Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011373.1 Kokia drynarioides strain JFW-HI SEQ_126354, whole genome shotgun sequence
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: 611466
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 148 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:362279 original size:18 final size:18
Alignment explanation
Indices: 362238--362293 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
362228 ATGCAACTAC
362238 AATGCAAATGCACTAAAT-AA
1 AATGC-AATG-AC-AAATAAA
362258 AATGCAATGACAAATAAA
1 AATGCAATGACAAATAAA
*
362276 AATGCAATGACAACTAAA
1 AATGCAATGACAAATAAA
362294 TGCTATGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.12
18 21 0.62
19 4 0.12
20 5 0.15
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.18
Consensus pattern (18 bp):
AATGCAATGACAAATAAA
Found at i:364591 original size:16 final size:16
Alignment explanation
Indices: 364567--364606 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
364557 CATAGAATCT
*
364567 AAAAAGAAATAGA-TA
1 AAAAAGAAATAAAGTA
364582 AAAGAAGAAATAAAGTA
1 AAA-AAGAAATAAAGTA
364599 AAAAAGAA
1 AAAAAGAA
364607 GAAGAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.64
17 5 0.23
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (16 bp):
AAAAAGAAATAAAGTA
Found at i:371979 original size:50 final size:48
Alignment explanation
Indices: 371923--372069 Score: 136
Period size: 50 Copynumber: 3.0 Consensus size: 48
371913 TTAATTCGAT
*
371923 CCTTGCAACTTCAAGTATATAGGATTTGGTGTTGTAGCTTCATCTTGTA
1 CCTTGCAACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTG-A
* * * * ** * * *
371972 CCGTTGCAACTTCAGGGAGATAAAGATCTT-CTAATGTTAGTTTTAGTC-CGA
1 CC-TTGCAACTTCAAGGATAT-AGGAT-TTGGTGTTG-TAGCTTCA-TCTTGA
372023 CCTTGCAACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTG
1 CCTTGCAACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTG
372070 CTCCACTGTA
Statistics
Matches: 72, Mismatches: 19, Indels: 15
0.68 0.18 0.14
Matches are distributed among these distances:
47 2 0.03
48 9 0.12
49 9 0.12
50 31 0.43
51 10 0.14
52 9 0.12
53 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (48 bp):
CCTTGCAACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTGA
Found at i:372083 original size:50 final size:50
Alignment explanation
Indices: 372029--372186 Score: 140
Period size: 50 Copynumber: 3.1 Consensus size: 50
372019 CCGACCTTGC
372029 AACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCCACTGT
1 AACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCCACTGT
* * * ***** * * ** *
372079 AACTTCAGGGAGATAAAGATTTTCCAATGTTAGTTTTAAT-TTAATCC-TTGT
1 AACTTCAAGGATAT-AGGATTTGGTGTTG-TAG-CTTCATCTTGCTCCACTGT
* *
372130 AAATTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCCACTGC
1 AACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCCACTGT
372180 AACTTCA
1 AACTTCA
372187 GGGAGATAAA
Statistics
Matches: 74, Mismatches: 29, Indels: 10
0.65 0.26 0.09
Matches are distributed among these distances:
48 4 0.05
49 8 0.11
50 28 0.38
51 22 0.30
52 8 0.11
53 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (50 bp):
AACTTCAAGGATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCCACTGT
Found at i:372169 original size:101 final size:101
Alignment explanation
Indices: 371857--372352 Score: 550
Period size: 101 Copynumber: 5.0 Consensus size: 101
371847 AATGTTATCA
* * *
371857 AGCTTCATCTTACTTCATTGTAACTTCAGGGAGATAAAGATTTGT-CAATGTTAGTTTTAATTCG
1 AGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAAGATTT-TCCAATGTTAGTTTTAATTCG
*
371921 ATCCTTGCAACTTCAAGTATATAGGATTTGGTGTTGT
65 ATCCTTGCAACTTCAAGGATATAGGATTTGGTGTTGT
** * * * * *
371958 AGCTTCATCTTG-TACCGTTGCAACTTCAGGGAGATAAAGATCTTCTAATGTTAGTTTTAGTCCG
1 AGCTTCATCTTGCT-CCACTGTAACTTCAGGGAGATAAAGATTTTCCAATGTTAGTTTTAATTCG
372022 A-CCTTGCAACTTCAAGGATATAGGATTTGGTGTTGT
65 ATCCTTGCAACTTCAAGGATATAGGATTTGGTGTTGT
**
372058 AGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAAGATTTTCCAATGTTAGTTTTAATTTAA
1 AGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAAGATTTTCCAATGTTAGTTTTAATTCGA
* *
372123 TCCTTGTAAATTCAAGGATATAGGATTTGGTGTTGT
66 TCCTTGCAACTTCAAGGATATAGGATTTGGTGTTGT
* * ** * *
372159 AGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAAGA-TTTGC--TACTA-CTTTAA-TCCA
1 AGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAAGATTTTCCAATGTTAGTTTTAATTCGA
* * * *
372219 CTTCAC-TACAAATTC-AGGAAGATAGGATTTGGTG-CG-
66 --TC-CTTGCAACTTCAAGG-ATATAGGATTTGGTGTTGT
* * * * * *
372255 A-CTTCATCTTGCTCTAGTGTAACTTCAGGGAGATAAAGATCTGCTAATGTTAGTTTTAATTTGA
1 AGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAAGATTTTCCAATGTTAGTTTTAATTCGA
* *
372319 TCCTTGCAACTTCAAGGATATAAGATTTGTTGTT
66 TCCTTGCAACTTCAAGGATATAGGATTTGGTGTT
372353 TCATTGATCC
Statistics
Matches: 330, Mismatches: 49, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
95 35 0.11
96 4 0.01
97 10 0.03
98 50 0.15
99 9 0.03
100 96 0.29
101 126 0.38
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (101 bp):
AGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAAGATTTTCCAATGTTAGTTTTAATTCGA
TCCTTGCAACTTCAAGGATATAGGATTTGGTGTTGT
Found at i:373250 original size:20 final size:20
Alignment explanation
Indices: 373222--373276 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
373212 TCATCTCGAC
*
373222 CTCTCCTTTTTCTTTTTCTT
1 CTCTTCTTTTTCTTTTTCTT
373242 -TCATTCTTTCTT-TTTTTCTT
1 CTC-TTCTTT-TTCTTTTTCTT
373262 CTCTT-TTTTTCTTTT
1 CTCTTCTTTTTCTTTT
373277 CCCCCTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 9 0.30
20 15 0.50
21 4 0.13
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (20 bp):
CTCTTCTTTTTCTTTTTCTT
Found at i:373268 original size:13 final size:12
Alignment explanation
Indices: 373227--373275 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
373217 TCGACCTCTC
373227 CTTTTTCTT-TTT
1 CTTTTT-TTCTTT
**
373239 CTTTCATTCTTT
1 CTTTTTTTCTTT
373251 CTTTTTTTCTTCT
1 CTTTTTTTCTT-T
373264 CTTTTTTTCTTT
1 CTTTTTTTCTTT
373276 TCCCCCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 2 0.06
12 17 0.55
13 12 0.39
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
CTTTTTTTCTTT
Found at i:374186 original size:16 final size:15
Alignment explanation
Indices: 374167--374221 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
374157 TCATCTTGAC
374167 TTTTTCTTTTCTTCTT
1 TTTTTCTTTTCTT-TT
*
374183 TTTTTC-TTTCCTTT
1 TTTTTCTTTTCTTTT
*
374197 TTTTTCTTTTTTTTT
1 TTTTTCTTTTCTTTT
*
374212 TTTTTGTTTT
1 TTTTTCTTTT
374222 AAGATGCCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 8 0.24
15 20 0.59
16 6 0.18
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (15 bp):
TTTTTCTTTTCTTTT
Found at i:374207 original size:8 final size:8
Alignment explanation
Indices: 374167--374221 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 8
374157 TCATCTTGAC
374167 TTTTTCTT
1 TTTTTCTT
*
374175 TTCTTCTT
1 TTTTTCTT
374183 TTTTTC-T
1 TTTTTCTT
**
374190 TTCCT-TT
1 TTTTTCTT
374197 TTTTTCTT
1 TTTTTCTT
374205 TTTTT-TT
1 TTTTTCTT
*
374212 TTTTTGTT
1 TTTTTCTT
374220 TT
1 TT
374222 AAGATGCCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 15 0.39
8 23 0.61
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:374211 original size:14 final size:14
Alignment explanation
Indices: 374167--374215 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
374157 TCATCTTGAC
374167 TTTTTCTTTTCTTCTT
1 TTTTTCTTTT-TT-TT
**
374183 TTTTTCTTTCCTTT
1 TTTTTCTTTTTTTT
374197 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
374211 TTTTT
1 TTTTT
374216 TGTTTTAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 19 0.66
15 1 0.03
16 9 0.31
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:375109 original size:3 final size:3
Alignment explanation
Indices: 375095--375125 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
375085 ATATGAGATT
375095 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
375126 TTTAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:377270 original size:16 final size:16
Alignment explanation
Indices: 377249--377280 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
377239 TACTAACTTG
377249 TTTTCTTTTTGTCGCT
1 TTTTCTTTTTGTCGCT
377265 TTTTCTTTTTGTCGCT
1 TTTTCTTTTTGTCGCT
377281 ACTTGAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.12, T:0.69
Consensus pattern (16 bp):
TTTTCTTTTTGTCGCT
Found at i:384392 original size:27 final size:27
Alignment explanation
Indices: 384356--384417 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
384346 ATTTTTTTAG
384356 AAAAATTCATTTTTTCTTCAATCTCAA
1 AAAAATTCATTTTTTCTTCAATCTCAA
384383 AAAAATTCATTTTTTCTTCAATCTCAA
1 AAAAATTCATTTTTTCTTCAATCTCAA
384410 AAAAATTC
1 AAAAATTC
384418 CCCTTTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAATTCATTTTTTCTTCAATCTCAA
Found at i:384424 original size:26 final size:27
Alignment explanation
Indices: 384368--384426 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
384358 AAATTCATTT
***
384368 TTTCTTCAATCTCAAAAAAATTCATTT
1 TTTCTTCAATCTCAAAAAAATTCACCC
384395 TTTCTTCAATCTCAAAAAAATTC-CCC
1 TTTCTTCAATCTCAAAAAAATTCACCC
384421 TTTCTT
1 TTTCTT
384427 TGTCTTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTCTTCAATCTCAAAAAAATTCACCC
Found at i:385291 original size:12 final size:12
Alignment explanation
Indices: 385274--385298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
385264 AATAAAGGAG
385274 TTTTTATTTGTT
1 TTTTTATTTGTT
385286 TTTTTATTTGTT
1 TTTTTATTTGTT
385298 T
1 T
385299 GGGTCTTGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TTTTTATTTGTT
Found at i:387971 original size:21 final size:19
Alignment explanation
Indices: 387947--387992 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
387937 AAAAAACATA
387947 AAATAAAAAACATGAACAAAC
1 AAATAAAAAACAT-AA-AAAC
*
387968 AAATAAAATACATAAAAAC
1 AAATAAAAAACATAAAAAC
387987 -AATAAA
1 AAATAAA
387993 TAACTAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 4 0.17
20 2 0.08
21 12 0.50
ACGTcount: A:0.74, C:0.11, G:0.02, T:0.13
Consensus pattern (19 bp):
AAATAAAAAACATAAAAAC
Found at i:388033 original size:23 final size:23
Alignment explanation
Indices: 388007--388075 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
387997 TAAAGGTAAG
388007 AATATAAACAAC-ATAAATAAATA
1 AATA-AAACAACAATAAATAAATA
* *
388030 AATAAAATATCAATAAATAAA-A
1 AATAAAACAACAATAAATAAATA
**
388052 AACTAAAATTA-AATAAA-AAATA
1 AA-TAAAACAACAATAAATAAATA
388074 AA
1 AA
388076 ACAATACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 3 0.08
22 17 0.44
23 19 0.49
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (23 bp):
AATAAAACAACAATAAATAAATA
Found at i:388066 original size:18 final size:17
Alignment explanation
Indices: 388043--388076 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
388033 AAAATATCAA
388043 TAAATAAAAAACTAAAAT
1 TAAATAAAAAA-TAAAAT
388061 TAAATAAAAAATAAAA
1 TAAATAAAAAATAAAA
388077 CAATACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAATAAAAAATAAAAT
Found at i:388089 original size:8 final size:7
Alignment explanation
Indices: 388021--388093 Score: 56
Period size: 8 Copynumber: 9.3 Consensus size: 7
388011 TAAACAACAT
388021 AAATAAA
1 AAATAAA
388028 TAAATAAA
1 -AAATAAA
* *
388036 ATATCAAT
1 AAAT-AAA
388044 AAATAAA
1 AAATAAA
388051 AAACTAAAA
1 AAA-T-AAA
388060 TTAAATAAA
1 --AAATAAA
388069 AAATAAA
1 AAATAAA
388076 ACAATACAA
1 A-AATA-AA
388085 AAATAAA
1 AAATAAA
388092 AA
1 AA
388094 GTGAGATCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
7 20 0.37
8 21 0.39
9 9 0.17
10 1 0.02
11 3 0.06
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.19
Consensus pattern (7 bp):
AAATAAA
Found at i:388482 original size:68 final size:69
Alignment explanation
Indices: 388410--388545 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 69
388400 AAAATTAGAA
* * *
388410 CAAAGTAAAAATGTAGAAAGACTAAAGAAATAAATAACTCATTTTA-AAAAAATACGCGGGTCTT
1 CAAAGTAAAAATGCAGAAAGACTAAAGAAATAAATAACTCATTTTACAAAAAACACGCGGGTCCT
388474 GGGG
66 GGGG
* *
388478 CAAAGTAAAAATGCAGAAGGACTAAGGAAATAAATAACTCATTTTACAAAAAACACGCGGGTCCT
1 CAAAGTAAAAATGCAGAAAGACTAAAGAAATAAATAACTCATTTTACAAAAAACACGCGGGTCCT
388543 GGG
66 GGG
388546 TCAATTCAGG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
68 43 0.69
69 19 0.31
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (69 bp):
CAAAGTAAAAATGCAGAAAGACTAAAGAAATAAATAACTCATTTTACAAAAAACACGCGGGTCCT
GGGG
Found at i:390207 original size:20 final size:20
Alignment explanation
Indices: 390184--390224 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
390174 TTGTAGTTTC
390184 ATTTATTTAGTTGTTTAATT
1 ATTTATTTAGTTGTTTAATT
390204 ATTTATTTAGTTGTTTAATT
1 ATTTATTTAGTTGTTTAATT
390224 A
1 A
390225 CTTGTCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (20 bp):
ATTTATTTAGTTGTTTAATT
Found at i:390673 original size:16 final size:15
Alignment explanation
Indices: 390652--390687 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
390642 TACCATAAAA
*
390652 TTTTTTTTTCT-GTT
1 TTTTTTTTTTTAGTT
390666 TTTTTTTTTTTAGTT
1 TTTTTTTTTTTAGTT
390681 TTTTTTT
1 TTTTTTT
390688 GAAATAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTTAGTT
Found at i:391372 original size:12 final size:12
Alignment explanation
Indices: 391355--391388 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
391345 CTCTTATACC
*
391355 TCTTTTTCTTTT
1 TCTTTTTCCTTT
*
391367 TCTTTTCCCTTT
1 TCTTTTTCCTTT
391379 TCTTTTTCCT
1 TCTTTTTCCT
391389 ACCCTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TCTTTTTCCTTT
Found at i:408462 original size:18 final size:18
Alignment explanation
Indices: 408441--408475 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
408431 CATCTGAGTT
* *
408441 TGTGATCGCATTTGATCA
1 TGTGATCACATCTGATCA
408459 TGTGATCACATCTGATC
1 TGTGATCACATCTGATC
408476 TGGGTGCGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (18 bp):
TGTGATCACATCTGATCA
Found at i:415035 original size:11 final size:11
Alignment explanation
Indices: 415019--415043 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
415009 TATTTATCTC
415019 AAAAAAAAGAA
1 AAAAAAAAGAA
415030 AAAAAAAAGAA
1 AAAAAAAAGAA
415041 AAA
1 AAA
415044 GAGAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:419659 original size:82 final size:82
Alignment explanation
Indices: 419566--419731 Score: 332
Period size: 82 Copynumber: 2.0 Consensus size: 82
419556 TTTAGTATTC
419566 TCAAAATAAAATAATCCCTTTAGCTAGCCTATGAGTATTTTCTCTCTTTTTGATTCTTTGAGTAA
1 TCAAAATAAAATAATCCCTTTAGCTAGCCTATGAGTATTTTCTCTCTTTTTGATTCTTTGAGTAA
419631 GATTTCTTTCTTCTTCA
66 GATTTCTTTCTTCTTCA
419648 TCAAAATAAAATAATCCCTTTAGCTAGCCTATGAGTATTTTCTCTCTTTTTGATTCTTTGAGTAA
1 TCAAAATAAAATAATCCCTTTAGCTAGCCTATGAGTATTTTCTCTCTTTTTGATTCTTTGAGTAA
419713 GATTTCTTTCTTCTTCA
66 GATTTCTTTCTTCTTCA
419730 TC
1 TC
419732 TTATTGGTGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (82 bp):
TCAAAATAAAATAATCCCTTTAGCTAGCCTATGAGTATTTTCTCTCTTTTTGATTCTTTGAGTAA
GATTTCTTTCTTCTTCA
Found at i:432710 original size:109 final size:112
Alignment explanation
Indices: 432507--432714 Score: 280
Period size: 109 Copynumber: 1.9 Consensus size: 112
432497 AATAAAAAAC
* *
432507 ATTTATCGATTTTTAAATAGAATGTTCAATTACTTAGGTTCCAAGAAAAAAATCATACCCAACAT
1 ATTTATCGATTTTTAAATAGAATATTCAATTACTTAGGTTCAAAGAAAAAAATCATACCCAACAT
* *
432572 GTTAAAGCACAATTTCTCAAGTTCCCTAAAATAACAGAACATTAAGT
66 ATTAAAGCACAATTTCTCAAATTCCCTAAAATAACAGAACATTAAGT
* * * * *
432619 ATTTCTCGA-TTTTAAATAGGATATTCAATTATTTAGGTTCAAAG-AAAAACT-GTACCCAACAT
1 ATTTATCGATTTTTAAATAGAATATTCAATTACTTAGGTTCAAAGAAAAAAATCATACCCAACAT
* *
432681 ATT-AGGACATAATTTCTCAAATTCCCTAAAATAA
66 ATTAAAG-CACAATTTCTCAAATTCCCTAAAATAA
432715 AATAATATTG
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
108 2 0.02
109 37 0.44
110 6 0.07
111 31 0.37
112 8 0.10
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (112 bp):
ATTTATCGATTTTTAAATAGAATATTCAATTACTTAGGTTCAAAGAAAAAAATCATACCCAACAT
ATTAAAGCACAATTTCTCAAATTCCCTAAAATAACAGAACATTAAGT
Found at i:433110 original size:18 final size:17
Alignment explanation
Indices: 433083--433120 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
433073 CATGTATATT
*
433083 AAATATAAAAATGAATA
1 AAATATAAAAATAAATA
433100 AAATAATAAAAATAAATA
1 AAAT-ATAAAAATAAATA
433118 AAA
1 AAA
433121 GGGGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATATAAAAATAAATA
Found at i:433651 original size:28 final size:29
Alignment explanation
Indices: 433620--433686 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
433610 TTAAAAAAAC
*
433620 CTTCAAACCCC-TTTTATTTTTCTCTCAA
1 CTTCAAACCCCTTTTTATTTTTCCCTCAA
433648 CTTCAAACCCCTTTTTATTTTTCCCTCAA
1 CTTCAAACCCCTTTTTATTTTTCCCTCAA
*
433677 CTTTAAACCC
1 CTTCAAACCC
433687 TAGACCAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.22, C:0.34, G:0.00, T:0.43
Consensus pattern (29 bp):
CTTCAAACCCCTTTTTATTTTTCCCTCAA
Found at i:437912 original size:15 final size:15
Alignment explanation
Indices: 437886--437934 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
437876 ATAAAAAATA
* *
437886 AAAAATAGAAAAGAG
1 AAAAAGAGAAAAGGG
437901 -AAAAGAGAAAAAGGG
1 AAAAAGAG-AAAAGGG
*
437916 AAAAAGGGAAAAGGG
1 AAAAAGAGAAAAGGG
437931 AAAA
1 AAAA
437935 GAAAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 6 0.21
15 17 0.59
16 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (15 bp):
AAAAAGAGAAAAGGG
Found at i:439926 original size:39 final size:39
Alignment explanation
Indices: 439867--440914 Score: 727
Period size: 39 Copynumber: 26.1 Consensus size: 39
439857 CAGATTAGAT
* * *
439867 GATGTCTTCAACCTACCCCATGATCGGGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * * *
439906 GATGACTTCAGTCTACCCCATGGTTAGGGATAAGAGATTGGG
1 GATGACTTCAATCTGCCCCAT-GATCGGGGTAAGAGATT--G
* * * **
439948 TGGTGTCTTCAATCTGCCTCATGATTAGGGTAAGAGATTG
1 -GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * * * *
439988 GATGGCTTCGATCTGCCTCACGGTCAGGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * **** *
440027 GATGATGTCTTTAATATATATCATGATTC-GGGTAAGAGATTT
1 GATGA---CTTCAATCTGCCCCATGA-TCGGGGTAAGAGATTG
* * *
440069 GATGACTTCAATCTGCCGCATGGTCAGGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* *
440108 GATGATGTCTTCTATCTGCCCCATGATTGGGGTAAGAGATTG
1 GATGA---CTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
*
440150 GATG------A--TGCCCCATGAT-AGGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * * * *
440180 GATGGCTTCAATCTACCCTTATTAACTTAGGGGGTAAAAGATTG
1 GATGACTTCAATCTGCCC-CA-TGA--T-CGGGGTAAGAGATTG
* * * *
440224 GATGATGTTTTAATCTACCCCATGATCAGGGTAAGAGATTG
1 GATGA--CTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * *
440265 GATGGCTTCAATCTGCCTCTTGGTCGGGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
440304 GATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
1 GATGA---CTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
** * **
440346 GATGGTTTCAATTTGCCCCATGATCAAGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
** * *
440385 GATGGGTTCAATTTGCCCCATGGTCGGGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* ** * * *
440424 AATGATGTCTTCAATCTATCCCATGATCGTGGTAAGATATTC
1 ---GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * **
440466 GATGGCTTCAATCTGCCTCATGGTCAAGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* *
440505 GATGATGTCTTCAGTCTGCCCCATAATCGGGGTAAGAGATTG
1 GATGA---CTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * **
440547 GATGGCTTCAATTTGCCCCATGGTTAGGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* ** * *
440586 GATGATGTCTTCAATCTGTCTTATGATCGGGGTAAGAGAATC
1 GATGA---CTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * *
440628 GATGGCTTCAATCTGCCCCATGGTCGGGGTACGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
*
440667 GATGATGTCTTCAATCTGCCCCATAATCGGGGTAAGAGATTG
1 GATGA---CTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * ** *
440709 GATGGCATT-AATTTGCCCCATGGTCGACGTAAGAGATAG
1 GATGAC-TTCAATCTGCCCCATGATCGGGGTAAGAGATTG
*
440748 AATGATGTCTTTC-ATCT-CCCTCATGATCGGGGTAAGAGATTG
1 ---GATGAC-TTCAATCTGCCC-CATGATCGGGGTAAGAGATTG
* * * * * *
440790 AATGGCTTCAATTTGCCCCATGGTCGGAGTGAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * *
440829 GATGATGTCTTTAGTCTACCCCATGATCGGGGTAAGAGATTG
1 GATGA---CTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* *
440871 GATGACTTCAATCTACCCCATGGTCGGGGTAAGAGATTG
1 GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
440910 GATGA
1 GATGA
440915 TGATGTAACT
Statistics
Matches: 790, Mismatches: 165, Indels: 108
0.74 0.16 0.10
Matches are distributed among these distances:
30 17 0.02
31 11 0.01
33 1 0.00
36 1 0.00
38 9 0.01
39 366 0.46
40 22 0.03
41 19 0.02
42 296 0.37
43 18 0.02
44 18 0.02
45 1 0.00
46 11 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (39 bp):
GATGACTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
Found at i:440052 original size:81 final size:81
Alignment explanation
Indices: 439851--440916 Score: 1082
Period size: 81 Copynumber: 13.2 Consensus size: 81
439841 ATTGACTTAG
* * * * *
439851 GGGTAACAGATTAGATGATGTCTTCAACCTACCCCATGATCGGGGTAAGAGATTGGATGACTTCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
* * *
439916 GTCTACCCCATGGTTA
66 ATCTGCCCCATGGTCA
* * * **
439932 GGGATAAGAGATTGGGTGGTGTCTTCAATCTGCCTCATGATTAGGGTAAGAGATTGGATGGCTTC
1 GGG-TAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTC
* * *
439997 GATCTGCCTCACGGTCA
65 AATCTGCCCCATGGTCA
* * **** * *
440014 GGGTAAGAGATTGGATGATGTCTTTAATATATATCATGATTC-GGGTAAGAGATTTGATGACTTC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGA-TCGGGGTAAGAGATTGGATGGCTTC
*
440078 AATCTGCCGCATGGTCA
65 AATCTGCCCCATGGTCA
* *
440095 GGGTAAGAGATTGGATGATGTCTTCTATCTGCCCCATGATTGGGGTAAGAGATTGGAT-G-----
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
*
440154 A--TGCCCCATGAT-A
66 ATCTGCCCCATGGTCA
* * * * *
440167 GGGTAAGAGATTGGATG--G-CTTCAATCTACCCTTATTAACTTAGGGGGTAAAAGATTGGATGA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCC-CA-TGA--T-CGGGGTAAGAGATTGGATG-
* * * *
440229 TGTTTTAATCTACCCCATGATCA
60 -GCTTCAATCTGCCCCATGGTCA
* * *
440252 GGGTAAGAGATTGGATG--G-CTTCAATCTGCCTCTTGGTCGGGGTAAGAGATTGGATGATGTCT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG--G-CT
* *
440314 TCAATCTGCCCCATGATCG
63 TCAATCTGCCCCATGGTCA
* ** *
440333 GGGTAAGAGATTGGATG--GT-TTCAATTTGCCCCATGATCAAGGTAAGAGATTGGATGGGTTCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
* *
440395 ATTTGCCCCATGGTCG
66 ATCTGCCCCATGGTCA
* ** * * *
440411 GGGTAAGAGATTGAATGATGTCTTCAATCTATCCCATGATCGTGGTAAGATATTCGATGGCTTCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
*
440476 ATCTGCCTCATGGTCA
66 ATCTGCCCCATGGTCA
* * *
440492 AGGTAAGAGATTGGATGATGTCTTCAGTCTGCCCCATAATCGGGGTAAGAGATTGGATGGCTTCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
* *
440557 ATTTGCCCCATGGTTA
66 ATCTGCCCCATGGTCA
* ** * *
440573 GGGTAAGAGATTGGATGATGTCTTCAATCTGTCTTATGATCGGGGTAAGAGAATCGATGGCTTCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
*
440638 ATCTGCCCCATGGTCG
66 ATCTGCCCCATGGTCA
* *
440654 GGGTACGAGATTGGATGATGTCTTCAATCTGCCCCATAATCGGGGTAAGAGATTGGATGGCATT-
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGC-TTC
*
440718 AATTTGCCCCATGGTC-
65 AATCTGCCCCATGGTCA
* * * *
440734 GACGTAAGAGATAGAATGATGTCTTTC-ATCT-CCCTCATGATCGGGGTAAGAGATTGAATGGCT
1 G-GGTAAGAGATTGGATGATGTC-TTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGGCT
*
440797 TCAATTTGCCCCATGGTC-
63 TCAATCTGCCCCATGGTCA
* * * * *
440815 GGAGTGAGAGATTGGATGATGTCTTTAGTCTACCCCATGATCGGGGTAAGAGATTGGATGACTTC
1 GG-GTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTC
* *
440880 AATCTACCCCATGGTCG
65 AATCTGCCCCATGGTCA
440897 GGGTAAGAGATTGGATGATG
1 GGGTAAGAGATTGGATGATG
440917 ATGTAACTTC
Statistics
Matches: 823, Mismatches: 129, Indels: 66
0.81 0.13 0.06
Matches are distributed among these distances:
69 11 0.01
70 2 0.00
71 2 0.00
72 18 0.02
73 10 0.01
74 16 0.02
75 1 0.00
77 1 0.00
78 34 0.04
79 1 0.00
80 31 0.04
81 578 0.70
82 77 0.09
83 1 0.00
84 10 0.01
85 30 0.04
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (81 bp):
GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
ATCTGCCCCATGGTCA
Found at i:440173 original size:30 final size:31
Alignment explanation
Indices: 440124--440183 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
440114 GTCTTCTATC
*
440124 TGCCCCATGATTGGGGTAAGAGATTGGATGA
1 TGCCCCATGATTAGGGTAAGAGATTGGATGA
440155 TGCCCCATGA-TAGGGTAAGAGATTGGATG
1 TGCCCCATGATTAGGGTAAGAGATTGGATG
440184 GCTTCAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.27, C:0.13, G:0.35, T:0.25
Consensus pattern (31 bp):
TGCCCCATGATTAGGGTAAGAGATTGGATGA
Found at i:441220 original size:49 final size:49
Alignment explanation
Indices: 441141--441512 Score: 322
Period size: 49 Copynumber: 7.6 Consensus size: 49
441131 AGATTCGCCT
* * * * * ** *
441141 TTGCGGCTTCGATCTATT-TCTCCTCTTCTTTAGGCTATAAGATTTGTCA
1 TTGCGGCTTCAATCT-TTCCCTCCACATCTTTAGGGTATAAGATTCATCG
* * **
441190 TTGCGGCTTTAATCTTTCCCTTCACATCTTTAGGGTATAAGATTCGCCG
1 TTGCGGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAAGATTCATCG
* ** ** * * *
441239 TTGTGGCTTTTAGATTTCCCTCCACATCTATAGGGTATAAGGTTCACCG
1 TTGCGGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAAGATTCATCG
* * *
441288 TTGCGGCTTCAACCTTTCCCTCCATATGTTTAGGGTATAAGATTC-TCTG
1 TTGCGGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAAGATTCATC-G
* * * *
441337 TTGTGGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAATG-TTCATCG
1 TTGCGGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAA-GATTCATCG
* * * * *
441386 TTGTGGCTTCAA-CTTTTCCCTCCACATCTCTT-GGGCATGAGATTCGTCA
1 TTGCGGCTTCAATC-TTTCCCTCCACATCT-TTAGGGTATAAGATTCATCG
* * * *
441435 TTGCGGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTTATCG
1 TTGCGGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAAGATTCATCG
* *
441484 TTACGGCTTCAACCTTTCCCTCCACATCT
1 TTGCGGCTTCAATCTTTCCCTCCACATCT
441513 CTATGTAGGA
Statistics
Matches: 260, Mismatches: 54, Indels: 18
0.78 0.16 0.05
Matches are distributed among these distances:
48 6 0.02
49 249 0.96
50 5 0.02
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.39
Consensus pattern (49 bp):
TTGCGGCTTCAATCTTTCCCTCCACATCTTTAGGGTATAAGATTCATCG
Found at i:441278 original size:98 final size:98
Alignment explanation
Indices: 441190--441512 Score: 405
Period size: 98 Copynumber: 3.3 Consensus size: 98
441180 AGATTTGTCA
* * * ** **
441190 TTGCGGCTTTAATCTTTCCCTTCACATCTTTAGGGTATAAGATTCGCCGTTGTGGCTTTTAGATT
1 TTGCGGCTTCAACCTTTCCCTCCACATCTTTAGGGTATAAGATTCGCCGTTGTGGCTTCAATCTT
* * *
441255 TCCCTCCACATCTATAGGGTATAAGGTTCACCG
66 TCCCTTCACATCTCTAGGGTATAAGGTTCATCG
* * * *
441288 TTGCGGCTTCAACCTTTCCCTCCATATGTTTAGGGTATAAGATTCTCTGTTGTGGCTTCAATCTT
1 TTGCGGCTTCAACCTTTCCCTCCACATCTTTAGGGTATAAGATTCGCCGTTGTGGCTTCAATCTT
* *
441353 TCCCTTCACATCTCTAAGGTATAATGTTCATCG
66 TCCCTTCACATCTCTAGGGTATAAGGTTCATCG
* * * * * * *
441386 TTGTGGCTTCAACTTTTCCCTCCACATCTCTT-GGGCATGAGATTCGTCATTGCGGCTTCAATCT
1 TTGCGGCTTCAACCTTTCCCTCCACATCT-TTAGGGTATAAGATTCGCCGTTGTGGCTTCAATCT
*
441450 TTCCCTTCACATCTCTAGGGTATAAGGTTTATCG
65 TTCCCTTCACATCTCTAGGGTATAAGGTTCATCG
*
441484 TTACGGCTTCAACCTTTCCCTCCACATCT
1 TTGCGGCTTCAACCTTTCCCTCCACATCT
441513 CTATGTAGGA
Statistics
Matches: 191, Mismatches: 33, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
98 189 0.99
99 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (98 bp):
TTGCGGCTTCAACCTTTCCCTCCACATCTTTAGGGTATAAGATTCGCCGTTGTGGCTTCAATCTT
TCCCTTCACATCTCTAGGGTATAAGGTTCATCG
Found at i:441353 original size:147 final size:147
Alignment explanation
Indices: 441171--441515 Score: 370
Period size: 147 Copynumber: 2.3 Consensus size: 147
441161 TCCTCTTCTT
* * * * * * *
441171 TAGGCTATAAGATTTGTCATTGCGGCTTTAATCTTTCCCTTCACATCTTTAGGGTATAA-GATTC
1 TAGGGTATAAGATTTATCGTTACGGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAATG-TTC
* ** * * * *
441235 GCCGTTGTGGCTTTTAGATTTCCCTCCACATCTATAGGGTATAAGGTTCACCGTTGCGGCTTCAA
65 ACCGTTGTGGCTTCAACATTTCCCTCCACATCTATAGGGCATAAGATTCACCATTGCGGCTTCAA
* * *
441300 CCTTTCCCTCCATATGTT
130 CCTTTCCCTCCACATCTC
* **
441318 TAGGGTATAAGA-TTCTCTGTTGTGGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAATGTTC
1 TAGGGTATAAGATTTATC-GTTACGGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAATGTTC
* * * * * **
441382 ATCGTTGTGGCTTCAACTTTTCCCTCCACATCTCTTGGGCATGAGATTCGTCATTGCGGCTTCAA
65 ACCGTTGTGGCTTCAACATTTCCCTCCACATCTATAGGGCATAAGATTCACCATTGCGGCTTCAA
* *
441447 TCTTTCCCTTCACATCTC
130 CCTTTCCCTCCACATCTC
* * *
441465 TAGGGTATAAGGTTTATCGTTACGGCTTCAACCTTTCCCTCCACATCTCTA
1 TAGGGTATAAGATTTATCGTTACGGCTTCAATCTTTCCCTTCACATCTCTA
441516 TGTAGGACAA
Statistics
Matches: 163, Mismatches: 32, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
146 4 0.02
147 154 0.94
148 5 0.03
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (147 bp):
TAGGGTATAAGATTTATCGTTACGGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAATGTTCA
CCGTTGTGGCTTCAACATTTCCCTCCACATCTATAGGGCATAAGATTCACCATTGCGGCTTCAAC
CTTTCCCTCCACATCTC
Found at i:442265 original size:7 final size:7
Alignment explanation
Indices: 442253--442357 Score: 101
Period size: 7 Copynumber: 15.0 Consensus size: 7
442243 CTCGACCTCC
442253 CTTTTTT
1 CTTTTTT
442260 C-TTTTT
1 CTTTTTT
*
442266 CTTTCTT
1 CTTTTTT
442273 CTTTTTT
1 CTTTTTT
***
442280 CCTTTAGC
1 -CTTTTTT
442288 CTTTTTT
1 CTTTTTT
442295 CTTTTTT
1 CTTTTTT
442302 C-TTTTT
1 CTTTTTT
442308 C-TTTTT
1 CTTTTTT
442314 C-TTTTT
1 CTTTTTT
442320 CTTTTTT
1 CTTTTTT
*
442327 CTTTTTC
1 CTTTTTT
442334 CTTTTTTT
1 C-TTTTTT
442342 CTTTTCTT
1 CTTTT-TT
442350 CTCTTTTT
1 CT-TTTTT
442358 TTTGGGTGAG
Statistics
Matches: 82, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
6 24 0.29
7 39 0.48
8 16 0.20
9 3 0.04
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.78
Consensus pattern (7 bp):
CTTTTTT
Found at i:442266 original size:6 final size:6
Alignment explanation
Indices: 442255--442349 Score: 82
Period size: 6 Copynumber: 14.3 Consensus size: 6
442245 CGACCTCCCT
**
442255 TTTTTC TTTTTC TTTCTTC TTTTTTCC TTTAGCC TTTTTTC TTTTTTC
1 TTTTTC TTTTTC TTT-TTC -TTTTT-C TTT-TTC -TTTTTC -TTTTTC
*
442303 TTTTTC TTTTTC TTTTTC TTTTTTC TTTTTCC TTTTTT TCTTTTC TT
1 TTTTTC TTTTTC TTTTTC -TTTTTC TTTTT-C TTTTTC T-TTTTC TT
442350 CTCTTTTTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
6 34 0.45
7 34 0.45
8 7 0.09
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:442274 original size:13 final size:13
Alignment explanation
Indices: 442253--442359 Score: 78
Period size: 13 Copynumber: 8.0 Consensus size: 13
442243 CTCGACCTCC
*
442253 CTTTTTTCTTTTT
1 CTTTCTTCTTTTT
442266 CTTTCTTCTTTTTT
1 CTTTCTTC-TTTTT
*
442280 CCTTTAGCCT-TTTTT
1 -CTTT--CTTCTTTTT
*
442295 CTTTTTTCTTTTT
1 CTTTCTTCTTTTT
442308 CTTT-TTCTTTTT
1 CTTTCTTCTTTTT
*
442320 CTTTTTTCTTTTT
1 CTTTCTTCTTTTT
*
442333 CCTTT-TTTTCTTTT
1 -CTTTCTTCT-TTTT
442347 CTTCTCTT-TTTTT
1 CTT-TCTTCTTTTT
442360 TGGGTGAGAT
Statistics
Matches: 79, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
12 13 0.16
13 34 0.43
14 19 0.24
15 11 0.14
17 2 0.03
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.79
Consensus pattern (13 bp):
CTTTCTTCTTTTT
Found at i:442360 original size:19 final size:20
Alignment explanation
Indices: 442254--442360 Score: 87
Period size: 19 Copynumber: 5.3 Consensus size: 20
442244 TCGACCTCCC
442254 TTTTTTCTTTTTCTTTCTTC-T
1 TTTTTTC-TTTTCTTT-TTCTT
* * *
442275 TTTTTCCTTTAGCCTTTTT-TC
1 TTTTTTCTTT--TCTTTTTCTT
442296 TTTTTTCTTTTTCTTTTTCTT
1 TTTTTTC-TTTTCTTTTTCTT
* *
442317 TTTCTT-TTTTCTTTTTCCT
1 TTTTTTCTTTTCTTTTTCTT
*
442336 TTTTTTCTTTTC-TTCTCTT
1 TTTTTTCTTTTCTTTTTCTT
442355 TTTTTT
1 TTTTTT
442361 GGGTGAGATA
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
19 28 0.41
20 14 0.20
21 20 0.29
22 7 0.10
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (20 bp):
TTTTTTCTTTTCTTTTTCTT
Found at i:445719 original size:103 final size:105
Alignment explanation
Indices: 445525--445750 Score: 262
Period size: 103 Copynumber: 2.2 Consensus size: 105
445515 TGAATCTTCG
** ** *
445525 AAAAT-AAAGAACATT-TATCGATTTTTAAATAGAATGTTCAATTACTTAGGTTCCAAGAAAAAA
1 AAAATAAAAGAACATTGCCTCGATTTTTAAATAGAATACTCAATTACTTAGGTTCAAAGAAAAAA
* * ** * *
445588 TCATACCCAATACGTTAGGGCACAATTTCTCGAATTCTCA
66 CCATACCCAACACGTTAGAACACAATTTCTCAAATTCCCA
* * *
445628 AAAATAAAAGAACATTGCCTCGA-TTTTAAATAGGATACTCGATTATTTAGGTTCAAAG-AAAAA
1 AAAATAAAAGAACATTGCCTCGATTTTTAAATAGAATACTCAATTACTTAGGTTCAAAGAAAAAA
* *
445691 CCGTACCCAACACGTTAGAACACAATTTCTCAAATTCCCT
66 CCATACCCAACACGTTAGAACACAATTTCTCAAATTCCCA
* *
445731 AAAATAAAATAATATTGCCT
1 AAAATAAAAGAACATTGCCT
445751 TTTTTAAAAA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
103 60 0.58
104 39 0.38
105 4 0.04
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (105 bp):
AAAATAAAAGAACATTGCCTCGATTTTTAAATAGAATACTCAATTACTTAGGTTCAAAGAAAAAA
CCATACCCAACACGTTAGAACACAATTTCTCAAATTCCCA
Found at i:446712 original size:28 final size:28
Alignment explanation
Indices: 446667--446733 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
446657 TTTAAAAAAC
* *
446667 CTTCAACCCCGCTTTTATTTTTCTCTCAA
1 CTTCAAACCC-CTTTTATTTCTCTCTCAA
*
446696 CTTCCAACCCCTTTTATTTCTCTCTCAA
1 CTTCAAACCCCTTTTATTTCTCTCTCAA
446724 CTTCAAACCC
1 CTTCAAACCC
446734 TAGGCCAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 26 0.76
29 8 0.24
ACGTcount: A:0.19, C:0.39, G:0.01, T:0.40
Consensus pattern (28 bp):
CTTCAAACCCCTTTTATTTCTCTCTCAA
Found at i:447658 original size:16 final size:18
Alignment explanation
Indices: 447629--447671 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
447619 TAAATGTATT
*
447629 TTTTATTTGTGTTTT-TA
1 TTTTATTTGAGTTTTCTA
447646 TTTT-TTTGAGTTTTCTA
1 TTTTATTTGAGTTTTCTA
*
447663 TTTTGTTTG
1 TTTTATTTG
447672 GGTCTTGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.09, C:0.02, G:0.14, T:0.74
Consensus pattern (18 bp):
TTTTATTTGAGTTTTCTA
Found at i:447869 original size:14 final size:15
Alignment explanation
Indices: 447846--447882 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
447836 TAATTTTTAT
*
447846 ATTGAATTTTATTTA
1 ATTGAATTTTAATTA
447861 ATT-AATTTTAATTA
1 ATTGAATTTTAATTA
447875 ATTGAATT
1 ATTGAATT
447883 AATGATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (15 bp):
ATTGAATTTTAATTA
Found at i:449877 original size:13 final size:13
Alignment explanation
Indices: 449859--449883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
449849 CCCATTTTAT
449859 CATTTTTAGCATG
1 CATTTTTAGCATG
449872 CATTTTTAGCAT
1 CATTTTTAGCAT
449884 TTTTAACTTA
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:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:450725 original size:21 final size:21
Alignment explanation
Indices: 450701--450746 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
450691 CAAGAAGAAC
*
450701 TACTTGCCAATGGTTGACAAA
1 TACTTGCCAATGCTTGACAAA
* *
450722 TACTTGGCAATGCTTGATAAA
1 TACTTGCCAATGCTTGACAAA
450743 TACT
1 TACT
450747 AAAAGAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TACTTGCCAATGCTTGACAAA
Found at i:451964 original size:21 final size:21
Alignment explanation
Indices: 451938--451981 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
451928 AGAATATATT
*
451938 CTTGGCAATGGTTGATAAATA
1 CTTGGCAATGCTTGATAAATA
451959 CTTGGCAATGCTTGATAAATA
1 CTTGGCAATGCTTGATAAATA
451980 CT
1 CT
451982 GATACAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (21 bp):
CTTGGCAATGCTTGATAAATA
Found at i:453267 original size:21 final size:21
Alignment explanation
Indices: 453241--453284 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
453231 AGAAGATCTT
*
453241 CTTGGCAATGGTTGATAAATA
1 CTTGGCAATGCTTGATAAATA
453262 CTTGGCAATGCTTGATAAATA
1 CTTGGCAATGCTTGATAAATA
453283 CT
1 CT
453285 GAAAGAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (21 bp):
CTTGGCAATGCTTGATAAATA
Found at i:455764 original size:21 final size:21
Alignment explanation
Indices: 455738--455781 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
455728 AGAAGATCTT
* *
455738 CTTGGCAATGGTTGATAAATA
1 CTTGGCAATGCTTCATAAATA
*
455759 CTTGGCATTGCTTCATAAATA
1 CTTGGCAATGCTTCATAAATA
455780 CT
1 CT
455782 GAAACAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (21 bp):
CTTGGCAATGCTTCATAAATA
Found at i:461004 original size:21 final size:21
Alignment explanation
Indices: 460978--461021 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
460968 CAAACATCTT
** *
460978 CTTGGCAATGGTTGATAAGTA
1 CTTGGCAATACTTGATAAATA
460999 CTTGGCAATACTTGATAAATA
1 CTTGGCAATACTTGATAAATA
461020 CT
1 CT
461022 GAAAGAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (21 bp):
CTTGGCAATACTTGATAAATA
Found at i:470752 original size:21 final size:21
Alignment explanation
Indices: 470728--470773 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
470718 AGGACACCTG
*
470728 TACTTGGCAATGGTTGATAAA
1 TACTTGGCAATGCTTGATAAA
470749 TACTTGGCAATGCTTGATAAA
1 TACTTGGCAATGCTTGATAAA
470770 TACT
1 TACT
470774 GAAAGAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (21 bp):
TACTTGGCAATGCTTGATAAA
Found at i:470800 original size:63 final size:64
Alignment explanation
Indices: 470687--470815 Score: 197
Period size: 63 Copynumber: 2.0 Consensus size: 64
470677 CTTTGATCTT
* * * * * *
470687 CTTGGTAATGGTTGATAAATACTGATGAGAGAGGACACCTGTACTTGGCAATGGTTGATAAATA
1 CTTGGCAATGCTTGATAAATACTGATAAGAAAGGACACCTATACTTGGCAACGGTTGATAAATA
470751 CTTGGCAATGCTTGATAAATACTGA-AAGAAAGGACACCTATACTTGGCAACGGTTGATAAATA
1 CTTGGCAATGCTTGATAAATACTGATAAGAAAGGACACCTATACTTGGCAACGGTTGATAAATA
470814 CT
1 CT
470816 AACAAGAGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
63 36 0.61
64 23 0.39
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (64 bp):
CTTGGCAATGCTTGATAAATACTGATAAGAAAGGACACCTATACTTGGCAACGGTTGATAAATA
Found at i:472107 original size:21 final size:21
Alignment explanation
Indices: 472077--472120 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
472067 GACACCTGTT
*
472077 CTTGGAAATGGTTGATAAATA
1 CTTGGAAATGCTTGATAAATA
*
472098 CTTGGCAATGCTTGATAAATA
1 CTTGGAAATGCTTGATAAATA
472119 CT
1 CT
472121 GAAAGAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (21 bp):
CTTGGAAATGCTTGATAAATA
Found at i:472150 original size:63 final size:64
Alignment explanation
Indices: 472034--472162 Score: 188
Period size: 63 Copynumber: 2.0 Consensus size: 64
472024 AGAATAACTT
* * * * * *
472034 CTTGGTAATGGTTGATAAATACTGACGAGAGAGGACACCTGTTCTTGGAAATGGTTGATAAATA
1 CTTGGCAATGCTTGATAAATACTGACAAGAAAGGACACCTATACTTGGAAATGGTTGATAAATA
*
472098 CTTGGCAATGCTTGATAAATACTGA-AAGAAAGGACACCTATACTTGGTAATGGTTGATAAATA
1 CTTGGCAATGCTTGATAAATACTGACAAGAAAGGACACCTATACTTGGAAATGGTTGATAAATA
472161 CT
1 CT
472163 GACGAAAGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
63 35 0.60
64 23 0.40
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (64 bp):
CTTGGCAATGCTTGATAAATACTGACAAGAAAGGACACCTATACTTGGAAATGGTTGATAAATA
Found at i:473425 original size:43 final size:43
Alignment explanation
Indices: 473364--473483 Score: 143
Period size: 42 Copynumber: 2.8 Consensus size: 43
473354 AGAAGATCTT
* *
473364 CTTGGCAATGGTTGATAAATACTGATGAGAGAGGACACTTAAA
1 CTTGGCAATGGTTGATAAATACTGAAGAGAGAGGACACCTAAA
* * * * **
473407 CTTGGCAATGTTTGATAAATACT-AAAAGAAAAGACACCTGTA
1 CTTGGCAATGGTTGATAAATACTGAAGAGAGAGGACACCTAAA
* *
473449 CTTGGCAAAGGTTGATAAATACTGACGAGAGAGGA
1 CTTGGCAATGGTTGATAAATACTGAAGAGAGAGGA
473484 TCTTCTTCAA
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 33 0.53
43 29 0.47
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (43 bp):
CTTGGCAATGGTTGATAAATACTGAAGAGAGAGGACACCTAAA
Found at i:480096 original size:15 final size:15
Alignment explanation
Indices: 480071--480106 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
480061 TTGGTATGAC
480071 TTTAC-TAGCATTTG
1 TTTACTTAGCATTTG
480085 TTTACTTAGCATTTG
1 TTTACTTAGCATTTG
480100 TTTACTT
1 TTTACTT
480107 GAGGACAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (15 bp):
TTTACTTAGCATTTG
Found at i:481845 original size:37 final size:36
Alignment explanation
Indices: 481740--481845 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 36
481730 CTTTGTGCTG
* * *
481740 GTGAAATCGGGCTTTGTGCTTAGTTGGCTTCATGCCA
1 GTGAAATC-GGCTTTGTGCCTAGTAGGCTTCGTGCCA
*
481777 GTGAAATCGGACTTTGTGGCTAGTAGGCTTCGTGCCTA
1 GTGAAATCGG-CTTTGTGCCTAGTAGGCTTCGTGCC-A
*
481815 -TGAAATCTGGCTTTTTGCCTAGTAGGCTTCG
1 GTGAAATC-GGCTTTGTGCCTAGTAGGCTTCG
481846 AACCGGTGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
36 2 0.03
37 55 0.92
38 3 0.05
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (36 bp):
GTGAAATCGGCTTTGTGCCTAGTAGGCTTCGTGCCA
Found at i:487447 original size:22 final size:22
Alignment explanation
Indices: 487422--487484 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
487412 GTGTTATTAG
487422 TGGC-ATTTCATCTACAAATCAA
1 TGGCAATTT-ATCTACAAATCAA
* *
487444 TGGCAATTTATCTGCAAATCAG
1 TGGCAATTTATCTACAAATCAA
*
487466 TGG-AAGTTTATCTGCAAAT
1 TGGCAA-TTTATCTACAAAT
487485 TAGTGGTCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.05
22 31 0.84
23 4 0.11
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (22 bp):
TGGCAATTTATCTACAAATCAA
Found at i:493642 original size:215 final size:219
Alignment explanation
Indices: 493103--493656 Score: 548
Period size: 219 Copynumber: 2.5 Consensus size: 219
493093 TTGTTTTCTA
* * * * * * * *
493103 AAATACATAAATTGTTTTTATAAAAAATTAAGGCAAGGTTCTTTTATTTTAGTAAATTCGAAAGG
1 AAATTCATAAATTG--TTT-TAAAAAATAAAAGCAATGTTCTTTTAGTTTAGGAAATTCAAAAAG
* * * * ** * * * * *
493168 TGGTG-CCATAACGTATTGGGTACGGTTTTTCTTCGAACTTAAATAATCGAATATCCTATTTGAA
63 TGCTGTAC-TAACGTGTTGAGTACAATCTTCCTTCGAACCTAAATAATTGAATATCCTATTTAAA
* ** * * * *
493232 ATTGATAATCGTTATTTTTACTTGTAAATTACATGGGTTTATCCATCTTTTTGCAAAGCATTTTG
127 ATCGATAATCGCCATTTTTAATTGTAAATTACAAGGATTTATCCATCTTTTTGCAAAACATTTTG
*
493297 AACGAAATAAAATGTATATCATTTATTT
192 AACAAAATAAAATGTATATCATTTATTT
* * *
493325 AAATTCATGAATTGTTTTAAAAAATAAAAGCAATGTTCTTTTATTTTAGGGAATTCAAAAAGTGC
1 AAATTCATAAATTGTTTTAAAAAATAAAAGCAATGTTCTTTTAGTTTAGGAAATTCAAAAAGTGC
* * * * *
493390 TGTACTAACGTGTTGGGTACAATTTTTCTTCGAACCTAAATAATTGGATATTCTATTTAAAATCG
66 TGTACTAACGTGTTGAGTACAATCTTCCTTCGAACCTAAATAATTGAATATCCTATTTAAAATCG
* * * *
493455 ATAATCGCCA-TTTTAATTGTAAATTACAAGTATTTATCTATC-TTTTGCAAAATATTTTTAACA
131 ATAATCGCCATTTTTAATTGTAAATTACAAGGATTTATCCATCTTTTTGCAAAACATTTTGAACA
*
493518 AAATAAAATGTATATCGTTT-TTT
196 AAATAAAATGTATATCATTTATTT
* * * *
493541 GAATAT-ATAAATTGTTTT-AAAAATAAAGGTAA-GATTCTTTTAGTTTAGGAAATTCAAGAAAT
1 AAAT-TCATAAATTGTTTTAAAAAATAAAAGCAATG-TTCTTTTAGTTTAGGAAATTCAA-AAAG
** * * *
493603 TG-TGTTTTAACGTGTTGAGTACGATCTTCCTTTGAACCTAAATAATTGAGTATC
63 TGCTGTACTAACGTGTTGAGTACAATCTTCCTTCGAACCTAAATAATTGAATATC
493657 TTCCTTAAAT
Statistics
Matches: 279, Mismatches: 49, Indels: 15
0.81 0.14 0.04
Matches are distributed among these distances:
214 1 0.00
215 75 0.27
216 22 0.08
217 37 0.13
218 27 0.10
219 101 0.36
220 4 0.01
222 12 0.04
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (219 bp):
AAATTCATAAATTGTTTTAAAAAATAAAAGCAATGTTCTTTTAGTTTAGGAAATTCAAAAAGTGC
TGTACTAACGTGTTGAGTACAATCTTCCTTCGAACCTAAATAATTGAATATCCTATTTAAAATCG
ATAATCGCCATTTTTAATTGTAAATTACAAGGATTTATCCATCTTTTTGCAAAACATTTTGAACA
AAATAAAATGTATATCATTTATTT
Found at i:494390 original size:19 final size:20
Alignment explanation
Indices: 494366--494404 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
494356 TTTTTGATTG
494366 AAAA-TTGAGAAATTGGTTT
1 AAAATTTGAGAAATTGGTTT
494385 AAAATTTGAGAAATTGGTTT
1 AAAATTTGAGAAATTGGTTT
494405 CGATGAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (20 bp):
AAAATTTGAGAAATTGGTTT
Found at i:496493 original size:39 final size:39
Alignment explanation
Indices: 496438--497203 Score: 996
Period size: 39 Copynumber: 19.4 Consensus size: 39
496428 CTTTAGGACC
* *
496438 CGGGGTAAGAGATTGGATGGCTCCAATCTACCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
*
496477 TGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* *
496516 CGGGGTAAGAGATTGAATGGCTTCAATCTACCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* * * **
496555 CGAGGTAAGAGATT-GAAGGTCTTCAATCTACCTTATGGT
1 CGGGGTAAGAGATTGGATGG-CTTCAATCTGCCCCATGGT
*
496594 CGAGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
*
496633 CGGGGTAAGAGATTGGATGACTTCAATCTGCCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* * *
496672 CGGAGTAAGAGATTAGATGACTTCAATCTGCCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* * *
496711 CGGGGTAAGAGATTAGATGGCTTCAATCTACCCTATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* * * *
496750 CGAGGTAAGTGATTGGATGTCTTCAATTTGCCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
*
496789 CGGGGGTAAGAGATTGGATGGCTTCAATCTGCCTCATGGT
1 C-GGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* *
496829 CGGGGTAAGAGATTGGATGATGTCTTCATTTTGCCCCATGGT
1 CGGGGTAAGAGATTGGATG--G-CTTCAATCTGCCCCATGGT
** *
496871 CGGGGTAAGAGATTTAATGTCTTCAATCTGCCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* * *
496910 TGAGGTAAGAGATTGGATGATGTCTTTAATCTGCCCCATGGT
1 CGGGGTAAGAGATTGGATG--G-CTTCAATCTGCCCCATGGT
* *
496952 CGGGGTAAGAGATTGGATGGCTCCAATCTACCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
*
496991 TGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* *
497030 CGGGGTAAGAGATTGAATGGCTTCAATCTACCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* * * **
497069 TGAGGTAAGAGATTGGA-GGTCTTCAATCTACCTTATGGT
1 CGGGGTAAGAGATTGGATGG-CTTCAATCTGCCCCATGGT
*
497108 CGAGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
1 CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
* * **
497147 CGGGGTAAGAGTTTGGATGACTTCTTCAATCTGTGCCATGGT
1 CGGGGTAAGAGATTGGATG---GCTTCAATCTGCCCCATGGT
497189 CGGGGTAAGAGATTG
1 CGGGGTAAGAGATTG
497204 TATTGTAGTT
Statistics
Matches: 638, Mismatches: 75, Indels: 25
0.86 0.10 0.03
Matches are distributed among these distances:
38 5 0.01
39 492 0.77
40 41 0.06
41 1 0.00
42 99 0.16
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (39 bp):
CGGGGTAAGAGATTGGATGGCTTCAATCTGCCCCATGGT
Found at i:507413 original size:39 final size:39
Alignment explanation
Indices: 507328--507877 Score: 582
Period size: 39 Copynumber: 13.8 Consensus size: 39
507318 TTGAGCATTA
* * *
507328 ACCATGGGGCAGATTAAAGACATCATCCAATCTCTTACCTCA
1 ACCATGGGGCAGATTGAAG--A-CATCCAATCTCTTACCCCG
* **
507370 ACCATAGGGCAGATTGAAGACATTAAATCTCTTACCCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
* *
507409 ACCATGGGGCAAAATGAAGACATCATCCAATCTCTTACCCCG
1 ACCATGGGGCAGATTGAAG--A-CATCCAATCTCTTACCCCG
* *
507451 ACCATGAGGCAGATTGAAGCCATCCAATCTCTTACCCCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTA-CCCCG
* * *
507491 ACCATGGGGCAAATTGAAGACATCCAATCACTTACCTCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
** * *
507530 ACCATACGACAGATTGAAGCCATCCAATCTCTTACCCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
* * *
507569 ACCATGGGGCAGATTGAAGTCATCTAATCTCTTACTCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
*
507608 ACCATGGGGCAGATTGAAGTCATCCAATCTCTTACCCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
* * * **
507647 ACCATGGGGTAGATTGAAGCCATCAAATCTCTTACATCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
* * *
507686 ATCATGGGGCATATTGAAGACATCATCCAATCTCTTACCCCA
1 ACCATGGGGCAGATTGAAG--A-CATCCAATCTCTTACCCCG
* * **
507728 ACCATAGGGTAGATTGAAGACATCTTCCAATCTCTTACCCTA
1 ACCATGGGGCAGATTGAAGACA---TCCAATCTCTTACCCCG
* * * *
507770 ACCATGAGGTAGATTGAAGCCATCCAGTCTCTTACCCTC-
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCC-CG
* *
507809 ACCATGGGGCAAATTGAA-ACCATCCAATCTCTTACCTCG
1 ACCATGGGGCAGATTGAAGA-CATCCAATCTCTTACCCCG
* *
507848 ACCATGGGGAAGATTGAAGCCATCCAATCT
1 ACCATGGGGCAGATTGAAGACATCCAATCT
507878 TTTAGCCTAA
Statistics
Matches: 427, Mismatches: 67, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.00
39 273 0.64
40 37 0.09
41 1 0.00
42 115 0.27
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (39 bp):
ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
Found at i:509413 original size:26 final size:26
Alignment explanation
Indices: 509384--509466 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
509374 TAAATTTTAT
*
509384 TTTTAAATTTTACCTCTTTAAATTAC
1 TTTTAAATTTTACTTCTTTAAATTAC
* ** *
509410 TTTT--ATTTTATTTCATATTATTTTAT
1 TTTTAAATTTTACTTC-T-TTAAATTAC
509436 TTTTAAATTTTACTTCTTTAAATTAC
1 TTTTAAATTTTACTTCTTTAAATTAC
509462 TTTTA
1 TTTTA
509467 TTTGTTTACT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
24 8 0.18
25 1 0.02
26 25 0.57
27 1 0.02
28 9 0.20
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTAAATTTTACTTCTTTAAATTAC
Found at i:509455 original size:15 final size:14
Alignment explanation
Indices: 509371--509459 Score: 59
Period size: 15 Copynumber: 6.6 Consensus size: 14
509361 ATTTTTTTCC
509371 TTTTAAATTTTA-T
1 TTTTAAATTTTACT
509384 TTTTAAATTTTACCT
1 TTTTAAATTTTA-CT
*
509399 CTTTAAA--TTAC-
1 TTTTAAATTTTACT
509410 TTTT--ATTTTA-T
1 TTTTAAATTTTACT
* *
509421 TTCATATTATTTTA-T
1 TT-TTA-AATTTTACT
509436 TTTTAAATTTTACT
1 TTTTAAATTTTACT
509450 TCTTTAAATT
1 T-TTTAAATT
509460 ACTTTTATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
9 1 0.02
11 8 0.13
12 2 0.03
13 21 0.35
14 4 0.07
15 24 0.40
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAATTTTACT
Found at i:510626 original size:39 final size:39
Alignment explanation
Indices: 510541--511090 Score: 582
Period size: 39 Copynumber: 13.8 Consensus size: 39
510531 TTGAGCATTA
* * *
510541 ACCATGGGGCAGATTAAAGACATCATCCAATCTCTTACCTCA
1 ACCATGGGGCAGATTGAAG--A-CATCCAATCTCTTACCCCG
* **
510583 ACCATAGGGCAGATTGAAGACATTAAATCTCTTACCCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
* *
510622 ACCATGGGGCAAAATGAAGACATCATCCAATCTCTTACCCCG
1 ACCATGGGGCAGATTGAAG--A-CATCCAATCTCTTACCCCG
* *
510664 ACCATGAGGCAGATTGAAGCCATCCAATCTCTTACCCCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTA-CCCCG
* * *
510704 ACCATGGGGCAAATTGAAGACATCCAATCACTTACCTCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
** * *
510743 ACCATACGACAGATTGAAGCCATCCAATCTCTTACCCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
* * *
510782 ACCATGGGGCAGATTGAAGTCATCTAATCTCTTACTCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
*
510821 ACCATGGGGCAGATTGAAGTCATCCAATCTCTTACCCCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
* * * **
510860 ACCATGGGGTAGATTGAAGCCATCAAATCTCTTACATCG
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
* * *
510899 ATCATGGGGCATATTGAAGACATCATCCAATCTCTTACCCCA
1 ACCATGGGGCAGATTGAAG--A-CATCCAATCTCTTACCCCG
* * **
510941 ACCATAGGGTAGATTGAAGACATCTTCCAATCTCTTACCCTA
1 ACCATGGGGCAGATTGAAGACA---TCCAATCTCTTACCCCG
* * * *
510983 ACCATGAGGTAGATTGAAGCCATCCAGTCTCTTACCCTC-
1 ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCC-CG
* *
511022 ACCATGGGGCAAATTGAA-ACCATCCAATCTCTTACCTCG
1 ACCATGGGGCAGATTGAAGA-CATCCAATCTCTTACCCCG
* *
511061 ACCATGGGGAAGATTGAAGCCATCCAATCT
1 ACCATGGGGCAGATTGAAGACATCCAATCT
511091 TTTAGCCTAA
Statistics
Matches: 427, Mismatches: 67, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.00
39 273 0.64
40 37 0.09
41 1 0.00
42 115 0.27
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (39 bp):
ACCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCG
Found at i:512626 original size:26 final size:26
Alignment explanation
Indices: 512597--512679 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
512587 TAAATTTTAT
*
512597 TTTTAAATTTTACCTCTTTAAATTAC
1 TTTTAAATTTTACTTCTTTAAATTAC
* ** *
512623 TTTT--ATTTTATTTCATATTATTTTAT
1 TTTTAAATTTTACTTC-T-TTAAATTAC
512649 TTTTAAATTTTACTTCTTTAAATTAC
1 TTTTAAATTTTACTTCTTTAAATTAC
512675 TTTTA
1 TTTTA
512680 TTTGTTTACT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
24 8 0.18
25 1 0.02
26 25 0.57
27 1 0.02
28 9 0.20
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTAAATTTTACTTCTTTAAATTAC
Found at i:512668 original size:15 final size:14
Alignment explanation
Indices: 512584--512672 Score: 59
Period size: 15 Copynumber: 6.6 Consensus size: 14
512574 ATTTTTTTCC
512584 TTTTAAATTTTA-T
1 TTTTAAATTTTACT
512597 TTTTAAATTTTACCT
1 TTTTAAATTTTA-CT
*
512612 CTTTAAA--TTAC-
1 TTTTAAATTTTACT
512623 TTTT--ATTTTA-T
1 TTTTAAATTTTACT
* *
512634 TTCATATTATTTTA-T
1 TT-TTA-AATTTTACT
512649 TTTTAAATTTTACT
1 TTTTAAATTTTACT
512663 TCTTTAAATT
1 T-TTTAAATT
512673 ACTTTTATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
9 1 0.02
11 8 0.13
12 2 0.03
13 21 0.35
14 4 0.07
15 24 0.40
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAATTTTACT
Found at i:513444 original size:216 final size:219
Alignment explanation
Indices: 512879--513450 Score: 692
Period size: 219 Copynumber: 2.6 Consensus size: 219
512869 AAAATATTTT
* * * ** **
512879 AAAA-AAAATTGTATGTTGTTT-TCTAAAATACATAAATTGTTTTCATAATAAATTAAGGCAAGG
1 AAAATAAAA-TGTATATTGTTTAT-TTAAATACATAAATTGTTTT-A-AA-AAATAAAAACAATA
* *
512942 TT-TTTCTATTTTAGGGTATTCGAAAAGTGGTGCCCTAACGTGTTGGGTACGATTTTTCTTCGAA
61 TTATTT-TATTTTAGGGAATTTGAAAAGTGGTGCCCTAACGTGTTGGGTACGATTTTTCTTCGAA
* * * * *
513006 CCTAAAAAATCGAATATCCTATTTAAAGTCAATAATCACTATTTTTACTTGTATATTACATGGGT
125 CCTAAATAATCGAATATCCTATTTAAAATCAATAATCACCATTTTTACTTGTAAATTACATGGAT
* *
513071 TTATCCATCTTTTTGCAAAGCATTTTTAAC
190 TTATCCATCTTTTCGCAAAACATTTTTAAC
* * * *
513101 GAAATAAAATGTATATTGTTTATTTAAATGCATGAATTGTTTTAAAAAATAAAAACAATGTTATT
1 AAAATAAAATGTATATTGTTTATTTAAATACATAAATTGTTTTAAAAAATAAAAACAATATTATT
*
513166 TTATTTTAGGAAATTTGAAAAGTGGTGCCCTAACGTGTTGGGTACGATTTTTCTTCGAACCTAAA
66 TTATTTTAGGGAATTTGAAAAGTGGTGCCCTAACGTGTTGGGTACGATTTTTCTTCGAACCTAAA
* * * **
513231 TAATCGGATATTCTATTTAAAATCGATAATTGCCA-TTTTACTTGTAAATTACATGGATTTATCC
131 TAATCGAATATCCTATTTAAAATCAATAATCACCATTTTTACTTGTAAATTACATGGATTTATCC
*
513295 ATC-TTTCGCAAAATATTTTTAAC
196 ATCTTTTCGCAAAACATTTTTAAC
* * * * *
513318 AAAATAAAATGTATATTGCTTT-TTTGAATATATAAATTGTTTT-AAAAATAAAGATAATATTCT
1 AAAATAAAATGTATATTG-TTTATTTAAATACATAAATTGTTTTAAAAAATAAAAACAATATTAT
* * * *
513381 TTTATTTTAGGGAATTTGAGAAA-TTGTGCCCTAACGTATTGGGTACGATTTTCCTTTGAACCTA
65 TTTATTTTAGGGAATTTGA-AAAGTGGTGCCCTAACGTGTTGGGTACGATTTTTCTTCGAACCTA
513445 AATAAT
129 AATAAT
513451 TGAGTATCTT
Statistics
Matches: 306, Mismatches: 39, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
216 77 0.25
217 54 0.18
218 33 0.11
219 100 0.33
220 5 0.02
221 1 0.00
222 31 0.10
223 5 0.02
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (219 bp):
AAAATAAAATGTATATTGTTTATTTAAATACATAAATTGTTTTAAAAAATAAAAACAATATTATT
TTATTTTAGGGAATTTGAAAAGTGGTGCCCTAACGTGTTGGGTACGATTTTTCTTCGAACCTAAA
TAATCGAATATCCTATTTAAAATCAATAATCACCATTTTTACTTGTAAATTACATGGATTTATCC
ATCTTTTCGCAAAACATTTTTAAC
Found at i:513588 original size:14 final size:15
Alignment explanation
Indices: 513569--513600 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
513559 TAAAATATAT
513569 AAATTAT-TTTAAAA
1 AAATTATATTTAAAA
513583 AAATTATATTTAAAA
1 AAATTATATTTAAAA
513598 AAA
1 AAA
513601 ATTTAGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTATATTTAAAA
Found at i:513808 original size:36 final size:36
Alignment explanation
Indices: 513757--513845 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 36
513747 AATCGTGCCT
* *
513757 AGATTGCGCCCAAAACTACCGCCGCATGAGCACTTCC
1 AGATTGC-ACCAAAACTACAGCCGCATGAGCACTTCC
** * *
513794 AGATTGCACCAAAACTGTAGTCGCATGAGCACTTCT
1 AGATTGCACCAAAACTACAGCCGCATGAGCACTTCC
*
513830 AGATTACACCAAAACT
1 AGATTGCACCAAAACT
513846 GTCACCGTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 38 0.84
37 7 0.16
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (36 bp):
AGATTGCACCAAAACTACAGCCGCATGAGCACTTCC
Found at i:513846 original size:36 final size:36
Alignment explanation
Indices: 513779--513847 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
513769 AAACTACCGC
*
513779 CGCATGAGCACTTCCAGATTGCACCAAAACTGTAGT
1 CGCATGAGCACTTCCAGATTACACCAAAACTGTAGT
*
513815 CGCATGAGCACTTCTAGATTACACCAAAACTGT
1 CGCATGAGCACTTCCAGATTACACCAAAACTGT
513848 CACCGTAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (36 bp):
CGCATGAGCACTTCCAGATTACACCAAAACTGTAGT
Found at i:513963 original size:37 final size:38
Alignment explanation
Indices: 513882--513963 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
513872 CACCTAAGAT
*
513882 TGTCGCTGCATAAATATTCTTCAAATTGCATCCAGAAC
1 TGTCGCTGCATAAATATTCTTCAAATTGCACCCAGAAC
* *
513920 TATCGCTGCATAAGTATTCTTC-AATTGCACCCAGGAA-
1 TGTCGCTGCATAAATATTCTTCAAATTGCACCCA-GAAC
513957 TGTCGCT
1 TGTCGCT
513964 ACATGAACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
37 16 0.41
38 23 0.59
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (38 bp):
TGTCGCTGCATAAATATTCTTCAAATTGCACCCAGAAC
Found at i:518692 original size:37 final size:37
Alignment explanation
Indices: 518632--518847 Score: 256
Period size: 37 Copynumber: 5.8 Consensus size: 37
518622 TCGATAACCG
* * *
518632 GCACAAAGTCTGCTAGGCACATAGCCTGAATACACTA
1 GCACAAAGCCTGCTAGGCACACAGCCTGAATACACCA
* * * *
518669 GCACGAAGCTTGCTAGGCACATAGCCTGAATACA-CT
1 GCACAAAGCCTGCTAGGCACACAGCCTGAATACACCA
* * *
518705 GACTCAAAGCCTGCTAGGCATACAGCCTGAATACACCG
1 G-CACAAAGCCTGCTAGGCACACAGCCTGAATACACCA
* * *
518743 GCACAAAGCCTACTAGGCACACAACCTGATTACACCA
1 GCACAAAGCCTGCTAGGCACACAGCCTGAATACACCA
***
518780 ATGCAAAGCCTGCTAAGGCACACAGCCTGAATACACCA
1 GCACAAAGCCTGCT-AGGCACACAGCCTGAATACACCA
518818 -CACAAAGCCTGCTAGGCACACAGCCTGAAT
1 GCACAAAGCCTGCTAGGCACACAGCCTGAAT
518848 TTGTAAATGC
Statistics
Matches: 151, Mismatches: 25, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
36 18 0.12
37 110 0.73
38 23 0.15
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (37 bp):
GCACAAAGCCTGCTAGGCACACAGCCTGAATACACCA
Found at i:518824 original size:111 final size:110
Alignment explanation
Indices: 518628--518847 Score: 291
Period size: 111 Copynumber: 2.0 Consensus size: 110
518618 TTCTTCGATA
* * * * * * *
518628 ACCGGCACAAAGTCTGCTAGGCACATAGCCTGAATACACTAGCACGAAGCTTGCTAGGCACATAG
1 ACCGGCACAAAGCCTACTAGGCACACAACCTGAATACACAAGCAC-AAGCCTGCTAGGCACACAG
* * *
518693 CCTGAATACACTGACTCAAAGCCTGCTAGGCATACAGCCTGAATAC
65 CCTGAATACACTCACACAAAGCCTGCTAGGCACACAGCCTGAATAC
*
518739 ACCGGCACAAAGCCTACTAGGCACACAACCTGATTACACCAATGCA-AAGCCTGCTAAGGCACAC
1 ACCGGCACAAAGCCTACTAGGCACACAACCTGAATACA-CAA-GCACAAGCCTGCT-AGGCACAC
518803 AGCCTGAATACAC-CACACAAAGCCTGCTAGGCACACAGCCTGAAT
63 AGCCTGAATACACTCACACAAAGCCTGCTAGGCACACAGCCTGAAT
518848 TTGTAAATGC
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
111 70 0.74
112 22 0.23
113 3 0.03
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.15
Consensus pattern (110 bp):
ACCGGCACAAAGCCTACTAGGCACACAACCTGAATACACAAGCACAAGCCTGCTAGGCACACAGC
CTGAATACACTCACACAAAGCCTGCTAGGCACACAGCCTGAATAC
Found at i:524743 original size:34 final size:34
Alignment explanation
Indices: 524705--524785 Score: 144
Period size: 34 Copynumber: 2.4 Consensus size: 34
524695 ACGTATATGG
*
524705 AAATGCAATGACAATGTAGATGCAGCGATAATAA
1 AAATGCAATGACAATGTAGATGCAGCGACAATAA
524739 AAATGCAATGACAATGTAGATGCAGCGACAATAA
1 AAATGCAATGACAATGTAGATGCAGCGACAATAA
*
524773 CAATGCAATGACA
1 AAATGCAATGACA
524786 TTAATAATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.19
Consensus pattern (34 bp):
AAATGCAATGACAATGTAGATGCAGCGACAATAA
Found at i:524761 original size:17 final size:17
Alignment explanation
Indices: 524707--524762 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
524697 GTATATGGAA
524707 ATGCAATGACAATGTAG
1 ATGCAATGACAATGTAG
** * ** *
524724 ATGCAGCGATAATAAAA
1 ATGCAATGACAATGTAG
524741 ATGCAATGACAATGTAG
1 ATGCAATGACAATGTAG
524758 ATGCA
1 ATGCA
524763 GCGACAATAA
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (17 bp):
ATGCAATGACAATGTAG
Found at i:524768 original size:17 final size:17
Alignment explanation
Indices: 524714--524770 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
524704 GAAATGCAAT
524714 GACAATGTAGATGCAGC
1 GACAATGTAGATGCAGC
* ** * **
524731 GATAATAAAAATGCAAT
1 GACAATGTAGATGCAGC
524748 GACAATGTAGATGCAGC
1 GACAATGTAGATGCAGC
524765 GACAAT
1 GACAAT
524771 AACAATGCAA
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (17 bp):
GACAATGTAGATGCAGC
Found at i:524803 original size:34 final size:34
Alignment explanation
Indices: 524705--524804 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 34
524695 ACGTATATGG
* * *
524705 AAATGCAATGACAATGTAGATGCAGCGATAATAA
1 AAATGCAATGACAATATAGATGAAGCGACAATAA
* *
524739 AAATGCAATGACAATGTAGATGCAGCGACAATAA
1 AAATGCAATGACAATATAGATGAAGCGACAATAA
* * *
524773 CAATGCAATGACATTAATA-ATGAAGGGACAAT
1 AAATGCAATGACAAT-ATAGATGAAGCGACAAT
524805 TACACTACAG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 57 0.97
35 2 0.03
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGAAGCGACAATAA
Found at i:525351 original size:21 final size:21
Alignment explanation
Indices: 525301--525352 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
525291 TGCGCCAAGC
**
525301 CTTCAGGTATTTCACCCACAA
1 CTTCAGGTGCTTCACCCACAA
525322 CTTCAGGTGCTTCACCCACAA
1 CTTCAGGTGCTTCACCCACAA
525343 CTTCAGGTGC
1 CTTCAGGTGC
525353 AGGGACAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (21 bp):
CTTCAGGTGCTTCACCCACAA
Found at i:534577 original size:238 final size:237
Alignment explanation
Indices: 534154--534633 Score: 723
Period size: 238 Copynumber: 2.0 Consensus size: 237
534144 CATGCCTCCA
*
534154 ATTTACTTGTAACTTGACTAAGACGTGTTCATCAAACTTATCTAATTTAAAACTTAAATTAGAGA
1 ATTTACTTGTAACTTGACTAAGACGTATTCATCAAACTTATCTAATTTAAAACTTAAATTAGAGA
* * ** * *
534219 TTTTTACTCCTAATAAGAACCCTAAGGATACCTTAATAATTCTTGTAAAATACTTTCAATTCTTC
66 TTTTTACTCCTAACAAGAACCCTAAAGATACCTTAATAATTCAAGTAAAATACCTTCAATTCTTA
* *
534284 AAATTAATTTTATTTTAGAATCCTAAAAAAGCCTAAAAAAATTACTAATGAATTAAGAGAAATAT
131 AAATTAATTTTATTTTAGAATCCTAAAAAAACCT-AAAAAATTACTAAGGAATTAAGAGAAATAT
* *
534349 TAAAATTCATCTACAACTTATTCGATCTTTTATCATTACTCTG
195 TAAAATTAATCTACAACTTATTCGATCTTTTATCATTACTATG
*
534392 ATTTCCTTGTAACTTGACTATA-ACGTATTCATCAAACTTATCTAATTTAAAACTTAAATTAGAG
1 ATTTACTTGTAACTTGACTA-AGACGTATTCATCAAACTTATCTAATTTAAAACTTAAATTAGAG
* * * *
534456 ATTTTTACTTCTAACGAGAATCCTAAAAGAT-TCTTAAATAATTCAAGTAAAATACCTTCAATTC
65 ATTTTTACTCCTAACAAGAACCCT-AAAGATACCTT-AATAATTCAAGTAAAATACCTTCAATTC
*
534520 TTAAAATTAATTTTATTTTAGAATCCTAAAAAAAACCT-AAAAGTTACTAAGGAATTAAGAGAAA
128 TTAAAATTAATTTTATTTTAGAATCCT-AAAAAAACCTAAAAAATTACTAAGGAATTAAGAGAAA
* *
534584 TATTAACATTAATCTACAACTTATTCGATCTTTTATCATTATTATG
192 TATTAAAATTAATCTACAACTTATTCGATCTTTTATCATTACTATG
534630 ATTT
1 ATTT
534634 TAAAAGATTT
Statistics
Matches: 219, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
238 153 0.70
239 57 0.26
240 9 0.04
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (237 bp):
ATTTACTTGTAACTTGACTAAGACGTATTCATCAAACTTATCTAATTTAAAACTTAAATTAGAGA
TTTTTACTCCTAACAAGAACCCTAAAGATACCTTAATAATTCAAGTAAAATACCTTCAATTCTTA
AAATTAATTTTATTTTAGAATCCTAAAAAAACCTAAAAAATTACTAAGGAATTAAGAGAAATATT
AAAATTAATCTACAACTTATTCGATCTTTTATCATTACTATG
Found at i:535765 original size:148 final size:145
Alignment explanation
Indices: 535613--536182 Score: 557
Period size: 148 Copynumber: 3.8 Consensus size: 145
535603 TTCTTCTTTT
* * ** * *
535613 TTTTTAAAAAAAGTAAAAGTTTTCTTTTTATTAAAACAAAATCACTACTTTACTTCAAAATCAAA
1 TTTTTAAAAAAA-TAAAAGTTTTCTTTTTTTTTAATGAAAATCACTACTTTACTTAAAAATCTAA
* *
535678 ACTTTTATTTCGATATAGTTAAAAAAAATCAAAATTTTATTTAAAAATTTAAACTTTTTTCTTTC
65 ACTTTTATTTCGAAATAGTTAAAAAAAATCAAAATTTT-TTTAAAAATTTAAAC-TTTTTCTTTA
* *
535743 AAATCATTAAAAAACATA
128 AAATAACTAAAAAACATA
***** * **
535761 TTTTT-ATTTTTTAAAAATCTAAACTTTTTTTTTAATGAAAATC-CTACTTTACTTAAAAATCTA
1 TTTTTAAAAAAATAAAAGT-T-TTCTTTTTTTTTAATGAAAATCACTACTTTACTTAAAAATCTA
* **
535824 AATTTTTATTTTAAAATAGTTAAAAAAAAAATCAAAACTTTTTTTAAAAATTTAAACTTTTTCTT
64 AACTTTTATTTCGAAATAGTT--AAAAAAAATCAAAA-TTTTTTTAAAAATTTAAACTTTTTCTT
*
535889 TAAAATAACTATAAAACATA
126 TAAAATAACTAAAAAACATA
* *
535909 TTTTTTTAAAAAAA-ATATAGACTTTCTTTCTTTTTTAATGAAAATCACTACTTTACTTAAAAAT
1 --TTTTTAAAAAAATA-AAAG-TTTTCTTT-TTTTTTAATGAAAATCACTACTTTACTTAAAAAT
* * *
535973 -TCAAACTTTTATTTCGAAATAGTTAAAAAATAA--AAACTTTCTTTAAAAAATTAAACTTTTTC
61 CT-AAACTTTTATTTCGAAATAGTTAAAAAA-AATCAAAATTTTTTTAAAAATTTAAACTTTTTC
536035 TTTAAAATAACT-AAAAACATA
124 TTTAAAATAACTAAAAAACATA
** *
536056 TTTTTATTTTTAAAAATATAAAA--TTTCTCCTTTTTTAATGAAAATCACTACTTT-TTTAAAAA
1 TTTTTA-----AAAAA-ATAAAAGTTTTCTTTTTTTTTAATGAAAATCACTACTTTACTT--AAA
* * *
536118 AATCTAAACTTTTATTTTGAAATAATTAAAAAAAATCAAAAGTTTGTTTAAAAATTTAAACTTTT
58 AATCTAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAA-TTTTTTTAAAAATTTAAACTTTT
536183 CTAAAAAAAT
Statistics
Matches: 347, Mismatches: 48, Indels: 52
0.78 0.11 0.12
Matches are distributed among these distances:
145 6 0.02
146 8 0.02
147 71 0.20
148 117 0.34
149 36 0.10
150 46 0.13
151 26 0.07
152 37 0.11
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (145 bp):
TTTTTAAAAAAATAAAAGTTTTCTTTTTTTTTAATGAAAATCACTACTTTACTTAAAAATCTAAA
CTTTTATTTCGAAATAGTTAAAAAAAATCAAAATTTTTTTAAAAATTTAAACTTTTTCTTTAAAA
TAACTAAAAAACATA
Found at i:536020 original size:20 final size:21
Alignment explanation
Indices: 535995--536052 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
535985 TTCGAAATAG
535995 TTAAAAAATAAAAAC-TTTCT
1 TTAAAAAATAAAAACTTTTCT
*
536015 TTAAAAAAT-TAAACTTTTTCT
1 TTAAAAAATAAAAAC-TTTTCT
536036 TTAAAATAACTAAAAAC
1 TTAAAA-AA-TAAAAAC
536053 ATATTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 4 0.13
20 9 0.29
21 11 0.35
22 2 0.06
23 1 0.03
24 4 0.13
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAAAAATAAAAACTTTTCT
Found at i:536208 original size:148 final size:147
Alignment explanation
Indices: 535650--536301 Score: 533
Period size: 148 Copynumber: 4.5 Consensus size: 147
535640 TTATTAAAAC
* * * * *
535650 AAAATCACTACTTTACTT-CAAAATCAAAACTTTTATTTCGATATAGTTAAAAAAAATCAAAATT
1 AAAATCACTACTTTACTTAAAAAATCTAAACTTTTATTTTGAAATAGTTAAAAAAAATCAAAACT
* * ***
535714 TTATTTAAAAATTTAAACTTTTTTCTTTCAAATCATTAAA-AAACATATTTTTATTTTTTAAAAA
66 TTCTTTAAAAATTTAAAC-TTTTTC-TT-AAA--A-TAAATAAAAATA-TTTT-TTTAAAAAAAA
* *
535778 TCT-AAA---CTT-TTTTTTTAATG
123 TATAAAATTTCTTCCTTTTTTAATG
* *
535798 AAAATC-CTACTTTACTT-AAAAATCTAAATTTTTATTTTAAAATAGTTAAAAAAAAAATCAAAA
1 AAAATCACTACTTTACTTAAAAAATCTAAACTTTTATTTTGAAATAGTT--AAAAAAAATCAAAA
*
535861 CTTTTTTTAAAAATTTAAACTTTTTCTTTAAAATAACTATAAAACATATTTTTTTAAAAAAAATA
64 CTTTCTTTAAAAATTTAAACTTTTTC-TTAAAATAA--ATAAAA-ATATTTTTTTAAAAAAAATA
* * *
535926 TAGACTTTCTTTCTTTTTTAATG
125 TAAAATTTCTTCCTTTTTTAATG
* * *
535949 AAAATCACTACTTTACTTAAAAATTC-AAACTTTTATTTCGAAATAGTT--AAAAAATAAAAACT
1 AAAATCACTACTTTACTTAAAAAATCTAAACTTTTATTTTGAAATAGTTAAAAAAAATCAAAACT
* * ***
536011 TTCTTTAAAAAATTAAACTTTTTCTTTAAAATAACTAAAAACATATTTTTATTTTTAAAAATATA
66 TTCTTTAAAAATTTAAACTTTTTC-TTAAAATAAAT-AAAA-ATATTTTT-TTAAAAAAAATATA
536076 AAATTTC-TCCTTTTTTAATG
127 AAATTTCTTCCTTTTTTAATG
* * *
536096 AAAATCACTACTTT-TTTAAAAAAATCTAAACTTTTATTTTGAAATAATTAAAAAAAATCAAAAG
1 AAAATCACTACTTTACTT-AAAAAATCTAAACTTTTATTTTGAAATAGTTAAAAAAAATCAAAAC
* *** *
536160 TTTGTTTAAAAATTTAAAC-TTTTC-TAAAA-AAATAGATTTTTATTTTTTT----AAAATCTAA
65 TTTCTTTAAAAATTTAAACTTTTTCTTAAAATAAATA-A-AAATATTTTTTTAAAAAAAATATAA
* * * *
536218 ACTTT-GT-CTTTTTAAAAG
128 AATTTCTTCCTTTTTTAATG
* * * * * * * *
536236 AAAATCACTATTTTA-TTTAAAAATCAAAACTTTTATTTCGATATTGTTTAAAAAAACCAAAACT
1 AAAATCACTACTTTACTTAAAAAATCTAAACTTTTATTTTGAAATAGTTAAAAAAAATCAAAACT
536300 TT
66 TT
536302 TCCCAAAATT
Statistics
Matches: 425, Mismatches: 56, Indels: 55
0.79 0.10 0.10
Matches are distributed among these distances:
139 40 0.09
140 24 0.06
141 13 0.03
144 3 0.01
145 4 0.01
146 25 0.06
147 97 0.23
148 99 0.23
149 37 0.09
150 31 0.07
151 16 0.04
152 30 0.07
153 6 0.01
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (147 bp):
AAAATCACTACTTTACTTAAAAAATCTAAACTTTTATTTTGAAATAGTTAAAAAAAATCAAAACT
TTCTTTAAAAATTTAAACTTTTTCTTAAAATAAATAAAAATATTTTTTTAAAAAAAATATAAAAT
TTCTTCCTTTTTTAATG
Found at i:536324 original size:140 final size:140
Alignment explanation
Indices: 536055--536316 Score: 309
Period size: 139 Copynumber: 1.9 Consensus size: 140
536045 CTAAAAACAT
* *
536055 ATTTTTATTTTTAAAAATATAAAATTTCTCCTTTTTTAATGAAAATCACTACTTTTTTAAAAAAA
1 ATTTTTATTTTTAAAAATATAAAATTTCTCCTTTTTAAAAGAAAATCACTACTTTTTTAAAAAAA
* * * * **
536120 TCTAAACTTTTATTTTGAAATAATTAAAAAAAATCAAAAGTTTGTTTAAAAATTTAAACTTTTCT
66 TCAAAACTTTTATTTCGAAATAATTAAAAAAAACCAAAACTTTGTCCAAAAATTTAAACTTTTCT
536185 AAAAAAATAG
131 AAAAAAATAG
* * * * *
536195 ATTTTTATTTTTTTAAAATCTAAACTTTGT-CTTTTTAAAAGAAAATCACTA-TTTTATT-TAAA
1 ATTTTTA-TTTTTAAAAATATAAAATTTCTCCTTTTTAAAAGAAAATCACTACTTTT-TTAAAAA
* ** * *
536257 AATCAAAACTTTTATTTCGATATTGTTTAAAAAAACCAAAACTTT-TCCCAAAA-TTAAACT
64 AATCAAAACTTTTATTTCGAAATAATTAAAAAAAACCAAAACTTTGTCCAAAAATTTAAACT
536317 ATTTTTCTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
137 7 0.07
138 5 0.05
139 44 0.43
140 28 0.27
141 18 0.18
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (140 bp):
ATTTTTATTTTTAAAAATATAAAATTTCTCCTTTTTAAAAGAAAATCACTACTTTTTTAAAAAAA
TCAAAACTTTTATTTCGAAATAATTAAAAAAAACCAAAACTTTGTCCAAAAATTTAAACTTTTCT
AAAAAAATAG
Found at i:536731 original size:3 final size:3
Alignment explanation
Indices: 536723--536751 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
536713 AGGAAACCCT
536723 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
536752 TTGGGCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:542762 original size:41 final size:41
Alignment explanation
Indices: 542693--542908 Score: 249
Period size: 41 Copynumber: 5.2 Consensus size: 41
542683 ACTTGATGTA
** *
542693 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGAATCGAAATGAGCATGAGATTATAT
* *
542735 TAAAAGAAGACTCGTGAATCGAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGAATCGAAATGAGCATGAGATTATAT
* * *
542776 TAAAGGAAGACTCATGACTCAAAATGAGCATGAGATTAAAT
1 TAAAGGAAGACTCATGAATCGAAATGAGCATGAGATTATAT
* *
542817 TAAAGGAAGACTCGTGACTC-AAGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCATGAATCGAA-ATGAGCATGAGATTATA-T
* * * *
542859 TAAAGGAAGACTTATGAATCGATA-GAGCATAAGATTGT-T
1 TAAAGGAAGACTCATGAATCGAAATGAGCATGAGATTATAT
542898 TAAAAGGAAGA
1 T-AAAGGAAGA
542909 TCTACGACTT
Statistics
Matches: 152, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.01
40 11 0.07
41 115 0.76
42 23 0.15
43 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (41 bp):
TAAAGGAAGACTCATGAATCGAAATGAGCATGAGATTATAT
Found at i:543577 original size:21 final size:21
Alignment explanation
Indices: 543548--543596 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
543538 TTTAGTATTA
*
543548 GTAGAAGCATGACTTGTTTCG
1 GTAGTAGCATGACTTGTTTCG
*
543569 GTAGTAGCATGACTTGTTTTG
1 GTAGTAGCATGACTTGTTTCG
543590 GTAGTAG
1 GTAGTAG
543597 TGTCACATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.10, G:0.31, T:0.37
Consensus pattern (21 bp):
GTAGTAGCATGACTTGTTTCG
Found at i:557664 original size:21 final size:21
Alignment explanation
Indices: 557640--557686 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
557630 TCACTCACAC
557640 TTTCATCACTCTCACTTTCTT-
1 TTTCATCACTCTCACTTT-TTG
* *
557661 TTTCCTCACTCTCTCTTTTTG
1 TTTCATCACTCTCACTTTTTG
557682 TTTCA
1 TTTCA
557687 GCTTCTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.11, C:0.32, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTCATCACTCTCACTTTTTG
Found at i:557835 original size:19 final size:18
Alignment explanation
Indices: 557807--557854 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
557797 TTCAAGTACT
557807 TTTC-TTTTTCTCTTTCA
1 TTTCTTTTTTCTCTTTCA
557824 GTTTCTTTTTTCTC--TCA
1 -TTTCTTTTTTCTCTTTCA
557841 TTTCTTTTTT-TCTT
1 TTTCTTTTTTCTCTT
557855 CTCTCAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 10 0.37
17 3 0.11
18 4 0.15
19 8 0.30
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTCTTTTTTCTCTTTCA
Found at i:557857 original size:18 final size:19
Alignment explanation
Indices: 557807--557857 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 19
557797 TTCAAGTACT
*
557807 TTTCTTTTTCTCTT-TCAG
1 TTTCTTTTTTTCTTCTCAG
557825 TTTC-TTTTTTC-TCTCA-
1 TTTCTTTTTTTCTTCTCAG
557841 TTTCTTTTTTTCTTCTC
1 TTTCTTTTTTTCTTCTC
557858 TCAAACTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 5 0.17
17 16 0.55
18 8 0.28
ACGTcount: A:0.04, C:0.24, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTCTTTTTTTCTTCTCAG
Found at i:569069 original size:21 final size:21
Alignment explanation
Indices: 569045--569094 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
569035 GAGTTTTTAG
*
569045 TATCGGTAGAGGAGTCACTTA
1 TATCGGTAGAAGAGTCACTTA
** *
569066 TATCGGTAGAATTGTCACTTG
1 TATCGGTAGAAGAGTCACTTA
569087 TATCGGTA
1 TATCGGTA
569095 CAAATCTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (21 bp):
TATCGGTAGAAGAGTCACTTA
Found at i:576249 original size:21 final size:21
Alignment explanation
Indices: 576225--576277 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
576215 CTATGACAGT
*
576225 TCTACCGATACAAGT-GAGACA
1 TCTACCGATACAAGTCAAG-CA
* * *
576246 TCTATCAATACAAGTCAAGCT
1 TCTACCGATACAAGTCAAGCA
576267 TCTACCGATAC
1 TCTACCGATAC
576278 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (21 bp):
TCTACCGATACAAGTCAAGCA
Found at i:577052 original size:51 final size:51
Alignment explanation
Indices: 576987--577117 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 51
576977 GCCCAGATAG
* * *
576987 ATTTACACTCTTATGAGTCAAACAAAATTACGCTCTTACGAGCCAAACATAA
1 ATTT-CACTCTTATGAGCCAAACAAAATTACGCTCTTACAAGCCAAACAGAA
* * * *
577039 ATTTCACTCTTATGAGCCAGAGAAAATTACGCTCTTACAAGCCAGATAGAA
1 ATTTCACTCTTATGAGCCAAACAAAATTACGCTCTTACAAGCCAAACAGAA
* * *
577090 ATTTCGCTCTTACGAGCCAAACAGAATT
1 ATTTCACTCTTATGAGCCAAACAAAATT
577118 TTACTCTTAC
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 63 0.94
52 4 0.06
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (51 bp):
ATTTCACTCTTATGAGCCAAACAAAATTACGCTCTTACAAGCCAAACAGAA
Found at i:577127 original size:25 final size:25
Alignment explanation
Indices: 576994--577156 Score: 130
Period size: 25 Copynumber: 6.4 Consensus size: 25
576984 TAGATTTACA
* * * *
576994 CTCTTATGAGTCAAACAAAATTACG
1 CTCTTACGAGCCAAACAGAATTTCG
* *
577019 CTCTTACGAGCCAAACATAAATTTCA
1 CTCTTACGAGCCAAACA-GAATTTCG
* * * * *
577045 CTCTTATGAGCCAGAGAAAATTACG
1 CTCTTACGAGCCAAACAGAATTTCG
* * *
577070 CTCTTACAAGCCAGATAGAAATTTCG
1 CTCTTACGAGCCAAACAG-AATTTCG
**
577096 CTCTTACGAGCCAAACAGAATTTTA
1 CTCTTACGAGCCAAACAGAATTTCG
* *
577121 CTCTTACCAG-CAAGACAGAATTACG
1 CTCTTACGAGCCAA-ACAGAATTTCG
577146 CTCTTACGAGC
1 CTCTTACGAGC
577157 TAGAATTCAA
Statistics
Matches: 110, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
24 3 0.03
25 66 0.60
26 41 0.37
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (25 bp):
CTCTTACGAGCCAAACAGAATTTCG
Found at i:583905 original size:26 final size:25
Alignment explanation
Indices: 583875--584061 Score: 140
Period size: 25 Copynumber: 7.4 Consensus size: 25
583865 ATTTAACTTA
* *
583875 TACGAGCCTAGACATATTTACGCTCT
1 TACGAGCC-AGACAAAATTACGCTCT
* * *
583901 TACGAGCCAAACAGAATTATGCTCT
1 TACGAGCCAGACAAAATTACGCTCT
583926 TACGAGCCAGACAAAAATTACGCTCT
1 TACGAGCCAGAC-AAAATTACGCTCT
* * * *
583952 TACGAACTAGACAAAAATTTCACTCT
1 TACGAGCCAGAC-AAAATTACGCTCT
* * * * * *
583978 TATGAGCCAAATAGAATCATGCTCT
1 TACGAGCCAGACAAAATTACGCTCT
* * * *
584003 TTCGAGCCATACAGAATTATGCTCT
1 TACGAGCCAGACAAAATTACGCTCT
* * * *
584028 TATGAGCTAGATAGAATTACGCTCT
1 TACGAGCCAGACAAAATTACGCTCT
584053 TACGAGCCA
1 TACGAGCCA
584062 AACTTTAGAA
Statistics
Matches: 126, Mismatches: 34, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
25 78 0.62
26 48 0.38
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (25 bp):
TACGAGCCAGACAAAATTACGCTCT
Found at i:583928 original size:25 final size:25
Alignment explanation
Indices: 583896--584064 Score: 142
Period size: 25 Copynumber: 6.7 Consensus size: 25
583886 ACATATTTAC
583896 GCTCTTACGAGCCAAACAGAATTAT
1 GCTCTTACGAGCCAAACAGAATTAT
* * *
583921 GCTCTTACGAGCCAGACAAAAATTAC
1 GCTCTTACGAGCCAAAC-AGAATTAT
* * * *
583947 GCTCTTACGAACTAGACAAAAATT-T
1 GCTCTTACGAGCCAAAC-AGAATTAT
* * * *
583972 CACTCTTATGAGCCAAATAGAATCAT
1 -GCTCTTACGAGCCAAACAGAATTAT
* *
583998 GCTCTTTCGAGCCATACAGAATTAT
1 GCTCTTACGAGCCAAACAGAATTAT
* * * * *
584023 GCTCTTATGAGCTAGATAGAATTAC
1 GCTCTTACGAGCCAAACAGAATTAT
584048 GCTCTTACGAGCCAAAC
1 GCTCTTACGAGCCAAAC
584065 TTTAGAATTA
Statistics
Matches: 111, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
25 71 0.64
26 40 0.36
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (25 bp):
GCTCTTACGAGCCAAACAGAATTAT
Found at i:583978 original size:77 final size:75
Alignment explanation
Indices: 583892--584064 Score: 202
Period size: 77 Copynumber: 2.3 Consensus size: 75
583882 CTAGACATAT
* *
583892 TTACGCTCTTACGAGCCAAACAGAATTATGCTCTTACGAGCCAGACAAAAATTACGCTCTTACGA
1 TTACACTCTTACGAGCCAAACAGAATCATGCTCTTACGAGCCAGAC-AAAATTACGCTCTTACGA
583957 ACTAGACAAAAA
65 ACTAGA-AAAAA
* * * * * * * * *
583969 TTTCACTCTTATGAGCCAAATAGAATCATGCTCTTTCGAGCCATACAGAATTATGCTCTTATGAG
1 TTACACTCTTACGAGCCAAACAGAATCATGCTCTTACGAGCCAGACAAAATTACGCTCTTACGAA
* *
584034 CTAGATAGAA
66 CTAGAAAAAA
*
584044 TTACGCTCTTACGAGCCAAAC
1 TTACACTCTTACGAGCCAAAC
584065 TTTAGAATTA
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
75 20 0.25
76 20 0.25
77 39 0.49
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (75 bp):
TTACACTCTTACGAGCCAAACAGAATCATGCTCTTACGAGCCAGACAAAATTACGCTCTTACGAA
CTAGAAAAAA
Found at i:588032 original size:18 final size:18
Alignment explanation
Indices: 588006--588044 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
587996 CTGAAAAGTG
*
588006 AAAGATTTTTAGGGTTTT
1 AAAGATTTTTAGAGTTTT
*
588024 AAAGGTTTTTAGAGTTTT
1 AAAGATTTTTAGAGTTTT
588042 AAA
1 AAA
588045 ATGTAATGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (18 bp):
AAAGATTTTTAGAGTTTT
Found at i:589270 original size:24 final size:23
Alignment explanation
Indices: 589229--589281 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
589219 TTTAGCCCAC
* *
589229 ACGAACCCGAATGGTTAGCTCTT
1 ACGAGCCCGAATGATTAGCTCTT
589252 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCC-GAATGATTAGCTCTT
589276 ACGAGC
1 ACGAGC
589282 TTAGATAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
ACGAGCCCGAATGATTAGCTCTT
Found at i:591335 original size:15 final size:15
Alignment explanation
Indices: 591312--591348 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
591302 TGGTTTACAT
*
591312 TCTTGTTATTTTATC
1 TCTTTTTATTTTATC
591327 TCTTTTTATTTTATC
1 TCTTTTTATTTTATC
591342 TCTTTTT
1 TCTTTTT
591349 GTGCACTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.73
Consensus pattern (15 bp):
TCTTTTTATTTTATC
Found at i:602139 original size:48 final size:48
Alignment explanation
Indices: 602087--602228 Score: 212
Period size: 48 Copynumber: 2.9 Consensus size: 48
602077 ATGTATTAAT
* * *
602087 GCAAAACATTAAATAAAGATGCATTTAAGAAACAAAACACATATTGAA
1 GCAAAACATTAAACAAAGATGCATTTAACAAACAAAACACATAATGAA
* *
602135 GCAAATCATTAAACAAAGATGCATTTAACAAACAAAACACATAATGAT
1 GCAAAACATTAAACAAAGATGCATTTAACAAACAAAACACATAATGAA
* *
602183 GCAGAACATTAAACAAAGATGCATTTAACCAAACAAAACATATAAT
1 GCAAAACATTAAACAAAGATGCATTTAA-CAAACAAAACACATAAT
602229 TAAAACTGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
48 69 0.81
49 16 0.19
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.20
Consensus pattern (48 bp):
GCAAAACATTAAACAAAGATGCATTTAACAAACAAAACACATAATGAA
Found at i:607604 original size:19 final size:19
Alignment explanation
Indices: 607569--607756 Score: 158
Period size: 19 Copynumber: 10.2 Consensus size: 19
607559 TCAGTAATTT
*
607569 GCTCTTACGAGCAAGTATC
1 GCTCTTACGAGCCAGTATC
* *
607588 GCTTTTATGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
607607 GCTCTTACGAGCCTA-TATC
1 GCTCTTACGAGCC-AGTATC
607626 GCTCTTACGAGCCAGTAT-
1 GCTCTTACGAGCCAGTATC
** * * *
607644 GCTCAAACAAGCCAATATT
1 GCTCTTACGAGCCAGTATC
607663 GCTCTTACGAGCCAGTAT-
1 GCTCTTACGAGCCAGTATC
* *
607681 GCTC-AAGCGAGCCAATAT-
1 GCTCTTA-CGAGCCAGTATC
* *
607699 GCCCTTACGAGCCAATA-C
1 GCTCTTACGAGCCAGTATC
* * *
607717 ACTC-AAGCGAGCTAGTAT-
1 GCTCTTA-CGAGCCAGTATC
607735 GCTCTTACGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
607754 GCT
1 GCT
607757 ATTCCTTCCG
Statistics
Matches: 134, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
17 2 0.01
18 65 0.49
19 66 0.49
20 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (19 bp):
GCTCTTACGAGCCAGTATC
Found at i:607722 original size:36 final size:36
Alignment explanation
Indices: 607596--607752 Score: 181
Period size: 36 Copynumber: 4.3 Consensus size: 36
607586 TCGCTTTTAT
* *
607596 GAGCCAGTATCGCTCTTA-CGAGCCTATATCGCTCTTAC
1 GAGCCAGTAT-GCTC-AAGCGAGCCAATAT-GCTCTTAC
* *
607634 GAGCCAGTATGCTCAAACAAGCCAATATTGCTCTTAC
1 GAGCCAGTATGCTCAAGCGAGCCAATA-TGCTCTTAC
*
607671 GAGCCAGTATGCTCAAGCGAGCCAATATGCCCTTAC
1 GAGCCAGTATGCTCAAGCGAGCCAATATGCTCTTAC
* ** * *
607707 GAGCCAATACACTCAAGCGAGCTAGTATGCTCTTAC
1 GAGCCAGTATGCTCAAGCGAGCCAATATGCTCTTAC
607743 GAGCCAGTAT
1 GAGCCAGTAT
607753 CGCTATTCCT
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
36 47 0.46
37 45 0.44
38 11 0.11
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (36 bp):
GAGCCAGTATGCTCAAGCGAGCCAATATGCTCTTAC
Found at i:607751 original size:18 final size:18
Alignment explanation
Indices: 607568--607752 Score: 151
Period size: 18 Copynumber: 10.1 Consensus size: 18
607558 GTCAGTAATT
*
607568 TGCTCTTACGAGCAAGTA
1 TGCTCTTACGAGCCAGTA
* *
607586 TCGCTTTTATGAGCCAGTA
1 T-GCTCTTACGAGCCAGTA
607605 TCGCTCTTACGAGCCTA-TA
1 T-GCTCTTACGAGCC-AGTA
607624 TCGCTCTTACGAGCCAGTA
1 T-GCTCTTACGAGCCAGTA
** * *
607643 TGCTCAAACAAGCCAATA
1 TGCTCTTACGAGCCAGTA
607661 TTGCTCTTACGAGCCAGTA
1 -TGCTCTTACGAGCCAGTA
* *
607680 TGCTC-AAGCGAGCCAATA
1 TGCTCTTA-CGAGCCAGTA
* *
607698 TGCCCTTACGAGCCAATA
1 TGCTCTTACGAGCCAGTA
** * *
607716 CACTC-AAGCGAGCTAGTA
1 TGCTCTTA-CGAGCCAGTA
607734 TGCTCTTACGAGCCAGTA
1 TGCTCTTACGAGCCAGTA
607752 T
1 T
607753 CGCTATTCCT
Statistics
Matches: 132, Mismatches: 27, Indels: 16
0.75 0.15 0.09
Matches are distributed among these distances:
17 2 0.02
18 66 0.50
19 63 0.48
20 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (18 bp):
TGCTCTTACGAGCCAGTA
Found at i:611438 original size:2 final size:2
Alignment explanation
Indices: 611425--611466 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
611415 TTGTATAATA
*
611425 AT AT AA 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
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.