Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_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: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:864211 original size:204 final size:207
Alignment explanation
Indices: 863632--864319 Score: 947
Period size: 204 Copynumber: 3.3 Consensus size: 207
863622 TTGATCCCTT
*
863632 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTTATATTTGTTCAATTTAGTCCTTAAAATT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATA-TTGTTCAATTTAGTCCTT-AAATT
* *
863697 ATATTTGCATCTAAAATT-ATCCCATACTTATACTTATATCTATTTTTTAATTGGCCCATAACTT
64 -TATTTGCATCTGAAATTGA-CCCATACTTATACTTAT-TTTATTTTTTAATTGGCCCATAACTT
* *
863761 TTTAAATGGGTATAA-TTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTTG
126 TTTAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCG
863825 A-TTGATCCCTCATCTATGTG
190 ATTTGAT-CCTCA-C-ATGTG
*
863845 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTGTTCAATTTAGTCCTTAAAATTA
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTGTTCAATTTAGTCCTTAAATTTA
* * * * *
863910 TATTGCATCTGAAATTGGCCAATACTTAT--TAATTTTATATTTTT--TTGGCCGAGAACTTTTT
66 T-TTGCATCTGAAATTGACCCATACTTATACTTATTTTAT-TTTTTAATTGGCCCATAACTTTTT
* * *
863971 AAATAGGTATAATTTAGTACTTTTTGAATTAATTTCAACCTCACAACTTAAAATTATTTCGATTT
129 AAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTT
864036 GAT-C-C-C-T-TG
194 GATCCTCACATGTG
*
864045 TG-TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATA-TTGTTCAATTTAGTCCT-TAAATT
864109 CTATTTGCATCTGAAATTGACCCATACTTATACTTATTTATATTTTTTAATTGGCCCATAAC-TT
64 -TATTTGCATCTGAAATTGACCCATACTTATACTTATTT-TATTTTTTAATTGGCCCATAACTTT
*
864173 TTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCAAT
127 TTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
864238 TTGATCCCTCATCAATGTG
192 TTGAT-CCTCA-C-ATGTG
* *
864257 TGTTGTTTAATTT-TTTAAATTTTAATTTGTAATTTCATATTGTTCAATTTAATTCTTAAATTT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTGTTCAATTTAGTCCTTAAATTT
864320 GTATTTTTCA
Statistics
Matches: 425, Mismatches: 28, Indels: 48
0.85 0.06 0.10
Matches are distributed among these distances:
199 36 0.08
200 21 0.05
201 31 0.07
202 3 0.01
203 11 0.03
204 71 0.17
205 11 0.03
206 2 0.00
207 65 0.15
208 16 0.04
209 10 0.02
210 9 0.02
211 43 0.10
212 47 0.11
213 49 0.12
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (207 bp):
TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTGTTCAATTTAGTCCTTAAATTTA
TTTGCATCTGAAATTGACCCATACTTATACTTATTTTATTTTTTAATTGGCCCATAACTTTTTAA
ATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGA
TCCTCACATGTG
Found at i:867229 original size:40 final size:41
Alignment explanation
Indices: 867167--867244 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
867157 ACAAAAATAT
* *
867167 TTTTTTCACTAGTCTTAGTTTGTGATTTGTGATGACAATTA
1 TTTTTTCACTAGTCTTAATTTGTGATTTGTGACGACAATTA
867208 TTTTTTCACTAGT-TTAATTTGTGATTTGTGACGACAA
1 TTTTTTCACTAGTCTTAATTTGTGATTTGTGACGACAA
867245 ACTTTATCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 22 0.63
41 13 0.37
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (41 bp):
TTTTTTCACTAGTCTTAATTTGTGATTTGTGACGACAATTA
Found at i:869678 original size:18 final size:19
Alignment explanation
Indices: 869655--869693 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
869645 TTTCTTTTCT
*
869655 TAAAAATAAG-GCTTAATA
1 TAAAAATAAGTGCTAAATA
869673 TAAAAATAAGTGCTAAATA
1 TAAAAATAAGTGCTAAATA
869692 TA
1 TA
869694 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (19 bp):
TAAAAATAAGTGCTAAATA
Found at i:872524 original size:96 final size:94
Alignment explanation
Indices: 872369--872597 Score: 263
Period size: 97 Copynumber: 2.4 Consensus size: 94
872359 CACCGATTAT
* *
872369 TTTCTTTTACAAATCATGAAAATAAATCCAATGA--TTATTTTCTTTCACAAACAAGAATCATAC
1 TTTCTTTTAC-AATTAGGAAAATAAATCCAATGATTTTATTTTCTTTCACAAACAAGAATCATAC
* *
872432 AATATTC-CAAAAA-AACATCCAATGATTTA
65 AAGATTCTCAAAAATAA-ATCCAATAATTTA
* * *
872461 TTTCTTTTACAATTAGGAAAATAAATCCAATGATTTGTTTATTTCTTTTTACAAAGAAGAATCAT
1 TTTCTTTTACAATTAGGAAAATAAATCCAATGATTT-TAT-TTTC-TTTCACAAACAAGAATCAT
*
872526 ACAAGATTCTCAAAAATGAATCCAATAATTTA
63 ACAAGATTCTCAAAAATAAATCCAATAATTTA
* * *
872558 TTTCCCTTTACAAATAGG-AAATAAATCCAACGA-TTTATTT
1 TTT-CTTTTACAATTAGGAAAATAAATCCAATGATTTTATTT
872598 CGGTTTATTT
Statistics
Matches: 117, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
91 21 0.18
92 10 0.09
93 1 0.01
94 4 0.03
95 6 0.05
96 27 0.23
97 35 0.30
98 13 0.11
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (94 bp):
TTTCTTTTACAATTAGGAAAATAAATCCAATGATTTTATTTTCTTTCACAAACAAGAATCATACA
AGATTCTCAAAAATAAATCCAATAATTTA
Found at i:872641 original size:48 final size:47
Alignment explanation
Indices: 872554--872645 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 47
872544 AATCCAATAA
872554 TTTATTTCCCTTTACAAATAGGAAATAAATCCAACGATTTATTTCGG
1 TTTATTTCCCTTTACAAATAGGAAATAAATCCAACGATTTATTTCGG
* * * * *
872601 TTTATTTTCTTTTACAAAATA-GAAACTAAATTCTATGATTTATTT
1 TTTATTTCCCTTTAC-AAATAGGAAA-TAAATCCAACGATTTATTT
872646 TCTTTTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 17 0.45
48 21 0.55
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (47 bp):
TTTATTTCCCTTTACAAATAGGAAATAAATCCAACGATTTATTTCGG
Found at i:872643 original size:38 final size:39
Alignment explanation
Indices: 872601--872692 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 39
872591 TTTATTTCGG
* * *
872601 TTTATTTTCTTTTACAAAATA-GAAACTAAATTCTATGA
1 TTTATTTTCTTTTACAAAATAGGAAAATAAATCCAATGA
*
872639 TTTATTTTCTTTTTCAAAATAGGAAAATAAATCCAATGA
1 TTTATTTTCTTTTACAAAATAGGAAAATAAATCCAATGA
*
872678 TTT-TTTCCTTTTACA
1 TTTATTTTCTTTTACA
872693 TATAGAATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 30 0.64
39 17 0.36
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (39 bp):
TTTATTTTCTTTTACAAAATAGGAAAATAAATCCAATGA
Found at i:872799 original size:39 final size:39
Alignment explanation
Indices: 872718--872799 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
872708 GATTCTTGAA
* *
872718 AAAATAAATTTACCGATGTATTTCCTTTTTCAAAACAGG
1 AAAATAAATTTACCGATGTATTTCCTTTTACAAAACACG
* * *
872757 AAAATAAATTCTA-CGATTTATTTCCTTTTACACAATACG
1 AAAATAAATT-TACCGATGTATTTCCTTTTACAAAACACG
872796 AAAA
1 AAAA
872800 GATTTATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.35
Consensus pattern (39 bp):
AAAATAAATTTACCGATGTATTTCCTTTTACAAAACACG
Found at i:873656 original size:14 final size:15
Alignment explanation
Indices: 873637--873669 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
873627 GTTATATGGT
873637 AATAATACCAT-AAC
1 AATAATACCATGAAC
*
873651 AATAATATCATGAAC
1 AATAATACCATGAAC
873666 AATA
1 AATA
873670 TCATGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATACCATGAAC
Found at i:875382 original size:21 final size:21
Alignment explanation
Indices: 875340--875378 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
875330 TTATTTATTT
*
875340 AAATATCAAAATTATTAATAA
1 AAATATCAAAATTATAAATAA
*
875361 AAATATCAAGATTA-AAAT
1 AAATATCAAAATTATAAAT
875379 TAAATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 3 0.19
21 13 0.81
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (21 bp):
AAATATCAAAATTATAAATAA
Found at i:876652 original size:28 final size:28
Alignment explanation
Indices: 876619--876711 Score: 96
Period size: 30 Copynumber: 3.2 Consensus size: 28
876609 ATATAATTTA
876619 TAAAATAAATAAAATTAAGAGACCGAAT
1 TAAAATAAATAAAATTAAGAGACCGAAT
* * * * **
876647 TAAAATATATAAATAAGTCAGTGACTAAATT
1 TAAAATAAAT-AA-AATTAAGAGACCGAA-T
876678 ATAAAATAAATAAAATTAAGAGACCGAAT
1 -TAAAATAAATAAAATTAAGAGACCGAAT
876707 TAAAA
1 TAAAA
876712 GGATCAAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
28 14 0.29
29 3 0.06
30 20 0.41
31 3 0.06
32 9 0.18
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.25
Consensus pattern (28 bp):
TAAAATAAATAAAATTAAGAGACCGAAT
Found at i:877825 original size:3 final size:3
Alignment explanation
Indices: 877819--877906 Score: 94
Period size: 3 Copynumber: 30.0 Consensus size: 3
877809 TTTTTATTAT
*
877819 TAA TAA TAA TAA TAAA TAA TAA -AA TAA TAA TAA TAG T-A TAAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* * *
877864 -AA TAA TAC TAA TAA T-A TAA TAA TAA TAA TAA CAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
877907 AAAAACCAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
2 7 0.10
3 60 0.83
4 5 0.07
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:877870 original size:26 final size:26
Alignment explanation
Indices: 877819--877905 Score: 101
Period size: 26 Copynumber: 3.4 Consensus size: 26
877809 TTTTTATTAT
877819 TAATAATAATA-ATAAATAATAA-AA
1 TAATAATAATATATAAATAATAATAA
877843 TAATAATAATAGTATAAATAA-AATAA
1 TAATAATAATA-TATAAATAATAATAA
*
877869 TACTAATAATATA-ATAATAATAATAA
1 TAATAATAATATATA-AATAATAATAA
* *
877895 CAAAAATAATA
1 TAATAATAATA
877906 AAAAAACCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
24 12 0.22
25 9 0.17
26 33 0.61
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (26 bp):
TAATAATAATATATAAATAATAATAA
Found at i:877902 original size:23 final size:23
Alignment explanation
Indices: 877819--877902 Score: 61
Period size: 23 Copynumber: 3.7 Consensus size: 23
877809 TTTTTATTAT
*
877819 TAATAATAATAATAAATAATAA-AA
1 TAATAATAACAA-AAAT-ATAATAA
* **
877843 TAATAATAA-TAGTATA-AATAA
1 TAATAATAACAAAAATATAATAA
*
877864 -AATAAT-ACTAATAATATAATAA
1 TAATAATAAC-AAAAATATAATAA
877886 TAATAATAACAAAAATA
1 TAATAATAACAAAAATA
877903 ATAAAAAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
19 1 0.02
20 8 0.17
21 7 0.15
22 7 0.15
23 13 0.28
24 11 0.23
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (23 bp):
TAATAATAACAAAAATATAATAA
Found at i:878352 original size:131 final size:132
Alignment explanation
Indices: 878191--878531 Score: 465
Period size: 137 Copynumber: 2.6 Consensus size: 132
878181 AGTCGAGTAA
* *
878191 AAGGTTGAATAAGTTCTTCAT-ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTG
1 AAGGTTGAACAAGTTCTTC-TCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* * ** *
878255 TGAAATTCAAATGTTGATCCTCAAAAGAGGTTC-CGTTGATTCAACTTTATATG-TGATGAATTA
65 TGAACTTCAAATGTTGATCCTCAAAAGAGGTTCTCGTTCATTCAACTCCATA-GATGATGAATCA
878318 AGGC-
129 A-GCT
*
878322 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* ** *
878387 GAACTCTCTGAAAATGTTGATCCTCCAGGGAGGTTCTTCTTTCATTCAACTCCATAGATGATGAA
66 GAACT-TC---AAATGTTGATCCTCAAAAGAGGTTC-TCGTTCATTCAACTCCATAGATGATGAA
878452 TCAAGCT
126 TCAAGCT
*
878459 AAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
878524 GAACTTCA
66 GAACTTCA
878532 TCTGGAAACG
Statistics
Matches: 187, Mismatches: 14, Indels: 16
0.86 0.06 0.07
Matches are distributed among these distances:
130 1 0.01
131 64 0.34
132 2 0.01
133 1 0.01
135 22 0.12
136 5 0.03
137 92 0.49
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (132 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTTCAAATGTTGATCCTCAAAAGAGGTTCTCGTTCATTCAACTCCATAGATGATGAATCAAG
CT
Found at i:878608 original size:123 final size:112
Alignment explanation
Indices: 878565--878877 Score: 504
Period size: 113 Copynumber: 2.8 Consensus size: 112
878555 ATCTCCTTCT
* *
878565 GTGATAGAATT-GAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTTTTCTTCC-TCTTCA
1 GTGAT-GAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
878628 GATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGA
65 GATGAGTTCTTCTCATTATGAACTT-CTCTGGAAAAGTTGATCCATCGA
* * * * *
878677 GTGATGAATTCAAGCAAAAGGTTGAACAAATTATTCTCATTATGAATTTCTTCTTCCTTCTTTAG
1 GTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
878742 ATGAGTTCTTCTCATTATGAACTCTCTCAGGAAAAGTTGATCCATCGA
66 ATGAGTTCTTCTCATTATGAACT-TCTCTGGAAAAGTTGATCCATCGA
*
878790 GTGATGAATTCGAGCAAAAGTTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
878855 ATGAGTTCTTCTCATTATGAACT
66 ATGAGTTCTTCTCATTATGAACT
878878 CTACCCGACA
Statistics
Matches: 184, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
111 5 0.03
112 45 0.24
113 133 0.72
114 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (112 bp):
GTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGA
Found at i:879296 original size:22 final size:22
Alignment explanation
Indices: 879266--879322 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
879256 AATAAAGCTT
*
879266 TCATCTTTGAAGAGTGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
879288 TCATTTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
879310 TTATCTTTGAAGA
1 TCATCTTTGAAGA
879323 ATGTAGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:879801 original size:54 final size:54
Alignment explanation
Indices: 879739--879957 Score: 237
Period size: 54 Copynumber: 4.1 Consensus size: 54
879729 TGCTTGGATT
* * *
879739 TTCGTAAAGCTTTTGATAACACATTCATCATTTCTTGTGGCTTCTGGC-CAGATG
1 TTCGTAAAGCATTTGACAACATATTCATCATTTCTTGTGGCTTCT-GCACAGATG
* * * ** *
879793 TTCATAAAGCATTTGACAACATATTCATCTTTTCATGTGATTTCTGCACAAATG
1 TTCGTAAAGCATTTGACAACATATTCATCATTTCTTGTGGCTTCTGCACAGATG
* * * *
879847 TTTGTAAAACATTTGACAACATATTCATCATTT-TCTGTGGTTTCTGCTCAGATG
1 TTCGTAAAGCATTTGACAACATATTCATCATTTCT-TGTGGCTTCTGCACAGATG
* * **
879901 TTTCGTAAA-CATTTGACAACATATTCATCATTTCCTATGGCTTCTGCTTAGATG
1 -TTCGTAAAGCATTTGACAACATATTCATCATTTCTTGTGGCTTCTGCACAGATG
879955 TTC
1 TTC
879958 AATTATTGAA
Statistics
Matches: 139, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
53 5 0.04
54 127 0.91
55 7 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (54 bp):
TTCGTAAAGCATTTGACAACATATTCATCATTTCTTGTGGCTTCTGCACAGATG
Found at i:879956 original size:108 final size:109
Alignment explanation
Indices: 879707--879956 Score: 269
Period size: 108 Copynumber: 2.3 Consensus size: 109
879697 ACATGTGACA
* * * * * *
879707 ATTCATCCTTT-CTCATGGCTTTTGCTTGGAT-TTTCGTAAAGCTTTTGATAACACATTCATCAT
1 ATTCATCATTTCCT-ATGGCTTCTGCTTAGATGTTTCGTAAAACATTTGACAACACATTCATCAT
879770 TTCTTGTGGCTTCTGGCCAGATGTTCATAAAGCATTTGACAACAT
65 TTCTTGTGGCTTCTGGCCAGATGTTCATAAAGCATTTGACAACAT
* * * ** ** * *
879815 ATTCATCTTTTCATGTGATTTCTGCACAAATGTTT-GTAAAACATTTGACAACATATTCATCATT
1 ATTCATCATTTCCTATGGCTTCTGCTTAGATGTTTCGTAAAACATTTGACAACACATTCATCATT
* *
879879 T-TCTGTGGTTTCT-GCTCAGATGTTTCGTAAA-CATTTGACAACAT
66 TCT-TGTGGCTTCTGGC-CAGATG-TTCATAAAGCATTTGACAACAT
879923 ATTCATCATTTCCTATGGCTTCTGCTTAGATGTT
1 ATTCATCATTTCCTATGGCTTCTGCTTAGATGTT
879957 CAATTATTGA
Statistics
Matches: 113, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
107 3 0.03
108 99 0.88
109 11 0.10
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.42
Consensus pattern (109 bp):
ATTCATCATTTCCTATGGCTTCTGCTTAGATGTTTCGTAAAACATTTGACAACACATTCATCATT
TCTTGTGGCTTCTGGCCAGATGTTCATAAAGCATTTGACAACAT
Found at i:884118 original size:71 final size:72
Alignment explanation
Indices: 883988--884122 Score: 254
Period size: 71 Copynumber: 1.9 Consensus size: 72
883978 GTATAATAAG
*
883988 TTAGCTGAATATTATCCATAAAGCCAGGGTGATTAACCAATTGCTTTAGGGGGATAACTCAAGCT
1 TTAGCTAAATATTATCCATAAAGCCAGGGTGATTAACCAATTGCTTTAGGGGGATAACTCAAGCT
884053 TAACAGA
66 TAACAGA
884060 TTAGCTAAATATTATCCATAAAGCCAGGGT-ATTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 TTAGCTAAATATTATCCATAAAGCCAGGGTGATTAACCAATTGCTTTAGGGGGATAACTCAAGC
884123 GTTATTGTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
71 33 0.53
72 29 0.47
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (72 bp):
TTAGCTAAATATTATCCATAAAGCCAGGGTGATTAACCAATTGCTTTAGGGGGATAACTCAAGCT
TAACAGA
Found at i:885348 original size:18 final size:18
Alignment explanation
Indices: 885325--885359 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
885315 TCCCTGAACT
*
885325 AAGAGTTCTTAAACCACC
1 AAGAGTTATTAAACCACC
*
885343 AAGAGTTATTGAACCAC
1 AAGAGTTATTAAACCAC
885360 TCGTTTGAAG
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:0.23, G:0.14, T:0.23
Consensus pattern (18 bp):
AAGAGTTATTAAACCACC
Found at i:886832 original size:43 final size:44
Alignment explanation
Indices: 886751--886837 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
886741 CCGTGCATCA
* * *
886751 AACAAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAAGGGACAACTTTCACTCCTAACTTC
* * *
886795 AACAAAAC-TTTATATATAAGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTTACATATAAGGGACAACTTTCACTCCTAACTTC
886838 TCTAAAGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 29 0.78
44 8 0.22
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAAGGGACAACTTTCACTCCTAACTTC
Found at i:888919 original size:136 final size:138
Alignment explanation
Indices: 888756--889002 Score: 403
Period size: 136 Copynumber: 1.8 Consensus size: 138
888746 CTATATCTAT
*
888756 ATATATATATTTTATAAATAAGATATTTATTTACTT-AGAAATATCAGAAAAG-ACTTCTAGGTG
1 ATATATATATTTTAAAAATAAGATATTTATTTACTTAAG-AATATCAGAAAAGAACTTCTAGGTG
*
888819 CTTTAAGACAGCCCATTTCTTAATATT-AAAAATAAATAAATATTAATAAAACATTTCTCTAAAA
65 CTTTAAGACAGCCAATTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAA
888883 ATAATTAAA
130 ATAATTAAA
* *
888892 ATATATA-ATTTATAAAAATAGGATATTTATTTATTTAAGAATATCAGAAAAGAACTTCTAGGTG
1 ATATATATATTT-TAAAAATAAGATATTTATTTACTTAAGAATATCAGAAAAGAACTTCTAGGTG
*
888956 TTTTAAGACAGCCAATTTCTTAATATTAAAAAATAAATAAATATTAA
65 CTTTAAGACAGCCAATTTCTTAATATTAAAAAATAAATAAATATTAA
889003 AATATGATTA
Statistics
Matches: 102, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
135 4 0.04
136 41 0.40
137 38 0.37
138 19 0.19
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (138 bp):
ATATATATATTTTAAAAATAAGATATTTATTTACTTAAGAATATCAGAAAAGAACTTCTAGGTGC
TTTAAGACAGCCAATTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAA
TAATTAAA
Found at i:889144 original size:8 final size:7
Alignment explanation
Indices: 889133--889217 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 7
889123 TAATAATAAT
889133 TAAATATA
1 TAAA-ATA
889141 TAAACATA
1 TAAA-ATA
889149 TAAAAT-
1 TAAAATA
889155 TAAAATA
1 TAAAATA
889162 T-AAATA
1 TAAAATA
*
889168 AAAAATGA
1 TAAAAT-A
889176 TTAAAATAAA
1 -TAAAAT--A
889186 TAAAAT-
1 TAAAATA
889192 TAAAACTA
1 TAAAA-TA
**
889200 TAGTAT-
1 TAAAATA
889206 TAAAATA
1 TAAAATA
889213 TAAAA
1 TAAAA
889218 GTTAATAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
6 20 0.33
7 14 0.23
8 15 0.25
9 11 0.18
10 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (7 bp):
TAAAATA
Found at i:890645 original size:3 final size:3
Alignment explanation
Indices: 890639--890711 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
890629 TATTTTTTAT
* *
890639 TAA TAA TAA TAAA TAA T-A TAA TAA TAG T-A TAAA TAA -AA TAA TAC
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
890683 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
890712 ACAAATGGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 7 0.12
3 48 0.80
4 5 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:890670 original size:23 final size:21
Alignment explanation
Indices: 890639--890711 Score: 94
Period size: 20 Copynumber: 3.4 Consensus size: 21
890629 TATTTTTTAT
890639 TAATAATAATAAATAATATAA
1 TAATAATAATAAATAATATAA
* *
890660 TAATAGT-ATAAATAAAATAA
1 TAATAATAATAAATAATATAA
*
890680 TACTAATAATAATAATAATATAA
1 TAATAATAAT-A-AATAATATAA
890703 TAATAATAA
1 TAATAATAA
890712 ACAAATGGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 17 0.40
21 8 0.19
22 1 0.02
23 17 0.40
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:890670 original size:26 final size:25
Alignment explanation
Indices: 890639--890707 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 25
890629 TATTTTTTAT
890639 TAATAATAATAAATAATA-TAATAA
1 TAATAATAATAAATAATACTAATAA
*
890663 TAGT-ATAAATAAAATAATACTAATAA
1 TAATAAT-AAT-AAATAATACTAATAA
890689 TAATAATAATATAATAATA
1 TAATAATAATA-AATAATA
890708 ATAAACAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 2 0.05
24 6 0.16
25 9 0.24
26 19 0.50
27 2 0.05
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (25 bp):
TAATAATAATAAATAATACTAATAA
Found at i:892070 original size:29 final size:29
Alignment explanation
Indices: 892023--892105 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
892013 TTCACCTAAC
*
892023 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGTAATGACATCATTACT
*
892053 TAAATGATGTAAGTAATGACATCTTTACT
1 TAAATGATGTAAGTAATGACATCATTACT
892082 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGTAATGACATCA
892106 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGTAATGACATCATTACT
Found at i:895485 original size:15 final size:15
Alignment explanation
Indices: 895465--895499 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
895455 CTCATAGTTT
895465 TTGTTGCAATTGTTG
1 TTGTTGCAATTGTTG
*
895480 TTGTTGGAATTGTTG
1 TTGTTGCAATTGTTG
895495 TTGTT
1 TTGTT
895500 ATAATTCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.03, G:0.29, T:0.57
Consensus pattern (15 bp):
TTGTTGCAATTGTTG
Found at i:895505 original size:15 final size:15
Alignment explanation
Indices: 895472--895505 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
895462 TTTTTGTTGC
*
895472 AATTGTTGTTGTTGG
1 AATTGTTGTTGTTAG
*
895487 AATTGTTGTTGTTAT
1 AATTGTTGTTGTTAG
895502 AATT
1 AATT
895506 CCAGCCTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.56
Consensus pattern (15 bp):
AATTGTTGTTGTTAG
Found at i:896816 original size:29 final size:29
Alignment explanation
Indices: 896773--896855 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
896763 CTCACCTAAC
*
896773 TAAATTGATGTAAGCAATGACATCATTACA
1 TAAA-TGATGTAAGCAATGATATCATTACA
* *
896803 TAAATGATGTAAGCAATGATATCTTTACT
1 TAAATGATGTAAGCAATGATATCATTACA
*
896832 TAAATAATGTAAGCAATGATATCA
1 TAAATGATGTAAGCAATGATATCA
896856 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGATATCATTACA
Found at i:898291 original size:18 final size:17
Alignment explanation
Indices: 898259--898302 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
898249 CAAGTGCAGG
*
898259 AGGAGTTAGCATGTCCA
1 AGGAGTTTGCATGTCCA
898276 AGGAGTTTGCCATGTCCA
1 AGGAGTTTG-CATGTCCA
898294 AGGAGTTTG
1 AGGAGTTTG
898303 TCGAGCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (17 bp):
AGGAGTTTGCATGTCCA
Found at i:898834 original size:19 final size:19
Alignment explanation
Indices: 898810--898854 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
898800 TTTAGTTTCA
*
898810 AAATCATCCAAAAATCCCT
1 AAATCATCCAAAAATCCCC
*
898829 AAATCATCCCAAAATCCCC
1 AAATCATCCAAAAATCCCC
898848 AAATCAT
1 AAATCAT
898855 TCTAGCTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (19 bp):
AAATCATCCAAAAATCCCC
Found at i:900629 original size:23 final size:23
Alignment explanation
Indices: 900594--900652 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
900584 ATCAAGTATA
*
900594 ATAACATATTAGGTAGAGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
* *
900617 ATAACGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
* *
900640 ATAAGAAAATAGG
1 ATAACATAATAGG
900653 AATTTAACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (23 bp):
ATAACATAATAGGTAGAGCTTAT
Found at i:900713 original size:87 final size:87
Alignment explanation
Indices: 900567--900728 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 87
900557 ATGTTATATC
* *
900567 ATTTAACCGGAAATATTATCAAGTATAATAACATATTAGGTAGAGCTTATATAACGTAATAGGTA
1 ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGAGCTTATATAACGTAATAGGTA
**
900632 GTGCTTATATAAGAAAATAGGA
66 GCACTTATATAAGAAAATAGGA
** *
900654 ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGTA
1 ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGAGCTTATATAACGTAATAGGTA
900719 GCACTTATAT
66 GCACTTATAT
900729 TGACCTATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGAGCTTATATAACGTAATAGGTA
GCACTTATATAAGAAAATAGGA
Found at i:901384 original size:201 final size:198
Alignment explanation
Indices: 900723--901448 Score: 822
Period size: 201 Copynumber: 3.6 Consensus size: 198
900713 TAGGTAGCAC
* * * * * * *
900723 TTATATTGACCTATTTTCTAAGT-AAACCGATATATTTACACTGATAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTAA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTA
* * * * * *
900787 TTACATTATAATTATCAGTTTCGATATTTTTTGGATTGATACAATTT--TAAATGCAACGACACT
65 TTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACT
* *
900850 TTATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACATAAAAAGTGTC
129 TTATGCGTGCACCTCGTTGGGCATTCATTCTGG-AAAAAGTATCGACACAAACTTAACAAGTGTC
900915 GATACA
193 GATACA
* * * * * *
900921 TTAT-TTAGACCTATTTTCTCATAAAATCGGAATACTTT-TATCGGGTATATTGTAAATTTACCT
1 TTATGTT-GACCTATTTTCTAATAAAACCGGTATA-TTTATACCGGTTACATTGTAAATTTACCT
* ** *
900984 ATCACATCGTAATTATTGGTTTCGATATTTTTGGGATCGATACTTTTAATAAATGTATCGACACT
64 ATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTAATAAATGTATCGACACT
* * * * * *
901049 TTGTGTGTGCATCC-CGTTTGACATTCATTATGGACAAAATGTATCGACACAAATTTAACAAGTG
129 TTATGCGTGCA-CCTCGTTGGGCATTCATTCTGGA-AAAA-GTATCGACACAAACTTAACAAGTG
*
901113 TCGATACT
191 TCGATACA
* * ** *
901121 TTATGCTGACCTATTTTCTCATAAAAATGGTATATTTATACCTGTTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* *
901186 TACATTATAATTATCGGTTTCGA-AGTTATTGGGATCGATACTTTTAATAAATGTATCGACACGT
66 TACATTATAATTATCGGTTTCGATA-TTTTTGGGATCGATACTTTTAATAAATGTATCGACACTT
*
901250 TATGCGTGCACCTTGTTGGGGCATTCATTCTGGATAATAAGTATCGACACAAA-TTACACAAGTG
130 TATGCGTGCACCTCGTT-GGGCATTCATTCTGGA-AA-AAGTATCGACACAAACTTA-ACAAGTG
*
901314 TCGGTACA
191 TCGATACA
* * * * *
901322 TTATGTTGACTTGTTTTCTAATTAACCCGGTATATTTATACCGGTTACATTGTTAATTTACCTAT
1 TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
* * *
901387 TACATTATAATTATTGGTTTCGATGTTTTTGGGCTCGATACTTTTAGA-AAATGTATCGACAC
66 TACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
901449 ATATTTAGGT
Statistics
Matches: 443, Mismatches: 68, Indels: 31
0.82 0.13 0.06
Matches are distributed among these distances:
197 6 0.01
198 79 0.18
199 52 0.12
200 151 0.34
201 152 0.34
202 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (198 bp):
TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
ATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAGTATCGACACAAACTTAACAAGTGTCGAT
ACA
Found at i:903951 original size:19 final size:19
Alignment explanation
Indices: 903927--903975 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
903917 TTACATTCAC
903927 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
903946 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
903965 ATACAAAATTA
1 ATACAAAATTA
903976 ACCCTACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:910931 original size:14 final size:14
Alignment explanation
Indices: 910912--911023 Score: 224
Period size: 14 Copynumber: 8.0 Consensus size: 14
910902 GGAAAAGTTG
910912 AGATGAATTCTAAA
1 AGATGAATTCTAAA
910926 AGATGAATTCTAAA
1 AGATGAATTCTAAA
910940 AGATGAATTCTAAA
1 AGATGAATTCTAAA
910954 AGATGAATTCTAAA
1 AGATGAATTCTAAA
910968 AGATGAATTCTAAA
1 AGATGAATTCTAAA
910982 AGATGAATTCTAAA
1 AGATGAATTCTAAA
910996 AGATGAATTCTAAA
1 AGATGAATTCTAAA
911010 AGATGAATTCTAAA
1 AGATGAATTCTAAA
911024 CTTGTGGTTA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 98 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
AGATGAATTCTAAA
Found at i:912079 original size:7 final size:7
Alignment explanation
Indices: 912067--912093 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
912057 GTGAACATTG
912067 GCTTAAA
1 GCTTAAA
912074 GCTTAAA
1 GCTTAAA
912081 GCTTAAA
1 GCTTAAA
912088 GCTTAA
1 GCTTAA
912094 TGAGGCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (7 bp):
GCTTAAA
Found at i:913146 original size:26 final size:26
Alignment explanation
Indices: 913114--913167 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
913104 ATTTAGTGTG
* *
913114 TATGGTGGGTACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTAGGTGTAT
913140 TATGGTGGGCACGACCTTAGGTGTAT
1 TATGGTGGGCACGACCTTAGGTGTAT
913166 TA
1 TA
913168 GCACTTCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.35
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTAGGTGTAT
Found at i:918023 original size:17 final size:16
Alignment explanation
Indices: 918001--918041 Score: 59
Period size: 14 Copynumber: 2.6 Consensus size: 16
917991 GGAAAAGTTG
918001 AGATGAATTCTACTAAA
1 AGATGAATTCT-CTAAA
918018 AGATGAA-T-TCTAAA
1 AGATGAATTCTCTAAA
918032 AGATGAATTC
1 AGATGAATTC
918042 ATAACTTGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 1 0.05
17 7 0.32
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (16 bp):
AGATGAATTCTCTAAA
Found at i:919463 original size:26 final size:26
Alignment explanation
Indices: 919431--919484 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
919421 ACTTAGTGTG
* * *
919431 TATGGTGGACACGACCTTATGTGTAT
1 TATGGTGGACACAAACTTATGTGCAT
*
919457 TATGGTGGGCACAAACTTATGTGCAT
1 TATGGTGGACACAAACTTATGTGCAT
919483 TA
1 TA
919485 GCACTTCGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (26 bp):
TATGGTGGACACAAACTTATGTGCAT
Found at i:926473 original size:15 final size:15
Alignment explanation
Indices: 926449--926538 Score: 83
Period size: 15 Copynumber: 5.9 Consensus size: 15
926439 AATAAAATAT
* *
926449 AAAATTCAATATCAG
1 AAAATACAATAACAG
*
926464 AAAATACAATAACATA
1 AAAATACAATAACA-G
926480 AAAATACAAT-ACTAG
1 AAAATACAATAAC-AG
* *
926495 AAGATACAATAACAT
1 AAAATACAATAACAG
* **
926510 AAAACACAATATTAG
1 AAAATACAATAACAG
926525 AAAATACAATAACA
1 AAAATACAATAACA
926539 TAATTATTAG
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
15 45 0.78
16 13 0.22
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.20
Consensus pattern (15 bp):
AAAATACAATAACAG
Found at i:926481 original size:30 final size:30
Alignment explanation
Indices: 926447--926541 Score: 129
Period size: 30 Copynumber: 3.1 Consensus size: 30
926437 GTAATAAAAT
*
926447 ATAAAATTCAATATCAGAAAATACAATAAC
1 ATAAAATACAATATCAGAAAATACAATAAC
*
926477 ATAAAAATACAATA-CTAGAAGATACAATAAC
1 AT-AAAATACAATATC-AGAAAATACAATAAC
* *
926508 ATAAAACACAATATTAGAAAATACAATAAC
1 ATAAAATACAATATCAGAAAATACAATAAC
926538 ATAA
1 ATAA
926542 TTATTAGAGG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 31 0.54
31 26 0.46
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (30 bp):
ATAAAATACAATATCAGAAAATACAATAAC
Found at i:927805 original size:42 final size:43
Alignment explanation
Indices: 927716--927810 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 43
927706 CTTTTTTACA
* * *
927716 TTTATAATTGATGACCCTAAGTTTTTCAATTTCACTTTGTACT
1 TTTATAATTGATGACCCTAAGTTTTTCAATTTCAATTTCTACC
*
927759 TTTATAATTGA-G-CTCCTATGTTTTTCAATCTT-AATTTCTACC
1 TTTATAATTGATGAC-CCTAAGTTTTTCAAT-TTCAATTTCTACC
927801 TTTATAATTG
1 TTTATAATTG
927811 GGCCCCCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 1 0.02
42 32 0.70
43 13 0.28
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51
Consensus pattern (43 bp):
TTTATAATTGATGACCCTAAGTTTTTCAATTTCAATTTCTACC
Found at i:927876 original size:15 final size:15
Alignment explanation
Indices: 927856--927887 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
927846 AAAATTAAGG
*
927856 TCCCTAATTTTTTAA
1 TCCCTAATTTTTCAA
927871 TCCCTAATTTTTCAA
1 TCCCTAATTTTTCAA
927886 TC
1 TC
927888 ATACTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (15 bp):
TCCCTAATTTTTCAA
Found at i:933062 original size:3 final size:3
Alignment explanation
Indices: 933054--933105 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
933044 CAAAAAATAT
*
933054 TTA TTA TTA TTA TATA TATA TATA TAA TTA -TA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
933100 TTA TTA
1 TTA TTA
933106 ATACTAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 29 0.66
4 11 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:933095 original size:8 final size:8
Alignment explanation
Indices: 933058--933105 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
933048 AAATATTTAT
933058 TATTATTA
1 TATTATTA
933066 TATATATATA
1 TAT-TAT-TA
*
933076 TATAATTA
1 TATTATTA
933084 TATTATTA
1 TATTATTA
933092 TATTATTA
1 TATTATTA
933100 TTATTA
1 -TATTA
933106 ATACTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 20 0.57
9 10 0.29
10 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATTATTA
Found at i:938321 original size:13 final size:13
Alignment explanation
Indices: 938305--938354 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
938295 GAACAAAGAG
938305 AAGAAAAAAAGCA
1 AAGAAAAAAAGCA
938318 AAGAAAGAAAAGAGCA
1 AAG-AA-AAAA-AGCA
938334 AAGAAAAAAA-CA
1 AAGAAAAAAAGCA
938346 CAAGAAAAA
1 -AAGAAAAA
938355 GTAAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.06
13 12 0.36
14 6 0.18
15 6 0.18
16 7 0.21
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGCA
Found at i:938328 original size:16 final size:16
Alignment explanation
Indices: 938298--938343 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
938288 CCAATCAGAA
938298 CAAAGAGAAGAAAAAAAG
1 CAAAGA-AAG-AAAAAAG
*
938316 CAAAGAAAGAAAAGAG
1 CAAAGAAAGAAAAAAG
938332 CAAAGAAA-AAAA
1 CAAAGAAAGAAAA
938344 CACAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
17 3 0.11
18 6 0.22
ACGTcount: A:0.74, C:0.07, G:0.20, T:0.00
Consensus pattern (16 bp):
CAAAGAAAGAAAAAAG
Found at i:938373 original size:25 final size:25
Alignment explanation
Indices: 938317--938373 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
938307 GAAAAAAAGC
938317 AAAGA-AAGAAAAGAGCAAAGAAAA
1 AAAGACAAGAAAAGAGCAAAGAAAA
* *
938341 AAACACAAGAAAA-AGTAAAGAAAA
1 AAAGACAAGAAAAGAGCAAAGAAAA
938365 AGAAGACAA
1 A-AAGACAA
938374 AAAGCACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.74, C:0.07, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAGACAAGAAAAGAGCAAAGAAAA
Found at i:939989 original size:66 final size:64
Alignment explanation
Indices: 939910--940130 Score: 268
Period size: 66 Copynumber: 3.4 Consensus size: 64
939900 ATTTTGCCTT
*
939910 TCTTGAGACAGTTTCTCTTGAAACATAACCATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGT
1 TCTTGAGACAGTTTCTCTTGAAACATAA-CATCTTTGAG-TCGTTTCCCTTGAAACAAATTTTGT
939975 C
64 C
* * * * *
939976 TCTTGAGACAGTTTCCCTTGCAACAT--CATCTTTAAGTTTGTTTCTCTTGAAACAAATTTTGTC
1 TCTTGAGACAGTTTCTCTTGAAACATAACATCTTTGAG-TCGTTTCCCTTGAAACAAATTTTGTC
* * *
940039 TCCCTTGAGATAGTTTCTCTTGAAACACAA-ATCTTTGAGTCTGTTTCCCTTGAAAAAAATTTGT
1 T--CTTGAGACAGTTTCTCTTGAAACATAACATCTTTGAGTC-GTTTCCCTTGAAACAAATTT-T
*
940103 CTC
62 GTC
940106 TCTTGAGACAGTTTCTCTTGAAACA
1 TCTTGAGACAGTTTCTCTTGAAACA
940131 AATCCATGGC
Statistics
Matches: 132, Mismatches: 17, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
63 33 0.25
65 45 0.34
66 50 0.38
67 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (64 bp):
TCTTGAGACAGTTTCTCTTGAAACATAACATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTC
Found at i:940111 original size:65 final size:65
Alignment explanation
Indices: 939851--940130 Score: 271
Period size: 65 Copynumber: 4.2 Consensus size: 65
939841 ATTTGAAATT
* * * ** * * *
939851 GTTTCCCTTGAAACAAAAATCTTTGAGTCTTTTTCTTTTAAAAACAAAAATTTTGCCTTTCTTGA
1 GTTTCTCTTGAAACACAAATCTTTGAGTCTGTTTCCCTT--GAA-AAAAA-TTTGTCTCTCTTGA
939916 GACA
62 GACA
* ** *
939920 GTTTCTCTTGAAACATAACCATCTTTGAGATC-GTTTCCCTTGAAACGAATTT-TGTCTCTTGAG
1 GTTTCTCTTGAAACACAA--ATCTTTGAG-TCTGTTTCCCTTGAAAAAAATTTGTCTCTCTTGAG
939983 ACA
63 ACA
* * * * * * *
939986 GTTTCCCTTGCAACATC--ATCTTTAAGTTTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACA-CAAATCTTTGAGTCTGTTTCCCTTGAAA-AAAATTTGTCTCTCTTGAGA
*
940049 TA
64 CA
940051 GTTTCTCTTGAAACACAAATCTTTGAGTCTGTTTCCCTTGAAAAAAATTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACACAAATCTTTGAGTCTGTTTCCCTTGAAAAAAATTTGTCTCTCTTGAGACA
940116 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
940131 AATCCATGGC
Statistics
Matches: 171, Mismatches: 31, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
62 1 0.01
63 20 0.12
64 5 0.03
65 58 0.34
66 46 0.27
67 3 0.02
68 3 0.02
69 18 0.11
71 15 0.09
72 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (65 bp):
GTTTCTCTTGAAACACAAATCTTTGAGTCTGTTTCCCTTGAAAAAAATTTGTCTCTCTTGAGACA
Found at i:940676 original size:3 final size:3
Alignment explanation
Indices: 940668--940701 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
940658 GGTCAACAAA
940668 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
940702 ATACTAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:943765 original size:24 final size:24
Alignment explanation
Indices: 943729--943785 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
943719 AATTAAATGT
*
943729 AATAA-TACAATCTATCCACCATG
1 AATAACTAAAATCTATCCACCATG
*
943752 AATAACTAAAATCTATCTACCATG
1 AATAACTAAAATCTATCCACCATG
943776 AATAACTAAA
1 AATAACTAAA
943786 GTAGACATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (24 bp):
AATAACTAAAATCTATCCACCATG
Found at i:944353 original size:14 final size:14
Alignment explanation
Indices: 944334--944360 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
944324 AGTTAAAGTG
944334 TTAAATAATAAAGC
1 TTAAATAATAAAGC
944348 TTAAATAATAAAG
1 TTAAATAATAAAG
944361 AGAAGGAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
TTAAATAATAAAGC
Found at i:946874 original size:23 final size:25
Alignment explanation
Indices: 946833--946884 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
946823 TCTGGCAATT
946833 TTTTGTAGTTTAATAAATACTTATA
1 TTTTGTAGTTTAATAAATACTTATA
* * *
946858 TTTTGT-G-TTAATTAATATTTATT
1 TTTTGTAGTTTAATAAATACTTATA
946881 TTTT
1 TTTT
946885 ACAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 1 0.04
25 6 0.25
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTTGTAGTTTAATAAATACTTATA
Found at i:947346 original size:56 final size:55
Alignment explanation
Indices: 947282--947428 Score: 186
Period size: 56 Copynumber: 2.6 Consensus size: 55
947272 CGCATGGCCT
* * *
947282 CAAAAAAATAGGGTACCCGAAATCGAATATATCTATCAGTTTTTGCCATTAATAAG
1 CAAAAAAATAGGGT-CCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAGAAA
* * * *
947338 CATAAAAATAGGGGTCCCAAAATTGAATATATCTATCAGTTGTTGTCATTAAGAAA
1 CAAAAAAATA-GGGTCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAGAAA
**
947394 CAAAAAAATAGGACCCCCGAAATCGAATATATCTA
1 CAAAAAAATAGG-GTCCCGAAATCGAATATATCTA
947429 GAAAATAGGG
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
55 2 0.03
56 71 0.92
57 4 0.05
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (55 bp):
CAAAAAAATAGGGTCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAGAAA
Found at i:948493 original size:30 final size:31
Alignment explanation
Indices: 948459--948518 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
948449 AAATAAGTGC
*
948459 CTAACATTTT-TCCATTATACTTTTAGGTGG
1 CTAACATTTTCTCCATTACACTTTTAGGTGG
* *
948489 CTAACGTTTTCTCCGTTACACTTTTAGGTG
1 CTAACATTTTCTCCATTACACTTTTAGGTG
948519 CTACATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (31 bp):
CTAACATTTTCTCCATTACACTTTTAGGTGG
Found at i:948574 original size:186 final size:187
Alignment explanation
Indices: 948230--948654 Score: 563
Period size: 186 Copynumber: 2.3 Consensus size: 187
948220 ATATCTTAAG
* * * * *
948230 TTAACTTTAGGTGCCTAAATAATTTTTCGTTAAAAATAGGTGTCTAACATTTTTTCCATTACCTT
1 TTAACTTTAAGTGTCTAAAGAATTTTTCATTAAAAATAGGTGTCTAACA-TTTTTCCATTAACTT
* *
948295 TTTGGGTGCCTAACATTTTTCGTTACACTTTTAGGTGTCTGCATAGTAACGGTCGTTAATTGACA
65 TTTAGGTGCCTAACATTTTTCGTTACACTTTTAGGTGTCTACATAGTAACGGTCGTTAATTGACA
* * *
948360 CGTGTTATGTTTATATTTTGGCTTAATGCAAAAGTAAGTTCCTAAATTATACCCT-AA
130 CATGTTATGTTTATATTTTGGCTTAATGCAAAAATAAGTACCTAAATTATACCCTAAA
* * *
948417 TTTACTTTAAGTGTCTAAAGAA-TTTTCATTAAAAATAAGTGCCTAACATTTTTCCATTATAC-T
1 TTAACTTTAAGTGTCTAAAGAATTTTTCATTAAAAATAGGTGTCTAACATTTTTCCATTA-ACTT
* * *
948480 TTTAGGTGGCTAACGTTTTCTCCGTTACACTTTTAGGTG-CTACATAGTAATGGTCGTT-ATGTG
65 TTTAGGTGCCTAACATTTT-T-CGTTACACTTTTAGGTGTCTACATAGTAACGGTCGTTAAT-TG
* * * * * *
948543 ACGCATGTTGTGTTTCTATTTTGGTTTAATGCAAAAATAAGTACCTAAATTATTCCTTAAA
127 ACACATGTTATGTTTATATTTTGGCTTAATGCAAAAATAAGTACCTAAATTATACCCTAAA
*
948604 TTAACATTAAGTGTCTAAAGAATTTTTCATTAAAAATAGGTGTCTAACATT
1 TTAACTTTAAGTGTCTAAAGAATTTTTCATTAAAAATAGGTGTCTAACATT
948655 CCAACGTTAA
Statistics
Matches: 206, Mismatches: 26, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
185 30 0.15
186 93 0.45
187 57 0.28
188 26 0.13
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (187 bp):
TTAACTTTAAGTGTCTAAAGAATTTTTCATTAAAAATAGGTGTCTAACATTTTTCCATTAACTTT
TTAGGTGCCTAACATTTTTCGTTACACTTTTAGGTGTCTACATAGTAACGGTCGTTAATTGACAC
ATGTTATGTTTATATTTTGGCTTAATGCAAAAATAAGTACCTAAATTATACCCTAAA
Found at i:950141 original size:30 final size:30
Alignment explanation
Indices: 950078--950142 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
950068 TTTAGGTATA
* ** * *
950078 AATTTAACTAAAATTTCATTTTGGTCCTTG
1 AATTTAACTAAAATTTCAATTTACTCATCG
*
950108 AATTTAATTAAAATTTCAATTTACTCATCG
1 AATTTAACTAAAATTTCAATTTACTCATCG
950138 AATTT
1 AATTT
950143 CTTTTTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (30 bp):
AATTTAACTAAAATTTCAATTTACTCATCG
Found at i:955842 original size:24 final size:27
Alignment explanation
Indices: 955784--955840 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 27
955774 CAAAAAAAAA
955784 AATATTCACATTTTTGTGATAAATTAAAT
1 AATATTCACATTTTTGTGATAAATT--AT
955813 AATATTCACATTTTTGTGATAAATTAT
1 AATATTCACATTTTTGTGATAAATTAT
955840 A
1 A
955841 TTTGTAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.11
29 25 0.89
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (27 bp):
AATATTCACATTTTTGTGATAAATTAT
Found at i:957818 original size:2 final size:2
Alignment explanation
Indices: 957811--957860 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
957801 AACATTTATC
957811 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
957853 AT AT AT AT
1 AT AT AT AT
957861 CATTCATACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:966755 original size:8 final size:8
Alignment explanation
Indices: 966742--966768 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
966732 ACTAATTAGT
966742 AAGAATGG
1 AAGAATGG
966750 AAGAATGG
1 AAGAATGG
966758 AAGAATGG
1 AAGAATGG
966766 AAG
1 AAG
966769 GACATTATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.37, T:0.11
Consensus pattern (8 bp):
AAGAATGG
Found at i:968314 original size:139 final size:138
Alignment explanation
Indices: 968090--968344 Score: 359
Period size: 139 Copynumber: 1.8 Consensus size: 138
968080 GTATGTAATG
* * *
968090 GTTATCGATCGATTTTGTGTAATATATAACAGTGCATTTTCATATTAGTACTATGTGTACTTTCG
1 GTTATCGATCGATTTTGTGTAATACATAACAGTGCATTTTCATATCAGTACTATATGTACTTTCG
*
968155 GAACTAAAGGTGCAACCATGGTATTCATAATGAGTTTATGAACTTACCATTTGGACATATAATTA
66 GAACTAAAGGTGCAACCATGGAATTCATAATGAGTTTATGAA-TTACCATTTGGACATATAATTA
968220 TGTATAAAA
130 TGTATAAAA
* * * *
968229 GTTATCGATCGATTTTGTTTAATACATAACGGTGCATTTTCGTATCATTACTATATGTACTTTC-
1 GTTATCGATCGATTTTGTGTAATACATAACAGTGCATTTTCATATCAGTACTATATGTACTTTCG
** ** * *
968293 GACACTATGGGTGCATTCATGGAATTCATAATGAGTTTGTGAATTTCCATTT
66 GA-ACTAAAGGTGCAACCATGGAATTCATAATGAGTTTATGAATTACCATTT
968345 CAGCACTTAG
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
138 10 0.10
139 91 0.90
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (138 bp):
GTTATCGATCGATTTTGTGTAATACATAACAGTGCATTTTCATATCAGTACTATATGTACTTTCG
GAACTAAAGGTGCAACCATGGAATTCATAATGAGTTTATGAATTACCATTTGGACATATAATTAT
GTATAAAA
Found at i:968857 original size:3 final size:3
Alignment explanation
Indices: 968849--968882 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
968839 AACGAATGTT
968849 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
968883 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:974617 original size:10 final size:10
Alignment explanation
Indices: 974602--974627 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
974592 GAGTATCAAG
974602 TAGCTCGTTT
1 TAGCTCGTTT
974612 TAGCTCGTTT
1 TAGCTCGTTT
974622 TAGCTC
1 TAGCTC
974628 AGGTCGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (10 bp):
TAGCTCGTTT
Found at i:977395 original size:14 final size:15
Alignment explanation
Indices: 977359--977396 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
977349 GAAATCATTG
977359 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
977374 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
977389 AAAAATTA
1 AAAAATTA
977397 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:977561 original size:20 final size:20
Alignment explanation
Indices: 977527--977664 Score: 127
Period size: 20 Copynumber: 6.8 Consensus size: 20
977517 ATATACCCAA
977527 AAAATTCGTGTTGCGAAAAAG
1 AAAA-TCGTGTTGCGAAAAAG
*
977548 AAAATCGAGTTGCGAAAAAG
1 AAAATCGTGTTGCGAAAAAG
*
977568 AAATTCGTGTTGCGAAAAAG
1 AAAATCGTGTTGCGAAAAAG
* * **
977588 AAATTCGTGTTGAGAATTCA-
1 AAAATCGTGTTGCGAA-AAAG
* * *
977608 AAAATCGAGTGGCGAAATTA-
1 AAAATCGTGTTGCGAAA-AAG
*
977628 AAAATCGTGTTGCGAAAAAT
1 AAAATCGTGTTGCGAAAAAG
**
977648 AACTTCGTGTTGCGAAA
1 AAAATCGTGTTGCGAAA
977665 TTGTCAAAAT
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.01
20 91 0.94
21 5 0.05
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (20 bp):
AAAATCGTGTTGCGAAAAAG
Found at i:977577 original size:40 final size:39
Alignment explanation
Indices: 977525--977685 Score: 146
Period size: 40 Copynumber: 4.0 Consensus size: 39
977515 TTATATACCC
977525 AAAAAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAA
1 AAAAAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAA
* * *
977564 AAAGAAATTCGTGTTGCGAAAAAGAAATTCGTGTTGAGAA
1 AAA-AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAA
* * * * *
977604 TTCAAAAA-TCGAGTGGCGAAATTA-AAAATCGTGTTGCGAA
1 --AAAAAATTCGTGTTGCGAAA-AAGAAAATCGAGTTGCGAA
* **
977644 AAATAACTTCGTGTTGCGAAATTGTCAAAATCGAGTTGCGAA
1 AAA-AAATTCGTGTTGCGAAAAAG--AAAATCGAGTTGCGAA
977686 TTTGACTTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
38 2 0.02
39 6 0.06
40 69 0.70
41 4 0.04
42 17 0.17
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (39 bp):
AAAAAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAA
Found at i:977592 original size:60 final size:59
Alignment explanation
Indices: 977528--977685 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 59
977518 TATACCCAAA
977528 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAA-AAGAAATTCGTGTTGCGAAAAAG
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAATAA-AAA-TCGTGTTGCGAAAAAG
* ** * *
977588 AAATTCGTGTTGAGAATTCA-AAAATCGAGTGGCGAAATTAAAAATCGTGTTGCGAAAAAT
1 AAATTCGTGTTGCGAA-AAAGAAAATCGAGTTGCGAAA-TAAAAATCGTGTTGCGAAAAAG
* **
977648 AACTTCGTGTTGCGAAATTGTCAAAATCGAGTTGCGAA
1 AAATTCGTGTTGCGAAAAAG--AAAATCGAGTTGCGAA
977686 TTTGACTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
60 60 0.74
61 4 0.05
62 17 0.21
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.25
Consensus pattern (59 bp):
AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAATAAAAATCGTGTTGCGAAAAAG
Found at i:977721 original size:21 final size:21
Alignment explanation
Indices: 977695--977747 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
977685 ATTTGACTTT
977695 TGTGTTGCGAATTCCAAATTA
1 TGTGTTGCGAATTCCAAATTA
977716 TGTGTTGCGAATTCCAAATTA
1 TGTGTTGCGAATTCCAAATTA
977737 TGTGTTGCGAA
1 TGTGTTGCGAA
977748 ATTGAAGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (21 bp):
TGTGTTGCGAATTCCAAATTA
Found at i:980097 original size:15 final size:15
Alignment explanation
Indices: 980077--980115 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
980067 AAGGGTAAGG
980077 GGAAGAGAGTGAAGA
1 GGAAGAGAGTGAAGA
980092 GGAAGAGAGTGAAGA
1 GGAAGAGAGTGAAGA
980107 GGAAGAGAG
1 GGAAGAGAG
980116 GGAATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.05
Consensus pattern (15 bp):
GGAAGAGAGTGAAGA
Found at i:980291 original size:29 final size:27
Alignment explanation
Indices: 980247--980301 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
980237 TGGAATGAAT
* *
980247 CGTTAGGTACCTAACTCGAACAAAAAAAA
1 CGTTAGGCACCAAACT-GAA-AAAAAAAA
980276 CGTTAGGCACCAAACTGAAAAAAAAA
1 CGTTAGGCACCAAACTGAAAAAAAAA
980302 GAATACGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 3 0.12
29 14 0.58
ACGTcount: A:0.51, C:0.20, G:0.15, T:0.15
Consensus pattern (27 bp):
CGTTAGGCACCAAACTGAAAAAAAAAA
Found at i:980931 original size:13 final size:14
Alignment explanation
Indices: 980903--980935 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
980893 TTAGAAACAA
980903 TTCTTTCTTGTTCT
1 TTCTTTCTTGTTCT
980917 TTCTTTCTT-TTCT
1 TTCTTTCTTGTTCT
980930 TTCTTT
1 TTCTTT
980936 TATAAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
TTCTTTCTTGTTCT
Found at i:982451 original size:44 final size:44
Alignment explanation
Indices: 982401--982799 Score: 566
Period size: 44 Copynumber: 9.1 Consensus size: 44
982391 TTATTTTTAT
* * * * *
982401 TTATGGCATCCTTTCATGCCTTACTGCATCGTTATTCATTTCAT
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
* *
982445 TTATGGCATCCTTTCATTCTTTAATGCACCATTATGCATTTCAG
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
*
982489 TTATTGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
* *
982533 TTATGGCATCCTTTCATTCCTTAATGCACCATTATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
* * * *
982577 TTATGGCATCATTTTATGCCTTAATGCATCATTATGCATATCAG
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
* * *
982621 TTATGACATCCTTTCATGCCTTACTGCACCATTATGCATTTCAT
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
* *
982665 TTATGGCATCCTTTCATGCTTTAAT-AACCATTATGCATTTCAG
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
** *
982708 TTATGGCATCCTTTCATGCCTTAATATACCATTATGCATTTCAT
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
* * *
982752 TTATAGCATCCTCTCATGCCTTAATGCACCATTATGCATTTCAA
1 TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
982796 TTAT
1 TTAT
982800 TAATTATGTT
Statistics
Matches: 315, Mismatches: 39, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
43 40 0.13
44 275 0.87
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (44 bp):
TTATGGCATCCTTTCATGCCTTAATGCACCATTATGCATTTCAG
Found at i:982589 original size:24 final size:24
Alignment explanation
Indices: 982518--982589 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
982508 CTTAATGCAC
*
982518 CATTATGCATTTCAGTTATGGCAT
1 CATTATGCATTTTAGTTATGGCAT
* *
982542 CCTT-T-CATTCCTTA---AT-GCAC
1 CATTATGCATT--TTAGTTATGGCAT
982562 CATTATGCATTTTAGTTATGGCAT
1 CATTATGCATTTTAGTTATGGCAT
982586 CATT
1 CATT
982590 TTATGCCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 16
0.62 0.09 0.29
Matches are distributed among these distances:
20 9 0.26
21 3 0.09
22 8 0.23
23 3 0.09
24 12 0.34
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (24 bp):
CATTATGCATTTTAGTTATGGCAT
Found at i:987885 original size:44 final size:44
Alignment explanation
Indices: 987822--988140 Score: 440
Period size: 44 Copynumber: 7.2 Consensus size: 44
987812 TATTTATTAT
* ** ** *
987822 TTTCATTTATGGCATCCTTTCATGCCTTGCTGCACTGTTATACA
1 TTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCATTATGCA
* *
987866 TTTCATTTATGGCATCCTTTCATGCCTTAATGCACTATTATGCA
1 TTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCATTATGCA
*
987910 TTTCAGTTATGGCATCCATTCATGCCTTAATGCACCATTATGCA
1 TTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCATTATGCA
* *
987954 TTTCAGTTATGGCATCCTTTCATGCCTTAACGCACCATTACGCA
1 TTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCATTATGCA
* * * * *
987998 TTTCGGTTATCGCATCGTTTCATTCCTTACTGCACCATTATGCA
1 TTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCATTATGCA
* * *
988042 TTTCATTTATGGCATCCTTTCATGCCTTAATGAACCATTATACA
1 TTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCATTATGCA
* *
988086 TTTCAGTTATGGCATCCTTTTAATGCCTTAATCCACCATTATGCA
1 TTTCAGTTATGGCATCC-TTTCATGCCTTAATGCACCATTATGCA
988131 TTTCAGTTAT
1 TTTCAGTTAT
988141 TAATTCGGTT
Statistics
Matches: 244, Mismatches: 30, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
44 211 0.86
45 33 0.14
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (44 bp):
TTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCATTATGCA
Found at i:992332 original size:24 final size:24
Alignment explanation
Indices: 992281--992336 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
992271 TTATTTCAAT
*
992281 TTTTTGTTTTTATTTTCAACTTTAG
1 TTTTT-TTTTTATTTTAAACTTTAG
* * *
992306 TTTTTTTTTTCTTTTAAATTTTTG
1 TTTTTTTTTTATTTTAAACTTTAG
992330 TTTTTTT
1 TTTTTTT
992337 AGGTACCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.77
Consensus pattern (24 bp):
TTTTTTTTTTATTTTAAACTTTAG
Found at i:992968 original size:20 final size:20
Alignment explanation
Indices: 992904--992968 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
992894 ATGTTGCATT
*
992904 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTG-AAA
** * **
992925 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTT-GAAA
992945 TCGCGTTGCGATAGTTGAAA
1 TCGCGTTGCGATAGTTGAAA
992965 TCGC
1 TCGC
992969 AACGCGATCT
Statistics
Matches: 31, Mismatches: 11, Indels: 5
0.66 0.23 0.11
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGATAGTTGAAA
Found at i:993017 original size:20 final size:20
Alignment explanation
Indices: 992992--993065 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
992982 CTATCGCAAA
*
992992 TTCGCGTTGAGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
993012 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
993033 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
993053 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
993066 AGTTGAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:993038 original size:21 final size:21
Alignment explanation
Indices: 993012--993085 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
993002 GATTTTCCAT
993012 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
* ** *
993033 TTCGCGTTGCGAT-TTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
993053 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
993074 TTCGCGTTGCGA
1 TTCGCGTTGCGA
993086 GCATTGCGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTTGAAA
Found at i:993083 original size:41 final size:41
Alignment explanation
Indices: 992989--993085 Score: 185
Period size: 41 Copynumber: 2.4 Consensus size: 41
992979 CCACTATCGC
*
992989 AAATTCGCGTTGAGATTTTCCATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
993030 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
993071 AAATTCGCGTTGCGA
1 AAATTCGCGTTGCGA
993086 GCATTGCGAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
AAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
Found at i:993135 original size:22 final size:22
Alignment explanation
Indices: 993107--993178 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
993097 TTCCATTTCG
*
993107 CGTTGCGATAGTCTGCAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
993129 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
993148 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
993170 CGTTGCGAT
1 CGTTGCGAT
993179 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:993152 original size:19 final size:19
Alignment explanation
Indices: 993128--993193 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
993118 TCTGCAGTTG
993128 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
993147 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
993168 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
993188 TCGTTG
1 TCGTTG
993194 AAAAAAAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:993160 original size:41 final size:41
Alignment explanation
Indices: 993089--993193 Score: 167
Period size: 41 Copynumber: 2.5 Consensus size: 41
993079 GTTGCGAGCA
* *
993089 TTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTGCAGTTGTCG
1 TTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGTCG
993131 TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCG
1 TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCG
993172 TTGCGATTTTCCAAATTCGTTG
1 TTGCGATTTTCCAAATTCGTTG
993194 AAAAAAAAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
41 45 0.75
42 12 0.20
43 3 0.05
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (41 bp):
TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCG
Found at i:993281 original size:6 final size:6
Alignment explanation
Indices: 993270--993349 Score: 160
Period size: 6 Copynumber: 13.3 Consensus size: 6
993260 ACACGTATTT
993270 CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA
1 CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA
993318 CCACGA CCACGA CCACGA CCACGA CCACGA CC
1 CCACGA CCACGA CCACGA CCACGA CCACGA CC
993350 CGAGACGAGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
CCACGA
Found at i:993863 original size:6 final size:6
Alignment explanation
Indices: 993852--993883 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
993842 TCGTCTCGTC
993852 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
993884 ATACGTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:993959 original size:20 final size:20
Alignment explanation
Indices: 993934--993982 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
993924 AGAGAAAATT
993934 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
993954 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
993974 ATCGCAACG
1 ATCGCAACG
993983 ACACTGTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:994007 original size:20 final size:21
Alignment explanation
Indices: 993974--994023 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
993964 GAAATGGAAA
*
993974 ATCGCAACGACACTGTACACT
1 ATCGCAACGACACTATACACT
*
993995 ATCGCAA-GACACTATAGACT
1 ATCGCAACGACACTATACACT
994015 ATCGCAACG
1 ATCGCAACG
994024 CGAAAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (21 bp):
ATCGCAACGACACTATACACT
Found at i:994177 original size:19 final size:19
Alignment explanation
Indices: 994153--994218 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
994143 TTAACTATCA
994153 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
994172 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
994194 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
994213 CAACGA
1 CAACGA
994219 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:994195 original size:22 final size:22
Alignment explanation
Indices: 994168--994239 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
994158 AATTTGGAAA
994168 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
994190 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
994209 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
994231 ATCGCAACG
1 ATCGCAACG
994240 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:994203 original size:41 final size:41
Alignment explanation
Indices: 994162--994382 Score: 231
Period size: 41 Copynumber: 5.4 Consensus size: 41
994152 ACAACGAATT
*
994162 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA-CGAATT
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACCGAA-A
994203 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAAC-CGAAA
* * *
994245 TGGAAAATCGCAAC-ACGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAAC-CGAAA
* * *
994286 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAAC-CGAAA
* * *
994327 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAAC-CGAAA
994368 TGGAAAATCGCAACG
1 TGGAAAATCGCAACG
994383 CGATTTTCAA
Statistics
Matches: 172, Mismatches: 4, Indels: 8
0.93 0.02 0.04
Matches are distributed among these distances:
41 153 0.89
42 15 0.09
43 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAACCGAAA
Found at i:994256 original size:20 final size:20
Alignment explanation
Indices: 994231--994385 Score: 139
Period size: 20 Copynumber: 7.6 Consensus size: 20
994221 ACTGTAGACT
994231 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
994251 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
994272 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
994292 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
994313 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
994333 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
994354 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
994374 ATCGCAACGCGA
1 ATCGCAACGCGA
994386 TTTTCAACTA
Statistics
Matches: 100, Mismatches: 32, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
20 56 0.56
21 44 0.44
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:994277 original size:21 final size:21
Alignment explanation
Indices: 994251--994406 Score: 147
Period size: 21 Copynumber: 7.6 Consensus size: 21
994241 GAAATGGAAA
*
994251 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
994272 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
994292 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
994313 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
994333 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
994354 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
994374 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
994395 ATCGCAACGCGA
1 ATCGCAACGCGA
994407 AATGCAACGC
Statistics
Matches: 101, Mismatches: 31, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
20 45 0.45
21 56 0.55
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:994317 original size:123 final size:122
Alignment explanation
Indices: 994187--994410 Score: 353
Period size: 123 Copynumber: 1.8 Consensus size: 122
994177 ACAACTGTAG
*
994187 ACTATCGCAA-CGAATTTGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAATGGAA
1 ACTATCGCAACCGAA-ATGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAATGGAA
994250 AATCGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
63 AATCGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * *
994310 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAAC-CGAAATGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAATGGAAAA
*
994375 TCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
65 TCGCAACACGATTTTCAACTATCGCAACGCGAAATG
994411 CAACGCGAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
123 73 0.78
124 16 0.17
125 4 0.04
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (122 bp):
ACTATCGCAACCGAAATGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAATGGAAAAT
CGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:994427 original size:41 final size:41
Alignment explanation
Indices: 994228--994410 Score: 357
Period size: 41 Copynumber: 4.5 Consensus size: 41
994218 ACAACTGTAG
*
994228 ACTATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
994269 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
994310 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
994351 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
994392 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
994411 CAACGCGAAT
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 141 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:997739 original size:20 final size:20
Alignment explanation
Indices: 997710--997751 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
997700 TTCTCTCTTT
997710 TCGTTCTTTTCTATTTTCTC
1 TCGTTCTTTTCTATTTTCTC
* *
997730 TCGTTGTTTTCTGTTTTCTC
1 TCGTTCTTTTCTATTTTCTC
997750 TC
1 TC
997752 CTTTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.24, G:0.10, T:0.64
Consensus pattern (20 bp):
TCGTTCTTTTCTATTTTCTC
Found at i:997759 original size:20 final size:20
Alignment explanation
Indices: 997716--997758 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
997706 CTTTTCGTTC
*
997716 TTTTCTATTTTCTCTCGTTG
1 TTTTCTATTTTCTCTCCTTG
*
997736 TTTTCTGTTTTCTCTCCTT-
1 TTTTCTATTTTCTCTCCTTG
997755 TTTT
1 TTTT
997759 TAAAAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.02, C:0.21, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTTCTATTTTCTCTCCTTG
Found at i:998326 original size:3 final size:3
Alignment explanation
Indices: 998318--998345 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
998308 AACGTAATTT
998318 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
998346 ATAAAAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:998668 original size:47 final size:46
Alignment explanation
Indices: 998550--998669 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 46
998540 CATCTTTAGG
* * *
998550 AAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGTTGGTTATCT
1 AAGGGTGATGACACGGTTCCTACGTGATGAGGACGGTTGGTCATCT
* * *
998596 AA-GG-G-TGACATGGCTCCTACGTGATGAGGA-GGTCTGGTCGTCT
1 AAGGGTGATGACACGGTTCCTACGTGATGAGGACGGT-TGGTCATCT
*
998639 AAGGGTAGATGACACGGTTCATACGTGATGA
1 AAGGGT-GATGACACGGTTCCTACGTGATGA
998670 AGAATTCTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 3 0.05
43 30 0.50
44 3 0.05
45 2 0.03
46 3 0.05
47 19 0.32
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27
Consensus pattern (46 bp):
AAGGGTGATGACACGGTTCCTACGTGATGAGGACGGTTGGTCATCT
Found at i:998716 original size:51 final size:46
Alignment explanation
Indices: 998519--998720 Score: 133
Period size: 51 Copynumber: 4.2 Consensus size: 46
998509 ACACTGCTCA
*
998519 TACGCGATGAAGAAGTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
1 TACGTGATGAAGAAGTCTGGCCATC--T---AAGGGTGATAACTCGGTTCC
* * ** * *
998570 TACGTGATGAGGACGGT-TGGTTATCTAAGGGTGA-CA-T-GGCTCC
1 TACGTGATGAAGA-AGTCTGGCCATCTAAGGGTGATAACTCGGTTCC
* * * * * * *
998613 TACGTGATGAGGAGGTCTGGTCGTCTAAGGGTAGATGACACGGTTCA
1 TACGTGATGAAGAAGTCTGGCCATCTAAGGGT-GATAACTCGGTTCC
*
998660 TACGTGATGAAGAATTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
1 TACGTGATGAAGAAGTCTGGCCATC--T---AAGGGTGATAACTCGGTTCC
998711 TACGTGATGA
1 TACGTGATGA
998721 GGACGCCTGG
Statistics
Matches: 119, Mismatches: 21, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
42 3 0.03
43 31 0.26
44 3 0.03
45 2 0.02
46 8 0.07
47 24 0.20
49 2 0.02
51 38 0.32
52 8 0.07
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (46 bp):
TACGTGATGAAGAAGTCTGGCCATCTAAGGGTGATAACTCGGTTCC
Found at i:998759 original size:141 final size:140
Alignment explanation
Indices: 998505--998775 Score: 400
Period size: 141 Copynumber: 1.9 Consensus size: 140
998495 TGTTGTTGGG
*
998505 GATGACACTGCTCATACGCGATGAAGAAGTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
1 GATGACACGGCTCATACGCGATGAAGAAGTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
** * * *
998570 TACGTGATGAGGACGGTTGGTTATCTAAGGGTGACATGGCTCCTACGTGATGAGGAGGTCTGGTC
66 TACGTGATGAGGACGCCTGGTTATCTAAGGGTAACAT-GCTCCTACGTGACGAGGAGATCTGGTC
998635 GTCTAAGGGTA
130 GTCTAAGGGTA
* * *
998646 GATGACACGGTTCATACGTGATGAAGAATTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
1 GATGACACGGCTCATACGCGATGAAGAAGTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
* * *
998711 TACGTGATGAGGACGCCTGGTTATCCTAATGTTAACACT-CTCCTACGTGCCGAGGAGATCTGGT
66 TACGTGATGAGGACGCCTGGTTAT-CTAAGGGTAACA-TGCTCCTACGTGACGAGGAGATCTGGT
998775 C
129 C
998776 AGTTGATGTT
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
141 106 0.91
142 9 0.08
143 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.27
Consensus pattern (140 bp):
GATGACACGGCTCATACGCGATGAAGAAGTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
TACGTGATGAGGACGCCTGGTTATCTAAGGGTAACATGCTCCTACGTGACGAGGAGATCTGGTCG
TCTAAGGGTA
Found at i:999833 original size:18 final size:17
Alignment explanation
Indices: 999807--999875 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
999797 TTTCTTTCTT
999807 TTTTCTCTCATTTTTCTCA
1 TTTT-TCTCATTTTT-TCA
*
999826 TTTTTCTCATTTTTTAA
1 TTTTTCTCATTTTTTCA
* *
999843 TTTTT-TAATTTTTTTCC
1 TTTTTCTCA-TTTTTTCA
*
999860 TTTTTCTCTTTTTTTC
1 TTTTTCTCATTTTTTC
999876 TTCTTCAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.05
17 25 0.60
18 11 0.26
19 4 0.10
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTCTCATTTTTTCA
Found at i:999840 original size:11 final size:9
Alignment explanation
Indices: 999807--999872 Score: 66
Period size: 9 Copynumber: 7.6 Consensus size: 9
999797 TTTCTTTCTT
999807 TTTTCTCTCA
1 TTTT-TCTCA
999817 TTTTTCTCA
1 TTTTTCTCA
999826 TTTTTCTCA
1 TTTTTCTCA
*
999835 TTTTT-TAA
1 TTTTTCTCA
*
999843 TTTTT-TAA
1 TTTTTCTCA
* *
999851 TTTTTTTCC
1 TTTTTCTCA
999860 TTTTTCTC-
1 TTTTTCTCA
999868 TTTTT
1 TTTTT
999873 TTCTTCTTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
8 20 0.39
9 27 0.53
10 4 0.08
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCTCA
Found at i:1003870 original size:32 final size:32
Alignment explanation
Indices: 1003829--1003895 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1003819 TGCGTTCTGT
1003829 CCCATCAAATGCCCTTACAATATTGCCATAAA
1 CCCATCAAATGCCCTTACAATATTGCCATAAA
1003861 CCCATCAAATGCCCTTACAATATTGCCATAAA
1 CCCATCAAATGCCCTTACAATATTGCCATAAA
1003893 CCC
1 CCC
1003896 TTACTTCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.36, C:0.34, G:0.06, T:0.24
Consensus pattern (32 bp):
CCCATCAAATGCCCTTACAATATTGCCATAAA
Found at i:1007831 original size:207 final size:207
Alignment explanation
Indices: 1007476--1007891 Score: 726
Period size: 207 Copynumber: 2.0 Consensus size: 207
1007466 TGCTGTGGCG
1007476 CCTTACTTGAACCAAGTCTCTTTCTCACTTACTGCACCCTTTGATAATACTTTTTTAGGTCTTCT
1 CCTTACTTGAACCAAGTCTCTTTCTCACTTACTGCACCCTTTGATAATACTTTTTTAGGTCTTCT
* *
1007541 AAATCAACTTCCATCTCCTCTTTCCATTCCCCCATCATTATAAACTGTCTGGCATGAAATTCAGC
66 AAATCAACTTCCACCTCCTCTTTCCATTCCCCCATCATTATAAACAGTCTGGCATGAAATTCAGC
* * *
1007606 CTTGATAGTTAACATGAAGTTTTCTCTCTCCATCTCTTCTATTTTCTTGGAATCTTTAGCCTTTT
131 CTCGATAGTTAACATGAAGTTTTCTATCTCCATCTCATCTATTTTCTTGGAATCTTTAGCCTTTT
*
1007671 CGATCTCAAACT
196 AGATCTCAAACT
*
1007683 CCTTACTTGAACCAAGTCTCTTTCTCACTTACTGCACCCTTTGATAATCCTTTTTTAGGTCTTCT
1 CCTTACTTGAACCAAGTCTCTTTCTCACTTACTGCACCCTTTGATAATACTTTTTTAGGTCTTCT
* * *
1007748 AAATTAGCTTTCACCTCCTCTTTCCA-TCCCCTCATCATTATAAACAGTCTGGCATGAAATTCAG
66 AAATCAACTTCCACCTCCTCTTTCCATTCCCC-CATCATTATAAACAGTCTGGCATGAAATTCAG
1007812 CCTCGATAGTTAACATGAAGTTTTCTATCTCCATCTCATCTATTTTCTTGGAATCTTTAGCCTTT
130 CCTCGATAGTTAACATGAAGTTTTCTATCTCCATCTCATCTATTTTCTTGGAATCTTTAGCCTTT
1007877 TAGATCTCAAACT
195 TAGATCTCAAACT
1007890 CC
1 CC
1007892 ATTCTTTGGA
Statistics
Matches: 198, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
206 5 0.03
207 193 0.97
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (207 bp):
CCTTACTTGAACCAAGTCTCTTTCTCACTTACTGCACCCTTTGATAATACTTTTTTAGGTCTTCT
AAATCAACTTCCACCTCCTCTTTCCATTCCCCCATCATTATAAACAGTCTGGCATGAAATTCAGC
CTCGATAGTTAACATGAAGTTTTCTATCTCCATCTCATCTATTTTCTTGGAATCTTTAGCCTTTT
AGATCTCAAACT
Found at i:1010974 original size:18 final size:18
Alignment explanation
Indices: 1010940--1010988 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1010930 AATTGAAATT
*
1010940 TATTAAACA-ATAGTAGAC
1 TATTAATCATATA-TAGAC
1010958 TATTAATCATATATAGAC
1 TATTAATCATATATAGAC
*
1010976 -ATTTAT-ATATATA
1 TATTAATCATATATA
1010989 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 5 0.18
18 13 0.46
19 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (18 bp):
TATTAATCATATATAGAC
Found at i:1011964 original size:20 final size:20
Alignment explanation
Indices: 1011915--1011965 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1011905 TTCTCTCTTT
*
1011915 TCCTTCTTTTCTATTTTCTC
1 TCCTTCTTTTATATTTTCTC
* *
1011935 TCGTTGTTTTATATTTTCTC
1 TCCTTCTTTTATATTTTCTC
*
1011955 TCCTTTTTTTA
1 TCCTTCTTTTA
1011966 AAAAACCCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.08, C:0.22, G:0.04, T:0.67
Consensus pattern (20 bp):
TCCTTCTTTTATATTTTCTC
Found at i:1012526 original size:3 final size:3
Alignment explanation
Indices: 1012518--1012561 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1012508 AAAAAATGTA
1012518 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1012562 ATAAAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1016884 original size:25 final size:25
Alignment explanation
Indices: 1016834--1016941 Score: 135
Period size: 25 Copynumber: 4.2 Consensus size: 25
1016824 AAGTTTGCTA
* **
1016834 AAAATGAAAGGAAAATAAAACGAAAT
1 AAAATGAAA-TAAAATAAAATAAAAT
*
1016860 AAAATGAAATGAAATAAAATAAAAT
1 AAAATGAAATAAAATAAAATAAAAT
*
1016885 AAAAAGAAATAAAATAAAATAAAAT
1 AAAATGAAATAAAATAAAATAAAAT
*
1016910 AAAAAGAAATAAAATAAAAATAAAAT
1 AAAATGAAATAAAAT-AAAATAAAAT
*
1016936 GAAATG
1 AAAATG
1016942 GGTTTCCTCC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
25 50 0.68
26 23 0.32
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (25 bp):
AAAATGAAATAAAATAAAATAAAAT
Found at i:1016941 original size:5 final size:5
Alignment explanation
Indices: 1016845--1016940 Score: 106
Period size: 5 Copynumber: 19.0 Consensus size: 5
1016835 AAATGAAAGG
* * * *
1016845 AAAAT AAAAC GAAAT AAAAT GAAAT GAAAT AAAAT AAAAT AAAA- AGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
*
1016895 AAAAT AAAAT AAAAT AAAA- AGAAAT AAAAT AAAAAT AAAAT GAAAT
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT -AAAAT AAAAT AAAAT
1016941 GGGTTTCCTC
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
4 2 0.03
5 70 0.89
6 7 0.09
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1019458 original size:30 final size:30
Alignment explanation
Indices: 1019424--1019502 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
1019414 TACAGTGTTA
* * *
1019424 TAGTGTGTAAGGACATTTAGTATAACACTG
1 TAGTGTGTAAGGACACTCAGTACAACACTG
* *
1019454 TAGTGTGTAACGACACTCAGTGCAACACTG
1 TAGTGTGTAAGGACACTCAGTACAACACTG
*
1019484 TAGTGTGTAAGGAAACTCA
1 TAGTGTGTAAGGACACTCA
1019503 ATGTATATGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (30 bp):
TAGTGTGTAAGGACACTCAGTACAACACTG
Found at i:1019997 original size:18 final size:20
Alignment explanation
Indices: 1019974--1020020 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
1019964 TTATTATAAT
1019974 TAGTATTAAATAAAT-TTA-
1 TAGTATTAAATAAATATTAC
1019992 TAGTA-TAAATAAATATTAC
1 TAGTATTAAATAAATATTAC
1020011 TA-TATTAAAT
1 TAGTATTAAAT
1020021 TATATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.35
18 10 0.38
19 7 0.27
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (20 bp):
TAGTATTAAATAAATATTAC
Found at i:1024444 original size:20 final size:20
Alignment explanation
Indices: 1024405--1024444 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1024395 TAATATGATG
* *
1024405 GAAATTAATGTTTGAGTGTT
1 GAAATTAATGTTAGAATGTT
*
1024425 GAAATTGATGTTAGAATGTT
1 GAAATTAATGTTAGAATGTT
1024445 AAGTTGGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:1025925 original size:30 final size:30
Alignment explanation
Indices: 1025891--1025950 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1025881 AGTGCATATG
* * *
1025891 GTACTACGGTGTGTAAGGATACTTTGTACA
1 GTACTACAGTGTGTAAGGACACTTAGTACA
*
1025921 GTACTATAGTGTGTAAGGACACTTAGTACA
1 GTACTACAGTGTGTAAGGACACTTAGTACA
1025951 ACACTGTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (30 bp):
GTACTACAGTGTGTAAGGACACTTAGTACA
Found at i:1025966 original size:30 final size:30
Alignment explanation
Indices: 1025927--1026068 Score: 187
Period size: 30 Copynumber: 4.7 Consensus size: 30
1025917 TACAGTACTA
* * *
1025927 TAGTGTGTAAGGACACTTAGTACAACACTG
1 TAGTCTGTAAGGACACTCAGTGCAACACTG
*
1025957 TAGTCTGTAAGGACACACAGTGCAACACTG
1 TAGTCTGTAAGGACACTCAGTGCAACACTG
*
1025987 TAGTCTGTAAGGACACACAGTGCAACACTG
1 TAGTCTGTAAGGACACTCAGTGCAACACTG
* *
1026017 TAGTCTGTAAGGACA-TAGAGTGCAACACTT
1 TAGTCTGTAAGGACACT-CAGTGCAACACTG
* *
1026047 TGGTGTGTAAGGACACTCAGTG
1 TAGTCTGTAAGGACACTCAGTG
1026069 TATATGGTAA
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
30 99 0.99
31 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (30 bp):
TAGTCTGTAAGGACACTCAGTGCAACACTG
Found at i:1026068 original size:60 final size:60
Alignment explanation
Indices: 1025927--1026068 Score: 212
Period size: 60 Copynumber: 2.4 Consensus size: 60
1025917 TACAGTACTA
* *
1025927 TAGTGTGTAAGGACACTTAGTACAACACTGTAGTCTGTAAGGACACACAGTGCAACACTG
1 TAGTGTGTAAGGACACTCAGTGCAACACTGTAGTCTGTAAGGACACACAGTGCAACACTG
* * * * *
1025987 TAGTCTGTAAGGACACACAGTGCAACACTGTAGTCTGTAAGGACATAGAGTGCAACACTT
1 TAGTGTGTAAGGACACTCAGTGCAACACTGTAGTCTGTAAGGACACACAGTGCAACACTG
*
1026047 TGGTGTGTAAGGACACTCAGTG
1 TAGTGTGTAAGGACACTCAGTG
1026069 TATATGGTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (60 bp):
TAGTGTGTAAGGACACTCAGTGCAACACTGTAGTCTGTAAGGACACACAGTGCAACACTG
Found at i:1029935 original size:45 final size:45
Alignment explanation
Indices: 1029866--1030188 Score: 409
Period size: 45 Copynumber: 7.2 Consensus size: 45
1029856 AATACACCAT
* * * * *
1029866 TATGCACTTTAAATTATAGCATACTCTTATGTTGATAATGCACCCA
1 TATGCA-TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
*
1029912 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGTACCCA
1 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* **
1029957 TATACATTTCAACTATAGTATACTTTTCTGTTGATAATATACCCA
1 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* ** * *
1030002 TATACATTTCAACTATAACATA-TTTATATGTTCATAATGCACCCA
1 TATGCATTTCAACTATAGTATACTTT-TCTGTTGATAATGCACCCA
* *
1030047 TATGCATTTCAACTATA-TCATACTCTTCTCTTGATAATGCACCCA
1 TATGCATTTCAACTATAGT-ATACTTTTCTGTTGATAATGCACCCA
* * *
1030092 TATGCATTTCAACTATAGTATAATTTTCTGTTGATAATGTACCTA
1 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* *
1030137 TATACATTTCAACAATAGTATACTTTT-TGTTGATAATGCACCCA
1 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
1030181 TATGCATT
1 TATGCATT
1030189 ATTATTTTCA
Statistics
Matches: 242, Mismatches: 31, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
44 25 0.10
45 208 0.86
46 9 0.04
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (45 bp):
TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
Found at i:1030140 original size:135 final size:135
Alignment explanation
Indices: 1029885--1030188 Score: 461
Period size: 135 Copynumber: 2.3 Consensus size: 135
1029875 TAAATTATAG
* * *
1029885 CATACTCTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGATAAT
1 CATACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTCTTCTCTTGATAAT
* *
1029950 GTACCCATATACATTTCAACTATAGTATACTTTTCTGTTGATAATATACCCATATACATTTCAAC
66 GCACCCATATACATTTCAACTATAGTATAATTTTCTGTTGATAATATACCCATATACATTTCAAC
*
1030015 TATAA
131 AATAA
*
1030020 CATA-TTTATATGTTCATAATGCACCCATATGCATTTCAACTATA-TCATACTCTTCTCTTGATA
1 CATACTTT-TATGTTGATAATGCACCCATATGCATTTCAACTATAGT-ATACTCTTCTCTTGATA
* * *
1030083 ATGCACCCATATGCATTTCAACTATAGTATAATTTTCTGTTGATAATGTACCTATATACATTTCA
64 ATGCACCCATATACATTTCAACTATAGTATAATTTTCTGTTGATAATATACCCATATACATTTCA
*
1030148 ACAATAG
129 ACAATAA
*
1030155 TATACTTTT-TGTTGATAATGCACCCATATGCATT
1 CATACTTTTATGTTGATAATGCACCCATATGCATT
1030189 ATTATTTTCA
Statistics
Matches: 153, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
134 27 0.18
135 123 0.80
136 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (135 bp):
CATACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTCTTCTCTTGATAAT
GCACCCATATACATTTCAACTATAGTATAATTTTCTGTTGATAATATACCCATATACATTTCAAC
AATAA
Found at i:1030738 original size:22 final size:19
Alignment explanation
Indices: 1030710--1030764 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
1030700 TACCCCATTC
1030710 TATGGTATCGATACTACTATA
1 TATGGTATCGATAC--CTATA
* *
1030731 TTATGGTACCGATACCTCTA
1 -TATGGTATCGATACCTATA
1030751 TATGGTATCGATAC
1 TATGGTATCGATAC
1030765 AAAAATTAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
22 13 0.43
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (19 bp):
TATGGTATCGATACCTATA
Done.