Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 70 of 171
Found at i:25411616 original size:20 final size:20
Alignment explanation
Indices: 25411562--25411616 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
25411552 TCAACGGTCG
* *
25411562 GTCAACGTCGATAAATGCCA
1 GTCAACGTCGATCAACGCCA
25411582 GTCAACGTCGATCAACGCCA
1 GTCAACGTCGATCAACGCCA
*
25411602 GTCAACGTCGGTCAA
1 GTCAACGTCGATCAA
25411617 TGGTTTGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (20 bp):
GTCAACGTCGATCAACGCCA
Found at i:25411673 original size:15 final size:15
Alignment explanation
Indices: 25411653--25411682 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25411643 TGGTTCATTT
25411653 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
25411668 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
25411683 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:25411692 original size:21 final size:21
Alignment explanation
Indices: 25411666--25411733 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
25411656 TTGGTTCAAA
25411666 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
25411687 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
*
25411708 TGAGTTTGGTTTAAATAGAATT
1 TGGGTTTGGTTTAAAT-GAATT
25411730 TGGG
1 TGGG
25411734 CTTAATGGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 35 0.83
22 7 0.17
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:25412127 original size:12 final size:12
Alignment explanation
Indices: 25412112--25412176 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
25412102 TTAAAAGAGG
*
25412112 AAGAAAATAGAA
1 AAGAAAAGAGAA
25412124 AAGAAAAGAGAA
1 AAGAAAAGAGAA
25412136 AA-AAATA-AGAA
1 AAGAAA-AGAGAA
* *
25412147 ATG-AATGAGAAA
1 AAGAAAAGAG-AA
25412159 AAGAAAAGAGAA
1 AAGAAAAGAGAA
*
25412171 AGGAAA
1 AAGAAA
25412177 GATGAGAGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
11 12 0.29
12 25 0.60
13 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (12 bp):
AAGAAAAGAGAA
Found at i:25412130 original size:23 final size:23
Alignment explanation
Indices: 25412104--25412178 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
25412094 AAGTATTATT
*
25412104 AAAAGAGGAAGAAAAT-AGAAAAG
1 AAAAGA-GAAAAAAATAAGAAAAG
*
25412127 AAAAGAGAAAAAAATAAGAAATG
1 AAAAGAGAAAAAAATAAGAAAAG
*
25412150 -AATGAGAAAAAGAA-AAGAGAAAG
1 AAAAGAGAAAAA-AATAAGA-AAAG
*
25412173 GAAAGA
1 AAAAGA
25412179 TGAGAGGCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 22 0.51
23 17 0.40
24 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAAAAATAAGAAAAG
Found at i:25412172 original size:11 final size:11
Alignment explanation
Indices: 25412104--25412178 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
25412094 AAGTATTATT
*
25412104 AAAAGAGGAAG
1 AAAAGAGAAAG
*
25412115 AAAATAGAAAAG
1 AAAAGAG-AAAG
25412127 AAAAGAGAAA-
1 AAAAGAGAAAG
*
25412137 AAAATAAGAAATG
1 AAAA-GAGAAA-G
* *
25412150 AATGAGAAAAAG
1 AA-AAGAGAAAG
25412162 AAAAGAGAAAG
1 AAAAGAGAAAG
*
25412173 GAAAGA
1 AAAAGA
25412179 TGAGAGGCTT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
10 4 0.08
11 26 0.53
12 12 0.24
13 6 0.12
14 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:25417568 original size:3 final size:3
Alignment explanation
Indices: 25417560--25417592 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
25417550 TACATCCCAA
25417560 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
25417593 GAATAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:25418656 original size:20 final size:20
Alignment explanation
Indices: 25418625--25418676 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
25418615 GTTTTTCAAA
*
25418625 AAAGTTAACGGTCAA-AGTC
1 AAAGTCAACGGTCAACAGTC
*
25418644 AAAGGTCAACGGTCAACGGTC
1 AAA-GTCAACGGTCAACAGTC
25418665 AAAGTCAACGGT
1 AAAGTCAACGGT
25418677 TAACGTTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 20 0.69
21 6 0.21
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGGTCAACAGTC
Found at i:25418657 original size:7 final size:7
Alignment explanation
Indices: 25418631--25418681 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
25418621 CAAAAAAGTT
25418631 AACGGTC
1 AACGGTC
*
25418638 AA-AGTC
1 AACGGTC
*
25418644 AAAGGTC
1 AACGGTC
25418651 AACGGTC
1 AACGGTC
25418658 AACGGTC
1 AACGGTC
*
25418665 AA-AGTC
1 AACGGTC
*
25418671 AACGGTT
1 AACGGTC
25418678 AACG
1 AACG
25418682 TTCGGTCAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 10 0.28
7 26 0.72
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (7 bp):
AACGGTC
Found at i:25418673 original size:13 final size:13
Alignment explanation
Indices: 25418625--25418676 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
25418615 GTTTTTCAAA
*
25418625 AAAGTTAACGGTC
1 AAAGTCAACGGTC
*
25418638 AAAGTCAAAGGTC
1 AAAGTCAACGGTC
*
25418651 AACGGTCAACGGTC
1 AA-AGTCAACGGTC
25418665 AAAGTCAACGGT
1 AAAGTCAACGGT
25418677 TAACGTTCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:25418777 original size:15 final size:15
Alignment explanation
Indices: 25418757--25418786 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25418747 TGGTTAATTT
25418757 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
25418772 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
25418787 AATTTGAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:25418799 original size:21 final size:21
Alignment explanation
Indices: 25418773--25418835 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
25418763 GTTCAAATGG
25418773 GTTTGGTTTAAATGAATTTGA
1 GTTTGGTTTAAATGAATTTGA
* *
25418794 GTTTGGTTTAAATGAATGTGG
1 GTTTGGTTTAAATGAATTTGA
25418815 GTTTGGTTTAAATAGAATTTG
1 GTTTGGTTTAAAT-GAATTTG
25418836 GGCTTAATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 32 0.84
22 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
GTTTGGTTTAAATGAATTTGA
Found at i:25419241 original size:11 final size:11
Alignment explanation
Indices: 25419208--25419282 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
25419198 AAGTGTGATT
* *
25419208 AAAAGAGGATG
1 AAAAGAGAAAG
*
25419219 AAAATAGAAAAG
1 AAAAGAG-AAAG
25419231 AAAAGAGAAAG
1 AAAAGAGAAAG
25419242 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
25419254 AATGAGAAAAAG
1 AA-AAGAGAAAG
25419266 AAAAGAGAAAG
1 AAAAGAGAAAG
*
25419277 GAAAGA
1 AAAAGA
25419283 TGAGAGGCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
11 30 0.60
12 16 0.32
13 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.25, T:0.07
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:25419459 original size:13 final size:13
Alignment explanation
Indices: 25419441--25419491 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
25419431 CCAAAAATTT
25419441 AACATACATTATC
1 AACATACATTATC
25419454 AACATACATTAT-
1 AACATACATTATC
*
25419466 ATGCATGACATTATC
1 A-ACAT-ACATTATC
25419481 AACATACATTA
1 AACATACATTA
25419492 CACAACTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 1 0.03
13 21 0.64
14 10 0.30
15 1 0.03
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (13 bp):
AACATACATTATC
Found at i:25420547 original size:18 final size:18
Alignment explanation
Indices: 25420526--25420560 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25420516 AATGATATAT
*
25420526 TAATTAATAATAATATTA
1 TAATAAATAATAATATTA
25420544 TAATAAATAATAATATT
1 TAATAAATAATAATATT
25420561 TTATTATTTA
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:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:25422015 original size:18 final size:19
Alignment explanation
Indices: 25421989--25422029 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
25421979 AAATTTCCTT
*
25421989 ATTATGTGA-ATTAAATTG
1 ATTAAGTGATATTAAATTG
*
25422007 ATTAAGTGATTTTAAATTG
1 ATTAAGTGATATTAAATTG
25422026 ATTA
1 ATTA
25422030 CAAAGCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (19 bp):
ATTAAGTGATATTAAATTG
Found at i:25422079 original size:11 final size:11
Alignment explanation
Indices: 25422063--25422089 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
25422053 CTTTTATTAA
25422063 TTAATCTATAT
1 TTAATCTATAT
25422074 TTAATCTATAT
1 TTAATCTATAT
25422085 TTAAT
1 TTAAT
25422090 GATTTATACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAATCTATAT
Found at i:25427619 original size:7 final size:7
Alignment explanation
Indices: 25427607--25427631 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25427597 AATTAAGTCC
25427607 AAATTTT
1 AAATTTT
25427614 AAATTTT
1 AAATTTT
25427621 AAATTTT
1 AAATTTT
25427628 AAAT
1 AAAT
25427632 AAGTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:25427686 original size:17 final size:17
Alignment explanation
Indices: 25427666--25427702 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
25427656 TTTGAGTTTC
25427666 AATTTACTTTAAATTAA
1 AATTTACTTTAAATTAA
*
25427683 AATTTATTTTAAATTAA
1 AATTTACTTTAAATTAA
25427700 AAT
1 AAT
25427703 AAAATTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTACTTTAAATTAA
Found at i:25428493 original size:3 final size:3
Alignment explanation
Indices: 25428485--25428541 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
25428475 CAGAACGTTT
*
25428485 TAA TAA TAA TAA TAA TAA T-A TATA TAA -AA -AA TTAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA -TAA TAA TAA TAA
25428529 TAA -AA TAA TAA TA
1 TAA TAA TAA TAA TA
25428542 TTAAAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 34 0.72
4 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:25428522 original size:20 final size:17
Alignment explanation
Indices: 25428495--25428549 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
25428485 TAATAATAAT
25428495 AATAATAATATATATAAAA
1 AATAATAATAT-TA-AAAA
*
25428514 AATTAATAATATTAATAA
1 AA-TAATAATATTAAAAA
25428532 AATAATAATATTAAAAA
1 AATAATAATATTAAAAA
25428549 A
1 A
25428550 GATTTGAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 15 0.45
18 5 0.15
19 4 0.12
20 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATATTAAAAA
Found at i:25428537 original size:17 final size:16
Alignment explanation
Indices: 25428485--25428549 Score: 71
Period size: 17 Copynumber: 4.0 Consensus size: 16
25428475 CAGAACGTTT
* *
25428485 TAATAATAAT-AATAA
1 TAATAATATTAAAAAA
25428500 TAAT-ATATATAAAAAA
1 TAATAATAT-TAAAAAA
25428516 TTAATAATATTAATAAAA
1 -TAATAATATTAA-AAAA
25428534 TAATAATATTAAAAAA
1 TAATAATATTAAAAAA
25428550 GATTTGAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
14 3 0.07
15 5 0.12
16 8 0.19
17 19 0.44
18 8 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATAATATTAAAAAA
Found at i:25429810 original size:29 final size:29
Alignment explanation
Indices: 25429647--25429859 Score: 147
Period size: 29 Copynumber: 7.4 Consensus size: 29
25429637 AAGGTCCCTA
* *
25429647 AACTGTCCAAAAATTATATTTTCA-CCTCCG
1 AACT-TCCAAAAATTACATTTTTACCCT-CG
* * **
25429677 AACTTCTAAAAATTACATTTTTGGCCCTAA
1 AACTTCCAAAAATTACATTTTT-ACCCTCG
* *
25429707 AACTTTCAAAAATTACA-TTTTACCC-AG
1 AACTTCCAAAAATTACATTTTTACCCTCG
* * *
25429734 AACTT-CAAAAATTCCATTTTTAACC-CA
1 AACTTCCAAAAATTACATTTTTACCCTCG
*
25429761 AACCTTCCCAAAATTACATTTTTACCCTCG
1 AA-CTTCCAAAAATTACATTTTTACCCTCG
*
25429791 AACTTCCAAAAATT-CTATTTTTGACCC-CAA
1 AACTTCCAAAAATTAC-ATTTTT-ACCCTC-G
* **
25429821 AACTTTC-AAAATTACCCTTTTACCCTCG
1 AACTTCCAAAAATTACATTTTTACCCTCG
25429849 AA-TGTCCAAAA
1 AACT-TCCAAAA
25429860 TTCTATTTTT
Statistics
Matches: 145, Mismatches: 25, Indels: 27
0.74 0.13 0.14
Matches are distributed among these distances:
26 10 0.07
27 16 0.11
28 15 0.10
29 68 0.47
30 33 0.23
31 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCG
Found at i:25429811 original size:58 final size:57
Alignment explanation
Indices: 25429646--25429869 Score: 201
Period size: 58 Copynumber: 3.9 Consensus size: 57
25429636 GAAGGTCCCT
* * * **
25429646 AAACTGTCCAAAAATTATATTTTCA-CCTCCGAACTTCTAAAAATTAC-ATTTTTGGCCCTA
1 AAACT-TCC-AAAATTACATTTTTACCCT-CGAACTTCCAAAAATT-CTATTTTTAACCC-A
* * *
25429706 AAACTTTCAAAAATTACA-TTTTACCC-AGAACTT-CAAAAATTCCATTTTTAACCCA
1 AAAC-TTCCAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCTATTTTTAACCCA
* *
25429761 AACCTTCCCAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCTATTTTTGACCCCA
1 AAACTT-CCAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCTATTTTT-AACCCA
* **
25429820 AAACTTTCAAAATTACCCTTTTACCCTCGAA-TGTCC-AAAATTCTATTTTT
1 AAACTTCCAAAATTACATTTTTACCCTCGAACT-TCCAAAAATTCTATTTTT
25429870 GATCCCGATT
Statistics
Matches: 139, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
54 2 0.01
55 15 0.11
56 24 0.17
57 27 0.19
58 44 0.32
59 20 0.14
60 6 0.04
61 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (57 bp):
AAACTTCCAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCTATTTTTAACCCA
Found at i:25429890 original size:58 final size:58
Alignment explanation
Indices: 25429770--25429968 Score: 184
Period size: 58 Copynumber: 3.5 Consensus size: 58
25429760 AAACCTTCCC
* * **
25429770 AAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCTATTTTTGACCCCAAAACTTTC--
1 AAAATTACCA-TTTTACCCTCGAA-TGTCC-AAAATTCTATTTTTGATCCC-GATTTTTCTA
*
25429828 AAAATTACCCTTTTACCCTCGAATGTCCAAAATTCTATTTTTGATCCCGATTTTTCTA
1 AAAATTACCATTTTACCCTCGAATGTCCAAAATTCTATTTTTGATCCCGATTTTTCTA
*
25429886 AAAATTACCATTTTACCCTC-AGATGTCCAAAA--CGT-TTTTT-ATCCTGATTTTT-TA
1 AAAATTACCATTTTACCCTCGA-ATGTCCAAAATTC-TATTTTTGATCCCGATTTTTCTA
* *
25429940 TAAAAGTTACCGTTTTACCCTCGGATGTC
1 -AAAA-TTACCATTTTACCCTCGAATGTC
25429969 TAAAGTTTCA
Statistics
Matches: 123, Mismatches: 9, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
54 2 0.02
55 15 0.12
56 31 0.25
57 22 0.18
58 52 0.42
59 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAATGTCCAAAATTCTATTTTTGATCCCGATTTTTCTA
Found at i:25434864 original size:54 final size:56
Alignment explanation
Indices: 25434783--25434909 Score: 195
Period size: 54 Copynumber: 2.3 Consensus size: 56
25434773 GTGTTATAAA
25434783 AAAAAAAAAAAAAAAGATAGGTCGAAAATTCGCAAAAGGCATTTTAAAAACCCAA-T
1 AAAAAAAAAAAAAAA-ATAGGTCGAAAATTCGCAAAAGGCATTTTAAAAACCCAATT
* * *
25434839 -AAAAAAATAAAAAAATGGGTCGAAAATTCGCAAAAGGTATTTTAAAAACCCAATT
1 AAAAAAAAAAAAAAAATAGGTCGAAAATTCGCAAAAGGCATTTTAAAAACCCAATT
*
25434894 AAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAA
25434910 GAAAAAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
54 37 0.57
55 14 0.22
56 14 0.22
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (56 bp):
AAAAAAAAAAAAAAAATAGGTCGAAAATTCGCAAAAGGCATTTTAAAAACCCAATT
Found at i:25435731 original size:9 final size:8
Alignment explanation
Indices: 25435665--25435738 Score: 62
Period size: 8 Copynumber: 9.0 Consensus size: 8
25435655 TTCAATGAAT
25435665 AAAGAAAA
1 AAAGAAAA
25435673 AAA-AAAA
1 AAAGAAAA
25435680 AAAGAAGAA
1 AAAGAA-AA
*
25435689 GAAGAAGAA
1 AAAGAA-AA
*
25435698 GAAA-AAGCA
1 -AAAGAA-AA
25435707 AAAGAAAA
1 AAAGAAAA
*
25435715 AAACAAAA
1 AAAGAAAA
*
25435723 AAGGAAAA
1 AAAGAAAA
25435731 AAAGAAAA
1 AAAGAAAA
25435739 GGAGAGGTCG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
7 7 0.13
8 29 0.54
9 16 0.30
10 2 0.04
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:25435739 original size:14 final size:14
Alignment explanation
Indices: 25435699--25435741 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
25435689 GAAGAAGAAG
*
25435699 AAAAAGCAAAAGAAA
1 AAAAAG-AAAAGGAA
*
25435714 AAAACAAAAAAGGAA
1 AAAA-AGAAAAGGAA
25435729 AAAAAGAAAAGGA
1 AAAAAGAAAAGGA
25435742 GAGGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 15 0.62
16 1 0.04
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGGAA
Found at i:25437041 original size:49 final size:49
Alignment explanation
Indices: 25436937--25437177 Score: 301
Period size: 49 Copynumber: 4.9 Consensus size: 49
25436927 CAGGTTTGAC
* * * *
25436937 AGGGAAAGATCTAA-GCCGCGACTGCGGATCCAGTACCACAAAAACACGA
1 AGGGAAAGATCTAAGGCCGCAACGGCGGATCCAGTACCACGAAGACAC-A
* *
25436986 CA-GGAAAGATCTAAGGCCGCAACGGCGGATCCAGTATCGCGAAGACACA
1 -AGGGAAAGATCTAAGGCCGCAACGGCGGATCCAGTACCACGAAGACACA
* * * *
25437035 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
1 AGGGAAAGATCTAAGGCCGCAACGGCGGATCCAGTACCACGAAG--ACACA
* * *
25437086 AGGGAAAGATCTAAGACCGCAACGACAGATCCAGTACCACGAAGACAC-
1 AGGGAAAGATCTAAGGCCGCAACGGCGGATCCAGTACCACGAAGACACA
25437134 AGGGAAAGATCTAA-GCCGCAACGGCGGATCCAGTACCACGAAGA
1 AGGGAAAGATCTAAGGCCGCAACGGCGGATCCAGTACCACGAAGA
25437178 TTTGAAGGGA
Statistics
Matches: 169, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
47 27 0.16
48 15 0.09
49 53 0.31
50 28 0.17
51 46 0.27
ACGTcount: A:0.39, C:0.26, G:0.26, T:0.10
Consensus pattern (49 bp):
AGGGAAAGATCTAAGGCCGCAACGGCGGATCCAGTACCACGAAGACACA
Found at i:25437626 original size:79 final size:79
Alignment explanation
Indices: 25437485--25437637 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 79
25437475 TTACATCATC
* * * * * * *
25437485 AACCAATCTCTTACCCTGAGCCTGGGGCATGCATTACAGCCATTGATCTTTTACCTCGAGCCTGG
1 AACCAATCTCTTACCCCGAGCCAGGGGCATGCATTACAACCATTGATCTCTTACCCCAAGCCTGA
25437550 GGCAGATCATCTTT
66 GGCAGATCATCTTT
*
25437564 AACCAAGTCTCTTACCCCGAGCCAGGGGCA-G-ATTACAATCATTCGATCTCTTACCCCAAGCCT
1 AACCAA-TCTCTTACCCCGAGCCAGGGGCATGCATTACAACCATT-GATCTCTTACCCCAAGCCT
25437627 GAGGCAGATCA
64 GAGGCAGATCA
25437638 CCATCAATCG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 10 0.16
79 33 0.52
80 21 0.33
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (79 bp):
AACCAATCTCTTACCCCGAGCCAGGGGCATGCATTACAACCATTGATCTCTTACCCCAAGCCTGA
GGCAGATCATCTTT
Found at i:25437633 original size:39 final size:39
Alignment explanation
Indices: 25437571--25437659 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
25437561 TTTAACCAAG
* * * *
25437571 TCTCTTACCCCGAGCCAGGGGCAGATTACAATCATTCGA
1 TCTCTTACCCCAAGCCAGAGGCAGATCACAATCAATCGA
* *
25437610 TCTCTTACCCCAAGCCTGAGGCAGATCACCATCAATCGA
1 TCTCTTACCCCAAGCCAGAGGCAGATCACAATCAATCGA
25437649 TCTCCTTACCC
1 TCT-CTTACCC
25437660 TGATCACGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 36 0.84
40 7 0.16
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.24
Consensus pattern (39 bp):
TCTCTTACCCCAAGCCAGAGGCAGATCACAATCAATCGA
Found at i:25437657 original size:79 final size:79
Alignment explanation
Indices: 25437481--25437659 Score: 200
Period size: 79 Copynumber: 2.3 Consensus size: 79
25437471 GAAGTTACAT
* * * * * *
25437481 CATCAACCAATCTCTTACCCTGAGCCTGGGGCATGCATTACAGCCATTGATCTTTTACCTCGAGC
1 CATCAACCAATCTCTTACCCCGAGCCAGGGGCATGCATTACAACCATTGATCTCTTACCCCAAGC
* *
25437546 CTGGGGCAGATCAT
66 CTGAGGCAGATCAC
* * *
25437560 CTTTAACCAAGTCTCTTACCCCGAGCCAGGGGCA-G-ATTACAATCATTCGATCTCTTACCCCAA
1 CATCAACCAA-TCTCTTACCCCGAGCCAGGGGCATGCATTACAACCATT-GATCTCTTACCCCAA
25437623 GCCTGAGGCAGATCAC
64 GCCTGAGGCAGATCAC
* *
25437639 CATCAATCGATCTCCTTACCC
1 CATCAACCAATCT-CTTACCC
25437660 TGATCACGGG
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
78 13 0.16
79 48 0.59
80 21 0.26
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (79 bp):
CATCAACCAATCTCTTACCCCGAGCCAGGGGCATGCATTACAACCATTGATCTCTTACCCCAAGC
CTGAGGCAGATCAC
Found at i:25438692 original size:17 final size:17
Alignment explanation
Indices: 25438647--25438716 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 17
25438637 AATTTTTAAA
*
25438647 TAAGTTTGAATTTATTT
1 TAAGTTTGAATTCATTT
* **
25438664 TAAATTCAAATTCATTT
1 TAAGTTTGAATTCATTT
* * *
25438681 TGAGTTTGAATTTACTT
1 TAAGTTTGAATTCATTT
* *
25438698 TAA-TTTAAATTTATTT
1 TAAGTTTGAATTCATTT
25438714 TAA
1 TAA
25438717 ATTAAAATAA
Statistics
Matches: 40, Mismatches: 13, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
16 14 0.35
17 26 0.65
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.54
Consensus pattern (17 bp):
TAAGTTTGAATTCATTT
Found at i:25438692 original size:34 final size:33
Alignment explanation
Indices: 25438649--25438714 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
25438639 TTTTTAAATA
*
25438649 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
1 AGTTTGAATTTACTTT-AATTCAAATTCATTTTG
* *
25438683 AGTTTGAATTTACTTTAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAATTCAAATTCATTTT
25438715 AAATTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.56
Consensus pattern (33 bp):
AGTTTGAATTTACTTTAATTCAAATTCATTTTG
Found at i:25438710 original size:16 final size:16
Alignment explanation
Indices: 25438689--25438722 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25438679 TTTGAGTTTG
*
25438689 AATTTACTTTAATTTA
1 AATTTACTTTAAATTA
*
25438705 AATTTATTTTAAATTA
1 AATTTACTTTAAATTA
25438721 AA
1 AA
25438723 ATAAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTACTTTAAATTA
Found at i:25438724 original size:17 final size:17
Alignment explanation
Indices: 25438655--25438724 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 17
25438645 AATAAGTTTG
*
25438655 AATTTATTTTAAATTCA
1 AATTTATTTTAAATTTA
* * * *
25438672 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
*
25438689 AATTTACTTT-AATTTA
1 AATTTATTTTAAATTTA
*
25438705 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
25438722 AAT
1 AAT
25438725 AAAATTAAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
16 13 0.32
17 28 0.68
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:25439528 original size:16 final size:17
Alignment explanation
Indices: 25439502--25439554 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
25439492 CAGAACGTTT
*
25439502 TTAATATATAATAAATA
1 TTAATAAATAATAAATA
25439519 -TAATAAATAAT-AATA
1 TTAATAAATAATAAATA
25439534 TTAATAAAATAAT-AATA
1 TTAAT-AAATAATAAATA
25439551 TTAA
1 TTAA
25439555 AAAAGATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 4 0.12
16 14 0.42
17 15 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAATAAATAATAAATA
Found at i:25439545 original size:17 final size:17
Alignment explanation
Indices: 25439509--25439558 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
25439499 TTTTTAATAT
25439509 ATAATAA-ATATAAT-AA
1 ATAATAATAT-TAATAAA
25439525 ATAATAATATTAATAAA
1 ATAATAATATTAATAAA
25439542 ATAATAATATTAA-AAA
1 ATAATAATATTAATAAA
25439558 A
1 A
25439559 GATTTGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.47
17 17 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAATATTAATAAA
Found at i:25439555 original size:14 final size:14
Alignment explanation
Indices: 25439503--25439556 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
25439493 AGAACGTTTT
25439503 TAATATATAAT-AAA
1 TAATA-ATAATAAAA
*
25439517 T-ATAATAA-ATAA
1 TAATAATAATAAAA
*
25439529 TAATATTAATAAAA
1 TAATAATAATAAAA
*
25439543 TAATAATATTAAAA
1 TAATAATAATAAAA
25439557 AAGATTTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 7 0.22
13 9 0.28
14 16 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:25440730 original size:29 final size:29
Alignment explanation
Indices: 25440684--25440864 Score: 150
Period size: 29 Copynumber: 6.1 Consensus size: 29
25440674 CTCTAAAGGT
* *
25440684 CCCTGAACTGTCCAAAAATTACATTTTTAA
1 CCCTAAACT-TCCAAAAATTACATTTTTAC
* * *
25440714 CCTTGAACTTCCAAAAATTCCATTTTTGACC
1 CCCTAAACTTCCAAAAATTACATTTTT-A-C
* *
25440745 CCCAAAACTTCCAAAAATT-CTAGTTTTGAC
1 CCCTAAACTTCCAAAAATTAC-A-TTTTTAC
* *
25440775 CCCAAAACTTCCAAAAATTTCATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * *
25440804 CCCCAAACTTCCAAAAATTCCATTTTTAA
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * **
25440833 CCTTGAAACTTTC-AAAATTACCCTTTTAC
1 CCCT-AAACTTCCAAAAATTACATTTTTAC
25440862 CCC
1 CCC
25440865 CGATGTCCAA
Statistics
Matches: 126, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
29 65 0.52
30 38 0.30
31 19 0.15
32 4 0.03
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:25440757 original size:31 final size:31
Alignment explanation
Indices: 25440719--25440830 Score: 176
Period size: 30 Copynumber: 3.7 Consensus size: 31
25440709 TTTAACCTTG
25440719 AACTTCCAAAAATTCCATTTTTGACCCCCAA
1 AACTTCCAAAAATTCCATTTTTGACCCCCAA
* *
25440750 AACTTCCAAAAATTCTAGTTTTGA-CCCCAA
1 AACTTCCAAAAATTCCATTTTTGACCCCCAA
*
25440780 AACTTCCAAAAATTTCATTTTT-ACCCCC-A
1 AACTTCCAAAAATTCCATTTTTGACCCCCAA
25440809 AACTTCCAAAAATTCCATTTTT
1 AACTTCCAAAAATTCCATTTTT
25440831 AACCTTGAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
29 23 0.31
30 29 0.39
31 22 0.30
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.33
Consensus pattern (31 bp):
AACTTCCAAAAATTCCATTTTTGACCCCCAA
Found at i:25440849 original size:30 final size:30
Alignment explanation
Indices: 25440689--25440834 Score: 170
Period size: 29 Copynumber: 4.9 Consensus size: 30
25440679 AAGGTCCCTG
* ***
25440689 AACTGTCCAAAAATTACATTTTTAA-CCTTG
1 AACT-TCCAAAAATTCCATTTTTAACCCCAA
*
25440719 AACTTCCAAAAATTCCATTTTTGACCCCCAA
1 AACTTCCAAAAATTCCATTTTT-AACCCCAA
* * *
25440750 AACTTCCAAAAATTCTAGTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* *
25440780 AACTTCCAAAAATTTCATTTTT-ACCCCCA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
25440809 AACTTCCAAAAATTCCATTTTTAACC
1 AACTTCCAAAAATTCCATTTTTAACC
25440835 TTGAAACTTT
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
29 44 0.44
30 33 0.33
31 22 0.22
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTAACCCCAA
Found at i:25440957 original size:58 final size:58
Alignment explanation
Indices: 25440846--25440989 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 58
25440836 TGAAACTTTC
* *
25440846 AAAATTACCCTTTTACCCCCGATGTCCAAAATTCTATTTTTGATCCCGA-TTTTTCTA
1 AAAATTACCATTTTACCCCCGATGTCCAAAATACTATTTTTGATCCCGATTTTTTCTA
* * *
25440903 AAAATTACCATTTTACCCTCGAATGTCCAAAAATAAC-GTTTTT-ATCCTGATTTTTTTCTA
1 AAAATTACCATTTTACCCCCG-ATGTCC-AAAAT-ACTATTTTTGATCCCGA-TTTTTTCTA
* *
25440963 AAAGTTACCGTTTTACCCCCGGATGTC
1 AAAATTACCATTTTACCCCC-GATGTC
25440990 TAAAGTTTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
57 19 0.26
58 12 0.16
59 10 0.14
60 31 0.42
61 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGATGTCCAAAATACTATTTTTGATCCCGATTTTTTCTA
Found at i:25441413 original size:96 final size:96
Alignment explanation
Indices: 25441296--25441477 Score: 262
Period size: 96 Copynumber: 1.9 Consensus size: 96
25441286 AAAACTTTAA
*
25441296 AATCGAGGCAATATTCTTTTAT-TTCGAGTT-TGGAAAATTTGTGCCTTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTCTTTTATATTCGA-TTCT-GAAAATTTGCGCCTTAACTTACTAGGTGCAA
**
25441359 TTTTTCTTCAAATCAAAATAATCAAATACCCTT
64 CCTTTCTTCAAATCAAAATAATCAAATACCCTT
*
25441392 AATCGAGGCAA-ATTTTCTTTATATTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAAC
1 AATCGAGGCAATATTCT-TTTATATTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAAC
* *
25441456 CTTTCTTCAAATCGAGATAATC
65 CTTTCTTCAAATCAAAATAATC
25441478 CTTTTCCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
95 4 0.05
96 67 0.87
97 6 0.08
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATATTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAAATAATCAAATACCCTT
Found at i:25452653 original size:29 final size:29
Alignment explanation
Indices: 25452621--25452847 Score: 94
Period size: 30 Copynumber: 7.7 Consensus size: 29
25452611 TATGGATACC
*
25452621 CGGGGGCAAAATGGTAATTTTGGTGTAAT
1 CGGGGGAAAAATGGTAATTTTGGTGTAAT
* * * * * **
25452650 CGGGGTGAAAAACGGGACTTATGG-ATACC
1 CGGGG-GAAAAATGGTAATTTTGGTGTAAT
*
25452679 CGGGGGTAAAATGGTAATTTTCGGTG-AGAT
1 CGGGGGAAAAATGGTAATTTT-GGTGTA-AT
* *
25452709 CGGGGTTAAAAATGG-AATTTTGGAAGCT--T
1 CGGGG-GAAAAATGGTAATTTTGG-TG-TAAT
* *
25452738 CGGGGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGAAAAATGGTAATTTT-GGTGTAAT
* * **
25452768 CGGGGTTAAAAAT-GAAATTTTAGAAGCT--T
1 CGGGG-GAAAAATGGTAATTTT-GGTG-TAAT
** *
25452797 CGGGGGTCAAATGGTAATTTTTGGTGAAAT
1 CGGGGGAAAAATGGTAA-TTTTGGTGTAAT
*
25452827 CGGGGTTAAAAATGG-AATTTT
1 CGGGG-GAAAAATGGTAATTTT
25452848 AAAAGATTTG
Statistics
Matches: 139, Mismatches: 40, Indels: 38
0.64 0.18 0.18
Matches are distributed among these distances:
28 22 0.16
29 45 0.32
30 54 0.39
31 18 0.13
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (29 bp):
CGGGGGAAAAATGGTAATTTTGGTGTAAT
Found at i:25452661 original size:58 final size:58
Alignment explanation
Indices: 25452589--25452838 Score: 258
Period size: 59 Copynumber: 4.3 Consensus size: 58
25452579 TAAATGATGA
* *
25452589 AATCGGGGTAAAAAACGGGACTTATGGATACCCGGGGGCAAAATGGTAATTTT-GGTG
1 AATCGGGGTTAAAAACGGGACTTATGGATACCCGGGGGTAAAATGGTAATTTTCGGTG
*
25452646 TAATCGGGGTGAAAAACGGGACTTATGGATACCCGGGGGTAAAATGGTAATTTTCGGTG
1 -AATCGGGGTTAAAAACGGGACTTATGGATACCCGGGGGTAAAATGGTAATTTTCGGTG
* * * *
25452705 AGATCGGGGTTAAAAA-TGGAATTTTGGA-AGCTTCGGGGGTAAAATGGTAATTTTCGGTG
1 A-ATCGGGGTTAAAAACGGGACTTATGGATA-C-CCGGGGGTAAAATGGTAATTTTCGGTG
* * * * * * * *
25452764 AAATCGGGGTTAAAAA-TGAAATTTTAGA-AGCTTCGGGGGTCAAATGGTAATTTTTGGTG
1 -AATCGGGGTTAAAAACGGGACTTATGGATA-C-CCGGGGGTAAAATGGTAATTTTCGGTG
25452823 AAATCGGGGTTAAAAA
1 -AATCGGGGTTAAAAA
25452839 TGGAATTTTA
Statistics
Matches: 176, Mismatches: 11, Indels: 9
0.90 0.06 0.05
Matches are distributed among these distances:
57 1 0.01
58 62 0.35
59 112 0.64
60 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.27
Consensus pattern (58 bp):
AATCGGGGTTAAAAACGGGACTTATGGATACCCGGGGGTAAAATGGTAATTTTCGGTG
Found at i:25452713 original size:30 final size:30
Alignment explanation
Indices: 25452679--25452847 Score: 129
Period size: 30 Copynumber: 5.7 Consensus size: 30
25452669 TATGGATACC
25452679 CGGGGGT-AAAATGGTAATTTTCGGTGAGAT
1 CGGGGGTAAAAATGGTAATTTT-GGTGAGAT
* * *
25452709 CGGGGTTAAAAATGG-AATTTTGG-AAGCTT
1 CGGGGGTAAAAATGGTAATTTTGGTGAG-AT
*
25452738 CGGGGGT-AAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAAATGGTAATTTT-GGTGAGAT
* * * * *
25452768 CGGGGTTAAAAAT-GAAATTTTAG-AAGCTT
1 CGGGGGTAAAAATGGTAATTTTGGTGAG-AT
* *
25452797 CGGGGGT-CAAATGGTAATTTTTGGTGAAAT
1 CGGGGGTAAAAATGGTAA-TTTTGGTGAGAT
*
25452827 CGGGGTTAAAAATGG-AATTTT
1 CGGGGGTAAAAATGGTAATTTT
25452848 AAAAGATTTG
Statistics
Matches: 106, Mismatches: 22, Indels: 23
0.70 0.15 0.15
Matches are distributed among these distances:
28 14 0.13
29 30 0.28
30 42 0.40
31 20 0.19
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (30 bp):
CGGGGGTAAAAATGGTAATTTTGGTGAGAT
Found at i:25452878 original size:59 final size:59
Alignment explanation
Indices: 25452621--25452876 Score: 320
Period size: 59 Copynumber: 4.4 Consensus size: 59
25452611 TATGGATACC
* * * * * * * *
25452621 CGGGGGCAAAATGGTAATTTT-GGTGTAATCGGGGTGAAAAACGGGACTTATGGATA-C-C
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAA-TGGAATTTTAGA-AGCTT
* *
25452679 CGGGGGTAAAATGGTAATTTTCGGTGAGATCGGGGTTAAAAATGGAATTTTGGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
*
25452738 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * * *
25452797 CGGGGGTCAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* *
25452856 TGGGGGTAAATTGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
25452877 TGAAAGTTTT
Statistics
Matches: 176, Mismatches: 19, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
57 1 0.01
58 30 0.17
59 145 0.82
ACGTcount: A:0.31, C:0.07, G:0.32, T:0.30
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
Found at i:25453155 original size:30 final size:30
Alignment explanation
Indices: 25452828--25453149 Score: 373
Period size: 30 Copynumber: 10.7 Consensus size: 30
25452818 TGGTGAAATC
*
25452828 GGGGTTAAAA-ATGGAATTTT--AAAAGATTT
1 GGGGTTAAAATAT--AATTTTGGAAAAGTTTT
* * * *
25452857 GGGGGTAAATTGGTAATTTTTG-AAAGTTTT
1 GGGGTTAAAAT-ATAATTTTGGAAAAGTTTT
** *
25452887 TAGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
* * *
25452917 AGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
*
25452947 AGGGTTAAAATATAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
*
25452977 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
* *
25453007 GGGATTAAAATATAATTTTGGAAAAGTCTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
*
25453037 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
*
25453067 GGGGTTAAAATATAATTTTGGAAAAGTATT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
** * * *
25453097 GGGGGCAAAATATAATTTTGAAAAAATTTC
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
*
25453127 GGGGTTAAAAGATAATTTCTGGA
1 GGGGTTAAAATATAATTT-TGGA
25453150 CAATTTAGGG
Statistics
Matches: 253, Mismatches: 34, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
29 23 0.09
30 226 0.89
31 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
GGGGTTAAAATATAATTTTGGAAAAGTTTT
Found at i:25453935 original size:18 final size:17
Alignment explanation
Indices: 25453894--25453942 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
25453884 CTCCTTTTTC
*
25453894 CTTTCTTCTCTTCTGTTT
1 CTTTCTT-TCTTCTATTT
25453912 CTTTCTTTCTTCTATTT
1 CTTTCTTTCTTCTATTT
* *
25453929 TTGTTCTTTATTCT
1 CT-TTCTTTCTTCT
25453943 TTATTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.69
Consensus pattern (17 bp):
CTTTCTTTCTTCTATTT
Found at i:25453955 original size:22 final size:23
Alignment explanation
Indices: 25453904--25453955 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
25453894 CTTTCTTCTC
*
25453904 TTCTGTTTCTTTCTTTCTTCTATT
1 TTCTG-TTCTTTCATTCTTCTATT
25453928 TT-TGTTCTTT-ATTCTT-TATTT
1 TTCTGTTCTTTCATTCTTCTA-TT
25453949 TTCTGTT
1 TTCTGTT
25453956 TTATGTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 9 0.36
22 10 0.40
23 2 0.08
24 2 0.08
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (23 bp):
TTCTGTTCTTTCATTCTTCTATT
Found at i:25455053 original size:17 final size:17
Alignment explanation
Indices: 25455033--25455117 Score: 70
Period size: 17 Copynumber: 5.2 Consensus size: 17
25455023 TAATTTTTAT
25455033 TTAAATTTAAATTCAAA
1 TTAAATTTAAATTCAAA
* *
25455050 TTAAATTCAAA-T--AT
1 TTAAATTTAAATTCAAA
*
25455064 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTCAAA
* * *
25455081 ATAAATCTAAATTTAAA
1 TTAAATTTAAATTCAAA
* *
25455098 -TAAATTTAAAATCAAT
1 TTAAATTTAAATTCAAA
25455114 TTAA
1 TTAA
25455118 CTCAAAAGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
14 11 0.20
15 1 0.02
16 13 0.24
17 29 0.54
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATTTAAATTCAAA
Found at i:25455065 original size:31 final size:30
Alignment explanation
Indices: 25455030--25455098 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
25455020 TTTTAATTTT
*
25455030 TATTTAAATTTAAATTCAAATTAAATTCAAA
1 TATTTAAATTTAAATTCAAAATAAA-TCAAA
* *
25455061 TATTTAAATTTAAATTTAAAATAAATCTAA
1 TATTTAAATTTAAATTCAAAATAAATCAAA
25455091 -ATTTAAAT
1 TATTTAAAT
25455099 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 8 0.23
30 4 0.11
31 23 0.66
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (30 bp):
TATTTAAATTTAAATTCAAAATAAATCAAA
Found at i:25455071 original size:6 final size:6
Alignment explanation
Indices: 25455031--25455107 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
25455021 TTTAATTTTT
* *
25455031 ATTTAA ATTTAA ATTCAA A-TTAA ATTCAAA TATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATT-TAA -ATTTAA ATTTAA ATTTAA
* *
25455080 A-ATAA ATCTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
25455108 ATCAATTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
4 4 0.07
5 8 0.14
6 39 0.67
7 4 0.07
8 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:25455100 original size:16 final size:17
Alignment explanation
Indices: 25455031--25455107 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
25455021 TTTAATTTTT
*
25455031 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAAAT-AA
*
25455049 A-TTAAATTCAAATATTTAA
1 ATTTAAATTTAAA-A--TAA
25455068 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
25455085 ATCTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
25455101 ATTTAAA
1 ATTTAAA
25455108 ATCAATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 12 0.24
17 22 0.44
18 1 0.02
19 4 0.08
20 11 0.22
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:25455565 original size:69 final size:69
Alignment explanation
Indices: 25455426--25456037 Score: 926
Period size: 69 Copynumber: 9.0 Consensus size: 69
25455416 GGAAATGATC
* * *
25455426 TTGCTCTTACTTCAATTTCAGAGATGATGACGT-ATTATCC-ACTCTACTTCAATTTCGAGGGGA
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGA-TATCCAACTCTACTTCAATTTCAAGAGGA
25455489 TGACG
65 TGACG
* * *
25455494 TTGTTCTTGCTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
25455559 GACG
66 GACG
25455563 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
25455628 GACG
66 GACG
* *
25455632 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATTCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
25455697 GACG
66 GACG
* *
25455701 TTGCTCTTACTTCAATTTCAGAGGTAAAGACGT-ATTATCCAACTCTACTTCAATTTCAAGAGGA
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGA-TATCCAACTCTACTTCAATTTCAAGAGGA
25455765 TGACG
65 TGACG
*
25455770 TTGCTCTTACTTCAATTTCAGAGATGGAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
25455835 GAC-
66 GACG
* *
25455838 --G----T--TTCAATTTTAGAGATAAAGACGT-ATTATCCAACTCTACTTCAATTTCAAGAGGA
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGA-TATCCAACTCTACTTCAATTTCAAGAGGA
25455894 TGACG
65 TGACG
* * *
25455899 TCGCTCTTACTTCAATTTCAGAGATGGAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
25455964 GACG
66 GACG
* * * *
25455968 TCGCTCTTACTTCAATTTCAGAGATGGAGACGTGTTATCCAACTCTACTTCAATTTCGAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
25456033 GACG
66 GACG
25456037 T
1 T
25456038 CGGTGACCTG
Statistics
Matches: 503, Mismatches: 26, Indels: 29
0.90 0.05 0.05
Matches are distributed among these distances:
59 1 0.00
60 53 0.11
62 1 0.00
63 1 0.00
66 1 0.00
67 1 0.00
68 34 0.07
69 410 0.82
70 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
GACG
Found at i:25455750 original size:38 final size:37
Alignment explanation
Indices: 25455503--25455832 Score: 198
Period size: 38 Copynumber: 9.4 Consensus size: 37
25455493 GTTGTTCTTG
*
25455503 CTTCAATTTC-AGAGATAAAGACGTGATATCCAACTCTA
1 CTTCAATTTCAAGAGGT-AAGACGT-ATATCCAACTCTA
* * *
25455541 CTTCAATTTCAAGAGG-ATGACG--T-TGC-TCT-TA
1 CTTCAATTTCAAGAGGTAAGACGTATATCCAACTCTA
*
25455572 CTTCAATTTC-AGAGATGAAGACGTGATATCCAACTCTA
1 CTTCAATTTCAAGAGGT-AAGACGT-ATATCCAACTCTA
* * *
25455610 CTTCAATTTCAAGAGG-ATGACG--T-TGC-TCT-TA
1 CTTCAATTTCAAGAGGTAAGACGTATATCCAACTCTA
* * *
25455641 CTTCAATTTC-AGAGATGAAGACGTGTTATTCAACTCTA
1 CTTCAATTTCAAGAGGT-AAGACGT-ATATCCAACTCTA
* * *
25455679 CTTCAATTTCAAGAGG-ATGACG--T-TGC-TCT-TA
1 CTTCAATTTCAAGAGGTAAGACGTATATCCAACTCTA
25455710 CTTCAATTTC-AGAGGTAAAGACGTATTATCCAACTCTA
1 CTTCAATTTCAAGAGGT-AAGACGTA-TATCCAACTCTA
* * *
25455748 CTTCAATTTCAAGAGG-ATGACG--T-TGC-TCT-TA
1 CTTCAATTTCAAGAGGTAAGACGTATATCCAACTCTA
25455779 CTTCAATTTCAGAGATGG--AGACGTGATATCCAACTCTA
1 CTTCAATTTCA-AGA-GGTAAGACGT-ATATCCAACTCTA
25455817 CTTCAATTTCAAGAGG
1 CTTCAATTTCAAGAGG
25455833 ATGACGTTTC
Statistics
Matches: 227, Mismatches: 29, Indels: 74
0.69 0.09 0.22
Matches are distributed among these distances:
30 13 0.06
31 49 0.22
32 30 0.13
33 10 0.04
34 4 0.02
35 4 0.02
36 10 0.04
37 31 0.14
38 59 0.26
39 17 0.07
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (37 bp):
CTTCAATTTCAAGAGGTAAGACGTATATCCAACTCTA
Found at i:25467965 original size:24 final size:24
Alignment explanation
Indices: 25467933--25467978 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25467923 CGATCACGAT
* *
25467933 CCTTTTCTCGGTCCCTATCCCTAC
1 CCTTATCTCGATCCCTATCCCTAC
*
25467957 CCTTATCTCTATCCCTATCCCT
1 CCTTATCTCGATCCCTATCCCT
25467979 GTGGCGATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.46, G:0.04, T:0.39
Consensus pattern (24 bp):
CCTTATCTCGATCCCTATCCCTAC
Found at i:25470938 original size:3 final size:3
Alignment explanation
Indices: 25470930--25470972 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
25470920 TACGAATGTG
*
25470930 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25470973 CTCATAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:25471642 original size:33 final size:33
Alignment explanation
Indices: 25471572--25471642 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
25471562 GTTTCTAAAT
*
25471572 TTTTTTTGCTCAATTTGATACTCAAACTTGACA
1 TTTTTTTCCTCAATTTGATACTCAAACTTGACA
*
25471605 TTTTTTTCCT-AATTTGGTA-TCTAAACTTGACA
1 TTTTTTTCCTCAATTTGATACTC-AAACTTGACA
*
25471637 CTTTTT
1 TTTTTT
25471643 ATATTGGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 2 0.06
32 23 0.68
33 9 0.26
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (33 bp):
TTTTTTTCCTCAATTTGATACTCAAACTTGACA
Found at i:25471978 original size:57 final size:58
Alignment explanation
Indices: 25471864--25471990 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 58
25471854 TAATAAATTT
* * *
25471864 AGGTATCAAATTGAATCTAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTTAAGTTC
1 AGGTACCAAATTGAATCTAAAAAAGTTTAGGTACAAAATT-AGAAAAAATGTCAAGTTC
* * *
25471923 AGGTACTAAATTGAGTC-AAAAAAGGTTTAGGTACAAAATT-TAAAAAATGTCAAGTTC
1 AGGTACCAAATTGAATCTAAAAAA-GTTTAGGTACAAAATTAGAAAAAATGTCAAGTTC
*
25471980 ATGTACCAAAT
1 AGGTACCAAAT
25471991 GTTATATTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 24 0.41
58 6 0.10
59 29 0.49
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.28
Consensus pattern (58 bp):
AGGTACCAAATTGAATCTAAAAAAGTTTAGGTACAAAATTAGAAAAAATGTCAAGTTC
Found at i:25472049 original size:29 final size:30
Alignment explanation
Indices: 25472004--25472077 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
25471994 ATATTAAGCC
* *
25472004 TACTATAAAATAACTTTTCAC-CAAAAAAA
1 TACTATAAAATACCTTTTCACAAAAAAAAA
*
25472033 TACTACAAAATACCTTTTCACAAAAAAAAA
1 TACTATAAAATACCTTTTCACAAAAAAAAA
25472063 TACTATAAAATACCT
1 TACTATAAAATACCT
25472078 AACTATATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 19 0.47
30 21 0.52
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (30 bp):
TACTATAAAATACCTTTTCACAAAAAAAAA
Found at i:25475921 original size:50 final size:50
Alignment explanation
Indices: 25475817--25475921 Score: 138
Period size: 50 Copynumber: 2.1 Consensus size: 50
25475807 CACGGGTAAA
* * * *
25475817 CACACGGACATGTGTCCAGGTCGTGTAGCTCACTGTTTGTGTATTAAGGC
1 CACACGGACATGTGTCCAGGCCGTGTAACTCACTGTTTATGCATTAAGGC
* * * *
25475867 CACACGGGCGTGTGTCCAGGCCGTGTAACTCACTGTTTATGCATTAGGGT
1 CACACGGACATGTGTCCAGGCCGTGTAACTCACTGTTTATGCATTAAGGC
25475917 CACAC
1 CACAC
25475922 AGGCAGGGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (50 bp):
CACACGGACATGTGTCCAGGCCGTGTAACTCACTGTTTATGCATTAAGGC
Found at i:25478461 original size:18 final size:18
Alignment explanation
Indices: 25478440--25478474 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25478430 AATGATATAT
*
25478440 TAATTAATAATAATATTA
1 TAATAAATAATAATATTA
25478458 TAATAAATAATAATATT
1 TAATAAATAATAATATT
25478475 TTATTATTTA
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:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:25479924 original size:18 final size:19
Alignment explanation
Indices: 25479898--25479938 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
25479888 AAATTTCCTT
*
25479898 ATTATGTGA-ATTAAATTG
1 ATTAAGTGATATTAAATTG
*
25479916 ATTAAGTGATTTTAAATTG
1 ATTAAGTGATATTAAATTG
25479935 ATTA
1 ATTA
25479939 CAAAGCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (19 bp):
ATTAAGTGATATTAAATTG
Found at i:25485533 original size:17 final size:17
Alignment explanation
Indices: 25485508--25485578 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
25485498 AATAAGTTTG
*
25485508 AATTTATTTTAAATTCA
1 AATTTATTTTAAATTTA
* * * *
25485525 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
*
25485542 AATTTACTTTAAATTTA
1 AATTTATTTTAAATTTA
*
25485559 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
25485576 AAT
1 AAT
25485579 AAAATTAAAG
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:25485545 original size:34 final size:34
Alignment explanation
Indices: 25485502--25485568 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
25485492 TTTTTAAATA
*
25485502 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
* *
25485536 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTT
25485569 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
Found at i:25486369 original size:3 final size:3
Alignment explanation
Indices: 25486361--25486412 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
25486351 CAGAACGTTT
*
25486361 TAA TAA TAA TAA TAA -ATA TAA TAA -AA TTAA TAA TAT TAA TAA -AA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA -TAA TAA TAA TAA TAA TAA
25486405 TAA TAA TA
1 TAA TAA TA
25486413 TTAAAAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 5 0.12
3 34 0.81
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:25486384 original size:18 final size:18
Alignment explanation
Indices: 25486360--25486420 Score: 76
Period size: 17 Copynumber: 3.5 Consensus size: 18
25486350 TCAGAACGTT
25486360 TTAATAATAATAATAAATA
1 TTAATAA-AATAATAAATA
25486379 -TAATAAAATTAAT-AATA
1 TTAATAAAA-TAATAAATA
25486396 TTAATAAAATAAT-AATA
1 TTAATAAAATAATAAATA
25486413 TTAA-AAAA
1 TTAATAAAA
25486421 GATTTGAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.10
17 18 0.45
18 18 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAATAAAATAATAAATA
Found at i:25486408 original size:17 final size:17
Alignment explanation
Indices: 25486360--25486420 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 17
25486350 TCAGAACGTT
25486360 TTAATAATAATAATAA-A
1 TTAATAA-AATAATAATA
25486377 TATAATAAAATTAATAATA
1 T-TAATAAAA-TAATAATA
25486396 TTAATAAAATAATAATA
1 TTAATAAAATAATAATA
25486413 TTAA-AAAA
1 TTAATAAAA
25486421 GATTTGAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.10
17 15 0.37
18 20 0.49
19 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAATAAAATAATAATA
Found at i:25487583 original size:30 final size:29
Alignment explanation
Indices: 25487503--25487648 Score: 161
Period size: 29 Copynumber: 5.0 Consensus size: 29
25487493 GAAGGTCCCT
*
25487503 AAACTGTCCAAAAATTACATTTTTACCCTA
1 AAACT-TCCAAAAATTACATTTTTACCCCA
* *
25487533 AAACTTCTAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACATTTTT-ACCCCA
* * *
25487563 AACCTTCCCAAAATTACATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCA
*
25487592 GAACTTCCAAAAATT-CTATTTTTGACCCCA
1 AAACTTCCAAAAATTAC-ATTTTT-ACCCCA
* *
25487622 AAACTTTC-AAAATTACCTTTTTACCCC
1 AAACTTCCAAAAATTACATTTTTACCCC
25487649 CGAATGTCCA
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.06
29 50 0.52
30 41 0.42
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCA
Found at i:25487604 original size:59 final size:58
Alignment explanation
Indices: 25487503--25487673 Score: 220
Period size: 59 Copynumber: 2.9 Consensus size: 58
25487493 GAAGGTCCCT
*** * *
25487503 AAACTGTCCAAAAATTACATTTTTACCCTAAAACTTCTAAAAATTCCATTTTTGACCCCA
1 AAACT-TCC-AAAATTACATTTTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCCA
*
25487563 AACCTTCCCAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCCA
1 AAACTT-CCAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCCA
* *
25487622 AAACTTTCAAAATTACCTTTTTACCCCCGAA-TGTCC-AAAATTCTATTTTTGA
1 AAACTTCCAAAATTACATTTTTACCCCCGAACT-TCCAAAAATTCTATTTTTGA
25487674 TCCCGATTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
57 17 0.17
58 26 0.26
59 51 0.51
60 6 0.06
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (58 bp):
AAACTTCCAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCTATTTTTGACCCCA
Found at i:25487659 original size:58 final size:58
Alignment explanation
Indices: 25487541--25487721 Score: 199
Period size: 58 Copynumber: 3.1 Consensus size: 58
25487531 TAAAACTTCT
* * * *
25487541 AAAAATTCCATTTTTGACCCCAAACCTTCCCAAAATTACATTTTTACCCCCGAACT-TCC
1 AAAAATTCTATTTTTGACCCCAAAACTT-TCAAAATTACCTTTTTACCCCCGAA-TGTCC
25487600 AAAAATTCTATTTTTGACCCCAAAACTTTCAAAATTACCTTTTTACCCCCGAATGTCC
1 AAAAATTCTATTTTTGACCCCAAAACTTTCAAAATTACCTTTTTACCCCCGAATGTCC
* * ** * *
25487658 -AAAATTCTATTTTTGATCCC-GATTTTTCTAAAAATTACCATTTTACCCTC-AGATGTCC
1 AAAAATTCTATTTTTGACCCCAAAACTTTC--AAAATTACCTTTTTACCCCCGA-ATGTCC
25487716 AAAAAT
1 AAAAAT
25487722 AACGTTTTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
56 5 0.05
57 21 0.20
58 50 0.47
59 31 0.29
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (58 bp):
AAAAATTCTATTTTTGACCCCAAAACTTTCAAAATTACCTTTTTACCCCCGAATGTCC
Found at i:25487671 original size:28 final size:28
Alignment explanation
Indices: 25487504--25487671 Score: 119
Period size: 29 Copynumber: 5.8 Consensus size: 28
25487494 AAGGTCCCTA
***
25487504 AACTGTCCAAAAATTACATTTTTACCCTAA
1 AACT-TCC-AAAATTACATTTTTACCCCCG
* * *
25487534 AACTTCTAAAAATTCCATTTTTGA-CCCCA
1 AACTTC-CAAAATTACATTTTT-ACCCCCG
25487563 AACCTTCCCAAAATTACATTTTTACCCCCG
1 AA-CTT-CCAAAATTACATTTTTACCCCCG
**
25487593 AACTTCCAAAAATT-CTATTTTTGACCCCAA
1 AACTTCC-AAAATTAC-ATTTTT-ACCCCCG
* *
25487623 AACTTTCAAAATTACCTTTTTACCCCCG
1 AACTTCCAAAATTACATTTTTACCCCCG
25487651 AA-TGTCCAAAATT-CTATTTTT
1 AACT-TCCAAAATTAC-ATTTTT
25487672 GATCCCGATT
Statistics
Matches: 112, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
27 2 0.02
28 23 0.21
29 47 0.42
30 39 0.35
31 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (28 bp):
AACTTCCAAAATTACATTTTTACCCCCG
Found at i:25487671 original size:29 final size:29
Alignment explanation
Indices: 25487542--25487671 Score: 92
Period size: 30 Copynumber: 4.5 Consensus size: 29
25487532 AAAACTTCTA
* * *
25487542 AAAATTCCATTTTTGA-CCCCAAACCTTCCC
1 AAAATTCTATTTTTTACCCCCGAA-CTT-CC
25487572 AAAATTAC-A-TTTTTACCCCCGAACTTCC
1 AAAATT-CTATTTTTTACCCCCGAACTTCC
* ** *
25487600 AAAAATTCTATTTTTGACCCCAAAACTTTC
1 -AAAATTCTATTTTTTACCCCCGAACTTCC
*
25487630 AAAA-T-TACCTTTTTACCCCCGAA-TGTCC
1 AAAATTCTA-TTTTTTACCCCCGAACT-TCC
25487658 AAAATTCTATTTTT
1 AAAATTCTATTTTT
25487672 GATCCCGATT
Statistics
Matches: 79, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
27 3 0.04
28 21 0.27
29 24 0.30
30 30 0.38
31 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATTCTATTTTTTACCCCCGAACTTCC
Found at i:25492677 original size:54 final size:55
Alignment explanation
Indices: 25492591--25492717 Score: 193
Period size: 54 Copynumber: 2.3 Consensus size: 55
25492581 GTGTTATAAA
*
25492591 AAAACAAAAAAAAAAGATAGGTCGAAAATTCGCAAAAGGCATTTTAAAAACCCAA-T
1 AAAA-AAAAAAAAAA-ATAGGTCAAAAATTCGCAAAAGGCATTTTAAAAACCCAATT
* *
25492647 AAAAAAATAAAAAAATAGGTCAAAAATTCGCAAAAGGTATTTTAAAAACCCAATT
1 AAAAAAAAAAAAAAATAGGTCAAAAATTCGCAAAAGGCATTTTAAAAACCCAATT
25492702 AAAAAAAAGAAAAAAA
1 AAAAAAAA-AAAAAAA
25492718 AAAAAAAAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
54 37 0.57
55 17 0.26
56 11 0.17
ACGTcount: A:0.62, C:0.11, G:0.10, T:0.17
Consensus pattern (55 bp):
AAAAAAAAAAAAAAATAGGTCAAAAATTCGCAAAAGGCATTTTAAAAACCCAATT
Found at i:25493510 original size:15 final size:15
Alignment explanation
Indices: 25493474--25493530 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
25493464 AATAAAGAAA
*
25493474 AAAAGAAAGAAGAAG-
1 AAAAG-AAGAAAAAGC
25493489 AAGAAGAAGAAAAAGC
1 AA-AAGAAGAAAAAGC
25493505 AAAAGAA-AAAAA-C
1 AAAAGAAGAAAAAGC
25493518 AAAA-AAGGAAAAA
1 AAAAGAA-GAAAAA
25493531 AAGAAAAGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 2 0.05
13 5 0.14
14 10 0.27
15 15 0.41
16 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAAGC
Found at i:25493530 original size:9 final size:8
Alignment explanation
Indices: 25493467--25493537 Score: 58
Period size: 8 Copynumber: 9.0 Consensus size: 8
25493457 TTCAATGAAT
25493467 AAAGAAAA
1 AAAGAAAA
25493475 AAAG-AAA
1 AAAGAAAA
*
25493482 GAAGAAGAA
1 AAAGAA-AA
*
25493491 GAAGAAGAA
1 AAAGAA-AA
*
25493500 AAAG--CA
1 AAAGAAAA
25493506 AAAGAAAA
1 AAAGAAAA
*
25493514 AAACAAAA
1 AAAGAAAA
*
25493522 AAGGAAAA
1 AAAGAAAA
25493530 AAAGAAAA
1 AAAGAAAA
25493538 GGAGAGGTCG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
6 5 0.10
7 6 0.12
8 26 0.51
9 14 0.27
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:25493538 original size:14 final size:14
Alignment explanation
Indices: 25493498--25493540 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
25493488 GAAGAAGAAG
*
25493498 AAAAAGCAAAAGAAA
1 AAAAAG-AAAAGGAA
*
25493513 AAAACAAAAAAGGAA
1 AAAA-AGAAAAGGAA
25493528 AAAAAGAAAAGGA
1 AAAAAGAAAAGGA
25493541 GAGGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 15 0.62
16 1 0.04
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGGAA
Found at i:25494853 original size:49 final size:48
Alignment explanation
Indices: 25494749--25494939 Score: 231
Period size: 49 Copynumber: 3.9 Consensus size: 48
25494739 CAAGTTTGAC
* * * * *
25494749 AGGGAAAGATCTAAGTCGCGACTGCGGATCCAGTACCACAAAAACACGA
1 AGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACAC-A
* *
25494798 TA-GGAAAGATCTAAGGCCGCAACGGCGGATCCAGTATCGCGAAGACACA
1 -AGGGAAAGATCTAA-GCCGCAACGGCGGATCCAGTACCACGAAGACACA
* * * *
25494847 AGGGAAAGATCTAAGACCGCAACGACAGATCCAGTACCGCGAAGGCACA
1 AGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAGACACA
*
25494896 AGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACGAAGA
1 AGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGA
25494940 TTTGAAGGGA
Statistics
Matches: 122, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
48 26 0.21
49 69 0.57
50 27 0.22
ACGTcount: A:0.38, C:0.25, G:0.27, T:0.10
Consensus pattern (48 bp):
AGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACACA
Found at i:25495391 original size:79 final size:78
Alignment explanation
Indices: 25495251--25495402 Score: 205
Period size: 79 Copynumber: 1.9 Consensus size: 78
25495241 TTACATCATC
* * * * * * * * *
25495251 AACCAATCTCTTACCCTGAGCCTGGGGCAGGTTACAGCCATTTGATCTTTTACCTCGAGCCTGGG
1 AACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAACCATTCGATCTCTTACCCCAAGCCTGAG
25495316 GCAGATCATCTTT
66 GCAGATCATCTTT
*
25495329 AACCAAGTCTCTTACCCCGAGCCAGGGGCAGATTACAATCATTCGATCTCTTACCCCAAGCCTGA
1 AACCAA-TCTCTTACCCCGAGCCAGGGGCAGATTACAACCATTCGATCTCTTACCCCAAGCCTGA
25495394 GGCAGATCA
65 GGCAGATCA
25495403 CCATCAATCG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
78 6 0.10
79 57 0.90
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (78 bp):
AACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAACCATTCGATCTCTTACCCCAAGCCTGAG
GCAGATCATCTTT
Found at i:25495398 original size:39 final size:39
Alignment explanation
Indices: 25495336--25495423 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
25495326 TTTAACCAAG
* * * *
25495336 TCTCTTACCCCGAGCCAGGGGCAGATTACAATCATTCGA
1 TCTCTTACCCCAAGCCAGAGGCAGATCACAATCAATCGA
* *
25495375 TCTCTTACCCCAAGCCTGAGGCAGATCACCATCAATCGA
1 TCTCTTACCCCAAGCCAGAGGCAGATCACAATCAATCGA
25495414 TCTCCTTACC
1 TCT-CTTACC
25495424 TTGATCACGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 36 0.86
40 6 0.14
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (39 bp):
TCTCTTACCCCAAGCCAGAGGCAGATCACAATCAATCGA
Found at i:25495422 original size:79 final size:78
Alignment explanation
Indices: 25495247--25495423 Score: 201
Period size: 79 Copynumber: 2.2 Consensus size: 78
25495237 GAAGTTACAT
* * * * * * * *
25495247 CATCAACCAATCTCTTACCCTGAGCCTGGGGCAGGTTACAGCCATTTGATCTTTTACCTCGAGCC
1 CATCAACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAACCATTCGATCTCTTACCCCAAGCC
* *
25495312 TGGGGCAGATCAT
66 TGAGGCAGATCAC
* * *
25495325 CTTTAACCAAGTCTCTTACCCCGAGCCAGGGGCAGATTACAATCATTCGATCTCTTACCCCAAGC
1 CATCAACCAA-TCTCTTACCCCGAGCCAGGGGCAGATTACAACCATTCGATCTCTTACCCCAAGC
25495390 CTGAGGCAGATCAC
65 CTGAGGCAGATCAC
* *
25495404 CATCAATCGATCTCCTTACC
1 CATCAACCAATCT-CTTACC
25495424 TTGATCACGG
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
78 11 0.14
79 69 0.86
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.25
Consensus pattern (78 bp):
CATCAACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAACCATTCGATCTCTTACCCCAAGCC
TGAGGCAGATCAC
Found at i:25495793 original size:194 final size:193
Alignment explanation
Indices: 25495454--25496300 Score: 1005
Period size: 194 Copynumber: 4.3 Consensus size: 193
25495444 GATTATCCAT
* *
25495454 AAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTT
1 AAGTGA-GCGGTCATCTTCCTGATGAGATATAGAGAAGTAAACCAACTCAATGCGAACAAATCTT
*
25495519 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAATGGTTAGCTTCCTG
65 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
* * * * * * *
25495584 ATGTGACATTGAGAAGTTGACCAAATTCGTTTTCCTGATGAGGTATAGAGAAGCGGATTGAAAC
130 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
* *
25495648 AAGTGAGATGGTCATCTTCCTGATGAGATATAGAGAAGTACACCAACTCAATGCGAACAAATCTT
1 AAGTGAG-CGGTCATCTTCCTGATGAGATATAGAGAAGTAAACCAACTCAATGCGAACAAATCTT
25495713 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
65 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
*
25495778 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAAC
130 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
** * * * * * * * *
25495842 AAACAGGGCAGTTATCTTCCTGATGAGGTACAGAGAAGTATACCAACTCAAGGCTCAAAGTGAGC
1 -AAGTGAGCGGTCATCTTCCTGATGAGATATAGAGAAG--TA--AAC-CAA--CTCAATGCGAAC
* * * * *
25495907 AAATCTTCGAACCCCAGCTTCTTGATGATATACTAAGAAGCAGGTCGGAGTAATAAAATGGTTAG
58 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
*
25495972 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
123 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
25496037 TGAAAC
188 TGAAAC
* * *
25496043 AAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATG
1 AAGTGA-GCGGTCATCTTCCTGATGAGATA-T-AG-AGAAG------T-AAA-CCA-ACTCAATG
* * * * *
25496108 TGAGCAAATCTTTGAACCCTAGCTTCCTGATGTGATACTGAGAAGCAGGTCGAAGCAATAAAATG
53 CGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATG
* * * * * *
25496173 GTTAGCTTTCTGATGAGATACGGAGAAGTGAACCAAA-TCTGTCTTCCTGATGAAACATAGAGAA
118 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTC-GTCTTCCTGATGAGATACAGAGAA
* **
25496237 GTGGATCAAAAC
182 GCGGATTGAAAC
* *
25496249 AAGTGATGCGGTTATCTTCCTGATGAGATACT-GAGAAGAAAACCAAACTCAA
1 AAGTGA-GCGGTCATCTTCCTGATGAGATA-TAGAGAAGTAAACC-AACTCAA
25496301 AGACTACGGT
Statistics
Matches: 568, Mismatches: 63, Indels: 43
0.84 0.09 0.06
Matches are distributed among these distances:
193 1 0.00
194 207 0.36
195 10 0.02
196 6 0.01
198 2 0.00
199 3 0.01
200 3 0.01
201 158 0.28
203 7 0.01
204 6 0.01
205 2 0.00
206 155 0.27
207 4 0.01
208 3 0.01
209 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (193 bp):
AAGTGAGCGGTCATCTTCCTGATGAGATATAGAGAAGTAAACCAACTCAATGCGAACAAATCTTC
GAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC
Found at i:25496221 original size:206 final size:204
Alignment explanation
Indices: 25495495--25496301 Score: 989
Period size: 201 Copynumber: 4.0 Consensus size: 204
25495485 AGAGAAGTAT
* * * *
25495495 ACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAA
1 ACCAGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGA
* * * * *
25495560 AGCAATAAAATGGTTAGCTTCCTGATGTGACATTGAGAAGTTGACCAAATTCGTTTTCCTGATGA
66 AGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
* * * *
25495625 GGTATAGAGAAGCGGATTGAAACAAGTGA-GATGGTCATCTTCCTGATGAGATA-T-AG-AGAAG
131 GATACAGAGAAGCGGATTGAAACAAGCGATG-CGGTCATCTTCCTGATGAGATACTGAGAAGAAG
*
25495686 ------T-AC
195 ACCAAATCAA
* * *
25495689 ACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGA
1 ACCAGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGA
25495754 AGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
66 AGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
* * * * * * * * *
25495819 GGTACAGAGAAGCGGATTGAAACAAAC-AGGGCAGTTATCTTCCTGATGAGGTACAGAGAAGTAT
131 GATACAGAGAAGCGGATTGAAACAAGCGA-TGCGGTCATCTTCCTGATGAGATACTGAGAAGAAG
*
25495883 ACCAACTC-A
195 ACCAAATCAA
* * * * * *
25495892 A--GGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGATATACTAAGAAGCAGGTCGG
1 ACCAGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGA
*
25495955 AGTAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
66 AGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
*
25496020 GATACAGAGAAGCGAATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA
131 GATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA
25496085 CCAAATCAA
196 CCAAATCAA
* * * *
25496094 ACCCACGCTCGATGTGAGCAAATCTTTGAACCCTAGCTTCCTGATGTGATACTGAGAAGCAGGTC
1 A-CCA-GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTC
* * *
25496159 GAAGCAATAAAATGGTTAGCTTTCTGATGAGATACGGAGAAGTGAACCAAA-TCTGTCTTCCTGA
64 GAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTC-GTCTTCCTGA
* * * * ** * *
25496223 TGAAACATAGAGAAGTGGATCAAAACAAGTGATGCGGTTATCTTCCTGATGAGATACTGAGAAGA
128 TGAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGA
*
25496288 AAACCAAACTCAA
193 AGACCAAA-TCAA
25496301 A
1 A
25496302 GACTACGGTG
Statistics
Matches: 531, Mismatches: 62, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
193 1 0.00
194 166 0.31
195 1 0.00
196 2 0.00
197 3 0.01
201 176 0.33
202 3 0.01
203 2 0.00
205 2 0.00
206 170 0.32
207 5 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (204 bp):
ACCAGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGA
AGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA
GATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA
CCAAATCAA
Found at i:25496675 original size:17 final size:17
Alignment explanation
Indices: 25496650--25496720 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
25496640 AATAAGTTTG
*
25496650 AATTTATTTTAAATTCA
1 AATTTATTTTAAATTTA
* * * *
25496667 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
*
25496684 AATTTACTTTAAATTTA
1 AATTTATTTTAAATTTA
*
25496701 AATTTATTTTAAATTAA
1 AATTTATTTTAAATTTA
25496718 AAT
1 AAT
25496721 AAAATTAAAG
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:25496684 original size:34 final size:34
Alignment explanation
Indices: 25496644--25496710 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
25496634 TTTTTAAATA
*
25496644 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
* *
25496678 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTT
25496711 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
Found at i:25497514 original size:9 final size:9
Alignment explanation
Indices: 25497500--25497554 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
25497490 GAACGTTTTA
25497500 ATAATAAAT
1 ATAATAAAT
25497509 ATAATAAAT
1 ATAATAAAT
25497518 ATAAT-AAT
1 ATAATAAAT
25497526 ATTAATAAA-
1 A-TAATAAAT
25497535 ATAAT-AAT
1 ATAATAAAT
*
25497543 ATTAAAAAAT
1 A-TAATAAAT
25497553 AT
1 AT
25497555 TTGAAGAGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
7 2 0.05
8 9 0.22
9 23 0.57
10 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAATAAAT
Found at i:25497538 original size:17 final size:17
Alignment explanation
Indices: 25497499--25497553 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 17
25497489 AGAACGTTTT
25497499 AATAATAA-ATATAATAA
1 AATAATAATAT-TAATAA
25497516 ATATAATAATATTAATAA
1 A-ATAATAATATTAATAA
25497534 AATAATAATATTAA-AA
1 AATAATAATATTAATAA
25497550 AATA
1 AATA
25497554 TTTGAAGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.17
17 14 0.39
18 14 0.39
19 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATATTAATAA
Found at i:25498729 original size:29 final size:29
Alignment explanation
Indices: 25498688--25498862 Score: 138
Period size: 29 Copynumber: 5.9 Consensus size: 29
25498678 AAGGTCCCTG
* *
25498688 AACTGTCCAAAAATTACATTTTTAACCTTG
1 AACT-TCCAAAAATTACATTTTTACCCTTA
* *
25498718 AACTTCCAAAAATTCCATTTTTGACCCTCAA
1 AACTTCCAAAAATTACATTTTT-ACCCT-TA
* * **
25498749 AACTTCCAAAAATT-CTAGCTTTGACCCCAA
1 AACTTCCAAAAATTAC-A-TTTTTACCCTTA
* **
25498779 AACTTCCAAAAATTTCATTTTTACCCCCA
1 AACTTCCAAAAATTACATTTTTACCCTTA
* *
25498808 AACTTCCAAAAATTCCATTTTTAACCTTGA
1 AACTTCCAAAAATTACATTTTTACCCTT-A
* **
25498838 AACTTTC-AAAATTACCCTTTTACCC
1 AACTTCCAAAAATTACATTTTTACCC
25498863 CGGATGTCCA
Statistics
Matches: 120, Mismatches: 19, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
29 64 0.53
30 33 0.28
31 20 0.17
32 3 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTTA
Found at i:25498848 original size:30 final size:30
Alignment explanation
Indices: 25498688--25498848 Score: 155
Period size: 30 Copynumber: 5.4 Consensus size: 30
25498678 AAGGTCCCTG
* **
25498688 AACTGTCCAAAAATTACATTTTTAACCT-TG
1 AACT-TCCAAAAATTCCATTTTTAACCTCAA
*
25498718 AACTTCCAAAAATTCCATTTTTGACCCTCAA
1 AACTTCCAAAAATTCCATTTTT-AACCTCAA
* ** * *
25498749 AACTTCCAAAAATTCTAGCTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTAACCTCAA
* * *
25498779 AACTTCCAAAAATTTCATTTTT-ACCCCCA
1 AACTTCCAAAAATTCCATTTTTAACCTCAA
**
25498808 AACTTCCAAAAATTCCATTTTTAACCTTGA
1 AACTTCCAAAAATTCCATTTTTAACCTCAA
*
25498838 AACTTTCAAAA
1 AACTTCCAAAA
25498849 TTACCCTTTT
Statistics
Matches: 108, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
29 44 0.41
30 45 0.42
31 19 0.18
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTAACCTCAA
Found at i:25498970 original size:60 final size:56
Alignment explanation
Indices: 25498841--25498988 Score: 172
Period size: 60 Copynumber: 2.6 Consensus size: 56
25498831 ACCTTGAAAC
* ***
25498841 TTTC-AAAATTACCCTTTTACCCCGGATGTCCAAAATTTTATTTTTGATCCCGATT
1 TTTCTAAAATTACCATTTTACCCCGGATGTCCAAAATAACATTTTTGATCCCGATT
* *
25498896 TTTCTAAAAATTACCATTTTACCCTCGGATGTCCAAAAATAACATTTTTTATCCTGATTT
1 TTTCT-AAAATTACCATTTTACCC-CGGATGTCC-AAAATAACATTTTTGATCCCGA-TT
*
25498956 TTTCTAAAAGTTACCGTTTTACCACCGGATGTC
1 TTTCTAAAA-TTACCATTTTACC-CCGGATGTC
25498989 TAAAGTTTCA
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
55 4 0.05
57 17 0.22
58 9 0.11
59 21 0.27
60 27 0.34
61 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (56 bp):
TTTCTAAAATTACCATTTTACCCCGGATGTCCAAAATAACATTTTTGATCCCGATT
Found at i:25499002 original size:59 final size:56
Alignment explanation
Indices: 25498841--25499003 Score: 175
Period size: 59 Copynumber: 2.8 Consensus size: 56
25498831 ACCTTGAAAC
* * *
25498841 TTTC-AAAATTACCCTTTTACCCCGGATGTCCAAAATTTTATTTTTGATCCCGATT
1 TTTCTAAAATTACCATTTTACCCCGGATGTCAAAAATTTCATTTTTGATCCCGATT
** * *
25498896 TTTCTAAAAATTACCATTTTACCCTCGGATGTCCAAAAATAACATTTTTTATCCTGATTT
1 TTTCT-AAAATTACCATTTTACCC-CGGATGT-CAAAAATTTCATTTTTGATCCCGA-TT
* * *
25498956 TTTCTAAAAGTTACCGTTTTACCACCGGATGTCTAAAGTTTCATTTTT
1 TTTCTAAAA-TTACCATTTTACC-CCGGATGTCAAAAATTTCATTTTT
25499004 AACCTCGAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.04
57 17 0.19
58 7 0.08
59 34 0.38
60 26 0.29
61 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (56 bp):
TTTCTAAAATTACCATTTTACCCCGGATGTCAAAAATTTCATTTTTGATCCCGATT
Found at i:25499413 original size:96 final size:96
Alignment explanation
Indices: 25499296--25499480 Score: 268
Period size: 96 Copynumber: 1.9 Consensus size: 96
25499286 AAAACTTTAA
*
25499296 AATCGAGGCAATATTCTTTTAT-TTCGAGTT-TGGAAAATTTGTGCCTTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTCTTTTATATTCGA-TTCT-GAAAATTTGCGCCTTAACTTACTAGGTGCAA
**
25499359 TTTTTCTTCAAATCAAAATAATCAAATACCCTT
64 CCTTTCTTCAAATCAAAATAATCAAATACCCTT
* *
25499392 AATCGAGGCAATGTT-TCTTTATATTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGTAAC
1 AATCGAGGCAATATTCT-TTTATATTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAAC
*
25499456 CTTTCTTCAAATCAAGATAATCAAA
65 CTTTCTTCAAATCAAAATAATCAAA
25499481 CATCCTTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
95 1 0.01
96 73 0.91
97 6 0.08
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATATTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAAATAATCAAATACCCTT
Found at i:25506802 original size:100 final size:99
Alignment explanation
Indices: 25506630--25506821 Score: 273
Period size: 100 Copynumber: 1.9 Consensus size: 99
25506620 AATGCACCTG
* * *
25506630 CATATTTCGTGTAAAAATTTGCGATTCCAGAAAGAGAAAAAAGATACGTTTTTACCCAAAAGAAT
1 CATATTTCGTGTAAAAATTTGCAATTCCAGAAAGAGAAAAAAGACACATTTTTACCCAAAAGAAT
*
25506695 AGGTTAGAGAAAGCATTGTCAAATATACATAGGT
66 AGGTTAGAGAAAGCAGTGTCAAATATACATAGGT
* *
25506729 CATATTTTC-TGTAAAAATTT-CAATTCCAGAAAGACCGGAAAAAG-CACATTTTTGTCCCAAAA
1 CATA-TTTCGTGTAAAAATTTGCAATTCCAGAAAGA--GAAAAAAGACACATTTTT-ACCCAAAA
25506791 GAATAGGTTAGAGAAAGCAGTGTCAAATATA
62 GAATAGGTTAGAGAAAGCAGTGTCAAATATA
25506822 TTAGGGGGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
98 13 0.16
99 22 0.27
100 48 0.58
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (99 bp):
CATATTTCGTGTAAAAATTTGCAATTCCAGAAAGAGAAAAAAGACACATTTTTACCCAAAAGAAT
AGGTTAGAGAAAGCAGTGTCAAATATACATAGGT
Found at i:25509595 original size:24 final size:24
Alignment explanation
Indices: 25509563--25509608 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25509553 CGATCACGAT
* *
25509563 CCTTTTCTCGGTCCCTATCCCTAC
1 CCTTATCTCGATCCCTATCCCTAC
*
25509587 CCTTATCTCTATCCCTATCCCT
1 CCTTATCTCGATCCCTATCCCT
25509609 GTGGCGATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.46, G:0.04, T:0.39
Consensus pattern (24 bp):
CCTTATCTCGATCCCTATCCCTAC
Found at i:25511053 original size:19 final size:19
Alignment explanation
Indices: 25511020--25511079 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 19
25511010 AAAGTAATAT
25511020 ATAATTATATTTAAAAATAAA
1 ATAA-TATA-TTAAAAATAAA
25511041 A-AATATATCTAAAAACTAAA
1 ATAATATAT-TAAAAA-TAAA
*
25511061 ATATTATTATTAAAAATAA
1 ATAATA-TATTAAAAATAA
25511080 TTTCTTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 1 0.03
19 10 0.29
20 10 0.29
21 10 0.29
22 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAATATATTAAAAATAAA
Found at i:25511496 original size:15 final size:15
Alignment explanation
Indices: 25511476--25511520 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
25511466 TATCGTCAAC
25511476 AATTATTTTTATTTT
1 AATTATTTTTATTTT
*
25511491 AATTA-TTTAATTTT
1 AATTATTTTTATTTT
*
25511505 AATAAATTTTTATTTT
1 AAT-TATTTTTATTTT
25511521 GATAACTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 11 0.44
15 6 0.24
16 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTATTTTTATTTT
Found at i:25511553 original size:21 final size:21
Alignment explanation
Indices: 25511529--25511575 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
25511519 TTGATAACTC
25511529 ATTTTA-TATTTTTAAAATTTA
1 ATTTTACTATTTTTAAAA-TTA
* *
25511550 A-TTTACTTTTTTTAATATTA
1 ATTTTACTATTTTTAAAATTA
25511570 ATTTTA
1 ATTTTA
25511576 GTTTTTTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTACTATTTTTAAAATTA
Found at i:25511554 original size:20 final size:20
Alignment explanation
Indices: 25511531--25511573 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
25511521 GATAACTCAT
25511531 TTTA-TATTTTTAAAATTTAA
1 TTTACTATTTTTAAAA-TTAA
* *
25511551 TTTACTTTTTTTAATATTAA
1 TTTACTATTTTTAAAATTAA
25511571 TTT
1 TTT
25511574 TAGTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTACTATTTTTAAAATTAA
Found at i:25512530 original size:3 final size:3
Alignment explanation
Indices: 25512522--25512550 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
25512512 TACGAATTTG
25512522 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
25512551 GTAAATATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:25513281 original size:29 final size:31
Alignment explanation
Indices: 25513196--25513284 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 31
25513186 TTTCTAAATT
* * *
25513196 TTTTTTGCTCAATTTGATACTCAAACTTGACAT
1 TTTTTT-CT-AATTTGGTACTTAAACTTGACAC
25513229 TTTTTTCGTAATTTGGTA-TCTAAACTTGACAC
1 TTTTTTC-TAATTTGGTACT-TAAACTTGACAC
25513261 TTTTTT-T-ATTTGGTACTTAAACTT
1 TTTTTTCTAATTTGGTACTTAAACTT
25513285 TTTGGGTCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
29 15 0.30
30 2 0.04
31 1 0.02
32 25 0.50
33 7 0.14
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.51
Consensus pattern (31 bp):
TTTTTTCTAATTTGGTACTTAAACTTGACAC
Found at i:25513604 original size:58 final size:59
Alignment explanation
Indices: 25513489--25513616 Score: 161
Period size: 58 Copynumber: 2.2 Consensus size: 59
25513479 TAATAAATTT
* * *
25513489 AGGTATCAAATTGAATCTAAAAAAGTTTAGATACCAAATTAGAAAAAAATGTTAAGTTC
1 AGGTACCAAATTGAATCTAAAAAAGTTTAGATACAAAATTAGAAAAAAATGTCAAGTTC
* * * *
25513548 AGGTACTAAATTGAGTC-AAAAAAGGTTTAGGTACAAAATT-TAAAAAAATGTCAAGTTC
1 AGGTACCAAATTGAATCTAAAAAA-GTTTAGATACAAAATTAGAAAAAAATGTCAAGTTC
*
25513606 ATGTACCAAAT
1 AGGTACCAAAT
25513617 GTTATATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 31 0.53
59 28 0.47
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (59 bp):
AGGTACCAAATTGAATCTAAAAAAGTTTAGATACAAAATTAGAAAAAAATGTCAAGTTC
Found at i:25513674 original size:28 final size:29
Alignment explanation
Indices: 25513630--25513701 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
25513620 ATATTAAGCC
* * *
25513630 TACTATAAAATAACTTTTGACCAAAAAAA
1 TACTATAAAATACCTTTTCACAAAAAAAA
*
25513659 TACTA-CAAATACCTTTTCACAAAAAAAA
1 TACTATAAAATACCTTTTCACAAAAAAAA
25513687 TACTATAAAATACCT
1 TACTATAAAATACCT
25513702 AACTATATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 24 0.65
29 13 0.35
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (29 bp):
TACTATAAAATACCTTTTCACAAAAAAAA
Found at i:25514039 original size:23 final size:23
Alignment explanation
Indices: 25514012--25514071 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
25514002 CAAATGTTTA
* *
25514012 TAAAAATTCTAAAATTATATTTT
1 TAAAAATTCTAAAATTAAATTCT
*
25514035 TAAAAATTATAAAATTAAATTCT
1 TAAAAATTCTAAAATTAAATTCT
*
25514058 AAACAAATTCTAAA
1 TAA-AAATTCTAAA
25514072 GAACATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAAATTCTAAAATTAAATTCT
Found at i:25517583 original size:50 final size:50
Alignment explanation
Indices: 25517479--25517574 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
25517469 TACGGGTAAA
* * * **
25517479 CACACGGACATGTGTCCAGGTCGTGTAGCTCACTGTTTGTGTATTAAAGC
1 CACACGGACATGTGTCCAGGCCGTGTAACTCACTGTTTATACATTAAAGC
* *
25517529 CACACGGGCGTGTGTCCAGGCCGTGTAACTCACTGTTTATACATTA
1 CACACGGACATGTGTCCAGGCCGTGTAACTCACTGTTTATACATTA
25517575 GGGTCACACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (50 bp):
CACACGGACATGTGTCCAGGCCGTGTAACTCACTGTTTATACATTAAAGC
Found at i:25518757 original size:20 final size:21
Alignment explanation
Indices: 25518703--25518758 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
25518693 GTTTAAGGAA
25518703 TTATTTTTAATAATA-ATATTT
1 TTATTTTTAA-AATATATATTT
* *
25518724 TAATTTTT-AGATATAT-TTT
1 TTATTTTTAAAATATATATTT
25518743 TTATTTTTAAAATATA
1 TTATTTTTAAAATATA
25518759 ATTATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 13 0.45
20 9 0.31
21 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATTTTTAAAATATATATTT
Found at i:25520009 original size:39 final size:39
Alignment explanation
Indices: 25519934--25520011 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
25519924 TTATGCCTGT
* * *
25519934 TCTACATTTGGGCTTTTAGTGTTATGGATTACATGCAAC
1 TCTACATTTGGGCTCTTAGTGTTATAGATTAAATGCAAC
*
25519973 TCTACATTTGGTCTCTTAGTGTTATA-AGTTAAATGCAAC
1 TCTACATTTGGGCTCTTAGTGTTATAGA-TTAAATGCAAC
25520012 CTTAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (39 bp):
TCTACATTTGGGCTCTTAGTGTTATAGATTAAATGCAAC
Found at i:25520166 original size:24 final size:24
Alignment explanation
Indices: 25520126--25520171 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25520116 TGATCGCCAC
* *
25520126 AGGGATAGGGATAGAGATAAGGGT
1 AGGGATAGGGACAGAGAAAAGGGT
*
25520150 AGGGATAGGGACCGAGAAAAGG
1 AGGGATAGGGACAGAGAAAAGG
25520172 ATCGTGATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.04, G:0.46, T:0.11
Consensus pattern (24 bp):
AGGGATAGGGACAGAGAAAAGGGT
Found at i:25525277 original size:2 final size:2
Alignment explanation
Indices: 25525270--25525326 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
25525260 CCAGATAAAT
*
25525270 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
25525312 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
25525327 TATATATATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25531223 original size:96 final size:95
Alignment explanation
Indices: 25531060--25531240 Score: 249
Period size: 96 Copynumber: 1.9 Consensus size: 95
25531050 TTTGGAAAAG
* ** *
25531060 GATTATCTCGATTTGAAGAAAGGTTGCACTAGTAAGTTAAGGCGCAAATTTTCAAAATCGAATAT
1 GATTATCTCGATTTGAAAAAAAATTGCACTAGTAAGTTAAGGCACAAATTTTCAAAATCGAATAT
25531125 -AAAGAAACATTGCCTCGATTAAGGGTATAT
66 AAAAG-AACATTGCCTCGATTAAGGGTATAT
* *
25531155 GATTATTTCGATTTGAAAAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCCAAACTCGAA-
1 GATTATCTCGATTTGAAAAAAAATTGCA-CTAGTAAGTTAAGGCACAAATTTT-CAAAATCGAAT
* *
25531219 ATAAAAGAATATTGCCTTGATT
64 ATAAAAGAACATTGCCTCGATT
25531241 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
95 24 0.32
96 38 0.51
97 13 0.17
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (95 bp):
GATTATCTCGATTTGAAAAAAAATTGCACTAGTAAGTTAAGGCACAAATTTTCAAAATCGAATAT
AAAAGAACATTGCCTCGATTAAGGGTATAT
Found at i:25531634 original size:29 final size:29
Alignment explanation
Indices: 25531592--25531816 Score: 134
Period size: 29 Copynumber: 7.6 Consensus size: 29
25531582 AATCAGGATC
** *
25531592 AAAAATGTTATTTTTGGACA-TCCGAGGTT
1 AAAAATGAAATTTTTGGA-AGTCCGAGGGT
* * *
25531621 AAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGAAATTTTTGGAAGTCCGAGGGT
**
25531650 AAAAATGAAATTTTTGGAAGTTTTG-GGGT
1 AAAAATGAAATTTTTGGAAG-TCCGAGGGT
* ** *
25531679 CAAAACT-AGAATTTTTGGAAGTTTTGGGGGT
1 -AAAAATGA-AATTTTTGGAAG-TCCGAGGGT
* * *
25531710 CAAAAATGAAATTTTTGGAAGTTCAAGAGT
1 -AAAAATGAAATTTTTGGAAGTCCGAGGGT
* * ***
25531740 AAAAATGTAATTTTTGAAAGTTTTAGGGT
1 AAAAATGAAATTTTTGGAAGTCCGAGGGT
* * *
25531769 CAAAAAT-AGAATTTTTGCAAGTTCGAGGTT
1 -AAAAATGA-AATTTTTGGAAGTCCGAGGGT
*
25531799 AAAAATGTAATTTTTGGA
1 AAAAATGAAATTTTTGGA
25531817 CAGTTCAGGG
Statistics
Matches: 162, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.01
29 85 0.52
30 53 0.33
31 22 0.14
32 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAAATGAAATTTTTGGAAGTCCGAGGGT
Found at i:25531694 original size:30 final size:30
Alignment explanation
Indices: 25531621--25531821 Score: 187
Period size: 29 Copynumber: 6.7 Consensus size: 30
25531611 ATCCGAGGTT
* **
25531621 AAAAATGGAATTTTTGGAAGTTCGGGGGT-
1 AAAAATGAAATTTTTGGAAGTTTTGGGGTC
25531650 AAAAATGAAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGAAATTTTTGGAAGTTTTGGGGTC
*
25531680 AAAACT-AGAATTTTTGGAAGTTTTGGGGGTC
1 AAAAATGA-AATTTTTGGAAGTTTT-GGGGTC
*** *
25531711 AAAAATGAAATTTTTGGAAGTTCAAGAGT-
1 AAAAATGAAATTTTTGGAAGTTTTGGGGTC
* * *
25531740 AAAAATGTAATTTTTGAAAGTTTTAGGGTC
1 AAAAATGAAATTTTTGGAAGTTTTGGGGTC
* * * *
25531770 AAAAAT-AGAATTTTTGCAAG-TTCGAGGTT
1 AAAAATGA-AATTTTTGGAAGTTTTGGGGTC
*
25531799 AAAAATGTAATTTTTGGACAGTT
1 AAAAATGAAATTTTTGGA-AGTT
25531822 CAGGGACCTT
Statistics
Matches: 141, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
29 71 0.50
30 43 0.30
31 26 0.18
32 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAAATGAAATTTTTGGAAGTTTTGGGGTC
Found at i:25531791 original size:59 final size:60
Alignment explanation
Indices: 25531616--25531814 Score: 194
Period size: 59 Copynumber: 3.4 Consensus size: 60
25531606 TGGACATCCG
* * * * * **
25531616 AGGTTAAAAATGGAATTTTTGGAAG-TTCGGGGGT-AAAAATGAAATTTTTGGAAGTTTTG
1 AGGTTAAAAATGTAATTTTTGAAAGTTTTGAGGGTCAAAAATGAAATTTTTGCAAG-TTCA
* * * * * *
25531675 GGGTCAAAACTAG-AATTTTTGGAAGTTTTGGGGGTCAAAAATGAAATTTTTGGAAGTTCA
1 AGGTTAAAAAT-GTAATTTTTGAAAGTTTTGAGGGTCAAAAATGAAATTTTTGCAAGTTCA
*
25531735 AGAG-TAAAAATGTAATTTTTGAAAGTTTT-AGGGTCAAAAAT-AGAATTTTTGCAAGTTCG
1 AG-GTTAAAAATGTAATTTTTGAAAGTTTTGAGGGTCAAAAATGA-AATTTTTGCAAGTTCA
25531794 AGGTTAAAAATGTAATTTTTG
1 AGGTTAAAAATGTAATTTTTG
25531815 GACAGTTCAG
Statistics
Matches: 120, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
58 2 0.02
59 65 0.54
60 32 0.27
61 21 0.17
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (60 bp):
AGGTTAAAAATGTAATTTTTGAAAGTTTTGAGGGTCAAAAATGAAATTTTTGCAAGTTCA
Found at i:25532986 original size:17 final size:17
Alignment explanation
Indices: 25532960--25533001 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
25532950 TCTTCAAATC
25532960 TTTT-TTAATATTATTA
1 TTTTATTAATATTATTA
25532976 TTTTATTAATATTATTA
1 TTTTATTAATATTATTA
25532993 TATTTATTA
1 T-TTTATTA
25533002 TTAAAACGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 4 0.17
17 13 0.54
18 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTAATATTATTA
Found at i:25533808 original size:17 final size:17
Alignment explanation
Indices: 25533783--25533853 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
25533773 CTTTAATTTT
*
25533783 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
25533800 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
* * * *
25533817 ATTCAAACTCAAAATGA
1 ATTTAAATTTAAAATAA
*
25533834 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
25533851 ATT
1 ATT
25533854 CAAACTTATT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:25533831 original size:34 final size:34
Alignment explanation
Indices: 25533793--25533859 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
25533783 ATTTTAATTT
*
25533793 AAAATAAATTTAAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
* *
25533827 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
25533860 TATTTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:25534572 original size:206 final size:204
Alignment explanation
Indices: 25534218--25535005 Score: 991
Period size: 206 Copynumber: 3.9 Consensus size: 204
25534208 TCTGGTTTTA
* ** *
25534218 TTGATTTGGTTTTCTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTCAATCCGCTT
* *** * * *
25534283 CTCTATGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
25534348 TTTATTGCTTCGACCTGCTTCTCAGTATCACATCAGGAAGCTAGGGTTCAAAGATTTTCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCACATCAGGAAGCTGGGGTTCGAAGATTTTCTCACAT
*
25534413 CGAGCGTGGG
196 TGAGCGT-GG
** *
25534423 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGGCCGCATCGCTTGTTTCAATCCGCT
1 -TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTCAATCCGCT
*
25534488 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
65 TCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * * *
25534553 TTTTATTACTCCGACCTGCTTCTTAGTAT-ATCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCA-CATCAGGAAGCTGGGGTTCGAAGATTTTCTCAC
* *
25534617 TTTGAGC---C
194 ATTGAGCGTGG
* * * * * * **
25534625 TTGAGTTGGTATACTTCTCTGTACCTCATCAGGAAGATAACTAC-CCT-GTTTGTTTCAATCCGC
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAAC--CGCATCACTTGTTTCAATCCGC
25534688 TTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
64 TTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
** *
25534753 ATTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGT-TCG
129 ATTTTATTGCTTCGACCTGCTTCTCAGTATCACATCAGGAAGCTGGGGTTCGAAGATTT-TCTCA
*
25534817 CATTGAG-TTGG
193 CATTGAGCGTGG
* * *
25534828 -TG---T--ACTTC-TCT--GTATCTCATCAGGAAGATGACCATC-TCACTTGTTTCAATCCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACC-GCATCACTTGTTTCAATCCGCT
* *
25534883 TCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACCA
65 TCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* *
25534948 TTTTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCACATCAGGAAGCTGGGGTTCGAAGATTT
25535006 GTTCTTATTG
Statistics
Matches: 517, Mismatches: 54, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
192 1 0.00
193 1 0.00
194 154 0.30
196 3 0.01
197 2 0.00
199 1 0.00
201 173 0.33
202 4 0.01
203 1 0.00
205 1 0.00
206 176 0.34
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (204 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTCAATCCGCTT
CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCACATCAGGAAGCTGGGGTTCGAAGATTTTCTCACAT
TGAGCGTGG
Found at i:25534724 original size:201 final size:196
Alignment explanation
Indices: 25534231--25535053 Score: 1002
Period size: 194 Copynumber: 4.1 Consensus size: 196
25534221 ATTTGGTTTT
* * ** * * ***
25534231 CTTCTCAGTATCTCATCAGGAAGAT-A-ACCGCATCACTTGTTTTGATCCACTTCTCTATGTTTC
1 CTTCTCTGTATCTCATCAGGAAGATGACACC-C-TCGCTTGTTTCAATCCGCTTCTCTGTACCTC
* * *
25534294 ATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
64 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * * *
25534359 GACCTGCTTCTCAGTATCA-CATCAGGAAGCTAGGGTTCAAAGATTTTCTCACATCGAGCGTGGG
129 GACCTGCTTCTCAGTAT-ATCATCAGGAAGCTGGGGTTCGAAGA-TTTGT-AC-T-TAGC-----
* * *
25534423 TTTGATTTGGTCTT
184 -TTGAGTTGGTATA
* * * *
25534437 CTTCTCAGTATCTCATCAGGAAGATGGC-CGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCA
1 CTTCTCTGTATCTCATCAGGAAGATGACAC-CCTCGCTTGTTTCAATCCGCTTCTCTGTACCTCA
* *
25534501 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTCCG
65 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
* *
25534566 ACCTGCTTCTTAGTATATCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGT
130 ACCTGCTTCTCAGTATATCATCAGGAAGCTGGGGTTCGAAGATTTG-T-AC-TT-AG-CTTGAGT
25534631 TGGTATA
190 TGGTATA
* * *
25534638 CTTCTCTGTACCTCATCAGGAAGATAACTACCCT-GTTTGTTTCAATCCGCTTCTCTGTACCTCA
1 CTTCTCTGTATCTCATCAGGAAGATGAC-ACCCTCGCTTGTTTCAATCCGCTTCTCTGTACCTCA
25534702 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
65 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
* * *
25534767 ACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTG---TTCGCATTGAGTTGGT
130 ACCTGCTTCTCAGTATATCATCAGGAAGCTGGGGTTCGAAGATTTGTACTTAGC-TTGAGTTGGT
*
25534829 GTA
194 ATA
* *
25534832 CTTCTCTGTATCTCATCAGGAAGATGAC-CATCTCACTTGTTTCAATCCGCTTCTCTGTACCTCA
1 CTTCTCTGTATCTCATCAGGAAGATGACAC-CCTCGCTTGTTTCAATCCGCTTCTCTGTACCTCA
* * *
25534896 TCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACCATTTTATTGCTTTG
65 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
* *
25534961 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCTTA--TTGAGTTGGTA
130 ACCTGCTTCTCAGTATATCATCAGGAAGCTGGGGTTCGAAGATTTGTACTTAGCTTGAGTTGGTA
25535024 TA
195 TA
25535026 CTTCTCTGTATCTCATCAGGAAGATGAC
1 CTTCTCTGTATCTCATCAGGAAGATGAC
25535054 CGCCTCACTT
Statistics
Matches: 552, Mismatches: 50, Indels: 42
0.86 0.08 0.07
Matches are distributed among these distances:
192 1 0.00
193 3 0.01
194 214 0.39
195 2 0.00
197 2 0.00
201 167 0.30
202 2 0.00
203 1 0.00
205 4 0.01
206 153 0.28
207 2 0.00
208 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (196 bp):
CTTCTCTGTATCTCATCAGGAAGATGACACCCTCGCTTGTTTCAATCCGCTTCTCTGTACCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATATCATCAGGAAGCTGGGGTTCGAAGATTTGTACTTAGCTTGAGTTGGTAT
A
Found at i:25534994 original size:395 final size:394
Alignment explanation
Indices: 25534292--25535050 Score: 1102
Period size: 395 Copynumber: 1.9 Consensus size: 394
25534282 TCTCTATGTT
* * *
25534292 TCATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCATTTTATTGCT
1 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCT
25534357 TCGACCTGCTTCTCAGTATCACATCAGGAAGCTAGGGTTCAAAGATTTTCTCACATCGAGCGTGG
66 TCGACCTGCTTCTCAGTATCACATCAGGAAGCTAGGGTTCAAAGATTTTCTCACATCGA-CGTGG
* * *
25534422 GTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGGCCGCATCGCTTGTTTCAATCCGC
130 G-TTG--TT-GACTTCTTCT-AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGC
* *
25534487 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
190 TTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACC
*
25534552 ATTTTATTACTCCGACCTGCTTCTTAGTATATCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
255 ATTTTATTACTCCGACCTGCTTCTCAGTATATCATCAAGAAGCTGGGGTTCGAAGATTTG-T-AC
25534617 TTTGAGCCTTGAGTTGGTATACTTCTCTGTACCTCATCAGGAAGATAACTACCCTGTTTGTTTCA
318 -TT-A---TTGAGTTGGTATACTTCTCTGTACCTCATCAGGAAGATAACTACCCTGTTTGTTTCA
25534682 ATCCGCTTCTCTGTACC
378 ATCCGCTTCTCTGTACC
25534699 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCT
1 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCT
** * * * * *
25534764 TCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGT-TCGCATTGA-GTTG
66 TCGACCTGCTTCTCAGTATCACATCAGGAAGCTAGGGTTCAAAGATTT-TCTCACATCGACGTGG
*
25534827 G-TG-T-ACTTC-TCT-GTATCTCATCAGGAAGATGACCATC-TCACTTGTTTCAATCCGCTTCT
130 GTTGTTGACTTCTTCTAGTATCTCATCAGGAAGATGACC-GCATCACTTGTTTCAATCCGCTTCT
*
25534886 CTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACCATTT
194 CTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCATTT
* ** * * *
25534951 TATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCTTATTG
259 TATTACTCCGACCTGCTTCTCAGTATATCATCAAGAAGCTGGGGTTCGAAGATTTGTACTTATTG
*
25535016 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGAT
324 AGTTGGTATACTTCTCTGTACCTCATCAGGAAGAT
25535051 GACCGCCTCA
Statistics
Matches: 325, Mismatches: 25, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
388 37 0.11
391 1 0.00
392 2 0.01
393 1 0.00
394 1 0.00
395 154 0.47
396 1 0.00
397 3 0.01
398 4 0.01
400 1 0.00
403 2 0.01
405 4 0.01
407 113 0.35
408 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (394 bp):
TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCT
TCGACCTGCTTCTCAGTATCACATCAGGAAGCTAGGGTTCAAAGATTTTCTCACATCGACGTGGG
TTGTTGACTTCTTCTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCT
GTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCATTTTA
TTACTCCGACCTGCTTCTCAGTATATCATCAAGAAGCTGGGGTTCGAAGATTTGTACTTATTGAG
TTGGTATACTTCTCTGTACCTCATCAGGAAGATAACTACCCTGTTTGTTTCAATCCGCTTCTCTG
TACC
Done.