Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold76
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: 2182696
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.29
Warning! 286211 characters in sequence are not A, C, G, or T
File 2 of 13
Found at i:192770 original size:28 final size:28
Alignment explanation
Indices: 192738--192793 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
192728 TTGTCTTTCT
192738 TATGAGCAATTTCAATATATATATATAA
1 TATGAGCAATTTCAATATATATATATAA
192766 TATGAGCAATTTCAATATATATATATAA
1 TATGAGCAATTTCAATATATATATATAA
192794 ATACATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (28 bp):
TATGAGCAATTTCAATATATATATATAA
Found at i:192808 original size:6 final size:6
Alignment explanation
Indices: 192799--192840 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
192789 TATAAATACA
192799 TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG
192841 CATGCATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:193202 original size:29 final size:29
Alignment explanation
Indices: 193169--193231 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
193159 ATGTATTTTG
*
193169 GGCATGTTATTTGTTCTCTTTTGATTCTT
1 GGCATGTTACTTGTTCTCTTTTGATTCTT
193198 GGCATGTTACTTGTTCTCTTTTGATTCTT
1 GGCATGTTACTTGTTCTCTTTTGATTCTT
193227 GGCAT
1 GGCAT
193232 TTCATGATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.19, T:0.54
Consensus pattern (29 bp):
GGCATGTTACTTGTTCTCTTTTGATTCTT
Found at i:194238 original size:21 final size:22
Alignment explanation
Indices: 194207--194247 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
194197 ATTTTGAGAA
194207 ATTATTTATTTAAT-ATAATTAC
1 ATTATTTATTT-ATGATAATTAC
194229 ATTA-TTATTTATGATAATT
1 ATTATTTATTTATGATAATT
194248 TCAAATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.67
22 4 0.22
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTATTTATTTATGATAATTAC
Found at i:194477 original size:2 final size:2
Alignment explanation
Indices: 194470--194497 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
194460 TGTTGTTGCT
194470 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
194498 ACACACACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:194502 original size:2 final size:2
Alignment explanation
Indices: 194497--194523 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
194487 CTCTCTCTCT
194497 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
194524 TTTTACAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:194889 original size:2 final size:2
Alignment explanation
Indices: 194882--194919 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
194872 GTAGGTGGTC
194882 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
194920 TTTCAAGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:200001 original size:36 final size:36
Alignment explanation
Indices: 199929--200002 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
199919 GAAGGTAGTT
* * *
199929 ACTTAGTCTGGTTTTGAGACTCAGATTGTGGTAGTG
1 ACTTAGTCTGGTTTTGAGACTCAGAATATGGCAGTG
199965 ACTTAG-CTTGGTTTTGAGACTCAGAATATGGCAGTG
1 ACTTAGTC-TGGTTTTGAGACTCAGAATATGGCAGTG
200001 AC
1 AC
200003 AGATTTTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (36 bp):
ACTTAGTCTGGTTTTGAGACTCAGAATATGGCAGTG
Found at i:200012 original size:36 final size:36
Alignment explanation
Indices: 199937--200015 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
199927 TTACTTAGTC
* * * **
199937 TGGTTTTGAGACTCAGATTGTGGTAGTGACTTAGCT
1 TGGTTTTGAGACTCAGAATATGGCAGTGACAGAGCT
**
199973 TGGTTTTGAGACTCAGAATATGGCAGTGACAGATTT
1 TGGTTTTGAGACTCAGAATATGGCAGTGACAGAGCT
200009 TGGTTTT
1 TGGTTTT
200016 TGTTATGTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (36 bp):
TGGTTTTGAGACTCAGAATATGGCAGTGACAGAGCT
Found at i:215380 original size:19 final size:21
Alignment explanation
Indices: 215358--215403 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
215348 ATAAATAAAA
215358 ATAATTT-A-AATAATATTTT
1 ATAATTTAATAATAATATTTT
215377 ATAATTTAATAATAATA-TTT
1 ATAATTTAATAATAATATTTT
215397 A-AATTTA
1 ATAATTTA
215404 TACATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.52
20 5 0.20
21 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATTTAATAATAATATTTT
Found at i:216651 original size:12 final size:11
Alignment explanation
Indices: 216625--216655 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
216615 ACTCTTTCTT
216625 AAAATCACTTTA
1 AAAAT-ACTTTA
216637 AAAATACTTTA
1 AAAATACTTTA
216648 AAAATACT
1 AAAATACT
216656 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATACTTTA
Found at i:220746 original size:13 final size:13
Alignment explanation
Indices: 220728--220752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220718 AAAAAAAATA
220728 TGTATCGATACAT
1 TGTATCGATACAT
220741 TGTATCGATACA
1 TGTATCGATACA
220753 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:222737 original size:6 final size:6
Alignment explanation
Indices: 222728--222769 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
222718 TTTATGATTA
* *
222728 TTAATT TTAATT TTAATT TT-CTT TTAATT TT-CTT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TT
222770 GGGTTTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (6 bp):
TTAATT
Found at i:222754 original size:11 final size:11
Alignment explanation
Indices: 222728--222769 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
222718 TTTATGATTA
*
222728 TTAATTTTAATT
1 TTAATTTT-CTT
222740 TTAATTTTCTT
1 TTAATTTTCTT
222751 TTAATTTTCTT
1 TTAATTTTCTT
222762 TTAATTTT
1 TTAATTTT
222770 GGGTTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 21 0.72
12 8 0.28
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (11 bp):
TTAATTTTCTT
Found at i:224304 original size:20 final size:21
Alignment explanation
Indices: 224259--224314 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
224249 CATTAGAAAA
224259 TGTATCGATACATGTTTACAAT
1 TGTATCGATACAT-TTTACAAT
224281 TGTATCGATACATTTCT-C-AT
1 TGTATCGATACATTT-TACAAT
224301 TGTATCGATACATT
1 TGTATCGATACATT
224315 CTGGGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.48
21 3 0.09
22 14 0.42
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
TGTATCGATACATTTTACAAT
Found at i:226440 original size:14 final size:13
Alignment explanation
Indices: 226408--226444 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
226398 ATATTATGGG
226408 TTGTCCATATTCTT
1 TTGT-CATATTCTT
226422 TTGTCATATTCTT
1 TTGTCATATTCTT
226435 TGTGTCATAT
1 T-TGTCATAT
226445 CACTACATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.57
Consensus pattern (13 bp):
TTGTCATATTCTT
Found at i:238382 original size:20 final size:19
Alignment explanation
Indices: 238327--238382 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
238317 AAAACCCTTA
*
238327 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
238347 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
238367 AATGTATCGATACATG
1 AAAGTATCGATACATG
238383 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:238476 original size:20 final size:20
Alignment explanation
Indices: 238433--238484 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
238423 GTAGCCAAAC
*
238433 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
*
238453 -TGTATTGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
238472 TTGTATCGATACA
1 TTGTATCGATACA
238485 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:250206 original size:21 final size:21
Alignment explanation
Indices: 250173--250212 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
250163 GTTAAATCAT
250173 AAAAATGAAGAAATGAGAGAC
1 AAAAATGAAGAAATGAGAGAC
* * *
250194 AAAATTGATGAAATTAGAG
1 AAAAATGAAGAAATGAGAG
250213 CTTCAAAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (21 bp):
AAAAATGAAGAAATGAGAGAC
Found at i:256802 original size:13 final size:13
Alignment explanation
Indices: 256781--256816 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
256771 AGGATCTTTG
*
256781 TATCAATACATTA
1 TATCGATACATTA
*
256794 TATCGATACATTG
1 TATCGATACATTA
256807 TATCGATACA
1 TATCGATACA
256817 AGGGCACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:261293 original size:13 final size:13
Alignment explanation
Indices: 261275--261299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
261265 CAAAGATCAG
261275 TGTATCGATACAA
1 TGTATCGATACAA
261288 TGTATCGATACA
1 TGTATCGATACA
261300 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:261381 original size:33 final size:33
Alignment explanation
Indices: 261339--261408 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
261329 GGCAGTAGCT
261339 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
261372 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
261405 TACA
1 TACA
261409 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:261382 original size:13 final size:13
Alignment explanation
Indices: 261364--261388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
261354 CAAAAAAATA
261364 TGTATCGATACAT
1 TGTATCGATACAT
261377 TGTATCGATACA
1 TGTATCGATACA
261389 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:262289 original size:21 final size:22
Alignment explanation
Indices: 262243--262295 Score: 81
Period size: 21 Copynumber: 2.4 Consensus size: 22
262233 AGAGGAGAAA
262243 TTTTATTAAGGGGAAAGAAAAT
1 TTTTATTAAGGGGAAAGAAAAT
*
262265 TTTTATTAA-GGGAGAGAAAAT
1 TTTTATTAAGGGGAAAGAAAAT
262286 TTTTAATTAA
1 TTTT-ATTAA
262296 AAGGGAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (22 bp):
TTTTATTAAGGGGAAAGAAAAT
Found at i:262877 original size:33 final size:32
Alignment explanation
Indices: 262835--262898 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
262825 AAGCCTAGAA
*
262835 GTATCGATACATATTGCTTTGTATCCATACATT
1 GTATCGATACATATT-CATTGTATCCATACATT
*
262868 GTATCGATACATATTCATTGTATCGATACAT
1 GTATCGATACATATTCATTGTATCCATACAT
262899 AAAGAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (32 bp):
GTATCGATACATATTCATTGTATCCATACATT
Found at i:262888 original size:19 final size:20
Alignment explanation
Indices: 262864--262918 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
262854 TGTATCCATA
**
262864 CATTGTATCGATACAT-ATT
1 CATTGTATCGATACATAAAG
262883 CATTGTATCGATACATAAAG
1 CATTGTATCGATACATAAAG
*
262903 AATTGTATCGATACAT
1 CATTGTATCGATACAT
262919 GAAACTGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
CATTGTATCGATACATAAAG
Found at i:262909 original size:20 final size:19
Alignment explanation
Indices: 262865--262918 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
262855 GTATCCATAC
***
262865 ATTGTATCGATACATATTC
1 ATTGTATCGATACATAAGA
262884 ATTGTATCGATACATAAAGA
1 ATTGTATCGATACAT-AAGA
262904 ATTGTATCGATACAT
1 ATTGTATCGATACAT
262919 GAAACTGGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (19 bp):
ATTGTATCGATACATAAGA
Found at i:264578 original size:57 final size:57
Alignment explanation
Indices: 264506--264620 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
264496 GTTGTTAGAC
* * * *
264506 TATTTTCATTTTTATTTATGCGTTTGCACTATTCACTTGTTTACATCTTTTTGAGTT
1 TATTGTCATTTTTATTCATGCATTTGCACGATTCACTTGTTTACATCTTTTTGAGTT
*
264563 TATTGTCATTTTTATTCATGCATTTGCACGATTCACTTGTTTACTTCTTTTTGAGTT
1 TATTGTCATTTTTATTCATGCATTTGCACGATTCACTTGTTTACATCTTTTTGAGTT
264620 T
1 T
264621 TTTAAATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (57 bp):
TATTGTCATTTTTATTCATGCATTTGCACGATTCACTTGTTTACATCTTTTTGAGTT
Found at i:266722 original size:152 final size:154
Alignment explanation
Indices: 266540--266825 Score: 366
Period size: 153 Copynumber: 1.9 Consensus size: 154
266530 AATTCTCATG
* * *
266540 TTTTCAAAATACGGAGTTTTCTACTTCGTAAAT-TTT-TCGAGAGGA-TTTTCATT-GATCCAAA
1 TTTTCAAAATACGAAGTTTTCTACTACGTAAATATTTGTAGAGA-GATTTTTC-TTAGATCCAAA
* *
266601 GTTTTTAAAATTCATAAAATATTATTATTTAATTCATATTAAATTAGCTTTCAAAAATTCATTCA
64 -TTTTTAAAACTCATAAAATATTATTATTTAATTCATATTAAATCAGCTTTCAAAAATTCATTCA
266666 TTTTCATTTTTTCTTGAAATTTTTCTA
128 TTTTCATTTTTTCTTGAAATTTTTCTA
* ***
266693 TTTT-AAAATACGAAGTTTTCTACTACGTAAATATTTGTAGAGAGATTTTTCTTAGTTTTTAATT
1 TTTTCAAAATACGAAGTTTTCTACTACGTAAATATTTGTAGAGAGATTTTTCTTAGATCCAAATT
* * * * * **
266757 TTTAAAACTGATCAAATATTATTATTTAATTCATATTAGATCAGTTTTCATAAATTCATTTGTTT
66 TTTAAAACTCATAAAATATTATTATTTAATTCATATTAAATCAGCTTTCAAAAATTCATTCATTT
266822 TCAT
131 TCAT
266826 CAGTTTTGAA
Statistics
Matches: 113, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 26 0.23
153 73 0.65
154 14 0.12
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (154 bp):
TTTTCAAAATACGAAGTTTTCTACTACGTAAATATTTGTAGAGAGATTTTTCTTAGATCCAAATT
TTTAAAACTCATAAAATATTATTATTTAATTCATATTAAATCAGCTTTCAAAAATTCATTCATTT
TCATTTTTTCTTGAAATTTTTCTA
Found at i:266855 original size:14 final size:13
Alignment explanation
Indices: 266830--266854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
266820 TTTCATCAGT
266830 TTTGAATTTTTTC
1 TTTGAATTTTTTC
266843 TTTGAATTTTTT
1 TTTGAATTTTTT
266855 TATTACCGAA
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:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTGAATTTTTTC
Found at i:267349 original size:9 final size:10
Alignment explanation
Indices: 267329--267375 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
267319 TCAGCTGAAA
*
267329 AAGAAGAGAG
1 AAGAAAAGAG
267339 AA-AAAAGAG
1 AAGAAAAGAG
267348 AAGGAAAAGA-
1 AA-GAAAAGAG
267358 AAGAAAAAGAG
1 AAG-AAAAGAG
267369 AAGAAAA
1 AAGAAAA
267376 TATAGCGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 9 0.28
10 14 0.44
11 9 0.28
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAGAAAAGAG
Found at i:270840 original size:51 final size:51
Alignment explanation
Indices: 270780--270925 Score: 240
Period size: 51 Copynumber: 2.9 Consensus size: 51
270770 TTTTAACTAG
*
270780 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAAATAGA
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAAACAGA
* * *
270831 ATGTATCGATACATTAAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAAACAGA
*
270882 ATGTATCGACACATT-AAAAATGTATCGATACATCTAGGTAAAAA
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAA
270926 TATGACTTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 27 0.31
51 61 0.69
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.27
Consensus pattern (51 bp):
ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAAACAGA
Found at i:271287 original size:13 final size:13
Alignment explanation
Indices: 271269--271357 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 13
271259 ACATAAATGT
271269 TGTATCGATACAA
1 TGTATCGATACAA
271282 TGTATCGATACATAA
1 TGTATCGATAC--AA
271297 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
271314 GGTATCGATACATAA
1 TGTATCGATAC--AA
271329 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
271346 GGTATCGATACA
1 TGTATCGATACA
271358 TAAGTTTTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
13 32 0.52
15 4 0.07
17 4 0.07
19 21 0.34
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:271295 original size:32 final size:32
Alignment explanation
Indices: 271250--271384 Score: 216
Period size: 32 Copynumber: 4.2 Consensus size: 32
271240 TTCAGCAATT
* *
271250 TGTATCGAAACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
271282 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
271314 GGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
271346 GGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
271378 TGTATCG
1 TGTATCG
271385 CTAGGAAGCT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:271306 original size:19 final size:18
Alignment explanation
Indices: 271249--271376 Score: 88
Period size: 19 Copynumber: 7.7 Consensus size: 18
271239 TTTCAGCAAT
*
271249 TTGTATCGAAACATAAATG
1 TTGTATCGATACAT-AATG
271268 TTGTATCGATAC--AA--
1 TTGTATCGATACATAATG
271282 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAA-TG
271300 TTGTATCGATAC--AA-G
1 TTGTATCGATACATAATG
*
271315 --GTATCGATACATAAGTT
1 TTGTATCGATACATAA-TG
271332 TTGTATCGATAC--AA-G
1 TTGTATCGATACATAATG
*
271347 --GTATCGATACATAAGTT
1 TTGTATCGATACATAA-TG
271364 TTGTATCGATACA
1 TTGTATCGATACA
271377 ATGTATCGCT
Statistics
Matches: 87, Mismatches: 4, Indels: 36
0.69 0.03 0.28
Matches are distributed among these distances:
13 31 0.36
15 7 0.08
16 2 0.02
17 4 0.05
19 43 0.49
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACATAATG
Found at i:271472 original size:34 final size:33
Alignment explanation
Indices: 271408--271474 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
271398 GCCAAGGAAA
* *
271408 TGTATCGATAAATTTTTCTGTGTATTGATACAT
1 TGTATCGATAAATTATTCTGTGTATCGATACAT
* *
271441 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATAAAT-TATTCTGTGTATCGATACAT
271475 CTAGGAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (33 bp):
TGTATCGATAAATTATTCTGTGTATCGATACAT
Found at i:274170 original size:52 final size:51
Alignment explanation
Indices: 274043--274212 Score: 196
Period size: 52 Copynumber: 3.3 Consensus size: 51
274033 TTATCTCCGA
* * *
274043 GGGGATACTCCAACCCCAGTTTTATTTCCAAATCATCGATTTTCCATAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCATAATC
* * * *
274094 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCC-ATAATC
* * * * * *
274146 GGGGATACTCCAACTCCAATTTTATTTCCAAAAATACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCAGTTTTATTTCC-AAAACACCAATTTTCCATAATC
*
274198 GAGGATACTCCAACC
1 GGGGATACTCCAACC
274213 TCGTTATTTC
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
51 39 0.40
52 45 0.46
53 14 0.14
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCATAATC
Found at i:274403 original size:78 final size:79
Alignment explanation
Indices: 274223--274428 Score: 227
Period size: 78 Copynumber: 2.6 Consensus size: 79
274213 TCGTTATTTC
* ** *
274223 ATCGGAGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAAT
* *
274288 ATTGATTTCTCATA
66 ATCGATTTCTCACA
* * * * * ** *
274302 ATTGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCTC-GATTTTTTTTC-TAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAAT
274365 CATCGATTTCTCACA
66 -ATCGATTTCTCACA
* * * *
274380 ATCGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
274429 TTATTATCTC
Statistics
Matches: 103, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
77 3 0.03
78 59 0.57
79 41 0.40
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAAT
ATCGATTTCTCACA
Found at i:277919 original size:52 final size:52
Alignment explanation
Indices: 277830--277958 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
277820 CGAAATATGA
*
277830 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* * *
277882 AACTTTGCCTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
277934 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
277959 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:277971 original size:52 final size:51
Alignment explanation
Indices: 277830--277978 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 51
277820 CGAAATATGA
277830 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * * *
277882 AACTTTGCCTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
277934 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
277979 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:277985 original size:13 final size:13
Alignment explanation
Indices: 277967--277991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277957 CAAAGATCAG
277967 TGTATCGATACAA
1 TGTATCGATACAA
277980 TGTATCGATACA
1 TGTATCGATACA
277992 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:278092 original size:33 final size:33
Alignment explanation
Indices: 278032--278163 Score: 239
Period size: 33 Copynumber: 4.0 Consensus size: 33
278022 AGTAGCTTAA
*
278032 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
*
278064 ATTGTATGGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
278097 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
278130 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
278163 A
1 A
278164 AATCGTTGAA
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 16 0.17
33 80 0.83
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAACACTTTATGTATCGATAC
Found at i:278095 original size:20 final size:20
Alignment explanation
Indices: 278066--278164 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 20
278056 ATCGATACAT
*
278066 TGTATGGATACAACACTTTA
1 TGTATCGATACAACACTTTA
278086 TGTATCGAT---ACA---T-
1 TGTATCGATACAACACTTTA
278099 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
278119 TGTATCGAT---ACA---T-
1 TGTATCGATACAACACTTTA
278132 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
278152 TGTATCGATACAA
1 TGTATCGATACAA
278165 ATCGTTGAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 28
0.69 0.01 0.30
Matches are distributed among these distances:
13 18 0.28
14 2 0.03
16 6 0.09
17 6 0.09
19 2 0.03
20 30 0.47
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACACTTTA
Found at i:278104 original size:13 final size:13
Alignment explanation
Indices: 278086--278143 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
278076 CAACACTTTA
278086 TGTATCGATACAT
1 TGTATCGATACAT
278099 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
278118 ATGTATCGATACAT
1 -TGTATCGATACAT
278132 TGTATCGATACA
1 TGTATCGATACA
278144 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:279130 original size:55 final size:52
Alignment explanation
Indices: 279035--279565 Score: 276
Period size: 52 Copynumber: 10.8 Consensus size: 52
279025 GTGATAAAGA
* * * * * *
279035 TGCCAATATGTTGATTCACGGCCAACGATATT-AGGCTTAAAGATGAGAAAAATG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGA-ACTTAAAGATG-G-AAAATG
* *
279089 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
1 -TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
* *
279142 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G-----G
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
* * *
279185 TGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAA-G
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
* * * * * * * *
279233 ATGCCAATATGTTGATTCAAGGCCAGCGATATAGGACTTAAGGATGAAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
* * * * * *
279286 AGCCAATATGATGATTCAAGGCCAGCGATATTGGACTT--GGA-GG----TG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
* *
279331 T--CAATGTGCTGATTCAAGGCCAGCTACATT-AGACTTAAAGAT-G--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGA-ACTTAAAGATGGAAAATG
* * * * *
279378 TGCCAATATGCTGATTCAAGGCCAACGATATTGGAC-T-----TGG---AGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
* * *
279421 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
* * * * * * ** *
279470 TGCCAATGTGCTGATTCAAGGCCAGCAATATTGGACTTAGAGGTGCCAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
* * * *
279522 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTA-AAGA
279566 AGACGCCACC
Statistics
Matches: 391, Mismatches: 52, Indels: 68
0.77 0.10 0.13
Matches are distributed among these distances:
43 101 0.26
44 4 0.01
45 5 0.01
47 2 0.01
48 4 0.01
49 111 0.28
50 4 0.01
51 2 0.01
52 112 0.29
53 9 0.02
54 1 0.00
55 35 0.09
56 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG
Found at i:279184 original size:22 final size:22
Alignment explanation
Indices: 279159--279226 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
279149 ATGCTGATTC
279159 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * * *
279181 AAGGTGCCA-ATGTGTT-GA-TTC
1 AA-G-GCCAGCTATATTGGACTTA
*
279202 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
279224 AAG
1 AAG
279227 ATAAAGATGC
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.19
22 9 0.28
23 5 0.16
24 4 0.12
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:279202 original size:43 final size:43
Alignment explanation
Indices: 279141--279518 Score: 297
Period size: 43 Copynumber: 8.2 Consensus size: 43
279131 GATGGAAAAT
279141 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
279184 GTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
279227 ATAAAGATGCCAATATGTTGATTCAAGGCCAGCGATATAGGACTTAAGGATGAAAAAG
1 -----G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---AAAG
* * * **
279285 GAGCCAATATGATGATTCAAGGCCAGCGATATTGGACTTGGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * * *
279328 GTGTCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAG
* * **
279377 GTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTGGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* *
279420 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAG
* * *
279469 GTGCCAATGTGCTGATTCAAGGCCAGCAATATTGGACTTAGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
279512 GTGCCAA
1 GTGCCAA
279519 AGGCGCCAAT
Statistics
Matches: 270, Mismatches: 38, Indels: 54
0.75 0.10 0.15
Matches are distributed among these distances:
43 120 0.44
45 1 0.00
46 1 0.00
48 1 0.00
49 106 0.39
50 1 0.00
51 1 0.00
52 33 0.12
53 1 0.00
55 1 0.00
58 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (43 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
Found at i:279302 original size:144 final size:142
Alignment explanation
Indices: 279093--279560 Score: 545
Period size: 144 Copynumber: 3.3 Consensus size: 142
279083 AAAATGATGT
* * * * *
279093 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAGAT-GAAAAGGTGCCAATATGCTGATT
*
279158 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTT
64 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
279223 AAAGATAAAGATGC
129 AAAGATAAAGGTGC
* * * *
279237 CAATATGTTGATTCAAGGCCAGCGATATAGGACTTAAGGATGAAAAAGGAGCCAATATGATGATT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA-GATG-AAAAGGTGCCAATATGCTGATT
* ** * *
279302 CAAGGCCAGCGATATTGGACTTGGAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTAGACTT
64 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
279367 AAAGATGAAGGTGC
129 AAAGATAAAGGTGC
* *
279381 CAATATGCTGATTCAAGGCCAACGATATTGGACTT--G--G---AGGTGCCAATGTGCTGATTCA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGATGAAAAGGTGCCAATATGCTGATTCA
* * *
279439 AGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCAATATTGG
66 AGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
* * *
279504 ACTTAGAGGTGCCAAAGGCGC
125 ACTTAAAGAT---AAAGGTGC
279525 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
279561 GAAGAAGACG
Statistics
Matches: 276, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
135 36 0.13
139 1 0.00
141 42 0.15
143 3 0.01
144 194 0.70
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (142 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGATGAAAAGGTGCCAATATGCTGATTCA
AGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
AGATAAAGGTGC
Found at i:279408 original size:92 final size:92
Alignment explanation
Indices: 279141--279518 Score: 419
Period size: 92 Copynumber: 4.1 Consensus size: 92
279131 GATGGAAAAT
* * * * *
279141 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGTTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAGGTGCCAATATGCTGAT
* * *
279200 TCAAGGCCAGCTACATTGGACTTAAAGATAAAG
66 TCAAGGCCAGCGATATTGGACTT---G---GAG
* * * * * * * *
279233 ATGCCAATATGTTGATTCAAGGCCAGCGATA-TAGGACTTAAGGATGAAAAAGGAGCCAATATGA
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTA-GACTTAAAGATG---AAGGTGCCAATATGC
279297 TGATTCAAGGCCAGCGATATTGGACTTGGAG
62 TGATTCAAGGCCAGCGATATTGGACTTGGAG
*
279328 GTGTCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAGGTGCCAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAGGTGCCAATATGCTGAT
*
279393 TCAAGGCCAACGATATTGGACTTGGAG
66 TCAAGGCCAGCGATATTGGACTTGGAG
* *
279420 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAGGTGCCAATATGCTGAT
* *
279485 TCAAGGCCAGCAATATTGGACTTAGAG
66 TCAAGGCCAGCGATATTGGACTTGGAG
279512 GTGCCAA
1 GTGCCAA
279519 AGGCGCCAAT
Statistics
Matches: 249, Mismatches: 26, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
91 1 0.00
92 169 0.68
95 38 0.15
96 3 0.01
98 1 0.00
101 37 0.15
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (92 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAGGTGCCAATATGCTGAT
TCAAGGCCAGCGATATTGGACTTGGAG
Found at i:279508 original size:236 final size:238
Alignment explanation
Indices: 279090--279559 Score: 741
Period size: 236 Copynumber: 2.0 Consensus size: 238
279080 AGAAAAATGA
*
279090 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
1 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG-AAAGGTGCCAATATGCTG
* * *
279155 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGA
65 ATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
* *
279220 CTTAAAGATAAAGATGCCAATATGTTGATTCAAGGCCAGCGATATAGGACTTA-AGGATGAAAAA
130 CTTAAAGATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATAGGACTTAGAGG-TGAAAAA
279284 GGAGCCAATATGATGATTCAAGGCCAGCGATATTGGACTTGGAGG
194 GGAGCCAATATGATGATTCAAGGCCAGCGATATTGGACTTGGAGG
279329 TGTCAATGTGCTGATTCAAGGCCAGCTACATT-AGACTTAAAGAT-G-AAGGTGCCAATATGCTG
1 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGA-ACTTAAAGATGGAAAGGTGCCAATATGCTG
**
279391 ATTCAAGGCCAACGATATTGGACTTGGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
65 ATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
* * * * **
279456 CTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCAATATTGGACTTAGAGGTGCCAAAG
130 CTTAAAGATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATAGGACTTAGAGGTGAAAAAG
* *
279521 GCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
195 GAGCCAATATGATGATTCAAGGCCAGCGATATTGGACTT
279560 AGAAGAAGAC
Statistics
Matches: 213, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
236 166 0.78
237 3 0.01
238 2 0.01
239 42 0.20
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (238 bp):
TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGA
TTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
TTAAAGATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATAGGACTTAGAGGTGAAAAAGG
AGCCAATATGATGATTCAAGGCCAGCGATATTGGACTTGGAGG
Found at i:279639 original size:28 final size:28
Alignment explanation
Indices: 279582--279733 Score: 191
Period size: 28 Copynumber: 5.3 Consensus size: 28
279572 CACCAACTTG
*
279582 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-GACT
*
279611 TGTGTGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
279639 TGTGGGCTTTTAAAGATTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
279667 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* * *
279695 TGTAGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
279725 TGTGGGCTT
1 TGTGGGCTT
279734 AAAAGGAAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
27 3 0.03
28 73 0.66
29 11 0.10
30 23 0.21
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:279736 original size:84 final size:84
Alignment explanation
Indices: 279582--279738 Score: 196
Period size: 86 Copynumber: 1.8 Consensus size: 84
279572 CACCAACTTG
* *
279582 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGTGCTTTTAAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGTGCTTTTAAAGGGTGCCACTAACTTGTGGGC-
279647 TTTAAAGATTGCCACTGACT
65 TTTAAAGATTGCCACTGACT
*
279667 TGTGGGCTTTT-AAAGG-TTGCCA-CTGACTTGTAG-GCTTTTGAAAAGGGTGCCACTAACTTGT
1 TGTGGGCTTTTGAAAGGTTTG-CATC-AACTTGT-GTGCTTTT--AAAGGGTGCCACTAACTTGT
*
279728 GGGCTTAAAAG
61 GGGCTTTAAAG
279739 GAAAAAGAGT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
83 4 0.06
84 19 0.30
85 18 0.29
86 22 0.35
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (84 bp):
TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGTGCTTTTAAAGGGTGCCACTAACTTGTGGGCT
TTAAAGATTGCCACTGACT
Found at i:279762 original size:34 final size:35
Alignment explanation
Indices: 279724--279798 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
279714 TGCCACTAAC
* * * *
279724 TTGTGGGCTTA-AAAGGAAAAAGAGTGCTATGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAATGCCACGGAG
* *
279758 TTGTGAGCTTACAAAAGAAAAGGAATGCCACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAATGCCACGGAG
279793 TTGTGG
1 TTGTGG
279799 ACTTTGGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
34 10 0.30
35 23 0.70
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.23
Consensus pattern (35 bp):
TTGTGGGCTTACAAAAGAAAAAGAATGCCACGGAG
Found at i:279836 original size:29 final size:29
Alignment explanation
Indices: 279782--279947 Score: 174
Period size: 29 Copynumber: 5.8 Consensus size: 29
279772 AAGAAAAGGA
* * *
279782 ATGCCACGGAGTTGTGGACTTTGGAAAAG
1 ATGCCACTGACTTGTGGGCTTTGGAAAAG
* * *
279811 ATGCCACCGACTTATGGGCTTCGGAAAAGG
1 ATGCCACTGACTTGTGGGCTTTGGAAAA-G
* * *
279841 GTGCCACTGATTTGTGGGCTTT-G-AAGG
1 ATGCCACTGACTTGTGGGCTTTGGAAAAG
* * * *
279868 TTGCCACTGAGTTGTGGACTTTGAAAAAG
1 ATGCCACTGACTTGTGGGCTTTGGAAAAG
*
279897 ATGCCACTGACTTGTGGGCTTTGAAAAAG
1 ATGCCACTGACTTGTGGGCTTTGGAAAAG
*
279926 ATGCCACTAACTTGTGGGCTTT
1 ATGCCACTGACTTGTGGGCTTT
279948 TGAAGGGTGA
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
27 20 0.18
28 2 0.02
29 74 0.65
30 18 0.16
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (29 bp):
ATGCCACTGACTTGTGGGCTTTGGAAAAG
Found at i:279950 original size:86 final size:88
Alignment explanation
Indices: 279628--279953 Score: 265
Period size: 86 Copynumber: 3.7 Consensus size: 88
279618 TTTTAAAGGT
** * *
279628 TGCCACTGACTTGTGGGCTT---TTAAAGATTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCAC
1 TGCCACTGACTTGTGGGCTTAGGAAAAAGAGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCAC
* * *
279690 TGACTTGTAGG-CTTTTGAAAAGGG
66 TGAGTTGT-GGAC-TTTGAAAAAGA
* * * * **
279714 TGCCACTAACTTGTGGGCTTAAAAGGAAAAAGAGTGCTA-TGGAGTTGTGAGCTTACAAAAGAAA
1 TGCCACTGACTTGTGGGCTT---AGGAAAAAGAGTGCCACT-GACTTGTGGGCTT----TTG--A
* * *
279778 AGGAATGCCACGGAGTTGTGGACTTTGGAAAAGA
56 AGG-TTGCCACTGAGTTGTGGACTTTGAAAAAGA
* * * * *
279812 TGCCACCGACTTATGGGCTTCGG-AAAAGGGTGCCACTGATTTGTGGGC-TTTGAAGGTTGCCAC
1 TGCCACTGACTTGTGGGCTTAGGAAAAAGAGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCAC
279875 TGAGTTGTGGACTTTGAAAAAGA
66 TGAGTTGTGGACTTTGAAAAAGA
* *
279898 TGCCACTGACTTGTGGGCTT-TGAAAAAGA-TGCCACTAACTTGTGGGCTTTTGAAGG
1 TGCCACTGACTTGTGGGCTTAGGAAAAAGAGTGCCACTGACTTGTGGGCTTTTGAAGG
279954 GTGAGGAATG
Statistics
Matches: 187, Mismatches: 35, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
85 17 0.09
86 77 0.41
87 4 0.02
89 1 0.01
91 1 0.01
92 20 0.11
93 1 0.01
94 19 0.10
95 3 0.02
98 31 0.17
99 13 0.07
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (88 bp):
TGCCACTGACTTGTGGGCTTAGGAAAAAGAGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCAC
TGAGTTGTGGACTTTGAAAAAGA
Found at i:281163 original size:16 final size:15
Alignment explanation
Indices: 281139--281176 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
281129 GTTGTTGTTG
281139 TTTTTTTTTCTATTT
1 TTTTTTTTTCTATTT
*
281154 TTTTTATTTTTTATTT
1 TTTTT-TTTTCTATTT
281170 TTTTTTT
1 TTTTTTT
281177 GCGGAGGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.08, C:0.03, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTCTATTT
Found at i:294152 original size:21 final size:19
Alignment explanation
Indices: 294128--294168 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
294118 TGGAGGTGCT
294128 AAACATGCTGTAAAATGCATG
1 AAACATG-T-TAAAATGCATG
*
294149 AAACATGTTCAAATGCATG
1 AAACATGTTAAAATGCATG
294168 A
1 A
294169 TCATGGGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 1 0.05
21 7 0.37
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (19 bp):
AAACATGTTAAAATGCATG
Found at i:295127 original size:13 final size:13
Alignment explanation
Indices: 295109--295133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
295099 CAAAGATCAG
295109 TGTATCGATACAA
1 TGTATCGATACAA
295122 TGTATCGATACA
1 TGTATCGATACA
295134 TTGAGTAATG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:295210 original size:33 final size:33
Alignment explanation
Indices: 295173--295239 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
295163 AGTAGCTTAA
295173 ATTGTATCAATACAAAAAAATATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
* * ***
295206 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
295239 A
1 A
295240 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (33 bp):
ATTGTATCAATACAAAAAAATATGTATCGATAC
Found at i:295213 original size:13 final size:13
Alignment explanation
Indices: 295195--295219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
295185 CAAAAAAATA
295195 TGTATCGATACAT
1 TGTATCGATACAT
295208 TGTATCGATACA
1 TGTATCGATACA
295220 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:566672 original size:20 final size:20
Alignment explanation
Indices: 566647--566699 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
566637 TCCCGTAGCT
*
566647 ATGTATCAATACAATTCATA
1 ATGTATCAATACAAATCATA
566667 ATGTATCAATACAAATCATA
1 ATGTATCAATACAAATCATA
*
566687 ATGTATCGATACA
1 ATGTATCAATACA
566700 TGCATTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (20 bp):
ATGTATCAATACAAATCATA
Found at i:566778 original size:13 final size:13
Alignment explanation
Indices: 566760--566784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
566750 CAATTCATTA
566760 TATATCGATACAT
1 TATATCGATACAT
566773 TATATCGATACA
1 TATATCGATACA
566785 ATGCACCATG
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:566779 original size:33 final size:33
Alignment explanation
Indices: 566742--566804 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
566732 TAAAGCAATG
* **
566742 TATCGATACAATTCATTATATATCGATACATTA
1 TATCGATACAATGCACCATATATCGATACATTA
*
566775 TATCGATACAATGCACCATGTATCGATACA
1 TATCGATACAATGCACCATATATCGATACA
566805 AACAGTGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (33 bp):
TATCGATACAATGCACCATATATCGATACATTA
Found at i:566882 original size:19 final size:20
Alignment explanation
Indices: 566834--566887 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
566824 TTACCAGTTT
**
566834 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
* *
566854 CATATATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
566873 CATGTATCGATACAA
1 CATGTATCGATACAA
566888 AGCATAATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:567651 original size:21 final size:21
Alignment explanation
Indices: 567607--567661 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
567597 TTAGGCTTAG
*
567607 TGTATCGATACAA-TCCACTA
1 TGTATCGATACAATTCAACTA
*
567627 TGTATCGATACAATTCAAGTA
1 TGTATCGATACAATTCAACTA
*
567648 TGTATTGATACAAT
1 TGTATCGATACAAT
567662 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACAATTCAACTA
Found at i:567752 original size:74 final size:74
Alignment explanation
Indices: 567626--567805 Score: 272
Period size: 74 Copynumber: 2.4 Consensus size: 74
567616 ACAATCCACT
* * *
567626 ATGTATCGATACAATTCAAGTATGTATTGATACAATGTATCGATACTGAGTGAGTTTTAGCTACT
1 ATGTATCGATACAATTCAAGTATGTATCGATACAATGTATCAATACTAAGTGAGTTTTAGCTACT
*
567691 GCCAATTTC
66 ACCAATTTC
*
567700 ATGTATCGATACAATTCAAGTATTTATCGATACAATGTATCAATACTAAGTGAGTTTTAGCTACT
1 ATGTATCGATACAATTCAAGTATGTATCGATACAATGTATCAATACTAAGTGAGTTTTAGCTACT
* *
567765 ACCAGTTTT
66 ACCAATTTC
* *
567774 ATGTATCGATACAATTCAA-TGTGTATAGATAC
1 ATGTATCGATACAATTCAAGTATGTATCGATAC
567806 TATGAACATG
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 10 0.10
74 86 0.90
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (74 bp):
ATGTATCGATACAATTCAAGTATGTATCGATACAATGTATCAATACTAAGTGAGTTTTAGCTACT
ACCAATTTC
Found at i:567831 original size:13 final size:13
Alignment explanation
Indices: 567813--567837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
567803 TACTATGAAC
567813 ATGTATCGATACA
1 ATGTATCGATACA
567826 ATGTATCGATAC
1 ATGTATCGATAC
567838 TAAGCAATAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:567855 original size:33 final size:32
Alignment explanation
Indices: 567795--567858 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
567785 CAATTCAATG
*
567795 TGTATAGATACTATGAACATGTATCGATACAA
1 TGTATAGATACTAAGAACATGTATCGATACAA
* *
567827 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATAGATACTAAG-AACATGTATCGATACA
567859 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (32 bp):
TGTATAGATACTAAGAACATGTATCGATACAA
Found at i:569982 original size:3 final size:3
Alignment explanation
Indices: 569974--570015 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
569964 ATTTCATTTA
569974 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
570016 TAAAATACCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:571065 original size:21 final size:21
Alignment explanation
Indices: 571040--571081 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
571030 TAGTTTTCTA
571040 TTTTCTTCTCTATTTTCCTCT
1 TTTTCTTCTCTATTTTCCTCT
* * *
571061 TTTTCTTTTTTTTTTTCCTCT
1 TTTTCTTCTCTATTTTCCTCT
571082 CTAATTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTCTTCTCTATTTTCCTCT
Found at i:572132 original size:163 final size:163
Alignment explanation
Indices: 571443--572217 Score: 773
Period size: 164 Copynumber: 4.7 Consensus size: 163
571433 TGAAATAATT
* * * * *
571443 TGAATTTTTCAAAAATGACTTAATTTGAATTTAATAACAATA-TTAGATGAATTTT-AAAATTAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTA-ATGAATTTTAAAAATT-A
* * * ** * *
571506 AAACCAAGAAAAATCCCCCCA-AAAACATTTATGGAATTGAAAACTCCGTATTTCGGAAATATGA
64 AAACCAAGAAAAAT--CCCCAGAAAACATTTAAGGAGTAGAAAACTCTATATTTCAGAAACA-GA
*
571570 GAATTTCAAGAAAAAAATGAAAAATTTATAAAAATGAA
126 AAATTTCAAGAAAAAAATGAAAAATTTATAAAAATGAA
* * * *
571608 T-AATTTTTGAAAATTGACTTAATATGAATTAAATACA-AATATTTTATGAA-TTTCAAAATTAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATA-ATAATATTTAATGAATTTTAAAAATTAA
* ** * * * * *
571670 AAGCCTAGAAAAATCCTCTTGAAAATATTTACGAAGTAGAAAACTCTATATTTCAAAAATAGGAA
65 AA-CCAAGAAAAATCC-CCAGAAAACATTTAAGGAGTAGAAAACTCTATATTTCAGAAACA-GAA
* *
571735 AATTTCAA-AGAAAAAATGAAAAACTCATAAAAATGAA
127 AATTTCAAGA-AAAAAATGAAAAATTTATAAAAATGAA
** * * * *
571772 TGAATTTTTGAAAACCGATTTAGTATGAATTAAATAATAATAGTTGAT-AAATTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
* ** * * * ** * *
571836 ACCACGAAAAATCTCCTTGAAAACATTTACGGAGTATAAAACTTTATATTTTGGAAACCGAGAAT
66 ACCAAGAAAAATC-CCCAGAAAACATTTAAGGAGTAGAAAACTCTATATTTCAGAAACAGAAAAT
** *
571901 TTCAAGAAAAAAATTGAAAAATGAATGAAAATGAA
130 TTCAAGAAAAAAA-TGAAAAATTTATAAAAATGAA
*
571936 TGAATTTTTGAAAAATGATTTGATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
*
572001 ACCAAGAAAAATCCCCAGAAAACA-TTAAAGAGTAGAAAACTCTATATTTC-GAAACAGAAAAAT
66 ACCAAGAAAAATCCCCAGAAAACATTTAAGGAGTAGAAAACTCTATATTTCAGAAACAG-AAAAT
*
572064 TTCAAGGAAAAAAAT-AAAACATTTATGAAAATGAA
130 TTCAA-GAAAAAAATGAAAA-ATTTATAAAAATGAA
* * * * *
572099 TGAATTTTTTAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
1 TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATT-AA
* * * * *
572164 AACCAAGAAAAATCTCTCC-GAAAATATTTACGAAGTAAAAAACTCCATATTTCA
65 AACCAAGAAAAATC-C-CCAGAAAACATTTAAGGAGTAGAAAACTCTATATTTCA
572218 AAAATAGAGA
Statistics
Matches: 513, Mismatches: 75, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
162 12 0.02
163 125 0.24
164 263 0.51
165 90 0.18
166 23 0.04
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (163 bp):
TGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTAATGAATTTTAAAAATTAAA
ACCAAGAAAAATCCCCAGAAAACATTTAAGGAGTAGAAAACTCTATATTTCAGAAACAGAAAATT
TCAAGAAAAAAATGAAAAATTTATAAAAATGAA
Found at i:572132 original size:327 final size:329
Alignment explanation
Indices: 571470--572207 Score: 870
Period size: 329 Copynumber: 2.2 Consensus size: 329
571460 ACTTAATTTG
* * * * * *
571470 AATTTAATAACAATA-TTAGATG-AATTTTAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACA
1 AATTAAATAATAATAGTT-GATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTCCGAAAACA
* ** *** * ** **
571533 TTTATGGAA-TTGAAAACTCCGTATTTCGGAAATATGAGAATTTCAAGAAAAAAATGAAAAATTT
65 TTTA-CGAAGTAAAAAACTTTATATTTTGGAAA-CCGAGAATTTCAAGAAAAAAATGAAAAATGA
* * *
571597 ATAAAAATGAATAATTTTTGAAAATTGACTTAATATGAATTAAATACAAATATTTTATGAATTTC
128 ATAAAAATGAATAATTTTTGAAAAATGACTTAATATGAATTAAATACAAATATTTAATGAATTTA
* ** * * *
571662 AAAATTAAAAGCCTAGAAAAATCCTCTTGAAAATATTTACGAAGTAGAAAACTCTATATTTCAAA
193 AAAATTAAAAGCCAAGAAAAATCCTCCAGAAAACATTAAAGAAGTAGAAAACTCTATATTTCAAA
* * *
571727 AATAGGAAAATTTCAAAGAAAAAATGAAAAACTCATAAAAATGAATGAATTTTTGAAAACCGATT
258 AACAGAAAAATTTCAAAGAAAAAATGAAAAACTCATAAAAATGAATGAATTTTTGAAAACCAATT
* *
571792 TAGTATG
323 TAATATA
* *
571799 AATTAAATAATAATAGTTGAT-AAATTTAAAAATT-AAAACCACGAAAAATCTC-CTTGAAAACA
1 AATTAAATAATAATAGTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTC-CGAAAACA
* *
571861 TTTACGGAGTATAAAACTTTATATTTTGGAAACCGAGAATTTCAAGAAAAAAATTGAAAAATGAA
65 TTTACGAAGTAAAAAACTTTATATTTTGGAAACCGAGAATTTCAAGAAAAAAA-TGAAAAATGAA
* * *
571926 TGAAAATGAATGAATTTTTGAAAAATGATTTGATATGAATTAAATA-ATAATATTTAATGAATTT
129 TAAAAATGAAT-AATTTTTGAAAAATGACTTAATATGAATTAAATACA-AATATTTAATGAA-TT
571990 TAAAAATTAAAA-CCAAGAAAAATCC-CCAGAAAACATTAAAG-AGTAGAAAACTCTATATTTC-
191 TAAAAATTAAAAGCCAAGAAAAATCCTCCAGAAAACATTAAAGAAGTAGAAAACTCTATATTTCA
* * * * * * *
572051 GAAACAGAAAAATTTCAAGGAAAAAAAT-AAAACATTTATGAAAATGAATGAATTTTTTAAAACT
256 AAAACAGAAAAATTTCAAAG-AAAAAATGAAAA-ACTCATAAAAATGAATGAATTTTTGAAAACC
572115 AATTTAATATA
319 AATTTAATATA
* * *
572126 AATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCTCTCCGAAAATAT
1 AATTAAATAATAATAGTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTCCGAAAACAT
572191 TTACGAAGTAAAAAACT
66 TTACGAAGTAAAAAACT
572208 CCATATTTCA
Statistics
Matches: 346, Mismatches: 50, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
326 20 0.06
327 103 0.30
328 86 0.25
329 121 0.35
330 16 0.05
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (329 bp):
AATTAAATAATAATAGTTGATGAAATTTAAAAATTAAAAACCAAGAAAAATCTCTCCGAAAACAT
TTACGAAGTAAAAAACTTTATATTTTGGAAACCGAGAATTTCAAGAAAAAAATGAAAAATGAATA
AAAATGAATAATTTTTGAAAAATGACTTAATATGAATTAAATACAAATATTTAATGAATTTAAAA
ATTAAAAGCCAAGAAAAATCCTCCAGAAAACATTAAAGAAGTAGAAAACTCTATATTTCAAAAAC
AGAAAAATTTCAAAGAAAAAATGAAAAACTCATAAAAATGAATGAATTTTTGAAAACCAATTTAA
TATA
Found at i:572272 original size:329 final size:329
Alignment explanation
Indices: 571443--572311 Score: 858
Period size: 329 Copynumber: 2.6 Consensus size: 329
571433 TGAAATAATT
* * * * * *
571443 TGAATTTTTCAAAAATGACTTAATTTGAATTTAATAACAATATTAGATGAATTTT-AAAATTAAA
1 TGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
* * * ** * *
571507 AACCAAGAAAAATCCCCCCAAAAACATTTATGGAA-TTGAAAACTCCGTATTTCGGAAATA-TGA
66 AACCAAGAAAAAT-CTCCCGAAAACATTTA-CGAAGTAAAAAACTCCATATTTCGGAAATAGAGA
** * * *
571570 GAATT-TCAAGAAAAAAATGAAAAATTTATAAAA-ATGAATAATTTTTGAAAATTGACTTAATAT
129 GAATTCT-AAGAAAAAAATGAAAAA-TTA-AAAATAAAAAGAATTTTTGAAAAATGATTTAATAT
* * * ** *
571633 GAATTAAATACA-AATATTTTATGAATTTCAAAATTAAAAGCCTAGAAAAATCCTCTTGAAAATA
191 GAATTAAATA-ATAATATTTAATGAATTTAAAAATTAAAAGCCAAGAAAAATCCTCCAGAAAACA
* * * *
571697 TTTACGAAGTAGAAAACTCTATATTTCAAAAATAGGAAAATTTCAAAGAAAAAATGAAAAACTCA
255 TTAAAGAAGTAGAAAACTCTATATTTCAAAAACAGAAAAATTTCAAAGAAAAAATGAAAAACTCA
571762 TAAAAATGAA
320 TAAAAATGAA
* * * * *
571772 TGAATTTTTGAAAACCGATTTAGTATGAATTAAATAATAATAGTTGAT-AAATTTAAAAATT-AA
1 TGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
* * * * ** * **
571835 AACCACGAAAAATCTCCTTGAAAACATTTACGGAGTATAAAACTTTATATTTTGGAAACCGAGA-
66 AACCAAGAAAAATCTCC-CGAAAACATTTACGAAGTAAAAAACTCCATATTTCGGAAATAGAGAG
* * * * *
571899 ATTTC-AAGAAAAAAATTGAAAAATGAATGAAA-ATGAATGAATTTTTGAAAAATGATTTGATAT
130 AATTCTAAGAAAAAAA-TGAAAAATTAA--AAATA-AAAAGAATTTTTGAAAAATGATTTAATAT
571962 GAATTAAATAATAATATTTAATGAATTTTAAAAATTAAAA-CCAAGAAAAATCC-CCAGAAAACA
191 GAATTAAATAATAATATTTAATGAA-TTTAAAAATTAAAAGCCAAGAAAAATCCTCCAGAAAACA
* * *
572025 TTAAAG-AGTAGAAAACTCTATATTTC-GAAACAGAAAAATTTCAAGGAAAAAAAT-AAAACATT
255 TTAAAGAAGTAGAAAACTCTATATTTCAAAAACAGAAAAATTTCAAAG-AAAAAATGAAAA-ACT
* *
572087 TATGAAAATGAA
318 CATAAAAATGAA
* * *
572099 TGAATTTTTTAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
1 TGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
* **
572164 AACCAAGAAAAATCTCTCCGAAAATATTTACGAAGTAAAAAACTCCATATTTCAAAAATAGAGAG
66 AACCAAGAAAAATCTC-CCGAAAACATTTACGAAGTAAAAAACTCCATATTTCGGAAATAGAGAG
* * * * *
572229 AATTCTAA-AAGAAAATCAATAACTTAAAAATTAAAAAGAATTTTTCAAAGAA-GATTTAATGGT
130 AATTCTAAGAAAAAAATGAA-AAATTAAAAA-TAAAAAGAATTTTTGAAA-AATGATTTAAT-AT
*
572292 G-ATTAAATGATAATATTTAA
191 GAATTAAATAATAATATTTAA
572312 AAAAATTTTG
Statistics
Matches: 437, Mismatches: 80, Indels: 46
0.78 0.14 0.08
Matches are distributed among these distances:
326 21 0.05
327 98 0.22
328 87 0.20
329 195 0.45
330 34 0.08
331 2 0.00
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (329 bp):
TGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
AACCAAGAAAAATCTCCCGAAAACATTTACGAAGTAAAAAACTCCATATTTCGGAAATAGAGAGA
ATTCTAAGAAAAAAATGAAAAATTAAAAATAAAAAGAATTTTTGAAAAATGATTTAATATGAATT
AAATAATAATATTTAATGAATTTAAAAATTAAAAGCCAAGAAAAATCCTCCAGAAAACATTAAAG
AAGTAGAAAACTCTATATTTCAAAAACAGAAAAATTTCAAAGAAAAAATGAAAAACTCATAAAAA
TGAA
Found at i:573629 original size:79 final size:78
Alignment explanation
Indices: 573546--573746 Score: 269
Period size: 79 Copynumber: 2.5 Consensus size: 78
573536 AATAAAATTA
*
573546 GGGTTGGAGTATCCCTTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGCTT
1 GGGTTGGAGTATCCCTTCGAAAATAAC-GGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTT
* *
573611 TAGAAATAAGGTCG
65 TAGAAATAAAGCCG
* ** * * *
573625 GGGTTAGAGTATCCCCACAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTT
1 GGGTTGGAGTATCCCTTCGAAAATAAC-GGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTT
573690 TAGAAATAAAGCCG
65 TAGAAATAAAGCCG
*
573704 GGGTTGGAGTATCCCCTTAG-AAATAACGGGATTGGAGTATCCC
1 GGGTTGGAGTAT-CCCTTCGAAAATAACGGG-TTGGAGTATCCC
573747 AATGAAATAA
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
78 3 0.03
79 99 0.94
80 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (78 bp):
GGGTTGGAGTATCCCTTCGAAAATAACGGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTTT
AGAAATAAAGCCG
Found at i:573765 original size:27 final size:27
Alignment explanation
Indices: 573704--573771 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
573694 AATAAAGCCG
**
573704 GGGTTGGAGTATCCCCTTAGAAATAAC
1 GGGTTGGAGTATCCCAATAGAAATAAC
573731 GGGATTGGAGTATCCCAAT-GAAATAAC
1 GGG-TTGGAGTATCCCAATAGAAATAAC
573758 GAGGTTGGAGTATC
1 G-GGTTGGAGTATC
573772 TCCGATTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (27 bp):
GGGTTGGAGTATCCCAATAGAAATAAC
Found at i:573823 original size:51 final size:51
Alignment explanation
Indices: 573761--573857 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
573751 AAATAACGAG
*
573761 GTTGGAGTATCTCCGATTGTGAAAAATTGGTGTTTT-GAAAATAAAATCGAA
1 GTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTAG-AAATAAAATCGAA
*
573812 GTTGGAGTATCTCCGATTATGGAAAATTGGTGTTTTAGAAATAAAA
1 GTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTAGAAATAAAA
573858 CCAGGGTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (51 bp):
GTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATCGAA
Found at i:573872 original size:51 final size:51
Alignment explanation
Indices: 573757--573873 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 51
573747 AATGAAATAA
* *
573757 CGAGGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAT
1 CGAGGTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTGAAAATAAAAC
* *
573808 CGAAGTTGGAGTATCTCCGATTATGGAAAATTGGTGTTTT-AGAAATAAAAC
1 CGAGGTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTGA-AAATAAAAC
*
573859 C-AGGGTTGAAGTATC
1 CGA-GGTTGGAGTATC
573874 CTCTCGAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 2 0.03
51 56 0.97
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (51 bp):
CGAGGTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTGAAAATAAAAC
Found at i:576287 original size:49 final size:50
Alignment explanation
Indices: 576231--576364 Score: 209
Period size: 50 Copynumber: 2.7 Consensus size: 50
576221 AAAAATGCTT
* *
576231 GAATGTATCGATACATTGAAAAATGTATCGATACATCT-GCGT-AAACCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTAG-GTAAAACCCA
576280 GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAACCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAACCCA
* *
576330 AAATGTATCGATACAATGAACAACGTATCGATACA
1 GAATGTATCGATACAATGAACAATGTATCGATACA
576365 AATTGTGAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
49 38 0.48
50 41 0.52
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (50 bp):
GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAACCCA
Found at i:577072 original size:84 final size:85
Alignment explanation
Indices: 576974--577270 Score: 305
Period size: 84 Copynumber: 3.5 Consensus size: 85
576964 GATTAAGGAA
* * * * **
576974 AAGGATAATGAAATGGGTCCTGCTCCTTGGGGACTAAGGAAAAAAAGAAATAAAATGCATTATGC
1 AAGGA-AATGAAATGTGTCCTGCTCTTTGAGGACAAAGG-AAAAAAGAAATAAAATGCATCCTGC
*
577039 CCTTTGAAGACAAAAGG-AAA-
64 TCTTTGAAGACAAAAGGAAAAG
* * * * * *
577059 AAGGAAATTAAATGTGTCCTGCTTTTTGAGGACAAAGGAAAAAGGAGAATAAAGTACGTCCTGCT
1 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGA-AATAAAATGCATCCTGCT
* *
577124 CTTTG-AGAACTAGAAGGGAAAAT
65 CTTTGAAG-AC-A-AAAGGAAAAG
* * * *
577147 AAGGAAATGAAGTGCGTCATGCTCTTTGAGGACAAAGGAAAAAAGAAA-AAAAGGCATCCTGCTC
1 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAATGCATCCTGCTC
*
577211 TTTGAGGACAAAAGGGAAAAG
66 TTTGAAGACAAAA-GGAAAAG
* *
577232 AAGGAAATGAAATGTGTCCTGCTCTTTCAGGATAAAGGA
1 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGA
577271 GATAAGGAAA
Statistics
Matches: 172, Mismatches: 32, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
83 9 0.05
84 48 0.28
85 47 0.27
86 22 0.13
87 6 0.03
88 40 0.23
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.21
Consensus pattern (85 bp):
AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAATGCATCCTGCTC
TTTGAAGACAAAAGGAAAAG
Found at i:577096 original size:41 final size:41
Alignment explanation
Indices: 576950--577302 Score: 261
Period size: 42 Copynumber: 8.4 Consensus size: 41
576940 GAAGAGGGCA
** *
576950 TCCTGCTCTTTGAGGATTAAGG-AAAAGGATAATGAAATGGG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGGA-AATGAAATGCG
* * * * * *
576991 TCCTGCTCCTTGGGGACTAAGGAAAAAAAGAAATAAAATGCA
1 TCCTGCTCTTTGAGGACAAAGG-AAAAAGGAAATGAAATGCG
** * * * *
577033 TTATGCCCTTTGAAGACAAAAGGAAAAAGGAAATTAAATGTG
1 TCCTGCTCTTTGAGGAC-AAAGGAAAAAGGAAATGAAATGCG
* *
577075 TCCTGCTTTTTGAGGACAAAGGAAAAAGGAGAAT-AAAGTACG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGGA-AATGAAA-TGCG
* *
577117 TCCTGCTCTTTGAGAACTAGAAGGGAAAATAAGGAAATGAAGTGCG
1 TCCTGCTCTTTGAGGAC-A-AA-GG-AAA-AAGGAAATGAAATGCG
* * * * *
577163 TCATGCTCTTTGAGGACAAAGGAAAAAAGAAA-AAAAGGCA
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATGAAATGCG
*
577203 TCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAATGTG
1 TCCTGCTCTTTGAGGAC-AAA-GG-AAA-AAGGAAATGAAATGCG
* * *
577248 TCCTGCTCTTTCAGGATAAAGGAGATAAGG--A--AAATGCG
1 TCCTGCTCTTTGAGGACAAAGGA-AAAAGGAAATGAAATGCG
*
577286 TCCTACTCTTTGAGGAC
1 TCCTGCTCTTTGAGGAC
577303 TAAAAAGTGT
Statistics
Matches: 246, Mismatches: 49, Indels: 37
0.74 0.15 0.11
Matches are distributed among these distances:
38 20 0.08
40 21 0.09
41 44 0.18
42 76 0.31
43 19 0.08
44 13 0.05
45 22 0.09
46 24 0.10
47 7 0.03
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.22
Consensus pattern (41 bp):
TCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATGAAATGCG
Found at i:577183 original size:88 final size:85
Alignment explanation
Indices: 576974--577270 Score: 298
Period size: 85 Copynumber: 3.5 Consensus size: 85
576964 GATTAAGGAA
* * * * **
576974 AAGGATAATGAAATGGGTCCTGCTCCTTGGGGACTAAGGAAAAAAAGAAATAAAATG-CATTATG
1 AAGGA-AATGAAATGTGTCCTGCTCTTTGAGGACAAAGG-AAAAAAGAAA-AAAA-GACATCCTG
*
577038 CCCTTTGA-AGACAAAA-GG-AAA-
62 CTCTTTGAGA-ACAAAAGGGAAAAG
* * * * *
577059 AAGGAAATTAAATGTGTCCTGCTTTTTGAGGACAAAGGAAAAAGGAGAATAAAGTACGTCCTGCT
1 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGA-AAAAAAG-ACATCCTGCT
* *
577124 CTTTGAGAACTAGAAGGGAAAAT
64 CTTTGAGAAC-AAAAGGGAAAAG
* * * *
577147 AAGGAAATGAAGTGCGTCATGCTCTTTGAGGACAAAGGAAAAAAGAAAAAAAGGCATCCTGCTCT
1 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGAAAAAAAGACATCCTGCTCT
*
577212 TTGAGGACAAAAGGGAAAAG
66 TTGAGAACAAAAGGGAAAAG
* *
577232 AAGGAAATGAAATGTGTCCTGCTCTTTCAGGATAAAGGA
1 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGA
577271 GATAAGGAAA
Statistics
Matches: 174, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
82 1 0.01
83 10 0.06
84 42 0.24
85 53 0.30
86 19 0.11
87 9 0.05
88 40 0.23
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.21
Consensus pattern (85 bp):
AAGGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAAAAAAGAAAAAAAGACATCCTGCTCT
TTGAGAACAAAAGGGAAAAG
Found at i:577309 original size:85 final size:85
Alignment explanation
Indices: 577040--577307 Score: 260
Period size: 85 Copynumber: 3.2 Consensus size: 85
577030 GCATTATGCC
* * * * * *
577040 CTTTGAAGAC-AAAA-GG-AAA-AAGGAAATTAAATGTGTCCTGCTTTTTGAGGACAAAGGAAAA
1 CTTTGAGGACTAAAAGGGAAAAGAAGGAAATGAAATGCGTCATGCTCTTTCAGGACAAAGGAAAA
* *
577101 AGGAGAATAAAGTACGTCCTGCT
66 A--AGAAAAAAG-GCGTCCTGCT
* * * * *
577124 CTTTGAGAACTAGAAGGGAAAATAAGGAAATGAAGTGCGTCATGCTCTTTGAGGACAAAGGAAAA
1 CTTTGAGGACTAAAAGGGAAAAGAAGGAAATGAAATGCGTCATGCTCTTTCAGGACAAAGGAAAA
*
577189 AAGAAAAAAAGGCATCCTGCT
66 AAG-AAAAAAGGCGTCCTGCT
* * * * *
577210 CTTTGAGGAC-AAAAGGGAAAAGAAGGAAATGAAATGTGTCCTGCTCTTTCAGGATAAAGGAGAT
1 CTTTGAGGACTAAAAGGGAAAAGAAGGAAATGAAATGCGTCATGCTCTTTCAGGACAAAGGAAAA
* * *
577274 AAG-GAAAATGCGTCCTACT
66 AAGAAAAAAGGCGTCCTGCT
577293 CTTTGAGGACTAAAA
1 CTTTGAGGACTAAAA
577308 AGTGTCACCA
Statistics
Matches: 153, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
83 22 0.14
84 12 0.08
85 51 0.33
86 21 0.14
87 9 0.06
88 38 0.25
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (85 bp):
CTTTGAGGACTAAAAGGGAAAAGAAGGAAATGAAATGCGTCATGCTCTTTCAGGACAAAGGAAAA
AAGAAAAAAGGCGTCCTGCT
Found at i:577361 original size:61 final size:60
Alignment explanation
Indices: 577277--577764 Score: 464
Period size: 61 Copynumber: 8.0 Consensus size: 60
577267 AGGAGATAAG
* * * *
577277 GAAAATGCGTCCTACTCTTTGAGGACTAAAAAGTGTCACCAACTCGTGTGGACTTTGAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGACTTT-AAAA
* * * * * * *
577338 GAAAAGACATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTGCAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGACTTT-AAAA
* * ** ** *
577399 GAGAAA-GCATCATGCTCTTTGAGTTCTGGAAGGTGCCACCAACTTGTGT-GAGCTTTAAAA
1 GA-AAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGA-CTTTAAAA
* * * *
577459 GAAGAAGACGTCCTGCTCCTTAAGGACTGAAAAGTGCCACCAACTTGTGT-GAGCTTTAAAAA
1 GAA-AAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGA-CTTT-AAAA
* * * * *
577521 GAAAAGGCATCCTGCTCTTTGAGGACTAGAATGTGCCACTAACTTGTGTGGGCTTTAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGACTTTAAAA
* * *
577581 GGAAAAGGTGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGACTTTAAAA
* * *
577643 GGAAATGGCGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTTGG-CTTTAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTG-TGGACTTTAAAA
* * * * * ** *
577704 GGAAAAGGCGTCATGCTCCTCGAGGACT-GAAGGTGCCACCAGTTTGTGTGGACTTTGAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGACTTTAAAA
577764 G
1 G
577765 GCATCTTACT
Statistics
Matches: 361, Mismatches: 56, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
59 5 0.01
60 35 0.10
61 254 0.70
62 67 0.19
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (60 bp):
GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGACTTTAAAA
Found at i:577539 original size:183 final size:183
Alignment explanation
Indices: 577274--577744 Score: 587
Period size: 183 Copynumber: 2.6 Consensus size: 183
577264 TAAAGGAGAT
* * * * * *
577274 AAGGAAAATG-CGTCCTACTCTTTGAGGACTAAAAAGTGTCACCAACTCGTGTGGACTTTGAAAA
1 AAGGAAAA-GACGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGG-CTTTAAAAA
* *
577338 GAAAAGACATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTGCAAA-GAG
64 GAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTT-AAAAGGA-
** * *
577402 AAA-G-CATCATGCTCTTTGAGTTCT-GGAAGGTGCCACCAACTTGTGTGAGCTTTAA
127 AAAGGTCATC-TGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGAGCTTTAA
*
577457 AA-GAAGAAGACGTCCTGCTCCTTAAGGACTGAAAAGTGCCACCAACTTGTGTGAGCTTTAAAAA
1 AAGGAA-AAGACGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTG-GCTTTAAAAA
* * *
577521 GAAAAGGCATCCTGCTCTTTGAGGACTAGAATGTGCCACTAACTTGTGTGGGCTTTAAAAGGAAA
64 GAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAA
** *
577586 AGGTGTTCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
129 AGGTCATCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGAGCTTTAA
* * *
577641 AAGGAAATGGCGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTTGGCTTTAAAAGG
1 AAGGAAAAGACGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTG-TGGCTTTAAAAAG
* * * *
577706 AAAAGGCGTCATGCTCCTCGAGGACT-GAAGGTGCCACCA
65 AAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCA
577745 GTTTGTGTGG
Statistics
Matches: 250, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
182 10 0.04
183 128 0.51
184 107 0.43
185 5 0.02
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (183 bp):
AAGGAAAAGACGTCCTGCTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGCTTTAAAAAGA
AAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAG
GTCATCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGAGCTTTAA
Found at i:578585 original size:11 final size:12
Alignment explanation
Indices: 578571--578620 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 12
578561 TTTTTCTCTC
578571 TTTTTTCTTTGT
1 TTTTTTCTTTGT
*
578583 TTTGTTTTTGTTGT
1 TTT-TTTCT-TTGT
578597 TGTTTTTCTTTGT
1 T-TTTTTCTTTGT
578610 TTTTTTGCTTT
1 TTTTTT-CTTT
578621 TTTAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 8 0.25
13 13 0.41
14 9 0.28
15 2 0.06
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (12 bp):
TTTTTTCTTTGT
Found at i:591167 original size:79 final size:77
Alignment explanation
Indices: 591031--591282 Score: 324
Period size: 79 Copynumber: 3.2 Consensus size: 77
591021 ACAACGGGGC
** * * * * *
591031 TGGAGTATCCTTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGGGGTTAGAGTATCCCCTC
1 TGGAGTATCCCCGATTGT-GAAAATCGATGTTTAG-AAATAAAGTCGGGGTTGGAGTATCCCCTC
591096 GAAAATAACAGGGT
64 GAAAATAACAGGGT
* *
591110 TGGAGTATCCCCGATTGTGGAAAATCGATGCTTTAGAAATAAGGTCGGGGTTGGAGTATCCCCAC
1 TGGAGTATCCCCGATTGT-GAAAATCGATG-TTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTC
591175 GAAAATAACAGGGT
64 GAAAATAACAGGGT
* * * *
591189 TGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCTCCTC
1 TGGAGTATCCCCGATTGTGA-AAATCGAT-GTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTC
*
591254 GAAAATAACGGGGT
64 GAAAATAACAGGGT
591268 TGGAGTATCCCCGAT
1 TGGAGTATCCCCGAT
591283 GAAATAACAG
Statistics
Matches: 153, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
78 2 0.01
79 147 0.96
80 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (77 bp):
TGGAGTATCCCCGATTGTGAAAATCGATGTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTCGA
AAATAACAGGGT
Found at i:591268 original size:28 final size:27
Alignment explanation
Indices: 591234--591307 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
591224 GAAATAAAGC
591234 CGGGGTTGGAGTATCTCCTCGA-AAATAA
1 CGGGGTTGGAGTATC-CC-CGAGAAATAA
591262 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGA-GAAATAA
*
591290 CAGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
591308 AATTGTGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 3 0.07
27 2 0.05
28 38 0.88
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGAGAAATAA
Found at i:591349 original size:107 final size:107
Alignment explanation
Indices: 591155--591355 Score: 287
Period size: 107 Copynumber: 1.9 Consensus size: 107
591145 GAAATAAGGT
* *
591155 CGGGGTTGGAGTATCCCCACGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCACGAAAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAATCAATAT
* *
591220 TTTAGAAATAAAGCCGGGGTTGGAGTATCTCCTCGAAAATAA
66 TTTAGAAATAAAACCGGAGTTGGAGTATCTCCTCGAAAATAA
* *** *
591262 CGGGGTTGGAGTATCCCCGATG-AAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTG
1 CGGGGTTGGAGTATCCCC-ACGAAAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAATCAATA
**
591326 TTTTAGAAATAAAATTGGAGTTGGAGTATC
65 TTTTAGAAATAAAACCGGAGTTGGAGTATC
591356 CCCGATTATG
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 80 0.98
108 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.26
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCACGAAAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAATCAATAT
TTTAGAAATAAAACCGGAGTTGGAGTATCTCCTCGAAAATAA
Found at i:591357 original size:51 final size:51
Alignment explanation
Indices: 591294--591399 Score: 176
Period size: 51 Copynumber: 2.1 Consensus size: 51
591284 AAATAACAGG
* *
591294 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTAGAAATAAAATTGGA
1 GTTGGAGTATCCCCAATTATGAAAAATTGGTGTTTTAGAAATAAAACTGGA
* *
591345 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACTGGG
1 GTTGGAGTATCCCCAATTATGAAAAATTGGTGTTTTAGAAATAAAACTGGA
591396 GTTG
1 GTTG
591400 AAGCATCCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTATGAAAAATTGGTGTTTTAGAAATAAAACTGGA
Found at i:594366 original size:21 final size:22
Alignment explanation
Indices: 594332--594373 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
594322 TACGATAGCT
*
594332 AAATTTTCAAAATTTTCAAAAA
1 AAATTTTCAAAATTCTCAAAAA
594354 AAATTTT-AAAATTCTCAAAA
1 AAATTTTCAAAATTCTCAAAA
594374 TAGGAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTTTCAAAATTCTCAAAAA
Found at i:599412 original size:99 final size:97
Alignment explanation
Indices: 599173--599412 Score: 252
Period size: 99 Copynumber: 2.4 Consensus size: 97
599163 TATCGAGTAT
* * *
599173 ACTCCAACCCCATTCTTCCGAGGAA-ATACTCTAACCCTGTTTTTAAACTTGTCAAGATTTAAAT
1 ACTCAAACCTCATTCTTCCGA-GAAGATACTCTAACCCTTTTTTTAAACTTGTCAAGATTTAAAT
* *
599237 CTTATTTTTGTCTAAATTATTATCGTCGAGGAC
65 CTTATTTTTGTCCAAATTATTATCGTCGAAGAC
* * * * *
599270 ACTCCAACCT-ATTCTTCCAAGAGGATACTCCAACCCATTTTTTTTTAAACTTGTTAAGATTTAA
1 ACTCAAACCTCATTCTTCCGAGAAGATACTCTAACCC---TTTTTTTAAACTTGTCAAGATTTAA
* * *
599334 ATCTTATTTTTG-CCAGGATTGTTATCGTCGAAGAT
63 ATCTTATTTTTGTCCA-AATTATTATCGTCGAAGAC
* * * *
599369 ATTCAAACCTCATTCCTCCGAGAAGATATTCTAACTCCGTTTTT
1 ACTCAAACCTCATTCTTCCGAGAAGATACTCTAAC-CCTTTTTT
599413 CAACCAAAAT
Statistics
Matches: 117, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
95 2 0.02
96 20 0.17
97 9 0.08
98 7 0.06
99 58 0.50
100 19 0.16
101 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (97 bp):
ACTCAAACCTCATTCTTCCGAGAAGATACTCTAACCCTTTTTTTAAACTTGTCAAGATTTAAATC
TTATTTTTGTCCAAATTATTATCGTCGAAGAC
Found at i:599564 original size:21 final size:21
Alignment explanation
Indices: 599527--599567 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
599517 AGTTATATCA
*
599527 AGATAATCGATGGCTATTACG
1 AGATAATCGATGACTATTACG
599548 AGATACATCGA-GACTATTAC
1 AGATA-ATCGATGACTATTAC
599568 ACTTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (21 bp):
AGATAATCGATGACTATTACG
Found at i:601136 original size:23 final size:22
Alignment explanation
Indices: 601110--601156 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
601100 TTAGATTATT
* *
601110 TTTAAATTATTATTATTTTTAAA
1 TTTAAATTATT-TTATATTAAAA
601133 TTTAAATTATTTTATATTAAAA
1 TTTAAATTATTTTATATTAAAA
601155 TT
1 TT
601157 AATTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAATTATTTTATATTAAAA
Found at i:601145 original size:16 final size:17
Alignment explanation
Indices: 601096--601171 Score: 68
Period size: 16 Copynumber: 4.6 Consensus size: 17
601086 AAGTTTTAAA
*
601096 AAATTTAGATTATTTTT
1 AAATTTAAATTATTTTT
*
601113 AAA-TTATTATTATTTTT
1 AAATTTA-AATTATTTTT
601130 AAATTTAAATTA-TTTT
1 AAATTTAAATTATTTTT
* * *
601146 ATATTAAAATTA-ATTT
1 AAATTTAAATTATTTTT
*
601162 AATTTTAAAT
1 AAATTTAAAT
601172 AGTATCAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 27 0.55
17 19 0.39
18 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
AAATTTAAATTATTTTT
Found at i:601940 original size:29 final size:29
Alignment explanation
Indices: 601907--601999 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
601897 TTATTTTATT
*
601907 TAAATAAATTTATATATTTTTA-TCATATA
1 TAAATAAATTTTTA-ATTTTTATTCATATA
* * *
601936 TAAATAAATTTTTAAATTTTATTTATATT
1 TAAATAAATTTTTAATTTTTATTCATATA
*
601965 TAAATAAATTTTTAATTTTTAATTTATATA
1 TAAATAAATTTTTAATTTTT-ATTCATATA
*
601995 CAAAT
1 TAAAT
602000 CAATCATTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
28 6 0.11
29 37 0.67
30 12 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TAAATAAATTTTTAATTTTTATTCATATA
Found at i:602183 original size:50 final size:51
Alignment explanation
Indices: 602105--602205 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 51
602095 AACAATGTAA
602105 GTGAAAGAATCGAGGGATAATTTAGTAATTTAGAAGAAACCCTCTCAATTT
1 GTGAAAGAATCGAGGGATAATTTAGTAATTTAGAAGAAACCCTCTCAATTT
* *
602156 GTGAAAGAGTCGA-GGATATTTTAGTAATTTAGAAGAAACCCTCTCAATTT
1 GTGAAAGAATCGAGGGATAATTTAGTAATTTAGAAGAAACCCTCTCAATTT
602206 CAATTGCGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 36 0.75
51 12 0.25
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (51 bp):
GTGAAAGAATCGAGGGATAATTTAGTAATTTAGAAGAAACCCTCTCAATTT
Found at i:607397 original size:16 final size:16
Alignment explanation
Indices: 607376--607434 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
607366 TAAACCTGAT
*
607376 TGACCCGAATCCGAAA
1 TGACCCGAACCCGAAA
* *
607392 TGACCCAAACCCGAAG
1 TGACCCGAACCCGAAA
* *
607408 TGATCTGAACCCGAAA
1 TGACCCGAACCCGAAA
*
607424 TGACCTGAACC
1 TGACCCGAACC
607435 AAAAACGACC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.14
Consensus pattern (16 bp):
TGACCCGAACCCGAAA
Found at i:608971 original size:164 final size:163
Alignment explanation
Indices: 608722--609041 Score: 445
Period size: 174 Copynumber: 1.9 Consensus size: 163
608712 CATTATAATA
*
608722 GGCCATTTTACATTGAATTTCTTTATTCTTTTCCCTTATTTCTATTTCTTTTATTTTGTTTTGAA
1 GGCCATTTTACATTGAATTTCTTTATTCTTTTCCCTTATTTCTATTTCTTTTATTTTATTTTGAA
*
608787 AATTTATTAAAAAAATCAATTTTCT-AAAA-AT-A-TCAAAAAT-AAAAAAAGGGAAGTGAAAGA
66 AATTTATTAAAAAAATCAATTTTCTAAAAATATAATTCAAAAATAAAAAAAAGAGAAGTGAAAGA
608847 TTAAAGGAAAAGAAAGGTTCATTGGATCATTGT
131 TTAAAGGAAAAGAAAGGTTCATTGGATCATTGT
* *
608880 GGCCATTTTACATTGAATTTTTTTATTTCTTTTCCTTTATTTCTATTGTGTTTCTTTTATTTTAT
1 GGCCATTTTACATTGAATTTCTTTA-TTCTTTTCCCTTATTTCTA-----TTTCTTTTATTTTAT
608945 TTTGAAAATTTA-TAAAAACAATCAATTTTCTAAAAATATCAGAATTTTCAAAAATAAAAAAAAG
60 TTTGAAAATTTATTAAAAA-AATCAATTTTCTAAAAATAT---AA--TTCAAAAATAAAAAAAAG
*
609009 AGAAGTGAAAGATTGAAGGAAAAGAAAGGTTCA
119 AGAAGTGAAAGATTAAAGGAAAAGAAAGGTTCA
609042 AAAAAATATG
Statistics
Matches: 140, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
158 24 0.17
159 18 0.13
163 6 0.04
164 38 0.27
165 4 0.03
166 2 0.01
170 1 0.01
173 8 0.06
174 39 0.28
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (163 bp):
GGCCATTTTACATTGAATTTCTTTATTCTTTTCCCTTATTTCTATTTCTTTTATTTTATTTTGAA
AATTTATTAAAAAAATCAATTTTCTAAAAATATAATTCAAAAATAAAAAAAAGAGAAGTGAAAGA
TTAAAGGAAAAGAAAGGTTCATTGGATCATTGT
Found at i:609594 original size:15 final size:16
Alignment explanation
Indices: 609568--609610 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
609558 ATATAGTGTT
609568 AAATTC-AAATGA-TC
1 AAATTCGAAATGACTC
*
609582 CAATTCGAAATGACTC
1 AAATTCGAAATGACTC
*
609598 AAATTAGAAATGA
1 AAATTCGAAATGA
609611 ATCGAATCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.21
15 6 0.25
16 13 0.54
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (16 bp):
AAATTCGAAATGACTC
Found at i:610633 original size:20 final size:20
Alignment explanation
Indices: 610608--610661 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
610598 GTTTAGGACA
610608 ATGTATCGATACAAT-T-CTTC
1 ATGTATCGATACAATGTGC--C
610628 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
610648 ATGTATCGATACAA
1 ATGTATCGATACAA
610662 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:610734 original size:19 final size:18
Alignment explanation
Indices: 610689--610746 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
610679 ACTGCCAGTT
610689 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
610708 TGCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
610727 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
610746 T
1 T
610747 ATCGATACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.54
20 16 0.43
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:610748 original size:13 final size:13
Alignment explanation
Indices: 610730--610755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
610720 TACAATGATC
610730 ATGTATCGATACA
1 ATGTATCGATACA
610743 ATGTATCGATACA
1 ATGTATCGATACA
610756 TCTGGATGTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:614408 original size:15 final size:16
Alignment explanation
Indices: 614382--614411 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
614372 TTTAAATTCA
614382 GGTCATTTTTATTTTT
1 GGTCATTTTTATTTTT
614398 GGTCA-TTTTATTTT
1 GGTCATTTTTATTTT
614412 CGGGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (16 bp):
GGTCATTTTTATTTTT
Found at i:617865 original size:20 final size:19
Alignment explanation
Indices: 617836--617910 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
617826 AAAAAGACAT
617836 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
617855 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
617876 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
617896 AATGTATCGATACAT
1 AATGTATCGATACAT
617911 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:617893 original size:40 final size:39
Alignment explanation
Indices: 617833--617910 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
617823 GGTAAAAAGA
*
617833 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
617872 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
617911 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:618560 original size:29 final size:29
Alignment explanation
Indices: 618472--619023 Score: 717
Period size: 29 Copynumber: 18.9 Consensus size: 29
618462 AAAAAAAATG
*
618472 GTGCCACTAACTTGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
**
618503 GTTGCCACCAACTTGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGAC-T-TGTGGGCTTTGAAAAGA
* *
618535 GTGCTACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618563 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618592 GTGCCAC-GAACTTGTGGGCTTTG-AAAGG
1 GTGCCACTG-ACTTGTGGGCTTTGAAAAGA
*
618620 GTGCCACTGACTTACGTGGGCTTT-AAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
618650 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618679 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
618707 GTGCCACTGACTTTTGGTCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
618736 GTGCCACTTATTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618764 GTGCCACTGACTTGCATGGGCTTTG-AAAGG
1 GTGCCACTGACTTG--TGGGCTTTGAAAAGA
* * *
618794 GTGCCATTGATTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
618823 -TGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
618851 GTTGCCACTGACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
*
618883 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
618912 ATGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
618940 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618969 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618998 GTGCCACTGAATTGTGGGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
619024 GGGATGAACA
Statistics
Matches: 467, Mismatches: 37, Indels: 36
0.86 0.07 0.07
Matches are distributed among these distances:
28 150 0.32
29 186 0.40
30 65 0.14
31 18 0.04
32 48 0.10
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:618588 original size:57 final size:58
Alignment explanation
Indices: 618472--619023 Score: 690
Period size: 57 Copynumber: 9.4 Consensus size: 58
618462 AAAAAAAATG
* * **
618472 GTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAG-GGTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
* *
618535 GTGCTACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618592 GTGCCAC-GAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTACGTGGGCTTT-AAAAGG
1 GTGCCACTG-ACTTGTGGGCTTTGAAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAAGA
* *
618650 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * * * *
618707 GTGCCACTGACTTTTGGTCTTTGAAAAGAGTGCCACTTATTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
618764 GTGCCACTGACTTGCATGGGCTTTG-AAAGGGTGCCATTGATTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTG--TGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618823 -TGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGA
* ** *
618883 GTGCCACTGATTTGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
618940 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
618998 GTGCCACTGAATTGTGGGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
619024 GGGATGAACA
Statistics
Matches: 442, Mismatches: 32, Indels: 35
0.87 0.06 0.07
Matches are distributed among these distances:
56 10 0.02
57 191 0.43
58 115 0.26
59 48 0.11
60 31 0.07
61 37 0.08
62 1 0.00
63 9 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (58 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:618784 original size:144 final size:145
Alignment explanation
Indices: 618471--619023 Score: 765
Period size: 144 Copynumber: 3.8 Consensus size: 145
618461 TAAAAAAAAT
* * * **
618471 GGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAAAGAG
1 GGTGCCACTGACTTGCGTGGGCTTT-AAAAG-GGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAG
* * *
618536 TGCTACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACG
62 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT
*
618600 AACTTGTGGGCTTTGAAAG
127 AATTTGTGGGCTTTGAAAG
*
618619 GGTGCCACTGACTTACGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCC
1 GGTGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCC
* * *
618684 ACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTTTGGTCTTTGAAAAGAGTGCCACTTATT
66 ACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAATT
618748 TGTGGGCTTTGAAAG
131 TGTGGGCTTTGAAAG
* * * * *
618763 GGTGCCACTGACTTGCATGGGCTTTGAAAGGGTGCCATTGATTTGTGGGCTTTGAAAGGA-TGCC
1 GGTGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCC
* *
618827 ACTGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGTGGGCTTTGAAAAGAGTGCCACTG
66 ACTGACTTGTGGGCTTTGAAAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACTA
618892 ATTTGTGGGCTTTGAAAAG
128 ATTTGTGGGCTTTG-AAAG
** *
618911 AATGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCC
1 GGTGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCC
* * *
618974 ACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGAATTGTGGGCTTTGAAA
66 ACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
619024 GGGATGAACA
Statistics
Matches: 366, Mismatches: 33, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
143 22 0.06
144 166 0.45
145 13 0.04
146 59 0.16
147 68 0.19
148 38 0.10
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (145 bp):
GGTGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCC
ACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAATT
TGTGGGCTTTGAAAG
Found at i:620270 original size:1 final size:1
Alignment explanation
Indices: 620266--620313 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
620256 TTTTTCTTGG
* * * * *
620266 TTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
620314 AGGTGTAAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:620276 original size:8 final size:8
Alignment explanation
Indices: 620265--620312 Score: 71
Period size: 8 Copynumber: 6.0 Consensus size: 8
620255 TTTTTTCTTG
620265 GTTTTTTT
1 GTTTTTTT
620273 GTTTTTTTT
1 G-TTTTTTT
*
620282 GTTTTGTT
1 GTTTTTTT
620290 -TTTTTTT
1 GTTTTTTT
620297 GTTTTTTT
1 GTTTTTTT
620305 GTTTTTTT
1 GTTTTTTT
620313 TAGGTGTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
7 6 0.17
8 22 0.61
9 8 0.22
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
GTTTTTTT
Found at i:620278 original size:9 final size:9
Alignment explanation
Indices: 620255--620313 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
620245 TTTTTTGCTA
620255 TTTTTTCTTG
1 TTTTTT-TTG
*
620265 GTTTTTTTG
1 TTTTTTTTG
620274 TTTTTTTTG
1 TTTTTTTTG
*
620283 --TTTTGT-
1 TTTTTTTTG
620289 TTTTTTTTG
1 TTTTTTTTG
620298 -TTTTTTTG
1 TTTTTTTTG
620306 TTTTTTTT
1 TTTTTTTT
620314 AGGTGTAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 5 0.12
8 13 0.32
9 18 0.44
10 5 0.12
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:620279 original size:32 final size:32
Alignment explanation
Indices: 620243--620313 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
620233 GACCCCTTTC
620243 TTTTTTTTGCTAT-TTTTTCTTGGTTTTTTTG
1 TTTTTTTTGCTATGTTTTTCTTGGTTTTTTTG
* * * *
620274 TTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTG
1 TTTTTTTTGCTATGTTTTTCTTGGTTTTTTTG
620306 TTTTTTTT
1 TTTTTTTT
620314 AGGTGTAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 11 0.31
32 24 0.69
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (32 bp):
TTTTTTTTGCTATGTTTTTCTTGGTTTTTTTG
Found at i:620292 original size:15 final size:15
Alignment explanation
Indices: 620269--620311 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
620259 TTCTTGGTTT
620269 TTTTG-TTTTTTTTG
1 TTTTGTTTTTTTTTG
620283 TTTTGTTTTTTTTTG
1 TTTTGTTTTTTTTTG
620298 TTTT-TTTGTTTTTT
1 TTTTGTTT-TTTTTT
620312 TTAGGTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTGTTTTTTTTTG
Found at i:620305 original size:23 final size:23
Alignment explanation
Indices: 620266--620313 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
620256 TTTTTCTTGG
620266 TTTTTTTGTTTTTTTTGTTTTGTT
1 TTTTTTTGTTTTTTTTGTTTT-TT
620290 TTTTTTTG-TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTTTTGTTTTTT
620312 TT
1 TT
620314 AGGTGTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
23 12 0.50
24 8 0.33
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (23 bp):
TTTTTTTGTTTTTTTTGTTTTTT
Found at i:621135 original size:13 final size:13
Alignment explanation
Indices: 621117--621142 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
621107 TACAGCAAGT
621117 ATGTATCGATACA
1 ATGTATCGATACA
621130 ATGTATCGATACA
1 ATGTATCGATACA
621143 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:623386 original size:21 final size:21
Alignment explanation
Indices: 623353--623397 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
623343 TTGCAAGTTG
*
623353 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
623375 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
623395 AAA
1 AAA
623398 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:625219 original size:15 final size:15
Alignment explanation
Indices: 625201--625239 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
625191 TAAAAATGTC
625201 CAAAAT-AAGGAAGCT
1 CAAAATGAA-GAAGCT
625216 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
625231 CCAAATGAA
1 CAAAATGAA
625240 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:627319 original size:13 final size:13
Alignment explanation
Indices: 627301--627339 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
627291 ACATTTTTCT
627301 TTGTATCGATACA
1 TTGTATCGATACA
627314 TTGTATCGATACA
1 TTGTATCGATACA
627327 TTGTATCGATACA
1 TTGTATCGATACA
627340 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:629905 original size:13 final size:13
Alignment explanation
Indices: 629887--629912 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
629877 TACAGCAAGT
629887 ATGTATCGATACA
1 ATGTATCGATACA
629900 ATGTATCGATACA
1 ATGTATCGATACA
629913 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:631562 original size:13 final size:13
Alignment explanation
Indices: 631544--631571 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
631534 AACCATCTTT
631544 CTCTTCTTCCACA
1 CTCTTCTTCCACA
631557 CTCTTCTTCCACA
1 CTCTTCTTCCACA
631570 CT
1 CT
631572 ATGACAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.46, G:0.00, T:0.39
Consensus pattern (13 bp):
CTCTTCTTCCACA
Done.