Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 192 of 198
Found at i:59568038 original size:74 final size:78
Alignment explanation
Indices: 59567917--59568121 Score: 220
Period size: 86 Copynumber: 2.6 Consensus size: 78
59567907 CAAAATTAGT
* ** * *
59567917 GGCGTTTGTGGCAAAAGTACCGCTAAAAGTCATGATCTATAGCGGCGTTTGT-GGAAAA-AGC-G
1 GGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAACAGCAG
59567979 TC-GCTCTATAGC
66 TCAGCTCTATAGC
* *
59567991 GGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTTTGGGAAAAGCGCCG
1 GGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAA---CAG
* *
59568056 CTAAAGGTCATGGTCTATAGT
63 C---A-GTCA-GCTCTATAGC
*
59568077 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
1 GGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
59568122 AATTTTTCAT
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
74 46 0.42
75 6 0.06
79 2 0.02
84 3 0.03
86 52 0.48
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (78 bp):
GGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAACAGCAG
TCAGCTCTATAGC
Found at i:59568050 original size:43 final size:43
Alignment explanation
Indices: 59567983--59568121 Score: 251
Period size: 43 Copynumber: 3.2 Consensus size: 43
59567973 AAAGCGTCGC
*
59567983 TCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGG
1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
*
59568026 TCTATAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGG
1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
*
59568069 TCTATAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
1 TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
59568112 TCTATAGCGG
1 TCTATAGCGG
59568122 AATTTTTCAT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (43 bp):
TCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
Found at i:59572925 original size:20 final size:20
Alignment explanation
Indices: 59572900--59572945 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
59572890 AAAAAATAAA
59572900 AAAAAATCA-ATAAAATTTATT
1 AAAAAAT-ATATAAAA-TTATT
*
59572921 TAAAAATATATAAAATTATT
1 AAAAAATATATAAAATTATT
59572941 AAAAA
1 AAAAA
59572946 TTTATAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATATATAAAATTATT
Found at i:59572944 original size:19 final size:21
Alignment explanation
Indices: 59572901--59572953 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
59572891 AAAAATAAAA
59572901 AAAAATCA-ATAAAATTTATTT
1 AAAAAT-ATATAAAATTTATTT
59572922 AAAAATATATAAAA-TTA-TT
1 AAAAATATATAAAATTTATTT
*
59572941 AAAAATTTATAAA
1 AAAAATATATAAA
59572954 TGTATATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATATATAAAATTTATTT
Found at i:59572959 original size:27 final size:28
Alignment explanation
Indices: 59572918--59572973 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
59572908 AATAAAATTT
59572918 ATTTAAAAATATATA-AAATTATTA-AAA
1 ATTTAAAAATATATATAAA-TATTATAAA
* *
59572945 ATTTATAAATGTATATAAATATTATAAA
1 ATTTAAAAATATATATAAATATTATAAA
59572973 A
1 A
59572974 AATTATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
ATTTAAAAATATATATAAATATTATAAA
Found at i:59572979 original size:29 final size:30
Alignment explanation
Indices: 59572927--59572984 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
59572917 TATTTAAAAA
*
59572927 TATATAAAATTATTAAAAATTTAT-AAATG
1 TATATAAAATTATTAAAAAATTATCAAATG
59572956 TATATAAATATTA-TAAAAAATTATCAAAT
1 TATATAAA-ATTATTAAAAAATTATCAAAT
59572985 ATAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
TATATAAAATTATTAAAAAATTATCAAATG
Found at i:59572995 original size:30 final size:30
Alignment explanation
Indices: 59572935--59572996 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
59572925 AATATATAAA
* * * *
59572935 ATTATTAAAAATTTATAAATGTATATAAAT
1 ATTATTAAAAAATTATAAATATAAAAAAAT
59572965 ATTA-TAAAAAATTATCAAATATAAAAAAAT
1 ATTATTAAAAAATTAT-AAATATAAAAAAAT
59572995 AT
1 AT
59572997 AATTTCTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (30 bp):
ATTATTAAAAAATTATAAATATAAAAAAAT
Found at i:59573426 original size:10 final size:10
Alignment explanation
Indices: 59573383--59573492 Score: 52
Period size: 10 Copynumber: 11.0 Consensus size: 10
59573373 ACATCGTTTA
*
59573383 ATATATTTTT
1 ATATAATTTT
*
59573393 A-ATAAATTT
1 ATATAATTTT
* *
59573402 CTATAATTTAC
1 ATATAATTT-T
*
59573413 ATATACTTTT
1 ATATAATTTT
59573423 ATATAATTTT
1 ATATAATTTT
*
59573433 CCTAT-ATTTCT
1 -ATATAATTT-T
59573444 -TAT-ATTTT
1 ATATAATTTT
59573452 ATAATAATTTT
1 AT-ATAATTTT
59573463 -TATATATTCTT
1 ATATA-ATT-TT
*
59573474 A-ATAACTTT
1 ATATAATTTT
*
59573483 CTATAATTTT
1 ATATAATTTT
59573493 TATTTTTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
8 1 0.01
9 19 0.25
10 35 0.46
11 21 0.28
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATAATTTT
Found at i:59573438 original size:21 final size:22
Alignment explanation
Indices: 59573403--59573448 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
59573393 AATAAATTTC
59573403 TATAATTTACATATACTT-TTA
1 TATAATTTACATATACTTCTTA
* * *
59573424 TATAATTTTCCTATATTTCTTA
1 TATAATTTACATATACTTCTTA
59573446 TAT
1 TAT
59573449 TTTATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAATTTACATATACTTCTTA
Found at i:59573469 original size:30 final size:30
Alignment explanation
Indices: 59573384--59573474 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
59573374 CATCGTTTAA
* *
59573384 TATATTTT-TAATAAATTTCTATA-ATTTACA
1 TATATTTTATAAT-AATTTTTATATATTT-CT
**
59573414 TATACTTTTAT-ATAATTTTCCTATATTTCT
1 TATA-TTTTATAATAATTTTTATATATTTCT
59573444 TATATTTTATAATAATTTTTATATA-TTCT
1 TATATTTTATAATAATTTTTATATATTTCT
59573473 TA
1 TA
59573475 ATAACTTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
29 12 0.24
30 28 0.55
31 10 0.20
32 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (30 bp):
TATATTTTATAATAATTTTTATATATTTCT
Found at i:59573470 original size:21 final size:21
Alignment explanation
Indices: 59573383--59573494 Score: 78
Period size: 20 Copynumber: 5.5 Consensus size: 21
59573373 ACATCGTTTA
*
59573383 ATATATTTTTAATAAATTTCT
1 ATATATTTTTAATAACTTTCT
59573404 ATA-A--TTTACATATACTTT-T
1 ATATATTTTTA-ATA-ACTTTCT
* **
59573423 ATATAATTTTCCTATA-TTTCT
1 ATATATTTTTAATA-ACTTTCT
*
59573444 -TATATTTTATAATAA-TTTTT
1 ATATATTTT-TAATAACTTTCT
*
59573464 ATATATTCTTAATAACTTTCT
1 ATATATTTTTAATAACTTTCT
59573485 ATA-ATTTTTA
1 ATATATTTTTA
59573495 TTTTTTTAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
18 4 0.06
19 7 0.10
20 33 0.46
21 25 0.35
22 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTTTTAATAACTTTCT
Found at i:59573516 original size:26 final size:26
Alignment explanation
Indices: 59573487--59573562 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 26
59573477 AACTTTCTAT
59573487 AATTTTTATTTTTTTAATTTTAACAA-
1 AATTTTTATTTTTTTAATTTTAA-AAC
* *
59573513 AATTTAAATATTTTTCTATATTTTAAAAC
1 AATTT--TTATTTTTTTA-ATTTTAAAAC
*
59573542 AAGTTTTATTTATTTT-ATTTT
1 AATTTTTATTT-TTTTAATTTT
59573563 CTTACCACGT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 10 0.25
27 5 0.12
28 14 0.35
29 11 0.28
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (26 bp):
AATTTTTATTTTTTTAATTTTAAAAC
Found at i:59581122 original size:26 final size:26
Alignment explanation
Indices: 59581063--59581123 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
59581053 AGCCATATTG
*
59581063 GGAAGCTCACAAAGAGCCAATTAACG
1 GGAAGCTCACAAAGAGCCAATTAACA
59581089 GGAAGCTCACAAAGAGCC-ATATAACA
1 GGAAGCTCACAAAGAGCCAAT-TAACA
*
59581115 GGATGCTCA
1 GGAAGCTCA
59581124 TAAGAGCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.13
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCAATTAACA
Found at i:59582545 original size:2 final size:2
Alignment explanation
Indices: 59582529--59582570 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
59582519 TTACGAATGG
* *
59582529 TA TA TA GA TA AA 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
59582571 CCCATTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:59583205 original size:41 final size:41
Alignment explanation
Indices: 59583161--59583346 Score: 284
Period size: 41 Copynumber: 4.5 Consensus size: 41
59583151 AACTTTAAGT
*
59583161 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAT
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
59583202 CTAGTAGGCTAAGTGCCGGTGATCTGAATCAAGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
59583243 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * *
59583284 CTAGCAGGCTAAGTGCCAGTGAT-TGGAATTAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
*
59583325 CTAGCAGGCTAAGTGCTGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
59583347 ATATGTTAAA
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 1 0.01
41 132 0.99
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:59583891 original size:45 final size:45
Alignment explanation
Indices: 59583827--59583916 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
59583817 AGCCATACGA
59583827 AATTAGCTTATTTTTCTTATGGTTTAACTGAACTGAAATGTTATG
1 AATTAGCTTATTTTTCTTATGGTTTAACTGAACTGAAATGTTATG
59583872 AATTAGCTTATTTTTCTTATGGTTTAACTGAACTGAAATGTTATG
1 AATTAGCTTATTTTTCTTATGGTTTAACTGAACTGAAATGTTATG
59583917 TTTTGTTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (45 bp):
AATTAGCTTATTTTTCTTATGGTTTAACTGAACTGAAATGTTATG
Found at i:59590110 original size:2 final size:2
Alignment explanation
Indices: 59590105--59590158 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
59590095 TTTTTTTGAC
59590105 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
*
59590147 AT -T AT AA AT AT A
1 AT AT AT AT AT AT A
59590159 GTTTTGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59600695 original size:124 final size:124
Alignment explanation
Indices: 59600245--59600712 Score: 432
Period size: 124 Copynumber: 3.8 Consensus size: 124
59600235 TAAAAAGGAA
* * * ** * ** *
59600245 CATAAAACTTAGCTTCAATGCATGCAGTCCTTTGAATCTCGAAATATCGAATGTTACGATCATAT
1 CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCGAACATTTCGATCATAT
* * *
59600310 -AA-AAATCTACTATTTACTTGGGAAGCAAGAAACAATCAGACATCAATCTAAGAAACCAG
66 CAACAAA--TACTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAG
* * * * * *
59600369 CATACAACTTGGCTTCAATGCCTGCAATCAGTTGATTCTCGAAATATCGAACATTTCGATCACAT
1 CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCGAACATTTCGATCATAT
* ** * *
59600434 CAAC--AT-CT-CTTACTTGCTAAACAAGCAAGCATCAATCA-ACCAT-GAATC-AGAAAAACTC
66 CAACAAATACTATTTACTTGGGAAACAAG-AA--A-CAATCAGA-CATCG-ATCTA-AGAAACTA
59600492 G
124 G
* * * * *
59600493 CATACAGCTTAGCTTCGATGCATGCAGTCAGTTGAATCTTAAAATATCAAACATTTTGATCATAT
1 CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCGAACATTTCGATCATAT
* * ** *
59600558 TAGCATCTGCTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAG
66 CAACAAATACTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAG
* * * * *
59600617 AATACAACCTAGCTTCGATGCCTGCAGTCAGTTAAATCTCAAAATTTTGAACATTTCGATCATAT
1 CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCGAACATTTCGATCATAT
* *
59600682 CAACAAATACTATTTACTTAGGAAGCAAGAA
66 CAACAAATACTATTTACTTGGGAAACAAGAA
59600713 TCAGCATTAA
Statistics
Matches: 273, Mismatches: 55, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
120 13 0.05
121 4 0.01
122 1 0.00
123 3 0.01
124 227 0.83
125 6 0.02
126 1 0.00
127 4 0.01
128 14 0.05
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (124 bp):
CATACAACTTAGCTTCGATGCCTGCAGTCAGTTGAATCTCAAAATATCGAACATTTCGATCATAT
CAACAAATACTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAG
Found at i:59600710 original size:248 final size:248
Alignment explanation
Indices: 59600252--59600715 Score: 588
Period size: 248 Copynumber: 1.9 Consensus size: 248
59600242 GAACATAAAA
** * * **
59600252 CTTAGCTTCAATGCATGCAGTCCTTTGAATCTCGAAATATCGAATGTTACGATCATATAAAAATC
1 CTTAGCTTCAATGCATGCAGTCAGTTGAATCTCAAAATATCAAACATTACGATCATATAAAAATC
* * * *
59600317 TACTATTTACTTGGGAAGCAAGAAACAATCAGACATCAATCTAAGAAACCAGCATACAACTTGGC
66 TACTATTTACTTGGGAAACAAGAAACAATCAGACATCAATCTAAGAAACCAGAATACAACCTAGC
* * * **
59600382 TTCAATGCCTGCAATCAGTTGATTCTCGAAATATCGAACATTTCGATCACATCAACATCTCTTAC
131 TTCAATGCCTGCAATCAGTTAAATCTCAAAATATCGAACATTTCGATCACATCAACAAATCTTAC
* *
59600447 TTGCTAAACAAGCAAGCATCAATCAACCATGAATCAGAAAAACTCGCATACAG
196 TTACTAAACAAGCAAGAATCAATCAACCATGAATCAGAAAAACTCGCATACAG
* * ** * **
59600500 CTTAGCTTCGATGCATGCAGTCAGTTGAATCTTAAAATATCAAACATTTTGATCATATTAGCATC
1 CTTAGCTTCAATGCATGCAGTCAGTTGAATCTCAAAATATCAAACATTACGATCATATAAAAATC
* * *
59600565 TGCTATTTACTTGGGAAACAAGAAACAATCAGACATCGATCTAAGAAACTAGAATACAACCTAGC
66 TACTATTTACTTGGGAAACAAGAAACAATCAGACATCAATCTAAGAAACCAGAATACAACCTAGC
* * * * *
59600630 TTCGATGCCTGCAGTCAGTTAAATCTCAAAATTTTGAACATTTCGATCATATCAACAAATAC-TA
131 TTCAATGCCTGCAATCAGTTAAATCTCAAAATATCGAACATTTCGATCACATCAACAAAT-CTTA
* * **
59600694 TTTACTTAGGAAGCAAGAATCA
195 CTTACTAAACAAGCAAGAATCA
59600716 GCATTAAATC
Statistics
Matches: 179, Mismatches: 36, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
248 178 0.99
249 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (248 bp):
CTTAGCTTCAATGCATGCAGTCAGTTGAATCTCAAAATATCAAACATTACGATCATATAAAAATC
TACTATTTACTTGGGAAACAAGAAACAATCAGACATCAATCTAAGAAACCAGAATACAACCTAGC
TTCAATGCCTGCAATCAGTTAAATCTCAAAATATCGAACATTTCGATCACATCAACAAATCTTAC
TTACTAAACAAGCAAGAATCAATCAACCATGAATCAGAAAAACTCGCATACAG
Found at i:59600768 original size:115 final size:122
Alignment explanation
Indices: 59600626--59600852 Score: 292
Period size: 120 Copynumber: 1.9 Consensus size: 122
59600616 GAATACAACC
** *
59600626 TAGCTTCGATGCCTGCAGTCAGTTAAATCT-CAAA-AT-TTTGAACA-TTTCGATCATATCAAC-
1 TAGCTTCGATGCC-GCAGTCAGTTAAATCTCCAAATATCAATGAACATTTTCAATCATATCAACG
59600686 AAATACTATTTACTTAGGAAGCAAGAATCAGC-ATTAAATCTAAAAAACTGACAGTTTAT
65 AAA-ACTATTTACTTAGGAAGCAAGAATCAGCTA-TAAATCTAAAAAACTGACAGTTTAT
*
59600745 TAGCTTCGATG-C-CA-TCAGTTAAATCTCCAAATATCGAATGAACATTTTCAATCATATTAACG
1 TAGCTTCGATGCCGCAGTCAGTTAAATCTCCAAATATC-AATGAACATTTTCAATCATATCAACG
* * *
59600807 TAAACTATTTACTTATGAAGCAAGAATCAGCTATCAATCTAAAAAA
65 AAAACTATTTACTTAGGAAGCAAGAATCAGCTATAAATCTAAAAAA
59600853 ACTCGCATAC
Statistics
Matches: 94, Mismatches: 7, Indels: 13
0.82 0.06 0.11
Matches are distributed among these distances:
115 12 0.13
116 6 0.06
117 2 0.02
118 1 0.01
119 17 0.18
120 53 0.56
121 3 0.03
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (122 bp):
TAGCTTCGATGCCGCAGTCAGTTAAATCTCCAAATATCAATGAACATTTTCAATCATATCAACGA
AAACTATTTACTTAGGAAGCAAGAATCAGCTATAAATCTAAAAAACTGACAGTTTAT
Found at i:59605953 original size:16 final size:17
Alignment explanation
Indices: 59605917--59605962 Score: 85
Period size: 16 Copynumber: 2.8 Consensus size: 17
59605907 CCTCATCATA
59605917 TGTAGTAGAAAATTGAT
1 TGTAGTAGAAAATTGAT
59605934 TGTAGTAGAAAATT-AT
1 TGTAGTAGAAAATTGAT
59605950 TGTAGTAGAAAAT
1 TGTAGTAGAAAAT
59605963 AACTTTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (17 bp):
TGTAGTAGAAAATTGAT
Found at i:59607510 original size:220 final size:214
Alignment explanation
Indices: 59606991--59607519 Score: 682
Period size: 216 Copynumber: 2.4 Consensus size: 214
59606981 CATAAATTCG
* * * *
59606991 TTGAAGCAGTCGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTCACCCATAATCATTGA
1 TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTA-CCATAATTATTGA
* * * *
59607056 TTTTTAGTGTGCAAAACTGAAAATTTTGTTCATGTACTTATTGTTTGAAGTCAATTATTTACTGA
65 TTTTTAGTGT-CAAAACTGAAAATTCTGTTCATCTACTTATTGTTCGAAGTCAATTACTTACTGA
** * * *
59607121 ATAATTGAATGAGTAAAATTATATATTTTGCTATCTCTAAAGTTGAATTTTTGTTCTTCATCGAA
129 ATAATTGAATGAGTAAAACGATACATTGTGCTATCTCAAAAGTTGAATTTTTGTTCTTCATCGAA
*
59607186 TTATGTATAAATAGTTTAGGC
194 TTATGTATAAATACTTTAGGC
* *
59607207 TTGAACCACTTGATAATCATCAATTTTCGCTTTCTGGGTAGTTATTATTTACTCATAATTATTGA
1 TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTAC-CATAATTATTGA
* * *
59607272 TTTTTAGTGTTCAAAACTGAGAATTCTGTTTATCTAGTTATTGTTCGAAGTCAATTACTTACTGA
65 TTTTTAGTG-TCAAAACTGAAAATTCTGTTCATCTACTTATTGTTCGAAGTCAATTACTTACTGA
* * *
59607337 ATAATTGAATTAGTAAAACGATACATTGTGCTGTCTCAAAAGTT-AATTTTTTTTTGTTTTTCAT
129 ATAATTGAATGAGTAAAACGATACATTGTGCTATCTCAAAAGTTGAA----TTTTTGTTCTTCAT
* *
59607401 CGAATTGTGTCTAAATACTTTAAGGC
190 CGAATTATGTATAAATACTTT-AGGC
* ** * *
59607427 TTGAAGCACTTGATAACCATCCGTTTTCGCTTTCTGGGTAATTATTATTTACCATCATTGTTGAT
1 TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTACCATAATTATTGAT
*
59607492 TTTTAGTGCTCAAAAACTGAAAAATCTG
66 TTTTAGTG-TC-AAAACTGAAAATTCTG
59607520 CTTATTTTAC
Statistics
Matches: 271, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
215 3 0.01
216 150 0.55
217 1 0.00
219 52 0.19
220 65 0.24
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (214 bp):
TTGAAGCACTTGATAATCATCAATTTTCGCTTTCTGGGTAATTATTATTTACCATAATTATTGAT
TTTTAGTGTCAAAACTGAAAATTCTGTTCATCTACTTATTGTTCGAAGTCAATTACTTACTGAAT
AATTGAATGAGTAAAACGATACATTGTGCTATCTCAAAAGTTGAATTTTTGTTCTTCATCGAATT
ATGTATAAATACTTTAGGC
Found at i:59616909 original size:14 final size:14
Alignment explanation
Indices: 59616890--59616925 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
59616880 ATTGGTTTTC
59616890 GAAATGGGTTATTT
1 GAAATGGGTTATTT
59616904 GAAATGGGTTATTT
1 GAAATGGGTTATTT
59616918 GAAATGGG
1 GAAATGGG
59616926 ACCTTCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (14 bp):
GAAATGGGTTATTT
Found at i:59627187 original size:15 final size:16
Alignment explanation
Indices: 59627169--59627205 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
59627159 TTATAATATG
*
59627169 AAATTT-TATTATTAA
1 AAATTTGTAATATTAA
59627184 AAATTTGTAATATT-A
1 AAATTTGTAATATTAA
59627199 AAATTTG
1 AAATTTG
59627206 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
AAATTTGTAATATTAA
Found at i:59629426 original size:19 final size:18
Alignment explanation
Indices: 59629402--59629445 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
59629392 AATTATTAAT
59629402 AAATAAATATTAAAATATA
1 AAATAAAT-TTAAAATATA
*
59629421 AAAT-AATTTAAATTATA
1 AAATAAATTTAAAATATA
59629438 AAA-AAATT
1 AAATAAATT
59629446 AACAATAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 16 0.70
18 3 0.13
19 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAAATTTAAAATATA
Found at i:59629447 original size:16 final size:16
Alignment explanation
Indices: 59629400--59629452 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
59629390 TAAATTATTA
59629400 ATAAATAAATATTAAAAT
1 ATAAA-AAA-ATTAAAAT
* *
59629418 ATAAAATAATTTAAATT
1 ATAAAA-AAATTAAAAT
59629435 ATAAAAAAATTAACAAT
1 ATAAAAAAATTAA-AAT
59629452 A
1 A
59629453 ATCAACCCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 6 0.21
17 16 0.55
18 7 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAAAAATTAAAAT
Found at i:59629884 original size:55 final size:54
Alignment explanation
Indices: 59629818--59630088 Score: 301
Period size: 58 Copynumber: 4.8 Consensus size: 54
59629808 TCTTTTTTGA
* * * * *
59629818 GTTTTTGTTGCCTTTTGACTTGATGGGTACTTTTAATTTCATTGTTATTTTGCGG
1 GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTC-TTGTTAGTTTGTGG
*
59629873 GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATATCTTGTTTAGTTTGTGG
1 GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTCTTG-TTAGTTTGTGG
* * * *
59629928 GTTTTTCTTCTTGCCCTTCGGCTTGATGTGTAGTTTTAATTTCTTTGTTATTTTGTGG
1 G--TTT-TTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTC-TTGTTAGTTTGTGG
** *
59629986 GTTTTTTTTCTTGCCTTTTGATTTGATGGGTAATTTTAATTTCTTTGTTAGTTTGTAGG
1 G---TTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTC-TTGTTAGTTTGT-GG
* *
59630045 GTTCTT-TTGCCTTTTGGCTTGATGGGTAGTTTTAGTTTCTTGTT
1 GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTCTTGTT
59630089 TAATTTGAGG
Statistics
Matches: 186, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
54 8 0.04
55 75 0.40
56 4 0.02
57 3 0.02
58 85 0.46
59 11 0.06
ACGTcount: A:0.11, C:0.10, G:0.23, T:0.56
Consensus pattern (54 bp):
GTTTTTCTTGCCTTTTGGCTTGATGGGTAGTTTTAATTTCTTGTTAGTTTGTGG
Found at i:59634206 original size:5 final size:5
Alignment explanation
Indices: 59634196--59634234 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
59634186 AAAATTTAAA
59634196 AATAT AATAT AATAT -ATAT AATAT AAT-T -ATAT AA-AT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
59634235 GTGATATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 2 0.07
4 10 0.33
5 18 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:59634220 original size:19 final size:17
Alignment explanation
Indices: 59634192--59634234 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
59634182 ATTTAAAATT
59634192 TAAA-AATATAATATAATA
1 TAAATAATATAAT-T-ATA
*
59634210 TATATAATATAATTATA
1 TAAATAATATAATTATA
59634227 TAAATAAT
1 TAAATAAT
59634235 GTGATATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
19 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATAATATAATTATA
Found at i:59634241 original size:14 final size:13
Alignment explanation
Indices: 59634197--59634234 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
59634187 AAATTTAAAA
59634197 ATATAATATAATAT
1 ATATAATATAAT-T
59634211 ATATAATATAATT
1 ATATAATATAATT
59634224 ATATAA-ATAAT
1 ATATAATATAAT
59634235 GTGATATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:59636252 original size:43 final size:42
Alignment explanation
Indices: 59636160--59636252 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 42
59636150 CTTACGTATG
*
59636160 ATCACTTATCATTTGTCCCTGATCAGATAAGTGTAGCAAAGTT
1 ATCACTTATCATTTGTCCCTGATCAGATAAGTATAGC-AAGTT
* * *
59636203 ACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGC-ATTT
1 ATCACTTATCA-TTTGTC-CCTGATCAGATAAGTATAGCAAGTT
59636246 ATCACTT
1 ATCACTT
59636253 TTTCACTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
43 19 0.44
44 6 0.14
45 18 0.42
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (42 bp):
ATCACTTATCATTTGTCCCTGATCAGATAAGTATAGCAAGTT
Found at i:59636259 original size:36 final size:36
Alignment explanation
Indices: 59636205--59636313 Score: 173
Period size: 36 Copynumber: 3.0 Consensus size: 36
59636195 GCAAAGTTAC
*
59636205 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* * *
59636241 CATTTATCACTTTTTCACTTGATCAAATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
59636277 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
59636313 C
1 C
59636314 TAAAGCTACT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:59641119 original size:151 final size:151
Alignment explanation
Indices: 59640845--59641151 Score: 533
Period size: 151 Copynumber: 2.0 Consensus size: 151
59640835 GTATCCAAAA
* * *
59640845 CTACTAGGTTTAGTGATGATATTATCAGATCTAGATGGATTGATCCATTGTGAATGGTTGGGATT
1 CTACTAGGTCTAGTGATGATAATATCAGATCTAGATGGATTGATCCAGTGTGAATGGTTGGGATT
*
59640910 CCATGATTGTAGATGATAAGTTGTAGACAAAACGAACCAATGCTCAAGACCTAGAATAAGACCGA
66 CCATGATTGTAGATGATAAGTTGTAGACAAAACAAACCAATGCTCAAGACCTAGAATAAGACCGA
59640975 TTGAACTACAGTTATATAACT
131 TTGAACTACAGTTATATAACT
* *
59640996 CTACTAGGTCTAGTGATGATAATATTAGATTTAGATGGATTGATCCAGTGTGAATGGTTGGGATT
1 CTACTAGGTCTAGTGATGATAATATCAGATCTAGATGGATTGATCCAGTGTGAATGGTTGGGATT
* *
59641061 CCATGATTGTAGATGATAAGTTGTAGATAAAACAAACCAATGCTCAAGACCTAGAATAAGACTGA
66 CCATGATTGTAGATGATAAGTTGTAGACAAAACAAACCAATGCTCAAGACCTAGAATAAGACCGA
*
59641126 TTGAACTACGGTTATATAACT
131 TTGAACTACAGTTATATAACT
59641147 CTACT
1 CTACT
59641152 GTAACTACAA
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
151 147 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (151 bp):
CTACTAGGTCTAGTGATGATAATATCAGATCTAGATGGATTGATCCAGTGTGAATGGTTGGGATT
CCATGATTGTAGATGATAAGTTGTAGACAAAACAAACCAATGCTCAAGACCTAGAATAAGACCGA
TTGAACTACAGTTATATAACT
Found at i:59644176 original size:218 final size:215
Alignment explanation
Indices: 59643786--59644422 Score: 968
Period size: 218 Copynumber: 2.9 Consensus size: 215
59643776 TTTACATAAA
* * * * *
59643786 AAGACAAGATACATGAATGACGGACTTTTCCTTGTAAAATGTTTTAAATGCAACTACCATCCCTA
1 AAGACGAGATACATGAATGATGGCCTTTTCCTTGTAAAATGTTTCAAATGCAACTACCATCCATA
* * *
59643851 TTGAAGACAAACACAACTTTACGCAAAAGAATTGCAAAAAGCAAACCCTCCAAGGCCAAGGAGCT
66 TCGAAGACAAAAACAACTTTACGCAAAAGAATTACAAAAAGCAAACCCT-CAAGGCCAAGGAGCT
*
59643916 TACACTAGTTTACAGGTCTTTTGTGACATAAAACACACTATCCCTACATATAAAATGTACAAATC
130 TACACTAGTTTGCAGGTC-TTTGTGACATAAAACACACTATCCCTACATATAAAATGTACAAATC
*
59643981 ATGATGCATTCAACTGGGGATG
194 ATGATGCATTCAACTAGGGATG
*
59644003 AAGACGAGATACATGAATGGTGGCCTTTTCCTTTGTAAAATGTTTCAAATGCAACTACCATCCAT
1 AAGACGAGATACATGAATGATGGCCTTTTCC-TTGTAAAATGTTTCAAATGCAACTACCATCCAT
** *
59644068 ATCGAAGACAAAAACAACTTTGTGCAAAAGAATTACAAAAAGCAAACCCTGCGAGGCCAAGGAGC
65 ATCGAAGACAAAAACAACTTTACGCAAAAGAATTACAAAAAGCAAACCCT-CAAGGCCAAGGAGC
* *
59644133 TTACACTAATTTGCAGGTCTATTGTGACATAAAACATACTATCCCTACATATAAAATGTACAAAT
129 TTACACTAGTTTGCAGGTCT-TTGTGACATAAAACACACTATCCCTACATATAAAATGTACAAAT
59644198 CATGATGCATTCAACTAGGGATG
193 CATGATGCATTCAACTAGGGATG
* *
59644221 AAGACGAGATACATGAATGATGGCCTTTCTCCTTATAAAATGTTTCAAATGCAACTACCATCCAC
1 AAGACGAGATACATGAATGATGGCCTTT-TCCTTGTAAAATGTTTCAAATGCAACTACCATCCAT
* * * * *
59644286 ATCGAAAACAAAAACAACTTTACACAAAAGAAATACAAAAAACAAACCCTCCAGGGCCAAGGAGC
65 ATCGAAGACAAAAACAACTTTACGCAAAAGAATTACAAAAAGCAAACCCT-CAAGGCCAAGGAGC
* *
59644351 TTAAACTAGTTTGCAGGTCTTTTTACGACATAAAACACACTATCCCTACATATAAAATGTACAAA
129 TTACACTAGTTTGCAGGTCTTTGT--GACATAAAACACACTATCCCTACATATAAAATGTACAAA
59644416 TCATGAT
192 TCATGAT
59644423 CCACCATGCT
Statistics
Matches: 382, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
217 31 0.08
218 303 0.79
219 48 0.13
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (215 bp):
AAGACGAGATACATGAATGATGGCCTTTTCCTTGTAAAATGTTTCAAATGCAACTACCATCCATA
TCGAAGACAAAAACAACTTTACGCAAAAGAATTACAAAAAGCAAACCCTCAAGGCCAAGGAGCTT
ACACTAGTTTGCAGGTCTTTGTGACATAAAACACACTATCCCTACATATAAAATGTACAAATCAT
GATGCATTCAACTAGGGATG
Found at i:59650243 original size:15 final size:16
Alignment explanation
Indices: 59650210--59650244 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
59650200 TAAATCACTT
*
59650210 AAATAAACAGTAAATC
1 AAATAAACAGTAAAAC
59650226 AAATAAAC-GTAAAAC
1 AAATAAACAGTAAAAC
59650241 AAAT
1 AAAT
59650245 CCAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAACAGTAAAAC
Found at i:59650436 original size:3 final size:3
Alignment explanation
Indices: 59650430--59650459 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
59650420 TGATGATGAT
59650430 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
59650460 TATTCTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:59652840 original size:2 final size:2
Alignment explanation
Indices: 59652833--59652861 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59652823 ATCGAAGAGC
59652833 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59652862 TCAGTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59659518 original size:16 final size:17
Alignment explanation
Indices: 59659492--59659524 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
59659482 AGCATTTATT
59659492 TTAATATTTTTAATATA
1 TTAATATTTTTAATATA
*
59659509 TTAA-ATTTTTTATATA
1 TTAATATTTTTAATATA
59659525 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAATATTTTTAATATA
Found at i:59662512 original size:204 final size:206
Alignment explanation
Indices: 59662173--59662547 Score: 501
Period size: 204 Copynumber: 1.8 Consensus size: 206
59662163 TTAGAAAAAA
* * *
59662173 TTTGAAAGTGAAATGTAAAGCATCTAAAAGTGAAAAATTGAGAATCGAAGCATTCAAAATTTAAC
1 TTTGAAAGTGAAACGTAAAGCATCAAAAAGTGAAAAATGGAGAATCGAAGCATTC-AAATTT-AC
* * *
59662238 TCTAAAATGGAAAATCAAACTAGGTAGCAACATTTCGGCCAAACATCAAAGATCAACATTGTTAA
64 TCTAAAATGGAAAATCAAACTACGTAGAAACATTTCAGCCAAACATCAAAGATCAACATTGTTAA
* * *
59662303 AAACTTAAGTCAACGTATTCGTGGATC-ACAACAAAAACAACTATACTTCGCATCAAAAAAGATT
129 AAACTTAAGTCAACATATTCATAGATCAACAACAAAAACAACTATACTTCGCATCAAAAAAGATT
59662367 TTTTTTTTTAAAT
194 TTTTTTTTTAAAT
* *
59662380 TTTGAAATTGTAACGTAAAGCATCAAAAAAGTGAAAAAATGGA-AATCGAAGCATTC-AATTT-C
1 TTTGAAAGTGAAACGTAAAGCATC-AAAAAGTG-AAAAATGGAGAATCGAAGCATTCAAATTTAC
* * * * *
59662442 TCTAAAAATGGAAATTTTAAATTACGTA-AAACCTTTCAGCC-ATCATCAAAGATCAACATTGTT
64 TCT-AAAATGGAAA-ATCAAACTACGTAGAAACATTTCAGCCAAACATCAAAGATCAACATTGTT
*
59662505 GAAAACTTAAGTCAACATATTCATAGATCAACAACAAAAACAA
127 AAAAACTTAAGTCAACATATTCATAGATCAACAACAAAAACAA
59662548 TAATATTTCG
Statistics
Matches: 146, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
204 50 0.34
205 33 0.23
206 14 0.10
207 21 0.14
208 20 0.14
209 8 0.05
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (206 bp):
TTTGAAAGTGAAACGTAAAGCATCAAAAAGTGAAAAATGGAGAATCGAAGCATTCAAATTTACTC
TAAAATGGAAAATCAAACTACGTAGAAACATTTCAGCCAAACATCAAAGATCAACATTGTTAAAA
ACTTAAGTCAACATATTCATAGATCAACAACAAAAACAACTATACTTCGCATCAAAAAAGATTTT
TTTTTTTAAAT
Found at i:59662688 original size:197 final size:198
Alignment explanation
Indices: 59662376--59662746 Score: 466
Period size: 197 Copynumber: 1.9 Consensus size: 198
59662366 TTTTTTTTTT
* * *
59662376 AAATTTTGAAATTGTAACGTAAAGCATCAAAAAAGTGAAAAAATGGAAATCGAAGCATTCAATTT
1 AAATTTTGAAATTGTAACGTAAAGCATCAAAAAAGTAAAAAAATGGAAACCGAAGCATTCAAATT
* * * * *
59662441 CTCTAAAAATGGAAATTTTAAATTACGTAAAACCTTTCAGCCATCATCAAAGATCAACATTGTTG
66 CACTAAAAATGGAAATATTAAATTACGTAAAACCTTTCAGCCACCATCAAAGATAAACATTGTTA
* * *
59662506 AAAACTT-AAGTCAACATATTCATAGATCAACAACAAAAACAATAATATTTCGCTATTATTTTTT
131 AAAAATTGAAGGCAACATACTCATAGATCAACAACAAAAACAATAATATTTCGCTATTATTTTTT
59662570 GAA
196 GAA
* * **
59662573 AAATTTTGAAATTGTAATGTAAAGCATC-TAAGGGTAAAAAAATTCGG-AACCGAAGCATTCAAA
1 AAATTTTGAAATTGTAACGTAAAGCATCAAAAAAGTAAAAAAA-T-GGAAACCGAAGCATTCAAA
* * * * *
59662636 TTCAACTGAAACT-GAAA-ATTAAATTACGTGACAACCTTCTC-GTCACCATCAAAGATAAATAT
64 TTC-ACTAAAAATGGAAATATTAAATTACGT-AAAACCTT-TCAGCCACCATCAAAGATAAACAT
*
59662698 TGTTAAAAAATTGAAGGCAACATACTCATGGATCAACAACAAAAACAAT
126 TGTTAAAAAATTGAAGGCAACATACTCATAGATCAACAACAAAAACAAT
59662747 CAAACTTCGC
Statistics
Matches: 147, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
196 21 0.14
197 83 0.56
198 43 0.29
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (198 bp):
AAATTTTGAAATTGTAACGTAAAGCATCAAAAAAGTAAAAAAATGGAAACCGAAGCATTCAAATT
CACTAAAAATGGAAATATTAAATTACGTAAAACCTTTCAGCCACCATCAAAGATAAACATTGTTA
AAAAATTGAAGGCAACATACTCATAGATCAACAACAAAAACAATAATATTTCGCTATTATTTTTT
GAA
Found at i:59666143 original size:23 final size:24
Alignment explanation
Indices: 59666109--59666153 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
59666099 AAATGTATTT
*
59666109 ATAATATAAAATATTAATATTTTA
1 ATAATATAAAATATGAATATTTTA
59666133 ATAATAT-AAATATGAATATTT
1 ATAATATAAAATATGAATATTT
59666154 ATTTAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAATATAAAATATGAATATTTTA
Found at i:59684262 original size:23 final size:23
Alignment explanation
Indices: 59684232--59684279 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
59684222 TCGATGAATC
59684232 ATTTCTTTTGACAGAAGAAAATT
1 ATTTCTTTTGACAGAAGAAAATT
59684255 ATTTCTTTTGACAGAAGAAAATT
1 ATTTCTTTTGACAGAAGAAAATT
59684278 AT
1 AT
59684280 GTAAACACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (23 bp):
ATTTCTTTTGACAGAAGAAAATT
Found at i:59693694 original size:15 final size:15
Alignment explanation
Indices: 59693670--59693710 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
59693660 TCCTGATCGG
*
59693670 TAAACTTAAATGATT
1 TAAACCTAAATGATT
59693685 TAAACCTAAAATGATT
1 TAAACCT-AAATGATT
*
59693701 TGAACCTAAA
1 TAAACCTAAA
59693711 ATAATCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (15 bp):
TAAACCTAAATGATT
Found at i:59693698 original size:16 final size:16
Alignment explanation
Indices: 59693677--59693712 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
59693667 CGGTAAACTT
59693677 AAATGATTTAAACCTA
1 AAATGATTTAAACCTA
*
59693693 AAATGATTTGAACCTA
1 AAATGATTTAAACCTA
59693709 AAAT
1 AAAT
59693713 AATCTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (16 bp):
AAATGATTTAAACCTA
Found at i:59698816 original size:23 final size:23
Alignment explanation
Indices: 59698786--59698835 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
59698776 TTTCAATCCC
*
59698786 TTAA-AAATGATGAAACTATATA
1 TTAACAAATGATAAAACTATATA
* *
59698808 TTAACAAATGATAAAATTATATT
1 TTAACAAATGATAAAACTATATA
59698831 TTAAC
1 TTAAC
59698836 CTCTTAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (23 bp):
TTAACAAATGATAAAACTATATA
Found at i:59698830 original size:21 final size:22
Alignment explanation
Indices: 59698786--59698830 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
59698776 TTTCAATCCC
*
59698786 TTAAAAATGATGAAACTATATA
1 TTAAAAATGATGAAAATATATA
59698808 TTAACAAATGAT-AAAAT-TATA
1 TTAA-AAATGATGAAAATATATA
59698829 TT
1 TT
59698831 TTAACCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 8 0.38
23 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (22 bp):
TTAAAAATGATGAAAATATATA
Found at i:59701008 original size:8 final size:9
Alignment explanation
Indices: 59700985--59701011 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
59700975 TTACGTGACT
59700985 TTAAAAATA
1 TTAAAAATA
59700994 TTAAAAATA
1 TTAAAAATA
59701003 TTAAAAATA
1 TTAAAAATA
59701012 AATAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAATA
Found at i:59704069 original size:29 final size:29
Alignment explanation
Indices: 59704037--59704102 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
59704027 TCAAGTTTAC
* *
59704037 TATATAAGATTACACA-AAATCAAACTTCA
1 TATATAA-ATTACAAATAAATCAAAATTCA
59704066 TATATCAAATTACAAATTAAATCAAAATTCA
1 TATAT-AAATTACAAA-TAAATCAAAATTCA
59704097 TATATA
1 TATATA
59704103 TTTTTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 12 0.38
30 3 0.09
31 17 0.53
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.32
Consensus pattern (29 bp):
TATATAAATTACAAATAAATCAAAATTCA
Found at i:59705174 original size:15 final size:17
Alignment explanation
Indices: 59705154--59705186 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
59705144 GTTCCTCAAC
59705154 TTTGGT-TTTTA-CCAA
1 TTTGGTCTTTTATCCAA
59705169 TTTGGTCTTTTATCCAA
1 TTTGGTCTTTTATCCAA
59705186 T
1 T
59705187 AAGCACCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (17 bp):
TTTGGTCTTTTATCCAA
Found at i:59710219 original size:3 final size:3
Alignment explanation
Indices: 59710211--59710241 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59710201 TGTGTGTATT
59710211 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
59710242 GCTCTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:59710844 original size:41 final size:41
Alignment explanation
Indices: 59710787--59710867 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
59710777 ACCGAATTGA
59710787 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
*
59710828 GAAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
59710868 AATAAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (41 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
Found at i:59714708 original size:41 final size:41
Alignment explanation
Indices: 59714649--59714729 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
59714639 ACCTAATTGA
* * *
59714649 GAAAATAATTCCCTTATTCTATTAAATTACTAAAAGATAAG
1 GAAAATAATTCCCCTATTCTAATAAACTACTAAAAGATAAG
59714690 GAAAATAATTCCCCTATTCTAATAAACTACTAAAAGATAA
1 GAAAATAATTCCCCTATTCTAATAAACTACTAAAAGATAA
59714730 AATAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (41 bp):
GAAAATAATTCCCCTATTCTAATAAACTACTAAAAGATAAG
Found at i:59714791 original size:19 final size:19
Alignment explanation
Indices: 59714767--59714807 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
59714757 TGATTTATTC
59714767 TAAGATTTATCTAACTAAA
1 TAAGATTTATCTAACTAAA
*
59714786 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTAACTAAA
59714805 TAA
1 TAA
59714808 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAGATTTATCTAACTAAA
Found at i:59717207 original size:20 final size:20
Alignment explanation
Indices: 59717184--59717224 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
59717174 TTTTCTACGT
59717184 AATAAAGC-ATAAATGAAAAA
1 AATAAAGCAATAAA-GAAAAA
*
59717204 AATAAATCAATAAAGAAAAA
1 AATAAAGCAATAAAGAAAAA
59717224 A
1 A
59717225 CACTCATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (20 bp):
AATAAAGCAATAAAGAAAAA
Found at i:59720213 original size:14 final size:14
Alignment explanation
Indices: 59720179--59720213 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
59720169 TTGTCATTTC
*
59720179 ACTATTATGTTGTT
1 ACTATTTTGTTGTT
59720193 ACTATTTTGTTGTT
1 ACTATTTTGTTGTT
*
59720207 ATTATTT
1 ACTATTT
59720214 GGATATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (14 bp):
ACTATTTTGTTGTT
Found at i:59723868 original size:14 final size:14
Alignment explanation
Indices: 59723849--59723879 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59723839 ATGAGTTCAC
59723849 AAATATAATTACAG
1 AAATATAATTACAG
*
59723863 AAATATATTTACAG
1 AAATATAATTACAG
59723877 AAA
1 AAA
59723880 ATGAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (14 bp):
AAATATAATTACAG
Found at i:59737707 original size:11 final size:11
Alignment explanation
Indices: 59737693--59737722 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
59737683 TTTTTATTTT
59737693 TATTTTTAAAA
1 TATTTTTAAAA
59737704 TATTTTTAAAA
1 TATTTTTAAAA
59737715 TACTTTTT
1 TA-TTTTT
59737723 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:59740032 original size:26 final size:25
Alignment explanation
Indices: 59739979--59740044 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
59739969 TGCATTCGAA
*
59739979 TATTTTAATATTTGATTAAAATTATT
1 TATTTTAA-ATTTGATTAAAAATATT
59740005 TATTTTAAATTTGTATTAAAAA-ATTT
1 TATTTTAAATTTG-ATTAAAAATA-TT
* *
59740031 TAATTTAAACTTGA
1 TATTTTAAATTTGA
59740045 GTTTAATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.20
26 28 0.80
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (25 bp):
TATTTTAAATTTGATTAAAAATATT
Found at i:59740796 original size:25 final size:25
Alignment explanation
Indices: 59740760--59740808 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
59740750 AAGGAAGAAA
*
59740760 GTCTGCCGCTTTGGCACGTTTCTTC
1 GTCTGCCACTTTGGCACGTTTCTTC
59740785 GTCTGCCACTTTGGCACGTTTCTT
1 GTCTGCCACTTTGGCACGTTTCTT
59740809 ATTGGTCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.06, C:0.31, G:0.22, T:0.41
Consensus pattern (25 bp):
GTCTGCCACTTTGGCACGTTTCTTC
Found at i:59746172 original size:2 final size:2
Alignment explanation
Indices: 59746167--59746202 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
59746157 GTTTTTTACA
59746167 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
59746203 TAAAGGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59746651 original size:21 final size:21
Alignment explanation
Indices: 59746627--59746666 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59746617 CTAAAACCTT
*
59746627 AAACTCTAGA-TCATAAACTCG
1 AAACCCTAGACTC-TAAACTCG
59746648 AAACCCTAGACTCTAAACT
1 AAACCCTAGACTCTAAACT
59746667 TTTAAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (21 bp):
AAACCCTAGACTCTAAACTCG
Found at i:59748316 original size:24 final size:24
Alignment explanation
Indices: 59748295--59748342 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
59748285 AAGATTTATT
**
59748295 ATTTATGAGTATAATATATTTAAC
1 ATTTATGAACATAATATATTTAAC
*
59748319 ATTTATTAACATAATATATTTAAC
1 ATTTATGAACATAATATATTTAAC
59748343 TTTGATTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (24 bp):
ATTTATGAACATAATATATTTAAC
Found at i:59748350 original size:24 final size:24
Alignment explanation
Indices: 59748305--59748350 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
59748295 ATTTATGAGT
59748305 ATAATATATTTAACATTTATTAAC
1 ATAATATATTTAACATTTATTAAC
59748329 ATAATATATTTAAC-TTTGATTA
1 ATAATATATTTAACATTT-ATTA
59748351 GAATTAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (24 bp):
ATAATATATTTAACATTTATTAAC
Found at i:59757417 original size:98 final size:98
Alignment explanation
Indices: 59757302--59757499 Score: 396
Period size: 98 Copynumber: 2.0 Consensus size: 98
59757292 ATGATTGAGA
59757302 GTGATATTAACTCAACAAAATGCTTAAATAATAGTATAAATTACATAATGAATTTAAGTATTATT
1 GTGATATTAACTCAACAAAATGCTTAAATAATAGTATAAATTACATAATGAATTTAAGTATTATT
59757367 TTTGGAAGACCAAGACTTTTTGCTTGTGTTATT
66 TTTGGAAGACCAAGACTTTTTGCTTGTGTTATT
59757400 GTGATATTAACTCAACAAAATGCTTAAATAATAGTATAAATTACATAATGAATTTAAGTATTATT
1 GTGATATTAACTCAACAAAATGCTTAAATAATAGTATAAATTACATAATGAATTTAAGTATTATT
59757465 TTTGGAAGACCAAGACTTTTTGCTTGTGTTATT
66 TTTGGAAGACCAAGACTTTTTGCTTGTGTTATT
59757498 GT
1 GT
59757500 CTTCTCCCTA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (98 bp):
GTGATATTAACTCAACAAAATGCTTAAATAATAGTATAAATTACATAATGAATTTAAGTATTATT
TTTGGAAGACCAAGACTTTTTGCTTGTGTTATT
Found at i:59770333 original size:4 final size:4
Alignment explanation
Indices: 59770324--59770360 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
59770314 TTACTCAACT
*
59770324 CTAA CTAA CTAA CTAG CTAA CTAA CTAA CTAA CTAA C
1 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA C
59770361 CAGCCCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.27, G:0.03, T:0.24
Consensus pattern (4 bp):
CTAA
Found at i:59770842 original size:7 final size:7
Alignment explanation
Indices: 59770830--59770856 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
59770820 TGAATTGAAA
59770830 TTAAAAT
1 TTAAAAT
59770837 TTAAAAT
1 TTAAAAT
59770844 TTAAAAT
1 TTAAAAT
59770851 TTAAAA
1 TTAAAA
59770857 CCTGAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TTAAAAT
Found at i:59783540 original size:2 final size:2
Alignment explanation
Indices: 59783533--59783576 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
59783523 AAGTTAACAT
59783533 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
59783575 TA
1 TA
59783577 AAGAATGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59802830 original size:232 final size:232
Alignment explanation
Indices: 59802424--59802871 Score: 781
Period size: 232 Copynumber: 1.9 Consensus size: 232
59802414 TTAAATATTA
*
59802424 GGAGCAAATATATCACAATCTCAACATCAATATACTCAGTAACAAAGCAGGACTACATTCAACCA
1 GGAGCAAATATATCACAATCTCAACATCAATATACTAAGTAACAAAGCAGGACTACATTCAACCA
*
59802489 GTGTCCCACATTTAATATTTGCATACAATCTCTGCTCAGAGAAAAGTGAAACTAAATAAATATTA
66 GTGTACCACATTTAATATTTGCATACAATCTCTGCTCAGAGAAAAGTGAAACTAAATAAATATTA
* *
59802554 GGAACACAATAAAACCATGCAGCTTCCTCGTGTCCTTCTAATCTCACATATAAAAGGAGGGCTCT
131 GGAACACAATAAAACCATGCAGCTTCCTCATGTCCTTCTAATCTCACATATAAAAGGAGGACTCT
59802619 TTTATTAACCATTTATGGAAGTCCCAAGTATAGCAAT
196 TTTATTAACCATTTATGGAAGTCCCAAGTATAGCAAT
* * *
59802656 GGAGCAAATATATCATAATCTCAACATCAATATACTAAGTATCAAAGCAGGACTACATTCAACCG
1 GGAGCAAATATATCACAATCTCAACATCAATATACTAAGTAACAAAGCAGGACTACATTCAACCA
* * * *
59802721 GTGTACCATATTTAATATTTGCGTACAATCTCTGCTCGGAGAAAAGTGAAACTAATTAAATATTA
66 GTGTACCACATTTAATATTTGCATACAATCTCTGCTCAGAGAAAAGTGAAACTAAATAAATATTA
59802786 GGAACACAATAAAACCATAG-AGCTTCCTCATGTCCTTCTAATCTCACATATAAAAGGAGGACTC
131 GGAACACAATAAAACCAT-GCAGCTTCCTCATGTCCTTCTAATCTCACATATAAAAGGAGGACTC
59802850 TTTTATTAACCATTTATGGAAG
195 TTTTATTAACCATTTATGGAAG
59802872 CCCTAAGAAA
Statistics
Matches: 204, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
232 203 1.00
233 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (232 bp):
GGAGCAAATATATCACAATCTCAACATCAATATACTAAGTAACAAAGCAGGACTACATTCAACCA
GTGTACCACATTTAATATTTGCATACAATCTCTGCTCAGAGAAAAGTGAAACTAAATAAATATTA
GGAACACAATAAAACCATGCAGCTTCCTCATGTCCTTCTAATCTCACATATAAAAGGAGGACTCT
TTTATTAACCATTTATGGAAGTCCCAAGTATAGCAAT
Found at i:59808317 original size:22 final size:22
Alignment explanation
Indices: 59808291--59808346 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
59808281 ATATTATTCT
*
59808291 AATATTTTTAAA-TTTAT-AAT
1 AATATTTTTAAATTTTATAAAA
*
59808311 TATATATTTTAGAATTTTATAAAA
1 AATAT-TTTTA-AATTTTATAAAA
59808335 AATATTTTTAAA
1 AATATTTTTAAA
59808347 CATTTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.14
21 5 0.17
22 4 0.14
23 10 0.34
24 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATATTTTTAAATTTTATAAAA
Found at i:59810673 original size:23 final size:24
Alignment explanation
Indices: 59810629--59810676 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
59810619 TCCCCATTTT
* *
59810629 TTATTTTTATTTTTATTTAAATAA
1 TTATTGTTATTTTTATTAAAATAA
59810653 TTATTGTTATTTTT-TTAAAATAA
1 TTATTGTTATTTTTATTAAAATAA
59810676 T
1 T
59810677 AATAATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATTGTTATTTTTATTAAAATAA
Found at i:59810685 original size:23 final size:24
Alignment explanation
Indices: 59810635--59810685 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
59810625 TTTTTTATTT
* * **
59810635 TTATTTTTATTTAAATAATTATTG
1 TTATTTTTATTAAAATAATAATAA
59810659 TTATTTTT-TTAAAATAATAATAA
1 TTATTTTTATTAAAATAATAATAA
59810682 TTAT
1 TTAT
59810686 GGTGTGGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATTTTTATTAAAATAATAATAA
Found at i:59813153 original size:3 final size:3
Alignment explanation
Indices: 59813145--59813170 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59813135 CCAATTCAAC
59813145 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
59813171 TTGTCTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:59813711 original size:7 final size:7
Alignment explanation
Indices: 59813691--59813729 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
59813681 AGAAGATTTG
*
59813691 TAGGGTT
1 TAGGATT
*
59813698 TAAGATT
1 TAGGATT
59813705 TAGGATT
1 TAGGATT
59813712 TAGGATT
1 TAGGATT
59813719 TAGGATT
1 TAGGATT
59813726 TAGG
1 TAGG
59813730 GTGTGCTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (7 bp):
TAGGATT
Found at i:59814008 original size:2 final size:2
Alignment explanation
Indices: 59814003--59814029 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59813993 AAAAAAAATA
59814003 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59814030 AACATCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59822392 original size:41 final size:41
Alignment explanation
Indices: 59822270--59822405 Score: 158
Period size: 41 Copynumber: 3.4 Consensus size: 41
59822260 ACCAGTTTGG
* *
59822270 CACCCAGTGCCTCAT--AAGATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAA-TTAATCCGAAGTAATAAATTGA
* * * *
59822310 CACCCAGTGTCTCATCG-GTTAAACCGAAG---TAAATTGG
1 CACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGA
59822347 CACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGA
*
59822388 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
59822406 CTCGAAGTCG
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
37 23 0.29
38 10 0.13
40 22 0.28
41 24 0.30
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGA
Found at i:59822617 original size:25 final size:23
Alignment explanation
Indices: 59822569--59822614 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
59822559 TACCACTTCA
59822569 ATCAATATAAATTCAATAAATTC
1 ATCAATATAAATTCAATAAATTC
*
59822592 ATCACATAGTAAA-TCAATCAATT
1 ATCA-ATA-TAAATTCAATAAATT
59822615 TCAATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (23 bp):
ATCAATATAAATTCAATAAATTC
Found at i:59823414 original size:35 final size:34
Alignment explanation
Indices: 59823368--59823458 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 34
59823358 TTTATCATTA
* *
59823368 TAATATAATAATATATATACT-TGACTCTTAAGTTT
1 TAATATTATAATATATATACTAT-A-TCTTAACTTT
*
59823403 TAATATTATAATATTATTATA-TATATTTTAACTTT
1 TAATATTATAATA-TA-TATACTATATCTTAACTTT
*
59823438 AAATATTTATAATATATATAC
1 TAATA-TTATAATATATATAC
59823459 ACTTATCCCG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
34 4 0.09
35 26 0.55
36 12 0.26
37 5 0.11
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (34 bp):
TAATATTATAATATATATACTATATCTTAACTTT
Found at i:59844483 original size:3 final size:3
Alignment explanation
Indices: 59844475--59844535 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
59844465 TAGATATTTT
* * *
59844475 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTG TTA TTA TTA TT- TAA TTGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
59844523 -TA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA
59844536 GATCAATGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 43 0.90
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:59844702 original size:21 final size:21
Alignment explanation
Indices: 59844677--59844719 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
59844667 AAACTAAAGT
*
59844677 AAAATAAAAG-ATAAAACAAAC
1 AAAAT-AAAGCATAAAAAAAAC
59844698 AAAATAAAGCATAAAAAAAAC
1 AAAATAAAGCATAAAAAAAAC
59844719 A
1 A
59844720 GAACCATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.77, C:0.09, G:0.05, T:0.09
Consensus pattern (21 bp):
AAAATAAAGCATAAAAAAAAC
Found at i:59844878 original size:21 final size:20
Alignment explanation
Indices: 59844849--59844889 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
59844839 TTTTTGGAGT
59844849 TTTAGAGTTGAATATTATTGAA
1 TTTAGAGTTGAA-ATT-TTGAA
59844871 TTTA-AGTTGAAATTTTGAA
1 TTTAGAGTTGAAATTTTGAA
59844890 AATTAGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 7 0.37
22 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (20 bp):
TTTAGAGTTGAAATTTTGAA
Found at i:59844951 original size:29 final size:29
Alignment explanation
Indices: 59844910--59844967 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
59844900 TTTTTTAGCA
59844910 GGGTTCATGTTGAATA-AATGATTGAATTAG
1 GGGTTCATGTTG-ATAGAATGATTG-ATTAG
* *
59844940 GGGTTTAT-TTGATAGAATTATTGATTAG
1 GGGTTCATGTTGATAGAATGATTGATTAG
59844968 AATTGATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.32
29 10 0.40
30 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.41
Consensus pattern (29 bp):
GGGTTCATGTTGATAGAATGATTGATTAG
Found at i:59845687 original size:38 final size:39
Alignment explanation
Indices: 59845585--59845693 Score: 123
Period size: 38 Copynumber: 2.8 Consensus size: 39
59845575 GACCTCGAGT
* * **
59845585 CGATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATT
1 CGATGAGATACTGGGTGTCA--ACTTTACTTCGGATAGAGC
* *
59845626 CGATGAGATACTGGGTATC-ACTTTACTTCGGCTAG-GC
1 CGATGAGATACTGGGTGTCAACTTTACTTCGGATAGAGC
*
59845663 CGATGAGATACTGGGTGTCAACTTTGCTTCG
1 CGATGAGATACTGGGTGTCAACTTTACTTCG
59845694 AACTATCCGA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
37 18 0.31
38 24 0.41
41 17 0.29
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (39 bp):
CGATGAGATACTGGGTGTCAACTTTACTTCGGATAGAGC
Found at i:59845704 original size:38 final size:37
Alignment explanation
Indices: 59845585--59845717 Score: 108
Period size: 38 Copynumber: 3.5 Consensus size: 37
59845575 GACCTCGAGT
* **
59845585 CGATGAGACACTGGGTGTCACTATTTTACTTCGGA-TAGATT
1 CGATGAGATACTGGGTGTCAC---TTTACTTC-GACTAG-GC
* *
59845626 CGATGAGATACTGGGTATCACTTTACTTCGGCTAGGC
1 CGATGAGATACTGGGTGTCACTTTACTTCGACTAGGC
* *
59845663 CGATGAGATACTGGGTGTCAACTTTGCTTCGAACTA-TC
1 CGATGAGATACTGGGTGTC-ACTTTACTTCG-ACTAGGC
**
59845701 CGATGAGGCACTGGGTG
1 CGATGAGATACTGGGTG
59845718 CCAATCTGGT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
37 19 0.24
38 37 0.47
39 3 0.04
41 19 0.24
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (37 bp):
CGATGAGATACTGGGTGTCACTTTACTTCGACTAGGC
Found at i:59845991 original size:8 final size:8
Alignment explanation
Indices: 59845978--59846004 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
59845968 TTTAAAGTTA
59845978 AATGATTT
1 AATGATTT
59845986 AATGATTT
1 AATGATTT
59845994 AATGATTT
1 AATGATTT
59846002 AAT
1 AAT
59846005 TTACTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (8 bp):
AATGATTT
Found at i:59846889 original size:31 final size:33
Alignment explanation
Indices: 59846854--59846920 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 33
59846844 CAATTTGAAA
*
59846854 AAACTAAGGTACCA-AAA-TGAATATTGAAGTC
1 AAACTAAGGTACCACAAATTGAATATTGAAATC
* *
59846885 AAACTCATGTACCACCAAATTGAATATTGAAATC
1 AAACTAAGGTACCA-CAAATTGAATATTGAAATC
59846919 AA
1 AA
59846921 GTTCAAGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 12 0.40
33 3 0.10
34 15 0.50
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (33 bp):
AAACTAAGGTACCACAAATTGAATATTGAAATC
Found at i:59846931 original size:34 final size:34
Alignment explanation
Indices: 59846864--59846931 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
59846854 AAACTAAGGT
* *
59846864 ACCAAAATGAATATTGAAGTCAAACTCATGTACC
1 ACCAAAATGAATATTGAAATCAAACTCAAGTACC
* **
59846898 ACCAAATTGAATATTGAAATCAAGTTCAAGTACC
1 ACCAAAATGAATATTGAAATCAAACTCAAGTACC
59846932 GAATAGTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (34 bp):
ACCAAAATGAATATTGAAATCAAACTCAAGTACC
Found at i:59851657 original size:23 final size:23
Alignment explanation
Indices: 59851631--59851752 Score: 226
Period size: 23 Copynumber: 5.3 Consensus size: 23
59851621 ATAAGTGCCA
*
59851631 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
59851654 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
59851677 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
59851700 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
59851723 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
59851746 CACTGAT
1 CACTGAT
59851753 CAATAACATT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 96 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATACGTAGCCGAAGCTAC
Found at i:59852004 original size:18 final size:17
Alignment explanation
Indices: 59851978--59852016 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
59851968 ATTTTCCTTC
59851978 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
59851995 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
59852013 CACA
1 CACA
59852017 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:59856450 original size:22 final size:21
Alignment explanation
Indices: 59856410--59856456 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
59856400 GAAAATATAT
* *
59856410 AATTTAAAAAAAATCTAAAAG
1 AATTCAAAAAAAATATAAAAG
*
59856431 AATTCAAAAAAGAATATAAAAT
1 AATTCAAAAAA-AATATAAAAG
59856453 AATT
1 AATT
59856457 TAAGAGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (21 bp):
AATTCAAAAAAAATATAAAAG
Found at i:59862788 original size:32 final size:33
Alignment explanation
Indices: 59862723--59862799 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
59862713 CTGTCAGACT
59862723 TAAATTT--TAAATTTTAAAAAGTTAAAAAAAA
1 TAAATTTCATAAATTTTAAAAAGTTAAAAAAAA
59862754 TAAATTTCATAAATTTTAAAAAGTT-AAAAAAA
1 TAAATTTCATAAATTTTAAAAAGTTAAAAAAAA
59862786 TAAATTTCATAAAT
1 TAAATTTCATAAAT
59862800 AAAAGTAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
31 7 0.16
32 21 0.48
33 16 0.36
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (33 bp):
TAAATTTCATAAATTTTAAAAAGTTAAAAAAAA
Found at i:59865296 original size:22 final size:22
Alignment explanation
Indices: 59865270--59865316 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
59865260 ATGAGAATTT
*
59865270 TTAAAAATGTTGGAGGGTCTAA
1 TTAAAAATGTTGGAAGGTCTAA
* * *
59865292 TTAAAACTTTTGGAAGGTTTAA
1 TTAAAAATGTTGGAAGGTCTAA
59865314 TTA
1 TTA
59865317 GAATATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (22 bp):
TTAAAAATGTTGGAAGGTCTAA
Found at i:59865320 original size:53 final size:51
Alignment explanation
Indices: 59865222--59865355 Score: 144
Period size: 53 Copynumber: 2.5 Consensus size: 51
59865212 GGATTTAATT
* * * *
59865222 AAAATTTGGACGGTTTAGTTAAAATTTTGAGAGGATTAATGAGAATTTTTA
1 AAAATTTGGAGGGTCTAATTAAAATTTTGAGAGGATTAATGAGAATATTTA
* *
59865273 AAAATGTTGGAGGGTCTAATTAAAACTTTTG-GAAGGTTTAATTAGAATATTTA
1 AAAAT-TTGGAGGGTCTAATTAAAA-TTTTGAG-AGGATTAATGAGAATATTTA
* *
59865326 AAAATTTCGAGGGGAGCTAATTAAAATTTT
1 AAAATTTGGA-GGG-TCTAATTAAAATTTT
59865356 CAAAAATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
51 5 0.07
52 21 0.30
53 34 0.49
54 10 0.14
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (51 bp):
AAAATTTGGAGGGTCTAATTAAAATTTTGAGAGGATTAATGAGAATATTTA
Found at i:59870616 original size:95 final size:96
Alignment explanation
Indices: 59870450--59870623 Score: 251
Period size: 95 Copynumber: 1.8 Consensus size: 96
59870440 ATCCCCAGCT
* * * *
59870450 TTAGTCGAAAGTAAAAAAAAATGCCATGTTAGCAATCCGTTAATGGATTAACGAAATTTTTAACG
1 TTAGTCAAAAGTAAAAAAAAAT-CCATGTCAGCAATCCATTAATGGACTAACGAAATTTTTAACG
*
59870515 GCAGTGACAAATTCGAACAATTATCTTAATTG
65 ACAGTGACAAATTCGAACAATTATCTTAATTG
* *
59870547 TTAGTCAAAAGTAAAAAAATAT-CATGTCAGCAATCCATTAATGGACTAACGGAATTTTTAACGA
1 TTAGTCAAAAGTAAAAAAAAATCCATGTCAGCAATCCATTAATGGACTAACGAAATTTTTAACGA
* *
59870611 TAGTGACCAATTC
66 CAGTGACAAATTC
59870624 AGAGTGACTA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
95 48 0.71
97 20 0.29
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (96 bp):
TTAGTCAAAAGTAAAAAAAAATCCATGTCAGCAATCCATTAATGGACTAACGAAATTTTTAACGA
CAGTGACAAATTCGAACAATTATCTTAATTG
Found at i:59873603 original size:28 final size:27
Alignment explanation
Indices: 59873564--59873618 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
59873554 ACACCTTGAA
59873564 TTGTTCAATTTGACACCTAAATTTTTT
1 TTGTTCAATTTGACACCTAAATTTTTT
* * *
59873591 TTGTCTCAATTTGGCACCTCAGTTTTTT
1 TTGT-TCAATTTGACACCTAAATTTTTT
59873619 CAGTTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.51
Consensus pattern (27 bp):
TTGTTCAATTTGACACCTAAATTTTTT
Found at i:59874584 original size:17 final size:18
Alignment explanation
Indices: 59874562--59874595 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59874552 TTTTATTTTT
59874562 ATATAA-AAATTAAAAAA
1 ATATAATAAATTAAAAAA
*
59874579 ATATAATACATTAAAAA
1 ATATAATAAATTAAAAA
59874596 TATTAAAATA
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:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATATAATAAATTAAAAAA
Found at i:59886131 original size:134 final size:133
Alignment explanation
Indices: 59885987--59886232 Score: 366
Period size: 134 Copynumber: 1.8 Consensus size: 133
59885977 GCTTCACATC
** * * *
59885987 TTTTTCCTTCAATTTCGGGTCACGGCTTCTCACCTACATGGAAACATTGAAATTTCATGACAAAA
1 TTTTTCCTTCAATTTCGGACCACGGCTTCTCACCTACATGAAAACATTGAAATCTCAAGACAAAA
* *
59886052 AAATCACTAATAAATTGACAAAAATTTCAGTTTTCACACCAATTAGCAAAAAAAAAAAAAACAAC
66 AAATCACTAATAAATTAACAAAAATTTCAATTTTCACA-CAATTAGCAAAAAAAAAAAAAACAAC
59886117 ACTT
130 ACTT
* ** *
59886121 TTTTTCCTTCAATTTCGGACCACTGCTTCTCGTCTACATGAAAACATTGAAATCTCAAGATAAAA
1 TTTTTCCTTCAATTTCGGACCACGGCTTCTCACCTACATGAAAACATTGAAATCTCAAGACAAAA
* *
59886186 AGATCACTAATAAATTAACAAAAATTTCAATTTTCACACAGTTAGCA
66 AAATCACTAATAAATTAACAAAAATTTCAATTTTCACACAATTAGCA
59886233 GAACAACATC
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
133 8 0.08
134 91 0.92
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (133 bp):
TTTTTCCTTCAATTTCGGACCACGGCTTCTCACCTACATGAAAACATTGAAATCTCAAGACAAAA
AAATCACTAATAAATTAACAAAAATTTCAATTTTCACACAATTAGCAAAAAAAAAAAAAACAACA
CTT
Found at i:59897045 original size:23 final size:23
Alignment explanation
Indices: 59897019--59897062 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
59897009 TACATATTGT
59897019 TACTGTTCACGACATGACCCCAG
1 TACTGTTCACGACATGACCCCAG
* * *
59897042 TACTGTTTATGACTTGACCCC
1 TACTGTTCACGACATGACCCC
59897063 CATTACTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.30
Consensus pattern (23 bp):
TACTGTTCACGACATGACCCCAG
Found at i:59897069 original size:24 final size:23
Alignment explanation
Indices: 59897018--59897069 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
59897008 ATACATATTG
59897018 TTACTGTTCACGACATGACCCCA
1 TTACTGTTCACGACATGACCCCA
* * * *
59897041 GTACTGTTTATGACTTGACCCCCA
1 TTACTGTTCACGACATGA-CCCCA
59897065 TTACT
1 TTACT
59897070 CTTAGGACTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (23 bp):
TTACTGTTCACGACATGACCCCA
Found at i:59898764 original size:25 final size:24
Alignment explanation
Indices: 59898717--59898793 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
59898707 AGCTCCGAGT
* *
59898717 AGCCATATAACAGGAAGTTCA-AACG
1 AGCCATAT--CAGGAAGCTCACAAAG
59898742 AGCCATATCAGGAAGCTCACAAAG
1 AGCCATATCAGGAAGCTCACAAAG
* * *
59898766 AGTCTATATCAGGATGCTCATAAAG
1 AG-CCATATCAGGAAGCTCACAAAG
59898791 AGC
1 AGC
59898794 TGCGGTATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.22
24 6 0.13
25 29 0.64
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (24 bp):
AGCCATATCAGGAAGCTCACAAAG
Found at i:59906101 original size:32 final size:32
Alignment explanation
Indices: 59906065--59906140 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
59906055 AAAAAAATTT
* * *
59906065 AAGTACCGAATTAAGAAAAAAGTGTCAAGTCC
1 AAGTACCAAATTAAGAAAAAAGTATCAAGTAC
* *
59906097 AAGTATCAAATTAGGAAAAAAGTATCAAGTAC
1 AAGTACCAAATTAAGAAAAAAGTATCAAGTAC
*
59906129 AAGTACGAAATT
1 AAGTACCAAATT
59906141 GTATTAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (32 bp):
AAGTACCAAATTAAGAAAAAAGTATCAAGTAC
Found at i:59909853 original size:34 final size:34
Alignment explanation
Indices: 59909815--59909884 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
59909805 ATTGCAATTT
59909815 ATCAATAGTTTGTATATATACAATGAATTTTTTC
1 ATCAATAGTTTGTATATATACAATGAATTTTTTC
59909849 ATCAATAGTTTGTATATATACAATGAATTTTTTC
1 ATCAATAGTTTGTATATATACAATGAATTTTTTC
59909883 AT
1 AT
59909885 TCTTTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (34 bp):
ATCAATAGTTTGTATATATACAATGAATTTTTTC
Found at i:59915992 original size:14 final size:13
Alignment explanation
Indices: 59915975--59916084 Score: 54
Period size: 13 Copynumber: 8.5 Consensus size: 13
59915965 AAAATAAAAA
59915975 TTAAAAAAAGTATT
1 TTAAAAAAA-TATT
59915989 TT-AAAAAA-ATT
1 TTAAAAAAATATT
* **
59916000 TTAAAATTAAAAAAA
1 TTAAAA--AAATATT
59916015 TTAAAAAAAGTATT
1 TTAAAAAAA-TATT
59916029 TT-AAAAAA-A-T
1 TTAAAAAAATATT
59916039 TT-AAAAAA-ATT
1 TTAAAAAAATATT
* **
59916050 TTAAAATTAAAAAAA
1 TTAAAA--AAATATT
59916065 TTAAAAAAAGTATT
1 TTAAAAAAA-TATT
59916079 TTAAAA
1 TTAAAA
59916085 GTAATTTTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
10 10 0.13
11 9 0.12
12 6 0.08
13 18 0.24
14 18 0.24
15 14 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
TTAAAAAAATATT
Found at i:59916000 original size:11 final size:11
Alignment explanation
Indices: 59915986--59916055 Score: 64
Period size: 10 Copynumber: 6.8 Consensus size: 11
59915976 TAAAAAAAGT
59915986 ATTTTAAAAAA
1 ATTTTAAAAAA
59915997 ATTTT---AAA
1 ATTTTAAAAAA
59916005 A--TTAAAAAA
1 ATTTTAAAAAA
*
59916014 A-TTAAAAAAA
1 ATTTTAAAAAA
59916024 GTATTTTAAAAAA
1 --ATTTTAAAAAA
59916037 A-TTTAAAAAA
1 ATTTTAAAAAA
59916047 ATTTTAAAA
1 ATTTTAAAA
59916056 TTAAAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
6 2 0.04
8 4 0.08
9 4 0.08
10 17 0.35
11 13 0.27
12 1 0.02
13 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:59916014 original size:9 final size:9
Alignment explanation
Indices: 59915989--59916073 Score: 66
Period size: 9 Copynumber: 9.0 Consensus size: 9
59915979 AAAAAGTATT
59915989 TTAAAAAAA
1 TTAAAAAAA
**
59915998 TT-TTAAAA
1 TTAAAAAAA
59916006 TTAAAAAAA
1 TTAAAAAAA
59916015 TTAAAAAAAGTA
1 TT-AAAAAA--A
59916027 TTTTAAAAAAA
1 --TTAAAAAAA
59916038 TTTAAAAAAA
1 -TTAAAAAAA
**
59916048 TT-TTAAAA
1 TTAAAAAAA
59916056 TTAAAAAAA
1 TTAAAAAAA
59916065 TTAAAAAAA
1 TTAAAAAAA
59916074 GTATTTTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
8 12 0.20
9 23 0.38
10 16 0.26
11 1 0.02
12 1 0.02
13 6 0.10
14 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:59916045 original size:50 final size:50
Alignment explanation
Indices: 59915988--59916084 Score: 194
Period size: 50 Copynumber: 1.9 Consensus size: 50
59915978 AAAAAAGTAT
59915988 TTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAA
1 TTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAA
59916038 TTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
1 TTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
59916085 GTAATTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (50 bp):
TTTAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAA
Found at i:59916063 original size:40 final size:40
Alignment explanation
Indices: 59915955--59916045 Score: 146
Period size: 40 Copynumber: 2.2 Consensus size: 40
59915945 AAAAATTTAT
59915955 TTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAAAA
1 TTTAAAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAAAA
*
59915998 TTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAA
1 TTTAAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAA
59916038 TTTAAAAA
1 TTTAAAAA
59916046 AATTTTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
40 35 0.76
41 2 0.04
43 9 0.20
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (40 bp):
TTTAAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAAA
Found at i:59916380 original size:8 final size:8
Alignment explanation
Indices: 59916367--59916419 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
59916357 TAAAAAGTAT
59916367 TTTAAAAA
1 TTTAAAAA
59916375 TTT--AAA
1 TTTAAAAA
59916381 -TTAAAAA
1 TTTAAAAA
59916388 -TTAAAAGTA
1 TTTAAAA--A
59916397 TTTTAAAAA
1 -TTTAAAAA
59916406 TTTAAAAA
1 TTTAAAAA
59916414 TTTAAA
1 TTTAAA
59916420 TTAAAAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
5 2 0.05
6 3 0.08
7 9 0.23
8 17 0.44
9 2 0.05
11 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
TTTAAAAA
Found at i:59916394 original size:31 final size:31
Alignment explanation
Indices: 59916336--59916438 Score: 133
Period size: 31 Copynumber: 3.3 Consensus size: 31
59916326 TACCAAAATT
59916336 TATTTT-AAAA-TTAAA-TAAAATTAAAAAG
1 TATTTTAAAAATTTAAATTAAAATTAAAAAG
59916364 TATTTTAAAAATTTAAATTAAAAATT-AAAAG
1 TATTTTAAAAATTTAAATT-AAAATTAAAAAG
*
59916395 TATTTTAAAAATTTAAAAATTTAAATTAAAAAAG
1 TATTTTAAAAATTT--AAATTAAAATT-AAAAAG
59916429 TATTTTAAAA
1 TATTTTAAAA
59916439 GTTAAAGTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
28 6 0.09
29 4 0.06
30 5 0.08
31 20 0.30
32 11 0.17
33 5 0.08
34 15 0.23
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (31 bp):
TATTTTAAAAATTTAAATTAAAATTAAAAAG
Found at i:59916457 original size:15 final size:16
Alignment explanation
Indices: 59916425--59916459 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
59916415 TTAAATTAAA
59916425 AAAGTATTTTAAAAGTT
1 AAAGTATTTT-AAAGTT
59916442 AAAGTATTTT-AAGTT
1 AAAGTATTTTAAAGTT
59916457 AAA
1 AAA
59916460 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
17 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (16 bp):
AAAGTATTTTAAAGTT
Found at i:59916861 original size:18 final size:18
Alignment explanation
Indices: 59916820--59916859 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
59916810 TTTATATTTT
* *
59916820 TAAAATTATTAATTATTA
1 TAAAATTATCAATTATGA
59916838 TAAAATTATCAA-TATGA
1 TAAAATTATCAATTATGA
59916855 TAAAA
1 TAAAA
59916860 ATAATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAAATTATCAATTATGA
Found at i:59926904 original size:20 final size:20
Alignment explanation
Indices: 59926879--59926937 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
59926869 TGATTTGATT
59926879 AAAAAAATTATTAAAAATTC
1 AAAAAAATTATTAAAAATTC
59926899 AAAAAAATTA--AATAGAA--C
1 AAAAAAATTATTAA-A-AATTC
59926917 -AAAAAATTATTAAAAATTC
1 AAAAAAATTATTAAAAATTC
59926936 AA
1 AA
59926938 TTCAACCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
17 11 0.34
18 4 0.12
19 4 0.12
20 13 0.41
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAAATTATTAAAAATTC
Found at i:59926908 original size:17 final size:18
Alignment explanation
Indices: 59926880--59926937 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
59926870 GATTTGATTA
59926880 AAAAAATTATTAAAAATTC
1 AAAAAA-TATTAAAAATTC
*
59926899 AAAAAA-ATTAAATAGA-AC
1 AAAAAATATTAAA-A-ATTC
59926917 AAAAAATTATTAAAAATTC
1 AAAAAA-TATTAAAAATTC
59926936 AA
1 AA
59926938 TTCAACCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
17 6 0.19
18 9 0.28
19 11 0.34
20 6 0.19
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAAATATTAAAAATTC
Found at i:59927749 original size:22 final size:22
Alignment explanation
Indices: 59927723--59927765 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
59927713 TTAAAAAACT
*
59927723 TAAATATTTTTATAT-ATTTTTA
1 TAAATAATTTTA-ATGATTTTTA
59927745 TAAATAATTTTAATGATTTTT
1 TAAATAATTTTAATGATTTTT
59927766 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TAAATAATTTTAATGATTTTTA
Found at i:59927765 original size:23 final size:22
Alignment explanation
Indices: 59927723--59927768 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
59927713 TTAAAAAACT
*
59927723 TAAATATTTTTATATATTTTTA
1 TAAATATTTTAATATATTTTTA
59927745 TAAATAATTTTAATGAT-TTTTTA
1 TAAAT-ATTTTAAT-ATATTTTTA
59927768 T
1 T
59927769 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 14 0.67
24 2 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TAAATATTTTAATATATTTTTA
Found at i:59927807 original size:29 final size:29
Alignment explanation
Indices: 59927707--59927808 Score: 97
Period size: 29 Copynumber: 3.5 Consensus size: 29
59927697 CTCTATTTAA
*
59927707 TTAA-TTTTAAAAA-ACTTA-AATATTTT
1 TTAATTTTTAAAAATAATTATAATATTTT
* *
59927733 TATATATTTTTATAAATAATTTTAATGATTTT
1 T-TA-ATTTTTAAAAATAATTATAAT-ATTTT
59927765 TT-ATTTTTAAAAAATAAATTAT-ATATTTT
1 TTAATTTTT-AAAAAT-AATTATAATATTTT
59927794 TTAATTTTTAAAAAT
1 TTAATTTTTAAAAAT
59927809 TTTAAAAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
26 1 0.02
27 2 0.03
28 1 0.02
29 27 0.44
30 16 0.26
31 9 0.15
32 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (29 bp):
TTAATTTTTAAAAATAATTATAATATTTT
Found at i:59930296 original size:18 final size:18
Alignment explanation
Indices: 59930275--59930326 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
59930265 TAGTAACGAA
*
59930275 ATTAACAATAAAATAAAT
1 ATTAACAATAAAATAAAC
* **
59930293 ATTATAAAAT-ATTTAAAC
1 ATTA-ACAATAAAATAAAC
59930311 ATTAACAATAAAATAA
1 ATTAACAATAAAATAA
59930327 TAATAGCATA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTAACAATAAAATAAAC
Found at i:59930345 original size:36 final size:36
Alignment explanation
Indices: 59930275--59930354 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
59930265 TAGTAACGAA
* * *
59930275 ATTAACAATAAAATAAATATTATAAAATATTTAAAC
1 ATTAACAATAAAATAAATAATACAAAATAGTTAAAC
* *
59930311 ATTAACAATAAAAT-AATAATAGCATAATAGTTAAAT
1 ATTAACAATAAAATAAATAATA-CAAAATAGTTAAAC
*
59930347 AGTAACAA
1 ATTAACAA
59930355 AAACATTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 6 0.16
36 31 0.84
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (36 bp):
ATTAACAATAAAATAAATAATACAAAATAGTTAAAC
Found at i:59937490 original size:29 final size:29
Alignment explanation
Indices: 59937456--59937519 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
59937446 AATTATTACC
59937456 CTTAATATGTATATATTATTAACTCTAAA
1 CTTAATATGTATATATTATTAACTCTAAA
*
59937485 TTTAATATGTATATATTATTAACTCTAAA
1 CTTAATATGTATATATTATTAACTCTAAA
59937514 CTTAAT
1 CTTAAT
59937520 TATCGAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (29 bp):
CTTAATATGTATATATTATTAACTCTAAA
Found at i:59939869 original size:164 final size:164
Alignment explanation
Indices: 59939598--59939922 Score: 524
Period size: 164 Copynumber: 2.0 Consensus size: 164
59939588 TCAAAATTTC
* *** *
59939598 AACACTAAATCATGCGGATTTGGATGTAGTATGGTGCAGAGGAAGTAAACCTTGGTTGCTTATTG
1 AACACTAAATCATGCGGATTTAGATGTAGTATGGTGCAGAGGAAGTAAAAAGTGATTGCTTATTG
** *
59939663 CCTGCCAATAAATAACATTTAAATTTTCTATGTTCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
66 CCTGCCAATAAATAACATTTAAATTGGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
*
59939728 TGATTGAGGTCATGGTCATTTTTATCAATATGGT
131 TGATTGAGGTCATGATCATTTTTATCAATATGGT
* * *
59939762 AACACTAAATCATGTGGTTTTAGATTTAGTATGGTGCAGAGGAAGTAAAAAGTGATTGCTTATTG
1 AACACTAAATCATGCGGATTTAGATGTAGTATGGTGCAGAGGAAGTAAAAAGTGATTGCTTATTG
* *
59939827 TCTGCCAATAAATAACATTTTAATTGGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
66 CCTGCCAATAAATAACATTTAAATTGGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
59939892 TGATTGAGGTCATGATCATTTTTATCAATAT
131 TGATTGAGGTCATGATCATTTTTATCAATAT
59939923 AGTTAAATTC
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
164 147 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (164 bp):
AACACTAAATCATGCGGATTTAGATGTAGTATGGTGCAGAGGAAGTAAAAAGTGATTGCTTATTG
CCTGCCAATAAATAACATTTAAATTGGCTATGATCTTGTTGGTTGAGAATCTTCTGTTTTGATTC
TGATTGAGGTCATGATCATTTTTATCAATATGGT
Found at i:59946394 original size:47 final size:46
Alignment explanation
Indices: 59946333--59946440 Score: 137
Period size: 47 Copynumber: 2.3 Consensus size: 46
59946323 TGCAACTGAA
*
59946333 TAATATTTTCTGTAATTACACAAATACACATAACATTA-ACGAAGTTG
1 TAATATTTT-TGTAATTACACAAATACACAAAACATTACA-GAAGTTG
* *
59946380 TAATAGTTTTTGTAATTACATAAATATACAAAACATTACAGAAGTTG
1 TAATA-TTTTTGTAATTACACAAATACACAAAACATTACAGAAGTTG
*
59946427 TCATAATTTTTGTA
1 TAAT-ATTTTTGTA
59946441 GTTAGGTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
47 48 0.89
48 6 0.11
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (46 bp):
TAATATTTTTGTAATTACACAAATACACAAAACATTACAGAAGTTG
Done.