Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 166 of 186
Found at i:55286441 original size:28 final size:28
Alignment explanation
Indices: 55286409--55286536 Score: 157
Period size: 28 Copynumber: 4.5 Consensus size: 28
55286399 ATAGTAAGTC
* *
55286409 CGCACACTTAGTGTTATATAATAAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
55286437 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
*
55286466 CACACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
55286494 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
55286523 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55286537 AAATCTCATG
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
28 43 0.50
29 43 0.50
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55286471 original size:29 final size:29
Alignment explanation
Indices: 55286409--55286536 Score: 154
Period size: 29 Copynumber: 4.5 Consensus size: 29
55286399 ATAGTAAGTC
*
55286409 CGCACACTTAGTG-TTATATAATAAAACT
1 CGCACACTTAGTGCTTATATAATCAAACT
*
55286437 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTATATAATCAAACT
*
55286466 CACACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTATATAATCAAACT
* ** * *
55286494 TGCACACTTAGTGC-TATGCAATTTAAACC
1 CGCACACTTAGTGCTTATATAA-TCAAACT
55286523 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55286537 AAATCTCATG
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 43 0.49
29 44 0.51
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTTATATAATCAAACT
Found at i:55286529 original size:57 final size:57
Alignment explanation
Indices: 55286408--55286536 Score: 170
Period size: 57 Copynumber: 2.3 Consensus size: 57
55286398 TATAGTAAGT
*
55286408 CCGCACACTTAGTGTTATATAATAAAACTCGCACACTTAGTGCTTACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATAAAACTCGCACACTTAGTGCTTACATAATCAAAC
* * * * * * *
55286465 TCACACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCA-ATTTAAAC
1 CCGCACACTTAGTGCTATATAATAAAACTCGCACACTTAGTGCT-TACATAATCAAAC
55286522 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
55286537 AAATCTCATG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
57 58 0.95
58 3 0.05
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATAAAACTCGCACACTTAGTGCTTACATAATCAAAC
Found at i:55294009 original size:28 final size:28
Alignment explanation
Indices: 55293977--55294075 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
55293967 ATAGTAAGTC
*
55293977 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
55294005 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
55294033 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
55294062 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55294076 AAATCTCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 45 0.71
29 18 0.29
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55295858 original size:28 final size:27
Alignment explanation
Indices: 55295795--55295866 Score: 117
Period size: 27 Copynumber: 2.6 Consensus size: 27
55295785 ATATTAAGTC
*
55295795 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
55295822 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
*
55295850 TGCACACTTAGTGCTAT
1 CGCACACTTAGTGCTAT
55295867 GCAATTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 22 0.52
28 20 0.48
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:55295887 original size:29 final size:28
Alignment explanation
Indices: 55295794--55295892 Score: 110
Period size: 27 Copynumber: 3.5 Consensus size: 28
55295784 TATATTAAGT
* *
55295794 CCGCACACTCAGTGCTATATAATC-AAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* *
55295821 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
** * *
55295849 TTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATACAA-TCAAAC
55295878 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
55295893 CAATCTCATG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.35
28 22 0.35
29 18 0.29
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:55300950 original size:13 final size:13
Alignment explanation
Indices: 55300927--55300983 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
55300917 CTATTTCAAA
55300927 AAAAAATAAAAGAT
1 AAAAAA-AAAAGAT
*
55300941 AAAAAGAAAA-AT
1 AAAAAAAAAAGAT
55300953 AAAAATAAAAAAGAT
1 -AAAA-AAAAAAGAT
55300968 AAAAAAAAAAGA-
1 AAAAAAAAAAGAT
55300980 AAAA
1 AAAA
55300984 TAGAGAGGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 6 0.16
13 16 0.42
14 14 0.37
15 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAAGAT
Found at i:55300952 original size:19 final size:17
Alignment explanation
Indices: 55300924--55300985 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 17
55300914 CTTCTATTTC
55300924 AAAAAAAAATAAAAGATA
1 AAAAAAAAATAAAA-ATA
55300942 AAAAGAAAAATAAAAAT-
1 AAAA-AAAAATAAAAATA
*
55300959 -AAAAAAGATAAAAA-A
1 AAAAAAAAATAAAAATA
55300974 AAAAGAAAAATA
1 AAAA-AAAAATA
55300986 GAGAGGCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 10 0.26
16 6 0.16
17 6 0.16
18 6 0.16
19 10 0.26
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (17 bp):
AAAAAAAAATAAAAATA
Found at i:55300964 original size:27 final size:27
Alignment explanation
Indices: 55300925--55300985 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
55300915 TTCTATTTCA
* *
55300925 AAAAAAAATAAAAGATAAAAAGAAAAAT
1 AAAAATAATAAAAGATAAAAA-AAAAAG
55300953 AAAAATAA-AAAAGATAAAAAAAAAAG
1 AAAAATAATAAAAGATAAAAAAAAAAG
55300979 AAAAATA
1 AAAAATA
55300986 GAGAGGCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 12 0.39
27 12 0.39
28 7 0.23
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.10
Consensus pattern (27 bp):
AAAAATAATAAAAGATAAAAAAAAAAG
Found at i:55301686 original size:46 final size:46
Alignment explanation
Indices: 55301636--55301727 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
55301626 ATTTGAAGAA
55301636 TGATACAAGCCTACAGGCTGAGCAGGAAAGATACTTTGAGAGAAGT
1 TGATACAAGCCTACAGGCTGAGCAGGAAAGATACTTTGAGAGAAGT
*
55301682 TGATACAAGCCTACAGGCTGAGCAGGAATGATACTTTGAGAGAAGT
1 TGATACAAGCCTACAGGCTGAGCAGGAAAGATACTTTGAGAGAAGT
55301728 AAAGATAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (46 bp):
TGATACAAGCCTACAGGCTGAGCAGGAAAGATACTTTGAGAGAAGT
Found at i:55301981 original size:44 final size:43
Alignment explanation
Indices: 55301907--55302270 Score: 247
Period size: 44 Copynumber: 8.3 Consensus size: 43
55301897 GGGACAATGT
* *
55301907 AGATCAAAGA-AACAAGATTTGGCATCCCTGTGTTTATAGGGAAC
1 AGATCGAAGATAAC-AGATCTGGCAT-CCTGTGTTTATAGGGAAC
* * * *
55301951 AGATCGAAGATAACAGATCTGACACTCCTGTGCTTACAGCGAAGC
1 AGATCGAAGATAACAGATCTGGCA-TCCTGTGTTTATAGGGAA-C
* ** *
55301996 AGATCGAGGATTTCAG--CATGGCATCCCTGTGTTTATAGGGAAT
1 AGATCGAAGATAACAGATC-TGGCAT-CCTGTGTTTATAGGGAAC
* * * * *
55302039 A-AGTTGAAGATAGCAAATTTGGCATCACTGTGTTTATAGGGTAC
1 AGA-TCGAAGATAACAGATCTGGCATC-CTGTGTTTATAGGGAAC
* * ** * *
55302083 AGATCGAAGATAACAGATCTGACACTCCTATACTTACAGCGAAGC
1 AGATCGAAGATAACAGATCTGGCA-TCCTGTGTTTATAGGGAA-C
* ***
55302128 AGATCGAGGATTTTAG--CATGGCATCCCTGTGTTTATAGGGAAC
1 AGATCGAAGATAACAGATC-TGGCAT-CCTGTGTTTATAGGGAAC
* * *
55302171 A-AGTTGAAGATAGCAGATTTGGCATCTCTGTGTTTATAGGGAAC
1 AGA-TCGAAGATAACAGATCTGGCATC-CTGTGTTTATAGGGAAC
* * * *
55302215 AGATCGAAGATAACAGATCTGACACTCCTGTGCTTACAGCGAAGC
1 AGATCGAAGATAACAGATCTGGCA-TCCTGTGTTTATAGGGAA-C
55302260 AGATCGAAGAT
1 AGATCGAAGAT
55302271 TTTAGCATGG
Statistics
Matches: 243, Mismatches: 56, Indels: 41
0.71 0.16 0.12
Matches are distributed among these distances:
42 2 0.01
43 25 0.10
44 167 0.69
45 49 0.20
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
AGATCGAAGATAACAGATCTGGCATCCTGTGTTTATAGGGAAC
Found at i:55302245 original size:88 final size:87
Alignment explanation
Indices: 55301907--55302320 Score: 274
Period size: 88 Copynumber: 4.7 Consensus size: 87
55301897 GGGACAATGT
*
55301907 AGATCAAAGA-AACAAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCT
1 AGATCGAAGATAAC-AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCT
* * *
55301971 GACACTCCTGTGCTTACAGCGAAGC
65 GACA-TCCTGTGTTTATAGGGAA-C
* ** * * * * *
55301996 AGATCGAGGATTTCAGCA--TGGCATCCCTGTGTTTATAGGGAATA-AGTTGAAGATAGCAAATT
1 AGATCGAAGATAACAG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAACAGATC
* *
55302058 TGGCATCACTGTGTTTATAGGGTAC
64 TGACATC-CTGTGTTTATAGGGAAC
* * * ** * * * ***
55302083 AGATCGAAGATAACAGATCTGACA-CTCCTATACTTACAGCGAAGCAGATCGAGGATTTTAG--C
1 AGATCGAAGATAACAGATTTGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAACAGATC
*
55302145 ATGGCATCCCTGTGTTTATAGGGAAC
64 -TGACAT-CCTGTGTTTATAGGGAAC
* * *
55302171 A-AGTTGAAGATAGCAGATTTGGCATCTCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCT
1 AGA-TCGAAGATAACAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCT
* * *
55302235 GACACTCCTGTGCTTACAGCGAAGC
65 GACA-TCCTGTGTTTATAGGGAA-C
*** * * *
55302260 AGATCGAAGATTTTAGCA--TGGTATCCCTGTGTTTATAGGGAACA-AGTTGAAGACAACAGAT
1 AGATCGAAGATAACAG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAACAGAT
55302321 TCAGTATCTC
Statistics
Matches: 247, Mismatches: 58, Indels: 41
0.71 0.17 0.12
Matches are distributed among these distances:
86 1 0.00
87 33 0.13
88 175 0.71
89 33 0.13
90 5 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (87 bp):
AGATCGAAGATAACAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTG
ACATCCTGTGTTTATAGGGAAC
Found at i:55302333 original size:132 final size:132
Alignment explanation
Indices: 55301921--55302321 Score: 694
Period size: 132 Copynumber: 3.0 Consensus size: 132
55301911 CAAAGAAACA
*
55301921 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCTCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTT
* *
55301986 ACAGCGAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAATAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAGGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
55302051 GC
131 GC
* * * * *
55302053 AAATTTGGCATCACTGTGTTTATAGGGTACAGATCGAAGATAACAGATCTGACACTCCTATACTT
1 AGATTTGGCATCTCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTT
55302118 ACAGCGAAGCAGATCGAGGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAGGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
55302183 GC
131 GC
55302185 AGATTTGGCATCTCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCTCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTT
* * *
55302250 ACAGCGAAGCAGATCGAAGATTTTAGCATGGTATCCCTGTGTTTATAGGGAACAAGTTGAAGACA
66 ACAGCGAAGCAGATCGAGGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
55302315 AC
131 GC
55302317 AGATT
1 AGATT
55302322 CAGTATCTCT
Statistics
Matches: 253, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 253 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCTCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTT
ACAGCGAAGCAGATCGAGGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:55302749 original size:205 final size:205
Alignment explanation
Indices: 55302390--55302896 Score: 834
Period size: 205 Copynumber: 2.5 Consensus size: 205
55302380 TGGCGGAGAG
*
55302390 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACAATGAAGCAAATCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
*
55302455 TCATCTCTGTATTGTCAAAGAACAAATCGAAGTCTGGCATCTCTACTTCAATAGAGAGCAGATAC
66 TCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCTACTTCAATAGAGAGCAGATAC
* * *
55302520 ACAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGC
131 ACAGCAGATCTCACCTTCAGATGTTTATACTGAAACAGATCCAAGATGGTTTGGCATCCTTGTGC
55302585 TTAAAAGGAA
196 TTAAAAGGAA
* * * *
55302595 CAAATCAAAGACATAGCTGATTTGGCTTTCACGTATTTACGATGAAGCAAATCTAATATAATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
* *
55302660 TCGTCTCTGTAGTGTCAGAGAACAAATCGAAGTCTGGCATCTCTACTTCAATAGAGAGCAGATAC
66 TCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCTACTTCAATAGAGAGCAGATAC
* *
55302725 ATAGCAGATCTCACCTTCAGATGTTTATACTGAAATAGATCCAAGATGGTTTGGCATCCTTGTGC
131 ACAGCAGATCTCACCTTCAGATGTTTATACTGAAACAGATCCAAGATGGTTTGGCATCCTTGTGC
* *
55302790 TTACAAGGAG
196 TTAAAAGGAA
* * *
55302800 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCAAATCTAAGATGATTTG
1 CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
* *
55302865 GCATCTCTGTATTGTCAGGGAACAAATCGAAG
66 TCATCTCTGTATTGTCAGAGAACAAATCGAAG
55302897 AAGTTAATTT
Statistics
Matches: 276, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
205 276 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (205 bp):
CAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTG
TCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCTACTTCAATAGAGAGCAGATAC
ACAGCAGATCTCACCTTCAGATGTTTATACTGAAACAGATCCAAGATGGTTTGGCATCCTTGTGC
TTAAAAGGAA
Found at i:55303546 original size:18 final size:17
Alignment explanation
Indices: 55303522--55303581 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
55303512 CCAATATATT
55303522 TTATATTTTTTATATAA
1 TTATATTTTTTATATAA
*
55303539 TTAT-TATTCTTATA-AA
1 TTATAT-TTTTTATATAA
55303555 -TATATTTTTTATTATATA
1 TTATATTTTTTA-TATA-A
55303573 TTATATTTT
1 TTATATTTT
55303582 AAATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 12 0.34
18 1 0.03
19 8 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTTTTATATAA
Found at i:55303566 original size:15 final size:16
Alignment explanation
Indices: 55303523--55303581 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
55303513 CAATATATTT
55303523 TATATTTTTTATATAA
1 TATATTTTTTATATAA
55303539 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
55303555 TATATTTTTTATTATATA
1 TATATTTTTTA-TATA-A
55303573 TTATATTTT
1 -TATATTTT
55303582 AAATTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.19
16 10 0.28
17 10 0.28
18 1 0.03
19 8 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:55303606 original size:26 final size:26
Alignment explanation
Indices: 55303558--55303607 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
55303548 TTATAAATAT
* * * *
55303558 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
55303584 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
55303608 TTTATATGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:55307366 original size:16 final size:15
Alignment explanation
Indices: 55307300--55307373 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 15
55307290 ATAATTTACA
*
55307300 AATAAAATATGTAAT
1 AATAAAATATATAAT
*
55307315 AATATAAATCATATAGT
1 AATA-AAAT-ATATAAT
*
55307332 ACTAAAA-ATAT-AT
1 AATAAAATATATAAT
55307345 GGAATAAAATATATATAT
1 --AATAAAATATATA-AT
*
55307363 AATATAATATA
1 AATAAAATATA
55307374 CATAGAATGT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 10 0.22
16 21 0.46
17 8 0.17
18 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (15 bp):
AATAAAATATATAAT
Found at i:55307527 original size:16 final size:15
Alignment explanation
Indices: 55307506--55307657 Score: 62
Period size: 16 Copynumber: 9.5 Consensus size: 15
55307496 AGTATGAACA
*
55307506 ATATAATTAATAATAT
1 ATATAAATAAT-ATAT
55307522 ATATAAATAATATAT
1 ATATAAATAATATAT
* *
55307537 ACTAAAAACATATAATATAA
1 A-T--ATA-A-ATAATATAT
55307557 ATATAAATAA-ATAT
1 ATATAAATAATATAT
55307571 ATATATAATAA-AGTAT
1 ATATA-AATAATA-TAT
* *
55307587 ATGATGAAA-AATTTTAA
1 AT-AT-AAATAA-TATAT
*
55307604 ATGTATAATAATATAAT
1 ATATA-AATAATAT-AT
*
55307621 AGATAAAT-ATAGTA-
1 ATATAAATAATA-TAT
*
55307635 AAATAAATAATATAT
1 ATATAAATAATATAT
55307650 ATAATAAA
1 AT-ATAAA
55307658 ACAATAATAT
Statistics
Matches: 104, Mismatches: 14, Indels: 36
0.68 0.09 0.23
Matches are distributed among these distances:
14 17 0.16
15 24 0.23
16 33 0.32
17 16 0.15
18 3 0.03
19 2 0.02
20 9 0.09
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (15 bp):
ATATAAATAATATAT
Found at i:55307549 original size:15 final size:13
Alignment explanation
Indices: 55307517--55307598 Score: 53
Period size: 14 Copynumber: 6.2 Consensus size: 13
55307507 TATAATTAAT
*
55307517 AATATATATAAAT
1 AATATATATAAAA
55307530 AATATATACTAAAA
1 AATATATA-TAAAA
*
55307544 ACATATA-AT-ATA
1 A-ATATATATAAAA
*
55307556 AATATAAAT-AAA
1 AATATATATAAAA
*
55307568 TATATATATAATAA
1 AATATATATAA-AA
* *
55307582 AGTATATGATGAAA
1 AATATAT-ATAAAA
55307596 AAT
1 AAT
55307599 TTTAAATGTA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.09
12 14 0.26
13 10 0.19
14 17 0.31
15 8 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (13 bp):
AATATATATAAAA
Found at i:55307640 original size:21 final size:20
Alignment explanation
Indices: 55307607--55307666 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
55307597 ATTTTAAATG
*
55307607 TATAATAATATAATAGATAAA
1 TATAATAAAATAATA-ATAAA
* *
55307628 TATAGTAAAATAAATAATATA
1 TATAATAAAAT-AATAATAAA
*
55307649 TATAATAAAACAATAATA
1 TATAATAAAATAATAATA
55307667 TATTAGATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 7 0.21
21 22 0.67
22 4 0.12
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (20 bp):
TATAATAAAATAATAATAAA
Found at i:55307669 original size:18 final size:21
Alignment explanation
Indices: 55307639--55307688 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
55307629 ATAGTAAAAT
55307639 AAATAATATATATA-ATAA-AA
1 AAATAATATAT-TAGATAATAA
*
55307659 CAATAATATATTAGATAATAA
1 AAATAATATATTAGATAATAA
55307680 AAATAATAT
1 AAATAATAT
55307689 GTACTACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
AAATAATATATTAGATAATAA
Found at i:55309730 original size:5 final size:5
Alignment explanation
Indices: 55309715--55309756 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
55309705 AGTGGAAAAG
* *
55309715 TGAATT TGAAT TGAAT TGAAT TGAAT TGAAT GGAAT GGAAT T
1 TGAA-T TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT T
55309757 TTTATTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (5 bp):
TGAAT
Found at i:55310244 original size:45 final size:45
Alignment explanation
Indices: 55310175--55310391 Score: 241
Period size: 45 Copynumber: 5.0 Consensus size: 45
55310165 TACTGCTATT
* * *
55310175 GTTACCGATTTGGCACTTTGTGTGTC-AATTATTGTTACTATTACC
1 GTTACTGATTCGGCACTTTGTGTGTCGAA-TATTGTTACTGTTACC
* * * *
55310220 GTTATTGATTCGACACTTTATGTGTCAAATATTGTTAC---T---
1 GTTACTGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACC
* *
55310259 GTTACTGATTTGGCACTTTGTGTGTCGAATATTATTACTGTTACC
1 GTTACTGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACC
* *
55310304 GTTACTGATTCGGCATTTTATGTGTCGAATATTGTTACTGTTACC
1 GTTACTGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACC
* * * *
55310349 GTTACCGATTCGGCACTTTGTGTGTTGAATACTGTTACCGTTA
1 GTTACTGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTA
55310392 TTATTACTGT
Statistics
Matches: 144, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
39 32 0.22
42 2 0.01
45 108 0.75
46 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (45 bp):
GTTACTGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACC
Found at i:55310274 original size:84 final size:84
Alignment explanation
Indices: 55310174--55310349 Score: 273
Period size: 84 Copynumber: 2.1 Consensus size: 84
55310164 CTACTGCTAT
* *
55310174 TGTTACCGATTTGGCACTTTGTGTGTC-AATTATTGTTACTATTACCGTTATTGATTCGACACTT
1 TGTTACCGATTTGGCACTTTGTGTGTCGAA-TATTATTACTATTACCGTTACTGATTCGACACTT
55310238 TATGTGTCAAATATTGTTAC
65 TATGTGTCAAATATTGTTAC
* * * *
55310258 TGTTACTGATTTGGCACTTTGTGTGTCGAATATTATTACTGTTACCGTTACTGATTCGGCATTTT
1 TGTTACCGATTTGGCACTTTGTGTGTCGAATATTATTACTATTACCGTTACTGATTCGACACTTT
*
55310323 ATGTGTCGAATATTGTTAC
66 ATGTGTCAAATATTGTTAC
55310342 TGTTACCG
1 TGTTACCG
55310350 TTACCGATTC
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 81 0.98
85 2 0.02
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (84 bp):
TGTTACCGATTTGGCACTTTGTGTGTCGAATATTATTACTATTACCGTTACTGATTCGACACTTT
ATGTGTCAAATATTGTTAC
Found at i:55310382 original size:84 final size:81
Alignment explanation
Indices: 55310174--55310391 Score: 210
Period size: 84 Copynumber: 2.6 Consensus size: 81
55310164 CTACTGCTAT
* * * *
55310174 TGTTACCGATTTGGCACTTTGTGTGTC-AATTATTGTTACTATTACCGTTATTGATTCGACACTT
1 TGTTACTGATTCGGCACTTTGTGTGTCGAA-TA---TTACTGTTACCGTTACTGATTCGACACTT
55310238 TATGTGTCAAATATTGTTAC
62 TATGTGTCAAATATTGTTAC
* * *
55310258 TGTTACTGATTTGGCACTTTGTGTGTCGAATATTATTACTGTTACCGTTACTGATTCGGCATTTT
1 TGTTACTGATTCGGCACTTTGTGTGTCG-A-A-TATTACTGTTACCGTTACTGATTCGACACTTT
*
55310323 ATGTGTCGAATATTGTTAC
63 ATGTGTCAAATATTGTTAC
*
55310342 TGTTACCGTTACCGATTCGGCACTTTGTGTGTTG-A-A-TACTGTTACCGTTA
1 TGTTA-C--T---GATTCGGCACTTTGTGTGTCGAATATTACTGTTACCGTTA
55310392 TTATTACTGT
Statistics
Matches: 117, Mismatches: 8, Indels: 18
0.82 0.06 0.13
Matches are distributed among these distances:
84 89 0.76
85 2 0.02
86 1 0.01
87 6 0.05
90 19 0.16
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (81 bp):
TGTTACTGATTCGGCACTTTGTGTGTCGAATATTACTGTTACCGTTACTGATTCGACACTTTATG
TGTCAAATATTGTTAC
Found at i:55310404 original size:6 final size:6
Alignment explanation
Indices: 55310378--55310437 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
55310368 GTGTGTTGAA
* * * *
55310378 TACTGT TACCGT TATTAT TACTGT TACTGC TACTGT TACTGAT TACTGT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT
*
55310427 T-CTGG TACTGT
1 TACTGT TACTGT
55310438 GTACCGTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
5 4 0.10
6 32 0.76
7 6 0.14
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (6 bp):
TACTGT
Found at i:55311518 original size:27 final size:26
Alignment explanation
Indices: 55311485--55311583 Score: 135
Period size: 27 Copynumber: 3.7 Consensus size: 26
55311475 TATTGTGGAT
55311485 ATGTGGCAGAGCCACCAGATCAGATA
1 ATGTGGCAGAGCCACCAGATCAGATA
* *
55311511 ATCGTGGCATAGCCACCAGAACAGATA
1 AT-GTGGCAGAGCCACCAGATCAGATA
55311538 TATGTGGCAGAGCCACCAGATCAGATA
1 -ATGTGGCAGAGCCACCAGATCAGATA
* *
55311565 ATTGTGGCATAGTCACCAG
1 A-TGTGGCAGAGCCACCAG
55311584 GACGCTTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
26 3 0.05
27 59 0.92
28 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.18
Consensus pattern (26 bp):
ATGTGGCAGAGCCACCAGATCAGATA
Found at i:55313235 original size:26 final size:26
Alignment explanation
Indices: 55313204--55313311 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
55313194 TGAAATGCCC
*
55313204 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
55313230 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55313256 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55313282 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
55313308 ATCA
1 ATCA
55313312 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:55313833 original size:18 final size:19
Alignment explanation
Indices: 55313810--55313848 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
55313800 AGAAATTAAG
*
55313810 AATTGAAATGTGA-ATTGA
1 AATTGAAATATGAGATTGA
*
55313828 AATTGAGATATGAGATTGA
1 AATTGAAATATGAGATTGA
55313847 AA
1 AA
55313849 GCTTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (19 bp):
AATTGAAATATGAGATTGA
Found at i:55315294 original size:20 final size:20
Alignment explanation
Indices: 55315271--55315309 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55315261 TTAATTTAAT
55315271 TTTTAAATAA-TATTTTATTA
1 TTTT-AATAATTATTTTATTA
*
55315291 TTTTATTAATTATTTTATT
1 TTTTAATAATTATTTTATT
55315310 TAGTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATAATTATTTTATTA
Found at i:55318000 original size:24 final size:24
Alignment explanation
Indices: 55317964--55318009 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
55317954 TTTAATTTTC
*
55317964 AAAATTTTAAAAAAATAAAAATAA
1 AAAAATTTAAAAAAATAAAAATAA
*
55317988 AAAAATTTCAAAAAATAAAAAT
1 AAAAATTTAAAAAAATAAAAAT
55318010 TGCATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAAATTTAAAAAAATAAAAATAA
Found at i:55318046 original size:30 final size:29
Alignment explanation
Indices: 55318006--55318107 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 29
55317996 CAAAAAATAA
*
55318006 AAATTGCATTTTTACCCCTAAACTTTTCCT
1 AAATTGCATTTTGACCCCTAAAC-TTTCCT
* * *
55318036 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTGCATTTTGACCCCTAAACTTTC-CT
* * **
55318066 AAATTTCACTGAGACCCCTAAACTTTCCTT
1 AAATTGCATTTTGACCCCTAAACTTTCC-T
55318096 AAATTGCATTTT
1 AAATTGCATTTT
55318108 AACCTTAAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
29 4 0.07
30 53 0.93
ACGTcount: A:0.28, C:0.24, G:0.05, T:0.43
Consensus pattern (29 bp):
AAATTGCATTTTGACCCCTAAACTTTCCT
Found at i:55318269 original size:70 final size:70
Alignment explanation
Indices: 55318188--55318327 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
55318178 CAGATTACAT
*
55318188 GATTTGGGGTACCCACTTCCCAGATTTTCAGGCCACAAACATGGGTGGCTGCTCCTTCTTCACCC
1 GATTTGGGGTACCCACTTCCCAGATTTTCAGGCCACAAACATGGGTGCCTGCTCCTTCTTCACCC
55318253 ACTAC
66 ACTAC
55318258 GATTTGGGGTACCCACTTCCCAGATTTTCAGGCCACAAACATGGGTGCCTGCTCCTTCTTCACCC
1 GATTTGGGGTACCCACTTCCCAGATTTTCAGGCCACAAACATGGGTGCCTGCTCCTTCTTCACCC
55318323 ACTAC
66 ACTAC
55318328 CTGCAAATAG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.27
Consensus pattern (70 bp):
GATTTGGGGTACCCACTTCCCAGATTTTCAGGCCACAAACATGGGTGCCTGCTCCTTCTTCACCC
ACTAC
Found at i:55318452 original size:16 final size:15
Alignment explanation
Indices: 55318415--55318457 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
55318405 GAGAAAAAAA
55318415 AGCAAAAAAAAATTC
1 AGCAAAAAAAAATTC
*
55318430 AG-AAAAAAAATTTTCC
1 AGCAAAAAAAA-ATT-C
55318446 AGCAAAAAAAAA
1 AGCAAAAAAAAA
55318458 CAACAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 8 0.35
15 4 0.17
16 3 0.13
17 8 0.35
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (15 bp):
AGCAAAAAAAAATTC
Found at i:55319149 original size:74 final size:74
Alignment explanation
Indices: 55319023--55319169 Score: 267
Period size: 74 Copynumber: 2.0 Consensus size: 74
55319013 CAACAATAAA
* *
55319023 AAATATTAAATTTTAAAATGGTCTGGTCAACCTGACTCTATTTGCGGCAATCTGATCCGGTGAAG
1 AAATATTAAATTTTAAAATGGTCGGGTCAACCTGACTCTATTTGCGGCAATCTGATCCAGTGAAG
55319088 ATCACCAAT
66 ATCACCAAT
*
55319097 AAATTTTAAATTTTAAAATGGTCGGGTCAACCTGACTCTATTTGCGGCAATCTGATCCAGTGAAG
1 AAATATTAAATTTTAAAATGGTCGGGTCAACCTGACTCTATTTGCGGCAATCTGATCCAGTGAAG
55319162 ATCACCAA
66 ATCACCAA
55319170 CAAAGGCCCA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (74 bp):
AAATATTAAATTTTAAAATGGTCGGGTCAACCTGACTCTATTTGCGGCAATCTGATCCAGTGAAG
ATCACCAAT
Found at i:55319339 original size:17 final size:17
Alignment explanation
Indices: 55319281--55319341 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
55319271 TCCGAATTTA
55319281 ATATATATATTTT-T--
1 ATATATATATTTTGTAC
*
55319295 ATA-ACTATATTATGTAC
1 ATATA-TATATTTTGTAC
55319312 ATATATATATTTTGTAC
1 ATATATATATTTTGTAC
55319329 ATATCAT-TATTTT
1 ATAT-ATATATTTT
55319342 ATATTATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 1 0.03
17 24 0.62
18 3 0.08
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATATATTTTGTAC
Found at i:55319824 original size:61 final size:61
Alignment explanation
Indices: 55319729--55319850 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
55319719 GTACCGATTT
* *
55319729 AACATTAAGCCATCGATTTCATCGCTATGTTGGGTGAAATTCATCGGCTCGTGTTAAAAAC
1 AACATTAAGCCATCAATTTCATCGCTATGTTGGGTGAAATTCATCGGCTCATGTTAAAAAC
*
55319790 AACATTAAGCCATCAATTTCATCGTTATGTTGGGTGAAATTCATCGGCTCATGTTAAAAAC
1 AACATTAAGCCATCAATTTCATCGCTATGTTGGGTGAAATTCATCGGCTCATGTTAAAAAC
55319851 GGGACACCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (61 bp):
AACATTAAGCCATCAATTTCATCGCTATGTTGGGTGAAATTCATCGGCTCATGTTAAAAAC
Found at i:55331750 original size:14 final size:14
Alignment explanation
Indices: 55331731--55331761 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55331721 GAGGTAATTT
*
55331731 CAATTTATGTTTTG
1 CAATTTATATTTTG
55331745 CAATTTATATTTTG
1 CAATTTATATTTTG
55331759 CAA
1 CAA
55331762 AAATCAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (14 bp):
CAATTTATATTTTG
Found at i:55331804 original size:87 final size:86
Alignment explanation
Indices: 55331672--55332237 Score: 518
Period size: 87 Copynumber: 6.7 Consensus size: 86
55331662 TTGTCAAAAA
* * *
55331672 AAAAAGTCGACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
55331737 ATGTTTTGCAATTTATATTTTGC
65 ATGTTTT-CAATTTATATTTTTC
* * * *
55331760 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTA
* *
55331825 TGTTCTT-AA-TGACTGTTTTT-
66 TGTT-TTCAATTTA-TATTTTTC
* * *
55331845 --AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTAAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTA
*
55331908 TGTTTTTTCCAATCTATATTTTTC
66 TG--TTTT-CAATTTATATTTTTC
* * * *
55331932 AAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAAGACACGTTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-
*
55331997 CAT-TTTTCAATTTATGTTTTTC
65 -ATGTTTTCAATTTATATTTTTC
* * * *
55332019 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTC-GAGACACGCTGAGGTAATTTCAATTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GACACGCTGAGGTATTTTCAATTT
* **
55332083 CTG--TT---TTT-T-TTTTAA
65 ATGTTTTCAATTTATATTTTTC
** * **
55332098 AAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
55332163 CTG---TC--TTTCA-A------
65 ATGTTTTCAATTT-ATATTTTTC
* * **
55332174 AAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAGCTCACGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
55332238 TTTACTTTTT
Statistics
Matches: 402, Mismatches: 56, Indels: 53
0.79 0.11 0.10
Matches are distributed among these distances:
75 50 0.12
76 5 0.01
79 10 0.02
80 56 0.14
81 3 0.01
83 60 0.15
84 4 0.01
85 5 0.01
86 15 0.04
87 126 0.31
88 11 0.03
89 56 0.14
91 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (86 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTA
TGTTTTCAATTTATATTTTTC
Found at i:55331985 original size:172 final size:170
Alignment explanation
Indices: 55331681--55332237 Score: 580
Period size: 172 Copynumber: 3.3 Consensus size: 170
55331671 AAAAAAGTCG
* * *
55331681 ACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTTTGC
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCTGTTTT-C
* * * *
55331746 AATTTATATTTTGCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAG
65 AA-TTATATTTTACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAG
*
55331811 GTATTTTTAATTTCTGTTCTT-AA-TGACTGTTTTT-AAATCA
129 GTATTTTCAATTTCTGTTCTTCAATTGA-TGTTTTTAAAATCA
* *
55331851 ACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTAAGGTATTTTCAATTTCTGTTTTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCTG--TTTT
* * *
55331916 CCAATCTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAAGACACGTTG
64 -CAAT-TATATTTTACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTG
* ** * *
55331981 AGGTATTTTCGATTTCCATTTTTCAATTTATGTTTTTCAAAAATCA
127 AGGTATTTTCAATTTCTGTTCTTCAATTGATGTTTTT--AAAATCA
* * * *
55332027 ATTCATATTACGAGAGGTGAGTTGAGCC-TCGAGACACGCTGAGGTAATTTCAATTCCTG-TTT-
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTAG-GACACGCTGAGGTAATTTCAATTTCTGTTTTC
* **
55332089 --TT-T-TTTTAAAAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAG
65 AATTATATTTTACAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAG
55332150 GTATTTTCAATTTCTG-TCTTTCAA---A-------AAAATCA
129 GTATTTTCAATTTCTGTTC-TTCAATTGATGTTTTTAAAATCA
* * * ** *
55332182 ACTCATATTACGAGAGGTGAGTTAAGCCTCAGCTCACGCTGAGGTATTTTCAATTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTT
55332238 TTTACTTTTT
Statistics
Matches: 333, Mismatches: 42, Indels: 39
0.80 0.10 0.09
Matches are distributed among these distances:
155 53 0.16
156 1 0.00
164 1 0.00
166 10 0.03
167 61 0.18
168 1 0.00
169 1 0.00
170 54 0.16
171 1 0.00
172 78 0.23
173 12 0.04
174 2 0.01
175 2 0.01
176 56 0.17
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (170 bp):
ACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCA
ATTATATTTTACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGT
ATTTTCAATTTCTGTTCTTCAATTGATGTTTTTAAAATCA
Found at i:55332048 original size:259 final size:255
Alignment explanation
Indices: 55331672--55332166 Score: 642
Period size: 259 Copynumber: 1.9 Consensus size: 255
55331662 TTGTCAAAAA
* * *
55331672 AAAAAGTCGACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAGTCAACTCATATTGCGAAAGGTGAATTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
*
55331737 ATGTTTTGCAATTTATATTTTGCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTC-AGG
66 ATGTTTTGCAATTTATATTTTGCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGA-G
* * * *
55331801 ACACACTGAGGTATTTTTAATTTCTGTTCTTAATGACTGTTTT-TAAA-TCAACTCATATTGCGA
130 ACACACTGAGGTAATTTCAATTCCTGTT-TT--T---T-TTTTAAAAAGTCAACTCATATTGCGA
** * * *
55331864 GAGGTGAGTTGAGCCTTAGGACACGCTAAGGTATTTTCAATTTCTGTTTTTTCCAATCTATATTT
188 GAAATGAGTTGAGCCTCAAGACACACTAAGGTATTTTCAATTTCTGTTTTTTCCAATCTATATTT
55331929 TTC
253 TTC
* * * *
55331932 AAAAA-TCAACTCATATTGCGAGAGGTGAATTGAGCCTCAAGACACGTTGAGGTATTTTCGATTT
1 AAAAAGTCAACTCATATTGCGAAAGGTGAATTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
* *
55331996 CCAT-TTTT-CAATTTATGTTTTTCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGA
66 --ATGTTTTGCAATTTATATTTTGCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGA
*
55332059 GACACGCTGAGGTAATTTCAATTCCTGTTTTTTTTTTAAAAAAAGTCAACTCATATTGCGAGAAA
129 GACACACTGAGGTAATTTCAATTCCTGTTTTTTTTTT--AAAAAGTCAACTCATATTGCGAGAAA
* *
55332124 TGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGT
192 TGAGTTGAGCCTCAAGACACACTAAGGTATTTTCAATTTCTGT
55332167 CTTTCAAAAA
Statistics
Matches: 206, Mismatches: 22, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
252 4 0.02
253 1 0.00
255 3 0.01
256 57 0.28
258 2 0.01
259 127 0.62
260 10 0.05
261 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (255 bp):
AAAAAGTCAACTCATATTGCGAAAGGTGAATTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
ATGTTTTGCAATTTATATTTTGCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGAGA
CACACTGAGGTAATTTCAATTCCTGTTTTTTTTTTAAAAAGTCAACTCATATTGCGAGAAATGAG
TTGAGCCTCAAGACACACTAAGGTATTTTCAATTTCTGTTTTTTCCAATCTATATTTTTC
Found at i:55332128 original size:80 final size:74
Alignment explanation
Indices: 55332019--55332282 Score: 264
Period size: 80 Copynumber: 3.4 Consensus size: 74
55332009 TATGTTTTTC
* *
55332019 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGAGACACGCTGAGGTAATTTCAATTCC
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-AGACACGCTGAGGTATTTTCAATTCC
* *
55332084 TGTTTTTTTTTTAA
65 TG----TCTTTCAA
* ** ** *
55332098 AAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTT
1 AAAAA-TCAACTCATATTACGAGAGGTGAGTTGAGCCTC-AGACACGCTGAGGTATTTTCAATTC
55332163 CTGTCTTTCAA
64 CTGTCTTTCAA
* * *
55332174 AAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAGCTCACGCTGAGGTATTTTCAATT-T
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAG-ACACGCTGAGGTATTTTCAATTCC
*
55332238 TTTACTTTTTC-A
65 TGT-C--TTTCAA
*
55332250 AAATATCAACTCATAATT-CGAGAGGTGAGTTGA
1 AAAAATCAACTCAT-ATTACGAGAGGTGAGTTGA
55332283 ACTTCAGGTC
Statistics
Matches: 157, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
74 4 0.03
75 49 0.31
76 39 0.25
77 7 0.04
79 5 0.03
80 53 0.34
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (74 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTTTCAATTCCT
GTCTTTCAA
Found at i:55332210 original size:75 final size:73
Alignment explanation
Indices: 55332000--55332282 Score: 275
Period size: 75 Copynumber: 3.7 Consensus size: 73
55331990 CGATTTCCAT
* * *
55332000 TTTTCAATTTATGTTTTTC-AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGAGACAC
1 TTTTCAATTTCTGTCTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-AGACAC
55332064 GCTGAGGTA
65 GCTGAGGTA
* * * * * **
55332073 ATTTCAATTCCTGTTTTTTTTTTAAAAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
1 TTTTCAATTTCTG-----TCTTTCAAAAAA-TCAACTCATATTACGAGAGGTGAGTTGAGCCTC-
**
55332138 AGACACATTGAGGTA
59 AGACACGCTGAGGTA
* *
55332153 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCAGCTCA
1 TTTTCAATTTCTGTCTTTC-AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAG-ACA
55332218 CGCTGAGGTA
64 CGCTGAGGTA
* *
55332228 TTTTCAATTT-TTTACTTTTTCAAAATATCAACTCATAATT-CGAGAGGTGAGTTGA
1 TTTTCAATTTCTGT-C--TTTCAAAAAATCAACTCAT-ATTACGAGAGGTGAGTTGA
55332283 ACTTCAGGTC
Statistics
Matches: 172, Mismatches: 25, Indels: 23
0.78 0.11 0.10
Matches are distributed among these distances:
73 10 0.06
74 4 0.02
75 54 0.31
76 34 0.20
77 7 0.04
78 5 0.03
79 5 0.03
80 53 0.31
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (73 bp):
TTTTCAATTTCTGTCTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGACACG
CTGAGGTA
Found at i:55332567 original size:29 final size:29
Alignment explanation
Indices: 55332511--55332627 Score: 128
Period size: 30 Copynumber: 4.0 Consensus size: 29
55332501 CAAAAAATAA
* *
55332511 AAATTACATTTTTACCCCTAAACTTTTCTT
1 AAATTTCATTTTAACCCCTAAAC-TTTCTT
* *
55332541 AAATTTCATTTTCACCCTTAAACTTTCTTT
1 AAATTTCATTTTAACCCCTAAACTTTC-TT
* *
55332571 AAATTTCACTTAAACCCCTAAACTTTCCTT
1 AAATTTCATTTTAACCCCTAAACTTT-CTT
* *
55332601 AAATTGCATTTTAA-CCCTAAATTTTCT
1 AAATTTCATTTTAACCCCTAAACTTTCT
55332628 AAAAATTACA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.03
29 14 0.19
30 57 0.77
31 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.01, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTAACCCCTAAACTTTCTT
Found at i:55333257 original size:74 final size:74
Alignment explanation
Indices: 55333136--55333284 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
55333126 AAGGAGAGGG
55333136 AGAATAGACAGCTTGAAGTTTGGATTTTCTTTGTTTGCTGCTGGAACTTGTTTGTTTTGGGGGGG
1 AGAATAGACAGCTTGAAGTTTGGATTTTCTTTGTTTGCTGCTGGAACTTGTTTGTTTTGGGGGGG
55333201 TTTAGTATT
66 TTTAGTATT
55333210 AGAATAGACAGCTTGAAGTTTGGATTTTCTTTGTTTGCTGCTGGAACTTGTTTGTTTTGGGGGGG
1 AGAATAGACAGCTTGAAGTTTGGATTTTCTTTGTTTGCTGCTGGAACTTGTTTGTTTTGGGGGGG
55333275 TTTAGTATT
66 TTTAGTATT
55333284 A
1 A
55333285 AAAAAAAGAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.18, C:0.08, G:0.30, T:0.44
Consensus pattern (74 bp):
AGAATAGACAGCTTGAAGTTTGGATTTTCTTTGTTTGCTGCTGGAACTTGTTTGTTTTGGGGGGG
TTTAGTATT
Found at i:55333781 original size:17 final size:17
Alignment explanation
Indices: 55333723--55333783 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
55333713 TCCGAATTTA
55333723 ATATATATATTTT-T--
1 ATATATATATTTTGTAC
*
55333737 ATA-ACTATATTATGTAC
1 ATATA-TATATTTTGTAC
55333754 ATATATATATTTTGTAC
1 ATATATATATTTTGTAC
55333771 ATATCAT-TATTTT
1 ATAT-ATATATTTT
55333784 ATATTATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 1 0.03
17 24 0.62
18 3 0.08
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATATATTTTGTAC
Found at i:55333889 original size:19 final size:17
Alignment explanation
Indices: 55333868--55333900 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55333858 ATTATTATTA
55333868 TTATTAT-TACATATAT
1 TTATTATATACATATAT
55333884 TTATTATATACATATAT
1 TTATTATATACATATAT
55333901 ATATGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTATATACATATAT
Found at i:55334896 original size:16 final size:16
Alignment explanation
Indices: 55334877--55334908 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55334867 ATTTGTTTTA
55334877 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
55334893 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
55334909 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:55335241 original size:51 final size:50
Alignment explanation
Indices: 55335111--55335252 Score: 151
Period size: 50 Copynumber: 2.8 Consensus size: 50
55335101 GAAGCTCTCT
* * ***
55335111 GGTACGCATAGTTGCCTGCACTTAGTACTACACACGTGACTTAACCATTT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACTGAACCAACG
* * * * **
55335161 GATACACGTAGTAGCCTACACTTAGTACTACACACGTGA-TCGAAGTTAACG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACT-GAA-CCAACG
*
55335212 GGTACGCATAGTAGCCTGCACTTAGTACTACACACATGACT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACT
55335253 CACAACAAAT
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
49 1 0.01
50 36 0.49
51 35 0.48
52 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (50 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACTGAACCAACG
Found at i:55335631 original size:18 final size:20
Alignment explanation
Indices: 55335600--55335646 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
55335590 AAGAATAGGT
55335600 TATATCATCAAAAT-AATCACA
1 TATAT-ATC-AAATGAATCACA
*
55335621 TA-ATATCAAATGATTCACA
1 TATATATCAAATGAATCACA
55335640 TATATAT
1 TATATAT
55335647 ACTTACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 11 0.48
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (20 bp):
TATATATCAAATGAATCACA
Found at i:55337992 original size:9 final size:9
Alignment explanation
Indices: 55337950--55338050 Score: 50
Period size: 9 Copynumber: 11.1 Consensus size: 9
55337940 TCAAAATTAT
55337950 TATTTTAGAA
1 TATTTTA-AA
*
55337960 TAATTCTAAA
1 T-ATTTTAAA
55337970 -ATTTTAAA
1 TATTTTAAA
*
55337978 TTTTTTATATA
1 TATTTTA-A-A
*
55337989 TTTTTTAGAA
1 TATTTTA-AA
55337999 T-TTTTAAA
1 TATTTTAAA
*
55338007 TTTTTTAAA
1 TATTTTAAA
*
55338016 -A-TATAAA
1 TATTTTAAA
*
55338023 T-TTTAAAA
1 TATTTTAAA
*
55338031 TTTTTATAAA
1 TATTT-TAAA
55338041 TATTTTAAA
1 TATTTTAAA
55338050 T
1 T
55338051 TTTGAATTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
7 5 0.07
8 15 0.21
9 25 0.35
10 13 0.18
11 14 0.19
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (9 bp):
TATTTTAAA
Found at i:55338027 original size:32 final size:29
Alignment explanation
Indices: 55337971--55338036 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 29
55337961 AATTCTAAAA
** *
55337971 TTTTAAATTTTTTATATATTTTTTAGAAT
1 TTTTAAATTTTTTATATAAATTTTAAAAT
55338000 TTTTAAATTTTTTAAAATATAAATTTTAAAAT
1 TTTTAAATTTTTT---ATATAAATTTTAAAAT
55338032 TTTTA
1 TTTTA
55338037 TAAATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.42
32 18 0.58
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAAATTTTTTATATAAATTTTAAAAT
Found at i:55338040 original size:18 final size:19
Alignment explanation
Indices: 55338017--55338053 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55338007 TTTTTTAAAA
55338017 TATAAAT-TTTAAAATTTT
1 TATAAATATTTAAAATTTT
*
55338035 TATAAATATTTTAAATTTT
1 TATAAATATTTAAAATTTT
55338054 GAATTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAAAATTTT
Found at i:55338041 original size:34 final size:33
Alignment explanation
Indices: 55337991--55338072 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 33
55337981 TTTATATATT
* *
55337991 TTTTAGAA-TTTTTAAATTTTTTAAAATATAAA
1 TTTTAAAATTTTTTAAATATTTTAAAATATAAA
* * *
55338023 TTTTAAAATTTTTATAAATATTTTAAATTTTGAA
1 TTTTAAAATTTTT-TAAATATTTTAAAATATAAA
55338057 TTTTGAAAATTATTTT
1 TTTT-AAAATT-TTTT
55338073 CGAAAATCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 7 0.17
33 4 0.10
34 20 0.49
35 7 0.17
36 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (33 bp):
TTTTAAAATTTTTTAAATATTTTAAAATATAAA
Found at i:55340794 original size:16 final size:17
Alignment explanation
Indices: 55340744--55340794 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
55340734 ATGGAAATAT
*
55340744 AATCTTTAAGGATATGC
1 AATCTTGAAGGATATGC
*
55340761 AATCTTAGATATGATATGC
1 AATCTT-GA-AGGATATGC
55340780 AATCTTGAA-GATATG
1 AATCTTGAAGGATATG
55340795 ATCTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
AATCTTGAAGGATATGC
Found at i:55340813 original size:22 final size:21
Alignment explanation
Indices: 55340754--55340796 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
55340744 AATCTTTAAG
55340754 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
55340773 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
55340794 GAT
1 GAT
55340797 CTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:55342941 original size:8 final size:7
Alignment explanation
Indices: 55342913--55342963 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
55342903 TCTATTTCAA
55342913 AAAAAAG
1 AAAAAAG
*
55342920 GAAAAAG
1 AAAAAAG
55342927 --AAAAG
1 AAAAAAG
55342932 -AAAAAG
1 AAAAAAG
*
55342938 AGAAAA-
1 AAAAAAG
55342944 AAAAAAG
1 AAAAAAG
55342951 AAAAAAG
1 AAAAAAG
55342958 AAAAAA
1 AAAAAA
55342964 AATGGAGAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
5 5 0.13
6 10 0.26
7 23 0.61
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:55342941 original size:13 final size:13
Alignment explanation
Indices: 55342915--55342962 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
55342905 TATTTCAAAA
*
55342915 AAAAGGAAAA-AG
1 AAAAGAAAAAGAG
55342927 AAAAGAAAAAGAG
1 AAAAGAAAAAGAG
* *
55342940 AAAAAAAAAAGAA
1 AAAAGAAAAAGAG
55342953 AAAAGAAAAA
1 AAAAGAAAAA
55342963 AAATGGAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 9 0.29
13 22 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:55342942 original size:19 final size:19
Alignment explanation
Indices: 55342914--55342965 Score: 81
Period size: 18 Copynumber: 2.8 Consensus size: 19
55342904 CTATTTCAAA
*
55342914 AAAAAG-GAAAAAGAAAAG
1 AAAAAGAGAAAAAAAAAAG
55342932 AAAAAGAGAAAAAAAAAAG
1 AAAAAGAGAAAAAAAAAAG
55342951 AAAAA-AGAAAAAAAA
1 AAAAAGAGAAAAAAAA
55342966 TGGAGAGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAGAGAAAAAAAAAAG
Found at i:55344057 original size:84 final size:84
Alignment explanation
Indices: 55343914--55344656 Score: 1161
Period size: 84 Copynumber: 8.9 Consensus size: 84
55343904 AAAATTCAGT
* *
55343914 GCCTTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCTTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
55343979 TGGGGCAGATCGAAGACTC
66 TGGAGCAGATCGAAGACTC
*
55343998 GCCTTAATCCTCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
55344063 TGGAGCAGATCAAAGAC-C
66 TGGAGCAGATCGAAGACTC
55344081 AGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 -GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
55344146 GTGGAGCAGATCAAAGAC-C
65 GTGGAGCAGATCGAAGACTC
55344165 AGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 -GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
55344230 GTGGAGCAGATCAAAGAC-C
65 GTGGAGCAGATCGAAGACTC
*
55344249 AGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTAGATCTTATCTCCCTAAGCAGTA
1 -GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
55344314 GTGGAGCATATCGAAGACTC
65 GTGGAGCAGATCGAAGACTC
*
55344334 GCCTTAATTCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
55344399 TGGAGCAGATCGAAGAATC
66 TGGAGCAGATCGAAGACTC
* * *
55344418 GCCTTAATCCCCTAAGCAGTAGGGGAACAGG-----TTCGTAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
55344478 CGGAGCAGATCGACGACGACTC
66 TGGAGCAGATCGA--A-GACTC
*
55344500 GCCTTAATCCCCTAAGAAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
55344565 TGGAGCAGATCGAAGAATC
66 TGGAGCAGATCGAAGACTC
* *
55344584 GCCTTAATCCCCTAAGCAGTAGGGTAACAGG-----TTCGTAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
55344644 CGGAGCAGATCGA
66 TGGAGCAGATCGA
55344657 CGNNNNNNNN
Statistics
Matches: 620, Mismatches: 29, Indels: 25
0.92 0.04 0.04
Matches are distributed among these distances:
79 78 0.13
81 1 0.00
82 33 0.05
83 1 0.00
84 466 0.75
85 2 0.00
87 39 0.06
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (84 bp):
GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACTC
Found at i:55348425 original size:33 final size:33
Alignment explanation
Indices: 55348388--55348457 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
55348378 ATTATTTAAA
* *
55348388 TATGATTTGAACATGCTTTTGAGTATGTTTAGG
1 TATGATTTGAACATACTTTTGAGAATGTTTAGG
* * *
55348421 TATGATTTGAACATATTTTTGGGAATGTTTTGG
1 TATGATTTGAACATACTTTTGAGAATGTTTAGG
55348454 TATG
1 TATG
55348458 GTTGATAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.47
Consensus pattern (33 bp):
TATGATTTGAACATACTTTTGAGAATGTTTAGG
Found at i:55361468 original size:42 final size:42
Alignment explanation
Indices: 55361404--55361486 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
55361394 CCATAGTCGT
*
55361404 TACTCAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
1 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
55361446 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAG
1 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAG
55361487 ATGGCTGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (42 bp):
TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
Found at i:55364226 original size:35 final size:35
Alignment explanation
Indices: 55364180--55364252 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
55364170 CTAGTTGTAA
55364180 AAGTCTTAGAAACACAAAAATTATAAGAAAAAGGC
1 AAGTCTTAGAAACACAAAAATTATAAGAAAAAGGC
*
55364215 AAGTCTTAGAAACACAAAAATTATGAGAAAAAGGC
1 AAGTCTTAGAAACACAAAAATTATAAGAAAAAGGC
55364250 AAG
1 AAG
55364253 GATTAACTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.16
Consensus pattern (35 bp):
AAGTCTTAGAAACACAAAAATTATAAGAAAAAGGC
Found at i:55376067 original size:29 final size:29
Alignment explanation
Indices: 55376005--55376103 Score: 150
Period size: 28 Copynumber: 3.5 Consensus size: 29
55375995 AAAAATAAAA
*
55376005 ATTTACCAAAACATTACAAC-TTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
55376033 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
*
55376062 ATTTACCAAAATATATA-AA-TATTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTTT
55376090 ATTTACCAAAATAT
1 ATTTACCAAAATAT
55376104 ATCAAAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 41 0.61
29 24 0.36
30 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:55376175 original size:27 final size:27
Alignment explanation
Indices: 55376137--55376220 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
55376127 CCTGATCACC
55376137 CCAATGCCATTGGCGGCACCAAAGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
*
55376164 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
* *
55376191 CCAATGCCATTGGCGGTACC-AATGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
55376217 CCAA
1 CCAA
55376221 AGGACTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 8 0.15
27 45 0.85
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (27 bp):
CCAATGCCATTGGCGGCACCAAAGGTG
Found at i:55376761 original size:18 final size:19
Alignment explanation
Indices: 55376710--55376770 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
55376700 CTGATATTTC
*
55376710 TATTAATTTAAAATA-TAGT
1 TATTAAATTAAAATAGTA-T
* *
55376729 TATTAAATGAGAATAGT-T
1 TATTAAATTAAAATAGTAT
*
55376747 TATTAAATTAAAATAGAAT
1 TATTAAATTAAAATAGTAT
55376766 TATTA
1 TATTA
55376771 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.44
19 18 0.53
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
TATTAAATTAAAATAGTAT
Found at i:55377307 original size:27 final size:26
Alignment explanation
Indices: 55377269--55377325 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
55377259 TTTTAGTCCT
55377269 TTGGCACATTGGTGCCACCAATGGCA
1 TTGGCACATTGGTGCCACCAATGGCA
* *
55377295 TTGGCACCTTTGGTGCCGCCAATGGCA
1 TTGGCA-CATTGGTGCCACCAATGGCA
55377322 TTGG
1 TTGG
55377326 GGTGATCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (26 bp):
TTGGCACATTGGTGCCACCAATGGCA
Found at i:55377445 original size:29 final size:29
Alignment explanation
Indices: 55377368--55377468 Score: 161
Period size: 29 Copynumber: 3.5 Consensus size: 29
55377358 TTTTTTTGAT
55377368 ATATTTTGGTAAAT-AAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
*
55377395 TATATTTTGATAAATAATAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAA-AAAAAAAGTTGTA
55377426 ATATTTTGGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
55377455 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
55377469 TTTTATTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
28 13 0.19
29 28 0.41
30 25 0.37
31 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.39
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAGTTGTA
Found at i:55381900 original size:2 final size:2
Alignment explanation
Indices: 55381893--55381917 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55381883 AGACTAAATC
55381893 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
55381918 TTTAAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55383401 original size:88 final size:88
Alignment explanation
Indices: 55383220--55383923 Score: 1038
Period size: 88 Copynumber: 7.9 Consensus size: 88
55383210 AAATACCGGC
* *
55383220 CCTTATCTCCCTGAGAAGAAGTGGAGTAGGTTGAAGATAGCAGATCAGATTTTGTCTTCCTGTAC
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATC-----TTGTCTTCCTGTAC
**
55383285 TGGCAGCA-AAGTAGATCGAAGATACTAG
61 TGGCAG-AGAAGTAGATCGAAGACCCTAG
55383313 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
55383378 GAGAAGTAGATCGAAGACCCTAG
66 GAGAAGTAGATCGAAGACCCTAG
*
55383401 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATATTGTCTTCCTGTACTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
55383466 GAGAAGTAGATCGAAGACCCTAG
66 GAGAAGTAGATCGAAGACCCTAG
* * *
55383489 CCTTATCTCTCTAAGAAGCAGTGGAGTAGGTTGAAGAAAACAGATCTTGTCTTCCTGTACTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
*
55383554 GAGAAGTAAATCGAAGACCCTAG
66 GAGAAGTAGATCGAAGACCCTAG
* * * *
55383577 CCTTATCTCTCTAAGAAGCAGTAGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTAGTA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
* **
55383642 GCGAAGTAGATCGAAGATACTAG
66 GAGAAGTAGATCGAAGACCCTAG
* *
55383665 CCTTATCTCTCTGAGAAGCAGTGGAGTAGATTGAAGATAGCAGATCTTGTCTTCCTATACTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
* * *
55383730 GTGAAGTAGATCGAAAACCCTAA
66 GAGAAGTAGATCGAAGACCCTAG
* * *
55383753 CCTTATCTCTCTGAGTAGCAGTGAAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
* *
55383818 GCGAAGTAGGTCGAAGACTCC-AG
66 GAGAAGTAGATCGAAGAC-CCTAG
* *
55383841 CCTTATCTC-CTTGAGAAGCAATGGAGTAGGTTGAAGATAGCAGATCTTGTCTTTCTGTACTGGC
1 CCTTATCTCTC-TGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGC
*
55383905 A-ACGAAGCAGATCGAAGAC
65 AGA-GAAGTAGATCGAAGAC
55383924 ACCAGTCTTA
Statistics
Matches: 560, Mismatches: 47, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
87 2 0.00
88 512 0.91
89 2 0.00
93 44 0.08
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (88 bp):
CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
GAGAAGTAGATCGAAGACCCTAG
Found at i:55383658 original size:45 final size:45
Alignment explanation
Indices: 55383265--55383922 Score: 215
Period size: 43 Copynumber: 14.9 Consensus size: 45
55383255 GATAGCAGAT
* * **
55383265 CAGATTTTGTCTTCCTGTACTGGCAGCAAAGTAGATCGAAGATA-
1 CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * ** * * *
55383309 CTAG-CCTTATC-TCTCTG-AGAAGCAGTGGAGTAGGTTGAAGATAG
1 C-AGATCTTGTCTTC-CTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * **
55383353 CAGATCTTGTCTTCCTGTACTGGCAGAGAAGTAGATCGAAGA-CC
1 CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * ** * * *
55383397 CTAG-CCTTATC-TCTCTG-AGAAGCAGTGGAGTAGGTTGAAGATAG
1 C-AGATCTTGTCTTC-CTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * * **
55383441 CAGATATTGTCTTCCTGTACTGGCAGAGAAGTAGATCGAAGA-CC
1 CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * * ** * * * * *
55383485 CTAG-CCTTATC-TCTCT-AAGAAGCAGTGGAGTAGGTTGAAGAAAA
1 C-AGATCTTGTCTTC-CTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * * **
55383529 CAGATCTTGTCTTCCTGTACTGGCAGAGAAGTAAATCGAAGA-CC
1 CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * * ** * *
55383573 CTAG-CCTTATC-TCTCT-AAGAAGCAGT-AGAGTAGGTTGAAGATAG
1 C-AGATCTTGTCTTC-CTGTACTAGCAGTGA-AGTAGATCGAAGATAG
* *
55383617 CAGATCTTGTCTTCCTGTACTAGTAGCGAAGTAGATCGAAGATA-
1 CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * ** * *
55383661 CTAG-CCTTATC-TCTCTG-AGAAGCAGTGGAGTAGATTGAAGATAG
1 C-AGATCTTGTCTTC-CTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * *
55383705 CAGATCTTGTCTTCCTATACTGGCAGTGAAGTAGATCGAA-A-ACC
1 CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGATA-G
* * * * *
55383749 CTA-ACCTTATC-TCTCTG-AGTAGCAGTGAAGTAGGTTGAAGATAG
1 C-AGATCTTGTCTTC-CTGTACTAGCAGTGAAGTAGATCGAAGATAG
* * * * *
55383793 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGGTCGAAGACT-C
1 CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGA-TAG
* * ** * * * *
55383838 CAG-CCTTATC-TCCT-TGAGAAGCAATGGAGTAGGTTGAAGATAG
1 CAGATCTTGTCTTCCTGT-ACTAGCAGTGAAGTAGATCGAAGATAG
* * ** *
55383881 CAGATCTTGTCTTTCTGTACTGGCAACGAAGCAGATCGAAGA
1 CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGA
55383923 CACCAGTCTT
Statistics
Matches: 423, Mismatches: 145, Indels: 91
0.64 0.22 0.14
Matches are distributed among these distances:
42 3 0.01
43 153 0.36
44 113 0.27
45 151 0.36
46 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (45 bp):
CAGATCTTGTCTTCCTGTACTAGCAGTGAAGTAGATCGAAGATAG
Found at i:55386064 original size:16 final size:16
Alignment explanation
Indices: 55386043--55386099 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
55386033 TTTGGTTCGC
*
55386043 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
55386059 TGTATTGGATTAGATG
1 TGTAATGGATTAGAGG
*
55386075 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
55386091 TGTAATGGA
1 TGTAATGGA
55386100 AAAGCTGTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:55386109 original size:16 final size:16
Alignment explanation
Indices: 55386070--55386112 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
55386060 GTATTGGATT
*
55386070 AGATGTGTAATGGAAT
1 AGATGTGTAATGGAAA
*
55386086 AGAGGTGTAATGGAAA
1 AGATGTGTAATGGAAA
*
55386102 AGCTGTGTAAT
1 AGATGTGTAAT
55386113 AGCAAATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.33, T:0.28
Consensus pattern (16 bp):
AGATGTGTAATGGAAA
Found at i:55386109 original size:32 final size:32
Alignment explanation
Indices: 55386043--55386112 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
55386033 TTTGGTTCGC
* * * **
55386043 TGTATTGGATTAGAGGTGTATTGGATTAGATG
1 TGTAATGGAATAGAGGTGTAATGGAAAAGATG
*
55386075 TGTAATGGAATAGAGGTGTAATGGAAAAGCTG
1 TGTAATGGAATAGAGGTGTAATGGAAAAGATG
55386107 TGTAAT
1 TGTAAT
55386113 AGCAAATCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.01, G:0.33, T:0.34
Consensus pattern (32 bp):
TGTAATGGAATAGAGGTGTAATGGAAAAGATG
Found at i:55386366 original size:18 final size:17
Alignment explanation
Indices: 55386345--55386379 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55386335 TTATTATTAA
*
55386345 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55386363 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55386380 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55386426 original size:61 final size:61
Alignment explanation
Indices: 55386360--55386547 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
55386350 TTTTAATTAA
55386360 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
55386421 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
55386480 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
55386541 AATATAT
1 AATATAT
55386548 GATACTATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 23 0.24
61 37 0.39
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:55386493 original size:14 final size:15
Alignment explanation
Indices: 55386444--55386495 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
55386434 ATAAAATATA
55386444 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
55386459 TATTAAATATATTAT
1 AATTAAATATATTAT
55386474 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
55386487 AATTTAATA
1 AATTAAATA
55386496 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:55386541 original size:120 final size:121
Alignment explanation
Indices: 55386328--55386620 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 121
55386318 ATCATATTTA
55386328 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
55386393 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
55386448 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
55386513 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* * *
55386569 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGACTTAATAAAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
55386621 TAAAATAATT
Statistics
Matches: 164, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 162 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:55386668 original size:101 final size:92
Alignment explanation
Indices: 55386617--55386848 Score: 276
Period size: 91 Copynumber: 2.5 Consensus size: 92
55386607 GACTTAATAA
* *
55386617 AATTT-AAAATAATTATA-ACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTAT
1 AATTTCAAAA-AATTATACA-TAATAAATTATCTTATATGAATTTATATAATTTAAAATAATTAA
*
55386680 TATTACATATAATTTAA-TAATAATATAT
64 TATTAAATATAATTTAATTAATAATATAT
* * * * *
55386708 AATTTCATAAAATTCTTCATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATA
1 AATTTCAAAAAATTATACATAATAAATTATCTTATATGAATTTATATAATTTAAAATAATTAATA
*
55386773 TTAAATATAATTTAA-TAATGATATAT
66 TTAAATATAATTTAATTAATAATATAT
* * * *
55386799 AATTTCATAAAATTCTTA-ATAATAAAATATTCTTATATGAATTCATATAA
1 AATTTCAAAAAATT-ATACATAATAAATTA-TCTTATATGAATTTATATAA
55386849 GATAATTTAT
Statistics
Matches: 122, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
91 99 0.81
92 23 0.19
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (92 bp):
AATTTCAAAAAATTATACATAATAAATTATCTTATATGAATTTATATAATTTAAAATAATTAATA
TTAAATATAATTTAATTAATAATATAT
Found at i:55386690 original size:26 final size:28
Alignment explanation
Indices: 55386661--55386721 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
55386651 TATGAATTTG
*
55386661 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
55386687 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
55386715 TAAAATT
1 TATAATT
55386722 CTTCATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:55386719 original size:47 final size:46
Alignment explanation
Indices: 55386668--55386811 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
55386658 TTGTATAATT
55386668 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
55386715 TAAAAT--TCT-TCA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
55386759 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
55386806 TAAAAT
1 TAAAAT
55386812 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:55386731 original size:91 final size:91
Alignment explanation
Indices: 55386636--55386841 Score: 331
Period size: 91 Copynumber: 2.3 Consensus size: 91
55386626 TAATTATAAC
* * * *
55386636 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
55386701 AATATATAATTTCATAAAATTCTTCA
66 AATATATAATTTCATAAAATTCTTAA
*
55386727 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
55386792 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
55386818 TAATAAAATATTCTTATATGAATT
1 TAATAAATTA-TCTTATATGAATT
55386842 CATATAAGAT
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 92 0.88
92 13 0.12
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (91 bp):
TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:55386803 original size:44 final size:43
Alignment explanation
Indices: 55386661--55386803 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
55386651 TATGAATTTG
* *
55386661 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
55386705 TATAATTTCATAAAATTCTTCATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
55386752 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
55386796 TATAATTT
1 TATAATTT
55386804 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:55386818 original size:47 final size:47
Alignment explanation
Indices: 55386686--55386824 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
55386676 TTATTATTAC
* *
55386686 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTCATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
55386733 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
55386777 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
55386824 A
1 A
55386825 ATATTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:55394949 original size:15 final size:15
Alignment explanation
Indices: 55394931--55394963 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55394921 AACAATTATG
55394931 TTTCTTCTTCTTCCT
1 TTTCTTCTTCTTCCT
*
55394946 TTTCTTTTTCTTCCT
1 TTTCTTCTTCTTCCT
55394961 TTT
1 TTT
55394964 GTAGTTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTCTTCTTCCT
Found at i:55399699 original size:101 final size:101
Alignment explanation
Indices: 55399524--55399712 Score: 378
Period size: 101 Copynumber: 1.9 Consensus size: 101
55399514 AGATTGCATT
55399524 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATTGGCCATGAGAATTGCTATGCCAATCTTC
1 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATTGGCCATGAGAATTGCTATGCCAATCTTC
55399589 GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
66 GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
55399625 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATTGGCCATGAGAATTGCTATGCCAATCTTC
1 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATTGGCCATGAGAATTGCTATGCCAATCTTC
55399690 GGCTGTTTAAATTCCATAATGTT
66 GGCTGTTTAAATTCCATAATGTT
55399713 TAAATCACCC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 88 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (101 bp):
GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATTGGCCATGAGAATTGCTATGCCAATCTTC
GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
Found at i:55399981 original size:24 final size:23
Alignment explanation
Indices: 55399937--55399981 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
55399927 GGTACTGTAG
*
55399937 TTCATTTCATGTTATTTTGGTAT
1 TTCATTTCATGTTATTATGGTAT
* *
55399960 TTCATTTTCTTGTTCTTATGGT
1 TTCA-TTTCATGTTATTATGGT
55399982 CAATTTCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.62
Consensus pattern (23 bp):
TTCATTTCATGTTATTATGGTAT
Found at i:55401623 original size:21 final size:21
Alignment explanation
Indices: 55401559--55401631 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
55401549 ATTTTGATTT
*
55401559 TGAATGATTGAATTTAGAAAA
1 TGAAAGATTGAATTTAGAAAA
** * ***
55401580 TGGGAGAGTG-ATTT-GATTG
1 TGAAAGATTGAATTTAGAAAA
55401599 TGAAAGATTGAATTTAGAAAA
1 TGAAAGATTGAATTTAGAAAA
55401620 TGAAAGATTGAA
1 TGAAAGATTGAA
55401632 CGTGCAAGTA
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 20 0.54
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (21 bp):
TGAAAGATTGAATTTAGAAAA
Found at i:55411243 original size:17 final size:18
Alignment explanation
Indices: 55411221--55411262 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
55411211 GACATATTAC
55411221 CCCTAATTTCTAATT-GG
1 CCCTAATTTCTAATTAGG
55411238 CCCTAATTTCTAATTAGG
1 CCCTAATTTCTAATTAGG
*
55411256 CCTTAAT
1 CCCTAAT
55411263 CAATTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (18 bp):
CCCTAATTTCTAATTAGG
Found at i:55419043 original size:36 final size:37
Alignment explanation
Indices: 55419003--55419083 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 37
55418993 TGAAACATAG
*
55419003 AAAATATATAAAAGTATGT-GTATATGTATAT-TTATA
1 AAAATATA-AAAAATATGTAGTATATGTATATATTATA
* *
55419039 AAAAT-TAAAAAATGTGTAGGTATATGTATATATTGTA
1 AAAATATAAAAAATATGTA-GTATATGTATATATTATA
55419076 AAACATAT
1 AAA-ATAT
55419084 GTATGTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 8 0.22
35 2 0.05
36 17 0.46
37 7 0.19
38 2 0.05
39 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.38
Consensus pattern (37 bp):
AAAATATAAAAAATATGTAGTATATGTATATATTATA
Found at i:55419640 original size:23 final size:24
Alignment explanation
Indices: 55419610--55419656 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
55419600 AAATTAAATC
55419610 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
55419633 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
55419657 AAGATTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:55419659 original size:21 final size:21
Alignment explanation
Indices: 55419633--55419687 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
55419623 AATCATATCT
55419633 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
55419654 TCTAAGATTTC--ATATCATA
1 TCTAAGATTGCATATATCATA
55419673 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
55419688 TCTTGAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 18 0.60
21 12 0.40
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:55419673 original size:24 final size:21
Alignment explanation
Indices: 55419610--55419675 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
55419600 AAATTAAATC
55419610 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC--AATCATATCT
*
55419633 TCTAAGATTGC-AT-ATATCAT
1 TCTAAGATTACAATCATATC-T
*
55419653 ATCTAAGATTTCATATCATATCT
1 -TCTAAGATTACA-ATCATATCT
55419676 AAGATTGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 10 0.28
23 13 0.36
24 5 0.14
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (21 bp):
TCTAAGATTACAATCATATCT
Found at i:55421625 original size:46 final size:44
Alignment explanation
Indices: 55421524--55421803 Score: 317
Period size: 46 Copynumber: 6.6 Consensus size: 44
55421514 TACGTATGAT
*
55421524 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA-GCTAC
55421567 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
55421613 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
55421649 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
*
55421695 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
55421731 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
* *
55421777 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
55421804 AGTACTCAAA
Statistics
Matches: 206, Mismatches: 8, Indels: 43
0.80 0.03 0.17
Matches are distributed among these distances:
36 57 0.28
38 5 0.02
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.03
43 11 0.05
44 10 0.05
45 20 0.10
46 90 0.44
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (44 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
Found at i:55421654 original size:36 final size:36
Alignment explanation
Indices: 55421613--55421767 Score: 175
Period size: 36 Copynumber: 4.0 Consensus size: 36
55421603 CTAAGGCTAC
55421613 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
55421649 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* *
55421691 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
55421731 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
55421767 C
1 C
55421768 TAAAGCTACC
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 64 0.62
38 3 0.03
40 3 0.03
42 3 0.03
44 2 0.02
46 28 0.27
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:55421674 original size:82 final size:82
Alignment explanation
Indices: 55421567--55421803 Score: 429
Period size: 82 Copynumber: 2.9 Consensus size: 82
55421557 GCTAGGCTAC
* * *
55421567 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
55421632 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
55421649 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
*
55421714 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
*
55421731 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
55421796 TGATCAGA
66 TGATCAGA
55421804 AGTACTCAAA
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 150 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTATAG
Found at i:55425015 original size:19 final size:19
Alignment explanation
Indices: 55424991--55425029 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55424981 ACTTTTCACG
55424991 GCACTTTTCAACTTCAAAA
1 GCACTTTTCAACTTCAAAA
55425010 GCACTTTTCAACTTCAAAA
1 GCACTTTTCAACTTCAAAA
55425029 G
1 G
55425030 TAAACTGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (19 bp):
GCACTTTTCAACTTCAAAA
Found at i:55427572 original size:42 final size:42
Alignment explanation
Indices: 55427463--55427590 Score: 157
Period size: 43 Copynumber: 3.0 Consensus size: 42
55427453 AAGCTCGTAC
* * * *
55427463 GATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAAC
1 GATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAAT-AT
* * *
55427506 GATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATATAT
1 GATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATAT
* *
55427548 GATGCCAATGTCCCAAACATGGTCTTACACGTAAATCACATAT
1 GATGCCAATGTCCCAGACATGGTCTTACACGT-AATCAAATAT
55427591 CGAAACCCTA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 30 0.41
43 43 0.59
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (42 bp):
GATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATAT
Found at i:55436270 original size:37 final size:37
Alignment explanation
Indices: 55436209--55436354 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
55436199 TACGTATGAT
* *
55436209 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55436244 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55436281 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55436318 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55436355 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:55436371 original size:46 final size:46
Alignment explanation
Indices: 55436318--55436586 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
55436308 TAAGTGTAGC
* **
55436318 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
55436364 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
55436410 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
55436462 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
55436508 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
55436560 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
55436587 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:55436437 original size:52 final size:52
Alignment explanation
Indices: 55436361--55436580 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
55436351 TAGCTAAAGC
* *
55436361 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
55436414 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
55436466 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
55436512 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
55436564 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
55436581 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:55436483 original size:98 final size:98
Alignment explanation
Indices: 55436318--55436586 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
55436308 TAAGTGTAGC
* * *
55436318 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
55436383 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
55436417 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
55436482 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
55436515 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
55436580 GATCAGA
66 GATCAGA
55436587 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:55439161 original size:15 final size:15
Alignment explanation
Indices: 55439141--55439178 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
55439131 GTGTGACAGA
55439141 GCCCAGACCGTGTCG
1 GCCCAGACCGTGTCG
55439156 GCCCAGACCGTGTCG
1 GCCCAGACCGTGTCG
55439171 GCCCAGAC
1 GCCCAGAC
55439179 AAGGCCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.16, C:0.42, G:0.32, T:0.11
Consensus pattern (15 bp):
GCCCAGACCGTGTCG
Found at i:55442302 original size:21 final size:21
Alignment explanation
Indices: 55442253--55442304 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
55442243 AAATAAATAC
*
55442253 TAAAATCCTAAACCTTGAACT
1 TAAAATCCTAAACCCTGAACT
* * *
55442274 CAATATCCTAAACCCTGAGCT
1 TAAAATCCTAAACCCTGAACT
55442295 TAAAATCCTA
1 TAAAATCCTA
55442305 GATTTGAGAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.27, G:0.06, T:0.27
Consensus pattern (21 bp):
TAAAATCCTAAACCCTGAACT
Found at i:55442733 original size:10 final size:11
Alignment explanation
Indices: 55442697--55442733 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
55442687 AAAAAAATAA
55442697 AAAAAGTATTTT
1 AAAAA-TATTTT
55442709 AAAAATATTTT
1 AAAAATATTTT
55442720 -AAAAT-TTTT
1 AAAAATATTTT
55442729 AAAAA
1 AAAAA
55442734 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 4 0.17
10 9 0.38
11 6 0.25
12 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:55461383 original size:16 final size:17
Alignment explanation
Indices: 55461362--55461397 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
55461352 TTTTTTGTTT
55461362 TTTGGGC-TAGGTTTAG
1 TTTGGGCTTAGGTTTAG
55461378 TTTGGGCTTAGGTTTAG
1 TTTGGGCTTAGGTTTAG
55461395 TTT
1 TTT
55461398 ATTGGGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.11, C:0.06, G:0.33, T:0.50
Consensus pattern (17 bp):
TTTGGGCTTAGGTTTAG
Found at i:55461555 original size:27 final size:27
Alignment explanation
Indices: 55461515--55461572 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
55461505 TTGCTTTAAG
*
55461515 TTTTTTTTGATTGTTGTTTTACTGTCA
1 TTTTTTTTGATTGTTATTTTACTGTCA
*
55461542 TTTTGTTTTG-TTGTTATTTTATTGTCA
1 TTTT-TTTTGATTGTTATTTTACTGTCA
55461569 TTTT
1 TTTT
55461573 ATTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.10, C:0.05, G:0.14, T:0.71
Consensus pattern (27 bp):
TTTTTTTTGATTGTTATTTTACTGTCA
Found at i:55462958 original size:10 final size:10
Alignment explanation
Indices: 55462916--55462959 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
55462906 TTTTTCAAAT
55462916 AATTATAAAA
1 AATTATAAAA
*
55462926 TATTA-AAAA
1 AATTATAAAA
* *
55462935 AATTATTAAG
1 AATTATAAAA
55462945 AATTATAAAA
1 AATTATAAAA
55462955 AATTA
1 AATTA
55462960 AAATTAATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
AATTATAAAA
Found at i:55463319 original size:20 final size:21
Alignment explanation
Indices: 55463296--55463334 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55463286 TATTTATTGT
55463296 AATTTTAA-ATGTTTTTATTA
1 AATTTTAATATGTTTTTATTA
*
55463316 AATTTTAATATTTTTTTAT
1 AATTTTAATATGTTTTTAT
55463335 AATTATTTAA
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:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
AATTTTAATATGTTTTTATTA
Found at i:55463338 original size:19 final size:19
Alignment explanation
Indices: 55463295--55463338 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
55463285 ATATTTATTG
55463295 TAATTTTAAATGTTTTTAT
1 TAATTTTAAATGTTTTTAT
*
55463314 TAAATTTTAATATTTTTTTA-
1 T-AATTTTAA-ATGTTTTTAT
55463334 TAATT
1 TAATT
55463339 ATTTAAAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 9 0.41
21 8 0.36
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TAATTTTAAATGTTTTTAT
Found at i:55466533 original size:26 final size:26
Alignment explanation
Indices: 55466504--55466555 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
55466494 TAAAAGAAAA
55466504 ACACAACGAAAAATGATTTAGAACAT
1 ACACAACGAAAAATGATTTAGAACAT
55466530 ACACAACGAAAAATGATTTAGAACAT
1 ACACAACGAAAAATGATTTAGAACAT
55466556 CTATTTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (26 bp):
ACACAACGAAAAATGATTTAGAACAT
Found at i:55467045 original size:18 final size:18
Alignment explanation
Indices: 55467004--55467045 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
55466994 CTTCGGAAGC
* *
55467004 TTCTTCTTCTCCTTCGGA
1 TTCTTCTTCGCCTTCAGA
*
55467022 TGCTTCTTCGCCTTCAGA
1 TTCTTCTTCGCCTTCAGA
55467040 TTCTTC
1 TTCTTC
55467046 GTCTTCTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.33, G:0.12, T:0.48
Consensus pattern (18 bp):
TTCTTCTTCGCCTTCAGA
Found at i:55467258 original size:5 final size:5
Alignment explanation
Indices: 55467248--55467273 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55467238 TCTTTTCCCC
55467248 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
55467274 AACTTGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:55470275 original size:43 final size:40
Alignment explanation
Indices: 55470202--55470345 Score: 123
Period size: 43 Copynumber: 3.5 Consensus size: 40
55470192 AGCACCGCAT
* * *
55470202 TGCATCATCAGATAAATCGAAGGAAATATACTGGCACACATAG
1 TGCATCATCAGATAAA-CCAAAG-ATTATACT-GCACACATAG
*
55470245 TGCATCATCAGATAAACCAAAGTAGTTATAC--CACGCATAG
1 TGCATCATCAGATAAACCAAAG-A-TTATACTGCACACATAG
* * *
55470285 TGCATCATCGGATAAACCGAAAGATGAATACTGACACACATAA
1 TGCATCATCAGATAAACC-AAAGAT-TATACTG-CACACATAG
55470328 TGCATCATC-GAATAAACC
1 TGCATCATCAG-ATAAACC
55470346 GAAGGATGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
39 1 0.01
40 30 0.35
41 4 0.05
42 6 0.07
43 44 0.52
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.21
Consensus pattern (40 bp):
TGCATCATCAGATAAACCAAAGATTATACTGCACACATAG
Found at i:55470346 original size:43 final size:43
Alignment explanation
Indices: 55470280--55470366 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
55470270 TTATACCACG
* *
55470280 CATAGTGCATCATCGGATAAACCGAAAGATGAATACTGACACA
1 CATAATGCATCATCGAATAAACCGAAAGATGAATACTGACACA
*
55470323 CATAATGCATCATCGAATAAACCGAAGGATGAATACTGACACA
1 CATAATGCATCATCGAATAAACCGAAAGATGAATACTGACACA
55470366 C
1 C
55470367 TATACTAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (43 bp):
CATAATGCATCATCGAATAAACCGAAAGATGAATACTGACACA
Found at i:55470399 original size:56 final size:56
Alignment explanation
Indices: 55470312--55470422 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 56
55470302 CGAAAGATGA
* *
55470312 ATACTGACACACATAATGCATCATCGAATAAACCGAAGGA-TGAATACTGACACACT
1 ATACTAACACACATAATGCATCATCGAATAAACCGAAGCAGT-AATACTGACACACT
* * * *
55470368 ATACTAACACACATAGTGCATCATCGGATAAATCGAAGCAGTTATACTGACACAC
1 ATACTAACACACATAATGCATCATCGAATAAACCGAAGCAGTAATACTGACACAC
55470423 ATCATTGGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
56 47 0.98
57 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.21
Consensus pattern (56 bp):
ATACTAACACACATAATGCATCATCGAATAAACCGAAGCAGTAATACTGACACACT
Found at i:55471220 original size:16 final size:16
Alignment explanation
Indices: 55471199--55471250 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
55471189 TTTGGTTCGC
55471199 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55471215 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
55471231 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
55471247 TGTA
1 TGTA
55471251 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:55471297 original size:45 final size:44
Alignment explanation
Indices: 55471231--55471325 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
55471221 GGATTAGAGG
* *
55471231 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
55471276 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
55471320 TGTAAT
1 TGTAAT
55471326 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:55471495 original size:25 final size:25
Alignment explanation
Indices: 55471463--55471517 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
55471453 TAATTTAATC
*
55471463 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
55471487 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
55471512 ATATAT
1 ATATAT
55471518 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Done.