Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 95 of 171
Found at i:30941474 original size:21 final size:21
Alignment explanation
Indices: 30941435--30941476 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30941425 GATACCTGAT
* *
30941435 AAAAGGTATTGGTAATTTTTG
1 AAAAGGTATCGATAATTTTTG
*
30941456 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATAATTTTTG
30941477 TCATTATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.40
Consensus pattern (21 bp):
AAAAGGTATCGATAATTTTTG
Found at i:30942295 original size:19 final size:19
Alignment explanation
Indices: 30942263--30942371 Score: 82
Period size: 18 Copynumber: 5.7 Consensus size: 19
30942253 CGTTACAACC
**
30942263 TAAAAATTATTAAATTTTAA
1 TAAAAATTA-TAAAAATTAA
* *
30942283 TAAAAAATATAAAAATTAT
1 TAAAAATTATAAAAATTAA
*
30942302 TAAAAATTATAAAAA-TCA
1 TAAAAATTATAAAAATTAA
*
30942320 TAAAAATTGTAAAAA--AA
1 TAAAAATTATAAAAATTAA
*
30942337 TAAAAACATATAAAAA-TACA
1 TAAAAA-TTATAAAAATTA-A
30942357 GTAAAAAGTTATAAA
1 -TAAAAA-TTATAAA
30942372 TTTTTATAGT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
17 7 0.10
18 22 0.31
19 22 0.31
20 9 0.12
21 12 0.17
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
TAAAAATTATAAAAATTAA
Found at i:30942297 original size:10 final size:9
Alignment explanation
Indices: 30942282--30942352 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
30942272 TTAAATTTTA
30942282 ATAAAAAAT
1 ATAAAAAAT
*
30942291 ATAAAAATT
1 ATAAAAAAT
*
30942300 ATTAAAAAT
1 ATAAAAAAT
30942309 -TATAAAAAT
1 ATA-AAAAAT
*
30942318 CATAAAAATT
1 -ATAAAAAAT
*
30942328 GTAAAAAA-
1 ATAAAAAAT
30942336 ATAAAAACAT
1 ATAAAAA-AT
30942346 ATAAAAA
1 ATAAAAA
30942353 TACAGTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
8 7 0.14
9 28 0.57
10 12 0.24
11 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.25
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:30942698 original size:30 final size:29
Alignment explanation
Indices: 30942655--30942711 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
30942645 ATGACTTTAT
* *
30942655 AAATTTTACAATTTTTTTATATTTTTATTA
1 AAATTTAACAATTTTTATA-ATTTTTATTA
*
30942685 AAATTTAATAATTTTTATAATTTTTAT
1 AAATTTAACAATTTTTATAATTTTTAT
30942712 AATTTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
AAATTTAACAATTTTTATAATTTTTATTA
Found at i:30942715 original size:18 final size:18
Alignment explanation
Indices: 30942621--30942716 Score: 70
Period size: 18 Copynumber: 5.2 Consensus size: 18
30942611 AAAGAACTTT
30942621 TTTTTAT-ATATTTTATAA
1 TTTTTATAAT-TTTTATAA
* *
30942639 TTTTTTATGA-CTTTATAA
1 -TTTTTATAATTTTTATAA
* * *
30942657 ATTTTACAATTTTTTTATA
1 TTTTTATAATTTTTATA-A
* *
30942676 TTTTTATTAAAATTTAATAA
1 TTTTTA-T-AATTTTTATAA
30942696 TTTTTATAATTTTTATAA
1 TTTTTATAATTTTTATAA
30942714 TTT
1 TTT
30942717 AATTTATTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
17 6 0.10
18 24 0.41
19 14 0.24
20 8 0.14
21 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTTTATAATTTTTATAA
Found at i:30942735 original size:18 final size:19
Alignment explanation
Indices: 30942704--30942744 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
30942694 AATTTTTATA
30942704 ATTTTTATAATTTA-ATTT
1 ATTTTTATAATTTATATTT
**
30942722 ATTTTTATTTTTTATATTT
1 ATTTTTATAATTTATATTT
30942741 -TTTT
1 ATTTT
30942745 ATCATATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTTATAATTTATATTT
Found at i:30950309 original size:14 final size:14
Alignment explanation
Indices: 30950290--30950319 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30950280 TTCATCCTAA
30950290 AGGTCCTAGATTCG
1 AGGTCCTAGATTCG
30950304 AGGTCCTAGATTCG
1 AGGTCCTAGATTCG
30950318 AG
1 AG
30950320 CACCTATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (14 bp):
AGGTCCTAGATTCG
Found at i:30954847 original size:16 final size:15
Alignment explanation
Indices: 30954826--30954888 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 15
30954816 CACTAGAATT
30954826 GAATAAGTTTGTAATG
1 GAATAAG-TTGTAATG
30954842 GAATAAGGTTGTAATG
1 GAATAA-GTTGTAATG
* *
30954858 AAATAGAGCTGTAATG
1 GAATA-AGTTGTAATG
30954874 GAATAAAGTTGTAAT
1 GAAT-AAGTTGTAAT
30954889 CAATAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
16 37 0.93
17 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.32
Consensus pattern (15 bp):
GAATAAGTTGTAATG
Found at i:30957256 original size:62 final size:62
Alignment explanation
Indices: 30957159--30957292 Score: 232
Period size: 62 Copynumber: 2.2 Consensus size: 62
30957149 ACCAGTTTGG
*
30957159 CACCCAATGTCTCAACGGATAAACCGAAGTAATAGTCGCGTCCAGCGCTATAATGTAAGTGA
1 CACCCAGTGTCTCAACGGATAAACCGAAGTAATAGTCGCGTCCAGCGCTATAATGTAAGTGA
** *
30957221 CACCCAGTGTCTCATGGGTTAAACCGAAGTAATAGTCGCGTCCAGCGCTATAATGTAAGTGA
1 CACCCAGTGTCTCAACGGATAAACCGAAGTAATAGTCGCGTCCAGCGCTATAATGTAAGTGA
30957283 CACCCAGTGT
1 CACCCAGTGT
30957293 GTTATGATCG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (62 bp):
CACCCAGTGTCTCAACGGATAAACCGAAGTAATAGTCGCGTCCAGCGCTATAATGTAAGTGA
Found at i:30960224 original size:5 final size:5
Alignment explanation
Indices: 30960206--30960235 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
30960196 GATGTTATGA
30960206 AAAAT AATAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAA
30960236 AATAAGTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:30973205 original size:53 final size:52
Alignment explanation
Indices: 30973082--30973432 Score: 438
Period size: 53 Copynumber: 6.7 Consensus size: 52
30973072 ACCTTTGATA
* * * *
30973082 ACTCATGATGACACAAAGTCATCAGACCT-TTAATCCGTAATAGGATTCAT-T
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCAT-ATAGGATTCATAT
* * *
30973133 ACTCACGATGACACGTAGTCATCGGACCTGTAAATCCATAGT-GAGATTCGTAT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCATA-TAG-GATTCATAT
* * * *
30973186 ACTCACGATGGCACATAGTCATCTGACCTATTAATCCATTATAGGATTCATGT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCA-TATAGGATTCATAT
**
30973239 ACTCACGATGACACATAGTCATCGGACCTGTTAATCTGTAATAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCAT-ATAGGATTCATAT
* ** * *
30973292 ACTCACGATGACACGTAGTCATCGGACCTGTTAATTCGTTATAGCATTCATGT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAA-TCCATATAGGATTCATAT
*
30973345 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCAT-ATAGGATTCATAT
*
30973398 ACTCACGATGACACATAGTCATAGGACCTGTTAAT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAAT
30973433 TCCTTTCCTT
Statistics
Matches: 260, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
51 27 0.10
52 18 0.07
53 209 0.80
54 6 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCGGACCTGTTAATCCATATAGGATTCATAT
Found at i:30973373 original size:159 final size:158
Alignment explanation
Indices: 30973082--30973432 Score: 510
Period size: 159 Copynumber: 2.2 Consensus size: 158
30973072 ACCTTTGATA
* * *
30973082 ACTCATGATGACACAAAGTCATCAGACCT-TTAATCCGTAATAGGATTCATTACTCACGATGACA
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATTACTCACGATGACA
* * *
30973146 CGTAGTCATCGGACCTGTAAATCCATAGTGAGATTCGTATACTCACGATGGCACATAGTCATCTG
66 CGTAGTCATCGGACCTGTAAATCCATAGTGAGATTCATATACTCACGATGACACATAGTCATCGG
* *
30973211 ACCTATTAATCCATTATAGGATTCATGT
131 ACCTATTAATCCATAATAGGATTCATAT
*
30973239 ACTCACGATGACACATAGTCATCGGACCTGTTAATCTGTAATAGGATTCATATACTCACGATGAC
1 ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCAT-TACTCACGATGAC
* ** *
30973304 ACGTAGTCATCGGACCTGTTAATTCGTTA-T-AGCATTCATGTACTCACGATGACACATAGTCAT
65 ACGTAGTCATCGGACCTG-TAAATCCATAGTGAG-ATTCATATACTCACGATGACACATAGTCAT
* *
30973367 CGGACCTGTTAATCCGTAATAGGATTCATAT
128 CGGACCTATTAATCCATAATAGGATTCATAT
*
30973398 ACTCACGATGACACATAGTCATAGGACCTGTTAAT
1 ACTCACGATGACACATAGTCATCGGACCTGTTAAT
30973433 TCCTTTCCTT
Statistics
Matches: 174, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
157 26 0.15
158 22 0.13
159 119 0.68
160 7 0.04
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (158 bp):
ACTCACGATGACACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATTACTCACGATGACA
CGTAGTCATCGGACCTGTAAATCCATAGTGAGATTCATATACTCACGATGACACATAGTCATCGG
ACCTATTAATCCATAATAGGATTCATAT
Found at i:30973434 original size:106 final size:106
Alignment explanation
Indices: 30973082--30973432 Score: 494
Period size: 106 Copynumber: 3.3 Consensus size: 106
30973072 ACCTTTGATA
* * *
30973082 ACTCATGATGACACAAAGTCATCA-GACCT-TTAATCCGTAATAGGATTCAT-TACTCACGATGA
1 ACTCACGATGACACATAGTCAT-AGGACCTGTTAATCCGTTATAGGATTCATGTACTCACGATGA
* * * * *
30973144 CACGTAGTCATCGGACCTGTAAATCCATAGT-GAGATTCGTAT
65 CACATAGTCATCGGACCTGTTAATCCGTAATAG-GATTCATAT
* ** * *
30973186 ACTCACGATGGCACATAGTCATCTGACCTATTAATCCATTATAGGATTCATGTACTCACGATGAC
1 ACTCACGATGACACATAGTCATAGGACCTGTTAATCCGTTATAGGATTCATGTACTCACGATGAC
*
30973251 ACATAGTCATCGGACCTGTTAATCTGTAATAGGATTCATAT
66 ACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
* * * *
30973292 ACTCACGATGACACGTAGTCATCGGACCTGTTAATTCGTTATAGCATTCATGTACTCACGATGAC
1 ACTCACGATGACACATAGTCATAGGACCTGTTAATCCGTTATAGGATTCATGTACTCACGATGAC
30973357 ACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
66 ACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
30973398 ACTCACGATGACACATAGTCATAGGACCTGTTAAT
1 ACTCACGATGACACATAGTCATAGGACCTGTTAAT
30973433 TCCTTTCCTT
Statistics
Matches: 221, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
104 24 0.11
105 19 0.09
106 177 0.80
107 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (106 bp):
ACTCACGATGACACATAGTCATAGGACCTGTTAATCCGTTATAGGATTCATGTACTCACGATGAC
ACATAGTCATCGGACCTGTTAATCCGTAATAGGATTCATAT
Found at i:30975555 original size:24 final size:24
Alignment explanation
Indices: 30975527--30975585 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
30975517 TAGACTAATA
*
30975527 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
30975551 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
30975575 AGAGTTTAACT
1 AGAGTTTAACT
30975586 AAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:30988008 original size:16 final size:17
Alignment explanation
Indices: 30987987--30988020 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
30987977 ATTTATAAAT
30987987 ATTTTTGAAAG-TTTTA
1 ATTTTTGAAAGCTTTTA
*
30988003 ATTTTTTAAAGCTTTTA
1 ATTTTTGAAAGCTTTTA
30988020 A
1 A
30988021 AAAATGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (17 bp):
ATTTTTGAAAGCTTTTA
Found at i:30988463 original size:25 final size:26
Alignment explanation
Indices: 30988435--30988499 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 26
30988425 TACAAAATAT
30988435 TTAAAAATATTTAAT-TAATTTAGAA
1 TTAAAAATATTTAATGTAATTTAGAA
** * **
30988460 TTAATTATA-TTAATGTTATTTAGTT
1 TTAAAAATATTTAATGTAATTTAGAA
30988485 TTAAAAATATTTAAT
1 TTAAAAATATTTAAT
30988500 ATTAAAATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
24 5 0.16
25 21 0.68
26 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (26 bp):
TTAAAAATATTTAATGTAATTTAGAA
Found at i:30988536 original size:6 final size:6
Alignment explanation
Indices: 30988525--30988560 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
30988515 AAGGTTATCA
30988525 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
30988561 ATTATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATAT
Found at i:30993248 original size:81 final size:81
Alignment explanation
Indices: 30993070--30993397 Score: 399
Period size: 81 Copynumber: 4.0 Consensus size: 81
30993060 AAATATAAAA
* * * * * *
30993070 AATTGAATAGATCTATTTCGGGATTTATTCCTTCCGTTGAACAAATTTTATTTTATTTTTTATTT
1 AATTGAATAAATCTGTTTCGAGATTTATTCCTTCCATTGAACAAATTTTATTCTA-TTTTGATTT
30993135 GTTTCCAAACAAGAATT
65 GTTTCCAAACAAGAATT
* * * *
30993152 ATTTGAATAAATCTGTTTCGAGATTTATTCGTGCCATTGAATAAATTTTATTCTATTTTGATTTG
1 AATTGAATAAATCTGTTTCGAGATTTATTCCTTCCATTGAACAAATTTTATTCTATTTTGATTTG
*
30993217 TTTCCAAACAATAATT
66 TTTCCAAACAAGAATT
* * * * * *
30993233 AATTGAATAAATCTGTTTCGAGATTTATTCC-TACGTT-AATAGATTTTATTTTATTTTGATTTA
1 AATTGAATAAATCTGTTTCGAGATTTATTCCTTCCATTGAACAAATTTTATTCTATTTTGATTTG
* *
30993296 TTTCTAAATAAGAATT
66 TTTCCAAACAAGAATT
* * * *
30993312 AATTGAATAAATCTGCTTCGAGATTTATTCCTTCCATTCAACAAATTGTATTCCATTTTGATTTT
1 AATTGAATAAATCTGTTTCGAGATTTATTCCTTCCATTGAACAAATTTTATTCTATTTTGA-TTT
* *
30993377 GCTTCCAAACAAGAAAT
65 GTTTCCAAACAAGAATT
30993394 AATT
1 AATT
30993398 AAAATTTTTA
Statistics
Matches: 208, Mismatches: 35, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
79 66 0.32
80 7 0.03
81 70 0.34
82 65 0.31
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (81 bp):
AATTGAATAAATCTGTTTCGAGATTTATTCCTTCCATTGAACAAATTTTATTCTATTTTGATTTG
TTTCCAAACAAGAATT
Found at i:30993325 original size:160 final size:164
Alignment explanation
Indices: 30993070--30993397 Score: 439
Period size: 160 Copynumber: 2.0 Consensus size: 164
30993060 AAATATAAAA
* * * *
30993070 AATTGAATAGATCTATTTCGGGATTTATTCCTTCCGTTGAACAAATTTTATTTTATTTTTTATTT
1 AATTGAATAAATCTATTTCGAGATTTATTCCTTACGTTGAACAAATTTTATTTTATTTTTGATTT
* * * * * * *
30993135 GTTTCCAAACAAGAATTATTTGAATAAATCTGTTTCGAGATTTATTCGTGCCATTGAATAAATTT
66 ATTTCCAAACAAGAATTAATTGAATAAATCTGCTTCGAGATTTATTCCTGCCATTCAACAAATTG
* * * *
30993200 TATTCTATTTTGA-TTTGTTTCCAAACAATAATT
131 TATTCCATTTTGATTTTGCTTCCAAACAAGAAAT
* * *
30993233 AATTGAATAAATCTGTTTCGAGATTTATTCC-TACGTT-AATAGATTTTATTTTA-TTTTGATTT
1 AATTGAATAAATCTATTTCGAGATTTATTCCTTACGTTGAACAAATTTTATTTTATTTTTGATTT
* * *
30993295 ATTTCTAAATAAGAATTAATTGAATAAATCTGCTTCGAGATTTATTCCTTCCATTCAACAAATTG
66 ATTTCCAAACAAGAATTAATTGAATAAATCTGCTTCGAGATTTATTCCTGCCATTCAACAAATTG
30993360 TATTCCATTTTGATTTTGCTTCCAAACAAGAAAT
131 TATTCCATTTTGATTTTGCTTCCAAACAAGAAAT
30993394 AATT
1 AATT
30993398 AAAATTTTTA
Statistics
Matches: 143, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
160 75 0.52
161 35 0.24
162 5 0.03
163 28 0.20
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (164 bp):
AATTGAATAAATCTATTTCGAGATTTATTCCTTACGTTGAACAAATTTTATTTTATTTTTGATTT
ATTTCCAAACAAGAATTAATTGAATAAATCTGCTTCGAGATTTATTCCTGCCATTCAACAAATTG
TATTCCATTTTGATTTTGCTTCCAAACAAGAAAT
Found at i:30993543 original size:12 final size:13
Alignment explanation
Indices: 30993526--30993556 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
30993516 TTTTCTATTT
30993526 ATTGTGGTTTT-A
1 ATTGTGGTTTTAA
30993538 ATTGTGGTTTTAA
1 ATTGTGGTTTTAA
30993551 ATTGTG
1 ATTGTG
30993557 AAAGCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (13 bp):
ATTGTGGTTTTAA
Found at i:30996326 original size:158 final size:158
Alignment explanation
Indices: 30996038--30996371 Score: 470
Period size: 158 Copynumber: 2.1 Consensus size: 158
30996028 TGTAATCATA
* * *
30996038 AATGCTCACACGAGCTGTGAAATGGGCCTGCTCATACAAGTTGTAGGTCAAGATGTGGGGCTACA
1 AATGCTCACACGAGCTGTGAAATGGGCCTGCTCACACAAGCTGTAGGTCAAGATGTGAGGCTACA
* * *
30996103 CGATGTTGCTCACACGAGCTGTGGAGAATCCGTAATAAATGTCGAACCTCAGCCATTGGTAGGAC
66 CGATGTTGCTCACACGAGCTGTGGAGAATCCGCAACAAATGTAGAACCTCAGCCATTGGTAGGAC
* * *
30996168 ATCAAAGACTAGTACCCATATAACTTGT
131 ATCAAAGACCAGCACCCATATAACCTGT
** * * **
30996196 AATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATGAGCTGTGGGTCAAGATGTTAGGCTATG
1 AATGCTCACACGAGCTGTGAAATGGGCCTGCTCACACAAGCTGTAGGTCAAGATGTGAGGCTACA
* * * * **
30996261 CGATGTTGCTTACACGAGCTGTGGAGAATCTGCAACCAATGTAGGACCTCATTCATTGGTAGGAC
66 CGATGTTGCTCACACGAGCTGTGGAGAATCCGCAACAAATGTAGAACCTCAGCCATTGGTAGGAC
*
30996326 ATCTAAGACCAGCACCCATATAACCTGT
131 ATCAAAGACCAGCACCCATATAACCTGT
30996354 AATGCTCACACGAGCTGT
1 AATGCTCACACGAGCTGT
30996372 AACTGTAACA
Statistics
Matches: 154, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
158 154 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (158 bp):
AATGCTCACACGAGCTGTGAAATGGGCCTGCTCACACAAGCTGTAGGTCAAGATGTGAGGCTACA
CGATGTTGCTCACACGAGCTGTGGAGAATCCGCAACAAATGTAGAACCTCAGCCATTGGTAGGAC
ATCAAAGACCAGCACCCATATAACCTGT
Found at i:30996703 original size:23 final size:25
Alignment explanation
Indices: 30996654--30996704 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
30996644 TACCATTCCA
*
30996654 TTATATATTATATGAAGTTCATATT
1 TTATATATTATATGAACTTCATATT
* *
30996679 TTATATA-TATATGCACTTGAT-TT
1 TTATATATTATATGAACTTCATATT
30996702 TTA
1 TTA
30996705 ATTAACTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.22
24 11 0.48
25 7 0.30
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (25 bp):
TTATATATTATATGAACTTCATATT
Found at i:30998637 original size:24 final size:25
Alignment explanation
Indices: 30998588--30998647 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
30998578 TATGATGATT
*
30998588 ATGT-ATATGTGAATATAAATGTAA
1 ATGTGATATGTGAATATAAATGGAA
30998612 ATGTGATATGTGAA-AT-AATGAGAA
1 ATGTGATATGTGAATATAAATG-GAA
30998636 ATGATGAATATG
1 ATG-TG-ATATG
30998648 AGAGATTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 4 0.13
24 11 0.35
25 11 0.35
26 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.22, T:0.33
Consensus pattern (25 bp):
ATGTGATATGTGAATATAAATGGAA
Found at i:30998790 original size:25 final size:23
Alignment explanation
Indices: 30998720--30998820 Score: 86
Period size: 23 Copynumber: 4.3 Consensus size: 23
30998710 ACACTAGCGC
*
30998720 GCCCTC-TGTTTAGCACGTT-TCGT
1 GCCCTCTTGATTAGCAC-TTGT-GT
30998743 GCCCT-TTG-TTCAGCACTGTGTGT
1 GCCCTCTTGATT-AGCACT-TGTGT
*
30998766 GCCCTCTATTATTAGCACTTCGTGT
1 GCCCTCT-TGATTAGCACTT-GTGT
30998791 GCCCT-TTGATTAGCACTTTGTGT
1 GCCCTCTTGATTAGCAC-TTGTGT
30998814 GCCCTCT
1 GCCCTCT
30998821 GTTACCCAGC
Statistics
Matches: 66, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
22 3 0.05
23 38 0.58
24 7 0.11
25 16 0.24
26 2 0.03
ACGTcount: A:0.11, C:0.29, G:0.21, T:0.40
Consensus pattern (23 bp):
GCCCTCTTGATTAGCACTTGTGT
Found at i:31000400 original size:29 final size:29
Alignment explanation
Indices: 31000367--31000435 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
31000357 ATTTCTAGTC
* *
31000367 CTTTCTTTTTTTAATTCTTTTATTATTTT
1 CTTTCTTTTTTTAATTCTTTCATCATTTT
31000396 CTTTCTTTTTTTAATTCTTTCATCATTTT
1 CTTTCTTTTTTTAATTCTTTCATCATTTT
31000425 CATTTTCTTTT
1 C--TTTCTTTT
31000436 CATTATTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 28 0.78
31 8 0.22
ACGTcount: A:0.13, C:0.14, G:0.00, T:0.72
Consensus pattern (29 bp):
CTTTCTTTTTTTAATTCTTTCATCATTTT
Found at i:31004567 original size:158 final size:158
Alignment explanation
Indices: 31004288--31004616 Score: 455
Period size: 158 Copynumber: 2.1 Consensus size: 158
31004278 GTAACCATAT
* * * *
31004288 ATGCTCACACAAGTTGTGAAATGGGCCTGCTCACACGAGCTGTAGGTCGAGATGTGGGGTTACAC
1 ATGCTCACACGAGTAGTGAAATGGGCCTGCTCACACGAGCTGTAGGTCGAGATGTGAGGCTACAC
* * * *
31004353 GATGTTGTTCACACGAGTTGTGGAAAATCCGCAATAAATGTCAGACCTCATCCATCGGTAAGACA
66 GATGTTGCTCACACGAGTTGTGCAAAATCCGCAACAAATGTCAGACCTCAGCCATCGGTAAGACA
31004418 TCTAAGACCAGAACCCATATAACCTGTA
131 TCTAAGACCAGAACCCATATAACCTGTA
* * *
31004446 ATGCTCACACGAGTAGTGAAATGGGCCTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACGC
1 ATGCTCACACGAGTAGTGAAATGGGCCTGCTCACACGAGCTGTAGGTCGAGATGTGAGGCTACAC
* * * * * *
31004511 TATGTTGCTCACACGAGCTT-TGCAGAATTCGCAACCAATG-CAGGACCTTAGCCATCGGTAGGA
66 GATGTTGCTCACACGAG-TTGTGCAAAATCCGCAACAAATGTCA-GACCTCAGCCATCGGTAAGA
* *
31004574 CATCTAAGACCAGCACCCATATAACTTGTA
129 CATCTAAGACCAGAACCCATATAACCTGTA
31004604 ATGCTCACACGAG
1 ATGCTCACACGAG
31004617 CTGTAACTGT
Statistics
Matches: 150, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
157 2 0.01
158 146 0.97
159 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (158 bp):
ATGCTCACACGAGTAGTGAAATGGGCCTGCTCACACGAGCTGTAGGTCGAGATGTGAGGCTACAC
GATGTTGCTCACACGAGTTGTGCAAAATCCGCAACAAATGTCAGACCTCAGCCATCGGTAAGACA
TCTAAGACCAGAACCCATATAACCTGTA
Found at i:31006381 original size:58 final size:58
Alignment explanation
Indices: 31006319--31006438 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 58
31006309 AAAAGGAGTT
* * *
31006319 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGATTTACAAATATTTGGGTTTA
1 GTTTATAAGTGTT-TTTGAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
* *
31006377 GTTTATAAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATAAGTGTTTTTGAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
31006435 GTTT
1 GTTT
31006439 GTTAATGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 3 0.05
58 53 0.95
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (58 bp):
GTTTATAAGTGTTTTTGAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
Found at i:31006701 original size:23 final size:23
Alignment explanation
Indices: 31006658--31006702 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31006648 AAAAAAATTC
**
31006658 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
31006681 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
31006703 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:31010288 original size:44 final size:43
Alignment explanation
Indices: 31010137--31010272 Score: 139
Period size: 43 Copynumber: 3.1 Consensus size: 43
31010127 TAAAAACCAT
* * * * *
31010137 GCTAAA-AATCATGATCCTTAGCGGCGTTTTTCTCACAAACACC
1 GCTAAAGAA-CATGATCTTTAACGACGCTTTTCTCACAAACCCC
* * * ***
31010180 GCTAAAAAATATGATTTTTAACGGTACTTTTCTCACAAACCCC
1 GCTAAAGAACATGATCTTTAACGACGCTTTTCTCACAAACCCC
*
31010223 GCTAAAGAACATGATCTTTAACGACGCTTTTCTTACAAATCCCC
1 GCTAAAGAACATGATCTTTAACGACGCTTTTCTCACAAA-CCCC
31010267 GCTAAA
1 GCTAAA
31010273 ATTAACAGAT
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 64 0.84
44 12 0.16
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (43 bp):
GCTAAAGAACATGATCTTTAACGACGCTTTTCTCACAAACCCC
Found at i:31014803 original size:41 final size:41
Alignment explanation
Indices: 31014774--31014998 Score: 294
Period size: 41 Copynumber: 5.5 Consensus size: 41
31014764 TAAGTGCCGT
* * * *
31014774 TAATGTTCTGACCTTTAGAGGCGCTTTTTCATAAGCACCGC
1 TAATGCTCTGACCTTTAGCGACGCTTTCTCATAAGCACCGC
*
31014815 TAATGCTCTGACCTTTAGCGACGCTTTCTTATAAGCACCGC
1 TAATGCTCTGACCTTTAGCGACGCTTTCTCATAAGCACCGC
* *
31014856 TAATGCTCTGACTTTTAGCGACGC-TTCCCTATAAGCACCGC
1 TAATGCTCTGACCTTTAGCGACGCTTTCTC-ATAAGCACCGC
*
31014897 TAATGTTCTGACCTTTAGC-AGCGCTTTCTCATAAGCGA-CGC
1 TAATGCTCTGACCTTTAGCGA-CGCTTTCTCATAAGC-ACCGC
* * * *
31014938 TAATACTCTGACCTTTAGCGACACTTTCTCATAAGCGCTGC
1 TAATGCTCTGACCTTTAGCGACGCTTTCTCATAAGCACCGC
31014979 TAATGCTCTGACCTTTAGCG
1 TAATGCTCTGACCTTTAGCG
31014999 GCGTTTATGG
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
40 4 0.02
41 151 0.94
42 6 0.04
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (41 bp):
TAATGCTCTGACCTTTAGCGACGCTTTCTCATAAGCACCGC
Found at i:31014965 original size:123 final size:123
Alignment explanation
Indices: 31014774--31014998 Score: 355
Period size: 123 Copynumber: 1.8 Consensus size: 123
31014764 TAAGTGCCGT
* * *
31014774 TAATGTTCTGACCTTTAGAGGCGCTTTTTCATAAGCACCGCTAATGCTCTGACCTTTAGCGACGC
1 TAATGTTCTGACCTTTAGAGGCGCTTTCTCATAAGCACCGCTAATACTCTGACCTTTAGCGACAC
* *
31014839 TTTCTTATAAGCACCGCTAATGCTCTGACTTTTAGCGACGCTTCCCTATAAGCACCGC
66 TTTCTCATAAGCACCGCTAATGCTCTGACCTTTAGCGACGCTTCCCTATAAGCACCGC
31014897 TAATGTTCTGACCTTTAGCA-GCGCTTTCTCATAAGCGA-CGCTAATACTCTGACCTTTAGCGAC
1 TAATGTTCTGACCTTTAG-AGGCGCTTTCTCATAAGC-ACCGCTAATACTCTGACCTTTAGCGAC
* *
31014960 ACTTTCTCATAAGCGCTGCTAATGCTCTGACCTTTAGCG
64 ACTTTCTCATAAGCACCGCTAATGCTCTGACCTTTAGCG
31014999 GCGTTTATGG
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
123 91 0.98
124 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (123 bp):
TAATGTTCTGACCTTTAGAGGCGCTTTCTCATAAGCACCGCTAATACTCTGACCTTTAGCGACAC
TTTCTCATAAGCACCGCTAATGCTCTGACCTTTAGCGACGCTTCCCTATAAGCACCGC
Found at i:31015044 original size:40 final size:40
Alignment explanation
Indices: 31014989--31015084 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
31014979 TAATGCTCTG
* *
31014989 ACCTTTAGCGGCGTTTATGGAAAAACGACGTTAGTGCTTT
1 ACCTTTTGCGGCGTTTATGGAAAAACGACGCTAGTGCTTT
* * *
31015029 ACCTTTTGCGACGTTTATGGAAAAACGCCGCTATTGCTTT
1 ACCTTTTGCGGCGTTTATGGAAAAACGACGCTAGTGCTTT
*
31015069 ACCTTTTACGGCGTTT
1 ACCTTTTGCGGCGTTT
31015085 TCTATCCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (40 bp):
ACCTTTTGCGGCGTTTATGGAAAAACGACGCTAGTGCTTT
Found at i:31016003 original size:13 final size:13
Alignment explanation
Indices: 31015984--31016019 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
31015974 TCCTTTCTTC
31015984 TTCTTTTTTTA-T
1 TTCTTTTTTTATT
31015996 TTCTTTTTTTATT
1 TTCTTTTTTTATT
31016009 TTCTTTCTTTT
1 TTCTTT-TTTT
31016020 TTTAATTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (13 bp):
TTCTTTTTTTATT
Found at i:31016015 original size:17 final size:17
Alignment explanation
Indices: 31015976--31016023 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
31015966 ATTTCTAATC
31015976 CTTTCTTCTTCTTT-TTTT
1 CTTTCTT-TT-TTTATTTT
*
31015994 ATTTCTTTTTTTATTTT
1 CTTTCTTTTTTTATTTT
31016011 CTTTCTTTTTTTA
1 CTTTCTTTTTTTA
31016024 ATTCTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 3 0.11
17 18 0.67
18 6 0.22
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (17 bp):
CTTTCTTTTTTTATTTT
Found at i:31016038 original size:29 final size:29
Alignment explanation
Indices: 31015984--31016050 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
31015974 TCCTTTCTTC
* ** *
31015984 TTCTTTTTTTATTTCTTTTTTTATTTTCT
1 TTCTTTTTTTAATTCTTTCATCATTTTCT
31016013 TTCTTTTTTTAATTCTTTCATCATTTTCT
1 TTCTTTTTTTAATTCTTTCATCATTTTCT
*
31016042 CT-TTTTTTT
1 TTCTTTTTTT
31016051 CATTATTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (29 bp):
TTCTTTTTTTAATTCTTTCATCATTTTCT
Found at i:31019266 original size:27 final size:27
Alignment explanation
Indices: 31019236--31019310 Score: 109
Period size: 25 Copynumber: 2.9 Consensus size: 27
31019226 CGATAGAGAT
31019236 ATTCTGATTCTGGCTCGTAAGAGCATA
1 ATTCTGATTCTGGCTCGTAAGAGCATA
* *
31019263 ATTCTG--TCTTGCTCGTAAGAGCGTA
1 ATTCTGATTCTGGCTCGTAAGAGCATA
*
31019288 ATTCTGATTCTGGGTCGTAAGAG
1 ATTCTGATTCTGGCTCGTAAGAG
31019311 TGATGCTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 23 0.55
27 19 0.45
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (27 bp):
ATTCTGATTCTGGCTCGTAAGAGCATA
Found at i:31025057 original size:26 final size:26
Alignment explanation
Indices: 31025028--31025078 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
31025018 TCTGGCTCGT
**
31025028 AAGAGCGATTCTCTGTTTGGGCTTGG
1 AAGAGCGAAACTCTGTTTGGGCTTGG
* *
31025054 AAGAGCTAAACTTTGTTTGGGCTTG
1 AAGAGCGAAACTCTGTTTGGGCTTG
31025079 TATGAGCTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (26 bp):
AAGAGCGAAACTCTGTTTGGGCTTGG
Found at i:31025675 original size:21 final size:23
Alignment explanation
Indices: 31025651--31025706 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
31025641 GACTTGCATT
31025651 GTATCGGTAGTACT-ATAATA-A
1 GTATCGGTAGTACTGATAATAGA
* * *
31025672 GTATCGATAGTTCTGATCATAGTA
1 GTATCGGTAGTACTGATAATAG-A
31025696 GTATCGGTAGT
1 GTATCGGTAGT
31025707 TTGGGTACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 12 0.43
22 5 0.18
24 11 0.39
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (23 bp):
GTATCGGTAGTACTGATAATAGA
Found at i:31025822 original size:21 final size:21
Alignment explanation
Indices: 31025784--31025844 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
31025774 TAGATACATG
* * *
31025784 ATTTGTTTCGATAAAAGTCAC
1 ATTTGTATCGGTAGAAGTCAC
31025805 ATTTGTATCGGTAGAAGTATCAC
1 ATTTGTATCGGTAGAAG--TCAC
*
31025828 A--AGTATCGGTAGAAGTC
1 ATTTGTATCGGTAGAAGTC
31025845 TGCATTGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.06
21 27 0.79
23 5 0.15
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (21 bp):
ATTTGTATCGGTAGAAGTCAC
Found at i:31026364 original size:50 final size:50
Alignment explanation
Indices: 31026260--31026370 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 50
31026250 AGATATGATG
* * * *
31026260 TTTTAAATAAATATAAATATTTATTTAATTTGTTTTGTATAGATCTGGTG
1 TTTTAAATAAACATAAATATTTATTTAATTTATTTTGTATAAATCTGGTA
* *
31026310 TTTTACATAAACATAAATATTTATTT-ATATTATTTTGT-TCAAATCTTGTA
1 TTTTAAATAAACATAAATATTTATTTAAT-TTATTTTGTAT-AAATCTGGTA
*
31026360 TTTTATATAAA
1 TTTTAAATAAA
31026371 TATTTTATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 3 0.06
50 49 0.94
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (50 bp):
TTTTAAATAAACATAAATATTTATTTAATTTATTTTGTATAAATCTGGTA
Found at i:31026721 original size:15 final size:15
Alignment explanation
Indices: 31026701--31026730 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31026691 TGTAATTAAC
*
31026701 TAAAAAAATTAAATG
1 TAAAAAAATGAAATG
31026716 TAAAAAAATGAAATG
1 TAAAAAAATGAAATG
31026731 CAAGACTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (15 bp):
TAAAAAAATGAAATG
Found at i:31033207 original size:192 final size:194
Alignment explanation
Indices: 31032970--31033346 Score: 580
Period size: 198 Copynumber: 1.9 Consensus size: 194
31032960 TTAAGTACGT
* * * *
31032970 TTATAGGGATATAAGGCTCATTTCCTATTTTATCTTGTACAATTTTTGGTGATTTTTCAAAGTCA
1 TTATAGGGATATAAGGATCACTTCCTATTTTATCTTGTACAATTTTTGATAATTTTTCAAAGTCA
31033035 -C-ATCTGTTTTATAAGAATTCTGCTGCCAAATTTTTATGACCTTTCAACACTCAAAAATTCATA
66 CCAATCTGTTTTATAAGAATTCTGCTGCCAAATTTTTATGACCTTTCAACACTCAAAAATTCATA
* *
31033098 TCTTTTAAAATAAAAAT-AGAAATCAATCTCCTTTTGTTCTAAACAAAACTATACTTTCGTAGTA
131 TATTTTAAAATAAAAATCA-AAATCAATCTCCGTTTGTTCTAAACAAAACTATACTTTCGTAGTA
* *
31033162 TTATAGGGATATAAGGATCACTTCCTATTTTATCTTGTGCAATTTTTGATAATTTTTCAAATTCA
1 TTATAGGGATATAAGGATCACTTCCTATTTTATCTTGTACAATTTTTGATAATTTTTCAAAGTCA
* *
31033227 CTGCTAAATCTGTTTTATAAGAATTCTGCTGTCAAATTTTTATGATCTTTCAACACTCAAAAATT
66 C--C--AATCTGTTTTATAAGAATTCTGCTGCCAAATTTTTATGACCTTTCAACACTCAAAAATT
* *
31033292 CATATATTTTAAACTAAAAATCAAAATCAATTTCCGTTTGTTCTAAACAAAACTA
127 CATATATTTTAAAATAAAAATCAAAATCAATCTCCGTTTGTTCTAAACAAAACTA
31033347 GACTGACTCA
Statistics
Matches: 166, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
192 59 0.36
195 1 0.01
198 105 0.63
199 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (194 bp):
TTATAGGGATATAAGGATCACTTCCTATTTTATCTTGTACAATTTTTGATAATTTTTCAAAGTCA
CCAATCTGTTTTATAAGAATTCTGCTGCCAAATTTTTATGACCTTTCAACACTCAAAAATTCATA
TATTTTAAAATAAAAATCAAAATCAATCTCCGTTTGTTCTAAACAAAACTATACTTTCGTAGTA
Found at i:31033946 original size:15 final size:15
Alignment explanation
Indices: 31033926--31033956 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31033916 AAGAAAAAGA
31033926 AAGAAAAATAGGGTG
1 AAGAAAAATAGGGTG
31033941 AAGAAAAATAGGGTG
1 AAGAAAAATAGGGTG
31033956 A
1 A
31033957 TTATAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (15 bp):
AAGAAAAATAGGGTG
Found at i:31042858 original size:11 final size:11
Alignment explanation
Indices: 31042844--31042877 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
31042834 ATTTTTTTGG
31042844 TGCTATTTTTT
1 TGCTATTTTTT
*
31042855 TGCTATTTTGAT
1 TGCTATTTT-TT
31042867 TGCTATTTTTT
1 TGCTATTTTTT
31042878 GCTGTTTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.68
Consensus pattern (11 bp):
TGCTATTTTTT
Found at i:31042947 original size:23 final size:23
Alignment explanation
Indices: 31042919--31043007 Score: 74
Period size: 23 Copynumber: 3.8 Consensus size: 23
31042909 TGCTTTTTTA
*
31042919 CTATTTTTGTTT-CTGTTTTGATG
1 CTATTTTT-TTTACTATTTTGATG
*
31042942 CTATTTTTTTTACTATTTTGGTG
1 CTATTTTTTTTACTATTTTGATG
** *
31042965 CT-TTTTTTATTGTTATTTTTGTTG
1 CTATTTTTT-TTACTA-TTTTGATG
* *
31042989 CTATTTTTTCTATTATTTT
1 CTATTTTTTTTACTATTTT
31043008 TGCTCCTGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
22 9 0.16
23 27 0.49
24 13 0.24
25 6 0.11
ACGTcount: A:0.11, C:0.08, G:0.11, T:0.70
Consensus pattern (23 bp):
CTATTTTTTTTACTATTTTGATG
Found at i:31042972 original size:24 final size:23
Alignment explanation
Indices: 31042934--31043031 Score: 74
Period size: 24 Copynumber: 4.1 Consensus size: 23
31042924 TTTGTTTCTG
*
31042934 TTTTGATGCTA-TTTTTT-TTACT
1 TTTTGGTGCTATTTTTTTGTTA-T
*
31042956 ATTTTGGTGCTTTTTTTATTGTTAT
1 -TTTTGGTGCTATTTTT-TTGTTAT
* *
31042981 TTTTGTTGCTATTTTTTCTATTAT
1 TTTTGGTGCTATTTTTT-TGTTAT
* * *
31043005 TTTTGCTCCTGTTTTGTTTGTTAT
1 TTTTGGTGCTATTTT-TTTGTTAT
31043029 TTT
1 TTT
31043032 AGTTGTTTGG
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
23 10 0.16
24 43 0.70
25 5 0.08
26 3 0.05
ACGTcount: A:0.10, C:0.08, G:0.12, T:0.69
Consensus pattern (23 bp):
TTTTGGTGCTATTTTTTTGTTAT
Found at i:31042982 original size:35 final size:34
Alignment explanation
Indices: 31042912--31042995 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 34
31042902 GTTTTGGTGC
* *
31042912 TTTTTTACTATTTTTGTTTCTGTTTTGATGCTATT
1 TTTTTTACTA-TTTTGGTGCTGTTTTGATGCTATT
* * *
31042947 TTTTTTACTATTTTGGTGCTTTTTTTATTGTTATT
1 TTTTTTACTATTTTGGTGCTGTTTTGA-TGCTATT
* *
31042982 TTTGTTGCTATTTT
1 TTTTTTACTATTTT
31042996 TTCTATTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 13 0.32
35 28 0.68
ACGTcount: A:0.11, C:0.07, G:0.12, T:0.70
Consensus pattern (34 bp):
TTTTTTACTATTTTGGTGCTGTTTTGATGCTATT
Found at i:31044084 original size:23 final size:22
Alignment explanation
Indices: 31044033--31044075 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
31044023 ATCTTAAGAA
*
31044033 TATTTTATGTATATCTTTTCCT
1 TATTTTATGTATATATTTTCCT
31044055 TATTTTATGTATATTATTTTC
1 TATTTTATGTATA-TATTTTC
31044076 TTTGATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (22 bp):
TATTTTATGTATATATTTTCCT
Found at i:31051994 original size:22 final size:23
Alignment explanation
Indices: 31051966--31052016 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
31051956 ATCTCAGGAA
*
31051966 TATTTTATGTATA-TGTTTTCCT
1 TATTTTATGTATATTATTTTCCT
31051988 TATTTTATGTATATTATTTTCCT
1 TATTTTATGTATATTATTTTCCT
31052011 TGATTT
1 T-ATTT
31052017 ACGATAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 13 0.50
23 9 0.35
24 4 0.15
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.65
Consensus pattern (23 bp):
TATTTTATGTATATTATTTTCCT
Found at i:31052040 original size:61 final size:61
Alignment explanation
Indices: 31051961--31052080 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 61
31051951 CCATAATCTC
* *
31051961 AGGAATATTTTATGTATATGTTTTCCTTATTTTATGTATATTATTTTCCTTGATTTACGAT
1 AGGAATATTTTATATATATGTTTTCCTTATTTTATGTACATTATTTTCCTTGATTTACGAT
* *
31052022 AGGAATATTTTATATATATTTTTTCCTTATTTTATGTACATTATTTTTCTTGATTTACG
1 AGGAATATTTTATATATATGTTTTCCTTATTTTATGTACATTATTTTCCTTGATTTACG
31052081 GTCTAATTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (61 bp):
AGGAATATTTTATATATATGTTTTCCTTATTTTATGTACATTATTTTCCTTGATTTACGAT
Found at i:31053163 original size:81 final size:81
Alignment explanation
Indices: 31053007--31053174 Score: 185
Period size: 81 Copynumber: 2.1 Consensus size: 81
31052997 TCCCTACTGC
* ** ** * *
31053007 TATTATTTATTTTTCGGTAACTACTTTGCTATTCAATTTCTGGCTCTTCACATCTCTGCAACTGT
1 TATTTTTTATTTTTCGACAACTACTTTGCTATTCAATTGATGGCTCTTCACATCTATGCAACTGC
* *
31053072 TCCTTGCTGCTATTAT
66 TCCCTACTGCTATTAT
* * * * * *
31053088 TATTTTTTATTTTTCGACAATTGCTTTGCTATTCCATTGATGGCTCTTGACGTCTATGCAGCTGC
1 TATTTTTTATTTTTCGACAACTACTTTGCTATTCAATTGATGGCTCTTCACATCTATGCAACTGC
*
31053153 TCCCTACTGCTCTTAT
66 TCCCTACTGCTATTAT
31053169 T-TTTTT
1 TATTTTT
31053175 GTTTTTTATG
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
80 5 0.07
81 66 0.93
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (81 bp):
TATTTTTTATTTTTCGACAACTACTTTGCTATTCAATTGATGGCTCTTCACATCTATGCAACTGC
TCCCTACTGCTATTAT
Found at i:31053632 original size:21 final size:21
Alignment explanation
Indices: 31053584--31053643 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
31053574 GAACAGTGCA
* *
31053584 TACTTCTACTGATACAAGTGG
1 TACTTCTACCGATACAAGAGG
*
31053605 TAGTTCTACCGATACAAGAGG
1 TACTTCTACCGATACAAGAGG
*
31053626 CT-CTTCTACCGAAACAAG
1 -TACTTCTACCGATACAAG
31053644 TCATACTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (21 bp):
TACTTCTACCGATACAAGAGG
Found at i:31061878 original size:11 final size:11
Alignment explanation
Indices: 31061845--31061887 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
31061835 TGGCAATATA
*
31061845 TTTCTTTTCTC
1 TTTCTTTTTTC
*
31061856 TTT-TCTTCTTC
1 TTTCT-TTTTTC
31061867 TTTCTTTTTTC
1 TTTCTTTTTTC
31061878 TTTCTTTTTT
1 TTTCTTTTTT
31061888 AAATAAGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 1 0.04
11 25 0.93
12 1 0.04
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:31062960 original size:19 final size:21
Alignment explanation
Indices: 31062933--31062971 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
31062923 TTCTCATCAG
31062933 ATTCCCCTTC-C-TTTCCTTT
1 ATTCCCCTTCTCATTTCCTTT
*
31062952 ATTCTCCTTCTCATTTCCTT
1 ATTCCCCTTCTCATTTCCTT
31062972 CTTCTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTCCCCTTCTCATTTCCTTT
Found at i:31063544 original size:16 final size:16
Alignment explanation
Indices: 31063519--31063549 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31063509 TGGGCGTATT
31063519 TTCTTGCTTTTCCTTC
1 TTCTTGCTTTTCCTTC
*
31063535 TTCTTTCTTTTCCTT
1 TTCTTGCTTTTCCTT
31063550 TTATCCTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (16 bp):
TTCTTGCTTTTCCTTC
Found at i:31071892 original size:21 final size:19
Alignment explanation
Indices: 31071864--31071902 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
31071854 TTTTATATGG
31071864 AATTTTGAATTAAAGATTTT
1 AATTTTGAATTAAA-ATTTT
31071884 AATTATTGAATTAAAATTT
1 AATT-TTGAATTAAAATTT
31071903 AGTATAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (19 bp):
AATTTTGAATTAAAATTTT
Found at i:31074030 original size:195 final size:197
Alignment explanation
Indices: 31073579--31074030 Score: 522
Period size: 195 Copynumber: 2.3 Consensus size: 197
31073569 AACCGACGTT
* * * *
31073579 ATGGCTAAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGCGAGCAGCATCGTGAGTCGGG
1 ATGGCTGAGGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGGG
*
31073644 AAATGAGAAAAGAAATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGAGATTTATGCAT
66 -AATGAG--AAG-AATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGAGACTTATGCAT
* * * * * *
31073709 AAGTGCATATTCTCGACGGTTTGTGTGAGCAGCATCGTTAGGGAACAGTTATATGCACAGATACC
127 AAGTGCATACTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGACACC
*
31073774 GTATCG
192 GTACCG
*
31073780 ATGGCTGAGGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGTAGCATCGTGACTCGGG
1 ATGGCTGAGGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGGG
* * * * * *
31073845 -A-GAG-AG-ATATGGATCTTAAATGGATTACAGGCCCTATGATGGCTGGGACTT-TGC-TTATT
66 AATGAGAAGAATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGAGACTTATGCATAAGT
* *
31073904 GCATACTCTCGACAGCTCGTTTGAGCAGCATCGTTAGGGAATAGTTTATAGTACAAACA-AGCAC
131 GCATACTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAG-TTATA-TAC--ACAGA-CAC
31073968 CGTACCG
191 CGTACCG
* * * * ** *
31073975 ATTGTTGGGGTATTGCATATGTTATGAGTCCTCTACAGCTCGTGTGAGCAGCATCG
1 ATGGCTGAGGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
31074031 AGTACTGGTA
Statistics
Matches: 217, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
191 41 0.19
192 8 0.04
193 42 0.19
194 1 0.00
195 61 0.28
198 3 0.01
199 1 0.00
201 60 0.28
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (197 bp):
ATGGCTGAGGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGGG
AATGAGAAGAATATGGATCCTAAATGGATTACAAGCCCTACGATGGCTGAGACTTATGCATAAGT
GCATACTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGACACCGTAC
CG
Found at i:31074834 original size:21 final size:21
Alignment explanation
Indices: 31074783--31074834 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
31074773 AGAGGTTTTA
31074783 GTATCGGTAGAAGCATTACAT
1 GTATCGGTAGAAGCATTACAT
* *
31074804 GTTTCGGTAGAAGTCA-TACTT
1 GTATCGGTAGAAG-CATTACAT
*
31074825 GTATCAGTAG
1 GTATCGGTAG
31074835 TATTGTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGCATTACAT
Found at i:31077335 original size:15 final size:15
Alignment explanation
Indices: 31077303--31077331 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31077293 ATGTATGACG
31077303 CTTCTTCTTCCTCCT
1 CTTCTTCTTCCTCCT
31077318 CTTCTTC-TCCTCCT
1 CTTCTTCTTCCTCCT
31077332 TCTTGTGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (15 bp):
CTTCTTCTTCCTCCT
Found at i:31077694 original size:18 final size:19
Alignment explanation
Indices: 31077649--31077688 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
31077639 TTTCTTAACA
31077649 TTAACATGGGTTTCCTCCTC
1 TTAACA-GGGTTTCCTCCTC
31077669 TCTAACAGGAGTTTCCTCCT
1 T-TAACAGG-GTTTCCTCCT
31077689 TAACAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.17, C:0.30, G:0.15, T:0.38
Consensus pattern (19 bp):
TTAACAGGGTTTCCTCCTC
Found at i:31082321 original size:21 final size:21
Alignment explanation
Indices: 31082275--31082350 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
31082265 ACAGTGTAGA
*
31082275 CTTCTACTGATACAA-ATGAT
1 CTTCTACCGATACAAGATGAT
31082295 CGTTCTACCGATACAAGAT-ACT
1 C-TTCTACCGATACAAGATGA-T
* * *
31082317 CTTCTATCGAAACAAG-TCAT
1 CTTCTACCGATACAAGATGAT
*
31082337 ACTTCTACCTATAC
1 -CTTCTACCGATAC
31082351 TAAAAACTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.07
21 38 0.84
22 4 0.09
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (21 bp):
CTTCTACCGATACAAGATGAT
Found at i:31087902 original size:49 final size:47
Alignment explanation
Indices: 31087849--31087941 Score: 141
Period size: 47 Copynumber: 1.9 Consensus size: 47
31087839 CAAAAATATT
*
31087849 TCTCAAAAAGAAAACACTCATATATAATACGCATTTATTTTGTGTAAAA
1 TCTC-AAAA-AAAACACTCATATATAATACACATTTATTTTGTGTAAAA
* *
31087898 TCTCATAAAAAACACTCATATATAATACACATTTGTTTTGTGTA
1 TCTCAAAAAAAACACTCATATATAATACACATTTATTTTGTGTA
31087942 TCTCTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 34 0.83
48 3 0.07
49 4 0.10
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (47 bp):
TCTCAAAAAAAACACTCATATATAATACACATTTATTTTGTGTAAAA
Found at i:31090756 original size:22 final size:22
Alignment explanation
Indices: 31090728--31090770 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31090718 CTCTAGGTCG
*
31090728 TGACATAATGGGGTGCTTGTCT
1 TGACATAATGGAGTGCTTGTCT
31090750 TGACATAATGGAGTGCTTGTC
1 TGACATAATGGAGTGCTTGTC
31090771 GCAACATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (22 bp):
TGACATAATGGAGTGCTTGTCT
Found at i:31090777 original size:22 final size:22
Alignment explanation
Indices: 31090730--31090777 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
31090720 CTAGGTCGTG
* ***
31090730 ACATAATGGGGTGCTTGTCTTG
1 ACATAATGGAGTGCTTGTCGCA
31090752 ACATAATGGAGTGCTTGTCGCA
1 ACATAATGGAGTGCTTGTCGCA
31090774 ACAT
1 ACAT
31090778 TCTCCTTAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (22 bp):
ACATAATGGAGTGCTTGTCGCA
Found at i:31099395 original size:30 final size:30
Alignment explanation
Indices: 31099280--31099407 Score: 118
Period size: 30 Copynumber: 4.3 Consensus size: 30
31099270 AATTAAAACC
* * *
31099280 GGGTCAAATTTGAATTTTTGA-AAATTTTG
1 GGGTCAAATTAGAATTTTTGAGAAAATTTA
* * * *
31099309 GGGCCAAATTAGAAGTTCT-AGAAAGTTTA
1 GGGTCAAATTAGAATTTTTGAGAAAATTTA
* *
31099338 GAGGTCAAATTGGAATTTTTTAGAAAATTTAA
1 G-GGTCAAATTAGAATTTTTGAGAAAATTT-A
*
31099370 GGGTCGAATTAGAATTTTTGA-AAAATTTGA
1 GGGTCAAATTAGAATTTTTGAGAAAATTT-A
31099400 GGGTCAAA
1 GGGTCAAA
31099408 AAATAATTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
28 1 0.01
29 22 0.28
30 29 0.37
31 25 0.32
32 2 0.03
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
GGGTCAAATTAGAATTTTTGAGAAAATTTA
Found at i:31099405 original size:61 final size:58
Alignment explanation
Indices: 31099280--31099407 Score: 132
Period size: 61 Copynumber: 2.1 Consensus size: 58
31099270 AATTAAAACC
* ** *
31099280 GGGTCAAATTTGAATTTTTGAAAATTTTGGGGCCAAATTAGAAGTTCTAGAAAGTTTA
1 GGGTCAAATTGGAATTTTTGAAAATTTAAGGGCCAAATTAGAAGTTCTAGAAAATTTA
* * * *
31099338 GAGGTCAAATTGGAATTTTTTAGAAAATTTAAGGGTCGAATTAGAA-TTTTTGAAAAATTTGA
1 G-GGTCAAATTGGAA-TTTTT-GAAAATTTAAGGGCCAAATTAGAAGTTCTAG-AAAATTT-A
31099400 GGGTCAAA
1 GGGTCAAA
31099408 AAATAATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
58 1 0.02
59 12 0.21
60 9 0.16
61 33 0.58
62 2 0.04
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (58 bp):
GGGTCAAATTGGAATTTTTGAAAATTTAAGGGCCAAATTAGAAGTTCTAGAAAATTTA
Found at i:31101630 original size:80 final size:80
Alignment explanation
Indices: 31101026--31101633 Score: 894
Period size: 80 Copynumber: 7.6 Consensus size: 80
31101016 TCGGGGCAAG
* * * ** * * * *
31101026 AGATTAGATTATCTTCAATCTGCCTCATGGTTAGGGTAAAAGATCGGATGGTTTTTAATCTTACC
1 AGATTGGATT-TCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAATCTTGCC
*
31101091 CTTTAGTTAGGGTAAA
65 CTCTAGTTAGGGTAAA
* * *
31101107 AGATTGGATTTCTTCAATCTGTCCCATGATCGGGATAAAAGATTGGACGGTCTTCAATCTTGCCC
1 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAATCTTGCCC
*
31101172 TCTGGTTAGGGTAAA
66 TCTAGTTAGGGTAAA
* *
31101187 AGATTGGATTTTTTCAATCTGCCCCATGATCGGGGTAAAAGATCT-GATGGTCTTCAAGCTTGCC
1 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGAT-TGGATGGTCTTCAATCTTGCC
31101251 CTCTAGTTAGGGTAAA
65 CTCTAGTTAGGGTAAA
* * * * *
31101267 AGATTAGATTTCTTCAATCTGCTCCATGATCAGGGTAAAAGATCGGACGGTCTTCAATCTTGCCC
1 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAATCTTGCCC
31101332 TCTAGTTAGGGTAAA
66 TCTAGTTAGGGTAAA
* * *
31101347 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCTATCTTGTCC
1 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAATCTTGCCC
*
31101412 TCTGGTTAGGGTAAA
66 TCTAGTTAGGGTAAA
* * * *
31101427 AGATTAGATTTCTTCAATCTGCCCCAAGATCGGGGTAAAAGATTGGATGGACTTTAATCTTGCCC
1 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAATCTTGCCC
31101492 TCTAGTTAGGGTAAA
66 TCTAGTTAGGGTAAA
* *
31101507 AGATTGGATTTCTTCAATCTGCCTCATGATCGGGGTAAAAGATTGGACGGTCTTCAATCTTGCCC
1 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAATCTTGCCC
*
31101572 TCTGGTTAGGGTAAA
66 TCTAGTTAGGGTAAA
*
31101587 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
1 AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGA
31101634 GGTTGTCACT
Statistics
Matches: 474, Mismatches: 51, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
80 464 0.98
81 10 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (80 bp):
AGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAATCTTGCCC
TCTAGTTAGGGTAAA
Found at i:31101773 original size:50 final size:50
Alignment explanation
Indices: 31101687--31101813 Score: 157
Period size: 50 Copynumber: 2.6 Consensus size: 50
31101677 GTCCGTGTGA
* *
31101687 CTTCAATATGCCCC-CTACAGCTTTAGGTGAAAGAGATTTGTAATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAAAGAGATTTGCAATTGCGG
* * * * *
31101736 CTTCATTCTGCCCCTCTACAGGTTTAGGTGTATGAGATTTGCCATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAAAGAGATTTGCAATTGCGG
* * *
31101786 TTTCAATCTGCACCTCCACAGCTTTAGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGG
31101814 GGCAAAAGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
49 12 0.18
50 53 0.82
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (50 bp):
CTTCAATCTGCCCCTCTACAGCTTTAGGTGAAAGAGATTTGCAATTGCGG
Found at i:31109896 original size:8 final size:8
Alignment explanation
Indices: 31109877--31109907 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
31109867 AATGTATGAA
31109877 AATGCAATG
1 AATGC-ATG
31109886 AATGCATG
1 AATGCATG
31109894 AATGCATG
1 AATGCATG
31109902 AATGCA
1 AATGCA
31109908 AATGCAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (8 bp):
AATGCATG
Found at i:31113570 original size:30 final size:32
Alignment explanation
Indices: 31113515--31113582 Score: 97
Period size: 30 Copynumber: 2.2 Consensus size: 32
31113505 AAAGTTTAGA
*
31113515 GGTCAAATTAGAATTTTTTGGAAAATTT-AAG
1 GGTCAAATTAGAATTTTTTGAAAAATTTGAAG
*
31113546 GGTCGAATTAGAA-TTTTTGAAAAATTTGAA-
1 GGTCAAATTAGAATTTTTTGAAAAATTTGAAG
31113576 GGTCAAA
1 GGTCAAA
31113583 AAATAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (32 bp):
GGTCAAATTAGAATTTTTTGAAAAATTTGAAG
Found at i:31117495 original size:7 final size:7
Alignment explanation
Indices: 31117477--31117514 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
31117467 CAAGAGCAAA
31117477 CTTCCC-
1 CTTCCCT
31117483 CTTCCCT
1 CTTCCCT
31117490 CTTCCCT
1 CTTCCCT
31117497 CTTCCC-
1 CTTCCCT
31117503 CTTCCCT
1 CTTCCCT
31117510 CTTCC
1 CTTCC
31117515 TTGTCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (7 bp):
CTTCCCT
Found at i:31117495 original size:13 final size:14
Alignment explanation
Indices: 31117477--31117514 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
31117467 CAAGAGCAAA
31117477 CTTCCC-CTTCCCT
1 CTTCCCTCTTCCCT
31117490 CTTCCCTCTTCCC-
1 CTTCCCTCTTCCCT
31117503 CTTCCCTCTTCC
1 CTTCCCTCTTCC
31117515 TTGTCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (14 bp):
CTTCCCTCTTCCCT
Found at i:31117502 original size:20 final size:20
Alignment explanation
Indices: 31117477--31117514 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
31117467 CAAGAGCAAA
31117477 CTTCCCCTTCCCTCTTCCCT
1 CTTCCCCTTCCCTCTTCCCT
31117497 CTTCCCCTTCCCTCTTCC
1 CTTCCCCTTCCCTCTTCC
31117515 TTGTCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (20 bp):
CTTCCCCTTCCCTCTTCCCT
Found at i:31122741 original size:21 final size:20
Alignment explanation
Indices: 31122707--31122750 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
31122697 TTAGGAAAAC
*
31122707 TTTATTTTTATTAATTTAGT
1 TTTATTTTTATTAATTTAAT
*
31122727 TTTATTTTTGTTTAATTTAAT
1 TTTATTTTT-ATTAATTTAAT
31122748 TTT
1 TTT
31122751 TAAATTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTATTTTTATTAATTTAAT
Found at i:31124593 original size:6 final size:6
Alignment explanation
Indices: 31124582--31124631 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
31124572 AGGGGAGGGT
**
31124582 TTAATA TTAATA -TAATTA TTTTTA TTCAATA TTAATA TTAATA TTAATA
1 TTAATA TTAATA TTAA-TA TTAATA TT-AATA TTAATA TTAATA TTAATA
31124631 T
1 T
31124632 AAAATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 3 0.08
6 29 0.78
7 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAATA
Found at i:31124755 original size:23 final size:23
Alignment explanation
Indices: 31124729--31124795 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 23
31124719 ATTTTTTTAA
31124729 AAAAATTATTATTATATTTTTTG
1 AAAAATTATTATTATATTTTTTG
*
31124752 -AAAA-T-TTA-T-TA-TTGTT-
1 AAAAATTATTATTATATTTTTTG
31124768 AAAAATTTATTATTATATTTTTTG
1 AAAAA-TTATTATTATATTTTTTG
31124792 AAAA
1 AAAA
31124796 TATTTATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
17 8 0.24
18 2 0.06
19 2 0.06
20 6 0.18
21 2 0.06
22 6 0.18
23 4 0.12
24 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
AAAAATTATTATTATATTTTTTG
Found at i:31130252 original size:6 final size:6
Alignment explanation
Indices: 31130241--31130269 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31130231 TACTCATATT
31130241 ATATAA ATATAA ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATA
31130270 CAACCTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:31133534 original size:13 final size:13
Alignment explanation
Indices: 31133518--31133542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31133508 ATTCAAAAAA
31133518 AAAAAATTTAAAT
1 AAAAAATTTAAAT
31133531 AAAAAATTTAAA
1 AAAAAATTTAAA
31133543 AAATATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATTTAAAT
Found at i:31134291 original size:12 final size:12
Alignment explanation
Indices: 31134276--31134301 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31134266 ATACACTTAA
31134276 AAATATTAAAAC
1 AAATATTAAAAC
31134288 AAATATTAAAAC
1 AAATATTAAAAC
31134300 AA
1 AA
31134302 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:31137742 original size:19 final size:21
Alignment explanation
Indices: 31137718--31137769 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
31137708 AAGATCAAAT
31137718 GTATTGATACTTTTGA-A-AA
1 GTATTGATACTTTTGATATAA
* * *
31137737 GTATTGGTAC-TCTGATATGA
1 GTATTGATACTTTTGATATAA
31137757 GTATTGATACTTT
1 GTATTGATACTTT
31137770 AATTCGATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 4 0.16
19 10 0.40
20 10 0.40
21 1 0.04
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (21 bp):
GTATTGATACTTTTGATATAA
Found at i:31141605 original size:16 final size:17
Alignment explanation
Indices: 31141565--31141606 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
31141555 TAATAATTAT
31141565 TCAATTTCACATATAAC
1 TCAATTTCACATATAAC
* * *
31141582 TTAATTTCACATCTCA-
1 TCAATTTCACATATAAC
31141598 TCAATTTCA
1 TCAATTTCA
31141607 TTTCATATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (17 bp):
TCAATTTCACATATAAC
Found at i:31145173 original size:28 final size:28
Alignment explanation
Indices: 31145129--31145182 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
31145119 GGTAACAGGT
31145129 ATGACCTTTGGGACAACAGGGAGTAAGC
1 ATGACCTTTGGGACAACAGGGAGTAAGC
*
31145157 ATGACCTTTGGGTCAACAGGGAGTAA
1 ATGACCTTTGGGACAACAGGGAGTAA
31145183 ATCGGATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.20
Consensus pattern (28 bp):
ATGACCTTTGGGACAACAGGGAGTAAGC
Found at i:31151148 original size:30 final size:29
Alignment explanation
Indices: 31151110--31151173 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
31151100 CATTCCACAT
31151110 CTTTATACACACATACATTAATTATGAAC
1 CTTTATACACACATACATTAATTATGAAC
*
31151139 CTTTGATACACACGTACATTAATTATGAAC
1 CTTT-ATACACACATACATTAATTATGAAC
*
31151169 TTTTA
1 CTTTA
31151174 ATTTTGAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (29 bp):
CTTTATACACACATACATTAATTATGAAC
Found at i:31156859 original size:13 final size:14
Alignment explanation
Indices: 31156835--31156864 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
31156825 AATTATATGC
31156835 TAATTAATTTTAAT
1 TAATTAATTTTAAT
31156849 TAATT-ATTTTAAT
1 TAATTAATTTTAAT
31156862 TAA
1 TAA
31156865 GCTTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTAATTTTAAT
Found at i:31156861 original size:23 final size:22
Alignment explanation
Indices: 31156835--31156879 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
31156825 AATTATATGC
**
31156835 TAATTAATTTTAATTAATTATTT
1 TAATTAAGCTTAATT-ATTATTT
31156858 TAATTAAGCTTAATTATTATTT
1 TAATTAAGCTTAATTATTATTT
31156880 AATCTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TAATTAAGCTTAATTATTATTT
Found at i:31157962 original size:32 final size:29
Alignment explanation
Indices: 31157884--31157962 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
31157874 TTATCCAAAA
* **
31157884 GTACCTAGTTGGTACTTGAATTATTTTTT
1 GTACCTAGTTGGTACTTGAATTATATTCC
31157913 GTACCTAGTTGGTACTTGAACTTATATTCC
1 GTACCTAGTTGGTACTTGAA-TTATATTCC
*
31157943 GTCACCTAGGTTGATACTTG
1 GT-ACCTA-GTTGGTACTTG
31157963 TACTCTAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 20 0.47
30 8 0.19
31 5 0.12
32 10 0.23
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (29 bp):
GTACCTAGTTGGTACTTGAATTATATTCC
Found at i:31159286 original size:3 final size:3
Alignment explanation
Indices: 31159278--31159308 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31159268 TTAATATTTG
31159278 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
31159309 AAGTTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:31161091 original size:2 final size:2
Alignment explanation
Indices: 31161034--31161072 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31161024 TAAAAATAGT
31161034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31161073 TAATACTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31161179 original size:20 final size:17
Alignment explanation
Indices: 31161140--31161173 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
31161130 TAGAGTAGTA
31161140 TATAATATATTAATTAT
1 TATAATATATTAATTAT
31161157 TATAATATATT-ATTAT
1 TATAATATATTAATTAT
31161173 T
1 T
31161174 TATTATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATAATATATTAATTAT
Found at i:31161184 original size:20 final size:20
Alignment explanation
Indices: 31161147--31161184 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31161137 GTATATAATA
31161147 TATTAATTATTATAATATAT
1 TATTAATTATTATAATATAT
* *
31161167 TATTATTTATTATTATAT
1 TATTAATTATTATAATAT
31161185 TGATTGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTAATTATTATAATATAT
Found at i:31161959 original size:4 final size:4
Alignment explanation
Indices: 31161952--31161998 Score: 69
Period size: 4 Copynumber: 11.8 Consensus size: 4
31161942 AAAAATAAAT
*
31161952 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTTA A-TA ATTA AATA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A-TTA ATTA ATTA ATTA ATT
31161999 TTTCAACTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 3 0.08
4 32 0.82
5 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:31164206 original size:25 final size:25
Alignment explanation
Indices: 31164178--31164329 Score: 167
Period size: 25 Copynumber: 6.3 Consensus size: 25
31164168 TGACAAATTT
*
31164178 TATCATATCATAATGAATAATATCA
1 TATCATATCATAATGAATCATATCA
31164203 TATCATATC--AA--AA-CGA-ATCA
1 TATCATATCATAATGAATC-ATATCA
31164223 TATCATATCATAATGAATCATATCA
1 TATCATATCATAATGAATCATATCA
* *
31164248 TATCATATCAAAACGAATCATATCA
1 TATCATATCATAATGAATCATATCA
*
31164273 TATCATA--ATGAATCATATCATATCA
1 TATCATATCAT-AATGA-ATCATATCA
* *
31164298 TATCATAACATAACGAATCATATCA
1 TATCATATCATAATGAATCATATCA
31164323 TATCATA
1 TATCATA
31164330 ATATAGCATG
Statistics
Matches: 108, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
20 13 0.12
21 3 0.03
22 2 0.02
23 3 0.03
24 6 0.06
25 76 0.70
26 3 0.03
27 2 0.02
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (25 bp):
TATCATATCATAATGAATCATATCA
Found at i:31164227 original size:45 final size:45
Alignment explanation
Indices: 31164178--31164331 Score: 254
Period size: 45 Copynumber: 3.3 Consensus size: 45
31164168 TGACAAATTT
*
31164178 TATCATATCATAATGAATAATATCATATCATATCAAAACGAATCA
1 TATCATATCATAATGAATCATATCATATCATATCAAAACGAATCA
31164223 TATCATATCATAATGAATCATATCATATCATATCAAAACGAATCA
1 TATCATATCATAATGAATCATATCATATCATATCAAAACGAATCA
31164268 TATCATATCATAATGAATCATATCATATCATATCATAACATAACGAATCA
1 TATCATATCATAATGAATCATATCATATCATATC---A-A-AACGAATCA
31164318 TATCATATCATAAT
1 TATCATATCATAAT
31164332 ATAGCATGTC
Statistics
Matches: 103, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
45 78 0.76
48 1 0.01
49 1 0.01
50 23 0.22
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (45 bp):
TATCATATCATAATGAATCATATCATATCATATCAAAACGAATCA
Found at i:31164309 original size:20 final size:20
Alignment explanation
Indices: 31164197--31164329 Score: 94
Period size: 20 Copynumber: 6.4 Consensus size: 20
31164187 ATAATGAATA
*
31164197 ATATCATATCATATCAAAAC
1 ATATCATATCATATCATAAC
31164217 GA-ATCATATCATATCATAATGAATC
1 -ATATCATATCATATC---AT-AA-C
*
31164242 ATATCATATCATATCAAAAC
1 ATATCATATCATATCATAAC
*
31164262 GA-ATCATATCATATCATAATG
1 -ATATCATATCATATCATAA-C
*
31164283 A-ATCATATCATATCATATC
1 ATATCATATCATATCATAAC
* * *
31164302 ATAACATAACGA-ATCATATC
1 ATATCATATC-ATATCATAAC
31164322 ATATCATA
1 ATATCATA
31164330 ATATAGCATG
Statistics
Matches: 93, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.01
20 68 0.73
21 5 0.05
22 1 0.01
23 1 0.01
24 3 0.03
25 14 0.15
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.32
Consensus pattern (20 bp):
ATATCATATCATATCATAAC
Found at i:31164330 original size:20 final size:20
Alignment explanation
Indices: 31164199--31164299 Score: 130
Period size: 20 Copynumber: 4.8 Consensus size: 20
31164189 AATGAATAAT
*
31164199 ATCATATCATATCAAAACGA
1 ATCATATCATATCATAACGA
*
31164219 ATCATATCATATCATAATGA
1 ATCATATCATATCATAACGA
31164239 ATCATATCATATCATATCAAAACGA
1 ATCATATCATATC--AT---AACGA
*
31164264 ATCATATCATATCATAATGA
1 ATCATATCATATCATAACGA
31164284 ATCATATCATATCATA
1 ATCATATCATATCATA
31164300 TCATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
20 51 0.71
22 2 0.03
23 2 0.03
25 17 0.24
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.32
Consensus pattern (20 bp):
ATCATATCATATCATAACGA
Found at i:31165045 original size:49 final size:49
Alignment explanation
Indices: 31164992--31165208 Score: 222
Period size: 49 Copynumber: 4.4 Consensus size: 49
31164982 TGCAAGATTT
* *
31164992 CACACGGTTGTGTGCCTCACATAGCCTACCCACACGAGCTACAAAATTA
1 CACACGGTTGTGTGCCTCACATAGCCTACCCACACGGGCTACAAAATCA
* * * **
31165041 CACAC-ATTCGTGTGCCCCACA-GGACCTATTCACACGGGCTACAAAATCA
1 CACACGGTT-GTGTGCCTCACATAG-CCTACCCACACGGGCTACAAAATCA
** * * * *
31165090 CACACGGCCGTATGTCTCACACAGTCTACCCACACGGGCTACAAAATCA
1 CACACGGTTGTGTGCCTCACATAGCCTACCCACACGGGCTACAAAATCA
** * * *
31165139 CACACGACTGTGTGCCCCACATGGCCTACCCACACGGGCTACATAATCA
1 CACACGGTTGTGTGCCTCACATAGCCTACCCACACGGGCTACAAAATCA
* *
31165188 CACATGGTCGTGTGCCTCACA
1 CACACGGTTGTGTGCCTCACA
31165209 CGGGCTACAA
Statistics
Matches: 133, Mismatches: 31, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
48 3 0.02
49 129 0.97
50 1 0.01
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (49 bp):
CACACGGTTGTGTGCCTCACATAGCCTACCCACACGGGCTACAAAATCA
Found at i:31165109 original size:98 final size:98
Alignment explanation
Indices: 31165007--31165209 Score: 266
Period size: 98 Copynumber: 2.1 Consensus size: 98
31164997 GGTTGTGTGC
* * * *
31165007 CTCACATAGCCTACCCACACGAGCTACAAAATTACACAC-ATTCGTGTGCCCCACA-GGACCTAT
1 CTCACACAGCCTACCCACACGAGCTACAAAATCACACACGACT-GTGTGCCCCACATGG-CCTAC
*
31165070 TCACACGGGCTACAAAATCACACACGGCCGTATGT
64 CCACACGGGCTACAAAATCACACACGGCCGTATGT
* *
31165105 CTCACACAGTCTACCCACACGGGCTACAAAATCACACACGACTGTGTGCCCCACATGGCCTACCC
1 CTCACACAGCCTACCCACACGAGCTACAAAATCACACACGACTGTGTGCCCCACATGGCCTACCC
* * * * *
31165170 ACACGGGCTACATAATCACACATGGTCGTGTGC
66 ACACGGGCTACAAAATCACACACGGCCGTATGT
31165203 CTCACAC
1 CTCACAC
31165210 GGGCTACAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
98 87 0.96
99 4 0.04
ACGTcount: A:0.30, C:0.36, G:0.16, T:0.18
Consensus pattern (98 bp):
CTCACACAGCCTACCCACACGAGCTACAAAATCACACACGACTGTGTGCCCCACATGGCCTACCC
ACACGGGCTACAAAATCACACACGGCCGTATGT
Found at i:31165240 original size:85 final size:85
Alignment explanation
Indices: 31165120--31165285 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 85
31165110 ACAGTCTACC
** * ** *
31165120 CACACGGGCTACAAAATCACACACGACTGTGTGCCCCACATGGCCTACCCACACGGGCTACATAA
1 CACACGGGCTACAAAATCACACACGACCATATGCCCCACACAGCCTACCCACACGGGCTACAAAA
* *
31165185 TCACACATGGTCGTGTGCCT
66 TCACACACGATCGTGTGCCT
* * **
31165205 CACACGGGCTACAAAATCACACATCG-CCATATGCCCCATACAGCGTACTTACACGGGCTACAAA
1 CACACGGGCTACAAAATCACACA-CGACCATATGCCCCACACAGCCTACCCACACGGGCTACAAA
31165269 ATCACACACGATCGTGT
65 ATCACACACGATCGTGT
31165286 ATCCCACACG
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 66 0.97
86 2 0.03
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.17
Consensus pattern (85 bp):
CACACGGGCTACAAAATCACACACGACCATATGCCCCACACAGCCTACCCACACGGGCTACAAAA
TCACACACGATCGTGTGCCT
Found at i:31167155 original size:22 final size:22
Alignment explanation
Indices: 31167128--31167185 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
31167118 TATGCACTAA
*
31167128 TAAACGGAGAGCACCAAGGTGC
1 TAAACGGAGAGCACAAAGGTGC
* *
31167150 TAAACGGAGAGTACAAATGTGC
1 TAAACGGAGAGCACAAAGGTGC
31167172 TAAACGGAGAGCAC
1 TAAACGGAGAGCAC
31167186 TGTACGTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.29, T:0.12
Consensus pattern (22 bp):
TAAACGGAGAGCACAAAGGTGC
Found at i:31170106 original size:233 final size:234
Alignment explanation
Indices: 31169617--31170316 Score: 1289
Period size: 234 Copynumber: 3.0 Consensus size: 234
31169607 AAAAAAAAAA
* *
31169617 ACCAGTATTTAGAGAAAT--AAAAAAAGTTACCTTCAATTAATAGCTACAATAGTTAAAGATTAT
1 ACCAGTATTTAGAGAAATAAAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGATTAT
31169680 GTTTGGATGTTCATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAAC-TTTACCCATTAC
66 GTTTGGATGTTCATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTAC
31169744 AAGACTTGGAAATGTTAGACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAGAGCATGG
131 AAGACTTGGAAATGTTAGACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAGAGCATGG
31169809 TAGTGGAGAAAAGAAAGAGAATTCAGAGGTTGAAATAAC
196 TAGTGGAGAAAAGAAAGAGAATTCAGAGGTTGAAATAAC
* *
31169848 ACCAGTATTTATAGAAATAAAAAAAAAGTTACCTTTAATGAATAGCTGCAATAGTTAAAGATTAT
1 ACCAGTATTTAGAGAAATAAAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGATTAT
31169913 GTTTGGATGTTCATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTAC
66 GTTTGGATGTTCATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTAC
* *
31169978 AAGACTTGGAAATGTTAAACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAATAGAGCATGG
131 AAGACTTGGAAATGTTAGACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAGAGCATGG
31170043 TAGTGGAGAAAAGAAAGAGAATTCAGAGGTTGAAATAAC
196 TAGTGGAGAAAAGAAAGAGAATTCAGAGGTTGAAATAAC
*
31170082 ACCAGTATTTAGAGAAATAAAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGGTTAT
1 ACCAGTATTTAGAGAAATAAAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGATTAT
*
31170147 GTTTGGATGTTCATTACTATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTAC
66 GTTTGGATGTTCATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTAC
31170212 AAGACTTGGAAATGTTAGACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAGAGCATGG
131 AAGACTTGGAAATGTTAGACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAGAGCATGG
* *
31170277 TAATGGAGAAAAGAAAGAGAATTCAAAGGTTGAAATAAC
196 TAGTGGAGAAAAGAAAGAGAATTCAGAGGTTGAAATAAC
31170316 A
1 A
31170317 AAGGAACCTG
Statistics
Matches: 452, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
231 17 0.04
233 94 0.21
234 341 0.75
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (234 bp):
ACCAGTATTTAGAGAAATAAAAAAAAAGTTACCTTCAATGAATAGCTGCAATAGTTAAAGATTAT
GTTTGGATGTTCATTACCATAGACCATTGATTCAATCAAATTCGAGTTTAACTTTTACCCATTAC
AAGACTTGGAAATGTTAGACAGAGCTGAAGTAGGGTATTTGGATTTGTTAAGAAACAGAGCATGG
TAGTGGAGAAAAGAAAGAGAATTCAGAGGTTGAAATAAC
Found at i:31172262 original size:29 final size:28
Alignment explanation
Indices: 31172224--31172333 Score: 112
Period size: 29 Copynumber: 3.8 Consensus size: 28
31172214 TAACCCCTCA
31172224 AACTTCCAAAAATCACATTTTTGCCCCG
1 AACTTCCAAAAATCACATTTTTGCCCCG
* * * * *
31172252 AACTTGTCAAAAATTATATTTTTACCCTTG
1 AACTT-CCAAAAATCACATTTTTGCCC-CG
* *
31172282 AACTTCCAAAAATTACATTTTTTGCTCTCG
1 AACTTCCAAAAATCACA-TTTTTGC-CCCG
*
31172312 AACTTCCAAAAATCACGTTTTT
1 AACTTCCAAAAATCACATTTTT
31172334 ACCTTGAATT
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
28 5 0.08
29 32 0.48
30 28 0.42
31 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (28 bp):
AACTTCCAAAAATCACATTTTTGCCCCG
Found at i:31172286 original size:58 final size:57
Alignment explanation
Indices: 31172224--31172396 Score: 161
Period size: 59 Copynumber: 2.9 Consensus size: 57
31172214 TAACCCCTCA
*
31172224 AACTTCCAAAAATCACATTTTTGCCCCGAACTTGTCAAAAATTATATTTTTACCCTTG
1 AACTTCCAAAAATCACATTTTTGCCCCGAACTT-TCAAAAATTATGTTTTTACCCTTG
* * * * *
31172282 AACTTCCAAAAATTACATTTTTTGCTCTCGAACTTCCAAAAATCACGTTTTTA-CCTTG
1 AACTTCCAAAAATCACA-TTTTTGC-CCCGAACTTTCAAAAATTATGTTTTTACCCTTG
* * * * * *
31172340 AATTTTCCTAAAATGACA-TTTTGACCCCTAAACTTTTCCAAAATTATGTTTTAACCC
1 AA-CTTCCAAAAATCACATTTTTG-CCCC-GAAC-TTTCAAAAATTATGTTTTTACCC
31172397 CAAACTCTTC
Statistics
Matches: 92, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
57 7 0.08
58 27 0.29
59 48 0.52
60 10 0.11
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (57 bp):
AACTTCCAAAAATCACATTTTTGCCCCGAACTTTCAAAAATTATGTTTTTACCCTTG
Found at i:31172304 original size:30 final size:29
Alignment explanation
Indices: 31172169--31172336 Score: 126
Period size: 30 Copynumber: 5.7 Consensus size: 29
31172159 CCTTGAATTG
* * *
31172169 TCCAAAAATCATATTTTGACCCTCAAACTTT
1 TCCAAAAATCACATTTTTACCCTCGAAC--T
** * *
31172200 TCC-AAAATTGCA-TTTAACCCCTCAAACT
1 TCCAAAAATCACATTTTTA-CCCTCGAACT
*
31172228 TCCAAAAATCACATTTTTGCCC-CGAACT
1 TCCAAAAATCACATTTTTACCCTCGAACT
* * * *
31172256 TGTCAAAAATTATATTTTTACCCTTGAACT
1 T-CCAAAAATCACATTTTTACCCTCGAACT
* * *
31172286 TCCAAAAATTACATTTTTTGCTCTCGAACT
1 TCCAAAAATCACA-TTTTTACCCTCGAACT
*
31172316 TCCAAAAATCACGTTTTTACC
1 TCCAAAAATCACATTTTTACC
31172337 TTGAATTTTC
Statistics
Matches: 108, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
28 10 0.09
29 47 0.44
30 48 0.44
31 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.35
Consensus pattern (29 bp):
TCCAAAAATCACATTTTTACCCTCGAACT
Found at i:31172482 original size:22 final size:22
Alignment explanation
Indices: 31172443--31172484 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
31172433 TCTTTGTTCG
*
31172443 ACTTTTTTTATATAAAATTTTC
1 ACTTTTTTTATAAAAAATTTTC
31172465 ACTTTTTTT-TAAAGAAATTT
1 ACTTTTTTTATAAA-AAATTT
31172485 AATTTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
ACTTTTTTTATAAAAAATTTTC
Found at i:31172513 original size:16 final size:15
Alignment explanation
Indices: 31172492--31172544 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
31172482 TTTAATTTTG
31172492 TATTTTCTCATTTATT
1 TATTTTCTCA-TTATT
*
31172508 TATTTTTTCA-TATTT
1 TATTTTCTCATTA-TT
31172523 TATTTTTCTCA-TATT
1 TA-TTTTCTCATTATT
31172538 TATTTTC
1 TATTTTC
31172545 GTATATTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 7 0.21
15 8 0.24
16 18 0.55
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTCTCATTATT
Found at i:31172526 original size:15 final size:15
Alignment explanation
Indices: 31172492--31172543 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
31172482 TTTAATTTTG
* *
31172492 TATTTTCTCATTTATT
1 TATTTTTTCATAT-TT
31172508 TATTTTTTCATATTT
1 TATTTTTTCATATTT
31172523 TATTTTTCTCATA-TT
1 TATTTTT-TCATATTT
31172538 TATTTT
1 TATTTT
31172544 CGTATATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 17 0.52
16 16 0.48
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTTTCATATTT
Found at i:31172551 original size:30 final size:31
Alignment explanation
Indices: 31172494--31172552 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
31172484 TAATTTTGTA
*
31172494 TTTTCTCATTTATTTATTTTTTCATATTTTAT
1 TTTTCTCA-TTATTTATTTTGTCATATTTTAT
31172526 TTTTCTCA-TATTTATTTTCGT-ATATTT
1 TTTTCTCATTATTTATTTT-GTCATATTT
31172553 GTTCATTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 16 0.64
31 1 0.04
32 8 0.32
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (31 bp):
TTTTCTCATTATTTATTTTGTCATATTTTAT
Found at i:31172782 original size:97 final size:97
Alignment explanation
Indices: 31172674--31172867 Score: 271
Period size: 97 Copynumber: 2.0 Consensus size: 97
31172664 AAAATATTTA
* * * *
31172674 AAATCGAGGCAATATTCCTTTATTTCAGATTTTGAAAATTCGTGCCTTAACTTACTAGGCACGAT
1 AAATCGAGGCAATATTCCTTTATTTCAGATTTTGAAAATTCATGCCCTAACTTACTAGACACGAC
*
31172739 TTTTCTTCAAATCGAGATAATCAAATACCCTT
66 TTTTCTTAAAATCGAGATAATCAAATACCCTT
* * * * * *
31172771 AAATCGAGGCAATATTCTTTTATTTTAGTTTTTTAAAATTTATGCCCTAACTTACTAGACGCGAC
1 AAATCGAGGCAATATTCCTTTATTTCAGATTTTGAAAATTCATGCCCTAACTTACTAGACACGAC
* *
31172836 TTTTCTTAAAATCGGGATAATCGAATACCCTT
66 TTTTCTTAAAATCGAGATAATCAAATACCCTT
31172868 TTTCAAAGTT
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATTTCAGATTTTGAAAATTCATGCCCTAACTTACTAGACACGAC
TTTTCTTAAAATCGAGATAATCAAATACCCTT
Found at i:31175012 original size:41 final size:41
Alignment explanation
Indices: 31174934--31175203 Score: 292
Period size: 41 Copynumber: 6.6 Consensus size: 41
31174924 CATAAACACT
* * * *
31174934 GCAAAAGGTAA-AGTAATAGCGGCGTTTATGGGAAAAACGTC
1 GCAAAAGGTAAGAGCATTAGCGGCGTTTATGAG-AAAACGCC
* * * *
31174975 GCAAAAGGTCAGAACATTAGCGGCGTTTATGATAAAACACC
1 GCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCC
* * **
31175016 GCAGAAGGTAAGAGCATTAGCGGTGTTTATGAGAAAACATC
1 GCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCC
* * *
31175057 GAAAAAGGTAAGAGCATTAGTGGCATTTATGAGAAAACGCC
1 GCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCC
*
31175098 GCAAAAGGTAAGAGCATTAGTGGCGTTTATGAGAAAACGCC
1 GCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCC
* * * * *
31175139 ACAAAAGGTAGGAGCATTAGTGGTGTTTATGGGAAAAACGCC
1 GCAAAAGGTAAGAGCATTAGCGGCGTTTATGAG-AAAACGCC
* * *
31175181 GCTAAAGGTTA-AGCAATAGCGGC
1 GCAAAAGGTAAGAGCATTAGCGGC
31175204 ATTTTCCCAT
Statistics
Matches: 193, Mismatches: 34, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
41 162 0.84
42 31 0.16
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (41 bp):
GCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCC
Found at i:31175094 original size:123 final size:123
Alignment explanation
Indices: 31174936--31175207 Score: 330
Period size: 123 Copynumber: 2.2 Consensus size: 123
31174926 TAAACACTGC
* * * * *
31174936 AAAAGGTAAAGTAATAGCGGCGTTTATGGGAAAAACGTCGCAAAAGGTCAGAACATTAGCGGCGT
1 AAAAGGTAAAGCAATAGCGGCATTTATGAGAAAAACGCCGCAAAAGGTAAGAACATTAGCGGCGT
* * *
31175001 TTATGATAAAACACCGCAGAAGGTAAGAGCATTAGCGGTGTTTATGAGAAAACATCGA
66 TTATGAGAAAACACCACAAAAGGTAAGAGCATTAGCGGTGTTTATGAGAAAACATCGA
* * * *
31175059 AAAAGGTAAGAGCATTAGTGGCATTTATGAG-AAAACGCCGCAAAAGGTAAGAGCATTAGTGGCG
1 AAAAGGTAA-AGCAATAGCGGCATTTATGAGAAAAACGCCGCAAAAGGTAAGAACATTAGCGGCG
* * * * ** *
31175123 TTTATGAGAAAACGCCACAAAAGGTAGGAGCATTAGTGGTGTTTATGGGAAAAACGCCGC
65 TTTATGAGAAAACACCACAAAAGGTAAGAGCATTAGCGGTGTTTATGAG-AAAACATCGA
* *
31175183 TAAAGGTTAAGCAATAGCGGCATTT
1 AAAAGGTAAAGCAATAGCGGCATTT
31175208 TCCCATAAAT
Statistics
Matches: 124, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
123 94 0.76
124 30 0.24
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (123 bp):
AAAAGGTAAAGCAATAGCGGCATTTATGAGAAAAACGCCGCAAAAGGTAAGAACATTAGCGGCGT
TTATGAGAAAACACCACAAAAGGTAAGAGCATTAGCGGTGTTTATGAGAAAACATCGA
Found at i:31175145 original size:82 final size:82
Alignment explanation
Indices: 31174869--31175203 Score: 295
Period size: 82 Copynumber: 4.1 Consensus size: 82
31174859 AAAAAGGTTT
* * * * * * * *
31174869 TTAGCGGCGTTTGGAT-CGAAAACGCCATAAAAAGTAA-AGCAATAGTGGTGTTTTTCA-TAAAC
1 TTAGCGGCGTTT--ATGAGAAAACGCCACAAAAGGTAAGAGCATTAGTGGCGTTTATGAGAAAAC
* * *
31174931 ACTGCAAAAGGTAA-AGTA
64 GCCGCAAAAGGTAAGAGCA
* * * * * * * * *
31174949 ATAGCGGCGTTTATGGGAAAAACGTCGCAAAAGGTCAGAACATTAGCGGCGTTTATGATAAAACA
1 TTAGCGGCGTTTATGAG-AAAACGCCACAAAAGGTAAGAGCATTAGTGGCGTTTATGAGAAAACG
*
31175014 CCGCAGAAGGTAAGAGCA
65 CCGCAAAAGGTAAGAGCA
* * * *
31175032 TTAGCGGTGTTTATGAGAAAACATCGA-AAAAGGTAAGAGCATTAGTGGCATTTATGAGAAAACG
1 TTAGCGGCGTTTATGAGAAAAC-GCCACAAAAGGTAAGAGCATTAGTGGCGTTTATGAGAAAACG
31175096 CCGCAAAAGGTAAGAGCA
65 CCGCAAAAGGTAAGAGCA
* * * *
31175114 TTAGTGGCGTTTATGAGAAAACGCCACAAAAGGTAGGAGCATTAGTGGTGTTTATGGGAAAAACG
1 TTAGCGGCGTTTATGAGAAAACGCCACAAAAGGTAAGAGCATTAGTGGCGTTTATGAG-AAAACG
* *
31175179 CCGCTAAAGGTTA-AGCA
65 CCGCAAAAGGTAAGAGCA
*
31175196 ATAGCGGC
1 TTAGCGGC
31175204 ATTTTCCCAT
Statistics
Matches: 204, Mismatches: 43, Indels: 14
0.78 0.16 0.05
Matches are distributed among these distances:
78 2 0.01
79 1 0.00
80 25 0.12
81 16 0.08
82 126 0.62
83 34 0.17
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.21
Consensus pattern (82 bp):
TTAGCGGCGTTTATGAGAAAACGCCACAAAAGGTAAGAGCATTAGTGGCGTTTATGAGAAAACGC
CGCAAAAGGTAAGAGCA
Found at i:31176660 original size:44 final size:42
Alignment explanation
Indices: 31176610--31176721 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
31176600 TTAGAGGTCA
* * *
31176610 AGCAATAGCGGCATTTATGGGAAAAAATGTCGTAAAAGGTATAG
1 AGCAATAGCGGCATTTATGGGAAAAAA--CCGCAAAAGGTACAG
* * * *
31176654 AGCAATAGCGGCGTTTATGCGAAAACACCGCAAAAGGTCCAG
1 AGCAATAGCGGCATTTATGGGAAAAAACCGCAAAAGGTACAG
* * *
31176696 AGCATTAGCGACATTTATAGGAAAAA
1 AGCAATAGCGGCATTTATGGGAAAAA
31176722 CGTCGCTAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
42 31 0.56
44 24 0.44
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (42 bp):
AGCAATAGCGGCATTTATGGGAAAAAACCGCAAAAGGTACAG
Found at i:31177015 original size:38 final size:38
Alignment explanation
Indices: 31176934--31177015 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 38
31176924 GAAAAAGTTT
* * * *
31176934 GCTTTCCCTCTGTTTGATATTTCCCACCGGTCCTCTAT
1 GCTTTCCCTCTGTTTGATATTTCCCACCAGTCATCGAC
* * * *
31176972 ACTTTCTCTCTGTTTGGTTTTTCCCACCAGTCATCGAC
1 GCTTTCCCTCTGTTTGATATTTCCCACCAGTCATCGAC
31177010 GCTTTC
1 GCTTTC
31177016 GCTTTTATCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.11, C:0.33, G:0.13, T:0.43
Consensus pattern (38 bp):
GCTTTCCCTCTGTTTGATATTTCCCACCAGTCATCGAC
Found at i:31179884 original size:41 final size:38
Alignment explanation
Indices: 31179784--31179887 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
31179774 TTCGAAGCAA
* * *
31179784 TAAAGTGACACCCAGTGTCTCATCG-GTCTAACTGAAG
1 TAAAATGACACCCAGTGTCTCATCGAATCTAACCGAAG
* ** ** *
31179821 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAATCTAACCGAAG
31179859 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
31179888 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAATCTAACCGAAG
Found at i:31180013 original size:18 final size:18
Alignment explanation
Indices: 31179990--31180026 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31179980 ACAATTCATA
31179990 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
31180008 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
31180026 T
1 T
31180027 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:31180358 original size:17 final size:18
Alignment explanation
Indices: 31180324--31180359 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31180314 TAAATTTCTA
31180324 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
31180342 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
31180359 T
1 T
31180360 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:31187418 original size:6 final size:6
Alignment explanation
Indices: 31187393--31187431 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
31187383 ACAATTCATA
* * *
31187393 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
31187432 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:31187764 original size:17 final size:18
Alignment explanation
Indices: 31187734--31187767 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31187724 AATTTCTATT
31187734 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
31187752 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
31187768 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:31190642 original size:65 final size:65
Alignment explanation
Indices: 31190558--31190686 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
31190548 GCAAATTGCT
*
31190558 CAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCAAAGGCTCAAAGAAAATATGATGAACTTCAGCA
1 CAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCAAAGGCTCAAAGAAAATATGATGAACTGCAGCA
* * * * *
31190623 CAACTTGAAGCTA-AGGCAGCAGCGAGGGAAGCAGAGTCTCAAAGAAAGTATGATGAACTGCAGC
1 CAACTTAAAGC-AGAGGCAGCAGCGAGAGAAGCAAAGGCTCAAAGAAAATATGATGAACTGCAGC
31190687 TACAGCTTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 56 0.98
66 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCAAAGGCTCAAAGAAAATATGATGAACTGCAGCA
Found at i:31214251 original size:18 final size:19
Alignment explanation
Indices: 31214216--31214254 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
31214206 AATAAATATA
31214216 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
31214235 AATA-AATTGTAAA-TTAAT
1 AATACAATT-TAAATTTAAT
31214253 AA
1 AA
31214255 AAACAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Done.