Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014004.1 Kokia drynarioides strain JFW-HI SEQ_129035, 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: 196764
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 39 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3453 original size:45 final size:45
Alignment explanation
Indices: 3394--3490 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 45
3384 GCAGATATGC
* * *
3394 TTTTTAGTTCTTTTATGTATTTATACATTCTTATAAATTTATAAA
1 TTTTTAATTCTTTTATATACTTATACATTCTTATAAATTTATAAA
* * *
3439 TTTTTAATTGTTTTATATACTTATATATTTTTATAAATTTATAAA
1 TTTTTAATTCTTTTATATACTTATACATTCTTATAAATTTATAAA
*
3484 ATTTTAA
1 TTTTTAA
3491 AATTTTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (45 bp):
TTTTTAATTCTTTTATATACTTATACATTCTTATAAATTTATAAA
Found at i:3480 original size:18 final size:17
Alignment explanation
Indices: 3431--3495 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 17
3421 TTCTTATAAA
*
3431 TTTATAAATTTTTAATTGT
1 TTTATAAATTTATAA-T-T
* *
3450 TTTATATACTTATATATT
1 TTTATAAATTTATA-ATT
*
3468 TTTATAAATTTATAAAAT
1 TTTATAAATTTAT-AATT
3486 TTTA-AAATTT
1 TTTATAAATTT
3496 TTATTTATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.16
18 18 0.47
19 13 0.34
20 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTATAAATTTATAATT
Found at i:3541 original size:56 final size:57
Alignment explanation
Indices: 3451--3594 Score: 154
Period size: 56 Copynumber: 2.5 Consensus size: 57
3441 TTTAATTGTT
* * *
3451 TTATATACTTATATATTTTTATAAATTTATAAAAT-TT-TAAAATTTTTATTTATATA
1 TTATATA-TTGTATATTTTTATAAATTTATAAAATATTATAAAATTTATATATATATA
* **
3507 TTATATATTGTACATTTTTATATAATTT-TCAAAATATTATAAGCTTTATATATATATA
1 TTATATATTGTATATTTTTATA-AATTTAT-AAAATATTATAAAATTTATATATATATA
*
3565 TT-TA-ATTGTATATATTTTATAAGTTTATAA
1 TTATATATTGTATAT-TTTTATAAATTTATAA
3595 TTTATATATT
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
55 14 0.19
56 31 0.42
57 12 0.16
58 17 0.23
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (57 bp):
TTATATATTGTATATTTTTATAAATTTATAAAATATTATAAAATTTATATATATATA
Found at i:4265 original size:23 final size:23
Alignment explanation
Indices: 4227--4280 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
4217 AGTTCGACTT
*
4227 AAATT-AAAAAATTAAACATGTC
1 AAATTAAAAAAAATAAACATGTC
*
4249 AAATTAAAAAAAATAAATATGTC
1 AAATTAAAAAAAATAAACATGTC
4272 AAATTAAAA
1 AAATTAAAA
4281 TATTGTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.26
Consensus pattern (23 bp):
AAATTAAAAAAAATAAACATGTC
Found at i:4527 original size:18 final size:17
Alignment explanation
Indices: 4492--4531 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
4482 TATTTTTTAT
* *
4492 ATTTTTTAAAATTTTAAA
1 ATTTTTTAAAAATAT-AA
4510 ATTTTTTAAAAATATAA
1 ATTTTTTAAAAATATAA
4527 ATTTT
1 ATTTT
4532 AGAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTTAAAAATATAA
Found at i:4557 original size:19 final size:20
Alignment explanation
Indices: 4533--4579 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4523 ATAAATTTTA
* *
4533 GAATTTTT-ATAATCATTTC
1 GAATTTTTGAAAATAATTTC
*
4552 GAATTTTTGAAAATAATTTT
1 GAATTTTTGAAAATAATTTC
4572 GAATTTTT
1 GAATTTTT
4580 TTATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (20 bp):
GAATTTTTGAAAATAATTTC
Found at i:4559 original size:20 final size:21
Alignment explanation
Indices: 4536--4586 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
4526 AATTTTAGAA
*
4536 TTTTTATAATCATTTCGAA-T
1 TTTTTATAATAATTTCGAATT
* * *
4556 TTTTGAAAATAATTTTGAATT
1 TTTTTATAATAATTTCGAATT
4577 TTTTTATAAT
1 TTTTTATAAT
4587 TTTTGTTGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTTATAATAATTTCGAATT
Found at i:17739 original size:28 final size:28
Alignment explanation
Indices: 17657--17781 Score: 128
Period size: 28 Copynumber: 4.5 Consensus size: 28
17647 CTCTAGGCTT
*
17657 TGGCTCGAAAGAGCGTTACTT-TGTATTA
1 TGGCTCGAAAGAGCGTTA-TTCTGTATTC
* *
17685 TGGCTCGAAGGAGCGTTACTCTGTATTC
1 TGGCTCGAAAGAGCGTTATTCTGTATTC
* *
17713 TGGCTCGAAAGAGCGCTATTCTATATTC
1 TGGCTCGAAAGAGCGTTATTCTGTATTC
* ** * *
17741 TAGCTTAAAAGAACATTATTCTGTA-TC
1 TGGCTCGAAAGAGCGTTATTCTGTATTC
*
17768 TGGCTCGAATGAGC
1 TGGCTCGAAAGAGC
17782 AATAATCTGT
Statistics
Matches: 77, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
27 12 0.16
28 65 0.84
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (28 bp):
TGGCTCGAAAGAGCGTTATTCTGTATTC
Found at i:19891 original size:19 final size:19
Alignment explanation
Indices: 19869--19913 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
19859 TTATATTAGG
19869 ATTTAATATTTAAGA-TATT
1 ATTTAATATTTAA-ATTATT
* *
19888 ATTTATTATTTAAATTTTT
1 ATTTAATATTTAAATTATT
19907 ATTTAAT
1 ATTTAAT
19914 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAATATTTAAATTATT
Found at i:20740 original size:22 final size:22
Alignment explanation
Indices: 20714--20771 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
20704 GACTTCCCTA
20714 TTTTCTATTT-CTTTTAATTCTT
1 TTTTCT-TTTACTTTTAATTCTT
*
20736 TTTTCTTTTATTTTTAATTC-T
1 TTTTCTTTTACTTTTAATTCTT
*
20757 TTTTCTTTTATTTTT
1 TTTTCTTTTACTTTT
20772 CCTTTGATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTACTTTTAATTCTT
Found at i:20749 original size:21 final size:20
Alignment explanation
Indices: 20714--20770 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 20
20704 GACTTCCCTA
*
20714 TTTTCTATTTCTTTTAATTCTT
1 TTTTCT-TTTATTTTAATTC-T
20736 TTTTCTTTTATTTTTAATTCT
1 TTTTCTTTTA-TTTTAATTCT
20757 TTTTCTTTTATTTT
1 TTTTCTTTTATTTT
20771 TCCTTTGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 4 0.12
21 14 0.42
22 15 0.45
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTATTTTAATTCT
Found at i:20771 original size:21 final size:22
Alignment explanation
Indices: 20725--20771 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
20715 TTTCTATTTC
20725 TTTTAATTCTTTTTTCTTTTAT
1 TTTTAATTCTTTTTTCTTTTAT
20747 TTTTAATTC-TTTTTCTTTTAT
1 TTTTAATTCTTTTTTCTTTTAT
20768 TTTT
1 TTTT
20772 CCTTTGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTAATTCTTTTTTCTTTTAT
Found at i:24523 original size:102 final size:102
Alignment explanation
Indices: 24331--24515 Score: 259
Period size: 102 Copynumber: 1.8 Consensus size: 102
24321 AAAAAATATA
* *
24331 AATAAATAAATTTGGAGTGTGTTAGACTAAGTAATCGGGGTGGAGTGCTTGGTTGTCATTTCACT
1 AATAAATAAATTTGGAGTGTGTTAGACTAAGTAATCGGGATGGAGTGCTTGGGTGTCATTTCACT
*
24396 TCGCGTCAAAAGGGCTAACACATTCTAAAAAAAAGAG
66 TCGCGTCAAAAGGGCCAACACATTCTAAAAAAAAGAG
* *
24433 AATAAATAAA-TT-GAGTGCATGTTGGACTGAGTAA-CTGGGATGGAGTGCTTGGGTGTCATTTC
1 AATAAATAAATTTGGAGTG--TGTTAGACTAAGTAATC-GGGATGGAGTGCTTGGGTGTCATTTC
* *
24495 ATTTCGCGTCAAAAGGTCCAA
63 ACTTCGCGTCAAAAGGGCCAA
24516 TGTATTCTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 5 0.07
101 3 0.04
102 65 0.89
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (102 bp):
AATAAATAAATTTGGAGTGTGTTAGACTAAGTAATCGGGATGGAGTGCTTGGGTGTCATTTCACT
TCGCGTCAAAAGGGCCAACACATTCTAAAAAAAAGAG
Found at i:25973 original size:15 final size:16
Alignment explanation
Indices: 25955--25984 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25945 TTTCCCTATT
25955 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
25970 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
25985 TTTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:25977 original size:22 final size:22
Alignment explanation
Indices: 25950--25993 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
25940 TTCGATTTCC
25950 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
25972 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
25994 ATGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:37614 original size:30 final size:30
Alignment explanation
Indices: 37580--37673 Score: 59
Period size: 30 Copynumber: 3.2 Consensus size: 30
37570 GTAAAATGGT
* *
37580 AATTTATGGAAAGTTCGGGGTTAAAAATGA
1 AATTTTTGGAAAGTTTGGGGTTAAAAATGA
* * * *
37610 AATTTTTAGACA-TCTAGGGG-T-AAAATGGT
1 AATTTTTGGAAAGT-TTGGGGTTAAAAAT-GA
* ** *
37639 AATTTTTTGAAAGTTTAAGGTTAAAAACGA
1 AATTTTTGGAAAGTTTGGGGTTAAAAATGA
37669 AATTT
1 AATTT
37674 ATAGACATGC
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
28 5 0.11
29 16 0.34
30 22 0.47
31 4 0.09
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTGGGGTTAAAAATGA
Found at i:37641 original size:59 final size:58
Alignment explanation
Indices: 37508--37733 Score: 204
Period size: 59 Copynumber: 3.8 Consensus size: 58
37498 TCGGACACTT
* * * * * * * *
37508 GGGGCAAAATGGTAAATTTGGGAAATTTTGGGGTAAAAAATGGAACTTTTAGACAT-TCA
1 GGGGTAAAATGGT-AATTTTGGAAAGTTCGAGGTTAAAAATGAAATTTTTAGACATCT-A
* *
37567 AGGGTAAAATGGTAATTTATGGAAAGTTCGGGGTTAAAAATGAAATTTTTAGACATCTA
1 GGGGTAAAATGGTAATTT-TGGAAAGTTCGAGGTTAAAAATGAAATTTTTAGACATCTA
* ** * * *
37626 GGGGTAAAATGGTAATTTTTTGAAAGTTTAAGGTTAAAAACGAAATTTATAGACATGCGA
1 GGGGTAAAATGGTAA-TTTTGGAAAGTTCGAGGTTAAAAATGAAATTTTTAGACAT-CTA
* * * *
37686 -GAGTAAAATGGTAATTTTGGAAGGATTCGAGGTCAAAAATGGAATTTT
1 GGGGTAAAATGGTAATTTTGGAAAG-TTCGAGGTTAAAAATGAAATTTT
37734 GGAAAGTTTG
Statistics
Matches: 137, Mismatches: 25, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
58 13 0.09
59 118 0.86
60 6 0.04
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.31
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTCGAGGTTAAAAATGAAATTTTTAGACATCTA
Found at i:37734 original size:30 final size:30
Alignment explanation
Indices: 37690--37960 Score: 128
Period size: 29 Copynumber: 9.1 Consensus size: 30
37680 ATGCGAGAGT
* *
37690 AAAATGGTAATTTTGGAAGGATTCGAGGTCA
1 AAAATGG-AATTTTGGAAAGATTCGGGGTCA
* *
37721 AAAATGGAATTTTGGAAAG-TTTGGGGTTA
1 AAAATGGAATTTTGGAAAGATTCGGGGTCA
* * *
37750 AAAATGTAATTTTTGGAAAAATTCGGGGGCA
1 AAAATGGAA-TTTTGGAAAGATTCGGGGTCA
* * * *
37781 AAAAAGGAATTTTTGAAAG-TTTGAGGGT-T
1 AAAATGGAATTTTGGAAAGATTCG-GGGTCA
* **
37810 AAAATGTAATTTTTGGAAA-ATTTAGGGT-A
1 AAAATGGAA-TTTTGGAAAGATTCGGGGTCA
* ** *
37839 AAAAAGGAATTTTTAAAAG-TTTGAGGGT-A
1 AAAATGGAATTTTGGAAAGATTCG-GGGTCA
** ** *
37868 AAAATATAATTTTTGGAAA-ATTCAAGGTTA
1 AAAATGGAA-TTTTGGAAAGATTCGGGGTCA
** ** *
37898 AAAATGGAATTTTATAAAG-TTTAGGGTTA
1 AAAATGGAATTTTGGAAAGATTCGGGGTCA
* * * *
37927 AAAAGGGATTTTTAGGAAAGTTTAGGGGTCA
1 AAAATGGAATTTT-GGAAAGATTCGGGGTCA
37958 AAA
1 AAA
37961 TATGATTTGT
Statistics
Matches: 180, Mismatches: 47, Indels: 26
0.71 0.19 0.10
Matches are distributed among these distances:
28 10 0.06
29 76 0.42
30 63 0.35
31 31 0.17
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTGGAAAGATTCGGGGTCA
Found at i:37783 original size:60 final size:60
Alignment explanation
Indices: 37690--37930 Score: 280
Period size: 60 Copynumber: 4.1 Consensus size: 60
37680 ATGCGAGAGT
* * * *
37690 AAAATGGTAA-TTTTGGAAGGATTCGAGGTCAAAAATGGAATTTTGGAAAGTTTG-GGGTTA
1 AAAAT-GTAATTTTTGGAA-AATTCGAGGGCAAAAAAGGAATTTTTGAAAGTTTGAGGGTTA
*
37750 AAAATGTAATTTTTGGAAAAATTCGGGGGCAAAAAAGGAATTTTTGAAAGTTTGAGGGTT-
1 AAAATGTAATTTTTGG-AAAATTCGAGGGCAAAAAAGGAATTTTTGAAAGTTTGAGGGTTA
* * *
37810 AAAATGTAATTTTTGGAAAATT-TAGGGTAAAAAAGGAATTTTTAAAAGTTTGAGGG-TA
1 AAAATGTAATTTTTGGAAAATTCGAGGGCAAAAAAGGAATTTTTGAAAGTTTGAGGGTTA
* * ** *
37868 AAAATATAATTTTTGGAAAATTCAAGGTTAAAAATGGAATTTTAT-AAAGTTT-AGGGTTA
1 AAAATGTAATTTTTGGAAAATTCGAGGGCAAAAAAGGAATTTT-TGAAAGTTTGAGGGTTA
37927 AAAA
1 AAAA
37931 GGGATTTTTA
Statistics
Matches: 161, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
57 1 0.01
58 55 0.34
59 40 0.25
60 58 0.36
61 7 0.04
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (60 bp):
AAAATGTAATTTTTGGAAAATTCGAGGGCAAAAAAGGAATTTTTGAAAGTTTGAGGGTTA
Found at i:37836 original size:29 final size:29
Alignment explanation
Indices: 37721--37953 Score: 154
Period size: 29 Copynumber: 7.9 Consensus size: 29
37711 TTCGAGGTCA
* *
37721 AAAATGGAA-TTTTGGAAAGTTTGGGGTT
1 AAAATGGAATTTTTGGAAAATTTAGGGTT
* ** **
37749 AAAAATGTAATTTTTGGAAAAATTCGGGGGCA
1 -AAAATGGAATTTTTGG-AAAATT-TAGGGTT
* *
37781 AAAAAGGAATTTTT-GAAAGTTTGAGGGTT
1 AAAATGGAATTTTTGGAAAATTT-AGGGTT
* *
37810 AAAATGTAATTTTTGGAAAATTTAGGGTA
1 AAAATGGAATTTTTGGAAAATTTAGGGTT
* *
37839 AAAAAGGAATTTTT--AAAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAAA-TTT-AGGGTT
** * *
37868 AAAATATAATTTTTGGAAAATTCAAGGTT
1 AAAATGGAATTTTTGGAAAATTTAGGGTT
*
37897 AAAAATGGAATTTTAT--AAAGTTTAGGGTT
1 -AAAATGGAATTTT-TGGAAAATTTAGGGTT
* * *
37926 AAAAAGGGATTTTTAGGAAAGTTTAGGG
1 AAAATGGAATTTTT-GGAAAATTTAGGG
37954 GTCAAAATAT
Statistics
Matches: 159, Mismatches: 31, Indels: 27
0.73 0.14 0.12
Matches are distributed among these distances:
27 5 0.03
28 14 0.09
29 76 0.48
30 38 0.24
31 22 0.14
32 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAATTTAGGGTT
Found at i:37939 original size:58 final size:60
Alignment explanation
Indices: 37690--37930 Score: 271
Period size: 58 Copynumber: 4.1 Consensus size: 60
37680 ATGCGAGAGT
* * * **
37690 AAAATGGTAA-TTTTGGAAGGATTCGAGGTCAAAAATGGAATTTTGGAAAGTTTG-GGGTTA
1 AAAAT-GTAATTTTTGGAA-AATTCGAGGGCAAAAAAGGAATTTTTAAAAGTTTGAGGGTTA
* *
37750 AAAATGTAATTTTTGGAAAAATTCGGGGGCAAAAAAGGAATTTTTGAAAGTTTGAGGGTT-
1 AAAATGTAATTTTTGG-AAAATTCGAGGGCAAAAAAGGAATTTTTAAAAGTTTGAGGGTTA
* *
37810 AAAATGTAATTTTTGGAAAATT-TAGGGTAAAAAAGGAATTTTTAAAAGTTTGAGGG-TA
1 AAAATGTAATTTTTGGAAAATTCGAGGGCAAAAAAGGAATTTTTAAAAGTTTGAGGGTTA
* * ** *
37868 AAAATATAATTTTTGGAAAATTCAAGGTTAAAAATGGAA-TTTTATAAAGTTT-AGGGTTA
1 AAAATGTAATTTTTGGAAAATTCGAGGGCAAAAAAGGAATTTTTA-AAAGTTTGAGGGTTA
37927 AAAA
1 AAAA
37931 GGGATTTTTA
Statistics
Matches: 161, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
57 1 0.01
58 60 0.37
59 36 0.22
60 57 0.35
61 7 0.04
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (60 bp):
AAAATGTAATTTTTGGAAAATTCGAGGGCAAAAAAGGAATTTTTAAAAGTTTGAGGGTTA
Found at i:38529 original size:3 final size:3
Alignment explanation
Indices: 38518--38622 Score: 54
Period size: 3 Copynumber: 34.0 Consensus size: 3
38508 ATTTTTTTAT
* * *
38518 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA ATA TTTA TTA ATG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * *
38563 TT- TGTT TCTA CTA TTTA TTA TTGA -TG TTA TTA TTA ATG TTA TTA TTA
1 TTA T-TA T-TA TTA -TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
*
38610 TTAA TTA CTA TTA
1 TT-A TTA TTA TTA
38623 ATTCATTTAA
Statistics
Matches: 76, Mismatches: 18, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
2 3 0.04
3 63 0.83
4 10 0.13
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:39320 original size:17 final size:17
Alignment explanation
Indices: 39300--39379 Score: 97
Period size: 17 Copynumber: 4.7 Consensus size: 17
39290 AACTAAATTT
*
39300 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* **
39317 TAAAATTAAATTTCCAA
1 TAAATTTAAATTTAAAA
39334 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
39351 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
39368 TAAATCTAAATT
1 TAAATTTAAATT
39380 CTGTTGGGCC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:39919 original size:49 final size:49
Alignment explanation
Indices: 39861--40008 Score: 151
Period size: 49 Copynumber: 3.0 Consensus size: 49
39851 CCTTCGTATC
* *
39861 TTCGTGGTACTAGATTCGCTGTTGCGGCTTAAATCTTTTCCTTCATGCT
1 TTCGAGGTACTAGATTCGCTGTTGCGACTTAAATCTTTTCCTTCATGCT
* * * * *
39910 TTTGAGGTACAAGGTTCG-TCATTGTGACTTAAA-CTTTTCCCTTCGTAT-C-
1 TTCGAGGTACTAGATTCGCT-GTTGCGACTTAAATCTTTT-CCTTC--ATGCT
* *
39959 TTCGTGGTACTAGATTCGCTGTTGCGACTTAAATCTTTCCCTTCATGCT
1 TTCGAGGTACTAGATTCGCTGTTGCGACTTAAATCTTTTCCTTCATGCT
40008 T
1 T
40009 AAACTTTTCC
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
47 2 0.03
48 7 0.09
49 60 0.78
50 6 0.08
51 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (49 bp):
TTCGAGGTACTAGATTCGCTGTTGCGACTTAAATCTTTTCCTTCATGCT
Found at i:40056 original size:69 final size:69
Alignment explanation
Indices: 39937--40077 Score: 239
Period size: 69 Copynumber: 2.0 Consensus size: 69
39927 GTCATTGTGA
* *
39937 CTTAAACTTTTCCCTTCGTATCTTCGTGGTACTAGATTCGCTGTTGCGACTTAAATCTTTCCCTT
1 CTTAAACTTTTCCCTTCGTATCTTCGTGGTACTAGATTCGCTGTTACGACTTAAATATTTCCCTT
40002 CATG
66 CATG
*
40006 CTTAAACTTTTCCCTTCGTATCTTCGTGGTACTGGATTCG-TCGTTACGACTTAAATATTTCCCT
1 CTTAAACTTTTCCCTTCGTATCTTCGTGGTACTAGATTCGCT-GTTACGACTTAAATATTTCCCT
40070 TCATG
65 TCATG
40075 CTT
1 CTT
40078 CTGAGGTACA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.01
69 67 0.99
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.43
Consensus pattern (69 bp):
CTTAAACTTTTCCCTTCGTATCTTCGTGGTACTAGATTCGCTGTTACGACTTAAATATTTCCCTT
CATG
Found at i:40061 original size:167 final size:167
Alignment explanation
Indices: 39840--40172 Score: 497
Period size: 167 Copynumber: 2.0 Consensus size: 167
39830 AAGTTCACCG
* * * *
39840 TTAAACCTTTCCCTTCGTATCTTCGTGGTACTAGATTCGCTGTTGCGGCTTAAATCTTTTCCTTC
1 TTAAACCTTTCCCTTCGTATCTTCGTGGTACTAGATTCGCTGTTACGACTTAAATATTTCCCTTC
* * * * *
39905 ATGCTTTTGAGGTACAAGGTTCGTCATTGTGACTTAAACTTTTCCCTTCGTATCTTCGTGGTACT
66 ATGCTTCTGAGGTACAAGATTCGCCATTGCGACTTAAACCTTTCCCTTCGTATCTTCGTGGTACT
* **
39970 AGATTCGCTGTTGCGACTTAAATCTTTCCCTTCATGC
131 AGATTCACCATTGCGACTTAAATCTTTCCCTTCATGC
* *
40007 TTAAACTTTTCCCTTCGTATCTTCGTGGTACTGGATTCG-TCGTTACGACTTAAATATTTCCCTT
1 TTAAACCTTTCCCTTCGTATCTTCGTGGTACTAGATTCGCT-GTTACGACTTAAATATTTCCCTT
*
40071 CATGCTTCTGAGGTACAAGATTCGCCATTGCGACTTAAACCTTTCCTTTCGTATCTTCGTGGTAC
65 CATGCTTCTGAGGTACAAGATTCGCCATTGCGACTTAAACCTTTCCCTTCGTATCTTCGTGGTAC
* *
40136 TGGATTCACCATTGCGGCTTAAATCTTTCCCTTCATG
130 TAGATTCACCATTGCGACTTAAATCTTTCCCTTCATG
40173 TTTCTGAGGT
Statistics
Matches: 148, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
166 1 0.01
167 147 0.99
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (167 bp):
TTAAACCTTTCCCTTCGTATCTTCGTGGTACTAGATTCGCTGTTACGACTTAAATATTTCCCTTC
ATGCTTCTGAGGTACAAGATTCGCCATTGCGACTTAAACCTTTCCCTTCGTATCTTCGTGGTACT
AGATTCACCATTGCGACTTAAATCTTTCCCTTCATGC
Found at i:40086 original size:49 final size:49
Alignment explanation
Indices: 40033--40507 Score: 414
Period size: 49 Copynumber: 9.7 Consensus size: 49
40023 GTATCTTCGT
* * *
40033 GGTACTGGATTCGTCGTTACGACTTAAATATTTCCCTTCATGCTTCTGA
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGA
** * * * *
40082 GGTACAAGATTCGCCATTGCGACTTAAACCTTTCCTTTCGTAT-CTTC-GT
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTC--ATGCTTCTGA
* * * *
40131 GGTACTGGATTCACCATTGCGGCTTAAATCTTTCCCTTCATGTTTCTGA
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGA
* * * *
40180 GGTACAAGG-TTTGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTC--A
1 GGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GCTTCTGA
* * * * * *
40228 TGGTATTGGATTCGCCTTTACGGCTTAAATCTTTCCCTTCATGCTTTTAA
1 -GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGA
* * * * *
40278 GGTACAAGG-TTCGCCGTTGTGACTTAAACCTTTCCCTTCATATCTTC-GT
1 GGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GCTTCTGA
*
40327 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGA
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGA
* * * * *
40376 GGTACAAGG-TTTGCCATTGCGACTTAAACCTTTCCCTTCGTAT-CTTC-GT
1 GGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCCTTC--ATGCTTCTGA
* *
40425 GGTACTGGATTCGCCGTTGCGGCTTAAGTCTTTCCCTTCATGCTTCTGA
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGA
* * * *
40474 GGTACAAGG-TTCGCCATTGCAACTTAAACCTTTC
1 GGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTC
40508 GCTTTATGTC
Statistics
Matches: 335, Mismatches: 70, Indels: 42
0.75 0.16 0.09
Matches are distributed among these distances:
47 4 0.01
48 21 0.06
49 283 0.84
50 23 0.07
51 4 0.01
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (49 bp):
GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGA
Found at i:40178 original size:98 final size:98
Alignment explanation
Indices: 40006--40529 Score: 778
Period size: 98 Copynumber: 5.3 Consensus size: 98
39996 TCCCTTCATG
* * * * * *
40006 CTTAAACTTTTCCCTTCGTATCTTCGTGGTACTGGATTCGTCGTTACGACTTAAATATTTCCCTT
1 CTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
*
40071 CATGCTTCTGAGGTACAAGATTCGCCATTGCGA
66 CATGCTTCTGAGGTACAAGGTTCGCCATTGCGA
* * * *
40104 CTTAAACCTTTCCTTTCGTATCTTCGTGGTACTGGATTCACCATTGCGGCTTAAATCTTTCCCTT
1 CTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
* * *
40169 CATGTTTCTGAGGTACAAGGTTTGCCGTTGCGA
66 CATGCTTCTGAGGTACAAGGTTCGCCATTGCGA
* * * *
40202 CTTAAACCTTTCCCTTCATATCTTCATGGTATTGGATTCGCCTTTACGGCTTAAATCTTTCCCTT
1 CTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
* * * *
40267 CATGCTTTTAAGGTACAAGGTTCGCCGTTGTGA
66 CATGCTTCTGAGGTACAAGGTTCGCCATTGCGA
40300 CTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
1 CTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
*
40365 CATGCTTCTGAGGTACAAGGTTTGCCATTGCGA
66 CATGCTTCTGAGGTACAAGGTTCGCCATTGCGA
* *
40398 CTTAAACCTTTCCCTTCGTATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAGTCTTTCCCTT
1 CTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
*
40463 CATGCTTCTGAGGTACAAGGTTCGCCATTGCAA
66 CATGCTTCTGAGGTACAAGGTTCGCCATTGCGA
* * * *
40496 CTTAAACCTTTCGCTTTATGTCTTCATGGTACTG
1 CTTAAACCTTTCCCTTCATATCTTCGTGGTACTG
40530 AGACGTAAAG
Statistics
Matches: 384, Mismatches: 42, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 384 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
CTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
CATGCTTCTGAGGTACAAGGTTCGCCATTGCGA
Found at i:40969 original size:18 final size:18
Alignment explanation
Indices: 40943--40977 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40933 AAAATTGCCG
*
40943 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
40961 AATAATTACAAGGAACA
1 AATAATTACAAGGAACA
40978 GTATTAGATG
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:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:50919 original size:29 final size:29
Alignment explanation
Indices: 50883--51316 Score: 223
Period size: 30 Copynumber: 15.0 Consensus size: 29
50873 GGATGCTCAA
*
50883 GGGT-AAAATGGTAATTTTGGAAATTTTG
1 GGGTAAAAATGGTAATTTTGGAAATTTAG
* * *
50911 GGGTAAAAAATGG-AATTTT-TAGATATTCG
1 GGGT-AAAAATGGTAATTTTGGAAAT-TTAG
50940 AGGGT-AAAATGGTAATTTTGGAAAGTTT-G
1 -GGGTAAAAATGGTAATTTTGGAAA-TTTAG
** * *
50969 GGGTTAAAAAATGAAAATTTTAGATATTT-G
1 GGG-T-AAAAATGGTAATTTTGGAAATTTAG
50999 AGGGT-AAAATGGTAAATTTTGGAAAGTTTAG
1 -GGGTAAAAATGGT-AATTTTGGAAA-TTTAG
* * * *
51030 GGTTAAAAATAG-AATTTTTAGACA-TTAG
1 GGGTAAAAATGGTAA-TTTTGGAAATTTAG
*
51058 AGGGT-AAAAT-GTAATTTTGGAAGGA-TTCG
1 -GGGTAAAAATGGTAATTTTGGAA--ATTTAG
*
51087 AGGTCAAAAATGG-AATTTTGGAAAGTTTAG
1 GGGT-AAAAATGGTAATTTTGGAAA-TTTAG
*
51117 GGGTAAAAAT-GTAATTTTTAGAAA-TTAG
1 GGGTAAAAATGGTAA-TTTTGGAAATTTAG
* * *
51145 GGGTTAAAAATGG-ATTTTTGG-AAGTTCG
1 GGG-TAAAAATGGTAATTTTGGAAATTTAG
* * * *
51173 AGGAAAAAAT-GTACTTTTTTGAAAATTTAG
1 GGGTAAAAATGGTA--ATTTTGGAAATTTAG
* * *
51203 GGTTAAAAATGG-AATTTTGGAAAGTTCG
1 GGGTAAAAATGGTAATTTTGGAAATTTAG
*
51231 GGGTAAAAAT-GCAATTTTTGGAATATTTAG
1 GGGTAAAAATGGTAA-TTTTGGAA-ATTTAG
* **
51261 GGTTAAAAATGG-AA-TTTGGAAAGTTCGG
1 GGGTAAAAATGGTAATTTTGGAAA-TTTAG
51289 GGGT-AAAAT-GTAATTTTTGGAAAATTTA
1 GGGTAAAAATGGTAA-TTTTGG-AAATTTA
51317 TGGTTAAAGA
Statistics
Matches: 313, Mismatches: 49, Indels: 87
0.70 0.11 0.19
Matches are distributed among these distances:
26 2 0.01
27 25 0.08
28 91 0.29
29 72 0.23
30 94 0.30
31 29 0.09
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGTAATTTTGGAAATTTAG
Found at i:50949 original size:58 final size:58
Alignment explanation
Indices: 50882--51337 Score: 364
Period size: 58 Copynumber: 7.8 Consensus size: 58
50872 TGGATGCTCA
* * *
50882 AGGGTAAAATGGTAATTTTGGAAATTTTGGGGTAAAAAATGGAATTTTTAGATA-TTCG
1 AGGGTAAAAT-GTAATTTTGGAAATTTTGGGGTTAAAAATGGAATTTTTGGAAAGTTCG
* * * * * *
50940 AGGGTAAAATGGTAATTTTGGAAAGTTTGGGGTTAAAAAATGAAAATTTTAGATA-TTTG
1 AGGGTAAAAT-GTAATTTTGGAAATTTTGGGGTT-AAAAATGGAATTTTTGGAAAGTTCG
* * * * * *
50999 AGGGTAAAATGGTAAATTTTGGAAAGTTTAGGGTTAAAAATAGAATTTTTAGACA-TTAG
1 AGGGTAAAAT-GT-AATTTTGGAAATTTTGGGGTTAAAAATGGAATTTTTGGAAAGTTCG
* * * *
51058 AGGGTAAAATGTAATTTTGGAAGGA-TTCGAGGTCAAAAATGGAA-TTTTGGAAAGTT-T
1 AGGGTAAAATGTAATTTTGGAA--ATTTTGGGGTTAAAAATGGAATTTTTGGAAAGTTCG
* *
51115 AGGGGTAAAAATGTAATTTTTAGAAA-TTAGGGGTTAAAAATGG-ATTTTTGG-AAGTTCG
1 A-GGGT-AAAATGTAA-TTTTGGAAATTTTGGGGTTAAAAATGGAATTTTTGGAAAGTTCG
** * * * *
51173 AGGAAAAAATGTACTTTTTTGAAAATTTAGGGTTAAAAATGGAA-TTTTGGAAAGTTCG
1 AGGGTAAAATGTA-ATTTTGGAAATTTTGGGGTTAAAAATGGAATTTTTGGAAAGTTCG
* *
51231 -GGGTAAAAATGCAATTTTTGG-AATATTTAGGGTTAAAAATGGAA--TTTGGAAAGTTCG
1 AGGGT-AAAATGTAA-TTTTGGAAAT-TTTGGGGTTAAAAATGGAATTTTTGGAAAGTTCG
* * ** *
51288 GGGGTAAAATGTAATTTTTGGAAAATTTATGGTTAAAGAATGAAATTTTT
1 AGGGTAAAATGTAA-TTTTGGAAATTTTGGGGTTAAA-AATGGAATTTTT
51338 TAAGGTTTAG
Statistics
Matches: 336, Mismatches: 40, Indels: 42
0.80 0.10 0.10
Matches are distributed among these distances:
56 16 0.05
57 90 0.27
58 127 0.38
59 73 0.22
60 30 0.09
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (58 bp):
AGGGTAAAATGTAATTTTGGAAATTTTGGGGTTAAAAATGGAATTTTTGGAAAGTTCG
Found at i:51006 original size:59 final size:59
Alignment explanation
Indices: 50882--51079 Score: 287
Period size: 59 Copynumber: 3.4 Consensus size: 59
50872 TGGATGCTCA
* * *
50882 AGGGTAAAATGGTAATTTTGGAAATTTTGGGG-TAAAAAATGGAATTTTTAGATATTCG
1 AGGGTAAAATGGTAATTTTGGAAAGTTTGGGGTTAAAAAATGAAATTTTTAGATATTAG
* *
50940 AGGGTAAAATGGTAATTTTGGAAAGTTTGGGGTTAAAAAATGAAAATTTTAGATATTTG
1 AGGGTAAAATGGTAATTTTGGAAAGTTTGGGGTTAAAAAATGAAATTTTTAGATATTAG
* *
50999 AGGGTAAAATGGTAAATTTTGGAAAGTTTAGGGTT-AAAAAT-AGAATTTTTAGACATTAG
1 AGGGTAAAATGGT-AATTTTGGAAAGTTTGGGGTTAAAAAATGA-AATTTTTAGATATTAG
51058 AGGGTAAAAT-GTAATTTTGGAA
1 AGGGTAAAATGGTAATTTTGGAA
51080 GGATTCGAGG
Statistics
Matches: 129, Mismatches: 8, Indels: 7
0.90 0.06 0.05
Matches are distributed among these distances:
57 10 0.08
58 34 0.26
59 65 0.50
60 20 0.16
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (59 bp):
AGGGTAAAATGGTAATTTTGGAAAGTTTGGGGTTAAAAAATGAAATTTTTAGATATTAG
Found at i:51116 original size:87 final size:84
Alignment explanation
Indices: 51004--51253 Score: 256
Period size: 86 Copynumber: 2.9 Consensus size: 84
50994 ATTTGAGGGT
*
51004 AAAATGGTAAATTTTGGAAAGTTTAGGGTTAAAAATAGAATTTTTAGACATTAGAGGG-T-AAAA
1 AAAATGG--AATTTTGGAAAGTTTAGGGTTAAAAAT-GAATTTTTAGAAATTAG-GGGTTAAAAA
* *
51067 TGTAATTTTGGAAGGATTCGAGGTCA
62 TGGAATTTTGGAA-G-TTCGAGG-AA
*
51093 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTAGAAATTAGGGGTTAAAAATGG
1 AAAATGGAATTTTGGAAAGTTTAGGGTTAAAAATG-AATTTTTAGAAATTAGGGGTTAAAAATGG
*
51158 ATTTTTGGAAGTTCGAGGAA
65 AATTTTGGAAGTTCGAGGAA
* * * * * *
51178 AAAATGTACTTTTTTGAAAATTTAGGGTTAAAAATGGAA-TTTTGGAAAGTTCGGGG-TAAAAAT
1 AAAATGGA-ATTTTGGAAAGTTTAGGGTTAAAAAT-GAATTTTTAGAAA-TTAGGGGTTAAAAAT
*
51241 GCAATTTTTGGAA
63 GGAA-TTTTGGAA
51254 TATTTAGGGT
Statistics
Matches: 140, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
85 25 0.18
86 49 0.35
87 44 0.31
88 15 0.11
89 7 0.05
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (84 bp):
AAAATGGAATTTTGGAAAGTTTAGGGTTAAAAATGAATTTTTAGAAATTAGGGGTTAAAAATGGA
ATTTTGGAAGTTCGAGGAA
Found at i:51211 original size:115 final size:115
Alignment explanation
Indices: 51092--51336 Score: 334
Period size: 115 Copynumber: 2.1 Consensus size: 115
51082 ATTCGAGGTC
*
51092 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTAGAA-A-TTAGGGGTTAAAAA
1 AAAAATGGAATTTTGGAAAG-TTAGGGGTAAAAATGCAATTTTTAGAATATTTA-GGGTTAAAAA
* * *
51155 TGGATTTTTGG-AAGTTCGAGGAAAAAATGTACTTTTTTGAAAATTTAGGGTT
64 TGGA-ATTTGGAAAGTTCGAGGAAAAAATGTAATTTTTGGAAAATTTAGGGTT
* *
51207 AAAAATGGAATTTTGGAAAGTTCGGGGTAAAAATGCAATTTTTGGAATATTTAGGGTTAAAAATG
1 AAAAATGGAATTTTGGAAAGTTAGGGGTAAAAATGCAATTTTTAGAATATTTAGGGTTAAAAATG
* ** *
51272 GAATTTGGAAAGTTCGGGGGTAAAATGTAATTTTTGGAAAATTTATGGTT
66 GAATTTGGAAAGTTCGAGGAAAAAATGTAATTTTTGGAAAATTTAGGGTT
*
51322 AAAGAATGAAATTTT
1 AAA-AATGGAATTTT
51337 TTAAGGTTTA
Statistics
Matches: 115, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
114 29 0.25
115 73 0.63
116 13 0.11
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (115 bp):
AAAAATGGAATTTTGGAAAGTTAGGGGTAAAAATGCAATTTTTAGAATATTTAGGGTTAAAAATG
GAATTTGGAAAGTTCGAGGAAAAAATGTAATTTTTGGAAAATTTAGGGTT
Found at i:51324 original size:29 final size:29
Alignment explanation
Indices: 50882--51324 Score: 170
Period size: 29 Copynumber: 15.3 Consensus size: 29
50872 TGGATGCTCA
*
50882 AGGG-TAAAATGGTAA-TTTTGGAAATTTT
1 AGGGTTAAAATGG-AATTTTTGGAAAATTT
* * * * *
50910 GGGGTAAAAAATGGAATTTTTAG-ATATTCG
1 AGGGT-TAAAATGGAATTTTTGGAAAATT-T
*
50940 AGGG-TAAAATGGTAA-TTTTGGAAAGTTT
1 AGGGTTAAAATGG-AATTTTTGGAAAATTT
* * * * *
50968 GGGGTTAAAAAATGAAAATTTTAG-ATATTT
1 AGGGTT--AAAATGGAATTTTTGGAAAATTT
* *
50998 GAGGG-TAAAATGGTAAATTTTGGAAAGTTT
1 -AGGGTTAAAATGG-AATTTTTGGAAAATTT
* * *
51028 AGGGTTAAAAATAGAATTTTTAG-ACA-TT
1 AGGGTT-AAAATGGAATTTTTGGAAAATTT
* * *
51056 AGAGGGTAAAATGTAA-TTTTGGAAGGA-TT
1 AG-GGTTAAAATGGAATTTTTGGAA-AATTT
* * *
51085 CGAGGTCAAAAATGGAA-TTTTGGAAAGTTT
1 AG-GGT-TAAAATGGAATTTTTGGAAAATTT
* * *
51115 AGGGGTAAAAATGTAATTTTTAG-AAA-TT
1 A-GGGTTAAAATGGAATTTTTGGAAAATTT
*
51143 AGGGGTTAAAAATGG-ATTTTTGG--AAGTT
1 A-GGGTT-AAAATGGAATTTTTGGAAAATTT
* ** * * *
51171 CGAGGAAAAAATGTACTTTTTTGAAAATTT
1 AG-GGTTAAAATGGAATTTTTGGAAAATTT
* *
51201 AGGGTTAAAAATGGAA-TTTTGGAAAGTTC
1 AGGGTT-AAAATGGAATTTTTGGAAAATTT
* * * *
51230 GGGGTAAAAATGCAATTTTTGGAATATTT
1 AGGGTTAAAATGGAATTTTTGGAAAATTT
* *
51259 AGGGTTAAAAATGGAA--TTTGGAAAGTTC
1 AGGGTT-AAAATGGAATTTTTGGAAAATTT
* * *
51287 GGGGGTAAAATGTAATTTTTGGAAAATTT
1 AGGGTTAAAATGGAATTTTTGGAAAATTT
*
51316 ATGGTTAAA
1 AGGGTTAAA
51325 GAATGAAATT
Statistics
Matches: 302, Mismatches: 80, Indels: 65
0.68 0.18 0.15
Matches are distributed among these distances:
27 22 0.07
28 82 0.27
29 97 0.32
30 80 0.26
31 21 0.07
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.35
Consensus pattern (29 bp):
AGGGTTAAAATGGAATTTTTGGAAAATTT
Found at i:52514 original size:13 final size:13
Alignment explanation
Indices: 52496--52530 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
52486 TTTTTGTTAA
*
52496 TATTTATTAATGC
1 TATTTATTAATAC
*
52509 TATTTATTACTAC
1 TATTTATTAATAC
52522 TATTTATTA
1 TATTTATTA
52531 TTAATGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (13 bp):
TATTTATTAATAC
Found at i:52542 original size:12 final size:12
Alignment explanation
Indices: 52525--52572 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
52515 TTACTACTAT
*
52525 TTATTATTAATG
1 TTATTATTAATA
52537 TTATTATTAATA
1 TTATTATTAATA
52549 TTATTATTAATAA
1 TTATTATTAAT-A
*
52562 TTACTATTAAT
1 TTATTATTAAT
52573 TCATTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
12 22 0.67
13 11 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:53265 original size:23 final size:23
Alignment explanation
Indices: 53240--53285 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53230 TTCGACATTA
53240 TTTAAATAAAATTTAAATTTAAAT
1 TTTAAAT-AAATTTAAATTTAAAT
*
53264 TTTCAATAAATTTAAATTTAAA
1 TTTAAATAAATTTAAATTTAAA
53286 ATAAACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAATAAATTTAAATTTAAAT
Found at i:53273 original size:17 final size:17
Alignment explanation
Indices: 53253--53315 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
53243 AAATAAAATT
*
53253 TAAATTTAAATTTTCAA
1 TAAATTTAAATTTTAAA
*
53270 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTTAAA
*
53287 TAAACTT-AATTTTAAAA
1 TAAATTTAAATTTT-AAA
*
53304 TAAATCTAAATT
1 TAAATTTAAATT
53316 CTATTGGGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 5 0.13
17 29 0.76
18 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTTAAA
Found at i:53941 original size:53 final size:51
Alignment explanation
Indices: 53878--54058 Score: 240
Period size: 51 Copynumber: 3.5 Consensus size: 51
53868 CTCGCATTTA
* **
53878 TTACTCACGATGA-AATATAGTCATCGGACCTCTTGTTCCGTATAGGAATTCAT
1 TTACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTATAGG-ATTCAT
* * *
53931 ATACTCACGATGACACTGAGTCATCGGACCTTTAATCCATCAT-GGATTCAT
1 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGT-ATAGGATTCAT
* *
53982 TTATTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
1 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCAT
54033 TTACTCACGATGACACTTAGTCATCG
1 TTACTCACGATGACACTTAGTCATCG
54059 AATCCTTTCG
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
50 1 0.01
51 75 0.66
52 8 0.07
53 27 0.24
54 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (51 bp):
TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCAT
Found at i:56417 original size:32 final size:32
Alignment explanation
Indices: 56381--56444 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
56371 GCTTTGGTTT
*
56381 GTGCTGATGTGTATTAAATGTTGAAATTGTTA
1 GTGCTAATGTGTATTAAATGTTGAAATTGTTA
56413 GTGCTAATGTGTATTAAATGTTGAAATTGTTA
1 GTGCTAATGTGTATTAAATGTTGAAATTGTTA
56445 TTGAGGAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.44
Consensus pattern (32 bp):
GTGCTAATGTGTATTAAATGTTGAAATTGTTA
Found at i:61048 original size:21 final size:23
Alignment explanation
Indices: 60999--61050 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
60989 AGAGAGTTAA
60999 ATTTAATAAAATAATATGGATGTGT
1 ATTTAATAAAATAATAT-G-TGTGT
61024 -TTTAATAAAAT-ATAT-TGTGT
1 ATTTAATAAAATAATATGTGTGT
61044 ATTTAAT
1 ATTTAAT
61051 TTCGTAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
23 4 0.15
24 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (23 bp):
ATTTAATAAAATAATATGTGTGT
Found at i:64838 original size:52 final size:52
Alignment explanation
Indices: 64739--65029 Score: 424
Period size: 52 Copynumber: 5.6 Consensus size: 52
64729 TTCCCATTTA
* * *
64739 ATACTCACGATGACACAAAGTCATCGGACCTTA-AATCTGTAATAGGA-TCTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAA-AGGATTC-AT
* ** * *
64791 ATATTCAAAATGACACATAGTCATCGAACCTCAAAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
64843 ATACTCATGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
64895 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
64947 ATACTCACGATGACATATAGTCATCGGACCTCATAATTCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
64999 ATACTTACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
65030 TTTTGCATTT
Statistics
Matches: 217, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
52 207 0.95
53 10 0.05
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:72178 original size:20 final size:21
Alignment explanation
Indices: 72153--72197 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
72143 CAATGGTATA
*
72153 GATACCTTTTA-TAAAATATC
1 GATACCTTCTATTAAAATATC
*
72173 GATACCTTCTATTAAAGTATC
1 GATACCTTCTATTAAAATATC
72194 GATA
1 GATA
72198 TTTTACCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
GATACCTTCTATTAAAATATC
Found at i:72193 original size:21 final size:20
Alignment explanation
Indices: 72148--72197 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
72138 TTGTGCAATG
* *
72148 GTATAGATACCTTTTATAAA
1 GTATCGATACCTTCTATAAA
*
72168 ATATCGATACCTTCTATTAAA
1 GTATCGATACCTTCTA-TAAA
72189 GTATCGATA
1 GTATCGATA
72198 TTTTACCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (20 bp):
GTATCGATACCTTCTATAAA
Found at i:77317 original size:7 final size:7
Alignment explanation
Indices: 77293--77331 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
77283 TTGACCTACA
77293 GTTGACC
1 GTTGACC
*
77300 GTTTGATC
1 G-TTGACC
77308 GTTGACC
1 GTTGACC
77315 GTTGACC
1 GTTGACC
*
77322 GTTGATC
1 GTTGACC
77329 GTT
1 GTT
77332 AACTTTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.38
Consensus pattern (7 bp):
GTTGACC
Found at i:77981 original size:2 final size:2
Alignment explanation
Indices: 77974--78008 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
77964 TGGGATATAA
*
77974 AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
78009 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:80606 original size:12 final size:12
Alignment explanation
Indices: 80589--80615 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
80579 GAAAAGGGCA
80589 ACTCTGAGAACT
1 ACTCTGAGAACT
80601 ACTCTGAGAACT
1 ACTCTGAGAACT
80613 ACT
1 ACT
80616 GATGACCGAC
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:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (12 bp):
ACTCTGAGAACT
Found at i:82875 original size:50 final size:50
Alignment explanation
Indices: 82816--82918 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
82806 AGTTGGGAGG
82816 ATTTCTTACCACTGGTTGAATACGATTAAAATAACAATTACCAAGCCAGT
1 ATTTCTTACCACTGGTTGAATACGATTAAAATAACAATTACCAAGCCAGT
* *
82866 ATTTCTTACCACTGGTTGAATACGATTATAATAACAATTACCAGGCCAGT
1 ATTTCTTACCACTGGTTGAATACGATTAAAATAACAATTACCAAGCCAGT
82916 ATT
1 ATT
82919 AAGATGGCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (50 bp):
ATTTCTTACCACTGGTTGAATACGATTAAAATAACAATTACCAAGCCAGT
Found at i:83721 original size:25 final size:25
Alignment explanation
Indices: 83688--83739 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
83678 AATATTCCAA
83688 TTTTATTAGGTATAAAACCCATATT
1 TTTTATTAGGTATAAAACCCATATT
83713 TTTTATTAGGTATAAAACCCATATT
1 TTTTATTAGGTATAAAACCCATATT
83738 TT
1 TT
83740 CTCCTTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (25 bp):
TTTTATTAGGTATAAAACCCATATT
Found at i:93195 original size:55 final size:56
Alignment explanation
Indices: 93127--93232 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 56
93117 ATCAAAATCC
* * *
93127 AAAAGTTTGAGTTGAAAACCTGAAAGGGCAGTTCAAACTAGC-AAAAAAAACCCCA
1 AAAAGTTCGAGTTGAAAACCTGAAAGGACAGCTCAAACTAGCGAAAAAAAACCCCA
* *
93182 AAAAGTTCGAGTTGAAAACCTTAAAGGACAGCTCAAAGTAGCGAAAAAAAA
1 AAAAGTTCGAGTTGAAAACCTGAAAGGACAGCTCAAACTAGCGAAAAAAAA
93233 AAGAAAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 37 0.82
56 8 0.18
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (56 bp):
AAAAGTTCGAGTTGAAAACCTGAAAGGACAGCTCAAACTAGCGAAAAAAAACCCCA
Found at i:93239 original size:6 final size:6
Alignment explanation
Indices: 93224--93267 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
93214 TCAAAGTAGC
*
93224 GAAAAA -AAAAA G-AAAA GAAAAA G--AGA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
93268 AAGAGGGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
4 3 0.09
5 10 0.31
6 19 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:93252 original size:15 final size:16
Alignment explanation
Indices: 93236--93271 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
93226 AAAAAAAAAG
93236 AAAAGAAAAAGAGAGA
1 AAAAGAAAAAGAGAGA
93252 AAAAGAAAAAGA-A-A
1 AAAAGAAAAAGAGAGA
93266 AAAAGA
1 AAAAGA
93272 GGGAGGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 1 0.05
16 12 0.60
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAGAGA
Found at i:93261 original size:22 final size:21
Alignment explanation
Indices: 93230--93272 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
93220 TAGCGAAAAA
*
93230 AAAAAGAAAAGAAAAAGAGAG
1 AAAAAGAAAAGAAAAAAAGAG
93251 AAAAAGAAAAAGAAAAAAAGAG
1 AAAAAG-AAAAGAAAAAAAGAG
93273 GGAGGGGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAGAAAAAAAGAG
Found at i:93987 original size:28 final size:28
Alignment explanation
Indices: 93947--94010 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
93937 GATTTCACGT
93947 TGAGGACACCAGACTTGAAAAGAAGACA
1 TGAGGACACCAGACTTGAAAAGAAGACA
93975 TGAGGACACCAGACTTGAAAAGAAGACA
1 TGAGGACACCAGACTTGAAAAGAAGACA
*
94003 TGATGACA
1 TGAGGACA
94011 TATCAACGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.12
Consensus pattern (28 bp):
TGAGGACACCAGACTTGAAAAGAAGACA
Found at i:94594 original size:82 final size:82
Alignment explanation
Indices: 94437--94784 Score: 389
Period size: 82 Copynumber: 4.2 Consensus size: 82
94427 TACATCATCT
* * * * *
94437 CATCCAATCTCTTACCCCGACCAT-GGGCAGAGTAAAGAACATCTAATATTTTACCCTAACCAGA
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGATCATCCAATCTTTTACCCTAACCAGA
* * *
94501 AGGCAGATTGAAAACAC
66 GGGTAGATTGAAGACAC
* *
94518 CATCCAATCTCTTACCCCGACCATGGGGCAGATTAGAAG-TCATTCAATCTTTTACCCTAACAAG
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATT-GAAGATCATCCAATCTTTTACCCTAACCAG
94582 AGGGTAGATTGAAGACAC
65 AGGGTAGATTGAAGACAC
* * *
94600 CATCCAATCTCTTACCCTGACCATAGGGCAGATTGAAG-CCATCCAATCTTTTACCCTAACTCAG
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGATCATCCAATCTTTTACCCTAAC-CAG
*
94664 AGGGTAGATTGAAGCCAC
65 AGGGTAGATTGAAGACAC
* ** * * * *
94682 CATCCAATCTTTTACCCTAATC-TAGAGGGAAGATTGAAGCTACCATCCAATCTCTTACCCTAAT
1 CATCCAATCTCTTACCCCGACCAT-G-GGGCAGATTGAAG--ATCATCCAATCTTTTACCCTAA-
* *
94746 CTAGAGGGTAGATTGAAGCCAC
61 CCAGAGGGTAGATTGAAGACAC
*
94768 CATCCAATCTTTTACCC
1 CATCCAATCTCTTACCC
94785 TAATCCAAAG
Statistics
Matches: 235, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
81 49 0.21
82 113 0.48
83 15 0.06
86 57 0.24
87 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (82 bp):
CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGATCATCCAATCTTTTACCCTAACCAGA
GGGTAGATTGAAGACAC
Found at i:94759 original size:86 final size:84
Alignment explanation
Indices: 94476--94902 Score: 418
Period size: 82 Copynumber: 5.0 Consensus size: 84
94466 GAGTAAAGAA
* * * * * ** * **
94476 CATCTAATATTTTACCCTAACCAGAAGGCAGATTGAAAACACCATCCAATCTCTTACCCCGA-CC
1 CATCCAATCTTTTACCCTAACTAGAGGGTAGATTGAAGCCACCATCCAATCTTTTACCCTAATCC
94540 ATG-GGGCAGATTAGAAGT--
66 A-GAGGGCAGATT-GAAGTAC
* * * * *
94558 CATTCAATCTTTTACCCTAACAAGAGGGTAGATTGAAGACACCATCCAATCTCTTACCCTGA-CC
1 CATCCAATCTTTTACCCTAACTAGAGGGTAGATTGAAGCCACCATCCAATCTTTTACCCTAATCC
*
94622 ATAGGGCAGATTGAAG--C
66 AGAGGGCAGATTGAAGTAC
94639 CATCCAATCTTTTACCCTAACTCAGAGGGTAGATTGAAGCCACCATCCAATCTTTTACCCTAATC
1 CATCCAATCTTTTACCCTAACT-AGAGGGTAGATTGAAGCCACCATCCAATCTTTTACCCTAATC
* *
94704 TAGAGGGAAGATTGAAGCTAC
65 CAGAGGGCAGATTGAAG-TAC
*
94725 CATCCAATCTCTTACCCTAATCTAGAGGGTAGATTGAAGCCACCATCCAATCTTTTACCCTAATC
1 CATCCAATCTTTTACCCTAA-CTAGAGGGTAGATTGAAGCCACCATCCAATCTTTTACCCTAATC
* *
94790 CAAAGGGTAGATTGAAGTCAC
65 CAGAGGGCAGATTGAAGT-AC
* * ** * *
94811 TGTATCCAATCTTTTACCCCTAATCCAGAAGGACAGATTGAAGTCACCATTATCCAGTCTTTTAC
1 --CATCCAATCTTTTA-CCCTAA-CTAG-AGGGTAGATTGAAGCCACC---ATCCAATCTTTTA-
94876 CCCTAATCCAGAGGGGCAGATTGAAGT
57 CCCTAATCCAGA-GGGCAGATTGAAGT
94903 TACAACATCA
Statistics
Matches: 297, Mismatches: 30, Indels: 23
0.85 0.09 0.07
Matches are distributed among these distances:
81 24 0.08
82 103 0.35
83 15 0.05
85 1 0.00
86 78 0.26
87 2 0.01
88 12 0.04
89 10 0.03
90 16 0.05
93 12 0.04
94 11 0.04
95 13 0.04
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (84 bp):
CATCCAATCTTTTACCCTAACTAGAGGGTAGATTGAAGCCACCATCCAATCTTTTACCCTAATCC
AGAGGGCAGATTGAAGTAC
Found at i:94874 original size:48 final size:44
Alignment explanation
Indices: 94476--94902 Score: 365
Period size: 43 Copynumber: 9.9 Consensus size: 44
94466 GAGTAAAGAA
* * **
94476 CATCTAATATTTTACCCTAA-CCAGAA-GGCAGATTGAAAACAC
1 CATCCAATCTTTTACCCTAATCCAGAAGGGCAGATTGAAGTCAC
* **
94518 CATCCAATCTCTTACCCCGA-CCATG--GGGCAGATTAGAAGT---
1 CATCCAATCTTTTACCCTAATCCA-GAAGGGCAGATT-GAAGTCAC
* * * *
94558 CATTCAATCTTTTACCCTAA-CAAG-AGGGTAGATTGAAGACAC
1 CATCCAATCTTTTACCCTAATCCAGAAGGGCAGATTGAAGTCAC
* * *
94600 CATCCAATCTCTTACCCTGA-CCA-TAGGGCAGATTGAAG---C
1 CATCCAATCTTTTACCCTAATCCAGAAGGGCAGATTGAAGTCAC
* *
94639 CATCCAATCTTTTACCCTAA-CTCAG-AGGGTAGATTGAAGCCAC
1 CATCCAATCTTTTACCCTAATC-CAGAAGGGCAGATTGAAGTCAC
* *
94682 CATCCAATCTTTTACCCTAATCTAG-AGGGAAGATTGAAG-CTAC
1 CATCCAATCTTTTACCCTAATCCAGAAGGGCAGATTGAAGTC-AC
* * * *
94725 CATCCAATCTCTTACCCTAATCTAG-AGGGTAGATTGAAGCCAC
1 CATCCAATCTTTTACCCTAATCCAGAAGGGCAGATTGAAGTCAC
*
94768 CATCCAATCTTTTACCCTAATCCA-AAGGGTAGATTGAAGTCAC
1 CATCCAATCTTTTACCCTAATCCAGAAGGGCAGATTGAAGTCAC
* *
94811 TGTATCCAATCTTTTACCCCTAATCCAGAAGGACAGATTGAAGTCAC
1 --CATCCAATCTTTTA-CCCTAATCCAGAAGGGCAGATTGAAGTCAC
* *
94858 CATTATCCAGTCTTTTACCCCTAATCCAGAGGGGCAGATTGAAGT
1 C---ATCCAATCTTTTA-CCCTAATCCAGAAGGGCAGATTGAAGT
94903 TACAACATCA
Statistics
Matches: 325, Mismatches: 36, Indels: 42
0.81 0.09 0.10
Matches are distributed among these distances:
39 25 0.08
40 41 0.13
42 59 0.18
43 120 0.37
44 2 0.01
45 13 0.04
46 10 0.03
47 17 0.05
48 38 0.12
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (44 bp):
CATCCAATCTTTTACCCTAATCCAGAAGGGCAGATTGAAGTCAC
Found at i:95300 original size:25 final size:25
Alignment explanation
Indices: 95255--95303 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
95245 CCAATATAAA
* *
95255 CCCAAATTTTACCCAAGCCTAAAAG
1 CCCAAATTTAACCCAACCCTAAAAG
95280 CCCAAA-TTAACCCAACCCCTAAAA
1 CCCAAATTTAACCCAA-CCCTAAAA
95304 CAAAAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.43, C:0.37, G:0.04, T:0.16
Consensus pattern (25 bp):
CCCAAATTTAACCCAACCCTAAAAG
Found at i:105524 original size:22 final size:20
Alignment explanation
Indices: 105477--105525 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
105467 ATTTATTTTT
*
105477 ATATTATAAAAATTAAAAAA
1 ATATTTTAAAAATTAAAAAA
* *
105497 ACATTTTACAAATTAAATAAAA
1 ATATTTTAAAAATT-AA-AAAA
105519 ATATTTT
1 ATATTTT
105526 TTTTAACTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 11 0.48
21 2 0.09
22 10 0.43
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATTTTAAAAATTAAAAAA
Found at i:106056 original size:22 final size:21
Alignment explanation
Indices: 106031--106086 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
106021 ACTTTCTCTC
106031 AATTCATTCTCAATCCT-ATCTT
1 AATTC-TTCTCAATCCTCA-CTT
*
106053 AATTCTCTCTTAATCCTCACTT
1 AATTCT-TCTCAATCCTCACTT
106075 AATTC-TCTCAAT
1 AATTCTTCTCAAT
106087 TTAGTCTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 6 0.20
21 1 0.03
22 22 0.73
23 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTCTTCTCAATCCTCACTT
Found at i:106063 original size:11 final size:11
Alignment explanation
Indices: 106009--106083 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
105999 CCACTTTTTC
*
106009 AATTCACTCTT
1 AATTCTCTCTT
*
106020 AACTT-TCTCTC
1 AA-TTCTCTCTT
*
106031 AATTCAT-TCTC
1 AATTC-TCTCTT
* *
106042 AATCCTATCTT
1 AATTCTCTCTT
106053 AATTCTCTCTT
1 AATTCTCTCTT
* *
106064 AATCCTCACTT
1 AATTCTCTCTT
106075 AATTCTCTC
1 AATTCTCTC
106084 AATTTAGTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
10 3 0.06
11 44 0.88
12 3 0.06
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTCTCTCTT
Found at i:106303 original size:18 final size:17
Alignment explanation
Indices: 106262--106304 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
106252 AAATAATTTT
106262 AATTT-TAAAATTCAAA
1 AATTTATAAAATTCAAA
*
106278 ATATTTATAACAATTCTAA
1 A-ATTTATAA-AATTCAAA
106297 AATTTATA
1 AATTTATA
106305 TCTTCCACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 4 0.17
18 10 0.43
19 8 0.35
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTATAAAATTCAAA
Found at i:107026 original size:10 final size:10
Alignment explanation
Indices: 107011--107038 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
107001 CTCACATGTG
107011 ATAAAAAAAT
1 ATAAAAAAAT
107021 ATAAAAAAAT
1 ATAAAAAAAT
107031 ATAAAAAA
1 ATAAAAAA
107039 TTTAAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
ATAAAAAAAT
Found at i:111085 original size:76 final size:76
Alignment explanation
Indices: 110959--111249 Score: 500
Period size: 76 Copynumber: 3.9 Consensus size: 76
110949 TTTTTCCGAG
* *
110959 ATACCCATGTCTTATTTTTATTCGAACATATGTGTAAAGATACGTTTCGAATATACCCGAATTCG
1 ATACCCATGTCTTATTTATATTCGAACATGTGTGTAAAGATACGTTTCGAATATACCCGAATTCG
111024 AGCATTTCGAA
66 AGCATTTCGAA
111035 ATACCCATGTCTTATTTATATTCGAACATGTGTGTAAAGATACGTTTCGAATATACCCGAATTCG
1 ATACCCATGTCTTATTTATATTCGAACATGTGTGTAAAGATACGTTTCGAATATACCCGAATTCG
111100 AGCATTTCGAA
66 AGCATTTCGAA
* *
111111 ATACTCATGTCTTATTTATATTCAAACATGTGTGT--AGATACGTTTCGAATATACCCGAATTCG
1 ATACCCATGTCTTATTTATATTCGAACATGTGTGTAAAGATACGTTTCGAATATACCCGAATTCG
*
111174 AGTATTTCGAA
66 AGCATTTCGAA
*
111185 ATACCCATGTCTTACTTATATTCGAACA--TGTGTAAAGATACGTTTCGAATATACCCGAATTCG
1 ATACCCATGTCTTATTTATATTCGAACATGTGTGTAAAGATACGTTTCGAATATACCCGAATTCG
111248 AG
66 AG
111250 TAACATAACT
Statistics
Matches: 205, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
72 5 0.02
74 93 0.45
76 107 0.52
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (76 bp):
ATACCCATGTCTTATTTATATTCGAACATGTGTGTAAAGATACGTTTCGAATATACCCGAATTCG
AGCATTTCGAA
Found at i:111251 original size:74 final size:74
Alignment explanation
Indices: 110959--111249 Score: 483
Period size: 74 Copynumber: 3.9 Consensus size: 74
110949 TTTTTCCGAG
*
110959 ATACCCATGTCTTATTTTTATTCGAACATATGTGTAAAGATACGTTTCGAATATACCCGAATTCG
1 ATACCCATGTCTTATTTATATTCGAAC--ATGTGTAAAGATACGTTTCGAATATACCCGAATTCG
111024 AGCATTTCGAA
64 AGCATTTCGAA
111035 ATACCCATGTCTTATTTATATTCGAACATGTGTGTAAAGATACGTTTCGAATATACCCGAATTCG
1 ATACCCATGTCTTATTTATATTCGAACA--TGTGTAAAGATACGTTTCGAATATACCCGAATTCG
111100 AGCATTTCGAA
64 AGCATTTCGAA
* * **
111111 ATACTCATGTCTTATTTATATTCAAACATGTGTGTAGATACGTTTCGAATATACCCGAATTCGAG
1 ATACCCATGTCTTATTTATATTCGAACATGTGTAAAGATACGTTTCGAATATACCCGAATTCGAG
*
111176 TATTTCGAA
66 CATTTCGAA
*
111185 ATACCCATGTCTTACTTATATTCGAACATGTGTAAAGATACGTTTCGAATATACCCGAATTCGAG
1 ATACCCATGTCTTATTTATATTCGAACATGTGTAAAGATACGTTTCGAATATACCCGAATTCGAG
111250 TAACATAACT
Statistics
Matches: 202, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
74 104 0.51
76 98 0.49
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (74 bp):
ATACCCATGTCTTATTTATATTCGAACATGTGTAAAGATACGTTTCGAATATACCCGAATTCGAG
CATTTCGAA
Found at i:116152 original size:26 final size:24
Alignment explanation
Indices: 116111--116169 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
116101 TTAAGATGAT
116111 TATATAAAAATTTTAATAAATAAAAA
1 TATAT-AAAATTTTAA-AAATAAAAA
* *
116137 TATATAAAATTATTAAATATTAAAA
1 TATATAAAATT-TTAAAAATAAAAA
116162 TAATATAA
1 T-ATATAA
116170 TATAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATATAAAATTTTAAAAATAAAAA
Found at i:117469 original size:20 final size:19
Alignment explanation
Indices: 117435--117484 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
117425 TAAAAATTTT
* *
117435 AAAATTTATAATTTTTTAA
1 AAAATTTAAAATTTTCTAA
117454 AAAATTCTAAAATTTTCTAA
1 AAAATT-TAAAATTTTCTAA
*
117474 AAAATATAAAA
1 AAAATTTAAAA
117485 AGAAAGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTAAAATTTTCTAA
Found at i:118022 original size:24 final size:26
Alignment explanation
Indices: 117965--118022 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
117955 ATAATTTTTG
*
117965 TAATTTTATATTTTTTCTATTTTTTAA
1 TAATTTTATA-TTTTTCTATTTTCTAA
117992 TAA-TTTATA-TTTTCTA-TTTCTAA
1 TAATTTTATATTTTTCTATTTTCTAA
118015 TAATTTTA
1 TAATTTTA
118023 ATAAATTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 9 0.31
24 11 0.38
26 6 0.21
27 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (26 bp):
TAATTTTATATTTTTCTATTTTCTAA
Found at i:118045 original size:19 final size:20
Alignment explanation
Indices: 118018--118062 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
118008 TTTCTAATAA
118018 TTTTAATAAA-TTTTGTAAT
1 TTTTAATAAATTTTTGTAAT
*
118037 TTTTTATAAATTTTTGTAAT
1 TTTTAATAAATTTTTGTAAT
118057 TTTTAA
1 TTTTAA
118063 AGATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTAATAAATTTTTGTAAT
Found at i:119682 original size:17 final size:17
Alignment explanation
Indices: 119635--119685 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
119625 AATTAATAAC
*
119635 ATAACATAATCATAGTA
1 ATAATATAATCATAGTA
119652 ATAA-ATAA--A-A-TA
1 ATAATATAATCATAGTA
119664 ATAATATAATCATAGTA
1 ATAATATAATCATAGTA
119681 ATAAT
1 ATAAT
119686 GACAACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 6 0.21
13 5 0.17
14 1 0.03
15 1 0.03
16 5 0.17
17 11 0.38
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (17 bp):
ATAATATAATCATAGTA
Found at i:119892 original size:17 final size:18
Alignment explanation
Indices: 119868--119909 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
119858 TTTAAATAGC
119868 ATAAAATAACAATAAACA
1 ATAAAATAACAATAAACA
**
119886 A-AAAATAATTATAAACA
1 ATAAAATAACAATAAACA
119903 ATAAAAT
1 ATAAAAT
119910 TGTAGGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAAAATAACAATAAACA
Found at i:120021 original size:11 final size:11
Alignment explanation
Indices: 119960--120047 Score: 76
Period size: 11 Copynumber: 8.1 Consensus size: 11
119950 ATACCTATAA
119960 AAATAATAAAT
1 AAATAATAAAT
*
119971 AAA-ATTAAATT
1 AAATAATAAA-T
119982 AAAT-ATAAAGT
1 AAATAATAAA-T
*
119993 AAA-AATGAAT
1 AAATAATAAAT
*
120003 AAAAAATAAAT
1 AAATAATAAAT
*
120014 AAATAATAAGT
1 AAATAATAAAT
*
120025 AAATAATATAT
1 AAATAATAAAT
120036 AAA-AATTAAAT
1 AAATAA-TAAAT
120047 A
1 A
120048 CTACATAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
10 11 0.18
11 51 0.82
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:120038 original size:33 final size:32
Alignment explanation
Indices: 119960--120047 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 32
119950 ATACCTATAA
119960 AAATAATAA-ATAAAATTAAATTAAATATAAAGT
1 AAATAATAATA-AAAATTAAA-TAAATATAAAGT
*
119993 AAA-AATGAATAAAAAATAAATAAATA-ATAAGT
1 AAATAAT-AATAAAAATTAAATAAATATA-AAGT
120025 AAATAATATATAAAAATTAAATA
1 AAATAATA-ATAAAAATTAAATA
120048 CTACATAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
31 1 0.02
32 17 0.35
33 29 0.60
34 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (32 bp):
AAATAATAATAAAAATTAAATAAATATAAAGT
Found at i:120981 original size:14 final size:14
Alignment explanation
Indices: 120964--120994 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
120954 ATTTTTTACA
120964 TTTGATTTTGTGTT
1 TTTGATTTTGTGTT
120978 TTTGATTTTGTGTT
1 TTTGATTTTGTGTT
120992 TTT
1 TTT
120995 ATAACACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.19, T:0.74
Consensus pattern (14 bp):
TTTGATTTTGTGTT
Found at i:125215 original size:59 final size:59
Alignment explanation
Indices: 125152--125270 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
125142 ATAATTGTAC
125152 ATGATACATGAAAGGCGCAAGGAGCCTAGTTAATGAGCGTGGACGACATATTGAGTGAG
1 ATGATACATGAAAGGCGCAAGGAGCCTAGTTAATGAGCGTGGACGACATATTGAGTGAG
*
125211 ATGATACATGAAAGGCGCAAGGAGCCTAGTTAATGGGCGTGGACGACATATTGAGTGAG
1 ATGATACATGAAAGGCGCAAGGAGCCTAGTTAATGAGCGTGGACGACATATTGAGTGAG
125270 A
1 A
125271 GACTCTCTGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (59 bp):
ATGATACATGAAAGGCGCAAGGAGCCTAGTTAATGAGCGTGGACGACATATTGAGTGAG
Found at i:129743 original size:108 final size:110
Alignment explanation
Indices: 129554--129770 Score: 384
Period size: 108 Copynumber: 2.0 Consensus size: 110
129544 AAAGTGAATA
*
129554 AAGCCTTAGCACAGTTGGTAAAAGGTGGATGTCTTGGGTTGTAAGTACCCAAGTTGGAGAGTTAT
1 AAGCCTTAGCACAGTTGGTAAAAGGTGGATGCCTTGGGTTGTAAGTACCCAAGTTGGAGAGTTAT
129619 TATACATAATTATATGTGTGGGTCTCC-AA-CTATCGTGGGTTGT
66 TATACATAATTATATGTGTGGGTCTCCAAATCTATCGTGGGTTGT
*
129662 AAGCCTTAGCACAGTTGGTAAAAGGTGGATGCCTTGGGTTGTAAGTATCCAAGTTGGAGAGTTAT
1 AAGCCTTAGCACAGTTGGTAAAAGGTGGATGCCTTGGGTTGTAAGTACCCAAGTTGGAGAGTTAT
*
129727 TATACATAATTATATGTGTGGGTTTCCAAATTCTATCGTGGGTT
66 TATACATAATTATATGTGTGGGTCTCCAAA-TCTATCGTGGGTT
129771 ATTTTTATAC
Statistics
Matches: 103, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
108 89 0.86
109 2 0.02
111 12 0.12
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.34
Consensus pattern (110 bp):
AAGCCTTAGCACAGTTGGTAAAAGGTGGATGCCTTGGGTTGTAAGTACCCAAGTTGGAGAGTTAT
TATACATAATTATATGTGTGGGTCTCCAAATCTATCGTGGGTTGT
Found at i:132555 original size:16 final size:16
Alignment explanation
Indices: 132536--132573 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
132526 CTTTTTCTTC
132536 TTTTTTTTTT-TAAAT
1 TTTTTTTTTTCTAAAT
* *
132551 TTTTTATTTTCTCAAT
1 TTTTTTTTTTCTAAAT
132567 TTTTTTT
1 TTTTTTT
132574 CAATCAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTTCTAAAT
Found at i:134840 original size:40 final size:40
Alignment explanation
Indices: 134782--134917 Score: 173
Period size: 40 Copynumber: 3.4 Consensus size: 40
134772 TTCCCTGTTA
* * ***
134782 TATCGGGCTTAATACCTAGCAGGCTTCGTGTTGGTGTATT
1 TATCGGGCTTAGTGCCTAGCAGGCTTCGTGACAGTGTATT
* *
134822 TATCGAGCTTAGTGCCTAGCAGGCTTCGTGACATTGTATT
1 TATCGGGCTTAGTGCCTAGCAGGCTTCGTGACAGTGTATT
* *
134862 TATCGGGCTTAGTGCCTAGCAGGCTTCATGCCAGTGTATT
1 TATCGGGCTTAGTGCCTAGCAGGCTTCGTGACAGTGTATT
* *
134902 TATCGGGTTTCGTGCC
1 TATCGGGCTTAGTGCC
134918 AGTGTATTTA
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (40 bp):
TATCGGGCTTAGTGCCTAGCAGGCTTCGTGACAGTGTATT
Found at i:134929 original size:64 final size:64
Alignment explanation
Indices: 134846--134972 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 64
134836 CCTAGCAGGC
* *
134846 TTCGTGACATTGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCCAGTGTATTTATCGGGT
1 TTCGTGACAGTGTATTTATCCGGCTTAGTGCCTAGCAGGCTTCATGCCAGTGTATTTATCGGGT
* * * *
134910 TTCGTGCCAGTGTATTTATCCGGCTTAGTGCCTAGCAGGCTTCGTGTCGGTGTATTTATCGGG
1 TTCGTGACAGTGTATTTATCCGGCTTAGTGCCTAGCAGGCTTCATGCCAGTGTATTTATCGGG
134973 CTTAATGCCA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37
Consensus pattern (64 bp):
TTCGTGACAGTGTATTTATCCGGCTTAGTGCCTAGCAGGCTTCATGCCAGTGTATTTATCGGGT
Found at i:134940 original size:24 final size:24
Alignment explanation
Indices: 134890--134941 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
134880 GCAGGCTTCA
* * *
134890 TGCCAGTGTATTTATCGGGTTTCG
1 TGCCAGTGTATTTATCCGGCTTAG
134914 TGCCAGTGTATTTATCCGGCTTAG
1 TGCCAGTGTATTTATCCGGCTTAG
134938 TGCC
1 TGCC
134942 TAGCAGGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.38
Consensus pattern (24 bp):
TGCCAGTGTATTTATCCGGCTTAG
Found at i:134954 original size:40 final size:40
Alignment explanation
Indices: 134910--135028 Score: 139
Period size: 40 Copynumber: 3.0 Consensus size: 40
134900 TTTATCGGGT
*
134910 TTCGTGCCAGTGTATTTATCCGGCTTAGTGCCTAGCAGGC
1 TTCGTGCCAGTGTATTTATCAGGCTTAGTGCCTAGCAGGC
* * * * * *
134950 TTCGTGTCGGTGTATTTATCGGGCTTAATGCCAAGTAGGC
1 TTCGTGCCAGTGTATTTATCAGGCTTAGTGCCTAGCAGGC
* * *
134990 TTCGTGCCTGTGTATATTATCAGGCTTTGAGCCTAGCAG
1 TTCGTGCCAGTGTAT-TTATCAGGCTTAGTGCCTAGCAG
135029 ATTTCGTGTC
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 47 0.73
41 17 0.27
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (40 bp):
TTCGTGCCAGTGTATTTATCAGGCTTAGTGCCTAGCAGGC
Found at i:134990 original size:104 final size:105
Alignment explanation
Indices: 134815--135010 Score: 297
Period size: 104 Copynumber: 1.9 Consensus size: 105
134805 CTTCGTGTTG
* * *
134815 GTGTATTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGACATTGTATTTATCGGGCTTAGTGCCTA
1 GTGTATTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGACAGTGTATTTATCGGGCTTAATGCCAA
134880 GCAGGCTTCATGCCAGTGTAT-TTATCGGGTTTCGTGCCA
66 GCAGGCTTCATGCCAGTGTATATTATCGGGTTTCGTGCCA
* *
134919 GTGTATTTATCCG-GCTTAGTGCCTAGCAGGCTTCGTGTCGGTGTATTTATCGGGCTTAATGCCA
1 GTGTATTTAT-CGAGCTTAGTGCCTAGCAGGCTTCGTGACAGTGTATTTATCGGGCTTAATGCCA
* * *
134983 AGTAGGCTTCGTGCCTGTGTATATTATC
65 AGCAGGCTTCATGCCAGTGTATATTATC
135011 AGGCTTTGAG
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
104 75 0.91
105 7 0.09
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (105 bp):
GTGTATTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGACAGTGTATTTATCGGGCTTAATGCCAA
GCAGGCTTCATGCCAGTGTATATTATCGGGTTTCGTGCCA
Found at i:135766 original size:22 final size:22
Alignment explanation
Indices: 135738--135781 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
135728 ATATATTAAT
*
135738 AATCATACCTAGTTAGTTGATG
1 AATCATACCTAGTTAGCTGATG
135760 AATCATACCTAGTTAGCTGATG
1 AATCATACCTAGTTAGCTGATG
135782 CTTAGTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (22 bp):
AATCATACCTAGTTAGCTGATG
Found at i:138081 original size:7 final size:7
Alignment explanation
Indices: 138061--138180 Score: 135
Period size: 7 Copynumber: 17.9 Consensus size: 7
138051 AATTGAAAAC
138061 GAGAAAG
1 GAGAAAG
138068 G-GAAAG
1 GAGAAAG
138074 GAGAAAG
1 GAGAAAG
* *
138081 GGGGAAG
1 GAGAAAG
138088 G-GAAAG
1 GAGAAAG
138094 G-GAAAG
1 GAGAAAG
138100 GAGAAAG
1 GAGAAAG
138107 GAGAAAG
1 GAGAAAG
138114 GAGAAAG
1 GAGAAAG
138121 GAGAAAG
1 GAGAAAG
*
138128 GAAAAAGG
1 GAGAAA-G
* *
138136 GGGAAGG
1 GAGAAAG
*
138143 GGGAAAG
1 GAGAAAG
138150 G-GAAA-
1 GAGAAAG
138155 G-GAAAG
1 GAGAAAG
138161 GAGAAAG
1 GAGAAAG
138168 GAGAAAG
1 GAGAAAG
138175 GAGAAA
1 GAGAAA
138181 AGAGGAAGGG
Statistics
Matches: 100, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
5 5 0.05
6 22 0.22
7 69 0.69
8 4 0.04
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (7 bp):
GAGAAAG
Found at i:138136 original size:47 final size:45
Alignment explanation
Indices: 138107--138200 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 45
138097 AAGGAGAAAG
138107 GAGAAAGGAGAAAGGAGAAAGGAAAAAGGGGGAAGGGGGAAAGGGAAA
1 GAGAAAGGAGAAAGGAGAAAGGAAAAA--GGGAA-GGGGAAAGGGAAA
*
138155 G-GAAAGGAGAAAGGAGAAAGGAGAAAAGAGGAAGGGGGAAGGGAAA
1 GAGAAAGGAGAAAGGAGAAAGGA-AAAAG-GGAAGGGGAAAGGGAAA
138201 TGGGGGAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 13 0.30
47 25 0.58
48 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (45 bp):
GAGAAAGGAGAAAGGAGAAAGGAAAAAGGGAAGGGGAAAGGGAAA
Found at i:138142 original size:54 final size:52
Alignment explanation
Indices: 138061--138200 Score: 210
Period size: 54 Copynumber: 2.6 Consensus size: 52
138051 AATTGAAAAC
138061 GAGAAAGG-GAAAGGAGAAAGGGGGAAGGGAAAGGGAAAGGAGAAAGGAGAAAG
1 GAGAAAGGAGAAAGGAGAAAGGGGGAAGGGAAAGGGAAA-G-GAAAGGAGAAAG
*
138114 GAGAAAGGAGAAAGGAAAAAGGGGGAAGGGGGAAAGGGAAAGGAAAGGAGAAAG
1 GAGAAAGGAGAAAGGAGAAAGGGGGAA--GGGAAAGGGAAAGGAAAGGAGAAAG
* *
138168 GAGAAAGGAGAAAAGAGGAAGGGGGAAGGGAAA
1 GAGAAAGGAGAAAGGAGAAAGGGGGAAGGGAAA
138201 TGGGGGAGAG
Statistics
Matches: 80, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
52 6 0.08
53 8 0.10
54 53 0.66
55 1 0.01
56 12 0.15
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (52 bp):
GAGAAAGGAGAAAGGAGAAAGGGGGAAGGGAAAGGGAAAGGAAAGGAGAAAG
Found at i:138197 original size:61 final size:61
Alignment explanation
Indices: 138055--138189 Score: 193
Period size: 61 Copynumber: 2.2 Consensus size: 61
138045 CCTTAAAATT
* * *
138055 GAAAACGAGAAAGG-GAAAGGAGAAAGGGGGAAGGGAAAGGGAAAGGAGAAAGGAGAAAGGA
1 GAAAA-GAGAAAGGAAAAAGGGGGAAGGGGGAAGGGAAAGGGAAAGGAGAAAGGAGAAAGGA
*
138116 GAAAGGAGAAAGGAAAAAGGGGGAAGGGGGAAAGGGAAA-GGAAAGGAGAAAGGAGAAAGGA
1 GAAAAGAGAAAGGAAAAAGGGGGAAGGGGG-AAGGGAAAGGGAAAGGAGAAAGGAGAAAGGA
*
138177 GAAAAGAGGAAGG
1 GAAAAGAGAAAGG
138190 GGGAAGGGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
60 8 0.12
61 50 0.76
62 8 0.12
ACGTcount: A:0.53, C:0.01, G:0.47, T:0.00
Consensus pattern (61 bp):
GAAAAGAGAAAGGAAAAAGGGGGAAGGGGGAAGGGAAAGGGAAAGGAGAAAGGAGAAAGGA
Found at i:138206 original size:61 final size:61
Alignment explanation
Indices: 138055--138207 Score: 186
Period size: 61 Copynumber: 2.5 Consensus size: 61
138045 CCTTAAAATT
*
138055 GAAAACGAGAAAGG-GAAAGGAGAAAGGGGG-AAGGGAAAGGGAAAGGAGAAAGGAGAAAGGA
1 GAAAA-GAGAAAGGAAAAAGG-GAAAGGGGGAAAGGGAAAGGGAAAGGAGAAAGGAGAAAGGA
* *
138116 GAAAGGAGAAAGGAAAAAGGGGGAAGGGGGAAAGGGAAA-GGAAAGGAGAAAGGAGAAAGGA
1 GAAAAGAGAAAGGAAAAA-GGGAAAGGGGGAAAGGGAAAGGGAAAGGAGAAAGGAGAAAGGA
* ***
138177 GAAAAGAGGAAGGGGGAAGGGAAATGGGGGA
1 GAAAAGAGAAAGGAAAAAGGGAAA-GGGGGA
138208 GAGGCTTCGG
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
60 13 0.16
61 56 0.71
62 10 0.13
ACGTcount: A:0.50, C:0.01, G:0.48, T:0.01
Consensus pattern (61 bp):
GAAAAGAGAAAGGAAAAAGGGAAAGGGGGAAAGGGAAAGGGAAAGGAGAAAGGAGAAAGGA
Found at i:139415 original size:60 final size:59
Alignment explanation
Indices: 139347--139516 Score: 225
Period size: 60 Copynumber: 2.8 Consensus size: 59
139337 TTTAGGAAAC
* *
139347 TTTAGGGGTTAAAAAGTGATTTTGGAAAAGTTTGAGAGTAAAAATGTAATTCTTGAAAAG
1 TTTAGGGGTTAAAAAGTAATTTT-GAAAAGTTTGAGGGTAAAAATGTAATTCTTGAAAAG
* * *
139407 TTTAGGGGTTAAAATA-TAATTTTTGAAAAGTTTAAGGGTTAAAATGTAATTTTTGAAAAG
1 TTTAGGGGTTAAAA-AGTAA-TTTTGAAAAGTTTGAGGGTAAAAATGTAATTCTTGAAAAG
* * * *
139467 TTTAGGGGTTAAAATGTAATTTTAAAAATTTTGAGGGTAAAAATATAATT
1 TTTAGGGGTTAAAAAGTAATTTTGAAAAGTTTGAGGGTAAAAATGTAATT
139517 TTTAAATAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
59 26 0.27
60 65 0.68
61 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.38
Consensus pattern (59 bp):
TTTAGGGGTTAAAAAGTAATTTTGAAAAGTTTGAGGGTAAAAATGTAATTCTTGAAAAG
Found at i:139446 original size:90 final size:89
Alignment explanation
Indices: 139316--139519 Score: 227
Period size: 90 Copynumber: 2.3 Consensus size: 89
139306 AGTTTCGAAG
* * * * * *
139316 AATTT-GA-GGTTAAAATGTGATTTTAGGAAACTTTAGGGGTTAAAAAGTGATTTTGGAAAAGTT
1 AATTTAGAGGGTTAAAATATAATTTTTGAAAACTTTAAGGGTTAAAAAGTAATTTTGGAAAAGTT
139379 T-GAGAGTAAAAATGTAATTCTTGAAA
66 TAG-GAGTAAAAATGTAATT-TT-AAA
* * * *
139405 AGTTTAG-GGGTTAAAATATAATTTTTGAAAAGTTTAAGGGTTAAAATGTAATTTTTGAAAAGTT
1 AATTTAGAGGGTTAAAATATAATTTTTGAAAACTTTAAGGGTTAAAAAGTAATTTTGGAAAAGTT
* *
139469 TAGGGGTTAAAATGTAATTTTAAA
66 TAGGAGTAAAAATGTAATTTTAAA
* *
139493 AATTTTGAGGGTAAAAATATAATTTTT
1 AATTTAGAGGGTTAAAATATAATTTTT
139520 AAATAAAATA
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
88 8 0.08
89 24 0.25
90 63 0.66
91 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.38
Consensus pattern (89 bp):
AATTTAGAGGGTTAAAATATAATTTTTGAAAACTTTAAGGGTTAAAAAGTAATTTTGGAAAAGTT
TAGGAGTAAAAATGTAATTTTAAA
Found at i:139522 original size:30 final size:29
Alignment explanation
Indices: 139323--139519 Score: 198
Period size: 30 Copynumber: 6.6 Consensus size: 29
139313 AAGAATTTGA
* * * *
139323 GGTTAAAATGTGATTTTAGGAAACTTTAGG
1 GGTTAAAATGTAATTTTTGAAAAGTTTA-G
* * *
139353 GGTTAAAAAGTGATTTTGGAAAAGTTTGAG
1 GGTTAAAATGTAATTTTTGAAAAGTTT-AG
* * *
139383 AGTAAAAATGTAATTCTTGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTTGAAAAGTTTA-G
*
139413 GGTTAAAATATAATTTTTGAAAAGTTTAAG
1 GGTTAAAATGTAATTTTTGAAAAGTTT-AG
139443 GGTTAAAATGTAATTTTTGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTTGAAAAGTTTA-G
* *
139473 GGTTAAAATGTAA-TTTTAAAAATTTTGAG
1 GGTTAAAATGTAATTTTTGAAAAGTTT-AG
* *
139502 GGTAAAAATATAATTTTT
1 GGTTAAAATGTAATTTTT
139520 AAATAAAATA
Statistics
Matches: 142, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
29 25 0.18
30 115 0.81
31 2 0.01
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.38
Consensus pattern (29 bp):
GGTTAAAATGTAATTTTTGAAAAGTTTAG
Found at i:140295 original size:10 final size:10
Alignment explanation
Indices: 140282--140352 Score: 61
Period size: 10 Copynumber: 7.1 Consensus size: 10
140272 GTATGCGCAG
*
140282 ATATGTATGT
1 ATATGTATAT
* *
140292 ATATATACAT
1 ATATGTATAT
* *
140302 ACATATATAT
1 ATATGTATAT
140312 ATATGTATAT
1 ATATGTATAT
**
140322 ATATACATAT
1 ATATGTATAT
* *
140332 ATATGTTTGT
1 ATATGTATAT
140342 ATATGTATAT
1 ATATGTATAT
140352 A
1 A
140353 CAAATATCAA
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
10 46 1.00
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.46
Consensus pattern (10 bp):
ATATGTATAT
Found at i:140307 original size:12 final size:12
Alignment explanation
Indices: 140292--140335 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
140282 ATATGTATGT
*
140292 ATATATACATAC
1 ATATATATATAC
*
140304 ATATATATATAT
1 ATATATATATAC
*
140316 GTATATATATAC
1 ATATATATATAC
140328 ATATATAT
1 ATATATAT
140336 GTTTGTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (12 bp):
ATATATATATAC
Found at i:140334 original size:24 final size:24
Alignment explanation
Indices: 140282--140359 Score: 93
Period size: 26 Copynumber: 3.1 Consensus size: 24
140272 GTATGCGCAG
140282 ATATGTATGTATATATACATACATAT
1 ATATGTATGTATATAT--ATACATAT
*
140308 ATATATATGTATATATATACATAT
1 ATATGTATGTATATATATACATAT
* *
140332 ATATGTTTGTATATGTATATACAAAT
1 ATATGTATGTATA--TATATACATAT
140358 AT
1 AT
140360 CAATGTACGT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.41
26 27 0.59
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (24 bp):
ATATGTATGTATATATATACATAT
Found at i:140352 original size:2 final size:2
Alignment explanation
Indices: 140291--140335 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
140281 GATATGTATG
* * * *
140291 TA TA TA TA CA TA CA TA TA TA TA TA TG TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
140333 TA T
1 TA T
140336 GTTTGTATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:141604 original size:208 final size:207
Alignment explanation
Indices: 141205--142378 Score: 1361
Period size: 208 Copynumber: 5.7 Consensus size: 207
141195 GCTTTATCTC
* * * * *
141205 TTGGTCTACTTCTCTGCATCTCATTAGAAAGATGACTGCTTCATTGTTTTAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGT
* ** * *
141270 ATCTCATCAAAAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCAGGAAA-ATGAACACTTTAT
66 ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCA-GAAAGATGACCACTTTAT
* * * * * * * * * *
141334 TGCATCAATCCACTCCTCTGTATCTTATCAGAAAGATAAGGTCTGATGTTTCACTCATATTGAGC
130 TGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGAT-AGGTTTGAAGTCTCATTCATATTGAGC
*
141399 TTCACTTCATTGAA
194 TTCACTTCATTGAT
* * * *
141413 TTGATCTACTTCTTTGTATCTCATCAGGAAGATGACCGCTTCATTATTTTAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGT
* ** * * * * **
141478 ATCTCATCAGGAAGACGGATTTGGTTCATTTCTTTGCATCTCGTTAGAAAGATGAATACTTTATT
66 ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCAGAAAGATGACCACTTTATT
* * *
141543 GCTTCGACCCACTTCTCTGTATCTCATTAGGAAGATGAGGTTTGAAGTCTCATTAATATTGAGTT
131 GCTTCGACCCACTTCTCTGTATCTCATCAGGAAGAT-AGGTTTGAAGTCTCATTCATATTGAGCT
141608 TCACTTCATTGAT
195 TCACTTCATTGAT
* * * * *
141621 TTGTTCTACTTTTCTATATCTCATCAGGAAGATGACTGCCTCATTGTTTCAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGT
* * ** *
141686 ATCTCATCAGGAAGACAAATTTGGTTCACTTCTCTACATCTCGCCAGGAAGATGACCAC-TTATT
66 ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCAGAAAGATGACCACTTTATT
* * **
141750 GGTTCGACCCACTTCTCTGTATCTCATCAAGAAGACGGGGTTTGAAGTCTCATTCATATTGAGCT
131 GCTTCGACCCACTTCTCTGTATCTCATCAGGAAGA-TAGGTTTGAAGTCTCATTCATATTGAGCT
*
141815 TCGCTTCATTGAT
195 TCACTTCATTGAT
* * * * *
141828 TTGGTCTACTTCTTTGTATCTCATCAAGAAGATAACCGCCTCATTGTTTCAATCCACTTCTTTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGT
* * * ***
141893 ATCTCATCAAGAAGACAGATTTGG-TCTACTTCTCTGTATCTCATCAGGAAA-TTGATTGCTTTA
66 ATCTCATCAAGAAGACAAATTTGGTTC-ACTTCTCTGCATCTCATCA-GAAAGATGACCACTTTA
* *
141956 TTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGAGTTTGAAGTCTCATTCGTATTGAG
129 TTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATAG-GTTTGAAGTCTCATTCATATTGAG
*
142021 CTTCGCTTCATTGAT
193 CTTCACTTCATTGAT
* * * *
142036 TTGGTCTACTTCTCTATATCACATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTAT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGT
* ** * * * *
142101 ATCTCATCAGGAAGATGAATTTGGTCCACTTCTTTGTATCTCATCA-AGAAGATGACCTCTTTAT
66 ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCAGA-AAGATGACCACTTTAT
* * * * * * * * * *
142165 TACTTTGACCCACTTCTTTGTATCTCATCAAGAAGGTAGGGTTTGAAGTTTCACTCACACTGAGT
130 TGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATA-GGTTTGAAGTCTCATTCATATTGAGC
**
142230 TTCACTTCAACGAT
194 TTCACTTCATTGAT
* * * * *
142244 TAGGTCTACTTCTCTGTATCTCATAAGGAATATGACCACCTCATTGATTTAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGT
*
142309 ATCTCATCAAGAAGACAAATTTGGTTCAATTCTCTGCATCTCATCA-AGAAGATGACCACTTTAT
66 ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCAGA-AAGATGACCACTTTAT
142373 TGCTTC
130 TGCTTC
142379 TGATGATTGT
Statistics
Matches: 828, Mismatches: 128, Indels: 20
0.85 0.13 0.02
Matches are distributed among these distances:
206 3 0.00
207 179 0.22
208 644 0.78
209 2 0.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (207 bp):
TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGT
ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCAGAAAGATGACCACTTTATT
GCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATAGGTTTGAAGTCTCATTCATATTGAGCTT
CACTTCATTGAT
Found at i:141980 original size:415 final size:415
Alignment explanation
Indices: 141205--142378 Score: 1489
Period size: 415 Copynumber: 2.8 Consensus size: 415
141195 GCTTTATCTC
** * * *
141205 TTGGTCTACTTCTCTGCATCTCATTAGAAAGATGACTGCTTCATTGTTTTAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTGCCTCATTGTTTTAATCCACTTCTCTGT
** * * *
141270 ATCTCATCAAAAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCAGGAAAATGAACACTTTATT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGATGACCACTTTATT
* * * * * * * *
141335 GCATCAATCCACTCCTCTGTATCTTATC-AGAAAGATAAGGTCTGATGTTTCACTCATATTGAGC
131 GCTTCGACCCACTTCTCTGTATCTCATCAAG-AAGATAGGGTTTGAAGTTTCACTCATATTGAGC
* * * * *
141399 TTCACTTCATTGAATTGATCTACTTCTTTGTATCTCATCAGGAAGATGACCGCTTCATTATTTTA
195 TTCACTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCGCCTCATT-GTTTA
* * * * * *
141464 ATCCACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTCATTTCTTTGCATCTCGTTAGAAAG
259 ATCCACTTCTCTGTATCTCATCAAGAAGACAGATTTGGTTCAATTCTCTGCATCTCATCAGAAAG
*
141529 ATGAATACTTTATTGCTTCGACCCACTTCTCTGTATCTCATTAGGAAGAT-GAGGTTTGAAGTCT
324 ATGAATACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATAGA-GTTTGAAGTCT
*
141593 CATTAATATTGAGTTTCACTTCATTGAT
388 CATTAATATTGAGCTTCACTTCATTGAT
* * *
141621 TTGTTCTACTTTTCTATATCTCATCAGGAAGATGACTGCCTCATTGTTTCAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTGCCTCATTGTTTTAATCCACTTCTCTGT
* * *
141686 ATCTCATCAGGAAGACAAATTTGGTTCACTTCTCTACATCTCGCCAGGAAGATGACCAC-TTATT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGATGACCACTTTATT
* ** * *
141750 GGTTCGACCCACTTCTCTGTATCTCATCAAGAAGACGGGGTTTGAAGTCTCATTCATATTGAGCT
131 GCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTTTCACTCATATTGAGCT
* *
141815 TCGCTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATAACCGCCTCATTGTTTCAA
196 TCACTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCGCCTCATTGTTT-AA
* * *
141880 TCCACTTCTTTGTATCTCATCAAGAAGACAGATTTGG-TCTACTTCTCTGTATCTCATCAGGAAA
260 TCCACTTCTCTGTATCTCATCAAGAAGACAGATTTGGTTC-AATTCTCTGCATCTCATCA-GAAA
* * * *
141944 -TTGATTGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGAGTTTGAAGTCT
323 GATGAATACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATAGAGTTTGAAGTCT
** *
142008 CATTCGTATTGAGCTTCGCTTCATTGAT
388 CATTAATATTGAGCTTCACTTCATTGAT
* * * *
142036 TTGGTCTACTTCTCTATATCACATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTAT
1 TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTGCCTCATTGTTTTAATCCACTTCTCTGT
* * * * * * *
142101 ATCTCATCAGGAAGATGAATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCTCTTTATT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGATGACCACTTTATT
* * * * * * *
142166 ACTTTGACCCACTTCTTTGTATCTCATCAAGAAGGTAGGGTTTGAAGTTTCACTCACACTGAGTT
131 GCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTTTCACTCATATTGAGCT
** * * * *
142231 TCACTTCAACGATTAGGTCTACTTCTCTGTATCTCAT-AAGGAATATGACCACCTCATTGATTTA
196 TCACTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAA-GAAGATGACCGCCTCATTG-TTTA
*
142295 ATCCACTTCTCTGTATCTCATCAAGAAGACAAATTTGGTTCAATTCTCTGCATCTCATCA-AGAA
259 ATCCACTTCTCTGTATCTCATCAAGAAGACAGATTTGGTTCAATTCTCTGCATCTCATCAGA-AA
**
142359 GATGACCACTTTATTGCTTC
323 GATGAATACTTTATTGCTTC
142379 TGATGATTGT
Statistics
Matches: 648, Mismatches: 99, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
414 6 0.01
415 347 0.54
416 290 0.45
417 5 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (415 bp):
TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTGCCTCATTGTTTTAATCCACTTCTCTGT
ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGATGACCACTTTATT
GCTTCGACCCACTTCTCTGTATCTCATCAAGAAGATAGGGTTTGAAGTTTCACTCATATTGAGCT
TCACTTCATTGATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTAAT
CCACTTCTCTGTATCTCATCAAGAAGACAGATTTGGTTCAATTCTCTGCATCTCATCAGAAAGAT
GAATACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATAGAGTTTGAAGTCTCAT
TAATATTGAGCTTCACTTCATTGAT
Found at i:142178 original size:85 final size:85
Alignment explanation
Indices: 142034--142199 Score: 206
Period size: 85 Copynumber: 2.0 Consensus size: 85
142024 CGCTTCATTG
* ** *
142034 ATTTGGTCTACTTCTCTATATCACATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCT
1 ATTTGGTCCACTTCTCTATATCACATCAAGAAGATGACCGCCTCATTACTTTAACCCACTTCTCT
*
142099 ATATCTCATCAGGAAGATGA
66 ATATCTCATCAAGAAGATGA
* * * * * * * *
142119 ATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCTCTTTATTACTTTGACCCACTTCTTT
1 ATTTGGTCCACTTCTCTATATCACATCAAGAAGATGACCGCCTCATTACTTTAACCCACTTCTCT
*
142184 GTATCTCATCAAGAAG
66 ATATCTCATCAAGAAG
142200 GTAGGGTTTG
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTATATCACATCAAGAAGATGACCGCCTCATTACTTTAACCCACTTCTCT
ATATCTCATCAAGAAGATGA
Found at i:142495 original size:41 final size:41
Alignment explanation
Indices: 142428--142702 Score: 320
Period size: 41 Copynumber: 6.7 Consensus size: 41
142418 GGGTGGCTAT
* *
142428 AATCTGCTCC-TCTTGATTAGGGGTAAAAGA-TCGAAATCTCC
1 AATCTGC-CCTTCTTGATTAAGGGTAAAAGACT-GAAATCTTC
* * *
142469 AATCTGCCCTTCTTTATTAAGAGTAAAAGACTGGAATCTTC
1 AATCTGCCCTTCTTGATTAAGGGTAAAAGACTGAAATCTTC
*
142510 AATCTGCCCTTCTTGATTAGGGGTAAAAGACTGAAATCTTC
1 AATCTGCCCTTCTTGATTAAGGGTAAAAGACTGAAATCTTC
* * *
142551 AATGTGCCCCTCTTGATTAAGGATAAAAGACTGAAATCTTC
1 AATCTGCCCTTCTTGATTAAGGGTAAAAGACTGAAATCTTC
* * * *
142592 AATCTGCCCCTCTTGATTAGGGGTAAAAGACTGGAATATTC
1 AATCTGCCCTTCTTGATTAAGGGTAAAAGACTGAAATCTTC
* * * * * *
142633 AATTTGCCCTTATTTATTAAGGGTAAAAGATTGACATATTC
1 AATCTGCCCTTCTTGATTAAGGGTAAAAGACTGAAATCTTC
* *
142674 AATCTGCCCTTATTGATTTAGGGGTAAAA
1 AATCTGCCCTTCTTGA-TTAAGGGTAAAA
142703 CATTGGAATG
Statistics
Matches: 202, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
40 2 0.01
41 188 0.93
42 12 0.06
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (41 bp):
AATCTGCCCTTCTTGATTAAGGGTAAAAGACTGAAATCTTC
Found at i:143307 original size:147 final size:148
Alignment explanation
Indices: 143084--143420 Score: 417
Period size: 147 Copynumber: 2.3 Consensus size: 148
143074 CGGGTTTGCC
* * * * * * *
143084 GTTACTGCCTCAATCTTTCCCTTCACATTTTCTAAGGTACCGGGTTCACCGTTGTAGCCTCAATC
1 GTTACGGCCTCAACCTTTCCCTTCAAATCTTC-ATGGTACCGGGTTCACCGTTGCAGCCTCAACC
* * ** * *
143149 TTTCCCTTCACATTTTCTAAGGTACCGAGTTCGCCGTTACGGCCTCAACCTTT-CCTTTCATATC
65 TTTCCCATCACATCTTCTAAGGTACCGAGTTAACCGTTACGGCCTCAACCTTTCCCTCT-AAATC
* * *
143213 TTCATGGTATCGGGTTCACT
129 TTAATGGTACCGAGTTCACT
** * * *
143233 GTTGGGGCCTCAACCTTTCCCTT-ATATCTTCATGGTACCGGGTTCACTGTTGCGGCCTCAACCT
1 GTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCAGCCTCAACCT
* *
143297 TTCCCATCACATCTTCTAAGGTACCGGGTTAACCGTTGCGGCCTCAACCTTTCCCTCTAAATCTT
66 TTCCCATCACATCTTCTAAGGTACCGAGTTAACCGTTACGGCCTCAACCTTTCCCTCTAAATCTT
*
143362 AATGGTACCGAGTTCGCT
131 AATGGTACCGAGTTCACT
*
143380 GTTACGGCCTCAACCTTTCCCTTCAAATGTTCATGGTACCG
1 GTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCG
143421 TGACTCATTT
Statistics
Matches: 159, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
147 115 0.72
148 25 0.16
149 19 0.12
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (148 bp):
GTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCAGCCTCAACCT
TTCCCATCACATCTTCTAAGGTACCGAGTTAACCGTTACGGCCTCAACCTTTCCCTCTAAATCTT
AATGGTACCGAGTTCACT
Found at i:143335 original size:50 final size:50
Alignment explanation
Indices: 143005--143400 Score: 376
Period size: 50 Copynumber: 8.0 Consensus size: 50
142995 CAATCCTCCT
* * * *
143005 ATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGACCTTAATCC--TCCC
1 ATCACATCTTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAA-CCTTTCCC
** * * *
143054 TATCACATCTTCTAAGGTACCGGGTTTGCCGTTACTGCCTCAATCTTTCCC
1 -ATCACATCTTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
* * ** *
143105 TTCACATTTTCTAAGGTACCGGGTTCACCGTTGTAGCCTCAATCTTTCCC
1 ATCACATCTTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
* * * * * *
143155 TTCACATTTTCTAAGGTACCGAGTTCGCCGTTACGGCCTCAACCTTTCCT
1 ATCACATCTTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
* * * * * *
143205 TTCATATCTTC-ATGGTATCGGGTTCACTGTTGGGGCCTCAACCTTTCCC
1 ATCACATCTTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
* * * *
143254 -TTATATCTTC-ATGGTACCGGGTTCACTGTTGCGGCCTCAACCTTTCCC
1 ATCACATCTTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
*
143302 ATCACATCTTCTAAGGTACCGGGTTAACCGTTGCGGCCTCAACCTTTCCC
1 ATCACATCTTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
* * * * *
143352 -TCTAAATC-T-TAATGGTACCGAGTTCGCTGTTACGGCCTCAACCTTTCCC
1 ATC-ACATCTTCTAA-GGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
143401 TTCAAATGTT
Statistics
Matches: 295, Mismatches: 45, Indels: 13
0.84 0.13 0.04
Matches are distributed among these distances:
48 48 0.16
49 73 0.25
50 170 0.58
51 4 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (50 bp):
ATCACATCTTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
Found at i:144349 original size:8 final size:8
Alignment explanation
Indices: 144331--144377 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
144321 CGACCTCTCC
144331 TTTTC-TT
1 TTTTCTTT
144338 TTTTCTTT
1 TTTTCTTT
144346 TTTTCTTT
1 TTTTCTTT
*
144354 TTTTCCTT
1 TTTTCTTT
*
144362 TTTCCTTT
1 TTTTCTTT
*
144370 CTTTCTTT
1 TTTTCTTT
144378 CTTATTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 5 0.15
8 29 0.85
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTT
Found at i:145087 original size:9 final size:8
Alignment explanation
Indices: 145065--145096 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
145055 TTTTGACCCA
*
145065 TCTTTTCT
1 TCTTTTTT
145073 TCTTTTTT
1 TCTTTTTT
145081 TCTTTTTT
1 TCTTTTTT
145089 TCTTTTTT
1 TCTTTTTT
145097 ATTTGACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TCTTTTTT
Found at i:149631 original size:60 final size:59
Alignment explanation
Indices: 149511--149712 Score: 219
Period size: 60 Copynumber: 3.4 Consensus size: 59
149501 TTTGGGAAAC
* * * * * *
149511 TTTAAGGGTCAAAA-AAAGATTTCGGAAAAGTTTGGGGGTAAAAATGTAATTCTTGAAAAG
1 TTTAAGGGTTAAAATATA-ATTTCTGAAAAGTTT-GGGGTTAAAATGTAATTTTTAAAAAG
* **
149571 TTT-AGCGGTTAAAATATAATTTCTGAAAAGTTTAAGGGTTAAAATGTAATTTTTTTAAAG
1 TTTAAG-GGTTAAAATATAATTTCTGAAAAGTTT-GGGGTTAAAATGTAATTTTTAAAAAG
* * * *
149631 TTTAAGGGTTAAATTGTAATTTTTTAAAAGTTTGGAGGTTAAAATGTAATTTTTAAAAAG
1 TTTAAGGGTTAAAATATAATTTCTGAAAAGTTTGG-GGTTAAAATGTAATTTTTAAAAAG
*
149691 TTTGAGGGTTAAAATATAATTT
1 TTTAAGGGTTAAAATATAATTT
149713 TTAAATAAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
59 3 0.03
60 112 0.94
61 4 0.03
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (59 bp):
TTTAAGGGTTAAAATATAATTTCTGAAAAGTTTGGGGTTAAAATGTAATTTTTAAAAAG
Found at i:149671 original size:90 final size:90
Alignment explanation
Indices: 149537--149714 Score: 239
Period size: 90 Copynumber: 2.0 Consensus size: 90
149527 AGATTTCGGA
** * *
149537 AAAGTTTGGGGGTAAAAATGTAATTCTTGAAAAGTTTAGCGGTTAAAATATAATTTCTGAAAAGT
1 AAAGTTTAAGGGTAAAAATGTAATTCTTGAAAAGTTTAGAGGTTAAAATATAATTTCTAAAAAGT
*
149602 TTAAGGGTTAAAATGTAATTTTTTT
66 TTAAGGGTTAAAATATAATTTTTTT
* * * * * * *
149627 AAAGTTTAAGGGTTAAATTGTAATTTTTTAAAAGTTTGGAGGTTAAAATGTAATTTTTAAAAAGT
1 AAAGTTTAAGGGTAAAAATGTAATTCTTGAAAAGTTTAGAGGTTAAAATATAATTTCTAAAAAGT
*
149692 TTGAGGGTTAAAATATAATTTTT
66 TTAAGGGTTAAAATATAATTTTT
149715 AAATAAAATG
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (90 bp):
AAAGTTTAAGGGTAAAAATGTAATTCTTGAAAAGTTTAGAGGTTAAAATATAATTTCTAAAAAGT
TTAAGGGTTAAAATATAATTTTTTT
Found at i:149715 original size:30 final size:30
Alignment explanation
Indices: 149536--149717 Score: 206
Period size: 30 Copynumber: 6.1 Consensus size: 30
149526 AAGATTTCGG
* * * *
149536 AAAAGTTTGGGGGTAAAAATGTAATTCTTG
1 AAAAGTTTGAGGGTTAAAATGTAATTTTTA
* * *
149566 AAAAGTTT-AGCGGTTAAAATATAATTTCTG
1 AAAAGTTTGAG-GGTTAAAATGTAATTTTTA
* *
149596 AAAAGTTTAAGGGTTAAAATGTAATTTTTT
1 AAAAGTTTGAGGGTTAAAATGTAATTTTTA
* * * *
149626 TAAAGTTTAAGGGTTAAATTGTAATTTTTT
1 AAAAGTTTGAGGGTTAAAATGTAATTTTTA
149656 AAAAGTTTG-GAGGTTAAAATGTAATTTTTA
1 AAAAGTTTGAG-GGTTAAAATGTAATTTTTA
*
149686 AAAAGTTTGAGGGTTAAAATATAATTTTTA
1 AAAAGTTTGAGGGTTAAAATGTAATTTTTA
149716 AA
1 AA
149718 TAAAATGGGG
Statistics
Matches: 133, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.02
30 128 0.96
31 3 0.02
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (30 bp):
AAAAGTTTGAGGGTTAAAATGTAATTTTTA
Found at i:150505 original size:2 final size:2
Alignment explanation
Indices: 150498--150639 Score: 169
Period size: 2 Copynumber: 69.0 Consensus size: 2
150488 AAGTATGCGC
* ** **
150498 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AGT AT GC GC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
150541 AT AT AT AT AT GT 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 AT
150583 AT AT AT AT AT AT CAT AT AT ACT GAT AT AT AT AT ACT -T AT AT AT
1 AT AT AT AT AT AT -AT AT AT A-T -AT AT AT AT AT A-T AT AT AT AT
*
150626 AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT
150640 GTTTGTATAT
Statistics
Matches: 124, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
1 1 0.01
2 115 0.93
3 7 0.06
4 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:154066 original size:4 final size:4
Alignment explanation
Indices: 154057--154117 Score: 51
Period size: 4 Copynumber: 16.2 Consensus size: 4
154047 AAATAATAAT
* * *
154057 AATA AATA AATA AAT- AATA AA-A AATG AA-A ATTA AATA GAT- AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
154101 AAT- AATA AATGA AATA A
1 AATA AATA AAT-A AATA A
154118 CAATAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
3 12 0.27
4 29 0.64
5 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:154074 original size:18 final size:18
Alignment explanation
Indices: 154047--154110 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
154037 GAAGATTGGA
154047 AAAT-AATAATAATAAAT
1 AAATAAATAATAATAAAT
*
154064 AAATAAATAATAAAAAAT
1 AAATAAATAATAATAAAT
154082 GAAAATTAAATAGATAATAAAT
1 --AAA-TAAATA-ATAATAAAT
154104 -AATAAAT
1 AAATAAAT
154111 GAAATAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 4 0.10
18 17 0.43
19 2 0.05
20 3 0.08
21 6 0.15
22 8 0.20
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
AAATAAATAATAATAAAT
Found at i:154075 original size:7 final size:7
Alignment explanation
Indices: 154047--154110 Score: 58
Period size: 7 Copynumber: 8.6 Consensus size: 7
154037 GAAGATTGGA
154047 AAATAAT
1 AAATAAT
154054 -AATAAT
1 AAATAAT
154060 AAATAAAT
1 AAAT-AAT
154068 AAATAAT
1 AAATAAT
*
154075 AAAAAAT
1 AAATAAT
154082 GAAAATTAAAT
1 --AAA-T-AAT
*
154093 AGATAAT
1 AAATAAT
154100 AAATAAT
1 AAATAAT
154107 AAAT
1 AAAT
154111 GAAATAACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
6 6 0.13
7 25 0.53
8 8 0.17
9 5 0.11
11 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:154092 original size:29 final size:29
Alignment explanation
Indices: 154059--154114 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
154049 ATAATAATAA
154059 TAAATAAATAA-ATAATAAAAAATGAAAAT
1 TAAATAAATAATA-AATAAAAAATGAAAAT
* *
154088 TAAATAGATAATAAATAATAAATGAAA
1 TAAATAAATAATAAATAAAAAATGAAA
154115 TAACAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (29 bp):
TAAATAAATAATAAATAAAAAATGAAAAT
Found at i:154122 original size:18 final size:16
Alignment explanation
Indices: 154047--154123 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 16
154037 GAAGATTGGA
154047 AAATAATAATAATAAAT
1 AAATAA-AATAATAAAT
154064 AAAT-AAATAATAAA-
1 AAATAAAATAATAAAT
154078 AAATGAAAAT--TAAAT
1 AAAT-AAAATAATAAAT
*
154093 AGATAATAAATAATAAAT
1 AAAT-A-AAATAATAAAT
154111 GAAATAACAATAA
1 -AAATAA-AATAA
154124 AATAACAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
14 8 0.16
15 13 0.27
16 9 0.18
17 5 0.10
18 11 0.22
19 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (16 bp):
AAATAAAATAATAAAT
Found at i:164782 original size:26 final size:29
Alignment explanation
Indices: 164735--164792 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 29
164725 TTTGAGTTTT
*
164735 TTTTTATTATGTTTAAAATTTTTATTTAA
1 TTTTTATTATGTTTAAAATTTTAATTTAA
*
164764 TTTTTA-TAT-TTT-AATTTTTAATTTAA
1 TTTTTATTATGTTTAAAATTTTAATTTAA
164790 TTT
1 TTT
164793 ATTTTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 15 0.56
27 3 0.11
28 3 0.11
29 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (29 bp):
TTTTTATTATGTTTAAAATTTTAATTTAA
Found at i:164783 original size:25 final size:22
Alignment explanation
Indices: 164751--164808 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 22
164741 TTATGTTTAA
164751 AATTTTTATTTAATTTTTATATTTT
1 AATTTTTATTTAA--TTTAT-TTTT
164776 AATTTTTAATTTAATTTATTTTT
1 AATTTTT-ATTTAATTTATTTTT
164799 ATATTTTTAT
1 A-ATTTTTAT
164809 AATATTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.23
24 11 0.35
25 7 0.23
26 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
AATTTTTATTTAATTTATTTTT
Found at i:164790 original size:12 final size:12
Alignment explanation
Indices: 164751--164792 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 12
164741 TTATGTTTAA
164751 AATTTTT-ATTT
1 AATTTTTAATTT
164762 AATTTTTATATTTT
1 AATTTTTA-A-TTT
164776 AATTTTTAATTT
1 AATTTTTAATTT
164788 AATTT
1 AATTT
164793 ATTTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.25
12 8 0.29
13 2 0.07
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
AATTTTTAATTT
Found at i:166656 original size:17 final size:17
Alignment explanation
Indices: 166649--166684 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
166639 TTCATATGAG
166649 ATAGCAGTTCATACCAA
1 ATAGCAGTTCATACCAA
*
166666 ATAGCAGTTCATTCCAA
1 ATAGCAGTTCATACCAA
166683 AT
1 AT
166685 GGTAATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (17 bp):
ATAGCAGTTCATACCAA
Found at i:166708 original size:17 final size:18
Alignment explanation
Indices: 166688--166730 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
166678 TCCAAATGGT
166688 AATTCATACT-ACATAAC
1 AATTCATACTCACATAAC
166705 AATTCATA-TCACATAAC
1 AATTCATACTCACATAAC
166722 AATTCATAC
1 AATTCATAC
166731 CACTCCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTCATACTCACATAAC
Found at i:166942 original size:76 final size:76
Alignment explanation
Indices: 166769--166943 Score: 210
Period size: 76 Copynumber: 2.3 Consensus size: 76
166759 TCATCTCGAA
* * ** *
166769 TTGCTCAACAACGATGACCTACCACCCCAGATTGGTCTGCAACGATGGTTTATTGAATCAAATTT
1 TTGCTCGACAACGATGACCTACCACCACAGATTGCCCTGCAACGATGGTTTACTGAATCAAATTT
**
166834 GTCATCCTGGG
66 GTCATCCCAGG
* * * *
166845 TTG-TCCGACAACGATCACCTACCACCACGGATTGCCCTGTAACGATGGTTTACTGGATCAAATA
1 TTGCT-CGACAACGATGACCTACCACCACAGATTGCCCTGCAACGATGGTTTACTGAATCAAAT-
166909 TT-TCATCCCAGG
64 TTGTCATCCCAGG
*
166921 TTGCTCGACAACGATGGCCTACC
1 TTGCTCGACAACGATGACCTACC
166944 CCCTCGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
75 1 0.01
76 79 0.95
77 3 0.04
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (76 bp):
TTGCTCGACAACGATGACCTACCACCACAGATTGCCCTGCAACGATGGTTTACTGAATCAAATTT
GTCATCCCAGG
Found at i:167158 original size:18 final size:18
Alignment explanation
Indices: 167143--167197 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
167133 ATAGTTTGGT
167143 AAATTAATACAGTTTGCC
1 AAATTAATACAGTTTGCC
* ****
167161 ATATTAATACAGAACACC
1 AAATTAATACAGTTTGCC
*
167179 AAATTAATATAGTTTGCC
1 AAATTAATACAGTTTGCC
167197 A
1 A
167198 CAATAATATA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (18 bp):
AAATTAATACAGTTTGCC
Done.