Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 46 of 226
Found at i:19316447 original size:2 final size:2
Alignment explanation
Indices: 19316403--19316428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19316393 ACTGAAAATA
19316403 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
19316429 CTTACAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19325147 original size:31 final size:31
Alignment explanation
Indices: 19325112--19325184 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
19325102 CTCGACTAAC
19325112 CAATTTTTCTTACATTTAATCTTCAACTTAG
1 CAATTTTTCTTACATTTAATCTTCAACTTAG
*
19325143 CAATTTTTCTTACATTTGATCTTCAACTTAG
1 CAATTTTTCTTACATTTAATCTTCAACTTAG
19325174 CAATTTTTCTT
1 CAATTTTTCTT
19325185 GAAATCTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (31 bp):
CAATTTTTCTTACATTTAATCTTCAACTTAG
Found at i:19325405 original size:22 final size:22
Alignment explanation
Indices: 19325369--19325431 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 22
19325359 AAAGTTATAA
*
19325369 TTTAAA-ATTTTTTATTAATTT
1 TTTAAATAATTTTTATTAATTT
*
19325390 TGTT-TATAATTTTTA-T-ATTT
1 T-TTAAATAATTTTTATTAATTT
19325410 TTTAAATAATTTTT-TTAATTT
1 TTTAAATAATTTTTATTAATTT
19325431 T
1 T
19325432 AAAAGGGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 8 0.24
22 9 0.26
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTAAATAATTTTTATTAATTT
Found at i:19332067 original size:24 final size:25
Alignment explanation
Indices: 19332038--19332084 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
19332028 GAAAAATATT
19332038 AAATAT-ATA-TTTTTTCTATTTTTA
1 AAATATAATAGTTTTTT-TATTTTTA
19332062 AAATATAATAGTTTTTTTATTTT
1 AAATATAATAGTTTTTTTATTTT
19332085 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.29
25 9 0.43
26 6 0.29
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
AAATATAATAGTTTTTTTATTTTTA
Found at i:19332196 original size:9 final size:9
Alignment explanation
Indices: 19332182--19332209 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19332172 TTTTGTTACA
19332182 ACAATTAAT
1 ACAATTAAT
19332191 ACAATTAAT
1 ACAATTAAT
19332200 ACAATTAAT
1 ACAATTAAT
19332209 A
1 A
19332210 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:19332237 original size:68 final size:66
Alignment explanation
Indices: 19332152--19332293 Score: 239
Period size: 68 Copynumber: 2.1 Consensus size: 66
19332142 TCAAGTTTGT
*
19332152 TTTACTAATAAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATAAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
19332217 AAA
64 AAA
*
19332220 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATAAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
19332285 T
66 A
19332286 TTTACTAA
1 TTTACTAA
19332294 CAATTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 43 0.61
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATAAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:19332307 original size:22 final size:22
Alignment explanation
Indices: 19332297--19332411 Score: 66
Period size: 22 Copynumber: 5.4 Consensus size: 22
19332287 TTACTAACAA
* *
19332297 TTAATTTTAATAACAATTAGTT
1 TTAATTTTACTAACAATTAATT
* *
19332319 TTAATATTAAC-AATTAA-TAATT
1 TTAAT-TTTACTAA-CAATTAATT
19332341 TGATAATTTTACTAACAATTAATT
1 T--TAATTTTACTAACAATTAATT
*
19332365 TT-A----A-TAACAATTAGTT
1 TTAATTTTACTAACAATTAATT
* * *
19332381 TTAATTTTATTAAAAAATAATT
1 TTAATTTTACTAACAATTAATT
19332403 TTAATTTTA
1 TTAATTTTA
19332412 ATTAAAAACG
Statistics
Matches: 71, Mismatches: 10, Indels: 24
0.68 0.10 0.23
Matches are distributed among these distances:
16 13 0.18
17 2 0.03
21 2 0.03
22 31 0.44
23 11 0.15
24 12 0.17
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (22 bp):
TTAATTTTACTAACAATTAATT
Found at i:19332331 original size:19 final size:16
Alignment explanation
Indices: 19332282--19332385 Score: 83
Period size: 16 Copynumber: 6.6 Consensus size: 16
19332272 AATAATTTGA
*
19332282 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
19332298 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
19332314 TAGTTTTAATATTAACAAT
1 TAATTTT-A-A-TAACAAT
***
19332333 TAA---TAAT-TTGA-
1 TAATTTTAATAACAAT
*
19332344 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
19332360 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
19332376 TAGTTTTAAT
1 TAATTTTAAT
19332386 TTTATTAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
11 3 0.04
12 1 0.01
13 1 0.01
14 4 0.06
15 2 0.03
16 46 0.68
17 1 0.01
18 1 0.01
19 9 0.13
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:19332350 original size:62 final size:62
Alignment explanation
Indices: 19332262--19332385 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
19332252 AATTAATACA
19332262 ATTAACAATTAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
1 ATTAACAATTAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
19332324 ATTAACAATTAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
1 ATTAACAATTAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
19332386 TTTATTAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (62 bp):
ATTAACAATTAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
Found at i:19332400 original size:62 final size:62
Alignment explanation
Indices: 19332262--19332411 Score: 223
Period size: 62 Copynumber: 2.5 Consensus size: 62
19332252 AATTAATACA
**
19332262 ATTAACAATTAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
1 ATTAACAAAAAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
**
19332324 ATTAACAATTAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
1 ATTAACAAAAAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
* **
19332386 TTTATTAAAAAATAATTT--TAATTTTA
1 ATTAACAAAAAATAATTTGATAATTTTA
19332412 ATTAAAAACG
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 8 0.10
62 75 0.90
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (62 bp):
ATTAACAAAAAATAATTTGATAATTTTACTAACAATTAATTTTAATAACAATTAGTTTTAAT
Found at i:19332418 original size:22 final size:22
Alignment explanation
Indices: 19332359--19332419 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
19332349 TTACTAACAA
* *
19332359 TTAATTTTAA-TAACAATTAGTT
1 TTAATTTTAATTAA-AAATAATT
19332381 TTAATTTT-ATTAAAAAATAATT
1 TTAATTTTAATT-AAAAATAATT
19332403 TTAATTTTAATTAAAAA
1 TTAATTTTAATTAAAAA
19332420 CGGGCCGGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 28 0.82
23 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATTAAAAATAATT
Found at i:19343649 original size:79 final size:81
Alignment explanation
Indices: 19343508--19343691 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
19343498 TCAACAGAAG
* * *
19343508 AAATAGATGTAA-TTTAAACAAAATAATCAATTTGTTTTTTATCTAACATATAGGAATTAATTTA
1 AAATAGATATAATTTTAAACAAAATAATCAATTTGTTTTTAATCTAACATAGAGGAATTAATTTA
19343572 CCCATTTTTT-AATTAA
66 CCCATTTTTTGAA-TAA
* * * * * *
19343588 AAATGGATATAATTTTAAACAAAATTATCAGTTT-TTTTTAATTTTACATAGA-GAATTAATTTG
1 AAATAGATATAATTTTAAACAAAATAATCAATTTGTTTTTAATCTAACATAGAGGAATTAATTTA
*
19343651 TCCATTTTTTGAATAA
66 CCCATTTTTTGAATAA
* * *
19343667 AAATAGATGTGATTTTAAATAAAAT
1 AAATAGATATAATTTTAAACAAAAT
19343692 GACAAGTTGA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 43 0.49
80 26 0.30
81 19 0.22
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (81 bp):
AAATAGATATAATTTTAAACAAAATAATCAATTTGTTTTTAATCTAACATAGAGGAATTAATTTA
CCCATTTTTTGAATAA
Found at i:19348625 original size:2 final size:2
Alignment explanation
Indices: 19348620--19348670 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
19348610 TATATACATA
19348620 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19348662 TG TG TG TG T
1 TG TG TG TG T
19348671 TTAACAGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:19350353 original size:2 final size:2
Alignment explanation
Indices: 19350346--19350388 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
19350336 GAAAAGAAAA
19350346 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19350388 A
1 A
19350389 TTAAACCAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19355122 original size:20 final size:20
Alignment explanation
Indices: 19355032--19355123 Score: 59
Period size: 20 Copynumber: 4.7 Consensus size: 20
19355022 AATAAATAAT
* *
19355032 AAATTTTA-GAAAAATTATTA
1 AAATTTTATAAAAAATT-GTA
*
19355052 AAATTTTACTAAAAAATAG-A
1 AAATTTTA-TAAAAAATTGTA
* * *
19355072 AATTTTTTTATAAAAATCGTA
1 AAATTTTATA-AAAAATTGTA
*
19355093 AAA---AATAAAAAATTGTA
1 AAATTTTATAAAAAATTGTA
19355110 AAATTTTATAAAAA
1 AAATTTTATAAAAA
19355124 TCATAAAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
17 12 0.22
18 2 0.04
19 2 0.04
20 29 0.54
21 3 0.06
22 6 0.11
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (20 bp):
AAATTTTATAAAAAATTGTA
Found at i:19355130 original size:19 final size:19
Alignment explanation
Indices: 19355032--19355131 Score: 55
Period size: 19 Copynumber: 5.2 Consensus size: 19
19355022 AATAAATAAT
* *
19355032 AAATTTTAGAAAAATTATTA
1 AAATTTTATAAAAATCA-TA
19355052 AAATTTTACTAAAAA--ATA
1 AAATTTTA-TAAAAATCATA
*
19355070 GAAATTTTTTTATAAAAATCGTA
1 -AAA---TTTTATAAAAATCATA
** **
19355093 AAA-AATA-AAAAATTGTA
1 AAATTTTATAAAAATCATA
19355110 AAATTTTATAAAAATCATA
1 AAATTTTATAAAAATCATA
19355129 AAA
1 AAA
19355132 AAATTAACGA
Statistics
Matches: 62, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
17 12 0.19
18 6 0.10
19 15 0.24
20 8 0.13
21 11 0.18
22 8 0.13
23 2 0.03
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATTTTATAAAAATCATA
Found at i:19355132 original size:20 final size:20
Alignment explanation
Indices: 19355027--19355132 Score: 53
Period size: 20 Copynumber: 5.3 Consensus size: 20
19355017 ATAATAATAA
* *
19355027 ATAATAAATTTTAGAAAAATT
1 ATAA-AAATTTTATAAAAATC
*
19355048 ATTAAAATTTTACTAAAAA--
1 ATAAAAATTTTA-TAAAAATC
*
19355067 ATAGAAATTTTTTTATAAAAATC
1 ATA-AAA--ATTTTATAAAAATC
* * *
19355090 GTAAAAA--ATA-AAAAATT
1 ATAAAAATTTTATAAAAATC
*
19355107 GT-AAAATTTTATAAAAATC
1 ATAAAAATTTTATAAAAATC
19355126 ATAAAAA
1 ATAAAAA
19355133 AATTAACGAC
Statistics
Matches: 64, Mismatches: 11, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
16 4 0.06
17 8 0.12
18 4 0.06
19 9 0.14
20 15 0.23
21 14 0.22
22 8 0.12
23 2 0.03
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (20 bp):
ATAAAAATTTTATAAAAATC
Found at i:19355221 original size:16 final size:17
Alignment explanation
Indices: 19355200--19355232 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19355190 GCATATGGTG
19355200 AAAAATGATA-AAAAAT
1 AAAAATGATAGAAAAAT
*
19355216 AAAAATTATAGAAAAAT
1 AAAAATGATAGAAAAAT
19355233 TATAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAATGATAGAAAAAT
Found at i:19355961 original size:22 final size:22
Alignment explanation
Indices: 19355918--19355961 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19355908 TGATTATGAA
* *
19355918 GATTTATTTCATGTTTCTATTT
1 GATTTATTTCATGTATCAATTT
19355940 GATTTATTT-ATGTAATCAATTT
1 GATTTATTTCATGT-ATCAATTT
19355962 TCCATCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (22 bp):
GATTTATTTCATGTATCAATTT
Found at i:19356905 original size:17 final size:14
Alignment explanation
Indices: 19356873--19356908 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
19356863 AAATATAAAA
19356873 TTATTTATATAATT
1 TTATTTATATAATT
19356887 TTATTATATATAATT
1 TTATT-TATATAATT
*
19356902 TTTTTTA
1 TTATTTA
19356909 ATTTTTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTATATAATT
Found at i:19363352 original size:158 final size:158
Alignment explanation
Indices: 19363119--19363449 Score: 464
Period size: 158 Copynumber: 2.1 Consensus size: 158
19363109 CGGATCAGGA
* * * * *
19363119 TTGCTAACACTAACTTGGTTCGATGCTACTAACATTAGCTTCAGAGAATTCGCAACATATGTTGG
1 TTGCTAACACTAGCTCGGTTCGATGCTACTAACACTAGCTTCAAAGAATCCGCAACATATGTTGG
19363184 ATCTCAAGCCATCAAATTAATTCCTGATCACAACACCCATTTATTCATACAAACTGAAATACTCA
66 ATCTCAAGCCATCAAATTAATTCCTGATCACAACACCCATTTATTCATACAAACTGAAATACTCA
* *
19363249 TGCAGCTAACATTAGCTTCAAATCAAGG
131 GGCAGCAAACATTAGCTTCAAATCAAGG
* * * *
19363277 TTGCCAACACTAGCTCGGTTCGATGTTGCTAACACTAGCTTTAAAGAATCCGCAACATATGTTGG
1 TTGCTAACACTAGCTCGGTTCGATGCTACTAACACTAGCTTCAAAGAATCCGCAACATATGTTGG
* * * * * * * *
19363342 ATGTCAAGCCATCGAATTAATTCTTGATCATAACACCCATTTATTCATACAGACTTATATACTCG
66 ATCTCAAGCCATCAAATTAATTCCTGATCACAACACCCATTTATTCATACAAACTGAAATACTCA
* * *
19363407 GGCCGCAAACATTAGCTTCAGATCAATG
131 GGCAGCAAACATTAGCTTCAAATCAAGG
19363435 TTGCTAACACTAGCT
1 TTGCTAACACTAGCT
19363450 TCAAAGAATC
Statistics
Matches: 150, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 150 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (158 bp):
TTGCTAACACTAGCTCGGTTCGATGCTACTAACACTAGCTTCAAAGAATCCGCAACATATGTTGG
ATCTCAAGCCATCAAATTAATTCCTGATCACAACACCCATTTATTCATACAAACTGAAATACTCA
GGCAGCAAACATTAGCTTCAAATCAAGG
Found at i:19363718 original size:32 final size:34
Alignment explanation
Indices: 19363667--19363730 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
19363657 AGGTCCGCCC
* *
19363667 ATATTATTTTTAATTTTTAA-AAATTTTTATAGT
1 ATATTATTTTTAATATTTAATAAAATTTTATAGT
19363700 ATATTA-TTTTAATATTTAATAAAATTTTATA
1 ATATTATTTTTAATATTTAATAAAATTTTATA
19363731 TTTTTTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
ATATTATTTTTAATATTTAATAAAATTTTATAGT
Found at i:19365836 original size:6 final size:6
Alignment explanation
Indices: 19365825--19365872 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
19365815 ATTGCTTAAT
* *
19365825 AAAATA AAAATA AAAATA AAAATA GAAATATA AAAAGA AAAAGA AAAA
1 AAAATA AAAATA AAAATA AAAATA -AAA-ATA AAAATA AAAATA AAAA
19365873 AAATTGTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 30 0.77
7 6 0.15
8 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:19372567 original size:13 final size:13
Alignment explanation
Indices: 19372549--19372576 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19372539 TAATTTGATC
19372549 ATCTATTTTTATA
1 ATCTATTTTTATA
19372562 ATCTATTTTTATA
1 ATCTATTTTTATA
19372575 AT
1 AT
19372577 ATTATTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (13 bp):
ATCTATTTTTATA
Found at i:19387244 original size:22 final size:22
Alignment explanation
Indices: 19387216--19387284 Score: 77
Period size: 23 Copynumber: 3.1 Consensus size: 22
19387206 TATTAATTAC
*
19387216 AATTTTTATATTTAAATTATAA
1 AATTTTTATATTTAAATAATAA
* *
19387238 AATTTTTATTATATAAATAATTA
1 AATTTTTA-TATTTAAATAATAA
* *
19387261 AATTTTGATATTTAAA-ACTAA
1 AATTTTTATATTTAAATAATAA
19387282 AAT
1 AAT
19387285 AATCTCTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 6 0.15
22 15 0.38
23 18 0.46
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
AATTTTTATATTTAAATAATAA
Found at i:19403241 original size:38 final size:40
Alignment explanation
Indices: 19403183--19403271 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 40
19403173 AAAATTTTTA
* * * *
19403183 TTTAATACAATTAAATATTTATTATATTTAT-TTGTG-TT
1 TTTAATATAATAAAACATTTATTATATTTATGTAGTGTTT
19403221 TTTAATATAATAAAACATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTAT-GTAGTGTTT
19403262 TTTAATATAA
1 TTTAATATAA
19403272 ATATCTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 28 0.64
40 4 0.09
41 12 0.27
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (40 bp):
TTTAATATAATAAAACATTTATTATATTTATGTAGTGTTT
Found at i:19404189 original size:16 final size:15
Alignment explanation
Indices: 19404170--19404211 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
19404160 TTTAAAATAT
19404170 TTAATTTTTTATGAAC
1 TTAATTTTTTAT-AAC
19404186 TTAA-TTTTTA-AAC
1 TTAATTTTTTATAAC
19404199 TTAATATTTTTAT
1 TTAAT-TTTTTAT
19404212 TTAAAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.30
15 12 0.52
16 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (15 bp):
TTAATTTTTTATAAC
Found at i:19404857 original size:2 final size:2
Alignment explanation
Indices: 19404850--19404875 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19404840 TCGAAAATTA
19404850 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
19404876 TAAGTGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19411204 original size:109 final size:109
Alignment explanation
Indices: 19410906--19411223 Score: 441
Period size: 110 Copynumber: 2.9 Consensus size: 109
19410896 GACATGGATT
* ** *
19410906 AAAATTTAAGAGGATATTTAA-TTGTTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGG
1 AAAATTTAAAAGGATA-TTAAGCCGTTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGG
*
19410968 CATGTTTTCTCGAATTT-TCAAAC-GCAAAACAATGCCTTATTTTA
65 CATGTTTTCTCGAATTTCT-AAACAGCAAAACATTGCCTTATTTTA
* * * *
19411012 AAATTTTTAAAAGGATATTAAGCCATTTAGTTGAACGAGAAAAAATCGACACCCAGCACCTTAGG
1 AAA-ATTTAAAAGGATATTAAGCCGTTTGGTTAAACGAG-AAAAATCGACACCCAGCACCTTAGG
19411077 GCATGTTTTCTCGAATTTCTAAACAGCAAAACATTGCCTTATTTTA
64 GCATGTTTTCTCGAATTTCTAAACAGCAAAACATTGCCTTATTTTA
*
19411123 AAAATTTAAAAGGATATTAAGCCGTTTGGTTAAACGAGAAAAACCGACACCCAGCACCTTAGGGC
1 AAAATTTAAAAGGATATTAAGCCGTTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
* * *
19411188 ACGTTTTCTCGAATTTCCAAA-AGCAAAACATCGCCT
66 ATGTTTTCTCGAATTTCTAAACAGCAAAACATTGCCT
19411224 CAATTAGAAA
Statistics
Matches: 188, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
106 7 0.04
107 23 0.12
108 14 0.07
109 45 0.24
110 75 0.40
111 24 0.13
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (109 bp):
AAAATTTAAAAGGATATTAAGCCGTTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
ATGTTTTCTCGAATTTCTAAACAGCAAAACATTGCCTTATTTTA
Found at i:19413131 original size:13 final size:14
Alignment explanation
Indices: 19413115--19413144 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
19413105 GGACTGTTTA
19413115 TTTATTTA-TTGGT
1 TTTATTTATTTGGT
19413128 TTTATTTATTTGGT
1 TTTATTTATTTGGT
19413142 TTT
1 TTT
19413145 GGGCCCGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (14 bp):
TTTATTTATTTGGT
Found at i:19416332 original size:46 final size:46
Alignment explanation
Indices: 19416229--19416380 Score: 256
Period size: 46 Copynumber: 3.4 Consensus size: 46
19416219 TACGTATGAT
* *
19416229 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
19416272 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
19416318 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
19416364 CACTTATCACTTTGTCA
1 CACTTATCACTTTGTCA
19416381 TTTATCACTG
Statistics
Matches: 103, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
43 10 0.10
44 5 0.05
45 20 0.19
46 68 0.66
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:19420563 original size:21 final size:21
Alignment explanation
Indices: 19420521--19420568 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19420511 ATTTTTATGA
* **
19420521 AATTAACATAAAATTTTTAAT
1 AATTAACATAAAACTTCAAAT
*
19420542 AATTAACATATAACTTCAAAT
1 AATTAACATAAAACTTCAAAT
19420563 AATTAA
1 AATTAA
19420569 TTGAAATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAACATAAAACTTCAAAT
Found at i:19421919 original size:7 final size:7
Alignment explanation
Indices: 19421907--19421941 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
19421897 ATTATGAGGA
19421907 TGATGGG
1 TGATGGG
19421914 TGATGGG
1 TGATGGG
19421921 TGATGGG
1 TGATGGG
19421928 TGATGGG
1 TGATGGG
19421935 TGATGGG
1 TGATGGG
19421942 CAATGACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.57, T:0.29
Consensus pattern (7 bp):
TGATGGG
Found at i:19422587 original size:2 final size:2
Alignment explanation
Indices: 19422580--19422610 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19422570 TGATATTTAA
19422580 AT AT 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 AT AT A
19422611 GACAGGCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19435240 original size:18 final size:19
Alignment explanation
Indices: 19435206--19435241 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19435196 TAAATACATA
19435206 TAATTTTATTATTTACTTC
1 TAATTTTATTATTTACTTC
19435225 TAATTTTATT-TTTACTT
1 TAATTTTATTATTTACTT
19435242 TTTTTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (19 bp):
TAATTTTATTATTTACTTC
Found at i:19439874 original size:23 final size:23
Alignment explanation
Indices: 19439842--19439885 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
19439832 CCTTTGGGCA
*
19439842 TACCGTTTTCCCA-TTGCCCATCG
1 TACCGGTTT-CCATTTGCCCATCG
19439865 TACCGGTTTCCATTTGCCCAT
1 TACCGGTTTCCATTTGCCCAT
19439886 ATCAGGGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (23 bp):
TACCGGTTTCCATTTGCCCATCG
Found at i:19448513 original size:15 final size:14
Alignment explanation
Indices: 19448493--19448522 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
19448483 TTTAGATCAC
19448493 AATAAATAAGAAATA
1 AATAAATAA-AAATA
19448508 AATAAATAAAAATA
1 AATAAATAAAAATA
19448522 A
1 A
19448523 GATTCGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:19453263 original size:35 final size:36
Alignment explanation
Indices: 19453217--19453288 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
19453207 TTGTTTTCGG
*
19453217 ATTTTCAGAGTTTAG-TTTTTATCTCCATCTTTTGT
1 ATTTTCAGAGTTTAGTTTTTTATCTCCATATTTTGT
19453252 ATTTTCAGAGTTTAGTTTTTTATCTCCATATTTTGT
1 ATTTTCAGAGTTTAGTTTTTTATCTCCATATTTTGT
19453288 A
1 A
19453289 CTCTTCATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 15 0.43
36 20 0.57
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.57
Consensus pattern (36 bp):
ATTTTCAGAGTTTAGTTTTTTATCTCCATATTTTGT
Found at i:19459150 original size:20 final size:20
Alignment explanation
Indices: 19459127--19459167 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
19459117 ATATTTTTCA
*
19459127 AAAAAATATGCCAATTTTTT
1 AAAAAATATACCAATTTTTT
19459147 AAAAAATATACCAATTTTTT
1 AAAAAATATACCAATTTTTT
19459167 A
1 A
19459168 GGGGTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAAAATATACCAATTTTTT
Found at i:19459579 original size:14 final size:14
Alignment explanation
Indices: 19459558--19459591 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
19459548 TGGTATGGGT
19459558 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
19459571 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
19459585 TTATAGG
1 TTATAGG
19459592 TAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:19459749 original size:24 final size:25
Alignment explanation
Indices: 19459720--19459767 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
19459710 GAGAGGAAAG
19459720 TTTAAAAAACATAAAA-GAAAAAAA
1 TTTAAAAAACATAAAACGAAAAAAA
** *
19459744 TTTAAATTACTTAAAACGAAAAAA
1 TTTAAAAAACATAAAACGAAAAAA
19459768 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (25 bp):
TTTAAAAAACATAAAACGAAAAAAA
Found at i:19459926 original size:29 final size:29
Alignment explanation
Indices: 19459887--19459944 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
19459877 TAAAATGTTA
19459887 CAACATTTCAAACATAAGTGACTAAAACG
1 CAACATTTCAAACATAAGTGACTAAAACG
19459916 CAACATTTCAAACATAAGTGACTAAAACG
1 CAACATTTCAAACATAAGTGACTAAAACG
19459945 TAACCTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (29 bp):
CAACATTTCAAACATAAGTGACTAAAACG
Found at i:19473964 original size:16 final size:16
Alignment explanation
Indices: 19473943--19473973 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19473933 ACTCTCGAAT
*
19473943 AATACAACTTATTTTA
1 AATACAAATTATTTTA
19473959 AATACAAATTATTTT
1 AATACAAATTATTTT
19473974 TCGTAATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (16 bp):
AATACAAATTATTTTA
Found at i:19489318 original size:24 final size:24
Alignment explanation
Indices: 19489266--19489332 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
19489256 AAAAAAAAGA
*
19489266 ATTGCTA-TCTTTTTTATTGTTTT
1 ATTGCTATTTTTTTTTATTGTTTT
*
19489289 ATTGCTGTTTTTTTTTATTGTTTT
1 ATTGCTATTTTTTTTTATTGTTTT
*
19489313 GA-TGCTATTTTCTTATTATT
1 -ATTGCTATTTT-TTTTTATT
19489333 TTCTCATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.16
24 23 0.62
25 8 0.22
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.69
Consensus pattern (24 bp):
ATTGCTATTTTTTTTTATTGTTTT
Found at i:19492922 original size:21 final size:20
Alignment explanation
Indices: 19492894--19492933 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19492884 TGTGGTGAAA
* *
19492894 ATTAATAAATTTTAATATAT
1 ATTAATAAATATAAATATAT
19492914 ATTATATAAATATAAATATA
1 ATTA-ATAAATATAAATATA
19492934 AATATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAATAAATATAAATATAT
Found at i:19492928 original size:6 final size:6
Alignment explanation
Indices: 19492917--19492950 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
19492907 AATATATATT
19492917 ATATAA ATATAA ATATAA ATATAA AT-TAA A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
19492951 TAACAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 7 0.26
6 20 0.74
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:19509995 original size:20 final size:20
Alignment explanation
Indices: 19509958--19510007 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
19509948 TAATACTTAT
* *
19509958 CTTAATACT-ATTTTATTAA
1 CTTAATATTAATTTGATTAA
*
19509977 CTTAATATTAATTTGATTAT
1 CTTAATATTAATTTGATTAA
*
19509997 CTTATTATTAA
1 CTTAATATTAA
19510008 AATTAATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (20 bp):
CTTAATATTAATTTGATTAA
Found at i:19513024 original size:124 final size:125
Alignment explanation
Indices: 19512810--19513159 Score: 571
Period size: 124 Copynumber: 2.8 Consensus size: 125
19512800 TTATTTCAAG
19512810 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
* * * * *
19512874 GAAATTGCGCCATTGTGGACGTGATTTTGCTACAGTAGGTCATGTAAGAAAT-ATTTTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
* *
19512934 TTGACGTTTCTGAGCAAATAGTATAAAATCGGCTCTACCAAGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
19512999 AAATCGCGCCCTCGTGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
*
19513059 TT-ACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGGGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
19513123 AAATCGCGCTCTCATGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
19513160 CAAGTTTGGG
Statistics
Matches: 210, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
124 200 0.95
125 10 0.05
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTT
Found at i:19515579 original size:18 final size:18
Alignment explanation
Indices: 19515556--19515668 Score: 87
Period size: 18 Copynumber: 6.3 Consensus size: 18
19515546 GCAGTCCAGG
19515556 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
19515574 GTTAGGGTTTTTAATTAGGTTA
1 GTTAGGGTTTTTAATTA----A
19515596 GGGTTAGGGTTTTTAATTAA
1 --GTTAGGGTTTTTAATTAA
* **
19515616 ATTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
*
19515627 GTTAAGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
19515645 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
19515663 GTTAGG
1 GTTAGG
19515669 TTAGGGTTGG
Statistics
Matches: 75, Mismatches: 7, Indels: 26
0.69 0.06 0.24
Matches are distributed among these distances:
11 3 0.04
12 2 0.03
13 1 0.01
14 2 0.03
15 2 0.03
16 1 0.01
17 2 0.03
18 43 0.57
20 1 0.01
22 1 0.01
24 17 0.23
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:19515619 original size:29 final size:29
Alignment explanation
Indices: 19515586--19515741 Score: 135
Period size: 29 Copynumber: 5.8 Consensus size: 29
19515576 TAGGGTTTTT
19515586 AATTAGGTTAGGGTTAGGGTTTTTAATTA
1 AATTAGGTTAGGGTTAGGGTTTTTAATTA
*
19515615 AATTAGGTTAGGGTTAAGGTTTTTAATT-
1 AATTAGGTTAGGGTTAGGGTTTTTAATTA
19515643 -A--A-GTTAGGGTT----TTTAATTAAGTTA
1 AATTAGGTTAGGGTTAGGGTTT--TTAA-TTA
**
19515667 GGTTAGGGTT-GGGTT-----TTTTAATTA
1 AATTA-GGTTAGGGTTAGGGTTTTTAATTA
*
19515691 AATTAGGTTAGGGTTAGAGTTTTTAATTA
1 AATTAGGTTAGGGTTAGGGTTTTTAATTA
19515720 AATTAGGTTAGGGTTAGGGTTT
1 AATTAGGTTAGGGTTAGGGTTT
19515742 CTAGGGTTTA
Statistics
Matches: 107, Mismatches: 5, Indels: 30
0.75 0.04 0.21
Matches are distributed among these distances:
20 3 0.03
22 4 0.04
23 6 0.06
24 20 0.19
25 5 0.05
27 4 0.04
28 5 0.05
29 60 0.56
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.46
Consensus pattern (29 bp):
AATTAGGTTAGGGTTAGGGTTTTTAATTA
Found at i:19515790 original size:29 final size:29
Alignment explanation
Indices: 19515743--19515829 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
19515733 TTAGGGTTTC
*
19515743 TAGGGTTTAGGATTTTTAATTAAGTTAGGT
1 TAGGG-TTAGGGTTTTTAATTAAGTTAGGT
* *
19515773 TAGGGTTAGGGTTATTAATTAGGTTAGGT
1 TAGGGTTAGGGTTTTTAATTAAGTTAGGT
*
19515802 TAGAGTTAGGGTTTTTAATTAAGTTAGG
1 TAGGGTTAGGGTTTTTAATTAAGTTAGG
19515830 GTTTTTAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (29 bp):
TAGGGTTAGGGTTTTTAATTAAGTTAGGT
Found at i:19515791 original size:74 final size:74
Alignment explanation
Indices: 19515593--19515950 Score: 420
Period size: 74 Copynumber: 4.8 Consensus size: 74
19515583 TTTAATTAGG
* * * **
19515593 TTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAAGTTAGGGTTTTT
1 TTAGGGTTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA-GG-TTAG
** * *
19515657 AATTA-AGTTAGG
64 GGTTAGGGTT--T
* *
19515669 TTAGGG-TT-GGGTTTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTAGGG-TTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
19515732 GTTAGGGTTT
65 GTTAGGGTTT
* * * ** *
19515742 CTAGGGTTTAGGATTTTTAATTAAGTTAGGTTAGGGTTAGGGTTATTAATTAGGTTAGGTTAGAG
1 TTAGGGTTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
19515807 TTAGGGTTT
66 TTAGGGTTT
**
19515816 TTA-ATTAAGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
1 TTAGGGT---TTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
19515880 GGGTTAGGGTTT
63 GGGTTAGGGTTT
* *
19515892 TTTGGGTTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGG
1 TTAGGGTTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
19515951 GTTTTAAATT
Statistics
Matches: 245, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
73 6 0.02
74 115 0.47
75 10 0.04
76 113 0.46
77 1 0.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (74 bp):
TTAGGGTTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
TTAGGGTTT
Found at i:19515810 original size:103 final size:103
Alignment explanation
Indices: 19515586--19515829 Score: 339
Period size: 103 Copynumber: 2.3 Consensus size: 103
19515576 TAGGGTTTTT
* *
19515586 AATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAAGTTAGG
1 AATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTCTAAGT-A-TTAGG
* *
19515651 GTTTTTAATTAAGTTAGGTTAGGGTTGGGTTTTTTAATTA
64 ATTTTTAATTAAGTTAGGTTAGGGTTGGGTTTATTAATTA
* * *
19515691 AATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTCTAGGGT-TTAGGA
1 AATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTCTA-AGTATTAGGA
19515755 TTTTTAATTAAGTTAGGTTAGGGTTAGGG-TTATTAATTA
65 TTTTTAATTAAGTTAGGTTAGGGTT-GGGTTTATTAATTA
** * *
19515794 GGTTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAGG
1 AATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
19515830 GTTTTTAATT
Statistics
Matches: 125, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
103 70 0.56
104 3 0.02
105 51 0.41
106 1 0.01
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (103 bp):
AATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTCTAAGTATTAGGAT
TTTTAATTAAGTTAGGTTAGGGTTGGGTTTATTAATTA
Found at i:19515828 original size:18 final size:18
Alignment explanation
Indices: 19515805--19515847 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
19515795 GTTAGGTTAG
19515805 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
19515823 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
19515841 AGTTAGG
1 AGTTAGG
19515848 TTAGGGTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (18 bp):
AGTTAGGGTTTTTAATTA
Found at i:19515835 original size:150 final size:150
Alignment explanation
Indices: 19515681--19515950 Score: 477
Period size: 150 Copynumber: 1.8 Consensus size: 150
19515671 AGGGTTGGGT
19515681 TTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTCTAG
1 TTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTCTAG
*
19515746 GGTTTAGGATTTTTAATTAAGTTAGGTTAGGGTTAGGGTTATTAATTAGGTTAGGTTAGAGTTAG
66 GGTTTAGGATTTTTAATTAAGTTAGGTTAGGGTTAGGGTTATTAATTAAGTTAGGTTAGAGTTAG
19515811 GGTTTTTAATTAAGTTAGGG
131 GGTTTTTAATTAAGTTAGGG
* * * *
19515831 TTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTTG
1 TTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTCTAG
* *
19515896 GGTTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGG
66 GGTTTAGGATTTTTAATTAAGTTAGGTTAGGGTTAGGGTTATTAATTAAGTTAGG
19515951 GTTTTAAATT
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
150 113 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (150 bp):
TTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTCTAG
GGTTTAGGATTTTTAATTAAGTTAGGTTAGGGTTAGGGTTATTAATTAAGTTAGGTTAGAGTTAG
GGTTTTTAATTAAGTTAGGG
Found at i:19515856 original size:29 final size:29
Alignment explanation
Indices: 19515824--19515893 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
19515814 TTTTAATTAA
*
19515824 GTTAGGGTTTTTAATTAAGTTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
19515853 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
19515882 GTTAGGGTTTTT
1 GTTAGGGTTTTT
19515894 TGGGTTTAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGG
Found at i:19515950 original size:18 final size:18
Alignment explanation
Indices: 19515927--19515993 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
19515917 TTAGGTTAGG
19515927 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
19515945 GTTAGGGTTTTAAATTAA
1 GTTAGGGTTTTTAATTAA
*
19515963 GTTAGGGTTTTTAAATAA
1 GTTAGGGTTTTTAATTAA
*
19515981 ATTAGGGTTTTTA
1 GTTAGGGTTTTTA
19515994 TTACATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:19516041 original size:25 final size:26
Alignment explanation
Indices: 19515989--19516052 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
19515979 AAATTAGGGT
* *
19515989 TTTTATTACATCAAATTGAACTTCTA
1 TTTTATTACATCAAATTAAACTTATA
* *
19516015 TTTTATTATATTAAA-TAAACTTATA
1 TTTTATTACATCAAATTAAACTTATA
19516040 TTTTATTACATCA
1 TTTTATTACATCA
19516053 GATAATAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 19 0.59
26 13 0.41
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATTAAACTTATA
Found at i:19516488 original size:18 final size:18
Alignment explanation
Indices: 19516461--19516495 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19516451 CGGAAAAGGA
* *
19516461 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
19516479 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
19516496 AACCACACCT
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:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:19517157 original size:7 final size:7
Alignment explanation
Indices: 19517147--19517171 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19517137 TTATATACAT
19517147 AATACTA
1 AATACTA
19517154 AATACTA
1 AATACTA
19517161 AATACTA
1 AATACTA
19517168 AATA
1 AATA
19517172 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:19520606 original size:10 final size:10
Alignment explanation
Indices: 19520587--19520652 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
19520577 GCCATTGATG
*
19520587 AAAATATAAA
1 AAAATTTAAA
19520597 AAAATTTAAA
1 AAAATTTAAA
* * *
19520607 ATTATTTTTAA
1 A-AAATTTAAA
19520618 AAAATATT-AA
1 AAAAT-TTAAA
19520628 AAAATTTAAA
1 AAAATTTAAA
**
19520638 ATTATTTAAA
1 AAAATTTAAA
19520648 AAAAT
1 AAAAT
19520653 GAAATTGAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 2 0.05
10 32 0.74
11 9 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:19520623 original size:31 final size:30
Alignment explanation
Indices: 19520587--19520652 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
19520577 GCCATTGATG
*
19520587 AAAATATAAAAAAATTTAAAATTATTTTTAA
1 AAAATATAAAAAAATTTAAAATTA-TTTAAA
*
19520618 AAAATATTAAAAAATTTAAAATTATTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTAAA
19520648 AAAAT
1 AAAAT
19520653 GAAATTGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTTAAA
Found at i:19520634 original size:21 final size:21
Alignment explanation
Indices: 19520595--19520634 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19520585 TGAAAATATA
*
19520595 AAAAAATTTAAAATTATTTTT
1 AAAAAATTTAAAATAATTTTT
19520616 AAAAAATATTAAAA-AATTT
1 AAAAAAT-TTAAAATAATTT
19520635 AAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATTTAAAATAATTTTT
Found at i:19527765 original size:29 final size:29
Alignment explanation
Indices: 19527743--19527798 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
19527733 CTCTGTTTGT
* *
19527743 TTGAAGCACTTCGGTGCTACTCTGTTCAG
1 TTGAAGCACTTCAGTGCCACTCTGTTCAG
*
19527772 TTGAAGCATTTCAGTGCCACTCTGTTC
1 TTGAAGCACTTCAGTGCCACTCTGTTC
19527799 TAATAAAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (29 bp):
TTGAAGCACTTCAGTGCCACTCTGTTCAG
Found at i:19528550 original size:28 final size:28
Alignment explanation
Indices: 19528518--19528574 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
19528508 TTTTGTTTAC
*
19528518 TCTTGTAGTACGTTTTTTACTCTTGTAG
1 TCTTGTAGTACGATTTTTACTCTTGTAG
* *
19528546 TCTTGTAGTATGATTTTTAGTCTTGTAG
1 TCTTGTAGTACGATTTTTACTCTTGTAG
19528574 T
1 T
19528575 ACGCTTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.54
Consensus pattern (28 bp):
TCTTGTAGTACGATTTTTACTCTTGTAG
Found at i:19528582 original size:20 final size:20
Alignment explanation
Indices: 19528543--19528582 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19528533 TTTACTCTTG
*
19528543 TAGTCTTGTAGTATGATTTT
1 TAGTCTTGTAGTACGATTTT
*
19528563 TAGTCTTGTAGTACGCTTTT
1 TAGTCTTGTAGTACGATTTT
19528583 GCGAGTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (20 bp):
TAGTCTTGTAGTACGATTTT
Found at i:19531141 original size:57 final size:57
Alignment explanation
Indices: 19531027--19531174 Score: 181
Period size: 57 Copynumber: 2.5 Consensus size: 57
19531017 AATTGAAGGT
*
19531027 AAAAAGGATCTAGCCCGGACGGGTGATCTTATCCTGATATAGCCCTCTCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATC---T-CTGATATAGCCCTCCCGAAGAATATGTG-G
*
19531090 AAAAAGATCTAGCCCGGACTGGTGATCT-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCTCTGATATAGCCCTCCCGAAGAATATGTGG
* * *
19531146 AAAATGGATTTAGCCCGGACGGGTAATCT
1 AAAA-AGATCTAGCCCGGACGGGTGATCT
19531175 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
56 5 0.06
57 46 0.59
59 1 0.01
62 21 0.27
63 5 0.06
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGATCTCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:19532165 original size:4 final size:4
Alignment explanation
Indices: 19532158--19532182 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19532148 TTGCTTACAC
19532158 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
19532183 CTCTACAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:19533627 original size:320 final size:320
Alignment explanation
Indices: 19533045--19533685 Score: 994
Period size: 320 Copynumber: 2.0 Consensus size: 320
19533035 AACCGAAGGT
* *
19533045 CAAGATTACAATACATCGACAGACGAGATTCATCCTATCTTTTAAATCATGGGATTTACAAGATA
1 CAAGATTACAATACATCGACAGACGAGATTCATCCTATCCTTTAAATCATGAGATTTACAAGATA
* *
19533110 TGCCATATCAAATCAAATCTAATCTTTACAAGATATGATTCTATCAATCTTCTAATATTAGTTAC
66 TGCCATATCAAATCAAATATAATCTTTACAAGATATGATTCTATCAATCTTCTAAGATTAGTTAC
*
19533175 CAAAATAGCCTAAGTTGCCATATCTTCATTATCGGGCCAACCAGGCTTCAATCTAACGGGCTTCT
131 CAAAATAGCCTAAGTTGCCATATCTTCATTATCGGGCCAACCAGGCTTCAATCTAACAGGCTTCT
* * ** *
19533240 CCAATAAGTTACCGAATCAGGCCAGTTCTTACGGGCCAAATAATCCTTATCTACATAATAGACCT
196 CCAACAAGTTACCAAATCAGGCCAGTTCTTACGGGCCAAATAATCCCCATCTACACAATAGACCT
* * * *
19533305 TCATCGGATGCATTTGGTGCGATGCTCACAGGCTTTGAACTCTGGCCCGTGACATTCTCC
261 TCACCGGATGCATTTGGTGAGATGCTCACAGACTTTGAACTCCGGCCCGTGACATTCTCC
* *
19533365 CAAGATTACAATACATCGACGGATGAGATTCATCCTATCCTTTAAATCATGAGATTTACAAGATA
1 CAAGATTACAATACATCGACAGACGAGATTCATCCTATCCTTTAAATCATGAGATTTACAAGATA
* *
19533430 TGTCATATCAAATCTAATATAATCTTTACAAGATATGATTCTATCAATCTTCTAAGATTAGTTAC
66 TGCCATATCAAATCAAATATAATCTTTACAAGATATGATTCTATCAATCTTCTAAGATTAGTTAC
* * * * ** *
19533495 CAAAATAGCGTAAGTTGTCATATCTTTATTATCGGGCCAACCAGGCTTTAATCTGGCATGCTTCT
131 CAAAATAGCCTAAGTTGCCATATCTTCATTATCGGGCCAACCAGGCTTCAATCTAACAGGCTTCT
* ** *
19533560 CTAACAAGTTACCAAATTGGGCCAGTTCTTACGGGCCAAATGATCCCCATCTACACAATAGACCT
196 CCAACAAGTTACCAAATCAGGCCAGTTCTTACGGGCCAAATAATCCCCATCTACACAATAGACCT
* * *
19533625 TCACCGGATGCATTTGGTGAGATGGTCATAGACTTTGAACTCCGGCCCTTGACATTCTCC
261 TCACCGGATGCATTTGGTGAGATGCTCACAGACTTTGAACTCCGGCCCGTGACATTCTCC
19533685 C
1 C
19533686 CCACCCATTC
Statistics
Matches: 289, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
320 289 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (320 bp):
CAAGATTACAATACATCGACAGACGAGATTCATCCTATCCTTTAAATCATGAGATTTACAAGATA
TGCCATATCAAATCAAATATAATCTTTACAAGATATGATTCTATCAATCTTCTAAGATTAGTTAC
CAAAATAGCCTAAGTTGCCATATCTTCATTATCGGGCCAACCAGGCTTCAATCTAACAGGCTTCT
CCAACAAGTTACCAAATCAGGCCAGTTCTTACGGGCCAAATAATCCCCATCTACACAATAGACCT
TCACCGGATGCATTTGGTGAGATGCTCACAGACTTTGAACTCCGGCCCGTGACATTCTCC
Found at i:19550297 original size:25 final size:24
Alignment explanation
Indices: 19550254--19550300 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
19550244 TAATAAAAAC
* *
19550254 AAATAAATAAATAATAAATAGATA
1 AAATAAATAAAAAAGAAATAGATA
19550278 AAATAAATAGAAAAAGAAATAGA
1 AAATAAATA-AAAAAGAAATAGA
19550301 GATAGAAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (24 bp):
AAATAAATAAAAAAGAAATAGATA
Found at i:19550640 original size:18 final size:19
Alignment explanation
Indices: 19550605--19550642 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
19550595 GTGAAAATTT
*
19550605 TGAAATTTAGGAATTTAAA
1 TGAAATTTAGGAAGTTAAA
*
19550624 TGAAA-TTAGGGAGTTAAA
1 TGAAATTTAGGAAGTTAAA
19550642 T
1 T
19550643 TTAGTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (19 bp):
TGAAATTTAGGAAGTTAAA
Found at i:19551298 original size:37 final size:40
Alignment explanation
Indices: 19551201--19551300 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 40
19551191 TTCGAGTCAG
*
19551201 TGAGACACTGGGTGTCAATTTACTACTCTGGATTAATTCGA
1 TGAGACACTGGGTGTCAATTTACTA-TCTGGATTAACTCGA
* * * * * *
19551242 TAAGGCACGGGGTGCCAATTTACT-TC-GGTTTAGCT-GA
1 TGAGACACTGGGTGTCAATTTACTATCTGGATTAACTCGA
19551279 TGAGACACTGGGTGTCAATTTA
1 TGAGACACTGGGTGTCAATTTA
19551301 TTACTTCGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
37 20 0.42
38 6 0.12
39 2 0.04
41 20 0.42
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (40 bp):
TGAGACACTGGGTGTCAATTTACTATCTGGATTAACTCGA
Found at i:19551321 original size:40 final size:40
Alignment explanation
Indices: 19551201--19551332 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 40
19551191 TTCGAGTCAG
* *
19551201 TGAGACACTGGGTGTCAATTTACTAC-TCTGGATTAATTCGA
1 TGAGACACTGGGTGTCAATTTATTACTTC-GGATT-ATCCGA
* * * * * * *
19551242 TAAGGCACGGGGTGCCAA--T-TTACTTCGGTTTAGCTGA
1 TGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCGA
*
19551279 TGAGACACTGGGTGTCAATTTATTACTTCGAATTATCCGA
1 TGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCGA
*
19551319 TGAGGCACTGGGTG
1 TGAGACACTGGGTG
19551333 CCAAACTGGT
Statistics
Matches: 69, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
37 17 0.25
38 7 0.10
39 4 0.06
40 27 0.39
41 14 0.20
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (40 bp):
TGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCGA
Found at i:19552876 original size:22 final size:20
Alignment explanation
Indices: 19552836--19552901 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
19552826 TTCAGATGTC
*
19552836 TTTAGTTATTTTATATCATA
1 TTTAATTATTTTATATCATA
19552856 TTTAATTATTTTTCATATCATA
1 TTTAATTA-TTTT-ATATCATA
*
19552878 TTATAA--ATTTTATGTCATA
1 TT-TAATTATTTTATATCATA
19552897 GTTTA
1 -TTTA
19552902 TGCGATTGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 9 0.22
20 13 0.32
21 5 0.12
22 10 0.25
23 3 0.08
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTAATTATTTTATATCATA
Found at i:19558492 original size:11 final size:11
Alignment explanation
Indices: 19558478--19558509 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19558468 AAAGTGAAAG
19558478 AAAAGGAAAAT
1 AAAAGGAAAAT
19558489 AAAAGGAAAAT
1 AAAAGGAAAAT
*
19558500 AAAAAGAAAA
1 AAAAGGAAAA
19558510 GGGAGAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (11 bp):
AAAAGGAAAAT
Found at i:19571676 original size:13 final size:13
Alignment explanation
Indices: 19571658--19571683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19571648 AAAGAGATTT
19571658 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
19571671 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
19571684 AAATTGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:19571753 original size:19 final size:19
Alignment explanation
Indices: 19571713--19571754 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
19571703 GTCTCTTTTC
* *
19571713 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
19571732 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
19571751 GCAT
1 GCAT
19571755 CAAAGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:19574991 original size:13 final size:13
Alignment explanation
Indices: 19574975--19574999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19574965 TAAATCAATT
19574975 TCTTTGTTATCCA
1 TCTTTGTTATCCA
19574988 TCTTTGTTATCC
1 TCTTTGTTATCC
19575000 TCGACAATTT
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:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
TCTTTGTTATCCA
Found at i:19576029 original size:89 final size:89
Alignment explanation
Indices: 19575878--19576324 Score: 772
Period size: 89 Copynumber: 5.0 Consensus size: 89
19575868 AGTAGGCTAG
*
19575878 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTT
1 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
19575943 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
*
19575967 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATATCAGATCTTGTCTT
1 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
19576032 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
*
19576056 GAAGAAAACAGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
1 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
*
19576121 CCCATACTGGTGGCAAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* * *
19576145 GAAGAAAGCAGATCTTGTCTTCATGTACGGGCGTGAAGTAGATCAAAGACAACAGATCTTGTCTT
1 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
19576210 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* *
19576234 GAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AAGCAG-TCTGGTCT
1 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-CAGATCTTGTCT
* *
19576297 TCCAATACCGGTGGCGAAGTAGATC
65 TCCCATACTGGTGGCGAAGTAGATC
19576322 GAA
1 GAA
19576325 NNNNNNNNNN
Statistics
Matches: 344, Mismatches: 13, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
88 35 0.10
89 309 0.90
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (89 bp):
GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
CCCATACTGGTGGCGAAGTAGATC
Found at i:19576674 original size:2 final size:2
Alignment explanation
Indices: 19576662--19576714 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
19576652 ACGCATTTCT
* * *
19576662 TA TA TA GTA TA TA TA TA TA TA TA TA TA CA TA TT TC T- 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
19576704 -A TA TA TA TA TA
1 TA TA TA TA TA TA
19576715 ACTTTTATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19576826 original size:29 final size:30
Alignment explanation
Indices: 19576792--19576851 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
19576782 TTCATTATTT
* *
19576792 ATATATACTTATAC-TATTTTTATTTTTTTAA
1 ATATATA--TATACATAATTTTATCTTTTTAA
19576823 ATATATATATACATAATTTTATCTTTTTA
1 ATATATATATACATAATTTTATCTTTTTA
19576852 TTTTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 14 0.54
31 7 0.27
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (30 bp):
ATATATATATACATAATTTTATCTTTTTAA
Found at i:19580422 original size:65 final size:65
Alignment explanation
Indices: 19580318--19580451 Score: 205
Period size: 65 Copynumber: 2.1 Consensus size: 65
19580308 GGTTTAATAG
* * *
19580318 TAAATATATATATTTATAACCCTAAATCTCGAATTATAAAGAGGTGCTAATGTAATAAACTTAAT
1 TAAAAATATATATTTATAACCCTAAACCTCGAATCATAAAGAGGTGCTAATGTAATAAACTTAAT
* * * *
19580383 TAAAAATATATATTTATAATCCTAAACCTCGAATCATAAAGAGGTGTTGATGTAATAAACTTAGT
1 TAAAAATATATATTTATAACCCTAAACCTCGAATCATAAAGAGGTGCTAATGTAATAAACTTAAT
19580448 TAAA
1 TAAA
19580452 CTAAGACGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (65 bp):
TAAAAATATATATTTATAACCCTAAACCTCGAATCATAAAGAGGTGCTAATGTAATAAACTTAAT
Found at i:19581376 original size:7 final size:7
Alignment explanation
Indices: 19581364--19581392 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
19581354 CGAGAGTACA
19581364 TTTGTTT
1 TTTGTTT
19581371 TTTGTTT
1 TTTGTTT
19581378 TTTGTTT
1 TTTGTTT
19581385 TTTGTTT
1 TTTGTTT
19581392 T
1 T
19581393 ACACTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTGTTT
Found at i:19616817 original size:46 final size:46
Alignment explanation
Indices: 19616703--19616841 Score: 179
Period size: 46 Copynumber: 3.0 Consensus size: 46
19616693 ACAATGTTAT
* * * *
19616703 AACTTAGTATGGTTTTCTTCACTGAAATACCATACATACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* * *
19616749 AACTCAGTATGGTTTTCGTTACTAAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* * **
19616795 AACTCGGTATGGTTTTCTTTACTGAATTTTCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
19616841 A
1 A
19616842 CTTTGCCATG
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
Found at i:19619140 original size:24 final size:24
Alignment explanation
Indices: 19619109--19619171 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 24
19619099 AGGTTCAAGT
*
19619109 GAGCCAATATTGGGAAGCTCCGAA
1 GAGCCAATATCGGGAAGCTCCGAA
*
19619133 GAGCCAATTAATCGGGAAGCTTCGAA
1 GAGCCAA-T-ATCGGGAAGCTCCGAA
19619159 GAGCCATATATCG
1 GAGCCA-ATATCG
19619172 AGACGCTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 7 0.21
25 5 0.15
26 21 0.62
27 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (24 bp):
GAGCCAATATCGGGAAGCTCCGAA
Found at i:19620661 original size:13 final size:13
Alignment explanation
Indices: 19620643--19620674 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
19620633 TTGACTCATA
19620643 AATATTAAATAAT
1 AATATTAAATAAT
19620656 AATATTAAATAAT
1 AATATTAAATAAT
19620669 AATATT
1 AATATT
19620675 TATGAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATTAAATAAT
Found at i:19628491 original size:26 final size:27
Alignment explanation
Indices: 19628442--19628505 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
19628432 TATATATTAA
* * *
19628442 ATATATTTTTTTTATTTTTGATCAAAT
1 ATATATTATATTTATTTTTAATCAAAT
19628469 ATATA-TATATTTATTTTTAATCAAAT
1 ATATATTATATTTATTTTTAATCAAAT
19628495 ATATATTATAT
1 ATATATTATAT
19628506 ATTAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (27 bp):
ATATATTATATTTATTTTTAATCAAAT
Found at i:19628501 original size:18 final size:19
Alignment explanation
Indices: 19628475--19628524 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
19628465 AAATATATAT
* *
19628475 ATATTTATTTTTA-ATCAA
1 ATATATATTTATATATCAA
*
19628493 ATATATA-TTATATATTAA
1 ATATATATTTATATATCAA
*
19628511 ATATATATTAATAT
1 ATATATATTTATAT
19628525 GGGTCGGGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATATATTTATATATCAA
Found at i:19630165 original size:17 final size:15
Alignment explanation
Indices: 19630144--19630182 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
19630134 TAAGATAACC
19630144 ATATTTTATTCTATAA
1 ATATTTTATTCT-TAA
*
19630160 ATTATTTTATTGTTAA
1 A-TATTTTATTCTTAA
19630176 ATATTTT
1 ATATTTT
19630183 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 5 0.24
17 10 0.48
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
ATATTTTATTCTTAA
Found at i:19630285 original size:15 final size:15
Alignment explanation
Indices: 19630260--19630292 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
19630250 TATTATTTAA
19630260 ATTTTAAAA-TTATT
1 ATTTTAAAATTTATT
19630274 ATTTTCAAAATTTATT
1 ATTTT-AAAATTTATT
19630290 ATT
1 ATT
19630293 AAAATAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 4 0.24
16 8 0.47
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTAAAATTTATT
Found at i:19633910 original size:4 final size:4
Alignment explanation
Indices: 19633901--19633948 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
19633891 CAAAAAAGGC
19633901 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
19633949 GATTAGTACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:19637544 original size:26 final size:26
Alignment explanation
Indices: 19637505--19637558 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
19637495 AAAACACTTT
*
19637505 AAATAAAAAAATTTT-AAACAATTTAA
1 AAATAAAAAAATTTTCAAA-AATTCAA
* *
19637531 AAATATAAATATTTTCAAAAATTCAA
1 AAATAAAAAAATTTTCAAAAATTCAA
19637557 AA
1 AA
19637559 CATGTGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAAAAAAATTTTCAAAAATTCAA
Found at i:19639818 original size:16 final size:16
Alignment explanation
Indices: 19639777--19639819 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
19639767 AACTTAATAT
* *
19639777 AATAAATTAAATTGTA
1 AATAAATCATATTGTA
19639793 AATAAATCATATTGTA
1 AATAAATCATATTGTA
19639809 AATAAATCATA
1 AATAAATCATA
19639820 CATTTTTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (16 bp):
AATAAATCATATTGTA
Found at i:19666379 original size:25 final size:26
Alignment explanation
Indices: 19666351--19666404 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
19666341 ATAATATACG
19666351 ATAGA-TTTTTTTAGTGACATAAGAT
1 ATAGATTTTTTTTAGTGACATAAGAT
19666376 ATAGATTTTTTTTAGTGACATAAGAT
1 ATAGATTTTTTTTAGTGACATAAGAT
19666402 ATA
1 ATA
19666405 AAGAAAGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (26 bp):
ATAGATTTTTTTTAGTGACATAAGAT
Found at i:19672027 original size:20 final size:20
Alignment explanation
Indices: 19671982--19672031 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
19671972 TTATTTATTT
*
19671982 AGAAAAACAAAATAAAAAGA
1 AGAAAAAGAAAATAAAAAGA
* *
19672002 AAAAAAAGAAAATAACGAA-A
1 AGAAAAAGAAAATAA-AAAGA
19672022 AGAAAAAGAA
1 AGAAAAAGAA
19672032 CAAAAATCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAAAATAAAAAGA
Found at i:19673294 original size:88 final size:90
Alignment explanation
Indices: 19673200--19673446 Score: 291
Period size: 88 Copynumber: 2.7 Consensus size: 90
19673190 GGACCTAATA
* * *
19673200 TCTTTGATCTACTTCATGCCAGTACATGAAGACATGATCTGTTTTCTTCGACCTACTCCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTGCTCCACCACC
*
19673265 AGTATGGGGAGACAAGAT-C-TGTT
66 AGTATGGGAAGACAAGATACTTGTT
* * * * *
19673288 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTGCTCCACCACC
* *
19673353 AGTATGGGAAGGCAAGATCAACTTTTT
66 AGTATGGGAAGACAAGAT--ACTTGTT
* *
19673380 TCTGATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTTTCAACCTGCTCC
1 TC---T-T-TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTC-TTCGACCTGCTCC
19673445 AC
60 AC
19673447 TGCTGCTCAG
Statistics
Matches: 131, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
88 73 0.56
91 1 0.01
92 5 0.04
95 1 0.01
96 1 0.01
97 40 0.31
98 10 0.08
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (90 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTGCTCCACCACC
AGTATGGGAAGACAAGATACTTGTT
Found at i:19673370 original size:45 final size:43
Alignment explanation
Indices: 19673200--19673371 Score: 146
Period size: 44 Copynumber: 3.9 Consensus size: 43
19673190 GGACCTAATA
*** *** *
19673200 TCTTTGATCTACTTCATGCCAGTACATGAAGACATGATCTGTTT
1 TCTTTGATCTACTTCCCACCAGTATGGGAAGACAAGATCTG-TT
* * * *
19673244 TCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTC-CCACCAGTATGGGAAGACAAGATCTGTT
* * ***
19673288 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCCCACCAGTATGGGAAGACAAGATCTG-TT
* *
19673332 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATC
1 TCTTTGATCTACTTC-CCACCAGTATGGGAAGACAAGATC
19673372 AACTTTTTTC
Statistics
Matches: 98, Mismatches: 27, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
43 20 0.20
44 42 0.43
45 36 0.37
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
TCTTTGATCTACTTCCCACCAGTATGGGAAGACAAGATCTGTT
Found at i:19681626 original size:20 final size:20
Alignment explanation
Indices: 19681601--19681640 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19681591 TAAATGTCTT
*
19681601 TAATGCATATGATGTGATGC
1 TAATGCATATGATGCGATGC
19681621 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
19681641 ATGAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:19685674 original size:2 final size:2
Alignment explanation
Indices: 19685661--19685700 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
19685651 TATTAATAGG
*
19685661 AT AT AT AC 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
19685701 GGAAAATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19686434 original size:20 final size:22
Alignment explanation
Indices: 19686409--19686462 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
19686399 ATTTATTTAG
19686409 AAAAAACAAAAT-A-AAAAGAA
1 AAAAAACAAAATAACAAAAGAA
*
19686429 AAAAAAGAAAATAACGAAAAGAA
1 AAAAAACAAAATAAC-AAAAGAA
*
19686452 AAAGAACAAAA
1 AAAAAACAAAA
19686463 ATCCAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.39
21 1 0.04
23 16 0.57
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.04
Consensus pattern (22 bp):
AAAAAACAAAATAACAAAAGAA
Found at i:19686453 original size:29 final size:27
Alignment explanation
Indices: 19686407--19686463 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
19686397 TTATTTATTT
*
19686407 AGAAAAAACAAAATAAAAAGAAAAAAA
1 AGAAAAAACAAAAGAAAAAGAAAAAAA
*
19686434 AGAAAATAACGAAAAGAAAAAGAACAAAA
1 AGAAAA-AAC-AAAAGAAAAAGAAAAAAA
19686463 A
1 A
19686464 TCCAATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 6 0.23
28 3 0.12
29 17 0.65
ACGTcount: A:0.81, C:0.05, G:0.11, T:0.04
Consensus pattern (27 bp):
AGAAAAAACAAAAGAAAAAGAAAAAAA
Found at i:19687506 original size:16 final size:15
Alignment explanation
Indices: 19687485--19687534 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
19687475 CATTATGTTG
19687485 TGTTATGCGAACCCTA
1 TGTTATGCGAA-CCTA
*
19687501 TGTTATGTGAACCTA
1 TGTTATGCGAACCTA
*
19687516 TATTACTGCGAACCTA
1 TGTTA-TGCGAACCTA
19687532 TGT
1 TGT
19687535 GTATTGCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (15 bp):
TGTTATGCGAACCTA
Found at i:19688630 original size:144 final size:144
Alignment explanation
Indices: 19688370--19688660 Score: 573
Period size: 144 Copynumber: 2.0 Consensus size: 144
19688360 CACTACACAC
*
19688370 TGAGCAATGTATGACAAGAAACTCAATAATGCGGTCGTTGAAAACACCAAAAATATCATATCCCT
1 TGAGCAATGTATGACAAGAAACTCAATAATGAGGTCGTTGAAAACACCAAAAATATCATATCCCT
19688435 AATAAATAATGAAAAAGAATAGTAAAAGGGAAGTAAGGACAAATCCTCAGGGACTAAATTTGCAC
66 AATAAATAATGAAAAAGAATAGTAAAAGGGAAGTAAGGACAAATCCTCAGGGACTAAATTTGCAC
19688500 AATATCTTGTTCCG
131 AATATCTTGTTCCG
19688514 TGAGCAATGTATGACAAGAAACTCAATAATGAGGTCGTTGAAAACACCAAAAATATCATATCCCT
1 TGAGCAATGTATGACAAGAAACTCAATAATGAGGTCGTTGAAAACACCAAAAATATCATATCCCT
19688579 AATAAATAATGAAAAAGAATAGTAAAAGGGAAGTAAGGACAAATCCTCAGGGACTAAATTTGCAC
66 AATAAATAATGAAAAAGAATAGTAAAAGGGAAGTAAGGACAAATCCTCAGGGACTAAATTTGCAC
19688644 AATATCTTGTTCCG
131 AATATCTTGTTCCG
19688658 TGA
1 TGA
19688661 AATCTTAGGC
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 146 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (144 bp):
TGAGCAATGTATGACAAGAAACTCAATAATGAGGTCGTTGAAAACACCAAAAATATCATATCCCT
AATAAATAATGAAAAAGAATAGTAAAAGGGAAGTAAGGACAAATCCTCAGGGACTAAATTTGCAC
AATATCTTGTTCCG
Found at i:19693414 original size:19 final size:19
Alignment explanation
Indices: 19693386--19693433 Score: 73
Period size: 17 Copynumber: 2.6 Consensus size: 19
19693376 ATAAATAGAA
19693386 ATAAAAATTTAAAAAGTTC
1 ATAAAAATTTAAAAAGTTC
*
19693405 ATAAATATTT--AAAGTTC
1 ATAAAAATTTAAAAAGTTC
19693422 ATAAAAATTTAA
1 ATAAAAATTTAA
19693434 CATTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 16 0.64
19 9 0.36
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (19 bp):
ATAAAAATTTAAAAAGTTC
Found at i:19700857 original size:2 final size:2
Alignment explanation
Indices: 19700850--19700896 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
19700840 TTCTGTTTTA
19700850 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
19700892 AT AT A
1 AT AT A
19700897 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19711995 original size:3 final size:3
Alignment explanation
Indices: 19711989--19712043 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
19711979 TTGGGCTTCA
* * * * *
19711989 CTT CTT CTT CTT CTT CCT CTT CTT CTC CTT CAT CAT CAT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
19712037 CTT CTT C
1 CTT CTT C
19712044 ATCTCCCTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.56
Consensus pattern (3 bp):
CTT
Found at i:19712033 original size:33 final size:33
Alignment explanation
Indices: 19711994--19712060 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
19711984 CTTCACTTCT
* *
19711994 TCTTCTTCTTCCTCTTCTTCTCCTTCATCATCA
1 TCTTCTTCTTCCTCTTCATCTCCCTCATCATCA
* *
19712027 TCTTCTTCTTCTTCTTCATCTCCCTCTTCATCA
1 TCTTCTTCTTCCTCTTCATCTCCCTCATCATCA
19712060 T
1 T
19712061 TCTCGCTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.09, C:0.39, G:0.00, T:0.52
Consensus pattern (33 bp):
TCTTCTTCTTCCTCTTCATCTCCCTCATCATCA
Found at i:19723723 original size:17 final size:18
Alignment explanation
Indices: 19723695--19723728 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19723685 TTGCATGTTT
*
19723695 AGAAAGAAAAATGAGAGA
1 AGAAAGAAAAATAAGAGA
19723713 AGAAA-AAAAATAAGAG
1 AGAAAGAAAAATAAGAG
19723729 GGGTGACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (18 bp):
AGAAAGAAAAATAAGAGA
Found at i:19731642 original size:16 final size:16
Alignment explanation
Indices: 19731607--19731652 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
19731597 TAAAAAAGTT
*
19731607 ATATTATTTTAATTTA-
1 ATATTA-TTTATTTTAG
19731623 ATATTATTTATTTTAG
1 ATATTATTTATTTTAG
19731639 ATA-T-TTTATTTTAG
1 ATATTATTTATTTTAG
19731653 TAAAATTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.36
15 9 0.32
16 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
ATATTATTTATTTTAG
Found at i:19735897 original size:57 final size:57
Alignment explanation
Indices: 19735806--19735933 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 57
19735796 TTAACATGAG
* *
19735806 CCTAAAGTCACCAAAATAGAAACAGGGCCTACCTAAATTGACTCTAAAGGACCCAAA
1 CCTAAAGTCACCAAAACAGAAACAGGGCCCACCTAAATTGACTCTAAAGGACCCAAA
* * * *
19735863 CCTAAAGTTACCAAAACGGAAACAGGTCCCACCTAAATTGATTCTAAAGGACCCAAA
1 CCTAAAGTCACCAAAACAGAAACAGGGCCCACCTAAATTGACTCTAAAGGACCCAAA
19735920 CCTAAAGTCACCAA
1 CCTAAAGTCACCAA
19735934 GGAACCCAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.43, C:0.27, G:0.13, T:0.16
Consensus pattern (57 bp):
CCTAAAGTCACCAAAACAGAAACAGGGCCCACCTAAATTGACTCTAAAGGACCCAAA
Found at i:19739346 original size:26 final size:26
Alignment explanation
Indices: 19739317--19739392 Score: 125
Period size: 26 Copynumber: 2.9 Consensus size: 26
19739307 CTATATTTTC
*
19739317 AAATTAAACTATGATTTAAATTAATA
1 AAATTAAACCATGATTTAAATTAATA
*
19739343 AAATTAAACCATGATTTGAATTAATA
1 AAATTAAACCATGATTTAAATTAATA
*
19739369 AAACTAAACCATGATTTAAATTAA
1 AAATTAAACCATGATTTAAATTAA
19739393 CACTTCATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (26 bp):
AAATTAAACCATGATTTAAATTAATA
Found at i:19739456 original size:16 final size:16
Alignment explanation
Indices: 19739399--19739458 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
19739389 TTAACACTTC
*
19739399 ATTCAAATTGA-AATA
1 ATTCAAATTTATAATA
*
19739414 AGTCATAATTTAAATCAATA
1 ATTCA-AATTT--AT-AATA
19739434 TATTCAAATTTATAATA
1 -ATTCAAATTTATAATA
19739451 ATTCAAAT
1 ATTCAAAT
19739459 CAACGTAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
15 4 0.11
16 12 0.33
17 4 0.11
18 3 0.08
20 9 0.25
21 4 0.11
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.38
Consensus pattern (16 bp):
ATTCAAATTTATAATA
Found at i:19747887 original size:89 final size:89
Alignment explanation
Indices: 19747736--19747913 Score: 329
Period size: 89 Copynumber: 2.0 Consensus size: 89
19747726 GCACTTTGTA
19747736 GGCATTGGGTCTCTCTTAACCCGTCTCAATAAAAGATGGGCTGATGCTACCAAAGTTCAGTGGGA
1 GGCATTGGGTCTCTCTTAACCCGTCTCAATAAAAGATGGGCTGATGCTACCAAAGTTCAGTGGGA
*
19747801 GACTAAAACCTAAATGGGGGAGGG
66 GACTAAAACCTAAATAGGGGAGGG
* *
19747825 GGCATTGGGTCTCTCTTAACCCGTCTCAATAAAAGATGGGCTGATGTTGCCAAAGTTCAGTGGGA
1 GGCATTGGGTCTCTCTTAACCCGTCTCAATAAAAGATGGGCTGATGCTACCAAAGTTCAGTGGGA
19747890 GACTAAAACCTAAATAGGGGAGGG
66 GACTAAAACCTAAATAGGGGAGGG
19747914 TTGCCAAAGG
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (89 bp):
GGCATTGGGTCTCTCTTAACCCGTCTCAATAAAAGATGGGCTGATGCTACCAAAGTTCAGTGGGA
GACTAAAACCTAAATAGGGGAGGG
Found at i:19750384 original size:15 final size:15
Alignment explanation
Indices: 19750340--19750384 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
19750330 AATGGCTCTC
*
19750340 TAATTAATTTTTATA
1 TAATTAAATTTTATA
*
19750355 TAATGTAACTTTTATA
1 TAAT-TAAATTTTATA
19750371 TAATTAAATTTTAT
1 TAATTAAATTTTAT
19750385 TTGATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TAATTAAATTTTATA
Found at i:19754114 original size:12 final size:12
Alignment explanation
Indices: 19754097--19754149 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
19754087 AAATACCTAA
19754097 TTTTTCTTCTTC
1 TTTTTCTTCTTC
19754109 TTTTTCTTCCTTC
1 TTTTTCTT-CTTC
*
19754122 -TTTTCTTCTGC
1 TTTTTCTTCTTC
*
19754133 TTCCTTCCTTCTTC
1 TT--TTTCTTCTTC
19754147 TTT
1 TTT
19754150 CTTCCGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 3 0.09
12 17 0.50
13 4 0.12
14 10 0.29
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:19754153 original size:18 final size:17
Alignment explanation
Indices: 19754102--19754154 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
19754092 CCTAATTTTT
19754102 CTTCTTCTT-TTTCTTC
1 CTTCTTCTTCTTTCTTC
19754118 CTTCTT-TTCTTCTGCTTC
1 CTTCTTCTTCTT-T-CTTC
19754136 CTTCCTTCTTCTTTCTTC
1 CTT-CTTCTTCTTTCTTC
19754154 C
1 C
19754155 GTTTTTGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.06
16 8 0.25
17 1 0.03
18 12 0.38
19 4 0.12
20 5 0.16
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (17 bp):
CTTCTTCTTCTTTCTTC
Found at i:19754293 original size:54 final size:54
Alignment explanation
Indices: 19754211--19754313 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
19754201 AAAATCACAG
*
19754211 CATTGGCGCCTCCTAATATGGCACCACCATTGGCG-CATCCTAGATAGGCACCAC
1 CATTGGCGCCTCCAAATATGGCACCACCATTGGCGCCATCC-AGATAGGCACCAC
*
19754265 CATTGGCGCCTCCCAAATA-GGCACCACCATTGGCGCCTTCCAGATAGGC
1 CATTGGCGCCT-CCAAATATGGCACCACCATTGGCGCCATCCAGATAGGC
19754314 GCCAATACTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
54 35 0.78
55 10 0.22
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.19
Consensus pattern (54 bp):
CATTGGCGCCTCCAAATATGGCACCACCATTGGCGCCATCCAGATAGGCACCAC
Found at i:19754311 original size:27 final size:28
Alignment explanation
Indices: 19754211--19754313 Score: 135
Period size: 27 Copynumber: 3.8 Consensus size: 28
19754201 AAAATCACAG
19754211 CATTGGCGCC-TCCTA-ATATGGCACCAC
1 CATTGGCGCCTTCCTAGATA-GGCACCAC
*
19754238 CATTGGCG-CATCCTAGATAGGCACCAC
1 CATTGGCGCCTTCCTAGATAGGCACCAC
* *
19754265 CATTGGCGCC-TCCCAAATAGGCACCAC
1 CATTGGCGCCTTCCTAGATAGGCACCAC
19754292 CATTGGCGCCTTCC-AGATAGGC
1 CATTGGCGCCTTCCTAGATAGGC
19754314 GCCAATACTA
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
26 1 0.01
27 61 0.88
28 7 0.10
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.19
Consensus pattern (28 bp):
CATTGGCGCCTTCCTAGATAGGCACCAC
Found at i:19754957 original size:20 final size:20
Alignment explanation
Indices: 19754932--19754971 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19754922 CGTAAAATGA
*
19754932 TTTCTGAAAAATATTTTACT
1 TTTCTGAAAAATAATTTACT
*
19754952 TTTCTGTAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
19754972 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:19754961 original size:34 final size:35
Alignment explanation
Indices: 19754917--19754983 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
19754907 CAGTAAAATA
*
19754917 TTTTCCGTAAAATGATTT-CTGAAAAATATTTTAC
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
* *
19754951 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
19754984 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
Done.