Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 79 of 120
Found at i:23727568 original size:28 final size:27
Alignment explanation
Indices: 23727511--23727578 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
23727501 TTTAAAAAAA
* *
23727511 TTTATAATTTTTTAAAATATATATATT
1 TTTAGAATTTTTTAAAATATATATAAT
*
23727538 TTTAGAATTTTTTATAAATAT-TTTGAAT
1 TTTAGAATTTTTTA-AAATATATAT-AAT
*
23727566 TTTTGAATTTTTT
1 TTTAGAATTTTTT
23727579 TGTAACTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTAGAATTTTTTAAAATATATATAAT
Found at i:23729034 original size:9 final size:9
Alignment explanation
Indices: 23729020--23729078 Score: 100
Period size: 9 Copynumber: 6.6 Consensus size: 9
23729010 TTTGGTTAAA
23729020 AATTACCCG
1 AATTACCCG
23729029 AATTACCCG
1 AATTACCCG
23729038 AATTACCCG
1 AATTACCCG
*
23729047 AATTAACCG
1 AATTACCCG
23729056 AATTACCCG
1 AATTACCCG
*
23729065 AATTAACCG
1 AATTACCCG
23729074 AATTA
1 AATTA
23729079 ATCAAATTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:23729058 original size:27 final size:27
Alignment explanation
Indices: 23729020--23729089 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
23729010 TTTGGTTAAA
* *
23729020 AATTACCCGAATTACCCGAATTACCCG
1 AATTAACCGAATTACCCGAATTAACCG
23729047 AATTAACCGAATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
* *
23729074 AATTAATCAAATTACC
1 AATTAACCGAATTACC
23729090 GAAAAATACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTAACCG
Found at i:23729079 original size:9 final size:9
Alignment explanation
Indices: 23729020--23729092 Score: 85
Period size: 9 Copynumber: 8.2 Consensus size: 9
23729010 TTTGGTTAAA
*
23729020 AATTACCCG
1 AATTAACCG
*
23729029 AATTACCCG
1 AATTAACCG
*
23729038 AATTACCCG
1 AATTAACCG
23729047 AATTAACCG
1 AATTAACCG
*
23729056 AATTACCCG
1 AATTAACCG
23729065 AATTAACCG
1 AATTAACCG
* *
23729074 AATTAATCA
1 AATTAACCG
23729083 AATT-ACCG
1 AATTAACCG
23729091 AA
1 AA
23729093 AAATACCCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
8 4 0.07
9 53 0.93
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:23738018 original size:39 final size:39
Alignment explanation
Indices: 23737969--23738048 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
23737959 TTTCTAAGTA
23737969 TAAATTCTATTTTTCAGGAAAATCAATTTTATCGATTTC
1 TAAATTCTATTTTTCAGGAAAATCAATTTTATCGATTTC
23738008 TAAATTCTATTTTTCAGGAAAATCAATTTTATCGATTTC
1 TAAATTCTATTTTTCAGGAAAATCAATTTTATCGATTTC
23738047 TA
1 TA
23738049 TTGAGAGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (39 bp):
TAAATTCTATTTTTCAGGAAAATCAATTTTATCGATTTC
Found at i:23743225 original size:14 final size:14
Alignment explanation
Indices: 23743191--23743225 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
23743181 TTTAAAAAAT
23743191 ATATTTTTACATAA
1 ATATTTTTACATAA
*
23743205 GTATTTTTACATAA
1 ATATTTTTACATAA
23743219 AT-TTTTT
1 ATATTTTT
23743226 CATCTAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (14 bp):
ATATTTTTACATAA
Found at i:23747941 original size:18 final size:18
Alignment explanation
Indices: 23747918--23747960 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
23747908 AGGGTTAGTG
23747918 GGCCCAAGAGGAGCATTC
1 GGCCCAAGAGGAGCATTC
23747936 GGCCCAAGAGGAGCATTC
1 GGCCCAAGAGGAGCATTC
23747954 GGCCCAA
1 GGCCCAA
23747961 TATTAGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.33, T:0.09
Consensus pattern (18 bp):
GGCCCAAGAGGAGCATTC
Found at i:23748148 original size:21 final size:21
Alignment explanation
Indices: 23748124--23748164 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23748114 TATACCCATC
23748124 AGCACACA-CATTTTGACCAGA
1 AGCACA-ATCATTTTGACCAGA
*
23748145 AGCACAATTATTTTGACCAG
1 AGCACAATCATTTTGACCAG
23748165 CCCCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (21 bp):
AGCACAATCATTTTGACCAGA
Found at i:23753990 original size:19 final size:20
Alignment explanation
Indices: 23753953--23753994 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
23753943 AAAAAACTTT
23753953 CAAAATATAATTTTATTAAA
1 CAAAATATAATTTTATTAAA
23753973 CAAAA-ATAATATTT-TTAAA
1 CAAAATATAAT-TTTATTAAA
23753992 CAA
1 CAA
23753995 TAAGTGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAAATATAATTTTATTAAA
Found at i:23754406 original size:11 final size:11
Alignment explanation
Indices: 23754390--23754424 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
23754380 GTCAAATTTT
23754390 CTCTCAATCTC
1 CTCTCAATCTC
*
23754401 CTCTCAATTTC
1 CTCTCAATCTC
*
23754412 CTCTCAATGTC
1 CTCTCAATCTC
23754423 CT
1 CT
23754425 TCCAAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.17, C:0.40, G:0.03, T:0.40
Consensus pattern (11 bp):
CTCTCAATCTC
Found at i:23754415 original size:22 final size:22
Alignment explanation
Indices: 23754382--23754440 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
23754372 AATCCTCTGT
23754382 CAAATTTTCTCTCAATCTCC-TC
1 CAAA-TTTCTCTCAATCTCCTTC
*
23754404 TC-AATTTCCTCTCAATGTCCTTC
1 -CAAATTT-CTCTCAATCTCCTTC
23754427 CAAATTTCTCTCAA
1 CAAATTTCTCTCAA
23754441 ATTCATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.09
22 21 0.66
23 8 0.25
ACGTcount: A:0.24, C:0.34, G:0.02, T:0.41
Consensus pattern (22 bp):
CAAATTTCTCTCAATCTCCTTC
Found at i:23754501 original size:51 final size:51
Alignment explanation
Indices: 23754402--23754501 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
23754392 CTCAATCTCC
* *
23754402 TCTCAATTTCCTCTCAATGTCCTTCCAAATTTCTCTCAAATTCATATTTAA
1 TCTCAATTACCTCTCAATGTCCTTCCAAATTTCTCTCAAATCCATATTTAA
* ** * *
23754453 TCTCAATTAGCTCTCAAAT-TCCTTTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTACCTCTC-AATGTCCTTCCAAATTTCTCTCAAATCCATATTT
23754502 TTAAATAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 38 0.93
52 3 0.07
ACGTcount: A:0.27, C:0.26, G:0.02, T:0.45
Consensus pattern (51 bp):
TCTCAATTACCTCTCAATGTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:23757484 original size:16 final size:17
Alignment explanation
Indices: 23757445--23757491 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
23757435 TCATTTTATA
*
23757445 TATG-TTATTTTAAAAT
1 TATGTTTATTTTCAAAT
*
23757461 TTTGTTTATTTTCAAAT
1 TATGTTTATTTTCAAAT
*
23757478 TAT-TTTAATTTCAA
1 TATGTTTATTTTCAA
23757492 TTTTCTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (17 bp):
TATGTTTATTTTCAAAT
Found at i:23759841 original size:16 final size:15
Alignment explanation
Indices: 23759820--23759852 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
23759810 AATTTATTAA
23759820 AAATTTATAAATTTAT
1 AAATTTAT-AATTTAT
23759836 AAATTTATAATTTAT
1 AAATTTATAATTTAT
23759851 AA
1 AA
23759853 TTAAATGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTATAATTTAT
Found at i:23759854 original size:7 final size:8
Alignment explanation
Indices: 23759820--23759852 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
23759810 AATTTATTAA
23759820 AAATTTAT
1 AAATTTAT
23759828 AAATTTAT
1 AAATTTAT
23759836 AAATTTAT
1 AAATTTAT
23759844 -AATTTAT
1 AAATTTAT
23759851 AA
1 AA
23759853 TTAAATGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAATTTAT
Found at i:23759974 original size:22 final size:22
Alignment explanation
Indices: 23759913--23760143 Score: 228
Period size: 22 Copynumber: 10.6 Consensus size: 22
23759903 TAACCCTAAT
*
23759913 CCTAACCCTT-AACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
23759934 CCT-AACTCTTAAA-TTAAAAAC
1 CCTAAAC-CTTAAACTTAAAAAC
*
23759955 GCT-AACCTTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* *
23759976 CCCAAACCTTAAACCTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
*
23759998 CCTAAACCCTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
*
23760020 TCTAAACAC-TAAACTTAAAAAC
1 CCTAAAC-CTTAAACTTAAAAAC
*
23760042 CCTAAAACC-TAAACCTAAAAAAC
1 CCT-AAACCTTAAA-CTTAAAAAC
* * *
23760065 TCTAAACCCTAAACCTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
23760087 CAC-AAACAC-TAAACTT-AAAAC
1 C-CTAAAC-CTTAAACTTAAAAAC
*
23760108 CCTTAAACCCTAAACTTAAAAAC
1 CC-TAAACCTTAAACTTAAAAAC
*
23760131 CCTAAACCATAAA
1 CCTAAACCTTAAA
23760144 ACCTTAACTT
Statistics
Matches: 179, Mismatches: 17, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
20 9 0.05
21 35 0.20
22 107 0.60
23 28 0.16
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.19
Consensus pattern (22 bp):
CCTAAACCTTAAACTTAAAAAC
Found at i:23760130 original size:15 final size:15
Alignment explanation
Indices: 23760112--23760164 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
23760102 TAAAACCCTT
23760112 AAACCCTAAACTTAA
1 AAACCCTAAACTTAA
*
23760127 AAACCCTAAAC-CATA
1 AAACCCTAAACTTA-A
* *
23760142 AAA-CCTTAACTTTA
1 AAACCCTAAACTTAA
23760156 AAACCCTAA
1 AAACCCTAA
23760165 CCCTTAAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
AAACCCTAAACTTAA
Found at i:23763637 original size:126 final size:126
Alignment explanation
Indices: 23763348--23763690 Score: 356
Period size: 126 Copynumber: 2.7 Consensus size: 126
23763338 CCCAAACATG
* * *
23763348 CTACTGTAGCAAAAGCGCGTCCACGTGGGTGCGATTTCACAAATTTTTCTCATAAAGCA-TCTTG
1 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATTCTTG
* * * *
23763412 GTAGAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAGGAC
66 CTAGAAGCAATTTTATACTATTTGCTCAGAAACATCAACTCAAAATAATTTCTTCCAAGAC
* * * *
23763473 CAACTGTAGCCAAAGCACGTCCACGA-GGGCGCGATTTCAGAAATTCTTCTCA-AATAGCATTC-
1 CTACTGTAGCAAAAGCGCGTCCAC-ATGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATTCT
* ** * * * ** *
23763535 TGCTTGAAGCGTTTTTTTATTCTATTTGCTTAGAAACATCAATTTGAAATAATTT-TTTCAAGAC
64 TGCTAGAAGC--AATTTTATACTATTTGCTCAGAAACATCAACTCAAAATAATTTCTTCCAAGAC
* * *
23763599 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGGTTTCACATATTCTTCTCATAAAGCA-TCCTG
1 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATTCTTG
* * ** *
23763663 GTATAAGTGATTTTATACTATTTTCTCA
66 CTAGAAGCAATTTTATACTATTTGCTCA
23763691 AGGAGAAACT
Statistics
Matches: 175, Mismatches: 35, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
124 17 0.10
125 59 0.34
126 63 0.36
127 36 0.21
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATTCTTG
CTAGAAGCAATTTTATACTATTTGCTCAGAAACATCAACTCAAAATAATTTCTTCCAAGAC
Found at i:23766996 original size:27 final size:27
Alignment explanation
Indices: 23766963--23767019 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
23766953 AAGGAAAGGA
23766963 ATGGTAAGTGTTCAAAGGAACTATGTC
1 ATGGTAAGTGTTCAAAGGAACTATGTC
*
23766990 ATGGTAAGTGTTCAAATGAACTATGTC
1 ATGGTAAGTGTTCAAAGGAACTATGTC
23767017 ATG
1 ATG
23767020 AAGCTCTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (27 bp):
ATGGTAAGTGTTCAAAGGAACTATGTC
Found at i:23770674 original size:13 final size:14
Alignment explanation
Indices: 23770658--23770687 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23770648 AAAGCAATTG
23770658 AAAAA-GCATAACA
1 AAAAATGCATAACA
23770671 AAAAATGCATAACA
1 AAAAATGCATAACA
23770685 AAA
1 AAA
23770688 TAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATGCATAACA
Found at i:23770727 original size:32 final size:32
Alignment explanation
Indices: 23770678--23770756 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
23770668 ACAAAAAATG
*
23770678 CATAACAAA-ATA-AAATATATAAATCCAAAA
1 CATAAAAAATATATAAATATATAAATCCAAAA
23770708 CATAAAAAATATATAAATATATAAATCCAAAA
1 CATAAAAAATATATAAATATATAAATCCAAAA
* *
23770740 AATATAAAAATAAATAA
1 CATA-AAAAATATATAA
23770757 TAAAAATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 8 0.19
31 3 0.07
32 21 0.49
33 11 0.26
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (32 bp):
CATAAAAAATATATAAATATATAAATCCAAAA
Found at i:23770761 original size:13 final size:13
Alignment explanation
Indices: 23770739--23770770 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
23770729 TAAATCCAAA
23770739 AAAT-ATAAAAAT
1 AAATAATAAAAAT
23770751 AAATAATAAAAAT
1 AAATAATAAAAAT
23770764 AAA-AATA
1 AAATAATA
23770771 GGGTTGGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAATAAAAAT
Found at i:23771150 original size:37 final size:36
Alignment explanation
Indices: 23771104--23771183 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
23771094 AATTCATATT
* * *
23771104 CCCC-AAGCCCAAATATTTTTACTTTACCCTATTTCC
1 CCCCAAAGCCCAAA-ACTTTTACGTCACCCTATTTCC
*
23771140 CCCCAAAGCCCAAACCTTTTACGTCACCCTATTTCC
1 CCCCAAAGCCCAAAACTTTTACGTCACCCTATTTCC
*
23771176 CCCTAAAG
1 CCCCAAAG
23771184 GCCACCTGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
36 29 0.76
37 9 0.24
ACGTcount: A:0.26, C:0.40, G:0.05, T:0.29
Consensus pattern (36 bp):
CCCCAAAGCCCAAAACTTTTACGTCACCCTATTTCC
Found at i:23771392 original size:44 final size:42
Alignment explanation
Indices: 23771291--23771392 Score: 116
Period size: 44 Copynumber: 2.4 Consensus size: 42
23771281 AATGTCAAAT
*
23771291 TTCTTCTTCTCCTTCAAAAAAAACCCCTAAATTAAACCCCAA
1 TTCTTCTTCTTCTTCAAAAAAAACCCCTAAATTAAACCCCAA
* * * *
23771333 ATCAATTATTC-TCTTCTTAAAAAAACCCCTAAATTAAACTCCCCA
1 TTC--TTCTTCTTCTTC-AAAAAAAACCCCTAAATTAAAC-CCCAA
23771378 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTCTTC
23771393 CTCATCAGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.04
43 9 0.19
44 31 0.65
45 6 0.12
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.35
Consensus pattern (42 bp):
TTCTTCTTCTTCTTCAAAAAAAACCCCTAAATTAAACCCCAA
Found at i:23778877 original size:14 final size:14
Alignment explanation
Indices: 23778860--23778913 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
23778850 AAAAATAATA
23778860 ATTGAGAATTGAGG
1 ATTGAGAATTGAGG
* *
23778874 ATTGAAAATTGAGA
1 ATTGAGAATTGAGG
* * *
23778888 ATTTAGGATTGAAG
1 ATTGAGAATTGAGG
*
23778902 ATTGAGTATTGA
1 ATTGAGAATTGA
23778914 ATTAAAAATA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (14 bp):
ATTGAGAATTGAGG
Found at i:23778883 original size:21 final size:21
Alignment explanation
Indices: 23778859--23778913 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
23778849 TAAAAATAAT
23778859 AATTGAGAATTGAGGATTGAA
1 AATTGAGAATTGAGGATTGAA
*
23778880 AATTGAGAATTTAGGATTGAA
1 AATTGAGAATTGAGGATTGAA
* *
23778901 GATTGAGTATTGA
1 AATTGAGAATTGA
23778914 ATTAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (21 bp):
AATTGAGAATTGAGGATTGAA
Found at i:23789159 original size:41 final size:41
Alignment explanation
Indices: 23789101--23789435 Score: 526
Period size: 41 Copynumber: 8.1 Consensus size: 41
23789091 CTTAATTTAA
* * *
23789101 CAGATTCACCGACACTTAACCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
23789143 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
23789184 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
23789225 CAGATCAACGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * * *
23789266 CAGATCACCTGCACTTAGCCTGTTAGGTTTATAACCTAATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
23789307 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
23789348 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGACT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
23789389 CAGATCACGGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
23789430 CAGATC
1 CAGATC
23789436 GCATAAGATA
Statistics
Matches: 274, Mismatches: 19, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
41 270 0.99
42 4 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:23797102 original size:41 final size:41
Alignment explanation
Indices: 23797044--23797378 Score: 535
Period size: 41 Copynumber: 8.1 Consensus size: 41
23797034 CTTAATTTAA
* *
23797044 CAGATTCACCGGCACTTAACCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
23797086 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
23797127 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
23797168 CAGATCAACGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * * *
23797209 CAGATCACCTGCACTTAGCCTGTTAGGTTTATAACCTAATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
23797250 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
23797291 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGACT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
23797332 CAGATCACGGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
23797373 CAGATC
1 CAGATC
23797379 GCATAAGATA
Statistics
Matches: 275, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
41 271 0.99
42 4 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:23802496 original size:49 final size:49
Alignment explanation
Indices: 23802413--23802515 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
23802403 GTACATGTAT
* *
23802413 GCTCATACGAGCTTTGAATCGATATGCTCTTACGAGCTGTAAT-T-GGTAA
1 GCTCATACGAGC-TTGAATCGATAAGCTCATACGAGCTG-AATATCGGTAA
*
23802462 GCTCATACGAGC-TGAATAACGGTAAGCTCATACGAGCTGAATATCGGTAA
1 GCTCATACGAGCTTGAAT--CGATAAGCTCATACGAGCTGAATATCGGTAA
23802512 GCTC
1 GCTC
23802516 TCTCGAGTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
47 5 0.11
48 3 0.06
49 30 0.64
50 9 0.19
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (49 bp):
GCTCATACGAGCTTGAATCGATAAGCTCATACGAGCTGAATATCGGTAA
Found at i:23802522 original size:25 final size:25
Alignment explanation
Indices: 23802413--23802515 Score: 115
Period size: 25 Copynumber: 4.2 Consensus size: 25
23802403 GTACATGTAT
* *
23802413 GCTCATACGAGCTTTG-A-ATCGATAT
1 GCTCATACGAGC--TGAATATCGGTAA
*
23802438 GCTCTTACGAGCTGTAAT-T-GGTAA
1 GCTCATACGAGCTG-AATATCGGTAA
*
23802462 GCTCATACGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATATCGGTAA
23802487 GCTCATACGAGCTGAATATCGGTAA
1 GCTCATACGAGCTGAATATCGGTAA
23802512 GCTC
1 GCTC
23802516 TCTCGAGTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
23 5 0.07
24 16 0.24
25 46 0.69
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTGAATATCGGTAA
Found at i:23806724 original size:12 final size:12
Alignment explanation
Indices: 23806707--23806732 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23806697 GGTATAAGCA
23806707 ATCGTGGAGGAT
1 ATCGTGGAGGAT
23806719 ATCGTGGAGGAT
1 ATCGTGGAGGAT
23806731 AT
1 AT
23806733 AGAGGTGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.38, T:0.27
Consensus pattern (12 bp):
ATCGTGGAGGAT
Found at i:23809017 original size:21 final size:21
Alignment explanation
Indices: 23808992--23809031 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
23808982 GAAGATAAAG
*
23808992 TATATCGCTTGAAGAAAGCTT
1 TATATCGATTGAAGAAAGCTT
* *
23809013 TATATGGATTGAAGCAAGC
1 TATATCGATTGAAGAAAGC
23809032 CTCAAGAGCA
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:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TATATCGATTGAAGAAAGCTT
Found at i:23816914 original size:2 final size:2
Alignment explanation
Indices: 23816907--23816934 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23816897 TATTTAACTT
23816907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23816935 AATTTCCGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23818253 original size:11 final size:11
Alignment explanation
Indices: 23818237--23818275 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
23818227 TAGCAATGCC
23818237 TATTTTAATCA
1 TATTTTAATCA
*
23818248 TATTTTAATTA
1 TATTTTAATCA
23818259 TATTTTAATCA
1 TATTTTAATCA
23818270 TATTTT
1 TATTTT
23818276 TTTAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTAATCA
Found at i:23820720 original size:3 final size:3
Alignment explanation
Indices: 23820714--23820740 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
23820704 ATAATAATAA
23820714 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
23820741 GCTTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:23826670 original size:22 final size:20
Alignment explanation
Indices: 23826636--23826676 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
23826626 AATTGTTGAT
*
23826636 AAATTGATGAATTAGGCTTG
1 AAATTGATGAATTAAGCTTG
23826656 AAATTGATAGAAATTAAGCTT
1 AAATTGAT-G-AATTAAGCTT
23826677 AGATTATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (20 bp):
AAATTGATGAATTAAGCTTG
Found at i:23828026 original size:43 final size:43
Alignment explanation
Indices: 23827978--23828302 Score: 445
Period size: 43 Copynumber: 7.6 Consensus size: 43
23827968 TTTTAGAAAT
* *
23827978 AAACGCCACTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
23828021 AAACGCCGCTATAGATCAGGACCTTTAGTGGTGCTTTTTCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
23828064 AAACGCTGCTATAGATCAGGACCTTTAGTGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* *
23828106 AAACGCCGCTATAGCTCAGGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
23828149 AAATGCCGCTATAGCTCAGGACCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * * *
23828192 AAACGCCGCTATAGATTAAGACCTTTAACGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * * *
23828235 AAACGACACTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
*
23828278 AAACGCCGCTATAGATCAAGACCTT
1 AAACGCCGCTATAGATCAGGACCTT
23828303 AGTATTAAAT
Statistics
Matches: 252, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 37 0.15
43 215 0.85
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
Found at i:23829560 original size:192 final size:191
Alignment explanation
Indices: 23829310--23829667 Score: 481
Period size: 192 Copynumber: 1.9 Consensus size: 191
23829300 GGCTATTATG
* * * *
23829310 TTCATTAACATCATAAAAAATCATCAATTACATCCTAATAACAATTTCAACTCCAAAGTT-GACT
1 TTCATTAACATCATAAAAAAACATCAATTACATCCTAATAACAATTCCAACCCCAAAGTTCAACT
* * * * ** *
23829374 AAAGAAGCTTTGCAGGATATGA-AAACACAAGTGCATTTCCATTCAAGTAAATTGTTGTGTTGTA
66 AAA-AAGCATTGCAGGATA-CACAAACACAAATGCATTTCCATTAAAGT-AATAATAGTGTTGTA
* *
23829438 ATCACAAAG-TTCAAATGAAAACCATGACTTGAACCCATAAAAAATTCAATTTAGTCTATTGTA
128 ATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATAAAAAATTCAATTTAGTCTATTGTA
*
23829501 TTCATTAACATCA-ACATAAAAACATCAATTACTTCCTAATAACAATTCCAACCCCAAAGTTCAA
1 TTCATTAACATCATA-A-AAAAACATCAATTACATCCTAATAACAATTCCAACCCCAAAGTTCAA
* ** *
23829565 TTAAAAAGCATTGCAGGATACACAAATGCAAATGCATTTCCATTAAAGTAATAATAGTGTTTTAA
64 CTAAAAAGCATTGCAGGATACACAAACACAAATGCATTTCCATTAAAGTAATAATAGTGTTGTAA
23829630 TCACAAAGCTCCAAATGAAAACCATGACTTAAACCCAT
129 TCACAAAGCTCCAAATGAAAACCATGACTTAAACCCAT
23829668 TATAGATTAC
Statistics
Matches: 144, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
190 1 0.01
191 35 0.24
192 103 0.72
193 5 0.03
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.28
Consensus pattern (191 bp):
TTCATTAACATCATAAAAAAACATCAATTACATCCTAATAACAATTCCAACCCCAAAGTTCAACT
AAAAAGCATTGCAGGATACACAAACACAAATGCATTTCCATTAAAGTAATAATAGTGTTGTAATC
ACAAAGCTCCAAATGAAAACCATGACTTAAACCCATAAAAAATTCAATTTAGTCTATTGTA
Found at i:23836907 original size:9 final size:9
Alignment explanation
Indices: 23836893--23836931 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
23836883 TATAAAATTT
*
23836893 ATTATTCGA
1 ATTATTTGA
23836902 ATTATTTGA
1 ATTATTTGA
23836911 ATTATTTGA
1 ATTATTTGA
*
23836920 GTTATTTGA
1 ATTATTTGA
23836929 ATT
1 ATT
23836932 GCAATATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (9 bp):
ATTATTTGA
Found at i:23839493 original size:15 final size:15
Alignment explanation
Indices: 23839459--23839487 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23839449 AAATTTATAA
23839459 GAAAAGAATAAAATC
1 GAAAAGAATAAAATC
23839474 GAAAAGAATAAAAT
1 GAAAAGAATAAAAT
23839488 TTAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (15 bp):
GAAAAGAATAAAATC
Found at i:23839525 original size:14 final size:15
Alignment explanation
Indices: 23839506--23839536 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
23839496 TAATTGAGGA
23839506 TTGAAGATT-AAAAT
1 TTGAAGATTGAAAAT
23839520 TTGAAGATTGAAAAT
1 TTGAAGATTGAAAAT
23839535 TT
1 TT
23839537 AGGAAGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (15 bp):
TTGAAGATTGAAAAT
Found at i:23846588 original size:18 final size:18
Alignment explanation
Indices: 23846551--23846584 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23846541 AATAAAGGGG
23846551 AAGAAGAAAAAGAAAATA
1 AAGAAGAAAAAGAAAATA
*
23846569 AAGAAGTAAAA-AAAAT
1 AAGAAGAAAAAGAAAAT
23846585 TAAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AAGAAGAAAAAGAAAATA
Found at i:23853906 original size:23 final size:24
Alignment explanation
Indices: 23853858--23853919 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
23853848 ACATATCTAA
23853858 AATAATATTAAATTTTGCTTCAAT
1 AATAATATTAAATTTTGCTTCAAT
* *
23853882 AATAATATTAACTTTT-TTTCAAT
1 AATAATATTAAATTTTGCTTCAAT
23853905 AATAATATTAAATTT
1 AATAATATTAAATTT
23853920 CTGATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (24 bp):
AATAATATTAAATTTTGCTTCAAT
Found at i:23857355 original size:14 final size:14
Alignment explanation
Indices: 23857336--23857362 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23857326 ACTATATTCC
23857336 CACTTTTACTGGTT
1 CACTTTTACTGGTT
23857350 CACTTTTACTGGT
1 CACTTTTACTGGT
23857363 CCATGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (14 bp):
CACTTTTACTGGTT
Found at i:23860198 original size:64 final size:64
Alignment explanation
Indices: 23860089--23860229 Score: 237
Period size: 64 Copynumber: 2.2 Consensus size: 64
23860079 GACCAATGGC
*
23860089 ACGCTCTATAATTGACACATGTGCACTAAAATAAGTTAATTTATTAATCCTAAACATATTATAT
1 ACGCTCTATAATTGACACATGTGCACTAAAATAAGTTAATGTATTAATCCTAAACATATTATAT
* ** *
23860153 ACGCTCTATAATTGACACATGTGCACTGAAATGGGTTGATGTATTAATCCTAAACATATTATAT
1 ACGCTCTATAATTGACACATGTGCACTAAAATAAGTTAATGTATTAATCCTAAACATATTATAT
23860217 ACGCTCTATAATT
1 ACGCTCTATAATT
23860230 AGTCAAATTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 72 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (64 bp):
ACGCTCTATAATTGACACATGTGCACTAAAATAAGTTAATGTATTAATCCTAAACATATTATAT
Found at i:23865550 original size:23 final size:23
Alignment explanation
Indices: 23865520--23865563 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
23865510 GCCTGCTTTG
23865520 GTATGTATGCACTTTAGTCATAT
1 GTATGTATGCACTTTAGTCATAT
23865543 GTATGTATGCACTTTAGTCAT
1 GTATGTATGCACTTTAGTCAT
23865564 GGTAACTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (23 bp):
GTATGTATGCACTTTAGTCATAT
Found at i:23868354 original size:18 final size:18
Alignment explanation
Indices: 23868333--23868375 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
23868323 ATAATTTAAA
23868333 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
23868351 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
23868369 ATGTAAA
1 ATATAAA
23868376 AATAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:23868876 original size:2 final size:2
Alignment explanation
Indices: 23868869--23868898 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23868859 AAGTGAAACC
23868869 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
23868899 ATGGTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23877121 original size:9 final size:9
Alignment explanation
Indices: 23877107--23877131 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23877097 TTTCACATTA
23877107 TGTGAACTT
1 TGTGAACTT
23877116 TGTGAACTT
1 TGTGAACTT
23877125 TGTGAAC
1 TGTGAAC
23877132 ATGCTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (9 bp):
TGTGAACTT
Found at i:23891079 original size:5 final size:5
Alignment explanation
Indices: 23891069--23891108 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
23891059 TTATTTTTAA
23891069 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
23891109 TAGGCTAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:23891239 original size:37 final size:38
Alignment explanation
Indices: 23891164--23891239 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
23891154 ATAATATTAT
* *
23891164 AATTTTAGTATTAAAAATATATTAAATTATTTATATTTAG
1 AATTTTAG-ATTAAAAATATA-TAAATTATTAAAATTTAG
23891204 AATTTTA-ATTAAAACATATA-AAATTATTAAAATTTA
1 AATTTTAGATTAAAA-ATATATAAATTATTAAAATTTA
23891240 AGTTAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 14 0.42
38 7 0.21
39 5 0.15
40 7 0.21
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (38 bp):
AATTTTAGATTAAAAATATATAAATTATTAAAATTTAG
Found at i:23891371 original size:10 final size:10
Alignment explanation
Indices: 23891327--23891379 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
23891317 ATCAACTATT
23891327 TTTTATTCAA
1 TTTTATTCAA
**
23891337 TTTTAAACAAA
1 TTTTATTC-AA
*
23891348 TTATTTTGTCAA
1 TT-TTAT-TCAA
23891360 TTTTATTCAA
1 TTTTATTCAA
23891370 TTTTATTCAA
1 TTTTATTCAA
23891380 AACATTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 20 0.59
11 7 0.21
12 6 0.18
13 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (10 bp):
TTTTATTCAA
Found at i:23893249 original size:9 final size:9
Alignment explanation
Indices: 23893227--23893274 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
23893217 AACATATCAA
*
23893227 AAATTAACT
1 AAATTAACC
*
23893236 GAATTAACC
1 AAATTAACC
*
23893245 AAATTAATC
1 AAATTAACC
23893254 AAATTAACC
1 AAATTAACC
* *
23893263 GAATTAAAC
1 AAATTAACC
23893272 AAA
1 AAA
23893275 CAATCCTACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.25
Consensus pattern (9 bp):
AAATTAACC
Found at i:23893250 original size:18 final size:18
Alignment explanation
Indices: 23893237--23893274 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23893227 AAATTAACTG
23893237 AATTAACCAAATTAATCA
1 AATTAACCAAATTAATCA
* *
23893255 AATTAACCGAATTAAACA
1 AATTAACCAAATTAATCA
23893273 AA
1 AA
23893275 CAATCCTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTAACCAAATTAATCA
Found at i:23893321 original size:45 final size:45
Alignment explanation
Indices: 23893270--23893357 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
23893260 ACCGAATTAA
*
23893270 ACAAACAATCCTACCGTAATACCTACATTAAATGCACATAATTCT
1 ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATTCT
*
23893315 ACAAACAATCCTATCATAATACCTACATTAAATGCACATAATT
1 ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATT
23893358 AATTTACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.44, C:0.25, G:0.03, T:0.27
Consensus pattern (45 bp):
ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATTCT
Found at i:23901318 original size:30 final size:29
Alignment explanation
Indices: 23901272--23901350 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
23901262 AATTATTTAT
* * *
23901272 ATTTAGAATTTTAATTAAAACATATAAAA
1 ATTTAAAATTTAAATTAAAACAGATAAAA
*
23901301 TTATTAAAATTTAAATTAAAAACAGATAAAA
1 AT-TTAAAATTTAAATT-AAAACAGATAAAA
*
23901332 ATTTAAAA-ATAAATTAAAA
1 ATTTAAAATTTAAATTAAAA
23901351 TTTAAACTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 4 0.10
29 7 0.17
30 18 0.43
31 13 0.31
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (29 bp):
ATTTAAAATTTAAATTAAAACAGATAAAA
Found at i:23901339 original size:18 final size:18
Alignment explanation
Indices: 23901316--23901356 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
23901306 AAAATTTAAA
*
23901316 TTAAAAACAGATAAAAAT
1 TTAAAAACAAATAAAAAT
* *
23901334 TTAAAAATAAATTAAAAT
1 TTAAAAACAAATAAAAAT
23901352 TTAAA
1 TTAAA
23901357 CTTAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TTAAAAACAAATAAAAAT
Found at i:23902911 original size:49 final size:44
Alignment explanation
Indices: 23902852--23902943 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
23902842 GGTGTATCGA
*
23902852 TACCGAAAAATAATTTTAAAATTAAAATTAAATTTTTATTATTTATTTG
1 TACCAAAAAATAATTTT-AAA-T-AAATT--ATTTTTATTATTTATTTG
*
23902901 TACCAAAAAATAATTTTAAATATATTATTTTTATTATTTATTT
1 TACCAAAAAATAATTTTAAATAAATTATTTTTATTATTTATTT
23902944 TGGATTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
44 17 0.41
46 4 0.10
47 1 0.02
48 3 0.07
49 16 0.39
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (44 bp):
TACCAAAAAATAATTTTAAATAAATTATTTTTATTATTTATTTG
Found at i:23914964 original size:13 final size:13
Alignment explanation
Indices: 23914931--23914965 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
23914921 TATTTAAATG
* *
23914931 TTATTATCATTTA
1 TTATTATTATTAA
23914944 TTATTATTATTAA
1 TTATTATTATTAA
23914957 TTATTATTA
1 TTATTATTA
23914966 GTTTTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:23915148 original size:35 final size:33
Alignment explanation
Indices: 23915075--23915155 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 33
23915065 TATACCCATG
* * * *
23915075 TATAT-TTTTATATATGCGTACACATATATGTT
1 TATATATTTTATTTATGCATACACATACATGTC
*
23915107 TCTATATTTTATTTATGCATACCTACATACATGTC
1 TATATATTTTATTTATGCATA-C-ACATACATGTC
*
23915142 TATATATTTCATTT
1 TATATATTTTATTT
23915156 TCATAATGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 4 0.10
33 13 0.33
34 1 0.03
35 21 0.54
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.51
Consensus pattern (33 bp):
TATATATTTTATTTATGCATACACATACATGTC
Found at i:23915233 original size:33 final size:34
Alignment explanation
Indices: 23915173--23915237 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
23915163 GTGTATATAT
23915173 ATATATATATTCTTATATATTCCTTATATTTTCA
1 ATATATATATTCTTATATATTCCTTATATTTTCA
* * *
23915207 ATATATATTTTGTT-TATATTCTTTATATTTT
1 ATATATATATTCTTATATATTCCTTATATTTT
23915238 ACGATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (34 bp):
ATATATATATTCTTATATATTCCTTATATTTTCA
Found at i:23927740 original size:45 final size:45
Alignment explanation
Indices: 23927672--23927949 Score: 373
Period size: 45 Copynumber: 6.2 Consensus size: 45
23927662 CTCAGAGAAC
* * * *
23927672 AGATCGAATATAGCAGATATTGTCTTCCTGAATTGGCAGGGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
23927717 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * *
23927762 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGACAACAAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
23927807 AGATCAAAGATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGGAGT
1 AGATCGAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGT
*
23927852 AGATCGAAGATAGCA-AGTCTTGTCTTTCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
23927897 AGA-CTGAAGATAACAGATCTTGTCTTCCTGTACTAGCAGCGAAGC
1 AGATC-GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
23927942 AGATCGAA
1 AGATCGAA
23927950 AAACAACAAG
Statistics
Matches: 207, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
44 2 0.01
45 203 0.98
46 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (45 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
Found at i:23928008 original size:135 final size:135
Alignment explanation
Indices: 23927714--23928010 Score: 307
Period size: 135 Copynumber: 2.2 Consensus size: 135
23927704 TTGGCAGGGA
* * * * *
23927714 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAGA
1 AGTAGATCCAAAACAGCAAATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAACAGA
* * * * * * * * *
23927779 TCTTGTCTTCCTGTATTGACAACAAAGTAGATCAAAGATAGCAAGTCTTGTCTTCCTGTATTGGC
66 TCTTGTCTTCCTGTATAGACAACAAAGCAGATCAAAAACAACAAGTCTTATCTCCCTGTAGTCGC
23927844 AGCGG
131 AGCGG
* * * * * *
23927849 AGTAGATCGAAGATAGCAAGTCTTGTCTTTCTGTATTGGCAGCGAAGTAGA-CTGAAGATAACAG
1 AGTAGATCCAAAACAGCAAATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC-GAAGATAACAG
* *
23927913 ATCTTGTCTTCCTGTACTAG-CAGCGAAGCAGATCGAAAAACAACAAGTCTTATCTCCCTG-ACG
65 ATCTTGTCTTCCTGTA-TAGACAACAAAGCAGATC-AAAAACAACAAGTCTTATCTCCCTGTA-G
*
23927976 TCGCAGTGG
127 TCGCAGCGG
23927985 AGTAGA-CCAAAACCA-CAAATCTTGTC
1 AGTAGATCCAAAA-CAGCAAATCTTGTC
23928011 CCCCTGAAAT
Statistics
Matches: 136, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
134 1 0.01
135 99 0.73
136 36 0.26
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (135 bp):
AGTAGATCCAAAACAGCAAATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAACAGA
TCTTGTCTTCCTGTATAGACAACAAAGCAGATCAAAAACAACAAGTCTTATCTCCCTGTAGTCGC
AGCGG
Found at i:23929868 original size:39 final size:39
Alignment explanation
Indices: 23929782--23929869 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
23929772 AAAAAACGTT
* **
23929782 GCTAAAGATCGAGCATTAGCGGCGGTTTTAAAAAAATGCC
1 GCTAAAAAT-GAGCATTAGCGGCGGTTTTAAAAAAACACC
* *
23929822 GCTAAAAATGAGCATTAGCGGCGTTTTGTAAAAAAGCACC
1 GCTAAAAATGAGCATTAGCGGCGGTTT-TAAAAAAACACC
*
23929862 GCAAAAAA
1 GCTAAAAA
23929870 CCTAAGCCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 17 0.41
40 24 0.59
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (39 bp):
GCTAAAAATGAGCATTAGCGGCGGTTTTAAAAAAACACC
Found at i:23929869 original size:40 final size:39
Alignment explanation
Indices: 23929792--23929869 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
23929782 GCTAAAGATC
** *
23929792 GAGCATTAGCGGCGGTTTTAAAAAAATGCCGCTAAAAAT
1 GAGCATTAGCGGCGGTTTTAAAAAAACACCGCAAAAAAT
* *
23929831 GAGCATTAGCGGCGTTTTGTAAAAAAGCACCGCAAAAAA
1 GAGCATTAGCGGCGGTTT-TAAAAAAACACCGCAAAAAA
23929870 CCTAAGCCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 17 0.52
40 16 0.48
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (39 bp):
GAGCATTAGCGGCGGTTTTAAAAAAACACCGCAAAAAAT
Found at i:23930410 original size:14 final size:15
Alignment explanation
Indices: 23930382--23930414 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
23930372 AAGGTTTATA
23930382 GATTATGGAATTAGG
1 GATTATGGAATTAGG
23930397 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
23930411 GATT
1 GATT
23930415 TTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:23930580 original size:7 final size:7
Alignment explanation
Indices: 23930568--23930633 Score: 87
Period size: 7 Copynumber: 9.4 Consensus size: 7
23930558 TAAATAATGT
23930568 TTAGGGG
1 TTAGGGG
23930575 TTAGGGG
1 TTAGGGG
23930582 TTAGGGG
1 TTAGGGG
*
23930589 TTGGGGG
1 TTAGGGG
*
23930596 TTGGGGG
1 TTAGGGG
**
23930603 TTAGTAG
1 TTAGGGG
23930610 TTAGGGG
1 TTAGGGG
23930617 TTAGGGG
1 TTAGGGG
*
23930624 TTAGAGG
1 TTAGGGG
23930631 TTA
1 TTA
23930634 AGAGTCAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.15, C:0.00, G:0.53, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:23932241 original size:6 final size:6
Alignment explanation
Indices: 23932225--23932257 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
23932215 TGTGGTTTGA
23932225 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
23932258 TTTGAGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:23934864 original size:31 final size:31
Alignment explanation
Indices: 23934829--23934898 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
23934819 CAGCATAACT
23934829 TATTGCTGAAGTTATACAGCCACGTTGTTTG
1 TATTGCTGAAGTTATACAGCCACGTTGTTTG
23934860 TATTGCTGAAGTTATACAGCCACGTTGTTTG
1 TATTGCTGAAGTTATACAGCCACGTTGTTTG
*
23934891 CA-TGCTGA
1 TATTGCTGA
23934899 TTACCAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (31 bp):
TATTGCTGAAGTTATACAGCCACGTTGTTTG
Found at i:23935447 original size:43 final size:42
Alignment explanation
Indices: 23935339--23935470 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 42
23935329 TTAATTTTTT
* * * *
23935339 TAAAAGTCATG-TTTTTAGCGGCGTTTGTGAAAAAGCGTCGC
1 TAAAGGTCATGCTCTTTAGCGGCGTTTGTGTAAAAGCGCCGC
* ** *
23935380 TAAAGGTCATTCTCCATAGTGGCGTTTGTGGTAAAAGCGCCGC
1 TAAAGGTCATGCTCTTTAGCGGCGTTTGT-GTAAAAGCGCCGC
* * * *
23935423 TAAAGGTCCTAGC-CTTTAGCGGCGTTTTTATAAAAGTGCCGC
1 TAAAGGTCAT-GCTCTTTAGCGGCGTTTGTGTAAAAGCGCCGC
23935465 TAAAGG
1 TAAAGG
23935471 CCAAAAAAAC
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
41 9 0.12
42 30 0.42
43 32 0.44
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
TAAAGGTCATGCTCTTTAGCGGCGTTTGTGTAAAAGCGCCGC
Found at i:23935669 original size:18 final size:18
Alignment explanation
Indices: 23935646--23935681 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
23935636 ATATACTTAC
23935646 ATAATTTTTTCATGTATA
1 ATAATTTTTTCATGTATA
*
23935664 ATAATTTTTTTATGTATA
1 ATAATTTTTTCATGTATA
23935682 CATGCATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (18 bp):
ATAATTTTTTCATGTATA
Found at i:23935726 original size:2 final size:2
Alignment explanation
Indices: 23935719--23935773 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
23935709 ATTTTAGATG
23935719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23935761 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
23935774 CTTTATATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23940683 original size:21 final size:21
Alignment explanation
Indices: 23940658--23940699 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
23940648 TTACTGGACA
*
23940658 TTTTATTTATATATTTTTTAT
1 TTTTATATATATATTTTTTAT
*
23940679 TTTTATATATATGTTTTTTAT
1 TTTTATATATATATTTTTTAT
23940700 ATTATGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATATATATATTTTTTAT
Found at i:23940705 original size:14 final size:14
Alignment explanation
Indices: 23940678--23940716 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
23940668 ATATTTTTTA
*
23940678 TTTTTATATATATGT
1 TTTTTATAT-TATGG
23940693 TTTTTATATTATGG
1 TTTTTATATTATGG
*
23940707 TTTTAATATT
1 TTTTTATATT
23940717 TGGGCTCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (14 bp):
TTTTTATATTATGG
Found at i:23941038 original size:17 final size:18
Alignment explanation
Indices: 23941012--23941045 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23941002 AAATTTGAGA
23941012 ATAAAAAAATAA-AAATC
1 ATAAAAAAATAAGAAATC
*
23941029 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
23941046 AGAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATC
Found at i:23951326 original size:2 final size:2
Alignment explanation
Indices: 23951319--23951348 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23951309 CATATGCATA
23951319 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
23951349 TCATCTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23951892 original size:31 final size:31
Alignment explanation
Indices: 23951857--23951932 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
23951847 CTCCTCGAAT
23951857 GCATATAACCGAATATTGATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
* *
23951888 GCATATAACCGAGTATTTATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
* *
23951919 GAATATACCCGAAT
1 GCATATAACCGAAT
23951933 GTATGTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (31 bp):
GCATATAACCGAATATTGATATACATCAAGA
Found at i:23953402 original size:18 final size:18
Alignment explanation
Indices: 23953379--23953414 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
23953369 TTAGTCTCTC
23953379 AAAATTTTAATTTCGCAA
1 AAAATTTTAATTTCGCAA
23953397 AAAATTTTAATTTCGCAA
1 AAAATTTTAATTTCGCAA
23953415 TTTAGCCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
AAAATTTTAATTTCGCAA
Found at i:23957535 original size:19 final size:19
Alignment explanation
Indices: 23957492--23957536 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
23957482 AGCCAGGCCT
* *
23957492 CCTCCTCGCGCATGTTGCG
1 CCTCCGCGCGCATGTAGCG
23957511 --TCCGCGCGCATGTAGCG
1 CCTCCGCGCGCATGTAGCG
23957528 CCTCCGCGC
1 CCTCCGCGC
23957537 CAAATCCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 15 0.68
19 7 0.32
ACGTcount: A:0.07, C:0.44, G:0.29, T:0.20
Consensus pattern (19 bp):
CCTCCGCGCGCATGTAGCG
Found at i:23958896 original size:39 final size:41
Alignment explanation
Indices: 23958755--23958907 Score: 138
Period size: 40 Copynumber: 3.8 Consensus size: 41
23958745 AGCGGCACTT
* * * *
23958755 TTAGCGGCG-TTTGGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTT-TACAAAAAGCACCGCTAAAAATCAAGCA
* *
23958796 TTAGCGGCGCTTTTACAAAAA-CACCGCTAAAGATCGAGCA
1 TTAGCGGCGCTTTTACAAAAAGCACCGCTAAAAATCAAGCA
* ** *
23958836 TTAGCGACGCATTTT--GGAAAGCGCCGCTAAAAAT-AAGCA
1 TTAGCGGCGC-TTTTACAAAAAGCACCGCTAAAAATCAAGCA
* *
23958875 TTAGCGGCG-TTTTTCAAAAAGCACCGCAAAAAA
1 TTAGCGGCGCTTTTACAAAAAGCACCGCTAAAAA
23958908 CCTAAGCCCA
Statistics
Matches: 91, Mismatches: 16, Indels: 12
0.76 0.13 0.10
Matches are distributed among these distances:
37 4 0.04
39 29 0.32
40 35 0.38
41 20 0.22
42 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTTACAAAAAGCACCGCTAAAAATCAAGCA
Found at i:23958923 original size:79 final size:80
Alignment explanation
Indices: 23958777--23958924 Score: 176
Period size: 79 Copynumber: 1.9 Consensus size: 80
23958767 GGACAAAAAA
* * * * ** *
23958777 CGCCACTAAAAATCAAGCATTAGCGGCGCTTTTACAAAAACACCGCTAAAGATCGAGCATTAGCG
1 CGCCACTAAAAATCAAGCATTAGCGGCGCTTTTACAAAAACACCGCAAAAAACCAAGCACCAACG
23958842 ACGCATTTTGGAAAG
66 ACGCATTTTGGAAAG
* *
23958857 CGCCGCTAAAAAT-AAGCATTAGCGGCG-TTTTTCAAAAAGCACCGCAAAAAACCTAAGC-CCAA
1 CGCCACTAAAAATCAAGCATTAGCGGCGCTTTTACAAAAA-CACCGCAAAAAACC-AAGCACCAA
23958919 CGACGC
64 CGACGC
23958925 CGTTTTCAGC
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
78 10 0.18
79 32 0.56
80 15 0.26
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (80 bp):
CGCCACTAAAAATCAAGCATTAGCGGCGCTTTTACAAAAACACCGCAAAAAACCAAGCACCAACG
ACGCATTTTGGAAAG
Found at i:23959018 original size:41 final size:41
Alignment explanation
Indices: 23958956--23959183 Score: 307
Period size: 41 Copynumber: 5.6 Consensus size: 41
23958946 CTATAGTGGT
** * *
23958956 GTTTTTGAAAAAGCGTTGCTAATGCTCCTACCTTTAGCAGC
1 GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
* * *
23958997 GTTTTTGAACAAGCGCAGCTAATGCTCGTACCGTTAGCAGC
1 GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
*
23959038 GTTTTTGAACAAGCGCAG-TGAATGCTCGTACCTTTAGCGGC
1 GTTTTTGAAAAAGCGCAGCT-AATGCTCGTACCTTTAGCGGC
* *
23959079 GTTTTTGAAAAGGCGCCGCTAATGCTCGTACCTTTAGCGGC
1 GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
* * *
23959120 GTTTTTGAAGAAGCGCCGCTAATGCTTGTACCTTTAGCGGC
1 GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
23959161 GTTTTTGAAAAAGCGTC-GCTAAT
1 GTTTTTGAAAAAGCG-CAGCTAAT
23959184 AATAAAATCT
Statistics
Matches: 170, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 167 0.98
42 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (41 bp):
GTTTTTGAAAAAGCGCAGCTAATGCTCGTACCTTTAGCGGC
Found at i:23960137 original size:7 final size:7
Alignment explanation
Indices: 23960125--23960180 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
23960115 TCTTGAGTTC
23960125 AGGGTTT
1 AGGGTTT
23960132 AGGGTTT
1 AGGGTTT
23960139 A-GGTTT
1 AGGGTTT
*
23960145 AGGGCTT
1 AGGGTTT
*
23960152 AGGGATT
1 AGGGTTT
23960159 -GGAGTTT
1 AGG-GTTT
*
23960166 AAGGTTT
1 AGGGTTT
*
23960173 AGAGTTT
1 AGGGTTT
23960180 A
1 A
23960181 TATTTTAGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
6 8 0.20
7 31 0.77
8 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.38, T:0.39
Consensus pattern (7 bp):
AGGGTTT
Found at i:23960594 original size:20 final size:20
Alignment explanation
Indices: 23960572--23960633 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
23960562 TTTGTGATTT
23960572 AAAATTTTAAAATGAATTTTA
1 AAAATTTTAAAATG-ATTTTA
*
23960593 AAAGATTTT-AAAT-TTTTTA
1 AAA-ATTTTAAAATGATTTTA
*
23960612 AAAATTTTAAAAAGATTTTA
1 AAAATTTTAAAATGATTTTA
23960632 AA
1 AA
23960634 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 7 0.20
21 7 0.20
22 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATTTTAAAATGATTTTA
Found at i:23960599 original size:29 final size:29
Alignment explanation
Indices: 23960569--23960639 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
23960559 TTTTTTGTGA
23960569 TTTAAAATTTTAAAATGAATTTT-AAAAGAT
1 TTTAAAATTTTAAAA--AATTTTAAAAAGAT
* *
23960599 TTTAAATTTTTTAAAAATTTTAAAAAGAT
1 TTTAAAATTTTAAAAAATTTTAAAAAGAT
*
23960628 TTTAAACTTTTA
1 TTTAAAATTTTA
23960640 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.17
29 17 0.47
30 13 0.36
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (29 bp):
TTTAAAATTTTAAAAAATTTTAAAAAGAT
Found at i:23960619 original size:9 final size:9
Alignment explanation
Indices: 23960572--23960624 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
23960562 TTTGTGATTT
23960572 AAAATTTTAA
1 AAAATTTT-A
23960582 AATGAATTTTA
1 AA--AATTTTA
23960593 AAAGATTTTA
1 AAA-ATTTTA
**
23960603 AATTTTTTA
1 AAAATTTTA
23960612 AAAATTTTA
1 AAAATTTTA
23960621 AAAA
1 AAAA
23960625 GATTTTAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
9 17 0.47
10 10 0.28
11 3 0.08
12 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (9 bp):
AAAATTTTA
Found at i:23961070 original size:164 final size:163
Alignment explanation
Indices: 23960798--23961139 Score: 614
Period size: 164 Copynumber: 2.1 Consensus size: 163
23960788 TAACAGATTT
23960798 AAAATGAAATAATTTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGACGT
1 AAAATGAAATAA-TTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGACGT
*
23960863 TTTTATAAAAAACGCGACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAG
65 TTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAG
* *
23960928 ATTTTTAGCATAGAAAAACGGT-GTCGTTTTGTAC
130 ATTTTTAGCATAGAAAAAC-ATCGTCATTTTGTAC
*
23960962 AAAAATGAAATAATTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGGCGT
1 -AAAATGAAATAATTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGACGT
23961027 TTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAG
65 TTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAG
23961092 ATTTTTAGCATAGAAAAACATCGTCATTTTGTAC
130 ATTTTTAGCATAGAAAAACATCGTCATTTTGTAC
23961126 AAAATGAAATAATT
1 AAAATGAAATAATT
23961140 AAAAACGCCG
Statistics
Matches: 172, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
163 15 0.09
164 145 0.84
165 12 0.07
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (163 bp):
AAAATGAAATAATTTTTGCGGCGTTTTTATGAAAAATGCCGCAAAAGGTAAGCAATAGCGACGTT
TTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAATAATTTTTAGCAGAAAAAATATAAGA
TTTTTAGCATAGAAAAACATCGTCATTTTGTAC
Found at i:23963183 original size:12 final size:12
Alignment explanation
Indices: 23963166--23963217 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
23963156 TAGCAATTTC
23963166 ATTATTTAGT-TT
1 ATTA-TTAGTATT
*
23963178 ATTATTATTATT
1 ATTATTAGTATT
*
23963190 ATTATTAGTGTT
1 ATTATTAGTATT
* *
23963202 ATTATCATTATT
1 ATTATTAGTATT
23963214 ATTA
1 ATTA
23963218 CTATTATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 4 0.12
12 29 0.88
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (12 bp):
ATTATTAGTATT
Found at i:23963184 original size:3 final size:3
Alignment explanation
Indices: 23963176--23963236 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
23963166 ATTATTTAGT
* * * *
23963176 TTA TTA TTA TTA TTA TTA TTA GTG TTA TTA TCA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
23963224 TTAA CTA TTA TTA
1 TT-A TTA TTA TTA
23963237 ATTTTATTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:23969257 original size:87 final size:87
Alignment explanation
Indices: 23969111--23969388 Score: 470
Period size: 87 Copynumber: 3.2 Consensus size: 87
23969101 AGATCAGTGA
* *
23969111 AGATCGAAAACAATGTCTTGCCTCCATCTGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
23969176 CTTCCTGCGTTAACAACGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
*
23969198 AGATCGAAAACAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
23969263 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
23969285 AGATCGAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGC
1 AGATCGAAAACAAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
23969349 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
23969371 ATATCGAAATC-AAGTCTT
1 AGATCGAAAACAAAGTCTT
23969389 ATCTCCCTGA
Statistics
Matches: 182, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
85 6 0.03
86 43 0.24
87 133 0.73
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (87 bp):
AGATCGAAAACAAAGTCTTGCCTCCATCAGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:23969348 original size:43 final size:42
Alignment explanation
Indices: 23969126--23969350 Score: 111
Period size: 42 Copynumber: 5.2 Consensus size: 42
23969116 GAAAACAATG
*
23969126 TCTTGCCTCCATCTGTTGTAGTGGAGCTGGTTAAAGATAGCAGA
1 TCTTGCCTCCATC-GTTGCAGTGGAGCTGGTTAAAGA-AGCAGA
* ** * * * ** *
23969170 TCTTGCCTTCC-TGCGTTAACAACGAAGCAGATCGAA-AA-CAAA
1 TCTTGCC-TCCAT-CGTT-GCAGTGGAGCTGGTTAAAGAAGCAGA
*
23969212 GTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGA
1 -TCTTGCCTCCATC-GTTGCAGTGGAGCTGGTTAAAGA-AGCAGA
* * * * * ** *
23969257 TCTTGCCTTCC-TGCGTTAACAGCGAAGCAGATCGAA-AA-CAAA
1 TCTTGCC-TCCAT-CGTT-GCAGTGGAGCTGGTTAAAGAAGCAGA
*
23969299 GCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGAAGCAGA
1 -TCTTGCCTCCATC-GTTGCAGTGGAGCTGGTTAAAGAAGCAGA
23969343 TCTTGCCT
1 TCTTGCCT
23969351 TCCTGCGTTA
Statistics
Matches: 125, Mismatches: 39, Indels: 35
0.63 0.20 0.18
Matches are distributed among these distances:
42 34 0.27
43 33 0.26
44 28 0.22
45 30 0.24
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (42 bp):
TCTTGCCTCCATCGTTGCAGTGGAGCTGGTTAAAGAAGCAGA
Found at i:23969486 original size:44 final size:44
Alignment explanation
Indices: 23969385--23969721 Score: 215
Period size: 44 Copynumber: 7.7 Consensus size: 44
23969375 CGAAATCAAG
* ** **
23969385 TCTTATCTCCCTG-AGATTACAGCGGAGCAGA-TCGAATACACTA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATACAGGA
* * * *
23969428 TCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGGA
* * * ***
23969472 TCTTATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCAT-CAGG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGGA
* * * ** *
23969513 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCA-GA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-TACAGGA
* * * **
23969559 TCTTATCTCCCTGAGGTTACAGTGGAACAGATT-GAAGCCAGAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG-GA
* ** * **
23969603 TCTTATCTCCCTG-AGATTACAGCGGAGCAGA-TCGAAGACACTA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATACAGGA
* * *
23969646 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGGA
* * *
23969690 TCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGAT
23969722 CGCATCAGGT
Statistics
Matches: 229, Mismatches: 51, Indels: 27
0.75 0.17 0.09
Matches are distributed among these distances:
41 29 0.13
42 5 0.02
43 57 0.25
44 106 0.46
45 2 0.01
46 30 0.13
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGGA
Found at i:23969722 original size:87 final size:88
Alignment explanation
Indices: 23969513--23969723 Score: 214
Period size: 87 Copynumber: 2.4 Consensus size: 88
23969503 TCGCATCAGG
* * * *
23969513 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCGAAGAA--TCAGATCCTATCTCCCTGAAGTTA
* **
23969578 CAGTGGAACAGATTGAAGCCAGAGA
64 CAGTGGAACAGATTAAAGAAAGAGA
* * * *
23969603 TCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAG-A-CACTATCCTATCTCCCTGAAGTTA
1 TCTTATCTCTCTGAAG-TTACAGTGGAGTAGATCGAAGAATCA-GATCCTATCTCCCTGAAGTTA
* * *
23969665 CAGTGGAGCGGATTAAAATAAAG-GA
64 CAGTGGAACAGATT-AAAGAAAGAGA
*
23969690 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
1 TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCG
23969724 CATCAGGTCT
Statistics
Matches: 99, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
86 2 0.02
87 59 0.60
88 6 0.06
89 2 0.02
90 30 0.30
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTATCTCTCTGAAGTTACAGTGGAGTAGATCGAAGAATCAGATCCTATCTCCCTGAAGTTACA
GTGGAACAGATTAAAGAAAGAGA
Found at i:23969763 original size:218 final size:218
Alignment explanation
Indices: 23969385--23969788 Score: 765
Period size: 218 Copynumber: 1.9 Consensus size: 218
23969375 CGAAATCAAG
*
23969385 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAATACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
23969450 TAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTC
66 TAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTC
23969515 TTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACA
131 TTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACA
23969580 GTGGAACAGATTGAAGCCAGAGA
196 GTGGAACAGATTGAAGCCAGAGA
23969603 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
*
23969668 TGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTC
66 TAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTC
*
23969733 TTATCTC-CTTGAGGTTACAGTTGAGTAGACCGAAGAATTTCAGATCTTATCTCCCT
131 TTATCTCTC-TGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCT
23969789 AAGCAGTAGT
Statistics
Matches: 182, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
217 1 0.01
218 181 0.99
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (218 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
TAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTC
TTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACA
GTGGAACAGATTGAAGCCAGAGA
Found at i:23969821 original size:40 final size:40
Alignment explanation
Indices: 23969777--23970134 Score: 452
Period size: 40 Copynumber: 8.8 Consensus size: 40
23969767 GAATTTCAGA
*
23969777 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
23969817 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*
23969857 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
* **
23969897 TCTTATCTCCCCAAGCAAAAGTGGAGCAGATCGCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
23969937 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*
23969977 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAAGAAATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC----G-CATCAAG
* * * *
23970021 TCCTATCTTCCTAAGCAGTAGTGGAGTAGGA-CAAAGCTTGC-AG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCA-GATC---GCAT-CAAG
* * * * * *
23970064 ATTTTATCTCCCTAAGTAGTAATAGAGCAAATCACATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
23970105 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
23970135 CAGAACTAAT
Statistics
Matches: 277, Mismatches: 31, Indels: 20
0.84 0.09 0.06
Matches are distributed among these distances:
39 1 0.00
40 207 0.75
41 4 0.01
43 5 0.02
44 57 0.21
45 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
Found at i:23972801 original size:113 final size:109
Alignment explanation
Indices: 23972518--23972829 Score: 437
Period size: 108 Copynumber: 2.8 Consensus size: 109
23972508 TTTTTAATTG
* * *
23972518 AGGCAATATTTAGCGTTTGGAAATTTGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * *
23972583 CGTTCAACAAAATAGCTAAATGTCC-TTTCAAAATTTTAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATA
* * *
23972626 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACATGCCCTAAGGTGTTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
23972691 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAAAAATTTCGAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTT---AAAAATTTCAAAATA
*
23972738 AGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
* * *
23972803 TCATTTAACCAAATAGCCAAATATCCT
65 TCGTTCAACCAAATAGCTAAATATCCT
23972830 CTTGAATTTC
Statistics
Matches: 179, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
108 81 0.45
109 3 0.02
112 29 0.16
113 66 0.37
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTCAAAATA
Found at i:23973643 original size:15 final size:15
Alignment explanation
Indices: 23973625--23973653 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23973615 AGCTTGTATT
23973625 ATTCAGGTAATCACG
1 ATTCAGGTAATCACG
23973640 ATTCAGGTAATCAC
1 ATTCAGGTAATCAC
23973654 TATAATGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (15 bp):
ATTCAGGTAATCACG
Found at i:23975536 original size:20 final size:20
Alignment explanation
Indices: 23975513--23975552 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
23975503 GTAGCAGGTG
23975513 CTTGCTATA-AGCAGCAAAGT
1 CTTG-TATAGAGCAGCAAAGT
23975533 CTTGTATATGAGCAGCAAAG
1 CTTGTATA-GAGCAGCAAAG
23975553 GATATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 10 0.56
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (20 bp):
CTTGTATAGAGCAGCAAAGT
Found at i:23975589 original size:16 final size:16
Alignment explanation
Indices: 23975568--23975602 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
23975558 TCAAAAGGTA
*
23975568 TTGCCTTTGTTATATT
1 TTGCCTTTGTTATAAT
23975584 TTGCCTTTGTTATAAT
1 TTGCCTTTGTTATAAT
23975600 TTG
1 TTG
23975603 TCAGTGGAAA
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:0.14, C:0.11, G:0.14, T:0.60
Consensus pattern (16 bp):
TTGCCTTTGTTATAAT
Found at i:23977217 original size:86 final size:86
Alignment explanation
Indices: 23976924--23977221 Score: 345
Period size: 86 Copynumber: 3.5 Consensus size: 86
23976914 ATGATATGTT
* * * * * * *
23976924 TTTAGCGGCATTT-TGGCAAGAAGCACCGCTAAAGGT-TTGTTCTATAGCGGCGTTTTTGAGAAA
1 TTTAGCGGCGTTTGTGACAA-AAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGAG-GA
* *
23976987 AAACGCTGCTAAAGGTCAC-GTTC
64 AAACGCCGCTAAAGGTC-CTGGTC
* * *
23977010 TTTAGCGGCGTTTGTAACAAAAGCGCCGCTAAAGGCCATAGTCTATAGCGGCGTTTGTG-GGAAA
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGAGGAAA
*
23977074 AGCGCCGCTAAAGG-CCATGGTA
66 A-CGCCGCTAAAGGTCC-TGGTC
* * *
23977096 TATAGCGGTGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTATAGTGGCGTTTGTGAGGAAA
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGAGGAAA
23977161 ACGCCGCTAAAGGTCCTGGTC
66 ACGCCGCTAAAGGTCCTGGTC
** *
23977182 TTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCATG
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG
23977222 ACCTTTAGCG
Statistics
Matches: 180, Mismatches: 25, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
84 1 0.01
85 5 0.03
86 144 0.80
87 30 0.17
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGAGGAAA
ACGCCGCTAAAGGTCCTGGTC
Found at i:23977232 original size:43 final size:43
Alignment explanation
Indices: 23976926--23977221 Score: 310
Period size: 43 Copynumber: 6.9 Consensus size: 43
23976916 GATATGTTTT
* * * * *
23976926 TAGCGGCATTT-TGGCAAGAAGCACCGCTAAAGGT-TTGTTCTA
1 TAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGGTCATGGTCTA
* * * * * * *
23976968 TAGCGGCGTTTTTGAGAAAAAACGCTGCTAAAGGTCACGTTCTT
1 TAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGGTCATGGTCTA
*** * *
23977012 TAGCGGCGTTTGTAACAAAAGCGCCGCTAAAGGCCATAGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
23977055 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGCCATGGTATA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* **
23977098 TAGCGGTGTTTGTGACAAAAGCGCCGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
23977141 TAGTGGCGTTTGTGAGGAAAA-CGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGGTCATGGTCTA
*
23977184 TAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCATG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATG
23977222 ACCTTTAGCG
Statistics
Matches: 211, Mismatches: 38, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
42 16 0.08
43 171 0.81
44 24 0.11
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
Found at i:23992028 original size:14 final size:14
Alignment explanation
Indices: 23992007--23992040 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
23991997 AATATAAAAT
23992007 TAAA-TTGAAGAAA
1 TAAAGTTGAAGAAA
23992020 TAAAGTTGAAGAAA
1 TAAAGTTGAAGAAA
23992034 TAAAGTT
1 TAAAGTT
23992041 AGCCTCGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (14 bp):
TAAAGTTGAAGAAA
Found at i:23992598 original size:41 final size:40
Alignment explanation
Indices: 23992553--23992648 Score: 120
Period size: 41 Copynumber: 2.4 Consensus size: 40
23992543 AATTTAACCG
* * * *
23992553 ATGAGACACTGGGTGTTAATTTATTACTTTGAATTTATTCA
1 ATGAGACACTGGGTGTCAATTTAGTACTTCGAA-TTATCCA
* *
23992594 ATGAGATACTGGGTGTCAATTTAGTACTTCGAATTATCCG
1 ATGAGACACTGGGTGTCAATTTAGTACTTCGAATTATCCA
*
23992634 ATGAGGCACTGGGTG
1 ATGAGACACTGGGTG
23992649 CCAAATTGGC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 18 0.38
41 29 0.62
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAATTTAGTACTTCGAATTATCCA
Found at i:23996437 original size:2 final size:2
Alignment explanation
Indices: 23996430--23996484 Score: 87
Period size: 2 Copynumber: 28.0 Consensus size: 2
23996420 GATTGAATTG
23996430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GA- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
23996471 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
23996485 GTGCAATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 47 0.94
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23996695 original size:41 final size:41
Alignment explanation
Indices: 23996633--23996740 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 41
23996623 AATTGCTAAT
* *
23996633 TTACTTCGG-TTTATCCAATGAGACACTGGGTGTCAATTTA
1 TTACTTCGGATTTATCCGATGAGACACTGAGTGTCAATTTA
*
23996673 TTACTTCGGATTTATTCGATGAGACACTGAGTGTCAATTTA
1 TTACTTCGGATTTATCCGATGAGACACTGAGTGTCAATTTA
* * *
23996714 CTACTTC-GAATTATCCGATGAGGCACT
1 TTACTTCGGATTTATCCGATGAGACACT
23996741 ATGTGCCAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 26 0.43
41 34 0.57
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (41 bp):
TTACTTCGGATTTATCCGATGAGACACTGAGTGTCAATTTA
Found at i:23998448 original size:40 final size:39
Alignment explanation
Indices: 23998394--23998529 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 39
23998384 ACCAGTTTGG
* *
23998394 CACCCAGTGCCTCATCGGATAATTCGAAGTAGTAAATTTA
1 CACCCAGTGCCTCATCGGATAATACGAAGTA-TAAATTGA
* * * * *
23998434 CACCAAGTGTCTCATCTGTTAA-ACTGAAGTA-AAATTGG
1 CACCCAGTGCCTCATCGGATAATAC-GAAGTATAAATTGA
* * *
23998472 CACTCAGTGCCTCATCGAATAAATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGAT-AATACGAAGT-ATAAATTGA
*
23998513 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
23998530 ACTCGAAGTT
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
38 19 0.26
39 8 0.11
40 26 0.35
41 21 0.28
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATACGAAGTATAAATTGA
Found at i:23999365 original size:4 final size:4
Alignment explanation
Indices: 23999343--23999435 Score: 54
Period size: 4 Copynumber: 23.2 Consensus size: 4
23999333 AAACCCCTAG
* *
23999343 TCTT GTCTT TC-T CCTT TCTT TCTT TCCCT T-TT TC-T T-TT TCTT TCTT
1 TCTT -TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TCTT
* *
23999389 TCTT TC-T TCTT TCAATT TCATT T-TT ATCAT TCTT TCTT TATT TCTT
1 TCTT TCTT TCTT TC--TT TC-TT TCTT -TCTT TCTT TCTT TCTT TCTT
23999435 T
1 T
23999436 TTATTACTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
3 13 0.19
4 41 0.59
5 12 0.17
6 4 0.06
ACGTcount: A:0.06, C:0.24, G:0.01, T:0.69
Consensus pattern (4 bp):
TCTT
Found at i:24000747 original size:12 final size:12
Alignment explanation
Indices: 24000724--24000761 Score: 67
Period size: 12 Copynumber: 3.1 Consensus size: 12
24000714 GCCGAGCCAC
24000724 ACACCTGTGTGCT
1 ACACC-GTGTGCT
24000737 ACACCGTGTGCT
1 ACACCGTGTGCT
24000749 ACACCGTGTGCT
1 ACACCGTGTGCT
24000761 A
1 A
24000762 GCTGTGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.26
Consensus pattern (12 bp):
ACACCGTGTGCT
Found at i:24001761 original size:40 final size:38
Alignment explanation
Indices: 24001717--24001857 Score: 149
Period size: 40 Copynumber: 3.6 Consensus size: 38
24001707 ACACACCAAT
* *
24001717 TTGACACTTAGTGCCTCATCAGATAATTCGAAGTAGTAAA
1 TTGACACTCAGTGCCTCATC-GATAAATCGAAGTA-TAAA
* * *
24001757 TTGACACCCAGTGTCTCATCGGATAAACCGAAGTA-AAA
1 TTGACACTCAGTGCCTCATC-GATAAATCGAAGTATAAA
*
24001795 TTGGCACTCAGTGCCTCATCGAATAAATCTGAAGTAATAAA
1 TTGACACTCAGTGCCTCATCG-ATAAATC-GAAGT-ATAAA
* *
24001836 TTGACACCCAGTGTCTCATCGA
1 TTGACACTCAGTGCCTCATCGA
24001858 CTCAAAGTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
37 1 0.01
38 26 0.31
39 5 0.06
40 31 0.37
41 21 0.25
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (38 bp):
TTGACACTCAGTGCCTCATCGATAAATCGAAGTATAAA
Found at i:24001854 original size:41 final size:40
Alignment explanation
Indices: 24001745--24001857 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 40
24001735 TCAGATAATT
* *
24001745 CGAAGTAGTAAATTGACACCCAGTGTCTCATCGGATAAAC
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAAC
* * *
24001785 CGAAGT-A-AAATTGGCACTCAGTGCCTCATCGAATAAATC
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAA-C
*
24001824 TGAAGTAATAAATTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGA
24001858 CTCAAAGTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
38 26 0.43
39 6 0.10
40 7 0.11
41 22 0.36
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (40 bp):
CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAAC
Found at i:24002718 original size:4 final size:4
Alignment explanation
Indices: 24002709--24002765 Score: 55
Period size: 4 Copynumber: 13.8 Consensus size: 4
24002699 CCTTTTTCTT
24002709 TTTC TTTC TTTC TTTC -TTC TTTC TGTTTC ATTT- TTATC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC --TTTC -TTTC TT-TC TTTC TTTC
*
24002755 TTTA TTTC TTT
1 TTTC TTTC TTT
24002766 TTATTACTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
3 5 0.11
4 31 0.69
5 5 0.11
6 4 0.09
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:24002822 original size:18 final size:18
Alignment explanation
Indices: 24002799--24002835 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24002789 CTATTATGTT
*
24002799 TTATTATACATTAATATA
1 TTATTATACAATAATATA
*
24002817 TTATTATATAATAATATA
1 TTATTATACAATAATATA
24002835 T
1 T
24002836 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTATACAATAATATA
Found at i:24002826 original size:2 final size:2
Alignment explanation
Indices: 24002812--24002860 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
24002802 TTATACATTA
24002812 AT AT AT -T AT -T AT AT A- AT A- 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 AT AT AT AT AT
24002850 AT AT AT AT AT A
1 AT AT AT AT AT A
24002861 CTTAACACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24008071 original size:47 final size:47
Alignment explanation
Indices: 24007917--24008069 Score: 243
Period size: 47 Copynumber: 3.3 Consensus size: 47
24007907 GTCACAGTAA
24007917 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
* *
24007964 TGCAAATAAACTACTAATAATCAAAATTGTGGATAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
* * * *
24008011 TACAGATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
*
24008058 TGTAAATAAACT
1 TGCAAATAAACT
24008070 GCTAAAAACT
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (47 bp):
TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
Found at i:24012316 original size:2 final size:2
Alignment explanation
Indices: 24012309--24012365 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
24012299 TCTTAAATTC
24012309 AT AT AT AT AT 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 AT AT AT AT AT
24012351 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
24012366 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24012502 original size:2 final size:2
Alignment explanation
Indices: 24012495--24012544 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
24012485 CTACTAACTA
24012495 AT AT AT AT AT 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 AT AT AT AT AT
24012537 AT AT AT AT
1 AT AT AT AT
24012545 TACATACTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24013361 original size:22 final size:24
Alignment explanation
Indices: 24013319--24013362 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
24013309 TAACTAAGCT
24013319 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
24013343 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
24013363 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:24013760 original size:15 final size:15
Alignment explanation
Indices: 24013740--24013768 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24013730 TTCTTTCCTG
24013740 TTTTTCTTTTGTTTC
1 TTTTTCTTTTGTTTC
24013755 TTTTTCTTTTGTTT
1 TTTTTCTTTTGTTT
24013769 TACTTACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTTGTTTC
Found at i:24013975 original size:17 final size:16
Alignment explanation
Indices: 24013952--24014009 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
24013942 GTTTATTTAA
24013952 TATATAATAATATAAT
1 TATATAATAATATAAT
24013968 TAATATAAT-ATAATATAT
1 T-ATATAATAAT-ATA-AT
*
24013986 TATATAATAAAATAAT
1 TATATAATAATATAAT
24014002 ATATATAA
1 -TATATAA
24014010 AACATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.14
17 27 0.75
18 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAATAATATAAT
Found at i:24013976 original size:5 final size:5
Alignment explanation
Indices: 24013949--24014009 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
24013939 TTGGTTTATT
24013949 TAATA T-ATAA TAATA TAAT- TAATA TAATA TAATA TATTATA TAATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TA--ATA TAATA
24013995 -AA-A TAATA T-ATA TAA
1 TAATA TAATA TAATA TAA
24014010 AACATAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
3 1 0.02
4 14 0.29
5 26 0.54
6 2 0.04
7 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Done.