Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006023.1 Hibiscus syriacus cultivar Beakdansim tig00014213_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: 1315283
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:947910 original size:9 final size:9
Alignment explanation
Indices: 947890--947920 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
947880 AATTAATTTA
947890 TTTTTCTA-
1 TTTTTCTAT
947898 TTTTTCTAT
1 TTTTTCTAT
947907 TTTTTCTAT
1 TTTTTCTAT
947916 TTTTT
1 TTTTT
947921 TCTTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTAT
Found at i:952009 original size:84 final size:84
Alignment explanation
Indices: 951868--953059 Score: 1393
Period size: 84 Copynumber: 14.3 Consensus size: 84
951858 TATTGGCAGT
* * *
951868 ATAACTCAAGACTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
*
951933 AAGGCACATTATTTGCAAC
66 AAGGCACATCATTTGCAAC
* * * * * * *
951952 ATAACTCAAGGCAAGAAGAGCTATTTGCCAACAAAAGACCTTCGAGTTCAACTACGCTCAGCTCT
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* *
952017 GAGGCACATCATTTGCAGC
66 AAGGCACATCATTTGCAAC
* * *
952036 ATAACTCAAGGCTAGAAGGGTTATGTGCCAACAAAAGACCTTCAAGTTC-ACCTACGCTCAGCTC
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA-CTACACTCAGCTC
* *
952100 CAAGGAACATTATTTGCAAC
65 CAAGGCACATCATTTGCAAC
* * * * * * *
952120 ATAGCTCAAGG-TAAGAATGGCTATTTGCAAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTC
1 ATAACTCAAGGCT-AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTC
* *
952184 CAAGGCACATCATTTGTAGC
65 CAAGGCACATCATTTGCAAC
* * *
952204 ATAACTCAAGGCTAGAAGAGTTATCTACCAACAGAAGACCTTCGAGTTCGACTACACTCAGCTCC
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* *
952269 AAGACACATCATTTGCAGC
66 AAGGCACATCATTTGCAAC
* * * * * *
952288 ATAACTCAAGGCTAGAAGGGTTATCTGCCAATAAAGGACCTTCGAGTTAGATTACAATCAGCTCA
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* *
952353 AAGGCACATCATTTGTAGC
66 AAGGCACATCATTTGCAAC
*
952372 ATAACTCAATGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAG-T----T--ACTCAGCTCC
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
952430 AAGGCACATCATTTGCAAC
66 AAGGCACATCATTTGCAAC
* * * * * * *
952449 ATAGCTCAAGGCAAGAAGGGTTATTTTCCAACAAAAGACCTTCGAGTTTGACTACGCTCATCTCC
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
952514 AAGGCACATCATTTGCAAC
66 AAGGCACATCATTTGCAAC
** * * *
952533 ATAACTCAAAACTAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* * *
952598 AAGACACATTATTTGTAAC
66 AAGGCACATCATTTGCAAC
* * * * * * *
952617 ATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGATTACGCTCAGCTCA
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
*
952682 AAGGCATATCATTTGCAAC
66 AAGGCACATCATTTGCAAC
* * * *
952701 ATAACTCAAGGCTAGAAGTGTTATCTGCC-A-AAAAGGCCTTCGAGTTCGATTACACTCAGCTCA
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* *
952764 AAGGCACAACATTTGCAGC
66 AAGGCACATCATTTGCAAC
* * * * *
952783 ATAGCTCAAGGCGAGAAGGGTTATCTTCCAACCAAAGACCTTCAAGTTCGACTACACTCAGCTCC
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
*
952848 AAGGCACATCATTTGTAAC
66 AAGGCACATCATTTGCAAC
* ** * * * * * *
952867 ATAGCTCAAGGAAAAAAGGGCTATTTGCCAACAAAATACCTTCGAGTTCGATTACACTCAGCTCA
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* * *
952932 AATGCACATCATTTACAGC
66 AAGGCACATCATTTGCAAC
* * * * *
952951 ATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTTGATTACACT-AACTCA
1 ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* *
953014 AAGGCACCTCATTTGCAGC
66 AAGGCACATCATTTGCAAC
* * *
953033 ATAGCTCAAGGCGAGAAGGGCTATCTG
1 ATAACTCAAGGCTAGAAGGGTTATCTG
953060 TCAAATACCT
Statistics
Matches: 946, Mismatches: 149, Indels: 28
0.84 0.13 0.02
Matches are distributed among these distances:
77 66 0.07
78 1 0.00
79 1 0.00
82 118 0.12
83 28 0.03
84 730 0.77
85 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (84 bp):
ATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCC
AAGGCACATCATTTGCAAC
Found at i:952591 original size:329 final size:330
Alignment explanation
Indices: 951868--953059 Score: 1484
Period size: 329 Copynumber: 3.6 Consensus size: 330
951858 TATTGGCAGT
* * * *
951868 ATAACTCAAGACTAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
1 ATAACTCAAAACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCA
* * * *
951933 AAGGCACATTATTTGCAACATAACTCAAGGCAAGAAGAGCTATTTGCCAACAAAAGACCTTCGAG
66 AAGACACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAG
* * ** *
951998 TTCA-ACTACGCTCAGCTCTGAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATGT
131 TT-AGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCT
* * * *
952062 GCCAACAAAAGACCTTCAAGTTCACCTACGCTCAGCTCCAAGGAACATTATTTGCAACATAGCTC
195 GCCAACAAAAGACCTTCGAG---A-TTA--CTCAGCTCCAAGGCACATCATTTGCAACATAGCTC
* * * * *
952127 AAGGTAAGAATGGCTATTTGCAAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCAC
254 AAGGCAAGAAGGGTTATTTTCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCAC
*
952192 ATCATTTGTAGC
319 ATCATTTGTAAC
** * * * *
952204 ATAACTCAAGGCTAGAAGAGTTATCTACCAACAGAAGACCTTCGAGTTCGACTACACTCAGCTCC
1 ATAACTCAAAACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCA
* * * * *
952269 AAGACACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATAAAGGACCTTCGAG
66 AAGACACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAG
* * *
952334 TTAGATTACAATCAGCTCAAAGGCACATCATTTGTAGCATAACTCAATGCTAGAAGGGTTATCTG
131 TTAGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTG
952399 CCAACAAAAGACCTTCGAG-TTACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAA
196 CCAACAAAAGACCTTCGAGATTACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAA
*
952463 GAAGGGTTATTTTCCAACAAAAGACCTTCGAGTTTGACTACGCTCATCTCCAAGGCACATCATTT
261 GAAGGGTTATTTTCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
*
952528 GCAAC
326 GTAAC
* *
952533 ATAACTCAAAACTAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 ATAACTCAAAACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCA
* * * *
952598 AAGACACATTATTTGTAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAG
66 AAGACACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAG
* * * * *
952663 TTCGATTACGCTCAGCTCAAAGGCATATCATTTGCAACATAACTCAAGGCTAGAAGTGTTATCTG
131 TTAGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTG
* * * *
952728 CC-A-AAAAGGCCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTTGCAGCATAGCTCA
196 CCAACAAAAGACCTTCGA----GATT--ACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCA
* * * * * *
952791 AGGCGAGAAGGGTTATCTTCCAACCAAAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCACA
255 AGGCAAGAAGGGTTATTTTCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACA
952856 TCATTTGTAAC
320 TCATTTGTAAC
* * * * * *
952867 ATAGCTCAAGGAA--AAAAGGGCTATTTGCCAACAAAATACCTTCGAGTTCGATTACACTCAGCT
1 ATAACTCAA--AACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCT
* * * * *
952930 CAAATG-CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTC
64 CAAA-GACACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTC
* * * * * *
952993 GAGTTTGATTACACT-AACTCAAAGGCACCTCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTAT
128 GAGTTAGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTAT
953057 CTG
193 CTG
953060 TCAAATACCT
Statistics
Matches: 748, Mismatches: 97, Indels: 26
0.86 0.11 0.03
Matches are distributed among these distances:
327 12 0.02
328 1 0.00
329 274 0.37
331 3 0.00
332 46 0.06
333 23 0.03
334 197 0.26
335 2 0.00
336 190 0.25
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (330 bp):
ATAACTCAAAACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCA
AAGACACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAG
TTAGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTG
CCAACAAAAGACCTTCGAGATTACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAA
GAAGGGTTATTTTCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
GTAAC
Found at i:953471 original size:83 final size:83
Alignment explanation
Indices: 953338--953537 Score: 283
Period size: 83 Copynumber: 2.4 Consensus size: 83
953328 TCAAGGAAAA
* * * * * *
953338 AAGGGCTATTTGCCAACAAAATACCTTCGAGTTCGATTACACTCAGCTCAAATGCACATCATTTA
1 AAGGGCTATCTGTCAAC-AAATACCTTCGAGTTTGATTACACTAAACTCAAAGGCACATCATTTA
*
953403 CAGCATAACTCAAGGCTAG
65 CAGCATAACTCAAGGCGAG
* * * *
953422 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTTGATTACACTAAACTCAAAGGCACCTCATTTGC
1 AAGGGCTATCTGTCAACAAATACCTTCGAGTTTGATTACACTAAACTCAAAGGCACATCATTTAC
*
953487 AGCATAGCTCAAGGCGAG
66 AGCATAACTCAAGGCGAG
953505 AAGGGCTATCTGTCAACAAATACCTTCGAGTTT
1 AAGGGCTATCTGTCAACAAATACCTTCGAGTTT
953538 AATTCCATTC
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 88 0.86
84 14 0.14
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (83 bp):
AAGGGCTATCTGTCAACAAATACCTTCGAGTTTGATTACACTAAACTCAAAGGCACATCATTTAC
AGCATAACTCAAGGCGAG
Found at i:954304 original size:37 final size:36
Alignment explanation
Indices: 954138--954573 Score: 423
Period size: 37 Copynumber: 11.6 Consensus size: 36
954128 ATATATATAT
* ** **
954138 ATATATATATTATATAGTTTGCAAATGATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACA-TTTTGAAA
*
954175 ATAAGTATATAATATATAATTTTTAAAAAACATTTTGAAA
1 AT-A-TATATAATATATAGTTTTT--AAAACATTTTGAAA
* * *
954215 ATGTATATAATATATAATTTTTTAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACA-TTTTGAAA
*
954252 A-CTATATAATATATAGTTTTTAAAACATTTTAGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTT-GAAA
954288 ATATATATAATATATAGTTTTTAAAATCATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAA-CATTTTGAAA
954325 ACT-TATATAATATATAG-TTTTAAAACTATTTTTGAAA
1 A-TATATATAATATATAGTTTTTAAAAC-A-TTTTGAAA
* *
954362 ATTTATATAATATATAGTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTGAAA
* *
954398 CATTTATATATTATATAGTTTTTAAAAACATTTTGAAAA
1 -ATATATATAATATATAGTTTTT-AAAACATTTTG-AAA
* *
954437 AAATATATAATATATAGTTTTTTAAAATATTTTTGAAAAA
1 ATATATATAATATATAG-TTTTTAAAACA-TTTTG--AAA
* *
954477 ATATATATATTATATAGTTTTTTAAAACGTTTTTGAAA
1 ATATATATAATATATAG-TTTTTAAAAC-ATTTTGAAA
** *
954515 ATACGTATAATATATATTTTTTAAAAAACATTTT-AGAA
1 ATATATATAATATATAGTTTTT--AAAACATTTTGA-AA
* *
954553 ATTTATATATTATAT-GTTTTT
1 ATATATATAATATATAGTTTTT
954574 GAAATTATTA
Statistics
Matches: 343, Mismatches: 33, Indels: 46
0.81 0.08 0.11
Matches are distributed among these distances:
35 5 0.01
36 51 0.15
37 108 0.31
38 98 0.29
39 33 0.10
40 44 0.13
41 4 0.01
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAACATTTTGAAA
Found at i:954573 original size:38 final size:38
Alignment explanation
Indices: 954138--954573 Score: 405
Period size: 38 Copynumber: 11.6 Consensus size: 38
954128 ATATATATAT
* ** ** *
954138 ATATATATATTATATAG-TTTGCAAATGATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTAGAAA
*
954175 ATAAGTATATAATATATAATTTTTAAAAAACATTTT-GAAA
1 AT-A-TATATAATATATAGTTTTT-AAAAACATTTTAGAAA
* * * *
954215 ATGTATATAATATATAATTTTT-TAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTAGAAA
*
954252 A-CTATATAATATATAGTTTTT-AAAACATTTTAGAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTAGAAA
*
954288 ATATATATAATATATAGTTTTTAAAATCATTTT-GAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTAGAAA
*
954325 ACT-TATATAATATATAG-TTTT-AAAACTATTTTTGAAA
1 A-TATATATAATATATAGTTTTTAAAAAC-ATTTTAGAAA
* *
954362 ATTTATATAATATATAG-TTTTGAAAACATTTT-GAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTAGAAA
* *
954398 CATTTATATATTATATAGTTTTTAAAAACATTTT-GAAAA
1 -ATATATATAATATATAGTTTTTAAAAACATTTTAG-AAA
* * * *
954437 AAATATATAATATATAGTTTTTTAAAATATTTTTGAAAAA
1 ATATATATAATATATAGTTTTTAAAAACA-TTTT-AGAAA
* * * *
954477 ATATATATATTATATAGTTTTTTAAAACGTTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTAGAAA
** *
954515 ATACGTATAATATATATTTTTTAAAAAACATTTTAG-AA
1 ATATATATAATATATAGTTTTT-AAAAACATTTTAGAAA
* *
954553 ATTTATATATTATAT-GTTTTT
1 ATATATATAATATATAGTTTTT
954574 GAAATTATTA
Statistics
Matches: 339, Mismatches: 41, Indels: 38
0.81 0.10 0.09
Matches are distributed among these distances:
35 4 0.01
36 55 0.16
37 94 0.28
38 108 0.32
39 33 0.10
40 37 0.11
41 8 0.02
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (38 bp):
ATATATATAATATATAGTTTTTAAAAACATTTTAGAAA
Found at i:954585 original size:3 final size:3
Alignment explanation
Indices: 954577--954615 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
954567 TGTTTTTGAA
954577 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
954616 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:955763 original size:16 final size:16
Alignment explanation
Indices: 955737--955822 Score: 63
Period size: 16 Copynumber: 5.3 Consensus size: 16
955727 AAAAAAATTA
955737 ATTTT-TTCTATTTTT
1 ATTTTATTCTATTTTT
955752 ATTTTATTCTATTTTCCT
1 ATTTTATTCTATTTT--T
* *
955770 -TTTTCTTCTATTTTG
1 ATTTTATTCTATTTTT
*
955785 ATTTTATT-TTTTATTT
1 ATTTTATTCTATT-TTT
*
955801 ATCTTATT-TAGTTTATT
1 ATTTTATTCTA-TTT-TT
955818 ATTTT
1 ATTTT
955823 TCTTCTATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
15 8 0.14
16 26 0.46
17 21 0.38
18 1 0.02
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.73
Consensus pattern (16 bp):
ATTTTATTCTATTTTT
Found at i:955809 original size:21 final size:21
Alignment explanation
Indices: 955787--955826 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
955777 CTATTTTGAT
*
955787 TTTA-TTTTTTATTTATCTTA
1 TTTAGTTTATTATTTATCTTA
*
955807 TTTAGTTTATTATTTTTCTT
1 TTTAGTTTATTATTTATCTT
955827 CTATATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTAGTTTATTATTTATCTTA
Found at i:957561 original size:12 final size:12
Alignment explanation
Indices: 957544--957568 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
957534 ATGTTATTAA
957544 TTCATGTGACAT
1 TTCATGTGACAT
957556 TTCATGTGACAT
1 TTCATGTGACAT
957568 T
1 T
957569 CCATATTAAT
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCATGTGACAT
Found at i:958845 original size:2 final size:2
Alignment explanation
Indices: 958840--958882 Score: 59
Period size: 2 Copynumber: 20.5 Consensus size: 2
958830 CGTCATGACA
*
958840 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AGT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A
958883 CTTTTACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 34 0.92
3 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:958941 original size:8 final size:8
Alignment explanation
Indices: 958857--958998 Score: 52
Period size: 7 Copynumber: 19.8 Consensus size: 8
958847 TATATATATA
958857 TATATAC-
1 TATATACT
*
958864 TATATAGT
1 TATATACT
958872 T-TATA--
1 TATATACT
958877 TATATACT
1 TATATACT
958885 T-T-TACT
1 TATATACT
*
958891 T-TATAGTT
1 TATATA-CT
* *
958899 TACATACA
1 TATATACT
*
958907 TACATACT
1 TATATACT
*
958915 TTTATA-T
1 TATATACT
*
958922 TTTATA-T
1 TATATACT
958929 TATATACT
1 TATATACT
958937 TATATACT
1 TATATACT
958945 T-TAGT-CT
1 TATA-TACT
*
958952 T-TATA-A
1 TATATACT
958958 T-TATACT
1 TATATACT
958965 T-TATA--
1 TATATACT
958970 TATATA-T
1 TATATACT
958977 ATATATACT
1 -TATATACT
958986 TATATACT
1 TATATACT
958994 T-TATA
1 TATATA
958999 TTTAAACTAT
Statistics
Matches: 109, Mismatches: 11, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
5 2 0.02
6 20 0.18
7 42 0.39
8 41 0.38
9 4 0.04
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (8 bp):
TATATACT
Found at i:958991 original size:29 final size:29
Alignment explanation
Indices: 958959--959027 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
958949 TCTTTATAAT
* *
958959 TATACTTTATATATATA-TATATATACTTA
1 TATACTTTATATATAAACTATATAAAC-TA
*
958988 TATACTTTATATTTAAACTATATAAACTA
1 TATACTTTATATATAAACTATATAAACTA
*
959017 TATAATTTATA
1 TATACTTTATA
959028 CATAGTGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 27 0.77
30 8 0.23
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.49
Consensus pattern (29 bp):
TATACTTTATATATAAACTATATAAACTA
Found at i:959112 original size:22 final size:21
Alignment explanation
Indices: 959076--959118 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
959066 ATATATGATG
959076 TATATATTTAAATATAATTCA
1 TATATATTTAAATATAATTCA
* *
959097 TATATAGTTTATATATAGTTCA
1 TATATA-TTTAAATATAATTCA
959119 ATGGTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
TATATATTTAAATATAATTCA
Found at i:960014 original size:23 final size:23
Alignment explanation
Indices: 959988--960048 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
959978 CTCATATAAA
959988 TGCACCGAAGTGCCAC-ATAGAAT
1 TGCACCGAAGTGCCACGA-AGAAT
*
960011 TGCACCGAAGTACCACGAAGAAT
1 TGCACCGAAGTGCCACGAAGAAT
960034 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
960049 TATAAAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGAAGAAT
Found at i:963858 original size:19 final size:20
Alignment explanation
Indices: 963818--963858 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
963808 ATCAGATTGT
963818 CCAGGGGGTACAGATTCTCC
1 CCAGGGGGTACAGATTCTCC
*
963838 CCAGGGGGTACCGATTC-CC
1 CCAGGGGGTACAGATTCTCC
963857 CC
1 CC
963859 TGTCTAACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.17, C:0.37, G:0.29, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCTCC
Found at i:966639 original size:20 final size:20
Alignment explanation
Indices: 966614--966676 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
966604 ATAAGATTGT
966614 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
966634 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATT-CCCC
966655 CCAGGGGGTACCA-ATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
966675 CC
1 CC
966677 TGTCTAACGG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 21 0.54
21 16 0.41
22 2 0.05
ACGTcount: A:0.21, C:0.40, G:0.27, T:0.13
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:966654 original size:21 final size:21
Alignment explanation
Indices: 966614--966676 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
966604 ATAAGATTGT
*
966614 CCAGGGGGTACAGATT-CCCC
1 CCAGGGGGAACAGATTCCCCC
966634 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
*
966655 CCAGGGGGTACCA-ATTCCCCC
1 CCAGGGGG-AACAGATTCCCCC
966676 C
1 C
966677 TGTCTAACGG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
20 15 0.38
21 21 0.54
22 3 0.08
ACGTcount: A:0.21, C:0.40, G:0.27, T:0.13
Consensus pattern (21 bp):
CCAGGGGGAACAGATTCCCCC
Found at i:969125 original size:23 final size:23
Alignment explanation
Indices: 969099--969159 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
969089 CTCATATAAA
* *
969099 TGCATCGAAGTGCTAC-ATAGAAT
1 TGCACCGAAGTGCCACGA-AGAAT
969122 TGCACCGAAGTGCCACGAAGAAT
1 TGCACCGAAGTGCCACGAAGAAT
969145 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
969160 TATAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGAAGAAT
Found at i:970727 original size:24 final size:24
Alignment explanation
Indices: 970695--970751 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
970685 TCTATAGTGT
970695 ATCGATGCATCCCTAAACATGTGC
1 ATCGATGCATCCCTAAACATGTGC
970719 ATCGATGCATCCCTAAACATGTGC
1 ATCGATGCATCCCTAAACATGTGC
970743 ATCGATGCA
1 ATCGATGCA
970752 CTCCTTATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCGATGCATCCCTAAACATGTGC
Found at i:974485 original size:23 final size:23
Alignment explanation
Indices: 974454--974531 Score: 129
Period size: 23 Copynumber: 3.4 Consensus size: 23
974444 CATATAAATA
974454 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
* *
974477 CACCAAAGTGCCACATAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
974500 CACCGAAGTGCTACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
974523 CACCGAAGT
1 CACCGAAGT
974532 TCCATATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:981459 original size:103 final size:102
Alignment explanation
Indices: 981235--981451 Score: 389
Period size: 103 Copynumber: 2.1 Consensus size: 102
981225 GTCGAGGGTC
981235 TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACT
* *
981300 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
981337 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
*
981402 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
981440 TATGTGGTCCTT
1 TATGTGGTCCTT
981452 ATGGACATTA
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 13 0.12
103 97 0.88
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:981501 original size:23 final size:23
Alignment explanation
Indices: 981469--981535 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
981459 TTATTATATG
981469 GCACTACGGTGCAATTCTACGCA
1 GCACTACGGTGCAATTCTACGCA
* **
981492 GCACTCCGGTGCAATTCTACGTG
1 GCACTACGGTGCAATTCTACGCA
* *
981515 GCACTTCGGTGCAATTATACG
1 GCACTACGGTGCAATTCTACG
981536 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCA
Found at i:983542 original size:23 final size:22
Alignment explanation
Indices: 983512--983570 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
983502 CTCATATAAA
983512 TGCACCGAAAGTGCACGTAGAAT
1 TGCACCG-AAGTGCACGTAGAAT
* *
983535 TGCACCGAAGTTTCATGTAGAAT
1 TGCACCGAAG-TGCACGTAGAAT
983558 TGCACCGAAGTGC
1 TGCACCGAAGTGC
983571 CATATAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (22 bp):
TGCACCGAAGTGCACGTAGAAT
Found at i:984233 original size:20 final size:19
Alignment explanation
Indices: 984208--984258 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 19
984198 ACATAGATCC
984208 TATAACATATATTGTAGCA
1 TATAACATATATTGTAGCA
984227 TTATAACATATATTGTAGCA
1 -TATAACATATATTGTAGCA
984247 TACTAACATATA
1 TA-TAACATATA
984259 CCACTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (19 bp):
TATAACATATATTGTAGCA
Found at i:985181 original size:24 final size:24
Alignment explanation
Indices: 985143--985204 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
985133 TCTACAGTGT
985143 ATCGATGCA-TCCCTAAACATGTGC
1 ATCGATGCACT-CCTAAACATGTGC
*
985167 ATTGATGCACTCCTAAACATGTGC
1 ATCGATGCACTCCTAAACATGTGC
985191 ATCGATGCACTCCT
1 ATCGATGCACTCCT
985205 TATGCATCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 34 0.97
25 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (24 bp):
ATCGATGCACTCCTAAACATGTGC
Found at i:986043 original size:2 final size:2
Alignment explanation
Indices: 986036--986081 Score: 67
Period size: 2 Copynumber: 22.5 Consensus size: 2
986026 TTTATACATA
986036 AT AT AT AT AGT -T CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
986079 AT A
1 AT A
986082 ATTGTTTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:994648 original size:31 final size:31
Alignment explanation
Indices: 994576--994825 Score: 101
Period size: 31 Copynumber: 8.3 Consensus size: 31
994566 CTTAAATTTT
* *
994576 AAAAT-TATCTTTTATTTTTGTTTTAACTTA
1 AAAATATATATTTTATTTTTATTTTAACTTA
**
994606 TTAA-ATATATTTTATTTTTATTTTAA-TGTA
1 AAAATATATATTTTATTTTTATTTTAACT-TA
* ** *
994636 AAAATATATATTTTATCTTTATCGTCACTTA
1 AAAATATATATTTTATTTTTATTTTAACTTA
**** * *
994667 AAAATATAT-TTTTAAAAATATTGTAA-TTT
1 AAAATATATATTTTATTTTTATTTTAACTTA
** *
994696 AAAATATAT-TTAAATATTTTATTATTAATTTA
1 AAAATATATATTTTAT-TTTTATT-TTAACTTA
* * * * * * * *
994728 TATATATATATATTACTATTATATTCACATA
1 AAAATATATATTTTATTTTTATTTTAACTTA
* *
994759 AAAATATATA--TTA-TTTT-TTTCAAATT-
1 AAAATATATATTTTATTTTTATTTTAACTTA
* **
994785 AAAA-ATATATTTTATTATTAACTTAACTTTTA
1 AAAATATATATTTTATTTTTATTTTAAC--TTA
994817 AAAATATAT
1 AAAATATAT
994826 TAAAATATAT
Statistics
Matches: 155, Mismatches: 49, Indels: 29
0.67 0.21 0.12
Matches are distributed among these distances:
25 5 0.03
26 4 0.03
27 7 0.05
28 6 0.04
29 21 0.14
30 40 0.26
31 47 0.30
32 19 0.12
33 6 0.04
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (31 bp):
AAAATATATATTTTATTTTTATTTTAACTTA
Found at i:994936 original size:29 final size:30
Alignment explanation
Indices: 994873--994951 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
994863 TTTAAAAATT
*
994873 AAGATAATAAT-AAATATATTTTTAATTTG
1 AAGATAATAATAAAATATATTTTTAATGTG
*
994902 AA-ATAAGAATAAAATATATTTTTAA-GTG
1 AAGATAATAATAAAATATATTTTTAATGTG
* *
994930 AAGATAATATTAATATATATTT
1 AAGATAATAATAAAATATATTT
994952 ATATTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 11 0.26
29 32 0.74
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (30 bp):
AAGATAATAATAAAATATATTTTTAATGTG
Found at i:998061 original size:29 final size:29
Alignment explanation
Indices: 998023--998081 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
998013 ACACTTTTAA
* *
998023 AAGTTAAGATAATAATAAAATATATTTTT
1 AAGTGAAGATAATAATAAAATATATATTT
* *
998052 AAGTGAAGATAATATTAATATATATATTT
1 AAGTGAAGATAATAATAAAATATATATTT
998081 A
1 A
998082 TATTTATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (29 bp):
AAGTGAAGATAATAATAAAATATATATTT
Found at i:998127 original size:100 final size:100
Alignment explanation
Indices: 998023--998216 Score: 236
Period size: 101 Copynumber: 1.9 Consensus size: 100
998013 ACACTTTTAA
* *
998023 AAGTTAAGATAATAAT-AAAATATA-TTTTTAAGTGAAGATAATA-TTAATATATATATTTATA-
1 AAGTTAAGAT-ATAATAAAAATATATTTTTTAAGTGAAGATAA-AGATAAAATATATATTTATAC
* *
998084 TTTATATTAAATTAATAATAAAATAT-TTTAATATATTTT
64 TTTA-A--AAATAAAAAATAAAATATATTTAATATATTTT
** * *
998123 AAGTTAAGATATTTTAAAAATATATTTTTTAAGTGATGATAAAGATAAAATATATATTTTTACTT
1 AAGTTAAGATATAATAAAAATATATTTTTTAAGTGAAGATAAAGATAAAATATATATTTATACTT
998188 TAAAAATAAAAAATAAAATATATTTAATA
66 TAAAAATAAAAAATAAAATATATTTAATA
998217 AGTTAAAACA
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
99 19 0.23
100 26 0.32
101 32 0.40
102 4 0.05
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.43
Consensus pattern (100 bp):
AAGTTAAGATATAATAAAAATATATTTTTTAAGTGAAGATAAAGATAAAATATATATTTATACTT
TAAAAATAAAAAATAAAATATATTTAATATATTTT
Found at i:998688 original size:20 final size:20
Alignment explanation
Indices: 998663--998755 Score: 141
Period size: 20 Copynumber: 4.7 Consensus size: 20
998653 TAATACAAAA
998663 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
998683 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
998703 TCGCATCGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
* *
998723 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATACTGACTT
*
998743 TCGCAACGAGATA
1 TCGCAACGCGATA
998756 ATACAGAATC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:999503 original size:24 final size:24
Alignment explanation
Indices: 999476--999529 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
999466 GTATTCGAAA
*
999476 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
999500 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
999524 TTTGAT
1 TTTGAT
999530 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:999721 original size:12 final size:12
Alignment explanation
Indices: 999704--999728 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
999694 ATATAATCCT
999704 GAAGAAGAAAAA
1 GAAGAAGAAAAA
999716 GAAGAAGAAAAA
1 GAAGAAGAAAAA
999728 G
1 G
999729 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1000749 original size:39 final size:38
Alignment explanation
Indices: 1000706--1000784 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
1000696 TCTTTTGGTT
**
1000706 GAAATGAAAATCGCAACGCGAAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGCG-AAATGAAAATCGCAACGC
*
1000745 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1000783 GA
1 GA
1000785 TTTTGGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 17 0.46
39 20 0.54
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:1000751 original size:19 final size:19
Alignment explanation
Indices: 1000706--1000784 Score: 122
Period size: 19 Copynumber: 4.1 Consensus size: 19
1000696 TCTTTTGGTT
1000706 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
1000725 GAAAATGACTATCGCAACGC
1 G-AAATGAAAATCGCAACGC
1000745 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1000764 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1000783 GA
1 GA
1000785 TTTTGGTTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 37 0.69
20 17 0.31
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1000802 original size:19 final size:20
Alignment explanation
Indices: 1000780--1000831 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1000770 AAAATCGCAA
**
1000780 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTTCATTTCCGCGT
**
1000799 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTTCCGCGT
1000819 TGCGATTTTCATT
1 TGCGATTTTCATT
1000832 CTCAAAACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (20 bp):
TGCGATTTTCATTTCCGCGT
Found at i:1001444 original size:20 final size:20
Alignment explanation
Indices: 1001353--1001438 Score: 106
Period size: 20 Copynumber: 4.3 Consensus size: 20
1001343 GCAATATGTA
* *
1001353 AATCGCAATGCGA-ATACGT
1 AATCGCATTGCGATTTACGT
1001372 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
1001392 ATTCGCATTGCGATTCTGAC-T
1 AATCGCATTGCGATT-T-ACGT
1001413 -ATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
1001432 AATCGCA
1 AATCGCA
1001439 ACGCGAATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
18 2 0.03
19 14 0.24
20 38 0.66
21 2 0.03
22 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:1002768 original size:3 final size:3
Alignment explanation
Indices: 1002760--1002791 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1002750 TTTATGGTTA
*
1002760 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1002792 AAAGTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1004118 original size:3 final size:3
Alignment explanation
Indices: 1004110--1004171 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
1004100 GGCCTGTTTG
** *
1004110 TAA TAA TAA TTT TAA TAA TAA TAA AAA TATA TAA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A
1004157 TAAA TAA TAA TAA TA
1 T-AA TAA TAA TAA TA
1004172 GAAAATGGAG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
3 42 0.84
4 7 0.14
5 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1004145 original size:16 final size:16
Alignment explanation
Indices: 1004110--1004171 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
1004100 GGCCTGTTTG
**
1004110 TAATAATAATTTTA-A
1 TAATAATAATAATATA
*
1004125 TAATAATAAAAATATA
1 TAATAATAATAATATA
1004141 TAATAATAATAATATA
1 TAATAATAATAATATA
1004157 TAAATAATAATAATA
1 T-AATAATAATAATA
1004172 GAAAATGGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.27
16 17 0.41
17 13 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAATAATAATATA
Found at i:1004570 original size:123 final size:123
Alignment explanation
Indices: 1004368--1005627 Score: 840
Period size: 123 Copynumber: 10.8 Consensus size: 123
1004358 GGGATGATAA
* * * * * *
1004368 TATCTCCTTCTGTGAT-GTAATT-TGGAAAAGGTTGAACAAGTTATTCTTATTATAAAATTCTTC
1 TATCTCCTTCTGTGATAG-AATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC-TC
* * * * *
1004431 TTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCCTGGAAAAGTTGATGTTGACC
64 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
* * * * * *
1004491 TATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTCTT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCTT
* * *
1004556 TCTTCTTCAAATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGCTGATA
66 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
** *
1004614 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC-T-TC-T
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCTT
* * *
1004676 TCTTTTTGAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATGCTGATC
66 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
1004734 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TT-TC-T
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCTT
* *
1004796 TCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGG-CAA--TG-T--TGATC
66 TCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGCTGATC
* *** **
1004851 CA--T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC-TC
* * * *
1004910 TTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAAGCTGATGCTGATC
64 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
* * *
1004970 TATCTCCTTCTGTGATAAAATTATG-AATAAGGTTGAACAAATTCTTCTCATTATGAA-TTTTTT
1 TATCTCCTTCTGTGATAGAATTATGCAA-AAGGTTGAACAAATTCTTCTCATTATGAACTTCTCT
* *
1005033 CTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TT-TCTGGAAAAGTTGAT-C----C
65 -TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
*** *** * * *
1005086 -A--T-C--GAATGAT-GAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAA-TTTTTT
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCT
* *
1005143 CTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TT-TCTGGAAAAGTTGAT-C----C
65 -TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
*** ** *
1005196 -A--T-C--GAATGAT-GAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAA-TT-TC-
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCT
* *
1005251 TTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGG-CAA--TG-T--TGATC
65 TTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGCTGATC
* *** ** *
1005307 CA--T-C--AAATGAT-GAATTCAAACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC-TC
* *
1005366 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCCTGGAAAAGTTGAT-C----C
64 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
** * * *
1005421 -A--T-C--AAGTGATGGATTTGA-GCAAAAGATTGAACAAATTCTTCTCATTATGAA-TT-TC-
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCT
* *
1005476 TTCTTCTTCAGACGACGAGTTCTTCTCATTATGAACTCTAC-CTGG-AAA--T-AT--TGATC
65 TTCTTCTTC--A-GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGCTGATC
* *** **
1005532 CA--T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC-TC
* *
1005591 TTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTT
64 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
1005628 AACTGATACT
Statistics
Matches: 973, Mismatches: 99, Indels: 141
0.80 0.08 0.12
Matches are distributed among these distances:
107 12 0.01
108 3 0.00
109 16 0.02
110 165 0.17
111 20 0.02
112 165 0.17
113 119 0.12
114 12 0.01
115 8 0.01
116 36 0.04
117 8 0.01
119 7 0.01
120 124 0.13
121 16 0.02
122 8 0.01
123 182 0.19
124 68 0.07
125 4 0.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (123 bp):
TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCTT
TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
Found at i:1004730 original size:120 final size:120
Alignment explanation
Indices: 1004368--1005627 Score: 767
Period size: 112 Copynumber: 10.8 Consensus size: 120
1004358 GGGATGATAA
* * * * *
1004368 TATCTCCTTCTGTGAT-GTAATT-TGGAAAAGGTTGAACAAGTTATTCTTATTATAAAATTCTTC
1 TATCTCCTTCTGTGATAG-AATTATGCAAAAGGTTGAACAAATTCTTCTCATTAT-GAA--CTTC
* * * * *
1004431 TTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCCTGGAAAAGTTGATGTTGACC
62 TT-CTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
* * * * * *
1004491 TATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTCTT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC-T-TC-T
* * * *
1004556 TCTTCTTCAAATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGCTGATA
63 TCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
** *
1004614 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
* *
1004679 TTTTGAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATGCTGATC
66 TTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
*
1004734 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
* * *
1004799 TCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGG-CAA--TG-T--TGATC
66 TTTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGCTGATC
* *** **
1004851 CA--T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
* * *
1004910 TTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAAGCTGATGCTGATC
65 -T--TT-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
* * *
1004970 TATCTCCTTCTGTGATAAAATTATG-AATAAGGTTGAACAAATTCTTCTCATTATGAATTTTTTC
1 TATCTCCTTCTGTGATAGAATTATGCAA-AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
*
1005034 TTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TT-TCTGGAAAAGTTGAT-C----C
65 TT--T-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
*** *** * * *
1005086 -A--T-C--GAATGAT-GAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAATTTTTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
*
1005144 TTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TT-TCTGGAAAAGTTGAT-C----C
65 TT--T-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
*** ** * *
1005196 -A--T-C--GAATGAT-GAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
* * *
1005254 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGG-CAA--TG-T--TGATC
65 TTTTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGCTGATC
* *** ** *
1005307 CA--T-C--AAATGAT-GAATTCAAACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
*
1005366 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCCTGGAAAAGTTGAT-C----C
65 -T--TT-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
** * * * *
1005421 -A--T-C--AAGTGATGGATTTGA-GCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
* * *
1005479 TTCTTCAGACGACGAGTTCTTCTCATTATGAACTCTAC-CTGG-AAA--T-AT--TGATC
65 TTTTTC--A-GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGCTGATC
* *** **
1005532 CA--T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
1 TATCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
*
1005591 TTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTT
65 -T--TT-TTCAGATGAGTTCTTCTCATTATGAACTTT
1005628 AACTGATACT
Statistics
Matches: 969, Mismatches: 100, Indels: 147
0.80 0.08 0.12
Matches are distributed among these distances:
107 7 0.01
108 3 0.00
109 10 0.01
110 170 0.18
111 20 0.02
112 182 0.19
113 122 0.13
114 12 0.01
115 5 0.01
116 21 0.02
117 8 0.01
119 7 0.01
120 124 0.13
121 18 0.02
122 7 0.01
123 179 0.18
124 70 0.07
125 4 0.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (120 bp):
TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
TTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
Found at i:1004900 original size:112 final size:110
Alignment explanation
Indices: 1004759--1005626 Score: 1009
Period size: 112 Copynumber: 7.7 Consensus size: 110
1004749 TAGAATTATG
1004759 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCA
*
1004823 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
64 TTATGAACT-TACCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
*
1004871 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGAT-GAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TT-TTCTT-CTTCTTCAGATAGAGTTCTTCTC
* * * *** ** * **
1004935 ATTATGAACTTTCTCTGAAAAAGCTGATGCTGATCTATCTCCTTCTGTGATAAAATTA
63 ATTATGAACTTAC-CTG-GAAA--TG-T--TGATCCATCAAATGATG-AATTCAA--A
* *
1004993 TGAATAAGGTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTCTTCAGATA-AGTTCTTCT
1 -CAA-AAGGTTGAACAAATTCTTCTCATTATGAA--TTTTCTTCTTCTTCAGATAGAGTTCTTCT
* * *
1005057 CATTATGAACTT-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
62 CATTATGAACTTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
* * *
1005105 TAAAAAGTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTCTTCAGATA-AGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA--TTTTCTTCTTCTTCAGATAGAGTTCTTCTCA
* * *
1005169 TTATGAACTT-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
64 TTATGAACTTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
*
1005215 CAAAAAGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCA
*
1005279 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
64 TTATGAACT-TACCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
*
1005327 CAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TT-TTCTT-CTTCTTCAGATAGAGTTCTTCTC
* * * * ** *
1005391 ATTATGAACTTTCCCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
63 ATTATGAAC-TTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
* *
1005440 CAAAAGATTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCTTCAGACGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTTCTTCTTCTTCAGA-TA-GAGTTCTTCTCA
*
1005504 TTATGAACTCTACCTGGAAATATTGATCCATCAAATGATGAATTCAAA
64 TTATGAACT-TACCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
1005552 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TT-TTCTT-CTTCTTCAGATAGAGTTCTTCTC
*
1005616 ATTATAAACTT
63 ATTATGAACTT
1005627 TAACTGATAC
Statistics
Matches: 659, Mismatches: 61, Indels: 72
0.83 0.08 0.09
Matches are distributed among these distances:
107 16 0.02
108 1 0.00
109 10 0.02
110 162 0.25
111 5 0.01
112 179 0.27
113 124 0.19
114 10 0.02
115 26 0.04
116 33 0.05
117 2 0.00
118 1 0.00
119 11 0.02
120 7 0.01
121 3 0.00
122 1 0.00
123 32 0.05
124 34 0.05
125 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (110 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTTCTTCTTCTTCAGATAGAGTTCTTCTCATT
ATGAACTTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAA
Found at i:1005300 original size:456 final size:457
Alignment explanation
Indices: 1004393--1005627 Score: 1431
Period size: 456 Copynumber: 2.7 Consensus size: 457
1004383 TGTAATTTGG
* * * * * *
1004393 AAAAGGTTGAACAAGTTATTCTTATTATAAAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
1004458 TATGAACTTTCCCTGGAAAAGTTGATGTTGACCTATTTCCTTCTGTGATAGAGTCATTCAAAAGG
66 TATGAACTTTCCCTGGAAAAG-TGATG-TGATCTA-TTCCTTCTGTGATAGAATTA-TGAAAAGG
* * * * * *
1004523 TTGAATAAGTTCTTCTCATTATGAACTTCTCTTTCTTCTTCAAATGAGTTCTTCTTATTATGAAC
127 TTGAACAAATTCTTCTCATTATGAA-TTTTC-TTCTTCTTCAGATAAGTTCTTCTCATTATGAAC
* * ***
1004588 TTTCTCTGGAAAAGTTGATGC-T-GATAT-ATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGA
190 -TTATCTGGAAAAGTTGATCCATCGA-ATGAT-GAATTC------A-AA-TA---AAAA-GTTGA
** * *
1004650 ACAAGCTCTTCTCATTGTGAACTTCTTCTT--T-TTGAGATGAGTTCTTCTCATTATGAACTTTC
240 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-TT-
* ** ** *
1004712 TCTGGAAAAGCTGATGCTGATCTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAATT
303 TCTGGAAAA-C-GAT-CTGATCCA-CTCC-TCAATGATAGAATTAAACAAAAAGTTGAACAAATT
1004777 CTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCA
363 CTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCA
1004842 ATGTTGATCCATCAAATGATGAATTCAAAC
428 ATGTTGATCCATCAAATGATGAATTCAAAC
*
1004872 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
1004937 TATGAACTTTCTCTGAAAAAGCTGATGCTGATCTATCTCCTTCTGTGATAAAATTATGAATAAGG
66 TATGAACTTTCCCTGGAAAAG-TGATG-TGATCTAT-TCCTTCTGTGATAGAATTATGAA-AAGG
*
1005002 TTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC
127 TTGAACAAATTCTTCTCATTATGAA--TTTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAAC
1005067 TT-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCAT
190 TTATCTGGAAAAGTTGATCCATCGAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCAT
* * *
1005131 TATGAATTTTTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTGGAAAA-G-T-TGA
255 TATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAAAACGATCTGA
*
1005193 TCCA-T-C-GAATGAT-GAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTC
320 TCCACTCCTCAATGATAGAATT-AAACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTC
1005254 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATG
384 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATG
1005319 AATTCAAAC
449 AATTCAAAC
*
1005328 AAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** * * *
1005393 TATGAACTTTCCCTGGAAAA--G-T-TGATCCA-T-C--AAGTGATGGATTTGA-GCAAAAGATT
66 TATGAACTTTCCCTGGAAAAGTGATGTGATCTATTCCTTCTGTGATAGAATT-ATG-AAAAGGTT
*
1005449 GAACAAATTCTTCTCATTATGAA-TTTCTTCTTCTTCAGACGACGAGTTCTTCTCATTATGAACT
129 GAACAAATTCTTCTCATTATGAATTTTCTTCTTCTTCAGA-TA--AGTTCTTCTCATTATGAACT
* * * *
1005513 CTACCTGGAAATA-TTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCA
191 -TATCTGGAAA-AGTTGATCCATCGAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCA
*
1005577 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTT
254 TTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTTT
1005628 AACTGATACT
Statistics
Matches: 674, Mismatches: 63, Indels: 69
0.84 0.08 0.09
Matches are distributed among these distances:
442 15 0.02
443 1 0.00
445 57 0.08
446 4 0.01
447 72 0.11
448 32 0.05
450 6 0.01
452 1 0.00
453 1 0.00
455 5 0.01
456 198 0.29
458 1 0.00
459 1 0.00
461 6 0.01
463 1 0.00
464 1 0.00
466 30 0.04
467 13 0.02
468 3 0.00
469 25 0.04
470 2 0.00
471 2 0.00
472 1 0.00
477 16 0.02
478 12 0.02
479 164 0.24
480 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (457 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCCCTGGAAAAGTGATGTGATCTATTCCTTCTGTGATAGAATTATGAAAAGGTTGA
ACAAATTCTTCTCATTATGAATTTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTTATCT
GGAAAAGTTGATCCATCGAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTCTCATTATGAA
CTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAAAACGATCTGATCCACT
CCTCAATGATAGAATTAAACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCA
GATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAA
AC
Found at i:1005495 original size:225 final size:222
Alignment explanation
Indices: 1005001--1005627 Score: 962
Period size: 225 Copynumber: 2.8 Consensus size: 222
1004991 TATGAATAAG
* *
1005001 GTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTCTTCAGATA--AGTTCTTCTCATTATG
1 GTTGAACAAATTCTTCTCATTATGAA---TTTCTTCTTCTTCAGAGACGAGTTCTTCTCATTATG
* * * * *
1005064 AACT-T-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAATAAAAAGTTGAACAAATTCTTC
63 AACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTC
* * *
1005127 TCATTATGAATTTTTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTGGAAAAGTT
128 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAAAAGTT
1005191 GATCCATCGAATGATGAATTCAAACAAAAA
193 GATCCATCGAATGATGAATTCAAACAAAAA
1005221 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGA-GACGAGTTCTTCTCATTATGAA
* *
1005286 CTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATTCTTCTC
65 CTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTC
1005351 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCCTGGAAAAGTT
130 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT--CTGGAAAAGTT
* ** *
1005416 GATCCATC-AAGTGATGGATTTGAGC-AAAA
193 GATCCATCGAA-TGATGAATTCAAACAAAAA
1005445 GATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGACGACGAGTTCTTCTCATTATGA
1 G-TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGA-GACGAGTTCTTCTCATTATGA
*
1005510 ACTCTACCTGGAAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCT
64 ACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCT
*
1005575 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTT
129 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
1005628 AACTGATACT
Statistics
Matches: 376, Mismatches: 21, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
217 15 0.04
218 1 0.00
220 46 0.12
221 1 0.00
222 70 0.19
223 31 0.08
224 7 0.02
225 205 0.55
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (222 bp):
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGAGACGAGTTCTTCTCATTATGAAC
TCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCA
TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGGAAAAGTTGAT
CCATCGAATGATGAATTCAAACAAAAA
Found at i:1006556 original size:115 final size:114
Alignment explanation
Indices: 1006366--1006578 Score: 356
Period size: 115 Copynumber: 1.9 Consensus size: 114
1006356 TCATCTTCCT
*
1006366 AATCCAATGATTGGTTTTGGAATTCTTACCGAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATCCAATGATTGGTTTTGGAATTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
*
1006431 AGATGCTATTGGGCCTCCTTATTTCTACTATGAGCAAATTCATCTTTTA
66 AGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAATTCATCTTTTA
* **
1006480 AATCTAATGATTGGTTTTGGGGTT-TATACCAAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 AATCCAATGATTGGTTTTGGAATTCT-TACC-AAACCAGATCAGATAACTCAAAGAACACTTCCA
1006544 GAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
64 GAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
1006579 TAATGTGGCA
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
113 1 0.01
114 25 0.27
115 66 0.72
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (114 bp):
AATCCAATGATTGGTTTTGGAATTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
AGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAATTCATCTTTTA
Found at i:1007279 original size:16 final size:16
Alignment explanation
Indices: 1007258--1007333 Score: 79
Period size: 17 Copynumber: 4.9 Consensus size: 16
1007248 ACCCCCTTTT
1007258 TTCTCTTTTTCTTCTC
1 TTCTCTTTTTCTTCTC
*
1007274 TTCTCTTTTTTCTTCTT
1 TTCTC-TTTTTCTTCTC
*
1007291 TTTTCTTTTTC-T-TC
1 TTCTCTTTTTCTTCTC
*
1007305 TTCTTTTTTTCTTCT-
1 TTCTCTTTTTCTTCTC
1007320 TT-TCATTTTTCTTC
1 TTCTC-TTTTTCTTC
1007334 AAGCATAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
14 11 0.22
15 13 0.26
16 12 0.24
17 14 0.28
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTCTTTTTCTTCTC
Found at i:1007302 original size:33 final size:31
Alignment explanation
Indices: 1007255--1007322 Score: 102
Period size: 30 Copynumber: 2.1 Consensus size: 31
1007245 TTGACCCCCT
1007255 TTTTTCTCTTTTTCTTCTCTTCTCTTTTTTCTTC
1 TTTTTCTCTTTTTC-T-TCTTCT-TTTTTTCTTC
1007289 TTTTT-TCTTTTTCTTCTTCTTTTTTTCTTC
1 TTTTTCTCTTTTTCTTCTTCTTTTTTTCTTC
1007319 TTTT
1 TTTT
1007323 CATTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 14 0.41
31 6 0.18
32 1 0.03
33 8 0.24
34 5 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTTCTCTTTTTCTTCTTCTTTTTTTCTTC
Found at i:1007331 original size:23 final size:22
Alignment explanation
Indices: 1007255--1007332 Score: 77
Period size: 22 Copynumber: 3.4 Consensus size: 22
1007245 TTGACCCCCT
*
1007255 TTTTTCTCTTTTTCTTCTCTTCTC
1 TTTTTCTTTTTTTCTTCT-TT-TC
*
1007279 TTTTTTCTTCTTTT-TTCTTTTTC
1 -TTTTTCTTTTTTTCTTC-TTTTC
*
1007302 TTCTTCTTTTTTTCTTCTTTTC
1 TTTTTCTTTTTTTCTTCTTTTC
1007324 ATTTTTCTT
1 -TTTTTCTT
1007333 CAAGCATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
22 16 0.36
23 12 0.27
24 5 0.11
25 12 0.27
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTTTTCTTCTTTTC
Found at i:1014685 original size:15 final size:15
Alignment explanation
Indices: 1014662--1014693 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1014652 TGCAATGAAT
1014662 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1014677 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1014692 AA
1 AA
1014694 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1018615 original size:20 final size:19
Alignment explanation
Indices: 1018576--1018627 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1018566 TTTCTTTGAT
1018576 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1018595 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1018615 ATTTATAAAATAA
1 A-TTAAAAAATAA
1018628 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1018678 original size:121 final size:116
Alignment explanation
Indices: 1018484--1018719 Score: 267
Period size: 121 Copynumber: 2.0 Consensus size: 116
1018474 AATATATATT
* * * * * *
1018484 AATTTATATATATTTATATATAAAATATTTATTTATTTAGAAATAATCAGAAAAGGACTTCTAGG
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATAATCAGAAAAAGACATCCAGG
* * *
1018549 TGCCTTAAGACAGCTATTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 TACCTTAAGACAG-TACTTTC-TTAATATTAAAAAATAAATAAAT-ATTAAAAC
*
1018603 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAAT-ATCAGAAAATAGACATCC
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATAATCAGAAAA-AGACATCC
* ** * * *
1018667 AGTTATTTTAAGACTGTCCTTTCTTAATATTAGAAAATAAATAAATATTAAAA
63 AGGTACCTTAAGACAGTACTTTCTTAATATTAAAAAATAAATAAATATTAAAA
1018720 TAGGATTAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
118 7 0.07
119 31 0.32
120 20 0.20
121 40 0.41
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (116 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATAATCAGAAAAAGACATCCAGG
TACCTTAAGACAGTACTTTCTTAATATTAAAAAATAAATAAATATTAAAAC
Found at i:1018801 original size:3 final size:3
Alignment explanation
Indices: 1018793--1018818 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1018783 TTTATGGTTA
1018793 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1018819 ACATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1020143 original size:3 final size:3
Alignment explanation
Indices: 1020135--1020210 Score: 73
Period size: 3 Copynumber: 23.7 Consensus size: 3
1020125 GGCCTGTTTG
**
1020135 TAA TAA TAA TTT TAA TAA TAA TAAA TAA T-A TATA TATA TATA TATA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TA-A TA-A TA-A
1020181 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA
1020211 GAAAATGGAG
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
2 2 0.03
3 42 0.65
4 21 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1020163 original size:10 final size:10
Alignment explanation
Indices: 1020148--1020210 Score: 64
Period size: 10 Copynumber: 6.7 Consensus size: 10
1020138 TAATAATTTT
1020148 AATAATAATA
1 AATAATAATA
1020158 AATAAT-ATA
1 AATAATAATA
*
1020167 TAT-AT-ATA
1 AATAATAATA
*
1020175 TATATATAAT-
1 AATA-ATAATA
1020185 AATAATAATA
1 AATAATAATA
1020195 AATAATAAT-
1 AATAATAATA
1020204 AATAATA
1 AATAATA
1020211 GAAAATGGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
8 8 0.17
9 17 0.36
10 20 0.43
11 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AATAATAATA
Found at i:1023876 original size:29 final size:29
Alignment explanation
Indices: 1023803--1023904 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
1023793 ATATATTTAA
* *
1023803 ATATTTTATTATTAGTTT-AATATATATATAT
1 ATATTTTATTATTA-TTTCAA-AT-TAAAAAT
*
1023834 ATATTTACTATTA-TATTT--ACTTAAAAAT
1 ATATTT--TATTATTATTTCAAATTAAAAAT
*
1023862 ATATTTTATTCTTATTTCAAATTAAAAAT
1 ATATTTTATTATTATTTCAAATTAAAAAT
1023891 ATATTTTATTATTA
1 ATATTTTATTATTA
1023905 AGTTAACTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
26 4 0.07
27 5 0.08
28 11 0.18
29 23 0.38
30 1 0.02
31 9 0.15
32 2 0.03
33 5 0.08
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (29 bp):
ATATTTTATTATTATTTCAAATTAAAAAT
Found at i:1025159 original size:60 final size:59
Alignment explanation
Indices: 1025090--1025251 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 59
1025080 ATTAGCATAG
* * * * *
1025090 TAACATTAAAATAAATATATTATTTTTATCTTAAA-TAATTAAAAATATTTTATTCTTATTT
1 TAAC-TTAAAATATATATATTATTCTTATTTTAAACTAA--AAAAATATTTTAGTCTTATCT
* * *
1025151 TAACTTAAAATATATATGTCATTCTTATTTTAAACTTAAAAATATATTTTAGTCTTATCT
1 TAACTTAAAATATATATATTATTCTTATTTTAAAC-TAAAAAAATATTTTAGTCTTATCT
* *
1025211 TAACTTAAAATATATATTTTATTCTTATTTTAAACTTAAAA
1 TAACTTAAAATATATATATTATTCTTATTTTAAACTAAAAA
1025252 TAGAATATAT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
59 5 0.06
60 76 0.86
61 4 0.05
62 3 0.03
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.49
Consensus pattern (59 bp):
TAACTTAAAATATATATATTATTCTTATTTTAAACTAAAAAAATATTTTAGTCTTATCT
Found at i:1025176 original size:30 final size:31
Alignment explanation
Indices: 1025134--1025253 Score: 183
Period size: 30 Copynumber: 4.0 Consensus size: 31
1025124 ATAATTAAAA
1025134 ATATTTTATTCTTATTTT-AACTTAAAATAT
1 ATATTTTATTCTTATTTTAAACTTAAAATAT
* *
1025164 ATATGTCATTCTTATTTTAAACTTAAAA-AT
1 ATATTTTATTCTTATTTTAAACTTAAAATAT
* *
1025194 ATATTTTAGTCTTATCTT-AACTTAAAATAT
1 ATATTTTATTCTTATTTTAAACTTAAAATAT
1025224 ATATTTTATTCTTATTTTAAACTTAAAATA
1 ATATTTTATTCTTATTTTAAACTTAAAATA
1025254 GAATATATAT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
29 9 0.11
30 50 0.63
31 20 0.25
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (31 bp):
ATATTTTATTCTTATTTTAAACTTAAAATAT
Found at i:1030950 original size:26 final size:26
Alignment explanation
Indices: 1030921--1031002 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
1030911 TCGAGGATTG
1030921 AAAAGTAGCATAGACATTAGTAAGAT
1 AAAAGTAGCATAGACATTAGTAAGAT
** * *
1030947 AAAAAAAGC-T-CAC-TTA-TCGAGGATT
1 AAAAGTAGCATAGACATTAGT--AAGA-T
1030972 GAAAAGTAGCATAGACATTAGTAAGAT
1 -AAAAGTAGCATAGACATTAGTAAGAT
1030999 AAAA
1 AAAA
1031003 AAACGTTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
22 1 0.03
23 3 0.08
24 5 0.12
25 2 0.05
26 18 0.45
27 2 0.05
28 5 0.12
29 3 0.08
30 1 0.03
ACGTcount: A:0.50, C:0.10, G:0.18, T:0.22
Consensus pattern (26 bp):
AAAAGTAGCATAGACATTAGTAAGAT
Found at i:1030979 original size:52 final size:52
Alignment explanation
Indices: 1030901--1031005 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1030891 TTACTTGAAT
1030901 AGCTCACTTATCGAGGATTGAAAAGTAGCATAGACATTAGTAAGATAAAAAA
1 AGCTCACTTATCGAGGATTGAAAAGTAGCATAGACATTAGTAAGATAAAAAA
1030953 AGCTCACTTATCGAGGATTGAAAAGTAGCATAGACATTAGTAAGATAAAAAA
1 AGCTCACTTATCGAGGATTGAAAAGTAGCATAGACATTAGTAAGATAAAAAA
1031005 A
1 A
1031006 CGTTATTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (52 bp):
AGCTCACTTATCGAGGATTGAAAAGTAGCATAGACATTAGTAAGATAAAAAA
Found at i:1032834 original size:9 final size:9
Alignment explanation
Indices: 1032811--1032862 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
1032801 ATTCCAGTAC
*
1032811 TGGAATTTC
1 TGGAATTTA
*
1032820 TTGAATTTA
1 TGGAATTTA
1032829 TGGAATTTA
1 TGGAATTTA
1032838 TGGAA-TTA
1 TGGAATTTA
* *
1032846 CCGGAATTTC
1 -TGGAATTTA
1032856 TGGAATT
1 TGGAATT
1032863 GAATAAGTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 3 0.09
9 30 0.86
10 2 0.06
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (9 bp):
TGGAATTTA
Found at i:1032843 original size:18 final size:19
Alignment explanation
Indices: 1032808--1032862 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 19
1032798 ATAATTCCAG
*
1032808 TACTGGAATTTCTTGAATT
1 TACTGGAATTTCTGGAATT
*
1032827 TA-TGGAATTTATGGAA-T
1 TACTGGAATTTCTGGAATT
*
1032844 TACCGGAATTTCTGGAATT
1 TACTGGAATTTCTGGAATT
1032863 GAATAAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (19 bp):
TACTGGAATTTCTGGAATT
Found at i:1040486 original size:24 final size:24
Alignment explanation
Indices: 1040469--1040586 Score: 166
Period size: 24 Copynumber: 4.9 Consensus size: 24
1040459 TTGATTTGAT
1040469 TTCTGATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
1040493 TTATGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
1040517 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* *
1040541 CTCTGATATGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
1040565 TTTTGATATGATACTTGACATG
1 TTCTGATATGATACTTGACATG
1040587 AATTATGGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:1043535 original size:30 final size:30
Alignment explanation
Indices: 1043479--1043537 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1043469 ATTTAGTCTA
* * *
1043479 GTGATCAAATTATAAGATTTGGAAAGTTTG
1 GTGACCAAAGTATAAGATTTGAAAAGTTTG
1043509 GTGACCAAAGTATAA-ACTTTGAAAAGTTT
1 GTGACCAAAGTATAAGA-TTTGAAAAGTTT
1043538 AGGGACCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
GTGACCAAAGTATAAGATTTGAAAAGTTTG
Found at i:1044716 original size:9 final size:9
Alignment explanation
Indices: 1044704--1044753 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
1044694 TGAATTTCTT
1044704 GAATTTATG
1 GAATTTATG
1044713 GAATTTATG
1 GAATTTATG
1044722 GAATTTATG
1 GAATTTATG
*
1044731 GAA-TTACCG
1 GAATTTA-TG
*
1044740 GAATTTCTG
1 GAATTTATG
1044749 GAATT
1 GAATT
1044754 GAATAAGTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 3 0.08
9 31 0.86
10 2 0.06
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (9 bp):
GAATTTATG
Found at i:1045378 original size:2 final size:2
Alignment explanation
Indices: 1045371--1045405 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1045361 TGTACACTAG
1045371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1045406 TCTGATCTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1045777 original size:17 final size:18
Alignment explanation
Indices: 1045737--1045778 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1045727 ATTAGTCTAT
1045737 TTTATTTTAATGATCTTA
1 TTTATTTTAATGATCTTA
* * *
1045755 TATATTTTGAT-ATTTTA
1 TTTATTTTAATGATCTTA
1045772 TTTATTT
1 TTTATTT
1045779 GTTCTCACCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTATTTTAATGATCTTA
Found at i:1056878 original size:48 final size:48
Alignment explanation
Indices: 1056811--1056907 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1056801 ACATGTTGTG
1056811 AATATATAAGTTAATATGTTCGTGAACAATAAATAAACGAACACGAAT
1 AATATATAAGTTAATATGTTCGTGAACAATAAATAAACGAACACGAAT
1056859 AATATATAAGTTAATATGTTCGTGAACAATAAATAAACGAACACGAAT
1 AATATATAAGTTAATATGTTCGTGAACAATAAATAAACGAACACGAAT
1056907 A
1 A
1056908 TGATATTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (48 bp):
AATATATAAGTTAATATGTTCGTGAACAATAAATAAACGAACACGAAT
Found at i:1056889 original size:27 final size:27
Alignment explanation
Indices: 1056811--1056894 Score: 63
Period size: 27 Copynumber: 3.3 Consensus size: 27
1056801 ACATGTTGTG
1056811 AATATATAAGTTAATATGTTCGTGAAC
1 AATATATAAGTTAATATGTTCGTGAAC
* ** ** *
1056838 -A-ATA-AA--TAA-ACGAACACGAAT
1 AATATATAAGTTAATATGTTCGTGAAC
1056859 AATATATAAGTTAATATGTTCGTGAAC
1 AATATATAAGTTAATATGTTCGTGAAC
*
1056886 AATAAATAA
1 AATATATAA
1056895 ACGAACACGA
Statistics
Matches: 38, Mismatches: 13, Indels: 12
0.60 0.21 0.19
Matches are distributed among these distances:
21 6 0.16
22 4 0.11
23 3 0.08
24 4 0.11
25 3 0.08
26 4 0.11
27 14 0.37
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (27 bp):
AATATATAAGTTAATATGTTCGTGAAC
Found at i:1057163 original size:19 final size:19
Alignment explanation
Indices: 1057141--1057186 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1057131 TTAGAAAAAG
1057141 ATAAGAAATCTTCATAATT
1 ATAAGAAATCTTCATAATT
* *
1057160 ATAATG-AATGTTTATAATT
1 ATAA-GAAATCTTCATAATT
1057179 ATAA-AAAT
1 ATAAGAAAT
1057187 AAATTAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 3 0.13
19 19 0.83
20 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (19 bp):
ATAAGAAATCTTCATAATT
Found at i:1059266 original size:5 final size:6
Alignment explanation
Indices: 1059250--1059279 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1059240 AATTATTTTC
*
1059250 TAAAAA TAAAAA TAAAAA TAAAAA CAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1059280 ATATTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (6 bp):
TAAAAA
Found at i:1062147 original size:15 final size:16
Alignment explanation
Indices: 1062118--1062147 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1062108 TTAGAATCCG
1062118 AACCGATTATTTTATA
1 AACCGATTATTTTATA
1062134 AACCGATT-TTTTAT
1 AACCGATTATTTTAT
1062148 TTATGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (16 bp):
AACCGATTATTTTATA
Found at i:1069142 original size:27 final size:26
Alignment explanation
Indices: 1069086--1069139 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1069076 TAGATTTAGG
*
1069086 AAGGGTATTTTTTATTTGAGACCAAA
1 AAGGGCATTTTTTATTTGAGACCAAA
*
1069112 AAGGGCATTTTTTATTTGGGACCAAA
1 AAGGGCATTTTTTATTTGAGACCAAA
1069138 AA
1 AA
1069140 AGGAATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (26 bp):
AAGGGCATTTTTTATTTGAGACCAAA
Found at i:1070050 original size:21 final size:21
Alignment explanation
Indices: 1070024--1070063 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1070014 CCGAAGTACC
*
1070024 ACATATATGTTCCAAATGATT
1 ACATATATGTCCCAAATGATT
*
1070045 ACATATATGTCCCGAATGA
1 ACATATATGTCCCAAATGA
1070064 CCGCGTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (21 bp):
ACATATATGTCCCAAATGATT
Found at i:1070209 original size:15 final size:15
Alignment explanation
Indices: 1070189--1070232 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
1070179 CTCATGGCTC
1070189 CTTATCACATAGCTT
1 CTTATCACATAGCTT
1070204 CTTATCACATAGCTT
1 CTTATCACATAGCTT
1070219 CTTATCACATAGCT
1 CTTATCACATAGCT
1070233 CATATATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (15 bp):
CTTATCACATAGCTT
Found at i:1073012 original size:2 final size:2
Alignment explanation
Indices: 1073007--1073040 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1072997 TTACTAGCTT
1073007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1073041 GAGATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1082185 original size:64 final size:64
Alignment explanation
Indices: 1082103--1082253 Score: 204
Period size: 64 Copynumber: 2.4 Consensus size: 64
1082093 GATAGATTTT
* *
1082103 ACCTATGTCTTTCAGGACATATGGACA-ATATTACCTATGTCTTTCGGGATATATGGACAATATC
1 ACCTATGTCTTTCAGGACATATGGACAGA-ATTACCTACGTCTTTCGGGACATATGGACAATATC
* *
1082167 ACCTATGTCTTTCGGGACATATGGACAGAATTACCTACGTCTTTCGGGACATATGGACAGT-T-
1 ACCTATGTCTTTCAGGACATATGGACAGAATTACCTACGTCTTTCGGGACATATGGACAATATC
1082229 ACCTATGT-TCTT-AGGAACATATGGA
1 ACCTATGTCT-TTCAGG-ACATATGGA
1082254 TAGGTCTTTC
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
61 3 0.04
62 19 0.24
63 1 0.01
64 55 0.70
65 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (64 bp):
ACCTATGTCTTTCAGGACATATGGACAGAATTACCTACGTCTTTCGGGACATATGGACAATATC
Found at i:1082226 original size:32 final size:33
Alignment explanation
Indices: 1082068--1082226 Score: 209
Period size: 32 Copynumber: 4.9 Consensus size: 33
1082058 AGAGTCGATG
* * * *
1082068 TTACCGATGTCCTTT-GGTACATATGGATAGATT
1 TTACCTATGT-CTTTCGGGACATATGGACAGATA
*
1082101 TTACCTATGTCTTTCAGGACATATGGACA-ATA
1 TTACCTATGTCTTTCGGGACATATGGACAGATA
*
1082133 TTACCTATGTCTTTCGGGATATATGGACA-ATA
1 TTACCTATGTCTTTCGGGACATATGGACAGATA
*
1082165 TCACCTATGTCTTTCGGGACATATGGACAGA-A
1 TTACCTATGTCTTTCGGGACATATGGACAGATA
*
1082197 TTACCTACGTCTTTCGGGACATATGGACAG
1 TTACCTATGTCTTTCGGGACATATGGACAG
1082227 TTACCTATGT
Statistics
Matches: 113, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
32 92 0.81
33 21 0.19
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (33 bp):
TTACCTATGTCTTTCGGGACATATGGACAGATA
Found at i:1084302 original size:31 final size:31
Alignment explanation
Indices: 1084258--1084317 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
1084248 ATGACCTCCC
*
1084258 AAAATTTTGAAAAT-TTATAATTTAGTCCTTT
1 AAAATTTTGAAAATATT-TAATTCAGTCCTTT
1084289 AAAATATTT-AAAATATTTAATTCAGTCCT
1 AAAAT-TTTGAAAATATTTAATTCAGTCCT
1084318 CACAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (31 bp):
AAAATTTTGAAAATATTTAATTCAGTCCTTT
Found at i:1086438 original size:20 final size:22
Alignment explanation
Indices: 1086413--1086453 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1086403 TTTGTGTACA
1086413 TGAA-TTCTT-TCTTATGCTAC
1 TGAATTTCTTCTCTTATGCTAC
*
1086433 TGAATTTCTTCTCTTTTGCTA
1 TGAATTTCTTCTCTTATGCTA
1086454 ATTTTCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.17, C:0.20, G:0.10, T:0.54
Consensus pattern (22 bp):
TGAATTTCTTCTCTTATGCTAC
Found at i:1092145 original size:19 final size:20
Alignment explanation
Indices: 1092099--1092147 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1092089 ACTAACCGAA
*
1092099 AATATTATAA-AAAAGATAT
1 AATATTTTAAGAAAAGATAT
* *
1092118 AACATTTTAAGAAAA-ATGT
1 AATATTTTAAGAAAAGATAT
1092137 AATATTTTAAG
1 AATATTTTAAG
1092148 TTACACGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (20 bp):
AATATTTTAAGAAAAGATAT
Found at i:1095264 original size:125 final size:126
Alignment explanation
Indices: 1095098--1095345 Score: 398
Period size: 125 Copynumber: 2.0 Consensus size: 126
1095088 TTATTTTTGA
1095098 AGGTGTTTATGTTCATTTATTTATTGTTCTCGAACATATTCATTTATATGTTCATGAATATGTTC
1 AGGTGTTTATGTTCA-TTATTTATTGTTCTCGAACATATTCATTTATATGTTCATGAATATGTTC
1095163 TTCTAACGTTCGTTTATTTGTTC-AA-TT-TTATCCTTTCATTTGGCAAACTAAATAAAATAAAA
65 -T-TAACGTTCGTTTATTTGTTCAAATTTATTATCCTTTCA-TT-GCAAACTAAATAAAATAAAA
1095225 T
126 T
1095226 AGGTGTTTATGTTCA-T-TTTATTGTTCTCGAACATATTCATTTATATGTTCATGAATATGTTCT
1 AGGTGTTTATGTTCATTATTTATTGTTCTCGAACATATTCATTTATATGTTCATGAATATGTTCT
1095289 TAACGTTCGTTTATTTGTTCAAATTTTAGTTATCCTTTCATTGCAAACTAAATAAAA
66 TAACGTTCGTTTATTTGTTCAAA-TTTA-TTATCCTTTCATTGCAAACTAAATAAAA
1095346 ATAATAAAAC
Statistics
Matches: 115, Mismatches: 0, Indels: 12
0.91 0.00 0.09
Matches are distributed among these distances:
123 20 0.17
124 3 0.03
125 46 0.40
126 18 0.16
127 2 0.02
128 26 0.23
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (126 bp):
AGGTGTTTATGTTCATTATTTATTGTTCTCGAACATATTCATTTATATGTTCATGAATATGTTCT
TAACGTTCGTTTATTTGTTCAAATTTATTATCCTTTCATTGCAAACTAAATAAAATAAAAT
Found at i:1100639 original size:78 final size:79
Alignment explanation
Indices: 1100496--1100655 Score: 313
Period size: 78 Copynumber: 2.0 Consensus size: 79
1100486 ATACATCTTC
1100496 AATTTTATGGTTCCCACGCCAACAATCTTTAAGGTATGATCATTGTAACTATACACAGATCCTCC
1 AATTTTATGGTTCCCACGCCAACAATCTTTAAGGTATGATCATTGTAACTATACACAGATCCTCC
1100561 TAAGTTAGGTTCAT
66 TAAGTTAGGTTCAT
1100575 AATTTTATGGTTCCCACGCCAACAATCTTTAA-GTATGATCATTGTAACTATACACAGATCCTCC
1 AATTTTATGGTTCCCACGCCAACAATCTTTAAGGTATGATCATTGTAACTATACACAGATCCTCC
1100639 TAAGTTAGGTTCAT
66 TAAGTTAGGTTCAT
1100653 AAT
1 AAT
1100656 GATGAAACCA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 49 0.60
79 32 0.40
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (79 bp):
AATTTTATGGTTCCCACGCCAACAATCTTTAAGGTATGATCATTGTAACTATACACAGATCCTCC
TAAGTTAGGTTCAT
Found at i:1104035 original size:11 final size:11
Alignment explanation
Indices: 1104019--1104043 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1104009 TTTTAATTCA
1104019 AAAATCAATTT
1 AAAATCAATTT
1104030 AAAATCAATTT
1 AAAATCAATTT
1104041 AAA
1 AAA
1104044 TAATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATCAATTT
Found at i:1107236 original size:24 final size:25
Alignment explanation
Indices: 1107204--1107272 Score: 95
Period size: 26 Copynumber: 2.8 Consensus size: 25
1107194 TAGGATGAGC
1107204 AAACTTATAAAATTTTAA-AATAAA
1 AAACTTATAAAATTTTAAGAATAAA
* *
1107228 AAACTTATAAGATTTTAGAGGATAAA
1 AAACTTATAAAATTTTA-AGAATAAA
*
1107254 AAACTTATAAAACTTTAAG
1 AAACTTATAAAATTTTAAG
1107273 GTTTTAAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
24 16 0.41
25 3 0.08
26 20 0.51
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (25 bp):
AAACTTATAAAATTTTAAGAATAAA
Found at i:1118420 original size:10 final size:9
Alignment explanation
Indices: 1118400--1118565 Score: 73
Period size: 8 Copynumber: 18.3 Consensus size: 9
1118390 ACTTGAAGAA
1118400 AAAGAAAAAG
1 AAAG-AAAAG
1118410 ATAAGAAAAG
1 A-AAGAAAAG
*
1118420 AGAGAAAAG
1 AAAGAAAAG
1118429 AAA-AAAA-
1 AAAGAAAAG
1118436 AAAGAAAAATG
1 AAAG-AAAA-G
* *
1118447 AAAAAAGAAA
1 AAAGAA-AAG
*
1118457 AAAGAAAAA
1 AAAGAAAAG
1118466 AATAGGAAAAG
1 AA-A-GAAAAG
*
1118477 ATA-AAAAG
1 AAAGAAAAG
1118485 -AAGAAAA-
1 AAAGAAAAG
*
1118492 AATGAAAAATG
1 AAAG-AAAA-G
*
1118503 AAAAAAAAG
1 AAAGAAAAG
*
1118512 -AAGAAAAT
1 AAAGAAAAG
1118520 AGAA-AAAAG
1 A-AAGAAAAG
1118529 AAAG-AAA-
1 AAAGAAAAG
*
1118536 AATGAAAAG
1 AAAGAAAAG
1118545 AAA-AAAAG
1 AAAGAAAAG
*
1118553 AGAGAGAAAG
1 AAAGA-AAAG
1118563 AAA
1 AAA
1118566 AATAAAAAGG
Statistics
Matches: 118, Mismatches: 18, Indels: 40
0.67 0.10 0.23
Matches are distributed among these distances:
7 7 0.06
8 36 0.31
9 31 0.26
10 28 0.24
11 16 0.14
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:1118429 original size:25 final size:25
Alignment explanation
Indices: 1118398--1118553 Score: 133
Period size: 25 Copynumber: 6.3 Consensus size: 25
1118388 ACACTTGAAG
* * *
1118398 AAAAAGAAAAAGATAAGAAAAGAGA
1 AAAAAGAAAAAAAGAAGAAAATAGA
* *
1118423 GAAAAGAAAAAAAAAAGAAAA-ATGA
1 AAAAAGAAAAAAAGAAGAAAATA-GA
*
1118448 AAAAAG-AAAAAAGAAAAAAATAG-
1 AAAAAGAAAAAAAGAAGAAAATAGA
* * *
1118471 GAAAAGATAAAAAGAAGAAAAAATGA
1 AAAAAGAAAAAAAGAAGAAAATA-GA
*
1118497 AAAATGAAAAAAAAGAAGAAAATAGA
1 AAAAAG-AAAAAAAGAAGAAAATAGA
* *
1118523 AAAAAGAAAGAAAA-ATGAAAAGA-A
1 AAAAAGAAA-AAAAGAAGAAAATAGA
1118547 AAAAAGA
1 AAAAAGA
1118554 GAGAGAAAGA
Statistics
Matches: 107, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
23 5 0.05
24 35 0.33
25 37 0.35
26 15 0.14
27 15 0.14
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (25 bp):
AAAAAGAAAAAAAGAAGAAAATAGA
Found at i:1118431 original size:14 final size:12
Alignment explanation
Indices: 1118395--1118574 Score: 115
Period size: 11 Copynumber: 14.8 Consensus size: 12
1118385 GCTACACTTG
1118395 AAGAAAAAGAAA
1 AAGAAAAAGAAA
*
1118407 AAG-ATAAGAAA
1 AAGAAAAAGAAA
1118418 AGAGAGAAAAGAAA
1 A-AGA-AAAAGAAA
1118432 AA-AAAAAGAAA
1 AAGAAAAAGAAA
1118443 AATGAAAAAAGAAAA
1 AA-G-AAAAAG-AAA
*
1118458 AAGAAAAA-AAT
1 AAGAAAAAGAAA
* *
1118469 AGGAAAAGATAAA
1 AAGAAAA-AGAAA
*
1118482 AAGAAGAA-AAA
1 AAGAAAAAGAAA
*
1118493 ATGAAAAATGAAA
1 AAGAAAAA-GAAA
1118506 AA-AAAGAAGAAA
1 AAGAAA-AAGAAA
*
1118518 ATAGAAAAA-AGA
1 A-AGAAAAAGAAA
1118530 AAGAAAAATG-AA
1 AAGAAAAA-GAAA
1118542 AAGAAAAA-AAGA
1 AAGAAAAAGAA-A
* *
1118554 GAGAGAAAGAAA
1 AAGAAAAAGAAA
*
1118566 AATAAAAAG
1 AAGAAAAAG
1118575 GAGGGTTCAA
Statistics
Matches: 132, Mismatches: 17, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
11 43 0.33
12 42 0.32
13 24 0.18
14 18 0.14
15 5 0.04
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:1118431 original size:31 final size:29
Alignment explanation
Indices: 1118395--1118574 Score: 101
Period size: 30 Copynumber: 6.1 Consensus size: 29
1118385 GCTACACTTG
1118395 AAGAAAAAGAAAAAGATAAGAAAAGAGAGAA
1 AAGAAAAAGAAAAAGATAAGAAAAGA-A-AA
*
1118426 AAGAAAAA-AAAAAG--AA-AAATGAAAA
1 AAGAAAAAGAAAAAGATAAGAAAAGAAAA
* *
1118451 AAGAAAAAAGAAAAAAATAGGAAAAGATAAA
1 AAG-AAAAAGAAAAAGATAAGAAAAGA-AAA
* * *
1118482 AAGAAGAA-AAAATGAAAAATGAAAA-AAAA
1 AAGAAAAAGAAAAAG-ATAA-GAAAAGAAAA
1118511 GAAGAAAATAGAAAAAAGA-AAGAAAAATGAAAA
1 -AAGAAAA-AG-AAAAAGATAAG-AAAA-GAAAA
* *
1118544 GAA-AAAAAGAGAGAGA-AAGAAAA-ATAAA
1 -AAGAAAAAGAAAAAGATAAGAAAAGA-AAA
1118572 AAG
1 AAG
1118575 GAGGGTTCAA
Statistics
Matches: 119, Mismatches: 13, Indels: 37
0.70 0.08 0.22
Matches are distributed among these distances:
25 5 0.04
26 6 0.05
27 13 0.11
28 5 0.04
29 12 0.10
30 33 0.28
31 28 0.24
32 5 0.04
33 12 0.10
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (29 bp):
AAGAAAAAGAAAAAGATAAGAAAAGAAAA
Found at i:1118443 original size:7 final size:7
Alignment explanation
Indices: 1118398--1118550 Score: 77
Period size: 7 Copynumber: 20.7 Consensus size: 7
1118388 ACACTTGAAG
1118398 AAAAAGA
1 AAAAAGA
*
1118405 AAAAGATA
1 AAAA-AGA
1118413 AGAAAAGA
1 A-AAAAGA
1118421 GAGAAAAG-
1 -A-AAAAGA
1118429 -AAAA-A
1 AAAAAGA
1118434 AAAAAGA
1 AAAAAGA
*
1118441 AAAATGA
1 AAAAAGA
1118448 AAAAAGA
1 AAAAAGA
1118455 AAAAAGA
1 AAAAAGA
1118462 AAAAA-A
1 AAAAAGA
1118468 TAGGAAAAGATAA
1 -A--AAAAG---A
1118481 AAAGAAGA
1 AAA-AAGA
1118489 AAAAATGA
1 AAAAA-GA
*
1118497 AAAATG-
1 AAAAAGA
1118503 AAAAA-A
1 AAAAAGA
*
1118509 AAGAAGA
1 AAAAAGA
*
1118516 AAATAGA
1 AAAAAGA
1118523 AAAAAGA
1 AAAAAGA
1118530 AAGAAA-A
1 AA-AAAGA
1118537 ATGAAAAGA
1 A--AAAAGA
1118546 AAAAA
1 AAAAA
1118551 AGAGAGAGAA
Statistics
Matches: 115, Mismatches: 10, Indels: 42
0.69 0.06 0.25
Matches are distributed among these distances:
5 4 0.03
6 13 0.11
7 53 0.46
8 21 0.18
9 17 0.15
10 2 0.02
11 3 0.03
12 1 0.01
13 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (7 bp):
AAAAAGA
Found at i:1118449 original size:18 final size:18
Alignment explanation
Indices: 1118398--1118550 Score: 111
Period size: 18 Copynumber: 8.3 Consensus size: 18
1118388 ACACTTGAAG
*
1118398 AAAAAGAAAAA-GATAAGA
1 AAAAAGAAAAATGA-AAAA
*
1118416 AAAGAGAGAAAA-GAAAAA
1 AAAAAGA-AAAATGAAAAA
1118434 AAAAAGAAAAATGAAAAA
1 AAAAAGAAAAATGAAAAA
1118452 AGAAAA-AAGAAA--AAAATA
1 A-AAAAGAA-AAATGAAAA-A
* * *
1118470 GGAAAAGATAAAAAGAAGAA
1 -AAAAAGA-AAAATGAAAAA
*
1118490 AAAATGAAAAATGAAAAA
1 AAAAAGAAAAATGAAAAA
1118508 AAAGAAG-AAAATAGAAAAA
1 AAA-AAGAAAAAT-GAAAAA
*
1118527 AGAAAGAAAAATGAAAAGA
1 AAAAAGAAAAATGAAAA-A
1118546 AAAAA
1 AAAAA
1118551 AGAGAGAGAA
Statistics
Matches: 109, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
17 8 0.07
18 54 0.50
19 42 0.39
20 2 0.02
21 3 0.03
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAATGAAAAA
Found at i:1118451 original size:24 final size:24
Alignment explanation
Indices: 1118397--1118573 Score: 115
Period size: 24 Copynumber: 7.5 Consensus size: 24
1118387 TACACTTGAA
* *
1118397 GAAAAAGAAAAAGATAAGAAAAGA-
1 GAAAAAGAAAAAAAAAAGAAAA-AT
1118421 GAGAAAAGAAAAAAAAAAGAAAAAT
1 GA-AAAAGAAAAAAAAAAGAAAAAT
*
1118446 GAAAAA-AGAAAAAAGAA-AAAAAT
1 GAAAAAGA-AAAAAAAAAGAAAAAT
* * *
1118469 AGGAAAAGATAAAAAGAAGAAAAAAT
1 -GAAAAAGAAAAAAAAAAG-AAAAAT
1118495 GAAAAATG--AAAAAAAAG---AA-
1 GAAAAA-GAAAAAAAAAAGAAAAAT
*
1118514 GAAAATAGAAAAAAGAAAGAAAAAT
1 GAAAA-AGAAAAAAAAAAGAAAAAT
* *
1118539 GAAAA-GAAAAAAAGAGAGAGAAA-
1 GAAAAAGAAAAAAA-AAAGAAAAAT
*
1118562 GAAAAATAAAAA
1 GAAAAAGAAAAA
1118574 GGAGGGTTCA
Statistics
Matches: 124, Mismatches: 12, Indels: 34
0.73 0.07 0.20
Matches are distributed among these distances:
19 6 0.05
20 3 0.02
21 8 0.06
23 19 0.15
24 50 0.40
25 31 0.25
26 7 0.06
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (24 bp):
GAAAAAGAAAAAAAAAAGAAAAAT
Found at i:1118492 original size:56 final size:57
Alignment explanation
Indices: 1118398--1118551 Score: 172
Period size: 57 Copynumber: 2.7 Consensus size: 57
1118388 ACACTTGAAG
*
1118398 AAAAAGAAAAAGATAAGAAAAGAGAGAAAAGAAAAAAAAAAGAAAAATGAAAAAAGA
1 AAAAAGAAAAAAATAAGAAAAGAGAGAAAAGAAAAAAAAAAGAAAAATGAAAAAAGA
* * * *
1118455 AAAAAGAAAAAAATAGGAAAAGATA-AAAAGAAGAAAAAATGAAAAATGAAAAAAAAGAA
1 AAAAAGAAAAAAATAAGAAAAGAGAGAAAAGAAAAAAAAAAGAAAAATG--AAAAAAG-A
*
1118514 GAAAATAGAAAAAAGA-AAGAAAA-A-TGAAAAGAAAAAAA
1 -AAAA-AGAAAAAA-ATAAGAAAAGAGAGAAAAGAAAAAAA
1118552 GAGAGAGAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
56 21 0.26
57 22 0.27
58 7 0.09
59 1 0.01
60 16 0.20
61 14 0.17
62 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (57 bp):
AAAAAGAAAAAAATAAGAAAAGAGAGAAAAGAAAAAAAAAAGAAAAATGAAAAAAGA
Found at i:1118562 original size:18 final size:16
Alignment explanation
Indices: 1118405--1118567 Score: 111
Period size: 16 Copynumber: 9.6 Consensus size: 16
1118395 AAGAAAAAGA
1118405 AAAAGATAAGAAAAGAGAG
1 AAAAGA-AA-AAAAGA-AG
*
1118424 AAAAGAAAAAAAAAAG
1 AAAAGAAAAAAAGAAG
1118440 AAAA-ATGAAAAAAGAA-
1 AAAAGA--AAAAAAGAAG
* *
1118456 AAAAGAAAAAAATAGG
1 AAAAGAAAAAAAGAAG
*
1118472 AAAAGATAAAAAGAAG
1 AAAAGAAAAAAAGAAG
*
1118488 AAAA-AATGAAAAATGAAAA
1 AAAAGAA--AAAAA-G-AAG
1118507 AAAAGAAGAAAATAGAA-
1 AAAAGAA-AAAA-AGAAG
*
1118524 AAAAGAAAGAAAA-ATG
1 AAAAGAAA-AAAAGAAG
1118540 AAAAGAAAAAAAGAGAG
1 AAAAGAAAAAAAGA-AG
1118557 AGAAAGAAAAA
1 A-AAAGAAAAA
1118568 TAAAAAGGAG
Statistics
Matches: 118, Mismatches: 11, Indels: 31
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.12
16 38 0.32
17 31 0.26
18 14 0.12
19 18 0.15
20 3 0.03
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (16 bp):
AAAAGAAAAAAAGAAG
Found at i:1121083 original size:44 final size:44
Alignment explanation
Indices: 1120963--1121090 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 44
1120953 TTGTTCACCC
* * ** ***
1120963 TTTTGCTCGATTCTATCACA-AAAGGAGGTAGATCCGCATCAACA
1 TTTTGCTCGATTCCATCACAGAAA-GAGGTGGATCAACATTTTCA
*
1121007 TTTTGTTCGATTCCATCACAGAAAGAGGTGGATCAACATTTTCA
1 TTTTGCTCGATTCCATCACAGAAAGAGGTGGATCAACATTTTCA
** * *
1121051 TTTTGCTCGATTCCATCTTAGAAGGAGTTGGATCAACATT
1 TTTTGCTCGATTCCATCACAGAAAGAGGTGGATCAACATT
1121091 GTCTCCACTT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
44 67 0.96
45 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
TTTTGCTCGATTCCATCACAGAAAGAGGTGGATCAACATTTTCA
Found at i:1121499 original size:33 final size:32
Alignment explanation
Indices: 1121440--1121509 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
1121430 ATATAAAAAA
* * **
1121440 AGAAAAAAATAATAAAAAAATTAAAAAATTAG
1 AGAAAAAAAAAAGAAAAAAAGGAAAAAATTAG
*
1121472 AGAAAGAAAAAAAGAAAAAAAGGAAAAAA-TGG
1 AGAAA-AAAAAAAGAAAAAAAGGAAAAAATTAG
1121504 AGAAAA
1 AGAAAA
1121510 GTAGATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 1 0.03
32 12 0.38
33 19 0.59
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (32 bp):
AGAAAAAAAAAAGAAAAAAAGGAAAAAATTAG
Found at i:1128079 original size:32 final size:32
Alignment explanation
Indices: 1128017--1128079 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1128007 GAATTAATAC
** **
1128017 AAATATATAATTTTTATTTTATTTTTAAATTA
1 AAATATATAATTTTTATTTTACATAAAAATTA
1128049 AAATATAT-ATTTATTATTTTACATAAAAATT
1 AAATATATAATTT-TTATTTTACATAAAAATT
1128080 TTATTACGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (32 bp):
AAATATATAATTTTTATTTTACATAAAAATTA
Found at i:1129727 original size:85 final size:85
Alignment explanation
Indices: 1129584--1129755 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 85
1129574 CCTGTTACAC
*
1129584 AATGTCAAATTCATTTAGTTTTACATATATTTAAGGCCGTTAGATGAGTGAAATAAGATGATCGA
1 AATGTCAAATTCATTTAGTTTTACATATATTTAAGGCCGTTAGATGAGTGAAATAAGATGACCGA
1129649 GATTAACAGTAGGAAATAAG
66 GATTAACAGTAGGAAATAAG
1129669 AATGTCAAATTCATTTAGTTTTACATATATTTAAGGCCGTTAGATGAGTGAAATAAGATGACCGA
1 AATGTCAAATTCATTTAGTTTTACATATATTTAAGGCCGTTAGATGAGTGAAATAAGATGACCGA
1129734 GATTAACAGTAGGAAATAAG
66 GATTAACAGTAGGAAATAAG
1129754 AA
1 AA
1129756 GATATTCACT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.31
Consensus pattern (85 bp):
AATGTCAAATTCATTTAGTTTTACATATATTTAAGGCCGTTAGATGAGTGAAATAAGATGACCGA
GATTAACAGTAGGAAATAAG
Found at i:1141351 original size:43 final size:42
Alignment explanation
Indices: 1141267--1141406 Score: 147
Period size: 43 Copynumber: 3.2 Consensus size: 42
1141257 TCTAAAGTTC
* *
1141267 GCGGCGTTTGTTAACGAAAAACGCCGCAATAGGTAAC-GATATATA
1 GCGGCGTTTGTT-A--AAAAACGCCGCAATAGGT-GCTGATATTTA
*
1141312 GCGGCGTTTGTTAAAGAAATGCCGCAATAGGTGCTGATATTTA
1 GCGGCGTTTGTTAAA-AAACGCCGCAATAGGTGCTGATATTTA
* * * * *
1141355 GCGGCATTTGTCTTAAAAACGTCGCAATAGGTGTTGAGATTTA
1 GCGGCGTTTGT-TAAAAAACGCCGCAATAGGTGCTGATATTTA
1141398 GCGGCGTTT
1 GCGGCGTTT
1141407 TTTTGATGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
42 3 0.04
43 63 0.77
44 4 0.05
45 12 0.15
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (42 bp):
GCGGCGTTTGTTAAAAAACGCCGCAATAGGTGCTGATATTTA
Found at i:1141563 original size:44 final size:44
Alignment explanation
Indices: 1141488--1141627 Score: 201
Period size: 44 Copynumber: 3.2 Consensus size: 44
1141478 GTATTTAGAT
* *
1141488 GCGTTTTTAGGATACAAACATCGCGATAGGTCTAGTATATAGCG
1 GCGTTTTTAGGATACAAACATCGCTAAAGGTCTAGTATATAGCG
* * * *
1141532 GCGTTTTTAGGATACAAGCGTCGCTAAAGGTCTTGTATATAACG
1 GCGTTTTTAGGATACAAACATCGCTAAAGGTCTAGTATATAGCG
* *
1141576 GCGTTTTTAGGATACAAACACCGCTAAAGGT-TGGTATATAGCG
1 GCGTTTTTAGGATACAAACATCGCTAAAGGTCTAGTATATAGCG
1141619 GCGTTTTTA
1 GCGTTTTTA
1141628 TATAAACGCC
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
43 19 0.22
44 66 0.78
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
GCGTTTTTAGGATACAAACATCGCTAAAGGTCTAGTATATAGCG
Found at i:1145491 original size:21 final size:21
Alignment explanation
Indices: 1145448--1145520 Score: 110
Period size: 21 Copynumber: 3.4 Consensus size: 21
1145438 CAAAAGTCCT
*
1145448 CGAGTATTGGTACTGGCCCCCC
1 CGAGTATCGGTACTGG-CCCCC
*
1145470 CGAGTATCGGTATTGGCCCCC
1 CGAGTATCGGTACTGGCCCCC
*
1145491 CGAGTATCGGTACTGGCCCCT
1 CGAGTATCGGTACTGGCCCCC
1145512 CGAGTATCG
1 CGAGTATCG
1145521 ATACCCTATG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 33 0.70
22 14 0.30
ACGTcount: A:0.15, C:0.33, G:0.29, T:0.23
Consensus pattern (21 bp):
CGAGTATCGGTACTGGCCCCC
Found at i:1146263 original size:17 final size:17
Alignment explanation
Indices: 1146227--1146269 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1146217 ATGCGATTTT
* *
1146227 AGAAGAAGATGATGACAA
1 AGAAGAA-ATGAAGAAAA
1146245 AGAAGAAATGAAGAAAA
1 AGAAGAAATGAAGAAAA
*
1146262 AGATGAAA
1 AGAAGAAA
1146270 CATTCCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.63, C:0.02, G:0.26, T:0.09
Consensus pattern (17 bp):
AGAAGAAATGAAGAAAA
Found at i:1146948 original size:29 final size:31
Alignment explanation
Indices: 1146915--1146974 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
1146905 GTGATATGAT
1146915 ACATG-CA-TGCCACATTATCATCTTGGGTG
1 ACATGACAGTGCCACATTATCATCTTGGGTG
*
1146944 ACATGACATGTGTCACATTATCATCTTGGGT
1 ACATGACA-GTGCCACATTATCATCTTGGGT
1146975 AACGTGGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 2 0.07
32 20 0.74
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (31 bp):
ACATGACAGTGCCACATTATCATCTTGGGTG
Found at i:1146965 original size:32 final size:34
Alignment explanation
Indices: 1146888--1146974 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 34
1146878 ATGTTACATT
* * *
1146888 TCACATCATCAACTTGGGTGATATGATACATGCATG
1 TCACATTATCATCTTGGGTGACATGA-ACATG-ATG
*
1146924 CCACATTATCATCTTGGGTGACATG-ACATG-TG
1 TCACATTATCATCTTGGGTGACATGAACATGATG
1146956 TCACATTATCATCTTGGGT
1 TCACATTATCATCTTGGGT
1146975 AACGTGGATC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 20 0.43
34 5 0.11
36 21 0.46
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (34 bp):
TCACATTATCATCTTGGGTGACATGAACATGATG
Found at i:1150213 original size:63 final size:63
Alignment explanation
Indices: 1150113--1150238 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
1150103 CTGGAGTTTC
*
1150113 AATTTCAAATGTTAATTGCTAATATTATAGAGAAAATTAGAACCTAAACAGAAGCATTACATTT
1 AATTTCAAATGTTAATTGCTAATACTATAGAGAAAATTAGAACCTAAACAGAAGCATTA-ATTT
* *
1150177 AATTTCACAT-TTAATTGCTAATACTATAGAGAAAATTAGAACCTAAACAGAAGCTTTAATTT
1 AATTTCAAATGTTAATTGCTAATACTATAGAGAAAATTAGAACCTAAACAGAAGCATTAATTT
1150239 TTTTTAACTT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 4 0.07
63 46 0.78
64 9 0.15
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (63 bp):
AATTTCAAATGTTAATTGCTAATACTATAGAGAAAATTAGAACCTAAACAGAAGCATTAATTT
Found at i:1151756 original size:18 final size:17
Alignment explanation
Indices: 1151733--1151769 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
1151723 AATCAAAATG
1151733 AAATAAGACAACAATACA
1 AAATAAGACAACAA-ACA
1151751 AAATAAGACAACAAACA
1 AAATAAGACAACAAACA
1151768 AA
1 AA
1151770 CTAAACCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.08
Consensus pattern (17 bp):
AAATAAGACAACAAACA
Found at i:1156061 original size:20 final size:21
Alignment explanation
Indices: 1155988--1156069 Score: 78
Period size: 20 Copynumber: 3.9 Consensus size: 21
1155978 CAGAACCCCA
* *
1155988 GGGGGGTATCGATTCCCT-GT
1 GGGGGGAATCGATTCCCTCAT
* *
1156008 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATT-CCC-TCAT
* *
1156031 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGAATCGATTCCCTCAT
1156052 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
1156070 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
20 23 0.45
21 11 0.22
22 4 0.08
23 13 0.25
ACGTcount: A:0.15, C:0.24, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAT
Found at i:1159904 original size:22 final size:21
Alignment explanation
Indices: 1159862--1159901 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1159852 GAGTTTGTTT
*
1159862 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1159883 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1159902 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1164448 original size:20 final size:20
Alignment explanation
Indices: 1164425--1164484 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1164415 ATCTGAATCA
1164425 GCTTGAGTCAACCCAAACCG
1 GCTTGAGTCAACCCAAACCG
*
1164445 GCTTGAGTCAACCCAAA-CA
1 GCTTGAGTCAACCCAAACCG
*
1164464 GCTTGAGTCAACCCGAACCG
1 GCTTGAGTCAACCCAAACCG
1164484 G
1 G
1164485 TATGACCCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.15
Consensus pattern (20 bp):
GCTTGAGTCAACCCAAACCG
Found at i:1168395 original size:17 final size:17
Alignment explanation
Indices: 1168359--1168401 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1168349 TGAGTTTTTT
* *
1168359 AGAAGAAGATGATGACAA
1 AGAAGAA-ATGAAGAAAA
1168377 AGAAGAAATGAAGAAAA
1 AGAAGAAATGAAGAAAA
*
1168394 AGATGAAA
1 AGAAGAAA
1168402 CTCGTCATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.63, C:0.02, G:0.26, T:0.09
Consensus pattern (17 bp):
AGAAGAAATGAAGAAAA
Found at i:1169101 original size:32 final size:34
Alignment explanation
Indices: 1169025--1169116 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 34
1169015 TGTTACATTT
* *
1169025 CACATTATCAGCTTGGGTGATATGATACATGCATGC
1 CACATTATCATCTTGGGTGACATGA-ACATG-ATGC
*
1169061 CACGTTATCATCTTGGGTGACATG-ACATG-TGC
1 CACATTATCATCTTGGGTGACATGAACATGATGC
*
1169093 CATATTATCATCTTGGGTGACATG
1 CACATTATCATCTTGGGTGACATG
1169117 GATCTTGTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
32 25 0.49
34 5 0.10
36 21 0.41
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (34 bp):
CACATTATCATCTTGGGTGACATGAACATGATGC
Found at i:1170596 original size:36 final size:36
Alignment explanation
Indices: 1170527--1170596 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1170517 ATTGATGTAT
* * *
1170527 TACATGTCACCTCATTAACTTGAATGACGTGATACA
1 TACATGTCACATCATCAACTTGAATGACATGATACA
* **
1170563 TACATGTCACATTATCAACTTGGGTGACATGATA
1 TACATGTCACATCATCAACTTGAATGACATGATA
1170597 TGTGTCACAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (36 bp):
TACATGTCACATCATCAACTTGAATGACATGATACA
Found at i:1172277 original size:17 final size:16
Alignment explanation
Indices: 1172245--1172275 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1172235 GTTTTTTACA
*
1172245 ATTTTTATTTAAAAAT
1 ATTTTCATTTAAAAAT
1172261 ATTTTCATTTAAAAA
1 ATTTTCATTTAAAAA
1172276 ATTACTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTCATTTAAAAAT
Found at i:1179238 original size:15 final size:15
Alignment explanation
Indices: 1179215--1179247 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1179205 ACCTTACCCG
*
1179215 CCCCGCATCCGCCCA
1 CCCCACATCCGCCCA
1179230 CCCCACATCCGCCCA
1 CCCCACATCCGCCCA
1179245 CCC
1 CCC
1179248 AGCTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.70, G:0.09, T:0.06
Consensus pattern (15 bp):
CCCCACATCCGCCCA
Found at i:1185387 original size:59 final size:59
Alignment explanation
Indices: 1185270--1185430 Score: 148
Period size: 59 Copynumber: 2.7 Consensus size: 59
1185260 GTGCTTTATT
* * * ** * * *
1185270 AAAAGTTTAGGGA-TCAATATAGAATGAGAGCCATAGTTTGGGGATGAATTTGGTATGTTC
1 AAAAGTTTAGGGACT-AATTTTGAATGAAAG-CATAGTTTAAGGATGAAATTAGAATGTTC
*
1185330 AAAAGTTTAGGGACTAATTTTGAATGAAAGCATAGTTTAAGGATGAAATTAGAATGTTG
1 AAAAGTTTAGGGACTAATTTTGAATGAAAGCATAGTTTAAGGATGAAATTAGAATGTTC
* * *
1185389 AAAACTTTAGAGG-CCAA-TTTGAAATGAATATCATAGTTTAAG
1 AAAAGTTTAG-GGACTAATTTTG-AATGAA-AGCATAGTTTAAG
1185431 TACATATGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
58 4 0.05
59 41 0.48
60 39 0.46
61 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.32
Consensus pattern (59 bp):
AAAAGTTTAGGGACTAATTTTGAATGAAAGCATAGTTTAAGGATGAAATTAGAATGTTC
Found at i:1187570 original size:15 final size:15
Alignment explanation
Indices: 1187552--1187604 Score: 79
Period size: 15 Copynumber: 3.3 Consensus size: 15
1187542 CGAGGGTATT
1187552 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1187567 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1187582 GTAGTGGTCCTTCGGGAC
1 GTA---GTCCTTCGGGAC
1187600 GTAGT
1 GTAGT
1187605 GGTCCTACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 20 0.57
18 15 0.43
ACGTcount: A:0.13, C:0.23, G:0.36, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:1187593 original size:18 final size:18
Alignment explanation
Indices: 1187555--1187617 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
1187545 GGGTATTGTA
1187555 GTCCTTCGGGACGTA---
1 GTCCTTCGGGACGTAGTG
1187570 GTCCTTCGGGACGTAGTG
1 GTCCTTCGGGACGTAGTG
1187588 GTCCTTCGGGACGTAGTG
1 GTCCTTCGGGACGTAGTG
*
1187606 GTCCTACGGGAC
1 GTCCTTCGGGAC
1187618 ATATATAGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
15 15 0.34
18 29 0.66
ACGTcount: A:0.13, C:0.25, G:0.37, T:0.25
Consensus pattern (18 bp):
GTCCTTCGGGACGTAGTG
Found at i:1192351 original size:59 final size:60
Alignment explanation
Indices: 1192288--1192411 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
1192278 GATGATCCTC
* * *
1192288 GACTACAGGTTGATGTTTTGTTGAGTCAT-T-GA-TGATTAAAAGTTATAAAATGGTT-CATT
1 GACTACAGGATGATGTTTTGTTGAGTC-TCTCAACT-ATTAAAAGTTACAAAATGGTTACA-T
* *
1192347 GACTATAGGATGTTGTTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGGTTACAT
1 GACTACAGGATGATGTTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGGTTACAT
1192407 GACTA
1 GACTA
1192412 TTCATGTGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
58 1 0.02
59 25 0.45
60 27 0.48
61 3 0.05
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (60 bp):
GACTACAGGATGATGTTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATGGTTACAT
Found at i:1198953 original size:30 final size:28
Alignment explanation
Indices: 1198903--1198958 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 28
1198893 GTTAATTTAA
* *
1198903 AAAATATATACGTTAACTTTTTTTTTTT
1 AAAATATATACATTAACTTTTATTTTTT
*
1198931 AAAATATCATTACATTACCTTTTATTTT
1 AAAATAT-A-TACATTAACTTTTATTTT
1198959 CAGATATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 7 0.30
29 1 0.04
30 15 0.65
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.54
Consensus pattern (28 bp):
AAAATATATACATTAACTTTTATTTTTT
Done.