Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
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 67 of 135
Found at i:22368129 original size:112 final size:115
Alignment explanation
Indices: 22367923--22368183 Score: 377
Period size: 112 Copynumber: 2.3 Consensus size: 115
22367913 TTTTTGTCAA
* * *
22367923 AAAAAAATTCAAATTTTTTTGGTGTTGGCTATCAAATGGCCGACACACCGTTTTCTCGAAAAAAA
1 AAAAAAATTCAAA-TTTTTTGGTGTTGGCCATCAAATGGCCGACACACCCTATTCTC-AAAAAAA
22367988 ATTACATTTTTGGGTGTTAGCCATTGCATGGCCGACACCCCCTTTTCTCGAG
64 ATTACATTTTTGGGTGTTAGCCATTGCATGGCCGACACCCCCTTTTCTCGAG
* * *
22368040 AAAAAAATTCAAACTTTTT-GTGTTGGCCATCAAATGGTCGACACCCCCTATT-T-AAAAAAAAT
1 AAAAAAATTCAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACACCCTATTCTCAAAAAAAAT
* **
22368102 TACATTTTTGGGTGTTGGTTATTGCATGGCCGACACCCCCTTTTCTCGAG
66 TACATTTTTGGGTGTTAGCCATTGCATGGCCGACACCCCCTTTTCTCGAG
*
22368152 -AAAAAATTCAAAATTTTTTGGTGTTAGCCATC
1 AAAAAAATTC-AAATTTTTTGGTGTTGGCCATC
22368184 CCCTTTTCTC
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
111 9 0.07
112 64 0.49
113 11 0.08
114 1 0.01
115 28 0.21
116 5 0.04
117 13 0.10
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (115 bp):
AAAAAAATTCAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACACCCTATTCTCAAAAAAAAT
TACATTTTTGGGTGTTAGCCATTGCATGGCCGACACCCCCTTTTCTCGAG
Found at i:22368223 original size:48 final size:45
Alignment explanation
Indices: 22368138--22368230 Score: 132
Period size: 48 Copynumber: 2.0 Consensus size: 45
22368128 TGGCCGACAC
*
22368138 CCCCTTTTCTCGAGAAAAAATTCAAAATTTTTTGGTGTTAGCCAT
1 CCCCTTTTCTCGAAAAAAAATTCAAAATTTTTTGGTGTTAGCCAT
* *
22368183 CCCCTTTTCTCGGATAAAAAAATTACAAATTTTTTTGGTGTTGGCCAT
1 CCCCTTTTCTC-GA-AAAAAAATT-CAAAATTTTTTGGTGTTAGCCAT
22368231 GTAATGGTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 11 0.26
46 2 0.05
47 8 0.19
48 21 0.50
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (45 bp):
CCCCTTTTCTCGAAAAAAAATTCAAAATTTTTTGGTGTTAGCCAT
Found at i:22369081 original size:17 final size:16
Alignment explanation
Indices: 22369061--22369115 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
22369051 AAAAAATAAT
22369061 AATTAGAATATACAGGA
1 AATTAGAATATACA-GA
*
22369078 AATTAGAA-AGA-A-A
1 AATTAGAATATACAGA
*
22369091 AATTAAAATATACAAGA
1 AATTAGAATATAC-AGA
22369108 AATTAGAA
1 AATTAGAA
22369116 ATCAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
15 1 0.03
16 3 0.10
17 16 0.53
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.22
Consensus pattern (16 bp):
AATTAGAATATACAGA
Found at i:22369127 original size:30 final size:30
Alignment explanation
Indices: 22369054--22369158 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
22369044 AATTTTAAAA
* *
22369054 AAATAATAA-TTAGAATATACAGGAAATTAG
1 AAATAA-AATTTAAAATATACAAGAAATTAG
* *
22369084 AAAGAAAAATTAAAATATACAAGAAATTAG
1 AAATAAAATTTAAAATATACAAGAAATTAG
* * *
22369114 AAATCAAATTTAAAATA-AAAACGAAATTAC
1 AAATAAAATTTAAAATATACAA-GAAATTAG
*
22369144 AAATTAAATTTAAAA
1 AAATAAAATTTAAAA
22369159 AGTAAACGGA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
29 5 0.08
30 59 0.92
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.25
Consensus pattern (30 bp):
AAATAAAATTTAAAATATACAAGAAATTAG
Found at i:22370501 original size:20 final size:21
Alignment explanation
Indices: 22370464--22370507 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
22370454 ATGCCATCTG
22370464 AAAAATTGAAAAATAATTAGAA
1 AAAAATTGAAAAATAATTA-AA
*
22370486 AAAAATT-AATAA-AATTAAA
1 AAAAATTGAAAAATAATTAAA
22370505 AAA
1 AAA
22370508 TATATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 5 0.24
21 4 0.19
22 7 0.33
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAAATTGAAAAATAATTAAA
Found at i:22370507 original size:17 final size:17
Alignment explanation
Indices: 22370485--22370517 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22370475 AATAATTAGA
22370485 AAAAAAT-TAATAAAATT
1 AAAAAATAT-ATAAAATT
22370502 AAAAAATATATAAAAT
1 AAAAAATATATAAAAT
22370518 CAAGACATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAAATATATAAAATT
Found at i:22371441 original size:22 final size:22
Alignment explanation
Indices: 22371393--22371452 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
22371383 CGGGACGTTG
*
22371393 GTGAGCTGGAAT-TTCGGTTTTA
1 GTGAGCTGGAATATT-GGTTTAA
*
22371415 CTGAGCTGGAATATTGGTTTAA
1 GTGAGCTGGAATATTGGTTTAA
*
22371437 GTGAGGTGGAA-ATTGG
1 GTGAGCTGGAATATTGG
22371453 GTGGTCCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 5 0.15
22 26 0.79
23 2 0.06
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (22 bp):
GTGAGCTGGAATATTGGTTTAA
Found at i:22371694 original size:89 final size:89
Alignment explanation
Indices: 22371543--22371880 Score: 550
Period size: 89 Copynumber: 3.9 Consensus size: 89
22371533 TAAATTTAAA
* *
22371543 ATATGATAAAACTTGTAATATAATAATAATAATAATTTTTATTTAAAGATAAAAAATTAATAAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
*
22371608 AATGTATTATCAAATCAATACATT
66 AATGTATTGTCAAATCAATACATT
22371632 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
* *
22371697 AATGAATTGTCAAATCAATGCATT
66 AATGTATTGTCAAATCAATACATT
*
22371721 ATATGATAAAAA---T--TATAAT-ATAATAATAAGTTTTATTTAAAGATATAAAATTAATAAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
*
22371780 AATGTATTGTCAAATCAACACATT
66 AATGTATTGTCAAATCAATACATT
22371804 ATATGATAAAAATTGTAATATAATAATAATAAT-A--TTTATTTAAAGATATAAAATTAATAAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
22371866 AATGTATTGTCAAAT
66 AATGTATTGTCAAAT
22371881 TAAAACATGT
Statistics
Matches: 234, Mismatches: 9, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
83 72 0.31
84 6 0.03
86 45 0.19
88 7 0.03
89 104 0.44
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (89 bp):
ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
AATGTATTGTCAAATCAATACATT
Found at i:22371835 original size:172 final size:170
Alignment explanation
Indices: 22371561--22371880 Score: 561
Period size: 172 Copynumber: 1.9 Consensus size: 170
22371551 AAACTTGTAA
*
22371561 TATAATAATAATAATAATTTTTATTTAAAGATAAAAAATTAATAAATAATGTATTATCAAATCAA
1 TATAATAATAATAATAAGTTTTATTTAAAGATAAAAAATTAATAAATAATGTATTATCAAATCAA
*
22371626 TACATTATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTA
66 CACATTATATGATAAAAATTGTAATATAATAATAATAAT-A--TTTATTTAAAGATATAAAATTA
22371691 ATAAATAATGAATTGTCAAATCAATGCATTATATGATAAAAAT
128 ATAAATAATGAATTGTCAAATCAATGCATTATATGATAAAAAT
* *
22371734 TATAAT-ATAATAATAAGTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAA
1 TATAATAATAATAATAAGTTTTATTTAAAGATAAAAAATTAATAAATAATGTATTATCAAATCAA
22371798 CACATTATATGATAAAAATTGTAATATAATAATAATAATATTTATTTAAAGATATAAAATTAATA
66 CACATTATATGATAAAAATTGTAATATAATAATAATAATATTTATTTAAAGATATAAAATTAATA
*
22371863 AATAATGTATTGTCAAAT
131 AATAATGAATTGTCAAAT
22371881 TAAAACATGT
Statistics
Matches: 142, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
169 42 0.30
171 1 0.01
172 93 0.65
173 6 0.04
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (170 bp):
TATAATAATAATAATAAGTTTTATTTAAAGATAAAAAATTAATAAATAATGTATTATCAAATCAA
CACATTATATGATAAAAATTGTAATATAATAATAATAATATTTATTTAAAGATATAAAATTAATA
AATAATGAATTGTCAAATCAATGCATTATATGATAAAAAT
Found at i:22371909 original size:12 final size:12
Alignment explanation
Indices: 22371892--22371939 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
22371882 AAAACATGTT
22371892 ATTAATTTCCAA
1 ATTAATTTCCAA
22371904 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
22371920 ATTAATTTTCAA
1 ATTAATTTCCAA
22371932 ATTAATTT
1 ATTAATTT
22371940 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:22371938 original size:16 final size:16
Alignment explanation
Indices: 22371902--22371936 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
22371892 ATTAATTTCC
*
22371902 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
22371918 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
22371935 AA
1 AA
22371937 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:22371949 original size:28 final size:28
Alignment explanation
Indices: 22371892--22371949 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
22371882 AAAACATGTT
**
22371892 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
22371920 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
22371948 AT
1 AT
22371950 ATTCTTCGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:22375942 original size:96 final size:96
Alignment explanation
Indices: 22375769--22376074 Score: 265
Period size: 114 Copynumber: 3.0 Consensus size: 96
22375759 CAGCCATTTG
* * * * *
22375769 ATGGCCAATACCAAAAAATTTTGAATTTTTTTCTCGAGAAAAGGGGGTGTCAACCATGCAATGGT
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAGGGGTGTCAACCATGCAATGGC
* *
22375834 CAGCACCCAAAAATGCAA-ATTTTTTAAATA
66 CAACACCAAAAAATGCAATATTTTTTAAATA
* * **
22375864 ATGGCCGACACCAAAAAAATTTAAATTTTTTTTCTTGAGAAAAAGGGGTGTCGGCCATGCAATGG
1 ATGGCCAACACCAAAAAAATTTAAA-TTTTTTTCTCGAGAAAAAGGGGTGTCAACCATGCAATGG
*
22375929 CCAACACCAAAAAATGCAATTTTTTTTAAATTGGGGGTGTCGGCCA
65 CCAACACCAAAAAATGCAATATTTTTTAAA---------T-----A
* **
22375975 TTTGATGGCCAACA-CAAAAAAATTTTGAATTTTTTTCTCGAGAAAAAGGGGTGTCGGCCATGCA
1 ----ATGGCCAACACCAAAAAAA-TTTAAATTTTTTTCTCGAGAAAAAGGGGTGTCAACCATGCA
* *
22376039 ATGGCCAACACCCAAAAATGCAATTTTTTTTAAATA
61 ATGGCCAACACCAAAAAATGCAATATTTTTTAAATA
22376075 GGGAGTGTCG
Statistics
Matches: 174, Mismatches: 16, Indels: 37
0.77 0.07 0.16
Matches are distributed among these distances:
95 21 0.12
96 51 0.29
97 9 0.05
100 1 0.01
105 1 0.01
106 1 0.01
111 1 0.01
114 75 0.43
115 14 0.08
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (96 bp):
ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAAGGGGTGTCAACCATGCAATGGC
CAACACCAAAAAATGCAATATTTTTTAAATA
Found at i:22375983 original size:54 final size:54
Alignment explanation
Indices: 22375908--22376110 Score: 219
Period size: 54 Copynumber: 3.6 Consensus size: 54
22375898 TTGAGAAAAA
*
22375908 GGGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGCAATTTTTTTTAAATTG
1 GGGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGCAATTTTTTTTAAATAG
*** * * *
22375962 GGGGTGTCGGCCATTTGATGGCCAACACAAAAAAATTTTG-AATTTTTTTCTCGAGAAAAA
1 GGGGTGTCGGCCATGCAATGGCCAACACCAAAAAA---TGCAATTTTTTT-T--A-AATAG
*
22376022 GGGGTGTCGGCCATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTAAATAG
1 GGGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGCAATTTTTTTTAAATAG
* *** *
22376076 GGAGTGTCGGCCATTTGATGGCCAACACTAAAAAA
1 GGGGTGTCGGCCATGCAATGGCCAACACCAAAAAA
22376111 ATTTGAATTT
Statistics
Matches: 121, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
54 63 0.52
55 1 0.01
56 9 0.07
57 6 0.05
58 9 0.07
59 1 0.01
60 32 0.26
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (54 bp):
GGGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGCAATTTTTTTTAAATAG
Found at i:22376018 original size:114 final size:113
Alignment explanation
Indices: 22375864--22376123 Score: 430
Period size: 114 Copynumber: 2.3 Consensus size: 113
22375854 TTTTTAAATA
* * *
22375864 ATGGCCGACACCAAAAAAATTTAAATTTTTTTTCTTGAGAAAAAGGGGTGTCGGCCATGCAATGG
1 ATGGCCAACA-CAAAAAAATTTGAA-TTTTTTTCTCGAGAAAAAGGGGTGTCGGCCATGCAATGG
* *
22375929 CCAACACCAAAAAATGCAATTTTTTTTAAATTGGGGGTGTCGGCCATTTG
64 CCAACACCAAAAAATGCAATTTTTTTTAAATAGGGAGTGTCGGCCATTTG
22375979 ATGGCCAACACAAAAAAATTTTGAATTTTTTTCTCGAGAAAAAGGGGTGTCGGCCATGCAATGGC
1 ATGGCCAACACAAAAAAA-TTTGAATTTTTTTCTCGAGAAAAAGGGGTGTCGGCCATGCAATGGC
*
22376044 CAACACCCAAAAATGCAATTTTTTTTAAATAGGGAGTGTCGGCCATTTG
65 CAACACCAAAAAATGCAATTTTTTTTAAATAGGGAGTGTCGGCCATTTG
22376093 ATGGCCAACACTAAAAAAATTTGAATTTTTT
1 ATGGCCAACAC-AAAAAAATTTGAATTTTTT
22376124 CCTCAAACTA
Statistics
Matches: 137, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
114 116 0.85
115 21 0.15
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (113 bp):
ATGGCCAACACAAAAAAATTTGAATTTTTTTCTCGAGAAAAAGGGGTGTCGGCCATGCAATGGCC
AACACCAAAAAATGCAATTTTTTTTAAATAGGGAGTGTCGGCCATTTG
Found at i:22376162 original size:96 final size:97
Alignment explanation
Indices: 22376046--22376221 Score: 266
Period size: 99 Copynumber: 1.8 Consensus size: 97
22376036 GCAATGGCCA
* * *
22376046 ACACCCAAAAATGCAATTTTTTTT-A-AATAGGGAGTGTCGGCCATTTGATGGCCAACACTAAAA
1 ACACCCAAAAATGCAATTTTTTTTAAGAAAAGGGAGTATCGGCCATTTGATGGCCAACACCAAAA
22376109 AAATTTGAATTTTTTCCTCAAACTACATAGCCG
66 AAA-TTGAATTTTTTCCTCAAACTACATAGCCG
* * *
22376142 ACACGCAAAAATGCAATTTTTTTTAAAGAAAAGGGGGTATCGGCCATTTGATGGTCAACACCAAA
1 ACACCCAAAAATGCAATTTTTTTT-AAGAAAAGGGAGTATCGGCCATTTGATGGCCAACACCAAA
22376207 AAAATTGAATTTTTT
65 AAAATTGAATTTTTT
22376222 TCTGACAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
96 23 0.32
98 12 0.17
99 36 0.51
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (97 bp):
ACACCCAAAAATGCAATTTTTTTTAAGAAAAGGGAGTATCGGCCATTTGATGGCCAACACCAAAA
AAATTGAATTTTTTCCTCAAACTACATAGCCG
Found at i:22377371 original size:27 final size:27
Alignment explanation
Indices: 22377337--22377398 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
22377327 GTTAGAGAGA
* *
22377337 AAAAAAAT-CAAGGAATGAATTTTTTTT
1 AAAAAAATGAAAGAAATGAA-TTTTTTT
* *
22377364 AAACAAATGAAAGAAATGGATTTTTTT
1 AAAAAAATGAAAGAAATGAATTTTTTT
22377391 AAAAAAAT
1 AAAAAAAT
22377399 TTGACTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.32
Consensus pattern (27 bp):
AAAAAAATGAAAGAAATGAATTTTTTT
Found at i:22377893 original size:10 final size:10
Alignment explanation
Indices: 22377860--22377907 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
22377850 TCCCTGTTTG
22377860 TTTTAATATGT
1 TTTTAATAT-T
22377871 TTTTAATATT
1 TTTTAATATT
*
22377881 TTTTAA-ATC
1 TTTTAATATT
22377890 TTTT-AT-TT
1 TTTTAATATT
22377898 TTTTAA-ATT
1 TTTTAATATT
22377907 T
1 T
22377908 GATCATTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
8 6 0.19
9 10 0.31
10 7 0.22
11 9 0.28
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTAATATT
Found at i:22377976 original size:25 final size:24
Alignment explanation
Indices: 22377948--22377995 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
22377938 ATCCTTTCAT
22377948 TTTATTTTA-TATGTATATATATTTA
1 TTTATTTTAGTAT-TAT-TATATTTA
22377973 TTTATTTTAGTATTATTATATTT
1 TTTATTTTAGTATTATTATATTT
22377996 TGTTTTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 12 0.55
26 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTATTTTAGTATTATTATATTTA
Found at i:22377994 original size:20 final size:21
Alignment explanation
Indices: 22377967--22378022 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
22377957 TATGTATATA
22377967 TATT-TATTTATTTTA-GTAT-
1 TATTATATTTATTTTATGT-TC
*
22377986 TATTATATTTTGTTTTATGTTC
1 TATTATA-TTTATTTTATGTTC
22378008 TATTAT-TTTATTTTA
1 TATTATATTTATTTTA
22378023 ATGCGTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 4 0.13
20 10 0.32
21 9 0.29
22 8 0.26
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
TATTATATTTATTTTATGTTC
Found at i:22381178 original size:41 final size:41
Alignment explanation
Indices: 22381131--22381243 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 41
22381121 GAAGACTTGT
*
22381131 GACTCGAAACGAGCGTGAGGATATATTTAAGGAAGACTCAG
1 GACTCGAAATGAGCGTGAGGATATATTTAAGGAAGACTCAG
* ** * * *
22381172 GTCTCGAAATGAGAATGAGAATATGATTAAAGGAAGACTCAT
1 GACTCGAAATGAGCGTGAGGATAT-ATTTAAGGAAGACTCAG
* *
22381214 GACTTGAAATGAGCGTG-GGATTATGTTTAA
1 GACTCGAAATGAGCGTGAGGA-TATATTTAA
22381244 AAAGGAAGAC
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 25 0.45
42 31 0.55
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (41 bp):
GACTCGAAATGAGCGTGAGGATATATTTAAGGAAGACTCAG
Found at i:22381244 original size:42 final size:41
Alignment explanation
Indices: 22381120--22381264 Score: 130
Period size: 41 Copynumber: 3.4 Consensus size: 41
22381110 TCATATGAAT
** * *
22381120 GGAAGACTTGTGACTCGAAACGAGCGTGAGGATATATTT-AA
1 GGAAGACTCATGACTCGAAATGAGCGTG-GGATATGTTTAAA
* * ** * *
22381161 GGAAGACTCAGGTCTCGAAATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGACTCGAAATGAGCGTG-GGATATGTTTAAA
*
22381203 GGAAGACTCATGACTTGAAATGAGCGTGGGATTATGTTTAAAAA
1 GGAAGACTCATGACTCGAAATGAGCGTGGGA-TATGTTT--AAA
*
22381247 GGAAGACTAATGACTCGA
1 GGAAGACTCATGACTCGA
22381265 TAGAGCATAA
Statistics
Matches: 81, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
41 31 0.38
42 31 0.38
44 19 0.23
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (41 bp):
GGAAGACTCATGACTCGAAATGAGCGTGGGATATGTTTAAA
Found at i:22386368 original size:19 final size:19
Alignment explanation
Indices: 22386344--22386423 Score: 90
Period size: 19 Copynumber: 4.2 Consensus size: 19
22386334 AAGGAATCAA
22386344 CAATACTGGCTAGTAAGAG
1 CAATACTGGCTAGTAAGAG
* *
22386363 CAATACTGACTCGTAAGAG
1 CAATACTGGCTAGTAAGAG
* *
22386382 TAATACTGGCTCGTAAGAG
1 CAATACTGGCTAGTAAGAG
* *
22386401 CGATATTGGCTCA-TAAGAG
1 CAATACTGGCT-AGTAAGAG
22386420 CAAT
1 CAAT
22386424 TTACTAGCTG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (19 bp):
CAATACTGGCTAGTAAGAG
Found at i:22386398 original size:38 final size:38
Alignment explanation
Indices: 22386345--22386419 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
22386335 AGGAATCAAC
*
22386345 AATACTGGCTAGTAAGAGCAATACTGACTCGTAAGAGT
1 AATACTGGCTAGTAAGAGCAATACTGACTCATAAGAGT
* * * *
22386383 AATACTGGCTCGTAAGAGCGATATTGGCTCATAAGAG
1 AATACTGGCTAGTAAGAGCAATACTGACTCATAAGAG
22386420 CAATTTACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (38 bp):
AATACTGGCTAGTAAGAGCAATACTGACTCATAAGAGT
Found at i:22409616 original size:17 final size:17
Alignment explanation
Indices: 22409596--22409643 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
22409586 ACTACAATGC
*
22409596 AAATGCATTGACAAATA
1 AAATGCAATGACAAATA
*
22409613 AAATGCAGA-GACAATTA
1 AAATGCA-ATGACAAATA
22409630 AAATGCAATGACAA
1 AAATGCAATGACAA
22409644 CTATATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 26 0.96
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (17 bp):
AAATGCAATGACAAATA
Found at i:22410061 original size:6 final size:6
Alignment explanation
Indices: 22410046--22410080 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
22410036 TAGCTACAAA
* *
22410046 TTCTTC TTCTTT TTCTTT TTCTTT TTCTCT TTCTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT
22410081 CATATCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTCTTT
Found at i:22417183 original size:40 final size:40
Alignment explanation
Indices: 22417128--22417375 Score: 298
Period size: 40 Copynumber: 6.1 Consensus size: 40
22417118 AAGTTATGTT
22417128 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
1 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
* * * *
22417168 TGATAAAGTTCAAGCTATGACTTAGCAGGCGATAAGCTGG
1 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
* * *
22417208 TAATAAAGTTCAAGCTACGGTTTAGCAGGCTATAAGCCGA
1 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
* *
22417248 TGATAAAGTTCAAGCTACGGCTTAGTAGGCTATAAGTCGG
1 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
* * * *
22417288 TGATAAAGTTCAAGCTACAGCTTAGCAGGTTATGACCCGG
1 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
* * * *
22417328 TGTTAAAAATTCAAGCTAAGTTTAGCTTAGCAGGCGATAAGCCGG
1 TGAT-AAAGTTCAAGCTACG----GCTTAGCAGGCTATAAGCCGG
22417373 TGA
1 TGA
22417376 AAATCATATG
Statistics
Matches: 172, Mismatches: 31, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
40 141 0.82
41 12 0.07
45 19 0.11
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (40 bp):
TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATAAGCCGG
Found at i:22418305 original size:21 final size:21
Alignment explanation
Indices: 22418281--22418335 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
22418271 TACCATTTAA
*
22418281 AGTATCGGTAGAA-GACTAAAT
1 AGTATCGGTAGAATGAAT-AAT
*
22418302 AGTATCGGTAGAATGAATCAT
1 AGTATCGGTAGAATGAATAAT
22418323 AGTATCGGTAGAA
1 AGTATCGGTAGAA
22418336 CTAGTGAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (21 bp):
AGTATCGGTAGAATGAATAAT
Found at i:22423227 original size:22 final size:20
Alignment explanation
Indices: 22423200--22423240 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
22423190 AAAAATATTA
22423200 TATTATATTTAATTTTATTAAT
1 TATTATATTT-ATTTT-TTAAT
22423222 TATTATATTTATTTTTTAA
1 TATTATATTTATTTTTTAA
22423241 AAATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATATTTATTTTTTAAT
Found at i:22423711 original size:183 final size:182
Alignment explanation
Indices: 22423393--22423741 Score: 626
Period size: 183 Copynumber: 1.9 Consensus size: 182
22423383 ATTATTATGT
22423393 TTTTGTACCCATAAGCCTAGCCAAATGATAAGATGGTCAATGATAAGGTGGTATGGACGGAGTCC
1 TTTTGTACCCATAAGCCTAGCCAAATGATAAGATGGTCAATGATAAGGTGGTATGGACGGAGTCC
* * * **
22423458 TAAATTTTTGAATCATATTTTTTGTTATTTTAGATTGTTATATATGTTGGATCTGGTGTTTTAAG
66 TAAATTTGTGAATCATATTCTTTGTTATTTTAGATTGTTATATATGTTGAATCTAATGTTTTAAG
*
22423523 TGTAGCATATTCGTTTTGTATATTTGTATTTTTAGATTGTTATATATGATTC
131 TGTAGCATATTCGTTTTGTATACTTGTATTTTTAGATTGTTATATATGATTC
*
22423575 TTTTGTACCCATAAGCCTAGTCAAATGATAAGATGGTCAATGATAAGGTGGTATGGACGGAGTCC
1 TTTTGTACCCATAAGCCTAGCCAAATGATAAGATGGTCAATGATAAGGTGGTATGGACGGAGT-C
22423640 CTAAATTTGTGAATCATATTCTTTGTTATTTTAGATTGTTATATATGTTGAATCTAATGTTTTAA
65 CTAAATTTGTGAATCATATTCTTTGTTATTTTAGATTGTTATATATGTTGAATCTAATGTTTTAA
22423705 GTGTAGCATATTCGTTTTGTATACTTGTATTTTTAGA
130 GTGTAGCATATTCGTTTTGTATACTTGTATTTTTAGA
22423742 ACAAATTAAT
Statistics
Matches: 159, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
182 62 0.39
183 97 0.61
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.44
Consensus pattern (182 bp):
TTTTGTACCCATAAGCCTAGCCAAATGATAAGATGGTCAATGATAAGGTGGTATGGACGGAGTCC
TAAATTTGTGAATCATATTCTTTGTTATTTTAGATTGTTATATATGTTGAATCTAATGTTTTAAG
TGTAGCATATTCGTTTTGTATACTTGTATTTTTAGATTGTTATATATGATTC
Found at i:22423978 original size:22 final size:20
Alignment explanation
Indices: 22423951--22423991 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
22423941 AAAAATATTA
22423951 TATTATATTTAATTTTATTAAT
1 TATTATATTT-ATTTT-TTAAT
22423973 TATTATATTTATTTTTTAA
1 TATTATATTTATTTTTTAA
22423992 AAATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATATTTATTTTTTAAT
Found at i:22424736 original size:18 final size:18
Alignment explanation
Indices: 22424701--22424739 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
22424691 AAATGAAAAA
**
22424701 AAAATTATTTAAGTTTTT
1 AAAATTATTTAAAATTTT
*
22424719 AAAATTTTTTAAAATTTT
1 AAAATTATTTAAAATTTT
22424737 AAA
1 AAA
22424740 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAAATTATTTAAAATTTT
Found at i:22428600 original size:16 final size:17
Alignment explanation
Indices: 22428579--22428611 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22428569 TCTTACTGAA
22428579 ATTTTTT-TATAAAATT
1 ATTTTTTCTATAAAATT
22428595 ATTTTTTCCTATAAAAT
1 ATTTTTT-CTATAAAAT
22428612 CCCATGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTTTCTATAAAATT
Found at i:22436709 original size:22 final size:22
Alignment explanation
Indices: 22436683--22436736 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
22436673 TATACTAAAT
22436683 TTTAATTCAATAATTAAAATTC
1 TTTAATTCAATAATTAAAATTC
*
22436705 TTTAATTAAATAATTAAAATTC
1 TTTAATTCAATAATTAAAATTC
22436727 TTTAATTCAA
1 TTTAATTCAA
22436737 AGTTCCATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAATTCAATAATTAAAATTC
Found at i:22437105 original size:21 final size:21
Alignment explanation
Indices: 22437079--22437118 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22437069 TGCTCAATGT
22437079 GTCTAG-TCGAGCCTCGATGCA
1 GTCTAGAT-GAGCCTCGATGCA
*
22437100 GTCTAGATGGGCCTCGATG
1 GTCTAGATGAGCCTCGATG
22437119 GATTAAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.17, C:0.25, G:0.33, T:0.25
Consensus pattern (21 bp):
GTCTAGATGAGCCTCGATGCA
Found at i:22437479 original size:102 final size:102
Alignment explanation
Indices: 22437303--22437486 Score: 341
Period size: 102 Copynumber: 1.8 Consensus size: 102
22437293 AATTAAAAGC
* *
22437303 TTGAAGATCAATCCCTATAGGATTCAACTACATAGCTAAATGAGTAATGAATAGGCCCAAAATTT
1 TTGAAGATAAATCCCTATAGGATTCAACTACATAGATAAATGAGTAATGAATAGGCCCAAAATTT
22437368 AGAGGTCGATTAGCATGAGTAATGAATAGGCCCAAGA
66 AGAGGTCGATTAGCATGAGTAATGAATAGGCCCAAGA
*
22437405 TTGAAGATAAATCCCTATAGGATTCAACTACATTGATAAATGAGTAATGAATAGGCCCAAAATTT
1 TTGAAGATAAATCCCTATAGGATTCAACTACATAGATAAATGAGTAATGAATAGGCCCAAAATTT
22437470 AGAGGTCGATTAGCATG
66 AGAGGTCGATTAGCATG
22437487 CACAACATGC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 79 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (102 bp):
TTGAAGATAAATCCCTATAGGATTCAACTACATAGATAAATGAGTAATGAATAGGCCCAAAATTT
AGAGGTCGATTAGCATGAGTAATGAATAGGCCCAAGA
Found at i:22442900 original size:30 final size:29
Alignment explanation
Indices: 22442863--22443191 Score: 215
Period size: 30 Copynumber: 11.0 Consensus size: 29
22442853 CCCAAACTCT
22442863 TCCAAAATTACATTTTGACCCTTAAACTTC
1 TCCAAAATTACATTTTGACCC-TAAACTTC
* *
22442893 TCTAAAATTACATTTT-AGCCTTCAAAC-TC
1 TCCAAAATTACATTTTGA-CCCT-AAACTTC
* *
22442922 TTCCAGAATTATATTTTGACCCTCAAACTTC
1 -TCCAAAATTACATTTTGACCCT-AAACTTC
* * *
22442953 TCAAAAATTACATTTTTAACCCTTGAAA-TTT
1 TCCAAAATTACA-TTTTGACCC-T-AAACTTC
* *
22442984 TCTAAAATTACATTTTAGCCCCTAAAC-TC
1 TCCAAAATTACATTTT-GACCCTAAACTTC
* * * * * *
22443013 TTCTAATATTATATTTTAATCCCTAACCTTT
1 -TCCAAAATTACATTTTGA-CCCTAAACTTC
*
22443044 TCCAAAATTGCATTTTGACACCTAAACTT-
1 TCCAAAATTACATTTTGAC-CCTAAACTTC
* * *
22443073 TCCCAAAATCACATATTGACTCCCAAACCTT-
1 T-CCAAAATTACATTTTGAC-CCTAAA-CTTC
* * *
22443104 TCCAAAATCACATTTTGACCCCAAGCTT-
1 TCCAAAATTACATTTTGACCCTAAACTTC
* * *
22443132 TCCTAAAAATACATTTTGACCCTCAAATTTT
1 TCC-AAAATTACATTTTGACCCT-AAACTTC
*
22443163 TCCAAAATTACATTTTAACCCTAAA-TTC
1 TCCAAAATTACATTTTGACCCTAAACTTC
22443191 T
1 T
22443192 TTAAAACTTC
Statistics
Matches: 238, Mismatches: 43, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
28 9 0.04
29 34 0.14
30 156 0.66
31 35 0.15
32 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
TCCAAAATTACATTTTGACCCTAAACTTC
Found at i:22443051 original size:91 final size:91
Alignment explanation
Indices: 22442855--22443059 Score: 249
Period size: 91 Copynumber: 2.3 Consensus size: 91
22442845 AAAGAGCCCC
* * *
22442855 CAAACTCTTCCAAAATTACA-TTTTGACCCTTAAACTTCTCTAAAATTACATTTTAGCCTTCAAA
1 CAAACTTTTCCAAAATTACATTTTTAACCCTTAAACTTCTCTAAAATTACATTTTAGCCCTCAAA
*
22442919 CTCTTCCAGAATTATATTTTGACCCT
66 CTCTTCCAGAATTATATTTTAACCCT
* * *
22442945 CAAACTTCTCAAAAATTACATTTTTAACCCTTGAAA-TTTTCTAAAATTACATTTTAGCCC-CTA
1 CAAACTTTTCCAAAATTACATTTTTAACCCTT-AAACTTCTCTAAAATTACATTTTAGCCCTC-A
*
22443008 AACTCTTCTA-ATATTATATTTTAATCCCT
64 AACTCTTCCAGA-ATTATATTTTAA-CCCT
* *
22443037 -AACCTTTTCCAAAATTGCATTTT
1 CAAACTTTTCCAAAATTACATTTT
22443060 GACACCTAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
90 19 0.19
91 72 0.73
92 7 0.07
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (91 bp):
CAAACTTTTCCAAAATTACATTTTTAACCCTTAAACTTCTCTAAAATTACATTTTAGCCCTCAAA
CTCTTCCAGAATTATATTTTAACCCT
Found at i:22447519 original size:21 final size:20
Alignment explanation
Indices: 22447463--22447502 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
22447453 GTACCTGTGC
22447463 TAATTCTACCGATACAAGTA
1 TAATTCTACCGATACAAGTA
22447483 TAATTTCTACCGATACAAGT
1 TAA-TTCTACCGATACAAGT
22447503 CATGCATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (20 bp):
TAATTCTACCGATACAAGTA
Found at i:22457289 original size:41 final size:40
Alignment explanation
Indices: 22457224--22457307 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 40
22457214 AAATACACTT
*
22457224 AAAAATATTAAAACAAATATTAAAAAAACAAACAAATTAA
1 AAAAATATTAAAACAAATAGTAAAAAAACAAACAAATTAA
* * * *
22457264 AAAAGATATTAAAACAATTCGTAAAACAACAAACAAATTGA
1 AAAA-ATATTAAAACAAATAGTAAAAAAACAAACAAATTAA
22457305 AAA
1 AAA
22457308 TACAATAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.68, C:0.10, G:0.04, T:0.19
Consensus pattern (40 bp):
AAAAATATTAAAACAAATAGTAAAAAAACAAACAAATTAA
Found at i:22457526 original size:23 final size:22
Alignment explanation
Indices: 22457500--22457547 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
22457490 AACAGTACTG
* *
22457500 AAAATAGTACTAAAATAGAACCA
1 AAAACAGTACCAAAAT-GAACCA
*
22457523 AAAACAGTACCAAAATGCACCA
1 AAAACAGTACCAAAATGAACCA
22457545 AAA
1 AAA
22457548 TCAAATCAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.60, C:0.19, G:0.08, T:0.12
Consensus pattern (22 bp):
AAAACAGTACCAAAATGAACCA
Found at i:22461131 original size:20 final size:20
Alignment explanation
Indices: 22461103--22461164 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
22461093 GCTGCGATTT
* *
22461103 GCAACTGATGGAAGGACTTA
1 GCAATTGATGGAAGCACTTA
22461123 GCAATTGATGGAAGCACTTA
1 GCAATTGATGGAAGCACTTA
*
22461143 GCAATGGATGGAAGCACTTA
1 GCAATTGATGGAAGCACTTA
22461163 GC
1 GC
22461165 TTTTTTTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (20 bp):
GCAATTGATGGAAGCACTTA
Found at i:22461203 original size:7 final size:7
Alignment explanation
Indices: 22461191--22461229 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
22461181 AATTGATTTA
22461191 GGAATTG
1 GGAATTG
22461198 GGAATTG
1 GGAATTG
*
22461205 AGAATTG
1 GGAATTG
22461212 GGAATTG
1 GGAATTG
*
22461219 GGAAATG
1 GGAATTG
22461226 GGAA
1 GGAA
22461230 GGCTAAGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (7 bp):
GGAATTG
Found at i:22470968 original size:22 final size:22
Alignment explanation
Indices: 22470943--22470994 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
22470933 TTATTGATAC
22470943 GAAATGATGTGCGAGATATAAG
1 GAAATGATGTGCGAGATATAAG
22470965 GAAATGATGTGCGAGATATAAG
1 GAAATGATGTGCGAGATATAAG
22470987 GAAATGAT
1 GAAATGAT
22470995 AATTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.31, T:0.23
Consensus pattern (22 bp):
GAAATGATGTGCGAGATATAAG
Found at i:22471400 original size:21 final size:22
Alignment explanation
Indices: 22471374--22471414 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
22471364 ATCAAAAAGG
*
22471374 AAAGAAAAATTAGT-AGAAACA
1 AAAGAAAAATGAGTAAGAAACA
*
22471395 AAAGAATAATGAGTAAGAAA
1 AAAGAAAAATGAGTAAGAAA
22471415 ACATGTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.66, C:0.02, G:0.17, T:0.15
Consensus pattern (22 bp):
AAAGAAAAATGAGTAAGAAACA
Found at i:22474328 original size:55 final size:55
Alignment explanation
Indices: 22474269--22474439 Score: 184
Period size: 55 Copynumber: 3.1 Consensus size: 55
22474259 TGAATAGTAT
* *
22474269 TAGCTCGGGTAGAGCTTTGGCCTGCTTACGTCTCGATTAGAGCGTAATGCTATTA
1 TAGCTCGGGTAGAGCTTTAGACTGCTTACGTCTCGATTAGAGCGTAATGCTATTA
*** * * *
22474324 TAGCTTTAGTAGAGCTTCAGACTGCTTATGTCTC-AGTTAGAGCGCAATGCTATTA
1 TAGCTCGGGTAGAGCTTTAGACTGCTTACGTCTCGA-TTAGAGCGTAATGCTATTA
* * * * * *
22474379 TTA-CTCGGGTAGAGCTTTAGACTACTTACGTCTTGGTTAGAGCATAAAGCTATTT
1 -TAGCTCGGGTAGAGCTTTAGACTGCTTACGTCTCGATTAGAGCGTAATGCTATTA
22474434 TAGCTC
1 TAGCTC
22474440 AGAAAGAGCG
Statistics
Matches: 92, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
54 3 0.03
55 87 0.95
56 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (55 bp):
TAGCTCGGGTAGAGCTTTAGACTGCTTACGTCTCGATTAGAGCGTAATGCTATTA
Found at i:22477669 original size:42 final size:42
Alignment explanation
Indices: 22477622--22478177 Score: 638
Period size: 42 Copynumber: 13.3 Consensus size: 42
22477612 AAGGAAAACA
* *
22477622 TTCATTGCATTTATAGGTCCAAGG-GTGGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGG-CCAAGGTGTGGAGGTCCATTTACTT
* * *
22477664 TTCATTGCATTTAGAAGCCCAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
*
22477706 TTCATTGCATTGAGAGGCCCAA-GTGTGGAGGTCCATTT-CTT
1 TTCATTGCATTTAGAGG-CCAAGGTGTGGAGGTCCATTTACTT
*
22477747 TTCATTACATTTAGAGGCCCAA-GTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGG-CCAAGGTGTGGAGGTCCATTTACTT
* * ** * *
22477789 TTCATCGTATTTAGAGGCTGAGGTGTGGTGGTGCATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* * * * *
22477831 TTCATCGCATTTAAAGGCCTAGGTGTGGAGGTCTATTTACCT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* * * **
22477873 TTCATCGCATTTAGAGGCCTAGGTGTGAAGGTTTATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* * *
22477915 TTCATTACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
22477957 TTCATGGCATTTAGAGGCCCAA-GTGTGGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGG-CCAAGGTGTGGAGGTCCATTTACTT
* * * * *
22477999 TTCATTGCATTTAGAGGCCCATGTATAGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
22478041 TTCATTGCATTTAGATGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* *
22478083 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
* * * * *
22478125 TTCATTGCATGTAAAGGCCCAGGTGT-GAGGTCTATTTACAT
1 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
*
22478166 TTCTTCTGCATT
1 TTCAT-TGCATT
22478178 CTCATTTCAA
Statistics
Matches: 448, Mismatches: 59, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
41 65 0.15
42 377 0.84
43 6 0.01
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
Found at i:22479123 original size:96 final size:94
Alignment explanation
Indices: 22479001--22479414 Score: 228
Period size: 96 Copynumber: 4.3 Consensus size: 94
22478991 AATTAGTCAT
* *
22479001 TTTAAAGAA-AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTAACTATTTCGAAATAAAAA
1 TTTAAAAAATAAAAGTTTAAATTTTTAAATAAAATTTTGATTTTTTAACTATTT-GAAATAAAAA
22479065 TTTTGATTTTTAAGAAAAATAATGATTTTC
65 TTTTGATTTTTAAGAAAAATAATGATTTTC
* * * * *
22479095 TTTAAAAAATAGAAAGTTTAGATTTTTAAAATAAAAATATG-TTTTTTAA-TCATTTTAAAGAAA
1 TTTAAAAAATA-AAAGTTTAAATTTTT-AAATAAAATTTTGATTTTTTAACT-ATTTGAAATAAA
* * * *
22479158 AATTTTAAATTTTTAA-ACAAAGTATTGATTTTT
63 AATTTT-GATTTTTAAGA-AAAATAATGATTTTC
* ** **
22479191 TTTAACTATTTCGAAATAAAAATTTTTATTTTTAAGA-AAAATAGTGATTTTCTT-AC-A----A
1 TTTAA--A-----AAATAAAAGTTTAAATTTTTAA-ATAAAATTTTGATTTT-TTAACTATTTGA
* * * * *
22479249 AA-AAAAGTTTAGATTTTTAAAAATAAAAAACT-AGTTTTAG
57 AATAAAAATTTTGATTTTTAAGAA-AAATAA-TGA-TTTT-C
** ** * *
22479289 TATTTTAATTTAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAA
1 T-TTAAAAAATAAAAGTTTAAATTTTTAAATAAAATTTTGA-TTTTTTAACTATTT-GAAAT-AA
* *
22479354 AAAATTT-ATTTTTAAGAAAAATAGTGATTTTC
62 AAATTTTGATTTTTAAGAAAAATAATGATTTTC
* *
22479386 -TTAAAAAAAAGAAAGTTTAGATTTTTAAA
1 TTTAAAAAATA-AAAGTTTAAATTTTTAAA
22479415 AATAAAAAAC
Statistics
Matches: 237, Mismatches: 47, Indels: 70
0.67 0.13 0.20
Matches are distributed among these distances:
91 1 0.00
92 26 0.11
93 6 0.03
94 9 0.04
95 29 0.12
96 80 0.34
97 19 0.08
98 7 0.03
99 10 0.04
100 10 0.04
101 15 0.06
102 18 0.08
103 7 0.03
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (94 bp):
TTTAAAAAATAAAAGTTTAAATTTTTAAATAAAATTTTGATTTTTTAACTATTTGAAATAAAAAT
TTTGATTTTTAAGAAAAATAATGATTTTC
Found at i:22479530 original size:290 final size:296
Alignment explanation
Indices: 22478993--22479652 Score: 941
Period size: 290 Copynumber: 2.2 Consensus size: 296
22478983 AAAAAAAAAA
22478993 TTAGTCATTTTAAAGAAAAAAGTTTAAATTTTTAAATAAAGTTTTGA-TTTTTTAACTATTTCGA
1 TTAGTCATTTTAAAG-AAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGA
* *
22479057 AAT-AAAAATTTTGATTTTTAAGAAAAATAATGATTTTCTTTAAAAAATAGAAAGTTTAGATTTT
65 AATAAAAAAATTTGATTTTTAAGAAAAATAATGATTTTCTTTAAAAAAAAGAAAGTTTAGATTTT
* *
22479121 TAAAATAAAAATATGTTTTTTAATCATTTTAAAGAAAAATTTTAAATTTTTAAACAAAGTATTGA
130 TAAAATAAAAATATATTTTTTAATCATTTTAAAGAAAAATTTTAAAATTTTAAACAAAGTATTGA
* *
22479186 TTTTTTTTAACTATTTCGAAATAAAAATTTTTATTTTTAAGAAAAATAGTGATTTTCTTACAAAA
195 TTTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGAAAAATAGTGATTTTCTTAAAAAA
22479251 -AAA-AG-TTTAGATTTTTAAAAATAAAAA-ACTAG-TT
260 GAAAGAGATTTAGATTTTTAAAAATAAAAATA-T-GTTT
*** *
22479285 TTAGT-ATTTTAATTTAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAA
1 TTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAA
*
22479349 ATAAAAAAATTT-ATTTTTAAGAAAAATAGTGATTTTC-TTAAAAAAAAGAAAGTTTAGATTTTT
66 ATAAAAAAATTTGATTTTTAAGAAAAATAATGATTTTCTTTAAAAAAAAGAAAGTTTAGATTTTT
* *** *
22479412 AAAAATAAAAA-ACTATTTTTTAGTCATTTTAATTTAAAATTTTAAAATTTTAAACAAAGTTTTG
131 -AAAATAAAAATA-TATTTTTTAATCATTTTAAAGAAAAATTTTAAAATTTTAAACAAAGTATTG
* * *
22479476 A-TTTTTTTAACTGTTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTTTTTAAAAA
194 ATTTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGAAAAATAGTGATTTTCTTAAAAA
*
22479540 AGAAAGAGAAAATTTAGGTTTTTAAAAATAAAAATATGTTT
259 AGAAAGAG---ATTTAGATTTTTAAAAATAAAAATATGTTT
* *
22479581 TTAGTCATTTTAAAGAAACAAGTTTAAATTTTTAAATAAAG-TTTGATTTTTCTTAACCATTTCA
1 TTAGTCATTTTAAAGAAA-AAGTTTAAATTTTTAAATAAAGTTTTGATTTTT-TTAACTATTTCG
22479645 AAATAAAA
64 AAATAAAA
22479653 GTTTTGATTT
Statistics
Matches: 327, Mismatches: 26, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
290 114 0.35
291 109 0.33
292 15 0.05
295 1 0.00
296 29 0.09
297 20 0.06
298 39 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (296 bp):
TTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAA
ATAAAAAAATTTGATTTTTAAGAAAAATAATGATTTTCTTTAAAAAAAAGAAAGTTTAGATTTTT
AAAATAAAAATATATTTTTTAATCATTTTAAAGAAAAATTTTAAAATTTTAAACAAAGTATTGAT
TTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGAAAAATAGTGATTTTCTTAAAAAAG
AAAGAGATTTAGATTTTTAAAAATAAAAATATGTTT
Found at i:22480256 original size:21 final size:21
Alignment explanation
Indices: 22480232--22480272 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
22480222 TTATTCACAT
22480232 TTATATAATTTTTATTTATTC
1 TTATATAATTTTTATTTATTC
* *
22480253 TTATTTCATTTTTATTTATT
1 TTATATAATTTTTATTTATT
22480273 TTCATGTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (21 bp):
TTATATAATTTTTATTTATTC
Found at i:22480273 original size:10 final size:10
Alignment explanation
Indices: 22480239--22480302 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
22480229 CATTTATATA
22480239 ATTTTTATTT
1 ATTTTTATTT
*
22480249 ATTCTTATTT
1 ATTTTTATTT
22480259 CATTTTTATTT
1 -ATTTTTATTT
*
22480270 ATTTTCATGTCT
1 ATTTTTAT-T-T
*
22480282 ATTTATATTT
1 ATTTTTATTT
22480292 ATGTTTT-TTT
1 AT-TTTTATTT
22480302 A
1 A
22480303 CACATTTCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 23 0.52
11 14 0.32
12 7 0.16
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.70
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:22482457 original size:50 final size:50
Alignment explanation
Indices: 22482382--22482480 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
22482372 CTCCATGGCA
* *
22482382 TAATTCATGCATCATTTAAATACATGGGGCACAGTGTTGCATCTATATTC
1 TAATTCATGCATCATTTAAATACATGGGGCACAATGATGCATCTATATTC
22482432 TAATTCATGCATCATTTAAATACATGGGGCACAATGATGCATCTATATT
1 TAATTCATGCATCATTTAAATACATGGGGCACAATGATGCATCTATATT
22482481 AGACATGAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (50 bp):
TAATTCATGCATCATTTAAATACATGGGGCACAATGATGCATCTATATTC
Found at i:22485997 original size:17 final size:17
Alignment explanation
Indices: 22485975--22486021 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
22485965 CTGTAGTATA
*
22485975 ATTGTCCCTGCATTTTT
1 ATTGTCACTGCATTTTT
*
22485992 ATTGTCACTTCATTTTT
1 ATTGTCACTGCATTTTT
*
22486009 ATTTTCACTGCAT
1 ATTGTCACTGCAT
22486022 CTACATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.09, T:0.53
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Found at i:22486029 original size:17 final size:17
Alignment explanation
Indices: 22486009--22486055 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
22485999 CTTCATTTTT
*
22486009 ATTTTCACTGCATCTAC
1 ATTTTCATTGCATCTAC
* *
22486026 ATTTTTATTACATCTAC
1 ATTTTCATTGCATCTAC
*
22486043 ATTGTCATTGCAT
1 ATTTTCATTGCAT
22486056 TTCCAAATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTTTCATTGCATCTAC
Found at i:22486480 original size:39 final size:39
Alignment explanation
Indices: 22486423--22486518 Score: 156
Period size: 39 Copynumber: 2.5 Consensus size: 39
22486413 TAAATAAAAG
***
22486423 ACACTCCAATGTGGGTGTATTGTGAACTAACAAGGGGGA
1 ACACTCCAATGCAAGTGTATTGTGAACTAACAAGGGGGA
*
22486462 ACACTGCAATGCAAGTGTATTGTGAACTAACAAGGGGGA
1 ACACTCCAATGCAAGTGTATTGTGAACTAACAAGGGGGA
22486501 ACACTCCAATGCAAGTGT
1 ACACTCCAATGCAAGTGT
22486519 TAGAAAAAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (39 bp):
ACACTCCAATGCAAGTGTATTGTGAACTAACAAGGGGGA
Found at i:22492410 original size:12 final size:12
Alignment explanation
Indices: 22492388--22492495 Score: 71
Period size: 12 Copynumber: 9.3 Consensus size: 12
22492378 ATAACATCCA
*
22492388 AACAATAAAAAT
1 AACAACAAAAAT
* *
22492400 AACAACTAAAAC
1 AACAACAAAAAT
* *
22492412 AGCCACAAAAAT
1 AACAACAAAAAT
*
22492424 AACAGC-AAAAT
1 AACAACAAAAAT
**
22492435 AAC-A-TTAAA-
1 AACAACAAAAAT
*
22492444 AACAATAAAAAT
1 AACAACAAAAAT
* *
22492456 AGCAACAAAAAC
1 AACAACAAAAAT
22492468 AACAACAAAAAT
1 AACAACAAAAAT
* *
22492480 AACAGCAAAAAC
1 AACAACAAAAAT
22492492 AACA
1 AACA
22492496 CGAAAACAGC
Statistics
Matches: 71, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
9 3 0.04
10 4 0.06
11 11 0.15
12 53 0.75
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:22492462 original size:24 final size:24
Alignment explanation
Indices: 22492444--22492515 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
22492434 TAACATTAAA
*
22492444 AACAATAAAAATAGCAACAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
* *
22492468 AACAACAAAAATAACAGCAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
* * *
22492492 AAC-ACGAAAACAGCAACTAAAAC
1 AACAACAAAAATAGCAACAAAAAC
22492515 A
1 A
22492516 GTAAAAAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 16 0.40
24 24 0.60
ACGTcount: A:0.68, C:0.21, G:0.06, T:0.06
Consensus pattern (24 bp):
AACAACAAAAATAGCAACAAAAAC
Found at i:22492483 original size:21 final size:20
Alignment explanation
Indices: 22492416--22492495 Score: 54
Period size: 21 Copynumber: 3.7 Consensus size: 20
22492406 TAAAACAGCC
*
22492416 ACAAAAATAACAGC-AAAATA
1 ACAAAAA-AACAACAAAAATA
* *
22492436 ACATTAAAAACAATAAAAATAGCA
1 ACA-AAAAAACAACAAAAAT---A
22492460 ACAAAAACAACAACAAAAATA
1 ACAAAAA-AACAACAAAAATA
*
22492481 ACAGCAAAAACAACA
1 ACA-AAAAAACAACA
22492496 CGAAAACAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
20 7 0.15
21 19 0.40
22 3 0.06
23 3 0.06
24 15 0.32
ACGTcount: A:0.70, C:0.17, G:0.04, T:0.09
Consensus pattern (20 bp):
ACAAAAAAACAACAAAAATA
Found at i:22492502 original size:56 final size:56
Alignment explanation
Indices: 22492387--22492503 Score: 155
Period size: 56 Copynumber: 2.1 Consensus size: 56
22492377 AATAACATCC
* * * * *
22492387 AAACAATAAAAATAACAACTAAAACAGCCACAAAAATAACAGCAAAATAACATTAA
1 AAACAATAAAAATAACAACAAAAACAACAACAAAAATAACAGCAAAACAACATCAA
* *
22492443 AAACAATAAAAATAGCAACAAAAACAACAACAAAAATAACAGCAAAAACAACA-CGA
1 AAACAATAAAAATAACAACAAAAACAACAACAAAAATAACAGC-AAAACAACATCAA
22492499 AAACA
1 AAACA
22492504 GCAACTAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
56 45 0.85
57 8 0.15
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.09
Consensus pattern (56 bp):
AAACAATAAAAATAACAACAAAAACAACAACAAAAATAACAGCAAAACAACATCAA
Found at i:22492583 original size:21 final size:20
Alignment explanation
Indices: 22492558--22492598 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
22492548 TAAAAAGAGC
22492558 AAAAAAGAGCAACCAAAACAAT
1 AAAAAA-AGC-ACCAAAACAAT
*
22492580 AAAAAAAGCATCAAAACAA
1 AAAAAAAGCACCAAAACAA
22492599 CAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.71, C:0.17, G:0.07, T:0.05
Consensus pattern (20 bp):
AAAAAAAGCACCAAAACAAT
Found at i:22493054 original size:34 final size:34
Alignment explanation
Indices: 22493025--22493093 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
22493015 CTCAAAGTTT
22493025 TCATA-TAT-AAACTCAAAGAACTAATTCAAAAC
1 TCATAGTATGAAACTCAAAGAACTAATTCAAAAC
* *
22493057 TCATAGTTTGGAACTCAAAGAACTAATTCAAAAC
1 TCATAGTATGAAACTCAAAGAACTAATTCAAAAC
22493091 TCA
1 TCA
22493094 AACTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 5 0.15
33 2 0.06
34 26 0.79
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (34 bp):
TCATAGTATGAAACTCAAAGAACTAATTCAAAAC
Found at i:22493196 original size:23 final size:24
Alignment explanation
Indices: 22493165--22493219 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
22493155 AAAATTTAGA
22493165 ATATATTTTTATATT-AATCTTTT
1 ATATATTTTTATATTAAATCTTTT
* * *
22493188 ATATTTTTTTATTTTAAATTTTTT
1 ATATATTTTTATATTAAATCTTTT
22493212 ATATATTT
1 ATATATTT
22493220 GAATTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
ATATATTTTTATATTAAATCTTTT
Found at i:22493224 original size:17 final size:16
Alignment explanation
Indices: 22493184--22493235 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
22493174 TATATTAATC
*
22493184 TTTTATATTTTTT-TA
1 TTTTAAATTTTTTATA
22493199 TTTTAAATTTTTTATA
1 TTTTAAATTTTTTATA
*
22493215 TATTTGAATTTTTTATA
1 T-TTTAAATTTTTTATA
22493232 TTTT
1 TTTT
22493236 TTTAAATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 12 0.36
16 6 0.18
17 15 0.45
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTAAATTTTTTATA
Found at i:22493529 original size:2 final size:2
Alignment explanation
Indices: 22493522--22493553 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22493512 ACATACATAC
22493522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22493554 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22493558 original size:2 final size:2
Alignment explanation
Indices: 22493553--22493580 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22493543 TATATATATA
22493553 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
22493581 CGCGCGCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:22498045 original size:29 final size:29
Alignment explanation
Indices: 22497964--22498082 Score: 134
Period size: 29 Copynumber: 4.1 Consensus size: 29
22497954 CCACAAAGGC
22497964 CTTTAACA-AAGTCAGCCACAAAGGCTTCA
1 CTTTAACAGAA-TCAGCCACAAAGGCTTCA
* * ** *
22497993 ATTTAACAGAATCATCCATGAAGGCTTTA
1 CTTTAACAGAATCAGCCACAAAGGCTTCA
*
22498022 CTTTAACAGAATCAGCCACAAAGGC-TAA
1 CTTTAACAGAATCAGCCACAAAGGCTTCA
* * *
22498050 TTTTAACAAAATTAGCCACAAAGGCTTCA
1 CTTTAACAGAATCAGCCACAAAGGCTTCA
22498079 CTTT
1 CTTT
22498083 TATGAAAAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
28 24 0.33
29 47 0.64
30 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (29 bp):
CTTTAACAGAATCAGCCACAAAGGCTTCA
Found at i:22498294 original size:54 final size:54
Alignment explanation
Indices: 22498219--22498346 Score: 175
Period size: 54 Copynumber: 2.4 Consensus size: 54
22498209 CATGACTATT
* * * *
22498219 TCTTATACTATGTGGTTTTCATTCCTCATATGATGTCATAGCCACCAAACTAGG
1 TCTTACACTATATGGTCTTCATTCCTCATATGATGTCACAGCCACCAAACTAGG
* * * * *
22498273 TCTTACTCTATATGGTCTTCATTCCTTATATGATGTCACAGTCACCAGACTATG
1 TCTTACACTATATGGTCTTCATTCCTCATATGATGTCACAGCCACCAAACTAGG
22498327 TCTTACACTATATGGTCTTC
1 TCTTACACTATATGGTCTTC
22498347 GATTGCCATG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.39
Consensus pattern (54 bp):
TCTTACACTATATGGTCTTCATTCCTCATATGATGTCACAGCCACCAAACTAGG
Found at i:22503565 original size:16 final size:16
Alignment explanation
Indices: 22503524--22503555 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
22503514 ATATGAAAAT
22503524 AAAGATAAAATGTAATA
1 AAAG-TAAAATGTAATA
22503541 AAAGTAAAATGTAAT
1 AAAGTAAAATGTAAT
22503556 GATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (16 bp):
AAAGTAAAATGTAATA
Found at i:22503870 original size:62 final size:62
Alignment explanation
Indices: 22503794--22503928 Score: 207
Period size: 62 Copynumber: 2.2 Consensus size: 62
22503784 GCAACTTCCA
* * * * *
22503794 AACTTGTCAAAAACTTATTTAAGTGAGAATTGTTTCCCTCTTGGTTCTTGGACGAACATCCG
1 AACTTGTCAAAAACTTATTTAAGTAAGAATTATTTCCCTCTCGGTTCATGGACGAAAATCCG
* *
22503856 AACTTGTCAAAAACTTATTTACGTAAGAATTATTTCTCTCTCGGTTCATGGACGAAAATCCG
1 AACTTGTCAAAAACTTATTTAAGTAAGAATTATTTCCCTCTCGGTTCATGGACGAAAATCCG
22503918 AACTTGTCAAA
1 AACTTGTCAAA
22503929 CTTTTACGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (62 bp):
AACTTGTCAAAAACTTATTTAAGTAAGAATTATTTCCCTCTCGGTTCATGGACGAAAATCCG
Found at i:22504180 original size:62 final size:62
Alignment explanation
Indices: 22504083--22504330 Score: 363
Period size: 62 Copynumber: 4.0 Consensus size: 62
22504073 GTTAATTAAT
* * *
22504083 AACTTAGTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACCAACTTCCGAACTTGTCAAA
1 AACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTGTCAAA
* * *
22504145 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGCACGAACTTTCGAACTTGTCAAA
1 AACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTGTCAAA
* *
22504207 AACTTATTTACGTGAGAATTGGTTCTCTCTTAGTTTTTGGACGAACTTCCGAACTTGTCAAA
1 AACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTGTCAAA
* * * * *
22504269 AACATATTTACGTGAGTATTGTTTCTTTCTTAGTTCTTGGATGAACATCC-AACCTTGTCAAA
1 AACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAA-CTTGTCAAA
22504331 CTTTTGCGAT
Statistics
Matches: 169, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
61 2 0.01
62 167 0.99
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (62 bp):
AACTTATTTACGTGAGAATTGTTTCTCTCTTAGTTCTTGGACGAACTTCCGAACTTGTCAAA
Found at i:22508625 original size:20 final size:21
Alignment explanation
Indices: 22508589--22508627 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22508579 CTTTTTTTTA
*
22508589 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
22508610 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
22508628 AATTCCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:22509871 original size:17 final size:17
Alignment explanation
Indices: 22509849--22509902 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
22509839 AGGATGACAC
22509849 GTGGCCAAGATACACCA
1 GTGGCCAAGATACACCA
22509866 GTGGCC--G--ACA-C-
1 GTGGCCAAGATACACCA
22509877 GTGGCCAAGATACACCA
1 GTGGCCAAGATACACCA
22509894 GTGGCCAAG
1 GTGGCCAAG
22509903 GAAGCCTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
11 6 0.19
12 1 0.03
13 4 0.13
15 4 0.13
16 1 0.03
17 15 0.48
ACGTcount: A:0.30, C:0.30, G:0.30, T:0.11
Consensus pattern (17 bp):
GTGGCCAAGATACACCA
Found at i:22509884 original size:28 final size:28
Alignment explanation
Indices: 22509844--22509899 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
22509834 TTGAGAGGAT
22509844 GACACGTGGCCAAGATACACCAGTGGCC
1 GACACGTGGCCAAGATACACCAGTGGCC
22509872 GACACGTGGCCAAGATACACCAGTGGCC
1 GACACGTGGCCAAGATACACCAGTGGCC
22509900 AAGGAAGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.32, G:0.29, T:0.11
Consensus pattern (28 bp):
GACACGTGGCCAAGATACACCAGTGGCC
Found at i:22515591 original size:297 final size:297
Alignment explanation
Indices: 22515057--22515654 Score: 1142
Period size: 297 Copynumber: 2.0 Consensus size: 297
22515047 CTTCCATGGT
22515057 AGCTCACTTTAAGAAAATAAAAAAATGTGGAATTAATTTCTTCTTTAGCTTGATGATGATCTTTT
1 AGCTCACTTTAAGAAAATAAAAAAATGTGGAATTAATTTCTTCTTTAGCTTGATGATGATCTTTT
*
22515122 CTCACTCTCCTCTATTTATAACCACTGTAAAGTACAGGTCTACCCCCTTCTCAGATCTAACTCCC
66 CTCACTCTCCTCTATTTATAACCACTGTAAAGTACAAGTCTACCCCCTTCTCAGATCTAACTCCC
22515187 TTTTTACAACTGTAAAAGTTTGTTATTGCCAGCTATGCACTCACATAGATCTGGTTTGTGCATTA
131 TTTTTACAACTGTAAAAGTTTGTTATTGCCAGCTATGCACTCACATAGATCTGGTTTGTGCATTA
22515252 GGTAGTTGCAAATTGTCGCGACATCTTTGGACGCAAATTTTGATTTTTATTCACTGAGACAACTT
196 GGTAGTTGCAAATTGTCGCGACATCTTTGGACGCAAATTTTGATTTTTATTCACTGAGACAACTT
*
22515317 GACATGCTCCTACGCTGGTGCTTCTAGATATGTTAGC
261 GACATGCTCCTACGCTAGTGCTTCTAGATATGTTAGC
*
22515354 AGCTCACTTTAAGAAAATCAAAAAATGTGGAATTAATTTCTTCTTTAGCTTGATGATGATCTTTT
1 AGCTCACTTTAAGAAAATAAAAAAATGTGGAATTAATTTCTTCTTTAGCTTGATGATGATCTTTT
22515419 CTCACTCTCCTCTATTTATAACCACTGTAAAGTACAAGTCTACCCCCTTCTCAGATCTAACTCCC
66 CTCACTCTCCTCTATTTATAACCACTGTAAAGTACAAGTCTACCCCCTTCTCAGATCTAACTCCC
*
22515484 TTTTTACAACTGTAAAAGTTTGTTATTGCCAGCTATGCACTCACGTAGATCTGGTTTGTGCATTA
131 TTTTTACAACTGTAAAAGTTTGTTATTGCCAGCTATGCACTCACATAGATCTGGTTTGTGCATTA
* *
22515549 GGTAGTTGCAGATTGTCGCGACATCTTTGGACGCAAATTTTGATTTTTATTCACTTAGACAACTT
196 GGTAGTTGCAAATTGTCGCGACATCTTTGGACGCAAATTTTGATTTTTATTCACTGAGACAACTT
22515614 GACATGCTCCTACGCTAGTGCTTCTAGATATGTTAGC
261 GACATGCTCCTACGCTAGTGCTTCTAGATATGTTAGC
22515651 AGCT
1 AGCT
22515655 TAAAGTCCCT
Statistics
Matches: 295, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
297 295 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (297 bp):
AGCTCACTTTAAGAAAATAAAAAAATGTGGAATTAATTTCTTCTTTAGCTTGATGATGATCTTTT
CTCACTCTCCTCTATTTATAACCACTGTAAAGTACAAGTCTACCCCCTTCTCAGATCTAACTCCC
TTTTTACAACTGTAAAAGTTTGTTATTGCCAGCTATGCACTCACATAGATCTGGTTTGTGCATTA
GGTAGTTGCAAATTGTCGCGACATCTTTGGACGCAAATTTTGATTTTTATTCACTGAGACAACTT
GACATGCTCCTACGCTAGTGCTTCTAGATATGTTAGC
Found at i:22517322 original size:15 final size:14
Alignment explanation
Indices: 22517300--22517329 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
22517290 TTCTTTTTCT
22517300 TCTTCTTTCTCTTC
1 TCTTCTTTCTCTTC
22517314 TCTTCCTTTCTCTTC
1 TCTT-CTTTCTCTTC
22517329 T
1 T
22517330 TCCTCTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
TCTTCTTTCTCTTC
Found at i:22525994 original size:20 final size:20
Alignment explanation
Indices: 22525966--22526016 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
22525956 ACGGACCCAA
22525966 AAAAAGTCAACTGGTTAAAG
1 AAAAAGTCAACTGGTTAAAG
* *
22525986 AAAATGTCAACTGGTTAATG
1 AAAAAGTCAACTGGTTAAAG
22526006 AAAAAGTCAAC
1 AAAAAGTCAAC
22526017 AATCAATGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAAAGTCAACTGGTTAAAG
Found at i:22529119 original size:24 final size:23
Alignment explanation
Indices: 22529083--22529141 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
22529073 ATTTGTGGGG
*
22529083 TAAAGCTCGTATTCTTTTTCT-AGT
1 TAAA-CTCTTATT-TTTTTCTCAGT
22529107 TAAACCTCTTA-TTTTTTCTCAGT
1 TAAA-CTCTTATTTTTTTCTCAGT
22529130 TAAACTCTTATT
1 TAAACTCTTATT
22529142 ATTTAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 13 0.42
23 9 0.29
24 9 0.29
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.51
Consensus pattern (23 bp):
TAAACTCTTATTTTTTTCTCAGT
Found at i:22529125 original size:22 final size:22
Alignment explanation
Indices: 22529097--22529141 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
22529087 GCTCGTATTC
22529097 TTTTTCT-AGTTAAACCTCTTAT
1 TTTTTCTCAGTTAAA-CTCTTAT
22529119 TTTTTCTCAGTTAAACTCTTAT
1 TTTTTCTCAGTTAAACTCTTAT
22529141 T
1 T
22529142 ATTTAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTTCTCAGTTAAACTCTTAT
Found at i:22537305 original size:23 final size:23
Alignment explanation
Indices: 22537279--22537328 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
22537269 TACTTTTCTG
22537279 GCACAATTATGTTTGCTTCTATA
1 GCACAATTATGTTTGCTTCTATA
22537302 GCACAATTATGTTTGCTTCTATA
1 GCACAATTATGTTTGCTTCTATA
22537325 GCAC
1 GCAC
22537329 GATAGTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (23 bp):
GCACAATTATGTTTGCTTCTATA
Found at i:22539564 original size:19 final size:20
Alignment explanation
Indices: 22539527--22539564 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
22539517 TTTATGGTTT
*
22539527 TAAATAATTTTTGGGTAAAA
1 TAAATAATTTTAGGGTAAAA
*
22539547 TAAAT-ATTTTAGGTTAAA
1 TAAATAATTTTAGGGTAAA
22539565 TTGGAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (20 bp):
TAAATAATTTTAGGGTAAAA
Found at i:22542763 original size:47 final size:48
Alignment explanation
Indices: 22542712--22542826 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 48
22542702 AAGGTGGAAG
* * * *
22542712 TATGTGGCAATTTATCTGTAA-TTTGGTGACTTGTCCATGATTTTGAT
1 TATGTGGCAGTTTATATGCAATTTTGGTGACTTGTCCATAATTTTGAT
* *
22542759 TATGTGGCAGTATATATGCAATTTTGGTGGCTTGTCCATAATTTTGAT
1 TATGTGGCAGTTTATATGCAATTTTGGTGACTTGTCCATAATTTTGAT
*
22542807 TATGTGGCAGTTTATTTGCA
1 TATGTGGCAGTTTATATGCA
22542827 TTATTGTGAC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 17 0.29
48 42 0.71
ACGTcount: A:0.22, C:0.10, G:0.23, T:0.45
Consensus pattern (48 bp):
TATGTGGCAGTTTATATGCAATTTTGGTGACTTGTCCATAATTTTGAT
Found at i:22542850 original size:48 final size:48
Alignment explanation
Indices: 22542733--22542850 Score: 123
Period size: 48 Copynumber: 2.5 Consensus size: 48
22542723 TTATCTGTAA
* **
22542733 TTTGGTGACTTGTCCATGATTTTGATTATGTGGCAGTATATATGCAAT
1 TTTGGTGACGTGTCCACAATTTTGATTATGTGGCAGTATATATGCAAT
* * * * *
22542781 TTTGGTGGCTTGTCCATAATTTTGATTATGTGGCAGTTTATTTGC-AT
1 TTTGGTGACGTGTCCACAATTTTGATTATGTGGCAGTATATATGCAAT
*
22542828 TATT-GTGACAGTGTTCACAATTT
1 T-TTGGTGAC-GTGTCCACAATTT
22542851 GGTGTTTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 7 0.12
48 53 0.88
ACGTcount: A:0.21, C:0.11, G:0.22, T:0.46
Consensus pattern (48 bp):
TTTGGTGACGTGTCCACAATTTTGATTATGTGGCAGTATATATGCAAT
Found at i:22548431 original size:29 final size:29
Alignment explanation
Indices: 22548389--22548457 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
22548379 TAACGGTCTT
22548389 GCTGACGTGGTCGTTAAGGGACTATCGAC
1 GCTGACGTGGTCGTTAAGGGACTATCGAC
22548418 GCTGACGTGGTCGTTAAGGGACTATCGAC
1 GCTGACGTGGTCGTTAAGGGACTATCGAC
22548447 GCTGACGTGGT
1 GCTGACGTGGT
22548458 GATTTTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.19, C:0.20, G:0.36, T:0.25
Consensus pattern (29 bp):
GCTGACGTGGTCGTTAAGGGACTATCGAC
Found at i:22548615 original size:30 final size:29
Alignment explanation
Indices: 22548542--22548621 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 29
22548532 CAAATGATTT
22548542 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATT-AAATTATTTTTTTAAAATA
* *
22548572 TAAAATTATTAAATTTTTTTTTTGAAATAA
1 TAAAATTATTAAATTATTTTTTTAAAAT-A
*
22548602 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATTATTTT
22548622 AATTTCCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 16 0.36
30 29 0.64
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TAAAATTATTAAATTATTTTTTTAAAATA
Found at i:22548657 original size:12 final size:12
Alignment explanation
Indices: 22548640--22548664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22548630 ATTTCATCAA
22548640 CTTCTTCTTCAT
1 CTTCTTCTTCAT
22548652 CTTCTTCTTCAT
1 CTTCTTCTTCAT
22548664 C
1 C
22548665 ATTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTCTTCTTCAT
Found at i:22549734 original size:10 final size:11
Alignment explanation
Indices: 22549693--22549731 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
22549683 ATAATTTTAT
22549693 ATTTTAAAAACTA
1 ATTTT-AAAA-TA
*
22549706 ATTTTAAATTA
1 ATTTTAAAATA
22549717 ATTTTAAAATA
1 ATTTTAAAATA
22549728 ATTT
1 ATTT
22549732 AAACAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 16 0.67
12 3 0.12
13 5 0.21
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:22551156 original size:17 final size:16
Alignment explanation
Indices: 22551099--22551157 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
22551089 AATGGGATAT
22551099 AATTTAA-TT-TT-TA
1 AATTTAATTTATTATA
*
22551112 AA-TTAGATTTATTTTA
1 AATTTA-ATTTATTATA
22551128 AATTTAAGTTTATTATA
1 AATTTAA-TTTATTATA
22551145 AATTTGAATTTAT
1 AATTT-AATTTAT
22551158 AAATTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 2 0.05
15 2 0.05
16 5 0.13
17 21 0.55
18 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
AATTTAATTTATTATA
Found at i:22552973 original size:30 final size:30
Alignment explanation
Indices: 22552939--22553044 Score: 119
Period size: 30 Copynumber: 3.6 Consensus size: 30
22552929 AACTGTCCAG
*
22552939 AAATTATATTTTGACCCCAAAACTTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTCTAA
* * *
22552969 AAATTACATTTTGACCTCGAAAC-TTCTAT
1 AAATTACATTTTGACCCCAAAACTTTCTAA
*
22552998 AAATTACCATTTT-ACCCCCAAACTTTCT-A
1 AAATTA-CATTTTGACCCCAAAACTTTCTAA
* *
22553027 AAATTCCATTTTAACCCC
1 AAATTACATTTTGACCCC
22553045 GATTTAACCA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 6 0.09
29 29 0.45
30 30 0.46
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTCTAA
Found at i:22553020 original size:29 final size:30
Alignment explanation
Indices: 22552946--22553044 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 30
22552936 CAGAAATTAT
*
22552946 ATTTTGACCCCAAAACTTTCTAAAAATTA-C
1 ATTTTGACCCCCAAACTTTCT-AAAATTACC
* *
22552976 ATTTTGACCTCGAAAC-TTCTATAAATTACC
1 ATTTTGACCCCCAAACTTTCTA-AAATTACC
22553006 ATTTT-ACCCCCAAACTTTCTAAAATT-CC
1 ATTTTGACCCCCAAACTTTCTAAAATTACC
*
22553034 ATTTTAACCCC
1 ATTTTGACCCC
22553045 GATTTAACCA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
28 8 0.13
29 28 0.46
30 25 0.41
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (30 bp):
ATTTTGACCCCCAAACTTTCTAAAATTACC
Found at i:22553058 original size:29 final size:28
Alignment explanation
Indices: 22553026--22553308 Score: 97
Period size: 29 Copynumber: 9.7 Consensus size: 28
22553016 CAAACTTTCT
22553026 AAAATT-CCATTTTAACCCCGATTTAACCA
1 AAAATTACCATTTT-ACCCCGATTT-ACCA
22553055 AAAATTACCATTTTACCCTCGAACTTT-CC-
1 AAAATTACCATTTTACCC-CG-A-TTTACCA
* *
22553084 AAAATT-TCATTTTTAACCCCAATTTCACCA
1 AAAATTACCA-TTTT-ACCCCGATTT-ACCA
* ** *
22553114 AAAATTATCATTTTACCCC--TAAACTCTTT
1 AAAATTACCATTTTACCCCGATTTAC-C--A
* *
22553143 AAAATT-CCATTTTTAACCTCGATTTCACAA
1 AAAATTACCA-TTTT-ACCCCGATTT-ACCA
**
22553173 AAAATTACCATTTTACCCTTAAACTTT-CC-
1 AAAATTACCATTTTACCC--CGA-TTTACCA
** *
22553202 AAAATT-CCATTTTAACATCGATTTTACAA
1 AAAATTACCATTTT-ACCCCGA-TTTACCA
*
22553231 AAAATTACCATTTTACCCCTAAACTTT-CC-
1 AAAATTACCATTTTACCCC--GA-TTTACCA
* * *
22553260 AAAATT-CTATTTTTAACCCCGGTTTCATCA
1 AAAATTACCA-TTTT-ACCCCGATTT-ACCA
22553290 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
22553309 TAAACTCTCC
Statistics
Matches: 189, Mismatches: 31, Indels: 68
0.66 0.11 0.24
Matches are distributed among these distances:
26 2 0.01
27 12 0.06
28 15 0.08
29 74 0.39
30 63 0.33
31 14 0.07
32 7 0.04
33 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCGATTTACCA
Found at i:22553127 original size:59 final size:59
Alignment explanation
Indices: 22552998--22553331 Score: 451
Period size: 59 Copynumber: 5.7 Consensus size: 59
22552988 AAACTTCTAT
* * *
22552998 AAATTACCATTTTACCCCCAAACTTTCTAAAATTCCA-TTTTAACCCCGATTTAACCAA
1 AAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAA
* * *
22553056 AAATTACCATTTTA-CCCTCGAACTTTCCAAAATTTCATTTTTAACCCCAATTTCACCAA
1 AAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAA
* * * *
22553115 AAATTATCATTTTACCCCTAAACTCTT-TAAAATTCCATTTTTAACCTCGATTTCACAAA
1 AAATTACCATTTTACCCCTAAACT-TTCCAAAATTCCATTTTTAACCCCGATTTCACCAA
* ** * *
22553174 AAATTACCATTTTACCCTTAAACTTTCCAAAATTCCA-TTTTAACATCGATTTTACAAA
1 AAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAA
* * *
22553232 AAATTACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGGTTTCATCAA
1 AAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAA
*
22553291 AAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTT
1 AAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTT
22553332 ACCCTGAACT
Statistics
Matches: 242, Mismatches: 28, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
57 3 0.01
58 85 0.35
59 148 0.61
60 6 0.02
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.37
Consensus pattern (59 bp):
AAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAA
Found at i:22553146 original size:117 final size:118
Alignment explanation
Indices: 22552998--22553331 Score: 460
Period size: 117 Copynumber: 2.8 Consensus size: 118
22552988 AAACTTCTAT
* *
22552998 AAATTACCATTTTACCCCCAAACTTTCTAAAATTCCA-TTTTAACCCCGATTTAACCAAAAATTA
1 AAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* * * *
22553062 CCATTTTACCCTCGAACTTTCCAAAATTTCATTTTTAACCCCAATTTCACCAA
66 CCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACACCAATTTCACAAA
* * *
22553115 AAATTATCATTTTACCCCTAAACTCTT-TAAAATTCCATTTTTAACCTCGATTTCACAAAAAATT
1 AAATTACCATTTTACCCCTAAACT-TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* * * *
22553179 ACCATTTTACCCTTAAACTTTCCAAAATTCCA-TTTTAACATCGATTTTACAAA
65 ACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACACCAATTTCACAAA
* * * *
22553232 AAATTACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGGTTTCATCAAAAATTA
1 AAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
*
22553297 CCATTTTACCC-CTAAACTCTCCAAAATTCCATTTT
66 CCATTTTACCCTC-AAACTTTCCAAAATTCCATTTT
22553332 ACCCTGAACT
Statistics
Matches: 190, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
116 2 0.01
117 131 0.69
118 57 0.30
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.37
Consensus pattern (118 bp):
AAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
CCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACACCAATTTCACAAA
Found at i:22553236 original size:176 final size:176
Alignment explanation
Indices: 22552998--22553331 Score: 510
Period size: 176 Copynumber: 1.9 Consensus size: 176
22552988 AAACTTCTAT
* * *
22552998 AAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTAACCCCGATTTAACCAAAAATTAC
1 AAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACACCGATTTAACAAAAAATTAC
* *
22553063 CATTTTA-CCCTCGAACTTTCCAAAATT-TCATTTTTAACCCCAATTTCACCAAAAATTATCATT
66 CATTTTACCCCT-AAACTTTCCAAAATTCT-ATTTTTAACCCCAATTTCACCAAAAATTACCATT
**
22553126 TTACCCCTAAACTCTTTAAAATTCCATTTTTAACCTCGATTTCACAAA
129 TTACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCACAAA
** * *
22553174 AAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTAACATCGATTTTACAAAAAATTAC
1 AAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACACCGATTTAACAAAAAATTAC
** *
22553239 CATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGGTTTCATCAAAAATTACCATTTT
66 CATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCAATTTCACCAAAAATTACCATTTT
22553304 ACCCCTAAACTCTCCAAAATTCCATTTT
131 ACCCCTAAACTCTCCAAAATTCCATTTT
22553332 ACCCTGAACT
Statistics
Matches: 142, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
176 137 0.96
177 5 0.04
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.37
Consensus pattern (176 bp):
AAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACACCGATTTAACAAAAAATTAC
CATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCAATTTCACCAAAAATTACCATTTT
ACCCCTAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCACAAA
Found at i:22553360 original size:86 final size:87
Alignment explanation
Indices: 22553055--22553393 Score: 252
Period size: 88 Copynumber: 3.9 Consensus size: 87
22553045 GATTTAACCA
* * *
22553055 AAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTTCATTTTTAACCCCAATTTCACCAAAAAT
1 AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CAAAAAT
* **
22553119 TATCATTTTACCCCTAAACTCTTT
64 TACCATTTTACCCCTAAACTCTCC
* ** **
22553143 AAAATT-CCATTTTTA-ACCTCGA-TTTCACAAAAAATTACCA-TTTT-ACCCTTAAACTTTC-C
1 AAAATTACCA-TTTTACCCCTAAACTTTC-C--AAAATT-CCATTTTTAACCC--CGA-TTTCAC
* * ** * * *
22553202 -AAAATT-CCATTTTA-ACATCGATTTTACAA
58 AAAAATTACCATTTTACCCCTAAACTCT-C-C
* *
22553231 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGGTTTCATCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CAAAAATT
22553296 ACCATTTTACCCCTAAACTCTCC
65 ACCATTTTACCCCTAAACTCTCC
* * * *
22553319 AAAATT-CCATTTTA-CCCTGAACTTTCTAAAATTCCATTTTTAACCCTGATTTCACCAAAATTA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACAAAAATTA
*
22553382 CCATTTTCCCCC
66 CCATTTTACCCC
22553394 GGGTATCCAA
Statistics
Matches: 196, Mismatches: 35, Indels: 43
0.72 0.13 0.16
Matches are distributed among these distances:
85 23 0.12
86 46 0.23
87 31 0.16
88 51 0.26
89 28 0.14
90 13 0.07
91 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (87 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACAAAAATTA
CCATTTTACCCCTAAACTCTCC
Found at i:22565621 original size:76 final size:76
Alignment explanation
Indices: 22565492--22566269 Score: 1240
Period size: 76 Copynumber: 10.3 Consensus size: 76
22565482 CAATCCAACG
*
22565492 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
22565557 TAAGAGCAAGA
66 TAAGAGCAAGA
* ** *
22565568 TCTTTTCCTATCAGCTTGAAATTGAAGTAGAGTTGGATAACAAGTATTTATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
*
22565633 TAAGAGGAAGA
66 TAAGAGCAAGA
* * * *
22565644 TCTTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTTTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
22565708 TAAGAGCAAGA
66 TAAGAGCAAGA
* * * * *
22565719 TCTTTTCCTATCCGCTTGGAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAATTTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
*
22565783 TAAGAACAAGA
66 TAAGAGCAAGA
*
22565794 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
*
22565859 TCAGAGCAAGA
66 TAAGAGCAAGA
* *
22565870 TCATTACCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
*
22565935 TCAGAGCAAGA
66 TAAGAGCAAGA
*
22565946 TCATTACCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
22566011 TAAGAGCAAGA
66 TAAGAGCAAGA
* * * *
22566022 TCTTTTCCTAT-CTGCTTGAGATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAATTTGAA
1 TCATTTCCTATCCT-CTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
22566085 GTAAGAACAAGA
65 GTAAGAGCAAGA
*
22566097 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
*
22566162 TAAGAACAAGA
66 TAAGAGCAAGA
*
22566173 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
*
22566238 TAAGAACAAGA
66 TAAGAGCAAGA
22566249 TCATTTCCTATCCTCTTGAAA
1 TCATTTCCTATCCTCTTGAAA
22566270 CAAGCGAGGC
Statistics
Matches: 661, Mismatches: 37, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
75 208 0.31
76 453 0.69
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
TAAGAGCAAGA
Found at i:22566076 original size:227 final size:228
Alignment explanation
Indices: 22565492--22566269 Score: 1242
Period size: 227 Copynumber: 3.4 Consensus size: 228
22565482 CAATCCAACG
*
22565492 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
* * * *
22565557 TAAGAGCAAGATCTTTTCCTATCAGCTTGAAATTGAAGTAGAGTTGGATAACAAGTATTTATCTC
66 TAAGAACAAGATCATTTCCTATCTGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
* * * *
22565622 TGAAATTGAAGTAAGAGGAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACAC
131 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAA
* *
22565686 GTCTTTATCTTTGAAATTGAAGTAAGAGCAAGA
196 GTCTTCATCTCTGAAATTGAAGTAAGAGCAAGA
* * * * *
22565719 TCTTTTCCTATCCGCTTGGAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAATTTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
*
22565783 TAAGAACAAGATCATTTCCTATCCT-CTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCT
66 TAAGAACAAGATCATTTCCTAT-CTGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCT
* *
22565847 CTGAAATTGAAGTCAGAGCAAGATCATTACCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA
130 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA
*
22565912 AGTCTTCATCTCTGAAATTGAAGTCAGAGCAAGA
195 AGTCTTCATCTCTGAAATTGAAGTAAGAGCAAGA
*
22565946 TCATTACCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
* * * *
22566011 TAAGAGCAAGATCTTTTCCTATCTGCTTGAGATTGAAGTAGAG-TGGATAACACGTCTTTATCTC
66 TAAGAACAAGATCATTTCCTATCTGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
* *
22566075 TGAATTTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAA
131 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAA
*
22566140 GTCTTCATCTCTGAAATTGAAGTAAGAACAAGA
196 GTCTTCATCTCTGAAATTGAAGTAAGAGCAAGA
*
22566173 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
22566238 TAAGAACAAGATCATTTCCTATCCT-CTTGAAA
66 TAAGAACAAGATCATTTCCTAT-CTGCTTGAAA
22566270 CAAGCGAGGC
Statistics
Matches: 504, Mismatches: 42, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
226 136 0.27
227 299 0.59
228 69 0.14
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (228 bp):
TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAG
TAAGAACAAGATCATTTCCTATCTGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAA
GTCTTCATCTCTGAAATTGAAGTAAGAGCAAGA
Found at i:22566134 original size:303 final size:302
Alignment explanation
Indices: 22565492--22566269 Score: 1360
Period size: 303 Copynumber: 2.6 Consensus size: 302
22565482 CAATCCAACG
* *
22565492 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
* ** * *
22565557 TAAGAGCAAGATCTTTTCCTATCAGCTTGAAATTGAAGTAGAGTTGGATAACAAGTATTTATCTC
66 TAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
* * * *
22565622 TGAAATTGAAGTAAGAGGAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAACACG
131 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACAAG
*
22565687 TCTTTATCTTTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCGCTTGGAATTGAAGTAGAGT
196 TCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCGCTTGGAATTGAAGTAGAGT
22565752 GGATAACACGTCTTTATCTCTGAATTTGAAGTAAGAACAAGA
261 GGATAACACGTCTTTATCTCTGAATTTGAAGTAAGAACAAGA
22565794 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
* *
22565859 TCAGAGCAAGATCATTACCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
66 TAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
* *
22565924 TGAAATTGAAGTCAGAGCAAGATCATTACCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAA
131 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACAA
*
22565989 GTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCTGCTT-GAGATTGAAGTAGA
195 GTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCGCTTGGA-ATTGAAGTAGA
22566053 GTGGATAACACGTCTTTATCTCTGAATTTGAAGTAAGAACAAGA
259 GTGGATAACACGTCTTTATCTCTGAATTTGAAGTAAGAACAAGA
22566097 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
1 TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
*
22566162 TAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
66 TAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
*
22566227 TGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAA
131 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAA
22566270 CAAGCGAGGC
Statistics
Matches: 451, Mismatches: 23, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
302 172 0.38
303 279 0.62
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (302 bp):
TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAG
TAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACAAG
TCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCGCTTGGAATTGAAGTAGAGT
GGATAACACGTCTTTATCTCTGAATTTGAAGTAAGAACAAGA
Found at i:22566822 original size:17 final size:16
Alignment explanation
Indices: 22566765--22566823 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
22566755 AATGGGATAT
22566765 AATTTAA-TT-TT-TA
1 AATTTAATTTATTATA
*
22566778 AA-TTAGATTTATTTTA
1 AATTTA-ATTTATTATA
22566794 AATTTAAGTTTATTATA
1 AATTTAA-TTTATTATA
22566811 AATTTGAATTTAT
1 AATTT-AATTTAT
22566824 AAATTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 2 0.05
15 2 0.05
16 5 0.13
17 21 0.55
18 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
AATTTAATTTATTATA
Found at i:22567568 original size:18 final size:18
Alignment explanation
Indices: 22567524--22567568 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
22567514 TAACAATAGC
22567524 ATTA-AATAATAATTAAT
1 ATTACAATAATAATTAAT
**
22567541 ATTTTAATAATAATTAAT
1 ATTACAATAATAATTAAT
*
22567559 ATTACGATAA
1 ATTACAATAA
22567569 AAAAATAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTACAATAATAATTAAT
Found at i:22568212 original size:15 final size:15
Alignment explanation
Indices: 22568192--22568233 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
22568182 CAACCCGTTT
22568192 GACCCGACCCGATCC
1 GACCCGACCCGATCC
*
22568207 GACCCGAACCGATCC
1 GACCCGACCCGATCC
22568222 GACCCGAACCCG
1 GACCCG-ACCCG
22568234 CTATGGGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.24, C:0.50, G:0.21, T:0.05
Consensus pattern (15 bp):
GACCCGACCCGATCC
Found at i:22568654 original size:30 final size:29
Alignment explanation
Indices: 22568611--22568938 Score: 145
Period size: 29 Copynumber: 11.2 Consensus size: 29
22568601 GTAGGTCCCT
* *
22568611 AAACTATCCAAAAATTATATTTTGACCCCA
1 AAACTTTCCAAAAATTACATTTT-ACCCCA
* *
22568641 AAACTTTCTAAAAATTACATTTTAACCCCG
1 AAACTTTCCAAAAATTACATTTT-ACCCCA
*
22568671 AAACTTAT--AAAAATTACCATTTTACCCCC
1 AAACTT-TCCAAAAATTA-CATTTTACCCCA
* *
22568700 AAACTTTCC-AAAATTTCATTTTTAACCTC-
1 AAACTTTCCAAAAATTACA-TTTT-ACCCCA
* *
22568729 --AGTTTCACAAAAAATTACCATTTTACCCCT
1 AAACTTTC-C-AAAAATTA-CATTTTACCCCA
* *
22568759 AAACTCTCC-AAAATTCCATTTTAACCCC-
1 AAACTTTCCAAAAATTACATTTT-ACCCCA
* *
22568787 -GA-TTTCACCAAAAATTACCATTTTACCCCT
1 AAACTTT--CCAAAAATTA-CATTTTACCCCA
* *
22568817 GAACTTTCC-AAAATTTCATTTTTAACCCC-
1 AAACTTTCCAAAAATTACA-TTTT-ACCCCA
*
22568846 -GA-TTTCACCAAAAATTACCATTTTACCCTC-
1 AAACTTT--CCAAAAATTA-CATTTTACCC-CA
* *
22568876 GAACTTTCC-AAAATTCCATTTTAACCCC-
1 AAACTTTCCAAAAATTACATTTT-ACCCCA
*
22568904 -AA-TTTCATCAAAAATTACCATTTTACCCCT
1 AAACTTTC--CAAAAATTA-CATTTTACCCCA
22568934 AAACT
1 AAACT
22568939 CTCTAAAATC
Statistics
Matches: 236, Mismatches: 24, Indels: 74
0.71 0.07 0.22
Matches are distributed among these distances:
26 6 0.03
27 11 0.05
28 23 0.10
29 92 0.39
30 83 0.35
31 10 0.04
32 11 0.05
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTTCCAAAAATTACATTTTACCCCA
Found at i:22568786 original size:117 final size:116
Alignment explanation
Indices: 22568619--22569048 Score: 516
Period size: 117 Copynumber: 3.7 Consensus size: 116
22568609 CTAAACTATC
* * * * *
22568619 CAAAAATTA-TATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCCGAAACTT-ATAAA
1 CAAAAATTACCATTTT-ACCCCTAAACTTTC-CAAAATTCCATTTTAACCCCG-AATTTCATAAA
*
22568682 AATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCTC-AGTTTCA
63 AATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGA-TTTCA
* *
22568736 CAAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTAACCCCG-ATTTCACCAAAA
1 C-AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGAATTTCA-TAAAA
* *
22568800 ATTACCATTTTACCCCTGAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA
64 ATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGATTTCA
*
22568853 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTAACCCC-AATTTCATCAAA
1 -CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTAACCCCGAATTTCAT-AAA
* * **
22568916 AATTACCATTTTACCCCTAAACTCTCTAAAATCCCA-TTTTAACCTCGATTTCA
63 AATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGATTTCA
** * **
22568969 TCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCG-ATTTCACCAAA
1 -CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCCGAATTTCATAAAA
*
22569033 ATTACCATTTTGCCCC
64 ATTACCATTTTACCCC
22569049 CGGGTATCCA
Statistics
Matches: 276, Mismatches: 25, Indels: 25
0.85 0.08 0.08
Matches are distributed among these distances:
115 3 0.01
116 73 0.26
117 173 0.63
118 22 0.08
119 5 0.02
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (116 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGAATTTCATAAAAAT
TACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGATTTCA
Found at i:22568793 original size:58 final size:58
Alignment explanation
Indices: 22568619--22569048 Score: 498
Period size: 58 Copynumber: 7.4 Consensus size: 58
22568609 CTAAACTATC
* * * * *
22568619 CAAAAATTA-TATTTTGACCCCAAAACTTTCTAAAAATTACA-TTTTAACCCCGAAACTT-A
1 CAAAAATTACCATTTT-ACCCCTAAACTTTC-CAAAATTCCATTTTTAACCCCG--ATTTCA
* * * *
22568678 TAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCTC-AGTTTCA
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCA
*
22568736 CAAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCA-TTTTAACCCCGATTTCA
1 C-AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
22568794 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA
1 -CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
22568853 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCA-TTTTAACCCCAATTTCA
1 -CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
22568911 TCAAAAATTACCATTTTACCCCTAAACTCTCTAAAATCCCA-TTTTAACCTCGATTTCA
1 -CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
** *
22568969 TCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
1 -CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
22569028 CCAAAATTACCATTTTGCCCC
1 CAAAAATTACCATTTTACCCC
22569049 CGGGTATCCA
Statistics
Matches: 327, Mismatches: 33, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
56 1 0.00
57 2 0.01
58 179 0.55
59 140 0.43
60 5 0.02
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:22569086 original size:175 final size:175
Alignment explanation
Indices: 22568679--22569087 Score: 565
Period size: 175 Copynumber: 2.3 Consensus size: 175
22568669 CGAAACTTAT
* * * * * *
22568679 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCTCAGTTTCA-CAAAAAA
1 AAAAATTACCATTTTACCCCCGAACTATCCAAAATTCCA-TTTCAACCCCAATTTCATC-AAAAA
*
22568743 TTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTAACCCCGATTTCACCAAAAATTACCAT
64 TTACCATTTTACCCCTAAACTCTCCAAAATCCCATTTTAACCCCGATTTCACCAAAAATTACCAT
*
22568808 TTTACCCCTGAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACC
129 TTTACCCCCGAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACC
* * *
22568855 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCCCAATTTCATCAAAAATT
1 AAAAATTACCATTTTACCCCCGAACTATCCAAAATTCCATTTCAACCCCAATTTCATCAAAAATT
* * *
22568920 ACCATTTTACCCCTAAACTCTCTAAAATCCCATTTTAACCTCGATTTCATCAAAAATTACCATTT
66 ACCATTTTACCCCTAAACTCTCCAAAATCCCATTTTAACCCCGATTTCACCAAAAATTACCATTT
22568985 TACCCCCGAACTTTCCAAAA-TTCTATTTTTAACCCCGATTTCACC
131 TACCCCCGAACTTTCCAAAATTTC-ATTTTTAACCCCGATTTCACC
* ** * * *
22569030 -AAAATTACCATTTTGCCCCCG-GGTATCCAAAAGTCTCGATTTCATCCCCGATTTCATC
1 AAAAATTACCATTTTACCCCCGAACTATCCAAAA-T-TCCATTTCAACCCCAATTTCATC
22569088 GTTTCTTCTT
Statistics
Matches: 210, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
173 8 0.04
174 23 0.11
175 142 0.68
176 37 0.18
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.34
Consensus pattern (175 bp):
AAAAATTACCATTTTACCCCCGAACTATCCAAAATTCCATTTCAACCCCAATTTCATCAAAAATT
ACCATTTTACCCCTAAACTCTCCAAAATCCCATTTTAACCCCGATTTCACCAAAAATTACCATTT
TACCCCCGAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACC
Found at i:22570798 original size:20 final size:22
Alignment explanation
Indices: 22570752--22570801 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
22570742 CTCTTAACCA
*
22570752 TTCTTTCTTTTCTCCTTTTCCTC
1 TTCTTT-TTTTCTCCTTTTCATC
*
22570775 TTCTTTTTTT-TTCTTTTCAT-
1 TTCTTTTTTTCTCCTTTTCATC
22570795 TTCTTTT
1 TTCTTTT
22570802 GATTAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.28
21 8 0.32
22 4 0.16
23 6 0.24
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTTTTTCTCCTTTTCATC
Found at i:22571103 original size:16 final size:16
Alignment explanation
Indices: 22571078--22571112 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22571068 ACTCATCTTT
*
22571078 AGTATCTAAAAACGTA
1 AGTATCTAAAAAAGTA
*
22571094 AGTATTTAAAAAAGTA
1 AGTATCTAAAAAAGTA
22571110 AGT
1 AGT
22571113 TCAGTTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (16 bp):
AGTATCTAAAAAAGTA
Found at i:22572828 original size:11 final size:11
Alignment explanation
Indices: 22572814--22572858 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 11
22572804 GATAATCACT
22572814 TTAATATTAAA
1 TTAATATTAAA
22572825 TTAATA--AAA
1 TTAATATTAAA
22572834 TT-ATATTAAA
1 TTAATATTAAA
*
22572844 ATAAGTATTAAA
1 TTAA-TATTAAA
22572856 TTA
1 TTA
22572859 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
8 3 0.11
9 5 0.18
10 4 0.14
11 7 0.25
12 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:22587369 original size:52 final size:52
Alignment explanation
Indices: 22587309--22587411 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
22587299 GGCAACAAAA
22587309 TGAACACACGTCAACATAAGCATATGAAACCAAAACTGACAACGGGGACGAT
1 TGAACACACGTCAACATAAGCATATGAAACCAAAACTGACAACGGGGACGAT
* *
22587361 TGAACACACGTCAGCATAAGCATATGAAACCAAAAGTGACAACGGGGACGA
1 TGAACACACGTCAACATAAGCATATGAAACCAAAACTGACAACGGGGACGA
22587412 GAGATAATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (52 bp):
TGAACACACGTCAACATAAGCATATGAAACCAAAACTGACAACGGGGACGAT
Found at i:22595551 original size:26 final size:26
Alignment explanation
Indices: 22595515--22595568 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
22595505 AATTTGATAC
22595515 ATACCCTCTTAGCACTTGGAGATGTG
1 ATACCCTCTTAGCACTTGGAGATGTG
22595541 ATACCCTCTTAGCACTTGGAGATGTG
1 ATACCCTCTTAGCACTTGGAGATGTG
22595567 AT
1 AT
22595569 GAGATGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (26 bp):
ATACCCTCTTAGCACTTGGAGATGTG
Found at i:22597928 original size:30 final size:31
Alignment explanation
Indices: 22597877--22597935 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
22597867 CACCCTTAAA
**
22597877 ATATTTACACTATTGACCCTTCAAATTTTTC
1 ATATTTACACTATCAACCCTTCAAATTTTTC
22597908 ATATTTACACT-TCAACCCTTCAAATTTT
1 ATATTTACACTATCAACCCTTCAAATTTT
22597936 AAGTATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.44
Consensus pattern (31 bp):
ATATTTACACTATCAACCCTTCAAATTTTTC
Found at i:22597943 original size:30 final size:31
Alignment explanation
Indices: 22597876--22597945 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
22597866 ACACCCTTAA
**
22597876 AATATTTACACTATTGACCCTTCAAATTTTT
1 AATATTTACACTATCAACCCTTCAAATTTTT
*
22597907 CATATTTACACT-TCAACCCTTCAAA-TTTT
1 AATATTTACACTATCAACCCTTCAAATTTTT
22597936 AAGTATTTAC
1 AA-TATTTAC
22597946 TCTAGGGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.15
30 18 0.53
31 11 0.32
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (31 bp):
AATATTTACACTATCAACCCTTCAAATTTTT
Found at i:22612346 original size:78 final size:78
Alignment explanation
Indices: 22612261--22612456 Score: 196
Period size: 78 Copynumber: 2.5 Consensus size: 78
22612251 CAGATTGAAG
* * * * *
22612261 ATTCGATCTCTTACCCCGAGTTTGGGGTAGATCACTATTAACCAATCTGTTACCCTAAGCCTGAG
1 ATTCGATCTCTTACCCCGAGCTTGGGGTAGATCACTATTAACAAATCTCTTACCCCAAGCATGAG
22612326 GCAGATTACAGCC
66 GCAGATTACAGCC
*** * * ** * * *
22612339 ATTCGATCT-TCTACCCCGAGCCAAGGGTAGATCACCATCAGTAAATCTCTTACCCCGATCATGG
1 ATTCGATCTCT-TACCCCGAGCTTGGGGTAGATCACTATTAACAAATCTCTTACCCCAAGCATGA
*
22612403 GGCAGATTACAGCT
65 GGCAGATTACAGCC
* * **
22612417 ATTTGATCTCTTACCCTGAGCTTGGGCCAGATCACTATTA
1 ATTCGATCTCTTACCCCGAGCTTGGGGTAGATCACTATTA
22612457 TTTGATCTTT
Statistics
Matches: 91, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
77 1 0.01
78 89 0.98
79 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (78 bp):
ATTCGATCTCTTACCCCGAGCTTGGGGTAGATCACTATTAACAAATCTCTTACCCCAAGCATGAG
GCAGATTACAGCC
Found at i:22612426 original size:39 final size:39
Alignment explanation
Indices: 22612383--22612828 Score: 185
Period size: 39 Copynumber: 11.7 Consensus size: 39
22612373 CCATCAGTAA
* *
22612383 ATCTCTTACCCCGATCATGGGGCAGATTACAGCTATTTG
1 ATCTCTTACCCCGAGCATGGGGCAGATTACAGCTATTCG
* * * * * *
22612422 ATCTCTTACCCTGAGCTTGGGCCAGATCACTA-TTATTTG
1 ATCTCTTACCCCGAGCATGGGGCAGATTAC-AGCTATTCG
* * * * * * *
22612461 ATCTTTTACCCCGAACTTGGGGCAGATCATCATC-A-GCAA
1 ATCTCTTACCCCGAGCATGGGGCAGATTA-CAGCTATTC-G
* * * *
22612500 ATCTTTTACCCCGATCATGGGGTAGATTACAGCCATTCG
1 ATCTCTTACCCCGAGCATGGGGCAGATTACAGCTATTCG
* ** * * * * * **
22612539 ATCTCTTACCCCGAGCCTAAGGTAAATCATCATC-AGTAA
1 ATCTCTTACCCCGAGCATGGGGCAGATTA-CAGCTATTCG
* *
22612578 ATCTCTTACCCCGAG-AT----CACCA-T-CAACTA----
1 ATCTCTTACCCCGAGCATGGGGCA-GATTACAGCTATTCG
* * *
22612607 ATCTCCTACCCCGATCATGGGGCAGATTGCAGCTACTT-G
1 ATCTCTTACCCCGAGCATGGGGCAGATTACAGCTA-TTCG
* * * * **
22612646 ATCTCTTACCCCGAGCTTGGGGCAGATGATCATC-AGTAA
1 ATCTCTTACCCCGAGCATGGGGCAGATTA-CAGCTATTCG
* * * *
22612685 ATCTCTTACCCCGAGTC-TGGGGCAGATTGCAACCATCCG
1 ATCTCTTACCCCGAG-CATGGGGCAGATTACAGCTATTCG
* * *
22612724 ATCTCTTACACTGAGCATGGGGCAGATTGCAGCTATTCG
1 ATCTCTTACCCCGAGCATGGGGCAGATTACAGCTATTCG
* * * * * *
22612763 ATCTCTTACCCCGAGCCTAGGGTAGATCACCATC-A-ACG
1 ATCTCTTACCCCGAGCATGGGGCAGATTA-CAGCTATTCG
*
22612801 ATCTCTTACCCCGATCATGGGGCAGATT
1 ATCTCTTACCCCGAGCATGGGGCAGATT
22612829 GTAGTCATTC
Statistics
Matches: 306, Mismatches: 75, Indels: 53
0.71 0.17 0.12
Matches are distributed among these distances:
29 13 0.04
30 2 0.01
32 3 0.01
33 2 0.01
34 4 0.01
35 6 0.02
38 34 0.11
39 229 0.75
40 13 0.04
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCATGGGGCAGATTACAGCTATTCG
Found at i:22612472 original size:117 final size:117
Alignment explanation
Indices: 22612343--22612554 Score: 307
Period size: 117 Copynumber: 1.8 Consensus size: 117
22612333 ACAGCCATTC
* * *
22612343 GATCTTCTACCCCGAGCCAAGGGTAGATCACCATCAGTAAATCTCTTACCCCGATCATGGGGCAG
1 GATCTTCTACCCCGAACCAAGGGCAGATCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAG
* * *
22612408 ATTACAGCTATTTGATCTCTTACCCTGAGCTTGGGCCAGATCACTATTATTT
66 ATTACAGCCATTCGATCTCTTACCCCGAGCTTGGGCCAGATCACTATTATTT
* *** * * *
22612460 GATCTTTTACCCCGAACTTGGGGCAGATCATCATCAGCAAATCTTTTACCCCGATCATGGGGTAG
1 GATCTTCTACCCCGAACCAAGGGCAGATCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAG
22612525 ATTACAGCCATTCGATCTCTTACCCCGAGC
66 ATTACAGCCATTCGATCTCTTACCCCGAGC
22612555 CTAAGGTAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
117 82 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (117 bp):
GATCTTCTACCCCGAACCAAGGGCAGATCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAG
ATTACAGCCATTCGATCTCTTACCCCGAGCTTGGGCCAGATCACTATTATTT
Found at i:22612678 original size:107 final size:107
Alignment explanation
Indices: 22612506--22612699 Score: 291
Period size: 107 Copynumber: 1.8 Consensus size: 107
22612496 GCAAATCTTT
* *
22612506 TACCCCGATCATGGGGTAGATTACAGCCATTCGATCTCTTACCCCGAGCCTAAGGTAAATCATCA
1 TACCCCGATCATGGGGCAGATTACAGCCATTCGATCTCTTACCCCGAGCCTAAGGCAAATCATCA
22612571 TCAGTAAATCTCTTACCCCGAGATCACCATCAACTAATCTCC
66 TCAGTAAATCTCTTACCCCGAGATCACCATCAACTAATCTCC
* * * ** * *
22612613 TACCCCGATCATGGGGCAGATTGCAGCTACTT-GATCTCTTACCCCGAGCTTGGGGCAGATGATC
1 TACCCCGATCATGGGGCAGATTACAGCCA-TTCGATCTCTTACCCCGAGCCTAAGGCAAATCATC
22612677 ATCAGTAAATCTCTTACCCCGAG
65 ATCAGTAAATCTCTTACCCCGAG
22612700 TCTGGGGCAG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 75 0.97
108 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (107 bp):
TACCCCGATCATGGGGCAGATTACAGCCATTCGATCTCTTACCCCGAGCCTAAGGCAAATCATCA
TCAGTAAATCTCTTACCCCGAGATCACCATCAACTAATCTCC
Found at i:22612696 original size:224 final size:223
Alignment explanation
Indices: 22612367--22612814 Score: 541
Period size: 224 Copynumber: 2.0 Consensus size: 223
22612357 AGCCAAGGGT
* * *
22612367 AGATCACCATCAGTAAATCTCTTACCCCGATCATGGGGCAGATTACAGCTATTTGATCTCTTACC
1 AGATCACCATCACTAAATCTCCTACCCCGATCATGGGGCAGATTACAGCTACTTGATCTCTTACC
* * * ** * *
22612432 CTGAGCTTGGGCCAGATCACTATTATTTGATCTTTTACCCCGAACT-TGGGGCAGA-T-C-ATCA
66 CCGAGCTTGGGCCAGATCACTATCAGTAAATCTCTTACCCCG-ACTCTGGGGCAGATTGCAACCA
* * * *
22612493 TCAGCAAATCTTTTACCCCGATCATGGGGTAGATTACAGCCATTCGATCTCTTACCCCGAGCCTA
130 TC--C-AATCTCTTACACCGAGCATGGGGCAGATTACAGCCATTCGATCTCTTACCCCGAGCCTA
*
22612558 AGGTAAATCATCATCAGTA-AATCTCTTACCCCG
192 AGGTAAATCACCATCA--ACAATCTCTTACCCCG
*
22612591 AGATCACCATCAACT-AATCTCCTACCCCGATCATGGGGCAGATTGCAGCTACTTGATCTCTTAC
1 AGATCACCATC-ACTAAATCTCCTACCCCGATCATGGGGCAGATTACAGCTACTTGATCTCTTAC
* * *
22612655 CCCGAGCTTGGGGCAGATGA-TCATCAGTAAATCTCTTACCCCGAGTCTGGGGCAGATTGCAACC
65 CCCGAGCTTGGGCCAGATCACT-ATCAGTAAATCTCTTACCCCGACTCTGGGGCAGATTGCAACC
* * * * *
22612719 ATCCGATCTCTTACACTGAGCATGGGGCAGATTGCAGCTATTCGATCTCTTACCCCGAGCCTAGG
129 ATCCAATCTCTTACACCGAGCATGGGGCAGATTACAGCCATTCGATCTCTTACCCCGAGCCTAAG
* *
22612784 GTAGATCACCATCAACGATCTCTTACCCCG
194 GTAAATCACCATCAACAATCTCTTACCCCG
22612814 A
1 A
22612815 TCATGGGGCA
Statistics
Matches: 191, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
222 1 0.01
223 17 0.09
224 163 0.85
225 4 0.02
226 1 0.01
227 5 0.03
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (223 bp):
AGATCACCATCACTAAATCTCCTACCCCGATCATGGGGCAGATTACAGCTACTTGATCTCTTACC
CCGAGCTTGGGCCAGATCACTATCAGTAAATCTCTTACCCCGACTCTGGGGCAGATTGCAACCAT
CCAATCTCTTACACCGAGCATGGGGCAGATTACAGCCATTCGATCTCTTACCCCGAGCCTAAGGT
AAATCACCATCAACAATCTCTTACCCCG
Found at i:22612828 original size:77 final size:78
Alignment explanation
Indices: 22612685--22612829 Score: 197
Period size: 77 Copynumber: 1.9 Consensus size: 78
22612675 TCATCAGTAA
* * *
22612685 ATCTCTTACCCCGAGTCTGGGGCAGATTGCAACCATCCGATCTCTTACACTGAGCATGGGGCAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATCCGATCTCTTACACCGAGCATGGGGCAGA
22612750 TTGCAGCTATTCG
66 TTGCAGCTATTCG
* * *
22612763 ATCTCTTACCCCGAGCCTAGGGTAGA-T-C-ACCATCAACGATCTCTTACCCCGATCATGGGGCA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATC--CGATCTCTTACACCGAGCATGGGGCA
22612825 GATTG
64 GATTG
22612830 TAGTCATTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
75 6 0.10
76 1 0.02
77 29 0.49
78 23 0.39
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATCCGATCTCTTACACCGAGCATGGGGCAGA
TTGCAGCTATTCG
Found at i:22612839 original size:77 final size:78
Alignment explanation
Indices: 22612645--22612840 Score: 206
Period size: 78 Copynumber: 2.5 Consensus size: 78
22612635 GCAGCTACTT
* * ** * *
22612645 GATCTCTTACCCCGAGCTTGGGGCAGA-TGATCA-TCAGTAAATCTCTTACCCCGAGTCTGGGGC
1 GATCTCTTACCCCGAGCATGGGGCAGATTG-T-AGTCATTCGATCTCTTACCCCGAGCCTAGGGC
22612708 AGATTGCAACCATCC
64 AGATTGCAACCATCC
* * * *
22612723 GATCTCTTACACTGAGCATGGGGCAGATTGCAG-CTATTCGATCTCTTACCCCGAGCCTAGGGTA
1 GATCTCTTACCCCGAGCATGGGGCAGATTGTAGTC-ATTCGATCTCTTACCCCGAGCCTAGGGCA
22612787 GA-T-C-ACCATCAAC
65 GATTGCAACCATC--C
*
22612800 GATCTCTTACCCCGATCATGGGGCAGATTGTAGTCATTCGA
1 GATCTCTTACCCCGAGCATGGGGCAGATTGTAGTCATTCGA
22612841 AGCAATAAAG
Statistics
Matches: 98, Mismatches: 14, Indels: 13
0.78 0.11 0.10
Matches are distributed among these distances:
75 6 0.06
76 1 0.01
77 39 0.40
78 50 0.51
79 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (78 bp):
GATCTCTTACCCCGAGCATGGGGCAGATTGTAGTCATTCGATCTCTTACCCCGAGCCTAGGGCAG
ATTGCAACCATCC
Found at i:22615093 original size:30 final size:30
Alignment explanation
Indices: 22615020--22615340 Score: 279
Period size: 30 Copynumber: 11.0 Consensus size: 30
22615010 GAAGGTCCTT
* *
22615020 GAACTGTC-CAAAAATCATA-TTTTGCCC-C
1 GAACT-TCTCAAAAATCACATTTTTACCCTC
** *
22615048 GAACTT-TTGAAAATCACATGTTTACCCTC
1 GAACTTCTCAAAAATCACATTTTTACCCTC
*
22615077 GAACTTCTCAAAAATCATATTTTTACCC-C
1 GAACTTCTCAAAAATCACATTTTTACCCTC
* **
22615106 TGAACTT-TCAAAAATTATGTTTTTACCCTC
1 -GAACTTCTCAAAAATCACATTTTTACCCTC
* *
22615136 AAACTTTTCAAAAAAT-ACATTTTTACCCTC
1 GAACTTCTC-AAAAATCACATTTTTACCCTC
*
22615166 GATCTTC-CAAAAATCACATTTTTACCCTC
1 GAACTTCTCAAAAATCACATTTTTACCCTC
* *
22615195 GAACTTCTCAAAAATCACATTTTTGCCCCC
1 GAACTTCTCAAAAATCACATTTTTACCCTC
* * *
22615225 GAACTTCTCAAAAATTATATTTTTGCCCTC
1 GAACTTCTCAAAAATCACATTTTTACCCTC
*
22615255 AAACTTC-CAAAAATCACATTTTTACCC-C
1 GAACTTCTCAAAAATCACATTTTTACCCTC
* * * * *
22615283 GAA-TTTTGAAAAATGACATTTTAACCCCTA
1 GAACTTCTCAAAAATCACATTTTTA-CCCTC
* * * *
22615313 AAACTT-TCCAAAATTACATTTTAACCCT
1 GAACTTCTCAAAAATCACATTTTTACCCT
22615341 AAACTCTCTA
Statistics
Matches: 242, Mismatches: 37, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
27 11 0.05
28 34 0.14
29 77 0.32
30 112 0.46
31 8 0.03
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (30 bp):
GAACTTCTCAAAAATCACATTTTTACCCTC
Found at i:22615141 original size:59 final size:58
Alignment explanation
Indices: 22615028--22615339 Score: 308
Period size: 59 Copynumber: 5.3 Consensus size: 58
22615018 TTGAACTGTC
* * ** * *
22615028 CAAAAATCATA-TTTTGCCCCGAACTTTTGAAAATCACATGTTTACCCTCGAACTTCT
1 CAAAAATCACATTTTTACCCCGAACTTTCAAAAATCACATTTTTACCCTCAAACTTCT
* * ** *
22615085 CAAAAATCATATTTTTACCCCTGAACTTTCAAAAATTATGTTTTTACCCTCAAACTTTT
1 CAAAAATCACATTTTTACCCC-GAACTTTCAAAAATCACATTTTTACCCTCAAACTTCT
* * *
22615144 CAAAAAAT-ACATTTTTACCCTCGATCTTCCAAAAATCACATTTTTACCCTCGAACTTCT
1 C-AAAAATCACATTTTTACCC-CGAACTTTCAAAAATCACATTTTTACCCTCAAACTTCT
* * * *
22615203 CAAAAATCACATTTTTGCCCCCGAACTTCTCAAAAATTATATTTTTGCCCTCAAACTTC-
1 CAAAAATCACATTTTT-ACCCCGAACTT-TCAAAAATCACATTTTTACCCTCAAACTTCT
* * * * *
22615262 CAAAAATCACATTTTTACCCCGAATTTTGAAAAATGACATTTTAACCCCTAAAACTT-T
1 CAAAAATCACATTTTTACCCCGAACTTTCAAAAATCACATTTTTA-CCCTCAAACTTCT
* * *
22615320 CCAAAATTACATTTTAACCC
1 CAAAAATCACATTTTTACCC
22615340 TAAACTCTCT
Statistics
Matches: 211, Mismatches: 35, Indels: 17
0.80 0.13 0.06
Matches are distributed among these distances:
57 24 0.11
58 50 0.24
59 102 0.48
60 35 0.17
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.35
Consensus pattern (58 bp):
CAAAAATCACATTTTTACCCCGAACTTTCAAAAATCACATTTTTACCCTCAAACTTCT
Done.