Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008511.1 Hibiscus syriacus cultivar Beakdansim tig00111366_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: 2221980
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 5 of 9
Found at i:942242 original size:42 final size:41
Alignment explanation
Indices: 942157--942277 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 41
942147 TGTGAATCGA
* * * *
942157 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
942199 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
942241 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACA
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACA
942278 TGCGAGTCGG
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 55 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:942713 original size:21 final size:21
Alignment explanation
Indices: 942676--942732 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
942666 TCTGGAACTT
* *
942676 AAAATCACAACGTGAAAAATG
1 AAAATCGCAACGCGAAAAATG
**
942697 ACTATCGCAACGCG--AAATG
1 AAAATCGCAACGCGAAAAATG
942716 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
942733 CCAAAAGACA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 17 0.61
21 11 0.39
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACGCGAAAAATG
Found at i:942738 original size:19 final size:19
Alignment explanation
Indices: 942700--942738 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
942690 AAAAATGACT
**
942700 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAACCAAA
942719 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAACCAAA
942738 A
1 A
942739 GACAAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.08
Consensus pattern (19 bp):
ATCGCAACGCGAAACCAAA
Found at i:942939 original size:94 final size:94
Alignment explanation
Indices: 942829--943084 Score: 426
Period size: 94 Copynumber: 2.7 Consensus size: 94
942819 ATGGATTGTA
* *
942829 TTAC-TTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
942893 TTAACAGAATTGGCAGCAAACGAACAAAT
66 TTAACAGAATTGGCAGCAAACGAACAAAT
* *
942922 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
* * *
942987 TTAGCAGAATTGGCAGCAACCGAACAATT
66 TTAACAGAATTGGCAGCAAACGAACAAAT
943016 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGA-TAAAGAATACACAG
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGT-ATTAAAGAATACACAG
943080 TTTAA
65 TTTAA
943085 TCTAAGTGAA
Statistics
Matches: 151, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
93 4 0.03
94 147 0.97
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
TTAACAGAATTGGCAGCAAACGAACAAAT
Found at i:943893 original size:23 final size:23
Alignment explanation
Indices: 943867--943911 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
943857 CACCACAGCT
*
943867 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
943890 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
943912 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:944657 original size:64 final size:63
Alignment explanation
Indices: 944524--944680 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
944514 TAATGAAGGT
* * * ** *
944524 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
944588 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
944650 G
63 G
*
944651 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
944681 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:950809 original size:23 final size:23
Alignment explanation
Indices: 950783--950827 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
950773 CACCACAGCT
* *
950783 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
950806 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
950828 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:951573 original size:64 final size:63
Alignment explanation
Indices: 951440--951596 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
951430 TAATGAAGGT
* * * ** *
951440 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
951504 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
951566 G
63 G
*
951567 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
951597 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:953861 original size:20 final size:19
Alignment explanation
Indices: 953834--953941 Score: 120
Period size: 20 Copynumber: 5.8 Consensus size: 19
953824 TCTTTTGGTT
953834 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
953853 GATAATGAAAATCGCAACGCA
1 GA-AATGAAAATCGCAACG-A
** *
953874 GAAATGACTATTGCAACGA
1 GAAATGAAAATCGCAACGA
953893 G--A-G--AATCGCAAC-A
1 GAAATGAAAATCGCAACGA
953906 CGAAATGAAAATCGCAACGA
1 -GAAATGAAAATCGCAACGA
953926 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
953942 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
13 1 0.01
14 8 0.11
16 2 0.03
17 2 0.03
19 29 0.39
20 30 0.40
21 3 0.04
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:953920 original size:19 final size:19
Alignment explanation
Indices: 953834--953941 Score: 86
Period size: 19 Copynumber: 5.8 Consensus size: 19
953824 TCTTTTGGTT
953834 GAAATGAAAATCGCAACGA-
1 GAAATGAAAATCGCAAC-AC
*
953853 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACAC
** *
953873 AGAAATGACTATTGC-A-AC
1 -GAAATGAAAATCGCAACAC
*
953891 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACAC
953907 GAAATGAAAATCGCAACGA-
1 GAAATGAAAATCGCAAC-AC
953926 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
953942 TGCGATTTTG
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
14 6 0.08
15 2 0.03
16 3 0.04
17 1 0.01
18 2 0.03
19 30 0.42
20 25 0.35
21 2 0.03
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACAC
Found at i:953964 original size:19 final size:20
Alignment explanation
Indices: 953942--953993 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
953932 AAAATCGCAA
**
953942 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTTCATTTCCGCGT
**
953961 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTTCCGCGT
953981 TGCGATTTTCATT
1 TGCGATTTTCATT
953994 CTCGAAACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (20 bp):
TGCGATTTTCATTTCCGCGT
Found at i:955720 original size:33 final size:33
Alignment explanation
Indices: 955679--955745 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
955669 GCGACTTACC
*
955679 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
955712 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
955745 C
1 C
955746 CCGTTCGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.09, C:0.42, G:0.24, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:955735 original size:10 final size:10
Alignment explanation
Indices: 955691--955803 Score: 55
Period size: 10 Copynumber: 10.3 Consensus size: 10
955681 CGCTCGGCTT
*
955691 CCCTCGGATT
1 CCCTCGGATG
*
955701 CCCTCGCATAG
1 CCCTCGGAT-G
*
955712 CTCGCTCGGTTG
1 C-C-CTCGGATG
955724 CCCTCGGATG
1 CCCTCGGATG
*
955734 CCCTCGCATAG
1 CCCTCGGAT-G
*
955745 CCCGTTCGAATGG
1 CCC--TCGGAT-G
955758 CCTCGGTCGGATG
1 CC-C--TCGGATG
*
955771 GCCTCGGATG
1 CCCTCGGATG
*
955781 CTCTCGGATG
1 CCCTCGGATG
* *
955791 GCCTCAGATG
1 CCCTCGGATG
955801 CCC
1 CCC
955804 AGCGTGTTGG
Statistics
Matches: 79, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
10 47 0.59
11 6 0.08
12 4 0.05
13 15 0.19
14 7 0.09
ACGTcount: A:0.12, C:0.37, G:0.28, T:0.23
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:955762 original size:33 final size:33
Alignment explanation
Indices: 955691--955763 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
955681 CGCTCGGCTT
* * **
955691 CCCTCGGATTCCCTCGCATAGCTCGCTCGGTTG
1 CCCTCGGATGCCCTCGCATAGCCCGCTCGAATG
*
955724 CCCTCGGATGCCCTCGCATAGCCCGTTCGAATG
1 CCCTCGGATGCCCTCGCATAGCCCGCTCGAATG
*
955757 GCCTCGG
1 CCCTCGG
955764 TCGGATGGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.40, G:0.26, T:0.23
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCCCGCTCGAATG
Found at i:955789 original size:20 final size:20
Alignment explanation
Indices: 955764--955801 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
955754 ATGGCCTCGG
*
955764 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCAGATGCTC
955784 TCGGATGGCCTCAGATGC
1 TCGGATGGCCTCAGATGC
955802 CCAGCGTGTT
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:0.29, G:0.34, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCAGATGCTC
Found at i:955877 original size:29 final size:29
Alignment explanation
Indices: 955840--955897 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
955830 GCAATCTCTT
*
955840 GTAGCTTGCCGGGAAGACATGGCGACCTA
1 GTAGCTTGCCCGGAAGACATGGCGACCTA
* *
955869 GTAGGTTGCCCGGAAGGCATGGCGACCTA
1 GTAGCTTGCCCGGAAGACATGGCGACCTA
955898 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.36, T:0.17
Consensus pattern (29 bp):
GTAGCTTGCCCGGAAGACATGGCGACCTA
Found at i:961466 original size:15 final size:16
Alignment explanation
Indices: 961427--961468 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
961417 ATATGGTTTT
961427 AAACCCCCAAAGCTAG
1 AAACCCCCAAAGCTAG
* * *
961443 ACACACCCATAG-TAG
1 AAACCCCCAAAGCTAG
961458 AAACCCCCAAA
1 AAACCCCCAAA
961469 TATTTGAATC
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.45, C:0.38, G:0.10, T:0.07
Consensus pattern (16 bp):
AAACCCCCAAAGCTAG
Found at i:961661 original size:57 final size:57
Alignment explanation
Indices: 961573--961686 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
961563 CATTATGAGA
961573 AGCCTCGTCGTCAGTCCTAAAAAGCCTTGTAAAGATAGTCGGAGTTTAAGCTATCCC
1 AGCCTCGTCGTCAGTCCTAAAAAGCCTTGTAAAGATAGTCGGAGTTTAAGCTATCCC
961630 AGCCTCGTCGTCAGTCCTAAAAAGCCTTGTAAAGATAGTCGGAGTTTAAGCTATCCC
1 AGCCTCGTCGTCAGTCCTAAAAAGCCTTGTAAAGATAGTCGGAGTTTAAGCTATCCC
961687 CTTCGGTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (57 bp):
AGCCTCGTCGTCAGTCCTAAAAAGCCTTGTAAAGATAGTCGGAGTTTAAGCTATCCC
Found at i:964688 original size:28 final size:27
Alignment explanation
Indices: 964635--964690 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
964625 TTCGAGTCTG
964635 GAATTTGTTTTAAATAATGGATATGATT
1 GAATTTGTTTTAAATAATGGA-ATGATT
*
964663 GAATTCTGTTTTTAATATATGG-ATGATT
1 GAATT-TGTTTTAAATA-ATGGAATGATT
964691 TTCTGAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 11 0.44
29 10 0.40
30 4 0.16
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (27 bp):
GAATTTGTTTTAAATAATGGAATGATT
Found at i:966018 original size:2 final size:2
Alignment explanation
Indices: 966011--966044 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
966001 TATTTCAAAC
966011 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
966045 CCCTCCATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:968972 original size:18 final size:18
Alignment explanation
Indices: 968949--968983 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
968939 TTCCATCCGG
*
968949 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
968967 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
968984 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:970293 original size:13 final size:13
Alignment explanation
Indices: 970271--970301 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
970261 CGACGGTCAA
*
970271 CGGGTCAACGGGT
1 CGGGTAAACGGGT
970284 CGGGTAAACGGGT
1 CGGGTAAACGGGT
970297 CGGGT
1 CGGGT
970302 CGGGTTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:971239 original size:16 final size:16
Alignment explanation
Indices: 971218--971285 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
971208 TATATAATAA
971218 TATTATATATTAAATT
1 TATTATATATTAAATT
*
971234 TATTATATTTTAAAGGATAAT
1 TATTATATATT-AA--AT--T
*
971255 AATTATTATATTAAATT
1 TATTA-TATATTAAATT
*
971272 TATTATATTTTAAA
1 TATTATATATTAAA
971286 GGATGACTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
16 18 0.44
17 7 0.17
19 4 0.10
21 7 0.17
22 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TATTATATATTAAATT
Found at i:971268 original size:38 final size:36
Alignment explanation
Indices: 971214--971289 Score: 134
Period size: 38 Copynumber: 2.1 Consensus size: 36
971204 AAAATATATA
971214 ATAATATTATATATTAAATTTATTATATTTTAAAGG
1 ATAATATTATATATTAAATTTATTATATTTTAAAGG
971250 ATAATAATTATTATATTAAATTTATTATATTTTAAAGG
1 ATAAT-ATTA-TATATTAAATTTATTATATTTTAAAGG
971288 AT
1 AT
971290 GACTATACGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 5 0.13
37 4 0.11
38 29 0.76
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (36 bp):
ATAATATTATATATTAAATTTATTATATTTTAAAGG
Found at i:972235 original size:16 final size:17
Alignment explanation
Indices: 972216--972252 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
972206 TAAAATATTA
972216 TTTTA-AATAATTAC-AT
1 TTTTATAATAA-TACGAT
972232 TTTTATAATAATACGAT
1 TTTTATAATAATACGAT
972249 TTTT
1 TTTT
972253 TCATCCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTTATAATAATACGAT
Found at i:972305 original size:16 final size:15
Alignment explanation
Indices: 972261--972307 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
972251 TTTCATCCCA
*
972261 TAAAATTATAAATAT
1 TAAAAATATAAATAT
*
972276 T-AAAATATTGAATAT
1 TAAAAATA-TAAATAT
972291 TAAAAATATAAAATAT
1 TAAAAATAT-AAATAT
972307 T
1 T
972308 TTAAATTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.19
15 9 0.35
16 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TAAAAATATAAATAT
Found at i:976954 original size:36 final size:36
Alignment explanation
Indices: 976886--977002 Score: 166
Period size: 35 Copynumber: 3.2 Consensus size: 36
976876 CCCATTATCA
* *
976886 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACTAT
*
976922 TTTTCAAAGAAACATTTACAAAACTTTGAAAACTA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACTAT
*
976957 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACTA-T
976994 TTTTCAAAG
1 TTTTCAAAG
977003 TTGGTTACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.45
36 12 0.16
37 28 0.38
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACTAT
Found at i:980837 original size:16 final size:16
Alignment explanation
Indices: 980813--980845 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
980803 TGAGGCCGAC
*
980813 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
980829 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
980845 C
1 C
980846 GTGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:981325 original size:36 final size:36
Alignment explanation
Indices: 981254--981367 Score: 169
Period size: 35 Copynumber: 3.2 Consensus size: 36
981244 ATCCCATTAT
* *
981254 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
* *
981290 TATTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
981326 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
981361 CATTTTT
1 CATTTTT
981368 TTAAAGTTGG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
35 34 0.49
36 17 0.24
37 19 0.27
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:981330 original size:21 final size:21
Alignment explanation
Indices: 981306--981365 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
981296 TCAAAGAAAT
981306 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
*
981327 ATTT-TCAAA----G-AAA-C
1 ATTTACCAAACTTTGAAAACC
981341 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
981362 ATTT
1 ATTT
981366 TTTTAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAACC
Found at i:981806 original size:2 final size:2
Alignment explanation
Indices: 981799--981826 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
981789 AATTAATGGT
981799 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
981827 ACTCATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:990411 original size:43 final size:43
Alignment explanation
Indices: 990347--990429 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
990337 TTTTTAATCT
* * **
990347 ATAAACGTCGCTAAAGTTTATGAGT-TTTAGTTGCGTTGTTTCC
1 ATAAACGCCGCTAAAGGTTATGA-TATTTAGCGGCGTTGTTTCC
990390 ATAAACGCCGCTAAAGGTTATGATATTTAGCGGCGTTGTT
1 ATAAACGCCGCTAAAGGTTATGATATTTAGCGGCGTTGTT
990430 GAAAAACGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 34 0.97
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (43 bp):
ATAAACGCCGCTAAAGGTTATGATATTTAGCGGCGTTGTTTCC
Found at i:990521 original size:21 final size:21
Alignment explanation
Indices: 990497--990538 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
990487 AATGTTATGA
990497 CATATAGTTGCATTTGTTCCC
1 CATATAGTTGCATTTGTTCCC
*
990518 CATATAGTTGCGTTTGTTCCC
1 CATATAGTTGCATTTGTTCCC
990539 AAAAACGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (21 bp):
CATATAGTTGCATTTGTTCCC
Found at i:990838 original size:21 final size:21
Alignment explanation
Indices: 990812--990859 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
990802 AAAGTATAAC
990812 ATCCATAACAACAAACTTTAA
1 ATCCATAACAACAAACTTTAA
*
990833 ATCCATAACAACCAACTTTAA
1 ATCCATAACAACAAACTTTAA
990854 ATCCAT
1 ATCCAT
990860 TATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (21 bp):
ATCCATAACAACAAACTTTAA
Found at i:991967 original size:23 final size:23
Alignment explanation
Indices: 991937--991984 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
991927 GAGAGTTGGA
*
991937 AGAGGAAAGGAGCAGCGGAGAGC
1 AGAGGAAAGGAGCACCGGAGAGC
*
991960 AGAGGAAAGGAGGACCGGAGAGC
1 AGAGGAAAGGAGCACCGGAGAGC
991983 AG
1 AG
991985 CGAGCTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.48, T:0.00
Consensus pattern (23 bp):
AGAGGAAAGGAGCACCGGAGAGC
Found at i:992346 original size:41 final size:41
Alignment explanation
Indices: 992258--992375 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 41
992248 ATCGTTTATT
* * * * *
992258 ACAAAAATGCCACTAAATTA-AAGGACTATTGCGACGTTTGA
1 ACAAAAATGCCACTAAAATACAA-GTCTATAGCGGCGCTTGA
*
992299 ACAAAAATGCCACTAAAATACAAGTCTATAGCGGCGCTTGT
1 ACAAAAATGCCACTAAAATACAAGTCTATAGCGGCGCTTGA
* ** * * *
992340 ATAAAAACACCACTATAATGCAACTCTATAGCGGCG
1 ACAAAAATGCCACTAAAATACAAGTCTATAGCGGCG
992376 TTTGCTAAAG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 62 0.97
42 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (41 bp):
ACAAAAATGCCACTAAAATACAAGTCTATAGCGGCGCTTGA
Found at i:992820 original size:42 final size:42
Alignment explanation
Indices: 992773--992878 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
992763 CGCCACTTAG
* *
992773 GTACATGACTATTACGACGTTTATTATAAAAAAACAACTAAA
1 GTACATGACTATTGCGGCGTTTATTATAAAAAAACAACTAAA
* ** * * * *
992815 TTACATGGTTATTGCGGCATTTATTATACAAAAGCCACTAAA
1 GTACATGACTATTGCGGCGTTTATTATAAAAAAACAACTAAA
992857 GTACATGACTATTGCGGCGTTT
1 GTACATGACTATTGCGGCGTTT
992879 GAAAAAAATA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (42 bp):
GTACATGACTATTGCGGCGTTTATTATAAAAAAACAACTAAA
Found at i:994582 original size:64 final size:65
Alignment explanation
Indices: 994491--994612 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
994481 ATGCACTCTC
* *
994491 AAATAAATTAACATCGATTGCAATTGGTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCT
1 AAATAAA-TAACATCGAATGCAATTGGTGCATCAATGCAT-AGGTAGTGCATCGATGCATCCCCT
994555 TA
64 TA
* * *
994557 AAATAAA-AACATCGAATGTAATTGGTGTATCAATGCATGGGTAGTGCATCGATGCA
1 AAATAAATAACATCGAATGCAATTGGTGCATCAATGCATAGGTAGTGCATCGATGCA
994613 CATGTTAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.04
64 41 0.82
66 7 0.14
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (65 bp):
AAATAAATAACATCGAATGCAATTGGTGCATCAATGCATAGGTAGTGCATCGATGCATCCCCTTA
Found at i:994646 original size:20 final size:20
Alignment explanation
Indices: 994621--994658 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
994611 CACATGTTAA
994621 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
994641 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
994659 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:995720 original size:23 final size:23
Alignment explanation
Indices: 995652--995712 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
995642 ACATTTTATA
995652 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
995675 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
995698 TGGCACTTCGATGCA
1 TGGCACTTCGGTGCA
995713 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:999771 original size:9 final size:8
Alignment explanation
Indices: 999756--999780 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
999746 AATTAAATCG
999756 ATTTTTTT
1 ATTTTTTT
999764 ATTTTTTT
1 ATTTTTTT
999772 ATTTTTTT
1 ATTTTTTT
999780 A
1 A
999781 AAAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:1000043 original size:31 final size:32
Alignment explanation
Indices: 1000008--1000089 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 32
999998 TTTATGAGTT
*
1000008 AAATTAATATTTTATTTAAAGTTAAAATG-TC-
1 AAATTAATATTTTATTTAAAATT-AAATGATCG
*
1000039 AAATTGATATTTTATTTAAAATTAAATGATCG
1 AAATTAATATTTTATTTAAAATTAAATGATCG
* *
1000071 AAA-TATTATTTTATCTAAA
1 AAATTAATATTTTATTTAAA
1000090 CTTCATAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
30 5 0.11
31 36 0.82
32 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (32 bp):
AAATTAATATTTTATTTAAAATTAAATGATCG
Found at i:1001868 original size:15 final size:15
Alignment explanation
Indices: 1001848--1001889 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1001838 ACTTCTGTGT
1001848 TGAATCATTCAGCAC
1 TGAATCATTCAGCAC
*
1001863 TGAATCAGTCAGCAC
1 TGAATCATTCAGCAC
*
1001878 TAAATCATTCAG
1 TGAATCATTCAG
1001890 AGGTGCGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (15 bp):
TGAATCATTCAGCAC
Found at i:1012015 original size:21 final size:20
Alignment explanation
Indices: 1011929--1012085 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
1011919 AAATGACCAA
**
1011929 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1011948 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1011968 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1011988 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
1012009 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
1012029 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1012049 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1012070 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1012086 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1012038 original size:41 final size:41
Alignment explanation
Indices: 1011929--1012085 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
1011919 AAATGACCAA
* **
1011929 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
1011968 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
1012009 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
1012050 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
1012086 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:1012095 original size:20 final size:20
Alignment explanation
Indices: 1012072--1012245 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
1012062 GCGAATATGA
1012072 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
1012092 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
1012112 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
1012132 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
1012152 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
1012172 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
1012192 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
1012212 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
1012233 AAATCGCAACGCG
1 AAATCGCAACGCG
1012246 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:1012116 original size:40 final size:39
Alignment explanation
Indices: 1012052--1012246 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
1012042 CGATTTTCCA
* ** *
1012052 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
1012092 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
1012132 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
1012172 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
1012212 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1012247 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:1012137 original size:60 final size:60
Alignment explanation
Indices: 1012052--1012245 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1012042 CGATTTTCCA
* ** * *
1012052 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
1012112 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
1012172 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
1012233 AAATCGCAACGCG
1 AAATCGCAACGCG
1012246 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:1012666 original size:33 final size:33
Alignment explanation
Indices: 1012627--1012697 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1012617 TTCACTTAGA
1012627 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1012660 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1012693 TTTCA
1 TTTCA
1012698 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1012834 original size:19 final size:20
Alignment explanation
Indices: 1012777--1012851 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1012767 TGCAGAAGAG
* *
1012777 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
1012798 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
1012818 TCGCAACGCGA-AATGACAA
1 TCGCAACGAGAGAATGACAA
1012837 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1012852 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.36
20 18 0.40
21 11 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:1012839 original size:39 final size:35
Alignment explanation
Indices: 1012789--1012906 Score: 129
Period size: 32 Copynumber: 3.4 Consensus size: 35
1012779 GCAACGAGAT
1012789 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAAT-A---TCGCAACGCG
*
1012828 AAATGACAATCGCAACGAGAG-A-ATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATATCGCAACGCG
*
1012861 -AATGAAAATCGCAACGAGAG-A-ATCACAACGCG
1 AAATGAAAATCGCAACGAGAGAATATCGCAACGCG
**
1012893 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1012907 TTGCGATTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
32 30 0.41
33 21 0.29
36 1 0.01
38 1 0.01
39 20 0.27
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.10
Consensus pattern (35 bp):
AAATGAAAATCGCAACGAGAGAATATCGCAACGCG
Found at i:1012854 original size:14 final size:14
Alignment explanation
Indices: 1012835--1012890 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
1012825 GCGAAATGAC
1012835 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1012849 AATCGCAACGCGAATGAA
1 AATCGCAA--CG-A-GAG
1012867 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1012881 AATCACAACG
1 AATCGCAACG
1012891 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 4 0.11
17 1 0.03
18 10 0.29
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1012943 original size:14 final size:14
Alignment explanation
Indices: 1012924--1012979 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
1012914 TTTTATTTCG
1012924 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1012938 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
1012956 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1012970 CGTTGCGATT
1 CGTTGCGATT
1012980 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 20 0.56
15 3 0.08
17 3 0.08
18 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1013014 original size:20 final size:20
Alignment explanation
Indices: 1012963--1013016 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1012953 TCGCGTTGCG
**
1012963 ATTCTCTCGTTGCGATTGTC
1 ATTCTCTCGTTGCGACAGTC
*
1012983 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
1013002 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
1013017 TTTTCATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:1013023 original size:20 final size:20
Alignment explanation
Indices: 1012963--1013024 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1012953 TCGCGTTGCG
1012963 ATTCTCTCGTTGCGATTGTC
1 ATTCTCTCGTTGCGATTGTC
* **
1012983 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTC
*
1013002 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTGTC
1013022 ATT
1 ATT
1013025 TCAACCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTGTC
Found at i:1013024 original size:39 final size:33
Alignment explanation
Indices: 1012907--1013026 Score: 161
Period size: 32 Copynumber: 3.5 Consensus size: 33
1012897 CAAAATCGCA
*
1012907 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1012940 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1012972 TTGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCG
1013011 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1013027 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
32 31 0.40
33 19 0.25
35 1 0.01
36 1 0.01
37 1 0.01
39 24 0.31
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1015650 original size:14 final size:14
Alignment explanation
Indices: 1015631--1015666 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1015621 CTTATTTAAT
1015631 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1015645 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1015659 TGATTTGT
1 TGATTTGT
1015667 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:1015789 original size:19 final size:19
Alignment explanation
Indices: 1015773--1015874 Score: 144
Period size: 19 Copynumber: 5.6 Consensus size: 19
1015763 AAAAATGACT
1015773 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1015792 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1015811 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1015825 ATCGCAATGCG-AATGAAA
1 ATCGCAATGCGAAATGAAA
1015843 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1015863 ATCGCAATGCGA
1 ATCGCAATGCGA
1015875 TTTTCATTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 3 0.04
18 13 0.17
19 29 0.39
20 17 0.23
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1015892 original size:19 final size:19
Alignment explanation
Indices: 1015864--1016185 Score: 450
Period size: 19 Copynumber: 17.9 Consensus size: 19
1015854 GAAATGAAAA
*
1015864 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1015883 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1015899 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1015916 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
1015932 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1015949 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1015968 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1015987 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1016006 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1016025 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1016044 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1016063 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1016082 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1016098 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1016115 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1016134 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
1016148 TCTCATTGCGATTTTCATTT
1 TCGCATTGCGATTTTCA-TT
1016168 TCGCATTGCGATTTTCAT
1 TCGCATTGCGATTTTCAT
1016186 GTTGGGATTT
Statistics
Matches: 273, Mismatches: 9, Indels: 42
0.84 0.03 0.13
Matches are distributed among these distances:
14 28 0.10
16 25 0.09
17 25 0.09
19 179 0.66
20 16 0.06
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1015907 original size:14 final size:14
Alignment explanation
Indices: 1015888--1015942 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1015878 TCATTTCGCA
*
1015888 TTGCGATTCTCTCG
1 TTGCGATTCTTTCG
1015902 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
1015919 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
1015935 TTGCGATT
1 TTGCGATT
1015943 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 8 0.23
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:1016872 original size:20 final size:20
Alignment explanation
Indices: 1016844--1017053 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
1016834 AAATTTCAGT
* * *
1016844 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1016864 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1016884 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1016904 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1016924 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
1016944 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
1016964 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1016984 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1017004 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1017024 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1017044 GTTGCGATTT
1 GTTGCGATTT
1017054 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1017070 original size:21 final size:20
Alignment explanation
Indices: 1017020--1017117 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
1017010 ATTTATGTGT
* * * *
1017020 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
1017040 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
1017061 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
1017081 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
1017102 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
1017118 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:1017112 original size:41 final size:41
Alignment explanation
Indices: 1017020--1017176 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
1017010 ATTTATGTGT
* * *
1017020 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
1017061 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
1017102 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
1017142 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
1017177 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:1019057 original size:28 final size:29
Alignment explanation
Indices: 1019026--1019081 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1019016 TTTAATCAAG
1019026 AAAAATA-TTAAAAATTA-ATATAGAATAC
1 AAAAATAGTTAAAAATTATATATA-AATAC
* *
1019054 AAAATTAGTTAAAATTTATATATAAATA
1 AAAAATAGTTAAAAATTATATATAAATA
1019082 TGTTATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 13 0.54
30 5 0.21
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATAGTTAAAAATTATATATAAATAC
Found at i:1020574 original size:23 final size:24
Alignment explanation
Indices: 1020548--1020597 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1020538 AAATTTTTTG
1020548 TTTATTTTG-ATACAAAAAATTAA
1 TTTATTTTGCATACAAAAAATTAA
* * *
1020571 TTTATTTTGCATATAAAATATTTA
1 TTTATTTTGCATACAAAAAATTAA
1020595 TTT
1 TTT
1020598 TGCAACCTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTATTTTGCATACAAAAAATTAA
Found at i:1021602 original size:2 final size:2
Alignment explanation
Indices: 1021537--1021589 Score: 74
Period size: 2 Copynumber: 27.0 Consensus size: 2
1021527 CCGCTCAAAT
*
1021537 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
1021579 TA T- TA TA TA TA
1 TA TA TA TA TA TA
1021590 ATTAACATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1023075 original size:16 final size:16
Alignment explanation
Indices: 1023054--1023087 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1023044 ATGTTATTGC
* *
1023054 TTATTTTTTTTTTTAT
1 TTATTTTATTTCTTAT
1023070 TTATTTTATTTCTTAT
1 TTATTTTATTTCTTAT
1023086 TT
1 TT
1023088 TTCTTTTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTTTATTTCTTAT
Found at i:1028243 original size:164 final size:164
Alignment explanation
Indices: 1027970--1028908 Score: 1133
Period size: 164 Copynumber: 5.7 Consensus size: 164
1027960 TAAACAAACT
*
1027970 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* *
1028035 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACC-AAAGACC
1028100 TTTGAGTTCGACTACGCTCAGCT-CAACGGCAC-TC
130 TTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
1028134 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * *
1028199 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ACCAAAGACC
1028264 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
1028299 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * *
1028363 GCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCT
*
1028428 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
1028462 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACCCCCGAGTTCGATTACACTC
* * * *
1028527 AGCTT-GAGGGCATATCATTTACAGCATAACTCAAGGCTATAA-GGTTATATGTCACCAAAGACC
65 AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACC
* *
1028590 TTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * * * *** **
1028625 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGATTATG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGATTACA
* * * ** * * * *
1028690 CTCAGC-TCCAAGGCATATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAG
62 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAG
* * * * * * *
1028751 ACCCTTAAGTTTGATTACACTCAGCTTCAAGGGCATATC
127 ACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
* * * * * * * * ***
1028790 ATTTACAACATAACTCAAGGCTAGAAGAGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACAC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCCCGAGTTCGATTACAC
* * * * * * *
1028855 TCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
63 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
1028909 CCAAAGACCC
Statistics
Matches: 703, Mismatches: 61, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
163 166 0.24
164 360 0.51
165 116 0.17
166 54 0.08
167 7 0.01
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (164 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAGACCT
TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:1028836 original size:411 final size:410
Alignment explanation
Indices: 1028170--1028973 Score: 1306
Period size: 411 Copynumber: 2.0 Consensus size: 410
1028160 GGGCTATCTG
* * * *
1028170 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCCCCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGCACAACTTAAGT
*
1028235 CGAGAAGGGTTATATGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
66 CGAGAAGGGTTATATGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
*
1028300 TTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGACCCCCGAGTTCGATTACACTCAGC
131 TTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGACCCCCAAGTTCGATTACACTCAGC
* * * * *
1028365 TTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAGACCTTC
196 TTCAAGGGCATATCATTTACAACATAACTCAAGGCTAGAAGAGTTATCTGTCAACAAAGACCTTC
*
1028430 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
261 GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
* *
1028495 CTGCCAAAAGACCCCCGAGTTCGATTACACTCAGCTT-GAGGGCATATCATTTACAGCATAACTC
326 CTGCC-AAAGA-CCCCGAGTTCGATTACACTCAACTTCGAGGGCATATCATTTACAACATAACTC
1028559 AAGGCTATAAGGTTATATGTCA
389 AAGGCTATAAGGTTATATGTCA
**
1028581 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCACAACTTAAGT
1 CCAAAGACCCCCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGCACAACTTAAGT
* * * * * *
1028645 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGATTATGCTCAGCTCCAAGGCATATCA
66 CGAGAAGGGTTATATGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
** *
1028710 TTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTTGATTACACTCAG
131 TTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAGACCCCCAAGTTCGATTACACTCAG
1028775 CTTCAAGGGCATATCATTTACAACATAACTCAAGGCTAGAAGAGTTATCTGTCAACAAAGACCTT
195 CTTCAAGGGCATATCATTTACAACATAACTCAAGGCTAGAAGAGTTATCTGTCAACAAAGACCTT
* *
1028840 TGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
260 CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
* *
1028905 TCTGCCAAAGACCCCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTACAACATAGCTCA
325 TCTGCCAAAGACCCCGAGTTCGATTACACTCAACTTCGAGGGCATATCATTTACAACATAACTCA
1028970 AGGC
390 AGGC
1028974 AAGAAGGACT
Statistics
Matches: 362, Mismatches: 29, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
409 24 0.07
410 159 0.44
411 179 0.49
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (410 bp):
CCAAAGACCCCCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGCACAACTTAAGT
CGAGAAGGGTTATATGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
TTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGACCCCCAAGTTCGATTACACTCAGC
TTCAAGGGCATATCATTTACAACATAACTCAAGGCTAGAAGAGTTATCTGTCAACAAAGACCTTC
GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
CTGCCAAAGACCCCGAGTTCGATTACACTCAACTTCGAGGGCATATCATTTACAACATAACTCAA
GGCTATAAGGTTATATGTCA
Found at i:1030830 original size:13 final size:13
Alignment explanation
Indices: 1030797--1030821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1030787 TATTGCTTAT
1030797 TTTATTTTATTTA
1 TTTATTTTATTTA
1030810 TTTATTTTATTT
1 TTTATTTTATTT
1030822 CTTATTTTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:1031088 original size:6 final size:6
Alignment explanation
Indices: 1031077--1031104 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1031067 CGAAATGAAT
1031077 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1031105 CGTAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:1036785 original size:17 final size:16
Alignment explanation
Indices: 1036753--1036789 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1036743 CATCAAATTT
1036753 TATA-TAAATTATTAA
1 TATATTAAATTATTAA
1036768 TATATTAAATTAATTAA
1 TATATTAAATT-ATTAA
1036785 TATAT
1 TATAT
1036790 AGTATTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATTAAATTATTAA
Found at i:1038841 original size:13 final size:13
Alignment explanation
Indices: 1038823--1038847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1038813 ATAGTTGAAC
1038823 AGTCTTCATATGT
1 AGTCTTCATATGT
1038836 AGTCTTCATATG
1 AGTCTTCATATG
1038848 CGAATATGTA
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
AGTCTTCATATGT
Found at i:1039180 original size:2 final size:2
Alignment explanation
Indices: 1039173--1039210 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1039163 AGATTTAGAA
*
1039173 AT AT AT AT AT AA 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
1039211 GGCGGCTGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1039495 original size:13 final size:13
Alignment explanation
Indices: 1039477--1039509 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1039467 TTAGTACACT
1039477 TATAATAGATAAA
1 TATAATAGATAAA
1039490 TATAATAGATAAA
1 TATAATAGATAAA
*
1039503 AATAATA
1 TATAATA
1039510 TCATTCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (13 bp):
TATAATAGATAAA
Found at i:1051952 original size:60 final size:59
Alignment explanation
Indices: 1051834--1051965 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 59
1051824 CAGATGATCA
* * * * *
1051834 TTTTGTAAGTTTTAATAGTCAAGTGACTCAACAAAGTAACTTTCTATAGTTGGGGGACTT
1 TTTTATAACTTTTAATAGTCAAGAGACTCAACAAAGTAACTATCTATAGTTGAGGGAC-T
* * *
1051894 TTTTATAACTTTTAATAGTCGAGAGACTCAATAAAGTAA-TATCATATAGTTGATGGACT
1 TTTTATAACTTTTAATAGTCAAGAGACTCAACAAAGTAACTATC-TATAGTTGAGGGACT
*
1051953 ATTTATATACTTT
1 TTTTATA-ACTTT
1051966 ACCCTAAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 10 0.16
60 51 0.84
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (59 bp):
TTTTATAACTTTTAATAGTCAAGAGACTCAACAAAGTAACTATCTATAGTTGAGGGACT
Found at i:1055933 original size:257 final size:257
Alignment explanation
Indices: 1055477--1055990 Score: 1028
Period size: 257 Copynumber: 2.0 Consensus size: 257
1055467 AGTGCGTAAG
1055477 TGTAATGATTGTTCTTGCCTTTATTTTGTATGTCTACTCAAGATAGTATTTGCATTTCTATCATT
1 TGTAATGATTGTTCTTGCCTTTATTTTGTATGTCTACTCAAGATAGTATTTGCATTTCTATCATT
1055542 AGGTTGAGTTCTCATGATATGCTTGCTTGGTTTTTCTCTTCTGTGGCTTCTACCAGGGTTGCTGC
66 AGGTTGAGTTCTCATGATATGCTTGCTTGGTTTTTCTCTTCTGTGGCTTCTACCAGGGTTGCTGC
1055607 AACTAAGAGTCCTGTCATATTTATAGGAACGGGAGAGCACATGGATGAGTTTGAAGTGTTTGATG
131 AACTAAGAGTCCTGTCATATTTATAGGAACGGGAGAGCACATGGATGAGTTTGAAGTGTTTGATG
1055672 TTAAACCATTTGTAAGCCGCCTTTTAGGTATACATCTCCTTTTCCTGTTATGTATTCTTCTC
196 TTAAACCATTTGTAAGCCGCCTTTTAGGTATACATCTCCTTTTCCTGTTATGTATTCTTCTC
1055734 TGTAATGATTGTTCTTGCCTTTATTTTGTATGTCTACTCAAGATAGTATTTGCATTTCTATCATT
1 TGTAATGATTGTTCTTGCCTTTATTTTGTATGTCTACTCAAGATAGTATTTGCATTTCTATCATT
1055799 AGGTTGAGTTCTCATGATATGCTTGCTTGGTTTTTCTCTTCTGTGGCTTCTACCAGGGTTGCTGC
66 AGGTTGAGTTCTCATGATATGCTTGCTTGGTTTTTCTCTTCTGTGGCTTCTACCAGGGTTGCTGC
1055864 AACTAAGAGTCCTGTCATATTTATAGGAACGGGAGAGCACATGGATGAGTTTGAAGTGTTTGATG
131 AACTAAGAGTCCTGTCATATTTATAGGAACGGGAGAGCACATGGATGAGTTTGAAGTGTTTGATG
1055929 TTAAACCATTTGTAAGCCGCCTTTTAGGTATACATCTCCTTTTCCTGTTATGTATTCTTCTC
196 TTAAACCATTTGTAAGCCGCCTTTTAGGTATACATCTCCTTTTCCTGTTATGTATTCTTCTC
1055991 AACACATAAA
Statistics
Matches: 257, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
257 257 1.00
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (257 bp):
TGTAATGATTGTTCTTGCCTTTATTTTGTATGTCTACTCAAGATAGTATTTGCATTTCTATCATT
AGGTTGAGTTCTCATGATATGCTTGCTTGGTTTTTCTCTTCTGTGGCTTCTACCAGGGTTGCTGC
AACTAAGAGTCCTGTCATATTTATAGGAACGGGAGAGCACATGGATGAGTTTGAAGTGTTTGATG
TTAAACCATTTGTAAGCCGCCTTTTAGGTATACATCTCCTTTTCCTGTTATGTATTCTTCTC
Found at i:1066534 original size:30 final size:30
Alignment explanation
Indices: 1066498--1066557 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1066488 ATCTTAGTTT
1066498 AGACAATATGCACTAATTCAAAAGTATTGA
1 AGACAATATGCACTAATTCAAAAGTATTGA
*
1066528 AGACAATATGCACTAATTCAAAGGTATTGA
1 AGACAATATGCACTAATTCAAAAGTATTGA
1066558 GTTTTATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (30 bp):
AGACAATATGCACTAATTCAAAAGTATTGA
Found at i:1075337 original size:21 final size:20
Alignment explanation
Indices: 1075315--1075376 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
1075305 TACAACATAT
1075315 TTTTAATAATATAAATAAAA
1 TTTTAATAATATAAATAAAA
*
1075335 -TTTAATAAATATAGATAAAA
1 TTTTAAT-AATATAAATAAAA
*
1075355 TTTTAATAACATAAATTAAAA
1 TTTTAATAATATAAA-TAAAA
1075376 T
1 T
1075377 AAATCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.17
20 18 0.50
21 12 0.33
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TTTTAATAATATAAATAAAA
Found at i:1075347 original size:20 final size:20
Alignment explanation
Indices: 1075316--1075376 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
1075306 ACAACATATT
1075316 TTTAAT-AATATAAATAAAA
1 TTTAATAAATATAAATAAAA
*
1075335 TTTAATAAATATAGATAAAA
1 TTTAATAAATATAAATAAAA
*
1075355 TTTTAATAACATA-AATTAAAA
1 -TTTAATAA-ATATAAATAAAA
1075376 T
1 T
1075377 AAATCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.17
20 13 0.36
21 14 0.39
22 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAATAAATATAAATAAAA
Found at i:1075581 original size:39 final size:40
Alignment explanation
Indices: 1075527--1075604 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
1075517 TAACGGACAA
*
1075527 CAATCAAAGTTTCAATAAAAAGTTTA-GGAACCAAAGCAG
1 CAATCAAAGCTTCAATAAAAAGTTTAGGGAACCAAAGCAG
1075566 CAATCAAAGCTTCAATAAAAAGTTTAGGGAACCAAAGCA
1 CAATCAAAGCTTCAATAAAAAGTTTAGGGAACCAAAGCA
1075605 AAAATAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 25 0.68
40 12 0.32
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (40 bp):
CAATCAAAGCTTCAATAAAAAGTTTAGGGAACCAAAGCAG
Found at i:1075754 original size:22 final size:22
Alignment explanation
Indices: 1075729--1075778 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1075719 AATGGAATCA
*
1075729 TTCAGCGATGAATGCTGAACCG
1 TTCAGCGATGAATACTGAACCG
1075751 TTCAGCGATGAATACTGAACCG
1 TTCAGCGATGAATACTGAACCG
1075773 TTCAGC
1 TTCAGC
1075779 ATTCAGCGCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (22 bp):
TTCAGCGATGAATACTGAACCG
Found at i:1087827 original size:37 final size:37
Alignment explanation
Indices: 1087777--1087856 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
1087767 TTGAGGTGAG
1087777 AATAAGCAGACATTTTAGGACGAGAAATGAAAGCGAA
1 AATAAGCAGACATTTTAGGACGAGAAATGAAAGCGAA
*
1087814 AATAAGCAGACATTTTAGGACGAGAAATGAAAGTGAA
1 AATAAGCAGACATTTTAGGACGAGAAATGAAAGCGAA
1087851 AATAAG
1 AATAAG
1087857 GGTTAACATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.17
Consensus pattern (37 bp):
AATAAGCAGACATTTTAGGACGAGAAATGAAAGCGAA
Found at i:1092299 original size:37 final size:36
Alignment explanation
Indices: 1092254--1092355 Score: 152
Period size: 35 Copynumber: 2.8 Consensus size: 36
1092244 TCAACAAATC
*
1092254 TACCAAACTTTGAAAAACTATTTTTCAAAGAAACATT
1 TACCAAACTTTG-AAAACCATTTTTCAAAGAAACATT
*
1092291 TACCAAACTTTGAAAACCA-TTTTCAAATAAACATT
1 TACCAAACTTTGAAAACCATTTTTCAAAGAAACATT
*
1092326 TACCAAACATTGAAAACCATTTTTTCAAAG
1 TACCAAACTTTGAAAACCA-TTTTTCAAAG
1092356 TTGGTTACCA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.56
36 6 0.10
37 20 0.34
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTCAAAGAAACATT
Found at i:1092311 original size:21 final size:20
Alignment explanation
Indices: 1092287--1092347 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
1092277 TTCAAAGAAA
1092287 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAAC-TTGAAAAC
*
1092308 CATTT-TCAAA--T--AAA-
1 CATTTACCAAACTTGAAAAC
1092322 CATTTACCAAACATTGAAAAC
1 CATTTACCAAAC-TTGAAAAC
1092343 CATTT
1 CATTT
1092348 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
17 1 0.03
18 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.31
Consensus pattern (20 bp):
CATTTACCAAACTTGAAAAC
Found at i:1096902 original size:32 final size:33
Alignment explanation
Indices: 1096809--1096951 Score: 148
Period size: 32 Copynumber: 4.2 Consensus size: 33
1096799 ATCCCATTAT
* *
1096809 CATTTTTCAACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAA-AGA-ATTTACCAAACTTTG-AAAAC
*
1096845 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAG--A-ATTTACCAAACTTTGAAAAC
1096881 CA-TTTTCAAAGAATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAATTTACCAAACTTTGAAAAC
*
1096913 CATTTTTTCAAAG-TTGGTTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAT--TTACCAAACTTTGAAAAC
1096947 CATTT
1 CATTT
1096952 AATACTTTCA
Statistics
Matches: 96, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
32 22 0.23
33 5 0.05
34 19 0.20
35 19 0.20
36 15 0.16
37 16 0.17
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (33 bp):
CATTTTTCAAAGAATTTACCAAACTTTGAAAAC
Found at i:1097190 original size:50 final size:50
Alignment explanation
Indices: 1097132--1097231 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1097122 TTACGAATGG
1097132 GGAAGAATACTACAAAAGAGTAGGCAAAGCCTAGAAACGTGGATATCTGT
1 GGAAGAATACTACAAAAGAGTAGGCAAAGCCTAGAAACGTGGATATCTGT
1097182 GGAAGAATACTACAAAAGAGTAGGCAAAGCCTAGAAACGTGGATATCTGT
1 GGAAGAATACTACAAAAGAGTAGGCAAAGCCTAGAAACGTGGATATCTGT
1097232 TGTACGGTCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (50 bp):
GGAAGAATACTACAAAAGAGTAGGCAAAGCCTAGAAACGTGGATATCTGT
Found at i:1098729 original size:13 final size:13
Alignment explanation
Indices: 1098711--1098737 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1098701 AAAGATATGC
1098711 TTGTAAGTATTGT
1 TTGTAAGTATTGT
1098724 TTGTAAGTATTGT
1 TTGTAAGTATTGT
1098737 T
1 T
1098738 AGCAAGTACT
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:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (13 bp):
TTGTAAGTATTGT
Found at i:1113817 original size:48 final size:48
Alignment explanation
Indices: 1113761--1113856 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1113751 ATGATCATTG
*
1113761 GAACTAGAGGGAATTCCATCCCGAGCGAAGAATGAAAGCTTAGTGAAC
1 GAACTAGAGGGAATTCCATCCCGAGCGAAGAATGAAAGCTTAGCGAAC
1113809 GAACTAGAGGGAATTCCATCCCGAGCGAAGAATGAAAGCTTAGCGAAC
1 GAACTAGAGGGAATTCCATCCCGAGCGAAGAATGAAAGCTTAGCGAAC
1113857 TCACAGGTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.16
Consensus pattern (48 bp):
GAACTAGAGGGAATTCCATCCCGAGCGAAGAATGAAAGCTTAGCGAAC
Found at i:1114515 original size:2 final size:2
Alignment explanation
Indices: 1114508--1114550 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1114498 TTTAATTGAA
1114508 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
1114550 A
1 A
1114551 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1114555 original size:2 final size:2
Alignment explanation
Indices: 1114550--1114585 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1114540 ATATATATAT
*
1114550 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1114586 GTATTATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1117353 original size:21 final size:20
Alignment explanation
Indices: 1117328--1117384 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
1117318 AACATATTTT
1117328 TAATATAAAATAAAATTTAA
1 TAATATAAAATAAAATTTAA
*
1117348 TAA-ATATAGATAAAATTTTAA
1 TAATATA-AAATAAAA-TTTAA
* *
1117369 TAACATAAATTAAAAT
1 TAATATAAAATAAAAT
1117385 AATCATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 3 0.10
20 11 0.35
21 14 0.45
22 3 0.10
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TAATATAAAATAAAATTTAA
Found at i:1126561 original size:81 final size:80
Alignment explanation
Indices: 1126366--1126677 Score: 473
Period size: 80 Copynumber: 3.9 Consensus size: 80
1126356 GCTTGCCTCA
* * ** *
1126366 GCACACAGCAAAAAGGGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAG
1 GCACACAGC--AAA-GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAA-GATATCCTTAG
* *
1126430 ATCCGTAGGGTTACCTTAA
62 GTCCGTAGGGTTACCTTAT
* *
1126449 GCACACAGCTAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAATATATCCTTAGGTCC
1 GCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCC
1126514 GTAGGGTTACCTTAT
66 GTAGGGTTACCTTAT
*
1126529 GCACACAGCAAAAGGGAACTAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTC
1 GCACACAGC-AAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTC
*
1126594 CGTAGGGTTACGTTAT
65 CGTAGGGTTACCTTAT
1126610 GCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCC
1 GCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCC
1126675 GTA
66 GTA
1126678 ATGACTTACA
Statistics
Matches: 213, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
80 116 0.54
81 88 0.41
83 9 0.04
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (80 bp):
GCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCC
GTAGGGTTACCTTAT
Found at i:1126642 original size:161 final size:163
Alignment explanation
Indices: 1126366--1126677 Score: 495
Period size: 161 Copynumber: 1.9 Consensus size: 163
1126356 GCTTGCCTCA
* *
1126366 GCACACAGCAAAAAGGGGAGCCAACCTAAGGATATACCTTGGATCTACCCAAGGACATCCTTAGA
1 GCACACAGCAAAAAGGGGAACCAACCTAAGGATATACCTTGGACCTACCCAAGGACATCCTTAGA
*
1126431 TCCGTAGGGTTACCTTAAGCACACAGCTAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACC
66 TCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACC
*
1126496 CAATATATCCTTAGGTCCGTAGGGTTACCTTAT
131 CAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
* * * *
1126529 GCACACAGC-AAAA-GGGAACTAACCTAAGGATATGCCTTGGGGCCTACCCAA-GATATCCTTAG
1 GCACACAGCAAAAAGGGGAACCAACCTAAGGATATACCTT-GGACCTACCCAAGGACATCCTTAG
* * *
1126591 GTCCGTAGGGTTACGTTATGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAC
65 ATCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAC
1126656 CCAAGATATCCTTAGGTCCGTA
130 CCAAGATATCCTTAGGTCCGTA
1126678 ATGACTTACA
Statistics
Matches: 137, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
161 114 0.83
162 14 0.10
163 9 0.07
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (163 bp):
GCACACAGCAAAAAGGGGAACCAACCTAAGGATATACCTTGGACCTACCCAAGGACATCCTTAGA
TCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACC
CAAGATATCCTTAGGTCCGTAGGGTTACCTTAT
Found at i:1130718 original size:35 final size:35
Alignment explanation
Indices: 1130645--1130719 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
1130635 CGTCATGTCC
* **
1130645 AGTAAGGCCCTGAGCACACAGCCGAGGAACTGGTA
1 AGTAAGGCCCTGAGCACACAACCGAGGAACTGCCA
1130680 AGTAAGGCCCTGAGCACACAACCGAGGAACCT-CCA
1 AGTAAGGCCCTGAGCACACAACCGAGGAA-CTGCCA
1130715 AGTAA
1 AGTAA
1130720 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 34 0.94
36 2 0.06
ACGTcount: A:0.35, C:0.28, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAACCGAGGAACTGCCA
Found at i:1130824 original size:24 final size:24
Alignment explanation
Indices: 1130797--1130887 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
1130787 CATAATTCAA
*
1130797 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
1130821 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
1130845 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
1130868 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
1130888 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:1130867 original size:47 final size:48
Alignment explanation
Indices: 1130797--1130887 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
1130787 CATAATTCAA
* * *
1130797 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
1130845 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
1130888 TCAAATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:1133375 original size:13 final size:13
Alignment explanation
Indices: 1133357--1133432 Score: 89
Period size: 13 Copynumber: 5.5 Consensus size: 13
1133347 CAATGGTCAA
1133357 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1133370 CGGGTCAACGGGTTGGGT
1 CGGGTCAAC-----GGGT
1133388 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
1133401 CGGGTCAACAGGT
1 CGGGTCAACGGGT
*
1133414 CGGGTAAACGGGT
1 CGGGTCAACGGGT
1133427 CGGGTC
1 CGGGTC
1133433 GGGTTATGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1133393 original size:31 final size:31
Alignment explanation
Indices: 1133357--1133418 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1133347 CAATGGTCAA
* *
1133357 CGGGTCAACGGGTCGGGTCAACGGGTTGGGT
1 CGGGTCAACGGGTCGGGTCAACAGGTCGGGT
1133388 CGGGTCAACGGGTCGGGTCAACAGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACAGGTCGGGT
1133419 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACAGGTCGGGT
Found at i:1133414 original size:26 final size:27
Alignment explanation
Indices: 1133357--1133432 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 27
1133347 CAATGGTCAA
*
1133357 CGGGTCAACGGGTCGGGTCAACGGGTTGGGT
1 CGGGTCAACGGGTCGGGTCAAC--G--AGGT
1133388 CGGGTCAACGGGTCGGGTCAAC-AGGT
1 CGGGTCAACGGGTCGGGTCAACGAGGT
*
1133414 CGGGTAAACGGGTCGGGTC
1 CGGGTCAACGGGTCGGGTC
1133433 GGGTTATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 21 0.49
31 22 0.51
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (27 bp):
CGGGTCAACGGGTCGGGTCAACGAGGT
Found at i:1133418 original size:18 final size:18
Alignment explanation
Indices: 1133351--1133406 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
1133341 GCCGGTCAAT
1133351 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
*
1133372 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTCGGGTCG
1133390 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1133407 AACAGGTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.14, C:0.21, G:0.46, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1136104 original size:2 final size:2
Alignment explanation
Indices: 1136056--1136087 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1136046 ACTATGTCTG
1136056 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
1136088 TGCATATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1136199 original size:24 final size:23
Alignment explanation
Indices: 1136171--1136228 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
1136161 TGATTAAATT
* *
1136171 TTAACATAAACTCGAACAATTTGA
1 TTAACTTAAACTC-AACAATTCGA
*
1136195 TTAACTTAAGACTCATCAATTCGA
1 TTAACTTAA-ACTCAACAATTCGA
1136219 TTAACTTAAA
1 TTAACTTAAA
1136229 AATATTTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 25 0.83
25 4 0.13
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (23 bp):
TTAACTTAAACTCAACAATTCGA
Found at i:1149348 original size:170 final size:170
Alignment explanation
Indices: 1149066--1149413 Score: 687
Period size: 170 Copynumber: 2.0 Consensus size: 170
1149056 ACCGGTATTT
1149066 ATGTTCCAATTTATGTTGTTAGGAGATATTAATAACCACGTGTTTTACTCTGAGTTTCTTATCAA
1 ATGTTCCAATTTATGTTGTTAGGAGATATTAATAACCACGTGTTTTACTCTGAGTTTCTTATCAA
1149131 GAGATGGAAATGAACATGTGGAAGGGAAGTGTTTATGAAAGAACTTCGTCAGATATTTTGCATAC
66 GAGATGGAAATGAACATGTGGAAGGGAAGTGTTTATGAAAGAACTTCGTCAGATATTTTGCATAC
1149196 TTGAGGGATTTGTTTCCAAACTTACTAGTTTTATTTTTTC
131 TTGAGGGATTTGTTTCCAAACTTACTAGTTTTATTTTTTC
1149236 ATGTTCCAATTTATGTTGTTAGGAGATATTAATAACCACGTGTTTTACTCTGAGTTTCTTATCAA
1 ATGTTCCAATTTATGTTGTTAGGAGATATTAATAACCACGTGTTTTACTCTGAGTTTCTTATCAA
1149301 GAGATGGAAATGAACATGTGGAAGGGAAGTGTTTATGAAAGAACTTCGTCAGATATTTTGCATAC
66 GAGATGGAAATGAACATGTGGAAGGGAAGTGTTTATGAAAGAACTTCGTCAGATATTTTGCATAC
1149366 TTGAGGGATTTGTTTCCAAACTTACTAGTTTTATTTTTTC
131 TTGAGGGATTTGTTTCCAAACTTACTAGTTTTATTTTTTC
*
1149406 ATGATCCA
1 ATGTTCCA
1149414 TAATTTATAA
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 177 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (170 bp):
ATGTTCCAATTTATGTTGTTAGGAGATATTAATAACCACGTGTTTTACTCTGAGTTTCTTATCAA
GAGATGGAAATGAACATGTGGAAGGGAAGTGTTTATGAAAGAACTTCGTCAGATATTTTGCATAC
TTGAGGGATTTGTTTCCAAACTTACTAGTTTTATTTTTTC
Found at i:1160390 original size:24 final size:24
Alignment explanation
Indices: 1160375--1160489 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
1160365 CATAATTCAC
* *
1160375 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAT
* * * *
1160399 GTTAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
*
1160423 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
1160447 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
1160471 GTCAAGTATCATATCAGAA
1 GTCAAGTATCATATCAGAA
1160490 ATCAAATCGA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:1166141 original size:25 final size:22
Alignment explanation
Indices: 1166112--1166157 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1166102 TTTTTAACCC
1166112 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
1166137 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
1166158 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:1173814 original size:88 final size:88
Alignment explanation
Indices: 1173660--1173836 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
1173650 ACAAACATGG
*
1173660 AGTTTCGGCTGCAATACAACATGTTAAGCCTTTTTTAACCATGAAGAGTCGGTCTGGAAGACTTT
1 AGTTTCGGCTGCAATACAACATGCTAAGCCTTTTTTAACCATGAAGAGTCGGTCTGGAAGACTTT
1173725 GAAAATCACACAAGAAAAGGAAA
66 GAAAATCACACAAGAAAAGGAAA
*
1173748 AGTTTCGGCTGCAATACAACATGCTAAGCCTTTTTTAACCATGAAGAGTCGGTCTGGAAGAGTTT
1 AGTTTCGGCTGCAATACAACATGCTAAGCCTTTTTTAACCATGAAGAGTCGGTCTGGAAGACTTT
1173813 GAAAATCACACAAGAAAAGGAAA
66 GAAAATCACACAAGAAAAGGAAA
1173836 A
1 A
1173837 AGAGAAAGGA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (88 bp):
AGTTTCGGCTGCAATACAACATGCTAAGCCTTTTTTAACCATGAAGAGTCGGTCTGGAAGACTTT
GAAAATCACACAAGAAAAGGAAA
Found at i:1175924 original size:21 final size:20
Alignment explanation
Indices: 1175902--1175963 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
1175892 TATAACGTAT
1175902 TTTTAATAATATAAATAAAA
1 TTTTAATAATATAAATAAAA
*
1175922 -TTTAATAAATATAGATAAAA
1 TTTTAAT-AATATAAATAAAA
*
1175942 TTTTAATAACATAAATTAAAA
1 TTTTAATAATATAAA-TAAAA
1175963 T
1 T
1175964 AAATCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.17
20 18 0.50
21 12 0.33
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TTTTAATAATATAAATAAAA
Found at i:1175934 original size:20 final size:20
Alignment explanation
Indices: 1175903--1175963 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
1175893 ATAACGTATT
1175903 TTTAAT-AATATAAATAAAA
1 TTTAATAAATATAAATAAAA
*
1175922 TTTAATAAATATAGATAAAA
1 TTTAATAAATATAAATAAAA
*
1175942 TTTTAATAACATA-AATTAAAA
1 -TTTAATAA-ATATAAATAAAA
1175963 T
1 T
1175964 AAATCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.17
20 13 0.36
21 14 0.39
22 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAATAAATATAAATAAAA
Found at i:1176161 original size:27 final size:28
Alignment explanation
Indices: 1176119--1176179 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
1176109 GGACAGCAAT
*
1176119 CAAAGTTTCAACAAAAAGTTTA-GGAAC
1 CAAAGCTTCAACAAAAAGTTTAGGGAAC
*
1176146 CAAAGCTTCAATAAAAAGTTTAGGGAAC
1 CAAAGCTTCAACAAAAAGTTTAGGGAAC
1176174 CAAAGC
1 CAAAGC
1176180 AAAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (28 bp):
CAAAGCTTCAACAAAAAGTTTAGGGAAC
Found at i:1176186 original size:28 final size:27
Alignment explanation
Indices: 1176131--1176188 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
1176121 AAGTTTCAAC
***
1176131 AAAAAGTTTAGGAACCAAAGCTTCAAT
1 AAAAAGTTTAGGAACCAAAGCAAAAAT
1176158 AAAAAGTTTAGGGAACCAAAGCAAAAAT
1 AAAAAGTTTA-GGAACCAAAGCAAAAAT
1176186 AAA
1 AAA
1176189 TAAATAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.17
Consensus pattern (27 bp):
AAAAAGTTTAGGAACCAAAGCAAAAAT
Found at i:1181093 original size:13 final size:13
Alignment explanation
Indices: 1181075--1181104 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1181065 GTCACAACCC
1181075 GACCCGACCCGTT
1 GACCCGACCCGTT
1181088 GACCCGACCCGTT
1 GACCCGACCCGTT
1181101 GACC
1 GACC
1181105 GGCGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1182443 original size:18 final size:18
Alignment explanation
Indices: 1182417--1182452 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1182407 TCGAAAGGAC
*
1182417 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1182435 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1182453 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1183609 original size:24 final size:24
Alignment explanation
Indices: 1183495--1183606 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
1183485 ATTTGAATTA
*
1183495 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATAGATTC
1183519 TGATCTGATA-TATGACATAGATTC
1 TGATCTGATACT-TGACATAGATTC
*
1183543 TGATCTGATACTTGACTTAGATTC
1 TGATCTGATACTTGACATAGATTC
* * *
1183567 TGATCTGATACTTGACCTGGATTT
1 TGATCTGATACTTGACATAGATTC
*
1183591 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
1183607 CTGATTTATG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
TGATCTGATACTTGACATAGATTC
Found at i:1185771 original size:13 final size:13
Alignment explanation
Indices: 1185752--1185793 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1185742 GTCACAACCC
*
1185752 GACCCGACTCGTT
1 GACCCGACCCGTT
*
1185765 TACCCGACCCGTT
1 GACCCGACCCGTT
1185778 GACCCGACCCCGTT
1 GACCCGA-CCCGTT
1185792 GA
1 GA
1185794 TCCGTTGACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1187142 original size:18 final size:18
Alignment explanation
Indices: 1187116--1187151 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1187106 TCGAAAGGAC
*
1187116 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1187134 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1187152 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1188309 original size:24 final size:24
Alignment explanation
Indices: 1188195--1188306 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
1188185 ATTTGAATTA
1188195 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
*
1188219 TGATCTGATA-TCTGACATAGATTC
1 TGATCTGATACT-TGACATGGATTC
*
1188243 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
1188267 TGATCTGATACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTC
*
1188291 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
1188307 CTGATTTATG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1194065 original size:37 final size:37
Alignment explanation
Indices: 1194010--1194131 Score: 217
Period size: 37 Copynumber: 3.3 Consensus size: 37
1194000 AGATATTGAG
* *
1194010 GTGAGAATAAACAGACATTTTAGGACGAGAAATGAAA
1 GTGAAAATAAGCAGACATTTTAGGACGAGAAATGAAA
*
1194047 GTGAAAATAAGCAGACATTTTAGGACGAGAAATAAAA
1 GTGAAAATAAGCAGACATTTTAGGACGAGAAATGAAA
1194084 GTGAAAATAAGCAGACATTTTAGGACGAGAAATGAAA
1 GTGAAAATAAGCAGACATTTTAGGACGAGAAATGAAA
1194121 GTGAAAATAAG
1 GTGAAAATAAG
1194132 GGTTAACATT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 81 1.00
ACGTcount: A:0.50, C:0.07, G:0.24, T:0.19
Consensus pattern (37 bp):
GTGAAAATAAGCAGACATTTTAGGACGAGAAATGAAA
Found at i:1199922 original size:25 final size:25
Alignment explanation
Indices: 1199888--1199942 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
1199878 GGATTTTATT
1199888 TTATAAAAAAAATAAAGAGATAAAA
1 TTATAAAAAAAATAAAGAGATAAAA
*
1199913 TTAT-AAAAAAATAAAGAGGTAAAA
1 TTATAAAAAAAATAAAGAGATAAAA
1199937 TT-TAAA
1 TTATAAA
1199943 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 1 0.04
24 23 0.82
25 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (25 bp):
TTATAAAAAAAATAAAGAGATAAAA
Found at i:1200464 original size:29 final size:28
Alignment explanation
Indices: 1200421--1200475 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
1200411 GTCCCCGGGT
*
1200421 AGGTCGTCATACACGCCCAACGACCTACC
1 AGGTCGCCATACACGCCC-ACGACCTACC
*
1200450 AGGTCGCCATGCACGCCCACGACCTA
1 AGGTCGCCATACACGCCCACGACCTA
1200476 GGTAGGCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.25, C:0.42, G:0.20, T:0.13
Consensus pattern (28 bp):
AGGTCGCCATACACGCCCACGACCTACC
Done.