Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 159 of 295
Found at i:54101263 original size:37 final size:37
Alignment explanation
Indices: 54101213--54101329 Score: 180
Period size: 37 Copynumber: 3.2 Consensus size: 37
54101203 CTTATTACAA
* * * *
54101213 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
54101250 AGTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
1 AGTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
*
54101287 GGTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
1 AGTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
*
54101324 GGTCTT
1 AGTCTT
54101330 TAGAGCTCGG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.22
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
Found at i:54101526 original size:47 final size:47
Alignment explanation
Indices: 54101448--54101859 Score: 630
Period size: 47 Copynumber: 8.7 Consensus size: 47
54101438 CCCTTCGGGA
* * * * * *
54101448 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54101495 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54101542 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54101589 CTTATCACATATATACAC-TTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54101635 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54101682 CTTATCACATGTATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54101729 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54101776 CTTATCACATGTATATACACTTTCGCATTCATTACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54101825 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
54101860 AGAATCCTAA
Statistics
Matches: 336, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
46 46 0.14
47 246 0.73
49 44 0.13
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54101763 original size:187 final size:189
Alignment explanation
Indices: 54101448--54101859 Score: 641
Period size: 187 Copynumber: 2.2 Consensus size: 189
54101438 CCCTTCGGGA
* * * ** *
54101448 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAAGCCCTATCACATATATACAC
54101513 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
54101578 GGCCATTAGGCCTTATCACA-TATATACAC-TTCACATTCATCACATCGGCTATTAGGC
131 GGCCATTAGGCCTTATCACAGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
54101635 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATGTATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAAGCCCTATCACATATATACAC
*
54101700 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
* *
54101765 GGCCATTAGGCCTTATCACATGTATATACACTTTCGCATTCATTACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACA-GTATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54101825 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATCCATCACAT
54101860 AGAATCCTAA
Statistics
Matches: 204, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
187 139 0.68
189 10 0.05
190 55 0.27
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (189 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAAGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACAGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54110215 original size:6 final size:6
Alignment explanation
Indices: 54110206--54110237 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
54110196 TGTGTGTCTG
*
54110206 TGTGTA TGTGTA CGTGTA TGTGTA TGTGTA TG
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TG
54110238 ACAACGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.47
Consensus pattern (6 bp):
TGTGTA
Found at i:54118511 original size:13 final size:13
Alignment explanation
Indices: 54118493--54118517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54118483 AAGTCATGAG
54118493 TGAGGGAAAAATT
1 TGAGGGAAAAATT
54118506 TGAGGGAAAAAT
1 TGAGGGAAAAAT
54118518 ATTTTGATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
TGAGGGAAAAATT
Found at i:54118690 original size:21 final size:20
Alignment explanation
Indices: 54118643--54118684 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
54118633 TGACTAAGTT
54118643 AAATTTACCTCATATGTAGTC
1 AAATTTACCTCATATGTA-TC
54118664 AAATTTACCTCATATGT-TC
1 AAATTTACCTCATATGTATC
54118683 AA
1 AA
54118685 TTATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
21 17 0.81
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (20 bp):
AAATTTACCTCATATGTATC
Found at i:54120207 original size:18 final size:18
Alignment explanation
Indices: 54120180--54120216 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54120170 TCTAGTTCTT
54120180 TAATAATTCTTTAATGAA
1 TAATAATTCTTTAATGAA
*
54120198 TAATAGTTCTTTAATGAA
1 TAATAATTCTTTAATGAA
54120216 T
1 T
54120217 GTCTATATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (18 bp):
TAATAATTCTTTAATGAA
Found at i:54120754 original size:25 final size:25
Alignment explanation
Indices: 54120720--54120770 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
54120710 ATAGATATTG
54120720 CACAATCAAATATTTTGTTTTCAAC
1 CACAATCAAATATTTTGTTTTCAAC
54120745 CACAATCAAATATTTTGTTTTCAAC
1 CACAATCAAATATTTTGTTTTCAAC
54120770 C
1 C
54120771 CCTTAACAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (25 bp):
CACAATCAAATATTTTGTTTTCAAC
Found at i:54127670 original size:46 final size:46
Alignment explanation
Indices: 54127620--54127791 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
54127610 TGAGCATCCG
*
54127620 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCA
* * * *
54127666 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG--TCCA
* * * *
54127713 AACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCA
* *
54127759 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54127792 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
43 5 0.05
45 4 0.04
46 57 0.54
47 29 0.28
48 4 0.04
50 6 0.06
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCA
Found at i:54127772 original size:93 final size:93
Alignment explanation
Indices: 54127613--54127784 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
54127603 GGATGGTTGA
* * * * *
54127613 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCAAACTCGTTGAGT
54127678 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
54127706 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCAAACTCGTTGAGT
54127771 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
54127785 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCAAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54130192 original size:14 final size:15
Alignment explanation
Indices: 54130175--54130210 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
54130165 CTTGAGACAC
54130175 TAAACCCTAAA-CCT
1 TAAACCCTAAACCCT
*
54130189 TAAATCCTAAACCCT
1 TAAACCCTAAACCCT
54130204 TAAACCC
1 TAAACCC
54130211 ATGATCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAACCCTAAACCCT
Found at i:54136875 original size:20 final size:20
Alignment explanation
Indices: 54136850--54136894 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
54136840 AGAGGCTAAA
* *
54136850 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
54136870 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
54136890 ATGAA
1 ATGAA
54136895 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:54142568 original size:42 final size:41
Alignment explanation
Indices: 54142488--54142637 Score: 162
Period size: 41 Copynumber: 3.6 Consensus size: 41
54142478 GAGCTTGGTC
54142488 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* *
54142529 TCGAAGGGCTTTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
54142571 CCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
*
54142612 TCGAAGGGCTTTTGAGCCGGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
54142638 GAGTCGGACT
Statistics
Matches: 90, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
39 4 0.04
40 9 0.10
41 37 0.41
42 28 0.31
43 12 0.13
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:54142620 original size:41 final size:40
Alignment explanation
Indices: 54142468--54142637 Score: 161
Period size: 41 Copynumber: 4.2 Consensus size: 40
54142458 GCTAATCGGG
*
54142468 GTCTAAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGT
1 GTCT-AATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
* *
54142509 G-CTAATAACCGAACTTAGTTTCGAAGGGCTTTTTAGAGCCAGT
1 GTCTAAT--CCGAGCTTAGTCTCGAAGGGC-TTTT-GAGCCAGT
* *
54142552 GTCATAA-CCG-GACTTAGT-TCCGAAGGGCCTTCGAGCCAGT
1 GTC-TAATCCGAG-CTTAGTCT-CGAAGGGCTTTTGAGCCAGT
* *
54142592 AGTCTAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCGGT
1 -GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
54142633 G-CTAA
1 GTCTAA
54142638 GAGTCGGACT
Statistics
Matches: 107, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
39 7 0.07
40 14 0.13
41 50 0.47
42 23 0.21
43 9 0.08
44 1 0.01
45 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
Found at i:54149341 original size:13 final size:13
Alignment explanation
Indices: 54149323--54149347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54149313 TATTATAAAC
54149323 ATTTTATGTTAGT
1 ATTTTATGTTAGT
54149336 ATTTTATGTTAG
1 ATTTTATGTTAG
54149348 AAATAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
ATTTTATGTTAGT
Found at i:54150892 original size:42 final size:41
Alignment explanation
Indices: 54150812--54150961 Score: 153
Period size: 41 Copynumber: 3.6 Consensus size: 41
54150802 GAGCTTGGTC
54150812 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* *
54150853 TCGAAGGGCTTTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * * *
54150895 CCGAAGGGCCTTCGAGCCAATAGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
*
54150936 TCGAAGGGCTTTTGAGCCGGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
54150962 GAGTCGGACT
Statistics
Matches: 88, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
39 4 0.05
40 8 0.09
41 36 0.41
42 28 0.32
43 12 0.14
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:54150944 original size:41 final size:40
Alignment explanation
Indices: 54150792--54150961 Score: 152
Period size: 41 Copynumber: 4.2 Consensus size: 40
54150782 GCTAATCGGG
*
54150792 GTCTAAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGT
1 GTCT-AATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
* *
54150833 G-CTAATAACCGAACTTAGTTTCGAAGGGCTTTTTAGAGCCAGT
1 GTCTAAT--CCGAGCTTAGTCTCGAAGGGC-TTTT-GAGCCAGT
* * *
54150876 GTCATAA-CCG-GACTTAGT-TCCGAAGGGCCTTCGAGCCAAT
1 GTC-TAATCCGAG-CTTAGTCT-CGAAGGGCTTTTGAGCCAGT
* *
54150916 AGTCTAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCGGT
1 -GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
54150957 G-CTAA
1 GTCTAA
54150962 GAGTCGGACT
Statistics
Matches: 105, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
39 7 0.07
40 13 0.12
41 49 0.47
42 23 0.22
43 9 0.09
44 1 0.01
45 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
Found at i:54156442 original size:40 final size:40
Alignment explanation
Indices: 54156398--54156535 Score: 179
Period size: 40 Copynumber: 3.4 Consensus size: 40
54156388 TGTTTTACCA
*
54156398 AAAACGCCACTAAAAATAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCACTAAAAACAGAGCATTAGCGGCGCTTTTGGT
**
54156438 AAAACGCTGCTAAAAACCAGA-CATTAGCGGCGCTTTTGGT
1 AAAACGCCACTAAAAA-CAGAGCATTAGCGGCGCTTTTGGT
* * *
54156478 AAAATGCTACTAAAAAAAACAGAGCATTAGCGGCTCTTTTGGT
1 AAAACGCCACT---AAAAACAGAGCATTAGCGGCGCTTTTGGT
54156521 AAAACGCCACTAAAA
1 AAAACGCCACTAAAA
54156536 GTCATATAAC
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
40 46 0.54
41 3 0.04
42 4 0.05
43 32 0.38
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (40 bp):
AAAACGCCACTAAAAACAGAGCATTAGCGGCGCTTTTGGT
Found at i:54156510 original size:43 final size:43
Alignment explanation
Indices: 54156409--54156535 Score: 179
Period size: 43 Copynumber: 3.0 Consensus size: 43
54156399 AAACGCCACT
* *
54156409 AAAAATAGAGCATTAGCGGCGCTTTTGGTAAAACGCTGCT--A
1 AAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCTACTAAA
* *
54156450 AAAACCAGA-CATTAGCGGCGCTTTTGGTAAAATGCTACTAAA
1 AAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCTACTAAA
* *
54156492 AAAAACAGAGCATTAGCGGCTCTTTTGGTAAAACGCCACTAAA
1 AAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCTACTAAA
54156535 A
1 A
54156536 GTCATATAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 28 0.37
41 7 0.09
42 9 0.12
43 31 0.41
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (43 bp):
AAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCTACTAAA
Found at i:54156633 original size:17 final size:18
Alignment explanation
Indices: 54156606--54156639 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54156596 TAAAAATAGT
*
54156606 AAACCCTTAAACCCTAAC
1 AAACCCTTAAACACTAAC
54156624 AAACCC-TAAACACTAA
1 AAACCCTTAAACACTAA
54156640 ACTATAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (18 bp):
AAACCCTTAAACACTAAC
Found at i:54157177 original size:24 final size:24
Alignment explanation
Indices: 54157150--54157198 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
54157140 CGTATATTTG
*
54157150 TTAAAAGTTTATATAAACATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
54157174 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
54157198 T
1 T
54157199 GTTATTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAGTTTATATAAAAATTAAT
Found at i:54157802 original size:18 final size:19
Alignment explanation
Indices: 54157779--54157817 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
54157769 AGATCTTTTT
54157779 TATTTTT-TATCAAAATAA
1 TATTTTTATATCAAAATAA
*
54157797 TATTTTTATATGAAAATAA
1 TATTTTTATATCAAAATAA
54157816 TA
1 TA
54157818 AATATGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTTTTATATCAAAATAA
Found at i:54162925 original size:42 final size:43
Alignment explanation
Indices: 54162862--54163017 Score: 149
Period size: 42 Copynumber: 3.7 Consensus size: 43
54162852 AAAAAATGTT
* * * * * *
54162862 GCTAAAGGTC-TATTATATAGTGGCGTTTT-GGGAAAAGTGTC
1 GCTAAAGGTCATAGTCTTTAGTGGCGTTTTCAGGAAAAGCGCC
* **
54162903 GCTAAAGGTCATAGTCTTTAGTGGTGTTTTCAAAAAAAGCGCC
1 GCTAAAGGTCATAGTCTTTAGTGGCGTTTTCAGGAAAAGCGCC
*
54162946 GCTAGAA-GTCAT-GGCTTTAGTGGCGTTTTCAGGAAAAGCGCC
1 GCTA-AAGGTCATAGTCTTTAGTGGCGTTTTCAGGAAAAGCGCC
* * * *
54162988 TCTAAAAGTCATGGTCTTTAGCGGCGTTTT
1 GCTAAAGGTCATAGTCTTTAGTGGCGTTTT
54163018 TTTAAATAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
41 12 0.13
42 49 0.52
43 31 0.33
44 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (43 bp):
GCTAAAGGTCATAGTCTTTAGTGGCGTTTTCAGGAAAAGCGCC
Found at i:54173705 original size:47 final size:47
Alignment explanation
Indices: 54173651--54174057 Score: 661
Period size: 47 Copynumber: 8.6 Consensus size: 47
54173641 TATTTGAATA
* *
54173651 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54173698 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
54173747 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54173794 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54173841 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54173890 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54173937 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
54173984 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54174031 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
54174058 TCCCGAAGGG
Statistics
Matches: 338, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 248 0.73
49 90 0.27
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:54173759 original size:96 final size:94
Alignment explanation
Indices: 54173651--54174057 Score: 661
Period size: 96 Copynumber: 4.3 Consensus size: 94
54173641 TATTTGAATA
* *
54173651 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
* *
54173716 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCGAATGGCCAATGTGATG
54173747 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
54173812 TGTGATAAGGCCGAATGGCCAATGTGATG
66 TGTGATAAGGCCGAATGGCCAATGTGATG
54173841 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * *
54173906 TATGTGATAAGGCCTAATAGCCGATGTGATG
64 TATGTGATAAGGCCGAATGGCCAATGTGATG
54173937 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * *
54174002 TGTGACAGGGCCGAGTGGCCAACGTGATG
66 TGTGATAAGGCCGAATGGCCAATGTGATG
* *
54174031 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
54174058 TCCCGAAGGG
Statistics
Matches: 293, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
94 145 0.49
96 148 0.51
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:54173909 original size:143 final size:143
Alignment explanation
Indices: 54173651--54174057 Score: 701
Period size: 143 Copynumber: 2.9 Consensus size: 143
54173641 TATTTGAATA
54173651 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
54173716 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
*
54173781 GGCCGATGTGATG
131 AGCCGATGTGATG
54173794 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
54173859 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
54173924 AGCCGATGTGATG
131 AGCCGATGTGATG
* *
54173937 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
54174000 TATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
54174058 TCCCGAAGGG
Statistics
Matches: 253, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
141 54 0.21
143 199 0.79
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (143 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
AGCCGATGTGATG
Found at i:54176537 original size:38 final size:38
Alignment explanation
Indices: 54176481--54176555 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
54176471 AATCCGAGTT
*
54176481 TAAAGACCCGCTGACTATGTGA-AGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATGT-ACAGAGATTATGTCCGGG
*
54176519 TAAAGACCCGATGGCTATGTACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATGTACAGAGATTATGTCCGG
54176556 ATTAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATGTACAGAGATTATGTCCGGG
Found at i:54176657 original size:40 final size:40
Alignment explanation
Indices: 54176613--54176769 Score: 197
Period size: 40 Copynumber: 3.9 Consensus size: 40
54176603 CTCGACGATG
* *
54176613 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* *
54176653 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* ** * * *
54176693 ATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* * *
54176733 ATCCGGGCTATGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
54176770 CGTGTATTCG
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
Found at i:54180281 original size:49 final size:47
Alignment explanation
Indices: 54180197--54180650 Score: 721
Period size: 47 Copynumber: 9.5 Consensus size: 47
54180187 TATTTGAATA
* *
54180197 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54180244 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54180293 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC-ATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54180339 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
54180388 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
54180437 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54180486 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54180533 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
54180580 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54180627 GATGTGAAAGTGTATAAATGTGAT
1 AATGTGAAAGTGTATATATGTGAT
54180651 GTCACACCCC
Statistics
Matches: 387, Mismatches: 15, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 20 0.05
47 179 0.46
48 25 0.06
49 163 0.42
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:54182085 original size:37 final size:37
Alignment explanation
Indices: 54182012--54182090 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
54182002 TTATTACGAA
* * * *
54182012 GTCTTACCCAGACATAATCTCCACCCGAAGTTATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
* *
54182049 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
54182086 GTCTT
1 GTCTT
54182091 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
Found at i:54182393 original size:93 final size:93
Alignment explanation
Indices: 54182209--54182446 Score: 377
Period size: 93 Copynumber: 2.5 Consensus size: 93
54182199 CCCTTCGGGA
* * * * * * *
54182209 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CCTATCACATATATACAC
54182274 TTTCACATTCATCACATCGGCCATTAGGC
65 TTTCACATTCATCACATCGGCCATTAGGC
*
54182303 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACGTATATACACT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACACT
54182368 TTCACATTCATCACATCGGCCATTAGGC
66 TTCACATTCATCACATCGGCCATTAGGC
54182396 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
54182447 TACTATCATT
Statistics
Matches: 134, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
93 53 0.40
94 40 0.30
95 41 0.31
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (93 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATACACT
TTCACATTCATCACATCGGCCATTAGGC
Found at i:54182430 original size:49 final size:47
Alignment explanation
Indices: 54182209--54182448 Score: 374
Period size: 47 Copynumber: 5.1 Consensus size: 47
54182199 CCCTTCGGGA
* * * * * *
54182209 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54182256 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54182303 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54182350 C-TATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54182396 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54182445 CTTA
1 CTTA
54182449 CTATCATTTC
Statistics
Matches: 178, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
46 45 0.25
47 91 0.51
49 42 0.24
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54187835 original size:25 final size:25
Alignment explanation
Indices: 54187807--54187855 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54187797 AGGAATTCGT
54187807 ACACACAGTGC-CTCTAATCATTCAC
1 ACACACAGTGCTCT-TAATCATTCAC
* *
54187832 ACACATAGTGCTCTTATTCATTCA
1 ACACACAGTGCTCTTAATCATTCA
54187856 TTATTACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (25 bp):
ACACACAGTGCTCTTAATCATTCAC
Found at i:54188066 original size:40 final size:40
Alignment explanation
Indices: 54188019--54188254 Score: 400
Period size: 40 Copynumber: 5.9 Consensus size: 40
54188009 GAATACACAT
* *
54188019 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
1 CACCGGCACGAATACCCTTCGGGACTTAGCCCGGATATAA
* *
54188059 CATCGGCACGAATACCCTTCGGGATTTAGCCCGGATATAA
1 CACCGGCACGAATACCCTTCGGGACTTAGCCCGGATATAA
*
54188099 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
1 CACCGGCACGAATACCCTTCGGGACTTAGCCCGGATATAA
*
54188139 CACCGGCACGAATACCCTTTGGGACTTAGCCCGGATATAA
1 CACCGGCACGAATACCCTTCGGGACTTAGCCCGGATATAA
54188179 CACCGGCACGAATACCCTTCGGGACTTAGCCCGGATATAA
1 CACCGGCACGAATACCCTTCGGGACTTAGCCCGGATATAA
* *
54188219 CACTGGCACGAATGCCCTTCGGGACTTAGCCCGGAT
1 CACCGGCACGAATACCCTTCGGGACTTAGCCCGGAT
54188255 CGTCGTCGAG
Statistics
Matches: 186, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 186 1.00
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.19
Consensus pattern (40 bp):
CACCGGCACGAATACCCTTCGGGACTTAGCCCGGATATAA
Found at i:54188381 original size:38 final size:38
Alignment explanation
Indices: 54188295--54188386 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 38
54188285 CTCTATATGA
* * **
54188295 AGCCAGTGGGTCTTAATCC-GGACATAATCTCTGTACAT
1 AGCCAGCGGGTCTTTA-CCTGGACATAATCTCTACACAT
* *
54188333 AGCCATCGGGTCTTTACCTGGACATAATCTCTACATAT
1 AGCCAGCGGGTCTTTACCTGGACATAATCTCTACACAT
*
54188371 AGTCAGCGGGTCTTTA
1 AGCCAGCGGGTCTTTA
54188387 AACTCGGATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
37 2 0.04
38 43 0.96
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (38 bp):
AGCCAGCGGGTCTTTACCTGGACATAATCTCTACACAT
Found at i:54198014 original size:48 final size:48
Alignment explanation
Indices: 54197953--54198182 Score: 212
Period size: 46 Copynumber: 4.9 Consensus size: 48
54197943 CGGCCATATT
* *
54197953 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAG
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCATCGAG
* * *
54198001 ATGAGAGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAG
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCATCGAG
**
54198047 ATGTA-AGAC-AGTGTAAGA-CATGTCTGGGACAT-GCATTGGC-TACGAG
1 ATG-AGAG-CTAGTGTAAGACCATGTCTGGGACATGGCATCAGCAT-CGAG
* * * * *
54198093 AT--GTGTTAGTGTAAGACCATGTCTAGGACATGGCTTCAGCA-CG-T
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCATCGAG
* *
54198137 ATAGAGTTGTTAGTGTAAGACCATGTCTGGGACATGGCATCAGCAT
1 AT-GAG-AGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCAT
54198183 TATACCCTAT
Statistics
Matches: 153, Mismatches: 16, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
44 12 0.08
45 16 0.10
46 56 0.37
47 16 0.10
48 53 0.35
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (48 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCATCGAG
Found at i:54198060 original size:46 final size:45
Alignment explanation
Indices: 54197920--54198124 Score: 168
Period size: 46 Copynumber: 4.4 Consensus size: 45
54197910 TGTGCTAGTA
* * * *
54197920 TAAGGCATGTTTGGGACATGCATCGGCCAT--ATTATGAGAGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGGCC-TCGA-GATGA-AGACAGTG
* * *
54197966 TAAGACCATGTCTGGGACATGGCATCAGCATTGAGATG-AGAGCTAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGAAGA-C-AGTG
*
54198014 TAAGACATGTTTGGGACATGCATCGGCCTCGAGATGTAAGACAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AAGACAGTG
* * **
54198060 TAAGACATGTCTGGGACATGCATTGG-CTACGAGATG-TGTTAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAAGACAGTG
*
54198104 TAAGACCATGTCTAGGACATG
1 TAAGA-CATGTCTGGGACATG
54198125 GCTTCAGCAC
Statistics
Matches: 133, Mismatches: 16, Indels: 21
0.78 0.09 0.12
Matches are distributed among these distances:
44 10 0.08
45 16 0.12
46 55 0.41
47 29 0.22
48 22 0.17
49 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (45 bp):
TAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAAGACAGTG
Found at i:54205243 original size:24 final size:24
Alignment explanation
Indices: 54205216--54205261 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54205206 ATTTTTGGAC
*
54205216 CTAGGGGTAAAACGATCATTTTAA
1 CTAGGGGCAAAACGATCATTTTAA
* *
54205240 CTAGGGGCAAAATGGTCATTTT
1 CTAGGGGCAAAACGATCATTTT
54205262 GCCCAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (24 bp):
CTAGGGGCAAAACGATCATTTTAA
Found at i:54205742 original size:46 final size:46
Alignment explanation
Indices: 54205594--54205817 Score: 176
Period size: 46 Copynumber: 4.8 Consensus size: 46
54205584 TCGGGTTATT
* * *
54205594 TGTAGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTA
1 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GA
* * * * ** * **
54205640 TG-AGAGCCAATGTAAGACCATGTTTGGGATATGGCATCAACATTAAGA
1 TGTA-AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGA
*
54205688 CG-AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
1 TGTA-AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
**
54205734 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATTAG-CTACGAGA
1 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGA
54205780 TGT--G-TCAGTGTAAGACCATGTCTGGG-CATGGCATCGGC
1 TGTAAGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
54205818 ACGTATAGAG
Statistics
Matches: 142, Mismatches: 26, Indels: 20
0.76 0.14 0.11
Matches are distributed among these distances:
43 1 0.01
44 13 0.09
45 18 0.13
46 63 0.44
47 25 0.18
48 21 0.15
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
Found at i:54205837 original size:47 final size:49
Alignment explanation
Indices: 54205696--54206009 Score: 207
Period size: 47 Copynumber: 6.6 Consensus size: 49
54205686 GACGAGAGCT
* * * *
54205696 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGAT-GTAAG-CT-
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGTGATAG-AGGTGTC
** *
54205742 AGTGTAAGA-CATGTCTGGGACAT-GCATTAGCTAC--G--AGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGTGATAGAGGTGTC
54205786 AGTGTAAGACCATGTCTGGG-CATGGCATCGGCACGT-ATAGAGGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTGATAGAGGTGTC
* * * *
54205833 AGTGTAAGACCATGTCTGGGACATGGAATTGGCACG-GATATGTGCGAG-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTGATA-GAG-GTGTC
* ** * * *** *
54205882 TAGTGTAAGACCATGTTTGGGACATGGTGTCAGC-CTTGATTTCGATAGTC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTGATAGAGGT-GTC
* * * *
54205932 AGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTGATGGATGAG-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTGATAGAGGTGTC
54205978 AAGTGTAAGACCATGTCTGGGACATGGCATCG
1 -AGTGTAAGACCATGTCTGGGACATGGCATCG
54206010 ACATTATACC
Statistics
Matches: 215, Mismatches: 32, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.01
43 2 0.01
44 15 0.07
45 17 0.08
46 30 0.14
47 59 0.27
48 23 0.11
49 33 0.15
50 34 0.16
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTGATAGAGGTGTC
Found at i:54206010 original size:47 final size:47
Alignment explanation
Indices: 54205602--54206011 Score: 195
Period size: 47 Copynumber: 8.7 Consensus size: 47
54205592 TTTGTAGGCT
*
54205602 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATT-AT-GA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G--AC-TTGATGGATGAGTC
* * * * *
54205648 AATGTAAGACCATGTTTGGGATATGGCATCAACATTAAGA-CGA-GAG-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-TT--GATGGATGAGTC
* *
54205695 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGA--GATGTAAG-C
1 -AGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGATGGATG--AGTC
* * *
54205741 TAGTGTAAGA-CATGTCTGGGACAT-GCAT-TAGC-T-ACGAGATGTGTC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGA-CTTGATG-GATGAGTC
* * * *
54205786 AGTGTAAGACCATGTCTGGG-CATGGCATCGGCACGT-ATAGAGGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTGATGGATGAGTC
* * * *
54205833 AGTGTAAGACCATGTCTGGGACATGGAATTGGCAC-GGATATGTG-CGAG-C
1 AGTGTAAGACCATGTCTGGGACATGGCA-TCG-ACTTG--ATG-GATGAGTC
* ** * *
54205882 TAGTGTAAGACCATGTTTGGGACATGGTGTCAGCCTTGATTTCGAT-AGTC
1 -AGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGA--TGGATGAGTC
54205932 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATGAG-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATGAGTC
54205978 AAGTGTAAGACCATGTCTGGGACATGGCATCGAC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGAC
54206012 ATTATACCCT
Statistics
Matches: 290, Mismatches: 37, Indels: 73
0.73 0.09 0.18
Matches are distributed among these distances:
43 3 0.01
44 16 0.06
45 21 0.07
46 54 0.19
47 89 0.31
48 39 0.13
49 34 0.12
50 33 0.11
51 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATGAGTC
Found at i:54210262 original size:75 final size:74
Alignment explanation
Indices: 54210090--54210281 Score: 221
Period size: 75 Copynumber: 2.6 Consensus size: 74
54210080 AAAAAGTTTC
* * * ** *
54210090 TCTATTGTATTTTACATCAATAATATACTTATTTACAATCTACAAAAAAAATTTAAAAATTGTTT
1 TCTATCGTATTTTATATAAATAATATACTTATTTACAATCTACAAAAAAAATGGAAAAATAGTTT
*
54210155 GTATTGCAT
66 GCATTGCAT
* *
54210164 TCTATTGTATTTTATATCAATAATATATACTTATTTACAATCTAC-AAAAAAATGGAATAAA-AG
1 TCTATCGTATTTTATATAAAT-A-ATATACTTATTTACAATCTACAAAAAAAATGGAA-AAATAG
*
54210227 TTTGCATTGTAT
63 TTTGCATTGCAT
54210239 TCTATCGTATGCTTT-T-TAAATAATATACTTATTTACAATCTAC
1 TCTATCGTAT--TTTATATAAATAATATACTTATTTACAATCTAC
54210282 GAGAAATGAA
Statistics
Matches: 105, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
73 21 0.20
74 21 0.20
75 35 0.33
76 25 0.24
77 3 0.03
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.43
Consensus pattern (74 bp):
TCTATCGTATTTTATATAAATAATATACTTATTTACAATCTACAAAAAAAATGGAAAAATAGTTT
GCATTGCAT
Found at i:54212002 original size:20 final size:20
Alignment explanation
Indices: 54211956--54212005 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
54211946 GATACCCCGA
* *
54211956 GTTTGGTGGTTTTGTGGTGT
1 GTTTGGTGGTTTTGTAGTGC
**
54211976 GAATGGTGGTTTTGTAGTGC
1 GTTTGGTGGTTTTGTAGTGC
54211996 GTTTGGTGGT
1 GTTTGGTGGT
54212006 CGGTAAGGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.06, C:0.02, G:0.44, T:0.48
Consensus pattern (20 bp):
GTTTGGTGGTTTTGTAGTGC
Found at i:54219664 original size:40 final size:40
Alignment explanation
Indices: 54219620--54219844 Score: 271
Period size: 40 Copynumber: 5.6 Consensus size: 40
54219610 GCTACTTGTT
*
54219620 CAAATGCCTTCGGGA-CATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGCCCGGTTATAGTAACTCGCA
*
54219660 CAAATGCCTTCGGATCTTAGTCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGCCCGGTTATAGTAACTCGCA
*
54219700 CAAATGCCTTCGGATCTTAGTCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGCCCGGTTATAGTAACTCGCA
* *
54219740 CAAATGCCCTCGGGA-CTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGCCCGG-TTATAGTAACTCGCA
* * * * * *
54219780 CCAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGCCCGGTTATAGTAAC-TCGCA
54219821 CAAA-GCCTTCGGGA-CTTAGCCCGG
1 CAAATGCCTTC-GGATCTTAGCCCGG
54219845 ACATCATTCG
Statistics
Matches: 163, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
39 7 0.04
40 141 0.87
41 15 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGCCCGGTTATAGTAACTCGCA
Found at i:54219839 original size:120 final size:120
Alignment explanation
Indices: 54219620--54219844 Score: 321
Period size: 120 Copynumber: 1.9 Consensus size: 120
54219610 GCTACTTGTT
* *
54219620 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCCTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
* * *
54219685 TTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGTTATAGTAACTCGCA
66 ATATAGTAACTAGCACAAATGCCTTCGGATCTTAGCCCGGTTATAGTAACTCGCA
* *
54219740 CAAATGCCCTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCCTCGGGACATAACCCGG-TTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
* *
54219804 GATATGGTCACTTAGCACAAA-GCCTTCGGGA-CTTAGCCCGG
65 GATATAGTAAC-TAGCACAAATGCCTTC-GGATCTTAGCCCGG
54219845 ACATCATTCG
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
120 80 0.86
121 13 0.14
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (120 bp):
CAAATGCCCTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
ATATAGTAACTAGCACAAATGCCTTCGGATCTTAGCCCGGTTATAGTAACTCGCA
Found at i:54222224 original size:28 final size:28
Alignment explanation
Indices: 54222161--54222311 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
54222151 ATATTAAGTC
*
54222161 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
54222188 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
54222216 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
54222244 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
54222272 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
54222301 CGCACACTTAG
1 CGCACACTTAG
54222312 CGCCAATCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 77 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54229797 original size:12 final size:12
Alignment explanation
Indices: 54229782--54229850 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 12
54229772 AAAAAGCCTT
*
54229782 TGAAAAACAAAA
1 TGAAAAAGAAAA
54229794 TGAAAAAGAAAA
1 TGAAAAAGAAAA
*
54229806 AGAAAAAGAAAA
1 TGAAAAAGAAAA
* ** * *
54229818 TGAGATTGAGAT
1 TGAAAAAGAAAA
*
54229830 TGAAAAAGAAAG
1 TGAAAAAGAAAA
54229842 TGAAAAAGA
1 TGAAAAAGA
54229851 GTTTGAAAGT
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.67, C:0.01, G:0.20, T:0.12
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:54229805 original size:5 final size:6
Alignment explanation
Indices: 54229783--54229817 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
54229773 AAAAGCCTTT
* *
54229783 GAAAAA CAAAAT GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
54229818 TGAGATTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:54246944 original size:40 final size:40
Alignment explanation
Indices: 54246838--54246981 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
54246828 ACCAGCTCGA
* * * **
54246838 AGCCTGCGGGACTTT-TGCCCGGACATATTTCCAGCGCAT
1 AGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCATAT
* * *
54246877 AGCCTGC-GGACCTTAAGTCCGGGTATAATTCCAGCATAT
1 AGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCATAT
*
54246916 AGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATAT
1 AGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCATAT
*
54246956 AGCCTGCGGGTCTTTAAGCCCGGATA
1 AGCCTGCGGGACTTTAAGCCCGGATA
54246982 CACATCAAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 6 0.07
39 31 0.34
40 54 0.59
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (40 bp):
AGCCTGCGGGACTTTAAGCCCGGATATAATTCCAGCATAT
Found at i:54252705 original size:16 final size:15
Alignment explanation
Indices: 54252680--54252709 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54252670 ATGTATCGGC
54252680 AAAAGCCAAAATGCA
1 AAAAGCCAAAATGCA
54252695 AAAATGCCAAAATGC
1 AAAA-GCCAAAATGC
54252710 CGAAAGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (15 bp):
AAAAGCCAAAATGCA
Found at i:54252971 original size:29 final size:29
Alignment explanation
Indices: 54252938--54253048 Score: 134
Period size: 29 Copynumber: 3.9 Consensus size: 29
54252928 TGAATGTAAC
*
54252938 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
54252967 TGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
54252996 TGGGCCTAATGGGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
* * * *
54253024 TGGGCTTAATTGGCCAGATACATGT
1 TGGGCCTAATGGGCCATATAAATGT
54253049 ATGTGAAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
28 20 0.29
29 49 0.71
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:54260110 original size:12 final size:13
Alignment explanation
Indices: 54260082--54260114 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54260072 TTATTTCTTT
54260082 TTCTCCATCTACC
1 TTCTCCATCTACC
*
54260095 TTCTCC-TCTTCC
1 TTCTCCATCTACC
54260107 TTCTCCAT
1 TTCTCCAT
54260115 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:54261390 original size:28 final size:27
Alignment explanation
Indices: 54261349--54261438 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
54261339 AGGAAGCATC
54261349 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* **
54261377 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
54261404 CTGGTGGCACTACCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
54261433 CTGGTG
1 CTGGTG
54261439 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:54261407 original size:27 final size:28
Alignment explanation
Indices: 54261361--54261438 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
54261351 GGTGGCTATG
* * *
54261361 CCACAAATTATCTGTTCTGGTGGCCCTG
1 CCACAAAATATCTGTTCTGGTGGCACTA
**
54261389 CCAC-GTATATCTGTTCTGGTGGCACTA
1 CCACAAAATATCTGTTCTGGTGGCACTA
54261416 CCACAAAATATCTGTATCTGGTG
1 CCACAAAATATCTGT-TCTGGTG
54261439 ACTCTGTCAC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 22 0.54
28 12 0.29
29 7 0.17
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
CCACAAAATATCTGTTCTGGTGGCACTA
Found at i:54267951 original size:12 final size:13
Alignment explanation
Indices: 54267923--54267955 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54267913 TTATTTCTTT
54267923 TTCTCCATCTACC
1 TTCTCCATCTACC
*
54267936 TTCTCC-TCTTCC
1 TTCTCCATCTACC
54267948 TTCTCCAT
1 TTCTCCAT
54267956 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:54269231 original size:28 final size:27
Alignment explanation
Indices: 54269190--54269279 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
54269180 AGCAAGCGTC
*
54269190 CTGGTGGCTA-TGCCACAAATTATTTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* **
54269218 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
54269245 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
54269274 CTGGTG
1 CTGGTG
54269280 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:54269252 original size:27 final size:28
Alignment explanation
Indices: 54269190--54269279 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 28
54269180 AGCAAGCGTC
* *
54269190 CTGGTGGCTA-TGCCACAAATTATTTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
54269218 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
54269245 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
54269274 CTGGTG
1 CTGGTG
54269280 ACTCTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.43
28 22 0.43
29 7 0.14
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:54269290 original size:29 final size:28
Alignment explanation
Indices: 54269200--54269290 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
54269190 CTGGTGGCTA
* * * *
54269200 TGCCACAAATTATTTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
54269228 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
54269255 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
54269284 TGTCACA
1 TGCCACA
54269291 TTTTCTATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 22 0.43
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:54273439 original size:65 final size:65
Alignment explanation
Indices: 54273358--54273483 Score: 200
Period size: 65 Copynumber: 1.9 Consensus size: 65
54273348 CTACCGCAGC
* *
54273358 TCTTTATGAGCATCCTGTTTAT-TGATTGGTTGTGATCCTGCATATGTTGCAGACACAAATGTAG
1 TCTTTATGAGAATCCTG-TTATGTGATCGGTTGTGATCCTGCATATGTTGCAGACACAAATGTAG
54273422 T
65 T
* *
54273423 TCTTTGTGAGAATCCTGTTATGTGATCGGTTGTGGTCCTGCATATGTTGCAGACACAAATG
1 TCTTTATGAGAATCCTGTTATGTGATCGGTTGTGATCCTGCATATGTTGCAGACACAAATG
54273484 CAACTCTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
64 4 0.07
65 52 0.93
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (65 bp):
TCTTTATGAGAATCCTGTTATGTGATCGGTTGTGATCCTGCATATGTTGCAGACACAAATGTAGT
Found at i:54273492 original size:65 final size:65
Alignment explanation
Indices: 54273357--54273504 Score: 199
Period size: 65 Copynumber: 2.3 Consensus size: 65
54273347 ACTACCGCAG
* * * *
54273357 CTCTTTATGAGCATCCTGTTTATTGATTGGTTGTGATCCTGCATATGTTGCAGACACAAATGTAG
1 CTCTTTATGAGAATCCTGTTTATTGATCGGTTGTGATCCTGCATATGTTGCAGACACAAATGCAA
* * *
54273422 TTCTTTGTGAGAATCCTG-TTATGTGATCGGTTGTGGTCCTGCATATGTTGCAGACACAAATGCA
1 CTCTTTATGAGAATCCTGTTTAT-TGATCGGTTGTGATCCTGCATATGTTGCAGACACAAATGCA
54273486 A
65 A
* *
54273487 CTCTTTATAAGCATCCTG
1 CTCTTTATGAGAATCCTG
54273505 ATATGGCTCG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 4 0.06
65 67 0.94
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (65 bp):
CTCTTTATGAGAATCCTGTTTATTGATCGGTTGTGATCCTGCATATGTTGCAGACACAAATGCAA
Found at i:54279181 original size:13 final size:13
Alignment explanation
Indices: 54279163--54279193 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
54279153 TGGAAGCCCT
54279163 CGATTACTACAGA
1 CGATTACTACAGA
54279176 CGATTACTACAGA
1 CGATTACTACAGA
54279189 CGATT
1 CGATT
54279194 TGTAAAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (13 bp):
CGATTACTACAGA
Found at i:54282342 original size:43 final size:43
Alignment explanation
Indices: 54282270--54282379 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 43
54282260 TGTAAGACTG
* * **
54282270 TGTCTGGGACACAGGCCTCGAT-TGAGATTTACGTATAAGACCA
1 TGTCTGGGACAGAGGCATCGATATTTGATTT-CGTATAAGACCA
** * * *
54282313 TGTCTGGGACATCGGCATC-ATATTTGATTTTGTGTAAGACCC
1 TGTCTGGGACAGAGGCATCGATATTTGATTTCGTATAAGACCA
54282355 TGTCTGGGACAGAGGCATCGATATT
1 TGTCTGGGACAGAGGCATCGATATT
54282380 GAATTACATG
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 28 0.51
43 27 0.49
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
TGTCTGGGACAGAGGCATCGATATTTGATTTCGTATAAGACCA
Found at i:54282393 original size:43 final size:43
Alignment explanation
Indices: 54282258--54282394 Score: 122
Period size: 43 Copynumber: 3.2 Consensus size: 43
54282248 TCTGAGATAT
** *
54282258 CGTGTAAGACTGTGTCTGGGACACAGGCCTCG--ATTGAGATTTA
1 CGTGTAAGACCATGTCTGGGACACAGGCATCGATATTGA-A-TTA
* *
54282301 CGTATAAGACCATGTCTGGGACATC-GGCATC-ATATTTG-ATTT
1 CGTGTAAGACCATGTCTGGGACA-CAGGCATCGATA-TTGAATTA
* * *
54282343 TGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGAATTA
1 CGTGTAAGACCATGTCTGGGACACAGGCATCGATATTGAATTA
*
54282386 CATGTAAGA
1 CGTGTAAGA
54282395 TCACATCTGG
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
42 31 0.41
43 39 0.52
44 2 0.03
45 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACACAGGCATCGATATTGAATTA
Found at i:54288217 original size:22 final size:21
Alignment explanation
Indices: 54288177--54288217 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
54288167 TACTAGACAC
*
54288177 AGGGGCACACACCCGTGTGGG
1 AGGGGCACACACCCATGTGGG
*
54288198 AGGGGCAACACGCCCATGTG
1 AGGGGC-ACACACCCATGTG
54288218 ACTCATCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.22, C:0.29, G:0.39, T:0.10
Consensus pattern (21 bp):
AGGGGCACACACCCATGTGGG
Found at i:54289459 original size:46 final size:45
Alignment explanation
Indices: 54289379--54289574 Score: 191
Period size: 46 Copynumber: 4.2 Consensus size: 45
54289369 CATGTCCTGC
* *
54289379 ACATGGTCTTACACTAGC-TCAACTCGTA-GCCGATGCATGTCCCAG
1 ACAT-GTCTTACACTGGCTTCATCTCG-AGGCCGATGCATGTCCCAG
*
54289424 ACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATGTCCTAG
1 ACATGTCTTACACTGGCTT-CATCTCGAGGCCGATGCATGTCCCAG
* * * * *
54289470 ACATGTCTTACACTAGCTTTCGTCTCAATGCTGATGCCATGTCCCAG
1 ACATGTCTTACACTGGC-TTCATCTCGAGGCCGATG-CATGTCCCAG
* * * *
54289517 ACATGGTCTTACACTGGCTCTCATAAT-GTGGCCAATGCATGTCTCAG
1 ACAT-GTCTTACACTGGCT-TCAT-CTCGAGGCCGATGCATGTCCCAG
54289564 ACATGTCTTAC
1 ACATGTCTTAC
54289575 GCTAGCACAC
Statistics
Matches: 125, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
44 12 0.10
45 6 0.05
46 57 0.46
47 29 0.23
48 20 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (45 bp):
ACATGTCTTACACTGGCTTCATCTCGAGGCCGATGCATGTCCCAG
Found at i:54289555 original size:94 final size:92
Alignment explanation
Indices: 54289410--54289580 Score: 240
Period size: 94 Copynumber: 1.8 Consensus size: 92
54289400 ACTCGTAGCC
* *
54289410 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATGTC-CTAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCAATGCATGTCTC-AGACAT
54289474 GTCTTACACTAGCTTTCGTCTCAATGCT
65 GTCTTACACTAGCTTTCGTCTCAATGCT
*
54289502 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCAATGCATGTCTCAGA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-ATCGAGGCCAATGCATGTCTCAGA
*
54289565 CATGTCTTACGCTAGC
62 CATGTCTTACACTAGC
54289581 ACACAAATGA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
92 4 0.06
93 14 0.20
94 49 0.70
95 3 0.04
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCAATGCATGTCTCAGACATG
TCTTACACTAGCTTTCGTCTCAATGCT
Found at i:54290942 original size:40 final size:40
Alignment explanation
Indices: 54290863--54291064 Score: 273
Period size: 40 Copynumber: 5.0 Consensus size: 40
54290853 TGAATGATAA
* * * *
54290863 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
54290903 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
54290943 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTT-TCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGT-TATAT
* *
54290983 TCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
54291023 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
54291063 CC
1 CC
54291065 AGCTAAATCC
Statistics
Matches: 141, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 137 0.97
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:54291347 original size:22 final size:22
Alignment explanation
Indices: 54291307--54291348 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54291297 GAATGTGAAT
*
54291307 ATATGATGTTATTCATTTAGCC
1 ATATGATGTTATACATTTAGCC
54291329 ATATGAATGTTATAC-TTTAG
1 ATATG-ATGTTATACATTTAG
54291349 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (22 bp):
ATATGATGTTATACATTTAGCC
Found at i:54294814 original size:40 final size:40
Alignment explanation
Indices: 54294759--54295060 Score: 446
Period size: 40 Copynumber: 7.6 Consensus size: 40
54294749 TATTCGAATG
* *
54294759 ATATCCGGGTTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
*
54294799 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
54294839 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* *
54294879 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
54294919 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * * * *
54294959 ATATTCGGGCTAAGTCCCGGAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * * *
54294999 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGT-TTCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAT-T
*
54295039 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
54295061 TTCTTGGGTT
Statistics
Matches: 236, Mismatches: 25, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
39 14 0.06
40 222 0.94
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
Found at i:54302728 original size:40 final size:40
Alignment explanation
Indices: 54302649--54302865 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
54302639 CGAATGATAA
* * * *
54302649 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
54302689 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
54302729 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTT-TCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGT-TATAT
* *
54302769 CTGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
54302809 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
54302849 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
54302866 ATACTTGGGT
Statistics
Matches: 156, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
38 1 0.01
39 16 0.10
40 137 0.88
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:54303133 original size:22 final size:22
Alignment explanation
Indices: 54303093--54303134 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54303083 GAATGTGCAT
*
54303093 ATATGATGTTATTCATTTAGCC
1 ATATGATGTTATACATTTAGCC
54303115 ATATGAATGTTATAC-TTTAG
1 ATATG-ATGTTATACATTTAG
54303135 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (22 bp):
ATATGATGTTATACATTTAGCC
Found at i:54304900 original size:10 final size:10
Alignment explanation
Indices: 54304885--54304923 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
54304875 TGCTTTTGTA
54304885 CATGATATGC
1 CATGATATGC
54304895 CATGATATGC
1 CATGATATGC
54304905 ACATGATATGC
1 -CATGATATGC
54304916 CATGATAT
1 CATGATAT
54304924 ATTCACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:54304909 original size:21 final size:21
Alignment explanation
Indices: 54304884--54304923 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
54304874 CTGCTTTTGT
54304884 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
54304905 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
54304924 ATTCACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:54305004 original size:25 final size:25
Alignment explanation
Indices: 54304970--54305039 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
54304960 AGGAAGTGCT
* *
54304970 AAAAGGGCTTTGCCCCAGTTTACTG
1 AAAAGGGCTTTGCCCCAGTTCACCG
54304995 AAAAGGGCTTTGCCCCAGTTCACCG
1 AAAAGGGCTTTGCCCCAGTTCACCG
54305020 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54305040 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTCACCG
Found at i:54307984 original size:27 final size:28
Alignment explanation
Indices: 54307946--54308034 Score: 128
Period size: 27 Copynumber: 3.2 Consensus size: 28
54307936 GAGGAAGCAT
54307946 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAAATATCTGTA
*
54307973 TCTGGTGGCTCTGCCACAAATATCTGTT
1 TCTGGTGGCTCTGCCACAAATATCTGTA
* * *
54308001 TCTAGTGGTTCTACCAC-AATATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTGTA
54308028 TCTGGTG
1 TCTGGTG
54308035 ACTTTGTCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 41 0.75
28 14 0.25
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:54308046 original size:55 final size:54
Alignment explanation
Indices: 54307945--54308054 Score: 132
Period size: 55 Copynumber: 2.0 Consensus size: 54
54307935 GGAGGAAGCA
* * *
54307945 TTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTAGTGGCTCTACCACAAATATCTGATCTGGTGACTCTGCCAC-AATATCTGT
* * * *
54308000 TTCTAGTGGTTCTACCAC-AATATCTGTATCTGGTGACTTTGTCACAATATGTGT
1 TTCTAGTGGCTCTACCACAAATATCTG-ATCTGGTGACTCTGCCACAATATCTGT
54308054 T
1 T
54308055 CTGGCAGCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
54 17 0.36
55 30 0.64
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (54 bp):
TTCTAGTGGCTCTACCACAAATATCTGATCTGGTGACTCTGCCACAATATCTGT
Found at i:54311282 original size:27 final size:27
Alignment explanation
Indices: 54311249--54311453 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
54311239 TATATAAGTC
* *
54311249 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
54311276 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
54311304 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
54311331 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
** **
54311358 CGCACACTTAGTGC-ATCATTTTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* ** *
54311385 CGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
** *
54311412 CGCACACTTAGTGCTACATAGCCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
54311439 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54311454 GTACAATTTA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.83
28 26 0.17
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54311388 original size:54 final size:54
Alignment explanation
Indices: 54311249--54311452 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
54311239 TATATAAGTC
* * * **
54311249 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAA-T
* *
54311304 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
** ** *
54311358 CGCACACTTAGTGC-ATCATTTTCATTTCGCACACTTAGTGCAACATGGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
* *
54311412 CGCACACTTAGTGCTACATAGCCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGC
54311453 TGTACAATTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCACATGGTCAAAT
Found at i:54311418 original size:81 final size:81
Alignment explanation
Indices: 54311303--54311452 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
54311293 ATAATCAAAC
* * * * * *
54311303 TCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
54311368 GTGCATCATTTTCATT
66 GTGCATCATTTTCATT
* *
54311384 TCGCACACTTAGTGCAACATGGTCAAATCGCACACTTAGTGCTACATAGCCAAATCGCACACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
54311449 GTGC
66 GTGC
54311453 TGTACAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCACATAGCCAAATCGCACACTTA
GTGCATCATTTTCATT
Found at i:54315198 original size:28 final size:28
Alignment explanation
Indices: 54315144--54315200 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
54315134 ATGAAGTCTT
* * *
54315144 GCACACTCAGTGCTATATAATCCAACTC
1 GCACACTCAGTGCCACATAATCAAACTC
* *
54315172 GCACACTTAGTGCCACATAATTAAACTC
1 GCACACTCAGTGCCACATAATCAAACTC
54315200 G
1 G
54315201 GCAACCACTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (28 bp):
GCACACTCAGTGCCACATAATCAAACTC
Found at i:54317296 original size:47 final size:48
Alignment explanation
Indices: 54317179--54317724 Score: 735
Period size: 47 Copynumber: 11.8 Consensus size: 48
54317169 TTAGGATTCT
* * *
54317179 ATGTGATG-GATGTGAAA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
54317225 ATGTGATG-AATGTGAAAGTTTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAAATGTGAAAG--TGTATATATGTGATAAGGCCTAATGGCCG
54317274 ATGATG-TGAAA-GT----GTGTATATATGTGATAAGGCCTAATGGCCG
1 ATG-TGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
54317317 ATGTGAT-AAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54317364 ATGTGATG-AATGTGAAAGTGTATATATATGTGATAAGGCCTAAT-GCCG
1 ATGTGATGAAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
54317412 ATGTGATG-AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
54317459 ATATGAT--AATGTGAAAGTGTATATATGTGATAAGGCCTAATAG-CG
1 ATGTGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54317504 ATGTGATG-AATGTGAAAGTGTATATATGT-ATAAGGCCTAATGGCCG
1 ATGTGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54317550 ATGTGAT--AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
54317596 ATGTGA--AAGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAA-ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
54317643 ATGTGATG-AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
54317690 ACGTGATG-GATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAAATGTGAAAGTGTATATATGTGATAAG
54317725 TCCCGAAGGG
Statistics
Matches: 458, Mismatches: 20, Indels: 43
0.88 0.04 0.08
Matches are distributed among these distances:
42 5 0.01
43 34 0.07
45 43 0.09
46 127 0.28
47 165 0.36
48 25 0.05
49 55 0.12
50 4 0.01
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (48 bp):
ATGTGATGAAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:54317308 original size:92 final size:91
Alignment explanation
Indices: 54317199--54317724 Score: 651
Period size: 92 Copynumber: 5.7 Consensus size: 91
54317189 TGTGAAATGC
* *
54317199 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTTTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG--TGTATATATGTGATAAGGC
54317264 CTAATGGCCGATG-ATGTGAAAGTGTGT
64 CTAATGGCCGATGAATGTGAAAGTGTGT
*
54317291 ATATATGTGATAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
* *
54317356 AATAGCCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCC-----GATGAATGTGAAAGTGTGT
54317387 ATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
54317451 AATGGCCGATATGATAATGTGAAA--GTGT
66 AATGGCCG--ATG--AATGTGAAAGTGTGT
*
54317479 ATATATGTGATAAGGCCTAATAG-CGATGTGATGAATGTGAAAGTGTATATATGT-ATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
54317542 AATGGCCGATGTGATAATGTGAAA--GTGT
66 AATGGCCGA--TG--AATGTGAAAGTGTGT
*
54317570 ATATATGTGATAAGGCCTAATGGCCGATGTGA-AAGATGTGAAAGTGTATATATGTGATAAGGCC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGA-ATGTGAAAGTGTATATATGTGATAAGGCC
54317634 TAATGGCCGATGTGATGAATGTGAAA--GTGT
65 TAATGGCC-----GATGAATGTGAAAGTGTGT
* * * * * * * *
54317664 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
54317725 TCCCGAAGGG
Statistics
Matches: 393, Mismatches: 19, Indels: 42
0.87 0.04 0.09
Matches are distributed among these distances:
89 1 0.00
90 27 0.07
91 57 0.15
92 128 0.33
93 17 0.04
94 73 0.19
95 52 0.13
96 36 0.09
98 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (91 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCGATGAATGTGAAAGTGTGT
Found at i:54317669 original size:279 final size:276
Alignment explanation
Indices: 54317188--54317724 Score: 816
Period size: 279 Copynumber: 1.9 Consensus size: 276
54317178 TATGTGATGG
*
54317188 ATGTGAAATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTTTATATATA
1 ATGTGAAATGCATATATGAGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG-TTATATATA
54317253 TGTGATAAGGCCTAATGGCCGATGATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGA
65 TGTGATAAGGCCTAATGGCCGATGATGTGAAAG-GTGTATATATGTGATAAGGCCTAATGGCCGA
54317318 TGTGATAAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
129 TGTGATAAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
* * * * *
54317383 GTATATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
194 G--TATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAAG
54317447 GCCTAATGGCCGATATGATA
257 GCCTAATGGCCGATATGATA
* * *
54317467 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAG-CGATGTGATGAATGTGAAAG-TGTATATA
1 ATGTGAAA-TGCATATATGAGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTTATATATA
54317530 TGT-ATAAGGCCTAATGGCCGATGTGATAATGTGAAA-GTGTATATATGTGATAAGGCCTAATGG
65 TGTGATAAGGCCTAATGGCCGA--TG---ATGTGAAAGGTGTATATATGTGATAAGGCCTAATGG
*
54317593 CCGATGTGA-AAGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
125 CCGATGTGATAA-ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
* * *
54317657 AAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGAT
189 AAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGAT
54317722 AAG
254 AAG
54317725 TCCCGAAGGG
Statistics
Matches: 237, Mismatches: 13, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
276 18 0.08
277 28 0.12
278 39 0.16
279 121 0.51
280 23 0.10
281 8 0.03
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (276 bp):
ATGTGAAATGCATATATGAGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTTATATATAT
GTGATAAGGCCTAATGGCCGATGATGTGAAAGGTGTATATATGTGATAAGGCCTAATGGCCGATG
TGATAAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGT
ATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAAGGCCT
AATGGCCGATATGATA
Found at i:54317899 original size:37 final size:37
Alignment explanation
Indices: 54317843--54317921 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54317833 CCGAGCTCTA
* * *
54317843 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
54317880 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54317917 AAGAC
1 AAGAC
54317922 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54321167 original size:14 final size:14
Alignment explanation
Indices: 54321148--54321174 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54321138 TATCAAAACA
54321148 AGAATTAAGAATAC
1 AGAATTAAGAATAC
54321162 AGAATTAAGAATA
1 AGAATTAAGAATA
54321175 AGTTAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.15, T:0.22
Consensus pattern (14 bp):
AGAATTAAGAATAC
Found at i:54332519 original size:55 final size:53
Alignment explanation
Indices: 54332375--54332570 Score: 178
Period size: 55 Copynumber: 3.6 Consensus size: 53
54332365 ACTTACCTTT
* **
54332375 GCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAATTCACCATT
1 GCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAATTCACCAAA
* * * * * * * *
54332428 GTCAAGTCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTATCAAA
1 GCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G-AATTCACCAAA
* * * * *
54332483 GCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTT-ACCAAT
1 GCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA-TTCACCAAA
* * *
54332537 GCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 GCCATGTCTTGACATGGTCTTACATGGTATCCTT
54332571 AAACCCTAAT
Statistics
Matches: 112, Mismatches: 28, Indels: 5
0.77 0.19 0.03
Matches are distributed among these distances:
53 35 0.31
54 35 0.31
55 42 0.38
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.38
Consensus pattern (53 bp):
GCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAATTCACCAAA
Found at i:54334779 original size:28 final size:27
Alignment explanation
Indices: 54334747--54334828 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 27
54334737 GTCACTAGAT
*
54334747 ACAGATATTTTGTGGCAGTGCCACCATA
1 ACAGATA-TTTGTGGCAGTGCCACCAGA
** *
54334775 ACAGATATACGTGGCAGGGCCACCAGA
1 ACAGATATTTGTGGCAGTGCCACCAGA
54334802 ACAGATAATTTGTGGCA-TAGCCACCAG
1 ACAGAT-ATTTGTGGCAGT-GCCACCAG
54334829 GACGCTTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
27 22 0.49
28 23 0.51
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (27 bp):
ACAGATATTTGTGGCAGTGCCACCAGA
Found at i:54334981 original size:28 final size:28
Alignment explanation
Indices: 54334934--54334997 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
54334924 AAATTAACCC
*
54334934 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
54334962 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
54334990 TAGGGGTA
1 TAGGGGTA
54334998 CTCTAGTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:54342011 original size:29 final size:29
Alignment explanation
Indices: 54341969--54342069 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
54341959 CATGAAATTG
54341969 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
54341998 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
54342027 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
54342055 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
54342070 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:54345881 original size:28 final size:27
Alignment explanation
Indices: 54345841--54345917 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 27
54345831 ACAAAGTCAG
*
54345841 CAGATACAGATATTTTGTGGCAGTGCCAC
1 CAGA-ACAGATA-TTTGTGGCAGGGCCAC
**
54345870 CAGAACAGATATACGTGGCAGGGCCAC
1 CAGAACAGATATTTGTGGCAGGGCCAC
54345897 CAGAACAGATAATTTGTGGCA
1 CAGAACAGAT-ATTTGTGGCA
54345918 TAGCCACTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.55
28 15 0.36
29 4 0.10
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (27 bp):
CAGAACAGATATTTGTGGCAGGGCCAC
Found at i:54346080 original size:28 final size:28
Alignment explanation
Indices: 54346033--54346124 Score: 148
Period size: 28 Copynumber: 3.3 Consensus size: 28
54346023 AAATTAACCC
* * *
54346033 TAGGAGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
54346061 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
54346089 TAAGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
54346117 TAGGGGTA
1 TAGGGGTA
54346125 CTCTAGTACA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:54346727 original size:12 final size:13
Alignment explanation
Indices: 54346708--54346740 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54346698 GGGTTCAGCT
54346708 ATGGAGAAGGAAG
1 ATGGAGAAGGAAG
*
54346721 A-GGAGAAGGTAG
1 ATGGAGAAGGAAG
54346733 ATGGAGAA
1 ATGGAGAA
54346741 AAAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.09
Consensus pattern (13 bp):
ATGGAGAAGGAAG
Found at i:54349297 original size:11 final size:11
Alignment explanation
Indices: 54349283--54349307 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54349273 TGAGTATGAA
54349283 TTATATTAAAT
1 TTATATTAAAT
54349294 TTATATTAAAT
1 TTATATTAAAT
54349305 TTA
1 TTA
54349308 CATGTATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATATTAAAT
Found at i:54349934 original size:21 final size:23
Alignment explanation
Indices: 54349910--54349955 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
54349900 AAAAATTGAA
54349910 AAAC-AATTCAAAT-TTCGAGTT
1 AAACAAATTCAAATATTCGAGTT
* *
54349931 AAACAAATTGAATTATTCGAGTT
1 AAACAAATTCAAATATTCGAGTT
54349954 AA
1 AA
54349956 TCGAGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 7 0.33
23 10 0.48
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (23 bp):
AAACAAATTCAAATATTCGAGTT
Found at i:54350046 original size:9 final size:9
Alignment explanation
Indices: 54350022--54350067 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
54350012 TGAGTTTTCG
*
54350022 AATTCAAAT
1 AATTCGAAT
*
54350031 AACTCGAAT
1 AATTCGAAT
54350040 AATTCGAAT
1 AATTCGAAT
54350049 AATTCGAAT
1 AATTCGAAT
54350058 AATTCGAAT
1 AATTCGAAT
54350067 A
1 A
54350068 TCAAACTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:54350329 original size:30 final size:30
Alignment explanation
Indices: 54350280--54350338 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
54350270 AATTTTTTAA
* *
54350280 TTTCCCCCTAAATTTTTAC-TCCCTCCCAC
1 TTTCCCCCAAAACTTTTACTTCCCTCCCAC
*
54350309 TTTCCCCCAAAAACTTTTACTTCCTTCCCA
1 TTTCCCCC-AAAACTTTTACTTCCCTCCCA
54350339 TCCCACCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 9 0.36
31 8 0.32
ACGTcount: A:0.20, C:0.42, G:0.00, T:0.37
Consensus pattern (30 bp):
TTTCCCCCAAAACTTTTACTTCCCTCCCAC
Found at i:54353943 original size:64 final size:68
Alignment explanation
Indices: 54353835--54354006 Score: 203
Period size: 67 Copynumber: 2.6 Consensus size: 68
54353825 CATCATGTGT
** * * *
54353835 ACAAGAGAGCTACGAGATACTATGTGGTAGCTAGGTCACATGTGT-GATAC-GG-GATGTATACC
1 ACAAGAGAGCTACGAGATA--AAAT-GTAGCTAGGTCACATGTGTAGATACAGGTGAAGGACACC
54353897 ATGTAG
63 ATGTAG
* * *
54353903 ACAAGAGAGCTACGGGAT-AAATGTAGCTAGGTCACATGTGTAGCTCCAGGTGAAGGACACCATG
1 ACAAGAGAGCTACGAGATAAAATGTAGCTAGGTCACATGTGTAGATACAGGTGAAGGACACCATG
54353967 TAG
66 TAG
54353970 ACAAGAGAGCTACGAGATAAAATG--GCTAGGTCACATG
1 ACAAGAGAGCTACGAGATAAAATGTAGCTAGGTCACATG
54354007 GGTGGCACTA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
64 19 0.21
65 5 0.05
66 15 0.16
67 30 0.33
68 22 0.24
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGATAAAATGTAGCTAGGTCACATGTGTAGATACAGGTGAAGGACACCATG
TAG
Found at i:54358996 original size:37 final size:37
Alignment explanation
Indices: 54358946--54359024 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
54358936 TTATTACGAA
*
54358946 GTCTTACCCGGACATAA-TCTCCACACGAAGTCATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
54358983 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
54359020 GTCTT
1 GTCTT
54359025 TAGAGCTCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 37 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:54359221 original size:47 final size:47
Alignment explanation
Indices: 54359143--54359498 Score: 568
Period size: 47 Copynumber: 7.6 Consensus size: 47
54359133 CCCTTCGGGA
* * * * * * *
54359143 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54359190 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54359237 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54359284 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54359331 CTTATCACATATATACACTTTCACATTCATCCCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54359378 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54359425 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54359472 CTTATCACATATATACACTTATCACAT
1 CTTATCACATATATACACTT-TCACAT
54359499 ATATACACTT
Statistics
Matches: 288, Mismatches: 20, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
47 282 0.98
48 6 0.02
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54359397 original size:141 final size:141
Alignment explanation
Indices: 54359143--54359601 Score: 630
Period size: 141 Copynumber: 3.1 Consensus size: 141
54359133 CCCTTCGGGA
* * * * * * * * * *
54359143 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
54359208 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCCCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
54359273 GGCCATTAGGC
131 GGCTATTAGGC
*
54359284 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
54359349 TTTCACATTCATCCCATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCCCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
54359414 GGCTATTAGGC
131 GGCTATTAGGC
54359425 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
54359490 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACT
66 TT-T--C------ACA--TT--CA-TC--C-CATCGGCCATTAGGCCTTATCACATATATACACT
54359555 TTCACATTCATCACATCGGCTATTAGGC
114 TTCACATTCATCACATCGGCTATTAGGC
54359583 CTTATCACATATATACACT
1 CTTATCACATATATACACT
54359602 GTCTTGGCTG
Statistics
Matches: 284, Mismatches: 17, Indels: 17
0.89 0.05 0.05
Matches are distributed among these distances:
141 193 0.68
142 1 0.00
144 1 0.00
150 3 0.01
152 2 0.01
154 2 0.01
155 2 0.01
157 1 0.00
158 79 0.28
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCCCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCTATTAGGC
Found at i:54359494 original size:17 final size:17
Alignment explanation
Indices: 54359472--54359514 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
54359462 GCTATTAGGC
54359472 CTTATCACATATATACA
1 CTTATCACATATATACA
54359489 CTTATCACATATATACA
1 CTTATCACATATATACA
54359506 CTT-TCACAT
1 CTTATCACAT
54359515 TCATCACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (17 bp):
CTTATCACATATATACA
Found at i:54359511 original size:111 final size:111
Alignment explanation
Indices: 54359378--54359601 Score: 439
Period size: 111 Copynumber: 2.0 Consensus size: 111
54359368 GCCATTAGGC
*
54359378 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
54359443 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
66 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
54359489 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
54359554 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
66 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
54359600 CT
1 CT
54359602 GTCTTGGCTG
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (111 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
Found at i:54359512 original size:64 final size:64
Alignment explanation
Indices: 54359425--54359561 Score: 267
Period size: 64 Copynumber: 2.2 Consensus size: 64
54359415 GCTATTAGGC
54359425 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
54359489 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
54359553 CTT-TCACAT
1 CTTATCACAT
54359562 TCATCACATC
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
63 6 0.08
64 67 0.92
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (64 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACA
Found at i:54359542 original size:47 final size:47
Alignment explanation
Indices: 54359489--54359601 Score: 226
Period size: 47 Copynumber: 2.4 Consensus size: 47
54359479 CATATATACA
54359489 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
54359536 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
54359583 CTTATCACATATATACACT
1 CTTATCACATATATACACT
54359602 GTCTTGGCTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:54368517 original size:47 final size:47
Alignment explanation
Indices: 54368439--54368805 Score: 601
Period size: 47 Copynumber: 7.7 Consensus size: 47
54368429 CCCTTCGGGA
* * * * * *
54368439 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54368486 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54368533 CTTATCACATATATAGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATA-CACTTTCACATTCATCACATCGGCCATTAGGC
54368581 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54368628 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54368675 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54368724 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54368771 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
54368806 AGAATCCTAA
Statistics
Matches: 304, Mismatches: 12, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 209 0.69
48 47 0.15
49 47 0.15
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54368737 original size:96 final size:94
Alignment explanation
Indices: 54368439--54368805 Score: 601
Period size: 96 Copynumber: 3.9 Consensus size: 94
54368429 CCCTTCGGGA
* * * * * * * *
54368439 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
54368504 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
54368533 CTTATCACATATATAGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CTTATCACATATATA-CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
54368598 CTTTCACATTCATCACATCGGCCATTAGGC
65 CTTTCACATTCATCACATCGGCCATTAGGC
54368628 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
54368693 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
54368724 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCA-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
54368788 TGTTCACATCCATCACAT
66 T-TTCACATTCATCACAT
54368806 AGAATCCTAA
Statistics
Matches: 259, Mismatches: 10, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
93 1 0.00
94 77 0.30
95 87 0.34
96 94 0.36
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:54368755 original size:143 final size:142
Alignment explanation
Indices: 54368439--54368805 Score: 610
Period size: 143 Copynumber: 2.6 Consensus size: 142
54368429 CCCTTCGGGA
* * * * * * * *
54368439 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
54368504 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAGCACTTTCACATTCATCACAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAACACTTTCACATTCATCACAT
54368569 CGGCCATTAGGC
131 CGGCCATTAGGC
54368581 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
54368646 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA-ACACTTTCACATTCATCACA
54368711 TCGGCCATTAGGC
130 TCGGCCATTAGGC
*
54368724 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCA-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
54368788 TGTTCACATCCATCACAT
66 T-TTCACATTCATCACAT
54368806 AGAATCCTAA
Statistics
Matches: 212, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
142 102 0.48
143 110 0.52
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (142 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAACACTTTCACATTCATCACAT
CGGCCATTAGGC
Found at i:54376395 original size:16 final size:16
Alignment explanation
Indices: 54376374--54376407 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
54376364 CTGTAACGCC
54376374 CTAAAAATCCCAAAAT
1 CTAAAAATCCCAAAAT
*
54376390 CTAAAAATCCTAAAAT
1 CTAAAAATCCCAAAAT
54376406 CT
1 CT
54376408 TGAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
CTAAAAATCCCAAAAT
Found at i:54377961 original size:29 final size:28
Alignment explanation
Indices: 54377902--54378016 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 28
54377892 GTGAGCATGA
* **
54377902 ATATGAATGTGATTGGGCCTAACAGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
*
54377930 ATATAAATGTGAGTTGGGCCTAATGGGTC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* *
54377959 ATATATAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* *
54377988 ATATGAATATGATT-GGCCTTAATGGGCC
1 ATATAAATGTGATTGGGCC-TAATGGGCC
54378016 A
1 A
54378017 GATATAGGTA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
27 4 0.05
28 23 0.32
29 46 0.63
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:54378022 original size:57 final size:57
Alignment explanation
Indices: 54377910--54378025 Score: 146
Period size: 58 Copynumber: 2.0 Consensus size: 57
54377900 GAATATGAAT
* * *
54377910 GTGATTGGGCCTAACAGGCCATATAAATGTGAGTTGGGCCTAATGGGTCATATATAG
1 GTGATTGGGCCTAACAGGCCATATAAATATGAGTTGGGCCTAATGGGCCAGATATAG
** *
54377967 GTGATTTGGGCCTAATGGGCCATATGAATATGA-TT-GGCCTTAATGGGCCAGATATAG
1 GTGA-TTGGGCCTAACAGGCCATATAAATATGAGTTGGGCC-TAATGGGCCAGATATAG
54378024 GT
1 GT
54378026 ATGTGAATTC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
56 4 0.08
57 23 0.45
58 24 0.47
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (57 bp):
GTGATTGGGCCTAACAGGCCATATAAATATGAGTTGGGCCTAATGGGCCAGATATAG
Found at i:54397191 original size:46 final size:44
Alignment explanation
Indices: 54397100--54397257 Score: 156
Period size: 46 Copynumber: 3.4 Consensus size: 44
54397090 AATGTATGAC
* * *
54397100 CATGTCTGGGACATGGCATCGGCATTAAGACGAT-TGCTAGTGTAAGA
1 CATGTCTGGGACAT-GCATCGGC--TACGA-GATAAGCCAGTGTAAGA
* *
54397147 CATGTCTGGGACATGCGTCGGCTTCGAGACATAAGCCAGTGTAAGA
1 CATGTCTGGGACATGCATCGGCTACGAG--ATAAGCCAGTGTAAGA
* ** *
54397193 CATGTCTGGGACATGCATCTGCTACGAGATGTGTCAGTGTAAGA
1 CATGTCTGGGACATGCATCGGCTACGAGATAAGCCAGTGTAAGA
54397237 CCATGTCTGGGACATGACATC
1 -CATGTCTGGGACATG-CATC
54397258 AGCACCTGAC
Statistics
Matches: 95, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
43 1 0.01
44 16 0.17
45 17 0.18
46 47 0.49
47 14 0.15
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (44 bp):
CATGTCTGGGACATGCATCGGCTACGAGATAAGCCAGTGTAAGA
Found at i:54403248 original size:58 final size:58
Alignment explanation
Indices: 54403125--54403293 Score: 243
Period size: 58 Copynumber: 2.9 Consensus size: 58
54403115 GTGCCCACTA
* *
54403125 ACCGATCTCGCACACATAGTGCTCGGTTGAAA--AACTCACACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTT-AAAGGAATTTACACACACAGTGCCTCAATT
* ** *
54403182 ACCAATCTCGCACACATAGTGCTCGGTTAAAGGAATTTTTACACACAGCGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTACACACACAGTGCCTCAATT
* *
54403240 ACCGATCTCACACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTC
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTACACACACAGTGCCTC
54403294 TAATCATTCG
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
56 3 0.03
57 27 0.27
58 69 0.70
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (58 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTACACACACAGTGCCTCAATT
Found at i:54403508 original size:43 final size:43
Alignment explanation
Indices: 54403447--54403754 Score: 526
Period size: 43 Copynumber: 7.2 Consensus size: 43
54403437 CCTTGCTCGA
** * * *
54403447 ATCACCGGCATTAAGCCTGCTAGGTACGAAGACCCAAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* * * *
54403490 ATCACCTGCACGAAGCCTGCAATGCACGAAGGCTCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
54403533 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
54403576 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
54403619 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
54403662 ATCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
54403705 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
54403748 ATCACCG
1 ATCACCG
54403755 AGTTTCATGC
Statistics
Matches: 250, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 250 1.00
ACGTcount: A:0.31, C:0.34, G:0.24, T:0.11
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:54408208 original size:27 final size:27
Alignment explanation
Indices: 54408178--54408355 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54408168 ATATTGAGTC
* * * *
54408178 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54408205 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54408232 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54408260 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54408287 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54408314 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54408341 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54408356 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54408317 original size:82 final size:81
Alignment explanation
Indices: 54408199--54408354 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54408189 TGCTATATAA
* *
54408199 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54408264 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54408281 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54408345 CACTTAGTGC
65 CACTTAGTGC
54408355 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54416259 original size:27 final size:27
Alignment explanation
Indices: 54416229--54416406 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54416219 ATATTGAGTC
* * * *
54416229 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54416256 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54416283 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54416311 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54416338 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54416365 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54416392 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54416407 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54416368 original size:82 final size:81
Alignment explanation
Indices: 54416250--54416405 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54416240 TGCTATATAA
* *
54416250 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54416315 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54416332 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54416396 CACTTAGTGC
65 CACTTAGTGC
54416406 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54416552 original size:96 final size:94
Alignment explanation
Indices: 54416432--54416622 Score: 364
Period size: 96 Copynumber: 2.0 Consensus size: 94
54416422 GCGCACTTAG
54416432 CGCCAATCTCATGGTCATAAATGGTTATACCCGCACGTTTAGTGCCGAGATCAACAACTCAGTAC
1 CGCCAATCTCATGGTCATAAATGGTTATACCCGCACGTTTAGTGCCGAGATCAACAACTCAGTAC
54416497 ATCTTACCTCTTTTCTTTTCATTAACAATTT
66 ATCTTACCTCTTTTCTTTTCATT--CAATTT
54416528 CGCCAATCTCATGGTCATAAATGGTTATACCCGCACGTTTAGTGCCGAGATCAACAACTCAGTAC
1 CGCCAATCTCATGGTCATAAATGGTTATACCCGCACGTTTAGTGCCGAGATCAACAACTCAGTAC
54416593 ATCTTACCTCTTTTCTTTTCATTCAATTT
66 ATCTTACCTCTTTTCTTTTCATTCAATTT
54416622 C
1 C
54416623 ATCATCACAT
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
94 7 0.07
96 88 0.93
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.35
Consensus pattern (94 bp):
CGCCAATCTCATGGTCATAAATGGTTATACCCGCACGTTTAGTGCCGAGATCAACAACTCAGTAC
ATCTTACCTCTTTTCTTTTCATTCAATTT
Found at i:54427145 original size:46 final size:45
Alignment explanation
Indices: 54427000--54427168 Score: 170
Period size: 46 Copynumber: 3.8 Consensus size: 45
54426990 TGGTTGAGCA
*
54427000 GCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 GCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
* * * * *
54427045 GTCAAACTCG-TGA-TTGAGTCCGAGTTC-GTGA--GATG-TAAC
1 GCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
54427084 TAGGATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
1 ---G--CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
* *
54427134 GCCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 G-CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54427169 GGGCGGGTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
39 2 0.02
40 4 0.04
42 3 0.03
43 14 0.14
44 10 0.10
45 11 0.11
46 45 0.45
47 3 0.03
49 4 0.04
50 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (45 bp):
GCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
Found at i:54429057 original size:40 final size:40
Alignment explanation
Indices: 54429012--54429231 Score: 207
Period size: 40 Copynumber: 5.5 Consensus size: 40
54429002 CATTTGAATG
*
54429012 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * * * *
54429052 TTATCCAGGCTAAGAT-TCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAG-TGATT
* * * *
54429092 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
54429132 TTATCCGGGCTAAG-ACCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATT
* * * *
54429171 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* *
54429211 ATATCC-GGCTAAATTCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
54429232 AAACTTGGGT
Statistics
Matches: 142, Mismatches: 31, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
39 46 0.32
40 93 0.65
41 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
Done.