Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 88 of 182
Found at i:27958359 original size:19 final size:19
Alignment explanation
Indices: 27958335--27958379 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
27958325 GTGTTATGAA
27958335 TTCACATATTCTTCCTCAT
1 TTCACATATTCTTCCTCAT
27958354 TTCACATATTCTTCCTCAT
1 TTCACATATTCTTCCTCAT
27958373 TTCACAT
1 TTCACAT
27958380 TTAGTCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (19 bp):
TTCACATATTCTTCCTCAT
Found at i:27965640 original size:27 final size:27
Alignment explanation
Indices: 27965569--27965645 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 27
27965559 AGTTCGACAG
* * *
27965569 GACATTAAAAATGTGATAGTTTGATGA
1 GACATTAAAAATGAGGTAGTCTGATGA
* * * *
27965596 AACATTAAATACGGGGTAGTCTGATGA
1 GACATTAAAAATGAGGTAGTCTGATGA
*
27965623 GACATTAAACATGAGGTAGTCTG
1 GACATTAAAAATGAGGTAGTCTG
27965646 CCAGGACAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.29
Consensus pattern (27 bp):
GACATTAAAAATGAGGTAGTCTGATGA
Found at i:27965728 original size:36 final size:36
Alignment explanation
Indices: 27965681--27965749 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
27965671 ATGGTGCAAG
27965681 ATCATGGCTTGGATATGGCAACCAATGGATTCCACC
1 ATCATGGCTTGGATATGGCAACCAATGGATTCCACC
27965717 ATCATGGCTTGGATATGGCAACCAATGGATTCC
1 ATCATGGCTTGGATATGGCAACCAATGGATTCC
27965750 GCCAAGACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (36 bp):
ATCATGGCTTGGATATGGCAACCAATGGATTCCACC
Found at i:27968371 original size:28 final size:28
Alignment explanation
Indices: 27968340--27968394 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
27968330 TTTAGGGACT
27968340 AAAT-TGTAAA-ATATGTAAAAGTTAAGGA
1 AAATGTGTAAATA-ATG-AAAAGTTAAGGA
*
27968368 AAATGTGTAAATAATGAAAATTTAAGG
1 AAATGTGTAAATAATGAAAAGTTAAGG
27968395 GTTTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 14 0.58
29 9 0.38
30 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (28 bp):
AAATGTGTAAATAATGAAAAGTTAAGGA
Found at i:27968894 original size:20 final size:20
Alignment explanation
Indices: 27968830--27968936 Score: 87
Period size: 20 Copynumber: 5.3 Consensus size: 20
27968820 CTTCGGTGTT
* *
27968830 CCTGAATGCACATTAGAG-C
1 CCTGAATGCACATCAGTGCC
* *
27968849 CCTCGAATGCATATTAGTGCC
1 CCT-GAATGCACATCAGTGCC
* *
27968870 TCTGAATGCACATCAGTTCC
1 CCTGAATGCACATCAGTGCC
*
27968890 CCTGATTGCACATTCA-TGCC
1 CCTGAATGCACA-TCAGTGCC
27968910 CCT-AATTGCACATTC-GTGCC
1 CCTGAA-TGCACA-TCAGTGCC
27968930 CCTGAAT
1 CCTGAAT
27968937 ACACTTCCAT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
19 4 0.06
20 60 0.83
21 8 0.11
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (20 bp):
CCTGAATGCACATCAGTGCC
Found at i:27970803 original size:58 final size:58
Alignment explanation
Indices: 27970738--27970848 Score: 177
Period size: 58 Copynumber: 1.9 Consensus size: 58
27970728 TAAGGCGTAC
* * *
27970738 TTCCCAACATTAGATAGTCCTAATGGACATCCTCTTCATTCGATAGTCCTTGGCGGAG
1 TTCCCAACACTAGATAGTCCTAACGAACATCCTCTTCATTCGATAGTCCTTGGCGGAG
* *
27970796 TTCCCAACACTAGATAGTCCTAACGAACATCCTCTTCATTTGTTAGTCCTTGG
1 TTCCCAACACTAGATAGTCCTAACGAACATCCTCTTCATTCGATAGTCCTTGG
27970849 AGAATTCTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (58 bp):
TTCCCAACACTAGATAGTCCTAACGAACATCCTCTTCATTCGATAGTCCTTGGCGGAG
Found at i:27973701 original size:14 final size:14
Alignment explanation
Indices: 27973678--27973723 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
27973668 TAAACAATTG
27973678 TATTTATTTAGTAT
1 TATTTATTTAGTAT
*
27973692 TATTTTTTTAAAG-A-
1 TATTTATTT--AGTAT
27973706 TATTTATTTAGTAT
1 TATTTATTTAGTAT
27973720 TATT
1 TATT
27973724 AACTTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 2 0.08
13 1 0.04
14 20 0.77
15 1 0.04
16 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TATTTATTTAGTAT
Found at i:27976103 original size:144 final size:141
Alignment explanation
Indices: 27975909--27976187 Score: 400
Period size: 144 Copynumber: 2.0 Consensus size: 141
27975899 TAAAAAAGAG
* * *
27975909 AAAATTTAGATTTTAAAAAATAAAAATCTGTTTTTTGGTTATTTTAAAG-AAAAGTTTAAATTTT
1 AAAATTTAGATTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAAAAATTTAAATTTT
* * *
27975973 TTAACAAAGTTTTGATTTTTTTTTAACTATTTCGAAA-TAAAAGTTTGGATTTTTAAGTAAAGTA
66 TAAACAAAGTTTTGA-TTTTTTTTAACTATTTCAAAATTAAAA-TTTGGA-TTTGAAGTAAAGTA
*
27976037 GTGATTTTCATTAA
128 GTAATTTTCATTAA
*
27976051 AAAATTTAGATTTTTTAAAAAATAAAAATTTGTTTTTTAGTGATTTTAAAGAAAAAATTTAAATT
1 AAAATTTAGA--TTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAAAAATTTAAATT
* * *
27976116 TTTAAATAAAGTTTTGATTTTTTTTAACTATTTCAAAATTAAAATTTTGATTTGAAGTAAATTAG
64 TTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATTAAAATTTGGATTTGAAGTAAAGTAG
27976181 TAATTTT
129 TAATTTT
27976188 GTTTTAATCG
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
142 10 0.08
143 19 0.16
144 61 0.50
145 32 0.26
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.47
Consensus pattern (141 bp):
AAAATTTAGATTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAAAAATTTAAATTTT
TAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATTAAAATTTGGATTTGAAGTAAAGTAGTA
ATTTTCATTAA
Found at i:27979818 original size:17 final size:17
Alignment explanation
Indices: 27979796--27979832 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
27979786 ATTAAGCTTA
27979796 CAATCATGAACCTTTTT
1 CAATCATGAACCTTTTT
27979813 CAATCATGAACCTTTTT
1 CAATCATGAACCTTTTT
27979830 CAA
1 CAA
27979833 CTATTCCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (17 bp):
CAATCATGAACCTTTTT
Found at i:27984975 original size:62 final size:64
Alignment explanation
Indices: 27984902--27985022 Score: 194
Period size: 62 Copynumber: 1.9 Consensus size: 64
27984892 ATCTCCTTCT
* *
27984902 AAAAAAGAAGAAGAAACAGGAAAGCA-AATAAAAAA-A-TAGGAGTAAGAACGAAGAAAAAAAGA
1 AAAAAAAAAGAAGAAACAGGAAAG-AGAATAAAAAATAGAAGGAGTAAGAACGAAGAAAAAAAGA
27984964 AAAAAAAAAGAAGAAACAGGAAAGAGAATAAAAAATAGAAGGAGTAAGAACGAAGAAAA
1 AAAAAAAAAGAAGAAACAGGAAAGAGAATAAAAAATAGAAGGAGTAAGAACGAAGAAAA
27985023 GTGATTGGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 1 0.02
62 32 0.59
63 1 0.02
64 20 0.37
ACGTcount: A:0.69, C:0.04, G:0.21, T:0.05
Consensus pattern (64 bp):
AAAAAAAAAGAAGAAACAGGAAAGAGAATAAAAAATAGAAGGAGTAAGAACGAAGAAAAAAAGA
Found at i:27984986 original size:29 final size:30
Alignment explanation
Indices: 27984902--27984998 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
27984892 ATCTCCTTCT
* * *
27984902 AAAAAAGAAGAAGAAACAGGAAAGCAAATA
1 AAAAAAAAAGAAGAAACAGGAAAGAAAAGA
* *
27984932 AAAAAATAGGAGTAAG-AACGAAGAAA-AAAAGA
1 AAAAAA-A-AAG-AAGAAAC-AGGAAAGAAAAGA
* *
27984964 AAAAAAAAAGAAGAAACAGGAAAGAGAATA
1 AAAAAAAAAGAAGAAACAGGAAAGAAAAGA
27984994 AAAAA
1 AAAAA
27984999 TAGAAGGAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
29 8 0.15
30 20 0.38
31 1 0.02
32 15 0.29
33 8 0.15
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (30 bp):
AAAAAAAAAGAAGAAACAGGAAAGAAAAGA
Found at i:27985578 original size:23 final size:23
Alignment explanation
Indices: 27985535--27985583 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
27985525 TTGTTTAAAT
27985535 AAAAAAACACAAAAAAGAAG-AG
1 AAAAAAACACAAAAAAGAAGAAG
27985557 AAAAAAACAACAAAAATA-AAGAAG
1 AAAAAAAC-ACAAAAA-AGAAGAAG
27985581 AAA
1 AAA
27985584 TAAAGAGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.33
23 10 0.42
24 6 0.25
ACGTcount: A:0.80, C:0.08, G:0.10, T:0.02
Consensus pattern (23 bp):
AAAAAAACACAAAAAAGAAGAAG
Found at i:27986045 original size:42 final size:42
Alignment explanation
Indices: 27985986--27986526 Score: 698
Period size: 42 Copynumber: 12.9 Consensus size: 42
27985976 AAGGAAAGAA
* * * *
27985986 TTCATTGCATTTAGAGGCCTAGGTGTAGAGGTTCGTTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * *
27986028 TTCATCGCATTTAGAGGCGTAGGTGTGGAGGCCCGTTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
27986070 TTCATTGCATTTAGAGG-CTCAGGTGTGGAGG-CCTATTTACTT
1 TTCATCGCATTTAGAGGCCT-AGGTGTGGAGGTCC-ATTTACTT
* *
27986112 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTATTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
27986154 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
27986196 CTCATCGCATTTAGAGGTCC-AGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGG-CCTAGGTGTGGAGGTCCATTTACTT
* * * * *
27986238 TTCATTGCATTTAGAGGCCCAGGTGTGAAAGTCCATTTATTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
27986280 TTCATCGCATTTTGAGGCCCAGGTGTGGAGG-CTCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTC-CATTTACTT
* *
27986322 TTCCTCGCATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
27986364 TTCATCGTATTTAGAGGCCCAGGTGTAGAGGTCCGTTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
27986406 TTCATCGCATTTAGAGG-CTCAGGTGTGGAGGTCCATTTAGTT
1 TTCATCGCATTTAGAGGCCT-AGGTGTGGAGGTCCATTTACTT
*
27986448 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
** * * *
27986490 TTCATTACATTTAGAGGCCCAAGTGT-GAGGTCTATTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTT
27986527 GCATTCCTTT
Statistics
Matches: 442, Mismatches: 47, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
41 17 0.04
42 416 0.94
43 9 0.02
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (42 bp):
TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
Found at i:27987593 original size:145 final size:142
Alignment explanation
Indices: 27987371--27987630 Score: 405
Period size: 144 Copynumber: 1.8 Consensus size: 142
27987361 TTTTTAAACA
* *
27987371 ATTTCGAAATAAAAGTTTGATTTTTAAGGAAAATAGTGATTTCTTTAAAAAAGAGAAAGTTTAGA
1 ATTTCGAAATAAAAGTTTGATTTTTAAGGAAAATAATGATTTCTTTAAAAAAGAAAAAGTTTAGA
* *
27987436 TTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAATTTAAATTTTTTAATAAAGTT
66 TTTTTAAAAATAAAAATATG-TTTTTAGTCATTTTAAAGAAAAATTTAAATTTTTTAATAAAGTT
27987501 TTATTTTTTAATT
130 TTATTTTTTAATT
*
27987514 ATTTCGAAATAAAAGTTTGGATTTTTACA-GAAAATAATGATTTTTTTTAAAAAAGAAAAAGTTT
1 ATTTCGAAATAAAAGTTT-GATTTTTA-AGGAAAATAATGA-TTTCTTTAAAAAAGAAAAAGTTT
* * *
27987578 AGATTTTTAAAAATAAATATATGTTTTTAGTCCTTTTAAAGAAAAGTTTAAAT
63 AGATTTTTAAAAATAAAAATATGTTTTTAGTCATTTTAAAGAAAAATTTAAAT
27987631 GAGGAAGATA
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
143 18 0.17
144 45 0.42
145 43 0.41
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (142 bp):
ATTTCGAAATAAAAGTTTGATTTTTAAGGAAAATAATGATTTCTTTAAAAAAGAAAAAGTTTAGA
TTTTTAAAAATAAAAATATGTTTTTAGTCATTTTAAAGAAAAATTTAAATTTTTTAATAAAGTTT
TATTTTTTAATT
Found at i:27994830 original size:21 final size:20
Alignment explanation
Indices: 27994799--27994855 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
27994789 TAATTTTAAT
27994799 TTTTATGATTTTAAAATAAGTA
1 TTTTAT-ATTTTAAAA-AAGTA
**
27994821 TTTTATA-TTTAAAAATTTA
1 TTTTATATTTTAAAAAAGTA
*
27994840 TTATATATTTTAAAAA
1 TTTTATATTTTAAAAA
27994856 CAGTGTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 9 0.29
20 15 0.48
21 1 0.03
22 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTATATTTTAAAAAAGTA
Found at i:27997490 original size:25 final size:25
Alignment explanation
Indices: 27997456--27997506 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
27997446 ATGCTTAGTA
27997456 AGTTCAAATGAAAAATACCATACTT
1 AGTTCAAATGAAAAATACCATACTT
**
27997481 AGTTCAAATGGCAAATACCATACTT
1 AGTTCAAATGAAAAATACCATACTT
27997506 A
1 A
27997507 CCTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (25 bp):
AGTTCAAATGAAAAATACCATACTT
Found at i:28000200 original size:23 final size:23
Alignment explanation
Indices: 28000170--28000409 Score: 327
Period size: 23 Copynumber: 10.4 Consensus size: 23
28000160 TTCTTATATC
28000170 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
28000193 TATGCTTAAATATTATTGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
28000216 TATGCTTAAATGTTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
28000239 TATGCTTAAATAGTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* **
28000262 TGTGCTTAAATATTAATAAGATT
1 TATGCTTAAATATTAATGTGATT
* *
28000285 TTTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
28000308 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
28000331 TGTGCTTAAATATTAATCTGATT
1 TATGCTTAAATATTAATGTGATT
* * *
28000354 TGTGCTTAAATATTAATATTATT
1 TATGCTTAAATATTAATGTGATT
*
28000377 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
**
28000400 TGCGCTTAAA
1 TATGCTTAAA
28000410 GAATTAAGAT
Statistics
Matches: 189, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 189 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:28000519 original size:36 final size:36
Alignment explanation
Indices: 28000479--28000555 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
28000469 TGATGACTGT
**
28000479 TGTGAAAGTGAATATGTGGGTATGTTCTTCATACCA
1 TGTGAAAGAAAATATGTGGGTATGTTCTTCATACCA
* *
28000515 TGTGACAGAAAATATGTGGGTATGTTCTTCATGCCA
1 TGTGAAAGAAAATATGTGGGTATGTTCTTCATACCA
28000551 TGTGA
1 TGTGA
28000556 CTGATTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (36 bp):
TGTGAAAGAAAATATGTGGGTATGTTCTTCATACCA
Found at i:28005181 original size:21 final size:21
Alignment explanation
Indices: 28005127--28005184 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
28005117 TTAGTATCGT
*
28005127 TAGAAG-CATGACATGTTTCGG
1 TAGAAGTCAT-ACTTGTTTCGG
28005148 TAGAAGTCATACTTGTTTCGG
1 TAGAAGTCATACTTGTTTCGG
28005169 TAGAAGTCATACTTGT
1 TAGAAGTCATACTTGT
28005185 ATCGATAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (21 bp):
TAGAAGTCATACTTGTTTCGG
Found at i:28011770 original size:11 final size:12
Alignment explanation
Indices: 28011741--28011767 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28011731 GAGATGAAGA
28011741 TTTTGGAGTGTT
1 TTTTGGAGTGTT
28011753 TTTTGGAGTGTT
1 TTTTGGAGTGTT
28011765 TTT
1 TTT
28011768 GGATGCACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (12 bp):
TTTTGGAGTGTT
Found at i:28026383 original size:15 final size:15
Alignment explanation
Indices: 28026363--28026393 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28026353 TGTGAAGAGT
28026363 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
*
28026378 ATTAATCTAAATTAA
1 ATTAATCTAAACTAA
28026393 A
1 A
28026394 AATAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:28028583 original size:11 final size:11
Alignment explanation
Indices: 28028567--28028594 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28028557 ATATGCTCTA
28028567 TTTTTTTTCAT
1 TTTTTTTTCAT
28028578 TTTTTTTTCAT
1 TTTTTTTTCAT
28028589 TTTTTT
1 TTTTTT
28028595 CTGAGCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTCAT
Found at i:28030738 original size:24 final size:23
Alignment explanation
Indices: 28030692--28030742 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
28030682 TAACAATTTA
*
28030692 AAATAAATTAAAAGTTAATAAATT
1 AAATAAATTAAAAATTAATAAA-T
28030716 AAATAAATTAAAAATTAGA-AAAT
1 AAATAAATTAAAAATTA-ATAAAT
28030739 AAAT
1 AAAT
28030743 TTCTTACCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 5 0.20
24 19 0.76
25 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (23 bp):
AAATAAATTAAAAATTAATAAAT
Found at i:28037144 original size:9 final size:9
Alignment explanation
Indices: 28037118--28037147 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28037108 ACCCAAAAAC
*
28037118 CTTCATCAC
1 CTTCATCAT
28037127 CTTCATCAT
1 CTTCATCAT
28037136 CTTCATCAT
1 CTTCATCAT
28037145 CTT
1 CTT
28037148 TTCCAAACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (9 bp):
CTTCATCAT
Found at i:28039419 original size:19 final size:19
Alignment explanation
Indices: 28039392--28039436 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
28039382 CAACCCTTTG
*
28039392 ACATCGGTCACAACTTCTA
1 ACATAGGTCACAACTTCTA
*
28039411 ACATAGGTCACAACTTCTG
1 ACATAGGTCACAACTTCTA
28039430 ACATAGG
1 ACATAGG
28039437 CATACGCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
ACATAGGTCACAACTTCTA
Found at i:28054633 original size:15 final size:15
Alignment explanation
Indices: 28054609--28054642 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28054599 TGCATTTTCG
* *
28054609 ATTTTTCTTTTATTT
1 ATTTTACTTTTACTT
28054624 ATTTTACTTTTACTT
1 ATTTTACTTTTACTT
28054639 ATTT
1 ATTT
28054643 CGTTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTACTTTTACTT
Found at i:28057018 original size:19 final size:19
Alignment explanation
Indices: 28056991--28057037 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
28056981 ATAGTTTTCA
28056991 TGCATTTTTATTTTGTCAT
1 TGCATTTTTATTTTGTCAT
*
28057010 TGTATTTTTATTTTGTCAT
1 TGCATTTTTATTTTGTCAT
28057029 TGCATTTTT
1 TGCATTTTT
28057038 GTTAAGTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.15, C:0.09, G:0.11, T:0.66
Consensus pattern (19 bp):
TGCATTTTTATTTTGTCAT
Found at i:28060339 original size:195 final size:196
Alignment explanation
Indices: 28059891--28060342 Score: 520
Period size: 195 Copynumber: 2.3 Consensus size: 196
28059881 AACCGACGCA
* *
28059891 ATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGCGAGCAGCATCGTGAGTCGAG
1 ATGGATGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAG-C---
* * *
28059956 AAATGAGAAAAGAAATATGGATCCTAAATGGATTACAGGCCCTAAGATGGTTGAGATTTATGCAT
62 -AATGAGAAAAGAAATATGGATCCTAAATGGATTACAGACCCTAAGATGGCTGAGATCTATGCAT
* * * * *
28060021 AAATGCATATTCTCGATAATTCGTGTGAGCAGCATCGTTAGGGAACAATTATATGCACAGATATC
126 AAATGCATACTCTCGACAACTCGTGTGAGCAGCATCATTAGGGAACAATTATATGCACAGATACC
*
28060086 GTATCG
191 GTACCG
* * * * * *
28060092 ATGGCTGAGGTACCGCATATGTTACAAGTCCTCGACAACTCGTGTAAGCAGCATCGTGA-C-TTG
1 ATGGATGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGCAATG
* * * * *
28060155 AG-AAAGAGATATGGATCCTAAATGGATTACAGACCCTACGATGGCTGGGA-CTATGC-TTATTG
66 AGAAAAGAAATATGGATCCTAAATGGATTACAGACCCTAAGATGGCTGAGATCTATGCATAAATG
* * * *
28060217 CATACTCTCGACAGCTCGTGTGAGCAGCCTCATTAGGGAACAGTT-TATAGGACAGATAGGCACC
131 CATACTCTCGACAACTCGTGTGAGCAGCATCATTAGGGAACAATTATAT-GCACAGAT----ACC
28060281 GTACCG
191 GTACCG
* *
28060287 ATGGATGGGGTACCGCATACGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
1 ATGGATGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
28060343 AGTACTGGTA
Statistics
Matches: 214, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
190 3 0.01
191 49 0.23
192 5 0.02
193 43 0.20
194 4 0.02
195 56 0.26
199 1 0.00
201 53 0.25
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (196 bp):
ATGGATGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGCAATG
AGAAAAGAAATATGGATCCTAAATGGATTACAGACCCTAAGATGGCTGAGATCTATGCATAAATG
CATACTCTCGACAACTCGTGTGAGCAGCATCATTAGGGAACAATTATATGCACAGATACCGTACC
G
Found at i:28076183 original size:3 final size:3
Alignment explanation
Indices: 28076175--28076215 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28076165 CAAGATCTTG
28076175 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28076216 CAAGGTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28076806 original size:146 final size:145
Alignment explanation
Indices: 28076643--28077429 Score: 950
Period size: 146 Copynumber: 5.4 Consensus size: 145
28076633 AAAATTATGG
*
28076643 TTTTTTAAATAATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTTCTTTAACAAG
1 TTTTTTAACT-ATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTT-TTTAA-AAG
* * *
28076708 AAAAAGTTTATATTTTTAAAAGTAAAAATCAATTTTTTAGTTATTTTAAAG-AAAATTTTAAATT
63 AAAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATT
28076772 TTTAAACAAAGTTTTGAT
128 TTTAAACAAAGTTTTGAT
* *
28076790 TTTTTTAACTATTTCGAAAT-AAAAGTTTGAATTTTTAAGTAAAATAGTGATTTTTTTAAAAAAT
1 TTTTTTAACTATTTCGAAATAAAAATTTTG-ATTTTTAAGTAAAATAGTGATTTTTTTAAAAGA-
* * * *
28076854 AGAAAGTTTATATTTTTAATAGTAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTCAAATT
64 A-AAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATT
* *
28076919 TTTTAACAAAGTTTTGGTT
128 TTTAAACAAAGTTTT-GAT
28076938 TTTTTTAACTATTTCGAAATAAAAATTTAT-ATTTTTAAGTAAAATAGTGATTTTTTTTTAAAAA
1 TTTTTTAACTATTTCGAAATAAAAATTT-TGATTTTTAAGTAAAATAGTGA--TTTTTTT-AAAA
* *
28077002 GAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAATTATTTT-AA-AAAAAGTTTAAAT
62 GAAAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAAT
28077065 TTTTAAACAAAGTTTTGATT
127 TTTTAAACAAAGTTTTGA-T
* * * * * **
28077085 TTTTTTAAATACTTCGGAATAAAAGTTTGGATTTTTAAGTAAAGCAGTGATTTTTATT-AAA-AA
1 TTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTTT-TTAAAAGAA
* * * *
28077148 AAAGTTTAGATTTCTAGAAAATAAAAATTTATTTTTTAGTGATTTTAAAGAAAAAGTTTAAATTT
65 AAAGTTTATATTTTTA-AAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTT
*
28077213 TTAGACAAAGTTTTGAT
129 TTAAACAAAGTTTTGAT
* * * * *
28077230 TTTTTTAACTATTTTGAAATAAAAGTTTAGATTTTTAAATAAAATAGTGATTTTCATTAAAAAAG
1 TTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTT--TT-TAAAAG
* *
28077295 AAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTA-TTTTTAGTGATTTTAAAGAAAAAGTTTAA
63 -AA-AAAGTTTATATTTTT-AAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAA
*
28077359 ATTTTTAAATAAAGTTTTGA-
125 ATTTTTAAACAAAGTTTTGAT
* * * * * *
28077379 ---TTTAACTATTTCAAAATAAAAGTTTTTATTTTAAAATAAAGTAGTGATTTT
1 TTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTT
28077430 GTTTTAATCA
Statistics
Matches: 563, Mismatches: 53, Indels: 49
0.85 0.08 0.07
Matches are distributed among these distances:
143 15 0.03
144 32 0.06
145 68 0.12
146 159 0.28
147 105 0.19
148 47 0.08
149 47 0.08
150 57 0.10
151 32 0.06
152 1 0.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (145 bp):
TTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGTAAAATAGTGATTTTTTTAAAAGAAA
AAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTT
AAACAAAGTTTTGAT
Found at i:28077356 original size:51 final size:49
Alignment explanation
Indices: 28077141--28077367 Score: 142
Period size: 51 Copynumber: 4.5 Consensus size: 49
28077131 GTGATTTTTA
* *
28077141 TTAAA-AAAAAGTTTAGATTTCTAGAAAATAAAAATTTATTTTTTAGTGATT
1 TTAAAGAAAAAGTTTAGATTTTTAAAAAATAAAAA-TTA-TTTTTAGT-ATT
* * **** *
28077192 TTAAAGAAAAAGTTTAAATTTTTAGACAAAGTTTTGATT-TTTTTAACTATT
1 TTAAAGAAAAAGTTTAGATTTTTA-A-AAAATAAAAATTATTTTT-AGTATT
* * * * * * *
28077243 TTGAAA-TAAAAGTTTAGATTTTTAAATAA-AATAGTGATTTTCA-T-TA
1 TT-AAAGAAAAAGTTTAGATTTTTAAAAAATAAAAATTATTTTTAGTATT
**
28077289 AAAAAGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTATTTTTAGTGATT
1 TTAAAG-AA-AAAGTTTAGATTTTTAAAAAATAAAAAT-TATTTTTAGT-ATT
*
28077342 TTAAAGAAAAAGTTTAAATTTTTAAA
1 TTAAAGAAAAAGTTTAGATTTTTAAA
28077368 TAAAGTTTTG
Statistics
Matches: 130, Mismatches: 32, Indels: 28
0.68 0.17 0.15
Matches are distributed among these distances:
45 3 0.02
46 1 0.01
47 2 0.02
48 23 0.18
49 10 0.08
50 7 0.05
51 49 0.38
52 23 0.18
53 7 0.05
54 5 0.04
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (49 bp):
TTAAAGAAAAAGTTTAGATTTTTAAAAAATAAAAATTATTTTTAGTATT
Found at i:28081974 original size:16 final size:16
Alignment explanation
Indices: 28081926--28081988 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
28081916 CAATTTCAAT
*
28081926 CATTCAATCATTCATC
1 CATTCATTCATTCATC
* *
28081942 CATCCA-TCCTTCGATC
1 CATTCATTCATTC-ATC
28081958 CATTCATTCATTCATC
1 CATTCATTCATTCATC
*
28081974 CATTCATTCACTCAT
1 CATTCATTCATTCAT
28081989 TTGCTCATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 5 0.12
16 30 0.75
17 5 0.12
ACGTcount: A:0.25, C:0.35, G:0.02, T:0.38
Consensus pattern (16 bp):
CATTCATTCATTCATC
Found at i:28081977 original size:8 final size:8
Alignment explanation
Indices: 28081934--28081980 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
28081924 ATCATTCAAT
28081934 CATTCATC
1 CATTCATC
*
28081942 CATCCATC
1 CATTCATC
28081950 C-TTCGATC
1 CATTC-ATC
*
28081958 CATTCATT
1 CATTCATC
28081966 CATTCATC
1 CATTCATC
28081974 CATTCAT
1 CATTCAT
28081981 TCACTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 2 0.06
8 28 0.85
9 3 0.09
ACGTcount: A:0.23, C:0.36, G:0.02, T:0.38
Consensus pattern (8 bp):
CATTCATC
Found at i:28081981 original size:4 final size:4
Alignment explanation
Indices: 28081920--28081989 Score: 52
Period size: 4 Copynumber: 17.5 Consensus size: 4
28081910 GTGCCCCAAT
* * * * * *
28081920 TTCA ATCA TTCA ATCA TTCA TCCA TCCA -TCC TTCGA TCCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTC-A TTCA TTCA TTCA
* *
28081968 TTCA TCCA TTCA TTCA CTCA TT
1 TTCA TTCA TTCA TTCA TTCA TT
28081990 TGCTCATTTG
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
3 1 0.02
4 47 0.94
5 2 0.04
ACGTcount: A:0.26, C:0.33, G:0.01, T:0.40
Consensus pattern (4 bp):
TTCA
Found at i:28086709 original size:19 final size:19
Alignment explanation
Indices: 28086674--28086732 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
28086664 TGTATAAATC
*
28086674 AAGAAAAAAATAAAAAAAG
1 AAGAAAAAAAGAAAAAAAG
28086693 AAGAAAAAAAGAGAAAAAA-
1 AAGAAAAAAAGA-AAAAAAG
*
28086712 ACA-ACAAAAAAGAAGAAAAG
1 A-AGA-AAAAAAGAAAAAAAG
28086732 A
1 A
28086733 TGGAAAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.02
Consensus pattern (19 bp):
AAGAAAAAAAGAAAAAAAG
Found at i:28086709 original size:21 final size:20
Alignment explanation
Indices: 28086685--28086730 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
28086675 AGAAAAAAAT
*
28086685 AAAAAAAGAAGAAAAAAAGAG
1 AAAAAAACAA-AAAAAAAGAG
*
28086706 AAAAAAACAACAAAAAAGAAG
1 AAAAAAACAAAAAAAAAG-AG
28086727 AAAA
1 AAAA
28086731 GATGGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAAGAG
Found at i:28087444 original size:42 final size:42
Alignment explanation
Indices: 28087077--28087451 Score: 455
Period size: 42 Copynumber: 8.9 Consensus size: 42
28087067 AAGGAAAACA
* * * *
28087077 TTCATTGCATTTATAGGGCC-AGGTGTGGAGATCCATATACTT
1 TTCATTGCATTTAGA-GGCCTAAGTGTGGAGGTCCATTTACTT
* * *
28087119 TTCATTGCATTTAGAGGCCTGAGTGTGGAGATCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
*
28087161 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * * *
28087203 TTCATTGCATTTAAAGTCCTAGGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
28087245 TTCATTGCATTTAGAGGCCTAGGTTTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
28087287 TTCATTACATTTAGAGGCCTGAGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
28087329 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* ** * *
28087371 TTCGTTGCATTCGGAAGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * * * *
28087413 TTCATTGCAATTAGAGGCATAAGCGTAGAGGTTCATTTA
1 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTA
28087452 TTTATTTATT
Statistics
Matches: 289, Mismatches: 43, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
41 4 0.01
42 285 0.99
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
Found at i:28088964 original size:24 final size:24
Alignment explanation
Indices: 28088933--28088985 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
28088923 ACAGATAACA
28088933 TTAGCTCTCACAAGCCCAGAATGG
1 TTAGCTCTCACAAGCCCAGAATGG
* * *
28088957 TTAGCTCTTACGAGCCTAGAATGG
1 TTAGCTCTCACAAGCCCAGAATGG
28088981 TTAGC
1 TTAGC
28088986 CCTTACGAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (24 bp):
TTAGCTCTCACAAGCCCAGAATGG
Found at i:28088990 original size:24 final size:24
Alignment explanation
Indices: 28088945--28089007 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
28088935 AGCTCTCACA
* *
28088945 AGCCCAGAATGGTTAGCTCTTACG
1 AGCCTAGAATGGTTAGCCCTTACG
28088969 AGCCTAGAATGGTTAGCCCTTACG
1 AGCCTAGAATGGTTAGCCCTTACG
*
28088993 AGCCTAGAATAGTTA
1 AGCCTAGAATGGTTA
28089008 ACCAGTACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (24 bp):
AGCCTAGAATGGTTAGCCCTTACG
Found at i:28089016 original size:24 final size:24
Alignment explanation
Indices: 28088965--28089017 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
28088955 GGTTAGCTCT
* * **
28088965 TACGAGCCTAGAATGGTTAGCCCT
1 TACGAGCCTAGAATAGTTAACCAG
28088989 TACGAGCCTAGAATAGTTAACCAG
1 TACGAGCCTAGAATAGTTAACCAG
28089013 TACGA
1 TACGA
28089018 TGCTGCTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
TACGAGCCTAGAATAGTTAACCAG
Found at i:28090828 original size:51 final size:51
Alignment explanation
Indices: 28090612--28091139 Score: 151
Period size: 52 Copynumber: 10.5 Consensus size: 51
28090602 ATTTTTTTAA
* * * * *
28090612 AAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTT
1 AAAGAAAAAGTTTAAATTTTTAAAAATAAAAATATATTTTCTAATTATTTT
** * * * *
28090663 AAAGAAAAAGTTTAAATTTTTAAACAA-AGTTTAAT-TTTTTTTTAACTATTTCG
1 AAAGAAAAAGTTTAAATTTTTAAA-AATA--AAAATATATTTTCTAATTATTT-T
* * ** * ****
28090716 AAA-TAAAAGTTTAGATTTTT---AAGCAAAATAGTGATTTTCT-ATAAAAAA
1 AAAGAAAAAGTTTAAATTTTTAAAAATAAAAATA-T-ATTTTCTAATTATTTT
* *
28090764 AAAAAAGAAAGTTTATATTTTTAAAAATAAAAATATATTTTCTAATTATTTT
1 AAAGAA-AAAGTTTAAATTTTTAAAAATAAAAATATATTTTCTAATTATTTT
* * * * *
28090816 AAAGAAAAAGTTTAAATTTTT--AAATAAAATTTTGATTTTTTTTAACTATTTC
1 AAAGAAAAAGTTTAAATTTTTAAAAATAAAA--AT-ATATTTTCTAATTATTTT
* ** * * *
28090868 AAA-ATAAAGGTTTGGATTTTT--AAGT-AAAGTAGTGATTTTC--ATTA---A
1 AAAGA-AAAAGTTTAAATTTTTAAAAATAAAAATA-T-ATTTTCTAATTATTTT
* * * *
28090913 AAAAAAGAAAGTTTAGATTTTTAAAAAATAAAAATATA-TTTCTTAGTGATTTT
1 AAAGAA-AAAGTTTAAATTTTT-AAAAATAAAAATATATTTTC-TAATTATTTT
* * * * * * ** *
28090966 AAAGAAAAATTTTAAATTTTT--AGACAAAAGTTTGATTTTTTAACGATTTCG
1 AAAGAAAAAGTTTAAATTTTTAAAAATAAAAATAT-ATTTTCTAATTATTT-T
* ** * **
28091017 AAA-TAAAAGTTTGGATTTTT--AAATAAAGTAAT-GATTTTC--ATTA--AA
1 AAAGAAAAAGTTTAAATTTTTAAAAATAAA--AATATATTTTCTAATTATTTT
* * *
28091062 AAAGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATATATTTTTTAGTTATTTT
1 AAAG-AA-AAAGTTTAAATTTTT-AAAAATAAAAATATATTTTCTAATTATTTT
28091116 AAAGAAAAAGTTTAAATTTTTAAA
1 AAAGAAAAAGTTTAAATTTTTAAA
28091140 CAAAGTTTAA
Statistics
Matches: 344, Mismatches: 85, Indels: 96
0.66 0.16 0.18
Matches are distributed among these distances:
45 7 0.02
46 14 0.04
47 8 0.02
48 26 0.08
49 29 0.08
50 66 0.19
51 65 0.19
52 104 0.30
53 21 0.06
54 4 0.01
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (51 bp):
AAAGAAAAAGTTTAAATTTTTAAAAATAAAAATATATTTTCTAATTATTTT
Found at i:28091000 original size:150 final size:148
Alignment explanation
Indices: 28090550--28091230 Score: 843
Period size: 150 Copynumber: 4.5 Consensus size: 148
28090540 AAAGTTTTGG
* ** * * *
28090550 TTTTTTTAAATAATTTCGAAATAAAAGTTTTTAATTTTTAAGTAAAATAGTAATTTT--TTTAAA
1 TTTTTTTAACT-ATTTCGAAATAAAAG-TTTGGATTTTTAAGTAAAGTAGTGATTTTCATTAAAA
* * *
28090613 AAGAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAAAAGTTTAA
64 AAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAGTTTAA
*
28090678 ATTTTTAAACAAAGTTTAATT
129 ATTTTTAAACAAAGTTTGA-T
* * * *
28090699 TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGCAAAATAGTGATTTTCTATAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTC-AT---TAA
* * *
28090764 AAAAAAGAAAGTTTATATTTTTAAAAATAAAAATATATTTTCTAATTATTTTAAAGAAAAAGTTT
62 AAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAGTTT
* *
28090829 AAATTTTTAAATAAAATTTTGAT
127 AAATTTTTAAA-CAAAGTTTGAT
* *
28090852 TTTTTTTAACTATTTCAAAATAAAGGTTTGGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
* * *
28090917 AAGAAAGTTTAGATTTTTAAAAAATAAAAATATATTTCTTAGTGATTTTAAAGAAAAATTTTAAA
66 AAGAAAGTTTAGATTTTT-AAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAGTTTAAA
*
28090982 TTTTTAGACAAAAGTTTGA-
130 TTTTTAAAC-AAAGTTTGAT
* * *
28091001 -TTTTTTAACGATTTCGAAATAAAAGTTTGGATTTTTAAATAAAGTAATGATTTTCATTAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTCATT-AAAAA
28091065 GAAAGAAAGTTTAGATTTTTAAAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAGTTTA
65 -AAAGAAAGTTTAGATTTTT-AAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAGTTTA
*
28091130 AATTTTTAAACAAAGTTT-AA
128 AATTTTTAAACAAAGTTTGAT
** * * * * **
28091150 AATTTTTAACTATTTCGAAATAAAATTTTTGATTTTAAAGTAAAGTAGTCATTTTGTTTTAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTT-CATTAAAAA
* *
28091215 AAA-AAACTTTTGATTT
65 AAAGAAAGTTTAGATTT
28091231 AAAAAAAAAG
Statistics
Matches: 468, Mismatches: 50, Indels: 29
0.86 0.09 0.05
Matches are distributed among these distances:
147 25 0.05
148 80 0.17
149 48 0.10
150 179 0.38
151 2 0.00
152 2 0.00
153 125 0.27
154 7 0.01
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (148 bp):
TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
AAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAGTTTAAAT
TTTTAAACAAAGTTTGAT
Found at i:28094225 original size:122 final size:122
Alignment explanation
Indices: 28094008--28094255 Score: 478
Period size: 122 Copynumber: 2.0 Consensus size: 122
28093998 TCAAGACGCA
*
28094008 AAACTGACAGTAAATGTAATGACATTATTAGCATAAGTGGGATAAAATAGAAGAAAATTAAACCA
1 AAACTGACAGTAAATGTAATGACATTAATAGCATAAGTGGGATAAAATAGAAGAAAATTAAACCA
28094073 AACATCACTAACTTAGAAAATGCAATTACTAAATATAAAATGCTAAAAATGCATGCT
66 AACATCACTAACTTAGAAAATGCAATTACTAAATATAAAATGCTAAAAATGCATGCT
*
28094130 AAACTGACAGTAACTGTAATGACATTAATAGCATAAGTGGGATAAAATAGAAGAAAATTAAACCA
1 AAACTGACAGTAAATGTAATGACATTAATAGCATAAGTGGGATAAAATAGAAGAAAATTAAACCA
28094195 AACATCACTAACTTAGAAAATGCAATTACTAAATATAAAATGCTAAAAATGCATGCT
66 AACATCACTAACTTAGAAAATGCAATTACTAAATATAAAATGCTAAAAATGCATGCT
28094252 AAAC
1 AAAC
28094256 ATAATACAAA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (122 bp):
AAACTGACAGTAAATGTAATGACATTAATAGCATAAGTGGGATAAAATAGAAGAAAATTAAACCA
AACATCACTAACTTAGAAAATGCAATTACTAAATATAAAATGCTAAAAATGCATGCT
Found at i:28106132 original size:6 final size:6
Alignment explanation
Indices: 28106118--28106151 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
28106108 ATAACACATG
* *
28106118 AATCTC AATCAC AATCAC AATCAC AATCGC AATC
1 AATCAC AATCAC AATCAC AATCAC AATCAC AATC
28106152 TCATGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.32, G:0.03, T:0.21
Consensus pattern (6 bp):
AATCAC
Found at i:28107407 original size:22 final size:22
Alignment explanation
Indices: 28107382--28107423 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28107372 AAAAAAAAAC
* *
28107382 AAAGGTAAAAGAATGGGAGCTT
1 AAAGGTAAAACAATAGGAGCTT
*
28107404 AAAGGTCAAACAATAGGAGC
1 AAAGGTAAAACAATAGGAGC
28107424 AAAAAGGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.29, T:0.14
Consensus pattern (22 bp):
AAAGGTAAAACAATAGGAGCTT
Found at i:28124471 original size:28 final size:28
Alignment explanation
Indices: 28124401--28124455 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
28124391 AATAGGAGTT
*
28124401 AATAAAGATATTTTAAGTATAAAAAATC
1 AATAGAGATATTTTAAGTATAAAAAATC
*
28124429 AATAGAAATATTTTAAGTATAAAAAAT
1 AATAGAGATATTTTAAGTATAAAAAAT
28124456 TATTAGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (28 bp):
AATAGAGATATTTTAAGTATAAAAAATC
Found at i:28124557 original size:13 final size:14
Alignment explanation
Indices: 28124535--28124567 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28124525 ATTTATAAAT
28124535 TTTAATTA-TTATA
1 TTTAATTATTTATA
*
28124548 TTTAATTATTTTTA
1 TTTAATTATTTATA
28124562 TTTAAT
1 TTTAAT
28124568 GTGTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTATTTATA
Found at i:28126519 original size:6 final size:6
Alignment explanation
Indices: 28126501--28126530 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28126491 TAAATACATA
28126501 ATAAAT A-AAAT ATAAAT ATAAAT ATAAAT A
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT A
28126531 ATATAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
ATAAAT
Found at i:28128078 original size:25 final size:23
Alignment explanation
Indices: 28128050--28128095 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
28128040 GTTGGATCCA
28128050 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
28128075 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
28128096 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:28130116 original size:6 final size:6
Alignment explanation
Indices: 28130097--28130218 Score: 66
Period size: 6 Copynumber: 19.3 Consensus size: 6
28130087 AGTGCATAAT
* * * * ** *
28130097 AAAATA AAATTA AAAATA AAACTA ACACTA AAACCA AAACT- AAAATGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A
* *
28130145 AAAATGA AAAATGA AAAATGA AAAATGAA AAAATAA AAAATG AAAATG
1 AAAAT-A AAAAT-A AAAAT-A AAAAT--A AAAAT-A AAAATA AAAATA
* * *
28130193 AAAATG AAAGTA AAAATG AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
28130219 TGTACTAATT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.04
6 55 0.56
7 33 0.34
8 6 0.06
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:28130150 original size:7 final size:7
Alignment explanation
Indices: 28130138--28130214 Score: 99
Period size: 7 Copynumber: 11.4 Consensus size: 7
28130128 AACCAAAACT
28130138 AAAATGA
1 AAAATGA
28130145 AAAATGA
1 AAAATGA
28130152 AAAATGA
1 AAAATGA
28130159 AAAATGA
1 AAAATGA
28130166 AAAATGAA
1 AAAATG-A
*
28130174 AAAATAA
1 AAAATGA
28130181 AAAATG-
1 AAAATGA
28130187 AAAATG-
1 AAAATGA
28130193 AAAATG-
1 AAAATGA
*
28130199 AAAGT-A
1 AAAATGA
28130205 AAAATGA
1 AAAATGA
28130212 AAA
1 AAA
28130215 TAAATGTACT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
6 20 0.32
7 37 0.59
8 6 0.10
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.14
Consensus pattern (7 bp):
AAAATGA
Found at i:28133445 original size:25 final size:25
Alignment explanation
Indices: 28133388--28133437 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
28133378 TTTATCCCCT
28133388 ATTA-AATTAAATTCTAAAAAGATA
1 ATTAGAATTAAATTCTAAAAAGATA
*
28133412 ATTAGAATTAAA-TCTAAACA-ATA
1 ATTAGAATTAAATTCTAAAAAGATA
28133435 ATT
1 ATT
28133438 CGCTAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 11 0.46
25 7 0.29
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (25 bp):
ATTAGAATTAAATTCTAAAAAGATA
Found at i:28139415 original size:15 final size:15
Alignment explanation
Indices: 28139395--28139436 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
28139385 CAATTTATTC
28139395 TTCTTTTTCTTTC-CT
1 TTCTTTTT-TTTCTCT
28139410 TTCTTTTTTTTCTCT
1 TTCTTTTTTTTCTCT
28139425 TT-TTTGTTTTTC
1 TTCTTT-TTTTTC
28139437 AAGTGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (15 bp):
TTCTTTTTTTTCTCT
Found at i:28148465 original size:17 final size:18
Alignment explanation
Indices: 28148433--28148472 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28148423 ACTAAATTAT
* *
28148433 AATGACAAATGGAAATTC
1 AATGACAAATGCAAATGC
28148451 AATGAC-AATGCAAATGC
1 AATGACAAATGCAAATGC
28148468 AATGA
1 AATGA
28148473 AAACTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.20
Consensus pattern (18 bp):
AATGACAAATGCAAATGC
Found at i:28165561 original size:26 final size:26
Alignment explanation
Indices: 28165524--28165603 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 26
28165514 TATTTAGGCG
*
28165524 CAATTTTGGACATGCTCATGCAACGA
1 CAATTCTGGACATGCTCATGCAACGA
* * **
28165550 TAATTCTGGACATGTTCATGCAGTGA
1 CAATTCTGGACATGCTCATGCAACGA
**
28165576 CAATTCTGGACATGCTCAAACAACGA
1 CAATTCTGGACATGCTCATGCAACGA
28165602 CA
1 CA
28165604 TTAGTAGTAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (26 bp):
CAATTCTGGACATGCTCATGCAACGA
Found at i:28167608 original size:139 final size:138
Alignment explanation
Indices: 28167359--28167884 Score: 766
Period size: 138 Copynumber: 3.8 Consensus size: 138
28167349 GCATAGAAAA
* * * *
28167359 AATTAATATATGAATTTGATTCATAAAAAATATTAATTATATATATTATACCGAAATTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * *
28167424 TAAATAATTATAATAATTAATTTCTGTTAAAATACAAAAGACATGGAAATTAATATTCTTTTGGA
66 TAAATAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
28167489 AAAAATAT
131 AAAAATAT
* *
28167497 AATTAATATACGAATTTGATTCATACAAAATATTAATTGTATATATTTTTACTGAATTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATA-TTTTACCGAATTTATTAAT
* *
28167562 ATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGG
65 ATAAATAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGG
*
28167627 AAATAATAT
130 AAAAAATAT
*
28167636 AATTAATATATGAATTTGATCCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * * * * *
28167701 TAAATAATTGTATTAATTAAATTCGGTCAAAATAAAAAATATATGTAAATTAATATTCTTTTGGA
66 TAAATAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
*
28167766 AAGAATAT
131 AAAAATAT
* * * * **
28167774 AAGTCATATATGAATTTAATTCATACGAAATATTAATTGTATATATTTTACAAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
*
28167839 TGAAA-AATTATATTAATTAATTTCAATCAAAATATAAAAGACATGG
66 T-AAATAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGG
28167885 TTCCTTTTTC
Statistics
Matches: 345, Mismatches: 41, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
138 216 0.63
139 129 0.37
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
TAAATAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
AAAAATAT
Found at i:28167721 original size:17 final size:17
Alignment explanation
Indices: 28167689--28167722 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28167679 TATTTTACCG
28167689 AATTTATTAATATAAAT
1 AATTTATTAATATAAAT
28167706 AATTGTATTAAT-TAAAT
1 AATT-TATTAATATAAAT
28167723 TCGGTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTTATTAATATAAAT
Found at i:28169061 original size:24 final size:24
Alignment explanation
Indices: 28169004--28169062 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
28168994 AACATGAACA
*
28169004 AACTCGTTTAAAAGCTCCTTTATT
1 AACTCGTTTATAAGCTCCTTTATT
** * * *
28169028 GGCTCATTTATAAGTTCGTTTATT
1 AACTCGTTTATAAGCTCCTTTATT
28169052 AACTCGTTTAT
1 AACTCGTTTAT
28169063 GACTCATTTA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (24 bp):
AACTCGTTTATAAGCTCCTTTATT
Found at i:28178109 original size:17 final size:17
Alignment explanation
Indices: 28178077--28178111 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28178067 GAAGAGAGAA
28178077 AAAAGCAAAACAAAAGC
1 AAAAGCAAAACAAAAGC
28178094 AAAAG-AAAACAGAAAGC
1 AAAAGCAAAACA-AAAGC
28178111 A
1 A
28178112 TGAGGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAGCAAAACAAAAGC
Found at i:28181883 original size:50 final size:50
Alignment explanation
Indices: 28181787--28181942 Score: 136
Period size: 50 Copynumber: 3.1 Consensus size: 50
28181777 AACTAATGGA
** * * *
28181787 TTAC-TAAATGCATGACTTGATTTAAAGATGGAAACTTTAACTAACATGGGAG
1 TTACATAAA-GCATGACAGGATTT-ATGATGCAAA-TTTAACTAACATGAGAG
* *
28181839 TTACATAAAGCATGATAGGATTTATGATGCATATTTAACTAACATGTA-AG
1 TTACATAAAGCATGACAGGATTTATGATGCAAATTTAACTAACATG-AGAG
* * * ** *
28181889 TTACTTAATGCATGCCATTATTTATGATGCAAACTTAACTAATCATGAGAG
1 TTACATAAAGCATGACAGGATTTATGATGCAAATTTAACTAA-CATGAGAG
28181940 TTA
1 TTA
28181943 ATGGATGTCA
Statistics
Matches: 85, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
50 50 0.59
51 16 0.19
52 15 0.18
53 4 0.05
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (50 bp):
TTACATAAAGCATGACAGGATTTATGATGCAAATTTAACTAACATGAGAG
Found at i:28204517 original size:16 final size:17
Alignment explanation
Indices: 28204477--28204510 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28204467 GAAGCAGAAC
28204477 AAGAAGAAGGCAAAGAG
1 AAGAAGAAGGCAAAGAG
*
28204494 AAGGAGAAGG-AAAGAG
1 AAGAAGAAGGCAAAGAG
28204510 A
1 A
28204511 GAAAGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (17 bp):
AAGAAGAAGGCAAAGAG
Found at i:28210423 original size:18 final size:16
Alignment explanation
Indices: 28210392--28210432 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
28210382 ATTTCTTTCT
28210392 CTTTTTCTTTTTGTTC
1 CTTTTTCTTTTTGTTC
*
28210408 CTTTTTCTCATTTTGTTT
1 CTTTTTCT--TTTTGTTC
28210426 CTTTTTC
1 CTTTTTC
28210433 AATTGAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.02, C:0.20, G:0.05, T:0.73
Consensus pattern (16 bp):
CTTTTTCTTTTTGTTC
Found at i:28211202 original size:24 final size:25
Alignment explanation
Indices: 28211159--28211211 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
28211149 ACCCTCGTCT
* * *
28211159 TTGTGCTTCTTCTTCCTTTTGTCC-
1 TTGTGCCTCTTCATCCTTTTATCCG
*
28211183 TTGTGCCTCTTCATCTTTTTATCCG
1 TTGTGCCTCTTCATCCTTTTATCCG
28211208 TTGT
1 TTGT
28211212 ACCAACCAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.04, C:0.26, G:0.13, T:0.57
Consensus pattern (25 bp):
TTGTGCCTCTTCATCCTTTTATCCG
Found at i:28218743 original size:20 final size:20
Alignment explanation
Indices: 28218718--28218785 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
28218708 TGCATTAGTA
28218718 GCATTTTATACTTAATGTTT
1 GCATTTTATACTTAATGTTT
* *
28218738 GCATTTTCTAACTTAATG-AT
1 GCATTTTAT-ACTTAATGTTT
*
28218758 G-TTTTTAT-CTTAATGTCTT
1 GCATTTTATACTTAATGT-TT
*
28218777 TCATTTTAT
1 GCATTTTAT
28218786 CTTTTTTATG
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 7 0.19
19 6 0.16
20 16 0.43
21 8 0.22
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (20 bp):
GCATTTTATACTTAATGTTT
Found at i:28220673 original size:15 final size:15
Alignment explanation
Indices: 28220653--28220681 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28220643 TGCGAGAGAG
28220653 CATCTCAAATATTTT
1 CATCTCAAATATTTT
28220668 CATCTCAAATATTT
1 CATCTCAAATATTT
28220682 GCAAGGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (15 bp):
CATCTCAAATATTTT
Found at i:28231434 original size:80 final size:80
Alignment explanation
Indices: 28231301--28231453 Score: 218
Period size: 80 Copynumber: 1.9 Consensus size: 80
28231291 GGGCGCAAAC
* * * *
28231301 CGTTGGTTAATCCAACTAGAGTTGAGCTCATTTATTGCGGTTTGTCCGCTAGGCACTAGGTGCCA
1 CGTTGGTTAATCCAACTAGAGTAGAGCTCACTTATTGCGGTCTATCCGCTAGGCACTAGGTGCCA
*
28231366 TGAATTGAAGGAATT
66 GGAATTGAAGGAATT
* * *
28231381 CGTTGGTTAATCCAACTAGAGCTAG-GCTTACTTATTGCGGTCTATTCGCTAGGCACTGGGTGCC
1 CGTTGGTTAATCCAACTAGAG-TAGAGCTCACTTATTGCGGTCTATCCGCTAGGCACTAGGTGCC
28231445 AGGAATTGA
65 AGGAATTGA
28231454 CGGATTTGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 62 0.97
81 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (80 bp):
CGTTGGTTAATCCAACTAGAGTAGAGCTCACTTATTGCGGTCTATCCGCTAGGCACTAGGTGCCA
GGAATTGAAGGAATT
Found at i:28232459 original size:21 final size:21
Alignment explanation
Indices: 28232415--28232460 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
28232405 CGACCAAGGG
*
28232415 CACGGGCGTGGGTATGTGAAA
1 CACGGGCGTGGGTATGAGAAA
* * *
28232436 CACGGGCGTGTGTTTGAGATA
1 CACGGGCGTGGGTATGAGAAA
28232457 CACG
1 CACG
28232461 ATTGTGTGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (21 bp):
CACGGGCGTGGGTATGAGAAA
Found at i:28234918 original size:21 final size:20
Alignment explanation
Indices: 28234886--28234929 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
28234876 TTTACTAAAT
*
28234886 GGAGAGAAAAGGAGGGTGAGA
1 GGAGAGAAAAGGA-GGAGAGA
28234907 GGAGA-AATAAGGAGGAGAGA
1 GGAGAGAA-AAGGAGGAGAGA
28234927 GGA
1 GGA
28234930 AATTGGACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.50, T:0.05
Consensus pattern (20 bp):
GGAGAGAAAAGGAGGAGAGA
Found at i:28245673 original size:27 final size:29
Alignment explanation
Indices: 28245642--28245699 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
28245632 ATTGAAAAAT
*
28245642 TTTGTATGTTTTGT-TTTTT-TATAATTG
1 TTTGTATGTTTTATCTTTTTATATAATTG
* *
28245669 TTTGTTTGTTTTATCTTTTTATTTAATTG
1 TTTGTATGTTTTATCTTTTTATATAATTG
28245698 TT
1 TT
28245700 GCATGGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 12 0.46
28 5 0.19
29 9 0.35
ACGTcount: A:0.14, C:0.02, G:0.12, T:0.72
Consensus pattern (29 bp):
TTTGTATGTTTTATCTTTTTATATAATTG
Found at i:28251345 original size:22 final size:22
Alignment explanation
Indices: 28251320--28251362 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28251310 ACATTTATCA
28251320 AAATGACATGATTTT-ACTTTTT
1 AAATGA-ATGATTTTGACTTTTT
* *
28251342 AAATTAATGGTTTTGACTTTT
1 AAATGAATGATTTTGACTTTT
28251363 AACTTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (22 bp):
AAATGAATGATTTTGACTTTTT
Found at i:28251405 original size:70 final size:67
Alignment explanation
Indices: 28251279--28251411 Score: 169
Period size: 70 Copynumber: 1.9 Consensus size: 67
28251269 ATAAATAATA
* * * *
28251279 TAATGGTTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATGATTTTACTTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATGATTTTACCTTTTAA
28251344 AT
66 AT
* *
28251346 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAATATTTATCAAAACGACGT-AGTTTTACCTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATGA-TTTTACCTT
28251410 TT
62 TT
28251412 CTTATTTGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
67 19 0.34
68 2 0.04
69 1 0.02
70 34 0.61
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATGATTTTACCTTTTAA
AT
Found at i:28256930 original size:12 final size:13
Alignment explanation
Indices: 28256911--28256948 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
28256901 ACATGTGGAG
28256911 ACAGAGGAAGGAA
1 ACAGAGGAAGGAA
28256924 A-AGAGGAA-GAA
1 ACAGAGGAAGGAA
*
28256935 ACAAAGGAAGGAA
1 ACAGAGGAAGGAA
28256948 A
1 A
28256949 TGATGTCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 4 0.18
12 13 0.59
13 5 0.23
ACGTcount: A:0.61, C:0.05, G:0.34, T:0.00
Consensus pattern (13 bp):
ACAGAGGAAGGAA
Found at i:28273103 original size:13 final size:14
Alignment explanation
Indices: 28273085--28273114 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28273075 GTCAACACAA
28273085 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
28273098 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
28273112 TCA
1 TCA
28273115 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:28276808 original size:50 final size:50
Alignment explanation
Indices: 28276722--28276852 Score: 156
Period size: 50 Copynumber: 2.6 Consensus size: 50
28276712 TGCATGACTT
*
28276722 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAA-TTTAACTAACATGGAAGTTACATAATGCATG-TCAG
* * * *
28276774 GATTTATGATGCATATTTAACTAACATGTAAGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
* *
28276824 TATTTATGATGCAAACTTAACTAATCATG
1 GATTTATGATGCAAATTTAACTAA-CATG
28276853 AGAGTTAATG
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.01
50 50 0.72
51 13 0.19
52 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (50 bp):
GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
Found at i:28277075 original size:17 final size:17
Alignment explanation
Indices: 28277055--28277087 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28277045 CAAATACTTA
28277055 TTAAACTAAAA-TAAAAC
1 TTAAA-TAAAATTAAAAC
28277072 TTAAATAAAATTAAAA
1 TTAAATAAAATTAAAA
28277088 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAATAAAATTAAAAC
Found at i:28284936 original size:17 final size:17
Alignment explanation
Indices: 28284912--28284969 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
28284902 ATATATATGG
**
28284912 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
28284929 AGATGCAACGACAATAA
1 AAATGCAATGACAATAA
*
28284946 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
*
28284963 TAATGCA
1 AAATGCA
28284970 GAGATAATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:28290117 original size:21 final size:20
Alignment explanation
Indices: 28290089--28290128 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
28290079 ATTTATTATA
28290089 TTATATATATTT-TTTCTTTT
1 TTATATAT-TTTCTTTCTTTT
28290109 TTATCATATTTTCTTTCTTT
1 TTAT-ATATTTTCTTTCTTT
28290129 CTCTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATATATTTTCTTTCTTTT
Found at i:28307320 original size:32 final size:32
Alignment explanation
Indices: 28307283--28307370 Score: 167
Period size: 32 Copynumber: 2.8 Consensus size: 32
28307273 AAATTGATTT
*
28307283 TTAAAGATAATTTGATTTTGAAATCTTTGTAA
1 TTAAAGATAAATTGATTTTGAAATCTTTGTAA
28307315 TTAAAGATAAATTGATTTTGAAATCTTTGTAA
1 TTAAAGATAAATTGATTTTGAAATCTTTGTAA
28307347 TTAAAGATAAATTGATTTTGAAAT
1 TTAAAGATAAATTGATTTTGAAAT
28307371 TAAAAAACTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (32 bp):
TTAAAGATAAATTGATTTTGAAATCTTTGTAA
Found at i:28314978 original size:14 final size:15
Alignment explanation
Indices: 28314948--28314984 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
28314938 TAAAAAGTAT
*
28314948 TTTTCTTTTTACAAA
1 TTTTCTTTTAACAAA
28314963 TTTTCTTTTAAC-AA
1 TTTTCTTTTAACAAA
28314977 TTTTCTTT
1 TTTTCTTT
28314985 CTTTTTAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTCTTTTAACAAA
Found at i:28318729 original size:25 final size:27
Alignment explanation
Indices: 28318677--28318736 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
28318667 AATGTGCATG
*
28318677 AATATAATAAATACAATTAAGAGTAC-
1 AATAAAATAAATACAATTAAGAGTACA
*
28318703 AATAAAAT-AATACAATTATG-GTAACA
1 AATAAAATAAATACAATTAAGAGT-ACA
28318729 AATAAAAT
1 AATAAAAT
28318737 CATGATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 2 0.07
25 13 0.43
26 15 0.50
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (27 bp):
AATAAAATAAATACAATTAAGAGTACA
Found at i:28320552 original size:42 final size:42
Alignment explanation
Indices: 28320493--28320589 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
28320483 CTTACTCCAC
* *
28320493 TGCAACTTTAGGGAGATAAAAATTTGCTTTAATCTGACCTAT
1 TGCAACTTTAGGGAGATAAAAAATTGCTTTAATCTGACCCAT
28320535 TGCAACTTTAGGGAGATAAAAAATTGCTTTAATCTGACCCAT
1 TGCAACTTTAGGGAGATAAAAAATTGCTTTAATCTGACCCAT
*
28320577 TGTAACTTTAGGG
1 TGCAACTTTAGGG
28320590 GTATAGGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (42 bp):
TGCAACTTTAGGGAGATAAAAAATTGCTTTAATCTGACCCAT
Found at i:28323833 original size:20 final size:20
Alignment explanation
Indices: 28323797--28323834 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28323787 AGACTAAGAG
*
28323797 AAATAACTGAAATATAAACA
1 AAATAACTGAAAAATAAACA
28323817 AAATAAACT-AAAAATAAA
1 AAAT-AACTGAAAAATAAA
28323835 TGATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (20 bp):
AAATAACTGAAAAATAAACA
Found at i:28329436 original size:212 final size:212
Alignment explanation
Indices: 28329069--28329494 Score: 674
Period size: 212 Copynumber: 2.0 Consensus size: 212
28329059 TAATCGGATT
*
28329069 TAATTCAAAATTGCCAGCTTGAATAGCTAGTCGAACAACCCCTGGCTGCAAATCGTCTAACACAA
1 TAATTCAAAATTGCCAGCTTGAATAGCTAGTCGAACAACCCCTGGCTGCAAATCGTCCAACACAA
* * * *
28329134 GAACAACAAAGTCTCGAATAGTCCCATTTTGCATCTGTTCTTCTTGTTGCGGCAGCGATGGATTA
66 GAACAACAAAGTCTCGAAGAGTCCCATTCTGCATCTGTTCTTCTTGTTGCGACAACGATGGATTA
* ** * *
28329199 TTGATAATTTGTGGCTGTATCAGAGGGACAGGATTTTGTGATGGCAATTG-GCGTATGGCTGTAT
131 TTGATAATTTGTGGCTGTATCAGAGGGACAAGATTTTGTGACAGCAATTGTG-GTATGACTGCAT
* *
28329263 CATTTCTAGGCAGAGCCA
195 CATTTCCAAGCAGAGCCA
* *
28329281 TAATTCAAAATTGCCAGCTTGAATAGCTGGTCGAACAACCCCTGGCTGCAAATCGTCCAACACAG
1 TAATTCAAAATTGCCAGCTTGAATAGCTAGTCGAACAACCCCTGGCTGCAAATCGTCCAACACAA
* *
28329346 GAACAACAAAGTCTCGAAGAGTTCTATTCTGCATCTGTTCTTCTTGTTGCGACAACGATGGATTA
66 GAACAACAAAGTCTCGAAGAGTCCCATTCTGCATCTGTTCTTCTTGTTGCGACAACGATGGATTA
* *
28329411 TTGATAATTTGTGGTTGTATCAGAGGGACAAGATTTTGTGGCAGCAATTGTGGTATGACTGCATC
131 TTGATAATTTGTGGCTGTATCAGAGGGACAAGATTTTGTGACAGCAATTGTGGTATGACTGCATC
28329476 ATTTCCAAGCAGAGCCA
196 ATTTCCAAGCAGAGCCA
28329493 TA
1 TA
28329495 TTTCTTTGTT
Statistics
Matches: 195, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
212 194 0.99
213 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (212 bp):
TAATTCAAAATTGCCAGCTTGAATAGCTAGTCGAACAACCCCTGGCTGCAAATCGTCCAACACAA
GAACAACAAAGTCTCGAAGAGTCCCATTCTGCATCTGTTCTTCTTGTTGCGACAACGATGGATTA
TTGATAATTTGTGGCTGTATCAGAGGGACAAGATTTTGTGACAGCAATTGTGGTATGACTGCATC
ATTTCCAAGCAGAGCCA
Found at i:28359841 original size:37 final size:37
Alignment explanation
Indices: 28359789--28359862 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
28359779 TTCAGGCTAT
28359789 GTGCCAGTGTATTCAGGCTATG-GGCCTAGTACGCTTC
1 GTGCCAGTGTATTCAGGCTATGTGG-CTAGTACGCTTC
* *
28359826 GTGCCAGTGTTTTCAGGCTATGTGGCTAGTAGGCTTC
1 GTGCCAGTGTATTCAGGCTATGTGGCTAGTACGCTTC
28359863 ATGGCGATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 32 0.94
38 2 0.06
ACGTcount: A:0.15, C:0.22, G:0.31, T:0.32
Consensus pattern (37 bp):
GTGCCAGTGTATTCAGGCTATGTGGCTAGTACGCTTC
Found at i:28359841 original size:58 final size:58
Alignment explanation
Indices: 28359740--28359849 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 58
28359730 TGCATCTAAA
* * * **
28359740 TATTCAGGCTATGTGCCTACTAGGCTTTGTGCTGGTGTATTCAGGCTATGTGCCAGTG
1 TATTCAGGCTATGGGCCTACTACGCTTCGTGCCAGTGTATTCAGGCTATGTGCCAGTG
* *
28359798 TATTCAGGCTATGGGCCTAGTACGCTTCGTGCCAGTGTTTTCAGGCTATGTG
1 TATTCAGGCTATGGGCCTACTACGCTTCGTGCCAGTGTATTCAGGCTATGTG
28359850 GCTAGTAGGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.35
Consensus pattern (58 bp):
TATTCAGGCTATGGGCCTACTACGCTTCGTGCCAGTGTATTCAGGCTATGTGCCAGTG
Found at i:28359902 original size:16 final size:16
Alignment explanation
Indices: 28359878--28359920 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
28359868 GATGTATTTG
*
28359878 GGCTATGTGCCTAGCA
1 GGCTTTGTGCCTAGCA
*
28359894 GGCTTTGTGCTTAGCA
1 GGCTTTGTGCCTAGCA
*
28359910 AGCTTTGTGCC
1 GGCTTTGTGCC
28359921 GGTAATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.33
Consensus pattern (16 bp):
GGCTTTGTGCCTAGCA
Found at i:28362949 original size:21 final size:21
Alignment explanation
Indices: 28362925--28362964 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28362915 TTATATTGCT
*
28362925 TTGATTCTTGAACTATAGCGG
1 TTGACTCTTGAACTATAGCGG
28362946 TTGACTCTTGAACTATAGC
1 TTGACTCTTGAACTATAGC
28362965 CGTTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (21 bp):
TTGACTCTTGAACTATAGCGG
Found at i:28373434 original size:21 final size:21
Alignment explanation
Indices: 28373410--28373449 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28373400 TGCATTCGAT
*
28373410 TTTGATGTGGCTGCATCTGTC
1 TTTGATGTGGATGCATCTGTC
*
28373431 TTTGTTGTGGATGCATCTG
1 TTTGATGTGGATGCATCTG
28373450 AGTCTGCTGA
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:0.10, C:0.15, G:0.30, T:0.45
Consensus pattern (21 bp):
TTTGATGTGGATGCATCTGTC
Found at i:28375826 original size:26 final size:26
Alignment explanation
Indices: 28375794--28375862 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
28375784 CAAATGCTAT
*
28375794 GACAATTCTGGACGTGCTCATGCAGC
1 GACAATTCTGGACATGCTCATGCAGC
* * * *
28375820 GATAATTCTAGACATGTTCATGCAGT
1 GACAATTCTGGACATGCTCATGCAGC
*
28375846 GACAATTTTGGACATGC
1 GACAATTCTGGACATGC
28375863 CCATACAGGG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (26 bp):
GACAATTCTGGACATGCTCATGCAGC
Found at i:28376697 original size:18 final size:17
Alignment explanation
Indices: 28376665--28376698 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28376655 GTTTTCATTT
28376665 TATTTTTTTAATTTATC
1 TATTTTTTTAATTTATC
*
28376682 TATTTGTTTTATTTTAT
1 TATTT-TTTTAATTTAT
28376699 TTTACTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TATTTTTTTAATTTATC
Found at i:28384003 original size:18 final size:18
Alignment explanation
Indices: 28383961--28384004 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
28383951 AAAAAAAGTG
28383961 ATAAAAAAGTAGAGAAAA
1 ATAAAAAAGTAGAGAAAA
28383979 A-AGAAAAA-TACGAGAAAA
1 ATA-AAAAAGTA-GAGAAAA
28383997 ATAAAAAA
1 ATAAAAAA
28384005 AGAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.13
18 19 0.83
19 1 0.04
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.09
Consensus pattern (18 bp):
ATAAAAAAGTAGAGAAAA
Found at i:28385346 original size:91 final size:91
Alignment explanation
Indices: 28385191--28385372 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
28385181 GTGATCTCTC
28385191 ACATTTTGAACAATGTTATTGGTGTAGTTCAAAAGATCATGAGAGTTTTCGATGTTCAATCCAAT
1 ACATTTTGAACAATGTTATTGGTGTAGTTCAAAAGATCATGAGAGTTTTCGATGTTCAATCCAAT
28385256 ATCCAACTAGAGAAGAAAGTAAGTAT
66 ATCCAACTAGAGAAGAAAGTAAGTAT
28385282 ACATTTTGAACAATGTTATTGGTGTAGTTCAAAAGATCATGAGAGTTTTCGATGTTCAATCCAAT
1 ACATTTTGAACAATGTTATTGGTGTAGTTCAAAAGATCATGAGAGTTTTCGATGTTCAATCCAAT
28385347 ATCCAACTAGAGAAGAAAGTAAGTAT
66 ATCCAACTAGAGAAGAAAGTAAGTAT
28385373 GACTTTGTGC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (91 bp):
ACATTTTGAACAATGTTATTGGTGTAGTTCAAAAGATCATGAGAGTTTTCGATGTTCAATCCAAT
ATCCAACTAGAGAAGAAAGTAAGTAT
Found at i:28388840 original size:24 final size:24
Alignment explanation
Indices: 28388807--28388862 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
28388797 GGAGAGTTCT
*
28388807 CAAGAGGAAAAAGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
* *
28388831 CAATAAGAAAATGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
28388855 CAAGAAGA
1 CAAGAAGA
28388863 TACCCATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.70, C:0.05, G:0.18, T:0.07
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAATGAAAAA
Found at i:28390735 original size:8 final size:8
Alignment explanation
Indices: 28390706--28390744 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
28390696 AAAAGTAGAG
28390706 AAAAAAGA
1 AAAAAAGA
*
28390714 AAAATACGA
1 AAAA-AAGA
*
28390723 GAAAAAGA
1 AAAAAAGA
28390731 AAAAAAGA
1 AAAAAAGA
28390739 AAAAAA
1 AAAAAA
28390745 ATTCTGTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:28390735 original size:18 final size:17
Alignment explanation
Indices: 28390694--28390735 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28390684 CAAAGTGATC
28390694 AAAAAAGTAGAGAAAAA
1 AAAAAAGTAGAGAAAAA
28390711 AGAAAAA-TACGAGAAAAA
1 A-AAAAAGTA-GAGAAAAA
28390729 GAAAAAA
1 -AAAAAA
28390736 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.14
18 18 0.82
19 1 0.05
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAAGTAGAGAAAAA
Found at i:28390745 original size:17 final size:17
Alignment explanation
Indices: 28390706--28390744 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28390696 AAAAGTAGAG
*
28390706 AAAAAAGAAAAATACGA
1 AAAAAAGAAAAATAAGA
*
28390723 GAAAAAGAAAAA-AAGA
1 AAAAAAGAAAAATAAGA
28390739 AAAAAA
1 AAAAAA
28390745 ATTCTGTGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAAATAAGA
Found at i:28397656 original size:9 final size:9
Alignment explanation
Indices: 28397642--28397667 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28397632 TAATTTCACG
28397642 AATCAAGAA
1 AATCAAGAA
28397651 AATCAAGAA
1 AATCAAGAA
28397660 AATCAAGA
1 AATCAAGA
28397668 TTTTAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
AATCAAGAA
Found at i:28402656 original size:13 final size:14
Alignment explanation
Indices: 28402622--28402660 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
28402612 TATCTCTTTT
*
28402622 TCTTCCTTTTCATC
1 TCTTTCTTTTCATC
*
28402636 TTTTTCTTTTC-TC
1 TCTTTCTTTTCATC
28402649 TCTTTCTTTTCA
1 TCTTTCTTTTCA
28402661 CTTTCTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTCTTTTCATC
Found at i:28404785 original size:23 final size:24
Alignment explanation
Indices: 28404742--28404786 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28404732 TGCCCTTTTG
28404742 TTTTTTTTATACTTTCGAAACTCT
1 TTTTTTTTATACTTTCGAAACTCT
28404766 TTTTTTTTAATA-TTTC-AAACT
1 TTTTTTTT-ATACTTTCGAAACT
28404787 TTGCACTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.24, C:0.13, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTTTTATACTTTCGAAACTCT
Found at i:28407484 original size:48 final size:48
Alignment explanation
Indices: 28407405--28407534 Score: 201
Period size: 48 Copynumber: 2.8 Consensus size: 48
28407395 TATTTATGCT
*
28407405 TCATTAAGTG-TTT-TTTGTTAAATACATCTTTGTTTAATAATCTCCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTCCA
* * *
28407451 TCATTAAGTGTTTTGTTTATTAAATGCATCTTTGTTTAGTAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTCCA
*
28407499 TTATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
28407535 AAATGCCTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
46 10 0.13
47 3 0.04
48 63 0.83
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTCCA
Found at i:28408038 original size:80 final size:79
Alignment explanation
Indices: 28407945--28408108 Score: 251
Period size: 80 Copynumber: 2.1 Consensus size: 79
28407935 ACATTAAGGA
* * *
28407945 GAAA-TGCCATGCCTTTTCAGCTACATCAGATCCTAATGAAGAGACATAACTCATT-GACTTTCT
1 GAAATTGCCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATAACTCATTAG-CTTCCC
28408008 TACAAGAGTTAAAAAT
65 TACAAGAGTT-AAAAT
* *
28408024 GAAATTGCCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCT
1 GAAATTGCCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATAACTCATTAGCTTCCCT
28408089 ACAAGAGTTAAAAT
66 ACAAGAGTTAAAAT
28408103 GAAATT
1 GAAATT
28408109 AGTGCTTGTA
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
79 15 0.19
80 62 0.79
81 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (79 bp):
GAAATTGCCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATAACTCATTAGCTTCCCT
ACAAGAGTTAAAAT
Found at i:28414163 original size:48 final size:48
Alignment explanation
Indices: 28414065--28414240 Score: 275
Period size: 48 Copynumber: 3.7 Consensus size: 48
28414055 TTTGTGCTTC
* * * *
28414065 ATTAAGTGTTTT-TTTGTTAAATGCATATTTG-TTAATAATCTGCATC
1 ATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATT
* * *
28414111 ATTAAGTGTGTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGTATT
1 ATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATT
28414159 ATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATT
1 ATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATT
28414207 ATTAACTGTTTTGTTTGTTAAATGCATCTTTGTT
1 ATTAACTGTTTTGTTTGTTAAATGCATCTTTGTT
28414241 AAATGCCTTC
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
46 11 0.09
47 18 0.15
48 91 0.76
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (48 bp):
ATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATT
Found at i:28414783 original size:80 final size:80
Alignment explanation
Indices: 28414685--28414835 Score: 250
Period size: 80 Copynumber: 1.9 Consensus size: 80
28414675 CGGAGAAATG
* *
28414685 CCATGCCTTTTCAGCTACATCAGATCCTAATGAAGAGACATGACTCATTGGCTTTCC-TACAAGA
1 CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGC-TTCCTTACAAGA
28414749 GTTAAAAACGAAATTT
65 GTTAAAAACGAAATTT
* *
28414765 CCATGCCTTTTTAACTACATCAGATCCTAATGATGAGACATGACTCATTAGCTTCCTTACAAGAG
1 CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCTTACAAGAG
28414830 TTAAAA
66 TTAAAA
28414836 TGAAATTAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
79 4 0.06
80 62 0.94
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (80 bp):
CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCTTACAAGAG
TTAAAAACGAAATTT
Found at i:28416650 original size:14 final size:16
Alignment explanation
Indices: 28416631--28416668 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
28416621 GCTTAAAAAG
28416631 AAAGAAAAA-TGTT-A
1 AAAGAAAAATTGTTAA
*
28416645 AAAGAAAAATTTTTAA
1 AAAGAAAAATTGTTAA
28416661 AAAGAAAA
1 AAAGAAAA
28416669 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 3 0.14
16 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (16 bp):
AAAGAAAAATTGTTAA
Found at i:28418045 original size:13 final size:13
Alignment explanation
Indices: 28418027--28418051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28418017 TTTTGAGCTT
28418027 AAAAATCTGTTTA
1 AAAAATCTGTTTA
28418040 AAAAATCTGTTT
1 AAAAATCTGTTT
28418052 TGTTCCCCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAAAATCTGTTTA
Found at i:28418417 original size:5 final size:5
Alignment explanation
Indices: 28418407--28418440 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
28418397 GTTCGGTCTT
28418407 GAAAA GAAAA GAAAA -AAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
28418441 AATATCCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:28418427 original size:14 final size:15
Alignment explanation
Indices: 28418407--28418440 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
28418397 GTTCGGTCTT
28418407 GAAAAGAAAAGAAAA
1 GAAAAGAAAAGAAAA
28418422 -AAAAGAAAAGAAAA
1 GAAAAGAAAAGAAAA
28418436 GAAAA
1 GAAAA
28418441 AATATCCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
GAAAAGAAAAGAAAA
Found at i:28441604 original size:18 final size:19
Alignment explanation
Indices: 28441583--28441618 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28441573 ATCAAAAGTA
*
28441583 GAGAAAAA-AGAAAAATAT
1 GAGAAAAATAAAAAAATAT
28441601 GAGAAAAATAAAAAAATA
1 GAGAAAAATAAAAAAATA
28441619 AAAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (19 bp):
GAGAAAAATAAAAAAATAT
Found at i:28443203 original size:24 final size:24
Alignment explanation
Indices: 28443176--28443231 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
28443166 GGAGAGTTCT
*
28443176 CAAGAGGAAAAAGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
*
28443200 CAAGAAGAAAATGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
28443224 CAAGAAGA
1 CAAGAAGA
28443232 TATTCATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.70, C:0.05, G:0.20, T:0.05
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAATGAAAAA
Found at i:28474690 original size:17 final size:17
Alignment explanation
Indices: 28474670--28474702 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28474660 TTTAAGGAAT
28474670 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
28474687 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
28474703 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:28474962 original size:50 final size:50
Alignment explanation
Indices: 28474883--28475003 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
28474873 TGACATCCAT
* ***
28474883 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGA-CATGCATTAAG
1 TAACTCACATG-TTAGTTAAACATGCATCATAAATAAT-ATCATGCATTAAG
* ** *
28474934 TAACTTACATGTTAGTTAAACATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAACATGCATCATAAATAATATCATGCATTAAG
*
28474984 TAACTCCCATGTTAGTTAAA
1 TAACTCACATGTTAGTTAAA
28475004 GTTTACATCA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.02
50 49 0.83
51 9 0.15
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAACATGCATCATAAATAATATCATGCATTAAG
Found at i:28482309 original size:24 final size:24
Alignment explanation
Indices: 28482278--28482332 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
28482268 GTATGGGTAC
28482278 CTTCTTGTTTTTCATTTTCATTTT
1 CTTCTTGTTTTTCATTTTCATTTT
* *
28482302 CTTCTTGTTTTTTATTTTCTTTTT
1 CTTCTTGTTTTTCATTTTCATTTT
*
28482326 CCTCTTG
1 CTTCTTG
28482333 AGAACTCTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.71
Consensus pattern (24 bp):
CTTCTTGTTTTTCATTTTCATTTT
Found at i:28483999 original size:18 final size:19
Alignment explanation
Indices: 28483968--28484003 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28483958 ACCCATAAAA
*
28483968 TATTTTTTTATTTTTCTCG
1 TATTTTTGTATTTTTCTCG
28483987 TATTTTTGT-TTTTTCTC
1 TATTTTTGTATTTTTCTC
28484004 AACTTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.08, C:0.11, G:0.06, T:0.75
Consensus pattern (19 bp):
TATTTTTGTATTTTTCTCG
Found at i:28489241 original size:18 final size:18
Alignment explanation
Indices: 28489218--28489261 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
28489208 AATATTTTTT
28489218 TATTTTTTC-TTTTTCTC
1 TATTTTTTCTTTTTTCTC
28489235 GTA-TTTTTCTTTTTTCTC
1 -TATTTTTTCTTTTTTCTC
28489253 TACTTTTTT
1 TA-TTTTTT
28489262 TTATCACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (18 bp):
TATTTTTTCTTTTTTCTC
Found at i:28489259 original size:17 final size:18
Alignment explanation
Indices: 28489222--28489263 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
28489212 TTTTTTTATT
*
28489222 TTTTC-TTTTTCTCGTAT
1 TTTTCTTTTTTCTCGTAC
28489239 TTTTCTTTTTTCTC-TAC
1 TTTTCTTTTTTCTCGTAC
28489256 TTTT-TTTT
1 TTTTCTTTT
28489264 ATCACTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTTTCTCGTAC
Found at i:28496041 original size:34 final size:34
Alignment explanation
Indices: 28495997--28496072 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
28495987 ATAGTTTACA
* * *
28495997 TGCATCTTTATTGTCATTGCAT-TATTAATGTCAT
1 TGCATTTTTATTGTCACTGCATCTA-CAATGTCAT
* *
28496031 TGCATTTTTATTGTCGCTGCATCTACATTGTCAT
1 TGCATTTTTATTGTCACTGCATCTACAATGTCAT
28496065 TGCATTTT
1 TGCATTTT
28496073 CATATATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 34 0.94
35 2 0.06
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (34 bp):
TGCATTTTTATTGTCACTGCATCTACAATGTCAT
Found at i:28496045 original size:17 final size:17
Alignment explanation
Indices: 28495997--28496072 Score: 80
Period size: 17 Copynumber: 4.5 Consensus size: 17
28495987 ATAGTTTACA
*
28495997 TGCATCTTTATTGTCAT
1 TGCATTTTTATTGTCAT
* *
28496014 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
28496031 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
28496048 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
28496065 TGCATTTT
1 TGCATTTT
28496073 CATATATATA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:28512465 original size:17 final size:17
Alignment explanation
Indices: 28512445--28512482 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
28512435 TATCAAATTC
28512445 AAAAATAAA-ACA-AAAT
1 AAAAATAAATA-AGAAAT
28512461 AAAAATAAATAAGAAAT
1 AAAAATAAATAAGAAAT
28512478 AAAAA
1 AAAAA
28512483 AGAAACGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (17 bp):
AAAAATAAATAAGAAAT
Found at i:28515045 original size:26 final size:26
Alignment explanation
Indices: 28515011--28515069 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
28515001 TTTAAATTAA
28515011 TAAAAATAA-AATTATATTT-AGATTT
1 TAAAAATAAGAATTA-ATTTAAGATTT
*
28515036 TAAAATATAAGAATTAATTTAATATTT
1 TAAAA-ATAAGAATTAATTTAAGATTT
28515063 TAAAAAT
1 TAAAAAT
28515070 TATAAAGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.17
26 10 0.33
27 15 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (26 bp):
TAAAAATAAGAATTAATTTAAGATTT
Found at i:28515850 original size:25 final size:25
Alignment explanation
Indices: 28515817--28515868 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
28515807 ATACTAAATA
*
28515817 TCTTCTTCTCTTT-TGCTCTTTTATT
1 TCTTCTTCT-TTTATGCTCTTCTATT
* *
28515842 TCTTGTTCTTTTATTCTCTTCTATT
1 TCTTCTTCTTTTATGCTCTTCTATT
28515867 TC
1 TC
28515869 ATAACACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.06, C:0.23, G:0.04, T:0.67
Consensus pattern (25 bp):
TCTTCTTCTTTTATGCTCTTCTATT
Done.