Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 78 of 163
Found at i:25352541 original size:60 final size:59
Alignment explanation
Indices: 25352432--25352550 Score: 132
Period size: 60 Copynumber: 2.0 Consensus size: 59
25352422 GTATTGATGG
* * * * * * *
25352432 TTAAATTGGCAAATTTTGTAAATATTAAAGATTAAATTTATTGAATTTTTAGAATTTAAA
1 TTAAAATGACAAATTTTATAAACATCAAAGATTAAATTTAGTAAATTTTTA-AATTTAAA
* *
25352492 TTAAAATGACAAATTTTATAAACATCAAGGATTAAATTT-GTAAAGTTTTTACATTTAAA
1 TTAAAATGACAAATTTTATAAACATCAAAGATTAAATTTAGTAAA-TTTTTAAATTTAAA
25352551 ATCAAATTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
59 10 0.20
60 39 0.80
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (59 bp):
TTAAAATGACAAATTTTATAAACATCAAAGATTAAATTTAGTAAATTTTTAAATTTAAA
Found at i:25356266 original size:50 final size:50
Alignment explanation
Indices: 25356212--25356867 Score: 442
Period size: 50 Copynumber: 13.1 Consensus size: 50
25356202 TCGGGGAAAC
* * * *
25356212 AAGATTTGCCGTCGTAGCTTTAATCTGTTTCATTGCACGGCCAGGGAAGT
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
* * * * * * ** * *
25356262 AAGATTTGCTGTTGTAGCTTTAATATTTTTAACTGCAATTTCGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
* * * * * *
25356312 AAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCACCGCTAGGGAAGT
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
* * * * * * *
25356362 AAGATTCGCAGTTGTAGCTTTAATCTTTTTAATTGCAATGTCAGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
* * * * *
25356412 AAGATTCACC-TATGTGGCTTTAATCTGTTCCACTGCA-TCGCCTGGGGAGT
1 AAGATTCGCCGT-TGTAGCTTTAATCTGTTTCACTGCACT-GCCAGGGAAGT
* * * * * * * *
25356462 AAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
* * * * * *
25356512 AAGGTTCGCCGTTGTGGCCTTAATCTGTTCCACTGCACCGCCAGGGAAAT
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
* * * * * * * *
25356562 AAGATTCACTGTTGTAGCTTTAATATTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
** * * * *
25356612 AAGATTCATCGATGTGGCTTTAATCTGTTCCACTGCA-TCGCCTGGG-AGT
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACT-GCCAGGGAAGT
* * * * * *
25356661 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATG-TAGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCA-GGGAAGT
* * * * * *
25356711 AAGGTTCGCCGTTGTGGCGTTAATCTGTTCCACTGCACCGCCAGGGAAAT
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
**** * *** *
25356761 AAGATTAATTGTTGTAGCTTTAATCT-TTTCAACTGCAATGTTGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTC-ACTGCACTGCCAGGGAAGT
* * * * * *
25356811 AAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACTGCCCGGGAAAT
1 AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
25356861 AAGATTC
1 AAGATTC
25356868 TGTCTTCACC
Statistics
Matches: 447, Mismatches: 148, Indels: 22
0.72 0.24 0.04
Matches are distributed among these distances:
49 41 0.09
50 400 0.89
51 6 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (50 bp):
AAGATTCGCCGTTGTAGCTTTAATCTGTTTCACTGCACTGCCAGGGAAGT
Found at i:25356367 original size:100 final size:100
Alignment explanation
Indices: 25356201--25356867 Score: 906
Period size: 100 Copynumber: 6.7 Consensus size: 100
25356191 TGGCTGCAGC
* ** * * * * *
25356201 GTCGGGGAAACAAGATTTGCCGTCGTAGCTTTAATCTGTTTCATTGCACGGCCAGGGAAGTAAGA
1 GTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA
** *
25356266 TTTGCTGTTGTAGCTTTAATATTTTTAACTGCAAT
66 TTCACTGTTGTAGCTTTAATCTTTTTAACTGCAAT
* * *
25356301 TTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCACCGCTAGGGAAGTAAGA
1 GTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA
* * *
25356366 TTCGCAGTTGTAGCTTTAATCTTTTTAATTGCAAT
66 TTCACTGTTGTAGCTTTAATCTTTTTAACTGCAAT
* * * *
25356401 GTCAGGGAAGCAAGATTCACC-TATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGGGAGTAAG
1 GTCGGGGAAGCAAGATTCACCGT-TGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAG
25356465 ATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAAT
65 ATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAAT
* * * *
25356501 GTCGGGGAAGCAAGGTTCGCCGTTGTGGCCTTAATCTGTTCCACTGCACCGCCAGGGAAATAAGA
1 GTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA
*
25356566 TTCACTGTTGTAGCTTTAATATTTTTAACTGCAAT
66 TTCACTGTTGTAGCTTTAATCTTTTTAACTGCAAT
* * * * *
25356601 GTCAGGGAAGCAAGATTCATCGATGTGGCTTTAATCTGTTCCACTGCATCGCCTGGG-AGTAAGA
1 GTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA
*
25356665 TTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAAT
66 TTCACTGTTGTAGCTTTAATCTTTTTAACTGCAAT
* * * * *
25356700 GTAGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTGTTCCACTGCACCGCCAGGGAAATAAGA
1 GTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA
* * *
25356765 TTAATTGTTGTAGCTTTAATCTTTTCAACTGCAAT
66 TTCACTGTTGTAGCTTTAATCTTTTTAACTGCAAT
* * * * *
25356800 GTTGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACTGCCCGGGAAATAAGA
1 GTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA
25356865 TTC
66 TTC
25356868 TGTCTTCACC
Statistics
Matches: 497, Mismatches: 67, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
99 88 0.18
100 408 0.82
101 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (100 bp):
GTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA
TTCACTGTTGTAGCTTTAATCTTTTTAACTGCAAT
Found at i:25387672 original size:12 final size:11
Alignment explanation
Indices: 25387657--25387720 Score: 60
Period size: 12 Copynumber: 5.8 Consensus size: 11
25387647 GCAACCCAAT
25387657 TTTTATTTTTA
1 TTTTATTTTTA
*
25387668 TTTT-TATTTA
1 TTTTATTTTTA
*
25387678 TTTTTTTCTTTA
1 TTTTATT-TTTA
*
25387690 CTTTATTTATTA
1 TTTTATTT-TTA
*
25387702 CTTTA-TTTTA
1 TTTTATTTTTA
25387712 TTTTATTTT
1 TTTTATTTT
25387721 ACTTATTGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
10 16 0.36
11 11 0.25
12 17 0.39
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:25387681 original size:21 final size:21
Alignment explanation
Indices: 25387657--25387700 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25387647 GCAACCCAAT
*
25387657 TTTTATT-TTTATTTTTATTTA
1 TTTTATTCTTTA-CTTTATTTA
*
25387678 TTTTTTTCTTTACTTTATTTA
1 TTTTATTCTTTACTTTATTTA
25387699 TT
1 TT
25387701 ACTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTATTCTTTACTTTATTTA
Found at i:25387694 original size:17 final size:16
Alignment explanation
Indices: 25387658--25387715 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 16
25387648 CAACCCAATT
25387658 TTTATTTTTATT-TTTA
1 TTTATTTTT-TTCTTTA
25387674 TTTATTTTTTTCTTTA
1 TTTATTTTTTTCTTTA
* *
25387690 CTTTATTTATTACTTTA
1 -TTTATTTTTTTCTTTA
25387707 TTTTATTTT
1 -TTTATTTT
25387716 ATTTTACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 2 0.06
16 13 0.36
17 21 0.58
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTTTTTCTTTA
Found at i:25387716 original size:27 final size:28
Alignment explanation
Indices: 25387664--25387727 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
25387654 AATTTTTATT
*
25387664 TTTATTT-TTATTTATTTTTTTCTTTAC
1 TTTATTTATTATTTATTTTTATCTTTAC
*
25387691 TTTATTTATTACTTTA-TTTTAT-TTTAT
1 TTTATTTATTA-TTTATTTTTATCTTTAC
*
25387718 TTTACTTATT
1 TTTATTTATT
25387728 GGATATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 20 0.62
28 8 0.25
29 4 0.12
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTATTTATTATTTATTTTTATCTTTAC
Found at i:25390553 original size:22 final size:22
Alignment explanation
Indices: 25390523--25390564 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
25390513 ACACCAAAAC
*
25390523 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
25390545 AGGCCTTTAGCGGCGCTTTT
1 AGGCCTTTAGCGGCGCTTTT
25390565 CACACAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:25398693 original size:9 final size:9
Alignment explanation
Indices: 25398679--25398711 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
25398669 CAGCAATGGT
25398679 TGTAACCTC
1 TGTAACCTC
*
25398688 TGTAACCTA
1 TGTAACCTC
25398697 TGTAACCTC
1 TGTAACCTC
25398706 TGTAAC
1 TGTAAC
25398712 ATGTTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (9 bp):
TGTAACCTC
Found at i:25398838 original size:4 final size:4
Alignment explanation
Indices: 25398831--25398856 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
25398821 ATAATGTCGC
25398831 AGGG AGGG AGGG AGGG AGGG AGGG AG
1 AGGG AGGG AGGG AGGG AGGG AGGG AG
25398857 AGAAAGCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:25399923 original size:14 final size:14
Alignment explanation
Indices: 25399885--25399929 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
25399875 TTTTAAATCT
*
25399885 TAAACCTTAAACCA
1 TAAACCTTAAACTA
*
25399899 TATACAC-TAAACTA
1 TAAAC-CTTAAACTA
25399913 TAAACCTTAAACTA
1 TAAACCTTAAACTA
25399927 TAA
1 TAA
25399930 TGATAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCTTAAACTA
Found at i:25400000 original size:20 final size:22
Alignment explanation
Indices: 25399975--25400026 Score: 72
Period size: 20 Copynumber: 2.4 Consensus size: 22
25399965 ACTAGTTAAT
25399975 CTAAACCCT-AAATCATAAA-C
1 CTAAACCCTAAAATCATAAACC
*
25399995 CTAAACCCTAAAATTATAAACC
1 CTAAACCCTAAAATCATAAACC
25400017 CATAAACCCT
1 C-TAAACCCT
25400027 TAACACATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.32
21 9 0.32
22 2 0.07
23 8 0.29
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (22 bp):
CTAAACCCTAAAATCATAAACC
Found at i:25400074 original size:7 final size:7
Alignment explanation
Indices: 25400062--25400185 Score: 65
Period size: 7 Copynumber: 17.6 Consensus size: 7
25400052 CCCCAGCCTT
25400062 TAAACCA
1 TAAACCA
25400069 TAAACCA
1 TAAACCA
*
25400076 TAAATCA
1 TAAACCA
*
25400083 TAAACCT
1 TAAACCA
***
25400090 TAAAATGG
1 T-AAACCA
25400098 TAACACC-
1 TAA-ACCA
*
25400105 TAAACCT
1 TAAACCA
25400112 TAAACTC-
1 TAAAC-CA
25400119 TAAACCA
1 TAAACCA
* *
25400126 TATACCC
1 TAAACCA
25400133 TAAACCA
1 TAAACCA
* *
25400140 AAAACCC
1 TAAACCA
*
25400147 T-AATCA
1 TAAACCA
*
25400153 TAACCCA
1 TAAACCA
25400160 TAAACCCA
1 TAAA-CCA
*
25400168 TAATCCA
1 TAAACCA
*
25400175 TAAACCT
1 TAAACCA
25400182 TAAA
1 TAAA
25400186 ATGGTAACAC
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
6 8 0.09
7 67 0.77
8 12 0.14
ACGTcount: A:0.49, C:0.28, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:25400175 original size:15 final size:15
Alignment explanation
Indices: 25400151--25400180 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25400141 AAACCCTAAT
25400151 CATAACCCATAAACC
1 CATAACCCATAAACC
*
25400166 CATAATCCATAAACC
1 CATAACCCATAAACC
25400181 TTAAAATGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (15 bp):
CATAACCCATAAACC
Found at i:25400577 original size:15 final size:15
Alignment explanation
Indices: 25400553--25400582 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25400543 AACCATATAT
25400553 CATAACCCATAAACC
1 CATAACCCATAAACC
*
25400568 CATAATCCATAAACC
1 CATAACCCATAAACC
25400583 TTAAAATGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (15 bp):
CATAACCCATAAACC
Found at i:25400587 original size:22 final size:21
Alignment explanation
Indices: 25400541--25400587 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
25400531 AAAAACGCCG
*
25400541 TAAACCATATATCATAACCCA
1 TAAACCATATATCATAAACCA
*
25400562 TAAACCCATA-ATCCATAAACCT
1 TAAA-CCATATAT-CATAAACCA
25400584 TAAA
1 TAAA
25400588 ATGGTAACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCATATATCATAAACCA
Found at i:25400893 original size:402 final size:402
Alignment explanation
Indices: 25400141--25400947 Score: 1589
Period size: 402 Copynumber: 2.0 Consensus size: 402
25400131 CCTAAACCAA
*
25400141 AAACCCTAATCATAACCCATAAACCCATAATCCATAAACCTTAAAATGGTAACACCTAAACCTTA
1 AAACCATAATCATAACCCATAAACCCATAATCCATAAACCTTAAAATGGTAACACCTAAACCTTA
25400206 AACTCTAAACCATATACCCTAAACTATAGTGATAATTAATTCAATATTTTAAAATTAATATTATC
66 AACTCTAAACCATATACCCTAAACTATAGTGATAATTAATTCAATATTTTAAAATTAATATTATC
25400271 TCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACAATCAGTAATGTACCCAA
131 TCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACAATCAGTAATGTACCCAA
25400336 AAAAAACTTTAAAATTATTTTAAATAATAGTATTTTAATTTTTTTCATTTTCAACAAATATTTTT
196 AAAAAACTTTAAAATTATTTTAAATAATAGTATTTTAATTTTTTTCATTTTCAACAAATATTTTT
25400401 CTATGTTTTTTATTTCAAATTATTTCTACGTGTCATTTTTTTATGAAGATTTTAAATATTCAATT
261 CTATGTTTTTTATTTCAAATTATTTCTACGTGTCATTTTTTTATGAAGATTTTAAATATTCAATT
25400466 AAAAATAAATTGAATTTTAATTAATATAAATTAATTAAATCCCGGAGCATTAGCGGCGCTTCTCC
326 AAAAATAAATTGAATTTTAATTAATATAAATTAATTAAATCCCGGAGCATTAGCGGCGCTTCTCC
25400531 AAAAACGCCG-T
391 AAAAACGCCGCT
25400542 AAACCATATATCATAACCCATAAACCCATAATCCATAAACCTTAAAATGGTAACACCTAAACCTT
1 AAACCATA-ATCATAACCCATAAACCCATAATCCATAAACCTTAAAATGGTAACACCTAAACCTT
25400607 AAACTCTAAACCATATACCCTAAACTATAGTGATAATTAATTCAATATTTTAAAATTAATATTAT
65 AAACTCTAAACCATATACCCTAAACTATAGTGATAATTAATTCAATATTTTAAAATTAATATTAT
25400672 CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACAATCAGTAATGTACCCA
130 CTCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACAATCAGTAATGTACCCA
25400737 AAAAAAACTTTAAAATTATTTTAAATAATAGTATTTTAATTTTTTTCATTTTCAACAAATATTTT
195 AAAAAAACTTTAAAATTATTTTAAATAATAGTATTTTAATTTTTTTCATTTTCAACAAATATTTT
25400802 TCTATGTTTTTTATTTCAAATTATTTCTACGTGTCATTTTTTTATGAAGATTTTAAATATTCAAT
260 TCTATGTTTTTTATTTCAAATTATTTCTACGTGTCATTTTTTTATGAAGATTTTAAATATTCAAT
25400867 TAAAAATAAATTGAATTTTAATTAATATAAATTAATTAAATCCCGGAGCATTAGCGGCGCTTCTC
325 TAAAAATAAATTGAATTTTAATTAATATAAATTAATTAAATCCCGGAGCATTAGCGGCGCTTCTC
25400932 CAAAAACGCCGCT
390 CAAAAACGCCGCT
25400945 AAA
1 AAA
25400948 GTCCAGAGCA
Statistics
Matches: 403, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
401 7 0.02
402 392 0.97
403 4 0.01
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.38
Consensus pattern (402 bp):
AAACCATAATCATAACCCATAAACCCATAATCCATAAACCTTAAAATGGTAACACCTAAACCTTA
AACTCTAAACCATATACCCTAAACTATAGTGATAATTAATTCAATATTTTAAAATTAATATTATC
TCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAACAATCAGTAATGTACCCAA
AAAAAACTTTAAAATTATTTTAAATAATAGTATTTTAATTTTTTTCATTTTCAACAAATATTTTT
CTATGTTTTTTATTTCAAATTATTTCTACGTGTCATTTTTTTATGAAGATTTTAAATATTCAATT
AAAAATAAATTGAATTTTAATTAATATAAATTAATTAAATCCCGGAGCATTAGCGGCGCTTCTCC
AAAAACGCCGCT
Found at i:25400976 original size:41 final size:41
Alignment explanation
Indices: 25400903--25401196 Score: 426
Period size: 41 Copynumber: 7.2 Consensus size: 41
25400893 ATAAATTAAT
* *
25400903 TAAATCCCGGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
1 TAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
* * * *
25400944 TAAAGTCCAGAGCATTAGTGGCACTTCCCCAAAAACGCCGC
1 TAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
* * *
25400985 TAAAGCCCAGAGCATTAGCGGCGATTTTCCAAAAACACCGC
1 TAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
* * *
25401026 TAAAGCCCAGAACATTAGCGGCGCTTCTCTAAAAGCGCCGC
1 TAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
*
25401067 TAAAGCCCAGAGCATTAACGGCGCTTCTCCAAAAACGCCGC
1 TAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
* * *
25401108 TAAAGCCTAGAGCATTAGCGGCACTTCTCCAAAAACGCCAC
1 TAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
* *
25401149 TAAAGCCCAGAGCTTTAGCGGCGCTTTTCCAAAAACGCCGC
1 TAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
25401190 TAAAGCC
1 TAAAGCC
25401197 TCGAAAAGCT
Statistics
Matches: 221, Mismatches: 32, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 221 1.00
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.17
Consensus pattern (41 bp):
TAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCGC
Found at i:25401315 original size:40 final size:40
Alignment explanation
Indices: 25401263--25401368 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 40
25401253 AAAACGCCGC
*
25401263 TAATACTTTATTTTTAGCGGCGTTTTTC-AGAAAGCACCGA
1 TAATACTCTATTTTTAGCGGCGTTTTTCGA-AAAGCACCGA
* * * *
25401303 TAATGCTCTA-TTTTAGCGGTG-TTTTCGTAAAAGCGCCGC
1 TAATACTCTATTTTTAGCGGCGTTTTTCG-AAAAGCACCGA
* *
25401342 TAATACTCGATTTTTAGCGACGTTTTT
1 TAATACTCTATTTTTAGCGGCGTTTTT
25401369 TGTCCAAACG
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
38 5 0.09
39 26 0.49
40 18 0.34
41 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (40 bp):
TAATACTCTATTTTTAGCGGCGTTTTTCGAAAAGCACCGA
Found at i:25406846 original size:88 final size:89
Alignment explanation
Indices: 25406664--25406849 Score: 204
Period size: 88 Copynumber: 2.1 Consensus size: 89
25406654 NNNNNNNNNG
* * *
25406664 AGGCAAGGCTGGTATCTTCGATCTACTTCGCTGTCGATGCGGGAATGCAAGATCTGCTATCTTTA
1 AGGCAAGGCTGGTATCTTCGATCTACTTCGCTGTCGATACAGGAAGGCAAGATCTGCTATCTTTA
25406729 ACCTACTCCACTACAACCTAGGGA
66 ACCTACTCCACTACAACCTAGGGA
* * * * *
25406753 A-GCAAGGTTGGTATCTTTGATCTGCTTCG-TCGTC-AGTACAGGAAGGTAAGATCTGTTAT-TT
1 AGGCAAGGCTGGTATCTTCGATCTACTTCGCT-GTCGA-TACAGGAAGGCAAGATCTGCTATCTT
* *
25406814 TCAACCTGCTCCGCTACAAACC-A-GGA
64 T-AACCTACTCCACTAC-AACCTAGGGA
25406840 AGGCAAGGCT
1 AGGCAAGGCT
25406850 TTGTGATTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
87 9 0.11
88 67 0.83
89 5 0.06
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (89 bp):
AGGCAAGGCTGGTATCTTCGATCTACTTCGCTGTCGATACAGGAAGGCAAGATCTGCTATCTTTA
ACCTACTCCACTACAACCTAGGGA
Found at i:25413479 original size:19 final size:19
Alignment explanation
Indices: 25413455--25413526 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
25413445 CATATCTTCG
* *
25413455 AAGATTGCGTATCATATCC
1 AAGATTGCATATCATATCT
25413474 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCATATCT
25413495 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCT
25413514 AAGATTGCATATC
1 AAGATTGCATATC
25413527 CTTGAAGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 32 0.65
21 17 0.35
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (19 bp):
AAGATTGCATATCATATCT
Found at i:25414098 original size:50 final size:50
Alignment explanation
Indices: 25414036--25414214 Score: 155
Period size: 49 Copynumber: 3.5 Consensus size: 50
25414026 CAATGTCATA
* * * ** *
25414036 TCCCAGATATGGTCATACATTGGAGTTCTCATATCGGTGTCC-ATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG-CCAACGCCATG
* * *
25414086 TCCCAGACATGGTCTTAC-GGGGACCTCTCATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* * ***
25414135 TCCCAGACATGGTCTTACATGGGACCCCTCATAATCTCAGCAATGCCAATTTCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC-G--GTGCCAACGCCATG
25414191 TCCCAGACATGGTCTTACATGGGA
1 TCCCAGACATGGTCTTACATGGGA
25414215 TCTCATTCCT
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
48 2 0.02
49 39 0.38
50 27 0.26
53 1 0.01
54 1 0.01
56 34 0.33
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:25418620 original size:16 final size:17
Alignment explanation
Indices: 25418599--25418631 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25418589 CACATTGAAG
25418599 TGTTTT-TTGAAAACCT
1 TGTTTTATTGAAAACCT
25418615 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
25418632 CTTCTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTTTATTGAAAACCT
Found at i:25419559 original size:32 final size:32
Alignment explanation
Indices: 25419523--25419678 Score: 192
Period size: 32 Copynumber: 5.0 Consensus size: 32
25419513 CCGTAAGTAC
* *
25419523 AGTAATATGATTGGCACAAAGCCATCTGTAGT
1 AGTAATATGATCGGCACAAAGCCATCAGTAGT
* *
25419555 AGTAATATGATCGGCACACAGCCATCAGTAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAGT
*
25419587 GGTAATATGATCGGCACAAAGCCATC---AGT
1 AGTAATATGATCGGCACAAAGCCATCAGTAGT
* * *
25419616 AGTAATATGATCGGCACATAGCAATCAGTAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAGT
* * *
25419648 GGTAATATGATCGACACAAATCCATCAGTAG
1 AGTAATATGATCGGCACAAAGCCATCAGTAG
25419679 CATCGCAGCA
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
29 25 0.24
32 79 0.76
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (32 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAGT
Found at i:25419647 original size:61 final size:61
Alignment explanation
Indices: 25419524--25419678 Score: 238
Period size: 61 Copynumber: 2.5 Consensus size: 61
25419514 CGTAAGTACA
* *
25419524 GTAATATGATTGGCACAAAGCCATCTGTAGTAGTAATATGATCGGCACACAGCCATCAGTAATG
1 GTAATATGATCGGCACAAAGCCATC---AGTAGTAATATGATCGGCACACAGCAATCAGTAATG
*
25419588 GTAATATGATCGGCACAAAGCCATCAGTAGTAATATGATCGGCACATAGCAATCAGTAATG
1 GTAATATGATCGGCACAAAGCCATCAGTAGTAATATGATCGGCACACAGCAATCAGTAATG
* *
25419649 GTAATATGATCGACACAAATCCATCAGTAG
1 GTAATATGATCGGCACAAAGCCATCAGTAG
25419679 CATCGCAGCA
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
61 62 0.72
64 24 0.28
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (61 bp):
GTAATATGATCGGCACAAAGCCATCAGTAGTAATATGATCGGCACACAGCAATCAGTAATG
Found at i:25419871 original size:24 final size:24
Alignment explanation
Indices: 25419844--25419925 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
25419834 CCATGCTCAG
*
25419844 AATCAGTCACACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* * *
25419868 AATCAGTGATACCAATTACAGACA
1 AATCAGTCATACAAATCACAGACA
* **
25419892 AATCTGTCATTTAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
25419916 AATCTGTCAT
1 AATCAGTCAT
25419926 TTACATCTCG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:25419926 original size:24 final size:24
Alignment explanation
Indices: 25419856--25419977 Score: 118
Period size: 24 Copynumber: 5.1 Consensus size: 24
25419846 TCAGTCACAC
* **
25419856 AAATCACAGACAAATCAGTGATAC
1 AAATCACAGACAAATCAGTCATTT
* * *
25419880 CAATTACAGACAAATCTGTCATTT
1 AAATCACAGACAAATCAGTCATTT
*
25419904 AAATCACAGACAAATCTGTCATTT
1 AAATCACAGACAAATCAGTCATTT
* * * *
25419928 ACATCTCGGACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
* * *
25419952 ACATCACAGGCAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
25419976 AA
1 AA
25419978 CCCCAAGGGG
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 81 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (24 bp):
AAATCACAGACAAATCAGTCATTT
Found at i:25420037 original size:33 final size:33
Alignment explanation
Indices: 25419995--25420078 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 33
25419985 GGGCAAAATA
25419995 GTCATTTTACCCTACAGGGGCATTGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTGGTATTTTG
* *
25420028 GTCATTTTACCCTTC----G-A-GGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTGGTATTTTG
25420055 GTCATTTTACCCTACAGGGGCATT
1 GTCATTTTACCCTACAGGGGCATT
25420079 ACCGTCATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
27 23 0.56
28 1 0.02
29 1 0.02
31 1 0.02
32 1 0.02
33 14 0.34
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (33 bp):
GTCATTTTACCCTACAGGGGCATTGGTATTTTG
Found at i:25440578 original size:41 final size:44
Alignment explanation
Indices: 25440477--25440611 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 44
25440467 ATATTGAACA
* * * * * *
25440477 ATGCCAATGTGCCAGACGTGGTCTTACATGCT-ATCTCATAT-CG
1 ATGCCAATATCCCAGACATGGTCTTACACG-TAATCACATATATG
*
25440520 ATGCCACTATCCCAGACAAT-GTCTTACACG-AATCA-A-ATATG
1 ATGCCAATATCCCAGAC-ATGGTCTTACACGTAATCACATATATG
* * *
25440561 ATGCCAATGTCCTAGACATGGTCTTACATGTAATCACATATATTG
1 ATGCCAATATCCCAGACATGGTCTTACACGTAATCACATATA-TG
25440606 ATGCCA
1 ATGCCA
25440612 TCGTCCCAGA
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
40 4 0.05
41 25 0.34
42 8 0.11
43 24 0.33
44 4 0.05
45 8 0.11
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (44 bp):
ATGCCAATATCCCAGACATGGTCTTACACGTAATCACATATATG
Found at i:25446582 original size:54 final size:54
Alignment explanation
Indices: 25446517--25446898 Score: 414
Period size: 54 Copynumber: 7.1 Consensus size: 54
25446507 ATTCGTCGGC
**
25446517 AAATGACCGAAATAATCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
* * * * *
25446571 AAATGATCGAAACACCCCCATAGGAT-AAATGATTGAAATA-CCCCGAAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
* * * * * *
25446623 AAATGACCGAAATACACCCATAAGGTAAAATGA-CTGCAATGCCCCCGAAGGGAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCCAAAGGGTA
* * * * *
25446677 AAATGACCAAAACACCCCCATAGGGTAAAATGATCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
* *
25446731 AAATGACCGAAATACCCCCATAGGGTAAAAT-AACTGAAATACCCCTAAAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCCAAAGGGTA
** * * ** * *
25446785 AAATGAATGAAATACCCCCATAGGGTAGAATAATTAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
* * * * *
25446839 AAATGACTGGAACA-CCCCATAGGGTAAAATGATCGAAATACCCCGATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
25446892 AAATGAC
1 AAATGAC
25446899 TGTTATACCC
Statistics
Matches: 272, Mismatches: 50, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
52 32 0.12
53 65 0.24
54 173 0.64
55 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (54 bp):
AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
Found at i:25446906 original size:27 final size:27
Alignment explanation
Indices: 25446517--25446909 Score: 324
Period size: 27 Copynumber: 14.7 Consensus size: 27
25446507 ATTCGTCGGC
* *
25446517 AAATGACCGAAATAATCCC-ATAGGGTA
1 AAATGACTGAAAT-ACCCCGATAGGGTA
* *
25446544 AAATGA-TCGAAATACCCCCAAAGGGTA
1 AAATGACT-GAAATACCCCGATAGGGTA
* * *
25446571 AAATGA-TCGAAACACCCCCATAGGAT-
1 AAATGACT-GAAATACCCCGATAGGGTA
*
25446597 AAATGATTGAAATACCCCGA-AGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
* *
25446623 AAATGACCGAAATACACCC-ATAAGGTA
1 AAATGACTGAAATAC-CCCGATAGGGTA
* * *
25446650 AAATGACTGCAATGCCCCCGA-AGGGAA
1 AAATGACTGAAAT-ACCCCGATAGGGTA
** * *
25446677 AAATGACCAAAACACCCCCATAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
*
25446704 AAATGA-TCAAAATACCCTCGA-AGGGTA
1 AAATGACT-GAAATACCC-CGATAGGGTA
* *
25446731 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
* * *
25446758 AAATAACTGAAATACCCCTAAAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
* *
25446785 AAATGAATGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
* * * *
25446812 GAATAATTAAAATACCCTC-ATAGGGTA
1 AAATGACTGAAATACCC-CGATAGGGTA
* *
25446839 AAATGACTGGAACACCCC-ATAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
25446865 AAATGA-TCGAAATACCCCGATAGGGTA
1 AAATGACT-GAAATACCCCGATAGGGTA
**
25446892 AAATGACTGTTATACCCC
1 AAATGACTGAAATACCCC
25446910 TAGGAGATGA
Statistics
Matches: 297, Mismatches: 52, Indels: 34
0.78 0.14 0.09
Matches are distributed among these distances:
25 5 0.02
26 64 0.22
27 222 0.75
28 6 0.02
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (27 bp):
AAATGACTGAAATACCCCGATAGGGTA
Found at i:25447080 original size:26 final size:26
Alignment explanation
Indices: 25447051--25447113 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
25447041 TGATACTAGT
*
25447051 AGCTTTGCTGCGATACTATTACTGGC
1 AGCTTTGCTGCGATACTACTACTGGC
* * *
25447077 AGCTTTGTTGCGATGCTACTACTGGT
1 AGCTTTGCTGCGATACTACTACTGGC
25447103 AGCTTTGCTGC
1 AGCTTTGCTGC
25447114 AACATTGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (26 bp):
AGCTTTGCTGCGATACTACTACTGGC
Found at i:25447263 original size:28 final size:28
Alignment explanation
Indices: 25447220--25447313 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 28
25447210 ATTACATTGT
* * *
25447220 ACTGATACTGTGTTGGGCTAAGGCACAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
*
25447248 ACTGTTACTGTATTGGGTTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* * *
25447276 ATTGTTTCTGTATCGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
*
25447304 AATG-TACTGT
1 ACTGTTACTGT
25447314 TACTGAATAG
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 5 0.09
28 51 0.91
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:25451690 original size:19 final size:19
Alignment explanation
Indices: 25451666--25451732 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
25451656 AGTGCATTCA
25451666 AACATAATTCACTTGAATT
1 AACATAATTCACTTGAATT
* * * *
25451685 AACATAAAGTAAGTTGCATT
1 AACAT-AATTCACTTGAATT
25451705 CAAACATAATTCACTTGAATT
1 --AACATAATTCACTTGAATT
25451726 AACATAA
1 AACATAA
25451733 AGTAAGCCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 12 0.32
20 10 0.27
21 10 0.27
22 5 0.14
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (19 bp):
AACATAATTCACTTGAATT
Found at i:25451715 original size:41 final size:41
Alignment explanation
Indices: 25451658--25451738 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
25451648 CACATGTTAG
25451658 TGCATTCAAACATAATTCACTTGAATTAACATAAAGTAAGT
1 TGCATTCAAACATAATTCACTTGAATTAACATAAAGTAAGT
25451699 TGCATTCAAACATAATTCACTTGAATTAACATAAAGTAAG
1 TGCATTCAAACATAATTCACTTGAATTAACATAAAGTAAG
25451739 CCATTATACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (41 bp):
TGCATTCAAACATAATTCACTTGAATTAACATAAAGTAAGT
Found at i:25460109 original size:4 final size:4
Alignment explanation
Indices: 25460095--25460128 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
25460085 TTCAAAAAAG
*
25460095 GAAA TAAA GAAA GAAA GAAA GAAA GAAA -AAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
25460129 CAAAGGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:25463187 original size:11 final size:12
Alignment explanation
Indices: 25463156--25463180 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25463146 TAAACTTTCG
25463156 AAATATTTGAAA
1 AAATATTTGAAA
25463168 AAATATTTGAAA
1 AAATATTTGAAA
25463180 A
1 A
25463181 CTATTTGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AAATATTTGAAA
Found at i:25479840 original size:20 final size:20
Alignment explanation
Indices: 25479814--25479910 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
25479804 CTTGTATGAG
25479814 TTTGCACTTTGGTGCCTCTGA
1 TTTGCACTTTGGTGCCTCT-A
* *** *
25479835 -TTGCACATCAATTCCTCTA
1 TTTGCACTTTGGTGCCTCTA
* *
25479854 TTTGGACTTCGGTGCCTCTA
1 TTTGCACTTTGGTGCCTCTA
*
25479874 TTTGCACTTTGGTGCTTCTGA
1 TTTGCACTTTGGTGCCTCT-A
25479895 -TTGCACATTT-GTGCCT
1 TTTGCAC-TTTGGTGCCT
25479911 TTATCTAAAC
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.02
20 54 0.92
21 4 0.07
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (20 bp):
TTTGCACTTTGGTGCCTCTA
Found at i:25479930 original size:60 final size:60
Alignment explanation
Indices: 25479814--25479930 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
25479804 CTTGTATGAG
* * ** **
25479814 TTTGCACTTTGGTGCCTCTGATTGCACATCAATTCCTCTATTTGGACTTCGGTGCCTCTA
1 TTTGCACTTTGGTGCCTCTGATTGCACATCAATGCCTCTATCTAAACTTCAATGCCTCTA
* *** *
25479874 TTTGCACTTTGGTGCTTCTGATTGCACATTTGTGCCTTTATCTAAACTTCAATGCCT
1 TTTGCACTTTGGTGCCTCTGATTGCACATCAATGCCTCTATCTAAACTTCAATGCCT
25479931 TTGTTACGCA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (60 bp):
TTTGCACTTTGGTGCCTCTGATTGCACATCAATGCCTCTATCTAAACTTCAATGCCTCTA
Found at i:25484432 original size:2 final size:2
Alignment explanation
Indices: 25484425--25484454 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25484415 TTCAAGAAAC
*
25484425 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25484455 CATGCCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:25490724 original size:2 final size:2
Alignment explanation
Indices: 25490717--25490741 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25490707 GAAAGACACC
25490717 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
25490742 ATGGGCATAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:25493152 original size:30 final size:32
Alignment explanation
Indices: 25493100--25493158 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
25493090 AATTAGACAC
25493100 TTTTAAGAAGTTAATGATCAAATTCAACTATT
1 TTTTAAGAAGTTAATGATCAAATTCAACTATT
* *
25493132 TTTTAA-AAGTTTATG-TCAAATTTAACT
1 TTTTAAGAAGTTAATGATCAAATTCAACT
25493159 CTAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 8 0.32
32 6 0.24
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTTAAGAAGTTAATGATCAAATTCAACTATT
Found at i:25495455 original size:27 final size:27
Alignment explanation
Indices: 25495425--25495491 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
25495415 CCTATCTTAG
*
25495425 AGGCGCCAATGGTGGTGCC-TTTCTGAC
1 AGGCGCCAATGGTGGTGCCATGT-TGAC
* * * *
25495452 AGGCGCCACTAGTTGTGCCATGTTGAG
1 AGGCGCCAATGGTGGTGCCATGTTGAC
25495479 AGGCGCCAATGGT
1 AGGCGCCAATGGT
25495492 CTTATTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.24, G:0.34, T:0.24
Consensus pattern (27 bp):
AGGCGCCAATGGTGGTGCCATGTTGAC
Found at i:25498349 original size:18 final size:18
Alignment explanation
Indices: 25498328--25498381 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
25498318 AAGGCAACAT
25498328 AAATTAAATTGATAAATA
1 AAATTAAATTGATAAATA
*
25498346 AAATTAAA---AGAAA-A
1 AAATTAAATTGATAAATA
*
25498360 AATTTAAATTGATAAATA
1 AAATTAAATTGATAAATA
25498378 AAAT
1 AAAT
25498382 GCCAACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 8 0.29
15 4 0.14
17 4 0.14
18 12 0.43
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (18 bp):
AAATTAAATTGATAAATA
Found at i:25498380 original size:19 final size:19
Alignment explanation
Indices: 25498331--25498381 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 19
25498321 GCAACATAAA
25498331 TTAAATTGATAAATAAAA-
1 TTAAATTGATAAATAAAAT
*
25498349 TTAAA---A-GAA-AAAAT
1 TTAAATTGATAAATAAAAT
25498363 TTAAATTGATAAATAAAAT
1 TTAAATTGATAAATAAAAT
25498382 GCCAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 11
0.66 0.05 0.29
Matches are distributed among these distances:
13 4 0.16
14 7 0.28
15 1 0.04
17 1 0.04
18 7 0.28
19 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
TTAAATTGATAAATAAAAT
Found at i:25500386 original size:15 final size:16
Alignment explanation
Indices: 25500366--25500404 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
25500356 ATAAAAAATC
25500366 ATATAAAAA-TACATT
1 ATATAAAAATTACATT
25500381 ATATAAAAATTACATT
1 ATATAAAAATTACATT
25500397 ATATAAAA
1 ATATAAAA
25500405 TTTAAATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:25500714 original size:57 final size:58
Alignment explanation
Indices: 25500607--25500718 Score: 147
Period size: 57 Copynumber: 1.9 Consensus size: 58
25500597 CAATATTTAT
* *
25500607 TTAAACAAAAAATATTTTTAATATAAAAAATTGATTTGCGCCTGTTAGATAGGCGGGA
1 TTAAACAAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTCAGATAGGCGGGA
* * * *
25500665 TTAAA-AAAATATATTTTTCAGTAT-AAAAATTTATTCGCGTCTGTCAGATAGGCG
1 TTAAACAAAAAATATTTTT-AATATAAAAAATTGATTCGCGCCTGTCAGATAGGCG
25500719 CTATTAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 38 0.81
58 9 0.19
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (58 bp):
TTAAACAAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTCAGATAGGCGGGA
Found at i:25501674 original size:17 final size:17
Alignment explanation
Indices: 25501649--25501683 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
25501639 ATTAATAATT
25501649 AATAACAAAAAAATCAC
1 AATAACAAAAAAATCAC
*
25501666 AATATCAAAAAAATCAC
1 AATAACAAAAAAATCAC
25501683 A
1 A
25501684 TTACCTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (17 bp):
AATAACAAAAAAATCAC
Found at i:25512273 original size:44 final size:44
Alignment explanation
Indices: 25512210--25512385 Score: 352
Period size: 44 Copynumber: 4.0 Consensus size: 44
25512200 ATTTAAGAAC
25512210 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
1 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
25512254 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
1 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
25512298 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
1 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
25512342 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
1 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
25512386 TAGATCCGTG
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 132 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.55
Consensus pattern (44 bp):
CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
Found at i:25523941 original size:29 final size:30
Alignment explanation
Indices: 25523860--25523930 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
25523850 GATTAAATCA
*
25523860 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATATATTTGAACC
* * *
25523890 ACAACTAAAGTTTCACGTATATATTTGCACC
1 A-AATTAAAGTTTCAAGTATATATTTGAACC
25523921 AAATTAAAGT
1 AAATTAAAGT
25523931 CCATGTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 9 0.26
31 26 0.74
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATATATTTGAACC
Found at i:25525502 original size:26 final size:25
Alignment explanation
Indices: 25525469--25525540 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
25525459 TTAGCTCTTA
25525469 TAAGCTTCCCGATTATAGGCTCTTCG
1 TAAGCTTCCCGATTAT-GGCTCTTCG
* * *
25525495 TGAGCTT-CCTATTAATTGGCTCTTTG
1 TAAGCTTCCCGATT-A-TGGCTCTTCG
25525521 TAAGCTTCCCGA-TATGGCTC
1 TAAGCTTCCCGATTATGGCTC
25525541 GTTTGAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
24 6 0.16
25 6 0.16
26 22 0.58
27 4 0.11
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (25 bp):
TAAGCTTCCCGATTATGGCTCTTCG
Found at i:25525641 original size:24 final size:25
Alignment explanation
Indices: 25525609--25525678 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
25525599 AGCTACTCGT
25525609 TATAGGCTCGCATAAGCTTCCTG-AA
1 TATA-GCTCGCATAAGCTTCCTGTAA
** * *
25525634 TATAGCTCTTATGAGCTTCCTGTTA
1 TATAGCTCGCATAAGCTTCCTGTAA
* * *
25525659 TACAGCCCGGATAAGCTTCC
1 TATAGCTCGCATAAGCTTCC
25525679 CGTTACATGG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (25 bp):
TATAGCTCGCATAAGCTTCCTGTAA
Found at i:25527480 original size:21 final size:21
Alignment explanation
Indices: 25527451--25527497 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
25527441 CCCATATATT
*
25527451 TAATGTAAACATACTTTT-TCA
1 TAATATAAACAT-CTTTTCTCA
*
25527472 TAATATAAACATGTTTTCTCA
1 TAATATAAACATCTTTTCTCA
25527493 TAATA
1 TAATA
25527498 CAATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (21 bp):
TAATATAAACATCTTTTCTCA
Found at i:25529271 original size:22 final size:22
Alignment explanation
Indices: 25529246--25529291 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
25529236 AAAGTAGTAG
* * *
25529246 GCACTGAAGTGCGGAACGATAA
1 GCACCGAAGTACGAAACGATAA
*
25529268 GCACCGAAGTACGAAACGGTAA
1 GCACCGAAGTACGAAACGATAA
25529290 GC
1 GC
25529292 GTTAAAACGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.22, G:0.30, T:0.11
Consensus pattern (22 bp):
GCACCGAAGTACGAAACGATAA
Found at i:25531927 original size:45 final size:42
Alignment explanation
Indices: 25531835--25531966 Score: 140
Period size: 45 Copynumber: 3.0 Consensus size: 42
25531825 CAGATACATG
* ***
25531835 GTGGATCAGCACATAGC-ACCACCCTTATAGTCAATGATACTTG
1 GTGGATCAGCACATAGCAACCA-CCTTATAATCAATG-TACCCA
25531878 GTGGATTCAGCACATAGCAACCACCTTCATAATCAATAGTACCCA
1 GTGGA-TCAGCACATAGCAACCACCTT-ATAATCAAT-GTACCCA
*
25531923 GTGGAATCAGCACACAGCAACCACCTTTATAATCAATGGTACCC
1 GTGG-ATCAGCACATAGCAACCACC-TTATAATCAAT-GTACCC
25531967 GGTACACGTA
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
43 5 0.06
44 16 0.21
45 52 0.68
46 4 0.05
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (42 bp):
GTGGATCAGCACATAGCAACCACCTTATAATCAATGTACCCA
Found at i:25532237 original size:17 final size:17
Alignment explanation
Indices: 25532215--25532249 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25532205 CAATTTAGTC
25532215 CAAAAATCACATTTTTG
1 CAAAAATCACATTTTTG
* *
25532232 CAAAAATTATATTTTTG
1 CAAAAATCACATTTTTG
25532249 C
1 C
25532250 CCCTAACGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (17 bp):
CAAAAATCACATTTTTG
Found at i:25535261 original size:21 final size:22
Alignment explanation
Indices: 25535224--25535267 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
25535214 GTGGCATTAC
25535224 ATAATCTGTATAATC-TTTAAA
1 ATAATCTGTATAATCTTTTAAA
*
25535245 ATAATCTG-ATATTTCTTTTAAA
1 ATAATCTGTATA-ATCTTTTAAA
25535267 A
1 A
25535268 CTGAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 10 0.50
22 7 0.35
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
ATAATCTGTATAATCTTTTAAA
Found at i:25544147 original size:18 final size:18
Alignment explanation
Indices: 25544121--25544156 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25544111 AGATTGAATT
*
25544121 ATATTATTAAATTTATTA
1 ATATAATTAAATTTATTA
*
25544139 ATATAATTATATTTATTA
1 ATATAATTAAATTTATTA
25544157 TGCATGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATAATTAAATTTATTA
Found at i:25546518 original size:20 final size:21
Alignment explanation
Indices: 25546473--25546518 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
25546463 GCTCATCTGG
* *
25546473 TTTTGCTGCTGCTCCCTCCCT
1 TTTTCCTGCTGCTCCCGCCCT
*
25546494 GTTTCCTGCTGC-CCCGCCCT
1 TTTTCCTGCTGCTCCCGCCCT
25546514 TTTTC
1 TTTTC
25546519 TAATATTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.00, C:0.43, G:0.15, T:0.41
Consensus pattern (21 bp):
TTTTCCTGCTGCTCCCGCCCT
Found at i:25551789 original size:20 final size:22
Alignment explanation
Indices: 25551764--25551807 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
25551754 TAATTTAGAG
25551764 ATCACTTA-AACAAAAA-AAAA
1 ATCACTTATAACAAAAATAAAA
25551784 ATCACTTATAACAAAAATAAAA
1 ATCACTTATAACAAAAATAAAA
25551806 AT
1 AT
25551808 AAGTATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
21 8 0.36
22 6 0.27
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (22 bp):
ATCACTTATAACAAAAATAAAA
Found at i:25552321 original size:10 final size:10
Alignment explanation
Indices: 25552299--25552336 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
25552289 GCGGGTATTT
25552299 TACAAAAATAA
1 TACAAAAA-AA
25552310 TACAAAAAAA
1 TACAAAAAAA
25552320 TA-AAAAAAA
1 TACAAAAAAA
25552329 TACCAAAA
1 TA-CAAAA
25552337 TAGTATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
10 4 0.16
11 12 0.48
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (10 bp):
TACAAAAAAA
Found at i:25552742 original size:154 final size:152
Alignment explanation
Indices: 25552461--25552966 Score: 726
Period size: 154 Copynumber: 3.3 Consensus size: 152
25552451 CAATTGTTCG
* *
25552461 TATTTCAGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTTTTAAAAAATATAATATTTTC
1 TATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTACTTTTAAAAAATATAATATTTTC
*
25552526 TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTTAGTGTGTTTTT
65 TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTGTGTTTTT
25552591 TAAATAAATTTAAAAAAAACCCT
130 TAAATAAATTTAAAAAAAACCCT
** *
25552614 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACCTTCAATAAAAATATATTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTA-CTTTTA-AAAAATATAATATTTT
* * * * * *
25552679 CGT-ATTTTATTATTTTACATTGTTTTAGTACATTATGTTTGAAATGTATTAACTAATTTTGTTT
64 C-TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTGTGTTT
*
25552743 TTTAAATAAATTTAGTAAAAAACCCT
128 TTTAAATAAATTTA-AAAAAAACCCT
* * * *
25552769 TATTTTGACCCTTTGTTCGTATTTTTTCCCCAGATTTTATTACTTTTAAAAAATATACTATTTTC
1 TATTTCGGCCCTTTGTTCGTATTTTTT-CCCGGATTTTATTACTTTTAAAAAATATAATATTTTC
* * *
25552834 TAATTTTATTATTTTACATTATTTTAGTACATTACAATTGAAATGTATTCATTCAGTGTGTTTTT
65 TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTGTGTTTTT
*
25552899 TAAATAAATTTTAAAAAAACCCCT
130 TAAATAAA-TTTAAAAAAAACCCT
* * *
25552923 TATTTCGGTCCTTTGTTCGTATTTTTCCCCTGATTTTATTACTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTT
25552967 GCAAGAAAAA
Statistics
Matches: 311, Mismatches: 35, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
152 19 0.06
153 41 0.13
154 194 0.62
155 44 0.14
156 13 0.04
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (152 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATTTTATTACTTTTAAAAAATATAATATTTTCT
AATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTGTGTTTTTT
AAATAAATTTAAAAAAAACCCT
Found at i:25557802 original size:45 final size:45
Alignment explanation
Indices: 25557753--25558293 Score: 1082
Period size: 45 Copynumber: 12.0 Consensus size: 45
25557743 AAAATTGGAG
25557753 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25557798 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25557843 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25557888 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25557933 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25557978 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25558023 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25558068 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25558113 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25558158 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25558203 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25558248 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
1 ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
25558293 A
1 A
25558294 CATTCTCTTC
Statistics
Matches: 496, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 496 1.00
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.22
Consensus pattern (45 bp):
ATTGATTTATCACCCAACAATTGGTGACCAACAATGAAAACACAA
Found at i:25559051 original size:29 final size:29
Alignment explanation
Indices: 25559009--25559070 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
25558999 TATATTCTAT
25559009 GGTCTAGTTCAACAACTAGCCAAGTAACA
1 GGTCTAGTTCAACAACTAGCCAAGTAACA
25559038 GGTCTAGTTCAACAACTAGCCAAGTAACA
1 GGTCTAGTTCAACAACTAGCCAAGTAACA
25559067 GGTC
1 GGTC
25559071 ATGTACATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (29 bp):
GGTCTAGTTCAACAACTAGCCAAGTAACA
Found at i:25562613 original size:29 final size:29
Alignment explanation
Indices: 25562538--25562626 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
25562528 TTAATTAATT
*
25562538 TTTTAA-AATTTAAAATTATTAAAAATATAA
1 TTTTAATATTTTAAAATT-TTAAAAA-ATAA
25562568 TTTTAATGATTTT--AATTTTAAAAAATAA
1 TTTTAAT-ATTTTAAAATTTTAAAAAATAA
*
25562596 TTTT-ATATTTTTAAAATTTTAAAAATTAA
1 TTTTAATA-TTTTAAAATTTTAAAAAATAA
25562625 TT
1 TT
25562627 AAATGATGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
26 1 0.02
27 6 0.12
28 8 0.15
29 23 0.44
30 10 0.19
32 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TTTTAATATTTTAAAATTTTAAAAAATAA
Found at i:25567652 original size:29 final size:29
Alignment explanation
Indices: 25567577--25567665 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
25567567 TTAATTAATT
*
25567577 TTTTAA-AATTTAAAATTATTAAAAATATAA
1 TTTTAATATTTTAAAATT-TTAAAAA-ATAA
25567607 TTTTAATGATTTT--AATTTTAAAAAATAA
1 TTTTAAT-ATTTTAAAATTTTAAAAAATAA
*
25567635 TTTT-ATATTTTTAAAATTTTAAAAATTAA
1 TTTTAATA-TTTTAAAATTTTAAAAAATAA
25567664 TT
1 TT
25567666 AAATGATGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
26 1 0.02
27 6 0.12
28 8 0.15
29 23 0.44
30 10 0.19
32 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TTTTAATATTTTAAAATTTTAAAAAATAA
Found at i:25572123 original size:3 final size:3
Alignment explanation
Indices: 25572115--25572164 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
25572105 CCCTGTTTTC
25572115 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25572163 AT
1 AT
25572165 TGTTGATAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:25582489 original size:15 final size:15
Alignment explanation
Indices: 25582458--25582508 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
25582448 GAGCTATCAT
*
25582458 TAAAATCTAATTAAA
1 TAAAATATAATTAAA
25582473 TAAAATATATATTAATA
1 TAAAATATA-ATTAA-A
* *
25582490 TTAAATAAAATTAAA
1 TAAAATATAATTAAA
25582505 -AAAA
1 TAAAA
25582509 AATCCTCCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.10
15 9 0.30
16 10 0.33
17 8 0.27
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATATAATTAAA
Found at i:25585110 original size:9 final size:8
Alignment explanation
Indices: 25585076--25585111 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
25585066 TAATTTTTTT
25585076 AAAATTTA
1 AAAATTTA
25585084 AAAATTTA
1 AAAATTTA
25585092 AAAATTTA
1 AAAATTTA
25585100 AAAATTATA
1 AAAATT-TA
25585109 AAA
1 AAA
25585112 GTTATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATTTA
Found at i:25585116 original size:9 final size:9
Alignment explanation
Indices: 25585076--25585116 Score: 52
Period size: 8 Copynumber: 4.9 Consensus size: 9
25585066 TAATTTTTTT
25585076 AAAATT-TA
1 AAAATTATA
25585084 AAAATT-TA
1 AAAATTATA
25585092 AAAATT-TA
1 AAAATTATA
25585100 AAAATTATA
1 AAAATTATA
*
25585109 AAAGTTAT
1 AAAATTAT
25585117 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 22 0.71
9 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAATTATA
Found at i:25585130 original size:20 final size:22
Alignment explanation
Indices: 25585096--25585149 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
25585086 AATTTAAAAA
*
25585096 TTTAAAAATTATAAAAGTTATT
1 TTTAAAAATTATAAAAATTATT
25585118 TTTAAAAA-T-TAAAAATTA--
1 TTTAAAAATTATAAAAATTATT
*
25585136 TTAAAAAATTATAA
1 TTTAAAAATTATAA
25585150 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 7 0.25
19 1 0.04
20 11 0.39
21 1 0.04
22 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTAAAAATTATAAAAATTATT
Found at i:25596567 original size:6 final size:6
Alignment explanation
Indices: 25596481--25596564 Score: 141
Period size: 6 Copynumber: 14.0 Consensus size: 6
25596471 TTTATGTGTC
25596481 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * *
25596529 TATGTG TATGTG TATGTG CATGTG GATGTG CATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
25596565 CATTTATAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.17, C:0.02, G:0.35, T:0.46
Consensus pattern (6 bp):
TATGTG
Found at i:25609192 original size:13 final size:14
Alignment explanation
Indices: 25609176--25609205 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25609166 ATTTATAAAC
25609176 AATATTATG-ATAT
1 AATATTATGTATAT
25609189 AATATTATGTATAT
1 AATATTATGTATAT
25609203 AAT
1 AAT
25609206 CCGTTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
AATATTATGTATAT
Found at i:25612064 original size:4 final size:4
Alignment explanation
Indices: 25612041--25612108 Score: 118
Period size: 4 Copynumber: 16.8 Consensus size: 4
25612031 GTAAGGGCAG
*
25612041 CATA CATTA CATA TATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25612090 CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CAT
25612109 TCACATATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
4 57 0.93
5 4 0.07
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:25612684 original size:6 final size:6
Alignment explanation
Indices: 25612664--25612700 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
25612654 TTTATCAATC
*
25612664 TCTGAT TCATGAT TCTGAT TCTGGT TCTGAT TCTGAT
1 TCTGAT TC-TGAT TCTGAT TCTGAT TCTGAT TCTGAT
25612701 ATGTTTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (6 bp):
TCTGAT
Found at i:25615470 original size:27 final size:27
Alignment explanation
Indices: 25615426--25615480 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
25615416 TTTTGAAATT
*
25615426 ATTATGTCTTGAATTTGTTAGATATTG
1 ATTATGTCTTGAACTTGTTAGATATTG
25615453 ATTATGTCTT-AAGCTTGTTAGATATTG
1 ATTATGTCTTGAA-CTTGTTAGATATTG
25615480 A
1 A
25615481 ATTTATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.49
Consensus pattern (27 bp):
ATTATGTCTTGAACTTGTTAGATATTG
Found at i:25615497 original size:32 final size:32
Alignment explanation
Indices: 25615408--25615513 Score: 98
Period size: 32 Copynumber: 3.5 Consensus size: 32
25615398 AAATTTTAGT
* * * *
25615408 TTGTTGGATTTTGAAATTATTATGTCTTGAA-T
1 TTGTTAGATATTGAATTTATTATGTCTT-AAGC
25615440 TTGTTAGATATTG-----ATTATGTCTTAAGC
1 TTGTTAGATATTGAATTTATTATGTCTTAAGC
*
25615467 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTGAATTTATTATGTCTTAAGC
* *
25615499 TTGTTGGATGTTGAA
1 TTGTTAGATATTGAA
25615514 ATGATTGACA
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
26 2 0.03
27 23 0.37
32 37 0.60
ACGTcount: A:0.25, C:0.04, G:0.20, T:0.51
Consensus pattern (32 bp):
TTGTTAGATATTGAATTTATTATGTCTTAAGC
Found at i:25616712 original size:20 final size:20
Alignment explanation
Indices: 25616687--25616724 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
25616677 ATAATTTAAA
25616687 ATATAAATTTATTAATATGT
1 ATATAAATTTATTAATATGT
25616707 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
25616725 ATGTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:25616734 original size:20 final size:20
Alignment explanation
Indices: 25616691--25616734 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
25616681 TTTAAAATAT
* *
25616691 AAATTTATTAATATGTATAT
1 AAATTTATTAATATATATAA
*
25616711 AAATTTATTAATATATGTAA
1 AAATTTATTAATATATATAA
25616731 AAAT
1 AAAT
25616735 AGTTTTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTTATTAATATATATAA
Found at i:25616836 original size:14 final size:15
Alignment explanation
Indices: 25616817--25616854 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
25616807 CCAGAAACGT
25616817 AAATCATTTTC-CAA
1 AAATCATTTTCTCAA
*
25616831 AAATCATTTTCTGAA
1 AAATCATTTTCTCAA
25616846 AAA-CATTTT
1 AAATCATTTT
25616855 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATCATTTTCTCAA
Found at i:25618472 original size:27 final size:25
Alignment explanation
Indices: 25618408--25618477 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 25
25618398 CTGTACATGT
*
25618408 ATGCTCACACGAGCTGTGAATTAGA
1 ATGCTCACACGAGCTGTGAAATAGA
*
25618433 ATGCTCACACGAGCTGTGAAAATAGGC
1 ATGCTCACACGAGCTGTG-AAATA-GA
*
25618460 CTGCTCACACGAGCTGTG
1 ATGCTCACACGAGCTGTG
25618478 GGTGGAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.45
26 4 0.10
27 18 0.45
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAAATAGA
Found at i:25626931 original size:18 final size:18
Alignment explanation
Indices: 25626908--25626942 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25626898 TATTCATATC
*
25626908 TATTGTTGAAAATAAGAT
1 TATTGTTAAAAATAAGAT
25626926 TATTGTTAAAAATAAGA
1 TATTGTTAAAAATAAGA
25626943 AATTGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (18 bp):
TATTGTTAAAAATAAGAT
Found at i:25626947 original size:17 final size:18
Alignment explanation
Indices: 25626909--25626947 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25626899 ATTCATATCT
* *
25626909 ATTGTTGAAAATAAGATT
1 ATTGTTAAAAATAAGATA
25626927 ATTGTTAAAAATAAGA-A
1 ATTGTTAAAAATAAGATA
25626944 ATTG
1 ATTG
25626948 AATTAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTGTTAAAAATAAGATA
Found at i:25627083 original size:24 final size:25
Alignment explanation
Indices: 25627007--25627090 Score: 134
Period size: 25 Copynumber: 3.4 Consensus size: 25
25626997 GTGGAAAAAT
*
25627007 GATGAATTGATGGTAAAATGCAAAG
1 GATGAATTGACGGTAAAATGCAAAG
25627032 GATGAATTGACGGTAAAATGCAAAG
1 GATGAATTGACGGTAAAATGCAAAG
* *
25627057 GATGAATTGACGGT-ATATGCAAGG
1 GATGAATTGACGGTAAAATGCAAAG
25627081 GATGAATTGA
1 GATGAATTGA
25627091 TGACAAATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 18 0.32
25 38 0.68
ACGTcount: A:0.40, C:0.06, G:0.30, T:0.24
Consensus pattern (25 bp):
GATGAATTGACGGTAAAATGCAAAG
Found at i:25627256 original size:22 final size:21
Alignment explanation
Indices: 25627203--25627257 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
25627193 CTATTTAACC
* *
25627203 CTTATGGGTTTCCGTTCAGCT
1 CTTATGGGTTTCCATTCACCT
* *
25627224 CCTATGAGTTTCCATTCAACCT
1 CTTATGGGTTTCCATTC-ACCT
*
25627246 TTTATGGGTTTC
1 CTTATGGGTTTC
25627258 TGTTAGCACT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (21 bp):
CTTATGGGTTTCCATTCACCT
Found at i:25628986 original size:22 final size:22
Alignment explanation
Indices: 25628961--25629015 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
25628951 TGCACTAATG
25628961 AACAGAGAGCACTA-AAGTGCTA
1 AACAGAGAGCAC-AGAAGTGCTA
* *
25628983 AACAAAGAGCACAGATGTGCTA
1 AACAGAGAGCACAGAAGTGCTA
*
25629005 AACGGAGAGCA
1 AACAGAGAGCA
25629016 TTGTCATGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.11
Consensus pattern (22 bp):
AACAGAGAGCACAGAAGTGCTA
Found at i:25629511 original size:14 final size:14
Alignment explanation
Indices: 25629492--25629521 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25629482 ACACCATTCA
25629492 ATCTCACATTAAAT
1 ATCTCACATTAAAT
25629506 ATCTCACATTAAAT
1 ATCTCACATTAAAT
25629520 AT
1 AT
25629522 TTCCTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (14 bp):
ATCTCACATTAAAT
Found at i:25634137 original size:10 final size:10
Alignment explanation
Indices: 25634124--25634154 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
25634114 TTTTATGTTT
25634124 TTTTTAAATA
1 TTTTTAAATA
25634134 TTTTTAAATA
1 TTTTTAAATA
*
25634144 TTTTTTAATA
1 TTTTTAAATA
25634154 T
1 T
25634155 ATATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:25634170 original size:22 final size:21
Alignment explanation
Indices: 25634145--25634197 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
25634135 TTTTAAATAT
* *
25634145 TTTTTAATATATATTTTTTTAA
1 TTTTTAATATA-AGTTTTTGAA
*
25634167 TTTTTATTATAAGTTTTTGAA
1 TTTTTAATATAAGTTTTTGAA
*
25634188 ATTTTAATAT
1 TTTTTAATAT
25634198 TTTTTGTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTAATATAAGTTTTTGAA
Found at i:25634273 original size:23 final size:25
Alignment explanation
Indices: 25634238--25634283 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
25634228 TTTTTATGTA
25634238 TTTTGAGATTTTTT-TTCAAATTATT
1 TTTTGAGATTTTTTATT-AAATTATT
25634263 TTTTGA-A-TTTTTATTAAATTA
1 TTTTGAGATTTTTTATTAAATTA
25634284 AAAGAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.55
24 3 0.15
25 6 0.30
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (25 bp):
TTTTGAGATTTTTTATTAAATTATT
Found at i:25639749 original size:42 final size:41
Alignment explanation
Indices: 25639643--25639796 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 41
25639633 TGAGCTGTGT
* *
25639643 TTTCGTGTAAGACCATGTCTGGGACGTTCGCATCGATTTGAGA
1 TTTCGTGTAAGACCATGTCTGGGAC-ATCGCATCGATAT-AGA
25639686 TTTACGTGTAAGACCATGTCTGGGACATCGACATCG-TATATGA
1 TTT-CGTGTAAGACCATGTCTGGGACATCG-CATCGATATA-GA
* * *
25639729 TTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGA
1 TTTCGTGTAAGACCATGTCTGGGACA-TCGCATCGATA-TAGA
* * * *
25639772 TTACATGGAAGACCACGTCTGGGAC
1 TTTCGTGTAAGACCATGTCTGGGAC
25639797 GTTGGCATTG
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
42 28 0.29
43 39 0.41
44 28 0.29
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TTTCGTGTAAGACCATGTCTGGGACATCGCATCGATATAGA
Found at i:25639819 original size:86 final size:86
Alignment explanation
Indices: 25639640--25639796 Score: 212
Period size: 86 Copynumber: 1.8 Consensus size: 86
25639630 TTCTGAGCTG
* * *
25639640 TGTTTTCGTGTAAGACCATGTCTGGGACGTTCGCATCGATTTGAGATTTACGTGTAAGACCATGT
1 TGTTTTCGTGTAAGACCATGTCTGGGACGTTCGCATCGATTTGAGATTTACATGGAAGACCACGT
25639705 CTGGGACATCGACATCGTATA
66 CTGGGACATCGACATCGTATA
* * * *
25639726 TGATTTCGTGTAAGACCCTGTCTGGGACAG-TGGCATCGATATT-TGA-TTACATGGAAGACCAC
1 TGTTTTCGTGTAAGACCATGTCTGGGAC-GTTCGCATCGAT-TTGAGATTTACATGGAAGACCAC
25639788 GTCTGGGAC
64 GTCTGGGAC
25639797 GTTGGCATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
85 22 0.35
86 37 0.60
87 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (86 bp):
TGTTTTCGTGTAAGACCATGTCTGGGACGTTCGCATCGATTTGAGATTTACATGGAAGACCACGT
CTGGGACATCGACATCGTATA
Found at i:25660649 original size:43 final size:43
Alignment explanation
Indices: 25660588--25660775 Score: 288
Period size: 43 Copynumber: 4.3 Consensus size: 43
25660578 TCTGATGTGT
* *
25660588 GATTTCGTGTAAGACCATAGCTGAGCTATTGGCATCGATCTGA
1 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATCTGA
*
25660631 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
1 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATCTGA
* * *
25660674 GATTTCGTGTAAGACCATAGCTGGGCTATTGACATCGATTTGA
1 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATCTGA
25660717 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATAC-GA
1 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGAT-CTGA
*
25660760 GATTTCTATGTAAGAC
1 GATTT-TGTGTAAGAC
25660776 TATGTCTGAG
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
43 125 0.93
44 9 0.07
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATCTGA
Found at i:25663286 original size:34 final size:34
Alignment explanation
Indices: 25663248--25663316 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
25663238 CCTAGCAGCG
25663248 AAAAAATGATATTTATTCAGTTTTAATAACATAT
1 AAAAAATGATATTTATTCAGTTTTAATAACATAT
*
25663282 AAAAAGTGATATTTATTCAGTTTTAATAACATAT
1 AAAAAATGATATTTATTCAGTTTTAATAACATAT
25663316 A
1 A
25663317 TGTTTCGTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (34 bp):
AAAAAATGATATTTATTCAGTTTTAATAACATAT
Found at i:25663988 original size:91 final size:90
Alignment explanation
Indices: 25663829--25664032 Score: 257
Period size: 91 Copynumber: 2.3 Consensus size: 90
25663819 CTCTGTTTTG
* * * * * * *
25663829 TGGATAAACCACCAGTG-TTGCAGGTTAATACACTGCCATTAGTAGTGAGTATACAATGGGTTTG
1 TGGATAAACCACCAGTGTTTGCAGGTTAATACACTACCAGTAGTAGTAAATACACAACGGGTTTA
25663893 CAGATAAAAGTTGCCAATAAAAATTA
66 CAGATAAAAGTTGCCAAT-AAAATTA
* * *
25663919 TGGATAAACCACCAGTGTTTGCTGGTTAATACGCTACCAGTAGTTGTAAATACACAACGGGTTTA
1 TGGATAAACCACCAGTGTTTGCAGGTTAATACACTACCAGTAGTAGTAAATACACAACGGGTTTA
* ** *
25663984 CAGATAAAAGTTTCCAATAAGTTTG
66 CAGATAAAAGTTGCCAATAAAATTA
*
25664009 TGGACAAACCACCAGTGTTTGCAG
1 TGGATAAACCACCAGTGTTTGCAG
25664033 ATAAACTACC
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 43 0.44
91 54 0.56
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (90 bp):
TGGATAAACCACCAGTGTTTGCAGGTTAATACACTACCAGTAGTAGTAAATACACAACGGGTTTA
CAGATAAAAGTTGCCAATAAAATTA
Found at i:25673399 original size:9 final size:9
Alignment explanation
Indices: 25673377--25673436 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
25673367 TATTATATAT
25673377 AAAATCAATA
1 AAAAT-AATA
25673387 AAAATAATA
1 AAAATAATA
25673396 AAAAT-ATA
1 AAAATAATA
*
25673404 GAAAATCATAA
1 -AAAATAAT-A
25673415 AAAGATATATA
1 AAA-ATA-ATA
*
25673426 AAAATTATA
1 AAAATAATA
25673435 AA
1 AA
25673437 CAAATATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
8 3 0.07
9 19 0.44
10 12 0.28
11 7 0.16
12 2 0.05
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (9 bp):
AAAATAATA
Found at i:25673402 original size:28 final size:30
Alignment explanation
Indices: 25673371--25673436 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 30
25673361 AATAGGTATT
25673371 ATATATAAAATCA-ATAAAA-ATA-ATAAAA
1 ATATATAAAATCATA-AAAAGATATATAAAA
*
25673399 ATATAGAAAATCATAAAAAGATATATAAAA
1 ATATATAAAATCATAAAAAGATATATAAAA
25673429 AT-TATAAA
1 ATATATAAA
25673437 CAAATATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 16 0.48
29 9 0.27
30 8 0.24
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (30 bp):
ATATATAAAATCATAAAAAGATATATAAAA
Found at i:25673828 original size:21 final size:20
Alignment explanation
Indices: 25673799--25673858 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
25673789 NNNNNNNNNN
25673799 TATGAAAAAAATTGTAAAAAT
1 TATGAAAAAAATT-TAAAAAT
* *
25673820 TATGTAAAATATTT-AAAA-
1 TATGAAAAAAATTTAAAAAT
* *
25673838 TATAGAAAAATATTAAAAAAT
1 TAT-GAAAAAAATTTAAAAAT
25673859 ATAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.09
19 13 0.41
20 5 0.16
21 11 0.34
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (20 bp):
TATGAAAAAAATTTAAAAAT
Found at i:25673847 original size:10 final size:10
Alignment explanation
Indices: 25673834--25673905 Score: 57
Period size: 9 Copynumber: 7.7 Consensus size: 10
25673824 TAAAATATTT
25673834 AAAATATAGA
1 AAAATATAGA
25673844 AAAATATTA-A
1 AAAATA-TAGA
25673854 AAAATATAG-
1 AAAATATAGA
*
25673863 AAAA-GT-GA
1 AAAATATAGA
* *
25673871 AAACTATA-T
1 AAAATATAGA
25673880 AAAATATAGA
1 AAAATATAGA
*
25673890 AAATTAT-GA
1 AAAATATAGA
25673899 AAAATAT
1 AAAATAT
25673906 TATTTCAAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
7 1 0.02
8 4 0.08
9 22 0.46
10 19 0.40
11 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.25
Consensus pattern (10 bp):
AAAATATAGA
Found at i:25673859 original size:20 final size:19
Alignment explanation
Indices: 25673825--25673866 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
25673815 AAAATTATGT
*
25673825 AAAATATTTAAAATATAGA
1 AAAATATTAAAAATATAGA
25673844 AAAATATTAAAAAATATAGA
1 AAAATATT-AAAAATATAGA
25673864 AAA
1 AAA
25673867 GTGAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAATATTAAAAATATAGA
Found at i:25673905 original size:26 final size:25
Alignment explanation
Indices: 25673854--25673905 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
25673844 AAAATATTAA
*
25673854 AAAATATAGAAAAGTGAAAACTATAT
1 AAAATATAGAAAAATGAAAAC-ATAT
25673880 AAAATATAGAAAATTATGAAAA-ATAT
1 AAAATATAGAAAA--ATGAAAACATAT
25673906 TATTTCAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 17 0.74
28 6 0.26
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (25 bp):
AAAATATAGAAAAATGAAAACATAT
Found at i:25674281 original size:9 final size:9
Alignment explanation
Indices: 25674263--25674302 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
25674253 TTTGGTTAAA
*
25674263 AATTACCCG
1 AATTAACCG
25674272 AATTAACCG
1 AATTAACCG
*
25674281 AATTACCCG
1 AATTAACCG
25674290 AATTAACCG
1 AATTAACCG
25674299 AATT
1 AATT
25674303 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:25674286 original size:18 final size:18
Alignment explanation
Indices: 25674263--25674302 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
25674253 TTTGGTTAAA
25674263 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
25674281 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
25674299 AATT
1 AATT
25674303 GAATCACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:25674351 original size:37 final size:37
Alignment explanation
Indices: 25674301--25674375 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
25674291 ATTAACCGAA
25674301 TTGAATCACTACATAAATAAAAACATTACATAAGTCT
1 TTGAATCACTACATAAATAAAAACATTACATAAGTCT
*
25674338 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAAATAAAAACATTACATAAGTCT
25674375 T
1 T
25674376 GAAATTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (37 bp):
TTGAATCACTACATAAATAAAAACATTACATAAGTCT
Found at i:25674369 original size:17 final size:17
Alignment explanation
Indices: 25674310--25674370 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
25674300 ATTGAATCAC
*
25674310 TACATAAATAAAAACAT
1 TACATAATTAAAAACAT
** * *
25674327 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
25674347 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
25674364 TACATAA
1 TACATAA
25674371 GTCTTGAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 20 0.62
20 12 0.38
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:25674389 original size:37 final size:37
Alignment explanation
Indices: 25674301--25674392 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
25674291 ATTAACCGAA
* *
25674301 TTGAATCACTACATAAATAAAAACATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
*
25674338 TTGAATCACTACATAATTAAAAACATTACATAAGTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
25674374 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
25674393 GAAATGTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 45 0.88
38 3 0.06
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:25674516 original size:17 final size:17
Alignment explanation
Indices: 25674496--25674528 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25674486 CTATTTATAT
*
25674496 ATTATTTTTATTTTTAA
1 ATTATTTTCATTTTTAA
25674513 ATTATTTTCATTTTTA
1 ATTATTTTCATTTTTA
25674529 TTTATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTATTTTCATTTTTAA
Found at i:25674527 original size:24 final size:25
Alignment explanation
Indices: 25674499--25674554 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
25674489 TTTATATATT
*
25674499 ATTTTTATTT-TTAAATTATTT-TC
1 ATTTTTATTTATTAAATTATTTGTA
25674522 ATTTTTATTTATTAAATTATTTGTA
1 ATTTTTATTTATTAAATTATTTGTA
25674547 ATTTTTAT
1 ATTTTTAT
25674555 GATTGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 10 0.33
24 11 0.37
25 9 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (25 bp):
ATTTTTATTTATTAAATTATTTGTA
Found at i:25674580 original size:13 final size:13
Alignment explanation
Indices: 25674562--25674594 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
25674552 TATGATTGAG
25674562 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
25674575 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
25674588 TTGGGTT
1 TTGGGTT
25674595 TGGATTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.45, T:0.42
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:25679733 original size:27 final size:26
Alignment explanation
Indices: 25679679--25679742 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 26
25679669 TTTTGCTTAG
*
25679679 TTTTAATAAAATATACATTTCATGCA
1 TTTTAATAAAATATACATTTCATACA
*
25679705 TTATTAATTAAAATATATATTTCA-ACA
1 TT-TTAA-TAAAATATACATTTCATACA
*
25679732 TTTTAAAAAAA
1 TTTTAATAAAA
25679743 CAAATTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 4 0.12
26 6 0.18
27 8 0.24
28 15 0.45
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTTAATAAAATATACATTTCATACA
Found at i:25680309 original size:21 final size:21
Alignment explanation
Indices: 25680283--25680324 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25680273 CTGCCAGTAA
*
25680283 GTTTGTGGATAAACCACCAGT
1 GTTTGTAGATAAACCACCAGT
*
25680304 GTTTGTAGATAAACTACCAGT
1 GTTTGTAGATAAACCACCAGT
25680325 AGGTTGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (21 bp):
GTTTGTAGATAAACCACCAGT
Found at i:25680318 original size:44 final size:43
Alignment explanation
Indices: 25680270--25680405 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 43
25680260 TTGCAGATAA
* *
25680270 AAACTGCCAGTAAGTTTGTGGATAAACCACCAGTGTTTGTAGAT
1 AAACTACCAGTAAGTTTGTGGATGAACCACCA-TGTTTGTAGAT
* * * * *
25680314 AAACTACCAGT-AGGTTGTGAATGCACAACGCA--TTTGAAGAT
1 AAACTACCAGTAAGTTTGTGGATGAACCAC-CATGTTTGTAGAT
*
25680355 AAAAGCTACAAGTAAGTTTGTGGATGAACCACCAATGTTTGTAGAT
1 -AAA-CTACCAGTAAGTTTGTGGATGAACCACC-ATGTTTGTAGAT
25680401 AAACT
1 AAACT
25680406 GTCAGTAGGT
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
41 8 0.11
42 3 0.04
43 21 0.29
44 29 0.40
45 3 0.04
46 8 0.11
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (43 bp):
AAACTACCAGTAAGTTTGTGGATGAACCACCATGTTTGTAGAT
Found at i:25680340 original size:87 final size:87
Alignment explanation
Indices: 25680194--25680480 Score: 358
Period size: 87 Copynumber: 3.3 Consensus size: 87
25680184 CCGAACACTC
* * * * * * * * *
25680194 AAGTTTATGGATGAACCACCATTGTTTGCAAATAAACTGCCACTTGGTTGTGAATGCACAATGTA
1 AAGTTTGTGGATAAACCACCAATGTTTGTAGATAAACTGCCAGTAGGTTGTGAATGCACAACGAA
* * *
25680259 TTTGCAGATAAAAACTGCCAGT
66 TTTGAAGATAAAAGCTGCAAGT
* * *
25680281 AAGTTTGTGGATAAACCACCAGTGTTTGTAGATAAACTACCAGTAGGTTGTGAATGCACAACGCA
1 AAGTTTGTGGATAAACCACCAATGTTTGTAGATAAACTGCCAGTAGGTTGTGAATGCACAACGAA
*
25680346 TTTGAAGATAAAAGCTACAAGT
66 TTTGAAGATAAAAGCTGCAAGT
* * * *
25680368 AAGTTTGTGGATGAACCACCAATGTTTGTAGATAAACTGTCAGTAGGTTGTGAGTGCACAACAAA
1 AAGTTTGTGGATAAACCACCAATGTTTGTAGATAAACTGCCAGTAGGTTGTGAATGCACAACGAA
*
25680433 TTTGTAGATAAAAGCTGCAAGT
66 TTTGAAGATAAAAGCTGCAAGT
* * *
25680455 AAATTCGCGGATAAACCACCAATGTT
1 AAGTTTGTGGATAAACCACCAATGTT
25680481 GGCAATTATT
Statistics
Matches: 173, Mismatches: 27, Indels: 0
0.87 0.14 0.00
Matches are distributed among these distances:
87 173 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (87 bp):
AAGTTTGTGGATAAACCACCAATGTTTGTAGATAAACTGCCAGTAGGTTGTGAATGCACAACGAA
TTTGAAGATAAAAGCTGCAAGT
Found at i:25680667 original size:38 final size:38
Alignment explanation
Indices: 25680570--25680695 Score: 164
Period size: 38 Copynumber: 3.3 Consensus size: 38
25680560 ACAATATTGA
**
25680570 AACAATAGACATGCTTAATGTGTATTCGGTTCAACAGT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAGT
* * * *
25680608 AA-AATAGACATGCTTATCATGTATTCAGCTCAACGGT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAGT
* *
25680645 AACAATAGCCATGTTTAACATGTATTCGGTTCAACAGT
1 AACAATAGACATGCTTAACATGTATTCGGTTCAACAGT
*
25680683 AACAATAGGCATG
1 AACAATAGACATG
25680696 AAATCATTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
37 31 0.42
38 43 0.58
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (38 bp):
AACAATAGACATGCTTAACATGTATTCGGTTCAACAGT
Found at i:25682567 original size:29 final size:29
Alignment explanation
Indices: 25682521--25682582 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
25682511 TTTTTCATAA
*
25682521 AATCACATATATAGACATGAATTAAATTC
1 AATCACATATATACACATGAATTAAATTC
25682550 AATCACATATATACACATGAATTAAATTC
1 AATCACATATATACACATGAATTAAATTC
25682579 AATC
1 AATC
25682583 TATAATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (29 bp):
AATCACATATATACACATGAATTAAATTC
Found at i:25690548 original size:18 final size:18
Alignment explanation
Indices: 25690525--25690563 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25690515 CGTTCTCTCC
25690525 TTTCTCCCCTTCTTTCTT
1 TTTCTCCCCTTCTTTCTT
* *
25690543 TTTCTCTCTTTCTTTCTT
1 TTTCTCCCCTTCTTTCTT
25690561 TTT
1 TTT
25690564 AATACTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTCTCCCCTTCTTTCTT
Found at i:25691685 original size:21 final size:23
Alignment explanation
Indices: 25691645--25691687 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
25691635 ATACGAGAAA
25691645 GAAAATACTTGATAGTAAAAGATG
1 GAAAATAC-TGATAGTAAAAGATG
25691669 GAAAATA-TGAT-GTAAAAGA
1 GAAAATACTGATAGTAAAAGA
25691688 GAGTAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
24 7 0.37
ACGTcount: A:0.53, C:0.02, G:0.21, T:0.23
Consensus pattern (23 bp):
GAAAATACTGATAGTAAAAGATG
Found at i:25692421 original size:24 final size:24
Alignment explanation
Indices: 25692394--25692449 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
25692384 AAGATATGCG
25692394 AAATATTAATAGGCAAAA-ATGTGC
1 AAATATTAATAGGCAAAATA-GTGC
* **
25692418 AAATTTTAATAGGCACCATAGTGC
1 AAATATTAATAGGCAAAATAGTGC
25692442 AAATATTA
1 AAATATTA
25692450 CGAATATCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (24 bp):
AAATATTAATAGGCAAAATAGTGC
Found at i:25693343 original size:27 final size:27
Alignment explanation
Indices: 25693304--25693365 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
25693294 AGAGGGTTTT
*
25693304 TGATTGGCGGCACCAAAGGTGCC-TAAC
1 TGATTGGCAGCACCAAAGGTGCCAT-AC
* * *
25693331 TGATTTGCAGCACCGATGGTGCCATAC
1 TGATTGGCAGCACCAAAGGTGCCATAC
25693358 TGATTGGC
1 TGATTGGC
25693366 GGGACTACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (27 bp):
TGATTGGCAGCACCAAAGGTGCCATAC
Found at i:25693619 original size:3 final size:3
Alignment explanation
Indices: 25693611--25693635 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25693601 TTTTAGTTAG
25693611 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
25693636 GTTNNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.