Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 36 of 132
Found at i:9658395 original size:18 final size:18
Alignment explanation
Indices: 9658369--9658411 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
9658359 GCAGTTGAAT
* *
9658369 AATTCAATTTTCTTCAAA
1 AATTTAATTTTCTTAAAA
*
9658387 AATTTAATTTTTTTAAAA
1 AATTTAATTTTCTTAAAA
*
9658405 AAATTAA
1 AATTTAA
9658412 AAATGAGTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTAATTTTCTTAAAA
Found at i:9665092 original size:4 final size:4
Alignment explanation
Indices: 9665083--9665107 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9665073 CTAATCCTAC
9665083 CAAT CAAT CAAT CAAT CAAT CAAT C
1 CAAT CAAT CAAT CAAT CAAT CAAT C
9665108 CCCTCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CAAT
Found at i:9666265 original size:22 final size:22
Alignment explanation
Indices: 9666238--9666306 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
9666228 GTGACATATG
9666238 AAAAAATATTATAAAAAATAAA
1 AAAAAATATTATAAAAAATAAA
* *
9666260 AAAAAA-AGTTATAAAAATTAATT
1 AAAAAATA-TTATAAAAAATAA-A
*
9666283 AAAAATTATTA-AAAAATATAAA
1 AAAAAATATTATAAAAA-ATAAA
9666305 AA
1 AA
9666307 TGGTAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
21 1 0.03
22 25 0.66
23 11 0.29
24 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (22 bp):
AAAAAATATTATAAAAAATAAA
Found at i:9666285 original size:11 final size:10
Alignment explanation
Indices: 9666262--9666307 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
9666252 AAAATAAAAA
9666262 AAAAAGTTA-T
1 AAAAA-TTATT
9666272 AAAAATTAATT
1 AAAAATT-ATT
9666283 AAAAATTATT
1 AAAAATTATT
*
9666293 AAAAAATA-T
1 AAAAATTATT
9666302 AAAAAT
1 AAAAAT
9666308 GGTAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAATTATT
Found at i:9666416 original size:19 final size:19
Alignment explanation
Indices: 9666394--9666450 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
9666384 TGATAAAATT
9666394 TTATAAAA-TCGTAAAAAAA
1 TTATAAAAGT-GTAAAAAAA
*
9666413 TTATAAAAAGTGTAAAGAAA
1 TTAT-AAAAGTGTAAAAAAA
*
9666433 -TATAAAATTTGTAAAAAA
1 TTATAAAA-GTGTAAAAAA
9666451 TTAGAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.12
19 15 0.47
20 12 0.38
21 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.28
Consensus pattern (19 bp):
TTATAAAAGTGTAAAAAAA
Found at i:9666458 original size:19 final size:19
Alignment explanation
Indices: 9666407--9666459 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
9666397 TAAAATCGTA
9666407 AAAAAATTATAAAAAGTGT
1 AAAAAATTATAAAAAGTGT
**
9666426 AAAGAAA-TATAAAATTTGT
1 AAA-AAATTATAAAAAGTGT
*
9666445 AAAAAATTAGAAAAA
1 AAAAAATTATAAAAA
9666460 TTATCATACC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.11
19 22 0.79
20 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (19 bp):
AAAAAATTATAAAAAGTGT
Found at i:9670373 original size:43 final size:43
Alignment explanation
Indices: 9670312--9670528 Score: 197
Period size: 43 Copynumber: 5.1 Consensus size: 43
9670302 CATAACGTCA
* * *
9670312 CTATAAAACATGGTCTTTAGCGGTGCTTTTCCCACAAATGCCG
1 CTATAGAACATGTTCTTTAGCGGTGCTTTTCCCACAAACGCCG
* * **
9670355 CTATAGTACATGTTCTTTAGTGACGCTTTTCCCACAAACGCCG
1 CTATAGAACATGTTCTTTAGCGGTGCTTTTCCCACAAACGCCG
* * * *
9670398 ATATAGAACATGTTCTTTAGCGGCGCTTCTTTTCC-C--ACGCCT
1 CTATAGAACATGTTCTTTAGCGGTGC-T-TTTCCCACAAACGCCG
* ** * * *
9670440 CTATAGAACGTGTTCTTTAATGGTGTTTTTCCCACAAATGCCT
1 CTATAGAACATGTTCTTTAGCGGTGCTTTTCCCACAAACGCCG
* * * * *
9670483 TTATAGAACATATTCTTTAACAGTGCTTTTACCACAAACGCCG
1 CTATAGAACATGTTCTTTAGCGGTGCTTTTCCCACAAACGCCG
9670526 CTA
1 CTA
9670529 ACATTAACAG
Statistics
Matches: 138, Mismatches: 31, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
40 5 0.04
41 2 0.01
42 25 0.18
43 99 0.72
44 2 0.01
45 5 0.04
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (43 bp):
CTATAGAACATGTTCTTTAGCGGTGCTTTTCCCACAAACGCCG
Found at i:9670617 original size:15 final size:15
Alignment explanation
Indices: 9670597--9670629 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9670587 TTTTCCTATA
*
9670597 AATTCAAATCTAACC
1 AATTCAAATCCAACC
9670612 AATTCAAATCCAACC
1 AATTCAAATCCAACC
9670627 AAT
1 AAT
9670630 AACTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTCAAATCCAACC
Found at i:9675795 original size:20 final size:20
Alignment explanation
Indices: 9675763--9675821 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
9675753 AGAGTTAAGG
*
9675763 GTTTGAGTTTAA-GTTTATT
1 GTTTGAGTTTAAGGTTTAGT
9675782 GTTTGAGATTTAAGGTTTAGT
1 GTTTGAG-TTTAAGGTTTAGT
9675803 GTTT-AGGTTTAAGGTTTAG
1 GTTTGA-GTTTAAGGTTTAG
9675822 GATTTTGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 7 0.19
20 18 0.50
21 11 0.31
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (20 bp):
GTTTGAGTTTAAGGTTTAGT
Found at i:9676063 original size:25 final size:26
Alignment explanation
Indices: 9676013--9676086 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
9676003 TGGAACTAAT
* *
9676013 TATTTAATTTTG-AATTTTTTTGATAA
1 TATTTAATTTTGAAAATATTTT-ATAA
9676039 -ATTTAATTTTGAAAATATTTTATAA
1 TATTTAATTTTGAAAATATTTTATAA
* *
9676064 TTTTATAATTTTTAAAA-ATTTTA
1 TATT-TAATTTTGAAAATATTTTA
9676087 GAGTTAACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 15 0.37
26 15 0.37
27 11 0.27
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
TATTTAATTTTGAAAATATTTTATAA
Found at i:9679843 original size:31 final size:31
Alignment explanation
Indices: 9679755--9679844 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 31
9679745 CCCTCAAATT
* *
9679755 TTTTATTTCTTTTAAAAA-TCTTATCCTTTTA
1 TTTTATTTTTTTTAAAAATTC-AATCCTTTTA
*
9679786 TTTTATTTTCTTT-AAAATT-AAGTCCTTTT-
1 TTTTATTTTTTTTAAAAATTCAA-TCCTTTTA
*
9679815 TCTTTCTTTTTTTTAAAAATTCAATCCTTT
1 T-TTTATTTTTTTTAAAAATTCAATCCTTT
9679845 AAATAATTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
29 2 0.04
30 21 0.43
31 24 0.49
32 2 0.04
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.61
Consensus pattern (31 bp):
TTTTATTTTTTTTAAAAATTCAATCCTTTTA
Found at i:9680522 original size:220 final size:220
Alignment explanation
Indices: 9680013--9680588 Score: 647
Period size: 223 Copynumber: 2.6 Consensus size: 220
9680003 AATTGTATTG
* *
9680013 TTTTTTT--AATACATAAATTGTTTTAAAACAA-TAAGACAATGTTCTTTTATTTTAGGGAATTC
1 TTTTTTTAAAATACATAAATTGTTTTAAAAAAATTAAGGCAATGTTCTTTTATTTTAGGGAATTC
* * * *
9680075 GAGAAATTGTTCTTTAACA-TGTTGGGTATAATTTTTCTTAT-AACATAAATAATCAAATATCCT
66 GAAAAATTGTGC-TCAA-ATTGTTGGGTATAA-TTTTCTT-TGAACCTAAATAATCAAATATCCT
* ** * *
9680138 ATTTAAAATTTAAAATTTTCGTTTTTTTTATTTGTAAATTACATGAATTAATCCATCTTTTGCAA
127 ATTTAAAATTGAAAA-TTTCGTCCTTTTTATTTGTAAATTACATGAATTAACCCATATTTTGCAA
* *
9680203 AATATTTTCAACAAAATAAAATGTATGTCA
191 AACATTTTCAACAAAATAAAATGTATATCA
* * *
9680233 -TTTTTAAAAATACATAAATCGTTTTAAATAAAATAAAGGCAATGTTCTTTTATTTTAGGGAATT
1 TTTTTTTAAAATACATAAATTGTTTTAAA-AAAATTAAGGCAATGTTCTTTTATTTTAGGGAATT
* * *
9680297 CGAAAAATTATGCTCAAATGTGTTGGGTATAATTTTCATTTGAACCTAAATAATCAAGTATCCTC
65 CGAAAAATTGTGCTCAAAT-TGTTGGGTATAATTTTC-TTTGAACCTAAATAATCAAATATCCTA
* * * *
9680362 TTT-AAATTGATAA-TT-G-CCTTTTT-TTT-TAAGTTACATAGTTATTTACCCATATTTTGCAA
128 TTTAAAATTGAAAATTTCGTCCTTTTTATTTGTAAATTACAT-G-AATTAACCCATATTTTGCAA
*
9680421 AACATTTTTAACAAAATAAAATGTATATCA
191 AACATTTTCAACAAAATAAAATGTATATCA
*
9680451 TTTTTTTAAAATACATAAATTGTTTTTTAAAAAAATTAAGGCAATGTTTTTTTATTTTAGGGAAT
1 TTTTTTTAAAATACATAAATTG--TTTTAAAAAAATTAAGGCAATGTTCTTTTATTTTAGGGAAT
* * * ** **
9680516 TCGAAAAATTGTGC-CATAACTTGTTGAGTATGATTTTTTTTGAACCTAAATAATTGAGCATCCT
64 TCGAAAAATTGTGCTCA-AA-TTGTTGGGTATAATTTTCTTTGAACCTAAATAATCAAATATCCT
9680580 ATTTAAAAT
127 ATTTAAAAT
9680589 CAATAAGTGC
Statistics
Matches: 304, Mismatches: 36, Indels: 32
0.82 0.10 0.09
Matches are distributed among these distances:
216 9 0.03
217 4 0.01
218 48 0.16
219 53 0.17
220 67 0.22
221 28 0.09
222 20 0.07
223 75 0.25
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (220 bp):
TTTTTTTAAAATACATAAATTGTTTTAAAAAAATTAAGGCAATGTTCTTTTATTTTAGGGAATTC
GAAAAATTGTGCTCAAATTGTTGGGTATAATTTTCTTTGAACCTAAATAATCAAATATCCTATTT
AAAATTGAAAATTTCGTCCTTTTTATTTGTAAATTACATGAATTAACCCATATTTTGCAAAACAT
TTTCAACAAAATAAAATGTATATCA
Found at i:9680630 original size:107 final size:109
Alignment explanation
Indices: 9680492--9680693 Score: 304
Period size: 108 Copynumber: 1.9 Consensus size: 109
9680482 AAAATTAAGG
* * *
9680492 CAATGTTTTTTTATTTTAGGGAATTCGAAAAATTGTGC-CATAACTTGTT-GAGTAT-GATTTTT
1 CAATGTTCTGTTATTTTAGGGAATTCGAAAAATTGTGCTC-TAACATGTTGGA-TATGGATTTTT
*
9680554 TTTGAACCTAAATAATTGAGCATCCTATTTAAAATCAATAAGTGCT
64 TTTGAACCTAAATAATTGAACATCCTATTTAAAATCAATAAGTGCT
* *
9680600 CAATGTTCTGTTA-TTTAGGGGATTCGAAAAATTGTGCTCTAACATGTTGGATATGGTTTTTTTT
1 CAATGTTCTGTTATTTTAGGGAATTCGAAAAATTGTGCTCTAACATGTTGGATATGGATTTTTTT
9680664 TGAACCTAAATAATTGAACATCCTATTTAA
66 TGAACCTAAATAATTGAACATCCTATTTAA
9680694 CATCTCATTC
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
107 34 0.40
108 51 0.60
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (109 bp):
CAATGTTCTGTTATTTTAGGGAATTCGAAAAATTGTGCTCTAACATGTTGGATATGGATTTTTTT
TGAACCTAAATAATTGAACATCCTATTTAAAATCAATAAGTGCT
Found at i:9688308 original size:25 final size:25
Alignment explanation
Indices: 9688254--9688320 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
9688244 TTTTTATATG
* *
9688254 CTTTATTTATTTGTTATTATTTTAT
1 CTTTATTTATATGTTATTATTTAAT
* *
9688279 TTTTATTT-TATGTTTTCTATTTAAT
1 CTTTATTTATATGTTAT-TATTTAAT
*
9688304 CTTTAATTAT-TGTTATT
1 CTTTATTTATATGTTATT
9688321 TTTTTGTGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
24 7 0.21
25 25 0.76
26 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (25 bp):
CTTTATTTATATGTTATTATTTAAT
Found at i:9688429 original size:4 final size:4
Alignment explanation
Indices: 9688390--9688497 Score: 62
Period size: 4 Copynumber: 26.0 Consensus size: 4
9688380 ACATGCTTGC
* *
9688390 ATTT ATTT AATTT -TATT ATTT -TTT ATGT ATTTT ATTT ATTT GTTAT
1 ATTT ATTT -ATTT AT-TT ATTT ATTT ATTT A-TTT ATTT ATTT ATT-T
* * * *
9688436 TTTT ATGCT ATTT ATAT ATTT -TTT AATTTT ATTT ATTT ATTG ATATT
1 ATTT AT-TT ATTT ATTT ATTT ATTT -A-TTT ATTT ATTT ATTT AT-TT
9688483 -TTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT
9688498 GTATGTCATA
Statistics
Matches: 81, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
3 9 0.11
4 53 0.65
5 16 0.20
6 3 0.04
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:9688441 original size:17 final size:16
Alignment explanation
Indices: 9688390--9688495 Score: 71
Period size: 16 Copynumber: 6.6 Consensus size: 16
9688380 ACATGCTTGC
9688390 ATTTATTTA-ATTTTATT
1 ATTTATTTATA-TTT-TT
*
9688407 ATTT-TTTATGTATTTT
1 ATTTATTTATAT-TTTT
*
9688423 ATTTATTTGTTATTTTT
1 ATTTATTT-ATATTTTT
*
9688440 ATGCTATTTATATATTTT
1 AT-TTATTTATAT-TTTT
*
9688458 -TTAATTT-TA--TTT
1 ATTTATTTATATTTTT
*
9688470 ATTTATTGATATTTTT
1 ATTTATTTATATTTTT
9688486 ATTTATTTAT
1 ATTTATTTAT
9688496 TTGTATGTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
12 3 0.04
13 5 0.07
14 2 0.03
15 2 0.03
16 27 0.39
17 19 0.28
18 11 0.16
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.71
Consensus pattern (16 bp):
ATTTATTTATATTTTT
Found at i:9688449 original size:26 final size:24
Alignment explanation
Indices: 9688390--9688489 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 24
9688380 ACATGCTTGC
9688390 ATTTATTTAATTTTATTATTTTTTATGT
1 ATTTATTT-A-TTT-TTA-TTTTTATGT
9688418 ATTTTATTTATTTGTTATTTTTATGCT
1 A-TTTATTTATTT-TTATTTTTATG-T
* * *
9688445 ATTTATATATTTTTTAATTTTATTT
1 ATTTATTTA-TTTTTATTTTTATGT
9688470 ATTTATTGATATTTTTATTT
1 ATTTATT--TATTTTTATTT
9688490 ATTTATTTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.11
26 32 0.52
27 13 0.21
28 2 0.03
29 7 0.11
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (24 bp):
ATTTATTTATTTTTATTTTTATGT
Found at i:9688656 original size:17 final size:17
Alignment explanation
Indices: 9688634--9688685 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
9688624 ATTTTTTACC
9688634 ATTATTACTATGATTAT
1 ATTATTACTATGATTAT
9688651 ATTATTA-T-T--TTAT
1 ATTATTACTATGATTAT
*
9688664 -TTATTACGATGATTAT
1 ATTATTACTATGATTAT
*
9688680 GTTATT
1 ATTATT
9688686 TTATATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 1 0.03
15 1 0.03
16 5 0.17
17 12 0.41
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.58
Consensus pattern (17 bp):
ATTATTACTATGATTAT
Found at i:9699510 original size:33 final size:33
Alignment explanation
Indices: 9699473--9699547 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
9699463 TCTCAAATTG
9699473 TCGAAGCATTTCCAGATGAGCAATTATTCTTTA
1 TCGAAGCATTTCCAGATGAGCAATTATTCTTTA
*
9699506 TCGAAGCATTTCCAGATGAGCAATTATTCTTTG
1 TCGAAGCATTTCCAGATGAGCAATTATTCTTTA
*
9699539 TCGATGCAT
1 TCGAAGCAT
9699548 CACCTTGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (33 bp):
TCGAAGCATTTCCAGATGAGCAATTATTCTTTA
Found at i:9703537 original size:22 final size:22
Alignment explanation
Indices: 9703493--9703537 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9703483 TCTGCTATTT
* *
9703493 TTTAATGAATGATTGGAATTGC
1 TTTAATGAATGAATGGAAATGC
9703515 TTTAAT-AATGAATGGATAATGC
1 TTTAATGAATGAATGGA-AATGC
9703537 T
1 T
9703538 GATGTTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (22 bp):
TTTAATGAATGAATGGAAATGC
Found at i:9706791 original size:67 final size:70
Alignment explanation
Indices: 9706701--9706838 Score: 194
Period size: 70 Copynumber: 2.0 Consensus size: 70
9706691 ACTACAGAAA
** * *
9706701 TAACATAATGGTTTTACCTTTTAAC-TTA-ATGAG-TAAACATTTATGAAAACGACGTAGTTTTG
1 TAACATAATGGTTTTACCTTTTAACTTTAGAAAAGATAAACATTTATCAAAACGACATAGTTTTG
9706763 CCTTT
66 CCTTT
*
9706768 TAACTTAATGGTTTTGA-CTTTTAACTTTAGAAAAGATAAACATTTATCAAAACGACATAGTTTT
1 TAACATAATGGTTTT-ACCTTTTAACTTTAGAAAAGATAAACATTTATCAAAACGACATAGTTTT
9706832 GCCTTT
65 GCCTTT
9706838 T
1 T
9706839 CTTATTCGGA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
67 22 0.35
68 4 0.06
69 3 0.05
70 33 0.53
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (70 bp):
TAACATAATGGTTTTACCTTTTAACTTTAGAAAAGATAAACATTTATCAAAACGACATAGTTTTG
CCTTT
Found at i:9710660 original size:31 final size:31
Alignment explanation
Indices: 9710625--9710685 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
9710615 TTTAAGTCCA
*
9710625 TTAAAAATTAGTAAAAA-AA-ATTTTGGGCCCT
1 TTAAAAATT-G-AAAAACAATATTTTAGGCCCT
9710656 TTAAAAATTGAAAAACAATATTTTAGGCCC
1 TTAAAAATTGAAAAACAATATTTTAGGCCC
9710686 CTTTCAGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 5 0.19
30 3 0.11
31 19 0.70
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (31 bp):
TTAAAAATTGAAAAACAATATTTTAGGCCCT
Found at i:9717486 original size:18 final size:20
Alignment explanation
Indices: 9717449--9717488 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
9717439 TTTTAACTCT
9717449 AATAAAATAAAAATCCTAAA
1 AATAAAATAAAAATCCTAAA
9717469 AATAAAAT-AAAA-CCTAAA
1 AATAAAATAAAAATCCTAAA
9717487 AA
1 AA
9717489 CCCTAAGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (20 bp):
AATAAAATAAAAATCCTAAA
Found at i:9728633 original size:17 final size:18
Alignment explanation
Indices: 9728613--9728651 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
9728603 TAAATTATTT
9728613 AAAAAATTAAAA-AATAA
1 AAAAAATTAAAATAATAA
*
9728630 AAAATATTAAAATTAATAA
1 AAAAAATTAAAA-TAATAA
9728649 AAA
1 AAA
9728652 TCAATTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAATTAAAATAATAA
Found at i:9731304 original size:22 final size:22
Alignment explanation
Indices: 9731279--9731328 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
9731269 GTGTGTCTCA
*
9731279 AGACATTTGCTC-ATATGTCTTG
1 AGACATTTACTCGA-ATGTCTTG
*
9731301 AGACAATTACTCGAATGTCTTG
1 AGACATTTACTCGAATGTCTTG
9731323 AGACAT
1 AGACAT
9731329 GACTCCCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (22 bp):
AGACATTTACTCGAATGTCTTG
Found at i:9733047 original size:24 final size:24
Alignment explanation
Indices: 9733015--9733065 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
9733005 CAATTTTAAC
*
9733015 AAAATTCATAGTTGGATGACAAAA
1 AAAAATCATAGTTGGATGACAAAA
* * *
9733039 AAAAATCATATTTGGGTGACTAAA
1 AAAAATCATAGTTGGATGACAAAA
9733063 AAA
1 AAA
9733066 GAAAATGACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (24 bp):
AAAAATCATAGTTGGATGACAAAA
Found at i:9734465 original size:12 final size:13
Alignment explanation
Indices: 9734448--9734478 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
9734438 GATTTTCTCA
9734448 AAATGAAAAT-AG
1 AAATGAAAATGAG
9734460 AAATGAAAATGAG
1 AAATGAAAATGAG
9734473 AAATGA
1 AAATGA
9734479 TTCATTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (13 bp):
AAATGAAAATGAG
Found at i:9737517 original size:6 final size:6
Alignment explanation
Indices: 9737508--9737544 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
9737498 GGTGAAAATA
9737508 AAAAAG AAAAAG AAAAAG -AAAAG -AAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
9737545 TGTAGATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:9737529 original size:11 final size:11
Alignment explanation
Indices: 9737509--9737544 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
9737499 GTGAAAATAA
9737509 AAAAGAAAAAG
1 AAAAGAAAAAG
9737520 AAAA-AGAAAAG
1 AAAAGA-AAAAG
9737531 AAAAGAAAAAG
1 AAAAGAAAAAG
9737542 AAA
1 AAA
9737545 TGTAGATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:9740580 original size:39 final size:40
Alignment explanation
Indices: 9740526--9740606 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
9740516 GTTCTAATCA
9740526 TTACCAATGTCAC-AAAAGGCTAAAAGATGAAAAAAGTAG
1 TTACCAATGTCACAAAAAGGCTAAAAGATGAAAAAAGTAG
9740565 TTACCAATGTCACAAAAAGGCTAAAAGATGAAAAAAGTAG
1 TTACCAATGTCACAAAAAGGCTAAAAGATGAAAAAAGTAG
9740605 TT
1 TT
9740607 GACATACTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 13 0.32
40 28 0.68
ACGTcount: A:0.51, C:0.12, G:0.17, T:0.20
Consensus pattern (40 bp):
TTACCAATGTCACAAAAAGGCTAAAAGATGAAAAAAGTAG
Found at i:9741251 original size:27 final size:27
Alignment explanation
Indices: 9741194--9741243 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
9741184 CAATAGAAGT
*
9741194 TTAAAATATGTTATTTTTATAAAATTA
1 TTAAAATATGTTATTTTAATAAAATTA
*
9741221 TTAAAAT-TTTTA-TTTAATAAAAT
1 TTAAAATATGTTATTTTAATAAAAT
9741244 CATATTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 4 0.19
27 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTAAAATATGTTATTTTAATAAAATTA
Found at i:9752572 original size:22 final size:21
Alignment explanation
Indices: 9752541--9752590 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
9752531 AAATATACAT
*
9752541 AAAAAATCATTCAAAACTTCAA
1 AAAAAATCATACAAAACTT-AA
* *
9752563 AAATAATCATACAAAATTTAA
1 AAAAAATCATACAAAACTTAA
9752584 AAAAAAT
1 AAAAAAT
9752591 ATATATTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATCATACAAAACTTAA
Found at i:9753780 original size:22 final size:23
Alignment explanation
Indices: 9753738--9753782 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
9753728 TATGTTTTTG
9753738 AAAATAAAGGACTAAATTTAAAAA
1 AAAATAAA-GACTAAATTTAAAAA
9753762 AAAATAAA-ACTGAAA-TTAAAA
1 AAAATAAAGACT-AAATTTAAAA
9753783 TTAAAATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (23 bp):
AAAATAAAGACTAAATTTAAAAA
Found at i:9766576 original size:21 final size:21
Alignment explanation
Indices: 9766550--9766603 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
9766540 GGAGTTTTTA
*
9766550 GTTTCGGTAGAAGTAAGACTT
1 GTTTCGGTAGAAGTAACACTT
*
9766571 GTTTCGGTAGAAGTTACACTT
1 GTTTCGGTAGAAGTAACACTT
9766592 GTATT-GGTAGAA
1 GT-TTCGGTAGAA
9766604 CTTTCTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (21 bp):
GTTTCGGTAGAAGTAACACTT
Found at i:9769795 original size:13 final size:13
Alignment explanation
Indices: 9769771--9769812 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
9769761 ACCCAAATTC
*
9769771 ATTTTAATTTTTA
1 ATTTTAATTTTCA
9769784 ATTTTTAATTTTCA
1 A-TTTTAATTTTCA
*
9769798 AGTTTAA-TTTCA
1 ATTTTAATTTTCA
9769810 ATT
1 ATT
9769813 GAACAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 12 0.48
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (13 bp):
ATTTTAATTTTCA
Found at i:9772165 original size:20 final size:20
Alignment explanation
Indices: 9772132--9772175 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9772122 TGCATCAAGA
*
9772132 TTTATTTCACTTTA-TTTAT
1 TTTATTTCACTTTAGTTTAG
*
9772151 TTTATTTTCATTTTAGTTTAG
1 TTTA-TTTCACTTTAGTTTAG
9772172 TTTA
1 TTTA
9772176 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTATTTCACTTTAGTTTAG
Found at i:9775039 original size:5 final size:5
Alignment explanation
Indices: 9775029--9775055 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9775019 GCATTCCTCG
9775029 CCCAA CCCAA CCCAA CCCAA CCCAA CC
1 CCCAA CCCAA CCCAA CCCAA CCCAA CC
9775056 TTCCCTTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.63, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCAA
Found at i:9775062 original size:5 final size:5
Alignment explanation
Indices: 9775054--9775078 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9775044 CCCAACCCAA
9775054 CCTTC CCTTC CCTTC CCTTC CCTTC
1 CCTTC CCTTC CCTTC CCTTC CCTTC
9775079 AAAAGGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CCTTC
Found at i:9782022 original size:12 final size:12
Alignment explanation
Indices: 9782005--9782034 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
9781995 ATGGTGGTCA
9782005 GCGGCGTTGCTG
1 GCGGCGTTGCTG
*
9782017 GCGGCGTTGCTT
1 GCGGCGTTGCTG
9782029 GCGGCG
1 GCGGCG
9782035 GTGGATGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.50, T:0.23
Consensus pattern (12 bp):
GCGGCGTTGCTG
Found at i:9782398 original size:17 final size:18
Alignment explanation
Indices: 9782372--9782406 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9782362 GGATGGTGAA
9782372 TTTAAAGGTTA-TGGGTT
1 TTTAAAGGTTATTGGGTT
*
9782389 TTTAATGGTTATTGGGTT
1 TTTAAAGGTTATTGGGTT
9782407 GATTTAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (18 bp):
TTTAAAGGTTATTGGGTT
Found at i:9796166 original size:9 final size:9
Alignment explanation
Indices: 9796152--9796225 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 9
9796142 TTTATAGAAT
9796152 TTTTTAAAA
1 TTTTTAAAA
9796161 TTTTTAAAA
1 TTTTTAAAA
9796170 TTTTTTTAAAA
1 --TTTTTAAAA
*
9796181 --TAT-AAA
1 TTTTTAAAA
*
9796187 TTTTT-AAT
1 TTTTTAAAA
9796195 TTTTTATAAA
1 TTTTTA-AAA
9796205 TATTTT-AAA
1 T-TTTTAAAA
9796214 TTTTTGAAAA
1 TTTTT-AAAA
9796224 TT
1 TT
9796226 ATTTTGAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
6 3 0.06
7 2 0.04
8 13 0.25
9 13 0.25
10 8 0.15
11 13 0.25
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:9796189 original size:26 final size:28
Alignment explanation
Indices: 9796158--9796230 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
9796148 GAATTTTTTA
9796158 AAATTTTTAAAATTTTTTTAAA-A-TAT
1 AAATTTTTAAAATTTTTTTAAATATTAT
*
9796184 AAATTTTT--AATTTTTTATAAATATTTT
1 AAATTTTTAAAATTTTTT-TAAATATTAT
*
9796211 AAATTTTTGAAAATTATTTT
1 AAATTTTT-AAAATTTTTTT
9796231 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 8 0.21
25 4 0.10
26 9 0.23
27 10 0.26
29 1 0.03
30 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (28 bp):
AAATTTTTAAAATTTTTTTAAATATTAT
Found at i:9796215 original size:20 final size:20
Alignment explanation
Indices: 9796102--9796239 Score: 72
Period size: 20 Copynumber: 6.8 Consensus size: 20
9796092 TCAAAATTAT
*
9796102 TATTTTAGAAATTTTT-TAAA
1 TATTTTA-AATTTTTTATAAA
* **
9796122 -ATTTTAACTTTTTT-TATG
1 TATTTTAAATTTTTTATAAA
*
9796140 TCTTTATAGAATTTTTTA-AAA
1 TATTT-TA-AATTTTTTATAAA
*
9796161 T-TTTTAAAATTTTTTTAAAATA
1 TATTTT-AAA-TTTTTTATAA-A
*
9796183 TAAATTTTTAATTTTTTATAAA
1 T--ATTTTAAATTTTTTATAAA
*
9796205 TATTTTAAATTTTTGA-AAA
1 TATTTTAAATTTTTTATAAA
*
9796224 TTATTTTGAATTTTTT
1 -TATTTTAAATTTTTT
9796240 TTTTGTAATT
Statistics
Matches: 92, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
18 8 0.09
19 15 0.16
20 39 0.42
21 11 0.12
22 4 0.04
23 9 0.10
24 2 0.02
25 4 0.04
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (20 bp):
TATTTTAAATTTTTTATAAA
Found at i:9797770 original size:20 final size:20
Alignment explanation
Indices: 9797745--9797782 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9797735 AATAATATTA
9797745 TAATATATAAA-TATTATACT
1 TAATATA-AAAGTATTATACT
9797765 TAATATAAAAGTATTATA
1 TAATATAAAAGTATTATA
9797783 ATTAGTCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
TAATATAAAAGTATTATACT
Found at i:9797772 original size:18 final size:18
Alignment explanation
Indices: 9797727--9797773 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
9797717 AATTAACTAA
*
9797727 ACTTAATAAATAATATTAT
1 ACTTAATATA-AATATTAT
*
9797746 A-AT-ATATAAATATTAT
1 ACTTAATATAAATATTAT
9797762 ACTTAATATAAA
1 ACTTAATATAAA
9797774 AGTATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
18 8 0.35
19 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
ACTTAATATAAATATTAT
Found at i:9801640 original size:9 final size:9
Alignment explanation
Indices: 9801626--9801665 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
9801616 GTTTAATTAT
*
9801626 ATAATTTAA
1 ATAATTCAA
*
9801635 ATAATTCGA
1 ATAATTCAA
*
9801644 ATAATTTAA
1 ATAATTCAA
9801653 ATAATTCAA
1 ATAATTCAA
9801662 ATAA
1 ATAA
9801666 CATATTACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (9 bp):
ATAATTCAA
Found at i:9801647 original size:18 final size:18
Alignment explanation
Indices: 9801626--9801665 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
9801616 GTTTAATTAT
*
9801626 ATAATTTAAATAATTCGA
1 ATAATTTAAATAATTCAA
9801644 ATAATTTAAATAATTCAA
1 ATAATTTAAATAATTCAA
9801662 ATAA
1 ATAA
9801666 CATATTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAATTTAAATAATTCAA
Found at i:9801749 original size:19 final size:19
Alignment explanation
Indices: 9801713--9801777 Score: 87
Period size: 19 Copynumber: 3.3 Consensus size: 19
9801703 AAAATTAAAA
9801713 TAAAATAACTTTTAAAAATT
1 TAAAATAA-TTTTAAAAATT
*
9801733 TAAAATAATTTTTAAAATT
1 TAAAATAATTTTAAAAATT
9801752 TAAAAT-ATTTATAAAAATT
1 TAAAATAATTT-TAAAAATT
9801771 TCAAAAT
1 T-AAAAT
9801778 TTATATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.10
19 24 0.59
20 13 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATAATTTTAAAAATT
Found at i:9801776 original size:27 final size:27
Alignment explanation
Indices: 9801723--9801780 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
9801713 TAAAATAACT
*
9801723 TTTAAAAATTTAAAATAATTTTTAAAA
1 TTTAAAAATTTAAAATAATTTTCAAAA
9801750 TTTAAAATATTTATAAA-AA-TTTCAAAA
1 TTTAAAA-ATTTA-AAATAATTTTCAAAA
9801777 TTTA
1 TTTA
9801781 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 18 0.64
28 7 0.25
29 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTAAAAATTTAAAATAATTTTCAAAA
Found at i:9803256 original size:25 final size:27
Alignment explanation
Indices: 9803200--9803259 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
9803190 AAATAATTTT
*
9803200 TAAATTTTAAAATATTTATAAAAATTC
1 TAAATTTTAAAATATTTATAAAAATTA
* * *
9803227 CAAATTTT-ATAT-TTTTTAAAAATTA
1 TAAATTTTAAAATATTTATAAAAATTA
9803252 TAAATTTT
1 TAAATTTT
9803260 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 18 0.64
26 3 0.11
27 7 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
TAAATTTTAAAATATTTATAAAAATTA
Found at i:9806164 original size:52 final size:52
Alignment explanation
Indices: 9806080--9806251 Score: 263
Period size: 52 Copynumber: 3.3 Consensus size: 52
9806070 GTAAAAAAAG
* * *
9806080 GGTCCAATGACTATGTGTCATCGTGAGTATATGAATATTTTACAGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGA
* **
9806132 GGTCTGATGACTAAATGTCATCGTGAGTATATGAATCTTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGA
* *
9806184 GGTCCGATGACTATGTGTCATCGTGATTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGA
*
9806236 GGTCCAATGACTATGT
1 GGTCCGATGACTATGT
9806252 TATACATTAA
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 108 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGA
Found at i:9811337 original size:604 final size:604
Alignment explanation
Indices: 9810180--9811993 Score: 3362
Period size: 604 Copynumber: 3.0 Consensus size: 604
9810170 CTCCTGAAAG
*
9810180 ATTTCTGAGA-TTTTGCCTAAATCCAATAAGGGAATAAATTCAAGATATAAAATAAAAAATATAT
1 ATTTCTGAGATTTTTGCCTAAATCCGATAAGGGAATAAATTCAAGATATAAAATAAAAAATATAT
9810244 ATTTTATATAGAAGACTTGTTCAATAAGTTAAAAGGATGTAACAATGTATTTGAAAATTAATAAA
66 ATTTTATATAGAAGACTTGTTCAATAAGTTAAAAGGATGTAACAATGTATTTGAAAATTAATAAA
9810309 GATTCAGTTATTCAGTTCTAGTTAAAGGTATGAGATGCTGAAGA-TTTTTTTGAACTTGAGATAA
131 GATTCAGTTATTCAGTTCTAGTTAAAGGTATGAGATGCTGAAGATTTTTTTTGAACTTGAGATAA
*
9810373 TCATTAAGAATTCTAATAATATTGTCTAGATTAACTAATGTCTCTGTTGAATTATGAATATGATG
196 TCATTAAGAATTCTAGTAATATTGTCTAGATTAACTAATGTCTCTGTTGAATTATGAATATGATG
*
9810438 AATCGGATTGTTCAATCTTATCTAAATATTTAGATACAGTCATAATTATGATTATTGATGATATT
261 AATCGGATTGTTCAATCTTATCTAGATATTTAGATACAGTCATAATTATGATTATTGATGATATT
* * *
9810503 CTGATATGCTACAAATAGAATCTGTGTATGTGTAATATGTGATAAATGTATTATAGACTATGTGT
326 CTGATATACTACAAATAGAATCTGTGTATGCGTAATATGTGAGAAATGTATTATAGACTATGTGT
9810568 GAGAAATAATCTACGTGAAAACTATCAACGGTGAGTTTTGGTTTAGTGAGGTTGGTTTTCTTGGT
391 GAGAAATAATCTACGTGAAAACTATCAACGGTGAGTTTTGGTTTAGTGAGGTTGGTTTTCTTGGT
*
9810633 TATGTAAATTTGAGAGATGAATTTGAATAGGTTTGGGTAAAAAGATTTTTCTATTGTTATATGAA
456 TATGTAAATTTGAGAGATGAATTTGAATAGGTTCGGGTAAAAAGATTTTTCTATTGTTATATGAA
* *
9810698 AACTTCAAAAACATCTTTGGAAATTTTTGTTTCGATCTATCTTGAATTTGGGAAAGAAATTGAAC
521 AACTTCAAAAACATCTCTGGAAATTTTTGTTTCGATCTATCTTGAATCTGGGAAAGAAATTGAAC
* *
9810763 ATCAAGTACCATCTAAATT
586 ATCAAGTATCGTCTAAATT
9810782 ATTTCTGAGATTTTTGCCTAAATCCGATAAGGGAATAAATTCAAGATATAAAATAAAAAATATAT
1 ATTTCTGAGATTTTTGCCTAAATCCGATAAGGGAATAAATTCAAGATATAAAATAAAAAATATAT
* *
9810847 ATTTTATATAGAAGACTTGTTCAATAAGTTAAAAGGATGTAACAATATCTTTGAAAATTAATAAA
66 ATTTTATATAGAAGACTTGTTCAATAAGTTAAAAGGATGTAACAATGTATTTGAAAATTAATAAA
9810912 GATTCAGTTATTCAGTTCTAGTTAAAGGTATGAGATGCTGAAGATTTTTTTTGAACTTGAGATAA
131 GATTCAGTTATTCAGTTCTAGTTAAAGGTATGAGATGCTGAAGATTTTTTTTGAACTTGAGATAA
*
9810977 TCATTAAGAATTCTAGTAATATTGTCTAGATTAACTAATGTCTCTGTTGAATTATAAATATGATG
196 TCATTAAGAATTCTAGTAATATTGTCTAGATTAACTAATGTCTCTGTTGAATTATGAATATGATG
*
9811042 AATCGGATTGTTCAATCTTATTTAGATATTTAGATACAGTCATAATTATGATTATTGATGATATT
261 AATCGGATTGTTCAATCTTATCTAGATATTTAGATACAGTCATAATTATGATTATTGATGATATT
9811107 CTGATATACTACAAATAGAATCTGTGTATGCGTAATATGTGAGAAATGTATTATAGACTATGTGT
326 CTGATATACTACAAATAGAATCTGTGTATGCGTAATATGTGAGAAATGTATTATAGACTATGTGT
*
9811172 GAGAAATAATCTACGTGAAAACTATCAACGGTGAGTTTTGGTTTAGTAAGGTTGGTTTTCTTGGT
391 GAGAAATAATCTACGTGAAAACTATCAACGGTGAGTTTTGGTTTAGTGAGGTTGGTTTTCTTGGT
* * *
9811237 TATGTAATTTTGAGAGATGAATTTGAATAGGTTCGAGTAAAAAGATTTTTCTATTGTTATATAAA
456 TATGTAAATTTGAGAGATGAATTTGAATAGGTTCGGGTAAAAAGATTTTTCTATTGTTATATGAA
*
9811302 AACTTCAAAAACATCTCTGGAAATTTTTGTTTCGATCTATCTTGAATCTAGGAAAGAAATTGAAC
521 AACTTCAAAAACATCTCTGGAAATTTTTGTTTCGATCTATCTTGAATCTGGGAAAGAAATTGAAC
9811367 ATCAAGTATCGTCTAAATT
586 ATCAAGTATCGTCTAAATT
9811386 ATTTCTGAGATTTTTGCCTAAATCCGATAAGGGAATAAATTCAAGATATAAAATAAAAAATATAT
1 ATTTCTGAGATTTTTGCCTAAATCCGATAAGGGAATAAATTCAAGATATAAAATAAAAAATATAT
*
9811451 ATTTTATATAGAAGACTTGTTCAATAAGTTAAAAGGATGTAATAATGTATTTGAAAATTAATAAA
66 ATTTTATATAGAAGACTTGTTCAATAAGTTAAAAGGATGTAACAATGTATTTGAAAATTAATAAA
9811516 GATTCAGTTATTCAGTTCTAGTTAAAGGTATGAGATGCTGAAGATTTTTTTTTGAACTTGAGATA
131 GATTCAGTTATTCAGTTCTAGTTAAAGGTATGAGATGCTGAAGA-TTTTTTTTGAACTTGAGATA
9811581 ATCATTAAGAATTCTAGTAATATTGTCTAGATTAACTAATGTCTCTGTTGAATTATGAATATGAT
195 ATCATTAAGAATTCTAGTAATATTGTCTAGATTAACTAATGTCTCTGTTGAATTATGAATATGAT
* *
9811646 GAATCAGATTGTTCAATCTTATCTAGATATTTAGATACAGTCATAATTATGATTATTGATGATGT
260 GAATCGGATTGTTCAATCTTATCTAGATATTTAGATACAGTCATAATTATGATTATTGATGATAT
*
9811711 TCTGATATACTACAAATAGAATCTGTGTATGCGTAATATGTGTGAAATGTATTATAGACTATGTG
325 TCTGATATACTACAAATAGAATCTGTGTATGCGTAATATGTGAGAAATGTATTATAGACTATGTG
9811776 TGAGAAATAATCTACGTGAAAACTATCAACGGTGAGTTTTGGTTTAGTGAGGTTGGTTTTCTTGG
390 TGAGAAATAATCTACGTGAAAACTATCAACGGTGAGTTTTGGTTTAGTGAGGTTGGTTTTCTTGG
*
9811841 TTATGTAAATTTGAGAGATAAATTTGAATAGGTTCGGGTAAAAAGATTTTTCTATTGTTATATGA
455 TTATGTAAATTTGAGAGATGAATTTGAATAGGTTCGGGTAAAAAGATTTTTCTATTGTTATATGA
* *
9811906 AAACTTCAAAAACATATCTGGAAATTTCTGTTTCGATCTATCTTGAATCTGGGAAAGAAATTGAA
520 AAACTTCAAAAACATCTCTGGAAATTTTTGTTTCGATCTATCTTGAATCTGGGAAAGAAATTGAA
9811971 CATCAAGTATCGTCTAAATT
585 CATCAAGTATCGTCTAAATT
9811991 ATT
1 ATT
9811994 ACTGCTAATT
Statistics
Matches: 1173, Mismatches: 36, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
602 10 0.01
603 160 0.14
604 583 0.50
605 420 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (604 bp):
ATTTCTGAGATTTTTGCCTAAATCCGATAAGGGAATAAATTCAAGATATAAAATAAAAAATATAT
ATTTTATATAGAAGACTTGTTCAATAAGTTAAAAGGATGTAACAATGTATTTGAAAATTAATAAA
GATTCAGTTATTCAGTTCTAGTTAAAGGTATGAGATGCTGAAGATTTTTTTTGAACTTGAGATAA
TCATTAAGAATTCTAGTAATATTGTCTAGATTAACTAATGTCTCTGTTGAATTATGAATATGATG
AATCGGATTGTTCAATCTTATCTAGATATTTAGATACAGTCATAATTATGATTATTGATGATATT
CTGATATACTACAAATAGAATCTGTGTATGCGTAATATGTGAGAAATGTATTATAGACTATGTGT
GAGAAATAATCTACGTGAAAACTATCAACGGTGAGTTTTGGTTTAGTGAGGTTGGTTTTCTTGGT
TATGTAAATTTGAGAGATGAATTTGAATAGGTTCGGGTAAAAAGATTTTTCTATTGTTATATGAA
AACTTCAAAAACATCTCTGGAAATTTTTGTTTCGATCTATCTTGAATCTGGGAAAGAAATTGAAC
ATCAAGTATCGTCTAAATT
Found at i:9814072 original size:52 final size:52
Alignment explanation
Indices: 9814005--9814190 Score: 257
Period size: 52 Copynumber: 3.6 Consensus size: 52
9813995 AAAAAAAAAG
*
9814005 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATACTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * * * *
9814057 GCTCCGATGATTATGTGTCATTGTGATTATATGAATCCTTTAAGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* ** *
9814109 GGTCCGATGACTATGTGTCATCGTGAGTATATGGATCCTATTACATATT-TAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACGGATTATGA
*
9814161 GGTCCGATGACTTTGTGTCATCGTGAGTAT
1 GGTCCGATGACTATGTGTCATCGTGAGTAT
9814191 TAAATGGAAA
Statistics
Matches: 117, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 111 0.95
53 6 0.05
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:9816597 original size:42 final size:42
Alignment explanation
Indices: 9816551--9816635 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
9816541 ATTATCAGAA
* *
9816551 TGTAAGATTACTTAGCATATTAGTGAGTATTATTATATTATT
1 TGTAAGATTACTTAGCATATTAGTAAGTATTATTACATTATT
* *
9816593 TGTAAGATTACTTAGTATATTATTAAGTATTATTACATTATT
1 TGTAAGATTACTTAGCATATTAGTAAGTATTATTACATTATT
9816635 T
1 T
9816636 TGTTTGATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (42 bp):
TGTAAGATTACTTAGCATATTAGTAAGTATTATTACATTATT
Found at i:9816619 original size:21 final size:22
Alignment explanation
Indices: 9816553--9816624 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
9816543 TATCAGAATG
* *
9816553 TAAG-ATTACTTAGCATATTAG
1 TAAGTATTACTTAGTATATTAT
*
9816574 TGAGTATTA-TTA-TATTATT-T
1 TAAGTATTACTTAGTA-TATTAT
9816594 GTAAG-ATTACTTAGTATATTAT
1 -TAAGTATTACTTAGTATATTAT
9816616 TAAGTATTA
1 TAAGTATTA
9816625 TTACATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
20 5 0.12
21 24 0.60
22 11 0.28
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.47
Consensus pattern (22 bp):
TAAGTATTACTTAGTATATTAT
Found at i:9816634 original size:21 final size:20
Alignment explanation
Indices: 9816576--9816635 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
9816566 CATATTAGTG
9816576 AGTATTATTATATTATTTGTA
1 AGTATTATTA-ATTATTTGTA
*
9816597 AG-ATTACTTAGTATATTAT-TA
1 AGTATTA-TTAAT-TATT-TGTA
9816618 AGTATTATTACATTATTT
1 AGTATTATTA-ATTATTT
9816636 TGTTTGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (20 bp):
AGTATTATTAATTATTTGTA
Found at i:9819169 original size:2 final size:2
Alignment explanation
Indices: 9819162--9819201 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9819152 TTATATCCTC
9819162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9819202 GTTTAGATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9820452 original size:22 final size:22
Alignment explanation
Indices: 9820426--9820467 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9820416 GAGTCCAGGA
*
9820426 TTGAATTGTTTCCTTACGGATT
1 TTGAATTGATTCCTTACGGATT
9820448 TTGAATTGATTCCTTACGGA
1 TTGAATTGATTCCTTACGGA
9820468 CAGTCTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.45
Consensus pattern (22 bp):
TTGAATTGATTCCTTACGGATT
Found at i:9827122 original size:30 final size:30
Alignment explanation
Indices: 9827087--9827209 Score: 108
Period size: 30 Copynumber: 4.1 Consensus size: 30
9827077 ATTTTATTTT
* *
9827087 AAAATTATGTTTTAGCCCCTAAACTTTCCA
1 AAAATTATATTTTAGCCCCTAAACTTTCTA
* * * *
9827117 AAAATTCAAATTTGA-TCCCTAAACTTTTTA
1 AAAATT-ATATTTTAGCCCCTAAACTTTCTA
* *
9827147 AAAATT-TCATTTTAGCCCCTTAATTTTCTA
1 AAAATTAT-ATTTTAGCCCCTAAACTTTCTA
* *
9827177 AAAATTACATTTT-GACCCTCAAACTTTCTA
1 AAAATTATATTTTAGCCCCT-AAACTTTCTA
9827207 AAA
1 AAA
9827210 TTTTGATTTT
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
29 10 0.14
30 57 0.79
31 5 0.07
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAATTATATTTTAGCCCCTAAACTTTCTA
Found at i:9827180 original size:60 final size:60
Alignment explanation
Indices: 9827096--9827219 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
9827086 TAAAATTATG
*
9827096 TTTTAGCCCCTAAACTTTCCAAAAATT-CAAATTTGATCCCT-AAACTTTTTAAAAATTTCA
1 TTTTAGCCCCTAAACTTTCCAAAAATTAC-AATTTGA-CCCTCAAACTTTCTAAAAATTTCA
* * * * * *
9827156 TTTTAGCCCCTTAATTTTCTAAAAATTACATTTTGACCCTCAAACTTTCTAAAATTTTGA
1 TTTTAGCCCCTAAACTTTCCAAAAATTACAATTTGACCCTCAAACTTTCTAAAAATTTCA
9827216 TTTT
1 TTTT
9827220 GACGTATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 4 0.07
60 50 0.91
61 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (60 bp):
TTTTAGCCCCTAAACTTTCCAAAAATTACAATTTGACCCTCAAACTTTCTAAAAATTTCA
Found at i:9827219 original size:30 final size:29
Alignment explanation
Indices: 9827103--9827222 Score: 116
Period size: 30 Copynumber: 4.0 Consensus size: 29
9827093 ATGTTTTAGC
* *
9827103 CCCTAAACTTTCCAAAAA-TTCAAATTTGA
1 CCCTAAACTTTCTAAAAATTTC-ATTTTGA
* *
9827132 TCCCTAAACTTTTTAAAAATTTCATTTTAGC
1 -CCCTAAACTTTCTAAAAATTTCATTTT-GA
* * *
9827163 CCCTTAATTTTCTAAAAATTACATTTTGA
1 CCCTAAACTTTCTAAAAATTTCATTTTGA
* *
9827192 CCCTCAAACTTTCTAAAATTTTGATTTTGA
1 CCCT-AAACTTTCTAAAAATTTCATTTTGA
9827222 C
1 C
9827223 GTATTTTTCC
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
29 5 0.07
30 64 0.88
31 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (29 bp):
CCCTAAACTTTCTAAAAATTTCATTTTGA
Found at i:9832300 original size:10 final size:10
Alignment explanation
Indices: 9832285--9832314 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
9832275 TTCACCTTAA
9832285 AAAAAAGAAG
1 AAAAAAGAAG
9832295 AAAAAAGAAAG
1 AAAAAAG-AAG
9832306 AAAAAAGAA
1 AAAAAAGAA
9832315 AAAGGAGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:9832776 original size:112 final size:115
Alignment explanation
Indices: 9832633--9832847 Score: 328
Period size: 112 Copynumber: 1.9 Consensus size: 115
9832623 TTGTCATTTT
* * *
9832633 TAATCTTTACATTCAAATGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAACCTTG
1 TAATCTTTACATTCAAACGAGCTTTGCCTCCAATAAAACTCAATTTCATCCACCTTACAACCTTG
*
9832698 -TTCAAACA-TTTTTGCA-TCGAAATAACGGTTAGTGGACCAATGATTCG
66 ATTCAAACATTTTTTGCATTCGAAATAACAGTTAGTGGACCAATGATTCG
* * *
9832745 TAATCTTTTCATTCATACGAGCTTTGTCTCCAATAAAACTCAATTTCATCCACCTTACAACCTTG
1 TAATCTTTACATTCAAACGAGCTTTGCCTCCAATAAAACTCAATTTCATCCACCTTACAACCTTG
* *
9832810 ATTCAAGCATTTTTTGCATTTGAAATAACAGTTAGTGG
66 ATTCAAACATTTTTTGCATTCGAAATAACAGTTAGTGG
9832848 TCTAACAATA
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
112 59 0.65
113 7 0.08
114 8 0.09
115 17 0.19
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (115 bp):
TAATCTTTACATTCAAACGAGCTTTGCCTCCAATAAAACTCAATTTCATCCACCTTACAACCTTG
ATTCAAACATTTTTTGCATTCGAAATAACAGTTAGTGGACCAATGATTCG
Found at i:9833305 original size:49 final size:49
Alignment explanation
Indices: 9833243--9833647 Score: 226
Period size: 49 Copynumber: 8.2 Consensus size: 49
9833233 ACAGGTTTTA
* * * * *
9833243 AGGGAAAGATTGAAGCCGCAACGACAAATCTTATACCCTAAAGATGTGG
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGATGTGG
* **
9833292 AGGGAAAGGTTGAAGCCGCAAC-AGTGAACCTTATACCTTAGAGACAT-G
1 AGGGAAAGGTTGAAGCCGCAACGA-CGAACCTTATACCTTAGAGATGTGG
* * * * * ** * * *
9833340 ATGGGAAAGATTAAAGCCGGAATTG-TGATTCTTATACCATGGAGATTTGG
1 A-GGGAAAGGTTGAAGCCGCAA-CGACGAACCTTATACCTTAGAGATGTGG
* ** * *
9833390 AGGGAAAGGTTGCAGCTACAACGGCGAACCTTGTACCTTAGAGATGT-G
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGATGTGG
** * * * * *
9833438 ATGGG-AAGGATTGAAGCCGCAACGATAAATCTTGTACCATAGAGATATAG
1 A-GGGAAAGG-TTGAAGCCGCAACGACGAACCTTATACCTTAGAGATGTGG
* * * ** * *
9833488 AGAGAAAGGTTAAAGCCGAAACGGTGAACCTTGTACCGTAGAGACATGATGGG
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAG--ATG-T-GG
** * ** * * * * *
9833541 ATGGGAAATATTAAAATCGTAACGACGAATCTTATACCCTAAAGATGTGA
1 A-GGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGATGTGG
* * * *
9833591 AGGGAAAGGTTGAAGACGCAATGGCGAACCTTATACCTTAGAGATGTGA
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGATGTGG
9833640 AGGGAAAG
1 AGGGAAAG
9833648 ATTAAGGCCA
Statistics
Matches: 267, Mismatches: 74, Indels: 30
0.72 0.20 0.08
Matches are distributed among these distances:
48 10 0.04
49 208 0.78
50 10 0.04
51 3 0.01
52 4 0.01
53 2 0.01
54 30 0.11
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (49 bp):
AGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAGATGTGG
Found at i:9833419 original size:98 final size:98
Alignment explanation
Indices: 9833244--9833652 Score: 345
Period size: 98 Copynumber: 4.1 Consensus size: 98
9833234 CAGGTTTTAA
* * * * *
9833244 GGGAAAGATTGAAGCCGCAACGACAAATCTTATACCCTAAAGATGTGGAGGGAAAGGTTGAAGCC
1 GGGAAAGATTAAAGCCGCAACGATAAATCTTATACCATAGAGATATGGAGGGAAAGGTTGAAGCC
* * *
9833309 GCAACAGTGAACCTTATACCTTAGAGACATGAT
66 ACAACGGTGAACCTTGTACCTTAGAGACATGAT
* * * * * * *
9833342 GGGAAAGATTAAAGCCGGAATTG-TGATTCTTATACCATGGAGATTTGGAGGGAAAGGTTGCAGC
1 GGGAAAGATTAAAGCCGCAA-CGATAAATCTTATACCATAGAGATATGGAGGGAAAGGTTGAAGC
* * **
9833406 TACAACGGCGAACCTTGTACCTTAGAGATGTGAT
65 CACAACGGTGAACCTTGTACCTTAGAGACATGAT
* * * * * *
9833440 GGGAAGGATTGAAGCCGCAACGATAAATCTTGTACCATAGAGATATAGAGAGAAAGGTTAAAGCC
1 GGGAAAGATTAAAGCCGCAACGATAAATCTTATACCATAGAGATATGGAGGGAAAGGTTGAAGCC
*
9833505 GA-AACGGTGAACCTTGTACCGTAGAGACATGATGGGAT
66 -ACAACGGTGAACCTTGTACCTTAGAGAC---AT--GAT
* ** * ** * * * * *
9833543 GGGAAATATTAAAATCGTAACGACGAATCTTATACCCTAAAGATGTGAAGGGAAAGGTTGAAGAC
1 GGGAAAGATTAAAGCCGCAACGATAAATCTTATACCATAGAGATATGGAGGGAAAGGTTGAAGCC
* * * * ** *
9833608 GCAATGGCGAACCTTATACCTTAGAGATGTGAA
66 ACAACGGTGAACCTTGTACCTTAGAGACATGAT
9833641 GGGAAAGATTAA
1 GGGAAAGATTAA
9833653 GGCCACAATA
Statistics
Matches: 240, Mismatches: 62, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
97 1 0.00
98 163 0.68
99 2 0.01
100 1 0.00
101 1 0.00
103 72 0.30
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (98 bp):
GGGAAAGATTAAAGCCGCAACGATAAATCTTATACCATAGAGATATGGAGGGAAAGGTTGAAGCC
ACAACGGTGAACCTTGTACCTTAGAGACATGAT
Found at i:9834012 original size:78 final size:78
Alignment explanation
Indices: 9833845--9834162 Score: 487
Period size: 77 Copynumber: 4.1 Consensus size: 78
9833835 AAGCTACCAT
* * *
9833845 CCAATCTCATACCCTAATCATGGGGCAGATTGAAGTATCCAATC-TTTACCCTAATTAGAGGGTA
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGTA
9833909 GATTGAAGACACA
66 GATTGAAGACACA
* ** * *
9833922 CCAATCTCATACCCCGATCATGGGATAGATTGAAGCATCCAATCTTTTACCCTAATCAAAGGGTT
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGTA
*
9833987 GATTGAAGAAACA
66 GATTGAAGACACA
* *
9834000 CCAATCTCATA-CCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATTAGAGGGTA
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGTA
*
9834064 GATTAAAGACACA
66 GATTGAAGACACA
* * *
9834077 CCAATCTCATACCCCAATCATGGGGCAAATTGAAGCATCTAATCTTTTACCCTAATCAGAGGGCA
1 CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGTA
9834142 GATTGAAGACACA
66 GATTGAAGACACA
9834155 CCAATCTC
1 CCAATCTC
9834163 TTAACCTTAA
Statistics
Matches: 217, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
77 109 0.50
78 108 0.50
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (78 bp):
CCAATCTCATACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGTA
GATTGAAGACACA
Found at i:9834127 original size:155 final size:155
Alignment explanation
Indices: 9833845--9834162 Score: 512
Period size: 155 Copynumber: 2.1 Consensus size: 155
9833835 AAGCTACCAT
*
9833845 CCAATCTCATACCCTAATCATGGGGCAGATTGAAGTATCCAATCTTTACCCTAATTAGAGGGTAG
1 CCAATCTCATACCCTAATCATGGGGCAGATTGAAGCATCCAATCTTTACCCTAATTAGAGGGTAG
* * * *
9833910 ATTGAAGACACACCAATCTCATACCCCGATCATGGGATAGATTGAAGCATCCAATCTTTTACCCT
66 ATTAAAGACACACCAATCTCATACCCCAATCATGGGACAAATTGAAGCATCCAATCTTTTACCCT
**
9833975 AATCAAAGGGTTGATTGAAGAAACA
131 AATCAAAGGGCAGATTGAAGAAACA
*
9834000 CCAATCTCATACCC-GATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATTAGAGGGTA
1 CCAATCTCATACCCTAATCATGGGGCAGATTGAAGCATCCAATC-TTTACCCTAATTAGAGGGTA
* *
9834064 GATTAAAGACACACCAATCTCATACCCCAATCATGGGGCAAATTGAAGCATCTAATCTTTTACCC
65 GATTAAAGACACACCAATCTCATACCCCAATCATGGGACAAATTGAAGCATCCAATCTTTTACCC
* *
9834129 TAATCAGAGGGCAGATTGAAGACACA
130 TAATCAAAGGGCAGATTGAAGAAACA
9834155 CCAATCTC
1 CCAATCTC
9834163 TTAACCTTAA
Statistics
Matches: 150, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
154 27 0.18
155 123 0.82
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (155 bp):
CCAATCTCATACCCTAATCATGGGGCAGATTGAAGCATCCAATCTTTACCCTAATTAGAGGGTAG
ATTAAAGACACACCAATCTCATACCCCAATCATGGGACAAATTGAAGCATCCAATCTTTTACCCT
AATCAAAGGGCAGATTGAAGAAACA
Found at i:9834191 original size:44 final size:46
Alignment explanation
Indices: 9834112--9834340 Score: 254
Period size: 46 Copynumber: 5.1 Consensus size: 46
9834102 CAAATTGAAG
* *
9834112 CATCTAATCTTTTACCC-TAA-TC-AGA-GGGCAGATTGAAGACA-
1 CATCCAATCTTTTACCCTTAAGTCAAGAGGGGCAGATTGAAGCCAC
* * *
9834153 CA-CCAATCTCTTAACCTTAAGTCAAGAGGGGCATATTGAAGCCAC
1 CATCCAATCTTTTACCCTTAAGTCAAGAGGGGCAGATTGAAGCCAC
* * *
9834198 CATCCAATCTTTTACCCCTAAGTCAAGAGAGGCAAATTGAAGCCAC
1 CATCCAATCTTTTACCCTTAAGTCAAGAGGGGCAGATTGAAGCCAC
* * *
9834244 CATCCAATATTTTACCCTTAACTCAAGAGGGGCAGATTGAAGCTAC
1 CATCCAATCTTTTACCCTTAAGTCAAGAGGGGCAGATTGAAGCCAC
* * * * * *
9834290 TATCTAATCTTTTACCCCTAAAATCAAGAGGGGCAAATTGAAGCTAC
1 CATCCAATCTTTTA-CCCTTAAGTCAAGAGGGGCAGATTGAAGCCAC
9834337 CATC
1 CATC
9834341 TCACATAAGT
Statistics
Matches: 158, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
40 11 0.07
41 5 0.03
42 2 0.01
43 3 0.02
44 14 0.09
45 2 0.01
46 89 0.56
47 32 0.20
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (46 bp):
CATCCAATCTTTTACCCTTAAGTCAAGAGGGGCAGATTGAAGCCAC
Found at i:9834270 original size:92 final size:90
Alignment explanation
Indices: 9834112--9834340 Score: 286
Period size: 92 Copynumber: 2.5 Consensus size: 90
9834102 CAAATTGAAG
* * *
9834112 CATCTAATCTTTTA-CCCTAATC-AGAGGGCAGATTGAAGACA-CA-CCAATCTCTTAACCTTAA
1 CATCTAATCTTTTACCCCTAATCAAGAGGGCAAATTGAAGCCACCATCCAATATCTTAACCTTAA
* *
9834173 GTCAAGAGGGGCATATTGAAGCCAC
66 CTCAAGAGGGGCAGATTGAAGCCAC
* * *
9834198 CATCCAATCTTTTACCCCTAAGTCAAGAGAGGCAAATTGAAGCCACCATCCAATATTTTACCCTT
1 CATCTAATCTTTTACCCCTAA-TCAAGAG-GGCAAATTGAAGCCACCATCCAATATCTTAACCTT
*
9834263 AACTCAAGAGGGGCAGATTGAAGCTAC
64 AACTCAAGAGGGGCAGATTGAAGCCAC
* *
9834290 TATCTAATCTTTTACCCCTAAAATCAAGAGGGGCAAATTGAAGCTACCATC
1 CATCTAATCTTTTACCCCT--AATCAAGA-GGGCAAATTGAAGCCACCATC
9834341 TCACATAAGT
Statistics
Matches: 122, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
86 13 0.11
87 6 0.05
88 2 0.02
89 4 0.03
90 13 0.11
91 2 0.02
92 54 0.44
93 25 0.20
94 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (90 bp):
CATCTAATCTTTTACCCCTAATCAAGAGGGCAAATTGAAGCCACCATCCAATATCTTAACCTTAA
CTCAAGAGGGGCAGATTGAAGCCAC
Found at i:9836078 original size:60 final size:60
Alignment explanation
Indices: 9836008--9836121 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
9835998 GCCCTTAAAC
* * * *
9836008 TTTTCAAAAAATTTAAATTT-TATCCCTAAACTTTCTAAAAATTTCATTTTGGCCCCCTAA
1 TTTTCAAAAAA-TTAAATTTCAATCCCCAAACTTTCCAAAAATTTAATTTTGGCCCCCTAA
* * *
9836068 TTTTCTAAAAATTACATTTCAATCCCCAAACTTTCCAAAATTTTAATTTTGGCC
1 TTTTCAAAAAATTAAATTTCAATCCCCAAACTTTCCAAAAATTTAATTTTGGCC
9836122 TCATTTTTCC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 7 0.15
60 39 0.85
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (60 bp):
TTTTCAAAAAATTAAATTTCAATCCCCAAACTTTCCAAAAATTTAATTTTGGCCCCCTAA
Found at i:9839332 original size:28 final size:27
Alignment explanation
Indices: 9839300--9839358 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
9839290 CTTTTCCTTA
* **
9839300 TATATTTTTTAAAATTTTTTAAATTTTT
1 TATATATTTTAAAAAATTTT-AATTTTT
*
9839328 TATATATTTTAAAAAATTTTGATTTTT
1 TATATATTTTAAAAAATTTTAATTTTT
9839355 TATA
1 TATA
9839359 AATATTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TATATATTTTAAAAAATTTTAATTTTT
Found at i:9842992 original size:10 final size:9
Alignment explanation
Indices: 9842944--9843024 Score: 60
Period size: 10 Copynumber: 8.8 Consensus size: 9
9842934 ATGCAAATTT
*
9842944 ATTTTCATA
1 ATTTTTATA
9842953 ATTTTATATA
1 ATTTT-TATA
*
9842963 CTTTTT-TA
1 ATTTTTATA
*
9842971 ATGTTTTGTA
1 AT-TTTTATA
9842981 ATTTTATATA
1 ATTTT-TATA
9842991 ATTTTTAATA
1 ATTTTT-ATA
9843001 ATTTTT-TCA
1 ATTTTTAT-A
9843010 ATTTTT-TA
1 ATTTTTATA
*
9843018 TTTTTTA
1 ATTTTTA
9843025 AATAATTTCT
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
8 10 0.17
9 22 0.37
10 28 0.47
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:9843005 original size:28 final size:28
Alignment explanation
Indices: 9842951--9843032 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
9842941 TTTATTTTCA
*
9842951 TAATTTTATATACTTTTTTAAT-GTTTTG
1 TAATTTTATATA-TTTTTTAATAATTTTG
* *
9842979 TAATTTTATATAATTTTTAATAATTTTT
1 TAATTTTATATATTTTTTAATAATTTTG
9843007 TCAATTTT-T-TATTTTTTAAATAATTT
1 T-AATTTTATATATTTTTT-AATAATTT
9843033 CTATTATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 15 0.32
28 26 0.55
29 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (28 bp):
TAATTTTATATATTTTTTAATAATTTTG
Found at i:9843006 original size:38 final size:39
Alignment explanation
Indices: 9842950--9843032 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 39
9842940 ATTTATTTTC
* *
9842950 ATAA-TTTTATATACTTTTTT-AATGTTTTGTA-ATTTTAT
1 ATAATTTTTATATAATTTTTTCAAT-TTTT-TATATTTTAA
*
9842988 ATAATTTTTA-ATAATTTTTTCAATTTTTTATTTTTTAA
1 ATAATTTTTATATAATTTTTTCAATTTTTTATATTTTAA
9843026 ATAATTT
1 ATAATTT
9843033 CTATTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
37 2 0.05
38 29 0.74
39 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (39 bp):
ATAATTTTTATATAATTTTTTCAATTTTTTATATTTTAA
Found at i:9853273 original size:12 final size:12
Alignment explanation
Indices: 9853256--9853280 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9853246 TAGACGCTAT
9853256 TAACAATATTTA
1 TAACAATATTTA
9853268 TAACAATATTTA
1 TAACAATATTTA
9853280 T
1 T
9853281 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:9859295 original size:2 final size:2
Alignment explanation
Indices: 9859290--9859408 Score: 53
Period size: 2 Copynumber: 64.5 Consensus size: 2
9859280 AAAAATAGAA
* *
9859290 AT AT AT AT AT AT AT AT AT A- AT A- AT A- AT AT AT AA AA AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
9859328 AT AT AT AA AT AT A- AA AT AT AT CAA AT AT TT AG A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
* * * *
9859369 A- AA AT A- AA AT AG AT AT A- AT AT AT AA AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9859406 AT A
1 AT A
9859409 AAAAAATTGA
Statistics
Matches: 89, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
1 11 0.12
2 77 0.87
3 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.37
Consensus pattern (2 bp):
AT
Found at i:9859304 original size:25 final size:25
Alignment explanation
Indices: 9859265--9859321 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
9859255 TTTTGTATTG
*
9859265 TATATAATGTATATAAAAAATAGA-AA
1 TATAT-ATATATATAAAAAATA-ATAA
* *
9859291 TATATATATATATATATAATAATAA
1 TATATATATATATAAAAAATAATAA
9859316 TATATA
1 TATATA
9859322 AAAATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.78
26 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
TATATATATATATAAAAAATAATAA
Found at i:9859329 original size:16 final size:17
Alignment explanation
Indices: 9859274--9859412 Score: 90
Period size: 16 Copynumber: 8.0 Consensus size: 17
9859264 GTATATAATG
* * *
9859274 TATATAAAAAATAGAAA
1 TATATAATATATAAAAA
*
9859291 TATATATATATATATATAA
1 TATATA-ATATATA-AAAA
9859310 TA-ATAATATATAAAAA
1 TATATAATATATAAAAA
*
9859326 TA-ATATATAAATATAAAA
1 TATATA-ATATATA-AAAA
* *
9859344 TATATCAAATATTTAGAATA
1 TATAT--AATATATA-AAAA
9859364 TATATAA-A-ATAAAATA
1 TATATAATATATAAAA-A
* *
9859380 GATATAATATATAAATA
1 TATATAATATATAAAAA
9859397 -ATATAATATATAAAAA
1 TATATAATATATAAAAA
9859413 AATTGAATAT
Statistics
Matches: 97, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.02
16 32 0.33
17 22 0.23
18 21 0.22
19 6 0.06
20 13 0.13
21 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.35
Consensus pattern (17 bp):
TATATAATATATAAAAA
Found at i:9859332 original size:34 final size:35
Alignment explanation
Indices: 9859288--9859411 Score: 107
Period size: 34 Copynumber: 3.6 Consensus size: 35
9859278 TAAAAAATAG
*
9859288 AAATATATATATATATATATAATA-ATAATATATAA
1 AAATA-ATATATATATATAAAATAGATAATATATAA
* * *
9859323 AAATAATATATAAATATAAAATATATCAA-ATATTTA
1 AAATAATATATATATATAAAATAGAT-AATATA-TAA
* * *
9859359 GAAT-ATATATA-AAATAAAATAGAT-ATAATATAT
1 AAATAATATATATATATAAAATAGATAAT-ATATAA
9859392 AAATAATATA-ATATATAAAA
1 AAATAATATATATATATAAAA
9859412 AAATTGAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
32 1 0.01
33 5 0.07
34 42 0.58
35 17 0.24
36 7 0.10
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (35 bp):
AAATAATATATATATATAAAATAGATAATATATAA
Found at i:9859378 original size:25 final size:25
Alignment explanation
Indices: 9859314--9859408 Score: 85
Period size: 25 Copynumber: 4.0 Consensus size: 25
9859304 ATATAATAAT
9859314 AATATATAAA-AAT--AATATATA-
1 AATATATAAATAATAAAATATATAG
* *
9859335 AATATA-AAATATATCAAATATTTAG
1 AATATATAAATA-ATAAAATATATAG
* *
9859360 AATATATATAA-AATAAAATAGATAT
1 AATATATA-AATAATAAAATATATAG
*
9859385 AATATATAAATAATATAATATATA
1 AATATATAAATAATAAAATATATA
9859409 AAAAAATTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.05
21 7 0.12
22 2 0.03
24 9 0.15
25 34 0.58
26 2 0.03
27 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (25 bp):
AATATATAAATAATAAAATATATAG
Found at i:9860050 original size:25 final size:24
Alignment explanation
Indices: 9859994--9860051 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
9859984 ATTCATTATC
9859994 ATTATATTATAATAATATAATGATA
1 ATTAT-TTATAATAATATAATGATA
*
9860019 ATT-TTTATAATATTATATAT-ATA
1 ATTATTTATAATAATATA-ATGATA
9860042 TATTATTTAT
1 -ATTATTTAT
9860052 CTATATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 15 0.52
24 6 0.21
25 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTATTTATAATAATATAATGATA
Found at i:9860077 original size:21 final size:22
Alignment explanation
Indices: 9860053--9860097 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
9860043 ATTATTTATC
*
9860053 TATATATTAAATATCTTT-TTT
1 TATATATTAAATATATTTCTTT
* *
9860074 TATATCTTAATTATATTTCTTT
1 TATATATTAAATATATTTCTTT
9860096 TA
1 TA
9860098 CATTATATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATATTAAATATATTTCTTT
Found at i:9861017 original size:18 final size:18
Alignment explanation
Indices: 9860991--9861032 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9860981 TCGCATAAAA
* *
9860991 AAAGCAAATAAATAAACG
1 AAAGAAAATAAACAAACG
*
9861009 AAAGAAAATAAACAAATG
1 AAAGAAAATAAACAAACG
9861027 AAAGAA
1 AAAGAA
9861033 GGGGGAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.07, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAGAAAATAAACAAACG
Found at i:9861042 original size:11 final size:11
Alignment explanation
Indices: 9861026--9861060 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9861016 ATAAACAAAT
9861026 GAAAGAAGGGG
1 GAAAGAAGGGG
9861037 GAAAG-AGGGG
1 GAAAGAAGGGG
*
9861047 GAAAAAAGGGG
1 GAAAGAAGGGG
9861058 GAA
1 GAA
9861061 GGAGGGGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (11 bp):
GAAAGAAGGGG
Found at i:9861055 original size:21 final size:21
Alignment explanation
Indices: 9861026--9861067 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9861016 ATAAACAAAT
*
9861026 GAAAGAAGGGGGAAAGAGGGG
1 GAAAAAAGGGGGAAAGAGGGG
*
9861047 GAAAAAAGGGGGAAGGAGGGG
1 GAAAAAAGGGGGAAAGAGGGG
9861068 CATCCTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (21 bp):
GAAAAAAGGGGGAAAGAGGGG
Found at i:9861911 original size:10 final size:10
Alignment explanation
Indices: 9861896--9861937 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
9861886 TTATCACAAG
9861896 TATTGTGATA
1 TATTGTGATA
9861906 TATTGTGATA
1 TATTGTGATA
9861916 TA-T-TGATA
1 TATTGTGATA
*
9861924 TATATATGATA
1 TAT-TGTGATA
9861935 TAT
1 TAT
9861938 GTAGAAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 7 0.24
9 1 0.03
10 13 0.45
11 8 0.28
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (10 bp):
TATTGTGATA
Found at i:9872464 original size:21 final size:21
Alignment explanation
Indices: 9872434--9872522 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
9872424 CTCACAAAGA
* *
9872434 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
9872454 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
9872475 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
9872496 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
9872520 AAA
1 AAA
9872523 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:9872515 original size:24 final size:21
Alignment explanation
Indices: 9872434--9872502 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
9872424 CTCACAAAGA
* * *
9872434 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
9872454 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
9872475 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
9872496 AAAAAGA
1 AAAAAGA
9872503 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:9877947 original size:14 final size:14
Alignment explanation
Indices: 9877928--9877969 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
9877918 AATCTTTATA
9877928 TTTATATATTATTT
1 TTTATATATTATTT
9877942 TTTATATATTA-TT
1 TTTATATATTATTT
*
9877955 ATTATATA-TATTT
1 TTTATATATTATTT
9877968 TT
1 TT
9877970 ATTTCTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
14 11 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATATATTATTT
Found at i:9877947 original size:20 final size:20
Alignment explanation
Indices: 9877922--9877959 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9877912 CTAATGAATC
9877922 TTTATAT-TTATATATTATTT
1 TTTATATATTAT-TATTATTT
9877942 TTTATATATTATTATTAT
1 TTTATATATTATTATTAT
9877960 ATATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATATATTATTATTATTT
Found at i:9882133 original size:12 final size:12
Alignment explanation
Indices: 9882116--9882144 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
9882106 ATCTCAATGC
9882116 TTTCAAGTATAT
1 TTTCAAGTATAT
9882128 TTTCAAGTATAT
1 TTTCAAGTATAT
9882140 TTTCA
1 TTTCA
9882145 TTCAAGATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (12 bp):
TTTCAAGTATAT
Found at i:9886051 original size:40 final size:39
Alignment explanation
Indices: 9885949--9886078 Score: 111
Period size: 40 Copynumber: 3.2 Consensus size: 39
9885939 GCGGCACTTT
* * *
9885949 TAGCGGCGTTTGGATAGAAAACGCCGTAAAAGGTAAAGCAA
1 TAGCGGCGTTT--ATAAAAAATGCCGCAAAAGGTAAAGCAA
* * * *
9885990 TAGCAGCGTTT-TCCCATAAATGCCGCAAAAGGTAAAGTAA
1 TAGCGGCGTTTAT--AAAAAATGCCGCAAAAGGTAAAGCAA
*
9886030 TAGCGGCGTTTATAAAAAAATGCCGCTAAAA-GTCAAAGCAT
1 TAGCGGCGTTTAT-AAAAAATGCCGC-AAAAGGT-AAAGCAA
9886071 TAGCGGCG
1 TAGCGGCG
9886079 CTTGTCAGAG
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
38 1 0.01
40 42 0.59
41 28 0.39
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.20
Consensus pattern (39 bp):
TAGCGGCGTTTATAAAAAATGCCGCAAAAGGTAAAGCAA
Found at i:9886085 original size:21 final size:21
Alignment explanation
Indices: 9886061--9886104 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
9886051 GCCGCTAAAA
9886061 GTCAAAGCATTAGCGGCGCTT
1 GTCAAAGCATTAGCGGCGCTT
* *
9886082 GTCAGAGTATTAGCGGCGCTT
1 GTCAAAGCATTAGCGGCGCTT
9886103 GT
1 GT
9886105 GGGAAAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.27
Consensus pattern (21 bp):
GTCAAAGCATTAGCGGCGCTT
Found at i:9886163 original size:41 final size:40
Alignment explanation
Indices: 9886082--9886206 Score: 126
Period size: 41 Copynumber: 3.0 Consensus size: 40
9886072 AGCGGCGCTT
* * * * *
9886082 GTCAGAGTATTAGCGGCGCTTGTGGGAAAGCACCCTTAAAG
1 GTCAGAGCATTAGCAGCGCTTGTGTGAAAGTACGC-TAAAG
*
9886123 GTCAGAGCATTAGCAGCGCTTGTGTGAAAGTGTCGCTAAAG
1 GTCAGAGCATTAGCAGCGCTTGTGTGAAAGT-ACGCTAAAG
* * *
9886164 GCCAAAGCATTAG-AGGCGCTTGTGTGAAAGCTCCGCTAAAG
1 GTCAGAGCATTAGCA-GCGCTTGTGTGAAAG-TACGCTAAAG
9886205 GT
1 GT
9886207 TAAGCAATAG
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.01
41 67 0.94
42 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.22
Consensus pattern (40 bp):
GTCAGAGCATTAGCAGCGCTTGTGTGAAAGTACGCTAAAG
Found at i:9887701 original size:11 final size:12
Alignment explanation
Indices: 9887674--9887706 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
9887664 CAATTTTAAG
9887674 TTTAAATTTATT
1 TTTAAATTTATT
9887686 TTTAAATTTA-T
1 TTTAAATTTATT
9887697 TTTAAATTTA
1 TTTAAATTTA
9887707 AATTTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:9887722 original size:16 final size:17
Alignment explanation
Indices: 9887686--9887724 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
9887676 TAAATTTATT
9887686 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
9887703 TTTAAATTTA-TTTGAA
1 TTTAAATTTATTTTAAA
9887719 TTTAAA
1 TTTAAA
9887725 AAAATATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:9888292 original size:7 final size:7
Alignment explanation
Indices: 9888272--9888317 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
9888262 ATTTCAAAGT
9888272 ATAATAA
1 ATAATAA
9888279 ATAAATAA
1 AT-AATAA
9888287 ATAATAA
1 ATAATAA
9888294 ATACAT-A
1 ATA-ATAA
*
9888301 ATATTAA
1 ATAATAA
9888308 ATAA-AA
1 ATAATAA
9888314 ATAA
1 ATAA
9888318 AAAGAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
6 7 0.21
7 18 0.53
8 9 0.26
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAA
Found at i:9888292 original size:11 final size:11
Alignment explanation
Indices: 9888278--9888318 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
9888268 AAGTATAATA
9888278 AATAAATAAAT
1 AATAAATAAAT
*
9888289 AATAAATACAT
1 AATAAATAAAT
*
9888300 AAT-ATTAAAT
1 AATAAATAAAT
9888310 AA-AAATAAA
1 AATAAATAAA
9888319 AAGAAATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 12 0.48
11 13 0.52
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:9894692 original size:78 final size:77
Alignment explanation
Indices: 9894632--9895303 Score: 736
Period size: 78 Copynumber: 8.6 Consensus size: 77
9894622 CAGTCATCTA
** * * * *
9894632 ATCTTTTACCTTGAGCATGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCTTGAGGCAAA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT-AGGCAGA
*
9894697 TTGTAGCCATTCG
65 TTGCAGCCATTCG
* * *
9894710 ATCTTTTACCTCGAGCTTAGGGCAGATCACTATCAGCCAATCTCTTACCCCGAGCCTAAGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT-AGGCAGA
*
9894775 TTGCAACCATTCG
65 TTGCAGCCATTCG
* *
9894788 ATCTTTTACCCCGAGCTTAGGGTAGATCACCATCAGCCAATCTCTTTA-CCCGAGCCTAGAGCAG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC-TTACCCCGAGCCTAG-GCAG
*
9894852 ATTGCAGCCATTTG
64 ATTGCAGCCATTCG
* * *
9894866 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCAAGCTTAGGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTA-GGCAGA
* *
9894931 TTGCAGTCATTCA
65 TTGCAGCCATTCG
* * * * * ** **
9894944 ATCTTCTACCCCGAGCCTGAGGAAGATCACGATCAGTGAATCTCTTACCCCGAGCCCGGGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG-CCTAGGCAGA
*
9895009 TTGCAGCTATTCG
65 TTGCAGCCATTCG
* * * * * * *
9895022 ATCTTTTACCCCGAGCTTGGGACAAATCACCATCAGCTAATCTTTTACCCTGAGCATGACGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT-AGGCAGA
** *
9895087 TTATAGCTATTCG
65 TTGCAGCCATTCG
* * *
9895100 ATCTTTTACCCCGAGCTTGGGGCAGATCACTATCAGCCAATCTCTTACCCCGAGCCTGGGGTAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT-AGGCAGA
*
9895165 TTGCAACCATTCG
65 TTGCAGCCATTCG
* * * * * * *
9895178 ATCTTTTACCCTGAGCTTGGAGCAGATCCCCATTAGCTAATCTCTTACCCTGAGCTTAGGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTA-GGCAGA
*
9895243 TTGCAACCATTCG
65 TTGCAGCCATTCG
* * ** *
9895256 ATCTTTTACCTCGA-TTATGAAGCAGATCACCGTCAGCCAATCTCTTAC
1 ATCTTTTACCCCGAGCT-TGGGGCAGATCACCATCAGCCAATCTCTTAC
9895304 TCCGTGACAG
Statistics
Matches: 499, Mismatches: 87, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
77 7 0.01
78 487 0.98
79 5 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (77 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGCAGAT
TGCAGCCATTCG
Found at i:9894758 original size:39 final size:39
Alignment explanation
Indices: 9894651--9895243 Score: 241
Period size: 39 Copynumber: 15.2 Consensus size: 39
9894641 CTTGAGCATG
*
9894651 GGGCAGATCACCATCAACCAATCTCTTACCCCGAGCTT-
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
* * * *
9894689 GAGGCAAATTGTAGCCATTC-G---ATCTTTTACCTCGAGCTTA
1 G-GGCAGA-T-CA-CCA-TCAGCCAATCTCTTACCCCGAGCTTA
* *
9894729 GGGCAGATCACTATCAGCCAATCTCTTACCCCGAGCCTA
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
* ** * * ** * *
9894768 AGGCAGATTGCAACCATTCGATCTTTTACCCCGAGCTTA
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
* *
9894807 GGGTAGATCACCATCAGCCAATCTCTTTA-CCCGAGCCTA
1 GGGCAGATCACCATCAGCCAATCTC-TTACCCCGAGCTTA
* ** * *
9894846 GAGCAGATTGCAGCCATTTG---ATCTTTTACCCCGAGCTTG
1 GGGCAGA-T-CA-CCATCAGCCAATCTCTTACCCCGAGCTTA
* *
9894885 GGGCAGATCACCATCAGCCAATCTCTTACCTCAAGCTTA
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
** ** *
9894924 GGGCAGAT-TGCAGTCATTCAATCT-TCTACCCCGAGCCT-
1 GGGCAGATCACCA-TCAGCCAATCTCT-TACCCCGAGCTTA
* * ** ***
9894962 GAGGAAGATCACGATCAGTGAATCTCTTACCCCGAGCCCG
1 G-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
* ** * *
9895002 GGGCAGATTGCAGC-T-ATTCGATCTTTTACCCCGAGCTT-
1 GGGCAGA-T-CACCATCAGCCAATCTCTTACCCCGAGCTTA
* * * * *
9895040 GGGACAAATCACCATCAGCTAATCTTTTACCCTGAGCAT-
1 GGG-CAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
* * * * ** * * *
9895079 GACGCAGATTA-TAGCTATTCGATCTTTTACCCCGAGCTTG
1 G-GGCAGATCACCATC-AGCCAATCTCTTACCCCGAGCTTA
* * *
9895119 GGGCAGATCACTATCAGCCAATCTCTTACCCCGAGCCTG
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
* ** * * ** * * *
9895158 GGGTAGATTGCAACCATTCGATCTTTTACCCTGAGCTT-
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
* * * *
9895196 GGAGCAGATCCCCATTAGCTAATCTCTTACCCTGAGCTTA
1 GG-GCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
9895236 GGGCAGAT
1 GGGCAGAT
9895244 TGCAACCATT
Statistics
Matches: 402, Mismatches: 118, Indels: 69
0.68 0.20 0.12
Matches are distributed among these distances:
35 2 0.00
36 8 0.02
37 6 0.01
38 19 0.05
39 334 0.83
40 18 0.04
41 5 0.01
42 8 0.02
43 2 0.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA
Found at i:9895982 original size:17 final size:17
Alignment explanation
Indices: 9895947--9896007 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
9895937 AATTGAACCC
* *
9895947 AATTTTAAGTTTAAATTT
1 AATTTTAAATTT-ATTTT
*
9895965 ATTTTTAAATTTATTTT
1 AATTTTAAATTTATTTT
* *
9895982 AAATTTAAATTTATTTG
1 AATTTTAAATTTATTTT
9895999 AATTTTAAA
1 AATTTTAAA
9896008 AAAAAGAATG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 26 0.72
18 10 0.28
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
AATTTTAAATTTATTTT
Found at i:9895983 original size:11 final size:12
Alignment explanation
Indices: 9895956--9895988 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
9895946 CAATTTTAAG
9895956 TTTAAATTTATT
1 TTTAAATTTATT
9895968 TTTAAATTTA-T
1 TTTAAATTTATT
9895979 TTTAAATTTA
1 TTTAAATTTA
9895989 AATTTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:9895994 original size:12 final size:12
Alignment explanation
Indices: 9895950--9896007 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
9895940 TGAACCCAAT
*
9895950 TTTAAGTTTAAA
1 TTTAATTTTAAA
*
9895962 TTTATTTTTAAA
1 TTTAATTTTAAA
9895974 TTT-ATTTTAAA
1 TTTAATTTTAAA
*
9895985 TTTAAATTT--A
1 TTTAATTTTAAA
9895995 TTTGAATTTTAAA
1 TTT-AATTTTAAA
9896008 AAAAAGAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 4 0.11
11 15 0.41
12 17 0.46
13 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:9896350 original size:148 final size:147
Alignment explanation
Indices: 9896083--9896377 Score: 536
Period size: 148 Copynumber: 2.0 Consensus size: 147
9896073 AACCAAACAG
*
9896083 ATCCAAATTACATAACCCAAACACTTAAGGGTCCAAAAGGCCAAACCAAAACAACCCTAATCTGC
1 ATCCAAATTACATAACCCAAACACTTAAGGGTCCAAAAGGCCAAACCAAAAAAACCCTAATCTGC
* * *
9896148 TAAGCCACTTGCTTCGGCCACCTCCATCCCACCCATTCAGAGCATGCCACGTCAGCAACACCGCT
66 TAAGCCACTTGCTTCGACCACCTCCATCCCACCCATTCAGAGCATGCCACGTCAGCAACACCACC
9896213 CTCACCAACTTGCCACT
131 CTCACCAACTTGCCACT
*
9896230 ATCCAAATTACATAACTCAAACACTTAAGGGTCCAAAAGGCCCAAACCAAAAAAACCCTAATCTG
1 ATCCAAATTACATAACCCAAACACTTAAGGGTCCAAAAGG-CCAAACCAAAAAAACCCTAATCTG
9896295 CTAAGCCACTTGCTTCGACCACCTCCATCCCACCCATTCAGAGCATGCCACGTCAGCAACACCAC
65 CTAAGCCACTTGCTTCGACCACCTCCATCCCACCCATTCAGAGCATGCCACGTCAGCAACACCAC
9896360 CCTCACCAACTTGCCACT
130 CCTCACCAACTTGCCACT
9896378 GCCACACCAC
Statistics
Matches: 142, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
147 39 0.27
148 103 0.73
ACGTcount: A:0.34, C:0.38, G:0.11, T:0.18
Consensus pattern (147 bp):
ATCCAAATTACATAACCCAAACACTTAAGGGTCCAAAAGGCCAAACCAAAAAAACCCTAATCTGC
TAAGCCACTTGCTTCGACCACCTCCATCCCACCCATTCAGAGCATGCCACGTCAGCAACACCACC
CTCACCAACTTGCCACT
Found at i:9896729 original size:15 final size:15
Alignment explanation
Indices: 9896709--9896738 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9896699 TTTCAAAGTA
*
9896709 TAATAAATACATAAT
1 TAATAAAAACATAAT
9896724 TAATAAAAACATAAT
1 TAATAAAAACATAAT
9896739 ATTAAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATAAAAACATAAT
Found at i:9897758 original size:30 final size:30
Alignment explanation
Indices: 9897702--9897926 Score: 267
Period size: 30 Copynumber: 7.5 Consensus size: 30
9897692 CTTAAGTTTC
* *
9897702 TCCAAAATTATATTTTAACCTC-AAATTTT
1 TCCAAAATTACATTTTAACCCCTAAATTTT
*
9897731 TCCAAAAATACATTTTAACCCCTAAATTTT
1 TCCAAAATTACATTTTAACCCCTAAATTTT
* * *
9897761 TCTAAAATTATATTTTAACCCCTAAACTTT
1 TCCAAAATTACATTTTAACCCCTAAATTTT
*
9897791 GCCAAAATTACATTTTAACCCC-AAATTTT
1 TCCAAAATTACATTTTAACCCCTAAATTTT
* * * *
9897820 TGCAAAATTACATTTTGACCACTAAATTTC
1 TCCAAAATTACATTTTAACCCCTAAATTTT
* * *
9897850 TCCAAAATTACATTTTCACCTCCCAAACTTT
1 TCCAAAATTACATTTTAACC-CCTAAATTTT
*
9897881 TCCAAAATTACATTTTGA-CCCTAAATTTT
1 TCCAAAATTACATTTTAACCCCTAAATTTT
*
9897910 TCCAAAAATTACGTTTT
1 TCC-AAAATTACATTTT
9897927 GGTCTTAAAT
Statistics
Matches: 166, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
29 54 0.33
30 89 0.54
31 23 0.14
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.39
Consensus pattern (30 bp):
TCCAAAATTACATTTTAACCCCTAAATTTT
Found at i:9897768 original size:59 final size:57
Alignment explanation
Indices: 9897704--9897918 Score: 243
Period size: 59 Copynumber: 3.6 Consensus size: 57
9897694 TAAGTTTCTC
*
9897704 CAAAATTATATTTTAA-CCTCAAATTTTTCCAAAAATACATTTTAACCCCTAAATTTTT
1 CAAAATTACATTTTAACCCT-AAATTTTTCCAAAAATACATTTTAACCCC-AAATTTTT
* * * *
9897762 CTAAAATTATATTTTAACCCCTAAACTTTGCCAAAATTACATTTTAACCCCAAATTTTT
1 C-AAAATTACATTTTAA-CCCTAAATTTTTCCAAAAATACATTTTAACCCCAAATTTTT
* * * * *
9897821 GCAAAATTACATTTTGACCACTAAATTTCTCCAAAATTACATTTTCACCTCCCAAACTTTTC
1 -CAAAATTACATTTTAACC-CTAAATTTTTCCAAAAATACATTTT-AAC-CCCAAA-TTTTT
*
9897883 CAAAATTACATTTTGACCCTAAATTTTTCCAAAAAT
1 CAAAATTACATTTTAACCCTAAATTTTTCCAAAAAT
9897919 TACGTTTTGG
Statistics
Matches: 137, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
58 3 0.02
59 58 0.42
60 45 0.33
61 27 0.20
62 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (57 bp):
CAAAATTACATTTTAACCCTAAATTTTTCCAAAAATACATTTTAACCCCAAATTTTT
Found at i:9897798 original size:89 final size:89
Alignment explanation
Indices: 9897703--9897918 Score: 290
Period size: 89 Copynumber: 2.4 Consensus size: 89
9897693 TTAAGTTTCT
* * * *
9897703 CCAAAATTATATTTTAACCTCAAATTTTTCCAAAAATACATTTTAACCCCTAAATTTTTCTAAAA
1 CCAAAATTACATTTTAACC-CAAATTTTTCCAAAAATACATTTTAACCACTAAATTTCTCCAAAA
* *
9897768 TTATATTTTAACC-CCTAAACTTTG
65 TTACATTTTAACCTCCCAAACTTTG
* * *
9897792 CCAAAATTACATTTTAACCCCAAATTTTTGCAAAATTACATTTTGACCACTAAATTTCTCCAAAA
1 CCAAAATTACATTTTAA-CCCAAATTTTTCCAAAAATACATTTTAACCACTAAATTTCTCCAAAA
* *
9897857 TTACATTTTCACCTCCCAAACTTTT
65 TTACATTTTAACCTCCCAAACTTTG
*
9897882 CCAAAATTACATTTTGACCCTAAATTTTTCCAAAAAT
1 CCAAAATTACATTTTAACCC-AAATTTTTCCAAAAAT
9897919 TACGTTTTGG
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
89 69 0.63
90 41 0.37
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (89 bp):
CCAAAATTACATTTTAACCCAAATTTTTCCAAAAATACATTTTAACCACTAAATTTCTCCAAAAT
TACATTTTAACCTCCCAAACTTTG
Found at i:9902096 original size:8 final size:8
Alignment explanation
Indices: 9902071--9902126 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
9902061 ATAACTCAAA
9902071 TATTTAAT
1 TATTTAAT
* *
9902079 TAGTTGAT
1 TATTTAAT
9902087 TATTTAATT
1 TATTTAA-T
9902096 ATATTTAAT
1 -TATTTAAT
9902105 TATTTAAT
1 TATTTAAT
* *
9902113 TAGTTATT
1 TATTTAAT
9902121 TATTTA
1 TATTTA
9902127 CAACTATGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 30 0.77
9 2 0.05
10 7 0.18
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (8 bp):
TATTTAAT
Found at i:9908258 original size:43 final size:43
Alignment explanation
Indices: 9908211--9908480 Score: 256
Period size: 43 Copynumber: 6.3 Consensus size: 43
9908201 ATCTGTGAAT
* * *
9908211 TTTAGCGACATTTGTGGAGAAAGCGTCGTTAAAGACCATGTTC
1 TTTAGCGGCATTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
* * * * * **
9908254 TTTAGCAGCCTCTGTGGAAAAAGCGTCGCTAAAGGTCATGTTC
1 TTTAGCGGCATTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
* * * *
9908297 TTTAGCGGCGTTTGTGGGGAAAGCACCGCTAAAGATCATGTTC
1 TTTAGCGGCATTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
* * * * * * *
9908340 TTCAGCGGTATTTATGGGGAAAGAGCCGCTGAAGACCATGGTC
1 TTTAGCGGCATTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
* * * *
9908383 TTCAGCGGCGTTTGTGG-GAAAAGCACCGCTAAAGACCATATTC
1 TTTAGCGGCATTTGTGGAG-AAAGCGCCGCTAAAGACCATGTTC
* * *
9908426 TTTAGCGGTATTTGT-GAAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCATTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
*
9908468 TATAGCGGCATTT
1 TTTAGCGGCATTT
9908481 TTCCTAATAA
Statistics
Matches: 183, Mismatches: 42, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
42 34 0.19
43 149 0.81
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCATTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
Found at i:9908944 original size:45 final size:45
Alignment explanation
Indices: 9908878--9908968 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
9908868 ATAATCAAGG
*
9908878 TTTCCATAGAAAATTTCATCCGCAAAGAAACAAATAGCCATAAGC
1 TTTCCATAGAAAATTTAATCCGCAAAGAAACAAATAGCCATAAGC
*
9908923 TTTCCATAGAAAATTTAATCCGTAAAGAAACAAATAGCCATAAGC
1 TTTCCATAGAAAATTTAATCCGCAAAGAAACAAATAGCCATAAGC
9908968 T
1 T
9908969 ATGTCATATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (45 bp):
TTTCCATAGAAAATTTAATCCGCAAAGAAACAAATAGCCATAAGC
Found at i:9909689 original size:17 final size:17
Alignment explanation
Indices: 9909663--9909722 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
9909653 AAAAATATGA
9909663 AAGGTTAAAGAAGATGG
1 AAGGTTAAAGAAGATGG
* * *
9909680 AAGATTAAAG-ATATGA
1 AAGGTTAAAGAAGATGG
9909696 AAGGTTAAAGAAGATGG
1 AAGGTTAAAGAAGATGG
9909713 AAGGTTAAAG
1 AAGGTTAAAG
9909723 GTTAAACGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.36
17 23 0.64
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (17 bp):
AAGGTTAAAGAAGATGG
Found at i:9909699 original size:33 final size:33
Alignment explanation
Indices: 9909657--9909722 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
9909647 AGTTACAAAA
9909657 ATATGAAAGGTTAAAGAAGATGGAAGATTAAAG
1 ATATGAAAGGTTAAAGAAGATGGAAGATTAAAG
*
9909690 ATATGAAAGGTTAAAGAAGATGGAAGGTTAAAG
1 ATATGAAAGGTTAAAGAAGATGGAAGATTAAAG
9909723 GTTAAACGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (33 bp):
ATATGAAAGGTTAAAGAAGATGGAAGATTAAAG
Found at i:9911405 original size:19 final size:19
Alignment explanation
Indices: 9911366--9911407 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
9911356 ATCTAACTAT
9911366 TTAAGTATCATTTTTTAAA
1 TTAAGTATCATTTTTTAAA
9911385 TTAA-TATCATATTATTT-AA
1 TTAAGTATCAT-TT-TTTAAA
9911404 TTAA
1 TTAA
9911408 ATTCCTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
19 12 0.57
20 3 0.14
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (19 bp):
TTAAGTATCATTTTTTAAA
Found at i:9912020 original size:3 final size:3
Alignment explanation
Indices: 9912012--9912049 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
9912002 AGCATTAAAT
9912012 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9912050 TATTTTTCAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9915987 original size:22 final size:22
Alignment explanation
Indices: 9915930--9915988 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
9915920 CTAATATATC
*
9915930 AAATATATGTAAAT-ATTTTCAAA
1 AAATATA-G-AAATAATTTTAAAA
9915953 AAATATA-ATAATAATTTTAAAA
1 AAATATAGA-AATAATTTTAAAA
9915975 AAATATAGAAATAA
1 AAATATAGAAATAA
9915989 AAATATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 3 0.09
22 20 0.62
23 8 0.25
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (22 bp):
AAATATAGAAATAATTTTAAAA
Found at i:9916011 original size:24 final size:24
Alignment explanation
Indices: 9915940--9916013 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
9915930 AAATATATGT
*
9915940 AAATATTTTCAAAAAAT-ATAATAA
1 AAATATTTT-AAAATATAATAATAA
* *
9915964 TAAT-TTTAAAAAAATATAGA-AATAA
1 AAATATTT--TAAAATATA-ATAATAA
9915989 AAATATTTTAAAATATAATAATAA
1 AAATATTTTAAAATATAATAATAA
9916013 A
1 A
9916014 TTTAATATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
23 4 0.10
24 23 0.59
25 8 0.21
26 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (24 bp):
AAATATTTTAAAATATAATAATAA
Found at i:9916780 original size:6 final size:6
Alignment explanation
Indices: 9916769--9916814 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
9916759 ACAACAAAGA
9916769 GGGATG GGGATG GGGATG GGGATG GGGATG GGGATG GGGATG GGGA
1 GGGATG GGGATG GGGATG GGGATG GGGATG GGGATG GGGATG GGGA
9916815 AGGAACGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.00, G:0.67, T:0.15
Consensus pattern (6 bp):
GGGATG
Found at i:9916893 original size:18 final size:17
Alignment explanation
Indices: 9916850--9916898 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
9916840 TATTTTATTT
*
9916850 AATATTAATATAATATA
1 AATATTAATATAATACA
**
9916867 CTTATTTAATATCAATACA
1 AATA-TTAATAT-AATACA
9916886 AATATTAATATAA
1 AATATTAATATAA
9916899 AATTTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 4 0.16
18 14 0.56
19 7 0.28
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATTAATATAATACA
Found at i:9917774 original size:28 final size:29
Alignment explanation
Indices: 9917719--9917774 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
9917709 CTTCTCTCAA
**
9917719 ATTGATATTTATAATTTATTTTGTTTCAG
1 ATTGATATTTATAATTTATTTTCCTTCAG
*
9917748 ATTGATATTTA-AATTTTTTTTCCTTCA
1 ATTGATATTTATAATTTATTTTCCTTCA
9917775 CTATATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (29 bp):
ATTGATATTTATAATTTATTTTCCTTCAG
Done.