Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 1 of 378
Found at i:4334 original size:16 final size:16
Alignment explanation
Indices: 4285--4338 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
4275 TCCGCAGAGT
4285 GGGATATACCTAAGCC
1 GGGATATACCTAAGCC
* **
4301 GGGCTAT-CCTAATTC
1 GGGATATACCTAAGCC
4316 GGGATATACCTAAGCC
1 GGGATATACCTAAGCC
4332 GGGATAT
1 GGGATAT
4339 CCTCGGAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (16 bp):
GGGATATACCTAAGCC
Found at i:4551 original size:41 final size:41
Alignment explanation
Indices: 4457--4551 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
4447 TCCGAACCGG
* * * *
4457 GATGGGATATCAGAGGGATATCCCGGAATTGATTATTCTAA
1 GATGGGATATGAGAGGGATAACCCGGAATAGATTATTCCAA
* *
4498 GAGGGGAAATGAGAGGGATAACCCTGGAATAGATTATTCCAA
1 GATGGGATATGAGAGGGATAACCC-GGAATAGATTATTCCAA
4540 G-TGGGATATGAG
1 GATGGGATATGAG
4552 CGGTATTTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 29 0.64
42 16 0.36
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.24
Consensus pattern (41 bp):
GATGGGATATGAGAGGGATAACCCGGAATAGATTATTCCAA
Found at i:4841 original size:115 final size:117
Alignment explanation
Indices: 4649--4861 Score: 358
Period size: 116 Copynumber: 1.8 Consensus size: 117
4639 ATATCTTCGC
* *
4649 TATAAAACCTCATTAATGGGATTCAATCATTCAAAGATTTGCAAGAAAATGTCGTTAAATACAAA
1 TATAAAACCTAATTAATGGGATTCAATCATTCAAAGATTTACAAGAAAATGTCGTTAAATACAAA
*
4714 GGGAAACTAACAATCA-AAAAAATAAAATAAAATAAAACACATAACAGGCAA
66 GGGAAACAAACAATCAGAAAAAATAAAATAAAATAAAACACATAACAGGCAA
* * *
4765 TATAAAATCTAATTAATGGGATTCAATTATTCAAATATTTAC-AGAAAATGTCGTTAAATACAAA
1 TATAAAACCTAATTAATGGGATTCAATCATTCAAAGATTTACAAGAAAATGTCGTTAAATACAAA
4829 GGGAAACAAACAATCAGAAAAAATAAAATAAAA
66 GGGAAACAAACAATCAGAAAAAATAAAATAAAA
4862 CACATTACAG
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 37 0.41
116 53 0.59
ACGTcount: A:0.54, C:0.12, G:0.11, T:0.23
Consensus pattern (117 bp):
TATAAAACCTAATTAATGGGATTCAATCATTCAAAGATTTACAAGAAAATGTCGTTAAATACAAA
GGGAAACAAACAATCAGAAAAAATAAAATAAAATAAAACACATAACAGGCAA
Found at i:9535 original size:31 final size:31
Alignment explanation
Indices: 9500--9562 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
9490 AGTACGAGAA
9500 GGGAGGAAGAGAGAATAATGAAAACAAAAAG
1 GGGAGGAAGAGAGAATAATGAAAACAAAAAG
9531 GGGAGGAAGAGAGAATAATGAAAACAAAAAG
1 GGGAGGAAGAGAGAATAATGAAAACAAAAAG
9562 G
1 G
9563 AAATAAGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.57, C:0.03, G:0.33, T:0.06
Consensus pattern (31 bp):
GGGAGGAAGAGAGAATAATGAAAACAAAAAG
Found at i:11899 original size:39 final size:39
Alignment explanation
Indices: 11845--11927 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
11835 GGTGGTGACG
*
11845 GGTGGACCAATGGTGACTACCTGACTGGTGAACGATGAT
1 GGTGGACCAATGGTGACTACCTGACTGGTGAACGACGAT
** *
11884 GGTGGACCGGTGGTGACTGCCTGACTGGTGAACGACGAT
1 GGTGGACCAATGGTGACTACCTGACTGGTGAACGACGAT
11923 GGTGG
1 GGTGG
11928 TGGCCAGTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (39 bp):
GGTGGACCAATGGTGACTACCTGACTGGTGAACGACGAT
Found at i:14998 original size:16 final size:16
Alignment explanation
Indices: 14977--15008 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
14967 TAATATTCAA
14977 CTGAAACTATTCTCTT
1 CTGAAACTATTCTCTT
14993 CTGAAACTATTCTCTT
1 CTGAAACTATTCTCTT
15009 TCTTCCACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (16 bp):
CTGAAACTATTCTCTT
Found at i:18332 original size:21 final size:21
Alignment explanation
Indices: 18301--18358 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
18291 CAAATAGGTT
18301 AAAAATA-TGAACCGGACACC
1 AAAAATACTGAACCGGACACC
*
18321 AAAACA-ACTGAACCGGACACT
1 AAAA-ATACTGAACCGGACACC
18342 AAAAATACTGAACCGGA
1 AAAAATACTGAACCGGA
18359 ACGGAATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (21 bp):
AAAAATACTGAACCGGACACC
Found at i:25420 original size:132 final size:132
Alignment explanation
Indices: 25183--25444 Score: 452
Period size: 132 Copynumber: 2.0 Consensus size: 132
25173 CGACTGTGGA
* * * *
25183 ATATCCTTATAATGACATGTACTTCCAACAGAATACCCCTTTTAGATAGAATCACTAGGCGGAAT
1 ATATCCTTATAATGACATGTACTTCCAACAGAATACCCCTTTCAGATAAAATCACCAGGCGAAAT
*
25248 ACTCCTGTAATGGGATATCACCATTTTCAGTCAAACATACCGACCCTTAATCAAACTTAATATTC
66 ACTCCTATAATGGGATATCACCATTTTCAGTCAAACATACCGACCCTTAATCAAACTTAATATTC
25313 GG
131 GG
* *
25315 ATATCCTTGTAATGACATGTACTTCCAACAGAATATCCCTTTCAGATAAAATCACCAGGCGAAAT
1 ATATCCTTATAATGACATGTACTTCCAACAGAATACCCCTTTCAGATAAAATCACCAGGCGAAAT
*
25380 ACTCCTATAATGGGATATCACCATTTTCAGTCAAACATACCGACCCTTAATCGAACTTAATATTC
66 ACTCCTATAATGGGATATCACCATTTTCAGTCAAACATACCGACCCTTAATCAAACTTAATATTC
25445 AAACCTAAGG
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 122 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (132 bp):
ATATCCTTATAATGACATGTACTTCCAACAGAATACCCCTTTCAGATAAAATCACCAGGCGAAAT
ACTCCTATAATGGGATATCACCATTTTCAGTCAAACATACCGACCCTTAATCAAACTTAATATTC
GG
Found at i:33398 original size:3 final size:3
Alignment explanation
Indices: 33390--33415 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33380 AATTAACCTT
33390 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
33416 TTTTTTTTTT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:34927 original size:15 final size:16
Alignment explanation
Indices: 34885--34930 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
34875 TTTTTCGTTT
34885 AAACATTGAAATTTGC
1 AAACATTGAAATTTGC
*
34901 AATATGATTGAAATTTGC
1 AA-A-CATTGAAATTTGC
34919 -AACATTGAAATT
1 AAACATTGAAATT
34931 AGCCTACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 2 0.08
18 12 0.46
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (16 bp):
AAACATTGAAATTTGC
Found at i:36413 original size:25 final size:25
Alignment explanation
Indices: 36360--36418 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
36350 CTTATTTCAT
* * *
36360 TAAATAAA-AAATTTTAAAATATAA
1 TAAATAAATACATTTAAAAACATAA
36384 TAAATCAAATACATTTAAAAACATAA
1 TAAAT-AAATACATTTAAAAACATAA
36410 -AAATAAATA
1 TAAATAAATA
36419 TTAAAACAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.33
25 7 0.23
26 13 0.43
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAATACATTTAAAAACATAA
Found at i:36443 original size:19 final size:20
Alignment explanation
Indices: 36400--36443 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
36390 AAATACATTT
*
36400 AAAAACATAAAAATAAATAT
1 AAAAACATAAAAATAAATAA
* *
36420 TAAAACA-AGAAATAAATAA
1 AAAAACATAAAAATAAATAA
36439 AAAAA
1 AAAAA
36444 TGAAACTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAACATAAAAATAAATAA
Found at i:39146 original size:49 final size:49
Alignment explanation
Indices: 39086--39381 Score: 443
Period size: 49 Copynumber: 5.9 Consensus size: 49
39076 GTATGAGATA
*
39086 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
39135 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTG------TG
**
39192 TTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAAAAAGTGTG
1 -TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
39242 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* *
39291 TATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
39338 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
39382 TATATGTGTG
Statistics
Matches: 227, Mismatches: 11, Indels: 20
0.88 0.04 0.08
Matches are distributed among these distances:
47 44 0.19
49 131 0.58
50 2 0.01
51 3 0.01
56 3 0.01
57 2 0.01
58 42 0.19
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:39199 original size:107 final size:98
Alignment explanation
Indices: 39084--39381 Score: 465
Period size: 107 Copynumber: 3.0 Consensus size: 98
39074 ATGTATGAGA
39084 TATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTGTATATATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTGTATATATGTGATAA
39149 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
66 GGCCTAATGGCCGATGTGATGAATGTGAAA--GTG
* **
39184 TATATATGTTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAAAAAGTGTGTATATAT
1 ----TA---TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTGTATATAT
39249 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
59 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39289 TATATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAAA--GTGTATATATGTGATAA
1 TATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTGTATATATGTGATAA
39352 GGCCTAATGGCCGATGTGATGAATGTGAAA
66 GGCCTAATGGCCGATGTGATGAATGTGAAA
39382 TATATGTGTG
Statistics
Matches: 184, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
96 47 0.26
98 40 0.22
101 2 0.01
104 2 0.01
105 3 0.02
107 90 0.49
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.31
Consensus pattern (98 bp):
TATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTGTATATATGTGATAA
GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:39364 original size:96 final size:97
Alignment explanation
Indices: 39193--39381 Score: 326
Period size: 96 Copynumber: 1.9 Consensus size: 97
39183 GTATATATGT
* *
39193 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAAAAAGTGTGTATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGAAAAAG-GTGTATATATGTGATAAGG
39258 CCTAATGGCCGATGTGATGAATGTGAAAGTGTA
65 CCTAATGGCCGATGTGATGAATGTGAAAGTGTA
**
39291 TATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAAA-GTGTATATATGTGATAAGGC
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGAAAAAGGTGTATATATGTGATAAGGC
39355 CTAATGGCCGATGTGATGAATGTGAAA
66 CTAATGGCCGATGTGATGAATGTGAAA
39382 TATATGTGTG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
96 47 0.54
98 40 0.46
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (97 bp):
TATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGAAAAAGGTGTATATATGTGATAAGGC
CTAATGGCCGATGTGATGAATGTGAAAGTGTA
Found at i:39522 original size:37 final size:37
Alignment explanation
Indices: 39468--39558 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
39458 AACTTGGAAA
*
39468 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGTAAGACCCGATGACTACGTGTGGAGAT
39506 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
39543 TATGTCCGGGTAAGAC
1 TATGTCCGGGTAAGAC
39559 TTCGTAATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 48 0.92
38 4 0.08
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (37 bp):
TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
Found at i:48717 original size:15 final size:15
Alignment explanation
Indices: 48697--48727 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
48687 AACTTATCTT
48697 AAATCTTAAATTATG
1 AAATCTTAAATTATG
48712 AAATCTTAAATTATG
1 AAATCTTAAATTATG
48727 A
1 A
48728 CATTTGGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
AAATCTTAAATTATG
Found at i:51456 original size:35 final size:35
Alignment explanation
Indices: 51355--51459 Score: 174
Period size: 35 Copynumber: 3.0 Consensus size: 35
51345 GACGAGCTTG
* * *
51355 CTGCTTGCGAGCTGCGCAATTGACTACCGATCGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
51390 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
*
51425 CTGCTTGCGAGTTGCGCGACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
51460 AGGGCTGAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (35 bp):
CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
Found at i:51458 original size:19 final size:19
Alignment explanation
Indices: 51402--51458 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
51392 GCTTGCGAGC
51402 TGCGCGACTGACTACCGAT
1 TGCGCGACTGACTACCGAT
**
51421 T--GC-ACTG-CTTGCGAGT
1 TGCGCGACTGACTACCGA-T
51437 TGCGCGACTGACTACCGAT
1 TGCGCGACTGACTACCGAT
51456 TGC
1 TGC
51459 AAGGGCTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
15 5 0.17
16 6 0.21
17 2 0.07
18 2 0.07
19 9 0.31
20 5 0.17
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (19 bp):
TGCGCGACTGACTACCGAT
Found at i:51477 original size:33 final size:34
Alignment explanation
Indices: 51375--51477 Score: 102
Period size: 35 Copynumber: 3.0 Consensus size: 34
51365 GCTGCGCAAT
* * * *
51375 TGACTACCGATCGCACTGCTTGCGAGCTGCGCGAC
1 TGACTACCGATTGCACGGCTT-CGAGTTGAGCGAC
* *
51410 TGACTACCGATTGCACTGCTTGCGAGTTGCGCGAC
1 TGACTACCGATTGCACGGCTT-CGAGTTGAGCGAC
*
51445 TGACTACCGATTGCAAGGGC-T-GAGTTGAGCGAC
1 TGACTACCGATTGC-ACGGCTTCGAGTTGAGCGAC
51478 GGAAAGAGGC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
33 11 0.18
35 48 0.77
36 3 0.05
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.22
Consensus pattern (34 bp):
TGACTACCGATTGCACGGCTTCGAGTTGAGCGAC
Found at i:54738 original size:42 final size:42
Alignment explanation
Indices: 54679--54764 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
54669 TAAAGTTTAG
*
54679 GAAGAAATGGAAGTAATCCCTGAAAACTATCGTTTAATTAAT
1 GAAGAAATGGAAGTAATCCCTGAAAACTATCATTTAATTAAT
*
54721 GAAGAAATGGAAGTAATCCCTGCAAACTATCATTTAATTAAT
1 GAAGAAATGGAAGTAATCCCTGAAAACTATCATTTAATTAAT
54763 GA
1 GA
54765 GCAAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (42 bp):
GAAGAAATGGAAGTAATCCCTGAAAACTATCATTTAATTAAT
Found at i:61638 original size:46 final size:44
Alignment explanation
Indices: 61579--61693 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
61569 ACAGGACAGA
* *
61579 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
61625 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
61669 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
61694 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:61674 original size:44 final size:45
Alignment explanation
Indices: 61579--61712 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
61569 ACAGGACAGA
* *
61579 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
61625 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
61669 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
61713 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:66606 original size:35 final size:35
Alignment explanation
Indices: 66562--66727 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
66552 TCCTCATTGA
** *
66562 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
66597 AATGCCATACCTACATTT-TTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
66636 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
66671 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
66706 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
66728 CTTTGCCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
34 12 0.10
35 75 0.65
38 2 0.02
39 18 0.16
40 9 0.08
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:66647 original size:74 final size:73
Alignment explanation
Indices: 66557--66727 Score: 217
Period size: 74 Copynumber: 2.4 Consensus size: 73
66547 GGTTTTCCTC
** * * **
66557 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTT-TTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
66620 TCAGTATGG
65 TCAGTATGG
*
66629 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
66694 CTCAGTATGG
64 CTCAGTATGG
66704 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
66728 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
70 21 0.24
72 1 0.01
73 9 0.10
74 44 0.50
75 13 0.15
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:68769 original size:46 final size:44
Alignment explanation
Indices: 68710--68824 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
68700 ACAGGACAGA
* *
68710 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
68756 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
68800 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
68825 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:68805 original size:44 final size:45
Alignment explanation
Indices: 68710--68843 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
68700 ACAGGACAGA
* *
68710 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
68756 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
68800 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
68844 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:86686 original size:17 final size:17
Alignment explanation
Indices: 86664--86698 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
86654 CTTTGGGCTG
* *
86664 TGATTTGAATGGGGTTT
1 TGATTTCAATGGGCTTT
86681 TGATTTCAATGGGCTTT
1 TGATTTCAATGGGCTTT
86698 T
1 T
86699 CCGGAACAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.49
Consensus pattern (17 bp):
TGATTTCAATGGGCTTT
Found at i:105710 original size:12 final size:12
Alignment explanation
Indices: 105695--105719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105685 TTGGATATTC
105695 ATATATTTTTAG
1 ATATATTTTTAG
105707 ATATATTTTTAG
1 ATATATTTTTAG
105719 A
1 A
105720 AATAGAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
ATATATTTTTAG
Found at i:113421 original size:2 final size:2
Alignment explanation
Indices: 113414--113442 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
113404 GCATGGTTGG
113414 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 T
113443 GACCCAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:119030 original size:21 final size:21
Alignment explanation
Indices: 119004--119044 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
118994 AGACAAGCGA
* *
119004 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
119025 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
119045 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:122518 original size:22 final size:22
Alignment explanation
Indices: 122493--122541 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
122483 ACTTTCGCTC
122493 AATA-ATTAAATTTAGAAT-TAAT
1 AATATATTAAA-TTA-AATATAAT
122515 AATATATTAAATTAAATATAAT
1 AATATATTAAATTAAATATAAT
122537 AATAT
1 AATAT
122542 GATATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.12
22 16 0.64
23 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATATTAAATTAAATATAAT
Found at i:127257 original size:36 final size:36
Alignment explanation
Indices: 127217--127326 Score: 220
Period size: 36 Copynumber: 3.1 Consensus size: 36
127207 TTTTTAATAC
127217 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
127253 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
127289 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
1 TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
127325 TT
1 TT
127327 ATTAATTTGC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (36 bp):
TTGATCAAAATAGAATCCTTCTTTTGGATGACTGCA
Found at i:130075 original size:34 final size:34
Alignment explanation
Indices: 130032--130098 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
130022 ATGGATGATA
130032 ATCGAGATCTTATACTTGATACTTTGATAGTTTT
1 ATCGAGATCTTATACTTGATACTTTGATAGTTTT
130066 ATCGAGATCTTATACTTGATACTTTGATAGTTT
1 ATCGAGATCTTATACTTGATACTTTGATAGTTT
130099 GTCTTTCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (34 bp):
ATCGAGATCTTATACTTGATACTTTGATAGTTTT
Found at i:130393 original size:2 final size:2
Alignment explanation
Indices: 130386--130424 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
130376 GCATTTTAAC
130386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
130425 AAGATAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:138416 original size:44 final size:44
Alignment explanation
Indices: 138366--138455 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
138356 TTGCTAGATG
*
138366 CTGAATATTTTCAAATAGCTTATAGACTAAATTACTGTGACATA
1 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
138410 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
1 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
138454 CT
1 CT
138456 TTTATTGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (44 bp):
CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
Found at i:150128 original size:23 final size:23
Alignment explanation
Indices: 150076--150129 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
150066 TCATAGTATT
*
150076 ATTAGAAAATAAAGTTATGATAA
1 ATTACAAAATAAAGTTATGATAA
* *
150099 AAT-CAAATATAAAGTTA-GGTAA
1 ATTACAAA-ATAAAGTTATGATAA
150121 ATTACAAAA
1 ATTACAAAA
150130 ATAGTTACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (23 bp):
ATTACAAAATAAAGTTATGATAA
Found at i:155068 original size:11 final size:10
Alignment explanation
Indices: 155027--155068 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
155017 GATGATTTAA
155027 TTTAAAAATT
1 TTTAAAAATT
*
155037 ATTAAATAATT
1 TTTAAA-AATT
155048 TTT-AAAATT
1 TTTAAAAATT
155057 TTTAAAAGATT
1 TTTAAAA-ATT
155068 T
1 T
155069 CTTTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.26
10 10 0.37
11 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
TTTAAAAATT
Found at i:163468 original size:28 final size:28
Alignment explanation
Indices: 163422--163477 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
163412 CATTATTTTA
* *
163422 TGTGTATGATCACACTAAATCAAAATTT
1 TGTGTATAATCACAATAAATCAAAATTT
*
163450 TGTGTATAATTACAATAAATCAAAATTT
1 TGTGTATAATCACAATAAATCAAAATTT
163478 CATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (28 bp):
TGTGTATAATCACAATAAATCAAAATTT
Found at i:171593 original size:26 final size:26
Alignment explanation
Indices: 171563--171614 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
171553 CCCCCAAAGA
171563 AAGGGAAACACTTAAATCTATTGAAG
1 AAGGGAAACACTTAAATCTATTGAAG
171589 AAGGGAAACACTTAAATCTATTGAAG
1 AAGGGAAACACTTAAATCTATTGAAG
171615 GAGAGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (26 bp):
AAGGGAAACACTTAAATCTATTGAAG
Found at i:173513 original size:14 final size:15
Alignment explanation
Indices: 173478--173522 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
173468 ACTCTAACTA
173478 AATTATTAATAAATTT
1 AATT-TTAATAAATTT
173494 ATATTTTAAT-AATTT
1 A-ATTTTAATAAATTT
*
173509 AATTTTAAAAAATT
1 AATTTTAATAAATT
173523 ATAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.27
15 10 0.38
16 6 0.23
17 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTTAATAAATTT
Found at i:174943 original size:13 final size:14
Alignment explanation
Indices: 174925--174978 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 14
174915 AGAGTAGTAT
174925 AAAGAT-AATCATG
1 AAAGATCAATCATG
*
174938 AAAGATCAATCTAGTAT
1 AAAGATCAATC-A-T-G
174955 AAAGAT-AATCATG
1 AAAGATCAATCATG
174968 AAAGATCAATC
1 AAAGATCAATC
174979 TAGTTACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 12 0.35
14 9 0.26
15 2 0.06
16 5 0.15
17 6 0.18
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (14 bp):
AAAGATCAATCATG
Found at i:174996 original size:30 final size:30
Alignment explanation
Indices: 174919--174982 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
174909 ATAGTAAGAG
174919 TAGTATAAAGATAATCATGAAAGATCAATC
1 TAGTATAAAGATAATCATGAAAGATCAATC
174949 TAGTATAAAGATAATCATGAAAGATCAATC
1 TAGTATAAAGATAATCATGAAAGATCAATC
174979 TAGT
1 TAGT
174983 TACTAACTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGTATAAAGATAATCATGAAAGATCAATC
Found at i:175459 original size:63 final size:62
Alignment explanation
Indices: 175366--175487 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 62
175356 AAAAAATTGC
* *
175366 CATGAATAAATCAATATGTAAATCCCACTTCGAC-CTGACTTCCAAAAATTATCTTAAAATCGG
1 CATGAAGAAATCAATATGTAAATCCCACTTCGACAC-AACTTCC-AAAATTATCTTAAAATCGG
* *
175429 CATGAAGAAATCAATACT-TAAATCCGACTTCGACACAACTTTCAAAATTATCTTAAAAT
1 CATGAAGAAATCAATA-TGTAAATCCCACTTCGACACAACTTCCAAAATTATCTTAAAAT
175488 TTGTTGACTG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
62 16 0.30
63 35 0.66
64 2 0.04
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (62 bp):
CATGAAGAAATCAATATGTAAATCCCACTTCGACACAACTTCCAAAATTATCTTAAAATCGG
Found at i:178622 original size:8 final size:8
Alignment explanation
Indices: 178609--178643 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
178599 AACTAACTTC
178609 AGCATGTG
1 AGCATGTG
178617 AGCATGTG
1 AGCATGTG
178625 AGCATGTG
1 AGCATGTG
178633 AGCATGTG
1 AGCATGTG
178641 AGC
1 AGC
178644 TTACACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.26, C:0.14, G:0.37, T:0.23
Consensus pattern (8 bp):
AGCATGTG
Found at i:197803 original size:31 final size:31
Alignment explanation
Indices: 197762--197825 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
197752 TTATAAAATG
*
197762 GTTATTAAACTATTCGAAAATTTTCATTTAA
1 GTTATCAAACTATTCGAAAATTTTCATTTAA
* *
197793 GTTATCAAACTATTCGAAAGTTTTTATTTAA
1 GTTATCAAACTATTCGAAAATTTTCATTTAA
197824 GT
1 GT
197826 CATTGGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (31 bp):
GTTATCAAACTATTCGAAAATTTTCATTTAA
Found at i:199911 original size:16 final size:17
Alignment explanation
Indices: 199887--199924 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
199877 GGTATAAATA
* *
199887 ATTTAAATATTT-CTTT
1 ATTTGAATATTTAATTT
199903 ATTTGAATATTTAATTT
1 ATTTGAATATTTAATTT
199920 ATTTG
1 ATTTG
199925 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (17 bp):
ATTTGAATATTTAATTT
Found at i:204193 original size:22 final size:22
Alignment explanation
Indices: 204168--204211 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
204158 GACTTGATTA
**
204168 ATATAATATTAATAGTTTGAAG
1 ATATAATAAAAATAGTTTGAAG
*
204190 ATATAATAAAAATATTTTGAAG
1 ATATAATAAAAATAGTTTGAAG
204212 TTTAGAGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (22 bp):
ATATAATAAAAATAGTTTGAAG
Found at i:205349 original size:17 final size:17
Alignment explanation
Indices: 205329--205365 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
205319 AAATAGATTT
205329 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
205346 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
205363 TTA
1 TTA
205366 TTCTTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:208540 original size:13 final size:13
Alignment explanation
Indices: 208522--208552 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
208512 GGCACCCTGC
208522 AAAATAATTTTTA
1 AAAATAATTTTTA
208535 AAAAT-ATTTTTA
1 AAAATAATTTTTA
208547 AAAATA
1 AAAATA
208553 GAAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATAATTTTTA
Found at i:210618 original size:23 final size:22
Alignment explanation
Indices: 210584--210641 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
210574 TGTTATATTA
210584 ATTTTAAATATATATCTTAAAAT
1 ATTTTAAATATA-ATCTTAAAAT
* * *
210607 ATTTTAATTATAATTTTAAAAA
1 ATTTTAAATATAATCTTAAAAT
210629 ATTATTATAATAT
1 ATT-TTA-AATAT
210642 TTGAATGGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 11 0.38
23 14 0.48
24 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTAAATATAATCTTAAAAT
Found at i:213697 original size:16 final size:16
Alignment explanation
Indices: 213676--213706 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
213666 AGTATCGGCC
213676 GTGAAAATCAATGGAT
1 GTGAAAATCAATGGAT
213692 GTGAAAATCAATGGA
1 GTGAAAATCAATGGA
213707 CTTTCGAATA
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:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
GTGAAAATCAATGGAT
Found at i:215116 original size:18 final size:18
Alignment explanation
Indices: 215078--215117 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
215068 AACTGGTCGG
* *
215078 TTAACCGAAAAAATTTGA
1 TTAACCGAAAAAAATTAA
215096 TTAACCGAAAAAAATTAA
1 TTAACCGAAAAAAATTAA
215114 TTAA
1 TTAA
215118 AAAAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (18 bp):
TTAACCGAAAAAAATTAA
Found at i:215228 original size:18 final size:18
Alignment explanation
Indices: 215202--215236 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
215192 ATATATTAAT
215202 CCAAGTACCCAACCCAAC
1 CCAAGTACCCAACCCAAC
*
215220 CCAATTACCCAACCCAA
1 CCAAGTACCCAACCCAA
215237 TTATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.49, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAGTACCCAACCCAAC
Found at i:215229 original size:13 final size:13
Alignment explanation
Indices: 215213--215239 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
215203 CAAGTACCCA
215213 ACCCAACCCAATT
1 ACCCAACCCAATT
215226 ACCCAACCCAATT
1 ACCCAACCCAATT
215239 A
1 A
215240 TAAAAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:215862 original size:28 final size:28
Alignment explanation
Indices: 215822--215881 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
215812 CAAATGTGTC
215822 AGATAGAAGTATTGGGTATTGTTGAGGG
1 AGATAGAAGTATTGGGTATTGTTGAGGG
215850 AGATAGAAGTATTGGGTATTGTTGAGGG
1 AGATAGAAGTATTGGGTATTGTTGAGGG
215878 AGAT
1 AGAT
215882 TAGCTCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (28 bp):
AGATAGAAGTATTGGGTATTGTTGAGGG
Found at i:217962 original size:172 final size:171
Alignment explanation
Indices: 217659--217968 Score: 480
Period size: 172 Copynumber: 1.8 Consensus size: 171
217649 TAATGTCATC
* * * *
217659 AACAATACATGACATAAAATCAAATAATTCTTGTACTGAAATAAATAGTAAATCTTAAAACATCC
1 AACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCTTAAAACAACC
*
217724 AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAACTATGGAACTCAAACCCAAGATAACTG
66 AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTG
217789 CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
131 CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
* * * *
217830 AACAATACATGACAATACAATCAAAGAATGTC-TGTACTGAAATAAAGACTAAATCTTCATATAA
1 AACAATACATGAC-ATAAAATCAAAGAAT-TCTTGTACTGAAATAAAGACTAAATCTTAAAACAA
* *
217894 CCAACCGTCTTTCGATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCC-AGATAA
64 CCAACCATCTTTCGATT-TCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAA
217958 CTGCAGACATG
128 CTGCAGACATG
217969 TCATAGAAAC
Statistics
Matches: 125, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
171 13 0.10
172 72 0.58
173 40 0.32
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (171 bp):
AACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCTTAAAACAACC
AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTG
CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
Found at i:218187 original size:148 final size:147
Alignment explanation
Indices: 217841--218257 Score: 563
Period size: 148 Copynumber: 2.8 Consensus size: 147
217831 ACAATACATG
* * *
217841 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTAAATCTTCATATAACCAACCGTCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
* * *
217906 CGATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAGACATGTC
66 CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAAACACGTC
*
217971 ATAGAAACACGCCACCA
131 ATACAAACACGCCACCA
* * * *
217988 ACAACACAATCAAAGAATGTCTGTACTGAAATGAAGACAGTATCTTCACATAACCAACCATCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
* * * *
218053 CGGTTATCTCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCATATCA-TAG-AAACACGA
66 CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACT-GCAAACACG-
* * *
218116 ATACA-ACATATATGCCACCA
129 -T-CATACAAACACGCCACCA
* *
218136 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGCATCTTCACATAACCACCCGTCTCT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCT-T
* *
218201 T-GATTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCTAACCCAGATAACTGCA
65 TCGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCA
218258 GACAACTGAG
Statistics
Matches: 234, Mismatches: 29, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
146 6 0.03
147 106 0.45
148 116 0.50
149 6 0.03
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (147 bp):
ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAAACACGTC
ATACAAACACGCCACCA
Found at i:218488 original size:164 final size:162
Alignment explanation
Indices: 218300--218844 Score: 590
Period size: 164 Copynumber: 3.3 Consensus size: 162
218290 CACATGAACA
* * *
218300 ATGCCACCAACAATACATGACAATAAAACCAAAGAATGCCCATACTGCAATAAAGACTAAATGTT
1 ATGCCACCAACAATACATGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAAT-TT
* * * *
218365 CACACATCCATCTGACTTTCAATCAGTCAAACTAAAATACTACAGAACACAAACCCGAGACAACC
65 CACATATCCAAC-AACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAACC
* *
218430 AGCGACTTGTCGGAGGAACATGAACACAACATAT
129 ACCGACTTGTCGGAGGAACATGAACATAACATAT
* **
218464 ATGCCACCAACAATACACGACAATAAAATCAAAGAAAACCTATACTACAATAAAGACTAAATTTC
1 ATGCCACCAACAATACATGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATTT-
* * * * *
218529 CATATATACAACCAACTTTCAATCAATCAAGCTAAAGTACTACGGAACACAAACCCGAGACAACC
65 CACATATCCAA-CAACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAACC
*
218594 ACCAACTTGTCGGAGGAACATAGACATGACATATATGCCATAT
129 ACCGACTTGTCGGAGGAACAT-G--A--ACATA-A---CATAT
* * * * * *
218637 ATGCCACTAACAATACATAACAACACAATCAAAGAATGCCTGT-GTAACAATAAAGACTAAATCT
1 ATGCCACCAACAATACATGACAATAAAATCAAAGAATGCCTATACT-ACAATAAAGACTAAAT-T
* * * *
218701 CCACATATCTAAACAACTTTCAATCAGTCAAACTAAAGTCCTACAGAACACAAACCCAAGACAAC
64 TCACATATC-CAACAACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAAC
* * *
218766 CACCGAC-TGTTTGGAGGAATATGAACATGACATAT
128 CACCGACTTG-TCGGAGGAACATGAACATAACATAT
* * * * * *
218801 GTGCCACTAACAATACATGACAACACAATCAATGAATGCATATA
1 ATGCCACCAACAATACATGACAATAAAATCAAAGAATGCCTATA
218845 TATTGTCCAA
Statistics
Matches: 320, Mismatches: 45, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
163 2 0.01
164 172 0.54
165 2 0.01
167 2 0.01
168 4 0.01
169 4 0.01
170 2 0.01
172 4 0.01
173 125 0.39
174 3 0.01
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (162 bp):
ATGCCACCAACAATACATGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATTTC
ACATATCCAACAACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAACCAC
CGACTTGTCGGAGGAACATGAACATAACATAT
Found at i:218720 original size:173 final size:172
Alignment explanation
Indices: 218300--218806 Score: 534
Period size: 173 Copynumber: 3.0 Consensus size: 172
218290 CACATGAACA
** * * ** * * * *
218300 ATGCCACCAACAATACATGACAATAAAACCAAAGAATGCCCATACTGCAATAAAGACTAAATGTT
1 ATGCCACCAACAATACACAACAACAAAATCAAAGAAAACCTATACTACAATAAAGACTAAATCTC
* * * * *
218365 CACACAT-CCATCTGACTTTCAATCAGTCAAACTAAAATACTACAGAACACAAACCCGAGACAAC
66 CACATATACAAAC-AACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAAC
* *
218429 CAGCGACTTGTCGGAGGAACATG--A--ACACA-A---CATAT
130 CACCGACTTGTCGGAGGAACATGACATGACATATATGCCATAT
* * *
218464 ATGCCACCAACAATACACGACAATAAAATCAAAGAAAACCTATACTACAATAAAGACTAAATTTC
1 ATGCCACCAACAATACACAACAACAAAATCAAAGAAAACCTATACTACAATAAAGACTAAATCTC
* * * * *
218529 CATATATACAACCAACTTTCAATCAATCAAGCTAAAGTACTACGGAACACAAACCCGAGACAACC
66 CACATATACAAACAACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAACC
*
218594 ACCAACTTGTCGGAGGAACATAGACATGACATATATGCCATAT
131 ACCGACTTGTCGGAGGAACAT-GACATGACATATATGCCATAT
* * * ** * *
218637 ATGCCACTAACAATACATAACAACACAATCAAAGAATGCCTGT-GTAACAATAAAGACTAAATCT
1 ATGCCACCAACAATACACAACAACAAAATCAAAGAAAACCTATACT-ACAATAAAGACTAAATCT
* *
218701 CCACATAT-CTAAACAACTTTCAATCAGTCAAACTAAAGTCCTACAGAACACAAACCCAAGACAA
65 CCACATATAC-AAACAACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAA
* * *
218765 CCACCGAC-TGTTTGGAGGAATATGAACATGACATATGTGCCA
129 CCACCGACTTG-TCGGAGGAACATG-ACATGACATATATGCCA
218807 CTAACAATAC
Statistics
Matches: 288, Mismatches: 41, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
164 128 0.44
165 4 0.01
167 1 0.00
169 4 0.01
170 1 0.00
172 5 0.02
173 145 0.50
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (172 bp):
ATGCCACCAACAATACACAACAACAAAATCAAAGAAAACCTATACTACAATAAAGACTAAATCTC
CACATATACAAACAACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAACC
ACCGACTTGTCGGAGGAACATGACATGACATATATGCCATAT
Found at i:219152 original size:10 final size:10
Alignment explanation
Indices: 219132--219164 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
219122 AAGTTTAACC
219132 AAAAT-AAAA
1 AAAATAAAAA
219141 AAAATAAAAA
1 AAAATAAAAA
*
219151 AAAACAAAAA
1 AAAATAAAAA
219161 AAAA
1 AAAA
219165 ACCTCAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.91, C:0.03, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:221952 original size:30 final size:30
Alignment explanation
Indices: 221918--221985 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
221908 CATTTAAAAG
*
221918 TTAAATTAACTGTATTAATAATGGAAGAAC
1 TTAAATTAACGGTATTAATAATGGAAGAAC
221948 TTAAATTAACGGTATTAATAATGGAAGAAC
1 TTAAATTAACGGTATTAATAATGGAAGAAC
*
221978 CT-AATTAA
1 TTAAATTAA
221986 TATAAGCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 6 0.17
30 30 0.83
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.32
Consensus pattern (30 bp):
TTAAATTAACGGTATTAATAATGGAAGAAC
Found at i:226963 original size:31 final size:31
Alignment explanation
Indices: 226914--226974 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
226904 GCTATCATAT
**
226914 AATTAAATAAATGTTTTTAAAAATTAATTAA
1 AATTAAATAAATAATTTTAAAAATTAATTAA
* **
226945 AATTAAATACATAATTTTATTAATTAATTA
1 AATTAAATAAATAATTTTAAAAATTAATTA
226975 CTATATTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
AATTAAATAAATAATTTTAAAAATTAATTAA
Found at i:228046 original size:4 final size:4
Alignment explanation
Indices: 228037--228068 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
228027 AATGCACCAG
*
228037 GTAT GTAT GTAT GTAT GTAT GTAT GTAA GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
228069 CAAGGCGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:232253 original size:22 final size:22
Alignment explanation
Indices: 232213--232254 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
232203 TTTTTTTTTT
* **
232213 TAAATTTAAAATATCACAATAA
1 TAAATTTAAAAAAAAACAATAA
232235 TAAATTTAAAAAAAAACAAT
1 TAAATTTAAAAAAAAACAAT
232255 TTAACAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATTTAAAAAAAAACAATAA
Found at i:234324 original size:46 final size:46
Alignment explanation
Indices: 234143--234324 Score: 258
Period size: 46 Copynumber: 4.0 Consensus size: 46
234133 TTTGACATGA
* * * * * *
234143 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
234189 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
234235 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
234281 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
234325 AGAGCACACT
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.03
46 120 0.97
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:242313 original size:24 final size:25
Alignment explanation
Indices: 242263--242313 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
242253 TAAATCAATT
* *
242263 TTTTAAATATATTTTATTTTTTGAA
1 TTTTAAATATATTTTATTTATTAAA
242288 TTTTAAATA-A-TTTATTTAATTAAA
1 TTTTAAATATATTTTATTT-ATTAAA
242312 TT
1 TT
242314 GAACTAGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 7 0.30
25 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTAAATATATTTTATTTATTAAA
Found at i:246022 original size:190 final size:190
Alignment explanation
Indices: 245689--246153 Score: 540
Period size: 190 Copynumber: 2.4 Consensus size: 190
245679 TTCTATTTGT
* * *
245689 TTTATGTTTGTTTATCAAGCTAAATAAATGAACATGAACAAGATTTTGAGGCTAATTTCTTAACT
1 TTTATG-TTGTTTATCAAGCTAAATAAATGAACATGAACAATATTTTGAGGCTCATTTATT-A--
* * * *
245754 GAACCGAACACGAACCTAACAAGAACAAGTTTAAAAATAAACTAATATGAACAAAGATTCCTTTG
62 -AACTGAAC-CGAA-C--AC-AGAACAAGTTTAAAAATAAACGAACATGAACAAAGATTCCTTAG
* ** * *
245819 TCCAACCTCGGTTCATTCACAGCCGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCT
121 TCCAACCTCGGTTCATTCACAGCCATGAATATATCCATAAACAGTTCATAAATCATCCTGGTCCA
245884 GTTCA
186 GTTCA
* *
245889 TTTATGTTCGTTTATCAA-CTAAATAAATGAATATGAACAATATTTTGAAGCTCCATTTATTAAA
1 TTTATGTT-GTTTATCAAGCTAAATAAATGAACATGAACAATATTTTGAGGCT-CATTTATTAAA
* ** * *
245953 CTGAACCGAACAC-GAACAAGTTTAAAAATAAACGAACATGACCAGTGATTCCTTAGTTCAAGCT
64 CTGAACCGAACACAGAACAAGTTTAAAAATAAACGAACATGAACAAAGATTCCTTAGTCCAACCT
* * * * * * **
246017 CGGTTCATTTACAGCCATGAATATATCCATGAATAGTTCATAAATCGTCCTGTTTCAGTTTG
129 CGGTTCATTCACAGCCATGAATATATCCATAAACAGTTCATAAATCATCCTGGTCCAGTTCA
246079 TTTA-GCTTGTTTATCAAGCTAAATAAATGAACATGAACAATATTTTGAGGCTCATTTATTAAAC
1 TTTATG-TTGTTTATCAAGCTAAATAAATGAACATGAACAATATTTTGAGGCTCATTTATTAAAC
*
246143 TGAATCGAACA
65 TGAACCGAACA
246154 TATGCAGTGA
Statistics
Matches: 231, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
189 32 0.14
190 130 0.56
192 2 0.01
194 1 0.00
195 4 0.02
196 7 0.03
199 34 0.15
200 21 0.09
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (190 bp):
TTTATGTTGTTTATCAAGCTAAATAAATGAACATGAACAATATTTTGAGGCTCATTTATTAAACT
GAACCGAACACAGAACAAGTTTAAAAATAAACGAACATGAACAAAGATTCCTTAGTCCAACCTCG
GTTCATTCACAGCCATGAATATATCCATAAACAGTTCATAAATCATCCTGGTCCAGTTCA
Found at i:248530 original size:20 final size:18
Alignment explanation
Indices: 248505--248543 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
248495 AATTTGTATT
248505 AAATATTTATATTATATTTA
1 AAATATTT-TATT-TATTTA
248525 AAATATTTTATTTATTTA
1 AAATATTTTATTTATTTA
248543 A
1 A
248544 TGTGACAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATTTTATTTATTTA
Found at i:251634 original size:18 final size:20
Alignment explanation
Indices: 251611--251650 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
251601 CAATAAAGTT
251611 TAAAAAATT-AT-AAAAAAA
1 TAAAAAATTCATGAAAAAAA
*
251629 TAAAAATTTCATGAAAAAAA
1 TAAAAAATTCATGAAAAAAA
251649 TA
1 TA
251651 GGAATATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (20 bp):
TAAAAAATTCATGAAAAAAA
Found at i:253235 original size:23 final size:23
Alignment explanation
Indices: 253205--253250 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
253195 AAATTTAATT
253205 TAATAGTAAAAATACACTTTGAC
1 TAATAGTAAAAATACACTTTGAC
253228 TAATAGTAAAAATACACTTTGAC
1 TAATAGTAAAAATACACTTTGAC
253251 CTCCATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (23 bp):
TAATAGTAAAAATACACTTTGAC
Found at i:259597 original size:15 final size:15
Alignment explanation
Indices: 259553--259622 Score: 59
Period size: 16 Copynumber: 4.5 Consensus size: 15
259543 ACATCCGTTG
259553 ATATTATTTTAATTTA
1 ATATT-TTTTAATTTA
**
259569 ATATTTAATAATTTA
1 ATATTTTTTAATTTA
*
259584 ATATTTTTTTATTTA
1 ATATTTTTTAATTTA
* * *
259599 TTAATTTTTTTATATA
1 AT-ATTTTTTAATTTA
259615 ATAATTTT
1 AT-ATTTT
259623 AATATCTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
15 21 0.47
16 24 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATTTTTTAATTTA
Found at i:262603 original size:3 final size:3
Alignment explanation
Indices: 262595--262624 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
262585 ATGTTTTTTA
262595 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
262625 TTGTTATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:263489 original size:35 final size:36
Alignment explanation
Indices: 263418--263489 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
263408 TGTCAAGTCT
*
263418 AATAGATTTTATCCATAATATTTGAGTGTTGGATAA
1 AATAGATTTTATCCATAAGATTTGAGTGTTGGATAA
* *
263454 AATAGATTTTATCCGTAAGA-TTGAGTGTTGTATAA
1 AATAGATTTTATCCATAAGATTTGAGTGTTGGATAA
263489 A
1 A
263490 GATCGTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 15 0.45
36 18 0.55
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (36 bp):
AATAGATTTTATCCATAAGATTTGAGTGTTGGATAA
Found at i:279116 original size:42 final size:42
Alignment explanation
Indices: 279068--279152 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
279058 ACACTCTAAT
279068 TTTTATTTTTATTTTATATCAACCTCAGAGATAAAATTTCTA
1 TTTTATTTTTATTTTATATCAACCTCAGAGATAAAATTTCTA
279110 TTTTATTTTTATTTTATATCAACCTCAGAGATAAAATTTCTA
1 TTTTATTTTTATTTTATATCAACCTCAGAGATAAAATTTCTA
279152 T
1 T
279153 CTTTGTCCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (42 bp):
TTTTATTTTTATTTTATATCAACCTCAGAGATAAAATTTCTA
Found at i:281177 original size:50 final size:50
Alignment explanation
Indices: 281123--281222 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
281113 ATTTTTCCTT
281123 AGTTTCTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
1 AGTTTCTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
*
281173 AGTTTTTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
1 AGTTTCTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
281223 TTATTTAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (50 bp):
AGTTTCTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
Found at i:284049 original size:60 final size:60
Alignment explanation
Indices: 283982--284096 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
283972 TAGTCCTGAC
* * *
283982 CAAAAAAGACAAAATT-GAGTAGTTGAGTGATCATTTTGTAACTTTTCATAATTAGGTTAT
1 CAAAAAAGA-AAAATTCGAATAGTTAAGTGATCATTTTATAACTTTTCATAATTAGGTTAT
** * *
284042 CAAAAAAGAAATTTTCTAATAGTTAAGTGATCATTTTATAACTTTTCATTATTAG
1 CAAAAAAGAAAAATTCGAATAGTTAAGTGATCATTTTATAACTTTTCATAATTAG
284097 ACGGCAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (60 bp):
CAAAAAAGAAAAATTCGAATAGTTAAGTGATCATTTTATAACTTTTCATAATTAGGTTAT
Found at i:284774 original size:29 final size:30
Alignment explanation
Indices: 284724--284793 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
284714 TTTATCAAAT
* *
284724 ATAAGTACTAGATTGAATAAAAA-AATAAC
1 ATAAGTACCAGATTGAATAAAAATAATAAA
* *
284753 ATAAGTACCATATTAGAA-AAAAATATTAAA
1 ATAAGTACCAGATT-GAATAAAAATAATAAA
284783 ATCAAGTACCA
1 AT-AAGTACCA
284794 AATGATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 17 0.50
30 9 0.26
31 8 0.24
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (30 bp):
ATAAGTACCAGATTGAATAAAAATAATAAA
Found at i:288063 original size:18 final size:18
Alignment explanation
Indices: 288042--288083 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
288032 AACCTTAAGG
288042 TCTGTTTGAACTTTAAAT
1 TCTGTTTGAACTTTAAAT
288060 TCTGTTTGAACTTTAAAT
1 TCTGTTTGAACTTTAAAT
*
288078 TATGTT
1 TCTGTT
288084 ACTTGTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (18 bp):
TCTGTTTGAACTTTAAAT
Found at i:292683 original size:12 final size:12
Alignment explanation
Indices: 292666--292692 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
292656 TTTGAATGAG
292666 TTTTAATTGAAT
1 TTTTAATTGAAT
292678 TTTTAATTGAAT
1 TTTTAATTGAAT
292690 TTT
1 TTT
292693 AACATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTTAATTGAAT
Found at i:292692 original size:11 final size:11
Alignment explanation
Indices: 292653--292694 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
292643 TTGAACAAAC
*
292653 GAATTTGAA-T
1 GAATTTTAATT
*
292663 GAGTTTTAATT
1 GAATTTTAATT
292674 GAATTTTTAATT
1 GAA-TTTTAATT
292686 GAATTTTAA
1 GAATTTTAA
292695 CATAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 7 0.26
11 9 0.33
12 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (11 bp):
GAATTTTAATT
Found at i:301408 original size:42 final size:42
Alignment explanation
Indices: 301349--301433 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
301339 TAGGTCTAAA
301349 ACTAGTCAATTCACGTTTCGAAACATTGTATTATGGATTGAT
1 ACTAGTCAATTCACGTTTCGAAACATTGTATTATGGATTGAT
*
301391 ACTAGTCAATTCACGTTTCGAAACATTTTATTATGGATTGAT
1 ACTAGTCAATTCACGTTTCGAAACATTGTATTATGGATTGAT
301433 A
1 A
301434 TCATTAGGGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (42 bp):
ACTAGTCAATTCACGTTTCGAAACATTGTATTATGGATTGAT
Found at i:302919 original size:12 final size:12
Alignment explanation
Indices: 302902--302928 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
302892 AATGTTATTA
302902 TTTCATACAAAC
1 TTTCATACAAAC
302914 TTTCATACAAAC
1 TTTCATACAAAC
302926 TTT
1 TTT
302929 TTTTCGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTCATACAAAC
Found at i:313422 original size:10 final size:10
Alignment explanation
Indices: 313402--313435 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
313392 TATAAGTTTG
313402 TTACTTTATTT
1 TTAC-TTATTT
313413 TTACTTA-TT
1 TTACTTATTT
313422 TTACTTATTT
1 TTACTTATTT
313432 TTAC
1 TTAC
313436 ATTTGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 9 0.41
11 4 0.18
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (10 bp):
TTACTTATTT
Found at i:320009 original size:20 final size:20
Alignment explanation
Indices: 319964--320026 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
319954 AGTTTTCCTT
* *
319964 TTTTAATTTTTTCTATAAATA
1 TTTTAATTATTT-GATAAATA
319985 TTTTATATTATTTGATAAA-A
1 TTTTA-ATTATTTGATAAATA
* *
320005 TTTTAATTTTTTTATAAATA
1 TTTTAATTATTTGATAAATA
320025 TT
1 TT
320027 AAAAAAGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 11 0.31
20 9 0.25
21 10 0.28
22 6 0.17
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAATTATTTGATAAATA
Found at i:320112 original size:32 final size:32
Alignment explanation
Indices: 320052--320113 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
320042 TAAGTAAATT
*
320052 AAAAATTATAAATCTTATAAAATATATTTTTA
1 AAAAATTATAAATATTATAAAATATATTTTTA
* *
320084 AAAAATTATATAATATTTTAATAT-TATTTT
1 AAAAATTATA-AATATTATAAAATATATTTT
320114 CAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
AAAAATTATAAATATTATAAAATATATTTTTA
Found at i:320204 original size:33 final size:32
Alignment explanation
Indices: 320143--320230 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 32
320133 TCTCATCATT
320143 TTAAAAAAATATTTTCTAATCA----TAAAAA
1 TTAAAAAAATATTTTCTAATCATTTTTAAAAA
320171 TTAAAAAAATATTTTCTAATCATTTTTAAAAAA
1 TTAAAAAAATATTTTCTAATCATTTTT-AAAAA
* * *
320204 TCT-TATAAATATTTTCTCATCATTTTT
1 T-TAAAAAAATATTTTCTAATCATTTTT
320231 TTCTCGGCCC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 22 0.43
32 1 0.02
33 27 0.53
34 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (32 bp):
TTAAAAAAATATTTTCTAATCATTTTTAAAAA
Found at i:323146 original size:31 final size:31
Alignment explanation
Indices: 323092--323178 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
323082 ATTATAAAAT
*
323092 AATCATTAAATTATTTATAAGTTT-TCATTGA
1 AATCATTAAATTATTTATAAGTTTGT-ATTCA
*
323123 AATCATTAAATTATTTGA-GAGTTTGTATTCA
1 AATCATTAAATTATTT-ATAAGTTTGTATTCA
* *
323154 AGTCATTAAATT-TTTTTATAGTTTG
1 AATCATTAAATTATTTATA-AGTTTG
323179 ATTGGCGAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
30 3 0.06
31 42 0.89
32 2 0.04
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.49
Consensus pattern (31 bp):
AATCATTAAATTATTTATAAGTTTGTATTCA
Found at i:328566 original size:142 final size:140
Alignment explanation
Indices: 328377--328631 Score: 354
Period size: 142 Copynumber: 1.8 Consensus size: 140
328367 TTCTATTATG
* * *
328377 TTAATTTAAAATATTGTTTATATCATTATATTTTTAATGGTTGAA-TTTTTACATAAATATATAA
1 TTAATTTAAAATACTGTTTATATCATTATAATTTTAATGGTTAAATTTTTTACATAAA-ATA-AA
* * *
328441 T-TTTAAAAAATTAAATTATTATTTCAAAC-TTGAAATACATTATTTAATTTATGTCAATAAAAC
64 TAATT-AAAAATTAAA-T-TTATTACAAACTTTAAAATACATTATTTAATTTATGTCAATAAAAC
328504 AAATAAAATTGTATA
126 AAATAAAATTGTATA
*
328519 TTAATTTAAAATACTGTTTATTTCATTATAATTTTAATGGTTAAATTTTTTACATAAAATAAATA
1 TTAATTTAAAATACTGTTTATATCATTATAATTTTAATGGTTAAATTTTTTACATAAAATAAATA
* * *
328584 ATTAAAATTTTAATTTATTACAAACTTTAAAATACATTATTTTATTTA
66 ATTAAAAATTAAATTTATTACAAACTTTAAAATACATTATTTAATTTA
328632 CTTAAGTAAC
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
139 10 0.10
140 21 0.21
141 11 0.11
142 46 0.46
143 12 0.12
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (140 bp):
TTAATTTAAAATACTGTTTATATCATTATAATTTTAATGGTTAAATTTTTTACATAAAATAAATA
ATTAAAAATTAAATTTATTACAAACTTTAAAATACATTATTTAATTTATGTCAATAAAACAAATA
AAATTGTATA
Found at i:331250 original size:29 final size:31
Alignment explanation
Indices: 331218--331280 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
331208 TCAACAATTT
*
331218 AAAATTTAGTCTCTTTA-TTTTTAT-TATAA
1 AAAATTTAATCTCTTTACTTTTTATATATAA
* *
331247 AAAATTTAATCTTTTTACTTTTTATATTTAA
1 AAAATTTAATCTCTTTACTTTTTATATATAA
331278 AAA
1 AAA
331281 TATAAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.52
30 7 0.24
31 7 0.24
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (31 bp):
AAAATTTAATCTCTTTACTTTTTATATATAA
Found at i:331782 original size:12 final size:12
Alignment explanation
Indices: 331761--331790 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
331751 AAATTAGTTT
*
331761 TTAATAAAAATA
1 TTAATTAAAATA
331773 TTAATTAAAATA
1 TTAATTAAAATA
331785 TTAATT
1 TTAATT
331791 TTTTAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAATTAAAATA
Found at i:334779 original size:28 final size:28
Alignment explanation
Indices: 334739--334796 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
334729 GGTCCTCAAG
334739 AATGTTAAGTCCTCATGCCTCATGTAGT
1 AATGTTAAGTCCTCATGCCTCATGTAGT
334767 AATGTTAAGTCCTCATGCCTCATGTAGT
1 AATGTTAAGTCCTCATGCCTCATGTAGT
334795 AA
1 AA
334797 CCCTTGGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (28 bp):
AATGTTAAGTCCTCATGCCTCATGTAGT
Found at i:335310 original size:18 final size:19
Alignment explanation
Indices: 335283--335320 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
335273 AGTACTCATT
*
335283 TTTTTTGTAAAATAT-TAA
1 TTTTTGGTAAAATATGTAA
335301 TTTTTGGTAAAATATGTAA
1 TTTTTGGTAAAATATGTAA
335320 T
1 T
335321 ATACTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTTGGTAAAATATGTAA
Found at i:339385 original size:58 final size:58
Alignment explanation
Indices: 339295--339409 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
339285 GGGGTTGGAG
*
339295 CATGCATATGTTTCTTGTAGTGTGATTTTGAGGGTTTGGAGTCAAAATTAAATTATAA
1 CATGCATACGTTTCTTGTAGTGTGATTTTGAGGGTTTGGAGTCAAAATTAAATTATAA
* * * *
339353 CATGCATGCGTTTCTTGTGGTGTGATTTTGAGGGTTTGGAGTCGAAATTATATTATA
1 CATGCATACGTTTCTTGTAGTGTGATTTTGAGGGTTTGGAGTCAAAATTAAATTATA
339410 CTTTTTTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (58 bp):
CATGCATACGTTTCTTGTAGTGTGATTTTGAGGGTTTGGAGTCAAAATTAAATTATAA
Found at i:339809 original size:32 final size:30
Alignment explanation
Indices: 339768--339921 Score: 125
Period size: 32 Copynumber: 4.9 Consensus size: 30
339758 TTAATTGAAA
339768 TTTTAAAAAATTTTAAGAGGTTTAATAAGAA-T
1 TTTTAAAAAA-TTTAA-AGGTTTAATAA-AATT
*
339800 TTTTAAAAAA-TT-AGGGTTTAATTAAAATT
1 TTTTAAAAAATTTAAAGGTTTAA-TAAAATT
* * *
339829 TTTTTAAAAATTTAAAAGATTTAATGATAATTT
1 TTTTAAAAAATTT-AAAGGTTTAAT-A-AAATT
** *
339862 TTTTAAAAAAAATAAAGATTTAATTAAAATT
1 TTTTAAAAAATTTAAAGGTTTAA-TAAAATT
* *
339893 TTTAAAAAAATTGAAAGGTTTAATGAAAA
1 TTTTAAAAAATTTAAAGGTTTAAT-AAAA
339922 GTTGTGAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
28 9 0.09
29 14 0.14
30 5 0.05
31 27 0.27
32 29 0.29
33 15 0.15
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (30 bp):
TTTTAAAAAATTTAAAGGTTTAATAAAATT
Found at i:339915 original size:31 final size:30
Alignment explanation
Indices: 339758--339921 Score: 129
Period size: 30 Copynumber: 5.3 Consensus size: 30
339748 TTTCGGATGC
* *
339758 TTAATTGAAA-TTTTAAAAAATTTTAAGAGGT
1 TTAATTAAAATTTTTAAAAAA-ATTAA-AGGT
*
339789 TTAA-TAAGAATTTTT-AAAAAATT-AGGGT
1 TTAATTAA-AATTTTTAAAAAAATTAAAGGT
* * *
339817 TTAATTAAAATTTTTTTAAAAATTTAAAAGAT
1 TTAATTAAAA-TTTTTAAAAAAATT-AAAGGT
** * *
339849 TTAATGATAATTTTTTTAAAAAAAATAAAGAT
1 TTAAT--TAAAATTTTTAAAAAAATTAAAGGT
339881 TTAATTAAAATTTTTAAAAAAATTGAAAGGT
1 TTAATTAAAATTTTTAAAAAAATT-AAAGGT
*
339912 TTAATGAAAA
1 TTAATTAAAA
339922 GTTGTGAAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
28 9 0.08
29 9 0.08
30 27 0.25
31 25 0.23
32 23 0.21
33 11 0.10
34 3 0.03
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (30 bp):
TTAATTAAAATTTTTAAAAAAATTAAAGGT
Found at i:343632 original size:69 final size:69
Alignment explanation
Indices: 343557--343696 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
343547 GTATGGGATG
343557 ATGATGGGTCAAATGTAAGCAAAGACAAAGTTAGAAATTTAATATCAAGGATGGAATAAAATTAT
1 ATGATGGGTCAAATGTAAGCAAAGACAAAGTTAGAAATTTAATATCAAGGATGGAATAAAATTAT
343622 AAAT
66 AAAT
343626 ATGATGGGTCAAATGTAAGCAAAGACAAAGTTAGAAATTTAATATCAAGGATGGAATAAAATTAT
1 ATGATGGGTCAAATGTAAGCAAAGACAAAGTTAGAAATTTAATATCAAGGATGGAATAAAATTAT
343691 AAAT
66 AAAT
343695 AT
1 AT
343697 TTGAGAGACT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (69 bp):
ATGATGGGTCAAATGTAAGCAAAGACAAAGTTAGAAATTTAATATCAAGGATGGAATAAAATTAT
AAAT
Found at i:345758 original size:2 final size:2
Alignment explanation
Indices: 345747--345788 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
345737 ATATGCTCTC
*
345747 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
345788 A
1 A
345789 CACATTTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345996 original size:2 final size:2
Alignment explanation
Indices: 345989--346017 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
345979 GCTACATAAT
345989 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 T
346018 TACAATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:348045 original size:2 final size:2
Alignment explanation
Indices: 348040--348064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
348030 TAAAAAAGTA
348040 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 A
348065 AATTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:349874 original size:18 final size:18
Alignment explanation
Indices: 349851--349888 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
349841 AAAAATGAAA
349851 ATTTGTTTGCTTAGTCTC
1 ATTTGTTTGCTTAGTCTC
349869 ATTTGTTTGCTTAGTCTC
1 ATTTGTTTGCTTAGTCTC
349887 AT
1 AT
349889 CTAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.55
Consensus pattern (18 bp):
ATTTGTTTGCTTAGTCTC
Found at i:350672 original size:2 final size:2
Alignment explanation
Indices: 350660--350692 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
350650 TTTTGGGATT
*
350660 TA TA CA 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 T
350693 TTGAAGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:351518 original size:3 final size:3
Alignment explanation
Indices: 351510--351549 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
351500 ACTATATTTA
351510 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
351550 TAGACAAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:351519 original size:20 final size:21
Alignment explanation
Indices: 351474--351538 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
351464 AGTAATATAT
*
351474 ATAATTACTAAATATTAAATA
1 ATAATAACTAAATATTAAATA
*
351495 A-AATAACTATAT-TTAAATA
1 ATAATAACTAAATATTAAATA
*
351514 ATAATAA-T-AATAAT-AATA
1 ATAATAACTAAATATTAAATA
351532 ATAATAA
1 ATAATAA
351539 TAATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 13 0.34
19 10 0.26
20 14 0.37
21 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATAACTAAATATTAAATA
Found at i:353673 original size:19 final size:19
Alignment explanation
Indices: 353649--353686 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
353639 CCATTTAGTG
353649 AAGTAT-TATAACATGATTT
1 AAGTATGTATAA-ATGATTT
*
353668 AAGTATGTCTAAATGATTT
1 AAGTATGTATAAATGATTT
353687 CAATATCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (19 bp):
AAGTATGTATAAATGATTT
Found at i:357855 original size:35 final size:35
Alignment explanation
Indices: 357828--357993 Score: 181
Period size: 35 Copynumber: 4.6 Consensus size: 35
357818 CATGGCAAAG
*
357828 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
357863 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
357898 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * *
357938 TAAGAAATGTAGGTATGGCAT-TTCCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
357973 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
357994 TTCAATGAGG
Statistics
Matches: 114, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
34 1 0.01
35 80 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:357947 original size:75 final size:75
Alignment explanation
Indices: 357828--357998 Score: 230
Period size: 75 Copynumber: 2.4 Consensus size: 75
357818 CATGGCAAAG
** *
357828 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
357887 CCATACTGAGC
65 CCATACTGAGC
357898 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
357963 CATACTGAGT
66 CATACTGAGC
**
357973 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
357999 TGAGGAAAAC
Statistics
Matches: 89, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.04
74 5 0.06
75 62 0.70
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACTGAGC
Found at i:361702 original size:20 final size:20
Alignment explanation
Indices: 361677--361721 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
361667 TTGGTTGCAT
361677 GAAAA-AGTGAAAGGTTGAAAA
1 GAAAAGAGTGAAA-G-TGAAAA
361698 GAAAAGAGTGAAAGTGAAAA
1 GAAAAGAGTGAAAGTGAAAA
361718 GAAA
1 GAAA
361722 TAAATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.43
21 6 0.26
22 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (20 bp):
GAAAAGAGTGAAAGTGAAAA
Found at i:365594 original size:15 final size:15
Alignment explanation
Indices: 365550--365598 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
365540 CAGTGGCGGC
* *
365550 GGTGATGATGATAGT
1 GGTGATAATGATGGT
*
365565 GATGATAATGATGGT
1 GGTGATAATGATGGT
*
365580 GGTGATAATGGTGGT
1 GGTGATAATGATGGT
365595 GGTG
1 GGTG
365599 GTGATGGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (15 bp):
GGTGATAATGATGGT
Found at i:375011 original size:2 final size:2
Alignment explanation
Indices: 375004--375035 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
374994 CTGATCAGGT
*
375004 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
375036 GTTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:379692 original size:39 final size:39
Alignment explanation
Indices: 379635--379878 Score: 375
Period size: 39 Copynumber: 6.3 Consensus size: 39
379625 CAGGACTTTA
*
379635 AGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
379674 AGCCCGGATGTAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
379713 AGCCC-GATATAGCACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* * **
379751 AGCCCGGATATAATACCAGCACGTATGCCTTTAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* * *
379790 AGCCCGGATATAATACCAGCACGAATGTCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
379829 AGCCCGGATATAACACCAGCATGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
379868 A-CCCGGATATA
1 AGCCCGGATATA
379879 TTTCCACCAT
Statistics
Matches: 188, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
38 46 0.24
39 142 0.76
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:379771 original size:116 final size:117
Alignment explanation
Indices: 379635--379878 Score: 393
Period size: 116 Copynumber: 2.1 Consensus size: 117
379625 CAGGACTTTA
* *
379635 AGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGATGTAACACCAGCACGAAT
1 AGCCCGGATATAATACCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACACCAGCACGAAT
* *
379700 GCCTTCGGGACTTAGCCC-GATATAGCACCAGCACGAATGCCTTCGGGACTT
66 GCCTTCAGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* * *
379751 AGCCCGGATATAATACCAGCACGTATGCCTTTAGGACTTAGCCCGGATATAATACCAGCACGAAT
1 AGCCCGGATATAATACCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACACCAGCACGAAT
* *
379816 GTCTTCAGGACTTAGCCCGGATATAACACCAGCATGAATGCCTTCGGGACTT
66 GCCTTCAGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
379868 A-CCCGGATATA
1 AGCCCGGATATA
379879 TTTCCACCAT
Statistics
Matches: 118, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 86 0.73
117 32 0.27
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (117 bp):
AGCCCGGATATAATACCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACACCAGCACGAAT
GCCTTCAGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:379916 original size:39 final size:39
Alignment explanation
Indices: 379870--379962 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
379860 CGGGACTTAC
379870 CCGGATATATTTCCACCATAAAGCCTGCGGACTTCAAGT
1 CCGGATATATTTCCACCATAAAGCCTGCGGACTTCAAGT
*
379909 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
1 CCGGATATATTTCCACCATAAAGCCTGCGGACTTCAAGT
*
379948 CCGGATATTTTTCCA
1 CCGGATATATTTCCA
379963 ATACCATGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (39 bp):
CCGGATATATTTCCACCATAAAGCCTGCGGACTTCAAGT
Found at i:379917 original size:155 final size:157
Alignment explanation
Indices: 379626--379926 Score: 414
Period size: 155 Copynumber: 1.9 Consensus size: 157
379616 CAAAGCATGC
* *
379626 AGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGATGTAACACC
1 AGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACACC
* * *
379691 AGCACGAATGCCTTCGGGACTTAGCCCGATATAGCACCAGCACGAATGCCTTCGGGACTTAGCCC
66 AGCACGAATGCCTTCGGGACTTAGCCCGATATAGCACCACCACGAAAGCCTGCGGGACTTAGCCC
379756 GGATATAATACCAGCACGTATGCCTTT
131 GGATATAATACCAGCACGTATGCCTTT
*
379783 AGGAC-TT-AGCCCGGATATAATACCAGCACGAATGTCTTCAGGACTTAGCCCGGATATAACACC
1 AGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACACC
* *** *
379846 AGCATGAATGCCTTCGGGACTTA-CCCGGATATATTTCCACCA-TAAAGCCTGC-GGACTTCAAG
66 AGCACGAATGCCTTCGGGACTTAGCCC-GATATAGCACCACCACGAAAGCCTGCGGGACTT--AG
* * *
379908 TCCGGATATATTTCCAGCA
128 CCCGGATATAATACCAGCA
379927 TAAAGCCTGC
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
153 6 0.05
154 10 0.08
155 104 0.82
156 2 0.02
157 5 0.04
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (157 bp):
AGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCAGGACTTAGCCCGGATATAACACC
AGCACGAATGCCTTCGGGACTTAGCCCGATATAGCACCACCACGAAAGCCTGCGGGACTTAGCCC
GGATATAATACCAGCACGTATGCCTTT
Found at i:379952 original size:155 final size:155
Alignment explanation
Indices: 379609--379955 Score: 393
Period size: 155 Copynumber: 2.2 Consensus size: 155
379599 AAATCAAATC
* * *
379609 ACCACCAC-AAAGCATGCAGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACT
1 ACCAGCACTAAAGCCTGC-GGAC-TTAAGCCCGGATATAATACCAGCACGAATGCCTTCAGGACT
* * *
379673 TAGCCCGGATGTAACACCAGCACGAATGCCTTCGGGACTTAGCCCGATATAGCACCAGCACGAAT
64 TAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGATATAGCACCACCACGAAA
*
379738 GCCTTCGGGACTTAGCCCGGATATAAT
129 GCCTGCGGGACTTAGCCCGGATATAAT
* ** *
379765 ACCAGCACGT-ATGCCTTTAGGACTT-AGCCCGGATATAATACCAGCACGAATGTCTTCAGGACT
1 ACCAGCAC-TAAAGCC-TGCGGACTTAAGCCCGGATATAATACCAGCACGAATGCCTTCAGGACT
* *** *
379828 TAGCCCGGATATAACACCAGCATGAATGCCTTCGGGACTTA-CCCGGATATATTTCCACCA-TAA
64 TAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCC-GATATAGCACCACCACGAA
* *
379891 AGCCTGC-GGACTTCAAGTCCGGATATATT
128 AGCCTGCGGGACTT--AGCCCGGATATAAT
* *
379920 TCCAGCA-TAAAGCCTGCGGACTTCAAGTCCGGATAT
1 ACCAGCACTAAAGCCTGCGGACTT-AAGCCCGGATAT
379956 TTTTCCAATA
Statistics
Matches: 159, Mismatches: 23, Indels: 19
0.79 0.11 0.09
Matches are distributed among these distances:
153 14 0.09
154 14 0.09
155 114 0.72
156 9 0.06
157 7 0.04
158 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (155 bp):
ACCAGCACTAAAGCCTGCGGACTTAAGCCCGGATATAATACCAGCACGAATGCCTTCAGGACTTA
GCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGATATAGCACCACCACGAAAGC
CTGCGGGACTTAGCCCGGATATAAT
Found at i:382117 original size:31 final size:28
Alignment explanation
Indices: 382041--382119 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 28
382031 AAATTAGATC
*
382041 AAATCAAAATTTCATGTATAAAATTCATA
1 AAATCAAAA-TTCATATATAAAATTCATA
* * *
382070 AAATCAAACTTTATATATAAAATTGCACATC
1 AAATCAAAATTCATATATAAAATT---CATA
*
382101 GAATCAAAATTCATATATA
1 AAATCAAAATTCATATATA
382120 GTTTTGAGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 13 0.32
29 8 0.20
31 19 0.47
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.33
Consensus pattern (28 bp):
AAATCAAAATTCATATATAAAATTCATA
Found at i:391452 original size:18 final size:18
Alignment explanation
Indices: 391429--391464 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
391419 TTTTTTTCTC
391429 TTTATTGGTGCTAACAAT
1 TTTATTGGTGCTAACAAT
*
391447 TTTATTGGTGCTACCAAT
1 TTTATTGGTGCTAACAAT
391465 AAATTTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (18 bp):
TTTATTGGTGCTAACAAT
Found at i:394714 original size:2 final size:2
Alignment explanation
Indices: 394707--394746 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
394697 GTCCTTGTGA
394707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
394747 GAACCTTGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:395193 original size:23 final size:22
Alignment explanation
Indices: 395167--395212 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
395157 AGAAATTGTG
*
395167 ATATGAATGAAAGATAATTAAAA
1 ATATGAAT-AAAAATAATTAAAA
* *
395190 ATATTAATAAAAATAATTTAAA
1 ATATGAATAAAAATAATTAAAA
395212 A
1 A
395213 CTGAAAATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
ATATGAATAAAAATAATTAAAA
Found at i:397962 original size:21 final size:23
Alignment explanation
Indices: 397929--397971 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
397919 GCAAAAAATA
*
397929 AAAATTGA-TTTTTCTTTTATTT
1 AAAATTGATTTTTTATTTTATTT
397951 AAAATT-ATTTTTTATTTTATT
1 AAAATTGATTTTTTATTTTATT
397972 AATTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
AAAATTGATTTTTTATTTTATTT
Done.