Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 92 of 132
Found at i:28362275 original size:50 final size:49
Alignment explanation
Indices: 28362125--28362451 Score: 286
Period size: 50 Copynumber: 6.7 Consensus size: 49
28362115 CCATTGTGGT
* * * *
28362125 CTCAACCTTTCCCATCACATCTTTTAAGGTACCGAATTTATCGTTACGGC
1 CTCAACCTTTCCCATCACATCTTTTAAGGTACCG-GTTCACCGTTGCGGC
* * * * * * * *
28362175 CTTAATCTTTCCCTTCATATC-TTCATGGTATCGGGTTCACCGTTGTGGC
1 CTCAACCTTTCCCATCACATCTTTTAAGGTA-CCGGTTCACCGTTGCGGC
28362224 CTCAACCTTTCCCATCACATCTTTTAAGGTACCGAGTTCACCGTTGCGGC
1 CTCAACCTTTCCCATCACATCTTTTAAGGTACCG-GTTCACCGTTGCGGC
* * * * *
28362274 CTTAACCTTTCCCATCACATCTTCTAAGGTACTGGGTTCGCCGTTGTGGC
1 CTCAACCTTTCCCATCACATCTTTTAAGGTAC-CGGTTCACCGTTGCGGC
* * * * * * *
28362324 CTTAACCTTTCCCTTCAAATC-TTCATGGTACCGGTTCGCCGTTGCAGC
1 CTCAACCTTTCCCATCACATCTTTTAAGGTACCGGTTCACCGTTGCGGC
* * *
28362372 TTCAACCTTTCCCATCACA--TTTCATA-GTACCGGATTTACCGTTGCGGC
1 CTCAACCTTTCCCATCACATCTTTTA-AGGTACCGG-TTCACCGTTGCGGC
** * *
28362420 CTCAATATTTCCCATCACATCTTCTGAGGTAC
1 CTCAACCTTTCCCATCACATCTTTTAAGGTAC
28362452 TAGGTTCTTC
Statistics
Matches: 220, Mismatches: 47, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
47 11 0.05
48 56 0.25
49 44 0.20
50 108 0.49
51 1 0.00
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (49 bp):
CTCAACCTTTCCCATCACATCTTTTAAGGTACCGGTTCACCGTTGCGGC
Found at i:28362450 original size:146 final size:149
Alignment explanation
Indices: 28362172--28362458 Score: 395
Period size: 146 Copynumber: 1.9 Consensus size: 149
28362162 TTATCGTTAC
* * * **
28362172 GGCCTTAATCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGTGGCCTCAACCTTTCCC
1 GGCCTTAACCTTTCCCTTCAAATCTTCATGGTATCCGGTTCACCGTTGCAGCCTCAACCTTTCCC
* * *
28362237 ATCACATCTTTTAAGGTACCGAGTTCACCGTTGCGGCCTTAACCTTTCCCATCACATCTTCTAAG
66 ATCACATCTTATAAGGTACCGAGTTCACCGTTGCGGCCTCAACATTTCCCATCACATCTTCTAAG
*
28362302 GTACTGGGTTCGCCGTTGT
131 GTACTAGGTTCGCCGTTGT
* *
28362321 GGCCTTAACCTTTCCCTTCAAATCTTCATGGTA-CCGGTTCGCCGTTGCAGCTTCAACCTTTCCC
1 GGCCTTAACCTTTCCCTTCAAATCTTCATGGTATCCGGTTCACCGTTGCAGCCTCAACCTTTCCC
* * *
28362385 ATCACAT-TTCAT-A-GTACCG-GATTTACCGTTGCGGCCTCAATATTTCCCATCACATCTTCTG
66 ATCACATCTT-ATAAGGTACCGAG-TTCACCGTTGCGGCCTCAACATTTCCCATCACATCTTCTA
28362446 AGGTACTAGGTTC
129 AGGTACTAGGTTC
28362459 TTCATTGCGA
Statistics
Matches: 122, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
145 1 0.01
146 53 0.43
147 3 0.02
148 34 0.28
149 31 0.25
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (149 bp):
GGCCTTAACCTTTCCCTTCAAATCTTCATGGTATCCGGTTCACCGTTGCAGCCTCAACCTTTCCC
ATCACATCTTATAAGGTACCGAGTTCACCGTTGCGGCCTCAACATTTCCCATCACATCTTCTAAG
GTACTAGGTTCGCCGTTGT
Found at i:28362477 original size:146 final size:149
Alignment explanation
Indices: 28362181--28362496 Score: 381
Period size: 146 Copynumber: 2.1 Consensus size: 149
28362171 CGGCCTTAAT
* * **
28362181 CTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGTGGCCTCAACCTTTCCCATCACATCT
1 CTTTCCCTTCAAATCTTCATGGTATCCGGTTCACCGTTGCAGCCTCAACCTTTCCCATCACATCT
* * * *
28362246 TTTAAGGTACCGAGTTCACCGTTGCGGCCTTAACCTTTCCCATCACATCTTCTAAGGTACTGGGT
66 TATAAGGTACCGAGTTCACCGTTGCGGCCTCAACATTTCCCATCACATCTTCTAAGGTACTAGGT
* * * *
28362311 TCGCCGTTGTGGCCTTAAC
131 TCGCCATTGCGACCTCAAC
* *
28362330 CTTTCCCTTCAAATCTTCATGGTA-CCGGTTCGCCGTTGCAGCTTCAACCTTTCCCATCACAT-T
1 CTTTCCCTTCAAATCTTCATGGTATCCGGTTCACCGTTGCAGCCTCAACCTTTCCCATCACATCT
* * *
28362393 TCAT-A-GTACCG-GATTTACCGTTGCGGCCTCAATATTTCCCATCACATCTTCTGAGGTACTAG
66 T-ATAAGGTACCGAG-TTCACCGTTGCGGCCTCAACATTTCCCATCACATCTTCTAAGGTACTAG
** *
28362455 GTTCTTCATTGCGATCTCAAC
129 GTTCGCCATTGCGACCTCAAC
* *
28362476 CTTTTCCTTTAAATCTTCATG
1 CTTTCCCTTCAAATCTTCATG
28362497 TTTTCTCAGT
Statistics
Matches: 143, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
145 1 0.01
146 82 0.57
147 3 0.02
148 34 0.24
149 23 0.16
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.35
Consensus pattern (149 bp):
CTTTCCCTTCAAATCTTCATGGTATCCGGTTCACCGTTGCAGCCTCAACCTTTCCCATCACATCT
TATAAGGTACCGAGTTCACCGTTGCGGCCTCAACATTTCCCATCACATCTTCTAAGGTACTAGGT
TCGCCATTGCGACCTCAAC
Found at i:28363974 original size:3 final size:3
Alignment explanation
Indices: 28363966--28363999 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28363956 CCCCATTCAC
28363966 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
28364000 TTGCGATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:28368506 original size:58 final size:58
Alignment explanation
Indices: 28368425--28368882 Score: 184
Period size: 58 Copynumber: 7.7 Consensus size: 58
28368415 TTTCAGAGAA
* *
28368425 TTTACGGTCAAAATGTAATTTTGGAAAAGTTTGAGGTAAAAATGCGATTTT-AGGAAAT
1 TTTAAGGTCAAAATGTAATTTTGGAAAAGTTTGAGGTAAAAATGCGATTTTGA-GAAAG
** * * * *
28368483 TTTAAGGTCAAAATGTGGTTTTGGGAAAGTTCGAGGTCAAAATGTGATTTTGAGAAAG
1 TTTAAGGTCAAAATGTAATTTTGGAAAAGTTTGAGGTAAAAATGCGATTTTGAGAAAG
* * * * * *
28368541 TGTAGGGGTCAAAATGCAATTTTGGAAAAGTTTGAGGGGGTTAAAATGTGATTTTGA-AAAA
1 TTTA-AGGTCAAAATGTAATTTTGGAAAAGTTTGA---GGTAAAAATGCGATTTTGAGAAAG
* * * ** * * * *
28368602 TTTAGGAGTTGAAAATGTTA-TTTCAAGAAAGTTT-AGGGTTAAAATGTGGTTTTGGGAAAG
1 TTTA--AGGTCAAAATGTAATTTTGGA-AAAGTTTGA-GGTAAAAATGCGATTTTGAGAAAG
* ** * * * * * *
28368662 TCTGGGGTTAAAATGTGATTTT-AAGAAAGTTTAGGGGTTAAAATGTGATTTTG-GAAATG
1 TTTAAGGTCAAAATGTAATTTTGGA-AAAGTTT-GAGGTAAAAATGCGATTTTGAGAAA-G
* * * * * ** *
28368721 TTTAGGGGTAAAAATGTGATTTTAGAAAAGTTTTG-GGT--TAATGTAATTTT-AGAAAAT
1 TTTA-AGGTCAAAATGTAATTTTGGAAAAG-TTTGAGGTAAAAATGCGATTTTGAG-AAAG
* * * * **
28368778 TTTAAGGGTCAAAATGTGATTTT-AAAGAAGTTTAAGGGTTAAAATGTAATTTTG-GAAAAG
1 TTTAA-GGTCAAAATGTAATTTTGGAA-AAGTTTGA-GGTAAAAATGCGATTTTGAG-AAAG
* * * * *
28368838 TTTAAGGGTTAAAATATAATTTTAGAGAAGTTTGGGGGTAAAAAT
1 TTTAA-GGTCAAAATGTAATTTTGGAAAAGTTT-GAGGTAAAAAT
28368883 ATGATTTTTG
Statistics
Matches: 317, Mismatches: 57, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
56 5 0.02
57 34 0.11
58 81 0.26
59 69 0.22
60 77 0.24
61 16 0.05
62 35 0.11
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (58 bp):
TTTAAGGTCAAAATGTAATTTTGGAAAAGTTTGAGGTAAAAATGCGATTTTGAGAAAG
Found at i:28368553 original size:30 final size:30
Alignment explanation
Indices: 28368434--28368890 Score: 320
Period size: 30 Copynumber: 15.4 Consensus size: 30
28368424 ATTTACGGTC
* * *
28368434 AAAATGTAATTTTG-GAAAAGTTT-GAGGTA
1 AAAATGTGATTTTGAG-AAAGTTTAGGGGTT
* * * *
28368463 AAAATGCGATTTT-AGGAAATTTTA-AGGTC
1 AAAATGTGATTTTGA-GAAAGTTTAGGGGTT
* * * * *
28368492 AAAATGTGGTTTTGGGAAAG-TTCGAGGTC
1 AAAATGTGATTTTGAGAAAGTTTAGGGGTT
* *
28368521 AAAATGTGATTTTGAGAAAGTGTAGGGGTC
1 AAAATGTGATTTTGAGAAAGTTTAGGGGTT
**
28368551 AAAATGCAATTTTG-GAAAAGTTTGAGGGGGTT
1 AAAATGTGATTTTGAG-AAAGTTT-A-GGGGTT
* *
28368583 AAAATGTGATTTTGA-AAAATTTAGGAGTT
1 AAAATGTGATTTTGAGAAAGTTTAGGGGTT
* **
28368612 GAAAATGTTATTTCAAGAAAGTTTA-GGGTT
1 -AAAATGTGATTTTGAGAAAGTTTAGGGGTT
* * *
28368642 AAAATGTGGTTTTGGGAAAGTCT-GGGGTT
1 AAAATGTGATTTTGAGAAAGTTTAGGGGTT
*
28368671 AAAATGTGATTTTAAGAAAGTTTAGGGGTT
1 AAAATGTGATTTTGAGAAAGTTTAGGGGTT
*
28368701 AAAATGTGATTTTG-GAAATGTTTAGGGGTA
1 AAAATGTGATTTTGAGAAA-GTTTAGGGGTT
*
28368731 AAAATGTGATTTT-AGAAAAGTTT-TGGGTT
1 AAAATGTGATTTTGAG-AAAGTTTAGGGGTT
* * * *
28368760 --AATGTAATTTT-AGAAAATTTTAAGGGTC
1 AAAATGTGATTTTGAG-AAAGTTTAGGGGTT
* *
28368788 AAAATGTGATTTT-AAAGAAGTTTAAGGGTT
1 AAAATGTGATTTTGAGA-AAGTTTAGGGGTT
* *
28368818 AAAATGTAATTTTG-GAAAAGTTTAAGGGTT
1 AAAATGTGATTTTGAG-AAAGTTTAGGGGTT
* * * *
28368848 AAAATATAATTTT-AGAGAAGTTTGGGGGTA
1 AAAATGTGATTTTGAGA-AAGTTTAGGGGTT
*
28368878 AAAATATGATTTT
1 AAAATGTGATTTT
28368891 TGTAAAGTTC
Statistics
Matches: 347, Mismatches: 56, Indels: 49
0.77 0.12 0.11
Matches are distributed among these distances:
27 19 0.05
28 6 0.02
29 116 0.33
30 171 0.49
31 18 0.05
32 17 0.05
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAATGTGATTTTGAGAAAGTTTAGGGGTT
Found at i:28368659 original size:150 final size:149
Alignment explanation
Indices: 28368478--28368749 Score: 395
Period size: 150 Copynumber: 1.8 Consensus size: 149
28368468 GCGATTTTAG
* *
28368478 GAAATTTTAAGGTCAAAATGTGGTTTTGGGAAAGT-TCGAGGTCAAAATGTGATTTTGAGAAAGT
1 GAAAGTTTAAGGTCAAAATGTGGTTTTGGGAAAGTCT-GAGGTCAAAATGTGATTTTAAGAAAGT
*
28368542 GTAGGGGTCAAAATGCAATTTTGGAAAAGTTTGAGGGGGTTAAAATGTGATTTT-GAAAAATTTA
65 GTAGGGGTCAAAATGCAATTTTGGAAAAGTTT-A-GGGGTAAAAATGTGATTTTAGAAAAATTTA
28368606 GGAGTTGAAAATGTTATTTCAA
128 GGAGTTGAAAATGTTATTTCAA
* * * * *
28368628 GAAAGTTTAGGGTTAAAATGTGGTTTTGGGAAAGTCTGGGGTTAAAATGTGATTTTAAGAAAGTT
1 GAAAGTTTAAGGTCAAAATGTGGTTTTGGGAAAGTCTGAGGTCAAAATGTGATTTTAAGAAAGTG
* ** *
28368693 TAGGGGTTAAAATGTGATTTTGGAAATGTTTAGGGGTAAAAATGTGATTTTAGAAAA
66 TAGGGGTCAAAATGCAATTTTGGAAAAGTTTAGGGGTAAAAATGTGATTTTAGAAAA
28368750 GTTTTGGGTT
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
148 18 0.17
149 6 0.06
150 83 0.77
151 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (149 bp):
GAAAGTTTAAGGTCAAAATGTGGTTTTGGGAAAGTCTGAGGTCAAAATGTGATTTTAAGAAAGTG
TAGGGGTCAAAATGCAATTTTGGAAAAGTTTAGGGGTAAAAATGTGATTTTAGAAAAATTTAGGA
GTTGAAAATGTTATTTCAA
Found at i:28380827 original size:18 final size:18
Alignment explanation
Indices: 28380781--28380830 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
28380771 TCTCTCTCAA
*
28380781 CAAAAATTATAAAAAAATT
1 CAAAAATT-TATAAAAATT
28380800 CAAAATATTTATAAAAATT
1 CAAAA-ATTTATAAAAATT
28380819 -ATAAAATTTATA
1 CA-AAAATTTATA
28380831 TTTTTAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.29
19 17 0.61
20 3 0.11
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (18 bp):
CAAAAATTTATAAAAATT
Found at i:28380847 original size:25 final size:24
Alignment explanation
Indices: 28380804--28380861 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
28380794 AAAATTCAAA
* *
28380804 ATATTTATAAAAATTATAA-AATTT
1 ATATTTTTAAAAATGATAATAA-TT
28380828 ATATTTTTAAGAAATGATAATAATT
1 ATATTTTTAA-AAATGATAATAATT
28380853 ATAATTTTT
1 AT-ATTTTT
28380862 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 12 0.41
26 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
ATATTTTTAAAAATGATAATAATT
Found at i:28381375 original size:18 final size:19
Alignment explanation
Indices: 28381320--28381378 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 19
28381310 TCTTTCAACA
*
28381320 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAAT-ATTTAT
28381340 GAAAAATTCAAAATATTTAT
1 -AAAAATTCAAAATATTTAT
*
28381360 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
28381378 A
1 A
28381379 TTTTTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 7 0.19
19 11 0.31
20 5 0.14
21 13 0.36
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:28381409 original size:44 final size:39
Alignment explanation
Indices: 28381319--28381409 Score: 94
Period size: 44 Copynumber: 2.2 Consensus size: 39
28381309 CTCTTTCAAC
*
28381319 AAAAAATTCAAAATAATTTTTGAAAAATTCAAAATATTT
1 AAAAAATTCAAAATAATTTTTGAAAAATTCAAAAAATTT
*
28381358 ATAAAAATTCCAAAATTTATATTTTTTAAAAATT-ATAAAAATTCT
1 A-AAAAATT-CAAAA--TA-ATTTTTGAAAAATTCA-AAAAATT-T
28381403 AAAAAAT
1 AAAAAAT
28381410 AAATAAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
39 1 0.02
40 7 0.16
41 5 0.12
43 3 0.07
44 25 0.58
45 2 0.05
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.37
Consensus pattern (39 bp):
AAAAAATTCAAAATAATTTTTGAAAAATTCAAAAAATTT
Found at i:28383980 original size:23 final size:24
Alignment explanation
Indices: 28383950--28383994 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
28383940 GAGTTTGGAC
28383950 AAAAATATAGGTC-CAAAAATGAT
1 AAAAATATAGGTCTCAAAAATGAT
*
28383973 AAAAATATAGGTCTGAAAAATG
1 AAAAATATAGGTCTCAAAAATG
28383995 GACTTGGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.22
Consensus pattern (24 bp):
AAAAATATAGGTCTCAAAAATGAT
Found at i:28384161 original size:21 final size:21
Alignment explanation
Indices: 28384114--28384182 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
28384104 AATTATATTA
28384114 TTGTTTTTTGCTA--TTGATG
1 TTGTTTTTTGCTATTTTGATG
* *
28384133 CTAG-TTTTTGCTGTTTTGATG
1 -TTGTTTTTTGCTATTTTGATG
* * *
28384154 TTTTTTTTTTCTATTTTGGTG
1 TTGTTTTTTGCTATTTTGATG
28384175 TTGTTTTT
1 TTGTTTTT
28384183 ACTATTATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
19 8 0.21
20 3 0.08
21 27 0.71
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.68
Consensus pattern (21 bp):
TTGTTTTTTGCTATTTTGATG
Found at i:28384197 original size:21 final size:21
Alignment explanation
Indices: 28384173--28384266 Score: 100
Period size: 21 Copynumber: 4.4 Consensus size: 21
28384163 TCTATTTTGG
28384173 TGTTGTTTTTACTATTATTTT
1 TGTTGTTTTTACTATTATTTT
*
28384194 TGTTGTTTTTACTATCATTTT
1 TGTTGTTTTTACTATTATTTT
* * *
28384215 TATTG-TTTTGCTGTTATTTT
1 TGTTGTTTTTACTATTATTTT
* *
28384235 TGTTGTTGTTTTGATTATTGTTTT
1 TGTTG-T-TTTT-ACTATTATTTT
28384259 TGTTGTTT
1 TGTTGTTT
28384267 GGGTGCTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 16 0.27
21 24 0.41
22 2 0.03
23 5 0.08
24 12 0.20
ACGTcount: A:0.11, C:0.04, G:0.15, T:0.70
Consensus pattern (21 bp):
TGTTGTTTTTACTATTATTTT
Found at i:28384277 original size:44 final size:43
Alignment explanation
Indices: 28384184--28384281 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 43
28384174 GTTGTTTTTA
* *
28384184 CTATTATTTTTGTTGTTTTTACTATCATTTTTATTGTTTTGCTG
1 CTATT-TTTTTGTTGTTTTGACTATCATTTTTATTGTTTGGCTG
* * ** * *
28384228 TTATTTTTGTTGTTGTTTTGATTATTGTTTTTGTTGTTTGGGTG
1 CTATTTTT-TTGTTGTTTTGACTATCATTTTTATTGTTTGGCTG
28384272 CTATTTTTTT
1 CTATTTTTTT
28384282 TTGCATTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
43 5 0.11
44 39 0.89
ACGTcount: A:0.10, C:0.05, G:0.16, T:0.68
Consensus pattern (43 bp):
CTATTTTTTTGTTGTTTTGACTATCATTTTTATTGTTTGGCTG
Found at i:28400434 original size:22 final size:20
Alignment explanation
Indices: 28400401--28400440 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
28400391 AGATAAAAAA
28400401 TATTTTTTAAATTTTTTATT
1 TATTTTTTAAATTTTTTATT
28400421 TATTATTTTGAAATTTTTTA
1 TATT-TTTT-AAATTTTTTA
28400441 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TATTTTTTAAATTTTTTATT
Found at i:28403128 original size:19 final size:19
Alignment explanation
Indices: 28403106--28403152 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
28403096 TTGCTCTCAT
* *
28403106 GAGCTAGTAAAGCTCTTGC
1 GAGCCAGTAAAGCTCTTAC
**
28403125 GAGCCAGTATTGCTCTTAC
1 GAGCCAGTAAAGCTCTTAC
28403144 GAGCCAGTA
1 GAGCCAGTA
28403153 TTGCATTCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (19 bp):
GAGCCAGTAAAGCTCTTAC
Found at i:28403153 original size:19 final size:19
Alignment explanation
Indices: 28403117--28403156 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
28403107 AGCTAGTAAA
*
28403117 GCTCTTGCGAGCCAGTATT
1 GCTCTTACGAGCCAGTATT
28403136 GCTCTTACGAGCCAGTATT
1 GCTCTTACGAGCCAGTATT
28403155 GC
1 GC
28403157 ATTCCTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (19 bp):
GCTCTTACGAGCCAGTATT
Found at i:28414076 original size:13 final size:13
Alignment explanation
Indices: 28414060--28414116 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
28414050 GTATAAATAC
28414060 TTCATATAACCAT
1 TTCATATAACCAT
28414073 TTCATAATAA-CAT
1 TTCAT-ATAACCAT
* *
28414086 TTCGTATAACTAT
1 TTCATATAACCAT
* *
28414099 TTCATCTAAGCAT
1 TTCATATAACCAT
28414112 TTCAT
1 TTCAT
28414117 TTTACCAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
12 4 0.11
13 28 0.78
14 4 0.11
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:28420146 original size:17 final size:17
Alignment explanation
Indices: 28420112--28420149 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
28420102 TACATATATA
28420112 TTTTTCTTCTTTTCCTT
1 TTTTTCTTCTTTTCCTT
28420129 TTTTCTCTTCTTTT-CTT
1 TTTT-TCTTCTTTTCCTT
28420146 TTTT
1 TTTT
28420150 ATATGTGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTCTTTTCCTT
Found at i:28427068 original size:21 final size:21
Alignment explanation
Indices: 28427042--28427094 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
28427032 ACTTGGGTTA
28427042 TATCGGTAGTTGAATTACAAG
1 TATCGGTAGTTGAATTACAAG
28427063 TATCGGTAGTTGAATTACAAG
1 TATCGGTAGTTGAATTACAAG
28427084 TATCGGTAGTT
1 TATCGGTAGTT
28427095 TATAGTACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (21 bp):
TATCGGTAGTTGAATTACAAG
Found at i:28429424 original size:16 final size:16
Alignment explanation
Indices: 28429393--28429426 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28429383 TATAATACTT
**
28429393 TATATTATGTTTTTTA
1 TATATTATGTAATTTA
28429409 TATATTATGTAATTTA
1 TATATTATGTAATTTA
28429425 TA
1 TA
28429427 ACATTTTAAA
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:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TATATTATGTAATTTA
Found at i:28434868 original size:31 final size:30
Alignment explanation
Indices: 28434807--28434884 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
28434797 TAGACCCACC
*
28434807 TATTTATTTTTTAATTTTTTAAAATATTTA
1 TATTTATTTTTTAATTATTTAAAATATTTA
28434837 TATTATATTATTTTAA-TATTTAATAAT-TTTA
1 TATT-TATT-TTTTAATTATTTAA-AATATTTA
*
28434868 TA--TATTTTTTATTTATT
1 TATTTATTTTTTAATTATT
28434885 AAATTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
27 5 0.12
28 8 0.19
30 4 0.10
31 16 0.38
32 9 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (30 bp):
TATTTATTTTTTAATTATTTAAAATATTTA
Found at i:28444219 original size:30 final size:30
Alignment explanation
Indices: 28444183--28444252 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
28444173 TTCTATGGAT
28444183 ACAAACTCACTAGCATACTTACTGAGTTGA
1 ACAAACTCACTAGCATACTTACTGAGTTGA
*
28444213 ACAAACTCATTAGCATACTTACTGAGTTGA
1 ACAAACTCACTAGCATACTTACTGAGTTGA
28444243 ACAAACTCAC
1 ACAAACTCAC
28444253 GCTCATATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (30 bp):
ACAAACTCACTAGCATACTTACTGAGTTGA
Found at i:28446285 original size:26 final size:25
Alignment explanation
Indices: 28446252--28446325 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 25
28446242 TTCTAAGCAT
28446252 TCACAGGCTCGAAGCCTGCTAATGAA
1 TCACAGGCTCGAAGCCTGCTAAT-AA
* * *
28446278 TCATAGGCTCAAAGCCTGCTAAATAT
1 TCACAGGCTCGAAGCCTGCT-AATAA
* *
28446304 TCACCGACTCGAAGCCTGCTAA
1 TCACAGGCTCGAAGCCTGCTAA
28446326 AAGTCACCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 2 0.05
26 35 0.88
27 3 0.08
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (25 bp):
TCACAGGCTCGAAGCCTGCTAATAA
Found at i:28447918 original size:19 final size:19
Alignment explanation
Indices: 28447887--28447934 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
28447877 GAGAGGGGGT
* *
28447887 TGCTGGCTGTCCTATCTGC
1 TGCTGGCTCTCCTATCTGA
* *
28447906 TGCTTGCTCTCCTCTCTGA
1 TGCTGGCTCTCCTATCTGA
28447925 TGCTGGCTCT
1 TGCTGGCTCT
28447935 ATGCTCCTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.04, C:0.33, G:0.23, T:0.40
Consensus pattern (19 bp):
TGCTGGCTCTCCTATCTGA
Found at i:28452726 original size:53 final size:51
Alignment explanation
Indices: 28452665--28452763 Score: 137
Period size: 53 Copynumber: 1.9 Consensus size: 51
28452655 GGAAAATTTT
* * *
28452665 TAAATTTTGAATTTTTTTTATATATTTTTCGAATTTTTT-TAAGTTTTTAAATA
1 TAAATTTTGAAATTTTTATAAATA-TTTT-GAATTTTTTGTAA-TTTTTAAATA
28452718 TAAATTTTGAAATTTTTATAAATATTTTGAATTTTTTGTAATTTTT
1 TAAATTTTGAAATTTTTATAAATATTTTGAATTTTTTGTAATTTTT
28452764 GTTAAGAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 14 0.33
52 7 0.17
53 21 0.50
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (51 bp):
TAAATTTTGAAATTTTTATAAATATTTTGAATTTTTTGTAATTTTTAAATA
Found at i:28454064 original size:2 final size:2
Alignment explanation
Indices: 28454057--28454092 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28454047 GTATTCTGTT
28454057 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28454093 TATATATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28454129 original size:21 final size:22
Alignment explanation
Indices: 28454105--28454148 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28454095 TATATTTACT
28454105 TTATATT-TTACTTA-TTTTATA
1 TTATATTATTA-TTATTTTTATA
*
28454126 TTATGTTATTATTATTTTTATA
1 TTATATTATTATTATTTTTATA
28454148 T
1 T
28454149 CGAAACTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (22 bp):
TTATATTATTATTATTTTTATA
Found at i:28454882 original size:29 final size:30
Alignment explanation
Indices: 28454849--28454930 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
28454839 GCATTTGCTT
* * *
28454849 TATTTTAAAATTGT-TTTTTACCCCCAAAC
1 TATTTAAAAATTATATTTTGACCCCCAAAC
*
28454878 TATTTAAAAATTATATTTTGACCCCTAAAC
1 TATTTAAAAATTATATTTTGACCCCCAAAC
* *
28454908 TATCTAAAAATTATGTTTTGACC
1 TATTTAAAAATTATATTTTGACC
28454931 TTCAAACTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 12 0.26
30 34 0.74
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (30 bp):
TATTTAAAAATTATATTTTGACCCCCAAAC
Found at i:28454938 original size:30 final size:29
Alignment explanation
Indices: 28454870--28454949 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
28454860 TGTTTTTTAC
*
28454870 CCCCAAACTATTTAAAAATTATATTTTGA
1 CCCCAAACTATCTAAAAATTATATTTTGA
*
28454899 CCCCTAAACTATCTAAAAATTATGTTTTGA
1 CCCC-AAACTATCTAAAAATTATATTTTGA
* * *
28454929 CCTTCAAACTTTCCAAAAATT
1 CC-CCAAACTATCTAAAAATT
28454950 CAAATTTGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 4 0.09
30 39 0.89
31 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (29 bp):
CCCCAAACTATCTAAAAATTATATTTTGA
Found at i:28454958 original size:30 final size:30
Alignment explanation
Indices: 28454894--28455050 Score: 158
Period size: 30 Copynumber: 5.3 Consensus size: 30
28454884 AAAATTATAT
* * **
28454894 TTTGACCCCTAAACTATCTAAAAATT-ATGT
1 TTTGACCCCTAAACTTTCCAAAAATTCA-AA
*
28454924 TTTGA-CCTTCAAACTTTCCAAAAATTCAAA
1 TTTGACCCCT-AAACTTTCCAAAAATTCAAA
* * * *
28454954 TTTGACTCCTAAA-TTTCCAAGACTACAAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
** *
28454983 TTTGACCCCTAAACTTTTTAAAAATTCTAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
*
28455013 TTTGACCCCTGAACTTTCCAAAAATTCAAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
28455043 TTTGACCC
1 TTTGACCC
28455051 GATTTTAATG
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
29 28 0.27
30 71 0.70
31 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (30 bp):
TTTGACCCCTAAACTTTCCAAAAATTCAAA
Found at i:28455006 original size:59 final size:60
Alignment explanation
Indices: 28454934--28455050 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 60
28454924 TTTGACCTTC
* * *
28454934 AAACTTTCCAAAAATTCAAATTTGACTCCT-AAATTTCCAAGACTACAAATTTGACCCCT
1 AAACTTTCCAAAAATTCAAATTTGACCCCTGAAATTTCCAAAAATACAAATTTGACCCCT
** * * *
28454993 AAACTTTTTAAAAATTCTAATTTGACCCCTGAACTTTCCAAAAATTCAAATTTGACCC
1 AAACTTTCCAAAAATTCAAATTTGACCCCTGAAATTTCCAAAAATACAAATTTGACCC
28455051 GATTTTAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 26 0.53
60 23 0.47
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.32
Consensus pattern (60 bp):
AAACTTTCCAAAAATTCAAATTTGACCCCTGAAATTTCCAAAAATACAAATTTGACCCCT
Found at i:28458726 original size:40 final size:39
Alignment explanation
Indices: 28458615--28458726 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 39
28458605 TAAAAACATC
* *
28458615 ATCCAGTCTCTTACCCCGACCATGGGGCATATTGAAACA
1 ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAACA
* ** * *
28458654 ATCCAATCTTTTACCTTGACCATGGGACAGATTGAAGACC
1 ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAA-ACA
* * *
28458694 ATTCGATCTCTTACCCCGACCATGGGGTAGATT
1 ATCCAATCTCTTACCCCGACCATGGGGCAGATT
28458727 AAGGTAGTCC
Statistics
Matches: 58, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
39 30 0.52
40 28 0.48
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (39 bp):
ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAACA
Found at i:28458798 original size:50 final size:49
Alignment explanation
Indices: 28458744--28458911 Score: 185
Period size: 50 Copynumber: 3.4 Consensus size: 49
28458734 TCCAATCTTT
*
28458744 TACACCTAAAGCTGTAGAAGTGCAAATTAAAGCTGCAATGACAAATCTCA
1 TACACCTAAAGCTGTAGAAGTGCAAATTGAAGCTGCAATG-CAAATCTCA
* * * *
28458794 TACACCTAAAGCTGTAGAGGTGCAGATTGAAGCCGTAATGGCAAATCTCA
1 TACACCTAAAGCTGTAGAAGTGCAAATTGAAGCTGCAAT-GCAAATCTCA
* * * * *
28458844 TACACCTAAAGCTATA-AAGGGGCAAATTGAAGCTACAGAAGCAAATCTTA
1 TACACCTAAAGCTGTAGAA-GTGCAAATTGAAGCTGCA-ATGCAAATCTCA
* *
28458894 TACCCCTAAAGTTGTAGA
1 TACACCTAAAGCTGTAGA
28458912 GGGGCAGATT
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
49 1 0.01
50 93 0.96
51 3 0.03
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (49 bp):
TACACCTAAAGCTGTAGAAGTGCAAATTGAAGCTGCAATGCAAATCTCA
Found at i:28459130 original size:101 final size:101
Alignment explanation
Indices: 28458987--28459168 Score: 267
Period size: 101 Copynumber: 1.8 Consensus size: 101
28458977 AGCTACAAAG
* * * *
28458987 GCAAATCTTTATCTCTCTAAAGTTACAGTAGAGCAGGATGAAGCTACGAGAACAAATCATATACC
1 GCAAATATTTATCTCTCTAAAGCTACAGTAGAGCAAGATGAAGCTACGACAACAAATCATATACC
28459052 CCTGAAGTTGCAGTGGGTCAGATTAAAGTCATGAAA
66 CCTGAAGTTGCAGTGGGTCAGATTAAAGTCATGAAA
* * * * *
28459088 GCAAATATTTATCTC-CTTGAAGCTACAGTGGAGCAAGATGAAGCTACGACATCAAATCCTATAT
1 GCAAATATTTATCTCTC-TAAAGCTACAGTAGAGCAAGATGAAGCTACGACAACAAATCATATAC
28459152 CCCTGAAGTTGCAGTGG
65 CCCTGAAGTTGCAGTGG
28459169 ATTGGATTGA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 1 0.01
101 70 0.99
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (101 bp):
GCAAATATTTATCTCTCTAAAGCTACAGTAGAGCAAGATGAAGCTACGACAACAAATCATATACC
CCTGAAGTTGCAGTGGGTCAGATTAAAGTCATGAAA
Found at i:28459168 original size:50 final size:50
Alignment explanation
Indices: 28459006--28459169 Score: 129
Period size: 50 Copynumber: 3.3 Consensus size: 50
28458996 TATCTCTCTA
* * * *
28459006 AAGTTACAGTAGAGCAGGATGAAGCTACGAGAACAAATCATATACCCCTG
1 AAGTTACAGTGGAGCAAGATGAAGCTACGAAAACAAATCATATATCCCTG
* * * * *
28459056 AAGTTGCAGTGG-GTC-AGATTAAAG-TCATGAAAGCAAAT-ATTTATCTCCTTG
1 AAGTTACAGTGGAG-CAAGA-TGAAGCT-ACGAAAACAAATCATATATC-CC-TG
* * * *
28459107 AAGCTACAGTGGAGCAAGATGAAGCTACGACATCAAATCCTATATCCCTG
1 AAGTTACAGTGGAGCAAGATGAAGCTACGAAAACAAATCATATATCCCTG
*
28459157 AAGTTGCAGTGGA
1 AAGTTACAGTGGA
28459170 TTGGATTGAG
Statistics
Matches: 86, Mismatches: 19, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
49 9 0.10
50 39 0.45
51 28 0.33
52 10 0.12
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (50 bp):
AAGTTACAGTGGAGCAAGATGAAGCTACGAAAACAAATCATATATCCCTG
Found at i:28459987 original size:16 final size:16
Alignment explanation
Indices: 28459937--28459987 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
28459927 CACACATATA
* *
28459937 TATATTATATTTACTT
1 TATATTATACTTATTT
*
28459953 TATATTTTACTTATTT
1 TATATTATACTTATTT
28459969 TATATTATA-TTATTAT
1 TATATTATACTTATT-T
28459985 TAT
1 TAT
28459988 TATTTATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 5 0.17
16 25 0.83
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTATACTTATTT
Found at i:28460819 original size:30 final size:30
Alignment explanation
Indices: 28460703--28461019 Score: 247
Period size: 30 Copynumber: 10.7 Consensus size: 30
28460693 ACTTTATTTT
* * *
28460703 AAAATCAT-TTTTAACCCC-AAACCATCCA
1 AAAATTATGTTTTGACCCCTAAACTATCCA
28460731 AAAATTATGTTTTGACCCCTCAAACTATCCA
1 AAAATTATGTTTTGACCCCT-AAACTATCCA
28460762 AAAATTATGTTTTGACCCCTCAAACTATCCA
1 AAAATTATGTTTTGACCCCT-AAACTATCCA
* *
28460793 AAAATTATGTTTTAACCCCTAAACTATTCA
1 AAAATTATGTTTTGACCCCTAAACTATCCA
* * * *
28460823 AAAATTATTTTTTGACCCATAAACTTTCTA
1 AAAATTATGTTTTGACCCCTAAACTATCCA
* * *
28460853 AAAATTATGTCTTGA-CCCTAAAACTTTCTA
1 AAAATTATGTTTTGACCCCT-AAACTATCCA
* * * *
28460883 AAAAATATGTTTTGACCCTTGAACT-TTCA
1 AAAATTATGTTTTGACCCCTAAACTATCCA
** * * *
28460912 AAAATTCA-AATTTGACCTC-AAACTTTCTA
1 AAAATT-ATGTTTTGACCCCTAAACTATCCA
* * *
28460941 AAAATT-TGAATTTGACCCCTGAACTTTCCA
1 AAAATTATG-TTTTGACCCCTAAACTATCCA
** * *
28460971 AAAATTCA-AATTTGACCCCTAAACT-TTCT
1 AAAATT-ATGTTTTGACCCCTAAACTATCCA
* *
28461000 AAAATTTTGATTTGACCCCT
1 AAAATTATGTTTTGACCCCT
28461020 GAATTTTCTA
Statistics
Matches: 238, Mismatches: 38, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.05
29 62 0.26
30 103 0.43
31 62 0.26
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (30 bp):
AAAATTATGTTTTGACCCCTAAACTATCCA
Found at i:28460877 original size:60 final size:59
Alignment explanation
Indices: 28460729--28461035 Score: 243
Period size: 59 Copynumber: 5.1 Consensus size: 59
28460719 CCAAACCATC
* * *
28460729 CAAAAATTATGTTTTGACCCCTCAAACTATCCAAAAATTATGTTTTGACCCCTCAAACTATC
1 CAAAAATTATGTTTTGACCCCT-AAACTATTCAAAAATTATGTTTTGACCCAT-AAACT-TT
* *
28460791 CAAAAATTATGTTTTAACCCCTAAACTATTCAAAAATTATTTTTTGACCCATAAACTTT
1 CAAAAATTATGTTTTGACCCCTAAACTATTCAAAAATTATGTTTTGACCCATAAACTTT
* * * *
28460850 CTAAAAATTATGTCTTGA-CCCTAAAACT-TTCTAAAAAATATGTTTTGACCCTTGAACTTT
1 C-AAAAATTATGTTTTGACCCCT-AAACTATTC-AAAAATTATGTTTTGACCCATAAACTTT
** * * * *
28460910 CAAAAATTCA-AATTTGACCTC-AAACT-TTCTAAAAATT-TGAATTTGACCCCTGAACTTT
1 CAAAAATT-ATGTTTTGACCCCTAAACTATTC-AAAAATTATG-TTTTGACCCATAAACTTT
** * * * * * *
28460968 CCAAAAATTCA-AATTTGACCCCTAAACT-TTCTAAAATTTTGATTTGACCCCTGAATTTT
1 -CAAAAATT-ATGTTTTGACCCCTAAACTATTCAAAAATTATGTTTTGACCCATAAACTTT
28461027 CTAAAAATT
1 C-AAAAATT
28461036 CATATTTGAC
Statistics
Matches: 214, Mismatches: 21, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
57 2 0.01
58 32 0.15
59 70 0.33
60 62 0.29
61 27 0.13
62 21 0.10
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (59 bp):
CAAAAATTATGTTTTGACCCCTAAACTATTCAAAAATTATGTTTTGACCCATAAACTTT
Found at i:28460925 original size:29 final size:29
Alignment explanation
Indices: 28460893--28461047 Score: 168
Period size: 29 Copynumber: 5.3 Consensus size: 29
28460883 AAAAATATGT
*
28460893 TTTGACCCTTGAACTTTCAAAAATTCAAA
1 TTTGACCCCTGAACTTTCAAAAATTCAAA
* * **
28460922 TTTGACCTC-AAACTTTCTAAAAATTTGAA
1 TTTGACCCCTGAACTTTC-AAAAATTCAAA
28460951 TTTGACCCCTGAACTTTCCAAAAATTCAAA
1 TTTGACCCCTGAACTTT-CAAAAATTCAAA
* * ***
28460981 TTTGACCCCTAAACTTTCTAAAATTTTGA
1 TTTGACCCCTGAACTTTCAAAAATTCAAA
* *
28461010 TTTGACCCCTGAATTTTCTAAAAATTCATA
1 TTTGACCCCTGAACTTTC-AAAAATTCAAA
28461040 TTTGACCC
1 TTTGACCC
28461048 GATTTTAATG
Statistics
Matches: 102, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
28 7 0.07
29 48 0.47
30 46 0.45
31 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TTTGACCCCTGAACTTTCAAAAATTCAAA
Found at i:28460927 original size:59 final size:58
Alignment explanation
Indices: 28460809--28461047 Score: 252
Period size: 59 Copynumber: 4.1 Consensus size: 58
28460799 ATGTTTTAAC
** * * **
28460809 CCCTAAACTATTC-AAAAATTATTTTTTGACCCATAAACTTTCTAAAAATT-ATGTCTTGA
1 CCCTAAACT-TTCTAAAAA-TATGATTTGACCCCTGAACTTTCTAAAAATTCAAAT-TTGA
* *
28460868 CCCTAAAACTTTCTAAAAAATATGTTTTGACCCTTGAACTTTC-AAAAATTCAAATTTGA
1 CCCT-AAACTTTCT-AAAAATATGATTTGACCCCTGAACTTTCTAAAAATTCAAATTTGA
* *
28460927 -CCTCAAACTTTCTAAAAATTTGAATTTGACCCCTGAACTTTCCAAAAATTCAAATTTGA
1 CCCT-AAACTTTCTAAAAATATG-ATTTGACCCCTGAACTTTCTAAAAATTCAAATTTGA
* * * *
28460986 CCCCTAAACTTTCTAAAATTTTGATTTGACCCCTGAATTTTCTAAAAATTCATATTTGA
1 -CCCTAAACTTTCTAAAAATATGATTTGACCCCTGAACTTTCTAAAAATTCAAATTTGA
28461045 CCC
1 CCC
28461048 GATTTTAATG
Statistics
Matches: 159, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
57 8 0.05
58 32 0.20
59 67 0.42
60 44 0.28
61 8 0.05
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (58 bp):
CCCTAAACTTTCTAAAAATATGATTTGACCCCTGAACTTTCTAAAAATTCAAATTTGA
Found at i:28461984 original size:43 final size:43
Alignment explanation
Indices: 28461917--28462100 Score: 228
Period size: 43 Copynumber: 4.3 Consensus size: 43
28461907 CGCTAATGAT
* *
28461917 AACGCCGCAAAAGAACATGGTCTTTAGTGGCGCTTTACCTACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTACCTACA
* * *
28461960 AACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTCT-TCTACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TACCTACA
* * * * *
28462003 AACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATCTAGA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTACCTACA
* *
28462046 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCC-ACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCG-CTTTACCTACA
28462089 AACGCCGCTAAA
1 AACGCCGCTAAA
28462101 ATTAACAGAT
Statistics
Matches: 124, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 120 0.97
44 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTACCTACA
Found at i:28462070 original size:86 final size:86
Alignment explanation
Indices: 28461917--28462100 Score: 260
Period size: 86 Copynumber: 2.1 Consensus size: 86
28461907 CGCTAATGAT
* * * * *
28461917 AACGCCGCAAAAGAACATGGTCTTTAGTGGCGCTTTACCTACAAACGCCGCTAAAGACCATGTTC
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAACCTACAAACGCCGCTAAAGAACATGGTC
*
28461982 TTTAGCGGCGCTTCTTCTACA
66 TTTAGCGGCGCTTCTTCCACA
* * * *
28462003 AACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATCTAGAAACGCCGCTAAAGAACATGGTC
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAACCTACAAACGCCGCTAAAGAACATGGTC
* *
28462068 TTTAGCGGCGTTTTTTCCACA
66 TTTAGCGGCGCTTCTTCCACA
28462089 AACGCCGCTAAA
1 AACGCCGCTAAA
28462101 ATTAACAGAT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (86 bp):
AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAACCTACAAACGCCGCTAAAGAACATGGTC
TTTAGCGGCGCTTCTTCCACA
Found at i:28462891 original size:13 final size:14
Alignment explanation
Indices: 28462864--28462892 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28462854 ACAAATGATG
28462864 AATTAAACTATTAT
1 AATTAAACTATTAT
28462878 AATTAAAC-ATTAT
1 AATTAAACTATTAT
28462891 AA
1 AA
28462893 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAACTATTAT
Found at i:28468157 original size:8 final size:8
Alignment explanation
Indices: 28468155--28468180 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28468145 ATTAAATATT
28468155 TAATTAAA
1 TAATTAAA
28468163 TAATTAAA
1 TAATTAAA
28468171 TAATTAAA
1 TAATTAAA
28468179 TA
1 TA
28468181 TTTTGAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:28468160 original size:12 final size:12
Alignment explanation
Indices: 28468143--28468197 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 12
28468133 TTGTTTTTAA
28468143 TAATTAAATATT
1 TAATTAAATATT
28468155 TAATTAAATAATT
1 TAATTAAAT-ATT
28468168 AAATAATTAAATATTT
1 ---TAATTAAATA-TT
28468184 TGAATTAAATATT
1 T-AATTAAATATT
28468197 T
1 T
28468198 GGGTTGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.24
13 7 0.19
14 9 0.24
15 1 0.03
16 11 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
TAATTAAATATT
Found at i:28468253 original size:50 final size:47
Alignment explanation
Indices: 28468161--28468281 Score: 127
Period size: 50 Copynumber: 2.5 Consensus size: 47
28468151 TATTTAATTA
* * *
28468161 AATAATTAAATAATTAAATATTTTGAATTAAATATTTGGGTTGTTTTT
1 AATAATTAAATAAATAAATATTTTGAATTAAATAATTGGGTTG-ATTT
* *
28468209 AATATTTAAATAAATAAATAATTAATT-AATTAATTAATTGGGTTGATTT
1 AATAATTAAATAAATAAAT-ATT--TTGAATTAAATAATTGGGTTGATTT
* *
28468258 AACTAATTAAATAATTAAGTATTT
1 AA-TAATTAAATAAATAAATATTT
28468282 GGGTTGTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
47 1 0.02
48 17 0.28
49 11 0.18
50 30 0.49
51 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (47 bp):
AATAATTAAATAAATAAATATTTTGAATTAAATAATTGGGTTGATTT
Found at i:28468265 original size:34 final size:34
Alignment explanation
Indices: 28468225--28468313 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 34
28468215 TAAATAAATA
*
28468225 AATAATTAATTAATTAATTAATTGGGTTG-ATTT
1 AATAATTAAATAATTAATTAATTGGGTTGTATTT
* * *
28468258 AACTAATTAAATAATTAAGTATTTGGGTTGTTTTT
1 AA-TAATTAAATAATTAATTAATTGGGTTGTATTT
*
28468293 AATAATTAAATATTTAATTAA
1 AATAATTAAATAATTAATTAA
28468314 ATAATTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 2 0.04
34 40 0.85
35 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (34 bp):
AATAATTAAATAATTAATTAATTGGGTTGTATTT
Found at i:28468312 original size:12 final size:12
Alignment explanation
Indices: 28468295--28468371 Score: 66
Period size: 10 Copynumber: 7.1 Consensus size: 12
28468285 TTGTTTTTAA
28468295 TAATTAAATATT
1 TAATTAAATATT
28468307 TAATT-AA-A--
1 TAATTAAATATT
28468315 TAATTAAATATT
1 TAATTAAATATT
28468327 TAATT-AA-A--
1 TAATTAAATATT
28468335 TAATTAAATA--
1 TAATTAAATATT
28468345 TAATTAAATATTT
1 TAATTAAATA-TT
28468358 TGAATTAAATATT
1 T-AATTAAATATT
28468371 T
1 T
28468372 GGGTTGTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 19
0.74 0.00 0.26
Matches are distributed among these distances:
8 10 0.18
9 4 0.07
10 14 0.25
11 4 0.07
12 10 0.18
13 4 0.07
14 9 0.16
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (12 bp):
TAATTAAATATT
Found at i:28468318 original size:20 final size:20
Alignment explanation
Indices: 28468293--28468354 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
28468283 GGTTGTTTTT
28468293 AATAATTAAATATTTAATTA
1 AATAATTAAATATTTAATTA
28468313 AATAATTAAATATTTAATTA
1 AATAATTAAATATTTAATTA
28468333 AATAATTAAATA--TAATTA
1 AATAATTAAATATTTAATTA
28468351 AATA
1 AATA
28468355 TTTTGAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.24
20 32 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAATTAAATATTTAATTA
Found at i:28468348 original size:76 final size:76
Alignment explanation
Indices: 28468125--28469341 Score: 536
Period size: 70 Copynumber: 15.8 Consensus size: 76
28468115 TCATCAAAAT
*
28468125 TATTTGAGTTGTTTTTAATAATTAAATATTTAATTAAATAATT-AA-A--TAATTAAAT-ATT--
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
28468183 -T-TGAATTAAA
66 ATAT-AATTAAA
* * * * *** **
28468193 TATTTGGGTTGTTTTTAATATTTAAATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTT
1 TATTTGGGTTGTTTTTAATAATTAAAT--AT--TTAATTAAATAATTAAAT-ATTTAATT-AAAT
* * *
28468258 AACTAATTAAATAATTAAG
60 AATTAA--ATATAATTAAA
28468277 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
28468342 ATATAATTAAA
66 ATATAATTAAA
** * ** * * * *
28468353 TATTTTGAATTAAATATTTGGGTTGT-TTTTAATATTTGAATAAATAAATAATTAATTAATTAAT
1 TA-TTTGGGTT--GT-TTT---TAATAATTAAATATTT-AAT---TAAATAATTAAATATTTAAT
* * * *
28468417 TAATTGGGTTGATTTAACTAATTAAATAATTAA
55 TAA-----AT-AATTAAAT-A-TAATTA---AA
28468450 GTATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATA--TAATTAAAT-ATT-
1 -TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTA
28468511 --T-TGAATTAAA
65 AATAT-AATTAAA
* * * * * *** * * *
28468521 TATTTGAGTTGTTTTTAATATTTATATAATTAATTAATTAATT--GGGTTGATTTAACTAATT-A
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
*
28468583 A-ATAATTAAG
66 ATATAATTAAA
28468593 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATA--TAATTAAAT-ATT--
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
28468653 -T-TGAATTAAA
66 ATAT-AATTAAA
* ** * * *** **
28468663 TATTTGGGTTGTTTTTAATATTTGAATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTT
1 TATTTGGGTTGTTTTTAATA----ATTAAATATTTAATTAAATAATTAAAT-ATTTAATT-AAAT
* * *
28468728 AACTAATTAAATAATTAAG
60 AATTAA--ATATAATTAAA
28468747 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATA--TAATTAAAT-ATT--
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
28468807 -T-TGAATTAAA
66 ATAT-AATTAAA
* ** * * *** **
28468817 TATTTGAGTTGTTTTTAATATTTATATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTT
1 TATTTGGGTTGTTTTTAATA---AT-TAAATATTTAATTAAATAATTAAAT-ATTTAATT-AAAT
* * *
28468882 AACTAATTAAATAATTAAG
60 AATTAA--ATATAATTAAA
28468901 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATA--TAATTAAAT-ATT--
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
28468961 -T-TGAATTAAA
66 ATAT-AATTAAA
** * * * * *
28468971 TATTTGGGTTGTTTTTCATATTTATATAAATAAATAAATAATTAATTAATTAATTGGGTTGATTT
1 TATTTGGGTTGTTTTT-A-A--TA-AT---TAAATATTTAATTAAATAATTAAAT--ATTTAATT
* *
28469036 AACTAATT-AA-ATAATTAAG
56 AAATAATTAAATATAATTAAA
*
28469055 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATA--TAATTAGATAATTAA
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
28469118 ATATTTTGAATTAAA
66 ATA---T-AATTAAA
* * ** * * *
28469133 TATTTGAGTTGTTTTTAATATTTAAATAAATAAATAAATAATTAATTAATTAATTAATTGAGTTG
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAA---A--T-
* *
28469198 ATTTAAATAATTAAATAATTCA
60 AATTAAAT-A-TAATTAA---A
28469220 GTATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATT-AA-A--TAATTAAAT-ATT-
1 -TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTA
28469279 --T-TGAATTAAA
65 AATAT-AATTAAA
* * *
28469289 TATTTGGGTTGTTTTTAATATTTAAATA---AA-TAAATAATTAATTAATTAATTAA
1 TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAA
28469342 TTGGGTTGAT
Statistics
Matches: 862, Mismatches: 163, Indels: 248
0.68 0.13 0.19
Matches are distributed among these distances:
64 9 0.01
65 3 0.00
66 1 0.00
68 59 0.07
69 4 0.00
70 119 0.14
71 10 0.01
72 77 0.09
73 7 0.01
74 51 0.06
75 9 0.01
76 37 0.04
77 19 0.02
78 82 0.10
79 19 0.02
80 69 0.08
81 4 0.00
82 18 0.02
83 10 0.01
84 117 0.14
85 7 0.01
86 36 0.04
87 3 0.00
88 51 0.06
91 6 0.01
92 15 0.02
93 1 0.00
94 8 0.01
95 1 0.00
97 8 0.01
98 2 0.00
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.48
Consensus pattern (76 bp):
TATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTAATTAAATAATTAA
ATATAATTAAA
Found at i:28468439 original size:34 final size:34
Alignment explanation
Indices: 28468399--28468629 Score: 153
Period size: 34 Copynumber: 6.6 Consensus size: 34
28468389 TGAATAAATA
*
28468399 AATAATTAATTAATTAATTAATTGGGTTG-ATTT
1 AATAATTAAATAATTAATTAATTGGGTTGTATTT
* * *
28468432 AACTAATTAAATAATTAAGTATTTGGGTTGTTTTT
1 AA-TAATTAAATAATTAATTAATTGGGTTGTATTT
* * ** ** *
28468467 AATAATTAAATATTTAATTAAAT-AATTAAATAT
1 AATAATTAAATAATTAATTAATTGGGTTGTATTT
* ** * * * *
28468500 AATTAAATATTTTGAATTAAATATTTGAGTTGTTTTT
1 AA-TAATTA-AAT-AATTAATTAATTGGGTTGTATTT
*
28468537 AATATTTATATAATTAATTAATTAATTGGGTTG-ATTT
1 AATA---AT-TAAATAATTAATTAATTGGGTTGTATTT
* * *
28468574 AACTAATTAAATAATTAAGTATTTGGGTTGTTTTT
1 AA-TAATTAAATAATTAATTAATTGGGTTGTATTT
*
28468609 AATAATTAAATATTTAATTAA
1 AATAATTAAATAATTAATTAA
28468630 ATAATTAAAT
Statistics
Matches: 147, Mismatches: 39, Indels: 23
0.70 0.19 0.11
Matches are distributed among these distances:
33 8 0.05
34 82 0.56
35 13 0.09
36 10 0.07
37 12 0.08
38 17 0.12
39 3 0.02
40 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (34 bp):
AATAATTAAATAATTAATTAATTGGGTTGTATTT
Found at i:28468445 original size:50 final size:49
Alignment explanation
Indices: 28468333--28468553 Score: 128
Period size: 50 Copynumber: 4.4 Consensus size: 49
28468323 TATTTAATTA
* *
28468333 AATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTGTTTTT
1 AATAATTAAATA-AATTAAATATTTTGAATTAAATAATTGGGTTGTATTT
* * *
28468383 AATATTTGAATAAA-TAAATAATTAATT-AATTAATTAATTGGGTTG-ATTT
1 AATAATTAAATAAATTAAAT-ATT--TTGAATTAAATAATTGGGTTGTATTT
* ** * *** * *
28468432 AACTAATTAAAT-AATTAAGTATTTGGGTTGTTTTTAATAATTAAATATTTAATTA
1 AA-TAATTAAATAAATTAAATA-TT---TTGAATTAAATAATTGGGT-TGT-ATTT
* * *
28468487 AATAATTAAATATAATTAAATATTTTGAATTAAATATTTGAGTTGTTTTT
1 AATAATTAAATA-AATTAAATATTTTGAATTAAATAATTGGGTTGTATTT
* *
28468537 AATATTTATAT-AATTAA
1 AATAATTAAATAAATTAA
28468554 TTAATTAATT
Statistics
Matches: 127, Mismatches: 31, Indels: 28
0.68 0.17 0.15
Matches are distributed among these distances:
48 11 0.09
49 13 0.10
50 50 0.39
51 6 0.05
52 22 0.17
53 1 0.01
54 9 0.07
55 7 0.06
56 8 0.06
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (49 bp):
AATAATTAAATAAATTAAATATTTTGAATTAAATAATTGGGTTGTATTT
Found at i:28468492 original size:20 final size:18
Alignment explanation
Indices: 28468467--28468508 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
28468457 GGTTGTTTTT
28468467 AATAATTAAATATTTAATTA
1 AATAATTAAATA--TAATTA
28468487 AATAATTAAATATAATTA
1 AATAATTAAATATAATTA
28468505 AATA
1 AATA
28468509 TTTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:28468499 original size:154 final size:153
Alignment explanation
Indices: 28468313--28469405 Score: 1802
Period size: 154 Copynumber: 7.1 Consensus size: 153
28468303 TATTTAATTA
28468313 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
1 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
28468378 TTTTTAATATTTGAATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
66 TTTTTAATATTT-AATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
28468443 TAATTAAGTATTTGGGTTGTTTTT
130 TAATTAAGTATTTGGGTTGTTTTT
*
28468467 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGAGTTG
1 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
28468532 TTTTTAATA--T--T---T--AT-A-TAATTAATTAATTAATTGGGTTGATTTAACTAATTAAAT
66 TTTTTAATATTTAATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAAT
28468586 AATTAAGTATTTGGGTTGTTTTT
131 AATTAAGTATTTGGGTTGTTTTT
28468609 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
1 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
28468674 TTTTTAATATTTGAATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
66 TTTTTAATATTT-AATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
28468739 TAATTAAGTATTTGGGTTGTTTTT
130 TAATTAAGTATTTGGGTTGTTTTT
*
28468763 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGAGTTG
1 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
28468828 TTTTTAATATTTATATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
66 TTTTTAATATTTA-ATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
28468893 TAATTAAGTATTTGGGTTGTTTTT
130 TAATTAAGTATTTGGGTTGTTTTT
28468917 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
1 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
* *
28468982 TTTTTCATATTTATATAAATAAATAAATAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
66 TTTTTAATATTTA-ATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
28469047 TAATTAAGTATTTGGGTTGTTTTT
130 TAATTAAGTATTTGGGTTGTTTTT
28469071 AATAATTAAATATTTAATTAAATAATTAAATATAATTAGATAATTAAATATTTTGAATTAAATAT
1 AATAATTAAATATTTAATTAAATAA-T---TA-AA-T--ATAATTAAATATTTTGAATTAAATAT
* *
28469136 TTGAGTTGTTTTTAATATTTAAATAAATAAATAAATAATTAATTAATTAATTAATTGAGTTGATT
58 TTGGGTTGTTTTTAATA-TT---T-AATAAATAAATAATTAATTAATTAATTAATTGGGTTGATT
* *
28469201 TAAATAATTAAATAATTCAGTATTTGGGTTGTTTTT
118 TAACTAATTAAATAATTAAGTATTTGGGTTGTTTTT
28469237 AATAATTAAATATTTAATTAAATAATT-AA-ATAATTAAATATTTTGAATTAAATATTTGGGTTG
1 AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
*
28469300 TTTTTAATATTTAAATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAAGTAATTAAA
66 TTTTTAATATTT-AATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAA
*
28469365 TAATGAAGTATTTGGGTTGTGTTTT
130 TAATTAAGTATTTGGGTTGT-TTTT
*
28469390 -CTAATTTAAA-ATTTAA
1 AATAA-TTAAATATTTAA
28469406 AAAAAATTCA
Statistics
Matches: 893, Mismatches: 18, Indels: 58
0.92 0.02 0.06
Matches are distributed among these distances:
142 135 0.15
143 1 0.00
144 3 0.00
146 1 0.00
147 1 0.00
149 1 0.00
150 1 0.00
152 82 0.09
153 11 0.01
154 462 0.52
155 3 0.00
156 42 0.05
158 2 0.00
159 2 0.00
160 3 0.00
162 42 0.05
163 2 0.00
165 1 0.00
166 97 0.11
167 1 0.00
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (153 bp):
AATAATTAAATATTTAATTAAATAATTAAATATAATTAAATATTTTGAATTAAATATTTGGGTTG
TTTTTAATATTTAATAAATAAATAATTAATTAATTAATTAATTGGGTTGATTTAACTAATTAAAT
AATTAAGTATTTGGGTTGTTTTT
Found at i:28468634 original size:20 final size:18
Alignment explanation
Indices: 28468609--28468650 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
28468599 GGTTGTTTTT
28468609 AATAATTAAATATTTAATTA
1 AATAATTAAATA--TAATTA
28468629 AATAATTAAATATAATTA
1 AATAATTAAATATAATTA
28468647 AATA
1 AATA
28468651 TTTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:28468735 original size:34 final size:34
Alignment explanation
Indices: 28468695--28468783 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 34
28468685 TGAATAAATA
*
28468695 AATAATTAATTAATTAATTAATTGGGTTG-ATTT
1 AATAATTAAATAATTAATTAATTGGGTTGTATTT
* * *
28468728 AACTAATTAAATAATTAAGTATTTGGGTTGTTTTT
1 AA-TAATTAAATAATTAATTAATTGGGTTGTATTT
*
28468763 AATAATTAAATATTTAATTAA
1 AATAATTAAATAATTAATTAA
28468784 ATAATTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 2 0.04
34 40 0.85
35 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (34 bp):
AATAATTAAATAATTAATTAATTGGGTTGTATTT
Found at i:28468788 original size:20 final size:18
Alignment explanation
Indices: 28468763--28468804 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
28468753 GGTTGTTTTT
28468763 AATAATTAAATATTTAATTA
1 AATAATTAAATA--TAATTA
28468783 AATAATTAAATATAATTA
1 AATAATTAAATATAATTA
28468801 AATA
1 AATA
28468805 TTTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:28468889 original size:34 final size:34
Alignment explanation
Indices: 28468849--28468937 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 34
28468839 TATATAAATA
*
28468849 AATAATTAATTAATTAATTAATTGGGTTG-ATTT
1 AATAATTAAATAATTAATTAATTGGGTTGTATTT
* * *
28468882 AACTAATTAAATAATTAAGTATTTGGGTTGTTTTT
1 AA-TAATTAAATAATTAATTAATTGGGTTGTATTT
*
28468917 AATAATTAAATATTTAATTAA
1 AATAATTAAATAATTAATTAA
28468938 ATAATTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 2 0.04
34 40 0.85
35 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (34 bp):
AATAATTAAATAATTAATTAATTGGGTTGTATTT
Found at i:28468942 original size:20 final size:18
Alignment explanation
Indices: 28468917--28468958 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
28468907 GGTTGTTTTT
28468917 AATAATTAAATATTTAATTA
1 AATAATTAAATA--TAATTA
28468937 AATAATTAAATATAATTA
1 AATAATTAAATATAATTA
28468955 AATA
1 AATA
28468959 TTTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:28469062 original size:34 final size:34
Alignment explanation
Indices: 28469003--28469087 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
28468993 TATATAAATA
* * *
28469003 AATAAATAATTAATTAATTAATTGGGTTG-ATTT
1 AATAATTAAATAATTAAGTAATTGGGTTGTATTT
* *
28469036 AACTAATTAAATAATTAAGTATTTGGGTTGTTTTT
1 AA-TAATTAAATAATTAAGTAATTGGGTTGTATTT
*
28469071 AATAATTAAATATTTAA
1 AATAATTAAATAATTAA
28469088 TTAAATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 2 0.05
34 37 0.84
35 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (34 bp):
AATAATTAAATAATTAAGTAATTGGGTTGTATTT
Found at i:28469108 original size:18 final size:18
Alignment explanation
Indices: 28469071--28469121 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 18
28469061 GGTTGTTTTT
28469071 AATAATTAAATATTTAATTA
1 AATAATTAAATA--TAATTA
28469091 AATAATTAAATATAATTA
1 AATAATTAAATATAATTA
*
28469109 GATAATTAAATAT
1 AATAATTAAATAT
28469122 TTTGAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 18 0.60
20 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAATTAAATATAATTA
Found at i:28469210 original size:34 final size:34
Alignment explanation
Indices: 28469167--28469257 Score: 110
Period size: 34 Copynumber: 2.7 Consensus size: 34
28469157 AATAAATAAA
*
28469167 TAAATAATTAATTAATTAATTAATTGAGTTGATT
1 TAAATAATTAAATAATTAATTAATTGAGTTGATT
* * * * *
28469201 TAAATAATTAAATAATTCAGTATTTGGGTTGTTT
1 TAAATAATTAAATAATTAATTAATTGAGTTGATT
* *
28469235 TTAATAATTAAATATTTAATTAA
1 TAAATAATTAAATAATTAATTAA
28469258 ATAATTAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (34 bp):
TAAATAATTAAATAATTAATTAATTGAGTTGATT
Found at i:28469253 original size:8 final size:8
Alignment explanation
Indices: 28469251--28469276 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28469241 ATTAAATATT
28469251 TAATTAAA
1 TAATTAAA
28469259 TAATTAAA
1 TAATTAAA
28469267 TAATTAAA
1 TAATTAAA
28469275 TA
1 TA
28469277 TTTTGAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:28469256 original size:12 final size:12
Alignment explanation
Indices: 28469239--28469293 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 12
28469229 TTGTTTTTAA
28469239 TAATTAAATATT
1 TAATTAAATATT
28469251 TAATTAAATAATT
1 TAATTAAAT-ATT
28469264 AAATAATTAAATATTT
1 ---TAATTAAATA-TT
28469280 TGAATTAAATATT
1 T-AATTAAATATT
28469293 T
1 T
28469294 GGGTTGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.24
13 7 0.19
14 9 0.24
15 1 0.03
16 11 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
TAATTAAATATT
Found at i:28470916 original size:26 final size:26
Alignment explanation
Indices: 28470868--28470917 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
28470858 AGGCAATTAG
***
28470868 TTATTAAGGTACACTCTTTAATAACC
1 TTATTAAGGTACACTCCAGAATAACC
*
28470894 TTATTGAGGTACACTCCAGAATAA
1 TTATTAAGGTACACTCCAGAATAA
28470918 TTAAGAGAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (26 bp):
TTATTAAGGTACACTCCAGAATAACC
Found at i:28471890 original size:41 final size:41
Alignment explanation
Indices: 28471682--28471982 Score: 272
Period size: 41 Copynumber: 7.4 Consensus size: 41
28471672 ATGTAAAAAT
*
28471682 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCT-TAGACT
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTCT-GACC
* * *
28471723 TTTCGCAGCGCTTTTCCATAAGCGCCG-TAATTGCT-TAGACT
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCT-ATTGCTCT-GACC
* * *
28471764 TTTACCGGCGCATTTCCATAAGCGCCGCTATTGCT-TAGACT
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTCT-GACC
* * *
28471805 TTTAGCGGCGCTTTTCCATATGCGCCGCTATTGATCTGATC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTCTGACC
* * *
28471846 TTTAGCGGCGCTTTTGCAAAAGCGCCGCTAATT-CTCTTACC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCT-ATTGCTCTGACC
* ** * * * * *
28471887 TTTAGCAGCGCTTTTAAATAAACGCTGCTAATGGTCTTACC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTCTGACC
* * * *
28471928 TTTAGCGGCGCTTCTCAATAAACGCCGCTATTGCTCT-ATC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTCTGACC
* *
28471968 TTTTGCGGCGTTTTT
1 TTTAGCGGCGCTTTT
28471983 TTAGAAACGC
Statistics
Matches: 219, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
40 17 0.08
41 197 0.90
42 5 0.02
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.35
Consensus pattern (41 bp):
TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTCTGACC
Found at i:28478041 original size:15 final size:15
Alignment explanation
Indices: 28478021--28478050 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28478011 ATCCAAAGTC
28478021 CATTTTTCAAAACAA
1 CATTTTTCAAAACAA
28478036 CATTTTTCAAAACAA
1 CATTTTTCAAAACAA
28478051 TTTCCTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
CATTTTTCAAAACAA
Found at i:28497515 original size:17 final size:17
Alignment explanation
Indices: 28497493--28497526 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28497483 ATAGACTCAC
*
28497493 TTAGATATACTTAGTAT
1 TTAGATATAATTAGTAT
28497510 TTAGATATAATTAGTAT
1 TTAGATATAATTAGTAT
28497527 AATATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGATATAATTAGTAT
Found at i:28504888 original size:3 final size:3
Alignment explanation
Indices: 28504880--28504916 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28504870 GTGGGCTTGG
28504880 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28504917 ATATAATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28507275 original size:13 final size:13
Alignment explanation
Indices: 28507259--28507324 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
28507249 AAATACATAG
*
28507259 ATGAAATAGTTAC
1 ATGAAATAGTTAT
28507272 ATGAAAT-GTTATT
1 ATGAAATAGTTA-T
* *
28507285 ATGAAAGTAGATGT
1 ATGAAA-TAGTTAT
*
28507299 ATGAAACAGTTAT
1 ATGAAATAGTTAT
*
28507312 ATGAAATATTTAT
1 ATGAAATAGTTAT
28507325 TTGTAATATT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
12 4 0.10
13 28 0.67
14 8 0.19
15 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (13 bp):
ATGAAATAGTTAT
Found at i:28513506 original size:7 final size:7
Alignment explanation
Indices: 28513494--28513527 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
28513484 AACCAAAGGG
28513494 TCCAAAT
1 TCCAAAT
28513501 TCCAAAT
1 TCCAAAT
28513508 TCCAAAT
1 TCCAAAT
28513515 TCCAAAT
1 TCCAAAT
28513522 TCCAAA
1 TCCAAA
28513528 ACAAACCTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (7 bp):
TCCAAAT
Found at i:28533944 original size:20 final size:20
Alignment explanation
Indices: 28533894--28533945 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
28533884 TTTTTCTATT
28533894 TTTTATGG-TTTTTAATAAA
1 TTTTATGGTTTTTTAATAAA
* ** *
28533913 TTTAATTTTTTTTTTATAAA
1 TTTTATGGTTTTTTAATAAA
28533933 TTTTATGGTTTTT
1 TTTTATGGTTTTT
28533946 AATTTATTTC
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTATGGTTTTTTAATAAA
Found at i:28533988 original size:20 final size:20
Alignment explanation
Indices: 28533902--28533988 Score: 54
Period size: 20 Copynumber: 4.4 Consensus size: 20
28533892 TTTTTTATGG
* *
28533902 TTTTTAATAAA-TTTAATTTT
1 TTTTTTATAAATTTTAA-TTA
**
28533922 TTTTTTATAAATTTT-ATGG
1 TTTTTTATAAATTTTAATTA
* **
28533941 TTTTTAATTTATTTCTAA-TA
1 TTTTTTATAAATTT-TAATTA
* *
28533961 ATTATTATAAATTTTAATTA
1 TTTTTTATAAATTTTAATTA
28533981 TTTTTTAT
1 TTTTTTAT
28533989 TTTTTTATAT
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
19 15 0.31
20 29 0.60
21 4 0.08
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTTATAAATTTTAATTA
Found at i:28535691 original size:58 final size:60
Alignment explanation
Indices: 28535620--28535752 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 60
28535610 ATCACTTTAA
** * *
28535620 TATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGGTTAAATTTGATATTAAATC
1 TATTAAATTAATATAATACTTATTACAAGATAAATATTAAATTAAATTTAATATTAAAAC
* *
28535678 TATTAAATTAATATAATATTTATTTACAAGATAAATATTAAATTTAATTTAATATTAAAAC
1 TATTAAATTAATATAATACTTA-TTACAAGATAAATATTAAATTAAATTTAATATTAAAAC
*
28535739 TATTAAAATAATAT
1 TATTAAATTAATAT
28535753 TATTTTTGGA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 21 0.32
60 1 0.02
61 43 0.66
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (60 bp):
TATTAAATTAATATAATACTTATTACAAGATAAATATTAAATTAAATTTAATATTAAAAC
Found at i:28540734 original size:8 final size:8
Alignment explanation
Indices: 28540721--28540776 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
28540711 ACCCAATTAT
28540721 TTTTTTTA
1 TTTTTTTA
28540729 TTTTTTTTA
1 -TTTTTTTA
*
28540738 TTTTTCTA
1 TTTTTTTA
28540746 TCTTATTTTA
1 T-TT-TTTTA
*
28540756 TTTGTTTA
1 TTTTTTTA
*
28540764 TTTATTTA
1 TTTTTTTA
28540772 TTTTT
1 TTTTT
28540777 GTCTAGGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 23 0.57
9 12 0.30
10 5 0.12
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:28540751 original size:22 final size:21
Alignment explanation
Indices: 28540725--28540776 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
28540715 AATTATTTTT
28540725 TTTATTTTTTTTATTT-TTCTA
1 TTTATTTTTTTTATTTATT-TA
* *
28540746 TCTTATTTTATTTGTTTATTTA
1 T-TTATTTTTTTTATTTATTTA
28540768 TTTATTTTT
1 TTTATTTTT
28540777 GTCTAGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTATTTTTTTTATTTATTTA
Found at i:28542323 original size:19 final size:19
Alignment explanation
Indices: 28542301--28542345 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28542291 TTATATTAGG
28542301 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
28542320 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
28542339 ATTTAAT
1 ATTTAAT
28542346 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:28544877 original size:16 final size:16
Alignment explanation
Indices: 28544856--28544890 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28544846 AGTCCTCGTA
28544856 ATTTTA-TCACTTTAAC
1 ATTTTAGTC-CTTTAAC
28544872 ATTTTAGTCCTTTAAC
1 ATTTTAGTCCTTTAAC
28544888 ATT
1 ATT
28544891 AAAATTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTTAGTCCTTTAAC
Found at i:28545247 original size:16 final size:15
Alignment explanation
Indices: 28545226--28545255 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28545216 CTAATATCCA
28545226 TTATTTCTATTATTTT
1 TTATTTCTA-TATTTT
28545242 TTATTTCTATATTT
1 TTATTTCTATATTT
28545256 CAATGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTTCTATATTTT
Found at i:28556951 original size:20 final size:20
Alignment explanation
Indices: 28556903--28556951 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
28556893 ATTTAAAAAA
*
28556903 TAATATTTTTTAATAATATT
1 TAATATTTTTAAATAATATT
28556923 T-ATACTTTTTAAATAAT-TT
1 TAATA-TTTTTAAATAATATT
28556942 TAATGATTTT
1 TAAT-ATTTT
28556952 AATTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 6 0.24
20 18 0.72
21 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TAATATTTTTAAATAATATT
Found at i:28558216 original size:16 final size:16
Alignment explanation
Indices: 28558192--28558243 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
28558182 GGTTTAATCG
*
28558192 ATTTAGTTGTTTGTTT
1 ATTTTGTTGTTTGTTT
*
28558208 ATTTTGTTGTTTATTT
1 ATTTTGTTGTTTGTTT
*
28558224 ATTTTAGTTATTTAGTTT
1 ATTTT-GTTGTTT-GTTT
28558242 AT
1 AT
28558244 GATATTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 19 0.63
17 6 0.20
18 5 0.17
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.69
Consensus pattern (16 bp):
ATTTTGTTGTTTGTTT
Found at i:28558807 original size:20 final size:18
Alignment explanation
Indices: 28558782--28558829 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
28558772 TGAAATAAAT
*
28558782 TTATAAAATATTATGAAGAA
1 TTATAAAAT-TTAT-AAAAA
28558802 TTATAAGAATTTATAAAAA
1 TTATAA-AATTTATAAAAA
28558821 TTAATAAAA
1 TT-ATAAAA
28558830 ACATTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 8 0.32
20 14 0.56
21 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
TTATAAAATTTATAAAAA
Found at i:28561424 original size:27 final size:27
Alignment explanation
Indices: 28561392--28561445 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
28561382 GGGTTCATAA
*
28561392 AATTCTCT-TTGAGTTTTTTTTTA-AAG
1 AATT-TCTGTTGAGTTTTCTTTTAGAAG
28561418 AATTTCTGTTGAGTTTTCTTTTAGAAG
1 AATTTCTGTTGAGTTTTCTTTTAGAAG
28561445 A
1 A
28561446 GTTTTAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 3 0.12
26 18 0.72
27 4 0.16
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (27 bp):
AATTTCTGTTGAGTTTTCTTTTAGAAG
Found at i:28562539 original size:27 final size:26
Alignment explanation
Indices: 28562509--28562564 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
28562499 TATTTTTTAG
* *
28562509 TTAATAAAA-TTCTCTTTTAGTTTTCTT
1 TTAA-AAAATTTCTC-TTGAGTTTTATT
*
28562536 TTAAATAATTTCTCTTGAGTTTTATT
1 TTAAAAAATTTCTCTTGAGTTTTATT
28562562 TTA
1 TTA
28562565 GAATAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (26 bp):
TTAAAAAATTTCTCTTGAGTTTTATT
Found at i:28562569 original size:27 final size:27
Alignment explanation
Indices: 28562518--28562569 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
28562508 GTTAATAAAA
* *
28562518 TTCTCTTTTAGTTTTCTTTTAAATAAT
1 TTCTCTTTGAGTTTTATTTTAAATAAT
28562545 TTCTC-TTGAGTTTTATTTTAGAATA
1 TTCTCTTTGAGTTTTATTTTA-AATA
28562570 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.23, C:0.10, G:0.08, T:0.60
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTATTTTAAATAAT
Found at i:28565906 original size:21 final size:21
Alignment explanation
Indices: 28565880--28565956 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
28565870 GGAGTTTTTA
*
28565880 GTATCGGTAGAAGTAAGACTT
1 GTATCGATAGAAGTAAGACTT
28565901 GTATCGATAGAAG--AGTCACTT
1 GTATCGATAGAAGTAAG--ACTT
* * **
28565922 GTATCGGTAGAACTATCACTT
1 GTATCGATAGAAGTAAGACTT
28565943 GTATCGATAGAAGT
1 GTATCGATAGAAGT
28565957 CTGCACTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.04
21 43 0.96
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (21 bp):
GTATCGATAGAAGTAAGACTT
Found at i:28568170 original size:132 final size:132
Alignment explanation
Indices: 28567933--28568195 Score: 350
Period size: 132 Copynumber: 2.0 Consensus size: 132
28567923 AATGGGCCTC
* * * * * * *
28567933 CTCACACGAGCTGTGGGTCGAGATGTTAAGCTACACGATGCTATTTACACGAGCTGTGGAGAATC
1 CTCACACGAGCTGTGGGTCGAGAAGTTAACCTACAAGATGCTACTAACACGAGCTATAGAGAATC
*
28567998 CACAATAAATGATGAATCTCAGCAATCGGTAGGACATCTAAGACCAGTACCCATATAACATGTAA
66 CACAATAAATGATGAATCTCAGCAATCGGTAGGACATCTAAGACCAGCACCCATATAACATGTAA
28568063 TG
131 TG
* *
28568065 CTCACACGAGTTGTGGGTCGAGAAGTTGACCTACAAGATGCTACTAACACGAGCTATAGAGAATC
1 CTCACACGAGCTGTGGGTCGAGAAGTTAACCTACAAGATGCTACTAACACGAGCTATAGAGAATC
** * * * *
28568130 TGCAATAAATG-TCGGATCTCAG-ACATCGGTAGGACATCTAAGACCAGCACCTATGTAACCTGT
66 CACAATAAATGAT-GAATCTCAGCA-ATCGGTAGGACATCTAAGACCAGCACCCATATAACATGT
28568193 AAT
129 AAT
28568196 CCTGATGTCG
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
131 2 0.02
132 111 0.98
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (132 bp):
CTCACACGAGCTGTGGGTCGAGAAGTTAACCTACAAGATGCTACTAACACGAGCTATAGAGAATC
CACAATAAATGATGAATCTCAGCAATCGGTAGGACATCTAAGACCAGCACCCATATAACATGTAA
TG
Found at i:28568361 original size:2 final size:2
Alignment explanation
Indices: 28568354--28568419 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
28568344 AAATTTATTC
28568354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28568396 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
28568420 CCAAATTAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28569975 original size:13 final size:13
Alignment explanation
Indices: 28569945--28569988 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
28569935 TACAATTATC
*
28569945 AATTTCATATATT
1 AATTTCATATAAT
* *
28569958 TATTTCATATAAA
1 AATTTCATATAAT
*
28569971 AATTTCGTATAAT
1 AATTTCATATAAT
28569984 AATTT
1 AATTT
28569989 TATCTAAACA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (13 bp):
AATTTCATATAAT
Found at i:28572606 original size:2 final size:2
Alignment explanation
Indices: 28572599--28572633 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28572589 CAATTGAACT
28572599 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28572634 TTAACTTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28574023 original size:20 final size:20
Alignment explanation
Indices: 28574000--28574229 Score: 178
Period size: 20 Copynumber: 11.5 Consensus size: 20
28573990 ATTATGCGTT
28574000 CAGGGGCATCGAAGTGCAAA
1 CAGGGGCATCGAAGTGCAAA
* * *
28574020 CAGGGGCACCAAAGTGTAAA
1 CAGGGGCATCGAAGTGCAAA
* * *
28574040 CAAGGGCACCGTAGTGCAAA
1 CAGGGGCATCGAAGTGCAAA
** * *
28574060 CAGATGCA-CTGTAGTGTAAA
1 CAGGGGCATC-GAAGTGCAAA
* *
28574080 TAGGGGCAGCGAAGTGCAAA
1 CAGGGGCATCGAAGTGCAAA
** * *
28574100 CAAAGGCA-CCATAGTACAAA
1 CAGGGGCATCGA-AGTGCAAA
*
28574120 AAGGGGCATCGAAGTGCAAA
1 CAGGGGCATCGAAGTGCAAA
* *
28574140 CAAGGGCGTCGAAGTGCAAA
1 CAGGGGCATCGAAGTGCAAA
* *
28574160 CAGGGTCA-CCATAGTGCAAA
1 CAGGGGCATCGA-AGTGCAAA
**
28574180 CAAAGGCATCGAAGTGCAAA
1 CAGGGGCATCGAAGTGCAAA
* * *
28574200 CAGAGGCGTCGTAGTGCAAA
1 CAGGGGCATCGAAGTGCAAA
28574220 CAGGGGCATC
1 CAGGGGCATC
28574230 AAGGTGTAAA
Statistics
Matches: 162, Mismatches: 42, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
19 5 0.03
20 152 0.94
21 5 0.03
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.12
Consensus pattern (20 bp):
CAGGGGCATCGAAGTGCAAA
Found at i:28574153 original size:60 final size:60
Alignment explanation
Indices: 28574004--28574227 Score: 215
Period size: 60 Copynumber: 3.7 Consensus size: 60
28573994 TGCGTTCAGG
* ** * * * *
28574004 GGCATCGAAGTGCAAACAGGGGCACCAAAGTGTAAACAAGGGCACCGTAGTGCAAACAGA
1 GGCATCGAAGTGCAAACAAGGGCGTCGAAGTGCAAACAAGGGCACCATAGTGCAAAAAGA
* * * * * * * *
28574064 TGCA-CTGTAGTGTAAATAGGGGCAG-CGAAGTGCAAACAAAGGCACCATAGTACAAAAAGG
1 GGCATC-GAAGTGCAAACAAGGGC-GTCGAAGTGCAAACAAGGGCACCATAGTGCAAAAAGA
28574124 GGCATCGAAGTGCAAACAAGGGCGTCGAAGTGCAAAC-AGGGTCACCATAGTGCAAACAA-A
1 GGCATCGAAGTGCAAACAAGGGCGTCGAAGTGCAAACAAGGG-CACCATAGTGCAAA-AAGA
* *
28574184 GGCATCGAAGTGCAAAC-AGAGGCGTCGTAGTGCAAACAGGGGCA
1 GGCATCGAAGTGCAAACAAG-GGCGTCGAAGTGCAAACAAGGGCA
28574228 TCAAGGTGTA
Statistics
Matches: 134, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
59 7 0.05
60 121 0.90
61 6 0.04
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (60 bp):
GGCATCGAAGTGCAAACAAGGGCGTCGAAGTGCAAACAAGGGCACCATAGTGCAAAAAGA
Found at i:28574875 original size:26 final size:26
Alignment explanation
Indices: 28574845--28574894 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
28574835 ACTTGCAAGA
* * *
28574845 GAAGGATCAAGACAAGGAAGAAGAGG
1 GAAGGAACAAGAAAAGGAAAAAGAGG
*
28574871 GAAGGAAGAAGAAAAGGAAAAAGA
1 GAAGGAACAAGAAAAGGAAAAAGA
28574895 AGAGCCTACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.36, T:0.02
Consensus pattern (26 bp):
GAAGGAACAAGAAAAGGAAAAAGAGG
Found at i:28575233 original size:3 final size:3
Alignment explanation
Indices: 28575225--28575251 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28575215 GAGAGCGTCC
28575225 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
28575252 AACCAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28579762 original size:15 final size:17
Alignment explanation
Indices: 28579744--28579781 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
28579734 GAGGAGATAA
28579744 AAAAAAG-AAAA-GAAG
1 AAAAAAGAAAAAGGAAG
28579759 AAAAAAGAAAAAGGAAG
1 AAAAAAGAAAAAGGAAG
28579776 AAAAAA
1 AAAAAA
28579782 TAAAGTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 10 0.48
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAGGAAG
Found at i:28579762 original size:16 final size:18
Alignment explanation
Indices: 28579743--28579781 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
28579733 AGAGGAGATA
28579743 AAAAAAAG-AAAA-GAAG
1 AAAAAAAGAAAAAGGAAG
28579759 -AAAAAAGAAAAAGGAAG
1 AAAAAAAGAAAAAGGAAG
28579776 AAAAAA
1 AAAAAA
28579782 TAAAGTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.35
16 4 0.20
17 4 0.20
18 5 0.25
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAGGAAG
Found at i:28580673 original size:22 final size:21
Alignment explanation
Indices: 28580648--28580696 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
28580638 ACTTCACCCA
* *
28580648 AAAAATAAAAAGAGAGAGAAAG
1 AAAAA-AAAAAGAAAGAAAAAG
*
28580670 AAAAGAAAAAAGAAATAAAAAG
1 AAAA-AAAAAAGAAAGAAAAAG
28580692 AAAAA
1 AAAAA
28580697 GGAGAGGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.91
23 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAGAAAGAAAAAG
Found at i:28580697 original size:16 final size:16
Alignment explanation
Indices: 28580650--28580697 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
28580640 TTCACCCAAA
* *
28580650 AAATAAAAAGAGAGAG
1 AAATAAAAAGAAAAAG
*
28580666 AAA-GAAAAGAAAAAAG
1 AAATAAAAAG-AAAAAG
28580682 AAATAAAAAGAAAAAG
1 AAATAAAAAGAAAAAG
28580698 GAGAGGATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (16 bp):
AAATAAAAAGAAAAAG
Found at i:28581158 original size:112 final size:112
Alignment explanation
Indices: 28580999--28581220 Score: 311
Period size: 112 Copynumber: 2.0 Consensus size: 112
28580989 AATGTTTGTC
* * * * *
28580999 ATTTTTAATCTTTTCATTCATGCGAGTTTTTCCTCCAATAAAATTCAATTTTATCCATCTTACAA
1 ATTTTTAATCTTTTCATTCACGCAAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
**
28581064 CTTTGTTCAAGCACGTTTGCATTGAAATAACTG-TTAGTGGACTAATG
66 CCCTGTTCAAGCACGTTTGCATTGAAATAAC-GATTAGTGGACTAATG
* *
28581111 ATTTTTAATCTTTTCATTCACGCAAGCTTTGCCTCTAGTAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATCTTTTCATTCACGCAAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
* * * *
28581176 CCCTGTTCAAGCACTTTTTCATTGAAATGACGATTAGTGGTCTAA
66 CCCTGTTCAAGCACGTTTGCATTGAAATAACGATTAGTGGACTAA
28581221 CGATGTAAGG
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 1 0.01
112 95 0.99
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (112 bp):
ATTTTTAATCTTTTCATTCACGCAAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
CCCTGTTCAAGCACGTTTGCATTGAAATAACGATTAGTGGACTAATG
Found at i:28581715 original size:49 final size:49
Alignment explanation
Indices: 28581662--28582013 Score: 284
Period size: 49 Copynumber: 7.2 Consensus size: 49
28581652 GAGATATGGA
* * *
28581662 GGGAAAGGTTGAAGCCACAACGGCAAACCTTGTACCTTA-AGGACGTGAT
1 GGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGA-GACGTGAT
* * * * **
28581711 GGGAAATATTGAAGCCGTAACGACGAATCTTGTACCGTT-GAGATATGGA-
1 GGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACC-TTAGAGACGT-GAT
* * *
28581760 GAGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGACGTGAT
1 GGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGTGAT
* * * * *
28581809 GGGAAAGATTGAAGCTGCAACGGCGAATCTTGTACCATGGAGACATGGA-
1 GGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGT-GAT
* * ** * * *
28581858 GGGAAAGGTTAAAGCCGCAATAGCGAACCTTGTACGTTAGAGAAGTAAT
1 GGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGTGAT
** * * *
28581907 GGGAAAGATTGAAGCCGCAATAGCGAATCTTGTACCATGGAGATACG-GA-
1 GGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACC-T-TAGAGACGTGAT
* * * * * * *
28581956 GGGAAAGGTTGAAGCCGTAATGGCGAACCTTATACCCTAGAGATGTGAA
1 GGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGTGAT
28582005 GGGAAAGAT
1 GGGAAAGAT
28582014 GGAGGCTGTA
Statistics
Matches: 238, Mismatches: 54, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
47 5 0.02
48 7 0.03
49 212 0.89
50 9 0.04
51 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (49 bp):
GGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGTGAT
Found at i:28582034 original size:98 final size:98
Alignment explanation
Indices: 28581652--28582013 Score: 458
Period size: 98 Copynumber: 3.7 Consensus size: 98
28581642 TAATACCCTA
* * *
28581652 GAGATATGGAGGGAAAGGTTGAAGCCACAACGGCAAACCTTGTACCTTA-AGGACGTGATGGGAA
1 GAGATATGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGA-GACGTGAAGGGAA
* * * * *
28581716 ATATTGAAGCCGTAACGACGAATCTTGTACCGTT
65 AGATTGAAGCCGCAACGGCGAATCTTGTACCATG
* * *
28581750 GAGATATGGAGAGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGACGTGATGGGAAA
1 GAGATATGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGTGAAGGGAAA
*
28581815 GATTGAAGCTGCAACGGCGAATCTTGTACCATG
66 GATTGAAGCCGCAACGGCGAATCTTGTACCATG
* * ** * *
28581848 GAGACATGGAGGGAAAGGTTAAAGCCGCAATAGCGAACCTTGTACGTTAGAGAAGT-AATGGGAA
1 GAGATATGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGTGAA-GGGAA
**
28581912 AGATTGAAGCCGCAATAGCGAATCTTGTACCATG
65 AGATTGAAGCCGCAACGGCGAATCTTGTACCATG
* * * * * *
28581946 GAGATACGGAGGGAAAGGTTGAAGCCGTAATGGCGAACCTTATACCCTAGAGATGTGAAGGGAAA
1 GAGATATGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGTGAAGGGAAA
28582011 GAT
66 GAT
28582014 GGAGGCTGTA
Statistics
Matches: 230, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
97 1 0.00
98 226 0.98
99 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (98 bp):
GAGATATGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACGTGAAGGGAAA
GATTGAAGCCGCAACGGCGAATCTTGTACCATG
Found at i:28582118 original size:42 final size:41
Alignment explanation
Indices: 28582055--28582169 Score: 117
Period size: 42 Copynumber: 2.8 Consensus size: 41
28582045 GAAGATAAGG
* *
28582055 AAAAGCAAATTAAAG-TCGTAAAGGTGAATCTC-AAGACTGTA
1 AAAAGCAAATTGAAGCT-GTAAAGGCGAATCTCAAAG-CTGTA
*
28582096 CAAAAGCATATTGAAGCTGTAAAGGCGAATCTCAAAGCTGTA
1 -AAAAGCAAATTGAAGCTGTAAAGGCGAATCTCAAAGCTGTA
** * *
28582138 AAGGGCTAGATTGAAGCTGAAAAGGCGAATCT
1 AAAAGC-AAATTGAAGCTGTAAAGGCGAATCT
28582170 TACGTCCCTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.06
42 55 0.87
43 4 0.06
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAAGCAAATTGAAGCTGTAAAGGCGAATCTCAAAGCTGTA
Found at i:28582154 original size:21 final size:20
Alignment explanation
Indices: 28582105--28582167 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
28582095 ACAAAAGCAT
28582105 ATTGAAGCTGTAAA-GGCGA
1 ATTGAAGCTGTAAAGGGCGA
* *
28582124 ATCTCAAAGCTGTAAAGGGCTA
1 AT-T-GAAGCTGTAAAGGGCGA
*
28582146 GATTGAAGCTG-AAAAGGCGA
1 -ATTGAAGCTGTAAAGGGCGA
28582166 AT
1 AT
28582168 CTTACGTCCC
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.11
20 8 0.23
21 16 0.46
22 5 0.14
23 2 0.06
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.21
Consensus pattern (20 bp):
ATTGAAGCTGTAAAGGGCGA
Found at i:28582500 original size:38 final size:38
Alignment explanation
Indices: 28582333--28583219 Score: 529
Period size: 38 Copynumber: 22.6 Consensus size: 38
28582323 CCCGATTATG
* **
28582333 GGGCAGATTGAAGACACACCAATCTCATA-CCTAAATCATG-
1 GGGCAGATTGAAG-CA-TCCAATCTTTTACCCT-AATCA-GA
* *
28582373 GGGCAGATTGAAACTGTCCAATCTTTTACCC-AGATCATG-
1 GGGCAGATTGAAGC-ATCCAATCTTTTACCCTA-ATCA-GA
* * * ** *
28582412 GGGTAGATTGAAGACATCATCCAATCTCTTGCCCCGATAATG-
1 GGGCAGATTGAAG----CATCCAATCTTTTACCCTAATCA-GA
* *
28582454 GGGCAGATTGAAGCATCCAATCTTTTACCCTTATCAAA
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* * * **
28582492 GGGTAGATTAAAGACATACCAATCTTATACCCCGATCATG-
1 GGGCAGATTGAAG-CAT-CCAATCTTTTACCCTAATCA-GA
* *
28582532 GGGCAGATTGAAGAATCCAATCTTTTACCCTAATTAGA
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* * ** *
28582570 GGGCAAATTGAAGACACACCAATCTCATA-CCTCGATCATG-
1 GGGCAGATTGAAG-CA-TCCAATCTTTTACCCT-AATCA-GA
*
28582610 GGACAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* * *
28582648 GGGCGGACTGAAGACACACCAATCTTTTACCCTAAT--GA
1 GGGCAGATTGAAG-CA-TCCAATCTTTTACCCTAATCAGA
*
28582686 AGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* *
28582724 GGGCATATTGAAGACACACCAATCTTTTACCCTAATCAGA
1 GGGCAGATTGAAG-CA-TCCAATCTTTTACCCTAATCAGA
* * * **
28582764 AGG-AAATTGAAGACACGCCAATCTCATACCCCT-ATCATG-
1 GGGCAGATTGAAG-CA-TCCAATCTTTTA-CCCTAATCA-GA
* *
28582803 GGGCAGATTAAAGCATCTAATCTTTTACCCTAATCAGA
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* * **
28582841 GGGCAGATTGAAAACATCATCTAATCTCTTACCCCGATCATGA
1 GGGCAGATTG-AAGCATC--C-AATCTTTTACCCTAATCA-GA
* * * *
28582884 -GGCAGATAGAAGCCATCATCCAATCTCTTA-CCTCGATCATA
1 GGGCAGATTGAAG----CATCCAATCTTTTACCCT-AATCAGA
* *
28582925 GGGCAAATTAAAGCATCCAATCTTTTACCCTAATCAGA
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* * * * * * *
28582963 GGGAAAACTAAAGACACGCCAAT-TTCATA-CCTCGATCATGA
1 GGGCAGATTGAAG-CA-TCCAATCTT-TTACCCT-AATCA-GA
28583004 -GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* ** **
28583041 GGGCAGATTGAAGACACACCAATCTCATACCCCGATCATG-
1 GGGCAGATTGAAG-CA-TCCAATCTTTTACCCTAATCA-GA
* *
28583081 GGGCAGATTAAAGCATCCAATATTTTACCCTAATCAGA
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
* * * * **
28583119 GGGCAGATTGAATACACACCATTCTCTTACCCCGATCATG-
1 GGGCAGATTGAA-GCA-TCCAATCTTTTACCCTAATCA-GA
* **
28583159 GGGCAGATTGAAGCATCCAATCTCTTACCCCGATCATG-
1 GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCA-GA
*
28583197 GGGCAGATTGAAGTATCCAATCT
1 GGGCAGATTGAAGCATCCAATCT
28583220 GACATCATTC
Statistics
Matches: 670, Mismatches: 120, Indels: 116
0.74 0.13 0.13
Matches are distributed among these distances:
36 18 0.03
37 12 0.02
38 248 0.37
39 105 0.16
40 193 0.29
41 10 0.01
42 76 0.11
43 4 0.01
45 4 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (38 bp):
GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
Found at i:28582550 original size:78 final size:78
Alignment explanation
Indices: 28582333--28583209 Score: 827
Period size: 78 Copynumber: 11.2 Consensus size: 78
28582323 CCCGATTATG
* *** * *
28582333 GGGCAGATTGAAGACACACCAATCTCATACCTAAATCATGGGGCAGATTGAAACTGTCCAATCTT
1 GGGCAGATTGAAGACACACCAATCTTATACCCCGATCATGGGGCAGATTGAAGC-ATCCAATCTT
28582398 TTACCC-AGATCATG-
65 TTACCCTA-ATCA-GA
* * *
28582412 GGGTAGATTGAAGACATCATCCAATCTCT-TGCCCCGATAATGGGGCAGATTGAAGCATCCAATC
1 GGGCAGATTGAAGACA-CA-CCAATCT-TATACCCCGATCATGGGGCAGATTGAAGCATCCAATC
* *
28582476 TTTTACCCTTATCAAA
63 TTTTACCCTAATCAGA
* * * *
28582492 GGGTAGATTAAAGACATACCAATCTTATACCCCGATCATGGGGCAGATTGAAGAATCCAATCTTT
1 GGGCAGATTGAAGACACACCAATCTTATACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTT
*
28582557 TACCCTAATTAGA
66 TACCCTAATCAGA
* * * *
28582570 GGGCAAATTGAAGACACACCAATCTCATACCTCGATCATGGGACAGATTGAAGCATCCAATCTTT
1 GGGCAGATTGAAGACACACCAATCTTATACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTT
28582635 TACCCTAATCAGA
66 TACCCTAATCAGA
* * * * *
28582648 GGGCGGACTGAAGACACACCAATCTTTTA-CCC--TAATGAAGGCAGATTGAAGCATCCAATCTT
1 GGGCAGATTGAAGACACACCAATCTTATACCCCGATCATG-GGGCAGATTGAAGCATCCAATCTT
28582710 TTACCCTAATCAGA
65 TTACCCTAATCAGA
* * ** * * *
28582724 GGGCATATTGAAGACACACCAATCTTTTACCCTAATCA-GAAGG-AAATTGAAGACACGCCAATC
1 GGGCAGATTGAAGACACACCAATCTTATACCCCGATCATG-GGGCAGATTGAAG-CA-TCCAATC
**
28582787 TCATACCCCT-ATCATG-
63 TTTTA-CCCTAATCA-GA
* * * * ** *
28582803 GGGCAGATTAAAG-CA-TCTAATCTTTTACCCTAATCA-GAGGGCAGATTGAAAACATCATCTAA
1 GGGCAGATTGAAGACACACCAATCTTATACCCCGATCATG-GGGCAGATTG-AAGCATC--C-AA
* **
28582865 TCTCTTACCCCGATCATGA
61 TCTTTTACCCTAATCA-GA
* * * * * *
28582884 -GGCAGATAGAAGCCATCATCCAATCTCT-TACCTCGATCATAGGGCAAATTAAAGCATCCAATC
1 GGGCAGATTGAAGACA-CA-CCAATCT-TATACCCCGATCATGGGGCAGATTGAAGCATCCAATC
28582947 TTTTACCCTAATCAGA
63 TTTTACCCTAATCAGA
* * * * * * *
28582963 GGGAAAACTAAAGACACGCCAAT-TTCATACCTCGATCATGAGGCAGATTGAAGCATCCAATCTT
1 GGGCAGATTGAAGACACACCAATCTT-ATACCCCGATCATGGGGCAGATTGAAGCATCCAATCTT
28583027 TTACCCTAATCAGA
65 TTACCCTAATCAGA
* * *
28583041 GGGCAGATTGAAGACACACCAATCTCATACCCCGATCATGGGGCAGATTAAAGCATCCAATATTT
1 GGGCAGATTGAAGACACACCAATCTTATACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTT
28583106 TACCCTAATCAGA
66 TACCCTAATCAGA
* * *
28583119 GGGCAGATTGAATACACACCATTCTCT-TACCCCGATCATGGGGCAGATTGAAGCATCCAATCTC
1 GGGCAGATTGAAGACACACCAATCT-TATACCCCGATCATGGGGCAGATTGAAGCATCCAATCTT
**
28583183 TTACCCCGATCATG-
65 TTACCCTAATCA-GA
28583197 GGGCAGATTGAAG
1 GGGCAGATTGAAG
28583210 TATCCAATCT
Statistics
Matches: 665, Mismatches: 100, Indels: 67
0.80 0.12 0.08
Matches are distributed among these distances:
75 4 0.01
76 63 0.09
77 38 0.06
78 358 0.54
79 53 0.08
80 89 0.13
81 31 0.05
83 6 0.01
84 22 0.03
85 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (78 bp):
GGGCAGATTGAAGACACACCAATCTTATACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTT
TACCCTAATCAGA
Found at i:28582832 original size:117 final size:120
Alignment explanation
Indices: 28582311--28583208 Score: 516
Period size: 116 Copynumber: 7.6 Consensus size: 120
28582301 AAGCTACCAT
* * * * * **
28582311 CCAATCTCATACCCCGATTATGGGGCAGATTGAAGACACACCAATCTCATA-CCTAAATCATG-G
1 CCAATCTCTTACCCCTATCATGGGGCAGATTAAAG-CA-TCCAATCTTTTACCCT-AATCA-GAG
* * *
28582374 GGCAGATTG-AAAC-T-GTCCAATCTTTTACCC-AGATCATG-GGGTAGATTGAAGACATCA
62 GGCAGATTGAAAACATCATCCAATCTTTTACCCTA-ATCA-GAAGGCAGATTGAAGACA-CA
* * * * * * *
28582431 TCCAATCTCTTGCCCCGATAATGGGGCAGATTGAAGCATCCAATCTTTTACCCTTATCAAAGGGT
1 -CCAATCTCTTACCCCTATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGC
* ** * *
28582496 AGATT-AAAGACAT-A-CCAATCTTATACCCCGATCATG-GGGCAGATTGAAGA-A-T
65 AGATTGAAA-ACATCATCCAATCTTTTACCCTAATCA-GAAGGCAGATTGAAGACACA
* * * * * ** *
28582548 CCAATCTTTTA-CCCTAATTA-GAGGGCAAATTGAAGACACACCAATCTCATA-CCTCGATCATG
1 CCAATCTCTTACCCCT-ATCATG-GGGCAGATTAAAG-CA-TCCAATCTTTTACCCT-AATCA-G
* * * * *
28582610 -GGACAGATTG---A-AGCATCCAATCTTTTACCCTAATCAGAGGGCGGACTGAAGACACA
60 AGGGCAGATTGAAAACATCATCCAATCTTTTACCCTAATCAGAAGGCAGATTGAAGACACA
* * *
28582666 CCAATCTTTTA-CCCTA--ATGAAGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGC
1 CCAATCTCTTACCCCTATCATG-GGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGC
* * * *
28582728 ATATTGAAGACA-CA-CCAATCTTTTACCCTAATCAGAAGG-AAATTGAAGACACG
65 AGATTGAAAACATCATCCAATCTTTTACCCTAATCAGAAGGCAGATTGAAGACACA
* *
28582781 CCAATCTCATACCCCTATCATGGGGCAGATTAAAGCATCTAATCTTTTACCCTAATCAGAGGGCA
1 CCAATCTCTTACCCCTATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
* * ** * *
28582846 GATTGAAAACATCATCTAATCTCTTACCCCGATCATG-AGGCAGATAGAAGCCATCA
66 GATTGAAAACATCATCCAATCTTTTACCCTAATCA-GAAGGCAGATTGAAGACA-CA
* * * * *
28582902 TCCAATCTCTTACCTCGATCATAGGGCAAATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGA
1 -CCAATCTCTTACCCCTATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGC
* * * * * *
28582967 AAACT-AAAGACA-C-GCCAAT-TTCATA-CCTCGATCATG-AGGCAGATTGAAG-CA-T
65 AGATTGAAA-ACATCATCCAATCTT-TTACCCT-AATCA-GAAGGCAGATTGAAGACACA
* * * ** **
28583019 CCAATCTTTTA-CCCTAATCA-GAGGGCAGATTGAAGACACACCAATCTCATACCCCGATCATG-
1 CCAATCTCTTACCCCT-ATCATG-GGGCAGATTAAAG-CA-TCCAATCTTTTACCCTAATCA-GA
* * * *
28583081 GGGCAGATT---AA-AGCATCCAATATTTTACCCTAATCAGAGGGCAGATTGAATACACA
61 GGGCAGATTGAAAACATCATCCAATCTTTTACCCTAATCAGAAGGCAGATTGAAGACACA
* * * * **
28583137 CCATTCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCCCGATCATG-GGGC
1 CCAATCTCTTACCCCTATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCA-GAGGGC
28583201 AGATTGAA
65 AGATTGAA
28583209 GTATCCAATC
Statistics
Matches: 621, Mismatches: 102, Indels: 110
0.75 0.12 0.13
Matches are distributed among these distances:
113 1 0.00
114 23 0.04
115 37 0.06
116 173 0.28
117 70 0.11
118 89 0.14
119 53 0.09
120 74 0.12
121 38 0.06
122 63 0.10
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (120 bp):
CCAATCTCTTACCCCTATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGCA
GATTGAAAACATCATCCAATCTTTTACCCTAATCAGAAGGCAGATTGAAGACACA
Found at i:28583044 original size:471 final size:471
Alignment explanation
Indices: 28582311--28583188 Score: 1230
Period size: 471 Copynumber: 1.9 Consensus size: 471
28582301 AAGCTACCAT
* *
28582311 CCAATCTCATACCCCGATTATGGGGCAGATTGAAGACACACCAATCTCATACCTAAATCATGGGG
1 CCAATCTCATACCCCGATCATGGGGCAGATTAAAGACACACCAATCTCATACCTAAATCATGGGG
* * * * *
28582376 CAGATTGAAACTGTCCAATCTTTTACCCAGATCATGGGGTAGATTGAAGACATCATCCAATCTCT
66 CAGATTGAAACTATCCAATCTCTTACCCAGATCATGAGGCAGATAGAAGACATCATCCAATCTCT
* * * * * * * *
28582441 TGCCCCGATAATGGGGCAGATTGAAGCATCCAATCTTTTACCCTTATCAAAGGGTAGATTAAAGA
131 TACCCCGATAATAGGGCAAATTAAAGCATCCAATCTTTTACCCTAATCAAAGGGAAAACTAAAGA
* * *
28582506 CATACCAATCTTATACCCCGATCATGGGGCAGATTGAAGAATCCAATCTTTTACCCTAATTAGAG
196 CACACCAATCTTATACCCCGATCATGAGGCAGATTGAAGAATCCAATCTTTTACCCTAATCAGAG
* * *
28582571 GGCAAATTGAAGACACACCAATCTCATACCTCGATCATGGGACAGATTGAAGCATCCAATCTTTT
261 GGCAAATTGAAGACACACCAATCTCATACCCCGATCATGGGACAGATTAAAGCATCCAATATTTT
* *
28582636 ACCCTAATCAGAGGGCGGACTGAAGACACACCAATCTTTTA-CCC-TAATGAAGGCAGATTGAAG
326 ACCCTAATCAGAGGGCAGACTGAAGACACACCAATCTCTTACCCCATAATG-AGGCAGATTGAAG
*
28582699 CATCCAATCTTTTACCCTAATCAGAGGGCATATTGAAGACACACCAATCTTTTACCCTAATCAGA
390 CATCCAATCTCTTACCCTAATCAGAGGGCATATTGAAGACACACCAATCTTTTACCCTAATCAGA
28582764 AGGAAATTGAAGACACG
455 AGGAAATTGAAGACACG
* * * **
28582781 CCAATCTCATACCCCTATCATGGGGCAGATTAAAG-CA-TCTAATCTTTTACCCT-AATCA-GAG
1 CCAATCTCATACCCCGATCATGGGGCAGATTAAAGACACACCAATCTCATA-CCTAAATCATG-G
* * *
28582842 GGCAGATTGAAAACATCATCTAATCTCTTACCCCGATCATGAGGCAGATAGAAGCCATCATCCAA
64 GGCAGATTG-AAAC-T-ATCCAATCTCTTACCCAGATCATGAGGCAGATAGAAGACATCATCCAA
* * *
28582907 TCTCTTACCTCGATCATAGGGCAAATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGAAAACT
126 TCTCTTACCCCGATAATAGGGCAAATTAAAGCATCCAATCTTTTACCCTAATCAAAGGGAAAACT
* * *
28582972 AAAGACACGCCAAT-TTCATACCTCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCCTAA
191 AAAGACACACCAATCTT-ATACCCCGATCATGAGGCAGATTGAAGAATCCAATCTTTTACCCTAA
* *
28583036 TCAGAGGGCAGATTGAAGACACACCAATCTCATACCCCGATCATGGGGCAGATTAAAGCATCCAA
255 TCAGAGGGCAAATTGAAGACACACCAATCTCATACCCCGATCATGGGACAGATTAAAGCATCCAA
* * * * *
28583101 TATTTTACCCTAATCAGAGGGCAGATTGAATACACACCATTCTCTTACCCCGATCATGGGGCAGA
320 TATTTTACCCTAATCAGAGGGCAGACTGAAGACACACCAATCTCTTACCCC-ATAATGAGGCAGA
28583166 TTGAAGCATCCAATCTCTTACCC
384 TTGAAGCATCCAATCTCTTACCC
28583189 CGATCATGGG
Statistics
Matches: 354, Mismatches: 45, Indels: 15
0.86 0.11 0.04
Matches are distributed among these distances:
467 1 0.00
468 23 0.06
469 9 0.03
470 35 0.10
471 251 0.71
472 3 0.01
473 28 0.08
474 4 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (471 bp):
CCAATCTCATACCCCGATCATGGGGCAGATTAAAGACACACCAATCTCATACCTAAATCATGGGG
CAGATTGAAACTATCCAATCTCTTACCCAGATCATGAGGCAGATAGAAGACATCATCCAATCTCT
TACCCCGATAATAGGGCAAATTAAAGCATCCAATCTTTTACCCTAATCAAAGGGAAAACTAAAGA
CACACCAATCTTATACCCCGATCATGAGGCAGATTGAAGAATCCAATCTTTTACCCTAATCAGAG
GGCAAATTGAAGACACACCAATCTCATACCCCGATCATGGGACAGATTAAAGCATCCAATATTTT
ACCCTAATCAGAGGGCAGACTGAAGACACACCAATCTCTTACCCCATAATGAGGCAGATTGAAGC
ATCCAATCTCTTACCCTAATCAGAGGGCATATTGAAGACACACCAATCTTTTACCCTAATCAGAA
GGAAATTGAAGACACG
Found at i:28583310 original size:46 final size:46
Alignment explanation
Indices: 28583249--28583454 Score: 349
Period size: 46 Copynumber: 4.5 Consensus size: 46
28583239 CCCTTATTAT
*
28583249 GGGGCAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGA
1 GGGGTAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGA
28583295 GGGGTAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGA
1 GGGGTAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGA
28583341 GGGGTAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGA
1 GGGGTAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGA
* * * *
28583387 GGGGTAGATTGAAGCCACAATGCAATCTTTTACCCCTAAATCAAGA
1 GGGGTAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGA
* *
28583433 GGGGCAGATTGAAGCTACCATC
1 GGGGTAGATTGAAGCCACCATC
28583455 TCATAGAAGT
Statistics
Matches: 151, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 151 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (46 bp):
GGGGTAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGA
Found at i:28583808 original size:11 final size:11
Alignment explanation
Indices: 28583771--28583813 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
28583761 GGCCTAGTAC
*
28583771 AAAATAAACCA
1 AAAATAAAACA
*
28583782 AAAACCAAAACAA
1 AAAA-TAAAAC-A
28583795 AAAATAAAACA
1 AAAATAAAACA
28583806 AAAATAAA
1 AAAATAAA
28583814 TAATAAACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 13 0.48
12 9 0.33
13 5 0.19
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAATAAAACA
Found at i:28583809 original size:18 final size:18
Alignment explanation
Indices: 28583782--28583825 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28583772 AAATAAACCA
*
28583782 AAAACCAAAACAAAAAAT
1 AAAACAAAAACAAAAAAT
* *
28583800 AAAACAAAAATAAATAAT
1 AAAACAAAAACAAAAAAT
*
28583818 AAACCAAA
1 AAAACAAA
28583826 CTGCATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (18 bp):
AAAACAAAAACAAAAAAT
Found at i:28584326 original size:13 final size:14
Alignment explanation
Indices: 28584307--28584338 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
28584297 TTTTACATAT
28584307 ATTTTATTTTTTTC
1 ATTTTATTTTTTTC
28584321 -TTTTATTTTTTTC
1 ATTTTATTTTTTTC
28584334 ATTTT
1 ATTTT
28584339 CGAAAGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTATTTTTTTC
Found at i:28587832 original size:53 final size:53
Alignment explanation
Indices: 28587747--28588060 Score: 425
Period size: 53 Copynumber: 5.9 Consensus size: 53
28587737 GGGTGTTACA
*
28587747 AATCCTATTAAGGATTAAGGGTCCGATGACTATGTGTCATCGTGAGTTATATG
1 AATCCTATTATGGATTAAGGGTCCGATGACTATGTGTCATCGTGAGTTATATG
* * * *
28587800 AATCATATTACGGATTAAGGGTTCGATGACTATGTGTCATCGTGAGTTATATC
1 AATCCTATTATGGATTAAGGGTCCGATGACTATGTGTCATCGTGAGTTATATG
* *
28587853 AATCCTATTACT-GATTAAGGGTCTGATGACTGTGTGTCATCGTGAGTTATATG
1 AATCCTATTA-TGGATTAAGGGTCCGATGACTATGTGTCATCGTGAGTTATATG
* * *
28587906 AATCCTATCATGGATTAAAGGTCCGATGACTATGTGTTATCGTGAGTTATATG
1 AATCCTATTATGGATTAAGGGTCCGATGACTATGTGTCATCGTGAGTTATATG
* * ** * *
28587959 AATCCTATTATGGATTAAGGGTCCGATAACTTTGTGTCATAATAAGATATATG
1 AATCCTATTATGGATTAAGGGTCCGATGACTATGTGTCATCGTGAGTTATATG
* * * *
28588012 AATCC-ATCATGGATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTAT
1 AATCCTATTATGGATTAAGGGTCCGATGACTATGTGTCATCGTGAGTTAT
28588061 CAAATGTGAA
Statistics
Matches: 226, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
52 36 0.16
53 190 0.84
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (53 bp):
AATCCTATTATGGATTAAGGGTCCGATGACTATGTGTCATCGTGAGTTATATG
Found at i:28595103 original size:53 final size:53
Alignment explanation
Indices: 28595041--28595395 Score: 496
Period size: 53 Copynumber: 6.7 Consensus size: 53
28595031 TTGTGCCAAA
* * * *
28595041 GATTAAAGGTCCGATGACTATGTGTCATTGTGAGTCATATGAATCCTGTTATG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCATG
* *
28595094 GATTAAAGGTTCGATGACTATGTGTCATTGTGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCATG
* * * * * * *
28595147 GATTAAAGATCCGATGACTATATGTCATCATTAGTTATATGAATCTTATTACG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCATG
* *
28595200 GATTAAGGGTCTGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCATG
*
28595253 GATTAAAGGTCCGATGGCTATGTGTCATCGTGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCATG
* * * *
28595306 GATTAAAGGTCCGATGACTATGTGTTATCATGAGATATACGAATCCT-TCATG
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCATG
* * *
28595358 GATTAAAGGTCTGATGACTCTATGTCATCGTGAGTTAT
1 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTAT
28595396 CAAATTTGAA
Statistics
Matches: 266, Mismatches: 36, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
52 37 0.14
53 229 0.86
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATCATG
Found at i:28610028 original size:45 final size:46
Alignment explanation
Indices: 28609973--28610061 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
28609963 AAACTAGAAG
** *
28609973 ATAATAAG-AAAAGGAAAACACATAGATGTTTGCAAAACTGAGATA
1 ATAATAAGAAAAAAAAAAACACATAGATGTTTGCAAAACAGAGATA
*
28610018 ATAATAAGAAAAAAAAAAATACATAGATGTTTGCAAAACAGAGA
1 ATAATAAGAAAAAAAAAAACACATAGATGTTTGCAAAACAGAGA
28610062 AGAACATAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 8 0.21
46 31 0.79
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (46 bp):
ATAATAAGAAAAAAAAAAACACATAGATGTTTGCAAAACAGAGATA
Found at i:28611824 original size:129 final size:130
Alignment explanation
Indices: 28611593--28611842 Score: 355
Period size: 129 Copynumber: 1.9 Consensus size: 130
28611583 AGGAGTCCTC
* *
28611593 AATTCAAGTCAAATATAAACCATTAAATTAAAATAAAAACAAGAATCTTAAGTGCCTGTTCAATG
1 AATTCAAGTAAAATATAAACCATTAAATTAAAATAAAAACAACAATCTTAAGTGCCTGTTCAATG
*
28611658 AATGGCTTCAGTGGTTAGGGAATTCATTCTCACCTCA-TTCTCCCAACACTAGAGTCATGCAACA
66 AATGGCTTCAGTGGTTAGGGAATTCATTCTCACCTCATTTCCCCCAACACTAGAGTCATGCAACA
* * * *
28611722 AATTCAAGTAAAATATAAA-CAGTTAAATTAAGATGGAAAACAACAGTC-TAAGTGCCTGTTCAG
1 AATTCAAGTAAAATATAAACCA-TTAAATTAAAAT-AAAAACAACAATCTTAAGTGCCTGTTCAA
* * *
28611785 TGAATGGCTTCAGT-GTATTGGGAATTCATTCTCATCTCATTTCCCCCGACACTAGAGT
64 TGAATGGCTTCAGTGGT-TAGGGAATTCATTCTCACCTCATTTCCCCCAACACTAGAGT
28611843 TATAAAACAG
Statistics
Matches: 107, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
128 4 0.04
129 77 0.72
130 26 0.24
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (130 bp):
AATTCAAGTAAAATATAAACCATTAAATTAAAATAAAAACAACAATCTTAAGTGCCTGTTCAATG
AATGGCTTCAGTGGTTAGGGAATTCATTCTCACCTCATTTCCCCCAACACTAGAGTCATGCAACA
Found at i:28615134 original size:2 final size:2
Alignment explanation
Indices: 28615124--28615156 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28615114 TTTTTAAAAT
*
28615124 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28615157 GAAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28616932 original size:16 final size:16
Alignment explanation
Indices: 28616911--28616941 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28616901 ATTCGACTCA
28616911 TAAATATTAAATAATG
1 TAAATATTAAATAATG
28616927 TAAATATTAAATAAT
1 TAAATATTAAATAAT
28616942 AATATTTACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TAAATATTAAATAATG
Found at i:28618201 original size:21 final size:21
Alignment explanation
Indices: 28618162--28618201 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28618152 TCTAAAATCA
*
28618162 AAAACCCTAAACTCAAATATT
1 AAAACCCTAAACCCAAATATT
* *
28618183 AAAAGCCTAAACCCTAATA
1 AAAACCCTAAACCCAAATA
28618202 AAGTTAACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAACCCTAAACCCAAATATT
Done.