Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 61 of 259
Found at i:19683732 original size:19 final size:20
Alignment explanation
Indices: 19683710--19683747 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19683700 TTAAGCATTC
*
19683710 ATCAATGGC-ACTTCAAAAA
1 ATCAATGACAACTTCAAAAA
*
19683729 ATCATTGACAACTTCAAAA
1 ATCAATGACAACTTCAAAA
19683748 GTTAAGGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.24
Consensus pattern (20 bp):
ATCAATGACAACTTCAAAAA
Found at i:19687654 original size:108 final size:109
Alignment explanation
Indices: 19687456--19687679 Score: 290
Period size: 108 Copynumber: 2.1 Consensus size: 109
19687446 AGGTATTTAA
* * * * *
19687456 ACGGCCTGGCACACGGGCGTGTGGCATGGCCGTGTGACCCAACTTCAAAAGTTACACAGGCACGG
1 ACGGCCTAGCACACGGGCATGTGGCATGGCCATGTGACCCAAATTCAAAAGTTACACAGGCACAG
* * * *
19687521 ACATGGGTTGGGACACAGTCGTGTGTCCCTATTTTGATTGTTAC
66 ACATGGGCTGGGACACAGCCATGTGTCCCTATTTCGATTGTTAC
* * * ** *
19687565 ATGGCCTAGCATACGGGCATGTGGCTTGGCCATGTGACCCAAATT-TGAAGTTACACGGGCACAG
1 ACGGCCTAGCACACGGGCATGTGGCATGGCCATGTGACCCAAATTCAAAAGTTACACAGGCACAG
19687629 ACATGGGCTGGGACAC-GACCATGTGTCCCTATTTCGATTGTTAC
66 ACATGGGCTGGGACACAG-CCATGTGTCCCTATTTCGATTGTTAC
19687673 ACGGCCT
1 ACGGCCT
19687680 GAGACACAGG
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
107 1 0.01
108 59 0.60
109 38 0.39
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (109 bp):
ACGGCCTAGCACACGGGCATGTGGCATGGCCATGTGACCCAAATTCAAAAGTTACACAGGCACAG
ACATGGGCTGGGACACAGCCATGTGTCCCTATTTCGATTGTTAC
Found at i:19696116 original size:40 final size:40
Alignment explanation
Indices: 19696046--19696263 Score: 253
Period size: 40 Copynumber: 5.5 Consensus size: 40
19696036 AAACCAAGTA
* * *
19696046 CCTTCGAGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
19696085 CCGTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
19696125 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * ** * * *
19696165 CCTTCGGGACTTAGCTCGGATATAATCGCTTGCATAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* ** *
19696205 CCTTCGGAACACAGCCCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
19696245 CCTTC-GGATCTTAGCCCGG
1 CCTTCGGGA-CTTAGCCCGG
19696264 TTATCATCCG
Statistics
Matches: 148, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 14 0.09
40 134 0.91
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:19704153 original size:40 final size:40
Alignment explanation
Indices: 19704076--19704316 Score: 280
Period size: 40 Copynumber: 6.2 Consensus size: 40
19704066 AAACCAAGTA
* *
19704076 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
19704115 CCTTCGTGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
19704155 CCTT-GGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
19704194 CCTTCGAGACTTAGCCCGGATATAGTAATTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* ** * ** *
19704234 CCTT-TGGACTTAG-CCGGAT-TA-TTGCTAGCTTAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** *
19704270 CCTTCGGGACACAGCCCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
19704310 CCTTCGG
1 CCTTCGG
19704317 ATCTTAGTCT
Statistics
Matches: 168, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
36 12 0.07
37 8 0.05
38 12 0.07
39 59 0.35
40 77 0.46
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:19704221 original size:79 final size:77
Alignment explanation
Indices: 19704076--19704323 Score: 300
Period size: 79 Copynumber: 3.2 Consensus size: 77
19704066 AAACCAAGTA
* * *
19704076 CCTTCGGGATTTAGCCGGATATAGCTACTCGCTCAAATGCCTTCGTGACTTAGCCCGGTTATAGT
1 CCTT-GGGACTTAGCCGGATATAG-TACTCGCTCAAATGCCTTCGAGACTTAGCCCGGATATAGT
19704141 AACTCGCACAAATG
64 AACTCGCACAAATG
*
19704155 CCTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGGATATAGT
1 CCTTGGGACTTAG-CCGGATATAGT-ACTCGCTCAAATGCCTTCGAGACTTAGCCCGGATATAGT
*
19704220 AATTCGCACAAATG
64 AACTCGCACAAATG
* * * * * * * ** *
19704234 CCTTTGGACTTAGCCGGAT-TATTGCTAGCTTAAATACCTTCGGGACACAGCCCGGATATAGCAA
1 CCTTGGGACTTAGCCGGATATAGTACTCGCTCAAATGCCTTCGAGACTTAGCCCGGATATAGTAA
19704298 CTCGCACAAATG
66 CTCGCACAAATG
*
19704310 CCTTCGGATCTTAG
1 CCTTGGGA-CTTAG
19704324 TCTGGTTATC
Statistics
Matches: 148, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
76 50 0.34
77 8 0.05
78 15 0.10
79 75 0.51
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (77 bp):
CCTTGGGACTTAGCCGGATATAGTACTCGCTCAAATGCCTTCGAGACTTAGCCCGGATATAGTAA
CTCGCACAAATG
Found at i:19722308 original size:21 final size:20
Alignment explanation
Indices: 19722280--19722318 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19722270 GAATCGTCAT
19722280 GGAGTTGAAAAGGCTATGTG
1 GGAGTTGAAAAGGCTATGTG
*
19722300 GGAGCTTGAAAATGCTATG
1 GGAG-TTGAAAAGGCTATG
19722319 AAACAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.26
Consensus pattern (20 bp):
GGAGTTGAAAAGGCTATGTG
Found at i:19729487 original size:50 final size:50
Alignment explanation
Indices: 19729404--19729651 Score: 289
Period size: 50 Copynumber: 4.9 Consensus size: 50
19729394 TATGTGGGTT
19729404 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * * * * * *
19729454 TTAGGTCGCATGTGTAGTACTAAGTACAAGCTACTATGCGTACCCGATAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * ** * *
19729504 CTTCGATCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGG
1 -TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* * * *
19729555 TTAGGTCACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACTAGATTA
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
* ** * *
19729605 TTAGGTCGCAAGTGTAGTACTAAGTTCAGGCTACTATGCGTACCAGA
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
19729652 GAGGTTCGGC
Statistics
Matches: 162, Mismatches: 35, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
50 124 0.77
51 38 0.23
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG
Found at i:19729590 original size:101 final size:101
Alignment explanation
Indices: 19729409--19729590 Score: 283
Period size: 101 Copynumber: 1.8 Consensus size: 101
19729399 GGGTTTTAGG
** * *
19729409 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGTTAGGTCACATGTGTAGTAC
*
19729474 TAAGTACAAGCTACTATGCGTACCCGATAGCTTCGA
66 TAAGTACAAGATACTATGCGTACCCGATAGCTTCGA
* *
19729510 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGTTAGGTCACATGTGTAGTAC
* *
19729575 TAAGTGCAGGATACTA
66 TAAGTACAAGATACTA
19729591 CGTGTACTAG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 72 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGTTAGGTCACATGTGTAGTAC
TAAGTACAAGATACTATGCGTACCCGATAGCTTCGA
Found at i:19744809 original size:43 final size:42
Alignment explanation
Indices: 19744725--19744865 Score: 124
Period size: 43 Copynumber: 3.3 Consensus size: 42
19744715 TCCCAGTTAT
* * **
19744725 GGTCTTACATGTTATCAT-ATATCGATGCCACTATCGTAGACAG
1 GGTCTTACATG-TATCATAATA-CGATGCCAATGTCCCAGACAG
* *
19744768 GGTCTTAGATGATATCATAATACGATGCCAATGTCCCAGACAT
1 GGTCTTACATG-TATCATAATACGATGCCAATGTCCCAGACAG
* * * * * *
19744811 TGTCTTACACGTAATCACAATACAATGCCAATGTCCCAAAC-T
1 GGTCTTACATGT-ATCATAATACGATGCCAATGTCCCAGACAG
19744853 GGTCTTACATGTA
1 GGTCTTACATGTA
19744866 ATCACATATC
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 12 0.15
43 65 0.80
44 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (42 bp):
GGTCTTACATGTATCATAATACGATGCCAATGTCCCAGACAG
Found at i:19744871 original size:42 final size:43
Alignment explanation
Indices: 19744768--19744871 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 43
19744758 TCGTAGACAG
* * * *
19744768 GGTCTTAGATG-ATATCATAATACGATGCCAATGTCCCAGACAT
1 GGTCTTACATGTA-ATCACAATACAATGCCAATGTCCCAAACAT
* *
19744811 TGTCTTACACGTAATCACAATACAATGCCAATGTCCCAAAC-T
1 GGTCTTACATGTAATCACAATACAATGCCAATGTCCCAAACAT
19744853 GGTCTTACATGTAATCACA
1 GGTCTTACATGTAATCACA
19744872 TATCGATAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
42 18 0.35
43 33 0.63
44 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (43 bp):
GGTCTTACATGTAATCACAATACAATGCCAATGTCCCAAACAT
Found at i:19750958 original size:27 final size:27
Alignment explanation
Indices: 19750927--19751104 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
19750917 TAAATTGTAC
19750927 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
19750954 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19750980 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
19751008 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
** *
19751036 AGCACTAAGTGTGCGATTTGGTTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19751063 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
19751090 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19751105 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:19751068 original size:82 final size:81
Alignment explanation
Indices: 19750928--19751083 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
19750918 AAATTGTACA
* *
19750928 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
19750993 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** **
19751009 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGGTTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGT
*
19751073 GTGCGAGTTGA
64 GTGCGAATTGA
19751084 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:19751095 original size:82 final size:81
Alignment explanation
Indices: 19750924--19751104 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
19750914 GATTAAATTG
* *
19750924 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
19750989 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** **
19751005 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGGTTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
19751069 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
19751087 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
19751105 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:19755834 original size:16 final size:16
Alignment explanation
Indices: 19755815--19755851 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
19755805 AAAAATCCCA
*
19755815 AAAAGTTGAAATGCCG
1 AAAAGTCGAAATGCCG
19755831 AAAAGTCGAAATGCCG
1 AAAAGTCGAAATGCCG
19755847 AAAAG
1 AAAAG
19755852 CCAAAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.24, T:0.14
Consensus pattern (16 bp):
AAAAGTCGAAATGCCG
Found at i:19756099 original size:28 final size:28
Alignment explanation
Indices: 19756067--19756178 Score: 120
Period size: 28 Copynumber: 4.0 Consensus size: 28
19756057 TATGAGCATG
19756067 AATATAAATGTGATTTGGGCCTAAT-GGC
1 AATATAAATGTGA-TTGGGCCTAATGGGC
* *
19756095 AATATGAATGTGGTTTGGGCCTAATGGGCC
1 AATATAAATGT-GATTGGGCCTAATGGG-C
*
19756125 AA-ATAAATGTGAATGGGCCTAATGGGC
1 AATATAAATGTGATTGGGCCTAATGGGC
* * * *
19756152 TATATAAAAGAGATTGGGCCTAGTGGG
1 AATATAAATGTGATTGGGCCTAATGGG
19756179 TCATATGCAT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.03
28 55 0.79
29 10 0.14
30 3 0.04
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.28
Consensus pattern (28 bp):
AATATAAATGTGATTGGGCCTAATGGGC
Found at i:19759019 original size:37 final size:37
Alignment explanation
Indices: 19758945--19759019 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
19758935 GTTCCAACTG
* * *
19758945 AAACACCAATCGCTTGTAAGAGCTAATCCATCTGATA
1 AAACACCAATCGCTTATAAGAGCTAATCCACCCGATA
19758982 AAACACCAGAT-GCTTATAAGAGCTAATCCACCCGATA
1 AAACACCA-ATCGCTTATAAGAGCTAATCCACCCGATA
19759019 A
1 A
19759020 CACGCCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 32 0.94
38 2 0.06
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.21
Consensus pattern (37 bp):
AAACACCAATCGCTTATAAGAGCTAATCCACCCGATA
Found at i:19761044 original size:15 final size:15
Alignment explanation
Indices: 19761024--19761055 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19761014 TCAGAAAGGG
19761024 GAAGAGCAAGAAAGT
1 GAAGAGCAAGAAAGT
*
19761039 GAAGAGGAAGAAAGT
1 GAAGAGCAAGAAAGT
19761054 GA
1 GA
19761056 TGGAACAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.38, T:0.06
Consensus pattern (15 bp):
GAAGAGCAAGAAAGT
Found at i:19763916 original size:20 final size:21
Alignment explanation
Indices: 19763888--19763927 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
19763878 ATATTTGATT
19763888 ATTTGATTTCTCATTT-TTTTC
1 ATTTGATTTC-CATTTATTTTC
19763909 ATTT-ATTTCCATTTATTTT
1 ATTTGATTTCCATTTATTTT
19763928 TACTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.17, C:0.12, G:0.03, T:0.68
Consensus pattern (21 bp):
ATTTGATTTCCATTTATTTTC
Found at i:19769653 original size:41 final size:42
Alignment explanation
Indices: 19769567--19769653 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
19769557 TTTCAAAAAA
**
19769567 TTTTCAAAAATCCCAAAAATATTTTCTATTTTTATTTTTAAT
1 TTTTCAAAAATCCCAAAAATATTTTCTATCATTATTTTTAAT
*
19769609 TTTTTAAAAAT-CCAAAAATATTTTTCT-TCATTATTTTTAAT
1 TTTTCAAAAATCCCAAAAATA-TTTTCTATCATTATTTTTAAT
19769650 TTTT
1 TTTT
19769654 GTTATTGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 25 0.61
42 16 0.39
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (42 bp):
TTTTCAAAAATCCCAAAAATATTTTCTATCATTATTTTTAAT
Found at i:19776937 original size:22 final size:22
Alignment explanation
Indices: 19776905--19776947 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19776895 CTAAGTCAAC
*
19776905 AGGACGACTCAACGTCGTAGAT
1 AGGACGACTCAACGCCGTAGAT
* *
19776927 AGGACGGCTCAATGCCGTAGA
1 AGGACGACTCAACGCCGTAGA
19776948 CATTGCAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.16
Consensus pattern (22 bp):
AGGACGACTCAACGCCGTAGAT
Found at i:19782629 original size:42 final size:43
Alignment explanation
Indices: 19782516--19782631 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
19782506 GGGATTTAGA
* *
19782516 AATCCGAGCTCGTTGAGCGGTCCGAGTTCGTGATATATATGAG
1 AATCCGAGCTCGTTGAGAGGTCCGAGTTCATGATATATATGAG
* * * * * *
19782559 AATCTGAACTTGTTGAGTGGTCCAAGTTCATGATATATGTG-G
1 AATCCGAGCTCGTTGAGAGGTCCGAGTTCATGATATATATGAG
* *
19782601 CATCCGAGCTCGTTGAGAGGTCTGAGTTCAT
1 AATCCGAGCTCGTTGAGAGGTCCGAGTTCAT
19782632 TATGGATGTA
Statistics
Matches: 59, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
42 25 0.42
43 34 0.58
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
AATCCGAGCTCGTTGAGAGGTCCGAGTTCATGATATATATGAG
Found at i:19794480 original size:15 final size:15
Alignment explanation
Indices: 19794460--19794488 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19794450 TATCACATAG
19794460 TTCTAAAAAGGTTAA
1 TTCTAAAAAGGTTAA
19794475 TTCTAAAAAGGTTA
1 TTCTAAAAAGGTTA
19794489 CTAAGTGAGC
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:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (15 bp):
TTCTAAAAAGGTTAA
Found at i:19796989 original size:39 final size:40
Alignment explanation
Indices: 19796890--19797074 Score: 169
Period size: 40 Copynumber: 4.7 Consensus size: 40
19796880 TCGAATGATG
* * * * * *
19796890 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
19796930 TCCAGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTAAA
*
19796970 TCCGGGCTAA-ACCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
19797009 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTA-AA
** * *
19797050 -CCGGGCTCTGTCTCGAAGGCATTTG
1 TCCGGGCTAAGACCCGAAGGCATTTG
19797075 AACGAGTAGC
Statistics
Matches: 118, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
39 34 0.29
40 75 0.64
41 9 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:19797038 original size:40 final size:39
Alignment explanation
Indices: 19796943--19797056 Score: 158
Period size: 39 Copynumber: 2.9 Consensus size: 39
19796933 AGACTAAGAT
*
19796943 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAAC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAAC
* * * *
19796982 CCGAAGGCATTGGTGCGAGTTACTAAATCTGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAA-AC
19797022 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCT
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCT
19797057 CTGTCTCGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
39 33 0.51
40 30 0.46
41 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAAC
Found at i:19813108 original size:6 final size:6
Alignment explanation
Indices: 19813097--19813132 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
19813087 TTCAATTTTT
* *
19813097 TCTCAA TATCAA TATCAA TCTCAA TCTCAA TCTCAA
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA
19813133 ATTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCAA
Found at i:19813184 original size:21 final size:20
Alignment explanation
Indices: 19813140--19813184 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19813130 CAAATTCTTT
*
19813140 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
19813160 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
19813181 TTTC
1 TTTC
19813185 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:19814017 original size:17 final size:17
Alignment explanation
Indices: 19813995--19814049 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
19813985 AATCACTCTT
19813995 TTTTTTTTCAATTTTGA
1 TTTTTTTTCAATTTTGA
*
19814012 TTTTTTTTC--TTCT--
1 TTTTTTTTCAATTTTGA
*
19814025 TTTTTTTT-AATTTCGA
1 TTTTTTTTCAATTTTGA
19814041 TTTTTTTTC
1 TTTTTTTTC
19814050 TTCTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
15 3 0.10
16 8 0.27
17 9 0.30
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCAATTTTGA
Found at i:19814027 original size:12 final size:13
Alignment explanation
Indices: 19814011--19814065 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 13
19814001 TTCAATTTTG
19814011 ATTTTTTTTCTTC
1 ATTTTTTTTCTTC
* *
19814024 TTTTTTTTTAATTTC
1 ATTTTTTTT--CTTC
19814039 GATTTTTTTTCTTC
1 -ATTTTTTTTCTTC
19814053 -TTTTTTTTCTTC
1 ATTTTTTTTCTTC
19814065 A
1 A
19814066 ATACTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 12 0.35
13 8 0.24
14 3 0.09
15 3 0.09
16 8 0.24
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (13 bp):
ATTTTTTTTCTTC
Found at i:19814036 original size:29 final size:30
Alignment explanation
Indices: 19813994--19814060 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
19813984 CAATCACTCT
*
19813994 TTTTTTTTTCAATTTTGATTTTTTTTCTTC
1 TTTTTTTTTCAATTTCGATTTTTTTTCTTC
19814024 TTTTTTTTT-AATTTCGATTTTTTTTCTTC
1 TTTTTTTTTCAATTTCGATTTTTTTTCTTC
19814053 TTTTTTTT
1 TTTTTTTT
19814061 CTTCAATACT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (30 bp):
TTTTTTTTTCAATTTCGATTTTTTTTCTTC
Found at i:19814123 original size:13 final size:13
Alignment explanation
Indices: 19814105--19814150 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
19814095 GAATACAAAC
19814105 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
***
19814118 TTTTTTTCAAAAT
1 TTTTTTTTTGAAT
19814131 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
19814144 TTTTTTT
1 TTTTTTT
19814151 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:19814159 original size:13 final size:12
Alignment explanation
Indices: 19814105--19814161 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
19814095 GAATACAAAC
*
19814105 TTTTTTTTTGAA
1 TTTTTTTTTTAA
**
19814117 TTTTTTTTCAAAA
1 TTTTTTTT-TTAA
19814130 TTTTTTTTTTGAA
1 TTTTTTTTTT-AA
*
19814143 TTTTTTTTAT-A
1 TTTTTTTTTTAA
19814154 TTTTTTTT
1 TTTTTTTT
19814162 ACAATACCGT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
11 9 0.24
12 8 0.21
13 21 0.55
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:19819562 original size:15 final size:14
Alignment explanation
Indices: 19819542--19819589 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
19819532 CTCATTTTCA
19819542 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
19819557 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
19819571 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
19819586 TCTT
1 TCTT
19819590 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:19819594 original size:22 final size:21
Alignment explanation
Indices: 19819542--19819600 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
19819532 CTCATTTTCA
* *
19819542 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
19819563 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
19819584 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
19819601 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:19820629 original size:12 final size:12
Alignment explanation
Indices: 19820587--19820646 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
19820577 TTTTTTTAAC
19820587 TCGATTTTTTTT
1 TCGATTTTTTTT
*
19820599 GTC-ACTTTTTTT
1 -TCGATTTTTTTT
*
19820611 TC--CTTTTTTT
1 TCGATTTTTTTT
19820621 TCGATTTTTTTT
1 TCGATTTTTTTT
19820633 T-GAATTTTTTTT
1 TCG-ATTTTTTTT
19820645 TC
1 TC
19820647 TGAATTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 10 0.24
11 3 0.07
12 26 0.63
13 2 0.05
ACGTcount: A:0.08, C:0.12, G:0.07, T:0.73
Consensus pattern (12 bp):
TCGATTTTTTTT
Found at i:19820642 original size:14 final size:14
Alignment explanation
Indices: 19820614--19820653 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 14
19820604 TTTTTTTTCC
19820614 TTTTTTTTC-G-A-
1 TTTTTTTTCTGAAT
19820625 TTTTTTTT-TGAAT
1 TTTTTTTTCTGAAT
19820638 TTTTTTTTCTGAAT
1 TTTTTTTTCTGAAT
19820652 TT
1 TT
19820654 CTTCTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 8 0.32
14 7 0.28
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (14 bp):
TTTTTTTTCTGAAT
Found at i:19824152 original size:20 final size:20
Alignment explanation
Indices: 19824106--19824152 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19824096 AGCTCGTTTC
*
19824106 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
19824126 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
19824146 CAGCTCA
1 CAGCTCA
19824153 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:19825711 original size:22 final size:22
Alignment explanation
Indices: 19825686--19825730 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19825676 AGAAGTGAGC
*
19825686 AAAAAAAGAAAAAAAAGTAAAA
1 AAAAAAACAAAAAAAAGTAAAA
** *
19825708 AAAAGGACAAAAAAAAGTGAAA
1 AAAAAAACAAAAAAAAGTAAAA
19825730 A
1 A
19825731 GTCTTGCGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAGTAAAA
Found at i:19826830 original size:48 final size:47
Alignment explanation
Indices: 19826751--19826855 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 47
19826741 GAGTGTCATG
*
19826751 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
19826799 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
19826847 GAAAAAGAA
1 GAAAAAGAA
19826856 TGAAAAGAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 39 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:19828573 original size:20 final size:20
Alignment explanation
Indices: 19828527--19828573 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19828517 AGCTCGTTTC
*
19828527 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
19828547 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
19828567 CAGCTCA
1 CAGCTCA
19828574 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:19829422 original size:20 final size:20
Alignment explanation
Indices: 19829399--19829445 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19829389 GGGTTAAGAT
*
19829399 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
19829419 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
19829439 TGAGCTG
1 TGAGCTG
19829446 CAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:19831586 original size:18 final size:18
Alignment explanation
Indices: 19831535--19831620 Score: 73
Period size: 18 Copynumber: 4.6 Consensus size: 18
19831525 GAGAAAAATG
* **
19831535 AAAGAAAAAGAACGAAAA
1 AAAGAAAAAGAAAGTGAA
**
19831553 AAAGAATGAGAAAGTGAA
1 AAAGAAAAAGAAAGTGAA
*
19831571 AAAGAAAAAGAGAGTGAAA
1 AAAGAAAAAGAAAGTG-AA
* *
19831590 GAAAGGAAAAACAAATTGAA
1 -AAA-GAAAAAGAAAGTGAA
19831610 AAAGAAAAAGA
1 AAAGAAAAAGA
19831621 TTTCAAGCAA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
18 33 0.62
19 5 0.09
20 5 0.09
21 10 0.19
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.06
Consensus pattern (18 bp):
AAAGAAAAAGAAAGTGAA
Found at i:19832632 original size:23 final size:21
Alignment explanation
Indices: 19832606--19832649 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
19832596 GTGTTTTATG
19832606 TGTTTAAATGTGTTTAATATGCA
1 TGTTTAAATGTG-TTAAT-TGCA
*
19832629 TGTTTTAATGTGTTAATTGCA
1 TGTTTAAATGTGTTAATTGCA
19832650 GGTGTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (21 bp):
TGTTTAAATGTGTTAATTGCA
Found at i:19834121 original size:28 final size:28
Alignment explanation
Indices: 19834069--19834146 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
19834059 CAATTTATGT
** *
19834069 ATATGGCACTTAGTGTGAAAAATATT-A
1 ATATGGCACTTAGTGTGCGAGATATTGA
*
19834096 ATAGTGGCACTTGGTGTGCGAGATATTGA
1 ATA-TGGCACTTAGTGTGCGAGATATTGA
* *
19834125 GTATGGCACTTAGTGTACGAGA
1 ATATGGCACTTAGTGTGCGAGA
19834147 CATCGAAGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.07
28 36 0.86
29 3 0.07
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (28 bp):
ATATGGCACTTAGTGTGCGAGATATTGA
Found at i:19836601 original size:11 final size:10
Alignment explanation
Indices: 19836576--19836636 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
19836566 ACCAATAAAA
19836576 TAAA-TGAGC
1 TAAATTGAGC
*
19836585 TGAATTGTAGC
1 TAAATTG-AGC
19836596 TAAATTGAGC
1 TAAATTGAGC
**
19836606 TTGATTGAGC
1 TAAATTGAGC
19836616 TGAAA-TGAGC
1 T-AAATTGAGC
*
19836626 TCAATTGAGC
1 TAAATTGAGC
19836636 T
1 T
19836637 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:19836637 original size:20 final size:20
Alignment explanation
Indices: 19836577--19836637 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
19836567 CCAATAAAAT
*
19836577 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
**
19836597 AAATTGAGCTTGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
19836618 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
19836638 GTCGGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:19853247 original size:20 final size:20
Alignment explanation
Indices: 19853224--19853277 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
19853214 AGTTTTTCCC
*
19853224 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
19853244 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
19853264 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
19853278 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:19853259 original size:30 final size:30
Alignment explanation
Indices: 19853224--19853297 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
19853214 AGTTTTTCCC
19853224 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19853254 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19853284 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
19853298 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19853287 original size:20 final size:20
Alignment explanation
Indices: 19853224--19853288 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
19853214 AGTTTTTCCC
* * * *
19853224 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
19853244 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
19853263 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
19853284 AGCTC
1 AGCTC
19853289 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:19854932 original size:12 final size:12
Alignment explanation
Indices: 19854897--19854938 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
19854887 AAAAGAGAAG
19854897 AAATTCAAAAATA
1 AAATTCAAAAA-A
19854910 AAATTTCAAAAAA
1 AAA-TTCAAAAAA
*
19854923 AAATTGAAAAAA
1 AAATTCAAAAAA
19854935 AAAT
1 AAAT
19854939 AAAAAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.44
13 7 0.26
14 8 0.30
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:19856042 original size:6 final size:6
Alignment explanation
Indices: 19856009--19856116 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
19855999 AAAGAAATTG
* * * ** *
19856009 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
19856056 AAAGAA ATTA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
19856107 AAAGAA AAAG
1 AAAGAA AAAG
19856117 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
5 4 0.05
6 57 0.78
7 8 0.11
8 4 0.05
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:19856070 original size:18 final size:18
Alignment explanation
Indices: 19855996--19856071 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
19855986 TAAAGAGATT
19855996 GAAAAAGAAATTGAAAGAAAA
1 GAAAAAGAAATT--AA-AAAA
* *** *
19856017 CAAAAAGAAAACGAAGAA
1 GAAAAAGAAATTAAAAAA
**
19856035 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATTAAAAAA
19856053 GAAAAAGAAATTAAAAAA
1 GAAAAAGAAATTAAAAAA
19856071 G
1 G
19856072 TGAGAGAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
18 33 0.77
19 1 0.02
21 9 0.21
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAATTAAAAAA
Found at i:19856096 original size:14 final size:13
Alignment explanation
Indices: 19856077--19856114 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
19856067 AAAAGTGAGA
19856077 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
19856089 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
19856104 GAAAAAGAAAA
1 GAAAAAGAAAA
19856115 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:19856111 original size:13 final size:12
Alignment explanation
Indices: 19855995--19856114 Score: 61
Period size: 12 Copynumber: 10.0 Consensus size: 12
19855985 GTAAAGAGAT
*
19855995 TGAAAAAGAAAT
1 TGAAAAAGAAAA
19856007 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
19856017 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* *
19856028 CGAAGAAGAAAA
1 TGAAAAAGAAAA
* **
19856040 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
*
19856053 -GAAAAAGAAAT
1 TGAAAAAGAAAA
* * *
19856064 TAAAAAAGTGAGA
1 TGAAAAAG-AAAA
19856077 -GAAAAAGAAAA
1 TGAAAAAGAAAA
19856088 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
19856102 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
19856115 AGCGAAAAAA
Statistics
Matches: 80, Mismatches: 18, Indels: 19
0.68 0.15 0.16
Matches are distributed among these distances:
10 7 0.09
11 13 0.16
12 33 0.41
13 15 0.19
14 10 0.12
15 2 0.03
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:19856128 original size:21 final size:21
Alignment explanation
Indices: 19856078--19856128 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
19856068 AAAGTGAGAG
*
19856078 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
19856099 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
19856120 AAAAAGAAA
1 AAAAAGAAA
19856129 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:19856132 original size:27 final size:27
Alignment explanation
Indices: 19856030--19856134 Score: 79
Period size: 27 Copynumber: 3.8 Consensus size: 27
19856020 AAAGAAAACG
* *
19856030 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
* **
19856057 AAGAA-ATTAAAAAAGTGAGAGAAAAAGAAA
1 AAGAAGA--AAAAAA--AATTGAAAAAGAAA
* *
19856087 ATGAAGAAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*
19856114 AAG-CGAAAAAAGAAATTGAAA
1 AAGAAGAAAAAA-AAATTGAAA
19856135 GAGAGCTTGA
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
26 7 0.12
27 27 0.46
28 5 0.08
29 5 0.08
30 14 0.24
31 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.10
Consensus pattern (27 bp):
AAGAAGAAAAAAAAATTGAAAAAGAAA
Found at i:19856168 original size:33 final size:33
Alignment explanation
Indices: 19856131--19856193 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
19856121 AAAAGAAATT
19856131 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
19856164 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
19856194 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:19857993 original size:20 final size:20
Alignment explanation
Indices: 19857970--19858023 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
19857960 AGTTTTTCCC
*
19857970 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
19857990 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
19858010 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
19858024 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:19858005 original size:30 final size:30
Alignment explanation
Indices: 19857970--19858043 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
19857960 AGTTTTTCCC
19857970 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19858000 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19858030 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
19858044 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19858033 original size:20 final size:20
Alignment explanation
Indices: 19857970--19858034 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
19857960 AGTTTTTCCC
* * * *
19857970 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
19857990 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
19858009 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
19858030 AGCTC
1 AGCTC
19858035 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:19860171 original size:30 final size:30
Alignment explanation
Indices: 19860137--19860233 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
19860127 TAAACTAAAA
19860137 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
19860167 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
19860197 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
19860227 TGAGCTA
1 TGAGCTA
19860234 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:19863217 original size:13 final size:13
Alignment explanation
Indices: 19863199--19863223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19863189 TGGTCATCAT
19863199 GGTGTGAACACAA
1 GGTGTGAACACAA
19863212 GGTGTGAACACA
1 GGTGTGAACACA
19863224 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:19864574 original size:21 final size:22
Alignment explanation
Indices: 19864548--19864591 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
19864538 AAACGAGCTC
19864548 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
19864569 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
19864591 G
1 G
19864592 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTGAGCTTGAA
Found at i:19867622 original size:15 final size:15
Alignment explanation
Indices: 19867602--19867635 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19867592 CTCTCTTTTG
19867602 TTTTCT-TTTTCTTAT
1 TTTTCTCTTTT-TTAT
19867617 TTTTCTCTTTTTTAT
1 TTTTCTCTTTTTTAT
19867632 TTTT
1 TTTT
19867636 TTACAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTCTTTTTTAT
Found at i:19871743 original size:20 final size:20
Alignment explanation
Indices: 19871720--19871766 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19871710 GGGTTAAGAT
*
19871720 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
19871740 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
19871760 TGAGCTG
1 TGAGCTG
19871767 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:19872997 original size:17 final size:18
Alignment explanation
Indices: 19872975--19873008 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19872965 ACAACACTCC
*
19872975 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
19872992 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
19873009 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:19873116 original size:15 final size:16
Alignment explanation
Indices: 19873091--19873122 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
19873081 TATCTCACAC
19873091 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
19873107 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
19873122 T
1 T
19873123 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:19874062 original size:13 final size:13
Alignment explanation
Indices: 19874041--19874170 Score: 52
Period size: 12 Copynumber: 9.2 Consensus size: 13
19874031 CTCGCAAGAC
*
19874041 TTTTCACTTTTTT
1 TTTTAACTTTTTT
19874054 TTTTAACTTGATTTT
1 TTTTAACTT--TTTT
*
19874069 TTTGGTCACCTTTTTT
1 TTT--T-AACTTTTTT
19874085 TTTGCTCAA--TTTTT
1 TTT--T-AACTTTTTT
*
19874099 TTTTCACTTTTTT
1 TTTTAACTTTTTT
*
19874112 TTTTGAATATTTTTT
1 TTTT-AA-CTTTTTT
19874127 TTTTCAATCAATTTTTT
1 TTTT-AA-C--TTTTTT
*
19874144 TTTGAA-TTTTTT
1 TTTTAACTTTTTT
*
19874156 TTTTGA-TTTTTT
1 TTTTAACTTTTTT
19874168 TTT
1 TTT
19874171 GTTACTCCAA
Statistics
Matches: 94, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
11 1 0.01
12 20 0.21
13 17 0.18
14 9 0.10
15 20 0.21
16 13 0.14
17 10 0.11
18 4 0.04
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTAACTTTTTT
Found at i:19874097 original size:15 final size:16
Alignment explanation
Indices: 19874065--19874102 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19874055 TTTAACTTGA
* *
19874065 TTTTTTTGGTCACCTT
1 TTTTTTTGCTCACATT
19874081 TTTTTTTGCTCA-ATT
1 TTTTTTTGCTCACATT
19874096 TTTTTTT
1 TTTTTTT
19874103 CACTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.71
Consensus pattern (16 bp):
TTTTTTTGCTCACATT
Found at i:19874113 original size:44 final size:43
Alignment explanation
Indices: 19874079--19874170 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 43
19874069 TTTGGTCACC
*
19874079 TTTTTTTTTGC-TCAATTTTTTTTTCACTTTTTTTTTTGAATA
1 TTTTTTTTTGCATCAATTTTTTTTTAACTTTTTTTTTTGAATA
*
19874121 TTTTTTTTTTCAATCAATTTTTTTTTGAA-TTTTTTTTTTG-AT-
1 TTTTTTTTTGC-ATCAATTTTTTTTT-AACTTTTTTTTTTGAATA
19874163 TTTTTTTT
1 TTTTTTTT
19874171 GTTACTCCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
42 18 0.40
43 2 0.04
44 24 0.53
45 1 0.02
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (43 bp):
TTTTTTTTTGCATCAATTTTTTTTTAACTTTTTTTTTTGAATA
Found at i:19874125 original size:28 final size:29
Alignment explanation
Indices: 19874041--19874159 Score: 95
Period size: 28 Copynumber: 4.1 Consensus size: 29
19874031 CTCGCAAGAC
*
19874041 TTTTCACTTTTTTTTTT-AACTTGATTTTTT
1 TTTTCACTTTTTTTTTTGAA--TCATTTTTT
** * * *
19874071 TGGTCACCTTTTTTTTTG-CTCAATTTTT
1 TTTTCACTTTTTTTTTTGAATCATTTTTT
19874099 TTTTCACTTTTTTTTTTGAAT-ATTTTTT
1 TTTTCACTTTTTTTTTTGAATCATTTTTT
*
19874127 TTTTCAATCAATTTTTTTTTGAAT--TTTTTT
1 TTTTC-A-C-TTTTTTTTTTGAATCATTTTTT
19874157 TTT
1 TTT
19874160 GATTTTTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
28 33 0.46
29 2 0.03
30 24 0.33
31 13 0.18
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.71
Consensus pattern (29 bp):
TTTTCACTTTTTTTTTTGAATCATTTTTT
Found at i:19874153 original size:11 final size:12
Alignment explanation
Indices: 19874136--19874171 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
19874126 TTTTTCAATC
19874136 AATTTTTTTTTG
1 AATTTTTTTTTG
19874148 AATTTTTTTTTTG
1 AA-TTTTTTTTTG
19874161 -ATTTTTTTTTG
1 AATTTTTTTTTG
19874172 TTACTCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.43
12 3 0.13
13 10 0.43
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:19875681 original size:20 final size:20
Alignment explanation
Indices: 19875658--19875704 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19875648 GGGTTAAGAT
*
19875658 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
19875678 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
19875698 TGAGCTG
1 TGAGCTG
19875705 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:19876833 original size:21 final size:22
Alignment explanation
Indices: 19876807--19876850 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
19876797 AAACGAGCTC
19876807 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
19876828 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
19876850 G
1 G
19876851 GAGTATGCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTGAGCTTGAA
Found at i:19877920 original size:6 final size:6
Alignment explanation
Indices: 19877887--19877919 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
19877877 CTCAAACTCT
*
19877887 TTTTCA TTCTCA TTTTCA TTTTCA TTTTC- TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
19877920 TGTTTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCA
Found at i:19877920 original size:18 final size:18
Alignment explanation
Indices: 19877884--19877928 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
19877874 TCTCTCAAAC
19877884 TCTTTTTCATTCTCATTT
1 TCTTTTTCATTCTCATTT
* * *
19877902 TCATTTTCATTTTCTTTT
1 TCTTTTTCATTCTCATTT
*
19877920 TGTTTTTCA
1 TCTTTTTCA
19877929 AAGGATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.02, T:0.69
Consensus pattern (18 bp):
TCTTTTTCATTCTCATTT
Found at i:19877950 original size:13 final size:12
Alignment explanation
Indices: 19877922--19877953 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19877912 TTTCTTTTTG
19877922 TTTTTCAAAGGA
1 TTTTTCAAAGGA
*
19877934 TTTTTCAAAGGC
1 TTTTTCAAAGGA
19877946 TTTTTCAA
1 TTTTTCAA
19877954 GTTCCCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (12 bp):
TTTTTCAAAGGA
Found at i:19878009 original size:5 final size:5
Alignment explanation
Indices: 19877999--19878057 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
19877989 GCCTCTTGCC
*
19877999 TTTCT TTTCT TTT-T ATTTCAT TTTCT TTT-T CTTCT TTTGCTT TTTCT
1 TTTCT TTTCT TTTCT -TTTC-T TTTCT TTTCT TTTCT TTT-C-T TTTCT
19878046 TTTCT TTTCT TT
1 TTTCT TTTCT TT
19878058 GTTTTCTCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
4 4 0.09
5 31 0.67
6 6 0.13
7 5 0.11
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:19878041 original size:15 final size:14
Alignment explanation
Indices: 19878000--19878057 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 14
19877990 CCTCTTGCCT
*
19878000 TTCTTTTCTTTTTAT
1 TTCTTTTCTTTTT-C
19878015 TTCATTTTCTTTTTC
1 TTC-TTTTCTTTTTC
19878030 TTCTTTTGCTTTTTC
1 TTCTTTT-CTTTTTC
19878045 TTTTCTTTTCTTT
1 --TTCTTTTCTTT
19878058 GTTTTCTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
14 4 0.11
15 13 0.34
16 14 0.37
17 7 0.18
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (14 bp):
TTCTTTTCTTTTTC
Found at i:19878058 original size:21 final size:21
Alignment explanation
Indices: 19877999--19878068 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
19877989 GCCTCTTGCC
* *
19877999 TTTCTTTTCTTTT-TATTTCAT
1 TTTCTTTTCTTTTCT-TTGCTT
*
19878020 TTTCTTTT-TCTTCTTTTGCTT
1 TTTCTTTTCTTTTC-TTTGCTT
19878041 TTTCTTTTCTTTTCTTTG-TT
1 TTTCTTTTCTTTTCTTTGCTT
19878061 TTCTCTTT
1 TT-TCTTT
19878069 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.17
21 29 0.71
22 5 0.12
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCTTTTCTTTGCTT
Found at i:19880759 original size:30 final size:30
Alignment explanation
Indices: 19880674--19880770 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19880664 TAAACTAAAA
* *
19880674 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
19880704 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
19880734 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
19880763 ATGAGCTA
1 -TGAGCTA
19880771 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:19882876 original size:12 final size:12
Alignment explanation
Indices: 19882834--19882870 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
19882824 GAAGTCCTTT
*
19882834 TCTTTTTCATTC
1 TCTTTTTCAATC
19882846 TCTTTTTCAATC
1 TCTTTTTCAATC
19882858 TCTTTTTCAATC
1 TCTTTTTCAATC
19882870 T
1 T
19882871 TATTTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (12 bp):
TCTTTTTCAATC
Found at i:19885065 original size:30 final size:30
Alignment explanation
Indices: 19885031--19885127 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19885021 AGCTCACTCC
19885031 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
19885061 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
19885091 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
19885121 TAGCTCA
1 TAGCTCA
19885128 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:19887827 original size:37 final size:37
Alignment explanation
Indices: 19887776--19887846 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
19887766 CATTCTTGTA
19887776 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
19887813 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
19887847 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:19887846 original size:6 final size:6
Alignment explanation
Indices: 19887786--19887835 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
19887776 AAGAGAAAAC
*
19887786 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
19887835 A
1 A
19887836 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:19887928 original size:11 final size:12
Alignment explanation
Indices: 19887896--19887926 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
19887886 TTGAGAGAAC
19887896 TTGAAAAAGCCT
1 TTGAAAAAGCCT
19887908 TTGAAAAAGCCT
1 TTGAAAAAGCCT
19887920 TTGAAAA
1 TTGAAAA
19887927 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:19890141 original size:30 final size:30
Alignment explanation
Indices: 19890107--19890203 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19890097 AGCTCACTCC
19890107 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
19890137 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
19890167 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
19890197 TAGCTCA
1 TAGCTCA
19890204 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:19896341 original size:20 final size:20
Alignment explanation
Indices: 19896316--19896370 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
19896306 TGTGGTTCAA
*
19896316 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
19896336 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
19896356 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
19896371 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:19898156 original size:20 final size:20
Alignment explanation
Indices: 19898131--19898185 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
19898121 TGTGGTTCAA
*
19898131 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
19898151 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
19898171 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
19898186 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:19907290 original size:10 final size:10
Alignment explanation
Indices: 19907274--19907331 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
19907264 CAACTCCGAC
19907274 CAGCTCAATT
1 CAGCTCAATT
* *
19907284 GAGCTCATTT
1 CAGCTCAATT
19907294 CAGCTCAA-T
1 CAGCTCAATT
19907303 CGAGCTCAATT
1 C-AGCTCAATT
*
19907314 TAGCTACAATT
1 CAGCT-CAATT
19907325 CAGCTCA
1 CAGCTCA
19907332 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:19907297 original size:20 final size:20
Alignment explanation
Indices: 19907274--19907334 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
19907264 CAACTCCGAC
19907274 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
19907294 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
19907315 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
19907335 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:19912372 original size:12 final size:12
Alignment explanation
Indices: 19912357--19912392 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
19912347 TCTTTTTCAA
*
19912357 TTTCTTTTTCTT
1 TTTCGTTTTCTT
19912369 TTTCGTTTTCTT
1 TTTCGTTTTCTT
19912381 TTT-GTTTTCTT
1 TTTCGTTTTCTT
19912392 T
1 T
19912393 CAATTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTCGTTTTCTT
Found at i:19913486 original size:32 final size:30
Alignment explanation
Indices: 19913426--19913491 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 30
19913416 TTAAACTTGA
*
19913426 TTTTTTTTGCTCACCTTTTTTTTTCTTTTCTT
1 TTTTTTTTGCTCA-CTTTTTTTTACTTTT-TT
19913458 TTTTTTTTGCTCTA-TTTTTTTTCACTTTTTT
1 TTTTTTTTGCTC-ACTTTTTTTT-ACTTTTTT
19913489 TTT
1 TTT
19913492 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 13 0.42
32 17 0.55
33 1 0.03
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (30 bp):
TTTTTTTTGCTCACTTTTTTTTACTTTTTT
Found at i:19913499 original size:13 final size:13
Alignment explanation
Indices: 19913483--19913543 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
19913473 TTTTTTTCAC
19913483 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
19913496 TTTTTTTTTCAAT
1 TTTTTTTTTGAAT
19913509 CAAATTTTTTTTTCGAA-
1 ----TTTTTTTTT-GAAT
19913526 TTTTTTTTTG-AT
1 TTTTTTTTTGAAT
19913538 TTTTTT
1 TTTTTT
19913544 GTTACTCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
11 1 0.03
12 7 0.17
13 21 0.52
17 9 0.22
18 2 0.05
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:19915580 original size:11 final size:13
Alignment explanation
Indices: 19915549--19915580 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
19915539 ACGTATGCAA
19915549 ATTTTTTTTCTCG
1 ATTTTTTTTCTCG
19915562 ATTTTTTTT-T-G
1 ATTTTTTTTCTCG
19915573 ATTTTTTT
1 ATTTTTTT
19915581 GAATCTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 1 0.05
13 9 0.47
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.78
Consensus pattern (13 bp):
ATTTTTTTTCTCG
Found at i:19922228 original size:20 final size:20
Alignment explanation
Indices: 19922205--19922258 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
19922195 AGTTTTTCCC
*
19922205 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
19922225 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
19922245 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
19922259 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:19922240 original size:30 final size:30
Alignment explanation
Indices: 19922205--19922278 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
19922195 AGTTTTTCCC
19922205 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19922235 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19922265 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
19922279 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19922268 original size:20 final size:20
Alignment explanation
Indices: 19922205--19922269 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
19922195 AGTTTTTCCC
* * * *
19922205 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
19922225 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
19922244 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
19922265 AGCTC
1 AGCTC
19922270 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:19923894 original size:12 final size:12
Alignment explanation
Indices: 19923877--19923947 Score: 72
Period size: 12 Copynumber: 5.7 Consensus size: 12
19923867 TTGGAGTAAC
19923877 AAAAAAA-TCAA
1 AAAAAAATTCAA
19923888 AAAAAAATTCGAA
1 AAAAAAATTC-AA
*
19923901 AAAAAATTGATTGAA
1 AAAAAA---ATTCAA
19923916 AAAAAAATTCAA
1 AAAAAAATTCAA
* *
19923928 AAAAAAAGTGAA
1 AAAAAAATTCAA
19923940 AAAAAAAT
1 AAAAAAAT
19923948 CGAGTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
11 7 0.14
12 24 0.48
13 8 0.16
15 8 0.16
16 3 0.06
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:19923945 original size:28 final size:28
Alignment explanation
Indices: 19923886--19923946 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
19923876 CAAAAAAATC
* * ***
19923886 AAAAAAAAATTCGAAAAAAAATTGATTG
1 AAAAAAAAATTCAAAAAAAAAGTGAAAA
19923914 AAAAAAAAATTCAAAAAAAAAGTGAAAA
1 AAAAAAAAATTCAAAAAAAAAGTGAAAA
19923942 AAAAA
1 AAAAA
19923947 TCGAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (28 bp):
AAAAAAAAATTCAAAAAAAAAGTGAAAA
Found at i:19923946 original size:40 final size:39
Alignment explanation
Indices: 19923877--19924007 Score: 113
Period size: 40 Copynumber: 3.2 Consensus size: 39
19923867 TTGGAGTAAC
* *
19923877 AAAAAAATCAAAAAAAAATTCGAAAAAAAATTGA-TTGAA
1 AAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGAGTT-AA
19923916 AAAAAAATTCAAAAAAAAAGT-GAAAAAAAAATCGAGTTAA
1 AAAAAAA-TCAAAAAAAAAGTCG-AAAAAAAATCGAGTTAA
** * *
19923956 AAAAAAGAAGAAAAAAAAAGGTGAGCAAAAAAAAATCAAGTTTAA
1 AAAAAA-ATCAAAAAAAAA-GT---CGAAAAAAAATCGAG-TTAA
19924001 AAAAAAA
1 AAAAAAA
19924008 AGTGAAAAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
39 8 0.11
40 40 0.53
41 5 0.07
44 13 0.17
45 10 0.13
ACGTcount: A:0.71, C:0.05, G:0.11, T:0.14
Consensus pattern (39 bp):
AAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGAGTTAA
Found at i:19925026 original size:12 final size:12
Alignment explanation
Indices: 19924995--19925131 Score: 54
Period size: 12 Copynumber: 11.4 Consensus size: 12
19924985 CCATTGAGCG
19924995 AGAAA-AGAAGAA
1 AGAAATAGAA-AA
* *
19925007 AGAGATTGAAAA
1 AGAAATAGAAAA
*
19925019 AGAAATTG--AA
1 AGAAATAGAAAA
*
19925029 AGAAA-ACAAAA
1 AGAAATAGAAAA
19925040 AGAAA-ACGAAAA
1 AGAAATA-GAAAA
* *
19925052 AGAAAAAGAAAT
1 AGAAATAGAAAA
*
19925064 TGCAAA-AGAAAA
1 AG-AAATAGAAAA
*
19925076 AGAAATCGAAAA
1 AGAAATAGAAAA
** *
19925088 AGTGAGAGAAAA
1 AGAAATAGAAAA
19925100 AGAAA-ATGAAGAA
1 AGAAATA-GAA-AA
*
19925113 ATGAAAATTGAAAA
1 A-G-AAATAGAAAA
19925127 AGAAA
1 AGAAA
19925132 AAGCGAAAAA
Statistics
Matches: 95, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
10 7 0.07
11 12 0.13
12 55 0.58
13 11 0.12
14 4 0.04
15 6 0.06
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (12 bp):
AGAAATAGAAAA
Found at i:19925057 original size:18 final size:18
Alignment explanation
Indices: 19925031--19925134 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
19925021 AAATTGAAAG
*
19925031 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
19925049 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
19925067 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
19925085 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
19925103 AAATGAAGAAATGAAAATTGA
1 AAAAGAA-AAA-GAAAA-CGA
19925124 AAAAGAAAAAG
1 AAAAGAAAAAG
19925135 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.70, C:0.04, G:0.18, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:19925059 original size:6 final size:6
Alignment explanation
Indices: 19925027--19925134 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
19925017 AAAGAAATTG
* * ** *
19925027 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
19925074 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAA GAAATGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -AAA-GAA AA-AGAA
19925125 AAAGAA AAAG
1 AAAGAA AAAG
19925135 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 60 0.80
7 9 0.12
8 3 0.04
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:19925120 original size:14 final size:13
Alignment explanation
Indices: 19925095--19925132 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
19925085 AAAAGTGAGA
19925095 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
19925107 GAAGAAATGAAAATT
1 GAA-AAA-GAAAATT
19925122 GAAAAAGAAAA
1 GAAAAAGAAAA
19925133 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 8 0.35
15 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:19925146 original size:21 final size:21
Alignment explanation
Indices: 19925096--19925146 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
19925086 AAAGTGAGAG
* *
19925096 AAAAAGAAAATGAAGAAATGA
1 AAAAAGAAAAAGAAGAAACGA
**
19925117 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-CGA
19925138 AAAAAGAAA
1 AAAAAGAAA
19925147 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.08
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAACGA
Found at i:19925186 original size:33 final size:33
Alignment explanation
Indices: 19925149--19925211 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
19925139 AAAAGAAATT
19925149 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
19925182 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
19925212 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:19927012 original size:20 final size:20
Alignment explanation
Indices: 19926989--19927042 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
19926979 AGTTTTTCCC
*
19926989 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
19927009 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
19927029 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
19927043 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:19927024 original size:30 final size:30
Alignment explanation
Indices: 19926989--19927059 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
19926979 AGTTTTTCCC
19926989 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19927019 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19927049 AGCTCGTTTGA
1 AGCTCGTTTGA
19927060 TCTTGGCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19927052 original size:20 final size:20
Alignment explanation
Indices: 19926989--19927053 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
19926979 AGTTTTTCCC
* * * *
19926989 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
19927009 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
19927028 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
19927049 AGCTC
1 AGCTC
19927054 GTTTGATCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:19929660 original size:12 final size:12
Alignment explanation
Indices: 19929638--19929669 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
19929628 CATAAAAATT
19929638 TAAACTAAGTAAA
1 TAAA-TAAGTAAA
19929651 TAAATAAGTAAA
1 TAAATAAGTAAA
19929663 TAAATAA
1 TAAATAA
19929670 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (12 bp):
TAAATAAGTAAA
Found at i:19931082 original size:23 final size:22
Alignment explanation
Indices: 19931030--19931082 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
19931020 TCCACGTCTT
*
19931030 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
19931052 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
19931075 TTTCTTTT
1 TTTCTTTT
19931083 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:19933449 original size:12 final size:12
Alignment explanation
Indices: 19933427--19933458 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
19933417 CATAAAAATT
19933427 TAAACTAAGTAAA
1 TAAA-TAAGTAAA
19933440 TAAATAAGTAAA
1 TAAATAAGTAAA
19933452 TAAATAA
1 TAAATAA
19933459 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (12 bp):
TAAATAAGTAAA
Found at i:19936845 original size:30 final size:29
Alignment explanation
Indices: 19936762--19936856 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
19936752 AACTAAAAAT
* *
19936762 AGCTAAGCTTTAGCTCTTGAGCTAAAGTTG
1 AGCTAAGATTTAGCTC-TGAGCTGAAGTTG
* * * *
19936792 AGCTGAGATTAAACTCTCAAGCTGAAGTTG
1 AGCTAAGATTTAGCTCT-GAGCTGAAGTTG
*
19936822 AGCTAAGGTTTAGCTCGTGAGCTGAA-TATG
1 AGCTAAGATTTAGCTC-TGAGCTGAAGT-TG
19936852 AGCTA
1 AGCTA
19936857 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 2 0.04
30 48 0.94
31 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (29 bp):
AGCTAAGATTTAGCTCTGAGCTGAAGTTG
Found at i:19937085 original size:17 final size:16
Alignment explanation
Indices: 19937055--19937089 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
19937045 CTTTCCTCTC
*
19937055 TTTTCTTTTGATCTTT
1 TTTTCTTTTCATCTTT
19937071 TTTTGCTTTTCATCTTT
1 TTTT-CTTTTCATCTTT
19937088 TT
1 TT
19937090 CTTTTCTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTCTTTTCATCTTT
Found at i:19938098 original size:9 final size:9
Alignment explanation
Indices: 19938076--19938109 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19938066 AAGTCAAGAA
*
19938076 TTTTTTAAT
1 TTTTTTTAT
19938085 ATTTTTTTAT
1 -TTTTTTTAT
19938095 TTTTTTTAT
1 TTTTTTTAT
19938104 TTTTTT
1 TTTTTT
19938110 CACTTTACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:19940533 original size:26 final size:26
Alignment explanation
Indices: 19940477--19940533 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
19940467 GACTTGAATA
* *
19940477 CAAGAGAGCTACTGATTTAGTTCTTC
1 CAAGTGAGCTACTGATTTAGTTCTCC
* *
19940503 AAAGTGAGCTATTGATTTAGTTCTCC
1 CAAGTGAGCTACTGATTTAGTTCTCC
19940529 CAAGT
1 CAAGT
19940534 ACCCTTCGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (26 bp):
CAAGTGAGCTACTGATTTAGTTCTCC
Found at i:19941084 original size:30 final size:30
Alignment explanation
Indices: 19941050--19941146 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19941040 AGCTCACTCC
19941050 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
19941080 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
19941110 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
19941140 TAGCTCA
1 TAGCTCA
19941147 TTTTTAGTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:19942283 original size:20 final size:20
Alignment explanation
Indices: 19942237--19942283 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19942227 AGCTCGTTTC
*
19942237 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
19942257 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
19942277 CAGCTCA
1 CAGCTCA
19942284 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:19944311 original size:30 final size:30
Alignment explanation
Indices: 19944216--19944312 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
19944206 ATCTCACTCC
*
19944216 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAAGCT
* * * * **
19944246 TATCTCAACTTCAACTTAGGAG-TTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAAG-CT
* *
19944276 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAAGCT
19944306 TAGCTCA
1 TAGCTCA
19944313 TTTTTAGTTT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 3 0.06
30 42 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAAGCT
Found at i:19944855 original size:30 final size:30
Alignment explanation
Indices: 19944821--19944917 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19944811 AGCTCACTCC
19944821 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
19944851 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
19944881 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
19944911 TAGCTCA
1 TAGCTCA
19944918 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Done.