Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 9 of 167
Found at i:2805600 original size:16 final size:16
Alignment explanation
Indices: 2805579--2805609 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2805569 TCTGTGCTTG
2805579 TAACTGATCAAAGTTT
1 TAACTGATCAAAGTTT
*
2805595 TAACTGCTCAAAGTT
1 TAACTGATCAAAGTT
2805610 CACAACTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (16 bp):
TAACTGATCAAAGTTT
Found at i:2807541 original size:27 final size:26
Alignment explanation
Indices: 2807497--2807550 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
2807487 GGAAAAATTA
* * *
2807497 GTAGAACTAGAAAAAGAAGAGAATTTT
1 GTAGAAATACAAAAAGAA-AGAAGTTT
*
2807524 GTAGAAATACAAATAGAAAGAAGTTT
1 GTAGAAATACAAAAAGAAAGAAGTTT
2807550 G
1 G
2807551 ATTTAAAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (26 bp):
GTAGAAATACAAAAAGAAAGAAGTTT
Found at i:2809370 original size:30 final size:30
Alignment explanation
Indices: 2809334--2809395 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2809324 GAAAATAGGG
2809334 TAAGTTTTGTGATGAAATGAATTATGATAC
1 TAAGTTTTGTGATGAAATGAATTATGATAC
2809364 TAAGTTTTGTGATGAAATGAATTATGATAC
1 TAAGTTTTGTGATGAAATGAATTATGATAC
2809394 TA
1 TA
2809396 TGGTAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.40
Consensus pattern (30 bp):
TAAGTTTTGTGATGAAATGAATTATGATAC
Found at i:2812437 original size:29 final size:29
Alignment explanation
Indices: 2812403--2812468 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
2812393 TTTTCCTGGT
*
2812403 GGACTTCCATGATCGGGCCAATCCTTAGC
1 GGACTTCCATGATCGGGCCAATCCTCAGC
* * *
2812432 GGACTTTCATGATGGGGCCAATCCTCAGT
1 GGACTTCCATGATCGGGCCAATCCTCAGC
2812461 GGACTTCC
1 GGACTTCC
2812469 TTTTTCCATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.20, C:0.29, G:0.26, T:0.26
Consensus pattern (29 bp):
GGACTTCCATGATCGGGCCAATCCTCAGC
Found at i:2814357 original size:52 final size:51
Alignment explanation
Indices: 2814278--2814412 Score: 129
Period size: 47 Copynumber: 2.7 Consensus size: 51
2814268 TGTGCTCCAT
* * *
2814278 TATAAGACCATAGCT-AGACTATAGCATCAGTGTGATGAGATAT-TGTTTTCCG
1 TATAAGACCATATCTGAGA-TATGGCATCAGTGTGAT-AGATATGTG-CTTCCG
* * *
2814330 TATAAGACCATATCTGGGATATGGCATC-G-GT--TATATATGTGCTTCTG
1 TATAAGACCATATCTGAGATATGGCATCAGTGTGATAGATATGTGCTTCCG
* *
2814377 TGTAAGACCATATCTGAGATATGACATCAGTGTGAT
1 TATAAGACCATATCTGAGATATGGCATCAGTGTGAT
2814413 TTTTGACCAT
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
47 34 0.50
48 4 0.06
49 2 0.03
50 2 0.03
51 2 0.03
52 22 0.32
53 2 0.03
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (51 bp):
TATAAGACCATATCTGAGATATGGCATCAGTGTGATAGATATGTGCTTCCG
Found at i:2815248 original size:13 final size:13
Alignment explanation
Indices: 2815230--2815255 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2815220 AAGTAATCGA
2815230 ACACGGGCGTGTC
1 ACACGGGCGTGTC
2815243 ACACGGGCGTGTC
1 ACACGGGCGTGTC
2815256 CCTGCCGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:2825818 original size:54 final size:54
Alignment explanation
Indices: 2825759--2825861 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
2825749 CCAAATTGCA
*
2825759 AAAAACAATCATAATTTGGCCCTTATACATTAACCCTTAAATTTTTCATAATAT
1 AAAAACAATCATAATTTGGCCCTTATACATTAACCCTTAAATTTATCATAATAT
2825813 AAAAACAATCATAATTTGGCCCTTATACATTAACCCTTAAATTTATCAT
1 AAAAACAATCATAATTTGGCCCTTATACATTAACCCTTAAATTTATCAT
2825862 TTTATGCAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (54 bp):
AAAAACAATCATAATTTGGCCCTTATACATTAACCCTTAAATTTATCATAATAT
Found at i:2828923 original size:5 final size:6
Alignment explanation
Indices: 2828896--2828920 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2828886 ATTTCTCCCC
2828896 TTCTTT TTCTTT TTCTTT TTCTTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT T
2828921 CTTCCTAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:2832198 original size:21 final size:21
Alignment explanation
Indices: 2832172--2832214 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2832162 GAGTCCTAAA
2832172 AAGTGAATTCAAAATTTTAAG
1 AAGTGAATTCAAAATTTTAAG
*
2832193 AAGTGAATTCAACATTTTAAG
1 AAGTGAATTCAAAATTTTAAG
2832214 A
1 A
2832215 TAAATATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
AAGTGAATTCAAAATTTTAAG
Found at i:2834982 original size:51 final size:51
Alignment explanation
Indices: 2834900--2835013 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 51
2834890 CTGTCTCTGT
* * * * *
2834900 TGTCACGACACCACAAGTTAGTGTCGCGACATTGGAGTATTCTACTCTCAG
1 TGTCATGACACCAAAAGTTAGTATCACGACATTGGAGTATTCTACCCTCAG
* *
2834951 TGTCGTGACACCAAAAGTTAGTATCATGACATTGGAGTATTCTACCCTCAG
1 TGTCATGACACCAAAAGTTAGTATCACGACATTGGAGTATTCTACCCTCAG
2835002 TGTCATGACACC
1 TGTCATGACACC
2835014 CATTTTCCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (51 bp):
TGTCATGACACCAAAAGTTAGTATCACGACATTGGAGTATTCTACCCTCAG
Found at i:2838272 original size:24 final size:24
Alignment explanation
Indices: 2838240--2838296 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2838230 TCTAAAATAG
*
2838240 ATAATATATAAAATAGTTTTAAACAA
1 ATAATATAT-AAATA-TTTGAAACAA
* *
2838266 ATAATATATATATATTTGAAATAA
1 ATAATATATAAATATTTGAAACAA
2838290 ATAATAT
1 ATAATAT
2838297 GTGAAAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 15 0.54
25 4 0.14
26 9 0.32
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (24 bp):
ATAATATATAAATATTTGAAACAA
Found at i:2839250 original size:15 final size:15
Alignment explanation
Indices: 2839232--2839261 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2839222 ATAGATTTAT
*
2839232 AATAAAACATAAAAA
1 AATAAAAAATAAAAA
2839247 AATAAAAAATAAAAA
1 AATAAAAAATAAAAA
2839262 GGAAATCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AATAAAAAATAAAAA
Found at i:2841502 original size:25 final size:23
Alignment explanation
Indices: 2841468--2841532 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
2841458 GTGTTCAGAA
*
2841468 TTTTAAAATTATTATTATTATATAT
1 TTTTAGAATTATTATTATTA-A-AT
2841493 TTTTAGAATTATT-TTA-TAAAT
1 TTTTAGAATTATTATTATTAAAT
*
2841514 TGTTTAGAATTATCATTAT
1 T-TTTAGAATTATTATTAT
2841533 AGTTCAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 3 0.09
22 12 0.34
23 5 0.14
24 3 0.09
25 12 0.34
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTAGAATTATTATTATTAAAT
Found at i:2841519 original size:22 final size:22
Alignment explanation
Indices: 2841478--2841533 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
2841468 TTTTAAAATT
*
2841478 ATTATTATTATATATTTTTAGA
1 ATTATTATTATAAATTTTTAGA
2841500 ATTATT-TTATAAATTGTTTAGA
1 ATTATTATTATAAATT-TTTAGA
*
2841522 ATTATCATTATA
1 ATTATTATTATA
2841534 GTTCAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 8 0.27
22 17 0.57
23 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTATTATTATAAATTTTTAGA
Found at i:2855869 original size:52 final size:52
Alignment explanation
Indices: 2855787--2855943 Score: 296
Period size: 52 Copynumber: 3.0 Consensus size: 52
2855777 GAACCTCCTA
*
2855787 TTTCGTATGGCAAAGGTGATTGATCATAACAACAGAGGAAAGCCAAAGCAAC
1 TTTCGTATGGCAAAGGTGATTGATCGTAACAACAGAGGAAAGCCAAAGCAAC
*
2855839 TTTCGTATGGCAAAGGTGATTGATCGTAACAACAAAGGAAAGCCAAAGCAAC
1 TTTCGTATGGCAAAGGTGATTGATCGTAACAACAGAGGAAAGCCAAAGCAAC
2855891 TTTCGTATGGCAAAGGTGATTGATCGTAACAACAGAGGAAAGCCAAAGCAAC
1 TTTCGTATGGCAAAGGTGATTGATCGTAACAACAGAGGAAAGCCAAAGCAAC
2855943 T
1 T
2855944 ATGTAACAAC
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 102 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (52 bp):
TTTCGTATGGCAAAGGTGATTGATCGTAACAACAGAGGAAAGCCAAAGCAAC
Found at i:2857500 original size:35 final size:35
Alignment explanation
Indices: 2857454--2857525 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
2857444 GGTATGTGTT
2857454 TGGGATGATTTTATGCGGGTAAGATTGTGCAATTA
1 TGGGATGATTTTATGCGGGTAAGATTGTGCAATTA
2857489 TGGGATGATTTTATGCGGGTAAGATTGTGCAATTA
1 TGGGATGATTTTATGCGGGTAAGATTGTGCAATTA
2857524 TG
1 TG
2857526 CACCAAACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.25, C:0.06, G:0.32, T:0.38
Consensus pattern (35 bp):
TGGGATGATTTTATGCGGGTAAGATTGTGCAATTA
Found at i:2860709 original size:15 final size:15
Alignment explanation
Indices: 2860689--2860718 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2860679 ACAAAAGAAT
2860689 TAGTCACTATTGTCG
1 TAGTCACTATTGTCG
2860704 TAGTCACTATTGTCG
1 TAGTCACTATTGTCG
2860719 CTATGGATAC
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:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
TAGTCACTATTGTCG
Found at i:2864194 original size:16 final size:16
Alignment explanation
Indices: 2864173--2864203 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2864163 TGAAGCTTTG
2864173 ATAGTTAATATAAATT
1 ATAGTTAATATAAATT
*
2864189 ATAGTTAATGTAAAT
1 ATAGTTAATATAAAT
2864204 CCTAATCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
ATAGTTAATATAAATT
Found at i:2866293 original size:30 final size:30
Alignment explanation
Indices: 2866253--2866311 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2866243 AATTCAATTG
**
2866253 AATTAATCTATATATGAATGTAACGACATC
1 AATTAATCTATATATGAAAATAACGACATC
* *
2866283 AATTAGTCTATGTATGAAAATAACGACAT
1 AATTAATCTATATATGAAAATAACGACAT
2866312 TATGGTGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (30 bp):
AATTAATCTATATATGAAAATAACGACATC
Found at i:2866591 original size:16 final size:16
Alignment explanation
Indices: 2866546--2866585 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2866536 ATATTCTTAT
* *
2866546 ATATAAGTTCGAAATG
1 ATATAAATTAGAAATG
2866562 ATATAAATTAGAAATG
1 ATATAAATTAGAAATG
*
2866578 ATTTAAAT
1 ATATAAAT
2866586 CTGAAAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (16 bp):
ATATAAATTAGAAATG
Found at i:2873710 original size:14 final size:15
Alignment explanation
Indices: 2873688--2873764 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2873678 CAATCAAACA
2873688 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
2873702 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
2873717 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
2873737 CCA-AAAATCATTTT
1 CCAGAAAATCATTTT
* *
2873751 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
2873765 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.40
15 16 0.32
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:2873748 original size:34 final size:35
Alignment explanation
Indices: 2873692--2873758 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2873682 CAAACACCAG
* *
2873692 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
*
2873727 AAAACATTTTCCA-AAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
2873759 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
Found at i:2880663 original size:21 final size:21
Alignment explanation
Indices: 2880638--2880706 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
2880628 TATAATGATT
2880638 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
2880659 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
2880679 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
2880699 ATTATTAT
1 ATTATTAT
2880707 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:2880719 original size:15 final size:14
Alignment explanation
Indices: 2880693--2880723 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2880683 TATGGTTTTA
2880693 TATTAGATTATTAT
1 TATTAGATTATTAT
2880707 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
2880722 TA
1 TA
2880724 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:2881062 original size:14 final size:14
Alignment explanation
Indices: 2881038--2881070 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2881028 AAGAATTAAG
2881038 GAAACAAAGAAACA
1 GAAACAAAGAAACA
2881052 -AAACAAAAGAAACA
1 GAAAC-AAAGAAACA
2881066 GAAAC
1 GAAAC
2881071 GAAGCAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 9 0.53
15 4 0.24
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (14 bp):
GAAACAAAGAAACA
Found at i:2884085 original size:24 final size:24
Alignment explanation
Indices: 2884058--2884141 Score: 62
Period size: 24 Copynumber: 3.4 Consensus size: 24
2884048 CGGGCTATAA
* *
2884058 CGGGAAGCTCA-ATAGAGCCGAAAT
1 CGGGAAGCTCACAAAGAACC-AAAT
* * *
2884082 CGGGTAGTTCACAAAGAACCATAT
1 CGGGAAGCTCACAAAGAACCAAAT
* *
2884106 CGGGAAGCTCACGAAGAGCCATATAT
1 CGGGAAGCTCACAAAGAACCA-A-AT
*
2884132 CGGGACGCTC
1 CGGGAAGCTC
2884142 TTAAGAGCTA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
24 29 0.63
25 6 0.13
26 11 0.24
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.15
Consensus pattern (24 bp):
CGGGAAGCTCACAAAGAACCAAAT
Found at i:2884213 original size:23 final size:22
Alignment explanation
Indices: 2884187--2884246 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 22
2884177 TACAATCTAT
*
2884187 CGGGACGCTCCGAAGAGCTATAA
1 CGGGAAGCT-CGAAGAGCTATAA
*
2884210 CGGGAAGCTCGCAAGAACCATATAA
1 CGGGAAGCTCG-AAG-AGC-TATAA
2884235 CGGGAAGCTCGA
1 CGGGAAGCTCGA
2884247 GAGGGCTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 2 0.06
23 11 0.34
24 3 0.09
25 16 0.50
ACGTcount: A:0.33, C:0.25, G:0.30, T:0.12
Consensus pattern (22 bp):
CGGGAAGCTCGAAGAGCTATAA
Found at i:2885711 original size:153 final size:153
Alignment explanation
Indices: 2885433--2885744 Score: 606
Period size: 153 Copynumber: 2.0 Consensus size: 153
2885423 TTAATTATCT
2885433 CCTTGTACATAATTCAAATGATGTTTCCGTTTGTTTATATTGAAGATAGACTCATTAAAGATTCT
1 CCTTGTACATAATTCAAATGATGTTTCCGTTTGTTTATATTGAAGATAGACTCATTAAAGATTCT
2885498 AAAAATATAAATTTAAGCCCATAATTATTTTTATCCAATTTTTTATGATTTTAAAAAGTCAGAAT
66 AAAAATATAAATTTAAGCCCATAATTATTTTTATCCAATTTTTTATGATTTTAAAAAGTCAGAAT
2885563 AGGGGAACCAGAAATCATTCTGA
131 AGGGGAACCAGAAATCATTCTGA
* *
2885586 CCTTGTACATAATTCAAATGATGTTTCCGTTTGTTTATATTGAAGATAGACTCATTCAGGATTCT
1 CCTTGTACATAATTCAAATGATGTTTCCGTTTGTTTATATTGAAGATAGACTCATTAAAGATTCT
2885651 AAAAATATAAATTTAAGCCCATAATTATTTTTATCCAATTTTTTATGATTTTAAAAAGTCAGAAT
66 AAAAATATAAATTTAAGCCCATAATTATTTTTATCCAATTTTTTATGATTTTAAAAAGTCAGAAT
2885716 AGGGGAACCAGAAATCATTCTGA
131 AGGGGAACCAGAAATCATTCTGA
2885739 CCTTGT
1 CCTTGT
2885745 CTCACAAAAT
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 157 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (153 bp):
CCTTGTACATAATTCAAATGATGTTTCCGTTTGTTTATATTGAAGATAGACTCATTAAAGATTCT
AAAAATATAAATTTAAGCCCATAATTATTTTTATCCAATTTTTTATGATTTTAAAAAGTCAGAAT
AGGGGAACCAGAAATCATTCTGA
Found at i:2885890 original size:18 final size:18
Alignment explanation
Indices: 2885867--2885904 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2885857 CTATTTCTAA
*
2885867 AATTTTTGGTGATTTTTC
1 AATTTTTGATGATTTTTC
2885885 AATTTTTGATGATTTTTC
1 AATTTTTGATGATTTTTC
2885903 AA
1 AA
2885905 AGTTAGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58
Consensus pattern (18 bp):
AATTTTTGATGATTTTTC
Found at i:2886459 original size:18 final size:20
Alignment explanation
Indices: 2886444--2886480 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2886434 TAATAATAAA
*
2886444 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
2886464 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
2886481 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:2895166 original size:30 final size:30
Alignment explanation
Indices: 2895105--2895168 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
2895095 AACATATGTC
* *
2895105 TTTATAATTTTTAAAAGATTAAATTAAAAT
1 TTTATAATTTTTAAAAGATAAAAGTAAAAT
* * **
2895135 TTTATCATTTTTAAAAGGTAAAAGTGTAAT
1 TTTATAATTTTTAAAAGATAAAAGTAAAAT
2895165 TTTA
1 TTTA
2895169 ATTTTATAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (30 bp):
TTTATAATTTTTAAAAGATAAAAGTAAAAT
Found at i:2899582 original size:21 final size:21
Alignment explanation
Indices: 2899558--2899600 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2899548 GAGTCGATGG
*
2899558 GTGA-TATGAAGTCAGCTCTCT
1 GTGATTATGAAG-CAGCACTCT
*
2899579 GTGATTGTGAAGCAGCACTCT
1 GTGATTATGAAGCAGCACTCT
2899600 G
1 G
2899601 CTTGGAACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGATTATGAAGCAGCACTCT
Found at i:2902066 original size:22 final size:23
Alignment explanation
Indices: 2902019--2902067 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
2902009 TTTTTATTTT
2902019 AAATATTTATTTTTAGATATCATA
1 AAATATTTATTTTTA-ATATCATA
*
2902043 AAATATTTATTTTT-ATATCCTA
1 AAATATTTATTTTTAATATCATA
2902065 AAA
1 AAA
2902068 AGGAATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.42
24 14 0.58
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATATTTATTTTTAATATCATA
Found at i:2910843 original size:18 final size:17
Alignment explanation
Indices: 2910801--2910843 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2910791 TTTCCAAGTT
*
2910801 TGTAATGTTTTATATTA
1 TGTAATTTTTTATATTA
* *
2910818 TATTATTTTTATATATTA
1 TGTAATTTTT-TATATTA
2910836 TGTAATTT
1 TGTAATTT
2910844 ATAATATATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (17 bp):
TGTAATTTTTTATATTA
Found at i:2912341 original size:14 final size:14
Alignment explanation
Indices: 2912324--2912362 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2912314 TATTTTTCGA
2912324 AAAATAATTTCTGG
1 AAAATAATTTCTGG
*
2912338 AAAATAATTTTTTGG
1 AAAATAA-TTTCTGG
*
2912353 AAAATGATTT
1 AAAATAATTT
2912363 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (14 bp):
AAAATAATTTCTGG
Found at i:2912353 original size:15 final size:15
Alignment explanation
Indices: 2912310--2912362 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 15
2912300 GTTTGCAGGT
* *
2912310 AAAAT-ATTTTTCGA
1 AAAATAATTTTTTGG
*
2912324 AAAATAA-TTTCTGG
1 AAAATAATTTTTTGG
2912338 AAAATAATTTTTTGG
1 AAAATAATTTTTTGG
*
2912353 AAAATGATTT
1 AAAATAATTT
2912363 ACTTTTCTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (15 bp):
AAAATAATTTTTTGG
Found at i:2914528 original size:742 final size:743
Alignment explanation
Indices: 2913048--2914534 Score: 2805
Period size: 742 Copynumber: 2.0 Consensus size: 743
2913038 GTAAATTGTT
2913048 CCAAAGCATTAGCAATTTTGCCAAGTTGTTCACCCACAAATTTAATTTGTTCATCAACGACACTT
1 CCAAAGCATTAGCAATTTTGCCAAGTTGTTCACCCACAAATTTAATTTGTTCAT--ACGACACTT
2913113 TCTTGAGCCTTTTTTCTTTTACGTTTGGATGTGCCAGATGAAGATACATTTGTTCTTACCTCTTC
64 TCTTGAGCCTTTTTTCTTTTACGTTTGGATGTGCCAGATGAAGATACATTTGTTCTTACCTCTTC
*
2913178 AGTCGCTTCATTCTCGCAGTCTATAGGCACTGAATCTATGTTATCATCATCCAAATCTATGTCAG
129 AGTCGCTTCATTCTCACAGTCTATAGGCACTGAATCTATGTTATCATCATCCAAATCTATGTCAG
2913243 CAAATGTTCTGGCAAAACTCCCTGTTGCCATATCTTTGCCAACAACCAAAGCCATTTCATCATAA
194 CAAATGTTCTGGCAAAACTCCCTGTTGCCATATCTTTGCCAACAACCAAAGCCATTTCATCATAA
* *
2913308 TGATCAATGCTTTTATTCAAAAATGGTTCATACTTCTTGTGTGCCTGTTGGATATTATACACAAT
259 TGATCAATGCTTTTATTCAAAAATGGCTCATACTTCTTGTGTGCCTGTTGGATATTATACAAAAT
2913373 TAGAATAACAAGTAAAAAACAATTGAAATATACTTAACATATATATACATATATTACCATCACTG
324 TAGAATAACAAGTAAAAAACAATTGAAATATACTTAACATATATATACATATATTACCATCACTG
*
2913438 TTGCATCATATGTCGCTCTATCACATGTGATCATTTTCATGTTATCATCCCATCCAAAACCACTT
389 CTGCATCATATGTCGCTCTATCACATGTGATCATTTTCATGTTATCATCCCATCCAAAACCACTT
*
2913503 TCACCCCGAATTGTGCATATAATCTGCCACTGTTTTTTTACAGTCCTCAAATGATTTTCCACATG
454 TCACCCCGAATTGTACATATAATCTGCCACTGTTTTTTTACAGTCCTCAAATGATTTTCCACATG
2913568 TTTTGCATCGCATTGGACTTGAAATTTTTCAGAAATAGCTTCGACAACTCGATTAATAGAAACTG
519 TTTTGCATCGCATTGGACTTGAAATTTTTCAGAAATAGCTTCGACAACTCGATTAATAGAAACTG
*
2913633 CTTTGAAAGTATTAGAAGGCTTATTTCCTTTCTGGGCCTCCTCTGCTAAAATTTCAAGAAAAAGA
584 CTTTGAAAGTATTAGAAGGCTTATTTCCTTTCTGGGCCTACTCTGCTAAAATTTCAAGAAAAAGA
2913698 TGTTCCATCGGTTTTGTCCACCTGAATTGCTTGGAGGTCTCTTCTTTGTTGCCCTTACCCATTCT
649 TGTTCCATCGGTTTTGTCCACCTGAATTGCTTGGAGGTCTCTTCTTTGTTGCCCTTACCCATTCT
2913763 ACGTCAATAATTGTCATTGTCAATCATTTC
714 ACGTCAATAATTGTCATTGTCAATCATTTC
*
2913793 CCAAAGCATTAGCAATTTTGCCAAGTTGTTCACCTACAAATTTAATTTGTTCAT-CGACACTTTC
1 CCAAAGCATTAGCAATTTTGCCAAGTTGTTCACCCACAAATTTAATTTGTTCATACGACACTTTC
* *
2913857 TTGAGCCTTTTTTCTTTTACGTTTGTATGTGCCAGATGAAGATACATTTGTTCTTACTTCTTCAG
66 TTGAGCCTTTTTTCTTTTACGTTTGGATGTGCCAGATGAAGATACATTTGTTCTTACCTCTTCAG
*
2913922 TCGCTTCATTCTCACAGTCTATAGGCACTGAATCTATGTTATCATTATCCAAATCTATGTCAGCA
131 TCGCTTCATTCTCACAGTCTATAGGCACTGAATCTATGTTATCATCATCCAAATCTATGTCAGCA
2913987 AATGTTCTGGCAAAACTCCCTGTTGCCATATCTTTGCCAACAACCAAAGCCATTTCATCATAATG
196 AATGTTCTGGCAAAACTCCCTGTTGCCATATCTTTGCCAACAACCAAAGCCATTTCATCATAATG
2914052 ATCAATGCTTTTATTCAAAAATGGCTCATACTTCTTGTGTGCCTGTTGGATATTATACAAAATTA
261 ATCAATGCTTTTATTCAAAAATGGCTCATACTTCTTGTGTGCCTGTTGGATATTATACAAAATTA
* *
2914117 GAATAACAAGTAAAAAATAATTGAAATATACTTAACATATATATACATATATTACCATTACTGCT
326 GAATAACAAGTAAAAAACAATTGAAATATACTTAACATATATATACATATATTACCATCACTGCT
*
2914182 GCATCATATGTCGCTCTATCGCATGTGATCATTTTCATGTTATCATCCCATCCAAAACCACTTTC
391 GCATCATATGTCGCTCTATCACATGTGATCATTTTCATGTTATCATCCCATCCAAAACCACTTTC
*
2914247 ACCCCGAATTGTACATATAATCTGTCACTGTTTTTTTACAGTCCTCAAATGATTTTCCACATGTT
456 ACCCCGAATTGTACATATAATCTGCCACTGTTTTTTTACAGTCCTCAAATGATTTTCCACATGTT
*
2914312 TTGCATCGCATTGGACTTGAAATTTTTCAGAAATAGCTTTGACAACTCGATTAATAGAAACTGCT
521 TTGCATCGCATTGGACTTGAAATTTTTCAGAAATAGCTTCGACAACTCGATTAATAGAAACTGCT
*
2914377 TTGAAAGTATTAGAAGGCTTATTTCTTTTCTGGGCCTACTCTGCTAAAATTTCAAGAAAAAGATG
586 TTGAAAGTATTAGAAGGCTTATTTCCTTTCTGGGCCTACTCTGCTAAAATTTCAAGAAAAAGATG
2914442 TTCCATCGGTTTTGTCCACCTGAATTGCTTGGAGGTCTCTTCTTTGTTGCCCTTACCCATTCTAC
651 TTCCATCGGTTTTGTCCACCTGAATTGCTTGGAGGTCTCTTCTTTGTTGCCCTTACCCATTCTAC
2914507 GTCAATAATTGTCATTGTCAATCATTTC
716 GTCAATAATTGTCATTGTCAATCATTTC
2914535 TGTAACGCCC
Statistics
Matches: 726, Mismatches: 16, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
742 673 0.93
745 53 0.07
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (743 bp):
CCAAAGCATTAGCAATTTTGCCAAGTTGTTCACCCACAAATTTAATTTGTTCATACGACACTTTC
TTGAGCCTTTTTTCTTTTACGTTTGGATGTGCCAGATGAAGATACATTTGTTCTTACCTCTTCAG
TCGCTTCATTCTCACAGTCTATAGGCACTGAATCTATGTTATCATCATCCAAATCTATGTCAGCA
AATGTTCTGGCAAAACTCCCTGTTGCCATATCTTTGCCAACAACCAAAGCCATTTCATCATAATG
ATCAATGCTTTTATTCAAAAATGGCTCATACTTCTTGTGTGCCTGTTGGATATTATACAAAATTA
GAATAACAAGTAAAAAACAATTGAAATATACTTAACATATATATACATATATTACCATCACTGCT
GCATCATATGTCGCTCTATCACATGTGATCATTTTCATGTTATCATCCCATCCAAAACCACTTTC
ACCCCGAATTGTACATATAATCTGCCACTGTTTTTTTACAGTCCTCAAATGATTTTCCACATGTT
TTGCATCGCATTGGACTTGAAATTTTTCAGAAATAGCTTCGACAACTCGATTAATAGAAACTGCT
TTGAAAGTATTAGAAGGCTTATTTCCTTTCTGGGCCTACTCTGCTAAAATTTCAAGAAAAAGATG
TTCCATCGGTTTTGTCCACCTGAATTGCTTGGAGGTCTCTTCTTTGTTGCCCTTACCCATTCTAC
GTCAATAATTGTCATTGTCAATCATTTC
Found at i:2916784 original size:12 final size:12
Alignment explanation
Indices: 2916767--2916792 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2916757 ATGAAAGTTT
2916767 CTCAAGCAATGA
1 CTCAAGCAATGA
2916779 CTCAAGCAATGA
1 CTCAAGCAATGA
2916791 CT
1 CT
2916793 AAAGTTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.19
Consensus pattern (12 bp):
CTCAAGCAATGA
Found at i:2917831 original size:13 final size:11
Alignment explanation
Indices: 2917800--2917829 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2917790 ATTTACTTTT
2917800 AAATATATCAA
1 AAATATATCAA
2917811 AAATATATCAA
1 AAATATATCAA
2917822 AAATATAT
1 AAATATAT
2917830 ATATAGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATATATCAA
Found at i:2918586 original size:64 final size:64
Alignment explanation
Indices: 2918511--2918638 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
2918501 GTGAGATGAT
*
2918511 TGAGAAGAAAGTGACAGAAGCCAAGCAAGTTTGTGAAGGAGATGAGACATCTGATGAATGCAAA
1 TGAGAAAAAAGTGACAGAAGCCAAGCAAGTTTGTGAAGGAGATGAGACATCTGATGAATGCAAA
2918575 TGAGAAAAAAGTGACAGAAGCCAAGCAAGTTTGTGAAGGAGATGAGACATCTGATGAATGCAAA
1 TGAGAAAAAAGTGACAGAAGCCAAGCAAGTTTGTGAAGGAGATGAGACATCTGATGAATGCAAA
2918639 GTAGCTTGGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (64 bp):
TGAGAAAAAAGTGACAGAAGCCAAGCAAGTTTGTGAAGGAGATGAGACATCTGATGAATGCAAA
Found at i:2928792 original size:6 final size:6
Alignment explanation
Indices: 2928781--2928815 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2928771 CACAAGCAGA
2928781 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
2928816 CATCAGTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:2937112 original size:12 final size:12
Alignment explanation
Indices: 2937095--2937127 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2937085 TAGCCCGCCC
2937095 ATATTAATTTTT
1 ATATTAATTTTT
2937107 ATATT-ATTTTT
1 ATATTAATTTTT
2937118 ATA-TAATTTT
1 ATATTAATTTT
2937128 AAAAGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:2937339 original size:22 final size:22
Alignment explanation
Indices: 2937314--2937356 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2937304 TATCCAAACA
*
2937314 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAACAGTAGCAAC
* *
2937336 ATAATAGCAAAACAGTAGCAA
1 ATAACAACAAAACAGTAGCAA
2937357 AACAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.14
Consensus pattern (22 bp):
ATAACAACAAAACAGTAGCAAC
Found at i:2940936 original size:18 final size:18
Alignment explanation
Indices: 2940882--2940953 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
2940872 TATACACTTG
*
2940882 TATTAT-AATTAAA-AAA
1 TATTATAAATTAAATAAT
*
2940898 TATTTATTAATTAAATAAT
1 TA-TTATAAATTAAATAAT
* *
2940917 TATTATAAATTATATTAT
1 TATTATAAATTAAATAAT
*
2940935 TATAATATAAAGTAAATAA
1 TAT--TATAAATTAAATAA
2940954 ATAAAAATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
16 2 0.05
17 4 0.09
18 23 0.52
19 4 0.09
20 11 0.25
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (18 bp):
TATTATAAATTAAATAAT
Found at i:2941845 original size:21 final size:21
Alignment explanation
Indices: 2941819--2941869 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2941809 GGCTTTGCCG
2941819 ATCAGGCACTATATGTGTCAT
1 ATCAGGCACTATATGTGTCAT
* * **
2941840 ATCAGGTACTGTATGTGTTGT
1 ATCAGGCACTATATGTGTCAT
2941861 ATCAGGCAC
1 ATCAGGCAC
2941870 CTCGTGTGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (21 bp):
ATCAGGCACTATATGTGTCAT
Found at i:2943302 original size:46 final size:46
Alignment explanation
Indices: 2943251--2943344 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
2943241 AATAGGCTTC
*
2943251 TCAAATATGGTTGATAAATGTTTGCATTTCTTTAAAGGATTGAAGG
1 TCAAATATGGTTGATAAATGTTTGCATTTCTTCAAAGGATTGAAGG
2943297 TCAAATATGGTTGATAAATGTTTGCATTTCTTCAAAGGATTGAAGG
1 TCAAATATGGTTGATAAATGTTTGCATTTCTTCAAAGGATTGAAGG
2943343 TC
1 TC
2943345 CATTTCCAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (46 bp):
TCAAATATGGTTGATAAATGTTTGCATTTCTTCAAAGGATTGAAGG
Found at i:2946982 original size:2 final size:2
Alignment explanation
Indices: 2946975--2947009 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2946965 AAACATATGT
2946975 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2947010 TAATTTCTAC
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2950057 original size:17 final size:18
Alignment explanation
Indices: 2950016--2950049 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2950006 TAAAAATGGT
2950016 AATAATTATATATTTAAA
1 AATAATTATATATTTAAA
2950034 AATAATTATA-ATTTAA
1 AATAATTATATATTTAA
2950050 TATAAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAATTATATATTTAAA
Found at i:2950222 original size:16 final size:16
Alignment explanation
Indices: 2950201--2950268 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
2950191 TTTGGTTCGC
2950201 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2950217 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
2950233 TGTATTGGATTAAATG
1 TGTATTGGATTAGAGG
2950249 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2950265 TGTA
1 TGTA
2950269 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:2950316 original size:45 final size:44
Alignment explanation
Indices: 2950249--2950343 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
2950239 GGATTAAATG
* * *
2950249 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
2950294 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
2950338 TGTAAT
1 TGTAAT
2950344 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 22 0.51
45 21 0.49
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:2950524 original size:16 final size:16
Alignment explanation
Indices: 2950484--2950538 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
2950474 TTAATCATAT
*
2950484 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
2950500 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
2950515 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
2950533 -TAAAAT
1 TTAAAAT
2950539 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:2950531 original size:18 final size:17
Alignment explanation
Indices: 2950504--2950538 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2950494 TTTTTATTAA
*
2950504 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2950522 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2950539 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2950651 original size:18 final size:17
Alignment explanation
Indices: 2950624--2950658 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2950614 TTACTATTAA
*
2950624 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2950642 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2950659 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2950704 original size:61 final size:60
Alignment explanation
Indices: 2950519--2950709 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
2950509 TTTTAATTAA
* *
2950519 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATTAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATAAATTTTCT-AAATCAT
* * * * * *
2950580 AATATATGATACT-GTAAAA-T-ATAA-ATTAACATAATTAC-TAT-TAAATATATT-TTAATTA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATT-CTTATATAAAT-T-TTCTAAATCA
*
2950638 A
60 T
*
2950639 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCT-AAATCAT
2950700 AATATATAAT
1 AATATATAAT
2950710 ACTATGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 30 0.31
60 18 0.18
61 39 0.40
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAATCAT
Found at i:2950787 original size:120 final size:120
Alignment explanation
Indices: 2950482--2950765 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
2950472 ATTTAATCAT
*
2950482 ATTTAAACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAAT-
* * * *
2950547 ATT-AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
64 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
* *
2950603 AATTAACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
* *
2950668 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
2950723 ATTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
2950766 TTTTCAATTA
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 133 0.89
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:2961543 original size:26 final size:26
Alignment explanation
Indices: 2961508--2961557 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2961498 TACTTATATT
2961508 TTTATTTGCGTGTAAGAATCTGTTAA
1 TTTATTTGCGTGTAAGAATCTGTTAA
2961534 TTTATTTGCGTGTAAGAATCTGTT
1 TTTATTTGCGTGTAAGAATCTGTT
2961558 GAGGACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (26 bp):
TTTATTTGCGTGTAAGAATCTGTTAA
Found at i:2962400 original size:16 final size:16
Alignment explanation
Indices: 2962379--2962411 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2962369 CATAGTTTCA
2962379 CTTTCGTTTTTTCCTG
1 CTTTCGTTTTTTCCTG
2962395 CTTTCGTTTTTTCCTG
1 CTTTCGTTTTTTCCTG
2962411 C
1 C
2962412 CTTAGTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.12, T:0.61
Consensus pattern (16 bp):
CTTTCGTTTTTTCCTG
Found at i:2970112 original size:87 final size:87
Alignment explanation
Indices: 2969966--2970142 Score: 345
Period size: 87 Copynumber: 2.0 Consensus size: 87
2969956 TGAGTTCGAA
2969966 TGTTAATTAGTAAGTCATTCTAGTCTTTTAAAGATCCAATGAAATTGAAATGAGAGAATAGATCT
1 TGTTAATTAGTAAGTCATTCTAGTCTTTTAAAGATCCAATGAAATTGAAATGAGAGAATAGATCT
2970031 ATCAATTCACGATTAATAAAGG
66 ATCAATTCACGATTAATAAAGG
2970053 TGTTAATTAGTAAGTCATTCTAGTCTTTTAAAGATCCAATGAAATTGAAATGAGAGAATAGATCT
1 TGTTAATTAGTAAGTCATTCTAGTCTTTTAAAGATCCAATGAAATTGAAATGAGAGAATAGATCT
*
2970118 ATCAATTCATGATTAATAAAGG
66 ATCAATTCACGATTAATAAAGG
2970140 TGT
1 TGT
2970143 GCAATATGTT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (87 bp):
TGTTAATTAGTAAGTCATTCTAGTCTTTTAAAGATCCAATGAAATTGAAATGAGAGAATAGATCT
ATCAATTCACGATTAATAAAGG
Found at i:2977823 original size:21 final size:21
Alignment explanation
Indices: 2977799--2977839 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2977789 TTTATAATAT
* *
2977799 AAAAAAATATTTTATATTTAA
1 AAAAAAATATATTAAATTTAA
*
2977820 AAAATAATATATTAAATTTA
1 AAAAAAATATATTAAATTTA
2977840 TTGATGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAAAATATATTAAATTTAA
Found at i:2983136 original size:19 final size:19
Alignment explanation
Indices: 2983108--2983145 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2983098 GGGTGCTACA
2983108 ATAATATTTATAT-ATTTTT
1 ATAATATTTA-ATCATTTTT
*
2983127 ATAATTTTTAATCATTTTT
1 ATAATATTTAATCATTTTT
2983146 TGAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
ATAATATTTAATCATTTTT
Found at i:2983401 original size:21 final size:22
Alignment explanation
Indices: 2983375--2983430 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
2983365 TTAGCCAATA
2983375 ATTATTAATATTTATGTTT-TT
1 ATTATTAATATTTATGTTTATT
** *
2983396 ATTATTTTTATTTTTGTTTATT
1 ATTATTAATATTTATGTTTATT
2983418 AGTTATTAATATT
1 A-TTATTAATATT
2983431 GTTCAACGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 16 0.57
22 3 0.11
23 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
ATTATTAATATTTATGTTTATT
Found at i:2985695 original size:15 final size:16
Alignment explanation
Indices: 2985675--2985718 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
2985665 TCCCGAACAC
*
2985675 TTTTATCTAAATTTA-
1 TTTTATCTAAATTAAT
2985690 TTTTAT-T-AATTAAT
1 TTTTATCTAAATTAAT
2985704 TTTTATC-AAATTAAT
1 TTTTATCTAAATTAAT
2985719 CTTAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTATCTAAATTAAT
Found at i:2992201 original size:19 final size:18
Alignment explanation
Indices: 2992179--2992221 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
2992169 ATTATTGAAT
2992179 ATAATTAAATAAATTAAAA
1 ATAATTAAATAAA-TAAAA
* *
2992198 ATAATTAATTAAATAAAT
1 ATAATTAAATAAATAAAA
2992216 ATAATT
1 ATAATT
2992222 TATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATTAAATAAATAAAA
Found at i:2992220 original size:14 final size:13
Alignment explanation
Indices: 2992180--2992221 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 13
2992170 TTATTGAATA
2992180 TAATTAAATAAAT
1 TAATTAAATAAAT
2992193 TAA--AAAT-AAT
1 TAATTAAATAAAT
2992203 TAATTAAATAAAT
1 TAATTAAATAAAT
2992216 ATAATT
1 -TAATT
2992222 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 6 0.24
11 4 0.16
12 4 0.16
13 6 0.24
14 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATTAAATAAAT
Found at i:2994166 original size:51 final size:51
Alignment explanation
Indices: 2994102--2994255 Score: 254
Period size: 51 Copynumber: 3.0 Consensus size: 51
2994092 CATTTCTCAT
* *
2994102 TTGTCACTGATCAGATAAGCGTAGCTAAAACTACCACTTATCACTTATCAC
1 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCAC
2994153 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCAC
1 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCAC
* * * *
2994204 TTGTCACTAATCAGATAAGTGTAGCTGAGGCTACCACTTATCACTTGTCAC
1 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCAC
2994255 T
1 T
2994256 GATCAGAAGT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 97 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (51 bp):
TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCAC
Found at i:2994417 original size:78 final size:77
Alignment explanation
Indices: 2994286--2994438 Score: 216
Period size: 78 Copynumber: 2.0 Consensus size: 77
2994276 GACGTTCCGT
* *
2994286 TCAATTTGATTATTTATTCGGTTTTCGCATTGTTATTTTATTCTCAATCCATCAACAAATATATA
1 TCAATTTGATCATTTATTCGATTTTCGCATTGTTATTTTATTCTCAATCCATCAACAAATATATA
2994351 TCATCATACACNC
66 TCATCATACAC-C
* ** * * * *
2994364 TCAATTTGATCATTTATTTGATTTTCGGGTTGTTATTTTATTCTCTATTCATCAATAAATATATT
1 TCAATTTGATCATTTATTCGATTTTCGCATTGTTATTTTATTCTCAATCCATCAACAAATATATA
2994429 TCATCATACA
66 TCATCATACA
2994439 TTATATAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.47
Consensus pattern (77 bp):
TCAATTTGATCATTTATTCGATTTTCGCATTGTTATTTTATTCTCAATCCATCAACAAATATATA
TCATCATACACC
Found at i:2996282 original size:33 final size:32
Alignment explanation
Indices: 2996223--2996285 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
2996213 AATAAAAGAG
* *
2996223 AGTTCTTACAAAATTTAACTGTTTTATTTAAT
1 AGTTCTTACAAAATTAAACTCTTTTATTTAAT
2996255 AGTTC-TACAATAACTTAAACTCTTTTATTTA
1 AGTTCTTACAA-AA-TTAAACTCTTTTATTTA
2996286 TTATTGGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 7 0.26
33 15 0.56
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.48
Consensus pattern (32 bp):
AGTTCTTACAAAATTAAACTCTTTTATTTAAT
Found at i:2999240 original size:33 final size:32
Alignment explanation
Indices: 2999203--2999300 Score: 99
Period size: 32 Copynumber: 3.0 Consensus size: 32
2999193 TACCCAAATG
*
2999203 GTACAACTTGAAAAGGTTATGTACACTTTGTGT
1 GTAC-ACTTGAAAAGGTTAGGTACACTTTGTGT
* *
2999236 GTACACTTGGAAAGGTTAGGTATACTTTGTGT
1 GTACACTTGAAAAGGTTAGGTACACTTTGTGT
* ** *
2999268 ATA-ACATATGAAAAGGAAAGGTATACTTTGTGT
1 GTACAC-T-TGAAAAGGTTAGGTACACTTTGTGT
2999301 ATACCATATG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 2 0.04
32 28 0.50
33 26 0.46
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (32 bp):
GTACACTTGAAAAGGTTAGGTACACTTTGTGT
Found at i:2999337 original size:33 final size:33
Alignment explanation
Indices: 2999253--2999339 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
2999243 TGGAAAGGTT
*
2999253 AGGTATACTTTGTGTATAACATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
2999286 AGGTATACTTTGTGTATACCATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
*
2999319 AGGTATACTTTATGTATACCA
1 AGGTATACTTTGTGTATACCA
2999340 CTTAGAAAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (33 bp):
AGGTATACTTTGTGTATACCATATGAAAAGGAA
Found at i:2999349 original size:33 final size:35
Alignment explanation
Indices: 2999253--2999351 Score: 138
Period size: 33 Copynumber: 3.0 Consensus size: 35
2999243 TGGAAAGGTT
*
2999253 AGGTATACTTTGTGTATA--ACATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCACTTATGAAAAGGAA
2999286 AGGTATACTTTGTGTATACCA--TATGAAAAGGAA
1 AGGTATACTTTGTGTATACCACTTATGAAAAGGAA
*
2999319 AGGTATACTTTATGTATACCACTTA-G-AAAGGAA
1 AGGTATACTTTGTGTATACCACTTATGAAAAGGAA
2999352 TGTACACCTC
Statistics
Matches: 61, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
33 57 0.93
34 1 0.02
35 3 0.05
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.30
Consensus pattern (35 bp):
AGGTATACTTTGTGTATACCACTTATGAAAAGGAA
Found at i:3000054 original size:8 final size:8
Alignment explanation
Indices: 3000041--3000069 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3000031 TTATGTTTAA
3000041 TATATTAT
1 TATATTAT
3000049 TATATTAT
1 TATATTAT
3000057 TATATTAT
1 TATATTAT
3000065 TATAT
1 TATAT
3000070 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:3000141 original size:20 final size:21
Alignment explanation
Indices: 3000116--3000155 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3000106 TATAAACTAA
*
3000116 AGAAACAAAA-GAAAGGAAAT
1 AGAAACAAAATGAAACGAAAT
3000136 AGAAACAAAATGAAACGAAA
1 AGAAACAAAATGAAACGAAA
3000156 CAGAGAGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.05
Consensus pattern (21 bp):
AGAAACAAAATGAAACGAAAT
Found at i:3001401 original size:15 final size:15
Alignment explanation
Indices: 3001381--3001437 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
3001371 CGATGAATTT
3001381 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
3001396 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
3001411 ATTGAATTTATATTG
1 ATTGAATTTATATTG
3001426 ATTGAA-TTATAT
1 ATTGAATTTATAT
3001438 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:3003505 original size:8 final size:8
Alignment explanation
Indices: 3003492--3003520 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3003482 TTATGTTTAG
3003492 TATATTAT
1 TATATTAT
3003500 TATATTAT
1 TATATTAT
3003508 TATATTAT
1 TATATTAT
3003516 TATAT
1 TATAT
3003521 AATAAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:3003555 original size:5 final size:5
Alignment explanation
Indices: 3003545--3003584 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
3003535 ATGTTTTAAC
3003545 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
3003585 AAACTAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:3004611 original size:15 final size:15
Alignment explanation
Indices: 3004591--3004647 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
3004581 CGATGAATTT
3004591 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
3004606 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
3004621 ATTGAATTTATATTG
1 ATTGAATTTATATTG
3004636 ATTGAA-TTATAT
1 ATTGAATTTATAT
3004648 AATATATGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:3008564 original size:41 final size:40
Alignment explanation
Indices: 3008508--3008595 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
3008498 ACTTAAACCG
* *
3008508 TTGATTTTTACTAATTTGCATATATATATATTGTT-ACACTA
1 TTGATTTTTACTAATTT-CATATATATAAATTATTGA-ACTA
** * *
3008549 TTGATTTTTGTTAATTTTATGTATATAAATTATTGAACTA
1 TTGATTTTTACTAATTTCATATATATAAATTATTGAACTA
3008589 TTGATTT
1 TTGATTT
3008596 CTAGGTCAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 24 0.60
41 16 0.40
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.55
Consensus pattern (40 bp):
TTGATTTTTACTAATTTCATATATATAAATTATTGAACTA
Found at i:3010338 original size:19 final size:19
Alignment explanation
Indices: 3010306--3010348 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3010296 ATTTCATACC
*
3010306 TTTTAAAAGTACTTGAATTT
1 TTTTAAAAGAACTT-AATTT
*
3010326 TTTTAAAA-AACTTATTTT
1 TTTTAAAAGAACTTAATTT
3010344 TTTTA
1 TTTTA
3010349 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 4 0.19
20 8 0.38
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTAAAAGAACTTAATTT
Found at i:3019223 original size:20 final size:22
Alignment explanation
Indices: 3019200--3019247 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 22
3019190 ATCTTTAGAT
3019200 ATTTGGTA-AAATCCTAA-AAA
1 ATTTGGTAGAAATCCTAAGAAA
3019220 ATTT-G-AGAAATCCTAAGAAA
1 ATTTGGTAGAAATCCTAAGAAA
*
3019240 TTTTGGTA
1 ATTTGGTA
3019248 TGCAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 10 0.43
20 10 0.43
21 1 0.04
22 1 0.04
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (22 bp):
ATTTGGTAGAAATCCTAAGAAA
Found at i:3019500 original size:19 final size:20
Alignment explanation
Indices: 3019478--3019523 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3019468 ATAACCTGAG
*
3019478 AAATTTT-GATAACTATTTA
1 AAATTTTCGATAAATATTTA
* *
3019497 AAATTTTCTATAAATCTTTA
1 AAATTTTCGATAAATATTTA
3019517 AAATTTT
1 AAATTTT
3019524 TGGTATTGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (20 bp):
AAATTTTCGATAAATATTTA
Found at i:3020398 original size:25 final size:25
Alignment explanation
Indices: 3020369--3020440 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
3020359 TCAATCCACA
*
3020369 TGTCCATAGTTTTATAGTTTTATTC
1 TGTCCATAGTTTCATAGTTTTATTC
*
3020394 TGTCCACT-GTTTCATAGTTTTATTT
1 TGTCCA-TAGTTTCATAGTTTTATTC
* * *
3020419 TGTTCATATTATTCATGGTTTT
1 TGTCCATAGT-TTCATAGTTTT
3020441 TTGTTTTGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 1 0.03
25 27 0.69
26 11 0.28
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.57
Consensus pattern (25 bp):
TGTCCATAGTTTCATAGTTTTATTC
Found at i:3034810 original size:37 final size:37
Alignment explanation
Indices: 3034769--3034981 Score: 399
Period size: 37 Copynumber: 5.8 Consensus size: 37
3034759 TTTGAGTACT
3034769 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
3034806 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
3034843 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
3034880 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
3034917 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
3034954 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
3034982 TAGCTTCAGC
Statistics
Matches: 173, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 173 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:3035053 original size:45 final size:46
Alignment explanation
Indices: 3034944--3035067 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
3034934 GTGATAAGTG
* *
3034944 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
3034990 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
3035035 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
3035068 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:3046376 original size:21 final size:21
Alignment explanation
Indices: 3046350--3046390 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3046340 ATCTGCTCAA
* *
3046350 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3046371 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3046391 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3052976 original size:12 final size:13
Alignment explanation
Indices: 3052953--3052982 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3052943 TTTTATATTT
3052953 ATTATAATAGAAA
1 ATTATAATAGAAA
3052966 ATTAT-ATAGAAA
1 ATTATAATAGAAA
3052978 ATTAT
1 ATTAT
3052983 TTGATACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATTATAATAGAAA
Found at i:3055932 original size:21 final size:20
Alignment explanation
Indices: 3055908--3055977 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
3055898 AAGTCTAGCT
3055908 GAAGCACATAAGTGCTAAACG
1 GAAGCACA-AAGTGCTAAACG
* *
3055929 GAAGCCCAAAG-GCT-AACT
1 GAAGCACAAAGTGCTAAACG
*
3055947 GAAGCACACAAGTGTTAAACG
1 GAAGCACA-AAGTGCTAAACG
*
3055968 GAAGCCCAAA
1 GAAGCACAAA
3055978 AGCTAACTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 10 0.25
19 6 0.15
20 7 0.17
21 17 0.43
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (20 bp):
GAAGCACAAAGTGCTAAACG
Found at i:3055949 original size:39 final size:39
Alignment explanation
Indices: 3055890--3055990 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
3055880 ATCGTGATTT
* * * *
3055890 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCAAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
3055929 GAAGCCCAAAGGCTAACTGAAGCACACAAGTGTTAAACG
1 GAAGCCCAAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
3055968 GAAGCCCAAAAGCTAACTGAAGC
1 GAAGCCCAAAGGCTAACTGAAGC
3055991 TCATTAGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.13
Consensus pattern (39 bp):
GAAGCCCAAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:3060077 original size:10 final size:10
Alignment explanation
Indices: 3060062--3060089 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3060052 ACTTGTCTTG
3060062 ATTTCATACT
1 ATTTCATACT
3060072 ATTTCATACT
1 ATTTCATACT
3060082 ATTTCATA
1 ATTTCATA
3060090 TTTAAGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTTCATACT
Found at i:3063566 original size:27 final size:25
Alignment explanation
Indices: 3063507--3063569 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
3063497 CACCATTGTG
*
3063507 GTTTTGTCCACATTTTTTTAGTTTT
1 GTTTTGTCCACATTTTTGTAGTTTT
* * *
3063532 ATTTTGTCCATATTTTTCGTGGTTTTT
1 GTTTTGTCCACATTTTT-GTAG-TTTT
3063559 GTTTTGTCCAC
1 GTTTTGTCCAC
3063570 TTTGTTTTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 15 0.50
26 2 0.07
27 13 0.43
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.60
Consensus pattern (25 bp):
GTTTTGTCCACATTTTTGTAGTTTT
Found at i:3067499 original size:2 final size:2
Alignment explanation
Indices: 3067492--3067520 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3067482 ACCATTGACG
3067492 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3067521 CAAAGCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3073880 original size:19 final size:19
Alignment explanation
Indices: 3073858--3073901 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3073848 CCTTTCTTTT
3073858 GCATT-CATTCCATACATTG
1 GCATTACATTCCA-ACATTG
* *
3073877 GCATTACATTGCAACATTT
1 GCATTACATTCCAACATTG
3073896 GCATTA
1 GCATTA
3073902 AACTTTCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (19 bp):
GCATTACATTCCAACATTG
Found at i:3075967 original size:39 final size:35
Alignment explanation
Indices: 3075881--3075954 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
3075871 TAAAATTTGG
*
3075881 TTAAA-ATAGTTTGACATATGTATGTTTGTCGATT
1 TTAAACATAGTTTGACATATGTATGTTAGTCGATT
3075915 TTAAACATAGTTTGACATATGTATGTTAGTCGATT
1 TTAAACATAGTTTGACATATGTATGTTAGTCGATT
3075950 TTAAA
1 TTAAA
3075955 TCAAGATAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (35 bp):
TTAAACATAGTTTGACATATGTATGTTAGTCGATT
Found at i:3081755 original size:122 final size:122
Alignment explanation
Indices: 3081594--3081837 Score: 461
Period size: 122 Copynumber: 2.0 Consensus size: 122
3081584 TCTGTTTGAT
*
3081594 TTACGAGCTATGAATACCCGGTTATCATTGACTGATGATGGTTCAATCCTAGCTGAATTGAGAGC
1 TTACGAGCTATGAATACCCGGTTATCATTGACTGATGATGGTTCAATCCTAGCTGAATTGAAAGC
3081659 TAAACCGACATTTTTACAGCAAATATGTGAAGCTCAGAAGAATGATGAGAAGTTACA
66 TAAACCGACATTTTTACAGCAAATATGTGAAGCTCAGAAGAATGATGAGAAGTTACA
3081716 TTACGAGCTATGAATACCCGGTTATCATTGACTGATGATGGTTCAATCCTAGCTGAATTGAAAGC
1 TTACGAGCTATGAATACCCGGTTATCATTGACTGATGATGGTTCAATCCTAGCTGAATTGAAAGC
**
3081781 TAAACCGATTTTTTTACAGCAAATATGTGAAGCTCAGAAGAATGATGAGAAGTTACA
66 TAAACCGACATTTTTACAGCAAATATGTGAAGCTCAGAAGAATGATGAGAAGTTACA
3081838 GGTTAAACGG
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (122 bp):
TTACGAGCTATGAATACCCGGTTATCATTGACTGATGATGGTTCAATCCTAGCTGAATTGAAAGC
TAAACCGACATTTTTACAGCAAATATGTGAAGCTCAGAAGAATGATGAGAAGTTACA
Found at i:3083039 original size:12 final size:12
Alignment explanation
Indices: 3083006--3083039 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3082996 TTAGTTAGAA
*
3083006 AAAGAAATTATT
1 AAAGAAATTGTT
*
3083018 GAAGAAATTGTT
1 AAAGAAATTGTT
3083030 AAAGAAATTG
1 AAAGAAATTG
3083040 GGTAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (12 bp):
AAAGAAATTGTT
Found at i:3095493 original size:2 final size:2
Alignment explanation
Indices: 3095486--3095514 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3095476 ACCATTGACG
3095486 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3095515 CAAAGCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3098454 original size:11 final size:11
Alignment explanation
Indices: 3098419--3098454 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
3098409 TTTTGATGTA
*
3098419 ATTTTGCTATT
1 ATTTTGTTATT
*
3098430 ATATTGTTATT
1 ATTTTGTTATT
3098441 ATTTTGTTATT
1 ATTTTGTTATT
3098452 ATT
1 ATT
3098455 ATTTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.67
Consensus pattern (11 bp):
ATTTTGTTATT
Found at i:3098561 original size:18 final size:18
Alignment explanation
Indices: 3098538--3098572 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3098528 TAACTATTTT
3098538 AATTTTATTTA-AATATAA
1 AATTTT-TTTATAATATAA
3098556 AATTTTTTTATAATATA
1 AATTTTTTTATAATATA
3098573 TTTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTTTTATAATATAA
Found at i:3114055 original size:31 final size:31
Alignment explanation
Indices: 3114017--3114084 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
3114007 CTACAAAAAC
3114017 AGTCACTTTTATTTGTTT-AAA-ATTACATTTT
1 AGTCACTTTTA--TGTTTGAAATATTACATTTT
3114048 AGTCAC--TTATGTTTGAAATATTACATTTT
1 AGTCACTTTTATGTTTGAAATATTACATTTT
3114077 AGTCACTT
1 AGTCACTT
3114085 ACGCTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
27 5 0.15
28 3 0.09
29 19 0.58
31 6 0.18
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (31 bp):
AGTCACTTTTATGTTTGAAATATTACATTTT
Found at i:3114060 original size:27 final size:29
Alignment explanation
Indices: 3114030--3114085 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3114020 CACTTTTATT
3114030 TGTTT-AAA-ATTACATTTTAGTCACTTA
1 TGTTTGAAATATTACATTTTAGTCACTTA
3114057 TGTTTGAAATATTACATTTTAGTCACTTA
1 TGTTTGAAATATTACATTTTAGTCACTTA
3114086 CGCTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 5 0.19
28 3 0.11
29 19 0.70
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (29 bp):
TGTTTGAAATATTACATTTTAGTCACTTA
Found at i:3114823 original size:21 final size:21
Alignment explanation
Indices: 3114805--3114852 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3114795 AATTTTAATT
3114805 ATTG-ATTAATTTTATTTAAA
1 ATTGAATTAATTTTATTTAAA
3114825 ATTGAATTAATTTTATTTAAA
1 ATTGAATTAATTTTATTTAAA
3114846 ATTGAAT
1 ATTGAAT
3114853 AATATCAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
ATTGAATTAATTTTATTTAAA
Found at i:3117037 original size:80 final size:80
Alignment explanation
Indices: 3116950--3117106 Score: 287
Period size: 80 Copynumber: 2.0 Consensus size: 80
3116940 ATTAATTTAA
* *
3116950 TTGTTAACATCATTAAAATTTTCATAATAAATTTAAGTTTATTACATAATTATCAAGTGATACTT
1 TTGTTAACATCATTAAAATTTTCATAATAAATTTAAATTTATTACATAATTATCAAATGATACTT
3117015 TTTATTTTAAAATAT
66 TTTATTTTAAAATAT
*
3117030 TTGTTAACATCATTAAAATTTTCATAGTAAATTTAAATTTATTACATAATTATCAAATGATACTT
1 TTGTTAACATCATTAAAATTTTCATAATAAATTTAAATTTATTACATAATTATCAAATGATACTT
3117095 TTTATTTTAAAA
66 TTTATTTTAAAA
3117107 AATTATATAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (80 bp):
TTGTTAACATCATTAAAATTTTCATAATAAATTTAAATTTATTACATAATTATCAAATGATACTT
TTTATTTTAAAATAT
Found at i:3126252 original size:5 final size:5
Alignment explanation
Indices: 3126242--3126313 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
3126232 TGTTAAAAAA
* *
3126242 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
3126288 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
3126314 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:3126295 original size:19 final size:19
Alignment explanation
Indices: 3126271--3126313 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3126261 ATTATGTTTT
3126271 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
3126290 TATATTATATTATATTATA
1 TATATTATATTATATTATA
3126309 TATAT
1 TATAT
3126314 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:3126346 original size:18 final size:19
Alignment explanation
Indices: 3126318--3126357 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3126308 ATATATACAT
*
3126318 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
3126337 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
3126355 AAA
1 AAA
3126358 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:3127334 original size:44 final size:45
Alignment explanation
Indices: 3127237--3127361 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 45
3127227 AACAGAAATG
* * *
3127237 AGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAAGATTG
1 AGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAAGAATA
* *
3127283 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAATA
1 AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
** * *
3127327 ATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 AGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3127362 CAGGATATTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 36 0.54
45 1 0.01
46 30 0.45
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (45 bp):
AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
Found at i:3129236 original size:15 final size:15
Alignment explanation
Indices: 3129213--3129242 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3129203 GTGAAGAGAA
3129213 ATATCTGAAATAATG
1 ATATCTGAAATAATG
*
3129228 ATATGTGAAATAATG
1 ATATCTGAAATAATG
3129243 TACAGAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (15 bp):
ATATCTGAAATAATG
Found at i:3129814 original size:25 final size:25
Alignment explanation
Indices: 3129760--3129817 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3129750 ATCTTAGCAC
* * * *
3129760 GCTCTCTAATTATTAGTACGTTAGT
1 GCTCTCTGATTATTAGCACGTCAAT
*
3129785 ACTCTCTGATTATTAGCACGTCAAT
1 GCTCTCTGATTATTAGCACGTCAAT
3129810 GCTCTCTG
1 GCTCTCTG
3129818 TTCAACCGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAAT
Found at i:3133108 original size:16 final size:16
Alignment explanation
Indices: 3133087--3133119 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3133077 TGAGGACATT
3133087 TGCTGTAATTAACCCA
1 TGCTGTAATTAACCCA
*
3133103 TGCTGTAATTTACCCA
1 TGCTGTAATTAACCCA
3133119 T
1 T
3133120 TTGAAGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (16 bp):
TGCTGTAATTAACCCA
Found at i:3141943 original size:22 final size:21
Alignment explanation
Indices: 3141916--3141980 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
3141906 TTAGTTAAAC
*
3141916 TTTAATTTTCGAATTAAATATT
1 TTTAATTATC-AATTAAATATT
* *
3141938 TTTAATTAT-AATTAATTATA
1 TTTAATTATCAATTAAATATT
* *
3141958 TTTAACTGTCTAATTAAATATT
1 TTTAATTATC-AATTAAATATT
3141980 T
1 T
3141981 AGATAAATGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 16 0.47
22 18 0.53
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTAATTATCAATTAAATATT
Found at i:3141952 original size:20 final size:22
Alignment explanation
Indices: 3141927--3141980 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
3141917 TTAATTTTCG
3141927 AATTAAATATTTTTAA-T-TAT
1 AATTAAATATTTTTAACTGTAT
* * *
3141947 AATTAATTATATTTAACTGTCT
1 AATTAAATATTTTTAACTGTAT
3141969 AATTAAATATTT
1 AATTAAATATTT
3141981 AGATAAATGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 14 0.52
21 1 0.04
22 12 0.44
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTAAATATTTTTAACTGTAT
Found at i:3141962 original size:42 final size:43
Alignment explanation
Indices: 3141889--3141980 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 43
3141879 TTTCCTTCAT
* * * *
3141889 ATATATTTTAATTACAGTTAGTTAAACTTTAATTTTCGAATTAA
1 ATAT-TTTTAATTACAATTAATTAAACTTTAACTGTCGAATTAA
* * *
3141933 ATATTTTTAATTATAATTAATTATA-TTTAACTGTCTAATTAA
1 ATATTTTTAATTACAATTAATTAAACTTTAACTGTCGAATTAA
3141975 ATATTT
1 ATATTT
3141981 AGATAAATGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 20 0.49
43 17 0.41
44 4 0.10
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.51
Consensus pattern (43 bp):
ATATTTTTAATTACAATTAATTAAACTTTAACTGTCGAATTAA
Found at i:3144616 original size:8 final size:9
Alignment explanation
Indices: 3144587--3144656 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
3144577 TTTTGATGCA
*
3144587 TTTTACAAT
1 TTTTAAAAT
* *
3144596 TTTTTATAT
1 TTTTAAAAT
3144605 TTTTAAAAT
1 TTTTAAAAT
3144614 TTTTAAAAAAT
1 TTTT--AAAAT
*
3144625 TTTTAAAAA
1 TTTTAAAAT
*
3144634 ATTTAATAAT
1 TTTTAA-AAT
3144644 TTTTATAAAT
1 TTTTA-AAAT
3144654 TTT
1 TTT
3144657 ATTTATTTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
9 26 0.54
10 12 0.25
11 10 0.21
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:3144625 original size:11 final size:11
Alignment explanation
Indices: 3144609--3144637 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3144599 TTATATTTTT
3144609 AAAATTTTTAA
1 AAAATTTTTAA
3144620 AAAATTTTTAA
1 AAAATTTTTAA
3144631 AAAATTT
1 AAAATTT
3144638 AATAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAAATTTTTAA
Found at i:3144633 original size:10 final size:10
Alignment explanation
Indices: 3144603--3144656 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
3144593 AATTTTTTAT
3144603 ATTTTT-AAA
1 ATTTTTAAAA
3144612 ATTTTTAAAAA
1 ATTTTT-AAAA
3144623 ATTTTTAAAA
1 ATTTTTAAAA
* *
3144633 A-ATTTAATA
1 ATTTTTAAAA
*
3144642 ATTTTTATAA
1 ATTTTTAAAA
3144652 ATTTT
1 ATTTT
3144657 ATTTATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
9 13 0.35
10 15 0.41
11 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTTTAAAA
Found at i:3144657 original size:19 final size:19
Alignment explanation
Indices: 3144603--3144668 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
3144593 AATTTTTTAT
*
3144603 ATTTTTA-AAATTTTTAAAAA
1 ATTTTTATAAA-TTTT-AATA
* *
3144623 ATTTTTAAAAAATTTAATA
1 ATTTTTATAAATTTTAATA
* *
3144642 ATTTTTATAAATTTTATTT
1 ATTTTTATAAATTTTAATA
3144661 ATTTTTAT
1 ATTTTTAT
3144669 TTATTTATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 26 0.67
20 10 0.26
21 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTATAAATTTTAATA
Found at i:3144674 original size:19 final size:20
Alignment explanation
Indices: 3144642--3144684 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3144632 AAATTTAATA
3144642 ATTTTTATAAATTT-TATTT
1 ATTTTTATAAATTTATATTT
**
3144661 ATTTTTATTTATTTATATTT
1 ATTTTTATAAATTTATATTT
3144681 -TTTT
1 ATTTT
3144685 GCTACATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTTATAAATTTATATTT
Found at i:3148150 original size:7 final size:7
Alignment explanation
Indices: 3148138--3148165 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3148128 TCGAATTGAC
3148138 AAAGAAG
1 AAAGAAG
3148145 AAAGAAG
1 AAAGAAG
3148152 AAAGAAG
1 AAAGAAG
3148159 AAAGAAG
1 AAAGAAG
3148166 TAGAAAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:3152764 original size:29 final size:29
Alignment explanation
Indices: 3152729--3152786 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
3152719 TTATATGTAT
3152729 AATTACAAC-AAATCAAAATTCATGTATCA
1 AATTAC-ACTAAATCAAAATTCATGTATCA
*
3152758 AATTACACGTTGAATCAAAATTCATGTAT
1 AATTACAC--TAAATCAAAATTCATGTAT
3152787 AATTGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 6 0.24
31 17 0.68
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.31
Consensus pattern (29 bp):
AATTACACTAAATCAAAATTCATGTATCA
Found at i:3158936 original size:44 final size:44
Alignment explanation
Indices: 3158888--3158977 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
3158878 CTTAGTATGT
*
3158888 TACCAACAATGTTGAAGTCTCATTGGCAAATTTTAAAATATTAG
1 TACCAACAATGTTGAAGTCCCATTGGCAAATTTTAAAATATTAG
3158932 TACCAACAATGTTGAAGTCCCATTGGCAAATTTTAAAATATTAG
1 TACCAACAATGTTGAAGTCCCATTGGCAAATTTTAAAATATTAG
3158976 TA
1 TA
3158978 TCAATCAAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (44 bp):
TACCAACAATGTTGAAGTCCCATTGGCAAATTTTAAAATATTAG
Found at i:3163552 original size:20 final size:20
Alignment explanation
Indices: 3163524--3163586 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
3163514 ATTTTTCATT
* *
3163524 ATTGGGTAATATTTTGTATA
1 ATTGAGTAATATTTTGTGTA
* * *
3163544 ATTTAGTAATGTTTTTTGTA
1 ATTGAGTAATATTTTGTGTA
* *
3163564 ATTGGGTAATATCTTGTGTA
1 ATTGAGTAATATTTTGTGTA
3163584 ATT
1 ATT
3163587 ATTTAAAAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.52
Consensus pattern (20 bp):
ATTGAGTAATATTTTGTGTA
Done.