Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 175 of 206
Found at i:53344624 original size:42 final size:42
Alignment explanation
Indices: 53344578--53344659 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
53344568 AGATATCATA
53344578 AAAAAAAATCCGCAGATGATTTTCTAGCAAAACATTTTTAAT
1 AAAAAAAATCCGCAGATGATTTTCTAGCAAAACATTTTTAAT
53344620 AAAAAAAATCCGCAGATGATTTTCTAGCAAAACATTTTTA
1 AAAAAAAATCCGCAGATGATTTTCTAGCAAAACATTTTTA
53344660 CATGATTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (42 bp):
AAAAAAAATCCGCAGATGATTTTCTAGCAAAACATTTTTAAT
Found at i:53346834 original size:21 final size:21
Alignment explanation
Indices: 53346805--53346852 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
53346795 ATAGTTACCT
* *
53346805 ATCCATAACCCCTAACCCTTA
1 ATCCTTAACCCCTAACCCCTA
*
53346826 ATCCTTAACCTCTAACCCCTA
1 ATCCTTAACCCCTAACCCCTA
*
53346847 ACCCTT
1 ATCCTT
53346853 CTTTTATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (21 bp):
ATCCTTAACCCCTAACCCCTA
Found at i:53346848 original size:14 final size:14
Alignment explanation
Indices: 53346810--53346852 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53346800 TACCTATCCA
53346810 TAACCCCTAACCCT
1 TAACCCCTAACCCT
* *
53346824 TAATCCTTAA-CCT
1 TAACCCCTAACCCT
53346837 CTAACCCCTAACCCT
1 -TAACCCCTAACCCT
53346852 T
1 T
53346853 CTTTTATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 3 0.13
14 17 0.74
15 3 0.13
ACGTcount: A:0.28, C:0.44, G:0.00, T:0.28
Consensus pattern (14 bp):
TAACCCCTAACCCT
Found at i:53347075 original size:67 final size:69
Alignment explanation
Indices: 53346939--53347097 Score: 216
Period size: 67 Copynumber: 2.3 Consensus size: 69
53346929 TGCCCGAGTC
* *
53346939 TCTAAACCCTAAACCACTAACTACTAACCCCTAAACCTTATTTAATATATAAATTTAAAAACACT
1 TCTAAACCCTAAACC-CTAACTACAAACCCCTAAACCTTATTT-AGATATAAATTTAAAAACACT
53347004 AATTAA
64 AATTAA
* * *
53347010 TCTAAACCCTAAACCCTAAC-CCAAATCCCTAAATCTTATTT-GATATAAA-TTAAAACACACTA
1 TCTAAACCCTAAACCCTAACTACAAACCCCTAAACCTTATTTAGATATAAATTTAAAA-ACACTA
53347072 ATTAA
65 ATTAA
*
53347077 TCTAAACCCTAAAGCCTAACT
1 TCTAAACCCTAAACCCTAACT
53347098 TGACACTGAA
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
66 6 0.08
67 37 0.46
69 17 0.21
70 5 0.06
71 15 0.19
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (69 bp):
TCTAAACCCTAAACCCTAACTACAAACCCCTAAACCTTATTTAGATATAAATTTAAAAACACTAA
TTAA
Found at i:53347622 original size:40 final size:40
Alignment explanation
Indices: 53347578--53347803 Score: 141
Period size: 41 Copynumber: 5.8 Consensus size: 40
53347568 ATAAAATGTT
*
53347578 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAAGCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCGAGCA
* * * *
53347618 TTAGCGGCGATTTTT-AAAAATGCCGCTAAAGATCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAA-AGCCGAGCA
* * * *
53347658 TTAGCGACGCTCTTCCAAAAGCGCCGCT-AAAGCTCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGC-C-GAGCA
* * * *
53347699 TTAGCAGCG--------AAAACACCACT-AAAGCCCAGGGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAG-CC-GAGCA
** * * *
53347732 TTAGCTACGCTTTTTTAAAAACGCTGCTAAAAGCCCGATCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAG-CCGAGCA
* *
53347773 TTAGTGGCACTTTTTCAAAAACGCCGCTAAA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
53347804 GCCCCGAAAG
Statistics
Matches: 139, Mismatches: 33, Indels: 27
0.70 0.17 0.14
Matches are distributed among these distances:
33 24 0.17
34 1 0.01
39 16 0.12
40 33 0.24
41 58 0.42
42 7 0.05
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCGAGCA
Found at i:53347645 original size:39 final size:41
Alignment explanation
Indices: 53347578--53347708 Score: 122
Period size: 40 Copynumber: 3.2 Consensus size: 41
53347568 ATAAAATGTT
* *
53347578 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAA-AGCCGAGCA
1 TTAGCGGCGATTTTTCAAAAACGCCGCTAAAGAGCCGAGCA
* * *
53347618 TTAGCGGCGATTTTT-AAAAATGCCGCTAAAGATCTGAGCA
1 TTAGCGGCGATTTTTCAAAAACGCCGCTAAAGAGCCGAGCA
* * * * * ** *
53347658 TTAGCGACGCTCTTCCAAAAGCGCCGCTAAAGCTCTGAGCA
1 TTAGCGGCGATTTTTCAAAAACGCCGCTAAAGAGCCGAGCA
*
53347699 TTAGCAGCGA
1 TTAGCGGCGA
53347709 AAACACCACT
Statistics
Matches: 74, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
39 14 0.19
40 31 0.42
41 29 0.39
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGATTTTTCAAAAACGCCGCTAAAGAGCCGAGCA
Found at i:53347953 original size:13 final size:13
Alignment explanation
Indices: 53347920--53347952 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
53347910 CGCTAATACT
53347920 CGATTTTTAGCGG
1 CGATTTTTAGCGG
53347933 CGATTTTTAGCGG
1 CGATTTTTAGCGG
53347946 CG-TTTTT
1 CGATTTTT
53347953 TGTCCAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.45
Consensus pattern (13 bp):
CGATTTTTAGCGG
Found at i:53368911 original size:16 final size:17
Alignment explanation
Indices: 53368890--53368921 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53368880 CTAATTAATA
53368890 AAAAAGG-ACAAAACTG
1 AAAAAGGTACAAAACTG
53368906 AAAAAGGTACAAAACT
1 AAAAAGGTACAAAACT
53368922 TGCTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.09
Consensus pattern (17 bp):
AAAAAGGTACAAAACTG
Found at i:53369080 original size:5 final size:5
Alignment explanation
Indices: 53369072--53369096 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53369062 AAATTGAAAT
53369072 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
53369097 GTGAAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:53370126 original size:24 final size:24
Alignment explanation
Indices: 53370090--53370140 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
53370080 TGGCACTACG
*
53370090 AATGTAAATGATGAATTGACGGAA
1 AATGTAAAGGATGAATTGACGGAA
*
53370114 AATGTAAAGGATGAATTGACGGCA
1 AATGTAAAGGATGAATTGACGGAA
53370138 AAT
1 AAT
53370141 TACCCAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.06, G:0.25, T:0.24
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGGAA
Found at i:53380662 original size:159 final size:159
Alignment explanation
Indices: 53380373--53380693 Score: 624
Period size: 159 Copynumber: 2.0 Consensus size: 159
53380363 ACTATCTCCT
53380373 TTTTGTTTGATCCGAGCCATGACCCATTGCTCACCCCGCAATGCTCTTTAGTTTCTTTGAGACGT
1 TTTTGTTTGATCCGAGCCATGACCCATTGCTCACCCCGCAATGCTCTTTAGTTTCTTTGAGACGT
*
53380438 GACAGCTCTCGAATAATCTTTGTCAGTTTGAATCCTCAAGCAGCGAAGCATATTCGTATATTCCT
66 GACAACTCTCGAATAATCTTTGTCAGTTTGAATCCTCAAGCAGCGAAGCATATTCGTATATTCCT
53380503 CCACGAACTTCCAGCCTTCTCTCATTGTG
131 CCACGAACTTCCAGCCTTCTCTCATTGTG
*
53380532 TTTTGTTTGATCCGAGCCATGACCCATTGCTCACCCCGCGATGCTCTTTAGTTTCTTTGAGACGT
1 TTTTGTTTGATCCGAGCCATGACCCATTGCTCACCCCGCAATGCTCTTTAGTTTCTTTGAGACGT
53380597 GACAACTCTCGAATAATCTTTGTCAGTTTGAATCCTCAAGCAGCGAAGCATATTCGTATATTCCT
66 GACAACTCTCGAATAATCTTTGTCAGTTTGAATCCTCAAGCAGCGAAGCATATTCGTATATTCCT
53380662 CCACGAACTTCCAGCCTTCTCTCATTGTG
131 CCACGAACTTCCAGCCTTCTCTCATTGTG
53380691 TTT
1 TTT
53380694 AATCAGACCA
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 160 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (159 bp):
TTTTGTTTGATCCGAGCCATGACCCATTGCTCACCCCGCAATGCTCTTTAGTTTCTTTGAGACGT
GACAACTCTCGAATAATCTTTGTCAGTTTGAATCCTCAAGCAGCGAAGCATATTCGTATATTCCT
CCACGAACTTCCAGCCTTCTCTCATTGTG
Found at i:53382213 original size:50 final size:50
Alignment explanation
Indices: 53382138--53382734 Score: 438
Period size: 50 Copynumber: 12.0 Consensus size: 50
53382128 TAATGAATTT
* *
53382138 TTAAAAAGATTGAAGCTACAACGGCGAATCCTGCTTCCCCGACATTGCAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * * * * *
53382188 TTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAGTACAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * * * *
53382238 TGGAACAA-ATTGAAGCTACAACGGTGAATCATGCTTCCCCGACATTGCAA
1 T-TAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* *** * ** *
53382288 TTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTTAGGCGGTGCAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
** * * *
53382338 TGGAATAGATTGAAGCTACAACGGCGAATCCTGCTTCCCCGACATTGCAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* * * * * ** *
53382388 TTAAAAAGATTGAAGCCACAACGACAAATCTTACTT-CCAGGCGGTGCAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
** * *
53382437 TGGAATAGAATGAAGCTACAACGGCGAATCTT-CTCTCCCCGACATTGCAA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACT-TCCCCGACATTGCAA
* * * * * **
53382487 TTTAAAAGATCGAAGCCACAACGGCTAATCTTACTTCCCAGGA-GGTGTC--
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC-CGACATTG-CAA
* * * * * *
53382536 GTAGAATAGGTTAAAGCTAGAACGACGAATCTT-CTTTCCCCGACATTGCAA
1 TTA-AAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCCGACATTGCAA
* * * * * ** *
53382587 TCAAAAAGATTGATGCCACAACGGTGAATCTTATTTCCCC-AGCGGTGCAG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGA-CATTGCAA
** * * ** * **
53382637 TGGAATAGATTAAAGCTACAACGGCGAATCTCGCTTCCCTGACATTGCGG
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
* *
53382687 TT-AATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCA
1 TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCA
53382735 GTTGAACAGG
Statistics
Matches: 404, Mismatches: 128, Indels: 31
0.72 0.23 0.06
Matches are distributed among these distances:
48 2 0.00
49 84 0.21
50 307 0.76
51 11 0.03
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
TTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAA
Found at i:53382319 original size:100 final size:99
Alignment explanation
Indices: 53382144--53382724 Score: 774
Period size: 100 Copynumber: 5.8 Consensus size: 99
53382134 ATTTTTAAAA
53382144 AGATTGAAGCTACAACGGCGAATCCTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAAT-CTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * *
53382209 CGGCGAATCTTACTTCCCAGGCAGTACAGTGGAAC
65 CGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAT
* *
53382244 AAATTGAAGCTACAACGGTGAATCATGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATC-TGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
**
53382309 CGGCGAATCTTACTTCTTAGGCGGTGCAGTGGAAT
65 CGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAT
53382344 AGATTGAAGCTACAACGGCGAATCCTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAAT-CTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* *
53382409 CGACAAATCTTACTT-CCAGGCGGTGCAGTGGAAT
65 CGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAT
* * * *
53382443 AGAATGAAGCTACAACGGCGAATCTTCTCTCCCCGACATTGCAATTTAAAAGATCGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTGCT-TCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * *
53382508 CGGCTAATCTTACTTCCCAGGAGGTGTC-GTAGAAT
65 CGGCGAATCTTACTTCCCAGGCGGTG-CAGTGGAAT
* * * * * * *
53382543 AGGTTAAAGCTAGAACGACGAATCTTCTTTCCCCGACATTGCAATCAAAAAGATTGATGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTGC-TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* *
53382608 CGGTGAATCTTATTTCCCCA-GCGGTGCAGTGGAAT
65 CGGCGAATCTTACTT-CCCAGGCGGTGCAGTGGAAT
* * ** * *
53382643 AGATTAAAGCTACAACGGCGAATCTCGCTTCCCTGACATTGCGGTT-AATAGATTGAAGCTACAA
1 AGATTGAAGCTACAACGGCGAATCT-GCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
*
53382707 CAGCGAATCTTACTTCCC
65 CGGCGAATCTTACTTCCC
53382725 CGACATTGCA
Statistics
Matches: 423, Mismatches: 49, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
98 7 0.02
99 115 0.27
100 293 0.69
101 8 0.02
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (99 bp):
AGATTGAAGCTACAACGGCGAATCTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAAC
GGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAT
Found at i:53384532 original size:50 final size:50
Alignment explanation
Indices: 53384419--53384527 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 50
53384409 TATTATTACC
53384419 ACTATTATTAAT-TATTATTAGTTTTATTTTCTTTTTATTTATTTGTTATT
1 ACTA-TATTAATGTATTATTAGTTTTATTTTCTTTTTATTTATTTGTTATT
*
53384469 ATTATATTAATGTATTAATTAGTTTTATATTT-TTTTTCAACTTTATTT-TTATT
1 ACTATATTAATGTATT-ATTAGTTTTAT-TTTCTTTTT--A-TTTATTTGTTATT
53384522 -CTATAT
1 ACTATAT
53384528 ATGTACATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
49 7 0.14
50 7 0.14
51 16 0.31
52 8 0.16
53 6 0.12
54 7 0.14
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.65
Consensus pattern (50 bp):
ACTATATTAATGTATTATTAGTTTTATTTTCTTTTTATTTATTTGTTATT
Found at i:53396810 original size:21 final size:21
Alignment explanation
Indices: 53396784--53396826 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53396774 ACAAACTATT
*
53396784 GATTTTCAAAAGAAAATAGAG
1 GATTTTCAAAAGAAAACAGAG
*
53396805 GATTTTCAATAGAAAACAGAG
1 GATTTTCAAAAGAAAACAGAG
53396826 G
1 G
53396827 CATCTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (21 bp):
GATTTTCAAAAGAAAACAGAG
Found at i:53398218 original size:7 final size:7
Alignment explanation
Indices: 53398197--53398288 Score: 75
Period size: 7 Copynumber: 13.3 Consensus size: 7
53398187 GGCAACCCAA
53398197 TTTTA-T
1 TTTTATT
53398203 TTTTA-T
1 TTTTATT
53398209 TTTTA-T
1 TTTTATT
53398215 TTTTA-T
1 TTTTATT
53398221 TTTTATTT
1 TTTTA-TT
53398229 TTTTATAT
1 TTTTAT-T
53398237 TTTATATT
1 TTT-TATT
*
53398245 TTATATT
1 TTTTATT
*
53398252 TTATATT
1 TTTTATT
*
53398259 TTATATT
1 TTTTATT
*
53398266 TTATATT
1 TTTTATT
*
53398273 TTATATT
1 TTTTATT
*
53398280 CTTTATT
1 TTTTATT
53398287 TT
1 TT
53398289 CTTACATGTT
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
6 23 0.29
7 39 0.50
8 13 0.17
9 3 0.04
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTATT
Found at i:53398286 original size:14 final size:13
Alignment explanation
Indices: 53398197--53398288 Score: 107
Period size: 14 Copynumber: 6.7 Consensus size: 13
53398187 GGCAACCCAA
53398197 TTTTATTTT-TAT
1 TTTTATTTTATAT
53398209 TTTTATTTT-TAT
1 TTTTATTTTATAT
53398221 TTTTATTTTTTTATAT
1 TTTTA---TTTTATAT
53398237 TTTATATTTTATAT
1 TTT-TATTTTATAT
53398251 TTTATATTTTATAT
1 TTT-TATTTTATAT
53398265 TTTATATTTTATAT
1 TTT-TATTTTATAT
53398279 TCTTTATTTT
1 T-TTTATTTT
53398289 CTTACATGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
12 17 0.23
14 43 0.58
15 6 0.08
16 6 0.08
17 2 0.03
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTTATAT
Found at i:53398286 original size:21 final size:20
Alignment explanation
Indices: 53398197--53398288 Score: 116
Period size: 21 Copynumber: 4.5 Consensus size: 20
53398187 GGCAACCCAA
53398197 TTTTATTTT-TATTTT-TAT
1 TTTTATTTTATATTTTATAT
*
53398215 TTTTATTTTTATTTTTTTATAT
1 TTTTA-TTTTA-TATTTTATAT
53398237 TTTATATTTTATATTTTATAT
1 TTT-TATTTTATATTTTATAT
53398258 TTTATATTTTATATTTTATAT
1 TTT-TATTTTATATTTTATAT
53398279 TCTTTATTTT
1 T-TTTATTTT
53398289 CTTACATGTT
Statistics
Matches: 66, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
18 5 0.08
19 4 0.06
21 42 0.64
22 13 0.20
23 2 0.03
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTTATATTTTATAT
Found at i:53402422 original size:20 final size:19
Alignment explanation
Indices: 53402358--53402424 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
53402348 GAACTACTCT
53402358 ATTT-CTTACTTATCATTCC
1 ATTTACTTACTT-TCATTCC
* *
53402377 ATTTTCTTACTTTTCATTTC
1 ATTTACTTAC-TTTCATTCC
53402397 ATTTACTTACTTTCCATTCC
1 ATTTACTTACTTT-CATTCC
*
53402417 ACTTACTT
1 ATTTACTT
53402425 GGCATAAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.17
20 32 0.78
21 2 0.05
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTACTTACTTTCATTCC
Found at i:53412582 original size:72 final size:72
Alignment explanation
Indices: 53412496--53412639 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
53412486 TTACTTATAA
53412496 CGCCTTTGTAGCGTATTTTGTATGTGCCTTTGTGGCGTATTCGGGATTACCTACATGGCAGAATC
1 CGCCTTTGTAGCGTATTTTGTATGTGCCTTTGTGGCGTATTCGGGATTACCTACATGGCAGAATC
53412561 TAGTTAT
66 TAGTTAT
53412568 CGCCTTTGTAGCGTATTTTGTATGTGCCTTTGTGGCGTATTCGGGATTACCTACATGGCAGAATC
1 CGCCTTTGTAGCGTATTTTGTATGTGCCTTTGTGGCGTATTCGGGATTACCTACATGGCAGAATC
53412633 TAGTTAT
66 TAGTTAT
53412640 TTCATGTGGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (72 bp):
CGCCTTTGTAGCGTATTTTGTATGTGCCTTTGTGGCGTATTCGGGATTACCTACATGGCAGAATC
TAGTTAT
Found at i:53417043 original size:6 final size:7
Alignment explanation
Indices: 53417026--53417052 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53417016 AATCATTATT
53417026 TTTTTTC
1 TTTTTTC
53417033 TTTTTTC
1 TTTTTTC
53417040 TTTTTTC
1 TTTTTTC
53417047 TTTTTT
1 TTTTTT
53417053 TTACAAGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:53418241 original size:5 final size:5
Alignment explanation
Indices: 53418231--53418272 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
53418221 GAAATAGATC
* *
53418231 AATAA AATAA AA-ATA AATAA TATAA AATAA TATAA AATAA AA
1 AATAA AATAA AATA-A AATAA AATAA AATAA AATAA AATAA AA
53418273 AAGGGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 1 0.03
5 29 0.94
6 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:53418249 original size:15 final size:15
Alignment explanation
Indices: 53418231--53418273 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
53418221 GAAATAGATC
53418231 AATAAAATAAAAATA
1 AATAAAATAAAAATA
*
53418246 AATAATAT-AAAATA
1 AATAAAATAAAAATA
53418260 ATATAAAATAAAAA
1 A-ATAAAATAAAAA
53418274 AGGGAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 13 0.54
16 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAAATAAAAATA
Found at i:53423686 original size:16 final size:17
Alignment explanation
Indices: 53423654--53423686 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53423644 GAATACAAGT
53423654 ATTTTCATTATGTTTTA
1 ATTTTCATTATGTTTTA
*
53423671 ATTTTCTTTA-GTTTTA
1 ATTTTCATTATGTTTTA
53423687 CTTACATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTTTCATTATGTTTTA
Found at i:53430751 original size:20 final size:20
Alignment explanation
Indices: 53430728--53430770 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
53430718 AGTGAAACTG
53430728 CCCT-CGATGTCGTGACATGA
1 CCCTCCGATGTCGTGACAT-A
*
53430748 CCCTCCTATGTCGTGACATA
1 CCCTCCGATGTCGTGACATA
53430768 CCC
1 CCC
53430771 CCTCTGGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.19, C:0.37, G:0.19, T:0.26
Consensus pattern (20 bp):
CCCTCCGATGTCGTGACATA
Found at i:53438168 original size:41 final size:40
Alignment explanation
Indices: 53438107--53438259 Score: 182
Period size: 41 Copynumber: 3.7 Consensus size: 40
53438097 AATTAATTAT
*
53438107 ACCCTGAATTGCACACACGTGCCCCTATTTGTACTTCGGTA
1 ACCCTGAA-TGCACATACGTGCCCCTATTTGTACTTCGGTA
* *
53438148 ACCCTAAATGCCACATACGTGCCCCTATTTGTACTTCGATA
1 ACCCTGAATG-CACATACGTGCCCCTATTTGTACTTCGGTA
* * * *
53438189 CCCCTGAATTACACATACGTGCCCCTTTTTGTACTTCAGT-
1 ACCCTGAA-TGCACATACGTGCCCCTATTTGTACTTCGGTA
*
53438229 ACCCTTGAATAGCACATGCGTGCCCCTATTT
1 ACCC-TGAAT-GCACATACGTGCCCCTATTT
53438260 ACACTCTAGT
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
40 6 0.06
41 88 0.93
42 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (40 bp):
ACCCTGAATGCACATACGTGCCCCTATTTGTACTTCGGTA
Found at i:53438209 original size:82 final size:82
Alignment explanation
Indices: 53438108--53438259 Score: 218
Period size: 82 Copynumber: 1.9 Consensus size: 82
53438098 ATTAATTATA
* *
53438108 CCCTGAATTGCACACACGTGCCCCTATTTGTACTTCGGTAACCC-TAAAT-GCCACATACGTGCC
1 CCCTGAATTACACACACGTGCCCCTATTTGTACTTCAGT-ACCCTTAAATAG-CACATACGTGCC
53438171 CCTATTTGTACTTCGATAC
64 CCTATTTGTACTTCGATAC
* * * *
53438190 CCCTGAATTACACATACGTGCCCCTTTTTGTACTTCAGTACCCTTGAATAGCACATGCGTGCCCC
1 CCCTGAATTACACACACGTGCCCCTATTTGTACTTCAGTACCCTTAAATAGCACATACGTGCCCC
53438255 TATTT
66 TATTT
53438260 ACACTCTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
81 4 0.06
82 57 0.92
83 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.31
Consensus pattern (82 bp):
CCCTGAATTACACACACGTGCCCCTATTTGTACTTCAGTACCCTTAAATAGCACATACGTGCCCC
TATTTGTACTTCGATAC
Found at i:53445502 original size:41 final size:41
Alignment explanation
Indices: 53445445--53445598 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
53445435 TAATTAATTA
* * *
53445445 TACCC-TGAATTGCACATACGTGCCCCTGTTTGTACTTCGG
1 TACCCTTGAATTGCACATACATGCCCCTATTTGTACTTTGG
53445485 TACCCTTGAA-TGCCACATACATGCCCCTATTTGTACTTTGG
1 TACCCTTGAATTG-CACATACATGCCCCTATTTGTACTTTGG
*
53445526 TACCCTTGAATTGCACATACATGCCTCTATTTGTACTTTGG
1 TACCCTTGAATTGCACATACATGCCCCTATTTGTACTTTGG
* * *
53445567 TACCCCTGAATAGCACATACGTGCCCCTATTT
1 TACCCTTGAATTGCACATACATGCCCCTATTT
53445599 ACACTATAGT
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
40 7 0.07
41 94 0.91
42 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (41 bp):
TACCCTTGAATTGCACATACATGCCCCTATTTGTACTTTGG
Found at i:53449411 original size:17 final size:17
Alignment explanation
Indices: 53449391--53449426 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
53449381 TAATTTAAAT
*
53449391 AATTAATTAATTTTCTC
1 AATTAAATAATTTTCTC
53449408 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
53449425 AA
1 AA
53449427 CTGAATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:53457365 original size:24 final size:22
Alignment explanation
Indices: 53457318--53457366 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 22
53457308 AAAATATTAG
53457318 TAGGTAATAGAGTAATATATAAA
1 TAGGTAATAGAG-AATATATAAA
53457341 TAGGTAAATAGA-AATATTATCAAA
1 TAGGT-AATAGAGAATA-TAT-AAA
53457365 TA
1 TA
53457367 TAATAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (22 bp):
TAGGTAATAGAGAATATATAAA
Found at i:53457389 original size:24 final size:23
Alignment explanation
Indices: 53457362--53457417 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
53457352 AAATATTATC
*
53457362 AAATATAATAGTAATAACAAGAAT
1 AAATATAATA-TAAAAACAAGAAT
* *
53457386 AAATAGTAATATAAAAATAATAAT
1 AAATA-TAATATAAAAACAAGAAT
53457410 AAAT-TAAT
1 AAATATAAT
53457418 TAATAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.14
24 19 0.68
25 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (23 bp):
AAATATAATATAAAAACAAGAAT
Found at i:53459220 original size:89 final size:88
Alignment explanation
Indices: 53459108--53459360 Score: 335
Period size: 89 Copynumber: 2.8 Consensus size: 88
53459098 GGTTGGTGTT
* * * * * * *
53459108 TTCGATCTGTTTTGCTGTCAGTACAAGAAGGCAAAATCTGTTTTATTCAGTCTACTCCGCTGGCA
1 TTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTTTCTTCAGTCTGCTCCGCT-GCA
* *
53459173 ACCCATGGAGGCAAGGCTGGTATC
65 ACCCAGGGAGGCAACGCTGGTATC
* * *
53459197 TTCGATCTGCTTCGCTGTCAGTACAGGAAGGCGAGATCTACTTTCTTCAGTCTGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTTTCTTCAGTCTGCTCCGCTGCAA
*
53459262 GCCCAGGGAGGCAACGCTGGTGTC
66 -CCCAGGGAGGCAACGCTGGTATC
* * *
53459286 TTCGATTTGGTTCGCTGTCAGTATAGGAAGGCAAGATCTGCTTTCTTCAGTCTGCTCCGCTGCAA
1 TTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTTTCTTCAGTCTGCTCCGCTGC-A
53459351 ACCCAGGGAG
65 ACCCAGGGAG
53459361 ATAAGACTTG
Statistics
Matches: 143, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
88 4 0.03
89 137 0.96
90 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (88 bp):
TTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTTTCTTCAGTCTGCTCCGCTGCAA
CCCAGGGAGGCAACGCTGGTATC
Found at i:53459251 original size:45 final size:44
Alignment explanation
Indices: 53459202--53459347 Score: 109
Period size: 45 Copynumber: 3.3 Consensus size: 44
53459192 GTATCTTCGA
* *
53459202 TCTGCTTCGCTGTCAGTACAGGAAGGCGAGATCTACTTTCTTCAG
1 TCTGCTCCGCTGTCAGTACAGGAAGGC-AGATCTGCTTTCTTCAG
* ** * * * *
53459247 TCTGCTCCACTG-CAAGCCCAGGGAGGCA-ACGCTGGTGTCTTC-G
1 TCTGCTCCGCTGTC-AGTACAGGAAGGCAGA-TCTGCTTTCTTCAG
* * * *
53459290 ATTTGGTTCGCTGTCAGTATAGGAAGGCAAGATCTGCTTTCTTCAG
1 -TCTGCTCCGCTGTCAGTACAGGAAGGC-AGATCTGCTTTCTTCAG
53459336 TCTGCTCCGCTG
1 TCTGCTCCGCTG
53459348 CAAACCCAGG
Statistics
Matches: 71, Mismatches: 23, Indels: 14
0.66 0.21 0.13
Matches are distributed among these distances:
43 2 0.03
44 27 0.38
45 40 0.56
46 2 0.03
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (44 bp):
TCTGCTCCGCTGTCAGTACAGGAAGGCAGATCTGCTTTCTTCAG
Found at i:53459923 original size:88 final size:87
Alignment explanation
Indices: 53459767--53460105 Score: 271
Period size: 88 Copynumber: 3.9 Consensus size: 87
53459757 ACCTGATGTG
* * * ** * *
53459767 ATCTGCTCTACTGCAAATTCAGAGAGATAAGATCTATTAT-TT-GAATCTTCTCCACTGCCA-CT
1 ATCTGCTCCACTACAAACTCAGAGAGATAAGATCTACCATCTTCG-ATCTGCTCCACT-ACAGCT
*
53459829 TCAGGGAGATAGGATTACTGGCTTCA
64 T-AGGGAGATAAGATTACT-GCTTCA
* *
53459855 ATATGCTCCCCTACAAACTCAGAGAGATAAGAT-TCACCATCTTCGATCTGCTCCACTACAGCTT
1 ATCTGCTCCACTACAAACTCAGAGAGATAAGATCT-ACCATCTTCGATCTGCTCCACTACAGCTT
* * * *
53459919 AGGGAGATAAGA--CCTGATGCT
65 AGGGAGATAAGATTACTGCTTCA
* * * *** ** ** *
53459940 ATCTACTCTACTGC-AACTTCAGAGAGATAAGATCTATTGT-TTTAATCTGCTCCACTGTAACTT
1 ATCTGCTCCACTACAAAC-TCAGAGAGATAAGATCTACCATCTTCGATCTGCTCCACTACAGCTT
* *
53460003 CAGGGAGATAGGATTATCAGCTTCA
65 -AGGGAGATAAGATTA-CTGCTTCA
* * * *
53460028 ATCTGCTCCACTACAACCTCAGCGAGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTA
1 ATCTGCTCCACTACAAACTCAGAGAGATAAGATCTACCATCTTCGATCTGCTCCACTACAGCTTA
53460093 GGGAGATAAGATT
66 GGGAGATAAGATT
53460106 TGCTTCTTCG
Statistics
Matches: 190, Mismatches: 49, Indels: 24
0.72 0.19 0.09
Matches are distributed among these distances:
84 21 0.11
85 40 0.21
86 3 0.02
87 1 0.01
88 89 0.47
89 35 0.18
90 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (87 bp):
ATCTGCTCCACTACAAACTCAGAGAGATAAGATCTACCATCTTCGATCTGCTCCACTACAGCTTA
GGGAGATAAGATTACTGCTTCA
Found at i:53459951 original size:173 final size:173
Alignment explanation
Indices: 53459746--53460103 Score: 542
Period size: 173 Copynumber: 2.1 Consensus size: 173
53459736 CTACAACCTC
*
53459746 AGGGAGATAAGACCTGATGTGATCTGCTCTACTGCAAATTCAGAGAGATAAGATCTATTATTTGA
1 AGGGAGATAAGACCTGATGTGATCTACTCTACTGCAAATTCAGAGAGATAAGATCTATTATTTGA
* * * *
53459811 ATCTTCTCCACTGCCACTTCAGGGAGATAGGATTA-CTGGCTTCAATATGCTCCCCTACAAACTC
66 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATC-AGCTTCAATATGCTCCACTACAAACTC
53459875 AGAGAGATAAGAT-TCACCATCTTCGATCTGCTCCACTACAGCTT
130 AGAGAGATAAGATCT-ACCATCTTCGATCTGCTCCACTACAGCTT
* * *
53459919 AGGGAGATAAGACCTGATGCT-ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTT
1 AGGGAGATAAGACCTGATG-TGATCTACTCTACTGCAAATTCAGAGAGATAAGATCTATTATTTG
* * *
53459983 AATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTACAACCTC
65 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTCAATATGCTCCACTACAAACTC
* * *
53460048 AGCGAGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTT
130 AGAGAGATAAGATCTACCATCTTCGATCTGCTCCACTACAGCTT
53460092 AGGGAGATAAGA
1 AGGGAGATAAGA
53460104 TTTGCTTCTT
Statistics
Matches: 168, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
173 165 0.98
174 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (173 bp):
AGGGAGATAAGACCTGATGTGATCTACTCTACTGCAAATTCAGAGAGATAAGATCTATTATTTGA
ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTCAATATGCTCCACTACAAACTCA
GAGAGATAAGATCTACCATCTTCGATCTGCTCCACTACAGCTT
Found at i:53460005 original size:391 final size:376
Alignment explanation
Indices: 53459324--53460321 Score: 1102
Period size: 391 Copynumber: 2.6 Consensus size: 376
53459314 AGGCAAGATC
* *
53459324 TGCTTTCTTCAGTCTGCTCCGCTGCAAACC-CAGGGAGATAAGACTTGATGTGATCTGCTCTACT
1 TGCTTTCTTCAGTCTACTCCGCTGC-AACCTCAGGGAGATAAGACCTGATGTGATCTGCTCTACT
* * * *
53459388 GCAACTTCAGGGAGATAAGATCTATTATTTGATTCCACTCAACTGCCACTTTAGGGAGATAGGAT
65 GCAACTTCAGAGAGATAAGATCTATTATTTGAAT-CACTCCACTGCCACTTCAGGGAGATAGGAT
* * * *
53459453 TACTGGCTTTAATTCACCATCTTCAGTCTGCCCC-ACTGCAACTTCAGGGGGATAAGACTT--GC
129 TACTGGC-----TTCA--AT-AT--G-CT-CCCCTAC--AAAC-TCAGGGAGATAAGA-TTCACC
* * * * * *
53459515 TTCCTCAGTCTGCTTCGCTGCAACCTCAGGGAGATAAGACCTGATGTGATCTGCTCTACTGCAAC
178 ATCTTCAGTCTGCTCCACTGCAA-CTTAGGGAGATAAGACCTGATGTGATCTACTCTACTGCAAC
* *
53459580 TTCAGAGAGATAAGATCTATTATTTGCCACTTCAGGGAGATAGGATTA-CTGGCTTCAATCTGCT
242 TTCAGAGAGATAAGATCTATTATTTCCCACTTCAGGGAGATAGGATTATC-AGCTTCAATCTGCT
* * *
53459644 CCACTGCAAACTCAGGGAGATAAGAT-T-CACTATCTTC-AGTCTGCCCCACTGCAACTTTAGGG
306 CCACTACAAACTCAGCGAGATAAGATCTGC-C-ATCTTCGA-TCTGCCCCACTACAAC-TTAGGG
*
53459706 GGATAAGACT
367 AGATAAGACT
*
53459716 TGCTTTC-TCAGTCTACTCCGCTACAACCTCAGGGAGATAAGACCTGATGTGATCTGCTCTACTG
1 TGCTTTCTTCAGTCTACTCCGCTGCAACCTCAGGGAGATAAGACCTGATGTGATCTGCTCTACTG
* *
53459780 CAAATTCAGAGAGATAAGATCTATTATTTGAATCTTCTCCACTGCCACTTCAGGGAGATAGGATT
66 CAACTTCAGAGAGATAAGATCTATTATTTGAATC-ACTCCACTGCCACTTCAGGGAGATAGGATT
*
53459845 ACTGGCTTCAATATGCTCCCCTACAAACTCAGAGAGATAAGATTCACCATCTTC-GATCTGCTCC
130 ACTGGCTTCAATATGCTCCCCTACAAACTCAGGGAGATAAGATTCACCATCTTCAG-TCTGCTCC
* *
53459909 ACTACAGCTTAGGGAGATAAGACCTGATGCT-ATCTACTCTACTGCAACTTCAGAGAGATAAGAT
194 ACTGCAACTTAGGGAGATAAGACCTGATG-TGATCTACTCTACTGCAACTTCAGAGAGATAAGAT
53459973 CTATTGTTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCA
258 CTA-----TT-AT-T--TCC-C----ACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCA
* * **
53460038 CTACAACCTCAGCGAGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
309 CTACAAACTCAGCGAGATAAGATCTGCCATCTTCGATCTGCCCCACTACAACTTAGGGAGATAAG
*
53460103 ATT
374 ACT
* * * * *
53460106 TGC-TTCTTCGGTCTACTCTGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTG
1 TGCTTTCTTCAGTCTACTCCGCTGCAACCTCAGGGAGATAAGACCTGATGTGATCTGCTCTACTG
* * * * *
53460170 CAACTTCAGAGAGATAAGATCTATTGTTTTAATCCCTCCACTACAACTTCAGGGAGATAGGATTA
66 CAACTTCAGAGAGATAAGATCTATTATTTGAATCACTCCACTGCCACTTCAGGGAGATAGGATTA
* * * *
53460235 CTGGCTTTAATCTGCTCCACTACAAACTCAGGGAGATAAGATTCACCATCTTCAGTCTGCCCCAC
131 CTGGCTTCAATATGCTCCCCTACAAACTCAGGGAGATAAGATTCACCATCTTCAGTCTGCTCCAC
*
53460300 TGCAACTTCAGGGGGATAAGAC
196 TGCAACTT-AGGGAGATAAGAC
53460322 TAGCGGTTTC
Statistics
Matches: 525, Mismatches: 53, Indels: 58
0.83 0.08 0.09
Matches are distributed among these distances:
376 2 0.00
377 69 0.13
378 20 0.04
379 4 0.01
380 4 0.01
381 1 0.00
382 2 0.00
383 3 0.01
384 3 0.01
386 6 0.01
387 1 0.00
389 95 0.18
390 117 0.22
391 186 0.35
392 11 0.02
393 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (376 bp):
TGCTTTCTTCAGTCTACTCCGCTGCAACCTCAGGGAGATAAGACCTGATGTGATCTGCTCTACTG
CAACTTCAGAGAGATAAGATCTATTATTTGAATCACTCCACTGCCACTTCAGGGAGATAGGATTA
CTGGCTTCAATATGCTCCCCTACAAACTCAGGGAGATAAGATTCACCATCTTCAGTCTGCTCCAC
TGCAACTTAGGGAGATAAGACCTGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTA
TTATTTCCCACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTACAAACTCAGCGAGA
TAAGATCTGCCATCTTCGATCTGCCCCACTACAACTTAGGGAGATAAGACT
Found at i:53460011 original size:44 final size:44
Alignment explanation
Indices: 53459608--53460320 Score: 228
Period size: 44 Copynumber: 16.4 Consensus size: 44
53459598 ATTATTTGCC
* * * *
53459608 ACTTCAGGGAGATAGGAT-TACTGGCTTCAATCTGCTCCACTGCAA
1 ACTTCAGGGAGATAAGATCTA-TTGTTTTAATCTGCTCCACTGC-A
* * * * *
53459653 AC-TCAGGGAGATAAGAT-TCACTATCTTCAGTCTGCCCCACTGCA
1 ACTTCAGGGAGATAAGATCT-ATTGT-TTTAATCTGCTCCACTGCA
* * * * * *
53459697 ACTTTAGGGGGATAAGA-C--TTGCTTTCTCAGTCTACTCCGCTACA
1 ACTTCAGGGAGATAAGATCTATTG-TTT-T-AATCTGCTCCACTGCA
* * * *
53459741 ACCTCAGGGAGATAAGACCTGA-TG---TGATCTGCTCTACTGCA
1 ACTTCAGGGAGATAAGATCT-ATTGTTTTAATCTGCTCCACTGCA
* * * * * *
53459782 AATTCAGAGAGATAAGATCTATTATTTGAATCTTCTCCACTGCC
1 ACTTCAGGGAGATAAGATCTATTGTTTTAATCTGCTCCACTGCA
* * * * * * *
53459826 ACTTCAGGGAGATAGGAT-TACTGGCTTCAATATGCTCCCCTACAA
1 ACTTCAGGGAGATAAGATCTA-TTGTTTTAATCTGCTCCACTGC-A
* *** ** *
53459871 AC-TCAGAGAGATAAGAT-TCACCATCTTCGATCTGCTCCACTACA
1 ACTTCAGGGAGATAAGATCT-ATTGT-TTTAATCTGCTCCACTGCA
* * * * *
53459915 GCTT-AGGGAGATAAGACCTGA-TG--CT-ATCTACTCTACTGCA
1 ACTTCAGGGAGATAAGATCT-ATTGTTTTAATCTGCTCCACTGCA
* *
53459955 ACTTCAGAGAGATAAGATCTATTGTTTTAATCTGCTCCACTGTA
1 ACTTCAGGGAGATAAGATCTATTGTTTTAATCTGCTCCACTGCA
* * * * *
53459999 ACTTCAGGGAGATAGGAT-TATCAGCTTCAATCTGCTCCACTACA
1 ACTTCAGGGAGATAAGATCTAT-TGTTTTAATCTGCTCCACTGCA
* * **** ** * *
53460043 ACCTCAGCGAGATAAGATCTGCCATCTTCGATCTGCTCCACTACT
1 ACTTCAGGGAGATAAGATCTATTGT-TTTAATCTGCTCCACTGCA
* ** * **
53460088 GCTT-AGGGAGATAAGA--T-TTGCTTCTTCGGTCTACTCTGCTGCA
1 ACTTCAGGGAGATAAGATCTATTG-TT-TT-AATCTGCTCCACTGCA
* ** * *
53460131 ACTTCAGGGAGATAAGACCTGA-TG---CGATCTACTCTACTGCA
1 ACTTCAGGGAGATAAGATCT-ATTGTTTTAATCTGCTCCACTGCA
* * *
53460172 ACTTCAGAGAGATAAGATCTATTGTTTTAATC-CCTCCACTACA
1 ACTTCAGGGAGATAAGATCTATTGTTTTAATCTGCTCCACTGCA
* * * *
53460215 ACTTCAGGGAGATAGGAT-TACTGGCTTTAATCTGCTCCACTACAA
1 ACTTCAGGGAGATAAGATCTA-TTGTTTTAATCTGCTCCACTGC-A
*** * * *
53460260 AC-TCAGGGAGATAAGAT-TCACCATCTTCAGTCTGCCCCACTGCA
1 ACTTCAGGGAGATAAGATCT-ATTGT-TTTAATCTGCTCCACTGCA
*
53460304 ACTTCAGGGGGATAAGA
1 ACTTCAGGGAGATAAGA
53460321 CTAGCGGTTT
Statistics
Matches: 491, Mismatches: 130, Indels: 94
0.69 0.18 0.13
Matches are distributed among these distances:
40 18 0.04
41 77 0.16
42 9 0.02
43 53 0.11
44 225 0.46
45 104 0.21
46 1 0.00
47 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
ACTTCAGGGAGATAAGATCTATTGTTTTAATCTGCTCCACTGCA
Found at i:53460105 original size:217 final size:216
Alignment explanation
Indices: 53459878--53460276 Score: 604
Period size: 216 Copynumber: 1.8 Consensus size: 216
53459868 CAAACTCAGA
* * *
53459878 GAGATAAGATTCACCATCTTCGATCTGCTCCACTACAGCTT-AGGGAGATAAGACCTGATGCTAT
1 GAGATAAGATT-ACCATCTTCGATCTACTCCACTACAACTTCAGGGAGATAAGACCTGATGCGAT
* **
53459942 CTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCTGCTCCACTGTAACTTCAGG
65 CTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATC-CCTCCACTACAACTTCAGG
*
53460007 GAGATAGGATTA-TCAGCTTCAATCTGCTCCACTACAACCTCAGCGAGATAAGATCTGCCATCTT
129 GAGATAGGATTACT-AGCTTCAATCTGCTCCACTACAAACTCAGCGAGATAAGATCTGCCATCTT
53460071 CGATCTGCTCCACTACTGCTTAGG
193 CGATCTGCTCCACTACTGCTTAGG
** * * ** *
53460095 GAGATAAGATTTGCTTCTTCGGTCTACTCTGCTGCAACTTCAGGGAGATAAGACCTGATGCGATC
1 GAGATAAGATTACCATCTTCGATCTACTCCACTACAACTTCAGGGAGATAAGACCTGATGCGATC
53460160 TACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCCCTCCACTACAACTTCAGGGA
66 TACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCCCTCCACTACAACTTCAGGGA
* * *
53460225 GATAGGATTACTGGCTTTAATCTGCTCCACTACAAACTCAGGGAGATAAGAT
131 GATAGGATTACTAGCTTCAATCTGCTCCACTACAAACTCAGCGAGATAAGAT
53460277 TCACCATCTT
Statistics
Matches: 163, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
216 84 0.52
217 79 0.48
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (216 bp):
GAGATAAGATTACCATCTTCGATCTACTCCACTACAACTTCAGGGAGATAAGACCTGATGCGATC
TACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCCCTCCACTACAACTTCAGGGA
GATAGGATTACTAGCTTCAATCTGCTCCACTACAAACTCAGCGAGATAAGATCTGCCATCTTCGA
TCTGCTCCACTACTGCTTAGG
Found at i:53460143 original size:88 final size:87
Alignment explanation
Indices: 53459767--53460147 Score: 251
Period size: 88 Copynumber: 4.4 Consensus size: 87
53459757 ACCTGATGTG
* * ** * * **
53459767 ATCTGCTCTACTGCAAATTCAGAGAGATAAGATCTATTAT-TT-GAATCTTCTCCACTGCCACTT
1 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTACCATCTTCG-ATCTGCTCCACTACTGCTT
* *
53459830 CAGGGAGATAGGA-TTACTGGCTTC
65 -AGGGAGATAAGATTTGCT-GCTTC
* * ** * *
53459854 AATATGCTCCCCTACAAAC-TCAGAGAGATAAGAT-TCACCATCTTCGATCTGCTCCACTACAGC
1 -ATCTACTCTACTGC-AACTTCAGAGAGATAAGATCT-ACCATCTTCGATCTGCTCCACTACTGC
** *
53459917 TTAGGGAGATAAGACCTGATGC-T-
63 TTAGGGAGATAAGATTTGCTGCTTC
*** ** * *
53459940 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGT-TTTAATCTGCTCCACT-GTAACTT
1 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTACCATCTTCGATCTGCTCCACTACT-GCTT
* *
53460003 CAGGGAGATAGGATTAT-CAGCTTC
65 -AGGGAGATAAGATT-TGCTGCTTC
* * * * * *
53460027 AATCTGCTCCACTACAACCTCAGCGAGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTT
1 -ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTACCATCTTCGATCTGCTCCACTACTGCTT
*
53460092 AGGGAGATAAGATTTGCTTCTTC
65 AGGGAGATAAGATTTGCTGCTTC
* * *
53460115 GGTCTACTCTGCTGCAACTTCAGGGAGATAAGA
1 -ATCTACTCTACTGCAACTTCAGAGAGATAAGA
53460148 CCTGATGCGA
Statistics
Matches: 220, Mismatches: 57, Indels: 32
0.71 0.18 0.10
Matches are distributed among these distances:
84 20 0.09
85 39 0.18
86 3 0.01
87 3 0.01
88 115 0.52
89 38 0.17
90 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (87 bp):
ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTACCATCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATTTGCTGCTTC
Found at i:53460177 original size:173 final size:171
Alignment explanation
Indices: 53459746--53460275 Score: 500
Period size: 173 Copynumber: 3.1 Consensus size: 171
53459736 CTACAACCTC
* * * * *
53459746 AGGGAGATAAGACCTGATG-TGATCTGCTCTACTGCAAATTCAGAGAGATAAGATCTATTATTTG
1 AGGGAGATAAGACCTGATGCT-ATCTACTCTACTGCAACTTCAGAGAGATAAGACCTA-T-TGTC
* * * * * *
53459810 AATCTTCTCCACTGCCACTTCAGGGAGATAGGATTA-CTGGCTTCAATATGCTCCCCTACAAACT
63 AATCTACTCCACTGCAACTTCAGGGAGATAGGATTATC-AGCTTCAATCTGCTCCACTACAACCT
53459874 CAGAGAGATAAGATTCACCATCTTCGATCTGCTCCACTACAGCTT
127 CAGAGAGATAAGATTCACCATCTTCGATCTGCTCCACTACAGCTT
* *
53459919 AGGGAGATAAGACCTGATGCTATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTA
1 AGGGAGATAAGACCTGATGCTATCTACTCTACTGCAACTTCAGAGAGATAAGACCTATTG--TCA
* *
53459984 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTACAACCTCA
64 ATCTACTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTACAACCTCA
* * *
53460049 GCGAGATAAGA-TCTGCCATCTTCGATCTGCTCCACTACTGCTT
129 GAGAGATAAGATTC-ACCATCTTCGATCTGCTCCACTACAGCTT
** * * * * *
53460092 AGGGAGATAAGATTTGCTTCTTCGGTCTACTCTGCTGCAACTTCAGGGAGATAAGACCTGA-TG-
1 AGGGAGATAAGACCTGATGC-T--ATCTACTCTACTGCAACTTCAGAGAGATAAGACCT-ATTGT
* * * * * * * * *
53460155 CGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTAT-TGTTTTAATC-CCTCCACTACAACT
62 CAATCTACTCCACTGCAACTTCAGGGAGATAGGAT-TATCAGCTTCAATCTGCTCCACTACAACC
* * *** ** * *
53460218 TCAGGGAGATAGGATT-ACTGGCTTTAATCTGCTCCACTACAAACTC
126 TCAGAGAGATAAGATTCACCATCTTCGATCTGCTCCACTAC-AGCTT
53460264 AGGGAGATAAGA
1 AGGGAGATAAGA
53460276 TTCACCATCT
Statistics
Matches: 300, Mismatches: 45, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
171 19 0.06
172 41 0.14
173 200 0.67
174 6 0.02
176 33 0.11
177 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (171 bp):
AGGGAGATAAGACCTGATGCTATCTACTCTACTGCAACTTCAGAGAGATAAGACCTATTGTCAAT
CTACTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTACAACCTCAGA
GAGATAAGATTCACCATCTTCGATCTGCTCCACTACAGCTT
Found at i:53460221 original size:43 final size:44
Alignment explanation
Indices: 53460170--53460277 Score: 132
Period size: 43 Copynumber: 2.5 Consensus size: 44
53460160 TACTCTACTG
* * *
53460170 CAACTTCAGAGAGATAAGATCTA-TTGTTTTAATC-CCTCCACTA
1 CAACTTCAGGGAGATAAGAT-TACTGGCTTTAATCTCCTCCACTA
* *
53460213 CAACTTCAGGGAGATAGGATTACTGGCTTTAATCTGCTCCACTA
1 CAACTTCAGGGAGATAAGATTACTGGCTTTAATCTCCTCCACTA
53460257 CAAAC-TCAGGGAGATAAGATT
1 C-AACTTCAGGGAGATAAGATT
53460278 CACCATCTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.04
43 27 0.48
44 24 0.43
45 3 0.05
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATTACTGGCTTTAATCTCCTCCACTA
Found at i:53460320 original size:217 final size:217
Alignment explanation
Indices: 53459919--53460320 Score: 614
Period size: 216 Copynumber: 1.9 Consensus size: 217
53459909 ACTACAGCTT
*
53459919 AGGGAGATAAGACCTGATGCTATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTA
1 AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTA
* ** *
53459984 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTACAACCTCA
66 ATCTCCTCCACTACAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTACAAACTCA
* * **
53460049 GCGAGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGCTTCTT
131 GCGAGATAAGATCTACCATCTTCGATCTGCCCCACTACAACTTAGGGAGATAAGATTTGCTTCTT
53460114 CGGTCTACTCTGCTGCAACTTC
196 CGGTCTACTCTGCTGCAACTTC
53460136 AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTA
1 AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTA
* *
53460201 ATC-CCTCCACTACAACTTCAGGGAGATAGGATTA-CTGGCTTTAATCTGCTCCACTACAAACTC
66 ATCTCCTCCACTACAACTTCAGGGAGATAGGATTATC-AGCTTCAATCTGCTCCACTACAAACTC
* * *
53460264 AGGGAGATAAGAT-TCACCATCTTC-AGTCTGCCCCACTGCAACTTCAGGGGGATAAGA
130 AGCGAGATAAGATCT-ACCATCTTCGA-TCTGCCCCACTACAACTT-AGGGAGATAAGA
53460321 CTAGCGGTTT
Statistics
Matches: 167, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
215 3 0.02
216 86 0.51
217 78 0.47
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (217 bp):
AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTGTTTTA
ATCTCCTCCACTACAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTACAAACTCA
GCGAGATAAGATCTACCATCTTCGATCTGCCCCACTACAACTTAGGGAGATAAGATTTGCTTCTT
CGGTCTACTCTGCTGCAACTTC
Found at i:53461446 original size:14 final size:14
Alignment explanation
Indices: 53461429--53461507 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
53461419 AGCCTCTTCA
53461429 ATTTTTCTTTTTCC
1 ATTTTTCTTTTTCC
* *
53461443 ATTTTCCATTTTCC
1 ATTTTTCTTTTTCC
*
53461457 ATTTTTCATTTT-C
1 ATTTTTCTTTTTCC
* *
53461470 TTTTTTCTTTTTTC
1 ATTTTTCTTTTTCC
* *
53461484 TTTTTTCTTTTTTC
1 ATTTTTCTTTTTCC
53461498 -TTTTT-TTTTT
1 ATTTTTCTTTTT
53461508 TACGACTCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
12 5 0.08
13 16 0.27
14 38 0.64
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTTTTCTTTTTCC
Found at i:53461447 original size:7 final size:7
Alignment explanation
Indices: 53461437--53461469 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
53461427 CAATTTTTCT
53461437 TTTTCCA
1 TTTTCCA
53461444 TTTTCCA
1 TTTTCCA
53461451 TTTTCCA
1 TTTTCCA
*
53461458 TTTTTCA
1 TTTTCCA
53461465 TTTTC
1 TTTTC
53461470 TTTTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTCCA
Found at i:53461453 original size:21 final size:19
Alignment explanation
Indices: 53461429--53461502 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 19
53461419 AGCCTCTTCA
53461429 ATTTTTCTTTTTCCATTTTCC
1 ATTTTTCTTTTT-CATTTT-C
*
53461450 ATTTTCCATTTTTCATTTTC
1 ATTTTTC-TTTTTCATTTTC
* *
53461470 TTTTTTCTTTTTTCTTTTTTC
1 ATTTTTC-TTTTTC-ATTTTC
*
53461491 TTTTTTCTTTTT
1 ATTTTTCTTTTT
53461503 TTTTTTACGA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.37
21 24 0.52
22 5 0.11
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTTCTTTTTCATTTTC
Found at i:53461475 original size:7 final size:7
Alignment explanation
Indices: 53461465--53461508 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
53461455 CCATTTTTCA
53461465 TTTTCTT
1 TTTTCTT
53461472 TTTTCTT
1 TTTTCTT
53461479 TTTTCTT
1 TTTTCTT
53461486 TTTTCTT
1 TTTTCTT
53461493 TTTTCTT
1 TTTTCTT
53461500 TTTT-TT
1 TTTTCTT
53461506 TTT
1 TTT
53461509 ACGACTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTCTT
Found at i:53462419 original size:15 final size:15
Alignment explanation
Indices: 53462399--53462441 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
53462389 TTGACCTCTC
53462399 TTTTTTCTTTTTCTT
1 TTTTTTCTTTTTCTT
*
53462414 TTTTTTCTTCTTCTT
1 TTTTTTCTTTTTCTT
53462429 TTTTTTCATTTTT
1 TTTTTTC-TTTTT
53462442 GATTTGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTCTTTTTCTT
Found at i:53466998 original size:24 final size:23
Alignment explanation
Indices: 53466971--53467026 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
53466961 AAATATTATC
*
53466971 AAATATAATAGTAATAACAAGAAT
1 AAATATAATA-TAAAAACAAGAAT
* *
53466995 AAATAGTAATATAAAAATAATAAT
1 AAATA-TAATATAAAAACAAGAAT
53467019 AAAT-TAAT
1 AAATATAAT
53467027 TAATAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.14
24 19 0.68
25 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (23 bp):
AAATATAATATAAAAACAAGAAT
Found at i:53473858 original size:2 final size:2
Alignment explanation
Indices: 53473845--53473887 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
53473835 ATTCTCCTTT
*
53473845 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53473887 T
1 T
53473888 TAAGTTCCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:53476307 original size:26 final size:26
Alignment explanation
Indices: 53476278--53476329 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
53476268 TTTTAATTAC
*
53476278 ATGTGTTTCTATT-TGTTTTTTATTTG
1 ATGTATTTC-ATTCTGTTTTTTATTTG
* *
53476304 ATGTATTTCATTCTTTTTTTTGTTTG
1 ATGTATTTCATTCTGTTTTTTATTTG
53476330 CAAATTTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.12, C:0.06, G:0.13, T:0.69
Consensus pattern (26 bp):
ATGTATTTCATTCTGTTTTTTATTTG
Found at i:53497527 original size:2 final size:2
Alignment explanation
Indices: 53497520--53497562 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
53497510 TCCCTCTTGA
53497520 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
53497562 A
1 A
53497563 AGAACTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53498945 original size:31 final size:29
Alignment explanation
Indices: 53498909--53498975 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
53498899 ATATGCCCTC
*
53498909 AGTCCCTGTACTTTTCACTATTTTGAAATT-T
1 AGTCCCTGTACTTTT-A-T-TTTTAAAATTAT
* *
53498940 AGTCCCTTTGCTTTTATTTTTAAAATTAT
1 AGTCCCTGTACTTTTATTTTTAAAATTAT
53498969 AGTCCCT
1 AGTCCCT
53498976 TTGATTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.28
29 9 0.28
30 1 0.03
31 13 0.41
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.49
Consensus pattern (29 bp):
AGTCCCTGTACTTTTATTTTTAAAATTAT
Found at i:53502242 original size:23 final size:24
Alignment explanation
Indices: 53502208--53502262 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
53502198 TATATATATT
53502208 TATTTCTTTTAT-T-CACATACATA
1 TATTT-TTTTATATGCACATACATA
* *
53502231 TATTTTTCTTATATGTACATATATA
1 TATTTTT-TTATATGCACATACATA
53502256 TATTTTT
1 TATTTTT
53502263 ATATTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 9 0.33
24 1 0.04
25 15 0.56
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTTTTTTATATGCACATACATA
Found at i:53503910 original size:20 final size:20
Alignment explanation
Indices: 53503885--53503924 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53503875 CGTAAAATGA
*
53503885 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
53503905 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
53503925 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:53503914 original size:34 final size:35
Alignment explanation
Indices: 53503870--53503936 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
53503860 CAGTAAAATA
*
53503870 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
53503904 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
53503937 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:53503940 original size:14 final size:15
Alignment explanation
Indices: 53503864--53503940 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
53503854 GATTGCCAGT
* *
53503864 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
53503878 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
53503892 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
53503912 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
53503927 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
53503941 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:53509231 original size:15 final size:14
Alignment explanation
Indices: 53509196--53509242 Score: 60
Period size: 13 Copynumber: 3.3 Consensus size: 14
53509186 AGCTCAATTC
53509196 CAAAATATTTTTT-
1 CAAAATATTTTTTA
*
53509209 CAATATATTTTTTA
1 CAAAATATTTTTTA
53509223 CAAACATATGTTTTTA
1 CAAA-ATAT-TTTTTA
53509239 CAAA
1 CAAA
53509243 TGATTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 12 0.41
14 3 0.10
15 4 0.14
16 10 0.34
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (14 bp):
CAAAATATTTTTTA
Found at i:53515942 original size:3 final size:3
Alignment explanation
Indices: 53515931--53515997 Score: 125
Period size: 3 Copynumber: 22.0 Consensus size: 3
53515921 ATGATGTATG
53515931 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53515977 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
53515998 TTCATCTTGA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53522502 original size:21 final size:19
Alignment explanation
Indices: 53522464--53522715 Score: 153
Period size: 19 Copynumber: 12.6 Consensus size: 19
53522454 GGCGCCAATG
* *
53522464 GTAATTTTGTACGTATATT
1 GTAATTTTGTATGAATATT
*
53522483 GTAACTTTTTGTGTGAATATT
1 GTAA--TTTTGTATGAATATT
*
53522504 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
53522523 GTAATTATTTTAT--A-ATT
1 GTAATT-TTGTATGAATATT
*
53522540 -T-ATTTTGTATTTATAGTTATT
1 GTAATTTTGTA-TGA-A--TATT
53522561 GATTAGTATTTTGTATGAATATT
1 G--TA--ATTTTGTATGAATATT
*
53522584 GTAATTTTGAATGAATATT
1 GTAATTTTGTATGAATATT
*
53522603 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
53522626 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
53522646 GT-ATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
53522664 GTAATTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
53522685 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
53522704 GTAATTTTGTAT
1 GTAATTTTGTAT
53522716 AATTAATTTG
Statistics
Matches: 185, Mismatches: 19, Indels: 58
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.02
15 4 0.02
16 1 0.01
17 8 0.04
18 6 0.03
19 75 0.41
20 17 0.09
21 41 0.22
22 4 0.02
23 9 0.05
24 4 0.02
25 2 0.01
26 2 0.01
27 8 0.04
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.56
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:53522612 original size:61 final size:58
Alignment explanation
Indices: 53522507--53522715 Score: 167
Period size: 61 Copynumber: 3.5 Consensus size: 58
53522497 GAATATTATA
* * **
53522507 ATTTTGTATGAATATTGTAATTATTTTAT-AAT-TTATTTTGTATTTATAGTTATTGATTAGT
1 ATTTTGTATGAATATTGTAATT-TTGTATGAATATTGTAAT-TATTTATA-TTATT-ATT-GT
*
53522568 ATTTTGTATGAATATTGTAATTTTGAATGAATATTGTAATTATTTTATAATTAATT-TTGT
1 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTA-TTTAT-ATT-ATTATTGT
* * * * * * *
53522628 ATTTATAGTTTTGGAT-TAGT-ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGT
1 ATTT-T-G-TATGAATATTGTAATTTTGTATGAATATTGTAATTATTTATATTATTATTGT
53522687 AATTTTGTATGAATATTGTAATTTTGTAT
1 -ATTTTGTATGAATATTGTAATTTTGTAT
53522716 AATTAATTTG
Statistics
Matches: 120, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
57 5 0.04
58 6 0.05
59 16 0.13
60 18 0.15
61 51 0.43
62 15 0.12
63 9 0.08
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.56
Consensus pattern (58 bp):
ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTATATTATTATTGT
Found at i:53522625 original size:80 final size:80
Alignment explanation
Indices: 53522489--53522690 Score: 334
Period size: 80 Copynumber: 2.5 Consensus size: 80
53522479 TATTGTAACT
* * *
53522489 TTTTGTGTGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTTATTTTGTATTTAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
53522554 AGTTATT-GATTAGTA
66 AGTT-TTGGATTAGTA
*
53522569 TTTTGTATGAATATTGTAATTTTGAATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
53522634 AGTTTTGGATTAGTA
66 AGTTTTGGATTAGTA
53522649 TTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAA--TTTTGTATGAATATTGTAATT
53522691 TTGTATGAAT
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
79 2 0.02
80 92 0.81
82 20 0.18
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.56
Consensus pattern (80 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
AGTTTTGGATTAGTA
Found at i:53522703 original size:40 final size:40
Alignment explanation
Indices: 53522568--53522711 Score: 129
Period size: 40 Copynumber: 3.6 Consensus size: 40
53522558 ATTGATTAGT
*
53522568 ATTTTGTATGAATATTGTAA--TTTTGAATGAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTA
* * * * * *
53522606 ATTATTTTAT-AATTAATTTTGT-ATTTATAGTTTTGGAT-TAGT-
1 ATT-TTGTATGAA-T-A--TTGTAATTTTTTG-TATGAATATTGTA
53522648 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTA
53522688 ATTTTGTATGAATATTGTAATTTT
1 ATTTTGTATGAATATTGTAATTTT
53522712 GTATAATTAA
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
38 14 0.17
39 15 0.19
40 26 0.32
41 7 0.09
42 9 0.11
43 6 0.07
44 4 0.05
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (40 bp):
ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTA
Found at i:53522765 original size:59 final size:60
Alignment explanation
Indices: 53522702--53522822 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
53522692 TGTATGAATA
* * ** *
53522702 TTGTAATT-TTGTATAA-TTAATTTGTTAGTAATTTAAGATTATGCTATAAATTTTTGTGT
1 TTGTAATTATT-TAAAATTTAATTTATTAGTAATTTAAGATTAAACTATAAATTGTTGTGT
*
53522761 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAACTATAAATTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAAGATTAAACTATAAATTGTTGTGT
53522821 TT
1 TT
53522823 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
59 12 0.22
60 42 0.78
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAAGATTAAACTATAAATTGTTGTGT
Found at i:53528569 original size:21 final size:21
Alignment explanation
Indices: 53528545--53528586 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53528535 TAATTTAAAT
* *
53528545 TAGAATAAAATCTAGATTTTA
1 TAGAATAAAATATAAATTTTA
*
53528566 TAGAATTAAATATAAATTTTA
1 TAGAATAAAATATAAATTTTA
53528587 AAACAAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
TAGAATAAAATATAAATTTTA
Found at i:53532798 original size:5 final size:6
Alignment explanation
Indices: 53532781--53532806 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53532771 AATGATAATG
53532781 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
53532807 AAATAGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:53532937 original size:25 final size:26
Alignment explanation
Indices: 53532891--53532939 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
53532881 GTTTTTAATT
*
53532891 TATTTTAAAGTTATTTTGTTAGTTAC
1 TATTATAAAGTTATTTTGTTAGTTAC
53532917 TATTATAAA-TTA-TTTGTTTAGTT
1 TATTATAAAGTTATTTTG-TTAGTT
53532940 TAATGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (26 bp):
TATTATAAAGTTATTTTGTTAGTTAC
Found at i:53536901 original size:33 final size:33
Alignment explanation
Indices: 53536848--53536936 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
53536838 CAATGAACTT
* *
53536848 GAGCTCGA-AGGAGTGAAGTACTGCGGTGGATA-
1 GAGCT-GAGAGGAGTGGAGTACTGAGGTGGATAC
* * * *
53536880 TAGGTCGGGAGGAGTGGAGTACTAAGGTGGATAC
1 GAGCT-GAGAGGAGTGGAGTACTGAGGTGGATAC
53536914 GAGCTGAGAGGAGTGGAGTACTG
1 GAGCTGAGAGGAGTGGAGTACTG
53536937 TGATGGTAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
32 5 0.11
33 37 0.82
34 3 0.07
ACGTcount: A:0.27, C:0.10, G:0.44, T:0.19
Consensus pattern (33 bp):
GAGCTGAGAGGAGTGGAGTACTGAGGTGGATAC
Found at i:53538700 original size:27 final size:27
Alignment explanation
Indices: 53538670--53538756 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
53538660 ACACAGTGAA
*
53538670 AACATAGTAAATACGTGAGTAACAAAG
1 AACACAGTAAATACGTGAGTAACAAAG
* * *
53538697 AACACAGTAAAAAAC---A-CAATAAA-
1 AACACAGT-AAATACGTGAGTAACAAAG
*
53538720 AA-ATAGTAAATACGTGAGTAACAAAG
1 AACACAGTAAATACGTGAGTAACAAAG
53538746 AACACAGTAAA
1 AACACAGTAAA
53538757 AAACACAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
21 5 0.11
22 4 0.09
23 2 0.05
24 6 0.14
25 6 0.14
26 2 0.05
27 14 0.32
28 5 0.11
ACGTcount: A:0.59, C:0.13, G:0.14, T:0.15
Consensus pattern (27 bp):
AACACAGTAAATACGTGAGTAACAAAG
Found at i:53538726 original size:49 final size:49
Alignment explanation
Indices: 53538655--53538773 Score: 211
Period size: 49 Copynumber: 2.4 Consensus size: 49
53538645 TTGATAAACA
* *
53538655 AAAAAACACAGTGAAAACATAGTAAATACGTGAGTAACAAAGAACACAGT
1 AAAAAACACAAT-AAAAAATAGTAAATACGTGAGTAACAAAGAACACAGT
53538705 AAAAAACACAATAAAAAATAGTAAATACGTGAGTAACAAAGAACACAGT
1 AAAAAACACAATAAAAAATAGTAAATACGTGAGTAACAAAGAACACAGT
53538754 AAAAAACACAATAAAAAATA
1 AAAAAACACAATAAAAAATA
53538774 TCTCATAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
49 56 0.84
50 11 0.16
ACGTcount: A:0.62, C:0.13, G:0.12, T:0.13
Consensus pattern (49 bp):
AAAAAACACAATAAAAAATAGTAAATACGTGAGTAACAAAGAACACAGT
Found at i:53539051 original size:109 final size:108
Alignment explanation
Indices: 53538887--53539686 Score: 802
Period size: 109 Copynumber: 7.4 Consensus size: 108
53538877 AATAAAATTT
* * * ** * *
53538887 ACATT-ATAACAAATCACAATACACATTAAACT--GTACAAATAATTTATAGCCTAATCATAAAT
1 ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAAT
53538949 TACTAACAAAATAACTTTAAAATAATTTAAAAAAAACAAAAAAA
66 TACTAACAAAATAACTTTAAAATAATTT-AAAAAAACAAAAAAA
* * *
53538993 AAATTCATAAAAAATCACAATAAATACTAAACTAAACACAAACAATTTATAATCTAATCATAAAT
1 ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAAT
* * **
53539058 TACTAACAAAATAAATTTAAAATAATTTAAAAAATAGAAAAATTT
66 TACTAACAAAATAACTTTAAAATAATTTAAAAAA-ACAAAAA-AA
* * * * * *
53539103 ACATTTATAACAAGTCACAATAAACACTAAACTAAATACAAAAAATTTATAATCTAATCATAAAT
1 ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAAT
* *
53539168 TGCTAACAAAATAACTTTAAAATAATTTTAAAAAACAAAAAAA
66 TACTAACAAAATAACTTTAAAATAATTTAAAAAAACAAAAAAA
* *
53539211 TACATTCATAAAAGATCACAATAAACACTAAACTAAATACAAACAATTTATAACCTAATCATAAA
1 -ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAA
* * * *
53539276 TTACTAACAAAACAACATTCAAATAA-TTAAGAAAACAAAAATAAA
65 TTACTAACAAAATAACTTTAAAATAATTTAAAAAAAC-AAAA-AAA
* * *
53539321 TTTACATTAATAAAAAATCACAATAAACATTAAACTAAAGACACAAACAATTTATAACCTAACCA
1 ---ACATTCATAAAAAATCACAATAAACACTAAACT-AA-ACACAAACAATTTATAACCTAATCA
* * *
53539386 TAAATTACTAACAAAATGACTATAAAATAATTTAAAAAATATAAAAAAA
61 TAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAA-ACAAAAAAA
* * *
53539435 TTACATTCATAAAAAATCAC-A-GAACACTAAACTAAACACAAACAATTTATAATCTAACCATAA
1 --ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAA
* * ********
53539498 ATTACTAACAAAATAACTATAAAATAA-CT----AAATTTTTTTT
64 ATTACTAACAAAATAACTTTAAAATAATTTAAAAAAACAAAAAAA
* * * *
53539538 ACATTAATAAAAATTCAC-A-AAACGCTAAACTAAACACAAACAATTTAGAACCTAATCATAAAT
1 ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAAT
* * * *
53539601 TACTAACAAAAAAACTTTAAAATAATTTTAAAATATAAAAAAA
66 TACTAACAAAATAACTTTAAAATAATTTAAAAAAACAAAAAAA
* * * * *
53539644 TTTAAATTCATAACAAAGCAC-A-AATCACTAAACTAAATACAAA
1 ---ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAA
53539687 AAAAAAAACT
Statistics
Matches: 582, Mismatches: 90, Indels: 41
0.82 0.13 0.06
Matches are distributed among these distances:
101 79 0.14
102 1 0.00
103 2 0.00
104 2 0.00
106 7 0.01
107 23 0.04
108 15 0.03
109 233 0.40
110 94 0.16
111 10 0.02
112 32 0.05
113 21 0.04
114 51 0.09
115 11 0.02
116 1 0.00
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (108 bp):
ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAAT
TACTAACAAAATAACTTTAAAATAATTTAAAAAAACAAAAAAA
Found at i:53539166 original size:219 final size:218
Alignment explanation
Indices: 53538880--53539686 Score: 930
Period size: 219 Copynumber: 3.7 Consensus size: 218
53538870 AATCATAAAT
* * * * * *
53538880 AAAATTTACATT-ATAACAAATCACAATACACATTAAACT--GTACAAATAATTTATAGCCTAAT
1 AAAATTTACATTAATAAAAAATCACAATAAACACTAAACTAAATACAAAAAATTTATAACCTAAT
*
53538942 CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAACAAAAAAA-AAATTCATAAAAA
66 CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAACAAAAAAATACATTCATAAAAA
*
53539006 ATCACAATAAATACTAAACTAAACACAAACAATTTATAATCTAATCATAAATTACTAACAAAATA
131 ATCACAATAAACACTAAACTAAACACAAACAATTTATAATCTAATCATAAATTACTAACAAAATA
53539071 AATTTAAAATAATTTAAAAAATAGA
196 AATTTAAAATAA-TTAAAAAATA-A
* * * *
53539096 AAAATTTACATTTATAACAAGTCACAATAAACACTAAACTAAATACAAAAAATTTATAATCTAAT
1 AAAATTTACATTAATAAAAAATCACAATAAACACTAAACTAAATACAAAAAATTTATAACCTAAT
* * *
53539161 CATAAATTGCTAACAAAATAACTTTAAAATAATTT-TAAAAAACAAAAAAATACATTCATAAAAG
66 CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAACAAAAAAATACATTCATAAAAA
* * *
53539225 ATCACAATAAACACTAAACTAAATACAAACAATTTATAACCTAATCATAAATTACTAACAAAACA
131 ATCACAATAAACACTAAACTAAACACAAACAATTTATAATCTAATCATAAATTACTAACAAAATA
* *
53539290 ACA-TTCAAATAATTAAGAAAACAAAA
196 A-ATTTAAAATAATT-A-AAAA-ATAA
* *
53539316 ATAAATTTACATTAATAAAAAATCACAATAAACATTAAACTAAAGACACAAACAATTTATAACCT
1 A-AAATTTACATTAATAAAAAATCACAATAAACACTAAACTAAATACA-AAA-AATTTATAACCT
* * * * *
53539381 AACCATAAATTACTAACAAAATGACTATAAAATAATTTAAAAAATATAAAAAAATTACATTCATA
63 AATCATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAACAAAAAAA-TACATTCATA
* *
53539446 AAAAATCAC-A-GAACACTAAACTAAACACAAACAATTTATAATCTAACCATAAATTACTAACAA
127 AAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAATCTAATCATAAATTACTAACAA
* * *
53539509 AATAACTATAAAATAACT---AAAT--
192 AATAAATTTAAAATAATTAAAAAATAA
**** * * * * *
53539531 TTTTTTTACATTAATAAAAATTCAC-A-AAACGCTAAACTAAACACAAACAATTTAGAACCTAAT
1 AAAATTTACATTAATAAAAAATCACAATAAACACTAAACTAAATACAAAAAATTTATAACCTAAT
* * ** * *
53539594 CATAAATTACTAACAAAAAAACTTTAAAATAATTTTAAAATATAA-AAAAATTTAAATTCATAAC
66 CATAAATTACTAACAAAATAACTTTAAAATAA-TTTAAAA-AAAACAAAAAAATACATTCATAAA
* * *
53539658 AAAGCAC-A-AATCACTAAACTAAATACAAA
129 AAATCACAATAAACACTAAACTAAACACAAA
53539687 AAAAAAAACT
Statistics
Matches: 510, Mismatches: 65, Indels: 38
0.83 0.11 0.06
Matches are distributed among these distances:
210 77 0.15
211 14 0.03
212 18 0.04
213 1 0.00
214 20 0.04
216 12 0.02
217 25 0.05
218 18 0.04
219 135 0.26
220 7 0.01
221 43 0.08
222 3 0.01
223 106 0.21
224 13 0.03
225 18 0.04
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (218 bp):
AAAATTTACATTAATAAAAAATCACAATAAACACTAAACTAAATACAAAAAATTTATAACCTAAT
CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAACAAAAAAATACATTCATAAAAA
ATCACAATAAACACTAAACTAAACACAAACAATTTATAATCTAATCATAAATTACTAACAAAATA
AATTTAAAATAATTAAAAAATAA
Found at i:53539556 original size:101 final size:101
Alignment explanation
Indices: 53539435--53539625 Score: 301
Period size: 101 Copynumber: 1.9 Consensus size: 101
53539425 TATAAAAAAA
* * * *
53539435 TTACATTCATAAAAAATCACAGAACACTAAACTAAACACAAACAATTTATAATCTAACCATAAAT
1 TTACATTAATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTAGAACCTAACCATAAAT
*
53539500 TACTAACAAAATAACTATAAAATAACTAAATTTTTT
66 TACTAACAAAAAAACTATAAAATAACTAAATTTTTT
* * *
53539536 TTACATTAATAAAAATTCACAAAACGCTAAACTAAACACAAACAATTTAGAACCTAATCATAAAT
1 TTACATTAATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTAGAACCTAACCATAAAT
*
53539601 TACTAACAAAAAAACTTTAAAATAA
66 TACTAACAAAAAAACTATAAAATAA
53539626 TTTTAAAATA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.27
Consensus pattern (101 bp):
TTACATTAATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTAGAACCTAACCATAAAT
TACTAACAAAAAAACTATAAAATAACTAAATTTTTT
Found at i:53539746 original size:4 final size:4
Alignment explanation
Indices: 53539737--53539822 Score: 172
Period size: 4 Copynumber: 21.5 Consensus size: 4
53539727 TACTAAAATG
53539737 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53539785 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
53539823 TCATTCATTC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 82 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:53541673 original size:2 final size:2
Alignment explanation
Indices: 53541666--53541713 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
53541656 AATGAAGTGT
53541666 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53541708 TA TA TA
1 TA TA TA
53541714 ATTGAGGTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53547422 original size:37 final size:37
Alignment explanation
Indices: 53547381--53547455 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
53547371 AATTAATGAA
*
53547381 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATGGAAGTGAATATGATATTGAGT
*
53547418 TGATTAATAGATAATGGAAGTGAATGTGATATTGAGT
1 TGATTAATAGATAATGGAAGTGAATATGATATTGAGT
53547455 T
1 T
53547456 ATGAAATGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (37 bp):
TGATTAATAGATAATGGAAGTGAATATGATATTGAGT
Found at i:53550209 original size:25 final size:25
Alignment explanation
Indices: 53550180--53550230 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
53550170 AGGAGAGAAA
53550180 GAATGCGAGAGAAAGAAAGTAAGTG
1 GAATGCGAGAGAAAGAAAGTAAGTG
53550205 GAATGCGAGAGAAAGAAAGTAAGTG
1 GAATGCGAGAGAAAGAAAGTAAGTG
53550230 G
1 G
53550231 GGAAAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.04, G:0.37, T:0.12
Consensus pattern (25 bp):
GAATGCGAGAGAAAGAAAGTAAGTG
Found at i:53552080 original size:35 final size:35
Alignment explanation
Indices: 53551975--53552086 Score: 116
Period size: 35 Copynumber: 3.1 Consensus size: 35
53551965 AGTGAGCCCT
*
53551975 GATAAACCAACAATGTTTGCGCCCAGCGCTAGTTG
1 GATAAACCGACAATGTTTGCGCCCAGCGCTAGTTG
* * ** * *
53552010 AATATACCGACAATTGAAAGTGAGCCCAGCTCTAGTTG
1 GATAAACCGACAA-TG--TTTGCGCCCAGCGCTAGTTG
* *
53552048 GATAAATCGACAATGTTTGCGCCCAGCGCTAGTCG
1 GATAAACCGACAATGTTTGCGCCCAGCGCTAGTTG
53552083 GATA
1 GATA
53552087 TACCAACGAT
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
35 29 0.49
36 2 0.03
37 2 0.03
38 26 0.44
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (35 bp):
GATAAACCGACAATGTTTGCGCCCAGCGCTAGTTG
Found at i:53552144 original size:75 final size:73
Alignment explanation
Indices: 53551975--53552161 Score: 223
Period size: 75 Copynumber: 2.5 Consensus size: 73
53551965 AGTGAGCCCT
* * * * * *
53551975 GATAAACCAACAATGTTTGCGCCCAGCGCTAGTTGAATATACCGACAATTGAAAGTGAGCCCAGC
1 GATAAATCAACAATGTTTGCGCCCAGCGCTAGTCGGATATACCAACAAATAAAAGTGAGCCCAGC
53552040 TCTAGTTG
66 TCTAGTTG
* * *
53552048 GATAAATCGACAATGTTTGCGCCCAGCGCTAGTCGGATATACCAACGATAATAAAAGTGAGTCTA
1 GATAAATCAACAATGTTTGCGCCCAGCGCTAGTCGGATATACCAAC-A-AATAAAAGTGAGCCCA
53552113 GCTCTAGTTG
64 GCTCTAGTTG
** * *
53552123 GATGAAA-CAACGGTGTTTGCGCCCAGCGTTAATCGGATA
1 GAT-AAATCAACAATGTTTGCGCCCAGCGCTAGTCGGATA
53552162 AACCGATAGT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
73 41 0.42
74 1 0.01
75 52 0.54
76 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (73 bp):
GATAAATCAACAATGTTTGCGCCCAGCGCTAGTCGGATATACCAACAAATAAAAGTGAGCCCAGC
TCTAGTTG
Found at i:53558793 original size:15 final size:15
Alignment explanation
Indices: 53558773--53558802 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53558763 TTCACTATTA
*
53558773 TGTCTTTTGTATTTT
1 TGTCTTTTATATTTT
53558788 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
53558803 GCATGCATAG
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:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATATTTT
Found at i:53560461 original size:37 final size:38
Alignment explanation
Indices: 53560415--53560486 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
53560405 AAAAATATTA
*
53560415 TTATTTTAATAGT-TTAATATTAAATTAA-ATTAAATAC
1 TTATCTTAATAGTATT-ATATTAAATTAATATTAAATAC
* *
53560452 TTATCTTAATAGTATTTTATTAATTTAATATTAAA
1 TTATCTTAATAGTATTATATTAAATTAATATTAAA
53560487 GTGATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 22 0.73
38 8 0.27
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
TTATCTTAATAGTATTATATTAAATTAATATTAAATAC
Found at i:53566098 original size:18 final size:18
Alignment explanation
Indices: 53566064--53566098 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53566054 ATTATATTTT
*
53566064 TATCGATATCATCTTTGA
1 TATCGATACCATCTTTGA
*
53566082 TATCGATACCATTTTTG
1 TATCGATACCATCTTTG
53566099 CATTCTGACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (18 bp):
TATCGATACCATCTTTGA
Found at i:53566155 original size:21 final size:21
Alignment explanation
Indices: 53566130--53566171 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53566120 CAATCAATTA
*
53566130 CAAAAGGTATCAATACCTTTT
1 CAAAAAGTATCAATACCTTTT
* *
53566151 CAAAAATTATCGATACCTTTT
1 CAAAAAGTATCAATACCTTTT
53566172 ACCAGGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (21 bp):
CAAAAAGTATCAATACCTTTT
Found at i:53566675 original size:73 final size:75
Alignment explanation
Indices: 53566598--53566736 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 75
53566588 ATAGTTTAAT
* ** *
53566598 TTTTTTCAATTTAGTCCTTTGTAAATATACTATAGCCCTCCTAAAAA-ATAAGTAGG-CCCTCCA
1 TTTTTGCAATTTACCCCTTTGTAAATATACTATAGCCCTCCTAAAAATAGAAGTAGGCCCCTCCA
53566661 AGGTTTAAGA
66 AGGTTTAAGA
* * *
53566671 TTTTTGCAATTTCCCCCTTTGTATATATATTATAGCCCTCCTAAAAATAGAAGTAGGCCCCTCCA
1 TTTTTGCAATTTACCCCTTTGTAAATATACTATAGCCCTCCTAAAAATAGAAGTAGGCCCCTCCA
53566736 A
66 A
53566737 TATTTTTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 41 0.72
74 8 0.14
75 8 0.14
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (75 bp):
TTTTTGCAATTTACCCCTTTGTAAATATACTATAGCCCTCCTAAAAATAGAAGTAGGCCCCTCCA
AGGTTTAAGA
Found at i:53566911 original size:2 final size:2
Alignment explanation
Indices: 53566904--53566937 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
53566894 GTAATACAAT
53566904 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53566938 AAGAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53566973 original size:25 final size:25
Alignment explanation
Indices: 53566939--53566991 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
53566929 ATATATATAA
53566939 AGAAAAGAAAAGATGATAGATGACC
1 AGAAAAGAAAAGATGATAGATGACC
53566964 AGAAAAGAAAAGATGATAGATGACC
1 AGAAAAGAAAAGATGATAGATGACC
53566989 AGA
1 AGA
53566992 CTTTTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.57, C:0.08, G:0.25, T:0.11
Consensus pattern (25 bp):
AGAAAAGAAAAGATGATAGATGACC
Found at i:53567800 original size:17 final size:16
Alignment explanation
Indices: 53567756--53567808 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
53567746 TATGCGATTT
* *
53567756 ATGATTTGAATATGAA
1 ATGATATGAAAATGAA
* *
53567772 ATGAAATTAAAATGAGA
1 ATGATATGAAAATGA-A
53567789 ATGATATGAAAATGGAA
1 ATGATATGAAAAT-GAA
53567806 ATG
1 ATG
53567809 GATTATAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 11 0.38
17 16 0.55
18 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (16 bp):
ATGATATGAAAATGAA
Found at i:53570532 original size:55 final size:55
Alignment explanation
Indices: 53570466--53570578 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
53570456 TCTTCTTAAT
*
53570466 TGTTGGAATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTATTA
1 TGTTGGAATATTACTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTATTA
* * *
53570521 TGTTGGAATATTACTTCTTTTGAATCGATTGTTTATATGTTTACATTGATTGTTA
1 TGTTGGAATATTACTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTATTA
53570576 TGT
1 TGT
53570579 AGCACATCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (55 bp):
TGTTGGAATATTACTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTATTA
Found at i:53583128 original size:41 final size:42
Alignment explanation
Indices: 53583020--53583129 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 42
53583010 TTGTATATAA
** *
53583020 CACCGGCATAAAGCCTGCTAGGCA-CCAAGCTCGATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAAGCTCGATACAATT
* * * *
53583061 CACCGGCACAAAGCCTGCTAGACATAAAATCT-GATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAAGCTCGATACAATT
53583102 CACCGGCATAAAGCCTGCTAGGCATAAA
1 CACCGGCATAAAGCCTGCTAGGCATAAA
53583130 GCCTGAACTT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 55 0.93
42 4 0.07
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (42 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAAGCTCGATACAATT
Found at i:53584316 original size:16 final size:17
Alignment explanation
Indices: 53584295--53584326 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53584285 AAATATGCAA
53584295 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
53584311 TCACATAACTTCATAT
1 TCACATAACTTCATAT
53584327 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:53584635 original size:42 final size:42
Alignment explanation
Indices: 53584488--53584642 Score: 144
Period size: 42 Copynumber: 3.7 Consensus size: 42
53584478 GGCTCGTACA
*
53584488 ATGCCAACGTCCCAGACGTGGTCTTACATGTA-ATCACATAT-G
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATA-CACA-ATCG
**
53584530 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAT-CA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTATACACAAT-CG
* ** *
53584571 ATGCCAATGTCCGGGACATGGTC-TACACGTATACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAA-TCG
53584613 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
53584643 AAAATACATA
Statistics
Matches: 89, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
39 2 0.02
40 8 0.09
41 23 0.26
42 48 0.54
43 8 0.09
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAATCG
Found at i:53588863 original size:10 final size:10
Alignment explanation
Indices: 53588848--53588890 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
53588838 ATATGCAAGA
53588848 GATGTTCATG
1 GATGTTCATG
53588858 GATGTTCATG
1 GATGTTCATG
*
53588868 GATG--CAAG
1 GATGTTCATG
53588876 AGATGTTCATG
1 -GATGTTCATG
53588887 GATG
1 GATG
53588891 CTCAAACAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 3 0.11
9 4 0.14
10 18 0.64
11 3 0.11
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.33
Consensus pattern (10 bp):
GATGTTCATG
Found at i:53589416 original size:22 final size:22
Alignment explanation
Indices: 53589386--53589428 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
53589376 ACACCAAAAC
*
53589386 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
53589408 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
53589429 ATCTCCGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:53589664 original size:43 final size:42
Alignment explanation
Indices: 53589565--53589687 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
53589555 CTTCTAGCAC
* * * * *
53589565 AAACGCCGCTGAAGACTA-AGACCTTTAGCGGCGCTTTAGTGG
1 AAACGCCGCTAAAGACCAGA-ATCTTTAGCGGCGTTTTTGTGG
**
53589607 AAACGCCGCTAAAGACCTTAATCTTTAGCGGCGTTTTTG-GG
1 AAACGCCGCTAAAGACCAGAATCTTTAGCGGCGTTTTTGTGG
* **
53589648 AGAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTT
1 A-AA-CGCCGCTAAAGACCAGAATCTTTAGCGGCGTTTTT
53589688 TTCTCAAATG
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 3 0.04
42 33 0.49
43 31 0.46
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCAGAATCTTTAGCGGCGTTTTTGTGG
Found at i:53589920 original size:43 final size:43
Alignment explanation
Indices: 53589562--53589920 Score: 233
Period size: 43 Copynumber: 8.4 Consensus size: 43
53589552 GCTCTTCTAG
* *** * *
53589562 CACAAACGCCGCTGAAGACTAAGACCTTTAGCGGCGCTTT-AG
1 CACAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGAC
*** * * * *
53589604 TGGAAACGCCGCTAAAGACCTTAATCTTTAGCGGCGTTTTTG-G
1 CACAAACGCCGCTAAAGACCCTGATCTTTAGCGGCG-CTTTGAC
* * * * ** * * ***
53589647 GAGAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTTT
1 CACAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGAC
* * * *
53589690 CTCAAATGCCGC-AATAGACCTTGATCTATAGCGGCGCTTTGAC
1 CACAAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTGAC
* * * * * *
53589733 CACAAACGCCACGAAAAAACCTAATCTTTAGCGGCGCTTT-CC
1 CACAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGAC
* * **
53589775 CTTCAAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTCCC
1 C-ACAAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTGAC
* * **
53589819 CACAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTC
1 CACAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGAC
* *
53589862 CACAAACGCCGCTAAAGACCCTTATCTTTAGTGGCGCTTTGAC
1 CACAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGAC
* *
53589905 CAAAAACGCCACTAAA
1 CACAAACGCCGCTAAA
53589921 TTTGGCAGAT
Statistics
Matches: 247, Mismatches: 61, Indels: 17
0.76 0.19 0.05
Matches are distributed among these distances:
42 37 0.15
43 203 0.82
44 7 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (43 bp):
CACAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGAC
Found at i:53589920 original size:86 final size:86
Alignment explanation
Indices: 53589607--53589920 Score: 280
Period size: 86 Copynumber: 3.7 Consensus size: 86
53589597 GCTTTAGTGG
* * ** * * * * *
53589607 AAACGCCGCTAA-AGACCTTAATCTTTAGCGGCGTTTTTG-GGAGAAGCGCCGCTAAAGATCAGG
1 AAACGCCGC-AATAGACCTTAATCTATAGCGGCG-CTTTGACCACAAACGCCACTAAAGACCATG
* * *
53589670 GTCTTTAGCGGCGTTTTTTTCTC
64 ATCTTTAGCGGCGCTTTTTCCTC
* * * * *
53589693 AAATGCCGCAATAGACCTTGATCTATAGCGGCGCTTTGACCACAAACGCCACGAAAAAACC-TAA
1 AAACGCCGCAATAGACCTTAATCTATAGCGGCGCTTTGACCACAAACGCCAC-TAAAGACCATGA
*
53589757 TCTTTAGCGGCGC-TTTCCCTTC
65 TCTTTAGCGGCGCTTTTTCC-TC
* * ** *
53589779 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGAT
1 AAACGCCGCAATAGACCTTAATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGACCATGAT
* *
53589844 CTTTAGTGGCGCTTTTTCCAC
66 CTTTAGCGGCGCTTTTTCCTC
* * *
53589865 AAACGCCGCTAA-AGACCCTT-ATCTTTAGTGGCGCTTTGACCAAAAACGCCACTAAA
1 AAACGCCGC-AATAGA-CCTTAATCTATAGCGGCGCTTTGACCACAAACGCCACTAAA
53589921 TTTGGCAGAT
Statistics
Matches: 184, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
85 16 0.09
86 153 0.83
87 15 0.08
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (86 bp):
AAACGCCGCAATAGACCTTAATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGACCATGAT
CTTTAGCGGCGCTTTTTCCTC
Found at i:53590339 original size:21 final size:21
Alignment explanation
Indices: 53590313--53590425 Score: 118
Period size: 21 Copynumber: 5.4 Consensus size: 21
53590303 TTTGACGCTG
53590313 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
53590334 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
53590355 CTCTGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
53590376 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
53590397 CTCTACTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
53590418 ATCTGCTT
1 CTCTGCTT
53590426 TAAGCTGCTG
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 78 1.00
ACGTcount: A:0.05, C:0.42, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:53590474 original size:66 final size:66
Alignment explanation
Indices: 53590402--53590542 Score: 205
Period size: 66 Copynumber: 2.1 Consensus size: 66
53590392 GCCGCCTCTA
*
53590402 CTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTTGAACCT
1 CTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTTGAACCT
53590465 CAG
64 CAG
* * * *
53590468 CTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCA
1 CTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCA
53590533 G
66 G
53590534 CTTCTCTCG
1 CTTCTCTCG
53590543 ATGTTGCCTC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.93
67 4 0.06
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCA
G
Found at i:53590558 original size:66 final size:66
Alignment explanation
Indices: 53590402--53590565 Score: 197
Period size: 66 Copynumber: 2.5 Consensus size: 66
53590392 GCCGCCTCTA
* * * * *
53590402 CTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATACTTTCGTTGAACCTC
1 CTTCTCTCGATGCTGCATCCGCTTTAAGTTG-TAGCTGGAGTTCTTCATACTTTCGTTGAACCTC
53590466 AG
65 AG
* * * *
53590468 CTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACCTC
1 CTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATA-CTTTCGTTGAACCTC
53590532 AG
65 AG
* *
53590534 CTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 CTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
53590566 GTAATTTGCT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 1 0.01
66 81 0.94
67 4 0.05
ACGTcount: A:0.13, C:0.27, G:0.19, T:0.41
Consensus pattern (66 bp):
CTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATACTTTCGTTGAACCTCA
G
Found at i:53592723 original size:25 final size:25
Alignment explanation
Indices: 53592671--53592727 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
53592661 AGTATTTCCT
* *
53592671 AATTATGTAAGTTATTTATTACCCA
1 AATTATGTAAGTTATGTATTACCAA
* **
53592696 AATTATGTAAGTTGTGTATTATGAA
1 AATTATGTAAGTTATGTATTACCAA
53592721 AATTATG
1 AATTATG
53592728 CTATGTAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (25 bp):
AATTATGTAAGTTATGTATTACCAA
Found at i:53592741 original size:9 final size:9
Alignment explanation
Indices: 53592729--53592812 Score: 50
Period size: 9 Copynumber: 9.8 Consensus size: 9
53592719 AAAATTATGC
53592729 TATGTAAGT
1 TATGTAAGT
53592738 TATGTAAGT
1 TATGTAAGT
* **
53592747 CACATAAGT
1 TATGTAAGT
53592756 TATGTAAG-
1 TATGTAAGT
* * *
53592764 -AAGTTATT
1 TATGTAAGT
53592772 TATGTAAGT
1 TATGTAAGT
*
53592781 TAT-TTA-T
1 TATGTAAGT
* *
53592788 TATGAAAAT
1 TATGTAAGT
*
53592797 TAAGTAAGT
1 TATGTAAGT
53592806 TATGTAA
1 TATGTAA
53592813 TTTACGAATA
Statistics
Matches: 52, Mismatches: 19, Indels: 8
0.66 0.24 0.10
Matches are distributed among these distances:
7 8 0.15
8 3 0.06
9 41 0.79
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.42
Consensus pattern (9 bp):
TATGTAAGT
Found at i:53592893 original size:33 final size:31
Alignment explanation
Indices: 53592856--53592927 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 31
53592846 AGTTGTAAGT
*
53592856 TGTAAGTTATGTATAATATTAATAACTAACTTA
1 TGTAAGTTAAGTATAATATTAAT--CTAACTTA
* * *
53592889 TGTAATTTAAGTATAATATTAATGTAAGTTA
1 TGTAAGTTAAGTATAATATTAATCTAACTTA
53592920 TGTAAGTT
1 TGTAAGTT
53592928 GTAAGTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 13 0.38
33 21 0.62
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.44
Consensus pattern (31 bp):
TGTAAGTTAAGTATAATATTAATCTAACTTA
Found at i:53592905 original size:81 final size:82
Alignment explanation
Indices: 53592751--53593070 Score: 316
Period size: 81 Copynumber: 3.9 Consensus size: 82
53592741 GTAAGTCACA
** * * * * * * *
53592751 TAAGTTATGTAAGAAGTTATTTATGTAAGTTATTTATTATGA-AAATTAAGTAAGTTATGTAATT
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAAT-ATTAATTAACTAACTTATGTAATT
* *
53592815 TACGAATAATTAAAAAAATG
65 TAAGTATAATT--AAAAATG
53592835 TAAGTTATGTAAGTTGTAAG-T-TGTAAGTTATGTATAATATTAA-TAACTAACTTATGTAATTT
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTT
**
53592897 AAGTATAA-TATTAATG
66 AAGTATAATTAAAAATG
53592913 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTT
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTT
**
53592978 AAGTATAA-TATTAATG
66 AAGTATAATTAAAAATG
* *
53592994 TAAGTTATGTATAATATAAGTGTAATTAGTTATGTAATTTATGTAT--T-TTAATTAACTAACTT
1 TAAGTTATG--TAA-GT---TGT-A--AGTTATGTAAGTTATGTATAATATTAATTAACTAACTT
53593056 ATGTAATTTAAGTAT
57 ATGTAATTTAAGTAT
53593071 TATTTTAAGC
Statistics
Matches: 208, Mismatches: 15, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
78 25 0.12
79 1 0.00
80 23 0.11
81 68 0.33
82 17 0.08
83 4 0.02
84 17 0.08
87 33 0.16
88 2 0.01
90 18 0.09
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (82 bp):
TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTT
AAGTATAATTAAAAATG
Found at i:53592924 original size:9 final size:9
Alignment explanation
Indices: 53592910--53592948 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
53592900 TATAATATTA
53592910 ATGTAAGTT
1 ATGTAAGTT
53592919 ATGTAAG-T
1 ATGTAAGTT
53592927 -TGTAAGTT
1 ATGTAAGTT
53592935 ATGTAAGTT
1 ATGTAAGTT
53592944 ATGTA
1 ATGTA
53592949 TAATATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.21
8 2 0.07
9 20 0.71
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:53592932 original size:16 final size:16
Alignment explanation
Indices: 53592911--53592943 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
53592901 ATAATATTAA
53592911 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
53592927 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
53592943 T
1 T
53592944 ATGTATAATA
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:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:53592994 original size:22 final size:21
Alignment explanation
Indices: 53592969--53593020 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
53592959 TAACTAACTT
53592969 ATGTAATTTAAGTATAATATTA
1 ATGTAATTTAAGTATAATA-TA
* *
53592991 ATGTAAGTTATGTATAATATA
1 ATGTAATTTAAGTATAATATA
53593012 AGTGTAATT
1 A-TGTAATT
53593021 AGTTATGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (21 bp):
ATGTAATTTAAGTATAATATA
Found at i:53593058 original size:56 final size:54
Alignment explanation
Indices: 53592856--53593060 Score: 125
Period size: 56 Copynumber: 3.6 Consensus size: 54
53592846 AGTTGTAAGT
*
53592856 TGTAAGTTATGTATAATATTAA-TAACTAACTTATG--TAATTTAAGTATAA-TATTAA
1 TGTAAGTTATGTAT--T-TTAATTAACTAACTTATGTATAATATAAGT-TAATTATT-A
* ** * *
53592911 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAA-TTAACTAACTTA
1 TGTAAGTTATGT-A-TTTTAA-TTAACTAACTTATGTATAATA-TAAGTTAA-TTA-TTA
* * ** * *
53592970 TGTAATTTAAGTATAAT-ATTAATGTAAGTTATGTATAATATAAGTGTAATTAGTTA
1 TGTAAGTTATGTATTTTAATTAA-CTAACTTATGTATAATATAAGT-TAATTA-TTA
*
53593026 TGTAATTTATGTATTTTAATTAACTAACTTATGTA
1 TGTAAGTTATGTATTTTAATTAACTAACTTATGTA
53593061 ATTTAAGTAT
Statistics
Matches: 118, Mismatches: 18, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
54 3 0.03
55 19 0.16
56 59 0.50
57 14 0.12
58 6 0.05
59 15 0.13
60 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (54 bp):
TGTAAGTTATGTATTTTAATTAACTAACTTATGTATAATATAAGTTAATTATTA
Found at i:53594486 original size:29 final size:30
Alignment explanation
Indices: 53594427--53594484 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53594417 TCCGAGCCTG
*
53594427 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
53594457 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
53594485 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:53594714 original size:13 final size:13
Alignment explanation
Indices: 53594696--53594727 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53594686 TTTCCAGCAA
53594696 TTATGAATTTATT
1 TTATGAATTTATT
53594709 TTATGAATTTATT
1 TTATGAATTTATT
*
53594722 TGATGA
1 TTATGA
53594728 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:53594952 original size:50 final size:50
Alignment explanation
Indices: 53594822--53595050 Score: 253
Period size: 50 Copynumber: 4.4 Consensus size: 50
53594812 ATTTGGGTAA
* *
53594822 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
53594878 AGAGGTCTCC-TGTAAGACCATGTCTGGGACATGACATGGGCACCGAGACG
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
53594928 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
53594978 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
53595028 AGAACATCCCATGTAAGACCATG
1 AG-AGGTCCCATGTAAGACCATG
53595051 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
49 2 0.01
50 90 0.59
51 16 0.11
52 1 0.01
53 3 0.02
55 2 0.01
56 36 0.24
57 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:53595016 original size:100 final size:103
Alignment explanation
Indices: 53594822--53595050 Score: 311
Period size: 100 Copynumber: 2.2 Consensus size: 103
53594812 ATTTGGGTAA
*
53594822 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCTC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* * *
53594887 CTGTAAGACCATGTCTGGGACATGACATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGACATGGGCACCAACACG
* * *
53594928 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
* *
53594990 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGACATGGGCACCAACACG
*
53595028 AGAACATCCCATGTAAGACCATG
1 AG-AGATCCCATGTAAGACCATG
53595051 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
100 49 0.44
101 20 0.18
105 2 0.02
106 40 0.36
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGACATGGGCACCAACACG
Found at i:53597532 original size:21 final size:21
Alignment explanation
Indices: 53597508--53597553 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
53597498 ACATTATTAG
53597508 TTTTTTTATTTCCTTT-TTATAT
1 TTTTTTTATTT--TTTCTTATAT
53597530 TTTTTTTATTTTTTCTTATAT
1 TTTTTTTATTTTTTCTTATAT
53597551 TTT
1 TTT
53597554 GGTCCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.13
21 9 0.39
22 11 0.48
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTATTTTTTCTTATAT
Found at i:53597899 original size:17 final size:18
Alignment explanation
Indices: 53597866--53597904 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
53597856 ATAAAACTAA
53597866 TTAATCTGAGCTTAAACC
1 TTAATCTGAGCTTAAACC
*
53597884 TTAATCTGA-TTTAAACC
1 TTAATCTGAGCTTAAACC
53597901 TTAA
1 TTAA
53597905 ATCACTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (18 bp):
TTAATCTGAGCTTAAACC
Found at i:53598083 original size:91 final size:91
Alignment explanation
Indices: 53597950--53598192 Score: 440
Period size: 91 Copynumber: 2.7 Consensus size: 91
53597940 AACCCTTAAA
53597950 CCCTAAACATTATTTAATATA-A-AAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
1 CCCTAAACATTATTTAATATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
53598013 TCGACCCCGAATCACTAACCCCAAAC
66 TCGACCCCGAATCACTAACCCCAAAC
53598039 CCCTAAACATTATTTAATATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
1 CCCTAAACATTATTTAATATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
*
53598104 TCGACCCCGAATCACTAACCCCTAAC
66 TCGACCCCGAATCACTAACCCCAAAC
*
53598130 CCCTAAATATTATTT-A-ATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
1 CCCTAAACATTATTTAATATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
53598193 CCTAAATCCC
Statistics
Matches: 150, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
89 68 0.45
90 2 0.01
91 80 0.53
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.27
Consensus pattern (91 bp):
CCCTAAACATTATTTAATATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
TCGACCCCGAATCACTAACCCCAAAC
Found at i:53598199 original size:20 final size:21
Alignment explanation
Indices: 53598174--53598212 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53598164 ACTAATTAAT
53598174 CTAAAT-CCTAAACCCTAACC
1 CTAAATCCCTAAACCCTAACC
*
53598194 CTAAATCCCTAACCCCTAA
1 CTAAATCCCTAAACCCTAA
53598213 ACATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAAATCCCTAAACCCTAACC
Found at i:53598955 original size:113 final size:113
Alignment explanation
Indices: 53598757--53599467 Score: 1138
Period size: 113 Copynumber: 6.3 Consensus size: 113
53598747 AGATAAAATG
* * *
53598757 TTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTCAGAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTT-TACAGAAAC
*
53598822 GCCGCTAAAG-CCCCAAAAACTCAGAAAACGGTGCCGTCGGGCTTAGGC
65 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * *
53598870 TTTTTGCGGCGCATTTAGAAAAACGCCGTTAAAGACCTGAGCATTAGCGGCGCTTTACAGAAACG
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTTTACAGAAACG
53598935 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
66 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
53598983 TTTTTGCGGCGCTTTTAAAAAAACGCTGCTAAACACCTGAGCATTAGCGGCGCTTTACAGAAACG
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTTTACAGAAACG
53599048 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
66 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
53599096 TTTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCAGCGCATTACAGAATC
1 -TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTTTACAGAAAC
*
53599161 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGTTTAGGC
65 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
53599210 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCATTACAGAAACA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTTTACAGAAACG
*
53599275 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGTTTAGGC
66 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * * *
53599323 TTTTTGCGGCGCTTTTAAAAAAAGGCCACTAAAGACCTGAGAATTAGCGGCGCTGTATAGAAATG
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTTTACAGAAACG
*
53599388 CCGCTAAAGACCCCCAAAAACTCAG-AAACGGTGCCGTTTGGCTTAGGC
66 CCGCTAAAGA-CCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
53599436 TTTTTGCGGCGCTTTCAAATAAATGCCGCTAA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAA
53599468 TGCTTATTTT
Statistics
Matches: 561, Mismatches: 34, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
112 18 0.03
113 423 0.75
114 120 0.21
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (113 bp):
TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTTTACAGAAACG
CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
Found at i:53599210 original size:227 final size:225
Alignment explanation
Indices: 53598757--53599467 Score: 1131
Period size: 227 Copynumber: 3.1 Consensus size: 225
53598747 AGATAAAATG
* *
53598757 TTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTCAGAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TACAGAAAC
* *
53598822 GCCGCTAAAG-CCCCAAAAACTCAGAAAACGGTGCCGTCGGGCTTAGGCTTTTTGCGGCGCATTT
65 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTT
* * * *
53598886 AGAAAAACGCCGTTAAAGACCTGAGCATTAGCGGCGCTTTACAGAAACGCCGCTAAAGACCCCAA
130 AAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGC-TTACAGAATCGCCGCTAAAGACCCCAA
53598951 AAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
194 AAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
53598983 TTTTTGCGGCGCTTTTAAAAAAACGCTGCTAAACACCTGAGCATTAGCGGCGCTTTACAGAAACG
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACAGAAACG
53599048 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTTGCGGCGCTTTT
66 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC-TTTTTGCGGCGCTTTT
*
53599113 AAAAAAACGCCGCTAAAGACCTGAGAATTAGCAGCGCATTACAGAATCGCCGCTAAAGACCCCAA
130 AAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGC-TTACAGAATCGCCGCTAAAGACCCCAA
*
53599178 AAACTCAGAAAACGGTGCCGTTGGGTTTAGGC
194 AAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
53599210 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCATTACAGAAACA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACAGAAACG
*
53599275 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGTTTAGGCTTTTTGCGGCGCTTTTA
66 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTA
* * *
53599340 AAAAAAGGCCACTAAAGACCTGAGAATTAGCGGCGCTGTATAGAAAT-GCCGCTAAAGACCCCCA
131 AAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCT-TACAG-AATCGCCGCTAAAGA-CCCCA
*
53599404 AAAACTCAG-AAACGGTGCCGTTTGGCTTAGGC
193 AAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
53599436 TTTTTGCGGCGCTTTCAAATAAATGCCGCTAA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAA
53599468 TGCTTATTTT
Statistics
Matches: 452, Mismatches: 28, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
225 19 0.04
226 204 0.45
227 229 0.51
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (225 bp):
TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACAGAAACG
CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTA
AAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCTTACAGAATCGCCGCTAAAGACCCCAAAA
ACTCAGAAAACGGTGCCGTTGGGCTTAGGC
Found at i:53599393 original size:340 final size:338
Alignment explanation
Indices: 53598757--53599467 Score: 1138
Period size: 340 Copynumber: 2.1 Consensus size: 338
53598747 AGATAAAATG
* * *
53598757 TTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTATTCAGAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCAGCGCTTA-TCAGAAAC
53598822 GCCGCTAAAGCCCCAAAAACTCAGAAAACGGTGCCGTCGGGCTTAGGCTTTTTGCGGCGCATTTA
65 GCCGCTAAAGCCCCAAAAACTCAGAAAACGGTGCCGTCGGGCTTAGGCTTTTTGCGGCGCATTTA
* * * * *
53598887 GAAAAACGCCGTTAAAGACCTGAGCATTAGCGGCGCTTTACAGAAACGCCGCTAAAGACCCCAAA
130 AAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCATTACAGAAACACCGCTAAAGACCCCAAA
**
53598952 AACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCTGCTAAAC
195 AACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCCACTAAAC
* *
53599017 ACCTGAGCATTAGCGGCGCTTTACAGAAACGCCGCTAAAGA-CCCCAAAAACTCAGAAAACGGTG
260 ACCTGAGAATTAGCGGCGCTGTACAGAAACGCCGCTAAAGACCCCCAAAAACTCAG-AAACGGTG
53599081 CCGTTGGGCTTAGGC
324 CCGTTGGGCTTAGGC
*
53599096 TTTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCAGCGCATTA-CAGAAT
1 -TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCAGCGC-TTATCAGAAA
* * *
53599160 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGTTTAGGCTTTTTGCGGCGCTTT
64 CGCCGCTAAAG-CCCCAAAAACTCAGAAAACGGTGCCGTCGGGCTTAGGCTTTTTGCGGCGCATT
53599225 TAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCATTACAGAAACACCGCTAAAGACCCCA
128 TAAAAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCATTACAGAAACACCGCTAAAGACCCCA
* *
53599290 AAAACTCAGAAAACGGTGCCGTTGGGTTTAGGCTTTTTGCGGCGCTTTTAAAAAAAGGCCACTAA
193 AAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCCACTAA
* * *
53599355 AGACCTGAGAATTAGCGGCGCTGTATAGAAATGCCGCTAAAGACCCCCAAAAACTCAGAAACGGT
258 ACACCTGAGAATTAGCGGCGCTGTACAGAAACGCCGCTAAAGACCCCCAAAAACTCAGAAACGGT
*
53599420 GCCGTTTGGCTTAGGC
323 GCCGTTGGGCTTAGGC
* * *
53599436 TTTTTGCGGCGCTTTCAAATAAATGCCGCTAA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAA
53599468 TGCTTATTTT
Statistics
Matches: 343, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
339 45 0.13
340 281 0.82
341 17 0.05
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (338 bp):
TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGAATTAGCAGCGCTTATCAGAAACG
CCGCTAAAGCCCCAAAAACTCAGAAAACGGTGCCGTCGGGCTTAGGCTTTTTGCGGCGCATTTAA
AAAAACGCCGCTAAAGACCTGAGAATTAGCGGCGCATTACAGAAACACCGCTAAAGACCCCAAAA
ACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAAAAAAACGCCACTAAACA
CCTGAGAATTAGCGGCGCTGTACAGAAACGCCGCTAAAGACCCCCAAAAACTCAGAAACGGTGCC
GTTGGGCTTAGGC
Found at i:53599560 original size:40 final size:39
Alignment explanation
Indices: 53599436--53599570 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 39
53599426 TGGCTTAGGC
* *
53599436 TTTTT-GCGGCGCTTTCAAATAAATGCCGCTAATGCTT-A
1 TTTTTAGCGGCGTTTTTAAA-AAATGCCGCTAATGCTTGA
* ** *
53599474 TTTTTAGCGGCGATTTTTAAAAAACGCCGCTAATAATCGA
1 TTTTTAGCGGCG-TTTTTAAAAAATGCCGCTAATGCTTGA
** *
53599514 CCTTTAGCGGCGTTTTCCT-AAAAGTGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTT--TAAAAAATGCCGCTAATGCTTGA
*
53599554 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
53599571 TGTCTAAACG
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
38 6 0.08
39 23 0.30
40 46 0.61
41 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTAAAAAATGCCGCTAATGCTTGA
Found at i:53600157 original size:18 final size:17
Alignment explanation
Indices: 53600134--53600186 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
53600124 ATATATTATG
*
53600134 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
53600152 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53600169 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
53600187 TTAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:53600222 original size:119 final size:120
Alignment explanation
Indices: 53599957--53600214 Score: 332
Period size: 119 Copynumber: 2.2 Consensus size: 120
53599947 AAAGTAGATT
*
53599957 ATAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAG
1 ATAAATTATATTAAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAG
* **
53600022 TAAATTCATATAAGAATATTTAATACTAGGAATTTTATCAAATTATATATTTTTA
66 TAAATTCATATAAGAATATTAAATACTAGGAATTTTATCAAATTATATATTAATA
* *
53600077 TTAAATTATATTTAATAATAATTATTTTAAATTAT-TTTTATAGTATTATATATTATGATTTTAG
1 ATAAATTATATTAAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAG
*** * * *
53600141 TAAATTCATAT-ATTTTATTAAATTA-TA-TATTTTTATTAAATTATAT-TTAATA
66 TAAATTCATATAAGAATATTAAA-TACTAGGAATTTTATCAAATTATATATTAATA
* *
53600193 AT-AATTATGTTAAA-AATGATTA
1 ATAAATTATATTAAATAATAATTA
53600215 AATTATTTAT
Statistics
Matches: 123, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
114 7 0.06
115 10 0.08
116 5 0.04
117 16 0.13
118 9 0.07
119 42 0.34
120 34 0.28
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (120 bp):
ATAAATTATATTAAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAG
TAAATTCATATAAGAATATTAAATACTAGGAATTTTATCAAATTATATATTAATA
Done.