Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 16
Found at i:2797013 original size:19 final size:19
Alignment explanation
Indices: 2796951--2797013 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
2796941 GCAACTGGAT
*
2796951 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
* *
2796970 AATCGCAACGCAAAACCAA
1 AATCGCAACGCGAAACTAA
2796989 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
2797008 ATTCGC
1 AATCGC
2797014 GTTGCGATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:2797069 original size:33 final size:34
Alignment explanation
Indices: 2797013--2797111 Score: 128
Period size: 33 Copynumber: 2.9 Consensus size: 34
2797003 ACTAAATTCG
2797013 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
** * * * *
2797047 CGTTGCGATTTTTA-TTTCGCATTACGATTATCC
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
*
2797080 CGTTGCGATAGTCATTTTCGCGTTGCGATTTT
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTT
2797112 TAAGTTTTGT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
Found at i:2799047 original size:20 final size:20
Alignment explanation
Indices: 2799024--2799076 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2799014 GAAACTTAAA
2799024 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
2799044 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
*
2799064 ATCGCAACGCGAA
1 ATCGCAACACGAA
2799077 TTAAACTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.13
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:2799491 original size:22 final size:22
Alignment explanation
Indices: 2799464--2799516 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
2799454 GGAGATAGAT
2799464 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
2799486 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
2799508 GGATGTCGC
1 GGATTTCGC
2799517 TGTAGAGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAC
Found at i:2799702 original size:20 final size:20
Alignment explanation
Indices: 2799677--2799768 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
2799667 ATTTTGTATT
*
2799677 ATCGCGTTGGGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
2799697 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
2799717 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * *
2799737 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAGA
2799757 ATCGCGTTGCGA
1 ATCGCGTTGCGA
2799769 ATCTGGAAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
19 1 0.02
20 59 0.97
21 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:2801957 original size:20 final size:20
Alignment explanation
Indices: 2801932--2801976 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2801922 ATCAAGTAAT
2801932 TTTAAT-TTATACAATACAAA
1 TTTAATATT-TACAATACAAA
* *
2801952 TTTAATATTTATAATATAAA
1 TTTAATATTTACAATACAAA
2801972 TTTAA
1 TTTAA
2801977 AAATGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAATATTTACAATACAAA
Found at i:2818740 original size:9 final size:10
Alignment explanation
Indices: 2818707--2818745 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
2818697 TGGGCTTGTA
2818707 ATTTAATATT
1 ATTTAATATT
2818717 ATTTATATATGT
1 ATTTA-ATAT-T
2818729 ATTTAATA-T
1 ATTTAATATT
2818738 ATTTAATA
1 ATTTAATA
2818746 ATAATAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:2818749 original size:3 final size:3
Alignment explanation
Indices: 2818741--2818832 Score: 114
Period size: 3 Copynumber: 30.7 Consensus size: 3
2818731 TTAATATATT
* * *
2818741 TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA T-A TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
2818788 TAG TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TATA TTA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA
2818833 TGGGTAAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.03
3 72 0.95
4 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2819300 original size:17 final size:17
Alignment explanation
Indices: 2819278--2819329 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2819268 GTTGAACAAA
2819278 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* * *
2819295 TTCTTCTTCATAACG-AG
1 TTCTTC-TCATTATGAAC
2819312 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
2819329 T
1 T
2819330 CTACCTAGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 6 0.22
17 15 0.56
18 6 0.22
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:2819486 original size:113 final size:112
Alignment explanation
Indices: 2819149--2819707 Score: 740
Period size: 113 Copynumber: 5.0 Consensus size: 112
2819139 ATAGAATTAT
* * * * *
2819149 GCAAAAAGTTGAACAAGTTCTTTTTATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
2819214 ATTATGAAC-TTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT-GATTTGA
* *
2819261 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA---CTTCTT-CTTCAT-A-ACGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * **
2819320 ATTATGAACTCTAC-CTAGCAATGTTGATCCATCAAATGATGAATTCAA
66 ATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGATG-ATTTGA
* *
2819368 ACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
2819433 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTAATAGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT-GATTTGA
2819481 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
2819546 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTT-A
66 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATG-ATTTGA
* * *
2819593 GGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTGCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
2819658 CATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTTGA
65 CATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT-GATTTGA
2819707 G
1 G
2819708 TCTTTGCTAA
Statistics
Matches: 393, Mismatches: 39, Indels: 29
0.85 0.08 0.06
Matches are distributed among these distances:
106 22 0.06
107 56 0.14
108 7 0.02
109 5 0.01
110 6 0.02
111 5 0.01
112 34 0.09
113 255 0.65
114 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGATTTGA
Found at i:2820596 original size:83 final size:83
Alignment explanation
Indices: 2820491--2821422 Score: 1522
Period size: 83 Copynumber: 11.3 Consensus size: 83
2820481 CTTATTTCTA
* * *
2820491 CTATGAGTAAATTCATCTTCCAAATTCAATGATTTGTTCTGTCC-AACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
2820555 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * *
2820574 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTT-TACCAAACTAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
2820638 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
2820656 CTATTG-GCAAATTCATCTTCCAAATTCAATGATTGGTT-TACCAAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
2820719 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
*
2820738 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTT-TACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
2820802 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
2820820 CTATTG-GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
2820884 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
2820903 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
2820968 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
**
2820986 CTATTG-GCAAATTCATCTTTTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
2821050 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
2821069 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
2821134 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
2821152 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
2821217 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
2821235 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
2821300 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
** * *
2821318 CTATTG-GCAAATTCATCTTTTAAATTCGATGATTGGTTCTGTCC-AACCAAATCAGATAACTCA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCA
*
2821381 AAGAAAACTTCCAGAAGATG
64 AAGAACACTTCCAGAAGATG
* *
2821401 ATATGAGCACATTCATCTTCCA
1 CTATGAGCAAATTCATCTTCCA
2821423 GTTAATGTTT
Statistics
Matches: 814, Mismatches: 24, Indels: 22
0.95 0.03 0.03
Matches are distributed among these distances:
81 4 0.00
82 235 0.29
83 569 0.70
84 6 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:2822222 original size:16 final size:18
Alignment explanation
Indices: 2822185--2822228 Score: 65
Period size: 16 Copynumber: 2.5 Consensus size: 18
2822175 AATAAAAGAG
2822185 TAAATTGAATCTTCGAAAA
1 TAAATTGAATCTTC-AAAA
2822204 TAAATTGAATC-TC-AAA
1 TAAATTGAATCTTCAAAA
2822220 TAAATTGAA
1 TAAATTGAA
2822229 CTTGAAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.48
18 2 0.08
19 11 0.44
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (18 bp):
TAAATTGAATCTTCAAAA
Found at i:2822236 original size:16 final size:16
Alignment explanation
Indices: 2822185--2822237 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
2822175 AATAAAAGAG
2822185 TAAATTGAATCTTCGAAAA
1 TAAATTGAA-CTT-G-AAA
*
2822204 TAAATTGAA-TCTCAAA
1 TAAATTGAACT-TGAAA
2822220 TAAATTGAACTTGAAA
1 TAAATTGAACTTGAAA
2822236 TA
1 TA
2822238 GATAGAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 18 0.60
17 2 0.07
18 1 0.03
19 9 0.30
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (16 bp):
TAAATTGAACTTGAAA
Found at i:2822577 original size:10 final size:10
Alignment explanation
Indices: 2822558--2822594 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
2822548 TTGACCCCCC
2822558 TTTTTC-TTT
1 TTTTTCTTTT
*
2822567 TTTCTCTTTT
1 TTTTTCTTTT
2822577 TTTTTCTTTT
1 TTTTTCTTTT
2822587 TTTTTCTT
1 TTTTTCTT
2822595 CTTCTTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 5 0.20
10 20 0.80
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:2833241 original size:15 final size:13
Alignment explanation
Indices: 2833208--2833246 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
2833198 CTTTGACAGA
2833208 GAAAT-AAATAAT
1 GAAATAAAATAAT
2833220 GAAATAAAATAATT
1 GAAATAAAATAA-T
2833234 GCAAATAAAATAA
1 G-AAATAAAATAA
2833247 AACATATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.21
13 6 0.25
14 2 0.08
15 11 0.46
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.23
Consensus pattern (13 bp):
GAAATAAAATAAT
Found at i:2835286 original size:9 final size:10
Alignment explanation
Indices: 2835253--2835291 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
2835243 TGGGCTTGTA
2835253 ATTTAATATT
1 ATTTAATATT
2835263 ATTTATATATGT
1 ATTTA-ATAT-T
2835275 ATTTAATA-T
1 ATTTAATATT
2835284 ATTTAATA
1 ATTTAATA
2835292 ATAATAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:2835295 original size:3 final size:3
Alignment explanation
Indices: 2835287--2835360 Score: 103
Period size: 3 Copynumber: 24.7 Consensus size: 3
2835277 TTAATATATT
* * *
2835287 TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2835335 TAG TAA TAA TAA TAA TTA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2835361 TTTATAATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2835310 original size:18 final size:17
Alignment explanation
Indices: 2835287--2835370 Score: 91
Period size: 18 Copynumber: 4.9 Consensus size: 17
2835277 TTAATATATT
2835287 TAATAATAATAATGATAA
1 TAATAATAATAAT-ATAA
*
2835305 TGATAATAAT-A-ATAA
1 TAATAATAATAATATAA
*
2835320 TAATAATAATAATTATAG
1 TAATAATAATAA-TATAA
2835338 TAATAATAATAATTATAA
1 TAATAATAATAA-TATAA
* *
2835356 TAATATTTATAATAT
1 TAATAATAATAATAT
2835371 GGGTAAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
15 13 0.23
16 1 0.02
17 4 0.07
18 39 0.68
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
TAATAATAATAATATAA
Found at i:2843503 original size:18 final size:18
Alignment explanation
Indices: 2843476--2843510 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2843466 AGATGATGAA
2843476 TTTTAATAAAATATATTT
1 TTTTAATAAAATATATTT
* *
2843494 TTTTATTAAAATTTATT
1 TTTTAATAAAATATATT
2843511 ACATCAAAGT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATAAAATATATTT
Found at i:2851444 original size:2 final size:2
Alignment explanation
Indices: 2851437--2851463 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2851427 GCACTTATGT
2851437 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2851464 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2851468 original size:2 final size:2
Alignment explanation
Indices: 2851463--2851490 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2851453 TCTCTCTCTC
2851463 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
2851491 AAGCCAATTA
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:2852619 original size:32 final size:32
Alignment explanation
Indices: 2852553--2852620 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
2852543 AAAAAGGTGA
* *
2852553 ATTACAAACTTGTTATCATATATATAATGGTC
1 ATTACAAACTTGCTATCATATATATAATGATC
* * *
2852585 ATTACAATCTTGCTATCATATATTTGATGATC
1 ATTACAAACTTGCTATCATATATATAATGATC
2852617 ATTA
1 ATTA
2852621 GTGAAAACCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (32 bp):
ATTACAAACTTGCTATCATATATATAATGATC
Found at i:2854625 original size:15 final size:14
Alignment explanation
Indices: 2854578--2854636 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
2854568 ATTAATTTGT
2854578 AATATTATAATATA
1 AATATTATAATATA
* *
2854592 AAAATTA-AATGT-
1 AATATTATAATATA
2854604 -ATA--ATAATATA
1 AATATTATAATATA
2854615 TAATATTATAATATA
1 -AATATTATAATATA
2854630 AATATTA
1 AATATTA
2854637 GAAAGTATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
9 1 0.03
10 4 0.11
11 2 0.06
13 7 0.20
14 13 0.37
15 8 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
AATATTATAATATA
Found at i:2854629 original size:23 final size:23
Alignment explanation
Indices: 2854565--2854630 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
2854555 TCTGGACCTC
* *
2854565 AATAT-TAAT-TTGTAATATTAT
1 AATATATAATATTATAATATAAT
*
2854586 AATATA-AAAATTA-AATGTATAAT
1 AATATATAATATTATAA--TATAAT
2854609 AATATATAATATTATAATATAA
1 AATATATAATATTATAATATAA
2854631 ATATTAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
21 9 0.26
22 2 0.06
23 16 0.46
24 6 0.17
25 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
AATATATAATATTATAATATAAT
Found at i:2857479 original size:16 final size:17
Alignment explanation
Indices: 2857451--2857486 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2857441 CGATGTCTAA
2857451 AAATAACGTGATCGGTT
1 AAATAACGTGATCGGTT
2857468 AAATAA-GTGATCGGTT
1 AAATAACGTGATCGGTT
2857484 AAA
1 AAA
2857487 ATTTGGACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (17 bp):
AAATAACGTGATCGGTT
Found at i:2857993 original size:200 final size:198
Alignment explanation
Indices: 2857609--2858278 Score: 848
Period size: 200 Copynumber: 3.4 Consensus size: 198
2857599 GTAACATTAA
* **
2857609 AAATTTACCTATTACATTATAATTATCG-GTTTCGATATTTTTGGGATCGATACAATTT-TAAAT
1 AAATTTACCTATTACATTATAATTAT-GAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAAT
* * * * * * *
2857672 GTATCGACACTTTATCCATGCACCTCGTTGGGCATTCATTCTGGA-AAAAAGTATCGACACAAAC
65 GTATCGACACTTTATGCGTGAACCCCGTTTGGCATTCATTATGGACAAAAAGTATCGACAC-AAG
* * * * * *
2857736 TT-AAAAAGTGTCGATACATTATGTAGAACTATTTTATGATAAAACCGGTATATTTCTATCGGGT
129 TTCAACAAGTGTCGATACATTATGTAGACCTATTTT-TTATAAAA-CTGTAAATTTCTATCGGTT
2857800 ACATTGT
192 ACATTGT
* *
2857807 AAATTTACCTATTACATTGTAATTATCG-GTTTCGATGTTTTTGGGATCGATACTTTTAATAAAT
1 AAATTTACCTATTACATTATAATTAT-GAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAAT
* *
2857871 GTATCGATACTTTATGCGTGAACCCCGTTTGGTATTCATTATGGACAAAAAGTATCGACACAAGT
65 GTATCGACACTTTATGCGTGAACCCCGTTTGGCATTCATTATGGACAAAAAGTATCGACACAAGT
* *
2857936 TCCACAAGTGTCGATACATTATATAGACCTATTTTTTCATAAAACATGTAAATTTCTATCGGTTA
130 TCAACAAGTGTCGATACATTATGTAGACCTATTTTTT-ATAAAAC-TGTAAATTTCTATCGGTTA
*
2858001 CATTAT
193 CATTGT
* * * * *
2858007 AAATTTACATATTATATTATAATTATGAGTTTCAATGTTTTTGGGATCTATACTTTTTATAAATA
1 AAATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATG
* * * * * *
2858072 TAACGACACTTTATGTGTGTA-CCCTTTTGGGCATTCATTTTGGACAACAAGTATCGACACAAGT
66 TATCGACACTTTATGCGTGAACCCCGTTT-GGCATTCATTATGGACAAAAAGTATCGACACAAGT
* * *
2858136 TCTACAAGTGTCGATACATTATGTAGACCTATTTTCTTATAAAACTGGTAAATTTATATTGGTTA
130 TCAACAAGTGTCGATACATTATGTAGACCTATTTT-TTATAAAACT-GTAAATTTCTATCGGTTA
2858201 CATTGT
193 CATTGT
* * *
2858207 AAAATTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGAGATCAATACTTTTTATAAATG
1 AAATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATG
2858272 TATCGAC
66 TATCGAC
2858279 GCATATTTAG
Statistics
Matches: 412, Mismatches: 51, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
198 53 0.13
199 56 0.14
200 301 0.73
201 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (198 bp):
AAATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATG
TATCGACACTTTATGCGTGAACCCCGTTTGGCATTCATTATGGACAAAAAGTATCGACACAAGTT
CAACAAGTGTCGATACATTATGTAGACCTATTTTTTATAAAACTGTAAATTTCTATCGGTTACAT
TGT
Found at i:2860139 original size:20 final size:21
Alignment explanation
Indices: 2860114--2860152 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2860104 GTGGCTCTTT
*
2860114 ACCGGTTTTGTCAT-TTTTAG
1 ACCGGTTTTATCATATTTTAG
2860134 ACCGGTTTTATCATATTTT
1 ACCGGTTTTATCATATTTT
2860153 TACCTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (21 bp):
ACCGGTTTTATCATATTTTAG
Found at i:2860552 original size:183 final size:181
Alignment explanation
Indices: 2859994--2860551 Score: 821
Period size: 182 Copynumber: 3.1 Consensus size: 181
2859984 CCTAAGTGTA
*
2859994 GATACATTTTTATAAAGTATCAACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
1 GATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
**
2860059 AGTGATGATACTTATAATAAAGTATCGACACTTTTAACATATATGGTGGCTCTTTACCGGTTTTG
66 AGTG-TGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTTTG
* *
2860124 TCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATTTTGTTATGGATC
130 TCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATT
* * *
2860176 GATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATTATTGCTTCTCTTTTAAATTCCAAA
1 GATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
*
2860241 AGTGTTAATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTTTG
66 AGTG-TGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTTTG
* *
2860306 TCATTTTTAGACTGGTTTTATCATATTTTTACATGTTATATTGTTATGGATT
130 TCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATT
* * ** * *
2860358 GATACATTTTTTTTAAAGTATCGACATTTTATAAACGTTATTACTGCTTGTCTTTTAAATTCCAA
1 GATACA-TTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAA
* * * * *
2860423 AAATGTCGATATTTATAATAAAATATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTT
65 AAGTGT-GATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGC-TCTTTACCGGTTT
* * ** *
2860487 GGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTAATATAGATT
128 TGTCATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATT
2860541 GATACATTTTT
1 GATACATTTTT
2860552 TATTTGTATC
Statistics
Matches: 340, Mismatches: 33, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
182 181 0.53
183 158 0.46
184 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44
Consensus pattern (181 bp):
GATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTATCTTTTAAATTCCAAA
AGTGTGATACTTATAATAAAGTATCGACACTTTTAACATATCCGGTGGCTCTTTACCGGTTTTGT
CATTTTTAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATT
Found at i:2867296 original size:20 final size:20
Alignment explanation
Indices: 2867271--2867309 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2867261 CAAGTGGGAG
2867271 ATTATTAGTTGTCATACAAA
1 ATTATTAGTTGTCATACAAA
2867291 ATTATTAGTTGTCATACAA
1 ATTATTAGTTGTCATACAA
2867310 CTAATAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTATTAGTTGTCATACAAA
Found at i:2867335 original size:21 final size:20
Alignment explanation
Indices: 2867311--2867352 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2867301 GTCATACAAC
*
2867311 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
2867332 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
2867352 T
1 T
2867353 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:2874143 original size:48 final size:48
Alignment explanation
Indices: 2874072--2874216 Score: 281
Period size: 48 Copynumber: 3.0 Consensus size: 48
2874062 TGTCTTACTT
2874072 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
1 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
*
2874120 TAGAGTGATCAGTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
1 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
2874168 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
1 TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
2874216 T
1 T
2874217 GGATGCTTCG
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 95 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (48 bp):
TAGAGTGATCATTCATCGGGTTCATACTCTGTACGATCAGGCTACAAA
Found at i:2875202 original size:23 final size:25
Alignment explanation
Indices: 2875162--2875209 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2875152 TTGTATTTCA
**
2875162 AATGGTATAATGCTTGAC-TTTATT
1 AATGGTATAATGAATGACGTTTATT
2875186 AATGGT-TAATGAATGACGTTTATT
1 AATGGTATAATGAATGACGTTTATT
2875210 TCAACAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (25 bp):
AATGGTATAATGAATGACGTTTATT
Found at i:2876913 original size:19 final size:19
Alignment explanation
Indices: 2876889--2876931 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2876879 TAGTATTGGT
2876889 TGGACTGGTCTAAACCGAC
1 TGGACTGGTCTAAACCGAC
*
2876908 TGGACTGGTCTAAACCGGC
1 TGGACTGGTCTAAACCGAC
2876927 TGGAC
1 TGGAC
2876932 CGGACTGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (19 bp):
TGGACTGGTCTAAACCGAC
Found at i:2882165 original size:170 final size:170
Alignment explanation
Indices: 2881883--2882222 Score: 662
Period size: 170 Copynumber: 2.0 Consensus size: 170
2881873 TTTATAAATC
2881883 CACATCCGTCCACTACCCGCTAAAATTATAGCTATCCCGCTCCGATTGAAACAAAATTGTATCCG
1 CACATCCGTCCACTACCCGCTAAAATTATAGCTATCCCGCTCCGATTGAAACAAAATTGTATCCG
2881948 TTTACCATCCTAGTTCGACGGATAAACCCAAATGGATTTTCACTCCTTTGTCATTTTGTACTTCG
66 TTTACCATCCTAGTTCGACGGATAAACCCAAATGGATTTTCACTCCTTTGTCATTTTGTACTTCG
*
2882013 GCGTCCAAACAAATGAAGCTGGTTCTCTACTCAAAGCCTG
131 GCGTCCAAACAAAGGAAGCTGGTTCTCTACTCAAAGCCTG
2882053 CACATCCGTCCACTACCCGCTAAAATTATAGCTATCCCGCTCCGATTGAAACAAAATTGTATCCG
1 CACATCCGTCCACTACCCGCTAAAATTATAGCTATCCCGCTCCGATTGAAACAAAATTGTATCCG
*
2882118 TTTACCATCCTAGTTCGGCGGATAAACCCAAATGGATTTTCACTCCTTTGTCATTTTGTACTTCG
66 TTTACCATCCTAGTTCGACGGATAAACCCAAATGGATTTTCACTCCTTTGTCATTTTGTACTTCG
2882183 GCGTCCAAACAAAGGAAGCTGGTTCTCTACTCAAAGCCTG
131 GCGTCCAAACAAAGGAAGCTGGTTCTCTACTCAAAGCCTG
2882223 GTTGCTGTTT
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 168 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (170 bp):
CACATCCGTCCACTACCCGCTAAAATTATAGCTATCCCGCTCCGATTGAAACAAAATTGTATCCG
TTTACCATCCTAGTTCGACGGATAAACCCAAATGGATTTTCACTCCTTTGTCATTTTGTACTTCG
GCGTCCAAACAAAGGAAGCTGGTTCTCTACTCAAAGCCTG
Found at i:2882943 original size:27 final size:27
Alignment explanation
Indices: 2882905--2882959 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2882895 TTGTTAGCCA
2882905 GGTTACTTCAAGGCCTACTTAATTTAT
1 GGTTACTTCAAGGCCTACTTAATTTAT
2882932 GGTTACTTCAAGGCCTACTTAATTTAT
1 GGTTACTTCAAGGCCTACTTAATTTAT
2882959 G
1 G
2882960 AATAAAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (27 bp):
GGTTACTTCAAGGCCTACTTAATTTAT
Found at i:2886451 original size:17 final size:17
Alignment explanation
Indices: 2886429--2886494 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 17
2886419 CAAAAGCAAA
2886429 ATATAAATTCGTATTCG
1 ATATAAATTCGTATTCG
*
2886446 ATAT-AATT--TAATC-
1 ATATAAATTCGTATTCG
* *
2886459 ATATAAGATTCATATTCAA
1 ATATAA-ATTCGTATTC-G
*
2886478 ATATAACTTCGTATTCG
1 ATATAAATTCGTATTCG
2886495 TCGTAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
13 4 0.11
14 5 0.13
15 3 0.08
16 4 0.11
17 8 0.21
18 8 0.21
19 6 0.16
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (17 bp):
ATATAAATTCGTATTCG
Found at i:2892215 original size:2 final size:2
Alignment explanation
Indices: 2892208--2892235 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2892198 TGATAAAATA
2892208 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
2892236 TTAAATTTAT
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):
AT
Found at i:2892397 original size:31 final size:31
Alignment explanation
Indices: 2892359--2892422 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
2892349 GAAACATAAA
**
2892359 ATATGATCACTTTTGTTTTTAA-TTAATTAAG
1 ATATGATCAC-TTTCATTTTAATTTAATTAAG
2892390 ATATGATCACTTTCATTTTAATTTAATTAAG
1 ATATGATCACTTTCATTTTAATTTAATTAAG
2892421 AT
1 AT
2892423 GTGCTCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (31 bp):
ATATGATCACTTTCATTTTAATTTAATTAAG
Found at i:2892663 original size:26 final size:26
Alignment explanation
Indices: 2892600--2892673 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 26
2892590 GTGTTTTAAA
*
2892600 ATTAAGTTAATA-ATAAAATATATTT
1 ATTAAGTTAATATATAAAAAATATTT
* *
2892625 AATAAATT-A-ATATAAAAAATATTT
1 ATTAAGTTAATATATAAAAAATATTT
* *
2892649 TTTAAGTTAATATATATAAAATATT
1 ATTAAGTTAATATATAAAAAATATT
2892674 ATGCATTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 1 0.03
24 18 0.46
25 7 0.18
26 13 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
ATTAAGTTAATATATAAAAAATATTT
Found at i:2906805 original size:23 final size:23
Alignment explanation
Indices: 2906779--2906870 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
2906769 CACCACAGCT
*
2906779 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * **
2906802 CGTAGAATTGCACCGTAGTGCTG
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2906825 CGTAGAAATGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
2906848 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2906871 TATAAGGTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2906852 original size:46 final size:46
Alignment explanation
Indices: 2906779--2906868 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
2906769 CACCACAGCT
* * *
2906779 CGTATAAATGCACCGAAGTGCCACGTAGAATTGCACCGTAGTGCTG
1 CGTAGAAATGCACCGAAGTGCCACGTAGAAATGCACCGAAGTGCTG
* * *
2906825 CGTAGAAATGCACTGTAGTGCCGCGTAGAAATGCACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGCCACGTAGAAATGCACCGAAGTGC
2906869 CATATAAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (46 bp):
CGTAGAAATGCACCGAAGTGCCACGTAGAAATGCACCGAAGTGCTG
Found at i:2907267 original size:2 final size:2
Alignment explanation
Indices: 2907260--2907294 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2907250 TGTCTTATCC
2907260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2907295 TCACATATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2908462 original size:24 final size:20
Alignment explanation
Indices: 2908405--2908482 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
2908395 TTTCCCTTGA
*
2908405 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
2908425 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
2908448 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
2908469 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
2908483 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:2912889 original size:27 final size:27
Alignment explanation
Indices: 2912859--2912912 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2912849 GGTCACTGAA
*
2912859 TGTGGAATGTTGTTGTTGTACATGGTG
1 TGTGGAATGTTATTGTTGTACATGGTG
*
2912886 TGTGGAATGTTATTGTTGTGCATGGTG
1 TGTGGAATGTTATTGTTGTACATGGTG
2912913 CATGGTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.04, G:0.37, T:0.44
Consensus pattern (27 bp):
TGTGGAATGTTATTGTTGTACATGGTG
Found at i:2913426 original size:47 final size:46
Alignment explanation
Indices: 2913358--2913453 Score: 174
Period size: 47 Copynumber: 2.1 Consensus size: 46
2913348 GACATTGAAC
2913358 CATCGTGATACAATCATCGTGTTAAAAAAAACTTAAAAGTGAATTT
1 CATCGTGATACAATCATCGTGTTAAAAAAAACTTAAAAGTGAATTT
*
2913404 CATCGATGGTACAATCATCGTGTTAAAAAAAACTTAAAAGTGAATTT
1 CATCG-TGATACAATCATCGTGTTAAAAAAAACTTAAAAGTGAATTT
2913451 CAT
1 CAT
2913454 TAATAAGAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 5 0.10
47 43 0.90
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (46 bp):
CATCGTGATACAATCATCGTGTTAAAAAAAACTTAAAAGTGAATTT
Found at i:2916125 original size:153 final size:154
Alignment explanation
Indices: 2915847--2916135 Score: 481
Period size: 153 Copynumber: 1.9 Consensus size: 154
2915837 TAAACCGTAT
*
2915847 ATATAACTATTCAAACTTTTATCCTCTAATGAGAACAATAATTCTTATTATCATTAAGGTAACTC
1 ATATAACTATTCAAACTTTTATCCTCTAACGAGAACAATAATTCTTATTATCATTAAGGTAACTC
*
2915912 AATAAATATTAGAATGCATTAGTTAAATATGTTCCTATATACCAAAAAGATTAATTATAAAAAAT
66 AATAAATATTAGAATGCAATAGTTAAATATGTTCCTATATACCAAAAAGATTAATTATAAAAAAT
2915977 -ATCACTATTCATACACCATATAA
131 GATCACTATTCATACACCATATAA
* * *
2916000 ATATAACTATTCTAACTTTTATTCTCTAACGAGAACAATGATTCTTATTATCATTAAGGTAACTC
1 ATATAACTATTCAAACTTTTATCCTCTAACGAGAACAATAATTCTTATTATCATTAAGGTAACTC
* ** * *
2916065 AATAAATATTAGAATGGAATAGTTAAATATGTTGTTATATACCTAAACGATTAATTATAAAAAAT
66 AATAAATATTAGAATGCAATAGTTAAATATGTTCCTATATACCAAAAAGATTAATTATAAAAAAT
2916130 GATCAC
131 GATCAC
2916136 GTTAGCGTGT
Statistics
Matches: 125, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
153 120 0.96
154 5 0.04
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (154 bp):
ATATAACTATTCAAACTTTTATCCTCTAACGAGAACAATAATTCTTATTATCATTAAGGTAACTC
AATAAATATTAGAATGCAATAGTTAAATATGTTCCTATATACCAAAAAGATTAATTATAAAAAAT
GATCACTATTCATACACCATATAA
Found at i:2919190 original size:17 final size:17
Alignment explanation
Indices: 2919168--2919208 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2919158 CCACTATTAT
2919168 AAGCACCCACACTTAAC
1 AAGCACCCACACTTAAC
2919185 AAGCACCCACACTTAAC
1 AAGCACCCACACTTAAC
*
2919202 AAACACC
1 AAGCACC
2919209 ACAAGAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.44, C:0.41, G:0.05, T:0.10
Consensus pattern (17 bp):
AAGCACCCACACTTAAC
Found at i:2919405 original size:29 final size:29
Alignment explanation
Indices: 2919373--2919432 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
2919363 AAAGTTATCT
* * *
2919373 TTTTTCTGTTAAAATAGGTATCTAAAATA
1 TTTTTCGGTCAAAATAAGTATCTAAAATA
*
2919402 TTTTTCGGTCAAAATAAGTATCTAAAGTA
1 TTTTTCGGTCAAAATAAGTATCTAAAATA
2919431 TT
1 TT
2919433 CAATTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (29 bp):
TTTTTCGGTCAAAATAAGTATCTAAAATA
Found at i:2919553 original size:28 final size:28
Alignment explanation
Indices: 2919517--2919595 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
2919507 AAAAAGTTTG
* * *
2919517 AATAGTTTAGGTACCTATTTTGACATAA
1 AATACTTTAAGTACATATTTTGACATAA
*
2919545 AATACTTTATGTACATATTTTGACATAA
1 AATACTTTAAGTACATATTTTGACATAA
2919573 AATACTTTAAGTACATATTTTGA
1 AATACTTTAAGTACATATTTTGA
2919596 TCTATTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (28 bp):
AATACTTTAAGTACATATTTTGACATAA
Found at i:2920336 original size:43 final size:45
Alignment explanation
Indices: 2920273--2920385 Score: 167
Period size: 45 Copynumber: 2.6 Consensus size: 45
2920263 TTCTATCCAA
* * *
2920273 AATTATATGGATTTTGAATTTAAAATAAA-AAAAAATTA-GATAT
1 AATTATATGAATTTTGAATTTAAAATAAATAAAAAAATAGGATAC
**
2920316 AATTATATGAATTTAAAATTTAAAATAAATAAAAAAATAGGATAC
1 AATTATATGAATTTTGAATTTAAAATAAATAAAAAAATAGGATAC
2920361 AATTATATGAATTTTGAATTTAAAA
1 AATTATATGAATTTTGAATTTAAAA
2920386 GAGATAATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 26 0.43
44 8 0.13
45 27 0.44
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (45 bp):
AATTATATGAATTTTGAATTTAAAATAAATAAAAAAATAGGATAC
Found at i:2920924 original size:29 final size:31
Alignment explanation
Indices: 2920860--2920924 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
2920850 AATTCTCAAA
*
2920860 ATAAAATGATATTTATAATTTGATGACTAAT
1 ATAAAATGATATTTATAATTTGATGACCAAT
*
2920891 ATAAAAT-ATTTTTA-AATTT-ATGAACCAAT
1 ATAAAATGATATTTATAATTTGATG-ACCAAT
*
2920920 TTAAA
1 ATAAA
2920925 TAAAGTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 3 0.10
29 14 0.47
30 6 0.20
31 7 0.23
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (31 bp):
ATAAAATGATATTTATAATTTGATGACCAAT
Found at i:2924131 original size:239 final size:236
Alignment explanation
Indices: 2923659--2924131 Score: 889
Period size: 239 Copynumber: 2.0 Consensus size: 236
2923649 TTTACTAAAC
2923659 TGCACAAGTTACAAGCATAAATCTTTAACTATCTGCTAGCTCAAGATACACGTGACTAACCTACA
1 TGCACAAGTTACAAGCATAAATCTTTAACTATCTGCTAGCTCAAGATACACGTGACTAACCTACA
2923724 AACATACAGTTTGTTCATGTCTTCAATGAAGCTAATAAAGTGTTAGAGTTTTATTAAAATTTAAA
66 AACATACAGTTTGTTCATGTCTTCAATGAAGCTAATAAAGTGTTAGAGTTTTATTAAAATTTAAA
2923789 GTGACACAAATTAATTAATATATAAATATTAAGAAAGTACGAAAGCTAGTTTGATTAAAAGTAAA
131 GTGACACAAATTAATT-ATATATAAATATTAAGAAAGTACGAAAGCTAGTTTGATTAAAAGTAAA
2923854 AAAATTTATTAAGTAAATTTTCCTTTATTTAATTTTTTTTTT
195 AAAATTTATTAAGTAAATTTTCCTTTATTTAATTTTTTTTTT
2923896 TGCACAAGTTACAAAGCAATAAATCTTTAACTATCTGCTAGCTCAAGATACACGTGACTAACCTA
1 TGCACAAGTTAC-AAGC-ATAAATCTTTAACTATCTGCTAGCTCAAGATACACGTGACTAACCTA
2923961 CAAACATACAGTTTGTTCATGTCTTCAATGAAGCTAATAAAGTGTTAGAGTTTTATTAAAATTTA
64 CAAACATACAGTTTGTTCATGTCTTCAATGAAGCTAATAAAGTGTTAGAGTTTTATTAAAATTTA
2924026 AAGTGACACAAATTAA-T-TATATAAATATTAAGAAAGTACGAAAGCTAGTTTGATTAAAAGT-A
129 AAGTGACACAAATTAATTATATATAAATATTAAGAAAGTACGAAAGCTAGTTTGATTAAAAGTAA
2924088 AAAAATTTATTAAAGTAAATTTTCCTTTATTTAATTTTTTTTTT
194 AAAAATTTATT-AAGTAAATTTTCCTTTATTTAATTTTTTTTTT
2924132 GTAATCAAAT
Statistics
Matches: 233, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
235 12 0.05
236 76 0.33
237 12 0.05
238 5 0.02
239 128 0.55
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (236 bp):
TGCACAAGTTACAAGCATAAATCTTTAACTATCTGCTAGCTCAAGATACACGTGACTAACCTACA
AACATACAGTTTGTTCATGTCTTCAATGAAGCTAATAAAGTGTTAGAGTTTTATTAAAATTTAAA
GTGACACAAATTAATTATATATAAATATTAAGAAAGTACGAAAGCTAGTTTGATTAAAAGTAAAA
AAATTTATTAAGTAAATTTTCCTTTATTTAATTTTTTTTTT
Found at i:2927932 original size:19 final size:19
Alignment explanation
Indices: 2927908--2927947 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2927898 ACACTTCTCT
2927908 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
2927927 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
2927946 CA
1 CA
2927948 CTAAAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:2929812 original size:17 final size:17
Alignment explanation
Indices: 2929790--2929823 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2929780 AAAATTCGAA
*
2929790 AAAATTTTCGAAAATTT
1 AAAATTTTAGAAAATTT
2929807 AAAATTTTAGAAAATTT
1 AAAATTTTAGAAAATTT
2929824 TGTTTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (17 bp):
AAAATTTTAGAAAATTT
Found at i:2930180 original size:21 final size:21
Alignment explanation
Indices: 2930150--2930207 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
2930140 AGAACCCCAT
*
2930150 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTGTG
2930171 GGGGGAATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTGTG
*
2930192 GGGGGAATCGGTTCCC
1 GGGGGAATCGATTCCC
2930208 ATTCAAAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTGTG
Found at i:2930241 original size:21 final size:21
Alignment explanation
Indices: 2930150--2930252 Score: 86
Period size: 21 Copynumber: 4.9 Consensus size: 21
2930140 AGAACCCCAT
* *
2930150 GGGGGTATCGATTCCC-CTGTG
1 GGGGGAATCGATTCCCTC-ATG
*
2930171 GGGGGAATCGATTCCC-CTGTG
1 GGGGGAATCGATTCCCTC-ATG
* **
2930192 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGATTCCC--TCATG
*
2930215 GGGGGAATCGGTTCCCTCATG
1 GGGGGAATCGATTCCCTCATG
2930236 GGGGG-ATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2930253 TGCACCAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
20 11 0.15
21 43 0.61
23 16 0.23
24 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCATG
Found at i:2930244 original size:20 final size:21
Alignment explanation
Indices: 2930190--2930252 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
2930180 GATTCCCCTG
2930190 TGGGGGGAATCGGTTCCCATTCAA
1 TGGGGGG-ATCGGTTCCC--TCAA
* *
2930214 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
2930234 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
2930253 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
23 10 0.29
24 5 0.15
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:2931979 original size:22 final size:22
Alignment explanation
Indices: 2931952--2931996 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2931942 GTTTCCTCAT
2931952 TTTTCGTTTCTTCCTTTGATGA
1 TTTTCGTTTCTTCCTTTGATGA
2931974 TTTTCGTTTCTTCCTTTGATGA
1 TTTTCGTTTCTTCCTTTGATGA
2931996 T
1 T
2931997 GGTTCTCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.13, T:0.60
Consensus pattern (22 bp):
TTTTCGTTTCTTCCTTTGATGA
Found at i:2937783 original size:21 final size:21
Alignment explanation
Indices: 2937757--2937819 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
2937747 GTCGAGGGTT
2937757 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
* *
2937778 TCATAGGTCCTTCGGAACATAT
1 TCATAGGTCCTTCGGGACA-AC
*
2937800 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
2937820 AATTTCATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:2938435 original size:22 final size:21
Alignment explanation
Indices: 2938364--2938419 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
2938354 CCGAAATTAT
*
2938364 TGTAGCAAGGGTATCGGTACAC
1 TGTAGC-AGGGTATCAGTACAC
2938386 TGTAGCAGGGTATCAGTACAC
1 TGTAGCAGGGTATCAGTACAC
2938407 TGTAGCAGGGTAT
1 TGTAGCAGGGTAT
2938420 TGATACCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (21 bp):
TGTAGCAGGGTATCAGTACAC
Found at i:2938487 original size:22 final size:22
Alignment explanation
Indices: 2938459--2938511 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
2938449 TTAGAATCAC
* * *
2938459 TACTGTTCACGGTACTATTTAT
1 TACTGTTCACGATACTATTCAG
*
2938481 TACTGTTCACGATACTGTTCAG
1 TACTGTTCACGATACTATTCAG
2938503 TACTGTTCA
1 TACTGTTCA
2938512 TATTGTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (22 bp):
TACTGTTCACGATACTATTCAG
Found at i:2939645 original size:3 final size:3
Alignment explanation
Indices: 2939639--2939663 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2939629 AATGATAATG
2939639 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
2939664 TGGTGGTGAT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:2941749 original size:19 final size:19
Alignment explanation
Indices: 2941722--2941759 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2941712 TGTTTAAAAC
*
2941722 TATCGATACTTATATAAAG
1 TATCAATACTTATATAAAG
2941741 TATCAATACTTATATAAAG
1 TATCAATACTTATATAAAG
2941760 CATTGAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (19 bp):
TATCAATACTTATATAAAG
Found at i:2942926 original size:48 final size:48
Alignment explanation
Indices: 2942862--2942954 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
2942852 AAGTGACTAG
*
2942862 GTTGCCTCCTTTAGCTGTTTTAACACCCCTCACATCAATGTTTAATAT
1 GTTGCCTCCTTCAGCTGTTTTAACACCCCTCACATCAATGTTTAATAT
* *
2942910 GTTGTCTCCTTCAGCTGTTTTAACACCCCTCACATCAGTGTTTAA
1 GTTGCCTCCTTCAGCTGTTTTAACACCCCTCACATCAATGTTTAA
2942955 AAAAGGCGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.39
Consensus pattern (48 bp):
GTTGCCTCCTTCAGCTGTTTTAACACCCCTCACATCAATGTTTAATAT
Found at i:2947465 original size:15 final size:15
Alignment explanation
Indices: 2947429--2947527 Score: 153
Period size: 15 Copynumber: 6.5 Consensus size: 15
2947419 AGAGCCTCTG
**
2947429 AATCATTCAGCATTT
1 AATCATTCAGCGCTT
2947444 GAATCATTCAGCGCTT
1 -AATCATTCAGCGCTT
*
2947460 AATCATTCAGTGCTT
1 AATCATTCAGCGCTT
2947475 AATCATTCAGCGCTT
1 AATCATTCAGCGCTT
*
2947490 AATCATTCAGTGCTT
1 AATCATTCAGCGCTT
2947505 AATCATTCAGCGCTT
1 AATCATTCAGCGCTT
2947520 AATCATTC
1 AATCATTC
2947528 TGAAGTAAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
15 64 0.83
16 13 0.17
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (15 bp):
AATCATTCAGCGCTT
Found at i:2953470 original size:92 final size:93
Alignment explanation
Indices: 2953320--2953496 Score: 257
Period size: 92 Copynumber: 1.9 Consensus size: 93
2953310 ATCAATCACA
* * * **
2953320 ACATGGTTTAAAGTTAAAAGCAATATGAGCATGAAAACTTAAAAGACACGAAAATCTACATGAAC
1 ACATGGTTTAAAGTTAAAAGAAAAAAGAGCATGAAAACTTAAAAGACACGAAAATCTACACCAAC
*
2953385 AGGCTTTGGAAGATGTATGACAATCATT
66 AGACTTTGGAAGATGTATGACAATCATT
** * *
2953413 ACATGGTTTAAAGTT-AAAGAAAAAAGAGCATGAAAACTTACGAGGCACGAAAATCTACGCCAAC
1 ACATGGTTTAAAGTTAAAAGAAAAAAGAGCATGAAAACTTAAAAGACACGAAAATCTACACCAAC
2953477 AGACTTTGGAAGATGTATGA
66 AGACTTTGGAAGATGTATGA
2953497 AACTGCGAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
92 59 0.80
93 15 0.20
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.23
Consensus pattern (93 bp):
ACATGGTTTAAAGTTAAAAGAAAAAAGAGCATGAAAACTTAAAAGACACGAAAATCTACACCAAC
AGACTTTGGAAGATGTATGACAATCATT
Found at i:2959534 original size:46 final size:46
Alignment explanation
Indices: 2959478--2959566 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
2959468 CAGTACTAGT
2959478 GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCAAGA
1 GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCAAGA
2959524 GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCA
1 GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCA
2959567 CTTGAACGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (46 bp):
GTGTTATAAACTAGTGGCAGATTTGTGCAGTAATTGTTATTCAAGA
Found at i:2961942 original size:33 final size:33
Alignment explanation
Indices: 2961900--2961966 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2961890 TGTGAAGGGT
2961900 TGAACTTTAATTTTCACCATTTAACTATTTTTA
1 TGAACTTTAATTTTCACCATTTAACTATTTTTA
2961933 TGAACTTTAATTTTCACCATTTAACTATTTTTA
1 TGAACTTTAATTTTCACCATTTAACTATTTTTA
2961966 T
1 T
2961967 TTTATGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (33 bp):
TGAACTTTAATTTTCACCATTTAACTATTTTTA
Found at i:2962382 original size:22 final size:22
Alignment explanation
Indices: 2962339--2962386 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2962329 ATATAAATAA
*
2962339 ATATTCTTGAATTTATTCATAT
1 ATATTCTTGAAATTATTCATAT
2962361 GATATT-TTGAAATTATAT-ATAT
1 -ATATTCTTGAAATTAT-TCATAT
2962383 ATAT
1 ATAT
2962387 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 13 0.57
23 6 0.26
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (22 bp):
ATATTCTTGAAATTATTCATAT
Found at i:2972616 original size:18 final size:17
Alignment explanation
Indices: 2972593--2972627 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2972583 AAACCTGTCA
2972593 GACTGGATGTATGGTTAG
1 GACTGG-TGTATGGTTAG
*
2972611 GACTGGTTTATGGTTAG
1 GACTGGTGTATGGTTAG
2972628 TGTTACTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.06, G:0.37, T:0.37
Consensus pattern (17 bp):
GACTGGTGTATGGTTAG
Found at i:2974113 original size:35 final size:36
Alignment explanation
Indices: 2974062--2974133 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
2974052 GATGGAGAAA
* *
2974062 GTTTCGTTCTTTTCTTTC-TGTCTAGTTTGTGTGTG
1 GTTTCGTTCTTCTCTTTCTTGTCTAATTTGTGTGTG
*
2974097 GTTTTGTTCTTCTCTTTCTTTGTCTAATTTGTGTGTG
1 GTTTCGTTCTTCTCTTTC-TTGTCTAATTTGTGTGTG
2974134 CTTTATCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 16 0.50
37 16 0.50
ACGTcount: A:0.04, C:0.14, G:0.21, T:0.61
Consensus pattern (36 bp):
GTTTCGTTCTTCTCTTTCTTGTCTAATTTGTGTGTG
Found at i:2975309 original size:13 final size:13
Alignment explanation
Indices: 2975291--2975319 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2975281 AATTATTTGA
2975291 ACTATACGTGATT
1 ACTATACGTGATT
2975304 ACTATACGTGATT
1 ACTATACGTGATT
2975317 ACT
1 ACT
2975320 GTTATGGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
ACTATACGTGATT
Found at i:2978005 original size:14 final size:15
Alignment explanation
Indices: 2977976--2978010 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
2977966 CAACTACTTT
2977976 TTTTTAATAAATTTAA
1 TTTTTAAT-AATTTAA
2977992 TTTTTAAT-ATTTAA
1 TTTTTAATAATTTAA
2978006 TTTTT
1 TTTTT
2978011 TTTATCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
16 8 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATAATTTAA
Found at i:2978011 original size:16 final size:17
Alignment explanation
Indices: 2977974--2978022 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
2977964 TACAACTACT
2977974 TTTTTTTAATAAATTTAA
1 TTTTTTTAAT-AATTTAA
2977992 --TTTTTAAT-ATTTAA
1 TTTTTTTAATAATTTAA
*
2978006 TTTTTTTTATCAATTTA
1 TTTTTTTAAT-AATTTA
2978023 GTTCATTTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 6 0.23
16 15 0.58
18 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTTAATAATTTAA
Found at i:2985159 original size:29 final size:29
Alignment explanation
Indices: 2985113--2985193 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
2985103 ACCGTTAACC
*
2985113 GGTGCTATTATGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2985142 GGTGCTATTCTGGCAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2985171 GGTGCTATTCTGGTAATTAATTC
1 GGTGCTATTCTGGTAAATAATTC
2985194 AAAATGGGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:2985203 original size:29 final size:29
Alignment explanation
Indices: 2985171--2985245 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
2985161 ATTCGGTTTT
* *
2985171 GGTGCTATTCTGGTAATTAATTCAAAATG
1 GGTGCTATTCTGGTAAATAATTCAAAAAG
* * *
2985200 GGTGCTATTTTGGTAAATATTTTAAAAAG
1 GGTGCTATTCTGGTAAATAATTCAAAAAG
2985229 GGTGCTATT-TGTGTAAA
1 GGTGCTATTCTG-GTAAA
2985246 ATGTTCAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 2 0.05
29 38 0.95
ACGTcount: A:0.31, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAAAAAG
Found at i:2988233 original size:19 final size:16
Alignment explanation
Indices: 2988196--2988227 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2988186 TTCAAGAGTC
2988196 AAGCAAATTGATATTT
1 AAGCAAATTGATATTT
2988212 AAGCAAATTGATATTT
1 AAGCAAATTGATATTT
2988228 TTTAAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
AAGCAAATTGATATTT
Found at i:2997121 original size:151 final size:147
Alignment explanation
Indices: 2996857--2997154 Score: 544
Period size: 151 Copynumber: 2.0 Consensus size: 147
2996847 ATCCTTTGTC
2996857 CTTACAATCCTTGTTCAATATTTTATTTATGTATTTGATCTTCATGTGTAATTTTCCCGCATAAA
1 CTTACAATCCTTGTTCAATATTTTATTTATGTATTTGATCTTCATGTGTAATTTTCCCGCATAAA
2996922 CATTCTTAAATGGCATACAATAATTTAACGAAAGAAATTTTCTATTGTATTATAAATTAGACTT-
66 CATTCTTAAATGGCATACAATAATTTAACGAAAGAAATTTTCTATTGTATTATAAATTAGACTTC
2996986 CCCATTATTGAATTAAA
131 CCCATTATTGAATTAAA
2997003 CTTACAATCCTTGTTCAATATTTTTATTTATGTATTTGATCTTTCATGTGTAATTTTCCCGCATA
1 CTTACAATCCTTGTTCAATA-TTTTATTTATGTATTTGATC-TTCATGTGTAATTTTCCCGCATA
2997068 AACATTTCTTAAATGGCATACAATATAATTTAACGAAAGAAATTTTCTATTGTATTATAAATTAG
64 AACA-TTCTTAAATGGCATAC-A-ATAATTTAACGAAAGAAATTTTCTATTGTATTATAAATTAG
2997133 ACTTCCCCATTATTGAATTAAA
126 ACTTCCCCATTATTGAATTAAA
2997155 AGAGCAGATA
Statistics
Matches: 146, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
146 20 0.14
147 20 0.14
148 27 0.18
149 16 0.11
150 1 0.01
151 45 0.31
152 17 0.12
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (147 bp):
CTTACAATCCTTGTTCAATATTTTATTTATGTATTTGATCTTCATGTGTAATTTTCCCGCATAAA
CATTCTTAAATGGCATACAATAATTTAACGAAAGAAATTTTCTATTGTATTATAAATTAGACTTC
CCCATTATTGAATTAAA
Found at i:2997405 original size:21 final size:20
Alignment explanation
Indices: 2997354--2997406 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
2997344 ATTATGACTA
*
2997354 TCGCAATGCGATTTTCCAAT
1 TCGCAGTGCGATTTTCCAAT
*
2997374 T-TCACGTTGCGATTTTCCCAAT
1 TCGCA-G-TGCGATTTT-CCAAT
2997396 TCGCAGTGCGA
1 TCGCAGTGCGA
2997407 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 14 0.54
22 7 0.27
23 2 0.08
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (20 bp):
TCGCAGTGCGATTTTCCAAT
Found at i:2997439 original size:21 final size:21
Alignment explanation
Indices: 2997413--2997489 Score: 145
Period size: 21 Copynumber: 3.7 Consensus size: 21
2997403 GCGAATAAGT
2997413 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
2997434 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
2997455 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
*
2997476 AAATCGCAACGCGA
1 AAATCGCAATGCGA
2997490 TACTGACTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:2997503 original size:20 final size:20
Alignment explanation
Indices: 2997478--2997592 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
2997468 AATTTGGAAA
2997478 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
2997498 ATCGCAACGCGCTAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
2997519 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2997539 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2997559 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
2997579 TTCACAACGAGATA
1 ATCGCAACGCGATA
2997593 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 63 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2997520 original size:41 final size:41
Alignment explanation
Indices: 2997475--2997612 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
2997465 GCGAATTTGG
* *
2997475 AAAATCGCAACGCGATACTGACTATCGCAACGCGCTAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
2997516 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** * *
2997558 --TTTCGCAACGCGATACTGACTTTCACAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
2997597 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
2997613 TTTCAAAGCG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.37
41 46 0.55
42 3 0.04
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:2998015 original size:19 final size:19
Alignment explanation
Indices: 2997968--2998022 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
2997958 TTTATTCTCT
* **
2997968 CGTTGCGATAGTCAAATCG
1 CGTTGCGATTGTCATTTCG
2997987 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTGTCATTTCG
* *
2998006 TGTTGCGATTTTCATTT
1 CGTTGCGATTGTCATTT
2998023 TCAGAACTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTGTCATTTCG
Found at i:2998208 original size:25 final size:24
Alignment explanation
Indices: 2998154--2998208 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2998144 ATGTTATTAT
* *
2998154 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2998178 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2998204 TGTTT
1 TGTTT
2998209 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2998885 original size:97 final size:97
Alignment explanation
Indices: 2998719--2998913 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
2998709 TTTTAGGCAG
2998719 AGAGTCCAGACAACCTATTCCGAATGATCTAATCAAATTGGTAGAAGACCTAAATGTGGAACCTG
1 AGAGTCCAGACAACCTATTCCGAATGATCTAATCAAATTGGTAGAAGACCTAAATGTGGAACCTG
2998784 TTTCCGTGGGGCTCGTATTTATAGAAAGCTAC
66 TTTCCGTGGGGCTCGTATTTATAGAAAGCTAC
2998816 AGAGTCCAGACAACCTATTCCGAATGATCTAATCAAATTGGTAGAAGACCTAAATGTGGAACCTG
1 AGAGTCCAGACAACCTATTCCGAATGATCTAATCAAATTGGTAGAAGACCTAAATGTGGAACCTG
2998881 TTTCCGTGGGGCTCGTATTTATAGAAAGCTAC
66 TTTCCGTGGGGCTCGTATTTATAGAAAGCTAC
2998913 A
1 A
2998914 TGGAAAAGTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (97 bp):
AGAGTCCAGACAACCTATTCCGAATGATCTAATCAAATTGGTAGAAGACCTAAATGTGGAACCTG
TTTCCGTGGGGCTCGTATTTATAGAAAGCTAC
Found at i:2999286 original size:17 final size:17
Alignment explanation
Indices: 2999260--2999305 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
2999250 TCCACTTCGG
2999260 GAGCATCACCTCA-CCA
1 GAGCATCACCTCACCCA
2999276 GAGCTATCACCTCACCCA
1 GAGC-ATCACCTCACCCA
2999294 GAGCCATCACCT
1 GAG-CATCACCT
2999306 AACGACCCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.15
17 9 0.33
18 13 0.48
19 1 0.04
ACGTcount: A:0.28, C:0.43, G:0.13, T:0.15
Consensus pattern (17 bp):
GAGCATCACCTCACCCA
Found at i:2999859 original size:20 final size:21
Alignment explanation
Indices: 2999834--2999880 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2999824 ATAGTTACTT
2999834 TCGCAACAC-GAAAATGACTA
1 TCGCAACACGGAAAATGACTA
** *
2999854 TCGCAATGCGGAAAATGGCTA
1 TCGCAACACGGAAAATGACTA
2999875 TCGCAA
1 TCGCAA
2999881 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACACGGAAAATGACTA
Found at i:2999869 original size:21 final size:21
Alignment explanation
Indices: 2999843--2999884 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2999833 TTCGCAACAC
2999843 GAAAATGACTATCGCAATGCG
1 GAAAATGACTATCGCAATGCG
*
2999864 GAAAATGGCTATCGCAATGCG
1 GAAAATGACTATCGCAATGCG
2999885 AAATGAAAAT
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:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (21 bp):
GAAAATGACTATCGCAATGCG
Found at i:2999942 original size:18 final size:19
Alignment explanation
Indices: 2999900--2999950 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
2999890 AAAATCCGAC
2999900 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
*
2999919 AAATCGCAACGCGAAATG-
1 AAATCGCAATGCGAAATGA
2999937 AAATCGCAATGCGA
1 AAATCGCAATGCGA
2999951 TTTGTGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:2999991 original size:19 final size:18
Alignment explanation
Indices: 2999969--3000027 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
2999959 TCGCGTTGCG
2999969 ATTTATCGTTGCGATTTTC
1 ATTT-TCGTTGCGATTTTC
2999988 A-TTTCGCATTGCGA--TT-
1 ATTTTCG--TTGCGATTTTC
3000004 -TTTTCGTTGCGATTTTC
1 ATTTTCGTTGCGATTTTC
3000021 ATTTTCG
1 ATTTTCG
3000028 CATTGCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 15
0.69 0.00 0.31
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 5 0.15
18 8 0.24
19 7 0.21
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.53
Consensus pattern (18 bp):
ATTTTCGTTGCGATTTTC
Found at i:3000016 original size:33 final size:34
Alignment explanation
Indices: 2999957--3000036 Score: 128
Period size: 33 Copynumber: 2.4 Consensus size: 34
2999947 GCGATTTGTG
*
2999957 TTTCGCGTTGCGA-TTTATCGTTGCGATTTTCA-
1 TTTCGCATTGCGATTTTATCGTTGCGATTTTCAT
*
2999989 TTTCGCATTGCGATTTTTTCGTTGCGATTTTCAT
1 TTTCGCATTGCGATTTTATCGTTGCGATTTTCAT
3000023 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
3000037 AGTGTAACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 12 0.27
33 18 0.41
34 14 0.32
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (34 bp):
TTTCGCATTGCGATTTTATCGTTGCGATTTTCAT
Found at i:3000019 original size:13 final size:14
Alignment explanation
Indices: 2999962--3000019 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2999952 TTGTGTTTCG
*
2999962 CGTTGCGA-TTTAT
1 CGTTGCGATTTTTT
2999975 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
2999992 CGCATTGCGATTTTTT
1 CG--TTGCGATTTTTT
3000008 CGTTGCGATTTT
1 CGTTGCGATTTT
3000020 CATTTTCGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 8 0.21
14 10 0.26
15 2 0.05
16 5 0.13
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:3000033 original size:20 final size:20
Alignment explanation
Indices: 2999977--3000036 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 20
2999967 CGATTTATCG
2999977 TTGCGATTTTCA-TTTCGCA
1 TTGCGATTTTCATTTTCGCA
2999996 TTGCGA--TT--TTTTCG--
1 TTGCGATTTTCATTTTCGCA
3000010 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCATTTTCGCA
3000030 TTGCGAT
1 TTGCGAT
3000037 AGTGTAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 2 0.06
18 6 0.18
19 6 0.18
20 7 0.21
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.50
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCGCA
Found at i:3000951 original size:31 final size:31
Alignment explanation
Indices: 3000906--3000984 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
3000896 CAGAGGTCAT
*
3000906 AAAGATCATCGGTAAACTGTCCATAGGTCCCG
1 AAAGA-CATAGGTAAACTGTCCATAGGTCCCG
* * *
3000938 -AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAAG-ACATAGGTAAACTGTCCATAGGTCCCG
3000969 AAAGACATAGGTAAAC
1 AAAGACATAGGTAAAC
3000985 CCTCGACTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
AAAGACATAGGTAAACTGTCCATAGGTCCCG
Found at i:3001709 original size:64 final size:64
Alignment explanation
Indices: 3001628--3001789 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 64
3001618 TCTTTCAATG
* *
3001628 AAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTA
1 AAAGTATGCATCGATGCACTACTGATGCATCGATGCATAAAATACATTCGATGTTTGTATT-TTA
*** * * * *
3001692 CTGGTATGCATCGATGCACTACTTATGCATCGATGCATGAATTACATTCGATGTTTTTATTTTA
1 AAAGTATGCATCGATGCACTACTGATGCATCGATGCATAAAATACATTCGATGTTTGTATTTTA
*
3001756 AAAG-AGTGCATCGATGCACTAATGATGCATCGAT
1 AAAGTA-TGCATCGATGCACTACTGATGCATCGAT
3001790 ACACCTTCAA
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 75 0.91
65 6 0.07
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (64 bp):
AAAGTATGCATCGATGCACTACTGATGCATCGATGCATAAAATACATTCGATGTTTGTATTTTA
Found at i:3004241 original size:17 final size:18
Alignment explanation
Indices: 3004209--3004242 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3004199 CATTGTAAAC
3004209 ACATCAAAATATCATTCA
1 ACATCAAAATATCATTCA
*
3004227 ACATCATAA-ATCATTC
1 ACATCAAAATATCATTC
3004243 TCTAATCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (18 bp):
ACATCAAAATATCATTCA
Found at i:3005458 original size:31 final size:30
Alignment explanation
Indices: 3005389--3005483 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 30
3005379 GAAGGACCTA
*
3005389 TCCAGAGGTCACAAAGACC-CGGGT-AACTA
1 TCCAGAGGTCACAAAGACCTC-GGTAAACTG
*
3005418 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCACAAAGA-CCTCGGTAAACTG
* * * *
3005449 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAG-ACCTCGGTAAACTG
3005480 TCCA
1 TCCA
3005484 TATGTCTCGA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 16 0.29
30 5 0.09
31 33 0.60
32 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGACCTCGGTAAACTG
Found at i:3005484 original size:31 final size:31
Alignment explanation
Indices: 3005431--3005508 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
3005421 AGAGGTCATA
* *
3005431 AAGATCCTCGGTAAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
* *
3005462 AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
*
3005493 AA-AGACATAGGTAAAC
1 AAGA-ACCTAGGTAAAC
3005509 CCTCGACTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (31 bp):
AAGAACCTAGGTAAACTGTCCATAGGTCCCG
Found at i:3006268 original size:65 final size:65
Alignment explanation
Indices: 3006155--3006317 Score: 199
Period size: 65 Copynumber: 2.5 Consensus size: 65
3006145 TCTTTCAATG
* *
3006155 AAAGTATGCATCGATGCACT-ACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATT
1 AAAGTATGCATCGATGCACTAACTGATGCATCGATGCATAAAATACATTCGATGTTTGTATT-TT
3006218 A
65 A
*** * * * *
3006219 CTGGTATGCATCGATGCACTAACTTATGCATCGATGCATGAATTACATTCGATGTTTTTATTTTA
1 AAAGTATGCATCGATGCACTAACTGATGCATCGATGCATAAAATACATTCGATGTTTGTATTTTA
3006284 AAAG-AGTGCATCGATGCACTAA-TGATGCATCGAT
1 AAAGTA-TGCATCGATGCACTAACTGATGCATCGAT
3006318 ACACCTTCAA
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
64 29 0.35
65 48 0.58
66 6 0.07
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (65 bp):
AAAGTATGCATCGATGCACTAACTGATGCATCGATGCATAAAATACATTCGATGTTTGTATTTTA
Found at i:3007490 original size:42 final size:41
Alignment explanation
Indices: 3007431--3007509 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
3007421 GACTCACCTG
* * *
3007431 TCATCCCTTAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCAACCATTCAAGAGGCCCCTA
*
3007473 TCATCCCTCAAGAGTCCCCCCCACCATTCAAGAGGCC
1 TCATCCCTCAAGAGTCCCCCCAACCATTCAAGAGGCC
3007510 AGTGTCATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 15 0.45
42 18 0.55
ACGTcount: A:0.24, C:0.42, G:0.14, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCAACCATTCAAGAGGCCCCTA
Found at i:3008087 original size:13 final size:13
Alignment explanation
Indices: 3008069--3008100 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3008059 TTCACTTGAA
3008069 GAATCAACGAGAT
1 GAATCAACGAGAT
3008082 GAATCAACGAGAT
1 GAATCAACGAGAT
3008095 GAATCA
1 GAATCA
3008101 TTTTCGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (13 bp):
GAATCAACGAGAT
Found at i:3008975 original size:14 final size:14
Alignment explanation
Indices: 3008941--3008979 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3008931 TTGATTGTTT
3008941 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3008955 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
3008969 TGTTGATTTGT
1 AATTGATTTGT
3008980 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3009143 original size:19 final size:19
Alignment explanation
Indices: 3009119--3009183 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
3009109 GCAACGAGAG
3009119 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3009138 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
3009157 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
3009171 AATCGCAATGCGA
1 AATCGCAATGCGA
3009184 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3009232 original size:20 final size:20
Alignment explanation
Indices: 3009209--3009277 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
3009199 GCGATTTCCT
3009209 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
3009229 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
*
3009249 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGCCATTTTCG
*
3009269 CGTTACGAT
1 CGTTGCGAT
3009278 TTCCCCGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:3009235 original size:34 final size:34
Alignment explanation
Indices: 3009190--3009293 Score: 91
Period size: 40 Copynumber: 2.9 Consensus size: 34
3009180 GCGATTTTCA
* *
3009190 TTTCGCATTGCGATTTCCTCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTCCCCGTTGCGATAGCCAT
* * *
3009224 TTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGC----G--ATTTCCCCGTTGCGATAGCCAT
* *
3009264 TTTCGCGTTACGATTTCCCCGTTGTGATAG
1 TTTCGCGTTGCGATTTCCCCGTTGCGATAG
3009294 TCAAATGAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
34 25 0.45
36 1 0.02
38 1 0.02
40 29 0.52
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.38
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTCCCCGTTGCGATAGCCAT
Found at i:3009551 original size:21 final size:21
Alignment explanation
Indices: 3009525--3009579 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
3009515 GAAAGTCAGA
3009525 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
3009546 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
3009567 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
3009580 AGTCAGTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:3009591 original size:20 final size:19
Alignment explanation
Indices: 3009509--3009599 Score: 65
Period size: 21 Copynumber: 4.5 Consensus size: 19
3009499 TTCAGAATCT
* *
3009509 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGATAGT-AGTATCG
* *
3009529 CGTTGCGATTTTGTATTATCG
1 CGTTGCGA--TAGTAGTATCG
* *
3009550 CGTTGCGATTTTGTATTATCG
1 CGTTGCGA--TAGTAGTATCG
3009571 CGTTGCGATAGTCAGTATCG
1 CGTTGCGATAGT-AGTATCG
*
3009591 CATTGCGAT
1 CGTTGCGAT
3009600 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
19 3 0.05
20 22 0.36
21 34 0.56
22 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTAGTATCG
Found at i:3009681 original size:21 final size:22
Alignment explanation
Indices: 3009629--3009681 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3009619 ATTTACTTAT
*
3009629 TCGCATTGTG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
** *
3009650 TCGCAACGCGAAATT-GTAAAA
1 TCGCATTGCGAAATTGGGAAAA
3009671 TCGCATTGCGA
1 TCGCATTGCGA
3009682 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:3011402 original size:60 final size:60
Alignment explanation
Indices: 3011338--3011464 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
3011328 TCTCACCCTT
* * * * *
3011338 AAACTATGATA-ACAATTCTAAATTAGTCCTCAAA-TTTTTGAACATTTCAATTTCATCCCC
1 AAACTATGACATAC-ATTCTAAATTACTCCCCAAACTGTTTGAACATTCCAATTTCAT-CCC
* * **
3011398 AAACTATGACATTCATTCTAAATTACTCCCCAAACTGTTTGAATATTCCAATTTTGTCCC
1 AAACTATGACATACATTCTAAATTACTCCCCAAACTGTTTGAACATTCCAATTTCATCCC
3011458 AAACTAT
1 AAACTAT
3011465 ACACATATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 38 0.68
61 18 0.32
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (60 bp):
AAACTATGACATACATTCTAAATTACTCCCCAAACTGTTTGAACATTCCAATTTCATCCC
Found at i:3019197 original size:22 final size:22
Alignment explanation
Indices: 3019169--3019217 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
3019159 CTACTTGTTG
*
3019169 TTATAGATAATAATTTAGA-ATA
1 TTATAGATAATAATCTA-ATATA
3019191 TTATAGATAATAATCTAATATA
1 TTATAGATAATAATCTAATATA
3019213 TTATA
1 TTATA
3019218 ATATATAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (22 bp):
TTATAGATAATAATCTAATATA
Found at i:3022457 original size:21 final size:21
Alignment explanation
Indices: 3022433--3022474 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3022423 AGTAGAAGAT
* *
3022433 GAGGAAGGATTACCTTCGTAA
1 GAGGAAGAAGTACCTTCGTAA
*
3022454 GAGGATGAAGTACCTTCGTAA
1 GAGGAAGAAGTACCTTCGTAA
3022475 TGTTCTCTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (21 bp):
GAGGAAGAAGTACCTTCGTAA
Found at i:3033275 original size:13 final size:13
Alignment explanation
Indices: 3033259--3033316 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 13
3033249 TAATATGATT
3033259 TATTAAATAAAAA
1 TATTAAATAAAAA
3033272 TATTAAAATAAAAA
1 TATT-AAATAAAAA
3033286 TATTAGAATAAATAAA
1 TATTA-AAT-AA-AAA
*
3033302 TATTTAATATAAAA
1 TATTAAATA-AAAA
3033316 T
1 T
3033317 TAAGAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 5 0.13
14 21 0.54
15 6 0.15
16 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
TATTAAATAAAAA
Found at i:3034135 original size:14 final size:14
Alignment explanation
Indices: 3034118--3034168 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
3034108 AAATATAATA
3034118 AATATTATTTTTAT
1 AATATTATTTTTAT
*
3034132 AATATTAAATCTATTA-
1 AATATT--AT-TTTTAT
3034148 AATATTATTTTTAT
1 AATATTATTTTTAT
3034162 AATATTA
1 AATATTA
3034169 AATCTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
16 8 0.26
17 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATTATTTTTAT
Found at i:3034140 original size:30 final size:30
Alignment explanation
Indices: 3034095--3034207 Score: 136
Period size: 30 Copynumber: 3.6 Consensus size: 30
3034085 TTGTGTTTGA
3034095 TTTATAATCTATTAAATATAATAAATATTATT
1 TTTATAA--TATTAAATATAATAAATATTATT
* *
3034127 TTTATAATATTAAATCTATTAAATATTATT
1 TTTATAATATTAAATATAATAAATATTATT
* *
3034157 TTTATAATATTAAATCTATTAAATATTATAT
1 TTTATAATATTAAATATAATAAATATTAT-T
* *
3034188 TAATATTATATTAAATATAA
1 T-TTATAATATTAAATATAA
3034208 AGTTATTATT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
30 50 0.68
31 2 0.03
32 21 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTATAATATTAAATATAATAAATATTATT
Found at i:3034153 original size:16 final size:16
Alignment explanation
Indices: 3034132--3034184 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
3034122 TTATTTTTAT
3034132 AATATTAAATCTATTA
1 AATATTAAATCTATTA
*
3034148 AATATT--AT-TTTTA
1 AATATTAAATCTATTA
3034161 TAATATTAAATCTATTA
1 -AATATTAAATCTATTA
3034178 AATATTA
1 AATATTA
3034185 TATTAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 4 0.13
14 8 0.26
16 15 0.48
17 4 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATTAAATCTATTA
Found at i:3036316 original size:31 final size:31
Alignment explanation
Indices: 3036243--3036328 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
3036233 GAACTGCTAC
* * *
3036243 GCATTATCTAAATGCAAACATGACATATTGT
1 GCATTATCTAAATGCAAACCTGACATACTAT
* *
3036274 GGATTATCTAAATGCAAACCTGATATACTAT
1 GCATTATCTAAATGCAAACCTGACATACTAT
*
3036305 GCATTAACTAAATGTC-AACCTGAC
1 GCATTATCTAAATG-CAAACCTGAC
3036329 TAGTATCTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 45 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (31 bp):
GCATTATCTAAATGCAAACCTGACATACTAT
Found at i:3037135 original size:16 final size:17
Alignment explanation
Indices: 3037114--3037151 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3037104 GGTAAAAATG
*
3037114 GAATTTTTAATT-AATT
1 GAATTTTAAATTCAATT
3037130 GAATTTTAAATTCAATT
1 GAATTTTAAATTCAATT
*
3037147 AAATT
1 GAATT
3037152 ATATTAAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (17 bp):
GAATTTTAAATTCAATT
Found at i:3037690 original size:39 final size:40
Alignment explanation
Indices: 3037606--3037696 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
3037596 TAAAAAATGA
* ***
3037606 AAATGATATATATATATATATATATTAAATTATTTGTATAC
1 AAATTATAT-TATATATATATATATTAAATTATAAATATAC
*
3037647 AAATT-TATTATATATATATATA-TAAATTATAAATAATAG
1 AAATTATATTATATATATATATATTAAATTATAAAT-ATAC
3037686 AAATTATATTA
1 AAATTATATTA
3037697 AGTTATTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 9 0.21
39 22 0.51
40 8 0.19
41 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (40 bp):
AAATTATATTATATATATATATATTAAATTATAAATATAC
Found at i:3053551 original size:21 final size:21
Alignment explanation
Indices: 3053525--3053647 Score: 101
Period size: 21 Copynumber: 5.8 Consensus size: 21
3053515 TTATGTGCAC
*
3053525 TAGGTATCGATACCCCCTTTA
1 TAGGTATCGATACCCCCTTGA
*
3053546 TAGGTATCGATACCCCCTTGC
1 TAGGTATCGATACCCCCTTGA
* *
3053567 TAGGTATCAATA-CCCCTTCA
1 TAGGTATCGATACCCCCTTGA
*
3053587 -ACGTGTATCGATACCCTCTTTGA
1 TA-G-GTATCGATACCC-CCTTGA
*
3053610 -ATGTGTAAT-GATACCCCCTTGC
1 TA-G-GT-ATCGATACCCCCTTGA
*
3053632 TAGGTATCAATACCCC
1 TAGGTATCGATACCCC
3053648 TTCAACGTGT
Statistics
Matches: 83, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.01
20 9 0.11
21 47 0.57
22 7 0.08
23 17 0.20
24 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (21 bp):
TAGGTATCGATACCCCCTTGA
Found at i:3053630 original size:65 final size:64
Alignment explanation
Indices: 3053554--3053690 Score: 247
Period size: 65 Copynumber: 2.1 Consensus size: 64
3053544 TATAGGTATC
*
3053554 GATACCCCCTTGCTAGGTATCAATACCCCTTCAACGTGTATCGATACCCTCTTTGAATGTGTAAT
1 GATACCCCCTTGCTAGGTATCAATACCCCTTCAACGTGTATC-ACACCCTCTTTGAATGTGTAAT
*
3053619 GATACCCCCTTGCTAGGTATCAATACCCCTTCAACGTGTATCACACCCTCTTTGAATGTGTATT
1 GATACCCCCTTGCTAGGTATCAATACCCCTTCAACGTGTATCACACCCTCTTTGAATGTGTAAT
3053683 GATACCCC
1 GATACCCC
3053691 TATAAGGGTA
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 28 0.40
65 42 0.60
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (64 bp):
GATACCCCCTTGCTAGGTATCAATACCCCTTCAACGTGTATCACACCCTCTTTGAATGTGTAAT
Done.