
Indices: 978403--978442 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
978393 TTACCCTTTA
978403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
978443 TGTTTTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:986968 original size:30 final size:31
Alignment explanation
Indices: 986905--986975 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
986895 ATTTGTACAC
* * *
986905 TTTTGGTCACTTATATTATCGTTTTATTGAG
1 TTTTGGTCACTTACATTATCGTTTCATTAAG
*
986936 TTTTGGTCACTTACGTT-TCGTTTCATTAAG
1 TTTTGGTCACTTACATTATCGTTTCATTAAG
986966 -TTTGGTCACT
1 TTTTGGTCACT
986976 CGAAAATGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 10 0.28
30 11 0.31
31 15 0.42
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (31 bp):
TTTTGGTCACTTACATTATCGTTTCATTAAG
Found at i:991906 original size:65 final size:65
Alignment explanation
Indices: 991832--991961 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
991822 CTATCTCGAC
991832 CAGGGTCGGGTCGGCACCCTTTAATCCCCCGAAACAAAGGCCGAAAGGTAGCCCTGCCGTATTGT
1 CAGGGTCGGGTCGGCACCCTTTAATCCCCCGAAACAAAGGCCGAAAGGTAGCCCTGCCGTATTGT
991897 CAGGGTCGGGTCGGCACCCTTTAATCCCCCGAAACAAAGGCCGAAAGGTAGCCCTGCCGTATTGT
1 CAGGGTCGGGTCGGCACCCTTTAATCCCCCGAAACAAAGGCCGAAAGGTAGCCCTGCCGTATTGT
991962 ATCCGGCCGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.18
Consensus pattern (65 bp):
CAGGGTCGGGTCGGCACCCTTTAATCCCCCGAAACAAAGGCCGAAAGGTAGCCCTGCCGTATTGT
Found at i:995059 original size:3 final size:3
Alignment explanation
Indices: 995053--995181 Score: 163
Period size: 3 Copynumber: 43.7 Consensus size: 3
995043 TTTTTTTATT
* *
995053 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
995101 -AA CAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
995148 TAA AAA TAA TAA TAA TAA -AA CAA AAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
995182 GTAAAAAAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
2 4 0.04
3 106 0.96
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:995143 original size:65 final size:65
Alignment explanation
Indices: 995053--995181 Score: 249
Period size: 65 Copynumber: 2.0 Consensus size: 65
995043 TTTTTTTATT
995053 TAATAATAATAATAATAATAATAATATTAATAAAAATAATAATAATAAAACAAAAATAATAATAA
1 TAATAATAATAATAATAATAATAATATTAATAAAAATAATAATAATAAAACAAAAATAATAATAA
*
995118 TAATAATAATAATAATAATACTAATATTAATAAAAATAATAATAATAAAACAAAAATAATAATA
1 TAATAATAATAATAATAATAATAATATTAATAAAAATAATAATAATAAAACAAAAATAATAATA
995182 GTAAAAAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (65 bp):
TAATAATAATAATAATAATAATAATATTAATAAAAATAATAATAATAAAACAAAAATAATAATAA
Found at i:995639 original size:76 final size:75
Alignment explanation
Indices: 995349--996012 Score: 1221
Period size: 76 Copynumber: 8.9 Consensus size: 75
995339 CCCCCGAGGG
*
995349 TTTGAAAACATC-AAAAGATCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
995413 ACCCTAAGGC
66 ACCCTAAGGC
* *
995423 TTTGAAAACATCAAAAAGCTCCCGAAGGCCTTTGAAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
*
995488 ACCCGAAGGC
66 ACCCTAAGGC
995498 TTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
995562 ACCCTAAGGC
66 ACCCTAAGGC
995572 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGAT
995637 GACCCTAAGGC
65 GACCCTAAGGC
995648 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
995713 ACCCTAAGGC
66 ACCCTAAGGC
995723 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGAT
995788 GACCCTAAGGC
65 GACCCTAAGGC
995799 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGAT
995864 GACCCTAAGGC
65 GACCCTAAGGC
995875 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGAT
995940 GACCCTAAGGC
65 GACCCTAAGGC
995951 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTGGAAACATCAT-C-CTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
996013 TGAGAAATAG
Statistics
Matches: 579, Mismatches: 7, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
72 18 0.03
73 1 0.00
74 97 0.17
75 161 0.28
76 302 0.52
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (75 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
ACCCTAAGGC
Found at i:995745 original size:151 final size:151
Alignment explanation
Indices: 995349--996012 Score: 1241
Period size: 151 Copynumber: 4.4 Consensus size: 151
995339 CCCCCGAGGG
*
995349 TTTGAAAACATC-AAAAGATCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
* *
995413 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-CTTTGAAAACATCATGCACTGAAGG
66 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
*
995477 ACTTACAGATGACCCGAAGGC
131 ACTTACAGATGACCCTAAGGC
995498 TTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
995562 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
66 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
995627 ACTTACAGATGACCCTAAGGC
131 ACTTACAGATGACCCTAAGGC
995648 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
995713 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
66 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
995778 ACTTACAGATGACCCTAAGGC
131 ACTTACAGATGACCCTAAGGC
995799 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGAT
995864 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
65 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
995929 GACTTACAGATGACCCTAAGGC
130 GACTTACAGATGACCCTAAGGC
995951 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTGGAAACATCAT-C-CTGAAGGACTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
996013 TGAGAAATAG
Statistics
Matches: 508, Mismatches: 4, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
148 18 0.04
149 103 0.20
150 69 0.14
151 167 0.33
152 151 0.30
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (151 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
ACTTACAGATGACCCTAAGGC
Found at i:999568 original size:82 final size:82
Alignment explanation
Indices: 999456--999716 Score: 434
Period size: 82 Copynumber: 3.2 Consensus size: 82
999446 CTTATTTCTC
* * *
999456 CTATGAGCAAATTTATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCACA-TTCTCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
999521 GAACACTTCCAGAAGATG
65 GAACACTTCCAGAAGATG
999539 CTATGAGCACATTCTCTTCTAAATTCAATGATTGGTTCTGTCT-ACCAGATCAGATAACTCAAAG
1 CTATGAGCACATTCTCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAAG
999603 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
* * *
999620 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCCGATAACTCAAA
1 CTATGAGCACATTC-TCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
999685 GAACACTTCCAGAAGATG
65 GAACACTTCCAGAAGATG
999703 CTATGGAGCACATT
1 CTAT-GAGCACATT
999717 ACATTTGTTC
Statistics
Matches: 169, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
81 52 0.31
82 57 0.34
83 51 0.30
84 9 0.05
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (82 bp):
CTATGAGCACATTCTCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATG
Found at i:1004580 original size:27 final size:27
Alignment explanation
Indices: 1004528--1004581 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1004518 GTACATCAAA
* *
1004528 CAAAACTTTACATGTAGGGGACAACTT
1 CAAAACTTTACATATAGGGAACAACTT
*
1004555 CAAAACTTTACATATAGGGAATAACTT
1 CAAAACTTTACATATAGGGAACAACTT
1004582 TCCCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (27 bp):
CAAAACTTTACATATAGGGAACAACTT
Found at i:1006416 original size:24 final size:23
Alignment explanation
Indices: 1006389--1006453 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
1006379 AATGAAATAT
1006389 AAATAATATATATAAATACTATAA
1 AAATAATATATATAAATA-TATAA
* *
1006413 AAATAATATGTATATATATATAA
1 AAATAATATATATAAATATATAA
* *
1006436 AAAAAATTATAAATAAAT
1 AAATAA-TATATATAAAT
1006454 TAAATATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 10 0.29
24 24 0.71
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATAATATATATAAATATATAA
Found at i:1008947 original size:3 final size:3
Alignment explanation
Indices: 1008941--1009043 Score: 127
Period size: 3 Copynumber: 34.7 Consensus size: 3
1008931 TTTTTTTATT
* * *
1008941 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA AAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1008989 TAA TAA TAA TAC TAA TAT TAA TAA AAA TAA TAA TAA TAA -AA CAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1009036 TAA TAA TA
1 TAA TAA TA
1009044 GTAAAAAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 2 0.02
3 85 0.98
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1015496 original size:18 final size:18
Alignment explanation
Indices: 1015452--1015499 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1015442 TTTTTAAAGA
*
1015452 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
1015471 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
1015488 AAATATATAATA
1 AAATATATAATA
1015500 AGGATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:1019676 original size:24 final size:24
Alignment explanation
Indices: 1019609--1019669 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
1019599 CGTCTTCACT
1019609 GTTGACATCATCACCGTCATTTTC
1 GTTGACATCATCACCGTCATTTTC
1019633 GTTGACATCATCACCGTCATTTTC
1 GTTGACATCATCACCGTCATTTTC
* *
1019657 GTTGTCGTCATCA
1 GTTGACATCATCA
1019670 TCATCATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (24 bp):
GTTGACATCATCACCGTCATTTTC
Found at i:1019681 original size:12 final size:12
Alignment explanation
Indices: 1019664--1019714 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1019654 TTCGTTGTCG
*
1019664 TCATCATCATCA
1 TCATAATCATCA
1019676 TCATCAATC-TCA
1 TCAT-AATCATCA
*
1019688 TCATAAACATCA
1 TCATAATCATCA
**
1019700 AGATAATCATCA
1 TCATAATCATCA
1019712 TCA
1 TCA
1019715 GAGTCATCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 3 0.10
12 24 0.80
13 3 0.10
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.29
Consensus pattern (12 bp):
TCATAATCATCA
Found at i:1019742 original size:27 final size:29
Alignment explanation
Indices: 1019706--1019773 Score: 113
Period size: 30 Copynumber: 2.4 Consensus size: 29
1019696 ATCAAGATAA
1019706 TCATCATCAGAGTCATC-T-TCCTCACCC
1 TCATCATCAGAGTCATCTTCTCCTCACCC
1019733 TCATCATCAGAGTCATCTTCCTCCTCACCC
1 TCATCATCAGAGTCATCTT-CTCCTCACCC
1019763 TCATCATCAGA
1 TCATCATCAGA
1019774 ATACTCAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 17 0.45
28 1 0.03
30 20 0.53
ACGTcount: A:0.24, C:0.40, G:0.07, T:0.29
Consensus pattern (29 bp):
TCATCATCAGAGTCATCTTCTCCTCACCC
Found at i:1021305 original size:34 final size:34
Alignment explanation
Indices: 1021262--1021336 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
1021252 AAAGGTGCAG
* *
1021262 ACAAAAAATCAGGTTATAGA-AGCTAGACCATAAT
1 ACAACAAATCAGATTATA-ATAGCTAGACCATAAT
* *
1021296 ACAACAAATCAGATTATAATAGCTAGATCATCAT
1 ACAACAAATCAGATTATAATAGCTAGACCATAAT
*
1021330 AGAACAA
1 ACAACAA
1021337 TAAGAATAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACAAATCAGATTATAATAGCTAGACCATAAT
Found at i:1023747 original size:15 final size:16
Alignment explanation
Indices: 1023726--1023761 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
1023716 GTTTTTATAA
1023726 ATAAATTTAAAAAAAT
1 ATAAATTTAAAAAAAT
1023742 -TAAA-TTAAAAAAAT
1 ATAAATTTAAAAAAAT
1023756 ATAAAT
1 ATAAAT
1023762 ATTATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATTTAAAAAAAT
Found at i:1027219 original size:97 final size:97
Alignment explanation
Indices: 1027053--1027228 Score: 307
Period size: 97 Copynumber: 1.8 Consensus size: 97
1027043 AGTGTAAACC
1027053 AGCATCACTGAATTCTCTAGCCGTGTCTTCTAAGCACTGCACATCGAGTTGAGACGTATTTGAAA
1 AGCATCACTGAATTCTCTAGCCGTGTCTTCTAAGCACTGCACATCGAGTTGAGACGTATTTGAAA
1027118 CACGACCAGCTTGATTATCCACCAACGAGTGT
66 CACGACCAGCTTGATTATCCACCAACGAGTGT
* * * * *
1027150 AGCATCACTGATTTCTCTAGCTGTGTCTTCTAAGCACTGCTCATCGGGTTGAGAGGTATTTGAAA
1 AGCATCACTGAATTCTCTAGCCGTGTCTTCTAAGCACTGCACATCGAGTTGAGACGTATTTGAAA
1027215 CACGACCAGCTTGA
66 CACGACCAGCTTGA
1027229 ATATTCACAC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 74 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (97 bp):
AGCATCACTGAATTCTCTAGCCGTGTCTTCTAAGCACTGCACATCGAGTTGAGACGTATTTGAAA
CACGACCAGCTTGATTATCCACCAACGAGTGT
Found at i:1027419 original size:53 final size:53
Alignment explanation
Indices: 1027339--1027445 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
1027329 AATGCATCCT
1027339 TATTAAACTGAACATGCCGCAATATATAAACCTTACCCTCATCATCAAGACAC
1 TATTAAACTGAACATGCCGCAATATATAAACCTTACCCTCATCATCAAGACAC
1027392 TATTAAACTGAACATGCCGCAATATATAAACCTTACCCTCATCATCAAGACAC
1 TATTAAACTGAACATGCCGCAATATATAAACCTTACCCTCATCATCAAGACAC
1027445 T
1 T
1027446 TGTAGCCGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.25
Consensus pattern (53 bp):
TATTAAACTGAACATGCCGCAATATATAAACCTTACCCTCATCATCAAGACAC
Found at i:1035592 original size:22 final size:23
Alignment explanation
Indices: 1035558--1035604 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
1035548 ATATGACGAG
1035558 TTGAATTTTTTTAATATATATTA
1 TTGAATTTTTTTAATATATATTA
1035581 TTGAA-TTTTTTAATATATATTA
1 TTGAATTTTTTTAATATATATTA
1035603 TT
1 TT
1035605 AAACGCATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TTGAATTTTTTTAATATATATTA
Found at i:1035969 original size:21 final size:20
Alignment explanation
Indices: 1035937--1035980 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1035927 CCAAAAATAT
* * *
1035937 TAAAAAATTAATGTTTTAGA
1 TAAAAAAATAATATTTTAAA
1035957 TAAAAATAATAATATTTTAAA
1 TAAAAA-AATAATATTTTAAA
1035978 TAA
1 TAA
1035981 TTTTTACCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
TAAAAAAATAATATTTTAAA
Found at i:1045109 original size:30 final size:30
Alignment explanation
Indices: 1045069--1045135 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1045059 AATGATGATA
*
1045069 ATAATTTTTGATAAACTTAATGATTGATTT
1 ATAATATTTGATAAACTTAATGATTGATTT
* * *
1045099 ATAATATTTGATAAATTTAATTATTGTTTT
1 ATAATATTTGATAAACTTAATGATTGATTT
1045129 ATAATAT
1 ATAATAT
1045136 CGTGACAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.52
Consensus pattern (30 bp):
ATAATATTTGATAAACTTAATGATTGATTT
Found at i:1045614 original size:22 final size:22
Alignment explanation
Indices: 1045589--1045649 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
1045579 TAGTTTAGAC
*
1045589 ACTTACTTTTATATTAATCCTT
1 ACTTATTTTTATATTAATCCTT
*
1045611 ACTTATTTTTATATTCATCCTT
1 ACTTATTTTTATATTAATCCTT
1045633 ACTT-TTTTTAATATTAA
1 ACTTATTTTT-ATATTAA
1045650 ACCGATAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 5 0.14
22 30 0.86
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (22 bp):
ACTTATTTTTATATTAATCCTT
Found at i:1046552 original size:4 final size:4
Alignment explanation
Indices: 1046543--1046568 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1046533 TTTTATTCAA
1046543 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1046569 TTGAAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1048151 original size:34 final size:34
Alignment explanation
Indices: 1048039--1048153 Score: 99
Period size: 34 Copynumber: 3.4 Consensus size: 34
1048029 TGTGTGAATT
*
1048039 ATTTAATTTATTTATTTAACTTTTTCTTTATATG
1 ATTTAATTTATTTATTTAACTTTTTCTTTATAGG
* * ** ** * *
1048073 ATTTTATTT-TTATCATATAACGATTAGTTT-TTGCT
1 ATTTAATTTATT-T-ATTTAACTTTTTCTTTATAG-G
1048108 ATTTAATTTATTTATTTAACTTTTTCTTTATAGG
1 ATTTAATTTATTTATTTAACTTTTTCTTTATAGG
*
1048142 ATTTTATTTATT
1 ATTTAATTTATT
1048154 ATCAGTACTT
Statistics
Matches: 58, Mismatches: 18, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
33 2 0.03
34 32 0.55
35 22 0.38
36 2 0.03
ACGTcount: A:0.26, C:0.06, G:0.05, T:0.63
Consensus pattern (34 bp):
ATTTAATTTATTTATTTAACTTTTTCTTTATAGG
Found at i:1049134 original size:3 final size:3
Alignment explanation
Indices: 1049128--1049178 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
1049118 TATTATTATT
1049128 ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1049175 ATA A
1 ATA A
1049179 ATACTAACTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1053603 original size:21 final size:21
Alignment explanation
Indices: 1053577--1053617 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1053567 ACATAATAGG
1053577 GGGTATCTGTACCCCTTCATA
1 GGGTATCTGTACCCCTTCATA
*
1053598 GGGTATCTGTACTCCTTCAT
1 GGGTATCTGTACCCCTTCAT
1053618 TCAATTCAAA
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:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (21 bp):
GGGTATCTGTACCCCTTCATA
Found at i:1062367 original size:35 final size:35
Alignment explanation
Indices: 1062328--1062399 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1062318 TCTCCTGAAT
1062328 TGTGCTTGAGCACTATCATTATGGAACATTCTTTC
1 TGTGCTTGAGCACTATCATTATGGAACATTCTTTC
1062363 TGTGCTTGAGCACTATCATTATGGAACATTCTTTC
1 TGTGCTTGAGCACTATCATTATGGAACATTCTTTC
1062398 TG
1 TG
1062400 CCATGGCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (35 bp):
TGTGCTTGAGCACTATCATTATGGAACATTCTTTC
Found at i:1063369 original size:21 final size:21
Alignment explanation
Indices: 1063325--1063369 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1063315 GATTTCTGGG
* * *
1063325 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1063346 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1063367 CAA
1 CAA
1063370 ACGAACATGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1063442 original size:23 final size:22
Alignment explanation
Indices: 1063398--1063442 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1063388 AATGCCAGAG
*
1063398 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1063420 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1063443 AAATTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1065161 original size:21 final size:21
Alignment explanation
Indices: 1065132--1065177 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1065122 GATTTCTGGG
* *
1065132 CAAGAGGAATCGGTACCCATT
1 CAAGAGGAACCGATACCCATT
* *
1065153 CAAGGGGAACCGATACCCCTT
1 CAAGAGGAACCGATACCCATT
1065174 CAAG
1 CAAG
1065178 CGAATAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (21 bp):
CAAGAGGAACCGATACCCATT
Found at i:1065248 original size:23 final size:22
Alignment explanation
Indices: 1065204--1065248 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1065194 AAGGTCATGG
*
1065204 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1065226 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1065249 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1066648 original size:31 final size:31
Alignment explanation
Indices: 1066549--1066674 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 31
1066539 AGAGTCGAGG
*
1066549 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
**
1066580 GTTTTACCTATGTT-T-TCGAGACATAT-GACA
1 G-TTTACCTATGTTCTAAGGA-ACATATGGACA
* *
1066610 GTATACCTATGTTCTAAGGAATATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* ** * *
1066641 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
1066672 GTT
1 GTT
1066675 ACCGAGGATC
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
29 11 0.14
30 13 0.17
31 41 0.53
32 12 0.16
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:1066694 original size:30 final size:30
Alignment explanation
Indices: 1066633--1066729 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
1066623 CTAAGGAATA
* * ***
1066633 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
1066664 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
1066694 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
1066724 TCTGGA
1 TATGGA
1066730 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:1066730 original size:30 final size:30
Alignment explanation
Indices: 1066660--1066732 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1066650 GGTTCTTCGG
* *
1066660 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1066690 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1066720 GACCTCTGGATAG
1 GACCTCTGGATAG
1066733 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1070181 original size:21 final size:21
Alignment explanation
Indices: 1070155--1070200 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1070145 GATTTCTGGG
* *
1070155 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1070176 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1070197 CAAG
1 CAAG
1070201 CGAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1070271 original size:23 final size:22
Alignment explanation
Indices: 1070227--1070271 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1070217 AAGGTCATGG
*
1070227 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1070249 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1070272 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1071658 original size:29 final size:30
Alignment explanation
Indices: 1071560--1071685 Score: 139
Period size: 32 Copynumber: 4.1 Consensus size: 30
1071550 AGAGTCGAGG
1071560 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGG-ACATATGGACA
*
1071591 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTC-TACG-GACATATGGACA
* *
1071623 GTATACCTATGTTCTAAGGA-ATATGGACA
1 GTTTACCTATGTTCTACGGACATATGGACA
* * *
1071652 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTAC-GGACATATGGACA
1071683 GTT
1 GTT
1071686 ACCGAGGATC
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
29 22 0.28
30 5 0.06
31 25 0.31
32 27 0.34
33 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (30 bp):
GTTTACCTATGTTCTACGGACATATGGACA
Found at i:1071679 original size:60 final size:62
Alignment explanation
Indices: 1071562--1071688 Score: 172
Period size: 60 Copynumber: 2.1 Consensus size: 62
1071552 AGTCGAGGGT
* *
1071562 TTACCTATGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTCGAGACATATGGACAG
* *
1071624 TATACCTATGTTCTAAGG-A-ATATGGACAG-TTTACCTAGGT-TCTTCGGGACCTATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCT-TTCGAGACATATGGACAG
1071684 TTACC
1 TTACC
1071689 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
59 5 0.08
60 27 0.46
61 10 0.17
62 2 0.03
63 15 0.25
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (62 bp):
TTACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTCGAGACATATGGACAG
Found at i:1071705 original size:30 final size:30
Alignment explanation
Indices: 1071644--1071740 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
1071634 TTCTAAGGAA
* * ***
1071644 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
1071675 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
1071705 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
1071735 TCTGGA
1 TATGGA
1071741 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:1071741 original size:30 final size:30
Alignment explanation
Indices: 1071671--1071743 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1071661 GGTTCTTCGG
* *
1071671 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1071701 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1071731 GACCTCTGGATAG
1 GACCTCTGGATAG
1071744 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1073290 original size:103 final size:103
Alignment explanation
Indices: 1073065--1073282 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1073055 GTCGAGGGTC
*
1073065 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1073130 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1073168 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1073233 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1073271 TATGTGGTCCTT
1 TATGTGGTCCTT
1073283 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1073329 original size:23 final size:23
Alignment explanation
Indices: 1073299--1073381 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
1073289 ATTATTATAT
1073299 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
1073322 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
** * *
1073345 GGCACTACGGTTTAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
1073368 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
1073382 TTTATATGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1076715 original size:23 final size:22
Alignment explanation
Indices: 1076671--1076715 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1076661 AATGCCAGAG
*
1076671 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1076693 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1076716 AAATTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1077049 original size:18 final size:17
Alignment explanation
Indices: 1077022--1077056 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1077012 TAACTATATG
1077022 TGATTATATGTATTACAT
1 TGATTATATGTA-TACAT
*
1077040 TGATTGTATGTATACAT
1 TGATTATATGTATACAT
1077057 GACTAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (17 bp):
TGATTATATGTATACAT
Found at i:1078593 original size:23 final size:23
Alignment explanation
Indices: 1078511--1078585 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
1078501 ATTATTATAT
*
1078511 GGCACTACGATGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
1078534 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1078557 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
1078580 GGCACT
1 GGCACT
1078586 TCAGTGCATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1078601 original size:23 final size:23
Alignment explanation
Indices: 1078501--1078601 Score: 69
Period size: 23 Copynumber: 4.3 Consensus size: 23
1078491 CCTTATGAAC
*
1078501 ATTATTATATGGCACTAC-GATGCA
1 ATTA-TATGTGGCACTACAG-TGCA
* * * *
1078525 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACAGTGCA
* * * *
1078548 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACAGTGCA
* *
1078571 ATTCTATGTGGCACTTCAGTGCA
1 ATTATATGTGGCACTACAGTGCA
*
1078594 TTTATATG
1 ATTATATG
1078602 AGCTGTGGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
23 62 0.94
24 4 0.06
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACAGTGCA
Done.