Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 142 of 770
Found at i:41822871 original size:71 final size:70
Alignment explanation
Indices: 41822670--41822867 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
41822660 CGATTTGTCT
* * * *
41822670 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41822735 CTTTCA
65 CTTTCA
* * * *
41822741 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41822806 CTTTCA
65 CTTTCA
* *
41822812 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
41822868 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:41831489 original size:29 final size:28
Alignment explanation
Indices: 41831457--41831559 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41831447 GTGACGAGAT
* *
41831457 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
41831486 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
41831515 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
41831544 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41831560 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:41833795 original size:2 final size:2
Alignment explanation
Indices: 41833788--41833814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41833778 CTTTAACTGA
41833788 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
41833815 ACATGCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41835526 original size:40 final size:40
Alignment explanation
Indices: 41835481--41835647 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
41835471 CGGAATATAA
41835481 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41835521 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41835561 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41835601 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41835640 CCGGATAT
1 CCGGATAT
41835648 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41835631 original size:80 final size:79
Alignment explanation
Indices: 41835497--41835647 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
41835487 ATAATCACGT
*
41835497 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
41835562 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
41835577 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
41835640 CCGGATAT
64 CCGGATAT
41835648 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:41836496 original size:17 final size:19
Alignment explanation
Indices: 41836473--41836518 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
41836463 AAGAAGCATG
41836473 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
41836491 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
41836509 AATCATGCTC
1 AATCATGCTC
41836519 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:41843528 original size:40 final size:40
Alignment explanation
Indices: 41843483--41843649 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
41843473 CGGAATATAA
41843483 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41843523 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41843563 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41843603 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41843642 CCGGATAT
1 CCGGATAT
41843650 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41843633 original size:80 final size:79
Alignment explanation
Indices: 41843499--41843649 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
41843489 ATAATCACGT
*
41843499 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
41843564 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
41843579 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
41843642 CCGGATAT
64 CCGGATAT
41843650 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:41844498 original size:17 final size:19
Alignment explanation
Indices: 41844475--41844520 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
41844465 AAGAAGCATG
41844475 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
41844493 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
41844511 AATCATGCTC
1 AATCATGCTC
41844521 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:41846134 original size:45 final size:45
Alignment explanation
Indices: 41846015--41846136 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 45
41846005 GATACCGATG
* * *
41846015 TCCCAGACATGGTCTTACACGTAACCACATATATCTATGCCAACG
1 TCCCAGACATGGTCTTACACGAAAACACATATATCTATGCCAACA
* ** * * * *
41846060 TCCCAAATTTGGTCTTAAACTACAGCACATATAT-TGATGCCAACA
1 TCCCAGACATGGTCTTACACGAAAACACATATATCT-ATGCCAACA
* *
41846105 TCCTAGACGTGGTCTTACACGAAAACACATAT
1 TCCCAGACATGGTCTTACACGAAAACACATAT
41846137 CAAAATCCTT
Statistics
Matches: 59, Mismatches: 17, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
44 1 0.02
45 58 0.98
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (45 bp):
TCCCAGACATGGTCTTACACGAAAACACATATATCTATGCCAACA
Found at i:41851465 original size:20 final size:20
Alignment explanation
Indices: 41851442--41851485 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
41851432 ATGATTTTGA
41851442 GTAATTTGAATGACTAAAAT
1 GTAATTTGAATGACTAAAAT
41851462 GTAATTTGAATGACTAAAAT
1 GTAATTTGAATGACTAAAAT
41851482 GTAA
1 GTAA
41851486 AATAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (20 bp):
GTAATTTGAATGACTAAAAT
Found at i:41851493 original size:20 final size:20
Alignment explanation
Indices: 41851450--41851494 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41851440 GAGTAATTTG
** *
41851450 AATGACTAAAATGTAATTTG
1 AATGACTAAAATGTAAAATA
41851470 AATGACTAAAATGTAAAATA
1 AATGACTAAAATGTAAAATA
41851490 AATGA
1 AATGA
41851495 AATGTATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.29
Consensus pattern (20 bp):
AATGACTAAAATGTAAAATA
Found at i:41852032 original size:45 final size:45
Alignment explanation
Indices: 41851967--41852143 Score: 177
Period size: 45 Copynumber: 4.0 Consensus size: 45
41851957 TACAATTTTG
* *
41851967 ATATGTGTTTTCATGTAAGACCACGTTTGGGACATCGGCATCGAT
1 ATATGTGTTTTCATGTAAGACCATGTCTGGGACATCGGCATCGAT
* * ** *
41852012 ATATGTGTTTTCATGAAAGACTATGTCTGGGACATTAGCATCTAT
1 ATATGTGTTTTCATGTAAGACCATGTCTGGGACATCGGCATCGAT
* * *
41852057 ATATGTGGTTACGTGTAAGACCATGTCTGGGACATCGGCAT---T
1 ATATGTGTTTTCATGTAAGACCATGTCTGGGACATCGGCATCGAT
* * * *
41852099 GTA-CTG-ATTCATGTAAGACCCTGTCTGGGACAGT-GGCATCGAT
1 ATATGTGTTTTCATGTAAGACCATGTCTGGGACA-TCGGCATCGAT
41852142 AT
1 AT
41852144 GAGATAGCAT
Statistics
Matches: 107, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
40 27 0.25
41 3 0.03
42 3 0.03
43 2 0.02
45 72 0.67
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (45 bp):
ATATGTGTTTTCATGTAAGACCATGTCTGGGACATCGGCATCGAT
Found at i:41852860 original size:51 final size:51
Alignment explanation
Indices: 41852796--41852896 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
41852786 GCCACTTAGA
41852796 GTGTAGGGAGGTGGCGTTAATAGCTAGCAAGGAGGTCCAAGGTTTGAATCT
1 GTGTAGGGAGGTGGCGTTAATAGCTAGCAAGGAGGTCCAAGGTTTGAATCT
*
41852847 GTGTAGGGGGGTGGCGTTAATAGCTAGCAAGGAGGTCCAAGGTTTGAATC
1 GTGTAGGGAGGTGGCGTTAATAGCTAGCAAGGAGGTCCAAGGTTTGAATC
41852897 CTAGCTTAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.25, C:0.12, G:0.39, T:0.25
Consensus pattern (51 bp):
GTGTAGGGAGGTGGCGTTAATAGCTAGCAAGGAGGTCCAAGGTTTGAATCT
Found at i:41854121 original size:29 final size:29
Alignment explanation
Indices: 41854089--41854236 Score: 138
Period size: 29 Copynumber: 5.1 Consensus size: 29
41854079 GTGAGCATGA
* * *
41854089 ATATAAAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGAATTGGGCCTGATGGGCC
* *
41854118 ATATTAATATGAATTGGGCCTGATGGGCC
1 ATATAAATGTGAATTGGGCCTGATGGGCC
* * *
41854147 GTATGAATGTGAATTGGGCTTGATGGGCC
1 ATATAAATGTGAATTGGGCCTGATGGGCC
* * * *
41854176 GTATGAATGTGAATTGGGCCTGATAGACC
1 ATATAAATGTGAATTGGGCCTGATGGGCC
* * *
41854205 ACATAAATGAG-ATTGGGCC-AAGTGGGCC
1 ATATAAATGTGAATTGGGCCTGA-TGGGCC
41854233 ATAT
1 ATAT
41854237 GCATGTATAT
Statistics
Matches: 98, Mismatches: 20, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
27 1 0.01
28 15 0.15
29 82 0.84
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (29 bp):
ATATAAATGTGAATTGGGCCTGATGGGCC
Found at i:41857298 original size:27 final size:27
Alignment explanation
Indices: 41857251--41857304 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
41857241 CCGGCTGTAC
*
41857251 AACAACCTCCACCCCTAATTAATCCTT
1 AACAACCTCCAACCCTAATTAATCCTT
* *
41857278 AACAACCTCCAACCTTGATTAATCCTT
1 AACAACCTCCAACCCTAATTAATCCTT
41857305 TTCTGATAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.28
Consensus pattern (27 bp):
AACAACCTCCAACCCTAATTAATCCTT
Found at i:41861107 original size:8 final size:8
Alignment explanation
Indices: 41861094--41861132 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
41861084 ATAGACAAAA
41861094 GCCGAAAT
1 GCCGAAAT
*
41861102 GCCGAAAA
1 GCCGAAAT
*
41861110 GCCAAAAT
1 GCCGAAAT
41861118 GCCGAAAT
1 GCCGAAAT
*
41861126 GCTGAAA
1 GCCGAAA
41861133 AGCTGAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (8 bp):
GCCGAAAT
Found at i:41861111 original size:16 final size:16
Alignment explanation
Indices: 41861090--41861124 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
41861080 ATGTATAGAC
*
41861090 AAAAGCCGAAATGCCG
1 AAAAGCCAAAATGCCG
41861106 AAAAGCCAAAATGCCG
1 AAAAGCCAAAATGCCG
41861122 AAA
1 AAA
41861125 TGCTGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.23, G:0.20, T:0.06
Consensus pattern (16 bp):
AAAAGCCAAAATGCCG
Found at i:41861122 original size:24 final size:23
Alignment explanation
Indices: 41861089--41861135 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
41861079 TATGTATAGA
41861089 CAAAAGCCGAAATGCCGAAAAGC
1 CAAAAGCCGAAATGCCGAAAAGC
*
41861112 CAAAATGCCGAAATGCTGAAAAGC
1 CAAAA-GCCGAAATGCCGAAAAGC
41861136 TGAAAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (23 bp):
CAAAAGCCGAAATGCCGAAAAGC
Found at i:41861137 original size:8 final size:8
Alignment explanation
Indices: 41861090--41861140 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
41861080 ATGTATAGAC
41861090 AAAAGCCG
1 AAAAGCCG
*
41861098 AAATGCCG
1 AAAAGCCG
41861106 AAAAGCC-
1 AAAAGCCG
41861113 AAAATGCCG
1 AAAA-GCCG
* *
41861122 AAATGCTG
1 AAAAGCCG
*
41861130 AAAAGCTG
1 AAAAGCCG
41861138 AAA
1 AAA
41861141 GTTTAGCTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 4 0.11
8 29 0.81
9 3 0.08
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.10
Consensus pattern (8 bp):
AAAAGCCG
Found at i:41861409 original size:29 final size:29
Alignment explanation
Indices: 41861365--41861464 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 29
41861355 GAATGTGACT
* *
41861365 GGCCTAACGGGACATATAAATGTGATTTG
1 GGCCTAATGGGCCATATAAATGTGATTTG
* * *
41861394 GGCCGAATGGGCCATATACAGGTGATTTG
1 GGCCTAATGGGCCATATAAATGTGATTTG
* * *
41861423 AGCCTAATGGGCCATATGAATATGA-TTG
1 GGCCTAATGGGCCATATAAATGTGATTTG
*
41861451 GGCTTAATGGGCCA
1 GGCCTAATGGGCCA
41861465 GATACAGGTA
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 15 0.26
29 43 0.74
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (29 bp):
GGCCTAATGGGCCATATAAATGTGATTTG
Found at i:41870195 original size:40 final size:40
Alignment explanation
Indices: 41870137--41870275 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 40
41870127 ATTGAATGAC
* *
41870137 ATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATTAT
1 ATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTAT
* * * ***
41870176 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTAT
1 ATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTAT
* * * ** * *
41870216 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATTCT
1 ATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACTAT
41870256 ATCCGGGCTAAGACCCGAAG
1 ATCCGGGCTAAGACCCGAAG
41870276 GCATTTGTGC
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 14 0.17
40 70 0.83
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTAT
Found at i:41870276 original size:40 final size:39
Alignment explanation
Indices: 41870173--41870301 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
41870163 TGCTGGAAAT
* * *
41870173 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
41870213 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
41870253 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
41870293 TATATCCGG
1 TATATCCGG
41870302 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:41878181 original size:40 final size:40
Alignment explanation
Indices: 41878115--41878281 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
41878105 GAAATGAATG
* * *
41878115 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
41878154 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41878194 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41878234 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41878274 ATATCCGG
1 ATATCCGG
41878282 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41881369 original size:2 final size:2
Alignment explanation
Indices: 41881362--41881387 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41881352 ATGTGCAAAC
41881362 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41881388 GTGCAAGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41888567 original size:40 final size:40
Alignment explanation
Indices: 41888543--41888708 Score: 230
Period size: 40 Copynumber: 4.2 Consensus size: 40
41888533 AGGGACATGG
41888543 CCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAA
1 CCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAA
41888583 CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA
1 CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA
*
41888623 CCCGGATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAG
1 CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAA
* * * * *
41888663 TCCGGATATAGTTACTTAGCACAAA-GCCTTCGGGACTTAG
1 CCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAA
41888703 CCCGGA
1 CCCGGA
41888709 CATCATTCAA
Statistics
Matches: 116, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
39 3 0.03
40 100 0.86
41 13 0.11
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA
Found at i:41894629 original size:31 final size:31
Alignment explanation
Indices: 41894594--41894655 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
41894584 TACTTTTTCT
41894594 TCGTAAGTCAAATCTAGTTGAATTTTTTTTA
1 TCGTAAGTCAAATCTAGTTGAATTTTTTTTA
41894625 TCGTAAGTCAAATCTAGTTGAATTTTTTTTA
1 TCGTAAGTCAAATCTAGTTGAATTTTTTTTA
41894656 CTTCAGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (31 bp):
TCGTAAGTCAAATCTAGTTGAATTTTTTTTA
Found at i:41898511 original size:30 final size:30
Alignment explanation
Indices: 41898470--41898532 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
41898460 CCAGACAGGT
* * *
41898470 AACCTTGATATAATGTTAGCTTGTGTAAGC
1 AACCCTGATATAATGTCAACTTGTGTAAGC
*
41898500 AACCCTGATATAATGTCAACTTGTGTGAGC
1 AACCCTGATATAATGTCAACTTGTGTAAGC
41898530 AAC
1 AAC
41898533 TTATTCCCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (30 bp):
AACCCTGATATAATGTCAACTTGTGTAAGC
Found at i:41901196 original size:19 final size:19
Alignment explanation
Indices: 41901159--41901197 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41901149 CCGAATTTGT
*
41901159 TAAAATTAAACTTTTTGTA
1 TAAAATTAAACTTTATGTA
41901178 TAAAATTAAA-TTATATGTA
1 TAAAATTAAACTT-TATGTA
41901197 T
1 T
41901198 GGTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (19 bp):
TAAAATTAAACTTTATGTA
Found at i:41901260 original size:27 final size:27
Alignment explanation
Indices: 41901225--41901276 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
41901215 AAATGCTTAA
**
41901225 TATAATATTTTTTTCTAATTTGGTAAC
1 TATAATATTTTAGTCTAATTTGGTAAC
*
41901252 TATATTATTTTAGTCTAATTTGGTA
1 TATAATATTTTAGTCTAATTTGGTA
41901277 TTTAAATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.56
Consensus pattern (27 bp):
TATAATATTTTAGTCTAATTTGGTAAC
Found at i:41902631 original size:19 final size:18
Alignment explanation
Indices: 41902592--41902711 Score: 96
Period size: 19 Copynumber: 6.1 Consensus size: 18
41902582 AATATTAATA
41902592 TTTAAATAAACTTATAAAAAT
1 TTTAAA-AAA-TT-TAAAAAT
* *
41902613 ATTAAAAATTTTAAAAAAT
1 TTTAAAAAATTT-AAAAAT
*
41902632 TTATAAAAACTTATAAAAAT
1 TT-TAAAAAATT-TAAAAAT
* *
41902652 TCTAATAAATTATAAAAAT
1 TTTAAAAAATT-TAAAAAT
41902671 ATTTAAAAATATTTAAAAAT
1 -TTTAAAAA-ATTTAAAAAT
*
41902691 CTTAAAAATATTTAAAAAT
1 TTTAAAAA-ATTTAAAAAT
41902710 TT
1 TT
41902712 CTGTAAACTT
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
18 1 0.01
19 43 0.52
20 30 0.36
21 9 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTAAAAAATTTAAAAAT
Found at i:41902634 original size:39 final size:38
Alignment explanation
Indices: 41902591--41902708 Score: 134
Period size: 39 Copynumber: 3.0 Consensus size: 38
41902581 CAATATTAAT
41902591 ATTTAAATAAACTTATAAAAATATTAAAAATTTTAAAAA
1 ATTTAAA-AAACTTATAAAAATATTAAAAATTTTAAAAA
*
41902630 ATTTATAAAAACTTATAAAAAT-TCTAATAAATTATAAAAA
1 ATTTA-AAAAACTTATAAAAATAT-TAA-AAATTTTAAAAA
*
41902670 TATTTAAAAATA-TT-TAAAAATCTTAAAAATATTTAAAAA
1 -ATTTAAAAA-ACTTATAAAAATATTAAAAAT-TTTAAAAA
41902709 TTTCTGTAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
38 5 0.07
39 39 0.56
40 20 0.29
41 6 0.09
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (38 bp):
ATTTAAAAAACTTATAAAAATATTAAAAATTTTAAAAA
Found at i:41902635 original size:29 final size:30
Alignment explanation
Indices: 41902592--41902711 Score: 133
Period size: 29 Copynumber: 4.1 Consensus size: 30
41902582 AATATTAATA
*
41902592 TTTAAATAAACTTATAAAAATA-TTAAAAAT
1 TTTAAA-AAATTTATAAAAATATTTAAAAAT
*
41902622 TTTAAAAAATTTATAAAAACT-TATAAAAAT
1 TTTAAAAAATTTATAAAAA-TATTTAAAAAT
* *
41902652 TCTAATAAA-TTATAAAAATATTTAAAAAT
1 TTTAAAAAATTTATAAAAATATTTAAAAAT
*
41902681 ATTT-AAAAATCT-TAAAAATATTTAAAAAT
1 -TTTAAAAAATTTATAAAAATATTTAAAAAT
41902710 TT
1 TT
41902712 CTGTAAACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
28 3 0.04
29 50 0.65
30 24 0.31
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
TTTAAAAAATTTATAAAAATATTTAAAAAT
Found at i:41902727 original size:29 final size:28
Alignment explanation
Indices: 41902591--41902737 Score: 122
Period size: 29 Copynumber: 5.0 Consensus size: 28
41902581 CAATATTAAT
*
41902591 ATTTAAATAAACTTATAAAAATATTAAAA
1 ATTTTAATAAACTTATAAAAAT-TTAAAA
* *
41902620 ATTTTAAAAAATTTATAAAAACTTATAAAA
1 ATTTTAATAAACTTATAAAAA-TT-TAAAA
*
41902650 ATTCTAATAAA-TTATAAAAATATTTAAAA
1 ATTTTAATAAACTTAT-AAAA-ATTTAAAA
41902679 ATATTTAA-AAATCTTA-AAAATATTTAAAA
1 AT-TTTAATAAA-CTTATAAAA-ATTTAAAA
* *
41902708 ATTTCT-GTAAACTTATAAAAAATTCAAAA
1 ATTT-TAATAAACTTAT-AAAAATTTAAAA
41902737 A
1 A
41902738 AACTTATGAA
Statistics
Matches: 99, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
28 6 0.06
29 60 0.61
30 29 0.29
31 4 0.04
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.36
Consensus pattern (28 bp):
ATTTTAATAAACTTATAAAAATTTAAAA
Found at i:41902817 original size:10 final size:9
Alignment explanation
Indices: 41902603--41902882 Score: 100
Period size: 10 Copynumber: 28.2 Consensus size: 9
41902593 TTAAATAAAC
41902603 TTATAAAAA
1 TTATAAAAA
41902612 -TATTAAAAA
1 TTA-TAAAAA
*
41902621 TTTTAAAAAA
1 TTAT-AAAAA
41902631 TTTATAAAAA
1 -TTATAAAAA
41902641 CTTATAAAAA
1 -TTATAAAAA
*
41902651 TTCTAATAAA
1 TTATAA-AAA
41902661 TTATAAAAA
1 TTATAAAAA
*
41902670 TATTTAAAAA
1 T-TATAAAAA
*
41902680 TATTTAAAAA
1 T-TATAAAAA
41902690 TCT-TAAAAA
1 T-TATAAAAA
*
41902699 TATTTAAAAA
1 T-TATAAAAA
* * *
41902709 TTTCTGTAAAC
1 -TTAT-AAAAA
41902720 TTATAAAAAA
1 TTAT-AAAAA
*
41902730 TTCAAAAAAA
1 TT-ATAAAAA
41902740 CTTATGAAAAAA
1 -TTAT--AAAAA
*
41902752 TCTAAAAAAA
1 T-TATAAAAA
*
41902762 TTTGTAAAAA
1 -TTATAAAAA
* **
41902772 TCATCAGTAA
1 TTAT-AAAAA
*
41902782 TTATAAAAC
1 TTATAAAAA
41902791 TTATACAAAA
1 TTATA-AAAA
41902801 TTCATAAAAA
1 TT-ATAAAAA
41902811 CTTATAAAAGA
1 -TTATAAAA-A
*
41902822 TTCTAATAAA
1 TTATAA-AAA
*
41902832 GTATAAAAAA
1 TTAT-AAAAA
*
41902842 TAATTTAAAAA
1 T--TATAAAAA
41902853 TT-TATAAAA
1 TTATA-AAAA
41902862 -TATTAAAAA
1 TTA-TAAAAA
41902871 TATATAAAAA
1 T-TATAAAAA
41902881 TT
1 TT
41902883 TATTTGTCCT
Statistics
Matches: 208, Mismatches: 34, Indels: 58
0.69 0.11 0.19
Matches are distributed among these distances:
8 5 0.02
9 43 0.21
10 121 0.58
11 30 0.14
12 9 0.04
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:41902859 original size:29 final size:28
Alignment explanation
Indices: 41902804--41902885 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
41902794 TACAAAATTC
* *
41902804 ATAAAAACT-TATAAAAGATTCTAATAAAGT
1 ATAAAAAATATATAAAA-ATT-T-ATAAAAT
*
41902834 ATAAAAAATAATTTAAAAATTTATAAAAT
1 ATAAAAAAT-ATATAAAAATTTATAAAAT
*
41902863 ATTAAAAATATATAAAAATTTAT
1 ATAAAAAATATATAAAAATTTAT
41902886 TTGTCCTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 13 0.29
29 14 0.31
30 9 0.20
31 3 0.07
32 6 0.13
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
ATAAAAAATATATAAAAATTTATAAAAT
Found at i:41903176 original size:20 final size:20
Alignment explanation
Indices: 41903152--41903202 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
41903142 AAGTTTTAAA
41903152 AATAAAAATAATAATTTATCT
1 AATAAAAATAATAATTTAT-T
41903173 -ATAAAAATAATAATTTATT
1 AATAAAAATAATAATTTATT
41903192 AATAAAAATAA
1 AATAAAAATAA
41903203 GAGAGTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAAAAATAATAATTTATT
Found at i:41903354 original size:9 final size:9
Alignment explanation
Indices: 41903342--41903433 Score: 60
Period size: 9 Copynumber: 9.4 Consensus size: 9
41903332 ATTTATAAAA
41903342 TTTTAATAT
1 TTTTAATAT
41903351 TTTTAATAAAT
1 TTTTAAT--AT
41903362 TTTATAAT-T
1 TTT-TAATAT
* *
41903371 TTTTTATAA
1 TTTTAATAT
*
41903380 TTTTAATAA
1 TTTTAATAT
* *
41903389 GTTTATATCAA
1 TTTTA-AT-AT
41903400 TTTTAATAT
1 TTTTAATAT
41903409 TTTTAATAAT
1 TTTTAAT-AT
41903419 ATTTTAATAAT
1 -TTTTAAT-AT
41903430 TTTT
1 TTTT
41903434 GGTAAAAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
8 3 0.04
9 31 0.45
10 10 0.14
11 21 0.30
12 4 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTAATAT
Found at i:41903367 original size:29 final size:29
Alignment explanation
Indices: 41903333--41903432 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
41903323 GTAAGTTTTA
41903333 TTTATAAAATTTTAATATTTTTAATAAAT
1 TTTATAAAATTTTAATATTTTTAATAAAT
** * * *
41903362 TTTATAATTTTTTTATAATTTTAAT-AAG
1 TTTATAAAATTTTAATATTTTTAATAAAT
*
41903390 TTTATATCAATTTTAATATTTTTAATAATAT
1 TTTATA-AAATTTTAATATTTTTAATAA-AT
*
41903421 TTTA-ATAATTTT
1 TTTATAAAATTTT
41903433 TGGTAAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
28 8 0.14
29 41 0.73
30 2 0.04
31 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (29 bp):
TTTATAAAATTTTAATATTTTTAATAAAT
Found at i:41903373 original size:20 final size:20
Alignment explanation
Indices: 41903336--41903433 Score: 71
Period size: 20 Copynumber: 4.9 Consensus size: 20
41903326 AGTTTTATTT
*
41903336 ATAAAATTT-TAATATTTTTA
1 ATAAATTTTATAAT-TTTTTA
*
41903356 ATAAATTTTATAATTTTTTT
1 ATAAATTTTATAATTTTTTA
* *
41903376 AT-AATTTTAATAAGTTTAT-
1 ATAAATTTT-ATAATTTTTTA
*
41903395 ATCAA-TTT-TAATATTTTTA
1 ATAAATTTTATAAT-TTTTTA
41903414 ATAATATTTTAATAATTTTT
1 ATAA-ATTTT-ATAATTTTT
41903434 GGTAAAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
17 3 0.05
18 4 0.06
19 14 0.23
20 26 0.42
21 7 0.11
22 4 0.06
23 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
ATAAATTTTATAATTTTTTA
Found at i:41903666 original size:60 final size:60
Alignment explanation
Indices: 41903599--41903723 Score: 241
Period size: 60 Copynumber: 2.1 Consensus size: 60
41903589 TTTTAAAGGC
41903599 ATTTTGTATTTATAAGGCTAAAAAGTAAAGTAAAATAATAGGATTGGGATGATTTTCAAT
1 ATTTTGTATTTATAAGGCTAAAAAGTAAAGTAAAATAATAGGATTGGGATGATTTTCAAT
*
41903659 ATTTTGTATTTATAAGGCTAAAAAGTAAAGTCAAATAATAGGATTGGGATGATTTTCAAT
1 ATTTTGTATTTATAAGGCTAAAAAGTAAAGTAAAATAATAGGATTGGGATGATTTTCAAT
41903719 ATTTT
1 ATTTT
41903724 TGTGTTTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (60 bp):
ATTTTGTATTTATAAGGCTAAAAAGTAAAGTAAAATAATAGGATTGGGATGATTTTCAAT
Found at i:41904590 original size:18 final size:17
Alignment explanation
Indices: 41904569--41904626 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
41904559 GGTTTATGGG
41904569 TTTAGGATTTTTTATAAC
1 TTTA-GATTTTTTATAAC
*
41904587 TTTAAAATTTTTTATATATTC
1 TTT-AGATTTTTTATA-A--C
41904608 TTTAGA-TTTTTATAAC
1 TTTAGATTTTTTATAAC
41904624 TTT
1 TTT
41904627 TTGAGTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 4 0.12
18 14 0.41
19 10 0.29
20 2 0.06
21 4 0.12
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTAGATTTTTTATAAC
Found at i:41908161 original size:37 final size:37
Alignment explanation
Indices: 41908115--41908227 Score: 226
Period size: 37 Copynumber: 3.1 Consensus size: 37
41908105 AAGAAGTTAG
41908115 AACCCTTGTAAAGTTATAGAGGTTTATTTTAAATAGA
1 AACCCTTGTAAAGTTATAGAGGTTTATTTTAAATAGA
41908152 AACCCTTGTAAAGTTATAGAGGTTTATTTTAAATAGA
1 AACCCTTGTAAAGTTATAGAGGTTTATTTTAAATAGA
41908189 AACCCTTGTAAAGTTATAGAGGTTTATTTTAAATAGA
1 AACCCTTGTAAAGTTATAGAGGTTTATTTTAAATAGA
41908226 AA
1 AA
41908228 AACAACATCC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (37 bp):
AACCCTTGTAAAGTTATAGAGGTTTATTTTAAATAGA
Found at i:41915497 original size:28 final size:28
Alignment explanation
Indices: 41915432--41915532 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41915422 ATAGTGAATC
*
41915432 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
41915461 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41915489 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
41915519 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41915533 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41925125 original size:20 final size:20
Alignment explanation
Indices: 41925087--41925125 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41925077 TTGAATTATT
**
41925087 GTTCTATTTTGAAGTTTAAG
1 GTTCTATTTTGAACATTAAG
*
41925107 GTTCTATTTTGTACATTAA
1 GTTCTATTTTGAACATTAA
41925126 TGCCCCGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (20 bp):
GTTCTATTTTGAACATTAAG
Found at i:41927221 original size:28 final size:29
Alignment explanation
Indices: 41927159--41927222 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
41927149 GTGACGAGAT
** *
41927159 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCAAGCTGGAAAAATA
*
41927188 TGGCACTAAGTGTGCAAGCT-GAAAAATA
1 CGGCACTAAGTGTGCAAGCTGGAAAAATA
41927216 CGGCACT
1 CGGCACT
41927223 GGGTGTGCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCAAGCTGGAAAAATA
Found at i:41935072 original size:28 final size:29
Alignment explanation
Indices: 41935010--41935073 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
41935000 GTGACGAGAT
** *
41935010 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCAAGCTGGAAAAATA
*
41935039 TGGCACTAAGTGTGCAAGCT-GAAAAATA
1 CGGCACTAAGTGTGCAAGCTGGAAAAATA
41935067 CGGCACT
1 CGGCACT
41935074 GGGTGTGCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCAAGCTGGAAAAATA
Found at i:41939791 original size:69 final size:69
Alignment explanation
Indices: 41939717--41940038 Score: 261
Period size: 69 Copynumber: 4.7 Consensus size: 69
41939707 CTTCACCTGT
* * * * *
41939717 GAACCTTAATATTATAGCTGGGAGTTTTGCTCTCGCTAATTGTTTTGGAGATTACGGCTCTTCGC
1 GAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTACGGCTCTTCGC
*
41939782 CTGC
66 TTGC
* * * * * * * * **
41939786 AAACCTTAATATGAAAACTGAGAGCTTTGCTCTTATTAACTGTTTTGGAGGTTACGACTATTCAA
1 GAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTACGGCTCTTCGC
41939851 TTGC
66 TTGC
* * * **
41939855 GAACCTTAATATGATAGCTGGGAGCTTTGCTCCCACTAACTATTTTAGAGGTTGTGGCTCTTCGC
1 GAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTACGGCTCTTCGC
*
41939920 TTGT
66 TTGC
* * * * * * *** **
41939924 GAACCTTAATATGA-CGATTGGGAGCTTTGTTCTCGCTAATTGTTTT-GATGTTGTAGCTCTTTA
1 GAACCTTAATATGATAG-CTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTACGGCTCTTCG
* *
41939987 CCTAC
65 CTTGC
* * * **
41939992 GAACCTTAATATGACAGCTAGGAGCTTTTCTCTTGCTAACTGTTTTG
1 GAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTTTG
41940039 AGTCACACGA
Statistics
Matches: 197, Mismatches: 53, Indels: 6
0.77 0.21 0.02
Matches are distributed among these distances:
68 53 0.27
69 144 0.73
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (69 bp):
GAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTACGGCTCTTCGC
TTGC
Found at i:41939968 original size:138 final size:138
Alignment explanation
Indices: 41939717--41939970 Score: 310
Period size: 138 Copynumber: 1.8 Consensus size: 138
41939707 CTTCACCTGT
* * * * * * *
41939717 GAACCTTAATATTATAGCTGGGAGTTTTGCTCTCGCTAATTGTTTTGGAGATTACGGCTCTTCGC
1 GAACCTTAATATGATAGCTGGGAGCTTTGCTCCCACTAACTATTTTAGAGATTACGGCTCTTCGC
* *
41939782 CTGCAAACCTTAATATGAAAACTGAGAGCTTTGCTCTTATTAACTGTTTTGGAGGTTACGACTAT
66 CTGCAAACCTTAATATGAAAACTGAGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTACGACTAT
41939847 TCAATTGC
131 TCAATTGC
* **
41939855 GAACCTTAATATGATAGCTGGGAGCTTTGCTCCCACTAACTATTTTAGAGGTTGTGGCTCTTCGC
1 GAACCTTAATATGATAGCTGGGAGCTTTGCTCCCACTAACTATTTTAGAGATTACGGCTCTTCGC
* ** ** * * * * *
41939920 TTGTGAACCTTAATATGACGATTGGGAGCTTTGTTCTCGCTAATTGTTTTG
66 CTGCAAACCTTAATATGAAAACTGAGAGCTTTGCTCTCACTAACTGTTTTG
41939971 ATGTTGTAGC
Statistics
Matches: 94, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
138 94 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (138 bp):
GAACCTTAATATGATAGCTGGGAGCTTTGCTCCCACTAACTATTTTAGAGATTACGGCTCTTCGC
CTGCAAACCTTAATATGAAAACTGAGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTACGACTAT
TCAATTGC
Found at i:41941099 original size:16 final size:16
Alignment explanation
Indices: 41941078--41941113 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41941068 TTGCCTAAAG
*
41941078 ATCTTCTGTGCAAACA
1 ATCTTCTATGCAAACA
*
41941094 ATCTTCTATGCTAACA
1 ATCTTCTATGCAAACA
41941110 ATCT
1 ATCT
41941114 ACATCCTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (16 bp):
ATCTTCTATGCAAACA
Found at i:41944136 original size:18 final size:18
Alignment explanation
Indices: 41944113--41944157 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
41944103 GTGTATTCAT
41944113 GTTGTCCTG-GGAACCAAA
1 GTTGTCC-GCGGAACCAAA
41944131 GTTGTCCGCGGAACCAAA
1 GTTGTCCGCGGAACCAAA
41944149 GTTGTCCGC
1 GTTGTCCGC
41944158 ATGTATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (18 bp):
GTTGTCCGCGGAACCAAA
Found at i:41950972 original size:19 final size:19
Alignment explanation
Indices: 41950930--41951000 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 19
41950920 ATTAATATTA
* *
41950930 AAAAATATTTTTTATTTTT
1 AAAAATATTTTATAATTTT
* *
41950949 TAATA-ATTTT-TAATTTT
1 AAAAATATTTTATAATTTT
*
41950966 AAAAATATTTTATACTTTT
1 AAAAATATTTTATAATTTT
* *
41950985 TAAAAT-TTTTAAAATT
1 AAAAATATTTTATAATT
41951001 AAAAAAATAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
17 9 0.22
18 18 0.44
19 14 0.34
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
AAAAATATTTTATAATTTT
Found at i:41950993 original size:9 final size:9
Alignment explanation
Indices: 41950945--41951000 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
41950935 TATTTTTTAT
41950945 TTTTTAATAA
1 TTTTTAA-AA
41950955 TTTTT--AA
1 TTTTTAAAA
*
41950962 TTTTAAAAA
1 TTTTTAAAA
* *
41950971 TATTTTATAC
1 T-TTTTAAAA
41950981 TTTTTAAAA
1 TTTTTAAAA
41950990 TTTTTAAAA
1 TTTTTAAAA
41950999 TT
1 TT
41951001 AAAAAAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
7 6 0.16
9 20 0.54
10 11 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:41950995 original size:18 final size:17
Alignment explanation
Indices: 41950938--41950995 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
41950928 TAAAAAATAT
41950938 TTTTTAT-TTTTTAATAA
1 TTTTTATATTTTTAA-AA
*
41950955 TTTTTA-ATTTTAAAAA
1 TTTTTATATTTTTAAAA
41950971 TATTTTATACTTTTTAAAA
1 T-TTTTATA-TTTTTAAAA
41950990 TTTTTA
1 TTTTTA
41950996 AAATTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 3 0.09
17 17 0.49
18 6 0.17
19 9 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTATATTTTTAAAA
Found at i:41951003 original size:35 final size:36
Alignment explanation
Indices: 41950921--41951005 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
41950911 CAGTATTTAA
* *
41950921 TTAATATTAAAAAATATTTTTTATTTTTTAATAATTT
1 TTAATATT-AAAAATATTTTATACTTTTTAATAATTT
*
41950958 TTAATTTTAAAAATATTTTATACTTTTTAA-AATTT
1 TTAATATTAAAAATATTTTATACTTTTTAATAATTT
*
41950993 TTAAAATTAAAAA
1 TTAATATTAAAAA
41951006 AATAATTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 16 0.37
36 20 0.47
37 7 0.16
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (36 bp):
TTAATATTAAAAATATTTTATACTTTTTAATAATTT
Found at i:41964369 original size:27 final size:27
Alignment explanation
Indices: 41964337--41964392 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
41964327 TTTAGCCGTA
41964337 TGTCACACAGGCGTGTCTTAGGTCGTG
1 TGTCACACAGGCGTGTCTTAGGTCGTG
* *
41964364 TGTCACACGGGCGTGTCTTAGGTTGTG
1 TGTCACACAGGCGTGTCTTAGGTCGTG
41964391 TG
1 TG
41964393 AATCTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.12, C:0.20, G:0.36, T:0.32
Consensus pattern (27 bp):
TGTCACACAGGCGTGTCTTAGGTCGTG
Found at i:41966752 original size:17 final size:18
Alignment explanation
Indices: 41966724--41966759 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41966714 TATGTGACTC
*
41966724 GCCTCGCTCGACACTTCG
1 GCCTCGCTCGACACATCG
41966742 GCCTC-CTCGACACATCG
1 GCCTCGCTCGACACATCG
41966759 G
1 G
41966760 AGTAGTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.14, C:0.44, G:0.22, T:0.19
Consensus pattern (18 bp):
GCCTCGCTCGACACATCG
Found at i:41967014 original size:14 final size:14
Alignment explanation
Indices: 41966995--41967031 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
41966985 CTGCTAGCTT
41966995 CCGAAGAGTATCCA
1 CCGAAGAGTATCCA
41967009 CCGAAGAGTATCCA
1 CCGAAGAGTATCCA
*
41967023 CTGAAGAGT
1 CCGAAGAGT
41967032 TCACTAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (14 bp):
CCGAAGAGTATCCA
Found at i:41969961 original size:30 final size:30
Alignment explanation
Indices: 41969925--41969986 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
41969915 AGTTAGTTAG
41969925 TTAAATTTAGATTAAAAACATCCCTTTTAA
1 TTAAATTTAGATTAAAAACATCCCTTTTAA
41969955 TTAAATTTAGATTAAAAACATCCCTTTTAA
1 TTAAATTTAGATTAAAAACATCCCTTTTAA
41969985 TT
1 TT
41969987 TATAGGCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (30 bp):
TTAAATTTAGATTAAAAACATCCCTTTTAA
Found at i:41970267 original size:18 final size:16
Alignment explanation
Indices: 41970231--41970269 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
41970221 TTTATATGGG
41970231 TTTTACTTTTATTTCA
1 TTTTACTTTTATTTCA
*
41970247 TTTTACTATTGTATTTTA
1 TTTTACT-TT-TATTTCA
41970265 TTTTA
1 TTTTA
41970270 ACAAGGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTACTTTTATTTCA
Found at i:41970416 original size:26 final size:26
Alignment explanation
Indices: 41970387--41970436 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
41970377 TAGGTAAATC
*
41970387 AGTATATAAAATCATCAAATCAATTT
1 AGTACATAAAATCATCAAATCAATTT
*
41970413 AGTACCTAAAATCATCAAATCAAT
1 AGTACATAAAATCATCAAATCAAT
41970437 ACTAACTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (26 bp):
AGTACATAAAATCATCAAATCAATTT
Found at i:41975087 original size:35 final size:35
Alignment explanation
Indices: 41975047--41975114 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
41975037 TAGCTCACAC
* *
41975047 TTTGATGTGCTCACA-ACTTTAGTTGAGCTCGCAGG
1 TTTGATGAGCTCACATA-TTTAGGTGAGCTCGCAGG
* *
41975082 TTTGATGAGTTCGCATATTTAGGTGAGCTCGCA
1 TTTGATGAGCTCACATATTTAGGTGAGCTCGCA
41975115 AGTGTAGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (35 bp):
TTTGATGAGCTCACATATTTAGGTGAGCTCGCAGG
Found at i:41975113 original size:18 final size:18
Alignment explanation
Indices: 41975064--41975114 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
41975054 TGCTCACAAC
* *
41975064 TTTAGTTGAGCTCGCAGG
1 TTTAGATGAGCTCGCAGA
* *
41975082 TTT-GATGAGTTCGCATA
1 TTTAGATGAGCTCGCAGA
*
41975099 TTTAGGTGAGCTCGCA
1 TTTAGATGAGCTCGCA
41975115 AGTGTAGACC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (18 bp):
TTTAGATGAGCTCGCAGA
Found at i:41975158 original size:18 final size:18
Alignment explanation
Indices: 41975124--41975161 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41975114 AAGTGTAGAC
*
41975124 CTCACATACTTGTTTGAG
1 CTCACATACTTGGTTGAG
41975142 CTCACA-ACTTGAGTTGAG
1 CTCACATACTTG-GTTGAG
41975160 CT
1 CT
41975162 TGCAACTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (18 bp):
CTCACATACTTGGTTGAG
Found at i:41979420 original size:2 final size:2
Alignment explanation
Indices: 41979415--41979446 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41979405 TTCGGCTTGA
41979415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41979447 TAGTCCCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41979990 original size:21 final size:21
Alignment explanation
Indices: 41979952--41979991 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41979942 AATCAAGATT
* **
41979952 AAAAATGTTGTATTTAGAAGG
1 AAAAATATTGTACGTAGAAGG
41979973 AAAAATATTGTACGTAGAA
1 AAAAATATTGTACGTAGAA
41979992 CACAAACAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (21 bp):
AAAAATATTGTACGTAGAAGG
Found at i:41980533 original size:12 final size:12
Alignment explanation
Indices: 41980485--41980526 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
41980475 GTCCAAATGA
*
41980485 AAGCGAGGGCCC
1 AAGCGAGGACCC
* *
41980497 AAGTGAGGAACC
1 AAGCGAGGACCC
41980509 AAGCGAGGACCC
1 AAGCGAGGACCC
41980521 AAGCGA
1 AAGCGA
41980527 AGGCCCAGCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.36, T:0.02
Consensus pattern (12 bp):
AAGCGAGGACCC
Found at i:41989286 original size:28 final size:28
Alignment explanation
Indices: 41989255--41989345 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
41989245 ATTTATACAA
*
41989255 ACTCATAAGTATGGATTCATATATGTGG
1 ACTCATAAGTATGGATTCATATATGCGG
* *
41989283 ACTCA-AAG-ATGCAGAATCATATATGCAG
1 ACTCATAAGTATG--GATTCATATATGCGG
* *
41989311 ATTCATAAGTACAGG-TTCATATATGCGG
1 ACTCATAAGTA-TGGATTCATATATGCGG
*
41989339 ATTCATA
1 ACTCATA
41989346 GATCCAGATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 39 0.76
29 4 0.08
30 1 0.02
31 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (28 bp):
ACTCATAAGTATGGATTCATATATGCGG
Found at i:41989301 original size:56 final size:56
Alignment explanation
Indices: 41989223--41989358 Score: 148
Period size: 56 Copynumber: 2.4 Consensus size: 56
41989213 AAAATCATAA
* * * *
41989223 GTGGATTCAGAGATGCAAAATCATTTATACAAACTCATAAGTA-TGGATTCATATAT
1 GTGGATTCAAAGATGCAGAATCATATATACAAACTCATAAGTACAGG-TTCATATAT
* * * *
41989279 GTGGACTCAAAGATGCAGAATCATATATGCAGATTCATAAGTACAGGTTCATATAT
1 GTGGATTCAAAGATGCAGAATCATATATACAAACTCATAAGTACAGGTTCATATAT
* * * *
41989335 GCGGATTCATAGATCCAGATTCAT
1 GTGGATTCAAAGATGCAGAATCAT
41989359 GCGTACGGAC
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
56 64 0.97
57 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (56 bp):
GTGGATTCAAAGATGCAGAATCATATATACAAACTCATAAGTACAGGTTCATATAT
Found at i:41989343 original size:14 final size:14
Alignment explanation
Indices: 41989267--41989345 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
41989257 TCATAAGTAT
*
41989267 GGATTCATATATGT
1 GGATTCATATATGC
* * *
41989281 GGACTCAAAGATGC
1 GGATTCATATATGC
* *
41989295 AGAATCATATATGC
1 GGATTCATATATGC
* *
41989309 AGATTCATA-AGTAC
1 GGATTCATATA-TGC
41989323 AGG-TTCATATATGC
1 -GGATTCATATATGC
41989337 GGATTCATA
1 GGATTCATA
41989346 GATCCAGATT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
13 3 0.06
14 44 0.90
15 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (14 bp):
GGATTCATATATGC
Found at i:41989355 original size:14 final size:14
Alignment explanation
Indices: 41989289--41989358 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 14
41989279 GTGGACTCAA
*
41989289 AGATGCAGAATCAT
1 AGATGCAGATTCAT
*
41989303 ATATGCAGATTCAT
1 AGATGCAGATTCAT
* *
41989317 A-AGTACAGGTTCAT
1 AGA-TGCAGATTCAT
* *
41989331 ATATGCGGATTCAT
1 AGATGCAGATTCAT
*
41989345 AGATCCAGATTCAT
1 AGATGCAGATTCAT
41989359 GCGTACGGAC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
13 1 0.02
14 42 0.95
15 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (14 bp):
AGATGCAGATTCAT
Found at i:41989357 original size:28 final size:28
Alignment explanation
Indices: 41989268--41989358 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
41989258 CATAAGTATG
* * * *
41989268 GATTCATATATGTGGACTCAAAGATGCA
1 GATTCATATATGCGGATTCATAGATACA
* *
41989296 GAATCATATATGCAGATTCATA-AGTACA
1 GATTCATATATGCGGATTCATAGA-TACA
* *
41989324 GGTTCATATATGCGGATTCATAGATCCA
1 GATTCATATATGCGGATTCATAGATACA
41989352 GATTCAT
1 GATTCAT
41989359 GCGTACGGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
27 1 0.02
28 48 0.96
29 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (28 bp):
GATTCATATATGCGGATTCATAGATACA
Found at i:41992774 original size:29 final size:29
Alignment explanation
Indices: 41992645--41992774 Score: 156
Period size: 29 Copynumber: 4.6 Consensus size: 29
41992635 CCTTCGAGCT
** * *
41992645 CGCACACCCAGTGCCGTAT-TTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* * * *
41992673 TGCACACATAGTG-TATATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
41992701 TGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41992730 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41992759 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
41992775 ATCTCGTCAC
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
27 3 0.03
28 30 0.34
29 55 0.62
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:41993422 original size:141 final size:142
Alignment explanation
Indices: 41993257--41993549 Score: 552
Period size: 143 Copynumber: 2.1 Consensus size: 142
41993247 TATACCCCAT
*
41993257 ATGGCCGAATGCTCATG-CACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTTT
1 ATGGCCGAATACTCATGACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTTT
41993321 GTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAGG
66 GTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAGG
*
41993386 AAGACAACATGC
131 AAAACAACATGC
41993398 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 ATGGCCGAATACTCATG-ACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
41993463 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
65 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
41993528 GAAAACAACATGC
130 GAAAACAACATGC
41993541 ATGGCCGAA
1 ATGGCCGAA
41993550 ATTTAACTCA
Statistics
Matches: 148, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
141 16 0.11
143 132 0.89
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.22
Consensus pattern (142 bp):
ATGGCCGAATACTCATGACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTTT
GTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAGG
AAAACAACATGC
Found at i:42000468 original size:29 final size:29
Alignment explanation
Indices: 42000436--42000571 Score: 157
Period size: 29 Copynumber: 4.7 Consensus size: 29
42000426 ATACCCTTCG
** * *
42000436 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
42000465 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
42000494 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
42000523 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
42000552 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
42000572 ATCTCGTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 93 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:42000563 original size:58 final size:58
Alignment explanation
Indices: 42000411--42000570 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 58
42000401 AATTTAAGCC
* *** * * ** * *
42000411 CGCACACACAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
* * * * *
42000469 TGCACACATAGTGTCATATTTTTCCAGCATGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
*
42000527 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
42000571 AATCTCGTCA
Statistics
Matches: 83, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.28
Consensus pattern (58 bp):
CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
Found at i:42001296 original size:137 final size:135
Alignment explanation
Indices: 42001054--42001338 Score: 443
Period size: 133 Copynumber: 2.1 Consensus size: 135
42001044 TATACCCCAT
*
42001054 ATGGCCGAATACTTCATTCCACACACACATAACAACAAGAACTCAGCACAAATTTCCTTTTTGTT
1 ATGGCCGAATACTTCATGCCACACACACATAACAACAAGAACTCAGCACAAATTTCCTTTTTGTT
42001119 AAACATTCGAACTCACTCATCATGCTTTCATCACAACAACATCAAAACA-TCA-CAAGG-AAACA
66 AAACATTCGAACTCACTCATCATGCTTTCAT-ACAACAACATCAAAACACTCACCAAGGAAAACA
42001181 ACATGC
130 ACATGC
42001187 ATGGCCGAATAC-TCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTT
1 ATGGCCGAATACTTCATGC-CACACACACATAACAACAAGAACTC-A--GCAC-AAATTTCCTTT
42001251 TTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAA
61 TTGTTAAACATTCGAACTCACTCA--T-CATGCTTTCAT-ACAACAACATCAAAACACTCACCAA
42001316 GGAAAACAACATGC
122 GGAAAACAACATGC
42001330 ATGGCCGAA
1 ATGGCCGAA
42001339 ATTTAACTCA
Statistics
Matches: 140, Mismatches: 1, Indels: 12
0.92 0.01 0.08
Matches are distributed among these distances:
132 5 0.04
133 37 0.26
134 1 0.01
136 4 0.03
137 35 0.25
139 1 0.01
140 29 0.21
141 3 0.02
142 5 0.04
143 20 0.14
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.22
Consensus pattern (135 bp):
ATGGCCGAATACTTCATGCCACACACACATAACAACAAGAACTCAGCACAAATTTCCTTTTTGTT
AAACATTCGAACTCACTCATCATGCTTTCATACAACAACATCAAAACACTCACCAAGGAAAACAA
CATGC
Found at i:42002101 original size:37 final size:37
Alignment explanation
Indices: 42002060--42002146 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
42002050 CCAATAGATG
* * * *
42002060 GTCTTAGCTTGAAACATTAGGATAAGTCCAGC-TATTT
1 GTCTTAGCTTGAAACATGAGGACAAGTCCAGCGGA-CT
* *
42002097 GTCTTTGTTTGAAACATGAGGACAAGTCCAGCGGACT
1 GTCTTAGCTTGAAACATGAGGACAAGTCCAGCGGACT
42002134 GTCTTAGCTTGAA
1 GTCTTAGCTTGAA
42002147 GCATAAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 40 0.98
38 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (37 bp):
GTCTTAGCTTGAAACATGAGGACAAGTCCAGCGGACT
Found at i:42010920 original size:80 final size:80
Alignment explanation
Indices: 42010836--42010984 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
42010826 TATGGTAACC
* * * *
42010836 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
42010900 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
42010916 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
42010981 CCGG
66 CCGG
42010985 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:42010926 original size:40 final size:38
Alignment explanation
Indices: 42010877--42010984 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42010867 ATCACGATTT
*
42010877 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42010917 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42010957 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42010985 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42014511 original size:58 final size:57
Alignment explanation
Indices: 42014440--42014695 Score: 246
Period size: 58 Copynumber: 4.4 Consensus size: 57
42014430 TTGTTGACGG
** * * ** *
42014440 GATTTAGGATGGACTGGTAATCCTGATATAATCCC-TCTTGAGCATATGTTACAATTAG
1 GATTTAGCCTGGACTGGTAATCCTGAT-TAAGCCCTTC-TGAGCATATATTACAAAAAA
* * * *
42014498 GATTTAGCCTGGACTAGTAATCCTAATTGAGCACTTCTGAGCATATATTACAAAAAA
1 GATTTAGCCTGGACTGGTAATCCTGATTAAGCCCTTCTGAGCATATATTACAAAAAA
* * * * **
42014555 GATTTAGCCTCGACTGGTAATCTTGATATAATCCC-TCTTGAGCATATGTTACAATTAA
1 GATTTAGCCTGGACTGGTAATCCTGAT-TAAGCCCTTC-TGAGCATATATTACAAAAAA
* * * * * *
42014613 GATTCAACCTAGACTGGTAATCCTAATTGAGCTCTTCTGAGCATATATTACAAAAAAA
1 GATTTAGCCTGGACTGGTAATCCTGATTAAGCCCTTCTGAGCATATATTAC-AAAAAA
42014671 GATTTAGCCTGGACTGGTAATCCTG
1 GATTTAGCCTGGACTGGTAATCCTG
42014696 TTATGTGTTA
Statistics
Matches: 157, Mismatches: 36, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
57 62 0.39
58 95 0.61
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (57 bp):
GATTTAGCCTGGACTGGTAATCCTGATTAAGCCCTTCTGAGCATATATTACAAAAAA
Found at i:42014642 original size:115 final size:116
Alignment explanation
Indices: 42014451--42014695 Score: 411
Period size: 115 Copynumber: 2.1 Consensus size: 116
42014441 ATTTAGGATG
* * * *
42014451 GACTGGTAATCCTGATATAATCCCTCTTGAGCATATGTTACAATTAGGATTTAGCCTGGACTAGT
1 GACTGGTAATCCTGATATAATCCCTCTTGAGCATATGTTACAATTAAGATTCAACCTAGACTAGT
42014516 AATCCTAATTGAGCACTTCTGAGCATATATTAC-AAAAAAGATTTAGCCTC
66 AATCCTAATTGAGCACTTCTGAGCATATATTACAAAAAAAGATTTAGCCTC
* *
42014566 GACTGGTAATCTTGATATAATCCCTCTTGAGCATATGTTACAATTAAGATTCAACCTAGACTGGT
1 GACTGGTAATCCTGATATAATCCCTCTTGAGCATATGTTACAATTAAGATTCAACCTAGACTAGT
* *
42014631 AATCCTAATTGAGCTCTTCTGAGCATATATTACAAAAAAAGATTTAGCCTG
66 AATCCTAATTGAGCACTTCTGAGCATATATTACAAAAAAAGATTTAGCCTC
42014682 GACTGGTAATCCTG
1 GACTGGTAATCCTG
42014696 TTATGTGTTA
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
115 91 0.76
116 29 0.24
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (116 bp):
GACTGGTAATCCTGATATAATCCCTCTTGAGCATATGTTACAATTAAGATTCAACCTAGACTAGT
AATCCTAATTGAGCACTTCTGAGCATATATTACAAAAAAAGATTTAGCCTC
Found at i:42020369 original size:164 final size:164
Alignment explanation
Indices: 42020098--42020426 Score: 523
Period size: 164 Copynumber: 2.0 Consensus size: 164
42020088 GGAAGCCCGT
* *
42020098 TCTATATTAAAACCTCTTTGCGCTTTTAATGAAAATTTAGGATTTCTTGCTCATGGTTAAGACTC
1 TCTATATTAAAACCTCTTTGCGCTCTTAATGAAAATTTAGGATTTCTTGCTCATGGTGAAGACTC
* * *
42020163 AAATCATTTTGGAAAAACGTTGATCCTACTAGATTGTTATTACACTTTAAAATAGTGTTTATTGT
66 AAATCATTTTAGAAAAACGTTGATCCTACTAGATTGTTATTACACTTTAAAACAGTGTTTATTGA
*
42020228 GGAAGCTTTCAAAATTTATTGTATAAAAGTGGTG
131 GGAAGCTTTCAAAATTTATTATATAAAAGTGGTG
*
42020262 TCTATATTAAAACCTCTTTGCGCTCTTAATGAAAATTTAGGATTTCTTGTTCATGGTGAAGACTC
1 TCTATATTAAAACCTCTTTGCGCTCTTAATGAAAATTTAGGATTTCTTGCTCATGGTGAAGACTC
* * * ** *
42020327 AAGTCGTTTTAGCAAAATTTTGATCCTATTAGATTGTTATTACACTTTAAAACAGTGTTTATTGA
66 AAATCATTTTAGAAAAACGTTGATCCTACTAGATTGTTATTACACTTTAAAACAGTGTTTATTGA
* *
42020392 GGAAGCTTTCAAAATTTGTTATATAAACGTGGTG
131 GGAAGCTTTCAAAATTTATTATATAAAAGTGGTG
42020426 T
1 T
42020427 TTTGGAAAAT
Statistics
Matches: 150, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
164 150 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (164 bp):
TCTATATTAAAACCTCTTTGCGCTCTTAATGAAAATTTAGGATTTCTTGCTCATGGTGAAGACTC
AAATCATTTTAGAAAAACGTTGATCCTACTAGATTGTTATTACACTTTAAAACAGTGTTTATTGA
GGAAGCTTTCAAAATTTATTATATAAAAGTGGTG
Found at i:42039286 original size:17 final size:17
Alignment explanation
Indices: 42039264--42039300 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42039254 ATTCAAGCCG
42039264 AAAATAAAATTTATTTT
1 AAAATAAAATTTATTTT
42039281 AAAATAAAATTTATTTT
1 AAAATAAAATTTATTTT
42039298 AAA
1 AAA
42039301 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATAAAATTTATTTT
Found at i:42048054 original size:9 final size:10
Alignment explanation
Indices: 42048021--42048078 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
42048011 AAATTTTTAA
42048021 TTTTTA-AAT
1 TTTTTATAAT
42048030 TTCTTTATATAT
1 TT-TTTATA-AT
42048042 TTTTTATAAT
1 TTTTTATAAT
**
42048052 TTTTGTGGAAGT
1 TTTT-TATAA-T
42048064 TTTTTATAAT
1 TTTTTATAAT
42048074 TTTTT
1 TTTTT
42048079 TAAAAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 2 0.05
10 16 0.40
11 13 0.32
12 9 0.22
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:42048079 original size:11 final size:11
Alignment explanation
Indices: 42048021--42048080 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
42048011 AAATTTTTAA
42048021 TTTTTA-AATT
1 TTTTTATAATT
*
42048031 TCTTTAT-ATAT
1 TTTTTATAAT-T
42048042 TTTTTATAATT
1 TTTTTATAATT
* ** *
42048053 TTTGTGGAAGT
1 TTTTTATAATT
42048064 TTTTTATAATT
1 TTTTTATAATT
42048075 TTTTTA
1 TTTTTA
42048081 AAAATATAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
10 7 0.19
11 28 0.76
12 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:42048139 original size:19 final size:19
Alignment explanation
Indices: 42048076--42048138 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 19
42048066 TTTATAATTT
42048076 TTTTAAAAATATAAATTTTAGAA
1 TTTTAAAAAT-T--ATTTT-GAA
*
42048099 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
42048117 TTTTAAAAATTATTTTG-A
1 TTTTAAAAATTATTTTGAA
42048135 TTTT
1 TTTT
42048139 TTTTTGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 16 0.43
19 12 0.32
21 1 0.03
23 8 0.22
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:42051399 original size:58 final size:58
Alignment explanation
Indices: 42051309--42051441 Score: 205
Period size: 58 Copynumber: 2.3 Consensus size: 58
42051299 TGTAGATAGA
* * *
42051309 ATTTAGCCCGGACA-GATAATTCTAATGTAAGCCCTCTTGAGCTTAGGTTACAAATTGG
1 ATTTAGCCCGGA-AGGGTGATTCTAATGTAAGCCCTCTTGAGCTTAGGTAACAAATTGG
*
42051367 ATTTAGCCTGGAAGGGTGATTCTAATGTAAGCCCTCTTGAGCTTAGGTAACAAATTGG
1 ATTTAGCCCGGAAGGGTGATTCTAATGTAAGCCCTCTTGAGCTTAGGTAACAAATTGG
*
42051425 ATTTAGCCCGGACGGGT
1 ATTTAGCCCGGAAGGGT
42051442 AATCCAAATT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 1 0.01
58 67 0.99
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (58 bp):
ATTTAGCCCGGAAGGGTGATTCTAATGTAAGCCCTCTTGAGCTTAGGTAACAAATTGG
Found at i:42054578 original size:30 final size:30
Alignment explanation
Indices: 42054520--42054579 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
42054510 CAAACTTGTT
* *
42054520 CTTGGCAAACTTAGATTTGCGGAATCATAC
1 CTTGGCAAACTTAAACTTGCGGAATCATAC
* * *
42054550 CTTGGCGAACTTAAACTTGTGGATTCATAC
1 CTTGGCAAACTTAAACTTGCGGAATCATAC
42054580 TCATTGAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (30 bp):
CTTGGCAAACTTAAACTTGCGGAATCATAC
Found at i:42054697 original size:14 final size:14
Alignment explanation
Indices: 42054678--42054783 Score: 64
Period size: 14 Copynumber: 7.6 Consensus size: 14
42054668 TCACATATGA
42054678 AGATTCATAAGTAC
1 AGATTCATAAGTAC
*
42054692 AGATTCATATA-TGC
1 AGATTCATA-AGTAC
42054706 AGATTCATAGATGT--
1 AGATTCATA-A-GTAC
* *
42054720 AGAATCATATA-TGC
1 AGATTCATA-AGTAC
*
42054734 GGATTCATAAGTAC
1 AGATTCATAAGTAC
42054748 AGATTCAT-A-TATC
1 AGATTCATAAGTA-C
42054761 TAGATTCAT-AGATAC
1 -AGATTCATAAG-TAC
42054776 AGATTCAT
1 AGATTCAT
42054784 GCTTACAGAC
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
12 3 0.04
13 3 0.04
14 63 0.85
15 2 0.03
16 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (14 bp):
AGATTCATAAGTAC
Found at i:42054709 original size:28 final size:28
Alignment explanation
Indices: 42054672--42054783 Score: 133
Period size: 28 Copynumber: 4.0 Consensus size: 28
42054662 TATGAATCAC
*
42054672 ATATGAAGATTCATAAGTACAGATTCAT
1 ATATGCAGATTCATAAGTACAGATTCAT
*
42054700 ATATGCAGATTCATAGATGT--AGAATCAT
1 ATATGCAGATTCATA-A-GTACAGATTCAT
*
42054728 ATATGCGGATTCATAAGTACAGATTCAT
1 ATATGCAGATTCATAAGTACAGATTCAT
42054756 ATAT-CTAGATTCAT-AGATACAGATTCAT
1 ATATGC-AGATTCATAAG-TACAGATTCAT
42054784 GCTTACAGAC
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.03
27 4 0.05
28 64 0.88
29 1 0.01
30 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (28 bp):
ATATGCAGATTCATAAGTACAGATTCAT
Found at i:42054732 original size:56 final size:56
Alignment explanation
Indices: 42054665--42054773 Score: 175
Period size: 56 Copynumber: 1.9 Consensus size: 56
42054655 AATCACATAT
42054665 GAATCACATATGAAGATTCATAAGTACAGATTCATATATGC-AGATTCATAGATGTA
1 GAATCACATATGAAGATTCATAAGTACAGATTCATATAT-CTAGATTCATAGATGTA
* **
42054721 GAATCATATATGCGGATTCATAAGTACAGATTCATATATCTAGATTCATAGAT
1 GAATCACATATGAAGATTCATAAGTACAGATTCATATATCTAGATTCATAGAT
42054774 ACAGATTCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
55 1 0.02
56 48 0.98
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (56 bp):
GAATCACATATGAAGATTCATAAGTACAGATTCATATATCTAGATTCATAGATGTA
Found at i:42059007 original size:39 final size:39
Alignment explanation
Indices: 42058954--42059123 Score: 250
Period size: 39 Copynumber: 4.4 Consensus size: 39
42058944 TATAATTATA
** *
42058954 CCCTGATCGCACTTACATGCCTTTGTTGTAATTCGGTAC
1 CCCTGATCGCACTTACATGCCCCTGTTGTACTTCGGTAC
* *
42058993 CCCTAATCGCACTTACATGCCCCTATTGTACTTCGGTAC
1 CCCTGATCGCACTTACATGCCCCTGTTGTACTTCGGTAC
* *
42059032 CCCTGATCACACTTACATGCCCCTGTTGTACTTCGATAC
1 CCCTGATCGCACTTACATGCCCCTGTTGTACTTCGGTAC
* *
42059071 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCAGTAC
1 CCCTGATCGCACTTACATGCCCCTGTTGTACTTCGGTAC
*
42059110 CCCTGATTGCACTT
1 CCCTGATCGCACTT
42059124 TTTTGTTTTG
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 117 1.00
ACGTcount: A:0.18, C:0.34, G:0.15, T:0.32
Consensus pattern (39 bp):
CCCTGATCGCACTTACATGCCCCTGTTGTACTTCGGTAC
Found at i:42059054 original size:20 final size:20
Alignment explanation
Indices: 42058992--42059095 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 20
42058982 TAATTCGGTA
*
42058992 CCCCTAATCGCACTTACATG
1 CCCCTGATCGCACTTACATG
* * * *
42059012 CCCCT-ATTGTACTT-CGGTA
1 CCCCTGATCGCACTTAC-ATG
*
42059031 CCCCTGATCACACTTACATG
1 CCCCTGATCGCACTTACATG
* * *
42059051 CCCCTG-TTGTACTT-CGATA
1 CCCCTGATCGCACTTAC-ATG
*
42059070 CCCCTGATCGCACTTACGTG
1 CCCCTGATCGCACTTACATG
42059090 CCCCTG
1 CCCCTG
42059096 TTGTACTTCA
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
18 2 0.03
19 26 0.43
20 31 0.51
21 2 0.03
ACGTcount: A:0.18, C:0.38, G:0.14, T:0.29
Consensus pattern (20 bp):
CCCCTGATCGCACTTACATG
Found at i:42059073 original size:19 final size:19
Alignment explanation
Indices: 42059051--42059114 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
42059041 CACTTACATG
42059051 CCCCTGTTGTACTTCGATA
1 CCCCTGTTGTACTTCGATA
* * *
42059070 CCCCTGATCGCACTTACG-TG
1 CCCCTG-TTGTACTT-CGATA
42059090 CCCCTGTTGTACTTC-AGTA
1 CCCCTGTTGTACTTCGA-TA
42059109 CCCCTG
1 CCCCTG
42059115 ATTGCACTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 19 0.54
20 13 0.37
21 2 0.06
ACGTcount: A:0.14, C:0.38, G:0.17, T:0.31
Consensus pattern (19 bp):
CCCCTGTTGTACTTCGATA
Found at i:42060832 original size:43 final size:43
Alignment explanation
Indices: 42060729--42060849 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
42060719 TAGGGTTACT
* * *
42060729 GAGATTTACATGTAAGACCATATCTGGGATATGACA-CGATAT
1 GAGACTTACATGTAAGACCATATCTGGGATATGGCATCGATAG
* * * *
42060771 GAGACTT-CGTGTAAGACCATAGCTGGGCTATTGGCATCTATAG
1 GAGACTTACATGTAAGACCATATCTGGGATA-TGGCATCGATAG
42060814 GAGA-TTACATGTAAGACCATATCTGGGATATGGCAT
1 GAGACTTACATGTAAGACCATATCTGGGATATGGCAT
42060850 TGGTACGATA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
41 20 0.30
42 18 0.27
43 28 0.42
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (43 bp):
GAGACTTACATGTAAGACCATATCTGGGATATGGCATCGATAG
Found at i:42063714 original size:43 final size:43
Alignment explanation
Indices: 42063665--42063864 Score: 366
Period size: 43 Copynumber: 4.7 Consensus size: 43
42063655 GGAAAAAAAT
*
42063665 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGTAAAAGC
1 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGC
42063708 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGC
1 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGC
42063751 GCCGCTAAAGGTCAAGGCTTTTAGCGGCG-TTGTGGGAAAAGC
1 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGC
*
42063793 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGTAAAGC
1 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGC
*
42063836 GCCGCTAAACGTCAAGGCTTTTAGCGGCG
1 GCCGCTAAAGGTCAAGGCTTTTAGCGGCG
42063865 CTTTTTTTAC
Statistics
Matches: 153, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
42 42 0.27
43 111 0.73
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGC
Found at i:42063811 original size:85 final size:86
Alignment explanation
Indices: 42063665--42063864 Score: 366
Period size: 85 Copynumber: 2.3 Consensus size: 86
42063655 GGAAAAAAAT
*
42063665 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCAAGGCTTTT
1 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTT
42063730 AGCGGCGTTTGTGGGAAAAGC
66 AGCGGCGTTTGTGGGAAAAGC
42063751 GCCGCTAAAGGTCAAGGCTTTTAGCGGCG-TTGTGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTT
1 GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTT
*
42063815 AGCGGCGTTTGTGGGTAAAGC
66 AGCGGCGTTTGTGGGAAAAGC
*
42063836 GCCGCTAAACGTCAAGGCTTTTAGCGGCG
1 GCCGCTAAAGGTCAAGGCTTTTAGCGGCG
42063865 CTTTTTTTAC
Statistics
Matches: 111, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
85 82 0.74
86 29 0.26
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (86 bp):
GCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTT
AGCGGCGTTTGTGGGAAAAGC
Found at i:42063974 original size:31 final size:31
Alignment explanation
Indices: 42063939--42064019 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
42063929 CTTCCTGCAT
* *
42063939 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * * *
42063970 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
*
42064001 TAAAAAATACAACCAAAAA
1 T--AAAATCCAACCAAAAA
42064020 TATTAATTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 26 0.65
33 14 0.35
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:42064289 original size:21 final size:21
Alignment explanation
Indices: 42064265--42064310 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
42064255 GCTCGTGCCT
*
42064265 CTGCCTCTCTCGCTGCAGCCG
1 CTGCCTCCCTCGCTGCAGCCG
* * *
42064286 CTGCCTCCCTCTCTGCTGCCT
1 CTGCCTCCCTCGCTGCAGCCG
42064307 CTGC
1 CTGC
42064311 TCTAAGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.50, G:0.20, T:0.28
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCAGCCG
Found at i:42069969 original size:9 final size:9
Alignment explanation
Indices: 42069955--42070180 Score: 143
Period size: 9 Copynumber: 24.6 Consensus size: 9
42069945 TATTTAAGTA
42069955 TTATGTAAG
1 TTATGTAAG
*
42069964 TTATGTAAT
1 TTATGTAAG
*
42069973 TTATGATATG
1 TTATG-TAAG
* * *
42069983 ATATAT-AT
1 TTATGTAAG
*
42069991 TTATGTAAA
1 TTATGTAAG
* *
42070000 TTATAT-AT
1 TTATGTAAG
*
42070008 TTATCTAAG
1 TTATGTAAG
*
42070017 TTATATAAG
1 TTATGTAAG
42070026 TTATGTAAG
1 TTATGTAAG
*
42070035 TTATGTAAA
1 TTATGTAAG
*
42070044 TTATGATATAAAA
1 TTATG---T-AAG
*
42070057 TATATTTAAG
1 T-TATGTAAG
42070067 TATTATGTAAG
1 --TTATGTAAG
42070078 TTATGTAAG
1 TTATGTAAG
* *
42070087 TTATAT-AT
1 TTATGTAAG
*
42070095 TTATCTAAG
1 TTATGTAAG
*
42070104 TTATATAAG
1 TTATGTAAG
*
42070113 TTATATAAG
1 TTATGTAAG
*
42070122 TTATGTATG
1 TTATGTAAG
*
42070131 TTATATAAG
1 TTATGTAAG
42070140 TTATGTAAG
1 TTATGTAAG
* *
42070149 TTATATATG
1 TTATGTAAG
*
42070158 TTATATAAG
1 TTATGTAAG
*
42070167 TTATGTAAA
1 TTATGTAAG
42070176 TTATG
1 TTATG
42070181 ATATCAAATA
Statistics
Matches: 171, Mismatches: 35, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
8 16 0.09
9 131 0.77
10 7 0.04
11 8 0.05
12 2 0.01
13 4 0.02
14 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:42070034 original size:18 final size:18
Alignment explanation
Indices: 42069955--42070180 Score: 161
Period size: 18 Copynumber: 12.3 Consensus size: 18
42069945 TATTTAAGTA
* *
42069955 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
42069973 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
* *
42069991 TTATGTAAATTATAT-AT
1 TTATGTAAGTTATATAAG
*
42070008 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
42070026 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
* *
42070044 TTATGATATAAAATATATTTAAG
1 TTATG---T-AAGT-TATATAAG
*
42070067 TATTATGTAAGTTATGTAAG
1 --TTATGTAAGTTATATAAG
* * *
42070087 TTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
*
42070104 TTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAG
*
42070122 TTATGTATGTTATATAAG
1 TTATGTAAGTTATATAAG
*
42070140 TTATGTAAGTTATATATG
1 TTATGTAAGTTATATAAG
* * *
42070158 TTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
42070176 TTATG
1 TTATG
42070181 ATATCAAATA
Statistics
Matches: 167, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
17 37 0.22
18 97 0.58
19 7 0.04
20 7 0.04
21 4 0.02
22 4 0.02
23 6 0.04
25 5 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:42070047 original size:27 final size:27
Alignment explanation
Indices: 42070008--42070180 Score: 159
Period size: 27 Copynumber: 6.2 Consensus size: 27
42069998 AATTATATAT
*
42070008 TTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* * *
42070035 TTATGTAAATTATGATATAAAATATATTTAAG
1 TTATGT-AAGT-T-ATAT-AAGT-TATGTAAG
* * *
42070067 TATTATGTAAGTTATGTAAGTTATAT-AT
1 --TTATGTAAGTTATATAAGTTATGTAAG
* *
42070095 TTATCTAAGTTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
*
42070122 TTATGTATGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* * *
42070149 TTATATATGTTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAGTTATGTAAG
42070176 TTATG
1 TTATG
42070181 ATATCAAATA
Statistics
Matches: 120, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
26 22 0.18
27 59 0.49
28 4 0.03
29 5 0.04
30 7 0.06
31 6 0.05
32 8 0.07
33 3 0.03
34 6 0.05
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATATAAGTTATGTAAG
Found at i:42070065 original size:114 final size:114
Alignment explanation
Indices: 42069931--42070152 Score: 313
Period size: 114 Copynumber: 1.9 Consensus size: 114
42069921 ACTAGTTATG
* * * *
42069931 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAATTTATGATATGATATAT-ATTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-ATATATAAGTTAT
* *
42069995 GTAAATTATAT-ATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
64 ATAAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
* *
42070045 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
* * *
42070110 AAGTTATATAAGTTATGTATGTTATATAAGTTATGTAAGTTAT
66 AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTAT
42070153 ATATGTTATA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
112 4 0.04
113 18 0.19
114 73 0.77
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.48
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATATATATAAGTTATAT
AAATTATATAAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
Found at i:42070305 original size:15 final size:15
Alignment explanation
Indices: 42070285--42070340 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
42070275 AAGTAGCGGG
42070285 ATTAAATAATATTTA
1 ATTAAATAATATTTA
42070300 ATTAAATAATATTT-
1 ATTAAATAATATTTA
42070314 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
42070329 ATTAAATAATAT
1 ATTAAATAATAT
42070341 ACATGTCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:42070544 original size:24 final size:24
Alignment explanation
Indices: 42070516--42070583 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
42070506 ACTTAAATGG
42070516 TAAAACGGACGATAATATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
*
42070540 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
*
42070564 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
42070584 CAATAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:42071522 original size:378 final size:370
Alignment explanation
Indices: 42070671--42071587 Score: 1694
Period size: 371 Copynumber: 2.5 Consensus size: 370
42070661 AATTGAAACA
42070671 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
*
42070736 TAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
42070801 AATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
131 AATAAGGTTGGAGAGAAGGT-AGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
42070866 GAAATTTAAAAATATTAAATATTAAAATAAAATATTATTAATATAAAAAAATAGTAATTTGAATA
195 GAAATTTAAAAATATTAAATATTAAAATAAAATATTATTAATATAAAAAAATAGTAATTTGAATA
42070931 TAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGTTATA
260 TAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGTTATA
42070996 TAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTCAAGTCTT
325 TAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTCAAGTCTT
*
42071042 TTTGAATTTTTTAAGATTCATCATATGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
42071107 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
42071172 AATAAGGTTGGAGAGAAGGT-GCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAAG
131 AATAAGGTTGGAGAGAAGGTAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAAG
42071236 AAATTTAAAAATATTAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAAATAGTAATT
196 AAATTTAAAAATATTAAATATTAAA-A-TAAAAT-----ATTATTAATATAAAAAAATAGTAATT
42071301 TGAATATAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAA
254 TGAATATAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAA
42071366 GGTTATATAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTT
319 -GTTATATAAATATTCAATAGTAAATGAGCTCGATAGAAC-TTTTTCAAGTCTT
42071420 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
42071485 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
*
42071550 AATAA-GTTGGAGAGAAAGTCAGCTATTGTTGTAATTTT
131 AATAAGGTTGGAGAGAAGGT-AGCTATTGTTGTAATTTT
42071588 AATGGACAAG
Statistics
Matches: 531, Mismatches: 4, Indels: 14
0.97 0.01 0.03
Matches are distributed among these distances:
369 69 0.13
370 1 0.00
371 154 0.29
376 91 0.17
377 52 0.10
378 147 0.28
379 17 0.03
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (370 bp):
TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
AATAAGGTTGGAGAGAAGGTAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAAG
AAATTTAAAAATATTAAATATTAAAATAAAATATTATTAATATAAAAAAATAGTAATTTGAATAT
AATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGTTATAT
AAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTCAAGTCTT
Found at i:42074728 original size:59 final size:58
Alignment explanation
Indices: 42074655--42074786 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 58
42074645 ATTTAAGCCC
* * * * *
42074655 GCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATTTTTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATA-TATTTCCAGCAT
* * **
42074714 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
42074772 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
42074787 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 26 0.41
59 36 0.57
60 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (58 bp):
GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Found at i:42074744 original size:29 final size:29
Alignment explanation
Indices: 42074704--42074786 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
42074694 TGCCGTATTT
42074704 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
42074733 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
42074762 TTTCCAGCATGCACACTTAGTGCCA
1 TTTCCAGCATGCACACTTAGTGCCA
42074787 ATCTCGTCAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:42079444 original size:13 final size:15
Alignment explanation
Indices: 42079406--42079440 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
42079396 AAATAATAAT
*
42079406 TTATATATATTTATC
1 TTATATACATTTATC
42079421 TTATATACATTTATC
1 TTATATACATTTATC
42079436 TTATA
1 TTATA
42079441 CATTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:42079883 original size:20 final size:18
Alignment explanation
Indices: 42079857--42079907 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
42079847 TTACACCCTA
42079857 AATATATATTATAA-TCTT
1 AATATATATTATAAGT-TT
*
42079875 AATATATATTAGAAGTTT
1 AATATATATTATAAGTTT
42079893 AATATATATATATAA
1 AATATATAT-TATAA
42079908 CAAGGGACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (18 bp):
AATATATATTATAAGTTT
Found at i:42080245 original size:41 final size:41
Alignment explanation
Indices: 42080196--42080467 Score: 402
Period size: 41 Copynumber: 6.6 Consensus size: 41
42080186 TTACTTTTTT
* **
42080196 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACATCGGCCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCTACCTATA
* *
42080237 GCGACGTTTTTCCAAAAGCGCCGCTAAAACATC-AGCCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCTA-CCTATA
* *
42080278 GCGGCATTTTTACAAAAGCGCCGCTAAAACCTCTACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCTACCTATA
* * *
42080319 GCGGCGTTTTTACAAAAGCGCAGCTAAAACCTCTAACTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCTACCTATA
*
42080360 GCGGCGTTTTTCCAGAAGCGCCGCTAAAACCTCTACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCTACCTATA
* *
42080401 GCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCTACCTATA
*
42080442 GCGGCATTTTTCCAAAAGCGCCGCTA
1 GCGGCGTTTTTCCAAAAGCGCCGCTA
42080468 TTGTTCTGTT
Statistics
Matches: 211, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
41 210 1.00
42 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (41 bp):
GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCTACCTATA
Found at i:42083382 original size:5 final size:6
Alignment explanation
Indices: 42083354--42083389 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
42083344 TATAATACCA
*
42083354 AAAAAGC AAAAGC AAAAAC AAAAAC AAAAAC AAAAA
1 AAAAA-C AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
42083390 AGTCATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.81, C:0.14, G:0.06, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:42092157 original size:16 final size:17
Alignment explanation
Indices: 42092118--42092162 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
42092108 ATTTTTCCAA
*
42092118 CAAGCCTGA-AAAAGTC
1 CAAGCTTGAGAAAAGTC
*
42092134 CAAACTTGAGAAAA-TC
1 CAAGCTTGAGAAAAGTC
42092150 CAAGCTTGAGAAA
1 CAAGCTTGAGAAA
42092163 TCTTAAGCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.16
Consensus pattern (17 bp):
CAAGCTTGAGAAAAGTC
Found at i:42092498 original size:16 final size:17
Alignment explanation
Indices: 42092477--42092551 Score: 50
Period size: 16 Copynumber: 4.6 Consensus size: 17
42092467 GCTATAATTT
*
42092477 TATATATAA-TAATAAA
1 TATATAAAATTAATAAA
*
42092493 TATATAAAATTAATAAT
1 TATATAAAATTAATAAA
* *
42092510 TAT-TAAAGTTTATAAA
1 TATATAAAATTAATAAA
* * *
42092526 -ATTTAAATTTAAT-GA
1 TATATAAAATTAATAAA
42092541 TAATATAAAAT
1 T-ATATAAAAT
42092552 ATATAATGAC
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
15 3 0.07
16 26 0.58
17 16 0.36
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATATAAAATTAATAAA
Found at i:42093062 original size:15 final size:17
Alignment explanation
Indices: 42093032--42093069 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
42093022 AACATATTTT
42093032 ATAGTATATAATATAAG
1 ATAGTATATAATATAAG
*
42093049 ATAGTAT-T-ATATAAT
1 ATAGTATATAATATAAG
42093064 ATAGTA
1 ATAGTA
42093070 GGACTGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 1 0.05
17 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (17 bp):
ATAGTATATAATATAAG
Found at i:42093231 original size:19 final size:18
Alignment explanation
Indices: 42093207--42093247 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
42093197 AATAATGTAA
*
42093207 TAATATATTTTAAAACTAT
1 TAATATA-TATAAAACTAT
*
42093226 TAATATATATATAACTAT
1 TAATATATATAAAACTAT
42093244 TAAT
1 TAAT
42093248 TGGTCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATATATAAAACTAT
Found at i:42100060 original size:21 final size:19
Alignment explanation
Indices: 42100004--42100061 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
42099994 TAATATCCTA
*
42100004 AAATCTTTCAATAAAAAAATT
1 AAATC-TTC-ATAAAAAAATC
*
42100025 AAATCTT-ATATAAAAATC
1 AAATCTTCATAAAAAAATC
42100043 ATAATCTATCATAAAAAAA
1 A-AATCT-TCATAAAAAAA
42100062 ACTACAATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 10 0.32
19 5 0.16
20 3 0.10
21 13 0.42
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATCTTCATAAAAAAATC
Found at i:42101097 original size:22 final size:23
Alignment explanation
Indices: 42101056--42101099 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
42101046 TTTCTATTTC
* *
42101056 TTAAAATATTATTTATTTAATTA
1 TTAAAATATAATTTAATTAATTA
42101079 TTAAAATA-AATTTAATTAATT
1 TTAAAATATAATTTAATTAATT
42101100 CACTCAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAAATATAATTTAATTAATTA
Found at i:42102410 original size:37 final size:37
Alignment explanation
Indices: 42102360--42102433 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
42102350 CAATCGTCTT
42102360 GCTCAATAAAAATGCGATGACTAATTAATTTAATTTC
1 GCTCAATAAAAATGCGATGACTAATTAATTTAATTTC
42102397 GCTCAATAAAAATGCGATGACTAATTAATTTAATTTC
1 GCTCAATAAAAATGCGATGACTAATTAATTTAATTTC
42102434 TACTTTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (37 bp):
GCTCAATAAAAATGCGATGACTAATTAATTTAATTTC
Done.