Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 59 of 221
Found at i:17076051 original size:61 final size:61
Alignment explanation
Indices: 17075873--17076147 Score: 221
Period size: 61 Copynumber: 4.5 Consensus size: 61
17075863 ACAAAGGTTG
* * * * ** * * * *
17075873 CCACAAAGGCCTACCTTTCCAAAGTTTTGCCACAAAAG-CATCTTTTACATTCAATACT-A
1 CCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAAGTTGTCCTGTACATCCAGTACTCA
** * * ** * * * *
17075932 GCCACAAACACTTTCCTGTCCAGAGATTTACTGCAGAAGCTGTTCTTTACATCCAGTACTCA
1 -CCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAAGTTGTCCTGTACATCCAGTACTCA
* * * * *
17075994 CCACAAAGGTTTTCCTATCCGGAGTTTTGCCACAAAAGTTTTCCTGTACATCTAGTACTCA
1 CCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAAGTTGTCCTGTACATCCAGTACTCA
* * * * * * **
17076055 CCACAAAGGCTTTCATGTCCAAAGTTTTACCACAAAGGTTGTCCTTTACATCCAATACTTG
1 CCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAAGTTGTCCTGTACATCCAGTACTCA
*
17076116 CCACAAAGGCTTTCCTGTCTAGAGTTTTGCCA
1 CCACAAAGGCTTTCCTGTCCAGAGTTTTGCCA
17076148 TAAAGCCTAT
Statistics
Matches: 164, Mismatches: 49, Indels: 3
0.76 0.23 0.01
Matches are distributed among these distances:
60 27 0.16
61 136 0.83
62 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (61 bp):
CCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAAGTTGTCCTGTACATCCAGTACTCA
Found at i:17082231 original size:30 final size:31
Alignment explanation
Indices: 17082186--17082245 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
17082176 GGAGGTGGGA
* *
17082186 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATATTAGGGGAAAAG
* *
17082217 TGGG-AGGGAGTAAAAATATTGGGGGAAAA
1 TGGGAAGGGAATAAAAATATTAGGGGAAAA
17082246 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.18
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATATTAGGGGAAAAG
Found at i:17082473 original size:9 final size:9
Alignment explanation
Indices: 17082459--17082495 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
17082449 TATAGTTTGA
17082459 TATTCGAAT
1 TATTCGAAT
17082468 TATTCGAAT
1 TATTCGAAT
*
17082477 TATTCGAGT
1 TATTCGAAT
17082486 TATTCGAAT
1 TATTCGAAT
17082495 T
1 T
17082496 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17085652 original size:24 final size:26
Alignment explanation
Indices: 17085596--17085660 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
17085586 GAATACGCTT
*
17085596 CAAAGGCAATTCTTTCACAGTTCACCA
1 CAAAGGCTATTCTTTCACAG-TCACCA
*
17085623 CAAAGGCTATTCTTTCA-A-TCGCCA
1 CAAAGGCTATTCTTTCACAGTCACCA
*
17085647 CAAAGGCTACTCTT
1 CAAAGGCTATTCTT
17085661 AGAAGTCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.51
26 1 0.03
27 16 0.46
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (26 bp):
CAAAGGCTATTCTTTCACAGTCACCA
Found at i:17088118 original size:30 final size:30
Alignment explanation
Indices: 17088078--17088148 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
17088068 AAAAAGGTTT
*
17088078 ACAAAAGCTTTTCCTTTACAGAG-TCTTGCC
1 ACAAAGGCTTTTCCTTTACAGAGAT-TTGCC
*
17088108 ACAAAGGCTTTTTCTTTACAGAGATTTGCC
1 ACAAAGGCTTTTCCTTTACAGAGATTTGCC
* *
17088138 ATAAAGACTTT
1 ACAAAGGCTTT
17088149 CATTTTCTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (30 bp):
ACAAAGGCTTTTCCTTTACAGAGATTTGCC
Found at i:17093432 original size:41 final size:41
Alignment explanation
Indices: 17093386--17093495 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
17093376 CATTGAATGT
*
17093386 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
***
17093427 AAGGGGTTGCTAAGTGCAGATTTTTCGAATCACTAATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
* *
17093468 AAGGGGTTACTAAGTGTAGATTCCCCGA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGA
17093496 GAGGTTACTA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
Found at i:17097276 original size:17 final size:18
Alignment explanation
Indices: 17097251--17097284 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17097241 ACAAGTAGCA
17097251 AGAAAGCAAA-AAGCAAC
1 AGAAAGCAAAGAAGCAAC
*
17097268 AGAAGGCAAAGAAGCAA
1 AGAAAGCAAAGAAGCAA
17097285 TAGTGGTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.15, G:0.24, T:0.00
Consensus pattern (18 bp):
AGAAAGCAAAGAAGCAAC
Found at i:17099656 original size:47 final size:46
Alignment explanation
Indices: 17099540--17099662 Score: 147
Period size: 47 Copynumber: 2.6 Consensus size: 46
17099530 GTATATATAA
** *
17099540 ATATATTTGTTATGCATGAAAATGAATTAATTTATAGCTGAATGTAT
1 ATATATTTGTTATGCATG-AAATGAATTAAACTATAGCCGAATGTAT
* * * *
17099587 ATGTAATTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATGTAT
1 ATATATTTGTTATGCA-TGAAATGAATTAAACTATAGCCGAATGTAT
*
17099634 ATATATTTGTTATGCATTGAAATAAATTA
1 ATATATTTGTTATGCA-TGAAATGAATTA
17099663 TTTGAAATTA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
47 62 0.98
48 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (46 bp):
ATATATTTGTTATGCATGAAATGAATTAAACTATAGCCGAATGTAT
Found at i:17099693 original size:161 final size:162
Alignment explanation
Indices: 17099525--17099827 Score: 502
Period size: 161 Copynumber: 1.9 Consensus size: 162
17099515 AAATTAACTA
* *
17099525 CGAATGTATATATAAATATATTTGTTATGCA-TGAAAATGAATTAATTTATAGCTGAATGTATAT
1 CGAATGTATATATAAATATATTTGTTATACATTG-AAATGAATTAATCTATAGCTGAATGTATAT
* *
17099589 GTAATTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATG-TATATATATTTGTTATGCATTG
65 GTAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGATATATATATTTGTTATACATTG
17099653 AAATAAATTATTTGAAATTACATAGGTTATGGC
130 AAATAAATTATTTGAAATTACATAGGTTATGGC
*
17099686 CGAATGTATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATG
1 CGAATGTATATATAAATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATG
17099751 TAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGTATATATATATATTTGTTATACAT
66 TAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATG---ATATATATATTTGTTATACAT
*
17099816 TGAAATGAATTA
128 TGAAATAAATTA
17099828 ATCTATAGCT
Statistics
Matches: 131, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
161 99 0.76
162 2 0.02
165 30 0.23
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (162 bp):
CGAATGTATATATAAATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATG
TAATTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGATATATATATTTGTTATACATTGA
AATAAATTATTTGAAATTACATAGGTTATGGC
Found at i:17099770 original size:47 final size:47
Alignment explanation
Indices: 17099719--17100000 Score: 249
Period size: 47 Copynumber: 5.7 Consensus size: 47
17099709 GTTATACATT
*
17099719 GAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTATGCAGA
1 GAAATGAATTAAACTATAGCTGAATGTATATGTAATTGTTATGCAGA
* * * * * **
17099766 GAAATAAATTAAACTATGGCCGAATGTATATATATATATTTGTTATACATT
1 GAAATGAATTAAACTATAGCTGAATG--TATATGTA-A-TTGTTATGCAGA
* *
17099817 GAAATGAATTAATCTATAGCTGAATGTATATGTACTTGTTATGCAGA
1 GAAATGAATTAAACTATAGCTGAATGTATATGTAATTGTTATGCAGA
* * * * **
17099864 GAAATAAATTAAACTATGGCCGAATGTATATATATATATATATATATTTGTTATGCATT
1 GAAATGAATTAAACTATAG-C---TG-----A-ATGTATATGTA-A-TTGTTATGCAGA
*
17099923 GAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTATGCAGA
1 GAAATGAATTAAACTATAGCTGAATGTATATGTAATTGTTATGCAGA
* *
17099970 GAAATGAATTAAACTATGGCCGAATGTATAT
1 GAAATGAATTAAACTATAGCTGAATGTATAT
17100001 ATATATGTTA
Statistics
Matches: 184, Mismatches: 35, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
47 85 0.46
48 2 0.01
49 23 0.12
50 2 0.01
51 33 0.18
55 2 0.01
56 1 0.01
57 9 0.05
58 1 0.01
59 26 0.14
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.37
Consensus pattern (47 bp):
GAAATGAATTAAACTATAGCTGAATGTATATGTAATTGTTATGCAGA
Found at i:17099837 original size:98 final size:99
Alignment explanation
Indices: 17099680--17100006 Score: 541
Period size: 98 Copynumber: 3.2 Consensus size: 99
17099670 TTACATAGGT
17099680 TATGGCCGAATGTATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
1 TATGGCCGAATG-ATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
17099745 TATATGTAATTGTTATGCAGAGAAATAAATTAAAC
65 TATATGTAATTGTTATGCAGAGAAATAAATTAAAC
17099780 TATGGCCGAATG-TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGT
1 TATGGCCGAATGATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGT
*
17099844 ATATGTACTTGTTATGCAGAGAAATAAATTAAAC
66 ATATGTAATTGTTATGCAGAGAAATAAATTAAAC
*
17099878 TATGGCCGAATGTATATATATATATATATATATTTGTTATGCATTGAAATGAATTAATCTATAGC
1 TATGGCCGAATG-------ATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGC
*
17099943 TGAATGTATATGTAATTGTTATGCAGAGAAATGAATTAAAC
59 TGAATGTATATGTAATTGTTATGCAGAGAAATAAATTAAAC
17099984 TATGGCCGAATG-TATATATATAT
1 TATGGCCGAATGATATATATATAT
17100007 GTTACACATT
Statistics
Matches: 215, Mismatches: 4, Indels: 18
0.91 0.02 0.08
Matches are distributed among these distances:
98 108 0.50
100 12 0.06
106 95 0.44
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (99 bp):
TATGGCCGAATGATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGT
ATATGTAATTGTTATGCAGAGAAATAAATTAAAC
Found at i:17099908 original size:106 final size:106
Alignment explanation
Indices: 17099792--17100006 Score: 403
Period size: 106 Copynumber: 2.0 Consensus size: 106
17099782 TGGCCGAATG
*
17099792 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTACTTGTT
1 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
17099857 ATGCAGAGAAATAAATTAAACTATGGCCGAATGTATATATA
66 ATGCAGAGAAATAAATTAAACTATGGCCGAATGTATATATA
*
17099898 TATATATATATATTTGTTATGCATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
1 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
*
17099963 ATGCAGAGAAATGAATTAAACTATGGCCGAATGTATATATA
66 ATGCAGAGAAATAAATTAAACTATGGCCGAATGTATATATA
17100004 TAT
1 TAT
17100007 GTTACACATT
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (106 bp):
TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
ATGCAGAGAAATAAATTAAACTATGGCCGAATGTATATATA
Found at i:17100021 original size:47 final size:47
Alignment explanation
Indices: 17099902--17100027 Score: 146
Period size: 47 Copynumber: 2.7 Consensus size: 47
17099892 TATATATATA
* * *
17099902 TATATATATTTGTTATGCATTGAAATGAATTAATCTATAGCTGAATG
1 TATATATATATGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
* ** *
17099949 TATATGTA-ATTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATG
1 TATATATATA-TGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
** *
17099996 TATATATATATGTTACACATTGAAATAAATTA
1 TATATATATATGTTATGCATTGAAATGAATTA
17100028 TTTGAAGTTA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
47 63 0.98
48 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (47 bp):
TATATATATATGTTATGCATTGAAATGAATTAAACTATAGCCGAATG
Found at i:17100194 original size:41 final size:40
Alignment explanation
Indices: 17100134--17100242 Score: 137
Period size: 41 Copynumber: 2.7 Consensus size: 40
17100124 TGTAAGTTCG
*
17100134 GGCTTTATGCCTAGTAGGCTCTATGCCGGTGAAATGTATC
1 GGCTTTATGCCTAGCAGGCTCTATGCCGGTGAAATGTATC
** *
17100174 AGGCTTTATGCCTAGCAGGCTCTGCGCCGGTGAAATGTTTC
1 -GGCTTTATGCCTAGCAGGCTCTATGCCGGTGAAATGTATC
* * *
17100215 GGCCTTTGTGTCTAGCAGGCTTTATGCC
1 GG-CTTTATGCCTAGCAGGCTCTATGCC
17100243 AGTGTTTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 2 0.03
41 56 0.97
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (40 bp):
GGCTTTATGCCTAGCAGGCTCTATGCCGGTGAAATGTATC
Found at i:17105285 original size:27 final size:27
Alignment explanation
Indices: 17105241--17105337 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
17105231 GTATTGAATA
*
17105241 CGCCAAAAAGG-TAGTTCTTTCAGAGTT
1 CGCCATAAAGGCTA-TTCTTTCAGAGTT
* * *
17105268 CACCATAAAGACTATTCTTTTAGAGTT
1 CGCCATAAAGGCTATTCTTTCAGAGTT
* * * *
17105295 TGCCACAAAGGTTATTCTTTCAAAGTT
1 CGCCATAAAGGCTATTCTTTCAGAGTT
17105322 CGCCATAAAGGCTATT
1 CGCCATAAAGGCTATT
17105338 ATTAATTGTC
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
27 53 0.96
28 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (27 bp):
CGCCATAAAGGCTATTCTTTCAGAGTT
Found at i:17106186 original size:3 final size:3
Alignment explanation
Indices: 17106171--17106204 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
17106161 ACCACTTGAG
*
17106171 GAA GAA CAA GAA GAA GAA GAA GAA GAAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA
17106205 TCCTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17114317 original size:31 final size:30
Alignment explanation
Indices: 17114250--17114317 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
17114240 TATGTTAAAT
17114250 AATTATTAAATTATTTAAAAAATTTATTCA
1 AATTATTAAATTATTTAAAAAATTTATTCA
* ** *
17114280 AGTTATTAAATTATTTGAAAATTTTTATTTA
1 AATTATTAAATTATTT-AAAAAATTTATTCA
17114311 AATTATT
1 AATTATT
17114318 GATTTGTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
AATTATTAAATTATTTAAAAAATTTATTCA
Found at i:17114998 original size:27 final size:27
Alignment explanation
Indices: 17114968--17115026 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
17114958 ACTGATAGGC
*
17114968 GGCACCAAAGGTGCCATTCCCATGGGT
1 GGCACCAAAGGTGCCATTCCCATGGGA
***
17114995 GGCACCGGTGGTGCCATTCCCATGGGA
1 GGCACCAAAGGTGCCATTCCCATGGGA
17115022 GGCAC
1 GGCAC
17115027 TGCCCTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.19, C:0.31, G:0.34, T:0.17
Consensus pattern (27 bp):
GGCACCAAAGGTGCCATTCCCATGGGA
Found at i:17115096 original size:10 final size:10
Alignment explanation
Indices: 17115081--17115202 Score: 57
Period size: 10 Copynumber: 12.2 Consensus size: 10
17115071 GAAGGAGAGG
17115081 GAAAGAAGAA
1 GAAAGAAGAA
17115091 GAAAGAAAGAAA
1 GAAAG-AAG-AA
17115103 GAAA-AAGAA
1 GAAAGAAGAA
17115112 GGAAAGAA-AA
1 -GAAAGAAGAA
17115122 GGAAAGGATAAGAA
1 -GAAA-G--AAGAA
*
17115136 GAAAAAAGAA
1 GAAAGAAGAA
17115146 GGAAA-AAGAA
1 -GAAAGAAGAA
17115156 GGAAAGAA-AA
1 -GAAAGAAGAA
* *
17115166 GGAAAGGAGAC
1 -GAAAGAAGAA
17115177 G--AGAAG-A
1 GAAAGAAGAA
17115184 GAAA-AA-AA
1 GAAAGAAGAA
17115192 -AAAGAAGAA
1 GAAAGAAGAA
17115201 GA
1 GA
17115203 GGGGAGGAAG
Statistics
Matches: 90, Mismatches: 5, Indels: 34
0.70 0.04 0.26
Matches are distributed among these distances:
7 4 0.04
8 9 0.10
9 5 0.06
10 45 0.50
11 13 0.14
12 6 0.07
13 6 0.07
14 2 0.02
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.01
Consensus pattern (10 bp):
GAAAGAAGAA
Found at i:17115098 original size:14 final size:14
Alignment explanation
Indices: 17115081--17115171 Score: 87
Period size: 14 Copynumber: 6.4 Consensus size: 14
17115071 GAAGGAGAGG
17115081 GAAAG-AAGAAGAAA
1 GAAAGAAAGAA-AAA
17115095 GAAAGAAAGAAAAA
1 GAAAGAAAGAAAAA
* *
17115109 GAAGGAAAGAAAAG
1 GAAAGAAAGAAAAA
17115123 GAAAGGATAAGAAGAAA
1 GAAA-GA-AAGAA-AAA
*
17115140 -AAAGAAGGAAAAA
1 GAAAGAAAGAAAAA
* *
17115153 GAAGGAAAGAAAAG
1 GAAAGAAAGAAAAA
17115167 GAAAG
1 GAAAG
17115172 GAGACGAGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
13 3 0.05
14 41 0.65
15 9 0.14
16 8 0.13
17 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (14 bp):
GAAAGAAAGAAAAA
Found at i:17115142 original size:34 final size:34
Alignment explanation
Indices: 17115080--17115171 Score: 113
Period size: 34 Copynumber: 2.8 Consensus size: 34
17115070 AGAAGGAGAG
17115080 GGAAAGAAGAA-GAAA-GAAAGAAAGAAAAAGAA
1 GGAAAGAAGAAGGAAAGGAAAGAAAGAAAAAGAA
17115112 GGAAAGAA-AAGGAAAGGATAAG-AAGAAAAAAGAA
1 GGAAAGAAGAAGGAAAGGA-AAGAAAG-AAAAAGAA
*
17115146 GGAAA-AAGAAGGAAAGAAAAGGAAAG
1 GGAAAGAAGAAGGAAAGGAAA-GAAAG
17115172 GAGACGAGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
31 2 0.04
32 12 0.23
33 9 0.17
34 26 0.50
35 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (34 bp):
GGAAAGAAGAAGGAAAGGAAAGAAAGAAAAAGAA
Found at i:17115159 original size:44 final size:45
Alignment explanation
Indices: 17115086--17115173 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 45
17115076 AGAGGGAAAG
17115086 AAGAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAT
1 AAGAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAT
*
17115131 AAGAAGAAA-AAAGAAGGAAAAAGAAGGAAAGAAAAGGAAAGGA
1 AAGAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGA
17115174 GACGAGAAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 33 0.79
45 9 0.21
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (45 bp):
AAGAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAT
Found at i:17115165 original size:24 final size:24
Alignment explanation
Indices: 17115082--17115150 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
17115072 AAGGAGAGGG
*
17115082 AAAGAA-GAAGAAAGAAAGAAAGAA
1 AAAGAAGGAA-AAAGAAGGAAAGAA
*
17115106 AAAGAAGGAAAGAA-AAGGAAAGGA
1 AAAGAAGGAAA-AAGAAGGAAAGAA
* *
17115130 TAAGAAGAAAAAAGAAGGAAA
1 AAAGAAGGAAAAAGAAGGAAA
17115151 AAGAAGGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 2 0.05
24 31 0.82
25 5 0.13
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (24 bp):
AAAGAAGGAAAAAGAAGGAAAGAA
Found at i:17115190 original size:48 final size:46
Alignment explanation
Indices: 17115084--17115202 Score: 154
Period size: 44 Copynumber: 2.6 Consensus size: 46
17115074 GGAGAGGGAA
*
17115084 AGAAGAAGA-AAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
* *
17115129 ATAAG-A-AGAAAAAAGAAGGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
* *
17115173 AGACGAGAAGAGAAAAAAAAAAGAAGAAGA
1 AGA--AGAAGAGAAAAAAGAAAGAAAAAGA
17115203 GGGGAGGAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.02
44 37 0.60
45 4 0.06
46 2 0.03
47 1 0.02
48 17 0.27
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.01
Consensus pattern (46 bp):
AGAAGAAGAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
Found at i:17115350 original size:27 final size:28
Alignment explanation
Indices: 17115318--17115371 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
17115308 TTTTATTATG
* *
17115318 TTATTTAGCAT-ATAAATTTTATGAAAT
1 TTATTTAGCATGACAAAATTTATGAAAT
17115345 TTATTTAGCATGACAAAATTTATGAAA
1 TTATTTAGCATGACAAAATTTATGAAA
17115372 AAATTCATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (28 bp):
TTATTTAGCATGACAAAATTTATGAAAT
Found at i:17116043 original size:285 final size:285
Alignment explanation
Indices: 17115611--17116857 Score: 2083
Period size: 286 Copynumber: 4.3 Consensus size: 285
17115601 AAAGTAAAAG
17115611 TATAAAATTAGAAATTATGAATTTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
1 TATAAAATTAGAAATTATGAA-TTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
** *
17115676 AACCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAGATATTTGA
65 GGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGA
17115741 AACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTA
130 AACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTA
* *
17115806 ATAAAATTCAGGAAAATAATACGAGAAAATGGCGTGAATAAGGGTTTTTTTACACTAAATTAATT
195 ATAAAATTTAGGAAAATAATACGAGCAAATGGCGTGAATAAGGGTTTTTTTACACTAAATTAATT
17115871 TAAAAAAACACACTAAATTAATAAATT
260 T-AAAAAACACACTAAATTAATAAATT
17115898 TATAAAATTAGAAATTATGAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAATG
1 TATAAAATTAGAAATTATGAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAATG
17115963 GCCGAGGTAAGAGTGTTTTAC-AAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAA
66 GCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAA
17116027 ACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTAA
131 ACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTAA
* **
17116092 TAAAATTTAGGAAAATAATACGAGCAAATGGCGGGAATAAGATTTTTTTTACACTAAATTAATTT
196 TAAAATTTAGGAAAATAATACGAGCAAATGGCGTGAATAAGGGTTTTTTTACACTAAATTAATTT
* *
17116157 TAAAAATACACTAAATTAATAAATT
261 AAAAAACACACTAAATTAATAAATT
*
17116182 TATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATGTGGAGAAAAAAATACGAAGAAAT
1 TATAAAATTAGAAATTATG-AATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
17116247 GGTCGAGGTAAGAGTGTTTTACAAATTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGA
65 GGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGA
*
17116312 AACAAAATGTACTGAAATAATATAAAATAATAAAATATGAAAATAAAATTATTTTATTGAAAGTA
130 AACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTA
*
17116377 ATAAAATTT-GAGAAAATAATACGAGCAAATGGC-TGGAATAAGGATTTTTTTACACTAAATTAA
195 ATAAAATTTAG-GAAAATAATACGAGCAAATGGCGT-GAATAAGGGTTTTTTTACACTAAATTAA
17116440 TTT-AAAAACACACTAAATTAATAAATTT
258 TTTAAAAAACACACTAAATTAATAAA-TT
* *
17116468 ATAAAATTAGAAATTATGAAATTATGAAATTTTTTAAAGTAATAAAATACAGAGAAAAAAATACG
1 -T---A-TA-AAATTA-GAAATTATG-AATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACG
*
17116533 AAGAAATGGCCGATGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAA
58 AAGAAATGGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAA
17116598 TATTTGAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATT-TTTTATT
123 TATTTGAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATT
*
17116662 GAAAGTAATAAAATTTGGGAAAATAATACGAGCAAATGGCAG-GAATAAGGGTTTTTTTTACACT
188 GAAAGTAATAAAATTTAGGAAAATAATACGAGCAAATGGC-GTGAATAAGGG-TTTTTTTACACT
*
17116726 AAATTAATTTAAAAAACATACTAAATTAATAAATT
251 AAATTAATTTAAAAAACACACTAAATTAATAAATT
* *
17116761 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAGAGAAAAAAAAACGAAGAAAT
1 TATAAAATTAGAAATTATGA-ATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
17116826 GGCCGAGGTAAGAGTGTTTTACTAACTTTTTT
65 GGCCGAGGTAAGAGTGTTTTACAAAATTTTTT
17116858 TTCAACATGC
Statistics
Matches: 910, Mismatches: 32, Indels: 37
0.93 0.03 0.04
Matches are distributed among these distances:
284 42 0.05
285 255 0.28
286 310 0.34
287 28 0.03
288 2 0.00
289 1 0.00
290 1 0.00
291 2 0.00
292 60 0.07
293 188 0.21
294 21 0.02
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (285 bp):
TATAAAATTAGAAATTATGAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAATG
GCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTGAA
ACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTAA
TAAAATTTAGGAAAATAATACGAGCAAATGGCGTGAATAAGGGTTTTTTTACACTAAATTAATTT
AAAAAACACACTAAATTAATAAATT
Found at i:17116481 original size:16 final size:17
Alignment explanation
Indices: 17116462--17116499 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
17116452 CTAAATTAAT
17116462 AAATTTATAAAATTA-G
1 AAATTTATAAAATTATG
*
17116478 AAA-TTATGAAATTATG
1 AAATTTATAAAATTATG
17116494 AAATTT
1 AAATTT
17116500 TTTAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 7 0.37
17 2 0.11
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (17 bp):
AAATTTATAAAATTATG
Found at i:17116488 original size:8 final size:8
Alignment explanation
Indices: 17116466--17116498 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
17116456 ATTAATAAAT
*
17116466 TTATAAAA
1 TTATGAAA
17116474 TTA-GAAA
1 TTATGAAA
17116481 TTATGAAA
1 TTATGAAA
17116489 TTATGAAA
1 TTATGAAA
17116497 TT
1 TT
17116499 TTTTAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (8 bp):
TTATGAAA
Found at i:17116489 original size:24 final size:23
Alignment explanation
Indices: 17116454--17116498 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
17116444 AAAACACACT
17116454 AAATTAATAAATTTATAAAATTAG
1 AAATTAATAAA-TTATAAAATTAG
*
17116478 AAATT-ATGAAATTATGAAATT
1 AAATTAAT-AAATTATAAAATT
17116499 TTTTAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATTAATAAATTATAAAATTAG
Found at i:17119608 original size:18 final size:18
Alignment explanation
Indices: 17119585--17119629 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
17119575 ATCCCAATGA
17119585 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
17119603 TCGCCACCATCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
17119621 TCACCACCA
1 TCGCCACCA
17119630 ACCATATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.49, G:0.04, T:0.31
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:17127254 original size:13 final size:13
Alignment explanation
Indices: 17127238--17127264 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17127228 TTAAAAACAC
17127238 TTTTCAAAAGTAT
1 TTTTCAAAAGTAT
17127251 TTTTCAAAAGTAT
1 TTTTCAAAAGTAT
17127264 T
1 T
17127265 ACTAAACTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTTCAAAAGTAT
Found at i:17132551 original size:43 final size:42
Alignment explanation
Indices: 17132498--17132774 Score: 272
Period size: 43 Copynumber: 6.5 Consensus size: 42
17132488 TTTTTAAAAT
* *
17132498 AAACGCCGCTATAGATCATGATCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTC-CAC
* * * * *
17132541 AAACCCCGCTAAAGAACAAGACCTTTAGCGGTGCTTCTACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTT-TTCCAC
17132584 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT-CCAC
* * *
17132627 TAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTT-TTCCAC
* * * * *
17132670 AAACGTCGCTAAAGAACATAACCTTTAGCGACGCTTATACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTT-TTCCAC
* * * * * **
17132713 AAACGCCACTAACA-A-GATGACTTTTAACAGCGCTTTTTGAC
1 AAACGCCGCTAA-AGATCATGACCTTTAGCGGCGCTTTTCCAC
*
17132754 AAACGCCGCTAAA-AACATGAC
1 AAACGCCGCTAAAGATCATGAC
17132775 TTTTTAAAAA
Statistics
Matches: 194, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
40 2 0.01
41 19 0.10
42 15 0.08
43 154 0.79
44 4 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCAC
Found at i:17132650 original size:86 final size:86
Alignment explanation
Indices: 17132498--17132724 Score: 312
Period size: 86 Copynumber: 2.6 Consensus size: 86
17132488 TTTTTAAAAT
* * *
17132498 AAACGCCGCTATAGATCATGATCTTTAGCGGCGCTTTT-CTCACAAACCCCGCTAAAGAACAAGA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTAC-CACAAACGCCGCTAAAGAACAAGA
* *
17132562 CCTTTAGCGGTGCTTCTACCAC
65 CCTTTAACGGCGCTTCTACCAC
* * *
17132584 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACTAACGCCGCTAAAGATCATGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACAAGAC
17132649 CTTTAACGGCGCTTCTACCAC
66 CTTTAACGGCGCTTCTACCAC
* * * * * *
17132670 AAACGTCGCTAAAGAACATAACCTTTAGCGACGCTTATACCACAAACGCCACTAA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAA
17132725 CAAGATGACT
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 124 0.99
87 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (86 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACAAGAC
CTTTAACGGCGCTTCTACCAC
Found at i:17136186 original size:22 final size:22
Alignment explanation
Indices: 17136123--17136188 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
17136113 GTATGTTTGT
* *
17136123 AAAGTTGGGGGTTTCAAGGGGG
1 AAAGTTGGGGATTTCAGGGGGG
*
17136145 AAAGTTGGGGATTTTAGGGGGG
1 AAAGTTGGGGATTTCAGGGGGG
17136167 AAAGTTGGGGATTTC-GGGGGG
1 AAAGTTGGGGATTTCAGGGGGG
17136188 A
1 A
17136189 GGGATTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 7 0.17
22 33 0.82
ACGTcount: A:0.23, C:0.03, G:0.50, T:0.24
Consensus pattern (22 bp):
AAAGTTGGGGATTTCAGGGGGG
Found at i:17137299 original size:82 final size:82
Alignment explanation
Indices: 17137213--17137372 Score: 268
Period size: 82 Copynumber: 2.0 Consensus size: 82
17137203 CAAACTCCAA
*
17137213 ACCCCAAA-CCACTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
1 ACCCCAAATCC-CTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
*
17137277 ATCCTAAACCCTAACTCG
65 ACCCTAAACCCTAACTCG
* *
17137295 ACCCCAAATTCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAA
1 ACCCCAAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAA
17137360 CCCTAAACCCTAA
66 CCCTAAACCCTAA
17137373 TCTGATACTG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
82 72 0.99
83 1 0.01
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.26
Consensus pattern (82 bp):
ACCCCAAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAA
CCCTAAACCCTAACTCG
Found at i:17137397 original size:82 final size:82
Alignment explanation
Indices: 17137229--17137399 Score: 236
Period size: 82 Copynumber: 2.1 Consensus size: 82
17137219 AACCACTAAC
* *
17137229 CCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAACTC
1 CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTC
* * * *
17137294 GACCCCAAATTCCTAAC
66 GACACCAAATACATAAA
*
17137311 CCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCTAA-TC
1 CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTC
* **
17137375 TGATACTGAATACATAAA
66 -GACACCAAATACATAAA
17137393 CCCTAAA
1 CCCTAAA
17137400 TCCTTAACTC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 2 0.03
82 76 0.97
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.28
Consensus pattern (82 bp):
CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAACTC
GACACCAAATACATAAA
Found at i:17137485 original size:14 final size:15
Alignment explanation
Indices: 17137468--17137501 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17137458 CTTAAATCAG
17137468 AATCTTTAA-TCCAT
1 AATCTTTAATTCCAT
*
17137482 AATCCTTAATTCCAT
1 AATCTTTAATTCCAT
17137497 AATCT
1 AATCT
17137502 ATAAACCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (15 bp):
AATCTTTAATTCCAT
Found at i:17137968 original size:41 final size:41
Alignment explanation
Indices: 17137910--17138150 Score: 275
Period size: 41 Copynumber: 5.9 Consensus size: 41
17137900 AAATGTTTTT
* *
17137910 GCGGCACTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* * *
17137951 GCGGCGCTTTTTAAAAAACACCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATTA
** * * * *
17137992 ATGGCGCTTTTCCAAAAACACCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* *
17138033 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* * * * *
17138074 GCGGCCCATTTTCAAAAACGCAGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* * * *
17138115 GCGACGCTTTTTTTAAAAACGTCGCTAAAGCCCCGA
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAGACCCGA
17138151 AAGGTAGAAA
Statistics
Matches: 173, Mismatches: 26, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
41 152 0.88
42 21 0.12
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATTA
Found at i:17141346 original size:3 final size:3
Alignment explanation
Indices: 17141338--17141371 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
17141328 ATGATCATTT
*
17141338 ATC ATC ATC ATC ATC ATC ATC ATC ATC AAC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
17141372 GCAGCAGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:17143553 original size:22 final size:21
Alignment explanation
Indices: 17143505--17143553 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
17143495 AACTAAATCC
** *
17143505 TTTCTCTCAATTTTTCTCTAA
1 TTTCTCTCAATTCCTCTCAAA
17143526 TATTCTCTCAAATTCCTCTCAAA
1 T-TTCTCTC-AATTCCTCTCAAA
17143549 TTTCT
1 TTTCT
17143554 ATTTAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.48
23 11 0.48
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTCTCTCAATTCCTCTCAAA
Found at i:17145375 original size:18 final size:18
Alignment explanation
Indices: 17145352--17145394 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17145342 TGCCAGGTGC
*
17145352 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTTTAT
17145370 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTTTAT
*
17145388 GTTTCCT
1 GTATCCT
17145395 TTTTCTACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTTTAT
Found at i:17145657 original size:21 final size:22
Alignment explanation
Indices: 17145633--17145675 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
17145623 TTATCTGATG
17145633 AACCAGAATCCCC-GCC-GAAGC
1 AACCAGAA-CCCCTGCCGGAAGC
*
17145654 AACCATAACCCCTGCCGGAAGC
1 AACCAGAACCCCTGCCGGAAGC
17145676 TGGACAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.33, C:0.42, G:0.19, T:0.07
Consensus pattern (22 bp):
AACCAGAACCCCTGCCGGAAGC
Found at i:17145852 original size:49 final size:49
Alignment explanation
Indices: 17145791--17146058 Score: 448
Period size: 49 Copynumber: 5.5 Consensus size: 49
17145781 GTTTATATTA
17145791 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
17145840 ATGTAATCAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
17145889 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
17145938 ATGTAATAAAATACAAAATAGTTTATTTTGAATAGTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* * *
17145987 ATTTAATAAAATAAAAAATAGTTTATTTTGAATATTTTGATGTTATTTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTA-TTTG
*
17146037 -TTTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
17146059 AATATTCTTA
Statistics
Matches: 207, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
49 204 0.99
50 3 0.01
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:17145915 original size:29 final size:29
Alignment explanation
Indices: 17145882--17145965 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
17145872 TATTTTGATA
17145882 TTATTTGATGTAATAAAATACAAAATAGT
1 TTATTTGATGTAATAAAATACAAAATAGT
***
17145911 TTATTT--TG-AAT--AAT--TTGATA--
1 TTATTTGATGTAATAAAATACAAAATAGT
17145931 TTATTTGATGTAATAAAATACAAAATAGT
1 TTATTTGATGTAATAAAATACAAAATAGT
17145960 TTATTT
1 TTATTT
17145966 TGAATAGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
20 6 0.15
22 5 0.12
23 3 0.08
24 3 0.08
25 3 0.08
26 3 0.08
27 5 0.12
29 12 0.30
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (29 bp):
TTATTTGATGTAATAAAATACAAAATAGT
Found at i:17149524 original size:125 final size:124
Alignment explanation
Indices: 17149263--17149644 Score: 568
Period size: 125 Copynumber: 3.1 Consensus size: 124
17149253 TCCAAACATG
* * *
17149263 CTACTGTATCAAAAACGCGTCCACGTGGGAGTGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
*
17149328 TTGAAGCGTTTTTATACTATTTGTTCAGAAACGTCAACTCAAAATTATTTTTTTAGGAC
66 TTGAAGCGTTTTTATACTATTTGTTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * *
17149387 CTACTGTAGCAAAAGCGCGTCTACGTGGGAGCAATTTCAAAAATTCTTCTGATAAAAG-ATCCTG
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGAT-AAAGCATCCTG
* ** *
17149451 GTTGAAGCGGTTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
65 CTTGAAGC-GTTTTTATACTATTTGTTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * *
17149512 CTACTGTAGCAAAAACGCGTCCACGTGAGTGCGATTTCAAAAATTCTTCTGATAAAGCATCTTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
17149577 TTGAAGCAATTTTTATACTATTTGTTCAGAAAAGTCAACTCAAAATTATTTTTTCAAGAC
66 TTGAAGC-GTTTTTATACTATTTGTTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
*
17149637 ATACTGTA
1 CTACTGTA
17149645 ATAAGCCTAA
Statistics
Matches: 229, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
124 64 0.28
125 165 0.72
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (124 bp):
CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTATACTATTTGTTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:17158192 original size:17 final size:17
Alignment explanation
Indices: 17158170--17158203 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17158160 TTTTTTTTTA
17158170 TTGTTTACTACATAAAG
1 TTGTTTACTACATAAAG
17158187 TTGTTTACTACATAAAG
1 TTGTTTACTACATAAAG
17158204 GTTAAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
TTGTTTACTACATAAAG
Found at i:17159328 original size:61 final size:63
Alignment explanation
Indices: 17159220--17159349 Score: 187
Period size: 61 Copynumber: 2.1 Consensus size: 63
17159210 GCTGAATTTG
*
17159220 TATTAGATATTATAATTATTTAAGTTTAATTTTTTACCTAATTAATATTTAGATACCA-TTTA
1 TATTAGATATTATAATTATTTAAGTTTAATTTTTTACCAAATTAATATTTAGATACCACTTTA
* *
17159282 TACTTAGATATTGTAATTA-TTAAGCTTT-A-TTTTTACCAAATTAATATTTAGATACTACTTTA
1 TA-TTAGATATTATAATTATTTAAG-TTTAATTTTTTACCAAATTAATATTTAGATACCACTTTA
17159344 TATTAG
1 TATTAG
17159350 TTTATGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
61 30 0.48
62 14 0.23
63 18 0.29
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (63 bp):
TATTAGATATTATAATTATTTAAGTTTAATTTTTTACCAAATTAATATTTAGATACCACTTTA
Found at i:17161498 original size:22 final size:23
Alignment explanation
Indices: 17161473--17161517 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
17161463 GTAATTGATT
17161473 ATTATTATTAAAT-TTTAATAAG
1 ATTATTATTAAATATTTAATAAG
17161495 ATTATTATTAAATAATTTAATAA
1 ATTATTATTAAAT-ATTTAATAA
17161518 AAATAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.62
24 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTATTATTAAATATTTAATAAG
Found at i:17161511 original size:25 final size:24
Alignment explanation
Indices: 17161469--17161517 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
17161459 TTAGGTAATT
*
17161469 GATTATTATTATTAAATTTTAATAA
1 GATTATTATTAATAAA-TTTAATAA
17161494 GATTATTATTAA-ATAATTTAATAA
1 GATTATTATTAATA-AATTTAATAA
17161518 AAATAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
GATTATTATTAATAAATTTAATAA
Found at i:17161550 original size:21 final size:22
Alignment explanation
Indices: 17161473--17161550 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 22
17161463 GTAATTGATT
*
17161473 ATTATTATTA-AATTTTAATAAG
1 ATTATTATTATAA-TTTAATAAA
17161495 ATTATTATTAAATAATTTAATAAA
1 ATTATTATT--ATAATTTAATAAA
* *
17161519 AATAATA-TATAATTTAATAAA
1 ATTATTATTATAATTTAATAAA
17161540 ATTATT-TTATA
1 ATTATTATTATA
17161551 TTAAATTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 21 0.45
22 9 0.19
23 1 0.02
24 14 0.30
25 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
ATTATTATTATAATTTAATAAA
Found at i:17161597 original size:21 final size:23
Alignment explanation
Indices: 17161556--17161599 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
17161546 TTATATTAAA
*
17161556 TTATATTAAAAGATTTTTTATTT
1 TTATATTAAAAGATATTTTATTT
17161579 TTATATT-AAA-ATATTTTATTT
1 TTATATTAAAAGATATTTTATTT
17161600 ACTGCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 3 0.15
23 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATATTAAAAGATATTTTATTT
Found at i:17175676 original size:20 final size:20
Alignment explanation
Indices: 17175653--17175690 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17175643 CTTGATAAAA
*
17175653 GGTATCGATATAATTTTATG
1 GGTATCAATATAATTTTATG
17175673 GGTATCAATATAATTTTA
1 GGTATCAATATAATTTTA
17175691 CAAGTACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (20 bp):
GGTATCAATATAATTTTATG
Found at i:17176939 original size:36 final size:38
Alignment explanation
Indices: 17176866--17176941 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 38
17176856 TTAAAAATAT
**
17176866 TTATATTAAAAAACACCTATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACAAATAAATATAAT-AATATTTTA
*
17176905 TTATATTAAAAAACACAAATAAATATAATAATTTTTT
1 TTATATTAAAAAACACAAATAAATATAATAATATTTT
17176942 TAATGTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 7 0.21
39 27 0.79
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (38 bp):
TTATATTAAAAAACACAAATAAATATAATAATATTTTA
Found at i:17177387 original size:40 final size:41
Alignment explanation
Indices: 17177299--17177388 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 41
17177289 ATTTTCCCCG
* * *
17177299 AAATCGCGTCCACGTCAGCGCGATGTTAGGGGACGTGTCAG
1 AAATCGCGTCCACGTCAGCGCGATGTTAGCGGACGTGACAC
* **
17177340 AACATCGCGTCCACGTCAGCGCGCT-TT-GCTTACGTGGACAC
1 AA-ATCGCGTCCACGTCAGCGCGATGTTAGCGGACGT-GACAC
17177381 AAATCGCG
1 AAATCGCG
17177389 CCTACGAGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
40 11 0.27
41 9 0.22
42 21 0.51
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.20
Consensus pattern (41 bp):
AAATCGCGTCCACGTCAGCGCGATGTTAGCGGACGTGACAC
Found at i:17179106 original size:31 final size:29
Alignment explanation
Indices: 17179050--17179107 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
17179040 ATGTAGCACC
*
17179050 TGTATTTTAAATTGATTAATATTAGTCAT
1 TGTATTTTAAATTGATAAATATTAGTCAT
* *
17179079 TGTATTTTTCAAATTGGTAAATTTTAGTC
1 TGTA-TTTT-AAATTGATAAATATTAGTC
17179108 CCTACACTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.17
30 4 0.17
31 16 0.67
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (29 bp):
TGTATTTTAAATTGATAAATATTAGTCAT
Found at i:17187997 original size:21 final size:21
Alignment explanation
Indices: 17187943--17187997 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
17187933 ACCATTGTTT
* *
17187943 CTAATCTCACCGCTACAGTAT
1 CTAATCTCACCGTTACAGTAA
*
17187964 CCAATCTCACCGTTACAGTAA
1 CTAATCTCACCGTTACAGTAA
*
17187985 CTAATCTCGCCGT
1 CTAATCTCACCGT
17187998 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (21 bp):
CTAATCTCACCGTTACAGTAA
Found at i:17191657 original size:15 final size:15
Alignment explanation
Indices: 17191637--17191670 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
17191627 ATGAGAAAAT
17191637 AAACCTAAATGTATG
1 AAACCTAAATGTATG
17191652 AAACCTAAATGTATG
1 AAACCTAAATGTATG
17191667 AAAC
1 AAAC
17191671 GTACAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (15 bp):
AAACCTAAATGTATG
Found at i:17193760 original size:12 final size:12
Alignment explanation
Indices: 17193738--17193767 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
17193728 ATCAAATATT
17193738 AGAACAATAAAGA
1 AGAA-AATAAAGA
17193751 AGAAAATAAAGA
1 AGAAAATAAAGA
17193763 AGAAA
1 AGAAA
17193768 GATGGAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (12 bp):
AGAAAATAAAGA
Found at i:17194926 original size:21 final size:22
Alignment explanation
Indices: 17194902--17194950 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
17194892 CACAATGACC
17194902 ACATGCCAAAGT-CACATTCAA
1 ACATGCCAAAGTGCACATTCAA
* * **
17194923 ACATACCAAATTGGTCATTCAA
1 ACATGCCAAAGTGCACATTCAA
17194945 ACATGC
1 ACATGC
17194951 ATTAACCCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (22 bp):
ACATGCCAAAGTGCACATTCAA
Found at i:17196131 original size:20 final size:20
Alignment explanation
Indices: 17196108--17196154 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17196098 ATAGAGACAT
* * *
17196108 CGAAGTGTATACAGGGGCAC
1 CGAAGTGCAAACAAGGGCAC
17196128 CGAAGTGCAAACAAGGGCAC
1 CGAAGTGCAAACAAGGGCAC
17196148 CGAAGTG
1 CGAAGTG
17196155 AAAATCCCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.34, T:0.11
Consensus pattern (20 bp):
CGAAGTGCAAACAAGGGCAC
Found at i:17196152 original size:40 final size:40
Alignment explanation
Indices: 17196078--17196154 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
17196068 GACTATACAA
* * *
17196078 ACAGGGGCACCGTAGTGCAAATAGAGACATCGAAGTGTAT
1 ACAGGGGCACCGAAGTGCAAAAAGAGACACCGAAGTGTAT
*
17196118 ACAGGGGCACCGAAGTGCAAACAAG-GGCACCGAAGTG
1 ACAGGGGCACCGAAGTGCAAA-AAGAGACACCGAAGTG
17196155 AAAATCCCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.35, C:0.21, G:0.32, T:0.12
Consensus pattern (40 bp):
ACAGGGGCACCGAAGTGCAAAAAGAGACACCGAAGTGTAT
Found at i:17197025 original size:21 final size:20
Alignment explanation
Indices: 17196997--17197040 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
17196987 AAATACTTTT
*
17196997 AATTATAAATAAACATTAAA
1 AATTATAAATAAACATAAAA
* *
17197017 AATTCATAATTTAACATAAAA
1 AATT-ATAAATAAACATAAAA
17197038 AAT
1 AAT
17197041 CACAATATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTATAAATAAACATAAAA
Found at i:17202490 original size:84 final size:84
Alignment explanation
Indices: 17202343--17202514 Score: 308
Period size: 84 Copynumber: 2.0 Consensus size: 84
17202333 TGTATCCTAT
*
17202343 ATATTCCTAAGGTTCAAACGGGGCTCGATAGTCATCGTAACATCGTTGGATTTTCTGTCGAAGCA
1 ATATTCATAAGGTTCAAACGGGGCTCGATAGTCATCGTAACATCGTTGGATTTTCTGTCGAAGCA
17202408 TAATATGATAAATAACATA
66 TAATATGATAAATAACATA
* * *
17202427 ATATTCATAAGGTTCAAACGGGGCTCGATAGTCGTCGTAACATCGTTGGATTTTTTGTTGAAGCA
1 ATATTCATAAGGTTCAAACGGGGCTCGATAGTCATCGTAACATCGTTGGATTTTCTGTCGAAGCA
17202492 TAATATGATAAATAACATA
66 TAATATGATAAATAACATA
17202511 ATAT
1 ATAT
17202515 CATTTAAATC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (84 bp):
ATATTCATAAGGTTCAAACGGGGCTCGATAGTCATCGTAACATCGTTGGATTTTCTGTCGAAGCA
TAATATGATAAATAACATA
Found at i:17205765 original size:23 final size:23
Alignment explanation
Indices: 17205720--17205765 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17205710 TTATTAATAT
* *
17205720 TGTTTGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
17205743 TGTTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTCGATTAA
17205766 GTTAAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.46
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:17205934 original size:15 final size:15
Alignment explanation
Indices: 17205914--17205947 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
17205904 ACAGGGATTT
17205914 GTTCGTTCAAGCTCG
1 GTTCGTTCAAGCTCG
17205929 GTTCGTTCAAGCTCG
1 GTTCGTTCAAGCTCG
17205944 GTTC
1 GTTC
17205948 ATTTATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.26, G:0.26, T:0.35
Consensus pattern (15 bp):
GTTCGTTCAAGCTCG
Found at i:17209143 original size:17 final size:17
Alignment explanation
Indices: 17209118--17209151 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17209108 CTCCACTCAA
*
17209118 TTAAGCAAGATCTACTC
1 TTAAACAAGATCTACTC
*
17209135 TTAAACAAGGTCTACTC
1 TTAAACAAGATCTACTC
17209152 AACCACCGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
TTAAACAAGATCTACTC
Found at i:17215992 original size:74 final size:72
Alignment explanation
Indices: 17215904--17216041 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
17215894 GGCATCCATG
* *
17215904 TGTATGCCAAGTTAGCAATTAGTTAATTTTTTTAAAAAATAAAAAATATATTTTTATAAACTTTA
1 TGTATGCCAAGTTAGCAATTAATTAA-TTGTTT-AAAAATAAAAAATATATTTTTATAAACTTTA
17215969 TTATTAAAA
64 TTATTAAAA
* * * *
17215978 TGTATGCCACGTTAGCAATTAATTAATTGTTTAAAATTACAAATTATATTTTTATAAACTTTAT
1 TGTATGCCAAGTTAGCAATTAATTAATTGTTTAAAAATAAAAAATATATTTTTATAAACTTTAT
17216042 ACTTTTTAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 29 0.50
73 5 0.09
74 24 0.41
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (72 bp):
TGTATGCCAAGTTAGCAATTAATTAATTGTTTAAAAATAAAAAATATATTTTTATAAACTTTATT
ATTAAAA
Found at i:17217743 original size:114 final size:114
Alignment explanation
Indices: 17217615--17217902 Score: 332
Period size: 114 Copynumber: 2.5 Consensus size: 114
17217605 AAACGTTGCA
* * * * * *
17217615 AAAACTGTTAAGAAAACGCTGCCGTTTTCAGTTTAGGTTTTGGGGACTTTAGTGGCGCTTACT-G
1 AAAACTGTTAAGAAAACGATGTCGTTTTCAGTTTAGGTTTTAGAGACGTTAGTGGCGCTT-CTCA
* * * *
17217679 GAAAACGCCGCTA-TAGTC-AAGAATTAGCGGCGCTTTATCATAAGCGCCGT
65 GAAAACACCGC-AGTAG-CGAAGAATTAGCGGCACTTTATCAGAAGCGCCGC
* ** * * *
17217729 AAAACTGTTAAGAAAACGTTGTCGTTTTTCA-TTTATCTTTTCGAGACGTTAGTGGCGATTTTCA
1 AAAACTGTTAAGAAAACGATGTCG-TTTTCAGTTTAGGTTTTAGAGACGTTAGTGGCGCTTCTCA
** *
17217793 GAAAACACCGCAGTAGCGAAGCTTTAGTGGCACTTTATCAGAAGCGCCGC
65 GAAAACACCGCAGTAGCGAAGAATTAGCGGCACTTTATCAGAAGCGCCGC
*
17217843 AAAACTGTTAAGAAAACGATGTCGTTTTTAGTTTAGGTTTTAGAGACGTTAGTGGCGCTT
1 AAAACTGTTAAGAAAACGATGTCGTTTTCAGTTTAGGTTTTAGAGACGTTAGTGGCGCTT
17217903 GTCTAAAAAT
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
113 8 0.05
114 132 0.90
115 6 0.04
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (114 bp):
AAAACTGTTAAGAAAACGATGTCGTTTTCAGTTTAGGTTTTAGAGACGTTAGTGGCGCTTCTCAG
AAAACACCGCAGTAGCGAAGAATTAGCGGCACTTTATCAGAAGCGCCGC
Found at i:17218612 original size:28 final size:28
Alignment explanation
Indices: 17218579--17218636 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
17218569 TGGATATGGT
*
17218579 TTAAGGATTGGGGTTAAGGGTTTAGGGG
1 TTAAGGACTGGGGTTAAGGGTTTAGGGG
* *
17218607 TTAAGGGCTGGGGTTAGGGGTTTAGGGG
1 TTAAGGACTGGGGTTAAGGGTTTAGGGG
17218635 TT
1 TT
17218637 TATAGTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.17, C:0.02, G:0.48, T:0.33
Consensus pattern (28 bp):
TTAAGGACTGGGGTTAAGGGTTTAGGGG
Found at i:17218827 original size:21 final size:22
Alignment explanation
Indices: 17218801--17218847 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
17218791 TATGGATTAT
*
17218801 GGTTTAAGGGTT-GGGGTTAAG
1 GGTTTAAGGGTTAAGGGTTAAG
* *
17218822 GGTTTATGGGTTAAGGGTTATG
1 GGTTTAAGGGTTAAGGGTTAAG
17218844 GGTT
1 GGTT
17218848 AGGGGTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (22 bp):
GGTTTAAGGGTTAAGGGTTAAG
Found at i:17218833 original size:29 final size:30
Alignment explanation
Indices: 17218797--17218870 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 30
17218787 GGCTTATGGA
17218797 TTAT-GGTTTAAGGGTT-GGGGTTAAGGGT
1 TTATGGGTTTAAGGGTTAGGGGTTAAGGGT
* *
17218825 TTATGGG-TTAAGGGTTATGGGTTAGGGGT
1 TTATGGGTTTAAGGGTTAGGGGTTAAGGGT
* *
17218854 TTAGGGGTTTAGGGGTT
1 TTATGGGTTTAAGGGTT
17218871 TATAGTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 13 0.33
29 18 0.46
30 8 0.21
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (30 bp):
TTATGGGTTTAAGGGTTAGGGGTTAAGGGT
Found at i:17218839 original size:7 final size:7
Alignment explanation
Indices: 17218763--17218859 Score: 52
Period size: 7 Copynumber: 13.7 Consensus size: 7
17218753 TCTACGATTC
*
17218763 AAGGTTT
1 AAGGGTT
*
17218770 AAGGGAT
1 AAGGGTT
*
17218777 ATGGGTT
1 AAGGGTT
*
17218784 AGAGGCTT
1 A-AGGGTT
* *
17218792 ATGGATT
1 AAGGGTT
* *
17218799 ATGGTTT
1 AAGGGTT
17218806 AAGGGTT
1 AAGGGTT
*
17218813 -GGGGTT
1 AAGGGTT
17218819 AAGGGTTT
1 AAGGG-TT
*
17218827 ATGGGTT
1 AAGGGTT
17218834 AAGGGTT
1 AAGGGTT
*
17218841 ATGGGTT
1 AAGGGTT
*
17218848 AGGGGTT
1 AAGGGTT
*
17218855 TAGGG
1 AAGGG
17218860 GTTTAGGGGT
Statistics
Matches: 68, Mismatches: 19, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
6 5 0.07
7 52 0.76
8 11 0.16
ACGTcount: A:0.22, C:0.01, G:0.42, T:0.35
Consensus pattern (7 bp):
AAGGGTT
Found at i:17218844 original size:14 final size:14
Alignment explanation
Indices: 17218797--17218854 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
17218787 GGCTTATGGA
*
17218797 TTATGGTTTAAGGG
1 TTATGGGTTAAGGG
*
17218811 TT-GGGGTTAAGGG
1 TTATGGGTTAAGGG
17218824 TTTATGGGTTAAGGG
1 -TTATGGGTTAAGGG
*
17218839 TTATGGGTTAGGGG
1 TTATGGGTTAAGGG
17218853 TT
1 TT
17218855 TAGGGGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 9 0.24
14 19 0.50
15 10 0.26
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (14 bp):
TTATGGGTTAAGGG
Found at i:17218872 original size:8 final size:7
Alignment explanation
Indices: 17218808--17218870 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
17218798 TATGGTTTAA
17218808 GGGTT-G
1 GGGTTAG
17218814 GGGTTAAG
1 GGGTT-AG
* *
17218822 GGTTTAT
1 GGGTTAG
*
17218829 GGGTTAA
1 GGGTTAG
*
17218836 GGGTTAT
1 GGGTTAG
17218843 GGGTTAG
1 GGGTTAG
17218850 GGGTTTAG
1 GGG-TTAG
17218858 GGGTTTAG
1 GGG-TTAG
17218866 GGGTT
1 GGGTT
17218871 TATAGTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
6 5 0.10
7 23 0.48
8 20 0.42
ACGTcount: A:0.14, C:0.00, G:0.49, T:0.37
Consensus pattern (7 bp):
GGGTTAG
Found at i:17222804 original size:23 final size:24
Alignment explanation
Indices: 17222778--17222832 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
17222768 TTTTAACTAA
*
17222778 TTTTTATAAATATG-AACATAT-TT
1 TTTTTATAAAAATGCAA-ATATATT
*
17222801 TTTTTAAAAAAATGCAAATATATT
1 TTTTTATAAAAATGCAAATATATT
17222825 TTTTTATA
1 TTTTTATA
17222833 TACTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTTTATAAAAATGCAAATATATT
Found at i:17226206 original size:21 final size:21
Alignment explanation
Indices: 17226180--17226245 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
17226170 CTACAACTTA
* *
17226180 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
17226201 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
* *
17226222 AAGTACAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
17226243 AAG
1 AAG
17226246 TAGTGAGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.33, C:0.18, G:0.44, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:17226801 original size:85 final size:84
Alignment explanation
Indices: 17226695--17227031 Score: 298
Period size: 85 Copynumber: 4.0 Consensus size: 84
17226685 GTTTGTCAAG
*
17226695 AAAGCGCCGCTAAAGAACATTACTTTTCGCGGCGTTTGAGATAAAAAGCAG-CGCTAAAGAACAT
1 AAAGCGCCGCTAAAGAACATTACTTTTCACGGCGTTTGAGAT-AAAAGC-GCCGCTAAAGAACAT
17226759 GATCTTTAGCGGCGTCTTTTT-
64 GATCTTTAGCGGCGT-TTTTTA
* * *
17226780 TAAGCGCCGCTAAAGAACATTACTTTTCACGGCGTTTGTGATAAAAGCGCCGCTAAAGGACATGA
1 AAAGCGCCGCTAAAGAACATTACTTTTCACGGCGTTTGAGATAAAAGCGCCGCTAAAGAACATGA
17226845 TCTTTAGCGGCGTTTTTTA
66 TCTTTAGCGGCGTTTTTTA
* ** **
17226864 CAAAGCGCCGCTAAAGAACATGA-TCTTT-AGCGGCGTCTT--TTTTTAAGCGCCGCTAAAGAAC
1 -AAAGCGCCGCTAAAGAACATTACT-TTTCA-CGGCGT-TTGAGATAAAAGCGCCGCTAAAGAAC
* * *
17226925 ATTA-CTTTTAGCGGAGTTTGTGATA
62 ATGATC-TTTAGCGGCGTTT-T-TTA
* * *** ** * *
17226950 ATAGCGCCGCTAAAGAACATGA-TCTTT-AGCGGCGTTT-TTTTCCAAGTGCTGCTAAAGAACAT
1 AAAGCGCCGCTAAAGAACATTACT-TTTCA-CGGCGTTTGAGATAAAAGCGCCGCTAAAGAACAT
*
17227012 GACCTTTAGCGGCGTTTTTT
64 GATCTTTAGCGGCGTTTTTT
17227032 CTGTAAACGC
Statistics
Matches: 219, Mismatches: 22, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
83 8 0.04
84 70 0.32
85 136 0.62
86 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (84 bp):
AAAGCGCCGCTAAAGAACATTACTTTTCACGGCGTTTGAGATAAAAGCGCCGCTAAAGAACATGA
TCTTTAGCGGCGTTTTTTA
Found at i:17226885 original size:42 final size:41
Alignment explanation
Indices: 17226695--17227031 Score: 317
Period size: 42 Copynumber: 8.0 Consensus size: 41
17226685 GTTTGTCAAG
* * * *
17226695 AAAGCGCCGCTAAAGAACATTA-CTTTTCGCGGCGTTTGAGATAA
1 AAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT---TTTA
17226739 AAAGCAG-CGCTAAAGAACATGATCTTTAGCGGCGTCTTTTT-
1 AAAGC-GCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTA
* * *
17226780 TAAGCGCCGCTAAAGAACATTA-CTTTTCA-CGGCGTTTGTGATA
1 AAAGCGCCGCTAAAGAACATGATC-TTT-AGCGGCGTTT-T-TTA
*
17226823 AAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTTTTA
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTA
*
17226864 CAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTT
1 -AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTA
* * * *
17226907 TAAGCGCCGCTAAAGAACATTA-CTTTTAGCGGAGTTTGTGATA
1 AAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT-T-TTA
* *
17226950 ATAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTA
* * * *
17226992 CAAGTGCTGCTAAAGAACATGACCTTTAGCGGCGTTTTTT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
17227032 CTGTAAACGC
Statistics
Matches: 246, Mismatches: 29, Indels: 39
0.78 0.09 0.12
Matches are distributed among these distances:
40 4 0.02
41 39 0.16
42 100 0.41
43 65 0.26
44 34 0.14
45 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (41 bp):
AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTA
Found at i:17226947 original size:127 final size:127
Alignment explanation
Indices: 17226695--17227031 Score: 477
Period size: 127 Copynumber: 2.7 Consensus size: 127
17226685 GTTTGTCAAG
* * ** *
17226695 AAAGCGCCGCTAAAGAACATTA-CTTTTCGCGGCGTTTGAGATAAAAAGCAG-CGCTAAAGAACA
1 AAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT--TTTACAAAGC-GCCGCTAAAGAACA
*
17226758 TGATCTTTAGCGGCGTC-TTTTTTAAGCGCCGCTAAAGAACATTACTTTTCACGGCGTTTGTGAT
62 TGATCTTTAGCGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACTTTTCACGGAGTTTGTGAT
17226822 A
127 A
*
17226823 AAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAAAGAACATGAT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAAAGAACATGAT
17226888 CTTTAGCGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACTTTT-AGCGGAGTTTGTGATA
66 CTTTAGCGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACTTTTCA-CGGAGTTTGTGATA
* * * * * *
17226950 ATAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCAAGTGCTGCTAAAGAACATGAC
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAAAGAACATGAT
17227015 CTTTAGCGGCGT-TTTTT
66 CTTTAGCGGCGTCTTTTT
17227032 CTGTAAACGC
Statistics
Matches: 191, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
125 1 0.01
126 42 0.22
127 115 0.60
128 32 0.17
129 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (127 bp):
AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAAAGAACATGAT
CTTTAGCGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACTTTTCACGGAGTTTGTGATA
Found at i:17228744 original size:31 final size:31
Alignment explanation
Indices: 17228706--17228771 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
17228696 AACAATCTAA
*
17228706 TGACTTAAATAAAAACTTAT-GAATAGTTAAG
1 TGACTTAAATAAAAACTT-TCAAATAGTTAAG
* *
17228737 TGACTTAAATGAAAACTTTCAAATAGTTTAG
1 TGACTTAAATAAAAACTTTCAAATAGTTAAG
17228768 TGAC
1 TGAC
17228772 CTAATTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTAAG
Found at i:17232209 original size:38 final size:38
Alignment explanation
Indices: 17232158--17232234 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
17232148 AACAAGAGTC
*
17232158 ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
1 ATTATCCTCCTTGGTTAAATGGGAAAAAAAATCCTTTT
17232196 ATTATCCTCCTTGGTTAAATGGGAAAAAAAATCCTTTT
1 ATTATCCTCCTTGGTTAAATGGGAAAAAAAATCCTTTT
17232234 A
1 A
17232235 GCCCTCCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (38 bp):
ATTATCCTCCTTGGTTAAATGGGAAAAAAAATCCTTTT
Found at i:17233072 original size:32 final size:32
Alignment explanation
Indices: 17233001--17233074 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
17232991 TTAAAGACCC
*
17233001 ATGGCTTTTGCAACTCCAATTATTTGCAACTA
1 ATGGCTTTTGCAACTCCAATTATTTACAACTA
* * *
17233033 ATGGCTTTTGCAACTCCGATTATTTATAACTC
1 ATGGCTTTTGCAACTCCAATTATTTACAACTA
*
17233065 ATTGCTTTTG
1 ATGGCTTTTG
17233075 AAAATGTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (32 bp):
ATGGCTTTTGCAACTCCAATTATTTACAACTA
Found at i:17238240 original size:3 final size:3
Alignment explanation
Indices: 17238186--17238222 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
17238176 AATTAGTCTC
17238186 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17238223 CTAATGTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17240763 original size:38 final size:38
Alignment explanation
Indices: 17240712--17240799 Score: 176
Period size: 38 Copynumber: 2.3 Consensus size: 38
17240702 TGGTACTACT
17240712 TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
1 TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
17240750 TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
1 TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
17240788 TGGAGTGTAGGG
1 TGGAGTGTAGGG
17240800 TTGGATGGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.20, C:0.11, G:0.40, T:0.28
Consensus pattern (38 bp):
TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
Found at i:17243957 original size:45 final size:45
Alignment explanation
Indices: 17243906--17244332 Score: 593
Period size: 45 Copynumber: 9.5 Consensus size: 45
17243896 GATCAAGACA
* *
17243906 AGTAAGACCATAGCTGAAAGATGCTATGGCATCATTATTCAAATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* * * * *
17243951 AGTAAGACTAGAGCTGAAAGACGTTATGACATCATTATTCAGACG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* * * *
17243996 AGAAAGACCATAGTTGAAAGACGTTATGGCATCATTATTCAGACG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
*
17244041 AGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* * **
17244086 AGTAAGACCATAGCTGAAAGACACTATGGCATCATTATTCAAACA
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* *
17244131 AGTAAGACCATAGCTGAAAGATGCTATGGCATCATGATTCAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* *
17244176 AGTAAGACCATAGTTGAAAGACGTTATGGCATCATTATTCAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* **
17244221 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAAACA
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
** * * *
17244266 AGTAAGTGCATAGCTGAAAGATGCTATGGAATCATGATTCAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
*
17244311 AGTAAGACCATAGTTGAAAGAC
1 AGTAAGACCATAGCTGAAAGAC
17244333 ATTATAGCAT
Statistics
Matches: 335, Mismatches: 47, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 335 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
Found at i:17244138 original size:135 final size:135
Alignment explanation
Indices: 17243901--17244390 Score: 653
Period size: 135 Copynumber: 3.6 Consensus size: 135
17243891 ATCAAGATCA
* * * * *
17243901 AGACAAGTAAGACCATAGCTGAAAGATGCTATGGCATCATTATTCAAATGAGTAAGACTAGAGCT
1 AGACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAAATGAGTAAGACCATAGCT
** * * * * * * *
17243966 GAAAGACGTTATGACATCATTATTCAGACGAGAAAGACCATAGTTGAAAGACGTTATGGCATCAT
66 GAAAGACACTATGGCATCATTATTCAAACAAGTAAGACCATAGCTGAAAGATGCTATGGCATCAT
*
17244031 TATTC
131 GATTC
*
17244036 AGACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAGATGAGTAAGACCATAGCT
1 AGACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAAATGAGTAAGACCATAGCT
17244101 GAAAGACACTATGGCATCATTATTCAAACAAGTAAGACCATAGCTGAAAGATGCTATGGCATCAT
66 GAAAGACACTATGGCATCATTATTCAAACAAGTAAGACCATAGCTGAAAGATGCTATGGCATCAT
17244166 GATTC
131 GATTC
* * *
17244171 AGATGAGTAAGACCATAGTTGAAAGACGTTATGGCATCATTATTCAGATGAGTAAGACCATAGCT
1 AGACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAAATGAGTAAGACCATAGCT
* ** *
17244236 GAAAGACGCTATGGCATCATTATTCAAACAAGTAAGTGCATAGCTGAAAGATGCTATGGAATCAT
66 GAAAGACACTATGGCATCATTATTCAAACAAGTAAGACCATAGCTGAAAGATGCTATGGCATCAT
17244301 GATTC
131 GATTC
* * * * * *
17244306 AGATGAGTAAGACCATAGTTGAAAGACATTATAGCATCCA--ATTGAAAATGAATAAGACCATAG
1 AGACGAGTAAGACCATAGCTGAAAGACGTTATGGCAT-CATTATT-CAAATGAGTAAGACCATAG
* *
17244369 -TGGAAAGGCACTGTGGCATCAT
64 CT-GAAAGACACTATGGCATCAT
17244391 ATCGGAAAGT
Statistics
Matches: 322, Mismatches: 30, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
134 4 0.01
135 316 0.98
136 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (135 bp):
AGACGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAAATGAGTAAGACCATAGCT
GAAAGACACTATGGCATCATTATTCAAACAAGTAAGACCATAGCTGAAAGATGCTATGGCATCAT
GATTC
Found at i:17244390 original size:90 final size:89
Alignment explanation
Indices: 17243906--17244481 Score: 528
Period size: 90 Copynumber: 6.4 Consensus size: 89
17243896 GATCAAGACA
* ** * * *
17243906 AGTAAGACCATAGCTGAAAGATGCTATGGCATCATTATTCAAATGAGTAAGACTAGAGCTGAAAG
1 AGTAAGACCATAGTTGAAAGACACTATGGCATCATTATTCAGATGAGTAAGACCATAGCTGAAAG
* * * * *
17243971 ACGTTATGACATCATTATTCAGACG
66 ACGCTATGGCATCA-TATTAAAATG
* ** *
17243996 AGAAAGACCATAGTTGAAAGACGTTATGGCATCATTATTCAGACGAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGTTGAAAGACACTATGGCATCATTATTCAGATGAGTAAGACCATAGCTGAAAG
* * *
17244061 ACGTTATGGCATCATTATTCAGATG
66 ACGCTATGGCATCA-TATTAAAATG
* * **
17244086 AGTAAGACCATAGCTGAAAGACACTATGGCATCATTATTCAAACAAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGTTGAAAGACACTATGGCATCATTATTCAGATGAGTAAGACCATAGCTGAAAG
* * *
17244151 ATGCTATGGCATCATGATTCAGATG
66 ACGCTATGGCATCAT-ATTAAAATG
**
17244176 AGTAAGACCATAGTTGAAAGACGTTATGGCATCATTATTCAGATGAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGTTGAAAGACACTATGGCATCATTATTCAGATGAGTAAGACCATAGCTGAAAG
* **
17244241 ACGCTATGGCATCATTATTCAAACA
66 ACGCTATGGCATCA-TATTAAAATG
** * ** * * *
17244266 AGTAAGTGCATAGCTGAAAGATGCTATGGAATCATGATTCAGATGAGTAAGACCATAGTTGAAAG
1 AGTAAGACCATAGTTGAAAGACACTATGGCATCATTATTCAGATGAGTAAGACCATAGCTGAAAG
** *
17244331 ACATTATAGCATCCA-ATTGAAAATG
66 ACGCTATGGCAT-CATATT-AAAATG
* * * * * * * *
17244356 AATAAGACCATAGTGGAAAGGCACTGTGGCATCA-TA-TCGGAAAGTGAATAAGACCATGGTTGA
1 AGTAAGACCATAGTTGAAAGACACTATGGCATCATTATTC--AGA-TGAGTAAGACCATAGCTGA
* * *
17244419 AAGACACTATTGCATCATATCAGAAAGTG
63 AAGACGCTATGGCATCATATTA-AAA-TG
* * * *
17244448 ACTAAGACCATGGTTGAAAGGCATTATGGCATCA
1 AGTAAGACCATAGTTGAAAGACACTATGGCATCA
17244482 AGTGGAGAAT
Statistics
Matches: 412, Mismatches: 64, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
88 2 0.00
89 5 0.01
90 336 0.82
91 38 0.09
92 31 0.08
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (89 bp):
AGTAAGACCATAGTTGAAAGACACTATGGCATCATTATTCAGATGAGTAAGACCATAGCTGAAAG
ACGCTATGGCATCATATTAAAATG
Found at i:17244421 original size:46 final size:46
Alignment explanation
Indices: 17244313--17244512 Score: 203
Period size: 46 Copynumber: 4.4 Consensus size: 46
17244303 TTCAGATGAG
* * * * * *
17244313 TAAGACCATAGTTGAAAGACATTATAGCATCCA-AT-TGAAAATGAA
1 TAAGACCATGGTTGAAAGGCACTATGGCAT-CATATCGGAAAGTGAA
* * *
17244358 TAAGACCATAGTGGAAAGGCACTGTGGCATCATATCGGAAAGTGAA
1 TAAGACCATGGTTGAAAGGCACTATGGCATCATATCGGAAAGTGAA
* * * *
17244404 TAAGACCATGGTTGAAAGACACTATTGCATCATATCAGAAAGTGAC
1 TAAGACCATGGTTGAAAGGCACTATGGCATCATATCGGAAAGTGAA
* *
17244450 TAAGACCATGGTTGAAAGGCATTATGGCATCA-AGT-GGAGAA-TAAA
1 TAAGACCATGGTTGAAAGGCACTATGGCATCATA-TCGGA-AAGTGAA
17244495 TAAGACCATGGTTGAAAG
1 TAAGACCATGGTTGAAAG
17244513 ACAACATGAC
Statistics
Matches: 131, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
44 2 0.02
45 50 0.38
46 79 0.60
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGGCACTATGGCATCATATCGGAAAGTGAA
Found at i:17244424 original size:91 final size:91
Alignment explanation
Indices: 17244313--17244515 Score: 243
Period size: 91 Copynumber: 2.2 Consensus size: 91
17244303 TTCAGATGAG
* * *
17244313 TAAGACCATAGTTGAAAGACATTATAGCATCCA-AT-TGAAAATGAATAAGACCATAGTGGAAAG
1 TAAGACCATGGTTGAAAGACACTATAGCAT-CATATCAGAAAATGAATAAGACCATAGTGGAAAG
* *
17244376 GCACTGTGGCATCATA-TCGGA-AAGTGAA
65 GCACTATGGCATCA-AGT-GGAGAA-TAAA
* * * * *
17244404 TAAGACCATGGTTGAAAGACACTATTGCATCATATCAGAAAGTGACTAAGACCATGGTTGAAAGG
1 TAAGACCATGGTTGAAAGACACTATAGCATCATATCAGAAAATGAATAAGACCATAGTGGAAAGG
*
17244469 CATTATGGCATCAAGTGGAGAATAAA
66 CACTATGGCATCAAGTGGAGAATAAA
17244495 TAAGACCATGGTTGAAAGACA
1 TAAGACCATGGTTGAAAGACA
17244516 ACATGACATC
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
90 2 0.02
91 57 0.59
92 38 0.39
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (91 bp):
TAAGACCATGGTTGAAAGACACTATAGCATCATATCAGAAAATGAATAAGACCATAGTGGAAAGG
CACTATGGCATCAAGTGGAGAATAAA
Found at i:17246012 original size:7 final size:8
Alignment explanation
Indices: 17245940--17246013 Score: 94
Period size: 8 Copynumber: 8.6 Consensus size: 8
17245930 TTTCCCAAGT
17245940 TTTTTCGAA
1 TTTTT-GAA
17245949 TTTTTGAA
1 TTTTTGAA
17245957 TTTTTGAA
1 TTTTTGAA
17245965 TTTTTGAA
1 TTTTTGAA
17245973 TTTTTGAA
1 TTTTTGAA
*
17245981 TTTTTTCCCAAA
1 -TTTTT---GAA
17245993 TTTTTGAA
1 TTTTTGAA
17246001 TTTTTGAA
1 TTTTTGAA
17246009 TTTTT
1 TTTTT
17246014 TCCTTGGTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
8 42 0.71
9 10 0.17
11 5 0.08
12 2 0.03
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.62
Consensus pattern (8 bp):
TTTTTGAA
Found at i:17249287 original size:20 final size:20
Alignment explanation
Indices: 17249262--17249328 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
17249252 TGCACATTCG
*
17249262 TGCTCTTATTAGTACTACGA
1 TGCTCTTATTAGCACTACGA
* *
17249282 TGCTCTTAATAGCACATTCG-
1 TGCTCTTATTAGCAC-TACGA
* *
17249302 TGCTCATGTTAGCACTACGA
1 TGCTCTTATTAGCACTACGA
17249322 TGCTCTT
1 TGCTCTT
17249329 GAAAGCACAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.08
20 31 0.84
21 3 0.08
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (20 bp):
TGCTCTTATTAGCACTACGA
Found at i:17249319 original size:40 final size:40
Alignment explanation
Indices: 17249253--17249355 Score: 145
Period size: 40 Copynumber: 2.6 Consensus size: 40
17249243 GATCCTGAGT
* * *
17249253 GCACATTCGTGCTCTTATTAGTACTACGATGCTCTT-AATA
1 GCACATTCGTGCTCATGTTAGCACTACGATGCTCTTGAA-A
17249293 GCACATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAA
1 GCACATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAA
* *
17249333 GCACATTCGTGCTCCTGATAGCA
1 GCACATTCGTGCTCATGTTAGCA
17249356 TATTTATGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 55 0.96
41 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (40 bp):
GCACATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAA
Found at i:17249335 original size:20 final size:20
Alignment explanation
Indices: 17249275--17249336 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
17249265 TCTTATTAGT
17249275 ACTACGATGCTCTT-AATAGC
1 ACTACGATGCTCTTGAA-AGC
* * **
17249295 ACATTCG-TGCTCATGTTAGC
1 AC-TACGATGCTCTTGAAAGC
17249315 ACTACGATGCTCTTGAAAGC
1 ACTACGATGCTCTTGAAAGC
17249335 AC
1 AC
17249337 ATTCGTGCTC
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (20 bp):
ACTACGATGCTCTTGAAAGC
Found at i:17249345 original size:20 final size:20
Alignment explanation
Indices: 17249282--17249369 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 20
17249272 AGTACTACGA
17249282 TGCTCTT-AATAGCACATTCG
1 TGCTCTTGAA-AGCACATTCG
* ** *
17249302 TGCTCATGTTAGCAC-TACG
1 TGCTCTTGAAAGCACATTCG
17249321 ATGCTCTTGAAAGCACATTCG
1 -TGCTCTTGAAAGCACATTCG
* * * **
17249342 TGCTCCTGATAGCATATTTA
1 TGCTCTTGAAAGCACATTCG
17249362 TGCTCTTG
1 TGCTCTTG
17249370 TTTGTTTTAC
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.06
20 45 0.88
21 3 0.06
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (20 bp):
TGCTCTTGAAAGCACATTCG
Found at i:17251397 original size:25 final size:25
Alignment explanation
Indices: 17251363--17251502 Score: 129
Period size: 25 Copynumber: 5.6 Consensus size: 25
17251353 AGATAACTTG
* *
17251363 GCCACTTAGGCTTCCCAAATAATAA
1 GCCACATAGGCTTTCCAAATAATAA
** ** *
17251388 GTTACATAGGCTTTTTAAATAACAA
1 GCCACATAGGCTTTCCAAATAATAA
* * * *
17251413 GGCACAAAGGCTTCCCAAATAATAT
1 GCCACATAGGCTTTCCAAATAATAA
*
17251438 GCCACATAGGCTTTTCAAATAACT-A
1 GCCACATAGGCTTTCCAAATAA-TAA
* *
17251463 GCCACAAAGGCTTTCCAAATAATAT
1 GCCACATAGGCTTTCCAAATAATAA
*
17251488 GCCACATAAGCTTTC
1 GCCACATAGGCTTTC
17251503 TAGATAGCCA
Statistics
Matches: 88, Mismatches: 25, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
24 1 0.01
25 86 0.98
26 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (25 bp):
GCCACATAGGCTTTCCAAATAATAA
Found at i:17251431 original size:50 final size:50
Alignment explanation
Indices: 17251370--17251501 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
17251360 TTGGCCACTT
** * *
17251370 AGGCTTCCCAAATAATAAGTTACATAGGCTTTTTAAATAACAAGGCACAA
1 AGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAATAACAAGCCACAA
* *
17251420 AGGCTTCCCAAATAATATGCCACATAGGCTTTTCAAATAACTAGCCACAA
1 AGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAATAACAAGCCACAA
* * *
17251470 AGGCTTTCCAAATAATATGCCACATAAGCTTT
1 AGGCTTCCCAAATAATAAGCCACATAGGCTTT
17251502 CTAGATAGCC
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.27
Consensus pattern (50 bp):
AGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAATAACAAGCCACAA
Found at i:17251521 original size:21 final size:22
Alignment explanation
Indices: 17251415--17251521 Score: 67
Period size: 25 Copynumber: 4.5 Consensus size: 22
17251405 AATAACAAGG
*
17251415 CACAAAGGCTTCCCAAATAATATGC
1 CACAAAGGCTTTCC--ATAATA-GC
* *
17251440 CACATAGGCTTTTCAAATAACTAGC
1 CACAAAGGC-TTTC-CATAA-TAGC
17251465 CACAAAGGCTTTCCAAATAATATGC
1 CACAAAGGCTTTCC--ATAATA-GC
17251490 CACATAA-GCTTT-C-TAGATAGC
1 CACA-AAGGCTTTCCATA-ATAGC
17251511 CACAAAGGCTT
1 CACAAAGGCTT
17251522 ATTTGGTTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
20 2 0.03
21 12 0.18
22 3 0.04
24 7 0.10
25 37 0.54
26 7 0.10
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CACAAAGGCTTTCCATAATAGC
Found at i:17256140 original size:16 final size:16
Alignment explanation
Indices: 17256108--17256142 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17256098 GTAGATCGAA
*
17256108 AAATGCCGAAATCTCG
1 AAATGCCGAAAACTCG
*
17256124 AAATGCCGAAAAGTCG
1 AAATGCCGAAAACTCG
17256140 AAA
1 AAA
17256143 AGTAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (16 bp):
AAATGCCGAAAACTCG
Found at i:17256571 original size:26 final size:27
Alignment explanation
Indices: 17256519--17256575 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
17256509 AAAGGTTGCT
17256519 AAATGACCAAAATACCATTGAAGGGTA
1 AAATGACCAAAATACCATTGAAGGGTA
* *
17256546 AAATGACCAAAATACCCTTGGA-GGTA
1 AAATGACCAAAATACCATTGAAGGGTA
17256572 AAAT
1 AAAT
17256576 TATCATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATACCATTGAAGGGTA
Found at i:17275411 original size:18 final size:18
Alignment explanation
Indices: 17275388--17275423 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
17275378 TCTCCATCCC
17275388 ACATCCTTTATGTATATA
1 ACATCCTTTATGTATATA
17275406 ACATCCTTTATGTATATA
1 ACATCCTTTATGTATATA
17275424 CATTTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (18 bp):
ACATCCTTTATGTATATA
Found at i:17276226 original size:43 final size:43
Alignment explanation
Indices: 17276138--17276335 Score: 176
Period size: 43 Copynumber: 4.7 Consensus size: 43
17276128 CTCGGTGGAT
* * **
17276138 TCAGCACTTAGCAACCACC-TT-AAATTCAGTGATACGGGGAA
1 TCAGCACATAGCAACCACCTTTCAAAATCAAAGATACGGGGAA
* * *
17276179 TCAGCACATAGCAACC-CCTTTCACAGTCAAAGATACGGTAGAA
1 TCAGCACATAGCAACCACCTTTCAAAATCAAAGATACGG-GGAA
* * * ***
17276222 TCAGCACTTAGCAACCACC-TT-ATATTCAGTTATACGGGGAA
1 TCAGCACATAGCAACCACCTTTCAAAATCAAAGATACGGGGAA
* *
17276263 TCAGCACATAGCAACC-CCTTTCAAAATCAAATATACGGTCGAA
1 TCAGCACATAGCAACCACCTTTCAAAATCAAAGATACGG-GGAA
* *
17276306 TCAGCACTTAGCAACCACCTTT-AGAATCAA
1 TCAGCACATAGCAACCACCTTTCAAAATCAA
17276336 TAATTTATGG
Statistics
Matches: 128, Mismatches: 21, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
40 4 0.03
41 37 0.29
42 35 0.27
43 45 0.35
44 7 0.05
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (43 bp):
TCAGCACATAGCAACCACCTTTCAAAATCAAAGATACGGGGAA
Found at i:17276275 original size:41 final size:43
Alignment explanation
Indices: 17276130--17276326 Score: 199
Period size: 41 Copynumber: 4.7 Consensus size: 43
17276120 ATCCGTTACT
* **
17276130 CGGTGGATTCAGCACTTAGCAACCACCTT-AAATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTCAAATTCAAAGATA
* * *
17276172 CGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCACC-TTCAAATTCAAAGATA
* * ***
17276214 CGGTAGAATCAGCACTTAGCAACCACCTT-ATATTCAGTTATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTCAAATTCAAAGATA
* * *
17276256 CGG-GGAATCAGCACATAGCAACC-CCTTTCAAAATCAAATATA
1 CGGTGGAATCAGCACTTAGCAACCACC-TTCAAATTCAAAGATA
*
17276298 CGGTCGAATCAGCACTTAGCAACCACCTT
1 CGGTGGAATCAGCACTTAGCAACCACCTT
17276327 TAGAATCAAT
Statistics
Matches: 126, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
40 4 0.03
41 40 0.32
42 38 0.30
43 40 0.32
44 4 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTCAAATTCAAAGATA
Found at i:17276279 original size:84 final size:84
Alignment explanation
Indices: 17276138--17276326 Score: 324
Period size: 84 Copynumber: 2.2 Consensus size: 84
17276128 CTCGGTGGAT
*
17276138 TCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCAC
1 TCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCAA
*
17276203 AGTCAAAGATACGGTAGAA
66 AATCAAAGATACGGTAGAA
* *
17276222 TCAGCACTTAGCAACCACCTTATATTCAGTTATACGGGGAATCAGCACATAGCAACCCCTTTCAA
1 TCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCAA
* *
17276287 AATCAAATATACGGTCGAA
66 AATCAAAGATACGGTAGAA
17276306 TCAGCACTTAGCAACCACCTT
1 TCAGCACTTAGCAACCACCTT
17276327 TAGAATCAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 99 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (84 bp):
TCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCAA
AATCAAAGATACGGTAGAA
Found at i:17276373 original size:26 final size:26
Alignment explanation
Indices: 17276344--17276393 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
17276334 AATAATTTAT
*
17276344 GGAATCAGCACTTAGCAAGCCCTTGG
1 GGAATCAGCACTTAGCAACCCCTTGG
*
17276370 GGAATCTGCACTTAGCAACCCCTT
1 GGAATCAGCACTTAGCAACCCCTT
17276394 TTTATCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (26 bp):
GGAATCAGCACTTAGCAACCCCTTGG
Found at i:17279709 original size:42 final size:42
Alignment explanation
Indices: 17279629--17279710 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
17279619 CATTTTCTCT
* * **
17279629 ATGCCATAGTCCAACTATGGTCTTACACATGTTTACATATTG
1 ATGCCATAGCCCAACTATGATCTTACACATGTGCACATATTG
*
17279671 ATGCCATAGCCCAGCTATGATCTTACACA-GTAGCACATAT
1 ATGCCATAGCCCAACTATGATCTTACACATGT-GCACATAT
17279711 CACACCAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGATCTTACACATGTGCACATATTG
Found at i:17282344 original size:43 final size:42
Alignment explanation
Indices: 17282225--17282357 Score: 162
Period size: 43 Copynumber: 3.2 Consensus size: 42
17282215 CTCGGTGGAT
*
17282225 TCAGCTCTTAGCAACCACC-TTAAATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
* * * **
17282266 TCAGCACATAGCAACC-CCTTTCACAGTCAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-AAATTCAGTGATACGG-GGAA
* *
17282309 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGAGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
17282351 TCAGCAC
1 TCAGCAC
17282358 ACCTTTAGAA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
40 2 0.03
41 16 0.21
42 22 0.29
43 31 0.41
44 5 0.07
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
Found at i:17282743 original size:28 final size:28
Alignment explanation
Indices: 17282703--17282757 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
17282693 TTTAACTTAT
17282703 TTAACATGCACATTCATCAAAACAGTCC
1 TTAACATGCACATTCATCAAAACAGTCC
17282731 TTAACATGCACATTCATCAAAACAGTC
1 TTAACATGCACATTCATCAAAACAGTC
17282758 AATAACTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.25
Consensus pattern (28 bp):
TTAACATGCACATTCATCAAAACAGTCC
Found at i:17283530 original size:11 final size:13
Alignment explanation
Indices: 17283500--17283531 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17283490 TGCCCAAACG
17283500 TCGAAATTTTTGA
1 TCGAAATTTTTGA
17283513 TCGAAATTTTT-A
1 TCGAAATTTTTGA
17283525 -CGAAATT
1 TCGAAATT
17283532 ATTTTGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.37
12 1 0.05
13 11 0.58
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (13 bp):
TCGAAATTTTTGA
Found at i:17289814 original size:13 final size:13
Alignment explanation
Indices: 17289796--17289822 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17289786 ATATGGGTAC
17289796 CCCTGTGTTGTGA
1 CCCTGTGTTGTGA
17289809 CCCTGTGTTGTGA
1 CCCTGTGTTGTGA
17289822 C
1 C
17289823 ACACAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.26, G:0.30, T:0.37
Consensus pattern (13 bp):
CCCTGTGTTGTGA
Found at i:17290915 original size:12 final size:12
Alignment explanation
Indices: 17290898--17290924 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17290888 CACACGCCCG
17290898 TGTGCTAGGCCA
1 TGTGCTAGGCCA
17290910 TGTGCTAGGCCA
1 TGTGCTAGGCCA
17290922 TGT
1 TGT
17290925 AAGTCACTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (12 bp):
TGTGCTAGGCCA
Found at i:17295013 original size:14 final size:14
Alignment explanation
Indices: 17294994--17295020 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17294984 TCAAATGACA
17294994 TAGGTATTTATGAG
1 TAGGTATTTATGAG
17295008 TAGGTATTTATGA
1 TAGGTATTTATGA
17295021 TTGATGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
TAGGTATTTATGAG
Found at i:17305111 original size:274 final size:276
Alignment explanation
Indices: 17304566--17305141 Score: 829
Period size: 274 Copynumber: 2.1 Consensus size: 276
17304556 ACATAGATAA
* * * *
17304566 AATTAATATGTGAATTTGATTCATACAAAAATATTAATTATATATATTTTACCGAATTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAAATATTAATTATATACATTTTACCAAATTTATAAAT
* ** *
17304631 ATAGACAGTTATATTAATTAATTTAAAATCAAAATATAAAAGATGTGGAAATTAATGTTCTTTTG
66 ATAGACAGTTAGATTAATTAATTTAAAATCAAAATATAAAAGACATGGAAATTAATATTCTTTTG
* * *
17304696 AAAAGTATAATTAATATATGAATTTGGTTCATACAAAATATTAATTATATATAGTTGACCGAATT
131 AAAAATATAATTAATATATAAATTTGATTCATACAAAATATTAATTATATATAGTTGACCGAATT
* * * *
17304761 TATTAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAATACATGGAAGTTAATATT
196 TATTAATATAAACAATTATATTAATGAATTTCAGTCAAAATATAAAAGACATAGAAATTAATATT
17304826 CATTTGGAAAGAATAT
261 CATTTGGAAAGAATAT
* * *
17304842 AATTAATATATGAATTTAATTCATAC-AAAATATTAATTTTATACATTTTATCAAATTTATAAAT
1 AATTAATATATGAATTTGATTCATACAAAAATATTAATTATATACATTTTACCAAATTTATAAAT
* ** *
17304906 AT-GAATAGTTAGATTAATTAATTT-TGATCAAAATATAAAAGACATGGAAATTAATATTTTTTT
66 ATAG-ACAGTTAGATTAATTAATTTAAAATCAAAATATAAAAGACATGGAAATTAATATTCTTTT
* * * *
17304969 GGAAAGAATATAATTAATATTTAAATTTGATTCATACAAAATATTAATTTTATATATTTTACCGA
130 -GAAA-AATATAATTAATATATAAATTTGATTCATACAAAATATTAATTATATATAGTTGACCGA
*
17305034 ATTTATTAATAT-AA-AATTATATTAATGAATTTCAGTCAAAATATAAAAGACGTAGAAATTAAT
193 ATTTATTAATATAAACAATTATATTAATGAATTTCAGTCAAAATATAAAAGACATAGAAATTAAT
*
17305097 ATTCTTTTGGAAAGAATAT
258 ATTCATTTGGAAAGAATAT
*
17305116 AATTAATATAAGAATTTGATTCATAC
1 AATTAATATATGAATTTGATTCATAC
17305142 TGTAAAAGCT
Statistics
Matches: 267, Mismatches: 30, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
274 120 0.45
275 59 0.22
276 88 0.33
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (276 bp):
AATTAATATATGAATTTGATTCATACAAAAATATTAATTATATACATTTTACCAAATTTATAAAT
ATAGACAGTTAGATTAATTAATTTAAAATCAAAATATAAAAGACATGGAAATTAATATTCTTTTG
AAAAATATAATTAATATATAAATTTGATTCATACAAAATATTAATTATATATAGTTGACCGAATT
TATTAATATAAACAATTATATTAATGAATTTCAGTCAAAATATAAAAGACATAGAAATTAATATT
CATTTGGAAAGAATAT
Found at i:17305132 original size:136 final size:138
Alignment explanation
Indices: 17304566--17305141 Score: 784
Period size: 138 Copynumber: 4.2 Consensus size: 138
17304556 ACATAGATAA
*
17304566 AATTAATATGTGAATTTGATTCATACAAAAATATTAATTATATATATTTTACCGAATTTATTAAT
1 AATTAATATATGAATTTGATTCATAC-AAAATATTAATTATATATATTTTACCGAATTTATTAAT
* * * * ** *
17304631 ATAGACAGTTATATTAATTAATTTAAAATCAAAATATAAAAGATGTGGAAATTAATGTTCTTTT-
65 ATAAACAATTATATTAATTAATTT-CAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTG
*
17304695 GAAA-AGTAT
129 GAAAGAATAT
* * *
17304704 AATTAATATATGAATTTGGTTCATACAAAATATTAATTATATATAGTTGACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
* * *
17304769 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAATACATGGAAGTTAATATTCATTTGGA
66 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
17304834 AAGAATAT
131 AAGAATAT
* * * * * *
17304842 AATTAATATATGAATTTAATTCATACAAAATATTAATTTTATACATTTTATCAAATTTATAAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
* * * * * *
17304907 TGAATAGTTAGATTAATTAATTT-TGATCAAAATATAAAAGACATGGAAATTAATATTTTTTTGG
66 TAAACAATTATATTAATTAATTTCAG-TCAAAATATAAAAGACATGGAAATTAATATTCTTTTGG
17304971 AAAGAATAT
130 AAAGAATAT
* * *
17304980 AATTAATATTTAAATTTGATTCATACAAAATATTAATTTTATATATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
* * *
17305045 T-AA-AATTATATTAATGAATTTCAGTCAAAATATAAAAGACGTAGAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
17305108 AAGAATAT
131 AAGAATAT
*
17305116 AATTAATATAAGAATTTGATTCATAC
1 AATTAATATATGAATTTGATTCATAC
17305142 TGTAAAAGCT
Statistics
Matches: 384, Mismatches: 50, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
136 113 0.29
137 66 0.17
138 205 0.53
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCGAATTTATTAATA
TAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:17308003 original size:25 final size:25
Alignment explanation
Indices: 17307970--17308033 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
17307960 ACGGACACAC
*
17307970 CACAGCTCGTATGAGCTTACTGATT
1 CACAGCTCGTATGAGCTTACCGATT
** *
17307995 TGCATCTCGTGA-GAGCTTACCGATT
1 CACAGCTCGT-ATGAGCTTACCGATT
17308020 CACAGCTCGTATGA
1 CACAGCTCGTATGA
17308034 CCATACATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 1 0.03
25 28 0.93
26 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTACCGATT
Found at i:17311267 original size:50 final size:50
Alignment explanation
Indices: 17311197--17311312 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
17311187 CACACCACAG
* * * * *
17311197 CTCGTATGAGCTTACCGATTTGCAGCTCTTGAGAGCTTACCAATTC-TCAA
1 CTCGTATGACCTTACAGATTTACAGCTCGTGAGAGCATACCAATTCAT-AA
* * * *
17311247 CTCGTATGACCTTGCAGATTTACAGCTCGTGAGAGCATATCGATTCATAG
1 CTCGTATGACCTTACAGATTTACAGCTCGTGAGAGCATACCAATTCATAA
17311297 CTCGTATGACCTTACA
1 CTCGTATGACCTTACA
17311313 TGTACAAGAG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 54 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (50 bp):
CTCGTATGACCTTACAGATTTACAGCTCGTGAGAGCATACCAATTCATAA
Found at i:17320451 original size:18 final size:19
Alignment explanation
Indices: 17320416--17320452 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17320406 TATAGTAGAA
17320416 GAGAAAGTAAATAATTTAG
1 GAGAAAGTAAATAATTTAG
*
17320435 GAGAAATTAAA-AATTTAG
1 GAGAAAGTAAATAATTTAG
17320453 ATTTAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (19 bp):
GAGAAAGTAAATAATTTAG
Found at i:17320523 original size:3 final size:3
Alignment explanation
Indices: 17320515--17320539 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17320505 TCAGGTTATA
17320515 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
17320540 TAAATCAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17322034 original size:22 final size:22
Alignment explanation
Indices: 17321994--17322035 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17321984 TTTACATTAA
17321994 TTTTCTCTTTAATTTTTTCTAC
1 TTTTCTCTTTAATTTTTTCTAC
*
17322016 TTTTC-CTTTATTTTCTTTCT
1 TTTTCTCTTTAATTT-TTTCT
17322036 TCATCCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTCTCTTTAATTTTTTCTAC
Found at i:17324066 original size:14 final size:15
Alignment explanation
Indices: 17324035--17324067 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17324025 AAATTTTAAG
17324035 AAAAATGAATATTGT
1 AAAAATGAATATTGT
*
17324050 AAAAATGGATATT-T
1 AAAAATGAATATTGT
17324064 AAAA
1 AAAA
17324068 CAATTCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:17324159 original size:18 final size:18
Alignment explanation
Indices: 17324121--17324164 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
17324111 TAGTTCACTC
17324121 TTACTTTATTTTTTTAGTT
1 TTACTTTA-TTTTTTAGTT
17324140 TTACTTTA-TTTTTAGTTT
1 TTACTTTATTTTTTAG-TT
17324158 TTACTTT
1 TTACTTT
17324165 TACAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.73
Consensus pattern (18 bp):
TTACTTTATTTTTTAGTT
Done.