Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015005.1 Kokia drynarioides strain JFW-HI SEQ_130049, 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: 495468
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 326 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:677 original size:29 final size:27
Alignment explanation
Indices: 602--885 Score: 177
Period size: 29 Copynumber: 9.8 Consensus size: 27
592 AGACACTTTG
602 GGGGTAAAATGGTAATTTTTGGAAAATTC
1 GGGGTAAAATGGTAATTTTTGG--AATTC
*
631 GAGGTCAAAAAT-GT-ATTTTTGGATATTC
1 GGGGT--AAAATGGTAATTTTTGGA-ATTC
*
659 AGGGGTAAAATGGTAATTTTTAGAAGTTTC
1 -GGGGTAAAATGGTAATTTTTGGAA--TTC
** *
689 GAAGTCAAAATTGG-AATTTTTGGACATCTA
1 GGGGT-AAAA-TGGTAATTTTTGGA-AT-TC
* *
719 GGGGTAAAATGGTAATTTTTGAAGGATTT
1 GGGGTAAAATGGTAATTTTTG--GAATTC
748 GGGGTCAAAAATGG-AATTTTTGGACATTC
1 GGGGT--AAAATGGTAATTTTTGGA-ATTC
*
777 GAGGGTAAAATGGTAATTTTTAGAAGTTTC
1 G-GGGTAAAATGGTAATTTTTGGAA--TTC
*
807 GAGGTTAAAACTGG-AATTTTTGGATATTC
1 G-GGGTAAAA-TGGTAATTTTTGGA-ATTC
*
836 GAGGGTAAAATGGTAA-TTTTAGAAGTTTC
1 G-GGGTAAAATGGTAATTTTTGGAA--TTC
*
865 GAGGTCAAAAT-GTAATTTTTG
1 GGGGT-AAAATGGTAATTTTTG
886 AAGACTTCAA
Statistics
Matches: 206, Mismatches: 20, Indels: 58
0.73 0.07 0.20
Matches are distributed among these distances:
27 7 0.03
28 35 0.17
29 86 0.42
30 57 0.28
31 21 0.10
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (27 bp):
GGGGTAAAATGGTAATTTTTGGAATTC
Found at i:737 original size:59 final size:58
Alignment explanation
Indices: 602--885 Score: 353
Period size: 59 Copynumber: 4.9 Consensus size: 58
592 AGACACTTTG
* ** * *
602 GGGGTAAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAAT-GTATTTTTGGATATTCA
1 GGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGACATT-A
* *
660 GGGGTAAAATGGTAATTTTTAGAAGTTTCGAAGTCAAAATTGGAATTTTTGGACATCTA
1 GGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGACAT-TA
* *
719 GGGGTAAAATGGTAATTTTT-GAAGGATTT-GGGGTCAAAAATGGAATTTTTGGACATTC
1 GGGGTAAAATGGTAATTTTTAGAA-G-TTTCGAGGTCAAAAATGGAATTTTTGGACATTA
* * * *
777 GAGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTTAAAACTGGAATTTTTGGATATTC
1 G-GGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGACATTA
*
836 GAGGGTAAAATGGTAA-TTTTAGAAGTTTCGAGGTC-AAAATGTAATTTTTG
1 G-GGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGAATTTTTG
886 AAGACTTCAA
Statistics
Matches: 201, Mismatches: 18, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
57 13 0.06
58 62 0.31
59 119 0.59
60 7 0.03
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGACATTA
Found at i:898 original size:29 final size:28
Alignment explanation
Indices: 783--913 Score: 75
Period size: 29 Copynumber: 4.5 Consensus size: 28
773 ATTCGAGGGT
* * *
783 AAAATGGTAATTTTTAGAAGTTTCGAGGTT
1 AAAAT-GTAATTTTT-GAAGCTTCAAGGTC
* * ** *
813 AAAACTGGAATTTTTGGATATTCGAGGGT-
1 AAAA-TGTAATTTTTGAAGCTTC-AAGGTC
* * *
842 AAAATGGTAATTTTAGAAGTTTCGAGGTC
1 AAAAT-GTAATTTTTGAAGCTTCAAGGTC
871 AAAATGTAATTTTTGAAGACTTCAAGGTC
1 AAAATGTAATTTTTGAAG-CTTCAAGGTC
* * *
900 GAAATATGATTTTT
1 AAAATGTAATTTTT
914 TGACAGTTTA
Statistics
Matches: 77, Mismatches: 19, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
28 16 0.21
29 45 0.58
30 15 0.19
31 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTTGAAGCTTCAAGGTC
Found at i:2250 original size:18 final size:17
Alignment explanation
Indices: 2184--2262 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
2174 CAATTCTTTT
2184 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
* *
2201 AATTTAAAGTAAATTTA
1 AATTTAAAATAAATTCA
* * * *
2218 AACTCAAAATGAATTTA
1 AATTTAAAATAAATTCA
2235 AATTTAAAAATAAATTCA
1 AATTT-AAAATAAATTCA
2253 AATTTTAAAA
1 AA-TTTAAAA
2263 ATTAAAAGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 31 0.62
18 16 0.32
19 3 0.06
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:2753 original size:39 final size:39
Alignment explanation
Indices: 2710--2968 Score: 170
Period size: 39 Copynumber: 6.6 Consensus size: 39
2700 GATGTTGATA
* *
2710 TGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA-ATC
1 TGCCCCAGGCTCGGGGTAAAAGATCGG-TGGATGCAGATC
* * * * *
2749 TGCCCCAGGCTCAGGGTAAGAGATTGGTTGAT-AATGATC
1 TGCCCCAGGCTCGGGGTAAAAGATCGGTGGATGCA-GATC
* ** *
2788 TGCCCCAGGCTCGAGGTAAAAGATCAAATGGTTGCA-ATC
1 TGCCCCAGGCTCGGGGTAAAAGATC-GGTGGATGCAGATC
* * * * * *
2827 TACCCCAGGCTCAGGGTAAGAGATTGGTTGAT-AATGATC
1 TGCCCCAGGCTCGGGGTAAAAGATCGGTGGATGCA-GATC
* ** * *
2866 TGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTACA-ATC
1 TGCCCCAGGCTCGGGGTAAAAGATC-GGTGGATGCAGATC
* * * * *
2905 TACCCCAGGCTTGGGGTAAGAGATTGGTCGATG-ATGATC
1 TGCCCCAGGCTCGGGGTAAAAGATCGGTGGATGCA-GATC
*
2944 TGCCCCAAGCTCGGGGTAAAAGATC
1 TGCCCCAGGCTCGGGGTAAAAGATC
2969 AGAATCTTCA
Statistics
Matches: 159, Mismatches: 51, Indels: 20
0.69 0.22 0.09
Matches are distributed among these distances:
37 3 0.02
38 9 0.06
39 139 0.87
40 6 0.04
41 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (39 bp):
TGCCCCAGGCTCGGGGTAAAAGATCGGTGGATGCAGATC
Found at i:2792 original size:78 final size:78
Alignment explanation
Indices: 2663--2969 Score: 452
Period size: 78 Copynumber: 3.9 Consensus size: 78
2653 TTTTGGATAA
* * * * ** *
2663 CTGCAATCTGCCCCAGGCTCAGGGTAGGAGACTAGTTGATGTTGATATGCCCCAAGCTCGGGGTA
1 CTGCAATCTACCCCAGGCTCAGGGTAAGAGATTGGTTGATAATGATCTGCCCCAAGCTCGGGGTA
**
2728 AAAGATCGGATGG
66 AAAGATCAAATGG
* * *
2741 CTGCAATCTGCCCCAGGCTCAGGGTAAGAGATTGGTTGATAATGATCTGCCCCAGGCTCGAGGTA
1 CTGCAATCTACCCCAGGCTCAGGGTAAGAGATTGGTTGATAATGATCTGCCCCAAGCTCGGGGTA
2806 AAAGATCAAATGG
66 AAAGATCAAATGG
*
2819 TTGCAATCTACCCCAGGCTCAGGGTAAGAGATTGGTTGATAATGATCTGCCCCAAGCTCGGGGTA
1 CTGCAATCTACCCCAGGCTCAGGGTAAGAGATTGGTTGATAATGATCTGCCCCAAGCTCGGGGTA
2884 AAAGATCAAATGG
66 AAAGATCAAATGG
* ** * *
2897 CTACAATCTACCCCAGGCTTGGGGTAAGAGATTGGTCGATGATGATCTGCCCCAAGCTCGGGGTA
1 CTGCAATCTACCCCAGGCTCAGGGTAAGAGATTGGTTGATAATGATCTGCCCCAAGCTCGGGGTA
2962 AAAGATCA
66 AAAGATCA
2970 GAATCTTCAT
Statistics
Matches: 209, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 209 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (78 bp):
CTGCAATCTACCCCAGGCTCAGGGTAAGAGATTGGTTGATAATGATCTGCCCCAAGCTCGGGGTA
AAAGATCAAATGG
Found at i:3304 original size:49 final size:49
Alignment explanation
Indices: 3215--4220 Score: 578
Period size: 49 Copynumber: 20.6 Consensus size: 49
3205 ATCGGGTTCA
* * * *
3215 CCGTTGCGATCGT-AATCTTTCCCTCCATATCTTC-GTGGTACTGGATTCG
1 CCGTTGCGA-CTTAAATCTTTCCCTTCAT-GCTTCTGAGGTACTGGATTCG
* * * *
3264 CCATTGCGACTTAAATCCTTCCCTTCATGCTTCTGAGGTACAAGG-TTTG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATTCG
* * * * * * *
3313 CCATTGCGACTTAAATTTTTCCCTCCAT-ATCCTTGTGGTACTAGATTCG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTC-TGAGGTACTGGATTCG
* * * * *
3362 CCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTGCAAGG-TTCA
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATTCG
* * * * *
3411 CTGTTGCGACTTAAA-CTATTCCTTTCATG-TCCTCGTGGTACTGGATTTG
1 CCGTTGCGACTTAAATCT-TTCCCTTCATGCTTCT-GAGGTACTGGATTCG
* * * * * *
3460 CCGTTACGGCTTAAATCTTTCTCTTTATGCTTTTGAGATA-TAAGG-TTCG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACT--GGATTCG
* ** * *
3509 TCGTTGCGACTTAAA-CATTTCCCTTTGTGTCTTC-GTGGTACTGGATTCA
1 CCGTTGCGACTTAAATC-TTTCCCTTCATG-CTTCTGAGGTACTGGATTCG
* * ** * * * *
3558 CCGTTACGGCTTAAATCTTTTTCTTCATGTTTCTAAGGTACAAGG-TTTG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATTCG
* * * * * * * *
3607 TCGTTGTGACTTAAACCATTCCCTCCATG-TCCTTGTGGTACTAGATTCG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTC-TGAGGTACTGGATTCG
* * * * *
3656 CCGTTACGACTTAAATTTTTCCCTTCATGCTTCTAAGGTACAAGG-TTCA
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATTCG
* * * * * *
3705 CCGTTGCGACTTAAACCTTTCCCTCCATATCTTC-GTGGCACTAGATTCG
1 CCGTTGCGACTTAAATCTTTCCCTTCAT-GCTTCTGAGGTACTGGATTCG
* * * * *
3754 TCGTTGCGGCTTAAATCTTTCTCTTCATGCTTTTGAGGTACAAGG-TTCG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATTCG
* * * * *
3803 CCGTTGCGACTTAAACCTTTCCCTCCATATCTTC--ATGGTACTAGATTTG
1 CCGTTGCGACTTAAATCTTTCCCTTCAT-GCTTCTGA-GGTACTGGATTCG
* * *
3852 CCGTTGC-AGCTTTAATCTTTCCCTTCATGCTTCTGAGGTACAAGG-TTTG
1 CCGTTGCGA-CTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATTCG
* * * *
3901 CCGTTGCGACTTAAA-CATTTCCCTCCATATCTTC-GTGGTACTAGATTCG
1 CCGTTGCGACTTAAATC-TTTCCCTTCAT-GCTTCTGAGGTACTGGATTCG
* * * * **
3950 TCGTTGTGGCTTAAATCTTTCCCTTCATACTTCTGAGGTACAACG-TTCG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATTCG
* * * * * *
3999 TCATTGCGACTTAAA-CATTTCCCTCCATATCTTC-GTGGTACTAGATTCG
1 CCGTTGCGACTTAAATC-TTTCCCTTCAT-GCTTCTGAGGTACTGGATTCG
* * * *
4048 CCGTTGTGATTTAAATCTTTCCCTTCATGC-TC-GTGGTACTAGATTCG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACTGGATTCG
* * * *
4095 CCATTGCGGCTTAAATTTTTCCCTTCATGCTTCTGAGGTACAAGG-TTCG
1 CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTAC-TGGATTCG
* * * * * * *
4144 CCATTGCGACTTAAACCTTT-CCTTCTAT-ATCCTCGTGGTACTAGATTTG
1 CCGTTGCGACTTAAATCTTTCCCTTC-ATGCTTCT-GAGGTACTGGATTCG
*
4193 CCGTTGCGGCTTAAATCTTTCCCTTCAT
1 CCGTTGCGACTTAAATCTTTCCCTTCAT
4221 TTTCATGGTA
Statistics
Matches: 716, Mismatches: 187, Indels: 108
0.71 0.18 0.11
Matches are distributed among these distances:
47 42 0.06
48 57 0.08
49 568 0.79
50 49 0.07
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (49 bp):
CCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTACTGGATTCG
Found at i:3360 original size:98 final size:98
Alignment explanation
Indices: 3209--4165 Score: 1041
Period size: 98 Copynumber: 9.8 Consensus size: 98
3199 TAAGGTATCG
* * * * *
3209 GGTTCACCGTTGCGATCGTAATC-TTTCCCTCCATATCTTCGTGGTACTGGATTCGCCATTGCGA
1 GGTTCGCCGTTGCGA-CTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGA
*
3273 CTTAAATCCTTCCCTTCATGCTTCTGAGGTACAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * ** * *
3307 GGTTTGCCATTGCGACTTAAATTTTTCCCTCCATATCCTT-GTGGTACTAGATTCGCCGTTGTGG
1 GGTTCGCCGTTGCGACTTAAACATTTCCCTCCATAT-CTTCGTGGTACTAGATTCGCCGTTGCGA
*
3371 CTTAAATCTTTCCCTTCATGCTTCTGAGGTGCAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * * * * * * * *
3405 GGTTCACTGTTGCGACTTAAAC-TATTCCTTTCATGTCCTCGTGGTACTGGATTTGCCGTTACGG
1 GGTTCGCCGTTGCGACTTAAACAT-TTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGA
* * * * *
3469 CTTAAATCTTTCTCTTTATGCTTTTGAGATATAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* *** * * * * *
3503 GGTTCGTCGTTGCGACTTAAACATTTCCCTTTGTGTCTTCGTGGTACTGGATTCACCGTTACGGC
1 GGTTCGCCGTTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGAC
** * *
3568 TTAAATCTTTTTCTTCATGTTTCTAAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * * *
3601 GGTTTGTCGTTGTGACTTAAACCA-TTCCCTCCATGTCCTT-GTGGTACTAGATTCGCCGTTACG
1 GGTTCGCCGTTGCGACTTAAA-CATTTCCCTCCATAT-CTTCGTGGTACTAGATTCGCCGTTGCG
* *
3664 ACTTAAATTTTTCCCTTCATGCTTCTAAGGTACAA
64 ACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * * *
3699 GGTTCACCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGCACTAGATTCGTCGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGAC
* *
3764 TTAAATCTTTCTCTTCATGCTTTTGAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * *
3797 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCATGGTACTAGATTTGCCGTTGC-AG
1 GGTTCGCCGTTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGA-
*
3861 CTTTAATCTTTCCCTTCATGCTTCTGAGGTACAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * *
3895 GGTTTGCCGTTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGTGGC
1 GGTTCGCCGTTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGAC
*
3960 TTAAATCTTTCCCTTCATACTTCTGAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * * *
3993 CGTTCGTCATTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGTGAT
1 GGTTCGCCGTTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGAC
* *
4058 TTAAATCTTTCCCTTCATGC-TC-GTGGTACTA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * ** * * * * * *
4089 GATTCGCCATTGCGGCTTAAATTTTTCCCTTCAT-GCTTCTGAGGTACAAGGTTCGCCATTGCGA
1 GGTTCGCCGTTGCGACTTAAACATTTCCCTCCATATCTTC-GTGGTACTAGATTCGCCGTTGCGA
*
4153 CTTAAACCTTTCC
65 CTTAAATCTTTCC
4166 TTCTATATCC
Statistics
Matches: 731, Mismatches: 116, Indels: 26
0.84 0.13 0.03
Matches are distributed among these distances:
95 4 0.01
96 64 0.09
97 13 0.02
98 641 0.88
99 9 0.01
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
GGTTCGCCGTTGCGACTTAAACATTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGAC
TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
Found at i:5270 original size:16 final size:16
Alignment explanation
Indices: 5245--5310 Score: 68
Period size: 15 Copynumber: 4.4 Consensus size: 16
5235 CACCTCGACC
5245 TCTCTTTTTTTATTTT
1 TCTCTTTTTTTATTTT
* *
5261 TCTC-TATTTTCTTTT
1 TCTCTTTTTTTATTTT
5276 TC-C-TTTTTT-TTTT
1 TCTCTTTTTTTATTTT
*
5289 TCTTTTTTTTTATTTT
1 TCTCTTTTTTTATTTT
*
5305 TTTCTT
1 TCTCTT
5311 CATTGCATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
13 6 0.15
14 6 0.15
15 17 0.41
16 12 0.29
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (16 bp):
TCTCTTTTTTTATTTT
Found at i:5275 original size:15 final size:14
Alignment explanation
Indices: 5251--5299 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 14
5241 GACCTCTCTT
5251 TTTTTATTTTTCTC
1 TTTTTATTTTTCTC
*
5265 TATTTTCTTTTTC-C
1 T-TTTTATTTTTCTC
5279 TTTTT-TTTTT-TC
1 TTTTTATTTTTCTC
5291 TTTTT-TTTT
1 TTTTTATTTT
5300 ATTTTTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 15 0.47
13 4 0.12
14 3 0.09
15 10 0.31
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTTTTCTC
Found at i:6349 original size:33 final size:33
Alignment explanation
Indices: 6307--6375 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
6297 TCGTATCCTT
6307 GATATCAAGGGACCCAGCATAAAGACAAAAGGG
1 GATATCAAGGGACCCAGCATAAAGACAAAAGGG
6340 GATATCAAGGGACCCAGCATAAAGACAAAAGGG
1 GATATCAAGGGACCCAGCATAAAGACAAAAGGG
6373 GAT
1 GAT
6376 CCAAAGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.28, T:0.10
Consensus pattern (33 bp):
GATATCAAGGGACCCAGCATAAAGACAAAAGGG
Found at i:9964 original size:97 final size:97
Alignment explanation
Indices: 9789--9964 Score: 266
Period size: 97 Copynumber: 1.8 Consensus size: 97
9779 AACGTTCGAA
* * *
9789 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGTCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTCCA
* *
9854 GAATCAGAGATAAAGAAACATTACCTTGATTT
66 AAATCAGAAATAAAGAAACATTACCTTGATTT
*
9886 AAGGGTATTCGATTAT-TCTGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTCC
1 AAGGATATTCGATTATCTC-GATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTCC
9950 AAAACTC-GAAATAAA
65 AAAA-TCAGAAATAAA
9965 AGAATATTGC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
96 2 0.03
97 67 0.94
98 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTCCA
AAATCAGAAATAAAGAAACATTACCTTGATTT
Found at i:10009 original size:97 final size:97
Alignment explanation
Indices: 9809--10005 Score: 213
Period size: 97 Copynumber: 2.0 Consensus size: 97
9799 GATTATCTCG
* * * * *
9809 ATTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGTCACAAATTTTCAGAATCAGAGATAAAGAAACA
1 ATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTCCAAAATCAGAAATAAAGAAACA
* * * *** *
9874 TTACCTTGATTTAAGGGTATTCGATTATTCTG
66 TTACCTCGATTTAAAGGTATTCGATGAAAATA
9906 ATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTCCAAAACTC-GAAATAAA-AGAA
1 ATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTCCAAAA-TCAGAAATAAAGA-AA
* *
9969 TATTGCCTCGATTTTAAAGGT-TTC-ATGAAAATA
64 CATTACCTCGA-TTTAAAGGTATTCGATGAAAATA
10002 ATTT
1 ATTT
10006 TGAAAACAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
96 9 0.11
97 64 0.77
98 10 0.12
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (97 bp):
ATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTCCAAAATCAGAAATAAAGAAACA
TTACCTCGATTTAAAGGTATTCGATGAAAATA
Found at i:16623 original size:9 final size:9
Alignment explanation
Indices: 16609--16633 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16599 TGCCATGACT
16609 GCGGCGAAG
1 GCGGCGAAG
16618 GCGGCGAAG
1 GCGGCGAAG
16627 GCGGCGA
1 GCGGCGA
16634 GGGAGGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.24, G:0.56, T:0.00
Consensus pattern (9 bp):
GCGGCGAAG
Found at i:18126 original size:2 final size:2
Alignment explanation
Indices: 18119--18145 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18109 AGGGGGTTAA
18119 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
18146 CGCTTTTCTT
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:21680 original size:96 final size:96
Alignment explanation
Indices: 21496--21687 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
21486 TTTTTGCGAA
* ** *
21496 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAAGCGCAATATTTCA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAATATTTCA
*
21561 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAGAAAACATTGCCTCGATT
* * * *
21592 AAGGGTATTCAATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAATA-TTTC
*
21656 -GAAACTCGAA-ATAA-AATAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAGAA-AACATTGCCTCGATT
21688 TTAAAACTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 3 0.04
96 74 0.90
97 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAATATTTCA
GAATCGAAGATAAGAAAACATTGCCTCGATT
Found at i:22060 original size:30 final size:30
Alignment explanation
Indices: 21945--22383 Score: 344
Period size: 30 Copynumber: 14.9 Consensus size: 30
21935 ATTTGGGGTT
*
21945 TAAAAATGGAATTTTTAG-A-TATTCG-GGG
1 TAAAAATGGAATTTTTGGAAGT-TTCGAGGG
* * * *
21973 GAAAAAGGGAAATATT-GAGAGTTTCGA-GG
1 TAAAAATGGAATTTTTGGA-AGTTTCGAGGG
*
22002 TCGAAAATGGAGA-TTTTGGAAG-TTCGAGGG
1 T-AAAAATGGA-ATTTTTGGAAGTTTCGAGGG
*
22032 CAAAAATGGAATTTTTGGAAGTTTCGA-GG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGG
*
22061 TAAAAAATGGAATTTTTTGGAAGTTTAG-GGG
1 T-AAAAATGGAA-TTTTTGGAAGTTTCGAGGG
* * *
22092 TAAAAATAGAATTTTTGAAAGTTT-TAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGG
* * *
22121 TTAAGATGTGATTTTTTGGAAG-TTCGAGGG
1 TAAAAATG-GAATTTTTGGAAGTTTCGAGGG
* *
22151 TAAAAATGGAATTTTTGAAAGTTTC-AAGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGG
* * *
22180 TCAAAAATAGG-ATTTCTAGAAG-TTCGGGGG
1 T-AAAAAT-GGAATTTTTGGAAGTTTCGAGGG
** *
22210 TAAAAATGGAATTTTTAAAAGTTT-TAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGG
*
22239 TTAAAAATAGG-ATTTTTGGAAG-CTCGAGGG
1 -TAAAAAT-GGAATTTTTGGAAGTTTCGAGGG
* *
22269 TAAAAATGGAATTTTTGGAAGTTTTGAGGT
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGG
*
22299 TAAAAATGGGATTTTTGGAAGTTTCG-GGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGG
*
22328 TTAAAAATGGGA-TTTTGGAATGTTT-G-GTGG
1 -TAAAAATGGAATTTTTGGAA-GTTTCGAG-GG
* *
22358 AAAAAATGGAATTTTTGAAAGTTTCG
1 TAAAAATGGAATTTTTGGAAGTTTCG
22384 GGAACTCTAG
Statistics
Matches: 331, Mismatches: 48, Indels: 62
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.00
28 17 0.05
29 133 0.40
30 156 0.47
31 24 0.07
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
TAAAAATGGAATTTTTGGAAGTTTCGAGGG
Found at i:22108 original size:89 final size:89
Alignment explanation
Indices: 22015--22380 Score: 338
Period size: 89 Copynumber: 4.1 Consensus size: 89
22005 AAAATGGAGA
* *
22015 TTTTGGAAGTTCGAGGGCAAAAATGGAATTTTTGGAAGTTTCGA-GGTAAAAAATGGAATTTTTT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAATGGAA-TTTTT
22079 GGAAGTTTAGGGGTAAAAATAGAAT
65 GGAAGTTTAGGGGTAAAAATAGAAT
* ** * * *
22104 TTTTGAAAGTTTTAGGGTTAAGATGTGATTTTTTGGAAG-TTCGAGGG-TAAAAATGGAATTTTT
1 TTTTGGAAGTTCGAGGGTAAAAATG-GAATTTTTGGAAGTTTCGAGGGTTAAAAATGGAATTTTT
* * *
22167 GAAAGTTTCA-AGGTCAAAAATAGGAT
65 GGAAGTTT-AGGGGT-AAAAATAGAAT
* * * ** *
22193 TTCTAGAAGTTCGGGGGTAAAAATGGAATTTTTAAAAGTTT-TAGGGTTAAAAATAGG-ATTTTT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAAT-GGAATTTTT
* * *
22256 GGAAG-CTCGAGGGTAAAAATGGAAT
65 GGAAGTTTAG-GGGTAAAAATAGAAT
* * * *
22281 TTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTCG-GGGTTAAAAATGGGA-TTTT
1 TTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAATGGAATTTTT
* *
22344 GGAATGTTT-GGTGGAAAAAATGGAAT
65 GGAA-GTTTAGG-GGTAAAAATAGAAT
*
22370 TTTTGAAAGTT
1 TTTTGGAAGTT
22381 TCGGGAACTC
Statistics
Matches: 221, Mismatches: 41, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
88 59 0.27
89 145 0.66
90 17 0.08
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (89 bp):
TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTTAAAAATGGAATTTTTG
GAAGTTTAGGGGTAAAAATAGAAT
Found at i:22363 original size:59 final size:58
Alignment explanation
Indices: 21944--22385 Score: 344
Period size: 59 Copynumber: 7.5 Consensus size: 58
21934 AATTTGGGGT
* * * * * *
21944 TTAAAAATGGAATTTTTAGATA-TTCGGGGGAAAAAGGGAAATATT-GAGAGTTTCGAGG
1 TTAAAAATGGGATTTTTGGA-AGTTCGGGGTAAAAATGG-AATTTTGGAAAGTTTCGAGG
** *
22002 TCGAAAATGGAGA-TTTTGGAAGTTCGAGGGCAAAAATGGAATTTTTGG-AAGTTTCGAGG
1 TTAAAAATGG-GATTTTTGGAAGTTCG-GGGTAAAAATGGAA-TTTTGGAAAGTTTCGAGG
* * * * * *
22061 TAAAAAATGGAATTTTTTGGAAGTTTAGGGGTAAAAATAGAATTTTTGAAAGTTT-TAGGG
1 TTAAAAATGGGA-TTTTTGGAAG-TTCGGGGTAAAAATGGAATTTTGGAAAGTTTCGA-GG
* * * *
22121 TT-AAGATGTGATTTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGTTTCAAGG
1 TTAAAAATGGGA-TTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTGGAAAGTTTCGAGG
* * * * ** *
22180 TCAAAAATAGGATTTCTAGAAGTTCGGGGGTAAAAATGGAATTTTTAAAAGTTT-TAGGG
1 TTAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAAATGGAATTTTGGAAAGTTTCGA-GG
* * *
22239 TTAAAAATAGGATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTGG-AAGTTTTGAGG
1 TTAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAAATGGAA-TTTTGGAAAGTTTCGAGG
* * * *
22298 TTAAAAATGGGATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTTTGGAATGTTTGGTGG
1 TTAAAAATGGGATTTTTGGAAG-TTCGGGG-TAAAAATGGAATTTTGGAAAGTTTCGAGG
* * *
22358 -AAAAAATGGAATTTTTGAAAGTTTCGGG
1 TTAAAAATGGGATTTTTGGAAG-TTCGGG
22386 AACTCTAGGG
Statistics
Matches: 316, Mismatches: 47, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
57 1 0.00
58 26 0.08
59 221 0.70
60 65 0.21
61 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (58 bp):
TTAAAAATGGGATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTGGAAAGTTTCGAGG
Found at i:24664 original size:195 final size:196
Alignment explanation
Indices: 24238--24683 Score: 716
Period size: 196 Copynumber: 2.3 Consensus size: 196
24228 TCGCTTTGAG
* *
24238 CGTGGGTTTGATTTTGTCTTCTTCTCAGTATCTCA-CAAGGAAGATGACCGCATCGCTTGTTTCA
1 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAA-GAAGATGACCGCATCGATTGTTTCA
* * * *
24302 ATCCACTTCTCTGTATCTTATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAG
65 ATCCACTTCTCTATATCTCATCAAGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGAAG
* *
24367 CTGACCATTTTATTGCTTCGACTTGCTTCTCAGTATCGCATCAAGAAGCTGGAGTTCGAAGATCG
130 CTAACCATTTTATTGCTTCGACTTGCTTCTCAATATCGCATCAAGAAGCTGGAGTTCGAAGATCG
24432 AA
195 AA
*
24434 CGTGGGTTTCATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCGATTGTTTCAA
1 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCGATTGTTTCAA
* * * *
24499 TTCGCTTCTCTATATCTCATCAGGAAGATGAATTTGATCCACTTCTCAGTATCTCATCAGGAAGC
66 TCCACTTCTCTATATCTCATCAAGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGAAGC
* * *
24564 TAACC-TTTTATTGCTTCGACTTGTTTCTCAATGTCGTATCAAGAAGCTGGAGTTCGAAGATCGA
131 TAACCATTTTATTGCTTCGACTTGCTTCTCAATATCGCATCAAGAAGCTGGAGTTCGAAGATCGA
24628 A
196 A
*
24629 CGTGGGTTTGATTTGGTCTTTTTCTCAGTATCTCATCAAGAAGATGACCGCATCG
1 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCG
24684 CTGTTTGTGG
Statistics
Matches: 231, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
195 109 0.47
196 119 0.52
197 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (196 bp):
CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCGATTGTTTCAA
TCCACTTCTCTATATCTCATCAAGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGAAGC
TAACCATTTTATTGCTTCGACTTGCTTCTCAATATCGCATCAAGAAGCTGGAGTTCGAAGATCGA
A
Found at i:30226 original size:29 final size:27
Alignment explanation
Indices: 30192--30635 Score: 217
Period size: 29 Copynumber: 15.1 Consensus size: 27
30182 TTTTGAGAGT
*
30192 TTCGAGGTCGAAAATGGAGATTTTGGAAG
1 TTCGAGGT-AAAAATGGA-ATTTTGGAAG
30221 TTCGAGGGTAAAAATGGAATTTTTGGAAG
1 TTCGA-GGTAAAAATGGAA-TTTTGGAAG
* *
30250 TTTCGTGGTAAAAATGGCATTTTTGGAAG
1 -TTCGAGGTAAAAATGG-AATTTTGGAAG
* * *
30279 TTCGGGGGTAAAAATAGAATTTTTGAAAG
1 TTC-GAGGTAAAAATGGAA-TTTTGGAAG
** * *
30308 TTTTAGGGTTAAAAATGTGATTTTTTTGAAG
1 TTCGA-GG-TAAAAATG-GA-ATTTTGGAAG
*
30339 TTCGAGGGTAAAAATTGAATTTTTGGAAG
1 TTCGA-GGTAAAAATGGAA-TTTTGGAAG
* *
30368 TTTTGAGGTAAAAAATAGGATTTTTGGAAG
1 -TTCGAGGT-AAAAAT-GGAATTTTGGAAG
* * **
30398 TTCGTGGGTAAAAATGAAATTTTTAAAAG
1 TTCG-AGGTAAAAATGGAA-TTTTGGAAG
* * *
30427 TTTTGGGGTTAAAAATAGGATTTTTTGGAAG
1 -TTCGAGG-TAAAAAT-GGA-ATTTTGGAAG
* **
30458 TTCGAGATTAAAAATAAAATTTTTGGAAG
1 TTCGAG-GTAAAAATGGAA-TTTTGGAAG
* *
30487 TTTCGGGGTTAAAAATGGGATTTTTGGAAG
1 -TTCGAGG-TAAAAAT-GGAATTTTGGAAG
* *
30517 TTTAGGGGTAAAAATGGAATTTTTGGAAG
1 -TTCGAGGTAAAAATGGAA-TTTTGGAAG
*
30546 TT-TAGGGTTAAAAAT-GAGATTTTGAGAAG
1 TTCGA-GG-TAAAAATGGA-ATTTTG-GAAG
* * *
30575 TTCGTGGTTAAAAATGAAATTTTTAGAAG
1 TTCGAGG-TAAAAATGGAA-TTTTGGAAG
* * *
30604 TTTTGGGTGTAAAAATAGAATTTTTGGAAG
1 -TTCGAG-GTAAAAATGGAA-TTTTGGAAG
30634 TT
1 TT
30636 TCGAAACTCC
Statistics
Matches: 323, Mismatches: 57, Indels: 70
0.72 0.13 0.16
Matches are distributed among these distances:
28 21 0.07
29 154 0.48
30 120 0.37
31 28 0.09
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.36
Consensus pattern (27 bp):
TTCGAGGTAAAAATGGAATTTTGGAAG
Found at i:30380 original size:59 final size:58
Alignment explanation
Indices: 30202--30635 Score: 450
Period size: 59 Copynumber: 7.3 Consensus size: 58
30192 TTCGAGGTCG
* * * *
30202 AAAATGGAGATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGTGG-TA
1 AAAATGGA-TTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTGGGGTTA
* * * *
30260 AAAATGGCATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGTTTTAGGGTTA
1 AAAATGG-ATTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTGGGGTTA
* * *
30319 AAAATGTGATTTTTTTGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTGAGGTAA
1 AAAATG-GA-TTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTGGGGTTA
* **
30379 AAAATAGGATTTTTGGAAGTTCGTGGGTAAAAA-TGAAATTTTTAAAAGTTTTGGGGTTA
1 AAAAT-GGATTTTTGGAAGTTCGAGGGTAAAAATTG-AATTTTTGGAAGTTTTGGGGTTA
** ** *
30438 AAAATAGGATTTTTTGGAAGTTCGAGATTAAAAATAAAATTTTTGGAAGTTTCGGGGTTA
1 AAAAT-GGA-TTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTGGGGTTA
* * *
30498 AAAATGGGATTTTTGGAAGTT-TAGGGGTAAAAATGGAATTTTTGGAAG-TTTAGGGTTA
1 AAAAT-GGATTTTTGGAAGTTCGA-GGGTAAAAATTGAATTTTTGGAAGTTTTGGGGTTA
* * *
30556 AAAATGAGA-TTTTGAGAAGTTCGTGGTTAAAAA-TGAAATTTTTAGAAGTTTT-GGGTGTA
1 AAAATG-GATTTTTG-GAAGTTCGAGGGTAAAAATTG-AATTTTTGGAAGTTTTGGGGT-TA
*
30615 AAAATAGAATTTTTGGAAGTT
1 AAAAT-GGATTTTTGGAAGTT
30636 TCGAAACTCC
Statistics
Matches: 317, Mismatches: 42, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
57 7 0.02
58 94 0.30
59 109 0.34
60 106 0.33
61 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (58 bp):
AAAATGGATTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTGGGGTTA
Found at i:30427 original size:119 final size:116
Alignment explanation
Indices: 30202--30635 Score: 504
Period size: 119 Copynumber: 3.7 Consensus size: 116
30192 TTCGAGGTCG
** *
30202 AAAATGGAGATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGTGG-TAAAAAT-
1 AAAATGGATTTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTCG-GGTTAAAAATA
30265 GGCATTTTTGGAAGTTCGGGGGTAAAAAT-AGAATTTTTGAAAGTTTTAGGGTTA
65 GG-ATTTTTGGAAGTTC-GGGGTAAAAATGA-AATTTTTGAAAGTTTTAGGGTTA
* * *
30319 AAAATGTGATTTTTTTGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTTGAGGTAAAAAAT
1 AAAATG-GATTTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTCG-GGTTAAAAAT
* *
30384 AGGATTTTTGGAAGTTCGTGGGTAAAAATGAAATTTTTAAAAGTTTTGGGGTTA
64 AGGATTTTTGGAAGTTCG-GGGTAAAAATGAAATTTTTGAAAGTTTTAGGGTTA
** **
30438 AAAATAGGATTTTTTGGAAGTTCGAGATTAAAAATAAAATTTTTGGAAGTTTCGGGGTTAAAAAT
1 AAAAT-GGATTTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTC-GGGTTAAAAAT
* * * *
30503 GGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAG-TTTAGGGTTA
64 AGGATTTTTGGAAG-TTCGGGGTAAAAATGAAATTTTTGAAAGTTTTAGGGTTA
* * * *
30556 AAAATGAGA--TTTTGAGAAGTTCGTGGTTAAAAA-TGAAATTTTTAGAAGTTTTGGGTGTAAAA
1 AAAATG-GATTTTTTG-GAAGTTCGAGGGTAAAAATTG-AATTTTTGGAAGTTTCGGGT-TAAAA
*
30618 ATAGAATTTTTGGAAGTT
62 ATAGGATTTTTGGAAGTT
30636 TCGAAACTCC
Statistics
Matches: 275, Mismatches: 30, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
116 11 0.04
117 56 0.20
118 61 0.22
119 139 0.51
120 8 0.03
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (116 bp):
AAAATGGATTTTTTGGAAGTTCGAGGGTAAAAATTGAATTTTTGGAAGTTTCGGGTTAAAAATAG
GATTTTTGGAAGTTCGGGGTAAAAATGAAATTTTTGAAAGTTTTAGGGTTA
Found at i:31641 original size:9 final size:9
Alignment explanation
Indices: 31622--31655 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
31612 TTTTTTTATT
31622 TATTAATTAA
1 TATT-ATTAA
31632 TATTATTAA
1 TATTATTAA
*
31641 TATTATTAT
1 TATTATTAA
31650 TATTAT
1 TATTAT
31656 GGATGTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:31711 original size:18 final size:19
Alignment explanation
Indices: 31670--31717 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
31660 GTGGTAATTA
31670 ATAATAATTAATATTATGT
1 ATAATAATTAATATTATGT
*
31689 TTAAT-ATTAATATTAATG-
1 ATAATAATTAATATT-ATGT
*
31707 ATAATCATTAA
1 ATAATAATTAA
31718 CACAGTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
ATAATAATTAATATTATGT
Found at i:32366 original size:15 final size:15
Alignment explanation
Indices: 32346--32378 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
32336 TTTTTTGGTT
32346 CAAATTGGG-TCCGAA
1 CAAATTGGGCTCC-AA
32361 CAAATTGGGCTCCAA
1 CAAATTGGGCTCCAA
32376 CAA
1 CAA
32379 TATTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (15 bp):
CAAATTGGGCTCCAA
Found at i:33697 original size:15 final size:15
Alignment explanation
Indices: 33677--33743 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
33667 ATTTATAACA
*
33677 ATTTTATATTAAAGT
1 ATTTTAGATTAAAGT
*
33692 ATTTTAGGTTAAAGTAT
1 ATTTTAGATTAAAG--T
*
33709 ACAATTTTACATTAAAGT
1 ---ATTTTAGATTAAAGT
*
33727 ATTTTAGGTTAAAGT
1 ATTTTAGATTAAAGT
33742 AT
1 AT
33744 ACAATTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
15 27 0.66
17 1 0.02
18 1 0.02
20 12 0.29
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (15 bp):
ATTTTAGATTAAAGT
Found at i:33717 original size:20 final size:20
Alignment explanation
Indices: 33692--33752 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
33682 ATATTAAAGT
33692 ATTTTAGGTTAAAGTATACA
1 ATTTTAGGTTAAAGTATACA
**
33712 ATTTTACATTAAAG--T---
1 ATTTTAGGTTAAAGTATACA
33727 ATTTTAGGTTAAAGTATACA
1 ATTTTAGGTTAAAGTATACA
33747 ATTTTA
1 ATTTTA
33753 TATTAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 12 0.38
17 1 0.03
18 1 0.03
20 18 0.56
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.44
Consensus pattern (20 bp):
ATTTTAGGTTAAAGTATACA
Found at i:33723 original size:35 final size:35
Alignment explanation
Indices: 33674--33759 Score: 163
Period size: 35 Copynumber: 2.5 Consensus size: 35
33664 AATATTTATA
33674 ACAATTTTATATTAAAGTATTTTAGGTTAAAGTAT
1 ACAATTTTATATTAAAGTATTTTAGGTTAAAGTAT
*
33709 ACAATTTTACATTAAAGTATTTTAGGTTAAAGTAT
1 ACAATTTTATATTAAAGTATTTTAGGTTAAAGTAT
33744 ACAATTTTATATTAAA
1 ACAATTTTATATTAAA
33760 ATTAGTCCAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (35 bp):
ACAATTTTATATTAAAGTATTTTAGGTTAAAGTAT
Found at i:34372 original size:15 final size:15
Alignment explanation
Indices: 34335--34427 Score: 102
Period size: 15 Copynumber: 6.4 Consensus size: 15
34325 TATGGACTGG
34335 TGGAGTACTGGTAAT
1 TGGAGTACTGGTAAT
34350 T-G-G-ACTGGTAAT
1 TGGAGTACTGGTAAT
* *
34362 TGGAGTTCTGGTAAC
1 TGGAGTACTGGTAAT
34377 TGGAGTACTGGTAAT
1 TGGAGTACTGGTAAT
*
34392 TGGAGTTCTGGTAAT
1 TGGAGTACTGGTAAT
*** *
34407 TATTGGACTGGTAAT
1 TGGAGTACTGGTAAT
34422 TGGAGT
1 TGGAGT
34428 TCGAACACGA
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
12 10 0.16
13 2 0.03
14 2 0.03
15 47 0.77
ACGTcount: A:0.24, C:0.08, G:0.33, T:0.35
Consensus pattern (15 bp):
TGGAGTACTGGTAAT
Found at i:34389 original size:30 final size:30
Alignment explanation
Indices: 34351--34429 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
34341 ACTGGTAATT
*
34351 GGACTGGTAATTGGAGTTCTGGTAACTGGA
1 GGACTGGTAATTGGAGTTCTGGTAACTAGA
* * **
34381 GTACTGGTAATTGGAGTTCTGGTAATTATT
1 GGACTGGTAATTGGAGTTCTGGTAACTAGA
34411 GGACTGGTAATTGGAGTTC
1 GGACTGGTAATTGGAGTTC
34430 GAACACGATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.23, C:0.09, G:0.33, T:0.35
Consensus pattern (30 bp):
GGACTGGTAATTGGAGTTCTGGTAACTAGA
Found at i:35595 original size:21 final size:19
Alignment explanation
Indices: 35564--35619 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
35554 CAATTATTTT
35564 TATTATATTATTCTTTAAA
1 TATTATATTATTCTTTAAA
* * *
35583 TATTTTATT-TTATTTTAA
1 TATTATATTATTCTTTAAA
*
35601 TATTATGTTATTCTTTAAA
1 TATTATATTATTCTTTAAA
35620 AAAATTAGGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTATATTATTCTTTAAA
Found at i:43611 original size:59 final size:58
Alignment explanation
Indices: 43514--43879 Score: 486
Period size: 59 Copynumber: 6.2 Consensus size: 58
43504 TTCGGATGCA
* * * * * *
43514 CGAGGGAAAAATGGTAGTTTTGGAAGGTTTGGAGTCAAAAATGAGATTTTTGGAAGTT
1 CGAGGGTAAAATAGTAATTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
*
43572 CGAGGGTAAAATAGTAATTTTCGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGAGGGTAAAATAGTAATTTT-GAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
*
43631 CG-GAGGTAAAATAGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGAG-GGTAAAATAGTAA-TTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
* *
43690 CG-GGTGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGAGG-GTAAAATAGTAATTTTGA-AAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
43749 CGGAGAGTAAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTTGAAGTT
1 C-GAGGGTAAAATAGTAA-TTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
*
43809 CGAGGGTAAAAATGAG-AATTTTGAAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 CGAGGGT-AAAAT-AGTAATTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAG-TT
*
43869 CGAGGTTAAAA
1 CGAGGGTAAAA
43880 ACGAGATTTT
Statistics
Matches: 279, Mismatches: 18, Indels: 21
0.88 0.06 0.07
Matches are distributed among these distances:
58 25 0.09
59 180 0.65
60 67 0.24
61 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
CGAGGGTAAAATAGTAATTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:43818 original size:119 final size:118
Alignment explanation
Indices: 43521--43867 Score: 506
Period size: 119 Copynumber: 2.9 Consensus size: 118
43511 GCACGAGGGA
* * * * *
43521 AAAATGGT-AGTTTTGGAAGGTTTGGAGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATA
1 AAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
* *
43585 GTAA-TTTTCGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGAGGT
66 GTAATTTTTAG-AAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGAGGT
* *
43638 AAAATAGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGTGTAAAAT
1 AAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGG-GTAAAAT
43702 GGTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGAGAGT
65 GGTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGAG-GT
*
43757 AAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTTGAAGTTCGAGGGTAAAAAT
1 AAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT-AAAAT
* *
43822 GAG-AATTTTGA-AAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
65 G-GTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
43868 TCGAGGTTAA
Statistics
Matches: 209, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
117 9 0.04
118 90 0.43
119 94 0.45
120 15 0.07
121 1 0.00
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (118 bp):
AAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
GTAATTTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGAGGT
Found at i:43867 original size:30 final size:29
Alignment explanation
Indices: 43520--43890 Score: 283
Period size: 30 Copynumber: 12.5 Consensus size: 29
43510 TGCACGAGGG
* * * *
43520 AAAAATGGTAGTTTTGGAAGGTTTGGAGTC
1 AAAAATGGGATTTTTGGAA-GTTCGGGGTC
*
43550 AAAAATGAGATTTTTGGAAGTTCGAGGGT-
1 AAAAATGGGATTTTTGGAAGTTCG-GGGTC
** * *
43579 -AAAATAGTAATTTTCGAAAGGTTCGGGGTC
1 AAAAAT-GGGATTTTTGGAA-GTTCGGGGTC
43609 AAAAATGGGATTTTTGGAAGTTCGGAGGT-
1 AAAAATGGGATTTTTGGAAGTTCGG-GGTC
** *
43638 -AAAATAGTAATTTTTGAAAGGTTCGGGGTC
1 AAAAAT-GGGATTTTTGGAA-GTTCGGGGTC
43668 AAAAATGGGATTTTTGGAAGTTCGGGTGT-
1 AAAAATGGGATTTTTGGAAGTTCGGG-GTC
* * *
43697 -AAAATGGTAATTTTTAGAAGGTTTGGGGTC
1 AAAAATGG-GATTTTTGGAA-GTTCGGGGTC
43727 AAAAATGGGATTTTTGGAAGTTCGGAGAGT-
1 AAAAATGGGATTTTTGGAAGTTCGG-G-GTC
* * *
43757 -AAAATGGTAATTTTTGAAAGGTTTGGGGTC
1 AAAAATGG-GATTTTTGGAA-GTTCGGGGTC
*
43787 AAAAATGGGATTTTTTGAAGTTCGAGGGT-
1 AAAAATGGGATTTTTGGAAGTTCG-GGGTC
* * * *
43816 AAAAATGAGAATTTTGAAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGGAAG-TTCGGGGTC
* *
43846 AAAAATGGGATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGGATTTTTGGAAG-TTCGGGGTC
* *
43876 AAAAACGAGATTTTT
1 AAAAATGGGATTTTT
43891 TGACAATCTA
Statistics
Matches: 272, Mismatches: 45, Indels: 48
0.75 0.12 0.13
Matches are distributed among these distances:
28 17 0.06
29 92 0.34
30 132 0.49
31 31 0.11
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTCGGGGTC
Found at i:44967 original size:46 final size:46
Alignment explanation
Indices: 44917--45013 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
44907 TTAATAGCAT
*
44917 TTATTAATATTAATAATTATTATTACTGTCATTAATATTACTAATG
1 TTATTAATAATAATAATTATTATTACTGTCATTAATATTACTAATG
* * * * * * *
44963 TTATTAGTAATATTTATTATTATTATTGTTATTAATATTATTGATG
1 TTATTAATAATAATAATTATTATTACTGTCATTAATATTACTAATG
45009 TTATT
1 TTATT
45014 GTTATTATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (46 bp):
TTATTAATAATAATAATTATTATTACTGTCATTAATATTACTAATG
Found at i:44996 original size:15 final size:15
Alignment explanation
Indices: 44932--45019 Score: 54
Period size: 15 Copynumber: 5.8 Consensus size: 15
44922 AATATTAATA
* *
44932 ATTATTATTACTGTC
1 ATTATTATTATTGTT
*
44947 ATTAATATTACTAATGTT
1 ATTATTATTA-T--TGTT
* *
44965 ATTAGTAATA-T-TT
1 ATTATTATTATTGTT
44978 ATTATTATTATTGTT
1 ATTATTATTATTGTT
* *
44993 ATTAATATTATTGAT
1 ATTATTATTATTGTT
* *
45008 GTTATTGTTATT
1 ATTATTATTATT
45020 ATAACCAAAG
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
13 10 0.18
14 2 0.04
15 33 0.59
18 11 0.20
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (15 bp):
ATTATTATTATTGTT
Found at i:45754 original size:6 final size:6
Alignment explanation
Indices: 45711--45808 Score: 66
Period size: 6 Copynumber: 17.0 Consensus size: 6
45701 TTTTATTTAT
* * *
45711 TTTAAA TTTTAAA TTTGAAA -ATAAT TTTAAA CTT-AA TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
45759 TTTAAA -ATAAA TTTAAA TTTTAAA ---AAA ATTAAT TTTAAA -TTAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
45803 TTTAAA
1 TTTAAA
45809 GGGAGTATGG
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
3 3 0.04
5 15 0.21
6 38 0.54
7 15 0.21
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:45757 original size:11 final size:11
Alignment explanation
Indices: 45705--45808 Score: 52
Period size: 11 Copynumber: 9.1 Consensus size: 11
45695 TTTGAGTTTT
*
45705 ATTTATTTTAA
1 ATTTAATTTAA
45716 ATTTTAAATTTGAA
1 A-TTT-AATTT-AA
*
45730 A-ATAATTTTAA
1 ATTTAA-TTTAA
*
45741 ACTTAATTTAA
1 ATTTAATTTAA
45752 ATTTAAATTTAA
1 ATTT-AATTTAA
* *
45764 AATAAATTTAA
1 ATTTAATTTAA
*
45775 ATTTTAA--AAA
1 A-TTTAATTTAA
*
45785 AATTAATTTTAA
1 ATTTAA-TTTAA
*
45797 ATTAAATTTAA
1 ATTTAATTTAA
45808 A
1 A
45809 GGGAGTATGG
Statistics
Matches: 70, Mismatches: 13, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
9 4 0.06
10 3 0.04
11 28 0.40
12 28 0.40
13 4 0.06
14 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:45758 original size:17 final size:17
Alignment explanation
Indices: 45713--45808 Score: 70
Period size: 17 Copynumber: 5.6 Consensus size: 17
45703 TTATTTATTT
*
45713 TAAATTTTAAATTTGAAAA
1 TAAA-TTTAAACTT-AAAA
* **
45732 TAATTTTAAACTTAATT
1 TAAATTTAAACTTAAAA
*
45749 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
*
45766 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-CTTAAAA
** *
45784 -AAA-TTAATTTTAAAT
1 TAAATTTAAACTTAAAA
45799 TAAATTTAAA
1 TAAATTTAAA
45809 GGGAGTATGG
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
15 6 0.10
16 7 0.11
17 32 0.51
18 15 0.24
19 3 0.05
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:46250 original size:15 final size:16
Alignment explanation
Indices: 46208--46272 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
46198 AATTATTTTG
46208 AAATTTAAAATATATA
1 AAATTTAAAATATATA
* *
46224 AAATCTAAAA-ATAAA
1 AAATTTAAAATATATA
*
46239 AAATTTATAAATTTATAA
1 AAATTTA-AAATATAT-A
46257 AAATATTAGAAATATA
1 AAAT-TTA-AAATATA
46273 ATTTGACACT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 10 0.26
16 12 0.32
17 2 0.05
18 5 0.13
19 9 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATTTAAAATATATA
Found at i:60794 original size:18 final size:20
Alignment explanation
Indices: 60760--60810 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
60750 CAAAAATAAT
60760 TAAAATAATTT-TCAAAA-TTC
1 TAAAAT-ATTTAT-AAAATTTC
60780 -AAAATATTTATAAAATTTC
1 TAAAATATTTATAAAATTTC
*
60799 TAAAATTTTTAT
1 TAAAATATTTAT
60811 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.30
19 9 0.33
20 10 0.37
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAATATTTATAAAATTTC
Found at i:62006 original size:29 final size:30
Alignment explanation
Indices: 61960--62019 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
61950 AATAAACAAC
*
61960 AAAAGAGAAGATGCAGAG-GAGTTGTTGGAG
1 AAAAGAGAAGATGCAGAGAG-GTTGCTGGAG
*
61990 AAAA-AGAAGATGGAGAGAGGTTGCTGGAG
1 AAAAGAGAAGATGCAGAGAGGTTGCTGGAG
62019 A
1 A
62020 GGGGGGCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.42, C:0.03, G:0.40, T:0.15
Consensus pattern (30 bp):
AAAAGAGAAGATGCAGAGAGGTTGCTGGAG
Found at i:71477 original size:19 final size:17
Alignment explanation
Indices: 71450--71488 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
71440 ATTTTGATAA
71450 AAATATAGATCTAAAAAAT
1 AAATATAGA--TAAAAAAT
*
71469 AAATGTAGATAAAAAAT
1 AAATATAGATAAAAAAT
71486 AAA
1 AAA
71489 GTTCATTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.23
Consensus pattern (17 bp):
AAATATAGATAAAAAAT
Found at i:79459 original size:15 final size:15
Alignment explanation
Indices: 79439--79468 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
79429 TTCTCTCTTC
79439 CCCTTTGGCAGTGAT
1 CCCTTTGGCAGTGAT
*
79454 CCCTTTGGTAGTGAT
1 CCCTTTGGCAGTGAT
79469 GTTGGCATCT
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:0.27, T:0.37
Consensus pattern (15 bp):
CCCTTTGGCAGTGAT
Found at i:80430 original size:14 final size:16
Alignment explanation
Indices: 80411--80447 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
80401 AGAGTAGAAG
80411 AAAATTATA-ATAT-T
1 AAAATTATATATATAT
*
80425 AAAATTATATTTATAT
1 AAAATTATATATATAT
80441 AAAATTA
1 AAAATTA
80448 ATTAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTATATATATAT
Found at i:82356 original size:3 final size:3
Alignment explanation
Indices: 82348--82373 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
82338 TTTTGAAGCT
82348 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
82374 TTGAACCGTT
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:88755 original size:19 final size:19
Alignment explanation
Indices: 88731--88768 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
88721 GACCAAAATG
*
88731 ATATTTGATTATTTTGTTA
1 ATATTTGACTATTTTGTTA
88750 ATATTTGACTATTTTGTTA
1 ATATTTGACTATTTTGTTA
88769 TATAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.61
Consensus pattern (19 bp):
ATATTTGACTATTTTGTTA
Found at i:89105 original size:3 final size:3
Alignment explanation
Indices: 89097--89146 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
89087 CCTGATCGAT
89097 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
89145 TA
1 TA
89147 TATTGGTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:98541 original size:18 final size:18
Alignment explanation
Indices: 98511--98545 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
98501 AAAATATTCG
98511 TATAAATATTAAATATAT
1 TATAAATATTAAATATAT
98529 TATAGAATA-TAAATATA
1 TATA-AATATTAAATATA
98546 AAATTTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TATAAATATTAAATATAT
Found at i:101589 original size:6 final size:6
Alignment explanation
Indices: 101580--101607 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
101570 CATTAAAACA
101580 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
101608 CCTGTATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:104926 original size:20 final size:19
Alignment explanation
Indices: 104898--104936 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
104888 TGCTTTTACC
*
104898 TCAATTTTAAATAACTTAAT
1 TCAACTTTAAATAA-TTAAT
*
104918 TCAACTTTAATTAATTAAT
1 TCAACTTTAAATAATTAAT
104937 CAATTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (19 bp):
TCAACTTTAAATAATTAAT
Found at i:106699 original size:22 final size:22
Alignment explanation
Indices: 106661--106703 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
106651 AAAAATTACC
*
106661 AAAAAGATGTGTTAATGACATG
1 AAAAAGATGTGTAAATGACATG
106683 AAAAAGATGCTG-AAATGACAT
1 AAAAAGATG-TGTAAATGACAT
106704 TAAATAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (22 bp):
AAAAAGATGTGTAAATGACATG
Found at i:109467 original size:2 final size:2
Alignment explanation
Indices: 109460--109485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
109450 AATACATTAA
109460 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
109486 TTCTCATTGC
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:110983 original size:31 final size:31
Alignment explanation
Indices: 110923--110998 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
110913 TTTTATAAAA
*
110923 TTTTAAATTAATAA-TAAAATTACACTTTAACT
1 TTTTAAA-AAATAATTAAAATTACACTTTAA-T
110955 TCTTT-AAAAATAATTAAAATTTA-A-TTTAAT
1 T-TTTAAAAAATAATTAAAA-TTACACTTTAAT
110985 TTTTAAAAAATAAT
1 TTTTAAAAAATAAT
110999 AAAGATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
29 3 0.08
30 11 0.28
31 10 0.26
32 9 0.23
33 6 0.15
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTTAAAAAATAATTAAAATTACACTTTAAT
Found at i:124640 original size:20 final size:20
Alignment explanation
Indices: 124615--124654 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
124605 GGTTTTTCAA
*
124615 GTAAAATATTTGTGTTCGTT
1 GTAAAATATTTGTATTCGTT
124635 GTAAAATATTTGTATTCGTT
1 GTAAAATATTTGTATTCGTT
124655 CTTTTTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.50
Consensus pattern (20 bp):
GTAAAATATTTGTATTCGTT
Found at i:130404 original size:52 final size:53
Alignment explanation
Indices: 130319--130424 Score: 160
Period size: 52 Copynumber: 2.0 Consensus size: 53
130309 CTTTTCTTTA
* ** *
130319 ATTTGATTATCCTCACCTATATATACGTCGCTGCTGGGCTACACTTA-TATAT
1 ATTTGATTATCCTCACCTATATATACGTAGCTGCTCCGCTACACCTATTATAT
*
130371 ATTTGATTATCCTCACCTATATATATGTAGCTGCTCCGCTACACCTATTATAT
1 ATTTGATTATCCTCACCTATATATACGTAGCTGCTCCGCTACACCTATTATAT
130424 A
1 A
130425 ATCGATAGGC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 42 0.88
53 6 0.12
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (53 bp):
ATTTGATTATCCTCACCTATATATACGTAGCTGCTCCGCTACACCTATTATAT
Found at i:136671 original size:2 final size:2
Alignment explanation
Indices: 136664--136696 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
136654 AAATTGATAA
136664 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 A
136697 AATTAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:137006 original size:2 final size:2
Alignment explanation
Indices: 137001--137034 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
136991 AAAAACGTTT
*
137001 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
137035 GTCTTTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:137671 original size:29 final size:29
Alignment explanation
Indices: 137630--137697 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
137620 TAATTTTTAA
137630 AAAATTCAGAAAAATATA-A-AAATTACTTTT
1 AAAATT-A-AAAAATATATATAAA-TACTTTT
*
137660 AAGAATTAAAAAATATATATAAATATTTTT
1 AA-AATTAAAAAATATATATAAATACTTTT
137690 AAAATTAA
1 AAAATTAA
137698 TTAAATGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 15 0.44
30 12 0.35
31 7 0.21
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTAAAAAATATATATAAATACTTTT
Found at i:141023 original size:33 final size:33
Alignment explanation
Indices: 140975--141047 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
140965 GAGTAGGTGG
** *
140975 ATTTCGATTTTGAAACAGGGACCACTTCCATAA
1 ATTTCGATTACGAAACAGGGACCAATTCCATAA
*
141008 ATTTCGATTACGAAACAGGGACTAATTCCATAA
1 ATTTCGATTACGAAACAGGGACCAATTCCATAA
141041 ATTTCGA
1 ATTTCGA
141048 CAGTCAAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (33 bp):
ATTTCGATTACGAAACAGGGACCAATTCCATAA
Found at i:141638 original size:15 final size:16
Alignment explanation
Indices: 141620--141657 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
141610 TAAATTAAAA
141620 ATTAAAAAATATA-AT
1 ATTAAAAAATATAGAT
*
141635 ATT-AAATATATAGAT
1 ATTAAAAAATATAGAT
141650 ATTAAAAA
1 ATTAAAAA
141658 TCACTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 8 0.42
15 8 0.42
16 3 0.16
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTAAAAAATATAGAT
Found at i:141763 original size:3 final size:3
Alignment explanation
Indices: 141751--141785 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
141741 ACGTCATATA
141751 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TGAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TA
141786 AAATGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:142064 original size:28 final size:29
Alignment explanation
Indices: 142033--142093 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
142023 ATTGTAATTT
*
142033 TGTTTTTATAATT-TTTTTATA-ATTTATA
1 TGTTTTT-TAATTGATTTTATATATTTATA
**
142061 TGTTTTTTTCTTGATTTTATATATTTATA
1 TGTTTTTTAATTGATTTTATATATTTATA
142090 TGTT
1 TGTT
142094 CATATTCCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.11
28 14 0.50
29 11 0.39
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.69
Consensus pattern (29 bp):
TGTTTTTTAATTGATTTTATATATTTATA
Found at i:151689 original size:2 final size:2
Alignment explanation
Indices: 151682--151727 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
151672 AATTTTGGTA
*
151682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
151724 AT AT
1 AT AT
151728 TTTTAGAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:151763 original size:24 final size:23
Alignment explanation
Indices: 151736--151786 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
151726 ATTTTTAGAA
*
151736 TTTTAGAATTTTATAATGTCATAT
1 TTTTAGAATTTTATAATAT-ATAT
* * *
151760 TTTTTGTATTTTTTAATATATAT
1 TTTTAGAATTTTATAATATATAT
151783 TTTT
1 TTTT
151787 TATTTGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTTAGAATTTTATAATATATAT
Found at i:151799 original size:23 final size:25
Alignment explanation
Indices: 151744--151799 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 25
151734 AATTTTAGAA
*
151744 TTTTATAATGTCATATTTTTTGTAT
1 TTTTATAATATCATATTTTTTGTAT
151769 TTTT-TAATAT-ATA-TTTTT-TAT
1 TTTTATAATATCATATTTTTTGTAT
151790 TTGTTATAAT
1 TT-TTATAAT
151800 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 5 0.18
22 7 0.25
23 7 0.25
24 5 0.18
25 4 0.14
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (25 bp):
TTTTATAATATCATATTTTTTGTAT
Found at i:158198 original size:16 final size:16
Alignment explanation
Indices: 158177--158210 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
158167 TCACCGGTAT
158177 TGTCCACTTATCTCGG
1 TGTCCACTTATCTCGG
158193 TGTCCACTTATCTCGG
1 TGTCCACTTATCTCGG
158209 TG
1 TG
158211 ATAATGCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.38
Consensus pattern (16 bp):
TGTCCACTTATCTCGG
Found at i:159397 original size:5 final size:5
Alignment explanation
Indices: 159391--159420 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
159381 AATACTCATT
*
159391 CCATT CCATC CCATC CCATC CCATC CCATC
1 CCATC CCATC CCATC CCATC CCATC CCATC
159421 TGACCAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.20, C:0.57, G:0.00, T:0.23
Consensus pattern (5 bp):
CCATC
Found at i:163474 original size:33 final size:32
Alignment explanation
Indices: 163405--163476 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
163395 AAATCGAACT
* *** *
163405 TTAAAAAAAAAAACTTAAAACAATTCATTGAT
1 TTAAATAAAAAAACTTAAAACAATTCACAAAC
*
163437 TTAAATAAAAAAACTATTAAACAATTCACAAAC
1 TTAAATAAAAAAACT-TAAAACAATTCACAAAC
163470 TTAAATA
1 TTAAATA
163477 GAAATTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.60, C:0.11, G:0.01, T:0.28
Consensus pattern (32 bp):
TTAAATAAAAAAACTTAAAACAATTCACAAAC
Found at i:163511 original size:46 final size:46
Alignment explanation
Indices: 163444--163536 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
163434 GATTTAAATA
163444 AAAAAACTATTAAACAATTCACAAACTTAAATAGAAA-TTTTTTAAT
1 AAAAAACTATTAAACAATTCACAAACTTAAATA-AAACTTTTTTAAT
* * *
163490 AAAAAACTATTAAATAGTTCACTAACTTAAATAAAACTTTTTTAAT
1 AAAAAACTATTAAACAATTCACAAACTTAAATAAAACTTTTTTAAT
163536 A
1 A
163537 GTTCCGTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 3 0.07
46 40 0.93
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (46 bp):
AAAAAACTATTAAACAATTCACAAACTTAAATAAAACTTTTTTAAT
Found at i:164185 original size:18 final size:18
Alignment explanation
Indices: 164162--164199 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
164152 TTTCCTCTGC
164162 CTTATGACACGCTTTT-GT
1 CTTATGACACG-TTTTCGT
*
164180 CTTATGGCACGTTTTCGT
1 CTTATGACACGTTTTCGT
164198 CT
1 CT
164200 ACTTTTGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (18 bp):
CTTATGACACGTTTTCGT
Found at i:164788 original size:23 final size:22
Alignment explanation
Indices: 164760--164811 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
164750 ATAATTTGGG
*
164760 TTTTAAATATTAATGGTATTGAA
1 TTTTAAATATTAATGG-ATAGAA
* * *
164783 TTTTAATTTTTAATGGATAGAC
1 TTTTAAATATTAATGGATAGAA
164805 TTTTAAA
1 TTTTAAA
164812 AATTTTAAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.50
Consensus pattern (22 bp):
TTTTAAATATTAATGGATAGAA
Found at i:168543 original size:13 final size:12
Alignment explanation
Indices: 168525--168570 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
168515 TTTGATTTTT
168525 TTCTTATAAAAAA
1 TTCTTA-AAAAAA
*
168538 TTCTTAACAATAA
1 TTCTTAA-AAAAA
168551 TT-TTAAAAAAA
1 TTCTTAAAAAAA
168562 -TCTTAAAAA
1 TTCTTAAAAA
168571 TCAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 1 0.03
11 11 0.38
12 5 0.17
13 12 0.41
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (12 bp):
TTCTTAAAAAAA
Found at i:168580 original size:23 final size:23
Alignment explanation
Indices: 168528--168580 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
168518 GATTTTTTTC
* *
168528 TTATAAAAAATTCTTAACAATAA
1 TTATAAAAAAATCTTAAAAATAA
*
168551 TTTTAAAAAAATCTTAAAAATCAA
1 TTATAAAAAAATCTTAAAAAT-AA
168575 -TATAAA
1 TTATAAA
168581 TTATTAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (23 bp):
TTATAAAAAAATCTTAAAAATAA
Found at i:173289 original size:54 final size:54
Alignment explanation
Indices: 173207--173316 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
173197 TGATAGGTGA
173207 TGCATCATTGTTACAAGAATGCAGCTCAATTCACAAGAGTTGTACAGTCAAAAT
1 TGCATCATTGTTACAAGAATGCAGCTCAATTCACAAGAGTTGTACAGTCAAAAT
173261 TGCATCATTGTTACAAGAATGCAGCTCAATTCACAAGAGTTGTACAGTCAAAAT
1 TGCATCATTGTTACAAGAATGCAGCTCAATTCACAAGAGTTGTACAGTCAAAAT
173315 TG
1 TG
173317 TCGTTGGGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (54 bp):
TGCATCATTGTTACAAGAATGCAGCTCAATTCACAAGAGTTGTACAGTCAAAAT
Found at i:188644 original size:30 final size:30
Alignment explanation
Indices: 188610--188805 Score: 181
Period size: 29 Copynumber: 6.7 Consensus size: 30
188600 GTAAAACGGT
* *
188610 AATTTTTAGAGGTTTCGGGGTCAAAATTGG
1 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
* * *
188640 AATTTTTGGAAG-TTCGAGGCCAAAAATGG
1 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
* * * *
188669 AATTTGTGGAAGTTTCGAGGTTAAAAATGG
1 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
* *
188699 GATTTTTGGAAG-TTCGGGGGT-AAAAATGG
1 AATTTTTAGAAGTTTC-GGGGTCAAAAATGG
*
188728 AATTTTTAGAAGTTTTGGGGTC-AAAATGG
1 AATTTTTAGAAGTTTCGGGGTCAAAAATGG
* *
188757 GATTTTT-GAAAG-TTCGAGGGT-AAAAATGA
1 AATTTTTAG-AAGTTTCG-GGGTCAAAAATGG
*
188786 AATTTTTAGAAGTTTTGGGG
1 AATTTTTAGAAGTTTCGGGG
188806 ACCTCCAGGG
Statistics
Matches: 138, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
28 4 0.03
29 89 0.64
30 45 0.33
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (30 bp):
AATTTTTAGAAGTTTCGGGGTCAAAAATGG
Found at i:188704 original size:59 final size:58
Alignment explanation
Indices: 188610--188800 Score: 238
Period size: 59 Copynumber: 3.3 Consensus size: 58
188600 GTAAAACGGT
* * * * **
188610 AATTTTTAGAGGTTTCGGGGTCAAAATTGGAATTTTTGGAAGTTCGAGGCCAAAAATGG
1 AATTTTTAGAAGTTTC-GGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* * *
188669 AATTTGTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGG
1 AATTTTTAGAAGTTTCG-GGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* * * * *
188728 AATTTTTAGAAGTTTTGGGGTCAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGA
1 AATTTTTAGAAGTTTCGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
188786 AATTTTTAGAAGTTT
1 AATTTTTAGAAGTTT
188801 TGGGGACCTC
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
58 52 0.46
59 62 0.54
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.35
Consensus pattern (58 bp):
AATTTTTAGAAGTTTCGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
Found at i:191105 original size:47 final size:44
Alignment explanation
Indices: 191034--191152 Score: 141
Period size: 45 Copynumber: 2.6 Consensus size: 44
191024 ATTTTTGGTT
* * *
191034 TGCTTCACCGTAT-TCATCAAGAAGCTAATCGTTTTTCTCTCCGATC
1 TGCTTCTCGGTATCTCATCAAGAAGCTAATCG-TTTGCT-T-CGATC
* **
191080 TGCTTCTTGGTATCTCATCTGGAAGCTAAATCGTTTGCTTCGATC
1 TGCTTCTCGGTATCTCATCAAGAAGCT-AATCGTTTGCTTCGATC
191125 TGCTTCTCGGTATCTCATCAAGAAGCTA
1 TGCTTCTCGGTATCTCATCAAGAAGCTA
191153 GGGTTCGAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
44 1 0.02
45 29 0.47
46 11 0.18
47 16 0.26
48 5 0.08
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (44 bp):
TGCTTCTCGGTATCTCATCAAGAAGCTAATCGTTTGCTTCGATC
Found at i:191408 original size:208 final size:207
Alignment explanation
Indices: 191089--191564 Score: 681
Period size: 208 Copynumber: 2.3 Consensus size: 207
191079 CTGCTTCTTG
* ** * * *
191089 GTATCTCATCTGGAAGCTAA--ATCGT-TTGCTTCGATCTGCTTCTCGGTATCTCATCAAGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* *
191151 TAGGGTTCGAAGATTTACTCTCATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
66 TAGGGTTCGAAAATTTACTCGCATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
** * * *
191216 AGGAAGAATGAT-TGCGTCGTTTGTTTCAATCTGCTCCCCTGTATCTAATCAGAAAGATGAATTT
131 AGGAAGAATG-TCCACGTCGTTTGTTTCAATCCGCTCCCCTGTATCTAATCAGAAAGACGAATTC
191280 GGTCCACTTATCA
195 GGTCCACTTATCA
* *
191293 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGTTTCTCAGTATCTCCTCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* * * * *
191358 TGGGGTTCGAAAATTTTGCTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCGGTATCTCAT
66 TAGGGTTCGAAAA-TTTACTCGCATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCAT
* * *
191423 CAGGAAGAATGTCCACGTCGTTTGTTTCAATCCGCTCCTCTGTATCTCATCAGGAAGACGAATTC
130 CAGGAAGAATGTCCACGTCGTTTGTTTCAATCCGCTCCCCTGTATCTAATCAGAAAGACGAATTC
*
191488 GGTCCACTTCTCA
195 GGTCCACTTATCA
*
191501 GTATCCCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAG
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAG
191565 ATGACTGCAT
Statistics
Matches: 240, Mismatches: 27, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
204 19 0.08
206 3 0.01
207 44 0.18
208 174 0.73
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (207 bp):
GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
TAGGGTTCGAAAATTTACTCGCATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
AGGAAGAATGTCCACGTCGTTTGTTTCAATCCGCTCCCCTGTATCTAATCAGAAAGACGAATTCG
GTCCACTTATCA
Found at i:203430 original size:30 final size:30
Alignment explanation
Indices: 203372--203582 Score: 175
Period size: 29 Copynumber: 7.2 Consensus size: 30
203362 GTAAAACGGT
* * *
203372 AATTTTTAGAGGTTTC-GGGGTCAAAATGG
1 AATTTTTGGAAGTTTCAGGGGTAAAAATGG
*
203401 AATTTTTGGAAGTTTCAGGGTTAAAAATGG
1 AATTTTTGGAAGTTTCAGGGGTAAAAATGG
** * *
203431 GGTTTTTGAAAGTTT-GGGGGTAAAAATGG
1 AATTTTTGGAAGTTTCAGGGGTAAAAATGG
* * *
203460 AATTTTTTGAAGTTTTA-GGGTTAAAATGG
1 AATTTTTGGAAGTTTCAGGGGTAAAAATGG
* * *
203489 GATTTTTGAAAG-TTCGGGGGTAAAAATGG
1 AATTTTTGGAAGTTTCAGGGGTAAAAATGG
* * * *
203518 AATTTCTAGAAGTTT-TGGGGTCAAAATGG
1 AATTTTTGGAAGTTTCAGGGGTAAAAATGG
* * *
203547 GATTTTTGAAAG-TTC-GAGGGTAAAAATGA
1 AATTTTTGGAAGTTTCAG-GGGTAAAAATGG
203576 AATTTTT
1 AATTTTT
203583 AAAAGTTTTG
Statistics
Matches: 142, Mismatches: 34, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
28 5 0.04
29 112 0.79
30 25 0.18
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAGTTTCAGGGGTAAAAATGG
Found at i:203514 original size:58 final size:58
Alignment explanation
Indices: 203388--203591 Score: 291
Period size: 58 Copynumber: 3.5 Consensus size: 58
203378 TAGAGGTTTC
* * * * *
203388 GGGGTCAAAATGGAATTTTTGGAAGTTTCAGGGTTAAAAATGGGGTTTTTGAAAGTTTG
1 GGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTT-AAAATGGGATTTTTGAAAGTTCG
*
203447 GGGGTAAAAATGGAATTTTTTGAAGTTTTAGGGTTAAAATGGGATTTTTGAAAGTTCG
1 GGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTTAAAATGGGATTTTTGAAAGTTCG
* * *
203505 GGGGTAAAAATGGAATTTCTAGAAGTTTTGGGGTCAAAATGGGATTTTTGAAAGTTCG
1 GGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTTAAAATGGGATTTTTGAAAGTTCG
* * *
203563 AGGGTAAAAATGAAATTTTTAAAAGTTTT
1 GGGGTAAAAATGGAATTTTTAGAAGTTTT
203592 GGGGACCTCC
Statistics
Matches: 132, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 100 0.76
59 32 0.24
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (58 bp):
GGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTTAAAATGGGATTTTTGAAAGTTCG
Found at i:203553 original size:87 final size:87
Alignment explanation
Indices: 203385--203589 Score: 218
Period size: 87 Copynumber: 2.4 Consensus size: 87
203375 TTTTAGAGGT
* * * ** *
203385 TTCG-GGGTCAAAATGGAATTTTTGGAAGTTTCAGGGTTAAAAATGGGGTTTTTGAAAGTTTGGG
1 TTCGAGGGTAAAAATGGAATTTTTGAAAG-TTCAGGGGTAAAAATGGAATTTTAGAAAGTTTGGG
203449 GGTAAAAATGGAATTTTTTG-AAG
65 GGTAAAAATGGAA-TTTTTGAAAG
** * * * *
203472 TTTTAGGGTTAAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTCTAG-AAGTTTTGG
1 TTCGAGGGTAAAAATGGAATTTTTGAAAGTTCAGGGGTAAAAATGGAATTT-TAGAAAGTTTGGG
* *
203536 GGTCAAAATGGGATTTTTGAAAG
65 GGTAAAAATGGAATTTTTGAAAG
* *
203559 TTCGAGGGTAAAAATGAAATTTTTAAAAGTT
1 TTCGAGGGTAAAAATGGAATTTTTGAAAGTT
203590 TTGGGGACCT
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
86 6 0.06
87 67 0.70
88 23 0.24
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (87 bp):
TTCGAGGGTAAAAATGGAATTTTTGAAAGTTCAGGGGTAAAAATGGAATTTTAGAAAGTTTGGGG
GTAAAAATGGAATTTTTGAAAG
Found at i:205418 original size:17 final size:17
Alignment explanation
Indices: 205383--205431 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
205373 TTTTAATTAA
*
205383 AATTTTAAA-TTCAAATT
1 AATTTTAAACTT-AATTT
205400 AATTTTAAACTTAATTT
1 AATTTTAAACTTAATTT
**
205417 AAAATTAAACTTAAT
1 AATTTTAAACTTAAT
205432 AGAAAAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTAAACTTAATTT
Found at i:205437 original size:17 final size:17
Alignment explanation
Indices: 205404--205437 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
205394 CAAATTAATT
**
205404 TTAAACTTAATTTAAAA
1 TTAAACTTAATAGAAAA
205421 TTAAACTTAATAGAAAA
1 TTAAACTTAATAGAAAA
205438 GTTTAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (17 bp):
TTAAACTTAATAGAAAA
Found at i:212932 original size:2 final size:2
Alignment explanation
Indices: 212920--212964 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
212910 GCATATTGAA
*
212920 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
212961 AT AT
1 AT AT
212965 GTATCAGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:220333 original size:3 final size:3
Alignment explanation
Indices: 220325--220350 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
220315 TCGGGTGGCA
220325 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
220351 ACAGAGTATC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:224511 original size:18 final size:19
Alignment explanation
Indices: 224490--224534 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
224480 ATAAATTTTT
224490 TTAAAGTTTTAAA-AAATA
1 TTAAAGTTTTAAATAAATA
**
224508 TTAAAAATTTAAATAAATA
1 TTAAAGTTTTAAATAAATA
*
224527 TTATAGTT
1 TTAAAGTT
224535 GAACATTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
TTAAAGTTTTAAATAAATA
Found at i:225961 original size:20 final size:20
Alignment explanation
Indices: 225914--225961 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
225904 GTAGTCAAAA
* *
225914 ATTTTATTAATAATATAGAT
1 ATTTTAATAATAAAATAGAT
*
225934 ATTCTAATATATAAAATA-AT
1 ATTTTAATA-ATAAAATAGAT
225954 ATTTTAAT
1 ATTTTAAT
225962 TAAATACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTTTAATAATAAAATAGAT
Found at i:227884 original size:25 final size:27
Alignment explanation
Indices: 227848--227900 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
227838 GAGCTGAAAT
227848 GAACAATAAAG-TT-ATACAAGTTACA
1 GAACAATAAAGTTTGATACAAGTTACA
*
227873 GAACAA-ACAAGTTTGGTACAAGTTACA
1 GAACAATA-AAGTTTGATACAAGTTACA
227900 G
1 G
227901 TGTGTGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.04
25 9 0.38
26 2 0.08
27 12 0.50
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (27 bp):
GAACAATAAAGTTTGATACAAGTTACA
Found at i:239281 original size:45 final size:45
Alignment explanation
Indices: 239231--239321 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
239221 GGAGGACAAT
*
239231 ATGATTAGAACGATTCGAATTCAGATTATACTTAAAACAATGAAC
1 ATGATTAGAACGATTCGAATTCAGACTATACTTAAAACAATGAAC
* *
239276 ATGATTAGGACGATTCGAATTCAGACTATACTTAAAACGATGAAC
1 ATGATTAGAACGATTCGAATTCAGACTATACTTAAAACAATGAAC
239321 A
1 A
239322 CCTTGATCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (45 bp):
ATGATTAGAACGATTCGAATTCAGACTATACTTAAAACAATGAAC
Found at i:245687 original size:22 final size:22
Alignment explanation
Indices: 245640--245687 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
245630 TTTAAAAAAT
* * *
245640 AAAAATTATTAAAATTATTTTT
1 AAAAATTATTAAAATGATTATA
245662 AAAAATTATTTAAAA-GATTATA
1 AAAAATTA-TTAAAATGATTATA
245684 AAAA
1 AAAA
245688 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAATTATTAAAATGATTATA
Found at i:252066 original size:22 final size:19
Alignment explanation
Indices: 252025--252073 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
252015 TATTATTTCA
252025 ATAAAATATTTATATTTTT
1 ATAAAATATTTATATTTTT
252044 ATAAAATATATTAATCATTTTT
1 ATAAAATAT-TT-AT-ATTTTT
*
252066 ATTAAATA
1 ATAAAATA
252074 AAGGTAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.35
20 2 0.08
21 2 0.08
22 13 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAAATATTTATATTTTT
Found at i:252081 original size:23 final size:22
Alignment explanation
Indices: 252038--252082 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
252028 AAATATTTAT
* *
252038 ATTTTTATAAAATATATTAATC
1 ATTTTTATAAAATAAAGTAATC
*
252060 ATTTTTATTAAATAAAGGTAATC
1 ATTTTTATAAAATAAA-GTAATC
252083 TTTAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTTTTATAAAATAAAGTAATC
Found at i:255312 original size:22 final size:22
Alignment explanation
Indices: 255284--255328 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
255274 CGGATCGCAC
255284 AATCTCTAATAGTTAATAAAAA
1 AATCTCTAATAGTTAATAAAAA
255306 AATCTCTAATAGTTAATAAAAA
1 AATCTCTAATAGTTAATAAAAA
255328 A
1 A
255329 TAATCTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (22 bp):
AATCTCTAATAGTTAATAAAAA
Found at i:255654 original size:33 final size:33
Alignment explanation
Indices: 255593--255656 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
255583 TTTTAGGTCA
255593 AATTTAGTACTCAAACTTGACACTTTTTTTTTT
1 AATTTAGTACTCAAACTTGACACTTTTTTTTTT
255626 AATTTATGTA-TCTAAACTTGACACTTTTTTT
1 AATTTA-GTACTC-AAACTTGACACTTTTTTT
255657 AAGTTAGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (33 bp):
AATTTAGTACTCAAACTTGACACTTTTTTTTTT
Found at i:255672 original size:30 final size:31
Alignment explanation
Indices: 255596--255674 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 31
255586 TAGGTCAAAT
* *
255596 TTAGTACTCAAACTTGACACTTTTTTTTTTAAT
1 TTAGTACTTAAACTTGACAC--TTTTTTTTAAG
255629 TTATGTA-TCTAAACTTGACAC-TTTTTTTAAG
1 TTA-GTACT-TAAACTTGACACTTTTTTTTAAG
255660 TTAGTACTTAAACTT
1 TTAGTACTTAAACTT
255675 TTTAGGGTCC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 10 0.24
31 13 0.32
33 4 0.10
34 14 0.34
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (31 bp):
TTAGTACTTAAACTTGACACTTTTTTTTAAG
Found at i:255929 original size:26 final size:27
Alignment explanation
Indices: 255891--255942 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
255881 ATTGAATTTA
*
255891 AAAAAAAGCTTAAGTACCATATTAGGT
1 AAAAAAAGCTTAAGTACCAAATTAGGT
*
255918 AAAAAAA-TTTAAGTACCAAATTAGG
1 AAAAAAAGCTTAAGTACCAAATTAGG
255943 AGCAAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (27 bp):
AAAAAAAGCTTAAGTACCAAATTAGGT
Found at i:256349 original size:6 final size:6
Alignment explanation
Indices: 256338--256393 Score: 62
Period size: 6 Copynumber: 9.2 Consensus size: 6
256328 TATTTATTAA
*
256338 TAATAT TAATAT TAATAT TAATAT TAATA- TAAAATT TAA-AT TAATTAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATA-T TAATAT TAA-TAT
256386 TATATAT T
1 TA-ATAT T
256394 TTAACATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
5 8 0.18
6 24 0.55
7 11 0.25
8 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATAT
Found at i:256448 original size:3 final size:3
Alignment explanation
Indices: 256442--256498 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
256432 TTCTTGTCGA
256442 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
256490 TAT TAT TAT
1 TAT TAT TAT
256499 ATTTTCTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:256722 original size:11 final size:12
Alignment explanation
Indices: 256698--256727 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
256688 CAATTCAAAT
256698 TTTATTATTTTA
1 TTTATTATTTTA
256710 TTTATTA-TTTA
1 TTTATTATTTTA
256721 TTTATTA
1 TTTATTA
256728 AATAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:257988 original size:30 final size:30
Alignment explanation
Indices: 257937--258060 Score: 187
Period size: 30 Copynumber: 4.1 Consensus size: 30
257927 ATCATTTTTA
*
257937 ACCCCTAAAGTTTTC-AAAAATTCAAATTTG
1 ACCCTTAAA-TTTTCTAAAAATTCAAATTTG
257967 ACCCTTAAATTTTCTAAAAATTCAAATTTG
1 ACCCTTAAATTTTCTAAAAATTCAAATTTG
257997 ACCCTTAAATTTTCTAAAAATTCAAATTTG
1 ACCCTTAAATTTTCTAAAAATTCAAATTTG
* * * *
258027 ACCCTCAAAGTTTCCAAAAATTAAAATTTG
1 ACCCTTAAATTTTCTAAAAATTCAAATTTG
258057 ACCC
1 ACCC
258061 GTTTTAATGT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 5 0.06
30 83 0.94
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (30 bp):
ACCCTTAAATTTTCTAAAAATTCAAATTTG
Found at i:264644 original size:25 final size:25
Alignment explanation
Indices: 264566--264653 Score: 63
Period size: 25 Copynumber: 3.4 Consensus size: 25
264556 AATTATTTTT
* * *
264566 TAATTAATTTAAATTAATTAAGAAA
1 TAATTAAATTAAAATAATTAAGCAA
* * * *
264591 TAAAT-AA-TAAAAAATATATAATCAC
1 TAATTAAATTAAAATA-AT-TAAGCAA
264616 TAATTAAATTAAAATAATTAAGCAA
1 TAATTAAATTAAAATAATTAAGCAA
264641 TAATATTAAATTA
1 T-A-ATTAAATTA
264654 TCATTTATCT
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
23 5 0.11
24 3 0.07
25 18 0.39
26 5 0.11
27 15 0.33
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (25 bp):
TAATTAAATTAAAATAATTAAGCAA
Found at i:266035 original size:22 final size:22
Alignment explanation
Indices: 265982--266036 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
265972 TTTTAATTCT
*
265982 TTTATTTCTCTCTTGATTTTTTC
1 TTTATTCCTCTCTTGA-TTTTTC
*
266005 TATTTTTCCTCTCTTTG-TTTTTC
1 T-TTATTCCTCTC-TTGATTTTTC
266028 TTTATTCCT
1 TTTATTCCT
266037 TTATAATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 9 0.33
25 3 0.11
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTATTCCTCTCTTGATTTTTC
Found at i:273238 original size:2 final size:2
Alignment explanation
Indices: 273233--273259 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
273223 ATATATTTGT
273233 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 T
273260 TAATGTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:273642 original size:18 final size:18
Alignment explanation
Indices: 273621--273659 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
273611 AAGTTAATCT
*
273621 TAAAATTTTAAAATTGAA
1 TAAAATATTAAAATTGAA
* *
273639 TAAAATATTAATATTGTA
1 TAAAATATTAAAATTGAA
273657 TAA
1 TAA
273660 TTAAATTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TAAAATATTAAAATTGAA
Found at i:274180 original size:3 final size:3
Alignment explanation
Indices: 274172--274200 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
274162 AAGCCATCAC
274172 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
274201 GTATTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:288770 original size:2 final size:2
Alignment explanation
Indices: 288763--288788 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
288753 TTTATATCCA
288763 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
288789 CATTGCAGAA
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:299871 original size:3 final size:3
Alignment explanation
Indices: 299863--299904 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
299853 TCAAGGATAC
299863 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
299905 TACCTTCTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:303179 original size:14 final size:14
Alignment explanation
Indices: 303143--303179 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
303133 TTCAATACCC
*
303143 AAATAATAATAACA
1 AAATAATAGTAACA
303157 AAATAATAGTAACA
1 AAATAATAGTAACA
*
303171 TAATAATAG
1 AAATAATAG
303180 AATGGTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (14 bp):
AAATAATAGTAACA
Found at i:313095 original size:22 final size:22
Alignment explanation
Indices: 313067--313112 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
313057 AAAGAGAAAG
*
313067 TTAATTCAATCGGTTCAACCAA
1 TTAATTCAATCGATTCAACCAA
*
313089 TTAATTCAATCGATTCAATCAA
1 TTAATTCAATCGATTCAACCAA
313111 TT
1 TT
313113 CATGAGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (22 bp):
TTAATTCAATCGATTCAACCAA
Found at i:318052 original size:23 final size:23
Alignment explanation
Indices: 318026--318081 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
318016 AGCGCGCTTA
* *
318026 CTGATTAGCACTGTGTGTGCTCT
1 CTGATCAGCACTGTGTGTGCCCT
*
318049 CTGATCAGCACTTTGTGTGCCCT
1 CTGATCAGCACTGTGTGTGCCCT
318072 CTGATCAGCA
1 CTGATCAGCA
318082 ATAAACTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.34
Consensus pattern (23 bp):
CTGATCAGCACTGTGTGTGCCCT
Found at i:319026 original size:39 final size:39
Alignment explanation
Indices: 318972--319048 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
318962 CTCAATAAAC
318972 ATGCAAATTAATCTTATTAGCCCATATATATTAGAAAAT
1 ATGCAAATTAATCTTATTAGCCCATATATATTAGAAAAT
319011 ATGCAAATTAATCTTATTAGCCCATATATATTAGAAAA
1 ATGCAAATTAATCTTATTAGCCCATATATATTAGAAAA
319049 ATTCCTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (39 bp):
ATGCAAATTAATCTTATTAGCCCATATATATTAGAAAAT
Found at i:321463 original size:31 final size:29
Alignment explanation
Indices: 321425--321486 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
321415 ATTTCCAATC
321425 AAGTCATTGAACTATTCAAAAG-TTTTTATTT
1 AAGTCATTGAACTATT---AAGTTTTTTATTT
*
321456 AAGTCATTGGACTATTAAGTTTTTTATTT
1 AAGTCATTGAACTATTAAGTTTTTTATTT
321485 AA
1 AA
321487 AAAAAGTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 3 0.10
29 11 0.38
31 15 0.52
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (29 bp):
AAGTCATTGAACTATTAAGTTTTTTATTT
Found at i:324496 original size:22 final size:22
Alignment explanation
Indices: 324455--324496 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
324445 TACAACACGA
* *
324455 ATATACTAACATATCAAAATCT
1 ATATACTAAAAGATCAAAATCT
*
324477 ATATACTAAAAGATCGAAAT
1 ATATACTAAAAGATCAAAAT
324497 GATTGGGGCA
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:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (22 bp):
ATATACTAAAAGATCAAAATCT
Found at i:343172 original size:20 final size:21
Alignment explanation
Indices: 343134--343172 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
343124 TTAAATCTAA
* *
343134 GATATTATCAATATTTCTATT
1 GATATTATCAAAATATCTATT
343155 GATA-TATCAAAATATCTA
1 GATATTATCAAAATATCTA
343173 ATACCTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (21 bp):
GATATTATCAAAATATCTATT
Found at i:344528 original size:20 final size:21
Alignment explanation
Indices: 344493--344531 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
344483 ATTTTTGCTT
*
344493 TTGTTTTAGTTGTTATTTTGG
1 TTGTTTTAGATGTTATTTTGG
344514 TTGTTTT-GATGTTATTTT
1 TTGTTTTAGATGTTATTTT
344532 TATGCGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (21 bp):
TTGTTTTAGATGTTATTTTGG
Found at i:344532 original size:12 final size:12
Alignment explanation
Indices: 344463--344518 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
344453 GGTTTTTTTG
*
344463 TTGTTGCTATTT
1 TTGTTGTTATTT
344475 TTGTTGTTATTT
1 TTGTTGTTATTT
*
344487 TTGCTT-TTGTTT
1 TTG-TTGTTATTT
*
344499 TAGTTGTTATTT
1 TTGTTGTTATTT
*
344511 TGGTTGTT
1 TTGTTGTT
344519 TTGATGTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.70
Consensus pattern (12 bp):
TTGTTGTTATTT
Found at i:356251 original size:19 final size:17
Alignment explanation
Indices: 356229--356272 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 17
356219 TCACATCAAT
356229 AATTTTATCTTAAATTATA
1 AATTTTAT-TTAAATT-TA
356248 AATTTTTTATTTAAATTTA
1 AA--TTTTATTTAAATTTA
356267 AATTTT
1 AATTTT
356273 TTCAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.17
19 6 0.26
20 7 0.30
21 6 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTTATTTAAATTTA
Found at i:356273 original size:19 final size:21
Alignment explanation
Indices: 356231--356274 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
356221 ACATCAATAA
356231 TTTTATCTTAAATTATAAATT
1 TTTTATCTTAAATTATAAATT
356252 TTTTAT-TTAAATT-TAAATT
1 TTTTATCTTAAATTATAAATT
356271 TTTT
1 TTTT
356275 CAAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
21 6 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATCTTAAATTATAAATT
Done.