Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 172 of 318
Found at i:54318436 original size:54 final size:54
Alignment explanation
Indices: 54318367--54318557 Score: 256
Period size: 54 Copynumber: 3.5 Consensus size: 54
54318357 AATACCCTAG
* * *
54318367 GGGTAAAATGGTAATTCTGTAAATCAAGGGTAAAACAGTAATTTTGTAAATTGA
1 GGGTAAAATGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATTGA
* * * *
54318421 GGGTAAAATAATAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTCAATCGA
1 GGGTAAAATGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATTGA
* * * *
54318475 GGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATAATAATTCTATAAATTGA
1 GGGTAAAATGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATTGA
* * *
54318529 GGGTAAAACGGTAATTTTGTAAATCGAGG
1 GGGTAAAATGATAATTCTGTAAATCGAGG
54318558 ATATTTGGAT
Statistics
Matches: 120, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (54 bp):
GGGTAAAATGATAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATTGA
Found at i:54318504 original size:81 final size:81
Alignment explanation
Indices: 54318367--54318557 Score: 276
Period size: 81 Copynumber: 2.4 Consensus size: 81
54318357 AATACCCTAG
* * * *
54318367 GGGTAAAATGGTAATTCTGTAAATCAAGGGTAAAACAGTAATTTTGTAAATTGAGGGTAAAATAA
1 GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAA
* *
54318432 TAATTTTGTAAATCGA
66 TAATTCTATAAATCGA
* *
54318448 GGGTAAAACAGTAATTCTGTCAATCGAGGGTAAAAC-GATAATTCTGTAAATCGAGGGTAAAATA
1 GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG-TAATTCTGTAAATCGAGGGTAAAATA
*
54318512 ATAATTCTATAAATTGA
65 ATAATTCTATAAATCGA
*
54318529 GGGTAAAACGGTAATTTTGTAAATCGAGG
1 GGGTAAAACGGTAATTCTGTAAATCGAGG
54318558 ATATTTGGAT
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 96 0.99
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (81 bp):
GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATAA
TAATTCTATAAATCGA
Found at i:54318569 original size:81 final size:81
Alignment explanation
Indices: 54318367--54318587 Score: 255
Period size: 81 Copynumber: 2.7 Consensus size: 81
54318357 AATACCCTAG
** * * *
54318367 GGGTAAAATGGTAATTCTGTAAATCAAGGGTAAAAC-AGTAATTTTGTAAATTGAGGGTAAAATA
1 GGGTAAAACAGTAATTCTGTAAATCGAGGATAAAACGA-TAATTTTGTAAATCGAGGGTAAAATA
* *
54318431 ATAATTTTGTAAATCGA
65 ATAATTCTATAAATCGA
* * *
54318448 GGGTAAAACAGTAATTCTGTCAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATAA
1 GGGTAAAACAGTAATTCTGTAAATCGAGGATAAAACGATAATTTTGTAAATCGAGGGTAAAATAA
*
54318513 TAATTCTATAAATTGA
66 TAATTCTATAAATCGA
* * **** * *
54318529 GGGTAAAACGGTAATTTTGTAAATCGAGGATATTTGGATAATTTTATAAATCGGGGGTA
1 GGGTAAAACAGTAATTCTGTAAATCGAGGATAAAACGATAATTTTGTAAATCGAGGGTA
54318588 CTTTGGTAAT
Statistics
Matches: 119, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
81 118 0.99
82 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (81 bp):
GGGTAAAACAGTAATTCTGTAAATCGAGGATAAAACGATAATTTTGTAAATCGAGGGTAAAATAA
TAATTCTATAAATCGA
Found at i:54318570 original size:27 final size:27
Alignment explanation
Indices: 54318538--54318601 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
54318528 AGGGTAAAAC
*
54318538 GGTAATTTTGTAAATCGAGGATA-TTT
1 GGTAATTTTATAAATCGAGGATACTTT
* *
54318564 GGATAATTTTATAAATCGGGGGTACTTT
1 GG-TAATTTTATAAATCGAGGATACTTT
54318592 GGTAATTTTA
1 GGTAATTTTA
54318602 CAATTGGGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.06
27 26 0.79
28 5 0.15
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (27 bp):
GGTAATTTTATAAATCGAGGATACTTT
Found at i:54318622 original size:26 final size:27
Alignment explanation
Indices: 54318539--54318625 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
54318529 GGGTAAAACG
* * * *
54318539 GTAATTTTGTAAATCGAGGATA-TTTG
1 GTAATTTTATAAATCGGGGGTACTTTA
*
54318565 GATAATTTTATAAATCGGGGGTACTTTG
1 G-TAATTTTATAAATCGGGGGTACTTTA
* *
54318593 GTAATTTTA-CAATTGGGGGTA-TTTCA
1 GTAATTTTATAAATCGGGGGTACTTT-A
54318619 GTAATTT
1 GTAATTT
54318626 GGTAAACTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
25 3 0.06
26 18 0.35
27 26 0.50
28 5 0.10
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (27 bp):
GTAATTTTATAAATCGGGGGTACTTTA
Found at i:54323571 original size:31 final size:32
Alignment explanation
Indices: 54323481--54323601 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
54323471 TCATATGGCT
* * *
54323481 TTGATATTGAAATGCGCTAGGCCCAACTGATA
1 TTGATTTTGATATGGGCTAGGCCCAACTGATA
* *
54323513 TTGAGTCTGATATGGGCTAGGCCCAACTGATA
1 TTGATTTTGATATGGGCTAGGCCCAACTGATA
*
54323545 TTGATTTTGATATGGGCTA-GCCCAACTAATA
1 TTGATTTTGATATGGGCTAGGCCCAACTGATA
* * *
54323576 GTGATTTTGAGATTGGCTAGGCCCAA
1 TTGATTTTGATATGGGCTAGGCCCAA
54323602 TTGAGACTGT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
31 27 0.35
32 50 0.65
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (32 bp):
TTGATTTTGATATGGGCTAGGCCCAACTGATA
Found at i:54323594 original size:63 final size:64
Alignment explanation
Indices: 54323481--54323601 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 64
54323471 TCATATGGCT
* * *
54323481 TTGATATTGAAATGCGCTAGGCCCAACTGATATTGAGTCTGATATGGGCTAGGCCCAACTGATA
1 TTGATATTGAAATGCGCTAGGCCCAACTAATAGTGAGTCTGAGATGGGCTAGGCCCAACTGATA
* * * * * *
54323545 TTGATTTTGATATGGGCTA-GCCCAACTAATAGTGATTTTGAGATTGGCTAGGCCCAA
1 TTGATATTGAAATGCGCTAGGCCCAACTAATAGTGAGTCTGAGATGGGCTAGGCCCAA
54323602 TTGAGACTGT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
63 32 0.67
64 16 0.33
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (64 bp):
TTGATATTGAAATGCGCTAGGCCCAACTAATAGTGAGTCTGAGATGGGCTAGGCCCAACTGATA
Found at i:54326009 original size:36 final size:36
Alignment explanation
Indices: 54325962--54326035 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
54325952 TTAATAAAGA
*
54325962 TCAATGTGTGCCTAATATGTGAGCCCTAAATGGCTT
1 TCAATGTGTGCCTAATATGTGAGCCCTAAATGGATT
54325998 TCAATGTGTGCCTAATATGTGAGCCCTAAATGGATT
1 TCAATGTGTGCCTAATATGTGAGCCCTAAATGGATT
54326034 TC
1 TC
54326036 TTCTTTCTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (36 bp):
TCAATGTGTGCCTAATATGTGAGCCCTAAATGGATT
Found at i:54327021 original size:18 final size:19
Alignment explanation
Indices: 54326994--54327031 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
54326984 GTAGTTATAA
*
54326994 CCAAAGT-AAATTAAAATC
1 CCAAAGTAAAAATAAAATC
*
54327012 CCAAATTAAAAATAAAATC
1 CCAAAGTAAAAATAAAATC
54327031 C
1 C
54327032 AAAAAGGCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (19 bp):
CCAAAGTAAAAATAAAATC
Found at i:54327813 original size:18 final size:17
Alignment explanation
Indices: 54327787--54327820 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54327777 CATAATGCAG
54327787 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
54327805 GCCCGTGTGGCCCACA
1 GCCCATGTGGCCCACA
54327821 TAGCCCAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:54334270 original size:64 final size:64
Alignment explanation
Indices: 54334121--54334371 Score: 195
Period size: 68 Copynumber: 3.8 Consensus size: 64
54334111 TACAGATGGT
* ** * * * *
54334121 ATGTAGCTAGGTCACATGTATGGTGCTGA-GTGCACATCATGTGTACAAGAGAGCTACGAGACAT
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTGGACAAGAGAGCTACGAG--A-
*
54334185 TATG
62 TA-A
* * * *
54334189 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTGGATAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTGGACAAGAGAGCTACGAGATAA
* * * * * *
54334253 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTGGACAAGAGAGCTACGAGAT
54334318 AA
63 AA
* * * *
54334320 ACTG--GCTAGGTCACATGGGTGGTA-TAAGTGTTCACCATGTGTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTGGACAAGAGAGC
54334372 CGAACTATAT
Statistics
Matches: 147, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
62 19 0.13
63 1 0.01
64 24 0.16
65 3 0.02
66 20 0.14
67 30 0.20
68 50 0.34
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTGGACAAGAGAGCTACGAGATAA
Found at i:54344076 original size:27 final size:27
Alignment explanation
Indices: 54344038--54344135 Score: 133
Period size: 27 Copynumber: 3.6 Consensus size: 27
54344028 CGTACCTGAA
* *
54344038 CCCTTATCTGATAAAATAATAATTTTG
1 CCCTTATGTGATAAAATAACAATTTTG
* *
54344065 CCCTCATGTGATAAAATGACAATTTTG
1 CCCTTATGTGATAAAATAACAATTTTG
* * *
54344092 CCCTTACGTGATAAAATAACGATTTTT
1 CCCTTATGTGATAAAATAACAATTTTG
54344119 CCCTTATGTGATAAAAT
1 CCCTTATGTGATAAAAT
54344136 GACCGAAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (27 bp):
CCCTTATGTGATAAAATAACAATTTTG
Found at i:54344164 original size:27 final size:27
Alignment explanation
Indices: 54344133--54344246 Score: 72
Period size: 27 Copynumber: 4.2 Consensus size: 27
54344123 TATGTGATAA
*
54344133 AATGACCGAAATA-CCTTCATAGGGTA-
1 AATGACCGAAATACCCTT-ATAAGGTAG
* *
54344159 ACATGATCAAAATACCCTTATAAGGTAG
1 A-ATGACCGAAATACCCTTATAAGGTAG
* * * *
54344187 AATGACTGAAATATCCC-TGTAGGGTAA
1 AATGACCGAAATA-CCCTTATAAGGTAG
* * * * *
54344214 AATGACTGTAATACCCCTGTAAGGTAA
1 AATGACCGAAATACCCTTATAAGGTAG
54344241 AATGAC
1 AATGAC
54344247 TGATTTGCCC
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
26 4 0.06
27 60 0.83
28 8 0.11
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (27 bp):
AATGACCGAAATACCCTTATAAGGTAG
Found at i:54344247 original size:27 final size:27
Alignment explanation
Indices: 54344168--54344249 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
54344158 AACATGATCA
* * *
54344168 AAATACCCTTATAAGGTAGAATGACTG
1 AAATACCCCTGTAAGGTAAAATGACTG
* *
54344195 AAATATCCCTGTAGGGTAAAATGACTG
1 AAATACCCCTGTAAGGTAAAATGACTG
*
54344222 TAATACCCCTGTAAGGTAAAATGACTG
1 AAATACCCCTGTAAGGTAAAATGACTG
54344249 A
1 A
54344250 TTTGCCCGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (27 bp):
AAATACCCCTGTAAGGTAAAATGACTG
Found at i:54347685 original size:18 final size:18
Alignment explanation
Indices: 54347658--54347708 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
54347648 TGTTTGCATT
54347658 CTGCACTGATTACTGTTA
1 CTGCACTGATTACTGTTA
* *
54347676 CTGCATTGATCA-TGGTTA
1 CTGCACTGATTACT-GTTA
*
54347694 CTGTACTGATTACTG
1 CTGCACTGATTACTG
54347709 CCATTGCTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (18 bp):
CTGCACTGATTACTGTTA
Found at i:54353222 original size:50 final size:47
Alignment explanation
Indices: 54353156--54353326 Score: 183
Period size: 50 Copynumber: 3.7 Consensus size: 47
54353146 TAGGGTATGA
* *
54353156 TGCCGATGCCATGTCCCAGACATGGTCTTACAGTAACTCTCACATATCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACTCT--CGTATCC
* * * *
54353205 GTGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACTCGTA-GC
1 -TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCGTATCC
* * *
54353252 TG--G-TG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCGTATC-C
54353295 TGCCGATGCCATGTCCCAGACATGGTCTTACA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACA
54353327 ATGGCTCTCA
Statistics
Matches: 101, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
41 16 0.16
42 13 0.13
43 4 0.04
44 1 0.01
45 1 0.01
46 4 0.04
47 15 0.15
48 11 0.11
50 36 0.36
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (47 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCGTATCC
Found at i:54358513 original size:21 final size:20
Alignment explanation
Indices: 54358489--54358527 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54358479 AAATTATGAC
*
54358489 TTATAATTATATTTTTAAAAT
1 TTATAATGA-ATTTTTAAAAT
*
54358510 TTATGATGAATTTTTAAA
1 TTATAATGAATTTTTAAA
54358528 GTCAGAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTATAATGAATTTTTAAAAT
Found at i:54360004 original size:30 final size:30
Alignment explanation
Indices: 54359970--54360030 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
54359960 CATTTAATAC
*
54359970 AAACTTTGGAAAAATTACATTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
54360000 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
54360030 A
1 A
54360031 GTGTAATATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:54361372 original size:46 final size:46
Alignment explanation
Indices: 54361322--54361497 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
54361312 TGATTGAGCA
54361322 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54361368 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54361413 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54361461 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54361498 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54361478 original size:93 final size:93
Alignment explanation
Indices: 54361319--54361490 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
54361309 GGATGATTGA
*
54361319 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
54361384 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54361412 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
54361476 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
54361491 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54368946 original size:46 final size:46
Alignment explanation
Indices: 54368896--54369071 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
54368886 TGATTGAGCA
*
54368896 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54368942 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54368987 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54369035 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54369072 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 60 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54369052 original size:93 final size:93
Alignment explanation
Indices: 54368893--54369064 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
54368883 GGATGATTGA
* *
54368893 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
54368958 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54368986 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
54369050 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
54369065 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54377886 original size:27 final size:28
Alignment explanation
Indices: 54377802--54377896 Score: 113
Period size: 27 Copynumber: 3.4 Consensus size: 28
54377792 CATGAGATTG
* * *
54377802 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
*
54377831 GCACTAATTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
54377859 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
54377886 GCACTGAGTGT
1 GCACTAAGTGT
54377897 ACGGACTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
27 21 0.36
28 20 0.34
29 18 0.31
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:54377910 original size:27 final size:27
Alignment explanation
Indices: 54377830--54377912 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
54377820 TAAATTGTTC
* * * *
54377830 AGCACTAATTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTACGA-CTTGAATATAT
* * *
54377858 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTACGACTTGAATATAT
*
54377885 AGCACTGAGTGTACGGACTT-AATATAT
1 AGCACTAAGTGTAC-GACTTGAATATAT
54377912 A
1 A
54377913 TTTTTGAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 29 0.60
28 19 0.40
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTACGACTTGAATATAT
Found at i:54388851 original size:47 final size:47
Alignment explanation
Indices: 54388763--54388975 Score: 358
Period size: 47 Copynumber: 4.6 Consensus size: 47
54388753 NNNNNNNNNN
54388763 TCACATATATGCATGTTCACATTCATCACATT-GCCA-TCGGCCTTA
1 TCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
* * *
54388808 TCACACATATGCAAGTTCACATTGATCACATTGGCCATTCGGCCTTA
1 TCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
* *
54388855 TCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTA
1 TCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
*
54388902 TCACGTATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
1 TCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
54388949 TCACATATATGCATGTTCACATTCATC
1 TCACATATATGCATGTTCACATTCATC
54388976 TCATAAAATC
Statistics
Matches: 158, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 29 0.18
46 4 0.03
47 125 0.79
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (47 bp):
TCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
Found at i:54388859 original size:22 final size:22
Alignment explanation
Indices: 54388832--54388954 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
54388822 GTTCACATTG
54388832 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
54388854 ATCACACATAT-GCAAGTTC-ACATT
1 AT--CACAT-TGGCCA-TTCGGCCTT
54388878 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* *
54388901 ATCACGTATAT-G-CATGTTC-ACATT
1 ATCAC--AT-TGGCCA--TTCGGCCTT
54388925 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
54388948 ATCACAT
1 ATCACAT
54388955 ATATGCATGT
Statistics
Matches: 75, Mismatches: 10, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
22 22 0.29
23 19 0.25
24 19 0.25
25 15 0.20
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:54391896 original size:24 final size:24
Alignment explanation
Indices: 54391860--54391963 Score: 149
Period size: 23 Copynumber: 4.4 Consensus size: 24
54391850 CTGGAGGCCT
*
54391860 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
54391885 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
54391909 AGCCC-TTTAATAACTAGGGCACA
1 AGCCCTTTTAATAACTGGGGCATA
54391932 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
54391955 AGCCATTTT
1 AGCCCTTTT
54391964 TCACTTCCTC
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
23 41 0.57
24 27 0.38
25 4 0.06
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:54392041 original size:20 final size:20
Alignment explanation
Indices: 54392013--54392053 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54392003 TTATGATTAC
54392013 ATCACGTGCATATCATACAT
1 ATCACGTGCATATCATACAT
*
54392033 ATCATGTGCATATCATACAT
1 ATCACGTGCATATCATACAT
54392053 A
1 A
54392054 CCTTGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (20 bp):
ATCACGTGCATATCATACAT
Found at i:54394367 original size:40 final size:40
Alignment explanation
Indices: 54394317--54394507 Score: 269
Period size: 40 Copynumber: 4.7 Consensus size: 40
54394307 CTCGATATAT
*
54394317 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
54394357 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* * *
54394397 TATATATCCGGGTTAAATCCCGTAGGCTTTGTGTTGGTAATA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT-A-A
*
54394439 TATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGT-A
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* *
54394478 -CTATATCCGGGCTTAAAGTTCCGCAGGCTT
1 TATATATCCGGG-TTAAA-TCCCGCAGGCTT
54394508 TGAGCTAGTG
Statistics
Matches: 138, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
38 10 0.07
39 6 0.04
40 85 0.62
41 1 0.01
42 36 0.26
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (40 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
Found at i:54394424 original size:80 final size:82
Alignment explanation
Indices: 54394317--54394507 Score: 291
Period size: 82 Copynumber: 2.4 Consensus size: 82
54394307 CTCGATATAT
54394317 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGT-A-ATATATATCCGGGTTAAATCCCGC
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAATATATATATCCGGGTTAAATCCCGC
*
54394380 AGGCTTCGTGCTGGTAA
66 AGGCTTAGTGCTGGTAA
* *
54394397 TATATATCCGGGTTAAATCCCGTAGGCTTTGTGTTGGTAATATATATATCCGGGTTAAATCCCGC
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAATATATATATCCGGGTTAAATCCCGC
54394462 AGGCTTAGTGCTGGT-A
66 AGGCTTAGTGCTGGTAA
* *
54394478 -CTATATCCGGGCTTAAAGTTCCGCAGGCTT
1 TATATATCCGGG-TTAAA-TCCCGCAGGCTT
54394508 TGAGCTAGTG
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
80 46 0.46
81 7 0.07
82 48 0.48
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (82 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAATATATATATCCGGGTTAAATCCCGC
AGGCTTAGTGCTGGTAA
Found at i:54399165 original size:49 final size:49
Alignment explanation
Indices: 54399080--54399197 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 49
54399070 TGCGTGTCAT
*
54399080 TGTAAGACCTTTCTGGGACATGGCATCAACACCGATAGAT-AAGAGCCAA
1 TGTAAGACCTCTCTGGGACATGGCATCAACACCGATAGATGAA-AGCCAA
* * * * * *
54399129 TGTAAGATCTCTCTGGGACATGGGATCAGC-CTCGATATATGAAAGTCAG
1 TGTAAGACCTCTCTGGGACATGGCATCAACAC-CGATAGATGAAAGCCAA
*
54399178 TGTAAGACCTGTCTGGGACA
1 TGTAAGACCTCTCTGGGACA
54399198 CAGCATCGAC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
48 1 0.02
49 55 0.95
50 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (49 bp):
TGTAAGACCTCTCTGGGACATGGCATCAACACCGATAGATGAAAGCCAA
Found at i:54407477 original size:53 final size:54
Alignment explanation
Indices: 54407389--54407543 Score: 195
Period size: 53 Copynumber: 2.9 Consensus size: 54
54407379 ATTACCAAAG
* * *
54407389 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTT
* * * **
54407443 TACCCTCAATTTA-AAAATTACCGTTTTACCCTCGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTT
* * * *
54407496 TACCCTTGATTTACAGAATTACTGTTTTACCCTTGATTTACAAAATTA
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTA
54407544 TTAAAATACC
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
53 45 0.52
54 41 0.48
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (54 bp):
TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTT
Found at i:54407510 original size:80 final size:81
Alignment explanation
Indices: 54407389--54407543 Score: 231
Period size: 80 Copynumber: 1.9 Consensus size: 81
54407379 ATTACCAAAG
54407389 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCAATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCAATT
54407454 TA-AAAATTACCGTTT
66 TACAAAATTACCGTTT
*** * * * **
54407469 TACCCTCGATTTATAGAATTATTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCAATT
54407534 TACAAAATTA
66 TACAAAATTA
54407544 TTAAAATACC
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 59 0.89
81 7 0.11
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (81 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCAATT
TACAAAATTACCGTTT
Found at i:54407536 original size:27 final size:27
Alignment explanation
Indices: 54407389--54407543 Score: 195
Period size: 27 Copynumber: 5.8 Consensus size: 27
54407379 ATTACCAAAG
* *
54407389 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
54407416 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
54407443 TACCCTCAATTTA-AAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
54407469 TACCCTCGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
54407496 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
54407523 TACCCTTGATTTACAAAATTA
1 TACCCTCGATTTACAGAATTA
54407544 TTAAAATACC
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
26 24 0.21
27 89 0.79
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:54407553 original size:27 final size:27
Alignment explanation
Indices: 54407523--54407855 Score: 237
Period size: 27 Copynumber: 12.3 Consensus size: 27
54407513 ATTACTGTTT
* **
54407523 TACCCTTGATTTACAAAATTATTAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
54407550 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
** **
54407577 TACCCTCAATCAATAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * * *
54407604 TACCC-TGGTCTATAAAATTGCTAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
54407630 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTATAAAATTACCAAAA
* *
54407657 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTATAAAATTACCAAAA
* * * *
54407684 TACAAC-TGGTTTGTGAAATTACCAAAA
1 TAC-CCTTGATTTATAAAATTACCAAAA
* *
54407711 TACCCTTAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
54407738 TACCCCTGATTTATAAAATTACAAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
*
54407765 TACCCTTGACTGTCTA-AAAATTA-TAGAAA
1 TACCCTTGA-T-T-TATAAAATTACCA-AAA
* * * **
54407794 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * * *
54407821 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
*
54407848 CACCCTTG
1 TACCCTTG
54407856 TAGGATGAAA
Statistics
Matches: 251, Mismatches: 44, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
26 23 0.09
27 203 0.81
28 5 0.02
29 18 0.07
30 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
TACCCTTGATTTATAAAATTACCAAAA
Found at i:54407554 original size:54 final size:54
Alignment explanation
Indices: 54407451--54407572 Score: 147
Period size: 54 Copynumber: 2.3 Consensus size: 54
54407441 TTTACCCTCA
* * ****
54407451 ATTTA-AAAATTACCGTTTTACCCTCGATTTATAGAATTATTGTTTTACCCTTG
1 ATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTATTAAAATACCCTTG
* * *
54407504 ATTTACAGAATTACTGTTTTACCCTTGATTTACAAAATTATTAAAATACCCTTG
1 ATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTATTAAAATACCCTTG
*
54407558 GTTTACAAAATTACC
1 ATTTACAAAATTACC
54407573 AAAATACCCT
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
53 5 0.09
54 51 0.91
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (54 bp):
ATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTATTAAAATACCCTTG
Found at i:54407608 original size:81 final size:80
Alignment explanation
Indices: 54407523--54407825 Score: 270
Period size: 81 Copynumber: 3.7 Consensus size: 80
54407513 ATTACTGTTT
* * *
54407523 TACCCTTGATTTACAAAATTATTAAAATACCCTTGGTTTACAAAATTACCAAAATA-CCCTCAAT
1 TACCC-TGATTTATAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCT-AAT
**
54407587 CAATAAAATTACCAAAA
64 TTATAAAATTACCAAAA
* * * * ** *
54407604 TACCCTGGTCTATAAAATTGCTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTT
1 TACCCTGATTTATAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTAATTT
*
54407669 GTAAAATTACCAAAA
66 ATAAAATTACCAAAA
* * * * * * ** *
54407684 TACAACTGGTTTGTGAAATTACCAAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTGATT
1 TAC-CCTGATTTATAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTAATT
*
54407749 TATAAAATTACAAAAA
65 TATAAAATTACCAAAA
* * **
54407765 TACCCTTGACTGTCTA-AAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCC
1 TACCC-TGA-T-T-TATAAAATTACTA-AAATACCCTTAGTTTACAAAATTACCAAAATACCC
54407826 TTGGTTTGTA
Statistics
Matches: 178, Mismatches: 37, Indels: 12
0.78 0.16 0.05
Matches are distributed among these distances:
80 61 0.34
81 79 0.44
82 2 0.01
83 35 0.20
84 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (80 bp):
TACCCTGATTTATAAAATTACTAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTAATTT
ATAAAATTACCAAAA
Found at i:54407960 original size:26 final size:26
Alignment explanation
Indices: 54407873--54407964 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 26
54407863 AAATGACCAA
* *
54407873 AATACCCCT-AATAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGA-CGT
* * *
54407900 AA-AGCCTCTGTAGGGTAAAGTGACGT
1 AATA-CCCCTGTATGGTAAAATGACGT
*
54407926 AATACCCCTGTATGGTAAAATGATG-
1 AATACCCCTGTATGGTAAAATGACGT
54407951 AATACGCCCT-TATG
1 AATAC-CCCTGTATG
54407965 TTCCGTATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
25 9 0.17
26 27 0.52
27 15 0.29
28 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (26 bp):
AATACCCCTGTATGGTAAAATGACGT
Found at i:54415427 original size:24 final size:25
Alignment explanation
Indices: 54415400--54415462 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
54415390 TCAACCGTAT
* * *
54415400 TCGCACACATAGTGCTA-ATTACAC
1 TCGCACACATAGTGCCATAGTAAAC
54415424 TCGCACACATAGTGCCATAGTAAAC
1 TCGCACACATAGTGCCATAGTAAAC
54415449 -CGCACACATAGTGC
1 TCGCACACATAGTGC
54415463 ATTGGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (25 bp):
TCGCACACATAGTGCCATAGTAAAC
Found at i:54428717 original size:22 final size:24
Alignment explanation
Indices: 54428689--54428733 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
54428679 GCCATTCTTA
54428689 TTTTTATTTCAA-T-TTAATTTTG
1 TTTTTATTTCAATTATTAATTTTG
*
54428711 TTTTTATTTTAATTATTAATTTT
1 TTTTTATTTCAATTATTAATTTT
54428734 TTTATTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTTATTTCAATTATTAATTTTG
Found at i:54428736 original size:22 final size:21
Alignment explanation
Indices: 54428689--54428740 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
54428679 GCCATTCTTA
54428689 TTTTTATTTCAATTTAATTTTG
1 TTTTTATTTCAATTTAA-TTTG
*
54428711 TTTTTATTTTAATTATTAA-TT-
1 TTTTTATTTCAA-T-TTAATTTG
54428732 TTTTTATTT
1 TTTTTATTT
54428741 ACTTCTAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 9 0.33
22 13 0.48
23 1 0.04
24 4 0.15
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTATTTCAATTTAATTTG
Found at i:54437451 original size:14 final size:14
Alignment explanation
Indices: 54437420--54437467 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
54437410 TTGTATTTGT
*
54437420 GGTTTAGGGT-TTA
1 GGTTTAGGGTCTCA
*
54437433 GGTTTATGGTCTCA
1 GGTTTAGGGTCTCA
*
54437447 GGTTTAGGGTTTCA
1 GGTTTAGGGTCTCA
54437461 GGTTTAG
1 GGTTTAG
54437468 AGTATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
13 9 0.30
14 21 0.70
ACGTcount: A:0.15, C:0.06, G:0.35, T:0.44
Consensus pattern (14 bp):
GGTTTAGGGTCTCA
Found at i:54437512 original size:15 final size:15
Alignment explanation
Indices: 54437492--54437523 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54437482 TTTAATTTAG
54437492 AAGATAAATATAAAT
1 AAGATAAATATAAAT
*
54437507 AAGATAAATATATAT
1 AAGATAAATATAAAT
54437522 AA
1 AA
54437524 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
AAGATAAATATAAAT
Found at i:54437548 original size:37 final size:37
Alignment explanation
Indices: 54437498--54437578 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
54437488 TTAGAAGATA
54437498 AATATAAATAAGATAAATATATATAAATTATTATTTT
1 AATATAAATAAGATAAATATATATAAATTATTATTTT
54437535 AATATAAATAAGATAAATATATATAAATTATTATTTT
1 AATATAAATAAGATAAATATATATAAATTATTATTTT
*
54437572 AAAATAA
1 AATATAA
54437579 TATATATCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (37 bp):
AATATAAATAAGATAAATATATATAAATTATTATTTT
Found at i:54439520 original size:38 final size:38
Alignment explanation
Indices: 54439470--54439552 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 38
54439460 GTCCATATAT
*
54439470 GACTG-TCTTAAATTTGTTATTTTGCATGATTATTTGA
1 GACTGCTCTTAAATTTGTTATTCTGCATGATTATTTGA
54439507 GACTGCTCTTAAATTTGTTATTCTGCATGATTATTTGA
1 GACTGCTCTTAAATTTGTTATTCTGCATGATTATTTGA
54439545 GATCTGCT
1 GA-CTGCT
54439553 TCTGTCAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
37 5 0.12
38 33 0.77
39 5 0.12
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (38 bp):
GACTGCTCTTAAATTTGTTATTCTGCATGATTATTTGA
Found at i:54441093 original size:60 final size:60
Alignment explanation
Indices: 54441020--54441145 Score: 243
Period size: 60 Copynumber: 2.1 Consensus size: 60
54441010 TGGGCCTAAT
*
54441020 TTTATTTCCATGTTCTTTTGTAGAAATTAGTTATGAACAAGGTAATATATATAGATATAG
1 TTTATTTCCATGTTCTTTTGTACAAATTAGTTATGAACAAGGTAATATATATAGATATAG
54441080 TTTATTTCCATGTTCTTTTGTACAAATTAGTTATGAACAAGGTAATATATATAGATATAG
1 TTTATTTCCATGTTCTTTTGTACAAATTAGTTATGAACAAGGTAATATATATAGATATAG
54441140 TTTATT
1 TTTATT
54441146 AATGAACAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (60 bp):
TTTATTTCCATGTTCTTTTGTACAAATTAGTTATGAACAAGGTAATATATATAGATATAG
Found at i:54441710 original size:106 final size:105
Alignment explanation
Indices: 54441470--54442004 Score: 804
Period size: 106 Copynumber: 5.2 Consensus size: 105
54441460 TATTTTAAAA
* * * * * *
54441470 TTTTATTTTATTTTGAAATTATCGAATTAAATTAAAATGTATTTAAAGTTTTA-TTTGAATATTT
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATTT
* **
54441534 TATTTGATTTTAATTT-ATCACGGAAAATATTTTGTCTAC
66 TACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
54441573 -TTTA-TTT-TTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATTT
* *
54441635 TACTTGATTTGAATTTACTCACTAAAAATATTTTGTCTAC
66 TACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
*
54441675 TTTTATTTTAATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
1 TTTTATTTT-ATTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATT
*
54441740 TTA-TTAGATTTT--TTTAATCACAAAAAATATTTTGTCTAC
65 TTACTT-GATTTTAATTTAATCACTAAAAATATTTTGTCTAC
* *
54441779 TTTTATTTTATTTTTTAAATTACCTAACTAAATTAAAATGTCTTTAAAGTTTTATTTTAAATATT
1 TTTTATTTTA-TTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATT
54441844 TTACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
65 TTACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
* *
54441885 TTTTATTTTATTTTTTAAATTACCTAATTAAATTAATTTTTCTTTAAAGTTTTATTTTAAATATT
1 TTTTATTTTA-TTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATT
54441950 TTACTTGATTTTAATTTAATCACTAAAAATA--TTGTCTAC
65 TTACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
54441989 -TTTATTTTATTTTTAA
1 TTTTATTTTATTTTTAA
54442005 TTCAAAATAA
Statistics
Matches: 398, Mismatches: 23, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
100 38 0.10
101 27 0.07
102 31 0.08
103 14 0.04
104 105 0.26
105 4 0.01
106 179 0.45
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (105 bp):
TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATTT
TACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
Found at i:54441852 original size:210 final size:209
Alignment explanation
Indices: 54441470--54442002 Score: 805
Period size: 210 Copynumber: 2.6 Consensus size: 209
54441460 TATTTTAAAA
* * * * *
54441470 TTTTATTTT-ATTTTGAAATTATCGAATTAAATTAAAATGTATTTAAAGTTTTA-TTTGAATATT
1 TTTTATTTTAATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
**
54441533 TTATTTGATTTTAATTT-ATCACGGAAAATATTTTGTCTACTTTA--TT-TTTTTTAAATTACCT
66 TTA-TTGATTTT-ATTTAATCACAAAAAATATTTTGTCTACTTTATTTTATTTTTTAAATTACCT
* * *
54441594 AATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATTTTACTTGATTTGAATTTACTCACTA
129 AACTAAATTAAAATGTCTTTAAAGTTTTATTTTAAATATTTTACTTGATTTGAATTTAATCACTA
54441659 AAAATATTTTGTCTAC
194 AAAATATTTTGTCTAC
54441675 TTTTATTTTAATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
1 TTTTATTTTAATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
54441740 TTATTAGATTTT-TTTAATCACAAAAAATATTTTGTCTACTTTTATTTTATTTTTTAAATTACCT
66 TTATT-GATTTTATTTAATCACAAAAAATATTTTGTCTAC-TTTATTTTATTTTTTAAATTACCT
*
54441804 AACTAAATTAAAATGTCTTTAAAGTTTTATTTTAAATATTTTACTTGATTTTAATTTAATCACTA
129 AACTAAATTAAAATGTCTTTAAAGTTTTATTTTAAATATTTTACTTGATTTGAATTTAATCACTA
54441869 AAAATATTTTGTCTAC
194 AAAATATTTTGTCTAC
* * * *
54441885 TTTTATTTTATTTTTTAAATTACCTAATTAAATTAATTTTTCTTTAAAGTTTTATTTTAAATATT
1 TTTTATTTTAATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
*
54441950 TTACTTGATTTTAATTTAATCACTAAAAATA--TTGTCTACTTTATTTTATTTTT
66 TTA-TTGATTTT-ATTTAATCACAAAAAATATTTTGTCTACTTTATTTTATTTTT
54442003 AATTCAAAAT
Statistics
Matches: 301, Mismatches: 16, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
205 12 0.04
206 63 0.21
207 22 0.07
209 16 0.05
210 170 0.56
211 2 0.01
212 16 0.05
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (209 bp):
TTTTATTTTAATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
TTATTGATTTTATTTAATCACAAAAAATATTTTGTCTACTTTATTTTATTTTTTAAATTACCTAA
CTAAATTAAAATGTCTTTAAAGTTTTATTTTAAATATTTTACTTGATTTGAATTTAATCACTAAA
AATATTTTGTCTAC
Found at i:54442103 original size:9 final size:9
Alignment explanation
Indices: 54442089--54442371 Score: 72
Period size: 9 Copynumber: 30.7 Consensus size: 9
54442079 TCCCATCAAC
54442089 AACTTACAT
1 AACTTACAT
54442098 AACTTACAT
1 AACTTACAT
54442107 AA--TACAT
1 AACTTACAT
*
54442114 AAATATATATCAT
1 -AA-CT-TA-CAT
54442127 ATA-TTACAT
1 A-ACTTACAT
*
54442136 AAATTACAT
1 AACTTACAT
** * *
54442145 AAGATAAAC
1 AACTTACAT
54442154 AACTTACAT
1 AACTTACAT
*
54442163 AATTTACAT
1 AACTTACAT
*
54442172 AACTTACGT
1 AACTTACAT
54442181 AAC--ACAT
1 AACTTACAT
* *
54442188 AAGTATATATT
1 AACT-TACA-T
*
54442199 ATATCGTACAT
1 A-A-CTTACAT
*
54442210 -ATTTACAT
1 AACTTACAT
54442218 AA-TT-CGGAT
1 AACTTAC--AT
54442227 AACTTACAT
1 AACTTACAT
*
54442236 AATTTACAT
1 AACTTACAT
54442245 AACTTACAT
1 AACTTACAT
54442254 ATA-TAATACAT
1 A-ACT--TACAT
*
54442265 AAATATATATCAT
1 -AA-CT-TA-CAT
* *
54442278 ATCGTACAT
1 AACTTACAT
*
54442287 AATTTACAT
1 AACTTACAT
54442296 AA-TT-CGGAT
1 AACTTAC--AT
*
54442305 AACTTACAC
1 AACTTACAT
*
54442314 AATTTACAT
1 AACTTACAT
54442323 AACTTACAT
1 AACTTACAT
54442332 AA--TACAT
1 AACTTACAT
* *
54442339 AA-ATATAT
1 AACTTACAT
* *
54442347 ATCATATCAT
1 AACTTA-CAT
54442357 AACTTACAT
1 AACTTACAT
54442366 AACTTA
1 AACTTA
54442372 ATTATACTTA
Statistics
Matches: 205, Mismatches: 36, Indels: 66
0.67 0.12 0.21
Matches are distributed among these distances:
7 19 0.09
8 17 0.08
9 120 0.59
10 17 0.08
11 12 0.06
12 12 0.06
13 8 0.04
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:54442175 original size:18 final size:18
Alignment explanation
Indices: 54442092--54442334 Score: 100
Period size: 18 Copynumber: 13.0 Consensus size: 18
54442082 CATCAACAAC
54442092 TTACATAACTTACATAA-
1 TTACATAACTTACATAAT
* *
54442109 -TACATAAATATATATCATAT
1 TTACATAACT-TACAT-A-AT
* *
54442129 ATTACATAAATTACATAAG
1 -TTACATAACTTACATAAT
* * *
54442148 ATAAACAACTTACATAAT
1 TTACATAACTTACATAAT
*
54442166 TTACATAACTTACGTAA-
1 TTACATAACTTACATAAT
* * *
54442183 -CACATAAGTATATATTATAT
1 TTACATAACT-TACA-TA-AT
* *
54442203 CGTACAT-ATTTACATAAT
1 -TTACATAACTTACATAAT
***
54442221 TCGGATAACTTACATAAT
1 TTACATAACTTACATAAT
54442239 TTACATAACTTACATATAT
1 TTACATAACTTACATA-AT
* * *
54442258 AATACATAAATATATATCATAT
1 -TTACATAACT-TACAT-A-AT
* *
54442280 CGTACATAATTTACATAAT
1 -TTACATAACTTACATAAT
*** *
54442299 TCGGATAACTTACACAAT
1 TTACATAACTTACATAAT
54442317 TTACATAACTTACATAAT
1 TTACATAACTTACATAAT
54442335 ACATAAATAT
Statistics
Matches: 164, Mismatches: 45, Indels: 33
0.68 0.19 0.14
Matches are distributed among these distances:
16 15 0.09
17 8 0.05
18 80 0.49
19 9 0.05
20 13 0.08
21 14 0.09
22 25 0.15
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.36
Consensus pattern (18 bp):
TTACATAACTTACATAAT
Found at i:54460435 original size:49 final size:49
Alignment explanation
Indices: 54460369--54460556 Score: 241
Period size: 49 Copynumber: 3.8 Consensus size: 49
54460359 TAGACAAAGC
* * *
54460369 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * * *
54460418 TATCCGATACACGTAGTAGCCTGCATTTAGTACTACACACGTGATCGAAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
** *
54460469 TATTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
*
54460518 TATCCGGTACACATAGTAGCCTACACTTAGTACTACACA
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
54460557 CGTGACCTCA
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
49 73 0.63
50 6 0.05
51 36 0.31
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:54460509 original size:100 final size:100
Alignment explanation
Indices: 54460374--54460561 Score: 331
Period size: 100 Copynumber: 1.9 Consensus size: 100
54460364 AAAGCTATCT
*
54460374 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACATAGTAGCC
* *
54460439 TGCATTTAGTACTACACACGTGATCGAAGTTATTG
66 TACACTTAGTACTACACACGTGATCGAAGTTATTG
* *
54460474 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACATAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACATAGTAGCC
54460539 TACACTTAGTACTACACACGTGA
66 TACACTTAGTACTACACACGTGA
54460562 CCTCACAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGATACACATAGTAGCC
TACACTTAGTACTACACACGTGATCGAAGTTATTG
Found at i:54460863 original size:27 final size:27
Alignment explanation
Indices: 54460800--54460863 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
54460790 GTGTAGCAAT
* * * *
54460800 TCATGCAATCCATGTAATAGTAATTTA
1 TCATTCAATTCATGTAACAATAATTTA
* *
54460827 ACATTCAATTCATGTAACAATAATTTG
1 TCATTCAATTCATGTAACAATAATTTA
54460854 TCATTCAATT
1 TCATTCAATT
54460864 TCACATGACA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (27 bp):
TCATTCAATTCATGTAACAATAATTTA
Found at i:54462167 original size:24 final size:26
Alignment explanation
Indices: 54462138--54462186 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
54462128 CTTGTTTTAA
* *
54462138 TATTTG-TTT-TTATGTTTTTAAATG
1 TATTTGATTTATTATATTTTAAAATG
54462162 TATTTGATTTATTATATTTTAAAAT
1 TATTTGATTTATTATATTTTAAAAT
54462187 TTTTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (26 bp):
TATTTGATTTATTATATTTTAAAATG
Found at i:54468128 original size:13 final size:13
Alignment explanation
Indices: 54468110--54468152 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
54468100 TAGATTTTTC
54468110 CTAAATATTATCA
1 CTAAATATTATCA
54468123 CTAAATA--ATC-
1 CTAAATATTATCA
54468133 CTAAATATTATCA
1 CTAAATATTATCA
*
54468146 TTAAATA
1 CTAAATA
54468153 ATTCAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 3 0.12
13 13 0.50
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:54468135 original size:23 final size:23
Alignment explanation
Indices: 54468108--54468154 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
54468098 GTTAGATTTT
54468108 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
54468131 TCCTAAATATTATCATTAAATAA
1 TCCTAAATATTATCACTAAATAA
54468154 T
1 T
54468155 TCAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:54471862 original size:33 final size:33
Alignment explanation
Indices: 54471820--54472071 Score: 190
Period size: 33 Copynumber: 7.7 Consensus size: 33
54471810 TCTGAGGTGC
54471820 ACAT-TCCTTTTTCAAGTGGTACACACAAAGT-T
1 ACATATCC-TTTTCAAGTGGTACACACAAAGTAT
* * * **
54471852 ACATACCCTTTTCAATTTGTACACACAAAGTGC
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* * * * *
54471885 AGATAACCTTTTCAAGT-GTACACGCATAGTGT
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* * *
54471917 ACTTTTCCTTTTCAAGTGGTATACACAAAGTAT
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* * * * *
54471950 ACTTTTCCTTTTCAAGTGGCATAAACAAAGTAT
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* * *
54471983 ACCTTTCCTTTTCATA-TGGTATACACAAAGTAT
1 ACATATCCTTTTCA-AGTGGTACACACAAAGTAT
** * * * *
54472016 ACCCAACCTTTCCAAGT-GTACGCACAAAGTGT
1 ACATATCCTTTTCAAGTGGTACACACAAAGTAT
* *
54472048 ACATAGCCTTTTCAAGTTGTACAC
1 ACATATCCTTTTCAAGTGGTACAC
54472072 TTTCGGGTTA
Statistics
Matches: 179, Mismatches: 35, Indels: 11
0.80 0.16 0.05
Matches are distributed among these distances:
32 76 0.42
33 102 0.57
34 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (33 bp):
ACATATCCTTTTCAAGTGGTACACACAAAGTAT
Found at i:54471905 original size:32 final size:31
Alignment explanation
Indices: 54471828--54471907 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
54471818 GCACATTCCT
* *
54471828 TTTTCAAGTGGTACACACAAAGTTACATACCC
1 TTTTCAAGT-GTACACACAAAGTCACATAACC
* *
54471860 TTTTCAATTTGTACACACAAAGTGCAGATAACC
1 TTTTCAA-GTGTACACACAAAGT-CACATAACC
54471893 TTTTCAAGTGTACAC
1 TTTTCAAGTGTACAC
54471908 GCATAGTGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 27 0.66
33 14 0.34
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (31 bp):
TTTTCAAGTGTACACACAAAGTCACATAACC
Found at i:54472764 original size:21 final size:22
Alignment explanation
Indices: 54472718--54472760 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
54472708 TGTAAAAGTG
*
54472718 ATTTCTCTATCAATAACCTTTC
1 ATTTCTCTATCAATAAACTTTC
54472740 ATTTC-CTATC-ATAAACTTTC
1 ATTTCTCTATCAATAAACTTTC
54472760 A
1 A
54472761 ATTTACAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTCTCTATCAATAAACTTTC
Found at i:54475156 original size:40 final size:40
Alignment explanation
Indices: 54474925--54475149 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
54474915 TCGAATGATG
* * * *
54474925 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
54474965 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54475005 TCCGGGCTAAG-CCCAAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54475044 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54475084 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54475125 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54475150 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.20
40 120 0.75
41 9 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54475171 original size:119 final size:119
Alignment explanation
Indices: 54474925--54475182 Score: 274
Period size: 119 Copynumber: 2.2 Consensus size: 119
54474915 TCGAATGATG
* *
54474925 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* * **
54474990 GTGTGAGATACTAATTCCGGGCTAAGCCCAAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAA
* * * **
54475044 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * *
54475107 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-CTAAA
* *
54475164 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54475183 TACGTGATTT
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.72
120 30 0.26
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAA
Found at i:54481449 original size:66 final size:65
Alignment explanation
Indices: 54481370--54481494 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 65
54481360 GGACCTTTCC
* * **
54481370 TTTTCTAATTGTACAC-CTGAGGTGCACATTCCCTTTTCAAGTGGTACACACGA-AGTGTACATA
1 TTTTCTAATTGTACACAC-AAAGTGCACATAACCTTTTCAAGT-GTACACAC-ATAGTGTACATA
54481433 CCT
63 CCT
*
54481436 TTTTC-AATTTGTACACACAAAGTGCAGATAACCTTTTCAAGTGTACACACATAGTGTAC
1 TTTTCTAA-TTGTACACACAAAGTGCACATAACCTTTTCAAGTGTACACACATAGTGTAC
54481495 CTTTCCTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
64 1 0.02
65 17 0.33
66 32 0.63
67 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (65 bp):
TTTTCTAATTGTACACACAAAGTGCACATAACCTTTTCAAGTGTACACACATAGTGTACATACCT
Found at i:54481486 original size:32 final size:32
Alignment explanation
Indices: 54481401--54481645 Score: 167
Period size: 33 Copynumber: 7.5 Consensus size: 32
54481391 GTGCACATTC
*
54481401 CCTTTTCAAGTGGTACACACGAAGTGTACATA
1 CCTTTTCAAGTGGTACACACAAAGTGTACATA
* * * *
54481433 CCTTTTTCAATTTGTACACACAAAGTGCAGATAA
1 CC-TTTTCAAGTGGTACACACAAAGTGTACAT-A
* * *
54481467 CCTTTTCAAGT-GTACACACATAGTGTACCTTT
1 CCTTTTCAAGTGGTACACACAAAGTGTA-CATA
* * *
54481499 CCTTTTCAAGTGGTATACACAAAGTATACATTT
1 CCTTTTCAAGTGGTACACACAAAGTGTACA-TA
* * * * * *
54481532 TCTTTTCATA-TTGTATACACAAAGTATACCTTT
1 CCTTTTCA-AGTGGTACACACAAAGTGTA-CATA
* *
54481565 CCTTTTCATA-TGGTATACACAAAGTATACCCA-A
1 CCTTTTCA-AGTGGTACACACAAAGTGTA--CATA
*
54481598 CCTTTCCAAGT-GTACACACAAAGTGTACATA
1 CCTTTTCAAGTGGTACACACAAAGTGTACATA
* *
54481629 GCCTTTTAAAGTTGTAC
1 -CCTTTTCAAGTGGTAC
54481646 CCTTTCAGGA
Statistics
Matches: 174, Mismatches: 27, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
30 2 0.01
31 1 0.01
32 52 0.30
33 112 0.64
34 7 0.04
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (32 bp):
CCTTTTCAAGTGGTACACACAAAGTGTACATA
Found at i:54481503 original size:66 final size:65
Alignment explanation
Indices: 54481401--54481625 Score: 229
Period size: 66 Copynumber: 3.4 Consensus size: 65
54481391 GTGCACATTC
* * * * * ** *
54481401 CCTTTTCAAGTGGTACACACGAAGTGTA-CATACCTTTTTCAATTTGTACACACAAAGTGCAGAT
1 CCTTTTCAAGT-GTACACACAAAGTGTACCTTTCC-TTTTCAATTGGTATACACAAAGTATACAT
54481465 AA
64 AA
* * **
54481467 CCTTTTCAAGTGTACACACATAGTGTACCTTTCCTTTTCAAGTGGTATACACAAAGTATACATTT
1 CCTTTTCAAGTGTACACACAAAGTGTACCTTTCCTTTTCAATTGGTATACACAAAGTATACATAA
* * * * **
54481532 TCTTTTCATATTGTATACACAAAGTATACCTTTCCTTTTC-ATATGGTATACACAAAGTATACCC
1 CCTTTTCA-AGTGTACACACAAAGTGTACCTTTCCTTTTCAAT-TGGTATACACAAAGTATACAT
54481596 AA
64 AA
*
54481598 CCTTTCCAAGTGTACACACAAAGTGTAC
1 CCTTTTCAAGTGTACACACAAAGTGTAC
54481626 ATAGCCTTTT
Statistics
Matches: 129, Mismatches: 27, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
65 62 0.48
66 67 0.52
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (65 bp):
CCTTTTCAAGTGTACACACAAAGTGTACCTTTCCTTTTCAATTGGTATACACAAAGTATACATAA
Found at i:54482335 original size:21 final size:22
Alignment explanation
Indices: 54482289--54482331 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
54482279 TGTAAAAGTG
*
54482289 ATTTCTCTATCAATAACCTTTC
1 ATTTCTCTATCAATAAACTTTC
54482311 ATTTC-CTATC-ATAAACTTTC
1 ATTTCTCTATCAATAAACTTTC
54482331 A
1 A
54482332 ATTTAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 5 0.25
22 5 0.25
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTCTCTATCAATAAACTTTC
Found at i:54482585 original size:47 final size:47
Alignment explanation
Indices: 54482524--54482618 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
54482514 TTTTATGAAG
54482524 AAGAAGATGATATAAAATAGGTTTAATTCTATTTAATCATTTATCAT
1 AAGAAGATGATATAAAATAGGTTTAATTCTATTTAATCATTTATCAT
*
54482571 AAGAAGATGATATAAAATGGGTTTAATTCTATTTAATCATTTATCAT
1 AAGAAGATGATATAAAATAGGTTTAATTCTATTTAATCATTTATCAT
54482618 A
1 A
54482619 CTTTATTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (47 bp):
AAGAAGATGATATAAAATAGGTTTAATTCTATTTAATCATTTATCAT
Found at i:54486314 original size:50 final size:50
Alignment explanation
Indices: 54486249--54486445 Score: 304
Period size: 50 Copynumber: 3.9 Consensus size: 50
54486239 ACCGAAGCTC
*
54486249 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
* * * * *
54486299 TCTGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAACCA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
* *
54486349 CCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGATCTAACAA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
* *
54486399 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
1 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAA
54486446 AACCGTCCTA
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 130 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (50 bp):
TCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
Found at i:54486424 original size:100 final size:102
Alignment explanation
Indices: 54486250--54486485 Score: 370
Period size: 100 Copynumber: 2.3 Consensus size: 102
54486240 CCGAAGCTCT
54486250 CTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
1 CTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
54486315 GCCTACACTTAGTACTACACACGTGACCT-AACC-AC
66 GCCTACACTTAGTACTACACACGTGACCTAAACCGAC
* *
54486350 CTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGATCTAACAATCTGGTACACGTAGTA
1 CTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
* * *
54486415 GCCTGCACTTAGTACTACACATGTGACCTAAAACCGTC
66 GCCTACACTTAGTACTACACACGTGACCT-AAACCGAC
* * *
54486453 CT-AAACACATAGTAGCCTGTACATAGTACTACA
1 CTGATACACATAGTAGCCTGCACTTAGTACTACA
54486486 TATGTGTCCT
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
100 90 0.73
102 31 0.25
103 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (102 bp):
CTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTA
GCCTACACTTAGTACTACACACGTGACCTAAACCGAC
Found at i:54489097 original size:42 final size:42
Alignment explanation
Indices: 54488957--54489358 Score: 303
Period size: 43 Copynumber: 9.7 Consensus size: 42
54488947 AAAAGGCCAT
* * * * *
54488957 TAAAGAACATGACTTTTAGTGACG-TTTTTGAGAAAGCGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTTCA-AAAACGCCGC
* * * * **
54488999 TAAAGAACGTGACCTTTAGCGGTGC-CTTCCACACAAACATCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTTCA-A-AAACGCCGC
* * * *
54489042 TAAAGGACGTGACCTTTAGAGGCGCTTTTTTAAAAACGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTTCAAAAACGCCGC
*
54489084 TAAAGAACATGACCTTTAGCGGTGC-TTTTCATACAAACGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTTCA-A-AAACGCCGC
* *
54489127 TAAAGAACATGACCTTTAGTGGCGCTTTTCTCAAAATCGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTT-TCAAAAACGCCGC
* * * *
54489170 TAAAGAACAT-AACTTATAGTGGCACTTTTT---------TGC
1 TAAAGAACATGACCTT-TAGCGGCGCTTTTTCAAAAACGCCGC
* * *
54489203 TAAAGAA-ATGACCTTTAGCGGCACTTTTCTCGAAAACGCGGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTT-TCAAAAACGCCGC
* * * * *
54489245 TAAAGAACATGACATTTAGCGGCGCTTTTCTAAAAAATGACAC
1 TAAAGAACATGACCTTTAGCGGCGCTTTT-TCAAAAACGCCGC
* *
54489288 TAAAGAACGTGACCTTTAGCGGTGC-TTTTCATACAAACGCCGC
1 TAAAGAACATGACCTTTAGCGGCGCTTTTTCA-A-AAACGCCGC
*
54489331 TAAAGAACATGACCTTTAGCGGAGCTTT
1 TAAAGAACATGACCTTTAGCGGCGCTTT
54489359 CCTAAAAAAT
Statistics
Matches: 286, Mismatches: 51, Indels: 44
0.75 0.13 0.12
Matches are distributed among these distances:
32 14 0.05
33 14 0.05
41 7 0.02
42 70 0.24
43 169 0.59
44 9 0.03
45 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
TAAAGAACATGACCTTTAGCGGCGCTTTTTCAAAAACGCCGC
Found at i:54489100 original size:85 final size:86
Alignment explanation
Indices: 54488957--54489352 Score: 272
Period size: 85 Copynumber: 4.8 Consensus size: 86
54488947 AAAAGGCCAT
* * * * * *
54488957 TAAAGAACATGACTTTTAGTGACG-TTTT-TGAGAAAGCGCCGCTAAAGAACGTGACCTTTAGCG
1 TAAAGAACATGACCTTTAGAGGCGCTTTTCTCA-AAAACGCCGCTAAAGAACATGACCTTTAGCG
*
54489020 GTGCCTTCCACACAAACATCGC
65 GTGCCTTCCACACAAACACCGC
* * *
54489042 TAAAGGACGTGACCTTTAGAGGCGCTTTT-TTAAAAACGCCGCTAAAGAACATGACCTTTAGCGG
1 TAAAGAACATGACCTTTAGAGGCGCTTTTCTCAAAAACGCCGCTAAAGAACATGACCTTTAGCGG
* * * *
54489106 TGCTTTTCATACAAACGCCGC
66 TGCCTTCCACACAAACACCGC
* * * *
54489127 TAAAGAACATGACCTTTAGTGGCGCTTTTCTCAAAATCGCCGCTAAAGAACAT-AACTTATAG-T
1 TAAAGAACATGACCTTTAGAGGCGCTTTTCTCAAAAACGCCGCTAAAGAACATGACCTT-TAGCG
****
54489190 G-GCACTT---------TTTTGC
65 GTGC-CTTCCACACAAACACCGC
* * * * *
54489203 TAAAGAA-ATGACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGG
1 TAAAGAACATGACCTTTAGAGGCGCTTTTCTCAAAAACGCCGCTAAAGAACATGACCTTTAGCGG
* * * * * *
54489267 CGCTTTTCTA-AAAAATGA-CAC
66 TGC-CTTCCACACAAA-CACCGC
* * * *
54489288 TAAAGAACGTGACCTTTAGCGGTGCTTTTCAT-ACAAACGCCGCTAAAGAACATGACCTTTAGCG
1 TAAAGAACATGACCTTTAGAGGCGCTTTTC-TCAAAAACGCCGCTAAAGAACATGACCTTTAGCG
54489352 G
65 G
54489353 AGCTTTCCTA
Statistics
Matches: 247, Mismatches: 46, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
75 43 0.17
76 13 0.05
77 4 0.02
84 2 0.01
85 106 0.43
86 78 0.32
87 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (86 bp):
TAAAGAACATGACCTTTAGAGGCGCTTTTCTCAAAAACGCCGCTAAAGAACATGACCTTTAGCGG
TGCCTTCCACACAAACACCGC
Found at i:54489230 original size:32 final size:33
Alignment explanation
Indices: 54489168--54489230 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
54489158 CAAAATCGCC
*
54489168 GCTAAAGAACATAACTTATAGTGGCACTTTTTT
1 GCTAAAGAACATAACTTATAGCGGCACTTTTTT
*
54489201 GCTAAAGAA-ATGACCTT-TAGCGGCACTTTT
1 GCTAAAGAACAT-AACTTATAGCGGCACTTTT
54489231 CTCGAAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (33 bp):
GCTAAAGAACATAACTTATAGCGGCACTTTTTT
Found at i:54489251 original size:161 final size:160
Alignment explanation
Indices: 54489051--54489340 Score: 397
Period size: 161 Copynumber: 1.8 Consensus size: 160
54489041 CTAAAGGACG
* * * *
54489051 TGACCTTTAGAGGCGCTTTTTTAAAAACGCCGCTAAAGAACATGACCTTTAGCGGTGCTTTTC-A
1 TGACCTTTAGAGGCACTTTTTCAAAAACGCCGCTAAAGAACATGACATTTAGCGGCGCTTTTCTA
* * * *
54489115 TACAAACGCCGCTAAAGAACATGACCTTTAGTGGCGCTTTTC-T-CAAAATCGCCGCTAAAGAAC
66 -AAAAACGACACTAAAGAACATGACCTTTAGCGGCGCTTTTCATAC-AAA-CGCCGCTAAAGAAC
54489178 ATAACTTATAGTGGCACTTTTTTGCTAAAGAAA
128 ATAACTTATAGTGGCACTTTTTTGCTAAAGAAA
* * *
54489211 TGACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGGCGCTTTTCT
1 TGACCTTTAGAGGCACTTTT-TCAAAAACGCCGCTAAAGAACATGACATTTAGCGGCGCTTTTCT
* * *
54489276 AAAAAATGACACTAAAGAACGTGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACAT
65 AAAAAACGACACTAAAGAACATGACCTTTAGCGGCGCTTTTCATACAAACGCCGCTAAAGAACAT
54489341 GACCTTTAGC
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
160 18 0.16
161 88 0.79
162 5 0.04
163 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (160 bp):
TGACCTTTAGAGGCACTTTTTCAAAAACGCCGCTAAAGAACATGACATTTAGCGGCGCTTTTCTA
AAAAACGACACTAAAGAACATGACCTTTAGCGGCGCTTTTCATACAAACGCCGCTAAAGAACATA
ACTTATAGTGGCACTTTTTTGCTAAAGAAA
Found at i:54489273 original size:75 final size:76
Alignment explanation
Indices: 54489125--54489273 Score: 205
Period size: 75 Copynumber: 2.0 Consensus size: 76
54489115 TACAAACGCC
* * *
54489125 GCTAAAGAACATGACCTTTAGTGGCGCTTTTCTCAAAATCGCCGCTAAAGAACATAACTTATAGT
1 GCTAAAGAACATGACCTTTAGCGGCACTTTTCTCAAAATCGCCGCTAAAGAACATAACTTATAGC
54489190 GGCACTTTTTT
66 GGCACTTTTTT
* *
54489201 GCTAAAGAA-ATGACCTTTAGCGGCACTTTTCTCGAAAA-CGCGGCTAAAGAACATGACATT-TA
1 GCTAAAGAACATGACCTTTAGCGGCACTTTTCTC-AAAATCGCCGCTAAAGAACATAAC-TTATA
*
54489263 GCGGCGCTTTT
64 GCGGCACTTTT
54489274 CTAAAAAATG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
75 50 0.77
76 15 0.23
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (76 bp):
GCTAAAGAACATGACCTTTAGCGGCACTTTTCTCAAAATCGCCGCTAAAGAACATAACTTATAGC
GGCACTTTTTT
Found at i:54489316 original size:118 final size:119
Alignment explanation
Indices: 54489082--54489295 Score: 292
Period size: 118 Copynumber: 1.8 Consensus size: 119
54489072 TAAAAACGCC
** * *
54489082 GCTAAAGAACATGACCTTTAGCGGTGCTTTTCATACAAACGCCGCTAAAGAACATGACCTTTAGT
1 GCTAAAGAACATGACCTTTAGCGGCACTTTTCATACAAACGCCGCTAAAGAACATGACATTTAGC
* * * *
54489147 GGCGCTTTTCTCAAAATCGCCGCTAAAGAACATAACTTATAGTGGCACTTTTTT
66 GGCGCTTTTCTAAAAATCGACACTAAAGAACATAACTTATAGCGGCACTTTTTT
*
54489201 GCTAAAGAA-ATGACCTTTAGCGGCACTTTTC-T-CGAAAACGCGGCTAAAGAACATGACATTTA
1 GCTAAAGAACATGACCTTTAGCGGCACTTTTCATAC--AAACGCCGCTAAAGAACATGACATTTA
54489263 GCGGCGCTTTTCTAAAAAAT-GACACTAAAGAAC
64 GCGGCGCTTTTCT-AAAAATCGACACTAAAGAAC
54489296 GTGACCTTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
116 1 0.01
117 1 0.01
118 68 0.81
119 14 0.17
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (119 bp):
GCTAAAGAACATGACCTTTAGCGGCACTTTTCATACAAACGCCGCTAAAGAACATGACATTTAGC
GGCGCTTTTCTAAAAATCGACACTAAAGAACATAACTTATAGCGGCACTTTTTT
Found at i:54489358 original size:86 final size:84
Alignment explanation
Indices: 54489202--54489376 Score: 235
Period size: 86 Copynumber: 2.0 Consensus size: 84
54489192 CACTTTTTTG
*
54489202 CTAAAGAAATGACCTTTAGCGGCACTTTTCTCGAAAACGCGGCTAAAGAACATGACATTTAGCGG
1 CTAAAGAAATGACCTTTAGCGGCACTTTTCTC-AAAACGCCGCTAAAGAACATGACATTTAGCGG
* *
54489267 CGCTTTTCTAAAAAATGACA
65 AGCTTTCCTAAAAAATGACA
* ** *
54489287 CTAAAGAACGTGACCTTTAGCGGTGCTTTTCAT-ACAAACGCCGCTAAAGAACATGACCTTTAGC
1 CTAAAGAA-ATGACCTTTAGCGGCACTTTTC-TCA-AAACGCCGCTAAAGAACATGACATTTAGC
*
54489351 GGAGCTTTCCTAAAAAATGCCA
63 GGAGCTTTCCTAAAAAATGACA
54489373 CTAA
1 CTAA
54489377 TTTTAGTAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
85 9 0.11
86 69 0.87
87 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (84 bp):
CTAAAGAAATGACCTTTAGCGGCACTTTTCTCAAAACGCCGCTAAAGAACATGACATTTAGCGGA
GCTTTCCTAAAAAATGACA
Found at i:54493136 original size:50 final size:49
Alignment explanation
Indices: 54493029--54493226 Score: 182
Period size: 50 Copynumber: 4.0 Consensus size: 49
54493019 CAATTATAGA
* * * * *
54493029 AAATCAAATATAATATCACATATGTGCATACCTATATGGCCGAATATGC
1 AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
* * *
54493078 AAGATCAAATTTAACATTAAATATGTACTTACTTATATGGCCGAATATAC
1 AA-ATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
* * * * * *
54493128 GAATTCAAATATAATATCAAATTTGTGCATACCTT-CATGGCCGAATATTC
1 -AAATCAAATATAACATCAAATATGTACATA-CTTATATGGCCGAATATAC
* * * * *
54493178 TAAATCCAATATAACATCACATACGTACATACCTATGTGGCCGAATATA
1 -AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATA
54493227 TGCAAGGTCA
Statistics
Matches: 116, Mismatches: 29, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
49 4 0.03
50 107 0.92
51 5 0.04
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (49 bp):
AAATCAAATATAACATCAAATATGTACATACTTATATGGCCGAATATAC
Found at i:54493219 original size:100 final size:100
Alignment explanation
Indices: 54493032--54493226 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 100
54493022 TTATAGAAAA
* * *
54493032 TCAAATATAATATCACATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATTTAACATTA
1 TCAAATATAATATCAAATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATATAACATCA
* * *
54493097 AATATGTACTTACTTATATGGCCGAATATACGAAT
66 AATACGTACATACCTATATGGCCGAATATACGAAT
* * *
54493132 TCAAATATAATATCAAATTTGTGCATACCT-TCATGGCCGAATATTCTAA-ATCCAATATAACAT
1 TCAAATATAATATCAAATATGTGCATACCTAT-ATGGCCGAATATGC-AAGATCAAATATAACAT
* *
54493195 CACATACGTACATACCTATGTGGCCGAATATA
64 CAAATACGTACATACCTATATGGCCGAATATA
54493227 TGCAAGGTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
99 1 0.01
100 79 0.96
101 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (100 bp):
TCAAATATAATATCAAATATGTGCATACCTATATGGCCGAATATGCAAGATCAAATATAACATCA
AATACGTACATACCTATATGGCCGAATATACGAAT
Found at i:54498138 original size:27 final size:27
Alignment explanation
Indices: 54498108--54498285 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
54498098 ATATTGAGTC
* *
54498108 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54498135 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54498162 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
54498190 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54498217 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
54498244 CGTACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
54498271 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54498286 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54498251 original size:82 final size:81
Alignment explanation
Indices: 54498129--54498284 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
54498119 TGCTATATAA
* *
54498129 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54498194 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
54498211 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGTACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54498275 CACTTAGTGC
65 CACTTAGTGC
54498285 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54503397 original size:27 final size:27
Alignment explanation
Indices: 54503365--54503430 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
54503355 TAGTTGAACT
54503365 ATGGCAAAGTGATAAAGTGTGCCAAAC
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
*
54503392 ATGGCAAAGTGATAAAGTGTGCCAAAT
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
54503419 ATGGCAAAGTGA
1 ATGGCAAAGTGA
54503431 AATGTGACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (27 bp):
ATGGCAAAGTGATAAAGTGTGCCAAAC
Found at i:54508393 original size:23 final size:22
Alignment explanation
Indices: 54508362--54508405 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
54508352 TTGATTGTAT
*
54508362 GTTTAGGTATGATTTTAGTTTAA
1 GTTTAGGTATGAATTTA-TTTAA
*
54508385 GTTTTGGTATGAATTTATTTA
1 GTTTAGGTATGAATTTATTTA
54508406 TGAATTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (22 bp):
GTTTAGGTATGAATTTATTTAA
Found at i:54518138 original size:40 final size:40
Alignment explanation
Indices: 54518061--54518239 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
54518051 ACCCAAGTAT
* ** *
54518061 CTTCGGGATTTAG-CCGGATATAACCACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
54518100 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
54518140 CTTCGGGACTTAGCCCGGATATAGTCGCCAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
54518180 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAAGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
54518220 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACTTAGCCCGGAT
54518240 TTCATTCGAA
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
39 12 0.10
40 108 0.90
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:54521475 original size:23 final size:22
Alignment explanation
Indices: 54521444--54521487 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
54521434 TTGATCGTAT
*
54521444 GTTTAGGTATGATTTTAGTTTAA
1 GTTTAGGTATGAATTTA-TTTAA
*
54521467 GTTTTGGTATGAATTTATTTA
1 GTTTAGGTATGAATTTATTTA
54521488 TGAATTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (22 bp):
GTTTAGGTATGAATTTATTTAA
Found at i:54525284 original size:28 final size:29
Alignment explanation
Indices: 54525251--54525322 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
54525241 TATAGTAAGT
* *
54525251 CCGCACACTTAGTGTTATATAA-TCGAAC
1 CCGCACACTTAGTGCTATACAACTCGAAC
* *
54525279 TCGCACACTTAGTGCTATACAACTTGAAC
1 CCGCACACTTAGTGCTATACAACTCGAAC
54525308 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
54525323 CAATTTCATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 19 0.50
29 19 0.50
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATACAACTCGAAC
Found at i:54529255 original size:9 final size:9
Alignment explanation
Indices: 54529241--54529366 Score: 84
Period size: 9 Copynumber: 14.0 Consensus size: 9
54529231 TATTACGTAA
*
54529241 GTAAGTTTT
1 GTAAGTTAT
54529250 GTAAGTTAT
1 GTAAGTTAT
54529259 GTAAGTTAT
1 GTAAGTTAT
*
54529268 G-ATA-TGAT
1 GTA-AGTTAT
* *
54529276 ATACATTTAT
1 GTA-AGTTAT
*
54529286 GT-A-TTAC
1 GTAAGTTAT
54529293 GTAAGTTAT
1 GTAAGTTAT
54529302 GTCAAGTATGAT
1 GT-AAGT-T-AT
* *
54529314 ATATATTTAT
1 GTA-AGTTAT
54529324 GT-A-TTAT
1 GTAAGTTAT
54529331 GTAAGTTAT
1 GTAAGTTAT
*
54529340 GTAAGTTTT
1 GTAAGTTAT
54529349 GTAAGTTAT
1 GTAAGTTAT
54529358 GTAAGTTAT
1 GTAAGTTAT
54529367 TATATGCTAT
Statistics
Matches: 93, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
7 11 0.12
8 8 0.09
9 55 0.59
10 11 0.12
11 3 0.03
12 5 0.05
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:54529322 original size:38 final size:37
Alignment explanation
Indices: 54529259--54529345 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 37
54529249 TGTAAGTTAT
54529259 GTAAGTTATG--A-TATGATATACATTTATGTATTAC
1 GTAAGTTATGTAAGTATGATATACATTTATGTATTAC
* *
54529293 GTAAGTTATGTCAAGTATGATATATATTTATGTATTAT
1 GTAAGTTATGT-AAGTATGATATACATTTATGTATTAC
54529331 GTAAGTTATGTAAGT
1 GTAAGTTATGTAAGT
54529346 TTTGTAAGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
34 10 0.21
37 5 0.11
38 32 0.68
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.45
Consensus pattern (37 bp):
GTAAGTTATGTAAGTATGATATACATTTATGTATTAC
Found at i:54529597 original size:15 final size:14
Alignment explanation
Indices: 54529583--54529643 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 14
54529573 GGAAAAAAAT
54529583 TTATTTTAATTAAA
1 TTATTTTAATTAAA
* *
54529597 TAATATTTAAATAAA
1 TTAT-TTTAATTAAA
*
54529612 TTATTTTAGTTAAA
1 TTATTTTAATTAAA
* *
54529626 TAATATTTAAGTAAA
1 TTAT-TTTAATTAAA
54529641 TTA
1 TTA
54529644 ATCCAAATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
14 14 0.39
15 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TTATTTTAATTAAA
Found at i:54529618 original size:29 final size:29
Alignment explanation
Indices: 54529583--54529643 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
54529573 GGAAAAAAAT
54529583 TTATTTTAATTAAATAATATTTAAATAAA
1 TTATTTTAATTAAATAATATTTAAATAAA
* *
54529612 TTATTTTAGTTAAATAATATTTAAGTAAA
1 TTATTTTAATTAAATAATATTTAAATAAA
54529641 TTA
1 TTA
54529644 ATCCAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATTTTAATTAAATAATATTTAAATAAA
Found at i:54529758 original size:195 final size:194
Alignment explanation
Indices: 54529408--54529808 Score: 687
Period size: 195 Copynumber: 2.1 Consensus size: 194
54529398 ATTATTTCCC
* * *
54529408 TTTAAA-AAATTGTTTTAATTAAATAATATTTAAATTAATTAATCCAAATTATGTAATTTAAAAA
1 TTTAAATAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAA
*
54529472 ATTGTGTATAAAAAGTTGAAAATCGTATAAGATGAAATGTCAACTTTGTTACATGAAAAAGAAAT
66 ATTGTGTATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTACATGAAAAAGAAAT
*
54529537 AATAAACATAAAATTTGACGATGTGGAAAATCACATGGAAAAAAATTTATTTTAATTAAATAATA
131 AATAAAAATAAAATTTGACGATGTGGAAAATCACATGGAAAAAAA-TTATTTTAATTAAATAATA
* *
54529602 TTTAAATAAATTATTTTAGTTAAATAATATTTAAGTAAATTAATCCAAATTATATAATTTAAAAA
1 TTTAAATAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAA
*
54529667 ATTGTGTATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTCCATGAAAAAGAAAT
66 ATTGTGTATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTACATGAAAAAGAAAT
* * *
54529732 AATAAAAATAAAATTTGATGATGTGGAAAATCACATGGAAATAAATTATTTTAATTAAATGATA
131 AATAAAAATAAAATTTGACGATGTGGAAAATCACATGGAAAAAAATTATTTTAATTAAATAATA
54529796 TTTAAATAAATTA
1 TTTAAATAAATTA
54529809 ATACAAAATA
Statistics
Matches: 195, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
194 37 0.19
195 158 0.81
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.35
Consensus pattern (194 bp):
TTTAAATAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATATAATTTAAAAA
ATTGTGTATAAAAAGTTGAAAACCGTATAAGATGAAATGTCAACTTTGTTACATGAAAAAGAAAT
AATAAAAATAAAATTTGACGATGTGGAAAATCACATGGAAAAAAATTATTTTAATTAAATAATA
Found at i:54529941 original size:14 final size:14
Alignment explanation
Indices: 54529922--54529952 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54529912 CTTGTTTTAA
*
54529922 TATGGTAATGGCAT
1 TATGGTAATGACAT
54529936 TATGGTAATGACAT
1 TATGGTAATGACAT
54529950 TAT
1 TAT
54529953 CGACTAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (14 bp):
TATGGTAATGACAT
Found at i:54530216 original size:24 final size:24
Alignment explanation
Indices: 54530184--54530230 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
54530174 TTAACTTAAA
*
54530184 TGATAAAATGGATGATAATATTTG
1 TGATAAAATGGATGAGAATATTTG
54530208 TGATAAAATGGATGAGAATATTT
1 TGATAAAATGGATGAGAATATTT
54530231 CAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (24 bp):
TGATAAAATGGATGAGAATATTTG
Found at i:54532723 original size:17 final size:19
Alignment explanation
Indices: 54532687--54532723 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
54532677 ATAAAATTTG
*
54532687 AAATCTTGAGAATTATTTA
1 AAATCTTGAGAATTAATTA
54532706 AAAT-TTGA-AATTAATTA
1 AAATCTTGAGAATTAATTA
54532723 A
1 A
54532724 TATATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATCTTGAGAATTAATTA
Found at i:54532870 original size:7 final size:7
Alignment explanation
Indices: 54532860--54532946 Score: 86
Period size: 7 Copynumber: 12.0 Consensus size: 7
54532850 AACCCCTGTC
54532860 CCCTTAA
1 CCCTTAA
54532867 CCCTTAAA
1 CCCTT-AA
*
54532875 CCCCTAA
1 CCCTTAA
* *
54532882 CCCATAT
1 CCCTTAA
54532889 CCCATTAA
1 CCC-TTAA
*
54532897 CCCCTAAA
1 -CCCTTAA
54532905 CCCTTAA
1 CCCTTAA
54532912 CCCTTAA
1 CCCTTAA
54532919 CCCTTAA
1 CCCTTAA
54532926 CCAC-TAA
1 CC-CTTAA
54532933 CCCTTAA
1 CCCTTAA
*
54532940 CCTTTAA
1 CCCTTAA
54532947 ATCCTAAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
6 1 0.01
7 51 0.76
8 12 0.18
9 3 0.04
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.25
Consensus pattern (7 bp):
CCCTTAA
Found at i:54532884 original size:30 final size:30
Alignment explanation
Indices: 54532836--54532941 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 30
54532826 CTAAACCTTA
* * * * *
54532836 AACCCC-AAACTCCAAACCCCTGTCCCCTT
1 AACCCCTAAACCCCTAACCCATATCCCATT
*
54532865 AACCCTTAAACCCCTAACCCATATCCCATT
1 AACCCCTAAACCCCTAACCCATATCCCATT
* * *
54532895 AACCCCTAAACCCTTAACCCTTAACCC-TT
1 AACCCCTAAACCCCTAACCCATATCCCATT
* *
54532924 AACCACT-AACCCTTAACC
1 AACCCCTAAACCCCTAACC
54532942 TTTAAATCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.17
29 13 0.20
30 41 0.63
ACGTcount: A:0.32, C:0.46, G:0.01, T:0.21
Consensus pattern (30 bp):
AACCCCTAAACCCCTAACCCATATCCCATT
Found at i:54532901 original size:22 final size:21
Alignment explanation
Indices: 54532864--54532941 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 21
54532854 CCTGTCCCCT
54532864 TAACCCTTAAACCCCTAACCCA
1 TAACCCTT-AACCCCTAACCCA
* *
54532886 TATCCCATTAACCCCTAAACCCT
1 TAACCC-TTAACCCCT-AACCCA
*
54532909 TAACCCTTAACCCTTAA-CCA
1 TAACCCTTAACCCCTAACCCA
54532929 CTAACCCTTAACC
1 -TAACCCTTAACC
54532942 TTTAAATCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 2 0.04
21 14 0.29
22 20 0.42
23 12 0.25
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (21 bp):
TAACCCTTAACCCCTAACCCA
Found at i:54532971 original size:8 final size:7
Alignment explanation
Indices: 54532898--54532977 Score: 63
Period size: 7 Copynumber: 11.1 Consensus size: 7
54532888 TCCCATTAAC
54532898 CCCTAAA
1 CCCTAAA
*
54532905 CCCTTAA
1 CCCTAAA
*
54532912 CCCTTAA
1 CCCTAAA
*
54532919 CCCTTAA
1 CCCTAAA
54532926 CCACT-AA
1 CC-CTAAA
*
54532933 CCCTTAA
1 CCCTAAA
*
54532940 CCTTTAAA
1 CC-CTAAA
*
54532948 TCCTAAA
1 CCCTAAA
*
54532955 TCCTAAA
1 CCCTAAA
54532962 CCCATAAA
1 CCC-TAAA
54532970 CCCTAAA
1 CCCTAAA
54532977 C
1 C
54532978 TATAATGATA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
6 2 0.03
7 48 0.76
8 13 0.21
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.24
Consensus pattern (7 bp):
CCCTAAA
Found at i:54533219 original size:14 final size:15
Alignment explanation
Indices: 54533192--54533230 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
54533182 CCTAACCAAT
54533192 AACCCCTAAACTTTA
1 AACCCCTAAACTTTA
*
54533207 AACCCC-AACCTTTA
1 AACCCCTAAACTTTA
54533221 AA-CCCTAAAC
1 AACCCCTAAAC
54533231 CCATAATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 3 0.14
14 12 0.57
15 6 0.29
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCCTAAACTTTA
Found at i:54533288 original size:304 final size:302
Alignment explanation
Indices: 54532849--54533425 Score: 831
Period size: 304 Copynumber: 1.9 Consensus size: 302
54532839 CCCAAACTCC
* * * * * *
54532849 AAACCCCTGTCCCCTTAACCCTTAAACCCCTAACCCATATCCCATTAACCCCTAAACCCTTAACC
1 AAACCCCTGTCCCCTTAACCCCTAAACCCCTAACCAATAACCCACTAAACCCTAAACCCTCAACC
* * * * ** *
54532914 CTTAACCCTTAACCACTAACCCTTAACCTTTAAATCCTAAATCCTAAACCCATAAACCCTAAACT
66 CTTAACCCTAAACCACTAACCATAAACCTTAAAATAATAAATCATAAACCCATAAACCCTAAACT
*
54532979 ATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACGATTATATAAGAATTTA
131 ATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACAATTATATAAGAATTTA
*
54533044 TTTAATATATAAATTGACAAACATTCAGTCATATACCCAAAAAACCTTAAAATTATTTTAAATAA
196 TTTAATATATAAATTGACAAACAATCAGTCATATACCC-AAAAACCTTAAAA--A-TTTAAATAA
54533109 TAGTATTTTAATTTTTTTAACATATATTTTTCACACTAATTACCCT
257 TAGTATTTTAATTTTTTTAACATATATTTTTCACACTAATTACCCT
**
54533155 AAACCCCTGTCCCCTTAACCCCT-AACCCCTAACCAATAACCC-CTAAACTTTAAACCC-CAACC
1 AAACCCCTGTCCCCTTAACCCCTAAACCCCTAACCAATAACCCACTAAACCCTAAACCCTCAACC
* * *
54533217 TTTAAACCCTAAACC-CATAATCCATAAACCTTAAAATAATAACTCATAAA-CCATAAATCCTAA
66 CTT-AACCCTAAACCAC-TAA-CCATAAACCTTAAAATAATAAATCATAAACCCATAAACCCTAA
54533280 ACTATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACAATTATATAAGAAT
128 ACTATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACAATTATATAAGAAT
* * * *
54533345 TTATTTACTGTATAAATTGACAAACAATCAGTCATATACCCAAAAAGCTTTAAAATTTAAATAAT
193 TTATTTAATATATAAATTGACAAACAATCAGTCATATACCCAAAAACCTTAAAAATTTAAATAAT
*
54533410 AGTATTTTTATTTTTT
258 AGTATTTTAATTTTTT
54533426 CATTTTTAAC
Statistics
Matches: 243, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
300 25 0.10
301 1 0.00
303 18 0.07
304 138 0.57
305 39 0.16
306 22 0.09
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34
Consensus pattern (302 bp):
AAACCCCTGTCCCCTTAACCCCTAAACCCCTAACCAATAACCCACTAAACCCTAAACCCTCAACC
CTTAACCCTAAACCACTAACCATAAACCTTAAAATAATAAATCATAAACCCATAAACCCTAAACT
ATAATGATAATTAATTCAATATTTTAAAATTAATATTATCTCTTTTACAATTATATAAGAATTTA
TTTAATATATAAATTGACAAACAATCAGTCATATACCCAAAAACCTTAAAAATTTAAATAATAGT
ATTTTAATTTTTTTAACATATATTTTTCACACTAATTACCCT
Found at i:54533647 original size:40 final size:40
Alignment explanation
Indices: 54533597--54533690 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
54533587 CGCTTTGTCA
* *
54533597 GCTCAATCTATAG-TGGAGTTTTTCAAAAAGCACCGCTAAT
1 GCTCGATCTATAGCTGCA-TTTTTCAAAAAGCACCGCTAAT
* * *
54533637 GCTCGATCTATAGCTGCATTTTTCAGAAAGCGCTGCTAAT
1 GCTCGATCTATAGCTGCATTTTTCAAAAAGCACCGCTAAT
* *
54533677 GCTTGATCTGTAGC
1 GCTCGATCTATAGC
54533691 ACCGCTAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
40 43 0.93
41 3 0.07
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (40 bp):
GCTCGATCTATAGCTGCATTTTTCAAAAAGCACCGCTAAT
Found at i:54533794 original size:40 final size:40
Alignment explanation
Indices: 54533750--54533855 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 40
54533740 TTTTTTTGTG
* *
54533750 GCATTTTTAAAAAAGCACCGCTAATGGTCGAGCTATAGCA
1 GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
** * * * *
54533790 GCATTTTTTGAAAAGCGCCGGTAGTGCTCGATCTATAGCG
1 GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
* *
54533830 GCATTTTTCAAAAAGTGCCGCTAATG
1 GCATTTTTAAAAAAGCGCCGCTAATG
54533856 ACACTAAAGC
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (40 bp):
GCATTTTTAAAAAAGCGCCGCTAATGCTCGAGCTATAGCA
Found at i:54536482 original size:21 final size:22
Alignment explanation
Indices: 54536454--54536504 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
54536444 TTGAAATGGC
54536454 AAAT-ATGAGAAATG-AATATG
1 AAATGATGAGAAATGAAATATG
54536474 AGAA-GATGAGAAATGAAATATG
1 A-AATGATGAGAAATGAAATATG
54536496 AAATGATGA
1 AAATGATGA
54536505 AATAAGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.04
21 14 0.52
22 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.22
Consensus pattern (22 bp):
AAATGATGAGAAATGAAATATG
Found at i:54543658 original size:19 final size:19
Alignment explanation
Indices: 54543611--54543671 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
54543601 TTGTAATGCA
* *
54543611 AATAAAGGCACCGAAGTAC
1 AATAGAGGCACCGAAGTGC
* *
54543630 AAACAGAGGCATCGAAGTGC
1 -AATAGAGGCACCGAAGTGC
54543650 AATAGAGGCACCGAAGTGC
1 AATAGAGGCACCGAAGTGC
54543669 AAT
1 AAT
54543672 CCTGTACAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (19 bp):
AATAGAGGCACCGAAGTGC
Found at i:54544620 original size:17 final size:18
Alignment explanation
Indices: 54544586--54544621 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54544576 TGAATTTCTA
54544586 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
54544604 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
54544621 T
1 T
54544622 AACTCACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:54554584 original size:43 final size:43
Alignment explanation
Indices: 54554504--54554696 Score: 257
Period size: 43 Copynumber: 4.5 Consensus size: 43
54554494 TTGTACAATA
* *
54554504 CCAACGTCCCTA-ACGTGGTCTTACATGTAATCTCATATCGATG
1 CCAACGTCCC-AGACGTGGTCTTACACGTAATCACATATCGATG
* * * * *
54554547 CC-ACTATCCCAGACAG-GGTCTTACTCTTAAACACATATTGATG
1 CCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCGATG
54554590 CCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATG
1 CCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATG
54554633 CCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATG
1 CCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATG
* *
54554676 CCAACGTTCCGGACGTGGTCT
1 CCAACGTCCCAGACGTGGTCT
54554697 AATACATGAT
Statistics
Matches: 131, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
42 4 0.03
43 124 0.95
44 3 0.02
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (43 bp):
CCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATG
Found at i:54556118 original size:43 final size:43
Alignment explanation
Indices: 54556057--54556380 Score: 450
Period size: 43 Copynumber: 7.5 Consensus size: 43
54556047 TAGTTTATCA
* *
54556057 TGGTCTTATACGTAATCACATATCGATGCCAATGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
** * *
54556100 TGGTCTTATGCGTAATCACATATCGATGCCAACGTCCCAAACT
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * * *
54556143 TGGTCTTACAAGTAATAACATATCGATGCCAACATCCCAGATG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
** * *
54556186 TGGTCTTATGCTTAATCACATATTGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
*
54556229 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGAAG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* *
54556272 TGGTCTTACGCGTAATCACATATCGATGCCAATGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * * *
54556315 TGGCCTTACGCGTAATCACATGTCGATGCGAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
*
54556358 TAGTCTTACACGTAATCACATAT
1 TGGTCTTACACGTAATCACATAT
54556381 TGATATCTCA
Statistics
Matches: 245, Mismatches: 36, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 245 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
Found at i:54558755 original size:46 final size:46
Alignment explanation
Indices: 54558705--54558876 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
54558695 TGGTTGAGCA
*
54558705 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
* * * * *
54558751 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAA--A--CG
* *
54558798 TCCGAACTCGTTGAGTTGAGT-TCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCT-GAGTTCACTTATGGATGCAAACG
* *
54558844 CCCGAGCTCGTTGAGTTGAGTC-GAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTA
54558877 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
43 6 0.06
45 13 0.13
46 48 0.47
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
Found at i:54558861 original size:93 final size:92
Alignment explanation
Indices: 54558702--54558871 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 92
54558692 GGATGGTTGA
* *
54558702 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
54558767 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGT-CGAGTTCGTGAGATGTAACTAG
* * *
54558795 GCATCCGAACTCGTTGAGTTGAGT-TCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCT-GAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
54558859 TTGAGTCGAGTTC
65 TTGAGTCGAGTTC
54558872 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
92 8 0.11
93 63 0.89
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAGATGTAACTAG
Found at i:54567895 original size:46 final size:46
Alignment explanation
Indices: 54567845--54568017 Score: 167
Period size: 46 Copynumber: 3.7 Consensus size: 46
54567835 TGCTTGAGCA
* *
54567845 TCCGAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
54567891 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--A--CG
* * *
54567938 TCCAAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
54567984 -CCTAAGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
54568018 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 13, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 6 0.06
46 52 0.50
47 25 0.24
48 2 0.02
50 5 0.05
51 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:54568001 original size:93 final size:93
Alignment explanation
Indices: 54567842--54568011 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
54567832 GGATGCTTGA
* *
54567842 GCATCCGAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
54567907 TGAGTCCGAGTTTGTGAGATGTAACTAG
66 TGAGTCCGAGTTTGTGAGATGTAACTAG
* * * *
54567935 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CCTAAGCTCGTTGAG
1 GCATCCAAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAA-CTCGTTGAG
*
54567999 TTGAGTTCGAGTT
65 TTGAGTCCGAGTT
54568012 CACTTAGGGG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
92 4 0.06
93 65 0.94
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTAGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTTGTGAGATGTAACTAG
Found at i:54571240 original size:26 final size:26
Alignment explanation
Indices: 54571211--54571260 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
54571201 CATAGTGTCT
*
54571211 GTACCTCGTTCGGAAAGCAGTCTTCC
1 GTACCTCGTTCGAAAAGCAGTCTTCC
54571237 GTACCTCGTTCGAAAAGCAGTCTT
1 GTACCTCGTTCGAAAAGCAGTCTT
54571261 TGGCACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (26 bp):
GTACCTCGTTCGAAAAGCAGTCTTCC
Found at i:54574600 original size:43 final size:43
Alignment explanation
Indices: 54574279--54574602 Score: 355
Period size: 43 Copynumber: 7.5 Consensus size: 43
54574269 CTAACGTCCT
* * * **
54574279 AGACATGGTCTTACATGTAATCTCATATCGATATC-ACTATCCC
1 AGACGTGGTCTTACACGTAATCACATATCGATGCCAAC-ATCCC
* * * **
54574322 AGACAG-GGTCTTACTCTTAAACACATATCGATGCCAATGTCCC
1 AGAC-GTGGTCTTACACGTAATCACATATCGATGCCAACATCCC
*
54574365 AGACGTGGTCTTACACGTAATCACATATCGATGCCAACACCCC
1 AGACGTGGTCTTACACGTAATCACATATCGATGCCAACATCCC
* * * * * *
54574408 AAATGTGGTTTTACATGTAATCACTTATAGATGCCAACATCCC
1 AGACGTGGTCTTACACGTAATCACATATCGATGCCAACATCCC
* * * **
54574451 AGACATGGTTTTACACGTAATCACATATCGATGCTAATGTCCC
1 AGACGTGGTCTTACACGTAATCACATATCGATGCCAACATCCC
* * * *
54574494 AGACATGGTCTTACGCATAATCACATATCGATGCCAACGTCCC
1 AGACGTGGTCTTACACGTAATCACATATCGATGCCAACATCCC
* *
54574537 AGACGTGGTCTTACACGTAATCACATATCAATGCCAACATCCT
1 AGACGTGGTCTTACACGTAATCACATATCGATGCCAACATCCC
*
54574580 GGACGTGGTCTTACACGTAATCA
1 AGACGTGGTCTTACACGTAATCA
54574603 ACTTTCACTT
Statistics
Matches: 234, Mismatches: 44, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
42 1 0.00
43 232 0.99
44 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (43 bp):
AGACGTGGTCTTACACGTAATCACATATCGATGCCAACATCCC
Found at i:54582178 original size:18 final size:20
Alignment explanation
Indices: 54582140--54582179 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
54582130 AGGACTTGTC
*
54582140 TACTGCATTATTTGATGCTG
1 TACTGCATTATTTGATACTG
54582160 TACTG-ATTA-TTGATACTG
1 TACTGCATTATTTGATACTG
54582178 TA
1 TA
54582180 ATGGGTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (20 bp):
TACTGCATTATTTGATACTG
Found at i:54584272 original size:40 final size:40
Alignment explanation
Indices: 54584203--54584408 Score: 288
Period size: 40 Copynumber: 5.2 Consensus size: 40
54584193 AACCCAAGTA
* **
54584203 CCTTCGGGATTTAG-CCGGATATAACAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
54584242 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
54584282 CCTTCAGGACTTAGCCCGGGTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
54584322 CCTTCGGGACTTAACCCGGATATAGTAACTCACACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
54584362 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54584402 CCTTCGG
1 CCTTCGG
54584409 ATCTTAGTCC
Statistics
Matches: 148, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 12 0.08
40 136 0.92
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54587466 original size:40 final size:40
Alignment explanation
Indices: 54587391--54587674 Score: 430
Period size: 40 Copynumber: 7.2 Consensus size: 40
54587381 AACCCAAGTA
* ** *
54587391 CCTTCGGGATTTAG-CCGGATATAACAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54587430 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54587470 CCTTC-GGACTTAG-CCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54587508 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54587548 CCTTCGGGACTTAGCCCGGATCTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
54587588 CCTTCGGGACTTAACCCGGAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
54587628 CCTTCGAGACTTAACCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54587668 CCTTCGG
1 CCTTCGG
54587675 ATCTTAGTCC
Statistics
Matches: 225, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
38 29 0.13
39 28 0.12
40 168 0.75
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54595537 original size:40 final size:40
Alignment explanation
Indices: 54595468--54595652 Score: 309
Period size: 40 Copynumber: 4.7 Consensus size: 40
54595458 AACCCAAGTA
* **
54595468 CCTTCGGGATTTAG-CCGGATATAACAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54595507 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54595547 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54595587 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54595627 CCTTCGGGACTTAACCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGT
54595653 CACTGTGACA
Statistics
Matches: 139, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 12 0.09
40 127 0.91
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54597680 original size:40 final size:40
Alignment explanation
Indices: 54597461--54597673 Score: 281
Period size: 40 Copynumber: 5.3 Consensus size: 40
54597451 TGGCTAAGTC
* *
54597461 CCGAAGGC-TTTGTGCTAAGTGACTAAATCCGGACTAAGAT
1 CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGAT
* *
54597501 CCGAAGGCATTCGTACGAGTTACTAAATCCGGACTAAGAT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
*
54597541 CCGAAGGTATTTGTGCGAGTTACTAAATCCGGACTAAGAT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
**
54597581 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-T
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
* *
54597620 CCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATG-T
1 -CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGACTAAGAT
54597660 CCCGAAGGCATTTG
1 -CCGAAGGCATTTG
54597674 AACGAGTAGC
Statistics
Matches: 158, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
39 1 0.01
40 150 0.95
41 7 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGAT
Found at i:54603184 original size:24 final size:24
Alignment explanation
Indices: 54603157--54603236 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
54603147 TTTCATACTC
* *
54603157 ATCTTCATGTCGACCCTTGTCTTT
1 ATCTTCATCTCCACCCTTGTCTTT
54603181 ATCTTCATCTCCACCCTTGTCTTT
1 ATCTTCATCTCCACCCTTGTCTTT
* * * * * *
54603205 GTCTTCGTCTCTATCGTTGTCTTC
1 ATCTTCATCTCCACCCTTGTCTTT
54603229 ATCTTCAT
1 ATCTTCAT
54603237 TGTCGTCTTC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.11, C:0.31, G:0.10, T:0.47
Consensus pattern (24 bp):
ATCTTCATCTCCACCCTTGTCTTT
Found at i:54603226 original size:18 final size:18
Alignment explanation
Indices: 54603203--54603257 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
54603193 ACCCTTGTCT
54603203 TTGTCTTCGTCTCTATCG
1 TTGTCTTCGTCTCTATCG
* *
54603221 TTGTCTTCATCT-TCATTG
1 TTGTCTTCGTCTCT-ATCG
* *
54603239 TCGTCTTCGTCTCCATCG
1 TTGTCTTCGTCTCTATCG
54603257 T
1 T
54603258 CTTCCTCCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 28 0.97
ACGTcount: A:0.07, C:0.29, G:0.15, T:0.49
Consensus pattern (18 bp):
TTGTCTTCGTCTCTATCG
Found at i:54607224 original size:21 final size:21
Alignment explanation
Indices: 54607200--54607246 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
54607190 TGTGGATAGG
54607200 GGACACA-TCCGTGTGACTATA
1 GGACACACT-CGTGTGACTATA
*
54607221 GGACACACTCGTGTGACTATG
1 GGACACACTCGTGTGACTATA
54607242 GGACA
1 GGACA
54607247 TGCCCGTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (21 bp):
GGACACACTCGTGTGACTATA
Found at i:54609036 original size:40 final size:40
Alignment explanation
Indices: 54608965--54609121 Score: 271
Period size: 40 Copynumber: 4.0 Consensus size: 40
54608955 GAAAAAAATA
54608965 TATAACCGGGTTAAGT-CCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
54609004 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
*
54609044 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGTGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* * *
54609084 TATAACTGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
54609122 GTTACATCCG
Statistics
Matches: 112, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 16 0.14
40 96 0.86
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Done.