Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 88 of 173
Found at i:27500240 original size:44 final size:46
Alignment explanation
Indices: 27500185--27500279 Score: 149
Period size: 44 Copynumber: 2.1 Consensus size: 46
27500175 TACTATGTGA
* *
27500185 ACCGAACATCATTGATTAGTAAGGTGG-TTGCTATGTGCT-ATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTTGCTATGTGCTGAATCC
*
27500229 ACCGGACATCATTGATTAATAAGGTGGTTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTTGCTATGTGCTGAATCC
27500275 ACCGA
1 ACCGA
27500280 GTATATGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 25 0.56
45 12 0.27
46 8 0.18
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (46 bp):
ACCGAACATCATTGATTAATAAGGTGGTTTGCTATGTGCTGAATCC
Found at i:27509928 original size:29 final size:29
Alignment explanation
Indices: 27509823--27509931 Score: 80
Period size: 29 Copynumber: 3.8 Consensus size: 29
27509813 AAAGGTTTCC
*
27509823 TTATAATAGAGACCA-CCACAAAAGCATTCA
1 TTATAATAGAGA-TAGCCACAAAAGC-TTCA
* * *
27509853 TTCA-ACT-GAGATAGCCATAAAAGCTTCC
1 TT-ATAATAGAGATAGCCACAAAAGCTTCA
* * * ** *
27509881 TTTTAATAGTGGTCCCCACAAATGCTTCA
1 TTATAATAGAGATAGCCACAAAAGCTTCA
27509910 TTATAATAGAGATAGCCACAAA
1 TTATAATAGAGATAGCCACAAA
27509932 GGTGTCCATT
Statistics
Matches: 57, Mismatches: 18, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
28 8 0.14
29 44 0.77
30 4 0.07
31 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (29 bp):
TTATAATAGAGATAGCCACAAAAGCTTCA
Found at i:27512296 original size:27 final size:27
Alignment explanation
Indices: 27512266--27512335 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
27512256 AATTCACCAA
*
27512266 GCCTACTGGCGAATACAAACTCGCCAG
1 GCCTACTGGCGAACACAAACTCGCCAG
* * *
27512293 GCCTACTGGAGAACACAAAGTTGCCAG
1 GCCTACTGGCGAACACAAACTCGCCAG
**
27512320 ATCTACTGGCGAACAC
1 GCCTACTGGCGAACAC
27512336 CAGGTTGCCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.16
Consensus pattern (27 bp):
GCCTACTGGCGAACACAAACTCGCCAG
Found at i:27512355 original size:27 final size:27
Alignment explanation
Indices: 27512262--27512355 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 27
27512252 CATCAATTCA
* * * * *
27512262 CCAAGCCTACTGGCGAATACAAACTCG
1 CCAAACCTACTGGAGAACACAAAGTTG
**
27512289 CCAGGCCTACTGGAGAACACAAAGTTG
1 CCAAACCTACTGGAGAACACAAAGTTG
* * * * *
27512316 CCAGATCTACTGGCGAACACCAGGTTG
1 CCAAACCTACTGGAGAACACAAAGTTG
*
27512343 CCAAACCTTCTGG
1 CCAAACCTACTGG
27512356 TGTACCTGCT
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.30, C:0.31, G:0.22, T:0.17
Consensus pattern (27 bp):
CCAAACCTACTGGAGAACACAAAGTTG
Found at i:27519254 original size:28 final size:28
Alignment explanation
Indices: 27519177--27519266 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 28
27519167 AGGCTAAATG
*
27519177 GAGAGTTCGCACAAAGCAAA-CCAAACA
1 GAGAGCTCGCACAAAGCAAAGCCAAACA
* * * * *
27519204 AAGAGCTCGTACAAATCAGAGCCAAATA
1 GAGAGCTCGCACAAAGCAAAGCCAAACA
* *
27519232 GAGAGCTCGCATAAAGCAAAGCCAAACC
1 GAGAGCTCGCACAAAGCAAAGCCAAACA
27519260 GAGAGCT
1 GAGAGCT
27519267 AAAACATTAG
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
27 15 0.31
28 34 0.69
ACGTcount: A:0.44, C:0.24, G:0.21, T:0.10
Consensus pattern (28 bp):
GAGAGCTCGCACAAAGCAAAGCCAAACA
Found at i:27524506 original size:138 final size:138
Alignment explanation
Indices: 27524258--27524535 Score: 547
Period size: 138 Copynumber: 2.0 Consensus size: 138
27524248 CCTCGCAGTC
*
27524258 TTATAGTAATCCTGGTGGCTCGTCAAGAAACACATATGGGAAATCTTGAACAGTTTACATTTCGT
1 TTATAGTAATCCTGGTGGCTCGTCAAGAAACACATATGGGAAATCTTGAACAGTTTACATTTCGC
27524323 GAACCCCTTGTGCCAAAACATGCGACCTCATCACATATATGAGATAGGCCTTGAAGCTCTTTCCC
66 GAACCCCTTGTGCCAAAACATGCGACCTCATCACATATATGAGATAGGCCTTGAAGCTCTTTCCC
27524388 AACATCTT
131 AACATCTT
27524396 TTATAGTAATCCTGGTGGCTCGTCAAGAAACACATATGGGAAATCTTGAACAGTTTACATTTCGC
1 TTATAGTAATCCTGGTGGCTCGTCAAGAAACACATATGGGAAATCTTGAACAGTTTACATTTCGC
27524461 GAACCCCTTGTGCCAAAACATGCGACCTCATCACATATATGAGATAGGCCTTGAAGCTCTTTCCC
66 GAACCCCTTGTGCCAAAACATGCGACCTCATCACATATATGAGATAGGCCTTGAAGCTCTTTCCC
27524526 AACATCTT
131 AACATCTT
27524534 TT
1 TT
27524536 CTACCCTTAG
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (138 bp):
TTATAGTAATCCTGGTGGCTCGTCAAGAAACACATATGGGAAATCTTGAACAGTTTACATTTCGC
GAACCCCTTGTGCCAAAACATGCGACCTCATCACATATATGAGATAGGCCTTGAAGCTCTTTCCC
AACATCTT
Found at i:27528176 original size:27 final size:27
Alignment explanation
Indices: 27528163--27528266 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 27
27528153 ACAAAATGAA
27528163 CAAAGTAGAGAGCTTACACAAAACAAAC
1 CAAA-TAGAGAGCTTACACAAAACAAAC
* *
27528191 CAAATAGAGAGCTCACAC-AAGCAAAAC
1 CAAATAGAGAGCTTACACAAAAC-AAAC
* *** * *
27528218 CAAATAGAAAGCTCGTACAAAGCAGAGC
1 CAAATAGAGAGCTTACACAAAACA-AAC
* *
27528246 CAAAAAGAGAGCTCACACAAA
1 CAAATAGAGAGCTTACACAAA
27528267 GCAGAGCTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
26 3 0.05
27 33 0.52
28 27 0.43
ACGTcount: A:0.52, C:0.23, G:0.16, T:0.09
Consensus pattern (27 bp):
CAAATAGAGAGCTTACACAAAACAAAC
Found at i:27528249 original size:28 final size:26
Alignment explanation
Indices: 27528163--27528286 Score: 97
Period size: 28 Copynumber: 4.5 Consensus size: 26
27528153 ACAAAATGAA
* *
27528163 CAAAGTAGAGAGCTTACACAAAACA-AAC
1 CAAA-TAGAGAGC-T-CACAAAGCAGAGC
* *
27528191 CAAATAGAGAGCTCACACAAGCAAAAC
1 CAAATAGAGAGCTCACA-AAGCAGAGC
*
27528218 CAAATAGAAAGCTCGTACAAAGCAGAGC
1 CAAATAGAGAGCTC--ACAAAGCAGAGC
*
27528246 CAAAAAGAGAGCTCACACAAAGCAGAGC
1 CAAATAGAGAGCT--CACAAAGCAGAGC
* *
27528274 TAAACAGAGAGCT
1 CAAATAGAGAGCT
27528287 AAACATTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
25 4 0.05
26 5 0.06
27 24 0.29
28 45 0.55
29 3 0.04
30 1 0.01
ACGTcount: A:0.50, C:0.23, G:0.19, T:0.09
Consensus pattern (26 bp):
CAAATAGAGAGCTCACAAAGCAGAGC
Found at i:27528274 original size:16 final size:15
Alignment explanation
Indices: 27528234--27528279 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
27528224 GAAAGCTCGT
27528234 ACAAAGCAGAGC-CA
1 ACAAAGCAGAGCTCA
27528248 A-AAAG-AGAGCTCA
1 ACAAAGCAGAGCTCA
*
27528261 CACAAAGCAGAGCTAA
1 -ACAAAGCAGAGCTCA
27528277 ACA
1 ACA
27528280 GAGAGCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.19
13 6 0.22
14 2 0.07
15 7 0.26
16 7 0.26
ACGTcount: A:0.52, C:0.24, G:0.20, T:0.04
Consensus pattern (15 bp):
ACAAAGCAGAGCTCA
Found at i:27537437 original size:24 final size:24
Alignment explanation
Indices: 27537403--27537450 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27537393 TTTCTAGAAG
* *
27537403 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
27537427 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
27537451 GTTTGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:27541699 original size:24 final size:24
Alignment explanation
Indices: 27541672--27541723 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
27541662 TTTCTAGAAG
* *
27541672 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
27541696 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
27541720 ATTT
1 ATTT
27541724 GACTTTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:27548588 original size:12 final size:12
Alignment explanation
Indices: 27548555--27548601 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
27548545 ATAAACTGTT
27548555 TATTTATATAT-
1 TATTTATATATC
*
27548566 AATATTATATATC
1 TAT-TTATATATC
*
27548579 TATTTTTATATC
1 TATTTATATATC
27548591 TATTTATATAT
1 TATTTATATAT
27548602 ATAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 2 0.07
12 26 0.87
13 2 0.07
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTATATATC
Found at i:27548681 original size:43 final size:42
Alignment explanation
Indices: 27548629--27548709 Score: 126
Period size: 43 Copynumber: 1.9 Consensus size: 42
27548619 TTATATCTTA
*
27548629 CTATTTTATATATCTATACGTACATATTTATATACATTAATC
1 CTATTTTATATATCTATACGTACATATATATATACATTAATC
* *
27548671 CTATCTTTATATATCTATGCGTACATATATATTTACATT
1 CTAT-TTTATATATCTATACGTACATATATATATACATT
27548710 TTTTTCCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 4 0.11
43 31 0.89
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (42 bp):
CTATTTTATATATCTATACGTACATATATATATACATTAATC
Found at i:27548739 original size:17 final size:17
Alignment explanation
Indices: 27548717--27548752 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
27548707 ATTTTTTTCC
27548717 TATATATATTATGTTTA
1 TATATATATTATGTTTA
*
27548734 TATATATTTTATGTTTA
1 TATATATATTATGTTTA
27548751 TA
1 TA
27548753 AAAAATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TATATATATTATGTTTA
Found at i:27549330 original size:18 final size:18
Alignment explanation
Indices: 27549307--27549343 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27549297 TGCAAAAAAA
* *
27549307 TATTCTAGTTTTAAGAAT
1 TATTCTAGGTTCAAGAAT
27549325 TATTCTAGGTTCAAGAAT
1 TATTCTAGGTTCAAGAAT
27549343 T
1 T
27549344 CATATTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (18 bp):
TATTCTAGGTTCAAGAAT
Found at i:27550923 original size:30 final size:30
Alignment explanation
Indices: 27550804--27551056 Score: 161
Period size: 30 Copynumber: 8.7 Consensus size: 30
27550794 TCACAATAGA
* *
27550804 TAGATAGCCAAAAAGGCAT-C-CA-AACAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * * *
27550831 TAGATAGCCATAAAAGC-TTC-CAT-ACAGA
1 TAGATAGCCACAAAGGCGTCCACATAACA-T
* * *
27550859 TAGATAGCCATATAGGCGT-C-CAT-ACAGA
1 TAGATAGCCACAAAGGCGTCCACATAACA-T
* *
27550887 TAGATAGCCACAAAAGCATCCACATAACAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * *
27550917 TAGATAGCCATAAATGTGTCCACATAACAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * * * *
27550947 CAAAAAGCCACAAAGGTGT-C-CAT-ACAGA
1 TAGATAGCCACAAAGGCGTCCACATAACA-T
*
27550975 TAGATAGCCACAAAGGCATCCACATAACAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * *
27551005 TAGATAGCCATAAATGCGTCCACATAAAAT
1 TAGATAGCCACAAAGGCGTCCACATAACAT
* * *
27551035 CAAAAAGCCACAAAGGCGTCCA
1 TAGATAGCCACAAAGGCGTCCA
27551057 AACACATATA
Statistics
Matches: 180, Mismatches: 35, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.01
27 24 0.13
28 56 0.31
29 4 0.02
30 89 0.49
31 6 0.03
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (30 bp):
TAGATAGCCACAAAGGCGTCCACATAACAT
Found at i:27550978 original size:88 final size:88
Alignment explanation
Indices: 27550801--27551056 Score: 339
Period size: 88 Copynumber: 3.0 Consensus size: 88
27550791 CTTTCACAAT
* *
27550801 AGATAGATAGCCA-AAAAGGCAT-C-CA-AACATTAGATAGCCATAAAAGCT-T-C-CATACAGA
1 AGATAGATAGCCACAAAA-GCATCCACATAACATTAGATAGCCATAAATG-TGTCCACATA-AAA
* * * *
27550859 T-AGATAGCCATATAGGCGTCCATAC
63 TCAAAAAGCCACAAAGGCGTCCATAC
*
27550884 AGATAGATAGCCACAAAAGCATCCACATAACATTAGATAGCCATAAATGTGTCCACATAACATCA
1 AGATAGATAGCCACAAAAGCATCCACATAACATTAGATAGCCATAAATGTGTCCACATAAAATCA
*
27550949 AAAAGCCACAAAGGTGTCCATAC
66 AAAAGCCACAAAGGCGTCCATAC
* *
27550972 AGATAGATAGCCACAAAGGCATCCACATAACATTAGATAGCCATAAATGCGTCCACATAAAATCA
1 AGATAGATAGCCACAAAAGCATCCACATAACATTAGATAGCCATAAATGTGTCCACATAAAATCA
27551037 AAAAGCCACAAAGGCGTCCA
66 AAAAGCCACAAAGGCGTCCA
27551057 AACACATATA
Statistics
Matches: 154, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
83 17 0.11
84 5 0.03
85 3 0.02
86 21 0.14
87 4 0.03
88 104 0.68
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (88 bp):
AGATAGATAGCCACAAAAGCATCCACATAACATTAGATAGCCATAAATGTGTCCACATAAAATCA
AAAAGCCACAAAGGCGTCCATAC
Found at i:27550984 original size:28 final size:28
Alignment explanation
Indices: 27550801--27550996 Score: 137
Period size: 28 Copynumber: 6.9 Consensus size: 28
27550791 CTTTCACAAT
* * *
27550801 AGATAGATAGCCAAAAAGGCATCCAAAC
1 AGATAGATAGCCACAAAGGCGTCCATAC
* * * *
27550829 A-TTAGATAGCCATAAAAGCTTCCATAC
1 AGATAGATAGCCACAAAGGCGTCCATAC
* *
27550856 AGATAGATAGCCATATAGGCGTCCATAC
1 AGATAGATAGCCACAAAGGCGTCCATAC
* *
27550884 AGATAGATAGCCACAAAAGCATCCACATAAC
1 AGATAGATAGCCACAAAGGCGT-C-CAT-AC
* * * *
27550915 A-TTAGATAGCCATAAATGTGTCCACATA-
1 AGATAGATAGCCACAAAGGCGT-C-CATAC
* * * *
27550943 ACATCAAAAAGCCACAAAGGTGTCCATAC
1 AGAT-AGATAGCCACAAAGGCGTCCATAC
*
27550972 AGATAGATAGCCACAAAGGCATCCA
1 AGATAGATAGCCACAAAGGCGTCCA
27550997 CATAACATTA
Statistics
Matches: 133, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
27 22 0.17
28 63 0.47
29 7 0.05
30 38 0.29
31 3 0.02
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (28 bp):
AGATAGATAGCCACAAAGGCGTCCATAC
Found at i:27551529 original size:54 final size:54
Alignment explanation
Indices: 27551379--27551529 Score: 212
Period size: 56 Copynumber: 2.8 Consensus size: 54
27551369 TCCCTACATA
* * ** *
27551379 ATGCCATCGTCCCAGACTAGGTCTTACACTATGTGGTCTTCTTTTCCCCATATT
1 ATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCACTTCCCCATATG
* *
27551433 ATGCCATAGCCACCATGACTAGGTCTTACACTATATAGTCTTCACTTCCCCATATG
1 ATGCCATAGTC-CCA-GACTAGGTCTTACACTATATGGTCTTCACTTCCCCATATG
*
27551489 ATGCCATAGTCCCAGACTAGGTCTTACATTATATGGTCTTC
1 ATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTCTTC
27551530 TTGCCATGGC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
54 34 0.40
55 6 0.07
56 45 0.53
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (54 bp):
ATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTCTTCACTTCCCCATATG
Found at i:27556559 original size:14 final size:14
Alignment explanation
Indices: 27556537--27556566 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27556527 TGTTGCGCCG
*
27556537 TAGTTAAATTAGAT
1 TAGTAAAATTAGAT
27556551 TAGTAAAATTAGAT
1 TAGTAAAATTAGAT
27556565 TA
1 TA
27556567 AAAATAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (14 bp):
TAGTAAAATTAGAT
Found at i:27558345 original size:26 final size:22
Alignment explanation
Indices: 27558316--27558366 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 22
27558306 CAACTAAAGA
27558316 AAAATTAAAAAGAAAGATAAATAAAT
1 AAAA-TAAAAAGAAA-A-AAAT-AAT
*
27558342 AAAATAAAACGAAAAAAATAAT
1 AAAATAAAAAGAAAAAAATAAT
27558364 AAA
1 AAA
27558367 CTCAATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.25
23 4 0.17
24 1 0.04
25 9 0.38
26 4 0.17
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAATAAAAAGAAAAAAATAAT
Found at i:27565031 original size:45 final size:44
Alignment explanation
Indices: 27564964--27565051 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
27564954 TGTGAATCGA
* * *
27564964 ACATCATTGATTAGTAAAGTGGTTTCTATGTGTTGATTCCACCGG
1 ACATCATTGATTAATAAAGTGGTTGCTATGTGTT-AATCCACCGG
*
27565009 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTAATCCACCG
1 ACATCATTGATTAATAAAGTGGTTGCTATGTGTTAATCCACCG
27565052 AGTATCTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 8 0.21
45 31 0.79
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (44 bp):
ACATCATTGATTAATAAAGTGGTTGCTATGTGTTAATCCACCGG
Found at i:27569073 original size:23 final size:23
Alignment explanation
Indices: 27569039--27569092 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
27569029 AATTTTGGGG
27569039 AATTA-AAGGTTAATAGGTGTTTT
1 AATTAGAAGGTTAATAGG-GTTTT
* *
27569062 AATTAGAA-GTTAGTATGGTTTT
1 AATTAGAAGGTTAATAGGGTTTT
27569084 AAGTTAGAA
1 AA-TTAGAA
27569093 AATAGGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 7 0.26
23 18 0.67
24 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (23 bp):
AATTAGAAGGTTAATAGGGTTTT
Found at i:27574084 original size:17 final size:17
Alignment explanation
Indices: 27574062--27574094 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27574052 AATAAATACA
27574062 TATTATATGTTGTATGC
1 TATTATATGTTGTATGC
27574079 TATTATATGTTGTATG
1 TATTATATGTTGTATG
27574095 TTCTGATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (17 bp):
TATTATATGTTGTATGC
Found at i:27579012 original size:46 final size:46
Alignment explanation
Indices: 27578959--27579047 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
27578949 TAGATATTTG
27578959 ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCCTAA
1 ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCCTAA
27579005 ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCC
1 ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCC
27579048 CAAAGACCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.39
Consensus pattern (46 bp):
ATTGTTTGGTCTTAGTGCTAGTGGGAGATTGTTAGAGTATGCCTAA
Found at i:27580539 original size:17 final size:17
Alignment explanation
Indices: 27580514--27580548 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
27580504 AAGTTTTTTA
*
27580514 CCGTGACTATACTATTG
1 CCGTCACTATACTATTG
27580531 CCGTCACTATACTATTG
1 CCGTCACTATACTATTG
27580548 C
1 C
27580549 ATCGACAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (17 bp):
CCGTCACTATACTATTG
Found at i:27580700 original size:19 final size:19
Alignment explanation
Indices: 27580678--27580727 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
27580668 TAAAAATATG
27580678 AAAAATAAAAAAT-TATAAA
1 AAAAATAAAAAATCT-TAAA
* *
27580697 AAAAATAAAAACTCTTCAA
1 AAAAATAAAAAATCTTAAA
27580716 AAAAATAAAAAA
1 AAAAATAAAAAA
27580728 GATTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAATAAAAAATCTTAAA
Found at i:27581732 original size:14 final size:14
Alignment explanation
Indices: 27581678--27581733 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
27581668 TTATGGTTCA
* *
27581678 ATATGTAATTATAT
1 ATATGAAATTTTAT
27581692 ATATGAAA-TTTAT
1 ATATGAAATTTTAT
* *
27581705 TTTTGTATAATTTTAT
1 ATATG-A-AATTTTAT
27581721 ATATGAAATTTTA
1 ATATGAAATTTTA
27581734 ATTTGATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 7 0.21
14 15 0.45
15 3 0.09
16 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (14 bp):
ATATGAAATTTTAT
Found at i:27583790 original size:31 final size:33
Alignment explanation
Indices: 27583722--27583790 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
27583712 AATATTAGTC
*
27583722 ATATGATGACATTATATATTACATTGTCATCAAT
1 ATATGATGACATTATATATTA-ATCGTCATCAAT
*
27583756 ATATGATGACATTATATATT-ATCGTTA-CAAT
1 ATATGATGACATTATATATTAATCGTCATCAAT
27583787 ATAT
1 ATAT
27583791 TAGTATTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 8 0.24
32 5 0.15
34 20 0.61
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (33 bp):
ATATGATGACATTATATATTAATCGTCATCAAT
Found at i:27591685 original size:28 final size:27
Alignment explanation
Indices: 27591626--27591703 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 27
27591616 TCATGTTTAC
* *
27591626 TTTATGTATTTTTTTAAATTTTATGAACTT
1 TTTATATATTTTTTTAAA-ATT-TG-ACTT
*
27591656 TTTATATATTTTTTTAAAATTTGATTT
1 TTTATATATTTTTTTAAAATTTGACTT
* *
27591683 TTTA-ATATCTTTTTACAATTT
1 TTTATATATTTTTTTAAAATTT
27591704 TTAAATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 15 0.35
27 7 0.16
28 2 0.05
29 2 0.05
30 17 0.40
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (27 bp):
TTTATATATTTTTTTAAAATTTGACTT
Found at i:27594563 original size:25 final size:25
Alignment explanation
Indices: 27594489--27594566 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
27594479 TCATTAGGGT
*
27594489 TACCGATTC-TCAGCTCGTATGAGCT
1 TACCGATTCAT-AGCTCGTATGAGCA
* *
27594514 TACCGATTTACAGCTCGTGA-GAGCA
1 TACCGATTCATAGCTCGT-ATGAGCA
*
27594539 TACCGATTCATATCTCGTATGAGCA
1 TACCGATTCATAGCTCGTATGAGCA
27594564 TAC
1 TAC
27594567 ATGTACAGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 1 0.02
25 42 0.95
26 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (25 bp):
TACCGATTCATAGCTCGTATGAGCA
Found at i:27594754 original size:30 final size:29
Alignment explanation
Indices: 27594720--27594776 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
27594710 GAAATATATG
* *
27594720 GAAAT-GATGTTATATGATATATTGAAACAT
1 GAAATGGATGATACATG-TATA-TGAAACAT
27594750 GAAATGGATGATACATGTATATGAAAC
1 GAAATGGATGATACATGTATATGAAAC
27594777 TTGCTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 9 0.38
31 9 0.38
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (29 bp):
GAAATGGATGATACATGTATATGAAACAT
Found at i:27595440 original size:26 final size:27
Alignment explanation
Indices: 27595390--27595442 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
27595380 ATTAAGTGGT
*
27595390 ATAATTGATACCAAATGGTATGTTTTG
1 ATAATTGATACCAAATGGTAAGTTTTG
* *
27595417 ATAATTGAT-CTACATGGTAAGTTTTG
1 ATAATTGATACCAAATGGTAAGTTTTG
27595443 GTGCAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (27 bp):
ATAATTGATACCAAATGGTAAGTTTTG
Found at i:27601823 original size:25 final size:26
Alignment explanation
Indices: 27601785--27601862 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 26
27601775 TCATCAGGGT
*
27601785 TACCGATTCTCAGCTCGTATAAGCT-
1 TACCGATTCACAGCTCGTATAAGCTA
* *
27601810 TACTGATTTACAGCTCGTGA-AAG-TA
1 TACCGATTCACAGCTCGT-ATAAGCTA
*
27601835 TACCGATTCATAGCTCGTATAAGC-A
1 TACCGATTCACAGCTCGTATAAGCTA
27601860 TAC
1 TAC
27601863 ATGTATAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 2 0.05
25 40 0.93
26 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (26 bp):
TACCGATTCACAGCTCGTATAAGCTA
Found at i:27606588 original size:30 final size:30
Alignment explanation
Indices: 27606554--27606614 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
27606544 TAGAAATTGG
27606554 TAAGTTTCCTTACCTCTCTTTAATTATGGA
1 TAAGTTTCCTTACCTCTCTTTAATTATGGA
* * *
27606584 TAAGTTTTCTTACCTCTTTTTACTTATGGA
1 TAAGTTTCCTTACCTCTCTTTAATTATGGA
27606614 T
1 T
27606615 GAAAGAAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (30 bp):
TAAGTTTCCTTACCTCTCTTTAATTATGGA
Found at i:27607132 original size:12 final size:12
Alignment explanation
Indices: 27607115--27607149 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
27607105 GATGGCGAAT
27607115 GGAGGAATAGGC
1 GGAGGAATAGGC
27607127 GGAGGAATAGGC
1 GGAGGAATAGGC
27607139 GGAGGAATAGG
1 GGAGGAATAGG
27607150 GAAAAAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.06, G:0.51, T:0.09
Consensus pattern (12 bp):
GGAGGAATAGGC
Found at i:27609440 original size:56 final size:50
Alignment explanation
Indices: 27609361--27609555 Score: 201
Period size: 50 Copynumber: 3.8 Consensus size: 50
27609351 ATTTGGGTAA
* * *
27609361 AGAGATCCCATGTAAGACAATGTCTGGGACATGGCATTGACATCATTGATGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACA-C--CGA-G--ATG
* * *
27609417 AGAGGTCCCATGTATGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
* * * *
27609467 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
** * * *
27609517 AGAATTCCCATGTAAGACCATATCTGGGATATGACATTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTG
27609556 GAAGTAAAAG
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
50 80 0.66
52 1 0.01
53 2 0.02
55 1 0.01
56 37 0.31
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
Found at i:27618899 original size:26 final size:26
Alignment explanation
Indices: 27618870--27618921 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
27618860 GGTAGTAATT
27618870 CAATAATTCTATCAATATTCATAAAC
1 CAATAATTCTATCAATATTCATAAAC
27618896 CAATAATTCTATCAATATTCATAAAC
1 CAATAATTCTATCAATATTCATAAAC
27618922 AACTGAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (26 bp):
CAATAATTCTATCAATATTCATAAAC
Found at i:27640591 original size:35 final size:35
Alignment explanation
Indices: 27640545--27640616 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
27640535 TTATTATTAT
*
27640545 GATAGCAAAAATAGACTAAATGCTTACTCAATAAA
1 GATAGCAAAAATAGACTAAATGCTTACACAATAAA
*
27640580 GATAGCAAAAATAGACTAAATTCTTACACAATAAA
1 GATAGCAAAAATAGACTAAATGCTTACACAATAAA
27640615 GA
1 GA
27640617 CATGTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.22
Consensus pattern (35 bp):
GATAGCAAAAATAGACTAAATGCTTACACAATAAA
Found at i:27643189 original size:25 final size:26
Alignment explanation
Indices: 27643160--27643215 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
27643150 TTTATTAGTA
*
27643160 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
27643184 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
27643210 TAAAAT
1 TAAAAT
27643216 TTAGTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:27643909 original size:16 final size:15
Alignment explanation
Indices: 27643884--27643917 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
27643874 AAAGTTGATA
*
27643884 ATAATTAATATATATT
1 ATAATAAATATA-ATT
27643900 ATAATAAATATAATT
1 ATAATAAATATAATT
27643915 ATA
1 ATA
27643918 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:27646818 original size:28 final size:28
Alignment explanation
Indices: 27646750--27646903 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
27646740 CATGAGATTG
* * * *
27646750 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
27646779 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
27646807 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
27646835 GCACTAAGTGTGCAAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
27646863 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
27646890 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
27646904 GACTTAATAT
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.20
28 75 0.65
29 18 0.16
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:27654957 original size:28 final size:28
Alignment explanation
Indices: 27654889--27655042 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
27654879 CATGAGATTG
* * * *
27654889 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
27654918 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
27654946 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
27654974 GCACTAAGTGTGCAAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
27655002 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
27655029 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
27655043 GACTTAATAT
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.20
28 75 0.65
29 18 0.16
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:27658966 original size:22 final size:22
Alignment explanation
Indices: 27658936--27658979 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27658926 TTTGGTATTT
27658936 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
27658958 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
27658980 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:27670301 original size:20 final size:20
Alignment explanation
Indices: 27670276--27670324 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
27670266 TAAGTTATGC
27670276 TAAGTAAATGAAATGAAAAG
1 TAAGTAAATGAAATGAAAAG
* **
27670296 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATGAAAAG
*
27670316 AAAGTAAAT
1 TAAGTAAAT
27670325 TGAGTGCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGAAATGAAAAG
Found at i:27683695 original size:6 final size:6
Alignment explanation
Indices: 27683684--27683723 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
27683674 ATCTTGTGGC
27683684 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
27683724 GAAAGAGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:27696497 original size:28 final size:28
Alignment explanation
Indices: 27696466--27696550 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 28
27696456 AGTTCGTTAG
27696466 GATTGTCTTAAATGGGGATGTCCATCAA
1 GATTGTCTTAAATGGGGATGTCCATCAA
* * * * * *
27696494 GATTATCTT-AATGTGAAAGCCCGTCAA
1 GATTGTCTTAAATGGGGATGTCCATCAA
* * *
27696521 GACTGTATTAAATAGGGATGTCCATCAA
1 GATTGTCTTAAATGGGGATGTCCATCAA
27696549 GA
1 GA
27696551 CTATCATATG
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
27 19 0.46
28 22 0.54
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (28 bp):
GATTGTCTTAAATGGGGATGTCCATCAA
Found at i:27704829 original size:14 final size:15
Alignment explanation
Indices: 27704800--27704830 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27704790 AAACCTGTAA
27704800 AAGTTAAATAAAACT
1 AAGTTAAATAAAACT
27704815 AAGTTAAAT-AAACT
1 AAGTTAAATAAAACT
27704829 AA
1 AA
27704831 TGGAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AAGTTAAATAAAACT
Found at i:27706797 original size:9 final size:9
Alignment explanation
Indices: 27706783--27706815 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
27706773 TCTTCCTATC
27706783 GAGAAATAA
1 GAGAAATAA
27706792 GAGAAATAA
1 GAGAAATAA
27706801 GAGAAATAA
1 GAGAAATAA
27706810 GAGAAA
1 GAGAAA
27706816 ATTATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (9 bp):
GAGAAATAA
Found at i:27738417 original size:44 final size:45
Alignment explanation
Indices: 27738367--27738488 Score: 144
Period size: 45 Copynumber: 2.7 Consensus size: 45
27738357 TAACAGATCG
* *
27738367 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AA-GTAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGGTA-GAA
*
27738411 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGGTAGAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGGTAGAA
* *
27738456 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
27738489 TTAAAGCCGG
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
43 3 0.05
44 28 0.42
45 29 0.44
46 6 0.09
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGGTAGAA
Found at i:27738552 original size:43 final size:43
Alignment explanation
Indices: 27738456--27738563 Score: 105
Period size: 43 Copynumber: 2.5 Consensus size: 43
27738446 GAAGGTAGAA
* *
27738456 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGGT
1 AATCTTATCTCCTTAAAGTTGCAGTGGAG-AGATTAAAACCGGT
* *
27738500 AATCCTATCTCGC-TAAAGTTGCAGT-GAGAGGATTAAAACC-TT
1 AATCTTATCTC-CTTAAAGTTGCAGTGGAGA-GATTAAAACCGGT
* *
27738542 AGATCTTATCTCTTTGAAGTTG
1 A-ATCTTATCTCCTTAAAGTTG
27738564 TAGAGAGTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
42 3 0.06
43 28 0.53
44 21 0.40
45 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (43 bp):
AATCTTATCTCCTTAAAGTTGCAGTGGAGAGATTAAAACCGGT
Found at i:27738634 original size:44 final size:44
Alignment explanation
Indices: 27738367--27738833 Score: 161
Period size: 44 Copynumber: 10.8 Consensus size: 44
27738357 TAACAGATCG
* * * *
27738367 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATAAGCA
* * * *
27738411 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGGT-AGAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-ATAAGCA
* * *** *
27738456 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-TAAGCA
* * * * *
27738501 A-TCCTATCTCGCTAAAGTTGCAGT-GAG-AGGATT-AA-AACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTAAATAAGC-A
** * * * *** *
27738542 AGATCTTATCTCTTTGAAGTTGTAG-AGAGTAGATCGCAT---CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATAAGCA
* *
27738583 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATAAGCA
* ** * *
27738627 AGTCTTATC-CTCCTAAAGTTGCAG-CAAGGCAGATTGAAGAT-GGTA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATT-AA-ATAAGCA
* * *
27738672 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTGA-CA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA--TAAGCA
* * * * * *
27738717 A-TCCTATCTCCCTGAAGTTGTAGTGGAGCGGGTT-AA-AACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATAAGC-A
* * * *** *
27738759 AGATCTTATCTCTCTGAAGTTGCAG-AGAGTAGATCGCAT---CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATAAGCA
*
27738800 AGTATTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
27738834 CGAATACGGC
Statistics
Matches: 312, Mismatches: 75, Indels: 75
0.68 0.16 0.16
Matches are distributed among these distances:
40 40 0.13
41 22 0.07
42 6 0.02
43 43 0.14
44 128 0.41
45 65 0.21
46 8 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATAAGCA
Found at i:27738878 original size:217 final size:215
Alignment explanation
Indices: 27738371--27738853 Score: 635
Period size: 216 Copynumber: 2.2 Consensus size: 215
27738361 AGATCGAGTC
* * * * * ** *
27738371 TTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAGGCAAGTCTTATCCTCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACGAATTAAGCAAATCTTATCCTCCAAAAGTTG-AGC
* * * * * * * * **
27738436 GAGGTAGACTGAAGGTAGAAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTA
65 AAGGCAGATTGAAGATGGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGACA
* * *
27738501 ATCCTATCTCGCTAAAGTTGCAGTGAGAGGATTAAAACCTTAGATCTTATCTCTTTGAAGTTGTA
130 ATCCTATCTCCCTAAAGTTGCAGTGAGAGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCA
*
27738566 GAGAGTAGATCGCATCTAGTC
195 GAGAGTAGATCGCATCTAGTA
* * *
27738587 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAATTAAGCAAGTCTTATCCTCCTAAAGTTGCAGC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACGAATTAAGCAAATCTTATCCTCCAAAAGTTG-AGC
*
27738652 AAGGCAGATTGAAGATGGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTGACA
65 AAGGCAGATTGAAGATGGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGACA
* * * *
27738717 ATCCTATCTCCCTGAAGTTGTAGTGGAGCGGGTTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
130 ATCCTATCTCCCTAAAGTTGCAGT-GAGAGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGC
27738782 AGAGAGTAGATCGCATCTAGTA
194 AGAGAGTAGATCGCATCTAGTA
*
27738804 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAA-TACGGCAAATCTTATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAATTA-AGCAAATCTTATC
27738854 TTTCCAAGAT
Statistics
Matches: 237, Mismatches: 27, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
216 135 0.57
217 88 0.37
218 14 0.06
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (215 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACGAATTAAGCAAATCTTATCCTCCAAAAGTTGAGCA
AGGCAGATTGAAGATGGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGACAA
TCCTATCTCCCTAAAGTTGCAGTGAGAGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAG
AGAGTAGATCGCATCTAGTA
Found at i:27743141 original size:11 final size:10
Alignment explanation
Indices: 27743124--27743162 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
27743114 GTATTAAGCA
27743124 TTTTAAATAT
1 TTTTAAATAT
27743134 TATTTAAATAT
1 T-TTTAAATAT
* *
27743145 TTTAAAATAA
1 TTTTAAATAT
27743155 TTTTAAAT
1 TTTTAAAT
27743163 TAAATATAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAAATAT
Found at i:27743660 original size:21 final size:20
Alignment explanation
Indices: 27743622--27743684 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
27743612 ATTCAATTTC
27743622 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
27743639 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
27743660 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
27743679 TGCAAT
1 T-CAAT
27743685 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:27755678 original size:42 final size:43
Alignment explanation
Indices: 27755617--27755703 Score: 131
Period size: 42 Copynumber: 2.0 Consensus size: 43
27755607 CTGAGTTGCC
** **
27755617 GAACGATAAAGATTGAATTTTCCT-AACCATACACGATTAAAG
1 GAACGATAAAGATCAAATTTTCCTAAACCATACAAAATTAAAG
27755659 GAACGATAAAGATCAAATTTTCCTAAACCATACAAAATTAAAG
1 GAACGATAAAGATCAAATTTTCCTAAACCATACAAAATTAAAG
27755702 GA
1 GA
27755704 TGATTAGAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 22 0.55
43 18 0.45
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (43 bp):
GAACGATAAAGATCAAATTTTCCTAAACCATACAAAATTAAAG
Found at i:27756853 original size:74 final size:74
Alignment explanation
Indices: 27756732--27756879 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
27756722 TGAATTTGAA
27756732 ACCTCAATTTTTGCTAGTGGTTTCCCTCTCAACAAGGTACGTTTGATGACTATGTCTACTAAGGA
1 ACCTCAATTTTTGCTAGTGGTTTCCCTCTCAACAAGGTACGTTTGATGACTATGTCTACTAAGGA
27756797 AGTGTAGAT
66 AGTGTAGAT
27756806 ACCTCAATTTTTGCTAGTGGTTTCCCTCTCAACAAGGTACGTTTGATGACTATGTCTACTAAGGA
1 ACCTCAATTTTTGCTAGTGGTTTCCCTCTCAACAAGGTACGTTTGATGACTATGTCTACTAAGGA
27756871 AGTGTAGAT
66 AGTGTAGAT
27756880 CTGTAAGAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (74 bp):
ACCTCAATTTTTGCTAGTGGTTTCCCTCTCAACAAGGTACGTTTGATGACTATGTCTACTAAGGA
AGTGTAGAT
Found at i:27757662 original size:29 final size:29
Alignment explanation
Indices: 27757628--27757864 Score: 196
Period size: 29 Copynumber: 8.1 Consensus size: 29
27757618 TGTATAAGTG
* *
27757628 AGCCTTTGTGGATATCTCTATTATAAGGA
1 AGCCTTTGTGGCTATCTCTATTAAAAGGA
*
27757657 AGCCTTTGTGG-TGATCAT-TGTTAAAAGGA
1 AGCCTTTGTGGCT-ATC-TCTATTAAAAGGA
* * *
27757686 AGTCTTTGTGGCGATCTCTATTAAATGGA
1 AGCCTTTGTGGCTATCTCTATTAAAAGGA
* * *
27757715 AGCCTTTGTGGCGT-TCTTTGTTAAATGGA
1 AGCCTTTGTGGC-TATCTCTATTAAAAGGA
* *
27757744 AGCCTTGGT-GATGATCTCTATTAAAAGGA
1 AGCCTTTGTGGCT-ATCTCTATTAAAAGGA
* * * *
27757773 AGCTTTTGTGGCCATCTCTGTAAAATAGGA
1 AGCCTTTGTGGCTATCTCTATTAAA-AGGA
* * * *
27757803 TGCTTTTATGGCTATCTC-AGTTAAATGGA
1 AGCCTTTGTGGCTATCTCTA-TTAAAAGGA
* *
27757832 TGTCTTTGTGGCTATCTCTATTAAAAGGA
1 AGCCTTTGTGGCTATCTCTATTAAAAGGA
27757861 AGCC
1 AGCC
27757865 CTCACAGCGA
Statistics
Matches: 164, Mismatches: 33, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 3 0.02
29 134 0.82
30 26 0.16
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (29 bp):
AGCCTTTGTGGCTATCTCTATTAAAAGGA
Found at i:27757809 original size:30 final size:30
Alignment explanation
Indices: 27757769--27757850 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
27757759 CTCTATTAAA
* *
27757769 AGGAAGCTTTTGTGGCCATCTCTGTAAAAT
1 AGGATGCTTTTGTGGCTATCTCTGTAAAAT
* * *
27757799 AGGATGCTTTTATGGCTATCTCAGTTAAAT
1 AGGATGCTTTTGTGGCTATCTCTGTAAAAT
27757829 -GGATG-TCTTTGTGGCTATCTCT
1 AGGATGCT-TTTGTGGCTATCTCT
27757851 ATTAAAAGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.02
29 18 0.41
30 25 0.57
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (30 bp):
AGGATGCTTTTGTGGCTATCTCTGTAAAAT
Found at i:27760252 original size:18 final size:18
Alignment explanation
Indices: 27760231--27760273 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
27760221 TAATTTGGCC
*
27760231 ATTTTTATTTTTA-TTATA
1 ATTTTTATTTCTAGTT-TA
*
27760249 ATTTTTGTTTCTAGTTTA
1 ATTTTTATTTCTAGTTTA
27760267 ATTTTTA
1 ATTTTTA
27760274 CATTCTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (18 bp):
ATTTTTATTTCTAGTTTA
Found at i:27761927 original size:21 final size:21
Alignment explanation
Indices: 27761901--27761943 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27761891 CACATGAACG
*
27761901 AACAATTTTGTAAAATTCTCA
1 AACAATTTGGTAAAATTCTCA
27761922 AACAATTTGGTAAAATTCTCA
1 AACAATTTGGTAAAATTCTCA
27761943 A
1 A
27761944 GCTGTTAAAG
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:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (21 bp):
AACAATTTGGTAAAATTCTCA
Found at i:27763495 original size:20 final size:20
Alignment explanation
Indices: 27763470--27763546 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
27763460 AGCCGCACAA
*
27763470 GCGTGTAGGCTCTCACACGG
1 GCGTGTGGGCTCTCACACGG
*
27763490 GCGTGTGGGCTCTCACTCGG
1 GCGTGTGGGCTCTCACACGG
** * *
27763510 TTGTGTGGGCTCTCACTCGA
1 GCGTGTGGGCTCTCACACGG
*
27763530 GCATGTGGGCTCTCACA
1 GCGTGTGGGCTCTCACA
27763547 TAGGCGTGGA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.12, C:0.29, G:0.34, T:0.26
Consensus pattern (20 bp):
GCGTGTGGGCTCTCACACGG
Found at i:27764219 original size:18 final size:18
Alignment explanation
Indices: 27764196--27764288 Score: 65
Period size: 18 Copynumber: 5.4 Consensus size: 18
27764186 ACCCATTCCT
27764196 TTATTTTATTTTATTTTA
1 TTATTTTATTTTATTTTA
27764214 TTATTTTA--TTA-TTTA
1 TTATTTTATTTTATTTTA
* *
27764229 TTATTATT-TGTTATATTA
1 TTATT-TTATTTTATTTTA
* *
27764247 TT-TTTTA-TCTATTTTC
1 TTATTTTATTTTATTTTA
*
27764263 TTATTTT-TTCTTATTTGTT
1 TTATTTTATT-TTATTT-TA
27764282 TTATTTT
1 TTATTTT
27764289 TCTTATGCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
15 9 0.15
16 14 0.24
17 10 0.17
18 18 0.31
19 8 0.14
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.75
Consensus pattern (18 bp):
TTATTTTATTTTATTTTA
Found at i:27764242 original size:10 final size:9
Alignment explanation
Indices: 27764199--27764345 Score: 59
Period size: 9 Copynumber: 15.4 Consensus size: 9
27764189 CATTCCTTTA
*
27764199 TTTTATTTT
1 TTTTATTAT
27764208 ATTTTATTA-
1 -TTTTATTAT
27764217 TTTTATTAT
1 TTTTATTAT
27764226 TTATTATTATT
1 TT-TTATTA-T
27764237 TGTTATATTATT
1 T-TT-TATTA-T
27764249 TTTTATCTA-
1 TTTTAT-TAT
*
27764258 TTTTCTTATT
1 TTTTATTA-T
*
27764268 TTTTCTTAT
1 TTTTATTAT
27764277 TTGTT-TTAT
1 TT-TTATTAT
*
27764286 TTTTCTTAT
1 TTTTATTAT
** *
27764295 GCTTA-GAT
1 TTTTATTAT
* *
27764303 TTTAATTTT
1 TTTTATTAT
27764312 GTTTTAATTTAT
1 -TTTT-A-TTAT
*
27764324 TTATATTAT
1 TTTTATTAT
*
27764333 TTTTAGTAT
1 TTTTATTAT
27764342 TTTT
1 TTTT
27764346 TAGTATTATT
Statistics
Matches: 107, Mismatches: 16, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
8 16 0.15
9 38 0.36
10 30 0.28
11 11 0.10
12 12 0.11
ACGTcount: A:0.20, C:0.03, G:0.04, T:0.72
Consensus pattern (9 bp):
TTTTATTAT
Found at i:27764266 original size:19 final size:19
Alignment explanation
Indices: 27764209--27764289 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 19
27764199 TTTTATTTTA
*
27764209 TTTTATTATTT-TATTATT
1 TTTTATTATTTGTCTTATT
* *
27764227 TATTATTATTTGTTATATTATT
1 TTTTATTATTTG---TCTTATT
27764249 TTTTATCTATTT-TCTTATT
1 TTTTAT-TATTTGTCTTATT
* *
27764268 TTTTCTTATTTGTTTTATT
1 TTTTATTATTTGTCTTATT
27764287 TTT
1 TTT
27764290 CTTATGCTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
18 15 0.29
19 20 0.38
22 12 0.23
23 5 0.10
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTATTATTTGTCTTATT
Found at i:27764267 original size:41 final size:39
Alignment explanation
Indices: 27764202--27764294 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 39
27764192 TCCTTTATTT
27764202 TATTTTATTTTATTATTTTATTATTTATTATTATTTGTTA
1 TATTTT-TTTTATTATTTTATTATTTATTATTATTTGTTA
* * * *
27764242 TATTATTTTTTATCTATTTTCTTATTTTTTCTTATTTGTTT
1 TATT-TTTTTTAT-TATTTTATTATTTATTATTATTTGTTA
*
27764283 TATTTTTCTTAT
1 TATTTTTTTTAT
27764295 GCTTAGATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 17 0.37
41 29 0.63
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (39 bp):
TATTTTTTTTATTATTTTATTATTTATTATTATTTGTTA
Found at i:27764352 original size:22 final size:22
Alignment explanation
Indices: 27764318--27764364 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
27764308 TTTTGTTTTA
*
27764318 ATTTATTTATATTATTTTTAGT
1 ATTTATTTATATTATTTTTACT
27764340 ATTT-TTTAGTATTATTTTTACT
1 ATTTATTTA-TATTATTTTTACT
27764362 ATT
1 ATT
27764365 ACCTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (22 bp):
ATTTATTTATATTATTTTTACT
Found at i:27764357 original size:12 final size:12
Alignment explanation
Indices: 27764323--27764365 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
27764313 TTTTAATTTA
27764323 TTTA-TATTATT
1 TTTAGTATTATT
27764334 TTTAGTA-T-TT
1 TTTAGTATTATT
27764344 TTTAGTATTATT
1 TTTAGTATTATT
*
27764356 TTTACTATTA
1 TTTAGTATTA
27764366 CCTTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.32
11 6 0.21
12 13 0.46
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (12 bp):
TTTAGTATTATT
Found at i:27766559 original size:29 final size:28
Alignment explanation
Indices: 27766514--27766610 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 28
27766504 TGTATAAGTG
* * *
27766514 AGCCATTGTGGCT-ATCTCTATTATAAGAA
1 AGCCTTTGTGG-TGATCTCTGTTA-AAGGA
*
27766543 AGCCTTTGTGGTGATCTTTGTTAAATGGA
1 AGCCTTTGTGGTGATCTCTGTTAAA-GGA
* *
27766572 AGCCTTGGTGATGATCTCTGTTAAAAGGA
1 AGCCTTTGTGGTGATCTCTGTT-AAAGGA
27766601 AGCCTTTGTG
1 AGCCTTTGTG
27766611 ACCATCTCTG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
28 3 0.05
29 51 0.89
30 3 0.05
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (28 bp):
AGCCTTTGTGGTGATCTCTGTTAAAGGA
Found at i:27766611 original size:29 final size:29
Alignment explanation
Indices: 27766527--27766626 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
27766517 CATTGTGGCT
* * * *
27766527 ATCTCTATTATAAGAAAGCCTTTGTGGTG
1 ATCTCTGTTAAAAGGAAGCCTTTGTGATG
* * *
27766556 ATCTTTGTTAAATGGAAGCCTTGGTGATG
1 ATCTCTGTTAAAAGGAAGCCTTTGTGATG
**
27766585 ATCTCTGTTAAAAGGAAGCCTTTGTGACC
1 ATCTCTGTTAAAAGGAAGCCTTTGTGATG
*
27766614 ATCTCTGTAAAAA
1 ATCTCTGTTAAAA
27766627 AAAGATGCTT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (29 bp):
ATCTCTGTTAAAAGGAAGCCTTTGTGATG
Found at i:27770129 original size:26 final size:26
Alignment explanation
Indices: 27770088--27770157 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
27770078 ATATAAGTGA
* * *
27770088 GCCTTTTTGGCAATCTTTGAATGGAT
1 GCCTTTGTGGCTATCTCTGAATGGAT
27770114 G-CTTTGGTGGCTATCTCTGAATGGAT
1 GCCTTT-GTGGCTATCTCTGAATGGAT
27770140 GCCTTTGTGGCTATCTCT
1 GCCTTTGTGGCTATCTCT
27770158 ATTGTAAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
25 4 0.10
26 31 0.79
27 4 0.10
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.41
Consensus pattern (26 bp):
GCCTTTGTGGCTATCTCTGAATGGAT
Found at i:27770184 original size:29 final size:28
Alignment explanation
Indices: 27770140--27770243 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 28
27770130 CTGAATGGAT
* *
27770140 GCCTTTGTGGCTATCTCTATTGTAAGGAA
1 GCCTTTGTGGCGATCTCTATT-AAAGGAA
27770169 GCCTTTGTGGCGATCTCTATTAAATGGAA
1 GCCTTTGTGGCGATCTCTATTAAA-GGAA
* * * * *
27770198 GCTTTTGTGGTGACCTCTGTTAAAAGTAA
1 GCCTTTGTGGCGATCTCTATT-AAAGGAA
*
27770227 GCCTTTGTGGCCATCTC
1 GCCTTTGTGGCGATCTC
27770244 AGTAAAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 57 0.92
30 3 0.05
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (28 bp):
GCCTTTGTGGCGATCTCTATTAAAGGAA
Found at i:27770205 original size:58 final size:58
Alignment explanation
Indices: 27770133--27770243 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
27770123 GCTATCTCTG
* * ** *
27770133 AATGGATGCCTTTGTGGCT-ATCTCTATTGTAAGGAAGCCTTTGTGGCGATCTCTATTA
1 AATGGAAGCCTTTGTGG-TGACCTCTATTAAAAGGAAGCCTTTGTGGCCATCTCTATTA
* * *
27770191 AATGGAAGCTTTTGTGGTGACCTCTGTTAAAAGTAAGCCTTTGTGGCCATCTC
1 AATGGAAGCCTTTGTGGTGACCTCTATTAAAAGGAAGCCTTTGTGGCCATCTC
27770244 AGTAAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
57 1 0.02
58 43 0.98
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (58 bp):
AATGGAAGCCTTTGTGGTGACCTCTATTAAAAGGAAGCCTTTGTGGCCATCTCTATTA
Found at i:27770314 original size:29 final size:29
Alignment explanation
Indices: 27770136--27770317 Score: 106
Period size: 29 Copynumber: 6.2 Consensus size: 29
27770126 ATCTCTGAAT
27770136 GGATGCCTTTGTGGCTATCTCTATT-GTAA
1 GGATGCCTTTGTGGCTATCTCTATTAG-AA
* *
27770165 GGAAGCCTTTGTGGCGATCTCTATTA-AA
1 GGATGCCTTTGTGGCTATCTCTATTAGAA
* * * * *
27770193 TGGAAGCTTTTGTGG-TGACCTCTGTTAAAA
1 -GGATGCCTTTGTGGCT-ATCTCTATTAGAA
* * * * *
27770223 GTAAGCCTTTGTGGCCATCTC-AGTAAAAAA
1 GGATGCCTTTGTGGCTATCTCTA-T-TAGAA
* * * *
27770253 AGATGCTTTTATGGCTATCT-TAGT-GAAA
1 GGATGCCTTTGTGGCTATCTCTATTAG-AA
*
27770281 TGGATGTCTTTGTGGCTATCTCTATTAGAA
1 -GGATGCCTTTGTGGCTATCTCTATTAGAA
27770311 GGATGCC
1 GGATGCC
27770318 CTCATGACGA
Statistics
Matches: 114, Mismatches: 27, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
28 4 0.04
29 83 0.73
30 26 0.23
31 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (29 bp):
GGATGCCTTTGTGGCTATCTCTATTAGAA
Found at i:27772748 original size:22 final size:23
Alignment explanation
Indices: 27772706--27772748 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
27772696 TTTATTCAAA
*
27772706 ATTATTATTAAATAATATAAAAT
1 ATTATTATTAAAAAATATAAAAT
27772729 ATTA-TATTAATAAAAT-TAAA
1 ATTATTATTAA-AAAATATAAA
27772749 CTTATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTATTATTAAAAAATATAAAAT
Found at i:27773547 original size:18 final size:17
Alignment explanation
Indices: 27773521--27773560 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
27773511 AATATTTTAA
*
27773521 TATTATAATTATTATATT
1 TATTATAATAATT-TATT
*
27773539 TATTTTAATAATTTATT
1 TATTATAATAATTTATT
27773556 TATTA
1 TATTA
27773561 GTATTATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATAATAATTTATT
Found at i:27773558 original size:26 final size:28
Alignment explanation
Indices: 27773512--27773588 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 28
27773502 GCTAGACATA
27773512 ATATTTTAATATTATAATTATTA-TATT
1 ATATTTTAATATTATAATTATTAGTATT
*
27773539 -TATTTTAATAATT-TATTTATTAGTATT
1 ATATTTTAAT-ATTATAATTATTAGTATT
27773566 ATATTAATT-ATAGTTATAATTAT
1 ATATT--TTAATA-TTATAATTAT
27773589 AATTATAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
26 17 0.41
27 7 0.17
28 5 0.12
29 4 0.10
30 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
ATATTTTAATATTATAATTATTAGTATT
Found at i:27788760 original size:31 final size:31
Alignment explanation
Indices: 27788701--27788769 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
27788691 AAAAAAAATC
**
27788701 TAGTGACTTAAATAAAATCTTTTGAATAG-T
1 TAGTGACTTAAATAAAATCTTTCAAATAGCT
27788731 TCAGTGACTTAAATGAAAA-CTTTCAAATAGCT
1 T-AGTGACTTAAAT-AAAATCTTTCAAATAGCT
27788763 TAGTGAC
1 TAGTGAC
27788770 CGTTTTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.79
32 6 0.18
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (31 bp):
TAGTGACTTAAATAAAATCTTTCAAATAGCT
Found at i:27796735 original size:26 final size:26
Alignment explanation
Indices: 27796701--27796753 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
27796691 CAACAAGAAA
*
27796701 TTGAAGATTTTACCCTTGGTAAAATT
1 TTGAAGATTTTACCCCTGGTAAAATT
* * *
27796727 TTGACGATTTTGCCCCTGGTTAAATT
1 TTGAAGATTTTACCCCTGGTAAAATT
27796753 T
1 T
27796754 CGAGAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (26 bp):
TTGAAGATTTTACCCCTGGTAAAATT
Found at i:27796938 original size:18 final size:18
Alignment explanation
Indices: 27796915--27796953 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
27796905 CCATTTTTGG
27796915 AAACCTACAGTCATTTCC
1 AAACCTACAGTCATTTCC
*
27796933 AAACCTACATTCATTTCC
1 AAACCTACAGTCATTTCC
27796951 AAA
1 AAA
27796954 TGGCTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.31, G:0.03, T:0.28
Consensus pattern (18 bp):
AAACCTACAGTCATTTCC
Found at i:27799076 original size:20 final size:19
Alignment explanation
Indices: 27799050--27799101 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
27799040 CTTTAACCCC
27799050 AAGTATCGATACTCGAGCA
1 AAGTATCGATACTCGAGCA
*
27799069 AGAGTATCGATACTTGAGCA
1 A-AGTATCGATACTCGAGCA
27799089 AATGTATCGATAC
1 AA-GTATCGATAC
27799102 CAAATCTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (19 bp):
AAGTATCGATACTCGAGCA
Found at i:27803219 original size:41 final size:41
Alignment explanation
Indices: 27803170--27803279 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
27803160 TAGCAACCTC
*
27803170 TCGAGGAATCTGCACTTAGCAACCCCTTTTTGACCAGAGTT
1 TCGAGGAATCTGCACTTAGCAACCCCTTTTTGACCAGAGAT
* * *
27803211 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
1 TCGAGGAATCTGCACTTAGCAACCCCTTTTTGACCAGAGAT
* *
27803252 TCGAGGAATATACACTTAGCAACCCCTT
1 TCGAGGAATCTGCACTTAGCAACCCCTT
27803280 AAATTCAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (41 bp):
TCGAGGAATCTGCACTTAGCAACCCCTTTTTGACCAGAGAT
Found at i:27806024 original size:28 final size:28
Alignment explanation
Indices: 27805984--27806057 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
27805974 TAGCAAAGTC
*
27805984 ATGGACTACCCTCTACATATTTTGCGTT
1 ATGGACTACCCTCTACATATTTTGAGTT
27806012 ATGGACTACCCTCTACATATTTTGAGTT
1 ATGGACTACCCTCTACATATTTTGAGTT
*
27806040 ATGGAGTACCCTCTACAT
1 ATGGACTACCCTCTACAT
27806058 GTGCTCTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (28 bp):
ATGGACTACCCTCTACATATTTTGAGTT
Found at i:27806193 original size:93 final size:93
Alignment explanation
Indices: 27806011--27806191 Score: 319
Period size: 93 Copynumber: 2.0 Consensus size: 93
27806001 TATTTTGCGT
* * *
27806011 TATGGACTACCCTCTACATATTTTGAGTTATGGAGTACCCTCTACATGTGCTCTTTGATGTGATT
1 TATGGACTACCATCTACATATTTTGAGTTATGGACTACCCTCTACATGTGCTATTTGATGTGATT
*
27806076 AAAGATGTGTTGTTCTATCAGGGGAATC
66 AAAGAAGTGTTGTTCTATCAGGGGAATC
27806104 TATGGACTACCATCTACATATTTTGAGTTATGGACTACCCTCTACATGTGCTATTTGATGTGATT
1 TATGGACTACCATCTACATATTTTGAGTTATGGACTACCCTCTACATGTGCTATTTGATGTGATT
27806169 AAAGAAGTGTTGTTCTAT-AGGGG
66 AAAGAAGTGTTGTTCTATCAGGGG
27806192 GACCCTATAT
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
92 5 0.06
93 79 0.94
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (93 bp):
TATGGACTACCATCTACATATTTTGAGTTATGGACTACCCTCTACATGTGCTATTTGATGTGATT
AAAGAAGTGTTGTTCTATCAGGGGAATC
Found at i:27809860 original size:9 final size:9
Alignment explanation
Indices: 27809842--27809881 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
27809832 TTTGGTTAAA
*
27809842 AATTAGCCG
1 AATTAACCG
27809851 AATTAACCG
1 AATTAACCG
*
27809860 AATTACCCG
1 AATTAACCG
*
27809869 AATTATCCG
1 AATTAACCG
27809878 AATT
1 AATT
27809882 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:27809869 original size:18 final size:18
Alignment explanation
Indices: 27809842--27809881 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
27809832 TTTGGTTAAA
*
27809842 AATTAGCCGAATTAACCG
1 AATTACCCGAATTAACCG
*
27809860 AATTACCCGAATTATCCG
1 AATTACCCGAATTAACCG
27809878 AATT
1 AATT
27809882 GAATCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:27809921 original size:37 final size:37
Alignment explanation
Indices: 27809880--27809954 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
27809870 ATTATCCGAA
*
27809880 TTGAATCACTACATAATTA-AAAATATTACTTAAGTCT
1 TTGAATCACTACATAATTATAAAA-ATTACATAAGTCT
*
27809917 TTGAATCACTACATAATTATAAAAATTACATAATTCT
1 TTGAATCACTACATAATTATAAAAATTACATAAGTCT
27809954 T
1 T
27809955 GAAATTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 31 0.89
38 4 0.11
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (37 bp):
TTGAATCACTACATAATTATAAAAATTACATAAGTCT
Found at i:27821648 original size:24 final size:25
Alignment explanation
Indices: 27821587--27821648 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
27821577 TACTGATTTT
* * *
27821587 AGCTCTTATGAGCTTACTATTTTTC
1 AGCTCGTATGAGCTTACCATTTTAC
* * *
27821612 AGCTTGAAGGAGCTTACCA-TTTAC
1 AGCTCGTATGAGCTTACCATTTTAC
27821636 AGCTCGTATGAGC
1 AGCTCGTATGAGC
27821649 ATATATAGGA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCATTTTAC
Found at i:27821815 original size:26 final size:26
Alignment explanation
Indices: 27821786--27821837 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
27821776 CATAGGTATT
*
27821786 TACATGAGATATATGA-AAATGATTTG
1 TACACGAGATATA-GATAAATGATTTG
* *
27821812 TACACGATATATAGATACATGATTTG
1 TACACGAGATATAGATAAATGATTTG
27821838 GAAATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (26 bp):
TACACGAGATATAGATAAATGATTTG
Found at i:27828714 original size:61 final size:61
Alignment explanation
Indices: 27828612--27828869 Score: 193
Period size: 61 Copynumber: 4.2 Consensus size: 61
27828602 CAGGAGAAGC
* * * ** * * * *
27828612 AAAGCCCTTGTGGCAAGTACTGAATGTAAAATACAACCTTTGTGGTAAAAATTTTGACGAG
1 AAAGCCTTTGTGGCGAGTACTGAATATAAAGGATAGCCTTTGTGGAAAAAATCTTGACGAG
* * * * * * *
27828673 AAAGCCTTTGTGGCGAGTACTGGATATAAAGGATGGTCTTTGTGGCACAACTCTGGAC-ATG
1 AAAGCCTTTGTGGCGAGTACTGAATATAAAGGATAGCCTTTGTGGAAAAAATCTTGACGA-G
* * * * *
27828734 AAAGCCTTTATGGCAAGTACT-AATTGTAAAGGATAGCCTTTGTGGAAAAAATCTAGACAAG
1 AAAGCCTTTGTGGCGAGTACTGAA-TATAAAGGATAGCCTTTGTGGAAAAAATCTTGACGAG
* ** * * *
27828795 AAAGCTTTTGTGATGAGCA-TCGAATATAAAGGATAACCTTTGTGGAAAAAAT-TT-ATAGAG
1 AAAGCCTTTGTGGCGAGTACT-GAATATAAAGGATAGCCTTTGTGGAAAAAATCTTGA-CGAG
27828855 AAAAGCCTTTGTGGC
1 -AAAGCCTTTGTGGC
27828870 AACCTCTGTT
Statistics
Matches: 151, Mismatches: 39, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
59 1 0.01
60 6 0.04
61 141 0.93
62 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (61 bp):
AAAGCCTTTGTGGCGAGTACTGAATATAAAGGATAGCCTTTGTGGAAAAAATCTTGACGAG
Found at i:27828836 original size:122 final size:122
Alignment explanation
Indices: 27828612--27828839 Score: 262
Period size: 122 Copynumber: 1.9 Consensus size: 122
27828602 CAGGAGAAGC
* * * * * *
27828612 AAAGCCCTTGTGGCAAGTACTGAATGTAAAATACAACCTTTGTGGTAAAAATTTTGACGAGAAAG
1 AAAGCCCTTATGGCAAGTACTGAATGTAAAAGACAACCTTTGTGGAAAAAATCTAGACAAGAAAG
* * * ***
27828677 CCTTTGTGGCGAGTACTGGATATAAAGGATGGTCTTTGTGGCACAACTCTGGACATG
66 CCTTTGTGACGAGCACTGAATATAAAGGATAACCTTTGTGGCACAACTCTGGACATG
* * * *
27828734 AAAGCCTTTATGGCAAGTACT-AATTGTAAAGGATAGCCTTTGTGGAAAAAATCTAGACAAGAAA
1 AAAGCCCTTATGGCAAGTACTGAA-TGTAAAAGACAACCTTTGTGGAAAAAATCTAGACAAGAAA
* *
27828798 GCTTTTGTGATGAGCA-TCGAATATAAAGGATAACCTTTGTGG
65 GCCTTTGTGACGAGCACT-GAATATAAAGGATAACCTTTGTGG
27828840 AAAAAATTTA
Statistics
Matches: 86, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
121 3 0.03
122 83 0.97
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (122 bp):
AAAGCCCTTATGGCAAGTACTGAATGTAAAAGACAACCTTTGTGGAAAAAATCTAGACAAGAAAG
CCTTTGTGACGAGCACTGAATATAAAGGATAACCTTTGTGGCACAACTCTGGACATG
Found at i:27834109 original size:261 final size:262
Alignment explanation
Indices: 27833740--27834258 Score: 907
Period size: 262 Copynumber: 2.0 Consensus size: 262
27833730 CGCCTATGTG
* * *
27833740 CAAGAAATGGGGTTGTTTTGTTTCTTGGTTCTTCACTATATTTTTCCAGGATTAATTTTAGTTCT
1 CAAGAAAGGGGGTTGTTTTGTTTCTTGGTTCTTCACTATATTTTTCCAGCAATAATTTTAGTTCT
* * **
27833805 TGAGGACTCCTAATCAGCTTTTAAACCCATTTCAACTAGGGAAAAATGTTCTTGATCAA-TGGCC
66 TGAAGACTCCTAATAAGCTTTTAAACCCATTTCAACTAGGGAAAAAAATTCTTGATCAATTGGCC
27833869 ATTCGGATTCCACAAATCGGGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACAT
131 ATTCGGATTCCACAAATCGGGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACAT
*
27833934 AGTTGTTGGGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTAGCTACTTAGT
196 AGTTGTTGAGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTAGCTACTTAGT
27833999 TC
261 TC
27834001 CAAGAAAGGGGGTTGTTTTGTTTCTTGGTTCTTC-CTTATATTTTTCCAGCAATAATTTTAGTTC
1 CAAGAAAGGGGGTTGTTTTGTTTCTTGGTTCTTCAC-TATATTTTTCCAGCAATAATTTTAGTTC
*
27834065 TTGAAGACTCCTAATAAGCTTTTAAACCTATTTCAACTAGGGAAAAAAATTCTTGATCAATTGGC
65 TTGAAGACTCCTAATAAGCTTTTAAACCCATTTCAACTAGGGAAAAAAATTCTTGATCAATTGGC
* *
27834130 CATTCGTATTCCACAAATCGTGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACA
130 CATTCGGATTCCACAAATCGGGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACA
*
27834195 TGGTTGTTGAGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTAGCTACTTA
195 TAGTTGTTGAGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTAGCTACTTA
27834259 TTTTCCAATA
Statistics
Matches: 244, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
260 1 0.00
261 114 0.47
262 129 0.53
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (262 bp):
CAAGAAAGGGGGTTGTTTTGTTTCTTGGTTCTTCACTATATTTTTCCAGCAATAATTTTAGTTCT
TGAAGACTCCTAATAAGCTTTTAAACCCATTTCAACTAGGGAAAAAAATTCTTGATCAATTGGCC
ATTCGGATTCCACAAATCGGGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACAT
AGTTGTTGAGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTAGCTACTTAGT
TC
Found at i:27856723 original size:21 final size:22
Alignment explanation
Indices: 27856699--27856741 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
27856689 AAATGAAAAA
*
27856699 AATGCTAATTT-TTGTTATTTT
1 AATGATAATTTCTTGTTATTTT
* *
27856720 AATGATATTTTCTTGTTGTTTT
1 AATGATAATTTCTTGTTATTTT
27856742 CTCCCTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (22 bp):
AATGATAATTTCTTGTTATTTT
Found at i:27858416 original size:30 final size:30
Alignment explanation
Indices: 27858380--27858477 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
27858370 GGTTGGATAA
27858380 TGAATTTTTAGTTTAATTTTGGCACTGAGT
1 TGAATTTTTAGTTTAATTTTGGCACTGAGT
* * * *
27858410 TGAATTTTGA-TTTACTGTGTGG--TTG-GAT
1 TGAATTTTTAGTTTAAT-TTTGGCACTGAG-T
27858438 AATGAATTTTTAGTTTAATTTTGGCACTGAGT
1 --TGAATTTTTAGTTTAATTTTGGCACTGAGT
27858470 TGAATTTT
1 TGAATTTT
27858478 GATTTACTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
27 1 0.02
28 3 0.06
29 5 0.10
30 34 0.65
31 5 0.10
32 3 0.06
33 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.50
Consensus pattern (30 bp):
TGAATTTTTAGTTTAATTTTGGCACTGAGT
Found at i:27858433 original size:60 final size:60
Alignment explanation
Indices: 27858367--27858490 Score: 239
Period size: 60 Copynumber: 2.1 Consensus size: 60
27858357 ATTGAAACTC
27858367 TGTGGTTGGATAATGAATTTTTAGTTTAATTTTGGCACTGAGTTGAATTTTGATTTACTG
1 TGTGGTTGGATAATGAATTTTTAGTTTAATTTTGGCACTGAGTTGAATTTTGATTTACTG
*
27858427 TGTGGTTGGATAATGAATTTTTAGTTTAATTTTGGCACTGAGTTGAATTTTGATTTACTT
1 TGTGGTTGGATAATGAATTTTTAGTTTAATTTTGGCACTGAGTTGAATTTTGATTTACTG
27858487 TGTG
1 TGTG
27858491 AATTAAATAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (60 bp):
TGTGGTTGGATAATGAATTTTTAGTTTAATTTTGGCACTGAGTTGAATTTTGATTTACTG
Found at i:27860103 original size:25 final size:25
Alignment explanation
Indices: 27860075--27860124 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27860065 TATATTTTAC
27860075 TTACTTTTCATAATTTTTATTCTAT
1 TTACTTTTCATAATTTTTATTCTAT
27860100 TTACTTTTCATAATTTTTATTCTAT
1 TTACTTTTCATAATTTTTATTCTAT
27860125 CTCTTAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (25 bp):
TTACTTTTCATAATTTTTATTCTAT
Found at i:27860345 original size:25 final size:25
Alignment explanation
Indices: 27860310--27860359 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
27860300 AGTTAAGTGC
* *
27860310 TTAGTCCAACAAATTTAGCATCAAA
1 TTAGTCAAACAAATTCAGCATCAAA
*
27860335 TTAGTCAAACAAATTCGGCATCAAA
1 TTAGTCAAACAAATTCAGCATCAAA
27860360 CTAAAAACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (25 bp):
TTAGTCAAACAAATTCAGCATCAAA
Found at i:27861646 original size:42 final size:41
Alignment explanation
Indices: 27861588--27861675 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 41
27861578 CGAGCTAAAC
*
27861588 CAAAATCATCCCTATCATCTCCATTGTATCAAGGGCAAGGT
1 CAAAATCATCCCTATCATCTCCATTGCATCAAGGGCAAGGT
27861629 CAAAACTCATCCCTATCATCTCCATTGCATCAAGGGCAAGGT
1 CAAAA-TCATCCCTATCATCTCCATTGCATCAAGGGCAAGGT
27861671 CAAAA
1 CAAAA
27861676 AGTTGCTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 5 0.11
42 40 0.89
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (41 bp):
CAAAATCATCCCTATCATCTCCATTGCATCAAGGGCAAGGT
Found at i:27864582 original size:22 final size:21
Alignment explanation
Indices: 27864536--27864583 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
27864526 TCTATAAAAA
* *
27864536 AAATTGTTTATAAAAATTAAC
1 AAATTGTCTATAAAAATAAAC
*
27864557 AAATTGTCTATAAAAAATAAAT
1 AAATTGTCTAT-AAAAATAAAC
27864579 AAATT
1 AAATT
27864584 TGTTAACGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (21 bp):
AAATTGTCTATAAAAATAAAC
Found at i:27868737 original size:21 final size:24
Alignment explanation
Indices: 27868694--27868737 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
27868684 GGAATTTATT
*
27868694 TACAAATATGAATCTAGTCTTTAC
1 TACAAATATGAATCTAATCTTTAC
27868718 TACAAATAT-AA-CTAAT-TTTA
1 TACAAATATGAATCTAATCTTTA
27868738 ACCCCGAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 2 0.11
24 9 0.47
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (24 bp):
TACAAATATGAATCTAATCTTTAC
Found at i:27874847 original size:24 final size:24
Alignment explanation
Indices: 27874826--27874882 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
27874816 AAGATTTAGT
*
27874826 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
* *
27874850 ATTTATTAGCATAATTTATTTGAC
1 ATTTATTAGCATAATATATTTAAC
*
27874874 ATTGATTAG
1 ATTTATTAG
27874883 AATTAGGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:27878073 original size:29 final size:29
Alignment explanation
Indices: 27878033--27878089 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
27878023 TTGTTGAAGA
* *
27878033 GGTGGAGAACTTGTTCATTGAGAGTTCGT
1 GGTGAAGAACTTGTTCATTGAGAATTCGT
*
27878062 GGTGAAGAACTTGTTCCTTGAGAATTCG
1 GGTGAAGAACTTGTTCATTGAGAATTCG
27878090 AGTAAAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.32, T:0.33
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCATTGAGAATTCGT
Found at i:27878209 original size:24 final size:24
Alignment explanation
Indices: 27878189--27878245 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
27878179 AAGATTTAGT
*
27878189 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
* *
27878213 ATTTATTAGCATAATTTATTTGAC
1 ATTTATTAGCATAATATATTTAAC
*
27878237 ATTGATTAG
1 ATTTATTAG
27878246 AATTAGGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:27880741 original size:24 final size:23
Alignment explanation
Indices: 27880688--27880737 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
27880678 TTTATTTATT
*
27880688 ATTAAAATATTTTAAATAATGATA
1 ATTAATATATTTTAAATAA-GATA
27880712 ATTAATATATTTTAAATCAA-ATA
1 ATTAATATATTTTAAAT-AAGATA
27880735 ATT
1 ATT
27880738 TAATCTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 16 0.67
25 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTAATATATTTTAAATAAGATA
Found at i:27881318 original size:19 final size:19
Alignment explanation
Indices: 27881294--27881337 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
27881284 GCATATTAAA
27881294 AAAATGTATAAAAATGATT
1 AAAATGTATAAAAATGATT
27881313 AAAATGTATAAAAATGATT
1 AAAATGTATAAAAATGATT
27881332 AAAATG
1 AAAATG
27881338 AAGTTATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (19 bp):
AAAATGTATAAAAATGATT
Found at i:27881335 original size:9 final size:9
Alignment explanation
Indices: 27881293--27881338 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
27881283 TGCATATTAA
27881293 AAAAATGTAT
1 AAAAATG-AT
27881303 AAAAATGAT
1 AAAAATGAT
*
27881312 TAAAATGTAT
1 AAAAATG-AT
27881322 AAAAATGAT
1 AAAAATGAT
*
27881331 TAAAATGA
1 AAAAATGA
27881339 AGTTATAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 17 0.53
10 15 0.47
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (9 bp):
AAAAATGAT
Found at i:27884033 original size:16 final size:16
Alignment explanation
Indices: 27884002--27884032 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27883992 ATTTTCTATA
27884002 ACTTTTATTGATTTTT
1 ACTTTTATTGATTTTT
27884018 ACTTTTATT-ATTTTT
1 ACTTTTATTGATTTTT
27884033 TGTCACATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.71
Consensus pattern (16 bp):
ACTTTTATTGATTTTT
Found at i:27884159 original size:19 final size:18
Alignment explanation
Indices: 27884135--27884217 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 18
27884125 TGGTTAAATG
27884135 TAATTTTTTATGCATTTTA
1 TAATTTTTTATG-ATTTTA
27884154 TAATTTTTTATGATTTTTA
1 TAATTTTTTATGA-TTTTA
** *
27884173 TGAA-AATTTATAATTTTTA
1 T-AATTTTTTATGA-TTTTA
27884192 TAATTTTTTTATGATTTCTA
1 TAA-TTTTTTATGATTT-TA
27884212 T-ATTTT
1 TAATTTT
27884218 ACAAAGTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
18 7 0.13
19 35 0.66
20 11 0.21
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (18 bp):
TAATTTTTTATGATTTTA
Found at i:27884200 original size:10 final size:9
Alignment explanation
Indices: 27884149--27884199 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
27884139 TTTTTATGCA
27884149 TTTTATAATT
1 TTTTATAA-T
*
27884159 TTTTATGAT
1 TTTTATAAT
*
27884168 TTTTATGAAA
1 TTTTAT-AAT
*
27884178 ATTTATAAT
1 TTTTATAAT
27884187 TTTTATAAT
1 TTTTATAAT
27884196 TTTT
1 TTTT
27884200 TTATGATTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 21 0.62
10 13 0.38
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:27884200 original size:29 final size:30
Alignment explanation
Indices: 27884135--27884205 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 30
27884125 TGGTTAAATG
* *
27884135 TAATTTTTTATG-CATTTTATAATTTTTTA
1 TAATTTTTTATGAAAATTTATAATTTTTTA
*
27884164 TGA-TTTTTATGAAAATTTATAA-TTTTTA
1 TAATTTTTTATGAAAATTTATAATTTTTTA
27884192 TAATTTTTTTATGA
1 TAA-TTTTTTATGA
27884206 TTTCTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 16 0.46
29 10 0.29
30 9 0.26
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (30 bp):
TAATTTTTTATGAAAATTTATAATTTTTTA
Found at i:27884213 original size:29 final size:28
Alignment explanation
Indices: 27884138--27884217 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
27884128 TTAAATGTAA
*
27884138 TTTTTTATGCATTTTATAATTTTTTATG
1 TTTTTTATGAATTTTATAATTTTTTATG
* *
27884166 ATTTTTATGAAAATTTATAATTTTTATAAT-
1 TTTTTTATG-AATTTTATAATTTTT-T-ATG
27884196 TTTTTTATG-ATTTCTAT-ATTTT
1 TTTTTTATGAATTT-TATAATTTT
27884218 ACAAAGTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 16 0.37
29 16 0.37
30 9 0.21
31 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (28 bp):
TTTTTTATGAATTTTATAATTTTTTATG
Found at i:27889798 original size:72 final size:72
Alignment explanation
Indices: 27889681--27889831 Score: 293
Period size: 72 Copynumber: 2.1 Consensus size: 72
27889671 TAACCTTGAC
*
27889681 GTCACTCCTTATTCTAATAGTCTATATTCCTTGGTCACACCAACTCATTTCTTTATATGACTAAT
1 GTCACTCATTATTCTAATAGTCTATATTCCTTGGTCACACCAACTCATTTCTTTATATGACTAAT
27889746 CACTCCA
66 CACTCCA
27889753 GTCACTCATTATTCTAATAGTCTATATTCCTTGGTCACACCAACTCATTTCTTTATATGACTAAT
1 GTCACTCATTATTCTAATAGTCTATATTCCTTGGTCACACCAACTCATTTCTTTATATGACTAAT
27889818 CACTCCA
66 CACTCCA
27889825 GTCACTC
1 GTCACTC
27889832 GTGAACTCCA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.38
Consensus pattern (72 bp):
GTCACTCATTATTCTAATAGTCTATATTCCTTGGTCACACCAACTCATTTCTTTATATGACTAAT
CACTCCA
Found at i:27889829 original size:39 final size:39
Alignment explanation
Indices: 27889714--27889829 Score: 104
Period size: 39 Copynumber: 3.1 Consensus size: 39
27889704 ATATTCCTTG
27889714 GTCACACCAACTCATTTCTTTATATGACTAATCACTCCA
1 GTCACACCAACTCATTTCTTTATATGACTAATCACTCCA
* * * * **
27889753 GTCAC-TC-A-TTA-TTC-TAATA-GTCTATATTC-CT-TG
1 GTCACACCAACTCATTTCTTTATATGACTA-A-TCACTCCA
27889786 GTCACACCAACTCATTTCTTTATATGACTAATCACTCCA
1 GTCACACCAACTCATTTCTTTATATGACTAATCACTCCA
27889825 GTCAC
1 GTCAC
27889830 TCGTGAACTC
Statistics
Matches: 55, Mismatches: 12, Indels: 20
0.63 0.14 0.23
Matches are distributed among these distances:
33 9 0.16
34 8 0.15
35 6 0.11
36 4 0.07
37 6 0.11
38 8 0.15
39 14 0.25
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.36
Consensus pattern (39 bp):
GTCACACCAACTCATTTCTTTATATGACTAATCACTCCA
Found at i:27890158 original size:45 final size:45
Alignment explanation
Indices: 27890088--27890220 Score: 153
Period size: 45 Copynumber: 3.0 Consensus size: 45
27890078 TGTGCTTTCG
* * * * *
27890088 CATGATTCCATATCGTCTTTTAGCTATGGTCTTATTCAT-TTCTAT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTATTCATCTT-TAC
*
27890133 CATGATGCTATAACATCTTTCAGCTATGGTCTTACTT-ATCTTTAC
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTA-TTCATCTTTAC
* * *
27890178 CATGATGCCATAGCATCTTTCAACTATGGTCTTACTCATCTTT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTATTCATCTTT
27890221 GATGTATAGC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 1 0.01
45 70 0.93
46 4 0.05
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (45 bp):
CATGATGCCATAACATCTTTCAGCTATGGTCTTATTCATCTTTAC
Found at i:27896230 original size:51 final size:50
Alignment explanation
Indices: 27896100--27896232 Score: 160
Period size: 50 Copynumber: 2.6 Consensus size: 50
27896090 AAAGTGATGG
* * *
27896100 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGATAGA
* * * * * *
27896150 TCGCATGTCTAGTACTATGTGCAGGCTACTATGCGTACC-GGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAAT-G-ATAGA
27896201 TCACGTGTGTAGTACTATGTGCAGGCTACTAT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAT
27896233 ATGAACCAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 3 0.04
50 35 0.51
51 31 0.45
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGATAGA
Found at i:27896494 original size:15 final size:16
Alignment explanation
Indices: 27896460--27896495 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
27896450 TGATTGAAAG
*
27896460 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
27896476 TGAAAAAGTAAAATT-
1 TGAAAAAGTAAAATTA
27896491 TGAAA
1 TGAAA
27896496 CAGAATAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:27906240 original size:50 final size:50
Alignment explanation
Indices: 27906129--27906525 Score: 449
Period size: 50 Copynumber: 7.8 Consensus size: 50
27906119 ATTTGGGTAA
* * * *
27906129 AGAGATCCCATGTAAGACCATGTCTGGGACATGTCATTGGCATCATTAAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-GATG
* *
27906185 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
27906235 AGAGGTCCCATGTAAGACCATGTCTGGGAGATGACGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
27906285 AGATGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
27906335 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
27906385 AGAGGTCCC-TCGTAAGACCATGTTTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
27906435 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
27906484 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
27906526 TGTTATATCC
Statistics
Matches: 300, Mismatches: 38, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
49 37 0.12
50 221 0.74
51 3 0.01
55 1 0.00
56 38 0.13
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:27910265 original size:28 final size:28
Alignment explanation
Indices: 27910202--27910299 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
27910192 ATATTAAGTC
* *
27910202 CGCACACTCAGTGCTATATGATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
27910229 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
27910257 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
27910286 CGCACACTTAGTGC
1 CGCACACTTAGTGC
27910300 CAATCTCATG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
27 21 0.33
28 22 0.35
29 20 0.32
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:27918258 original size:28 final size:28
Alignment explanation
Indices: 27918195--27918292 Score: 128
Period size: 28 Copynumber: 3.5 Consensus size: 28
27918185 ATATTAAGTC
* *
27918195 CGCACACTCAGTGCTATATAA-TCAACT
1 CGCACACTTAGTGCTATATAATTAAACT
27918222 CGCACACTTAGTGCTATATAATTAAACT
1 CGCACACTTAGTGCTATATAATTAAACT
* *
27918250 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TTAAACT
27918279 CGCACACTTAGTGC
1 CGCACACTTAGTGC
27918293 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 20 0.31
28 23 0.36
29 21 0.33
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATTAAACT
Found at i:27933257 original size:71 final size:71
Alignment explanation
Indices: 27933141--27933280 Score: 280
Period size: 71 Copynumber: 2.0 Consensus size: 71
27933131 TAATTTCTTT
27933141 AACTAAGTTGGTGTCACGAATCTCAATCAAGGCTTTAAAAGTAATAGAGATAAACAATAGAAACC
1 AACTAAGTTGGTGTCACGAATCTCAATCAAGGCTTTAAAAGTAATAGAGATAAACAATAGAAACC
27933206 CAACTC
66 CAACTC
27933212 AACTAAGTTGGTGTCACGAATCTCAATCAAGGCTTTAAAAGTAATAGAGATAAACAATAGAAACC
1 AACTAAGTTGGTGTCACGAATCTCAATCAAGGCTTTAAAAGTAATAGAGATAAACAATAGAAACC
27933277 CAAC
66 CAAC
27933281 CAGCAAGTGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (71 bp):
AACTAAGTTGGTGTCACGAATCTCAATCAAGGCTTTAAAAGTAATAGAGATAAACAATAGAAACC
CAACTC
Done.