Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 31
Found at i:138227 original size:84 final size:83
Alignment explanation
Indices: 138024--138551 Score: 499
Period size: 84 Copynumber: 6.3 Consensus size: 83
138014 TGAAGAAACT
* * * * *
138024 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACA
* * * **
138089 CTCATCTTCGAGGGCATGTC
65 CTCAGC-TCCAAGGCACATC
* * * * * * *
138109 ATTTGAAGTATAACTTAAGTCGAGAAGGGTTATCTTCAAACCAAAGACCTTCGAGTTCAACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC-AACCAAAGACCTTCGAGTTCGACTACA
138174 CTCAGCTCCAAGGCACATC
65 CTCAGCTCCAAGGCACATC
* *
138193 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGATCC-CCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCAACCAAAGA-CCTTCGAGTTCGACTACA
* * *
138254 CTCAGCTTCGAGGACATATC
65 CTCAGCTCCAAGG-CACATC
* * * * * * * *
138274 ATTCGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACA
* *
138338 CTCAGCGTCGAGGGCACATC
65 CTCAGC-TCCAAGGCACATC
** * * **
138358 ATTTGCAATATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACA
138423 CTCAGCTCCAAGGCACATC
65 CTCAGCTCCAAGGCACATC
* * *
138442 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCAAACCAAAGACCTTTGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC-AACCAAAGACCTTCGAGTTCGACTACA
* ***
138507 CTCAGCTCGGAGAAAAACATC
65 CTCAGCTC-CA-AGGCACATC
* *
138528 ATTTACAGCATAGCTCAAGTCGAG
1 ATTTGCAGCATAGCTTAAGTCGAG
138552 GTTTTTCAAG
Statistics
Matches: 362, Mismatches: 69, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
80 29 0.08
81 37 0.10
83 3 0.01
84 176 0.49
85 90 0.25
86 27 0.07
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (83 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCAACCAAAGACCTTCGAGTTCGACTACAC
TCAGCTCCAAGGCACATC
Found at i:140289 original size:22 final size:21
Alignment explanation
Indices: 140250--140295 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
140240 ATGTTTTTGA
*
140250 TTATTTCATTTATTTTTTATT
1 TTATTTCATTTATATTTTATT
* *
140271 TTATTCTCATTTGTATTTTTTT
1 TTATT-TCATTTATATTTTATT
140293 TTA
1 TTA
140296 AAACCAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (21 bp):
TTATTTCATTTATATTTTATT
Found at i:142205 original size:18 final size:19
Alignment explanation
Indices: 142182--142224 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
142172 CAGTAATCCT
142182 ATTCC-CTGGTAATCTTAC
1 ATTCCTCTGGTAATCTTAC
142200 ATTCCCTCTGGTAATCTTAC
1 ATT-CCTCTGGTAATCTTAC
142220 ATTCC
1 ATTCC
142225 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCTCTGGTAATCTTAC
Found at i:142212 original size:20 final size:20
Alignment explanation
Indices: 142187--142224 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
142177 ATCCTATTCC
142187 CTGGTAATCTTACATTCCCT
1 CTGGTAATCTTACATTCCCT
142207 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
142225 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCT
Found at i:143825 original size:3 final size:3
Alignment explanation
Indices: 143811--143847 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
143801 TTTAAGATAT
143811 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
143848 TTGTTGAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:143996 original size:43 final size:43
Alignment explanation
Indices: 143935--144030 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 43
143925 AATGCGTTTA
143935 TGTTCGTTTATTTATTAAACGAACAAACATGAAAAAGATTTTG
1 TGTTCGTTTATTTATTAAACGAACAAACATGAAAAAGATTTTG
* * * * *
143978 TGTTCATTTATTTATTAAACGAACGAACCTGAACAATATTTTG
1 TGTTCGTTTATTTATTAAACGAACAAACATGAAAAAGATTTTG
144021 TGTTCGTTTA
1 TGTTCGTTTA
144031 ATTAAATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (43 bp):
TGTTCGTTTATTTATTAAACGAACAAACATGAAAAAGATTTTG
Found at i:144044 original size:40 final size:41
Alignment explanation
Indices: 143947--144045 Score: 119
Period size: 43 Copynumber: 2.4 Consensus size: 41
143937 TTCGTTTATT
*
143947 TATTAAACGAACAAACATGAAAAAGATTTTGTGTTCATTTA
1 TATTAAACGAACGAACATGAAAAAGATTTTGTGTTCATTTA
* * * *
143988 TTTATTAAACGAACGAACCTGAACAATATTTTGTGTTCGTTTA
1 --TATTAAACGAACGAACATGAAAAAGATTTTGTGTTCATTTA
*
144031 -ATTAAATGAACGAAC
1 TATTAAACGAACGAAC
144046 TTAAACAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 14 0.28
43 36 0.72
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (41 bp):
TATTAAACGAACGAACATGAAAAAGATTTTGTGTTCATTTA
Found at i:144121 original size:14 final size:14
Alignment explanation
Indices: 144102--144141 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
144092 AATATGTTAG
144102 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
*
144116 TTTATGTTCGTTCG
1 TTTATGTTCGTTCA
*
144130 TTTATATTCGTT
1 TTTATGTTCGTT
144142 TATGATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.60
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:151245 original size:17 final size:17
Alignment explanation
Indices: 151195--151254 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
151185 ATAAAGTTGG
*
151195 TTCATTAATTAAACTAG
1 TTCATTAATTAAACTAA
* *
151212 TTCATTCATCAAACTAA
1 TTCATTAATTAAACTAA
* *
151229 TTCATTTATTAGACTAA
1 TTCATTAATTAAACTAA
*
151246 CTC-TTAATT
1 TTCATTAATT
151255 GTTTCATGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 5 0.14
17 30 0.86
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (17 bp):
TTCATTAATTAAACTAA
Found at i:152763 original size:8 final size:8
Alignment explanation
Indices: 152727--152762 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
152717 AGTAAAAAAC
152727 AAAAATCA
1 AAAAATCA
152735 AAAAATCA
1 AAAAATCA
152743 AAAAATCA
1 AAAAATCA
152751 AAAAAT-A
1 AAAAATCA
152758 AAAAA
1 AAAAA
152763 AAAAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATCA
Found at i:154463 original size:15 final size:15
Alignment explanation
Indices: 154443--154473 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
154433 TCATTTTCAT
*
154443 TTTCATTTTGTTTTA
1 TTTCATTTTATTTTA
154458 TTTCATTTTATTTTA
1 TTTCATTTTATTTTA
154473 T
1 T
154474 CTTTGCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTCATTTTATTTTA
Found at i:154775 original size:33 final size:33
Alignment explanation
Indices: 154735--154802 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
154725 GAATGATCGT
154735 AATTTAAATATATTTTTGAGTTTGTAATTTCCC
1 AATTTAAATATATTTTTGAGTTTGTAATTTCCC
*
154768 AATTTAAATATATTTTTGAGTTTGTAATTTTCC
1 AATTTAAATATATTTTTGAGTTTGTAATTTCCC
154801 AA
1 AA
154803 CATTTAAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.51
Consensus pattern (33 bp):
AATTTAAATATATTTTTGAGTTTGTAATTTCCC
Found at i:155644 original size:18 final size:16
Alignment explanation
Indices: 155612--155642 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
155602 AATATTGAAA
155612 CTTGAACTCAAAAAAG
1 CTTGAACTCAAAAAAG
155628 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
155643 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:155714 original size:14 final size:14
Alignment explanation
Indices: 155695--155722 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
155685 AAGGGAAAGA
155695 ATAGTTATATAATT
1 ATAGTTATATAATT
155709 ATAGTTATATAATT
1 ATAGTTATATAATT
155723 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:157013 original size:137 final size:138
Alignment explanation
Indices: 156802--157137 Score: 491
Period size: 137 Copynumber: 2.4 Consensus size: 138
156792 TATTTGATTC
* * *
156802 ATTTAGTCCTTTAATTTAGGAAAATTCTTAATTTGGTC-TTCGTTTTTGCTCGAGGTTCCATTTT
1 ATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTAGTCATT-GTTTTTGCTCGAGGTTCCATTTA
* * * *
156866 AATTATTCGATTCAATAACTGATTAAAATTAATTAGTATTAAT-ATTAGGGCCTTCACTTTAGAC
65 AATTATTCGATTCAATAACTGACTAAAATGAACTAG-ATTAATAATTAGAGCCTTCACTTTAGAC
156930 TTAATTT-AA
129 TTAATTTCAA
* *
156939 ATTTAGTCCTTTAATTTAGGAGAATTTTTAATTTAGTCATTGCTTTTGCTCGAGGTTCCATTTAA
1 ATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTAGTCATTGTTTTTGCTCGAGGTTCCATTTAA
* * *
157004 ATTATTCGATTCAATAATTGACTAAAATGAACTAGGTTAATAATTAGAGCCTTCACTTTAGGCTT
66 ATTATTCGATTCAATAACTGACTAAAATGAACTAGATTAATAATTAGAGCCTTCACTTTAGACTT
*
157069 AATTTCAT
131 AATTTCAA
*
157077 ATTTAGTCCTTTAATTTAGGAGAATTCTTAA-TTAGTTCATCGTTTTTGCTCGAGGTTCCAT
1 ATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTAG-TCATTGTTTTTGCTCGAGGTTCCAT
157138 AATCGATTGC
Statistics
Matches: 179, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
136 5 0.03
137 118 0.66
138 56 0.31
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (138 bp):
ATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTAGTCATTGTTTTTGCTCGAGGTTCCATTTAA
ATTATTCGATTCAATAACTGACTAAAATGAACTAGATTAATAATTAGAGCCTTCACTTTAGACTT
AATTTCAA
Found at i:159947 original size:17 final size:17
Alignment explanation
Indices: 159925--159978 Score: 90
Period size: 17 Copynumber: 3.2 Consensus size: 17
159915 CGATTTGCAT
159925 AAAGTAGATGTGCATGG
1 AAAGTAGATGTGCATGG
*
159942 AAAGTATATGTGCATGG
1 AAAGTAGATGTGCATGG
*
159959 AAAGTAGATGCGCATGG
1 AAAGTAGATGTGCATGG
159976 AAA
1 AAA
159979 TTATATCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.39, C:0.07, G:0.31, T:0.22
Consensus pattern (17 bp):
AAAGTAGATGTGCATGG
Found at i:168759 original size:14 final size:14
Alignment explanation
Indices: 168740--168766 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
168730 ATACGGCGTC
168740 TTGAGAAAGATGAT
1 TTGAGAAAGATGAT
168754 TTGAGAAAGATGA
1 TTGAGAAAGATGA
168767 GGAGGTTTAA
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:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (14 bp):
TTGAGAAAGATGAT
Found at i:170659 original size:31 final size:31
Alignment explanation
Indices: 170623--170685 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
170613 TTCCTTTAAT
170623 AAAAATCAGACATTGTTGAGCAAAAAAAAAA
1 AAAAATCAGACATTGTTGAGCAAAAAAAAAA
170654 AAAAATCAGACATTGTTGAGCAAAAAAAAAA
1 AAAAATCAGACATTGTTGAGCAAAAAAAAAA
170685 A
1 A
170686 CTTGGCACCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.62, C:0.10, G:0.13, T:0.16
Consensus pattern (31 bp):
AAAAATCAGACATTGTTGAGCAAAAAAAAAA
Found at i:172962 original size:84 final size:82
Alignment explanation
Indices: 172658--173163 Score: 527
Period size: 84 Copynumber: 6.0 Consensus size: 82
172648 GCTCAAGGCC
* **
172658 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCATGTCAT
1 AGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCGA-GGCACATCAT
*
172723 TTGCAGTATAACTTAAGTCG
63 TTGCAGCATAACTTAAGTCG
* * * *
172743 AGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATC-TGCAACCAAAGACCTTCGAGTTCGACTACACTCAGCT-CGAGGCACATCATT
*
172808 TGCAGCATAGCTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * *
172827 AGAAGGGCTATCTG---CCAAAGATCC-CCGAGTTCGATTACACTCAGCTTCGAGGACATATCAT
1 AGAAGGGCTATCTGCAACCAAAGA-CCTTCGAGTTCGACTACACTCAGC-TCGAGG-CACATCAT
* * * *
172888 TCGCAGCATAACTCAAGGCT
63 TTGCAGCATAACTTAAGTCG
* * *
172908 AGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTACGCTCAGCGTCGAGGGCACATCAT
1 AGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCGA-GGCACATCAT
**
172972 TTGCAATATAACTTAAGTCG
63 TTGCAGCATAACTTAAGTCG
* * *
172992 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTG-CAACCAAAGACCTTCGAGTTCGACTACACTCAGCT-CGAGGCACATCATT
* *
173057 TGCAGTATAGCTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * **
173076 AGAAGGGCTATCTGCAAACCAAAGACCTTTGAGTTCGATTACACTCAGCTCGGAGAAAAACATCA
1 AGAAGGGCTATCTGC-AACCAAAGACCTTCGAGTTCGACTACACTCAGCTC-GAG--GCACATCA
* * *
173141 TTTACAGCATAGCTCAAGTCG
62 TTTGCAGCATAACTTAAGTCG
173162 AG
1 AG
173164 GTTTTTCAAG
Statistics
Matches: 356, Mismatches: 49, Indels: 31
0.82 0.11 0.07
Matches are distributed among these distances:
80 29 0.08
81 38 0.11
83 5 0.01
84 177 0.50
85 80 0.22
86 27 0.08
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (82 bp):
AGAAGGGCTATCTGCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCGAGGCACATCATTTG
CAGCATAACTTAAGTCG
Found at i:174067 original size:22 final size:22
Alignment explanation
Indices: 174050--174116 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
174040 CTCGTATAAA
174050 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
174072 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
174094 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
174116 T
1 T
174117 TGTCCATAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:174377 original size:30 final size:31
Alignment explanation
Indices: 174327--174385 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
174317 CGTAGACAGT
*
174327 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
* *
174357 ATTTACATACTTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
174386 GAACTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:174442 original size:29 final size:29
Alignment explanation
Indices: 174400--174478 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
174390 TTTTCTGCAT
**
174400 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
174429 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
174458 ATTCATGTCATGT-AT-CATATA
1 ATTCATGTCATGTAATACATATA
174479 TGGAATGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
27 5 0.11
28 2 0.04
29 38 0.84
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:174876 original size:64 final size:64
Alignment explanation
Indices: 174774--174938 Score: 199
Period size: 65 Copynumber: 2.6 Consensus size: 64
174764 TTTTTCTCAT
* * *
174774 GGGGGAATCGGTTCCCCCCCCTGGGTATCGATTCCCCTCAAGCAATCT-GAATTCATATACGATG
1 GGGGGTATCGG-T-CCCCCCCTGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
174838 A
64 A
* * * *
174839 GGGGGTATCGGTCCCCCCCTGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTGA
1 GGGGGTATCGGTCCCCCCCT-GGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATGA
* * *
174904 AGGGGTATCGGT-TCCCCTTGGGTACCGATTCCCCT
1 GGGGGTATCGGTCCCCCCCTGGGTACCGATTCCCCT
174939 AACCCAAAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
63 24 0.27
64 29 0.33
65 35 0.40
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (64 bp):
GGGGGTATCGGTCCCCCCCTGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATGA
Found at i:174934 original size:63 final size:63
Alignment explanation
Indices: 174788--174938 Score: 187
Period size: 64 Copynumber: 2.4 Consensus size: 63
174778 GAATCGGTTC
* * * *
174788 CCCCCCCTGGGTATCGATTCCCCTCAAGCAATCTGAATTCATATACGATGAGGGGGTATCGGT
1 CCCCCCTTGGGTACCGATTCCCCTCAAGCAATCTGAAATCATATACGATGAAGGGGTATCGGT
* * * * *
174851 CCCCCCCTGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTGAAGGGGTATCGGT
1 -CCCCCCTTGGGTACCGATTCCCCTCAAGCAATCT-GAAATCATATACGATGAAGGGGTATCGGT
*
174916 -TCCCCTTGGGTACCGATTCCCCT
1 CCCCCCTTGGGTACCGATTCCCCT
174939 AACCCAAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
63 21 0.28
64 29 0.39
65 25 0.33
ACGTcount: A:0.19, C:0.31, G:0.23, T:0.27
Consensus pattern (63 bp):
CCCCCCTTGGGTACCGATTCCCCTCAAGCAATCTGAAATCATATACGATGAAGGGGTATCGGT
Found at i:180890 original size:22 final size:22
Alignment explanation
Indices: 180873--180939 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
180863 CTCGTATAAA
180873 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
180895 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
180917 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
180939 T
1 T
180940 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:181724 original size:68 final size:66
Alignment explanation
Indices: 181587--181736 Score: 185
Period size: 67 Copynumber: 2.3 Consensus size: 66
181577 TTTTTCTCAT
* * * *
181587 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATTCATATACGATG
1 GGGGGTATCGGTCCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
181652 A
66 A
* * * *
181653 GGGGGTATCGGTCCCCCCCCCTGGGGGTACCGATT-CCCTCTAGCATTCTGGAAATCATATTCGT
1 GGGGGTATCGGT-CCCCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGA
181717 TGA
64 TGA
* *
181720 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTCCCCC
181737 TTGAATGGGT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
66 15 0.21
67 46 0.64
68 11 0.15
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (66 bp):
GGGGGTATCGGTCCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
A
Found at i:181746 original size:21 final size:21
Alignment explanation
Indices: 181716--181756 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
181706 ATCATATTCG
* *
181716 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
181737 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
181757 TAACCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:183870 original size:8 final size:8
Alignment explanation
Indices: 183857--183904 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
183847 TTTGACTTTC
183857 TTTTATTA
1 TTTTATTA
183865 TTTTATTA
1 TTTTATTA
183873 TTTT-TTA
1 TTTTATTA
*
183880 ATTT-TTA
1 TTTTATTA
183887 --TTATTA
1 TTTTATTA
*
183893 TTTTATTG
1 TTTTATTA
183901 TTTT
1 TTTT
183905 TGTATTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 2 0.06
6 3 0.09
7 9 0.26
8 21 0.60
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTATTA
Found at i:185702 original size:18 final size:19
Alignment explanation
Indices: 185679--185721 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
185669 CAGTAATCCT
185679 ATTCC-CTGGTAATCTTAC
1 ATTCCTCTGGTAATCTTAC
185697 ATTCCCTCTGGTAATCTTAC
1 ATT-CCTCTGGTAATCTTAC
185717 ATTCC
1 ATTCC
185722 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCTCTGGTAATCTTAC
Found at i:185709 original size:20 final size:20
Alignment explanation
Indices: 185684--185721 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
185674 ATCCTATTCC
185684 CTGGTAATCTTACATTCCCT
1 CTGGTAATCTTACATTCCCT
185704 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
185722 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCT
Found at i:187304 original size:3 final size:3
Alignment explanation
Indices: 187296--187327 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
187286 TTTAAGATAT
187296 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
187328 TTGTTGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:187473 original size:41 final size:42
Alignment explanation
Indices: 187422--187503 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
187412 TTATGTTCGT
187422 TTATTTATTAAACGAACAAACATGAA-AAGATTTTGTGTTCA
1 TTATTTATTAAACGAACAAACATGAACAAGATTTTGTGTTCA
* * *
187463 TTATTTATTAAACGAACGAACCTGAACAATATTTTGTGTTC
1 TTATTTATTAAACGAACAAACATGAACAAGATTTTGTGTTC
187504 GTTTAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 24 0.65
42 13 0.35
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (42 bp):
TTATTTATTAAACGAACAAACATGAACAAGATTTTGTGTTCA
Found at i:187520 original size:40 final size:41
Alignment explanation
Indices: 187423--187523 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
187413 TATGTTCGTT
* * *
187423 TATTTATTAAACGAACAAACATGAAAAGATTTTGTGTTCAT
1 TATTAATTAAACGAACGAACATGAAAAGATTTTGTGTTCAG
* * *
187464 TATTTATTAAACGAACGAACCTGAACAATATTTTGTGTTC-G
1 TATTAATTAAACGAACGAACATGAA-AAGATTTTGTGTTCAG
*
187505 T-TTAATTAAATGAACGAAC
1 TATTAATTAAACGAACGAAC
187524 TTAAACAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 16 0.30
41 24 0.45
42 13 0.25
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (41 bp):
TATTAATTAAACGAACGAACATGAAAAGATTTTGTGTTCAG
Found at i:187599 original size:14 final size:14
Alignment explanation
Indices: 187580--187619 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
187570 AATATGTTAG
187580 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
*
187594 TTTATGTTCGTTCG
1 TTTATGTTCGTTCA
*
187608 TTTATATTCGTT
1 TTTATGTTCGTT
187620 TATGATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.60
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:196195 original size:15 final size:15
Alignment explanation
Indices: 196175--196218 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
196165 TTGGGTTAGT
*
196175 AAAAAAACAAAAATC
1 AAAAAAACAAAAATA
*
196190 AAAAAATCAAAAAATA
1 AAAAAAAC-AAAAATA
*
196206 AAAAAAAGAAAAA
1 AAAAAAACAAAAA
196219 AATTTAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.84, C:0.07, G:0.02, T:0.07
Consensus pattern (15 bp):
AAAAAAACAAAAATA
Found at i:196217 original size:16 final size:16
Alignment explanation
Indices: 196175--196219 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
196165 TTGGGTTAGT
*
196175 AAAAAAAC-AAAAATC
1 AAAAAAACAAAAAATA
*
196190 AAAAAATCAAAAAATA
1 AAAAAAACAAAAAATA
*
196206 AAAAAAAGAAAAAA
1 AAAAAAACAAAAAA
196220 ATTTAAAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.84, C:0.07, G:0.02, T:0.07
Consensus pattern (16 bp):
AAAAAAACAAAAAATA
Found at i:198727 original size:17 final size:17
Alignment explanation
Indices: 198686--198757 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
198676 ATTCATGTAT
198686 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
198703 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
198721 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
198738 CTAGTTCATTTATTAGA
1 CTAGTTCATTAATTAAA
198755 CTA
1 CTA
198758 AATCTTAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:210336 original size:24 final size:24
Alignment explanation
Indices: 210309--210358 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
210299 ATGTTCAGGA
210309 ATAAGCTCGTTTATGAGTTCATTT
1 ATAAGCTCGTTTATGAGTTCATTT
* *
210333 ATAAGCTTGTTTATGAGTTCGTTT
1 ATAAGCTCGTTTATGAGTTCATTT
210357 AT
1 AT
210359 GCTCATGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (24 bp):
ATAAGCTCGTTTATGAGTTCATTT
Found at i:210356 original size:12 final size:12
Alignment explanation
Indices: 210315--210359 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
210305 AGGAATAAGC
210315 TCGTTTATGAGT
1 TCGTTTATGAGT
* *
210327 TCATTTATAAGCT
1 TCGTTTATGAG-T
210340 T-GTTTATGAGT
1 TCGTTTATGAGT
210351 TCGTTTATG
1 TCGTTTATG
210360 CTCATGAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 2 0.07
12 23 0.85
13 2 0.07
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (12 bp):
TCGTTTATGAGT
Found at i:211291 original size:30 final size:31
Alignment explanation
Indices: 211257--211315 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
211247 TCTTACTTGA
211257 AACCAC-ACA-TATGAAAATATTTATAAAAAT
1 AACCACGACATTATGAAAA-ATTTATAAAAAT
**
211287 AACCACGACATTATGAGTAATTTATAAAA
1 AACCACGACATTATGAAAAATTTATAAAA
211316 TCTACGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 13 0.52
32 6 0.24
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.27
Consensus pattern (31 bp):
AACCACGACATTATGAAAAATTTATAAAAAT
Found at i:212359 original size:22 final size:23
Alignment explanation
Indices: 212333--212376 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
212323 AAATTAAATA
* *
212333 AATATTTTAAA-ATACTTTTTAT
1 AATATTATAAATACACTTTTTAT
212355 AATATTATAAATACACTTTTTA
1 AATATTATAAATACACTTTTTA
212377 GAACGATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTATAAATACACTTTTTAT
Found at i:214559 original size:22 final size:22
Alignment explanation
Indices: 214533--214588 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
214523 AAAAAGGTTA
214533 GACAAGATAATCAAATAAAAGT
1 GACAAGATAATCAAATAAAAGT
214555 GACAAGATAATCAAATAAAAGT
1 GACAAGATAATCAAATAAAAGT
*
214577 GACAAGCTAATC
1 GACAAGATAATC
214589 CAATGAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.18
Consensus pattern (22 bp):
GACAAGATAATCAAATAAAAGT
Found at i:214794 original size:15 final size:16
Alignment explanation
Indices: 214774--214817 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
214764 CCTCTTTCTC
214774 TTTTCATTTTTTTA-T
1 TTTTCATTTTTTTATT
**
214789 TTTTCATTTTTCAATT
1 TTTTCATTTTTTTATT
214805 TTTTCATTTTTTT
1 TTTTCATTTTTTT
214818 TTGAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCATTTTTTTATT
Found at i:214807 original size:9 final size:8
Alignment explanation
Indices: 214774--214816 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
214764 CCTCTTTCTC
214774 TTTTCATT
1 TTTTCATT
*
214782 TTTTTA-T
1 TTTTCATT
214789 TTTTCA-T
1 TTTTCATT
214796 TTTTCAATT
1 TTTTC-ATT
214805 TTTTCATT
1 TTTTCATT
214813 TTTT
1 TTTT
214817 TTTGAAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 12 0.39
8 13 0.42
9 6 0.19
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:219242 original size:38 final size:40
Alignment explanation
Indices: 219197--219273 Score: 136
Period size: 41 Copynumber: 1.9 Consensus size: 40
219187 TCCTAAATAT
219197 AATAATAATAAAATAATCAAACTAAAAATCCTAAATAAAAA
1 AATAATAATAAAATAATCAAACTAAAAATCCTAAAT-AAAA
*
219238 AATAATAATAAAATACTCAAACTAAAAATCCTAAAT
1 AATAATAATAAAATAATCAAACTAAAAATCCTAAAT
219274 CTAAAAGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (40 bp):
AATAATAATAAAATAATCAAACTAAAAATCCTAAATAAAA
Found at i:236512 original size:18 final size:18
Alignment explanation
Indices: 236489--236532 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
236479 AACCCTTATT
236489 ATTATATAT-ATATATTTA
1 ATTATAT-TGATATATTTA
*
236507 ATTATATTGTTATATTTA
1 ATTATATTGATATATTTA
*
236525 TTTATATT
1 ATTATATT
236533 TTCTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTATATTGATATATTTA
Found at i:236546 original size:18 final size:18
Alignment explanation
Indices: 236499--236551 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
236489 ATTATATATA
* *
236499 TATATTTAATTATATTGT
1 TATATTTATTTATATTTT
236517 TATATTTATTTATATTTT
1 TATATTTATTTATATTTT
236535 CTATATTT-TTTA-ATTTT
1 -TATATTTATTTATATTTT
236552 GGTTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 5 0.16
18 20 0.62
19 7 0.22
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
TATATTTATTTATATTTT
Found at i:236602 original size:29 final size:28
Alignment explanation
Indices: 236570--236695 Score: 70
Period size: 26 Copynumber: 4.5 Consensus size: 28
236560 TTTATTTATG
236570 TTATATTATACTATTTATTATTATTATTA
1 TTATATTATA-TATTTATTATTATTATTA
* * *
236599 TTATTACTT-TACTATATTGTTCTCCATTATTA
1 TTA-TA-TTATA-TAT-TTATTAT-TATTATTA
*
236631 TT-T-TT-T-TCTTTATTATTA-TAGTTA
1 TTATATTATATATTTATTATTATTA-TTA
*
236655 TTATA-TATAT-TTTATTATTATTATATG
1 TTATATTATATATTTATTATTATTAT-TA
236682 TTATATATATATAT
1 TTATAT-TATATAT
236696 ATATATATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 27
0.68 0.07 0.25
Matches are distributed among these distances:
23 2 0.03
24 6 0.08
25 7 0.09
26 14 0.19
27 9 0.12
28 3 0.04
29 8 0.11
30 10 0.13
31 7 0.09
32 9 0.12
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (28 bp):
TTATATTATATATTTATTATTATTATTA
Found at i:236663 original size:2 final size:2
Alignment explanation
Indices: 236656--236709 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
236646 TTATAGTTAT
* *
236656 TA TA TA TA T- TT TA T- TA T- TA T- TA TA TG T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
236693 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
236710 GTTTTTCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
1 5 0.11
2 40 0.89
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (2 bp):
TA
Found at i:236815 original size:2 final size:2
Alignment explanation
Indices: 236808--236846 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
236798 ATCTTGCATT
236808 TA TA 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 TA TA T
236847 TATCATAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:237025 original size:9 final size:9
Alignment explanation
Indices: 237011--237121 Score: 51
Period size: 9 Copynumber: 12.9 Consensus size: 9
237001 CATTTTGTCT
237011 TTATTATTA
1 TTATTATTA
* *
237020 TTATTACTG
1 TTATTATTA
237029 TTA-TATATA
1 TTATTAT-TA
237038 TT-TTATTA
1 TTATTATTA
237046 TTATTATTA
1 TTATTATTA
* *
237055 GTATTGTATA
1 TTATTAT-TA
*
237065 TT-TTACATA
1 TTATTA-TTA
237074 TT-TT-TTAA
1 TTATTATT-A
*
237082 TTTTTATT-
1 TTATTATTA
*
237090 TTATTTTTA
1 TTATTATTA
237099 TTATT-TTA
1 TTATTATTA
*
237107 TT-CTATTA
1 TTATTATTA
237115 TT-TTATT
1 TTATTATT
237122 TCTCTTCTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
7 2 0.03
8 29 0.37
9 42 0.54
10 5 0.06
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (9 bp):
TTATTATTA
Found at i:237064 original size:29 final size:29
Alignment explanation
Indices: 237010--237065 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
237000 TCATTTTGTC
*
237010 TTTATTATTATTATTACTGTTATATATAT
1 TTTATTATTATTATTACTATTATATATAT
* *
237039 TTTATTATTATTATTAGTATTGTATAT
1 TTTATTATTATTATTACTATTATATAT
237066 TTTACATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.62
Consensus pattern (29 bp):
TTTATTATTATTATTACTATTATATATAT
Found at i:237096 original size:19 final size:20
Alignment explanation
Indices: 237072--237119 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
237062 ATATTTTACA
*
237072 TATTTTTTAAT-TTTTATTT
1 TATTTTTTAATATTTTATTC
*
237091 TA-TTTTTATTATTTTATTC
1 TATTTTTTAATATTTTATTC
237110 TATTATTTTA
1 TATT-TTTTA
237120 TTTCTCTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 11 0.46
20 1 0.04
21 5 0.21
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (20 bp):
TATTTTTTAATATTTTATTC
Found at i:237124 original size:14 final size:14
Alignment explanation
Indices: 237085--237124 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
237075 TTTTTAATTT
*
237085 TTATTTTATTTTTA
1 TTATTTTATTTCTA
237099 TTATTTTA-TTCTA
1 TTATTTTATTTCTA
237112 TTATTTTATTTCT
1 TTATTTTATTTCT
237125 CTTCTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTTATTTCTA
Found at i:239644 original size:83 final size:83
Alignment explanation
Indices: 239518--240488 Score: 1221
Period size: 83 Copynumber: 11.8 Consensus size: 83
239508 GGACATGGCC
* * * * * * * *
239518 TTGAGCTGAATGTAATTGAACTCGAGGGTATTTGTTGGCAGATAGCCCTTCTCGCCTTTAGCTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
* **
239583 GCCGCAAATGATACGCCT
66 GCTGCAAATGATGTGCCT
* ** * * * *
239601 TGGAGCTGAGCATAGTCGAACTCGAAGGTCTTGGTTAACAGATAGCCCTTCTTGCCTTGAGCTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
*
239666 ACTGCAAATGATGTGCCT
66 GCTGCAAATGATGTGCCT
* * * * *
239684 TTGAGCTGAGTGCAATCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTAGGCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
**
239749 GCTGTGAATG-TGTGCCT
66 GCTGCAAATGATGTGCCT
* *
239766 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTT-AGTAGATAACCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGA-CAGATAACCCTTCTTGCCTTGAGCTA
239830 TGCTGCAAATGATGTGCCT
65 TGCTGCAAATGATGTGCCT
* * * *
239849 TTGAGATGAGTATAATCGAACTCGAAGGTCTTTG--G-CAGATAGCTCTTCTTGCCTTGAGCTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
*
239911 GTTGCAAATGATGTGCCT
66 GCTGCAAATGATGTGCCT
* *
239929 TTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGT-CTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTA
*
239994 CT-CTACAAATGATGTGCCT
65 -TGCTGCAAATGATGTGCCT
* *
240013 TTGAGCTAAGTGTAATCGAACACGAAGGTCTTTGTTGGA-AGATAACCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTT-GACAGATAACCCTTCTTGCCTTGAGCTA
240077 TGCTGCAAATGATGTGCCT
65 TGCTGCAAATGATGTGCCT
* * * *
240096 TTGAGATGAGTGTAATCAAACTTGAAGGTCTTTG--G-CAGATATCCCTTCTTGCCTTGAGCTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
*
240158 GCTACAAATGATGTGCCT
66 GCTGCAAATGATGTGCCT
* *
240176 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACTCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTA
240241 TGCTGCAAATGATGTGCCT
65 TGCTGCAAATGATGTGCCT
* * *
240260 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTAACAGATAACCCTTCTAGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
*
240325 GCTGTAAATGATGTGCCT
66 GCTGCAAATGATGTGCCT
* * * * *
240343 TTGAGCTGAGTTTAATCGAACTCGAAGGTCTTTG--G-TAGATAGCCCTTCTTGTCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
* * *
240405 GTTGTAAATGATGTGTCT
66 GCTGCAAATGATGTGCCT
* * * * ** * *
240423 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGATGATAGAAAACAATTCTCGCCTTGAGTTAT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
240488 G
66 G
240489 TTGCCAATAG
Statistics
Matches: 775, Mismatches: 95, Indels: 36
0.86 0.10 0.04
Matches are distributed among these distances:
80 209 0.27
81 9 0.01
82 73 0.09
83 344 0.44
84 139 0.18
85 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (83 bp):
TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTAT
GCTGCAAATGATGTGCCT
Found at i:240082 original size:247 final size:246
Alignment explanation
Indices: 239518--240456 Score: 1303
Period size: 247 Copynumber: 3.8 Consensus size: 246
239508 GGACATGGCC
* * * * * * *
239518 TTGAGCTGAATGTAATTGAACTCGAGGGTATTTGTTGGCAGATAGCCCTTCTCGCCTTTAGCTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGGAAGATAACCCTTCTTGCCTTGAGCTAT
* ** * * * *
239583 GCCGCAAATGATACGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTC-TTGGTTAACAGATAGC
66 GCTGCAAATGATGTGCCTTTGAGATGAGTATAATCGAACTCGAAGGTCTTTGG----CAGATAGC
* *
239647 CCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTTGAGCTGAGTGCAATCGAACTCGAAGG
127 CCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * * * * **
239712 TCTTTGTTGACATATAACCCTTCTAGGCTTGAGTTATGCTGTGAATG-TGTGCCT
192 TTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCT
* *
239766 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTAGTAGATAACCCTTCTTGCCTTGAGCTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGGAAGATAACCCTTCTTGCCTTGAGCTAT
*
239831 GCTGCAAATGATGTGCCTTTGAGATGAGTATAATCGAACTCGAAGGTCTTTGGCAGATAGCTCTT
66 GCTGCAAATGATGTGCCTTTGAGATGAGTATAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTT
*
239896 CTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATT
131 CTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-TT
*
239961 TTGTTGGCAGATAACCCTTCTTGCCTTGAGCTACT-CTACAAATGATGTGCCT
195 TTGTTGGCAGATAACCCTTCTTGCCTTGAGCTA-TGCTGCAAATGATGTGCCT
*
240013 TTGAGCT-AAGTGTAATCGAACACGAAGGTCTTTGTTGGAAGATAACCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAA-TGTAATCGAACTCGAAGGTCTTTGTTGGAAGATAACCCTTCTTGCCTTGAGCTA
* * * *
240077 TGCTGCAAATGATGTGCCTTTGAGATGAGTGTAATCAAACTTGAAGGTCTTTGGCAGATATCCCT
65 TGCTGCAAATGATGTGCCTTTGAGATGAGTATAATCGAACTCGAAGGTCTTTGGCAGATAGCCCT
*
240142 TCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
130 TCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-T
*
240207 TTTGTTGGCAGATAACTCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCT
194 TTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCT
* * * *
240260 TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTT-AACAGATAACCCTTCTAGCCTTGAGTTA
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGGA-AGATAACCCTTCTTGCCTTGAGCTA
* * * *
240324 TGCTGTAAATGATGTGCCTTTGAGCTGAGTTTAATCGAACTCGAAGGTCTTTGGTAGATAGCCCT
65 TGCTGCAAATGATGTGCCTTTGAGATGAGTATAATCGAACTCGAAGGTCTTTGGCAGATAGCCCT
* * * * * * *
240389 TCTTGTCTTGAGTTATGTTGTAAATGATGTGTCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCT
130 TCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTTT
240454 TTG
195 TTG
240457 ATGATAGAAA
Statistics
Matches: 622, Mismatches: 61, Indels: 18
0.89 0.09 0.03
Matches are distributed among these distances:
245 70 0.11
246 43 0.07
247 406 0.65
248 99 0.16
249 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (246 bp):
TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGGAAGATAACCCTTCTTGCCTTGAGCTAT
GCTGCAAATGATGTGCCTTTGAGATGAGTATAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTT
CTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTTTT
TGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCT
Found at i:241814 original size:95 final size:95
Alignment explanation
Indices: 241614--241876 Score: 330
Period size: 95 Copynumber: 2.7 Consensus size: 95
241604 GGCTAGCTGA
* * * * * *
241614 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAGCTTAA-TATCATTGTATAGAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAAGTTTTATTG--T--AT
* *
241678 ATTGTAATCACCTTTATTAGGCTAGCTAAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTAAATATT
* * *
241712 ATCCATAAAGTCGGGGCGCTTAACCAATTTCTCTAGAGGGACAACTCAAGTTTTATTGTATATTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAAGTTTTATTGTATATTA
* *
241777 TAATCACCTTTATCAGGCTAGTTGAATATT
66 TAATCACCTTTATCAGGCTAGCTAAATATT
* * *
241807 ATCCATAAAGTCGGGGTGTTTAACCAATTACTTTAGAGGGACAGCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAAGTTTTATTGTATAT-T
241872 ATAAT
65 ATAAT
241877 ATTATAATAT
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
95 89 0.61
96 6 0.04
97 1 0.01
98 43 0.30
99 6 0.04
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAAGTTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTAAATATT
Found at i:242404 original size:35 final size:35
Alignment explanation
Indices: 242358--242424 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
242348 ATGTCCCCAT
*
242358 AAAAATAAATATG-GCAAAGTTCAAAAACAAGTTAC
1 AAAAAGAAATATGAG-AAAGTTCAAAAACAAGTTAC
242393 AAAAAGAAATATGAGAAAGTTCAAAAACAAGT
1 AAAAAGAAATATGAGAAAGTTCAAAAACAAGT
242425 CCAATCAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.18
Consensus pattern (35 bp):
AAAAAGAAATATGAGAAAGTTCAAAAACAAGTTAC
Found at i:243860 original size:19 final size:21
Alignment explanation
Indices: 243836--243888 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 21
243826 TTGTTCTCTT
243836 TATTATTATA-GTTAT-TATA
1 TATTATTATATGTTATCTATA
*
243855 TATTATTATATGTTCTCTATA
1 TATTATTATATGTTATCTATA
243876 TATATATATATAT
1 TAT-TAT-TATAT
243889 ATATTTCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.34
20 4 0.14
21 7 0.24
22 3 0.10
23 5 0.17
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
TATTATTATATGTTATCTATA
Found at i:244305 original size:29 final size:29
Alignment explanation
Indices: 244234--244311 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
244224 ATTTTTTTAA
244234 TTTATTTTAATTTATTTTTTATTTTCTCTTC
1 TTTATTTT-ATTTA-TTTTTATTTTCTCTTC
** *
244265 TTTATTACATTTGTTTTTATTTTACT-TTC
1 TTTATTTTATTTATTTTTATTTT-CTCTTC
244294 TTTATTTTATTTATTTTT
1 TTTATTTTATTTATTTTT
244312 TTCTGCTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 28 0.70
30 6 0.15
31 6 0.15
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (29 bp):
TTTATTTTATTTATTTTTATTTTCTCTTC
Found at i:252266 original size:42 final size:41
Alignment explanation
Indices: 252197--252304 Score: 155
Period size: 42 Copynumber: 2.6 Consensus size: 41
252187 TTATTCATAA
**
252197 TTGTGACGAAAACA-TTTTGTCACTAGTCTTAGTTGGTGAT
1 TTGTGACGAAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
* *
252237 TTGTGACGATAATTGTTTTTGTCAGTAGTCTTAGTTGGTGAT
1 TTGTGACGA-AATTATTTTTGTCACTAGTCTTAGTTGGTGAT
*
252279 TTGTGATGAAATTATTTTTGTCACTA
1 TTGTGACGAAATTATTTTTGTCACTA
252305 TTGAAGTGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 9 0.15
41 17 0.29
42 33 0.56
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.45
Consensus pattern (41 bp):
TTGTGACGAAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
Found at i:254340 original size:106 final size:105
Alignment explanation
Indices: 254149--254396 Score: 286
Period size: 106 Copynumber: 2.4 Consensus size: 105
254139 GTGACGAAGT
* * *
254149 TATTGATAATAGTGTCAAACATTTGGTCACTAAAAAACACATTGTGTGACAACATTGGTGGTCAC
1 TATTGATAATAGTATCAAACATTTGGTCACTAAAAAACACATTGTGTGAAAACATTGGTGATCAC
* * * *
254214 AAAATATATTTTTAGAGTCAAACAAATTTA-TATCAATTTC
66 AAAATATATTGTTAGAGTCAAACAAATTCACCA-CAATTTA
* * * *
254254 TATTGATAATAGTATCGAACATTTGGTCACTATAAAAATAC-TTAGTGTGAAAACGTTGTTGATC
1 TATTGATAATAGTATCAAACATTTGGTCACTA-AAAAACACATT-GTGTGAAAACATTGGTGATC
* *
254318 ACAAAGTATATTGTTAGTGTCAAACAAATTCACCACAATTTA
64 ACAAAATATATTGTTAGAGTCAAACAAATTCACCACAATTTA
* * * **
254360 TATTGATAATTGTGTCAAATAGATGGTCAC-AAAAAAC
1 TATTGATAATAGTATCAAACATTTGGTCACTAAAAAAC
254397 GTAACAATTG
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
104 5 0.04
105 33 0.28
106 81 0.68
107 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (105 bp):
TATTGATAATAGTATCAAACATTTGGTCACTAAAAAACACATTGTGTGAAAACATTGGTGATCAC
AAAATATATTGTTAGAGTCAAACAAATTCACCACAATTTA
Found at i:257358 original size:20 final size:20
Alignment explanation
Indices: 257333--257480 Score: 190
Period size: 20 Copynumber: 7.3 Consensus size: 20
257323 TGAAAATCGC
257333 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
257353 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
257373 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* * *
257393 TGCGATAGTCTACA-GTCGCGT
1 TGCGAT--TTTCCATTTCGCGT
257414 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* ** *
257434 TGCGATAGTTGAAATTCGCGT
1 TGCGAT-TTTCCATTTCGCGT
*
257455 TGCGATTTTCCATTTCGCAT
1 TGCGATTTTCCATTTCGCGT
257475 TGCGAT
1 TGCGAT
257481 AGTCTACAGT
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.04
20 73 0.67
21 28 0.26
22 4 0.04
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.41
Consensus pattern (20 bp):
TGCGATTTTCCATTTCGCGT
Found at i:257424 original size:41 final size:40
Alignment explanation
Indices: 257304--257526 Score: 258
Period size: 41 Copynumber: 5.5 Consensus size: 40
257294 ATTCGTGTTG
* *
257304 CATTTCGCGTTGCGATAGTTGAAAATCGC--TGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-ACAGTCGCGTTGCGATTTTC
* * *
257343 CATTTCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTACA-GTCGCGTTGCGATTTTC
257383 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TACAGTCGCGTTGCGATTTTC
* *
257424 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-ACAGTCGCGTTGCGATTTTC
* *
257465 CATTTCGCATTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TACAGTCG-CGTTGCGATTTTC
*
257507 CAAATT--CGTTGCGATAGTTA
1 C-ATTTCGCGTTGCGATAGTTA
257527 AAAAAAAGAT
Statistics
Matches: 160, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
37 1 0.01
38 6 0.04
39 16 0.10
40 29 0.18
41 87 0.54
42 18 0.11
43 3 0.02
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTACAGTCGCGTTGCGATTTTC
Found at i:257478 original size:61 final size:61
Alignment explanation
Indices: 257304--257480 Score: 227
Period size: 61 Copynumber: 2.9 Consensus size: 61
257294 ATTCGTGTTG
*
257304 CATTTCGCGTTGCGATAGTTGAAAATCGC--TGCGATTTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
* ** * * * *
257363 CATTTCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTCTACA-GTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGAT--TTTCCATTTCGCGTTGCGATTTTC
*
257424 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCATTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
257481 AGTCTACAGT
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
58 7 0.07
59 16 0.17
60 10 0.10
61 43 0.45
62 20 0.21
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (61 bp):
CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
Found at i:257478 original size:82 final size:82
Alignment explanation
Indices: 257304--257525 Score: 294
Period size: 82 Copynumber: 2.7 Consensus size: 82
257294 ATTCGTGTTG
* * * *
257304 CATTTCGCGTTGCGATAGT-TGAAAATCGC--TGCGATTTTCCATTTCGCGTTGCGAT-TTTCCA
1 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAA
*
257365 TTTCGCGTTGCGATTTTC
65 ATTCGCGTTGCGATTTTC
*
257383 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAA
257448 TTCGCGTTGCGATTTTC
66 TTCGCGTTGCGATTTTC
* * *
257465 CATTTCGCATTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTT
1 CATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTT
257526 AAAAAAAAGA
Statistics
Matches: 128, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
79 25 0.20
80 1 0.01
81 26 0.20
82 59 0.46
83 14 0.11
84 3 0.02
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (82 bp):
CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAA
TTCGCGTTGCGATTTTC
Found at i:257612 original size:6 final size:6
Alignment explanation
Indices: 257601--257653 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
257591 GACACGTATT
*
257601 ACCACG ACCACG ACCACG ACCACA ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
257649 ACCAC
1 ACCAC
257654 ATGCAGTCCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.36, C:0.51, G:0.13, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:261507 original size:12 final size:12
Alignment explanation
Indices: 261490--261514 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
261480 AATGCGTTTA
261490 TAGCGGCATTTT
1 TAGCGGCATTTT
261502 TAGCGGCATTTT
1 TAGCGGCATTTT
261514 T
1 T
261515 TGAATAAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (12 bp):
TAGCGGCATTTT
Found at i:261563 original size:41 final size:41
Alignment explanation
Indices: 261520--261923 Score: 259
Period size: 41 Copynumber: 9.9 Consensus size: 41
261510 TTTTTTGAAT
* * * *
261520 AAACGCCGCTAAATACTCGTACTTTAGTGGTGTTTCTATAT
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
261561 AAACACCGCTAAAGAC-GGTACTTTAGTGGCGTTTTTATGC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
261601 AAATGCCGCTAAAGACT-GTACTTTAGTGGCATTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGC-GTTTTTATAC
* * * * *
261642 AAACGCAGC-ATAGACTCGTACATTAATGGCGTTTTT-TGAAT
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT--AC
*** * *
261683 AAACGCCGC-AATTTCTCAGTACATTAGTGGCGTTTGTATAC
1 AAACGCCGCTAAAGACTC-GTACTTTAGTGGCGTTTTTATAC
* * *
261724 AAACGCCGCTAAAGACTCATACTTTAGTTGCGTTTTTAGAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * * * * * * *
261765 AAACGACGCTATAGACAT-ATACATTAATGAC-TTTTTTTAAT
1 AAACGCCGCTAAAGAC-TCGTACTTTAGTGGCGTTTTTAT-AC
* * *** * * *
261806 AAATGTCGC-AATTTCTCAATACCTTAGTGGCGTTTGTATAC
1 AAACGCCGCTAAAGACTC-GTACTTTAGTGGCGTTTTTATAC
* * *
261847 AAAAGCCGCTAAAGACTCGCACTTTAGT-GAGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * * * * *
261887 AAACGCCGGTATAGACTCATACATTAATGGCATTTTT
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTT
261924 CGAATAAACG
Statistics
Matches: 274, Mismatches: 74, Indels: 30
0.72 0.20 0.08
Matches are distributed among these distances:
39 2 0.01
40 95 0.35
41 143 0.52
42 33 0.12
43 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:261737 original size:123 final size:122
Alignment explanation
Indices: 261578--261965 Score: 480
Period size: 123 Copynumber: 3.2 Consensus size: 122
261568 GCTAAAGACG
* * * * *
261578 GTACTTTAGTGGCGTTTTTATGCAAATGCCGCTAAAGACT-GTACTTTAGTGGCATTTTTTATAC
1 GTACATTAGTGGCGTTTGTATACAAAAGCCGCTAAAGACTCGTACTTTAGT-GCAGTTTTTATAC
*
261642 AAACGCAGCATAGACTCGTACATTAATGGCGTTTTTTGAATAAACGCCGCAATTTCTCA
65 AAACGCAGCATAGACTCATACATTAATGGC-TTTTTTGAATAAACGCCGCAATTTCTCA
* * *
261701 GTACATTAGTGGCGTTTGTATACAAACGCCGCTAAAGACTCATACTTTAGTTGC-GTTTTTAGAC
1 GTACATTAGTGGCGTTTGTATACAAAAGCCGCTAAAGACTCGTACTTTAG-TGCAGTTTTTATAC
* * * *
261765 AAACG-ACGCTATAGACAT-ATACATTAATGACTTTTTTTAATAAATGTCGCAATTTCTCA
65 AAACGCA-GC-ATAGAC-TCATACATTAATGGCTTTTTTGAATAAACGCCGCAATTTCTCA
* * *
261824 ATACCTTAGTGGCGTTTGTATACAAAAGCCGCTAAAGACTCGCACTTTAGTG-AGTTTTTATACA
1 GTACATTAGTGGCGTTTGTATACAAAAGCCGCTAAAGACTCGTACTTTAGTGCAGTTTTTATACA
* * *
261888 AACGCCGGTATAGACTCATACATTAATGGCATTTTTCGAATAAACGCCGCAATTTCTCA
66 AACG-CAGCATAGACTCATACATTAATGGC-TTTTTTGAATAAACGCCGCAATTTCTCA
* *
261947 GTATATTTGTGGCGTTTGT
1 GTACATTAGTGGCGTTTGT
261966 GTTTACAAAC
Statistics
Matches: 226, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
121 1 0.00
122 35 0.15
123 161 0.71
124 27 0.12
125 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (122 bp):
GTACATTAGTGGCGTTTGTATACAAAAGCCGCTAAAGACTCGTACTTTAGTGCAGTTTTTATACA
AACGCAGCATAGACTCATACATTAATGGCTTTTTTGAATAAACGCCGCAATTTCTCA
Found at i:262264 original size:14 final size:13
Alignment explanation
Indices: 262222--262255 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
262212 TTGTGTTCCT
262222 TTCCTTTCATGGC
1 TTCCTTTCATGGC
262235 TTCCTTTCATGGC
1 TTCCTTTCATGGC
262248 TTCCTTTC
1 TTCCTTTC
262256 GCAGGCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.32, G:0.12, T:0.50
Consensus pattern (13 bp):
TTCCTTTCATGGC
Found at i:262598 original size:2 final size:2
Alignment explanation
Indices: 262591--262624 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
262581 GTTGTTGAAT
262591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
262625 GTAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:270178 original size:21 final size:21
Alignment explanation
Indices: 270136--270194 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
270126 TGATTTATTA
**
270136 TTATGGATTTCAAACTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
270157 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
270178 TTATAGATGTT-AAGTTT
1 TTATGGAT-TTCAAGTTT
270195 ATTGGATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:270459 original size:44 final size:43
Alignment explanation
Indices: 270411--270509 Score: 153
Period size: 44 Copynumber: 2.3 Consensus size: 43
270401 TTTTACATTC
270411 ACAAATGCCACTATATGACAGAACATTTAGCAGCATTTTTGGG
1 ACAAATGCCACTATATGACAGAACATTTAGCAGCATTTTTGGG
* * *
270454 AACAAATGTCACTATATGTCAGAACATTTAGCGGCATTTTTGGG
1 -ACAAATGCCACTATATGACAGAACATTTAGCAGCATTTTTGGG
270498 ACAAAATGCCAC
1 AC-AAATGCCAC
270510 AAAATAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 2 0.04
44 48 0.96
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (43 bp):
ACAAATGCCACTATATGACAGAACATTTAGCAGCATTTTTGGG
Found at i:274965 original size:40 final size:40
Alignment explanation
Indices: 274910--274990 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
274900 GGTCAAATGC
274910 ACATAGAGTGATGTTAAATTAATTTTATAAAAAATAAATA
1 ACATAGAGTGATGTTAAATTAATTTTATAAAAAATAAATA
274950 ACATAGAGTGATGTTAAATTAATTTTATAAAAAATAAATA
1 ACATAGAGTGATGTTAAATTAATTTTATAAAAAATAAATA
274990 A
1 A
274991 GATGAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (40 bp):
ACATAGAGTGATGTTAAATTAATTTTATAAAAAATAAATA
Found at i:280166 original size:3 final size:3
Alignment explanation
Indices: 280152--280183 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
280142 TTGTAAACAA
280152 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A
280184 TATTTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:280545 original size:21 final size:21
Alignment explanation
Indices: 280498--280546 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
280488 TGACTATCGT
280498 AATGCGATTTTCCAATTTCGC
1 AATGCGATTTTCCAATTTCGC
**
280519 GTTGCGATTTTCCCAA-TTCGC
1 AATGCGATTTT-CCAATTTCGC
280540 AATGCGA
1 AATGCGA
280547 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (21 bp):
AATGCGATTTTCCAATTTCGC
Found at i:280602 original size:20 final size:20
Alignment explanation
Indices: 280577--280649 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
280567 TAATACAAAA
280577 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
280597 TCGCAACGCGATACTTAATT
1 TCGCAACGCGATACTGACTT
*
280617 TCGCAACGCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
280637 TCGCAACGAGATA
1 TCGCAACGCGATA
280650 ATACATAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:280864 original size:22 final size:22
Alignment explanation
Indices: 280836--280879 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
280826 CACTCTCTCA
280836 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
280858 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
280880 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:281181 original size:20 final size:20
Alignment explanation
Indices: 281158--281200 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
281148 GATAGTCAAA
281158 TTCGCGTTACGATTGTCATT
1 TTCGCGTTACGATTGTCATT
* * *
281178 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTACGATTGTCATT
281198 TTC
1 TTC
281201 AGAAACTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
TTCGCGTTACGATTGTCATT
Found at i:281391 original size:25 final size:24
Alignment explanation
Indices: 281337--281391 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
281327 TGTTTATTAT
* *
281337 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
281361 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
281387 TGTTT
1 TGTTT
281392 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:282540 original size:18 final size:18
Alignment explanation
Indices: 282519--282566 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
282509 TCCACTTCGG
282519 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
282537 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
282555 GAGCCATTACCT
1 GAGCCATCACCT
282567 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:283155 original size:19 final size:20
Alignment explanation
Indices: 283101--283156 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
283091 TAGTTTACTT
* *
283101 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
283121 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
283141 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
283157 AAATCGCGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:283162 original size:19 final size:19
Alignment explanation
Indices: 283140--283216 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
283130 GGAAATGGCT
283140 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
283159 ATCGCGA--C--AA-CAAA
1 ATCGCAATGCGAAATGAAA
283173 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* * *
283192 ATCGCAACGTGAAATAAAA
1 ATCGCAATGCGAAATGAAA
283211 ATCGCA
1 ATCGCA
283217 TCAGACGGCG
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 9 0.20
15 2 0.04
16 1 0.02
17 1 0.02
18 2 0.04
19 31 0.67
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:283350 original size:21 final size:21
Alignment explanation
Indices: 283299--283358 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
283289 ACTCACCTGT
283299 AATCCCTCAAGAGTCCCCTCC
1 AATCCCTCAAGAGTCCCCTCC
** * *
283320 AATCGTTCAAGAGGCCCCTATC
1 AATCCCTCAAGAGTCCCCT-CC
283342 -ATCCCTCAAGAGTCCCC
1 AATCCCTCAAGAGTCCCC
283359 CCCCCACCGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.42, G:0.13, T:0.20
Consensus pattern (21 bp):
AATCCCTCAAGAGTCCCCTCC
Found at i:283387 original size:43 final size:42
Alignment explanation
Indices: 283295--283387 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 42
283285 CCCGACTCAC
* * * *
283295 CTGTAATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCA
* *
283337 CTATCATCCCTCAAGAGTCCCCCCCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGT-CCCCCCCAACCGTTCAAGAGGCCA
283380 CTGTCATC
1 CTGTCATC
283388 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 16 0.37
43 27 0.63
ACGTcount: A:0.23, C:0.42, G:0.15, T:0.20
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCA
Found at i:284830 original size:14 final size:14
Alignment explanation
Indices: 284796--284834 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
284786 TTGATTGTTT
284796 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
284810 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
284824 TGTTGATTTGT
1 AATTGATTTGT
284835 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:284960 original size:20 final size:20
Alignment explanation
Indices: 284932--284974 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
284922 GTTGAAGGCA
*
284932 AAACAGACTATCACAACGCG
1 AAACAGACTATCACAACGAG
* *
284952 AAACTGACTATCGCAACGAG
1 AAACAGACTATCACAACGAG
284972 AAA
1 AAA
284975 ATCGCAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
AAACAGACTATCACAACGAG
Found at i:284980 original size:14 final size:14
Alignment explanation
Indices: 284961--285014 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
284951 GAAACTGACT
284961 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
284975 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
284994 ATTGCAACGAGAAA
1 ATCGCAACGAGAAA
285008 ATCGCAA
1 ATCGCAA
285015 TGCGATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:285063 original size:20 final size:20
Alignment explanation
Indices: 285038--285075 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
285028 TCGCATTGCG
*
285038 ATTTTCGCGTTGTGATAGCC
1 ATTTTCGCGTTGCGATAGCC
285058 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
285076 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:287146 original size:19 final size:19
Alignment explanation
Indices: 287124--287254 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
287114 GGAAATTACT
287124 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
287143 ATCGCAAT--G--A-GATA
1 ATCGCAATGCGAAATGAAA
287157 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
287176 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
287190 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
287209 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
287223 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
287242 ATCGCAACGCGAA
1 ATCGCAATGCGAA
287255 TTTAGTTTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 29 0.34
15 3 0.03
16 5 0.06
17 5 0.06
18 3 0.03
19 41 0.48
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:287166 original size:33 final size:33
Alignment explanation
Indices: 287124--287250 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
287114 GGAAATTACT
* *
287124 ATCGCAATGCGAAATGAAAATCGCAATGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
287157 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
287190 ATCACAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
287223 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
287251 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:287304 original size:33 final size:33
Alignment explanation
Indices: 287260--287372 Score: 156
Period size: 33 Copynumber: 3.4 Consensus size: 33
287250 GCGAATTTAG
* * *
287260 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCATTGCGATTATCTCGTTGTGATTTTCA
*
287293 TTTCGCATTGCGATTCTCTCGTTGCT-ATTTTCA
1 TTTCGCATTGCGATTATCTCGTTG-TGATTTTCA
* *
287326 TTTCGCATTGTGATTATCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTATCTCGTTGTGATTTTCA
287359 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
287373 AGTAATTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
33 70 0.99
34 1 0.01
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTATCTCGTTGTGATTTTCA
Found at i:287371 original size:19 final size:19
Alignment explanation
Indices: 287285--287372 Score: 70
Period size: 16 Copynumber: 5.2 Consensus size: 19
287275 TTGTCGTTGT
287285 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
287304 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
* *
287318 TATTTTCATTTCGCATTGT
1 GATTTTCATTTCGCATTGC
*
287337 GA--TT-ATCTCG--TTGC
1 GATTTTCATTTCGCATTGC
287351 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
287370 GAT
1 GAT
287373 AGTAATTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
14 10 0.20
16 14 0.27
17 14 0.27
19 13 0.25
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:287498 original size:14 final size:14
Alignment explanation
Indices: 287479--287515 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
287469 CATCAATTAA
287479 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
287493 ACAAATCACCTTTT
1 ACAAATCAACTTTT
287507 ACAAATCAA
1 ACAAATCAA
287516 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:288958 original size:42 final size:42
Alignment explanation
Indices: 288891--288970 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
288881 CGATGACAGT
* * *
288891 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
288933 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
288971 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:289368 original size:91 final size:90
Alignment explanation
Indices: 289192--289376 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
289182 ATTTGAAACT
*
289192 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
289257 AGAATTGGCAACAACCGAATAAATTTAC
63 AGAATTGGCAACAACCGAATAAATTTAC
289285 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
289349 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAACAACCGAATAAATTTAC
289376 T
1 T
289377 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAACAACCGAATAAATTTAC
Found at i:291114 original size:20 final size:19
Alignment explanation
Indices: 291069--291256 Score: 87
Period size: 19 Copynumber: 10.8 Consensus size: 19
291059 TCTTTCGGTT
291069 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
291088 GATAATGAAAATCGCAAAGCG-
1 GA-AATGAAAATCGC-AA-CGA
**
291109 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
291128 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
291142 GAAAT-AACTATCGCAACGA
1 GAAATGAA-AATCGCAACGA
* *
291161 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
**
291175 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
291194 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
291208 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
291227 G--A-G--AATTGCAACGC
1 GAAATGAAAATCGCAACGA
291241 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
291257 TGCGATTTTG
Statistics
Matches: 125, Mismatches: 18, Indels: 52
0.64 0.09 0.27
Matches are distributed among these distances:
14 39 0.31
16 7 0.06
17 7 0.06
18 2 0.02
19 42 0.34
20 22 0.18
21 4 0.03
22 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:291137 original size:14 final size:14
Alignment explanation
Indices: 291118--291239 Score: 64
Period size: 14 Copynumber: 7.6 Consensus size: 14
291108 GGAAATGACT
291118 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
291132 ATCGCAACGCGAAATAA
1 ATCGCAA--CGAGA-GA
291149 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
291165 ATCGCAATGCGAAATGA
1 ATCGCAA--CGAGA-GA
291182 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
291198 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
291217 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
291231 ATTGCAACG
1 ATCGCAACG
291240 CGAAATGAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 30
0.68 0.07 0.24
Matches are distributed among these distances:
14 32 0.38
15 1 0.01
16 13 0.15
17 13 0.15
18 1 0.01
19 24 0.29
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:291183 original size:66 final size:66
Alignment explanation
Indices: 291069--291256 Score: 243
Period size: 66 Copynumber: 2.7 Consensus size: 66
291059 TCTTTCGGTT
291069 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAAAGCGGAAATGACTATCGCAACGAGAGAAT
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAAAGC-GAAATGACTATCGCAACGAGAGAAT
291134 CGCAACGC
59 CGCAACGC
* *
291142 GAAAT-AACTATCGCAACGAGAGAATCGCAATGCGAAATGACTATCGCAACGAGAGAATCGCAAC
1 GAAATGAA-AATCGCAACGAGAGAATCGCAAAGCGAAATGACTATCGCAACGAGAGAATCGCAAC
291206 GC
65 GC
* * **
291208 GAAATGAAAATCGCAACGAGAGAATTGCAACGCGAAATGAAAATCGCAA
1 GAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGACTATCGCAA
291257 TGCGATTTTG
Statistics
Matches: 106, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
66 74 0.70
67 12 0.11
69 1 0.01
70 1 0.01
72 2 0.02
73 16 0.15
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (66 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGACTATCGCAACGAGAGAATCGCAACG
C
Found at i:291189 original size:19 final size:18
Alignment explanation
Indices: 291098--291214 Score: 69
Period size: 14 Copynumber: 6.9 Consensus size: 18
291088 GATAATGAAA
291098 ATCGCAAAGCGGAAATGACT
1 ATCGC-AAGC-GAAATGACT
*
291118 ATCGCAA-CGAGA-GA--
1 ATCGCAAGCGAAATGACT
*
291132 ATCGCAACGCGAAATAACT
1 ATCGCAA-GCGAAATGACT
*
291151 ATCGCAA-CGAGA-GA--
1 ATCGCAAGCGAAATGACT
291165 ATCGCAATGCGAAATGACT
1 ATCGCAA-GCGAAATGACT
*
291184 ATCGCAA-CGAGA-GA--
1 ATCGCAAGCGAAATGACT
291198 ATCGCAACGCGAAATGA
1 ATCGCAA-GCGAAATGA
291215 AAATCGCAAC
Statistics
Matches: 76, Mismatches: 8, Indels: 29
0.67 0.07 0.26
Matches are distributed among these distances:
14 21 0.28
16 17 0.22
17 16 0.21
18 1 0.01
19 16 0.21
20 5 0.07
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGACT
Found at i:291246 original size:33 final size:33
Alignment explanation
Indices: 291097--291256 Score: 232
Period size: 33 Copynumber: 4.8 Consensus size: 33
291087 AGATAATGAA
* *
291097 AATCGCAAAGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAATATCGCAACGAGAG
291131 AATCGCAACGCGAAAT-AACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGAA-TATCGCAACGAGAG
* *
291164 AATCGCAATGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGAATATCGCAACGAGAG
*
291197 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAATATCGCAACGAGAG
* *
291230 AATTGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAATATCGCAA
291257 TGCGATTTTG
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.01
33 104 0.90
34 11 0.09
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAATATCGCAACGAGAG
Found at i:291290 original size:19 final size:19
Alignment explanation
Indices: 291257--291327 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
291247 AAAATCGCAA
**
291257 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
291276 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
291295 TGCGATGGTT-ATTTCCGCGT
1 TGCGAT-TTTCATTT-CGCGT
291315 TGCGATTTTCATT
1 TGCGATTTTCATT
291328 CTCGAAACTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:291870 original size:20 final size:20
Alignment explanation
Indices: 291845--292079 Score: 118
Period size: 20 Copynumber: 11.6 Consensus size: 20
291835 GCTATGTAAA
*
291845 TCGCATTGCGATATACGTAT
1 TCGCATTGCGATTTACGTAT
* *
291865 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
291886 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
* * *
291906 TCGCGTTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
**
291926 TCGTGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * * * *
291946 TCGTATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACG-TAT
** * *
291967 TCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGT-AT
* * * *
291987 TCGCAATGCGAATTAGGAAAAT
1 TCGCATTGCGATTTACG--TAT
*
292009 T-GCATTGCGATAGT-CAGTA-
1 TCGCATTGCGAT-TTAC-GTAT
* **
292028 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACGTAT
*
292049 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACGTAT
292069 TCGCATTGCGA
1 TCGCATTGCGA
292080 ATTGGGAAAA
Statistics
Matches: 166, Mismatches: 37, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.01
20 110 0.66
21 51 0.31
22 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:291890 original size:41 final size:41
Alignment explanation
Indices: 291845--292079 Score: 158
Period size: 41 Copynumber: 5.8 Consensus size: 41
291835 GCTATGTAAA
*
291845 TCGCATTGCGATATACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATATACGTATTCGCATTGCGATTTTCCAAAT
* * * * * **
291886 TCGCATTGCGATTTACTTAATCGCGTTGCGATTTACTTAA-
1 TCGCATTGCGATATACGTATTCGCATTGCGATTTTCCAAAT
** * * * * *
291926 TCGTGTTGCGATTTACGTATTCGTATTGCGAATTAT-GAAAA
1 TCGCATTGCGATATACGTATTCGCATTGCG-ATTTTCCAAAT
** * * ****
291967 TCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAAAT
1 TCGCATTGCGATATACGT-ATTCGCATTGCG-ATTTTCCAAAT
292009 T-GCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATA-TAC-GTATTCGCATTGCGATTTTCCAAAT
* *
292049 TCGCATTGCGATTTACTTATTCGCATTGCGA
1 TCGCATTGCGATATACGTATTCGCATTGCGA
292080 ATTGGGAAAA
Statistics
Matches: 148, Mismatches: 36, Indels: 20
0.73 0.18 0.10
Matches are distributed among these distances:
40 42 0.28
41 96 0.65
42 7 0.05
43 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (41 bp):
TCGCATTGCGATATACGTATTCGCATTGCGATTTTCCAAAT
Found at i:292017 original size:21 final size:21
Alignment explanation
Indices: 291952--292018 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
291942 GTATTCGTAT
*
291952 TGCGAATTATGAAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* *
291973 CGCGAA-TACGTAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* * *
291993 TGCGAATTAGGAAAATTGCAT
1 TGCGAATTACGAAAATCGCAA
292014 TGCGA
1 TGCGA
292019 TAGTCAGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCGAATTACGAAAATCGCAA
Found at i:292121 original size:21 final size:22
Alignment explanation
Indices: 292069--292121 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
292059 ATTTACTTAT
292069 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
292090 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
292111 TCGCATTGCGA
1 TCGCATTGCGA
292122 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:293452 original size:60 final size:60
Alignment explanation
Indices: 293387--293528 Score: 166
Period size: 61 Copynumber: 2.4 Consensus size: 60
293377 GGAATGTTAA
** *
293387 AAAAGTTTGGGGATCAATTTAGAATGA-AGGTAATAGTTTGAGGA-TGGAATTAAAAT-TTT
1 AAAAGTTTAAGGATCAATTTAGAATGATA-GTAATAGTTT-AGGATTGAAATTAAAATATTT
* *
293446 CAAAAGTTTTAAAGA-CTAATTTAGAATGATAGTCATAGTTTAGGATTGAAATTAAAATATTT
1 -AAAAG-TTTAAGGATC-AATTTAGAATGATAGTAATAGTTTAGGATTGAAATTAAAATATTT
293508 AAAAGTTTAAGGATCAATTTA
1 AAAAGTTTAAGGATCAATTTA
293529 ATATAAAGGT
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
60 23 0.33
61 43 0.61
62 4 0.06
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (60 bp):
AAAAGTTTAAGGATCAATTTAGAATGATAGTAATAGTTTAGGATTGAAATTAAAATATTT
Found at i:293541 original size:60 final size:60
Alignment explanation
Indices: 293387--293548 Score: 163
Period size: 61 Copynumber: 2.7 Consensus size: 60
293377 GGAATGTTAA
** * * *
293387 AAAAGTTTGGGGATCAATTTAGAATGAAGGTAATAGTTTGAGGATGGAATTAAAATTTTC
1 AAAAGTTTAAGGATCAATTTAGAATAAAGGTCATAGTTTGAGGATGAAATTAAAATTTTC
* *
293447 AAAAGTTTTAAAGA-CTAATTTAGAATGATA-GTCATAGTTT-AGGATTGAAATTAAAATATTT-
1 AAAAG-TTTAAGGATC-AATTTAGAAT-AAAGGTCATAGTTTGAGGA-TGAAATTAAAAT-TTTC
*
293508 AAAAGTTTAAGGATCAATTTA-ATATAAAGGTCATACTTTGA
1 AAAAGTTTAAGGATCAATTTAGA-ATAAAGGTCATAGTTTGA
293549 AGACATTTGA
Statistics
Matches: 83, Mismatches: 10, Indels: 17
0.75 0.09 0.15
Matches are distributed among these distances:
59 3 0.04
60 34 0.41
61 42 0.51
62 4 0.05
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (60 bp):
AAAAGTTTAAGGATCAATTTAGAATAAAGGTCATAGTTTGAGGATGAAATTAAAATTTTC
Found at i:303431 original size:44 final size:45
Alignment explanation
Indices: 303374--303462 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 45
303364 CCCACCTTAT
* * * *
303374 TATTATCTCTTTTTTAAATTTTAAACACCCTA-CTTTTCCTTTTA
1 TATTATATATTTTTTAAATTTTAAACACCCCACCTATTCCTTTTA
* *
303418 TATTATATATTTTTTTAATTTTAAACTCCCCACCTATTCCTTTTA
1 TATTATATATTTTTTAAATTTTAAACACCCCACCTATTCCTTTTA
303463 ATCAACCAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
44 27 0.71
45 11 0.29
ACGTcount: A:0.26, C:0.20, G:0.00, T:0.54
Consensus pattern (45 bp):
TATTATATATTTTTTAAATTTTAAACACCCCACCTATTCCTTTTA
Found at i:304374 original size:20 final size:20
Alignment explanation
Indices: 304351--304388 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
304341 TTTGAAACTT
304351 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
304371 AAATTCGCAACGCGAAAA
1 AAATTCGCAACACGAAAA
304389 CTAAAATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:304398 original size:20 final size:20
Alignment explanation
Indices: 304345--304398 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
304335 GTAGTTTTTG
304345 AAACTTAAATTCGCAACACGA
1 AAAC-TAAATTCGCAACACGA
*
304366 AAA-TGAAATTCGCAACGCGA
1 AAACT-AAATTCGCAACACGA
*
304386 AAACTAAAATCGC
1 AAACTAAATTCGC
304399 GTTGCGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 1 0.03
20 24 0.83
21 4 0.14
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (20 bp):
AAACTAAATTCGCAACACGA
Found at i:305971 original size:42 final size:42
Alignment explanation
Indices: 305909--306008 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
305899 ACCCCCACTT
* * * * **
305909 CGAGAGCAATCACCTGATCGAGCCGATTCTACAGCTTGACAC
1 CGAGAGCCATCACCTAATCGAGCCGATTATACACCTAAACAC
*
305951 CGAGAGCCATCACCTAATCGAGCTGATTATACACCTAAACAC
1 CGAGAGCCATCACCTAATCGAGCCGATTATACACCTAAACAC
305993 CGAGAGCCATCACCTA
1 CGAGAGCCATCACCTA
306009 TTCCATCACA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTAATCGAGCCGATTATACACCTAAACAC
Found at i:306617 original size:21 final size:21
Alignment explanation
Indices: 306591--306713 Score: 106
Period size: 21 Copynumber: 5.9 Consensus size: 21
306581 GATACACATA
*
306591 CCATTGTTCAGGATCCACCTC
1 CCATCGTTCAGGATCCACCTC
* * *
306612 CCATTGTTCAGGATTCACCTG
1 CCATCGTTCAGGATCCACCTC
* * *
306633 TCATCGTTCAAGAGGCC-CCTC
1 CCATCGTTCAGGA-TCCACCTC
* * *
306654 CCATCGTTCAAGAGGCC-CCTT
1 CCATCGTTCAGGA-TCCACCTC
*
306675 CCATCGTTCAGGATCCACTTC
1 CCATCGTTCAGGATCCACCTC
*
306696 CCACCGTTCAGGATCCAC
1 CCATCGTTCAGGATCCAC
306714 ATGGCATACT
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
20 2 0.02
21 82 0.96
22 1 0.01
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (21 bp):
CCATCGTTCAGGATCCACCTC
Found at i:308247 original size:20 final size:20
Alignment explanation
Indices: 308224--308270 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
308214 AAGAAAATCG
308224 AATTCGCAACGCGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
** *
308244 AATTTTCAACGCGAAATTCA
1 AATTCGCAACGCGAAAGTCA
308264 AATTCGC
1 AATTCGC
308271 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
AATTCGCAACGCGAAAGTCA
Found at i:308318 original size:20 final size:20
Alignment explanation
Indices: 308295--308368 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
308285 TTTCACGTGT
*
308295 CGAATTCGATTTTCGTGTAG
1 CGAATTTGATTTTCGTGTAG
* *
308315 CGAATTTGATTTTCGCGTTG
1 CGAATTTGATTTTCGTGTAG
* * *
308335 TGAATTTGACTTTCGTGTTG
1 CGAATTTGATTTTCGTGTAG
* *
308355 CAAATTTGACTTTC
1 CGAATTTGATTTTC
308369 AATTCAATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.45
Consensus pattern (20 bp):
CGAATTTGATTTTCGTGTAG
Found at i:308327 original size:40 final size:40
Alignment explanation
Indices: 308274--308369 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
308264 AATTCGCGTT
* * *
308274 GCGATTTTTATTTTCACG-TGTCGAATTCGATTTTCGTGTA
1 GCGAATTTGATTTTCACGTTGT-GAATTCGACTTTCGTGTA
* * *
308314 GCGAATTTGATTTTCGCGTTGTGAATTTGACTTTCGTGTT
1 GCGAATTTGATTTTCACGTTGTGAATTCGACTTTCGTGTA
* *
308354 GCAAATTTGACTTTCA
1 GCGAATTTGATTTTCA
308370 ATTCAATTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
40 43 0.93
41 3 0.07
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.46
Consensus pattern (40 bp):
GCGAATTTGATTTTCACGTTGTGAATTCGACTTTCGTGTA
Found at i:309123 original size:20 final size:20
Alignment explanation
Indices: 309095--309158 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
309085 AAATAAAAGC
*
309095 TGTTGCGAAATTAAAATTCG
1 TGTTACGAAATTAAAATTCG
309115 TGTTACG-AATTCGAAAA-TCG
1 TGTTACGAAATT--AAAATTCG
* * **
309135 AGTTCCGAAAACAAAATTCG
1 TGTTACGAAATTAAAATTCG
309155 TGTT
1 TGTT
309159 GTGAATTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 8 0.24
20 20 0.59
21 6 0.18
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
TGTTACGAAATTAAAATTCG
Found at i:309333 original size:21 final size:21
Alignment explanation
Indices: 309309--309371 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
309299 TGCTATTTAA
309309 GAAACTGAGTTGCGAATTTGG
1 GAAACTGAGTTGCGAATTTGG
* * *
309330 GAAATTCGCGTTACGAATTT-G
1 GAAACT-GAGTTGCGAATTTGG
* *
309351 GAAACTGTGTTGCGAAATTGG
1 GAAACTGAGTTGCGAATTTGG
309372 AGTTCACGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.30
21 12 0.36
22 11 0.33
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (21 bp):
GAAACTGAGTTGCGAATTTGG
Found at i:309363 original size:82 final size:81
Alignment explanation
Indices: 309186--309367 Score: 181
Period size: 82 Copynumber: 2.2 Consensus size: 81
309176 ATTGTGAAAA
*
309186 GGAAACTTGTGTTGCG-AAAAGAAATTCGCATTGCGAATTCAGAAATCGAGTTACGAATTTGAAA
1 GGAAAC-TGTGTTGCGAAAAAGAAATTCGCATTGCGAATTAAGAAATCGAGTTACGAATTTGAAA
* * **
309250 TTATGTGTTGTGAATTT
65 TTACGCGTTACGAATTT
** * * * * * *
309267 TTAAAATCGCGTTGCGAAAAAGAAATTCGCGTTGCTATTTAAGAAA-CTGAGTTGCGAATTTGGG
1 GGAAACT-GTGTTGCGAAAAAGAAATTCGCATTGCGAATTAAGAAATC-GAGTTACGAATTT--G
309331 AAATT-CGCGTTACGAATTT
62 AAATTACGCGTTACGAATTT
309350 GGAAACTGTGTTGCGAAA
1 GGAAACTGTGTTGCGAAA
309368 TTGGAGTTCA
Statistics
Matches: 79, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
80 1 0.01
81 11 0.14
82 47 0.59
83 14 0.18
84 6 0.08
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (81 bp):
GGAAACTGTGTTGCGAAAAAGAAATTCGCATTGCGAATTAAGAAATCGAGTTACGAATTTGAAAT
TACGCGTTACGAATTT
Done.