Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:774614 original size:24 final size:24
Alignment explanation
Indices: 774547--774614 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
774537 CTGAAAAATC
* * *
774547 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
774571 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
774595 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
774615 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:775865 original size:5 final size:5
Alignment explanation
Indices: 775855--775888 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
775845 GGATCGAATG
775855 GACTC GACTC GAGCTC GACTC GAGCTC GACTC GA
1 GACTC GACTC GA-CTC GACTC GA-CTC GACTC GA
775889 GTTCTTAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 17 0.63
6 10 0.37
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (5 bp):
GACTC
Found at i:775873 original size:11 final size:11
Alignment explanation
Indices: 775857--775889 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
775847 ATCGAATGGA
775857 CTCGACTCGAG
1 CTCGACTCGAG
775868 CTCGACTCGAG
1 CTCGACTCGAG
775879 CTCGACTCGAG
1 CTCGACTCGAG
775890 TTCTTAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.27, T:0.18
Consensus pattern (11 bp):
CTCGACTCGAG
Found at i:775876 original size:16 final size:16
Alignment explanation
Indices: 775855--775888 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
775845 GGATCGAATG
775855 GACTCGACTCGAGCTC
1 GACTCGACTCGAGCTC
775871 GACTCGAGCTCGA-CTC
1 GACTCGA-CTCGAGCTC
775887 GA
1 GA
775889 GTTCTTAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (16 bp):
GACTCGACTCGAGCTC
Found at i:776506 original size:29 final size:29
Alignment explanation
Indices: 776445--776506 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
776435 TTTAGAAAAT
** * *
776445 ATTTAAACTTAAATCTAATAAAATATTAT
1 ATTTAAACTTAAATAAAATAAAATATAAA
776474 ATTTAAACTTAAATAAAA-ATAAATATAAA
1 ATTTAAACTTAAATAAAATA-AAATATAAA
776503 ATTT
1 ATTT
776507 TAATAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTTAAACTTAAATAAAATAAAATATAAA
Found at i:776606 original size:64 final size:63
Alignment explanation
Indices: 776536--776693 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 63
776526 TTATATGATA
*
776536 TAAAATTAAATATCTATAACATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
776600 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
776664 TAAAATTAATATCTATAATATAAAATTAAA
1 TAAAATTAATATCTATAATATAATATTAAA
776694 TATAAAACTT
Statistics
Matches: 91, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
63 22 0.24
64 69 0.76
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:776635 original size:40 final size:37
Alignment explanation
Indices: 776557--776640 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 37
776547 ATCTATAACA
*
776557 TAATATTAAAAATTAATATTTAATTTATTTAAAAAAT
1 TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
776594 TAATATT-AAAATTAATATCTATAATATAATATTAAAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-TAAT-TTAAAAAAT
776634 TAATATT
1 TAATATT
776641 TAATTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
36 11 0.26
37 8 0.19
38 4 0.10
39 3 0.07
40 16 0.38
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (37 bp):
TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
Found at i:776644 original size:26 final size:26
Alignment explanation
Indices: 776591--776675 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 26
776581 TTATTTAAAA
776591 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
776616 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
* *
776642 AATTTAT-TTAAAAAATTAATATTAA
1 AATTAATATTAAAAAATTAATATTAT
776667 AATTAATAT
1 AATTAATAT
776676 CTATAATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
24 16 0.31
25 12 0.23
26 12 0.23
27 1 0.02
28 11 0.21
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:793292 original size:13 final size:13
Alignment explanation
Indices: 793274--793298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
793264 GCAAAAAGCA
793274 AAAAAATAAAAAT
1 AAAAAATAAAAAT
793287 AAAAAATAAAAA
1 AAAAAATAAAAA
793299 AATGTATGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:800030 original size:18 final size:18
Alignment explanation
Indices: 800007--800045 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
799997 CTTTAGGTAA
800007 CTTCTCAATCCCTAATCT
1 CTTCTCAATCCCTAATCT
*
800025 CTTCTCAATCCCTAATTT
1 CTTCTCAATCCCTAATCT
800043 CTT
1 CTT
800046 TCGATCCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (18 bp):
CTTCTCAATCCCTAATCT
Found at i:802552 original size:21 final size:22
Alignment explanation
Indices: 802511--802554 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
802501 AATGTCAGAG
*
802511 GGGAACCGATTCCCCTACTACA
1 GGGAACCGATTACCCTACTACA
*
802533 GGGAACCGA-TACCCTGCTACA
1 GGGAACCGATTACCCTACTACA
802554 G
1 G
802555 TACTTCCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTACCCTACTACA
Found at i:803196 original size:24 final size:24
Alignment explanation
Indices: 803169--803236 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
803159 CACCACAGCT
*
803169 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
803193 CGTAGAATTTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
* *
803217 TGTAGAAA-TGCACCGTAGTG
1 CGTAGAAATTGCACCGAAGTG
803237 TCATATAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 11 0.29
24 27 0.71
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:805820 original size:2 final size:2
Alignment explanation
Indices: 805761--805804 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
805751 AATATTTTGC
805761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
805803 TA
1 TA
805805 GCAAAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:806846 original size:19 final size:19
Alignment explanation
Indices: 806819--806855 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
806809 AAATGACCAA
*
806819 ATAAATCGCAATGCGATCG
1 ATAAATCGCAACGCGATCG
*
806838 ATAATTCGCAACGCGATC
1 ATAAATCGCAACGCGATC
806856 TCCGGTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (19 bp):
ATAAATCGCAACGCGATCG
Found at i:806934 original size:20 final size:21
Alignment explanation
Indices: 806883--806928 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
806873 GTTTCCAGAT
806883 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
806904 TCGCAACGCGAACTT-GACTA
1 TCGCAACGCGAACTTCGACTA
806924 TCGCA
1 TCGCA
806929 TTGCGATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:806948 original size:21 final size:21
Alignment explanation
Indices: 806924--807047 Score: 103
Period size: 21 Copynumber: 5.9 Consensus size: 21
806914 AACTTGACTA
*
806924 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
806945 TCGCGTTACGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
* * *
806966 TCGCGTTGCGATTTATTACAAAT
1 TCGCGTTGCGA--TAGTCCAAGT
*
806989 T--CGTTGTGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
807008 TCGCGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA--TAGTCCAAGT
807031 T--CGTTGCGATAGTCCAA
1 TCGCGTTGCGATAGTCCAA
807048 AATCGCAACG
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
19 15 0.19
21 50 0.62
23 16 0.20
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:807000 original size:42 final size:42
Alignment explanation
Indices: 806948--807047 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
806938 TCCAAGTTCG
* *
806948 CGTTACGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
* *
806990 CGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
807032 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
807048 AATCGCAACG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
Found at i:808218 original size:6 final size:6
Alignment explanation
Indices: 808207--808266 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
808197 GCCATCCCTA
* *
808207 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT AGTGGT AGTGGT
1 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
* *
808255 AGTGGT AGTGGT
1 CGTGGT CGTGGT
808267 AATACGTGTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.07, C:0.10, G:0.50, T:0.33
Consensus pattern (6 bp):
CGTGGT
Found at i:808379 original size:19 final size:19
Alignment explanation
Indices: 808355--808421 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 19
808345 TCGTTGCGAT
808355 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
808374 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
*
808397 CTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
808416 TTTGGA
1 TTTGGA
808422 AAATCGCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 16 0.40
21 14 0.35
23 10 0.25
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:808427 original size:19 final size:19
Alignment explanation
Indices: 808363--808429 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
808353 ATTTTGGACT
808363 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
* **
808384 ATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAA
808405 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
808424 ATCGCA
1 ATCGCA
808430 TTGCGATAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 15 0.39
21 14 0.37
22 1 0.03
23 8 0.21
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:808454 original size:21 final size:21
Alignment explanation
Indices: 808425--808477 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
808415 ATTTGGAAAA
* *
808425 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTAGAAGT
*
808446 TCGCGTTGCGATAGTAGATGT
1 TCGCGTTGCGATAGTAGAAGT
808467 TCGCGTTGCGA
1 TCGCGTTGCGA
808478 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTAGAAGT
Found at i:809562 original size:21 final size:22
Alignment explanation
Indices: 809524--809564 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
809514 TAAAATCTTA
*
809524 TTTAGAGATAAATTTATAAAAT
1 TTTAGAGATAAATATATAAAAT
*
809546 TTTAGA-ATATATATATAAA
1 TTTAGAGATAAATATATAAA
809565 CTTTCATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTAGAGATAAATATATAAAAT
Found at i:811696 original size:21 final size:21
Alignment explanation
Indices: 811655--811696 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
811645 TTATAATTCC
**
811655 ATTTAAATATAATTACTTTTA
1 ATTTAAATATAATTAAATTTA
811676 ATTTAAA-ATAAATTAAATTTA
1 ATTTAAATAT-AATTAAATTTA
811697 GTTTGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTAAATATAATTAAATTTA
Found at i:816174 original size:2 final size:2
Alignment explanation
Indices: 816167--816196 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
816157 TAACTTTTTA
816167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
816197 CACAAAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:818262 original size:3 final size:3
Alignment explanation
Indices: 818254--818310 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
818244 GTTTTATTTA
* *
818254 TAT TAT TAT TAT TAT TA- TAT TATT TAT TAT ATAT TTT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT TAT TAT TAT
818300 TAT TAT TAT TA
1 TAT TAT TAT TA
818311 CAACCATGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:818310 original size:12 final size:12
Alignment explanation
Indices: 818247--818310 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
818237 TGTCTCGGTT
*
818247 TTATTTATATTA
1 TTATTAATATTA
*
818259 TTATTATTATTA
1 TTATTAATATTA
818271 -TATT-AT-TTA
1 TTATTAATATTA
* *
818280 TTATATATTTTTA
1 TTAT-TAATATTA
818293 TTATTAATATTA
1 TTATTAATATTA
818305 TTATTA
1 TTATTA
818311 CAACCATGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 3 0.07
10 4 0.10
11 5 0.12
12 23 0.55
13 7 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:831058 original size:64 final size:64
Alignment explanation
Indices: 830957--831082 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 64
830947 AATGTACTCA
* *
830957 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
1 TAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATT
*
831021 TAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 TAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAA
831083 ATTGAAAGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (64 bp):
TAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATT
Found at i:831206 original size:64 final size:64
Alignment explanation
Indices: 831105--831227 Score: 228
Period size: 64 Copynumber: 1.9 Consensus size: 64
831095 ATGTGCATAA
*
831105 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAG
*
831169 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAA
831228 ATTGAAAGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (64 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAG
Found at i:831223 original size:145 final size:146
Alignment explanation
Indices: 830955--831313 Score: 666
Period size: 145 Copynumber: 2.5 Consensus size: 146
830945 GCAATGTACT
830955 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAAT
831020 TTAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAAT
66 TTAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAAT
831085 TGAAAGATGAATGTG-
131 TGAAAGATGAATGTGC
*
831100 CATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAAT
*
831165 TTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAAT
66 TTAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAAT
831230 TGAAAGATGAATGTGC
131 TGAAAGATGAATGTGC
* *
831246 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAA
1 -CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
831311 TTT
65 TTT
831314 GAAAGATGAA
Statistics
Matches: 207, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
145 143 0.69
147 64 0.31
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (146 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAAT
TTAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAAT
TGAAAGATGAATGTGC
Found at i:831309 original size:83 final size:83
Alignment explanation
Indices: 831166--831370 Score: 365
Period size: 83 Copynumber: 2.5 Consensus size: 83
831156 TCATTGAATT
*
831166 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAATT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAAATT
831231 GAAAGATGAATGTGCTCA
66 GAAAGATGAATGTGCTCA
* * * *
831249 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTT
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAAATT
831314 GAAAGATGAATGTGCTCA
66 GAAAGATGAATGTGCTCA
831332 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
831371 ATTCGGTAGG
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 117 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (83 bp):
TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAAATT
GAAAGATGAATGTGCTCA
Found at i:831531 original size:114 final size:114
Alignment explanation
Indices: 831331--831643 Score: 572
Period size: 114 Copynumber: 2.7 Consensus size: 114
831321 GAATGTGCTC
*
831331 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAACCAAT
1 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAACCAAT
831396 CATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
66 CATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
*
831445 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGAAACCCCAAAACCAAT
1 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAACCAAT
831510 CATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
66 CATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
* *
831559 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAGAACCGAT
1 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAACCAAT
* *
831624 CATTGGAATTGAAAGATGAA
66 CATTGGATTTAAAAGATGAA
831644 CTGCATGATC
Statistics
Matches: 192, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 192 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (114 bp):
ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAACCAAT
CATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
Found at i:832399 original size:36 final size:38
Alignment explanation
Indices: 832347--832442 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 38
832337 TTTCCAGAGA
*
832347 AAGTTCATAATAAGAAGAACTCATCTG-AA-GAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAG
832383 AAGTTCATAATGAGAAGAACTCATCTGAAAAAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTG---AAAGGAAGAAG
832424 AAGTTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
832443 TTTGTTCAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
36 26 0.48
40 2 0.04
41 26 0.48
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (38 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAG
Found at i:832721 original size:113 final size:113
Alignment explanation
Indices: 832383--833134 Score: 1090
Period size: 114 Copynumber: 6.7 Consensus size: 113
832373 GAAGAAGAAG
*
832383 AAGTTCATAATGAGAAGAACTCATCTGAAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAGTTCATAATGAGAAGAACTCATCTG-AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
832448 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAGA
65 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAGA
*
832497 AAGTTCATAATGAGAAGAACTCATCTGAAAAACGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAA-GGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * *
832562 TCAACTTTTTGTTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGA
65 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAGA
832611 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * * * * *
832676 CAACCTTTTGTTTAAATTCACCAATTGATGGATTAACTTTGCCAGAGG
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAGA
* *
832724 AAGTTCATAATGAGAAGAACTCATCTAAAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAGTTCATAATGAGAAGAACTCATCT-GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* *
832789 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGA
65 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAGA
832838 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * * * * *
832903 CAACCTTTTGTTTAAATTCATCAATTAATGGATTAACATTGCCAG-GTA
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAG-A
* *
832951 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATAAGAAGAATTT
1 AAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
* *
833012 GTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGA
63 GTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAGA
* * *
833063 AAGTTCATAATGAGAAGAACTCAT-T--TGAA-GAAGAAGAAGTTCACAATGAGAAGAGTTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
*
833124 CAGCCTTTTGC
66 CAACCTTTTGC
833135 ATAATTCTAT
Statistics
Matches: 575, Mismatches: 53, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
106 7 0.01
107 1 0.00
108 3 0.01
109 33 0.06
110 1 0.00
112 77 0.13
113 198 0.34
114 238 0.41
115 5 0.01
116 12 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAGA
Found at i:832779 original size:227 final size:227
Alignment explanation
Indices: 832383--833133 Score: 1201
Period size: 227 Copynumber: 3.3 Consensus size: 227
832373 GAAGAAGAAG
*
832383 AAGTTCATAATGAGAAGAACTCATCTGAAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAGTTCATAATGAGAAGAACTCATCTG-AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * * *
832448 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTGCCAGAGAAAGTTCATAATGAGAA
65 TCAACCTTTTGTTTAAATTCATCAATTGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAA
* * * *
832513 GAACTCATCTGAAAAACGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTCAA
130 GAACTCATCTAAAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAA
832578 ATCCATCACTTGATGGATCAGCTTTTCCAGAGA
195 ATCCATCACTTGATGGATCAGCTTTTCCAGAGA
832611 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* *
832676 CAACCTTTTGTTTAAATTCACCAATTGATGGATTAACTTTGCCAGAGGAAGTTCATAATGAGAAG
66 CAACCTTTTGTTTAAATTCATCAATTGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAG
832741 AACTCATCTAAAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAA
131 AACTCATCTAAAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAA
832806 TCCATCACTTGATGGATCAGCTTTTCCAGAGA
196 TCCATCACTTGATGGATCAGCTTTTCCAGAGA
832838 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
832903 CAACCTTTTGTTTAAATTCATCAATTAATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAA
66 CAACCTTTTGTTTAAATTCATCAATTGATGGATTAACTTTGCCAGAG-AAAGTTCATAATGAGAA
* **** * *
832967 GAACTCGTC-ATCTGAA-GAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAA
130 GAACTCATCTAAAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAA
833030 ATCCATCACTTGATGGATCAGCTTTTCCAGAGA
195 ATCCATCACTTGATGGATCAGCTTTTCCAGAGA
* * *
833063 AAGTTCATAATGAGAAGAACTCAT-T--TGAA-GAAGAAGAAGTTCACAATGAGAAGAGTTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
*
833124 CAGCCTTTTG
66 CAACCTTTTG
833134 CATAATTCTA
Statistics
Matches: 494, Mismatches: 28, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
221 39 0.08
222 3 0.01
224 1 0.00
225 102 0.21
226 4 0.01
227 318 0.64
228 27 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (227 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGTTTAAATTCATCAATTGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAG
AACTCATCTAAAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAA
TCCATCACTTGATGGATCAGCTTTTCCAGAGA
Found at i:833374 original size:3 final size:3
Alignment explanation
Indices: 833366--833422 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
833356 GTTTTATTTA
* *
833366 TAT TAT TAT TAT TA- TAT TAT TATT TAT TAT ATAT TTT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT TAT TAT TAT
833412 TAT TAT TAT TA
1 TAT TAT TAT TA
833423 CAACCAGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:841035 original size:54 final size:54
Alignment explanation
Indices: 840971--841084 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
840961 GAATGATATT
* * * ** *
840971 GATATTGTTCGTCGGGTATCAATATAATGGTATTGATG-TTTTTCGAGTAGTATC
1 GATACTGTTCGTCGGATACCAATATAATGGTATTGATGCCATTT-GAGGAGTATC
** *
841025 GATACTGTTCGTTTGATACCAATATAGTGGTATTGATGCCATTTGAGGAGTATC
1 GATACTGTTCGTCGGATACCAATATAATGGTATTGATGCCATTTGAGGAGTATC
841079 GATACT
1 GATACT
841085 TTTTGGAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 47 0.94
55 3 0.06
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.39
Consensus pattern (54 bp):
GATACTGTTCGTCGGATACCAATATAATGGTATTGATGCCATTTGAGGAGTATC
Found at i:846073 original size:16 final size:17
Alignment explanation
Indices: 846052--846085 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
846042 AAATGTTTTC
*
846052 ATTTTAATAAAAT-TTA
1 ATTTTAAAAAAATATTA
846068 ATTTTAAAAAAATATTA
1 ATTTTAAAAAAATATTA
846085 A
1 A
846086 AACAACGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTAAAAAAATATTA
Found at i:847655 original size:29 final size:30
Alignment explanation
Indices: 847586--847644 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
847576 AATTTAAGGT
847586 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
847617 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
847645 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:847750 original size:21 final size:21
Alignment explanation
Indices: 847724--847802 Score: 131
Period size: 21 Copynumber: 3.8 Consensus size: 21
847714 AGGGTGTCAA
847724 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
847745 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
847766 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
847787 AGTGCATCGATGCACC
1 AGTGCATCCATGCACC
847803 TGCACTAGTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:847869 original size:20 final size:20
Alignment explanation
Indices: 847844--847911 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
847834 AATGCAATTA
*
847844 GTGCATCGATGCATCCTTTT
1 GTGCATCGATGCATCCTATT
* *
847864 GTGCATCGATGAAT-CAAGGTT
1 GTGCATCGATGCATCCTA--TT
*
847885 GTGCATCGATGCATCCTACT
1 GTGCATCGATGCATCCTATT
847905 GTGCATC
1 GTGCATC
847912 CACGCACGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 21 0.54
21 15 0.38
22 2 0.05
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTATT
Found at i:848949 original size:30 final size:30
Alignment explanation
Indices: 848915--848971 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
848905 CAGAGGTTAC
*
848915 AAAGAACCCCGGTAACTATCCAGATGTCAT
1 AAAGAACCCCGGCAACTATCCAGATGTCAT
* * *
848945 AAAGATCCTCGGCAACTATCCATATGT
1 AAAGAACCCCGGCAACTATCCAGATGT
848972 TCCTTTCAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (30 bp):
AAAGAACCCCGGCAACTATCCAGATGTCAT
Found at i:862657 original size:64 final size:64
Alignment explanation
Indices: 862503--862659 Score: 146
Period size: 64 Copynumber: 2.5 Consensus size: 64
862493 CAATAAGGGT
* **
862503 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATACATTCGATGTTGTATTATTATTAAG
* * * * *
862567 ATGCATCGATGCA-TGCCTTATACATCGATGCACT-AATTGCATTCGATG-T-TATTATT-TTAA
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCGATGTTGTATTATTATT--
862627 AAG
62 AAG
862630 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
862660 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
61 2 0.03
62 7 0.09
63 4 0.05
64 57 0.76
65 5 0.07
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTGTATTATTATTAAG
Found at i:866366 original size:34 final size:30
Alignment explanation
Indices: 866327--866395 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
866317 TTGATATAAC
*
866327 AATTTAAGGCAAAATGGTTTTTTGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
866361 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
866390 AATTTA
1 AATTTA
866396 TTTAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:866406 original size:29 final size:30
Alignment explanation
Indices: 866336--866395 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
866326 CAATTTAAGG
*
866336 CAAAATGGTTTTTTGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
866367 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
866396 TTTAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:866501 original size:21 final size:20
Alignment explanation
Indices: 866475--866573 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
866465 AGGGTGTCAA
866475 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
866496 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
866517 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
** *
866538 TAGTGCATTGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
866559 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
866574 TCAAACACCG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.53
22 12 0.18
23 3 0.04
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:866619 original size:20 final size:20
Alignment explanation
Indices: 866594--866687 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
866584 AATGCAATTA
* *
866594 GTGCATCGATGCTTCCTTTT
1 GTGCATCGATGCATCCTGTT
*
866614 GTGCATCGATGCAAT-CTTTT
1 GTGCATCGATGC-ATCCTGTT
**
866634 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-CTGTT
*
866655 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGTT
*
866675 GTGCATCCATGCA
1 GTGCATCGATGCA
866688 CGAAGGCTGC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.68
21 18 0.29
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGTT
Found at i:869356 original size:39 final size:39
Alignment explanation
Indices: 869298--869372 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
869288 CTGCTTCAAT
*
869298 TTCACTTCTTGACAATGCTAAGCCAGACTCTACTTCCAA
1 TTCACTTCTTAACAATGCTAAGCCAGACTCTACTTCCAA
* * *
869337 TTCACTTGTTAACACTGCTAGGCCAGACTCTACTTC
1 TTCACTTCTTAACAATGCTAAGCCAGACTCTACTTC
869373 TACTTTGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (39 bp):
TTCACTTCTTAACAATGCTAAGCCAGACTCTACTTCCAA
Found at i:872241 original size:47 final size:47
Alignment explanation
Indices: 872171--872264 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
872161 ATACACTTTT
* *
872171 GCTCTTGGTAAGGATGATTCCTTATCTTTAGTTCATATATCTTTCAA
1 GCTCTTGGTAAGGATGATACCTTATCTTCAGTTCATATATCTTTCAA
* * *
872218 GCTCTTGGTAATGATGATACCTTATCTTCATTTCATATCTCTTTCAA
1 GCTCTTGGTAAGGATGATACCTTATCTTCAGTTCATATATCTTTCAA
872265 TAGAGTACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (47 bp):
GCTCTTGGTAAGGATGATACCTTATCTTCAGTTCATATATCTTTCAA
Found at i:880897 original size:3 final size:3
Alignment explanation
Indices: 880889--880913 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
880879 TCAAAATTGC
880889 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
880914 GGAATCCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:882510 original size:29 final size:30
Alignment explanation
Indices: 882457--882521 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
882447 AAAAAATTGA
882457 TATTTTATATAAATTCTAAGATT-AATTAG
1 TATTTTATATAAATTCTAAGATTAAATTAG
* *
882486 TATTTTCTATAAAATT-TAA-AGTTAAATTAT
1 TATTTTATAT-AAATTCTAAGA-TTAAATTAG
882516 TATTTT
1 TATTTT
882522 TAAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 14 0.45
30 16 0.52
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
TATTTTATATAAATTCTAAGATTAAATTAG
Found at i:882740 original size:2 final size:2
Alignment explanation
Indices: 882735--882782 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
882725 TAACTGAAAT
882735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
882777 TA -A TA T
1 TA TA TA T
882783 CGGTCCACCC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:882967 original size:22 final size:22
Alignment explanation
Indices: 882924--882971 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
882914 TCTTTTGTTT
* *
882924 TTTTCTAAAAATATATATTATA
1 TTTTCTAAAAATATAAAATATA
882946 TTTTCTCAAAAATA-AAAATATA
1 TTTTCT-AAAAATATAAAATATA
882968 TTTT
1 TTTT
882972 ATTTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTCTAAAAATATAAAATATA
Found at i:882983 original size:27 final size:29
Alignment explanation
Indices: 882929--883003 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 29
882919 TGTTTTTTTC
** *
882929 TAAAAATATATATTATATTTTCTCAAAAA
1 TAAAAATATATATTATATTTAATAAAAAA
882958 TAAAAATATAT-TT-TATTTAATAAAAAA
1 TAAAAATATATATTATATTTAATAAAAAA
* **
882985 TATATTTA-ATATTATATTT
1 TAAAAATATATATTATATTT
883004 TACAATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.05
27 18 0.47
28 7 0.18
29 11 0.29
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAAAATATATATTATATTTAATAAAAAA
Found at i:883016 original size:22 final size:20
Alignment explanation
Indices: 882986--883033 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
882976 AATAAAAAAT
*
882986 ATATTTAATATTATATTTTACA
1 ATATATAATA-TATATTTT-CA
*
883008 ATATATAATATATATTTTTA
1 ATATATAATATATATTTTCA
883028 ATATAT
1 ATATAT
883034 TTATTTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 8 0.33
22 9 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATATAATATATATTTTCA
Found at i:885031 original size:63 final size:63
Alignment explanation
Indices: 884932--885060 Score: 213
Period size: 63 Copynumber: 2.0 Consensus size: 63
884922 CAAATATTGA
* * *
884932 AAATCAAGTTGATAGGTCGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAAACAGATACATC
1 AAATCAAGTAGATAAGTCGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAAACAAATACATC
* *
884995 AAATCAAGTAGATAAGTTGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAGACAAATACATC
1 AAATCAAGTAGATAAGTCGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAAACAAATACATC
885058 AAA
1 AAA
885061 GAGTGCAACC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (63 bp):
AAATCAAGTAGATAAGTCGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAAACAAATACATC
Found at i:890118 original size:20 final size:20
Alignment explanation
Indices: 890093--890140 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
890083 ATAATACAAA
890093 ATCGCAACGCAATTCTGACT
1 ATCGCAACGCAATTCTGACT
*
890113 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCAATTCTGACT
890133 ATCGCAAC
1 ATCGCAAC
890141 ACTGAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCAATTCTGACT
Found at i:890312 original size:17 final size:17
Alignment explanation
Indices: 890290--890324 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
890280 TATCCGTTCT
890290 TATATCCAACGACATCC
1 TATATCCAACGACATCC
890307 TATATCCAACGACATCC
1 TATATCCAACGACATCC
890324 T
1 T
890325 TCCCCATCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (17 bp):
TATATCCAACGACATCC
Found at i:893143 original size:18 final size:18
Alignment explanation
Indices: 893111--893145 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
893101 AGCAAAAGGC
*
893111 AATCAAAATAGCAATCAA
1 AATCAAAATACCAATCAA
*
893129 AATCAAAATCCCAATCA
1 AATCAAAATACCAATCA
893146 CAACCAGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATACCAATCAA
Found at i:893341 original size:20 final size:20
Alignment explanation
Indices: 893316--893456 Score: 143
Period size: 20 Copynumber: 7.4 Consensus size: 20
893306 TTAGACATTC
* * *
893316 ATTTGAATATCTCAATGCGA
1 ATTTGACTATCGCAACGCGA
893336 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
893356 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
893376 ATTTGATTATCACAACGGGA
1 ATTTGACTATCGCAACGCGA
*
893396 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
893416 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
893430 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
893450 A-TTGACT
1 ATTTGACT
893457 TTTGTAACAC
Statistics
Matches: 100, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.10
16 1 0.01
18 1 0.01
19 5 0.05
20 83 0.83
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:893497 original size:20 final size:20
Alignment explanation
Indices: 893469--893513 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
893459 TGTAACACGA
* *
893469 TTTGACTTTTGCGTTGCGAT
1 TTTGACTTTCGCATTGCGAT
*
893489 TTTGGCTTTCGCATTGCGAT
1 TTTGACTTTCGCATTGCGAT
893509 TTTGA
1 TTTGA
893514 GTTTAGCGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTTGACTTTCGCATTGCGAT
Found at i:893691 original size:67 final size:66
Alignment explanation
Indices: 893581--893748 Score: 182
Period size: 71 Copynumber: 2.5 Consensus size: 66
893571 TTAAAATCAG
*
893581 CAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAAGAA-TTA-TTTACACATCAAT
1 CAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAATAAGAATTTATTTTACACATCAAT
893644 TAAA
63 TAAA
* * *
893648 CAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTCATC
1 CAAATCAACTTTTACATAATCAATTAAACAAGC---AAA-AATAAGAA-T-TTATTTTACACATC
893712 AATTAAA
60 AATTAAA
*
893719 CAAATCAACTTTTA-AGAATCAATTAAACAA
1 CAAATCAACTTTTACATAATCAATTAAACAA
893749 TAAAAAAAAG
Statistics
Matches: 88, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
63 16 0.18
66 2 0.02
67 23 0.26
70 4 0.05
71 43 0.49
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (66 bp):
CAAATCAACTTTTACATAATCAATTAAACAAGCAAAAATAAGAATTTATTTTACACATCAATTAA
A
Found at i:895106 original size:42 final size:42
Alignment explanation
Indices: 895047--895169 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
895037 GTGAATCGGG
* *
895047 CTCTTGAATGGTAGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGGGC
* ** *
895089 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTAGGA-GGGACCTCTTGAACGATGACAGGGGC
*
895131 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGGTAGGAG-GGACCTCTTGAACGATGACAGG
895170 TGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 62 0.93
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:895107 original size:21 final size:21
Alignment explanation
Indices: 895047--895161 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
895037 GTGAATCGGG
* * *
895047 CTCTTGAATGGTAGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
895068 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
895089 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
895110 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
895131 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
895152 CTCTTGAACG
1 CTCTTGAACG
895162 ATGACAGGTG
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.04
21 65 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:895671 original size:20 final size:20
Alignment explanation
Indices: 895646--895688 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
895636 ATAGTTTCTG
895646 AAACTTAAAATCGCAACACA
1 AAACTTAAAATCGCAACACA
*
895666 AAACTTAAAATCGCAACGCA
1 AAACTTAAAATCGCAACACA
895686 AAA
1 AAA
895689 ATGACTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.23, G:0.07, T:0.14
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACA
Found at i:895746 original size:33 final size:33
Alignment explanation
Indices: 895703--895777 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
895693 CTATCGTTCG
* * * *
895703 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTCT
1 CGTTGCGATTTTGATTTCGCATTGCGATTATCC
* *
895736 CGTTGTGATTTTTATTTCGCATTGCGATTATCC
1 CGTTGCGATTTTGATTTCGCATTGCGATTATCC
895769 CGTTGCGAT
1 CGTTGCGAT
895778 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTGATTTCGCATTGCGATTATCC
Found at i:895786 original size:33 final size:33
Alignment explanation
Indices: 895717--895797 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
895707 GCGATTTTGG
* * * ** *
895717 TTTCGCGTTGCGATTTTCTCGTTGTGATTTTTA
1 TTTCGCGTTGCGATTATCCCGTTGCGATAGTCA
*
895750 TTTCGCATTGCGATTATCCCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTATCCCGTTGCGATAGTCA
895783 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
895798 AATCATTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 29 0.74
34 10 0.26
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCCCGTTGCGATAGTCA
Found at i:895794 original size:20 final size:20
Alignment explanation
Indices: 895769--895817 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
895759 GCGATTATCC
*
895769 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAATCATTTCCG
*
895789 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCATTTCCG
895809 CGTTGCGAT
1 CGTTGCGAT
895818 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAATCATTTCCG
Found at i:896091 original size:14 final size:14
Alignment explanation
Indices: 896072--896098 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
896062 AGTATGAACC
896072 TCGTTGCGATTTTG
1 TCGTTGCGATTTTG
896086 TCGTTGCGATTTT
1 TCGTTGCGATTTT
896099 CATTTCGCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (14 bp):
TCGTTGCGATTTTG
Found at i:896684 original size:20 final size:20
Alignment explanation
Indices: 896654--896725 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
896644 ATTTTGTATT
* *
896654 ATCGCGTTGCGATAGTCAGA
1 ATCGCGCTGCGATAGTCAAA
* *
896674 ATCGTGCTGCGATAGTCATA
1 ATCGCGCTGCGATAGTCAAA
* *
896694 ATGGCGTTGCGATAGTCAAA
1 ATCGCGCTGCGATAGTCAAA
*
896714 ATCGCGTTGCGA
1 ATCGCGCTGCGA
896726 ATCTGGAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
ATCGCGCTGCGATAGTCAAA
Found at i:896775 original size:19 final size:19
Alignment explanation
Indices: 896751--896787 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
896741 TGCGATACTG
*
896751 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
896770 GAGATCGCATTTCGATTT
1 GAGATCGCATTGCGATTT
896788 TGCTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:902077 original size:2 final size:2
Alignment explanation
Indices: 902070--902105 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
902060 AATTATTGGC
902070 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
902106 ATTTGAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:911149 original size:867 final size:864
Alignment explanation
Indices: 909734--911467 Score: 3140
Period size: 867 Copynumber: 2.0 Consensus size: 864
909724 TACAATGACA
909734 TGTCACTTTTGAGTTGGAGGATTAAATTATTTAAATGAATTAAAATAATGACTAAACTAATAAAA
1 TGTCACTTTTGAGTTGGAGGATTAAATTATTTAAATGAATTAAAATAATGACTAAACTAAT-AAA
909799 TATGTAAATATCTATCAAGGACCAAATATATATTAGTCAATGTTATTGATGTGCCACATCACCAC
65 TATGTAAATATCTATCAAGGACCAAATATATATTAGTCAATGTTATTGATGTGCCACATCACCAC
909864 CTCGTTAAAAACTAACGACTAGTGGCTTGATTGAATTATTTAAATAGTTGGGTCTTTTTTAATCA
130 CTCGTTAAAAACTAACGACTAGTGGCTTGATTGAATTATTTAAATAGTTGGGTCTTTTTTAATCA
909929 AATTGAAACATCAGTGGTCAAAATAAATTTTGACATAGTTTGGTGGTCACCGTGTAGTTTATCTT
195 AATTGAAACATCAGTGGTCAAAATAAATTTTGACATAGTTTGGTGGTCACCGTGTAGTTTATCTT
909994 ATTTTTTAATATAATAAATATTAGATTATATGAATATAAAAAAGGAGGGAATTGTAAAATTTGAT
260 ATTTTTTAATATAAT-AATATTAGATTATATGAATATAAAAAAGGAGGGAATTGTAAAATTTGAT
910059 GTATAATAGCCATCGCGGACGGCGACCAATGCCCGTTGACAATGACAACAGTAAGTGGTGCTGCA
324 GTATAATAGCCATCGCGGACGGCGACCAATGCCCGTTGACAATGACAACAGTAAGTGGTGCTGCA
910124 ACATGAGACTTTGGTCGAATTTTAAAAGTCAAATTAATAATTTATCTAAAACTTAGGTCAATTGA
389 ACATGAGACTTTGGTCGAATTTTAAAAGTCAAATTAATAATTTATCTAAAACTTAGGTCAATTGA
910189 TACTTCATTATACAATTTAGGGCGTCATCAAACTAACGGGAGTTAACAACTCAATGACCAAAATG
454 TACTTCATTATACAATTTAGGGCGTCATCAAACTAACGGGAGTTAACAACTCAATGACCAAAATG
910254 TAACAATCGATATGTAAATGACTAAAATTTAATAAATCAATAACGTATATGACCGAAATTTAATA
519 TAACAATCGATATGTAAATGACTAAAATTTAATAAATCAATAACGTATATGACCGAAATTTAATA
910319 AATCAATTAAA-AAATGATCAAAGTATAATTTTTTTTTAAATTTAGT-G-AAAACTATATAAATA
584 AATCAATTAAATAAATGATCAAAGTATAATTTTTTTTTAAATTTAGTAGTAAAACTATAT-AA-A
910381 TGAAAGAAACCAATCCGGTAGTTTATCATTTTTAAACGGGGAACCCTTACATAATTA-TGTTCAT
647 TGAAAGAAACCAATCCGGTAGTTTATCATTTTTAAACGGGGAACCCTTACATAATTATTGTTCAT
910445 CTTAACGGGTAACTAAT-A-A-TATTGTGGAGAATCTTTCATAATGAAAAGACCATGGATTC-TA
712 CTTAACGGGTAACTAATAATATTATTGTGGAGAATCTTTCATAATGAAAAGACCATGGATTCTTA
910506 TAATGAAAAAGAAGCCGTGGTCAAGAATTAAACATATGAGTGCAGAAAGAAAGACCATACCTAAA
777 TAATG-AAAAGAAGCCGTGGTCAAGAATT-AA-ATATGAGTGCAGAAAG-AAGACCATACCTAAA
910571 GTTTAGTTTTTGTTTGATTTTAGTGTC
838 GTTTAGTTTTTGTTTGATTTTAGTGTC
*
910598 TGTCACTTTTGAGTTGGAGGATTAATTTATTTAAATGAATT-AAATAATGACTAAACTAAT-AAT
1 TGTCACTTTTGAGTTGGAGGATTAAATTATTTAAATGAATTAAAATAATGACTAAACTAATAAAT
910661 ATGTAAATATCTATCAAGGACCAAATATATAATTATGTCAATGTTATTGATGTGCCACATCACCA
66 ATGTAAATATCTATCAAGGACCAAATATAT-ATTA-GTCAATGTTATTGATGTGCCACATCACCA
*
910726 CCTCCGTTAAAAACTAACGACTAGTGGCTTGATTGAATTATTTAAATAGTTGGGTGGTCTTTTTA
129 CCT-CGTTAAAAACTAACGACTAGTGGCTTGATTGAATTATTTAAATAGTTGGGT-CT-TTTTTA
910791 ATCAAATTGAAACATCA-TGGTC-AAATAAATTTTGACATAGTTTGGTGGTCACCCGTGTAGTTT
191 ATCAAATTGAAACATCAGTGGTCAAAATAAATTTTGACATAGTTTGGTGGTCA-CCGTGTAGTTT
910854 ATCTTATTTTTTTAATATAAT-ATATTAGATTCATATTGAATATAAAAAAAGGAGGGAATTGTAA
255 ATCTTA-TTTTTTAATATAATAATATTAGATT-ATA-TGAATAT-AAAAAAGGAGGGAATTGTAA
910918 AATTTGATGTATAATAGCCATCGCGGACGGCGACCAATGCCCGTTGACAATGACAACAGTAAGTG
316 AATTTGATGTATAATAGCCATCGCGGACGGCGACCAATGCCCGTTGACAATGACAACAGTAAGTG
910983 GTGGCTGCAACATGAGACTTTGGTCGAA-TTTAAAAGTCAAATTAATAATTTATCTAAAACTTAG
381 GT-GCTGCAACATGAGACTTTGGTCGAATTTTAAAAGTCAAATTAATAATTTATCTAAAACTTA-
911047 GGTCAAATTGATACTTCATTATACAATTTAGGGCGTCATCAAACTAACGGGAGTTAACAACTCAA
444 GGTC-AATTGATACTTCATTATACAATTTAGGGCGTCATCAAACTAACGGGAGTTAACAACTCAA
911112 TGACCAAAATGT-ACAATCGATAT-TAAATGACTAAAATTTAATAAATCAATAACGTATATGACC
508 TGACCAAAATGTAACAATCGATATGTAAATGACTAAAATTTAATAAATCAATAACGTATATGACC
911175 GAAATTTAATAAATCAATTAAATAAATGATCAAAGTATAATTTTTTTTTAAATTTAGTGAGTAAA
573 GAAATTTAATAAATCAATTAAATAAATGATCAAAGTATAATTTTTTTTTAAATTTAGT-AGTAAA
911240 ACTATATAAATGAAAGAAACCAATCCGGTAGTTTATCATTTTTAAACGGGGAACCCTTACATAAT
637 ACTATATAAATGAAAGAAACCAATCCGGTAGTTTATCATTTTTAAACGGGGAACCCTTACATAAT
911305 TATTGTTCATCTTAACGGGTAACTAATAATATTATTGTGGAGAATCTTTCATAATGAAAAGACCA
702 TATTGTTCATCTTAACGGGTAACTAATAATATTATTGTGGAGAATCTTTCATAATGAAAAGACCA
911370 TGGATTCTTATAATGAAAAGAAGCCGTGGTCAAGAATTAAATATGAGTGCAGAAAGAAGACCATA
767 TGGATTCTTATAATGAAAAGAAGCCGTGGTCAAGAATTAAATATGAGTGCAGAAAGAAGACCATA
911435 CCTAAAGTTTAGTTTTTGTTTGATTTTAGTGTC
832 CCTAAAGTTTAGTTTTTGTTTGATTTTAGTGTC
911468 AGTTCAAAAC
Statistics
Matches: 846, Mismatches: 2, Indels: 38
0.95 0.00 0.04
Matches are distributed among these distances:
861 33 0.04
862 4 0.00
863 51 0.06
864 130 0.15
865 26 0.03
866 44 0.05
867 184 0.22
868 75 0.09
869 130 0.15
870 69 0.08
871 27 0.03
872 3 0.00
873 63 0.07
874 7 0.01
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (864 bp):
TGTCACTTTTGAGTTGGAGGATTAAATTATTTAAATGAATTAAAATAATGACTAAACTAATAAAT
ATGTAAATATCTATCAAGGACCAAATATATATTAGTCAATGTTATTGATGTGCCACATCACCACC
TCGTTAAAAACTAACGACTAGTGGCTTGATTGAATTATTTAAATAGTTGGGTCTTTTTTAATCAA
ATTGAAACATCAGTGGTCAAAATAAATTTTGACATAGTTTGGTGGTCACCGTGTAGTTTATCTTA
TTTTTTAATATAATAATATTAGATTATATGAATATAAAAAAGGAGGGAATTGTAAAATTTGATGT
ATAATAGCCATCGCGGACGGCGACCAATGCCCGTTGACAATGACAACAGTAAGTGGTGCTGCAAC
ATGAGACTTTGGTCGAATTTTAAAAGTCAAATTAATAATTTATCTAAAACTTAGGTCAATTGATA
CTTCATTATACAATTTAGGGCGTCATCAAACTAACGGGAGTTAACAACTCAATGACCAAAATGTA
ACAATCGATATGTAAATGACTAAAATTTAATAAATCAATAACGTATATGACCGAAATTTAATAAA
TCAATTAAATAAATGATCAAAGTATAATTTTTTTTTAAATTTAGTAGTAAAACTATATAAATGAA
AGAAACCAATCCGGTAGTTTATCATTTTTAAACGGGGAACCCTTACATAATTATTGTTCATCTTA
ACGGGTAACTAATAATATTATTGTGGAGAATCTTTCATAATGAAAAGACCATGGATTCTTATAAT
GAAAAGAAGCCGTGGTCAAGAATTAAATATGAGTGCAGAAAGAAGACCATACCTAAAGTTTAGTT
TTTGTTTGATTTTAGTGTC
Found at i:921806 original size:32 final size:32
Alignment explanation
Indices: 921716--921972 Score: 265
Period size: 32 Copynumber: 8.2 Consensus size: 32
921706 TAGCACAATG
* * *
921716 GTGTCCGTGTTGCATT--GATAATGCACAATA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * * *
921746 GTATCAATGTTGTATT-TGATAATGCATAGTA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * *
921777 GAGTCATTGTTGCATTCAGATAATACATAGTA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * **
921809 GTGTCAGTGTTGCATTCATATAATGCACAACA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
*
921841 GTGTCAGTGTTGCA-TCTAGATAATGCACAGTA
1 GTGTCAGTGTTGCATTC-AGATAATGCATAGTA
*
921873 GTGTCAGTGTTGCATTCAGATAATGCATAATA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * * *
921905 ATGTCAGTGTCGCATTTAGATAATACATAGTA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* *
921937 GTGTCAGTG-T-CATTTAGATAATACATAGTA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
921967 GTGTCA
1 GTGTCA
921973 CATTTAGATA
Statistics
Matches: 192, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
30 38 0.20
31 26 0.14
32 126 0.66
33 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (32 bp):
GTGTCAGTGTTGCATTCAGATAATGCATAGTA
Found at i:921884 original size:96 final size:94
Alignment explanation
Indices: 921716--921972 Score: 295
Period size: 96 Copynumber: 2.7 Consensus size: 94
921706 TAGCACAATG
* * * * * *
921716 GTGTCCGTGTTGCATT-GATAATGCACAATAGTATCAATGTTGTATTTGATAATGCATAGTAGAG
1 GTGTCAGTGTTGCATTAGATAATGCACAATAGTGTCAGTGTTGCATTAGATAATGCATAGTAGTG
* *
921780 TCATTGTTGCATTCAGATAATACATAGTA
66 TCAGTGTTGCATTCAGATAATACATAATA
* * *
921809 GTGTCAGTGTTGCATTCATATAATGCACAACAGTGTCAGTGTTGCATCTAGATAATGCACAGTAG
1 GTGTCAGTGTTGCATT-AGATAATGCACAATAGTGTCAGTGTTGCAT-TAGATAATGCATAGTAG
*
921874 TGTCAGTGTTGCATTCAGATAATGCATAATA
64 TGTCAGTGTTGCATTCAGATAATACATAATA
* * * * * *
921905 ATGTCAGTGTCGCATTTAGATAATACATAGTAGTGTCAGTG-T-CATTTAGATAATACATAGTAG
1 GTGTCAGTGTTGCA-TTAGATAATGCACAATAGTGTCAGTGTTGCA-TTAGATAATGCATAGTAG
921968 TGTCA
64 TGTCA
921973 CATTTAGATA
Statistics
Matches: 138, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
93 15 0.11
94 22 0.16
95 26 0.19
96 73 0.53
97 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (94 bp):
GTGTCAGTGTTGCATTAGATAATGCACAATAGTGTCAGTGTTGCATTAGATAATGCATAGTAGTG
TCAGTGTTGCATTCAGATAATACATAATA
Found at i:921941 original size:26 final size:26
Alignment explanation
Indices: 921910--921984 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 26
921900 TAATAATGTC
921910 AGTGTCGCATTTAGATAATACATAGT
1 AGTGTCGCATTTAGATAATACATAGT
921936 AGTGTCAGTGTCATTTAGATAATACATAGT
1 AGTGTC---G-CATTTAGATAATACATAGT
*
921966 AGTGTCACATTTAGATAAT
1 AGTGTCGCATTTAGATAAT
921985 GCACAACAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 18 0.41
29 1 0.02
30 25 0.57
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (26 bp):
AGTGTCGCATTTAGATAATACATAGT
Found at i:928523 original size:20 final size:20
Alignment explanation
Indices: 928486--928522 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
928476 TTTTGGTGCA
*
928486 GAGGGAATCGATATCCCCAT
1 GAGGGAACCGATATCCCCAT
928506 GAGGGAACCGAT-TCCCC
1 GAGGGAACCGATATCCCC
928523 CCACAGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATATCCCCAT
Found at i:930527 original size:17 final size:17
Alignment explanation
Indices: 930494--930527 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
930484 TTGAATATTT
* *
930494 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
930511 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
930528 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:930807 original size:13 final size:13
Alignment explanation
Indices: 930789--930814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
930779 GGAGAAGTGT
930789 TAAGTGTTTTAAA
1 TAAGTGTTTTAAA
930802 TAAGTGTTTTAAA
1 TAAGTGTTTTAAA
930815 GGGAGAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TAAGTGTTTTAAA
Found at i:932127 original size:13 final size:14
Alignment explanation
Indices: 932085--932126 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
932075 TCAAAAAAAT
932085 TAAATAATTAATT-
1 TAAATAATTAATTA
932098 TAAATAA-T-ATTA
1 TAAATAATTAATTA
932110 TAAA-AATTAATTA
1 TAAATAATTAATTA
932123 TAAA
1 TAAA
932127 AGTGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.19
12 6 0.23
13 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATAATTAATTA
Found at i:940597 original size:6 final size:6
Alignment explanation
Indices: 940588--940612 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
940578 TATGTATGTA
940588 TGTATG TGTATG TGTATG TGTATG T
1 TGTATG TGTATG TGTATG TGTATG T
940613 ATGTACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TGTATG
Found at i:943298 original size:17 final size:17
Alignment explanation
Indices: 943247--943300 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
943237 AGCTAAAATT
*
943247 AATTAGTATAATTTGTTA
1 AATTAGTATAAGTTG-TA
*
943265 AGATTGAGGACTAAGTTGTA
1 A-ATT-AGTA-TAAGTTGTA
943285 AATTAGTATAAGTTGT
1 AATTAGTATAAGTTGT
943301 GATCTGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 8 0.27
18 4 0.13
19 6 0.20
20 6 0.20
21 6 0.20
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (17 bp):
AATTAGTATAAGTTGTA
Found at i:945097 original size:19 final size:19
Alignment explanation
Indices: 945073--945116 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
945063 GACCATTAAC
945073 GATAAATGATTGATTAATT
1 GATAAATGATTGATTAATT
* *
945092 GATAAAGGATTGATTTATT
1 GATAAATGATTGATTAATT
945111 -ATAAAT
1 GATAAAT
945117 TAATAACGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (19 bp):
GATAAATGATTGATTAATT
Found at i:945200 original size:29 final size:29
Alignment explanation
Indices: 945166--945228 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
945156 TCAATTTGTT
945166 ACTTCTAAAACTTC-AATTTCAAATTGAAA
1 ACTTCTAAAACTTCAAATTTCAAATTG-AA
945195 ACTTCTAAAACTTCAAATTTCAAATTGAA
1 ACTTCTAAAACTTCAAATTTCAAATTGAA
945224 ACTTC
1 ACTTC
945229 AAGATCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (29 bp):
ACTTCTAAAACTTCAAATTTCAAATTGAA
Found at i:948605 original size:21 final size:21
Alignment explanation
Indices: 948579--948632 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
948569 GCGTTGCATT
948579 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
948600 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
948621 TCGCGTTGCGAT
1 TCGCGTTGCGAT
948633 TTTCCAGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:948788 original size:6 final size:6
Alignment explanation
Indices: 948777--948811 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
948767 GAAGACACGT
948777 ACGACC ACGACC ACGACC ACGACC ACGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
948812 CGAGACGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.31, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:949439 original size:22 final size:22
Alignment explanation
Indices: 949410--949500 Score: 91
Period size: 22 Copynumber: 4.3 Consensus size: 22
949400 AATTTGGAAA
949410 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
949432 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
949454 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
949473 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
949494 ATCGCAA
1 ATCGCAA
949501 AGCGAAATGA
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 13 0.24
20 3 0.06
21 11 0.20
22 27 0.50
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:949515 original size:41 final size:41
Alignment explanation
Indices: 949446--949550 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 41
949436 CAACAACAAC
* *
949446 TGTAGACTATCGC-AA-CGAATTTGGAAAATCGCAACGAC-AT
1 TGTAGACTATCGCAAAGCGAA-ATGAAAAATCGCAACG-CGAT
*
949486 TGTAGACTATCGCAAAGCGAAATGAAAAATCGTAACGCGAT
1 TGTAGACTATCGCAAAGCGAAATGAAAAATCGCAACGCGAT
* *
949527 TTTCA-ACTATCGCAACGCGAAATG
1 TGT-AGACTATCGCAAAGCGAAATG
949551 CAACGCGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
40 14 0.25
41 37 0.66
42 5 0.09
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (41 bp):
TGTAGACTATCGCAAAGCGAAATGAAAAATCGCAACGCGAT
Found at i:949554 original size:21 final size:21
Alignment explanation
Indices: 949491--949554 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
949481 GACATTGTAG
*
949491 ACTATCGCAAAGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** * ** *
949511 AAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
949532 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
949553 AC
1 AC
949555 GCGAATTTGC
Statistics
Matches: 30, Mismatches: 13, Indels: 1
0.68 0.30 0.02
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:969412 original size:2 final size:2
Alignment explanation
Indices: 969405--969434 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
969395 AACATCAAAC
*
969405 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
969435 GTGGATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:969568 original size:8 final size:8
Alignment explanation
Indices: 969550--969602 Score: 97
Period size: 8 Copynumber: 6.5 Consensus size: 8
969540 GCTTTAGATC
969550 TCTTCTTCT
1 TCTT-TTCT
969559 TCTTTTCT
1 TCTTTTCT
969567 TCTTTTCT
1 TCTTTTCT
969575 TCTTTTCT
1 TCTTTTCT
969583 TCTTTTCT
1 TCTTTTCT
969591 TCTTTTCT
1 TCTTTTCT
969599 TCTT
1 TCTT
969603 GCCTTTCTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
8 40 0.91
9 4 0.09
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (8 bp):
TCTTTTCT
Found at i:970508 original size:17 final size:18
Alignment explanation
Indices: 970486--970526 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
970476 AAAAAATATT
970486 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
970503 AGTAAAATGTTTAAATAA
1 AGTAAAATGATTAAATAA
*
970521 ATTAAA
1 AGTAAA
970527 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:976173 original size:2 final size:2
Alignment explanation
Indices: 976166--976196 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
976156 TGTAACAAAC
976166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
976197 AAAGAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:977013 original size:24 final size:23
Alignment explanation
Indices: 976984--977031 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
976974 TTTTGGTTCG
* *
976984 TTTTAATACCTAAACTTTCAATTT
1 TTTTAA-AACTAAACTTTAAATTT
*
977008 TTTTAAAACTTAACTTTAAATTT
1 TTTTAAAACTAAACTTTAAATTT
977031 T
1 T
977032 GAACATGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTAAAACTAAACTTTAAATTT
Found at i:977610 original size:23 final size:23
Alignment explanation
Indices: 977591--977648 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
977581 ACATGTCTTC
*
977591 TAGATTTACGACCGTCTGTCTCT
1 TAGATTTACAACCGTCTGTCTCT
*
977614 TAGATTTCCAACCGTCTGTCTCT
1 TAGATTTACAACCGTCTGTCTCT
*
977637 TAGATTTCCAAC
1 TAGATTTACAAC
977649 GGTTCTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.38
Consensus pattern (23 bp):
TAGATTTACAACCGTCTGTCTCT
Found at i:979848 original size:30 final size:30
Alignment explanation
Indices: 979812--979873 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
979802 GCTAAAGATG
979812 TATTTTTTCAATCAATTTATTCTATCTAAT
1 TATTTTTTCAATCAATTTATTCTATCTAAT
979842 TATTTTTTCAATCAATTTATTCTATCTAAT
1 TATTTTTTCAATCAATTTATTCTATCTAAT
979872 TA
1 TA
979874 GAAATGACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (30 bp):
TATTTTTTCAATCAATTTATTCTATCTAAT
Found at i:982121 original size:28 final size:28
Alignment explanation
Indices: 982089--982142 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
982079 TGGTATTTAA
982089 TCAAAAAAATAATTTGATATAAATATTT
1 TCAAAAAAATAATTTGATATAAATATTT
982117 TCAAAAAAATAATTTGATATAAATAT
1 TCAAAAAAATAATTTGATATAAATAT
982143 GAAATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (28 bp):
TCAAAAAAATAATTTGATATAAATATTT
Found at i:982126 original size:14 final size:14
Alignment explanation
Indices: 982089--982131 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
982079 TGGTATTTAA
982089 TCAAAAAAATAATT
1 TCAAAAAAATAATT
* * * *
982103 TGATATAAATATTT
1 TCAAAAAAATAATT
982117 TCAAAAAAATAATT
1 TCAAAAAAATAATT
982131 T
1 T
982132 GATATAAATA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (14 bp):
TCAAAAAAATAATT
Found at i:982140 original size:14 final size:14
Alignment explanation
Indices: 982095--982141 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
982085 TTAATCAAAA
982095 AAATAATTTGATAT
1 AAATAATTTGATAT
* * * *
982109 AAATATTTTCAAAA
1 AAATAATTTGATAT
982123 AAATAATTTGATAT
1 AAATAATTTGATAT
982137 AAATA
1 AAATA
982142 TGAAATTTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (14 bp):
AAATAATTTGATAT
Found at i:982521 original size:31 final size:31
Alignment explanation
Indices: 982483--982551 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
982473 GTTTAAAAAG
* * *
982483 TAACAAATTGGTCATTAACGTTATCGATTTA
1 TAACAAATGGGTCATTAACATTATCAATTTA
* *
982514 TAACAAATGGGTTATTGACATTATCAATTTA
1 TAACAAATGGGTCATTAACATTATCAATTTA
982545 TAACAAA
1 TAACAAA
982552 CCTATCACTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (31 bp):
TAACAAATGGGTCATTAACATTATCAATTTA
Found at i:983431 original size:21 final size:21
Alignment explanation
Indices: 983405--983454 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
983395 GGAGCGTGGG
983405 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
983426 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
983447 GGGAATCG
1 GGGAATCG
983455 ATTCCCTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.18
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTCATA
Found at i:983867 original size:13 final size:13
Alignment explanation
Indices: 983849--983875 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
983839 TAACACTTCT
983849 CCCCTTTAAAACA
1 CCCCTTTAAAACA
983862 CCCCTTTAAAACA
1 CCCCTTTAAAACA
983875 C
1 C
983876 TTTAACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (13 bp):
CCCCTTTAAAACA
Found at i:984623 original size:19 final size:20
Alignment explanation
Indices: 984586--984631 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
984576 TTGGAGCGTG
*
984586 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGATACCCCCTAT
984606 GGGGAATCGATA-CCCCTAT
1 GGGGAATCGATACCCCCTAT
984625 GGGGAAT
1 GGGGAAT
984632 TGGTTCCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.20
Consensus pattern (20 bp):
GGGGAATCGATACCCCCTAT
Found at i:987443 original size:20 final size:20
Alignment explanation
Indices: 987414--987451 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
987404 CAGTACCCCA
*
987414 GGGGGTATCGATTCCCTCAT
1 GGGGGGATCGATTCCCTCAT
987434 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
987452 TGCACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:991307 original size:22 final size:21
Alignment explanation
Indices: 991265--991304 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
991255 GAGCTTATTT
*
991265 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
991286 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
991305 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:994091 original size:18 final size:18
Alignment explanation
Indices: 994068--994108 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
994058 AGGCATTTGA
994068 TCCTCTGGTCATGCTTGT
1 TCCTCTGGTCATGCTTGT
**
994086 TCCTCTGGTTGTGCTTGT
1 TCCTCTGGTCATGCTTGT
994104 TCCTC
1 TCCTC
994109 ATGCAGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.29, G:0.22, T:0.46
Consensus pattern (18 bp):
TCCTCTGGTCATGCTTGT
Found at i:1005953 original size:231 final size:232
Alignment explanation
Indices: 1005541--1006003 Score: 919
Period size: 231 Copynumber: 2.0 Consensus size: 232
1005531 TCTCCCAGCC
1005541 TATCTTTCAAAGATATCCTCGGCCCGAGAAAGAGTATCAGTCTTTTTCACTTATATATAATGAGA
1 TATCTTTCAAAGATATCCTCGGCCCGAGAAAGAGTATCAGTCTTTTTCACTTATATATAATGAGA
1005606 GATCTCTAGATTTGGTAAGAATATGCCTCTTTGTAAGCGTGACTTCTTGTCTATCTGATTGCACC
66 GATCTCTAGATTTGGTAAGAATATGCCTCTTTGTAAGCGTGACTTCTTGTCTATCTGATTGCACC
1005671 TCTTTTCTTGTGCCATATCCAAACAGCTAAAAGTATTTATATTGTTATCATATATTAGATCTGCA
131 TCTTTTCTTGTGCCATATCCAAACAGCTAAAAGTATTTATATTGTTATCATATATTAGATCTGCA
1005736 AGGATAAAGATGAAGCTGAAGTCTGGTTTAGTGGTTT
196 AGGATAAAGATGAAGCTGAAGTCTGGTTTAGTGGTTT
1005773 TATCTTTC-AAGATATCCTCGGCCCGAGAAAGAGTATCAGTCTTTTTCACTTATATATAATGAGA
1 TATCTTTCAAAGATATCCTCGGCCCGAGAAAGAGTATCAGTCTTTTTCACTTATATATAATGAGA
1005837 GATCTCTAGATTTGGTAAGAATATGCCTCTTTGTAAGCGTGACTTCTTGTCTATCTGATTGCACC
66 GATCTCTAGATTTGGTAAGAATATGCCTCTTTGTAAGCGTGACTTCTTGTCTATCTGATTGCACC
1005902 TCTTTTCTTGTGCCATATCCAAACAGCTAAAAGTATTTATATTGTTATCATATATTAGATCTGCA
131 TCTTTTCTTGTGCCATATCCAAACAGCTAAAAGTATTTATATTGTTATCATATATTAGATCTGCA
1005967 AGGATAAAGATGAAGCTGAAGTCTGGTTTAGTGGTTT
196 AGGATAAAGATGAAGCTGAAGTCTGGTTTAGTGGTTT
1006004 AAAAACATTA
Statistics
Matches: 231, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
231 223 0.97
232 8 0.03
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (232 bp):
TATCTTTCAAAGATATCCTCGGCCCGAGAAAGAGTATCAGTCTTTTTCACTTATATATAATGAGA
GATCTCTAGATTTGGTAAGAATATGCCTCTTTGTAAGCGTGACTTCTTGTCTATCTGATTGCACC
TCTTTTCTTGTGCCATATCCAAACAGCTAAAAGTATTTATATTGTTATCATATATTAGATCTGCA
AGGATAAAGATGAAGCTGAAGTCTGGTTTAGTGGTTT
Found at i:1014007 original size:2 final size:2
Alignment explanation
Indices: 1014000--1014066 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
1013990 CAAGTAATTC
1014000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1014042 AT AT AT AT AT AT CT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1014067 GAGATAATCT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1018551 original size:3 final size:3
Alignment explanation
Indices: 1018525--1018583 Score: 68
Period size: 3 Copynumber: 19.3 Consensus size: 3
1018515 TTTATAAAAA
*
1018525 TAT T-T TAT T-T TAT TATT TAGT TAT TAT TAT TAT TAA TATT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TA-T TAT TAT
1018571 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
1018584 TTGGCCCTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
2 4 0.08
3 37 0.76
4 8 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1018567 original size:16 final size:16
Alignment explanation
Indices: 1018548--1018580 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1018538 TATTTAGTTA
1018548 TTATTATTATTAATAT
1 TTATTATTATTAATAT
*
1018564 TTATTATTATTATTAT
1 TTATTATTATTAATAT
1018580 T
1 T
1018581 ATTTTGGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTATTAATAT
Found at i:1018567 original size:19 final size:19
Alignment explanation
Indices: 1018523--1018584 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
1018513 GATTTATAAA
1018523 AATATTTTATT-TTATTATT
1 AATA-TTTATTATTATTATT
*
1018542 --TAGTTATTATTATTATT
1 AATATTTATTATTATTATT
1018559 AATATTTATTATTATTATT
1 AATATTTATTATTATTATT
*
1018578 ATTATTT
1 AATATTT
1018585 TGGCCCTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 5 0.14
17 10 0.27
19 22 0.59
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
AATATTTATTATTATTATT
Found at i:1019969 original size:14 final size:13
Alignment explanation
Indices: 1019950--1020016 Score: 61
Period size: 14 Copynumber: 5.2 Consensus size: 13
1019940 GTTACTCAAT
1019950 TTTATTTATCTTTA
1 TTTATTTAT-TTTA
1019964 TTTATTTATTTTA
1 TTTATTTATTTTA
1019977 TTT-TTTA-TTTA
1 TTTATTTATTTTA
*
1019988 -TTA-TTATTATA
1 TTTATTTATTTTA
*
1019999 TTAATATTTTTTTTA
1 TT--TATTTATTTTA
1020014 TTT
1 TTT
1020017 TTTTCATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
10 5 0.11
11 7 0.16
12 5 0.11
13 8 0.18
14 11 0.25
15 8 0.18
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:1020014 original size:20 final size:22
Alignment explanation
Indices: 1019982--1020034 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1019972 TTTTATTTTT
*
1019982 TATTTATTATTATTATATT-A-A
1 TATTT-TTTTTATTATATTCATA
* *
1020003 TATTTTTTTTATTTTTTTCATA
1 TATTTTTTTTATTATATTCATA
1020025 TATTTTTTTT
1 TATTTTTTTT
1020035 TTACAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.37
21 6 0.22
22 11 0.41
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTTTTTTATTATATTCATA
Found at i:1020025 original size:26 final size:24
Alignment explanation
Indices: 1019984--1020037 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1019974 TTATTTTTTA
1019984 TTTATTATTATTATATTAATATTTTT
1 TTTATTATTATTATA-T-ATATTTTT
* *
1020010 TTTATT-TTTTTCATATATTTTTTT
1 TTTATTATTATT-ATATATATTTTT
1020034 TTTA
1 TTTA
1020038 CAATTTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 11 0.44
25 5 0.20
26 9 0.36
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTATTATTATTATATATATTTTT
Found at i:1022079 original size:4 final size:4
Alignment explanation
Indices: 1022062--1022131 Score: 72
Period size: 4 Copynumber: 16.8 Consensus size: 4
1022052 TTTACTCAAT
*
1022062 TTTA TTTA TCTTTA TTTA TTTA TCTA TTTA TTTA TTTA TTTA TTTA -TTA
1 TTTA TTTA --TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1022111 TTATA TTAATA TTT- TTTA TTT
1 TT-TA TT--TA TTTA TTTA TTT
1022132 TTTTCATATT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
3 6 0.10
4 39 0.67
5 4 0.07
6 9 0.16
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1022117 original size:16 final size:15
Alignment explanation
Indices: 1022062--1022152 Score: 70
Period size: 16 Copynumber: 6.2 Consensus size: 15
1022052 TTTACTCAAT
*
1022062 TTTATTTA-TCTTTA
1 TTTATTTATTATTTA
1022076 TTTATTTATCTATTTA
1 TTTATTTAT-TATTTA
1022092 TTTATTTATTTATTTA
1 TTTATTTA-TTATTTA
*
1022108 -TTATTATATTA-ATA
1 TTTATT-TATTATTTA
1022122 TTT-TTTATT-TTT-
1 TTTATTTATTATTTA
1022134 TTCATATTTATT-TTTA
1 TT--TATTTATTATTTA
1022150 TTT
1 TTT
1022153 TATAATCTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
12 2 0.03
13 5 0.08
14 14 0.22
15 19 0.30
16 23 0.36
17 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTATTATTTA
Found at i:1022153 original size:18 final size:18
Alignment explanation
Indices: 1022102--1022154 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1022092 TTTATTTATT
* *
1022102 TATTTATTATTATATTAA
1 TATTTATTTTTATTTTAA
* *
1022120 TATTT-TTTATTTTTTTCA
1 TATTTATTT-TTATTTTAA
1022138 TATTTATTTTTATTTTA
1 TATTTATTTTTATTTTA
1022155 TAATCTAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 2 0.07
18 22 0.81
19 3 0.11
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTATTTTTATTTTAA
Found at i:1024702 original size:67 final size:69
Alignment explanation
Indices: 1024574--1024711 Score: 199
Period size: 67 Copynumber: 2.0 Consensus size: 69
1024564 CAAGGTAGTG
**
1024574 AGCCCAAGTGTAATTGCATTTTTTTTTCTTTCACTTGTGTTGTTGACTGCTTGTTGGTTGAAATT
1 AGCCCAAGTGTAATTGCA---TTTTTTCTTTCACTCATGTTGTTGACTGCTTGTTGGTTGAAATT
1024639 CAGGCCA
63 CAGGCCA
* *
1024646 AGCCCAAGTGTAATTGCA-TTTTT-TTTCACTCATGTTGTTTACTGTTTGTTGGTTGAAATTCAG
1 AGCCCAAGTGTAATTGCATTTTTTCTTTCACTCATGTTGTTGACTGCTTGTTGGTTGAAATTCAG
1024709 GCC
66 GCC
1024712 GTTAGTGAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 39 0.63
68 5 0.08
72 18 0.29
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (69 bp):
AGCCCAAGTGTAATTGCATTTTTTCTTTCACTCATGTTGTTGACTGCTTGTTGGTTGAAATTCAG
GCCA
Found at i:1034825 original size:33 final size:33
Alignment explanation
Indices: 1034782--1034844 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1034772 ACAACAGTTA
*
1034782 ATAATGTTTATTCAT-TTTTAATAAAATTAAAAT
1 ATAATATTTATTCATATTTT-ATAAAATTAAAAT
* *
1034815 ATAATATTTATTTATATTTTTTAAAATTAA
1 ATAATATTTATTCATATTTTATAAAATTAA
1034845 TATTAGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 22 0.85
34 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (33 bp):
ATAATATTTATTCATATTTTATAAAATTAAAAT
Found at i:1036606 original size:21 final size:20
Alignment explanation
Indices: 1036582--1036628 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
1036572 TAGTTAACTA
1036582 GTTTAT-GATTTTATAAAAGTT
1 GTTTATAGATTTTA-AAAA-TT
*
1036603 GTTTTATAGCTTTTAAAAATT
1 G-TTTATAGATTTTAAAAATT
1036624 GTTTA
1 GTTTA
1036629 GGGTATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 9 0.39
23 6 0.26
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (20 bp):
GTTTATAGATTTTAAAAATT
Found at i:1038747 original size:30 final size:30
Alignment explanation
Indices: 1038711--1038803 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
1038701 AATGCATTTT
1038711 TGACATCTGCATGGGATAAATTCCTCATTC
1 TGACATCTGCATGGGATAAATTCCTCATTC
* * *
1038741 TGACATCTGCATCGAATAAATTCCCCATTC
1 TGACATCTGCATGGGATAAATTCCTCATTC
* ** *
1038771 TAACATCTATATGGGAT-TATATCCTCATTC
1 TGACATCTGCATGGGATAAAT-TCCTCATTC
1038801 TGA
1 TGA
1038804 TTTATGCTTC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 2 0.04
30 49 0.96
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (30 bp):
TGACATCTGCATGGGATAAATTCCTCATTC
Done.