Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 98 of 120
Found at i:29015203 original size:16 final size:16
Alignment explanation
Indices: 29015182--29015215 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29015172 ATAGTTAAGC
29015182 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
29015198 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
29015214 TA
1 TA
29015216 CCCAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:29015267 original size:9 final size:9
Alignment explanation
Indices: 29015253--29015450 Score: 60
Period size: 9 Copynumber: 22.7 Consensus size: 9
29015243 AAAATTGTGC
29015253 TATGTAAGT
1 TATGTAAGT
29015262 TATGTAAGT
1 TATGTAAGT
* **
29015271 CACATAAGT
1 TATGTAAGT
29015280 TATGTAAG-
1 TATGTAAGT
* * *
29015288 -AAGTTATT
1 TATGTAAGT
29015296 TATGTAAGT
1 TATGTAAGT
*
29015305 TAT-TTA-T
1 TATGTAAGT
* *
29015312 TATGAAAAT
1 TATGTAAGT
*
29015321 TAAGTAAGT
1 TATGTAAGT
*
29015330 TATGTAATT
1 TATGTAAGT
*
29015339 TACG-AA-T
1 TATGTAAGT
* **
29015346 AAT-TAAAAA
1 TATGT-AAGT
29015355 TATGTAAGT
1 TATGTAAGT
29015364 TATGTAAG-
1 TATGTAAGT
29015372 T-TGTAAGT
1 TATGTAAGT
*
29015380 TATGTATA-A
1 TATGTA-AGT
29015389 TAT-TAA-T
1 TATGTAAGT
**
29015396 TAACTAAGT
1 TATGTAAGT
* *
29015405 TATGTCATT
1 TATGTAAGT
*
29015414 TATGTATCATAT
1 TATGTA--A-GT
29015426 TAATGTAAGT
1 T-ATGTAAGT
*
29015436 TATGTAATT
1 TATGTAAGT
29015445 TATGTA
1 TATGTA
29015451 TATTAACTAA
Statistics
Matches: 134, Mismatches: 38, Indels: 34
0.65 0.18 0.17
Matches are distributed among these distances:
7 19 0.14
8 14 0.10
9 88 0.66
10 4 0.03
11 2 0.01
12 2 0.01
13 5 0.04
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (9 bp):
TATGTAAGT
Found at i:29015333 original size:34 final size:34
Alignment explanation
Indices: 29015295--29015373 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
29015285 AAGAAGTTAT
*** * *
29015295 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
1 TTATGTAAGTTACGAATAATGAAAAATAAGTAAG
* * *
29015329 TTATGTAATTTACGAATAATTAAAAATATGTAAG
1 TTATGTAAGTTACGAATAATGAAAAATAAGTAAG
29015363 TTATGTAAGTT
1 TTATGTAAGTT
29015374 GTAAGTTATG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (34 bp):
TTATGTAAGTTACGAATAATGAAAAATAAGTAAG
Found at i:29015417 original size:34 final size:34
Alignment explanation
Indices: 29015373--29015525 Score: 183
Period size: 34 Copynumber: 4.7 Consensus size: 34
29015363 TTATGTAAGT
* *
29015373 TGTAAGTTATGTATAATATTAATTAACTAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
* * *
29015407 TGTCATTTATGTATCATATTAA-T--GTAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
* *
29015438 TGTAATTTATG--T-ATATTAACTAATTAATTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
*
29015469 TGTAAGTTATGTATAATATTAATTAATTAAGTTA
1 TGTAATTTATGTATAATATTAATTAATTAAGTTA
*
29015503 TGTCATTTATGTATAATATTAAT
1 TGTAATTTATGTATAATATTAAT
29015526 GTAAGTTATG
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.07
29 2 0.02
31 33 0.33
33 2 0.02
34 57 0.56
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.48
Consensus pattern (34 bp):
TGTAATTTATGTATAATATTAATTAATTAAGTTA
Found at i:29015434 original size:56 final size:56
Alignment explanation
Indices: 29015373--29015770 Score: 349
Period size: 56 Copynumber: 6.7 Consensus size: 56
29015363 TTATGTAAGT
* *
29015373 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTCATTTATGTATCATATTAA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAA
* * * *
29015429 TGTAAGTTATGTAATTTATGTATATTAACTAATTAATTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGT-A--TA---ATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAA
* * * *
29015491 TTAATTAAGTTATGTCAT-TTATGT-A-TAA-T-A-TTAATGTAAGTTATGTATAATATTAA
1 -T--GTAAGTTATGT-ATAATAT-TAATTAATTAAGTT-ATGTCATTTATGTATAATATTAA
* * * *
29015547 TTAATTAAGTTATGTCATTTATGTATCATATTAATGTAAGTTATGTAATTTATGTATATTAACTA
1 -T--GTAAGTTATGT-A--TA-ATATTA-ATTAAT-TAAGTTATGTCATTTATG--TA-TAA-T-
29015612 ATTAATTTA
52 ATT-A---A
29015621 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAA
*
29015677 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAA
29015733 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTC
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTC
29015771 CCTACAATAA
Statistics
Matches: 294, Mismatches: 17, Indels: 62
0.79 0.05 0.17
Matches are distributed among these distances:
55 2 0.01
56 147 0.50
57 2 0.01
58 4 0.01
59 7 0.02
60 7 0.02
61 2 0.01
62 41 0.14
63 4 0.01
64 1 0.00
65 40 0.14
66 8 0.03
67 6 0.02
68 5 0.02
69 1 0.00
70 4 0.01
71 11 0.04
73 1 0.00
74 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (56 bp):
TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAA
Found at i:29015485 original size:96 final size:96
Alignment explanation
Indices: 29015373--29015897 Score: 413
Period size: 96 Copynumber: 5.7 Consensus size: 96
29015363 TTATGTAAGT
* *
29015373 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTCATTTATGTATCATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAATGTAAGTTA
* * *
29015438 TGTAATTTATGTATATTAACTAATTAATTTA
66 TGTAAGTTATGTATATTAATTAATTAAGTTA
29015469 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAATGTAAGTTA
29015534 TGT-A--TA---ATATTAATTAATTAAGTTA
66 TGTAAGTTATGTATATTAATTAATTAAGTTA
* * * * * * * *
29015559 TGTCATTTATGTATCATATTAA-T--GTAAGTTATGTAATTTATGTATATTAACTAAT-TAATTT
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAAT-ATTAATGTAAGTT
29015620 ATGTAAGTTATGTATAATATTAATTAATTAAGTTA
65 ATGTAAGTTATG--T-ATATTAATTAATTAAGTTA
* * * * *
29015655 TGTCATTTATGTATAATATTAA-T--GTAAGTTATGT-A--TA-ATATTA-ATTAAT-TAAGTTA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAATGTAAGTTA
*
29015711 TGTCA-TCTATG--TA-TAA-T-ATT-A---A
66 TGTAAGT-TATGTATATTAATTAATTAAGTTA
** ** * ** *
29015733 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTC-CCTA-CAATAAGAGACAAATATTAA-
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTAT-A-ATATTAAT-GTAAG
*
29015795 TTAAT-TAAGTTATGTCAT-TT-ATGT-A-TAATATTAA
63 TT-ATGTAAGTTATGT-ATATTAAT-TAATTAA-GTT-A
*
29015829 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAATGTAAGTTA
29015894 TGTA
66 TGTA
29015898 TAATATNNNN
Statistics
Matches: 354, Mismatches: 35, Indels: 80
0.75 0.07 0.17
Matches are distributed among these distances:
78 21 0.06
79 1 0.00
81 11 0.03
82 3 0.01
83 5 0.01
84 3 0.01
85 3 0.01
86 4 0.01
87 39 0.11
88 12 0.03
89 3 0.01
90 60 0.17
91 3 0.01
92 3 0.01
93 4 0.01
95 7 0.02
96 166 0.47
97 4 0.01
98 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (96 bp):
TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAATGTAAGTTA
TGTAAGTTATGTATATTAATTAATTAAGTTA
Found at i:29015536 original size:152 final size:152
Alignment explanation
Indices: 29015373--29015897 Score: 839
Period size: 152 Copynumber: 3.5 Consensus size: 152
29015363 TTATGTAAGT
* * *
29015373 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTCATTTATGTATCATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTA
29015438 TGTAATTTATGTATATTAACTAATTAATTTATGTAAGTTATGTATAATATTAATTAATTAAGTTA
66 TGTAATTTATGTATATTAACTAATTAATTTATGTAAGTTATGTATAATATTAATTAATTAAGTTA
29015503 TGTCATTTATGTATAATATTAA
131 TGTCATTTATGTATAATATTAA
* *
29015525 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATCATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTA
29015590 TGTAATTTATGTATATTAACTAATTAATTTATGTAAGTTATGTATAATATTAATTAATTAAGTTA
66 TGTAATTTATGTATATTAACTAATTAATTTATGTAAGTTATGTATAATATTAATTAATTAAGTTA
29015655 TGTCATTTATGTATAATATTAA
131 TGTCATTTATGTATAATATTAA
29015677 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTA
* * * * * *
29015742 TGT-A--TA---ATATTAATTAATTAAGTTATGTCCCTACA-ATAAGAGACAAATATTAATTAAT
66 TGTAATTTATGTATATTAACTAATTAATTTATG----TA-AGTTATG-TA-TAATATTAATTAAT
29015800 TAAGTTATGTCATTTATGTATAATATTAA
124 TAAGTTATGTCATTTATGTATAATATTAA
29015829 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTA
29015894 TGTA
66 TGTA
29015898 TAATATNNNN
Statistics
Matches: 356, Mismatches: 9, Indels: 15
0.94 0.02 0.04
Matches are distributed among these distances:
146 19 0.05
149 2 0.01
150 5 0.01
151 3 0.01
152 327 0.92
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (152 bp):
TGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTA
TGTAATTTATGTATATTAACTAATTAATTTATGTAAGTTATGTATAATATTAATTAATTAAGTTA
TGTCATTTATGTATAATATTAA
Found at i:29015578 original size:34 final size:34
Alignment explanation
Indices: 29015524--29015677 Score: 194
Period size: 34 Copynumber: 4.7 Consensus size: 34
29015514 TATAATATTA
*
29015524 ATGTAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
* * *
29015558 ATGTCATTTATGTATCATATTAA-T--GTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
* *
29015589 ATGTAATTTATG--T-ATATTAACTAATTAATTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
*
29015620 ATGTAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
*
29015654 ATGTCATTTATGTATAATATTAAT
1 ATGTAATTTATGTATAATATTAAT
29015678 GTAAGTTATG
Statistics
Matches: 102, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.07
29 2 0.02
31 33 0.32
33 2 0.02
34 58 0.57
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (34 bp):
ATGTAATTTATGTATAATATTAATTAATTAAGTT
Found at i:29015699 original size:208 final size:208
Alignment explanation
Indices: 29015468--29015903 Score: 641
Period size: 208 Copynumber: 2.1 Consensus size: 208
29015458 TAATTAATTT
*
29015468 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAATGTAAGTT
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTT
** ** * * **
29015533 ATGTATAATATTAATTAATTAAGTTATGTCATTTA-TGTATCATATTAAT-GTAAGTT-ATGTAA
66 ATGTATAATATTAATTAATTAAGTTATGTC-CCTACAATAACAGACAAATAGTAA-TTAAT-TAA
*
29015595 TTTATGT-ATATTAACTAATTAAT-TT-ATGTAAGTTATGTATAATATTAATTAATTAAGTTATG
128 GTTATGTCAT-TTAACT-A-TAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATG
*
29015657 TCATTTATGTATAATATTA
190 TCATCTATGTATAATATTA
29015676 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTT
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTT
* *
29015741 ATGTATAATATTAATTAATTAAGTTATGTCCCTACAATAAGAGACAAATATTAATTAATTAAGTT
66 ATGTATAATATTAATTAATTAAGTTATGTCCCTACAATAACAGACAAATAGTAATTAATTAAGTT
**
29015806 ATGTCATTTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCT
131 ATGTCATTTAACTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCT
29015871 ATGTATAATATTA
196 ATGTATAATATTA
29015884 ATGTAAGTTATGTATAATAT
1 ATGTAAGTTATGTATAATAT
29015904 NNNNNNNNNN
Statistics
Matches: 207, Mismatches: 15, Indels: 12
0.88 0.06 0.05
Matches are distributed among these distances:
206 4 0.02
207 5 0.02
208 191 0.92
209 7 0.03
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.46
Consensus pattern (208 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTT
ATGTATAATATTAATTAATTAAGTTATGTCCCTACAATAACAGACAAATAGTAATTAATTAAGTT
ATGTCATTTAACTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTCATCT
ATGTATAATATTA
Found at i:29015874 original size:56 final size:56
Alignment explanation
Indices: 29015787--29015903 Score: 225
Period size: 56 Copynumber: 2.1 Consensus size: 56
29015777 ATAAGAGACA
*
29015787 AATATTAATTAATTAAGTTATGTCATTTATGTATAATATTAATGTAAGTTATGTAT
1 AATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTATGTAT
29015843 AATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTATGTAT
1 AATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTATGTAT
29015899 AATAT
1 AATAT
29015904 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (56 bp):
AATATTAATTAATTAAGTTATGTCATCTATGTATAATATTAATGTAAGTTATGTAT
Found at i:29017866 original size:33 final size:33
Alignment explanation
Indices: 29017819--29017892 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
29017809 ATATACATAT
*
29017819 ATTCATACCTAACACTAATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
*
29017852 ATTCATACCCAACACTCATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
29017885 ATATCATA
1 AT-TCATA
29017893 GATGGCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 33 0.87
34 5 0.13
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (33 bp):
ATTCATACCCAACACTAATCTCATTTAACTCGA
Found at i:29018127 original size:14 final size:15
Alignment explanation
Indices: 29018108--29018146 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
29018098 AATTGGGAAA
29018108 TTGGGGAAAAT-ACT
1 TTGGGGAAAATAACT
29018122 TTGGGGAAGAATAACT
1 TTGGGGAA-AATAACT
*
29018138 TGGGGGAAA
1 TTGGGGAAA
29018147 TTGGGGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 4 0.18
16 10 0.45
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (15 bp):
TTGGGGAAAATAACT
Found at i:29018151 original size:25 final size:22
Alignment explanation
Indices: 29018122--29018178 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
29018112 GGAAAATACT
*
29018122 TTGGGGAAGAATAACTTGGGGGAAA
1 TTGGGGAA-AAGAACTT--GGGAAA
*
29018147 TTGGGGGAAAAGAAGTTGGGAAA
1 TT-GGGGAAAAGAACTTGGGAAA
29018170 TTGGGGAAA
1 TTGGGGAAA
29018179 TGAAATCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
25 8 0.28
26 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.42, T:0.19
Consensus pattern (22 bp):
TTGGGGAAAAGAACTTGGGAAA
Found at i:29018191 original size:23 final size:23
Alignment explanation
Indices: 29018141--29018194 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
29018131 AATAACTTGG
* *
29018141 GGGAAATTGGGGGAAAAGAAGTT
1 GGGAAATTGGGGGAAAAGAAATC
*
29018164 GGGAAATT-GGGGAAATGAAATC
1 GGGAAATTGGGGGAAAAGAAATC
29018186 GTGGAAATT
1 G-GGAAATT
29018195 TGACTTGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.39, C:0.02, G:0.39, T:0.20
Consensus pattern (23 bp):
GGGAAATTGGGGGAAAAGAAATC
Found at i:29019841 original size:26 final size:27
Alignment explanation
Indices: 29019785--29019851 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
29019775 CCCTAAATCT
* *
29019785 TTAATATATATATATATATAATCATAA
1 TTAAAATAAATATATATATAATCATAA
* * **
29019812 TTAAATTAAATATATA-ATAATTATTG
1 TTAAAATAAATATATATATAATCATAA
*
29019838 TTAAAATATATATA
1 TTAAAATAAATATA
29019852 AATTAGTCGA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
TTAAAATAAATATATATATAATCATAA
Found at i:29020317 original size:41 final size:41
Alignment explanation
Indices: 29020190--29020593 Score: 407
Period size: 41 Copynumber: 9.8 Consensus size: 41
29020180 TTTTGTTACT
* * * * *
29020190 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGA-TTAATAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCTGA-GC
* * * * * ** *
29020231 ATTCGCGGCGCTTAGATACAAACGCCGCTGAATACAGGAGA
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCTGAGC
* * * *
29020272 ATTAGCAGCGCATATATAAAAACGCCGCTAAAGACCTGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCTGAGC
* * * * * *
29020313 ATTAGCGGCGCATAGGCGAAAACGCCACTATAGACACAGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGAC-CTGAGC
* * *
29020355 ATTATCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGAC-CTGAGC
* * * * *
29020397 ATTAGCGGCGCTTAGACGAAAGCACCACTAAAGACTCGGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGAC-CTGAGC
* * * *
29020439 ATTAGCGGCGCTTATACGAAAACGCTGCTATAGA-CTCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCT-GAGC
* *
29020480 ATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCTGAGC
*
29020521 ATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCTGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCTGAGC
29020562 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAA
29020594 TGTTTAAAAA
Statistics
Matches: 305, Mismatches: 54, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
40 1 0.00
41 196 0.64
42 108 0.35
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCTGAGC
Found at i:29020741 original size:40 final size:39
Alignment explanation
Indices: 29020693--29020768 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
29020683 CGCTTCCGTA
*
29020693 TAAACGCCGCTGATGCTCTACCTTTAGTGGCGCTTTGGC
1 TAAACGCCGCTAATGCTCTACCTTTAGTGGCGCTTTGGC
** *
29020732 TAAATCGCCGCTAATGCTCTATTTTTTGTGGCGCTTT
1 TAAA-CGCCGCTAATGCTCTACCTTTAGTGGCGCTTT
29020769 TGTTCCAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (39 bp):
TAAACGCCGCTAATGCTCTACCTTTAGTGGCGCTTTGGC
Found at i:29028328 original size:14 final size:14
Alignment explanation
Indices: 29028288--29028322 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
29028278 TATCACATTT
29028288 TAAATAATTAT-CAA
1 TAAAT-ATTATACAA
29028302 TAAATATTATACAA
1 TAAATATTATACAA
29028316 TAAATAT
1 TAAATAT
29028323 AGTACACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAATATTATACAA
Found at i:29028519 original size:20 final size:20
Alignment explanation
Indices: 29028494--29028535 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29028484 CCTACATAAA
*
29028494 AAAACAA-ATAAAATTATGTT
1 AAAACAACAT-AAATTATCTT
29028514 AAAACAACATAAATTATCTT
1 AAAACAACATAAATTATCTT
29028534 AA
1 AA
29028536 CATAATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAACAACATAAATTATCTT
Found at i:29029531 original size:125 final size:124
Alignment explanation
Indices: 29029265--29029699 Score: 600
Period size: 125 Copynumber: 3.5 Consensus size: 124
29029255 NNNNNNNNNN
* * * *
29029265 TGCTTTATCAGAAGAACTTCTGAAATTGCACCCACATGGACGCGCTTTTGGTACAGTAGGTCCTG
1 TGCTTTATCAGAAGAATTTCTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTG
* *
29029330 AAAAAATAATTTCAAGTTGACGTTTCTGAGAAAATAGTATAAAAAATTGCTTCAAGCAGGA
66 AAAAAA-AATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAA-CGCTTCAAGCAGGA
* * * *
29029391 TGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACACGCTTTTCCCACAGTAGGTCCTG
1 TGCTTTATCAGAAGAATTTCTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTG
* * *
29029456 AAAAAAAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACCGCTTCAAGTAGAA
66 AAAAAAAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAA-CGCTTCAAGCAGGA
* * * *
29029516 TGCTTTATCAAAAGAATTTCTTAAATTGCACCCACGTGGACGCGTTTTTGCTACAGTAGGTCCTG
1 TGCTTTATCAGAAGAATTTCTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTG
* * *
29029581 AAAAGATAATTTTGAGTTGACATTTCTGAGAAAATAGTATAAAAAACGCTTCAAGCAGGA
66 AAAA-AAAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTCAAGCAGGA
* * *** *
29029641 TGCTTTATCAGAAGAATTTTTGAAATCGCGCCCTTATGGACGCGTTTTTGCTACAGTAG
1 TGCTTTATCAGAAGAATTTCTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAG
29029700 CATGTTTGGG
Statistics
Matches: 272, Mismatches: 36, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
125 172 0.63
126 100 0.37
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (124 bp):
TGCTTTATCAGAAGAATTTCTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTG
AAAAAAAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTCAAGCAGGA
Found at i:29030174 original size:18 final size:18
Alignment explanation
Indices: 29030151--29030191 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
29030141 AATAGAAAAT
*
29030151 GGATACATAAAAGGGCTA
1 GGATACATAAAAGGGATA
29030169 GGATACATAAAAGGGATA
1 GGATACATAAAAGGGATA
29030187 GGATA
1 GGATA
29030192 AGCACCTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.29, T:0.17
Consensus pattern (18 bp):
GGATACATAAAAGGGATA
Found at i:29030850 original size:7 final size:7
Alignment explanation
Indices: 29030840--29030865 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29030830 TTATATACAT
29030840 AATACTA
1 AATACTA
29030847 AATACTA
1 AATACTA
29030854 AATACTA
1 AATACTA
29030861 AATAC
1 AATAC
29030866 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:29031363 original size:23 final size:23
Alignment explanation
Indices: 29031333--29031377 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
29031323 GGCATCAGAT
29031333 TGTAACACCCCCTAACCCCAAAA
1 TGTAACACCCCCTAACCCCAAAA
29031356 TGTAACACCCCCTAACCCCAAA
1 TGTAACACCCCCTAACCCCAAA
29031378 CCGTCGCCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.44, G:0.04, T:0.13
Consensus pattern (23 bp):
TGTAACACCCCCTAACCCCAAAA
Found at i:29031610 original size:17 final size:18
Alignment explanation
Indices: 29031590--29031629 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
29031580 CATCTTTTTT
29031590 TTTATATTTTA-TTTTAC
1 TTTATATTTTATTTTTAC
29031607 TTTAT-TTTTATTTTTAC
1 TTTATATTTTATTTTTAC
29031624 -TTATAT
1 TTTATAT
29031630 AATATAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATATTTTATTTTTAC
Found at i:29031634 original size:5 final size:5
Alignment explanation
Indices: 29031626--29031690 Score: 80
Period size: 5 Copynumber: 13.2 Consensus size: 5
29031616 ATTTTTACTT
* *
29031626 ATATA ATATA ATACA ATACA ATATA ATATA ATATA ATATA ATAT- A-ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
29031674 ATATA TATATA ACATA A
1 ATATA -ATATA ATATA A
29031691 AAATCTAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 45 0.83
6 5 0.09
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:29032672 original size:51 final size:51
Alignment explanation
Indices: 29032611--29032708 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
29032601 AATTAATTAA
29032611 AAATAGGGATTTAAGAGAAATTTAAG-AAGAAATTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGCAAGAAATTGAGAGCAAATTGAAATT
* * * *
29032662 AAATATGGATTTGAGAGAAATTTGGCAGGAAATTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGCAAGAAATTGAGAGCAAATTGA
29032709 GAGGAAATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 41 0.98
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGCAAGAAATTGAGAGCAAATTGAAATT
Found at i:29032697 original size:22 final size:22
Alignment explanation
Indices: 29032672--29032734 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
29032662 AAATATGGAT
29032672 TTGAGAGAAATTTG-GCAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
29032694 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAGAGGAAA
29032716 TTGAGA-AAATAATTGAGAG
1 TTGAGAGAAAT--TTGAGAG
29032735 AGGATTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.08
22 22 0.61
23 11 0.31
ACGTcount: A:0.44, C:0.03, G:0.30, T:0.22
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:29033272 original size:5 final size:5
Alignment explanation
Indices: 29033245--29033316 Score: 53
Period size: 5 Copynumber: 14.4 Consensus size: 5
29033235 TTTTTTTCCC
* * *
29033245 CTTCT CATTCT CTTCT -TTC- CTTCT CTTCT ATTCT -TT-T TTTCC CATTTCT
1 CTTCT C-TTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT C--TTCT
29033294 CCTTCT CTTCT CTTCT CTTCT CT
1 -CTTCT CTTCT CTTCT CTTCT CT
29033317 ATTCTACTAC
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
3 1 0.02
4 10 0.18
5 31 0.56
6 9 0.16
7 3 0.05
8 1 0.02
ACGTcount: A:0.04, C:0.36, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTCT
Found at i:29033318 original size:43 final size:42
Alignment explanation
Indices: 29033219--29033321 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 42
29033209 TTCTTTTTTC
* *
29033219 CTTCTCTTATCTTTTCTTTTTTTCCCCTTCTCATTCTCTTCT
1 CTTCTCTTCTCTATTCTTTTTTTCCCCTTCTCATTCTCTTCT
* *
29033261 -TTC-CTTCTCTTCTATTCTTTTTTTCCCATTTCTCCTTCTCTTCT
1 CTTCTC-T-TC-TCTATTCTTTTTTTCCC-CTTCTCATTCTCTTCT
29033305 CTTCTCTTCTCTATTCT
1 CTTCTCTTCTCTATTCT
29033322 ACTACTATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
40 1 0.02
41 4 0.08
42 1 0.02
43 24 0.47
44 16 0.31
45 4 0.08
46 1 0.02
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (42 bp):
CTTCTCTTCTCTATTCTTTTTTTCCCCTTCTCATTCTCTTCT
Found at i:29035166 original size:21 final size:21
Alignment explanation
Indices: 29035140--29035219 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
29035130 TTTGCTTTTT
*
29035140 TTTTAAATCGATTGTTTATTG
1 TTTTAAATCGATTCTTTATTG
29035161 TTTTAAATCGATTCTTT-TCT-
1 TTTTAAATCGATTCTTTAT-TG
* *
29035181 TCTTTGAATCGATTTTTTATTG
1 T-TTTAAATCGATTCTTTATTG
*
29035203 TTTTAAATAGATTCTTT
1 TTTTAAATCGATTCTTT
29035220 GCTTCTTTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
20 2 0.04
21 45 0.92
22 2 0.04
ACGTcount: A:0.23, C:0.09, G:0.10, T:0.59
Consensus pattern (21 bp):
TTTTAAATCGATTCTTTATTG
Found at i:29035193 original size:42 final size:42
Alignment explanation
Indices: 29035145--29035346 Score: 194
Period size: 42 Copynumber: 4.7 Consensus size: 42
29035135 TTTTTTTTTA
*
29035145 AATCGATTGTTTATTGTTTTAAATCGATTCTTTTCTTCTTTG
1 AATCGATTTTTTATTGTTTTAAATCGATTCTTTTCTTCTTTG
* *
29035187 AATCGATTTTTTATTGTTTTAAATAGATTCTTTGCTTCTTTG
1 AATCGATTTTTTATTGTTTTAAATCGATTCTTTTCTTCTTTG
* * *
29035229 AATCGATTCATTATTCTTTTTTTAAATCGATTGTTTGT-TTCTTTG
1 AATCGATT--TT-TTATTGTTTTAAATCGATTCTTT-TCTTCTTTG
* * *
29035274 AATCAATTAATTATTGTTGTTTTAAA-CGATTCTTTACTTCTTTG
1 AATCGATT--TT-TTATTGTTTTAAATCGATTCTTTTCTTCTTTG
** * * *
29035318 AATTTATTCTTTGTTG-TTTAACTCGATTC
1 AATCGATTTTTTATTGTTTTAAATCGATTC
29035347 AAACTCTAAT
Statistics
Matches: 136, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
40 5 0.04
41 12 0.09
42 48 0.35
44 23 0.17
45 48 0.35
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (42 bp):
AATCGATTTTTTATTGTTTTAAATCGATTCTTTTCTTCTTTG
Found at i:29035254 original size:45 final size:44
Alignment explanation
Indices: 29035155--29035320 Score: 212
Period size: 45 Copynumber: 3.8 Consensus size: 44
29035145 AATCGATTGT
*
29035155 TTATTGTTTTAAATCGATTCTTTTCTTCTTTGAATCGATT-TT-
1 TTATTGTTTTAAATCGATTCTTTGCTTCTTTGAATCGATTATTA
*
29035197 TTATTGTTTTAAATAGATTCTTTGCTTCTTTGAATCGATTCATTA
1 TTATTGTTTTAAATCGATTCTTTGCTTCTTTGAATCGATT-ATTA
* * * * *
29035242 TTCTTTTTTTAAATCGATTGTTTGTTTCTTTGAATCAATTAATTA
1 TTATTGTTTTAAATCGATTCTTTGCTTCTTTGAATCGATT-ATTA
* *
29035287 TTGTTGTTTTAAA-CGATTCTTTACTTCTTTGAAT
1 TTATTGTTTTAAATCGATTCTTTGCTTCTTTGAAT
29035321 TTATTCTTTG
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 38 0.36
44 20 0.19
45 49 0.46
ACGTcount: A:0.22, C:0.11, G:0.10, T:0.57
Consensus pattern (44 bp):
TTATTGTTTTAAATCGATTCTTTGCTTCTTTGAATCGATTATTA
Found at i:29039433 original size:18 final size:18
Alignment explanation
Indices: 29039410--29039476 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
29039400 TTATATGTCC
*
29039410 TAATATTATATTTTAAAT
1 TAATATTATAATTTAAAT
* *** **
29039428 TAATATTTTCCCTTATTT
1 TAATATTATAATTTAAAT
29039446 TTAATATTATAATTTAAAT
1 -TAATATTATAATTTAAAT
*
29039465 TAATATTTTAAT
1 TAATATTATAAT
29039477 AAATATATTT
Statistics
Matches: 35, Mismatches: 13, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
18 23 0.66
19 12 0.34
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATATTATAATTTAAAT
Found at i:29039435 original size:13 final size:13
Alignment explanation
Indices: 29039417--29039492 Score: 54
Period size: 13 Copynumber: 6.1 Consensus size: 13
29039407 TCCTAATATT
29039417 ATATTTTAAATTA
1 ATATTTTAAATTA
***
29039430 ATATTTTCCCTT-
1 ATATTTTAAATTA
29039442 AT-TTTTAATATT-
1 ATATTTTAA-ATTA
*
29039454 ATAATTTAAATTA
1 ATATTTTAAATTA
*
29039467 ATATTTT-AATAA
1 ATATTTTAAATTA
29039479 ATATATTT-AATTA
1 ATAT-TTTAAATTA
29039492 A
1 A
29039493 AATAATCTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
11 4 0.08
12 17 0.35
13 28 0.57
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTTTAAATTA
Found at i:29039486 original size:26 final size:25
Alignment explanation
Indices: 29039444--29039492 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
29039434 TTTCCCTTAT
*
29039444 TTTTAATATTATAATTTAAATTAATA
1 TTTTAATAATATAATTT-AATTAATA
29039470 TTTTAATAA-ATATATTTAATTAA
1 TTTTAATAATATA-ATTTAATTAA
29039493 AATAATCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTTAATAATATAATTTAATTAATA
Found at i:29039493 original size:14 final size:13
Alignment explanation
Indices: 29039457--29039515 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
29039447 TAATATTATA
*
29039457 ATTTAAATTAATAT
1 ATTT-AATTAAAAT
29039471 -TTTAA-TAAATAT
1 ATTTAATTAAA-AT
29039483 ATTTAATTAAAAT
1 ATTTAATTAAAAT
*
29039496 AATCTAATTAAAAT
1 -ATTTAATTAAAAT
29039510 -TTTAAT
1 ATTTAAT
29039516 GATATTTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
11 3 0.08
12 9 0.24
13 10 0.26
14 16 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTAATTAAAAT
Found at i:29039675 original size:22 final size:20
Alignment explanation
Indices: 29039633--29039679 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
29039623 TTATTTAATT
29039633 ATAAGAAAAATAATAAAATA
1 ATAAGAAAAATAATAAAATA
29039653 ATAATGAAAAGATAA-AAAGATA
1 ATAA-GAAAA-ATAATAAA-ATA
29039675 A-AAGA
1 ATAAGA
29039680 TCAATATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 6 0.25
21 10 0.42
22 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (20 bp):
ATAAGAAAAATAATAAAATA
Found at i:29041894 original size:31 final size:30
Alignment explanation
Indices: 29041821--29041895 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
29041811 CTGAGATTTC
* *
29041821 CCGACAATGATGACTTGCCAACTCGGATTG
1 CCGACAATGATGACTTACCAACCCGGATTG
** * *
29041851 CCTGACGGTGATGGCTTACCATCCCGGATTGG
1 CC-GACAATGATGACTTACCAACCCGGATT-G
29041883 CCGACAATGATGA
1 CCGACAATGATGA
29041896 TTTATCAAGT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
30 2 0.06
31 29 0.85
32 3 0.09
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.23
Consensus pattern (30 bp):
CCGACAATGATGACTTACCAACCCGGATTG
Found at i:29042245 original size:26 final size:27
Alignment explanation
Indices: 29042204--29042254 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
29042194 CAAACAGATC
*
29042204 CCAAATACCCACTTAACCTAGCCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
29042231 CCAAA-ACCCAATTAACCTAGCCCA
1 CCAAATACCCAATTAACCTAGCCCA
29042255 GCTAATGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.41, C:0.41, G:0.04, T:0.14
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:29043702 original size:14 final size:14
Alignment explanation
Indices: 29043683--29043709 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29043673 ATATAGATAT
29043683 ACTATTTTTATTAA
1 ACTATTTTTATTAA
29043697 ACTATTTTTATTA
1 ACTATTTTTATTA
29043710 TACATATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
ACTATTTTTATTAA
Found at i:29043898 original size:18 final size:17
Alignment explanation
Indices: 29043877--29043910 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29043867 AGCTTATTAT
29043877 CTTATGTGTATTGTATTG
1 CTTATGTGTATT-TATTG
*
29043895 CTTATTTGTATTTATT
1 CTTATGTGTATTTATT
29043911 AATTATTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (17 bp):
CTTATGTGTATTTATTG
Found at i:29045053 original size:15 final size:15
Alignment explanation
Indices: 29045033--29045064 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29045023 AAAATAATTA
29045033 TTAGTTTTATTATTT
1 TTAGTTTTATTATTT
29045048 TTAGTTTTATTATTT
1 TTAGTTTTATTATTT
29045063 TT
1 TT
29045065 GGTTACTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (15 bp):
TTAGTTTTATTATTT
Found at i:29049472 original size:16 final size:16
Alignment explanation
Indices: 29049451--29049486 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29049441 TGTTTAAGAA
*
29049451 ATTATTATTATATTAC
1 ATTATTATAATATTAC
*
29049467 ATTATTATAATATTAT
1 ATTATTATAATATTAC
29049483 ATTA
1 ATTA
29049487 ACTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTATAATATTAC
Found at i:29051711 original size:9 final size:9
Alignment explanation
Indices: 29051659--29051711 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
29051649 AATTCTTTTT
*
29051659 AAAAATTTA
1 AAAAATTAA
* *
29051668 GAAAATTAT
1 AAAAATTAA
29051677 AAAAATTAAA
1 AAAAATT-AA
*
29051687 ATAAAAGTAA
1 A-AAAATTAA
29051697 AAAAATTAA
1 AAAAATTAA
29051706 AAAAAT
1 AAAAAT
29051712 AGATAAAGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
9 25 0.71
10 5 0.14
11 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (9 bp):
AAAAATTAA
Found at i:29055398 original size:25 final size:25
Alignment explanation
Indices: 29055352--29055399 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29055342 TTGAGTTGAA
**
29055352 TATCGGTAAACTCATACTAGCTGAG
1 TATCGGTAAACTCATAAGAGCTGAG
*
29055377 TATCGGTAAGCTCATAAGAGCTG
1 TATCGGTAAACTCATAAGAGCTG
29055400 GAATTGGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (25 bp):
TATCGGTAAACTCATAAGAGCTGAG
Found at i:29061207 original size:19 final size:21
Alignment explanation
Indices: 29061169--29061209 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
29061159 TGAAATTCCA
*
29061169 AAATTAAAAAGTACAAGGATT
1 AAATTAAAAAGTAAAAGGATT
29061190 AAATT-AAAA-TAAAAGGATT
1 AAATTAAAAAGTAAAAGGATT
29061209 A
1 A
29061210 TATCCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.24
Consensus pattern (21 bp):
AAATTAAAAAGTAAAAGGATT
Found at i:29067442 original size:104 final size:104
Alignment explanation
Indices: 29067269--29067462 Score: 275
Period size: 104 Copynumber: 1.9 Consensus size: 104
29067259 GTCTTTTGAA
* * * *
29067269 GGTGTATGGGCTCTCCCAAGAATAAAGCCGTAAGGGCCATGTGAGCCCAAAGCGGACAATATCTT
1 GGTGTATGGGCGCTCCCAAGAACAAAACCGTAAGGGCCATGTGAGCCCAAAGCAGACAATATCTT
*
29067334 ATCGGGCTGGGTGTTGACTATGACAAGATGTTTTTTGGG
66 ATCGGGCTGGGTATTGACTATGACAAGATGTTTTTTGGG
* * *
29067373 GGTGTATGGGCGCTCCCAAGAACAAAACCGTGAA-GGCCATGTGCA-TCCAAAGTAGATAATATC
1 GGTGTATGGGCGCTCCCAAGAACAAAACCGT-AAGGGCCATGTG-AGCCCAAAGCAGACAATATC
*
29067436 TTATCGGGCTGGGTATTGGCTATGACA
64 TTATCGGGCTGGGTATTGACTATGACA
29067463 TCAAGGACTA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
104 76 0.96
105 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (104 bp):
GGTGTATGGGCGCTCCCAAGAACAAAACCGTAAGGGCCATGTGAGCCCAAAGCAGACAATATCTT
ATCGGGCTGGGTATTGACTATGACAAGATGTTTTTTGGG
Found at i:29071795 original size:13 final size:13
Alignment explanation
Indices: 29071777--29071807 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29071767 NNNNAGCAAC
29071777 TATGAATTTATTT
1 TATGAATTTATTT
29071790 TATGAATTTATTT
1 TATGAATTTATTT
*
29071803 GATGA
1 TATGA
29071808 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:29072016 original size:50 final size:50
Alignment explanation
Indices: 29071902--29072143 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
29071892 ATTTGGGTAA
* * *
29071902 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
29071958 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
29072008 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
29072058 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
29072108 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
29072144 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 92 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:29072094 original size:100 final size:103
Alignment explanation
Indices: 29071902--29072151 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
29071892 ATTTGGGTAA
29071902 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* * *
29071967 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * *
29072008 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
29072070 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
29072108 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
29072152 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:29086588 original size:11 final size:11
Alignment explanation
Indices: 29086572--29086609 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
29086562 TTTATATTTT
29086572 TAAAAAATATA
1 TAAAAAATATA
*
29086583 T-AAAAAT-TC
1 TAAAAAATATA
29086592 TAAAAAATATA
1 TAAAAAATATA
29086603 TAAAAAA
1 TAAAAAA
29086610 AGGTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.09
10 12 0.52
11 9 0.39
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
TAAAAAATATA
Found at i:29088889 original size:20 final size:20
Alignment explanation
Indices: 29088855--29088896 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29088845 AACTATTTAA
** *
29088855 ATAATATTATTTAAATAGTT
1 ATAATATTAAATAAATAATT
29088875 ATAATATTAAATAAATAATT
1 ATAATATTAAATAAATAATT
29088895 AT
1 AT
29088897 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATAAATAATT
Found at i:29100958 original size:71 final size:71
Alignment explanation
Indices: 29100866--29101038 Score: 188
Period size: 71 Copynumber: 2.4 Consensus size: 71
29100856 TAAACAAACC
* * ** *
29100866 TTAGCTTCGATGTTGGCTGGTCTTGAGACAAATGGACTTTTATCTTGAGACAGGGGCA-C-TTGA
1 TTAGCTTCGATGTTGGTTGGTCTCGAGACAAATGGACTTTTATCTCAAGACA-AGGCACCTTTGA
29100929 AGCAATAT
65 AGCAAT-T
* * * * *
29100937 TTAGCTTCGATGTTGGTTGGTCCCGTGACAAATGGGCTTTTGTCTCAAGATAAGGCACCTTTGAA
1 TTAGCTTCGATGTTGGTTGGTCTCGAGACAAATGGACTTTTATCTCAAGACAAGGCACCTTTGAA
*
29101002 GTAATT
66 GCAATT
* * *
29101008 TTAGCTTTGATATTGGTTTGTCTCGAGACAA
1 TTAGCTTCGATGTTGGTTGGTCTCGAGACAA
29101039 GGCCTGTGTC
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
70 4 0.05
71 71 0.85
72 9 0.11
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (71 bp):
TTAGCTTCGATGTTGGTTGGTCTCGAGACAAATGGACTTTTATCTCAAGACAAGGCACCTTTGAA
GCAATT
Found at i:29101050 original size:19 final size:19
Alignment explanation
Indices: 29101026--29101077 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
29101016 GATATTGGTT
29101026 TGTCTCGAGACAAGGCCTG
1 TGTCTCGAGACAAGGCCTG
29101045 TGTCTCGAGACAAGGCCTG
1 TGTCTCGAGACAAGGCCTG
*
29101064 TGTCTCAAGACAAG
1 TGTCTCGAGACAAG
29101078 ACTCAAATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (19 bp):
TGTCTCGAGACAAGGCCTG
Found at i:29101817 original size:19 final size:19
Alignment explanation
Indices: 29101795--29101924 Score: 64
Period size: 19 Copynumber: 6.7 Consensus size: 19
29101785 ATGCACCTCC
29101795 TGTGCTAGGATGCACTTTG
1 TGTGCTAGGATGCACTTTG
* ** **
29101814 TGTGCCAATATGTGCTTTG
1 TGTGCTAGGATGCACTTTG
** * * *
29101833 TGCCCCAGGAATGCATTTTT
1 TGTGCTAGG-ATGCACTTTG
*
29101853 TGTGCTAGGATGCACTTCG
1 TGTGCTAGGATGCACTTTG
* * * **
29101872 TGTACCAGTATGTGCTTTG
1 TGTGCTAGGATGCACTTTG
29101891 TGTGCTAGGGATGCA-TTTCG
1 TGTGCTA-GGATGCACTTT-G
* *
29101911 TCTGCTAGTATGCA
1 TGTGCTAGGATGCA
29101925 TTATACGTGC
Statistics
Matches: 76, Mismatches: 32, Indels: 6
0.67 0.28 0.05
Matches are distributed among these distances:
19 53 0.70
20 23 0.30
ACGTcount: A:0.17, C:0.18, G:0.28, T:0.37
Consensus pattern (19 bp):
TGTGCTAGGATGCACTTTG
Found at i:29101917 original size:58 final size:58
Alignment explanation
Indices: 29101797--29101924 Score: 157
Period size: 58 Copynumber: 2.2 Consensus size: 58
29101787 GCACCTCCTG
* * ** *
29101797 TGCTAGGATGCACTTTGTGTGCCAATATGTGCTTTGTGCCCCAGGAATGCATTTTTTG
1 TGCTAGGATGCACTTCGTGTACCAATATGTGCTTTGTGCCCCAGGAATGCATTTCGTC
* ** * *
29101855 TGCTAGGATGCACTTCGTGTACCAGTATGTGCTTTGTGTGCTAGGGATGCATTTCGTC
1 TGCTAGGATGCACTTCGTGTACCAATATGTGCTTTGTGCCCCAGGAATGCATTTCGTC
*
29101913 TGCTAGTATGCA
1 TGCTAGGATGCA
29101925 TTATACGTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (58 bp):
TGCTAGGATGCACTTCGTGTACCAATATGTGCTTTGTGCCCCAGGAATGCATTTCGTC
Found at i:29106653 original size:16 final size:17
Alignment explanation
Indices: 29106626--29106661 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
29106616 TTATAATTGG
29106626 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTATTTA
29106643 ATTGA-AAAATTATTTA
1 ATTGAGAAAATTATTTA
29106659 ATT
1 ATT
29106662 TAAATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTGAGAAAATTATTTA
Found at i:29113739 original size:31 final size:29
Alignment explanation
Indices: 29113704--29113778 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
29113694 AACGGCTCAA
*
29113704 TGACTAAAATGTTACAACACGATAACATAAG
1 TGACTAAAATGTAACAACAC-A-AACATAAG
* ***
29113735 TGACTAAAACGTAACATTTCAAACATAAG
1 TGACTAAAATGTAACAACACAAACATAAG
29113764 TGACTAAAATGTAAC
1 TGACTAAAATGTAAC
29113779 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 22 0.58
30 1 0.03
31 15 0.39
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (29 bp):
TGACTAAAATGTAACAACACAAACATAAG
Found at i:29116428 original size:18 final size:18
Alignment explanation
Indices: 29116405--29116444 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29116395 AATTTGAAAC
29116405 TTTTCTACTAAGGTTTAA
1 TTTTCTACTAAGGTTTAA
**
29116423 TTTTCTACTATTGTTTAA
1 TTTTCTACTAAGGTTTAA
29116441 TTTT
1 TTTT
29116445 ATAAATAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (18 bp):
TTTTCTACTAAGGTTTAA
Found at i:29119319 original size:37 final size:37
Alignment explanation
Indices: 29119278--29119353 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
29119268 TGCAAATTAG
*
29119278 TCCTCCATTTTGTTTTAATTGCATTTCTTCTTCTTCT
1 TCCTCCATTTTGTTTTAAATGCATTTCTTCTTCTTCT
29119315 TCCTCCATTTTGTTTTAAATGCATTTCTTCTTCTTCT
1 TCCTCCATTTTGTTTTAAATGCATTTCTTCTTCTTCT
29119352 TC
1 TC
29119354 TTCTTCTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.12, C:0.25, G:0.05, T:0.58
Consensus pattern (37 bp):
TCCTCCATTTTGTTTTAAATGCATTTCTTCTTCTTCT
Found at i:29119347 original size:3 final size:3
Alignment explanation
Indices: 29119339--29119376 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
29119329 TTAAATGCAT
29119339 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
29119377 TGCAATTCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:29119418 original size:3 final size:3
Alignment explanation
Indices: 29119405--29119472 Score: 91
Period size: 3 Copynumber: 22.3 Consensus size: 3
29119395 AAATAAATTG
* * *
29119405 TTA TCA TTA TTA TTA TTTA TTG TTA TTA TTA TTA TTA TGA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29119451 TTA CTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
29119473 ATTCATATGC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:29126057 original size:88 final size:88
Alignment explanation
Indices: 29125908--29126192 Score: 489
Period size: 88 Copynumber: 3.2 Consensus size: 88
29125898 AGCAGATCAG
* * *
29125908 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACCGCGAAGCAGATCGAAGACACTAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
29125973 CCCTGGGTTGCAGCGTAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
29125996 TAAAAATAACAGATCTTGTCTTCCTACGCCGACAGCGAAGCGGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
29126061 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
*
29126084 TAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTCGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
29126149 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
29126172 TAAAAATAGCAGATCTTGCCT
1 TAAAAATAGCAGATCTTGCCT
29126193 CTCTGGGTTG
Statistics
Matches: 184, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 184 1.00
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.20
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGT
Found at i:29126169 original size:43 final size:43
Alignment explanation
Indices: 29125942--29126169 Score: 150
Period size: 44 Copynumber: 5.2 Consensus size: 43
29125932 TGCACCGACC
*
29125942 GCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTTGCA
1 GCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
* * ** * * * * * * ** **
29125985 GCGTAGCAGGTTAAAAATAACAGATCTTGTCTTCCTACGCCGACA
1 GCGAAGCAGATCGAAGACACCAG-CCTTGCCTCCCTGGGTTG-CA
*
29126030 GCGAAGCGGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
1 GCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
* * ** * * * * * * **
29126073 GCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACA
1 GCGAAGCAGATCGAAGACACCAG-CCTTGCCTCCCTGGGTTG-CA
*
29126118 GCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGGGTTGCA
1 GCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
*
29126161 GCGGAGCAG
1 GCGAAGCAG
29126170 GTTAAAAATA
Statistics
Matches: 124, Mismatches: 57, Indels: 8
0.66 0.30 0.04
Matches are distributed among these distances:
43 42 0.34
44 47 0.38
45 35 0.28
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.18
Consensus pattern (43 bp):
GCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
Found at i:29126212 original size:132 final size:132
Alignment explanation
Indices: 29126054--29126324 Score: 461
Period size: 132 Copynumber: 2.1 Consensus size: 132
29126044 AGACACCAGC
* *
29126054 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAG
1 CTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
*
29126119 CGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAG
66 CGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAG
29126184 AT
131 AT
*
29126186 CTTGCCTCTCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
1 CTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
* * * * *
29126251 CGAAGCAGATCGAAGACATCAGCCTTGCCTTCCTAGGTTGTAGCGGAGTAGGTTAAAAATAGCAG
66 CGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAG
29126316 AT
131 AT
29126318 CTTGCCT
1 CTTGCCT
29126325 TCCTACGCCG
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 130 1.00
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (132 bp):
CTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
CGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAG
AT
Found at i:29126356 original size:220 final size:220
Alignment explanation
Indices: 29125966--29126417 Score: 735
Period size: 220 Copynumber: 2.1 Consensus size: 220
29125956 AGACACTAGC
*
29125966 CTTGCCTCCCTGGGTTGCAGCGTAGCAGGTTAAAAATAACAGATCTTGTCTTCCTACGCCGACAG
1 CTTGCCTCCCTGGGTTGCAGCGTAGCAGGTTAAAAATAACAGATCTTGCCTTCCTACGCCGACAG
* *
29126031 CGAAGCGGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAG
66 CGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAG
* * *
29126096 ATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGGGTTGCA
131 ATCTTGCCTTCCTACGCCGACAGCGAAGCAGATCGAAGACACCAACCTCGCCTCCCTAGGTTGCA
29126161 GCGGAGCAGGTTAAAAATAGCAGAT
196 GCGGAGCAGGTTAAAAATAGCAGAT
* *
29126186 CTTGCCTCTCTGGGTTGCAGCAG-AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACA
1 CTTGCCTCCCTGGGTTGCAGC-GTAGCAGGTTAAAAATAACAGATCTTGCCTTCCTACGCCGACA
* * * *
29126250 GCGAAGCAGATCGAAGACATCAGCCTTGCCTTCCTAGGTTGTAGCGGAGTAGGTTAAAAATAGCA
65 GCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCA
* * * *
29126315 GATCTTGCCTTCCTACGCCGACAGTGAAGCGGATTGAAGACACCAACCTTGCCTCCCTAGGTTGC
130 GATCTTGCCTTCCTACGCCGACAGCGAAGCAGATCGAAGACACCAACCTCGCCTCCCTAGGTTGC
29126380 AGCGGAGCAGGTTAAAAATAGCAGAT
195 AGCGGAGCAGGTTAAAAATAGCAGAT
*
29126406 CTTGCCTTCCTG
1 CTTGCCTCCCTG
29126418 CGCCGACAAT
Statistics
Matches: 213, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
220 212 1.00
221 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.21
Consensus pattern (220 bp):
CTTGCCTCCCTGGGTTGCAGCGTAGCAGGTTAAAAATAACAGATCTTGCCTTCCTACGCCGACAG
CGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAG
ATCTTGCCTTCCTACGCCGACAGCGAAGCAGATCGAAGACACCAACCTCGCCTCCCTAGGTTGCA
GCGGAGCAGGTTAAAAATAGCAGAT
Found at i:29126473 original size:308 final size:308
Alignment explanation
Indices: 29125908--29126500 Score: 963
Period size: 308 Copynumber: 1.9 Consensus size: 308
29125898 AGCAGATCAG
* *
29125908 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACCGCGAAGCAGATCGAAGACACTAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
* * *
29125973 CCCTGGGTTGCAGCGTAGCAGGTTAAAAATAACAGATCTTGTCTTCCTACGCCGACAGCGAAGCG
66 CCCTAGGTTGCAGCGGAGCAGGTTAAAAATAACAGATCTTGCCTTCCTACGCCGACAGCGAAGCG
* *
29126038 GATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGC
131 GATCGAAGACACCAACCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGC
* * * *
29126103 CTTCCTGCGCCGACAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGGGTTGCAGCGGAGC
196 CTTCCTGCGCCGACAACGAAGCAGATCAAAGACACCAGCCTCGCCTCACTGGGTTACAGCGGAGC
29126168 AGGTTAAAAATAGCAGATCTTGCCTCTCTGGGTTGCAGCAGAGCAGGT
261 AGGTTAAAAATAGCAGATCTTGCCTCTCTGGGTTGCAGCAGAGCAGGT
*
29126216 TAAAAATAGCAGATCTTGCCTTCCTACGCCGACAGCGAAGCAGATCGAAGACA-TCAGCCTTGCC
1 TAAAAATAGCAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACT-AGCCTTGCC
* * * * *
29126280 TTCCTAGGTTGTAGCGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAGTGAAGC
65 TCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAACAGATCTTGCCTTCCTACGCCGACAGCGAAGC
*
29126345 GGATTGAAGACACCAACCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTG
130 GGATCGAAGACACCAACCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTG
** * * *
29126410 CCTTCCTGCGCCGACAATTAAGCAGATCAAAGACATCAGCCTTGCCTCATTGGGTTACAGCGGAG
195 CCTTCCTGCGCCGACAACGAAGCAGATCAAAGACACCAGCCTCGCCTCACTGGGTTACAGCGGAG
29126475 CAGGTTAAAAATAGCAGATCTTGCCT
260 CAGGTTAAAAATAGCAGATCTTGCCT
29126501 TCTTGCGCCG
Statistics
Matches: 261, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
307 1 0.00
308 260 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.21
Consensus pattern (308 bp):
TAAAAATAGCAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
CCCTAGGTTGCAGCGGAGCAGGTTAAAAATAACAGATCTTGCCTTCCTACGCCGACAGCGAAGCG
GATCGAAGACACCAACCTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGC
CTTCCTGCGCCGACAACGAAGCAGATCAAAGACACCAGCCTCGCCTCACTGGGTTACAGCGGAGC
AGGTTAAAAATAGCAGATCTTGCCTCTCTGGGTTGCAGCAGAGCAGGT
Found at i:29126534 original size:264 final size:264
Alignment explanation
Indices: 29126186--29126717 Score: 832
Period size: 264 Copynumber: 2.0 Consensus size: 264
29126176 AATAGCAGAT
*
29126186 CTTGCCTCTCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
1 CTTGCCTCTCTGGGTTACAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
* * *
29126251 CGAAGCAGATCGAAGACATCAGCCTTGCCTTCCTAGGTTGTAGCGGAGTAGGTTAAAAATAGCAG
66 CGAAGCAGATCGAAGACATCAGCCTTGCCTCCCTAGGTTGTAGCAGAGCAGGTTAAAAATAGCAG
* * * *
29126316 ATCTTGCCTTCCTACGCCGACAGTGAAGCGGATTGAAGACACCAACCTTGCCTCCCTAGGTTGCA
131 ATCTTGCCTTCCTACGCCAACAGTGAAGCAGATCGAAGACACCAACCTTGCCTCCCGAGGTTGCA
* **
29126381 GCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAATTAAGCAGATCAAAGACAT
196 ACGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAACGAAGCAGATCAAAGACAT
*
29126446 CAGC
261 CAAC
* * * *
29126450 CTTGCCTCAT-TGGGTTACAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCTTGCGCCGATA
1 CTTGCCTC-TCTGGGTTACAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACA
* *
29126514 GCGAAGCAGATCGAAGACATCAGCCTTGCCTCCCTAGGTTGTCGTAGAGCAGGTTAAAAATAGCA
65 GCGAAGCAGATCGAAGACATCAGCCTTGCCTCCCTAGGTTGTAGCAGAGCAGGTTAAAAATAGCA
* * *
29126579 GATCTTGCCTTCCTGCGCCAACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCGGGGTTGC
130 GATCTTGCCTTCCTACGCCAACAGTGAAGCAGATCGAAGACACCAACCTTGCCTCCCGAGGTTGC
* * *
29126644 AACGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGGTGAAAGACA
195 AACGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAACGAAGCAGATCAAAGACA
29126709 TCAAC
260 TCAAC
29126714 CTTG
1 CTTG
29126718 TCTCCCTGAG
Statistics
Matches: 243, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
264 242 1.00
265 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (264 bp):
CTTGCCTCTCTGGGTTACAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
CGAAGCAGATCGAAGACATCAGCCTTGCCTCCCTAGGTTGTAGCAGAGCAGGTTAAAAATAGCAG
ATCTTGCCTTCCTACGCCAACAGTGAAGCAGATCGAAGACACCAACCTTGCCTCCCGAGGTTGCA
ACGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAACGAAGCAGATCAAAGACAT
CAAC
Found at i:29126745 original size:88 final size:88
Alignment explanation
Indices: 29126186--29126724 Score: 740
Period size: 88 Copynumber: 6.1 Consensus size: 88
29126176 AATAGCAGAT
* * * *
29126186 CTTGCCTCTCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
1 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAG
29126251 CGAAGCAGATCGAAGACATCAGC
66 CGAAGCAGATCGAAGACATCAGC
* * * *
29126274 CTTGCCTTCCTAGGTTGTAGCGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTACGCCGACAG
1 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAG
* * * * *
29126339 TGAAGCGGATTGAAGACACCAAC
66 CGAAGCAGATCGAAGACATCAGC
*
29126362 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAA
1 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAG
** *
29126427 TTAAGCAGATCAAAGACATCAGC
66 CGAAGCAGATCGAAGACATCAGC
** * * * *
29126450 CTTGCCTCATTGGGTTACAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCTTGCGCCGATAG
1 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAG
29126515 CGAAGCAGATCGAAGACATCAGC
66 CGAAGCAGATCGAAGACATCAGC
** *
29126538 CTTGCCTCCCTAGGTTGTC-GTAGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCAACA
1 CTTGCCTCCCTAGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACA
* *
29126602 GTGAAGCAGATCGAAGACACCAGC
65 GCGAAGCAGATCGAAGACATCAGC
** *
29126626 CTTGCCTCCCGGGGTTGCAACGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAG
1 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAG
* *
29126691 CGAAGCAGGT-GAAAGACATCAAC
66 CGAAGCAGATCG-AAGACATCAGC
*
29126714 CTTGTCTCCCT
1 CTTGCCTCCCT
29126725 GAGCAGCAGT
Statistics
Matches: 393, Mismatches: 55, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
87 2 0.01
88 390 0.99
89 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (88 bp):
CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAG
CGAAGCAGATCGAAGACATCAGC
Found at i:29126799 original size:43 final size:43
Alignment explanation
Indices: 29126751--29126891 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 43
29126741 GGTTACAGAT
29126751 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
* * * * * * ** *
29126794 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCCAG-C
* *
29126838 ATTATCTCCCCAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
29126881 CTTATCTCCCT
1 CTTATCTCCCT
29126892 GGTCAGCAGT
Statistics
Matches: 73, Mismatches: 22, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
43 42 0.58
44 31 0.42
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
Found at i:29126802 original size:80 final size:80
Alignment explanation
Indices: 29126713--29126911 Score: 283
Period size: 87 Copynumber: 2.4 Consensus size: 80
29126703 AAGACATCAA
* * *
29126713 CCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCA
1 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTACAGATATTATCTCCCCAAGCAGTAGTGGAGCA
29126778 GATCGAAGTCCCCAG
66 GATCGAAGTCCCCAG
29126793 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATATTATCTCCCCAAGCAGTAG
1 CCTTATCTCCCTGAGCAGCAGTGGAGTA-G--G----TTACAGATATTATCTCCCCAAGCAGTAG
29126858 TGGAGCAGATCGAAGTCCCCAG
59 TGGAGCAGATCGAAGTCCCCAG
*
29126880 CCTTATCTCCCTG-GTCAGCAGTGGAATAGGTT
1 CCTTATCTCCCTGAG-CAGCAGTGGAGTAGGTT
29126912 GAAGATTGTG
Statistics
Matches: 107, Mismatches: 4, Indels: 16
0.84 0.03 0.13
Matches are distributed among these distances:
80 29 0.27
81 1 0.01
83 1 0.01
84 1 0.01
86 2 0.02
87 73 0.68
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (80 bp):
CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTACAGATATTATCTCCCCAAGCAGTAGTGGAGCA
GATCGAAGTCCCCAG
Found at i:29126933 original size:44 final size:44
Alignment explanation
Indices: 29126883--29126969 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
29126873 TCCCCAGCCT
*
29126883 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCC
*
29126927 TATCTCCCTGGTCAGCTGTGGAATAGGTTGAAGATTGAGAATC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATC
29126970 TTACCTCTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCC
Found at i:29126948 original size:87 final size:87
Alignment explanation
Indices: 29126743--29126914 Score: 301
Period size: 87 Copynumber: 2.0 Consensus size: 87
29126733 GTGGAGTAGG
* *
29126743 TTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAG
1 TTACAGATATTATCTCCCCAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAG
*
29126808 CAGCAGTGGAGTAGGTTGAAAA
66 CAGCAGTGGAATAGGTTGAAAA
29126830 TTACAGATATTATCTCCCCAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTG-G
1 TTACAGATATTATCTCCCCAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAG
29126894 TCAGCAGTGGAATAGGTTGAA
66 -CAGCAGTGGAATAGGTTGAA
29126915 GATTGTGAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
86 1 0.01
87 80 0.99
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (87 bp):
TTACAGATATTATCTCCCCAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAG
CAGCAGTGGAATAGGTTGAAAA
Found at i:29127157 original size:44 final size:46
Alignment explanation
Indices: 29127109--29127210 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 46
29127099 TATCTTTCTG
* *
29127109 AAGTTGCAGTGGA-GCAGACT-AA-ATAAGCGACTTTTATC-CTCCTA
1 AAGTTGCAGTGGAGGCAGACTGAAGAT-AGCGAATCTTATCTC-CCTA
*
29127153 AAGTTGCAGT-GAGGCAGACTGAAGATGGCGAATCTTATCTCCCTA
1 AAGTTGCAGTGGAGGCAGACTGAAGATAGCGAATCTTATCTCCCTA
29127198 AAGTTGCAGTGGA
1 AAGTTGCAGTGGA
29127211 AAAGATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
43 2 0.04
44 17 0.34
45 26 0.52
46 5 0.10
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (46 bp):
AAGTTGCAGTGGAGGCAGACTGAAGATAGCGAATCTTATCTCCCTA
Found at i:29127204 original size:217 final size:219
Alignment explanation
Indices: 29126955--29127391 Score: 605
Period size: 217 Copynumber: 2.0 Consensus size: 219
29126945 TGGAATAGGT
* * *
29126955 TGAAGATTGAGAATCTTACCTCTCTGAAGTTGCAGT-AAAGAAGATTAAAGCCAATGATCCTATC
1 TGAAGATGGAGAATCTTACCTCCCTAAAGTTGCAGTGAAA-AAGATTAAAGCCAATGATCCTATC
*
29127019 TCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCCCTCTGAAGTTACAG-AAAGC
65 TCCCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCTTATCCCTCTGAAGTTACAGTAAAGC
* ** * *
29127083 AGATCGCATCCAGTCTTATCTTTCTGAAGTTGCAGTGGAGCAGACT-AA-ATAAGCGACTTTTAT
130 AGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAAGA-AAGCAACTTTTAT
*
29127146 CCTCCT-AAAGTTGCAGTGAGGCAGAC
194 CCCCCTGAAA-TTGCAGTGAGGCAGAC
* * *
29127172 TGAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAAAAGATTAAAGCCAATGATCCTATCT
1 TGAAGATGGAGAATCTTACCTCCCTAAAGTTGCAGTGAAAAAGATTAAAGCCAATGATCCTATCT
* ** * * *
29127237 CTCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCTTATCTTTCTGAAGTTGCAGTAGAGTA
66 CCCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCTTATCCCTCTGAAGTTACAGTAAAGCA
* * *
29127302 GATCACATCGAGTCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTCAAGAAAGCAAGTTTTATCC
131 GATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAAGAAAGCAACTTTTATCC
*
29127367 CCCTGAAATTGCAGTGGGGCAGAC
196 CCCTGAAATTGCAGTGAGGCAGAC
29127391 T
1 T
29127392 AAATACACAA
Statistics
Matches: 192, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
217 109 0.57
218 45 0.23
219 34 0.18
220 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (219 bp):
TGAAGATGGAGAATCTTACCTCCCTAAAGTTGCAGTGAAAAAGATTAAAGCCAATGATCCTATCT
CCCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCTTATCCCTCTGAAGTTACAGTAAAGCA
GATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTCAAGAAAGCAACTTTTATCC
CCCTGAAATTGCAGTGAGGCAGAC
Found at i:29127299 original size:44 final size:44
Alignment explanation
Indices: 29126967--29127344 Score: 201
Period size: 44 Copynumber: 8.7 Consensus size: 44
29126957 AAGATTGAGA
* * * *
29126967 ATCTTACCTCTCTGAAGTTGCAGTAAAGAAGATTAAAGCCA-ATG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCACA-G
* * * *
29127011 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCACAG
* * * *** *
29127055 ATCTTATCCCTCTGAAGTTACAG-AAAGCAGA-TCGCATC-CAG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCACAG
* * *
29127096 -TCTTATCTTTCTGAAGTTGCAGTGGAGCAGACTAAATA--AGC-G
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAA-ACCA-CAG
* * * * ***
29127138 ACTTTTATC-CTCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGGC-G
1 A-TCTTATCTCT-CTGAAGTTGCAGTAGA-GCAGA-TTAAAACCACAG
* * * ** *
29127183 AATCTTATCTCCCTAAAGTTGCAGTGGAAAAGATTAAAGCCA-ATG
1 -ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCACA-G
* *
29127228 ATCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAACCACAG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCACAG
* * * * * *
29127272 ATCTTATCTTTCTGAAGTTGCAGTAGAGTAGA-TCACATC-GAG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCACAG
* *
29127314 -TCTTATCTCCCTGAAGTTGTAGTAGAGCAGA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
29127345 CTCAAGAAAG
Statistics
Matches: 251, Mismatches: 64, Indels: 41
0.71 0.18 0.12
Matches are distributed among these distances:
40 19 0.08
41 36 0.14
42 7 0.03
43 14 0.06
44 142 0.57
45 29 0.12
46 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCACAG
Found at i:29128923 original size:3 final size:3
Alignment explanation
Indices: 29128910--29128971 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
29128900 AAATAAATTG
* *
29128910 TTA TCA TTA TTA TTA TTTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29128956 TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
29128972 ATTCATATGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:29129375 original size:8 final size:8
Alignment explanation
Indices: 29129364--29129459 Score: 58
Period size: 8 Copynumber: 11.6 Consensus size: 8
29129354 TTGCTTGTCA
*
29129364 TTATTTAT
1 TTATTCAT
29129372 TTATTCAT
1 TTATTCAT
29129380 TTATTCAT
1 TTATTCAT
29129388 ATTATT--T
1 -TTATTCAT
*
29129395 CTATGTCAT
1 TTAT-TCAT
29129404 TGT-TGTC-T
1 T-TAT-TCAT
29129412 TTATTACTAT
1 TTATT-C-AT
29129422 TGTATT-AT
1 T-TATTCAT
*
29129430 TTATTTAT
1 TTATTCAT
29129438 TTATTCAT
1 TTATTCAT
29129446 TTATTCAT
1 TTATTCAT
29129454 ATTATT
1 -TTATT
29129460 TCTATGCCAT
Statistics
Matches: 72, Mismatches: 4, Indels: 23
0.73 0.04 0.23
Matches are distributed among these distances:
6 3 0.04
7 8 0.11
8 39 0.54
9 15 0.21
10 3 0.04
11 4 0.06
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (8 bp):
TTATTCAT
Found at i:29129421 original size:23 final size:22
Alignment explanation
Indices: 29129389--29129487 Score: 64
Period size: 23 Copynumber: 4.5 Consensus size: 22
29129379 TTTATTCATA
*
29129389 TTATTTCTATGTCATTGTTGTCT
1 TTATTACTATGTCATTGTT-TCT
* *
29129412 TTATTACTATTGT-ATTATTTAT
1 TTATTACTA-TGTCATTGTTTCT
29129434 TTATT--TAT-TCATT-TATTCAT
1 TTATTACTATGTCATTGT-TTC-T
* *
29129454 ATTATTTCTATGCCATTGTTGTCT
1 -TTATTACTATGTCATTGTT-TCT
29129478 TTATTACTAT
1 TTATTACTAT
29129488 TGTATTTGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
18 2 0.03
19 6 0.10
20 3 0.05
21 5 0.08
22 7 0.12
23 25 0.42
24 9 0.15
25 3 0.05
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (22 bp):
TTATTACTATGTCATTGTTTCT
Found at i:29129434 original size:66 final size:66
Alignment explanation
Indices: 29129364--29129493 Score: 251
Period size: 66 Copynumber: 2.0 Consensus size: 66
29129354 TTGCTTGTCA
*
29129364 TTATTTATTTATTCATTTATTCATATTATTTCTATGTCATTGTTGTCTTTATTACTATTGTATTA
1 TTATTTATTTATTCATTTATTCATATTATTTCTATGCCATTGTTGTCTTTATTACTATTGTATTA
29129429 T
66 T
29129430 TTATTTATTTATTCATTTATTCATATTATTTCTATGCCATTGTTGTCTTTATTACTATTGTATT
1 TTATTTATTTATTCATTTATTCATATTATTTCTATGCCATTGTTGTCTTTATTACTATTGTATT
29129494 TGTTATCACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.62
Consensus pattern (66 bp):
TTATTTATTTATTCATTTATTCATATTATTTCTATGCCATTGTTGTCTTTATTACTATTGTATTA
T
Found at i:29140149 original size:20 final size:19
Alignment explanation
Indices: 29140112--29140153 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
29140102 TAGTAAAACA
29140112 TTATTTATTAAAATTTATAT
1 TTATTTATTAAAATTTAT-T
*
29140132 TTATTTTTTCAAAA-TTATT
1 TTATTTATT-AAAATTTATT
29140151 TTA
1 TTA
29140154 AGAAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTATTAAAATTTATT
Found at i:29140486 original size:26 final size:27
Alignment explanation
Indices: 29140453--29140520 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
29140443 TTTTTGGCAC
*
29140453 ATAA-AAATATAATTTTTAAAAA-AAT
1 ATAATAAATATAATTTTAAAAAATAAT
29140478 -TAATTAAATATATATTTTAAAAAATAAT
1 ATAA-TAAATATA-ATTTTAAAAAATAAT
29140506 ATAATAAATACTAAT
1 ATAATAAATA-TAAT
29140521 AATTTAACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
24 3 0.08
26 7 0.19
27 10 0.28
28 11 0.31
29 5 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
ATAATAAATATAATTTTAAAAAATAAT
Found at i:29152338 original size:12 final size:13
Alignment explanation
Indices: 29152312--29152337 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29152302 TTACAAATAT
29152312 ATATACAAGTAAA
1 ATATACAAGTAAA
29152325 ATATACAAGTAAA
1 ATATACAAGTAAA
29152338 TTTACAAGCA
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:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
ATATACAAGTAAA
Found at i:29152343 original size:12 final size:12
Alignment explanation
Indices: 29152312--29152345 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29152302 TTACAAATAT
29152312 ATATACAAGTAAA
1 ATATACAAGT-AA
29152325 ATATACAAGTAA
1 ATATACAAGTAA
*
29152337 ATTTACAAG
1 ATATACAAG
29152346 CATGTGTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (12 bp):
ATATACAAGTAA
Found at i:29152520 original size:23 final size:22
Alignment explanation
Indices: 29152494--29152543 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
29152484 AACATGTGTA
* *
29152494 TATATTTATAAAAAATGTATAAG
1 TATATGTATAAAAAATATA-AAG
* *
29152517 TATATGTATATACAATATAAAG
1 TATATGTATAAAAAATATAAAG
29152539 TATAT
1 TATAT
29152544 AAAAGTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (22 bp):
TATATGTATAAAAAATATAAAG
Found at i:29152828 original size:6 final size:6
Alignment explanation
Indices: 29152819--29152868 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
29152809 CATGTGCATG
* * *
29152819 TATATT TATATA TATATA TATATA TATATA TATATA TATACA TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
29152867 TA
1 TA
29152869 AAATAAAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATA
Found at i:29152834 original size:4 final size:4
Alignment explanation
Indices: 29152819--29152868 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
29152809 CATGTGCATG
* * *
29152819 TATA TTTA TATA TATA TATA TATA TATA TATA TATA TATA CATA TTTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
29152867 TA
1 TA
29152869 AAATAAAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (4 bp):
TATA
Found at i:29152838 original size:10 final size:10
Alignment explanation
Indices: 29152819--29152868 Score: 73
Period size: 10 Copynumber: 5.0 Consensus size: 10
29152809 CATGTGCATG
*
29152819 TATATTTATA
1 TATATATATA
29152829 TATATATATA
1 TATATATATA
29152839 TATATATATA
1 TATATATATA
29152849 TATATATATA
1 TATATATATA
* *
29152859 CATATTTATA
1 TATATATATA
29152869 AAATAAAGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATATATA
Found at i:29152995 original size:3 final size:3
Alignment explanation
Indices: 29152987--29153051 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
29152977 TGTATACGAA
* * * * *
29152987 AAT AAT AAT TAC AAT ATT AAT AAT AAT AGT AAAT AAT AAT AAA AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA-T
29153034 AAT AAT -AT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
29153052 CAACAAATAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 4 0.08
3 40 0.83
4 4 0.08
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29153023 original size:10 final size:10
Alignment explanation
Indices: 29152986--29153045 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
29152976 ATGTATACGA
29152986 AAATAATAATT
1 AAATAATAA-T
*
29152997 ACAATATTAAT
1 A-AATAATAAT
*
29153008 -AATAATAGT
1 AAATAATAAT
29153017 AAATAATAAT
1 AAATAATAAT
29153027 AAA-AAGTAAT
1 AAATAA-TAAT
29153037 AATATAATA
1 AA-ATAATA
29153046 TAATAACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 9 0.22
10 17 0.43
11 5 0.12
12 9 0.22
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (10 bp):
AAATAATAAT
Found at i:29153023 original size:13 final size:12
Alignment explanation
Indices: 29152999--29153051 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
29152989 TAATAATTAC
*
29152999 AATATTAATAAT
1 AATATAAATAAT
29153011 AATAGTAAATAAT
1 AATA-TAAATAAT
*
29153024 AATAAAAAGTAAT
1 AATATAAA-TAAT
29153037 AATATAATATAAT
1 AATATAA-ATAAT
29153050 AA
1 AA
29153052 CAACAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 7 0.20
13 27 0.77
14 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (12 bp):
AATATAAATAAT
Found at i:29153025 original size:16 final size:15
Alignment explanation
Indices: 29153004--29153051 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
29152994 ATTACAATAT
29153004 TAATAATAATAGTAAA
1 TAATAATAATAGT-AA
*
29153020 TAATAATAAAAAGTAA
1 TAATAAT-AATAGTAA
29153036 TAAT-ATAATA-TAA
1 TAATAATAATAGTAA
29153049 TAA
1 TAA
29153052 CAACAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 3 0.10
15 2 0.07
16 13 0.45
17 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
TAATAATAATAGTAA
Found at i:29153044 original size:31 final size:31
Alignment explanation
Indices: 29152986--29153045 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
29152976 ATGTATACGA
* * *
29152986 AAATAATAATTACAATATTAATAATAATAGT
1 AAATAATAATAAAAATAATAATAATAATAGT
29153017 AAATAATAATAAAAAGTAATAAT-ATAATA
1 AAATAATAATAAAAA-TAATAATAATAATA
29153046 TAATAACAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (31 bp):
AAATAATAATAAAAATAATAATAATAATAGT
Found at i:29155103 original size:11 final size:11
Alignment explanation
Indices: 29155089--29155118 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
29155079 TTACTAATTT
29155089 AAATTTAATAA
1 AAATTTAATAA
29155100 AAATTTAATAA
1 AAATTTAATAA
29155111 AAATTTAA
1 AAATTTAA
29155119 ATTTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATTTAATAA
Found at i:29155761 original size:13 final size:13
Alignment explanation
Indices: 29155743--29155767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29155733 AATTAAAGGG
29155743 TTAAAATTTAAAT
1 TTAAAATTTAAAT
29155756 TTAAAATTTAAA
1 TTAAAATTTAAA
29155768 GATGATAATC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAAATTTAAAT
Found at i:29161835 original size:43 final size:43
Alignment explanation
Indices: 29161788--29161939 Score: 180
Period size: 43 Copynumber: 3.5 Consensus size: 43
29161778 AAAGCGGTGT
* * * * *
29161788 TAAAGGTCATGTTCTATAGTGGTGTTTATTAGG-AAAGCCCCAT
1 TAAAGGTCATGTTCTATAGTGGCGTTT-GTGGGAAAAGCACCAC
* * * *
29161831 TAAAGGTCAAGTTCTTTAGTGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTATAGTGGCGTTTGTGGGAAAAGCACCAC
* * *
29161874 TAAAAGTCATGTTCTATAGCGGCATTTGTGGGAAAAGCACCAC
1 TAAAGGTCATGTTCTATAGTGGCGTTTGTGGGAAAAGCACCAC
29161917 TAAAGGTCATGTTCTATAGTGGC
1 TAAAGGTCATGTTCTATAGTGGC
29161940 ATTTTTCCAC
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 3 0.03
43 88 0.97
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (43 bp):
TAAAGGTCATGTTCTATAGTGGCGTTTGTGGGAAAAGCACCAC
Found at i:29161911 original size:86 final size:86
Alignment explanation
Indices: 29161756--29161939 Score: 217
Period size: 86 Copynumber: 2.1 Consensus size: 86
29161746 TAGCCGCGTT
* ** * * * ** *
29161756 TTCTTTAGCGGCGTTTGTAGGAAAAGCGGTGTTAAAGGTCATGTTCTATAGTGGTGTTTATTAGG
1 TTCTTTAGTGGCGTTTGTAGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTTAGTAGG
* *
29161821 AAAGCCCCATTAAAGGTCAAG
66 AAAGCACCACTAAAGGTCAAG
* *
29161842 TTCTTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTT-GTGGG
1 TTCTTTAGTGGCGTTTGTAGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTTAGTAGG
*
29161906 AAAAGCACCACTAAAGGTCATG
66 -AAAGCACCACTAAAGGTCAAG
*
29161928 TTCTATAGTGGC
1 TTCTTTAGTGGC
29161940 ATTTTTCCAC
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 3 0.04
86 79 0.96
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (86 bp):
TTCTTTAGTGGCGTTTGTAGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTTAGTAGG
AAAGCACCACTAAAGGTCAAG
Found at i:29163005 original size:20 final size:20
Alignment explanation
Indices: 29162974--29163025 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
29162964 AAACTATGAT
*
29162974 GCATGCTAGTTCTGTTTGAA
1 GCATGCTGGTTCTGTTTGAA
*
29162994 GCATGTTGGTTCTGTTTGAA
1 GCATGCTGGTTCTGTTTGAA
29163014 GCATGCTGGTTC
1 GCATGCTGGTTC
29163026 AGCTTTAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.40
Consensus pattern (20 bp):
GCATGCTGGTTCTGTTTGAA
Found at i:29165036 original size:22 final size:22
Alignment explanation
Indices: 29164990--29165055 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
29164980 TCAGTAGGAG
* *
29164990 GGGAA-AACTTAAG-TTTTACA
1 GGGAATAACTTGAGTTTTTATA
*
29165010 AGGAATAACTTGAGTTTTTATA
1 GGGAATAACTTGAGTTTTTATA
* *
29165032 GGGAATAACCTGAATTTTTATA
1 GGGAATAACTTGAGTTTTTATA
29165054 GG
1 GG
29165056 AAAAATCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.11
21 7 0.18
22 27 0.71
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (22 bp):
GGGAATAACTTGAGTTTTTATA
Found at i:29170005 original size:3 final size:3
Alignment explanation
Indices: 29169999--29170029 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29169989 AAAAAAATTT
29169999 GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
29170030 GAGCGGGAAG
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29170140 original size:48 final size:46
Alignment explanation
Indices: 29170035--29170140 Score: 108
Period size: 48 Copynumber: 2.2 Consensus size: 46
29170025 GAAGAGAGCG
* *
29170035 GGAAGGGA-AGGGAAGGGGAAAAAGAAAGAAAAAAAAAAAAGAGAA
1 GGAAAGGAGAGGGAAGGAGAAAAAGAAAGAAAAAAAAAAAAGAGAA
* * *
29170080 GCAAAATAGAGAGGGAAGGAGAAAGAGAAAGAAAAAAAATAAATAG-GAAA
1 G-GAAA-GGAGAGGGAAGGAGAAAAAGAAAGAAAAAAAA-AAA-AGAG-AA
29170130 GGAAAGGAGAG
1 GGAAAGGAGAG
29170141 ATTGTGTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
45 1 0.02
46 2 0.04
47 2 0.04
48 31 0.65
49 7 0.15
50 5 0.10
ACGTcount: A:0.62, C:0.01, G:0.34, T:0.03
Consensus pattern (46 bp):
GGAAAGGAGAGGGAAGGAGAAAAAGAAAGAAAAAAAAAAAAGAGAA
Found at i:29172172 original size:33 final size:34
Alignment explanation
Indices: 29172089--29172175 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 34
29172079 GACATTACTT
*
29172089 CACCGCAGTACAGCACTCCT-TCTGGCTCGTATC
1 CACCGCAGTATAGCACTCCTCTCTGGCTCGTATC
* * * *
29172122 CACCACATTACT-CCACTCCTCT-TGGGTCGTATC
1 CACCGCAGTA-TAGCACTCCTCTCTGGCTCGTATC
*
29172155 CATCGCAGTATAGCACTCCTC
1 CACCGCAGTATAGCACTCCTC
29172176 CCGGCTCAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
32 1 0.02
33 40 0.95
34 1 0.02
ACGTcount: A:0.20, C:0.39, G:0.15, T:0.26
Consensus pattern (34 bp):
CACCGCAGTATAGCACTCCTCTCTGGCTCGTATC
Found at i:29172513 original size:8 final size:8
Alignment explanation
Indices: 29172500--29172531 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
29172490 AGATTAATTG
29172500 CAACATTA
1 CAACATTA
29172508 CAACATTA
1 CAACATTA
29172516 CAACATTA
1 CAACATTA
29172524 CAACATTA
1 CAACATTA
29172532 AAACTTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (8 bp):
CAACATTA
Found at i:29172589 original size:48 final size:48
Alignment explanation
Indices: 29172518--29172610 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
29172508 CAACATTACA
*
29172518 ACATTACAACATTAAAACTTGGAACAAGCTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAAT
29172566 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTA
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTA
29172611 GGTATATTGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (48 bp):
ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAAT
Found at i:29176478 original size:14 final size:13
Alignment explanation
Indices: 29176455--29176489 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
29176445 AAAAATACAT
29176455 TTTC-TTTCTTTC
1 TTTCTTTTCTTTC
29176467 TTGTCTTTTCTTTC
1 TT-TCTTTTCTTTC
29176481 TTTCTTTTC
1 TTTCTTTTC
29176490 CCTCTCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.10
13 9 0.43
14 10 0.48
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:29176893 original size:17 final size:17
Alignment explanation
Indices: 29176827--29176893 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
29176817 ATTTAAATTC
*
29176827 ATTATTATGTTTTTAAAAT
1 ATTATTAT-TTTTT-ATAT
29176846 ATTTATGTA-TTTTTATAT
1 A-TTAT-TATTTTTTATAT
* *
29176864 ATTTTTAATTTTTATAT
1 ATTATTATTTTTTATAT
29176881 ATTATTATTTTTT
1 ATTATTATTTTTT
29176894 GTCAACATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.05
17 23 0.56
18 4 0.10
19 6 0.15
20 4 0.10
21 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTATTATTTTTTATAT
Found at i:29189353 original size:29 final size:29
Alignment explanation
Indices: 29189288--29189346 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
29189278 AACTATTTGT
* *
29189288 ACTAATCAATAACATTATAAAAATATTGA
1 ACTAATTAATAACATTATAAAAATATAGA
29189317 ACTAATTAATAACATTATAAAAATATAGA
1 ACTAATTAATAACATTATAAAAATATAGA
29189346 A
1 A
29189347 ACCATTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (29 bp):
ACTAATTAATAACATTATAAAAATATAGA
Found at i:29192350 original size:11 final size:11
Alignment explanation
Indices: 29192321--29192377 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
29192311 TAATAATTAA
29192321 AAATATTAAAAT
1 AAAT-TTAAAAT
*
29192333 CATATTTAAAAT
1 -AAATTTAAAAT
*
29192345 AAATTTTAAAT
1 AAATTTAAAAT
* * *
29192356 TATTTTAAATT
1 AAATTTAAAAT
29192367 AAATTTAAAAT
1 AAATTTAAAAT
29192378 TTTATAATAG
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
11 24 0.71
12 7 0.21
13 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:29192369 original size:22 final size:22
Alignment explanation
Indices: 29192321--29192378 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
29192311 TAATAATTAA
*
29192321 AAATATTAAAATCATATTTAAAAT
1 AAAT-TTAAAATTAT-TTTAAAAT
* *
29192345 AAATTTTAAATTATTTTAAATT
1 AAATTTAAAATTATTTTAAAAT
29192367 AAATTTAAAATT
1 AAATTTAAAATT
29192379 TTATAATAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.60
23 8 0.27
24 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTTAAAATTATTTTAAAAT
Found at i:29192378 original size:12 final size:12
Alignment explanation
Indices: 29192321--29192378 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
29192311 TAATAATTAA
*
29192321 AAATATTAAAATC
1 AAAT-TTAAAATT
*
29192334 ATATTTAAAA-T
1 AAATTTAAAATT
*
29192345 AAATTTTAAATT
1 AAATTTAAAATT
*
29192357 --ATTTTAAATT
1 AAATTTAAAATT
29192367 AAATTTAAAATT
1 AAATTTAAAATT
29192379 TTATAATAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 10 0.27
11 8 0.22
12 16 0.43
13 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATTTAAAATT
Found at i:29198811 original size:21 final size:20
Alignment explanation
Indices: 29198787--29198842 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
29198777 ATATTTATCA
*
29198787 TTATATCATTATTCATTATTG
1 TTATATCATTATT-ATTATGG
* *
29198808 TTATATTATTTATTATTGTGG
1 TTATATCA-TTATTATTATGG
29198829 TTATTATCATTATT
1 TTA-TATCATTATT
29198843 TCTATGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (20 bp):
TTATATCATTATTATTATGG
Found at i:29198880 original size:2 final size:2
Alignment explanation
Indices: 29198873--29198897 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29198863 GTTTTTACAG
29198873 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29198898 GCATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29198954 original size:25 final size:26
Alignment explanation
Indices: 29198881--29198970 Score: 98
Period size: 25 Copynumber: 3.6 Consensus size: 26
29198871 AGTATATATA
*
29198881 TATATATATATATATATGCATTTTTT
1 TATATATATATATATACGCATTTTTT
* * * *
29198907 TATGTAT-TA-A-ACACACATATTTT
1 TATATATATATATATACGCATTTTTT
29198930 TATATATA-ATATATACGCATTTTTT
1 TATATATATATATATACGCATTTTTT
*
29198955 TAAATATATATATATA
1 TATATATATATATATA
29198971 TTTTAAGCTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
23 16 0.32
24 2 0.04
25 19 0.38
26 13 0.26
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (26 bp):
TATATATATATATATACGCATTTTTT
Found at i:29202312 original size:35 final size:35
Alignment explanation
Indices: 29202172--29202318 Score: 231
Period size: 35 Copynumber: 4.2 Consensus size: 35
29202162 GGCGTGTTTC
*
29202172 GGTTGGATTAGCTCTTATGAGCATTGGCGTATTTT
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTATTAT
* * *
29202207 GGTTGGATTAGCTCTTATGAGCATTGGTGTGTTAC
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTATTAT
* *
29202242 GATTGGATTAGCTCTTATGAGCATTGGCGTGTTAT
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTATTAT
*
29202277 GGTTGGATTACCTCTTATGAGCATTGGCGTATTAT
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTATTAT
29202312 GGTTGGA
1 GGTTGGA
29202319 CTGATGATGT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 102 1.00
ACGTcount: A:0.18, C:0.12, G:0.30, T:0.40
Consensus pattern (35 bp):
GGTTGGATTAGCTCTTATGAGCATTGGCGTATTAT
Found at i:29205915 original size:9 final size:9
Alignment explanation
Indices: 29205870--29205943 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
29205860 ATAGTTTTTT
29205870 AAATTATAA
1 AAATTATAA
*
29205879 AAA-AATTAA
1 AAATTA-TAA
* *
29205888 AACTTTTAA
1 AAATTATAA
29205897 AAA-TAT-A
1 AAATTATAA
*
29205904 AAATTTTAA
1 AAATTATAA
*
29205913 AAATTGTAA
1 AAATTATAA
29205922 AATATTATAA
1 AA-ATTATAA
29205932 AAATTATAA
1 AAATTATAA
29205941 AAA
1 AAA
29205944 AATTGGAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
7 4 0.08
8 5 0.10
9 34 0.67
10 8 0.16
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:29205934 original size:19 final size:17
Alignment explanation
Indices: 29205879--29205942 Score: 78
Period size: 16 Copynumber: 3.8 Consensus size: 17
29205869 TAAATTATAA
*
29205879 AAAAATTA-AAACTTTT
1 AAAAATTATAAAATTTT
29205895 AAAAA-TATAAAATTTT
1 AAAAATTATAAAATTTT
*
29205911 AAAAATTGTAAAATATTAT
1 AAAAATTATAAAAT-TT-T
29205930 AAAAATTATAAAA
1 AAAAATTATAAAA
29205943 AAATTGGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 2 0.05
16 17 0.41
17 7 0.17
18 2 0.05
19 13 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAAATTATAAAATTTT
Found at i:29206508 original size:16 final size:16
Alignment explanation
Indices: 29206487--29206520 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29206477 TTATAATTTG
29206487 TAAAAAAAATTAAAAA
1 TAAAAAAAATTAAAAA
* *
29206503 TAAAAAAACTTGAAAA
1 TAAAAAAAATTAAAAA
29206519 TA
1 TA
29206521 TTACTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (16 bp):
TAAAAAAAATTAAAAA
Found at i:29206557 original size:29 final size:29
Alignment explanation
Indices: 29206486--29206559 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 29
29206476 TTTATAATTT
* *
29206486 GTAAAAAAA-ATTAAAAATAAAAAAACTT
1 GTAAAAAAATATTCAAAATAAAAAAACTA
* * * * *
29206514 G-AAAATATTACTCAAAATTATAAAACTA
1 GTAAAAAAATATTCAAAATAAAAAAACTA
29206542 GTAAAAAAATATTCAAAA
1 GTAAAAAAATATTCAAAA
29206560 AAATTTAAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
27 5 0.15
28 16 0.47
29 13 0.38
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (29 bp):
GTAAAAAAATATTCAAAATAAAAAAACTA
Found at i:29206559 original size:10 final size:10
Alignment explanation
Indices: 29206546--29206651 Score: 76
Period size: 10 Copynumber: 10.6 Consensus size: 10
29206536 AAACTAGTAA
*
29206546 AAAAATATTC
1 AAAAATATTT
*
29206556 AAAAAAATTT
1 AAAAATATTT
*
29206566 AAAATCTATTT
1 AAAA-ATATTT
* *
29206577 AAAAAAATTC
1 AAAAATATTT
29206587 AAAAA-ATTT
1 AAAAATATTT
*
29206596 AAAATCTATTT
1 AAAA-ATATTT
*
29206607 AAAAA-AATT
1 AAAAATATTT
29206616 AAAAATAATTT
1 AAAAAT-ATTT
*
29206627 -AAAATATTG
1 AAAAATATTT
29206636 AAAAAT-TTGT
1 AAAAATATT-T
29206646 AAAAAT
1 AAAAAT
29206652 TCTTAAACGT
Statistics
Matches: 75, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
9 20 0.27
10 36 0.48
11 19 0.25
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAAATATTT
Found at i:29206581 original size:31 final size:31
Alignment explanation
Indices: 29206527--29206631 Score: 144
Period size: 30 Copynumber: 3.4 Consensus size: 31
29206517 AATATTACTC
* *
29206527 AAAATTATAAAA-CTAGTAAAAAAATATTCAAA
1 AAAATT-TAAAATCTATTTAAAAAA-ATTCAAA
29206559 AAAATTTAAAATCTATTTAAAAAAATTC-AA
1 AAAATTTAAAATCTATTTAAAAAAATTCAAA
29206589 AAAATTTAAAATCTATTTAAAAAAATT-AAA
1 AAAATTTAAAATCTATTTAAAAAAATTCAAA
29206619 AATAATTTAAAAT
1 AA-AATTTAAAAT
29206632 ATTGAAAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
30 33 0.49
31 19 0.28
32 16 0.24
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.31
Consensus pattern (31 bp):
AAAATTTAAAATCTATTTAAAAAAATTCAAA
Done.