Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009099.1 Hibiscus syriacus cultivar Beakdansim tig00112553_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 322120
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:9301 original size:63 final size:63
Alignment explanation
Indices: 9222--9344 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
9212 AGGTATTTAT
*
9222 TATCTATTTAAATTTGAATATTAAAGATAAT-TATATAT-TTTTAAATATTTCAAATTAAAATAA
1 TATCTATTTAAATTTGAATAGTAAA-AT-ATGTATATATATTTTAAATATTTCAAATTAAAATAA
* * *
9285 TATCTATTTAAGTTTGAATAGTAAAATGTGTATATATATTTTACATATTTCAAATTAAAA
1 TATCTATTTAAATTTGAATAGTAAAATATGTATATATATTTTAAATATTTCAAATTAAAA
9345 GATAATATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
61 1 0.02
62 9 0.17
63 44 0.81
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (63 bp):
TATCTATTTAAATTTGAATAGTAAAATATGTATATATATTTTAAATATTTCAAATTAAAATAA
Found at i:10916 original size:16 final size:16
Alignment explanation
Indices: 10872--10916 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
10862 AACTAAAATT
* *
10872 ACCCGAATTGAAAGCA
1 ACCCGAACTAAAAGCA
* *
10888 ACCCAAACCAAAAGCA
1 ACCCGAACTAAAAGCA
10904 ACCCGAACTAAAA
1 ACCCGAACTAAAA
10917 TTAACCTGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.31, G:0.11, T:0.07
Consensus pattern (16 bp):
ACCCGAACTAAAAGCA
Found at i:10922 original size:16 final size:16
Alignment explanation
Indices: 10887--10996 Score: 60
Period size: 16 Copynumber: 6.9 Consensus size: 16
10877 AATTGAAAGC
* **
10887 AACCCAAACCAAAAGC
1 AACCCGAACCAAAATT
*
10903 AACCCGAACTAAAATT
1 AACCCGAACCAAAATT
* * *
10919 AACCTGAACCGATATT
1 AACCCGAACCAAAATT
* * *
10935 AACTCGAACCGAATTT
1 AACCCGAACCAAAATT
* **
10951 AACCCGACCCAAAAGC
1 AACCCGAACCAAAATT
*
10967 AACCC-AAACATAAATT
1 AACCCGAACCA-AAATT
* *
10983 AATCCGAACTAAAA
1 AACCCGAACCAAAA
10997 GCGACTTGAA
Statistics
Matches: 67, Mismatches: 25, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
15 3 0.04
16 61 0.91
17 3 0.04
ACGTcount: A:0.48, C:0.29, G:0.08, T:0.15
Consensus pattern (16 bp):
AACCCGAACCAAAATT
Found at i:11589 original size:17 final size:19
Alignment explanation
Indices: 11569--11605 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
11559 TAAAAAATTG
11569 ATAA-TTTAT-TAAAAATA
1 ATAAGTTTATATAAAAATA
11586 ATAAGTTTATAATAAAAATA
1 ATAAGTTTAT-ATAAAAATA
11606 CTGAAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
20 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAAGTTTATATAAAAATA
Found at i:12454 original size:16 final size:16
Alignment explanation
Indices: 12433--12463 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12423 ATGACCCAAC
12433 CCAAACCCGATCCGAT
1 CCAAACCCGATCCGAT
12449 CCAAACCCGATCCGA
1 CCAAACCCGATCCGA
12464 ATGGCATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.45, G:0.13, T:0.10
Consensus pattern (16 bp):
CCAAACCCGATCCGAT
Found at i:13892 original size:26 final size:23
Alignment explanation
Indices: 13835--13898 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 23
13825 TGATCGACCG
*
13835 AATCAAATTTTTATTAACCGAATT
1 AATCGAATTTTT-TTAACCGAATT
13859 AATCGAATTTTTTTAACCGTTAATT
1 AATCGAATTTTTTTAACCG--AATT
*
13884 GATCTGAATTTTTTT
1 AATC-GAATTTTTTT
13899 TGAAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 7 0.20
24 11 0.31
25 7 0.20
26 10 0.29
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (23 bp):
AATCGAATTTTTTTAACCGAATT
Found at i:29388 original size:57 final size:58
Alignment explanation
Indices: 29297--29422 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 58
29287 ACCATTTTGT
* * * * * ** *
29297 AATATAATTTAAGTTAAGATAAAAATAAAATATATTTATTAA-TTAAGATAGGATTAA
1 AATATATTTTTAGTTAAGATAAAAATAAAATATATTCAATAAGTTAAGAAAAAAATAA
*
29354 AATATATTTTTAGTTAAGATAAAAATAAAGTATATTCAATAAGTTAAGAAAAAAATAA
1 AATATATTTTTAGTTAAGATAAAAATAAAATATATTCAATAAGTTAAGAAAAAAATAA
29412 AATATATTTTT
1 AATATATTTTT
29423 TAATGTTAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
57 37 0.63
58 22 0.37
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (58 bp):
AATATATTTTTAGTTAAGATAAAAATAAAATATATTCAATAAGTTAAGAAAAAAATAA
Found at i:29401 original size:30 final size:29
Alignment explanation
Indices: 29297--29434 Score: 138
Period size: 30 Copynumber: 4.7 Consensus size: 29
29287 ACCATTTTGT
*
29297 AATATAAT-TTAAGTTAAGATAAAAATAA
1 AATATATTATTAAGTTAAGATAAAAATAA
** *
29325 AATATATTTATTAA-TTAAGATAGGATTAA
1 AATATA-TTATTAAGTTAAGATAAAAATAA
*
29354 AATATATT-TTTAGTTAAGATAAAAATAA
1 AATATATTATTAAGTTAAGATAAAAATAA
* * *
29382 AGTATATTCAATAAGTTAAGAAAAAAATAA
1 AATATATT-ATTAAGTTAAGATAAAAATAA
*
29412 AATATATTTTTTAATGTTAAGAT
1 AATATA-TTATTAA-GTTAAGAT
29435 GTGATTTTAA
Statistics
Matches: 87, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
27 3 0.03
28 27 0.31
29 19 0.22
30 29 0.33
31 9 0.10
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.38
Consensus pattern (29 bp):
AATATATTATTAAGTTAAGATAAAAATAA
Found at i:30287 original size:25 final size:23
Alignment explanation
Indices: 30220--30290 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 23
30210 AACAACTGCC
*
30220 ATAAACAATTATATTTCTAACAATT
1 ATAAACAA-TATATTTC-AACAAAT
*
30245 ATACTAACAATATTTTTCAACAAAT
1 ATA--AACAATATATTTCAACAAAT
30270 ATAAACAACTATGATTTCAAC
1 ATAAACAA-TAT-ATTTCAAC
30291 CATCGAATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 5 0.13
24 3 0.08
25 19 0.49
26 7 0.18
27 5 0.13
ACGTcount: A:0.48, C:0.15, G:0.01, T:0.35
Consensus pattern (23 bp):
ATAAACAATATATTTCAACAAAT
Found at i:44376 original size:35 final size:35
Alignment explanation
Indices: 44335--44409 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
44325 TTCATGTTCA
*
44335 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATCCTAAACCCT
* * * * *
44370 AAATTCCAAAATATTTTAATTATATCCTAAACCTT
1 AAATTCCAAAACACTTCAATTACATCCTAAACCCT
44405 AAATT
1 AAATT
44410 AAATTATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATCCTAAACCCT
Found at i:44452 original size:35 final size:35
Alignment explanation
Indices: 44405--44481 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
44395 CCTAAACCTT
* *
44405 AAATTAAATTATTTTAGAATTTGGGGTTTAAAATA
1 AAATTGAATTATTTTAGAATTTAGGGTTTAAAATA
* *
44440 TAATTGAATTATTTTAGAATTTAGGGTTTAGAATA
1 AAATTGAATTATTTTAGAATTTAGGGTTTAAAATA
44475 AAATTGA
1 AAATTGA
44482 GGATTGTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.43
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAGGGTTTAAAATA
Found at i:47518 original size:35 final size:35
Alignment explanation
Indices: 47462--47536 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
47452 TTCATGTTCA
*
47462 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTACATCCTAAACCCC
* * * * *
47497 AAATTCCAAAATATTTTAATTATATCCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATCCTAAACCCC
47532 AAATT
1 AAATT
47537 AAATTATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATCCTAAACCCC
Found at i:47579 original size:35 final size:35
Alignment explanation
Indices: 47533--47601 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
47523 CTAAACCCTA
*
47533 AATTAAATTATTTTAGAATTTGGGGTTTAAAATAT
1 AATTAAATTATTTTAGAATTTAGGGTTTAAAATAT
* *
47568 AATTGAATTATTTTAGAATTTAGGGTTTAGAATA
1 AATTAAATTATTTTAGAATTTAGGGTTTAAAATA
47602 AAAATTGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (35 bp):
AATTAAATTATTTTAGAATTTAGGGTTTAAAATAT
Found at i:51139 original size:54 final size:54
Alignment explanation
Indices: 51034--51142 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
51024 TTAAAAAAAT
* * **
51034 CTAACCCGATCAGATCGGGTTAGATTAAAACCCGTATGATGCTGGTGAAATTAC
1 CTAACCCAATCAGATCGGGTTAGATTAAAACCCGTATGATGCAGGCAAAATTAC
*
51088 CTAACCCAATCAGATCGGGTTGGATTAAAACCCGTATGATGCAGGCAAAATTAC
1 CTAACCCAATCAGATCGGGTTAGATTAAAACCCGTATGATGCAGGCAAAATTAC
51142 C
1 C
51143 ATCCCTGATC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (54 bp):
CTAACCCAATCAGATCGGGTTAGATTAAAACCCGTATGATGCAGGCAAAATTAC
Found at i:51663 original size:31 final size:28
Alignment explanation
Indices: 51598--51663 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 28
51588 GATATCTAGC
* * *
51598 TGCATCATTAAGAAAATAGGTATCTAGT
1 TGCATCATTAAGAAAATAAGTATATAAT
51626 TGCATCATTAAGAAAAAGTAAAGTATATAAT
1 TGCATCATTAAG-AAAA-T-AAGTATATAAT
51657 TGCATCA
1 TGCATCA
51664 AAAAGAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 12 0.38
29 4 0.12
30 1 0.03
31 15 0.47
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (28 bp):
TGCATCATTAAGAAAATAAGTATATAAT
Found at i:52338 original size:24 final size:23
Alignment explanation
Indices: 52310--52363 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
52300 ATTATATTAG
*
52310 AAATTTAGGGGTACCGAAATTACA
1 AAATTTAGAGGT-CCGAAATTACA
*
52334 AAATTTTAGAGGTGCGAAATTACA
1 AAA-TTTAGAGGTCCGAAATTACA
*
52358 AGATTT
1 AAATTT
52364 TAGAAGCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.12
24 15 0.58
25 8 0.31
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (23 bp):
AAATTTAGAGGTCCGAAATTACA
Found at i:52364 original size:24 final size:25
Alignment explanation
Indices: 52324--52380 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
52314 TTAGGGGTAC
*
52324 CGAAATTACAAAATTTTAG-AGGTG
1 CGAAATTACAAAATTTTAGAAGCTG
*
52348 CGAAATTACAAGATTTTAGAAGCTG
1 CGAAATTACAAAATTTTAGAAGCTG
52373 CGAAATTA
1 CGAAATTA
52381 TATAATCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (25 bp):
CGAAATTACAAAATTTTAGAAGCTG
Found at i:62494 original size:14 final size:15
Alignment explanation
Indices: 62477--62506 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
62467 TTTAATAAAT
62477 ATTTAAAT-TTTTAA
1 ATTTAAATATTTTAA
62491 ATTTAAATATTTTAA
1 ATTTAAATATTTTAA
62506 A
1 A
62507 ATTCTCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAATATTTTAA
Found at i:62502 original size:16 final size:15
Alignment explanation
Indices: 62477--62535 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
62467 TTTAATAAAT
62477 ATTTAA-ATTTTTAA
1 ATTTAATATTTTTAA
*
62491 ATTTAAATATTTTAAA
1 ATTT-AATATTTTTAA
**
62507 ATTCTCTTATTTTTAA
1 ATT-TAATATTTTTAA
*
62523 TTTTAATATTTTT
1 ATTTAATATTTTT
62536 TTATTTCATG
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.11
15 10 0.29
16 20 0.57
17 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTAATATTTTTAA
Found at i:65639 original size:23 final size:23
Alignment explanation
Indices: 65611--65654 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
65601 AAAACAAAAA
*
65611 AATAAAAAAAAAATAAAAAAATT
1 AATAAAAAAAAAACAAAAAAATT
**
65634 AATAAACGAAAAACAAAAAAA
1 AATAAAAAAAAAACAAAAAAA
65655 AAACTTCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.82, C:0.05, G:0.02, T:0.11
Consensus pattern (23 bp):
AATAAAAAAAAAACAAAAAAATT
Found at i:65658 original size:11 final size:11
Alignment explanation
Indices: 65606--65657 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
65596 AGAAGAAAAC
65606 AAAAAAATAAA
1 AAAAAAATAAA
65617 AAAAAAATAAA
1 AAAAAAATAAA
*
65628 AAAATTAATAAA
1 AAAA-AAATAAA
** *
65640 CGAAAAACAAA
1 AAAAAAATAAA
65651 AAAAAAA
1 AAAAAAA
65658 CTTCAACTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.85, C:0.04, G:0.02, T:0.10
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:67449 original size:28 final size:28
Alignment explanation
Indices: 67405--67462 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
67395 AATTACCAAG
67405 TTTGTAATTTACCCTTCTTTCAAAGAAA
1 TTTGTAATTTACCCTTCTTTCAAAGAAA
* * *
67433 TTTGTAATTTACGCTTCTTTTACAGAAA
1 TTTGTAATTTACCCTTCTTTCAAAGAAA
67461 TT
1 TT
67463 ATATTTAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (28 bp):
TTTGTAATTTACCCTTCTTTCAAAGAAA
Found at i:71182 original size:34 final size:34
Alignment explanation
Indices: 71135--71200 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
71125 CGAAATTCAC
* *
71135 GTTTCCCAGAAAATTCAGACATAATTATTTAAGT
1 GTTTCCCAAAAAATTCAAACATAATTATTTAAGT
*
71169 GTTTTCCAAAAAATTCAAACATAATTATTTAA
1 GTTTCCCAAAAAATTCAAACATAATTATTTAA
71201 TAATCTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (34 bp):
GTTTCCCAAAAAATTCAAACATAATTATTTAAGT
Found at i:79830 original size:4 final size:4
Alignment explanation
Indices: 79821--79851 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
79811 CATAGAGGCT
79821 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
79852 TATGGGGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:83133 original size:96 final size:96
Alignment explanation
Indices: 82998--83188 Score: 256
Period size: 96 Copynumber: 2.0 Consensus size: 96
82988 TTCAAGTAGT
* * * * *
82998 AACCAGTAGATTTCATAATCCGTAAATCAGGAACAATTATATTTTCTAGTGAAAACAAGAAACCA
1 AACCAGTAGATTCCATAATCCGTAAATCAAGAACAATTATACTTTCCAGGGAAAACAAGAAACCA
* *
83063 GATAACACATTTCAGGTAACCATAGTTCATA
66 GAGAACACATATCAGGTAACCATAGTTCATA
* * * * *
83094 AACCAGTAGATTCCATGATCCGTAAATCAAGAACGATTATACTTTCCAGGGAAAGCAGGAAATCA
1 AACCAGTAGATTCCATAATCCGTAAATCAAGAACAATTATACTTTCCAGGGAAAACAAGAAACCA
* *
83159 GAGAACACATATCATGTATCCATAGTTCAT
66 GAGAACACATATCAGGTAACCATAGTTCAT
83189 TAACAATTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (96 bp):
AACCAGTAGATTCCATAATCCGTAAATCAAGAACAATTATACTTTCCAGGGAAAACAAGAAACCA
GAGAACACATATCAGGTAACCATAGTTCATA
Found at i:83903 original size:2 final size:2
Alignment explanation
Indices: 83896--83929 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
83886 TGAGATTTCA
83896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83930 TGAATTATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84446 original size:27 final size:27
Alignment explanation
Indices: 84389--84446 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
84379 TAATATAGTC
* * * *
84389 ATTTTACAATTCAAGGGTATTTTGGTT
1 ATTTTACAATTCAAGGGCAATTTCGTA
* *
84416 ATTTTACACTTCAGGGGCAATTTCGTA
1 ATTTTACAATTCAAGGGCAATTTCGTA
84443 ATTT
1 ATTT
84447 CATAATCAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (27 bp):
ATTTTACAATTCAAGGGCAATTTCGTA
Found at i:86898 original size:12 final size:12
Alignment explanation
Indices: 86870--86936 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
86860 CTTGGTAATT
*
86870 GAATACATGCAC
1 GAATACATGTAC
* *
86882 AAATATATGTAC
1 GAATACATGTAC
*
86894 GAATACATGTAT
1 GAATACATGTAC
* *
86906 GTATACATGCAC
1 GAATACATGTAC
* * *
86918 AAATATATGTAT
1 GAATACATGTAC
86930 GAATACA
1 GAATACA
86937 CGTATGCATG
Statistics
Matches: 39, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (12 bp):
GAATACATGTAC
Found at i:86912 original size:36 final size:38
Alignment explanation
Indices: 86871--86969 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 38
86861 TTGGTAATTG
*
86871 AATACATGCACAAATATATGTACGAATACATGTATG-T
1 AATACATGCACAAATATATGTACGAATACACGTATGAT
*
86908 -ATACATGCACAAATATATGTATGAATACACGTATGCAT
1 AATACATGCACAAATATATGTACGAATACACGTATG-AT
86946 GAATACATGCACAAATACTATGTA
1 -AATACATGCACAAATA-TATGTA
86970 TGGATATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
36 33 0.60
38 1 0.02
40 15 0.27
41 6 0.11
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (38 bp):
AATACATGCACAAATATATGTACGAATACACGTATGAT
Found at i:86928 original size:20 final size:20
Alignment explanation
Indices: 86903--86970 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
86893 CGAATACATG
86903 TATGTATACATGCACAAATA
1 TATGTATACATGCACAAATA
* ** *
86923 TATGTATGA-ATACACGTATG
1 TATGTAT-ACATGCACAAATA
* *
86943 CATGAATACATGCACAAATA
1 TATGTATACATGCACAAATA
86963 CTATGTAT
1 -TATGTAT
86971 GGATATATAG
Statistics
Matches: 33, Mismatches: 12, Indels: 5
0.66 0.24 0.10
Matches are distributed among these distances:
19 1 0.03
20 26 0.79
21 6 0.18
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (20 bp):
TATGTATACATGCACAAATA
Found at i:88983 original size:16 final size:17
Alignment explanation
Indices: 88962--89001 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
88952 ACATTCTAAC
88962 TTATTTTTCAA-AA-TAT
1 TTATTTTT-AAGAAGTAT
88978 TTA-TTTTAAGAAGTAT
1 TTATTTTTAAGAAGTAT
88994 TTATTTTT
1 TTATTTTT
89002 TTTAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 6 0.29
16 9 0.43
17 4 0.19
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (17 bp):
TTATTTTTAAGAAGTAT
Found at i:92393 original size:2 final size:2
Alignment explanation
Indices: 92386--92416 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
92376 TAAAAATAAT
92386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92417 GAGATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92479 original size:2 final size:2
Alignment explanation
Indices: 92472--92497 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
92462 AGTTCAATAC
92472 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
92498 GTTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92756 original size:23 final size:23
Alignment explanation
Indices: 92696--92758 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 23
92686 ATCATTAAAT
92696 TGATTTTTTA-A-TTTAAA-TAA
1 TGATTTTTTATATTTTAAATTAA
* *
92716 T-A-ATTTTAT-TTTT-TATTAA
1 TGATTTTTTATATTTTAAATTAA
92735 TGATTTTTTATATTTTAAATTAA
1 TGATTTTTTATATTTTAAATTAA
92758 T
1 T
92759 TTGTTATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 11
0.68 0.09 0.23
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 2 0.06
21 6 0.19
22 4 0.12
23 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (23 bp):
TGATTTTTTATATTTTAAATTAA
Found at i:93239 original size:18 final size:18
Alignment explanation
Indices: 93216--93253 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
93206 ATGCCCTAAA
* *
93216 TATAATTTAGTTTATGTT
1 TATAATTTAGCTTACGTT
93234 TATAATTTAGCTTACGTT
1 TATAATTTAGCTTACGTT
93252 TA
1 TA
93254 CGATTATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (18 bp):
TATAATTTAGCTTACGTT
Found at i:95128 original size:228 final size:228
Alignment explanation
Indices: 94731--96064 Score: 1238
Period size: 228 Copynumber: 5.9 Consensus size: 228
94721 TGCATAACAG
* * * * * * *
94731 ATGCAGATATTTGTGAAAACTCTTACCGGTAAGACCATCACTCTGGAGGTGGAAAGCTCAGACAC
1 ATGCAGATATTTGTGAAAACTCTTACTGGAAAGACAATCACCCTTGAGGTGGAGAGCTCCGACAC
* * * * *
94796 AATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAAGGG-ATCCCTCCCGACCAACAGAGGCTT
66 AATTGATAATGTGAAGGCCAAGATCCAGGACAAGG-AGGGCATCCCACCAGACCAGCAGAGG-TT
* * *
94860 -ATCTTTGCTGGAAAACAGCTTGAGGATGGCCGTACACTTGCTGATTACAACATCCAGAAGGAGT
129 GATCTTTGCTGGAAAACAGCTTGAGGATGGGCGGACACTTGCTGACTACAACATCCAGAAGGAGT
* * * *
94924 CTACCCTACACCTT-GTCCTTCGGCTGAGGGGTGGT
194 CTACCCTACA-CTTGGTCCTTCGTCTCAGAGGTGGC
* * * * *
94959 ATGCAGATCTTTGTAAAAACACTTACTGGCAAGACAATCACCCTTGAGGTGGAAAGCTCCGACAC
1 ATGCAGATATTTGTGAAAACTCTTACTGGAAAGACAATCACCCTTGAGGTGGAGAGCTCCGACAC
* * *
95024 AATCGATAATGTCAAGGCCAAGATCCAGGACAAGGAGGGCATCCCACCGGACCAGCAGAGGCTT-
66 AATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAGGGCATCCCACCAGACCAGCAGAGG-TTG
* * *
95088 ATCTTTGCTGGAAAACAGCTTGAGGATGGTCGTACACTTGCTGACTACAACATCCAAAAGGAGTC
130 ATCTTTGCTGGAAAACAGCTTGAGGATGGGCGGACACTTGCTGACTACAACATCCAGAAGGAGTC
*
95153 TACCCTACACCTT-GTCCTTCGTCTCAGGGGTGGC
195 TACCCTACA-CTTGGTCCTTCGTCTCAGAGGTGGC
* *
95187 ATGCAGATCTTTGTGAAAACTCTTACTGGCAAGACAATCACCCTTGAGGTGGAGAGCTCCGACAC
1 ATGCAGATATTTGTGAAAACTCTTACTGGAAAGACAATCACCCTTGAGGTGGAGAGCTCCGACAC
* * * *
95252 AATTGATAATGTGAAGGCTAAGATTCAGGACAAGGAGGGCATCCCACCGGACCAGCAGAGGTTAA
66 AATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAGGGCATCCCACCAGACCAGCAGAGGTTGA
* * * * * * * * *
95317 TTTTTGCTGGGAAACAGCTTGAAGAT-GGCAGGACCCTAGCAGACTATAACATTCAAAAGGAGTC
131 TCTTTGCTGGAAAACAGCTTGAGGATGGGC-GGACACTTGCTGACTACAACATCCAGAAGGAGTC
* * * *
95381 TACCCTCCATTTGGT-GTTGCGTCTCCGAGGTGGC
195 TACCCTACACTTGGTCCTT-CGTCTCAGAGGTGGC
* * * * * * * * * * *
95415 ATGCAAATTTTTGTGAAGACTCTTACTGGAAAGACTATTA-CATTGGAAGTTGAGAGTTCTGATA
1 ATGCAGATATTTGTGAAAACTCTTACTGGAAAGACAATCACCCTT-GAGGTGGAGAGCTCCGACA
* * * * * * * *
95479 CAATTGACAATGTGAAAGCTAAGATCCAGGACAAGGAGGGGATTCCACCAGATCAACAGAGGCTG
65 CAATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAGGGCATCCCACCAGACCAGCAGAGGTTG
* * * * * * * * * * *
95544 ATCTTCGCTGGTAAGCAGCTGGAGGATGGGAGGACACTTGCCGATTATAATATTCAGAAAGAGTC
130 ATCTTTGCTGGAAAACAGCTTGAGGATGGGCGGACACTTGCTGACTACAACATCCAGAAGGAGTC
* * * * *
95609 GACCCTCCACTTGGTTCTTCGTCTGC-GTGGTGGG
195 TACCCTACACTTGGTCCTTCGTCT-CAGAGGTGGC
* * * * * * *
95643 ATGCAGATTTTTGTGAAAAC-CTTGACTGGTAAGACCATTA-CATTGGAGGTCGAGAGCTCCGAT
1 ATGCAGATATTTGTGAAAACTCTT-ACTGGAAAGACAATCACCCTT-GAGGTGGAGAGCTCCGAC
* * * * * *
95706 ACAATTGATAACGTTAAGGCCAAGATCCAAGATAAGGAGGGAATCCCACCTGACCAGCAGAGGTT
64 ACAATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAGGGCATCCCACCAGACCAGCAGAGGTT
* * * * * * * *
95771 GATATTTGCTGGAAAGCAGCTCGAGGACGGGAGGACTCTTGCTGACTATAACATTCAGAAGGAGT
129 GATCTTTGCTGGAAAACAGCTTGAGGATGGGCGGACACTTGCTGACTACAACATCCAGAAGGAGT
* * * * * * *
95836 CAACCCTGCATTTGGT-CTTGCGCCTTAGAGGAGGG
194 CTACCCTACACTTGGTCCTT-CGTCTCAGAGGTGGC
* * * * * * * * *
95871 ATGCAGATATTTGTCAAGACCCTGACTGGAAAAACTATCACCCTGGAGGTTGAGAGCTCGGACAC
1 ATGCAGATATTTGTGAAAACTCTTACTGGAAAGACAATCACCCTTGAGGTGGAGAGCTCCGACAC
* * * * *
95936 AATTGACAATGTGAAAGCAAAGATCCAGGACAAGGAGGGGATTCCC-CCAGATCAGCAGAGGTTG
66 AATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAGGGCA-TCCCACCAGACCAGCAGAGGTTG
* * * * * * *
96000 ATCTTTGCTGGGAAGCA-ATTGGAGGATGGTCGTACTCTTGCTGATTACAACATCCAGAAGGAGT
130 ATCTTTGCTGGAAAACAGCTT-GAGGATGGGCGGACACTTGCTGACTACAACATCCAGAAGGAGT
96064 C
194 C
96065 CACTCTGCAC
Statistics
Matches: 935, Mismatches: 155, Indels: 32
0.83 0.14 0.03
Matches are distributed among these distances:
227 22 0.02
228 900 0.96
229 13 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (228 bp):
ATGCAGATATTTGTGAAAACTCTTACTGGAAAGACAATCACCCTTGAGGTGGAGAGCTCCGACAC
AATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAGGGCATCCCACCAGACCAGCAGAGGTTGA
TCTTTGCTGGAAAACAGCTTGAGGATGGGCGGACACTTGCTGACTACAACATCCAGAAGGAGTCT
ACCCTACACTTGGTCCTTCGTCTCAGAGGTGGC
Found at i:96096 original size:456 final size:452
Alignment explanation
Indices: 94730--96097 Score: 1465
Period size: 456 Copynumber: 3.0 Consensus size: 452
94720 TTGCATAACA
* * *
94730 GATGCAGATATTTGTGAAAACTCTTACCGGTAAGACCATCACTCTGGAGGTGGAAAGCTCAGACA
1 GATGCAGATATTTGTGAAAACTCTTACTGGTAAGACCATCACT-TGGAGGTGGAGAGCTCCGACA
* *
94795 CAATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAAGGGATCCCTCCCGACCAACAGAGGCTT
65 CAATTGATAATGTCAAGGCCAAGATCCAGGATAAGG-AGGGATCCCACCCGACCAGCAGAGG-TT
* * * * * *
94860 ATCTTTGCTGGAAAACAGCTTGAGGATGGCCGTACACTTGCTGATTACAACATCCAGAAGGAGTC
128 ATATTTGCTGG-AAACAGCTTGAGGATGGCAGGACACTTGCTGACTATAACATTCAGAAGGAGTC
* * * * * * *
94925 TACCCTACACCTT-GTCCTT-CGGCTGAGGGGTGGTATGCAGATCTTTGTAAAAACACTTACTGG
192 TACCCTACA-TTTGGT-CTTGCGCCTCAGAGGTGGCATGCAGATATTTGTAAAGACACTTACTGG
* * * * * * * * * *
94988 CAAGACAATCACCCTTGAGGTGGAAAGCTCCGACACAATCGATAATGTCAAGGCCAAGATCCAGG
255 AAAGACTATCACCCTGGAGGTTGAGAGCTCCGACACAATTGACAATGTGAAAGCAAAGATCCAGG
* * * * *
95053 ACAAGGAGGGCA-TCCCACCGGACCAGCAGAGGCTT-ATCTTTGCTGGAAAACAGCTT-GAGGAT
320 ACAAGGAGGGGATTCCC-CCAGATCAGCAGAGG-TTGATCTTTGCTGGAAAGCA-ATTGGAGGAT
* * * *
95115 GGTCGTACACTTGCTGACTACAACATCCAAAAGGAGTCTACCCTACACCTTGTCCTTCGTCTCAG
382 GGTCGTACACTTGCTGATTACAACATCCAGAAGGAGTCCACCCTACACCTTGTCCTTCGTCTCCG
*
95180 GGGTGG
447 TGGTGG
* * * *
95186 CATGCAGATCTTTGTGAAAACTCTTACTGGCAAGACAATCACCCTT-GAGGTGGAGAGCTCCGAC
1 GATGCAGATATTTGTGAAAACTCTTACTGGTAAGACCATCA--CTTGGAGGTGGAGAGCTCCGAC
* * * * *
95250 ACAATTGATAATGTGAAGGCTAAGATTCAGGACAAGGAGGGCATCCCACCGGACCAGCAGAGGTT
64 ACAATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAGGG-ATCCCACCCGACCAGCAGAGGTT
* * * * * *
95315 AATTTTTGCTGGGAAACAGCTTGAAGATGGCAGGACCCTAGCAGACTATAACATTCAAAAGGAGT
128 -ATATTTGCT-GGAAACAGCTTGAGGATGGCAGGACACTTGCTGACTATAACATTCAGAAGGAGT
* * * * * * * *
95380 CTACCCTCCATTTGGTGTTGCGTCTCCGAGGTGGCATGCAAATTTTTGTGAAGACTCTTACTGGA
191 CTACCCTACATTTGGTCTTGCGCCTCAGAGGTGGCATGCAGATATTTGTAAAGACACTTACTGGA
* ** * * * * *
95445 AAGACTATTACATTGGAAGTTGAGAGTTCTGATACAATTGACAATGTGAAAGCTAAGATCCAGGA
256 AAGACTATCACCCTGGAGGTTGAGAGCTCCGACACAATTGACAATGTGAAAGCAAAGATCCAGGA
* * * * * ** **
95510 CAAGGAGGGGATTCCACCAGATCAACAGAGGCTGATCTTCGCTGGTAAGCAGCTGGAGGATGGGA
321 CAAGGAGGGGATTCCCCCAGATCAGCAGAGGTTGATCTTTGCTGGAAAGCAATTGGAGGATGGTC
* * * * * * * * * *
95575 GGACACTTGCCGATTATAATATTCAGAAAGAGTCGACCCTCCA-CTTGGTTCTTCGTCTGCGTGG
386 GTACACTTGCTGATTACAACATCCAGAAGGAGTCCACCCTACACCTT-GTCCTTCGTCTCCGTGG
95639 TGG
450 TGG
* * * *
95642 GATGCAGATTTTTGTGAAAAC-CTTGACTGGTAAGACCATTACATTGGAGGTCGAGAGCTCCGAT
1 GATGCAGATATTTGTGAAAACTCTT-ACTGGTAAGACCATCAC-TTGGAGGTGGAGAGCTCCGAC
* * * *
95706 ACAATTGATAACGTTAAGGCCAAGATCCAAGATAAGGAGGGAATCCCACCTGACCAGCAGAGGTT
64 ACAATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAGGG-ATCCCACCCGACCAGCAGAGGTT
* * * *
95771 GATATTTGCTGGAAAGCAGCTCGAGGACGGGAGGACTCTTGCTGACTATAACATTCAGAAGGAGT
128 -ATATTTGCTGGAAA-CAGCTTGAGGATGGCAGGACACTTGCTGACTATAACATTCAGAAGGAGT
* * * * * * * *
95836 CAACCCTGCATTTGGTCTTGCGCCTTAGAGGAGGGATGCAGATATTTGTCAAGACCCTGACTGGA
191 CTACCCTACATTTGGTCTTGCGCCTCAGAGGTGGCATGCAGATATTTGTAAAGACACTTACTGGA
* *
95901 AAAACTATCACCCTGGAGGTTGAGAGCTCGGACACAATTGACAATGTGAAAGCAAAGATCCAGGA
256 AAGACTATCACCCTGGAGGTTGAGAGCTCCGACACAATTGACAATGTGAAAGCAAAGATCCAGGA
*
95966 CAAGGAGGGGATTCCCCCAGATCAGCAGAGGTTGATCTTTGCTGGGAAGCAATTGGAGGATGGTC
321 CAAGGAGGGGATTCCCCCAGATCAGCAGAGGTTGATCTTTGCTGGAAAGCAATTGGAGGATGGTC
* * * *
96031 GTACTCTTGCTGATTACAACATCCAGAAGGAGTCCACTCTGCACCTTGTCCTTCGCCTCCGTGGT
386 GTACACTTGCTGATTACAACATCCAGAAGGAGTCCACCCTACACCTTGTCCTTCGTCTCCGTGGT
96096 GG
451 GG
96098 TCACTGATTT
Statistics
Matches: 745, Mismatches: 151, Indels: 32
0.80 0.16 0.03
Matches are distributed among these distances:
454 1 0.00
455 25 0.03
456 708 0.95
457 9 0.01
458 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (452 bp):
GATGCAGATATTTGTGAAAACTCTTACTGGTAAGACCATCACTTGGAGGTGGAGAGCTCCGACAC
AATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAGGGATCCCACCCGACCAGCAGAGGTTATA
TTTGCTGGAAACAGCTTGAGGATGGCAGGACACTTGCTGACTATAACATTCAGAAGGAGTCTACC
CTACATTTGGTCTTGCGCCTCAGAGGTGGCATGCAGATATTTGTAAAGACACTTACTGGAAAGAC
TATCACCCTGGAGGTTGAGAGCTCCGACACAATTGACAATGTGAAAGCAAAGATCCAGGACAAGG
AGGGGATTCCCCCAGATCAGCAGAGGTTGATCTTTGCTGGAAAGCAATTGGAGGATGGTCGTACA
CTTGCTGATTACAACATCCAGAAGGAGTCCACCCTACACCTTGTCCTTCGTCTCCGTGGTGG
Found at i:98551 original size:25 final size:21
Alignment explanation
Indices: 98524--98566 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
98514 CAAGCTCCAT
*
98524 ATTCTA-TTTGCCCAACTAAC
1 ATTCTATTTTTCCCAACTAAC
98544 ATTCTATTTTTCCCAACTAAC
1 ATTCTATTTTTCCCAACTAAC
98565 AT
1 AT
98567 ACAAGAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTCTATTTTTCCCAACTAAC
Found at i:106050 original size:3 final size:3
Alignment explanation
Indices: 106042--106073 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
106032 ATAATTTTGT
106042 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
106074 AGTAATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:106057 original size:23 final size:23
Alignment explanation
Indices: 106031--106087 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
106021 ACAAAATGTA
106031 AATAATTTTGTTAATAATAAAAT
1 AATAATTTTGTTAATAATAAAAT
** ** *
106054 AATAATAATAATAATAATAAAGT
1 AATAATTTTGTTAATAATAAAAT
*
106077 AATATTTTTGT
1 AATAATTTTGT
106088 ATACCCGGAC
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (23 bp):
AATAATTTTGTTAATAATAAAAT
Found at i:114893 original size:37 final size:36
Alignment explanation
Indices: 114818--114893 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
114808 TTTTTATATT
*
114818 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
114854 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
114891 TTT
1 TTT
114894 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:115056 original size:18 final size:19
Alignment explanation
Indices: 115033--115089 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 19
115023 CCAGTAATCC
115033 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
115051 TATTCCCACTGGTAATCTTT
1 TATT-CCACTGGTAATCTTT
115071 TATTCTCACTGGTAATCTT
1 TATTC-CACTGGTAATCTT
115090 ACATTCCGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 29 0.81
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:115095 original size:20 final size:20
Alignment explanation
Indices: 115039--115089 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
115029 ATCCTATTCC
115039 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
*
115059 CTGGTAATCTTTTATTCTCA
1 CTGGTAATCTTTTATTCCCA
115079 CTGGTAATCTT
1 CTGGTAATCTT
115090 ACATTCCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:115683 original size:34 final size:35
Alignment explanation
Indices: 115644--115728 Score: 149
Period size: 34 Copynumber: 2.5 Consensus size: 35
115634 TATATATATA
115644 TATATATAATAATATTTTATA-TTTTTATATTAAT
1 TATATATAATAATATTTTATATTTTTTATATTAAT
115678 TATATAT-ATAATATTTTATATTTTTTATATTAAT
1 TATATATAATAATATTTTATATTTTTTATATTAAT
115712 TATATATAA-AATATTTT
1 TATATATAATAATATTTT
115729 TGGGTTCGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
33 13 0.27
34 35 0.71
35 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (35 bp):
TATATATAATAATATTTTATATTTTTTATATTAAT
Found at i:115977 original size:8 final size:8
Alignment explanation
Indices: 115964--115990 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
115954 ATATGATTTG
115964 AGTTGTGA
1 AGTTGTGA
115972 AGTTGTGA
1 AGTTGTGA
115980 AGTTGTGA
1 AGTTGTGA
115988 AGT
1 AGT
115991 GATTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (8 bp):
AGTTGTGA
Found at i:122066 original size:2 final size:2
Alignment explanation
Indices: 122059--122084 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
122049 ATTACTATGC
122059 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
122085 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:122608 original size:23 final size:23
Alignment explanation
Indices: 122581--122629 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
122571 AATAGTTACG
* *
122581 AGAGACAAATTTTTAAAATTTTA
1 AGAGACAAATTTATAAAATTCTA
*
122604 AGAGACGAATTTATAAAATTCTA
1 AGAGACAAATTTATAAAATTCTA
122627 AGA
1 AGA
122630 AACGAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (23 bp):
AGAGACAAATTTATAAAATTCTA
Found at i:122634 original size:23 final size:23
Alignment explanation
Indices: 122588--122635 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
122578 ACGAGAGACA
* * *
122588 AATTTTTAAAATTTTAAGAGACG
1 AATTTATAAAATTCTAAGAAACG
122611 AATTTATAAAATTCTAAGAAACG
1 AATTTATAAAATTCTAAGAAACG
122634 AA
1 AA
122636 GAAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (23 bp):
AATTTATAAAATTCTAAGAAACG
Found at i:124209 original size:2 final size:2
Alignment explanation
Indices: 124117--124193 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
124107 CAACTAAAAC
124117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
124159 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
124194 TGAATTAATC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:124554 original size:16 final size:16
Alignment explanation
Indices: 124533--124563 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
124523 ATAAATAAAT
124533 GAACATAAACGAACAC
1 GAACATAAACGAACAC
124549 GAACATAAACGAACA
1 GAACATAAACGAACA
124564 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:124644 original size:10 final size:10
Alignment explanation
Indices: 124629--124703 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
124619 CATTTAATAA
124629 ATAAACGAAC
1 ATAAACGAAC
124639 ATAAACG--C
1 ATAAACGAAC
124647 AT--ACGAAC
1 ATAAACGAAC
124655 ATAAACGAAC
1 ATAAACGAAC
** *
124665 ACGAAC-ATAA
1 ATAAACGA-AC
124675 ATGAACACGAAC
1 AT-AA-ACGAAC
124687 ATAAACGAAC
1 ATAAACGAAC
124697 ATAAACG
1 ATAAACG
124704 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 3 0.06
8 6 0.12
9 1 0.02
10 32 0.63
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:124654 original size:16 final size:16
Alignment explanation
Indices: 124633--124697 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
124623 TAATAAATAA
* *
124633 ACGAACATAAACGCAT
1 ACGAACATAAACGAAC
124649 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
124665 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
124681 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
124697 A
1 A
124698 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:125787 original size:14 final size:14
Alignment explanation
Indices: 125770--125801 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
125760 AATGAACATA
125770 AACGAACATAAACG
1 AACGAACATAAACG
*
125784 AACGAACATAATCG
1 AACGAACATAAACG
125798 AACG
1 AACG
125802 TTCACGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.22, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:125811 original size:24 final size:24
Alignment explanation
Indices: 125750--125800 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
125740 GATTGGGTTA
* *
125750 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
125774 AACATAAACGAACGAACATAATCG
1 AACATAAACGAACGAACATAAACG
125798 AAC
1 AAC
125801 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:139020 original size:15 final size:15
Alignment explanation
Indices: 139000--139029 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
138990 TTCTTCATCC
139000 TCTCATTTCCATTTT
1 TCTCATTTCCATTTT
*
139015 TCTCATTTTCATTTT
1 TCTCATTTCCATTTT
139030 CTCTACTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (15 bp):
TCTCATTTCCATTTT
Found at i:139151 original size:22 final size:22
Alignment explanation
Indices: 139092--139151 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
139082 TGTATTTTCA
* * *
139092 TCCTTTTTATTGTTTCTATTTT
1 TCCTTTTTATTCTTTTTATTCT
* *
139114 TCCTCTTTATTCTTTTTCTTCT
1 TCCTTTTTATTCTTTTTATTCT
139136 TCCTTTTTATT-TTTTT
1 TCCTTTTTATTCTTTTT
139152 GGTATTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (22 bp):
TCCTTTTTATTCTTTTTATTCT
Found at i:144013 original size:3 final size:3
Alignment explanation
Indices: 144005--144030 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
143995 ACTATCTGTG
144005 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
144031 TAGAACGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:147191 original size:41 final size:40
Alignment explanation
Indices: 147131--147207 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 40
147121 GTGTTCGTGG
* * *
147131 ATATATTTATTTAATGTTCA-CATACATATTCGTTTATGCCA
1 ATATATTTATATAACGTTCATCAT-CACATT-GTTTATGCCA
*
147172 ATATATTTGTATAACGTTCATCATCACATTGTTTAT
1 ATATATTTATATAACGTTCATCATCACATTGTTTAT
147208 CGTTTGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
40 6 0.19
41 22 0.71
42 3 0.10
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (40 bp):
ATATATTTATATAACGTTCATCATCACATTGTTTATGCCA
Found at i:172831 original size:2 final size:2
Alignment explanation
Indices: 172824--172882 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
172814 AGTTAGTTAT
172824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
172866 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
172883 GGATTATTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:173541 original size:18 final size:16
Alignment explanation
Indices: 173510--173546 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
173500 AAAATTGACC
173510 ATAAAATATATATTAA
1 ATAAAATATATATTAA
173526 ATAAATATATTATATTAA
1 ATAAA-ATA-TATATTAA
173544 ATA
1 ATA
173547 TATAATATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 3 0.16
18 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAAATATATATTAA
Found at i:173546 original size:14 final size:14
Alignment explanation
Indices: 173517--173554 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
173507 ACCATAAAAT
*
173517 ATATATTA-AATAA
1 ATATATTATATTAA
173530 ATATATTATATTAA
1 ATATATTATATTAA
*
173544 ATATATAATAT
1 ATATATTATAT
173555 CTATCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATTATATTAA
Found at i:175360 original size:74 final size:74
Alignment explanation
Indices: 175259--175510 Score: 441
Period size: 74 Copynumber: 3.4 Consensus size: 74
175249 TTTTTCCTAA
* * * * *
175259 TCTGGGTATTGCTTTGTTGGGGTTGAAAGTGCTTAAATTCTTAATTTCTTCGAAGTTTTTGAAGT
1 TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTCAAATTCTTAATTTCTTCGAAGTTTTTGAAGT
175324 GTTCTCGTT
66 GTTCTCGTT
* *
175333 TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTCAAATTCTTAATTTCTTCCAAGTTTTTGGAGT
1 TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTCAAATTCTTAATTTCTTCGAAGTTTTTGAAGT
175398 GTTCTCGTT
66 GTTCTCGTT
175407 TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTCAAATTCTTAATTTCTTCGAAGTTTTTGAAGT
1 TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTCAAATTCTTAATTTCTTCGAAGTTTTTGAAGT
175472 GTTCTCGTT
66 GTTCTCGTT
175481 TCTGGGTATTGCTTGGTTTGAGCTGAAAGT
1 TCTGGGTATTGCTTGGTTTGAGCTGAAAGT
175511 TCTTGAACTT
Statistics
Matches: 169, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 169 1.00
ACGTcount: A:0.18, C:0.13, G:0.25, T:0.45
Consensus pattern (74 bp):
TCTGGGTATTGCTTGGTTTGAGCTGAAAGTGCTCAAATTCTTAATTTCTTCGAAGTTTTTGAAGT
GTTCTCGTT
Found at i:181657 original size:28 final size:29
Alignment explanation
Indices: 181616--181683 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
181606 AATTTTTATG
*
181616 TTAAGA-GTGAATTTAAAGTTT-TAAAATT
1 TTAAGAGGTAAATTTAAA-TTTATAAAATT
*
181644 TT-AGGGGTAAATTTAAATTTATAAAATT
1 TTAAGAGGTAAATTTAAATTTATAAAATT
181672 TTAAGAGGTAAA
1 TTAAGAGGTAAA
181684 AATAAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 5 0.15
28 21 0.62
29 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (29 bp):
TTAAGAGGTAAATTTAAATTTATAAAATT
Found at i:181689 original size:29 final size:27
Alignment explanation
Indices: 181629--181690 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
181619 AGAGTGAATT
* **
181629 TAAAGTTTTAAAATTTTAGGGGTAAATT
1 TAAA-TTTTAAAATTTTAGAGGTAAAAA
181657 TAAATTTATAAAATTTTAAGAGGTAAAAA
1 TAAATTT-TAAAATTTT-AGAGGTAAAAA
181686 TAAAT
1 TAAAT
181691 ATTTTAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.10
28 13 0.45
29 13 0.45
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (27 bp):
TAAATTTTAAAATTTTAGAGGTAAAAA
Found at i:187019 original size:37 final size:37
Alignment explanation
Indices: 186969--187045 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
186959 TTTAATGAAA
* *
186969 ATTGTTATTATAGAAAGTGAGAATTGAGGATGGTAGG
1 ATTGTCATTATAGAAAGTGAGAATCGAGGATGGTAGG
187006 ATTGTCATTATAGAAAGTGAGAATCGAGGATGGTAGG
1 ATTGTCATTATAGAAAGTGAGAATCGAGGATGGTAGG
187043 ATT
1 ATT
187046 TATAGTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.31
Consensus pattern (37 bp):
ATTGTCATTATAGAAAGTGAGAATCGAGGATGGTAGG
Found at i:191017 original size:111 final size:111
Alignment explanation
Indices: 190864--191085 Score: 300
Period size: 111 Copynumber: 2.0 Consensus size: 111
190854 AAAGGCGCAC
* * * * * *
190864 TGCTACACACATTCACGAAGATCCAGTTTGTTCTGGTGTTTCAACTTTTAGTCCAGTTACGGATG
1 TGCTACACACATTCACCAAGATCCAGTTTGTTCTGGTATTTCAACTTCTACTCCAGCTACAGATG
190929 TTTCCCTAGAATCATGCCACAGTTCATTTGCCGCTCCAACTCCCAT
66 TTTCCCTAGAATCATGCCACAGTTCATTTGCCGCTCCAACTCCCAT
* * * * *
190975 TGCTACAGACATTCCCCAATATCCTGTTTGTTCTGGTATTTCAACTTCTACTCCAGCTGCAGATG
1 TGCTACACACATTCACCAAGATCCAGTTTGTTCTGGTATTTCAACTTCTACTCCAGCTACAGATG
** * * *
191040 TTTCCCTAGAATCATGCCAGGGTTCATTTTCTGCTTCAACTCCCAT
66 TTTCCCTAGAATCATGCCACAGTTCATTTGCCGCTCCAACTCCCAT
191086 ACACCCTCCA
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
111 95 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (111 bp):
TGCTACACACATTCACCAAGATCCAGTTTGTTCTGGTATTTCAACTTCTACTCCAGCTACAGATG
TTTCCCTAGAATCATGCCACAGTTCATTTGCCGCTCCAACTCCCAT
Found at i:193121 original size:25 final size:22
Alignment explanation
Indices: 193093--193143 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 22
193083 TGTGAATCAT
193093 TCTAAATCAAATATAAAAAATATTA
1 TCTAAAT--AATA-AAAAAATATTA
*
193118 TCT-AATAATAATAAAATATTA
1 TCTAAATAATAAAAAAATATTA
193139 TCTAA
1 TCTAA
193144 TATTTTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 13 0.54
22 5 0.21
24 3 0.12
25 3 0.12
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (22 bp):
TCTAAATAATAAAAAAATATTA
Found at i:193135 original size:21 final size:20
Alignment explanation
Indices: 193105--193145 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
193095 TAAATCAAAT
193105 ATAAAAAATATTATCTAATA
1 ATAAAAAATATTATCTAATA
193125 ATAATAAAATATTATCTAATA
1 ATAA-AAAATATTATCTAATA
193146 TTTTGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAAAATATTATCTAATA
Found at i:199985 original size:16 final size:15
Alignment explanation
Indices: 199957--199986 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
199947 AGAGTGTAGA
199957 ATATTTAAATAATAT
1 ATATTTAAATAATAT
199972 ATATTTATAATAATA
1 ATATTTA-AATAATA
199987 GGACTTAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTTAAATAATAT
Found at i:201540 original size:50 final size:49
Alignment explanation
Indices: 201432--201572 Score: 160
Period size: 50 Copynumber: 2.9 Consensus size: 49
201422 TTCATATTAC
* * * *
201432 AAAAAA-TATAACACTTAACATATACTTACACCGGTGTAAGTAAAAAAT
1 AAAAAAGTGTAACACTTAATACATACTTACACCGGCGTAAGTAAAAAAT
* * * *
201480 AAACAAGTGTAGCACTTAATAGATAC-TACACCTGCGTAAGTAAATAAAAT
1 AAAAAAGTGTAACACTTAATACATACTTACACCGGCGTAAGT-AA-AAAAT
* *
201530 AAAAAAGTGTAACACTTAATACATACTTACACTGGTGTAAGTA
1 AAAAAAGTGTAACACTTAATACATACTTACACCGGCGTAAGTA
201573 TGTATATCTC
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
48 18 0.24
49 17 0.22
50 29 0.38
51 12 0.16
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.26
Consensus pattern (49 bp):
AAAAAAGTGTAACACTTAATACATACTTACACCGGCGTAAGTAAAAAAT
Found at i:208236 original size:18 final size:18
Alignment explanation
Indices: 208215--208249 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
208205 TGCTGAAATG
208215 GAAAGTGGAG-GAGAAAGA
1 GAAAG-GGAGTGAGAAAGA
208233 GAAAGGGAGTGAGAAAG
1 GAAAGGGAGTGAGAAAG
208250 GTTGTGAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.00, G:0.46, T:0.06
Consensus pattern (18 bp):
GAAAGGGAGTGAGAAAGA
Found at i:214324 original size:31 final size:32
Alignment explanation
Indices: 214289--214349 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
214279 TAATATTTAA
*
214289 TATTTTTAATTTAATTATTT-AACTTTCAAAT
1 TATTTTTAATTTAATCATTTCAACTTTCAAAT
*
214320 TATTTTTAATTTAATCGTTTCAACTTTCAA
1 TATTTTTAATTTAATCATTTCAACTTTCAA
214350 CTTTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.56
Consensus pattern (32 bp):
TATTTTTAATTTAATCATTTCAACTTTCAAAT
Found at i:217272 original size:11 final size:11
Alignment explanation
Indices: 217256--217288 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
217246 TCAACTTAAA
*
217256 AAATTAAAATT
1 AAATTAAAACT
217267 AAATTAAAACT
1 AAATTAAAACT
217278 AAATTAAAACT
1 AAATTAAAACT
217289 TTGAATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATTAAAACT
Found at i:217630 original size:6 final size:6
Alignment explanation
Indices: 217621--217665 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
217611 ATTTATTTAT
* * * *
217621 TTATTA TTATAA TTATAA TTATAA TAATAA TAATAA TTATTA TTA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTA
217666 AATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTATAA
Found at i:217674 original size:2 final size:2
Alignment explanation
Indices: 217667--217693 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
217657 TTATTATTAA
217667 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
217694 ATAATAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:217706 original size:12 final size:12
Alignment explanation
Indices: 217629--217709 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 12
217619 ATTTATTATT
* *
217629 ATAATTATAATT
1 ATAATAATAATA
217641 ATAATAATAATA
1 ATAATAATAATA
* * *
217653 ATAATTATTATT
1 ATAATAATAATA
217665 A-AATATATATATA
1 ATAATA-ATA-ATA
217678 TATATATATATATATA
1 -ATA-ATA-ATA-ATA
217694 ATAATAATAATA
1 ATAATAATAATA
217706 ATAA
1 ATAA
217710 AAAATACAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
11 3 0.05
12 29 0.52
13 5 0.09
14 4 0.07
15 4 0.07
16 11 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAATAATAATA
Found at i:219073 original size:23 final size:25
Alignment explanation
Indices: 219020--219073 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
219010 AATTGTATTT
* *
219020 TTATTATTTTAATTTTACTTGTTTA
1 TTATTATTTAAATATTACTTGTTTA
219045 -TA-TATTTAAATATTA-TT-TTTA
1 TTATTATTTAAATATTACTTGTTTA
219066 TTATTATT
1 TTATTATT
219074 ATATAGTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.16
22 4 0.16
23 15 0.60
24 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTATTATTTAAATATTACTTGTTTA
Found at i:223237 original size:15 final size:15
Alignment explanation
Indices: 223217--223248 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
223207 ATCAATACCT
223217 TTTTGCATACATACA
1 TTTTGCATACATACA
*
223232 TTTTGCATACATTCA
1 TTTTGCATACATACA
223247 TT
1 TT
223249 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:230590 original size:1 final size:1
Alignment explanation
Indices: 230584--230636 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
230574 ATGCTTGAAG
* * * * * *
230584 AAAAAAAAAAGAAAAAAGAAAAAAAAGAAAGAAAAAAAAAGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
230637 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:230600 original size:7 final size:7
Alignment explanation
Indices: 230584--230636 Score: 65
Period size: 7 Copynumber: 7.4 Consensus size: 7
230574 ATGCTTGAAG
230584 AAAA-AA
1 AAAAGAA
230590 AAAAGAA
1 AAAAGAA
230597 AAAAGAAAA
1 AAAAG--AA
230606 AAAAGAA
1 AAAAGAA
230613 AGAAA-AA
1 A-AAAGAA
230620 AAAAGAA
1 AAAAGAA
230627 AAAAGAA
1 AAAAGAA
230634 AAA
1 AAA
230637 GGGGGTCAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 7 0.17
7 25 0.60
8 3 0.07
9 7 0.17
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:230600 original size:10 final size:10
Alignment explanation
Indices: 230585--230630 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
230575 TGCTTGAAGA
230585 AAAAAAAAAG
1 AAAAAAAAAG
230595 AAAAAAGAAA-
1 AAAAAA-AAAG
*
230605 AAAAAGAAAG
1 AAAAAAAAAG
230615 AAAAAAAAAG
1 AAAAAAAAAG
230625 AAAAAA
1 AAAAAA
230631 GAAAAAGGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 3 0.09
10 26 0.81
11 3 0.09
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:230607 original size:16 final size:16
Alignment explanation
Indices: 230586--230636 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
230576 GCTTGAAGAA
230586 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
*
230602 AAAAAAAAG-AAAGA-
1 AAAAAAAAGAAAAAAG
230616 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
230632 AAAAA
1 AAAAA
230637 GGGGGTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 9 0.29
15 8 0.26
16 14 0.45
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:231822 original size:115 final size:115
Alignment explanation
Indices: 231620--231924 Score: 558
Period size: 115 Copynumber: 2.7 Consensus size: 115
231610 TCGTGTGCTC
231620 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTATGAAACCACAGAACCAA
231685 TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
66 TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
* *
231735 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTATGAAACCACAGAACCAA
231800 TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
66 TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
* *
231850 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTA-GGAATCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTATGAAACCACAGAACCAA
231914 TCATTGGAATT
66 TCATT-GAATT
231925 AAAAGATAAA
Statistics
Matches: 183, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
114 19 0.10
115 164 0.90
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (115 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTATGAAACCACAGAACCAA
TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
Found at i:232872 original size:73 final size:73
Alignment explanation
Indices: 232711--232882 Score: 179
Period size: 73 Copynumber: 2.4 Consensus size: 73
232701 TGAAGAAGGA
* * *
232711 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGCATGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCTGCATGAAC
** *
232775 AGCTTTTCC
65 AGCAGTACC
* * * *
232784 AGAAAAAGTTAATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCA-CT-CAGTGGAA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCTGCA-T-GAA
232847 CAGCAGTACC
64 CAGCAGTACC
** *
232857 AGTTAGAGTTCATAATGAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
232883 CACCTAAAGA
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
71 2 0.02
72 5 0.06
73 75 0.91
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (73 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCTGCATGAACA
GCAGTACC
Found at i:233112 original size:113 final size:113
Alignment explanation
Indices: 232784--233512 Score: 704
Period size: 113 Copynumber: 6.4 Consensus size: 113
232774 CAGCTTTTCC
* * * * *
232784 AGAAAAAGTTAATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCAC-TCAGTGGAAC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGA-TGGATC
* * * *
232848 AGCAGTACCAGTTAGAGTTCATAATGAGAAGAACTCACCTAAAGAAGGA
65 AACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
232897 AGAATAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTGCTTGAATTCATCA-TTCAATGGAT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-CTTTTGCTTAAATTCATCACTT-GATGGAT
* * *
232961 CAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
64 CAACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * *
233011 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCA
* *
233076 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
66 ACATTACCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGA
* * * *
233127 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCA
* * *
233192 GA-TTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 -ACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
233240 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCA
*** ***
233305 GTTTTTTTTAG--AGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-
66 -ACATTACCAGTTAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
233351 A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCAT-AATTCTATCACAGAAGCAGAT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTC-AT--C---A-C---T
* * * * ** * * *
233413 AGATTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAA
56 TGA-T-GGATCAACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
233473 AGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
233513 AATGACTCTA
Statistics
Matches: 529, Mismatches: 59, Indels: 45
0.84 0.09 0.07
Matches are distributed among these distances:
108 4 0.01
109 33 0.06
110 2 0.00
111 2 0.00
112 2 0.00
113 191 0.36
114 110 0.21
115 3 0.01
116 99 0.19
117 1 0.00
118 3 0.01
119 6 0.01
120 35 0.07
121 1 0.00
122 1 0.00
123 2 0.00
124 34 0.06
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCA
ACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:233325 original size:229 final size:228
Alignment explanation
Indices: 232784--233389 Score: 691
Period size: 229 Copynumber: 2.7 Consensus size: 228
232774 CAGCTTTTCC
* * * * * * * *
232784 AGAAAAAGTTAATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCAC-TCAGTGGAAC
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGA-TGGATC
* * * * *
232848 AGCAGTACCAGTTAGAGTTCATAATGAGAAGAACTCA-C--CTAAAGAAGGAAGAATAAGTTCAT
65 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAA-AAGTTCAT
* ** *
232910 AATGAGAAGAACTTGTTCAACTTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTT
129 AATGAGAAGAACTTGTTCAAC-CTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGTT
232975 CGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
193 CGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
* * * * * *
233011 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
*
233076 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAATTCATA
66 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAA-AAGTTCATA
* * *
233141 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGGATCAG-ATTTTCCAGTT
130 ATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCA-TTCAATGGATCAGCA-TTACCAGTT
* *
233204 TGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
193 CGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
*
233240 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
*** *** *
233305 GTTTTTTTTA-G-AGAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA-G-A-AAAAGTTCAC
66 -ACATTGCCAGGTAG-AGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAAAGTTCAT
* *
233362 AATGAGAAGAGCTTATTCAACCTTTTGC
129 AATGAGAAGAACTTGTTCAACCTTTTGC
233390 ATAATTCTAT
Statistics
Matches: 327, Mismatches: 44, Indels: 21
0.83 0.11 0.05
Matches are distributed among these distances:
222 31 0.09
223 2 0.01
224 1 0.00
225 1 0.00
226 12 0.04
227 85 0.26
228 6 0.02
229 143 0.44
230 46 0.14
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (228 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAGTTCGA
GTTCATAATAAGAAGAACTCATCTGAAGAAGGA
Found at i:233548 original size:124 final size:119
Alignment explanation
Indices: 233314--233597 Score: 378
Period size: 124 Copynumber: 2.4 Consensus size: 119
233304 AGTTTTTTTT
233314 AGAG-AAGTTCATAATGAGAAGAACTCATCTG-A-AGAAGAAAAAGTTCACAATGAGAAGAGCTT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAAGTTCACAATGAGAAGAGCTT
* * * * *
233376 ATTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATCAACCTTTCC
66 ATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACC---CC
* *
233433 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-GAG-AAGAAAAAGTTCACAATGAGAAGAGC
* * * *
233498 TTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCCCC
64 TTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACCCC
*
233554 AGCGAAAAGTTCATAATGAGAAGAACTCATCTGAAGA-AAGAAAA
1 AGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAA
233598 TGATTTATTC
Statistics
Matches: 146, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
119 10 0.07
120 27 0.18
121 8 0.05
122 30 0.21
123 2 0.01
124 69 0.47
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (119 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAAGTTCACAATGAGAAGAGCTT
ATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACCCC
Found at i:233766 original size:3 final size:3
Alignment explanation
Indices: 233760--233810 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
233750 TTATTATTAT
233760 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
233808 ATA
1 ATA
233811 TTATTAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:233853 original size:12 final size:12
Alignment explanation
Indices: 233760--233854 Score: 72
Period size: 12 Copynumber: 8.2 Consensus size: 12
233750 TTATTATTAT
*
233760 ATAATAATAATA
1 ATAATAATAAAA
*
233772 ATAATAATAATA
1 ATAATAATAAAA
*
233784 ATAATAATAATA
1 ATAATAATAAAA
*
233796 ATAATAATAATA
1 ATAATAATAAAA
* * *
233808 ATATTATTAAAT
1 ATAATAATAAAA
* *
233820 AT-AT-ATATAT
1 ATAATAATAAAA
*
233830 AT-AT-ATATAA
1 ATAATAATAAAA
233840 ATAATAATAAAA
1 ATAATAATAAAA
233852 ATA
1 ATA
233855 CAAGCCCAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
10 15 0.21
11 3 0.04
12 54 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATAATAAAA
Found at i:236279 original size:24 final size:24
Alignment explanation
Indices: 236252--236378 Score: 71
Period size: 24 Copynumber: 5.2 Consensus size: 24
236242 AATTATATTT
236252 TATTTAAATATAAATATTAAAATA
1 TATTTAAATATAAATATTAAAATA
* * *
236276 TA-TTAATTTAAAAATATTAAAATC
1 TATTTAA-ATATAAATATTAAAATA
* *
236300 TA-TTAATTTAAAAATATTAAAAT-
1 TATTTAA-ATATAAATATTAAAATA
* * * * * *
236323 TAGATTAAATATTTACTAAATAATATTT
1 TA-TTTAAATA-TAAAT-ATTAA-AATA
*
236351 TATTTAAATTTAAATATTAAAATA
1 TATTTAAATATAAATATTAAAATA
236375 TATT
1 TATT
236379 AAAAATTAGT
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
23 6 0.08
24 47 0.59
25 10 0.12
26 7 0.09
27 8 0.10
28 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (24 bp):
TATTTAAATATAAATATTAAAATA
Found at i:236292 original size:14 final size:14
Alignment explanation
Indices: 236257--236319 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
236247 TATTTTATTT
*
236257 AAATATAAATATTAA
1 AAATATTAAT-TTAA
236272 AATATATTAATTTAA
1 AA-ATATTAATTTAA
236287 AAATATT-A---AA
1 AAATATTAATTTAA
**
236297 ATCTATTAATTTAA
1 AAATATTAATTTAA
236311 AAATATTAA
1 AAATATTAA
236320 AATTAGATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
10 7 0.18
11 1 0.03
13 1 0.03
14 14 0.37
15 8 0.21
16 7 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATTAATTTAA
Found at i:236494 original size:22 final size:23
Alignment explanation
Indices: 236466--236510 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
236456 TTTACTAAAT
236466 AATATTTACTAAA-AATAGTTTA
1 AATATTTACTAAATAATAGTTTA
* *
236488 AATATTTATTAAATAATATTTTA
1 AATATTTACTAAATAATAGTTTA
236511 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AATATTTACTAAATAATAGTTTA
Found at i:236505 original size:158 final size:159
Alignment explanation
Indices: 236317--236613 Score: 533
Period size: 159 Copynumber: 1.9 Consensus size: 159
236307 TTAAAAATAT
*
236317 TAAAATTAGATTAAATATTTACTAAATAATATTTTATTTAAATTTAAATATTAAAATATATT-AA
1 TAAAAATAGATTAAATATTTACTAAATAATATTTTATTTAAATTTAAATATTAAAATATATTAAA
*
236381 AAATTAGTTTATTAATATTATATTCAAATATTGTATGGATTATACTTATTATTTTAAAAGTAATA
66 AAATTAGTTTATTAATATTATATTCAAATAATGTATGGATTATACTTATTATTTTAAAAGTAATA
236446 TTTTAAAATATTTACTAAATAATATTTAC
131 TTTTAAAATATTTACTAAATAATATTTAC
* *
236475 TAAAAATAGTTTAAATATTTATTAAATAATATTTTATTTAAATTTAAATATTAAAATATATTAAA
1 TAAAAATAGATTAAATATTTACTAAATAATATTTTATTTAAATTTAAATATTAAAATATATTAAA
*
236540 AAATTAGTTTATTAATATTCTATTCAAATAATGTATGGATTATACTTATTATTTTAAAAGTAATA
66 AAATTAGTTTATTAATATTATATTCAAATAATGTATGGATTATACTTATTATTTTAAAAGTAATA
*
236605 TTTTTAAAT
131 TTTTAAAAT
236614 TATCCATTAA
Statistics
Matches: 132, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
158 59 0.45
159 73 0.55
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (159 bp):
TAAAAATAGATTAAATATTTACTAAATAATATTTTATTTAAATTTAAATATTAAAATATATTAAA
AAATTAGTTTATTAATATTATATTCAAATAATGTATGGATTATACTTATTATTTTAAAAGTAATA
TTTTAAAATATTTACTAAATAATATTTAC
Found at i:236507 original size:14 final size:13
Alignment explanation
Indices: 236450--236487 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
236440 GTAATATTTT
236450 AAAATATTTACTA
1 AAAATATTTACTA
236463 AATAATATTTACTA
1 AA-AATATTTACTA
236477 AAAATAGTTTA
1 AAAATA-TTTA
236488 AATATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (13 bp):
AAAATATTTACTA
Found at i:238091 original size:15 final size:15
Alignment explanation
Indices: 238071--238107 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
238061 ATATTTAGTT
*
238071 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
238086 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
238101 GGGCGGG
1 GGGCGGG
238108 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:240388 original size:24 final size:24
Alignment explanation
Indices: 240349--240542 Score: 246
Period size: 24 Copynumber: 8.1 Consensus size: 24
240339 ATATGCATGG
* *
240349 CCACCAAAACCATTCCCTCCCCAT
1 CCACCAAGACCGTTCCCTCCCCAT
*
240373 CCGCCAAGACCGTTCCCTCCCCAT
1 CCACCAAGACCGTTCCCTCCCCAT
240397 CCACCAAGACCGTTCCCTCCCCAT
1 CCACCAAGACCGTTCCCTCCCCAT
* * *
240421 CCTCCACGACCGTTCCCTCCTC-T
1 CCACCAAGACCGTTCCCTCCCCAT
* * * *
240444 CCCGCCGAGACCATTCCCTCCCGAT
1 -CCACCAAGACCGTTCCCTCCCCAT
240469 CCACCAAGACCGTTCCCTCCCCAT
1 CCACCAAGACCGTTCCCTCCCCAT
* * *
240493 CCGCCACGACCGTTCCCTCCCGAT
1 CCACCAAGACCGTTCCCTCCCCAT
*
240517 CCACCAAGACCGTTCCCTCCTCAT
1 CCACCAAGACCGTTCCCTCCCCAT
240541 CC
1 CC
240543 TCCACACCCA
Statistics
Matches: 144, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
23 1 0.01
24 142 0.99
25 1 0.01
ACGTcount: A:0.18, C:0.54, G:0.10, T:0.18
Consensus pattern (24 bp):
CCACCAAGACCGTTCCCTCCCCAT
Found at i:250257 original size:25 final size:25
Alignment explanation
Indices: 250209--250257 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
250199 AAATTTATAA
*
250209 AATTTTAGAGAAAATAAACTTAAAG
1 AATTTTAGAGAAAATAAACATAAAG
*
250234 AATTTTATAGAAAAATAAA-ATAAA
1 AATTTTAGAG-AAAATAAACATAAA
250258 TTACCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAACATAAAG
Found at i:252504 original size:14 final size:13
Alignment explanation
Indices: 252480--252516 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
252470 CAATTAAATG
252480 AATAAATTAATAAT
1 AATAAA-TAATAAT
252494 AATATAATAATAAT
1 AATA-AATAATAAT
252508 AATAAATAA
1 AATAAATAA
252517 AGATAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:252636 original size:12 final size:12
Alignment explanation
Indices: 252619--252666 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
252609 ATTTGTATAC
252619 TATTTTCAAAAT
1 TATTTTCAAAAT
* *
252631 TATTTTTAAAAC
1 TATTTTCAAAAT
*
252643 TATTTTCCAAAT
1 TATTTTCAAAAT
252655 TATTTTCAAAAT
1 TATTTTCAAAAT
252667 ACAATAATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTTTCAAAAT
Found at i:252645 original size:24 final size:24
Alignment explanation
Indices: 252617--252665 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
252607 ATATTTGTAT
*
252617 ACTATTTTCAAAATTATTTTTAAA
1 ACTATTTTCAAAATTATTTTCAAA
*
252641 ACTATTTTCCAAATTATTTTCAAA
1 ACTATTTTCAAAATTATTTTCAAA
252665 A
1 A
252666 TACAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (24 bp):
ACTATTTTCAAAATTATTTTCAAA
Found at i:256784 original size:32 final size:32
Alignment explanation
Indices: 256747--256811 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
256737 TTTTCATTTT
256747 GATCTTTTACGAGCTTCAATTCATGGTTTTGA
1 GATCTTTTACGAGCTTCAATTCATGGTTTTGA
256779 GATCTTTTACGAGCTTCAATTCATGGTTTTGA
1 GATCTTTTACGAGCTTCAATTCATGGTTTTGA
256811 G
1 G
256812 TTCGAGTCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (32 bp):
GATCTTTTACGAGCTTCAATTCATGGTTTTGA
Found at i:257496 original size:29 final size:29
Alignment explanation
Indices: 257454--257510 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
257444 TAGGAGAAAC
*
257454 TTAAAATTTAAGTGATTAAATTAAAAATT
1 TTAAAATTTAAGTGATTAAAATAAAAATT
257483 TTAAAATGTT-AGTGATTAAAATAAAAAT
1 TTAAAAT-TTAAGTGATTAAAATAAAAAT
257511 GAGAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.39
Consensus pattern (29 bp):
TTAAAATTTAAGTGATTAAAATAAAAATT
Found at i:258953 original size:16 final size:18
Alignment explanation
Indices: 258932--258978 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
258922 ATATGGAATT
258932 AGATTCCAATTCC-T-AC
1 AGATTCCAATTCCTTCAC
*
258948 AGATTCTAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
*
258966 AGATTTCAATTCC
1 AGATTCCAATTCC
258979 CTTATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:259523 original size:60 final size:60
Alignment explanation
Indices: 259452--259568 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 60
259442 ATGGTTCGAT
* * *
259452 TATATGATGTTGTTTTGTCGAGTCGTTTGATTATTAAAAGTTATAAAATAATCCTTTGAC
1 TATATAATGTTGTTTTGTCGAGTCATTTGATTATCAAAAGTTATAAAATAATCCTTTGAC
*
259512 TATATAATGTTGTTTTGTCGAGTCATTTGATTATCAAAAGTTATAAAATAGTCCTTT
1 TATATAATGTTGTTTTGTCGAGTCATTTGATTATCAAAAGTTATAAAATAATCCTTT
259569 ATTTTTTTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (60 bp):
TATATAATGTTGTTTTGTCGAGTCATTTGATTATCAAAAGTTATAAAATAATCCTTTGAC
Found at i:261549 original size:120 final size:120
Alignment explanation
Indices: 261367--262688 Score: 1510
Period size: 120 Copynumber: 11.1 Consensus size: 120
261357 ATGATAGTGT
* * * * * * ** *
261367 TGAAGCCAATGTTTTCGATTTCAGGTCTAAAGGGAATAAAGAATCTGAAATAGCTGTAGCTGATG
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* * * *
261432 ATAGTGATTACAATGGAGATGGTCTAGCTAATGATAGTGCTAAGGCCCCTGTCTC
66 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * * * *
261487 TGTAGCCAATGATGTTGGTTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* * *
261552 ATGGTGATTGCAATGGAGACGGTTTAGCTAATGGT-GTGCTAAGGCCAGTGTCTC
66 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * * * * *
261606 TGAAGCCAATGTTCTTGATTTCAGATCAAAAGAGAATAAGGGCTCTGAAATGGCTGTAGCTGCTG
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* * * *
261671 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATGGTGCCAAAGCCACTGTGTC
66 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * * *
261726 TGAAGCCAATGTTCTCGATTTCAGGTCAAATGAGAATGAGGGGTCTGAAATGGCTGTAGCTGATG
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* * * * * *
261791 ACGGCGATTGCAGTGGAGAAGGTTTAG-T--T-ATAGTCCTATGGCCACTGTCTC
66 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* *
261842 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAACG-GAGGCTCTGAAATGGTTGTAGCTGAT
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAG-GGCTCTGAAATGGCTGTAGCTGAT
* *
261906 GATGGTGATTGCAATGGA-ATTGCTTTAGCTAATGATAGTGTCACTGTCAAGGCCACTGTCTA
65 GATGGTGATTGCAATGGAGA-TGGTTTAGCTAATGATAGTG---C--T-AAGGCCACTGTCTC
* * * * *
261968 GGAAGCCGATGTTATCGATTCCAGGTTAAAAGAGAATG-GAAGCTCTGAAATGGCTATAGCTGAT
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAG-GGCTCTGAAATGGCTGTAGCTGAT
* * * *
262032 GATGGTGATTGCAATGGAAAT-GTGTTAGCTAATGATAGTG-TCAAGTCCCACCGTCTA
65 GATGGTGATTGCAATGGAGATGGT-TTAGCTAATGATAGTGCT-AAG-GCCACTGTCTC
** * *
262089 TGAAGCCAATGTTATTTATTCCAGGTCAAAAGAGACA-GAGGGCTCTGAAATAGTTGTAGCTGAT
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGA-ATGAGGGCTCTGAAATGGCTGTAGCTGAT
* * *
262153 GATGGCGATTGCAATGGAGATGGTTTAGCTACTGATAGTGCTAAGGCCACTGTATC
65 GATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* ** *
262209 TGAAGCTAATGTTCA-CGATTCCAGGTTGAAAGAGAACGAGGGCTCTGAAATGGCTGTAGCTGAT
1 TGAAGCCAATGTT-ATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGAT
** * * *
262273 GATGGCAACTGCAATGAAGATGGTTTAGCTAATGATAGTGCCAAGGCCACTGTCTC
65 GATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
** *
262329 TGAAGCCAATGTTATCGATTCCAGGTTGAAAGAGAACGAGGGCTCTGAAATGGCTGTAGCTGATG
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
** * * *
262394 ATGGCAACTGCAACGGAGATGGTTTAGCTAATGATAGTGCCAAGGCCACTGTCTC
66 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * * * * *
262449 TGAAGCCAATGTTATTGATCCCAAGTCAGAAGAGAATGGGGGCTCTGAAATGGCCGTAGCTGATG
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* * ** * *
262514 ATGATGGTTGCCGTGGAGATGGTTTAGCTAATGATAGTTCTAAGGCCACTGTTTC
66 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * * * * *
262569 TGAAGCCAATGCTCTCGATTTCAGGTCAAAAGAGAATGAGAGTTCTGAAATGGTTGTAGC---TG
1 TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* *
262631 A---TGATTGCAATGGAGATGGTTTAGCTTATGATAGTGCTAAGACCACTGTCTC
66 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
262683 TGAAGC
1 TGAAGC
262689 TGCTGTAGAT
Statistics
Matches: 1034, Mismatches: 145, Indels: 52
0.84 0.12 0.04
Matches are distributed among these distances:
114 50 0.05
115 2 0.00
116 93 0.09
117 5 0.00
119 111 0.11
120 562 0.54
121 98 0.09
122 5 0.00
123 1 0.00
125 2 0.00
126 104 0.10
127 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (120 bp):
TGAAGCCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
Found at i:263096 original size:189 final size:186
Alignment explanation
Indices: 262779--263159 Score: 690
Period size: 189 Copynumber: 2.0 Consensus size: 186
262769 CTGACCGTGA
262779 TGGGGATTGTTTACTTGATGTTAGGGAAAAGGACACAGTTTCAGAAGCTCTTGCTGAATCCGGGG
1 TGGGGATTGTTTACTTGATGTTAGGGAAAAGGACACAGTTTCAGAAGCTCTTGCTGAATCCGGGG
262844 CTGAACAGAATGAGTCCTCTAACAGTGGTGAAGTTGAAGCTGATTCTGCATGTCCCGTCTCTAAT
66 CTGAACAGAATGAGTCCTCTAACAGTGGTGAAGTTGAAGCTGATTCTGCATGTCCCGTCTCTAAT
262909 GTTAATGTAGACAGGCCTGAACAAAATGTTGTGTCTGGAAATGAATCAGTTAAAGT
131 GTTAATGTAGACAGGCCTGAACAAAATGTTGTGTCTGGAAATGAATCAGTTAAAGT
* *
262965 TGGGGATTGTTTACTTGATGTTAGGGAAAAGGATACAGTTTCAGAAGCTGTTCTTGTTGAATCCG
1 TGGGGATTGTTTACTTGATGTTAGGGAAAAGGACACAGTTTCAGAAGC---TCTTGCTGAATCCG
* *
263030 GGGCTGAACAGAATGAGTCCTCTAACAGTGGTGAAGTTGAAGCTGATTCTGCATTTCCTGTCTCT
63 GGGCTGAACAGAATGAGTCCTCTAACAGTGGTGAAGTTGAAGCTGATTCTGCATGTCCCGTCTCT
*
263095 AATGTTAATGTAGACAGGCCTGAACAAAATGTTGTGTCTGGAAATGGATCAGTTAAAGT
128 AATGTTAATGTAGACAGGCCTGAACAAAATGTTGTGTCTGGAAATGAATCAGTTAAAGT
263154 TGGGGA
1 TGGGGA
263160 AAGCTTAACA
Statistics
Matches: 187, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
186 47 0.25
189 140 0.75
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (186 bp):
TGGGGATTGTTTACTTGATGTTAGGGAAAAGGACACAGTTTCAGAAGCTCTTGCTGAATCCGGGG
CTGAACAGAATGAGTCCTCTAACAGTGGTGAAGTTGAAGCTGATTCTGCATGTCCCGTCTCTAAT
GTTAATGTAGACAGGCCTGAACAAAATGTTGTGTCTGGAAATGAATCAGTTAAAGT
Found at i:266042 original size:21 final size:21
Alignment explanation
Indices: 266016--266064 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
266006 ACACAAGATA
266016 AAACAGCTCCCGCAAAAGTGG
1 AAACAGCTCCCGCAAAAGTGG
*
266037 AAACAGCTCCCGCGAAAGTGG
1 AAACAGCTCCCGCAAAAGTGG
266058 AAACAGC
1 AAACAGC
266065 AAAGGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.29, G:0.24, T:0.08
Consensus pattern (21 bp):
AAACAGCTCCCGCAAAAGTGG
Found at i:267429 original size:26 final size:26
Alignment explanation
Indices: 267381--267431 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
267371 GATGAGAATC
*
267381 TAATTTAAGGCTAAAGAACGATAGGT
1 TAATTTAAGGCTAAAGAAAGATAGGT
*
267407 TAATTTAGGGCT-AAGAAAAGATAGG
1 TAATTTAAGGCTAAAG-AAAGATAGG
267432 GATAGGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.25
Consensus pattern (26 bp):
TAATTTAAGGCTAAAGAAAGATAGGT
Found at i:267860 original size:2 final size:2
Alignment explanation
Indices: 267853--267878 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
267843 CTAACCCAAT
267853 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
267879 AGATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:268748 original size:35 final size:35
Alignment explanation
Indices: 268702--268774 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
268692 ATTACACCAC
268702 CATGTATTTCACAGGTTCCTTTTACCCCAAATTAA
1 CATGTATTTCACAGGTTCCTTTTACCCCAAATTAA
268737 CATGTATTTCACAGGTTCCTTTTACCCCAAATTAA
1 CATGTATTTCACAGGTTCCTTTTACCCCAAATTAA
268772 CAT
1 CAT
268775 ATCTTGACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (35 bp):
CATGTATTTCACAGGTTCCTTTTACCCCAAATTAA
Found at i:270791 original size:4 final size:4
Alignment explanation
Indices: 270782--270813 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
270772 TAAGGAATTA
270782 AATG AATG AATG AATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG
270814 TAATTCTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:271516 original size:7 final size:7
Alignment explanation
Indices: 271504--271533 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
271494 GGGATTGGAG
271504 AACGGGA
1 AACGGGA
271511 AACGGGA
1 AACGGGA
271518 AACGGGA
1 AACGGGA
271525 AACGGGA
1 AACGGGA
271532 AA
1 AA
271534 ATGAATTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.40, T:0.00
Consensus pattern (7 bp):
AACGGGA
Found at i:275998 original size:30 final size:30
Alignment explanation
Indices: 275964--276035 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
275954 CCCGAATGAC
275964 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
275994 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
276024 CTGTCCATAGGT
1 CTATCCAGAGGT
276036 TCCGAAGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:276057 original size:31 final size:31
Alignment explanation
Indices: 276022--276209 Score: 186
Period size: 31 Copynumber: 6.0 Consensus size: 31
276012 GATCCTCGGT
* *
276022 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
276053 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* *
276084 TACTGTCTATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
276115 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
* *
276147 TACTATCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
276178 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
276210 TACCCTCTAC
Statistics
Matches: 127, Mismatches: 20, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
30 6 0.05
31 71 0.56
32 44 0.35
33 6 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:276130 original size:63 final size:63
Alignment explanation
Indices: 276047--276212 Score: 289
Period size: 63 Copynumber: 2.7 Consensus size: 63
276037 CCGAAGAACC
* * * *
276047 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCTATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTATCCATATGTCTCGAAAGACA
276109 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTATCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTATCCATATGTCTCGAAAGACA
276172 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
276213 CCTCTACTCT
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 7 0.07
63 92 0.93
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTATCCATATGTCTCGAAAGACA
Found at i:286132 original size:24 final size:24
Alignment explanation
Indices: 286105--286154 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
286095 TGGTGGTTGA
*
286105 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
286129 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
286153 TT
1 TT
286155 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:292679 original size:64 final size:63
Alignment explanation
Indices: 292611--292791 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
292601 TTGGAACACT
* ***
292611 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * * **
292675 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAAAGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
292739 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
292792 CAATTAATTC
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
64 53 0.55
65 44 0.45
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:292763 original size:19 final size:19
Alignment explanation
Indices: 292739--292789 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
292729 GAAAATATTC
292739 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
292758 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
292777 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
292790 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:292765 original size:65 final size:65
Alignment explanation
Indices: 292632--292791 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
292622 TGCACCAAGT
* ***
292632 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* * **
292696 GTGCATCGATGCATCAAAAGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
292760 A
65 A
* *
292761 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
292792 CAATTAATTC
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.44
65 46 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:293031 original size:20 final size:21
Alignment explanation
Indices: 293008--293047 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
292998 GAATCGAATA
293008 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
293028 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
293048 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Done.