Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 83 of 133
Found at i:16317640 original size:18 final size:17
Alignment explanation
Indices: 16317593--16317642 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
16317583 TTTGTGGGTT
* *
16317593 TTTTTTTTCTTTTTCTC
1 TTTTTTTTCCTTTTCCC
16317610 TTTGTTTTT-CTTTTCCC
1 TTT-TTTTTCCTTTTCCC
16317627 TTTTTGTTTCCTTTTC
1 TTTTT-TTTCCTTTTC
16317643 TTTCTTTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.54
18 11 0.39
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCCTTTTCCC
Found at i:16318079 original size:25 final size:24
Alignment explanation
Indices: 16318051--16318098 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
16318041 TTTCTTGATT
* *
16318051 TTTTTTCCATTTTTGGTGTTTTTGG
1 TTTTTTCAATTTTT-GAGTTTTTGG
16318076 TTTTTTCAATTTTTGAGTTTTTG
1 TTTTTTCAATTTTTGAGTTTTTG
16318099 TTTGGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.69
Consensus pattern (24 bp):
TTTTTTCAATTTTTGAGTTTTTGG
Found at i:16319834 original size:20 final size:20
Alignment explanation
Indices: 16319798--16319856 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
16319788 AAAAAATATT
*
16319798 GAATCTTG-TCAAATCTTGAA
1 GAATCTTGAT-AATTCTTGAA
*
16319818 GAATCTTGATAATTCTTGAT
1 GAATCTTGATAATTCTTGAA
* *
16319838 CAATCTTGGATGATTCTTG
1 GAATCTT-GATAATTCTTG
16319857 GTGCATTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (20 bp):
GAATCTTGATAATTCTTGAA
Found at i:16333428 original size:182 final size:181
Alignment explanation
Indices: 16333121--16333476 Score: 604
Period size: 182 Copynumber: 2.0 Consensus size: 181
16333111 AATTTCAAGA
**
16333121 TCAAGTTGATTTTTGTCCAAGTCTTGAATTTCAAATAAATAAAATCCTACTCCAAGTTAAATTCT
1 TCAAGTTGATTTTTGTCCAAGTCTCAAATTTCAAATAAATAAAATCCTACTCCAAGTTAAATTCT
* * *
16333186 TCAAGGCTAAACAACAAGCTTCATCGTGGACTTCAAATCCCTCTTGGTATAATGCACCTAGTCTT
66 TCAAGGCTAAACAACAAGCTTCATCGTGGACTTCAAATCCCTCTTGGTAGAATACACCTAGCCTT
*
16333251 CATTATAGAAAAAGTACATGGTAGCTCTTTTGGATTGCTTTGGCCGAACATG
131 CATTAT-GAAAAAGTACATGGTAGCTCTTTTGGATTGCCTTGGCCGAACATG
*
16333303 TCAAGTTGATTTTTGTCCAAGTCTCAAATTTCAAATAGATAAAATCCTACTCCAAGTTAAATTCT
1 TCAAGTTGATTTTTGTCCAAGTCTCAAATTTCAAATAAATAAAATCCTACTCCAAGTTAAATTCT
* *
16333368 TCAAGGCTAAACAACAAGCTTTATCGTGGACTTCAAATTCCTCTTGGTAGAATACACCTAGCCTT
66 TCAAGGCTAAACAACAAGCTTCATCGTGGACTTCAAATCCCTCTTGGTAGAATACACCTAGCCTT
* *
16333433 CATTATGGATAAGTACATGGTAGCTCTTTTGGATTGCCTTGGCC
131 CATTATGAAAAAGTACATGGTAGCTCTTTTGGATTGCCTTGGCC
16333477 AAATATAATT
Statistics
Matches: 163, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
181 35 0.21
182 128 0.79
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (181 bp):
TCAAGTTGATTTTTGTCCAAGTCTCAAATTTCAAATAAATAAAATCCTACTCCAAGTTAAATTCT
TCAAGGCTAAACAACAAGCTTCATCGTGGACTTCAAATCCCTCTTGGTAGAATACACCTAGCCTT
CATTATGAAAAAGTACATGGTAGCTCTTTTGGATTGCCTTGGCCGAACATG
Found at i:16337825 original size:22 final size:21
Alignment explanation
Indices: 16337800--16337841 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
16337790 AAGGGGAGAG
*
16337800 AAAATTTTTTCTAAATTTTTTC
1 AAAATATTTTC-AAATTTTTTC
16337822 AAAATATTTTCAAATTTTTT
1 AAAATATTTTCAAATTTTTT
16337842 GTTTTAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
AAAATATTTTCAAATTTTTTC
Found at i:16337836 original size:10 final size:11
Alignment explanation
Indices: 16337800--16337841 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
16337790 AAGGGGAGAG
16337800 AAAATTTTTTC
1 AAAATTTTTTC
*
16337811 TAAATTTTTTC
1 AAAATTTTTTC
*
16337822 AAAATATTTTC
1 AAAATTTTTTC
16337833 -AAATTTTTT
1 AAAATTTTTT
16337842 GTTTTAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (11 bp):
AAAATTTTTTC
Found at i:16343358 original size:28 final size:28
Alignment explanation
Indices: 16343318--16343375 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
16343308 ATTGTAGAGG
16343318 TATTCATCTCATAAAAGCATAAAAACTT
1 TATTCATCTCATAAAAGCATAAAAACTT
16343346 TATTCATCTCATAAAAGCATAAAAACTT
1 TATTCATCTCATAAAAGCATAAAAACTT
16343374 TA
1 TA
16343376 CTTCCTCCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (28 bp):
TATTCATCTCATAAAAGCATAAAAACTT
Found at i:16343387 original size:27 final size:27
Alignment explanation
Indices: 16343318--16343389 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
16343308 ATTGTAGAGG
16343318 TATTCATCTCATAAAAGCATAAAAACTT
1 TATTCA-CTCATAAAAGCATAAAAACTT
16343346 TATTCATCTCATAAAAGCATAAAAACTT
1 TATTCA-CTCATAAAAGCATAAAAACTT
*
16343374 TACTTC-CTCCTAAAAG
1 TA-TTCACTCATAAAAG
16343390 GGTCATAGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 9 0.21
28 30 0.71
29 3 0.07
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (27 bp):
TATTCACTCATAAAAGCATAAAAACTT
Found at i:16345983 original size:158 final size:158
Alignment explanation
Indices: 16345783--16346094 Score: 588
Period size: 158 Copynumber: 2.0 Consensus size: 158
16345773 GTTTGATATT
16345783 TATTTATTCTAATCTAAAAATTTCTTAATTAAATTCTTTCAAAATACTACTTTTTGACCATGTTT
1 TATTTATTCTAATCTAAAAATTTCTTAATTAAATTCTTTCAAAATACTACTTTTTGACCATGTTT
16345848 GATCAAATGAGCTTGAATTTGACCAAATTTGTCTCTAGTTTGACAAAATATTTTACCAAAGTTTT
66 GATCAAATGAGCTTGAATTTGACCAAATTTGTCTCTAGTTTGACAAAATATTTTACCAAAGTTTT
16345913 TCAAAGCATTGACACACAAGTCAAAATC
131 TCAAAGCATTGACACACAAGTCAAAATC
* *
16345941 TATTTATTCTCATCTAAAATTTTCTTAATTAAATTCTTTCAAAATACTACTTTTTGACCATGTTT
1 TATTTATTCTAATCTAAAAATTTCTTAATTAAATTCTTTCAAAATACTACTTTTTGACCATGTTT
*
16346006 GATCAAATGAGCTTGAATTTGACCAAATTTGTCTCTAGTTTGACAAAATATTTTACCAGAGTTTT
66 GATCAAATGAGCTTGAATTTGACCAAATTTGTCTCTAGTTTGACAAAATATTTTACCAAAGTTTT
*
16346071 TCAAAGCATTGACACACAGGTCAA
131 TCAAAGCATTGACACACAAGTCAA
16346095 CCCACGATCC
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 150 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (158 bp):
TATTTATTCTAATCTAAAAATTTCTTAATTAAATTCTTTCAAAATACTACTTTTTGACCATGTTT
GATCAAATGAGCTTGAATTTGACCAAATTTGTCTCTAGTTTGACAAAATATTTTACCAAAGTTTT
TCAAAGCATTGACACACAAGTCAAAATC
Found at i:16351139 original size:18 final size:18
Alignment explanation
Indices: 16351116--16351151 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16351106 TTTTCTTAAT
*
16351116 AAATTTGGTAAGCTTTAC
1 AAATTTGGTAAGCATTAC
16351134 AAATTTGGTAAGCATTAC
1 AAATTTGGTAAGCATTAC
16351152 CACATTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (18 bp):
AAATTTGGTAAGCATTAC
Found at i:16362364 original size:10 final size:10
Alignment explanation
Indices: 16362349--16362376 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
16362339 TGCTAGAAAA
16362349 TGTGCATGTG
1 TGTGCATGTG
16362359 TGTGCATGTG
1 TGTGCATGTG
16362369 TGTGCATG
1 TGTGCATG
16362377 AAGTGGCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.39, T:0.39
Consensus pattern (10 bp):
TGTGCATGTG
Found at i:16363139 original size:79 final size:79
Alignment explanation
Indices: 16363000--16363156 Score: 244
Period size: 79 Copynumber: 2.0 Consensus size: 79
16362990 AAACTAACTA
* *
16363000 TGCTCAGAATCAAGTCTTTGGCTGATTTTGACTTAGCATTGAAGAAGGTGAACTTCTTTTTTGTT
1 TGCTCAGAATCAAGTCTTTGGCTGATTTTGACTTAGCATTAAAGAAGGTGAACTTCTTTTTTGCT
*
16363065 GATCTGGACTTTTT
66 AATCTGGACTTTTT
* * *
16363079 TGCTCAGAATCAAGTCTTTGGCT-ACTTTTGACTTAGCGTTAAAGAAGGTGAAGTTTTTTTTTGC
1 TGCTCAGAATCAAGTCTTTGGCTGA-TTTTGACTTAGCATTAAAGAAGGTGAACTTCTTTTTTGC
16363143 TAATCTGGACTTTT
65 TAATCTGGACTTTT
16363157 CCTTGATCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
78 1 0.01
79 70 0.99
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (79 bp):
TGCTCAGAATCAAGTCTTTGGCTGATTTTGACTTAGCATTAAAGAAGGTGAACTTCTTTTTTGCT
AATCTGGACTTTTT
Found at i:16372346 original size:43 final size:43
Alignment explanation
Indices: 16372292--16372437 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 43
16372282 ACTTGATAAC
*
16372292 TTTGAAAATTTTTAAAAATTCCTCTAAATAGAAGCTAGACAAT
1 TTTGAAAATTTTTAAAAATTCCTCTAAACAGAAGCTAGACAAT
* * * * * * * *
16372335 TTTGAGAATTTTTTAAAAACTCATTTAAACAGAGGCTTGGCAAC
1 TTTGA-AAATTTTTAAAAATTCCTCTAAACAGAAGCTAGACAAT
** * * *
16372379 TTAAAAAATTTTTAAAAGTTTCTCTAAACAAAAGCTTA-ACAAT
1 TTTGAAAATTTTTAAAAATTCCTCTAAACAGAAGC-TAGACAAT
16372422 TTTGAAAA-TTTTAAAA
1 TTTGAAAATTTTTAAAA
16372438 TTGATTTAAT
Statistics
Matches: 77, Mismatches: 24, Indels: 5
0.73 0.23 0.05
Matches are distributed among these distances:
42 8 0.10
43 36 0.47
44 33 0.43
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.36
Consensus pattern (43 bp):
TTTGAAAATTTTTAAAAATTCCTCTAAACAGAAGCTAGACAAT
Found at i:16377386 original size:44 final size:44
Alignment explanation
Indices: 16377328--16377618 Score: 247
Period size: 44 Copynumber: 6.7 Consensus size: 44
16377318 ATAGAGGCTT
*
16377328 ATGACTTTGAAAAAAATAAATAAGGCTCCTCTAAACAGAGACTCA
1 ATGACTTT-TAAAAAATAAATAAGGCTCCTCTAAACAGAGACTCA
* * *
16377373 ATGACTTCTAAAAAATAAATAAGGCT--T-TAAATAGAGGCTCA
1 ATGACTTTTAAAAAATAAATAAGGCTCCTCTAAACAGAGACTCA
** * * * * *
16377414 ATGACTTTGGAAAAATAAATAAGACGCATCTAAATAGAGGCTCA
1 ATGACTTTTAAAAAATAAATAAGGCTCCTCTAAACAGAGACTCA
* * * * * *
16377458 AAGACTTTTGAAAAATAAATAAAGCTCTTCTAAACAGAGGCTTA
1 ATGACTTTTAAAAAATAAATAAGGCTCCTCTAAACAGAGACTCA
** * *
16377502 ACAACTTTTAAAAAAAATAAATAAGGCTCCTTTAAATAGA-AGCTCA
1 ATGACTTTT--AAAAAATAAATAAGGCTCCTCTAAACAGAGA-CTCA
** * *
16377548 ACAACTTTTAAAAAATAAATAAGGTTCCTCTAAGCAGA-AGCTCA
1 ATGACTTTTAAAAAATAAATAAGGCTCCTCTAAACAGAGA-CTCA
*
16377592 ATGAC--TTAAAAAA-AAATAAAGCTCCTC
1 ATGACTTTTAAAAAATAAATAAGGCTCCTC
16377619 GACAATCATG
Statistics
Matches: 206, Mismatches: 34, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
41 45 0.22
42 9 0.04
43 1 0.00
44 108 0.52
45 7 0.03
46 36 0.17
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (44 bp):
ATGACTTTTAAAAAATAAATAAGGCTCCTCTAAACAGAGACTCA
Found at i:16377434 original size:85 final size:85
Alignment explanation
Indices: 16377317--16377618 Score: 265
Period size: 85 Copynumber: 3.5 Consensus size: 85
16377307 AACTCCTCTC
* * * *
16377317 AATAGAGGCTTATGACTTTGAAAAAAATAAATAAGGCTCCTCTAAACAGAGACTCAATGACTTCT
1 AATAGAGGCTAATGACTTTG-AAAAAATAAATAAGGCTCCTCTAAATAGAGACTCAAAGACTTTT
16377382 AAAAAATAAATAAGGCTT-TA
65 AAAAAATAAATAAGGCTTCTA
* * * * *
16377402 AATAGAGGCTCAATGACTTTGGAAAAATAAATAAGACGCATCTAAATAGAGGCTCAAAGACTTTT
1 AATAGAGGCT-AATGACTTTGAAAAAATAAATAAGGCTCCTCTAAATAGAGACTCAAAGACTTTT
* *
16377467 GAAAAATAAATAAAGCTCTTCTA
65 AAAAAATAAAT-AAG-GCTTCTA
* ** * *
16377490 AACAGAGGCTTAACAACTTTTAAAAAAAATAAATAAGGCTCCTTTAAATAGA-AGCTCAACA-AC
1 AATAGAGGC-TAATGAC-TTT-GAAAAAATAAATAAGGCTCCTCTAAATAGAGA-CTCAA-AGAC
*
16377553 TTTTAAAAAATAAATAAGGTTCCTCTA
61 TTTTAAAAAATAAATAAGG--CTTCTA
** * *
16377580 AGCAGAAGCTCAATGAC-TT-AAAAAA-AAATAAAGCTCCTC
1 AATAGAGGCT-AATGACTTTGAAAAAATAAATAAGGCTCCTC
16377619 GACAATCATG
Statistics
Matches: 175, Mismatches: 30, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
85 68 0.39
86 18 0.10
87 3 0.02
88 16 0.09
89 8 0.05
90 61 0.35
91 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (85 bp):
AATAGAGGCTAATGACTTTGAAAAAATAAATAAGGCTCCTCTAAATAGAGACTCAAAGACTTTTA
AAAAATAAATAAGGCTTCTA
Found at i:16377580 original size:90 final size:87
Alignment explanation
Indices: 16377310--16377611 Score: 281
Period size: 90 Copynumber: 3.4 Consensus size: 87
16377300 GAAATAAAAC
* * * * *
16377310 TCCTCTCAATAGAGGCT-TATGACTTTGAAAAAAATAAATAAGGCTCCTCTAAACAG-AGACTCA
1 TCCTCTAAACAGAGGCTCAATGACTTTAAAAAAAATAAATAAGGCTCCTCTAAATAGAAG-CTCA
* *
16377373 ATGACTTCTAAAAAATAAATAAGG
65 A-AACTTTTAAAAAATAAATAAGG
* * ** * * * *
16377397 --CTTTAAATAGAGGCTCAATGACTTT-GGAAAAATAAATAAGACGCATCTAAATAGAGGCTCAA
1 TCCTCTAAACAGAGGCTCAATGACTTTAAAAAAAATAAATAAGGCTCCTCTAAATAGAAGCTCAA
* *
16377459 AGACTTTTGAAAAATAAATAAAGC
66 A-ACTTTTAAAAAATAAAT-AAGG
* * ** *
16377483 TCTTCTAAACAGAGGCTTAACAACTTTTAAAAAAAATAAATAAGGCTCCTTTAAATAGAAGCTCA
1 TCCTCTAAACAGAGGCTCAATGAC-TTTAAAAAAAATAAATAAGGCTCCTCTAAATAGAAGCTCA
16377548 ACAACTTTTAAAAAATAAATAAGG
65 A-AACTTTTAAAAAATAAATAAGG
* * *
16377572 TTCCTCTAAGCAGAAGCTCAATGACTTAAAAAAAAATAAA
1 -TCCTCTAAACAGAGGCTCAATGACTTTAAAAAAAATAAA
16377612 GCTCCTCGAC
Statistics
Matches: 169, Mismatches: 36, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
85 56 0.33
86 12 0.07
88 16 0.09
89 20 0.12
90 64 0.38
91 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (87 bp):
TCCTCTAAACAGAGGCTCAATGACTTTAAAAAAAATAAATAAGGCTCCTCTAAATAGAAGCTCAA
AACTTTTAAAAAATAAATAAGG
Found at i:16377580 original size:134 final size:126
Alignment explanation
Indices: 16377339--16377618 Score: 299
Period size: 134 Copynumber: 2.2 Consensus size: 126
16377329 TGACTTTGAA
* **
16377339 AAAAATAAATAAGGCTCCTCTAAACAGAGACTCAATGACTTCTAAAAAATAAATAAGGCTTTAAA
1 AAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACAACTTCTAAAAAATAAATAAGGCTTTAAA
* ** * * *
16377404 TAGAGGCTCAATGACTTTGGAAAAATAAATAAGACGCATCTAAATAGAGGCTCAAAGACTTTT
66 TAGAAGCTCAACAACTTTGAAAAAATAAATAAGACGCATCTAAACAGAAGCTCAAAGAC--TT
* * * *
16377467 GAAAAATAAATAAAGCTCTTCTAAACAGAGGCTTAACAACTTTTAAAAAAAATAAATAAGGCTCC
1 -AAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACAACTTCT--AAAAAATAAATAAGG---C
* *** * * *
16377532 TTTAAATAGAAGCTCAACAACTTTTAAAAAATAAATAAGGTTCCTCTAAGCAGAAGCTCAATGAC
60 TTTAAATAGAAGCTCAACAACTTTGAAAAAATAAATAAGACGCATCTAAACAGAAGCTCAAAGAC
16377597 TT
125 TT
*
16377599 AAAAAAAAATAAAGCTCCTC
1 AAAAATAAATAAAGCTCCTC
16377619 GACAATCATG
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
129 36 0.29
131 33 0.27
132 2 0.02
134 53 0.43
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (126 bp):
AAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACAACTTCTAAAAAATAAATAAGGCTTTAAA
TAGAAGCTCAACAACTTTGAAAAAATAAATAAGACGCATCTAAACAGAAGCTCAAAGACTT
Found at i:16387661 original size:20 final size:21
Alignment explanation
Indices: 16387624--16387663 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16387614 AATTGAAAAT
**
16387624 AAATATTTATCATTATTATTG
1 AAATATTTATCAAAATTATTG
16387645 AAAT-TTTATCAAAATTATT
1 AAATATTTATCAAAATTATT
16387664 CCACCATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
AAATATTTATCAAAATTATTG
Found at i:16387716 original size:26 final size:24
Alignment explanation
Indices: 16387678--16387742 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 24
16387668 CATTTGAGAT
16387678 AAATTTTGA-AAAAATTTCTCACCTAG
1 AAATTTT-ATAAAAATTTC-CA-CTAG
* *
16387704 AAATTTTATAAAAATTTCCATTTG
1 AAATTTTATAAAAATTTCCACTAG
16387728 AAATTTT-TAAAAATT
1 AAATTTTATAAAAATT
16387743 CCATCATTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 8 0.22
24 9 0.25
25 3 0.08
26 16 0.44
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.42
Consensus pattern (24 bp):
AAATTTTATAAAAATTTCCACTAG
Found at i:16387757 original size:25 final size:24
Alignment explanation
Indices: 16387703--16387746 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
16387693 TTCTCACCTA
16387703 GAAATTTTATAAAAATTTCCATTT
1 GAAATTTTATAAAAATTTCCATTT
16387727 GAAATTTT-TAAAAA-TTCCAT
1 GAAATTTTATAAAAATTTCCAT
16387747 CATTGGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (24 bp):
GAAATTTTATAAAAATTTCCATTT
Found at i:16389119 original size:15 final size:16
Alignment explanation
Indices: 16389099--16389134 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
16389089 TTCCAATAAT
*
16389099 ATTTACTTTTCTTAC-
1 ATTTACTTTTCATACA
16389114 ATTTACTTTTCATACA
1 ATTTACTTTTCATACA
16389130 ATTTA
1 ATTTA
16389135 AGATTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTACTTTTCATACA
Found at i:16391801 original size:3 final size:3
Alignment explanation
Indices: 16391793--16391833 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
16391783 ATTTATCTTC
16391793 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16391834 TCGTTATTAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16391843 original size:3 final size:3
Alignment explanation
Indices: 16391837--16391862 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16391827 AATAATATCG
16391837 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
16391863 GAATTTCTAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16396998 original size:21 final size:21
Alignment explanation
Indices: 16396973--16397021 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
16396963 GTGTTTGTAC
*
16396973 TAAAATTGCCAAATTTTACTA
1 TAAAATCGCCAAATTTTACTA
16396994 TAAAATCGCCAAATTTTACTA
1 TAAAATCGCCAAATTTTACTA
16397015 TAAAATC
1 TAAAATC
16397022 TTGGATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (21 bp):
TAAAATCGCCAAATTTTACTA
Found at i:16402214 original size:23 final size:23
Alignment explanation
Indices: 16402180--16402237 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
16402170 ATTCAACTTA
*
16402180 CCTTATTTTTTTAGCAATTTTTTCT
1 CCTT-TTTTTTTAGC-ATTTTGTCT
* *
16402205 -CTTTTTTTTTATCGTTTTGTCT
1 CCTTTTTTTTTAGCATTTTGTCT
16402227 CCTTTTTTTTT
1 CCTTTTTTTTT
16402238 TCAATCTCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
23 19 0.66
24 3 0.10
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.71
Consensus pattern (23 bp):
CCTTTTTTTTTAGCATTTTGTCT
Found at i:16402893 original size:24 final size:25
Alignment explanation
Indices: 16402866--16402912 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
16402856 AAATTCACCA
16402866 AAAATC-ATGAAA-TATTATGAAATT
1 AAAATCTA-GAAAGTATTATGAAATT
*
16402890 AAAATCTAGAAAGTTTTATGAAA
1 AAAATCTAGAAAGTATTATGAAA
16402913 ATCCAAGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (25 bp):
AAAATCTAGAAAGTATTATGAAATT
Found at i:16402922 original size:144 final size:145
Alignment explanation
Indices: 16402562--16402973 Score: 499
Period size: 144 Copynumber: 2.9 Consensus size: 145
16402552 TCATTTTTGG
* * * *
16402562 GATTTTAAAAT-ACAAAAAATCATGAAATATTATAAAATTGAGAT-TTGAAAAGTTTCATAAAAA
1 GATTTTAAATTCACAAAAAATCATGAAATATTATGAAATTGAGATCTAG-AAAGTTTCATGAAAA
* * * * *
16402625 TCTAAGCTC-AATAAGGTCAAATTACGAAAATACCTTTGTAGGGGTATTTTGCTAATTTCATACT
65 TCTAAGCTCGAA-AAGGTCAAATTACGAAAATACCTTTATAGGGGTATTTTGGTAATTTTACACA
16402689 TCCTAGGGTACTACTAT
129 TCCTAGGGTACTACTAT
* * * * * *
16402706 GATTTCAAATGCATAAAATATCATGAAATATTATGAAATTGAGATCTAAAAAGTTTCGTGAAAAT
1 GATTTTAAATTCACAAAAAATCATGAAATATTATGAAATTGAGATCTAGAAAGTTTCATGAAAAT
* * **
16402771 ATGAGCTCGGGAAGGTCAAATTACGAAAATACCTTTATAGGGGTATTTTGGTAATTTTACACATC
66 CTAAGCTCGAAAAGGTCAAATTACGAAAATACCTTTATAGGGGTATTTTGGTAATTTTACACATC
* * *
16402836 TTA-GGTATTGCTAT
131 CTAGGGTACTACTAT
* * * *
16402850 GATTTTAAATTCACCAAAAATCATGAAATATTATGAAATTAAAATCTAGAAAGTTTTATGAAAAT
1 GATTTTAAATTCACAAAAAATCATGAAATATTATGAAATTGAGATCTAGAAAGTTTCATGAAAAT
* * * * *
16402915 CCAAGCTCGAAAAGGTCAAATTACGAAAAGACCCTTATAAGGGTATTTTAGTAATTTTA
66 CTAAGCTCGAAAAGGTCAAATTACGAAAATACCTTTATAGGGGTATTTTGGTAATTTTA
16402974 TACTTTTCTA
Statistics
Matches: 224, Mismatches: 41, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
144 122 0.54
145 101 0.45
146 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (145 bp):
GATTTTAAATTCACAAAAAATCATGAAATATTATGAAATTGAGATCTAGAAAGTTTCATGAAAAT
CTAAGCTCGAAAAGGTCAAATTACGAAAATACCTTTATAGGGGTATTTTGGTAATTTTACACATC
CTAGGGTACTACTAT
Found at i:16403686 original size:35 final size:35
Alignment explanation
Indices: 16403636--16403725 Score: 90
Period size: 37 Copynumber: 2.5 Consensus size: 35
16403626 ATAAAATATT
* * * * **
16403636 ATTTGAAACTTGCTCCTTAAGCAGAGGTTTTGAAA
1 ATTTGAAAATGGCTCCCTAAACAGAGACTTTGAAA
16403671 ATTTGAAAATGGCTCCCCCTAAACAGAGACTTTGAAA
1 ATTTGAAAATGGCT--CCCTAAACAGAGACTTTGAAA
* *
16403708 GTTTGAAAATGACTCCCT
1 ATTTGAAAATGGCTCCCT
16403726 CCAAATAGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 16 0.36
37 29 0.64
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (35 bp):
ATTTGAAAATGGCTCCCTAAACAGAGACTTTGAAA
Found at i:16404143 original size:41 final size:40
Alignment explanation
Indices: 16404053--16404164 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 40
16404043 CCTATGGTGC
* *
16404053 AAATGCAAATGTC-TTTTATAAATGTAA-ATGCAAGTGATGC
1 AAATGCAAATGTCTTTTTAT-GATG-AAGATGCAAGTGATGA
*
16404093 AAATACAAATGTCTTTCTTATGATGAAGATGCAAGTGATGA
1 AAATGCAAATGTCTTT-TTATGATGAAGATGCAAGTGATGA
*
16404134 AAATGCAAATGTCTTTTTTATGATGTAGATG
1 AAATGCAAATGTC-TTTTTATGATGAAGATG
16404165 TGAATGTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
40 14 0.22
41 42 0.67
42 7 0.11
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.35
Consensus pattern (40 bp):
AAATGCAAATGTCTTTTTATGATGAAGATGCAAGTGATGA
Found at i:16406774 original size:20 final size:19
Alignment explanation
Indices: 16406751--16406797 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
16406741 AGTTTTATTC
*
16406751 AATTTTGACTTTGTTTGACT
1 AATTTTGACTTT-ATTGACT
*
16406771 AATTTTAACTTTATTGACT
1 AATTTTGACTTTATTGACT
*
16406790 AAGTTTGA
1 AATTTTGA
16406798 TCGGATTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51
Consensus pattern (19 bp):
AATTTTGACTTTATTGACT
Found at i:16406789 original size:19 final size:20
Alignment explanation
Indices: 16406751--16406791 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16406741 AGTTTTATTC
* *
16406751 AATTTTGACTTTGTTTGACT
1 AATTTTAACTTTGATTGACT
16406771 AATTTTAACTTT-ATTGACT
1 AATTTTAACTTTGATTGACT
16406790 AA
1 AA
16406792 GTTTGATCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (20 bp):
AATTTTAACTTTGATTGACT
Found at i:16411713 original size:20 final size:20
Alignment explanation
Indices: 16411667--16411713 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16411657 AAAACTAAAA
16411667 AAAT-AATAATAAAAGAAAT
1 AAATGAATAATAAAAGAAAT
* *
16411686 AAAAGAATAAT-AAAGACAT
1 AAATGAATAATAAAAGAAAT
16411705 GAAATGAAT
1 -AAATGAAT
16411714 TTACTTGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (20 bp):
AAATGAATAATAAAAGAAAT
Found at i:16412186 original size:27 final size:27
Alignment explanation
Indices: 16412155--16412221 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
16412145 TTTTGATTTG
*
16412155 AATTTAAATAATTATCCAAATATATTA
1 AATTTAAATAATTATCCAAACATATTA
* *
16412182 AATTTACATAATTATCCAAACATTTTA
1 AATTTAAATAATTATCCAAACATATTA
16412209 AATTTAAATAATT
1 AATTTAAATAATT
16412222 TATTAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTTAAATAATTATCCAAACATATTA
Found at i:16423325 original size:2 final size:2
Alignment explanation
Indices: 16423320--16423351 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16423310 TTACCCTGAG
16423320 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16423352 TTGTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:16424279 original size:10 final size:10
Alignment explanation
Indices: 16424245--16424279 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
16424235 ATTATCTCTC
16424245 TTTTTCTTTT
1 TTTTTCTTTT
* *
16424255 TTTTTGTTGT
1 TTTTTCTTTT
16424265 TTTTTCTTTT
1 TTTTTCTTTT
16424275 TTTTT
1 TTTTT
16424280 TAATTAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:16424501 original size:13 final size:15
Alignment explanation
Indices: 16424474--16424506 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
16424464 CTTCCATATG
16424474 GTTTTTTTCTCTTTT
1 GTTTTTTTCTCTTTT
16424489 GTTTTTTT-T-TTTT
1 GTTTTTTTCTCTTTT
16424502 GTTTT
1 GTTTT
16424507 GGTATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 1 0.06
15 8 0.44
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (15 bp):
GTTTTTTTCTCTTTT
Found at i:16424924 original size:14 final size:15
Alignment explanation
Indices: 16424892--16424924 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16424882 TTTTTTACTT
*
16424892 TTTTATGATTTTTTG
1 TTTTATGATTTTTTA
16424907 TTTTATGA-TTTTTA
1 TTTTATGATTTTTTA
16424921 TTTT
1 TTTT
16424925 TTAGATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (15 bp):
TTTTATGATTTTTTA
Found at i:16424925 original size:15 final size:14
Alignment explanation
Indices: 16424890--16424925 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
16424880 ACTTTTTTAC
16424890 TTTTTTATGATTTT
1 TTTTTTATGATTTT
16424904 TTGTTTTATGATTTT
1 TT-TTTTATGATTTT
16424919 TATTTTT
1 T-TTTTT
16424926 TAGATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 17 0.85
16 1 0.05
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTTTTATGATTTT
Found at i:16425331 original size:20 final size:21
Alignment explanation
Indices: 16425294--16425335 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
16425284 CTATTAATTG
16425294 TTATTTATTTAAAATAAAATA
1 TTATTTATTTAAAATAAAATA
* *
16425315 TTATTT-TTTAGATTAAAATA
1 TTATTTATTTAAAATAAAATA
16425335 T
1 T
16425336 GTTACATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATTTATTTAAAATAAAATA
Found at i:16433206 original size:65 final size:68
Alignment explanation
Indices: 16433102--16433235 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 68
16433092 AGAATACCAA
* *
16433102 TAAAAAATATTTCAAAAAGATATTTTAAGGAAAAGTTGAAA-TATCTA-TTTTCTTTGAATAAAA
1 TAAAAAATATTTCAAAAAGATATTTTAAGGAAAAGTTGAAACTATCAATTTTTC-TTAAATAAAA
16433165 AAAT
65 AAAT
*
16433169 TAAAAAA-ATTTTAAAAA-A-AGTTTTAAGGAATAA-TTGAAACTATCAATTTTTCTTAAATAAA
1 TAAAAAATATTTCAAAAAGATA-TTTTAAGGAA-AAGTTGAAACTATCAATTTTTCTTAAATAAA
16433230 AAAAT
64 AAAAT
16433235 T
1 T
16433236 TCTTAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
64 1 0.02
65 17 0.28
66 30 0.50
67 12 0.20
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.36
Consensus pattern (68 bp):
TAAAAAATATTTCAAAAAGATATTTTAAGGAAAAGTTGAAACTATCAATTTTTCTTAAATAAAAA
AAT
Found at i:16433278 original size:61 final size:59
Alignment explanation
Indices: 16433169--16433355 Score: 211
Period size: 63 Copynumber: 3.1 Consensus size: 59
16433159 ATAAAAAAAT
* * *
16433169 TAAAAAAA-TTTTAAAAAAA-GTTTTAAGGAATAA-TTGAAACTATCAATTTTTCTTAAA
1 TAAAAAAATTTTTAAAAAAAGGTTTTAAAGAA-AAGTTGAAAGTATTAATTTTTCTTAAA
* *
16433226 TAAAAAAATTTCTTAAAAAAAGGGTTTTAAAGAAAAGTCGAAAGTATTAATTTTTTTTAAA
1 TAAAAAAATTT-TTAAAAAAA-GGTTTTAAAGAAAAGTTGAAAGTATTAATTTTTCTTAAA
* *
16433287 TAAAAAAATAATATTTCAAAAAAAGGTTTTACAA-AAATGTTGAAAGTATTAATTTTCCTTAAA
1 TAAAAAAAT--T-TTT-AAAAAAAGGTTTTA-AAGAAAAGTTGAAAGTATTAATTTTTCTTAAA
16433350 TAAAAA
1 TAAAAA
16433356 GCTTCCCAAT
Statistics
Matches: 111, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
57 8 0.07
58 2 0.02
59 9 0.08
60 2 0.02
61 39 0.35
63 41 0.37
64 10 0.09
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (59 bp):
TAAAAAAATTTTTAAAAAAAGGTTTTAAAGAAAAGTTGAAAGTATTAATTTTTCTTAAA
Found at i:16437806 original size:10 final size:9
Alignment explanation
Indices: 16437791--16437831 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
16437781 GTTGCAATAA
16437791 AAAAAAAAG
1 AAAAAAAAG
16437800 AACAAAAAAG
1 AA-AAAAAAG
16437810 -AAAAAAAG
1 AAAAAAAAG
16437818 AAAAAAAAAG
1 -AAAAAAAAG
16437828 AAAA
1 AAAA
16437832 GATATGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.24
9 7 0.24
10 15 0.52
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:16437813 original size:15 final size:15
Alignment explanation
Indices: 16437790--16437833 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
16437780 AGTTGCAATA
*
16437790 AAAAAAAAAGAACA-
1 AAAAAAAAAGAAAAG
*
16437804 AAAAAGAAA-AAAAG
1 AAAAAAAAAGAAAAG
16437818 AAAAAAAAAGAAAAG
1 AAAAAAAAAGAAAAG
16437833 A
1 A
16437834 TATGATTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.64
15 6 0.24
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:16437814 original size:8 final size:8
Alignment explanation
Indices: 16437792--16437833 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
16437782 TTGCAATAAA
16437792 AAAAAAAG
1 AAAAAAAG
16437800 AACAAAAAAG
1 -A-AAAAAAG
16437810 AAAAAAAG
1 AAAAAAAG
16437818 AAAAAAA-
1 AAAAAAAG
*
16437825 AAGAAAAG
1 AAAAAAAG
16437833 A
1 A
16437834 TATGATTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 6 0.20
8 15 0.50
9 2 0.07
10 7 0.23
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:16437815 original size:18 final size:18
Alignment explanation
Indices: 16437792--16437831 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
16437782 TTGCAATAAA
*
16437792 AAAAAAAGAACAAAAAAG
1 AAAAAAAGAAAAAAAAAG
16437810 AAAAAAAGAAAAAAAAAG
1 AAAAAAAGAAAAAAAAAG
16437828 AAAA
1 AAAA
16437832 GATATGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.88, C:0.03, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAAAG
Found at i:16438948 original size:141 final size:140
Alignment explanation
Indices: 16438674--16438960 Score: 538
Period size: 141 Copynumber: 2.0 Consensus size: 140
16438664 ACCTTCTCTT
16438674 TATTTCCCAAAGTTCGAAGCCTTGCATGACTAGTCTTGACATTTATTAAATTAATATATATCAAG
1 TATTTCCCAAAGTTCGAAGCCTTGCATGACTAGTCTTGACATTTATTAAATTAATATATATCAAG
*
16438739 ACTTAAAAGAGTTCTAAAATAGATTGTACTTTAAAAGATCATCTTTGTTGGTAGGCCTAAATGAA
66 ACTTAAAAGAGTGCTAAAATAGATTGTACTTTAAAAGATCATCTTTGTTGGTAGGCCTAAATGAA
16438804 GAGACATTGA
131 GAGACATTGA
16438814 TATTTCCCAAAGTTCGAAGCCTTGCATGACTAGTCTTGACATTTATTAAATTAATATATATCAAG
1 TATTTCCCAAAGTTCGAAGCCTTGCATGACTAGTCTTGACATTTATTAAATTAATATATATCAAG
* *
16438879 AACTTAAAAGAGTGCTAAACTAGATTGTACTTTAAAAGATCATCTTTGTTGGTGGGCCTAAATGA
66 -ACTTAAAAGAGTGCTAAAATAGATTGTACTTTAAAAGATCATCTTTGTTGGTAGGCCTAAATGA
16438944 AGAGACATTGA
130 AGAGACATTGA
16438955 TATTTC
1 TATTTC
16438961 TTTTCTTGTT
Statistics
Matches: 143, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
140 65 0.45
141 78 0.55
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (140 bp):
TATTTCCCAAAGTTCGAAGCCTTGCATGACTAGTCTTGACATTTATTAAATTAATATATATCAAG
ACTTAAAAGAGTGCTAAAATAGATTGTACTTTAAAAGATCATCTTTGTTGGTAGGCCTAAATGAA
GAGACATTGA
Found at i:16439813 original size:22 final size:23
Alignment explanation
Indices: 16439788--16439847 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
16439778 CATAATCACC
*
16439788 AAGTCCTCCGGGCATGATTTAT-
1 AAGTCCTCCGAGCATGATTTATA
* *
16439810 AAGTTCTCTGAGCATGATTTATA
1 AAGTCCTCCGAGCATGATTTATA
*
16439833 AAGTCCTTCGAGCAT
1 AAGTCCTCCGAGCAT
16439848 AATCACCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 19 0.61
23 12 0.39
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (23 bp):
AAGTCCTCCGAGCATGATTTATA
Found at i:16442485 original size:68 final size:66
Alignment explanation
Indices: 16442363--16442497 Score: 166
Period size: 68 Copynumber: 2.0 Consensus size: 66
16442353 TTAGAATACC
* * * *
16442363 AATAAAAAATGTTTCAAAAAAATATTTTTAGGAAAAGTTAAAATATCATTTTTTTCTTAAATAAA
1 AATAAAAAA-GTTTCAAAAAAAAATTTTAAGGAAAAATTAAAATATCATATTTTTCTTAAATAAA
16442428 AA
65 AA
*
16442430 AATAAAAAA-TTTCAAAAAAAAAGGGTTTTAAGGAAAAATTGAAAGTATCA-ATTTTTCTTAAAT
1 AATAAAAAAGTTTCAAAAAAAAA---TTTTAAGGAAAAATT-AAAATATCATATTTTTCTTAAAT
16442493 AAAAA
62 AAAAA
16442498 TCTTTCCAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
65 12 0.20
67 9 0.15
68 30 0.51
69 8 0.14
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (66 bp):
AATAAAAAAGTTTCAAAAAAAAATTTTAAGGAAAAATTAAAATATCATATTTTTCTTAAATAAAA
A
Found at i:16460236 original size:24 final size:25
Alignment explanation
Indices: 16460209--16460255 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
16460199 CATGAGATTC
16460209 AAGATATTCCATAAGAAG-TTCTAT
1 AAGATATTCCATAAGAAGATTCTAT
*
16460233 AAGATATTCCCTAAGAAGATTCT
1 AAGATATTCCATAAGAAGATTCT
16460256 TCTAGTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (25 bp):
AAGATATTCCATAAGAAGATTCTAT
Found at i:16462928 original size:30 final size:30
Alignment explanation
Indices: 16462894--16462953 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
16462884 GCAACATAAC
*
16462894 AATTTAGCAACAACTTTTCACTAGCAAATT
1 AATTTAGCAACAACTTTGCACTAGCAAATT
* *
16462924 AATTTAGCAATAGCTTTGCACTAGCAAATT
1 AATTTAGCAACAACTTTGCACTAGCAAATT
16462954 TTCATAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (30 bp):
AATTTAGCAACAACTTTGCACTAGCAAATT
Found at i:16470278 original size:13 final size:13
Alignment explanation
Indices: 16470260--16470302 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
16470250 GTTTCTAATT
*
16470260 TAAAGTAATTAAA
1 TAAAGTAATAAAA
16470273 TAAAGTAAATAAAA
1 TAAAGT-AATAAAA
16470287 TAAA-TAATAAAA
1 TAAAGTAATAAAA
16470299 TAAA
1 TAAA
16470303 ATTGGTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 11 0.39
13 7 0.25
14 10 0.36
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
TAAAGTAATAAAA
Found at i:16478187 original size:18 final size:17
Alignment explanation
Indices: 16478159--16478202 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
16478149 TTTGTTAAAA
16478159 AATTTTT-AGTAATATTT
1 AATTTTTAAGTAA-ATTT
*
16478176 TATTTTTAAGTAAATTT
1 AATTTTTAAGTAAATTT
16478193 AATATTTTAA
1 AAT-TTTTAA
16478203 TATGTTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
AATTTTTAAGTAAATTT
Found at i:16483389 original size:3 final size:3
Alignment explanation
Indices: 16483381--16483409 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16483371 GTTGCTCTCC
16483381 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16483410 GATTTAGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16485932 original size:16 final size:16
Alignment explanation
Indices: 16485911--16485948 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16485901 CAATATATAC
*
16485911 ATGTATATATACGTAT
1 ATGTATATATACATAT
*
16485927 ATGTATATATATATAT
1 ATGTATATATACATAT
16485943 ATGTAT
1 ATGTAT
16485949 TTGTATGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (16 bp):
ATGTATATATACATAT
Found at i:16487881 original size:195 final size:194
Alignment explanation
Indices: 16487550--16487941 Score: 757
Period size: 195 Copynumber: 2.0 Consensus size: 194
16487540 GTTTCAATTA
16487550 GGTTTAGGAAAATGAATATTGAGATTTCTCCATCTATTGACTTTTTTTTTTTCTCTCCCCTAATT
1 GGTTTAGGAAAATGAATATTGAGATTTCTCCATCTATTGACTTTTTTTTTTTCTCTCCCCTAATT
*
16487615 CTTCAATTCATCTCCCTATGTCATCTGTTTCTCCCTAATTGTTCTGCAGATCTCTGATTTTCCCT
66 CTTCAATTCATCTCCCTATGTCATCTGTTTCTCCCTAATTCTTCTGCAGATCTCTGATTTTCCCT
16487680 CTAAATTACTGTTTATATATCTACATCACCATGGCATCCTATCTACAACTATTTAATAATAAGT
131 CTAAATTACTGTTTATATATCTACATCACCATGGCATCCTATCTACAACTATTTAATAATAAGT
*
16487744 GGTTTAGGAAGATGAATATTGAGATTTCTCCATCTATTGACTTTTTTTTTTCTCTCTCCCCTAAT
1 GGTTTAGGAAAATGAATATTGAGATTTCTCCATCTATTGACTTTTTTTTTT-TCTCTCCCCTAAT
16487809 TCTTCAATTCATCTCCCTATGTCATCTGTTTCTCCCTAATTCTTCTGCAGATCTCTGATTTTCCC
65 TCTTCAATTCATCTCCCTATGTCATCTGTTTCTCCCTAATTCTTCTGCAGATCTCTGATTTTCCC
16487874 TCTAAATTACTGTTTATATATCTACATCACCATGGCATCCTATCTACAACTATTTAATAATAAGT
130 TCTAAATTACTGTTTATATATCTACATCACCATGGCATCCTATCTACAACTATTTAATAATAAGT
16487939 GGT
1 GGT
16487942 GGGACCAACA
Statistics
Matches: 195, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
194 50 0.26
195 145 0.74
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (194 bp):
GGTTTAGGAAAATGAATATTGAGATTTCTCCATCTATTGACTTTTTTTTTTTCTCTCCCCTAATT
CTTCAATTCATCTCCCTATGTCATCTGTTTCTCCCTAATTCTTCTGCAGATCTCTGATTTTCCCT
CTAAATTACTGTTTATATATCTACATCACCATGGCATCCTATCTACAACTATTTAATAATAAGT
Found at i:16497703 original size:17 final size:18
Alignment explanation
Indices: 16497670--16497704 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16497660 AACCAACACC
*
16497670 AATTTATTTGTAAAAGAT
1 AATTTAATTGTAAAAGAT
16497688 AATTTAATTG-AAAAGAT
1 AATTTAATTGTAAAAGAT
16497705 TAAAATGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (18 bp):
AATTTAATTGTAAAAGAT
Found at i:16498282 original size:19 final size:18
Alignment explanation
Indices: 16498246--16498284 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
16498236 TGTTGTTCTA
* *
16498246 AAAATAAAAAACTTAACT
1 AAAATAAAAAAATCAACT
16498264 AAAATAAATAAAATCAACT
1 AAAATAAA-AAAATCAACT
16498283 AA
1 AA
16498285 TTAAGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAAAAAAATCAACT
Found at i:16500215 original size:22 final size:22
Alignment explanation
Indices: 16500181--16500222 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16500171 GGCTTGAAGG
*
16500181 ATCTGATTGGATGTTTTAGAAA
1 ATCTGATTAGATGTTTTAGAAA
*
16500203 ATCTGGTTAGATGTTTTAGA
1 ATCTGATTAGATGTTTTAGA
16500223 CATGAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.43
Consensus pattern (22 bp):
ATCTGATTAGATGTTTTAGAAA
Found at i:16503156 original size:34 final size:34
Alignment explanation
Indices: 16503092--16503157 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
16503082 TGCATTTCTA
*
16503092 GTACAGTGAAAAAGTTTTCGAAAATGAATTTTCG
1 GTACAGTGAAAAAGTTTTAGAAAATGAATTTTCG
* *
16503126 GTACATTGAAAAAGTTTTTAG-AAATTAATTTT
1 GTACAGTGAAAAAG-TTTTAGAAAATGAATTTT
16503158 TGATAACTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 23 0.82
35 5 0.18
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (34 bp):
GTACAGTGAAAAAGTTTTAGAAAATGAATTTTCG
Found at i:16504242 original size:14 final size:15
Alignment explanation
Indices: 16504223--16504251 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16504213 AAAATATTTA
16504223 AATTTTT-TATTTTT
1 AATTTTTATATTTTT
16504237 AATTTTTATATTTTT
1 AATTTTTATATTTTT
16504252 TATAAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
AATTTTTATATTTTT
Found at i:16504560 original size:19 final size:20
Alignment explanation
Indices: 16504519--16504561 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
16504509 AAATAATGTG
* **
16504519 TAAATTTTTTTTAAAATTTA
1 TAAATTCTTTTTAAAATACA
16504539 TAAATTCTTTTTAAAA-ACA
1 TAAATTCTTTTTAAAATACA
16504558 TAAA
1 TAAA
16504562 AAATATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATTCTTTTTAAAATACA
Found at i:16506481 original size:55 final size:53
Alignment explanation
Indices: 16506401--16506547 Score: 177
Period size: 55 Copynumber: 2.7 Consensus size: 53
16506391 ACAACTTCGG
* * *
16506401 GAAAAATTTATATTTCAACTTTTTCCTTAATTTTCAAAACATTTTTTATTTCAAA
1 GAAAGATTGATATTTCAACTTTTTCCTTAATTTTCAAAACA--ATTTATTTCAAA
* * * *
16506456 GAAGGATTGATATTTCGACTCTTTCCTTAATTTTCAAAACAATTTATTTCAAG
1 GAAAGATTGATATTTCAACTTTTTCCTTAATTTTCAAAACAATTTATTTCAAA
* * *
16506509 GAAAGATTGATGTTTCAACTTTTTCATGACATTTTCAAA
1 GAAAGATTGATATTTCAACTTTTTCCTTA-ATTTTCAAA
16506548 TTTTATTTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 33 0.42
54 9 0.12
55 36 0.46
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (53 bp):
GAAAGATTGATATTTCAACTTTTTCCTTAATTTTCAAAACAATTTATTTCAAA
Found at i:16510416 original size:33 final size:33
Alignment explanation
Indices: 16510377--16510548 Score: 150
Period size: 33 Copynumber: 5.0 Consensus size: 33
16510367 ACATGGAAAT
16510377 CATGCAAACATAAATCAATCTTTAAACTTTAGAA
1 CATGCAAACATAAATCAATCTTTAAACTTTA-AA
* **
16510411 -ATGCAAACGTAAATCAATCTTTAAAGCAATAAA
1 CATGCAAACATAAATCAATCTTTAAA-CTTTAAA
* * * * ** **
16510444 TCATGCAACTCTACTAATTAAAACCCTAAACATGCAAA
1 -CATGCAA-AC-A-TAAATCAATCTTTAAAC-TTTAAA
16510482 TCATGCAAACATAAATCAATCTTTAAACTTTAGAA
1 -CATGCAAACATAAATCAATCTTTAAACTTTA-AA
16510517 -ATGCAAACATAAATCAATCTTTAAACTTTAAA
1 CATGCAAACATAAATCAATCTTTAAACTTTAAA
16510549 ACAATAACCG
Statistics
Matches: 109, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
32 2 0.02
33 56 0.51
34 5 0.05
35 20 0.18
36 2 0.02
37 2 0.02
38 22 0.20
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.28
Consensus pattern (33 bp):
CATGCAAACATAAATCAATCTTTAAACTTTAAA
Found at i:16510450 original size:106 final size:106
Alignment explanation
Indices: 16510320--16510541 Score: 390
Period size: 106 Copynumber: 2.1 Consensus size: 106
16510310 ATGTAAACCA
* * * *
16510320 AATCTTTCATGCAATAAATCATGCAACTCAACTAATTAAAACCTTAAACATGGAAATCATGCAAA
1 AATCTTTAAAGCAATAAATCATGCAACTCAACTAATTAAAACCCTAAACATGCAAATCATGCAAA
*
16510385 CATAAATCAATCTTTAAACTTTAGAAATGCAAACGTAAATC
66 CATAAATCAATCTTTAAACTTTAGAAATGCAAACATAAATC
*
16510426 AATCTTTAAAGCAATAAATCATGCAACTCTACTAATTAAAACCCTAAACATGCAAATCATGCAAA
1 AATCTTTAAAGCAATAAATCATGCAACTCAACTAATTAAAACCCTAAACATGCAAATCATGCAAA
16510491 CATAAATCAATCTTTAAACTTTAGAAATGCAAACATAAATC
66 CATAAATCAATCTTTAAACTTTAGAAATGCAAACATAAATC
16510532 AATCTTTAAA
1 AATCTTTAAA
16510542 CTTTAAAACA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 110 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.27
Consensus pattern (106 bp):
AATCTTTAAAGCAATAAATCATGCAACTCAACTAATTAAAACCCTAAACATGCAAATCATGCAAA
CATAAATCAATCTTTAAACTTTAGAAATGCAAACATAAATC
Found at i:16514716 original size:16 final size:18
Alignment explanation
Indices: 16514687--16514724 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
16514677 GTTACTCTAG
16514687 TTTTATTTTAAAAT-ACA
1 TTTTATTTTAAAATAACA
*
16514704 TTTT-TTTTGAAATAACA
1 TTTTATTTTAAAATAACA
16514721 TTTT
1 TTTT
16514725 CCATAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTATTTTAAAATAACA
Found at i:16517645 original size:14 final size:15
Alignment explanation
Indices: 16517615--16517647 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16517605 TTACACAAGG
16517615 CTAAGAAAATAAAAC
1 CTAAGAAAATAAAAC
*
16517630 CTAAGAAAGT-AAAC
1 CTAAGAAAATAAAAC
16517644 CTAA
1 CTAA
16517648 ACTAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.61, C:0.15, G:0.09, T:0.15
Consensus pattern (15 bp):
CTAAGAAAATAAAAC
Found at i:16532780 original size:33 final size:32
Alignment explanation
Indices: 16532743--16533137 Score: 190
Period size: 33 Copynumber: 12.4 Consensus size: 32
16532733 TAGGTGTTAG
*
16532743 CTAAACTAGGCTTAAATCTCGTTTAGGTGCCAA
1 CTAAACTAGGCTTAAATCTCATTT-GGTGCCAA
** * * * * *
16532776 CTAAACGGGGCATAACTCTCATCTGGGTGCTAG
1 CTAAACTAGGCTTAAATCTCAT-TTGGTGCCAA
* *
16532809 CTAAACTAGGCTTAAAGCTTATTTGTGTGCCAA
1 CTAAACTAGGCTTAAATCTCATTTG-GTGCCAA
* * * *
16532842 CTAAACTAGGCTTAACTCTTATCTGGGTGCCGA
1 CTAAACTAGGCTTAAATCTCAT-TTGGTGCCAA
*
16532875 CTAAACT-GAGCTTAAATCTCATTT-GT---AG
1 CTAAACTAG-GCTTAAATCTCATTTGGTGCCAA
* *
16532903 CTAAACTAGGCTTAAATCTCATCT-GT---AG
1 CTAAACTAGGCTTAAATCTCATTTGGTGCCAA
* *
16532931 CTAAATTAGGCTTAAATCTCATATGG-GCACCAA
1 CTAAACTAGGCTTAAATCTCATTTGGTG--CCAA
* ** * * *
16532964 CTAAACT-GAGCTTAAATATCATAAGATGCTAG
1 CTAAACTAG-GCTTAAATCTCATTTGGTGCCAA
* * *
16532996 CTAAACT-GAGCTTAAATATCATTTAAGTGCCAG
1 CTAAACTAG-GCTTAAATCTCATTT-GGTGCCAA
* * * * *
16533029 CTAAA-TTGGATTTAAATCTC-TTAGGGTGCTAG
1 CTAAACTAGG-CTTAAATCTCATT-TGGTGCCAA
* * * * *
16533061 CTAAATTAGACTTAACTTTCATCTAGGTGCCAA
1 CTAAACTAGGCTTAAATCTCAT-TTGGTGCCAA
* * *
16533094 CTAAATTGGGCTTAAATCTCA-ATGGTGCCAA
1 CTAAACTAGGCTTAAATCTCATTTGGTGCCAA
*
16533125 CCAAACTAGGCTT
1 CTAAACTAGGCTT
16533138 TTTCTCTTTT
Statistics
Matches: 279, Mismatches: 63, Indels: 42
0.73 0.16 0.11
Matches are distributed among these distances:
28 47 0.17
29 2 0.01
31 20 0.07
32 51 0.18
33 154 0.55
34 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (32 bp):
CTAAACTAGGCTTAAATCTCATTTGGTGCCAA
Found at i:16532906 original size:28 final size:28
Alignment explanation
Indices: 16532875--16532952 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
16532865 TGGGTGCCGA
*
16532875 CTAAACT-GAGCTTAAATCTCATTTGTAG
1 CTAAACTAG-GCTTAAATCTCATCTGTAG
16532903 CTAAACTAGGCTTAAATCTCATCTGTAG
1 CTAAACTAGGCTTAAATCTCATCTGTAG
*
16532931 CTAAATTAGGCTTAAATCTCAT
1 CTAAACTAGGCTTAAATCTCAT
16532953 ATGGGCACCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 46 0.98
29 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (28 bp):
CTAAACTAGGCTTAAATCTCATCTGTAG
Found at i:16533109 original size:65 final size:65
Alignment explanation
Indices: 16532928--16533114 Score: 178
Period size: 65 Copynumber: 2.9 Consensus size: 65
16532918 ATCTCATCTG
* * * ** * * *
16532928 TAGCTAAATTAGGCTTAAATCTCATATGGGCACCAACTAAACTGAGCTTAAATATCATAAGATGC
1 TAGCTAAATTAGACTTAAATATCATATAGGTGCCAACTAAATTGGGCTTAAATCTCATAAGATGC
* * * * ** * * *
16532993 TAGCTAAACT-GAGCTTAAATATCATTTAAGTGCCAGCTAAATTGGATTTAAATCTCTTAGGGTG
1 TAGCTAAATTAGA-CTTAAATATCATATAGGTGCCAACTAAATTGGGCTTAAATCTCATAAGATG
16533057 C
65 C
* * *
16533058 TAGCTAAATTAGACTTAACTTTCATCTAGGTGCCAACTAAATTGGGCTTAAATCTCA
1 TAGCTAAATTAGACTTAAATATCATATAGGTGCCAACTAAATTGGGCTTAAATCTCA
16533115 ATGGTGCCAA
Statistics
Matches: 94, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
64 1 0.01
65 91 0.97
66 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (65 bp):
TAGCTAAATTAGACTTAAATATCATATAGGTGCCAACTAAATTGGGCTTAAATCTCATAAGATGC
Found at i:16533290 original size:6 final size:6
Alignment explanation
Indices: 16533279--16533345 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
16533269 CATGCTATAC
* * * *
16533279 TTCTTT TTCTTTT TTCTTT TTTTTT TTCTCT ATCTCT TTC-TT TTC-TT
1 TTCTTT TTC-TTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
* *
16533326 TTCATT TTCTTT CTCTTT TT
1 TTCTTT TTCTTT TTCTTT TT
16533346 TCCTAAGCTC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
5 9 0.18
6 35 0.70
7 6 0.12
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (6 bp):
TTCTTT
Found at i:16534101 original size:23 final size:23
Alignment explanation
Indices: 16534070--16534114 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16534060 TCCTTCACTA
* *
16534070 TTTTGCCTTGTTT-CTTTATCAAT
1 TTTTACCTTATTTGCTTT-TCAAT
16534093 TTTTACCTTATTTGCTTTTCAA
1 TTTTACCTTATTTGCTTTTCAA
16534115 ATAGGCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.60
Consensus pattern (23 bp):
TTTTACCTTATTTGCTTTTCAAT
Found at i:16535969 original size:6 final size:6
Alignment explanation
Indices: 16535960--16536009 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
16535950 AATGAAAATG
* * * *
16535960 TTTTTC TTTTT- TTTTTC TTTCTC TCTCT- TTTTTC TTTTTC CTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
16536006 TTTT
1 TTTT
16536010 ACTTGTCTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:16542215 original size:19 final size:19
Alignment explanation
Indices: 16542177--16542215 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
16542167 AATTTTAATC
* *
16542177 TATTTATTTTTTTTATTAT
1 TATTCATTTTTTTTACTAT
*
16542196 TATTCATTTTTTTTGCTAT
1 TATTCATTTTTTTTACTAT
16542215 T
1 T
16542216 TTTGATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (19 bp):
TATTCATTTTTTTTACTAT
Found at i:16542585 original size:15 final size:15
Alignment explanation
Indices: 16542532--16542597 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
16542522 ACCTAAGTTT
16542532 TTTAATTTTTATTT-A
1 TTTAATTTTT-TTTAA
**
16542547 TTTGAATTTTTTTCCA
1 TTT-AATTTTTTTTAA
**
16542563 -TTCCTTTTTTTTAA
1 TTTAATTTTTTTTAA
16542577 TTTAATTTTTTTTAA
1 TTTAATTTTTTTTAA
16542592 TTTAAT
1 TTTAAT
16542598 ACCTCAACAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.20
15 25 0.61
16 8 0.20
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTTTTAA
Found at i:16547166 original size:3 final size:3
Alignment explanation
Indices: 16547158--16547231 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
16547148 AAATTTATGC
**
16547158 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GCA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16547206 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
16547232 GATGATGATG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16547575 original size:14 final size:15
Alignment explanation
Indices: 16547558--16547591 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
16547548 TTTGTTTTGT
16547558 TAAAATAACAAAT-A
1 TAAAATAACAAATAA
*
16547572 TAAAATAATAAATAA
1 TAAAATAACAAATAA
16547587 TAAAA
1 TAAAA
16547592 ATAATAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAATAACAAATAA
Found at i:16556894 original size:70 final size:69
Alignment explanation
Indices: 16556714--16557153 Score: 271
Period size: 70 Copynumber: 6.3 Consensus size: 69
16556704 CTTTGCCTCG
* * *
16556714 TGGTTCAATC-CTAGTCATATTT-ATTCTTCGAC-TAGAGGTTCAATCGTAGTCATTTTCATT-T
1 TGGTTCAATCTC-AATCAT-TTTCATTCTTCGACTTA-CGGTTCAATCTTAGTCATTTT-ATTCT
* *
16556775 CTCAACTTG
62 -TCGACTTA
***
16556784 TGGTTCAATCCCTACAAT-A-TTT-ATTCCTT-GACTCGTGGTTCAATCTTAGTCATTTTCATTC
1 TGGTTCAAT--CT-CAATCATTTTCATT-CTTCGACTTACGGTTCAATCTTAGTCATTTT-ATTC
16556845 TTCGACTTA
61 TTCGACTTA
* * * **
16556854 CGATTCAATCTCGATCATTTTCATTCTTCGACTTACGGTTCAATCCCAGTCATATTTATTCTTCG
1 TGGTTCAATCTCAATCATTTTCATTCTTCGACTTACGGTTCAATCTTAGTCAT-TTTATTCTTCG
16556919 ACTTA
65 ACTTA
** * * * * * *
16556924 TGGTTCAATCTTGAT-AATTTCAATTCCTCGACTTGCGGTTCAATGC-CAATCATTTTATTTTTC
1 TGGTTCAATCTCAATCATTTTC-ATTCTTCGACTTACGGTTCAAT-CTTAGTCATTTTATTCTTC
* *
16556987 AACTCA
64 GACTTA
* * * * * * *
16556993 TGGTTCAATCCCAATCATATTT-ATTATTTGACTCACGATTTAATTTTCA-TCATTTTCATTCCT
1 TGGTTCAATCTCAATCAT-TTTCATTCTTCGACTTACGGTTCAATCTT-AGTCATTTT-ATT-CT
16557056 T-GACTTA
62 TCGACTTA
* * * *
16557063 TGGTTCAATCTCAATCATTTTCATTTTTTGACTTGCAGTTCAAT-TCTAGTCATATTTATTCTTC
1 TGGTTCAATCTCAATCATTTTCATTCTTCGACTTACGGTTCAATCT-TAGTCAT-TTTATTCTTC
16557127 GAC-TA
64 GACTTA
* *
16557132 GTGGTTCAATCCCAATAATTTT
1 -TGGTTCAATCTCAATCATTTT
16557154 GATTTCCTGA
Statistics
Matches: 294, Mismatches: 50, Indels: 52
0.74 0.13 0.13
Matches are distributed among these distances:
67 3 0.01
68 3 0.01
69 68 0.23
70 199 0.68
71 16 0.05
72 2 0.01
73 2 0.01
74 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (69 bp):
TGGTTCAATCTCAATCATTTTCATTCTTCGACTTACGGTTCAATCTTAGTCATTTTATTCTTCGA
CTTA
Found at i:16556894 original size:105 final size:105
Alignment explanation
Indices: 16556710--16557240 Score: 367
Period size: 105 Copynumber: 5.1 Consensus size: 105
16556700 ACTTCTTTGC
* *
16556710 CTCGTGGTTCAATCCTAGTCATATTT-ATTCTTCGAC-TA-GAGGTTCAATCGT-AGTCATTTTC
1 CTCGTGGTTCAATCTTAGTCAT-TTTCATTCTTCGACTTACGA--TTCAATC-TCAATCATTTTC
* **
16556771 ATTTCTCAACTTGTGGTTCAATCCCTA-CAATATTTATTCCTT-GA
62 ATTTTTCAACTTACGGTTCAATCCCTATC-ATATTTATT-CTTCGA
* *
16556815 CTCGTGGTTCAATCTTAGTCATTTTCATTCTTCGACTTACGATTCAATCTCGATCATTTTCATTC
1 CTCGTGGTTCAATCTTAGTCATTTTCATTCTTCGACTTACGATTCAATCTCAATCATTTTCATTT
*
16556880 TTCGACTTACGGTTCAATCCC-AGTCATATTTATTCTTCGA
66 TTCAACTTACGGTTCAATCCCTA-TCATATTTATTCTTCGA
** * * * *
16556920 CTTATGGTTCAATCTT-GAT-AATTTCAATTCCTCGACTTGCGGTTCAATGC-CAATCATTTT-A
1 CTCGTGGTTCAATCTTAG-TCATTTTC-ATTCTTCGACTTACGATTCAAT-CTCAATCATTTTCA
* * * * *
16556981 TTTTTCAACTCATGGTTCAATCCCAATCATATTTATTATTTGA
63 TTTTTCAACTTACGGTTCAATCCCTATCATATTTATTCTTCGA
** * * * * *
16557024 CTCACGATTTAATTTTCA-TCATTTTCATTCCTT-GACTTATGGTTCAATCTCAATCATTTTCAT
1 CTCGTGGTTCAATCTT-AGTCATTTTCATT-CTTCGACTTACGATTCAATCTCAATCATTTTCAT
** * * *
16557087 TTTTTGACTTGCAGTTCAAT-TCTAGTCATATTTATTCTTCGA
64 TTTTCAACTTACGGTTCAATCCCTA-TCATATTTATTCTTCGA
* ** * * * * *** * * *
16557129 CTAGTGGTTCAATCCCAATAATTTTGATT-TCCTGACTGGTGATTCAATCCCAGTCACTTTT-GT
1 CTCGTGGTTCAATCTTAGTCATTTTCATTCTTC-GACTTACGATTCAATCTCAATCA-TTTTCAT
** * * *
16557192 TTTTTGACTCACAGTTCAATCCCTATCATATTTATTCTTTGA
64 TTTTCAACTTACGGTTCAATCCCTATCATATTTATTCTTCGA
16557234 CTC-TGGT
1 CTCGTGGT
16557241 CTAAACCCAG
Statistics
Matches: 341, Mismatches: 62, Indels: 47
0.76 0.14 0.10
Matches are distributed among these distances:
103 2 0.01
104 95 0.28
105 231 0.68
106 11 0.03
107 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (105 bp):
CTCGTGGTTCAATCTTAGTCATTTTCATTCTTCGACTTACGATTCAATCTCAATCATTTTCATTT
TTCAACTTACGGTTCAATCCCTATCATATTTATTCTTCGA
Found at i:16556922 original size:35 final size:35
Alignment explanation
Indices: 16556714--16557331 Score: 217
Period size: 35 Copynumber: 17.7 Consensus size: 35
16556704 CTTTGCCTCG
*
16556714 TGGTTCAATCCTAGTCATATTT-ATTCTTCGAC-TA
1 TGGTTCAATCCCAGTCAT-TTTCATTCTTCGACTTA
* ** * *
16556748 GAGGTTCAATCGTAGTCATTTTCATT-TCTCAACTTG
1 -TGGTTCAATCCCAGTCATTTTCATTCT-TCGACTTA
**
16556784 TGGTTCAATCCC--TACAATATTT-ATTCCTT-GACTCG
1 TGGTTCAATCCCAGT-C-AT-TTTCATT-CTTCGACTTA
**
16556819 TGGTTCAATCTTAGTCATTTTCATTCTTCGACTTA
1 TGGTTCAATCCCAGTCATTTTCATTCTTCGACTTA
* * *
16556854 CGATTCAATCTC-GATCATTTTCATTCTTCGACTTA
1 TGGTTCAATCCCAG-TCATTTTCATTCTTCGACTTA
*
16556889 CGGTTCAATCCCAGTCATATTT-ATTCTTCGACTTA
1 TGGTTCAATCCCAGTCAT-TTTCATTCTTCGACTTA
** * * *
16556924 TGGTTCAAT-CTTGAT-AATTTCAATTCCTCGACTTG
1 TGGTTCAATCCCAG-TCATTTTC-ATTCTTCGACTTA
* * * * * *
16556959 CGGTTCAATGCCAATCATTTT-ATTTTTCAACTCA
1 TGGTTCAATCCCAGTCATTTTCATTCTTCGACTTA
* * * *
16556993 TGGTTCAATCCCAATCATATTT-ATTATTTGACTCA
1 TGGTTCAATCCCAGTCAT-TTTCATTCTTCGACTTA
* * * **
16557028 CGATTTAATTTTCA-TCATTTTCATTCCTT-GACTTA
1 TGGTTCAA-TCCCAGTCATTTTCATT-CTTCGACTTA
* * * * *
16557063 TGGTTCAATCTCAATCATTTTCATTTTTTGACTTG
1 TGGTTCAATCCCAGTCATTTTCATTCTTCGACTTA
** * *
16557098 CAGTTCAATTCTAGTCATATTT-ATTCTTCGAC-TA
1 TGGTTCAATCCCAGTCAT-TTTCATTCTTCGACTTA
* * * * **
16557132 GTGGTTCAATCCCAATAATTTTGATT-TCCTGACTGG
1 -TGGTTCAATCCCAGTCATTTTCATTCTTC-GACTTA
* * * * *
16557168 TGATTCAATCCCAGTCACTTTT-GTTTTTTGACTCA
1 TGGTTCAATCCCAGTCA-TTTTCATTCTTCGACTTA
** * *
16557203 CAGTTCAATCCCTA-TCATATTT-ATTCTTTGAC-TC
1 TGGTTCAATCCC-AGTCAT-TTTCATTCTTCGACTTA
* * * *
16557237 TGG-TCTAAACCCAGCCATTTTCATT-TCCCAACTTA
1 TGGTTC-AATCCCAGTCATTTTCATTCT-TCGACTTA
* * * * *
16557272 CGGTTCAGTCCTAGCCATATTT-ATTCATT-GACTTG
1 TGGTTCAATCCCAGTCAT-TTTCATTC-TTCGACTTA
* *
16557307 TAGTTCAATCCAAGTCATTTTCATT
1 TGGTTCAATCCCAGTCATTTTCATT
16557332 TCTTGGCTTG
Statistics
Matches: 433, Mismatches: 105, Indels: 90
0.69 0.17 0.14
Matches are distributed among these distances:
33 11 0.03
34 72 0.17
35 313 0.72
36 34 0.08
37 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.43
Consensus pattern (35 bp):
TGGTTCAATCCCAGTCATTTTCATTCTTCGACTTA
Found at i:16557749 original size:11 final size:11
Alignment explanation
Indices: 16557733--16557764 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
16557723 AGTCTAAACA
16557733 AAGCCCATTTG
1 AAGCCCATTTG
16557744 AAGCCCATTTG
1 AAGCCCATTTG
16557755 AAGCCCATTT
1 AAGCCCATTT
16557765 TAAGAGCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (11 bp):
AAGCCCATTTG
Found at i:16558176 original size:11 final size:12
Alignment explanation
Indices: 16558150--16558176 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16558140 CTAAAATGCC
16558150 TTTTAAGGGCAT
1 TTTTAAGGGCAT
16558162 TTTTAAGGGCAT
1 TTTTAAGGGCAT
16558174 TTT
1 TTT
16558177 CATAATTTGA
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:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (12 bp):
TTTTAAGGGCAT
Found at i:16560274 original size:3 final size:3
Alignment explanation
Indices: 16560268--16560299 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16560258 AATAATAATA
16560268 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
16560300 TATAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:16567449 original size:41 final size:41
Alignment explanation
Indices: 16567396--16567525 Score: 224
Period size: 41 Copynumber: 3.1 Consensus size: 41
16567386 TTGAAATAAA
*
16567396 ACTCTTTAAAAAGAACTCTTCTAGATCATAAAAATCTTCTAT
1 ACTCTTT-AAAAGAACTCTTTTAGATCATAAAAATCTTCTAT
*
16567438 ACTCTTTAAAAGAACTCTTTTATATCATAAAAATCTTCTAT
1 ACTCTTTAAAAGAACTCTTTTAGATCATAAAAATCTTCTAT
*
16567479 ACTCTTTAAAAGAACTCTTTTAGATCATAAAAATCTTTTAT
1 ACTCTTTAAAAGAACTCTTTTAGATCATAAAAATCTTCTAT
16567520 ACTCTT
1 ACTCTT
16567526 CTTTTCTTAC
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
41 77 0.92
42 7 0.08
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (41 bp):
ACTCTTTAAAAGAACTCTTTTAGATCATAAAAATCTTCTAT
Found at i:16567461 original size:23 final size:23
Alignment explanation
Indices: 16567396--16567497 Score: 89
Period size: 18 Copynumber: 4.8 Consensus size: 23
16567386 TTGAAATAAA
*
16567396 ACTCTTTAAAAAGAACTCTTCTAG
1 ACTCTTT-AAAAGAACTCTTCTAT
*
16567420 A-TC-AT-AAA-AA-TCTTCTAT
1 ACTCTTTAAAAGAACTCTTCTAT
*
16567438 ACTCTTTAAAAGAACTCTTTTAT
1 ACTCTTTAAAAGAACTCTTCTAT
*
16567461 A-TC-AT-AAA-AA-TCTTCTAT
1 ACTCTTTAAAAGAACTCTTCTAT
16567479 ACTCTTTAAAAGAACTCTT
1 ACTCTTTAAAAGAACTCTT
16567498 TTAGATCATA
Statistics
Matches: 61, Mismatches: 7, Indels: 21
0.69 0.08 0.24
Matches are distributed among these distances:
18 16 0.26
19 8 0.13
20 8 0.13
21 7 0.11
22 7 0.11
23 14 0.23
24 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (23 bp):
ACTCTTTAAAAGAACTCTTCTAT
Found at i:16567509 original size:21 final size:21
Alignment explanation
Indices: 16567404--16567510 Score: 82
Period size: 18 Copynumber: 5.2 Consensus size: 21
16567394 AAACTCTTTA
*
16567404 AAAAGAACTCTTCTAGATCAT
1 AAAAGAACTCTTCTATATCAT
*
16567425 -AAA-AA-TCTTCTATACTCTTT
1 AAAAGAACTCTTCTATA-TC-AT
*
16567445 AAAAGAACTCTTTTATATCAT
1 AAAAGAACTCTTCTATATCAT
*
16567466 -AAA-AA-TCTTCTATACTCTTT
1 AAAAGAACTCTTCTATA-TC-AT
* *
16567486 AAAAGAACTCTTTTAGATCAT
1 AAAAGAACTCTTCTATATCAT
16567507 AAAA
1 AAAA
16567511 ATCTTTTATA
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
18 16 0.24
19 8 0.12
20 8 0.12
21 12 0.18
22 8 0.12
23 15 0.22
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAAGAACTCTTCTATATCAT
Found at i:16568779 original size:12 final size:13
Alignment explanation
Indices: 16568751--16568783 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
16568741 CAAAAATAAC
16568751 AAATAAACTAATA
1 AAATAAACTAATA
*
16568764 AAATAAA-TAATT
1 AAATAAACTAATA
16568776 AAATAAAC
1 AAATAAAC
16568784 GAAAAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAACTAATA
Found at i:16569671 original size:87 final size:87
Alignment explanation
Indices: 16569569--16569743 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 87
16569559 AAAAAGACTC
*
16569569 CTACATGTAATTGGTAAATTAAGATGTATACTTGGACAAGGACTCTTAAATATTTTTGGCTAAAA
1 CTACATGTAATTGGTAAATAAAGATGTATACTTGGACAAGGACTCTTAAATATTTTTGGCTAAAA
16569634 GGAGAGATTTTACAAGAAAAGG
66 GGAGAGATTTTACAAGAAAAGG
* *
16569656 CTACATGTAATTGGTAAATAAAGATGTATACTTGGACAAGGACTCTTTAATATTTTTGGTTAAAA
1 CTACATGTAATTGGTAAATAAAGATGTATACTTGGACAAGGACTCTTAAATATTTTTGGCTAAAA
16569721 GGAGAGATTTTACAAGAAAAGG
66 GGAGAGATTTTACAAGAAAAGG
16569743 C
1 C
16569744 CTCTTTGTTT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (87 bp):
CTACATGTAATTGGTAAATAAAGATGTATACTTGGACAAGGACTCTTAAATATTTTTGGCTAAAA
GGAGAGATTTTACAAGAAAAGG
Found at i:16570099 original size:14 final size:13
Alignment explanation
Indices: 16570061--16570103 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
16570051 CTCATTTCTC
16570061 TCTTTTCTTTTAGT
1 TCTTTT-TTTTAGT
*
16570075 TCTTAGTTTTTAGT
1 TCTT-TTTTTTAGT
16570089 TCTTTTATTTTAGT
1 TCTTTT-TTTTAGT
16570103 T
1 T
16570104 TGATTATTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 1 0.04
14 23 0.92
15 1 0.04
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (13 bp):
TCTTTTTTTTAGT
Found at i:16572504 original size:32 final size:33
Alignment explanation
Indices: 16572468--16572532 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
16572458 GAAAAATAGA
16572468 AATTAAGTC-TTTGATTAAACCGACCATAGAGG
1 AATTAAGTCATTTGATTAAACCGACCATAGAGG
16572500 AATTAAGTCATTTTGATTAAACCGACCATAGAG
1 AATTAAGTCA-TTTGATTAAACCGACCATAGAG
16572533 AAACCTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 9 0.29
34 22 0.71
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (33 bp):
AATTAAGTCATTTGATTAAACCGACCATAGAGG
Found at i:16589114 original size:20 final size:20
Alignment explanation
Indices: 16589086--16589145 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
16589076 TTCAATCAAG
16589086 TTTCTTTCAAGTTAATTTAAA
1 TTTC-TTCAAGTTAATTTAAA
* *
16589107 TTTCTTCAAATTAACTT-AA
1 TTTCTTCAAGTTAATTTAAA
* *
16589126 GTT-TTCAAG-CAATTTAAA
1 TTTCTTCAAGTTAATTTAAA
16589144 TT
1 TT
16589146 CTATTTTGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
17 4 0.13
18 8 0.26
19 4 0.13
20 11 0.35
21 4 0.13
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTCTTCAAGTTAATTTAAA
Found at i:16596431 original size:309 final size:310
Alignment explanation
Indices: 16595698--16596613 Score: 1638
Period size: 309 Copynumber: 3.0 Consensus size: 310
16595688 TAAGGTGAGA
16595698 TGGTGATCCAAGTTGGGGTGAATTGGATCTCTCTAAATTCTTCTTAAAATAATGATTTCAAGATA
1 TGGTGATCCAAGTTGGGGTGAATTGGATCTCTCTAAATTCTTCTTAAAATAATGATTTCAAGATA
*
16595763 ATTGAATGAGGAGTTAAATCAATAAGCACTTTTTATGAAAATATAATGCAATCAATAACAATTAA
66 ATTGAATGAGGAATTAAATCAATAAGCACTTTTTATGAAAATATAATGCAATCAATAACAATTAA
*
16595828 TGAACCTAGAATCAAATATAAACAACAATAAATGTAAAAAGATAGGGATAGAGAAATCAAACACA
131 TGAACCTAGAATCAAATATAAACAACAATAAATGTAAGAAGATAGGGATAGAGAAATCAAACACA
* * * *
16595893 ATGATTTATAGAGGTTCAACCTTTCTGCACAACACACCTATGTCTTCTCCTCTTGGTTGTCCACA
196 ATGATTTATAGAGGTTCGACCTTTCTCCACAACGCACCTATGTCCTCTCCTCTTGGTTGTCCACA
16595958 CCAAGGCTTCAATCCATTAATTGAAGAAAAAATCTTAAATTGATTTTTTC
261 CCAAGGCTTCAATCCATTAATTGAAGAAAAAATCTTAAATTGATTTTTTC
*
16596008 TGGTGATCCAAGTTGGGGTGAATTGGATCTCTCTAAATTCTTCTTAAAACAATGATTTCAAGATA
1 TGGTGATCCAAGTTGGGGTGAATTGGATCTCTCTAAATTCTTCTTAAAATAATGATTTCAAGATA
16596073 ATTGAATGAGGAATTAAATCAATAAGCACTTTTTATGAAAATATAATGCAATCAATAACAATTAA
66 ATTGAATGAGGAATTAAATCAATAAGCACTTTTTATGAAAATATAATGCAATCAATAACAATTAA
* *
16596138 TGAACCTAGAATCAAATATAAACAACAATAAATGTAAGAAGATAGGGATAAAAAAATCAAACACA
131 TGAACCTAGAATCAAATATAAACAACAATAAATGTAAGAAGATAGGGATAGAGAAATCAAACACA
* *
16596203 ATAATTTATAGAGGTTCGACCTTTCTCCACAACGCACCTATGTCCTCTCCT-TTGGTTATCCACA
196 ATGATTTATAGAGGTTCGACCTTTCTCCACAACGCACCTATGTCCTCTCCTCTTGGTTGTCCACA
* *
16596267 CCAAGGTTTCAATCCATTAATTGAAG-AAAAATCTTAAATTGATTTTTTTT
261 CCAAGGCTTCAATCCATTAATTGAAGAAAAAATCTTAAATTGA-TTTTTTC
*
16596317 TTGTGATCCAAGTTGGGGTGAATTGGATCTCTCTAAATTCTTCTTAAAATAATGATTTCAAGATA
1 TGGTGATCCAAGTTGGGGTGAATTGGATCTCTCTAAATTCTTCTTAAAATAATGATTTCAAGATA
*
16596382 ATTGAATGAGAAATTAAATCAATAAGCACTTTTTATGAAAATATAATGCAATCAATAACAATTAA
66 ATTGAATGAGGAATTAAATCAATAAGCACTTTTTATGAAAATATAATGCAATCAATAACAATTAA
16596447 TGAACCTAGAATCAAATATAAACAACAATAAATGTAAGAAGATAGGGATAGAGAAATCAAACACA
131 TGAACCTAGAATCAAATATAAACAACAATAAATGTAAGAAGATAGGGATAGAGAAATCAAACACA
* *
16596512 ATGATTTATAGAGGTTCGACCTTTCTTCAAAACGCACCTATGTCCTCTCCTCTTGGTTGTCCACA
196 ATGATTTATAGAGGTTCGACCTTTCTCCACAACGCACCTATGTCCTCTCCTCTTGGTTGTCCACA
* *
16596577 CTAAAGCTTCAATCCATTAATTGAAGAAAAAATCTTA
261 CCAAGGCTTCAATCCATTAATTGAAGAAAAAATCTTA
16596614 CAAGATACAA
Statistics
Matches: 578, Mismatches: 25, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
308 16 0.03
309 281 0.49
310 271 0.47
311 10 0.02
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (310 bp):
TGGTGATCCAAGTTGGGGTGAATTGGATCTCTCTAAATTCTTCTTAAAATAATGATTTCAAGATA
ATTGAATGAGGAATTAAATCAATAAGCACTTTTTATGAAAATATAATGCAATCAATAACAATTAA
TGAACCTAGAATCAAATATAAACAACAATAAATGTAAGAAGATAGGGATAGAGAAATCAAACACA
ATGATTTATAGAGGTTCGACCTTTCTCCACAACGCACCTATGTCCTCTCCTCTTGGTTGTCCACA
CCAAGGCTTCAATCCATTAATTGAAGAAAAAATCTTAAATTGATTTTTTC
Found at i:16598731 original size:117 final size:117
Alignment explanation
Indices: 16598604--16598839 Score: 472
Period size: 117 Copynumber: 2.0 Consensus size: 117
16598594 GAGCAAAGGA
16598604 TAATGAATGATATTCAACATACTCATAAATCATGTTAGCATAAGATGTACTTTGAACCTAAAACA
1 TAATGAATGATATTCAACATACTCATAAATCATGTTAGCATAAGATGTACTTTGAACCTAAAACA
16598669 TCAATAGCAATTAAGCATAAATTCAAGCACATGCATACAAGCTCATACTAAT
66 TCAATAGCAATTAAGCATAAATTCAAGCACATGCATACAAGCTCATACTAAT
16598721 TAATGAATGATATTCAACATACTCATAAATCATGTTAGCATAAGATGTACTTTGAACCTAAAACA
1 TAATGAATGATATTCAACATACTCATAAATCATGTTAGCATAAGATGTACTTTGAACCTAAAACA
16598786 TCAATAGCAATTAAGCATAAATTCAAGCACATGCATACAAGCTCATACTAAT
66 TCAATAGCAATTAAGCATAAATTCAAGCACATGCATACAAGCTCATACTAAT
16598838 TA
1 TA
16598840 TTCAGGATAC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 119 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (117 bp):
TAATGAATGATATTCAACATACTCATAAATCATGTTAGCATAAGATGTACTTTGAACCTAAAACA
TCAATAGCAATTAAGCATAAATTCAAGCACATGCATACAAGCTCATACTAAT
Found at i:16610776 original size:18 final size:18
Alignment explanation
Indices: 16610753--16610798 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
16610743 AATTCAGCCA
16610753 TCAAGTTTTCTTTATTTT
1 TCAAGTTTTCTTTATTTT
16610771 TCAAGTTTTCTTTATTTT
1 TCAAGTTTTCTTTATTTT
*
16610789 TAAAGTTTTC
1 TCAAGTTTTC
16610799 ATTCTTGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.63
Consensus pattern (18 bp):
TCAAGTTTTCTTTATTTT
Found at i:16615709 original size:59 final size:59
Alignment explanation
Indices: 16615584--16615828 Score: 316
Period size: 59 Copynumber: 4.1 Consensus size: 59
16615574 CTTTTATACA
* * * **
16615584 AAGAAAATTTGATACTTTTAACTTTTCCTTAAAAAGAT-TTTTTTT-ATTTTTTATTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTGAAATTTTATTTT
*
16615641 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTGAAATTTTATTTT
1 -AAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTGAAATTTTATTTT
* * * *
16615701 AAGAAAAATTGATACTTTTAACTTTTCCTTAAAAATGTTTTTTTTTCTAAAATTTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTTAAAAAT-ATATTTTTT-TGAAATTTTA-TTTT
* *
16615763 AAAAAAAATTGATACTTTCAACTTTTCATTAAAAATATA-TTTTTTGAAAATTTTATTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTG-AAATTTTATTTT
16615822 AAGAAAA
1 AAGAAAA
16615829 TCATTGAAAA
Statistics
Matches: 163, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
58 34 0.21
59 52 0.32
60 30 0.18
61 10 0.06
62 37 0.23
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (59 bp):
AAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTGAAATTTTATTTT
Found at i:16615801 original size:121 final size:117
Alignment explanation
Indices: 16615584--16615828 Score: 366
Period size: 121 Copynumber: 2.1 Consensus size: 117
16615574 CTTTTATACA
* ** **
16615584 AAGAAAATTTGATACTTTTAACTTTTCCTTAAAAAGATTTTTTTTATTTTTTATTTTCAAGGAAA
1 AAGAAAAATTGATACTTTTAACTTTTCCTTAAAAAGATTTTTTTTAAATTTTATTTTCAAAAAAA
*
16615649 ATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTG-AAATTTTATTTT
66 ATTGATACTTTCAACTTTTCATTAAAAATATA-TTTTTTGAAAATTTTATTTT
* *
16615701 AAGAAAAATTGATACTTTTAACTTTTCCTTAAAAATGTTTTTTTTTCTAAAATTTTATTTTTAAA
1 AAGAAAAATTGATACTTTTAACTTTTCCTTAAAAA-G-ATTTTTTT-T-AAATTTTATTTTCAAA
16615766 AAAAATTGATACTTTCAACTTTTCATTAAAAATATATTTTTTGAAAATTTTATTTT
62 AAAAATTGATACTTTCAACTTTTCATTAAAAATATATTTTTTGAAAATTTTATTTT
16615822 AAGAAAA
1 AAGAAAA
16615829 TCATTGAAAA
Statistics
Matches: 115, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
117 34 0.30
118 1 0.01
119 7 0.06
120 8 0.07
121 65 0.57
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (117 bp):
AAGAAAAATTGATACTTTTAACTTTTCCTTAAAAAGATTTTTTTTAAATTTTATTTTCAAAAAAA
ATTGATACTTTCAACTTTTCATTAAAAATATATTTTTTGAAAATTTTATTTT
Found at i:16616462 original size:42 final size:42
Alignment explanation
Indices: 16616416--16616614 Score: 328
Period size: 42 Copynumber: 4.8 Consensus size: 42
16616406 AATTTCCAGA
* * *
16616416 AAATAGAGGCAACCATAATTTTGAAAAATAAATTGCTCCTCA
1 AAATAGAGGCAACCACAACTTTGAAAAATAAATTGCTCCTCT
16616458 AAATAGAGGCAACCACAACTTTGAAAAATAAATTGCTCCTCT
1 AAATAGAGGCAACCACAACTTTGAAAAATAAATTGCTCCTCT
16616500 AAATAGAGGCAACCACAACTTTGAAAAATAAATTGCTCCTCT
1 AAATAGAGGCAACCACAACTTTGAAAAATAAATTGCTCCTCT
* *
16616542 AAATAGAGGCAACTACAACTTTGAAAAATAAATTACTCCTCT
1 AAATAGAGGCAACCACAACTTTGAAAAATAAATTGCTCCTCT
* *
16616584 AAACAGAGGC-ACCACAACTTTGGAAAATAAA
1 AAATAGAGGCAACCACAACTTTGAAAAATAAA
16616615 AATGCTTCTT
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 19 0.13
42 130 0.87
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (42 bp):
AAATAGAGGCAACCACAACTTTGAAAAATAAATTGCTCCTCT
Found at i:16616917 original size:20 final size:20
Alignment explanation
Indices: 16616892--16616930 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16616882 CACATCCAAA
16616892 AGTTCAAAGCTTCTCATTCG
1 AGTTCAAAGCTTCTCATTCG
* *
16616912 AGTTCAAAGGTTCTTATTC
1 AGTTCAAAGCTTCTCATTC
16616931 AATAAATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (20 bp):
AGTTCAAAGCTTCTCATTCG
Found at i:16616979 original size:21 final size:21
Alignment explanation
Indices: 16616953--16616992 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16616943 AGTTTCACAT
*
16616953 CTCAAAGTTTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
16616974 CTCAAAGATTCTCATTTGA
1 CTCAAAGATTCTCATTTGA
16616993 GTTTGAAGAT
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:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAA
Found at i:16617053 original size:137 final size:137
Alignment explanation
Indices: 16616902--16617201 Score: 379
Period size: 137 Copynumber: 2.2 Consensus size: 137
16616892 AGTTCAAAGC
* * * * **
16616902 TTCTCATTCGAGTTCAAAGGTTCTTATTCAATAAATCTTAGAGTTTCACA-TCTCAAAGTTTCTC
1 TTCTCATTTGAGTTCAAAGATTCTCATTCAACAAAT-TTAGAGTTTCACACT-TCAAACATTCTC
* * *
16616966 ATTTGAAACTCAAAGATTCTCATTTGAGTTTGAAGATTCAC-TTTAACAAATTTTGGGTTTCACA
64 ATTTAAAACTCAAAGATTCTCATTTGAGTTCGAAGATTCACATTCAACAAATTTTGGGTTTCACA
16617030 CCTTAAACA
129 CCTTAAACA
* * * * *
16617039 TTTTCATTTGAGTTCTAAGATTCACATTCAACAAATTTTGGGTTTCACACTTCAAACATTCTCAT
1 TTCTCATTTGAGTTCAAAGATTCTCATTCAACAAATTTAGAGTTTCACACTTCAAACATTCTCAT
* * *
16617104 TTAAAATTCAAAGATTCTCATTTGAGTTCGAAGATTCACATTCGACAAATTTTGGGTTTCATACC
66 TTAAAACTCAAAGATTCTCATTTGAGTTCGAAGATTCACATTCAACAAATTTTGGGTTTCACACC
**
16617169 TTAATGA
131 TTAAACA
*
16617176 TTCTCATTTGAAATTCAAAGATTCTC
1 TTCTCATTTG-AGTTCAAAGATTCTC
16617202 CTTTGAGAAC
Statistics
Matches: 137, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
136 59 0.43
137 66 0.48
138 12 0.09
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (137 bp):
TTCTCATTTGAGTTCAAAGATTCTCATTCAACAAATTTAGAGTTTCACACTTCAAACATTCTCAT
TTAAAACTCAAAGATTCTCATTTGAGTTCGAAGATTCACATTCAACAAATTTTGGGTTTCACACC
TTAAACA
Found at i:16617059 original size:57 final size:58
Alignment explanation
Indices: 16616975--16617105 Score: 196
Period size: 58 Copynumber: 2.3 Consensus size: 58
16616965 CATTTGAAAC
* *
16616975 TCAAAGATTCTCATTTGAGTTTGAAGATTCAC-TTTAACAAATTTTGGGTTTCACACCT
1 TCAAACATTCTCATTTGAGTTTGAAGATTCACATTCAACAAATTTTGGGTTTCACA-CT
*
16617033 T-AAACATTTTCATTTGAGTTCT-AAGATTCACATTCAACAAATTTTGGGTTTCACACT
1 TCAAACATTCTCATTTGAGTT-TGAAGATTCACATTCAACAAATTTTGGGTTTCACACT
16617090 TCAAACATTCTCATTT
1 TCAAACATTCTCATTT
16617106 AAAATTCAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
57 29 0.44
58 37 0.56
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (58 bp):
TCAAACATTCTCATTTGAGTTTGAAGATTCACATTCAACAAATTTTGGGTTTCACACT
Found at i:16617131 original size:79 final size:79
Alignment explanation
Indices: 16617042--16617208 Score: 255
Period size: 79 Copynumber: 2.1 Consensus size: 79
16617032 TTAAACATTT
*
16617042 TCATTTGAGTTCTAAGATTCACATTCAACAAATTTTGGGTTTCACA-CTTCAAACATTCTCATTT
1 TCATTTGAGTTCGAAGATTCACATTCAACAAATTTTGGGTTTCACACCTT-AAACATTCTCATTT
16617106 AAAATTCAAAGATTC
65 AAAATTCAAAGATTC
* * ** *
16617121 TCATTTGAGTTCGAAGATTCACATTCGACAAATTTTGGGTTTCATACCTTAATGATTCTCATTTG
1 TCATTTGAGTTCGAAGATTCACATTCAACAAATTTTGGGTTTCACACCTTAAACATTCTCATTTA
16617186 AAATTCAAAGATTC
66 AAATTCAAAGATTC
*
16617200 TCCTTTGAG
1 TCATTTGAG
16617209 AACTCAAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 77 0.96
80 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (79 bp):
TCATTTGAGTTCGAAGATTCACATTCAACAAATTTTGGGTTTCACACCTTAAACATTCTCATTTA
AAATTCAAAGATTC
Found at i:16617200 original size:21 final size:22
Alignment explanation
Indices: 16617174--16617225 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
16617164 ATACCTTAAT
*
16617174 GATTCTCATTTGA-AATTCAAA
1 GATTCTCATTTGAGAACTCAAA
*
16617195 GATTCTCCTTTGAGAACTCAAA
1 GATTCTCATTTGAGAACTCAAA
*
16617217 AATTCTCAT
1 GATTCTCAT
16617226 CAAAAGATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (22 bp):
GATTCTCATTTGAGAACTCAAA
Found at i:16618394 original size:11 final size:11
Alignment explanation
Indices: 16618380--16618413 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
16618370 CTCTTTTCTA
16618380 TTTTTTTTTCC
1 TTTTTTTTTCC
*
16618391 TTTTTTTTTTC
1 TTTTTTTTTCC
16618402 -TTTTTTTTCC
1 TTTTTTTTTCC
16618412 TT
1 TT
16618414 CCTTCATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTCC
Found at i:16618395 original size:12 final size:11
Alignment explanation
Indices: 16618373--16618409 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
16618363 ATTTTCTCTC
16618373 TTTTCTATTTTT
1 TTTTCT-TTTTT
16618385 TTTTCCTTTTTT
1 TTTT-CTTTTTT
16618397 TTTTCTTTTTT
1 TTTTCTTTTTT
16618408 TT
1 TT
16618410 CCTTCCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.38
12 13 0.54
13 2 0.08
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:16622423 original size:121 final size:121
Alignment explanation
Indices: 16622290--16622539 Score: 371
Period size: 121 Copynumber: 2.1 Consensus size: 121
16622280 TGCTTTTATA
* **
16622290 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAACATTTTTTTTAGAATTTTTTATTTTGAAA
1 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAACATTTTTTTTAGAAAATTTTATTTT-AAA
*
16622355 G-AAAATTGATACTTTCAACTTCTCCTTAAAAATTTTTTTTTTGAAAATTTTATTTT
65 GAAAAATTGATACTTTCAACTTCTCCTTAAAAATATTTTTTTTGAAAATTTTATTTT
** * *
16622411 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTTTTTGAAAATTTTATTTTCAAG
1 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAACATTTTTTTTAGAAAATTTTATTTTAAAG
* * *
16622476 AAAAATTGATACTTTTAACTTTTCTTTAAAAATATTTTTTTTGAAAATTTTATTTT
66 AAAAATTGATACTTTCAACTTCTCCTTAAAAATATTTTTTTTGAAAATTTTATTTT
16622532 -AA-GAAAAT
1 CAAGGAAAAT
16622540 CATTGAAAAA
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
119 6 0.05
120 5 0.04
121 106 0.91
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (121 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAACATTTTTTTTAGAAAATTTTATTTTAAAG
AAAAATTGATACTTTCAACTTCTCCTTAAAAATATTTTTTTTGAAAATTTTATTTT
Found at i:16622545 original size:61 final size:60
Alignment explanation
Indices: 16622290--16622538 Score: 367
Period size: 61 Copynumber: 4.1 Consensus size: 60
16622280 TGCTTTTATA
* **
16622290 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAACATTTTTTTTAGAATTTTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTT-GAAAATTTTATTTT
* * *
16622351 GAA-AGAAAATTGATACTTTCAACTTCTCCTTAAAAATTTTTTTTTTGAAAATTTTATTTT
1 CAAGA-AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAATTTTATTTT
* *
16622411 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTTTTTGAAAATTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAAT-ATTTTTTTTGAAAATTTTATTTT
* *
16622472 CAAGAAAAATTGATACTTTTAACTTTTCTTTAAAAATATTTTTTTTGAAAATTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAATTTTATTTT
16622532 -AAGAAAA
1 CAAGAAAA
16622539 TCATTGAAAA
Statistics
Matches: 172, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
59 7 0.04
60 68 0.40
61 97 0.56
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (60 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAATTTTATTTT
Found at i:16623417 original size:18 final size:18
Alignment explanation
Indices: 16623386--16623428 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
16623376 TTCAACCCGT
* *
16623386 ATTTTTTTTATTTTTCTC
1 ATTTTTTCTATTTTTATC
* *
16623404 ATTTTTTCTCTTTTTATT
1 ATTTTTTCTATTTTTATC
16623422 ATTTTTT
1 ATTTTTT
16623429 ATTTTTAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (18 bp):
ATTTTTTCTATTTTTATC
Found at i:16625267 original size:29 final size:29
Alignment explanation
Indices: 16625230--16625285 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
16625220 CTTGGATCTT
16625230 AAAAAAAGATTGCCAAA-TTCAAAGTAAAG
1 AAAAAAAGATTG-CAAACTTCAAAGTAAAG
* *
16625259 AAAACAAGATTGCAAACTTGAAAGTAA
1 AAAAAAAGATTGCAAACTTCAAAGTAA
16625286 TAAAAGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.18
Consensus pattern (29 bp):
AAAAAAAGATTGCAAACTTCAAAGTAAAG
Found at i:16625498 original size:13 final size:13
Alignment explanation
Indices: 16625480--16625506 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16625470 CTAAGGGCGA
16625480 TAGGCTATACAAG
1 TAGGCTATACAAG
16625493 TAGGCTATACAAG
1 TAGGCTATACAAG
16625506 T
1 T
16625507 GTTTGATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (13 bp):
TAGGCTATACAAG
Found at i:16629031 original size:17 final size:17
Alignment explanation
Indices: 16629009--16629045 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16628999 ACCAATAAGC
16629009 CTTTTCTTTGATTATAT
1 CTTTTCTTTGATTATAT
* *
16629026 CTTTTCTTTGGTTTTAT
1 CTTTTCTTTGATTATAT
16629043 CTT
1 CTT
16629046 ACCCAATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.14, G:0.08, T:0.68
Consensus pattern (17 bp):
CTTTTCTTTGATTATAT
Found at i:16630970 original size:18 final size:18
Alignment explanation
Indices: 16630927--16630972 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
16630917 CCTTTTGTTC
*
16630927 TCAAGTTCTTTTTATTTT
1 TCAAGTTTTTTTTATTTT
16630945 TCAAGTTTTTTTTATTTT
1 TCAAGTTTTTTTTATTTT
16630963 TCAAGTTTTT
1 TCAAGTTTTT
16630973 CATTCTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.09, G:0.07, T:0.67
Consensus pattern (18 bp):
TCAAGTTTTTTTTATTTT
Found at i:16641079 original size:54 final size:54
Alignment explanation
Indices: 16641015--16641122 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
16641005 TCCTTTCTTG
16641015 ACAAAGCATCGACTAGGAACAATTTAGGAATAATGATTTAATGCAATGATGATC
1 ACAAAGCATCGACTAGGAACAATTTAGGAATAATGATTTAATGCAATGATGATC
16641069 ACAAAGCATCGACTAGGAACAATTTAGGAATAATGATTTAATGCAATGATGATC
1 ACAAAGCATCGACTAGGAACAATTTAGGAATAATGATTTAATGCAATGATGATC
16641123 TCATAATTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (54 bp):
ACAAAGCATCGACTAGGAACAATTTAGGAATAATGATTTAATGCAATGATGATC
Found at i:16644984 original size:39 final size:38
Alignment explanation
Indices: 16644940--16645015 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
16644930 GAAACCTTGA
** * *
16644940 GTTACATTTAAGGGGAGTTAGACGAGAAAAAAATATTAT
1 GTTACATTTAAAAGGAGTAAAACGAGAAAAAAA-ATTAT
16644979 GTTACATTTAAAAGGAGTAAAACGAGAAAAAAAATTA
1 GTTACATTTAAAAGGAGTAAAACGAGAAAAAAAATTA
16645016 CAACTCTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 4 0.12
39 29 0.88
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (38 bp):
GTTACATTTAAAAGGAGTAAAACGAGAAAAAAAATTAT
Found at i:16650799 original size:18 final size:17
Alignment explanation
Indices: 16650772--16650807 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
16650762 AAGCATATAA
*
16650772 AGAAAAAAAAAGAAATG
1 AGAAAAAAAAAAAAATG
16650789 AGAACAAAAAAAAAAATG
1 AGAA-AAAAAAAAAAATG
16650807 A
1 A
16650808 AAAGATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.06
Consensus pattern (17 bp):
AGAAAAAAAAAAAAATG
Found at i:16652591 original size:22 final size:22
Alignment explanation
Indices: 16652548--16652592 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
16652538 TTCAAAGATA
*
16652548 GGCATGATCTATAAGACCTTTT
1 GGCATGATCTATAAAACCTTTT
* * *
16652570 GGCATGATTTTTAAAACTTTTT
1 GGCATGATCTATAAAACCTTTT
16652592 G
1 G
16652593 ATACCTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (22 bp):
GGCATGATCTATAAAACCTTTT
Found at i:16652908 original size:24 final size:21
Alignment explanation
Indices: 16652866--16652969 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 21
16652856 ATTTAAATTT
*
16652866 TTTAAATTTTGAATGTGAATC
1 TTTAAATTTTGAATATGAATC
16652887 TTTCAAATTTCTCGAATATGAATC
1 TTT-AAATTT-T-GAATATGAATC
* *
16652911 TTTGAATTTTTGGATATGAATC
1 TTT-AAATTTTGAATATGAATC
*
16652933 TTTAAGATTTTTGTTAATGTGAATC
1 TTTAA-A-TTTTG--AATATGAATC
16652958 TTTAAAATTTTG
1 TTT-AAATTTTG
16652970 GATGTAAATC
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.07
22 19 0.28
23 7 0.10
24 23 0.34
25 12 0.18
26 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (21 bp):
TTTAAATTTTGAATATGAATC
Found at i:16653204 original size:23 final size:22
Alignment explanation
Indices: 16652869--16653204 Score: 162
Period size: 22 Copynumber: 14.8 Consensus size: 22
16652859 TAAATTTTTT
*
16652869 AAATTTTGAATGTGAATCTTTC
1 AAATTTTGAATGTGAATCTTTA
* *
16652891 AAATTTCTCGAATATGAATCTTTG
1 AAATTT-T-GAATGTGAATCTTTA
* * *
16652915 AATTTTTGGATATGAATCTTTA
1 AAATTTTGAATGTGAATCTTTA
*
16652937 AGATTTTTGTTAATGTGAATCTTTA
1 A-AATTTTG--AATGTGAATCTTTA
* * **
16652962 AAATTTTGGATGTAAATCCCTA
1 AAATTTTGAATGTGAATCTTTA
*
16652984 AAATTTCTCGAATGTGAATATTT-
1 AAATTT-T-GAATGTGAATCTTTA
* * *
16653007 GAATTTTTAGATGTAAAT-TTTAAAA
1 AAATTTTGA-ATGTGAATCTTT---A
* *
16653032 AAATTTTGAATGAGAATCTTTG
1 AAATTTTGAATGTGAATCTTTA
*
16653054 AAATTTTAGAA-GTGAATCTCTA
1 AAATTTT-GAATGTGAATCTTTA
* * *
16653076 AAATTTTTTAATATGGATCTTT-
1 AAA-TTTTGAATGTGAATCTTTA
* * **
16653098 GAA-TTTCATATGTGAATCGCTA
1 AAATTTTGA-ATGTGAATCTTTA
* ** * *
16653120 AAAGCTCCGAATGAGAACCTTT-
1 AAA-TTTTGAATGTGAATCTTTA
* * *
16653142 GAATTTTGGATGTAAATCTTTA
1 AAATTTTGAATGTGAATCTTTA
*
16653164 AAATTTCTGAATGAGAATCTTTA
1 AAATTT-TGAATGTGAATCTTTA
*
16653187 AAATTTTGGGATGTGAAT
1 AAATTTT-GAATGTGAAT
16653205 TGCTAAATTT
Statistics
Matches: 231, Mismatches: 60, Indels: 45
0.69 0.18 0.13
Matches are distributed among these distances:
20 4 0.02
21 23 0.10
22 76 0.33
23 64 0.28
24 41 0.18
25 23 0.10
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (22 bp):
AAATTTTGAATGTGAATCTTTA
Found at i:16653291 original size:21 final size:21
Alignment explanation
Indices: 16653261--16653318 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
16653251 AACAAAAATC
* *
16653261 TTTTGAATGTGAATCTTTG-AA
1 TTTTGGATGTGAAT-TTAGAAA
*
16653282 TTTTGGATGTAAATTTAGAAA
1 TTTTGGATGTGAATTTAGAAA
*
16653303 TTTTGGATGTGGATTT
1 TTTTGGATGTGAATTT
16653319 CTAAACATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (21 bp):
TTTTGGATGTGAATTTAGAAA
Found at i:16653509 original size:22 final size:22
Alignment explanation
Indices: 16653468--16653548 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
16653458 AATTCTTGCA
*
16653468 AATCTTTGAATTT--AATTGTG
1 AATCCTTGAATTTCAAATTGTG
*
16653488 AATCCTTAAATTTCAAATTGTG
1 AATCCTTGAATTTCAAATTGTG
* *
16653510 AA-CCTTTGAATTTCAAGTTGGG
1 AATCC-TTGAATTTCAAATTGTG
16653532 AATCCTTGAATTTCAAA
1 AATCCTTGAATTTCAAA
16653549 CTATCAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.22
21 2 0.04
22 36 0.71
23 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (22 bp):
AATCCTTGAATTTCAAATTGTG
Found at i:16657242 original size:19 final size:19
Alignment explanation
Indices: 16657218--16657272 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
16657208 TATCTTGACA
16657218 ATTTATTATTAAGTATTTT-
1 ATTTATTATTAA-TATTTTC
* *
16657237 ATTTATTTTTAATCTTTTC
1 ATTTATTATTAATATTTTC
*
16657256 ATATTATTATTATTATT
1 AT-TTATTATTAATATT
16657273 ATTATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 5 0.17
19 13 0.45
20 11 0.38
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTATTATTAATATTTTC
Done.