Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 16 of 135
Found at i:4313147 original size:29 final size:29
Alignment explanation
Indices: 4313023--4313165 Score: 103
Period size: 29 Copynumber: 4.9 Consensus size: 29
4313013 ATGGGGGTAT
* *
4313023 CATGTTTGTATCTGTAATTGTATCCGT-A
1 CATGTCTGTATCTGTAATTGTATCTGTGA
* ** * * *
4313051 TCATGTCTGCATCCATAACTATATCGGTGA
1 -CATGTCTGTATCTGTAATTGTATCTGTGA
* * * * *
4313081 CATGACTGCATATGTAACTGTATCTCTGA
1 CATGTCTGTATCTGTAATTGTATCTGTGA
* *
4313110 -TTCGACTGTATCTGTAATTGTATCTGTGA
1 CAT-GTCTGTATCTGTAATTGTATCTGTGA
4313139 CATGTCTGTATCTGTAACTT-TATCTGT
1 CATGTCTGTATCTGTAA-TTGTATCTGT
4313166 ATTATTTCTA
Statistics
Matches: 89, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
28 1 0.01
29 84 0.94
30 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (29 bp):
CATGTCTGTATCTGTAATTGTATCTGTGA
Found at i:4321744 original size:85 final size:85
Alignment explanation
Indices: 4321601--4321862 Score: 470
Period size: 85 Copynumber: 3.1 Consensus size: 85
4321591 ATTTTAAACC
* *
4321601 AACTTATTTCATAAAGATAATAATCCTAACAAAACTTCACCATATGCTTATACAACATATAAAGT
1 AACTTACTTCATAAAGATAATAATCCTAACAAAACTTCACCATATGCATATACAACATATAAAGT
4321666 AGTCAAAGTAAAGCATACTG
66 AGTCAAAGTAAAGCATACTG
*
4321686 AACTTACTTCATAAAGATAATAATCCTAACGAAACTTCACCATATGCATATACAACATATAAAGT
1 AACTTACTTCATAAAGATAATAATCCTAACAAAACTTCACCATATGCATATACAACATATAAAGT
*
4321751 GGTCAAAGTAAAGCATACTG
66 AGTCAAAGTAAAGCATACTG
* *
4321771 AACTTACTTCATAAAGATAATAATCCTAACAAAACTTTACCATATGCATAAACAACATATAAAGT
1 AACTTACTTCATAAAGATAATAATCCTAACAAAACTTCACCATATGCATATACAACATATAAAGT
4321836 AGTCAAAGTAAAGCATACTG
66 AGTCAAAGTAAAGCATACTG
4321856 AACTTAC
1 AACTTAC
4321863 ATCCTTCTCC
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 169 1.00
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.27
Consensus pattern (85 bp):
AACTTACTTCATAAAGATAATAATCCTAACAAAACTTCACCATATGCATATACAACATATAAAGT
AGTCAAAGTAAAGCATACTG
Found at i:4323471 original size:104 final size:103
Alignment explanation
Indices: 4323278--4323592 Score: 297
Period size: 104 Copynumber: 3.0 Consensus size: 103
4323268 TGGTAAGGGC
* *
4323278 ATTTTATATTGTTCTATAAGCAGGGGCATAGTCAAGGGTACTGGTAGAGGGTTTCGGTATTTCTA
1 ATTTTATATTGTTCTATAAGCAGGGGCATAGTCAAGGGAACTGATAGAGGGTTTCGGTATTTCTA
*
4323343 AAATGAAAAATTTTCATTATATCCTTTAAATTTTTTAAA
66 AAATGAAAAATTTTCATTAGATCCTTTAAA-TTTTTAAA
* * *
4323382 ATTTTATATTGTTCTATAAGCAGGGG-AGTAGTCAAGGGAATTGATAG-GGGTCTT-GATTCTTT
1 ATTTTATATTGTTCTATAAGCAGGGGCA-TAGTCAAGGGAACTGATAGAGGGT-TTCG-GTATTT
* *
4323444 TTAAAATGAAAATTTTTTCA-TAGATCCTTTAAATTTTTAAA
63 CTAAAATGAAAA-ATTTTCATTAGATCCTTTAAATTTTTAAA
* * * * ** * * *
4323485 ATTTTTATATTGCTCTATAAGCA-AGG-ATAGTTAGGGGAGTTG--ACAGGATTCTCGG-ACTTC
1 A-TTTTATATTGTTCTATAAGCAGGGGCATAGTCAAGGGAACTGATAGAGGGTT-TCGGTA-TTT
* * *
4323545 CTTAAAATAGAAAATTTTTCATTAAATCTTTTAAATTTTTAAA
63 C-TAAAAT-GAAAAATTTTCATTAGATCCTTTAAATTTTTAAA
4323588 ATTTT
1 ATTTT
4323593 CAAATTAATA
Statistics
Matches: 178, Mismatches: 21, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
100 2 0.01
101 6 0.03
102 30 0.17
103 43 0.24
104 91 0.51
105 6 0.03
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.41
Consensus pattern (103 bp):
ATTTTATATTGTTCTATAAGCAGGGGCATAGTCAAGGGAACTGATAGAGGGTTTCGGTATTTCTA
AAATGAAAAATTTTCATTAGATCCTTTAAATTTTTAAA
Found at i:4323859 original size:3 final size:3
Alignment explanation
Indices: 4323853--4323888 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
4323843 TGATATGTTG
4323853 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
4323889 GGTATGATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4324067 original size:19 final size:18
Alignment explanation
Indices: 4324040--4324079 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4324030 AATATATTAT
4324040 TTTAAAATTTAAAAAATAA
1 TTTAAAATTT-AAAAATAA
* *
4324059 TTTATAATTTATAAATAA
1 TTTAAAATTTAAAAATAA
4324077 TTT
1 TTT
4324080 TCCATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAAATTTAAAAATAA
Found at i:4324944 original size:11 final size:11
Alignment explanation
Indices: 4324928--4324952 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4324918 CAACACCCTC
4324928 TTTTTTCTTTT
1 TTTTTTCTTTT
4324939 TTTTTTCTTTT
1 TTTTTTCTTTT
4324950 TTT
1 TTT
4324953 GAAAACTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:4325134 original size:56 final size:56
Alignment explanation
Indices: 4325059--4325169 Score: 177
Period size: 56 Copynumber: 2.0 Consensus size: 56
4325049 GCACCCTTGA
*
4325059 ACGTCGTAGAAATCCCCACCGCCAGTGATACGCAGATAAATAGCAATCAGAAAACG
1 ACGTCGTAGAAATCCCCACCGCCAGTGATACGCAGATAAACAGCAATCAGAAAACG
* ** *
4325115 ACGTCGTAGAAATCCCCACCGCGAGTGATGTGCAGATAAACGGCAATCAGAAAAC
1 ACGTCGTAGAAATCCCCACCGCCAGTGATACGCAGATAAACAGCAATCAGAAAAC
4325170 AACCATTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.14
Consensus pattern (56 bp):
ACGTCGTAGAAATCCCCACCGCCAGTGATACGCAGATAAACAGCAATCAGAAAACG
Found at i:4325260 original size:86 final size:85
Alignment explanation
Indices: 4325115--4325287 Score: 274
Period size: 86 Copynumber: 2.0 Consensus size: 85
4325105 TCAGAAAACG
* * *
4325115 ACGTCGTAGAAATCCCCACCGCGAGTGATGTGCAGATAAACGGCAATCAGAAAACAACCATTTTA
1 ACGTCGTAGAAATCCCCACCGCCAGTGATCTGCAGATAAACAGCAATCAGAAAACAACCATTTTA
*
4325180 GACAGTAACAGCACACCTTTA
66 GACAGTAACAACAC-CCTTTA
* **
4325201 ACGTCGTAGAGATCCCTGCCGCCAGTGATCTGCAGATAAACAGCAATCAGAAAACAACCATTTTA
1 ACGTCGTAGAAATCCCCACCGCCAGTGATCTGCAGATAAACAGCAATCAGAAAACAACCATTTTA
4325266 GACAGTAACAACACCCTTTA
66 GACAGTAACAACACCCTTTA
4325286 AC
1 AC
4325288 AAATGAGATG
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 8 0.10
86 72 0.90
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (85 bp):
ACGTCGTAGAAATCCCCACCGCCAGTGATCTGCAGATAAACAGCAATCAGAAAACAACCATTTTA
GACAGTAACAACACCCTTTA
Found at i:4328563 original size:80 final size:80
Alignment explanation
Indices: 4328430--4328586 Score: 305
Period size: 80 Copynumber: 2.0 Consensus size: 80
4328420 CGGAAGAACT
*
4328430 AATGCTTATCAACAAGGAAAAGCATTTGCCAGGTGTTTCACTCTAACAACATGAAGTGATAGCAT
1 AATGCTTATCAACAAGGAAAAGCATTTGCCAGATGTTTCACTCTAACAACATGAAGTGATAGCAT
4328495 CCTTATCTGATGACA
66 CCTTATCTGATGACA
4328510 AATGCTTATCAACAAGGAAAAGCATTTGCCAGATGTTTCACTCTAACAACATGAAGTGATAGCAT
1 AATGCTTATCAACAAGGAAAAGCATTTGCCAGATGTTTCACTCTAACAACATGAAGTGATAGCAT
4328575 CCTTATCTGATG
66 CCTTATCTGATG
4328587 GCATCCGGAC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (80 bp):
AATGCTTATCAACAAGGAAAAGCATTTGCCAGATGTTTCACTCTAACAACATGAAGTGATAGCAT
CCTTATCTGATGACA
Found at i:4335336 original size:80 final size:80
Alignment explanation
Indices: 4335203--4335359 Score: 305
Period size: 80 Copynumber: 2.0 Consensus size: 80
4335193 CGGAAGAACT
*
4335203 AATGCTTATCAACAAGGAAAAGCATTTGCCAGGTGTTTCACTCTAACAACATGAAGTGATAGCAT
1 AATGCTTATCAACAAGGAAAAGCATTTGCCAGATGTTTCACTCTAACAACATGAAGTGATAGCAT
4335268 CCTTATCTGATGACA
66 CCTTATCTGATGACA
4335283 AATGCTTATCAACAAGGAAAAGCATTTGCCAGATGTTTCACTCTAACAACATGAAGTGATAGCAT
1 AATGCTTATCAACAAGGAAAAGCATTTGCCAGATGTTTCACTCTAACAACATGAAGTGATAGCAT
4335348 CCTTATCTGATG
66 CCTTATCTGATG
4335360 GCATCCGGAC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (80 bp):
AATGCTTATCAACAAGGAAAAGCATTTGCCAGATGTTTCACTCTAACAACATGAAGTGATAGCAT
CCTTATCTGATGACA
Found at i:4337942 original size:11 final size:12
Alignment explanation
Indices: 4337906--4337940 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
4337896 TTATCTAAAA
4337906 TAAATATTATTT
1 TAAATATTATTT
*
4337918 TAAAGA-TATTT
1 TAAATATTATTT
4337929 TAAATATTATTT
1 TAAATATTATTT
4337941 AAGAAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TAAATATTATTT
Found at i:4338288 original size:25 final size:24
Alignment explanation
Indices: 4338256--4338305 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
4338246 TAAAATTTGT
*
4338256 AAAAAAATAATTGTT-TATAATTTA
1 AAAAAAATAATT-TTAAATAATTTA
*
4338280 AAAATAAATTATTTTAAATAATTTA
1 AAAA-AAATAATTTTAAATAATTTA
4338305 A
1 A
4338306 TTAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
AAAAAAATAATTTTAAATAATTTA
Found at i:4342039 original size:20 final size:20
Alignment explanation
Indices: 4342002--4342040 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4341992 TAATTTTAAG
* **
4342002 TATTAAAAAATATCAAAAAT
1 TATTAAAAAAAAAAAAAAAT
4342022 TATTAAAAAAAAAAAAAAA
1 TATTAAAAAAAAAAAAAAA
4342041 AACTAAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (20 bp):
TATTAAAAAAAAAAAAAAAT
Found at i:4342429 original size:17 final size:16
Alignment explanation
Indices: 4342408--4342448 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
4342398 TAAATTTTAT
4342408 AAAAAATTAAAAATAA
1 AAAAAATTAAAAATAA
*
4342424 ATAAAAATTAAAAATAT
1 A-AAAAATTAAAAATAA
4342441 AAAAAATT
1 AAAAAATT
4342449 GATAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATTAAAAATAA
Found at i:4342437 original size:26 final size:27
Alignment explanation
Indices: 4342403--4342468 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
4342393 TAATTTAAAT
*
4342403 TTTATAAAAAATTAAAAATAAATAAAAA
1 TTTA-AAAAAATAAAAAATAAATAAAAA
* **
4342431 -TTAAAAATATAAAAAATTGATAAAAA
1 TTTAAAAAAATAAAAAATAAATAAAAA
*
4342457 TTTTAAAAAATA
1 TTTAAAAAAATA
4342469 TCATGAAGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 19 0.61
27 12 0.39
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
TTTAAAAAAATAAAAAATAAATAAAAA
Found at i:4345866 original size:15 final size:16
Alignment explanation
Indices: 4345834--4345874 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
4345824 TAAATATAAT
4345834 TTTC-CTTTTAGTTCG
1 TTTCTCTTTTAGTTCG
*
4345849 TTTCTCTTTTA-TTTG
1 TTTCTCTTTTAGTTCG
*
4345864 TTTCTTTTTTA
1 TTTCTCTTTTA
4345875 ATAAAATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.71
Consensus pattern (16 bp):
TTTCTCTTTTAGTTCG
Found at i:4350452 original size:20 final size:19
Alignment explanation
Indices: 4350415--4350451 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4350405 TCAACAGAAT
4350415 GTTTTGAATTCATTTTTTC
1 GTTTTGAATTCATTTTTTC
4350434 GTTTTGAATTCATTTTTT
1 GTTTTGAATTCATTTTTT
4350452 TTAAACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.08, G:0.11, T:0.65
Consensus pattern (19 bp):
GTTTTGAATTCATTTTTTC
Found at i:4355800 original size:14 final size:15
Alignment explanation
Indices: 4355774--4355813 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
4355764 ATGGAATGAG
4355774 AATAAATTTTAATTA
1 AATAAATTTTAATTA
4355789 AATAAA-TTTAATTA
1 AATAAATTTTAATTA
*
4355803 ATTAAACTTTT
1 AATAAA-TTTT
4355814 TAAACTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 13 0.59
15 6 0.27
16 3 0.14
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTTTAATTA
Found at i:4358187 original size:45 final size:45
Alignment explanation
Indices: 4358111--4358196 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
4358101 ATTTTAATAA
4358111 TAGAGGTAAATTTAAATATTAGAATCCGTTAATTACAAAAAAATT
1 TAGAGGTAAATTTAAATATTAGAATCCGTTAATTACAAAAAAATT
* * * **
4358156 TAGATGTAGATTTAAATATTTGAATTTGTTAATTACAAAAA
1 TAGAGGTAAATTTAAATATTAGAATCCGTTAATTACAAAAA
4358197 GCTTATAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (45 bp):
TAGAGGTAAATTTAAATATTAGAATCCGTTAATTACAAAAAAATT
Found at i:4359107 original size:16 final size:16
Alignment explanation
Indices: 4359088--4359126 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4359078 AAAAATAAAA
*
4359088 AATTTTAAATTTATAT
1 AATTTTAAATTAATAT
*
4359104 AATTTTGAATTAATAT
1 AATTTTAAATTAATAT
4359120 ATATTTT
1 A-ATTTT
4359127 TTTCATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AATTTTAAATTAATAT
Found at i:4368245 original size:2 final size:2
Alignment explanation
Indices: 4368238--4368266 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4368228 ATCTTCATCC
4368238 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4368267 CAACTTCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4376745 original size:20 final size:20
Alignment explanation
Indices: 4376712--4376752 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4376702 TAAAGTGGTT
4376712 GTCAAAGGGCTTTCCCAGTG
1 GTCAAAGGGCTTTCCCAGTG
* * *
4376732 GTCAATGGGTTTTCCCGGTG
1 GTCAAAGGGCTTTCCCAGTG
4376752 G
1 G
4376753 GCTGCATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.34, T:0.29
Consensus pattern (20 bp):
GTCAAAGGGCTTTCCCAGTG
Found at i:4390575 original size:12 final size:12
Alignment explanation
Indices: 4390554--4390583 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4390544 TTTGAATCTC
*
4390554 AATTTCCATATA
1 AATTTTCATATA
4390566 AATTTTCATATA
1 AATTTTCATATA
4390578 AATTTT
1 AATTTT
4390584 AGGAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTTTCATATA
Found at i:4391791 original size:14 final size:13
Alignment explanation
Indices: 4391772--4391807 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
4391762 TTATGCGTTC
4391772 TTTTATTGATTTAT
1 TTTTATT-ATTTAT
4391786 TTTTATTATTTAT
1 TTTTATTATTTAT
4391799 TTATTATTA
1 TT-TTATTA
4391808 CAATTAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:4391889 original size:19 final size:19
Alignment explanation
Indices: 4391865--4391904 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
4391855 TAAATATTGC
*
4391865 TATACATATAACACTTTAA
1 TATACATAGAACACTTTAA
4391884 TATACATAGAACACTTTAA
1 TATACATAGAACACTTTAA
4391903 TA
1 TA
4391905 AAGAATCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (19 bp):
TATACATAGAACACTTTAA
Found at i:4392008 original size:14 final size:13
Alignment explanation
Indices: 4391989--4392024 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
4391979 TTGTGCGTTC
4391989 TTTTATTGATTTAT
1 TTTTATT-ATTTAT
4392003 TTTTATTATTTAT
1 TTTTATTATTTAT
4392016 TTATTATTA
1 TT-TTATTA
4392025 CAATTAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:4399543 original size:23 final size:23
Alignment explanation
Indices: 4399499--4399543 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4399489 TGATTATTCT
* *
4399499 TTTCAAAAAATTAAAACTTAAAC
1 TTTCAAAAAAATAAAACATAAAC
4399522 TTTCAATAAAAATAAAA-ATAAA
1 TTTCAA-AAAAATAAAACATAAA
4399544 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (23 bp):
TTTCAAAAAAATAAAACATAAAC
Found at i:4409251 original size:16 final size:15
Alignment explanation
Indices: 4409229--4409271 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
4409219 AAATTTTACA
*
4409229 AATTAAAAAATAATT
1 AATTAAAAAATAAAT
4409244 ATATT-AAAAATAAAT
1 A-ATTAAAAAATAAAT
4409259 AATATAAAAAATA
1 AAT-TAAAAAATA
4409272 TCCAATAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 12 0.50
16 10 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTAAAAAATAAAT
Found at i:4409254 original size:15 final size:15
Alignment explanation
Indices: 4409232--4409271 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
4409222 TTTTACAAAT
*
4409232 TAAAAAATAATTATA
1 TAAAAAATAATAATA
*
4409247 TTAAAAATAAATAATA
1 TAAAAAAT-AATAATA
4409263 TAAAAAATA
1 TAAAAAATA
4409272 TCCAATAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAAATAATAATA
Found at i:4409318 original size:19 final size:18
Alignment explanation
Indices: 4409290--4409327 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
4409280 GGATATCGTC
4409290 AAATTTTTTAAAATATAT
1 AAATTTTTTAAAATATAT
4409308 AAATATTTTTAAAATATAT
1 AAAT-TTTTTAAAATATAT
4409327 A
1 A
4409328 TTATAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTTTTTAAAATATAT
Found at i:4414889 original size:191 final size:191
Alignment explanation
Indices: 4414563--4414946 Score: 714
Period size: 191 Copynumber: 2.0 Consensus size: 191
4414553 CAAAAACACT
* *
4414563 AAGATAATATTTGGAAAGTTACCTAGTAACTGGATTTGAGTGTAATTACTTGTAATTACACAATG
1 AAGATAAAATTTGGAAAGTCACCTAGTAACTGGATTTGAGTGTAATTACTTGTAATTACACAATG
*
4414628 ATAGCATGTTTGGGTAATTATTGTGATTGATGGGATATGATATTGATACCATTTGAGAGAATGAT
66 ATAGCATGTTTGGGTAACTATTGTGATTGATGGGATATGATATTGATACCATTTGAGAGAATGAT
*
4414693 GCCAGACACAAGCATCATAGACAGCTCGCGAACTATGTGCTTTGAGACATTGAAGGCTTCG
131 GCCAGACACAAGCATCATAGACAGCTCGCGAACTATGTACTTTGAGACATTGAAGGCTTCG
4414754 AAGATAAAATTTGGAAAGTCACCTAGTAACTGGATTTGAGTGTAATTACTTGTAATTACACAATG
1 AAGATAAAATTTGGAAAGTCACCTAGTAACTGGATTTGAGTGTAATTACTTGTAATTACACAATG
*
4414819 ATAGCATGTTTGGGTAACTATTGTGATTGATGGGATATGATATTGATACCATTTGAGAGAATGTT
66 ATAGCATGTTTGGGTAACTATTGTGATTGATGGGATATGATATTGATACCATTTGAGAGAATGAT
*
4414884 GCCAGACACAAGCATCATAGACAGCTCGCGAACTATTTACTTTGAGACATTGAAGGCTTCG
131 GCCAGACACAAGCATCATAGACAGCTCGCGAACTATGTACTTTGAGACATTGAAGGCTTCG
4414945 AA
1 AA
4414947 ATGTGGTTGA
Statistics
Matches: 187, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
191 187 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (191 bp):
AAGATAAAATTTGGAAAGTCACCTAGTAACTGGATTTGAGTGTAATTACTTGTAATTACACAATG
ATAGCATGTTTGGGTAACTATTGTGATTGATGGGATATGATATTGATACCATTTGAGAGAATGAT
GCCAGACACAAGCATCATAGACAGCTCGCGAACTATGTACTTTGAGACATTGAAGGCTTCG
Found at i:4417153 original size:29 final size:30
Alignment explanation
Indices: 4417119--4417186 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
4417109 TCAGATTTTA
4417119 ATGTATAAAATT-ACA-GAAAATCAAAATTC
1 ATGTATAAAATTCACATGAAAAT-AAAATTC
* * *
4417148 ATGTATACAATTGCACATGAAACTATAATTC
1 ATGTATAAAATT-CACATGAAAATAAAATTC
4417179 ATGTATAA
1 ATGTATAA
4417187 TTTTGATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 11 0.34
31 16 0.50
32 5 0.16
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.31
Consensus pattern (30 bp):
ATGTATAAAATTCACATGAAAATAAAATTC
Found at i:4417974 original size:64 final size:64
Alignment explanation
Indices: 4417873--4417999 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
4417863 CCATGGGGTT
*
4417873 TGAGGGTCTTGATATTATGAAGGATCGAAGGGTTGGTTGATAGGGGTTAGGAATTGATGGTCAG
1 TGAGGGTCTTGATATTATGAAGGATCGAAGGGTTGGTTGACAGGGGTTAGGAATTGATGGTCAG
*
4417937 TGAGGGTCTTGGTATTATGAAGGATCGAAGGGTTGGTTGACAGGGGTTAGGAATTGATGGTCA
1 TGAGGGTCTTGATATTATGAAGGATCGAAGGGTTGGTTGACAGGGGTTAGGAATTGATGGTCA
4418000 CTAGCACTAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.24, C:0.06, G:0.39, T:0.31
Consensus pattern (64 bp):
TGAGGGTCTTGATATTATGAAGGATCGAAGGGTTGGTTGACAGGGGTTAGGAATTGATGGTCAG
Found at i:4418445 original size:14 final size:14
Alignment explanation
Indices: 4418408--4418449 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4418398 TTATATTTTA
4418408 AATATTTAAATA-T
1 AATATTTAAATATT
4418421 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
4418435 TATATTTAAATATT
1 AATATTTAAATATT
4418449 A
1 A
4418450 GCACAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:4419452 original size:25 final size:25
Alignment explanation
Indices: 4419418--4419468 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
4419408 AATCTAAGAA
*
4419418 ATATTTTTTTTA-ATTTATCATTTTT
1 ATATATTTTTTAGATTT-TCATTTTT
*
4419443 ATATATTTTTTAGATTTTTATTTTT
1 ATATATTTTTTAGATTTTCATTTTT
4419468 A
1 A
4419469 AAAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (25 bp):
ATATATTTTTTAGATTTTCATTTTT
Found at i:4422075 original size:16 final size:16
Alignment explanation
Indices: 4422049--4422104 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
4422039 CGTTTGGTTC
4422049 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
4422065 GGTGTACTGGAATAGA
1 GCTGTAATGGAATAGA
4422081 GCTGTAATGGAATAG-
1 GCTGTAATGGAATAGA
4422096 GACTGTAAT
1 G-CTGTAAT
4422105 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.03
16 34 0.97
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:4422343 original size:58 final size:59
Alignment explanation
Indices: 4422274--4422414 Score: 189
Period size: 58 Copynumber: 2.4 Consensus size: 59
4422264 AATTTTAATG
* *
4422274 ATTATTATTAAATATAATTTAATAAAAATATCAAT-TAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAAATTAATAAAAATAT-AATATAATTTAATAATATTTTTAACATA
* * *
4422332 ATTATTATTAAATATAACTTAAT-AAAATATTATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAAATTAATAAAAATATAATATAATTTAATAATATTTTTAACATA
*
4422390 ATTATTATCAAAATATAAATTAATA
1 ATTATTAT-TAAATATAAATTAATA
4422415 TATAATCTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
56 2 0.03
57 19 0.26
58 39 0.53
59 13 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (59 bp):
ATTATTATTAAATATAAATTAATAAAAATATAATATAATTTAATAATATTTTTAACATA
Found at i:4446518 original size:27 final size:27
Alignment explanation
Indices: 4446480--4446558 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 27
4446470 ATCTAAATCA
4446480 TCCAACACTTGTGTTTCG-CAACCAAAG
1 TCCAACACTTGTGTTTCGTC-ACCAAAG
4446507 TCCAACACTTGTGTTTCGTCACCAAAG
1 TCCAACACTTGTGTTTCGTCACCAAAG
* *
4446534 TCCAACACTTGAGTTTCCTCACCAA
1 TCCAACACTTGTGTTTCGTCACCAA
4446559 GGTTTAGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 48 0.98
28 1 0.02
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.28
Consensus pattern (27 bp):
TCCAACACTTGTGTTTCGTCACCAAAG
Found at i:4448329 original size:15 final size:16
Alignment explanation
Indices: 4448309--4448338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4448299 ATAATTATGA
4448309 TATTAT-TTTTTTAAT
1 TATTATATTTTTTAAT
4448324 TATTATATTTTTTAA
1 TATTATATTTTTTAA
4448339 ATAACATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATATTTTTTAAT
Found at i:4458446 original size:28 final size:28
Alignment explanation
Indices: 4458405--4458459 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4458395 AGTAAAGACT
4458405 TGATTTCAAGATTCAAACTTCATCCAAA
1 TGATTTCAAGATTCAAACTTCATCCAAA
* *
4458433 TGATTTCAATATTCAAACTTCTTCCAA
1 TGATTTCAAGATTCAAACTTCATCCAA
4458460 CTATTTGTTG
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:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (28 bp):
TGATTTCAAGATTCAAACTTCATCCAAA
Found at i:4466079 original size:17 final size:17
Alignment explanation
Indices: 4466044--4466085 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4466034 AGAAAAATTA
*
4466044 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
4466062 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
4466079 GTTAAAG
1 GTTAAAG
4466086 GTCAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:4468031 original size:17 final size:17
Alignment explanation
Indices: 4467989--4468038 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
4467979 AGTTTTTCTA
*
4467989 AAATTTAAACTTAACAT
1 AAATTTAAACTTAAAAT
*
4468006 AGATTTAAACTTAAAAT
1 AAATTTAAACTTAAAAT
* *
4468023 AAATATAAAATTAAAA
1 AAATTTAAACTTAAAA
4468039 GTCCAATTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (17 bp):
AAATTTAAACTTAAAAT
Found at i:4468149 original size:13 final size:15
Alignment explanation
Indices: 4468131--4468163 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4468121 TTACAATTTG
4468131 ACCCAAA-TAC-AAA
1 ACCCAAAGTACAAAA
4468144 ACCCAAAGTACAAAA
1 ACCCAAAGTACAAAA
4468159 ACCCA
1 ACCCA
4468164 GCAACCTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 3 0.17
15 8 0.44
ACGTcount: A:0.58, C:0.33, G:0.03, T:0.06
Consensus pattern (15 bp):
ACCCAAAGTACAAAA
Found at i:4468810 original size:16 final size:16
Alignment explanation
Indices: 4468772--4468817 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
4468762 GTTAACAAAT
4468772 ATTTTAATAATAATAA
1 ATTTTAATAATAATAA
*
4468788 ATATTAATAATAAT-A
1 ATTTTAATAATAATAA
4468803 ATGTTTAATATATAA
1 AT-TTTAATA-ATAA
4468818 AAAAAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 3 0.12
16 19 0.73
17 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATTTTAATAATAATAA
Found at i:4470107 original size:29 final size:28
Alignment explanation
Indices: 4470002--4470166 Score: 108
Period size: 29 Copynumber: 5.6 Consensus size: 28
4469992 AACTTCAAAA
* *
4470002 AAAATTCCATCTTTGACCCTAAACTTTCC
1 AAAATTCCAT-TTTAACCCTGAACTTTCC
*
4470031 AAAATTCCATTTTTGACCCTGAAACTTAT--
1 AAAATTCCA-TTTTAACCCTG-AACTT-TCC
*
4470060 AATAATTACTATTTTAACCCTGAACTTTCC
1 AA-AATT-CCATTTTAACCCTGAACTTTCC
4470090 AAAATTCCATTTTAAACCC-G-A-TTTCACC
1 AAAATTCCATTTT-AACCCTGAACTTT--CC
* * *
4470118 AAAAATTACCATTTTACCCCTAAACTTTTC
1 -AAAATT-CCATTTTAACCCTGAACTTTCC
4470148 AAAA-TCTCATTTTTAACCC
1 AAAATTC-CA-TTTTAACCC
4470167 CGATTTTACC
Statistics
Matches: 111, Mismatches: 8, Indels: 34
0.73 0.05 0.22
Matches are distributed among these distances:
26 3 0.03
27 2 0.02
28 13 0.12
29 56 0.50
30 30 0.27
31 4 0.04
32 3 0.03
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCTGAACTTTCC
Found at i:4470190 original size:59 final size:58
Alignment explanation
Indices: 4470001--4470196 Score: 177
Period size: 59 Copynumber: 3.3 Consensus size: 58
4469991 AAACTTCAAA
** * *
4470001 AAAAATT-CCATCTTTGA-CCCTAAACTTTCCAAAATTCCATTTTTGACCCTGAAACTT-A-T
1 AAAAATTACCAT-TTT-ACCCCTAAACTTTCCAAAATTCCATTTTAAACCC-G--ATTTCACC
* * * *
4470060 AATAATTACTATTTTAACCCTGAACTTTCCAAAATTCCATTTTAAACCCGATTTCACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAAACCCGATTTCACC
* * *
4470118 AAAAATTACCATTTTACCCCTAAACTTTTCAAAA-TCTCATTTTTAACCCCGATTTTACC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTC-CA-TTTTAAACCCGATTTCACC
* *
4470177 AAAAATTATCATTTCACCCC
1 AAAAATTACCATTTTACCCC
4470197 CGGGCATCCA
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
56 3 0.03
57 3 0.03
58 33 0.29
59 73 0.63
60 3 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAAACCCGATTTCACC
Found at i:4480659 original size:59 final size:59
Alignment explanation
Indices: 4480560--4480757 Score: 217
Period size: 59 Copynumber: 3.4 Consensus size: 59
4480550 AAACTTTAAA
* * *
4480560 AAAAATT-CCATCTTTGA-CCCCAAACTTTCCAAAATTCCATTTTTAACC-CCAGTTTCACC
1 AAAAATTACCAT-TTT-ACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGA-TTTCACC
* * *
4480619 AAAAATAACCATTTTACCCCCGAACTCTT-CACAATCCCATTTATAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCCGAACT-TTCCAAAATCCCATTTTTAACCTCGATTTCACC
* * ** *
4480678 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATCTTA-TTTTAACCTCGATTTTACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
*
4480736 AAAAATTACCATTTCACCCCCG
1 AAAAATTACCATTTTACCCCCG
4480758 GGCATCCAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
58 39 0.33
59 70 0.60
60 8 0.07
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACC
Found at i:4483323 original size:18 final size:20
Alignment explanation
Indices: 4483302--4483338 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
4483292 AAAATATCAA
4483302 TTAAAAATA-AAAA-AAAAC
1 TTAAAAATATAAAATAAAAC
4483320 TTAAAAATATAAAATAAAA
1 TTAAAAATATAAAATAAAA
4483339 ATACAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (20 bp):
TTAAAAATATAAAATAAAAC
Found at i:4496564 original size:29 final size:29
Alignment explanation
Indices: 4496509--4496564 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4496499 ACGGTTGATG
** *
4496509 ATTCAAGAAAAATGCATTTTTTTTATTAA
1 ATTCAAGAAAAATGCATTAATTGTATTAA
*
4496538 ATTCAAGAAAAATGTATTAATTGTATT
1 ATTCAAGAAAAATGCATTAATTGTATT
4496565 TTTTTCATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (29 bp):
ATTCAAGAAAAATGCATTAATTGTATTAA
Found at i:4498752 original size:17 final size:17
Alignment explanation
Indices: 4498720--4498764 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
4498710 CTTTTTCTCC
*
4498720 AAGTTTGGATAAAATATT
1 AAGTTT-GAGAAAATATT
4498738 AAG-TTGAGAAAA-A-T
1 AAGTTTGAGAAAATATT
4498752 AAGTTTGAGAAAA
1 AAGTTTGAGAAAA
4498765 ATATCCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 6 0.24
17 2 0.08
18 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (17 bp):
AAGTTTGAGAAAATATT
Found at i:4498756 original size:14 final size:15
Alignment explanation
Indices: 4498737--4498767 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4498727 GATAAAATAT
4498737 TAAG-TTGAGAAAAA
1 TAAGTTTGAGAAAAA
4498751 TAAGTTTGAGAAAAA
1 TAAGTTTGAGAAAAA
4498766 TA
1 TA
4498768 TCCATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (15 bp):
TAAGTTTGAGAAAAA
Found at i:4499678 original size:25 final size:28
Alignment explanation
Indices: 4499650--4499707 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 28
4499640 GTACATAAGT
*
4499650 TAAAATTAATTAAA-AAA-TATAAGG-C
1 TAAAATGAATTAAATAAACTATAAGGAC
4499675 TAAAATGAATTAAATTAAACTATAAGGAC
1 TAAAATGAATTAAA-TAAACTATAAGGAC
4499704 TAAA
1 TAAA
4499708 TCTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 13 0.46
27 3 0.11
28 7 0.25
29 5 0.18
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.28
Consensus pattern (28 bp):
TAAAATGAATTAAATAAACTATAAGGAC
Found at i:4506605 original size:28 final size:28
Alignment explanation
Indices: 4506574--4506647 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
4506564 ATATTTAAAT
*
4506574 TATATTATTTTAATATTTAATAA-TTTTA
1 TATATTATTTTAATATTGAA-AATTTTTA
*
4506602 TATATT-TTTTATTTATTGAAAATTTTTA
1 TATATTATTTTA-ATATTGAAAATTTTTA
* *
4506630 TATAGTCATCTTAATATT
1 TATA-TTATTTTAATATT
4506648 ATTTTAATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 7 0.19
28 21 0.57
29 5 0.14
30 4 0.11
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TATATTATTTTAATATTGAAAATTTTTA
Found at i:4506631 original size:26 final size:27
Alignment explanation
Indices: 4506573--4506632 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
4506563 AATATTTAAA
*
4506573 TTATATTATTTTAATATTTAATAATTT
1 TTATATTATTTTAATATTGAATAATTT
*
4506600 TATATATT-TTTTATTTATTGAA-AATTT
1 T-TATATTATTTTA-ATATTGAATAATTT
4506627 TTATAT
1 TTATAT
4506633 AGTCATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 12 0.41
28 12 0.41
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTATATTATTTTAATATTGAATAATTT
Found at i:4509916 original size:3 final size:3
Alignment explanation
Indices: 4509908--4509937 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4509898 ACATTATCAT
4509908 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4509938 ACACTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4511156 original size:2 final size:2
Alignment explanation
Indices: 4511149--4511173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4511139 CTAACCCCTC
4511149 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4511174 AAGACAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4515845 original size:17 final size:18
Alignment explanation
Indices: 4515814--4515849 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4515804 TAGATAAATG
*
4515814 AAAATATTTTATATTAAA
1 AAAATATATTATATTAAA
4515832 AAAATATATT-TATTAAA
1 AAAATATATTATATTAAA
4515849 A
1 A
4515850 TATATGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATATATTATATTAAA
Found at i:4517309 original size:15 final size:15
Alignment explanation
Indices: 4517271--4517310 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
4517261 TTTAATTTTA
4517271 ATATTTTTAAT-AAT
1 ATATTTTTAATAAAT
*
4517285 -T-TTTTGAATAAAT
1 ATATTTTTAATAAAT
4517298 ATATTTTTAATAA
1 ATATTTTTAATAA
4517311 TTTGAATGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
12 7 0.33
13 4 0.19
14 1 0.05
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATATTTTTAATAAAT
Found at i:4517343 original size:19 final size:19
Alignment explanation
Indices: 4517321--4517357 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4517311 TTTGAATGGC
4517321 TTTTAATTTTTTAAAAATA
1 TTTTAATTTTTTAAAAATA
**
4517340 TTTTTTTTTTTTAAAAAT
1 TTTTAATTTTTTAAAAAT
4517358 TTTAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTTTTAAAAATA
Found at i:4540870 original size:14 final size:14
Alignment explanation
Indices: 4540827--4540870 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4540817 AAAAATAGAG
4540827 AAATTAAATTTCTAA
1 AAATTAAATTT-TAA
* * *
4540842 AAATAAAAGTATAA
1 AAATTAAATTTTAA
4540856 AAATTAAATTTTAA
1 AAATTAAATTTTAA
4540870 A
1 A
4540871 TTTATGAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
AAATTAAATTTTAA
Found at i:4548573 original size:16 final size:16
Alignment explanation
Indices: 4548547--4548591 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
4548537 TTTGAAATTT
4548547 AATTATTTAATTATTAA
1 AATT-TTTAATTATTAA
*
4548564 AATTTTTAATTATTTA
1 AATTTTTAATTATTAA
*
4548580 TATTTTTGAATT
1 AATTTTT-AATT
4548592 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
AATTTTTAATTATTAA
Found at i:4548626 original size:15 final size:15
Alignment explanation
Indices: 4548588--4548626 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4548578 TATATTTTTG
4548588 AATTTAAAAAATTTA
1 AATTTAAAAAATTTA
*
4548603 AATTGTAAAAATTTTA
1 AATT-TAAAAAATTTA
*
4548619 TATTTAAA
1 AATTTAAA
4548627 TTAATTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AATTTAAAAAATTTA
Found at i:4574414 original size:23 final size:24
Alignment explanation
Indices: 4574388--4574432 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4574378 TTCTAAAAAA
4574388 ATAG-CAATTTTA-TTTTGCTTTAT
1 ATAGTCAATTTTACTTTT-CTTTAT
*
4574411 ATAGTCAGTTTTACTTTTCTTT
1 ATAGTCAATTTTACTTTTCTTT
4574433 TTATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 11 0.58
25 4 0.21
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (24 bp):
ATAGTCAATTTTACTTTTCTTTAT
Found at i:4576415 original size:17 final size:17
Alignment explanation
Indices: 4576395--4576443 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
4576385 AGTTTTTCTA
* *
4576395 AAATTTAAACTTAAAAT
1 AAATATAAAATTAAAAT
4576412 AAATATAAAATTAAAAT
1 AAATATAAAATTAAAAT
4576429 AAATATAAAATTAAA
1 AAATATAAAATTAAA
4576444 TGTCCATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATAAAATTAAAAT
Found at i:4578319 original size:29 final size:31
Alignment explanation
Indices: 4578286--4578352 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
4578276 ACTTATAGGT
4578286 CCCCAAACA-ATCCAAAAATTA-CATTTTGA-
1 CCCCAAACACATCCAAAAATTACCATTTT-AC
* *
4578315 CCCCAAA-ACTTCTAAAAATTACCATTTTAC
1 CCCCAAACACATCCAAAAATTACCATTTTAC
4578345 CCCCAAAC
1 CCCCAAAC
4578353 TTTCTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 1 0.03
29 18 0.56
30 13 0.41
ACGTcount: A:0.42, C:0.33, G:0.01, T:0.24
Consensus pattern (31 bp):
CCCCAAACACATCCAAAAATTACCATTTTAC
Found at i:4578349 original size:30 final size:29
Alignment explanation
Indices: 4578299--4578361 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 29
4578289 CAAACAATCC
4578299 AAAAATTACATTTTGACCCCAAAAC-TTCT
1 AAAAATTACATTTTGACCCC-AAACTTTCT
4578328 AAAAATTACCATTTT-ACCCCCAAACTTTCT
1 AAAAATTA-CATTTTGA-CCCCAAACTTTCT
4578358 AAAA
1 AAAA
4578362 TTCTATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCCAAACTTTCT
Found at i:4578362 original size:29 final size:29
Alignment explanation
Indices: 4578299--4578605 Score: 122
Period size: 29 Copynumber: 10.5 Consensus size: 29
4578289 CAAACAATCC
*
4578299 AAAAATTA-CATTTTGACCCCAAAAC-TTCT
1 AAAAATTACCATTTT-ACCCC-CAACTTTCT
4578328 AAAAATTACCATTTTACCCCCAAACTTTCT
1 AAAAATTACCATTTTACCCCC-AACTTTCT
* * * * *
4578358 -AAAATT-CTATTTTTAACCTCGATTTCTCT
1 AAAAATTACCA-TTTTACCCCCAACTT-TCT
* * **
4578387 GAAAATTACCGTTTTACCCTGAACTTTCT
1 AAAAATTACCATTTTACCCCCAACTTTCT
* * * *
4578416 -AAAA-T-CTCATTTTTAACCTCGATTTTACT
1 AAAAATTAC-CA-TTTTACCCCCAACTTT-CT
* *
4578445 AAAAATTACCAATTTACCCTCGAACTTTCT
1 AAAAATTACCATTTTACCC-CCAACTTTCT
* * *
4578475 -AAAA-TCCCATTTTTAACCCCGA-TTTCAGT
1 AAAAATTACCA-TTTTACCCCCAACTTTC--T
*
4578504 AAAAATTACCATTTTACCCCTGAACTTTCT
1 AAAAATTACCATTTTACCCC-CAACTTTCT
* * *
4578534 -AAAA-TCCCATTTTTAACCCCGA-TTTCACT
1 AAAAATTACCA-TTTTACCCCCAACTTT--CT
* *
4578563 GAAAATTACCATTTTACCCCTAAACTTT-T
1 AAAAATTACCATTTTACCCC-CAACTTTCT
*
4578592 TAAAATT-CCATTTT
1 AAAAATTACCATTTT
4578606 TAACCTCGAA
Statistics
Matches: 209, Mismatches: 41, Indels: 57
0.68 0.13 0.19
Matches are distributed among these distances:
26 1 0.00
27 9 0.04
28 39 0.19
29 70 0.33
30 64 0.31
31 18 0.09
32 8 0.04
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCAACTTTCT
Found at i:4578413 original size:58 final size:59
Alignment explanation
Indices: 4578326--4578614 Score: 395
Period size: 59 Copynumber: 4.9 Consensus size: 59
4578316 CCCAAAACTT
** * *
4578326 CTAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCTATTTTTAACCTCGATTTCT
1 CTAAAAATTACCATTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCTCGATTTCA
* * *
4578385 CTGAAAATTACCGTTTTA-CCCTGAACTTTCTAAAA-TCTCATTTTTAACCTCGATTTTA
1 CTAAAAATTACCATTTTACCCCTGAACTTTCTAAAATTC-CATTTTTAACCTCGATTTCA
* * *
4578443 CTAAAAATTACCAATTTA-CCCTCGAACTTTCTAAAATCCCATTTTTAACCCCGATTTCA
1 CTAAAAATTACCATTTTACCCCT-GAACTTTCTAAAATTCCATTTTTAACCTCGATTTCA
* * *
4578502 GTAAAAATTACCATTTTACCCCTGAACTTTCTAAAATCCCATTTTTAACCCCGATTTCA
1 CTAAAAATTACCATTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCTCGATTTCA
* * *
4578561 CTGAAAATTACCATTTTACCCCTAAACTTTTTAAAATTCCATTTTTAACCTCGA
1 CTAAAAATTACCATTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCTCGA
4578615 AAGTCAAAAA
Statistics
Matches: 205, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
57 2 0.01
58 51 0.25
59 147 0.72
60 5 0.02
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (59 bp):
CTAAAAATTACCATTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCTCGATTTCA
Found at i:4578450 original size:30 final size:30
Alignment explanation
Indices: 4578416--4578509 Score: 70
Period size: 30 Copynumber: 3.2 Consensus size: 30
4578406 TGAACTTTCT
4578416 AAAATCTCATTTTTAACCTCGATTTTACTA
1 AAAATCTCATTTTTAACCTCGATTTTACTA
* * *
4578446 AAAAT-TACCA-ATTTACCCTCGAACTTT-CT-
1 AAAATCT--CATTTTTAACCTCG-ATTTTACTA
* * * *
4578475 AAAATCCCATTTTTAACCCCGATTTCAGTA
1 AAAATCTCATTTTTAACCTCGATTTTACTA
4578505 AAAAT
1 AAAAT
4578510 TACCATTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
28 5 0.11
29 15 0.32
30 21 0.45
31 6 0.13
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATCTCATTTTTAACCTCGATTTTACTA
Found at i:4588095 original size:3 final size:3
Alignment explanation
Indices: 4588087--4588112 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4588077 CATGGTCGTA
4588087 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
4588113 ATGGAACACT
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:4591566 original size:75 final size:75
Alignment explanation
Indices: 4591443--4591586 Score: 243
Period size: 75 Copynumber: 1.9 Consensus size: 75
4591433 AATTAGTTCA
* * *
4591443 TTCCTAGCCAACCATAATGACCAACATGCAAGCAGCCGTTCAACAACAAAGCCACCATCTCCTTC
1 TTCCTAGCCAACCATAATGACCAACATGCAAGCAGCAGTCCAACAACAAAGCCACAATCTCCTTC
4591508 TTCTTCTTCT
66 TTCTTCTTCT
* *
4591518 TTCCTAGCCAATCATAATGACCAACATGCAAGCAGCAGTCCAACAACAAAGCCACAATCTTCTTC
1 TTCCTAGCCAACCATAATGACCAACATGCAAGCAGCAGTCCAACAACAAAGCCACAATCTCCTTC
4591583 TTCT
66 TTCT
4591587 GCTGCTGCTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.32, C:0.34, G:0.10, T:0.24
Consensus pattern (75 bp):
TTCCTAGCCAACCATAATGACCAACATGCAAGCAGCAGTCCAACAACAAAGCCACAATCTCCTTC
TTCTTCTTCT
Found at i:4593870 original size:36 final size:31
Alignment explanation
Indices: 4593789--4593851 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4593779 AACAACACCA
4593789 TGATAAACAATCTATGTGTATAAATTTTATT
1 TGATAAACAATCTATGTGTATAAATTTTATT
4593820 TGATAAACAATCTATGTGTATAAATTTTATT
1 TGATAAACAATCTATGTGTATAAATTTTATT
4593851 T
1 T
4593852 TACTCACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (31 bp):
TGATAAACAATCTATGTGTATAAATTTTATT
Found at i:4596946 original size:20 final size:19
Alignment explanation
Indices: 4596900--4596948 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
4596890 GAATGTACTT
*
4596900 ACAAACCAAATATAATAATA
1 ACAAA-CAAATATAATAAAA
**
4596920 ATTAACAAAGTATAATAAAA
1 ACAAACAAA-TATAATAAAA
4596940 ACAAACAAA
1 ACAAACAAA
4596949 AACAAAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.18
Consensus pattern (19 bp):
ACAAACAAATATAATAAAA
Found at i:4597501 original size:183 final size:183
Alignment explanation
Indices: 4597193--4597558 Score: 696
Period size: 183 Copynumber: 2.0 Consensus size: 183
4597183 ACACAGTGAA
*
4597193 AAGGTTCCCCAAAACCCTTTCCCAACCAATCGTCACCAATCGCAGTATAGTTTTAATATCAACCG
1 AAGGTTCCCCAAAACCCTTTCCCAACCAATCGTCACCAATCGCAGTATAATTTTAATATCAACCG
4597258 TTTAAAGGAATGATAACCACTTCTTCCACCGTACAATCTCACCCCATGAACACACAATGGTATTG
66 TTTAAAGGAATGATAACCACTTCTTCCACCGTACAATCTCACCCCATGAACACACAATGGTATTG
*
4597323 TTGGAGCCCAATTTTGATCGGGCCCCTTTAAATTTATTTTAAAATTAAATTTG
131 TTGGAGCCCAATTTTGACCGGGCCCCTTTAAATTTATTTTAAAATTAAATTTG
* *
4597376 AAGGTTCCCTAAAACCCTTTCCCAACCAATCGTCACCAATCGCAGTGTAATTTTAATATCAACCG
1 AAGGTTCCCCAAAACCCTTTCCCAACCAATCGTCACCAATCGCAGTATAATTTTAATATCAACCG
4597441 TTTAAAGGAATGATAACCACTTCTTCCACCGTACAATCTCACCCCATGAACACACAATGGTATTG
66 TTTAAAGGAATGATAACCACTTCTTCCACCGTACAATCTCACCCCATGAACACACAATGGTATTG
4597506 TTGGAGCCCAATTTTGACCGGGCCCCTTTAAATTTATTTTAAAATTAAATTTG
131 TTGGAGCCCAATTTTGACCGGGCCCCTTTAAATTTATTTTAAAATTAAATTTG
4597559 TTTTAAATTT
Statistics
Matches: 179, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 179 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30
Consensus pattern (183 bp):
AAGGTTCCCCAAAACCCTTTCCCAACCAATCGTCACCAATCGCAGTATAATTTTAATATCAACCG
TTTAAAGGAATGATAACCACTTCTTCCACCGTACAATCTCACCCCATGAACACACAATGGTATTG
TTGGAGCCCAATTTTGACCGGGCCCCTTTAAATTTATTTTAAAATTAAATTTG
Found at i:4597555 original size:17 final size:17
Alignment explanation
Indices: 4597532--4597652 Score: 115
Period size: 17 Copynumber: 7.4 Consensus size: 17
4597522 ACCGGGCCCC
4597532 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
4597549 ATTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
***
4597566 TTTAGCCTTATTTTAAA
1 TTTAAATTTATTTTAAA
4597583 TTT-AA---ATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
4597596 TTTGAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
4597613 TTTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
4597630 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
4597647 TTTAAA
1 TTTAAA
4597653 ATTAATAAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
13 11 0.13
14 2 0.02
17 71 0.85
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:4597586 original size:6 final size:6
Alignment explanation
Indices: 4597577--4597657 Score: 62
Period size: 6 Copynumber: 13.8 Consensus size: 6
4597567 TTAGCCTTAT
* * * *
4597577 TTTAAA TTTAAA TTTTAAA TTTGAA TTT-AA TTTAAG TTTGAA TTT-AT
1 TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
4597624 TTTAAA TTTAAA ATT--A TTATAAA TTTAAA ATTAA
1 TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAA
4597658 TAAAATGTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.03
5 10 0.17
6 39 0.65
7 9 0.15
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:4597653 original size:17 final size:17
Alignment explanation
Indices: 4597620--4597656 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
4597610 AAGTTTGAAT
*
4597620 TTATTTTAAATTTAAAA
1 TTATTATAAATTTAAAA
4597637 TTATTATAAATTTAAAA
1 TTATTATAAATTTAAAA
4597654 TTA
1 TTA
4597657 ATAAAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTATAAATTTAAAA
Found at i:4599282 original size:35 final size:36
Alignment explanation
Indices: 4599231--4599302 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
4599221 GACTCGCTCC
*
4599231 ACCAGGATCCGCGTGTTTTCAACTTTT-GGATATTT
1 ACCAAGATCCGCGTGTTTTCAACTTTTGGGATATTT
4599266 ACCAAGATCCGCGTGTTTTCAACTTTTGGGATATTT
1 ACCAAGATCCGCGTGTTTTCAACTTTTGGGATATTT
4599302 A
1 A
4599303 TGCATTTGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 26 0.74
36 9 0.26
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (36 bp):
ACCAAGATCCGCGTGTTTTCAACTTTTGGGATATTT
Found at i:4599715 original size:30 final size:29
Alignment explanation
Indices: 4599679--4599835 Score: 160
Period size: 30 Copynumber: 5.3 Consensus size: 29
4599669 CCCAAACTTC
4599679 TCCAAAAATCCCATTTTTAATCC-CGAAACT
1 TCCAAAAATCCCATTTTT-A-CCTCGAAACT
*
4599709 TCCAAAAATCACATTTTTACCCTCG-AACT
1 TCCAAAAATCCCATTTTTA-CCTCGAAACT
* *
4599738 TCCAAAAATTCCATTTTTAACCTCAAAACT
1 TCCAAAAATCCCATTTTT-ACCTCGAAACT
***
4599768 TCCAAAAATTATATTTTTACCCTC-AAACT
1 TCCAAAAATCCCATTTTTA-CCTCGAAACT
*
4599797 TCTAAAAA-CTCCATTTTTTACCTCGAAACT
1 TCCAAAAATC-CCA-TTTTTACCTCGAAACT
4599827 TCCAAAAAT
1 TCCAAAAAT
4599836 TAAATTTTTA
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
29 45 0.42
30 62 0.58
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (29 bp):
TCCAAAAATCCCATTTTTACCTCGAAACT
Found at i:4599756 original size:59 final size:59
Alignment explanation
Indices: 4599650--4599873 Score: 263
Period size: 59 Copynumber: 3.8 Consensus size: 59
4599640 CTAAACTATT
* * * * *
4599650 CAAAAATTATATTTTGACCCCCAAACTTCTCCAAAAATCCCATTTTTAATCC-CGAAACTTC
1 CAAAAATTAAATTTTTACCCTCGAAC-T-TCCAAAAATTCCATTTTTAA-CCTCGAAACTTC
* * *
4599711 CAAAAATCACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCAAAACTTC
1 CAAAAATTAAATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* * * * *
4599770 CAAAAATTATATTTTTACCCTCAAACTTCTAAAAACTCCATTTTTTACCTCGAAACTTC
1 CAAAAATTAAATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* *
4599829 CAAAAATTAAATTTTTACACTCGGA-TGTCCAAAAATTCCATTTTT
1 CAAAAATTAAATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
4599874 GATTCCGATT
Statistics
Matches: 141, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
58 3 0.02
59 116 0.82
60 1 0.01
61 21 0.15
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAAAATTAAATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
Found at i:4599843 original size:30 final size:31
Alignment explanation
Indices: 4599679--4599873 Score: 167
Period size: 29 Copynumber: 6.6 Consensus size: 31
4599669 CCCAAACTTC
** * *
4599679 TCCAAAAATCCCATTTTTAATCC-CGAAACT
1 TCCAAAAATTACATTTTTTACCCTCGAAACT
*
4599709 TCCAAAAATCACA-TTTTTACCCTCG-AACT
1 TCCAAAAATTACATTTTTTACCCTCGAAACT
* * *
4599738 TCCAAAAATTCCA-TTTTTAACCTCAAAACT
1 TCCAAAAATTACATTTTTTACCCTCGAAACT
*
4599768 TCCAAAAATTATA-TTTTTACCCTC-AAACT
1 TCCAAAAATTACATTTTTTACCCTCGAAACT
* * *
4599797 TCTAAAAACTCCATTTTTTA-CCTCGAAACT
1 TCCAAAAATTACATTTTTTACCCTCGAAACT
* * *
4599827 TCCAAAAATTA-AATTTTTACACTCG-GA-T
1 TCCAAAAATTACATTTTTTACCCTCGAAACT
*
4599855 GTCCAAAAATTCCATTTTT
1 -TCCAAAAATTACATTTTT
4599874 GATTCCGATT
Statistics
Matches: 136, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.01
29 68 0.50
30 67 0.49
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (31 bp):
TCCAAAAATTACATTTTTTACCCTCGAAACT
Found at i:4599991 original size:108 final size:110
Alignment explanation
Indices: 4599806--4600023 Score: 266
Period size: 108 Copynumber: 2.0 Consensus size: 110
4599796 TTCTAAAAAC
* *
4599806 TCCATTTTTTACCTCGAAACTTCCAAAAATTAAATTTTTACACTCGGATGTCCAAAAATTCCATT
1 TCCATGTTTTACCTCAAAACTTCCAAAAATTAAATTTTTACACTCGGATGTCCAAAAATTCCATT
* *
4599871 TTTGATTCCGA-TTCTCATAAAAATTACCGTTTTACCCTCGAATGT
66 TTTGATTCCGATTTCTC-TAAAAATTACCATTGTACCCTCGAATGT
* * * * *
4599916 TCCATGTTTTATCTCAAAACTT-TAAAAATTACCA-TTTTAC-CTCGGATGTCCAAAAATTTCGT
1 TCCATGTTTTACCTCAAAACTTCCAAAAATTA-AATTTTTACACTCGGATGTCCAAAAATTCCAT
* * *
4599978 TTTTG-CTCTCGATTTTTCTAAAAATTACCATTGTACCCTCGGATGT
65 TTTTGATTC-CGATTTCTCTAAAAATTACCATTGTACCCTCGAATGT
4600024 CCAAAATTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
107 2 0.02
108 53 0.57
109 18 0.19
110 20 0.22
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.39
Consensus pattern (110 bp):
TCCATGTTTTACCTCAAAACTTCCAAAAATTAAATTTTTACACTCGGATGTCCAAAAATTCCATT
TTTGATTCCGATTTCTCTAAAAATTACCATTGTACCCTCGAATGT
Found at i:4600115 original size:28 final size:30
Alignment explanation
Indices: 4600054--4600115 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
4600044 TTAAATTTCC
*
4600054 CCAAAATTACCATTTTGCCCCCGAGAGTAT
1 CCAAAATTACCATTTTACCCCCGAGAGTAT
4600084 --AAAATTACCATTTTACCCCCG-G-GTAT
1 CCAAAATTACCATTTTACCCCCGAGAGTAT
4600110 CCAAAA
1 CCAAAA
4600116 GGTCTCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
28 24 0.83
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (30 bp):
CCAAAATTACCATTTTACCCCCGAGAGTAT
Found at i:4602186 original size:16 final size:17
Alignment explanation
Indices: 4602153--4602188 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4602143 AAATAACAAG
*
4602153 AAATAAAATAACTAAGC
1 AAATAAAACAACTAAGC
4602170 AAATAAAACAA-TAAGC
1 AAATAAAACAACTAAGC
4602186 AAA
1 AAA
4602189 AATGAAACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (17 bp):
AAATAAAACAACTAAGC
Found at i:4602364 original size:59 final size:59
Alignment explanation
Indices: 4602305--4602612 Score: 320
Period size: 59 Copynumber: 5.2 Consensus size: 59
4602295 ACCCGAGGGT
* * * * *
4602305 AAAATAGTAATTTTTGGTAAAATCGGAGTAAAAAATAGAGTTTTGAAAAGTTTAGGGGT
1 AAAATAGTAATTTTTGGTAAAATCGGAGTTAAAAATAGAATTTTGGAAAGTTCAGGGGC
* * * * * *
4602364 AAAATGGTAA-TTTTGGAAAAATC-AAGGTTAAAAACAAAATTTTGGAAGGTTCAGGGGC
1 AAAATAGTAATTTTTGGTAAAATCGGA-GTTAAAAATAGAATTTTGGAAAGTTCAGGGGC
* * * * * *
4602422 AAAA-ATGTAATTTTTGGTGAAATTAGG-GTTAAAAATAAAATTTTGGCAAGTTCAAGGGT
1 AAAATA-GTAATTTTTGGT-AAAATCGGAGTTAAAAATAGAATTTTGGAAAGTTCAGGGGC
* * * *
4602481 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGC
1 AAAATAGTAATTTTTGGTAAAATCGGAGTTAAAAATAGAATTTTGGAAAGTTCAGGGGC
* * **
4602540 AAAATAGTAATTTTTGGTAGAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTGGGGGC
1 AAAATAGTAATTTTTGGTAAAATCGGAGTTAAAAATAGAATTTTGGAAAGTTCAGGGGC
4602599 AAAA-ATGTAATTTT
1 AAAATA-GTAATTTT
4602613 AGGAAGTTTT
Statistics
Matches: 207, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
57 1 0.00
58 50 0.24
59 152 0.73
60 4 0.02
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (59 bp):
AAAATAGTAATTTTTGGTAAAATCGGAGTTAAAAATAGAATTTTGGAAAGTTCAGGGGC
Found at i:4602456 original size:30 final size:31
Alignment explanation
Indices: 4602422--4602583 Score: 96
Period size: 30 Copynumber: 5.5 Consensus size: 31
4602412 GTTCAGGGGC
4602422 AAAAAT-GTAATTTTTGGTGAAATTAGGGTT
1 AAAAATAGTAATTTTTGGTGAAATTAGGGTT
* * *
4602452 AAAAATA--AAATTTTGG-CAAGTTCAAGGG-T
1 AAAAATAGTAATTTTTGGTGAAATT--AGGGTT
* **
4602481 -AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAAATAGTAATTTTTGGTGAAATTAGGGTT
* **
4602511 AAAAATAG-AA-TTTT-G-GAAAGTTCGGGGG
1 AAAAATAGTAATTTTTGGTGAAA-TTAGGGTT
* **
4602539 CAAAATAGTAATTTTTGGT-AGAATCGGGGTT
1 AAAAATAGTAATTTTTGGTGA-AATTAGGGTT
4602570 AAAAATAG-AATTTT
1 AAAAATAGTAATTTT
4602584 GGAAAGTTTG
Statistics
Matches: 98, Mismatches: 20, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
27 4 0.04
28 21 0.21
29 18 0.18
30 31 0.32
31 22 0.22
32 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (31 bp):
AAAAATAGTAATTTTTGGTGAAATTAGGGTT
Found at i:4602596 original size:29 final size:28
Alignment explanation
Indices: 4602301--4602641 Score: 112
Period size: 29 Copynumber: 11.6 Consensus size: 28
4602291 GGATACCCGA
*
4602301 GGGT-AAAATAGTAATTTTTGGTAAA-ATCG
1 GGGTAAAAATAG-AA-TTTTGG-AAAGTTCG
* * * *
4602330 GAGTAAAAAATAGAGTTTTGAAAAGTTTAG
1 GGGT-AAAAATAGAATTTTGGAAAG-TTCG
* ** *
4602360 GGGT-AAAATGGTAATTTTGGAAAAATCAA
1 GGGTAAAAATAG-AATTTTGGAAAGTTC-G
* * * *
4602389 GGTTAAAAACAAAATTTTGGAAGGTTCAG
1 GGGTAAAAATAGAATTTTGGAAAGTTC-G
* *
4602418 GGGCAAAAAT-GTAATTTTTGGTGAAA-TTAG
1 GGGTAAAAATAG-AA-TTTT-G-GAAAGTTCG
* * * *
4602448 GGTTAAAAATAAAATTTTGGCAAGTTCAA
1 GGGTAAAAATAGAATTTTGGAAAGTTC-G
*
4602477 GGGT-AAAATGGTAATTTTTGGTGAAA--TCG
1 GGGTAAAAATAG-AA-TTTT-G-GAAAGTTCG
4602506 GGGTTAAAAATAGAATTTTGGAAAGTTCG
1 GGG-TAAAAATAGAATTTTGGAAAGTTCG
**
4602535 GGGGCAAAATAGTAATTTTTGGTAGAA--TCG
1 GGGTAAAAATAG-AA-TTTTGG-A-AAGTTCG
*
4602565 GGGTTAAAAATAGAATTTTGGAAAGTTTGG
1 GGG-TAAAAATAGAATTTTGGAAAG-TTCG
* **
4602595 GGGCAAAAAT-GTAATTTTAGG-AAGTTTTT
1 GGGTAAAAATAG-AATTTT-GGAAAG-TTCG
*
4602624 GGGTAAAAATATAATTTT
1 GGGTAAAAATAGAATTTT
4602642 TAGATAATTT
Statistics
Matches: 230, Mismatches: 49, Indels: 66
0.67 0.14 0.19
Matches are distributed among these distances:
27 9 0.04
28 28 0.12
29 105 0.46
30 55 0.24
31 25 0.11
32 8 0.03
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (28 bp):
GGGTAAAAATAGAATTTTGGAAAGTTCG
Found at i:4602609 original size:118 final size:118
Alignment explanation
Indices: 4602305--4602617 Score: 373
Period size: 118 Copynumber: 2.7 Consensus size: 118
4602295 ACCCGAGGGT
* * * * *
4602305 AAAATAGTAATTTTTGGTAAAATCGGAGTAAAAAATAGAGTTTTGAAAAGTTTAGGGGTAAAATG
1 AAAATAGTAATTTTTGGTAGAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATG
*
4602370 GTAA-TTTTGGAAAAATCAAGGTTAAAAACAAAATTTTGGAAGGTTCAGGGGC
66 GTAATTTTTGGAAAAATCAAGGTTAAAAACAAAATTTTGGAAAGTTCAGGGGC
** * * * *
4602422 AAAA-ATGTAATTTTTGGT-GAAATTAGGGTTAAAAATAAAATTTTGGCAAGTTCAAGGGTAAAA
1 AAAATA-GTAATTTTTGGTAG-AATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAA
** ** * * *
4602485 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGC
64 TGGTAATTTTTGGAAAAATCAAGGTTAAAAACAAAATTTTGGAAAGTTCAGGGGC
* *
4602540 AAAATAGTAATTTTTGGTAGAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTGGGGGCAAAAAT
1 AAAATAGTAATTTTTGGTAGAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAGGGG-TAAAAT
*
4602605 -GTAATTTTAGGAA
65 GGTAATTTTTGGAA
4602618 GTTTTTGGGT
Statistics
Matches: 160, Mismatches: 30, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
116 1 0.01
117 55 0.34
118 97 0.61
119 7 0.04
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (118 bp):
AAAATAGTAATTTTTGGTAGAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATG
GTAATTTTTGGAAAAATCAAGGTTAAAAACAAAATTTTGGAAAGTTCAGGGGC
Found at i:4605428 original size:23 final size:23
Alignment explanation
Indices: 4605398--4605481 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
4605388 TAATAGGGAT
*
4605398 TTTCAATTTACAATTCATATCAC
1 TTTCAATTCACAATTCATATCAC
*
4605421 TTTCAATTCACAATTCATATCAT
1 TTTCAATTCACAATTCATATCAC
*
4605444 TTTCAATTC-CAATTTCACTTTCAC
1 TTTCAATTCACAA-TTCA-TATCAC
*
4605468 TTTCACTTC-CAATT
1 TTTCAATTCACAATT
4605482 TTGATCACAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 3 0.06
23 36 0.67
24 15 0.28
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTCAATTCACAATTCATATCAC
Found at i:4612880 original size:58 final size:58
Alignment explanation
Indices: 4612818--4613019 Score: 183
Period size: 58 Copynumber: 3.5 Consensus size: 58
4612808 ATAAGCAATG
* * *
4612818 AAATCGGGGTGAAAAATGAGACTTTTGG-ATACTCGGGGGCAAAATGGTAA-TTTCGGTA
1 AAATCGGGGT-AAAAATG-GAATTTTGGAAGACTCAGGGGCAAAATGGTAATTTTCGGTA
* * * *
4612876 AAATCGGGGTTAAAATGGAATTTTGGAAGATTCAGGGGTAAAATGGTAATTTTCGGTG
1 AAATCGGGGTAAAAATGGAATTTTGGAAGACTCAGGGGCAAAATGGTAATTTTCGGTA
* * ** * * * * *
4612934 AAATCAGGGTTAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTTGGTG
1 AAATCGGGGTAAAAATGGAATTTTGGAAGACTCAGGGGCAAAATGGTAATTTTCGGTA
** * * *
4612992 AAATATGGGTTAAAATGGGATTTAGGAA
1 AAATCGGGGTAAAAATGGAATTTTGGAA
4613020 AGTTTTAGGG
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
56 8 0.06
57 24 0.19
58 92 0.74
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (58 bp):
AAATCGGGGTAAAAATGGAATTTTGGAAGACTCAGGGGCAAAATGGTAATTTTCGGTA
Found at i:4612882 original size:29 final size:29
Alignment explanation
Indices: 4612850--4612985 Score: 113
Period size: 28 Copynumber: 4.7 Consensus size: 29
4612840 TTTTGGATAC
*
4612850 TCGGGGGCAAAATGGTAATTTCGGTAAAA
1 TCGGGGGTAAAATGGTAATTTCGGTAAAA
* * *
4612879 TCGGGGTTAAAATGG-AATTTTGG-AAGAT
1 TCGGGGGTAAAATGGTAATTTCGGTAA-AA
* *
4612907 TCAGGGGTAAAATGGTAATTTTCGGTGAAA
1 TCGGGGGTAAAATGGTAA-TTTCGGTAAAA
* *
4612937 TCAGGGTTAAAATGG-AATTT---TAAAAGA
1 TCGGGGGTAAAATGGTAATTTCGGT-AAA-A
4612964 TTCGGGGGTAAAATGGTAATTT
1 -TCGGGGGTAAAATGGTAATTT
4612986 TTGGTGAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
25 1 0.01
26 2 0.02
27 3 0.03
28 37 0.43
29 22 0.26
30 20 0.23
31 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTCGGTAAAA
Found at i:4612948 original size:30 final size:30
Alignment explanation
Indices: 4612858--4613009 Score: 122
Period size: 29 Copynumber: 5.2 Consensus size: 30
4612848 ACTCGGGGGC
* *
4612858 AAAATGGTAA-TTTCGGTAAAATCGGGGTT
1 AAAATGGTAATTTTCGGTGAAATCAGGGTT
*
4612887 AAAATGG-AATTTT--G-GAAGATTCAGGGGT
1 AAAATGGTAATTTTCGGTGAA-A-TCAGGGTT
4612915 AAAATGGTAATTTTCGGTGAAATCAGGGTT
1 AAAATGGTAATTTTCGGTGAAATCAGGGTT
**** * * *
4612945 AAAATGG-AATTTTAAAAG-ATTCGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCAGGGTT
*
4612973 AAAATGGTAATTTTTGGTGAAAT-ATGGGTT
1 AAAATGGTAATTTTCGGTGAAATCA-GGGTT
4613003 AAAATGG
1 AAAATGG
4613010 GATTTAGGAA
Statistics
Matches: 95, Mismatches: 18, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 29 0.31
29 30 0.32
30 27 0.28
31 2 0.02
32 3 0.03
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTCGGTGAAATCAGGGTT
Found at i:4613041 original size:58 final size:59
Alignment explanation
Indices: 4612853--4613046 Score: 229
Period size: 58 Copynumber: 3.4 Consensus size: 59
4612843 TGGATACTCG
* * * * *
4612853 GGGGCAAAATGGTAA-TTTCGGTAAAATCGGGGTTAAAATGGAATTTTGG-AAGATTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGAATTTAGGAAAGATTCA
* *
4612910 GGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAATGGAATTTTA--AAAGATTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGAA-TTTAGGAAAGATTCA
* * *
4612968 GGGGTAAAATGGTAATTTTTGGTGAAAT-ATGGGTTAAAATGGGATTTAGGAAAGTTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCA-GGGTTAAAATGGAATTTAGGAAAGATTCA
*
4613027 GGGTTAAAAT-GTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
4613047 AAAAGTTTTA
Statistics
Matches: 120, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
57 19 0.16
58 83 0.69
59 18 0.15
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGAATTTAGGAAAGATTCA
Found at i:4613054 original size:30 final size:30
Alignment explanation
Indices: 4613018--4613315 Score: 454
Period size: 30 Copynumber: 9.9 Consensus size: 30
4613008 GGGATTTAGG
* *
4613018 AAAGTTTTAGGGTTAAAATGTAATTTTTGA
1 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
4613048 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
*
4613078 AAAGTTTTAGGATCAAAATGTAATTTTGGA
1 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
* *
4613108 AAAGTTTTGGGGCCAAAATGTAATTTTGGA
1 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
* *
4613138 AAAGTTTTGGGGTCAAAATGGTAATTTTTGA
1 AAAGTTTTAGGGTCAAAAT-GTAATTTTGGA
*
4613169 AAAGTCTT-GAGGTCAAAATGTAATTTTGGA
1 AAAGTTTTAG-GGTCAAAATGTAATTTTGGA
**
4613199 AAAGTTTCGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
*
4613229 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
*
4613259 AAAGTTTTAAGGTCAAAATGTAATTTTGGA
1 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
*
4613289 AAAGTTTTAGGGTTAAAATGTAATTTT
1 AAAGTTTTAGGGTCAAAATGTAATTTT
4613316 TGGACAATTT
Statistics
Matches: 248, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
30 221 0.89
31 27 0.11
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (30 bp):
AAAGTTTTAGGGTCAAAATGTAATTTTGGA
Found at i:4613319 original size:121 final size:120
Alignment explanation
Indices: 4613018--4613315 Score: 481
Period size: 121 Copynumber: 2.5 Consensus size: 120
4613008 GGGATTTAGG
*
4613018 AAAGTTTTAGGGTTAAAATGTAATTTTTGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGT
1 AAAGTTTTAGGGTCAAAATGTAATTTTTGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGT
*
4613083 TTTAGGATCAAAATGTAATTTTGGAAAAGTTTTGGGGCCAAAATGTAATTTTGGA
66 TTCAGGATCAAAATGTAATTTTGGAAAAGTTTTGGGGCCAAAATGTAATTTTGGA
* *
4613138 AAAGTTTTGGGGTCAAAATGGTAATTTTTGAAAAGTCTT-GAGGTCAAAATGTAATTTTGGAAAA
1 AAAGTTTTAGGGTCAAAAT-GTAATTTTTGAAAAGTTTTAG-GGTCAAAATGTAATTTTGGAAAA
* * *
4613202 GTTTCGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGA
64 GTTTCAGGATCAAAATGTAATTTTGGAAAAGTTTTGGGGCCAAAATGTAATTTTGGA
* * *
4613259 AAAGTTTTAAGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTT
1 AAAGTTTTAGGGTCAAAATGTAATTTTTGAAAAGTTTTAGGGTCAAAATGTAATTTT
4613316 TGGACAATTT
Statistics
Matches: 163, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
120 51 0.31
121 112 0.69
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (120 bp):
AAAGTTTTAGGGTCAAAATGTAATTTTTGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGT
TTCAGGATCAAAATGTAATTTTGGAAAAGTTTTGGGGCCAAAATGTAATTTTGGA
Found at i:4614351 original size:3 final size:3
Alignment explanation
Indices: 4614345--4614370 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4614335 TTATTAATTC
4614345 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
4614371 ACAATATGAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4614905 original size:13 final size:14
Alignment explanation
Indices: 4614872--4614917 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
4614862 AGTCCTAGGC
*
4614872 ATTGGGCCATTGTA
1 ATTGGGCCTTTGTA
4614886 ATTGGGCCTTTG-A
1 ATTGGGCCTTTGTA
*
4614899 TTTGGGCCTTTGTA
1 ATTGGGCCTTTGTA
4614913 ATTGG
1 ATTGG
4614918 ACTCTGGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.15, C:0.13, G:0.30, T:0.41
Consensus pattern (14 bp):
ATTGGGCCTTTGTA
Found at i:4614927 original size:27 final size:27
Alignment explanation
Indices: 4614873--4614928 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
4614863 GTCCTAGGCA
* *
4614873 TTGGGCCATTGTAATTGGGCCTTTGAT
1 TTGGGCCATTGTAATTGGACCTTGGAT
*
4614900 TTGGGCCTTTGTAATTGGA-CTCTGGAT
1 TTGGGCCATTGTAATTGGACCT-TGGAT
4614927 TT
1 TT
4614929 TAATTTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (27 bp):
TTGGGCCATTGTAATTGGACCTTGGAT
Found at i:4614990 original size:17 final size:16
Alignment explanation
Indices: 4614960--4614999 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
4614950 AATTTATTCC
4614960 AAATTT-ACCAAATTT
1 AAATTTAACCAAATTT
4614975 AAATTTAACACAAATTT
1 AAATTTAAC-CAAATTT
4614992 AAATTTAA
1 AAATTTAA
4615000 AAATTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.26
16 2 0.09
17 15 0.65
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTAACCAAATTT
Found at i:4615030 original size:18 final size:18
Alignment explanation
Indices: 4615009--4615057 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
4614999 AAAATTGATT
4615009 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
**
4615027 TAAATCCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
4615045 TAAATTTAGAATT
1 TAAATTTA-AATT
4615058 AACTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:4615712 original size:76 final size:76
Alignment explanation
Indices: 4615584--4616955 Score: 2258
Period size: 76 Copynumber: 18.0 Consensus size: 76
4615574 TTGGTGCTTT
* * * *
4615584 ATCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
4615649 GATAGGAAACG
66 GATAGGAAATG
* * *
4615660 ATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4615725 GATAGGAAATG
66 GATAGGAAATG
* *
4615736 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4615801 GATAGGAAATG
66 GATAGGAAATG
* * * *
4615812 ATCTTGTTCTTATTTCAATTTCGGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
4615877 GATAGAAAATG
66 GATAGGAAATG
*
4615888 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4615953 GATAGGAAATG
66 GATAGGAAATG
* * *
4615964 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATTCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4616029 GATAGGAAATG
66 GATAGGAAATG
* * *
4616040 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4616105 GATAGGAAATG
66 GATAGGAAATG
* * *
4616116 ATCTTGTTCTTACTTCAATTTCGGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4616181 GATAGGAAATG
66 GATAGGAAATG
*
4616192 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
4616257 GATAAGAAATG
66 GATAGGAAATG
* * *
4616268 ATCTTGTTCTTACTTCAATTTCGGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4616333 GATAGGAAATG
66 GATAGGAAATG
*
4616344 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
4616409 AATAGGAAATG
66 GATAGGAAATG
* *
4616420 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4616485 GATAGGAAATG
66 GATAGGAAATG
* * *
4616496 ATCTTGTTCTTACTTCAATTTCGGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4616561 GATAGGAAATG
66 GATAGGAAATG
*
4616572 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
4616637 GATAAGAAATG
66 GATAGGAAATG
* *
4616648 ATCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
4616713 GATAAGAAAATG
66 GAT-AGGAAATG
* * * * *
4616725 ATGTTGTTCTTACTTCAATTTCGGAGTTGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
4616790 GATAGGAAATG
66 GATAGGAAATG
*
4616801 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
4616866 GATAAGAAATG
66 GATAGGAAATG
* *
4616877 ATCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
4616942 GATAAGAAAATG
66 GAT-AGGAAATG
4616954 AT
1 AT
4616956 GTTGGTGCTT
Statistics
Matches: 1214, Mismatches: 80, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
76 1139 0.94
77 75 0.06
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:4618508 original size:14 final size:14
Alignment explanation
Indices: 4618489--4618533 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
4618479 TTGGGCCTAT
*
4618489 TTGGGCCATTGTAA
1 TTGGGCCTTTGTAA
*
4618503 TTGGGCCTTTG-AT
1 TTGGGCCTTTGTAA
4618516 TTGGGCCTTTGTAA
1 TTGGGCCTTTGTAA
4618530 TTGG
1 TTGG
4618534 ACTCTGGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.13, C:0.13, G:0.31, T:0.42
Consensus pattern (14 bp):
TTGGGCCTTTGTAA
Found at i:4618543 original size:27 final size:27
Alignment explanation
Indices: 4618487--4618544 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4618477 CATTGGGCCT
* *
4618487 ATTTGGGCCATTGTAATTGGGCCTTTG
1 ATTTGGGCCATTGTAATTGGACCTTGG
*
4618514 ATTTGGGCCTTTGTAATTGGA-CTCTGG
1 ATTTGGGCCATTGTAATTGGACCT-TGG
4618541 ATTT
1 ATTT
4618545 TAATTTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.16, C:0.14, G:0.28, T:0.43
Consensus pattern (27 bp):
ATTTGGGCCATTGTAATTGGACCTTGG
Found at i:4618606 original size:17 final size:16
Alignment explanation
Indices: 4618576--4618615 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
4618566 AATTTATTCC
4618576 AAATTT-ACCAAATTT
1 AAATTTAACCAAATTT
4618591 AAATTTAACACAAATTT
1 AAATTTAAC-CAAATTT
4618608 AAATTTAA
1 AAATTTAA
4618616 AAATTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.26
16 2 0.09
17 15 0.65
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTAACCAAATTT
Found at i:4618646 original size:18 final size:18
Alignment explanation
Indices: 4618625--4618673 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
4618615 AAAATTGATT
4618625 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
**
4618643 TAAATCCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
4618661 TAAATTTAGAATT
1 TAAATTTA-AATT
4618674 AACTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:4627073 original size:5 final size:5
Alignment explanation
Indices: 4627063--4627089 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4627053 CCAAAAACTT
4627063 TCCTA TCCTA TCCTA TCCTA TCCTA TC
1 TCCTA TCCTA TCCTA TCCTA TCCTA TC
4627090 TACCCCATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (5 bp):
TCCTA
Found at i:4636999 original size:29 final size:29
Alignment explanation
Indices: 4636967--4637113 Score: 103
Period size: 30 Copynumber: 5.0 Consensus size: 29
4636957 TTTGGACATC
*
4636967 CGGGGGTAAAATGGTAGTTTTGGTGAAAT
1 CGGGGGTAAAATGGTAATTTTGGTGAAAT
*
4636996 C-GGGGTCAAAAATGG-AAATTT-G-GAAAGTT
1 CGGGGGT--AAAATGGTAATTTTGGTGAAA--T
* *
4637025 CAGGGGTAAAATGGTAATTTTTGGTGGAAT
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAAT
*
4637055 CGGGGTTAAAAATGG-AATTTT-G-GAAAGTT
1 CGGGGGT-AAAATGGTAATTTTGGTGAAA--T
4637084 CGGGGGGTAAAATGGTAAATTTTGGT-AAAT
1 C-GGGGGTAAAATGGT-AATTTTGGTGAAAT
4637114 TCGAGGTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 33
0.69 0.06 0.25
Matches are distributed among these distances:
27 7 0.08
28 14 0.15
29 22 0.24
30 29 0.31
31 14 0.15
32 7 0.08
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.30
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAAT
Found at i:4637057 original size:59 final size:59
Alignment explanation
Indices: 4636969--4637164 Score: 256
Period size: 59 Copynumber: 3.3 Consensus size: 59
4636959 TGGACATCCG
*
4636969 GGGGTAAAATGGT-AGTTTTGGTGAAATCGGGGTCAAAAATGGAAATTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAAATTTGGAAAGTTCA
* * * *
4637027 GGGGTAAAATGGTAATTTTTGGTGGAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAAATTTGGAAAGTTC-A
* * *
4637087 GGGGTAAAATGGTAAATTTTGGT-AAATTCGAGGTCAAAAA-CGAAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTCAAAAATGGAAA-TTTGGAAAGTTCA
4637146 GGGGTCAAAAT-GTAATTTT
1 GGGGT-AAAATGGTAATTTT
4637165 GGAAAAGGTC
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
58 13 0.11
59 57 0.47
60 50 0.42
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.30
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAAATTTGGAAAGTTCA
Found at i:4637126 original size:60 final size:58
Alignment explanation
Indices: 4636969--4637166 Score: 265
Period size: 60 Copynumber: 3.4 Consensus size: 58
4636959 TGGACATCCG
* *
4636969 GGGGTAAAATGGTAGTTTTGGTGAAATCGGGGTCAAAAATGGAAATTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCA
* * *
4637027 GGGGTAAAATGGTAATTTTTGGTGGAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGG
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTC-A
* * *
4637087 GGGGTAAAATGGTAAATTTTGGT-AAATTCGAGGTCAAAAACGAAATTTTGGAAAGTTCA
1 GGGGTAAAATGGT-AATTTTGGTGAAA-TCGGGGTCAAAAATGGAATTTTGGAAAGTTCA
4637146 GGGGTCAAAAT-GTAATTTTGG
1 GGGGT-AAAATGGTAATTTTGG
4637167 AAAAGGTCAA
Statistics
Matches: 124, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
58 22 0.18
59 48 0.39
60 52 0.42
61 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.30
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCA
Found at i:4637162 original size:29 final size:29
Alignment explanation
Indices: 4636997--4637350 Score: 194
Period size: 30 Copynumber: 12.1 Consensus size: 29
4636987 TGGTGAAATC
* * *
4636997 GGGGTCAAAAATGGAAATTTGGAAAGTTCA
1 GGGGTC-AAAATGTAATTTTGGAAAGTTTA
** ** *
4637027 GGGGT-AAAATGGTAATTTTTGG-TGGAATC
1 GGGGTCAAAAT-GTAA-TTTTGGAAAGTTTA
* * **
4637056 GGGGTTAAAAATGGAATTTTGGAAAGTTCGG
1 GGGG-TCAAAATGTAATTTTGGAAAGTT-TA
*
4637087 GGGGT-AAAATGGTAAATTTTGGTAAA--TTC
1 GGGGTCAAAAT-GT-AATTTTGG-AAAGTTTA
* * * *
4637116 GAGGTCAAAAACGAAATTTTGGAAAGTTCA
1 GGGGTC-AAAATGTAATTTTGGAAAGTTTA
4637146 GGGGTCAAAATGTAATTTTGGAAA----A
1 GGGGTCAAAATGTAATTTTGGAAAGTTTA
* *
4637171 --GGTCAAAATGTAATATTGAAAAAGTTTTA
1 GGGGTCAAAATGTAATTTTG-GAAAG-TTTA
* * * *
4637200 -GGGTTAAAATGTAATATTAGAAAAGTTTT
1 GGGGTCAAAATGTAAT-TTTGGAAAGTTTA
* * *
4637229 GGGGTTAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTA
* *
4637259 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTA
*
4637289 GGGGTTAAAATGTAATTTTGGAAAGTTTTA
1 GGGGTCAAAATGTAATTTTGGAAAG-TTTA
* *
4637319 -GGGTCAAAATATAATTTTTGGACAGTTTA
1 GGGGTCAAAATGTAA-TTTTGGAAAGTTTA
4637348 GGG
1 GGG
4637351 ACCCACAGAG
Statistics
Matches: 258, Mismatches: 40, Indels: 52
0.74 0.11 0.15
Matches are distributed among these distances:
23 17 0.07
24 3 0.01
25 1 0.00
28 8 0.03
29 74 0.29
30 129 0.50
31 23 0.09
32 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTGGAAAGTTTA
Found at i:4637174 original size:23 final size:23
Alignment explanation
Indices: 4637148--4637194 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4637138 AAAGTTCAGG
* *
4637148 GGTCAAAATGTAATTTTGGAAAA
1 GGTCAAAATGTAATATTGAAAAA
4637171 GGTCAAAATGTAATATTGAAAAA
1 GGTCAAAATGTAATATTGAAAAA
4637194 G
1 G
4637195 TTTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.21, T:0.28
Consensus pattern (23 bp):
GGTCAAAATGTAATATTGAAAAA
Found at i:4637211 original size:30 final size:30
Alignment explanation
Indices: 4637175--4637336 Score: 211
Period size: 30 Copynumber: 5.4 Consensus size: 30
4637165 GGAAAAGGTC
* *
4637175 AAAATGTAATATTGAAAAAGTTTTAGGGTT
1 AAAATGTAATTTTGAAAAAGTTTTGGGGTT
*
4637205 AAAATGTAATATT-AGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGA-AAAAGTTTTGGGGTT
* *
4637235 AAAATATAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGAAAAAGTTTTGGGGTT
*
4637265 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGAAAAAGTTTTGGGGTT
* * *
4637295 AAAATGTAATTTTG-GAAAGTTTTAGGGTC
1 AAAATGTAATTTTGAAAAAGTTTTGGGGTT
*
4637324 AAAATATAATTTT
1 AAAATGTAATTTT
4637337 TGGACAGTTT
Statistics
Matches: 121, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
29 25 0.21
30 96 0.79
ACGTcount: A:0.39, C:0.01, G:0.22, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTTGAAAAAGTTTTGGGGTT
Found at i:4637258 original size:60 final size:60
Alignment explanation
Indices: 4637175--4637333 Score: 239
Period size: 60 Copynumber: 2.7 Consensus size: 60
4637165 GGAAAAGGTC
* *
4637175 AAAATGTAATATTGAAAAAGTTTTAGGGTTAAAATGTAATATTAGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATATTAGAAAAGTTTTGGGGTT
* * * *
4637235 AAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATATTAGAAAAGTTTTGGGGTT
* *
4637295 AAAATGTAATTTTGG-AAAGTTTTAGGGTCAAAATATAAT
1 AAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAAT
4637334 TTTTGGACAG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 21 0.24
60 68 0.76
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.38
Consensus pattern (60 bp):
AAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATATTAGAAAAGTTTTGGGGTT
Found at i:4637279 original size:19 final size:19
Alignment explanation
Indices: 4637255--4637309 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
4637245 TTTGGAAAAG
4637255 TTTTGGGGTTAAAATGTAA
1 TTTTGGGGTTAAAATGTAA
4637274 TTTT--GG--AAAA-G---
1 TTTTGGGGTTAAAATGTAA
4637285 TTTTGGGGTTAAAATGTAA
1 TTTTGGGGTTAAAATGTAA
4637304 TTTTGG
1 TTTTGG
4637310 AAAGTTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (19 bp):
TTTTGGGGTTAAAATGTAA
Found at i:4637338 original size:30 final size:29
Alignment explanation
Indices: 4637130--4637350 Score: 206
Period size: 30 Copynumber: 7.7 Consensus size: 29
4637120 TCAAAAACGA
* *
4637130 AATTTTGGAAAG-TTCAGGGGTCAAAATGT
1 AATTTTGGAAAGTTTTA-GGGTTAAAATGT
*
4637159 AATTTTGGAAA-----A-GGTCAAAATGT
1 AATTTTGGAAAGTTTTAGGGTTAAAATGT
* *
4637182 AATATTGAAAAAGTTTTAGGGTTAAAATGT
1 AATTTTG-GAAAGTTTTAGGGTTAAAATGT
* * * *
4637212 AATATTAGAAAAGTTTTGGGGTTAAAATAT
1 AAT-TTTGGAAAGTTTTAGGGTTAAAATGT
*
4637242 AATTTTGGAAAAGTTTTGGGGTTAAAATGT
1 AATTTTGG-AAAGTTTTAGGGTTAAAATGT
*
4637272 AATTTTGGAAAAGTTTTGGGGTTAAAATGT
1 AATTTTGG-AAAGTTTTAGGGTTAAAATGT
* *
4637302 AATTTTGGAAAGTTTTAGGGTCAAAATAT
1 AATTTTGGAAAGTTTTAGGGTTAAAATGT
*
4637331 AATTTTTGGACAG-TTTAGGG
1 AA-TTTTGGAAAGTTTTAGGG
4637351 ACCCACAGAG
Statistics
Matches: 168, Mismatches: 14, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
23 17 0.10
24 3 0.02
25 1 0.01
29 42 0.25
30 103 0.61
31 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
AATTTTGGAAAGTTTTAGGGTTAAAATGT
Found at i:4638486 original size:18 final size:18
Alignment explanation
Indices: 4638463--4638515 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 18
4638453 ATAATAAATG
4638463 TTATTATTTAAACCATTA
1 TTATTATTTAAACCATTA
*
4638481 TTATTATTATTAAACCCCTTA
1 TTATTA-T-TTAAA-CCATTA
*
4638502 TTATTATTGAAACC
1 TTATTATTTAAACC
4638516 GTTTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 8 0.27
19 5 0.17
20 6 0.20
21 11 0.37
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.47
Consensus pattern (18 bp):
TTATTATTTAAACCATTA
Found at i:4638489 original size:21 final size:21
Alignment explanation
Indices: 4638463--4638509 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
4638453 ATAATAAATG
4638463 TTATTATTTAAA-CCATTATTA
1 TTATTA-TTAAACCCATTATTA
*
4638484 TTATTATTAAACCCCTTATTA
1 TTATTATTAAACCCATTATTA
4638505 TTATT
1 TTATT
4638510 GAAACCGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTATTAAACCCATTATTA
Found at i:4638578 original size:12 final size:12
Alignment explanation
Indices: 4638552--4638586 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
4638542 TCAAAATAGT
4638552 TATTATTATTTAA
1 TATTATTA-TTAA
4638565 TATTATTATTAA
1 TATTATTATTAA
4638577 TATTATTATT
1 TATTATTATT
4638587 GAAGTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:4639143 original size:15 final size:16
Alignment explanation
Indices: 4639112--4639145 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4639102 GTAGGGTTAG
4639112 AATCGGGCCAAATTTGT
1 AATCGGGCC-AATTTGT
4639129 AATCGGGCC-ATTTGT
1 AATCGGGCCAATTTGT
4639144 AA
1 AA
4639146 ATGGATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (16 bp):
AATCGGGCCAATTTGT
Found at i:4639265 original size:17 final size:16
Alignment explanation
Indices: 4639243--4639340 Score: 97
Period size: 17 Copynumber: 5.8 Consensus size: 16
4639233 GTTTCTCTTT
*
4639243 TTAAATTTATAATAATA
1 TTAAATTTAAAATAA-A
*
4639260 TTAAATTTAAATTAAA
1 TTAAATTTAAAATAAA
*
4639276 TTAAAATTAAAATTAAAA
1 TTAAATTTAAAA-T-AAA
*
4639294 TTGAATTTAAAATAAA
1 TTAAATTTAAAATAAA
*
4639310 TTTAAAATTAAAATAAA
1 -TTAAATTTAAAATAAA
*
4639327 TTTAATTTCAAAAT
1 TTAAATTT-AAAAT
4639341 GGTTTGGGCC
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
16 20 0.30
17 34 0.51
18 13 0.19
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Done.