Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009067.1 Hibiscus syriacus cultivar Beakdansim tig00112491_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: 2329927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2139016 original size:32 final size:32
Alignment explanation
Indices: 2138961--2139025 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
2138951 GAAAAAAGAG
*
2138961 AAAAAAGGAGGGTTCAAGATGAAAACCCGAAA
1 AAAAAAAGAGGGTTCAAGATGAAAACCCGAAA
2138993 AAAAAAAGAGAGGTTCAAG-TGAAAACCCGAAA
1 AAAAAAAGAG-GGTTCAAGATGAAAACCCGAAA
2139025 A
1 A
2139026 GGGCGTCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.55, C:0.12, G:0.23, T:0.09
Consensus pattern (32 bp):
AAAAAAAGAGGGTTCAAGATGAAAACCCGAAA
Found at i:2140544 original size:55 final size:54
Alignment explanation
Indices: 2140316--2140686 Score: 411
Period size: 55 Copynumber: 6.9 Consensus size: 54
2140306 GTTGAAGATT
* * * ** *
2140316 GAGT-CTATACTCTCTGAATGAATAGGGAGTGGACAAGTTCATTGAAGA--TT-
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTC
* * * ** **
2140366 GAGTCCTATACTCTCTGAATGAATAGGGAGTGGACAAGTTCGTTGAAGA--TT-
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTC
* *
2140417 GAGTCCTATACTCTCTG-AAGAAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAAG-AATAGAGAGCGGACCTG-TTTATTGAAGATT-TTC
2140473 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTC
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGA-TTTTC
* * * *
2140528 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTG-TTTATTGAAGATT-TTC
2140584 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTC
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGA-TTTTC
* * *
2140639 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACGT-TTTA-TGAAGAT
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGAT
2140687 CGAATCATTT
Statistics
Matches: 289, Mismatches: 20, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
50 6 0.02
51 75 0.26
52 11 0.04
53 6 0.02
54 4 0.01
55 99 0.34
56 85 0.29
57 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (54 bp):
GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTC
Found at i:2140567 original size:111 final size:111
Alignment explanation
Indices: 2140366--2140673 Score: 507
Period size: 111 Copynumber: 2.8 Consensus size: 111
2140356 ATTGAAGATT
* * * ** ** *
2140366 GAGTCCTATACTCTCTGAATGAATAGGGAGTGGACAAGTTCGTTGAAGA---TT-GAGTCCTATA
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
*
2140427 CTCTCTGAAGAAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
2140473 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
2140538 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
2140584 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
2140649 CTCTCTGAAGGAATAGAGAGCGGAC
66 CTCTCTGAAGGAATAGAGAGCGGAC
2140674 GTTTTATGAA
Statistics
Matches: 188, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
107 42 0.22
110 2 0.01
111 144 0.77
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (111 bp):
GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
Found at i:2156946 original size:30 final size:29
Alignment explanation
Indices: 2156859--2156951 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 29
2156849 AGAATTAATG
* * *
2156859 GGTCAAATTAATATTTTATCTAAAGTTTAG
1 GGTCAAA-TAATATTCTATTTAAAGTTTAA
* *
2156889 GAGTCAAAATGATA-TCTTTTTAGAAGTTTAA
1 G-GTC-AAATAATATTCTATTTA-AAGTTTAA
*
2156920 GGTCAAATCAATATTCTATTTAAAGTTCAA
1 GGTCAAAT-AATATTCTATTTAAAGTTTAA
2156950 GG
1 GG
2156952 GGCAAACTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
29 4 0.08
30 21 0.42
31 22 0.44
32 3 0.06
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (29 bp):
GGTCAAATAATATTCTATTTAAAGTTTAA
Found at i:2159411 original size:17 final size:17
Alignment explanation
Indices: 2159391--2159423 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2159381 CTCACTAACC
*
2159391 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
2159408 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
2159424 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:2160055 original size:19 final size:19
Alignment explanation
Indices: 2160033--2160078 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2160023 ATTTAGACAT
* *
2160033 TTTGCATTTTTTTATTTTC
1 TTTGCATTTTGTTAGTTTC
2160052 TTTGCATTTTGTTAGTTTC
1 TTTGCATTTTGTTAGTTTC
2160071 TTTGCATT
1 TTTGCATT
2160079 CACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTAGTTTC
Found at i:2163271 original size:16 final size:16
Alignment explanation
Indices: 2163247--2163282 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2163237 CGAGAACCAA
2163247 TTCAGACCAAATCCAG
1 TTCAGACCAAATCCAG
*
2163263 TTCATACCAAATCCAG
1 TTCAGACCAAATCCAG
2163279 TTCA
1 TTCA
2163283 ACAACTCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.08, T:0.25
Consensus pattern (16 bp):
TTCAGACCAAATCCAG
Found at i:2163945 original size:165 final size:165
Alignment explanation
Indices: 2163719--2164342 Score: 860
Period size: 165 Copynumber: 3.8 Consensus size: 165
2163709 CAAATACCTT
* * * * * * * * *
2163719 CGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTT
1 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
* * *
2163783 GTCTGCCAATAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCATATCATTTGCAGCAT
66 ATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCAT
*
2163847 AGCTTAAGTCGAGAAGGACTATCTGCCAAAGACCCC
130 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
* * *
2163883 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCT
1 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
* **
2163948 ATTTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATA
66 ATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
* *
2164013 GCTTAAGTCGAGAAGGGCTAGCTACCAAAGACCCC
131 GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
* * * *
2164048 CGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAATATAACTCAAGGGTAGAAGGGTT
1 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
* * * *
2164113 ATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATA
66 ATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
* *
2164177 GCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCT
131 GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
* * * * *
2164212 CGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTT
1 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
* * *
2164277 ATCTGTCAACCAAAGACCTTTGAGTTCGACTAC-CTCAGCTCCAAGGCACATCATTTACAGCATA
66 ATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
2164341 GC
131 GC
2164343 CCAAGGCAAG
Statistics
Matches: 406, Mismatches: 51, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
164 195 0.48
165 208 0.51
166 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
ATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
Found at i:2164316 original size:413 final size:409
Alignment explanation
Indices: 2163503--2164361 Score: 1238
Period size: 413 Copynumber: 2.1 Consensus size: 409
2163493 TTTAAGACAA
* * *
2163503 CATTTGCAATATAGCTCAAGACAAGAAGGGCTATTTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTAC
* * *
2163568 GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTATCAAAGACC
66 GCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTAGCTACCAAAGACC
* * *
2163633 CCCGAGTTCGATTACATTCAACTTCGAGGGCATATCATTTACAATATAACTCAAGGCTAGGAGGG
131 CCCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAATATAACTCAAGGCTAGAAGGG
* *
2163698 TTATCTGTCACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCAC
196 TTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAC
* * * * *
2163763 AACTTAAGTCTAGAAGGGTTGTCTGCCAATAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAC
261 AACTTAAGTCGAGAAGGGTTATCTGCC---AAAAGACCCTCGAGTTCGACTACACTCAGCTCAAC
* * *
2163828 GGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGACTATCTGCCAAAGACCCCCGAGTTCGAT
323 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGACTATCTGCCAAAGACCCCCGAGTTCGAC
* *
2163893 TACACTCAGCTTCGAGGGCACAT
388 TACACTCAGC-TCCAAGGCACAT
*
2163916 CATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTAC
* *
2163981 GCTCAGCTCCAAGGCACATCATTTGCAATATAGCTTAAGTCGAGAAGGGCTAGCTACCAAAGACC
66 GCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTAGCTACCAAAGACC
* * *
2164046 CCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAATATAACTCAAGGGTAGAAGGG
131 CCCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAATATAACTCAAGGCTAGAAGGG
* *
2164111 TTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCAT
196 TTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAC
* * *
2164176 AGCTTAAGTCGAGAAGGGTTATCTGCC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGA-GG
261 AACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCCTCGAGTTCGACTACACTCAGC-TCAACGG
** ***
2164239 ACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTC
325 -CACATCATTTGCAGCATAACTTAAGTCGAGAAGGACTATCTG----CCAAAGACCCCCGAGTTC
2164304 GACTAC-CTCAGCTCCAAGGCACAT
385 GACTACACTCAGCTCCAAGGCACAT
* * * *
2164328 CATTTACAGCATAGCCCAAGGCAAGAAGAGCTAT
1 CATTTGCAACATAGCTCAAGGCAAGAAGGGCTAT
2164362 CTGTCAAGAA
Statistics
Matches: 399, Mismatches: 41, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
409 27 0.07
410 41 0.10
412 40 0.10
413 271 0.68
414 20 0.05
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (409 bp):
CATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTAGCTACCAAAGACC
CCCGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAATATAACTCAAGGCTAGAAGGG
TTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAC
AACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCCTCGAGTTCGACTACACTCAGCTCAACGGC
ACATCATTTGCAGCATAACTTAAGTCGAGAAGGACTATCTGCCAAAGACCCCCGAGTTCGACTAC
ACTCAGCTCCAAGGCACAT
Found at i:2179051 original size:2 final size:2
Alignment explanation
Indices: 2179044--2179080 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2179034 TTAAAACTTA
2179044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2179081 AAAGTTTAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2180190 original size:30 final size:29
Alignment explanation
Indices: 2180103--2180195 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 29
2180093 AGAATTAATG
* * *
2180103 GGTCAAATTAATATTTTATCTAAAGTTTAG
1 GGTCAAA-TAATATTCTATTTAAAGTTTAA
* *
2180133 GAGTCAAAATGATA-TCTTTTTAGAAGTTTAA
1 G-GTC-AAATAATATTCTATTTA-AAGTTTAA
*
2180164 GGTCAAATCAATATTCTATTTAAAGTTCAA
1 GGTCAAAT-AATATTCTATTTAAAGTTTAA
2180194 GG
1 GG
2180196 GGCAAACTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
29 4 0.08
30 21 0.42
31 22 0.44
32 3 0.06
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (29 bp):
GGTCAAATAATATTCTATTTAAAGTTTAA
Found at i:2182782 original size:31 final size:33
Alignment explanation
Indices: 2182747--2182807 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
2182737 TTTTTAAAGA
2182747 GAAATTATATAT-T-CCTGTTTCTATACATACT
1 GAAATTATATATATGCCTGTTTCTATACATACT
2182778 GAAATTATATATATGCCTGTTTCTATACAT
1 GAAATTATATATATGCCTGTTTCTATACAT
2182808 CCTAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 12 0.43
32 1 0.04
33 15 0.54
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (33 bp):
GAAATTATATATATGCCTGTTTCTATACATACT
Found at i:2185262 original size:15 final size:14
Alignment explanation
Indices: 2185238--2185276 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2185228 ATCCATTTTT
2185238 CATAACATATCACA
1 CATAACATATCACA
2185252 CATACACATATCACA
1 CATA-ACATATCACA
* *
2185267 TATAATATAT
1 CATAACATAT
2185277 AATATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (14 bp):
CATAACATATCACA
Found at i:2185411 original size:23 final size:23
Alignment explanation
Indices: 2185376--2185441 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
2185366 CACCACAACT
*
2185376 CGTATAAATGCACCGAAGTGTCA
1 CGTAGAAATGCACCGAAGTGTCA
*
2185399 CGTAG-AATCGCACCGAAGTGTCG
1 CGTAGAAAT-GCACCGAAGTGTCA
*
2185422 CGTAGAAATGCACAGAAGTG
1 CGTAGAAATGCACCGAAGTG
2185442 CCATATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 3 0.08
23 32 0.84
24 3 0.08
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGTCA
Found at i:2185750 original size:170 final size:170
Alignment explanation
Indices: 2185468--2185807 Score: 662
Period size: 170 Copynumber: 2.0 Consensus size: 170
2185458 TAAGGACCAC
2185468 ATAGAAATTCCTTAAGAATCATATACATATACCAAGAATCAAGTAGGTGTCTCAAAAGACCTCAT
1 ATAGAAATTCCTTAAGAATCATATACATATACCAAGAATCAAGTAGGTGTCTCAAAAGACCTCAT
*
2185533 ACATGTTTCAAAGAATACATATATGTCCCGAAGAACCACGTAGAAATTTCCCGAATACACACTAT
66 ACATATTTCAAAGAATACATATATGTCCCGAAGAACCACGTAGAAATTTCCCGAATACACACTAT
2185598 AGTATTTGCTCACTTCATCATCTTTCTTATATTCTATGGA
131 AGTATTTGCTCACTTCATCATCTTTCTTATATTCTATGGA
*
2185638 ATAGAAATTCCTTAAGAATCATATACATATATCAAGAATCAAGTAGGTGTCTCAAAAGACCTCAT
1 ATAGAAATTCCTTAAGAATCATATACATATACCAAGAATCAAGTAGGTGTCTCAAAAGACCTCAT
2185703 ACATATTTCAAAGAATACATATATGTCCCGAAGAACCACGTAGAAATTTCCCGAATACACACTAT
66 ACATATTTCAAAGAATACATATATGTCCCGAAGAACCACGTAGAAATTTCCCGAATACACACTAT
2185768 AGTATTTGCTCACTTCATCATCTTTCTTATATTCTATGGA
131 AGTATTTGCTCACTTCATCATCTTTCTTATATTCTATGGA
2185808 CGAAAGATGT
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 168 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (170 bp):
ATAGAAATTCCTTAAGAATCATATACATATACCAAGAATCAAGTAGGTGTCTCAAAAGACCTCAT
ACATATTTCAAAGAATACATATATGTCCCGAAGAACCACGTAGAAATTTCCCGAATACACACTAT
AGTATTTGCTCACTTCATCATCTTTCTTATATTCTATGGA
Found at i:2187880 original size:26 final size:27
Alignment explanation
Indices: 2187820--2187880 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
2187810 TTTTTATTGT
*
2187820 TTTTAATTTTTATTAATGGAAGAAATAA
1 TTTTAACTTTTATTAAT-GAAGAAATAA
2187848 TTCTTAACTTTTATTAAT-AA-AAATAA
1 TT-TTAACTTTTATTAATGAAGAAATAA
2187874 TCTTTAA
1 T-TTTAA
2187881 ATAAAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 11 0.37
27 3 0.10
28 2 0.07
29 14 0.47
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (27 bp):
TTTTAACTTTTATTAATGAAGAAATAA
Found at i:2193645 original size:132 final size:133
Alignment explanation
Indices: 2193502--2193772 Score: 436
Period size: 136 Copynumber: 2.0 Consensus size: 133
2193492 AAGTCCTGCC
2193502 ACTTTCAAGAGTTAGACTGAATTTCCAGTCATCTCTATCTTTGTTTTCTTTTTA-TTCCTTCTGT
1 ACTTTCAAGAGTTAGACTGAATTTCCAGTCATCTCTATCTTTGTTTTCTTTTTATTTCCTTCTGT
* * *
2193566 TGATTTATTAAAATCTTATGGACTTCCAGCTCTTGCAATTAATTTTATCACTTCCTGCATCAGAG
66 TGATTTATTAAAATCTTATGGACTTCCAGCTCTTACAATTAATTTTATAACTTCCTGCATCAGAA
2193631 GAT
131 GAT
* *
2193634 ACTTTCGAGAGTTAGACTGAATTTCCAGTCATCTCTATCTTTGTTTTGTTTTTATCTTTTCCTTC
1 ACTTTCAAGAGTTAGACTGAATTTCCAGTCATCTCTATCTTTGTTTTCTTTTTA---TTTCCTTC
* * *
2193699 TGTTGGTTTATTAAAATTTTATGGACTTCCAGCTCTTACAATTAGTTTTATAACTTCCTGCATCA
63 TGTTGATTTATTAAAATCTTATGGACTTCCAGCTCTTACAATTAATTTTATAACTTCCTGCATCA
2193764 GAAGAT
128 GAAGAT
2193770 ACT
1 ACT
2193773 GAGCTCCAGT
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
132 52 0.41
136 75 0.59
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (133 bp):
ACTTTCAAGAGTTAGACTGAATTTCCAGTCATCTCTATCTTTGTTTTCTTTTTATTTCCTTCTGT
TGATTTATTAAAATCTTATGGACTTCCAGCTCTTACAATTAATTTTATAACTTCCTGCATCAGAA
GAT
Found at i:2206078 original size:13 final size:14
Alignment explanation
Indices: 2206035--2206083 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
2206025 CATAACATGG
2206035 ACATTTTCACTTATC
1 ACATTTTCAC-TATC
*
2206050 TCA-TTTCACTAT-
1 ACATTTTCACTATC
2206062 ACATTTTCA-TATC
1 ACATTTTCACTATC
*
2206075 ACATGTTCA
1 ACATTTTCA
2206084 TATAAGCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 5 0.17
13 16 0.55
14 6 0.21
15 2 0.07
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (14 bp):
ACATTTTCACTATC
Found at i:2206087 original size:25 final size:26
Alignment explanation
Indices: 2206035--2206087 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 26
2206025 CATAACATGG
*
2206035 ACATTTTCACTTATCTCATTTCACTAT
1 ACATTTTCAC-TATCACATTTCACTAT
2206062 ACATTTTCA-TATCACATGTTCA-TAT
1 ACATTTTCACTATCACAT-TTCACTAT
2206087 A
1 A
2206088 AGCTCATAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 11 0.46
26 4 0.17
27 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.45
Consensus pattern (26 bp):
ACATTTTCACTATCACATTTCACTAT
Found at i:2206774 original size:20 final size:22
Alignment explanation
Indices: 2206749--2206807 Score: 86
Period size: 20 Copynumber: 2.7 Consensus size: 22
2206739 TTCCCCTTGA
2206749 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
2206769 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
2206792 ATGTGCATCGATGCAT
1 A-GTGCATCGATGCAT
2206808 GGGTATCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.49
22 1 0.03
23 3 0.09
24 14 0.40
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:2211203 original size:20 final size:20
Alignment explanation
Indices: 2211178--2211235 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
2211168 TTTCCCTTGA
2211178 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
2211198 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
2211218 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
2211236 TGAACGTGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2211331 original size:19 final size:19
Alignment explanation
Indices: 2211307--2211359 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
2211297 TTTTAAGGGG
2211307 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
2211326 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
2211345 ATGCATCGATGCACT
1 ATGCATCGATGCACT
2211360 AATTGCATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:2212142 original size:2 final size:2
Alignment explanation
Indices: 2212135--2212179 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2212125 TTACAAATTG
2212135 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
2212177 AT A
1 AT A
2212180 CTCATCTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2224533 original size:41 final size:40
Alignment explanation
Indices: 2224488--2224832 Score: 227
Period size: 41 Copynumber: 8.5 Consensus size: 40
2224478 ATTCACGTTG
* *
2224488 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
* *
2224529 CATTTCGCGTTGCGATAGATGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAG-TTGAAATCGCGTTGCGATTTTC
***
2224570 CATTTCGCGTTGCGATAGTTGAAATCGCAACGCGA-TTTC
1 CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
* * ** * * *
2224609 CATCATCGCAAATT-CG-T-GTTGCATTTCGAGTTGCGATAGTTG
1 CAT-TTCGC--GTTGCGATAGTTG-AAATCGCGTTGCGAT-TTTC
* ** * * * ** * *
2224651 AAAATCGCGTTGTGAT-TTTCCATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTT-GAAATCGCGTTGCGAT-TTTC
* ** * * **
2224692 AAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-GAAATCGCGTTGCGATTTTC
*
2224732 CATTTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
*
2224773 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGA-AATCGCGTTGCGATTTTC
2224814 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2224833 CTACACTTGT
Statistics
Matches: 251, Mismatches: 39, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
39 13 0.05
40 41 0.16
41 189 0.75
42 8 0.03
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
Found at i:2224584 original size:20 final size:20
Alignment explanation
Indices: 2224513--2224585 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2224503 TAGTTGAAAA
*
2224513 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
** ** **
2224533 TCGCGTTGCGATAGATGGAGA
1 TCGCGTTGCGAT-TTTCCATT
2224554 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
2224574 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2224586 AGTTGAAATC
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:2224597 original size:20 final size:20
Alignment explanation
Indices: 2224492--2224597 Score: 54
Period size: 20 Copynumber: 5.2 Consensus size: 20
2224482 ACGTTGCATT
*
2224492 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTG-AAA
** * **
2224513 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTT-GAAA
* *
2224533 TCGCGTTGCGATAGATGGAGA
1 TCGCGTTGCGATAG-TTGAAA
* * **
2224554 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTT-GAAA
2224574 TCGCGTTGCGATAGTTGAAA
1 TCGCGTTGCGATAGTTGAAA
2224594 TCGC
1 TCGC
2224598 AACGCGATTT
Statistics
Matches: 59, Mismatches: 21, Indels: 11
0.65 0.23 0.12
Matches are distributed among these distances:
19 1 0.02
20 32 0.54
21 25 0.42
22 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGATAGTTGAAA
Found at i:2224708 original size:142 final size:142
Alignment explanation
Indices: 2224471--2224727 Score: 435
Period size: 142 Copynumber: 1.8 Consensus size: 142
2224461 GATCTCCACT
*
2224471 ATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTCCATTTCG
1 ATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCG
* *
2224536 CGTTGCGATAGATGGAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATCGCAAC
66 CGTTGCGATAGATGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATCGCAAC
2224601 GCGATTTCCATC
131 GCGATTTCCATC
** *
2224613 ATCGCAAATTCGTGTTGCATTTCG-AGTTGCGATAGTTGAAAATCGCGTTGTGATTTTCCATTTC
1 ATCGCAAATTCACGTTGCATTTCGCA-TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
*
2224677 GCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
65 GCGTTGCGATAGATGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
2224728 TTTCCATTTC
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
141 1 0.01
142 106 0.99
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (142 bp):
ATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCG
CGTTGCGATAGATGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATCGCAAC
GCGATTTCCATC
Found at i:2224731 original size:61 final size:61
Alignment explanation
Indices: 2224655--2224788 Score: 250
Period size: 61 Copynumber: 2.2 Consensus size: 61
2224645 TAGTTGAAAA
* *
2224655 TCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTCCATT
2224716 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTCCATT
2224777 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2224789 AGTCTACAGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:2224762 original size:102 final size:102
Alignment explanation
Indices: 2224513--2224829 Score: 419
Period size: 102 Copynumber: 3.1 Consensus size: 102
2224503 TAGTTGAAAA
* * * *
2224513 TCGCGTTGCGTTTTTCCATTTCGCGTTGCGATAGATGGAGATCGCGTTGCGATTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
*** *
2224578 GTTGCGATAGTTG-AAATCGCAACGCGA-TTTCCATCA
66 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT-T
* * * * *
2224614 TCGCAAATT-CG-TGTTGCATTTCGAGTTGCGATAGTTGAAAATCGCGTTGTGATTTTCCATTTC
1 TCGC--GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
2224677 GCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
64 GCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
*
2224716 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
* *
2224781 GTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATT
66 GTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATT
2224818 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2224830 AGTCTACACT
Statistics
Matches: 189, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
100 2 0.01
101 66 0.35
102 111 0.59
103 10 0.05
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (102 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:2224803 original size:21 final size:21
Alignment explanation
Indices: 2224777--2224851 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
2224767 ATTTTCCATT
*
2224777 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATAGTCTACAC
* * *
2224798 TCGCGTTGCGAT--TTTCCATT
1 TCGCGTTGCGATAGTCTACA-C
2224818 TCGCGTTGCGATAGTCTACAC
1 TCGCGTTGCGATAGTCTACAC
*
2224839 TTGTCGTTGCGAT
1 TCG-CGTTGCGAT
2224852 TTTCCAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 4 0.09
20 12 0.28
21 14 0.33
22 13 0.30
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCTACAC
Found at i:2224829 original size:61 final size:61
Alignment explanation
Indices: 2224655--2224809 Score: 186
Period size: 61 Copynumber: 2.5 Consensus size: 61
2224645 TAGTTGAAAA
* * * * * *
2224655 TCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTCTACATGTCGCGTTACGATAGTTCAAAATCGCGTTGCGATTTTCCATT
* * * *
2224716 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTCTACATGTCGCGTTACGATAGTTCAAAATCGCGTTGCGATTTTCCATT
*
2224777 TCGCGTTGCGATAGTCTACA-GTCGCGTTGCGAT
1 TCGCGTTGCGAT--TCTACATGTCGCGTTACGAT
2224810 TTTCCATTTC
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
61 71 0.83
62 11 0.13
63 4 0.05
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (61 bp):
TCGCGTTGCGATTCTACATGTCGCGTTACGATAGTTCAAAATCGCGTTGCGATTTTCCATT
Found at i:2224833 original size:41 final size:41
Alignment explanation
Indices: 2224716--2224898 Score: 228
Period size: 41 Copynumber: 4.4 Consensus size: 41
2224706 ATTTTCCATT
* *
2224716 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGT-TGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTCT-ACAC
* *
2224757 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTCTACAC
*
2224798 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAC
1 TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTCTACAC
* *
2224839 TTGTCGTTGCGATTTTCCAAATT--CGTTACGATAGTCTACAC
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTACGATAGTCTACAC
* *
2224880 TTGTCGTTGCGGTTTTCCA
1 TCG-CGTTGCGATTTTCCA
2224899 AATTCGTTGT
Statistics
Matches: 131, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.01
41 112 0.85
42 15 0.11
43 3 0.02
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTACGATAGTCTACAC
Found at i:2224899 original size:41 final size:41
Alignment explanation
Indices: 2224760--2224914 Score: 190
Period size: 41 Copynumber: 3.8 Consensus size: 41
2224750 TTGAAAATCG
* * *
2224760 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTCG-
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACACTTGT
*
2224801 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACACTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACACTTGT
*
2224843 CGTTGCGATTTTCCAAATTCGTTACGATAGTCTACACTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACACTTGT
* *
2224884 CGTTGCGGTTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
2224915 AAAAAAAAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
41 88 0.84
42 14 0.13
43 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACACTTGT
Found at i:2225003 original size:6 final size:6
Alignment explanation
Indices: 2224992--2225034 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
2224982 GACACGTATT
2224992 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
2225035 GACGAGACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2225535 original size:6 final size:6
Alignment explanation
Indices: 2225524--2225555 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2225514 CCGTCTCGTC
*
2225524 TCGTGG TTGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
2225556 ATACGTGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.16, G:0.47, T:0.38
Consensus pattern (6 bp):
TCGTGG
Found at i:2225702 original size:20 final size:20
Alignment explanation
Indices: 2225677--2225912 Score: 242
Period size: 20 Copynumber: 11.6 Consensus size: 20
2225667 ACTGTAGACT
*
2225677 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
2225697 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
2225718 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
2225738 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
2225759 ATCGCAACACGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
2225779 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
2225800 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
2225820 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
2225841 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2225861 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2225881 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2225901 ATCGCAACGCGA
1 ATCGCAACGCGA
2225913 TTTTCAACTA
Statistics
Matches: 173, Mismatches: 35, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
19 5 0.03
20 107 0.62
21 55 0.32
22 6 0.03
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2225721 original size:41 final size:41
Alignment explanation
Indices: 2225648--2225937 Score: 383
Period size: 41 Copynumber: 7.0 Consensus size: 41
2225638 ACAACGAATT
*
2225648 TGGAAAATCGCAACGGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAAC-G-CGACTGTAGACTATCGCAACGCGAAA
*
2225691 CGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
* * *
2225732 TGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACACGAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAA
* *
2225773 TGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAA
2225814 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
* **
2225855 TGGAAAATCGCAACGCGAAATG--GAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCG-ACTGTAGACTATCGCAACGCGAAA
* *
2225895 TGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAA
2225936 TG
1 TG
2225938 CAACGCGAAT
Statistics
Matches: 225, Mismatches: 16, Indels: 14
0.88 0.06 0.05
Matches are distributed among these distances:
39 2 0.01
40 34 0.15
41 171 0.76
42 5 0.02
43 13 0.06
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
Found at i:2226668 original size:32 final size:33
Alignment explanation
Indices: 2226627--2226704 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
2226617 TTATTTGTTT
2226627 GGGTCGGGTCGGGTTTTTT-AAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
2226659 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
2226692 GGGTCGGGTCGGG
1 GGGTCGGGTCGGG
2226705 ATCGGGTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 19 0.42
33 26 0.58
ACGTcount: A:0.12, C:0.10, G:0.42, T:0.36
Consensus pattern (33 bp):
GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
Found at i:2227277 original size:18 final size:17
Alignment explanation
Indices: 2227240--2227278 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2227230 TATGGAATTG
* *
2227240 GATTCCAATTCCTGACA
1 GATTACAATTCCTCACA
2227257 GATTACAATTCCTTCACA
1 GATTACAATTCC-TCACA
2227275 GATT
1 GATT
2227279 CTAATTCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (17 bp):
GATTACAATTCCTCACA
Found at i:2227490 original size:22 final size:22
Alignment explanation
Indices: 2227440--2227494 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
2227430 GTGCCTATAG
2227440 AATTTTGTAATTTTATATGCTAA
1 AATTTTGTAATTTTATA-GCTAA
* *
2227463 AATTTTGTACTTTTATCA-CTTA
1 AATTTTGTAATTTTAT-AGCTAA
2227485 AATTTT-TAAT
1 AATTTTGTAAT
2227495 ATAACTTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 3 0.11
22 9 0.32
23 15 0.54
24 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTTTGTAATTTTATAGCTAA
Found at i:2234095 original size:21 final size:21
Alignment explanation
Indices: 2234046--2234097 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2234036 TTATCGGAAA
* *
2234046 TATTATTATTTCTACTGATTT
1 TATTATTTTTTCTACCGATTT
2234067 TATTATTTTTTCTACCGATTT
1 TATTATTTTTTCTACCGATTT
*
2234088 TGTTATTTTT
1 TATTATTTTT
2234098 GAGCATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (21 bp):
TATTATTTTTTCTACCGATTT
Found at i:2238635 original size:35 final size:34
Alignment explanation
Indices: 2238596--2238727 Score: 147
Period size: 35 Copynumber: 3.8 Consensus size: 34
2238586 AAGTGTTTTA
* ** *
2238596 GAATTTGGAGTTTAAAATTTAATTGAATTATTTTG
1 GAATTTGG-GTTTAGAATGAAATTGAATTACTTTG
*
2238631 GAATTTAGGGTTTAGAATGAAATTAAATTACTTTG
1 GAATTT-GGGTTTAGAATGAAATTGAATTACTTTG
* *
2238666 GAAATTAGGGTTTAGAATGAAAGTGAATTACTTTG
1 G-AATTTGGGTTTAGAATGAAATTGAATTACTTTG
* *
2238701 GAAATTGGGGTTTACAATGAAATTGAA
1 G-AATTTGGGTTTAGAATGAAATTGAA
2238728 GACTGTTTTG
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
35 78 0.93
36 6 0.07
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (34 bp):
GAATTTGGGTTTAGAATGAAATTGAATTACTTTG
Found at i:2243902 original size:45 final size:47
Alignment explanation
Indices: 2243806--2243902 Score: 119
Period size: 45 Copynumber: 2.1 Consensus size: 47
2243796 TATTTTCGTT
* * * *
2243806 TTTTTGAATAAATGTATGCGAACTAGATATCATGCGGTTAGGTTTAT
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGAGGTTAGATTTAC
*
2243853 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGAGGTTATGATTT-C
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGAGGTTA-GATTTAC
2243898 TTTTT
1 TTTTT
2243903 ATGGATAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
45 29 0.66
46 6 0.14
47 9 0.20
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGAGGTTAGATTTAC
Found at i:2253583 original size:26 final size:26
Alignment explanation
Indices: 2253552--2253640 Score: 73
Period size: 26 Copynumber: 3.5 Consensus size: 26
2253542 AAGAAGAAAT
2253552 AAATGAGAAAAAATGAGAAAAAAGAA
1 AAATGAGAAAAAATGAGAAAAAAGAA
* *
2253578 AAATGATGGAAAAAACGA-AAAGAA-AA
1 AAATGA--GAAAAAATGAGAAAAAAGAA
2253604 AAATG-G--AAAATGGAAGAAAAAATGAA
1 AAATGAGAAAAAAT-G-AGAAAAAA-GAA
2253630 AAATGA-AAAAA
1 AAATGAGAAAAA
2253641 GAAAAATGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
21 4 0.08
22 1 0.02
23 2 0.04
24 5 0.10
26 20 0.41
27 5 0.10
28 12 0.24
ACGTcount: A:0.71, C:0.01, G:0.19, T:0.09
Consensus pattern (26 bp):
AAATGAGAAAAAATGAGAAAAAAGAA
Found at i:2253597 original size:19 final size:16
Alignment explanation
Indices: 2253560--2253655 Score: 78
Period size: 15 Copynumber: 5.9 Consensus size: 16
2253550 ATAAATGAGA
2253560 AAAAATGAGAAAAAAG
1 AAAAATGAGAAAAAAG
2253576 AAAAATGATGGAAAAAACG
1 AAAAATGA--GAAAAAA-G
2253595 -AAAA-GA-AAAAAATG
1 AAAAATGAGAAAAAA-G
*
2253609 GAAAATGGAAGAAAAAATG
1 AAAAAT-G-AGAAAAAA-G
2253628 AAAAAT--GAAAAAAG
1 AAAAATGAGAAAAAAG
2253642 AAAAATGA-AAAAAA
1 AAAAATGAGAAAAAA
2253656 AAGAGAAATA
Statistics
Matches: 68, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
14 14 0.21
15 17 0.25
16 8 0.12
17 3 0.04
18 12 0.18
19 14 0.21
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:2253631 original size:7 final size:7
Alignment explanation
Indices: 2253621--2253653 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2253611 AAATGGAAGA
2253621 AAAAATG
1 AAAAATG
2253628 AAAAATG
1 AAAAATG
*
2253635 AAAAAAG
1 AAAAATG
2253642 AAAAATG
1 AAAAATG
2253649 AAAAA
1 AAAAA
2253654 AAAAGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:2253644 original size:14 final size:15
Alignment explanation
Indices: 2253619--2253654 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
2253609 GAAAATGGAA
2253619 GAAAAAATGAAAAAT
1 GAAAAAATGAAAAAT
2253634 GAAAAAA-GAAAAAT
1 GAAAAAATGAAAAAT
2253648 GAAAAAA
1 GAAAAAA
2253655 AAAGAGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
GAAAAAATGAAAAAT
Found at i:2253647 original size:33 final size:30
Alignment explanation
Indices: 2253567--2253657 Score: 92
Period size: 33 Copynumber: 2.8 Consensus size: 30
2253557 AGAAAAAATG
*
2253567 AGAAAAAAGAAAAATGATGGAAAAAACGAAA
1 AGAAAAAAGAAAAATGA-AGAAAAAACGAAA
* *
2253598 AGAAAAAAATGGAAAATGGAAGAAAAAATGAAAA
1 AG-AAAAAA-GAAAAAT-GAAGAAAAAACG-AAA
*
2253632 ATGAAAAAAGAAAAATGAAAAAAAAA
1 A-GAAAAAAGAAAAATGAAGAAAAAA
2253658 GAGAAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
31 2 0.04
32 15 0.30
33 20 0.40
34 12 0.24
35 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.08
Consensus pattern (30 bp):
AGAAAAAAGAAAAATGAAGAAAAAACGAAA
Found at i:2255049 original size:51 final size:51
Alignment explanation
Indices: 2254982--2255303 Score: 365
Period size: 55 Copynumber: 6.1 Consensus size: 51
2254972 AGCAAATTCA
* *
2254982 TTTGTTTAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAACGGACAAG
1 TTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
*
2255033 TTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
1 TTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
*
2255084 TTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
1 TTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
* * **
2255135 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
1 TTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
* * * * * *
2255190 TTTGTTGAAGATTATTCGAGTCTTATAATCCCTGAACGAATAGGGAGCAGACACG
1 TTTGTTGAAG---ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
* * * * *
2255245 TTTGTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACG
1 TTTGTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
2255300 TTTG
1 TTTG
2255304 CAAAAGATTG
Statistics
Matches: 242, Mismatches: 18, Indels: 18
0.87 0.06 0.06
Matches are distributed among these distances:
51 109 0.45
52 1 0.00
54 2 0.01
55 127 0.52
56 2 0.01
58 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (51 bp):
TTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG
Found at i:2255186 original size:55 final size:55
Alignment explanation
Indices: 2254995--2255347 Score: 361
Period size: 55 Copynumber: 6.6 Consensus size: 55
2254985 GTTTAAGATT
* * *
2254995 GAGTCCTATACTCTCTGAAGGAATAGGGAACGGACAAGTTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
* *
2255046 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
*
2255097 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
* ** *
2255152 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTATTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
* * * * * *
2255207 GAG-TCTTATAATCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTT
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
* * * * ***
2255262 GAG-TCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCAAAAGATTGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
* *
2255317 GAG-TCTTATACTC-CTTAAAAGAATAGGGAGC
1 GAGTTC-TATACTCTC-TGAAGGAATAGGGAGC
2255348 AGACCCGTTA
Statistics
Matches: 273, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
51 98 0.36
54 5 0.02
55 170 0.62
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTC
Found at i:2255377 original size:110 final size:111
Alignment explanation
Indices: 2255117--2255378 Score: 316
Period size: 110 Copynumber: 2.4 Consensus size: 111
2255107 CTCTCTGAAG
* * * *
2255117 GAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGA
1 GAATAGGGAGCAGACACGTTTGTTGAAGATTTTTCGAGTCTCTATACTCCCTGAAGGAATAGAGA
* * *** * *
2255181 GCGGACCCGTTTGTTGAAGATTATTCGAGTCTTATAATCCCTGAAC
66 GCAGACACGTTTGCAAAAGATTATTCGAGTCTTATAATCCCTAAAA
* *
2255227 GAATAGGGAGCAGACACGTTTGTTGAAGATTGTTT-GAGTCT-TATACTCCCTGAATGAATAGGG
1 GAATAGGGAGCAGACACGTTTGTTGAAGATT-TTTCGAGTCTCTATACTCCCTGAAGGAATAGAG
* * *
2255290 AGCAGACACGTTTGCAAAAGATTGTTCGAGTCTTATACTCCTTAAAA
65 AGCAGACACGTTTGCAAAAGATTATTCGAGTCTTATAATCCCTAAAA
* *
2255337 GAATAGGGAGCAGACCCGTTAT-TTGAAGATTTTTCAAGTCTC
1 GAATAGGGAGCAGACACGTT-TGTTGAAGATTTTTCGAGTCTC
2255379 GCTTATCCTG
Statistics
Matches: 129, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
109 3 0.02
110 122 0.95
111 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (111 bp):
GAATAGGGAGCAGACACGTTTGTTGAAGATTTTTCGAGTCTCTATACTCCCTGAAGGAATAGAGA
GCAGACACGTTTGCAAAAGATTATTCGAGTCTTATAATCCCTAAAA
Found at i:2282536 original size:16 final size:16
Alignment explanation
Indices: 2282515--2282552 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
2282505 AAATAGTGGG
2282515 AGCTATCCGTAAAAGA
1 AGCTATCCGTAAAAGA
2282531 AGCTATCCGTAAAAGA
1 AGCTATCCGTAAAAGA
2282547 AGCTAT
1 AGCTAT
2282553 GGCAACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (16 bp):
AGCTATCCGTAAAAGA
Found at i:2290717 original size:21 final size:22
Alignment explanation
Indices: 2290687--2290727 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2290677 ACAAACATCG
*
2290687 TAATTGTCAA-ATAAATAAACA
1 TAATTCTCAATATAAATAAACA
*
2290708 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
2290728 TAAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACA
Found at i:2290869 original size:15 final size:15
Alignment explanation
Indices: 2290846--2290875 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2290836 TATCGAATTT
*
2290846 AATTGAATAAAATAA
1 AATTAAATAAAATAA
2290861 AATTAAATAAAATAA
1 AATTAAATAAAATAA
2290876 CAAAGAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATTAAATAAAATAA
Found at i:2294834 original size:23 final size:22
Alignment explanation
Indices: 2294774--2294835 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
2294764 TTAGGATGAG
*
2294774 AATTTAAGAAAT-TAAATTAAA
1 AATTTTAGAAATATAAATTAAA
**
2294795 AATTTT-GCACTTCATAAATTATAA
1 AATTTTAG-AAAT-ATAAATTA-AA
2294819 AATTTTAGAAATATAAA
1 AATTTTAGAAATATAAA
2294836 ATCATATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
20 1 0.03
21 7 0.23
23 12 0.39
24 10 0.32
25 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (22 bp):
AATTTTAGAAATATAAATTAAA
Found at i:2297967 original size:3 final size:3
Alignment explanation
Indices: 2297959--2297992 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2297949 ATATTAATTA
2297959 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2297993 TTTATAATAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2298378 original size:117 final size:112
Alignment explanation
Indices: 2298164--2298472 Score: 423
Period size: 117 Copynumber: 2.8 Consensus size: 112
2298154 AAGCGTTGGA
2298164 TTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CTCTTGTTGGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTC-T-TTGGATGAGTTCTTCTCATTATGAA
2298228 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCGAACCAAGG
64 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCG-A--AA-G
2298281 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTCTTTGGATGAGTTCTTCTCATTATGAAC
* * * * *
2298346 TCTTCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGATTTGAAAG
65 TCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCGAAAG
* * *
2298394 --GAACAAGTTCTTCTCATTATGAAC-T-TTATCCT-TTAGGATGAGTTCTTCTCATTATGAGCT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTTGGATGAGTTCTTCTCATTATGAACT
* *
2298454 CTCCATTGAAAATGTTGAT
66 CTTCACTGAAAATGTTGAT
2298473 GCGAAGTTGA
Statistics
Matches: 180, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
107 43 0.24
108 4 0.02
109 2 0.01
110 1 0.01
111 24 0.13
113 1 0.01
114 2 0.01
116 1 0.01
117 97 0.54
118 2 0.01
119 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (112 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTTGGATGAGTTCTTCTCATTATGAACT
CTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCGAAAG
Found at i:2298491 original size:87 final size:89
Alignment explanation
Indices: 2298394--2298563 Score: 238
Period size: 91 Copynumber: 1.9 Consensus size: 89
2298384 GATTTGAAAG
*
2298394 GAACAAGTTCTTCTCATTATGAACTT-TATC-CTT-TAGGATGAGTTCTTCTCATTATGAGCTCT
1 GAACAAGTTCTTCTCATTATGAACTTCT-TCTCTTCTAGGATGAGTTCTTCTCATTATGAACTCT
*
2298456 CCATTGAAAATGTTGATGCGAAGTT
65 CCACTGAAAATGTTGATGCGAAGTT
**
2298481 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCGTTTGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTC-TCTTC-TAGGATGAGTTCTTCTCATTATGAACTC
* *
2298546 TTCACTGGAAATGTTGAT
64 TCCACTGAAAATGTTGAT
2298564 CCCTCAAGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
87 28 0.39
88 1 0.01
89 3 0.04
91 40 0.56
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (89 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCTTCTAGGATGAGTTCTTCTCATTATGAACTCTC
CACTGAAAATGTTGATGCGAAGTT
Found at i:2298724 original size:136 final size:136
Alignment explanation
Indices: 2298481--2298829 Score: 547
Period size: 136 Copynumber: 2.6 Consensus size: 136
2298471 ATGCGAAGTT
* * * **
2298481 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTC-GTTTGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * ** * * *
2298545 CTTCACTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTTATGAATCGAGTGA
66 CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
2298610 TAGGTC
131 TAGGTC
2298616 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * *
2298681 ATCCATTGGAAATACTGATCCTTCAAGCAAGGTGTCACTGATTCAAAATGTCGTGAATCTAGTGA
66 CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
2298746 TAGGTC
131 TAGGTC
2298752 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
2298817 CTCCATTGGAAAT
66 CTCCATTGGAAAT
2298830 GTTGGTTCAC
Statistics
Matches: 196, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
135 33 0.17
136 163 0.83
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:2299732 original size:20 final size:20
Alignment explanation
Indices: 2299703--2299756 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 20
2299693 AACCCTCCTT
*
2299703 TTTCTCTTTTTATTTTTTCA
1 TTTCTCTTTTCATTTTTTCA
*
2299723 TTTCTTTTTTCA-TTTTT--
1 TTTCTCTTTTCATTTTTTCA
2299740 TTTCT-TTTTCATTTTTT
1 TTTCTCTTTTCATTTTTT
2299757 TTCATTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 6 0.19
17 10 0.32
19 5 0.16
20 10 0.32
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTCTTTTCATTTTTTCA
Found at i:2299740 original size:10 final size:10
Alignment explanation
Indices: 2299715--2299765 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
2299705 TCTCTTTTTA
2299715 TTTTTTCATTT
1 TTTTTTCA-TT
2299726 CTTTTTTCATT
1 -TTTTTTCATT
2299737 TTTTTTC---
1 TTTTTTCATT
2299744 -TTTTTCATT
1 TTTTTTCATT
2299753 TTTTTTCATT
1 TTTTTTCATT
2299763 TTT
1 TTT
2299766 CATCTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.17
10 19 0.54
11 2 0.06
12 8 0.23
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:2299749 original size:16 final size:16
Alignment explanation
Indices: 2299701--2299794 Score: 84
Period size: 16 Copynumber: 5.6 Consensus size: 16
2299691 CAAACCCTCC
*
2299701 TTTTTCTCTTTTT-ATT
1 TTTTTTTCTTTTTCA-T
2299717 TTTTCATTTCTTTTTTCAT
1 TTTT--TTTC-TTTTTCAT
2299736 TTTTTTTCTTTTTCAT
1 TTTTTTTCTTTTTCAT
2299752 TTTTTTTCATTTTTCAT
1 TTTTTTTC-TTTTTCAT
* * *
2299769 CTTTTTAT-TTGTTCCT
1 -TTTTTTTCTTTTTCAT
2299785 TTTTTTTCTT
1 TTTTTTTCTT
2299795 CAAGCATAGT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
15 6 0.09
16 28 0.42
17 12 0.18
18 9 0.14
19 10 0.15
20 1 0.02
ACGTcount: A:0.07, C:0.14, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTTTTCTTTTTCAT
Found at i:2299774 original size:33 final size:34
Alignment explanation
Indices: 2299700--2299792 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 34
2299690 TCAAACCCTC
* *
2299700 CTTTTTCTCTTTTT-ATTTTTTCATTTCTTTTTTCAT
1 CTTTTTATCTTTTTCA-TTTTT--TTTCATTTTTCAT
*
2299736 -TTTTTTTCTTTTTCATTTTTTTTCATTTTTCAT
1 CTTTTTATCTTTTTCATTTTTTTTCATTTTTCAT
* *
2299769 CTTTTTAT-TTGTTCCTTTTTTTTC
1 CTTTTTATCTTTTTCATTTTTTTTC
2299793 TTCAAGCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
33 26 0.52
34 6 0.12
35 17 0.34
36 1 0.02
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (34 bp):
CTTTTTATCTTTTTCATTTTTTTTCATTTTTCAT
Found at i:2312937 original size:3 final size:3
Alignment explanation
Indices: 2312929--2312965 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2312919 ATATTAATTA
2312929 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2312966 TTTATAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2313742 original size:21 final size:21
Alignment explanation
Indices: 2313718--2313757 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2313708 ATTAATTTGA
2313718 AATCTGAAA-TAACTCGAATCG
1 AATCT-AAATTAACTCGAATCG
*
2313739 AATCTAAATTGACTCGAAT
1 AATCTAAATTAACTCGAAT
2313758 TTTAGTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (21 bp):
AATCTAAATTAACTCGAATCG
Found at i:2318944 original size:18 final size:18
Alignment explanation
Indices: 2318921--2318961 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2318911 AACAGACCCA
2318921 TCACCGGATACATCATCT
1 TCACCGGATACATCATCT
2318939 TCACCGGATACATCATCT
1 TCACCGGATACATCATCT
2318957 TCACC
1 TCACC
2318962 AGAAATAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.27
Consensus pattern (18 bp):
TCACCGGATACATCATCT
Found at i:2321622 original size:21 final size:19
Alignment explanation
Indices: 2321589--2321808 Score: 98
Period size: 21 Copynumber: 10.7 Consensus size: 19
2321579 CGTTACGATT
* *
2321589 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
2321608 TTGGAATGAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
2321631 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
* * *
2321650 TTAGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
*
2321669 TTGTAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* * *
2321692 TTGGACTATCGCAACAAAT
1 TTGGAATATCGCAACGAAC
* ***
2321711 TTAGAATAAATTATAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
2321734 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
* *
2321753 TTGAAAAATCGCAACGCGAAC
1 TTGGAATATCGCAA--CGAAC
* *
2321774 TTCGACTATCGCAACGCGAAC
1 TTGGAATATCGCAA--CGAAC
*
2321795 TTGGACTATCGCAA
1 TTGGAATATCGCAA
2321809 TGCGAATATG
Statistics
Matches: 151, Mismatches: 36, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
19 55 0.36
21 70 0.46
23 26 0.17
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:2321687 original size:61 final size:61
Alignment explanation
Indices: 2321592--2321715 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
2321582 TACGATTTTG
* *
2321592 GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAACTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTA
* * *
2321653 GACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTATCGCAACAAATTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTA
2321714 GA
1 GA
2321716 ATAAATTATA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (61 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTA
Found at i:2321704 original size:42 final size:41
Alignment explanation
Indices: 2321638--2321789 Score: 211
Period size: 42 Copynumber: 3.7 Consensus size: 41
2321628 AACTTCGACT
*
2321638 ATCGCAA--CGAACTTAGACTATCGCAACGAATTTGTAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTG-AATAA
*
2321678 ATCGCAACGCGAACTTGGACTATCGCAACAAATTTAGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTT-GAATAA
***
2321720 ATTATAACGCGAACTTGGACTATCGCAACGAATTTGAA-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATAA
*
2321760 ATCGCAACGCGAACTTCGACTATCGCAACG
1 ATCGCAACGCGAACTTGGACTATCGCAACG
2321790 CGAACTTGGA
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 35 0.35
41 3 0.03
42 60 0.61
43 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATAA
Found at i:2321768 original size:103 final size:102
Alignment explanation
Indices: 2321589--2321808 Score: 266
Period size: 103 Copynumber: 2.1 Consensus size: 102
2321579 CGTTACGATT
* * * *
2321589 TTGGACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAG
1 TTGGACTATCGCAACAAATTTAGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTAG
** *
2321654 ACTATCGCAA-CGAA-TTTGTAATAAATCGCAACGCGAAC
66 AAAATCGCAACCGAACTTCG-AAT--ATCGCAACGCGAAC
* * * *
2321692 TTGGACTATCGCAACAAATTTAGAATAAATTATAACGCGAACTTGGACTATCGCAACGAA-TTTG
1 TTGGACTATCGCAACAAATTTAGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTAG
*
2321756 AAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
66 -AAAATCGCAAC-CGAACTTCGAATATCGCAACGCGAAC
2321795 TTGGACTATCGCAA
1 TTGGACTATCGCAA
2321809 TGCGAATATG
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
102 3 0.03
103 89 0.88
105 6 0.06
106 3 0.03
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (102 bp):
TTGGACTATCGCAACAAATTTAGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTAG
AAAATCGCAACCGAACTTCGAATATCGCAACGCGAAC
Done.