Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 10 of 290
Found at i:3311950 original size:176 final size:176
Alignment explanation
Indices: 3311656--3312009 Score: 690
Period size: 176 Copynumber: 2.0 Consensus size: 176
3311646 TTTTATCAAA
3311656 GTATAACTCAAAACATTTTTCATCAAATATAAAGTTTTAGAAAAATTCATATAAATTTTTATTTT
1 GTATAACTCAAAACATTTTTCATCAAATATAAAGTTTTAGAAAAATTCATATAAATTTTTATTTT
*
3311721 TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCGACTTCAATCTAATCTATTTA
66 TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCAACTTCAATCTAATCTATTTA
3311786 AAATTTAAGAATATATAAATATTTGAGTTGAGTTGTAATTAAATCC
131 AAATTTAAGAATATATAAATATTTGAGTTGAGTTGTAATTAAATCC
*
3311832 GTATAACTCAAAACATTTTTCATCAAATATAAAGTTTTAGAAAATTTCATATAAATTTTTATTTT
1 GTATAACTCAAAACATTTTTCATCAAATATAAAGTTTTAGAAAAATTCATATAAATTTTTATTTT
3311897 TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCAACTTCAATCTAATCTATTTA
66 TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCAACTTCAATCTAATCTATTTA
3311962 AAATTTAAGAATATATAAATATTTGAGTTGAGTTGTAATTAAATCC
131 AAATTTAAGAATATATAAATATTTGAGTTGAGTTGTAATTAAATCC
3312008 GT
1 GT
3312010 TTTAATAGTC
Statistics
Matches: 176, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 176 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (176 bp):
GTATAACTCAAAACATTTTTCATCAAATATAAAGTTTTAGAAAAATTCATATAAATTTTTATTTT
TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCAACTTCAATCTAATCTATTTA
AAATTTAAGAATATATAAATATTTGAGTTGAGTTGTAATTAAATCC
Found at i:3312181 original size:203 final size:203
Alignment explanation
Indices: 3311832--3312199 Score: 691
Period size: 203 Copynumber: 1.8 Consensus size: 203
3311822 AATTAAATCC
* *
3311832 GTATAACTCAAAACATTTTTCATCAAATATAAAGTTTTAGAAAATTTCATATAAATTTTTATTTT
1 GTATAACTCAAAACATTATTCATCAAATATAAAGTTTTAGAAAAATTCATATAAATTTTTATTTT
3311897 TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCAACTTCAATCTAATCTATTTA
66 TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCAACTTCAATCTAATCTATTTA
3311962 AAATTTAAGAATATATAAATATTTGAGTTGAGTTGTAATTAAATCCGTTTTAATAGTCTAAAGTT
131 AAATTTAAGAATATATAAATATTTGAGTTGAGTTGTAATTAAATCCGTTTTAATAGTCTAAAGTT
3312027 TTATCAAA
196 TTATCAAA
3312035 GTATAACTCAAAACATTATTCATCAAATATAAAGTTTTAGAAAAATTCATATAAATTTTTATTTT
1 GTATAACTCAAAACATTATTCATCAAATATAAAGTTTTAGAAAAATTCATATAAATTTTTATTTT
**
3312100 TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTTGACTTCAATCTAATCTATTTA
66 TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCAACTTCAATCTAATCTATTTA
*
3312165 AAATTTCAGAATATATAAATATTTGAGTTGAGTTG
131 AAATTTAAGAATATATAAATATTTGAGTTGAGTTG
3312200 AAGTCAAGTT
Statistics
Matches: 160, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
203 160 1.00
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (203 bp):
GTATAACTCAAAACATTATTCATCAAATATAAAGTTTTAGAAAAATTCATATAAATTTTTATTTT
TTCAAATAAAAGAATACTAATTAGTTTATCTAAAGAAAAAACTCAACTTCAATCTAATCTATTTA
AAATTTAAGAATATATAAATATTTGAGTTGAGTTGTAATTAAATCCGTTTTAATAGTCTAAAGTT
TTATCAAA
Found at i:3312418 original size:14 final size:14
Alignment explanation
Indices: 3312380--3312418 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3312370 TGTTTTTGAG
3312380 TTTATGATATTTTAT
1 TTTAT-ATATTTTAT
* *
3312395 TCTATTTATTTTAT
1 TTTATATATTTTAT
3312409 TTTATATATT
1 TTTATATATT
3312419 ATGTTATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTATATATTTTAT
Found at i:3317362 original size:41 final size:41
Alignment explanation
Indices: 3317196--3317351 Score: 226
Period size: 41 Copynumber: 3.8 Consensus size: 41
3317186 TTTATCGTTA
* * * * *
3317196 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAACGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
3317237 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
3317278 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
3317319 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
3317352 AAGAGCCGGT
Statistics
Matches: 106, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 101 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:3317626 original size:33 final size:33
Alignment explanation
Indices: 3317570--3317667 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
3317560 ATATGTATAT
*
3317570 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
3317602 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
3317635 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
3317668 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:3324989 original size:41 final size:41
Alignment explanation
Indices: 3324823--3324978 Score: 226
Period size: 41 Copynumber: 3.8 Consensus size: 41
3324813 TTTATCGTTA
* * * * *
3324823 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAACGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
3324864 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
3324905 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
3324946 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
3324979 AAGAGCCGGT
Statistics
Matches: 106, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 101 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:3325249 original size:33 final size:33
Alignment explanation
Indices: 3325193--3325290 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
3325183 ATAGATATGT
*
3325193 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
3325225 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
3325258 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
3325291 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:3551570 original size:44 final size:44
Alignment explanation
Indices: 3551422--3551859 Score: 211
Period size: 44 Copynumber: 10.0 Consensus size: 44
3551412 TAGGTTTATT
* **
3551422 ATACAGG-TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-A
* ** * *
3551467 ATTTCA-GATCTTATCTCCCTGAGATTACAACGGAGTAGATT-GA
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * *
3551510 A-GCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
1 ATAC-AG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * ** * ***
3551555 ATAAAGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * * * **
3551598 AT-CAGGATCTTATTTCCTTGAGGTTACAGTGGAGTAGACCGGAGAA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA--TTA-AA
* * * *
3551644 TTTCA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
** * **
3551686 AGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCGA
1 ATACAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* ** * *
3551730 AGACACTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * * ** * ***
3551774 ATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* *
3551817 AT-CAGG-TCTTATCTCCCTGATATTACAGTGGAGTAGACTTAAA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAAA
3551860 CCTAAAACCT
Statistics
Matches: 289, Mismatches: 82, Indels: 46
0.69 0.20 0.11
Matches are distributed among these distances:
41 27 0.09
42 36 0.12
43 38 0.13
44 119 0.41
45 6 0.02
46 61 0.21
47 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
Found at i:3551757 original size:87 final size:87
Alignment explanation
Indices: 3551654--3551815 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
3551644 TTTCAGATCT
* * * *
3551654 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
*
3551718 GGAGCAGATCGAAGACACTATCC
65 AGAGCAGATCGAAGACACTATCC
* * * *
3551741 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
*
3551806 GAGTAGATCG
66 GAGCAGATCG
3551816 CATCAGGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACTATCC
Found at i:3553379 original size:20 final size:20
Alignment explanation
Indices: 3553354--3553400 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3553344 GATATTTGTT
3553354 TTTATATTGATATT-ACTA-TA
1 TTTATATT-ATATTGA-TATTA
3553374 TTTATATTATATTGATATTA
1 TTTATATTATATTGATATTA
3553394 TTTATAT
1 TTTATAT
3553401 CTTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATATTATATTGATATTA
Found at i:3557079 original size:17 final size:18
Alignment explanation
Indices: 3557057--3557091 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3557047 TTAAATAATT
*
3557057 CTAAGGCTAAA-AAGCAA
1 CTAAGGCAAAACAAGCAA
3557074 CTAAGGCAAAACAAGCAA
1 CTAAGGCAAAACAAGCAA
3557092 GAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.20, G:0.17, T:0.09
Consensus pattern (18 bp):
CTAAGGCAAAACAAGCAA
Found at i:3560207 original size:50 final size:50
Alignment explanation
Indices: 3560153--3560247 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 50
3560143 AATTAAAAGG
* * *
3560153 ATTTAATTTTGAGTGACAAAAATAAAAACATCCTAAAAGTTGGGTCAAGA
1 ATTTAATTTTGAATGACAAAAATAAAAACACCCTAAAAATTGGGTCAAGA
* * *
3560203 ATTTAATTTTGAATGACCAAAATAAAAGCGCCCTAAAAATTGGGT
1 ATTTAATTTTGAATGACAAAAATAAAAACACCCTAAAAATTGGGT
3560248 GACCAACTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (50 bp):
ATTTAATTTTGAATGACAAAAATAAAAACACCCTAAAAATTGGGTCAAGA
Found at i:3560496 original size:11 final size:10
Alignment explanation
Indices: 3560461--3560495 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
3560451 ATAATTAACC
3560461 ATTTTTTATA
1 ATTTTTTATA
3560471 ATTTTTTATA
1 ATTTTTTATA
*
3560481 ATTTCTTATA
1 ATTTTTTATA
3560491 ATTTT
1 ATTTT
3560496 CATAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:3560720 original size:20 final size:22
Alignment explanation
Indices: 3560697--3560740 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3560687 AAAATATTAA
*
3560697 AAAAT-ATTTT-TATATTTTTT
1 AAAATAATTTTCTAAATTTTTT
3560717 AAAATAATTTTCTAAATTTTTT
1 AAAATAATTTTCTAAATTTTTT
3560739 AA
1 AA
3560741 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 5 0.24
22 11 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
AAAATAATTTTCTAAATTTTTT
Found at i:3564973 original size:10 final size:10
Alignment explanation
Indices: 3564958--3564982 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3564948 AGTTGATGAA
3564958 TAATACAAAT
1 TAATACAAAT
3564968 TAATACAAAT
1 TAATACAAAT
3564978 TAATA
1 TAATA
3564983 TTTTCGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
TAATACAAAT
Found at i:3565466 original size:45 final size:45
Alignment explanation
Indices: 3565402--3565491 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
3565392 TTTTGCCATG
3565402 GCATCCCCACCATCAATAAAATTAACACACTATCATTTCCATCTA
1 GCATCCCCACCATCAATAAAATTAACACACTATCATTTCCATCTA
3565447 GCATCCCCACCATCAATAAAATTAACACACTATCATTTCCATCTA
1 GCATCCCCACCATCAATAAAATTAACACACTATCATTTCCATCTA
3565492 TTTTGAGATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.27
Consensus pattern (45 bp):
GCATCCCCACCATCAATAAAATTAACACACTATCATTTCCATCTA
Found at i:3567867 original size:35 final size:35
Alignment explanation
Indices: 3567821--3567892 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3567811 GGTTCTTCCC
3567821 TTTTTATTTTGCTTTACAAATAATTTCAAAGAGGG
1 TTTTTATTTTGCTTTACAAATAATTTCAAAGAGGG
3567856 TTTTTATTTTGCTTTACAAATAATTTCAAAGAGGG
1 TTTTTATTTTGCTTTACAAATAATTTCAAAGAGGG
3567891 TT
1 TT
3567893 AATTGATGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (35 bp):
TTTTTATTTTGCTTTACAAATAATTTCAAAGAGGG
Found at i:3571764 original size:19 final size:19
Alignment explanation
Indices: 3571717--3571768 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
3571707 AGTAACAGTC
*
3571717 AATTTTTCAGTAA-AAATA
1 AATTATTCAGTAACAAATA
* * *
3571735 AAATATACAGTAACAATTA
1 AATTATTCAGTAACAAATA
3571754 AATTATTCAGTAACA
1 AATTATTCAGTAACA
3571769 GTCGATCTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (19 bp):
AATTATTCAGTAACAAATA
Found at i:3571924 original size:52 final size:51
Alignment explanation
Indices: 3571848--3572043 Score: 128
Period size: 47 Copynumber: 4.0 Consensus size: 51
3571838 ACCAACGCAC
* * * *
3571848 CAGTACGGCACATAGCGCCTCATCGG-CCGAAGCCGGAACAGTAACAGTAG
1 CAGTACGGCACAGAGCGCCTCATCGGAACAAAGCCAGAACAGTAACAGTAG
* *
3571898 CAGTACGGTACACAGAGTGCCTCATCGGAACAAATCCAGAACAGTAACAGTATG
1 CAGTACGG--CACAGAGCGCCTCATCGGAACAAAGCCAGAACAGTAACAGTA-G
** * *
3571952 --GTA---CACAGAGTACCTCATCGGAACAAATCC-GAAACAGCAACAGTA-
1 CAGTACGGCACAGAGCGCCTCATCGGAACAAAGCCAG-AACAGTAACAGTAG
* ** * *
3571997 CGGTA---CACAGAGTACCTCATCGAAACAAATCC-GAAACAGTAACAGTA
1 CAGTACGGCACAGAGCGCCTCATCGGAACAAAGCCAG-AACAGTAACAGTA
3572044 ACGGTAATAG
Statistics
Matches: 129, Mismatches: 10, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
46 1 0.01
47 81 0.63
50 8 0.06
52 19 0.15
53 19 0.15
54 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.14
Consensus pattern (51 bp):
CAGTACGGCACAGAGCGCCTCATCGGAACAAAGCCAGAACAGTAACAGTAG
Found at i:3571949 original size:47 final size:47
Alignment explanation
Indices: 3571890--3572049 Score: 250
Period size: 47 Copynumber: 3.4 Consensus size: 47
3571880 CCGGAACAGT
* *
3571890 AACAGTAGCAGTACGGTACACAGAGTGCCTCATCGGAACAAATCC-A
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
*
3571936 GAACAGTAACAGTATGGTACACAGAGTACCTCATCGGAACAAATCCGA
1 -AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
* *
3571984 AACAGCAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
3572031 AACAGTAACAGTAACGGTA
1 AACAGTAACAGT-ACGGTA
3572050 ATAGTAACAA
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
47 97 0.93
48 7 0.07
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:3575266 original size:46 final size:46
Alignment explanation
Indices: 3575199--3575324 Score: 182
Period size: 46 Copynumber: 2.7 Consensus size: 46
3575189 ATGAAATGTG
* * *
3575199 TAAGACCATGGTTGAAAGATACTATGGCAACGTGACATG-CAATGAA
1 TAAGACCATGGTTGAAAGATACTATGGCAACATGACA-GAAAACGAA
*
3575245 TAAGACCATGGTTGAAAGATACTATGGCAACATGACAGAAAACGAG
1 TAAGACCATGGTTGAAAGATACTATGGCAACATGACAGAAAACGAA
* *
3575291 TAAGACCATAGTTGAAAGATACTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACTATGGCAACATG
3575325 TCAAAGATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
45 1 0.01
46 72 0.99
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACTATGGCAACATGACAGAAAACGAA
Found at i:3580928 original size:39 final size:39
Alignment explanation
Indices: 3580872--3580981 Score: 175
Period size: 39 Copynumber: 2.8 Consensus size: 39
3580862 ACAAAGCATG
*
3580872 CGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
3580913 CGGGACTTAGCCCGGATATAACGCCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
3580952 CGGGACTTAGCCCGGATATAGCACCAGCAC
1 CGGGACTTAGCCCGGATATAACACCAGCAC
3580982 TTAGCCTGCG
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
39 57 0.88
40 2 0.03
41 6 0.09
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:3581006 original size:39 final size:39
Alignment explanation
Indices: 3580984--3581094 Score: 177
Period size: 39 Copynumber: 2.8 Consensus size: 39
3580974 ACCAGCACTT
*
3580984 AGCCTGCGGACTTTAAGTCCGGATATATTTCCAGCATAA
1 AGCCTGCGGACTTCAAGTCCGGATATATTTCCAGCATAA
* *
3581023 AGCCTGCGAACTTCAAGTCCTGATATATTTCCAGCATAA
1 AGCCTGCGGACTTCAAGTCCGGATATATTTCCAGCATAA
* *
3581062 AGCCTACGGACTTCAAGTCCGGATATTTTTCCA
1 AGCCTGCGGACTTCAAGTCCGGATATATTTCCA
3581095 ATACCATGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (39 bp):
AGCCTGCGGACTTCAAGTCCGGATATATTTCCAGCATAA
Found at i:3583458 original size:8 final size:8
Alignment explanation
Indices: 3583441--3583470 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3583431 TCACAGAAAT
3583441 CATACATG
1 CATACATG
*
3583449 CATGCATG
1 CATACATG
3583457 CATACATG
1 CATACATG
3583465 CATACA
1 CATACA
3583471 CATAAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (8 bp):
CATACATG
Found at i:3592775 original size:13 final size:13
Alignment explanation
Indices: 3592759--3592783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3592749 ATAAAATTAA
3592759 AGAAAAAAAAATT
1 AGAAAAAAAAATT
3592772 AGAAAAAAAAAT
1 AGAAAAAAAAAT
3592784 ATAGGAAGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAAAATT
Found at i:3610230 original size:34 final size:34
Alignment explanation
Indices: 3610192--3610260 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
3610182 TTTGACTGAG
*
3610192 TTGCTGCTAGAGTATGATTTTGAAACATAAGTTT
1 TTGCTGCTAGAATATGATTTTGAAACATAAGTTT
3610226 TTGCTGCTAGAATATGATTTTGAAACATAAGTTT
1 TTGCTGCTAGAATATGATTTTGAAACATAAGTTT
3610260 T
1 T
3610261 GTTTGGTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (34 bp):
TTGCTGCTAGAATATGATTTTGAAACATAAGTTT
Found at i:3623784 original size:46 final size:47
Alignment explanation
Indices: 3623724--3623987 Score: 326
Period size: 46 Copynumber: 5.7 Consensus size: 47
3623714 TGTCATAGTG
* * *
3623724 TCTTTTAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATGTCAGGTTGCCATGGTA
* *
3623770 TCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATGTCAGGTTGCCATGGTA
* * ** *
3623816 TCTTTCAACCATGGTCTTATTTA-TTTCCCGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATGTCAGGTTGCCATGGTA
* *
3623862 TCTTTCAACCATGGTCTTA--CATGTTTCATATCAGGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCAT-TTTCATGTCAGGTTGCCATGGTA
* *
3623908 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATGTCAGGTTGCCATGGTA
* *
3623954 TCTTTCAACCATGGTCTTACGCA-TTTCATATCAG
1 TCTTTCAACCATGGTCTTACTCATTTTCATGTCAG
3623988 AGAGCACACT
Statistics
Matches: 197, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
44 1 0.01
45 4 0.02
46 190 0.96
48 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.41
Consensus pattern (47 bp):
TCTTTCAACCATGGTCTTACTCATTTTCATGTCAGGTTGCCATGGTA
Found at i:3626163 original size:18 final size:20
Alignment explanation
Indices: 3626148--3626184 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3626138 TAATAATAAA
*
3626148 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
3626168 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
3626185 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:3638019 original size:99 final size:95
Alignment explanation
Indices: 3637786--3638141 Score: 383
Period size: 99 Copynumber: 3.7 Consensus size: 95
3637776 CAATTTATGC
* * *
3637786 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTC-GGGCACGCCGAGGTAATTTTT
1 TTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-A---TT
* * **
3637850 TTTAATTTCTGCTTTTCTCAATTTCTGCTTTTAATT
61 TTCAATTTCTGCTTTT-TCAATTTATGCTTCAAATT
*
3637886 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
1 TTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
*
3637951 ATTTCTG-TTTTTCAATTTTTGCCTTACAAATTCT
65 ATTTCTGCTTTTTCAATTTATG-CTT-CAAA-T-T
3637985 GCTTTTC-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
1 --TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* * *
3638049 AATTTC-GTTTTTTTAATTTATGTTTCTAAA--
64 AATTTCTGCTTTTTCAATTTATGCTTC-AAATT
* *
3638079 -----AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
1 TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
3638139 TTT
66 TTT
3638142 TTGTTTGTCA
Statistics
Matches: 234, Mismatches: 12, Indels: 32
0.84 0.04 0.12
Matches are distributed among these distances:
88 60 0.26
95 9 0.04
96 7 0.03
97 15 0.06
98 7 0.03
99 75 0.32
100 43 0.18
101 18 0.08
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (95 bp):
TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
TTTCTGCTTTTTCAATTTATGCTTCAAATT
Found at i:3638179 original size:73 final size:72
Alignment explanation
Indices: 3638078--3638649 Score: 695
Period size: 73 Copynumber: 7.9 Consensus size: 72
3638068 ATGTTTCTAA
* * *
3638078 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACGCTGAGGTATTTTCAATTTC
3638143 TGTTTGTC
65 TGTTTGTC
* *
3638151 AAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCT----CA-----AGGTATTTTCAATTTCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTTTCAATTTCT
*
3638207 GTTTTTC
66 GTTTGTC
* *
3638214 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACGCTGAGGTATTTTCAATT
*
3638279 TTTGTTTGTC
63 TCTGTTTGTC
*
3638289 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACACGCTGAGGTATTTTCAATTTC
*
3638354 TGTCTT-TAA
65 TGT-TTGT-C
* * *
3638363 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACACGCTGAGGTATTTTCAATTTC
*
3638428 TGTTTTTC
65 TGTTTGTC
* * * *
3638436 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCA-AGACGCTGAGGTAATTTCAATTT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTTTCAATTT
3638500 -TGTTTGTC
64 CTGTTTGTC
*
3638508 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACACGCTGAGGTATTTTCAATTTC
3638573 TGTCTT-TC
65 TGT-TTGTC
* * * * *
3638581 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA-AGACGCTGAGGTGTTTTCCATTT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTTTCAATTT
3638645 CTGTT
64 CTGTT
3638650 CTTCAATTTT
Statistics
Matches: 438, Mismatches: 37, Indels: 49
0.84 0.07 0.09
Matches are distributed among these distances:
63 21 0.05
65 34 0.08
68 2 0.00
70 38 0.09
71 1 0.00
72 28 0.06
73 147 0.34
74 74 0.17
75 93 0.21
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTTTCAATTTCT
GTTTGTC
Found at i:3638558 original size:145 final size:142
Alignment explanation
Indices: 3638078--3638655 Score: 733
Period size: 145 Copynumber: 4.0 Consensus size: 142
3638068 ATGTTTCTAA
* * *
3638078 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
* * *
3638143 TGTTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAG--G-T-A--T-TTTCA
66 TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTCA
3638201 ATTTCTGTTTTTC
131 ATTTCTG-TTTTC
* *
3638214 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATT
* * *
3638279 TTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAT
64 TCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTA-
*
3638344 TTTCAATTTCTGTCTTTAA
126 TTTCAATTTCTGT-TTT-C
* * * *
3638363 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
* *
3638428 TGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGACGCTGAGGTAATT
66 TGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGT-ATT
3638493 TCAATTT-TGTTTGTC
128 TCAATTTCTGTTT-TC
* *
3638508 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
* *
3638573 TGTCTT-TCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTT
66 TGT-TTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGT-AT
*
3638637 TTCCATTTCTGTTCTTC
127 TTCAATTTCTGTT-TTC
3638654 AA
1 AA
3638656 TTTTGTGTTT
Statistics
Matches: 397, Mismatches: 24, Indels: 30
0.88 0.05 0.07
Matches are distributed among these distances:
138 110 0.28
142 1 0.00
143 1 0.00
144 1 0.00
145 129 0.32
146 15 0.04
147 85 0.21
148 16 0.04
149 39 0.10
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (142 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTCA
ATTTCTGTTTTC
Found at i:3638776 original size:88 final size:88
Alignment explanation
Indices: 3638624--3639125 Score: 405
Period size: 88 Copynumber: 5.8 Consensus size: 88
3638614 GAACCTCAAG
* * * *
3638624 ACGCTGAGGTGTTTTCCATTTCTGTTCTTCAATTTTGTGTTTCAAAAAAATCAGCTCATATTGCG
1 ACGCTGAGGTATTTT-CAATTCTGTT-TTCAATTTTGTTTTTCAAAAAAATCAACTCATATTGCG
*
3638689 AGTGGTGAGTTGAGCCTTGACTCAC
64 AGAGGTGAGTTGAGCCTTGACTCAC
*
3638714 ACGCTGAGGTATTTTCAATTCTGTTTTCAATTTTGTTTTTCCAAAAAATCAACTCATATTGCGAG
1 ACGCTGAGGTATTTTCAATTCTGTTTTCAATTTTGTTTTTCAAAAAAATCAACTCATATTGCGAG
* **
3638779 AGGTGAGTTCAGCC-T--CAGAC
66 AGGTGAGTTGAGCCTTGACTCAC
* * *
3638799 ACG-TGAGATATTTTCAATTTCTTTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTG
1 ACGCTGAGGTATTTTCAA-TTC--TGTTTTCAATTT-TGTTTTTCAAAAAAATCAACTCATATTG
*
3638863 C--GAGGTGAGTTGAGCCTCAGA-TCAC
62 CGAGAGGTGAGTTGAGCCT-TGACTCAC
* * * * * * *
3638888 ACGCCGAGGT-TTTTCAATTGATTTTTTTTAATTTATGCTTTGC--AAAAATCAACTCATATTAC
1 ACGCTGAGGTATTTTCAATT--CTGTTTTCAATTT-TGTTTTTCAAAAAAATCAACTCATATTGC
* **
3638950 GAGAGGTGAGTTGAGCCTCGGGTCAC
63 GAGAGGTGAGTTGAGCCTTGACTCAC
** *
3638976 ATAC-GAGGTATTTTCAAATCT-TTTTACAAATTTT-TGTTTT---AAAAATCAA-TCATATTGC
1 ACGCTGAGGTATTTTCAATTCTGTTTT-C-AATTTTGT-TTTTCAAAAAAATCAACTCATATTGC
* *
3639034 GAGAAGTGAGTTGAGCCTTGGCTCAC
63 GAGAGGTGAGTTGAGCCTTGACTCAC
** * * * * *
3639060 GTGCTGAGCTATTTTCAATTTCTGTTTTTAATGTTTAG-TTTT--AAAGAGTCAATTCATATTGC
1 ACGCTGAGGTATTTTCAA-TTCTGTTTTCAAT-TTT-GTTTTTCAAAAAAATCAACTCATATTGC
3639122 GAGA
63 GAGA
3639126 AATGAGTTAA
Statistics
Matches: 341, Mismatches: 45, Indels: 54
0.77 0.10 0.12
Matches are distributed among these distances:
84 46 0.13
85 37 0.11
86 47 0.14
87 34 0.10
88 138 0.40
89 21 0.06
90 18 0.05
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (88 bp):
ACGCTGAGGTATTTTCAATTCTGTTTTCAATTTTGTTTTTCAAAAAAATCAACTCATATTGCGAG
AGGTGAGTTGAGCCTTGACTCAC
Found at i:3638872 original size:174 final size:171
Alignment explanation
Indices: 3638562--3639087 Score: 534
Period size: 174 Copynumber: 3.0 Consensus size: 171
3638552 CGTTGAGGTA
* * * * *
3638562 TTTTCAATTTCTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA-AGAC
1 TTTTCAATTTATG-CTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACAC
* * * * *
3638626 GCTGAGGTGTTTTCCATTTCTGTTCTTCAATTTTGTGTTTCAAAAAAATCAGCTCATATTGCGAG
65 G-TGAGGTATTTTCAATTTCTTTTTTTCAATTTTGT-TTTCAAAAAAATCAACTCATATTGCGA-
3638691 TGGTGAGTTGAGCCTTGACTCACACGCTGAGGTATTTTCAATTCTG
127 -GGTGAGTTGAGCCTTGACTCACACGCTGAGGTATTTTCAATTCTG
* *
3638737 TTTTCAATTT-TGTTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGACAC
1 TTTTCAATTTATG-CTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACAC
*
3638801 GTGAGATATTTTCAATTTCTTTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGA
65 GTGAGGTATTTTCAATTTC-TTTTTTTCAATTT-TGTTT-TCAAAAAAATCAACTCATATTGCGA
* * * *
3638866 GGTGAGTTGAGCCTCAGA-TCACACGCCGAGGT-TTTTCAATTGATTT
127 GGTGAGTTGAGCCT-TGACTCACACGCTGAGGTATTTTCAATT--CTG
* * * * *
3638912 TTTTTAATTTATGCTTTGC-AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTTCAATTTATGCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACAC
* * *
3638976 ATACGAGGTATTTTCAA-ATC-TTTTTACAAATTTTTGTTTT---AAAAATCAA-TCATATTGCG
65 GT--GAGGTATTTTCAATTTCTTTTTTTC-AA-TTTTGTTTTCAAAAAAATCAACTCATATTGCG
* ** *
3639035 AGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTG
126 AG--GTGAGTTGAGCCTTGACTCACACGCTGAGGTATTTTCAA-TTCTG
3639084 TTTT
1 TTTT
3639088 TAATGTTTAG
Statistics
Matches: 298, Mismatches: 35, Indels: 39
0.80 0.09 0.10
Matches are distributed among these distances:
170 12 0.04
171 10 0.03
172 28 0.09
173 16 0.05
174 131 0.44
175 55 0.18
176 34 0.11
177 12 0.04
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (171 bp):
TTTTCAATTTATGCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACG
TGAGGTATTTTCAATTTCTTTTTTTCAATTTTGTTTTCAAAAAAATCAACTCATATTGCGAGGTG
AGTTGAGCCTTGACTCACACGCTGAGGTATTTTCAATTCTG
Found at i:3658242 original size:14 final size:13
Alignment explanation
Indices: 3658220--3658291 Score: 99
Period size: 13 Copynumber: 5.4 Consensus size: 13
3658210 CGCTGAGGTA
*
3658220 TTTTTAATTTCTA
1 TTTTTAATTTCTG
3658233 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
*
3658247 CTTTTAATTTCTG
1 TTTTTAATTTCTG
3658260 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
*
3658274 CTTTTAATTTCTG
1 TTTTTAATTTCTG
3658287 TTTTT
1 TTTTT
3658292 CAAAAATCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
13 29 0.56
14 23 0.44
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.67
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:3658263 original size:27 final size:27
Alignment explanation
Indices: 3658221--3658294 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
3658211 GCTGAGGTAT
*
3658221 TTTTAATTTCTATTTTTCAATTTCTGC
1 TTTTAATTTCTGTTTTTCAATTTCTGC
3658248 TTTTAATTTCTGTTTTTCAATTTCTGC
1 TTTTAATTTCTGTTTTTCAATTTCTGC
3658275 TTTTAATTTCTGTTTTTCAA
1 TTTTAATTTCTGTTTTTCAA
3658295 AAATCAACTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.64
Consensus pattern (27 bp):
TTTTAATTTCTGTTTTTCAATTTCTGC
Found at i:3658424 original size:99 final size:99
Alignment explanation
Indices: 3658248--3658455 Score: 312
Period size: 99 Copynumber: 2.1 Consensus size: 99
3658238 CAATTTCTGC
** * *
3658248 TTTT-AATTTCTGTTTTTCAATTTCTGCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 TTTTCAATTTCTGTTTTTCAATTTCTGCTTACAAATTCTGCTTTTC-AAAATCAACTCATATTGC
* *
3658312 GAGAGGTGAGTTGAGCCTCAGGGCATGCTGAGGTA
65 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
* *
3658347 TTTTCAATTTCTGTTTTTCAATTTTTGCCTTACAAATTCTGCTTTTC-AAATCAACTCATATTGT
1 TTTTCAATTTCTGTTTTTCAATTTCTG-CTTACAAATTCTGCTTTTCAAAATCAACTCATATTGC
3658411 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
65 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
3658446 TTTTCAATTT
1 TTTTCAATTT
3658456 TCATTTTTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
99 63 0.64
100 21 0.21
101 15 0.15
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (99 bp):
TTTTCAATTTCTGTTTTTCAATTTCTGCTTACAAATTCTGCTTTTCAAAATCAACTCATATTGCG
AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
Found at i:3658678 original size:76 final size:76
Alignment explanation
Indices: 3658592--3659062 Score: 631
Period size: 76 Copynumber: 6.3 Consensus size: 76
3658582 TTGAGCCTCA
* *
3658592 AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTC
1 AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
3658657 AAGACACGCTG
66 AAGACACGCTG
* * * *
3658668 AGGTAATTTCAATTTTTGTTTGTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
*
3658730 AAGACACGTTG
66 AAGACACGCTG
* * *
3658741 AGGTATTTTCAATTTCTGTCTTT-AAAAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTC
1 AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
*
3658805 AAGACACGTTG
66 AAGACACGCTG
* *
3658816 AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATGAACTCATATTGCGATAGGTGAGTTGAACCTC
1 AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
3658881 AAG--ACGCTG
66 AAGACACGCTG
* * * * *
3658890 AGGTAATTTCAATTTTTGTTTGTC---AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC
1 AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
*
3658952 AAGACACGTTG
66 AAGACACGCTG
* * * *
3658963 ATGTATTTTCAATTTCTATCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTC
1 AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
3659028 AAG--ACGCTG
66 AAGACACGCTG
* * *
3659037 AGGTGTTTTCCATTTCTGTTCTTCAA
1 AGGTATTTTCAATTTCTGTTTTTCAA
3659063 TTTTTGTGTT
Statistics
Matches: 345, Mismatches: 41, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
71 37 0.11
73 89 0.26
74 51 0.15
75 68 0.20
76 100 0.29
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (76 bp):
AGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
AAGACACGCTG
Found at i:3658960 original size:147 final size:142
Alignment explanation
Indices: 3658481--3659062 Score: 633
Period size: 147 Copynumber: 4.0 Consensus size: 142
3658471 ATGTTTCTAA
* * * * *
3658481 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCTTTAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
* * *
3658546 TGTTTGTCAAAACTCAACTCA-ATTGCAAGAGGTGAGTTGAGCCTCAAG--G-T-A--T-TTTCA
66 TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTCA
3658603 ATTTCTGTTTTTC
131 ATTTCTG-TTTTC
* *
3658616 AAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
1 ---AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
* * *
3658681 TTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA
63 TTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTA
*
3658746 TTTTCAATTTCTGTCTTTAAA
126 -TTTCAATTTCTGT-TTT--C
* * * * * *
3658767 AAAAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
* * *
3658832 TGTTTTTCAAAAAAAATGAACTCATATTGCGATAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
66 TGTTTGTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGT-AT
*
3658897 TTCAATTTTTGTTTGTC
127 TTCAATTTCTGTTT-TC
* * *
3658914 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGATGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
* * *
3658979 TATCTT-TCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGT
66 TGT-TTGTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGT-A
*
3659043 TTTCCATTTCTGTTCTTC
126 TTTCAATTTCTGTT-TTC
3659061 AA
1 AA
3659063 TTTTTGTGTT
Statistics
Matches: 387, Mismatches: 36, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
138 79 0.20
139 26 0.07
143 1 0.00
144 1 0.00
145 1 0.00
147 132 0.34
148 71 0.18
149 37 0.10
150 1 0.00
151 38 0.10
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (142 bp):
AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTC
TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTCA
ATTTCTGTTTTC
Found at i:3658993 original size:222 final size:222
Alignment explanation
Indices: 3658481--3659062 Score: 814
Period size: 222 Copynumber: 2.7 Consensus size: 222
3658471 ATGTTTCTAA
* * * * * *
3658481 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCTTTAGGACACGCTGAGGTAATTTCAATTT-
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
* *** * * * *
3658545 T-TGTTT-GTCAAAACTCAACTCA-ATTGCAAGAGGTGAGTTGAGCCTC---A-----AGGTATT
66 TATCTTTAAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATT
*
3658599 TTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAAGACAC
131 TTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGA-AC
3658664 GCTGAGGTAATTTCAATTTTTGTTTGTC
195 GCTGAGGTAATTTCAATTTTTGTTTGTC
*
3658692 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
* * *
3658757 TGTCTTT-AAAAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTA
66 TATCTTTAAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTA
*
3658821 TTTTCAATTTCTGTTTTTCAAAAAAAATGAACTCATATTGCGATAGGTGAGTTGAACCTCAAG-A
129 TTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGAA
3658885 CGCTGAGGTAATTTCAATTTTTGTTTGTC
194 CGCTGAGGTAATTTCAATTTTTGTTTGTC
*
3658914 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGATGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
* *
3658979 TATCTTTCAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTT
66 TATCTTTAAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATT
* *
3659044 TTCCATTTCTGTTCTTCAA
131 TTCAATTTCTGTTTTTCAA
3659063 TTTTTGTGTT
Statistics
Matches: 331, Mismatches: 26, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
211 57 0.17
212 1 0.00
213 14 0.04
214 22 0.07
219 1 0.00
221 28 0.08
222 99 0.30
223 43 0.13
224 66 0.20
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (222 bp):
AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
TATCTTTAAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATT
TTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAGAACG
CTGAGGTAATTTCAATTTTTGTTTGTC
Found at i:3659169 original size:15 final size:14
Alignment explanation
Indices: 3659133--3659165 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3659123 CGCTGAGGTA
3659133 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
3659147 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
3659161 TTTTC
1 TTTTC
3659166 CAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:3659171 original size:91 final size:91
Alignment explanation
Indices: 3659031--3659508 Score: 424
Period size: 91 Copynumber: 5.3 Consensus size: 91
3659021 GAACCTCAAG
* * * * * * *
3659031 ACGCTGAGGTGTTTTCCATTTCTGTTCTTCAATTTTTGTGTTTCAAAAAAATCAGCTCATATTGC
1 ACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCAAAAAAATCAACTCATATTGC
*
3659096 GAGTGGTGAGTTGAGCCTTGACTCAC
66 GAGAGGTGAGTTGAGCCTTGACTCAC
* *
3659122 ACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCCAAAAAATCAACTCATATTCC
1 ACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCAAAAAAATCAACTCATATTGC
* * *
3659187 GAGATGTGAGTTCAGCCTCAGA---AC
66 GAGAGGTGAGTTGAGCCT-TGACTCAC
* * * *
3659211 ACGCTGAGATATTTTCAATTTCTTTTTTTTTC-AATTTATGTTTGTCAAAAAAATCAACTCATAT
1 ACGCTGAGGTATTTTCAAATTC--TGTTTTTCAAATTT-TGTTTTTCAAAAAAATCAACTCATAT
* *
3659275 TGCGAGAGGTGAGTTGAGCC-TCAGGTCAC
63 TGCGAGAGGTGAGTTGAGCCTTGA-CTCAC
* * * ** * *
3659304 ACGCCGATGTATTTTC-AATTGAT-TTTTTTTAATTTATGCTTTGC--AAAAATCAACTCATATT
1 ACGCTGAGGTATTTTCAAATT-CTGTTTTTCAAATTT-TGTTTTTCAAAAAAATCAACTCATATT
* * **
3659365 ACGAGAGGTGAGTTGAGCCTCGGGTCAC
64 GCGAGAGGTGAGTTGAGCCTTGACTCAC
** * * * *
3659393 ATACCGAGGTATTTTCAAAATCTATTTTACAAATTTTG-TTTT---AAAAATCAACTCATATTGC
1 ACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCAAAAAAATCAACTCATATTGC
* *
3659454 GAGAAGTGAGTTGAGCCTTGGCTCAC
66 GAGAGGTGAGTTGAGCCTTGACTCAC
** * *
3659480 GTGCTGAGCTATTTTCAATTTCTGTTTTT
1 ACGCTGAGGTATTTTCAAATTCTGTTTTT
3659509 AATGTCTAGT
Statistics
Matches: 317, Mismatches: 57, Indels: 30
0.78 0.14 0.07
Matches are distributed among these distances:
87 62 0.20
88 3 0.01
89 79 0.25
90 22 0.07
91 131 0.41
92 5 0.02
93 15 0.05
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (91 bp):
ACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCAAAAAAATCAACTCATATTGC
GAGAGGTGAGTTGAGCCTTGACTCAC
Found at i:3660230 original size:15 final size:15
Alignment explanation
Indices: 3660210--3660275 Score: 66
Period size: 15 Copynumber: 4.4 Consensus size: 15
3660200 CCACTAGCCA
3660210 CACTTGCTCCACCAC
1 CACTTGCTCCACCAC
3660225 CACTTGCTCCACCAC
1 CACTTGCTCCACCAC
* *
3660240 CTAC-TCCAT-TAGCCA-
1 C-ACTTGC-TCCA-CCAC
3660255 CACTTGCTCCACCAC
1 CACTTGCTCCACCAC
3660270 CACTTG
1 CACTTG
3660276 TACCTACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
14 6 0.15
15 29 0.71
16 6 0.15
ACGTcount: A:0.21, C:0.48, G:0.08, T:0.23
Consensus pattern (15 bp):
CACTTGCTCCACCAC
Found at i:3660253 original size:45 final size:45
Alignment explanation
Indices: 3660188--3660275 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
3660178 CTAGCCTTTG
3660188 CCACCACCAACTCCACTAGCCACACTTGCTCCACCACCACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCTCCACCACCACTTGCT
* *
3660233 CCACCACCTACTCCATTAGCCACACTTGCTCCACCACCACTTG
1 CCACCACCAACTCCACTAGCCACACTTGCTCCACCACCACTTG
3660276 TACCTACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.50, G:0.07, T:0.19
Consensus pattern (45 bp):
CCACCACCAACTCCACTAGCCACACTTGCTCCACCACCACTTGCT
Found at i:3660848 original size:23 final size:23
Alignment explanation
Indices: 3660776--3660888 Score: 84
Period size: 23 Copynumber: 4.8 Consensus size: 23
3660766 TTCTTAATAT
* *
3660776 TATATTATGTATATATTATTTTAA
1 TATATTATGTATATA-TATTATAC
* * * *
3660800 TATATTAGGTATAT-TCTAAATTC
1 TATATTATGTATATATAT-TATAC
*
3660823 TATATTACGTATATATATTATAC
1 TATATTATGTATATATATTATAC
* * *
3660846 TATTTTATGTACATATCTTTAATAC
1 TATATTATGTATATAT-ATT-ATAC
*
3660871 TATATTATTTATATATAT
1 TATATTATGTATATATAT
3660889 ATATTTTTTC
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
22 2 0.03
23 30 0.45
24 18 0.27
25 17 0.25
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (23 bp):
TATATTATGTATATATATTATAC
Found at i:3660861 original size:25 final size:26
Alignment explanation
Indices: 3660833--3660890 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
3660823 TATATTACGT
*
3660833 ATATATATT-ATACTATTTTATGTAC
1 ATATATATTAATACTATATTATGTAC
* * *
3660858 ATATCT-TTAATACTATATTATTTAT
1 ATATATATTAATACTATATTATGTAC
3660883 ATATATAT
1 ATATATAT
3660891 ATTTTTTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 2 0.08
25 23 0.88
26 1 0.04
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATATTAATACTATATTATGTAC
Found at i:3660935 original size:22 final size:22
Alignment explanation
Indices: 3660905--3660946 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3660895 TTTCTACATG
*
3660905 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
3660927 TTATATTATGTATGTATTTT
1 TTATATTATGTATATATTTT
3660947 TTTACACTAT
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:0.02, G:0.07, T:0.62
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:3660957 original size:26 final size:25
Alignment explanation
Indices: 3660911--3660975 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
3660901 CATGTTATCT
* *
3660911 TATGTATATATTTTAATTATATTATG
1 TATGTAT-TTTTTTAACTATATTATG
3660937 TATGTATTTTTTTACACTATATTATG
1 TATGTATTTTTTTA-ACTATATTATG
**
3660963 TACATATTTTTTT
1 TATGTATTTTTTT
3660976 TTATATCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 6 0.18
26 28 0.82
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (25 bp):
TATGTATTTTTTTAACTATATTATG
Found at i:3668460 original size:15 final size:17
Alignment explanation
Indices: 3668423--3668466 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3668413 CTAATATCCT
3668423 AATCCAAAAATTATCAG
1 AATCCAAAAATTATCAG
*
3668440 AATCCAAAAGTTA-CA-
1 AATCCAAAAATTATCAG
3668455 AATCCAACAAAT
1 AATCCAA-AAAT
3668467 GATGTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 12 0.50
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (17 bp):
AATCCAAAAATTATCAG
Found at i:3677146 original size:20 final size:21
Alignment explanation
Indices: 3677123--3677164 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3677113 GGTATCAGAG
*
3677123 CTTTTTCTGG-GATTTTTTTT
1 CTTTGTCTGGCGATTTTTTTT
3677143 CTTTGTCTGGCGATTTTTTTT
1 CTTTGTCTGGCGATTTTTTTT
3677164 C
1 C
3677165 CTGATTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.05, C:0.14, G:0.17, T:0.64
Consensus pattern (21 bp):
CTTTGTCTGGCGATTTTTTTT
Found at i:3679795 original size:33 final size:33
Alignment explanation
Indices: 3679698--3679796 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
3679688 TTTCTTCTTG
* *
3679698 ACATTCCAGCTCCTATCCAGCAACAAAACACCC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
*
3679731 ACATTCCAGCTCCTGTCCAGCAGCAAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
* *
3679764 ACATTCCAACTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
3679797 CCACTCAGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.33, C:0.41, G:0.08, T:0.17
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
Found at i:3685010 original size:19 final size:18
Alignment explanation
Indices: 3684970--3685010 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
3684960 TTTATAATAT
3684970 TTTATTTTATTATTTCAG
1 TTTATTTTATTATTTCAG
3684988 TTTATTTTATAGTATTT-AG
1 TTTATTTTAT--TATTTCAG
3685007 TTTA
1 TTTA
3685011 AGTATTGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTATTTTATTATTTCAG
Found at i:3691815 original size:25 final size:26
Alignment explanation
Indices: 3691783--3691837 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
3691773 TTATTAAATT
*
3691783 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
3691808 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
3691833 A-ATAT
1 ATATAT
3691838 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:3692024 original size:44 final size:45
Alignment explanation
Indices: 3691975--3692069 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
3691965 TTACACCTCT
* * *
3691975 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTTC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
3692019 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
3692064 ATTACA
1 ATTACA
3692070 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:3692069 original size:16 final size:16
Alignment explanation
Indices: 3692048--3692085 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3692038 TTGATTTGCT
*
3692048 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
3692064 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
3692080 AATACA
1 ATTACA
3692086 GCGAACCAAA
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:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:3693698 original size:30 final size:30
Alignment explanation
Indices: 3693633--3693700 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
3693623 AATTTTTGAA
*
3693633 TTAATAAA-GATAAAATTGTACTTTAGTCAT
1 TTAA-AAATGATAAAATTGTACTTTAATCAT
* *
3693663 CTAAAAATGATAAAATTTTGA-TTTAATCAT
1 TTAAAAATGATAAAATTGT-ACTTTAATCAT
3693693 TTAAAAAT
1 TTAAAAAT
3693701 TATATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 3 0.09
30 28 0.88
31 1 0.03
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (30 bp):
TTAAAAATGATAAAATTGTACTTTAATCAT
Found at i:3693709 original size:22 final size:23
Alignment explanation
Indices: 3693673--3693733 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
3693663 CTAAAAATGA
* *
3693673 TAAAATTTTGATTTAATC-ATT-
1 TAAAATTATAATTTAATCTATTG
*
3693694 TAAAAATTATATTTTAA-CTATTG
1 T-AAAATTATAATTTAATCTATTG
3693717 TAAAATTATAATTTAAT
1 TAAAATTATAATTTAAT
3693734 TTCGATCCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.06
22 29 0.91
23 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
TAAAATTATAATTTAATCTATTG
Found at i:3704781 original size:134 final size:133
Alignment explanation
Indices: 3704575--3704866 Score: 370
Period size: 134 Copynumber: 2.2 Consensus size: 133
3704565 TGTCAAACGC
* * * * * * * * *
3704575 CGAATATCGCTTTCGTTTTAAATAATTTTTTAAAATATATGAATGAATTTTTGAAGGGATACTCG
1 CGAATTTCGCCTTCGTTTTAAAGAATTTTTTAAAAGACATGAAGGAAATCTTGAAGGGACACTCG
*
3704640 ATCATTTT-AAGCAAACGCGAAATTGCAACCCAACACGTTAAGGCACTATTTCGCGAATTGCAAA
66 ATCATTTTGAA-CAAACGCGAAATTGCAACCCAACACGTTAAGGCACTATTCCGCGAATTGCAAA
3704704 ATAT
130 ATAT
* * *
3704708 CGAATTTCGCCTTCGTTTTAAAGAATTCTTTTAAAAGGCATGAGGGAAATCTTGAAGGGACATTC
1 CGAATTTCGCCTTCGTTTTAAAGAATT-TTTTAAAAGACATGAAGGAAATCTTGAAGGGACACTC
* * * * * *
3704773 GATTATTTTGCACAAACGCGAAATTGCCACCCAACACGTTAGGGCACTATTCCGCGGATTGCCAA
65 GATCATTTTGAACAAACGCGAAATTGCAACCCAACACGTTAAGGCACTATTCCGCGAATTGCAAA
3704838 ATAT
130 ATAT
* *
3704842 CGGATTTCACCTTCGTTTTAAAGAA
1 CGAATTTCGCCTTCGTTTTAAAGAA
3704867 AATTGTTTTA
Statistics
Matches: 136, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
133 24 0.18
134 111 0.82
135 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (133 bp):
CGAATTTCGCCTTCGTTTTAAAGAATTTTTTAAAAGACATGAAGGAAATCTTGAAGGGACACTCG
ATCATTTTGAACAAACGCGAAATTGCAACCCAACACGTTAAGGCACTATTCCGCGAATTGCAAAA
TAT
Found at i:3707414 original size:15 final size:15
Alignment explanation
Indices: 3707390--3707419 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3707380 TATTTATTTA
*
3707390 TTTATTTGTATATAT
1 TTTATATGTATATAT
3707405 TTTATATGTATATAT
1 TTTATATGTATATAT
3707420 GTGATTGGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTATATGTATATAT
Found at i:3716106 original size:43 final size:43
Alignment explanation
Indices: 3716045--3716131 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
3716035 TGTATGTATG
3716045 TATGTCGTATACGTACATGGATTCCACAATATTTATGGTATAA
1 TATGTCGTATACGTACATGGATTCCACAATATTTATGGTATAA
*
3716088 TATGTCGTATACGTACATGGATTCCACAATCTTTATGGTATAA
1 TATGTCGTATACGTACATGGATTCCACAATATTTATGGTATAA
3716131 T
1 T
3716132 TATTCTTTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (43 bp):
TATGTCGTATACGTACATGGATTCCACAATATTTATGGTATAA
Found at i:3723538 original size:21 final size:21
Alignment explanation
Indices: 3723514--3723556 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3723504 TCATTATCCC
*
3723514 CTCCTTGATCTCAAATAAATT
1 CTCCTTAATCTCAAATAAATT
3723535 CTCCTTAATCTCAAATAAATT
1 CTCCTTAATCTCAAATAAATT
3723556 C
1 C
3723557 AATAATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (21 bp):
CTCCTTAATCTCAAATAAATT
Found at i:3723985 original size:31 final size:31
Alignment explanation
Indices: 3723943--3724006 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
3723933 ATTTCTTTAA
3723943 ATATATATATTTGAA-TCACAATTAAAATTTT
1 ATATATATATTTGAACT-ACAATTAAAATTTT
*
3723974 ATATATCTATTTGAACTACAATTAAAATTTT
1 ATATATATATTTGAACTACAATTAAAATTTT
3724005 AT
1 AT
3724007 GTATGTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (31 bp):
ATATATATATTTGAACTACAATTAAAATTTT
Found at i:3732546 original size:20 final size:18
Alignment explanation
Indices: 3732502--3732548 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
3732492 TATACACATT
3732502 TAAAAATATAAAAAATTA
1 TAAAAATATAAAAAATTA
*
3732520 -AATAAATATATAAAACTTGA
1 TAA-AAATATA-AAAAATT-A
3732540 TAAAAATAT
1 TAAAAATAT
3732549 TTATAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 7 0.29
19 6 0.25
20 7 0.29
21 2 0.08
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAAAATATAAAAAATTA
Found at i:3732613 original size:31 final size:32
Alignment explanation
Indices: 3732551--3732614 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
3732541 AAAAATATTT
* *
3732551 ATAAAATCTAGAAAGAAATATAATTTATGAAA
1 ATAAAATCTACAAAGAAATATAATATATGAAA
*
3732583 ATAAAATTTACAAA-AAATATAATA-ATTGAAA
1 ATAAAATCTACAAAGAAATATAATATA-TGAAA
3732614 A
1 A
3732615 GAAATTAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 1 0.04
31 15 0.54
32 12 0.43
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (32 bp):
ATAAAATCTACAAAGAAATATAATATATGAAA
Found at i:3736356 original size:12 final size:12
Alignment explanation
Indices: 3736339--3736364 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3736329 TTAATCCCTT
3736339 TCAATTTTGATA
1 TCAATTTTGATA
3736351 TCAATTTTGATA
1 TCAATTTTGATA
3736363 TC
1 TC
3736365 GAGTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (12 bp):
TCAATTTTGATA
Found at i:3739097 original size:75 final size:75
Alignment explanation
Indices: 3739009--3739151 Score: 178
Period size: 75 Copynumber: 1.9 Consensus size: 75
3738999 ATTGTTTCTG
* * ** ** * *
3739009 ATTATGTATTGTTTCAAAACATAAAATTTTGGTTAATTTGGTTAACTTTCAAGATAAAAATATAT
1 ATTATATAGTGTTTCAAAACATAAAATTTCAGTTAATTCAGTTAACTTTCAAGACAAAAACATAT
3739074 ATTTCAATTA
66 ATTTCAATTA
* * * *
3739084 ATTATATAGTGTTTTAAGATATAAAATTTCAGTTTATTCAGTTAACTTTCAAGACAAAAACATAT
1 ATTATATAGTGTTTCAAAACATAAAATTTCAGTTAATTCAGTTAACTTTCAAGACAAAAACATAT
3739149 ATT
66 ATT
3739152 ATGTATTTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
75 56 1.00
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.43
Consensus pattern (75 bp):
ATTATATAGTGTTTCAAAACATAAAATTTCAGTTAATTCAGTTAACTTTCAAGACAAAAACATAT
ATTTCAATTA
Found at i:3740576 original size:18 final size:20
Alignment explanation
Indices: 3740553--3740589 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
3740543 ATTTAATCCC
3740553 TTTATTTT-TTAAA-ATAAA
1 TTTATTTTATTAAATATAAA
3740571 TTTATTTTATTAAATATAA
1 TTTATTTTATTAAATATAA
3740590 GTTCAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTTTATTAAATATAAA
Found at i:3750238 original size:37 final size:37
Alignment explanation
Indices: 3750176--3750248 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
3750166 ATTTAGTTGA
*
3750176 GAAATAATTTAAAGATAGTTATTTTTATAAAATAAAG
1 GAAATAATTTAAAAATAGTTATTTTTATAAAATAAAG
* *
3750213 GAAATAATTTAAAAATTA-TTGTTTTTATAAAGTAAA
1 GAAATAATTTAAAAA-TAGTTATTTTTATAAAATAAA
3750249 TTATATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.40
Consensus pattern (37 bp):
GAAATAATTTAAAAATAGTTATTTTTATAAAATAAAG
Found at i:3751793 original size:27 final size:26
Alignment explanation
Indices: 3751745--3751798 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
3751735 ATTTAACAAC
* * * *
3751745 TTATTTAGTTTAATATATTTTGTTAA
1 TTATTTAATTTAAAATAATTTGCTAA
3751771 TTATTTAATGTTAAAATAATTTGCTAA
1 TTATTTAAT-TTAAAATAATTTGCTAA
3751798 T
1 T
3751799 AATGAAAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (26 bp):
TTATTTAATTTAAAATAATTTGCTAA
Found at i:3761567 original size:19 final size:20
Alignment explanation
Indices: 3761520--3761569 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
3761510 GTACATTACA
3761520 AAAAAAAATTATAAAATTTC
1 AAAAAAAATTATAAAATTTC
3761540 ATAAAAAAATTA-AAAATTAT-
1 A-AAAAAAATTATAAAATT-TC
3761560 AAAAAAAATT
1 AAAAAAAATT
3761570 CTAAGCAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.32
20 8 0.29
21 11 0.39
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAAATTATAAAATTTC
Found at i:3765667 original size:9 final size:9
Alignment explanation
Indices: 3765640--3765680 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
3765630 TGGCTGAAGC
3765640 TCTTCCTCT
1 TCTTCCTCT
* *
3765649 TCCTCATCT
1 TCTTCCTCT
3765658 TCTTCCTCT
1 TCTTCCTCT
3765667 TCTTCCTCT
1 TCTTCCTCT
3765676 TCTTC
1 TCTTC
3765681 TTCACCTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:3765859 original size:21 final size:21
Alignment explanation
Indices: 3765835--3765874 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3765825 ATCTTCCTCC
3765835 TCACCTGCAT-CTTCATCTTGA
1 TCACCTGC-TGCTTCATCTTGA
3765856 TCACCTGCTGCTTCATCTT
1 TCACCTGCTGCTTCATCTT
3765875 CCTCATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.15, C:0.35, G:0.10, T:0.40
Consensus pattern (21 bp):
TCACCTGCTGCTTCATCTTGA
Found at i:3765882 original size:24 final size:24
Alignment explanation
Indices: 3765824--3765882 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 24
3765814 TCACCTGATC
*
3765824 CATCTTCCTCCTCACCTGCATCTT
1 CATCTTCCTCATCACCTGCATCTT
*
3765848 CATC-T--TGATCACCTGC-TGCTT
1 CATCTTCCTCATCACCTGCAT-CTT
3765869 CATCTTCCTCATCA
1 CATCTTCCTCATCA
3765883 TCATTGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 1 0.04
23 1 0.04
24 9 0.32
ACGTcount: A:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (24 bp):
CATCTTCCTCATCACCTGCATCTT
Found at i:3770499 original size:13 final size:13
Alignment explanation
Indices: 3770481--3770510 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3770471 TTATTAATAT
3770481 TTTAATAAGATAC
1 TTTAATAAGATAC
*
3770494 TTTAATAAGATAT
1 TTTAATAAGATAC
3770507 TTTA
1 TTTA
3770511 TTATTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (13 bp):
TTTAATAAGATAC
Found at i:3771354 original size:28 final size:28
Alignment explanation
Indices: 3771314--3771376 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
3771304 AAAAGAAGAT
3771314 AGAAAGACTAACAGAGAGCAAACGTGAA
1 AGAAAGACTAACAGAGAGCAAACGTGAA
3771342 AGAAAGACTAACAGAGAGCAAACGTGAA
1 AGAAAGACTAACAGAGAGCAAACGTGAA
3771370 AGAAAGA
1 AGAAAGA
3771377 AGAAAGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.56, C:0.13, G:0.25, T:0.06
Consensus pattern (28 bp):
AGAAAGACTAACAGAGAGCAAACGTGAA
Found at i:3784144 original size:19 final size:19
Alignment explanation
Indices: 3784101--3784144 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3784091 ATATTTATTT
3784101 TTTTATATTTTAAATATAA
1 TTTTATATTTTAAATATAA
*
3784120 -TTTATATTTTGAAT-TAAA
1 TTTTATATTTTAAATAT-AA
3784138 TTTTATA
1 TTTTATA
3784145 AATAGTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 15 0.68
19 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTATATTTTAAATATAA
Found at i:3793870 original size:15 final size:14
Alignment explanation
Indices: 3793850--3793880 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3793840 ATAATATTGG
3793850 ATATGCTGCAAGTGA
1 ATATGCTGCAA-TGA
3793865 ATATGCTGCAATGA
1 ATATGCTGCAATGA
3793879 AT
1 AT
3793881 CTGGTTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (14 bp):
ATATGCTGCAATGA
Found at i:3800520 original size:18 final size:19
Alignment explanation
Indices: 3800499--3800539 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3800489 TTATTGAATC
3800499 ACATATT-AAC-ATAAATAA
1 ACATATTAAACTATAAA-AA
3800517 ACATATTAAACTATAAAAA
1 ACATATTAAACTATAAAAA
3800536 ACAT
1 ACAT
3800540 TTACATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 9 0.43
20 5 0.24
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (19 bp):
ACATATTAAACTATAAAAA
Found at i:3801558 original size:23 final size:23
Alignment explanation
Indices: 3801528--3801575 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3801518 ACTTGCTTAT
3801528 ATCAAGTGCAAGAATTCAGCGGC
1 ATCAAGTGCAAGAATTCAGCGGC
3801551 ATCAAGTGCAAGAATTCAGCGGC
1 ATCAAGTGCAAGAATTCAGCGGC
3801574 AT
1 AT
3801576 TTTCGGCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (23 bp):
ATCAAGTGCAAGAATTCAGCGGC
Found at i:3802143 original size:79 final size:73
Alignment explanation
Indices: 3802082--3802289 Score: 201
Period size: 72 Copynumber: 2.8 Consensus size: 73
3802072 GTATGAATAT
* * * * *
3802082 GGAGGTGAACACTGAGTTG-CTACCATATCTTATAGAAGATTCTACAAGTGCT-AAAGAGATGGG
1 GGAGATGAACACTGAATTGTC-ACCAAAGCTTATAGAAGATTCTACAAGTACTAAAAGAGATGGG
3802145 TAAGACTAA
65 TAAGACTAA
*
3802154 GGAGATGAACATTGAATTGTCACCAAAGCTTATAGAAGATTCTACAAGTACTAAAAGAGATGGGT
1 GGAGATGAACACTGAATTGTCACCAAAGCTTATAGAAGATTCTACAAGTACTAAAAGAGATGGGT
* * * *
3802219 CATAATAT
66 AAGACTAA
* * * *
3802227 GGAGGAGTGGAGCA-TCGAATTGAT-ATCAAAGCTTATAGAAGATTCTCCAAGTGCT-AAAGAGA
1 GGA-GA-T-GAACACT-GAATTG-TCACCAAAGCTTATAGAAGATTCTACAAGTACTAAAAGAGA
3802289 T
61 T
3802290 AGATATGAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
72 44 0.38
73 20 0.17
74 2 0.02
75 10 0.09
76 38 0.33
77 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (73 bp):
GGAGATGAACACTGAATTGTCACCAAAGCTTATAGAAGATTCTACAAGTACTAAAAGAGATGGGT
AAGACTAA
Found at i:3802208 original size:72 final size:75
Alignment explanation
Indices: 3802110--3802371 Score: 264
Period size: 75 Copynumber: 3.5 Consensus size: 75
3802100 GCTACCATAT
* *
3802110 CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAAGACTAAGGA-GA-T-GAACATTGAATT
1 CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAAGAATAAGGAGGAGTGGAACATCGAATT
3802172 G-TCACCAAAG
66 GAT-ACCAAAG
* * * * *
3802182 CTTATAGAAGATTCTACAAGTACTAAAAGAGATGGGTCATAATATGGAGGAGTGGAGCATCGAAT
1 CTTATAGAAGATTCTACAAGTGCT-AAAGAGATGGGTAAGAATAAGGAGGAGTGGAACATCGAAT
*
3802247 TGATATCAAAG
65 TGATACCAAAG
* * * * * * *
3802258 CTTATAGAAGATTCTCCAAGTGCTAAAGAGATAGATATGAATATGGAGGAG-GAGAACGTTGAAT
1 CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAAGAATAAGGAGGAGTG-GAACATCGAAT
** * **
3802322 TGATGGCGATT
65 TGATACCAAAG
* *
3802333 CTTATAGAAGATTCTTCAAATGCTAAAGAGATGGGTAAG
1 CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAAG
3802372 GATGTGGCAG
Statistics
Matches: 156, Mismatches: 28, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
72 23 0.15
73 19 0.12
74 3 0.02
75 71 0.46
76 39 0.25
77 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.26
Consensus pattern (75 bp):
CTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAAGAATAAGGAGGAGTGGAACATCGAATT
GATACCAAAG
Found at i:3806731 original size:19 final size:19
Alignment explanation
Indices: 3806707--3806756 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3806697 TTGTTTGATA
3806707 AAATTAATCTTATTTTATT
1 AAATTAATCTTATTTTATT
*
3806726 AAATTAA--TTA-TTTCTT
1 AAATTAATCTTATTTTATT
3806742 AAATCTAATCTTATT
1 AAAT-TAATCTTATT
3806757 AATCTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 9 0.35
17 6 0.23
19 10 0.38
20 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATTAATCTTATTTTATT
Found at i:3807424 original size:18 final size:18
Alignment explanation
Indices: 3807399--3807464 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
3807389 ATTAGCAAGT
3807399 AATT-AAATTTTTTTAAA
1 AATTAAAATTTTTTTAAA
* * *
3807416 ATTTAAAATTTATTAAAA
1 AATTAAAATTTTTTTAAA
* *
3807434 AATTATAATTTTTTTTGTAA
1 AATTA-AAATTTTTTT-AAA
3807454 AATTAAAATTT
1 AATTAAAATTT
3807465 ATTAAAATTA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
17 3 0.08
18 15 0.41
19 12 0.32
20 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTAAAATTTTTTTAAA
Found at i:3812336 original size:16 final size:17
Alignment explanation
Indices: 3812312--3812363 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
3812302 AATTAACAGA
3812312 AATATTTATTGTTTTC-
1 AATATTTATTGTTTTCT
*
3812328 AATACTTATATAGTTTTCT
1 AATA-TT-TATTGTTTTCT
*
3812347 AATATTTGTTGTTTTCT
1 AATATTTATTGTTTTCT
3812364 TATTTGTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 11 0.37
18 11 0.37
19 4 0.13
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.60
Consensus pattern (17 bp):
AATATTTATTGTTTTCT
Found at i:3814080 original size:9 final size:9
Alignment explanation
Indices: 3814068--3814099 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
3814058 TCGAGGTCGA
3814068 CGCCTAGAT
1 CGCCTAGAT
3814077 CGCCTAGAT
1 CGCCTAGAT
3814086 CGCCTAGAT
1 CGCCTAGAT
3814095 CGCCT
1 CGCCT
3814100 TACTTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.19, C:0.38, G:0.22, T:0.22
Consensus pattern (9 bp):
CGCCTAGAT
Found at i:3815186 original size:21 final size:21
Alignment explanation
Indices: 3815160--3815203 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3815150 GTGATGATAC
3815160 TCACTATTACATACTCATAAT
1 TCACTATTACATACTCATAAT
3815181 TCACTATTACATACTCATAAT
1 TCACTATTACATACTCATAAT
3815202 TC
1 TC
3815204 GATTGAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (21 bp):
TCACTATTACATACTCATAAT
Found at i:3816327 original size:30 final size:30
Alignment explanation
Indices: 3816271--3816327 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3816261 TCTATGTATA
* *
3816271 AATATTAAATTTATATATGAATTTTTGTCT
1 AATATTAAATTTATACATGAAATTTTGTCT
*
3816301 AATATTCAATTTGATACAT-AAATTTTG
1 AATATTAAATTT-ATACATGAAATTTTG
3816328 ATTCGATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (30 bp):
AATATTAAATTTATACATGAAATTTTGTCT
Found at i:3816574 original size:29 final size:30
Alignment explanation
Indices: 3816542--3816606 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
3816532 CCAAAATTTT
3816542 ATATATAAAATTACACA-AAATTAAAACTC
1 ATATATAAAATTACACATAAATTAAAACTC
* * *
3816571 ATATATAACATTGCACATTAAATTAAAATTC
1 ATATATAAAATTACACA-TAAATTAAAACTC
3816602 ATATA
1 ATATA
3816607 AAACTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 15 0.48
31 16 0.52
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
ATATATAAAATTACACATAAATTAAAACTC
Found at i:3820750 original size:12 final size:12
Alignment explanation
Indices: 3820733--3820758 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3820723 CTTGTAACCC
3820733 TGTTTGAGTTCA
1 TGTTTGAGTTCA
3820745 TGTTTGAGTTCA
1 TGTTTGAGTTCA
3820757 TG
1 TG
3820759 CCTCACACGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50
Consensus pattern (12 bp):
TGTTTGAGTTCA
Found at i:3822668 original size:3 final size:3
Alignment explanation
Indices: 3822660--3822690 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3822650 GTGGGGGACC
3822660 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3822691 GGGTTGAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3828760 original size:14 final size:14
Alignment explanation
Indices: 3828723--3828770 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3828713 TATATTTAAA
3828723 AAAATATAAAAACTT
1 AAAATATAAAAA-TT
* * *
3828738 TATACATAAAAATT
1 AAAATATAAAAATT
*
3828752 AAAATATAAAAACT
1 AAAATATAAAAATT
3828766 AAAAT
1 AAAAT
3828771 TTAATTTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:3830010 original size:297 final size:296
Alignment explanation
Indices: 3829450--3830016 Score: 640
Period size: 300 Copynumber: 1.9 Consensus size: 296
3829440 CATATTATTA
* * * * * * *
3829450 ATATATACAATTTATGGAGATAATAAAGCGTGTATAGTAAAACAAAAATGTACAAAATATATTTA
1 ATATATACAATTGATGGAGATAATAAAGCATATATAGTAAAACAAAAATGTAAAAAAGACATTAA
* * * **
3829515 AATAAAGCTTTGGTTGAATGGTGAATTTAAGGTTTTAGTAATTTAATTGGTGCGATTCAAATGTC
66 AATAAAGCTTTGGTTGAACGATGAATTTAAGGTTTTAGTAATCTAATTAATGCGATTCAAATGTC
* *
3829580 ACCATATATAAGCTTTAATTGATTTTTGTTAAAATGAAAAGACTAAAATGCCTTCGAATAATATA
131 ACCATATATAAGATTTAATTGATTTTTGTTAAAATGAAAAGACTAAAATACCTTCGAATAATATA
* * * * * *
3829645 ATTTTTTTAAAATTACGAAAGAATATTTTCGTAATTTCTTGGCCAAATTGGTGACCAGGTTGAGG
196 ATTTTTTT---ATTAAGAAAGAACATTTTCGTAATTTCATGACCAAATTGGTGACCAGATTAAGG
3829710 GTGACACCAATTAAGTCAAAAGCTTAATAAATAGTATAT
258 GTGACACCAATTAAGTCAAAAGCTTAATAAATAGTATAT
** * * * *
3829749 ATATATACAATTGATGGAGATAATAAATTATATATATTAAAATAGAATTGTATAAAAAGACATTA
1 ATATATACAATTGATGGAGATAATAAAGCATATATAGTAAAACAAAAATGTA-AAAAAGACATTA
* * * *
3829814 AAATGAAGCTTTGGTTGAACGATGAATTTAATGTTTTAGTAATCTAATTAATGCGGGTTTAAAT-
65 AAATAAAGCTTTGGTTGAACGATGAATTTAAGGTTTTAGTAATCTAATTAATGC-GATTCAAATG
** * * * *
3829878 TC-CGTTATATGCATATTTCAATTGGTTTTTGTTAAAATGAGAAGACTAAAATACTCTT-GAATA
129 TCACCATATAT-AAGATTT-AATTGATTTTTGTTAAAATGAAAAGACTAAAATAC-CTTCGAATA
* ** * *
3829941 ATATTAA-TTTTTT-TTAAGGAAGAACATTTTCGTAATTTCATGATTAAGTTGGTGACCCGATTA
191 ATA-TAATTTTTTTATTAAGAAAGAACATTTTCGTAATTTCATGACCAAATTGGTGACCAGATTA
*
3830004 AGGGTGATACCAA
255 AGGGTGACACCAA
3830017 CTCAGTCATG
Statistics
Matches: 220, Mismatches: 42, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
297 51 0.23
299 49 0.22
300 61 0.28
301 53 0.24
302 6 0.03
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (296 bp):
ATATATACAATTGATGGAGATAATAAAGCATATATAGTAAAACAAAAATGTAAAAAAGACATTAA
AATAAAGCTTTGGTTGAACGATGAATTTAAGGTTTTAGTAATCTAATTAATGCGATTCAAATGTC
ACCATATATAAGATTTAATTGATTTTTGTTAAAATGAAAAGACTAAAATACCTTCGAATAATATA
ATTTTTTTATTAAGAAAGAACATTTTCGTAATTTCATGACCAAATTGGTGACCAGATTAAGGGTG
ACACCAATTAAGTCAAAAGCTTAATAAATAGTATAT
Found at i:3847725 original size:17 final size:17
Alignment explanation
Indices: 3847696--3847729 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3847686 TTCTTTATAT
3847696 ATTTAAAATTATTAAAA
1 ATTTAAAATTATTAAAA
3847713 ATTTATAAA-TATTAAAA
1 ATTTA-AAATTATTAAAA
3847730 TAGAGACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAATTATTAAAA
Found at i:3848028 original size:13 final size:13
Alignment explanation
Indices: 3848010--3848034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3848000 GCTGCCATGG
3848010 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
3848023 TTTTTTTTGTTT
1 TTTTTTTTGTTT
3848035 AATTTTTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTTTGTTTT
Found at i:3872675 original size:22 final size:20
Alignment explanation
Indices: 3872649--3872707 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
3872639 AGTTTATACA
*
3872649 TAATTTATATATTACAAATTT
1 TAATTTATATATTA-AAATCT
*
3872670 TCAATTTAAAATATTAAAATCT
1 T-AATTT-ATATATTAAAATCT
3872692 TAATTT-TATAGTTAAA
1 TAATTTATATA-TTAAA
3872708 TTACAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 6 0.19
22 11 0.34
23 7 0.22
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATTTATATATTAAAATCT
Found at i:3874698 original size:32 final size:32
Alignment explanation
Indices: 3874632--3874699 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
3874622 TTTTGGTTAA
* *
3874632 TGTTGGATTCTAAAATTTTAGTTTATTATATT
1 TGTTGGATTCTAAAATTTTAGTCTATGATATT
*
3874664 TGTTGGATTCTGAAATTATTATGTCT-TGAT-TT
1 TGTTGGATTCTAAAATT-TTA-GTCTATGATATT
3874696 TGTT
1 TGTT
3874700 AGATATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 22 0.71
33 6 0.19
34 3 0.10
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.56
Consensus pattern (32 bp):
TGTTGGATTCTAAAATTTTAGTCTATGATATT
Found at i:3874725 original size:27 final size:27
Alignment explanation
Indices: 3874695--3874767 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
3874685 TGTCTTGATT
3874695 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
3874722 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
3874754 TTGTTGGATATTGA
1 TTGTTAGATATTGA
3874768 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:3874747 original size:32 final size:32
Alignment explanation
Indices: 3874708--3874768 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3874698 TTAGATATTG
3874708 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
3874740 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
3874769 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:3875750 original size:22 final size:22
Alignment explanation
Indices: 3875682--3875770 Score: 92
Period size: 22 Copynumber: 4.0 Consensus size: 22
3875672 GATACTTTTA
3875682 ATGTGGTGTAATATTAGTTATGC
1 ATGTGGTGTAATATTAGTTAT-C
** *
3875705 ACT-TGG-ACAATATTGTTGTTATC
1 A-TGTGGTGTAATA-T-TAGTTATC
3875728 ATGTGGTGTAATATTAGTTATC
1 ATGTGGTGTAATATTAGTTATC
*
3875750 ATATGGTGTAATATTAGTTAT
1 ATGTGGTGTAATATTAGTTAT
3875771 GCACTTGGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
22 32 0.59
23 11 0.20
24 11 0.20
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (22 bp):
ATGTGGTGTAATATTAGTTATC
Found at i:3875830 original size:68 final size:68
Alignment explanation
Indices: 3875685--3875833 Score: 210
Period size: 68 Copynumber: 2.2 Consensus size: 68
3875675 ACTTTTAATG
* * *
3875685 TGGTGTAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATATTAGTTATC
1 TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
3875750 ATA
66 ATA
* * *
3875753 TGGTGTAATATTAGTTATGCACTTGGATAATGTTGTTGTTATCATGTGGTGTAATACTAATTATG
1 TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTAT-
* *
3875818 TATT
65 CATA
3875822 TGG-ATAATATTA
1 TGGTATAATATTA
3875834 TTAATTTCTA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 68 0.93
69 5 0.07
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (68 bp):
TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
ATA
Found at i:3876015 original size:18 final size:19
Alignment explanation
Indices: 3875989--3876024 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3875979 TTGAGTATTA
3875989 TTATATATTTA-AAATAAT
1 TTATATATTTATAAATAAT
*
3876007 TTATTTATTTATAAATAA
1 TTATATATTTATAAATAA
3876025 ATCATTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATATTTATAAATAAT
Found at i:3876290 original size:15 final size:14
Alignment explanation
Indices: 3876229--3876295 Score: 73
Period size: 14 Copynumber: 4.7 Consensus size: 14
3876219 CCAGAAAAGT
*
3876229 AAATCATTTTCCAG
1 AAATCATTTTCCAA
* *
3876243 AAATTATTTTTCAA
1 AAATCATTTTCCAA
*
3876257 TAAATCATTTTCTAA
1 -AAATCATTTTCCAA
3876272 AAATCATTTTCCGAA
1 AAATCATTTTCC-AA
3876287 AAAT-ATTTT
1 AAATCATTTT
3876296 ATCTGTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
14 27 0.61
15 17 0.39
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:3876290 original size:29 final size:29
Alignment explanation
Indices: 3876228--3876295 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
3876218 ACCAGAAAAG
* * *
3876228 TAAATCATTTTCCAGAAATTATTTTTCAA
1 TAAATCATTTTCCAAAAATCATTTTCCAA
*
3876257 TAAATCATTTTCTAAAAATCATTTTCCGAA
1 TAAATCATTTTCCAAAAATCATTTTCC-AA
3876287 -AAAT-ATTTT
1 TAAATCATTTT
3876296 ATCTGTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.15
29 27 0.79
30 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (29 bp):
TAAATCATTTTCCAAAAATCATTTTCCAA
Found at i:3878895 original size:14 final size:14
Alignment explanation
Indices: 3878876--3878906 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3878866 AGACGTGACA
3878876 TTTTTTGACTAAAG
1 TTTTTTGACTAAAG
3878890 TTTTTTGACTAAAG
1 TTTTTTGACTAAAG
3878904 TTT
1 TTT
3878907 AAGGAACTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (14 bp):
TTTTTTGACTAAAG
Found at i:3881411 original size:59 final size:59
Alignment explanation
Indices: 3881340--3881463 Score: 248
Period size: 59 Copynumber: 2.1 Consensus size: 59
3881330 AGAATTGAAT
3881340 AACTAACTTAACAGCTTACTAAACTCAAATTAATTAATTATAATTAGAATAAATCTGGG
1 AACTAACTTAACAGCTTACTAAACTCAAATTAATTAATTATAATTAGAATAAATCTGGG
3881399 AACTAACTTAACAGCTTACTAAACTCAAATTAATTAATTATAATTAGAATAAATCTGGG
1 AACTAACTTAACAGCTTACTAAACTCAAATTAATTAATTATAATTAGAATAAATCTGGG
3881458 AACTAA
1 AACTAA
3881464 TTATAACCAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (59 bp):
AACTAACTTAACAGCTTACTAAACTCAAATTAATTAATTATAATTAGAATAAATCTGGG
Found at i:3891929 original size:7 final size:7
Alignment explanation
Indices: 3891917--3891964 Score: 96
Period size: 7 Copynumber: 6.9 Consensus size: 7
3891907 CAACAAAACA
3891917 CCCTACT
1 CCCTACT
3891924 CCCTACT
1 CCCTACT
3891931 CCCTACT
1 CCCTACT
3891938 CCCTACT
1 CCCTACT
3891945 CCCTACT
1 CCCTACT
3891952 CCCTACT
1 CCCTACT
3891959 CCCTAC
1 CCCTAC
3891965 ACTTTTAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.15, C:0.58, G:0.00, T:0.27
Consensus pattern (7 bp):
CCCTACT
Found at i:3892676 original size:2 final size:2
Alignment explanation
Indices: 3892669--3892700 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3892659 TAGGTAAATT
3892669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3892701 AACCCTCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3896711 original size:18 final size:18
Alignment explanation
Indices: 3896640--3896711 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 18
3896630 TATTATCAAT
3896640 ATTATTCAGTAAC-GATCA
1 ATTATTCAGTAACAG-TCA
* * * *
3896658 ATTGTTTAGTGACAATCA
1 ATTATTCAGTAACAGTCA
* * *
3896676 GTTATTCAATATCAGTCA
1 ATTATTCAGTAACAGTCA
*
3896694 ATTATTCAGTAACTGTCA
1 ATTATTCAGTAACAGTCA
3896712 GTATCATTCA
Statistics
Matches: 38, Mismatches: 15, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
ATTATTCAGTAACAGTCA
Found at i:3896890 original size:18 final size:18
Alignment explanation
Indices: 3896849--3896890 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3896839 GTAATGATAA
*
3896849 CAGTAACAGTAACAGTAG
1 CAGTAGCAGTAACAGTAG
*
3896867 CAGTAGCAGTGACAGTAG
1 CAGTAGCAGTAACAGTAG
*
3896885 CTGTAG
1 CAGTAG
3896891 ACAGAGTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.19
Consensus pattern (18 bp):
CAGTAGCAGTAACAGTAG
Found at i:3898196 original size:17 final size:16
Alignment explanation
Indices: 3898170--3898202 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3898160 TTGTCTTTCT
3898170 TTTATTTATTTAATTA
1 TTTATTTATTTAATTA
3898186 TTTACTTTATTTAATTA
1 TTTA-TTTATTTAATTA
3898203 ATAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTATTTAATTA
Found at i:3904886 original size:16 final size:14
Alignment explanation
Indices: 3904857--3904890 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
3904847 TAAGTCAATA
3904857 ATAATATTAAATTT
1 ATAATATTAAATTT
3904871 ATAATATATAACATTT
1 ATAATAT-TAA-ATTT
3904887 ATAA
1 ATAA
3904891 GTAATGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 3 0.17
16 8 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATATTAAATTT
Found at i:3910242 original size:23 final size:22
Alignment explanation
Indices: 3910206--3910260 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
3910196 GTTTTTATAT
3910206 ATATTATAAATAAATATAATAA-A
1 ATATTATAAATAAA-A-AATAACA
* *
3910229 ATATTATTACTAAAAAATAACA
1 ATATTATAAATAAAAAATAACA
3910251 ATAATTATAA
1 AT-ATTATAA
3910261 TTGTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 18 0.67
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATTATAAATAAAAAATAACA
Found at i:3910253 original size:27 final size:27
Alignment explanation
Indices: 3910202--3910254 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3910192 TCGTGTTTTT
*
3910202 ATATATATTATAAATAAATATAATAAA
1 ATATATATTATAAATAAATACAATAAA
3910229 ATAT-TATTACTAAA-AAATAACAATAA
1 ATATATATTA-TAAATAAAT-ACAATAA
3910255 TTATAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATATATTATAAATAAATACAATAAA
Found at i:3913435 original size:117 final size:117
Alignment explanation
Indices: 3913229--3913461 Score: 430
Period size: 117 Copynumber: 2.0 Consensus size: 117
3913219 TAACATCGAG
3913229 GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGCTTACCTTGAGGTTTGCTTATGAAAGAAG
1 GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGCTTACCTTGAGGTTTGCTTATGAAAGAAG
*
3913294 AAGTGCAAAGGTAGTCGTGGGAGCTGGAAATAGGTGTGGAGACTTTGTGGTT
66 AAGTGCAAAGATAGTCGTGGGAGCTGGAAATAGGTGTGGAGACTTTGTGGTT
* *
3913346 GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGTTTACCTTGAGGTTTGCTTATGAAAGATG
1 GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGCTTACCTTGAGGTTTGCTTATGAAAGAAG
*
3913411 AAGTGCAAAGATAGTCGTGGGAGCTGGAAATGGGTGTGGAGACTTTGTGGT
66 AAGTGCAAAGATAGTCGTGGGAGCTGGAAATAGGTGTGGAGACTTTGTGGT
3913462 CCTCAACGAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.29, C:0.09, G:0.33, T:0.29
Consensus pattern (117 bp):
GATTTACCAAGATAGAGATGGGATAGTAAGTGCTAGCTTACCTTGAGGTTTGCTTATGAAAGAAG
AAGTGCAAAGATAGTCGTGGGAGCTGGAAATAGGTGTGGAGACTTTGTGGTT
Found at i:3915383 original size:40 final size:40
Alignment explanation
Indices: 3915337--3915413 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
3915327 TTAGGCATAA
*
3915337 ATAGAAGATTGAGTAGTTAATCTCTTTAATTGTACTAGTC
1 ATAGAAGATTGAGTAGTCAATCTCTTTAATTGTACTAGTC
3915377 ATAGAAGATTGAGTAGTCAATCTCTTTAATTGTACTA
1 ATAGAAGATTGAGTAGTCAATCTCTTTAATTGTACTA
3915414 TTTGGTGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (40 bp):
ATAGAAGATTGAGTAGTCAATCTCTTTAATTGTACTAGTC
Found at i:3917171 original size:16 final size:15
Alignment explanation
Indices: 3917152--3917181 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3917142 CTAGAACATT
3917152 AAAATAAAAGAAAAAA
1 AAAATAAAA-AAAAAA
3917168 AAAATAAAAAAAAA
1 AAAATAAAAAAAAA
3917182 GGGAGCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.07
Consensus pattern (15 bp):
AAAATAAAAAAAAAA
Found at i:3918186 original size:16 final size:17
Alignment explanation
Indices: 3918165--3918197 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3918155 CAAATAATTT
3918165 AAAATTTATA-AAAATA
1 AAAATTTATAGAAAATA
*
3918181 AAAATTTTTAGAAAATA
1 AAAATTTATAGAAAATA
3918198 TGAAAACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATTTATAGAAAATA
Found at i:3919176 original size:17 final size:17
Alignment explanation
Indices: 3919154--3919187 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3919144 ATCCACTAAT
*
3919154 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
3919171 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
3919188 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:3923806 original size:17 final size:17
Alignment explanation
Indices: 3923784--3923817 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3923774 ATCCACTAAT
*
3923784 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
3923801 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
3923818 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:3924401 original size:13 final size:14
Alignment explanation
Indices: 3924384--3924424 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
3924374 TAGAAAATAA
3924384 AAAATAAAAATT-T
1 AAAATAAAAATTAT
*
3924397 TAAATAAAAATTAT
1 AAAATAAAAATTAT
3924411 AAAATTAAAAATTA
1 AAAA-TAAAAATTA
3924425 CTACACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.46
14 4 0.17
15 9 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAATAAAAATTAT
Found at i:3924403 original size:20 final size:21
Alignment explanation
Indices: 3924378--3924416 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3924368 ATATTATAGA
3924378 AAATAAAAAATA-AAAATTTT
1 AAATAAAAAATATAAAATTTT
*
3924398 AAATAAAAATTATAAAATT
1 AAATAAAAAATATAAAATT
3924417 AAAAATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAAAAATATAAAATTTT
Done.