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 149 of 171
Found at i:44929534 original size:58 final size:58
Alignment explanation
Indices: 44929465--44929685 Score: 254
Period size: 58 Copynumber: 3.8 Consensus size: 58
44929455 ATTCTTACGA
*
44929465 ATATCTCTTTTCATT-AGTATTCTTACAAATATCCCTTTTCATATAATATCCTTATGGAT
1 ATATC-CTTTTCATTGA-TATTCTTACGAATATCCCTTTTCATATAATATCCTTATGGAT
* * * *
44929524 ATATCATTTTCGTTGATATTATTACGAATATCCCTTCTCATATAATATCCTTATGGAT
1 ATATCCTTTTCATTGATATTCTTACGAATATCCCTTTTCATATAATATCCTTATGGAT
* * * ** * *
44929582 AAATCCTTTTCATTGACATTCTTACGAATATCTCTTTTCAT-TGGTATTCTTA-CGA-
1 ATATCCTTTTCATTGATATTCTTACGAATATCCCTTTTCATATAATATCCTTATGGAT
*
44929637 ATATCCCTTTTCATTAATATTCTTACGAATAT-CCTTTCTCATATAATAT
1 ATAT-CCTTTTCATTGATATTCTTACGAATATCCCTTT-TCATATAATAT
44929686 TCCATTGGAT
Statistics
Matches: 136, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
55 7 0.05
56 31 0.23
57 12 0.09
58 80 0.59
59 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (58 bp):
ATATCCTTTTCATTGATATTCTTACGAATATCCCTTTTCATATAATATCCTTATGGAT
Found at i:44934263 original size:40 final size:40
Alignment explanation
Indices: 44934219--44934444 Score: 283
Period size: 40 Copynumber: 5.7 Consensus size: 40
44934209 ATCTGATCGA
* *
44934219 AGCCTGCTAAGTCGTAGCTT-TACTTTTAACACCAGCTCGT
1 AGCCTGCTAAGCCGTAGCTTGTA-TTTTAACACCGGCTCGT
* *
44934259 AGCCTACTAAGCCGTAGCTTGAATTTTAACACCGGCTCGT
1 AGCCTGCTAAGCCGTAGCTTGTATTTTAACACCGGCTCGT
* * * * *
44934299 AACCTGCTAAGCAGCAGCTTGTATTCTAACATCGGCTCGT
1 AGCCTGCTAAGCCGTAGCTTGTATTTTAACACCGGCTCGT
* **
44934339 AGCATGCTAAGCCGTAGCTTGTATTTTAACATTGGCTCGT
1 AGCCTGCTAAGCCGTAGCTTGTATTTTAACACCGGCTCGT
* * *
44934379 AGCCTGCTAAGCTGTAGCTTGTATTTAAACACTGGCTCGT
1 AGCCTGCTAAGCCGTAGCTTGTATTTTAACACCGGCTCGT
* *
44934419 AGCCTGCTAAGCCGTAGTTTGAATTT
1 AGCCTGCTAAGCCGTAGCTTGTATTT
44934445 GTTCAATCAT
Statistics
Matches: 161, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 160 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (40 bp):
AGCCTGCTAAGCCGTAGCTTGTATTTTAACACCGGCTCGT
Found at i:44936657 original size:9 final size:9
Alignment explanation
Indices: 44936630--44936669 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
44936620 TGAATTTTAC
44936630 AATTTGAAT
1 AATTTGAAT
* *
44936639 AACTTAAAT
1 AATTTGAAT
44936648 AATTTGAAT
1 AATTTGAAT
*
44936657 AATTCGAAT
1 AATTTGAAT
44936666 AATT
1 AATT
44936670 CAAATAATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (9 bp):
AATTTGAAT
Found at i:44936778 original size:19 final size:19
Alignment explanation
Indices: 44936756--44936819 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
44936746 AAATTACAAA
44936756 TAAAATTCAAAATAATTTT
1 TAAAATTCAAAATAATTTT
*
44936775 TAAAATTCATAAT-ATTTAT
1 TAAAATTCAAAATAATTT-T
*
44936794 AAAAATTTCAAAATATATTTT
1 TAAAA-TTCAAAATA-ATTTT
44936815 TAAAA
1 TAAAA
44936820 AAATTATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 4 0.11
19 17 0.46
20 7 0.19
21 5 0.14
22 4 0.11
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATTCAAAATAATTTT
Found at i:44936946 original size:14 final size:14
Alignment explanation
Indices: 44936929--44936956 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44936919 TTATTTTGCT
44936929 TTTAAAAAAAATTC
1 TTTAAAAAAAATTC
44936943 TTTAAAAAAAATTC
1 TTTAAAAAAAATTC
44936957 AAATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTAAAAAAAATTC
Found at i:44937117 original size:20 final size:20
Alignment explanation
Indices: 44937079--44937117 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44937069 ACTCAACTTG
**
44937079 AATTTTATTTCACTTAACTC
1 AATTTTATTTCACGCAACTC
*
44937099 AATTTTATTTCAGGCAACT
1 AATTTTATTTCACGCAACT
44937118 TGATTTGCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (20 bp):
AATTTTATTTCACGCAACTC
Found at i:44937123 original size:20 final size:20
Alignment explanation
Indices: 44937072--44937123 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
44937062 TAATTCAACT
*
44937072 CAACTTGAATTTTATTTCACT
1 CAACTTG-ATTTTATTTCACG
* ** *
44937093 TAACTCAATTTTATTTCAGG
1 CAACTTGATTTTATTTCACG
44937113 CAACTTGATTT
1 CAACTTGATTT
44937124 GCTTCTTATT
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (20 bp):
CAACTTGATTTTATTTCACG
Found at i:44938216 original size:44 final size:40
Alignment explanation
Indices: 44938153--44938268 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 40
44938143 TACTAAGCTG
* *
44938153 TAGCTTGAATGTTAACACCGGCTTGTAGCTTGCTAAGCCGTA
1 TAGCTTGTATTTTAACACCGGCTTGTAGCTTGCTAAGCC--A
* * *
44938195 GCTTGCTTGTATTTTAACACCGGCTCGTAGCCTGCTAAGCCA
1 --TAGCTTGTATTTTAACACCGGCTTGTAGCTTGCTAAGCCA
* *
44938237 TAGCTTATATTTTAACACTGGCTTGTAGCTTG
1 TAGCTTGTATTTTAACACCGGCTTGTAGCTTG
44938269 GTTTAACTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 27 0.44
42 1 0.02
44 34 0.55
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (40 bp):
TAGCTTGTATTTTAACACCGGCTTGTAGCTTGCTAAGCCA
Found at i:44939492 original size:18 final size:19
Alignment explanation
Indices: 44939469--44939507 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
44939459 ATTTGTTATT
44939469 TTATATTATTT-TTAAA-AA
1 TTATA-TATTTATTAAATAA
44939487 TTATATATTTATTAAATAA
1 TTATATATTTATTAAATAA
44939506 TT
1 TT
44939508 TCTTTCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATATATTTATTAAATAA
Found at i:44943779 original size:21 final size:19
Alignment explanation
Indices: 44943739--44943780 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
44943729 ACATCATAAC
*
44943739 CAAATAAGTTAACAAGTTA
1 CAAATAAATTAACAAGTTA
44943758 CAAACTAAATTAACATAGTTA
1 CAAA-TAAATTAACA-AGTTA
44943779 CA
1 CA
44943781 TTGAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.26
Consensus pattern (19 bp):
CAAATAAATTAACAAGTTA
Found at i:44949551 original size:21 final size:19
Alignment explanation
Indices: 44949511--44949552 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
44949501 ACATAATAAC
*
44949511 CAAATAAGTTAACAAGTTA
1 CAAATAAATTAACAAGTTA
44949530 CAAACTAAATTAACATAGTTA
1 CAAA-TAAATTAACA-AGTTA
44949551 CA
1 CA
44949553 TTGAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.26
Consensus pattern (19 bp):
CAAATAAATTAACAAGTTA
Found at i:44951101 original size:3 final size:3
Alignment explanation
Indices: 44951093--44951148 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
44951083 GCAATCTTCA
44951093 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44951141 ATT ATT AT
1 ATT ATT AT
44951149 ATACTTCTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44955622 original size:15 final size:15
Alignment explanation
Indices: 44955599--44955629 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44955589 TTCACTCAAT
*
44955599 TCGATTCAACCTGAA
1 TCGACTCAACCTGAA
44955614 TCGACTCAACCTGAA
1 TCGACTCAACCTGAA
44955629 T
1 T
44955630 TTCATTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (15 bp):
TCGACTCAACCTGAA
Found at i:44961854 original size:12 final size:12
Alignment explanation
Indices: 44961837--44961862 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44961827 AGAATTTCAC
44961837 TTAGGTGAAATA
1 TTAGGTGAAATA
44961849 TTAGGTGAAATA
1 TTAGGTGAAATA
44961861 TT
1 TT
44961863 GTTATCAGCC
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:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (12 bp):
TTAGGTGAAATA
Found at i:44967681 original size:21 final size:22
Alignment explanation
Indices: 44967649--44967689 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
44967639 TATAAAGTAA
44967649 AAAAGAAAGAAA-AAGAAAAGCG
1 AAAAGAAAGAAAGAA-AAAAGCG
44967671 AAAAG-AAGAAAGAAAAAAG
1 AAAAGAAAGAAAGAAAAAAG
44967690 ATGGGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (22 bp):
AAAAGAAAGAAAGAAAAAAGCG
Found at i:44971421 original size:21 final size:21
Alignment explanation
Indices: 44971379--44971417 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
44971369 TATCCAAAAT
*
44971379 CCCAAACATTTTTACTTTTCC
1 CCCAAACACTTTTACTTTTCC
44971400 CCCAAA-ACTTTTACTTTT
1 CCCAAACACTTTTACTTTT
44971418 TCCCACTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (21 bp):
CCCAAACACTTTTACTTTTCC
Found at i:44982726 original size:15 final size:16
Alignment explanation
Indices: 44982701--44982730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
44982691 TTTATATATA
44982701 AAAAATAAAATATTTT
1 AAAAATAAAATATTTT
44982717 AAAAAT-AAATATTT
1 AAAAATAAAATATTT
44982731 AGAAGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATAAAATATTTT
Found at i:44991844 original size:6 final size:6
Alignment explanation
Indices: 44991830--44991942 Score: 84
Period size: 6 Copynumber: 17.8 Consensus size: 6
44991820 ACAAACAACC
* ** *
44991830 ATAAGA ATAAAA ATAATGC ATAATAA AATAA-A ATAAAAA ATAAAA GTAAAAA
1 ATAAAA ATAAAA ATAA-AA ATAA-AA A-TAAAA ATA-AAA ATAAAA AT-AAAA
* * *
44991882 ATAAAA GTAAAA GTAAAA ATAAAA ATAAAA ATGAAA ATGAAAA ATGAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT-AAAA AT-AAAA
*
44991932 ATGAAA ATAAA
1 ATAAAA ATAAA
44991943 TTAACTAATT
Statistics
Matches: 88, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
5 2 0.02
6 56 0.64
7 27 0.31
8 3 0.03
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:44991845 original size:12 final size:11
Alignment explanation
Indices: 44991830--44991942 Score: 64
Period size: 13 Copynumber: 8.9 Consensus size: 11
44991820 ACAAACAACC
44991830 ATAAGAATAAAA
1 ATAA-AATAAAA
*
44991842 ATAATGCATAATAA
1 ATAA--AATAA-AA
44991856 AATAAAATAAAAA
1 A-TAAAAT-AAAA
44991869 ATAAAAGTAAAAA
1 ATAAAA-T-AAAA
44991882 ATAAAAGTAAAA
1 ATAAAA-TAAAA
*
44991894 GTAAAAATAAAA
1 AT-AAAATAAAA
*
44991906 ATAAAAATGAAA
1 AT-AAAATAAAA
44991918 ATGAAAAATGAAAA
1 AT--AAAAT-AAAA
44991932 ATGAAAATAAA
1 AT-AAAATAAA
44991943 TTAACTAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
12 34 0.40
13 39 0.45
14 10 0.12
15 3 0.03
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:44991869 original size:7 final size:6
Alignment explanation
Indices: 44991854--44991942 Score: 90
Period size: 6 Copynumber: 14.3 Consensus size: 6
44991844 AATGCATAAT
* * *
44991854 AAAAT- AAAATAA AAAATA AAAGTAA AAAATA AAAGTA AAAGTA AAAATA
1 AAAATA AAAAT-A AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA
* *
44991903 AAAATA AAAATG AAAATGA AAAATGA AAAATG AAAATA AA
1 AAAATA AAAATA AAAAT-A AAAAT-A AAAATA AAAATA AA
44991943 TTAACTAATT
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
5 5 0.07
6 45 0.62
7 22 0.31
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:44995879 original size:13 final size:13
Alignment explanation
Indices: 44995858--44995891 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
44995848 ACAATATAAT
44995858 AATAATAATCCTA
1 AATAATAATCCTA
*
44995871 AATATTAATCCTA
1 AATAATAATCCTA
*
44995884 AAAAATAA
1 AATAATAA
44995892 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:45001454 original size:26 final size:28
Alignment explanation
Indices: 45001413--45001465 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
45001403 AACAATCATT
45001413 GCATAGTCATGAATTAAGCAAA-GAAAA
1 GCATAGTCATGAATTAAGCAAATGAAAA
*
45001440 GCAT-GTCATGGATTAAGCAAATGAAA
1 GCATAGTCATGAATTAAGCAAATGAAA
45001466 GAAAATGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (28 bp):
GCATAGTCATGAATTAAGCAAATGAAAA
Found at i:45002560 original size:88 final size:89
Alignment explanation
Indices: 45002441--45002613 Score: 330
Period size: 88 Copynumber: 2.0 Consensus size: 89
45002431 ATTTCTTGAC
45002441 ATAATTTTTACATTATAAGAAAAGATAAAATTTTGAATATAATTTATTTTTACAATTTTGACTTT
1 ATAATTTTTACATTATAAGAAAAGATAAAATTTTGAATATAATTTATTTTTACAATTTTGACTTT
45002506 GAAAATAATTTACAGGTAATGAAA
66 GAAAATAATTTACAGGTAATGAAA
*
45002530 ATAATTTTTACATTA-AAGAACAGATAAAATTTTGAATATAATTTATTTTTACAATTTTGACTTT
1 ATAATTTTTACATTATAAGAAAAGATAAAATTTTGAATATAATTTATTTTTACAATTTTGACTTT
45002594 GAAAATAATTTACAGGTAAT
66 GAAAATAATTTACAGGTAAT
45002614 TTATTCATAC
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
88 68 0.82
89 15 0.18
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (89 bp):
ATAATTTTTACATTATAAGAAAAGATAAAATTTTGAATATAATTTATTTTTACAATTTTGACTTT
GAAAATAATTTACAGGTAATGAAA
Found at i:45004928 original size:40 final size:40
Alignment explanation
Indices: 45004855--45004941 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 40
45004845 TGAACACTCT
*
45004855 TTTGATAAAATATCAATACCCATCTTAAGGTATCGATAATA
1 TTTGA-AAAATATCAATACCCATATTAAGGTATCGATAATA
* * *
45004896 TTTGAAAAATATCGATACCCATATCTGA-GTATCGATCATA
1 TTTGAAAAATATCAATACCCATAT-TAAGGTATCGATAATA
*
45004936 TCTGAA
1 TTTGAA
45004942 TTCTATCGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
40 33 0.82
41 7 0.17
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (40 bp):
TTTGAAAAATATCAATACCCATATTAAGGTATCGATAATA
Found at i:45005810 original size:40 final size:39
Alignment explanation
Indices: 45005762--45005858 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 39
45005752 TGAAACATTA
*
45005762 GAAAAATATCGATACCCT-TTCAAAGGTATCGATAATTTTT
1 GAAAAATATCGATACCCTATTC-AA-GTATCGATAATATTT
*
45005802 GAAAAATATCGATACCTATATTCAAGTATCGATAATATTT
1 GAAAAATATCGATACC-CTATTCAAGTATCGATAATATTT
45005842 GAAAAA-ATCGATACCCT
1 GAAAAATATCGATACCCT
45005859 CTATTAAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
38 1 0.02
39 9 0.17
40 36 0.69
41 3 0.06
42 3 0.06
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (39 bp):
GAAAAATATCGATACCCTATTCAAGTATCGATAATATTT
Found at i:45006062 original size:20 final size:22
Alignment explanation
Indices: 45006037--45006090 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
45006027 GTATCGATCC
45006037 AAGTATCGAT-AT-TTTTATAA
1 AAGTATCGATAATATTTTATAA
45006057 AAGTATCGATAATATTTTAT--
1 AAGTATCGATAATATTTTATAA
*
45006077 AACTATCGATAATA
1 AAGTATCGATAATA
45006091 ACGGTCCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 23 0.74
21 2 0.06
22 6 0.19
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (22 bp):
AAGTATCGATAATATTTTATAA
Found at i:45014567 original size:20 final size:20
Alignment explanation
Indices: 45014520--45014573 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
45014510 GAAACATTAG
45014520 AAAAATATTGATACACTTTC
1 AAAAATATTGATACACTTTC
*
45014540 AAAGATATTGATA-A-TTTC
1 AAAAATATTGATACACTTTC
*
45014558 TAAAAAATATCGATAC
1 --AAAAATATTGATAC
45014574 CTATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.14
19 1 0.04
20 23 0.82
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (20 bp):
AAAAATATTGATACACTTTC
Found at i:45014837 original size:20 final size:22
Alignment explanation
Indices: 45014812--45014865 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
45014802 GTATCGATCC
45014812 AAGTATCGAT-AT-TTTTATAA
1 AAGTATCGATAATATTTTATAA
45014832 AAGTATCGATAATATTTTAT--
1 AAGTATCGATAATATTTTATAA
*
45014852 AAGTATTGATAATA
1 AAGTATCGATAATA
45014866 ACGGTCCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 23 0.74
21 2 0.06
22 6 0.19
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (22 bp):
AAGTATCGATAATATTTTATAA
Found at i:45027720 original size:10 final size:10
Alignment explanation
Indices: 45027697--45027770 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
45027687 AAATTTTAAT
*
45027697 AAAAATTATT
1 AAAAATTATA
*
45027707 AAAAATTAGA
1 AAAAATTATA
*
45027717 AAAATTTATA
1 AAAAATTATA
*
45027727 AAAAATTGTA
1 AAAAATTATA
**
45027737 AAATTTTAT-
1 AAAAATTATA
*
45027746 AAAAATCGTAAA
1 AAAAAT--TATA
45027758 AAAAATTATA
1 AAAAATTATA
45027768 AAA
1 AAA
45027771 TTTTATAAAG
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
9 4 0.08
10 36 0.75
11 2 0.04
12 6 0.12
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:45027739 original size:20 final size:19
Alignment explanation
Indices: 45027696--45027759 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
45027686 TAAATTTTAA
45027696 TAAAAA-TTATTAAAAATTAG
1 TAAAAATTTA-TAAAAATT-G
45027716 -AAAAATTTATAAAAAATTG
1 TAAAAATTTAT-AAAAATTG
* *
45027735 TAAAATTTTATAAAAATCG
1 TAAAAATTTATAAAAATTG
45027754 TAAAAA
1 TAAAAA
45027760 AAATTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAAAATTTATAAAAATTG
Found at i:45027802 original size:31 final size:31
Alignment explanation
Indices: 45027726--45027796 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
45027716 AAAAATTTAT
*
45027726 AAAAAATTGTAAAATTTTATAAAAATCGTAA
1 AAAAAATTATAAAATTTTATAAAAATCGTAA
*
45027757 AAAAAATTATAAAATTTTAT-AAAGTCGT-A
1 AAAAAATTATAAAATTTTATAAAAATCGTAA
*
45027786 AGAAAATTATA
1 AAAAAATTATA
45027797 CAAAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 11 0.30
30 7 0.19
31 19 0.51
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (31 bp):
AAAAAATTATAAAATTTTATAAAAATCGTAA
Found at i:45028124 original size:47 final size:46
Alignment explanation
Indices: 45028050--45028138 Score: 108
Period size: 47 Copynumber: 1.9 Consensus size: 46
45028040 ATGATTTCTA
*
45028050 TAAAATTTTATAAATTTTTTATATTTTACAATTTTTATAAAAAAATT
1 TAAAATTTTATAAATTTTTAATATTTTA-AATTTTTATAAAAAAATT
* * * *
45028097 TAAATTTTTAATAAA-TTTTAATCTTTTATATTTTTATTAAAA
1 TAAAATTTT-ATAAATTTTTAATATTTTAAATTTTTATAAAAA
45028139 CTTAATAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 12 0.33
47 19 0.53
48 5 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (46 bp):
TAAAATTTTATAAATTTTTAATATTTTAAATTTTTATAAAAAAATT
Found at i:45028143 original size:26 final size:26
Alignment explanation
Indices: 45028095--45028144 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
45028085 TATAAAAAAA
**
45028095 TTTAAATTTTTAATAAATTTTAATCT
1 TTTAAATTTTTAATAAAACTTAATCT
* *
45028121 TTTATATTTTTATTAAAACTTAAT
1 TTTAAATTTTTAATAAAACTTAAT
45028145 AATTTTCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTAAATTTTTAATAAAACTTAATCT
Found at i:45033332 original size:4 final size:4
Alignment explanation
Indices: 45033323--45033361 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
45033313 TTGATTTATA
45033323 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
45033362 AGATAGATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:45037388 original size:17 final size:17
Alignment explanation
Indices: 45037340--45037392 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
45037330 TTTTTGAAAA
45037340 ATAAATAAAATTTATTTTT
1 ATAAA-AAAATTT-TTTTT
* *
45037359 AGTTAGAATAATTTTTTTT
1 A--TAAAAAAATTTTTTTT
45037378 ATAAAAAAATTTTTT
1 ATAAAAAAATTTTTT
45037393 GATAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 12 0.43
19 7 0.25
20 6 0.21
21 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
ATAAAAAAATTTTTTTT
Found at i:45037405 original size:15 final size:16
Alignment explanation
Indices: 45037368--45037409 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
45037358 TAGTTAGAAT
45037368 AATTTTTTTT-ATAAA
1 AATTTTTTTTGATAAA
**
45037383 AAAATTTTTTGAT-AA
1 AATTTTTTTTGATAAA
45037398 AATTTTTTTTGA
1 AATTTTTTTTGA
45037410 ACTAATTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
AATTTTTTTTGATAAA
Found at i:45039002 original size:29 final size:29
Alignment explanation
Indices: 45038938--45039002 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
45038928 AAGGTCAGAC
*
45038938 ATGATACGAATACAACTCCAAATATAGAT
1 ATGATACGAATACAACTACAAATATAGAT
* ** * *
45038967 ATAATACGTGTACAACTACAAATGTAGTT
1 ATGATACGAATACAACTACAAATATAGAT
45038996 ATGATAC
1 ATGATAC
45039003 AGATATAGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (29 bp):
ATGATACGAATACAACTACAAATATAGAT
Found at i:45039015 original size:29 final size:29
Alignment explanation
Indices: 45038983--45039060 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
45038973 CGTGTACAAC
** *
45038983 TACAAATGTAGTTATGATACAGATATAGT
1 TACAAATGTAGACATGATACAGACATAGT
*
45039012 TACAGATGTAGACATGATACAGACATAGT
1 TACAAATGTAGACATGATACAGACATAGT
* **
45039041 TACAGATACAGACATGATAC
1 TACAAATGTAGACATGATAC
45039061 CCCCATCCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (29 bp):
TACAAATGTAGACATGATACAGACATAGT
Found at i:45039885 original size:53 final size:53
Alignment explanation
Indices: 45039799--45039936 Score: 181
Period size: 53 Copynumber: 2.6 Consensus size: 53
45039789 CCTTAAATAA
*
45039799 CAAAATAGTATACACACACCCT-ACCGCACGCCCGTGTGCCAAC-CAGTGCGCCT
1 CAAAATAGTATACACACACCCTGA-CACACGCCCGTGTGCCAACTCA-TGCGCCT
* * * * *
45039852 CAAAATAGTATATAGACACCCTGACACATGCCCGTGTGTCAACTCATGTGCCT
1 CAAAATAGTATACACACACCCTGACACACGCCCGTGTGCCAACTCATGCGCCT
*
45039905 CAAAATAGTATACACACACCTTGACACACGCC
1 CAAAATAGTATACACACACCCTGACACACGCC
45039937 TGCGTGCCTC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 70 0.96
54 3 0.04
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.19
Consensus pattern (53 bp):
CAAAATAGTATACACACACCCTGACACACGCCCGTGTGCCAACTCATGCGCCT
Found at i:45039987 original size:43 final size:41
Alignment explanation
Indices: 45039898--45039989 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 41
45039888 TGTCAACTCA
*
45039898 TGTGCCTCAAAATAGTATACACACACCTTGACACACGCCTG
1 TGTGCCTCAAAATAGTATACACACACCCTGACACACGCCTG
* *
45039939 CGTGCCTCAAAATAGTATATACGCACACCCTGACACACGTCC-G
1 TGTGCCTCAAAATAG--TATACACACACCCTGACACACG-CCTG
45039982 TGTGCCTC
1 TGTGCCTC
45039990 TTGCAACTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 14 0.32
43 28 0.64
44 2 0.05
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (41 bp):
TGTGCCTCAAAATAGTATACACACACCCTGACACACGCCTG
Found at i:45042120 original size:35 final size:35
Alignment explanation
Indices: 45042081--45042154 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
45042071 TGAGGTTATT
45042081 TTTATAAATCAAATAAAAAAGTATCCATAATAAAA
1 TTTATAAATCAAATAAAAAAGTATCCATAATAAAA
*
45042116 TTTATAAATCAAATAAAAAATTATCCATAATAAAA
1 TTTATAAATCAAATAAAAAAGTATCCATAATAAAA
45042151 TTTA
1 TTTA
45042155 AACTAAAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.32
Consensus pattern (35 bp):
TTTATAAATCAAATAAAAAAGTATCCATAATAAAA
Found at i:45042149 original size:17 final size:17
Alignment explanation
Indices: 45042092--45042150 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
45042082 TTATAAATCA
*
45042092 AATAAAAAAGTATCCAT
1 AATAAAAAATTATCCAT
* **
45042109 AAT-AAAATTTATAAAT
1 AATAAAAAATTATCCAT
45042125 CAAATAAAAAATTATCCAT
1 --AATAAAAAATTATCCAT
45042144 AATAAAA
1 AATAAAA
45042151 TTTAAACTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.28
17 10 0.31
18 3 0.09
19 10 0.31
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (17 bp):
AATAAAAAATTATCCAT
Found at i:45043486 original size:19 final size:19
Alignment explanation
Indices: 45043450--45043487 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
45043440 AAAGTTAATA
*
45043450 ACAAATTTGATAATGGTGG
1 ACAAATTTGATAACGGTGG
*
45043469 ACAAATTTGATTACGGTGG
1 ACAAATTTGATAACGGTGG
45043488 TGACAGTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (19 bp):
ACAAATTTGATAACGGTGG
Found at i:45044396 original size:35 final size:33
Alignment explanation
Indices: 45044351--45044417 Score: 107
Period size: 35 Copynumber: 2.0 Consensus size: 33
45044341 GTTAGGGTTA
45044351 TTTACCAAAATAATATAAAAAATTATTTATTTTAT
1 TTTACCAAAATAATAT-AAAAATTATTT-TTTTAT
*
45044386 TTTACTAAAATAATATAAAAATTATTTTTTTA
1 TTTACCAAAATAATATAAAAATTATTTTTTTA
45044418 CTAAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.16
34 11 0.35
35 15 0.48
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (33 bp):
TTTACCAAAATAATATAAAAATTATTTTTTTAT
Found at i:45044428 original size:30 final size:34
Alignment explanation
Indices: 45044348--45044428 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 34
45044338 TTTGTTAGGG
* *
45044348 TTATTTACCAAAATAATATAAAAAATTATTTATT
1 TTATCTACAAAAATAATATAAAAAATTATTTATT
* *
45044382 TTATTTTACTAAAATAATAT-AAAAATTATTT-TT
1 TTA-TCTACAAAAATAATATAAAAAATTATTTATT
45044415 TTA-CTA-AAAAATAA
1 TTATCTACAAAAATAA
45044429 AATTAAATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 7 0.16
31 2 0.05
33 5 0.12
34 14 0.33
35 15 0.35
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (34 bp):
TTATCTACAAAAATAATATAAAAAATTATTTATT
Found at i:45045234 original size:24 final size:24
Alignment explanation
Indices: 45045202--45045247 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
45045192 TAATGTGGAA
45045202 CCAGTAGAAAATGAAGATCCAAAT
1 CCAGTAGAAAATGAAGATCCAAAT
45045226 CCAGTAGAAAATGAAGATCCAA
1 CCAGTAGAAAATGAAGATCCAA
45045248 CTCCGTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (24 bp):
CCAGTAGAAAATGAAGATCCAAAT
Found at i:45047757 original size:7 final size:7
Alignment explanation
Indices: 45047747--45047847 Score: 55
Period size: 7 Copynumber: 14.3 Consensus size: 7
45047737 TTTATGATTA
45047747 TTTAAGG
1 TTTAAGG
45047754 TTTAAGG
1 TTTAAGG
*
45047761 TTTAGGG
1 TTTAAGG
45047768 TGTT-AGG
1 T-TTAAGG
*
45047775 TTAAAGAG
1 TTTAAG-G
*
45047783 TTTAAAG
1 TTTAAGG
* *
45047790 TATACGG
1 TTTAAGG
45047797 TTT-AGG
1 TTTAAGG
*
45047803 TTTTAGGG
1 -TTTAAGG
*
45047811 TCT-AGTG
1 TTTAAG-G
**
45047818 CATAAGG
1 TTTAAGG
45047825 TTTAAGG
1 TTTAAGG
*
45047832 TTTATGG
1 TTTAAGG
45047839 TTTAAGG
1 TTTAAGG
45047846 TT
1 TT
45047848 ATGGGTTTAT
Statistics
Matches: 68, Mismatches: 19, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
6 4 0.06
7 53 0.78
8 11 0.16
ACGTcount: A:0.26, C:0.03, G:0.30, T:0.42
Consensus pattern (7 bp):
TTTAAGG
Found at i:45047842 original size:14 final size:15
Alignment explanation
Indices: 45047823--45047863 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
45047813 TAGTGCATAA
45047823 GGTTTAAGGTTTAT-
1 GGTTTAAGGTTTATG
45047837 GGTTTAAGG-TTATG
1 GGTTTAAGGTTTATG
*
45047851 GGTTTATGGTTTA
1 GGTTTAAGGTTTA
45047864 GGATTTAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 17 0.71
15 3 0.12
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.49
Consensus pattern (15 bp):
GGTTTAAGGTTTATG
Found at i:45047844 original size:21 final size:21
Alignment explanation
Indices: 45047820--45047863 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45047810 GTCTAGTGCA
45047820 TAAGGTT-TAAGGTTTATGGTT
1 TAAGGTTAT-AGGTTTATGGTT
*
45047841 TAAGGTTATGGGTTTATGGTT
1 TAAGGTTATAGGTTTATGGTT
45047862 TA
1 TA
45047864 GGATTTAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
TAAGGTTATAGGTTTATGGTT
Found at i:45048306 original size:6 final size:6
Alignment explanation
Indices: 45048297--45048345 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
45048287 CCAATGCCTT
*
45048297 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTGCTC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC
45048345 T
1 T
45048346 GGCTCTAGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (6 bp):
TTCCTC
Found at i:45048862 original size:19 final size:19
Alignment explanation
Indices: 45048823--45048858 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45048813 GAACTGCACA
45048823 ATTAATAACATGTCAAGAT
1 ATTAATAACATGTCAAGAT
*
45048842 ATTAATAAGA-GTCAAGA
1 ATTAATAACATGTCAAGA
45048859 ATATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (19 bp):
ATTAATAACATGTCAAGAT
Found at i:45050362 original size:12 final size:11
Alignment explanation
Indices: 45050339--45050376 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
45050329 CTCAACTAAA
45050339 TAAA-AAAAAT
1 TAAATAAAAAT
45050349 TAAATAACAAAT
1 TAAATAA-AAAT
*
45050361 TAATTAAAAAT
1 TAAATAAAAAT
45050372 TAAAT
1 TAAAT
45050377 TAAACAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAATAAAAAT
Found at i:45050377 original size:12 final size:12
Alignment explanation
Indices: 45050343--45050380 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
45050333 ACTAAATAAA
45050343 AAAAATTAAA-T
1 AAAAATTAAATT
45050354 AACAAATT-AATT
1 AA-AAATTAAATT
45050366 AAAAATTAAATT
1 AAAAATTAAATT
45050378 AAA
1 AAA
45050381 CAAAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:45050665 original size:20 final size:19
Alignment explanation
Indices: 45050621--45050666 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
45050611 AGAAAATTAC
*
45050621 CTTTCTCTCCTTCTTCTTT
1 CTTTCTCTCCTTCTTCCTT
*
45050640 CTTTTCTCTCTTTCTTTCCTT
1 C-TTTCTCTCCTTC-TTCCTT
45050661 CTTTCT
1 CTTTCT
45050667 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 16 0.70
21 6 0.26
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (19 bp):
CTTTCTCTCCTTCTTCCTT
Found at i:45050681 original size:25 final size:24
Alignment explanation
Indices: 45050631--45050698 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
45050621 CTTTCTCTCC
45050631 TTCTTCTTTCTTTTCTCTCTTTCT
1 TTCTTCTTTCTTTTCTCTCTTTCT
* *
45050655 TTCCTTCTTTCTTTT-TTTTTTTACT
1 TT-CTTCTTTCTTTTCTCTCTTT-CT
* *
45050680 TTCTTCTCTCTTCTCTCTC
1 TTCTTCTTTCTTTTCTCTC
45050699 CCGTTTGATC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 17 0.49
25 18 0.51
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.69
Consensus pattern (24 bp):
TTCTTCTTTCTTTTCTCTCTTTCT
Found at i:45052903 original size:20 final size:21
Alignment explanation
Indices: 45052875--45052913 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
45052865 TAGTGAATAC
45052875 ATATATAAATATAA-ATATAA
1 ATATATAAATATAAGATATAA
*
45052895 ATATTTAAATATAAGATAT
1 ATATATAAATATAAGATAT
45052914 GTATAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
ATATATAAATATAAGATATAA
Found at i:45056710 original size:195 final size:195
Alignment explanation
Indices: 45056414--45056816 Score: 547
Period size: 195 Copynumber: 2.1 Consensus size: 195
45056404 CTAATGTGGT
* * * * *
45056414 ACCTCAGCCATCGATACGGTATCTATATATTTGTTCCCTAACGATGTTGCTCACATAAGCTATTG
1 ACCTCAGCCATCGATACGATATCTATATATCTGTTCCCTAACGATGCTACTCACACAAGCTATTG
* *
45056479 AGAATATGCAACATATGCATAGATATCAGCCATCGTAAGGCCATGTAATCCAATCCAAGATTCAT
66 AGAATATGCAACATACGCATAAATATCAGCCATCGTAAGGCCATGTAATCCAATCCAAGATTCAT
* * * * *
45056544 TTCAACATTTTCCCAATTCACGATGCTGTTCACACAAGCTGTTGAGATTCCATAACATATGCAGG
131 TTCAACATTTTCCCAACTCACGATGCTGCTCACACAAGCTATTGAGAATCCACAACATATGCAGG
* * *
45056609 ACCTCAGCCATC-ATTACGATATCTATATATCTGTTTCCTAAGGATGCTACTCACACAAGCTTTT
1 ACCTCAGCCATCGA-TACGATATCTATATATCTGTTCCCTAACGATGCTACTCACACAAGCTATT
* * * * *
45056673 GAGAATATGCAACATACGCTTAAATCTCAGCCATCGTAAGGCCATGTAATCCAATCTAGGATTTA
65 GAGAATATGCAACATACGCATAAATATCAGCCATCGTAAGGCCATGTAATCCAATCCAAGATTCA
* * * * *
45056738 TTTCAACATTTTCTCGACTCACGATGCTGCTCACATAAGCTATTGAGAATCCGCAACATATGTAG
130 TTTCAACATTTTCCCAACTCACGATGCTGCTCACACAAGCTATTGAGAATCCACAACATATGCAG
45056803 G
195 G
* *
45056804 ATCTCAACCATCG
1 ACCTCAGCCATCG
45056817 CATCGATTTA
Statistics
Matches: 179, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
194 1 0.01
195 178 0.99
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (195 bp):
ACCTCAGCCATCGATACGATATCTATATATCTGTTCCCTAACGATGCTACTCACACAAGCTATTG
AGAATATGCAACATACGCATAAATATCAGCCATCGTAAGGCCATGTAATCCAATCCAAGATTCAT
TTCAACATTTTCCCAACTCACGATGCTGCTCACACAAGCTATTGAGAATCCACAACATATGCAGG
Found at i:45058158 original size:22 final size:22
Alignment explanation
Indices: 45058145--45058199 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
45058135 TATTTTAATC
45058145 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* * *
45058167 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
45058190 TTAAAATTTA
1 TT-AAATTTA
45058200 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:45058175 original size:6 final size:6
Alignment explanation
Indices: 45058128--45058200 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
45058118 CATTTGAAAA
* * *
45058128 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
45058173 TTAAAT TTGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
45058201 TATTATTATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 27 0.50
7 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:45058175 original size:17 final size:17
Alignment explanation
Indices: 45058148--45058194 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
45058138 TTTAATCTTA
*
45058148 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
45058164 AATTTAAATTTAAATTTG
1 AATTT-AATTTAAATTTC
45058182 AATTTAATTTAAA
1 AATTTAATTTAAA
45058195 ATTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 5 0.19
17 15 0.56
18 7 0.26
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:45058185 original size:12 final size:12
Alignment explanation
Indices: 45058128--45058200 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
45058118 CATTTGAAAA
45058128 TTAAATTT--AT
1 TTAAATTTAAAT
*
45058138 TTTAATCTTAAAT
1 TTAAAT-TTAAAT
*
45058151 TT-ACTTTAAA-
1 TTAAATTTAAAT
*
45058161 TTCAATTTAAAT
1 TTAAATTTAAAT
*
45058173 TTAAATTTGAAT
1 TTAAATTTAAAT
45058185 TT-AATTTAAAAT
1 TTAAATTT-AAAT
45058197 TTAA
1 TTAA
45058201 TATTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
11 19 0.38
12 19 0.38
13 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:45058201 original size:12 final size:11
Alignment explanation
Indices: 45058125--45058201 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
45058115 AACCATTTGA
*
45058125 AAATTAAATTT
1 AAATTTAATTT
*
45058136 -ATTTTAATCTT
1 AAATTTAAT-TT
*
45058147 AAATTTACTTT
1 AAATTTAATTT
*
45058158 AAATTCAATTT
1 AAATTTAATTT
45058169 AAATTTAAATTT
1 AAATTT-AATTT
*
45058181 GAATTTAATTT
1 AAATTTAATTT
45058192 AAAATTTAAT
1 -AAATTTAAT
45058202 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.43
12 24 0.45
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:45059847 original size:162 final size:162
Alignment explanation
Indices: 45059669--45059982 Score: 436
Period size: 162 Copynumber: 1.9 Consensus size: 162
45059659 CTTTTCAATT
*
45059669 TAGTCATTTGACTGTTTGACTGTACCATG-AGCTGCCACGTGTC-TCTTTTTGGATTATTTATGC
1 TAGTCATTTGACTGTTTGACTGCACCA-GAAGCTGCCACGTGTCAT-TTTTTGGATTATTTATGC
* * *
45059732 ATTTAGTCCTTTTTATTTTTTATTTATTTTAATTTAATCCCCAAATCAAC-TTTATTTTAATTAC
64 ATTTAGTCCTTTTTATTTTTAATTTATTTTAATTTAATCCCCAAATCAACTTTTA-TATAATTAA
* * *
45059796 GAAATTGGCCCAATAATTTTTCAAGGTTTATAAAC
128 AAAATAGGCCCAAAAATTTTTCAAGGTTTATAAAC
* * * *
45059831 TAGTCCTTTGACTGTTTGACTGCACCAGAAGTTGCCACGTGTCATTTTTTGGATTATTTCTTCAT
1 TAGTCATTTGACTGTTTGACTGCACCAGAAGCTGCCACGTGTCATTTTTTGGATTATTTATGCAT
* ** *
45059896 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATATAATTAAAAA
66 TTAGTCCTTTTTATTTTTAATTTATTTTAATTTAATCCCCAAATCAACTTTTATATAATTAAAAA
*
45059961 ATAGGTCCAAAAATTTTTCAAG
131 ATAGGCCCAAAAATTTTTCAAG
45059983 ACTTTCAAAT
Statistics
Matches: 133, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
161 1 0.01
162 127 0.95
163 5 0.04
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (162 bp):
TAGTCATTTGACTGTTTGACTGCACCAGAAGCTGCCACGTGTCATTTTTTGGATTATTTATGCAT
TTAGTCCTTTTTATTTTTAATTTATTTTAATTTAATCCCCAAATCAACTTTTATATAATTAAAAA
ATAGGCCCAAAAATTTTTCAAGGTTTATAAAC
Found at i:45060153 original size:31 final size:30
Alignment explanation
Indices: 45060060--45060233 Score: 251
Period size: 30 Copynumber: 5.7 Consensus size: 30
45060050 CCCTAAATTG
45060060 TCCAGAAATTATATTTTGACCCCAAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACTTT
*
45060091 TCCAAAATTATATTTTGACCCAAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* *
45060121 TCCAAAATTACATTTTGGCCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* *
45060151 TTCAAAATTATATTTTGACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
45060181 TCCAAAATTATATTTTTGACCCCAAAAC-TT
1 TCCAAAATTATA-TTTTGACCCCAAAACTTT
* *
45060211 TACAAAAGTTACATTTTGACCCC
1 TCCAAAA-TTATATTTTGACCCC
45060234 GATTTCACCA
Statistics
Matches: 129, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
30 107 0.83
31 22 0.17
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.36
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACTTT
Found at i:45060217 original size:90 final size:91
Alignment explanation
Indices: 45060065--45060233 Score: 279
Period size: 90 Copynumber: 1.9 Consensus size: 91
45060055 AATTGTCCAG
*
45060065 AAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCAAAAACTTTTCCAAAA-T
1 AAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCAAAAACTTTTACAAAAGT
*
45060129 TACATTTTGGCCCCAAAACTTTTTCA
66 TACATTTTGACCCCAAAACTTTTTCA
* *
45060155 AAATTATATTTTGACCCCGAAACTTTTCCAAAATTATATTTTTGACCCCAAAAC-TTTACAAAAG
1 AAATTATATTTTGACCCCAAAACTTTTCCAAAATTATA-TTTTGACCCAAAAACTTTTACAAAAG
45060219 TTACATTTTGACCCC
65 TTACATTTTGACCCC
45060234 GATTTCACCA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
90 45 0.62
91 28 0.38
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (91 bp):
AAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCAAAAACTTTTACAAAAGT
TACATTTTGACCCCAAAACTTTTTCA
Found at i:45060248 original size:60 final size:57
Alignment explanation
Indices: 45060065--45060461 Score: 224
Period size: 59 Copynumber: 6.7 Consensus size: 57
45060055 AATTGTCCAG
* * ** *
45060065 AAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCAAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTT-CAAAATTACATTTTGACCC--CGACTTTACCA
* * *
45060125 AAATTACATTTTGGCCCCAAAACTTTTTCAAAATTATATTTTGACCCCGAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAAC-TTTTCAAAATTACATTTTGACCCCG--ACTTTACCA
* *
45060185 AAATTATATTTTTGACCCCAAAACTTTACAAAAGTTACATTTTGACCCCGA-TTTCACCAA
1 AAATTACA-TTTTGACCCCAAAACTTTTCAAAA-TTACATTTTGACCCCGACTTT-ACC-A
* * * *
45060245 AAATTACCATTTT-ACCCCCAAAGCTTTT-AAAATTCCATTTTTAACCCCGA-TTTCACTGA
1 AAATTA-CATTTTGA-CCCCAAAACTTTTCAAAATTACA-TTTTGACCCCGACTTT-AC-CA
* * * * *
45060304 AAATTACCATTTT-ACCCCCGAATCTTTT-AAAATTCCATTTTTAACCCCGA-TTTCATCGA
1 AAATTA-CATTTTGA-CCCCAAAACTTTTCAAAATTACA-TTTTGACCCCGACTTT-A-CCA
* * * * * *
45060363 AAATTACCATTTT-ATCCTCGAAGCTTCT-AAAATTCCATTTTAACCCCGA-TTTCACCGA
1 AAATTA-CATTTTGA-CCCCAAAACTTTTCAAAATTACATTTTGACCCCGACTTT-ACC-A
* * *
45060421 AAATTACCATTTT-ACCCCCGAATCTTTT-AAAATTCCATTTT
1 AAATTA-CATTTTGA-CCCCAAAACTTTTCAAAATTACATTTT
45060462 TAATACCGAT
Statistics
Matches: 298, Mismatches: 26, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
57 1 0.00
58 62 0.21
59 114 0.38
60 87 0.29
61 34 0.11
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (57 bp):
AAATTACATTTTGACCCCAAAACTTTTCAAAATTACATTTTGACCCCGACTTTACCA
Found at i:45060262 original size:90 final size:89
Alignment explanation
Indices: 45060065--45060272 Score: 235
Period size: 90 Copynumber: 2.3 Consensus size: 89
45060055 AATTGTCCAG
* *
45060065 AAATTATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCAAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCAAAAACTTTTACAAAATT
* **
45060130 ACATTTTGGCCCCAAAACTTTTTCA
66 ACATTTTGACCCC-AAACTTTACCA
* * *
45060155 AAATTATATTTTGACCCCGAAACTTTTCCAAAATTATATTTTTGACCCCAAAAC-TTTACAAAAG
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTATA-TTTTGACCCAAAAACTTTTACAAAA-
*
45060219 TTACATTTTGACCCC-GA-TTTCACCAA
64 TTACATTTTGACCCCAAACTTT-ACC-A
*
45060245 AAATTACCATTTT-ACCCCCAAAGCTTTT
1 AAATTA-CATTTTGA-CCCCAAAACTTTT
45060273 AAAATTCCAT
Statistics
Matches: 102, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
88 3 0.03
89 2 0.02
90 53 0.52
91 44 0.43
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (89 bp):
AAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCAAAAACTTTTACAAAATT
ACATTTTGACCCCAAACTTTACCA
Found at i:45060430 original size:58 final size:59
Alignment explanation
Indices: 45060224--45060498 Score: 401
Period size: 59 Copynumber: 4.7 Consensus size: 59
45060214 AAAAGTTACA
* * *
45060224 TTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAAGCTTTTAAAATTCCAT
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCAT
* *
45060283 TTTTAACCCCGATTTCACTGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCAT
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCAT
* * * *
45060342 TTTTAACCCCGATTTCATCGAAAATTACCATTTTATCCTCGAAGCTTCTAAAATTCCA-
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCAT
*
45060400 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCAT
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCAT
** * * *
45060459 TTTTAATACCGATTACACC-AAAATTACTATTTTGCCCCCG
1 TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCG
45060499 GGTATCCATA
Statistics
Matches: 194, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
58 72 0.37
59 122 0.63
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (59 bp):
TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCAT
Found at i:45060440 original size:30 final size:30
Alignment explanation
Indices: 45060214--45060441 Score: 157
Period size: 30 Copynumber: 7.7 Consensus size: 30
45060204 AAAACTTTAC
* * *
45060214 AAAAGTTA-CATTTTGACCCCGATTTCACCA
1 AAAA-TTACCATTTTAACCCCGATTTCATCG
* *** * **
45060244 AAAATTACCATTTT-ACCCCCAAAGCTTTT
1 AAAATTACCATTTTAACCCCGATTTCATCG
45060273 AAAATT-CCATTTTTAACCCCGATTTCA-CTG
1 AAAATTACCA-TTTTAACCCCGATTTCATC-G
* * * **
45060303 AAAATTACCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCATCG
45060332 AAAATT-CCATTTTTAACCCCGATTTCATCG
1 AAAATTACCA-TTTTAACCCCGATTTCATCG
* * ** * *
45060362 AAAATTACCATTTTATCCTCGA-AGCTTCT
1 AAAATTACCATTTTAACCCCGATTTCATCG
*
45060391 AAAATT-CCATTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTAACCCCGATTTCATCG
*
45060420 AAAATTACCATTTTACCCCCGA
1 AAAATTACCATTTTAACCCCGA
45060442 ATCTTTTAAA
Statistics
Matches: 148, Mismatches: 39, Indels: 22
0.71 0.19 0.11
Matches are distributed among these distances:
28 19 0.13
29 56 0.38
30 67 0.45
31 6 0.04
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCATCG
Found at i:45060441 original size:117 final size:117
Alignment explanation
Indices: 45060224--45060497 Score: 406
Period size: 117 Copynumber: 2.3 Consensus size: 117
45060214 AAAAGTTACA
* *
45060224 TTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAAGCTTTTAAAATTCCATTTTTAA
1 TTTTAACCCCGATTTCA-CAAAAATTACCATTTTACCCCCAAAGCTTCTAAAATTCCATTTTTAA
*
45060289 CCCCGATTTCACTGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCAT
65 CCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCAT
* * * *
45060342 TTTTAACCCCGATTTCATCGAAAATTACCATTTTATCCTCGAAGCTTCTAAAATTCCA-TTTTAA
1 TTTTAACCCCGATTTCA-CAAAAATTACCATTTTACCCCCAAAGCTTCTAAAATTCCATTTTTAA
45060406 CCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCAT
65 CCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCAT
** * * * *
45060459 TTTTAATACCGATTACACCAAAATTACTATTTTGCCCCC
1 TTTTAACCCCGATTTCACAAAAATTACCATTTTACCCCC
45060498 GGGTATCCAT
Statistics
Matches: 140, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
116 17 0.12
117 72 0.51
118 51 0.36
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (117 bp):
TTTTAACCCCGATTTCACAAAAATTACCATTTTACCCCCAAAGCTTCTAAAATTCCATTTTTAAC
CCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCAT
Found at i:45060526 original size:117 final size:116
Alignment explanation
Indices: 45060244--45060529 Score: 333
Period size: 117 Copynumber: 2.4 Consensus size: 116
45060234 GATTTCACCA
* ** * *
45060244 AAAATTACCATTTTACCCCCAAAGCTTTTAAAATTCCATTTTTAACCCCGATTTCACTGAAAATT
1 AAAATTACCATTTTACCCCC-GAGCTTCCAAAA-TCCCTTTTTAACCCCGATTTCACCGAAAATT
* * *
45060309 ACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCATCG
64 ACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACACCGATTACATCC
* * * * *
45060362 AAAATTACCATTTTATCCTCGAAGCTTCTAAAATTCCATTTTAACCCCGATTTCACCGAAAATTA
1 AAAATTACCATTTTACCCCCG-AGCTTCCAAAATCCCTTTTTAACCCCGATTTCACCGAAAATTA
*
45060427 CCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAATACCGATTACA-CC
65 CCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACACCGATTACATCC
* * * * *
45060478 AAAATTACTATTTTGCCCCCG-GGTATCCATAAGTCCCGTTTTTCACCCCGAT
1 AAAATTACCATTTTACCCCCGAGCT-TCCA-AAATCCC-TTTTTAACCCCGAT
45060530 CTCATCATTT
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
114 2 0.01
115 3 0.02
116 23 0.16
117 86 0.61
118 28 0.20
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (116 bp):
AAAATTACCATTTTACCCCCGAGCTTCCAAAATCCCTTTTTAACCCCGATTTCACCGAAAATTAC
CATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACACCGATTACATCC
Found at i:45068608 original size:33 final size:33
Alignment explanation
Indices: 45068564--45068630 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
45068554 GGATGACAGT
*
45068564 TTTCAGCTGGACATATTTGGTTTTGATTTTGAG
1 TTTCAGCTGGACATATTTGGTTTCGATTTTGAG
*
45068597 TTTCAGTTGGACATATTTGGTTTCGATTTTGAG
1 TTTCAGCTGGACATATTTGGTTTCGATTTTGAG
45068630 T
1 T
45068631 AGGTGATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.49
Consensus pattern (33 bp):
TTTCAGCTGGACATATTTGGTTTCGATTTTGAG
Found at i:45070105 original size:44 final size:44
Alignment explanation
Indices: 45070012--45070107 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
45070002 TTGCCATTTT
* * ** *
45070012 GGCTTGCACCCGCTCGATCTTGCATTTAGACTGTCCGCTGCTTC
1 GGCTTGCACCCACTCGATCTTGCATTTAGACCGTCCGCCACCTC
* *
45070056 AGCTTGCACCCACTCGGGT-TTGCATTTAGACCGTCCGCCACCTC
1 GGCTTGCACCCACTC-GATCTTGCATTTAGACCGTCCGCCACCTC
45070100 GGCTTGCA
1 GGCTTGCA
45070108 ATTCTACAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 41 0.95
45 2 0.05
ACGTcount: A:0.14, C:0.35, G:0.23, T:0.28
Consensus pattern (44 bp):
GGCTTGCACCCACTCGATCTTGCATTTAGACCGTCCGCCACCTC
Found at i:45070185 original size:30 final size:30
Alignment explanation
Indices: 45070137--45070232 Score: 149
Period size: 30 Copynumber: 3.2 Consensus size: 30
45070127 TGACAAACTT
* *
45070137 GCACTTT-GCTTGCTGTCTTCAACAGGCTC
1 GCACTTTGGCTTACTGTCTTTAACAGGCTC
45070166 GCACTTTGGCTTACTGTCTTTAACAGGCTC
1 GCACTTTGGCTTACTGTCTTTAACAGGCTC
* *
45070196 GCACTTTGGCTTACTATCTTTGACAGGCTC
1 GCACTTTGGCTTACTGTCTTTAACAGGCTC
45070226 GCACTTT
1 GCACTTT
45070233 TGATGGCTCG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 7 0.11
30 55 0.89
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (30 bp):
GCACTTTGGCTTACTGTCTTTAACAGGCTC
Found at i:45070257 original size:16 final size:16
Alignment explanation
Indices: 45070238--45070296 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
45070228 ACTTTTGATG
45070238 GCTCGCACCTTGTTGA
1 GCTCGCACCTTGTTGA
* *
45070254 GCTCGCATTCTTTTTACTGA
1 GCTCGCA--CCTTGT--TGA
*
45070274 ACTCGCACCTTGTTGA
1 GCTCGCACCTTGTTGA
45070290 GCTCGCA
1 GCTCGCA
45070297 GCTCGCACAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 16 0.48
18 8 0.24
20 9 0.27
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (16 bp):
GCTCGCACCTTGTTGA
Found at i:45073647 original size:17 final size:17
Alignment explanation
Indices: 45073627--45073659 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45073617 TTTTCAAAAC
*
45073627 AAAACCCTTTTTTACTA
1 AAAACCCTATTTTACTA
45073644 AAAACCCTATTTTACT
1 AAAACCCTATTTTACT
45073660 GTTAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAACCCTATTTTACTA
Found at i:45078217 original size:12 final size:13
Alignment explanation
Indices: 45078200--45078232 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
45078190 AGAAATCCCA
45078200 TCTTCTTTTA-CT
1 TCTTCTTTTACCT
45078212 TCTTCTTTTACCT
1 TCTTCTTTTACCT
*
45078225 TTTTCTTT
1 TCTTCTTT
45078233 GCTGTCTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (13 bp):
TCTTCTTTTACCT
Found at i:45079404 original size:165 final size:165
Alignment explanation
Indices: 45079127--45079508 Score: 595
Period size: 165 Copynumber: 2.3 Consensus size: 165
45079117 AGAAAAGCAT
* *
45079127 GTCATGAATTAAGAAAATGAAAGAAGATTACCTTTAACGGGATGCTTGAAATTTTGAGATAGACC
1 GTCATGAATTAAGAAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTTGAGATAGACC
* * * *
45079192 TTGACTGGGAGGTCAAAAGAAATTAAAATCATTGAAGAAGAAATAAAATTATGAGCCAAATTTTA
66 TTGACTGGGAGATCAAAAGAAATTAAAAACAGTGAAGAAGAAATAAAATTATGAGCCAAATTGTA
*
45079257 AGCAATAGCATATAATAAAAAACAATCAATGAATA
131 AGCAATAGCAGATAATAAAAAACAATCAATGAATA
* * *
45079292 GTCATGAATTACGAAAATCAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTTGTGATAGACC
1 GTCATGAATTAAGAAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTTGAGATAGACC
*
45079357 TTGACTGGGAGATCAAAAGAAATTAAAAACAGTGAAGAAGCAATAAAATTATGAGCCAAATTGTA
66 TTGACTGGGAGATCAAAAGAAATTAAAAACAGTGAAGAAGAAATAAAATTATGAGCCAAATTGTA
* * *
45079422 AGCAATAGCAGATAATAAAAGACAATCATTGCATA
131 AGCAATAGCAGATAATAAAAAACAATCAATGAATA
* * * *
45079457 GTCATGAATTAAGCAAATGAAAGAAACTTACC-TTGACTGGATGCTTAAAATT
1 GTCATGAATTAAGAAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATT
45079509 ATGTCCCTGC
Statistics
Matches: 197, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
164 18 0.09
165 179 0.91
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (165 bp):
GTCATGAATTAAGAAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTTGAGATAGACC
TTGACTGGGAGATCAAAAGAAATTAAAAACAGTGAAGAAGAAATAAAATTATGAGCCAAATTGTA
AGCAATAGCAGATAATAAAAAACAATCAATGAATA
Found at i:45080156 original size:11 final size:11
Alignment explanation
Indices: 45080125--45080161 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
45080115 TCCACCTTTC
*
45080125 TTTTTCTTTAG
1 TTTTTCTTTTG
45080136 TTTTTCTTTTG
1 TTTTTCTTTTG
*
45080147 TTTTTCTTTTA
1 TTTTTCTTTTG
45080158 TTTT
1 TTTT
45080162 CTCAAGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.81
Consensus pattern (11 bp):
TTTTTCTTTTG
Found at i:45080691 original size:15 final size:15
Alignment explanation
Indices: 45080671--45080709 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
45080661 CTCATTAAGC
45080671 CCAAACCAAGGTGAA
1 CCAAACCAAGGTGAA
* **
45080686 CCAAACCCATTTGAA
1 CCAAACCAAGGTGAA
45080701 CCAAACCAA
1 CCAAACCAA
45080710 TTGAACTAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.33, G:0.10, T:0.10
Consensus pattern (15 bp):
CCAAACCAAGGTGAA
Found at i:45081839 original size:3 final size:3
Alignment explanation
Indices: 45081822--45081865 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
45081812 AAATTTAGAA
45081822 TAT T-T TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
45081866 TTGGATTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:45087889 original size:15 final size:15
Alignment explanation
Indices: 45087869--45087907 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
45087859 TCCATTAAGC
45087869 CCAAACCAAGGTGAA
1 CCAAACCAAGGTGAA
* **
45087884 CCAAACCCATTTGAA
1 CCAAACCAAGGTGAA
45087899 CCAAACCAA
1 CCAAACCAA
45087908 ATGAACTAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.33, G:0.10, T:0.10
Consensus pattern (15 bp):
CCAAACCAAGGTGAA
Found at i:45087964 original size:11 final size:11
Alignment explanation
Indices: 45087950--45088001 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
45087940 CGTTGATCGG
45087950 CTGTTGACCGA
1 CTGTTGACCGA
* *
45087961 CTGTTGATCGG
1 CTGTTGACCGA
45087972 CTGTTGACCGA
1 CTGTTGACCGA
* *
45087983 CCGTTGACCGG
1 CTGTTGACCGA
45087994 CTGTTGAC
1 CTGTTGAC
45088002 TGGTCGTTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.13, C:0.27, G:0.31, T:0.29
Consensus pattern (11 bp):
CTGTTGACCGA
Found at i:45087969 original size:22 final size:22
Alignment explanation
Indices: 45087938--45088001 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
45087928 ACCAAGTCAA
45087938 ACCGTTGATCGGCTGTTGACCG
1 ACCGTTGATCGGCTGTTGACCG
*
45087960 ACTGTTGATCGGCTGTTGACCG
1 ACCGTTGATCGGCTGTTGACCG
*
45087982 ACCGTTGACCGGCTGTTGAC
1 ACCGTTGATCGGCTGTTGAC
45088002 TGGTCGTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.14, C:0.27, G:0.31, T:0.28
Consensus pattern (22 bp):
ACCGTTGATCGGCTGTTGACCG
Found at i:45088009 original size:22 final size:21
Alignment explanation
Indices: 45087940--45088012 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
45087930 CAAGTCAAAC
* *
45087940 CGTTGATCGGCTGTTGACCGA
1 CGTTGACCGGCTGTTGACGGA
* *
45087961 CTGTTGATCGGCTGTTGACCGA
1 C-GTTGACCGGCTGTTGACGGA
*
45087983 CCGTTGACCGGCTGTTGACTGGT
1 -CGTTGACCGGCTGTTGAC-GGA
45088006 CGTTGAC
1 CGTTGAC
45088013 TTTGATCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
21 1 0.02
22 43 0.93
23 2 0.04
ACGTcount: A:0.12, C:0.25, G:0.33, T:0.30
Consensus pattern (21 bp):
CGTTGACCGGCTGTTGACGGA
Found at i:45089714 original size:19 final size:19
Alignment explanation
Indices: 45089686--45089723 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
45089676 TTTGCGAGGA
*
45089686 GTGCTTGCAAGCCTAATTC
1 GTGCTCGCAAGCCTAATTC
45089705 GTGCTCGCAAGCCTAATTC
1 GTGCTCGCAAGCCTAATTC
45089724 ACATGTCCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (19 bp):
GTGCTCGCAAGCCTAATTC
Found at i:45090086 original size:39 final size:38
Alignment explanation
Indices: 45090035--45090108 Score: 121
Period size: 39 Copynumber: 1.9 Consensus size: 38
45090025 TAAAAGCAGT
45090035 GAAGAAGAAAGAATGTTGTGGGTACAATAGCCAGAAGAA
1 GAAGAAGAAAGAATGTTGTGGGTACAA-AGCCAGAAGAA
* *
45090074 GAAGAAGAAAGAATGTTTTGGGTACAAAGGCAGAA
1 GAAGAAGAAAGAATGTTGTGGGTACAAAGCCAGAA
45090109 CTGTTAAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 7 0.21
39 26 0.79
ACGTcount: A:0.46, C:0.07, G:0.31, T:0.16
Consensus pattern (38 bp):
GAAGAAGAAAGAATGTTGTGGGTACAAAGCCAGAAGAA
Found at i:45090531 original size:14 final size:14
Alignment explanation
Indices: 45090512--45090538 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45090502 TTAGATTGAA
45090512 GTTGTGGTTTATTG
1 GTTGTGGTTTATTG
45090526 GTTGTGGTTTATT
1 GTTGTGGTTTATT
45090539 AGTCATTAAA
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:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (14 bp):
GTTGTGGTTTATTG
Found at i:45091233 original size:12 final size:12
Alignment explanation
Indices: 45091217--45091245 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
45091207 TCAAGATTTT
45091217 ATTTTTCTATA-
1 ATTTTTCTATAC
45091228 ATTTTTCTATAC
1 ATTTTTCTATAC
45091240 ATTTTT
1 ATTTTT
45091246 ATATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTTTCTATAC
Found at i:45093720 original size:9 final size:9
Alignment explanation
Indices: 45093706--45093733 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
45093696 AGTGCCTATA
45093706 ATGGTAAGT
1 ATGGTAAGT
45093715 ATGGTAAGT
1 ATGGTAAGT
45093724 ATGGTAAGT
1 ATGGTAAGT
45093733 A
1 A
45093734 CACTTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (9 bp):
ATGGTAAGT
Found at i:45103463 original size:14 final size:14
Alignment explanation
Indices: 45103444--45103471 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45103434 AAATTGCATC
45103444 AATTTTGGTCAATT
1 AATTTTGGTCAATT
45103458 AATTTTGGTCAATT
1 AATTTTGGTCAATT
45103472 TTAGCCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
AATTTTGGTCAATT
Found at i:45104202 original size:16 final size:16
Alignment explanation
Indices: 45104181--45104214 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45104171 TTAATTATTG
*
45104181 AATTAAAAGCTAGTAT
1 AATTAAAAACTAGTAT
*
45104197 AATTAAAAATTAGTAT
1 AATTAAAAACTAGTAT
45104213 AA
1 AA
45104215 GTGATTATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (16 bp):
AATTAAAAACTAGTAT
Found at i:45113090 original size:17 final size:16
Alignment explanation
Indices: 45113064--45113095 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
45113054 TTCAGGGAAA
45113064 ATGTCAAAATATTCAC
1 ATGTCAAAATATTCAC
45113080 ATGTCCAAAATATTCA
1 ATGT-CAAAATATTCA
45113096 TAATTGCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
ATGTCAAAATATTCAC
Found at i:45118687 original size:16 final size:15
Alignment explanation
Indices: 45118666--45118695 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
45118656 TTTTATATAA
45118666 AAAAATAAAATATTTT
1 AAAAAT-AAATATTTT
45118682 AAAAATAAATATTT
1 AAAAATAAATATTT
45118696 AGAAGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAATAAATATTTT
Found at i:45118901 original size:35 final size:34
Alignment explanation
Indices: 45118862--45118927 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
45118852 TCCATCTTTC
45118862 CTTTTATT-CCCACTTT-CTCCCTCCTTTTCTACCAT
1 CTTTT-TTACCCACTTTCCT-CCT-CTTTTCTACCAT
*
45118897 CTTTTTTATCCACTTTCCTCCTCTTTTCTAC
1 CTTTTTTACCCACTTTCCTCCTCTTTTCTAC
45118928 TTCTTCCGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 11 0.39
35 15 0.54
36 2 0.07
ACGTcount: A:0.11, C:0.38, G:0.00, T:0.52
Consensus pattern (34 bp):
CTTTTTTACCCACTTTCCTCCTCTTTTCTACCAT
Found at i:45120336 original size:78 final size:78
Alignment explanation
Indices: 45120235--45120392 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
45120225 ATCGAAAGAC
45120235 AAGGCAGATCTCTTAATTCCCAACAGCCACGAAGCAGCAATGTTGTGAGGTTCTTTAGTTCAGAG
1 AAGGCAGATCTCTTAATTCCCAACAGCCACGAAGCAGCAATGTTGTGAGGTTCTTTAGTTCAGAG
45120300 ATGGAATTTGGTA
66 ATGGAATTTGGTA
45120313 AAGGCAGATCTCTTAATTCCCAACAGCCACGAAGCAGCAATGTTGTGAGGTTCTTTAGTTCAGAG
1 AAGGCAGATCTCTTAATTCCCAACAGCCACGAAGCAGCAATGTTGTGAGGTTCTTTAGTTCAGAG
45120378 ATGGAATTTGGTA
66 ATGGAATTTGGTA
45120391 AA
1 AA
45120393 CTCTCGATCA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (78 bp):
AAGGCAGATCTCTTAATTCCCAACAGCCACGAAGCAGCAATGTTGTGAGGTTCTTTAGTTCAGAG
ATGGAATTTGGTA
Found at i:45122716 original size:15 final size:14
Alignment explanation
Indices: 45122696--45122726 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
45122686 TCCCATCTTC
45122696 TTTAACTTTTTTTCT
1 TTTAAC-TTTTTTCT
45122711 TTTAACTTTTTTCT
1 TTTAACTTTTTTCT
45122725 TT
1 TT
45122727 GCTGTCAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTAACTTTTTTCT
Found at i:45128312 original size:24 final size:24
Alignment explanation
Indices: 45128281--45128328 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
45128271 AGAAATAATT
* *
45128281 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
45128305 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
45128329 ACTAAGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:45130283 original size:24 final size:25
Alignment explanation
Indices: 45130240--45130290 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
45130230 GTTAAACTTG
*
45130240 TTTATTTGTTTCAATTAAACT-TTA
1 TTTATTTGTTTCAATCAAACTCTTA
* *
45130264 TTTATTTGTTTGAGTCAAACTCTTA
1 TTTATTTGTTTCAATCAAACTCTTA
45130289 TT
1 TT
45130291 AGTCTAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (25 bp):
TTTATTTGTTTCAATCAAACTCTTA
Found at i:45131861 original size:58 final size:58
Alignment explanation
Indices: 45131788--45131905 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 58
45131778 TTTCACATTA
45131788 AATTACTAATATATGTAAAATTTTCATTTTATTCAATTTAGTCCCTAAAATTGAGACT
1 AATTACTAATATATGTAAAATTTTCATTTTATTCAATTTAGTCCCTAAAATTGAGACT
* * *
45131846 AATTACTAATTTATGTGAATTTTTCATTTTATTCAATTTAGTCCCTAAAATTGAGACT
1 AATTACTAATATATGTAAAATTTTCATTTTATTCAATTTAGTCCCTAAAATTGAGACT
45131904 AA
1 AA
45131906 CGTACTTTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (58 bp):
AATTACTAATATATGTAAAATTTTCATTTTATTCAATTTAGTCCCTAAAATTGAGACT
Found at i:45131933 original size:58 final size:57
Alignment explanation
Indices: 45131812--45131933 Score: 129
Period size: 58 Copynumber: 2.1 Consensus size: 57
45131802 GTAAAATTTT
* * ** * *** *
45131812 CATTTTATTCAATTTAGTCCCTAAAATTGAGACTAATTACTAATTTATGTGAATTTTT
1 CATTTTATTCAATTTAGTCCCTAAAATTGAGACTAAGTACT-ATTCAAATAAAGCCTC
45131870 CATTTTATTCAATTTAGTCCCTAAAATTGAGACTAACGTACT-TTCAAATAAAGCCTC
1 CATTTTATTCAATTTAGTCCCTAAAATTGAGACTAA-GTACTATTCAAATAAAGCCTC
45131927 CAATTTT
1 C-ATTTT
45131934 TATACCGATT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
57 8 0.15
58 41 0.77
59 4 0.08
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (57 bp):
CATTTTATTCAATTTAGTCCCTAAAATTGAGACTAAGTACTATTCAAATAAAGCCTC
Found at i:45133360 original size:16 final size:16
Alignment explanation
Indices: 45133321--45133360 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
45133311 CGTTTGGTTC
45133321 GCTGTAATAGAATAGA
1 GCTGTAATAGAATAGA
* *
45133337 GCTATAATGGAATAGA
1 GCTGTAATAGAATAGA
*
45133353 GTTGTAAT
1 GCTGTAAT
45133361 CAATATTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:45140400 original size:11 final size:11
Alignment explanation
Indices: 45140384--45140409 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45140374 AGTAAGATGA
45140384 TTATTATTTGC
1 TTATTATTTGC
45140395 TTATTATTTGC
1 TTATTATTTGC
45140406 TTAT
1 TTAT
45140410 ATGTGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (11 bp):
TTATTATTTGC
Found at i:45153726 original size:22 final size:22
Alignment explanation
Indices: 45153701--45153742 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45153691 CGATGGTGGT
*
45153701 CGACGGTTGGTACGGCAGTGAA
1 CGACGGTAGGTACGGCAGTGAA
*
45153723 CGACGGTAGGTACGGTAGTG
1 CGACGGTAGGTACGGCAGTG
45153743 GTGTTCGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (22 bp):
CGACGGTAGGTACGGCAGTGAA
Found at i:45154186 original size:31 final size:31
Alignment explanation
Indices: 45154122--45154191 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
45154112 GGACGACGGC
*
45154122 TTGCTTGCGGCGGTGGGTGGTGAACGGCGGT
1 TTGCTTGCGGCGGTGGGTGGTGAACGGCAGT
* *
45154153 TTGCTTGTGGCGGTGGGTGGTGAACGGTAGT
1 TTGCTTGCGGCGGTGGGTGGTGAACGGCAGT
45154184 TTGGCTTG
1 TT-GCTTG
45154192 AGAAAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 30 0.86
32 5 0.14
ACGTcount: A:0.07, C:0.13, G:0.49, T:0.31
Consensus pattern (31 bp):
TTGCTTGCGGCGGTGGGTGGTGAACGGCAGT
Found at i:45157793 original size:20 final size:20
Alignment explanation
Indices: 45157768--45157805 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
45157758 CAGGTAGCGG
45157768 CTTGCAATGTCATCTTGTAA
1 CTTGCAATGTCATCTTGTAA
45157788 CTTGCAATGTCATCTTGT
1 CTTGCAATGTCATCTTGT
45157806 CTCCTTCTGT
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:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (20 bp):
CTTGCAATGTCATCTTGTAA
Found at i:45158841 original size:18 final size:18
Alignment explanation
Indices: 45158818--45158854 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
45158808 TTACAAAGCT
45158818 AGCTGATAATAAAAAAAC
1 AGCTGATAATAAAAAAAC
45158836 AGCTGATAATAAAAAAAC
1 AGCTGATAATAAAAAAAC
45158854 A
1 A
45158855 ATCATTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (18 bp):
AGCTGATAATAAAAAAAC
Found at i:45161852 original size:11 final size:11
Alignment explanation
Indices: 45161836--45161860 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
45161826 TTTTATTATT
45161836 TTATTTATTTA
1 TTATTTATTTA
45161847 TTATTTATTTA
1 TTATTTATTTA
45161858 TTA
1 TTA
45161861 AATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:45162254 original size:15 final size:16
Alignment explanation
Indices: 45162234--45162271 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
45162224 GTAATTTTTC
45162234 ATACAC-AAAAAAATT
1 ATACACAAAAAAAATT
45162249 ATACACAAAAAAAAATT
1 ATACAC-AAAAAAAATT
45162266 ATACAC
1 ATACAC
45162272 GGAGAGGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.29
17 15 0.71
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (16 bp):
ATACACAAAAAAAATT
Found at i:45174606 original size:50 final size:50
Alignment explanation
Indices: 45174541--45174849 Score: 343
Period size: 50 Copynumber: 6.2 Consensus size: 50
45174531 ATCTTTTACC
* * * *
45174541 CCTAAAGCTATAGAGGTGCAGATTGAAACCGCAAAGGCAAATCTCATACA
1 CCTAAAGCTATAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATACA
* ** *
45174591 CTTAAAGCTGCAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTATAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATACA
** * *
45174641 CCTAAAGCTGCAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATTCT
1 CCTAAAGCTATAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATACA
** * * *
45174691 CCTAAAGCTATAGAGATGCAGATTGAAACCGCTAA-AGCAAATCTCATACA
1 CCTAAAGCTATAGAGGGGCAGAATGAAGCCGC-AATGGCAAATCTCATACA
* *
45174741 CCTAAAGTTATAGAAGGGCAGAATGAAGCCGCAATGGCAAATCTCATACA
1 CCTAAAGCTATAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATACA
* * * * * * *
45174791 TCTAAAGCTATAGAGGGGTAGATTGAAGTCACAA-GGACAAATCTTATACT
1 CCTAAAGCTATAGAGGGGCAGAATGAAGCCGCAATGG-CAAATCTCATACA
*
45174841 CCTGAAGCT
1 CCTAAAGCT
45174850 GAAATGAAGT
Statistics
Matches: 219, Mismatches: 37, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
49 4 0.02
50 213 0.97
51 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTATAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATACA
Found at i:45174806 original size:150 final size:150
Alignment explanation
Indices: 45174541--45174849 Score: 433
Period size: 150 Copynumber: 2.1 Consensus size: 150
45174531 ATCTTTTACC
* * * *
45174541 CCTAAAGCTATAGAGGTGCAGATTGAAACCGCAAAGGCAAATCTCATACACTTAAAGCTGCAGAG
1 CCTAAAGCTATAGAGATGCAGATTGAAACCGCAAAGGCAAATCTCATACACCTAAAGCTACAGAA
* *
45174606 GGGCAGAATGAAGCCGCAATGGCAAATCTCATTCACCTAAAGCTGCAGAGGGGCAGAATGAAGCC
66 GGGCAGAATGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTACAGAGGGGCAGAATGAAGCC
* *
45174671 GCAATGG-CAAATCTCATTCT
131 ACAA-GGACAAATCTCATACT
* *
45174691 CCTAAAGCTATAGAGATGCAGATTGAAACCGCTAAA-GCAAATCTCATACACCTAAAGTTATAGA
1 CCTAAAGCTATAGAGATGCAGATTGAAACCGC-AAAGGCAAATCTCATACACCTAAAGCTACAGA
* * * * *
45174755 AGGGCAGAATGAAGCCGCAATGGCAAATCTCATACATCTAAAGCTATAGAGGGGTAGATTGAAGT
65 AGGGCAGAATGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTACAGAGGGGCAGAATGAAGC
*
45174820 CACAAGGACAAATCTTATACT
130 CACAAGGACAAATCTCATACT
*
45174841 CCTGAAGCT
1 CCTAAAGCT
45174850 GAAATGAAGT
Statistics
Matches: 140, Mismatches: 17, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
149 2 0.01
150 135 0.96
151 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (150 bp):
CCTAAAGCTATAGAGATGCAGATTGAAACCGCAAAGGCAAATCTCATACACCTAAAGCTACAGAA
GGGCAGAATGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTACAGAGGGGCAGAATGAAGCC
ACAAGGACAAATCTCATACT
Found at i:45174969 original size:80 final size:80
Alignment explanation
Indices: 45174872--45175126 Score: 413
Period size: 80 Copynumber: 3.2 Consensus size: 80
45174862 AGTAACAACC
*
45174872 TCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGGG
1 TCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGG
* *
45174937 CAAGATGGAAGACCG
66 CAAGATTGAAGACCA
* * *
45174952 TCCAATATTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAAAGGG
1 TCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGG
*
45175017 CAAGATTGAATACCA
66 CAAGATTGAAGACCA
* *
45175032 TCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAATCAGAGGG
1 TCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGG
*
45175097 C-AGATTGAAGACAA
66 CAAGATTGAAGACCA
45175111 TCCAATCTTTTACCCC
1 TCCAATCTTTTACCCC
45175127 TAAAGTTACA
Statistics
Matches: 160, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
79 26 0.16
80 134 0.84
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (80 bp):
TCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGG
CAAGATTGAAGACCA
Found at i:45175023 original size:40 final size:40
Alignment explanation
Indices: 45174872--45175125 Score: 261
Period size: 39 Copynumber: 6.4 Consensus size: 40
45174862 AGTAACAACC
**
45174872 TCCAATCTTTTACCCCGATCATG-GGGCAGATTGAAGA-AA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACAA
* * * **
45174911 TCTAATCTTTTACCCTAACCAGAGGGCAAGATGGAAGACCG
1 TCCAATCTTTTACCCTAATCAGAGGGC-AGATTGAAGACAA
* **
45174952 TCCAATATTTTACCCCGATCATG-GGGCAGATTGAAGA-AA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACAA
* * *
45174991 TCCAATCTTTTACCCTAA-CTAAAGGGCAAGATTGAATACCA
1 TCCAATCTTTTACCCTAATC-AGAGGGC-AGATTGAAGACAA
* **
45175032 TCCGATCTTTTACCCCGATCATG-GGGCAGATTGAAGA-AA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACAA
45175071 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
45175111 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
45175126 CTAAAGTTAC
Statistics
Matches: 173, Mismatches: 30, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
38 3 0.02
39 74 0.43
40 53 0.31
41 41 0.24
42 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
Found at i:45175242 original size:50 final size:50
Alignment explanation
Indices: 45175121--45175249 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
45175111 TCCAATCTTT
** *
45175121 TACCCCTAAAGTTACAGAGGAACAGATTGAAGCTACAAAAACAAATCTCA
1 TACCCCTAAAGTTACAGAGGGGCAGATTAAAGCTACAAAAACAAATCTCA
* * ** * *
45175171 TACCCCTAAAGTTACAAAGGGGCAGATTAAAGCTACAAGAGTAAATTTTA
1 TACCCCTAAAGTTACAGAGGGGCAGATTAAAGCTACAAAAACAAATCTCA
* *
45175221 TACCCCTAAAGTAATAGAGGGGCAGATTA
1 TACCCCTAAAGTTACAGAGGGGCAGATTA
45175250 TCAATCTTCA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.21
Consensus pattern (50 bp):
TACCCCTAAAGTTACAGAGGGGCAGATTAAAGCTACAAAAACAAATCTCA
Found at i:45180128 original size:44 final size:42
Alignment explanation
Indices: 45180077--45180166 Score: 144
Period size: 44 Copynumber: 2.1 Consensus size: 42
45180067 GCTGCCTCAT
*
45180077 TTTTCTGTTGTTCAGCTTCTTTCTTTTTTGCTTCTTCTTTGGCC
1 TTTTCTGTTGTTCAGCTTCTTTCTTTTTTGCTTCCTC-TT-GCC
*
45180121 TTTTCTGTTGTTCAGCTTCTTTTTTTTTTGCTTCCTCTTGCC
1 TTTTCTGTTGTTCAGCTTCTTTCTTTTTTGCTTCCTCTTGCC
45180163 TTTT
1 TTTT
45180167 TATCTCTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 7 0.16
43 2 0.05
44 35 0.80
ACGTcount: A:0.02, C:0.22, G:0.12, T:0.63
Consensus pattern (42 bp):
TTTTCTGTTGTTCAGCTTCTTTCTTTTTTGCTTCCTCTTGCC
Found at i:45187725 original size:21 final size:21
Alignment explanation
Indices: 45187701--45187791 Score: 59
Period size: 21 Copynumber: 4.5 Consensus size: 21
45187691 AAAAAGTTGC
45187701 AGCAAAAAAGGCAAAAGAAGA
1 AGCAAAAAAGGCAAAAGAAGA
* **
45187722 AGC-AAAAA-GAAAGAAGTTGA
1 AGCAAAAAAGGCAA-AAGAAGA
* *
45187742 A-CAACAGAAA---AAAAGAGGT
1 AGCAA-A-AAAGGCAAAAGAAGA
45187761 AGCAAAAAAGGCAAAAGAAGA
1 AGCAAAAAAGGCAAAAGAAGA
*
45187782 AGCAATAAAG
1 AGCAAAAAAG
45187792 AAAGAAAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
18 3 0.06
19 10 0.19
20 17 0.32
21 20 0.38
22 3 0.06
ACGTcount: A:0.64, C:0.09, G:0.23, T:0.04
Consensus pattern (21 bp):
AGCAAAAAAGGCAAAAGAAGA
Found at i:45187767 original size:60 final size:60
Alignment explanation
Indices: 45187684--45187797 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
45187674 AGCTGCTGAG
**
45187684 CAACAGAAAAAAGTTGCAGCAAAAAAGGCAAAAGAAGAAGCAA-AAAGAAAGAAGTTGAA
1 CAACAGAAAAAAGAGGCAGCAAAAAAGGCAAAAGAAGAAGCAATAAAGAAAGAAGTTGAA
*
45187743 CAACAGAAAAAAAGAGGTAGCAAAAAAGGCAAAAGAAGAAGCAATAAAGAAAGAA
1 CAACAG-AAAAAAGAGGCAGCAAAAAAGGCAAAAGAAGAAGCAATAAAGAAAGAA
45187798 AAAAGCCTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 6 0.12
60 34 0.68
61 10 0.20
ACGTcount: A:0.63, C:0.10, G:0.22, T:0.05
Consensus pattern (60 bp):
CAACAGAAAAAAGAGGCAGCAAAAAAGGCAAAAGAAGAAGCAATAAAGAAAGAAGTTGAA
Found at i:45194792 original size:14 final size:14
Alignment explanation
Indices: 45194773--45194799 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45194763 GGCTAATTAC
45194773 AATTTTTTGTTAGT
1 AATTTTTTGTTAGT
45194787 AATTTTTTGTTAG
1 AATTTTTTGTTAG
45194800 ATTCATGTTA
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:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (14 bp):
AATTTTTTGTTAGT
Found at i:45197390 original size:17 final size:17
Alignment explanation
Indices: 45197368--45197400 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
45197358 ATACATAGTA
45197368 AACAGTAAAGATTCTTC
1 AACAGTAAAGATTCTTC
45197385 AACAGTAAAGATTCTT
1 AACAGTAAAGATTCTT
45197401 TACTTTAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (17 bp):
AACAGTAAAGATTCTTC
Found at i:45209575 original size:29 final size:29
Alignment explanation
Indices: 45209405--45209619 Score: 122
Period size: 30 Copynumber: 7.3 Consensus size: 29
45209395 TAGAAATTAT
* * *
45209405 ATTTTAACCCCCAAACTTCTCTAAAATTA-T
1 ATTTT-ACCCTCAAACTTC-CAAAAATTACC
* *
45209435 ATTTTTGACCCTAAAACTTTCAAAAATTA-C
1 A-TTTT-ACCCTCAAACTTCCAAAAATTACC
* *
45209465 ATTCTTACACTCAAACTCCCAAAAATT-CC
1 ATT-TTACCCTCAAACTTCCAAAAATTACC
* * *
45209494 ATTTTTGACCTTAAAACTTCCAAAAATTA-T
1 A-TTTT-ACCCTCAAACTTCCAAAAATTACC
* * *
45209524 A-TTTACCCCTAAAAGTT-CTAAAATTACC
1 ATTTTA-CCCTCAAACTTCCAAAAATTACC
* *
45209552 ATTTTACCCTCGAACTTCCAAAAACT-CC
1 ATTTTACCCTCAAACTTCCAAAAATTACC
* *
45209580 ATTTTTAACCC-CGAAACTTTCAAAAAATACC
1 A-TTTT-ACCCTC-AAACTTCCAAAAATTACC
45209611 ATTTTACCC
1 ATTTTACCC
45209620 CCGGATGTCC
Statistics
Matches: 144, Mismatches: 27, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
27 9 0.06
28 24 0.17
29 42 0.29
30 52 0.36
31 17 0.12
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (29 bp):
ATTTTACCCTCAAACTTCCAAAAATTACC
Done.