Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_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: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 15
Found at i:375906 original size:47 final size:49
Alignment explanation
Indices: 375818--375921 Score: 140
Period size: 47 Copynumber: 2.2 Consensus size: 49
375808 ACCAAAAAGG
* *
375818 GAGAAAAAAAGAAGGAAAAGTCGAACCAGAAAAGGGAGAGAAAATAAAA
1 GAGAAAAAAAGAAGGAAAAATCGAACCAGAAAAAGGAGAGAAAATAAAA
* * * *
375867 TAGAAAAAAAGAAGTAAAAATTGAA-CA-AAAAAGGAGAGAAAATACAA
1 GAGAAAAAAAGAAGGAAAAATCGAACCAGAAAAAGGAGAGAAAATAAAA
375914 GAGAAAAA
1 GAGAAAAA
375922 GAAAAGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 25 0.52
48 2 0.04
49 21 0.44
ACGTcount: A:0.66, C:0.05, G:0.22, T:0.07
Consensus pattern (49 bp):
GAGAAAAAAAGAAGGAAAAATCGAACCAGAAAAAGGAGAGAAAATAAAA
Found at i:376766 original size:14 final size:15
Alignment explanation
Indices: 376747--376784 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
376737 CTTATATTAA
376747 ATATTTATATG-TGT
1 ATATTTATATGCTGT
*
376761 ATATTTATGTGTCTGT
1 ATATTTATATG-CTGT
376777 ATATTTAT
1 ATATTTAT
376785 TTTTTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
16 11 0.52
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (15 bp):
ATATTTATATGCTGT
Found at i:379807 original size:12 final size:12
Alignment explanation
Indices: 379792--379857 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
379782 GTTATTTAAA
379792 CGGGTATTGGGC
1 CGGGTATTGGGC
*
379804 CGGGTATTGGGT
1 CGGGTATTGGGC
* *
379816 CGGCTATTGGGT
1 CGGGTATTGGGC
379828 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
379839 CGGGAATCGGGC
1 CGGGTATTGGGC
379851 CGGGTAT
1 CGGGTAT
379858 ATATATATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
11 9 0.20
12 37 0.80
ACGTcount: A:0.11, C:0.17, G:0.47, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:382544 original size:189 final size:192
Alignment explanation
Indices: 382189--382565 Score: 557
Period size: 189 Copynumber: 2.0 Consensus size: 192
382179 GCTTCTTTAA
* * *
382189 TCCTCTTATTGGTCATTGGATGAGATGAGCTTTAGCAATTCAATGGAGTATTTAGAATCATGTTC
1 TCCTCTTATTGGTCATTGAATCAGATGAGCTTTAGCAATTCAATGGAGCATTTAGAA-CATGTTC
* * *
382254 TGTAGCATCATGTTATCCTTGTGTGCGACTTGCTGATATCTCATCTTTTCAAATTAAGAGTTTCT
65 TGTAGCATCATGTTATCCTTGTGTGCAACTTGCTAATATCTCATCTTTCCAAATTAAGAGTTTCT
382319 CAAAATTTTATGTTTAAAACAATGCATAACATTTAAGTAATTGATGTCGAAGAATATCTTTGC
130 CAAAATTTTATGTTTAAAACAATGCATAACATTTAAGTAATTGATGTCGAAGAATATCTTTGC
* *
382382 TCCTCTTATTGGTCATTGAATCAGATGAGCTTTAGCAATTCAGTGGAGCATTTGGAA-A-GTTCT
1 TCCTCTTATTGGTCATTGAATCAGATGAGCTTTAGCAATTCAATGGAGCATTTAGAACATGTTCT
* * *
382445 GTAGCATTATGTTATCCTTGTGTGCAACTTGCTAATCTGTCATC-TTCCAAATTAATG-GTTTCT
66 GTAGCATCATGTTATCCTTGTGTGCAACTTGCTAATATCTCATCTTTCCAAATTAA-GAGTTTCT
* * * *
382508 CAACAA-TTTATGTTTAAAACAATGCATCATATTTAAGTAATTGATGTTGAAGGATATC
130 CAA-AATTTTATGTTTAAAACAATGCATAACATTTAAGTAATTGATGTCGAAGAATATC
382566 ATATATTATT
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
189 67 0.40
190 47 0.28
191 1 0.01
193 52 0.31
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (192 bp):
TCCTCTTATTGGTCATTGAATCAGATGAGCTTTAGCAATTCAATGGAGCATTTAGAACATGTTCT
GTAGCATCATGTTATCCTTGTGTGCAACTTGCTAATATCTCATCTTTCCAAATTAAGAGTTTCTC
AAAATTTTATGTTTAAAACAATGCATAACATTTAAGTAATTGATGTCGAAGAATATCTTTGC
Found at i:383565 original size:42 final size:36
Alignment explanation
Indices: 383499--383614 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 36
383489 TGACATATGA
* * *
383499 TGCACAAAGACCAAAGGGATTAAATTCACCTAGATCAGTC
1 TGCACAGAGACCAAGGGGAATAAATTCACCT--AT-A-TC
383539 GGTGCACAGAGACCAAGGGGAATAAATTCACCTATATC
1 --TGCACAGAGACCAAGGGGAATAAATTCACCTATATC
* * **
383577 TGAACAGAGACCAAGGGGAATAAACTCATTTATATC
1 TGCACAGAGACCAAGGGGAATAAATTCACCTATATC
383613 TG
1 TG
383615 AACGCCGTGT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
36 34 0.51
38 2 0.03
39 1 0.01
40 2 0.03
42 28 0.42
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (36 bp):
TGCACAGAGACCAAGGGGAATAAATTCACCTATATC
Found at i:383591 original size:36 final size:36
Alignment explanation
Indices: 383544--383617 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
383534 CAGTCGGTGC
*
383544 ACAGAGACCAAGGGGAATAAATTCACCTATATCTGA
1 ACAGAGACCAAGGGGAATAAACTCACCTATATCTGA
**
383580 ACAGAGACCAAGGGGAATAAACTCATTTATATCTGA
1 ACAGAGACCAAGGGGAATAAACTCACCTATATCTGA
383616 AC
1 AC
383618 GCCGTGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (36 bp):
ACAGAGACCAAGGGGAATAAACTCACCTATATCTGA
Found at i:393035 original size:32 final size:32
Alignment explanation
Indices: 392999--393084 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
392989 ATGACACTTC
*
392999 TGTGCATTATATAAATGCAACA-TCGACTCTAT
1 TGTGCATTATATGAATGCAACACT-GACTCTAT
* * * * *
393031 TGTGCATTATCTGAACGCATCACTGACTTTGT
1 TGTGCATTATATGAATGCAACACTGACTCTAT
*
393063 TGTGCATTATTTGAATGCAACA
1 TGTGCATTATATGAATGCAACA
393085 GTAACAATAC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTGCATTATATGAATGCAACACTGACTCTAT
Found at i:394287 original size:20 final size:21
Alignment explanation
Indices: 394262--394302 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
394252 TTGTGCCCCA
*
394262 ATTCATCC-AGTATTGATACT
1 ATTCATCCTAGTATCGATACT
394282 ATTCATCCTAGTATCGATACT
1 ATTCATCCTAGTATCGATACT
394303 CGAGCTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
ATTCATCCTAGTATCGATACT
Found at i:401852 original size:23 final size:23
Alignment explanation
Indices: 401826--401871 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
401816 CATTATTATA
*
401826 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGCATTTATACG
*
401849 TGGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCATTTATACG
401872 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTATACG
Found at i:402157 original size:21 final size:21
Alignment explanation
Indices: 402111--402157 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
402101 TAAATAATGT
*
402111 GATGATAATGATAATAATATA
1 GATGATAATGATAAGAATATA
* *
402132 TATGATAATGTTAAGAA-AGTA
1 GATGATAATGATAAGAATA-TA
402153 GATGA
1 GATGA
402158 CGATATATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (21 bp):
GATGATAATGATAAGAATATA
Found at i:404220 original size:16 final size:16
Alignment explanation
Indices: 404199--404229 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
404189 TACACCTATG
*
404199 AGTGTATCTATACACT
1 AGTGTATCGATACACT
404215 AGTGTATCGATACAC
1 AGTGTATCGATACAC
404230 CCTGCAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (16 bp):
AGTGTATCGATACACT
Found at i:406355 original size:18 final size:18
Alignment explanation
Indices: 406332--406388 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
406322 TATATTTTCC
406332 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
*
406350 AACAATTGATATCCTTTTGTT
1 AACAATTGGTAT-C-TTT-TT
406371 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
406389 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 4 0.12
21 13 0.38
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (18 bp):
AACAATTGGTATCTTTTT
Found at i:406374 original size:21 final size:20
Alignment explanation
Indices: 406332--406388 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
406322 TATATTTTCC
406332 AACAATTGGTAT-C-TTTTT
1 AACAATTGGTATCCTTTTTT
*
406350 AACAATTGATATCCTTTTGTT
1 AACAATTGGTATCCTTTT-TT
406371 AACAATTGGTAT-CTTTTT
1 AACAATTGGTATCCTTTTT
406389 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 11 0.32
19 2 0.06
20 8 0.24
21 13 0.38
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (20 bp):
AACAATTGGTATCCTTTTTT
Found at i:406714 original size:19 final size:18
Alignment explanation
Indices: 406690--406759 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 18
406680 GAATGGAAAT
*
406690 AGTGTAACGATACACTATG
1 AGTGTATCGATACACT-TG
*
406709 AGTGTATCTATACAC-T-
1 AGTGTATCGATACACTTG
406725 AGTGTATCGATACACTCTG
1 AGTGTATCGATACACT-TG
*
406744 CAGTGTATCCATACAC
1 -AGTGTATCGATACAC
406760 CATGGCTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
16 14 0.33
17 1 0.02
18 1 0.02
19 13 0.30
20 14 0.33
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (18 bp):
AGTGTATCGATACACTTG
Found at i:406736 original size:35 final size:36
Alignment explanation
Indices: 406689--406759 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
406679 CGAATGGAAA
*
406689 TAGTGTAACGATACACTATG-AGTGTATCTATACAC
1 TAGTGTAACGATACACTATGCAGTGTATCCATACAC
* *
406724 TAGTGTATCGATACACTCTGCAGTGTATCCATACAC
1 TAGTGTAACGATACACTATGCAGTGTATCCATACAC
406760 CATGGCTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 18 0.56
36 14 0.44
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (36 bp):
TAGTGTAACGATACACTATGCAGTGTATCCATACAC
Found at i:406750 original size:20 final size:19
Alignment explanation
Indices: 406690--406759 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
406680 GAATGGAAAT
* *
406690 AGTGTAACGATACACTATG
1 AGTGTATCGATACACTCTG
*
406709 AGTGTATCTATACA--CT-
1 AGTGTATCGATACACTCTG
406725 AGTGTATCGATACACTCTG
1 AGTGTATCGATACACTCTG
*
406744 CAGTGTATCCATACAC
1 -AGTGTATCGATACAC
406760 CATGGCTGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
16 13 0.31
17 1 0.02
18 2 0.05
19 12 0.29
20 14 0.33
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (19 bp):
AGTGTATCGATACACTCTG
Found at i:407150 original size:34 final size:34
Alignment explanation
Indices: 407111--407183 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
407101 TTTTGTAAAG
* *
407111 GGGAAAGATTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGATTCTAGCTAAGCCCGTGAAAAAACTA
* * * *
407145 GGGAAAGGTTCTAGTTTATCCCGTGAAAAAACTA
1 GGGAAAGATTCTAGCTAAGCCCGTGAAAAAACTA
407179 GGGAA
1 GGGAA
407184 TTGTAAAGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (34 bp):
GGGAAAGATTCTAGCTAAGCCCGTGAAAAAACTA
Found at i:411009 original size:20 final size:20
Alignment explanation
Indices: 410984--411022 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
410974 AGTCGTTAAG
410984 GCCTATGGTATCGATACTAT
1 GCCTATGGTATCGATACTAT
411004 GCCTATGGTATCGATACTA
1 GCCTATGGTATCGATACTA
411023 CTATACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
GCCTATGGTATCGATACTAT
Found at i:417937 original size:26 final size:26
Alignment explanation
Indices: 417887--417937 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
417877 AGGTACAATA
* * *
417887 CCCTTTGTTGTGAAGTTGTGGATGAC
1 CCCTTCGTTGTGAAGTTGAGCATGAC
417913 CCCTTCGTTGTGAAGTTGAGCATGA
1 CCCTTCGTTGTGAAGTTGAGCATGA
417938 GAATTATATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (26 bp):
CCCTTCGTTGTGAAGTTGAGCATGAC
Found at i:418249 original size:102 final size:106
Alignment explanation
Indices: 417991--418522 Score: 714
Period size: 106 Copynumber: 5.0 Consensus size: 106
417981 ACTGTTCTGA
* ** *
417991 TCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAACCA
1 TCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCA
418056 GTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
66 GTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
* * * *
418097 TCCAATATACTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGCTTGTTAACAACCA
1 TCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCA
418162 GTCGTCCCTTCGTTGTGAAGTTGAAC-T-TG-T-TCTCGAG
66 GTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
* * *
418199 TCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
1 TCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCA
* **
418264 GTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAG
66 GTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
* * * * *
418305 TCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTAAAATTAGGAAGTTGTTTTGTTGACAACC
1 TCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGACAACC
*
418370 AGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAG
65 AGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
* * * *
418412 TCCAATATCCTTCGATGTGAAGTTAAAATTGGCTCTGAATGAAACT-GAAAAGTGGTTTATTGAC
1 TCCAATATCCTTCGATGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAA-TTGTTTGTTGAC
** * * *
418476 AACCAACCGTCCCTTCATCGTGAAGTTGAACTTGTGTTATCTCGAG
61 AACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
418522 T
1 T
418523 GGCGCGATAT
Statistics
Matches: 379, Mismatches: 37, Indels: 16
0.88 0.09 0.04
Matches are distributed among these distances:
102 92 0.24
103 2 0.01
104 4 0.01
105 2 0.01
106 134 0.35
107 86 0.23
110 52 0.14
111 7 0.02
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (106 bp):
TCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCA
GTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
Found at i:429713 original size:2 final size:2
Alignment explanation
Indices: 429706--429736 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
429696 ATTGGTAGTG
429706 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
429737 ATGAAATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:429953 original size:12 final size:12
Alignment explanation
Indices: 429920--429954 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
429910 ATAGAAATAA
*
429920 AATAAAAAAAAT
1 AATAAATAAAAT
429932 AATCAAATAAAAT
1 AAT-AAATAAAAT
429945 AATAAATAAA
1 AATAAATAAA
429955 GGGTTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:437100 original size:17 final size:17
Alignment explanation
Indices: 437080--437116 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
437070 TTTTAATTTT
* *
437080 TTATTAAATGTGTTTAA
1 TTATTAAATATGATTAA
437097 TTATTAAATATGATTAA
1 TTATTAAATATGATTAA
437114 TTA
1 TTA
437117 AAAATATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
TTATTAAATATGATTAA
Found at i:437709 original size:14 final size:15
Alignment explanation
Indices: 437687--437715 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
437677 TTTAATTAGA
437687 AATAGATAATAATAT
1 AATAGATAATAATAT
437702 AATA-ATAATAATAT
1 AATAGATAATAATAT
437716 TTCTTCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AATAGATAATAATAT
Found at i:443919 original size:32 final size:31
Alignment explanation
Indices: 443879--443957 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
443869 TTATCACTCC
443879 TGTACATTATATGAATAAAACACTGACTCTGT
1 TGTACATTATATGAATAAAACACTGACT-TGT
* * * **
443911 TGTGCATTATCTAAATGCAACACTGACTTGT
1 TGTACATTATATGAATAAAACACTGACTTGT
*
443942 TGTACATTATTTGAAT
1 TGTACATTATATGAAT
443958 GTAACATTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 16 0.41
32 23 0.59
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (31 bp):
TGTACATTATATGAATAAAACACTGACTTGT
Found at i:444500 original size:12 final size:12
Alignment explanation
Indices: 444483--444516 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
444473 TTTACTATTC
444483 ACTGCTACAGTA
1 ACTGCTACAGTA
444495 ACTGCTACAGTA
1 ACTGCTACAGTA
444507 A--GCTACAGTA
1 ACTGCTACAGTA
444517 CTTCCGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:452344 original size:23 final size:22
Alignment explanation
Indices: 452288--452346 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
452278 GTCATAACCA
452288 TATTTTGAAAAATAATTAAATAT
1 TATTTT-AAAAATAATTAAATAT
* *
452311 TATTTAAAAAAATAATTATGACT-T
1 TATTT-TAAAAATAATTA--AATAT
452335 TATTTTAAAAAT
1 TATTTTAAAAAT
452347 TTTGTCGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 22 0.73
24 6 0.20
25 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (22 bp):
TATTTTAAAAATAATTAAATAT
Found at i:455257 original size:131 final size:131
Alignment explanation
Indices: 454897--455236 Score: 421
Period size: 131 Copynumber: 2.6 Consensus size: 131
454887 GTTATGGTAG
* * * *
454897 TCTAAGGGTGACACAACTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACTA
1 TCTAGGGGTGACACAGCTCCTACGTGATGAGGAGGTCTAGTCGGTGGATGACACGGTTCCTAC--
* * *
454962 GAGATGAGGATGACAGGCCATTTTTAGGGAGGGTGATAACACGGTTCCTACACGATGAGGACGGC
64 GAGATGAGGATGACAGGCCATCTTTAGGGA---TGATAACACGATTCCTACACGATGAGGACGAC
455027 TGGTTA
126 TGGTTA
* * * * *
455033 TCTAGAGGTGACACTGCTCCTACATGATGAGGAAGTCTAGTCGGTGGATGACACGGTTCTTAC-A
1 TCTAGGGGTGACACAGCTCCTACGTGATGAGGAGGTCTAGTCGGTGGATGACACGGTTCCTACGA
* ***
455097 TGATGAGGATGACAGGCCATCTTTAGGGATGGTAACACGATTCCTATGTGATGAGGACGACTGGT
66 -GATGAGGATGACAGGCCATCTTTAGGGATGATAACACGATTCCTACACGATGAGGACGACTGGT
455162 TA
130 TA
* * * * * *
455164 TCTAGGGGTGACACGGCTTCTATGTGATGAGGAGGTCTAGTCGGGGGATGATACGGTTCCTACGC
1 TCTAGGGGTGACACAGCTCCTACGTGATGAGGAGGTCTAGTCGGTGGATGACACGGTTCCTACGA
455229 GATGAGGA
66 GATGAGGA
455237 CGGATGTCCA
Statistics
Matches: 176, Mismatches: 26, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
131 94 0.53
133 1 0.01
134 27 0.15
136 54 0.31
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.25
Consensus pattern (131 bp):
TCTAGGGGTGACACAGCTCCTACGTGATGAGGAGGTCTAGTCGGTGGATGACACGGTTCCTACGA
GATGAGGATGACAGGCCATCTTTAGGGATGATAACACGATTCCTACACGATGAGGACGACTGGTT
A
Found at i:455530 original size:70 final size:67
Alignment explanation
Indices: 455261--455584 Score: 377
Period size: 66 Copynumber: 4.8 Consensus size: 67
455251 TAGGGATTTA
* * * * *
455261 TTTCAAGAGAAATTGTCTCAAGGGAGAAAAAACTTTGTTTCAAGGGAAATAGACTTAAAGATTTT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
455326 TG
66 TG
* * * *
455328 TTTCAAGGGAAA-CGTGTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGACTTT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
455392 TG
66 TG
* * *
455394 TTTCAAAAGAAATTGTCTCAAGAGTGACACAAA--TTGTTTCAAGGCAAACAAACTCAAAGATCT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACA-AAACTTTGTTTCAAGGGAAACAAACTCAAAGA--T
455457 TTTTACG
63 TTTT--G
* *
455464 TTTCAAGATAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATTTT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA---T
455529 TTTTG
63 TTTTG
* * * * *
455534 TTTCAAGAGAAACTGTCCCAAGGGAGACACAAC-TTGTTTCAAGAGAAACAA
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAA
455585 TCTCCAAGTT
Statistics
Matches: 219, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
66 82 0.37
67 24 0.11
68 7 0.03
69 19 0.09
70 56 0.26
71 25 0.11
72 6 0.03
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (67 bp):
TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
TG
Found at i:465236 original size:207 final size:206
Alignment explanation
Indices: 464881--465292 Score: 752
Period size: 207 Copynumber: 2.0 Consensus size: 206
464871 CTCAGCCTCT
464881 TCTACAACCTTTTGCAACGAAGTCTTGATTTGACCCCTTAACAAAGCCTCGCCACAACCAGGAGT
1 TCTACAACCTTTTGCAACGAAGTCTTGATTTGACCCCTTAACAAAGCCTCGCCACAACCAGGAGT
*
464946 CACCATCATGTTCTTGACTCCATTACCCCTCTGCTTGCCTACACCAGATGATGGCATCTCCATCG
66 CACCATCATGTTCTTGACTCCATTACCCCTCTGCTTACCTACACCAGATGATGGCATCTCCATCG
465011 CAACCCCAAAAATGGGTGAAAGAATCATTTGTTAATTCATTAAAAGCAGACCTTTCTTGAATATG
131 CAACCCCAAAAATGGGTG-AAGAATCATTTGTTAATTCATTAAAAGCAGACCTTTCTTGAATATG
465076 ATTCCCATTTCC
195 ATTCCCATTTCC
*
465088 TCTACAATCTTTTGCAACGAAGTCTTGATTTGACCCCTTAACAAAGCCTCGCCACAACCAGGAGT
1 TCTACAACCTTTTGCAACGAAGTCTTGATTTGACCCCTTAACAAAGCCTCGCCACAACCAGGAGT
*
465153 CACCATCATGTTCTTGACTCCATTACCCCTCTGCTTACCTACACCAGATGATGGCGTCTCCATCG
66 CACCATCATGTTCTTGACTCCATTACCCCTCTGCTTACCTACACCAGATGATGGCATCTCCATCG
* * * *
465218 CAACCCCGAAAATGGGTGAAGAATCATTTGTTAATTCATTAAAAGCAGACTTTTCTTGAATCTGT
131 CAACCCCAAAAATGGGTGAAGAATCATTTGTTAATTCATTAAAAGCAGACCTTTCTTGAATATGA
465283 TTCCCATTTC
196 TTCCCATTTC
465293 TTGTTCTTGT
Statistics
Matches: 198, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
206 54 0.27
207 144 0.73
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (206 bp):
TCTACAACCTTTTGCAACGAAGTCTTGATTTGACCCCTTAACAAAGCCTCGCCACAACCAGGAGT
CACCATCATGTTCTTGACTCCATTACCCCTCTGCTTACCTACACCAGATGATGGCATCTCCATCG
CAACCCCAAAAATGGGTGAAGAATCATTTGTTAATTCATTAAAAGCAGACCTTTCTTGAATATGA
TTCCCATTTCC
Found at i:468609 original size:24 final size:25
Alignment explanation
Indices: 468565--468639 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
468555 TTATGTCAAT
**
468565 ATTATTATTAAAAT-ATTATATCTATA
1 ATTATTA-TAAAATAAAAATAT-TATA
468591 ATT-TTAT-AAATAAAAATATTA-A
1 ATTATTATAAAATAAAAATATTATA
*
468613 TATTATTATAAAATAAAATTATTATA
1 -ATTATTATAAAATAAAAATATTATA
468639 A
1 A
468640 ATTACATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
22 1 0.02
23 9 0.22
24 10 0.24
25 17 0.41
26 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTATTATAAAATAAAAATATTATA
Found at i:468679 original size:42 final size:41
Alignment explanation
Indices: 468608--468762 Score: 137
Period size: 42 Copynumber: 3.9 Consensus size: 41
468598 AAATAAAAAT
*
468608 ATTAA-TA-TTATTATAA-AATAA-AAT-TATTATAAATTA
1 ATTAATTATTTATTAAAATAATAATAATATATTATAAATTA
* * *
468644 CATTAATTATTTATTAAAATAAGAATAATAAATTATTAATTA
1 -ATTAATTATTTATTAAAATAATAATAATATATTATAAATTA
* * *
468686 TATTAATTAGTTATTAAATTAATAAT-AT-TATTAAAATATTA
1 -ATTAATTATTTATTAAAATAATAATAATATATTATAA-ATTA
* *
468727 A-AAATTATTATATTAAAATAATAATATTATATTATA
1 ATTAATTATT-TATTAAAATAATAATAATATATTATA
468763 TTTTAAGAAA
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
37 5 0.05
38 2 0.02
39 14 0.15
40 24 0.26
41 10 0.11
42 38 0.41
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (41 bp):
ATTAATTATTTATTAAAATAATAATAATATATTATAAATTA
Found at i:468725 original size:11 final size:12
Alignment explanation
Indices: 468512--468726 Score: 67
Period size: 11 Copynumber: 17.9 Consensus size: 12
468502 AACAAAATAA
* *
468512 TAATATTATTTT
1 TAATAATATTAT
468524 TAA-AATATTA-
1 TAATAATATTAT
*
468534 GAATAAT-TTATT
1 TAATAATATTA-T
*
468546 TAATATTATTTAT
1 TAATAATA-TTAT
*
468559 GTCAATATTATTAT
1 -T-AATAATATTAT
468573 TAA-AATATTAT
1 TAATAATATTAT
* *
468584 ATCTATAATTTTAT
1 -T-AATAATATTAT
* * *
468598 AAATAAAAATAT
1 TAATAATATTAT
*
468610 TAATATTATTAT
1 TAATAATATTAT
* *
468622 AAAATAAAATTAT
1 -TAATAATATTAT
468635 T-ATAA-ATTACAT
1 TAATAATATT--AT
*
468647 TAATTAT-TTAT
1 TAATAATATTAT
** *
468658 TAA-AATAAGAA
1 TAATAATATTAT
468669 TAATAA-ATTAT
1 TAATAATATTAT
*
468680 TAATTATATTAAT
1 TAATAATATT-AT
*
468693 TAGT--TATTAAAT
1 TAATAATATT--AT
468705 TAATAATATTAT
1 TAATAATATTAT
468717 TAA-AATATTA
1 TAATAATATTA
468727 AAAATTATTA
Statistics
Matches: 149, Mismatches: 32, Indels: 45
0.66 0.14 0.20
Matches are distributed among these distances:
10 10 0.07
11 46 0.31
12 45 0.30
13 22 0.15
14 19 0.13
15 7 0.05
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:468753 original size:14 final size:14
Alignment explanation
Indices: 468697--468755 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
468687 ATTAATTAGT
*
468697 TATTAAATTAATAA
1 TATTAAAATAATAA
*
468711 TATT--ATTAA-AA
1 TATTAAAATAATAA
* *
468722 TATTAAAAATTATTA
1 TATT-AAAATAATAA
468737 TATTAAAATAATAA
1 TATTAAAATAATAA
468751 TATTA
1 TATTA
468756 TATTATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 6 0.17
12 5 0.14
14 20 0.56
15 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTAAAATAATAA
Found at i:468892 original size:23 final size:21
Alignment explanation
Indices: 468850--468897 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
468840 TTAATAATTT
*
468850 ATTATATATTGTTAAAATAAA
1 ATTATATATTATTAAAATAAA
*
468871 ATTATATATTA-TAATAATATA
1 ATTATATATTATTAA-AATAAA
468892 ATTATA
1 ATTATA
468898 ACAATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTATATATTATTAAAATAAA
Found at i:472337 original size:21 final size:21
Alignment explanation
Indices: 472309--472360 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
472299 GGATGAACTA
* *
472309 TATCGATATTGATGTAATTAG
1 TATCGATACTGATGCAATTAG
*
472330 TATTGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
472351 TATCGATACT
1 TATCGATACT
472361 AAGAGAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
TATCGATACTGATGCAATTAG
Found at i:472883 original size:54 final size:54
Alignment explanation
Indices: 472795--473358 Score: 783
Period size: 54 Copynumber: 10.4 Consensus size: 54
472785 CTATGTATAA
* * * * *
472795 TATCGACACTAAGTGTGCAACCCACGGAACTCATAATATGTTTATGAATGATCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* *
472849 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATATGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
*
472903 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * *
472957 TATCAGC-CTTAAGTGTGCAACCTACGGAATTCATAATATGTTTATGAACGACTG
1 TATCGGCAC-TAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
473011 TATCGACACTAAGTGTGCAACCCGC-GAAATTCATAATATGTTTATGAACGGCCG
1 TATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATATGTTTATGAACGACCG
* * * *
473065 TATTC-ACACTAAGTGTGCAACCCACAAAATTCATAATATGTTTATGAATGACTG
1 TA-TCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* *
473119 TATCGGTACTAAGTGTGCAACCCACAAAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
473173 TATCGGCACTAAGTGTTCAACCCACGGAATTCATAATATGTTTATGAACGACCT
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * **
473227 TATTGGCACTAAGTGTGTAACCCACAGAATTCATAATAGGTTTATGAACGACAT
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
*
473281 TATCGGCACTAAGTGTGAAACCCACAGAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
473335 TATCGACACTACGTGTGCACCCCA
1 TATCGGCACTAAGTGTGCAACCCA
473359 ACGACTTATA
Statistics
Matches: 458, Mismatches: 46, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
53 4 0.01
54 451 0.98
55 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
Found at i:479051 original size:54 final size:54
Alignment explanation
Indices: 478976--479526 Score: 700
Period size: 54 Copynumber: 10.3 Consensus size: 54
478966 TTATGTATAC
* * * *
478976 ATCGGCACTAAGTGTGAAACCCACGGAATTCATAAAATATTTATTAACGACCGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
* * *** *
479030 ATCGGCAATAAGAGTGCAACCCAAATAATTCATAATATGTTTATGAACGATCGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
* * * *
479084 ATCGACACTAAGTGTTCAACCCACAGAATTCATAATATGTTTATGAACGATCGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
* *
479138 ATCGACACTAAGTGTGCAACCCACGGAATTCATAATATATTTATGAACGACCGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
* *
479192 ATCAGCACTAAGTGTGCAACCCATGGAATTCATAATATGTTTATGAACGACCGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
* ** *
479246 ATCAGCACTAAGTGT--AACCCACATAATTCATTATATGTTTATGAACGACCGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
* *
479298 ATCGACACTAAGTGTGCAA--CAGGGAATTCATAATATGTTTATGAACGA-CGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
* * ** *
479349 ATCAGCACTAAGTGTGTAACCCA-GTGAATTCATAATATGTTTATGAATTAACGT
1 ATCGGCACTAAGTGTGCAACCCACG-GAATTCATAATATGTTTATGAACGACCGT
* *
479403 ATCGACACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
** * ** *
479457 ATCAACATTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGGCCGT
1 ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
* *
479511 ATTGGCACTACGTGTG
1 ATCGGCACTAAGTGTG
479527 TGCCTCAACG
Statistics
Matches: 434, Mismatches: 56, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
51 19 0.04
52 72 0.17
53 25 0.06
54 317 0.73
55 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (54 bp):
ATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGT
Found at i:479471 original size:265 final size:268
Alignment explanation
Indices: 478980--479512 Score: 770
Period size: 265 Copynumber: 2.0 Consensus size: 268
478970 GTATACATCG
* * *
478980 GCACTAAGTGTGAAACCCACGGAATTCATAAAATATTTATTAACGACCGTATCGGCAATAAGAGT
1 GCACTAAGTGT-AAACCCACAGAATTCATAAAATATTTATGAACGACCGTATCGACAATAAGAGT
*
479045 GCAACCCAAATAATTCATAATATGTTTATGAACGATCGTATCGACACTAAGTGTTCAACCCACAG
65 GCAA-CCAAAGAATTCATAATATGTTTATGAACGATCGTATCGACACTAAGTGTTCAACCCACAG
* *
479110 AATTCATAATATGTTTATGAACGATCGTATCGACACTAAGTGTGCAACCCACGGAATTCATAATA
129 AATTCATAATATGTTTATGAACGAACGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATA
* **
479175 TATTTATGAACGACCGTATCAGCACTAAGTGTGCAACCCATGGAATTCATAATATGTTTATGAAC
194 TATTTATGAACGACCGTATCAACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAAC
479240 GACCGTATCA
259 GACCGTATCA
* * * * * *
479250 GCACTAAGTGT-AACCCACATAATTCATTATATGTTTATGAACGACCGTATCGACACTAAGTGTG
1 GCACTAAGTGTAAACCCACAGAATTCATAAAATATTTATGAACGACCGTATCGACAATAAGAGTG
** **
479314 CAA-CAGGGAATTCATAATATGTTTATGAACGA-CGTATC-AGCACTAAGTGTGT-AACCCAGTG
66 CAACCAAAGAATTCATAATATGTTTATGAACGATCGTATCGA-CACTAAGTGT-TCAACCCACAG
**
479375 AATTCATAATATGTTTATGAATTAACGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATA
129 AATTCATAATATGTTTATGAACGAACGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATA
* * *
479440 TGTTTATGAACGACCGTATCAACATTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAAC
194 TATTTATGAACGACCGTATCAACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAAC
*
479505 GGCCGTAT
259 GACCGTAT
479513 TGGCACTACG
Statistics
Matches: 236, Mismatches: 25, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
264 1 0.00
265 150 0.64
266 27 0.11
268 47 0.20
270 11 0.05
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (268 bp):
GCACTAAGTGTAAACCCACAGAATTCATAAAATATTTATGAACGACCGTATCGACAATAAGAGTG
CAACCAAAGAATTCATAATATGTTTATGAACGATCGTATCGACACTAAGTGTTCAACCCACAGAA
TTCATAATATGTTTATGAACGAACGTATCGACACTAAGTGTGCAACCCACGAAATTCATAATATA
TTTATGAACGACCGTATCAACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGA
CCGTATCA
Found at i:481138 original size:22 final size:23
Alignment explanation
Indices: 481092--481134 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
481082 GTCGGTACTC
*
481092 GGGGAAGTATCGATACCACAAGA
1 GGGGAAGTACCGATACCACAAGA
481115 GGGG-AGTACCGATACC-CAAG
1 GGGGAAGTACCGATACCACAAG
481135 GAGGAGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.35, C:0.21, G:0.33, T:0.12
Consensus pattern (23 bp):
GGGGAAGTACCGATACCACAAGA
Found at i:481147 original size:20 final size:22
Alignment explanation
Indices: 481097--481148 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
481087 TACTCGGGGA
*
481097 AGTATCGATACCACAAGAGGGG
1 AGTATCGATACCACAAGAGAGG
*
481119 AGTACCGATACC-CAAG-GAGG
1 AGTATCGATACCACAAGAGAGG
*
481139 AGTGTCGATA
1 AGTATCGATA
481149 TCATTGTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 11 0.42
21 4 0.15
22 11 0.42
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (22 bp):
AGTATCGATACCACAAGAGAGG
Found at i:484285 original size:15 final size:16
Alignment explanation
Indices: 484267--484304 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
484257 TGATACTTTT
484267 AATTTATTT-TATTTA
1 AATTTATTTCTATTTA
* *
484282 AATTTATTTCTTTTTT
1 AATTTATTTCTATTTA
484298 AATTTAT
1 AATTTAT
484305 AAAATCTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTATTTCTATTTA
Found at i:485204 original size:17 final size:16
Alignment explanation
Indices: 485182--485223 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
485172 TTTACAAAAA
*
485182 TATTATATTATTATTAT
1 TATTATATTATTAAT-T
*
485199 TATTATTTTATTAATT
1 TATTATATTATTAATT
485215 TA-TATATTA
1 TATTATATTA
485224 CAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 6 0.27
16 3 0.14
17 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATATTATTAATT
Found at i:489015 original size:2 final size:2
Alignment explanation
Indices: 489010--489038 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
489000 CTATATATGC
489010 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 A
489039 CCTTGTTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:489254 original size:25 final size:25
Alignment explanation
Indices: 489226--489286 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
489216 AAAAGAGAAA
489226 AGAAGCAAAAA-AGAAAA-AAATAAAG
1 AGAA-CAAAAAGAGAAAATAAA-AAAG
489251 AGAA-AACAAAGAGAAAATAAAAAAG
1 AGAACAA-AAAGAGAAAATAAAAAAG
489276 AGAAACAAAAA
1 AG-AACAAAAA
489287 CAAAGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 2 0.06
24 3 0.10
25 16 0.52
26 8 0.26
27 2 0.06
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (25 bp):
AGAACAAAAAGAGAAAATAAAAAAG
Found at i:489256 original size:12 final size:11
Alignment explanation
Indices: 489242--489271 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
489232 AAAAAAGAAA
489242 AAAATAAAGAG
1 AAAATAAAGAG
*
489253 AAAACAAAGAG
1 AAAATAAAGAG
489264 AAAATAAA
1 AAAATAAA
489272 AAAGAGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (11 bp):
AAAATAAAGAG
Found at i:489256 original size:14 final size:13
Alignment explanation
Indices: 489215--489286 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 13
489205 CAATCAGAAC
489215 AAAAAGAGAAAAGA
1 AAAAAGAGAAAA-A
*
489229 AGCAAAAAAGAAAAA
1 A--AAAAGAGAAAAA
489244 AATAAAGAG--AAA
1 AA-AAAGAGAAAAA
*
489256 ACAAAGAGAAAATA
1 AAAAAGAGAAAA-A
489270 AAAAAGAGAAACAA
1 AAAAAGAGAAA-AA
489284 AAA
1 AAA
489287 CAAAGGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
11 6 0.13
12 4 0.09
13 3 0.06
14 21 0.45
15 3 0.06
16 10 0.21
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:489273 original size:30 final size:31
Alignment explanation
Indices: 489217--489297 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
489207 ATCAGAACAA
* * *
489217 AAAGAGAAAA-GAAGCAAAAAAGAAAAAA-AT
1 AAAGAGAAAACAAAG-AGAAAAGAAAAAAGAG
*
489247 AAAGAGAAAACAAAGAGAAAATAAAAAAGAG
1 AAAGAGAAAACAAAGAGAAAAGAAAAAAGAG
*
489278 AAACA-AAAACAAAG-GAAAAG
1 AAAGAGAAAACAAAGAGAAAAG
489298 TGAAGAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.12
30 30 0.70
31 8 0.19
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.02
Consensus pattern (31 bp):
AAAGAGAAAACAAAGAGAAAAGAAAAAAGAG
Found at i:489296 original size:24 final size:24
Alignment explanation
Indices: 489269--489333 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
489259 AAGAGAAAAT
489269 AAAAAAG-AGAAACAAAAACAAAGG
1 AAAAAAGAAGAAA-AAAAACAAAGG
**
489293 AAAAGTGAAGAAAAAAAACAAAGG
1 AAAAAAGAAGAAAAAAAACAAAGG
**
489317 -AAAGTGAAGAAAAAAAA
1 AAAAAAGAAGAAAAAAAA
489334 GACAAGATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 17 0.45
24 16 0.42
25 5 0.13
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (24 bp):
AAAAAAGAAGAAAAAAAACAAAGG
Found at i:489308 original size:23 final size:23
Alignment explanation
Indices: 489276--489333 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 23
489266 AATAAAAAAG
489276 AGAAACAAAAACAAAGGAAAAGTGA
1 AGAAA-AAAAACAAAGG-AAAGTGA
489301 AGAAAAAAAACAAAGGAAAGTGA
1 AGAAAAAAAACAAAGGAAAGTGA
489324 AGAAAAAAAA
1 AGAAAAAAAA
489334 GACAAGATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 17 0.52
24 11 0.33
25 5 0.15
ACGTcount: A:0.72, C:0.05, G:0.19, T:0.03
Consensus pattern (23 bp):
AGAAAAAAAACAAAGGAAAGTGA
Found at i:489338 original size:25 final size:25
Alignment explanation
Indices: 489276--489338 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
489266 AATAAAAAAG
*
489276 AGAAACAAAAACAAAGGAAAAGTGA
1 AGAAAAAAAAACAAAGGAAAAGTGA
489301 AG-AAAAAAAACAAAGG-AAAGTGA
1 AGAAAAAAAAACAAAGGAAAAGTGA
489324 AGAAAAAAAAGACAA
1 AGAAAAAAAA-ACAA
489339 GATGCATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 9 0.26
24 20 0.57
25 6 0.17
ACGTcount: A:0.71, C:0.06, G:0.19, T:0.03
Consensus pattern (25 bp):
AGAAAAAAAAACAAAGGAAAAGTGA
Found at i:490220 original size:32 final size:32
Alignment explanation
Indices: 490184--490271 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 32
490174 GGAACAATGA
*
490184 GGGCATCTTTCAAGATTCAACATTAAATATTG
1 GGGCATCTTTCAAGATTCAACATCAAATATTG
* ** *
490216 GGGCATTTTTGGAGATTCAACATCGAATATTG
1 GGGCATCTTTCAAGATTCAACATCAAATATTG
** *
490248 GGGCATCTTTGGAGAATCAACATC
1 GGGCATCTTTCAAGATTCAACATC
490272 CTGATATGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (32 bp):
GGGCATCTTTCAAGATTCAACATCAAATATTG
Found at i:491324 original size:85 final size:85
Alignment explanation
Indices: 491185--491501 Score: 395
Period size: 85 Copynumber: 3.7 Consensus size: 85
491175 CCTATTACAA
** * **
491185 CATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAAGACCTTTGAGTTTTATTACATTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCA
*
491250 AAGGCACATCAAATTTACAT
66 AAGGCACATCAAATTTAAAT
* * * *
491270 CATAACTCAAAGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCAATTACATTCAACTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCA
* *
491335 AAGGCACACCAAATTTATAT
66 AAGGCACATCAAATTTAAAT
* * * *
491355 CATAGC-CAAGGCGAGAAGGGTTATCTTTCAACCAAGACCTTTGAGTTCGATTACATTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCA
* * *
491419 AGGGCATATCAAATTTAAAG
66 AAGGCACATCAAATTTAAAT
* * * * *
491439 CATAGCTCAAGGCGAGAAGGGATATCTATCAACAAA-AACTGTCGAGTTCGATTTCATTAAGCT
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCT-TCGAGTTCGATTACATTCAGCT
491502 TGAAGATATA
Statistics
Matches: 200, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
84 75 0.38
85 125 0.62
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (85 bp):
CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCA
AAGGCACATCAAATTTAAAT
Found at i:491486 original size:169 final size:170
Alignment explanation
Indices: 491185--491496 Score: 439
Period size: 169 Copynumber: 1.8 Consensus size: 170
491175 CCTATTACAA
**
491185 CATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAAGACCTTTGAGTTTTATTACATTCAGCTCA
1 CATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAAGACCTTTGAGTTCGATTACATTCAGCTCA
* * * * *
491250 AAGGCACATCAAATTTACATCATAACTCAAAGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGA
66 AAGGCACATCAAATTTAAAGCATAACTCAAAGCGAGAAGGGATATCTATCAACAAAGAACTTCGA
491315 GTTCAATTACATTCAACTCAAAGGCACACCAAATTTATAT
131 GTTCAATTACATTCAACTCAAAGGCACACCAAATTTATAT
** * * *
491355 CATAGC-CAAGGCGAGAAGGGTTATCTTTCAACCAAGACCTTTGAGTTCGATTACATTCAGCTCA
1 CATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAAGACCTTTGAGTTCGATTACATTCAGCTCA
* * * *
491419 AGGGCATATCAAATTTAAAGCATAGCTCAAGGCGAGAAGGGATATCTATCAACAAA-AACTGTCG
66 AAGGCACATCAAATTTAAAGCATAACTCAAAGCGAGAAGGGATATCTATCAACAAAGAACT-TCG
* *
491483 AGTTCGATTTCATT
130 AGTTCAATTACATT
491497 AAGCTTGAAG
Statistics
Matches: 123, Mismatches: 18, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
168 3 0.02
169 114 0.93
170 6 0.05
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (170 bp):
CATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAAGACCTTTGAGTTCGATTACATTCAGCTCA
AAGGCACATCAAATTTAAAGCATAACTCAAAGCGAGAAGGGATATCTATCAACAAAGAACTTCGA
GTTCAATTACATTCAACTCAAAGGCACACCAAATTTATAT
Found at i:492983 original size:18 final size:19
Alignment explanation
Indices: 492954--492993 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
492944 AAATTTTATA
*
492954 TTATATTATTATTATTAAT
1 TTATATTATTATAATTAAT
*
492973 TTATA-TATTATAATTATT
1 TTATATTATTATAATTAAT
492991 TTA
1 TTA
492994 CAGGCCTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTATTATAATTAAT
Found at i:495606 original size:41 final size:41
Alignment explanation
Indices: 495487--495917 Score: 360
Period size: 41 Copynumber: 10.4 Consensus size: 41
495477 ATATAGCGGT
* * *
495487 GTTTTTGA-ACAAACGCCGCAAAATACTA-TATTTTAGTGGC
1 GTTTTT-ATACAAACGCCGCTATAGACTAGTATTTTAGTGGC
* * * * * * * * *
495527 GTTTGTATAAAAACGCCGCTAAAGAATCGAAATGTAGTGAC
1 GTTTTTATACAAACGCCGCTATAGACTAGTATTTTAGTGGC
* * *
495568 ATTTTTATACAAACGCCACTATAAACTAGTATTTTAGTGGC
1 GTTTTTATACAAACGCCGCTATAGACTAGTATTTTAGTGGC
**
495609 GTTTTTATATGAACGCCGCTATAGAC-ACGTACTTTT-GTGGC
1 GTTTTTATACAAACGCCGCTATAGACTA-GTA-TTTTAGTGGC
* * *
495650 GTTTTAATACCAAACGCCTCTATAGACTCA-TACTTTAGTGGC
1 GTTTTTATA-CAAACGCCGCTATAGACT-AGTATTTTAGTGGC
* * *
495692 ATTTTTACATAAACGCCGCTATAGAC-ACGTACTTTT-GTGGC
1 GTTTTTATACAAACGCCGCTATAGACTA-GTA-TTTTAGTGGC
* * * *
495733 GTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGC
1 GTTTTTATA-CAAACGCCGCTATAGACTAGTATTTTAGTGGC
*
495775 GTTTTTACACAAACGCCGCTATAGAC-ACGTACTTTT-GTGGC
1 GTTTTTATACAAACGCCGCTATAGACTA-GTA-TTTTAGTGGC
* * * *
495816 GTTTTAATACCAAATGCCACTATAGACTCGT-TCTTTAGTGGC
1 GTTTTTATA-CAAACGCCGCTATAGACTAGTAT-TTTAGTGGC
* *
495858 GTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGC
1 GTTTTTATACAAACGCCGCTATAGACTAGTATTTTAGTGGC
*
495899 GTTTTAATACCAAACGCCG
1 GTTTTTATA-CAAACGCCG
495918 TAATTGTCAT
Statistics
Matches: 309, Mismatches: 60, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.01
40 22 0.07
41 178 0.58
42 106 0.34
44 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (41 bp):
GTTTTTATACAAACGCCGCTATAGACTAGTATTTTAGTGGC
Found at i:495697 original size:83 final size:83
Alignment explanation
Indices: 495569--495916 Score: 511
Period size: 83 Copynumber: 4.2 Consensus size: 83
495559 TGTAGTGACA
* * * * **
495569 TTTTTATA-CAAACGCCACTATAAACT-AGTATTTTAGTGGCGTTTTTATATGAACGCCGCTATA
1 TTTTAATACCAAACGCCACTATAGACTCA-TACTTTAGTGGCGTTTTTACACAAACGCCGCTATA
495632 GACACGTACTTTTGTGGCG
65 GACACGTACTTTTGTGGCG
* * *
495651 TTTTAATACCAAACGCCTCTATAGACTCATACTTTAGTGGCATTTTTACATAAACGCCGCTATAG
1 TTTTAATACCAAACGCCACTATAGACTCATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAG
495716 ACACGTACTTTTGTGGCG
66 ACACGTACTTTTGTGGCG
* * *
495734 TTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTTTACACAAACGCCGCTATAG
1 TTTTAATACCAAACGCCACTATAGACTCATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAG
495799 ACACGTACTTTTGTGGCG
66 ACACGTACTTTTGTGGCG
* * * *
495817 TTTTAATACCAAATGCCACTATAGACTCGTTCTTTAGTGGCGTTTTTATACAAACGCCGCTATAG
1 TTTTAATACCAAACGCCACTATAGACTCATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAG
* *
495882 ACTCGTACTTTAGTGGCG
66 ACACGTACTTTTGTGGCG
495900 TTTTAATACCAAACGCC
1 TTTTAATACCAAACGCC
495917 GTAATTGTCA
Statistics
Matches: 244, Mismatches: 20, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
82 7 0.03
83 236 0.97
84 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (83 bp):
TTTTAATACCAAACGCCACTATAGACTCATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAG
ACACGTACTTTTGTGGCG
Found at i:499506 original size:42 final size:43
Alignment explanation
Indices: 499389--499695 Score: 238
Period size: 43 Copynumber: 7.2 Consensus size: 43
499379 AAGGTAATTA
* * *
499389 GCGGCGTTTATATCCAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGTATCTAAAAACGCCGCTATAGGTCTGACCTTTT
* *
499432 GCGGCGTTTGTGT-TCAAAAACGCCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGTATCT-AAAAACGCCGCTATAGGTCTGACCTTTT
**
499475 GCATCGTTTGT-TCTAAAAACGCCAG-TATAGGTCTG-CTCTTTT
1 GCGGCGTTTGTATCTAAAAACGCC-GCTATAGGTCTGAC-CTTTT
* * * * *
499517 GCGGCGTTTGTATCCAAAAACGCCACTATAGATTTGACATTTT
1 GCGGCGTTTGTATCTAAAAACGCCGCTATAGGTCTGACCTTTT
* * * ** * *
499560 --GGCGTTT-TTTCTAGAAACGTCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTATCTAAAAACGCCGCTATAGGTC-TGACCTTTT
* * *
499601 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTATCTAAAAACGCCGCTATAGGTCT-GACCTTTT
* * * * *
499644 GCGGCGTTTGT-TCAAAAAATGCCG-TAATAGATATTGACCTATT
1 GCGGCGTTTGTATCTAAAAACGCCGCT-ATAGGT-CTGACCTTTT
499687 GCGGCGTTT
1 GCGGCGTTT
499696 TTTGTTCTCA
Statistics
Matches: 216, Mismatches: 34, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
40 17 0.08
41 15 0.07
42 36 0.17
43 145 0.67
44 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (43 bp):
GCGGCGTTTGTATCTAAAAACGCCGCTATAGGTCTGACCTTTT
Found at i:499537 original size:85 final size:82
Alignment explanation
Indices: 499404--499667 Score: 280
Period size: 85 Copynumber: 3.1 Consensus size: 82
499394 GTTTATATCC
* * * *
499404 AAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTCAAAAACGCCGTTATAGGTCTGA
1 AAAAACGCCGCTATAGGTCTG-CTTTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGA
*
499469 CCTTTTGCATCGTTTGTTCT
64 CCTTTTGC-GCGTTTGTTCT
* *
499489 AAAAACGCCAG-TATAGGTCTGCTCTTTTGCGGCGTTTGTATCCAAAAACGCCACTATAGATTTG
1 AAAAACGCC-GCTATAGGTCTGCT-TTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATG
* *
499553 ACATTTTG-GCGTTTTTTCT
63 ACCTTTTGCGCGTTTGTTCT
* * ** *
499572 AGAAACGTCGCTATATATCATAACTTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATCG
1 AAAAACGCCGCTATAGGTC-T-GCTTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-G
*
499637 ACCTTTTGCGGCGTTTGTTCA
63 ACCTTTTGC-GCGTTTGTTCT
*
499658 AAAAATGCCG
1 AAAAACGCCG
499668 TAATAGATAT
Statistics
Matches: 149, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
82 1 0.01
83 43 0.29
84 26 0.17
85 62 0.42
86 17 0.11
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34
Consensus pattern (82 bp):
AAAAACGCCGCTATAGGTCTGCTTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACC
TTTTGCGCGTTTGTTCT
Found at i:501121 original size:313 final size:313
Alignment explanation
Indices: 500521--501146 Score: 1209
Period size: 313 Copynumber: 2.0 Consensus size: 313
500511 TCTACCTATC
* *
500521 CCCTTGCCGGTGAGCCTCAATCCAGATTCTGTGCTTTCCACCAGGAAACCTACTCTGAGCTCCAC
1 CCCTCGCCGGTGAGCCTCAATCCAGATTCTGTGCTTTCCACCAGGAAACCTACTCCGAGCTCCAC
*
500586 TCCGACCACCAACCATACCCTATTTGAACCGTCTCTTAGTCCTAAACTCGTTTCTAGTCTCAAAA
66 TCCGACCACCAACCATACCCTATTCGAACCGTCTCTTAGTCCTAAACTCGTTTCTAGTCTCAAAA
500651 TCTTCTAAAACAATCATGCAAACATAGATCTAAAGAAATATGTGTAATACCCTATTCTAGTCCGA
131 TCTTCTAAAACAATCATGCAAACATAGATCTAAAGAAATATGTGTAATACCCTATTCTAGTCCGA
500716 CCCAAAATCAATGGATCATGATGTCACGAGGGACCAACAAAGTGGCTAACCCAAAATATTTCTTT
196 CCCAAAATCAATGGATCATGATGTCACGAGGGACCAACAAAGTGGCTAACCCAAAATATTTCTTT
500781 AAAACAATTGTAAAATAACATATAAAATCCATCCCATGTAAAAT-AAATAAAA
261 AAAACAATTGTAAAATAACATATAAAATCCATCCCATGTAAAATAAAATAAAA
500833 CCCTCGCCGGTGAGCCTCAATCCAGATTCTGTGGCTTTCCACCAGGAAACCTACTCCGAGCTCCA
1 CCCTCGCCGGTGAGCCTCAATCCAGATTCTGT-GCTTTCCACCAGGAAACCTACTCCGAGCTCCA
500898 CTCCGACCACCAACCATACCCTATTCGAACCGTCTCTTAGTCCTAAACTCGTTTCTAGTCTCAAA
65 CTCCGACCACCAACCATACCCTATTCGAACCGTCTCTTAGTCCTAAACTCGTTTCTAGTCTCAAA
500963 ATCTTCTAAAACAATCATGCAAACATAGATCTAAAGAAATATGTGTAATACCCTATTCTAGTCCG
130 ATCTTCTAAAACAATCATGCAAACATAGATCTAAAGAAATATGTGTAATACCCTATTCTAGTCCG
501028 ACCCAAAATCAATGGATCATGATGTCACGAGGGACCAACAAAGTGGCTAACCCAAAATATTTCTT
195 ACCCAAAATCAATGGATCATGATGTCACGAGGGACCAACAAAGTGGCTAACCCAAAATATTTCTT
501093 TAAAACAATTGTAAAATAACATATAAAATCCATCCCATGTAAAATAAAATAAAA
260 TAAAACAATTGTAAAATAACATATAAAATCCATCCCATGTAAAATAAAATAAAA
501147 TGTGATAATT
Statistics
Matches: 309, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
312 31 0.10
313 270 0.87
314 8 0.03
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.25
Consensus pattern (313 bp):
CCCTCGCCGGTGAGCCTCAATCCAGATTCTGTGCTTTCCACCAGGAAACCTACTCCGAGCTCCAC
TCCGACCACCAACCATACCCTATTCGAACCGTCTCTTAGTCCTAAACTCGTTTCTAGTCTCAAAA
TCTTCTAAAACAATCATGCAAACATAGATCTAAAGAAATATGTGTAATACCCTATTCTAGTCCGA
CCCAAAATCAATGGATCATGATGTCACGAGGGACCAACAAAGTGGCTAACCCAAAATATTTCTTT
AAAACAATTGTAAAATAACATATAAAATCCATCCCATGTAAAATAAAATAAAA
Found at i:501698 original size:77 final size:77
Alignment explanation
Indices: 501571--501720 Score: 300
Period size: 77 Copynumber: 1.9 Consensus size: 77
501561 AACTGGCGGC
501571 TAAGTATCTTGGCATCAACGGGGATATCTGAACTGTACGATCGTATCTGCTAAAGTAAATCGAGT
1 TAAGTATCTTGGCATCAACGGGGATATCTGAACTGTACGATCGTATCTGCTAAAGTAAATCGAGT
501636 GTCTTAACGTCT
66 GTCTTAACGTCT
501648 TAAGTATCTTGGCATCAACGGGGATATCTGAACTGTACGATCGTATCTGCTAAAGTAAATCGAGT
1 TAAGTATCTTGGCATCAACGGGGATATCTGAACTGTACGATCGTATCTGCTAAAGTAAATCGAGT
501713 GTCTTAAC
66 GTCTTAAC
501721 TACGTCTTGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (77 bp):
TAAGTATCTTGGCATCAACGGGGATATCTGAACTGTACGATCGTATCTGCTAAAGTAAATCGAGT
GTCTTAACGTCT
Found at i:502308 original size:21 final size:20
Alignment explanation
Indices: 502222--502379 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
502212 AAATGACCAA
**
502222 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
502241 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
502261 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
502281 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
502302 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
502323 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
502343 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
502364 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
502380 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:502434 original size:58 final size:60
Alignment explanation
Indices: 502347--502535 Score: 224
Period size: 58 Copynumber: 3.2 Consensus size: 60
502337 GATTTTCAAT
* ** * *
502347 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTAT-CGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
502406 AATCGCAACGTGTATCCGT-AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT-
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
**
502464 -ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
502524 AATCGCAACGCG
1 AATCGCAACGCG
502536 ATATTTAAAG
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
57 17 0.16
58 42 0.40
59 36 0.34
61 11 0.10
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:502436 original size:38 final size:39
Alignment explanation
Indices: 502387--502533 Score: 183
Period size: 38 Copynumber: 3.8 Consensus size: 39
502377 CGAACACATA
502387 AATCGCAACGCGTAT-CGTAAATCGCAACGTGTATCCGT
1 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
** * *
502425 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
* * *
502464 -ATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACAT
1 AATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
502502 AAAATCGCAACGCGTATCCGTAAATCGCAACG
1 --AATCGCAACGCGTATCCGTAAATCGCAACG
502534 CGATATTTAA
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
38 45 0.48
39 20 0.21
41 29 0.31
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
Found at i:502450 original size:20 final size:20
Alignment explanation
Indices: 502347--502535 Score: 192
Period size: 20 Copynumber: 9.6 Consensus size: 20
502337 GATTTTCAAT
* ** *
502347 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
502367 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
502387 AATCGCAACGCGTAT-CGTA
1 AATCGCAACGCGTATCCGTA
*
502406 AATCGCAACGTGTATCCGT-
1 AATCGCAACGCGTATCCGTA
**
502425 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
502445 AATCGCAATGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
502464 -ATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
502483 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
502504 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
502524 AATCGCAACGCG
1 AATCGCAACGCG
502536 ATATTTAAAG
Statistics
Matches: 139, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
18 17 0.12
19 35 0.25
20 70 0.50
21 16 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:502703 original size:21 final size:22
Alignment explanation
Indices: 502679--502731 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
502669 CTCTCTACGG
502679 CGAAGAAATCCGTCCCC-TCTC
1 CGAAGAAATCCGTCCCCATCTC
*
502700 CGAAG-ATTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
502721 CGGCGAAATCC
1 CGAAGAAATCC
502732 CTCACAACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.38
21 12 0.46
22 4 0.15
ACGTcount: A:0.23, C:0.42, G:0.17, T:0.19
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:502971 original size:33 final size:31
Alignment explanation
Indices: 502913--502981 Score: 102
Period size: 33 Copynumber: 2.2 Consensus size: 31
502903 TTCACTTAGA
*
502913 TTTCATTCGCGTTCGATTCTGTCGTTGCGAT
1 TTTCATTCGCGTTCGATTCTCTCGTTGCGAT
*
502944 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCA-TTCGCGTT-CGATTCTCTCGTTGCGAT
502977 TTTCA
1 TTTCA
502982 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 5 0.15
32 8 0.24
33 21 0.62
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (31 bp):
TTTCATTCGCGTTCGATTCTCTCGTTGCGAT
Found at i:503120 original size:14 final size:14
Alignment explanation
Indices: 503101--503155 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
503091 GAGATGACTG
503101 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
503115 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
503134 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
503148 TCGCAACG
1 TCGCAACG
503156 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:503122 original size:33 final size:33
Alignment explanation
Indices: 503080--503171 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
503070 GATAAATGAA
* ***
503080 AATCGCAACGAGAGATGACTGTCGCAACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
*
503113 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
* **
503146 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGAGAAATGAAAATCGCA
503172 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.10
Consensus pattern (33 bp):
AATCGCAACGAGAAATGAAAATCGCAACGAGAG
Found at i:503208 original size:14 final size:14
Alignment explanation
Indices: 503189--503278 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
503179 TTTCATTTCG
503189 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
503203 CGTTGCGATTTTCCTTTCG
1 CGTTGCGA--TT-C--TCT
*
503222 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
503236 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
503253 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
503269 CGTTGCGATT
1 CGTTGCGATT
503279 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.08, C:0.27, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:503214 original size:33 final size:33
Alignment explanation
Indices: 503172--503286 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
503162 CAAAATCGCA
503172 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
503205 TTGCGATTTTCCTTTCGCGTTGCTATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
503238 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
503271 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
503287 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.09, C:0.25, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:503258 original size:19 final size:17
Alignment explanation
Indices: 503167--503279 Score: 73
Period size: 19 Copynumber: 6.8 Consensus size: 17
503157 GAAACCAAAA
* *
503167 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTC-TC
503186 TCGCGTTGCGA-TTCTC
1 TCGCGTTGCGATTTCTC
*
503202 T--CGTTGCGATTTTCCTT
1 TCGCGTTGCGA-TTT-CTC
*
503219 TCGCGTTGCTA-TTCTC
1 TCGCGTTGCGATTTCTC
503235 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TC-TC
503252 TCGCGTTGCGA-TTCTC
1 TCGCGTTGCGATTTCTC
503268 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
503280 TCATTTCAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 23 0.30
15 3 0.04
16 12 0.16
17 13 0.17
18 1 0.01
19 25 0.32
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (17 bp):
TCGCGTTGCGATTTCTC
Found at i:505165 original size:90 final size:93
Alignment explanation
Indices: 504970--505337 Score: 664
Period size: 90 Copynumber: 4.1 Consensus size: 93
504960 ATTGCTTAGT
*
504970 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTG-GTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
505034 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
505062 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATA-TATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
505125 TCTTTGTTTTGTC-TTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
505152 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
505216 TCTTTGTTTTGTCTTTTGG-TGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
505243 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTG-AATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
505306 TCTTTGTTTTGTC-TTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
505333 AATTT
1 AATTT
505338 ATCCATTCAA
Statistics
Matches: 270, Mismatches: 1, Indels: 12
0.95 0.00 0.04
Matches are distributed among these distances:
89 9 0.03
90 113 0.42
91 88 0.33
92 42 0.16
93 18 0.07
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGTA
Found at i:505306 original size:181 final size:182
Alignment explanation
Indices: 504970--505339 Score: 692
Period size: 181 Copynumber: 2.0 Consensus size: 182
504960 ATTGCTTAGT
504970 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTATTCTTTAACACTGTGAAATAGTATTTGT
1 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTATTCTTTAACACTGTGAAATAGTATTTGT
505035 CTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA
66 CTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA
505100 TTCTTTAACACTGTGAATATATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTA
131 TTCTTTAACACTGTGAATATATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTA
*
505152 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TATTTG
1 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTG-GTATTCTTTAACACTGTGAAATAGTATTTG
505216 TCTTTGTTTTGTCTTTTGG-TGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGT
65 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGT
505280 A-TCTTTAACACTGTGAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTA
130 ATTCTTTAACACTGTGAATA-TATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTA
505333 AATTTAT
1 AATTTAT
505340 CCATTCAAGT
Statistics
Matches: 184, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
180 18 0.10
181 85 0.46
182 58 0.32
183 23 0.12
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (182 bp):
AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGGTATTCTTTAACACTGTGAAATAGTATTTGT
CTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA
TTCTTTAACACTGTGAATATATTTGTCTTTGTTTTGTCTTTGGTTGAAAGTA
Found at i:505421 original size:19 final size:19
Alignment explanation
Indices: 505381--505507 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
505371 TAGTTTACTT
* *
505381 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
505401 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
505420 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACCAAAA
*
505438 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
505452 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
505471 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
505485 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
505503 TCGCA
1 TCGCA
505508 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 18 0.21
19 28 0.32
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:505477 original size:33 final size:31
Alignment explanation
Indices: 505417--505507 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 31
505407 CGCGAAACCA
**
505417 AAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAATCGCAACGAC
505448 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACC-AAATCGCAACGAC
505481 AAGATCGCAACGCGAAACCAAATCGCA
1 AA-ATCGCAACGCGAAACCAAATCGCA
505508 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 24 0.44
33 30 0.55
ACGTcount: A:0.45, C:0.29, G:0.19, T:0.08
Consensus pattern (31 bp):
AAATCGCAACGCGAAACCAAATCGCAACGAC
Found at i:505530 original size:19 final size:19
Alignment explanation
Indices: 505503--505637 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
505493 CGAAACCAAA
*
505503 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
505522 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
505538 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
505555 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
505571 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
505588 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
505607 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
505627 TCGTGTTGCGA
1 TCGCGTTGCGA
505638 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:505544 original size:14 final size:14
Alignment explanation
Indices: 505525--505581 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
505515 TTTCATTTCG
505525 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
505539 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
505556 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
505572 CGTTGCGATT
1 CGTTGCGATT
505582 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:505550 original size:33 final size:33
Alignment explanation
Indices: 505508--505600 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
505498 CCAAATCGCA
*
505508 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
505541 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
505574 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
505601 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:507535 original size:14 final size:14
Alignment explanation
Indices: 507516--507551 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
507506 ATTGTTTAAT
507516 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
507530 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
507544 TGATTTGT
1 TGATTTGT
507552 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:507725 original size:20 final size:19
Alignment explanation
Indices: 507657--507739 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
507647 AAAAATGACT
507657 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
507676 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
507690 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
507709 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
507729 ATCGCAATGCG
1 ATCGCAATGCG
507740 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:507792 original size:19 final size:19
Alignment explanation
Indices: 507768--508149 Score: 517
Period size: 19 Copynumber: 21.4 Consensus size: 19
507758 GATTATCTCG
507768 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
507787 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
507806 TGCGA--TTC-TTTCG--T
1 TGCGATTTTCATTTCGCAT
507820 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
507839 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
*
507858 TGCGATTTCCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
507877 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
507896 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
*
507915 TGCGA--TTC-TCTCG--T
1 TGCGATTTTCATTTCGCAT
507929 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
507948 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
*
507967 TGCGATTTCCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
507986 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
508005 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
*
508024 TGCGA--TTC-TCTCG--T
1 TGCGATTTTCATTTCGCAT
508038 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
508057 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
*
508076 TGCGA--TTC-TCTCG--T
1 TGCGATTTTCATTTCGCAT
508090 TGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTT-CGCAT
508110 TGCGATTTTCA--T-G--T
1 TGCGATTTTCATTTCGCAT
* *
508124 TGGGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCAT
508143 TGCGATT
1 TGCGATT
508150 GTATTTTCCG
Statistics
Matches: 325, Mismatches: 12, Indels: 52
0.84 0.03 0.13
Matches are distributed among these distances:
14 35 0.11
16 31 0.10
17 28 0.09
18 3 0.01
19 216 0.66
20 12 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCAT
Found at i:507862 original size:90 final size:91
Alignment explanation
Indices: 507746--508149 Score: 508
Period size: 90 Copynumber: 4.6 Consensus size: 91
507736 TGCGTTTATA
*
507746 ATTTCGCATTGCGA--TT-ATCTCG-TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
1 ATTTCGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
507807 GCGA-TTC-TTTCG-TTGCGATTTTC
66 GCGATTTCATTTCGATTGCGATTTTC
*
507830 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
507895 TTGCGATTTTCATTTCGCATTGCGA--TTC
64 TTGCGA-TTTCATTTCG-ATTGCGATTTTC
* *
507923 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
507985 TTGCGATTTTCATTTCGCATTGCGATTTTC
64 TTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
508015 ATTTCGCATTGCGA--TTC-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
1 ATTTCGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
*
508077 GCGA-TTC-TCTCG-TTGCGATTTTC
66 GCGATTTCATTTCGATTGCGATTTTC
* *
508100 ATTTCCGCATTGCGATTTTCA--T-GTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATT
508150 GTATTTTCCG
Statistics
Matches: 289, Mismatches: 11, Indels: 38
0.86 0.03 0.11
Matches are distributed among these distances:
84 14 0.05
85 15 0.05
86 38 0.13
87 10 0.03
88 6 0.02
90 165 0.57
92 14 0.05
93 15 0.05
95 12 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (91 bp):
ATTTCGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
GCGATTTCATTTCGATTGCGATTTTC
Found at i:507887 original size:109 final size:109
Alignment explanation
Indices: 507768--508121 Score: 646
Period size: 109 Copynumber: 3.3 Consensus size: 109
507758 GATTATCTCG
*
507768 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
507833 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCAT
66 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCAT
507877 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
507942 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCAT
66 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCAT
507986 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
508051 TCGCATTGCGATTTTCATTTCGCATTGCGA-TT-C-TCTCG--T
66 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCAT
508090 TGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCAT
508122 GTTGGGATTT
Statistics
Matches: 242, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
104 15 0.06
105 17 0.07
106 4 0.02
107 1 0.00
108 2 0.01
109 203 0.84
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCAT
Found at i:510641 original size:24 final size:23
Alignment explanation
Indices: 510607--510652 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
510597 CTGAAACATC
*
510607 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCG-ATATTGACCAAT
*
510631 ATCAAAGTCCGATATTGACCAA
1 ATCAAAATCCGATATTGACCAA
510653 GACCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
ATCAAAATCCGATATTGACCAAT
Found at i:511354 original size:20 final size:20
Alignment explanation
Indices: 511326--511714 Score: 448
Period size: 20 Copynumber: 19.4 Consensus size: 20
511316 AAATTTCAGT
* * * *
511326 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
511346 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
511366 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
511386 GTTGCGATTTAC-GATTA-TC
1 GTTGCGATTTACGGA-TACGC
511405 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
511425 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
511445 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
511465 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
511485 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
511505 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
511525 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
511545 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
511566 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
511586 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
511606 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
511626 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
511646 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
511666 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
511686 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
511706 GTTGCGATT
1 GTTGCGATT
511715 ATTGAAAATC
Statistics
Matches: 322, Mismatches: 35, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
19 23 0.07
20 279 0.87
21 18 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:513743 original size:5 final size:5
Alignment explanation
Indices: 513733--513772 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
513723 ATCATTTTAG
*
513733 AAAAT AAAAT AAACCT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAA
513773 ATATAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:513775 original size:16 final size:15
Alignment explanation
Indices: 513733--513772 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
513723 ATCATTTTAG
*
513733 AAAATAAAATAAACCT
1 AAAATAAAATAAA-AT
513749 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
513764 AAAATAAAA
1 AAAATAAAA
513773 ATATAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:513780 original size:21 final size:21
Alignment explanation
Indices: 513733--513772 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
513723 ATCATTTTAG
*
513733 AAAATAAAATAAACCTAAAAT
1 AAAATAAAATAAACATAAAAT
513754 AAAATAAAATAAA-ATAAAA
1 AAAATAAAATAAACATAAAA
513773 ATATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAATAAAATAAACATAAAAT
Found at i:513940 original size:22 final size:20
Alignment explanation
Indices: 513895--513943 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
513885 AACTATGTAT
513895 TATATATATGTTTTTAAACC
1 TATATATATGTTTTTAAACC
*
513915 TATATATGA-GTTTTTAAAAC
1 TATATAT-ATGTTTTTAAACC
*
513935 TGTATATAT
1 TATATATAT
513944 ACTATATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (20 bp):
TATATATATGTTTTTAAACC
Found at i:516948 original size:30 final size:28
Alignment explanation
Indices: 516912--517109 Score: 110
Period size: 30 Copynumber: 6.8 Consensus size: 28
516902 TTAAATTCAC
516912 ATCTTAACAGTAAAATTATATTTTACTTTT
1 ATCTTAACA-TAAAA-TATATTTTACTTTT
* *
516942 ATCTTAACTTATTAAATATATTTTATTTTT
1 ATCTTAAC--ATAAAATATATTTTACTTTT
* * * *
516972 ATTTTAACTTAAAAATATATTTTAGTCTT
1 ATCTTAACAT-AAAATATATTTTACTTTT
* * * * *
517001 ATTTTAACTTAAAAAATCTATTTTAATCTT
1 ATCTTAAC--ATAAAATATATTTTACTTTT
* * * * *
517031 ATTTTAGCTTAAAA-ATAATTTACTCTT
1 ATCTTAACATAAAATATATTTTACTTTT
* *
517058 ACCTTAACTTATAAAATATATATTACTTTT
1 ATCTTAAC--ATAAAATATATTTTACTTTT
* ** *
517088 ATTTTAATTTAAGATATATTTT
1 ATCTTAACATAAAATATATTTT
517110 TTAAAAAATA
Statistics
Matches: 130, Mismatches: 30, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
27 15 0.12
28 16 0.12
29 28 0.22
30 66 0.51
31 4 0.03
32 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (28 bp):
ATCTTAACATAAAATATATTTTACTTTT
Found at i:517008 original size:59 final size:59
Alignment explanation
Indices: 516922--517109 Score: 220
Period size: 59 Copynumber: 3.2 Consensus size: 59
516912 ATCTTAACAG
* * * *
516922 TAAAATTATATTTTACTTTTATCTTAACTTATTAAATATATTTTATTTTTATTTTAACT
1 TAAAAATATATTTTACTCTTATCTTAACTTATAAAATATATTTTAATTTTATTTTAACT
* * * * * *
516981 TAAAAATATATTTTAGTCTTATTTTAACTTAAAAAATCTATTTTAATCTTATTTTAGCT
1 TAAAAATATATTTTACTCTTATCTTAACTTATAAAATATATTTTAATTTTATTTTAACT
* * *
517040 TAAAAATA-A-TTTACTCTTACCTTAACTTATAAAATATATATTACTTTTATTTTAA-T
1 TAAAAATATATTTTACTCTTATCTTAACTTATAAAATATATTTTAATTTTATTTTAACT
* *
517096 TTAAGATATATTTT
1 TAAAAATATATTTT
517110 TTAAAAAATA
Statistics
Matches: 106, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
56 7 0.07
57 38 0.36
58 4 0.04
59 57 0.54
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (59 bp):
TAAAAATATATTTTACTCTTATCTTAACTTATAAAATATATTTTAATTTTATTTTAACT
Found at i:517437 original size:65 final size:65
Alignment explanation
Indices: 517333--517463 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
517323 TTAAACCAAA
*
517333 AATGCAAATTTTCAGGTTTTAAATCCTGTACATGCATTTGTGTGCTCTTATTTTCTTTCCACCAT
1 AATGCAAATTTTCAGGTTTTAAATCCTGTACATGCATTTGTGTGCACTTATTTTCTTTCCACCAT
*
517398 AATGCAAATTTTCAGGTTTTAAATCCTGTGCATGCATTTGTGTGCACTTATTTTCTTTCCACCAT
1 AATGCAAATTTTCAGGTTTTAAATCCTGTACATGCATTTGTGTGCACTTATTTTCTTTCCACCAT
517463 A
1 A
517464 GGTTGACATG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.44
Consensus pattern (65 bp):
AATGCAAATTTTCAGGTTTTAAATCCTGTACATGCATTTGTGTGCACTTATTTTCTTTCCACCAT
Found at i:518895 original size:21 final size:21
Alignment explanation
Indices: 518870--518917 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
518860 TGAATAATGG
518870 AATCACTCCTGTCATATCTGA
1 AATCACTCCTGTCATATCTGA
518891 AATCACTCCTGTCATATCTGA
1 AATCACTCCTGTCATATCTGA
518912 AATCAC
1 AATCAC
518918 AGATAACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (21 bp):
AATCACTCCTGTCATATCTGA
Found at i:531670 original size:18 final size:19
Alignment explanation
Indices: 531635--531675 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
531625 GTTTTTACAT
531635 AAAT-ATTATCATAATAGA
1 AAATAATTATCATAATAGA
*
531653 AAATAATTAT-ATATTAGA
1 AAATAATTATCATAATAGA
*
531671 CAATA
1 AAATA
531676 TTTTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
AAATAATTATCATAATAGA
Found at i:547171 original size:5 final size:5
Alignment explanation
Indices: 547161--547224 Score: 101
Period size: 5 Copynumber: 12.8 Consensus size: 5
547151 ACCACGACCA
* * *
547161 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
547211 CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAG
547225 ACGGACGGTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.16, C:0.39, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Found at i:561799 original size:33 final size:33
Alignment explanation
Indices: 561762--561824 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
561752 AAACTAAAAA
561762 TAACCAGAAT-CGAAAGAAACCTGAACCGAATTT
1 TAACCAG-ATCCGAAAGAAACCTGAACCGAATTT
* *
561795 TAACCAGATCCGAAAGCAATCTGAACCGAA
1 TAACCAGATCCGAAAGAAACCTGAACCGAA
561825 CTTAACCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (33 bp):
TAACCAGATCCGAAAGAAACCTGAACCGAATTT
Found at i:562699 original size:21 final size:19
Alignment explanation
Indices: 562673--562711 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
562663 CAAACTAGAT
*
562673 CTGAACCAAATCTAATCCGAC
1 CTGAACAAAAT-TAA-CCGAC
562694 CTGAACAAAATTAACCGA
1 CTGAACAAAATTAACCGA
562712 ATATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.44, C:0.28, G:0.10, T:0.18
Consensus pattern (19 bp):
CTGAACAAAATTAACCGAC
Found at i:563655 original size:3 final size:3
Alignment explanation
Indices: 563643--563695 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
563633 CAAAAACATT
*
563643 TTA TTA -TA TTA TTA TTTA TTA GTA TTA TTA TTA TTA TTA TTTA TT-
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
563688 TTA TTA TT
1 TTA TTA TT
563696 TTTGCAGGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:563696 original size:12 final size:13
Alignment explanation
Indices: 563649--563696 Score: 73
Period size: 12 Copynumber: 3.8 Consensus size: 13
563639 CATTTTATTA
563649 TATTATTATTTAT
1 TATTATTATTTAT
*
563662 TAGTATTA-TTAT
1 TATTATTATTTAT
563674 TATTATTATTTAT
1 TATTATTATTTAT
563687 T-TTATTATTT
1 TATTATTATTT
563697 TTGCAGGCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
12 20 0.62
13 12 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:564393 original size:25 final size:23
Alignment explanation
Indices: 564365--564424 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 23
564355 AATTTTAGCA
564365 TTTTTTATTATTATTATTTTTAT
1 TTTTTTATTATTATTATTTTTAT
*
564388 GTTTTTTACTTCTTATTATTTTTAT
1 -TTTTTTA-TTATTATTATTTTTAT
*
564413 TTTATT-TTATTA
1 TTTTTTATTATTA
564425 CTTTTAGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 5 0.16
24 12 0.38
25 15 0.47
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTTTATTATTATTATTTTTAT
Found at i:568710 original size:124 final size:124
Alignment explanation
Indices: 568485--569729 Score: 1374
Period size: 124 Copynumber: 9.9 Consensus size: 124
568475 TTGAACTCGA
*
568485 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGATCAAC
* * *
568550 TTCACAACGAATGGGTCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACC
66 TTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
* * * *
568609 AGCAGCATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGATATTCAATTCAAGGATCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGATCAAC
* *
568674 TTCACAATGAAGGGG-CTATCCATAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
66 TTCACAACGAAGGGGTC-ATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
* * * *
568733 AGCAACATTCATCTTTAGATTGGATTTCAACTTTACGA-GATTGGAT-TTCAACTTCACGATGAA
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGA-AGAATATCCAA-TTCA--A-G--
* * ** * * *** * *
568796 TGATATCCAA-TTCAAGGCTCAACTTCACAATGAATGAGCCATCTACGATTTCAATTTCACGACG
59 -G--AT-CAACTTC-A----CAAC--GA-AG-GGGTCATCCA-C-AATT--TCAACTTCACGAAG
*
568860 AAGAATATCGTGCCCACC
107 AAGGATATCGTGCCCACC
* * *
568878 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTTC-AGGCTCAA
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAA-TTCAAGGATCAA
* ** * **
568942 CTTCACAACAAAGGGGTCATCCATGATTTCAACTTCACGACGAAGGATATCGTGCGTACC
65 CTTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
** * *
569002 AGCAACATTCATCTTTAGATTAAATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGATCAAC
* * * ** * *
569067 TTCACAACGAAGAGGACATCTATGATTTCAACTTCACGATGAAGGATATCATGCCCACC
66 TTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
* * * *
569126 AGCAACATTCATCTTTAGATTGGATTTCAACTTCATGAAGAAGGATATCCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGATCAAC
* * * ** * *
569191 TTCACAACGAATGAGCCATCCACGGTTTCAACTTCACGACGAAGG--CTCGTGCCCACC
66 TTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
* * * * * *
569248 ATCAACATTCATCTTTAGATTAGATTTCAACTTCAAGATGAAGGATATCCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGATCAAC
* * * *
569313 TTCACAACGAAGGGGTTATCCACGATTTCAACTTCGCGACGAAGGATATCGTGCCCACC
66 TTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
* * * * *
569372 AGCAGCATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGATATTCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGATCAAC
* *
569437 TTCACAATGAAGGGGACATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
66 TTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
* * * *
569496 AACAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATTCAATTCAAGGCTCAAC
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGATCAAC
* * * **
569561 TTCACAACGAAGGGGCCATCTACTATTTCAACTTCACGTCGAAGGATATCGTGCCCACC
66 TTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
* * *
569620 AGCAACATTCATCTTTAGATTGGATTTTAACTTCACGATGAA-AGATATCCAATTCAAGGCTCAA
1 AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGA-ATATCCAATTCAAGGATCAA
** *
569684 CTTCACAACGAATAGGTCATCCACGATTTCAACTTCAC-AACGAAGG
65 CTTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAA-GAAGG
569730 GGTCATCCAC
Statistics
Matches: 971, Mismatches: 116, Indels: 68
0.84 0.10 0.06
Matches are distributed among these distances:
122 110 0.11
123 11 0.01
124 726 0.75
126 1 0.00
127 1 0.00
128 6 0.01
129 1 0.00
130 2 0.00
132 9 0.01
133 4 0.00
136 4 0.00
137 7 0.01
139 2 0.00
140 1 0.00
141 5 0.01
142 1 0.00
143 2 0.00
145 69 0.07
146 9 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (124 bp):
AGCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGAATATCCAATTCAAGGATCAAC
TTCACAACGAAGGGGTCATCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACC
Found at i:568766 original size:18 final size:19
Alignment explanation
Indices: 568740--568786 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
568730 ACCAGCAACA
*
568740 TTCATCTTT-AGATTGGAT
1 TTCAACTTTAAGATTGGAT
568758 TTCAACTTTACGAGATTGGAT
1 TTCAACTTTA--AGATTGGAT
568779 TTCAACTT
1 TTCAACTT
568787 CACGATGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
21 17 0.68
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (19 bp):
TTCAACTTTAAGATTGGAT
Found at i:568775 original size:21 final size:21
Alignment explanation
Indices: 568749--568791 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
568739 ATTCATCTTT
*
568749 AGATTGGATTTCAACTTTACG
1 AGATTGGATTTCAACTTCACG
568770 AGATTGGATTTCAACTTCACG
1 AGATTGGATTTCAACTTCACG
568791 A
1 A
568792 TGAATGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (21 bp):
AGATTGGATTTCAACTTCACG
Found at i:568888 original size:145 final size:145
Alignment explanation
Indices: 568625--568910 Score: 464
Period size: 145 Copynumber: 2.0 Consensus size: 145
568615 ATTCATCTTT
* *
568625 AGATTGGATTTCAACTTCACGATGAAGGATATTCAATTCAAGGATCAACTTCACAATGAAGGGGC
1 AGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGATCAACTTCACAATGAAGGAGC
* * *
568690 TATCCATAATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
66 CATCCACAATTTCAACTTCACGAAGAAGAATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
568755 GATTTCAACTTTACG
131 GATTTCAACTTTACG
* * *
568770 AGATTGGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAATGAATGAGC
1 AGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGATCAACTTCACAATGAAGGAGC
* * * *
568835 CATCTACGATTTCAATTTCACGACGAAGAATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
66 CATCCACAATTTCAACTTCACGAAGAAGAATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
568900 GATTTCAACTT
131 GATTTCAACTT
568911 CACAACGAAG
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
145 129 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (145 bp):
AGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGATCAACTTCACAATGAAGGAGC
CATCCACAATTTCAACTTCACGAAGAAGAATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
GATTTCAACTTTACG
Found at i:569707 original size:494 final size:494
Alignment explanation
Indices: 568770--569729 Score: 1514
Period size: 494 Copynumber: 1.9 Consensus size: 494
568760 CAACTTTACG
* * * * *
568770 AGATTGGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAATGAATGAGC
1 AGATTAGATTTCAACTTCAAGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGAGC
* *
568835 CATCTACGATTTCAATTTCACGACGAAGAATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
66 CATCCACGATTTCAACTTCACGACGAAGAATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
*
568900 GATTTCAACTTCACAACGAAGGATATCCAATTTCAGGCTCAACTTCACAACAAAGGGGTCATCCA
131 GATTTCAACTTCACAACGAAGGATATCCAATTTCAGGCTCAACTTCACAACAAAGGGGACATCCA
** * ** *
568965 TGATTTCAACTTCACGACGAAGGATATCGTGCGTACCAGCAACATTCATCTTTAGATTAAATTTC
196 CAATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAACAACATTCATCTTTAGATTAAATTTC
569030 AACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGACATCTATGATTT
261 AACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGACATCTATGATTT
569095 CAACTTCACGATGAAGGATATCATGCCCACCAGCAACATTCATCTTTAGATTGGATTTCAACTTC
326 CAACTTCACGATGAAGGATATCATGCCCACCAGCAACATTCATCTTTAGATTGGATTTCAACTTC
* * *
569160 ATGAAGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCACGGTTTCAACTT
391 ACGAAGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCACGATTTCAACTT
*
569225 CACGACGAAGGCTCGTGCCCACCATCAACATTCATCTTT
456 CACAACGAAGGCTCGTGCCCACCATCAACATTCATCTTT
* *
569264 AGATTAGATTTCAACTTCAAGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGT
1 AGATTAGATTTCAACTTCAAGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGAGC
* * * *
569329 TATCCACGATTTCAACTTCGCGACGAAGGATATCGTGCCCACCAGCAGCATTCATCTTTAGATTG
66 CATCCACGATTTCAACTTCACGACGAAGAATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
* * * **
569394 GATTTCAACTTCACGATGAAGGATATTCAA-TTCAAGGCTCAACTTCACAATGAAGGGGACATCC
131 GATTTCAACTTCACAACGAAGGATATCCAATTTC-AGGCTCAACTTCACAACAAAGGGGACATCC
**
569458 ACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAACAACATTCATCTTTAGATTGGATTT
195 ACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAACAACATTCATCTTTAGATTAAATTT
* * *
569523 CAACTTCACGACGAAGGATATTCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCTACT-AT
260 CAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGACATCTA-TGAT
* *
569587 TTCAACTTCACG-TCGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGATTGGATTTTAAC
324 TTCAACTTCACGAT-GAAGGATATCATGCCCACCAGCAACATTCATCTTTAGATTGGATTTCAAC
* *
569651 TTCACGATGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAT-AGGTCATCCACGATTTCA
388 TTCACGAAGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAATGA-GCCATCCACGATTTCA
569715 ACTTCACAACGAAGG
452 ACTTCACAACGAAGG
569730 GGTCATCCAC
Statistics
Matches: 424, Mismatches: 38, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
493 5 0.01
494 418 0.99
495 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (494 bp):
AGATTAGATTTCAACTTCAAGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGAGC
CATCCACGATTTCAACTTCACGACGAAGAATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
GATTTCAACTTCACAACGAAGGATATCCAATTTCAGGCTCAACTTCACAACAAAGGGGACATCCA
CAATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAACAACATTCATCTTTAGATTAAATTTC
AACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGACATCTATGATTT
CAACTTCACGATGAAGGATATCATGCCCACCAGCAACATTCATCTTTAGATTGGATTTCAACTTC
ACGAAGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCACGATTTCAACTT
CACAACGAAGGCTCGTGCCCACCATCAACATTCATCTTT
Found at i:569761 original size:32 final size:32
Alignment explanation
Indices: 569680--569761 Score: 128
Period size: 32 Copynumber: 2.6 Consensus size: 32
569670 AATTCAAGGC
**
569680 TCAACTTCACAACGAATAGGTCATCCACGATT
1 TCAACTTCACAACGAAGGGGTCATCCACGATT
569712 TCAACTTCACAACGAAGGGGTCATCCACGATT
1 TCAACTTCACAACGAAGGGGTCATCCACGATT
* *
569744 TCTACTTCACGACGAAGG
1 TCAACTTCACAACGAAGG
569762 TTATCGTACC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (32 bp):
TCAACTTCACAACGAAGGGGTCATCCACGATT
Found at i:569840 original size:156 final size:156
Alignment explanation
Indices: 569556--569877 Score: 520
Period size: 156 Copynumber: 2.1 Consensus size: 156
569546 AATTCAAGGC
* * * *
569556 TCAACTTCACAACGAAGGGGCCATCTACTATTTCAACTTCACGTCGAAGGATATCGTGCCCACCA
1 TCAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTACCCACCA
* *
569621 GCAACATTCATCTTTAGATTGGATTTTAACTTCACGATGAAAGATATCCAATTCAAGGCTCAACT
66 GCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACT
* *
569686 TCACAACGAATAGGTCATCCACGATT
131 TCACAACGAAGAGGCCATCCACGATT
* * *
569712 TCAACTTCACAACGAAGGGGTCATCCACGATTTCTACTTCACGACGAAGGTTATCGTACCCACCA
1 TCAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTACCCACCA
569777 GCAACATTCATCTTTAGATTGGATTTCAACTTCACGACG-AAGAATATCCAATTCAAGGCTCAAC
66 GCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAAG-ATATCCAATTCAAGGCTCAAC
*
569841 TTCACAACGAAGGGGCCATCCACGATT
130 TTCACAACGAAGAGGCCATCCACGATT
569868 TCAACTTCAC
1 TCAACTTCAC
569878 GACAAAGGAT
Statistics
Matches: 153, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
155 3 0.02
156 150 0.98
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (156 bp):
TCAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTACCCACCA
GCAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACT
TCACAACGAAGAGGCCATCCACGATT
Found at i:570154 original size:3 final size:3
Alignment explanation
Indices: 570138--570185 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
570128 TCTACAAAAA
570138 TAT T-T TAT TA- TAT TAT TATT TAT TAT TAT TAT TATT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT
570182 TAT T
1 TAT T
570186 TTTGCAGGCC
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.15
3 28 0.70
4 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:570164 original size:13 final size:13
Alignment explanation
Indices: 570138--570186 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
570128 TCTACAAAAA
570138 TATT-TTATTATAT
1 TATTATTATT-TAT
570151 TATTATT-TATTAT
1 TATTATTAT-TTAT
570164 TATTATTATTTAT
1 TATTATTATTTAT
570177 T-TTATTATTT
1 TATTATTATTT
570187 TTGCAGGCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 9 0.27
13 20 0.61
14 4 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:574780 original size:26 final size:26
Alignment explanation
Indices: 574750--574813 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
574740 TACTATATTG
* *
574750 TAATGTAATGTATGAGTTAATGCTTC
1 TAATGTAATGTAGGAGTTAATACTTC
*
574776 TAATGTAATGTAGGAGTTAATATTTC
1 TAATGTAATGTAGGAGTTAATACTTC
*
574802 TAATATAATGTA
1 TAATGTAATGTA
574814 ATGTATGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (26 bp):
TAATGTAATGTAGGAGTTAATACTTC
Found at i:574783 original size:31 final size:31
Alignment explanation
Indices: 574748--574838 Score: 90
Period size: 26 Copynumber: 3.2 Consensus size: 31
574738 TCTACTATAT
574748 TGTAATGTAATGTATGAGTTAATGCTTCTAA
1 TGTAATGTAATGTATGAGTTAATGCTTCTAA
**
574779 TGTAATGT-A-G---GAGTTAATATTTCTAA
1 TGTAATGTAATGTATGAGTTAATGCTTCTAA
*
574805 TATAATGTAATGTATGAG-T-ATGCTT-TGAA
1 TGTAATGTAATGTATGAGTTAATGCTTCT-AA
574834 TGTAA
1 TGTAA
574839 AATTTAGTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
26 21 0.44
27 1 0.02
28 2 0.04
29 11 0.23
30 2 0.04
31 11 0.23
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.42
Consensus pattern (31 bp):
TGTAATGTAATGTATGAGTTAATGCTTCTAA
Found at i:575862 original size:31 final size:30
Alignment explanation
Indices: 575780--575864 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 30
575770 AAAAAATTAA
* *
575780 AAAATTTAAAATATATCACAAAATAAAAAAT
1 AAAATTTAAAATATTTTA-AAAATAAAAAAT
*
575811 AATTAA-TT-ATATATTATTAAAAATAAAAAAT
1 AA--AATTTAAAATATT-TTAAAAATAAAAAAT
575842 AAAATTTCAAAATATTTTAAAAA
1 AAAATTT-AAAATATTTTAAAAA
575865 ATATATATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
29 2 0.05
30 2 0.05
31 28 0.64
32 10 0.23
33 2 0.05
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAATTTAAAATATTTTAAAAATAAAAAAT
Found at i:576385 original size:38 final size:38
Alignment explanation
Indices: 576306--576411 Score: 122
Period size: 38 Copynumber: 2.8 Consensus size: 38
576296 TTTAAAAAAG
* * * *
576306 TAAACGAGTTTGTTCATGAACATAAACGAACGAGTCGA
1 TAAACAAGTTTGTTCATGAACATAAATGAACAAGTCAA
*** *
576344 TAAATGCGTTTGTTCATGAACATAAATGAACAAGTTAA
1 TAAACAAGTTTGTTCATGAACATAAATGAACAAGTCAA
* *
576382 TAAACAAGCTTGTTCATGAACATTAATGAA
1 TAAACAAGTTTGTTCATGAACATAAATGAA
576412 TCGGACACAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (38 bp):
TAAACAAGTTTGTTCATGAACATAAATGAACAAGTCAA
Found at i:581184 original size:41 final size:41
Alignment explanation
Indices: 581105--581204 Score: 98
Period size: 41 Copynumber: 2.5 Consensus size: 41
581095 TACATATATC
* *
581105 GTGGCATTTTTAGACAAATGCCACTAAAACCTAGTACTTTA
1 GTGGCATTTTTAGACAAACGCCACTAAAACCTAATACTTTA
* *
581146 GTGGCATTTTTCA-ATAAACGCCGCTAAAACAC-AATACTTTA
1 GTGGCATTTTT-AGACAAACGCCACTAAAAC-CTAATACTTTA
* * *
581187 ATGGC-GTTTTAGGCAAAC
1 GTGGCATTTTTAGACAAAC
581205 ATGTCGTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
39 1 0.02
40 8 0.17
41 37 0.77
42 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (41 bp):
GTGGCATTTTTAGACAAACGCCACTAAAACCTAATACTTTA
Found at i:585096 original size:29 final size:25
Alignment explanation
Indices: 585026--585077 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
585016 AAATCGCCGC
*
585026 TATAGATCTGACCTTTTGCGGCGTT
1 TATAGATCTGACCTTTCGCGGCGTT
585051 TATAGATCTTGACCTTTCGCGGCGTT
1 TATAGATC-TGACCTTTCGCGGCGTT
585077 T
1 T
585078 TTGGAAGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.40
Consensus pattern (25 bp):
TATAGATCTGACCTTTCGCGGCGTT
Found at i:585180 original size:43 final size:43
Alignment explanation
Indices: 585083--585180 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
585073 CGTTTTTGGA
* *
585083 AGATCTCGACCTTTTTCGGAGTTTGTTCCAAAAACGCCGCTAT
1 AGATCTCGACCTTTTTCGGAGTTTGTTCAAAAAACGACGCTAT
* *
585126 AGATATCGACCTTTTGT-GGCGTTTGTTCAAAAAACGACGCTAT
1 AGATCTCGACCTTTT-TCGGAGTTTGTTCAAAAAACGACGCTAT
*
585169 AGATCTTGACCT
1 AGATCTCGACCT
585181 ATTGCTGCGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 47 0.98
44 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (43 bp):
AGATCTCGACCTTTTTCGGAGTTTGTTCAAAAAACGACGCTAT
Found at i:585191 original size:43 final size:43
Alignment explanation
Indices: 585103--585192 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
585093 CTTTTTCGGA
* * *
585103 GTTTGTTCCAAAAACGCCGCTATAGATATCGACCTTTTGTGGC
1 GTTTGTTCAAAAAACGACGCTATAGATATCGACCTATTGTGGC
* *
585146 GTTTGTTCAAAAAACGACGCTATAGATCTTGACCTATTGCT-GC
1 GTTTGTTCAAAAAACGACGCTATAGATATCGACCTATTG-TGGC
585189 GTTT
1 GTTT
585193 TTTGTTCTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
43 40 0.98
44 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34
Consensus pattern (43 bp):
GTTTGTTCAAAAAACGACGCTATAGATATCGACCTATTGTGGC
Found at i:587224 original size:195 final size:193
Alignment explanation
Indices: 586887--587252 Score: 714
Period size: 195 Copynumber: 1.9 Consensus size: 193
586877 ATCAAAGATA
586887 ATAATAACATAAAATTATAGAATAATTCTATGTTTTAAAGGGATCAGGACTATTAGAATAAGATT
1 ATAATAACATAAAATTATAGAATAATTCTATGTTTTAAAGGGATCAGGACTATTAGAATAAGATT
586952 ATCCTCAACAAAAAAATCCTTGCATAAACCTTAGAAATCTTTGTTACCATTGAACCCTAAACTCT
66 ATCCTCAACAAAAAAATCCTTGCATAAACCTTAGAAATCTTTGTTACCATTGAACCCTAAACTCT
587017 GTAAAACCGTTGTAATTAAGAAGCCTTAGCCTAATAGAGTTCAAAACAATTCACAGTCAACAAT
131 GTAAAACCGTTGTAATTAAGAAGCCTTAGCCTAATA-AGTTCAAAACAATTCACAGTCAACAAT
587081 ATAATAAACATAAAATTATAGAATAATTCTATGTTTTAAAGGGATCAGGACTATTAGAATAAGAT
1 ATAAT-AACATAAAATTATAGAATAATTCTATGTTTTAAAGGGATCAGGACTATTAGAATAAGAT
587146 TATCCTCAACAAAAAAATCCTTGCATAAACCTTAGAAATCTTTGTTACCATTGAACCCTAAACTC
65 TATCCTCAACAAAAAAATCCTTGCATAAACCTTAGAAATCTTTGTTACCATTGAACCCTAAACTC
587211 TGTAAAACCGTTGTAATTAAGAAGCCTTAGCCTAATAAGTTC
130 TGTAAAACCGTTGTAATTAAGAAGCCTTAGCCTAATAAGTTC
587253 CATGAAATTA
Statistics
Matches: 171, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
194 10 0.06
195 161 0.94
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (193 bp):
ATAATAACATAAAATTATAGAATAATTCTATGTTTTAAAGGGATCAGGACTATTAGAATAAGATT
ATCCTCAACAAAAAAATCCTTGCATAAACCTTAGAAATCTTTGTTACCATTGAACCCTAAACTCT
GTAAAACCGTTGTAATTAAGAAGCCTTAGCCTAATAAGTTCAAAACAATTCACAGTCAACAAT
Found at i:588075 original size:25 final size:25
Alignment explanation
Indices: 588017--588065 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
588007 ATATAACACG
*
588017 TATAACATAATTGGTCACTTATTTA
1 TATAACATAATTGATCACTTATTTA
588042 TATAACATAATTGATCACTTATTT
1 TATAACATAATTGATCACTTATTT
588066 TTGTGTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (25 bp):
TATAACATAATTGATCACTTATTTA
Done.