Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 123 of 171
Found at i:39131390 original size:25 final size:25
Alignment explanation
Indices: 39131342--39131408 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
39131332 AAGGAGAGAG
*
39131342 AAAGAAAAGAAAAAAAGAAAAAAAAA
1 AAAGAAAA-AGAAAAAGAAAAAAAAA
* *
39131368 AAAGAAAAAGAAGAAGAAGAAAAAA
1 AAAGAAAAAGAAAAAGAAAAAAAAA
*
39131393 AAGGAAAAAGAAAAAG
1 AAAGAAAAAGAAAAAG
39131409 GAGAGGTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 28 0.78
26 8 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAGAAAAAGAAAAAGAAAAAAAAA
Found at i:39131906 original size:112 final size:113
Alignment explanation
Indices: 39131720--39131929 Score: 296
Period size: 112 Copynumber: 1.9 Consensus size: 113
39131710 AATGTTTGTC
* ** *
39131720 ATTTTTAATATTTTCGTTCATTCGAGCTTTGTCTCCAATAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATATTTTCATTCACGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
*** * * *
39131785 CCTTGTTCAAGCACGTTTGCA-TTGGAATAACAATTAGTGAACTAATG
66 CCCAATTCAAACAAGTTTGCATTTGAAATAACAATTAGTGAACTAATG
* *
39131832 ATTTTTAATCTTTTCATTCACGCGAGCTTTGCCTGCAATAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATATTTTCATTCACGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
*
39131897 CCCAATTCAAACAATTTTGCATTTGAAATAACA
66 CCCAATTCAAACAAGTTTGCATTTGAAATAACA
39131930 GTTAATGATC
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
112 74 0.88
113 10 0.12
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (113 bp):
ATTTTTAATATTTTCATTCACGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
CCCAATTCAAACAAGTTTGCATTTGAAATAACAATTAGTGAACTAATG
Found at i:39132508 original size:49 final size:50
Alignment explanation
Indices: 39132360--39132940 Score: 357
Period size: 49 Copynumber: 11.8 Consensus size: 50
39132350 ACCGAGGGAA
* * *
39132360 CATA-AAGATATGAAGGGAAAGGTTGAGGTCGCATCGGCAAACCCGATAC
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATAC
* * * * **
39132409 CTTAGAAGATGTGAAGGG-AAGGATTGAGGCCGCAAC-AGCGAATCTAATAC
1 CATAGAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGA-CAAACCCGATAC
* * * *
39132459 CAT-GAAAATATAAAGGGAAAGGTTGAGGCTGCAACGACGAACCCGATAC
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATAC
* * * * * * ** *
39132508 CTTGGAAGATGTGATGGG-AAGGATTGAGGCCGCAATGGCAAATTCGGTAC
1 CATAGAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGACAAACCCGATAC
* *
39132558 CAT-GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATAC
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATAC
* * * * * * *
39132607 CTTAGAAGATGTGATGGG-AAGGATTGAGGCCGCAATGAAAAATCCGGTAC
1 CATAGAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGACAAACCCGATAC
* * *
39132657 CAT-GAAGATATGAAGGGAAAGGTTGAGGCCGTAATGGA-AAA-CCTAGTAC
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAA-CGACAAACCCGA-TAC
* * * * ** * *
39132706 CTTAGAAGGTGTG-ATGGAAAGGATTGAGGTAGCAACGACGAATCCGATAC
1 CATAGAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGACAAACCCGATAC
* * * * *
39132756 CAT-GAAGATATGAAGGGAAAGGTTGAGGTCGCAATGGCGAACCCGGTAC
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATAC
* * * * * * * **
39132805 CTTAGAAGATGTGATGGG-AAGAATTGAGGCCGCAATGGCGAATCTTG-TAC
1 CATAGAAGATATGAAGGGAAAG-GTTGAGGCCGCAACGAC-AAACCCGATAC
* * * * * * ***
39132855 CAT-GAATATATGGAGGGAAAGGTTGAAGTCGCAACGGCGAACTTTATAC
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATAC
* * *
39132904 CTTAG-AGATATGAAGGGAAAGATTGAGACCGCAACGA
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGA
39132941 TGAATCTCAT
Statistics
Matches: 407, Mismatches: 101, Indels: 48
0.73 0.18 0.09
Matches are distributed among these distances:
48 6 0.01
49 213 0.52
50 182 0.45
51 6 0.01
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.18
Consensus pattern (50 bp):
CATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATAC
Found at i:39132559 original size:99 final size:99
Alignment explanation
Indices: 39132364--39132937 Score: 654
Period size: 99 Copynumber: 5.8 Consensus size: 99
39132354 AGGGAACATA
* * *
39132364 AAGATATGAAGGGAAAGGTTGAGGTCGCATCGGCAAACCCGATACCTTAGAAGATGTGAAGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
** **
39132429 GGATTGAGGCCGCAACAGCGAA-TCTAATACCATG
66 GGATTGAGGCCGCAATGGCGAATTC-GGTACCATG
* * * *
39132463 AAAATATAAAGGGAAAGGTTGAGG-CTGCAACGACGAACCCGATACCTTGGAAGATGTGATGGGA
1 AAGATATGAAGGGAAAGGTTGAGGTC-GCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGA
*
39132527 AGGATTGAGGCCGCAATGGCAAATTCGGTACCATG
65 AGGATTGAGGCCGCAATGGCGAATTCGGTACCATG
* * *
39132562 AAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCTTAGAAGATGTGATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
*** *
39132627 GGATTGAGGCCGCAATGAAAAATCCGGTACCATG
66 GGATTGAGGCCGCAATGGCGAATTCGGTACCATG
* * * * * * * *
39132661 AAGATATGAAGGGAAAGGTTGAGGCCGTAATGG-AAAACCTAGTACCTTAGAAGGTGTGATGGAA
1 AAGATATGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGA-TACCTTAGAAGATGTGATGGGA
** * * * *
39132725 AGGATTGAGGTAGCAACGACGAATCCGATACCATG
65 AGGATTGAGGCCGCAATGGCGAATTCGGTACCATG
* *
39132760 AAGATATGAAGGGAAAGGTTGAGGTCGCAATGGCGAACCCGGTACCTTAGAAGATGTGATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
* *
39132825 GAATTGAGGCCGCAATGGCGAA-TCTTGTACCATG
66 GGATTGAGGCCGCAATGGCGAATTC-GGTACCATG
* * * *** * *
39132859 AATATATGGAGGGAAAGGTTGAAGTCGCAACGGCGAACTTTATACCTTAG-AGATATGAAGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
* *
39132923 AGATTGAGACCGCAA
66 GGATTGAGGCCGCAA
39132938 CGATGAATCT
Statistics
Matches: 406, Mismatches: 63, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
98 32 0.08
99 367 0.90
100 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.18
Consensus pattern (99 bp):
AAGATATGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAA
GGATTGAGGCCGCAATGGCGAATTCGGTACCATG
Found at i:39132906 original size:297 final size:296
Alignment explanation
Indices: 39132364--39132937 Score: 764
Period size: 297 Copynumber: 1.9 Consensus size: 296
39132354 AGGGAACATA
* * * * *
39132364 AAGATATGAAGGGAAAGGTTGAGGTCGCATCGGCAAACCCGATACCTTAGAAGATGTGAAGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGAATCGGAAAACCAGATACCTTAGAAGATGTGAAGGAAA
* *
39132429 GGATTGAGGCCGCAACAGCGAATCTAATACCATGAAAATATAAAGGGAAAGGTTGAGGCTGCAAC
66 GGATTGAGGCAGCAACAGCGAATCCAATACCATGAAAATATAAAGGGAAAGGTTGAGGCTGCAAC
* *
39132494 GACGAACCCGATACCTTGGAAGATGTGATGGGAAGGATTGAGGCCGCAATGGCAAATTCGGTACC
131 GACGAACCCGATACCTTAGAAGATGTGATGGGAAGAATTGAGGCCGCAATGGCAAATTCGGTACC
* *
39132559 ATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCTTAGAAGATGTGATGG
196 ATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCTTAG-AGATATGAAGG
* *
39132624 GAAGGATTGAGGCCGCAATGAAAAATCCGGTACCATG
260 GAAAGATTGAGACCGCAATGAAAAATCCGGTACCATG
* *
39132661 AAGATATGAAGGGAAAGGTTGAGGCCGTAAT-GGAAAACCTAG-TACCTTAGAAGGTGTGATGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCG-AATCGGAAAACC-AGATACCTTAGAAGATGTGAAGGA
* * * *
39132724 AAGGATTGAGGTAGCAAC-GACGAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGG-TCG
64 AAGGATTGAGGCAGCAACAG-CGAATCCAATACCATGAAAATATAAAGGGAAAGGTTGAGGCT-G
* * * * *
39132787 CAATGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAGAATTGAGGCCGCAATGGCGAA-TCTT
127 CAACGACGAACCCGATACCTTAGAAGATGTGATGGGAAGAATTGAGGCCGCAATGGCAAATTC-G
* * * * ***
39132851 GTACCATGAATATATGGAGGGAAAGGTTGAA-GTCGCAACGGCGAACTTTATACCTTAGAGATAT
191 GTACCATGAAGATATGAAGGGAAAGGTT-AAGGCCGCAACGGCAAACCCGATACCTTAGAGATAT
39132915 GAAGGGAAAGATTGAGACCGCAA
255 GAAGGGAAAGATTGAGACCGCAA
39132938 CGATGAATCT
Statistics
Matches: 240, Mismatches: 31, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
296 29 0.12
297 206 0.86
298 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.18
Consensus pattern (296 bp):
AAGATATGAAGGGAAAGGTTGAGGCCGAATCGGAAAACCAGATACCTTAGAAGATGTGAAGGAAA
GGATTGAGGCAGCAACAGCGAATCCAATACCATGAAAATATAAAGGGAAAGGTTGAGGCTGCAAC
GACGAACCCGATACCTTAGAAGATGTGATGGGAAGAATTGAGGCCGCAATGGCAAATTCGGTACC
ATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCTTAGAGATATGAAGGG
AAAGATTGAGACCGCAATGAAAAATCCGGTACCATG
Found at i:39133226 original size:42 final size:43
Alignment explanation
Indices: 39133175--39133392 Score: 171
Period size: 46 Copynumber: 5.0 Consensus size: 43
39133165 AAAGGGAAAA
* * *
39133175 CACA-CCAATCTCTTACCCC-AA-TCATGGGGCAGATTGAAGA
1 CACATCCAATCTTTTACCCCTAACTCAAGGGGCAGATTGAAGC
* * * *
39133215 CATTATCCAATCTCTTACCCC-GA-TCATGGGGCAGATTGAAG-
1 CA-CATCCAATCTTTTACCCCTAACTCAAGGGGCAGATTGAAGC
* * *
39133256 C-CGTCCAATCTTTTACCCCTAAGTCAAGAAGGGCAGTTTGAAGC
1 CACATCCAATCTTTTACCCCTAACTCAAG--GGGCAGATTGAAGC
*
39133300 CACCATCCAATCTTTTACCCCTAACTCAAGAGGGGTAGATTGAAGC
1 CA-CATCCAATCTTTTACCCCTAACTC-A-AGGGGCAGATTGAAGC
* * *
39133346 CAGTATCCAATCTTTTACCCTTAAAATCAAGAGGGGCAGATTGAAGC
1 CA-CATCCAATCTTTTACCCCT-AACTC-A-AGGGGCAGATTGAAGC
39133393 TACCATCTTA
Statistics
Matches: 149, Mismatches: 17, Indels: 17
0.81 0.09 0.09
Matches are distributed among these distances:
39 15 0.10
40 3 0.02
41 6 0.04
42 34 0.23
43 12 0.08
44 1 0.01
46 53 0.36
47 23 0.15
48 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (43 bp):
CACATCCAATCTTTTACCCCTAACTCAAGGGGCAGATTGAAGC
Found at i:39133310 original size:85 final size:92
Alignment explanation
Indices: 39133201--39133399 Score: 232
Period size: 85 Copynumber: 2.2 Consensus size: 92
39133191 CCCAATCATG
* ** * *
39133201 GGGCAGATTGAAGACATTATCCAATCTCTTACCCC-GA-TC-A-TGGGGCAGATTGAAGCC-G-T
1 GGGCAGATTGAAGCCACCATCCAATCTCTTACCCCTAACTCAAGAGGGGCAGATTGAAGCCAGAT
*
39133260 CCAATCTTTTACCCCT-AAGTCAAGAA
66 CCAATCTTTTACCCCTAAAATCAAGAA
* * *
39133286 GGGCAGTTTGAAGCCACCATCCAATCTTTTACCCCTAACTCAAGAGGGGTAGATTGAAGCCAGTA
1 GGGCAGATTGAAGCCACCATCCAATCTCTTACCCCTAACTCAAGAGGGGCAGATTGAAGCCAG-A
* *
39133351 TCCAATCTTTTACCCTTAAAATCAAGAG
65 TCCAATCTTTTACCCCTAAAATCAAGAA
*
39133379 GGGCAGATTGAAGCTACCATC
1 GGGCAGATTGAAGCCACCATC
39133400 TTATAGAAGC
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
85 30 0.32
86 1 0.01
87 2 0.02
88 1 0.01
89 15 0.16
90 1 0.01
92 16 0.17
93 27 0.29
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (92 bp):
GGGCAGATTGAAGCCACCATCCAATCTCTTACCCCTAACTCAAGAGGGGCAGATTGAAGCCAGAT
CCAATCTTTTACCCCTAAAATCAAGAA
Found at i:39133318 original size:46 final size:46
Alignment explanation
Indices: 39133200--39133399 Score: 198
Period size: 46 Copynumber: 4.5 Consensus size: 46
39133190 CCCCAATCAT
* ** * * *
39133200 GGGGCAGATTGAAGACATTATCCAATCTCTTACCCC--GATC-A-T
1 GGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCAAGA
* *
39133242 GGGGCAGATTGAAG---CCGTCCAATCTTTTACCCCTAAGTCAAGA
1 GGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCAAGA
* * *
39133285 AGGGCAGTTTGAAGCCACCATCCAATCTTTTACCCCTAACTCAAGA
1 GGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCAAGA
* ** *
39133331 GGGGTAGATTGAAGCCAGTATCCAATCTTTTACCCTTAAAATCAAGA
1 GGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCT-AAATCAAGA
*
39133378 GGGGCAGATTGAAGCTACCATC
1 GGGGCAGATTGAAGCCACCATC
39133400 TTATAGAAGC
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
39 15 0.12
41 2 0.02
42 15 0.12
43 12 0.09
46 58 0.45
47 26 0.20
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (46 bp):
GGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCAAGA
Found at i:39138933 original size:61 final size:61
Alignment explanation
Indices: 39138860--39138994 Score: 198
Period size: 61 Copynumber: 2.2 Consensus size: 61
39138850 CACGGTTGTC
* * * ** *
39138860 ACACGACCGTGTGCCACATTAAGGTGCAGTACAGGTCACATGGGCAGACACACGAGCTGGT
1 ACACGGCCGTGTGCCACATTAAAGTGCAGTACAGGTAACACAGGCAGACACACAAGCTGGT
*
39138921 ACACGGCCGTGTGCCACATTAAAGTGCAGTACAGGTAACACAGGCAGACACACAAGTTGGT
1 ACACGGCCGTGTGCCACATTAAAGTGCAGTACAGGTAACACAGGCAGACACACAAGCTGGT
*
39138982 ACACGGCCATGTG
1 ACACGGCCGTGTG
39138995 GCCCAATTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.16
Consensus pattern (61 bp):
ACACGGCCGTGTGCCACATTAAAGTGCAGTACAGGTAACACAGGCAGACACACAAGCTGGT
Found at i:39142066 original size:28 final size:28
Alignment explanation
Indices: 39141980--39142107 Score: 125
Period size: 28 Copynumber: 4.6 Consensus size: 28
39141970 ACAGAAAGTA
* *
39141980 GCTCATTCAAGCCAAATACAGA-ATATT
1 GCTCATTCGAGCCAAATACAGATTTATT
* * * * *
39142007 GCTCATTTGAGCTAGA-ACAGACTAATT
1 GCTCATTCGAGCCAAATACAGATTTATT
* *
39142034 TCTCATTCGAGCCAGATACAGATTTATT
1 GCTCATTCGAGCCAAATACAGATTTATT
* *
39142062 GCTCATTTGAGCCAAATACAAATTTATT
1 GCTCATTCGAGCCAAATACAGATTTATT
*
39142090 GCTCCTTTCGAGCCAAAT
1 GCT-CATTCGAGCCAAAT
39142108 TTAGACTGTT
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 5 0.06
27 28 0.35
28 36 0.44
29 12 0.15
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (28 bp):
GCTCATTCGAGCCAAATACAGATTTATT
Found at i:39179533 original size:7 final size:7
Alignment explanation
Indices: 39179521--39179548 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39179511 TAAATCAAAT
39179521 GTGTTGA
1 GTGTTGA
39179528 GTGTTGA
1 GTGTTGA
39179535 GTGTTGA
1 GTGTTGA
39179542 GTGTTGA
1 GTGTTGA
39179549 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTGTTGA
Found at i:39181818 original size:17 final size:17
Alignment explanation
Indices: 39181793--39181835 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
39181783 ATGCATCTCA
39181793 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* *
39181810 TTTAGTTGTCGTTGCAT
1 TTTAATTGTCATTGCAT
*
39181827 TTTACTTGT
1 TTTAATTGT
39181836 TAGTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:39182472 original size:18 final size:17
Alignment explanation
Indices: 39182425--39182474 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
39182415 GCGTCTACAA
* *
39182425 AAAAGAAGAAGAAAAAG
1 AAAAGCAGAAAAAAAAG
39182442 -AAAGCA-AAGAAAAAGAG
1 AAAAGCAGAA-AAAAA-AG
39182459 AAAAGCAGAAAAAAAA
1 AAAAGCAGAAAAAAAA
39182475 TATATGTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 2 0.07
16 9 0.33
17 3 0.11
18 11 0.41
19 2 0.07
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAGCAGAAAAAAAAG
Found at i:39192512 original size:17 final size:17
Alignment explanation
Indices: 39192464--39192512 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
39192454 ATAGTTTTCA
*
39192464 TGCA-TTCTTATTGTCAT
1 TGCATTTCTT-TTGTCAC
*
39192481 TGCATTTTGTTTTGTCAC
1 TGCA-TTTCTTTTGTCAC
39192499 TGCATTTCTTTTGT
1 TGCATTTCTTTTGT
39192513 TAACTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 13 0.48
18 10 0.37
19 4 0.15
ACGTcount: A:0.12, C:0.16, G:0.14, T:0.57
Consensus pattern (17 bp):
TGCATTTCTTTTGTCAC
Found at i:39196881 original size:16 final size:16
Alignment explanation
Indices: 39196850--39196895 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 16
39196840 AAACATCTTA
39196850 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
39196864 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
39196880 AAATAATTTTCTCAAT
1 AATTAA-TTTCTCAAT
39196896 CCAATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 9 0.32
17 9 0.32
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:39196892 original size:17 final size:16
Alignment explanation
Indices: 39196847--39196895 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
39196837 AATAAACATC
39196847 TTAAATTAATTT-T-AA
1 TTAAA-TAATTTCTCAA
*
39196862 TTAATTAATTTCTCAA
1 TTAAATAATTTCTCAA
39196878 TTAAATAATTTTCTCAA
1 TTAAATAA-TTTCTCAA
39196895 T
1 T
39196896 CCAATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.21
15 5 0.17
16 9 0.31
17 9 0.31
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATAATTTCTCAA
Found at i:39199881 original size:6 final size:6
Alignment explanation
Indices: 39199870--39199904 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
39199860 ACAATCATTC
39199870 ATAAAT ATAAAT ATAAAT ATAAAT ATATAAT ATAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATA-AAT ATAA
39199905 GGTCTATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:39201320 original size:23 final size:23
Alignment explanation
Indices: 39201218--39201321 Score: 99
Period size: 23 Copynumber: 4.7 Consensus size: 23
39201208 TAGTTCAATT
*
39201218 GGGTTT-GGTTT-GGTTTTTAAA
1 GGGTTTGGGTTTAGGTTTTAAAA
* *
39201239 GGGTTTGGGTTTGGGTTTAAAAA
1 GGGTTTGGGTTTAGGTTTTAAAA
* * *
39201262 GGTTATTGGATTTA-ATTTT-AAA
1 GGGT-TTGGGTTTAGGTTTTAAAA
*
39201284 GGATTTGGGTTTAGGTTTTAAAA
1 GGGTTTGGGTTTAGGTTTTAAAA
*
39201307 GGGTTTGGGCTTAGG
1 GGGTTTGGGTTTAGG
39201322 CACAAATTTG
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
21 14 0.21
22 15 0.23
23 30 0.45
24 7 0.11
ACGTcount: A:0.21, C:0.01, G:0.34, T:0.44
Consensus pattern (23 bp):
GGGTTTGGGTTTAGGTTTTAAAA
Found at i:39207137 original size:12 final size:13
Alignment explanation
Indices: 39207120--39207148 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39207110 ACAATCATTC
39207120 ATAAATATA-AAT
1 ATAAATATATAAT
39207132 ATAAATATATAAT
1 ATAAATATATAAT
39207145 ATAA
1 ATAA
39207149 GGTCTATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAATATATAAT
Found at i:39208359 original size:21 final size:21
Alignment explanation
Indices: 39208335--39208382 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
39208325 CTCAAAAAAA
39208335 GTCAACGATCAACTGTCAACG
1 GTCAACGATCAACTGTCAACG
* *
39208356 GTCAATGATTAACTGTCAACG
1 GTCAACGATCAACTGTCAACG
39208377 GTCAAC
1 GTCAAC
39208383 AGTCAATGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (21 bp):
GTCAACGATCAACTGTCAACG
Found at i:39208485 original size:23 final size:22
Alignment explanation
Indices: 39208442--39208543 Score: 82
Period size: 23 Copynumber: 4.6 Consensus size: 22
39208432 GGTTCAATTA
* *
39208442 GGTTT-GGTTTGGTTTTTAAAG
1 GGTTTGGGTTTAGTTTTAAAAG
*
39208463 GGTTTGGGTTTGAGTTTAAAAAG
1 GGTTTGGGTTT-AGTTTTAAAAG
* * * *
39208486 GTTATTAGATTTAATTTT-AAAG
1 GGT-TTGGGTTTAGTTTTAAAAG
*
39208508 GATTTGGGTTTAGGTTTTAAAAG
1 GGTTTGGGTTTA-GTTTTAAAAG
*
39208531 GGTTTGGGCTTAG
1 GGTTTGGGTTTAG
39208544 GCACAAATTT
Statistics
Matches: 62, Mismatches: 14, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
21 12 0.19
22 16 0.26
23 28 0.45
24 6 0.10
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (22 bp):
GGTTTGGGTTTAGTTTTAAAAG
Found at i:39208488 original size:22 final size:21
Alignment explanation
Indices: 39208441--39208488 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
39208431 TGGTTCAATT
*
39208441 AGGTTTGGTTTGGTTTTTAAA
1 AGGTTTGGTTTGGTTTTAAAA
*
39208462 GGGTTTGGGTTTGAG-TTTAAAA
1 AGGTTT-GGTTTG-GTTTTAAAA
39208484 AGGTT
1 AGGTT
39208489 ATTAGATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.23
22 16 0.73
23 1 0.05
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (21 bp):
AGGTTTGGTTTGGTTTTAAAA
Found at i:39221262 original size:29 final size:31
Alignment explanation
Indices: 39221194--39221262 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
39221184 AATGGATGAG
* *
39221194 TGACCAAAATATTAATTTTTGATAACGTTAA
1 TGACCAAAATATAAAATTTTGATAACGTTAA
* *
39221225 TGACTAAAATA-AAAATTTTGA-AACTTTAA
1 TGACCAAAATATAAAATTTTGATAACGTTAA
39221254 TGACCAAAA
1 TGACCAAAA
39221263 CAGAATCGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 15 0.45
30 8 0.24
31 10 0.30
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (31 bp):
TGACCAAAATATAAAATTTTGATAACGTTAA
Found at i:39222768 original size:50 final size:48
Alignment explanation
Indices: 39222675--39222794 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 48
39222665 TTTTCAGATC
* *
39222675 TATTGTTTTTAAATAAATATAAATATTTATTTAAAGTGATTTGTTTAAA
1 TATTG-TTTTATATAAATATAAATATTTATTTAAAGTGATTTGTTGAAA
* * * *
39222724 TATGATGTTTTATATAAATATAAATATTTGTTTATA-TTATTTTGTTGAGA
1 TAT--TGTTTTATATAAATATAAATATTTATTTAAAGTGA-TTTGTTGAAA
39222774 TATTGTATTTAATATAAATAT
1 TATTGT-TTT-ATATAAATAT
39222795 TTGTATTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
48 3 0.05
49 8 0.13
50 47 0.78
51 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (48 bp):
TATTGTTTTATATAAATATAAATATTTATTTAAAGTGATTTGTTGAAA
Found at i:39223215 original size:83 final size:81
Alignment explanation
Indices: 39222976--39223259 Score: 232
Period size: 83 Copynumber: 3.4 Consensus size: 81
39222966 TTTCCTGACA
* * *
39222976 TTTAACAAATTTTATTCTATTTTGAATTTATTTCCAAAACGAGAATAAGTTGAATAAATCTGTTT
1 TTTAACAAATTTTATTCTAATTTGATTTTATTTCC-AAACAAGAATAAGTTGAATAAATCTGTTT
**
39223041 CGAGATTTATTCCTGCCG
65 CG-GATTTATTCCCACCG
* * * * * * *
39223059 TTCAACATATTTGATTCTATATTTAGATTTT-TGGTTCCAAATAATAATTAAG-TAAAAAAATCT
1 TTTAACAAATTTTATTCTA-ATTT-GATTTTAT--TTCCAAACAAGAA-TAAGTTGAATAAATCT
* *
39223122 ATTTCGGGATTTATTCCCACTG
61 GTTTC-GGATTTATTCCCACCG
* * *
39223144 TTTAACAGATTTTATT-TCAATTTGATTTTATTTCCTAAACAAGAATAAGTTGACTAAATTTGTT
1 TTTAACAAATTTTATTCT-AATTTGATTTTATTTCC-AAACAAGAATAAGTTGAATAAATCTGTT
**
39223208 TCAGGATTTATTCCCGTCG
64 TC-GGATTTATTCCCACCG
* * *
39223227 ATTAACAGATTATATTCTATATTTGGATTTTAT
1 TTTAACAAATTTTATTCTA-ATTT-GATTTTAT
39223260 AATAATTAAT
Statistics
Matches: 158, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
82 8 0.05
83 68 0.43
84 15 0.09
85 58 0.37
86 9 0.06
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (81 bp):
TTTAACAAATTTTATTCTAATTTGATTTTATTTCCAAACAAGAATAAGTTGAATAAATCTGTTTC
GGATTTATTCCCACCG
Found at i:39226999 original size:6 final size:6
Alignment explanation
Indices: 39226988--39227019 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
39226978 GAAAATAAAG
39226988 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CC
39227020 ATTCTCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTTCC
Found at i:39232634 original size:101 final size:101
Alignment explanation
Indices: 39232457--39232676 Score: 332
Period size: 101 Copynumber: 2.2 Consensus size: 101
39232447 TAACACCAAC
**** *
39232457 TCCTATACCCCTAAAGTTGCAGAGGGGTGGATTAGAGCTACAGAAGCAAATCTTATCTCTCTGAA
1 TCCTATACCCCTAAAGTTGCAGAGGGACAAATTAGAGCTACAGAAGCAAATCTTATCTCTCTAAA
*
39232522 GATGCAATAGAGCAAGATTAAAGGTACAAAATCAAA
66 GATGCAATAGAGCAAGATTAAAGCTACAAAATCAAA
* *
39232558 TCCTATACCCCTAAAGTTGTAGAGGGACAAATTAGAGCTACAGAAGCAGATCTTATCTCTCTAAA
1 TCCTATACCCCTAAAGTTGCAGAGGGACAAATTAGAGCTACAGAAGCAAATCTTATCTCTCTAAA
* * *
39232623 GATGTAGTAGAGCAAGGTTAAAGCTACAAAATCAAA
66 GATGCAATAGAGCAAGATTAAAGCTACAAAATCAAA
*
39232659 TCCTATATCCCTAAAGTT
1 TCCTATACCCCTAAAGTT
39232677 ACGGAGGGTC
Statistics
Matches: 107, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 107 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (101 bp):
TCCTATACCCCTAAAGTTGCAGAGGGACAAATTAGAGCTACAGAAGCAAATCTTATCTCTCTAAA
GATGCAATAGAGCAAGATTAAAGCTACAAAATCAAA
Found at i:39232673 original size:51 final size:51
Alignment explanation
Indices: 39232486--39232674 Score: 166
Period size: 51 Copynumber: 3.7 Consensus size: 51
39232476 CAGAGGGGTG
* * * * * * * *
39232486 GATTAGAGCTACAGAAGCAAATCTTATCTCTCTGAAGATGCAATAGAGCAA
1 GATTAAAGCTACAAAAGCAAATCCTATATCCCTAAAGATGTAGTAGAGCAA
* * * * *
39232537 GATTAAAGGTACAAAATCAAATCCTATACCCCTAAAGTTGTAG-AGGGACAA
1 GATTAAAGCTACAAAAGCAAATCCTATATCCCTAAAGATGTAGTAGAG-CAA
* * * * * *
39232588 -ATTAGAGCTACAGAAGCAGATCTTATCTCTCTAAAGATGTAGTAGAGCAA
1 GATTAAAGCTACAAAAGCAAATCCTATATCCCTAAAGATGTAGTAGAGCAA
* *
39232638 GGTTAAAGCTACAAAATCAAATCCTATATCCCTAAAG
1 GATTAAAGCTACAAAAGCAAATCCTATATCCCTAAAG
39232675 TTACGGAGGG
Statistics
Matches: 103, Mismatches: 32, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
50 38 0.37
51 65 0.63
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (51 bp):
GATTAAAGCTACAAAAGCAAATCCTATATCCCTAAAGATGTAGTAGAGCAA
Found at i:39242469 original size:93 final size:93
Alignment explanation
Indices: 39242310--39242496 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
39242300 AGTCGATGCA
39242310 AATGAAACTAAGCAGAAAGAAAAAATTGCATCTGAAGAAGAAGCAGTAGAGATAAATGAGGAGGA
1 AATGAAACTAAGCAGAAAGAAAAAATTGCATCTGAAGAAGAAGCAGTAGAGATAAATGAGGAGGA
39242375 GTCACCAGTAATTACACCTATGTCAACC
66 GTCACCAGTAATTACACCTATGTCAACC
* *
39242403 AATGAAACTAAGTAGAAAGAAAAAATTGCATCTGAAGAAGAAGTAGTAGAGATAAATGAGGAGGA
1 AATGAAACTAAGCAGAAAGAAAAAATTGCATCTGAAGAAGAAGCAGTAGAGATAAATGAGGAGGA
39242468 GTCACCAGTAATTACACCTATGTCAACC
66 GTCACCAGTAATTACACCTATGTCAACC
39242496 A
1 A
39242497 TTCGACCTTC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.18
Consensus pattern (93 bp):
AATGAAACTAAGCAGAAAGAAAAAATTGCATCTGAAGAAGAAGCAGTAGAGATAAATGAGGAGGA
GTCACCAGTAATTACACCTATGTCAACC
Found at i:39248269 original size:12 final size:12
Alignment explanation
Indices: 39248243--39248296 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
39248233 GTGGGTATCG
*
39248243 AGAAGGAAAAGGA
1 AGAA-GAAAAAGA
39248256 AGAAGAAAAAGA
1 AGAAGAAAAAGA
* *
39248268 AGATGAAAGAGA
1 AGAAGAAAAAGA
*
39248280 AGAAGAGAAAGA
1 AGAAGAAAAAGA
*
39248292 GGAAG
1 AGAAG
39248297 TTCTTGTCGC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
12 30 0.88
13 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (12 bp):
AGAAGAAAAAGA
Found at i:39248296 original size:15 final size:15
Alignment explanation
Indices: 39248264--39248292 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39248254 GAAGAAGAAA
39248264 AAGAAGATGAAAGAG
1 AAGAAGATGAAAGAG
39248279 AAGAAGA-GAAAGAG
1 AAGAAGATGAAAGAG
39248293 GAAGTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (15 bp):
AAGAAGATGAAAGAG
Found at i:39263248 original size:6 final size:6
Alignment explanation
Indices: 39263237--39263265 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
39263227 ACCAAACCAC
39263237 ATACAT ATACAT ATACAT ATACAT ATACA
1 ATACAT ATACAT ATACAT ATACAT ATACA
39263266 AGTTGGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:39263861 original size:11 final size:11
Alignment explanation
Indices: 39263841--39263915 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
39263831 AAGCCTCTCA
*
39263841 TCTTTCCTTTC
1 TCTTTTCTTTC
*
39263852 TCTTTTCTTTT
1 TCTTTTCTTTC
* *
39263863 TCTCATCCATTTC
1 TCT-TTTC-TTTC
39263876 T-TATTTCTTTC
1 TCT-TTTCTTTC
39263887 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
39263899 TATTTTCTTCC
1 TCTTTTCTTTC
39263910 TCTTTT
1 TCTTTT
39263916 AATCACACTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
11 29 0.59
12 16 0.33
13 4 0.08
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:39264322 original size:21 final size:22
Alignment explanation
Indices: 39264286--39264332 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
39264276 ACCCATTAAG
39264286 CCCAAATTCTATTTAAATCAAA
1 CCCAAATTCTATTTAAATCAAA
39264308 CCCAAATTC-ATTTAAATCAAA
1 CCCAAATTCTATTTAAATCAAA
39264329 CCCA
1 CCCA
39264333 TTTGAACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (22 bp):
CCCAAATTCTATTTAAATCAAA
Found at i:39264453 original size:7 final size:7
Alignment explanation
Indices: 39264443--39264499 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
39264433 TTGATTGATT
39264443 GTTGACC
1 GTTGACC
39264450 GTTGACC
1 GTTGACC
39264457 GTTGA-C
1 GTTGACC
*
39264463 TTTGACC
1 GTTGACC
*
39264470 GTTAACC
1 GTTGACC
39264477 GTTGA-C
1 GTTGACC
*
39264483 TTTGACC
1 GTTGACC
39264490 GTTGACC
1 GTTGACC
39264497 GTT
1 GTT
39264500 AACTTTTTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
6 10 0.24
7 32 0.76
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.35
Consensus pattern (7 bp):
GTTGACC
Found at i:39264469 original size:20 final size:20
Alignment explanation
Indices: 39264444--39264505 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
39264434 TGATTGATTG
39264444 TTGACCGTTGACCGTTGACT
1 TTGACCGTTGACCGTTGACT
*
39264464 TTGACCGTTAACCGTTGACT
1 TTGACCGTTGACCGTTGACT
*
39264484 TTGACCGTTGACCGTTAACT
1 TTGACCGTTGACCGTTGACT
39264504 TT
1 TT
39264506 TTCAAAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:39264477 original size:27 final size:27
Alignment explanation
Indices: 39264447--39264502 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
39264437 TTGATTGTTG
*
39264447 ACCGTTGACCGTTGA-CTTTGACCGTTA
1 ACCGTTGA-CGTTGACCGTTGACCGTTA
*
39264474 ACCGTTGACTTTGACCGTTGACCGTTA
1 ACCGTTGACGTTGACCGTTGACCGTTA
39264501 AC
1 AC
39264503 TTTTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (27 bp):
ACCGTTGACGTTGACCGTTGACCGTTA
Found at i:39265562 original size:3 final size:3
Alignment explanation
Indices: 39265550--39265579 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
39265540 TATTCTATTC
39265550 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
39265580 TTGGGATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:39270351 original size:20 final size:20
Alignment explanation
Indices: 39270326--39270369 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
39270316 AGTGTCTCCA
39270326 TGGAAGAAGGTGCTTAGATT
1 TGGAAGAAGGTGCTTAGATT
39270346 TGGAAGAAGGTGCTTAGATT
1 TGGAAGAAGGTGCTTAGATT
39270366 TGGA
1 TGGA
39270370 GTTGTTGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (20 bp):
TGGAAGAAGGTGCTTAGATT
Found at i:39270630 original size:21 final size:21
Alignment explanation
Indices: 39270594--39270661 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
39270584 ACCCATTAAG
39270594 CCCAAATTCTATTTAAACCAAA
1 CCCAAATTC-ATTTAAACCAAA
*
39270616 CCCACATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
*
39270637 CCTAAATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
39270658 CCCA
1 CCCA
39270662 TTTGAACCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 34 0.81
22 8 0.19
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (21 bp):
CCCAAATTCATTTAAACCAAA
Found at i:39270669 original size:15 final size:15
Alignment explanation
Indices: 39270645--39270674 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39270635 AACCTAAATT
39270645 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
39270660 CATTTGAACCAAACC
1 CATTTAAACCAAACC
39270675 AAATGAACCA
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:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:39270755 original size:11 final size:10
Alignment explanation
Indices: 39270711--39270758 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
39270701 AGTCAAACCA
*
39270711 TTGACCGATG
1 TTGACCGACG
* *
39270721 TTGACTGGCG
1 TTGACCGACG
39270731 TTGACCGACG
1 TTGACCGACG
*
39270741 TTGATCGACCG
1 TTGACCGA-CG
39270752 TTGACCG
1 TTGACCG
39270759 GTGTTGATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (10 bp):
TTGACCGACG
Found at i:39270755 original size:21 final size:21
Alignment explanation
Indices: 39270729--39270778 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
39270719 TGTTGACTGG
39270729 CGTTGACCGACGTTGATCGAC
1 CGTTGACCGACGTTGATCGAC
** *
39270750 CGTTGACCGGTGTTGATTGAC
1 CGTTGACCGACGTTGATCGAC
*
39270771 CATTGACC
1 CGTTGACC
39270779 ATTGATCGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
CGTTGACCGACGTTGATCGAC
Found at i:39270775 original size:7 final size:7
Alignment explanation
Indices: 39270766--39270831 Score: 73
Period size: 7 Copynumber: 9.7 Consensus size: 7
39270756 CCGGTGTTGA
*
39270766 TTGACCA
1 TTGACCG
*
39270773 TTGACCA
1 TTGACCG
*
39270780 TTGATCG
1 TTGACCG
*
39270787 TTGA-CT
1 TTGACCG
39270793 TTGACCG
1 TTGACCG
39270800 TTGACCG
1 TTGACCG
*
39270807 TTG-CCT
1 TTGACCG
39270813 TTGACCG
1 TTGACCG
39270820 TTGACCG
1 TTGACCG
39270827 TTGAC
1 TTGAC
39270832 TTTTTCGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
6 10 0.20
7 41 0.80
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.35
Consensus pattern (7 bp):
TTGACCG
Found at i:39270798 original size:20 final size:20
Alignment explanation
Indices: 39270773--39270834 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
39270763 TGATTGACCA
* *
39270773 TTGACCATTGATCGTTGACT
1 TTGACCGTTGACCGTTGACT
*
39270793 TTGACCGTTGACCGTTGCCT
1 TTGACCGTTGACCGTTGACT
39270813 TTGACCGTTGACCGTTGACT
1 TTGACCGTTGACCGTTGACT
39270833 TT
1 TT
39270835 TTCGAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:39270803 original size:27 final size:27
Alignment explanation
Indices: 39270766--39270831 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
39270756 CCGGTGTTGA
* * *
39270766 TTGACCATTGACCATTGATCGTTGA-CT
1 TTGACCGTTGACCATTG-CCGTTGACCG
* *
39270793 TTGACCGTTGACCGTTGCCTTTGACCG
1 TTGACCGTTGACCATTGCCGTTGACCG
39270820 TTGACCGTTGAC
1 TTGACCGTTGAC
39270832 TTTTTCGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.35
Consensus pattern (27 bp):
TTGACCGTTGACCATTGCCGTTGACCG
Found at i:39273085 original size:76 final size:76
Alignment explanation
Indices: 39272976--39273169 Score: 257
Period size: 76 Copynumber: 2.6 Consensus size: 76
39272966 CGCCCAGAGT
* * * *
39272976 TAGTCGGAT-AATCGAAGATATCAAATGTATGCCCAGCACTAGACGAATAAATCGACGATGGATT
1 TAGTCGGATAAATCGATGATATTAAATGTGTGCCCAGCACTAGACGAATAAACCGACGATGGATT
*
39273040 GCGTC-CAACGC
66 GCG-CACAACAC
* * * *
39273051 TAGTCGGATAAATCGATGGTATTAAATATGTGCCCAGCACTAGTCGGATAAACCGACGATGGATT
1 TAGTCGGATAAATCGATGATATTAAATGTGTGCCCAGCACTAGACGAATAAACCGACGATGGATT
*
39273116 GCGCACAGCAC
66 GCGCACAACAC
* *
39273127 TAGTCCGATAAACCGATGATATTAAATGTGTGCCCAGCACTAG
1 TAGTCGGATAAATCGATGATATTAAATGTGTGCCCAGCACTAG
39273170 TTGGATATAC
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
75 10 0.10
76 93 0.90
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (76 bp):
TAGTCGGATAAATCGATGATATTAAATGTGTGCCCAGCACTAGACGAATAAACCGACGATGGATT
GCGCACAACAC
Found at i:39273098 original size:40 final size:39
Alignment explanation
Indices: 39273050--39273176 Score: 134
Period size: 40 Copynumber: 3.3 Consensus size: 39
39273040 GCGTCCAACG
*
39273050 CTAGTCGGATAAATCGATGGTATTAAATATGTGCCCAGCA
1 CTAGTCGGATAAACCGATGGTATTAAAT-TGTGCCCAGCA
* ** * *
39273090 CTAGTCGGATAAACCGA-CG-A-TGGATTGCGCACAGCA
1 CTAGTCGGATAAACCGATGGTATTAAATTGTGCCCAGCA
* *
39273126 CTAGTCCGATAAACCGATGATATTAAATGTGTGCCCAGCA
1 CTAGTCGGATAAACCGATGGTATTAAAT-TGTGCCCAGCA
*
39273166 CTAGTTGGATA
1 CTAGTCGGATA
39273177 TACCAACAAG
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
36 25 0.37
37 3 0.04
38 2 0.03
39 4 0.06
40 34 0.50
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (39 bp):
CTAGTCGGATAAACCGATGGTATTAAATTGTGCCCAGCA
Found at i:39273170 original size:76 final size:75
Alignment explanation
Indices: 39272992--39273251 Score: 256
Period size: 76 Copynumber: 3.4 Consensus size: 75
39272982 GATAATCGAA
* * * * * * *
39272992 GATATCAAATGTATGCCCAGCACTAGACGAATAAATCGACGATGGATTGCGTCCAACGCTAGTCG
1 GATATTAAATGTGTGCCCAGCACTAGTCGGATAAACCGACGATGGATTGCG-CCAACACTAGTCA
*
39273057 GATAAATCGAT
65 GATAAACCGAT
* * * *
39273068 GGTATTAAATATGTGCCCAGCACTAGTCGGATAAACCGACGATGGATTGCGCACAGCACTAGTCC
1 GATATTAAATGTGTGCCCAGCACTAGTCGGATAAACCGACGATGGATTGCGC-CAACACTAGTCA
39273133 GATAAACCGAT
65 GATAAACCGAT
* * * * *
39273144 GATATTAAATGTGTGCCCAGCACTAGTTGGATATACCAAC-A-AGATTTGCGCCCAACACTAATC
1 GATATTAAATGTGTGCCCAGCACTAGTCGGATAAACCGACGATGGA-TTGCG-CCAACACTAGTC
* * *
39273207 AGTTAAACTGAAG
64 AGATAAACCG-AT
* *
39273220 GA-ATTAAATGTGCGCCCAGCACTAGTTGGATA
1 GATATTAAATGTGTGCCCAGCACTAGTCGGATA
39273252 TACCAAAAAC
Statistics
Matches: 156, Mismatches: 24, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
74 2 0.01
75 52 0.33
76 102 0.65
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (75 bp):
GATATTAAATGTGTGCCCAGCACTAGTCGGATAAACCGACGATGGATTGCGCCAACACTAGTCAG
ATAAACCGAT
Found at i:39276970 original size:27 final size:27
Alignment explanation
Indices: 39276940--39277053 Score: 156
Period size: 27 Copynumber: 4.2 Consensus size: 27
39276930 AGGTTTAATA
*
39276940 GATATTCTGTTTCTGGCTCGTAAGAGC
1 GATATTCTGTTTCTGGCTCATAAGAGC
* * *
39276967 GATATTCTGTTTCAGGCTCGTAAGAGA
1 GATATTCTGTTTCTGGCTCATAAGAGC
*
39276994 GATATTCTGTTTCTGGCTCATAAGAGT
1 GATATTCTGTTTCTGGCTCATAAGAGC
* *
39277021 GATATTCTATTTCTGGCTCATAACAGC
1 GATATTCTGTTTCTGGCTCATAAGAGC
*
39277048 AATATT
1 GATATT
39277054 TTGGACTCTG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (27 bp):
GATATTCTGTTTCTGGCTCATAAGAGC
Found at i:39277130 original size:27 final size:28
Alignment explanation
Indices: 39277062--39277124 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
39277052 TTTTGGACTC
* **
39277062 TGGCTCGAAAAGAAAATTATTCTATTTT
1 TGGCTCGAAAGGAGCATTATTCTATTTT
*
39277090 TGGCTCGAAAGGAGCATTATTCTGTTTT
1 TGGCTCGAAAGGAGCATTATTCTATTTT
39277118 TGGCTCG
1 TGGCTCG
39277125 TAGGAGTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (28 bp):
TGGCTCGAAAGGAGCATTATTCTATTTT
Found at i:39277324 original size:18 final size:18
Alignment explanation
Indices: 39277303--39277344 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
39277293 ATTATGTGAA
39277303 CTTACTAAGCTATGTAAG
1 CTTACTAAGCTATGTAAG
39277321 CTTACTAAGCTATGTAAG
1 CTTACTAAGCTATGTAAG
39277339 CTTACT
1 CTTACT
39277345 TGTAGATCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (18 bp):
CTTACTAAGCTATGTAAG
Found at i:39280777 original size:9 final size:9
Alignment explanation
Indices: 39280765--39280808 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
39280755 ACATAATTTT
39280765 TTTTTCTTC
1 TTTTTCTTC
*
39280774 TTTTTCTTT
1 TTTTTCTTC
*
39280783 TTTTTTTTC
1 TTTTTCTTC
39280792 TTTTTC-TC
1 TTTTTCTTC
39280800 ATTTTTCTT
1 -TTTTTCTT
39280809 TTTAAGTGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 2 0.07
9 26 0.90
10 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:39280785 original size:18 final size:18
Alignment explanation
Indices: 39280762--39280808 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
39280752 CAAACATAAT
39280762 TTTTTTTTCTTCTTTTTC
1 TTTTTTTTCTTCTTTTTC
*
39280780 TTTTTTTTTTTCTTTTTC
1 TTTTTTTTCTTCTTTTTC
**
39280798 TCATTTTTCTT
1 TTTTTTTTCTT
39280809 TTTAAGTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTTCTTCTTTTTC
Found at i:39280787 original size:21 final size:21
Alignment explanation
Indices: 39280761--39280811 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
39280751 ACAAACATAA
*
39280761 TTTTTTTTTCTTCTTTTTC-TT
1 TTTTTTTTTCTT-TTTCTCATT
39280782 TTTTTTTTTCTTTTTCTCATT
1 TTTTTTTTTCTTTTTCTCATT
*
39280803 TTTCTTTTT
1 TTTTTTTTT
39280812 AAGTGACTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTTTTCTTTTTCTCATT
Found at i:39280804 original size:27 final size:26
Alignment explanation
Indices: 39280761--39280811 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
39280751 ACAAACATAA
39280761 TTTTTTTTTCTTCTTTTTCTTTTTTT
1 TTTTTTTTTCTTCTTTTTCTTTTTTT
39280787 TTTTCTTTTTC-TCATTTTTCTTTTT
1 TTTT-TTTTTCTTC-TTTTTCTTTTT
39280812 AAGTGACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (26 bp):
TTTTTTTTTCTTCTTTTTCTTTTTTT
Found at i:39281417 original size:19 final size:18
Alignment explanation
Indices: 39281387--39281427 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
39281377 AACTAAATTA
39281387 ACAAAAAAAAATGCAATG
1 ACAAAAAAAAATGCAATG
39281405 ACAAAATAAAAATGCAATG
1 ACAAAA-AAAAATGCAATG
39281424 ACAA
1 ACAA
39281428 TAAAGATCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.66, C:0.12, G:0.10, T:0.12
Consensus pattern (18 bp):
ACAAAAAAAAATGCAATG
Found at i:39288106 original size:282 final size:283
Alignment explanation
Indices: 39287601--39288171 Score: 1040
Period size: 282 Copynumber: 2.0 Consensus size: 283
39287591 ATTTCTAACA
39287601 ATACAACTCAAGTCAAAGAACAACCTCTCTCTTACCCTGTACTTCTACCGATACCTGTATAAGTT
1 ATACAACTCAAGTCAAAGAACAACCTCTCTCTTACCCTGTACTTCTACCGATACCTGTATAAGTT
*
39287666 CTACCGAAACATGTATGCAGAAACTCAAGAATTACTCTAAGACACAAGTCTAACATATCAAACAC
66 CTACCGAAACATGTATGCAAAAACTCAAGAATTACTCTAAGACACAAGTCTAACATATCAAACAC
* *
39287731 AAGTTATGCATTTAAACATCACACTACATACATAACTTCTAAGTTTTTCAAGCATCATAAGCTTA
131 AAGTTATGCATTTAAACATCACACTACATACATAACTGCTAAGTTTTACAAGCATCATAAGCTTA
*
39287796 AACTTATAAGTTGTACTTCATGCATTTACACAATCAAAATAGCAAGATTTCAACATCTTTAGTTC
196 AACTTATAAGTTGTACTTCATGCATTTACACAATCAAAATAGAAAGATTTCAACATCTTTAGTTC
39287861 AACATCAAAGTTAATATCATCCT
261 AACATCAAAGTTAATATCATCCT
39287884 ATACAACTCAAGTCAAAGAACAACCTCTCTCTTA-CCTAGTACTTCTACCGATACCTGTATAAGT
1 ATACAACTCAAGTCAAAGAACAACCTCTCTCTTACCCT-GTACTTCTACCGATACCTGTATAAGT
*
39287948 TCTACCGAAACATGTATG-AAAAACTCAAGAATTACTCTAAGACACAAGTCTAACATATCAAAGA
65 TCTACCGAAACATGTATGCAAAAACTCAAGAATTACTCTAAGACACAAGTCTAACATATCAAACA
*
39288012 CAAGTTATGCATTTAAACATCACTCTACATACATAACTGCTAAGTTTTACAAGCATCATAAGCTT
130 CAAGTTATGCATTTAAACATCACACTACATACATAACTGCTAAGTTTTACAAGCATCATAAGCTT
39288077 AAACTT-TAAAGTTGTACTTCATGCATTTACACAATCAAAATAGAAAGATTTCAACATCTTTAGT
195 AAACTTAT-AAGTTGTACTTCATGCATTTACACAATCAAAATAGAAAGATTTCAACATCTTTAGT
39288141 TCAACATCAAAGTTAATATCATCCT
259 TCAACATCAAAGTTAATATCATCCT
39288166 AGTACA
1 A-TACA
39288172 TGTCATAAGA
Statistics
Matches: 279, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
281 1 0.00
282 196 0.70
283 82 0.29
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.29
Consensus pattern (283 bp):
ATACAACTCAAGTCAAAGAACAACCTCTCTCTTACCCTGTACTTCTACCGATACCTGTATAAGTT
CTACCGAAACATGTATGCAAAAACTCAAGAATTACTCTAAGACACAAGTCTAACATATCAAACAC
AAGTTATGCATTTAAACATCACACTACATACATAACTGCTAAGTTTTACAAGCATCATAAGCTTA
AACTTATAAGTTGTACTTCATGCATTTACACAATCAAAATAGAAAGATTTCAACATCTTTAGTTC
AACATCAAAGTTAATATCATCCT
Found at i:39295505 original size:15 final size:15
Alignment explanation
Indices: 39295485--39295515 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39295475 TATTTCATTA
39295485 CTTCATTTCACAATT
1 CTTCATTTCACAATT
*
39295500 CTTCATTTCATAATT
1 CTTCATTTCACAATT
39295515 C
1 C
39295516 AACCATTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
CTTCATTTCACAATT
Found at i:39296289 original size:21 final size:22
Alignment explanation
Indices: 39296235--39296298 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
39296225 AGGAAATAGT
*
39296235 ACAGACTTCTACCGATACCTA-TG
1 ACAG-CTTCTACCGATA-CAAGTG
*
39296258 ACAG-TTTTACCGATACAAGTG
1 ACAGCTTCTACCGATACAAGTG
*
39296279 A-AGCTTCTACCGAAACAAGT
1 ACAGCTTCTACCGATACAAGT
39296299 ATGCAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 27 0.77
23 4 0.11
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (22 bp):
ACAGCTTCTACCGATACAAGTG
Found at i:39298871 original size:3 final size:3
Alignment explanation
Indices: 39298863--39298901 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
39298853 TACATCCCAA
39298863 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39298902 GAATAGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39299976 original size:13 final size:14
Alignment explanation
Indices: 39299951--39299982 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
39299941 TTTCAAAAAA
39299951 GTCAAAGGTCAACG
1 GTCAAAGGTCAACG
39299965 GTCAAA-GTCAACG
1 GTCAAAGGTCAACG
39299978 GTCAA
1 GTCAA
39299983 TCAACACCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.16
Consensus pattern (14 bp):
GTCAAAGGTCAACG
Found at i:39300012 original size:10 final size:10
Alignment explanation
Indices: 39299993--39300037 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
39299983 TCAACACCGA
39299993 TCAACGGTCGG
1 TCAAC-GTCGG
39300004 TCAACGTCGG
1 TCAACGTCGG
* **
39300014 TCAACGCCAA
1 TCAACGTCGG
39300024 TCAACGTCGG
1 TCAACGTCGG
39300034 TCAA
1 TCAA
39300038 TGGTTTGACT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
10 23 0.82
11 5 0.18
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAACGTCGG
Found at i:39300116 original size:21 final size:21
Alignment explanation
Indices: 39300090--39300144 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
39300080 GTTCAAATGG
*
39300090 GTTTGGTTTAAATGAATTTGA
1 GTTTGGTTTAAATGAATGTGA
*
39300111 GTTTGGTTTAAATGAATGTGG
1 GTTTGGTTTAAATGAATGTGA
39300132 GTTTGGTTTAAAT
1 GTTTGGTTTAAAT
39300145 AGGATTTGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (21 bp):
GTTTGGTTTAAATGAATGTGA
Found at i:39300558 original size:11 final size:11
Alignment explanation
Indices: 39300525--39300599 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
39300515 AAGTGTGATT
*
39300525 AAAAGAGGAAG
1 AAAAGAGAAAG
*
39300536 AAAATAGAAAAG
1 AAAAGAG-AAAG
39300548 AAAAGAGAAAG
1 AAAAGAGAAAG
39300559 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
39300571 AATGAGAAAAAG
1 AA-AAGAGAAAG
39300583 AAAAGAGAAAG
1 AAAAGAGAAAG
*
39300594 GAAAGA
1 AAAAGA
39300600 TGATAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:39300567 original size:23 final size:23
Alignment explanation
Indices: 39300525--39300597 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
39300515 AAGTGTGATT
*
39300525 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
39300548 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
39300571 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
39300595 AAA
1 AAA
39300598 GATGATAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:39301244 original size:42 final size:42
Alignment explanation
Indices: 39301177--39301267 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 42
39301167 CAATTGTACT
**
39301177 CTATCACTGTTCCAAATCCGATTCAAGCACGCAGATGTTACA
1 CTATCACTGTTCCAAATCCGATTCAAAAACGCAGATGTTACA
* * * * *
39301219 CTATTACTGTTCCAACTCTGGTTCAAAAACGCGGATGTTACA
1 CTATCACTGTTCCAAATCCGATTCAAAAACGCAGATGTTACA
*
39301261 ATATCAC
1 CTATCAC
39301268 ATTACTTAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (42 bp):
CTATCACTGTTCCAAATCCGATTCAAAAACGCAGATGTTACA
Found at i:39301735 original size:53 final size:53
Alignment explanation
Indices: 39301625--39301765 Score: 228
Period size: 53 Copynumber: 2.6 Consensus size: 53
39301615 TTCACGTTTA
**
39301625 ATAACTCACGATGACACAGAGTCATCGGACCCTTTAATCTGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGA-CCTTTAATCCATAATAGGATTCAT
* *
39301679 ATAACTCATGATGACACAGAGTCATTGGACCTTTAATCCATAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATAATAGGATTCAT
*
39301732 ATAACTCACAATGACACAGAGTCATCGGACCTTT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTT
39301766 TGCATTTACG
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
53 53 0.66
54 27 0.34
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATAATAGGATTCAT
Found at i:39305770 original size:30 final size:29
Alignment explanation
Indices: 39305734--39305811 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
39305724 ATTTTAACCC
* *
39305734 AAGGATTAAATTAGAATTTTTGTGAAATTT
1 AAGGATTAAATT-GAATTTTTATGAAACTT
* *
39305764 AAGGATTAATTTGTAA-ATTTATGAAACTT
1 AAGGATTAAATTG-AATTTTTATGAAACTT
*
39305793 AAGGACTAAATTGAATTTT
1 AAGGATTAAATTGAATTTT
39305812 AATTAAAGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.05
29 24 0.62
30 13 0.33
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (29 bp):
AAGGATTAAATTGAATTTTTATGAAACTT
Found at i:39309628 original size:3 final size:3
Alignment explanation
Indices: 39309620--39309663 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
39309610 GGCTGTGAAG
39309620 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39309664 GAAACGATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39312344 original size:14 final size:14
Alignment explanation
Indices: 39312298--39312348 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
39312288 AATGGTTCAG
*
39312298 GTCAACGTGTCAAA
1 GTCAACGGGTCAAA
* * *
39312312 TTCAATGGGTC-GA
1 GTCAACGGGTCAAA
39312325 -TCAACGGGTCAAA
1 GTCAACGGGTCAAA
39312338 GTCAACGGGTC
1 GTCAACGGGTC
39312349 GATCAATGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
14 18 0.62
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (14 bp):
GTCAACGGGTCAAA
Found at i:39312366 original size:25 final size:26
Alignment explanation
Indices: 39312299--39312367 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
39312289 ATGGTTCAGG
* * *
39312299 TCAACGTGTCAAATTCAATGGGTCGA
1 TCAACGGGTCAAAGTCAACGGGTCGA
39312325 TCAACGGGTCAAAGTCAACGGGTCGA
1 TCAACGGGTCAAAGTCAACGGGTCGA
* *
39312351 TCAA-TGGTCAAGGTCAA
1 TCAACGGGTCAAAGTCAA
39312368 TTGTTCAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 11 0.29
26 27 0.71
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (26 bp):
TCAACGGGTCAAAGTCAACGGGTCGA
Found at i:39314346 original size:31 final size:29
Alignment explanation
Indices: 39314311--39314380 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
39314301 TATTAGAGAT
*
39314311 AATGTTATATTTGGTACCTATATTTTCATAA
1 AATGTTATATATGGTACCTATATTTT-A-AA
* *
39314342 AATG-TATAATATGGTACTTATATTTTAAG
1 AATGTTAT-ATATGGTACCTATATTTTAAA
39314371 AATGTTATAT
1 AATGTTATAT
39314381 GTTTATAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 7 0.21
30 7 0.21
31 20 0.59
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (29 bp):
AATGTTATATATGGTACCTATATTTTAAA
Found at i:39314534 original size:17 final size:18
Alignment explanation
Indices: 39314512--39314547 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39314502 ATTATGTGAA
*
39314512 AAATTAAA-TAAAACAAT
1 AAATTAAATTAAAAAAAT
39314529 AAATTAAATTAAAAAAAT
1 AAATTAAATTAAAAAAAT
39314547 A
1 A
39314548 GATAAGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATTAAATTAAAAAAAT
Found at i:39317071 original size:163 final size:163
Alignment explanation
Indices: 39316790--39317121 Score: 592
Period size: 163 Copynumber: 2.0 Consensus size: 163
39316780 AGAGCTCTTG
* *
39316790 AAAACCGAGCAGTTGACTGATTTGATTTCTGAACCCGGAGTCCACTCCTTTTGAAAAGAAAATGT
1 AAAACCGAGCAGTTGACTGATGTGATTTCTGAACCCCGAGTCCACTCCTTTTGAAAAGAAAATGT
*
39316855 TACTTTTCCTTGAGCCAACCTTGTATCCTGAAATACCATAGAAAAGATTCAGAATATCAGTTAAT
66 TACTTTTCCTTGAGCCAACCTTGTATCCTGAAATACCACAGAAAAGATTCAGAATATCAGTTAAT
*
39316920 AGTTGTGCTTGATTTAGCTCCGCTTTGCAAAAT
131 AATTGTGCTTGATTTAGCTCCGCTTTGCAAAAT
*
39316953 AAAATCGAGCAGTTGACTGATGTGATTTCTGAACCCCGAGTCCACTCCTTTTGAAAAGAAAATGT
1 AAAACCGAGCAGTTGACTGATGTGATTTCTGAACCCCGAGTCCACTCCTTTTGAAAAGAAAATGT
* * *
39317018 TACTTTTCCTTGAGCTAACCTTGTGTCCTGAAATACCACAGAAAAGCTTCAGAATATCAGTTAAT
66 TACTTTTCCTTGAGCCAACCTTGTATCCTGAAATACCACAGAAAAGATTCAGAATATCAGTTAAT
39317083 AATTGTGCTTGATTTAGCTCCGCTTTGCAAAAT
131 AATTGTGCTTGATTTAGCTCCGCTTTGCAAAAT
39317116 AAAACC
1 AAAACC
39317122 AGATCATCTG
Statistics
Matches: 160, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
163 160 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (163 bp):
AAAACCGAGCAGTTGACTGATGTGATTTCTGAACCCCGAGTCCACTCCTTTTGAAAAGAAAATGT
TACTTTTCCTTGAGCCAACCTTGTATCCTGAAATACCACAGAAAAGATTCAGAATATCAGTTAAT
AATTGTGCTTGATTTAGCTCCGCTTTGCAAAAT
Found at i:39320014 original size:17 final size:18
Alignment explanation
Indices: 39319973--39320018 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
39319963 TTTTAATTAA
*
39319973 ATAAATATAATTTTATCT
1 ATAAATATGATTTTATCT
39319991 ATAAATATGATTTTAT-T
1 ATAAATATGATTTTATCT
*
39320008 TTAAATATGAT
1 ATAAATATGAT
39320019 AATAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
ATAAATATGATTTTATCT
Found at i:39320678 original size:20 final size:19
Alignment explanation
Indices: 39320653--39320705 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
39320643 TATTGGATTA
*
39320653 ATAATTTAATATAAATATAT
1 ATAA-TTAATATAAACATAT
* *
39320673 ATAATTATTATTTAACATAT
1 ATAATTAATA-TAAACATAT
39320693 ATAATTAATATAA
1 ATAATTAATATAA
39320706 CATTTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATTAATATAAACATAT
Found at i:39322466 original size:14 final size:14
Alignment explanation
Indices: 39322425--39322470 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
39322415 CATCTCCCCT
39322425 TTTTTTTAGTTTTC
1 TTTTTTTAGTTTTC
** *
39322439 TTTTCGTA-TCTTC
1 TTTTTTTAGTTTTC
39322452 TTTTTTTAGTTTTC
1 TTTTTTTAGTTTTC
39322466 TTTTT
1 TTTTT
39322471 CATTTGACTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.07, C:0.11, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTAGTTTTC
Found at i:39336368 original size:79 final size:81
Alignment explanation
Indices: 39336237--39336438 Score: 214
Period size: 79 Copynumber: 2.5 Consensus size: 81
39336227 AATTTAACTG
* ** * * * * * *
39336237 ACTAGAGCTGGGCTCACTTTTGCG-GTTTATCCTCCACGCACT-AGGTGTCAGGATTTGACGGAT
1 ACTAGAGCTAGGCTCACAATTGCGAGTTTATCCGCTAGGCACTCA-ATGCCAGGAATTGACGGAT
*
39336300 ATT-TTTGGTTAATCCA
65 ATTAGTTGGTTAATCCA
* *
39336316 ACTAGATCTAGGCTCACAATTGC-AGTTTATCCGCTAGGCACTCAATGCCAGGAATTGACGGTTA
1 ACTAGAGCTAGGCTCACAATTGCGAGTTTATCCGCTAGGCACTCAATGCCAGGAATTGACGGATA
39336380 TTAGTTGGTTAATCCA
66 TTAGTTGGTTAATCCA
* * ** *
39336396 ATTAGAGCTGGGCTCACTTTTGCGATTTTATCCGCTAGGCACT
1 ACTAGAGCTAGGCTCACAATTGCGAGTTTATCCGCTAGGCACT
39336439 GTCTGCCAAG
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
79 52 0.51
80 31 0.31
81 18 0.18
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (81 bp):
ACTAGAGCTAGGCTCACAATTGCGAGTTTATCCGCTAGGCACTCAATGCCAGGAATTGACGGATA
TTAGTTGGTTAATCCA
Found at i:39338791 original size:109 final size:109
Alignment explanation
Indices: 39338600--39338818 Score: 438
Period size: 109 Copynumber: 2.0 Consensus size: 109
39338590 TTTTTGTAAA
39338600 ACAAGGTCAGGGTAGGTTCGACTTCTCCTGTTCTGACTTTGAAAAATCATAGAAAAATGTAGAAA
1 ACAAGGTCAGGGTAGGTTCGACTTCTCCTGTTCTGACTTTGAAAAATCATAGAAAAATGTAGAAA
39338665 AATTATTAGAGACTGAAATTTATATGGCTGAATCCTTAATGAGT
66 AATTATTAGAGACTGAAATTTATATGGCTGAATCCTTAATGAGT
39338709 ACAAGGTCAGGGTAGGTTCGACTTCTCCTGTTCTGACTTTGAAAAATCATAGAAAAATGTAGAAA
1 ACAAGGTCAGGGTAGGTTCGACTTCTCCTGTTCTGACTTTGAAAAATCATAGAAAAATGTAGAAA
39338774 AATTATTAGAGACTGAAATTTATATGGCTGAATCCTTAATGAGT
66 AATTATTAGAGACTGAAATTTATATGGCTGAATCCTTAATGAGT
39338818 A
1 A
39338819 TATTTTCAAA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (109 bp):
ACAAGGTCAGGGTAGGTTCGACTTCTCCTGTTCTGACTTTGAAAAATCATAGAAAAATGTAGAAA
AATTATTAGAGACTGAAATTTATATGGCTGAATCCTTAATGAGT
Found at i:39339255 original size:22 final size:23
Alignment explanation
Indices: 39339225--39339318 Score: 122
Period size: 22 Copynumber: 4.1 Consensus size: 23
39339215 ACACTTGCGC
*
39339225 GCCTACTGTTCAGCATTGTGTGT
1 GCCTACTGTTCAGCACTGTGTGT
39339248 GCCT-CTGTTCAGCACTGTGTGT
1 GCCTACTGTTCAGCACTGTGTGT
*
39339270 G-CTTCTGTTCAGCACTGTGTGT
1 GCCTACTGTTCAGCACTGTGTGT
*
39339292 GCCTACTGTTTCCAGCACT-TATGT
1 GCCTACTG-TT-CAGCACTGTGTGT
39339316 GCC
1 GCC
39339319 CTCTGTTAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
21 2 0.03
22 37 0.58
23 9 0.14
24 9 0.14
25 7 0.11
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.37
Consensus pattern (23 bp):
GCCTACTGTTCAGCACTGTGTGT
Found at i:39343533 original size:80 final size:80
Alignment explanation
Indices: 39343397--39343544 Score: 262
Period size: 80 Copynumber: 1.9 Consensus size: 80
39343387 CAAACCGTTG
* *
39343397 GTTAATCCAACTAGAGCTGGGCTCACTTATCGAGGTTTATCCGCTAGGCACTGGGTGCCATGAAT
1 GTTAATCCAACTAGAGCTGGGCTCACTTATCGAGGTTTAACCGCTAGGCACCGGGTGCCATGAAT
39343462 TGACGGACTTTGTAA
66 TGACGGACTTTGTAA
39343477 GTTAATCCAACTAGAGCTGGGCTCACTTATCGCA-GTTTAACCGCTAGGCACCGGGTGCCATGAA
1 GTTAATCCAACTAGAGCTGGGCTCACTTATCG-AGGTTTAACCGCTAGGCACCGGGTGCCATGAA
39343541 TTGA
65 TTGA
39343545 TGAAAATTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
80 64 0.98
81 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (80 bp):
GTTAATCCAACTAGAGCTGGGCTCACTTATCGAGGTTTAACCGCTAGGCACCGGGTGCCATGAAT
TGACGGACTTTGTAA
Found at i:39344421 original size:93 final size:93
Alignment explanation
Indices: 39344262--39344455 Score: 388
Period size: 93 Copynumber: 2.1 Consensus size: 93
39344252 TTACAAATAG
39344262 CTATTTAGGGAATGGTCTTATTGATTAAGTTGGAAACGTCATGCTTAGGGTTTGGTTGATGCTTG
1 CTATTTAGGGAATGGTCTTATTGATTAAGTTGGAAACGTCATGCTTAGGGTTTGGTTGATGCTTG
39344327 GATGTTGTTTTGAATCCTAGAAATTGTA
66 GATGTTGTTTTGAATCCTAGAAATTGTA
39344355 CTATTTAGGGAATGGTCTTATTGATTAAGTTGGAAACGTCATGCTTAGGGTTTGGTTGATGCTTG
1 CTATTTAGGGAATGGTCTTATTGATTAAGTTGGAAACGTCATGCTTAGGGTTTGGTTGATGCTTG
39344420 GATGTTGTTTTGAATCCTAGAAATTGTA
66 GATGTTGTTTTGAATCCTAGAAATTGTA
39344448 CTATTTAG
1 CTATTTAG
39344456 TAATGCATCT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 101 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (93 bp):
CTATTTAGGGAATGGTCTTATTGATTAAGTTGGAAACGTCATGCTTAGGGTTTGGTTGATGCTTG
GATGTTGTTTTGAATCCTAGAAATTGTA
Found at i:39348567 original size:22 final size:22
Alignment explanation
Indices: 39348540--39348588 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
39348530 GGGCACGAGG
* *
39348540 GTGTGAATGTGGCCACACTGGT
1 GTGTGAATGTGACCACACAGGT
39348562 GTGTGAATGTGACCACACAGGT
1 GTGTGAATGTGACCACACAGGT
39348584 GTGTG
1 GTGTG
39348589 TTTGAGACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.37, T:0.27
Consensus pattern (22 bp):
GTGTGAATGTGACCACACAGGT
Found at i:39356435 original size:53 final size:52
Alignment explanation
Indices: 39356289--39356475 Score: 259
Period size: 52 Copynumber: 3.6 Consensus size: 52
39356279 AAAAGGTTCA
*
39356289 ATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCCG
* * * *
39356341 ATAACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGGTCTG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGA-GGTCCG
* * *
39356394 ATGACTTTGTGTCATCGTGAGTATATGAATCCCTTGTGGATTATA-AGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTA-AGAGGTCCG
* *
39356446 GTGGCTATGTGTCATCGTGAGTATATGAAT
1 ATGACTATGTGTCATCGTGAGTATATGAAT
39356476 GAAGTGAAAT
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
52 76 0.63
53 43 0.36
54 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (52 bp):
ATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCCG
Found at i:39357455 original size:14 final size:15
Alignment explanation
Indices: 39357430--39357458 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39357420 ATAAAATAAC
39357430 GATAACATGAACAGT
1 GATAACATGAACAGT
39357445 GATAA-ATGAACAGT
1 GATAACATGAACAGT
39357459 AAAACACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (15 bp):
GATAACATGAACAGT
Found at i:39359116 original size:47 final size:47
Alignment explanation
Indices: 39359047--39359140 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
39359037 GTATGTCGTA
*
39359047 AATGTCCACTGAGAATTTGGGACTGTAAGTTCCCTGTTGATTTGATG
1 AATGTCCACTGAGAATTTGGGACTGTAAGTTCCCTGCTGATTTGATG
* *
39359094 AATGTCCATTGAGAATTTGGGACTGTGAGTTCCCTGCTGATTTGATG
1 AATGTCCACTGAGAATTTGGGACTGTAAGTTCCCTGCTGATTTGATG
39359141 TTATTACCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (47 bp):
AATGTCCACTGAGAATTTGGGACTGTAAGTTCCCTGCTGATTTGATG
Found at i:39369940 original size:11 final size:11
Alignment explanation
Indices: 39369909--39370135 Score: 82
Period size: 11 Copynumber: 19.4 Consensus size: 11
39369899 CATGGAAATC
*
39369909 ATTTCAACTTAA
1 ATTTCAA-TTTA
*
39369921 ATTTAAATTTA
1 ATTTCAATTTA
*
39369932 ATTTCAATTTC
1 ATTTCAATTTA
39369943 ATTTCAACTTGTA
1 ATTTCAA-TT-TA
* * *
39369956 TTAATTAAACTTA
1 --ATTTCAATTTA
*
39369969 ATTTCAACTTAAA
1 ATTTCAA-TT-TA
39369982 ATTT-AATTTA
1 ATTTCAATTTA
*
39369992 ATTTCAATTTC
1 ATTTCAATTTA
39370003 ATTTCAACTTGTA
1 ATTTCAA-TT-TA
* * *
39370016 TTAATTAAACTTA
1 --ATTTCAATTTA
*
39370029 ATTTCAACTTAA
1 ATTTCAA-TTTA
*
39370041 ATTTAAATTTA
1 ATTTCAATTTA
*
39370052 ATTTCAACTTCA
1 ATTTCAA-TTTA
*
39370064 ACTTCAATTTTTTA
1 ATTTCAA---TTTA
*
39370078 ATTTCAACTTA
1 ATTTCAATTTA
*
39370089 AGTTC-ATTTCA
1 ATTTCAATTT-A
*
39370100 ATTTCAATTAA
1 ATTTCAATTTA
* * *
39370111 ACTT-AAGTTC
1 ATTTCAATTTA
*
39370121 ATTTCAATTTC
1 ATTTCAATTTA
39370132 ATTT
1 ATTT
39370136 AAACTTGTAT
Statistics
Matches: 156, Mismatches: 41, Indels: 37
0.67 0.18 0.16
Matches are distributed among these distances:
10 14 0.09
11 77 0.49
12 33 0.21
13 11 0.07
14 11 0.07
15 10 0.06
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (11 bp):
ATTTCAATTTA
Found at i:39369942 original size:6 final size:6
Alignment explanation
Indices: 39369909--39370108 Score: 54
Period size: 6 Copynumber: 35.5 Consensus size: 6
39369899 CATGGAAATC
* * * * **
39369909 ATTTCA ACTTAA ATTTAA ATTT-A ATTTCA ATTTC- ATTTCA ACTTGT
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA
* * **
39369955 A-TT-A A-TTAA ACTT-A ATTTCA ACTTAAA ATTT-A ATTT-A ATTTCA
1 ATTTCA ATTTCA ATTTCA ATTTCA A-TTTCA ATTTCA ATTTCA ATTTCA
* ** * * * *
39369998 ATTTC- ATTTCA ACTTGT A-TT-A A-TTAA ACTT-A ATTTCA ACTTAA
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA
* * * * *
39370041 ATTTAA ATTT-A ATTTCA ACTTCA ACTTCA ATTTTTTA ATTTCA ACTT-A
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA A--TTTCA ATTTCA ATTTCA
*
39370089 AGTTC- ATTTCA ATTTCA ATT
1 ATTTCA ATTTCA ATTTCA ATT
39370109 AAACTTAAGT
Statistics
Matches: 152, Mismatches: 26, Indels: 32
0.72 0.12 0.15
Matches are distributed among these distances:
4 6 0.04
5 54 0.36
6 84 0.55
7 4 0.03
8 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.48
Consensus pattern (6 bp):
ATTTCA
Found at i:39370002 original size:60 final size:60
Alignment explanation
Indices: 39369909--39370063 Score: 285
Period size: 60 Copynumber: 2.6 Consensus size: 60
39369899 CATGGAAATC
39369909 ATTTCAACTTAAATTTAAATTTAATTTCAATTTCATTTCAACTTGTATTAATTAAACTTA
1 ATTTCAACTTAAATTTAAATTTAATTTCAATTTCATTTCAACTTGTATTAATTAAACTTA
39369969 ATTTCAACTTAAAATTT-AATTTAATTTCAATTTCATTTCAACTTGTATTAATTAAACTTA
1 ATTTCAACTT-AAATTTAAATTTAATTTCAATTTCATTTCAACTTGTATTAATTAAACTTA
*
39370029 ATTTCAACTTAAATTTAAATTTAATTTCAACTTCA
1 ATTTCAACTTAAATTTAAATTTAATTTCAATTTCA
39370064 ACTTCAATTT
Statistics
Matches: 92, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
59 6 0.07
60 80 0.87
61 6 0.07
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (60 bp):
ATTTCAACTTAAATTTAAATTTAATTTCAATTTCATTTCAACTTGTATTAATTAAACTTA
Found at i:39370166 original size:41 final size:41
Alignment explanation
Indices: 39370119--39370258 Score: 149
Period size: 41 Copynumber: 3.7 Consensus size: 41
39370109 AAACTTAAGT
39370119 TCATTTCAATTTCA-TTTAAACTTGTATTTTAATTTTGAATA
1 TCATTTC-ATTTCATTTTAAACTTGTATTTTAATTTTGAATA
39370160 TCATTTCATTTCATTTTAAACTTGTATTTTAATTTTG---A
1 TCATTTCATTTCATTTTAAACTTGTATTTTAATTTTGAATA
* * * *
39370198 --ATTT-A----AATTTGAACTTGTATTATAATTTTGAATT
1 TCATTTCATTTCATTTTAAACTTGTATTTTAATTTTGAATA
*
39370232 TAATTTCATTTCATTTTAAACTTGTAT
1 TCATTTCATTTCATTTTAAACTTGTAT
39370259 AATTTGTATA
Statistics
Matches: 82, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
31 22 0.27
35 1 0.01
36 8 0.10
37 1 0.01
38 1 0.01
40 6 0.07
41 43 0.52
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.55
Consensus pattern (41 bp):
TCATTTCATTTCATTTTAAACTTGTATTTTAATTTTGAATA
Found at i:39381198 original size:12 final size:12
Alignment explanation
Indices: 39381181--39381206 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39381171 ATATTTACTC
39381181 TTTTTGACACAA
1 TTTTTGACACAA
39381193 TTTTTGACACAA
1 TTTTTGACACAA
39381205 TT
1 TT
39381207 CTTAAAAGTA
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:0.15, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTTTGACACAA
Found at i:39382106 original size:31 final size:30
Alignment explanation
Indices: 39382032--39382108 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
39382022 ATTGATATAA
* *
39382032 TAATAAATTTAATGTTTTAATATTTATAGAAT
1 TAATAAATTT-A-GTTTTAATATTTAAAAAAT
* * *
39382064 TTATTAATTTAGTTTTAAATCTTTAAAAAAT
1 TAATAAATTTAGTTTT-AATATTTAAAAAAT
39382095 TAATAAATTTAGTT
1 TAATAAATTTAGTT
39382109 ATCAATTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 5 0.14
31 24 0.65
32 8 0.22
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (30 bp):
TAATAAATTTAGTTTTAATATTTAAAAAAT
Found at i:39385409 original size:20 final size:21
Alignment explanation
Indices: 39385384--39385425 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
39385374 TTGACCGATA
*
39385384 GTTGACCGTTGA-TTTTTTTG
1 GTTGACCGTTAACTTTTTTTG
39385404 GTTGACCGTTAACTTTTTTTG
1 GTTGACCGTTAACTTTTTTTG
39385425 G
1 G
39385426 GAAACCTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (21 bp):
GTTGACCGTTAACTTTTTTTG
Found at i:39389715 original size:19 final size:18
Alignment explanation
Indices: 39389667--39389717 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
39389657 AGCTAATGGT
39389667 TTTA-TTTT-TTATTGTA
1 TTTATTTTTATTATTGTA
* *
39389683 TTTATTGTTCATTATTAGTC
1 TTTATT-TTTATTATT-GTA
39389703 TTTATTTTTATTATT
1 TTTATTTTTATTATT
39389718 TTGATTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.14
17 1 0.04
18 2 0.07
19 13 0.46
20 8 0.29
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTATTTTTATTATTGTA
Found at i:39391878 original size:29 final size:29
Alignment explanation
Indices: 39391824--39391902 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
39391814 AATATTAAAA
* * *
39391824 TTATACAT-AAATTATGATTTAATGTGTAAT
1 TTATACATGAAATTTTGA-TT-CTGTGCAAT
39391854 TATATACATG-AATTTTGATTCTGTGCAAT
1 T-TATACATGAAATTTTGATTCTGTGCAAT
*
39391883 TTGTACATGAAATTTTGATT
1 TTATACATGAAATTTTGATT
39391903 TGATCTATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.17
29 18 0.43
30 3 0.07
31 14 0.33
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (29 bp):
TTATACATGAAATTTTGATTCTGTGCAAT
Found at i:39396171 original size:22 final size:21
Alignment explanation
Indices: 39396137--39396186 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
39396127 AGTTAAGATA
*
39396137 CATTT-TTATTTAA-TTGATT
1 CATTTATTATTTAACTTGAGT
39396156 CATATTATTATCTTAACTTGAGT
1 CAT-TTATTAT-TTAACTTGAGT
39396179 CATTTATT
1 CATTTATT
39396187 TGGATTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 4 0.15
22 9 0.35
23 8 0.31
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.56
Consensus pattern (21 bp):
CATTTATTATTTAACTTGAGT
Found at i:39396247 original size:16 final size:17
Alignment explanation
Indices: 39396222--39396254 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39396212 GTTGGAATTA
39396222 AGTTTCTAGAA-ATGTT
1 AGTTTCTAGAATATGTT
*
39396238 AGTTTTTAGAATATGTT
1 AGTTTCTAGAATATGTT
39396255 TTTTTACTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.48
Consensus pattern (17 bp):
AGTTTCTAGAATATGTT
Found at i:39398196 original size:22 final size:21
Alignment explanation
Indices: 39398172--39398236 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 21
39398162 GCATAAGCAA
39398172 AAAATTAAAAATAAAAAAACT
1 AAAATTAAAAATAAAAAAACT
39398193 AAAATTAACAAATAAAAAAAGC-
1 AAAATTAA-AAATAAAAAAA-CT
*
39398215 AAAATT-GAAATAAAAAAGACT
1 AAAATTAAAAATAAAAAA-ACT
39398236 A
1 A
39398237 TAAGCAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
20 11 0.28
21 10 0.26
22 17 0.44
23 1 0.03
ACGTcount: A:0.72, C:0.06, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAATTAAAAATAAAAAAACT
Found at i:39398370 original size:24 final size:25
Alignment explanation
Indices: 39398324--39398370 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39398314 AAGAAATAAA
*
39398324 AAAAATTAAAAAATAAATGGCTATT
1 AAAAATTAAAAAATAAATAGCTATT
*
39398349 AAAAATTAAAAAA-GAATAGCTA
1 AAAAATTAAAAAATAAATAGCTA
39398371 AAAATGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (25 bp):
AAAAATTAAAAAATAAATAGCTATT
Found at i:39398969 original size:32 final size:31
Alignment explanation
Indices: 39398891--39398971 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 31
39398881 TTGTTGCTCC
39398891 AAGTTGGTACTTAAACTTGACACATTTTCCT
1 AAGTTGGTACTTAAACTTGACACATTTTCCT
* * ** **
39398922 AA-TTCGGTACCTAAACTTGATATTTTTTTTTT
1 AAGTT-GGTACTTAAACTTGACA-CATTTTCCT
39398954 AAGTTGGTACTTAAACTT
1 AAGTTGGTACTTAAACTT
39398972 TTTGGGATCC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 2 0.05
31 17 0.43
32 19 0.47
33 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (31 bp):
AAGTTGGTACTTAAACTTGACACATTTTCCT
Found at i:39399316 original size:59 final size:60
Alignment explanation
Indices: 39399196--39399365 Score: 175
Period size: 59 Copynumber: 2.9 Consensus size: 60
39399186 AATTGAATGT
* * ** * **
39399196 AAAAAAACTTATGTACCAAATTAGGAAAAAA-TGCCAAGTTTAGATACCAAATTGGGTTC
1 AAAAAAATTTAAGTACCAAATTAAAAAAAAAGTGTCAAGTTTAGATACCAAATTAAGTTC
* *
39399255 AAAAAAGTTTAAGTATCAAATTAAAAAAAAAGTGTCAAGTTTAGATACCAAATTAAG-TC
1 AAAAAAATTTAAGTACCAAATTAAAAAAAAAGTGTCAAGTTTAGATACCAAATTAAGTTC
* * * * * * *
39399314 AAAAAAATTTAGGTACCAAACT-AAGAAAACGTATCAAATTCAGATACCAAAT
1 AAAAAAATTTAAGTACCAAATTAAAAAAAAAGTGTCAAGTTTAGATACCAAAT
39399366 GTTATATTAA
Statistics
Matches: 92, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
58 25 0.27
59 45 0.49
60 22 0.24
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (60 bp):
AAAAAAATTTAAGTACCAAATTAAAAAAAAAGTGTCAAGTTTAGATACCAAATTAAGTTC
Found at i:39399559 original size:16 final size:17
Alignment explanation
Indices: 39399521--39399559 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
39399511 GATCTTAAAG
39399521 ATTTGATTATTAATACGTT
1 ATTTGATTATTAATAC--T
39399540 ATTTGATTATTAATAC-
1 ATTTGATTATTAATACT
39399556 ATTT
1 ATTT
39399560 CCCTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
19 16 0.80
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (17 bp):
ATTTGATTATTAATACT
Found at i:39405572 original size:12 final size:12
Alignment explanation
Indices: 39405555--39405589 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
39405545 TGGTCCGCCC
39405555 ATATTAATTTTT
1 ATATTAATTTTT
39405567 ATATT-ATTTTT
1 ATATTAATTTTT
39405578 ATA-TAATTTTT
1 ATATTAATTTTT
39405589 A
1 A
39405590 AATATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 16 0.73
12 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:39405741 original size:30 final size:30
Alignment explanation
Indices: 39405705--39405769 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
39405695 CAACTTAACA
* *
39405705 AACAAATGCCTTTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
*
39405735 AACAAATATCTCTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
39405765 AACAA
1 AACAA
39405770 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.25
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:39409381 original size:17 final size:17
Alignment explanation
Indices: 39409359--39409391 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39409349 AATGATAAAG
39409359 ATAAATGTCAGAGCAAA
1 ATAAATGTCAGAGCAAA
39409376 ATAAATGTCAGAGCAA
1 ATAAATGTCAGAGCAA
39409392 CTGAAAGTAA
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:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
ATAAATGTCAGAGCAAA
Found at i:39410951 original size:21 final size:22
Alignment explanation
Indices: 39410919--39410961 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
39410909 CATTTTTCTG
*
39410919 CTTTTCTCTTCTTCTTTGTTTT
1 CTTTTCTCTTCTTCTTTATTTT
*
39410941 CTTTT-TCTTCTTTTTTATTTT
1 CTTTTCTCTTCTTCTTTATTTT
39410962 TGTATGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (22 bp):
CTTTTCTCTTCTTCTTTATTTT
Found at i:39411584 original size:18 final size:18
Alignment explanation
Indices: 39411546--39411584 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39411536 ATGTACTAAC
* *
39411546 AAAAATGCAGTGATAAAT
1 AAAAATGCAATGACAAAT
*
39411564 AAAAATGCAATGACAACT
1 AAAAATGCAATGACAAAT
39411582 AAA
1 AAA
39411585 TGCTATGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (18 bp):
AAAAATGCAATGACAAAT
Found at i:39425289 original size:13 final size:13
Alignment explanation
Indices: 39425271--39425300 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39425261 TAAAAAAATG
*
39425271 AGAAAAAGAAGAA
1 AGAAAAAGAAAAA
39425284 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
39425297 AGAA
1 AGAA
39425301 GAATATGCTG
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:39425296 original size:20 final size:19
Alignment explanation
Indices: 39425246--39425303 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
39425236 TCAATCACTT
* *
39425246 AAAAAATAAAAAA-AATAA
1 AAAAAAGAAAAAAGAAGAA
*
39425264 AAAAATGAGAAAAAGAAGAA
1 AAAAAAGA-AAAAAGAAGAA
39425284 AGAAAAAGAAAAAAGAAGAA
1 A-AAAAAGAAAAAAGAAGAA
39425304 TATGCTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.18
19 5 0.15
20 16 0.48
21 6 0.18
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAAAAAGAAGAA
Found at i:39433691 original size:13 final size:13
Alignment explanation
Indices: 39433673--39433705 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
39433663 AATATCAAAC
39433673 AAAAAATA-TATTA
1 AAAAAATAGTA-TA
39433686 AAAAAATAGTATA
1 AAAAAATAGTATA
39433699 AAAAAAT
1 AAAAAAT
39433706 TCATTCATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAAAATAGTATA
Found at i:39443381 original size:42 final size:42
Alignment explanation
Indices: 39443307--39443426 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
39443297 GTAGATAGCG
* * * * * *
39443307 AAACAATCGATTGAAAAG-CAAAACACTCAATTGACACAAGA
1 AAACAATCGATTGTAAAGTGAAAAAAATCAATTGAAACAACA
39443348 AAACAATTC-ATTGTAAAGTGAAAAAAATCAATTGAAACAACA
1 AAACAA-TCGATTGTAAAGTGAAAAAAATCAATTGAAACAACA
* * * *
39443390 AAACAATCGATTTTAAATTGAAAACAATCGATTGAAA
1 AAACAATCGATTGTAAAGTGAAAAAAATCAATTGAAA
39443427 AGAATCATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
41 16 0.24
42 50 0.76
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (42 bp):
AAACAATCGATTGTAAAGTGAAAAAAATCAATTGAAACAACA
Found at i:39453585 original size:7 final size:7
Alignment explanation
Indices: 39453573--39453618 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
39453563 TTTTGAAAAA
39453573 GTCAACG
1 GTCAACG
39453580 GTCAACG
1 GTCAACG
* *
39453587 ATCAA-A
1 GTCAACG
39453593 GTCAACG
1 GTCAACG
39453600 GTCAACG
1 GTCAACG
39453607 GTCAACG
1 GTCAACG
*
39453614 ATCAA
1 GTCAA
39453619 TCAACACCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
6 4 0.12
7 29 0.88
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:39453595 original size:20 final size:20
Alignment explanation
Indices: 39453570--39453611 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
39453560 GTTTTTTGAA
39453570 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGGTCAACGATC
*
39453590 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGATC
39453610 AA
1 AA
39453612 CGATCAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGATC
Found at i:39453719 original size:15 final size:15
Alignment explanation
Indices: 39453699--39453728 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39453689 TGGTTCATTT
39453699 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
39453714 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
39453729 AATGTGGGTT
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:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:39454161 original size:11 final size:11
Alignment explanation
Indices: 39454128--39454202 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
39454118 AAGTGTGATT
*
39454128 AAAAGAGGAAG
1 AAAAGAGAAAG
*
39454139 AAAATAGAAAAG
1 AAAAGAG-AAAG
39454151 AAAAGAGAAAG
1 AAAAGAGAAAG
39454162 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
39454174 AATGAGAAAAAG
1 AA-AAGAGAAAG
39454186 AAAAGAGAAAG
1 AAAAGAGAAAG
*
39454197 GAAAGA
1 AAAAGA
39454203 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:39454170 original size:23 final size:23
Alignment explanation
Indices: 39454128--39454200 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
39454118 AAGTGTGATT
*
39454128 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
39454151 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
39454174 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
39454198 AAA
1 AAA
39454201 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:39456319 original size:48 final size:48
Alignment explanation
Indices: 39456248--39456345 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
39456238 GCATAAGCCA
*
39456248 CAACCTTTCCCTCTTGCATTAACACACATCCCAATCCAGTGTGAGAAG
1 CAACCTTTCCCTCTTGCATTAACACACATCCCAATCCAGTGCGAGAAG
39456296 CAACCTTTCCCTCTTGCATTAACACACATCCCAATCCAGTGCGAGAAG
1 CAACCTTTCCCTCTTGCATTAACACACATCCCAATCCAGTGCGAGAAG
39456344 CA
1 CA
39456346 TCACTGTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.30, C:0.35, G:0.12, T:0.23
Consensus pattern (48 bp):
CAACCTTTCCCTCTTGCATTAACACACATCCCAATCCAGTGCGAGAAG
Found at i:39460730 original size:20 final size:20
Alignment explanation
Indices: 39460705--39460746 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39460695 GTTTTTCGAA
39460705 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGGTCAACGATC
39460725 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGGTCAACGATC
39460745 AA
1 AA
39460747 CGATCAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGATC
Found at i:39460854 original size:15 final size:15
Alignment explanation
Indices: 39460834--39460863 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39460824 TGGTTCATTT
39460834 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
39460849 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
39460864 AATTTGGGTT
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:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Done.