Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009406.1 Hibiscus syriacus cultivar Beakdansim tig00113338_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 689325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:396 original size:18 final size:19
Alignment explanation
Indices: 365--407 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
355 CGATATACCA
365 GGTAAAATATGATAAAACC
1 GGTAAAATATGATAAAACC
384 GGTAAAA-ATGATAAAACC
1 GGTAAAATATGATAAAACC
402 GGTAAA
1 GGTAAA
408 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (19 bp):
GGTAAAATATGATAAAACC
Found at i:2806 original size:21 final size:21
Alignment explanation
Indices: 2759--2823 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2749 CAAAGAATCA
* *
2759 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2781 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2801 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2822 AG
1 AG
2824 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:2896 original size:31 final size:32
Alignment explanation
Indices: 2861--2920 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
2851 AGATGGAGTG
*
2861 GTGAAAGAAGTAGAGG-GTTGAGGGGTGAAGT
1 GTGAAAGAAGTAGAGGTGTTAAGGGGTGAAGT
* *
2892 GTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 GTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2921 TATTAAGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.22
Consensus pattern (32 bp):
GTGAAAGAAGTAGAGGTGTTAAGGGGTGAAGT
Found at i:4780 original size:23 final size:23
Alignment explanation
Indices: 4720--4782 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
4710 ATAGGTAAAC
*
4720 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
4743 ATATAAT-TAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
4765 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
4783 TGGTTATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:4789 original size:23 final size:23
Alignment explanation
Indices: 4720--4791 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
4710 ATAGGTAAAC
* **
4720 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
4743 ATATAAT-TAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
4765 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
4788 ATAT
1 ATAT
4792 TGTAAAATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 18 0.44
23 22 0.54
24 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:5171 original size:21 final size:23
Alignment explanation
Indices: 5140--5201 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 23
5130 ATAGGTAAAC
*
5140 ATATGATGTAATAGGTAGC-CCT
1 ATATAATGTAATAGGTAGCGCCT
* * **
5162 -TATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCCT
5184 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5202 TGATTATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 15 0.48
22 1 0.03
23 15 0.48
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCCT
Found at i:5208 original size:23 final size:23
Alignment explanation
Indices: 5162--5210 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5152 AGGTAGCCCT
* *
5162 TATAATGTAATATGTATCGTTTA
1 TATAATGTAATAGGTATCGATTA
5185 TATAATGTAATAGGTAGT-GATTA
1 TATAATGTAATAGGTA-TCGATTA
5208 TAT
1 TAT
5211 TGTAAAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (23 bp):
TATAATGTAATAGGTATCGATTA
Found at i:5505 original size:25 final size:25
Alignment explanation
Indices: 5477--5527 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5467 AACAACAATC
*
5477 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
5502 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
5527 A
1 A
5528 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:5790 original size:18 final size:18
Alignment explanation
Indices: 5769--5805 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5759 GTAATTGGAG
5769 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5787 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5805 T
1 T
5806 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5813 original size:24 final size:24
Alignment explanation
Indices: 5761--5807 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5751 TTTCATATGT
* *
5761 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
5785 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
5808 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:6102 original size:39 final size:39
Alignment explanation
Indices: 6059--6184 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
6049 TCCGATGCTC
* *
6059 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
6098 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
6137 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
6176 ATCAAAATC
1 ATCAAAATC
6185 TACAACTTGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:6616 original size:23 final size:23
Alignment explanation
Indices: 6585--6648 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
6575 ATAGGTAAAC
*
6585 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
6608 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
6631 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
6649 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:6655 original size:23 final size:23
Alignment explanation
Indices: 6585--6657 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6575 ATAGGTAAAC
* **
6585 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
6608 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
6631 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
6654 ATAT
1 ATAT
6658 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:12802 original size:15 final size:15
Alignment explanation
Indices: 12769--12802 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12759 CTTTTACTTT
*
12769 ATATTTTTATATTTT
1 ATATTTTTATATTTA
*
12784 ATATTTTTATGTTTA
1 ATATTTTTATATTTA
12799 ATAT
1 ATAT
12803 ATATTAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
ATATTTTTATATTTA
Found at i:16399 original size:3 final size:3
Alignment explanation
Indices: 16393--16430 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
16383 AAAAATGAAA
16393 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
16431 TATATATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16607 original size:35 final size:35
Alignment explanation
Indices: 16486--16726 Score: 163
Period size: 35 Copynumber: 6.6 Consensus size: 35
16476 CAAAATGTTT
*
16486 TTTTTAAAACTATATAATATACGAATGTTTTCCAACATG
1 TTTTCAAAACTATATAATATA--AATGTTTT-CAA-ATG
* * * * *
16525 TTTTCAAAA-AAGATTATATAAAT-TTTCCCAAAACG
1 TTTTCAAAACTATATAATATAAATGTTT-TC-AAATG
*
16560 TTTTAAAAACTATATAATATAAATGTTTTCAAATG
1 TTTTCAAAACTATATAATATAAATGTTTTCAAATG
* *
16595 CTTTCAAAAC--TATAATATATATGTTTTCAAAAATG
1 TTTTCAAAACTATATAATATAAATGTTTTC--AAATG
16630 TTTTCAAAACTATATATATATATAA-GTTTTCCAAATG
1 TTTTCAAAACTATATA-ATATA-AATGTTTT-CAAATG
* * * *
16667 ATTTT-AAAATTATATTATATATAT-TTTCTAAAATG
1 -TTTTCAAAACTATATAATATAAATGTTT-TCAAATG
*
16702 TTTTTTTAAAACTATATATATATAA
1 --TTTTCAAAACTATATA-ATATAA
16727 TTTTAAAAAC
Statistics
Matches: 160, Mismatches: 25, Indels: 35
0.73 0.11 0.16
Matches are distributed among these distances:
33 17 0.11
35 49 0.31
36 27 0.17
37 30 0.19
38 27 0.17
39 10 0.06
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (35 bp):
TTTTCAAAACTATATAATATAAATGTTTTCAAATG
Found at i:16694 original size:72 final size:69
Alignment explanation
Indices: 16464--16726 Score: 246
Period size: 72 Copynumber: 3.6 Consensus size: 69
16454 AAACATACAA
16464 TATATAAATTTTCAAAATGTTTTTTTTAAAACTATATAATATACGAATGTTTTCCAACATGTTTT
1 TATATAAATTTTCAAAATG--TTTTTTAAAACTATATAATATA--AATGTTTTCCAA-ATGTTTT
* *
16529 CAAAAAAGAT
61 -AAAATATAT
* * *
16539 TATATAAATTTTCCCAAAACG-TTTTAAAAACTATATAATATAAATGTTTT-CAAATGCTTTCAA
1 TATATAAATTTT--CAAAATGTTTTTTAAAACTATATAATATAAATGTTTTCCAAATG-TTTTAA
*
16602 AACTATAA
63 AA-TATAT
** *
16610 TATATATGTTTTCAAAAATG-TTTTCAAAACTATATATATATATAA-GTTTTCCAAATGATTTTA
1 TATATAAATTTTC-AAAATGTTTTTTAAAACTATATA-ATATA-AATGTTTTCCAAATG-TTTTA
16673 AAATTATAT
62 AAA-TATAT
*
16682 TATATATATTTTCTAAAATGTTTTTTTAAAACTATATATATATAA
1 TATATAAATTTTC-AAAATG-TTTTTTAAAACTATATA-ATATAA
16727 TTTTAAAAAC
Statistics
Matches: 161, Mismatches: 17, Indels: 22
0.81 0.09 0.11
Matches are distributed among these distances:
69 1 0.01
70 27 0.17
71 28 0.17
72 45 0.28
73 1 0.01
74 41 0.25
75 12 0.07
77 6 0.04
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.44
Consensus pattern (69 bp):
TATATAAATTTTCAAAATGTTTTTTAAAACTATATAATATAAATGTTTTCCAAATGTTTTAAAAT
ATAT
Found at i:16753 original size:72 final size:72
Alignment explanation
Indices: 16539--16759 Score: 183
Period size: 72 Copynumber: 3.1 Consensus size: 72
16529 CAAAAAAGAT
* * * * * * *
16539 TATATAAATTTTCCCAAAACGTTTTAAAAAC-TATATA-ATATAAATGTTTT-CAAATGCTTTCA
1 TATATATATTTT-CAAAAATGTTTTCAAAACATATATATATAT-AA-GTTTTAAAAATGATTTAA
16601 AAACTATA-A
63 AAACTATATA
* ** *
16610 TATATATGTTTTCAAAAATGTTTTCAAAACTATATATATATATAAGTTTTCCAAATGATTTTAAA
1 TATATATATTTTCAAAAATGTTTTCAAAAC-ATATATATATATAAGTTTTAAAAATGATTTAAAA
*
16675 ATTATAT-
65 ACTATATA
* *
16682 TATATATATTTTCTAAAATGTTTTTTTAAAAC-TATATATATATAA-TTTTAAAAACT-A-TTAA
1 TATATATATTTTCAAAAATG--TTTTCAAAACATATATATATATAAGTTTTAAAAA-TGATTTAA
16743 AAACTATATA
63 AAACTATATA
16753 T-TATATA
1 TATATATA
16760 CGTAGTTTCA
Statistics
Matches: 126, Mismatches: 15, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
70 32 0.25
71 24 0.19
72 57 0.45
73 4 0.03
74 9 0.07
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (72 bp):
TATATATATTTTCAAAAATGTTTTCAAAACATATATATATATAAGTTTTAAAAATGATTTAAAAA
CTATATA
Found at i:17952 original size:249 final size:249
Alignment explanation
Indices: 17419--18782 Score: 2205
Period size: 249 Copynumber: 5.5 Consensus size: 249
17409 TCGAACCCAG
* *
17419 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAG
1 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
* * *
17484 CGTAGTCGCACTCGAAGGTCTTTGATGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
* * * * * * * ** * *
17549 ATATGCCGTTG-AGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTAACAGATAACCCTTCTAGC
131 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGA
* * * * ** * **
17613 CTTGAGTTATGCTGTAAATGTTATGCCCTT-GAAGCTGAGTGTAATCGAACTTAA
196 CTTAAGTTATGCTGCAAATGATGTG-CCTTCGAAGCTGAACGTAGTCGAACTCGA
* *
17667 GGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
1 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
*
17732 CGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
*
17797 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGA
131 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGA
17862 CTTAAGTTATGCTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGA
196 CTTAAGTTATGCTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGA
*
17916 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAA
1 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
17981 CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
18046 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGA
131 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGA
18111 CTTAAGTTATGCTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGA
196 CTTAAGTTATGCTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGA
*
18165 AGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
1 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
18230 CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
*
18295 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGA
131 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGA
*
18360 CTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGA
196 CTTAAGTTATGCTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGA
18414 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
1 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
18479 CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
18544 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGA
131 ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGA
* * * *
18609 CTTAAGTTATGCTGCAAATGATGGGCCTT-GGAGCTGAGCGTAGTCGAACTCAA
196 CTTAAGTTATGCTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGA
* * * * * **
18662 AGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTCAAAG
1 GGGTC-TTTG---GCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTT-GGAG
* * * *
18727 CTGAACGTAGTCGAACTCGAAGGTC-TTGGTGGACAGATAGCCCTTCTGGCCTTGAG
61 CTGAGCGTAGTCGAACTCAAAGGTCTTTGGT-GACAGATAACCCTTCTAGCCTTGAG
18783 CTAAGCTGCA
Statistics
Matches: 1053, Mismatches: 55, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
248 161 0.15
249 796 0.76
252 48 0.05
253 48 0.05
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (249 bp):
GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
CGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
ATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGA
CTTAAGTTATGCTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGA
Found at i:22149 original size:18 final size:19
Alignment explanation
Indices: 22108--22152 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
22098 AGTTAATGTG
22108 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
22127 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
22145 AATGCAAA
1 AATGCAAA
22153 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:25041 original size:3 final size:3
Alignment explanation
Indices: 25035--25072 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
25025 AAAAATGAAA
25035 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
25073 TATATATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25237 original size:36 final size:36
Alignment explanation
Indices: 25130--25409 Score: 180
Period size: 34 Copynumber: 7.6 Consensus size: 36
25120 AAATGTTTTT
* *
25130 TTTTTAAAACTATATAATATACGAATGTTTTCCAACATG
1 TTTTAAAAACTATATAATATA--AATGTTTT-CAAAATG
* * * *
25169 TTTTCAAAAA--AGATTATATAAAT-TTTCCCAAAACG
1 TTTT-AAAAACTATATAATATAAATGTTT-TCAAAATG
25204 TTTTAAAAACTATATAATATAAATGTTTTCAAAATG
1 TTTTAAAAACTATATAATATAAATGTTTTCAAAATG
* * *
25240 CTTTCAAAAC--TATAATATATATGTTTTCAAAAATG
1 TTTTAAAAACTATATAATATAAATGTTTTC-AAAATG
* *
25275 TTTTCAAAAACTATATATATATATATAAGTTTTCCAAATG
1 TTTT-AAAAACTATATA-ATATA-A-ATGTTTTCAAAATG
* * * *
25315 ATTTTAAAAATTATATATTATATATATTTTCTAAAATG
1 -TTTTAAAAACTATATAATATAAATGTTTTC-AAAATG
* * **
25353 TTTTTTTAAAACTATATATTATATAA--TTTT-AAAAAC
1 --TTTTAAAAACTATATAATATA-AATGTTTTCAAAATG
* *
25389 TATTAAAAACTATATATTATA
1 TTTTAAAAACTATATAATATA
25410 TACGTAGTTT
Statistics
Matches: 193, Mismatches: 32, Indels: 37
0.74 0.12 0.14
Matches are distributed among these distances:
34 41 0.21
35 21 0.11
36 37 0.19
37 9 0.05
38 21 0.11
39 32 0.17
40 21 0.11
41 11 0.06
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATAAATGTTTTCAAAATG
Found at i:25277 original size:12 final size:12
Alignment explanation
Indices: 25260--25284 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25250 TATAATATAT
25260 ATGTTTTCAAAA
1 ATGTTTTCAAAA
25272 ATGTTTTCAAAA
1 ATGTTTTCAAAA
25284 A
1 A
25285 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:25337 original size:39 final size:39
Alignment explanation
Indices: 25183--25411 Score: 184
Period size: 36 Copynumber: 6.1 Consensus size: 39
25173 CAAAAAAGAT
* * *
25183 TATATAAATTTTCCCAAAACGTTTTAAAAACTATATA--A
1 TATATAAGTTTT-CAAAAATGTTTTAAAAACTATATATTA
* *
25221 TATA-AATGTTTTC-AAAATGCTTTCAAAACTATA-A-TA
1 TATATAA-GTTTTCAAAAATGTTTTAAAAACTATATATTA
25257 TATAT--GTTTTCAAAAATGTTTTCAAAAACTATATATATA
1 TATATAAGTTTTCAAAAATGTTTT-AAAAACTATATAT-TA
* *
25296 TATATAAGTTTTC-CAAATGATTTTAAAAATTATATATTA
1 TATATAAGTTTTCAAAAATG-TTTTAAAAACTATATATTA
* *
25335 TATAT-A-TTTTCTAAAATGTTTTTTTAAAACTATATA-T-
1 TATATAAGTTTTCAAAAATG--TTTTAAAAACTATATATTA
* *
25372 TATATAA-TTTT-AAAAA-CTATTAAAAACTATATATTA
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATATTA
25408 TATA
1 TATA
25412 CGTAGTTTCA
Statistics
Matches: 159, Mismatches: 16, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
34 20 0.13
35 11 0.07
36 35 0.22
37 18 0.11
38 20 0.13
39 28 0.18
40 17 0.11
41 10 0.06
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (39 bp):
TATATAAGTTTTCAAAAATGTTTTAAAAACTATATATTA
Found at i:26478 original size:15 final size:15
Alignment explanation
Indices: 26460--26506 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
26450 CCCGCATCCA
* *
26460 CCCGCATCCGTCCGT
1 CCCGCATCCGCCCGC
26475 CCCGCATCCGCCCGC
1 CCCGCATCCGCCCGC
*
26490 CCCACATCCGCCCGC
1 CCCGCATCCGCCCGC
26505 CC
1 CC
26507 AACTAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.09, C:0.64, G:0.17, T:0.11
Consensus pattern (15 bp):
CCCGCATCCGCCCGC
Found at i:27377 original size:2 final size:2
Alignment explanation
Indices: 27370--27397 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27360 AATGGGCTTA
27370 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
27398 TATTCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32392 original size:33 final size:33
Alignment explanation
Indices: 32350--32416 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
32340 TAGCACAAAA
32350 AAACAAAACACTAAAGTATATATATATATATAT
1 AAACAAAACACTAAAGTATATATATATATATAT
* *
32383 AAACAAAACACTAAAGTTTTTATATATATATAT
1 AAACAAAACACTAAAGTATATATATATATATAT
32416 A
1 A
32417 TATATATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (33 bp):
AAACAAAACACTAAAGTATATATATATATATAT
Found at i:39293 original size:22 final size:21
Alignment explanation
Indices: 39268--39315 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
39258 TATGATAAGT
39268 TTTTTTCTGCTTT-TATGACAC
1 TTTTTTCTG-TTTCTATGACAC
*
39289 ATTTTCTCTGTTTCTATGACAC
1 -TTTTTTCTGTTTCTATGACAC
39311 TTTTT
1 TTTTT
39316 GATCGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.58
Consensus pattern (21 bp):
TTTTTTCTGTTTCTATGACAC
Found at i:39323 original size:22 final size:22
Alignment explanation
Indices: 39268--39323 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
39258 TATGATAAGT
*
39268 TTTTTTCTGCTTT-TATGACACA
1 TTTTATCTG-TTTCTATGACACA
* *
39290 TTTTCTCTGTTTCTATGACACT
1 TTTTATCTGTTTCTATGACACA
39312 TTTTGATC-GTTT
1 TTTT-ATCTGTTT
39324 AACCGTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 24 0.83
23 2 0.07
ACGTcount: A:0.14, C:0.18, G:0.11, T:0.57
Consensus pattern (22 bp):
TTTTATCTGTTTCTATGACACA
Found at i:46215 original size:21 final size:21
Alignment explanation
Indices: 46173--46215 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
46163 CAACAAATAA
*
46173 ATTGATCATGTGGTTCGTTTT
1 ATTGATCATGTGGATCGTTTT
*
46194 ATTGAT-ATTTGGATCGTGTTT
1 ATTGATCATGTGGATCGT-TTT
46215 A
1 A
46216 ATTTCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.19, C:0.07, G:0.23, T:0.51
Consensus pattern (21 bp):
ATTGATCATGTGGATCGTTTT
Found at i:47421 original size:17 final size:17
Alignment explanation
Indices: 47399--47431 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
47389 TGAATGTATG
47399 TAAAATATTTTTTTATA
1 TAAAATATTTTTTTATA
47416 TAAAATATTTTTTTAT
1 TAAAATATTTTTTTAT
47432 CGTTTTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAAAATATTTTTTTATA
Found at i:49489 original size:15 final size:15
Alignment explanation
Indices: 49445--49492 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
49435 AACAATAAAG
*
49445 ATAATAGATGATTAG
1 ATAATAGATGATTAA
49460 ATAATAGATGATTAA
1 ATAATAGATGATTAA
49475 ATAATAGATGATTAA
1 ATAATAGATGATTAA
49490 ATA
1 ATA
49493 CACAATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (15 bp):
ATAATAGATGATTAA
Found at i:52331 original size:29 final size:32
Alignment explanation
Indices: 52276--52334 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 32
52266 GTTGTATTTT
**
52276 GTGTTTGTGTTTAACAGGAATGTAAGATTACC
1 GTGTTTGTGTTTAACAGGAATAAAAGATTACC
52308 GTGTTTG-G-TTAA-AGGAATAAAAGATTA
1 GTGTTTGTGTTTAACAGGAATAAAAGATTA
52335 TTAGAATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 4 0.16
31 1 0.04
32 7 0.28
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (32 bp):
GTGTTTGTGTTTAACAGGAATAAAAGATTACC
Found at i:54031 original size:31 final size:29
Alignment explanation
Indices: 53975--54032 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
53965 TTCATTTAAG
*
53975 TACCTAAAGTATTTTTTGTTTAAAATAAA
1 TACCTAAAGTATTTTTTGTTCAAAATAAA
54004 TACCTAAAGTTATCTTTTTAG-TCAAAATA
1 TACCTAAAG-TAT-TTTTT-GTTCAAAATA
54033 TGTACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 9 0.36
30 3 0.12
31 12 0.48
32 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (29 bp):
TACCTAAAGTATTTTTTGTTCAAAATAAA
Found at i:54888 original size:16 final size:15
Alignment explanation
Indices: 54862--54891 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54852 GACAGTTCAG
54862 AAATTATAATATAAT
1 AAATTATAATATAAT
54877 AAATTCATAATATAA
1 AAATT-ATAATATAA
54892 ATGATGAAAA
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:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTATAATATAAT
Found at i:55417 original size:15 final size:15
Alignment explanation
Indices: 55399--55429 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55389 ATAAAATTAA
55399 AAATATTATTAAAAT
1 AAATATTATTAAAAT
*
55414 AAATATTTTTAAAAT
1 AAATATTATTAAAAT
55429 A
1 A
55430 TATCTTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTATTAAAAT
Found at i:56238 original size:29 final size:29
Alignment explanation
Indices: 56205--56263 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
56195 ACCCAACCCA
* **
56205 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
56234 TAGGTCGCCATGCACTCCCAGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
56263 T
1 T
56264 CTCCTCTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.37, G:0.27, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTTG
Found at i:56539 original size:26 final size:26
Alignment explanation
Indices: 56510--56593 Score: 134
Period size: 26 Copynumber: 3.3 Consensus size: 26
56500 ACATAAAAGA
56510 AAGAAAGGGAGAAGAGATTGCAGCCG
1 AAGAAAGGGAGAAGAGATTGCAGCCG
* *
56536 AAGAAAGGGATAAGAGATTGTAGCCG
1 AAGAAAGGGAGAAGAGATTGCAGCCG
*
56562 AAGAAAGGGAGAAGATATTGCAGCCG
1 AAGAAAGGGAGAAGAGATTGCAGCCG
56588 -AGAAAG
1 AAGAAAG
56594 AAATAAAGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 6 0.11
26 47 0.89
ACGTcount: A:0.44, C:0.10, G:0.36, T:0.11
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAGATTGCAGCCG
Found at i:57032 original size:30 final size:30
Alignment explanation
Indices: 56964--57035 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 30
56954 AGTTAGTAAG
*
56964 TTTATTAGTAGTTTATTATAATGAAAAAATAG
1 TTTATTAGT--TTTATTATAATGAAAAAATAA
56996 TTTATTAGTTTTAGTTAT-AT-AAAAGAATAA
1 TTTATTAGTTTTA-TTATAATGAAAA-AATAA
57026 TTTATTAGTT
1 TTTATTAGTT
57036 GTTTAAGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 4 0.11
30 20 0.54
31 4 0.11
32 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (30 bp):
TTTATTAGTTTTATTATAATGAAAAAATAA
Found at i:59694 original size:378 final size:378
Alignment explanation
Indices: 58999--59753 Score: 1483
Period size: 378 Copynumber: 2.0 Consensus size: 378
58989 TATGACTTTG
58999 AACACATGACAGTTCATCTCAACATCGAATGATTCAGTCATTTGGTACGGAGGTAAATGTGGCAT
1 AACACATGACAGTTCATCTCAACATCGAATGATTCAGTCATTTGGTACGGAGGTAAATGTGGCAT
*
59064 GTCTGGGAATTCAGGTGCCCTCTTCGCATCATAGTCTATCTCGTACATGTGAGGAGTAGCTTCAT
66 GTCTGGGAATTCAGGTGCCCTCATCGCATCATAGTCTATCTCGTACATGTGAGGAGTAGCTTCAT
59129 ACGGTGTCAGAACTTCATCAATTGCACCCCCACCGAAAATATTTTCATCGCTGCCCAAAACGGGT
131 ACGGTGTCAGAACTTCATCAATTGCACCCCCACCGAAAATATTTTCATCGCTGCCCAAAACGGGT
59194 TCTTCGGTTTCTTCATCTTCGCTTGAATCATCATGAATTTCTCCCCATCGATTTTTAGCATCAAT
196 TCTTCGGTTTCTTCATCTTCGCTTGAATCATCATGAATTTCTCCCCATCGATTTTTAGCATCAAT
59259 ATCAACATCCAATTCCGGTATGTTTCTCGTCTCATACTCTGCTGCTGCAGATGTCCCTCTGACTC
261 ATCAACATCCAATTCCGGTATGTTTCTCGTCTCATACTCTGCTGCTGCAGATGTCCCTCTGACTC
*
59324 CATTTACACTTTTCATTAGTGCCATAAACTGTTCGAGAACCTGTATGTCAGCA
326 CATTTACACTTTCCATTAGTGCCATAAACTGTTCGAGAACCTGTATGTCAGCA
59377 AACACATGACAGTTCATCTCAACATCGAATGATTCAGTCATTTGGTACGGAGGTAAATGTGGCAT
1 AACACATGACAGTTCATCTCAACATCGAATGATTCAGTCATTTGGTACGGAGGTAAATGTGGCAT
59442 GTCTGGGAATTCAGGTGCCCTCATCGCATCATAGTCTATCTCGTACATGTGAGGAGTAGCTTCAT
66 GTCTGGGAATTCAGGTGCCCTCATCGCATCATAGTCTATCTCGTACATGTGAGGAGTAGCTTCAT
*
59507 ACGGTGTCAGAACTTCATCAATTGCACCTCCACCGAAAATATTTTCATCGCTGCCCAAAACGGGT
131 ACGGTGTCAGAACTTCATCAATTGCACCCCCACCGAAAATATTTTCATCGCTGCCCAAAACGGGT
59572 TCTTCGGTTTCTTCATCTTCGCTTGAATCATCATGAATTTCTCCCCATCGATTTTTAGCATCAAT
196 TCTTCGGTTTCTTCATCTTCGCTTGAATCATCATGAATTTCTCCCCATCGATTTTTAGCATCAAT
59637 ATCAACATCCAATTCCGGTATGTTTCTCGTCTCATACTCTGCTGCTGCAGATGTCCCTCTGACTC
261 ATCAACATCCAATTCCGGTATGTTTCTCGTCTCATACTCTGCTGCTGCAGATGTCCCTCTGACTC
59702 CATTTACACTTTCCATTAGTGCCATAAACTGTTCGAGAACCTGTATGTCAGC
326 CATTTACACTTTCCATTAGTGCCATAAACTGTTCGAGAACCTGTATGTCAGC
59754 TCCTCAAACT
Statistics
Matches: 374, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
378 374 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (378 bp):
AACACATGACAGTTCATCTCAACATCGAATGATTCAGTCATTTGGTACGGAGGTAAATGTGGCAT
GTCTGGGAATTCAGGTGCCCTCATCGCATCATAGTCTATCTCGTACATGTGAGGAGTAGCTTCAT
ACGGTGTCAGAACTTCATCAATTGCACCCCCACCGAAAATATTTTCATCGCTGCCCAAAACGGGT
TCTTCGGTTTCTTCATCTTCGCTTGAATCATCATGAATTTCTCCCCATCGATTTTTAGCATCAAT
ATCAACATCCAATTCCGGTATGTTTCTCGTCTCATACTCTGCTGCTGCAGATGTCCCTCTGACTC
CATTTACACTTTCCATTAGTGCCATAAACTGTTCGAGAACCTGTATGTCAGCA
Found at i:60557 original size:23 final size:23
Alignment explanation
Indices: 60531--60575 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
60521 CACCACAGCT
*
60531 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
60554 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
60576 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:62026 original size:19 final size:17
Alignment explanation
Indices: 61994--62028 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
61984 ACGTTTGGAG
61994 AAGGAAGAGAAGAAGAT
1 AAGGAAGAGAAGAAGAT
62011 AAGGAAGAAGGAAGAAGA
1 AAGGAAG-A-GAAGAAGA
62029 AATGAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (17 bp):
AAGGAAGAGAAGAAGAT
Found at i:63596 original size:12 final size:12
Alignment explanation
Indices: 63579--63614 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
63569 TATCATGTTC
63579 TCATATCACATG
1 TCATATCACATG
*
63591 TCATATCACATA
1 TCATATCACATG
63603 TCATATCACATG
1 TCATATCACATG
63615 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:63902 original size:26 final size:25
Alignment explanation
Indices: 63880--63930 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
63870 ATTTGATATT
63880 TAATGATTTAATAATAATATGATTTA
1 TAATGA-TTAATAATAATATGATTTA
*
63906 GTAATGATTACTAATAAT-T-ATTTA
1 -TAATGATTAATAATAATATGATTTA
63930 T
1 T
63931 TATAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 1 0.04
24 5 0.22
25 1 0.04
26 10 0.43
27 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TAATGATTAATAATAATATGATTTA
Found at i:64331 original size:17 final size:16
Alignment explanation
Indices: 64291--64333 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
64281 TTACACATAC
64291 ACAACAACAAAAAATGA
1 ACAACAA-AAAAAATGA
* *
64308 ACAA-AAACAAAATGG
1 ACAACAAAAAAAATGA
64323 ACAACAAAAAA
1 ACAACAAAAAA
64334 TAATAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.50
16 7 0.32
17 4 0.18
ACGTcount: A:0.72, C:0.16, G:0.07, T:0.05
Consensus pattern (16 bp):
ACAACAAAAAAAATGA
Found at i:64783 original size:28 final size:30
Alignment explanation
Indices: 64735--64797 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
64725 ATTTTTTATA
64735 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
64765 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
64793 TAATA
1 TAATA
64798 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:64804 original size:28 final size:28
Alignment explanation
Indices: 64739--64804 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
64729 TTTATATAAT
64739 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
64767 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
64795 ATAATTTATA
1 ATAATATATA
64805 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:64807 original size:21 final size:21
Alignment explanation
Indices: 64774--64822 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
64764 CTAATATAAT
64774 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
64795 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
64816 ATTAACT
1 A-TAACT
64823 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:64974 original size:6 final size:6
Alignment explanation
Indices: 64963--64996 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
64953 TCGGCAAAGT
64963 TTCTGC TTCTGC TTCTGC TTCTGC TTCTGC TTCT
1 TTCTGC TTCTGC TTCTGC TTCTGC TTCTGC TTCT
64997 ACCCTAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.15, T:0.53
Consensus pattern (6 bp):
TTCTGC
Found at i:65563 original size:29 final size:29
Alignment explanation
Indices: 65530--65591 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
65520 TTATCTTAGT
* * *
65530 AAATAATATGTCTAAAACATTATTTCGTG
1 AAATAAAAAGTCTAAAACATTATCTCGTG
* * *
65559 AAATAAAAAGTTTGAAACTTTATCTCGTG
1 AAATAAAAAGTCTAAAACATTATCTCGTG
65588 AAAT
1 AAAT
65592 TTGTCAGATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (29 bp):
AAATAAAAAGTCTAAAACATTATCTCGTG
Found at i:69597 original size:15 final size:17
Alignment explanation
Indices: 69577--69608 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
69567 CATAATATAA
69577 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
69592 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
69609 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:79060 original size:20 final size:19
Alignment explanation
Indices: 79018--79066 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
79008 TCAATTTAAT
* *
79018 ATTAAAATTAATGATCAAT
1 ATTAAAATTAACGATCAAA
*
79037 ATTAAAATTTACGTATCAAA
1 ATTAAAATTAACG-ATCAAA
*
79057 ATTAATATTA
1 ATTAAAATTA
79067 TCATGGTTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (19 bp):
ATTAAAATTAACGATCAAA
Found at i:79563 original size:32 final size:32
Alignment explanation
Indices: 79501--79563 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
79491 TAACTTCGTT
*
79501 CAAATCAATTGAAACACACGGGGGCACCGGCG
1 CAAATCAATTGAAACACACGGGAGCACCGGCG
*
79533 CAAATCAATTGAAACACA-GAGGAGCGCCGGC
1 CAAATCAATTGAAACACACG-GGAGCACCGGC
79564 TAACCTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.37, C:0.27, G:0.27, T:0.10
Consensus pattern (32 bp):
CAAATCAATTGAAACACACGGGAGCACCGGCG
Found at i:82437 original size:14 final size:14
Alignment explanation
Indices: 82414--82447 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
82404 AAATAACTTT
82414 TTATTATTATAATA
1 TTATTATTATAATA
* *
82428 TTATTTTTATAATT
1 TTATTATTATAATA
82442 TTATTA
1 TTATTA
82448 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTATTATAATA
Found at i:82631 original size:23 final size:21
Alignment explanation
Indices: 82593--82650 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
82583 ATATTAAATG
*
82593 TATAATTAATATTATTCATTAC
1 TATAATTAATAATATT-ATTAC
*
82615 TATAATTTAATAATATTATTTC
1 TATAA-TTAATAATATTATTAC
82637 TATGAAATTAATAA
1 TAT--AATTAATAA
82651 ATAATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 12 0.39
23 17 0.55
24 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
TATAATTAATAATATTATTAC
Found at i:82723 original size:22 final size:23
Alignment explanation
Indices: 82695--82744 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
82685 ATTAAAATAA
*
82695 AATATAATATCTTATATTA-TAT
1 AATATAATATATTATATTATTAT
* *
82717 AATATAATTTATTATTTTATTAT
1 AATATAATATATTATATTATTAT
82740 AATAT
1 AATAT
82745 TAAAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:89415 original size:2 final size:2
Alignment explanation
Indices: 89408--89449 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
89398 CTTCATGTTT
89408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89450 AACTAAAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96196 original size:5 final size:5
Alignment explanation
Indices: 96186--96219 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
96176 ATAGGCACTG
96186 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT CCAA
1 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT CCAA
96220 AATTGAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (5 bp):
CCAAT
Found at i:98527 original size:31 final size:32
Alignment explanation
Indices: 98492--98562 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
98482 TTGTATTGAT
98492 AAATTAAAATTT-AACTCAAACTCAAA-AA-TTA
1 AAATTAAAATTTCAA-T-AAACTCAAATAACTTA
*
98523 AAATT-AAATTTCAATATACTCAAATAACTTA
1 AAATTAAAATTTCAATAAACTCAAATAACTTA
98554 AAATTAAAA
1 AAATTAAAA
98563 ATTATGCTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
29 8 0.23
30 9 0.26
31 15 0.43
32 3 0.09
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (32 bp):
AAATTAAAATTTCAATAAACTCAAATAACTTA
Found at i:100310 original size:14 final size:14
Alignment explanation
Indices: 100291--100320 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
100281 CAAGTGATCA
100291 AAACTTAATAAAAC
1 AAACTTAATAAAAC
100305 AAACTTAATAAAAC
1 AAACTTAATAAAAC
100319 AA
1 AA
100321 TAATGTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACTTAATAAAAC
Found at i:100342 original size:31 final size:31
Alignment explanation
Indices: 100305--100404 Score: 139
Period size: 31 Copynumber: 3.2 Consensus size: 31
100295 TTAATAAAAC
100305 AAACTTAATAAAACAATAATGTAAGTGACCA
1 AAACTTAATAAAACAATAATGTAAGTGACCA
* * * *
100336 AAACTTAACAAAACGATCACT-TAAGTGATCA
1 AAACTTAATAAAACAAT-AATGTAAGTGACCA
*
100367 AAACTTAATAAAACAATAACGTAAGTGACCA
1 AAACTTAATAAAACAATAATGTAAGTGACCA
100398 AAACTTA
1 AAACTTA
100405 TGTTTCTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
30 1 0.02
31 55 0.95
32 2 0.03
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (31 bp):
AAACTTAATAAAACAATAATGTAAGTGACCA
Found at i:108412 original size:21 final size:22
Alignment explanation
Indices: 108387--108433 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
108377 ATATTATTAA
* * *
108387 AAAAATTATATTATTTATATAT
1 AAAATTTATAGTATTTAAATAT
108409 AAAATTTTATAGTATTTAAATAT
1 AAAA-TTTATAGTATTTAAATAT
108432 AA
1 AA
108434 GTTTTTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAATTTATAGTATTTAAATAT
Found at i:112418 original size:29 final size:29
Alignment explanation
Indices: 112384--112442 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
112374 CCTAAATTAA
112384 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
112413 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
112442 T
1 T
112443 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:115368 original size:27 final size:29
Alignment explanation
Indices: 115337--115393 Score: 100
Period size: 27 Copynumber: 2.0 Consensus size: 29
115327 CCTAAATTAA
115337 TTTGATGTCATTGCTTAC-TCAA-TTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
115364 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
115393 T
1 T
115394 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 18 0.64
28 4 0.14
29 6 0.21
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:117515 original size:32 final size:31
Alignment explanation
Indices: 117427--117535 Score: 111
Period size: 32 Copynumber: 3.6 Consensus size: 31
117417 TCTTTTAATA
***
117427 TTCGGGTCGGATTTTTTTATAAAACTTTCGAG
1 TTCGGGTCGGATTTTTTT-TAAAAAAATCGAG
* *
117459 ATCGGGTCGG----TTTTTAAAAAAATCGGG
1 TTCGGGTCGGATTTTTTTTAAAAAAATCGAG
117486 ATT-GGGTCGGATTTTTTTTAAAAAAAATCGAG
1 -TTCGGGTCGGATTTTTTTT-AAAAAAATCGAG
117518 TTCGGGTCGGATTTTTTT
1 TTCGGGTCGGATTTTTTT
117536 AAGTGTGATA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
27 16 0.25
28 5 0.08
31 7 0.11
32 35 0.56
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (31 bp):
TTCGGGTCGGATTTTTTTTAAAAAAATCGAG
Found at i:118154 original size:18 final size:16
Alignment explanation
Indices: 118105--118154 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
118095 AGGTTTCAGA
118105 TTCAGATTTCAATTCC
1 TTCAGATTTCAATTCC
*
118121 TTCAGATTCCAATTCC
1 TTCAGATTTCAATTCC
*
118137 TTCACAGATTTCATTTCC
1 TT--CAGATTTCAATTCC
118155 CTAAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 17 0.59
18 12 0.41
ACGTcount: A:0.24, C:0.28, G:0.06, T:0.42
Consensus pattern (16 bp):
TTCAGATTTCAATTCC
Found at i:118464 original size:3 final size:3
Alignment explanation
Indices: 118456--118483 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
118446 AAAATCTCAA
118456 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
118484 TTTCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:124776 original size:22 final size:22
Alignment explanation
Indices: 124733--124776 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
124723 AAATTTACAT
*
124733 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
124755 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
124777 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:127266 original size:3 final size:3
Alignment explanation
Indices: 127260--127320 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
127250 AAAAAATATG
* **
127260 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
127304 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
127321 CGGAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:127949 original size:129 final size:129
Alignment explanation
Indices: 127520--127968 Score: 670
Period size: 129 Copynumber: 3.5 Consensus size: 129
127510 CGTCTAAGGG
* * * * * **
127520 TGACATGGTTCCTACGTGATGAAGACATCTGGTC-GAAGGATGACACTACTCATACATGATGAAG
1 TGACACGGCTCCTACGTGATGAAGAGATCTGATCTG-GGGATGACACGGCTCATACATGATGAAG
*
127584 AGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGAC-GCT-GTTATCTATGG
65 AGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
127647 T
129 T
* *
127648 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAAGAGATCTGATCTGGGG-ATGACACGGCTCATACATGATGAAG
127713 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
65 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * * ** *
127778 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGATCTGGGGATGACACGGCTCATACATGATGAAGA
*
127843 ATTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * *
127907 TGACACGGCTCCTACGTGATGAAGAGCTCTGATCTGGGGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGATCTGGGGATGACACGGCTCATACATGATGA
127969 GGACGGCTGG
Statistics
Matches: 293, Mismatches: 24, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
128 73 0.25
129 173 0.59
130 47 0.16
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGATCTGGGGATGACACGGCTCATACATGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:127973 original size:83 final size:83
Alignment explanation
Indices: 127609--127984 Score: 307
Period size: 83 Copynumber: 4.4 Consensus size: 83
127599 TAAGGTGATA
* *
127609 ACACGGTTCCTACGTGATGAGGAC-GCT-GTTATCTATGGTTGACACGGCTCCTACGTGATGAGG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTCATCTATGGTTGACACGGCTCCTACGTGATGAAG
*
127672 AGATCTGATCTGGGGAATG
66 AGCTCTGATCTGGGG-ATG
* * * * * * * *
127691 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCATCT-ATGGT--TGACACGGCTCCTACGTGAT
* * * ** *
127755 GAGGACGGCTGGTTATCTATGGTTG
62 GAAGA--GCT-CTGATCTGGGGATG
* * * * *
127780 ACACGGCTCCTACGTGATGAGGA-GATCTGGTCAGC--T-GATGACACGGCTCATACGTGATGAA
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCATCTATGGTTGACACGGCTCCTACGTGATGAA
** * *
127841 GAATTCTGGCCATCTAAAGGTGATA
65 GAGCTCT-G--ATCT---GGGGATG
*
127866 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTCATCTATGGTTGACACGGCTCCTACGTGATGAAG
127931 AGCTCTGATCTGGGGATG
66 AGCTCTGATCTGGGGATG
* *
127949 ACACGGTTCCTACATGATGAGGACGGCTGGCCATCT
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTCATCT
127985 TTAGGATTTA
Statistics
Matches: 227, Mismatches: 48, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
80 1 0.00
81 1 0.00
82 20 0.09
83 65 0.29
84 5 0.02
85 5 0.02
86 35 0.15
87 24 0.11
88 2 0.01
89 62 0.27
90 7 0.03
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (83 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTCATCTATGGTTGACACGGCTCCTACGTGATGAAG
AGCTCTGATCTGGGGATG
Found at i:128047 original size:28 final size:28
Alignment explanation
Indices: 127997--128050 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
127987 AGGATTTATG
* *
127997 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
128025 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
128051 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:128242 original size:66 final size:65
Alignment explanation
Indices: 128066--128248 Score: 201
Period size: 66 Copynumber: 2.8 Consensus size: 65
128056 TTTTAAAAGC
* * *
128066 AACTGTCTCAAAAGAGACCAAATTCGTTTTAAGGGAAACGA-CTCAAAGATGACATTTAAAGGGA
1 AACTGTCTCAAATGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATGACATTTAAAGGGA
* * * * * *
128130 AACTGTCTC--GTGCAAGACAAAATTCGTTTTTAAGGGAAACGTTCTCAAAGATCGACGTTTCAT
1 AACTGTCTCAAATG--AGACAAAATTC-ATTTTAAGGGAAACGATCTCAAAGAT-GACATTTAAA
128193 GGGA
62 GGGA
* * *
128197 AATTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCACAGATG
1 AACTGTCTCAAATGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATG
128249 TTTGTTTTGT
Statistics
Matches: 98, Mismatches: 14, Indels: 13
0.78 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
64 19 0.19
65 15 0.15
66 31 0.32
67 30 0.31
69 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (65 bp):
AACTGTCTCAAATGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATGACATTTAAAGGGA
Found at i:128474 original size:15 final size:15
Alignment explanation
Indices: 128450--128493 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
128440 AAGATGATCT
*
128450 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
128465 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
128480 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
128494 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:128870 original size:1 final size:1
Alignment explanation
Indices: 128864--128893 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
128854 ACAACATTTG
128864 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
128894 AAAAAGACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:129125 original size:67 final size:65
Alignment explanation
Indices: 128967--129159 Score: 252
Period size: 67 Copynumber: 3.0 Consensus size: 65
128957 AAAGATTTAC
* * * * * *
128967 TTCAAAAG-ACTGTCTTAAGAGATACAAAA-TTCATTT-TAAGAGAAACAGATTCAAAGATTTTT
1 TTCAAAAGAACTATCTTAAGAGAGACAAAATTTTATTTCCAA-AGAAACAAACTCAAAGATTTTT
129029 T
65 T
*
129030 TTTAAAAGAA--ATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAAAGATTTTTG
1 TTCAAAAGAACTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAAAGATTTTT-
129093 T
65 T
*
129094 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAG-AACTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAAAGATTTTT
129159 T
65 T
129160 GAAAGAAACA
Statistics
Matches: 114, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
62 16 0.14
63 33 0.29
64 11 0.10
65 2 0.02
66 1 0.01
67 51 0.45
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (65 bp):
TTCAAAAGAACTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAAAGATTTTTT
Found at i:129164 original size:26 final size:26
Alignment explanation
Indices: 129135--129185 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
129125 TTTTGTTTCC
129135 AAAGAAACAAACTCAAAGATTTTTTG
1 AAAGAAACAAACTCAAAGATTTTTTG
*
129161 AAAGAAACAATCTCAAAGATTTTTT
1 AAAGAAACAAACTCAAAGATTTTTT
129186 TCACAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (26 bp):
AAAGAAACAAACTCAAAGATTTTTTG
Found at i:129338 original size:25 final size:27
Alignment explanation
Indices: 129292--129385 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 27
129282 AAAACTTTGT
* *
129292 TTCAAAATAAATAGACTCAAAGATTT-
1 TTCAAAAGAAACAGACTCAAAGATTTA
129318 TTCAAAAGAAACA-ACTCAAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGA--TTTA
*
129346 TTCAAAAGGAACAGACTCAAAGATTTA
1 TTCAAAAGAAACAGACTCAAAGATTTA
*
129373 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
129386 TGTCTCCAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.16
26 11 0.19
27 8 0.14
28 21 0.36
29 9 0.16
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (27 bp):
TTCAAAAGAAACAGACTCAAAGATTTA
Found at i:129591 original size:66 final size:67
Alignment explanation
Indices: 129520--129652 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
129510 TTTGTTTTAA
129520 AATTCTCAAAATTTGTGG-AAAAATGTCTCAAGCGAGACATAATATGTTTTAAAGAGAAAGTTGT
1 AATTCTCAAAATTTGTGGAAAAAATGTCTCAAGCGAGACATAATATGTTTTAAAGAGAAAGTTGT
129584 CT
66 CT
* *
129586 AATTCTCAAAATTTGTGGAAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAGAGTTGT
1 AATTCTCAAAATTTGTGGAAAAAATGTCTCAAGCGAGACATAATATGTTTTAAAGAGAAAGTTGT
129651 CT
66 CT
129653 CAAGCGAGAC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 18 0.28
67 46 0.72
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (67 bp):
AATTCTCAAAATTTGTGGAAAAAATGTCTCAAGCGAGACATAATATGTTTTAAAGAGAAAGTTGT
CT
Found at i:129698 original size:36 final size:38
Alignment explanation
Indices: 129612--129698 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
129602 GGAAAAAATG
* ** *
129612 TCTCAAGCGAGACATAATTTGTTTTAAAGAGAGAGTTG
1 TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAGAACTA
*
129650 TCTCAAGCGAGACAAAATTTGTTTTTAAGA-A-AACTA
1 TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAGAACTA
*
129686 TCTCAAGTGAGAC
1 TCTCAAGCGAGAC
129699 GACACTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 14 0.33
37 1 0.02
38 28 0.65
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (38 bp):
TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAGAACTA
Found at i:130074 original size:16 final size:16
Alignment explanation
Indices: 130053--130128 Score: 60
Period size: 16 Copynumber: 5.2 Consensus size: 16
130043 TGTAACATGC
130053 ATGTATGTGTTGATGT
1 ATGTATGTGTTGATGT
*
130069 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
*
130081 ATGTATGAGTTGATGT
1 ATGTATGTGTTGATGT
*
130097 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
*
130109 ATGTATGAGTTGATGT
1 ATGTATGTGTTGATGT
130125 ATGT
1 ATGT
130129 TTCTCAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
12 18 0.40
13 2 0.04
14 1 0.02
15 2 0.04
16 22 0.49
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
ATGTATGTGTTGATGT
Found at i:130085 original size:28 final size:28
Alignment explanation
Indices: 130053--130128 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
130043 TGTAACATGC
*
130053 ATGTATGTGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
130081 ATGTATGAGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
130109 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
130129 TTCTCAATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (28 bp):
ATGTATGAGTTGATGTATGTATATATGT
Found at i:130128 original size:4 final size:4
Alignment explanation
Indices: 130065--130115 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
130055 GTATGTGTTG
* *
130065 ATGT ATGT ATAT ATGT ATGT ATG- A-GT -TG- ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
130109 ATGT ATG
1 ATGT ATG
130116 AGTTGATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 1 0.03
3 4 0.10
4 34 0.87
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:131311 original size:11 final size:11
Alignment explanation
Indices: 131295--131331 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
131285 GTCCCTTTTG
*
131295 TTCTTTGCTTT
1 TTCTTTGATTT
131306 TTCTTTGATTT
1 TTCTTTGATTT
*
131317 TGCTTTGATTT
1 TTCTTTGATTT
131328 TTCT
1 TTCT
131332 CTTTGCTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.05, C:0.14, G:0.11, T:0.70
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:132002 original size:45 final size:44
Alignment explanation
Indices: 131932--132016 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 44
131922 ATAAATGCAG
* * *
131932 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGGAA
*
131976 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGCCTCAAAGAGA
132017 TAGAATGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 11 0.31
45 25 0.69
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (44 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGGAA
Found at i:138481 original size:3 final size:3
Alignment explanation
Indices: 138473--138533 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
138463 AAAAAATATG
* **
138473 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
138517 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
138534 CGGAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:140561 original size:20 final size:20
Alignment explanation
Indices: 140526--140579 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 20
140516 AAGGATAAAA
*
140526 AATTAAACAAATTATT-TGT
1 AATTAAACAAATTATTATTT
140545 --TTAAACAAATTATTATTT
1 AATTAAACAAATTATTATTT
*
140563 AATTAAATAAATTATTA
1 AATTAAACAAATTATTA
140580 ACGACTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 14 0.47
18 2 0.07
20 14 0.47
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTAAACAAATTATTATTT
Found at i:140807 original size:106 final size:105
Alignment explanation
Indices: 140682--140941 Score: 301
Period size: 106 Copynumber: 2.5 Consensus size: 105
140672 TTTGATGATT
* * *
140682 ATTAACCGAACC-GAATTAATTTGAAAATTGTTAACTGAACCGAATTAACCAATTTTTTTAAAAA
1 ATTAATCGAACCAAAATTAATTTGAAAATTATTAACTGAACCGAATTAACCAA--TTTTTAAAAA
* *
140746 AAAAT-TATTAATCGAAGCAAAAATTAGGTTAATTCGGTTCG
64 AAAATCAATTAATCGAAGCAAAAATTAGGTTAATTCGGCTCG
* * * * * * ** **
140787 GTTAATCGAACCAAAATTAATTCGTAAATTATTAACCGAACCTAATTAACCGATTTTTAATTATT
1 ATTAATCGAACCAAAATTAATTTGAAAATTATTAACTGAACCGAATTAACCAATTTTTAAAAAAA
*
140852 AATCGAATTAATCGAAGCAAAAATTCGGTTAATTCGGCTCG
66 AATC-AATTAATCGAAGCAAAAATTAGGTTAATTCGGCTCG
* *
140893 ATTAATCGAACCAAAATTTATTTGAAAATTATTAA-TCGAACTGAATTAA
1 ATTAATCGAACCAAAATTAATTTGAAAATTATTAACT-GAACCGAATTAA
140942 TTTGAAAATT
Statistics
Matches: 128, Mismatches: 23, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
104 11 0.09
105 10 0.08
106 107 0.84
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (105 bp):
ATTAATCGAACCAAAATTAATTTGAAAATTATTAACTGAACCGAATTAACCAATTTTTAAAAAAA
AATCAATTAATCGAAGCAAAAATTAGGTTAATTCGGCTCG
Found at i:140947 original size:29 final size:29
Alignment explanation
Indices: 140893--140970 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
140883 ATTCGGCTCG
** *
140893 ATTAATCGAACCAAAATTTATTTGAAAATT
1 ATTAATCGAA-CTGAATTAATTTGAAAATT
140923 ATTAATCGAACTGAATTAATTTGAAAATT
1 ATTAATCGAACTGAATTAATTTGAAAATT
*
140952 ATTAACCGAACTGAATTAA
1 ATTAATCGAACTGAATTAA
140971 CCGATTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 34 0.77
30 10 0.23
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (29 bp):
ATTAATCGAACTGAATTAATTTGAAAATT
Found at i:141029 original size:128 final size:132
Alignment explanation
Indices: 140801--141070 Score: 379
Period size: 128 Copynumber: 2.1 Consensus size: 132
140791 ATCGAACCAA
*
140801 AATTAATTCGTAAATTATTAACCGAACCTAATTAACCGATTTTTAATTATTAATCGAATTAATCG
1 AATTAATTCGAAAATTATTAACCGAACCTAATTAACCGA-TTTT-ATTATTAATC-AATTAATCG
* * *
140866 AAGCAAAAATTCGGTTAATTCGGCTCGATTAATCGAACCAAAATTTATTTGAAAATTATTAATCG
63 AAGCAAAAATTCGGTTAATTCGGCTCGATTAATCGAACCAAAATTAATTTGAAAAATATTAACCG
*
140931 AACTG
128 AACCG
* *
140936 AATTAATTTGAAAATTATTAACCGAA-CTGAATTAACCGA-TTT-TT-TTAAT-TATTAATCGAA
1 AATTAATTCGAAAATTATTAACCGAACCT-AATTAACCGATTTTATTATTAATCAATTAATCGAA
* * *
140996 GCAAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTAATTTGAAAAATATTAACCGAG
65 GCAAAAATTCGGTTAATTCGGCTCGATTAATCGAACCAAAATTAATTTGAAAAATATTAACCGAA
141061 CCG
130 CCG
141064 AATTAAT
1 AATTAAT
141071 CGATTTTTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
128 78 0.63
130 5 0.04
131 2 0.02
133 3 0.02
134 2 0.02
135 34 0.27
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (132 bp):
AATTAATTCGAAAATTATTAACCGAACCTAATTAACCGATTTTATTATTAATCAATTAATCGAAG
CAAAAATTCGGTTAATTCGGCTCGATTAATCGAACCAAAATTAATTTGAAAAATATTAACCGAAC
CG
Found at i:141077 original size:234 final size:235
Alignment explanation
Indices: 140629--141078 Score: 659
Period size: 241 Copynumber: 1.9 Consensus size: 235
140619 GGTTAAAGAA
* * **
140629 AAAAAATCAGTTAATTCGGTTCGGTTAATCGAACAAAAATTTATTTGATGATTATTAACCGAACC
1 AAAAAATCAGTTAATTCGGCTCGATTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACC
* *
140694 GAATTAATTTGAAAATTGTTAACTGAACCGAATTAACCAATTTTTTTAAAAAAAAATTATTAATC
66 GAATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTT------AAATTATTAATC
* *
140759 GAAGCAAAAATTAGGTTAATTCGGTTCGGTTAATCGAACCAAAATTAATTCGTAAATTATTAACC
125 GAAGCAAAAATTAGGTTAATTCGGTTCGGTTAATCGAACCAAAATTAATTCGAAAAATATTAACC
*
140824 GAACCTAATTAACCGATTTTTAATTATTAATCGAATTAATCGAAGC
190 GAACCGAATTAACCGATTTTTAATTATTAATCGAATTAATCGAAGC
* * * * *
140870 AAAAATTCGGTTAATTCGGCTCGATTAATCGAACCAAAATTTATTTGAAAATTATTAATCGAACT
1 AAAAAATCAGTTAATTCGGCTCGATTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACC
* *
140935 GAATTAATTTGAAAATTATTAACCGAACTGAATTAACCGATTTTTTT-AATTATTAATCGAAGCA
66 GAATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGAAGCA
* * *
140999 AAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTAATTTGAAAAATATTAACCGAGCCG
131 AAAATTAGGTTAATTCGGTTCGGTTAATCGAACCAAAATTAATTCGAAAAATATTAACCGAACCG
*
141064 AATTAATCGATTTTT
196 AATTAACCGATTTTT
141079 TTCTTTAACC
Statistics
Matches: 189, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
234 90 0.48
241 99 0.52
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (235 bp):
AAAAAATCAGTTAATTCGGCTCGATTAATCGAACAAAAATTTATTTGAAAATTATTAACCGAACC
GAATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGAAGCA
AAAATTAGGTTAATTCGGTTCGGTTAATCGAACCAAAATTAATTCGAAAAATATTAACCGAACCG
AATTAACCGATTTTTAATTATTAATCGAATTAATCGAAGC
Found at i:141657 original size:29 final size:29
Alignment explanation
Indices: 141625--141746 Score: 160
Period size: 29 Copynumber: 4.3 Consensus size: 29
141615 TTAACGGCGC
**
141625 GGTGGTCTGATTGA-ATCAATTAAAAGTTT
1 GGTGGTCTGATTGAGAT-AAAAAAAAGTTT
141654 GGTGGTCTGATTGAGATAAAAAAAAGTTT
1 GGTGGTCTGATTGAGATAAAAAAAAGTTT
*
141683 AGTGGTCTGATTGAGATAAAAAAAAGTTT
1 GGTGGTCTGATTGAGATAAAAAAAAGTTT
* * *
141712 AGTGGTCTGATTGAG--ACAAAAAAGTTC
1 GGTGGTCTGATTGAGATAAAAAAAAGTTT
141739 GGTGGTCT
1 GGTGGTCT
141747 CCCGTGTAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
27 17 0.20
29 67 0.78
30 2 0.02
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (29 bp):
GGTGGTCTGATTGAGATAAAAAAAAGTTT
Found at i:142198 original size:2 final size:2
Alignment explanation
Indices: 142191--142221 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
142181 TTAACTCCAA
142191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
142222 ATTCTTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:142246 original size:80 final size:75
Alignment explanation
Indices: 142090--142264 Score: 192
Period size: 80 Copynumber: 2.3 Consensus size: 75
142080 TTATTCTTAT
* * * *
142090 TATA-TTTATTATATCTTAACTTCAAATAAATATTATTAAAACAATATATTTTATTCTTTTATTA
1 TATATTTTATTATATCTTAACTCCAAATAAATATTATTAAAACAATATATATAATTCTTGTATTA
* *
142154 ACTTAAAGAA
66 ACCTAAAAAA
* * *
142164 TATATTTTATTATTATCTTAACTCCAAATATATATATATATATATATATATATATATAATTCTTG
1 TATATTTTATTA-TATCTTAACTCCAAATAAATAT-TAT-TA-AAACA-ATATATATAATTCTTG
142229 TATTAACCTAAAAAA
61 TATTAACCTAAAAAA
142244 TATATTTT-TTAAATATCTTAA
1 TATATTTTATT--ATATCTTAA
142265 GTTAATAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
74 4 0.05
75 7 0.08
76 20 0.24
77 3 0.04
78 2 0.02
79 5 0.06
80 42 0.50
81 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.48
Consensus pattern (75 bp):
TATATTTTATTATATCTTAACTCCAAATAAATATTATTAAAACAATATATATAATTCTTGTATTA
ACCTAAAAAA
Found at i:142328 original size:28 final size:31
Alignment explanation
Indices: 142256--142344 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 31
142246 TATTTTTTAA
*
142256 ATATCTTAAGTT-AATAAAATAATCAAATAT
1 ATATTTTAAGTTAAATAAAATAATCAAATAT
* * *
142286 ATTATTTGAATTTAAAT-TAATAA-CAAA-AT
1 A-TATTTTAAGTTAAATAAAATAATCAAATAT
* *
142315 ATATTTTAAGTT-AATAAAAGAATAAAATAT
1 ATATTTTAAGTTAAATAAAATAATCAAATAT
142345 GTTTTCAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
27 3 0.07
28 13 0.29
29 6 0.13
30 7 0.16
31 13 0.29
32 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.38
Consensus pattern (31 bp):
ATATTTTAAGTTAAATAAAATAATCAAATAT
Found at i:150167 original size:15 final size:16
Alignment explanation
Indices: 150147--150176 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
150137 ATCTAATTCT
150147 TAATTGA-TCTCAAAC
1 TAATTGAGTCTCAAAC
150162 TAATTGAGTCTCAAA
1 TAATTGAGTCTCAAA
150177 GTAAACACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (16 bp):
TAATTGAGTCTCAAAC
Found at i:151190 original size:21 final size:20
Alignment explanation
Indices: 151152--151190 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
151142 ATTTATTAAA
*
151152 CAAAATAAAATAACAAAACT
1 CAAAATAAAAGAACAAAACT
*
151172 CAAATATAAAAGAATAAAA
1 CAAA-ATAAAAGAACAAAA
151191 TTGAAGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (20 bp):
CAAAATAAAAGAACAAAACT
Found at i:152680 original size:7 final size:7
Alignment explanation
Indices: 152653--152760 Score: 76
Period size: 7 Copynumber: 15.7 Consensus size: 7
152643 GATTACACCA
*
152653 TAAACTC
1 TAAACCC
152660 TAAA-CC
1 TAAACCC
152666 TAAA-CC
1 TAAACCC
152672 TAAACCC
1 TAAACCC
* *
152679 TAAATCA
1 TAAACCC
* *
152686 TATACCA
1 TAAACCC
*
152693 TAAACTC
1 TAAACCC
* *
152700 TAAATCT
1 TAAACCC
*
152707 TAAATCC
1 TAAACCC
*
152714 TAAACCA
1 TAAACCC
*
152721 TAAACAC
1 TAAACCC
*
152728 TAAACCT
1 TAAACCC
*
152735 TAGACCC
1 TAAACCC
152742 TAAACCC
1 TAAACCC
*
152749 TAAGCCC
1 TAAACCC
152756 TAAAC
1 TAAAC
152761 TCTTAATCTG
Statistics
Matches: 77, Mismatches: 23, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
6 11 0.14
7 66 0.86
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:152736 original size:28 final size:27
Alignment explanation
Indices: 152659--152766 Score: 101
Period size: 28 Copynumber: 3.9 Consensus size: 27
152649 ACCATAAACT
*
152659 CTAAACC-TAAACCTAAACCCTAAATC
1 CTAAACCATAAACCTAAACCTTAAATC
* * *
152685 ATATACCATAAACTCTAAATCTTAAATC
1 CTAAACCATAAAC-CTAAACCTTAAATC
* *
152713 CTAAACCATAAACACTAAACCTTAGACC
1 CTAAACCATAAAC-CTAAACCTTAAATC
* *
152741 CTAAACCCTAAGCCCTAAACTCTTAA
1 CTAAACCATAA-ACCTAAAC-CTTAA
152767 TCTGATTATG
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
26 5 0.08
27 5 0.08
28 50 0.77
29 5 0.08
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.23
Consensus pattern (27 bp):
CTAAACCATAAACCTAAACCTTAAATC
Found at i:154672 original size:23 final size:24
Alignment explanation
Indices: 154640--154689 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
154630 AAAGAGGTAC
* *
154640 CAAAAGACATAAAAAAACGTGTCA
1 CAAAAGACATAAAAAAACATGCCA
154664 CAAAA-ACATAAAAAAACATGCCA
1 CAAAAGACATAAAAAAACATGCCA
154687 CAA
1 CAA
154690 TAGTAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.62, C:0.20, G:0.08, T:0.10
Consensus pattern (24 bp):
CAAAAGACATAAAAAAACATGCCA
Found at i:161069 original size:3 final size:3
Alignment explanation
Indices: 161061--161095 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
161051 TTGAGAAAAT
161061 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
161096 CTATATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:161362 original size:29 final size:29
Alignment explanation
Indices: 161320--161405 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 29
161310 AGTGTTGGCC
** *
161320 GTAGGTCGCCATGCACTATGGGTGACCTT
1 GTAGGTCGCCATGCACTACAGGCGACCTT
*
161349 GTAGGTCGCCATGCACTCCAGGCGACCTT
1 GTAGGTCGCCATGCACTACAGGCGACCTT
* *
161378 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTACAGGCGACCT
161406 ACCCTTGCTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTACAGGCGACCTT
Found at i:161498 original size:29 final size:29
Alignment explanation
Indices: 161464--161519 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
161454 TCCCAACACT
*
161464 TAGGTCACCATGCCCTCCGGGCAACCTTG
1 TAGGTCACCATGCACTCCGGGCAACCTTG
* *
161493 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCACCATGCACTCCGGGCAACCT
161520 ACCCTTGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.38, G:0.27, T:0.20
Consensus pattern (29 bp):
TAGGTCACCATGCACTCCGGGCAACCTTG
Found at i:161607 original size:33 final size:33
Alignment explanation
Indices: 161526--161592 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
161516 ACCTACCCTT
*
161526 GCTCGGCTT-CCCTCGGATTCCCTCGCATAGCTC
1 GCTCGG-TTGCCCTCGGATGCCCTCGCATAGCTC
161559 GCTCGGTTGCCCTCGGATGCCCTCGCATAGCTC
1 GCTCGGTTGCCCTCGGATGCCCTCGCATAGCTC
161592 G
1 G
161593 TTCGTATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.09, C:0.40, G:0.25, T:0.25
Consensus pattern (33 bp):
GCTCGGTTGCCCTCGGATGCCCTCGCATAGCTC
Found at i:161701 original size:29 final size:29
Alignment explanation
Indices: 161664--161721 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
161654 GCAATCTCTT
**
161664 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCAGAAGACATGGCGACCTA
* *
161693 GTAGGTCGCCCAGAAGGCATGGCGACCTA
1 GTAGCTCGCCCAGAAGACATGGCGACCTA
161722 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCAGAAGACATGGCGACCTA
Found at i:163490 original size:30 final size:30
Alignment explanation
Indices: 163456--163520 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
163446 CAACCAATAG
* *
163456 AAAATGAGAGG-GGCAAAATCAAAATAAATC
1 AAAATGAG-GGAGACAAAATCAAAATAAACC
*
163486 AAAATGAGGGAGACAAAATTAAAATAAACC
1 AAAATGAGGGAGACAAAATCAAAATAAACC
163516 AAAAT
1 AAAAT
163521 TTGAAGGTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.60, C:0.09, G:0.17, T:0.14
Consensus pattern (30 bp):
AAAATGAGGGAGACAAAATCAAAATAAACC
Found at i:175814 original size:42 final size:42
Alignment explanation
Indices: 175767--175863 Score: 106
Period size: 44 Copynumber: 2.3 Consensus size: 42
175757 ACCCAGCCTG
* *
175767 ATAAATTTAA-AAATGATTATTATATATATATATATAATATTA
1 ATAAATTTAATAAATGA-AAATATATATATATATATAATATTA
* * *
175809 ATAAATTCAATTTAAATTAAAATATATATATATATATAATATTT
1 ATAAATTTAA--TAAATGAAAATATATATATATATATAATATTA
*
175853 ATATATTTAAT
1 ATAAATTTAAT
175864 TTAAATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
42 10 0.22
44 30 0.67
45 5 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (42 bp):
ATAAATTTAATAAATGAAAATATATATATATATATAATATTA
Found at i:175837 original size:2 final size:2
Alignment explanation
Indices: 175830--175881 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
175820 TTAAATTAAA
* * * *
175830 AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
175870 AT AT AT AT AT AT
1 AT AT AT AT AT AT
175882 CCGGCCCGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:175850 original size:44 final size:42
Alignment explanation
Indices: 175787--175881 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 42
175777 AAATGATTAT
175787 TATATATATATATATAATATTAATAAATTCAATTTAAATTAAAA
1 TATATATATATATATAATATTAATAAATTCAATTTAAA-T-AAA
* * * *
175831 TATATATATATATATAATATTTATATATTTAATTTAAATATA
1 TATATATATATATATAATATTAATAAATTCAATTTAAATAAA
175873 TATATATAT
1 TATATATAT
175882 CCGGCCCGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 11 0.23
43 1 0.02
44 35 0.74
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (42 bp):
TATATATATATATATAATATTAATAAATTCAATTTAAATAAA
Found at i:178588 original size:127 final size:127
Alignment explanation
Indices: 178359--178797 Score: 729
Period size: 127 Copynumber: 3.5 Consensus size: 127
178349 GTACTATTCA
*
178359 CGTGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
178424 TATTATGTCACTTATGTCCCCCAGG-AACTATTAATGTCAATACATATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCC-GGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
*
178486 CGTGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
178551 TATTATATCACTTATGTCCCCCGGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
* * * * *
178613 CGTAAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATATTATAATTGCCA
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* *
178678 TATTATGTCACTTATGTCCCCCGGAAACTATTCATGTCAATACCTATTATTCCTTAGGGGAT
66 TATTATGTCACTTATGTCCCCCGGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
* **
178740 CATGAAGGCGCGTT-CCGGGGGCATGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
178798 GCAAAATAAA
Statistics
Matches: 291, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
126 42 0.14
127 249 0.86
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
TATTATGTCACTTATGTCCCCCGGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
Found at i:179232 original size:226 final size:227
Alignment explanation
Indices: 178809--179256 Score: 889
Period size: 226 Copynumber: 2.0 Consensus size: 227
178799 CAAAATAAAG
178809 GTAAAGCGCCTTCACACGTGGCAACTGAATCAGCAAAATAAAGGTAAAGCGCGTCCCCGGGGATG
1 GTAAAGCGCCTTCACACGTGGCAACTGAATCAGCAAAATAAAGGTAAAGCGCGTCCCCGGGGATG
178874 CACCTTTCGCCACTTCAGCCGAAAGGGTGCCACTTCGGGAAATATAGAACAAACAGTGCTAAAAA
66 CACCTTTCGCCACTTCAGCCGAAAGGGTGCCACTTCGGGAAATATAGAACAAACAGTGCTAAAAA
178939 GAGAGATATTCGGTTAAAGGGTGTCAGTTTGGTCAAATCGCCTAAATATTCGGTTCGCAGGGATT
131 GAGAGATATTCGGTTAAAGGGTGTCAGTTTGGTCAAATCGCCTAAATATTCGGTTCGCAGGGATT
179004 CCTCAGCATACGACACGTAATTAAACTCTATT
196 CCTCAGCATACGACACGTAATTAAACTCTATT
179036 GTAAAGCGCCTTCACACGTGGCAACTGAATCAGCAAAATAAAGGTAAAGCGCGTCCCCGGGGATG
1 GTAAAGCGCCTTCACACGTGGCAACTGAATCAGCAAAATAAAGGTAAAGCGCGTCCCCGGGGATG
179101 CACCTTTCGCCACTTCAGCCGAAAGGGTGCCAC-TCGGGAAATATAGAACAAACAGTGCTAAAAA
66 CACCTTTCGCCACTTCAGCCGAAAGGGTGCCACTTCGGGAAATATAGAACAAACAGTGCTAAAAA
179165 GAGAGATATTCGGTTAAAGGGTGTCAGTTTGGTCAAATCGCCTAAATATTCGGTTCGCAGGGATT
131 GAGAGATATTCGGTTAAAGGGTGTCAGTTTGGTCAAATCGCCTAAATATTCGGTTCGCAGGGATT
179230 CCTCAGCATACGACACGTAATTAAACT
196 CCTCAGCATACGACACGTAATTAAACT
179257 GTCTATTTTA
Statistics
Matches: 221, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
226 123 0.56
227 98 0.44
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (227 bp):
GTAAAGCGCCTTCACACGTGGCAACTGAATCAGCAAAATAAAGGTAAAGCGCGTCCCCGGGGATG
CACCTTTCGCCACTTCAGCCGAAAGGGTGCCACTTCGGGAAATATAGAACAAACAGTGCTAAAAA
GAGAGATATTCGGTTAAAGGGTGTCAGTTTGGTCAAATCGCCTAAATATTCGGTTCGCAGGGATT
CCTCAGCATACGACACGTAATTAAACTCTATT
Found at i:180113 original size:2 final size:2
Alignment explanation
Indices: 180102--180134 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
180092 GGAATTTATT
180102 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
180135 AATGATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:180931 original size:25 final size:25
Alignment explanation
Indices: 180901--180956 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
180891 ATATTAATGG
180901 TTAAAA-TTTATT-ATATTATCTTGAA
1 TTAAAATTTTATTAATATT-T-TTGAA
180926 TTAAAACTTTTTATTAATATTTTTGAA
1 TTAAAA--TTTTATTAATATTTTTGAA
180953 TTAA
1 TTAA
180957 GATTAAATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
25 6 0.22
27 9 0.33
28 7 0.26
29 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
TTAAAATTTTATTAATATTTTTGAA
Found at i:185066 original size:2 final size:2
Alignment explanation
Indices: 185059--185085 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
185049 TTATATTCAC
185059 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
185086 GGTCTCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:186092 original size:24 final size:23
Alignment explanation
Indices: 186065--186119 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
186055 TTATTTATTT
* * *
186065 TTAAAAATTAAAATTTATAAAATG
1 TTAAAAATAAAAATATA-AAAATA
186089 TTAAAATATAAAAATATAAAAATA
1 TTAAAA-ATAAAAATATAAAAATA
186113 TTAAAAA
1 TTAAAAA
186120 ACCAATTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 17 0.63
25 9 0.33
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAAAATAAAAATATAAAAATA
Found at i:186095 original size:8 final size:8
Alignment explanation
Indices: 186065--186118 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
186055 TTATTTATTT
186065 TTAAAA-A
1 TTAAAATA
*
186072 TTAAAATT
1 TTAAAATA
*
186080 TATAAAATG
1 T-TAAAATA
186089 TTAAAATA
1 TTAAAATA
*
186097 TAAAAATA
1 TTAAAATA
*
186105 TAAAAATA
1 TTAAAATA
186113 TTAAAA
1 TTAAAA
186119 AACCAATTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
7 6 0.15
8 27 0.68
9 7 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (8 bp):
TTAAAATA
Found at i:187634 original size:2 final size:2
Alignment explanation
Indices: 187629--187653 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
187619 TTAAACGTGT
187629 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
187654 GAAAGTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:188640 original size:64 final size:65
Alignment explanation
Indices: 188529--188672 Score: 193
Period size: 64 Copynumber: 2.2 Consensus size: 65
188519 TTTAAAATTA
* * *
188529 AAGTAAATTTAATATTTTTAAAATAAATTAAGGTTTGATTCATTTTATTGTTTTCATTATAATAC
1 AAGTAAATTTAATATTTCTAAAATAAATAAAGATTTGATTCATTTTATTGTTTTCATTATAATAC
* * *
188594 AAGTATATTTAATATTCTCT-AAA-AAATAAAGATTTGATTCATTTTATTGTTTTCGTTGTAATA
1 AAGTAAATTTAATATT-TCTAAAATAAATAAAGATTTGATTCATTTTATTGTTTTCATTATAATA
188657 C
65 C
*
188658 AAGTTAAATATAATA
1 AAG-TAAATTTAATA
188673 CGTTTTAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 40 0.58
65 27 0.39
66 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (65 bp):
AAGTAAATTTAATATTTCTAAAATAAATAAAGATTTGATTCATTTTATTGTTTTCATTATAATAC
Found at i:189102 original size:23 final size:23
Alignment explanation
Indices: 189049--189111 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
189039 TTTTTCAACA
*
189049 TATTCGTTTAGTGTTTGCCAAAT
1 TATTCGTTTAATGTTTGCCAAAT
* * *
189072 TATCCGTTTAATTTTTG-CGAAT
1 TATTCGTTTAATGTTTGCCAAAT
189094 GTATTCGTTTATATGTTT
1 -TATTCGTTTA-ATGTTT
189112 AGAAATTGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 4 0.12
23 23 0.72
24 5 0.16
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (23 bp):
TATTCGTTTAATGTTTGCCAAAT
Found at i:193891 original size:102 final size:101
Alignment explanation
Indices: 193719--193904 Score: 302
Period size: 104 Copynumber: 1.8 Consensus size: 101
193709 ATTCAAAAAA
*
193719 AAGATAGATAAAAATGCATTGAAATTAGATATATAAACATACTATTTTTTTGTAATTTTTCTGAT
1 AAGATAGATAAAAAT-CATTGAAATTAGATAAATAAACATACTATTTTTTTGTAATTTTTCTGAT
*
193784 TTTTTTTATTTTTTTAAATTCAAGTATATTAATTTGC
65 TTTTTGTATTTTTTTAAATTCAAGTATATTAATTTGC
193821 AAGATAGATAAAAAT-ATATGAAAATTAGATAAATAAACATACTAATTTTTTTTGTAATTTTTCT
1 AAGATAGATAAAAATCAT-TG-AAATTAGATAAATAAACATACT-A-TTTTTTTGTAATTTTTCT
193885 GATTTTTTGTATTTTTTTAA
62 GATTTTTTGTATTTTTTTAA
193905 TTTTTTAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
100 2 0.03
101 2 0.03
102 36 0.46
103 1 0.01
104 37 0.47
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (101 bp):
AAGATAGATAAAAATCATTGAAATTAGATAAATAAACATACTATTTTTTTGTAATTTTTCTGATT
TTTTGTATTTTTTTAAATTCAAGTATATTAATTTGC
Done.