Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold16
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: 5287347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 8769 characters in sequence are not A, C, G, or T
File 14 of 35
Found at i:2104294 original size:29 final size:27
Alignment explanation
Indices: 2104238--2104294 Score: 62
Period size: 29 Copynumber: 2.0 Consensus size: 27
2104228 AATCATCACA
*
2104238 CATTTTATTATGCATGGATATTCTTAAT
1 CATTTTATTAAGCAT-GATATTCTTAAT
2104266 CATTTTATTTAAGCAT-ATATATCTGTAAT
1 CATTTTA-TTAAGCATGATAT-TCT-TAAT
2104295 AACATATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.16
28 10 0.40
29 11 0.44
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (27 bp):
CATTTTATTAAGCATGATATTCTTAAT
Found at i:2105567 original size:21 final size:20
Alignment explanation
Indices: 2105531--2105591 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
2105521 ATGCAACAAA
*
2105531 TTACATAAAAAAATTACCAAG
1 TTACAT-AAAACATTACCAAG
*
2105552 TTACATACAAACATTACAAAG
1 TTACATA-AAACATTACCAAG
*
2105573 TTACATAAAACATGACCAA
1 TTACATAAAACATTACCAA
2105592 AACTATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.31
21 24 0.69
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (20 bp):
TTACATAAAACATTACCAAG
Found at i:2109303 original size:28 final size:28
Alignment explanation
Indices: 2109204--2109302 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
2109194 TTTTCGTCTC
*
2109204 GGGGATACTCCAACCCCGTTATTTCATT
1 GGGGATACTCCAACCCCGTTATTTCATA
2109232 GGGGATACTCCAACCCCGTTATTTCATA
1 GGGGATACTCCAACCCCGTTATTTCATA
* ** **
2109260 GGGGATACTCTAACCTAGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCATA
*
2109288 GGGCATACTCCAACC
1 GGGGATACTCCAACC
2109303 TCGATTTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCATA
Found at i:2109489 original size:78 final size:79
Alignment explanation
Indices: 2109261--2109488 Score: 253
Period size: 79 Copynumber: 2.9 Consensus size: 79
2109251 TATTTCATAG
* ** * * * * *
2109261 GGGATACTCTAACCTAGTTATTTCCGAGGGCATACTCCAACCTCGATTTTATTTCCAAAACATAA
1 GGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCA
**
2109326 ATTTTTTCACAATTG
66 A-TTTTTCACAATCA
** * *
2109341 GGGATACTCCAATGCCGTTATTTTCAA-AGGATACTCCAACCCC-AGTTTTATTTCCAAAACACC
1 GGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGA-TTTTATTTCCAAAACATC
2109404 AATTTTTCACAATCA
65 AATTTTTCACAATCA
* * * * *
2109419 GGGATACTCCAACCCCGTTATTTTTAAGGGGATACTCCAACCCCGAATTTATTTTCAGAACATCG
1 GGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCA
2109484 ATTTT
66 ATTTT
2109489 CCATGGTCAA
Statistics
Matches: 122, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
78 36 0.30
79 65 0.53
80 21 0.17
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCA
ATTTTTCACAATCA
Found at i:2110963 original size:13 final size:13
Alignment explanation
Indices: 2110945--2110970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2110935 CAATTTTTTG
2110945 TGTATCGATACAT
1 TGTATCGATACAT
2110958 TGTATCGATACAT
1 TGTATCGATACAT
2110971 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2110982 original size:32 final size:33
Alignment explanation
Indices: 2110925--2110988 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2110915 TACAAGCCAA
**
2110925 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
2110958 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
2110989 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:2112759 original size:4 final size:4
Alignment explanation
Indices: 2112750--2112780 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2112740 TTTTGAGGTG
2112750 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2112781 GTTTGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2118947 original size:92 final size:92
Alignment explanation
Indices: 2118785--2119371 Score: 978
Period size: 92 Copynumber: 6.3 Consensus size: 92
2118775 ACCAGGCGCC
2118785 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
* *
2118850 AGCACCTTCTTCTTTAAGTCCAATGTA
66 GGCACCTTCATCTTTAAGTCCAATGTA
***
2118877 GCTGGCCTTGAATCAGCACATTGGCACCACCAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
*
2118942 GGCACCTTCTTCTTTAAGTCCAATGTA
66 GGCACCTTCATCTTTAAGTCCAATGTA
*
2118969 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
*
2119034 GGCATCTTCATCTTTAAGTCCAATGTA
66 GGCACCTTCATCTTTAAGTCCAATGTA
* *
2119061 GCTGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCA-TTGGCCTTGAATCAGCATAT
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATAT
2119125 TGGCACCTTCATCTTTAAGTCCAATGTA
65 TGGCACCTTCATCTTTAAGTCCAATGTA
*
2119153 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
* *
2119218 GGCATCTTCTTCTTTAAGTCCAATGTA
66 GGCACCTTCATCTTTAAGTCCAATGTA
*
2119245 GCTGGCCTTGAATCAGTACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
1 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
*
2119310 GGCACCTTTTCCATCTTTAAGTTCAATGTA
66 GGCACC--TT-CATCTTTAAGTCCAATGTA
*
2119340 GCTGGCCTTGAATCAGCACATTGACATCCTTT
1 GCTGGCCTTGAATCAGCACATTGGCA-CCTTT
2119372 TTCTCATCTT
Statistics
Matches: 463, Mismatches: 26, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
92 415 0.90
94 2 0.00
95 41 0.09
96 5 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
GGCACCTTCATCTTTAAGTCCAATGTA
Found at i:2119128 original size:19 final size:19
Alignment explanation
Indices: 2119063--2119128 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
2119053 CCAATGTAGC
*
2119063 TGGCCTTGAATCAGCACAT
1 TGGCCTTGAATCAGCATAT
* **
2119082 TGGCACTTTTAAGTCCAATATCAT
1 TGGC-C-TTGAA-T-CAGCAT-AT
2119106 TGGCCTTGAATCAGCATAT
1 TGGCCTTGAATCAGCATAT
2119125 TGGC
1 TGGC
2119129 ACCTTCATCT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 10 0.29
20 5 0.14
21 5 0.14
22 5 0.14
23 4 0.11
24 6 0.17
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (19 bp):
TGGCCTTGAATCAGCATAT
Found at i:2119296 original size:22 final size:22
Alignment explanation
Indices: 2119229--2119296 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
2119219 GCATCTTCTT
*
2119229 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
* * * *
2119251 CTTGAA-T-CAGTACA-TTGGCAC
1 CTTTAAGTCCAATATAGCTGG--C
2119272 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
2119294 CTT
1 CTT
2119297 GAATCAGCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 10 0.31
23 5 0.16
24 3 0.09
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (22 bp):
CTTTAAGTCCAATATAGCTGGC
Found at i:2119350 original size:52 final size:55
Alignment explanation
Indices: 2119272--2119409 Score: 174
Period size: 52 Copynumber: 2.6 Consensus size: 55
2119262 ACATTGGCAC
* *
2119272 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
2119324 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
** * * *
2119379 CTTTAAACCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
2119410 ACGTATTGGT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
52 38 0.53
53 2 0.03
54 5 0.07
55 27 0.38
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:2119739 original size:19 final size:19
Alignment explanation
Indices: 2119715--2119782 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2119705 AATTCAACGA
2119715 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2119734 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2119749 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2119766 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2119783 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2119753 original size:32 final size:32
Alignment explanation
Indices: 2119717--2119779 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2119707 TTCAACGATT
*
2119717 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2119749 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2119780 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2119754 original size:13 final size:13
Alignment explanation
Indices: 2119736--2119760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2119726 ACATAAGTTT
2119736 TGTATCGATACAA
1 TGTATCGATACAA
2119749 TGTATCGATACA
1 TGTATCGATACA
2119761 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2119840 original size:13 final size:13
Alignment explanation
Indices: 2119822--2119847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2119812 CATTTTTCTG
2119822 TGTATCGATACAT
1 TGTATCGATACAT
2119835 TGTATCGATACAT
1 TGTATCGATACAT
2119848 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2119844 original size:33 final size:33
Alignment explanation
Indices: 2119802--2119868 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2119792 GCCAAGGAAA
***
2119802 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2119835 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2119868 T
1 T
2119869 TAGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2122273 original size:51 final size:53
Alignment explanation
Indices: 2122204--2122334 Score: 160
Period size: 51 Copynumber: 2.5 Consensus size: 53
2122194 AGTTTATCAA
* * * * *
2122204 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
2122255 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
2122309 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
2122335 CCCGTTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
50 2 0.03
51 32 0.48
53 9 0.14
54 20 0.30
55 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:2122422 original size:52 final size:51
Alignment explanation
Indices: 2122349--2122518 Score: 184
Period size: 52 Copynumber: 3.3 Consensus size: 51
2122339 TTATTTCCGA
*
2122349 GGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATC-CTAAAACACCAATTTTTCCACAATC
** **
2122401 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACACCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * *
2122453 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
*
2122505 GAGGATACTCCAAC
1 GGGGATACTCCAAC
2122519 CTCGTTATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
51 10 0.10
52 70 0.71
53 13 0.13
54 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:2122538 original size:28 final size:28
Alignment explanation
Indices: 2122502--2122578 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
2122492 ATTTTTCACA
* * *
2122502 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2122530 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2122558 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2122579 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2122542 original size:184 final size:185
Alignment explanation
Indices: 2122207--2122546 Score: 533
Period size: 185 Copynumber: 1.8 Consensus size: 185
2122197 TTATCAATTC
* *
2122207 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
2122272 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
2122337 CGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTT
131 CGTTATTTCAGAGGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTT
* * *
2122392 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
2122456 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* **
2122519 CTCGTTATTTCATCGGGGATACTCCAAC
129 CCCGTTATTTCAGAGGGGATACTCCAAC
2122547 CCCGTTACTT
Statistics
Matches: 141, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
184 49 0.35
185 57 0.40
186 35 0.25
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (185 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTATTTCAGAGGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTT
Found at i:2122645 original size:107 final size:107
Alignment explanation
Indices: 2122453--2122657 Score: 243
Period size: 107 Copynumber: 1.9 Consensus size: 107
2122443 TCCTTTAATC
* * * *
2122453 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACCCCAA
*
2122518 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * *
2122561 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACCCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACCCCAA
*
2122625 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
2122658 ATTTTTTTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
105 3 0.04
107 57 0.70
108 21 0.26
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACCCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:2122681 original size:79 final size:79
Alignment explanation
Indices: 2122532--2122734 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
2122522 GTTATTTCAT
* * * *
2122532 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
2122597 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * * ** *
2122611 TGGGGATACCCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
2122675 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
2122690 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
2122735 TGTTATTATC
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 8 0.08
79 94 0.92
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:2123791 original size:52 final size:52
Alignment explanation
Indices: 2123707--2123874 Score: 183
Period size: 52 Copynumber: 3.2 Consensus size: 52
2123697 CGTTGCGACA
* * *
2123707 GGCACCTTTTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
1 GGCACCTTTTCCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT
** *
2123759 GGCACCTTTTCCATCTTTAAGTTTAATGTAGCTGGCCTTGAATCAGCACATT
1 GGCACCTTTTCCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT
* * * * * * *
2123811 GACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATT
1 GGCA-CC-TTTTC-CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT
*
2123866 GGCATCTTT
1 GGCACCTTT
2123875 ATCACTTTTC
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
52 49 0.52
53 5 0.05
54 6 0.06
55 35 0.37
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (52 bp):
GGCACCTTTTCCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT
Found at i:2123856 original size:55 final size:53
Alignment explanation
Indices: 2123709--2123958 Score: 179
Period size: 52 Copynumber: 4.5 Consensus size: 53
2123699 TTGCGACAGG
* * *
2123709 CACCTTTT-TCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1 CACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
** *
2123761 CACCTTTTC-CATCTTTAAGTTTAATGTAGCTGGCCTTGAATCAGCACATTGA
1 CACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
* * * * * *
2123813 CATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCA
1 CA-CC-TTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-A
* * *
2123870 TCTTTATCACTTTTCTCATCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG
1 -C---A-C-CTTTTCTCA------TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
2123935 CACC--TT-T-ATCTTTAAGTCCAATAT
1 CACCTTTTCTCATCTTTAAGTCCAATAT
2123959 CGCTAGCCGC
Statistics
Matches: 158, Mismatches: 23, Indels: 37
0.72 0.11 0.17
Matches are distributed among these distances:
49 15 0.09
52 47 0.30
53 2 0.01
54 5 0.03
55 33 0.21
56 2 0.01
57 3 0.02
58 1 0.01
59 1 0.01
60 1 0.01
61 12 0.08
62 1 0.01
64 1 0.01
66 1 0.01
67 33 0.21
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (53 bp):
CACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
Found at i:2124949 original size:52 final size:52
Alignment explanation
Indices: 2124820--2124950 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
2124810 CACTGATCTT
* * *
2124820 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATAGATACACTATAAAA
*
2124872 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATAGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATAGATACACTATAAAA
*
2124924 TGTATCGATACATGCAGGTAAATTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
2124951 ATATTTCGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATAGATACACTATAAAA
Found at i:2133484 original size:61 final size:62
Alignment explanation
Indices: 2133290--2133703 Score: 433
Period size: 61 Copynumber: 6.9 Consensus size: 62
2133280 GAGAAGGACG
* * * * * *
2133290 CCTTTCAAAGCCTATACAAGTTAGTGGCA-TTTTCTAGTCCTCAAAGAGCACGATGCC-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * **
2133350 -C----AAAGCCCACACAAGCTGGTGGCAC-CTTC-AGTCTTCAAAGAGCAGGATGTTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
*
2133405 CCTTTTAAAGCCCACACAAGTTGATGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
2133467 -CTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCGAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
2133527 CCTGTTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
2133589 CCTTTTAAAGCCTACACAAGTTGGTGGTACCTTTC-AGTCCTCAAAGAACAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTT-T
** * * * * * * *
2133650 CCTTGCAAAACCCATACAAGCTGGTGGCAC-CTGCTAGTCCCCAAGGAGCAGGAC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGAC
2133704 CTATTTCATT
Statistics
Matches: 296, Mismatches: 45, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
54 18 0.06
55 25 0.08
56 1 0.00
59 1 0.00
60 57 0.19
61 115 0.39
62 79 0.27
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (62 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:2133608 original size:184 final size:174
Alignment explanation
Indices: 2133269--2133703 Score: 457
Period size: 184 Copynumber: 2.4 Consensus size: 174
2133259 TTTCACCCTT
* * * **
2133269 TAGTCCTCAAAGAGAAGGACGCC-TTTC--AAAGCCTATACAAGTTAGTGGCATTTTCTAGTCCT
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCTTAAAGCCCATACAAGTTGGTGGCACCTTCTAGTCCT
* * *
2133331 CAAAGAGCACGATGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCTTCAAAGAGCAGG
66 CAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGG
* ** *
2133396 ATGTTTTTTCCTTTTAAAGCCCACACAAGTTGATGGCACTTTTC
131 ACGCCTTTTCCTTTTAAAGCCCACACAAGTTGATGGCACCTTTC
* *
2133440 TAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCGAGTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTC--TTAAAGCCCATACAAGTTGGTGGCACCTTCTAGTC
* * *
2133505 CTCAAAGAGCAGGACGCCTTTTCCTGTTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTC
64 CTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGCTGGTGGCAC--CTTCAGTCCTC
* * * *
2133570 AAAGAGTAGGACGCCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGTACCTTTC
121 AAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGATGGCACCTTTC
* * * * *
2133624 -AGTCCTCAAAGAACAGGATG-CTTTCTCCTTGCAAAACCCATACAAGCTGGTGGCACCTGCTAG
1 TAGTCCTCAAAGAGCAGGACGCCTTT-T-CTT--AAAGCCCATACAAGTTGGTGGCACCTTCTAG
* *
2133687 TCCCCAAGGAGCAGGAC
62 TCCTCAAAGAGCAGGAC
2133704 CTATTTCATT
Statistics
Matches: 217, Mismatches: 30, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
171 22 0.10
172 4 0.02
176 43 0.20
177 3 0.01
178 1 0.00
182 29 0.13
183 19 0.09
184 96 0.44
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (174 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTCTTAAAGCCCATACAAGTTGGTGGCACCTTCTAGTCCT
CAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGG
ACGCCTTTTCCTTTTAAAGCCCACACAAGTTGATGGCACCTTTC
Found at i:2134381 original size:20 final size:20
Alignment explanation
Indices: 2134355--2134402 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2134345 CAGATGTATA
*
2134355 AATACATTGTTCATTATATC
1 AATACATTATTCATTATATC
* *
2134375 GATACATTATTCATTGTATC
1 AATACATTATTCATTATATC
2134395 AATACATT
1 AATACATT
2134403 CTGGGTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (20 bp):
AATACATTATTCATTATATC
Found at i:2136762 original size:28 final size:29
Alignment explanation
Indices: 2136719--2136802 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 29
2136709 ATTTCTAAAT
*
2136719 TTTTCATCTCGGGGATACTCTAACCCCGTTA
1 TTTTCAT-T-GGGGATACTCTAACCCCGCTA
* *
2136750 -TTTCATTGGGGATACTCCAACCCTGCTA
1 TTTTCATTGGGGATACTCTAACCCCGCTA
*
2136778 TTTTCGA--GGGGATACTCTAATCCCG
1 TTTTC-ATTGGGGATACTCTAACCCCG
2136803 ATTTTATTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
28 33 0.73
29 5 0.11
30 7 0.16
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTTCATTGGGGATACTCTAACCCCGCTA
Found at i:2136969 original size:78 final size:79
Alignment explanation
Indices: 2136758--2137013 Score: 261
Period size: 79 Copynumber: 3.2 Consensus size: 79
2136748 TATTTCATTG
* * *
2136758 GGGATACTCCAACCCTGCTATTTTCGAGGGGATACTCTAA-TCCCGATTTTATTTCCAAAACACC
1 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACT-CC-ATTTTATTTCCAAAACACC
2136822 AATTTTTTCACAATCA
64 AATTTTTTCACAATCA
* * * * * * *
2136838 GGGATGCTCCCACACCGTTATTTTCGA-GGGATACTCCAACCCCAGTTTTATTTCCAAAATATCG
1 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTCCA-TTTTATTTCCAAAACACCA
2136902 A-TTTTTCACAATC-
65 ATTTTTTCACAATCA
* * * * *
2136915 GGAGATACTCCAACCCCATTATTTTCAAGGGGATACTCCAACTCCAATTTATTTCCAGAACACCG
1 GG-GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTCCATTTTATTTCCAAAACACCA
* * *
2136980 A-TTTTCCATAGTCA
65 ATTTTTTCACAATCA
*
2136994 GGGGACACTCCAACCCCGTT
1 -GGGATACTCCAACCCCGTT
2137014 GTCATCTCCA
Statistics
Matches: 145, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
77 2 0.01
78 58 0.40
79 61 0.42
80 24 0.17
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTCCATTTTATTTCCAAAACACCAA
TTTTTTCACAATCA
Found at i:2138398 original size:19 final size:19
Alignment explanation
Indices: 2138374--2138410 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2138364 TAATTTTTTA
*
2138374 ATAAAAATTATTTAAAATT
1 ATAAAAATGATTTAAAATT
2138393 ATAAAAATGATTTAAAAT
1 ATAAAAATGATTTAAAAT
2138411 CTTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAAAAATGATTTAAAATT
Found at i:2138977 original size:4 final size:4
Alignment explanation
Indices: 2138963--2138992 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2138953 TAAAGTATGA
*
2138963 AATT CATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
2138993 AAAAATGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:2139803 original size:33 final size:33
Alignment explanation
Indices: 2139739--2139804 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2139729 GTTATTATAA
* *
2139739 TTTATATAAATTTTTGATACATTAATAATTTAT
1 TTTATATAAATATTTAATACATTAATAATTTAT
* *
2139772 TTTATATAAA-ATTTAATATATTCATACATTTAT
1 TTTATATAAATATTTAATACATTAATA-ATTTAT
2139805 ATCGTATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (33 bp):
TTTATATAAATATTTAATACATTAATAATTTAT
Found at i:2140886 original size:21 final size:20
Alignment explanation
Indices: 2140856--2140910 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
2140846 AGTTTTGTTG
*
2140856 TATATTAATTTATTTTATATTT
1 TATA-TAATTTATTATA-ATTT
2140878 TATATAATTTATTATAATTT
1 TATATAATTTATTATAATTT
*
2140898 T-T-TAATTTTTTAT
1 TATATAATTTATTAT
2140911 TTTAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 10 0.32
19 1 0.03
20 5 0.16
21 11 0.35
22 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATAATTTATTATAATTT
Found at i:2142297 original size:105 final size:105
Alignment explanation
Indices: 2142091--2142302 Score: 297
Period size: 105 Copynumber: 2.0 Consensus size: 105
2142081 TAAGGATCAT
* *
2142091 TTACATATATGTTTACATGGATATTTTCTCTAAGGATACCGAAGATAAAGAAAAAATAAAATTTA
1 TTACATATATATTTACATGGATATTTTCTCTAAGGACACCGAAGATAAAGAAAAAATAAAATTTA
*
2142156 ATATCATTAAATTTTTATTATTTTAGAAAGTGTTGTTTCA
66 ATATCATTAAATTTTTATTATTTTAAAAAGTGTTGTTTCA
* * *
2142196 TTACATATATATTTATATGGATATTTTTTTTAAGGACA-CGAAAGAT-AAG-AAAAA-AAAATTT
1 TTACATATATATTTACATGGATATTTTCTCTAAGGACACCG-AAGATAAAGAAAAAATAAAATTT
*
2142257 AATATCATTAAATTTTTATTATTTTAACAACAAGTTTTGTTTCA
65 AATATCATTAAATTTTTATTATTTT-A-AA-AAGTGTTGTTTCA
2142301 TT
1 TT
2142303 TTGAATTTTA
Statistics
Matches: 96, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
102 32 0.33
103 6 0.06
104 6 0.06
105 52 0.54
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (105 bp):
TTACATATATATTTACATGGATATTTTCTCTAAGGACACCGAAGATAAAGAAAAAATAAAATTTA
ATATCATTAAATTTTTATTATTTTAAAAAGTGTTGTTTCA
Found at i:2145376 original size:2 final size:2
Alignment explanation
Indices: 2145371--2145400 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2145361 GACAGATTTA
*
2145371 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2145401 TTAATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2145618 original size:17 final size:17
Alignment explanation
Indices: 2145596--2145668 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 17
2145586 TAACCATTAC
2145596 ATAATATAAAAAATAAA
1 ATAATATAAAAAATAAA
2145613 ATAATA-AAAATAATTTAAA
1 ATAATATAAAA-AA--TAAA
* *
2145632 A-ATTATAAAAATTAAA
1 ATAATATAAAAAATAAA
* *
2145648 A-AATTTTAAAAAT-AA
1 ATAATATAAAAAATAAA
2145663 ATAATA
1 ATAATA
2145669 AATAATATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
15 3 0.07
16 20 0.45
17 8 0.18
18 4 0.09
19 9 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATATAAAAAATAAA
Found at i:2145622 original size:9 final size:9
Alignment explanation
Indices: 2145596--2145675 Score: 58
Period size: 9 Copynumber: 8.7 Consensus size: 9
2145586 TAACCATTAC
2145596 ATAATATAAA
1 ATAATA-AAA
2145606 A-AAT-AAA
1 ATAATAAAA
2145613 ATAATAAAA
1 ATAATAAAA
2145622 ATAATTTAAAA
1 ATAA--TAAAA
*
2145633 ATTATAAAA
1 ATAATAAAA
*
2145642 ATTA-AAAA
1 ATAATAAAA
**
2145650 ATTTTAAAA
1 ATAATAAAA
2145659 ATAAATAATAA
1 AT-AATAA-AA
2145670 ATAATA
1 ATAATA
2145676 TAAGTAATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
7 4 0.07
8 10 0.17
9 25 0.42
10 8 0.14
11 12 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAATAAAA
Found at i:2145678 original size:9 final size:9
Alignment explanation
Indices: 2145596--2145686 Score: 54
Period size: 9 Copynumber: 10.9 Consensus size: 9
2145586 TAACCATTAC
2145596 ATAATATAA
1 ATAATATAA
*
2145605 AAAATA-AA
1 ATAATATAA
*
2145613 ATAATAAAA
1 ATAATATAA
*
2145622 ATAATTTAA
1 ATAATATAA
2145631 A-AATTATAA
1 ATAA-TATAA
2145640 A-AAT-TAA
1 ATAATATAA
* * *
2145647 AAAATTTTA
1 ATAATATAA
2145656 A-AA-ATAA
1 ATAATATAA
2145663 AT-A-ATAA
1 ATAATATAA
2145670 ATAATATAA
1 ATAATATAA
*
2145679 GTAATATA
1 ATAATATA
2145687 GAAGTTATAA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
7 14 0.21
8 16 0.24
9 36 0.55
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (9 bp):
ATAATATAA
Found at i:2145937 original size:15 final size:16
Alignment explanation
Indices: 2145917--2145948 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2145907 ATCAATATAC
2145917 AAAAAAATTAGTTTAA
1 AAAAAAATTAGTTTAA
*
2145933 AAAAAAATTGGTTTAA
1 AAAAAAATTAGTTTAA
2145949 TTTAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (16 bp):
AAAAAAATTAGTTTAA
Found at i:2153993 original size:20 final size:19
Alignment explanation
Indices: 2153959--2153996 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2153949 TTAAAAATTA
*
2153959 ATTTTATATATAAATATAG
1 ATTTTATAAATAAATATAG
2153978 ATTTTAATAAATAAATATA
1 ATTTT-ATAAATAAATATA
2153997 TTAAAATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTTATAAATAAATATAG
Found at i:2154695 original size:51 final size:52
Alignment explanation
Indices: 2154633--2154771 Score: 181
Period size: 52 Copynumber: 2.7 Consensus size: 52
2154623 TTTGAAATGA
* * * *
2154633 AAATGTATCGATATATTTTTCATTGTATCGATACATTTTGGG-TTTTGACTC
1 AAATGTATCGATACATTCTTCATTATATCGATACATTTTGGGTTTTTGACCC
* *
2154684 AAATGTATCGATACATTCTTCATTATATCAATAAATTTTGGGTTTTTGACCC
1 AAATGTATCGATACATTCTTCATTATATCGATACATTTTGGGTTTTTGACCC
* * * *
2154736 AAATATATTGATACATTCTTCAATATATTGATACAT
1 AAATGTATCGATACATTCTTCATTATATCGATACAT
2154772 AGAGGTAATT
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 37 0.49
52 38 0.51
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTATATCGATACATTTTGGGTTTTTGACCC
Found at i:2154750 original size:52 final size:51
Alignment explanation
Indices: 2154633--2154763 Score: 172
Period size: 51 Copynumber: 2.5 Consensus size: 51
2154623 TTTGAAATGA
* * * * * *
2154633 AAATGTATCGATATATTTTTCATTGTATCGATACATTTTGGGTTTTGACTC
1 AAATGTATCGATACATTCTTCATTATATCAATAAATTTTGGGTTTTGACCC
2154684 AAATGTATCGATACATTCTTCATTATATCAATAAATTTTGGGTTTTTGACCC
1 AAATGTATCGATACATTCTTCATTATATCAATAAATTTTGGG-TTTTGACCC
* * *
2154736 AAATATATTGATACATTCTTCAATATAT
1 AAATGTATCGATACATTCTTCATTATAT
2154764 TGATACATAG
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 37 0.53
52 33 0.47
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (51 bp):
AAATGTATCGATACATTCTTCATTATATCAATAAATTTTGGGTTTTGACCC
Found at i:2155387 original size:10 final size:10
Alignment explanation
Indices: 2155372--2155398 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2155362 AACTTCAACC
2155372 TCATTTTCTA
1 TCATTTTCTA
2155382 TCATTTTCTA
1 TCATTTTCTA
2155392 TCATTTT
1 TCATTTT
2155399 TGATACAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.63
Consensus pattern (10 bp):
TCATTTTCTA
Found at i:2155487 original size:13 final size:13
Alignment explanation
Indices: 2155466--2155496 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2155456 CGATACATGG
*
2155466 TACAATGTATCGA
1 TACATTGTATCGA
2155479 TACATTGTATCGA
1 TACATTGTATCGA
2155492 TACAT
1 TACAT
2155497 GATGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:2157711 original size:13 final size:13
Alignment explanation
Indices: 2157693--2157717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2157683 CAATTTTTTG
2157693 TGTATCGATACAT
1 TGTATCGATACAT
2157706 TGTATCGATACA
1 TGTATCGATACA
2157718 AACTTGCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2160276 original size:13 final size:13
Alignment explanation
Indices: 2160258--2160296 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2160248 ATAATCACCT
*
2160258 TGTATCGATACAG
1 TGTATCGATACAA
2160271 TGTATCGATACAA
1 TGTATCGATACAA
2160284 TGTATCGATACAA
1 TGTATCGATACAA
2160297 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2160307 original size:20 final size:20
Alignment explanation
Indices: 2160282--2160360 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
2160272 GTATCGATAC
2160282 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
2160302 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
2160327 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
2160347 CATGTATCGATACA
1 AATGTATCGATACA
2160361 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2160511 original size:8 final size:8
Alignment explanation
Indices: 2160498--2160529 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
2160488 CATCATTCAA
2160498 CACAAAAT
1 CACAAAAT
2160506 CACAAAAT
1 CACAAAAT
2160514 CACAAAAT
1 CACAAAAT
2160522 CACAAAAT
1 CACAAAAT
2160530 TTAATCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.12
Consensus pattern (8 bp):
CACAAAAT
Found at i:2166680 original size:13 final size:13
Alignment explanation
Indices: 2166662--2166686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2166652 CAATTTTTTG
2166662 TGTATCGATACAT
1 TGTATCGATACAT
2166675 TGTATCGATACA
1 TGTATCGATACA
2166687 AACTTGCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2167812 original size:23 final size:21
Alignment explanation
Indices: 2167786--2167827 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
2167776 AAAGGGAAAA
2167786 AAGAAAAAAGGAAAAGAGAAATG
1 AAGAAAAAA-G-AAAGAGAAATG
*
2167809 AAGAGAAAAGAAAGAGAAA
1 AAGAAAAAAGAAAGAGAAA
2167828 GAGAGAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 1 0.06
23 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (21 bp):
AAGAAAAAAGAAAGAGAAATG
Found at i:2167814 original size:10 final size:11
Alignment explanation
Indices: 2167798--2167844 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
2167788 GAAAAAAGGA
2167798 AAAGAGAAATG
1 AAAGAGAAATG
*
2167809 -AAGAGAAAAG
1 AAAGAGAAATG
2167819 AAAGAGAAA-G
1 AAAGAGAAATG
2167829 --AGAG-AATG
1 AAAGAGAAATG
2167837 AAAGAGAA
1 AAAGAGAA
2167845 GGAGATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
7 2 0.07
8 5 0.17
10 14 0.47
11 9 0.30
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (11 bp):
AAAGAGAAATG
Found at i:2167857 original size:28 final size:26
Alignment explanation
Indices: 2167787--2167844 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2167777 AAGGGAAAAA
*
2167787 AGAAAA-AAGGAAAAGAGAAATGAAG
1 AGAAAAGAAAGAAAAGAGAAATGAAG
2167812 AGAAAAGAAAGAGAAAGAGAGAATGAAAG
1 AGAAAAGAAAGA-AAAGAGA-AATG-AAG
2167841 AGAA
1 AGAA
2167845 GGAGATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 6 0.21
26 4 0.14
27 7 0.25
28 4 0.14
29 7 0.25
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.03
Consensus pattern (26 bp):
AGAAAAGAAAGAAAAGAGAAATGAAG
Found at i:2167897 original size:17 final size:17
Alignment explanation
Indices: 2167875--2167908 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2167865 AGGGAATTGC
2167875 GAAAGAAAAAAAAAAGA
1 GAAAGAAAAAAAAAAGA
*
2167892 GAAAGAAAGAAAAAAGA
1 GAAAGAAAAAAAAAAGA
2167909 AAGGGGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAAAAAAAGA
Found at i:2167900 original size:21 final size:21
Alignment explanation
Indices: 2167875--2167942 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
2167865 AGGGAATTGC
2167875 GAAAGAAAAAAAAAAGAGAAA
1 GAAAGAAAAAAAAAAGAGAAA
* **
2167896 GAAAGAAAAAAGAAAG-GGGA
1 GAAAGAAAAAAAAAAGAGAAA
2167916 GAAAAGAAAAAGAAAAA-AGATAA
1 G-AAAGAAAAA-AAAAAGAGA-AA
2167939 GAAA
1 GAAA
2167943 ATTTTGTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.08
21 24 0.65
22 8 0.22
23 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (21 bp):
GAAAGAAAAAAAAAAGAGAAA
Found at i:2168053 original size:20 final size:19
Alignment explanation
Indices: 2168030--2168096 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
2168020 AATAATTCAT
2168030 TTTATATATATTTTTATATA
1 TTTATAT-TATTTTTATATA
* *
2168050 TTTAT-GTATTTATATTATA
1 TTTATATTATTTTTA-TATA
2168069 TTTATATTATTTTTATACTA
1 TTTATATTATTTTTATA-TA
*
2168089 TTTTTATT
1 TTTATATT
2168097 CATATAGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.18
19 11 0.28
20 21 0.54
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTATATTATTTTTATATA
Found at i:2168072 original size:11 final size:11
Alignment explanation
Indices: 2168056--2168095 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2168046 TATATTTATG
2168056 TATTTATATTA
1 TATTTATATTA
2168067 TATTTATATTA
1 TATTTATATTA
* *
2168078 TTTTTATACTA
1 TATTTATATTA
*
2168089 TTTTTAT
1 TATTTAT
2168096 TCATATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTATATTA
Found at i:2168078 original size:16 final size:16
Alignment explanation
Indices: 2168031--2168078 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 16
2168021 ATAATTCATT
*
2168031 TTATA-TATATTTTTA
1 TTATATTATATTTATA
*
2168046 -TATATT-TATGTAT-
1 TTATATTATATTTATA
2168059 TTATATTATATTTATA
1 TTATATTATATTTATA
2168075 TTAT
1 TTAT
2168079 TTTTATACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
14 15 0.58
15 7 0.27
16 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATATTATATTTATA
Found at i:2168121 original size:20 final size:19
Alignment explanation
Indices: 2168089--2168127 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2168079 TTTTATACTA
*
2168089 TTTTTATTCATATAGATTT
1 TTTTTATTAATATAGATTT
*
2168108 TTTTATATTAATATTGATTT
1 TTTT-TATTAATATAGATTT
2168128 ATATAGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTATTAATATAGATTT
Found at i:2168134 original size:30 final size:30
Alignment explanation
Indices: 2168050--2168137 Score: 69
Period size: 30 Copynumber: 3.0 Consensus size: 30
2168040 TTTTTATATA
* * *
2168050 TTTATGTATTTATATTATATTTATAT-TATT
1 TTTATATATTAATATT-TATTTATATAGATT
*
2168080 TTTATACTA-T--T-TTTATTCATATAGATT
1 TTTATA-TATTAATATTTATTTATATAGATT
* *
2168107 TTTTTATATTAATATTGATTTATATAGATT
1 TTTATATATTAATATTTATTTATATAGATT
2168137 T
1 T
2168138 GATATGTTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
26 10 0.22
27 11 0.24
28 1 0.02
29 1 0.02
30 21 0.46
31 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTATATATTAATATTTATTTATATAGATT
Found at i:2168890 original size:15 final size:16
Alignment explanation
Indices: 2168860--2168892 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2168850 AAAAATTTAA
*
2168860 AATATAATTATAATTT
1 AATAAAATTATAATTT
2168876 AATAAAATT-TAATTT
1 AATAAAATTATAATTT
2168891 AA
1 AA
2168893 AATTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAAAATTATAATTT
Found at i:2168898 original size:21 final size:21
Alignment explanation
Indices: 2168857--2168899 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2168847 TAAAAAAATT
*
2168857 TAAAATATAATTATAATTTAA
1 TAAAATATAATTATAAATTAA
*
2168878 TAAAATTTAATT-TAAAATTAA
1 TAAAATATAATTAT-AAATTAA
2168899 T
1 T
2168900 TTTTATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATATAATTATAAATTAA
Found at i:2169598 original size:16 final size:16
Alignment explanation
Indices: 2169577--2169607 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2169567 GTGTTTATAA
2169577 AAATTAATAAATAAAT
1 AAATTAATAAATAAAT
*
2169593 AAATTATTAAATAAA
1 AAATTAATAAATAAA
2169608 CGTTTGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTAATAAATAAAT
Found at i:2188212 original size:32 final size:32
Alignment explanation
Indices: 2188153--2188232 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
2188143 ATATTATTTG
* * *
2188153 TAAATTTGAT-AA-ATTAAATATATTTACTTA
1 TAAATTTGATAAATATTAAATAAAATTACTCA
2188183 TAAATTTGATAAATATTAAATAAAATTACTCA
1 TAAATTTGATAAATATTAAATAAAATTACTCA
*
2188215 TAAATTTAATAAATATTA
1 TAAATTTGATAAATATTA
2188233 TAGTAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 10 0.23
31 2 0.05
32 32 0.73
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (32 bp):
TAAATTTGATAAATATTAAATAAAATTACTCA
Found at i:2188384 original size:22 final size:22
Alignment explanation
Indices: 2188356--2188405 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2188346 TTAAAATATT
2188356 ATATATAATTAATGAGTATTTG
1 ATATATAATTAATGAGTATTTG
*
2188378 ATATATAATTAGTGAGTATTTG
1 ATATATAATTAATGAGTATTTG
2188400 ATATAT
1 ATATAT
2188406 GAAATCTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (22 bp):
ATATATAATTAATGAGTATTTG
Found at i:2188446 original size:21 final size:21
Alignment explanation
Indices: 2188422--2188461 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2188412 TATTTAGTCT
*
2188422 TATTTATTTA-ATATTTAAAAA
1 TATTT-TTTATATATATAAAAA
2188443 TATTTTTTATATATATAAA
1 TATTTTTTATATATATAAA
2188462 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTTTATATATATAAAAA
Found at i:2192598 original size:13 final size:13
Alignment explanation
Indices: 2192580--2192607 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2192570 ATTACTCAAA
2192580 TGTATCGATACAT
1 TGTATCGATACAT
2192593 TGTATCGATACAT
1 TGTATCGATACAT
2192606 TG
1 TG
2192608 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2193221 original size:21 final size:21
Alignment explanation
Indices: 2193195--2193271 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
2193185 AAATAATCCA
2193195 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2193216 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
2193237 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
2193258 AATGTATCGATACA
1 AATGTATCGATACA
2193272 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2193331 original size:19 final size:18
Alignment explanation
Indices: 2193307--2193376 Score: 78
Period size: 19 Copynumber: 4.1 Consensus size: 18
2193297 AATTCAACAA
2193307 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAA-T
2193326 TTTGTATCGATAC--AA-
1 TTTGTATCGATACATAAT
2193341 --TGTATCGATACATAAAT
1 TTTGTATCGATACAT-AAT
*
2193358 ATTGTATCGATACATAAT
1 TTTGTATCGATACATAAT
2193376 T
1 T
2193377 AGCTACTGCC
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.25
16 2 0.05
17 2 0.05
18 3 0.07
19 26 0.59
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAT
Found at i:2193346 original size:13 final size:13
Alignment explanation
Indices: 2193328--2193352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2193318 ACATAAGTTT
2193328 TGTATCGATACAA
1 TGTATCGATACAA
2193341 TGTATCGATACA
1 TGTATCGATACA
2193353 TAAATATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2193350 original size:32 final size:32
Alignment explanation
Indices: 2193309--2193371 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2193299 TTCAACAATT
* *
2193309 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAATATTGTATCGATACAA
2193341 TGTATCGATACATAAATATTGTATCGATACA
1 TGTATCGATACATAAATATTGTATCGATACA
2193372 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCGATACAA
Found at i:2193432 original size:13 final size:13
Alignment explanation
Indices: 2193414--2193439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2193404 CATTTTTCTG
2193414 TGTATCGATACAT
1 TGTATCGATACAT
2193427 TGTATCGATACAT
1 TGTATCGATACAT
2193440 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2193436 original size:33 final size:33
Alignment explanation
Indices: 2193394--2193460 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2193384 GCCAAGGAAA
***
2193394 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2193427 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2193460 T
1 T
2193461 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2195967 original size:52 final size:50
Alignment explanation
Indices: 2195787--2196021 Score: 245
Period size: 51 Copynumber: 4.6 Consensus size: 50
2195777 TTGAGTTTCT
* * * *
2195787 CAATTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACAC
1 CAATTTTCCACAATCGGGGATACTCCAACT-CGATTTTATTTCCAAAACAC
* * * * * * *
2195838 TAATTTTCTATAATCGGGGATACTCAAACTCCGGTTTTATTTCCAAATCAT
1 CAATTTTCCACAATCGGGGATACTCCAACT-CGATTTTATTTCCAAAACAC
** *
2195889 CAATTTTCCACAATCGGGGATACTCCAACCTCGGCTTTATTTTCAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAA-CTCGATTTTATTTCCAAAACAC
**
2195940 CAATTTTCCTTTAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACTC-GATTTTATTTCC-AAAACAC
* * *
2195993 CAATTTTTCACAATTGAGGATACTCCAAC
1 CAATTTTCCACAATCGGGGATACTCCAAC
2196022 CTCGTTATTT
Statistics
Matches: 151, Mismatches: 29, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
51 92 0.61
52 44 0.29
53 15 0.10
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (50 bp):
CAATTTTCCACAATCGGGGATACTCCAACTCGATTTTATTTCCAAAACAC
Found at i:2208657 original size:14 final size:14
Alignment explanation
Indices: 2208638--2208672 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2208628 CTTCTCTTCC
2208638 AAAAAAAAAAACAA
1 AAAAAAAAAAACAA
*
2208652 AAAAAACAAAACAA
1 AAAAAAAAAAACAA
*
2208666 AGAAAAA
1 AAAAAAA
2208673 GAGAGAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAACAA
Found at i:2209762 original size:60 final size:55
Alignment explanation
Indices: 2209653--2210188 Score: 546
Period size: 55 Copynumber: 9.4 Consensus size: 55
2209643 TCCTTCCGCT
* * *
2209653 TTTTAGTCCTCAAAGAGTAGGACGC-CTTTTAAAGCCCACACAAGTTGGTGGCATT
1 TTTTAGTCCTCAAAGAGCAGGACGCTCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * * *
2209708 TTTTAGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACATAAGTTGGTGGGAC
1 TTTTAGTCCTCAAAGAGCAGGACGC----TCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
2209767 CTTTAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCAC
1 TTTTAGTCCTCAAAGAGCAGGACG-C---TCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
2209826 CTTCAGTCCTCAAAGAGCAGGATGCTTTTGCCTTTCAAAGCCCACACAAGTTGGTGGCAC
1 TTTTAGTCCTCAAAGAGCAGGACGC---T--CTTTCAAAGCCCACACAAGTTGGTGGCAC
* **
2209886 CTTTAGTCCTCAAAGAGCAGGATACTTTTTCTTGTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGG--AC--GCTCTT-TCAAAGCCCACACAAGTTGGTGGCA-C
* * * *
2209947 TTTCAGTCCCCAAAGAGCAGGAC-CCCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTTAGTCCTCAAAGAGCAGGACGCTCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
2210001 TTTCTAGTCCTCAAAGAGCAGGACAC-CTTTCAAAGCCTACACAAGTTGGTGGCA-
1 TTT-TAGTCCTCAAAGAGCAGGACGCTCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
2210055 TGTTCCAGTCCTCAAAGAGCAGGACAC-CTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 T-TT-TAGTCCTCAAAGAGCAGGACGCTCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
* *
2210112 TTTCAGTCCTCAAAGAGCAGGACGC-CTTTCAAAGCCCACACGAGTTGGTGGCAC
1 TTTTAGTCCTCAAAGAGCAGGACGCTCTTTCAAAGCCCACACAAGTTGGTGGCAC
2210166 TTTTTAGTCCTCAAAGAGCAGGA
1 -TTTTAGTCCTCAAAGAGCAGGA
2210189 TACACTTTAT
Statistics
Matches: 427, Mismatches: 32, Indels: 44
0.85 0.06 0.09
Matches are distributed among these distances:
54 7 0.02
55 207 0.48
56 8 0.02
57 1 0.00
58 5 0.01
59 79 0.19
60 99 0.23
61 20 0.05
62 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (55 bp):
TTTTAGTCCTCAAAGAGCAGGACGCTCTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:2210943 original size:19 final size:19
Alignment explanation
Indices: 2210919--2210986 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
2210909 AATTCAACAA
2210919 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2210938 TTTGTATCAATAC--AA--
1 TTTGTATCGATACATAAGT
2210953 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2210970 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2210987 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2210962 original size:32 final size:32
Alignment explanation
Indices: 2210921--2210983 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2210911 TTCAACAATT
*
2210921 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
*
2210953 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
2210984 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:2211044 original size:13 final size:13
Alignment explanation
Indices: 2211026--2211051 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2211016 CATTTTTCTG
2211026 TGTATCGATACAT
1 TGTATCGATACAT
2211039 TGTATCGATACAT
1 TGTATCGATACAT
2211052 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2211048 original size:33 final size:33
Alignment explanation
Indices: 2211006--2211072 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2210996 GCCAAGGAAA
***
2211006 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2211039 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2211072 T
1 T
2211073 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2213594 original size:52 final size:52
Alignment explanation
Indices: 2213412--2213635 Score: 213
Period size: 51 Copynumber: 4.3 Consensus size: 52
2213402 AATTCTCCAC
* * * *
2213412 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTT-CTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCTAT
* * * * * *
2213463 AATCGGGGATACTCTAACTCCGGTTTTATTTCCAAATCATCGATTTTCC-AC
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCTAT
** ** * *
2213514 AATAAGGGATACTCCAAC-CTCGGCTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACTC-CGATTTTATTTCCAAAACACCAATTTTCCTAT
* * *
2213566 AATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTC-AC
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACACCAATTTTCCTAT
* *
2213618 AATTGAGGATACTCCAAC
1 AATCGGGGATACTCCAAC
2213636 CTCGTTATTT
Statistics
Matches: 137, Mismatches: 31, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
50 1 0.01
51 78 0.57
52 42 0.31
53 16 0.12
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (52 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCTAT
Found at i:2225157 original size:1 final size:1
Alignment explanation
Indices: 2225151--2225189 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
2225141 AAAGTGTTTG
***
2225151 AAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2225190 TTTTAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.92, C:0.00, G:0.03, T:0.05
Consensus pattern (1 bp):
A
Found at i:2225172 original size:19 final size:19
Alignment explanation
Indices: 2225148--2225185 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2225138 GATAAAGTGT
2225148 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
2225167 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
2225186 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
TTGAAAAAAAAAAAAAAAA
Found at i:2225219 original size:21 final size:21
Alignment explanation
Indices: 2225195--2225251 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2225185 AAAAATTTTA
2225195 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2225216 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2225237 AATGTATCGATACAT
1 AATGTATCGATACAT
2225252 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2225331 original size:19 final size:19
Alignment explanation
Indices: 2225307--2225374 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2225297 AATTCAACAA
2225307 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2225326 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2225341 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2225358 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2225375 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2225346 original size:13 final size:13
Alignment explanation
Indices: 2225328--2225352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2225318 ACATAAGTTT
2225328 TGTATCGATACAA
1 TGTATCGATACAA
2225341 TGTATCGATACA
1 TGTATCGATACA
2225353 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2225350 original size:32 final size:32
Alignment explanation
Indices: 2225309--2225371 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2225299 TTCAACAATT
*
2225309 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2225341 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2225372 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2227986 original size:28 final size:27
Alignment explanation
Indices: 2227919--2227989 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
2227909 CTTCACAATC
* *
2227919 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
2227946 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
2227974 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
2227990 TGACTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:2228034 original size:51 final size:50
Alignment explanation
Indices: 2227974--2228145 Score: 173
Period size: 51 Copynumber: 3.3 Consensus size: 50
2227964 TTATTTCTGA
* * *
2227974 GGGGATACTCCAACCCTGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCC-GATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
2228025 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTCAAAATACCAATTT-TTC-AT-AATC
* * *
2228079 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
2228131 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2228146 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
51 33 0.34
52 21 0.22
53 1 0.01
54 31 0.32
55 11 0.11
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:2228164 original size:28 final size:28
Alignment explanation
Indices: 2228128--2228209 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
2228118 ATTTTTCACA
*
2228128 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
2228156 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
2228184 --CGAGGGAACACTCCAATCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
2228210 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 40 0.89
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:2231682 original size:52 final size:52
Alignment explanation
Indices: 2231604--2231752 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 52
2231594 CGAAATATGA
2231604 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* * *
2231656 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *** *
2231708 AAATTTTCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACA
2231753 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 87 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:2231759 original size:13 final size:13
Alignment explanation
Indices: 2231741--2231765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2231731 CAAAGATTAG
2231741 TGTATCGATACAA
1 TGTATCGATACAA
2231754 TGTATCGATACA
1 TGTATCGATACA
2231766 TTTTTTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2231822 original size:33 final size:33
Alignment explanation
Indices: 2231785--2231851 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2231775 AGTAGCTTAA
2231785 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2231818 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2231851 A
1 A
2231852 AATCGTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2231825 original size:13 final size:13
Alignment explanation
Indices: 2231807--2231831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2231797 CAAAAAAATA
2231807 TGTATCGATACAT
1 TGTATCGATACAT
2231820 TGTATCGATACA
1 TGTATCGATACA
2231832 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2237634 original size:56 final size:57
Alignment explanation
Indices: 2237551--2237663 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
2237541 TCACCCTTCA
* *
2237551 AAAGCCCAGAAGTCAGTGGCAACCTTC-AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
*
2237607 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCCGTGGCATCTTTTTC
1 AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
2237664 CTTTTAAGCC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 25 0.47
57 28 0.53
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (57 bp):
AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:2237653 original size:28 final size:27
Alignment explanation
Indices: 2237545--2237655 Score: 141
Period size: 27 Copynumber: 4.0 Consensus size: 27
2237535 CATTCCTCAC
*
2237545 CCTTCAAAAGCCCAGAAGTCAGTGGCAA
1 CCTTC-AAAGCCCACAAGTCAGTGGCAA
*
2237573 CCTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTCAAAGCCCACAAGTCAGTGGCAA
* *
2237600 CTTTTTCAAAGCCCACAAATCAGTGGCAA
1 C--CTTCAAAGCCCACAAGTCAGTGGCAA
*
2237629 CCTTCAAAAGCCCACAAGTCCGTGGCA
1 CCTTC-AAAGCCCACAAGTCAGTGGCA
2237656 TCTTTTTCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 24 0.33
28 24 0.33
29 24 0.33
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (27 bp):
CCTTCAAAGCCCACAAGTCAGTGGCAA
Found at i:2237701 original size:32 final size:32
Alignment explanation
Indices: 2237636--2237725 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
2237626 CAACCTTCAA
* *
2237636 AAGCCCACAAGTCCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTCCTTTT
* *
2237669 AAGCCCACAACTCCATGGCACCTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
2237701 AAGCCCACAACTCCGTGGCACCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
2237726 AAGCCCAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
32 34 0.65
33 18 0.35
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.31
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:2237830 original size:35 final size:33
Alignment explanation
Indices: 2237774--2237874 Score: 114
Period size: 35 Copynumber: 3.0 Consensus size: 33
2237764 CCTTTTGTTT
* *
2237774 TTTTAAGTCCACAATTCCGTGGCACTCCTTTTCT
1 TTTTAAGCCCACAATT-CGTGGCACTCCTTTTCC
* *
2237808 TTTGTAAGCTCACAACTTCGTGGCACTCTTTTTCC
1 TTT-TAAGCCCACAA-TTCGTGGCACTCCTTTTCC
*
2237843 TTTTAAGCCCACAAGTCAGTGGCAC-CCTTTTC
1 TTTTAAGCCCACAATTC-GTGGCACTCCTTTTC
2237875 AAAAGCCCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
33 8 0.14
34 20 0.35
35 27 0.47
36 2 0.04
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.38
Consensus pattern (33 bp):
TTTTAAGCCCACAATTCGTGGCACTCCTTTTCC
Found at i:2237882 original size:30 final size:29
Alignment explanation
Indices: 2237847--2237942 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 29
2237837 TTTTCCTTTT
2237847 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCACCC-TTTCAA
*
2237877 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCACCCTTTCAA
* **
2237905 AAGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAGTGGC-ACCCTTTCAA
2237934 AAGCCCACA
1 AAGCCCACA
2237943 CAAGTTGGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.03
28 21 0.36
29 13 0.22
30 22 0.38
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCACCCTTTCAA
Found at i:2237946 original size:31 final size:30
Alignment explanation
Indices: 2237866--2237952 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 30
2237856 AGTCAGTGGC
**
2237866 ACCCTTTTCAAAAGCC-CACAAGTCAGTGGCA
1 ACCC-TTTCAAAAGCCACACAAGTTGGT-GCA
2237897 A-CC-TTCAAAAG-CACACAAGTTGGTGCA
1 ACCCTTTCAAAAGCCACACAAGTTGGTGCA
2237924 ACCCTTTCAAAAGCCCACACAAGTTGGTG
1 ACCCTTTCAAAAG-CCACACAAGTTGGTG
2237953 GCGTCTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
27 5 0.10
28 19 0.39
29 8 0.16
30 2 0.04
31 15 0.31
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (30 bp):
ACCCTTTCAAAAGCCACACAAGTTGGTGCA
Found at i:2238031 original size:48 final size:48
Alignment explanation
Indices: 2237977--2238383 Score: 438
Period size: 48 Copynumber: 8.5 Consensus size: 48
2237967 GTCCAATATT
2237977 GCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTC
* * * * * *
2238025 GTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTATGTCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTC
* * * *
2238074 ACTGGTCC-TAAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTC
1 GCTGG-CCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTC
* * * * *
2238122 GTTGGCCTTGAATTAGCACATTGG---C--A----TAAGCCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTC
* *
2238161 GCTGGCCTTAAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTC
* *
2238209 GCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAACGTC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTC
*
2238257 GCTGGCCTTGAATCAGCATATTGGCACTTTAACCATCTTTAAGACCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCACCTT----ATCTTTAAGACCAATGTC
* * * * *
2238309 GCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATT
1 GCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTC
* *
2238358 GTTGGCCTTAAATCAGCATATTGGCA
1 GCTGGCCTTGAATCAGCATATTGGCA
2238384 TCTTTAACAT
Statistics
Matches: 299, Mismatches: 44, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
39 31 0.10
42 1 0.00
45 1 0.00
47 2 0.01
48 142 0.47
49 77 0.26
50 2 0.01
52 43 0.14
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (48 bp):
GCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTC
Found at i:2238168 original size:39 final size:39
Alignment explanation
Indices: 2238109--2238186 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
2238099 ACCTTGTCTC
* * * *
2238109 TAAGACCAATGTCGTTGGCCTTGAATTAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCA
* *
2238148 TAAGCCCAATATCGCTGGCCTTAAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCA
2238187 CCTTGTCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCA
Found at i:2238215 original size:87 final size:88
Alignment explanation
Indices: 2238066--2238334 Score: 299
Period size: 87 Copynumber: 2.9 Consensus size: 88
2238056 ATCTTTATGT
* * *
2238066 CCAATATCACTGGTCC-TAAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGTTGGCCT
1 CCAATATCGCTGG-CCTTAAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCT
* *
2238130 TGAATTAGCACATTGGCA-TAAGC
65 TGAATCAGCACATTGGCATTAAGA
2238153 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
*
2238218 GAATCAGCATATTGGCACCTTGTCTTTAAGA
66 GAATCAGCACATTGGCA--------TTAAGA
** * * *
2238249 CCAACGTCGCTGGCCTTGAATCAGCATATTGGCACTTTAACCATCTTTAAGACCAATGTCGCTGG
1 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTT----GTCTTTAAGACCAATGTCGCTGG
*
2238314 CCTTAAATCAGCACATTGGCA
62 CCTTGAATCAGCACATTGGCA
2238335 CCTTCATCTT
Statistics
Matches: 155, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
86 2 0.01
87 74 0.48
96 38 0.25
100 41 0.26
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (88 bp):
CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCATTAAGA
Found at i:2238263 original size:135 final size:136
Alignment explanation
Indices: 2238012--2238383 Score: 390
Period size: 135 Copynumber: 2.6 Consensus size: 136
2238002 ACCTTATCTT
* * * * * *
2238012 TAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTATGTCCAATATCACT
1 TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCACT
* * *
2238077 GGTCCTAAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGTTGGCCTTGAATTAGCACA
66 GGTCCTAAATCAGCATATTGGCACCTTGTCTCTAAGACCAACGTCGCTGGCCTTGAATCAGCACA
2238142 TTGGCA
131 TTGGCA
* * * * *
2238148 TAAGCCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCGCT
1 TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCACT
* * *
2238212 GG-CCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAACGTCGCTGGCCTTGAATCAGCAT
66 GGTCC-TAAATCAGCATATTGGCACCTTGTCTCTAAGACCAACGTCGCTGGCCTTGAATCAGCAC
2238276 ATTGGCACTTTAACCA
130 ATTGG---------CA
* *
2238292 TCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
1 ----TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGACCAATAT
***
2238357 TGTTGG-CCTTAAATCAGCATATTGGCA
62 CACTGGTCC-TAAATCAGCATATTGGCA
2238384 TCTTTAACAT
Statistics
Matches: 195, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
134 2 0.01
135 76 0.39
136 37 0.19
144 2 0.01
148 40 0.21
149 38 0.19
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (136 bp):
TAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCACT
GGTCCTAAATCAGCATATTGGCACCTTGTCTCTAAGACCAACGTCGCTGGCCTTGAATCAGCACA
TTGGCA
Found at i:2238332 original size:100 final size:100
Alignment explanation
Indices: 2238148--2238393 Score: 329
Period size: 100 Copynumber: 2.5 Consensus size: 100
2238138 CACATTGGCA
* * * *
2238148 TAAGCCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTT---GTCTTTAAGACCAATGTCG
1 TAAGACCAACATCGCTGGCCTTAAATCAGCATATTGGCACTTTAACATCTTTAAGACCAATGTCG
* * *
2238210 CTGGCCTTGAATCAGCATATTGGCACCTT-GTCTT
66 CTGGCCTTAAATCAGCACATTGGCACCTTCATCTT
* *
2238244 TAAGACCAACGTCGCTGGCCTTGAATCAGCATATTGGCACTTTAACCATCTTTAAGACCAATGTC
1 TAAGACCAACATCGCTGGCCTTAAATCAGCATATTGGCACTTTAA-CATCTTTAAGACCAATGTC
2238309 GCTGGCCTTAAATCAGCACATTGGCACCTTCATCTT
65 GCTGGCCTTAAATCAGCACATTGGCACCTTCATCTT
* * * *
2238345 TAAGTCCAATATTGTTGGCCTTAAATCAGCATATTGGCATCTTTAACAT
1 TAAGACCAACATCGCTGGCCTTAAATCAGCATATTGGCA-CTTTAACAT
2238394 TCCTAAGCCC
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
96 38 0.29
100 45 0.35
101 40 0.31
102 6 0.05
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (100 bp):
TAAGACCAACATCGCTGGCCTTAAATCAGCATATTGGCACTTTAACATCTTTAAGACCAATGTCG
CTGGCCTTAAATCAGCACATTGGCACCTTCATCTT
Found at i:2238410 original size:49 final size:47
Alignment explanation
Indices: 2238163--2238410 Score: 148
Period size: 48 Copynumber: 5.0 Consensus size: 47
2238153 CCAATATCGC
* ** *
2238163 TGGCCTTAAATCAGCATATTGGCACCTTGTC-TT-TAAGACCAATGT
1 TGGCCTTAAATCAGCATATTGGCACTTTAACATTCTAAGCCCAATGT
* * ** * *
2238208 CGCTGGCCTTGAATCAGCATATTGGCACCTTGTC-TT-TAAGACCAACGTCGC
1 ---TGGCCTTAAATCAGCATATTGGCACTTTAACATTCTAAGCCCAA--T-GT
* * *
2238259 TGGCCTTGAATCAGCATATTGGCACTTTAACCATCTTTAAGACCAATGT
1 TGGCCTTAAATCAGCATATTGGCACTTTAA-CAT-TCTAAGCCCAATGT
* * * *
2238308 CGCTGGCCTTAAATCAGCACATTGGCACCTT--CATCTTTAAGTCCAATATTGT
1 ---TGGCCTTAAATCAGCATATTGGCACTTTAACAT-TCTAAG-CCCA-A-TGT
2238360 TGGCCTTAAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGT
1 TGGCCTTAAATCAGCATATTGGCA-CTTTAACATT-CTAAGCCCAATGT
2238409 TG
1 TG
2238411 CTAGCTTTGT
Statistics
Matches: 168, Mismatches: 15, Indels: 33
0.78 0.07 0.15
Matches are distributed among these distances:
48 68 0.40
49 40 0.24
50 9 0.05
51 7 0.04
52 44 0.26
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (47 bp):
TGGCCTTAAATCAGCATATTGGCACTTTAACATTCTAAGCCCAATGT
Found at i:2245657 original size:13 final size:13
Alignment explanation
Indices: 2245639--2245676 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2245629 ATAATCCCCC
2245639 TGTATCGATACAG
1 TGTATCGATACAG
*
2245652 TGTATCGATACAT
1 TGTATCGATACAG
2245665 TGTATCGATACA
1 TGTATCGATACA
2245677 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2247775 original size:15 final size:15
Alignment explanation
Indices: 2247755--2247785 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2247745 ATTTCGTTTG
*
2247755 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2247770 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2247785 G
1 G
2247786 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2251859 original size:20 final size:20
Alignment explanation
Indices: 2251834--2251885 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
2251824 TACAAGCCAA
**
2251834 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
2251854 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
2251873 TGTATCGATACAA
1 TGTATCGATACAA
2251886 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:2252994 original size:76 final size:78
Alignment explanation
Indices: 2252893--2253096 Score: 227
Period size: 76 Copynumber: 2.6 Consensus size: 78
2252883 GAGATAATAA
* * * * *
2252893 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
2252957 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* **
2252969 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* *
2253034 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * *
2253048 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
2253097 GAAATAACGA
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
75 7 0.07
76 48 0.45
77 2 0.02
78 3 0.03
79 46 0.43
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:2253005 original size:28 final size:28
Alignment explanation
Indices: 2252961--2253014 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
2252951 TCGATGATTA
2252961 GAAAAAATCGGGATTGGAGTATCCCTTC
1 GAAAAAATCGGGATTGGAGTATCCCTTC
*
2252989 GAAAATAA-CGGGGTTGGAGTATCCCT
1 GAAAA-AATCGGGATTGGAGTATCCCT
2253015 AATTATGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (28 bp):
GAAAAAATCGGGATTGGAGTATCCCTTC
Found at i:2253088 original size:28 final size:28
Alignment explanation
Indices: 2253048--2253119 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2253038 GGAATAAAGC
** *
2253048 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2253076 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2253104 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2253120 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2253177 original size:52 final size:50
Alignment explanation
Indices: 2253108--2253277 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
2253098 AAATAACGAG
* * *
2253108 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
2253160 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
2253213 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
2253264 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
2253278 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:2253296 original size:28 final size:28
Alignment explanation
Indices: 2253251--2253332 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
2253241 AGTGTTTTAA
* *
2253251 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
2253278 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
2253305 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
2253333 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:2255798 original size:33 final size:33
Alignment explanation
Indices: 2255737--2255803 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2255727 AAAATTTCCA
*** *
2255737 AATGTATCGATACAAAGATCCATTTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2255770 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2255803 A
1 A
2255804 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2255847 original size:19 final size:18
Alignment explanation
Indices: 2255823--2255890 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2255813 CAGTAGCTAA
2255823 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2255842 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2255857 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2255874 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2255891 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2255863 original size:13 final size:13
Alignment explanation
Indices: 2255845--2255869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2255835 ACAATACTTA
2255845 TGTATCGATACAT
1 TGTATCGATACAT
2255858 TGTATCGATACA
1 TGTATCGATACA
2255870 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2255867 original size:32 final size:32
Alignment explanation
Indices: 2255826--2255888 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2255816 TAGCTAATTA
*
2255826 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2255858 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2255889 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2255970 original size:21 final size:21
Alignment explanation
Indices: 2255946--2256002 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2255936 CATTTGTAGG
2255946 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2255967 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
2255988 ATGTATCGATACATT
1 ATGTATCGATACATT
2256003 TAAAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2256014 original size:1 final size:1
Alignment explanation
Indices: 2256008--2256046 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
2255998 ACATTTAAAA
***
2256008 TTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2256047 CAAACACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.05, C:0.03, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Done.