Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 29 of 182
Found at i:11616613 original size:244 final size:240
Alignment explanation
Indices: 11616159--11616862 Score: 752
Period size: 244 Copynumber: 2.9 Consensus size: 240
11616149 TAATATAATG
* * *
11616159 TATTAT-TAT-ATTA-TAGATTATAAAAAAAATACAATATTACATGATATTATAATGTTTAATCA
1 TATTATATATAATTATTATATTATAATAAAAATATAATATTACATGATATTATAATGTTTAATCA
* *
11616221 TTGATGCATATAT-ATAAACTATTAATATATTATATACCATATGATATGATATAACATTATAAAA
66 TTAATGCATATATAATAAACTATTAATATATTATATACCATATGATATGATATAACATTATATAA
* * * *
11616285 TATAGCAGGAGGGCTAACTTTTAAATGTACGAAAAATATA-AGAATTTA-AAGCATATTTCAACT
131 TATAGTAGGAGAGCTAACTTTTAAATATACGAAAAATATAGAG-ACTTAGAA--ATATTTCAAC-
* * * **
11616348 AGTATAATAATAAACAATAATAGTTAATAGTTGGTATATAATATACTAC
192 AGTATAATAATAAAAAATAATAATTAATAATTAATATATAATATACTAC
* * * *
11616397 TATTATATATAATTATTATATTATAATAAAAATATAACATTAAATAATATTGTAATGTTTAATCA
1 TATTATATATAATTATTATATTATAATAAAAATATAATATTACATGATATTATAATGTTTAATCA
* *
11616462 TTAATGCATACATATAAATAAACCATTAATATATTATATACTATATGATATGATATAACATTATA
66 TTAATGCAT--ATAT-AATAAACTATTAATATATTATATACCATATGATATGATATAACATTATA
*
11616527 TAATAT-GATAGGA-AGCTAACTTTTAAATCTACGAAAAATATAGAGACTTAGAATATATTTCAA
128 TAATATAG-TAGGAGAGCTAACTTTTAAATATACGAAAAATATAGAGACTTAGAA-ATATTTCAA
* *
11616590 TCAGTATAATTATAAAAAATAATAATTAATAATTAATATATAATGTACTAC
191 -CAGTATAATAATAAAAAATAATAATTAATAATTAATATATAATATACTAC
*
11616641 TATTATATATAACTATTATTATATTATAGATTATACTAAATGATATAGTATTACATGTTATTATA
1 TATTATATAT-A--ATTATTATATTATA-A-TA-A--AAAT-ATA-A-TATTACATGATATTATA
* * * *
11616706 ATATTCAATCATTAATGCATATAT-ATATA-TATTATATTATATTATAT--GATAT--TATGATA
55 ATGTTTAATCATTAATGCATATATAATAAACTATTA-A-TATATTATATACCATATGATATGATA
* * * * * * *
11616765 TAACATTATATAATATAGTAGAATAACTAACTTTCAAATATACGAAAAGTATCGGGACTTAGAGA
118 TAACATTATATAATATAGTAGGAGAGCTAACTTTTAAATATACGAAAAATATAGAGACTTAGA-A
* *
11616830 ATATTTCAACCAATATAATAATAAATAATAATA
182 ATATTTCAA-CAGTATAATAATAAAAAATAATA
11616863 TATGATAACA
Statistics
Matches: 395, Mismatches: 44, Indels: 43
0.82 0.09 0.09
Matches are distributed among these distances:
238 6 0.02
239 3 0.01
240 4 0.01
241 50 0.13
243 4 0.01
244 93 0.24
245 61 0.15
247 14 0.04
248 28 0.07
249 65 0.16
250 10 0.03
251 5 0.01
252 14 0.04
253 7 0.02
254 1 0.00
255 30 0.08
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (240 bp):
TATTATATATAATTATTATATTATAATAAAAATATAATATTACATGATATTATAATGTTTAATCA
TTAATGCATATATAATAAACTATTAATATATTATATACCATATGATATGATATAACATTATATAA
TATAGTAGGAGAGCTAACTTTTAAATATACGAAAAATATAGAGACTTAGAAATATTTCAACAGTA
TAATAATAAAAAATAATAATTAATAATTAATATATAATATACTAC
Found at i:11616743 original size:5 final size:5
Alignment explanation
Indices: 11616727--11616760 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
11616717 TTAATGCATA
*
11616727 TATAT ATATAT TATAT TATAT TATAT GATAT TAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TAT
11616761 GATATAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:11616766 original size:15 final size:14
Alignment explanation
Indices: 11616724--11616766 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
11616714 TCATTAATGC
*
11616724 ATATATATATATATT
1 ATAT-TATATATATG
11616739 ATATTATATTATATG
1 ATATTATA-TATATG
11616754 ATATTATGATATA
1 ATATTAT-ATATA
11616767 ACATTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 20 0.80
16 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
ATATTATATATATG
Found at i:11621683 original size:6 final size:6
Alignment explanation
Indices: 11621674--11621703 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11621664 TTTTTTAAAC
11621674 ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA
1 ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA
11621704 TGGTTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
ATAGGA
Found at i:11622746 original size:6 final size:6
Alignment explanation
Indices: 11622735--11622769 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
11622725 GGTCAGCTCG
*
11622735 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCG GTGGC
1 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTGGC
11622770 TTCCAGCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.11, C:0.17, G:0.54, T:0.17
Consensus pattern (6 bp):
GTGGCA
Found at i:11626321 original size:9 final size:9
Alignment explanation
Indices: 11626306--11626337 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
11626296 GTGGTGGAAG
11626306 AGAGGAGGA
1 AGAGGAGGA
*
11626315 GGAGGAGGA
1 AGAGGAGGA
11626324 AGAGGAGGA
1 AGAGGAGGA
11626333 AGAGG
1 AGAGG
11626338 GTGGAGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (9 bp):
AGAGGAGGA
Found at i:11629493 original size:27 final size:27
Alignment explanation
Indices: 11629434--11629486 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
11629424 TCAATTAAGC
* *
11629434 CATCAATCCCAAACTCATCAACTATAA
1 CATCAATCACAAACTCATCAACAATAA
11629461 CATCAATCACAAACTCATCACACAAT
1 CATCAATCACAAACTCATCA-ACAAT
11629487 TCTTCAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (27 bp):
CATCAATCACAAACTCATCAACAATAA
Found at i:11633775 original size:17 final size:17
Alignment explanation
Indices: 11633753--11633803 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
11633743 AATTTTTATT
11633753 ATTTTTTTAAATTTTAA
1 ATTTTTTTAAATTTTAA
*
11633770 ATTTTTGTT-AATTTTGA
1 ATTTTT-TTAAATTTTAA
11633787 ATTTTATTTAATATTTT
1 ATTTT-TTTAA-ATTTT
11633804 TATAATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 20 0.69
18 4 0.14
19 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
ATTTTTTTAAATTTTAA
Found at i:11633988 original size:24 final size:23
Alignment explanation
Indices: 11633952--11633998 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
11633942 AAATTTTAAC
*
11633952 TTTTTTAGAGAAAATATTTCTAT
1 TTTTTTAGAGAAAAGATTTCTAT
*
11633975 TTTTCTTAGAGAAAAGCTTTCTAT
1 TTTT-TTAGAGAAAAGATTTCTAT
11633999 CATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (23 bp):
TTTTTTAGAGAAAAGATTTCTAT
Found at i:11636119 original size:91 final size:91
Alignment explanation
Indices: 11635957--11636165 Score: 283
Period size: 91 Copynumber: 2.3 Consensus size: 91
11635947 GGGTATCCAT
* * * * * * *
11635957 ACTTTTATAAAATGTCCAATGTGGTACTTGTGCTTTAAAAATGTCCAATGTGATTCTTGAATTAT
1 ACTTTCATAAAATGTCCAATGTGGTACGTATACTTTAAAAATGTCCAATGTGATACATGAACTAT
* *
11636022 CGATTTGTGTATTATTTGGTACTTGC
66 CAATTTGTGTATTATTGGGTACTTGC
* * * * *
11636048 ACTTTCATAAAATATCCAATGCGGTACGTATATTTTGAAAATGTCCAATGTGGTACATGAACTAT
1 ACTTTCATAAAATGTCCAATGTGGTACGTATACTTTAAAAATGTCCAATGTGATACATGAACTAT
*
11636113 CAATTTGTGTATTATTGGGTACTTGT
66 CAATTTGTGTATTATTGGGTACTTGC
11636139 ACTTTCATAAAATGTCCAATGTGGTAC
1 ACTTTCATAAAATGTCCAATGTGGTAC
11636166 TTGAACTATC
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
91 101 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (91 bp):
ACTTTCATAAAATGTCCAATGTGGTACGTATACTTTAAAAATGTCCAATGTGATACATGAACTAT
CAATTTGTGTATTATTGGGTACTTGC
Found at i:11636168 original size:31 final size:31
Alignment explanation
Indices: 11635956--11636168 Score: 86
Period size: 31 Copynumber: 7.0 Consensus size: 31
11635946 TGGGTATCCA
*
11635956 TACTTTTATAAAATGTCCAATGTGGTACTTG
1 TACTTTCATAAAATGTCCAATGTGGTACTTG
* * *
11635987 TGCTTT-A-AAAATGTCCAATGTGATTCTTG
1 TACTTTCATAAAATGTCCAATGTGGTACTTG
* *** *** *
11636016 -AATTATCGAT-TTGTGTATTATTTGGTACTTG
1 TACTT-TC-ATAAAATGTCCAATGTGGTACTTG
* * * * *
11636047 CACTTTCATAAAATATCCAATGCGGTACGTA
1 TACTTTCATAAAATGTCCAATGTGGTACTTG
*
11636078 TA-TTT--TGAAAATGTCCAATGTGGTACATG
1 TACTTTCAT-AAAATGTCCAATGTGGTACTTG
* * ** **
11636107 AACTATC--AATTTGTGTATTAT-TGGGTACTTG
1 TACTTTCATAAAATGTCCA--ATGT-GGTACTTG
11636138 TACTTTCATAAAATGTCCAATGTGGTACTTG
1 TACTTTCATAAAATGTCCAATGTGGTACTTG
11636169 AACTATCAAT
Statistics
Matches: 123, Mismatches: 44, Indels: 30
0.62 0.22 0.15
Matches are distributed among these distances:
28 3 0.02
29 46 0.37
30 9 0.07
31 55 0.45
32 4 0.03
33 6 0.05
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (31 bp):
TACTTTCATAAAATGTCCAATGTGGTACTTG
Found at i:11638367 original size:10 final size:9
Alignment explanation
Indices: 11638342--11638449 Score: 55
Period size: 9 Copynumber: 11.9 Consensus size: 9
11638332 AAAAATAAAA
*
11638342 ATAAAAATG
1 ATAAAAATT
*
11638351 AGTAAAAGTT
1 A-TAAAAATT
11638361 ATAAAAATT
1 ATAAAAATT
**
11638370 ATTAAATTTT
1 A-TAAAAATT
11638380 AATAAAAA-T
1 -ATAAAAATT
*
11638389 AT--ATATT
1 ATAAAAATT
11638396 -TAAAAATT
1 ATAAAAATT
11638404 ATAAAAA-T
1 ATAAAAATT
*
11638412 ATAAAGAAAT
1 ATAAA-AATT
*
11638422 ATAAAATTCGT
1 ATAAAAAT--T
*
11638433 AAAAAAATT
1 ATAAAAATT
11638442 ATAAAAAT
1 ATAAAAAT
11638450 ATCGTACCAA
Statistics
Matches: 74, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
6 3 0.04
7 1 0.01
8 12 0.16
9 27 0.36
10 23 0.31
11 8 0.11
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:11644976 original size:27 final size:27
Alignment explanation
Indices: 11644898--11644978 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
11644888 TATAAGGGGG
* * *
11644898 TGGTGCCTTCCTGACAGGCGGCACTAG
1 TGGTGCCTTCCTGTCAGGCGGCACCAA
* *
11644925 TGGTGCCTACCTGTCAGGCGACACCAA
1 TGGTGCCTTCCTGTCAGGCGGCACCAA
* *
11644952 TGGTGCCTTCCTGTTAAGCGGCACCAA
1 TGGTGCCTTCCTGTCAGGCGGCACCAA
11644979 CCCGTATTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.19, C:0.31, G:0.28, T:0.22
Consensus pattern (27 bp):
TGGTGCCTTCCTGTCAGGCGGCACCAA
Found at i:11649356 original size:6 final size:6
Alignment explanation
Indices: 11649345--11649385 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
11649335 ATATTTTCAT
*
11649345 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
11649386 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:11649852 original size:6 final size:6
Alignment explanation
Indices: 11649841--11649865 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11649831 ATAGTGCTAC
11649841 GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA G
11649866 CCGGTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:11652142 original size:23 final size:21
Alignment explanation
Indices: 11652087--11652142 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 21
11652077 TAGTAAAAAC
* *
11652087 TAAAGATAATTGTATTTTAAA
1 TAAAAATAATTTTATTTTAAA
*
11652108 -AAATATATATTTTATATTTCAAA
1 TAAAAATA-ATTTTAT-TTT-AAA
11652131 TAAAAATAATTT
1 TAAAAATAATTT
11652143 AGTTAAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 6 0.21
21 6 0.21
22 3 0.11
23 7 0.25
24 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
TAAAAATAATTTTATTTTAAA
Found at i:11652335 original size:17 final size:17
Alignment explanation
Indices: 11652313--11652346 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11652303 CTTACAATAA
*
11652313 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
11652330 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
11652347 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:11652558 original size:20 final size:20
Alignment explanation
Indices: 11652533--11652570 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11652523 ATTATAAGAT
11652533 CCCCA-TTTACCCCTCCCTCC
1 CCCCATTTTA-CCCTCCCTCC
11652553 CCCCATTTTACCCTCCCT
1 CCCCATTTTACCCTCCCT
11652571 TTAGGCAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.11, C:0.61, G:0.00, T:0.29
Consensus pattern (20 bp):
CCCCATTTTACCCTCCCTCC
Found at i:11652595 original size:10 final size:10
Alignment explanation
Indices: 11652580--11652634 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
11652570 TTTAGGCAGG
11652580 AGCAGGGAGC
1 AGCAGGGAGC
11652590 AGCAGGGAGC
1 AGCAGGGAGC
*
11652600 AGCAGGAAGC
1 AGCAGGGAGC
*
11652610 AGC-GTCGA-C
1 AGCAG-GGAGC
11652619 AAGCAGGGAGC
1 -AGCAGGGAGC
11652630 AGCAG
1 AGCAG
11652635 CAGCAGGGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 2 0.05
10 33 0.89
11 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.44, T:0.02
Consensus pattern (10 bp):
AGCAGGGAGC
Found at i:11652697 original size:27 final size:28
Alignment explanation
Indices: 11652658--11652713 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
11652648 GCAGCAAGCA
**
11652658 ATTAGGTGTCGCCTAGTAGGTAGGCACC
1 ATTAGGTGTCGCCTACCAGGTAGGCACC
11652686 ATTA-GTGTCGCCTACCAGGTAGGCACC
1 ATTAGGTGTCGCCTACCAGGTAGGCACC
11652713 A
1 A
11652714 CCCAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (28 bp):
ATTAGGTGTCGCCTACCAGGTAGGCACC
Found at i:11653351 original size:31 final size:30
Alignment explanation
Indices: 11653313--11653378 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
11653303 ATTTTTTAAG
11653313 TTTAATTTGATA-CTTAAACTTGACACTTTT
1 TTTAATTTGATATC-TAAACTTGACACTTTT
*
11653343 TCTTAATTTGGTATCTAAACTTGACACTTTT
1 T-TTAATTTGATATCTAAACTTGACACTTTT
11653374 TTTAA
1 TTTAA
11653379 GTTGGCACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 5 0.15
31 27 0.82
32 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.50
Consensus pattern (30 bp):
TTTAATTTGATATCTAAACTTGACACTTTT
Found at i:11658069 original size:15 final size:15
Alignment explanation
Indices: 11658049--11658100 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
11658039 TGATTCGTTA
*
11658049 ACTCGACTTGATTTG
1 ACTCGAATTGATTTG
**
11658064 ACTCGAATTTTTTTG
1 ACTCGAATTGATTTG
* *
11658079 ATTCGATTTGATTTG
1 ACTCGAATTGATTTG
*
11658094 ATTCGAA
1 ACTCGAA
11658101 AAAAATTTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (15 bp):
ACTCGAATTGATTTG
Found at i:11659925 original size:13 final size:13
Alignment explanation
Indices: 11659902--11659934 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11659892 TATATTAATT
11659902 AAAAT-TAAATAC
1 AAAATATAAATAC
11659914 AAAATATAAATAC
1 AAAATATAAATAC
11659927 AAAA-ATAA
1 AAAATATAA
11659935 TGTTAAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATATAAATAC
Found at i:11669228 original size:2 final size:2
Alignment explanation
Indices: 11669216--11669251 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11669206 GCTGGCCTTA
11669216 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11669252 TTCTAACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:11675481 original size:20 final size:21
Alignment explanation
Indices: 11675450--11675489 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11675440 ACTGCACGTG
*
11675450 GAAATAAATTAAATTTATTTA
1 GAAATAAATTAAAATTATTTA
11675471 GAAAT-AATTAAAATTATTT
1 GAAATAAATTAAAATTATTT
11675490 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
GAAATAAATTAAAATTATTTA
Found at i:11683403 original size:17 final size:17
Alignment explanation
Indices: 11683363--11683404 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
11683353 TAATAACTTT
*
11683363 ATAAATATTATGTCAAA
1 ATAAATAATATGTCAAA
* *
11683380 A-AAATAATATTTGAAA
1 ATAAATAATATGTCAAA
11683396 ATAAATAAT
1 ATAAATAAT
11683405 TTAACATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (17 bp):
ATAAATAATATGTCAAA
Found at i:11683454 original size:17 final size:18
Alignment explanation
Indices: 11683416--11683456 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
11683406 TAACATTTTA
*
11683416 TATTTAATAATAAAAAAT
1 TATTTAACAATAAAAAAT
*
11683434 TATTTAACAAT-AAATAT
1 TATTTAACAATAAAAAAT
11683451 TATTTA
1 TATTTA
11683457 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTTAACAATAAAAAAT
Found at i:11690024 original size:21 final size:19
Alignment explanation
Indices: 11690000--11690039 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
11689990 ATATTAATTA
*
11690000 AATATTATATTAAATGAAAAT
1 AATATT-TAATAAAT-AAAAT
11690021 AATATTTAATAAATAAAAT
1 AATATTTAATAAATAAAAT
11690040 TACATTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AATATTTAATAAATAAAAT
Found at i:11693104 original size:23 final size:23
Alignment explanation
Indices: 11693078--11693130 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
11693068 AATTAATTAT
11693078 ATTTTTTTATAAATTAAAATATA
1 ATTTTTTTATAAATTAAAATATA
* ** **
11693101 ATTTTATTATTTATTAATTTATA
1 ATTTTTTTATAAATTAAAATATA
11693124 ATTTTTT
1 ATTTTTT
11693131 CGGGACTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTTTTATAAATTAAAATATA
Found at i:11696754 original size:13 final size:14
Alignment explanation
Indices: 11696731--11696773 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
11696721 ATGATATTCG
11696731 TATTGATTTTTT-TA
1 TATT-ATTTTTTATA
11696745 TATTATTTTTTAATA
1 TATTATTTTTT-ATA
11696760 TAATTATTTTTTAT
1 T-ATTATTTTTTAT
11696774 TTGATAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
15 5 0.19
16 10 0.38
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TATTATTTTTTATA
Found at i:11697358 original size:13 final size:13
Alignment explanation
Indices: 11697283--11697363 Score: 60
Period size: 13 Copynumber: 6.3 Consensus size: 13
11697273 AAAATAATAT
11697283 TAATATATTTTTAA
1 TAATA-ATTTTTAA
* *
11697297 T-ATTA-TTTCAA
1 TAATAATTTTTAA
*
11697308 TAAT-ATTTTTAT
1 TAATAATTTTTAA
* *
11697320 TAATAAATATTAA
1 TAATAATTTTTAA
* *
11697333 AAATAAATATTTAA
1 TAAT-AATTTTTAA
11697347 TAATAATTTTTAA
1 TAATAATTTTTAA
11697360 TAAT
1 TAAT
11697364 CTTTATTATT
Statistics
Matches: 50, Mismatches: 13, Indels: 9
0.69 0.18 0.12
Matches are distributed among these distances:
11 7 0.14
12 11 0.22
13 22 0.44
14 10 0.20
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATAATTTTTAA
Found at i:11698325 original size:12 final size:14
Alignment explanation
Indices: 11698308--11698339 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
11698298 TTCATGAAAA
11698308 TATTTTTT-ATTT-
1 TATTTTTTCATTTC
11698320 TATTTTTTCATTTC
1 TATTTTTTCATTTC
11698334 TATTTT
1 TATTTT
11698340 CAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 4 0.22
14 6 0.33
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTTTTCATTTC
Found at i:11706066 original size:4 final size:4
Alignment explanation
Indices: 11706057--11706081 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
11706047 ATTCATCTCC
11706057 TGTT TGTT TGTT TGTT TGTT TGTT T
1 TGTT TGTT TGTT TGTT TGTT TGTT T
11706082 ATTATCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TGTT
Found at i:11710113 original size:22 final size:21
Alignment explanation
Indices: 11710087--11710138 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
11710077 TATAATTAAT
*
11710087 TTTAATTATATTTAAATAAAAA
1 TTTAATTATATTGAAA-AAAAA
*
11710109 TTTAAGTATTTATTGAAAAAAAA
1 TTTAA-T-TATATTGAAAAAAAA
11710132 TTTAATT
1 TTTAATT
11710139 TTTCGGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 6 0.23
23 11 0.42
24 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
TTTAATTATATTGAAAAAAAA
Found at i:11713811 original size:2 final size:2
Alignment explanation
Indices: 11713804--11713828 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11713794 GTCTCTATGT
11713804 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 T
11713829 CAAATTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11714109 original size:24 final size:24
Alignment explanation
Indices: 11714065--11714111 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11714055 ATTTATTGTA
* *
11714065 TTTTATAATATTTTATCGTAATTT
1 TTTTAAAATATTTAATCGTAATTT
11714089 TTTTAAAATATATTAAT-GTAATT
1 TTTTAAAATAT-TTAATCGTAATT
11714112 ACATGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTAAAATATTTAATCGTAATTT
Found at i:11715593 original size:15 final size:16
Alignment explanation
Indices: 11715573--11715607 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
11715563 ATCTTAATTA
*
11715573 TATAAAAAAT-GTAAT
1 TATAAAAAATAATAAT
11715588 TATAAAAAATAATAAT
1 TATAAAAAATAATAAT
11715604 TATA
1 TATA
11715608 TGACACCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TATAAAAAATAATAAT
Found at i:11716201 original size:24 final size:24
Alignment explanation
Indices: 11716144--11716204 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
11716134 CATACACCTA
* *
11716144 TTTTATTTTAT-TTTAGTTTTGTT
1 TTTTATTTGATATTTACTTTTGTT
11716167 TTTCTATTTTGATATTTACCTTTT-TT
1 TTT-TA-TTTGATATTTA-CTTTTGTT
11716193 TTTTATTTGATA
1 TTTTATTTGATA
11716205 CTTAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 3 0.09
24 9 0.28
25 7 0.22
26 9 0.28
27 4 0.12
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTTATTTGATATTTACTTTTGTT
Found at i:11716219 original size:25 final size:26
Alignment explanation
Indices: 11716160--11716219 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 26
11716150 TTTATTTTAG
* **
11716160 TTTTGTTTTTCTATTTTGATATTTACC
1 TTTT-TTTTTCTATTTTGATACTTAAA
11716187 TTTTTTTTT-TA-TTTGATACTTAAA
1 TTTTTTTTTCTATTTTGATACTTAAA
*
11716211 TTTTATTTT
1 TTTTTTTTT
11716220 ATCGCATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 18 0.62
25 2 0.07
26 5 0.17
27 4 0.14
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTTTTTTTCTATTTTGATACTTAAA
Found at i:11716639 original size:26 final size:27
Alignment explanation
Indices: 11716603--11716655 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
11716593 AAGTTTAAAT
*
11716603 AAAAAAATATAAATTC-A-AAAAATTG
1 AAAAAAATATAAAATCTAGAAAAATTG
11716628 AAAAAATATATAAAATCTAGAAAAATTG
1 AAAAAA-ATATAAAATCTAGAAAAATTG
11716656 TCATAATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 9 0.38
27 1 0.04
28 8 0.33
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.25
Consensus pattern (27 bp):
AAAAAAATATAAAATCTAGAAAAATTG
Found at i:11723108 original size:16 final size:16
Alignment explanation
Indices: 11723096--11723135 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
11723086 ATTGAATAGG
11723096 ATTGTAATAGAATAAA
1 ATTGTAATAGAATAAA
*
11723112 ATTGTAATAAAATAAA
1 ATTGTAATAGAATAAA
*
11723128 ACTGTAAT
1 ATTGTAAT
11723136 CAGTATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (16 bp):
ATTGTAATAGAATAAA
Found at i:11728953 original size:25 final size:24
Alignment explanation
Indices: 11728915--11728961 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
11728905 TGTAATTAAG
11728915 AAATAATTTCTAAA-ATCATAATAA
1 AAATAATTTCTAAATA-CATAATAA
*
11728939 AAATAATATTTTAAATACATAAT
1 AAATAAT-TTCTAAATACATAAT
11728962 TAACAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 12 0.60
26 1 0.05
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAATTTCTAAATACATAATAA
Found at i:11729713 original size:18 final size:19
Alignment explanation
Indices: 11729683--11729729 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
11729673 ATTTTTCCCT
11729683 AAAAATTAAAAAAA-CA-A
1 AAAAATTAAAAAAATCAGA
*
11729700 AAAGAATTATAAAAATCAGA
1 AAA-AATTAAAAAAATCAGA
11729720 AAAAATTAAA
1 AAAAATTAAA
11729730 TAGTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 3 0.12
18 10 0.40
19 8 0.32
20 4 0.16
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (19 bp):
AAAAATTAAAAAAATCAGA
Found at i:11730369 original size:9 final size:9
Alignment explanation
Indices: 11730357--11730448 Score: 78
Period size: 9 Copynumber: 9.9 Consensus size: 9
11730347 TTATGATTTT
11730357 TTTTTATAA
1 TTTTTATAA
11730366 TTTTTATAA
1 TTTTTATAA
11730375 TTTTATATCAA
1 TTTT-TAT-AA
*
11730386 TTTTAAT-A
1 TTTTTATAA
*
11730394 TTTTTAATAC
1 TTTTT-ATAA
*
11730404 TTTTTATAC
1 TTTTTATAA
*
11730413 TTTTTATACT
1 TTTTTATA-A
* *
11730423 TTTTTTTTA
1 TTTTTATAA
*
11730432 TTTTTATGA
1 TTTTTATAA
11730441 TTTTTATA
1 TTTTTATA
11730449 GAATTTTAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
8 5 0.07
9 41 0.60
10 16 0.24
11 6 0.09
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11730387 original size:20 final size:18
Alignment explanation
Indices: 11730357--11730505 Score: 66
Period size: 18 Copynumber: 7.8 Consensus size: 18
11730347 TTATGATTTT
*
11730357 TTTTTATAATTTTTATAA
1 TTTTAATAATTTTTATAA
* *
11730375 TTTTATATCAATTTTAATAT
1 TTTTA-AT-AATTTTTATAA
* *
11730395 TTTTAATACTTTTTATAC
1 TTTTAATAATTTTTATAA
* * * *
11730413 TTTTTATACTTTTTTTTTA
1 TTTTAATA-ATTTTTATAA
* *
11730432 TTTTTATGATTTTTATAGAA
1 TTTTAATAATTTTTAT--AA
* *
11730452 TTTTAACACCTTTTTATAAA
1 TTTTAATA-ATTTTTAT-AA
*
11730472 TTTTTAAAAATGTTTTAATAA
1 -TTTTAATAAT-TTTT-ATAA
*
11730493 -TTTAATAGTTTTT
1 TTTTAATAATTTTT
11730506 TATTATTTTT
Statistics
Matches: 98, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
18 29 0.30
19 24 0.24
20 23 0.23
21 20 0.20
22 2 0.02
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTAATAATTTTTATAA
Found at i:11730427 original size:19 final size:18
Alignment explanation
Indices: 11730356--11730448 Score: 78
Period size: 19 Copynumber: 5.0 Consensus size: 18
11730346 TTTATGATTT
11730356 TTTTTTATAATTTTTATAA
1 TTTTTTATAATTTTTAT-A
* *
11730375 TTTTATATCAATTTTAATA
1 TTTTTTAT-AATTTTTATA
* *
11730394 TTTTTAATACTTTTTATA
1 TTTTTTATAATTTTTATA
* * * *
11730412 CTTTTTATACTTTTTTTT
1 TTTTTTATAATTTTTATA
*
11730430 TATTTTTATGATTTTTATA
1 T-TTTTTATAATTTTTATA
11730449 GAATTTTAAC
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
18 22 0.39
19 27 0.47
20 8 0.14
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTTTATAATTTTTATA
Found at i:11734335 original size:11 final size:11
Alignment explanation
Indices: 11734319--11734347 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
11734309 ATGAAGAGTC
11734319 ACGTGGCACTG
1 ACGTGGCACTG
11734330 ACGTGGCACTG
1 ACGTGGCACTG
11734341 ACGTGGC
1 ACGTGGC
11734348 GGCTGTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.38, T:0.17
Consensus pattern (11 bp):
ACGTGGCACTG
Found at i:11734414 original size:16 final size:16
Alignment explanation
Indices: 11734393--11734423 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11734383 TTTTCATATT
11734393 TTGGGTGAATTTGGGC
1 TTGGGTGAATTTGGGC
*
11734409 TTGGGTGTATTTGGG
1 TTGGGTGAATTTGGG
11734424 TATTTGGGTA
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:0.10, C:0.03, G:0.45, T:0.42
Consensus pattern (16 bp):
TTGGGTGAATTTGGGC
Found at i:11734428 original size:8 final size:8
Alignment explanation
Indices: 11734415--11734439 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11734405 GGGCTTGGGT
11734415 GTATTTGG
1 GTATTTGG
11734423 GTATTTGG
1 GTATTTGG
11734431 GTATTTGG
1 GTATTTGG
11734439 G
1 G
11734440 CCTATTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (8 bp):
GTATTTGG
Found at i:11735045 original size:59 final size:59
Alignment explanation
Indices: 11734982--11735164 Score: 226
Period size: 59 Copynumber: 3.1 Consensus size: 59
11734972 TTTATATATT
* *
11734982 AAAAAAATAAAAAAATAAAATTATATTAATGGAGGATTATCAAATGACGACATTACAGG
1 AAAAAAATAAAAAAATAATATTATATTAGTGGAGGATTATCAAATGACGACATTACAGG
* * * ** *
11735041 -AAAAAATAAAAAAAATAATGTTATATTAGTGGAAGATTATCAAATGGCGACACCAGAGG
1 AAAAAAAT-AAAAAAATAATATTATATTAGTGGAGGATTATCAAATGACGACATTACAGG
* * * *
11735100 AAAAAAA-ATAAAAAATAATATTATATTAGTAGAGGGTTATCAAATGACGGCATTATAGG
1 AAAAAAATA-AAAAAATAATATTATATTAGTGGAGGATTATCAAATGACGACATTACAGG
11735159 AAAAAA
1 AAAAAA
11735165 TTATATAAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 8 0.08
59 90 0.87
60 6 0.06
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (59 bp):
AAAAAAATAAAAAAATAATATTATATTAGTGGAGGATTATCAAATGACGACATTACAGG
Found at i:11735184 original size:21 final size:21
Alignment explanation
Indices: 11735160--11735234 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
11735150 CATTATAGGA
11735160 AAAAATTATATAAAATACACG
1 AAAAATTATATAAAATACACG
* *** *
11735181 AAAAA-AATATTTGA-ACATTG
1 AAAAATTATATAAAATACA-CG
11735201 AAAAATTATATAAAATACACG
1 AAAAATTATATAAAATACACG
*
11735222 AAAAATTAAATAA
1 AAAAATTATATAA
11735235 CAAATCATTT
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 3 0.08
20 11 0.28
21 23 0.57
22 3 0.08
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAATTATATAAAATACACG
Found at i:11740453 original size:22 final size:22
Alignment explanation
Indices: 11740428--11740470 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11740418 TTAATGTCGA
11740428 TTTAAATTATT-CACAATATTAT
1 TTTAAATTATTACAC-ATATTAT
*
11740450 TTTACATTATTACACATATTA
1 TTTAAATTATTACACATATTA
11740471 ATTATAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAAATTATTACACATATTAT
Found at i:11743277 original size:5 final size:5
Alignment explanation
Indices: 11743269--11743296 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
11743259 TTTACTTTAA
11743269 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
11743297 TTTAGTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:11754325 original size:2 final size:2
Alignment explanation
Indices: 11754318--11754342 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11754308 TAGTGTAAGC
11754318 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 T
11754343 GATCTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11757526 original size:34 final size:32
Alignment explanation
Indices: 11757469--11757540 Score: 83
Period size: 35 Copynumber: 2.2 Consensus size: 32
11757459 TGTTTTAATA
11757469 AATTTTAAAATTTTAAATTAATAAAAATAAAATT
1 AATTTTAAAATTTTAAA-TAATAAAAA-AAAATT
* *
11757503 ATATTTTAAATTTCTTAAA-AATAATAAAAAATT
1 A-ATTTTAAAATT-TTAAATAATAAAAAAAAATT
11757536 AATTT
1 AATTT
11757541 AATCTTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
32 4 0.12
33 7 0.21
34 8 0.24
35 10 0.29
36 5 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
AATTTTAAAATTTTAAATAATAAAAAAAAATT
Found at i:11757542 original size:31 final size:32
Alignment explanation
Indices: 11757488--11757558 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 32
11757478 ATTTTAAATT
* *
11757488 AATAAAAATAAAATTATATTTTAAATTTCTTAAA
1 AATAATAATAAAATTATATTTT-AATCT-TTAAA
*
11757522 AATAATAA-AAAATTA-A-TTTAATCTTTCAA
1 AATAATAATAAAATTATATTTTAATCTTTAAA
11757551 AATAATAA
1 AATAATAA
11757559 GATTATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.35
30 4 0.12
31 3 0.09
32 1 0.03
33 7 0.21
34 7 0.21
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (32 bp):
AATAATAATAAAATTATATTTTAATCTTTAAA
Found at i:11768688 original size:17 final size:16
Alignment explanation
Indices: 11768666--11768754 Score: 72
Period size: 17 Copynumber: 5.4 Consensus size: 16
11768656 ACCGTTTTAG
11768666 AATTTATTTTGAAATTA
1 AATTTATTTT-AAATTA
11768683 AATTTATTTTAAATTTA
1 AATTTATTTTAAA-TTA
*
11768700 AATTTAATTTAAATT-
1 AATTTATTTTAAATTA
* * *
11768715 TATTTAAATTTAATTTA
1 AATTT-ATTTTAAATTA
* * *
11768732 AGTTTGAATTTAATTTA
1 AATTT-ATTTTAAATTA
11768749 AATTTA
1 AATTTA
11768755 ATATTATTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.06
16 15 0.24
17 43 0.69
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTTATTTTAAATTA
Found at i:11768696 original size:11 final size:11
Alignment explanation
Indices: 11768694--11768773 Score: 85
Period size: 11 Copynumber: 7.2 Consensus size: 11
11768684 ATTTATTTTA
11768694 AATTTAAATTT
1 AATTTAAATTT
11768705 AATTTAAATTT
1 AATTTAAATTT
11768716 -ATTTAAATTT
1 AATTTAAATTT
*
11768726 AATTTAAGTTT
1 AATTTAAATTT
11768737 GAATTT-AATTT
1 -AATTTAAATTT
11768748 AAATTT-AATATT
1 -AATTTAAAT-TT
*
11768760 ATTTGTAAATTT
1 AATT-TAAATTT
11768772 AA
1 AA
11768774 AATGTCTAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
10 10 0.17
11 35 0.59
12 11 0.19
13 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:11768697 original size:28 final size:27
Alignment explanation
Indices: 11768660--11768772 Score: 120
Period size: 28 Copynumber: 4.0 Consensus size: 27
11768650 GTCCAAACCG
* *
11768660 TTTTAGAATTTATTTTGAAATTAAATTTA
1 TTTTA-AATTTAATTT-AATTTAAATTTA
11768689 TTTTAAATTTAAATTTAATTTAAATTTA
1 TTTTAAATTT-AATTTAATTTAAATTTA
*
11768717 -TTTAAATTTAATTTAAGTTTGAATTTA
1 TTTTAAATTTAATTTAA-TTTAAATTTA
* *
11768744 ATTTAAATTTAATATTATTTGTAAATTTA
1 TTTTAAATTTAAT-TTAATT-TAAATTTA
11768773 AAATGTCTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.09
27 18 0.24
28 30 0.41
29 19 0.26
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (27 bp):
TTTTAAATTTAATTTAATTTAAATTTA
Found at i:11768723 original size:38 final size:38
Alignment explanation
Indices: 11768680--11768754 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
11768670 TATTTTGAAA
*
11768680 TTAAATTTATTTTAAATTTAAATTTAATTTAAATTTAT
1 TTAAATTTAATTTAAATTTAAATTTAATTTAAATTTAT
* *
11768718 TTAAATTTAATTTAAGTTTGAATTTAATTTAAATTTA
1 TTAAATTTAATTTAAATTTAAATTTAATTTAAATTTA
11768755 ATATTATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (38 bp):
TTAAATTTAATTTAAATTTAAATTTAATTTAAATTTAT
Found at i:11768774 original size:6 final size:6
Alignment explanation
Indices: 11768680--11768755 Score: 83
Period size: 6 Copynumber: 13.7 Consensus size: 6
11768670 TATTTTGAAA
*
11768680 TTAAAT TT-ATT TTAAAT TTAAAT TT-AAT TTAAAT TT--AT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
11768724 TT-AAT TTAAGT TTGAAT TT-AAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
11768756 TATTATTTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
4 4 0.07
5 19 0.32
6 36 0.61
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:11769605 original size:22 final size:23
Alignment explanation
Indices: 11769580--11769633 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 23
11769570 ATAAATGTTT
11769580 TTAATTAGTG-TTAATGAAATTA
1 TTAATTAGTGATTAATGAAATTA
*
11769602 TTAATGATGGTGATTAATGAAATTA
1 TTAAT--TAGTGATTAATGAAATTA
11769627 TTAATTA
1 TTAATTA
11769634 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 1 0.04
24 4 0.15
25 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (23 bp):
TTAATTAGTGATTAATGAAATTA
Found at i:11769885 original size:14 final size:14
Alignment explanation
Indices: 11769866--11769892 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11769856 ATGTTGAATA
11769866 TTTCCAGATCTGGG
1 TTTCCAGATCTGGG
11769880 TTTCCAGATCTGG
1 TTTCCAGATCTGG
11769893 TTTTGTTTAT
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:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (14 bp):
TTTCCAGATCTGGG
Found at i:11770609 original size:161 final size:163
Alignment explanation
Indices: 11770428--11770767 Score: 477
Period size: 164 Copynumber: 2.1 Consensus size: 163
11770418 AGTTTTCAAT
* * *
11770428 TTAGTCCTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGT-C-ATTTTTAGATTAGTTATGC
1 TTAGTCCTTTGACTGTTTGACTACACCAGAGGCTACCACGTGTCCTATTTTTAGATTAGTTATGC
* *
11770491 ATTTAGTCCCTGGCATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACA
66 ATTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAATTACA
* *
11770556 AAATTAGCCCAACAATTTTTCAAGGTTTATAAA
131 AAATTAGCCCAACAATTTTTCAAGATTTACAAA
* * * * *
11770589 TTAGTCCTTTGACTGTTTGACTACACCAGGGGCTACCACGTGTCGCTTTTTTTGGCTTATTTATG
1 TTAGTCCTTTGACTGTTTGACTACACCAGAGGCTACCACGTGTC-CTATTTTTAGATTAGTTATG
* *
11770654 CATTTAGTCCTTGACTTTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAATTAC
65 CATTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAATTAC
* * * *
11770719 GAAATTGGCCCAAGAATTTTTCAAGATTTACAAT
130 AAAATTAGCCCAACAATTTTTCAAGATTTACAAA
* *
11770753 TTAATCCCTTGACTG
1 TTAGTCCTTTGACTG
11770768 CTGGATGCCT
Statistics
Matches: 156, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
161 39 0.25
163 1 0.01
164 116 0.74
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (163 bp):
TTAGTCCTTTGACTGTTTGACTACACCAGAGGCTACCACGTGTCCTATTTTTAGATTAGTTATGC
ATTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAATTACA
AAATTAGCCCAACAATTTTTCAAGATTTACAAA
Found at i:11770902 original size:29 final size:28
Alignment explanation
Indices: 11770836--11771026 Score: 95
Period size: 29 Copynumber: 6.6 Consensus size: 28
11770826 CCCCAAACAG
*
11770836 TCCAAAAATTACATTTTGACCCC-AAAAT
1 TCCAAAAATTACA-TTTGACCCCGAAACT
** *
11770864 TTTAGGAAATTACATTCTGACCCCGAAACT
1 TCCA-AAAATTACATT-TGACCCCGAAACT
* *
11770894 TCCAAAAATTACCATTTTACCCTCGAACCT
1 TCCAAAAATTA-CATTTGACCC-CGAAACT
* * * **
11770924 T-CTAAAATTCCATTTTTAACCCC--AGTT
1 TCCAAAAATTACA--TTTGACCCCGAAACT
*
11770951 TCACCAAAAATTACTATTTTACCCCGAAACT
1 T--CCAAAAATTAC-ATTTGACCCCGAAACT
* *
11770982 TCCAAAAATTACCATTTTACCCCTAAACCT
1 TCCAAAAATTA-CATTTGACCCCGAAA-CT
* *
11771012 T-CTAAAATTCCATTT
1 TCCAAAAATTACATTT
11771027 TTCACCCCGA
Statistics
Matches: 126, Mismatches: 22, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
27 3 0.02
28 11 0.09
29 72 0.57
30 36 0.29
31 4 0.03
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (28 bp):
TCCAAAAATTACATTTGACCCCGAAACT
Found at i:11771034 original size:59 final size:58
Alignment explanation
Indices: 11770984--11771182 Score: 265
Period size: 59 Copynumber: 3.4 Consensus size: 58
11770974 CCGAAACTTC
**
11770984 CAAAAATTACCATTTTACCCCTAAACCTTCTAAAATTCCATTTTTCACCCCGATTTCA
1 CAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTCACCCCGATTTCA
* * * *
11771042 CTGAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCAATTTTA
1 C-AAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTCACCCCGATTTCA
* * * *
11771101 TCAAAAATTACCATTTCACCCCCGAACTTTCCAAAATTCCA-TTTTCAACCTCGATTTCA
1 -CAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTC-ACCCCGATTTCA
*
11771160 CCAAAATTACCATTTTACCCCCG
1 CAAAAATTACCATTTTACCCCCG
11771183 GGTATCCAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
58 26 0.21
59 95 0.78
60 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.33
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTCACCCCGATTTCA
Found at i:11771088 original size:88 final size:89
Alignment explanation
Indices: 11770870--11771086 Score: 293
Period size: 88 Copynumber: 2.5 Consensus size: 89
11770860 AAATTTTAGG
* *
11770870 AAATTA-CATTCTGACCCCGAAACTTCCAAAAATTACCATTTTA-CCCTCGAACCTTCTAAAATT
1 AAATTACCATT-TTACCCCGAAACTTCCAAAAATTACCATTTTACCCCTCAAACCTTCTAAAATT
11770933 CCATTTTTAACCCCAGTTTCACCAA
65 CCATTTTTAACCCCAGTTTCACCAA
*
11770958 AAATTACTATTTTACCCCGAAACTTCCAAAAATTACCATTTTACCCCT-AAACCTTCTAAAATTC
1 AAATTACCATTTTACCCCGAAACTTCCAAAAATTACCATTTTACCCCTCAAACCTTCTAAAATTC
* **
11771022 CATTTTTCACCCC-GATTTCACTGA
66 CATTTTTAACCCCAG-TTTCACCAA
* *
11771046 AAATTACCATTTTACCCCCGAACCTT-CTAAAATT-CCATTTT
1 AAATTACCATTTTA-CCCCGAAACTTCCAAAAATTACCATTTT
11771087 TAACCCCAAT
Statistics
Matches: 116, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
87 8 0.07
88 91 0.78
89 17 0.15
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (89 bp):
AAATTACCATTTTACCCCGAAACTTCCAAAAATTACCATTTTACCCCTCAAACCTTCTAAAATTC
CATTTTTAACCCCAGTTTCACCAA
Found at i:11771146 original size:29 final size:29
Alignment explanation
Indices: 11770884--11771182 Score: 167
Period size: 29 Copynumber: 10.2 Consensus size: 29
11770874 TACATTCTGA
11770884 CCCCGAAAC-TTCCAAAAATTACCATTTTAC
1 CCCCG-AACTTTCC-AAAATTACCATTTTAC
* * * *
11770914 CCTCGAACCTTCTAAAATT-CCATTTTTAA
1 CCCCGAACTTTCCAAAATTACCA-TTTTAC
* *
11770943 CCCC--AGTTTCACCAAAAATTACTATTTTA-
1 CCCCGAACTTT--CC-AAAATTACCATTTTAC
11770972 CCCCGAAAC-TTCCAAAAATTACCATTTTAC
1 CCCCG-AACTTTCC-AAAATTACCATTTTAC
** * * *
11771002 CCCTAAACCTTCTAAAATT-CCATTTTTC
1 CCCCGAACTTTCCAAAATTACCATTTTAC
11771030 ACCCCG-A-TTTCACTGAAAATTACCATTTTAC
1 -CCCCGAACTTTC-C--AAAATTACCATTTTAC
* * *
11771061 CCCCGAACCTTCTAAAATT-CCATTTTTAA
1 CCCCGAACTTTCCAAAATTACCA-TTTTAC
* * *
11771090 CCCC-AATTTTATCAAAAATTACCATTTCAC
1 CCCCGAA-CTT-TCCAAAATTACCATTTTAC
*
11771120 CCCCGAACTTTCCAAAATT-CCATTTTCAA
1 CCCCGAACTTTCCAAAATTACCATTTT-AC
*
11771149 CCTCG-A-TTTCACCAAAATTACCATTTTAC
1 CCCCGAACTTT--CCAAAATTACCATTTTAC
11771178 CCCCG
1 CCCCG
11771183 GGTATCCAAA
Statistics
Matches: 208, Mismatches: 34, Indels: 55
0.70 0.11 0.19
Matches are distributed among these distances:
27 9 0.04
28 24 0.12
29 93 0.45
30 60 0.29
31 18 0.09
32 4 0.02
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (29 bp):
CCCCGAACTTTCCAAAATTACCATTTTAC
Found at i:11773872 original size:4 final size:4
Alignment explanation
Indices: 11773865--11773901 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
11773855 ATTTATTATT
11773865 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
11773902 ATGGAATCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:11773887 original size:63 final size:64
Alignment explanation
Indices: 11773708--11773889 Score: 230
Period size: 63 Copynumber: 2.8 Consensus size: 64
11773698 TTTGGGTTTG
* *
11773708 TTTT-TATTTATTTATTTATCTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATAT
1 TTTTATATTTATTTATTTAT-TATATT-ATAATA-AATAAATAAATAATAAAATAAAATTAATAT
11773772 TA
63 TA
* **
11773774 TTTTACATTTATTTA--TATTCATACAATAATAAATAAATAAATAATAAAATAAAATTAATATTA
1 TTTTATATTTATTTATTTATT-ATATTATAATAAATAAATAAATAATAAAATAAAATTAATATTA
*
11773837 TTTTATATTTATTTATTTATT-TATTATTATAAATAAATAAATAA-ATAAATAAA
1 TTTTATATTTATTTATTTATTATATTATAATAAATAAATAAATAATA-AAATAAA
11773890 TAAATAAATA
Statistics
Matches: 102, Mismatches: 9, Indels: 13
0.82 0.07 0.10
Matches are distributed among these distances:
62 1 0.01
63 72 0.71
64 6 0.06
65 10 0.10
66 4 0.04
67 9 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (64 bp):
TTTTATATTTATTTATTTATTATATTATAATAAATAAATAAATAATAAAATAAAATTAATATTA
Found at i:11774072 original size:15 final size:15
Alignment explanation
Indices: 11774052--11774097 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
11774042 TTTGTCTTAG
11774052 CTTATATTTTAGTCA
1 CTTATATTTTAGTCA
*
11774067 CTTATATTTAAGAT-A
1 CTTATATTTTAG-TCA
*
11774082 -TTATGTTTTAGTCA
1 CTTATATTTTAGTCA
11774096 CT
1 CT
11774098 GAGCGTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.40
15 13 0.52
16 1 0.04
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (15 bp):
CTTATATTTTAGTCA
Found at i:11778688 original size:11 final size:11
Alignment explanation
Indices: 11778642--11778697 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
11778632 CCCAAACTAT
11778642 TTTAATTTTAAA
1 TTTAA-TTTAAA
* *
11778654 TTTATTTTGAA
1 TTTAATTTAAA
*
11778665 TTCAATTTAAA
1 TTTAATTTAAA
11778676 TTTAAATTT-AA
1 TTT-AATTTAAA
11778687 TTTAAATTTAA
1 TTT-AATTTAA
11778698 CATTATTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 26 0.72
12 10 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:11778696 original size:6 final size:6
Alignment explanation
Indices: 11778642--11778697 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
11778632 CCCAAACTAT
* * * *
11778642 TTTAAT TTTAAA TTT-AT TTTGAA -TTCAA TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
11778687 TTTAAA TTTAA
1 TTTAAA TTTAA
11778698 CATTATTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 13 0.31
6 29 0.69
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:11778710 original size:17 final size:17
Alignment explanation
Indices: 11778663--11778697 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11778653 ATTTATTTTG
*
11778663 AATTCAATTTAAATTTA
1 AATTTAATTTAAATTTA
11778680 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
11778697 A
1 A
11778698 CATTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:11779162 original size:14 final size:14
Alignment explanation
Indices: 11779110--11779149 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
11779100 TATTAACACC
11779110 CACATATACATATA
1 CACATATACATATA
11779124 CACATATACATATA
1 CACATATACATATA
11779138 CACATATACATA
1 CACATATACATA
11779150 AATTCATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (14 bp):
CACATATACATATA
Found at i:11780458 original size:90 final size:90
Alignment explanation
Indices: 11780305--11780532 Score: 318
Period size: 90 Copynumber: 2.5 Consensus size: 90
11780295 AATTGTTCAG
* * *
11780305 AAATTACATTTTGACCCCGAAACTTTCTAAAAATTTCATTTTGACCCTAAAACTATCTCAAAATT
1 AAATTATATTTTGACCCCGAAACTTTCTAAAAATTACATTTTGACCCCAAAACTATCTCAAAATT
*
11780370 ATATTTTGA-CCTCAAAACTTTTCCA
66 ACATTTTGACCCT-AAAACTTTTCCA
* * *
11780395 AAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACT-TTTCCAAAAT
1 AAATTATATTTTGACCCCGAAACTTTCTAAAAATTACATTTTGACCCCAAAACTATCT-CAAAAT
11780459 TACATTTTGACCCTAAAACTTTTCCA
65 TACATTTTGACCCTAAAACTTTTCCA
* * *
11780485 AAATTATACTTTGACCCCGAAACTTTC-AAAAATTGCCATTTTTACCCC
1 AAATTATATTTTGACCCCGAAACTTTCTAAAAATT-ACATTTTGACCCC
11780533 CGCATCTTTT
Statistics
Matches: 123, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
89 9 0.07
90 111 0.90
91 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (90 bp):
AAATTATATTTTGACCCCGAAACTTTCTAAAAATTACATTTTGACCCCAAAACTATCTCAAAATT
ACATTTTGACCCTAAAACTTTTCCA
Found at i:11780526 original size:60 final size:60
Alignment explanation
Indices: 11780305--11780518 Score: 263
Period size: 60 Copynumber: 3.6 Consensus size: 60
11780295 AATTGTTCAG
* * *
11780305 AAATTACATTTTGACCCCGAAAC-TTTCTAAAAATTTCATTTTGACCCTAAAACTATCTCA
1 AAATTACATTTTGACCCCAAAACTTTTC-AAAAATTACATTTTGACCCTAAAACTTTCTCA
* * * * * * *
11780365 AAATTATATTTTGACCTCAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTTCAAAAATTACATTTTGACCCTAAAACTTTCTCA
*
11780425 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTT-TCCA
1 AAATTACATTTTGACCCCAAAACTTTTCAAAAATTACATTTTGACCCTAAAACTTTCT-CA
* * *
11780485 AAATTATACTTTGACCCCGAAAC-TTTCAAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCAAAAATT
11780519 GCCATTTTTA
Statistics
Matches: 132, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
59 11 0.08
60 117 0.89
61 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (60 bp):
AAATTACATTTTGACCCCAAAACTTTTCAAAAATTACATTTTGACCCTAAAACTTTCTCA
Found at i:11780532 original size:30 final size:29
Alignment explanation
Indices: 11780300--11780532 Score: 234
Period size: 30 Copynumber: 7.8 Consensus size: 29
11780290 CCCTAAATTG
* *
11780300 TTCAGAAATTACATTTTGACCCCGAAACT
1 TTCAAAAATTACATTTTGACCCCAAAACT
* *
11780329 TTCTAAAAATTTCATTTTGACCCTAAAACT
1 TTC-AAAAATTACATTTTGACCCCAAAACT
* *
11780359 ATCTC-AAAATTATATTTTGACCTCAAAACTT
1 -T-TCAAAAATTACATTTTGACCCCAAAAC-T
* * *
11780390 TTCCAAAATTATATTTTAACCCCAAAACT
1 TTCAAAAATTACATTTTGACCCCAAAACT
11780419 TTCTAAAAATTACATTTTGACCCCAAAACTT
1 TTC-AAAAATTACATTTTGACCCCAAAAC-T
* *
11780450 TTCCAAAATTACATTTTGACCCTAAAACTT
1 TTCAAAAATTACATTTTGACCCCAAAAC-T
* * * *
11780480 TTCCAAAATTATACTTTGACCCCGAAACT
1 TTCAAAAATTACATTTTGACCCCAAAACT
* *
11780509 TTCAAAAATTGCCATTTTTACCCC
1 TTCAAAAATT-ACATTTTGACCCC
11780533 CGCATCTTTT
Statistics
Matches: 172, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.11
30 145 0.84
31 6 0.03
32 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCAAAAATTACATTTTGACCCCAAAACT
Found at i:11787962 original size:51 final size:50
Alignment explanation
Indices: 11787907--11788062 Score: 179
Period size: 50 Copynumber: 3.1 Consensus size: 50
11787897 AAGCATGGAC
* *
11787907 GGGAAATATCTAAGACCGCAATGGTAGATCCAGTACCACAAAGATACAGAA
1 GGGAAATATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGACAC-GAA
* ** * ** *
11787958 GGGAAAGATCTAAGATTGCAACGGTAGATCTAGTACCATGAAGACACGAC
1 GGGAAATATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGACACGAA
* * * *
11788008 GGGAAATATCTAAGCCCGCAACGGTAGATTCAGTATCACAAAGACA-AAA
1 GGGAAATATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGACACGAA
11788057 GGGAAA
1 GGGAAA
11788063 GGTCTAAGTT
Statistics
Matches: 85, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
49 7 0.08
50 39 0.46
51 39 0.46
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.16
Consensus pattern (50 bp):
GGGAAATATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGACACGAA
Found at i:11788029 original size:50 final size:51
Alignment explanation
Indices: 11787904--11788053 Score: 185
Period size: 51 Copynumber: 3.0 Consensus size: 51
11787894 CAAAAGCATG
* *
11787904 GACGGGAAATATCTAAGACCGCAATGGTAGATCCAGTACCACAAAGATACA
1 GACGGGAAATATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGACACA
* * ** * **
11787955 GAAGGGAAAGATCTAAGATTGCAACGGTAGATCTAGTACCATGAAGACAC-
1 GACGGGAAATATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGACACA
* * *
11788005 GACGGGAAATATCTAAGCCCGCAACGGTAGATTCAGTATCACAAAGACA
1 GACGGGAAATATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGACA
11788054 AAAGGGAAAG
Statistics
Matches: 80, Mismatches: 19, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
50 39 0.49
51 41 0.51
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (51 bp):
GACGGGAAATATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGACACA
Found at i:11788513 original size:78 final size:76
Alignment explanation
Indices: 11788348--11789136 Score: 968
Period size: 76 Copynumber: 9.9 Consensus size: 76
11788338 GTCAAATGTT
*
11788348 TATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
11788413 AGATCTTTTCC
66 AGATCATTTCC
*
11788424 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTTTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATC--TCTGAAATTGAAGTAAGAG
11788489 CAAGATCATTTCC
64 CAAGATCATTTCC
* *
11788502 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTC-TT-TATCTCTGAAA-T----T----G
11788567 TAAGATGAAGAGCAAGATCATTTCC
55 -AAG-T-AAGAGCAAGATCATTTCC
*
11788592 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGCCTTTATCTCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA--TCTCTGAAATTGAAGTAAGAG
* ** *
11788657 TAAGATGAAGCACCAACATCAT
64 CAAGAT-------C-ATTTC-C
* **** * * * * *
11788679 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATGTAAAGTCTTTATCTCTGAAATTGAAGTAA
1 TATCC--T-CTTGAAAT--TGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
*
11788744 GAGTAAGATCATTTCC
61 GAGCAAGATCATTTCC
11788760 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
11788825 AGATCTTTTCC
66 AGATCATTTCC
* *
11788836 TATTCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTA
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
11788901 AGATC-TATTCC
66 AGATCAT-TTCC
*
11788912 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
11788977 AGATCTTTTCC
66 AGATCATTTCC
*
11788988 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTTTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATC--TCTGAAATTGAAGTAAGAG
11789053 CAAGATCATTTCC
64 CAAGATCATTTCC
* * *
11789066 TATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAATTGAAGTAAAAG
1 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA--TCTCTGAAATTGAAGTAAGAG
11789131 CAAGAT
64 CAAGAT
11789137 GAAGCCTCGA
Statistics
Matches: 630, Mismatches: 45, Indels: 74
0.84 0.06 0.10
Matches are distributed among these distances:
75 1 0.00
76 285 0.45
77 1 0.00
78 183 0.29
79 5 0.01
80 8 0.01
81 5 0.01
82 3 0.00
83 2 0.00
85 2 0.00
86 3 0.00
87 5 0.01
88 4 0.01
89 5 0.01
90 95 0.15
92 23 0.04
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (76 bp):
TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
AGATCATTTCC
Found at i:11789087 original size:38 final size:37
Alignment explanation
Indices: 11788724--11789087 Score: 251
Period size: 38 Copynumber: 9.6 Consensus size: 37
11788714 GTAAAGTCTT
*
11788724 TATCTC-TGAAATTGAAGTAAGAGTAAGATCATTTCC
1 TATCTCTTGAAATTGAAGTAAGAGCAAGATCATTTCC
* * ** *
11788760 TATCCTCTTGAAATTGAAGTAA-AGCTGGATATCAAGTCTT
1 TAT-CTCTTGAAATTGAAGTAAGAGC--AAGATCATTTC-C
*
11788800 TATCTC-TGAAATTGAAGTAAGAGCAAGATCTTTTCC
1 TATCTCTTGAAATTGAAGTAAGAGCAAGATCATTTCC
* * ** *
11788836 TATTCTCTTGAAATTGAAGTAA-AGCTGGATATCAAGTCTT
1 TA-TCTCTTGAAATTGAAGTAAGAGC--AAGATCATTTC-C
*
11788876 TATCTC-TGAAATTGAAGTAAGAGTAAGATC-TATTCC
1 TATCTCTTGAAATTGAAGTAAGAGCAAGATCAT-TTCC
** * ** *
11788912 TATCCTCTTGAAATTGAAGTAA-AGTTGGATATCAAGTCTT
1 TAT-CTCTTGAAATTGAAGTAAGAG--CAAGATCATTTC-C
*
11788952 TATCTC-TGAAATTGAAGTAAGAGCAAGATCTTTTCC
1 TATCTCTTGAAATTGAAGTAAGAGCAAGATCATTTCC
** * ** *
11788988 TATCCTCTTGAAATTGAAGTAA-AGTTGGATATCAAGTCTT
1 TAT-CTCTTGAAATTGAAGTAAGAG--CAAGATCATTTC-C
*
11789028 TATCTTTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
1 TATCTCT-TGAAATTGAAGTAAGAGCAAGATCATTTCC
11789066 TATCCTCTTGAAATTGAAGTAA
1 TAT-CTCTTGAAATTGAAGTAA
11789088 AGTTGGATAG
Statistics
Matches: 248, Mismatches: 52, Indels: 54
0.70 0.15 0.15
Matches are distributed among these distances:
36 11 0.04
37 40 0.16
38 115 0.46
39 55 0.22
40 25 0.10
41 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (37 bp):
TATCTCTTGAAATTGAAGTAAGAGCAAGATCATTTCC
Found at i:11789430 original size:17 final size:17
Alignment explanation
Indices: 11789410--11789446 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
11789400 TTAAATTTAT
11789410 TTTGAATTCAATTTAAA
1 TTTGAATTCAATTTAAA
*
11789427 TTTGAATTTAATTTAAA
1 TTTGAATTCAATTTAAA
11789444 TTT
1 TTT
11789447 AACATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTGAATTCAATTTAAA
Found at i:11789439 original size:11 final size:11
Alignment explanation
Indices: 11789393--11789448 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
11789383 CCCAAACTAT
11789393 TTTAATTTTAAA
1 TTTAA-TTTAAA
* *
11789405 TTTATTTTGAA
1 TTTAATTTAAA
*
11789416 TTCAATTTAAA
1 TTTAATTTAAA
11789427 TTTGAATTT-AA
1 TTT-AATTTAAA
11789438 TTTAAATTTAA
1 TTT-AATTTAA
11789449 CATTATTATA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:11789894 original size:14 final size:14
Alignment explanation
Indices: 11789861--11789899 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11789851 TATTAACACC
*
11789861 CACATATACATATA
1 CACATATACATAAA
11789875 CACATATACATAAA
1 CACATATACATAAA
**
11789889 TTCATATACAT
1 CACATATACAT
11789900 GGATAATCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (14 bp):
CACATATACATAAA
Found at i:11791080 original size:30 final size:30
Alignment explanation
Indices: 11791040--11791237 Score: 231
Period size: 30 Copynumber: 6.6 Consensus size: 30
11791030 AATTGTTCAG
* *
11791040 AAATTACATTTTGACCCCGAAAC-TTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTTC-CA
* * *
11791070 AAATTTCATTTTGACCCTAAAAC-TATCTCA
1 AAATTACATTTTGACCCCAAAACTTTTC-CA
*
11791100 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
11791130 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
11791160 AAATTACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * * *
11791190 AAATTATACTTTGACCCCGAAAC-TTTCAA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
11791219 AAATTGCCATTTTTACCCC
1 AAATT-ACATTTTGACCCC
11791238 CGCATCTTTT
Statistics
Matches: 146, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
29 10 0.07
30 133 0.91
31 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:11791193 original size:90 final size:89
Alignment explanation
Indices: 11791035--11791237 Score: 266
Period size: 90 Copynumber: 2.3 Consensus size: 89
11791025 CCCTAAATTG
* * *
11791035 TTCAGAAATTACATTTTGACCCCGAAACTTTCTAAAAATTTCATTTTGACCCTAAAACTATCTCA
1 TTCAAAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCTAAAACTATCTCA
*
11791100 AAATTATATTTTGACCCCAAAACTT
66 AAATTATACTTTGACCCCAAAAC-T
* * *
11791125 TTCCAAAATTACATTTTGACCCCAAAACTTT-TCCAAAATTACATTTTGACCCTAAAACT-TTTC
1 TTCAAAAATTACATTTTGACCCCAAAACTTTCT-AAAAATTACATTTTGACCCTAAAACTATCT-
*
11791188 CAAAATTATACTTTGACCCCGAAACT
64 CAAAATTATACTTTGACCCCAAAACT
* *
11791214 TTCAAAAATTGCCATTTTTACCCC
1 TTCAAAAATT-ACATTTTGACCCC
11791238 CGCATCTTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
89 13 0.13
90 86 0.87
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (89 bp):
TTCAAAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCTAAAACTATCTCA
AAATTATACTTTGACCCCAAAACT
Found at i:11793129 original size:25 final size:24
Alignment explanation
Indices: 11793101--11793152 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
11793091 TTTTTAATTT
*
11793101 TTTTAAAAATATTTAT-ATTGTTTTA
1 TTTTAAAAAT-TTAATAATT-TTTTA
*
11793126 TTTTAATAATTTAATAATTTTTTA
1 TTTTAAAAATTTAATAATTTTTTA
11793150 TTT
1 TTT
11793153 ATTGAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTAAAAATTTAATAATTTTTTA
Found at i:11801088 original size:22 final size:22
Alignment explanation
Indices: 11801045--11801102 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
11801035 TGATCTTTAT
*
11801045 TATTATTATTTTTTTTGATGAAA
1 TATTATTA-TTATTTTGATGAAA
*
11801068 TATTATTATTATTTTGGTGAAA
1 TATTATTATTATTTTGATGAAA
11801090 TATTATTATTATT
1 TATTATTATTATT
11801103 ATTATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 25 0.76
23 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (22 bp):
TATTATTATTATTTTGATGAAA
Found at i:11803543 original size:31 final size:31
Alignment explanation
Indices: 11803508--11803574 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
11803498 TTAATAGCCT
*
11803508 AGTGACTTAAATA-AAATA-TTATGAATAGTTC
1 AGTGACTTAAA-AGAAA-ACTTATAAATAGTTC
* *
11803539 AGTGATTTAAAAGAAAACTTCTAAATAGTTC
1 AGTGACTTAAAAGAAAACTTATAAATAGTTC
11803570 AGTGA
1 AGTGA
11803575 TCATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (31 bp):
AGTGACTTAAAAGAAAACTTATAAATAGTTC
Found at i:11813694 original size:2 final size:2
Alignment explanation
Indices: 11813687--11813721 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11813677 TAATATTCTT
11813687 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 T
11813722 TTGGAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11818402 original size:59 final size:59
Alignment explanation
Indices: 11818310--11818421 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
11818300 CTAATATTAA
* * * *
11818310 TATATATTAAACAATTAGAGATTTAATTATTCTAATTGACTTGACAATCATTCAATTGC
1 TATATATTAAACAATTACAGATTCAATTATTCTAATTGACTTAACAACCATTCAATTGC
11818369 TATATATTAAACAATTACAGATTCAATTATTCTAATTGACTTAACAACCATTC
1 TATATATTAAACAATTACAGATTCAATTATTCTAATTGACTTAACAACCATTC
11818422 TAAGCAATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.39
Consensus pattern (59 bp):
TATATATTAAACAATTACAGATTCAATTATTCTAATTGACTTAACAACCATTCAATTGC
Found at i:11828333 original size:17 final size:18
Alignment explanation
Indices: 11828307--11828343 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
11828297 AAAGTGATCA
*
11828307 TTTTATTTCTTTT-ATCT
1 TTTTACTTCTTTTAATCT
11828324 TTTTACTTCTTTTAATCT
1 TTTTACTTCTTTTAATCT
11828342 TT
1 TT
11828344 GTATTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTACTTCTTTTAATCT
Found at i:11828350 original size:17 final size:17
Alignment explanation
Indices: 11828313--11828351 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
11828303 ATCATTTTAT
*
11828313 TTCTTTTATCTTTTTAC
1 TTCTTTTATCTTTGTAC
11828330 TTCTTTTAATCTTTGTA-
1 TTCTTTT-ATCTTTGTAC
11828347 TTCTT
1 TTCTT
11828352 CTATTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.13, C:0.15, G:0.03, T:0.69
Consensus pattern (17 bp):
TTCTTTTATCTTTGTAC
Found at i:11831633 original size:3 final size:3
Alignment explanation
Indices: 11831625--11831662 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
11831615 CATTCAGAAA
* *
11831625 TTC TTC TTC TTC TTC TTC TTC TTC ATC TTC TTC ATC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
11831663 TTGTTATTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:11832979 original size:17 final size:19
Alignment explanation
Indices: 11832957--11832994 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
11832947 AAATTCATTT
11832957 TTAAATCATT-A-TCAATA
1 TTAAATCATTCATTCAATA
*
11832974 TTAAATGATTCATTCAATA
1 TTAAATCATTCATTCAATA
11832993 TT
1 TT
11832995 CACTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (19 bp):
TTAAATCATTCATTCAATA
Found at i:11834336 original size:2 final size:2
Alignment explanation
Indices: 11834329--11834354 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11834319 AAGCCTATTT
11834329 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
11834355 ATGAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11836220 original size:6 final size:6
Alignment explanation
Indices: 11836211--11836245 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
11836201 CAGTGGCAGA
*
11836211 GACACC GACACC GACTCC GACACC GACACC GACAC
1 GACACC GACACC GACACC GACACC GACACC GACAC
11836246 AACCAATCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.49, G:0.17, T:0.03
Consensus pattern (6 bp):
GACACC
Found at i:11839422 original size:3 final size:3
Alignment explanation
Indices: 11839414--11839446 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
11839404 AATATGCTTT
11839414 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
11839447 ATCTCTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:11839602 original size:14 final size:14
Alignment explanation
Indices: 11839583--11839612 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11839573 TGGTTACTTT
*
11839583 TTCTTTTCTGTTTG
1 TTCTTTTCTATTTG
11839597 TTCTTTTCTATTTG
1 TTCTTTTCTATTTG
11839611 TT
1 TT
11839613 TGTCATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.13, G:0.10, T:0.73
Consensus pattern (14 bp):
TTCTTTTCTATTTG
Found at i:11842839 original size:21 final size:21
Alignment explanation
Indices: 11842800--11842839 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11842790 TGTGGAAATG
***
11842800 GGTTTAGGGTTTTTTAATTAA
1 GGTTTAGGGTTTAAAAATTAA
11842821 GGTTTAGGGTTTAAAAATT
1 GGTTTAGGGTTTAAAAATT
11842840 TTAATTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (21 bp):
GGTTTAGGGTTTAAAAATTAA
Found at i:11844234 original size:30 final size:28
Alignment explanation
Indices: 11844189--11844313 Score: 92
Period size: 30 Copynumber: 4.2 Consensus size: 28
11844179 ATGAAAACGT
*
11844189 AATTTTTGAGGAATTTGGGGTCAAAATTG
1 AATTTTTG-GAAATTTGGGGTCAAAATTG
* * * *
11844218 AATTTTTTGGATAATTTCGGATTAAAATCG
1 AA-TTTTTGGA-AATTTGGGGTCAAAATTG
* *
11844248 AACTTTTGGAAAATTTGAGGTCGAAAATGTG
1 AATTTTTGG-AAATTTGGGGTC-AAAAT-TG
*
11844279 -ATTTTTGGAAATTTGAGGG-CAAAATGG
1 AATTTTTGGAAATTTG-GGGTCAAAATTG
11844306 TAATTTTT
1 -AATTTTT
11844314 AGATGTTCGA
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
27 1 0.01
28 5 0.07
29 30 0.41
30 37 0.50
31 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (28 bp):
AATTTTTGGAAATTTGGGGTCAAAATTG
Found at i:11844311 original size:29 final size:29
Alignment explanation
Indices: 11844251--11844345 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
11844241 AAAATCGAAC
* *
11844251 TTTTGGAAAATTTGAGGTCGAAAAT-GTGAT
1 TTTTGG-AAATTTGAGGGC-AAAATGGTAAT
11844281 TTTTGGAAATTTGAGGGCAAAATGGTAAT
1 TTTTGGAAATTTGAGGGCAAAATGGTAAT
* ** * *
11844310 TTTTAGATGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAATTTGAGGGCAAAATGGTAAT
11844339 TTTTGGA
1 TTTTGGA
11844346 TGTTCGAGCA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 5 0.09
29 45 0.80
30 6 0.11
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (29 bp):
TTTTGGAAATTTGAGGGCAAAATGGTAAT
Found at i:11844347 original size:29 final size:29
Alignment explanation
Indices: 11844271--11844353 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
11844261 TTTGAGGTCG
* ** *
11844271 AAAAT-GTGATTTTTGGAAATTTGAGGGC
1 AAAATGGTAATTTTTGGATGTTCGAGGGC
* *
11844299 AAAATGGTAATTTTTAGATGTTCGAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGC
11844328 AAAATGGTAATTTTTGGATGTTCGAG
1 AAAATGGTAATTTTTGGATGTTCGAG
11844354 CAAAATCATA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 5 0.11
29 42 0.89
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATGTTCGAGGGC
Found at i:11844406 original size:29 final size:29
Alignment explanation
Indices: 11844368--11844449 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 29
11844358 ATCATAATTG
*
11844368 TGGAGGAGTTCGGGATCAAAATGGAAGTT
1 TGGAGAAGTTCGGGATCAAAATGGAAGTT
* * * *
11844397 TGGAGAAGTTCGAGGGTGAAAATGTAATTT
1 TGGAGAAGTTCG-GGATCAAAATGGAAGTT
* * *
11844427 TGGAAAATTTTGGGGATCAAAAT
1 TGGAGAA-GTTCGGGATCAAAAT
11844450 ATAATTTTGG
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
29 11 0.27
30 27 0.66
31 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.33, T:0.28
Consensus pattern (29 bp):
TGGAGAAGTTCGGGATCAAAATGGAAGTT
Found at i:11844429 original size:30 final size:30
Alignment explanation
Indices: 11844383--11844750 Score: 283
Period size: 29 Copynumber: 12.5 Consensus size: 30
11844373 GAGTTCGGGA
* * * *
11844383 TCAAAATGGAAGTTTGGAGAAGTTCGAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
* *
11844413 TGAAAATGTAATTTTGGAAAATTTTG-GGG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
*
11844442 ATCAAAATATAATTTTGGAAAAGTTT-AGGG
1 -TCAAAATGTAATTTTGGAAAAGTTTGAGGG
* * *
11844472 TGAAAATGTGATTTTAGAAAAGTTTGAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
* * *
11844502 TCAAAATGTAATTTTGGAAAAATAT-AGAG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
*
11844531 TCAAAATGTAATTTTTGG-AAAGTTTAAGGG
1 TCAAAATGTAA-TTTTGGAAAAGTTTGAGGG
* *
11844561 T-AGAAATGTAATTTT-GCAAAGTTTGA-TG
1 TCA-AAATGTAATTTTGGAAAAGTTTGAGGG
* * * *
11844589 TTAAAATATGATGTTGGAAAAGTTT-AGGG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
* * **
11844618 TGAAAATGTGATTTTAAAAAAGTTTGAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
* ** **
11844648 TCAAAATGTAATTTT-AAAAAAATCAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
*
11844677 TCAAAATTTAATTTTGTG--AAGTTTGAGGG
1 TCAAAATGTAATTTTG-GAAAAGTTTGAGGG
* * * *
11844706 TTAAAATGTGATTTTTGG-AATGTTTGGGGG
1 TCAAAATGT-AATTTTGGAAAAGTTTGAGGG
* *
11844736 TTAAAAAGTAATTTT
1 TCAAAATGTAATTTT
11844751 TAAACAATAT
Statistics
Matches: 270, Mismatches: 53, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
28 13 0.05
29 130 0.48
30 127 0.47
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
TCAAAATGTAATTTTGGAAAAGTTTGAGGG
Found at i:11844491 original size:29 final size:29
Alignment explanation
Indices: 11844383--11844725 Score: 257
Period size: 30 Copynumber: 11.7 Consensus size: 29
11844373 GAGTTCGGGA
* * * *
11844383 TCAAAATGGAAGTTTGGAGAAGTTCGAGGG
1 TCAAAATGTAATTTTGGAAAAGTT-TAGGG
* * *
11844413 TGAAAATGTAATTTTGGAAAATTTTGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAGGG
*
11844442 ATCAAAATATAATTTTGGAAAAGTTTAGGG
1 -TCAAAATGTAATTTTGGAAAAGTTTAGGG
* * *
11844472 TGAAAATGTGATTTTAGAAAAGTTTGAGGG
1 TCAAAATGTAATTTTGGAAAAGTTT-AGGG
* * *
11844502 TCAAAATGTAATTTTGGAAAAATATAGAG
1 TCAAAATGTAATTTTGGAAAAGTTTAGGG
11844531 TCAAAATGTAATTTTTGG-AAAGTTTAAGGG
1 TCAAAATGTAA-TTTTGGAAAAGTTT-AGGG
* *
11844561 T-AGAAATGTAATTTT-GCAAAGTTT-GATG
1 TCA-AAATGTAATTTTGGAAAAGTTTAG-GG
* * * *
11844589 TTAAAATATGATGTTGGAAAAGTTTAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAGGG
* * **
11844618 TGAAAATGTGATTTTAAAAAAGTTTGAGGG
1 TCAAAATGTAATTTTGGAAAAGTTT-AGGG
** * **
11844648 TCAAAATGTAATTTTAAAAAAATCAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAGGG
*
11844677 TCAAAATTTAATTTTGTG--AAGTTTGAGGG
1 TCAAAATGTAATTTTG-GAAAAGTTT-AGGG
* *
11844706 TTAAAATGTGATTTTTGGAA
1 TCAAAATGT-AATTTTGGAA
11844726 TGTTTGGGGG
Statistics
Matches: 248, Mismatches: 49, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.00
28 15 0.06
29 115 0.46
30 117 0.47
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
TCAAAATGTAATTTTGGAAAAGTTTAGGG
Found at i:11844492 original size:59 final size:60
Alignment explanation
Indices: 11844379--11844720 Score: 240
Period size: 59 Copynumber: 5.8 Consensus size: 60
11844369 GGAGGAGTTC
* * * * * *
11844379 GGGATCAAAATGGAAGTTTGGAGAAGTTCGAGGGTGAAAATGTAATTTTGGAAAATTTTG-
1 GGGATCAAAATGTAATTTTGGAAAAGTT-TAGGGTGAAAATGTAATTTTAGAAAAGTTTGA
* *
11844439 GGGATCAAAATATAATTTTGGAAAAGTTTAGGGTGAAAATGTGATTTTAGAAAAGTTTGA
1 GGGATCAAAATGTAATTTTGGAAAAGTTTAGGGTGAAAATGTAATTTTAGAAAAGTTTGA
* * * * * * *
11844499 GGG-TCAAAATGTAATTTTGGAAAAATATAGAGTCAAAATGTAATTTTTGGAAAGTTTAA
1 GGGATCAAAATGTAATTTTGGAAAAGTTTAGGGTGAAAATGTAATTTTAGAAAAGTTTGA
* * * * * * *
11844558 GGG-T-AGAAATGTAATTTT-GCAAAGTTT-GATGTTAAAATATGATGTTGGAAAAGTTT-A
1 GGGATCA-AAATGTAATTTTGGAAAAGTTTAG-GGTGAAAATGTAATTTTAGAAAAGTTTGA
* * ** * ** **
11844615 GGG-TGAAAATGTGATTTTAAAAAAGTTTGAGGGTCAAAATGTAATTTTA-AAAAAATCAA
1 GGGATCAAAATGTAATTTTGGAAAAGTTT-AGGGTGAAAATGTAATTTTAGAAAAGTTTGA
* * *
11844674 GGG-TCAAAATTTAATTTTGTG--AAGTTTGAGGGTTAAAATGTGATTTT
1 GGGATCAAAATGTAATTTTG-GAAAAGTTT-AGGGTGAAAATGTAATTTT
11844721 TGGAATGTTT
Statistics
Matches: 227, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
57 17 0.07
58 64 0.28
59 118 0.52
60 28 0.12
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (60 bp):
GGGATCAAAATGTAATTTTGGAAAAGTTTAGGGTGAAAATGTAATTTTAGAAAAGTTTGA
Found at i:11844624 original size:146 final size:145
Alignment explanation
Indices: 11844409--11844720 Score: 414
Period size: 146 Copynumber: 2.1 Consensus size: 145
11844399 GAGAAGTTCG
* * * ** * *
11844409 AGGGTGAAAATGTAATTTTGGAAAATTTTGGGGATCAAAATATAATTTTGGAAAAGTTTAGGGTG
1 AGGGTTAAAATGTAATTTT-GCAAAGTTTGATG-TTAAAATATAATGTTGGAAAAGTTTAGGGTG
* **
11844474 AAAATGTGATTTTAGAAAAGTTTGAGGGTCAAAATGTAATTTTGGAAAAAT-ATAGAGTCAAAAT
64 AAAATGTGATTTTAAAAAAGTTTGAGGGTCAAAATGTAATTTTAAAAAAATCA-AGAGTCAAAAT
11844538 GTAATTTT-TGGAAAGTTTA
128 GTAATTTTGT-G-AAGTTTA
*
11844557 AGGG-TAGAAATGTAATTTTGCAAAGTTTGATGTTAAAATATGATGTTGGAAAAGTTTAGGGTGA
1 AGGGTTA-AAATGTAATTTTGCAAAGTTTGATGTTAAAATATAATGTTGGAAAAGTTTAGGGTGA
* *
11844621 AAATGTGATTTTAAAAAAGTTTGAGGGTCAAAATGTAATTTTAAAAAAATCAAGGGTCAAAATTT
65 AAATGTGATTTTAAAAAAGTTTGAGGGTCAAAATGTAATTTTAAAAAAATCAAGAGTCAAAATGT
*
11844686 AATTTTGTGAAGTTTG
130 AATTTTGTGAAGTTTA
*
11844702 AGGGTTAAAATGTGATTTT
1 AGGGTTAAAATGTAATTTT
11844721 TGGAATGTTT
Statistics
Matches: 145, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
145 21 0.14
146 96 0.66
147 12 0.08
148 16 0.11
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (145 bp):
AGGGTTAAAATGTAATTTTGCAAAGTTTGATGTTAAAATATAATGTTGGAAAAGTTTAGGGTGAA
AATGTGATTTTAAAAAAGTTTGAGGGTCAAAATGTAATTTTAAAAAAATCAAGAGTCAAAATGTA
ATTTTGTGAAGTTTA
Found at i:11844731 original size:146 final size:146
Alignment explanation
Indices: 11844445--11844720 Score: 416
Period size: 146 Copynumber: 1.9 Consensus size: 146
11844435 TTTGGGGATC
* *
11844445 AAAATATAATTTTGGAAAAGTTTAGGGTGAAAATGTGATTTTAGAAAAGTTTGAGGGTCAAAATG
1 AAAATATAATGTTGGAAAAGTTTAGGGTGAAAATGTGATTTTAAAAAAGTTTGAGGGTCAAAATG
**
11844510 TAATTTTGGAAAAATATAGAGTCAAAATGTAATTTTTGGAAAGTTTAAGGGTAGAAATGTAATTT
66 TAATTTTAAAAAAATATAGAGTCAAAATGTAATTTTTGGAAAGTTTAAGGGTAGAAATGTAATTT
11844575 TGCAAAGTTTGATGTT
131 TGCAAAGTTTGATGTT
*
11844591 AAAATATGATGTTGGAAAAGTTTAGGGTGAAAATGTGATTTTAAAAAAGTTTGAGGGTCAAAATG
1 AAAATATAATGTTGGAAAAGTTTAGGGTGAAAATGTGATTTTAAAAAAGTTTGAGGGTCAAAATG
* * * *
11844656 TAATTTTAAAAAAATCA-AGGGTCAAAATTTAA-TTTTGTG-AAGTTTGAGGGTTA-AAATGTGA
66 TAATTTTAAAAAAAT-ATAGAGTCAAAATGTAATTTTTG-GAAAGTTTAAGGG-TAGAAATGTAA
11844717 TTTT
128 TTTT
11844721 TGGAATGTTT
Statistics
Matches: 118, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
145 26 0.22
146 91 0.77
147 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (146 bp):
AAAATATAATGTTGGAAAAGTTTAGGGTGAAAATGTGATTTTAAAAAAGTTTGAGGGTCAAAATG
TAATTTTAAAAAAATATAGAGTCAAAATGTAATTTTTGGAAAGTTTAAGGGTAGAAATGTAATTT
TGCAAAGTTTGATGTT
Found at i:11844751 original size:30 final size:30
Alignment explanation
Indices: 11844688--11844751 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
11844678 CAAAATTTAA
* *
11844688 TTTTGTGAAGTTTGAGGGTTAAAATGTGAT
1 TTTTGTGAAGTTTGAGGGTTAAAAAGTAAT
*
11844718 TTTTG-GAATGTTTGGGGGTTAAAAAGTAAT
1 TTTTGTGAA-GTTTGAGGGTTAAAAAGTAAT
11844748 TTTT
1 TTTT
11844752 AAACAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (30 bp):
TTTTGTGAAGTTTGAGGGTTAAAAAGTAAT
Found at i:11845869 original size:27 final size:28
Alignment explanation
Indices: 11845818--11845874 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
11845808 GACTGTTCTT
11845818 TTATTATTATTATTTTAATTATTAAATA
1 TTATTATTATTATTTTAATTATTAAATA
* *
11845846 TTATTCTTATTA-TTTATTTATTAAATA
1 TTATTATTATTATTTTAATTATTAAATA
11845873 TT
1 TT
11845875 GAATGCGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TTATTATTATTATTTTAATTATTAAATA
Found at i:11847871 original size:23 final size:23
Alignment explanation
Indices: 11847836--11847880 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11847826 TTAGTCCCTC
11847836 ATCAATTAAAAATTAGTT-ACTAG
1 ATCAATTAAAAA-TAGTTGACTAG
* *
11847859 ATCATTTACAAATAGTTGACTA
1 ATCAATTAAAAATAGTTGACTA
11847881 ATGCTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (23 bp):
ATCAATTAAAAATAGTTGACTAG
Found at i:11853019 original size:28 final size:28
Alignment explanation
Indices: 11852988--11853050 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
11852978 AAAACGGGAC
11852988 TTTTGGA-TACCCGGGCGCAAAATGGTAA
1 TTTTGGACT-CCCGGGCGCAAAATGGTAA
** * *
11853016 TTTTGGACTTTCGGGGGCAAAATTGTAA
1 TTTTGGACTCCCGGGCGCAAAATGGTAA
11853044 TTTTGGA
1 TTTTGGA
11853051 GAAATCGGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
TTTTGGACTCCCGGGCGCAAAATGGTAA
Found at i:11853162 original size:29 final size:29
Alignment explanation
Indices: 11853130--11853254 Score: 135
Period size: 30 Copynumber: 4.2 Consensus size: 29
11853120 GTCAAAACAA
* * *
11853130 AATTTTGG-AAGGTTCGAGGGTTAAAATGT
1 AATTTTGGAAAGTTTTG-GGGTCAAAATGT
11853159 AATTTTGGAAAAGTTTTGGGGTCAAAATGT
1 AATTTTGG-AAAGTTTTGGGGTCAAAATGT
11853189 AATTTTGGAAAAGTTTTGGGGTCAAAATGT
1 AATTTTGG-AAAGTTTTGGGGTCAAAATGT
** * * *
11853219 AATTTTCAAAAAGTTTTGAGGTAAAAATAT
1 AATTTT-GGAAAGTTTTGGGGTCAAAATGT
11853249 AATTTT
1 AATTTT
11853255 TAGACAATTT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
29 8 0.09
30 71 0.84
31 6 0.07
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTGGAAAGTTTTGGGGTCAAAATGT
Found at i:11853188 original size:30 final size:30
Alignment explanation
Indices: 11853147--11853254 Score: 162
Period size: 30 Copynumber: 3.6 Consensus size: 30
11853137 GAAGGTTCGA
*
11853147 GGGTTAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
11853177 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
**
11853207 GGGTCAAAATGTAATTTTCAAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTG
* * *
11853237 AGGTAAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
11853255 TAGACAATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTTG
Found at i:11855017 original size:17 final size:17
Alignment explanation
Indices: 11854997--11855053 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
11854987 TTATAATAAT
*
11854997 TTTAAATTTAATCCAAA
1 TTTAAATTAAATCCAAA
*
11855014 TTTAAATTAAATTCAAA
1 TTTAAATTAAATCCAAA
* **
11855031 TTTAAAATAAATTTAAA
1 TTTAAATTAAATCCAAA
11855048 TTTAAA
1 TTTAAA
11855054 ACAAATTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTAAATCCAAA
Found at i:11855020 original size:6 final size:6
Alignment explanation
Indices: 11854997--11855053 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
11854987 TTATAATAAT
** * *
11854997 TTTAAA TTT-AA TCCAAA TTTAAA -TTAAA TTCAAA TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
11855042 TTTAAA TTTAAA
1 TTTAAA TTTAAA
11855054 ACAAATTCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
5 12 0.30
6 28 0.70
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:11855054 original size:17 final size:17
Alignment explanation
Indices: 11855010--11855064 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
11855000 AAATTTAATC
*
11855010 CAAATTTAAATTAAATT
1 CAAATTTAAAATAAATT
11855027 CAAATTTAAAATAAATT
1 CAAATTTAAAATAAATT
* *
11855044 TAAATTTAAAACAAATT
1 CAAATTTAAAATAAATT
11855061 CAAA
1 CAAA
11855065 ATGGTTTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (17 bp):
CAAATTTAAAATAAATT
Found at i:11862367 original size:30 final size:27
Alignment explanation
Indices: 11862313--11862369 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 27
11862303 TTCTGGATCA
*
11862313 ATAAAAAATTTAAAATTTTTTAAAAAT
1 ATAAAAAATTTAAAATTATTTAAAAAT
11862340 ATAAAAAATTATTAATAATTATTTAAAAAT
1 ATAAAAAA-T-TTAA-AATTATTTAAAAAT
11862370 TCTAAATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.31
28 1 0.04
29 4 0.15
30 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAAAAAATTTAAAATTATTTAAAAAT
Done.