Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014617.1 Kokia drynarioides strain JFW-HI SEQ_129656, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 303807
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4174 original size:21 final size:21
Alignment explanation
Indices: 4150--4203 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
4140 CTTGTGATCG
*
4150 TTCTACTGATACAAGTGA-GAC
1 TTCTACTGATACAAGTCATG-C
*
4171 TTCTA-TCGAAACAAGTCATGC
1 TTCTACT-GATACAAGTCATGC
4192 TTCTACTGATAC
1 TTCTACTGATAC
4204 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (21 bp):
TTCTACTGATACAAGTCATGC
Found at i:4196 original size:42 final size:42
Alignment explanation
Indices: 4124--4203 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
4114 CGATTTTTTA
* ** *
4124 GAGACTTCTATCGATACTTGTGATCGTTCTACTGATACAAGT
1 GAGACTTCTATCGAAACAAGTCATCGTTCTACTGATACAAGT
4166 GAGACTTCTATCGAAACAAGTCAT-GCTTCTACTGATAC
1 GAGACTTCTATCGAAACAAGTCATCG-TTCTACTGATAC
4204 TAAAAACTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 32 0.97
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (42 bp):
GAGACTTCTATCGAAACAAGTCATCGTTCTACTGATACAAGT
Found at i:6640 original size:37 final size:37
Alignment explanation
Indices: 6597--6677 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
6587 AAATAGTGTC
*
6597 TTTTGAGCCTGGTTCAATAGGATCCAAAACGACACCG
1 TTTTGAGCCTAGTTCAATAGGATCCAAAACGACACCG
* *
6634 TTTTGAGCCTAGTTCAATAGGCTCCAAAACGACGCCG
1 TTTTGAGCCTAGTTCAATAGGATCCAAAACGACACCG
6671 TTTTGAG
1 TTTTGAG
6678 TCCAAACCCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (37 bp):
TTTTGAGCCTAGTTCAATAGGATCCAAAACGACACCG
Found at i:16398 original size:20 final size:20
Alignment explanation
Indices: 16375--16416 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
16365 TCATAAAAGC
16375 AATT-ATATAATCAAATATAA
1 AATTGATATAATCAAA-ATAA
* *
16395 AATTGATTTAATGAAAATAA
1 AATTGATATAATCAAAATAA
16415 AA
1 AA
16417 GAAACTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTGATATAATCAAAATAA
Found at i:22640 original size:35 final size:30
Alignment explanation
Indices: 22594--22661 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 30
22584 TTACTCAAGA
22594 TTTCTCTTGTTTTATATCTACTCATTCTTTTTCTT
1 TTTCTCTTGTTTT-T-TC-ACT-ATTC-TTTTCTT
*
22629 TTTCTTTTGTTTTTTCACTATTCTTTTCTT
1 TTTCTCTTGTTTTTTCACTATTCTTTTCTT
22659 TTT
1 TTT
22662 GGTTAAGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.31
31 4 0.12
32 3 0.09
33 2 0.06
34 1 0.03
35 12 0.38
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.71
Consensus pattern (30 bp):
TTTCTCTTGTTTTTTCACTATTCTTTTCTT
Found at i:30540 original size:15 final size:16
Alignment explanation
Indices: 30508--30549 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
30498 GGATCTCCCA
*
30508 ATCTTCATTG-TATCC
1 ATCTTCATAGATATCC
30523 ATCTTCATAGATAT-C
1 ATCTTCATAGATATCC
*
30538 ATCCTCATAGAT
1 ATCTTCATAGAT
30550 GTTATCATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (16 bp):
ATCTTCATAGATATCC
Found at i:39209 original size:79 final size:79
Alignment explanation
Indices: 39078--39399 Score: 531
Period size: 79 Copynumber: 4.1 Consensus size: 79
39068 AAAAGAGTAG
* * *
39078 TAAATTTTATGGGTTGAATTGAGAACTTAAGGACTAAATTGTAAAATAAGTAAAAACTGACAAAT
1 TAAATTCTATGGGTTGAATTGAGAAATTAAGGACTAAATTGTAAAATAAGTAAAAAGTGACAAAT
39143 GAGTATGATAATAA
66 GAGTATGATAATAA
* *
39157 TAAATTCTTTGGGTTGAATTGAGAAATTAAGGACTAAATTGTAAAATAAGTAAAAATTGACAAAT
1 TAAATTCTATGGGTTGAATTGAGAAATTAAGGACTAAATTGTAAAATAAGTAAAAAGTGACAAAT
39222 GAGTATGATAATAA
66 GAGTATGATAATAA
* *
39236 TAAATTCTATGGGTTGAATTGAGAACTTAAGGACTAAATTGTAAAATAAGTACAAAGTGACAAAT
1 TAAATTCTATGGGTTGAATTGAGAAATTAAGGACTAAATTGTAAAATAAGTAAAAAGTGACAAAT
39301 GAGTATGATAATAGA
66 GAGTATGATAATA-A
*
39316 -AAATTCTATGGGTTAAATTGA-AAACTTAAGGACTAAATTGTAAAATAAGTAAAAAGTGACAAA
1 TAAATTCTATGGGTTGAATTGAGAAA-TTAAGGACTAAATTGTAAAATAAGTAAAAAGTGACAAA
*
39379 TGATTATGATAATAA
65 TGAGTATGATAATAA
39394 TAAATT
1 TAAATT
39400 TAGATGTAAT
Statistics
Matches: 228, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
78 3 0.01
79 224 0.98
80 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.30
Consensus pattern (79 bp):
TAAATTCTATGGGTTGAATTGAGAAATTAAGGACTAAATTGTAAAATAAGTAAAAAGTGACAAAT
GAGTATGATAATAA
Found at i:44583 original size:46 final size:46
Alignment explanation
Indices: 44508--44601 Score: 120
Period size: 46 Copynumber: 2.0 Consensus size: 46
44498 AAAATAAAAC
*
44508 AATAAGGTCTAAATTGTAAAAAAACATAAATAAATGG-GCAAAATTA
1 AATAAGGACTAAATTGTAAAAAAACATAAATAAATGGTGC-AAATTA
** *
44554 AATAAGGACTAAATTGTAAATGTAA-ATAAATTAATGGTGCAAATTA
1 AATAAGGACTAAATTGTAAA-AAAACATAAATAAATGGTGCAAATTA
44600 AA
1 AA
44602 AATAAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 38 0.90
47 4 0.10
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (46 bp):
AATAAGGACTAAATTGTAAAAAAACATAAATAAATGGTGCAAATTA
Found at i:44610 original size:5 final size:5
Alignment explanation
Indices: 44600--44634 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
44590 GTGCAAATTA
*
44600 AAAAT AAAAT AAAATT AAATT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAA
44635 ATTACAGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:44618 original size:11 final size:11
Alignment explanation
Indices: 44594--44636 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
44584 TTAATGGTGC
44594 AAATTAAAAATA
1 AAATT-AAAATA
*
44606 AAA-TAAAATT
1 AAATTAAAATA
44616 AAATTAAAATA
1 AAATTAAAATA
*
44627 AAATAAAAAT
1 AAATTAAAAT
44637 TACAGGGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.30
11 16 0.59
12 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATTAAAATA
Found at i:44625 original size:16 final size:17
Alignment explanation
Indices: 44594--44636 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
44584 TTAATGGTGC
44594 AAATTAAAAATAAAATA
1 AAATTAAAAATAAAATA
*
44611 AAATT-AAATTAAAATA
1 AAATTAAAAATAAAATA
44627 AAA-TAAAAAT
1 AAATTAAAAAT
44637 TACAGGGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 1 0.04
16 17 0.74
17 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATTAAAAATAAAATA
Found at i:44638 original size:22 final size:22
Alignment explanation
Indices: 44594--44634 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
44584 TTAATGGTGC
44594 AAATTAAAAATAAAATAAAATT
1 AAATTAAAAATAAAATAAAATT
44616 AAATT-AAAATAAAATAAAA
1 AAATTAAAAATAAAATAAAA
44635 ATTACAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATTAAAAATAAAATAAAATT
Found at i:46521 original size:98 final size:98
Alignment explanation
Indices: 46351--46531 Score: 231
Period size: 98 Copynumber: 1.8 Consensus size: 98
46341 GTAACTTCAC
* * * *
46351 TCCATGCAACTTCAGTGGAGATTAAGGTTTGCTACTATGAGTTTTAATCCGCCCCTCTACAACTT
1 TCCATGCAACTTCAGTGGAGATTAAGATCTGCTACTAT-AGTTTTAATCCGACCCACTACAACTT
* *
46416 TAGGGGTATAGGATTTGGTGTGGCTTCACTCCAT
65 CAAGGGTATAGGATTTGGTGTGGCTTCACTCCAT
* * * *
46450 TCCACTGCAACTTCAGTGGAGATTGAGATCT-CTACTACT-TTTTTAATCTGACCCACTGCAACT
1 TCCA-TGCAACTTCAGTGGAGATTAAGATCTGCTACTA-TAGTTTTAATCCGACCCACTACAACT
46513 TCAAGGGTATAGGATTTGG
64 TCAAGGGTATAGGATTTGG
46532 GGTTGTAACT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
98 36 0.51
99 10 0.14
100 24 0.34
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (98 bp):
TCCATGCAACTTCAGTGGAGATTAAGATCTGCTACTATAGTTTTAATCCGACCCACTACAACTTC
AAGGGTATAGGATTTGGTGTGGCTTCACTCCAT
Found at i:47635 original size:26 final size:25
Alignment explanation
Indices: 47591--47663 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
47581 TCGGCATACT
** *
47591 TATGCGTTTACAATCGCCAGCTTATA
1 TATGCGTTTACGCTTGCCAGCTT-TA
*
47617 TATGCGTTTACGCTTGCCAGC-TTG
1 TATGCGTTTACGCTTGCCAGCTTTA
* *
47641 CACGCGTTTACGCTTGCCAGCTT
1 TATGCGTTTACGCTTGCCAGCTT
47664 GCACGCGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 20 0.50
25 2 0.05
26 18 0.45
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (25 bp):
TATGCGTTTACGCTTGCCAGCTTTA
Found at i:47652 original size:24 final size:24
Alignment explanation
Indices: 47620--47678 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
47610 GCTTATATAT
47620 GCGTTTACGCTTGCCAGCTTGCAC
1 GCGTTTACGCTTGCCAGCTTGCAC
47644 GCGTTTACGCTTGCCAGCTTGCAC
1 GCGTTTACGCTTGCCAGCTTGCAC
47668 GCGTTTACGCT
1 GCGTTTACGCT
47679 CATTAGCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.12, C:0.32, G:0.25, T:0.31
Consensus pattern (24 bp):
GCGTTTACGCTTGCCAGCTTGCAC
Found at i:47686 original size:24 final size:24
Alignment explanation
Indices: 47635--47714 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
47625 TACGCTTGCC
****
47635 AGCTTGCACGCGTTTACGCTTGCC
1 AGCTTGCACGCGTTTACGCTCATT
47659 AGCTTGCACGCGTTTACGCTCATT
1 AGCTTGCACGCGTTTACGCTCATT
** *
47683 AGCTTATATAAGCGTTTACGCTCATT
1 AGC-T-TGCACGCGTTTACGCTCATT
47709 AGCTTG
1 AGCTTG
47715 TACATGTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 24 0.52
25 2 0.04
26 20 0.43
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (24 bp):
AGCTTGCACGCGTTTACGCTCATT
Found at i:47698 original size:50 final size:50
Alignment explanation
Indices: 47644--47830 Score: 187
Period size: 50 Copynumber: 3.7 Consensus size: 50
47634 CAGCTTGCAC
* * * *
47644 GCGTTTACGCTTGCCAGCTTGCACGCGTTTACGCTCATTAGCTTATATAA
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCATCAGCTTATTTAA
*** * * * * * *
47694 GCGTTTACGCTCATTAGCTTGTACATGTTTATGCTCGTCAACTTATTTAT
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCATCAGCTTATTTAA
* * * *
47744 GTGTTTACGCTTGCCAGCTTGCACACATTTACGCTCGTCAGCTTATTTATA
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCATCAGCTTATTTA-A
* *
47795 -CTTTTATGCTCGCCAGCTTGCACACGTTTACGCTCA
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCA
47831 CTAGCTTGCA
Statistics
Matches: 106, Mismatches: 30, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
50 106 1.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (50 bp):
GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCATCAGCTTATTTAA
Found at i:47765 original size:124 final size:124
Alignment explanation
Indices: 47611--47892 Score: 307
Period size: 124 Copynumber: 2.3 Consensus size: 124
47601 CAATCGCCAG
* * * * * *
47611 CTTATATATGCGTTTACGCTTGCCAGCTTGCACGCGTTTACGCTTGCCAGC-T-TGCACGCGTTT
1 CTTATTTATGTGTTTACGCTTGCCAGCTTGCACACATTTACGCTCGCCAGCTTATGCACACGTTT
** * * * **
47674 ACGCTCATTAGCTTATATAAGCGTTTACGCTCATTAGCTTGTACATGTTTATGCTCGTCAA
66 ACGCTCACCAGCTTACA-AA-CGTTTACGCTCACTAGCTTGCACACATTTATGCTCGTCAA
* ** * *
47735 CTTATTTATGTGTTTACGCTTGCCAGCTTGCACACATTTACGCTCGTCAGCTTATTTATACTTTT
1 CTTATTTATGTGTTTACGCTTGCCAGCTTGCACACATTTACGCTCGCCAGCTTATGCACACGTTT
* * * * *
47800 ATGCTCGCCAGCTTGCACACGTTTACGCTCACTAGCTTGCACACATTTATGCTCGTCAT
66 ACGCTCACCAGCTTACAAACGTTTACGCTCACTAGCTTGCACACATTTATGCTCGTCAA
* *
47859 CTTATTTATTTGTTTACGCTCGCCAGCTTGCACA
1 CTTATTTATGTGTTTACGCTTGCCAGCTTGCACA
47893 ATATGTATAT
Statistics
Matches: 131, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
124 112 0.85
125 2 0.02
126 17 0.13
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (124 bp):
CTTATTTATGTGTTTACGCTTGCCAGCTTGCACACATTTACGCTCGCCAGCTTATGCACACGTTT
ACGCTCACCAGCTTACAAACGTTTACGCTCACTAGCTTGCACACATTTATGCTCGTCAA
Found at i:47785 original size:24 final size:24
Alignment explanation
Indices: 47747--47854 Score: 99
Period size: 24 Copynumber: 4.4 Consensus size: 24
47737 TATTTATGTG
*
47747 TTTACGCTTGCCAGCTTGCACACA
1 TTTACGCTCGCCAGCTTGCACACA
* ** * *
47771 TTTACGCTCGTCAGCTTATTTATACT
1 TTTACGCTCGCCAGC-T-TGCACACA
* *
47797 TTTATGCTCGCCAGCTTGCACACG
1 TTTACGCTCGCCAGCTTGCACACA
* *
47821 TTTACGCTCACTAGCTTGCACACA
1 TTTACGCTCGCCAGCTTGCACACA
*
47845 TTTATGCTCG
1 TTTACGCTCG
47855 TCATCTTATT
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
24 45 0.70
25 2 0.03
26 17 0.27
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTTGCACACA
Found at i:47824 original size:100 final size:100
Alignment explanation
Indices: 47646--47829 Score: 235
Period size: 100 Copynumber: 1.8 Consensus size: 100
47636 GCTTGCACGC
* * * **
47646 GTTTACGCTTGCCAGCTTGCACGCGTTTACGCTCATTAGCTTATATAAGCGTTTACGCTCATTAG
1 GTTTACGCTTGCCAGCTTGCACACATTTACGCTCATCAGCTTATATAAGCGTTTACGCTCACCAG
* * *
47711 CTTGTACATGTTTATGCTCGTCAACTTATTTATGT
66 CTTGCACACGTTTACGCTCGTCAACTTATTTATGT
* * * * *
47746 GTTTACGCTTGCCAGCTTGCACACATTTACGCTCGTCAGCTTATTTATA-CTTTTATGCTCGCCA
1 GTTTACGCTTGCCAGCTTGCACACATTTACGCTCATCAGCTTATATA-AGCGTTTACGCTCACCA
47810 GCTTGCACACGTTTACGCTC
65 GCTTGCACACGTTTACGCTC
47830 ACTAGCTTGC
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
100 69 0.99
101 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (100 bp):
GTTTACGCTTGCCAGCTTGCACACATTTACGCTCATCAGCTTATATAAGCGTTTACGCTCACCAG
CTTGCACACGTTTACGCTCGTCAACTTATTTATGT
Found at i:63954 original size:19 final size:21
Alignment explanation
Indices: 63930--63969 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
63920 TCACATTCAC
63930 ATTCTCTCAT-C-TTCTCTCA
1 ATTCTCTCATCCTTTCTCTCA
63949 ATTCTCTCATCCTTTCTCTCA
1 ATTCTCTCATCCTTTCTCTCA
63970 TTTTCCCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTCTCTCATCCTTTCTCTCA
Found at i:64088 original size:13 final size:13
Alignment explanation
Indices: 64070--64132 Score: 126
Period size: 13 Copynumber: 4.8 Consensus size: 13
64060 GCCATCAGCA
64070 AAGGAACGAAGTG
1 AAGGAACGAAGTG
64083 AAGGAACGAAGTG
1 AAGGAACGAAGTG
64096 AAGGAACGAAGTG
1 AAGGAACGAAGTG
64109 AAGGAACGAAGTG
1 AAGGAACGAAGTG
64122 AAGGAACGAAG
1 AAGGAACGAAG
64133 GAGTCTTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.48, C:0.08, G:0.38, T:0.06
Consensus pattern (13 bp):
AAGGAACGAAGTG
Found at i:75103 original size:18 final size:18
Alignment explanation
Indices: 75080--75149 Score: 104
Period size: 18 Copynumber: 3.8 Consensus size: 18
75070 TGGAAGGAAT
* *
75080 AGCATAGTGGCTCGTTTG
1 AGCATACTGGCTCGTATG
75098 AGCATACTGGCTCGTATG
1 AGCATACTGGCTCGTATG
75116 AGCATACTGGCTCGTATG
1 AGCATACTGGCTCGTATG
*
75134 AGCATTACTAGCTCGT
1 AGCA-TACTGGCTCGT
75150 GGGAACAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
18 38 0.79
19 10 0.21
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (18 bp):
AGCATACTGGCTCGTATG
Found at i:75920 original size:21 final size:21
Alignment explanation
Indices: 75896--75950 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
75886 AAGCATGATG
75896 TGTATCGATAGAAGTTACACT
1 TGTATCGATAGAAGTTACACT
75917 TGTATCGATAGAAGTTACACT
1 TGTATCGATAGAAGTTACACT
*
75938 TGTATCGGTAGAA
1 TGTATCGATAGAA
75951 CTTTCACAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (21 bp):
TGTATCGATAGAAGTTACACT
Found at i:82768 original size:37 final size:37
Alignment explanation
Indices: 82723--82873 Score: 214
Period size: 37 Copynumber: 4.1 Consensus size: 37
82713 CTGAGCGCAA
* * *
82723 AGCCCGAATACACCAGCATAAAGCCTACTAGGCACAT
1 AGCCCGAATTCACCAGCACAAAGCCTGCTAGGCACAT
* *
82760 AGCTCGAATTCACCGGCACAAAGCCTGCTAGGCACAT
1 AGCCCGAATTCACCAGCACAAAGCCTGCTAGGCACAT
* * *
82797 AACCCGAATTCACCGGCACAAAGCCTGCTAGGCATAT
1 AGCCCGAATTCACCAGCACAAAGCCTGCTAGGCACAT
82834 AGCCCGAATTCACC-GACACAAAGCCTGCTAGGCACAT
1 AGCCCGAATTCACCAG-CACAAAGCCTGCTAGGCACAT
82871 AGC
1 AGC
82874 TCAAATTTTT
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
36 1 0.01
37 102 0.99
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (37 bp):
AGCCCGAATTCACCAGCACAAAGCCTGCTAGGCACAT
Found at i:84319 original size:18 final size:18
Alignment explanation
Indices: 84290--84356 Score: 89
Period size: 18 Copynumber: 3.7 Consensus size: 18
84280 CGGAAGGAGT
* * *
84290 ATACTAGCTCGTTTAAGC
1 ATACTGGCTCGTATGAGC
*
84308 ATGCTGGCTCGTATGAGC
1 ATACTGGCTCGTATGAGC
*
84326 ATACTGGTTCGTATGAGC
1 ATACTGGCTCGTATGAGC
84344 ATACTGGCTCGTA
1 ATACTGGCTCGTA
84357 AAAGCATTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (18 bp):
ATACTGGCTCGTATGAGC
Found at i:84362 original size:18 final size:18
Alignment explanation
Indices: 84290--84368 Score: 86
Period size: 18 Copynumber: 4.3 Consensus size: 18
84280 CGGAAGGAGT
* *
84290 ATACTAGCTCGTTTAAGC
1 ATACTGGCTCGTATAAGC
* *
84308 ATGCTGGCTCGTATGAGC
1 ATACTGGCTCGTATAAGC
* *
84326 ATACTGGTTCGTATGAGC
1 ATACTGGCTCGTATAAGC
*
84344 ATACTGGCTCGTAAAAGC
1 ATACTGGCTCGTATAAGC
84362 ATTACTG
1 A-TACTG
84369 ACTTGTGAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
18 46 0.90
19 5 0.10
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (18 bp):
ATACTGGCTCGTATAAGC
Found at i:85153 original size:21 final size:21
Alignment explanation
Indices: 85114--85154 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
85104 TTTAGTACCG
* **
85114 GTAGAACCATGACGTGTATCT
1 GTAGAACCATCACAAGTATCT
85135 GTAGAACCATCACAAGTATC
1 GTAGAACCATCACAAGTATC
85155 GGTAAAAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
GTAGAACCATCACAAGTATCT
Found at i:91295 original size:18 final size:18
Alignment explanation
Indices: 91272--91320 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
91262 TGGAATGAAT
*
91272 AGCATACTGGCTCCTTTG
1 AGCATATTGGCTCCTTTG
**
91290 AGCATATTGGCTTTTTTG
1 AGCATATTGGCTCCTTTG
91308 AGCATATTGGCTC
1 AGCATATTGGCTC
91321 GTATGTGTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (18 bp):
AGCATATTGGCTCCTTTG
Found at i:103115 original size:21 final size:21
Alignment explanation
Indices: 103089--103130 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
103079 TTTTAGTACT
* * *
103089 GGTAGAAGCATGACATGTATC
1 GGTAGAACCATCACAAGTATC
103110 GGTAGAACCATCACAAGTATC
1 GGTAGAACCATCACAAGTATC
103131 AATAGAAGTC
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:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (21 bp):
GGTAGAACCATCACAAGTATC
Found at i:104717 original size:27 final size:27
Alignment explanation
Indices: 104658--104708 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 27
104648 ATTTGCATAC
104658 TTATAATATTTTTTTCACAATTTAAAT
1 TTATAATATTTTTTTCACAATTTAAAT
104685 TTATAAT-TTTTTTT-A-AATTTAAAT
1 TTATAATATTTTTTTCACAATTTAAAT
104709 CATGTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
25 1 0.04
26 7 0.29
27 7 0.29
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATAATATTTTTTTCACAATTTAAAT
Found at i:105004 original size:21 final size:22
Alignment explanation
Indices: 104956--105007 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
104946 TTTTAAAAAA
*
104956 ATTATTTATATTATTTTATTTT
1 ATTATTTATATTATTTCATTTT
*
104978 AATATTTA-ATTATTTACATTTT
1 ATTATTTATATTATTT-CATTTT
105000 -TTATTTAT
1 ATTATTTAT
105008 TGAAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTATTTATATTATTTCATTTT
Found at i:105143 original size:23 final size:23
Alignment explanation
Indices: 105113--105158 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
105103 ATTACATATT
* *
105113 ATATAAAAATAGCATAGTATAAA
1 ATATAAAAAAAACATAGTATAAA
105136 ATATAAAAAAAACATAGTATAAA
1 ATATAAAAAAAACATAGTATAAA
105159 GTATTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (23 bp):
ATATAAAAAAAACATAGTATAAA
Found at i:106534 original size:18 final size:18
Alignment explanation
Indices: 106502--106550 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
106492 AATAAATAAT
*
106502 AAAATAATTTTTAAAATTC
1 AAAAT-ATTTATAAAATTC
106521 AAAATATTTATAAAAATTC
1 AAAATATTTAT-AAAATTC
*
106540 CAAA-ATTTATA
1 AAAATATTTATA
106551 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 11 0.41
19 15 0.56
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATATTTATAAAATTC
Found at i:106569 original size:10 final size:10
Alignment explanation
Indices: 106554--106615 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
106544 ATTTATATTT
106554 TAAAAATATA
1 TAAAAATATA
106564 TAAAAAT-TA
1 TAAAAATATA
106573 TAAAAA-AT-
1 TAAAAATATA
*
106581 TAAAAAT-TC
1 TAAAAATATA
*
106590 TATAAAACATA
1 TA-AAAATATA
*
106601 TAAAAACAT-
1 TAAAAATATA
106610 TAAAAA
1 TAAAAA
106616 ATTTCTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 7 0.16
9 17 0.38
10 18 0.40
11 3 0.07
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAAATATA
Found at i:106586 original size:17 final size:19
Alignment explanation
Indices: 106554--106606 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 19
106544 ATTTATATTT
106554 TAAAAATATATAAAAATTA
1 TAAAAATATATAAAAATTA
*
106573 TAAAAA-AT-TAAAAATTC
1 TAAAAATATATAAAAATTA
*
106590 TATAAAACATATAAAAA
1 TA-AAAATATATAAAAA
106607 CATTAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 8 0.27
20 6 0.20
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATATATAAAAATTA
Found at i:106625 original size:29 final size:28
Alignment explanation
Indices: 106553--106615 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
106543 AATTTATATT
*
106553 TTAAAAA-TATATAAAA-ATTATAAAAAA
1 TTAAAAATTCTATAAAACA-TATAAAAAA
106580 TTAAAAATTCTATAAAACATATAAAAACA
1 TTAAAAATTCTATAAAACATATAAAAA-A
106609 TTAAAAA
1 TTAAAAA
106616 ATTTCTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.22
28 16 0.50
29 9 0.28
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (28 bp):
TTAAAAATTCTATAAAACATATAAAAAA
Found at i:106818 original size:22 final size:22
Alignment explanation
Indices: 106775--106819 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
106765 TATAATACAG
* *
106775 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGATCAATT
106797 TTTTAATTTAAC-TCGATCAATT
1 TTTTAATTTAACAT-GATCAATT
106819 T
1 T
106820 CATTTGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGATCAATT
Found at i:108453 original size:22 final size:22
Alignment explanation
Indices: 108396--108453 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
108386 TTTCTATTAA
*
108396 TTTAACCATTTTTTAATTTTTGT
1 TTTAA-CATTTTTTAATTTTAGT
*
108419 TTTAATATTTTTTAA-TTTAGT
1 TTTAACATTTTTTAATTTTAGT
*
108440 TTTTACATTCTTTT
1 TTTAACATT-TTTT
108454 GGTTTATGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 12 0.40
22 13 0.43
23 5 0.17
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.67
Consensus pattern (22 bp):
TTTAACATTTTTTAATTTTAGT
Found at i:111088 original size:20 final size:20
Alignment explanation
Indices: 111063--111154 Score: 103
Period size: 20 Copynumber: 4.6 Consensus size: 20
111053 TTATTGTTAA
*
111063 CCCTGTATGCACTTCGGTGC
1 CCCTGTATGCACTTCGATGC
* *
111083 CCCTGTATGCATTTTGATGC
1 CCCTGTATGCACTTCGATGC
* *
111103 TCTTGTATGCACTTCGATGC
1 CCCTGTATGCACTTCGATGC
* **
111123 CCCTATATGCACTTTTATGC
1 CCCTGTATGCACTTCGATGC
*
111143 CCCTTTATGCAC
1 CCCTGTATGCAC
111155 AATGGTGCCC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.15, C:0.30, G:0.17, T:0.37
Consensus pattern (20 bp):
CCCTGTATGCACTTCGATGC
Found at i:111110 original size:40 final size:41
Alignment explanation
Indices: 111066--111168 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 41
111056 TTGTTAACCC
*
111066 TGTATGCACTTCGGTGCCCCTGTATGCA-TTTTGATG-CTCT
1 TGTATGCACTTCGGTGCCCCTGTATGCACTTTT-ATGCCCCT
* *
111106 TGTATGCACTTCGATGCCCCTATATGCACTTTTATGCCCCT
1 TGTATGCACTTCGGTGCCCCTGTATGCACTTTTATGCCCCT
*
111147 T-TATGCACAAT-GGTGCCCCTGT
1 TGTATGCAC-TTCGGTGCCCCTGT
111169 GTGTTACAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 45 0.83
41 9 0.17
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (41 bp):
TGTATGCACTTCGGTGCCCCTGTATGCACTTTTATGCCCCT
Found at i:112154 original size:28 final size:29
Alignment explanation
Indices: 112114--112169 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
112104 CACACAGCCA
112114 TGTGCCCTTGTTTCACAAAA-TTTCTAAG
1 TGTGCCCTTGTTTCACAAAATTTTCTAAG
112142 TGTGCCCTTGTTTCACAAAATTTTCTAA
1 TGTGCCCTTGTTTCACAAAATTTTCTAA
112170 CTTTTTCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (29 bp):
TGTGCCCTTGTTTCACAAAATTTTCTAAG
Found at i:113476 original size:16 final size:17
Alignment explanation
Indices: 113455--113487 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
113445 TTTAGTATGT
113455 TTATGA-ACATTAATTC
1 TTATGATACATTAATTC
*
113471 TTATGATACTTTAATTC
1 TTATGATACATTAATTC
113488 CACCAAACTC
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:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
TTATGATACATTAATTC
Found at i:116025 original size:43 final size:43
Alignment explanation
Indices: 115977--116101 Score: 164
Period size: 43 Copynumber: 2.9 Consensus size: 43
115967 ACACCACTAT
*
115977 AGAACATGGTCTTTAGCTTCGCTTTTCCCACAAACGCCGCTAA
1 AGAACATGGTCTTTAGCTGCGCTTTTCCCACAAACGCCGCTAA
* * *
116020 AGAACATGGTCTTTAG-TGGCACTTTTCCTACAAATGCCGCTAA
1 AGAACATGGTCTTTAGCT-GCGCTTTTCCCACAAACGCCGCTAA
* *
116063 AGAACATGGTCTTTAGCGGCGTTTTTCCC-CAAAACGCCG
1 AGAACATGGTCTTTAGCTGCGCTTTTCCCAC-AAACGCCG
116102 TTAACATTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
42 2 0.03
43 68 0.97
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCTGCGCTTTTCCCACAAACGCCGCTAA
Found at i:118037 original size:32 final size:30
Alignment explanation
Indices: 117967--118044 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 30
117957 TATTATTTTG
117967 AGTAATAATTATTGATAAAATAATAAAATACA
1 AGTAATAATTATTGATAAAATAATAAAAT--A
* *
117999 ATTAATAATGTAATTGATAAAATAATGATAAT-
1 AGTAATAAT-T-ATTGATAAAATAAT-AAAATA
118031 AGTAATAAATTATT
1 AGTAAT-AATTATT
118045 TATATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
31 3 0.08
32 14 0.36
33 4 0.10
34 14 0.36
35 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (30 bp):
AGTAATAATTATTGATAAAATAATAAAATA
Found at i:120091 original size:41 final size:41
Alignment explanation
Indices: 119995--120144 Score: 158
Period size: 41 Copynumber: 3.7 Consensus size: 41
119985 ACTAACGCCG
* ** * *
119995 CTAATGCTCTGACCTTTAGTGACGTTTTCTCATAACA-TCA
1 CTAATGCTCTGACCTTTAGCGGGGTTTTCTCATAAAAGCCA
* *
120035 CTAATGCTCTGACCTTTAGCGGGGTTTTCTCATGAATGCCA
1 CTAATGCTCTGACCTTTAGCGGGGTTTTCTCATAAAAGCCA
* * * * *
120076 CTAATGCTTTTACCTTTAGCGGTGTTTTCTTATAAAAGCCG
1 CTAATGCTCTGACCTTTAGCGGGGTTTTCTCATAAAAGCCA
* * *
120117 CTAATGCTCTGACTTTTACCGGCGTTTT
1 CTAATGCTCTGACCTTTAGCGGGGTTTT
120145 ACCTATAAAC
Statistics
Matches: 90, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 31 0.34
41 59 0.66
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (41 bp):
CTAATGCTCTGACCTTTAGCGGGGTTTTCTCATAAAAGCCA
Found at i:120243 original size:40 final size:39
Alignment explanation
Indices: 120158--120258 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 39
120148 TATAAACGCT
*
120158 GCTATTGCTGTACTTCTTGTA-GCGTTTATGGAAAAACTCC
1 GCTATTGCTTTACTT-TT-TACGCGTTTATGGAAAAACTCC
*
120198 ACTATTGCTTTACTTTTTACGACGTTTATGGAAAAA-TGCC
1 GCTATTGCTTTACTTTTTACG-CGTTTATGGAAAAACT-CC
* *
120238 GCTATTGATTTACATTTTACG
1 GCTATTGCTTTACTTTTTACG
120259 GTGTTTTTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
38 2 0.04
39 4 0.08
40 47 0.89
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.41
Consensus pattern (39 bp):
GCTATTGCTTTACTTTTTACGCGTTTATGGAAAAACTCC
Found at i:128756 original size:18 final size:17
Alignment explanation
Indices: 128733--128766 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
128723 GAAAACAAAT
*
128733 AAGAAAATGAGAAAAAGG
1 AAGAAAAAGA-AAAAAGG
128751 AAGAAAAAGAAAAAAG
1 AAGAAAAAGAAAAAAG
128767 AAATAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (17 bp):
AAGAAAAAGAAAAAAGG
Found at i:152362 original size:61 final size:60
Alignment explanation
Indices: 152279--152446 Score: 264
Period size: 61 Copynumber: 2.8 Consensus size: 60
152269 TAAATTTTTG
*
152279 CTTAAAAAGAGGATAATGACTCCTTAATTTAAGATTAAAGATATCCTATAAGTGCAACACA
1 CTTAAAAAAAGGATAATGACTCC-TAATTTAAGATTAAAGATATCCTATAAGTGCAACACA
** * * *
152340 CTTATGACAAGGATAATGACTCCATAATTTAAGATTAAGGATATCCTATAAGTGTAACACA
1 CTTAAAAAAAGGATAATGACTCC-TAATTTAAGATTAAAGATATCCTATAAGTGCAACACA
152401 CTTAAAAAAAGGATAATGACTCCTAATTTAAGATTAAAGATATCCT
1 CTTAAAAAAAGGATAATGACTCCTAATTTAAGATTAAAGATATCCT
152447 TCAACTCATA
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
60 22 0.23
61 74 0.77
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (60 bp):
CTTAAAAAAAGGATAATGACTCCTAATTTAAGATTAAAGATATCCTATAAGTGCAACACA
Found at i:154003 original size:26 final size:26
Alignment explanation
Indices: 153967--154114 Score: 179
Period size: 26 Copynumber: 5.7 Consensus size: 26
153957 AGACTATGAA
* *
153967 GATATACTGAACTGGCTTGTAAGAGC
1 GATATATTGAACTGGCTCGTAAGAGC
* * ** *
153993 GATATACTGAACTGACTTATAAGAGT
1 GATATATTGAACTGGCTCGTAAGAGC
*
154019 GATATATTGAACTGGATCGTAAGAGC
1 GATATATTGAACTGGCTCGTAAGAGC
*
154045 GATATATTGAACTGGATCGTAAGAGC
1 GATATATTGAACTGGCTCGTAAGAGC
* *
154071 GATATATTGAACTGGCTCATAAGAGT
1 GATATATTGAACTGGCTCGTAAGAGC
* *
154097 AATATATTGTACTGGCTC
1 GATATATTGAACTGGCTC
154115 ATAGGAGCAA
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 108 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (26 bp):
GATATATTGAACTGGCTCGTAAGAGC
Found at i:154096 original size:78 final size:78
Alignment explanation
Indices: 153967--154111 Score: 218
Period size: 78 Copynumber: 1.9 Consensus size: 78
153957 AGACTATGAA
* * * *
153967 GATATACTGAACTGGCTTGTAAGAGCGATATACTGAACTGACTTATAAGAGTGATATATTGAACT
1 GATATACTGAACTGGATCGTAAGAGCGATATACTGAACTGACTCATAAGAGTAATATATTGAACT
154032 GGATCGTAAGAGC
66 GGATCGTAAGAGC
* * * *
154045 GATATATTGAACTGGATCGTAAGAGCGATATATTGAACTGGCTCATAAGAGTAATATATTGTACT
1 GATATACTGAACTGGATCGTAAGAGCGATATACTGAACTGACTCATAAGAGTAATATATTGAACT
154110 GG
66 GG
154112 CTCATAGGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 59 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (78 bp):
GATATACTGAACTGGATCGTAAGAGCGATATACTGAACTGACTCATAAGAGTAATATATTGAACT
GGATCGTAAGAGC
Found at i:160954 original size:11 final size:12
Alignment explanation
Indices: 160934--160977 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
160924 TCAGTCACAT
160934 AAAAAG-AAAG-
1 AAAAAGAAAAGA
160944 AAAAAGAAAAGA
1 AAAAAGAAAAGA
*
160956 AAAAGAGAAAAGC
1 AAAA-AGAAAAGA
160969 AAAAAGAAA
1 AAAAAGAAA
160978 CAAAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 6 0.20
11 4 0.13
12 9 0.30
13 11 0.37
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:160973 original size:7 final size:6
Alignment explanation
Indices: 160940--160977 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
160930 ACATAAAAAG
160940 AAAGAA AAAG-A AAAGAA AAAGAGA AAAGCAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGA-A AAAG-AA AAAGAA A
160978 CAAAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 13 0.45
7 10 0.34
8 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:165452 original size:13 final size:14
Alignment explanation
Indices: 165434--165463 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
165424 GTCAATGCAA
165434 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
165447 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
165461 TCA
1 TCA
165464 ATGTATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:168818 original size:26 final size:26
Alignment explanation
Indices: 168780--168878 Score: 146
Period size: 26 Copynumber: 3.8 Consensus size: 26
168770 AGACTCTGAA
168780 GATATACTGAACTGGCTCGTAAGAGC
1 GATATACTGAACTGGCTCGTAAGAGC
*
168806 GATATACTAAACTGGCTCGTAAGAGC
1 GATATACTGAACTGGCTCGTAAGAGC
* *
168832 GATATACTGTACTGGCTCGTAAGAGA
1 GATATACTGAACTGGCTCGTAAGAGC
*
168858 GATATTCTG-ACTGGGCTCGTA
1 GATATACTGAACT-GGCTCGTA
168879 TGTGCTAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
25 3 0.04
26 64 0.96
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (26 bp):
GATATACTGAACTGGCTCGTAAGAGC
Found at i:170063 original size:51 final size:52
Alignment explanation
Indices: 169955--170072 Score: 134
Period size: 51 Copynumber: 2.3 Consensus size: 52
169945 ATAGTAATCT
* * *
169955 TGAAAATGGAGAAATGAGAAACATATGGAAATGATTATGGTTTTCTCCGAAA
1 TGAAAATGGAGAAATGAGAAACATATGGAAATGAATATAGTTTTCTCCAAAA
* * * * * *
170007 GGAAAATGGAGAAGTG-GAATCATTTGGAGATGAATCTAGTTTTCTCCAAAA
1 TGAAAATGGAGAAATGAGAAACATATGGAAATGAATATAGTTTTCTCCAAAA
170058 TGAAAAT-GA-AAATGA
1 TGAAAATGGAGAAATGA
170073 AAATAACCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
49 4 0.07
50 2 0.04
51 34 0.63
52 14 0.26
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAGAAACATATGGAAATGAATATAGTTTTCTCCAAAA
Found at i:175179 original size:14 final size:14
Alignment explanation
Indices: 175158--175204 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
175148 TAAATTTCAG
175158 AATTGAGGATTGAA
1 AATTGAGGATTGAA
* *
175172 ATTTGAGGGTTGAA
1 AATTGAGGATTGAA
175186 AATTGAGGATTGAA
1 AATTGAGGATTGAA
*
175200 TATTG
1 AATTG
175205 TGTTGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (14 bp):
AATTGAGGATTGAA
Found at i:183575 original size:120 final size:120
Alignment explanation
Indices: 183362--183588 Score: 436
Period size: 120 Copynumber: 1.9 Consensus size: 120
183352 ATCAGTCTAA
*
183362 CAGCACCATCATCCTCTCATAGGTGAGTCATAGCTCGTCCGGAGATATTTGCCTAATGGTTGAGT
1 CAGCACCATCATCCTCTCATAGGTGAGTCATAGCTCGTCCGGAGATATTTGCCTAATGGTCGAGT
183427 TTACGATGATTGAACCATGTACATCAGAATTTTCCAGACTATCTTGTTCCTCGCC
66 TTACGATGATTGAACCATGTACATCAGAATTTTCCAGACTATCTTGTTCCTCGCC
*
183482 CAGCACCATCATCCTCTCATAGGTGAGTCATAGCTCGTCCGGAGATATTTGCCTGATGGTCGAGT
1 CAGCACCATCATCCTCTCATAGGTGAGTCATAGCTCGTCCGGAGATATTTGCCTAATGGTCGAGT
183547 TTACGATGATTGAACCATGTACATCAGAATTTTCCAGACTAT
66 TTACGATGATTGAACCATGTACATCAGAATTTTCCAGACTAT
183589 ATTGAACCAT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 105 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (120 bp):
CAGCACCATCATCCTCTCATAGGTGAGTCATAGCTCGTCCGGAGATATTTGCCTAATGGTCGAGT
TTACGATGATTGAACCATGTACATCAGAATTTTCCAGACTATCTTGTTCCTCGCC
Found at i:183598 original size:34 final size:34
Alignment explanation
Indices: 183555--183622 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
183545 GTTTACGATG
183555 ATTGAACCATGTACATCAGAATTTTCCAGACTAT
1 ATTGAACCATGTACATCAGAATTTTCCAGACTAT
183589 ATTGAACCATGTACATCAGAATTTTCCAGACTAT
1 ATTGAACCATGTACATCAGAATTTTCCAGACTAT
183623 CTTGTTCCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (34 bp):
ATTGAACCATGTACATCAGAATTTTCCAGACTAT
Found at i:190986 original size:42 final size:42
Alignment explanation
Indices: 190900--190986 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
190890 TCCACTATTG
* * *
190900 GTGGATTTTCCACATATTTCTAACAATTTATTTACATATTTA
1 GTGGATTTTCCACATATTTCTAACAATTTATTCAAATATCTA
* *
190942 GTGG-TTTATCCACATATTTCTAATAGTTTATTGCAAATA-CTA
1 GTGGATTT-TCCACATATTTCTAACAATTTATT-CAAATATCTA
190984 GTG
1 GTG
190987 ACTTGTCCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 3 0.08
42 31 0.82
43 4 0.11
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (42 bp):
GTGGATTTTCCACATATTTCTAACAATTTATTCAAATATCTA
Found at i:199972 original size:24 final size:24
Alignment explanation
Indices: 199919--199972 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
199909 TAATTAACAC
* *
199919 TTATAATTAAACATATCATTTTTA
1 TTATAATTAAACATATAATTTTAA
* *
199943 TCATAATTAACCATA-AATTTTAAA
1 TTATAATTAAACATATAATTTT-AA
199967 TTATAA
1 TTATAA
199973 ACACTTTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (24 bp):
TTATAATTAAACATATAATTTTAA
Found at i:201455 original size:40 final size:40
Alignment explanation
Indices: 201404--201586 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 40
201394 GCTTTGAAAC
* * **
201404 TAAATTTAAGCTTCGACTTAGTAGGTTATAAGTTGGTAAA
1 TAAATTCAAGCTTCGACTTAGTAGGTTACAAGCCGGTAAA
* * * * *
201444 TAAATTCAAGCTTCGATTTAGCAGGCTACGAGCCGATAAA
1 TAAATTCAAGCTTCGACTTAGTAGGTTACAAGCCGGTAAA
* * ** *
201484 TAAATTCAAGCTTCGGCTTAGCT-GGTTATAAGCTAGTGAA
1 TAAATTCAAGCTTCGACTTAG-TAGGTTACAAGCCGGTAAA
* * * * *
201524 TAAATTCAAGCTTTGGCTTAGCAGGTTACGAGCCGGTGAA
1 TAAATTCAAGCTTCGACTTAGTAGGTTACAAGCCGGTAAA
*
201564 TAAATTCAAGCTACGACTTAGTA
1 TAAATTCAAGCTTCGACTTAGTA
201587 AGCTACAGGC
Statistics
Matches: 112, Mismatches: 29, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
40 112 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (40 bp):
TAAATTCAAGCTTCGACTTAGTAGGTTACAAGCCGGTAAA
Found at i:201545 original size:80 final size:80
Alignment explanation
Indices: 201404--201586 Score: 242
Period size: 80 Copynumber: 2.3 Consensus size: 80
201394 GCTTTGAAAC
* * * *
201404 TAAATTTAAGCTTCGACTTAGTAGGTTATAAGTTGGTAAATAAATTCAAGCTTCGATTTAGCAGG
1 TAAATTCAAGCTTCGACTTAGTAGGTTATAAGCTAGTAAATAAATTCAAGCTTCGACTTAGCAGG
201469 CTACGAGCCGATAAA
66 CTACGAGCCGATAAA
* * * *
201484 TAAATTCAAGCTTCGGCTTAGCT-GGTTATAAGCTAGTGAATAAATTCAAGCTTTGGCTTAGCAG
1 TAAATTCAAGCTTCGACTTAG-TAGGTTATAAGCTAGTAAATAAATTCAAGCTTCGACTTAGCAG
* * *
201548 GTTACGAGCCGGTGAA
65 GCTACGAGCCGATAAA
*
201564 TAAATTCAAGCTACGACTTAGTA
1 TAAATTCAAGCTTCGACTTAGTA
201587 AGCTACAGGC
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 86 0.98
81 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (80 bp):
TAAATTCAAGCTTCGACTTAGTAGGTTATAAGCTAGTAAATAAATTCAAGCTTCGACTTAGCAGG
CTACGAGCCGATAAA
Found at i:201599 original size:80 final size:80
Alignment explanation
Indices: 201442--201624 Score: 201
Period size: 80 Copynumber: 2.3 Consensus size: 80
201432 TAAGTTGGTA
* * *
201442 AATAAATTCAAGC-TTCGATTTAGCAGGCTACGAGCCGATAAATAAATTCAAGCTTCGGCTTAGC
1 AATAAATTCAAGCTTTGGA-TTAGCAGGCTACGAGCCGATAAATAAATTCAAGCTACGACTTAGC
* * *
201506 TGGTTATAAGCTAGTG
65 TAGCTACAAGCTAGTG
* * * *
201522 AATAAATTCAAGCTTTGGCTTAGCAGGTTACGAGCCGGTGAATAAATTCAAGCTACGACTTAG-T
1 AATAAATTCAAGCTTTGGATTAGCAGGCTACGAGCCGATAAATAAATTCAAGCTACGACTTAGCT
*
201586 AAGCTACAGGCTAGTG
66 -AGCTACAAGCTAGTG
* *
201602 -TTAAAATTCAAGCTATGGATTAG
1 AAT-AAATTCAAGCTTTGGATTAG
201625 TAAGCTATGA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
79 2 0.02
80 81 0.94
81 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (80 bp):
AATAAATTCAAGCTTTGGATTAGCAGGCTACGAGCCGATAAATAAATTCAAGCTACGACTTAGCT
AGCTACAAGCTAGTG
Found at i:201943 original size:2 final size:2
Alignment explanation
Indices: 201936--201968 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
201926 AGGACATCTG
201936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
201969 GTAGATTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:210448 original size:106 final size:106
Alignment explanation
Indices: 210316--210534 Score: 341
Period size: 106 Copynumber: 2.1 Consensus size: 106
210306 TCCCTCAGAG
* *
210316 AAATATATGGAAGATTCATTAAAACATTATATCCTTTCCAAAAGGATATTATCTTTCATGTTTTA
1 AAAT-TATGGAAGATTCATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTA
*
210381 ATATTTAACGAAATCATTATAATTCATAATTATAATTACGTT
65 ATATTTAACGAAATCATTATAATTAATAATTATAATTACGTT
* * * *
210423 AAATTATGGAAGGTTTATTAAAACATTATATCCTTTTCTAAAGGATATTAACTTCCATGTTTTAA
1 AAATTATGGAAGATTCATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTAA
* *
210488 TATTTAACGAAATCATTATAATTAATAATTATATTTATGTT
66 TATTTAACGAAATCATTATAATTAATAATTATAATTACGTT
210529 -AATTAT
1 AAATTAT
210535 TTTTAGTAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 6 0.06
106 93 0.90
107 4 0.04
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (106 bp):
AAATTATGGAAGATTCATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTAA
TATTTAACGAAATCATTATAATTAATAATTATAATTACGTT
Found at i:217586 original size:18 final size:17
Alignment explanation
Indices: 217563--217631 Score: 66
Period size: 17 Copynumber: 4.0 Consensus size: 17
217553 CATTAATATA
217563 CAATGATATATGGAAATG
1 CAATGATA-ATGGAAATG
*
217581 CAATGATAATGTAAATG
1 CAATGATAATGGAAATG
* * **
217598 CAGTGACAATAAAAATG
1 CAATGATAATGGAAATG
* *
217615 CAATGACAAAGGAAATG
1 CAATGATAATGGAAATG
217632 TGGTGATAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
17 34 0.81
18 8 0.19
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.22
Consensus pattern (17 bp):
CAATGATAATGGAAATG
Found at i:226056 original size:105 final size:106
Alignment explanation
Indices: 225929--226147 Score: 332
Period size: 106 Copynumber: 2.1 Consensus size: 106
225919 TCCCTTAGAG
* *
225929 AAATATATAGAAGGTTTATTAAAACATTATATTCATTCC-AAAGGATATTATCTTCCACGTTTTA
1 AAAT-TATAGAAGGTTTATTAAAACATTATATCCATTCCAAAAGGATATTAACTTCCACGTTTTA
*
225993 ATATTTAACAAAATCATTATAATTAATAATTATAATTACATT
65 ATATTTAACAAAATCATCATAATTAATAATTATAATTACATT
* * * *
226035 AAATTATGGAAGGTTTATTAAAATATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTAA
1 AAATTATAGAAGGTTTATTAAAACATTATATCCATTCCAAAAGGATATTAACTTCCACGTTTTAA
* **
226100 TATTTAACGAAATCATCATAATTAATAATTATAATTATGTT
66 TATTTAACAAAATCATCATAATTAATAATTATAATTACATT
226141 AAATTAT
1 AAATTAT
226148 TTTCAGTAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 30 0.29
106 72 0.71
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (106 bp):
AAATTATAGAAGGTTTATTAAAACATTATATCCATTCCAAAAGGATATTAACTTCCACGTTTTAA
TATTTAACAAAATCATCATAATTAATAATTATAATTACATT
Found at i:227635 original size:392 final size:392
Alignment explanation
Indices: 226911--227694 Score: 1327
Period size: 392 Copynumber: 2.0 Consensus size: 392
226901 ATCCAAGAAA
* * * * **
226911 CATACTCATAGTGATTCAGTTCGATATGTTTTTCCCTAACACATACTCATATATTGATTTTGACA
1 CATACTCATAGCGAGTCAGTCCAATATGTCATTCCCTAACACATACTCATATATTGATTTTGACA
*
226976 TCCCTATGTCAATGACAACACTTTGTCATCAATCAACTACATATTAGTCTCAATGCATTATAGTT
66 TCCCTATGTCAATGACAACACTTTGTCATCAATAAACTACATATTAGTCTCAATGCATTATAGTT
* *
227041 GTCCACGTCCACAATAATACTTGACTAAGGACCTTTTAAGAATAATCTTATTATCCTCAGGACAT
131 GTCCACGCCCACAATAATACTTGACTAAGGACCTTTTAAGAATAATCATATTATCCTCAGGACAT
*
227106 TATTATAAATCAATTTATTTAAATACACAGAAAAAGAAACTGAAATAACAATGACAATGTCTTTT
196 TATTATAAATCAATTTATTTAAATACACAGAAAAAGAAACTAAAATAACAATGACAATGTCTTTT
*
227171 ATTAATAAACAAGGTAAAATGACTATGTGATTACAATCATCTCATGATTGATCTTTGGGCATACT
261 ATTAATAAACAAGGTAAAATGACTATGTGATTACAATAATCTCATGATTGATCTTTGGGCATACT
* * *
227236 CTAACATTTAGATCAAGAGACAAGTATGACTGTGGATAATCGGGGGAAGAGCAAGGTTGTTGAAT
326 CTAACATTTAGATCAAGAGACAAGTACGACTGTGGATAATCGGAGGAAGAGCAAGGTCGTTGAAT
227301 AG
391 AG
* * *
227303 CATACTCATAGCGAGTCAGTCCAATATGTCATTCTCTAACATATACTCATGTATTGATTTTGACA
1 CATACTCATAGCGAGTCAGTCCAATATGTCATTCCCTAACACATACTCATATATTGATTTTGACA
* *
227368 TCCTTATGTCAATGACAACACTTTGTCATCAATAAACTACATATTAGTCTCAATGCATTATTGTT
66 TCCCTATGTCAATGACAACACTTTGTCATCAATAAACTACATATTAGTCTCAATGCATTATAGTT
227433 GTCCACGCCCACAATAATACTTGACTAAGGACCTTTTAAGAATAATCATATTATCCTCAGGACAT
131 GTCCACGCCCACAATAATACTTGACTAAGGACCTTTTAAGAATAATCATATTATCCTCAGGACAT
* * *
227498 TATTGTAAATTAGTTTATTTAAATACACAGAAAAAGAAACTAAAATAACAATGACAATGTCTTTT
196 TATTATAAATCAATTTATTTAAATACACAGAAAAAGAAACTAAAATAACAATGACAATGTCTTTT
* * *
227563 ATTAATAAATAGGGTAAAATGAGTATGTGATTACAATAATCTCATGATT-AGTCTTTGGGCATAC
261 ATTAATAAACAAGGTAAAATGACTATGTGATTACAATAATCTCATGATTGA-TCTTTGGGCATAC
227627 TCTAACATTTAGATCAAGAGACAAGTACGACTGTGGATAATCGGAGGAAGAGCAAGGTCGTTGAA
325 TCTAACATTTAGATCAAGAGACAAGTACGACTGTGGATAATCGGAGGAAGAGCAAGGTCGTTGAA
227692 TAG
390 TAG
227695 ATATCTTCTA
Statistics
Matches: 366, Mismatches: 25, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
391 1 0.00
392 365 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (392 bp):
CATACTCATAGCGAGTCAGTCCAATATGTCATTCCCTAACACATACTCATATATTGATTTTGACA
TCCCTATGTCAATGACAACACTTTGTCATCAATAAACTACATATTAGTCTCAATGCATTATAGTT
GTCCACGCCCACAATAATACTTGACTAAGGACCTTTTAAGAATAATCATATTATCCTCAGGACAT
TATTATAAATCAATTTATTTAAATACACAGAAAAAGAAACTAAAATAACAATGACAATGTCTTTT
ATTAATAAACAAGGTAAAATGACTATGTGATTACAATAATCTCATGATTGATCTTTGGGCATACT
CTAACATTTAGATCAAGAGACAAGTACGACTGTGGATAATCGGAGGAAGAGCAAGGTCGTTGAAT
AG
Found at i:228046 original size:40 final size:40
Alignment explanation
Indices: 227884--228033 Score: 219
Period size: 40 Copynumber: 3.8 Consensus size: 40
227874 TTGCGTTGAA
* *
227884 AATAAATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGGTG
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTACAAGCCAGTG
* *
227924 AATAAATTCAAGCTTCGGCTTAGCAAGCTACAAGTCAGTG
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTACAAGCCAGTG
* *
227964 AATAAATTCAAGCTTTGCCTTAGCAGGCTACAAGCCAGTG
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTACAAGCCAGTG
* * *
228004 AATAAATTGAAGCTACGACTTAGCAGGCTA
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTA
228034 TGAGCCGGTG
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (40 bp):
AATAAATTCAAGCTTCGGCTTAGCAGGCTACAAGCCAGTG
Found at i:231806 original size:17 final size:17
Alignment explanation
Indices: 231773--231818 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
231763 CATTAATTTA
*
231773 CAATGACAAATGGAAATG
1 CAATGAC-AATGCAAATG
231791 CAATGACAATGCAAATG
1 CAATGACAATGCAAATG
* *
231808 TAGTGACAATG
1 CAATGACAATG
231819 AGAATGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.20
Consensus pattern (17 bp):
CAATGACAATGCAAATG
Found at i:231824 original size:17 final size:16
Alignment explanation
Indices: 231793--231836 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
231783 TGGAAATGCA
231793 ATGACAATGCAAATGT-
1 ATGACAATG-AAATGTG
231809 AGTGACAATGAGAATGTG
1 A-TGACAATGA-AATGTG
231827 ATGACAATGA
1 ATGACAATGA
231837 TTTCTAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (16 bp):
ATGACAATGAAATGTG
Found at i:231987 original size:21 final size:20
Alignment explanation
Indices: 231948--231994 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
231938 CTGCATGATG
* *
231948 TTTCTTCTTGTTGCGCTTCT
1 TTTCTTCTTGTGGCACTTCT
231968 TTTCTTCCTTGTGGCACTTCT
1 TTTCTT-CTTGTGGCACTTCT
*
231989 TATCTT
1 TTTCTT
231995 TGGCACACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.04, C:0.26, G:0.13, T:0.57
Consensus pattern (20 bp):
TTTCTTCTTGTGGCACTTCT
Found at i:249708 original size:12 final size:12
Alignment explanation
Indices: 249688--249739 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 12
249678 CAAGCAAAAA
249688 AAAAAAAACAAG
1 AAAAAAAACAAG
*
249700 AAAAGAAACAAG
1 AAAAAAAACAAG
249712 AAAGCAATAAAACAAG
1 -AA--AA-AAAACAAG
249728 AAAGAAAAACAA
1 AAA-AAAAACAA
249740 AAGAGCTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 11 0.33
13 10 0.30
14 1 0.03
15 4 0.12
16 7 0.21
ACGTcount: A:0.77, C:0.10, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAAAAAACAAG
Found at i:253197 original size:36 final size:36
Alignment explanation
Indices: 253153--253224 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
253143 AGAGAAAATA
*
253153 TTTGCAACTAAACTAAATACTGAAAAGTAAAACTAT
1 TTTGCAACTAAACTAAATACCGAAAAGTAAAACTAT
253189 TTTGCAACTAAACTAAATACCGAAAAGTAAAACTAT
1 TTTGCAACTAAACTAAATACCGAAAAGTAAAACTAT
253225 CTCAGTGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.26
Consensus pattern (36 bp):
TTTGCAACTAAACTAAATACCGAAAAGTAAAACTAT
Found at i:253619 original size:21 final size:20
Alignment explanation
Indices: 253584--253622 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
253574 GGGCAACTTC
*
253584 TTCTTTTTTTTCTTCTGCAT
1 TTCTTTTTCTTCTTCTGCAT
253604 TTCTTTCTTCTTCTTCTGC
1 TTCTTT-TTCTTCTTCTGC
253623 TTCAATACCC
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:0.03, C:0.26, G:0.05, T:0.67
Consensus pattern (20 bp):
TTCTTTTTCTTCTTCTGCAT
Found at i:269301 original size:17 final size:17
Alignment explanation
Indices: 269266--269328 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
269256 CATTAAATTA
*
269266 CAATGACAATTGGAAATG
1 CAATGACAA-TGAAAATG
*
269284 CAATGACAATGCAAATG
1 CAATGACAATGAAAATG
* * *
269301 CAGTGATAATTAAAATG
1 CAATGACAATGAAAATG
*
269318 TAATGACAATG
1 CAATGACAATG
269329 GGAATGTGAT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 27 0.75
18 9 0.25
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:276642 original size:21 final size:21
Alignment explanation
Indices: 276618--276664 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
276608 CTAAGAACGG
276618 TAGAA-GAGTAACTTGTATCGA
1 TAGAACGA-TAACTTGTATCGA
* *
276639 TAGAACTATCACTTGTATCGA
1 TAGAACGATAACTTGTATCGA
276660 TAGAA
1 TAGAA
276665 ATTTGCACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (21 bp):
TAGAACGATAACTTGTATCGA
Found at i:279700 original size:16 final size:18
Alignment explanation
Indices: 279679--279713 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
279669 TTTTTAGTTC
279679 AAAGACTT-T-ATTTTGA
1 AAAGACTTGTAATTTTGA
279695 AAAGACTTGTAATTTTGA
1 AAAGACTTGTAATTTTGA
279713 A
1 A
279714 TAACAGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (18 bp):
AAAGACTTGTAATTTTGA
Found at i:281721 original size:21 final size:22
Alignment explanation
Indices: 281695--281736 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
281685 GACTGCCTTC
*
281695 TGTGTCACAACA-CGACTCCTG
1 TGTGTCACAACATCAACTCCTG
281716 TGTGTCACAACATCAACTCCT
1 TGTGTCACAACATCAACTCCT
281737 TAACGTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.26
Consensus pattern (22 bp):
TGTGTCACAACATCAACTCCTG
Found at i:292587 original size:36 final size:36
Alignment explanation
Indices: 292547--292616 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
292537 TATTCCTGCA
* * *
292547 GCGATAGTTTTGGTGCAATCTGGAAGTGCTCATGTG
1 GCGATAGTTTGGGCGCAATCTAGAAGTGCTCATGTG
*
292583 GCGATAGTTTGGGCGCAATCTAGAGGTGCTCATG
1 GCGATAGTTTGGGCGCAATCTAGAAGTGCTCATG
292617 CGGTAACAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (36 bp):
GCGATAGTTTGGGCGCAATCTAGAAGTGCTCATGTG
Found at i:292628 original size:36 final size:36
Alignment explanation
Indices: 292552--292637 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 36
292542 CTGCAGCGAT
* * * * * *
292552 AGTTTTGGTGCAATCTGGAAGTGCTCATGTGGCGAT
1 AGTTTGGGCGCAATCTAGAAGTGCTCATGCGGCAAC
* *
292588 AGTTTGGGCGCAATCTAGAGGTGCTCATGCGGTAAC
1 AGTTTGGGCGCAATCTAGAAGTGCTCATGCGGCAAC
292624 AGTTTTGGGCGCAA
1 AG-TTTGGGCGCAA
292638 ATTTGGATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 30 0.73
37 11 0.27
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (36 bp):
AGTTTGGGCGCAATCTAGAAGTGCTCATGCGGCAAC
Found at i:293809 original size:17 final size:17
Alignment explanation
Indices: 293789--293835 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
293779 GACAATGGTG
293789 ATGCAGCGACAATAAAA
1 ATGCAGCGACAATAAAA
* *
293806 ATGCAGTGAAAATAAAA
1 ATGCAGCGACAATAAAA
* *
293823 ATGAAGGGACAAT
1 ATGCAGCGACAAT
293836 TATACTACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.15
Consensus pattern (17 bp):
ATGCAGCGACAATAAAA
Found at i:296551 original size:21 final size:21
Alignment explanation
Indices: 296530--296570 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
296520 AACTGTTTAC
296530 TGACTTAACAACTACCGATACT
1 TGAC-TAACAACTACCGATACT
* *
296552 TGTCTAACAAGTACCGATA
1 TGACTAACAACTACCGATA
296571 GAAGTCTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (21 bp):
TGACTAACAACTACCGATACT
Found at i:296577 original size:21 final size:21
Alignment explanation
Indices: 296535--296577 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
296525 TTTACTGACT
**
296535 TAACAACTACCGATACTTGTC
1 TAACAACTACCGATACAAGTC
* *
296556 TAACAAGTACCGATAGAAGTC
1 TAACAACTACCGATACAAGTC
296577 T
1 T
296578 CCAAAAATCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (21 bp):
TAACAACTACCGATACAAGTC
Found at i:303733 original size:21 final size:21
Alignment explanation
Indices: 303670--303739 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
303660 ATGACATGTT
303670 TCAGTAGAAGTCTCACTTGTA
1 TCAGTAGAAGTCTCACTTGTA
* * *
303691 TCAATA-ATACTGCCTCA--AGTA
1 TCAGTAGA-A--GTCTCACTTGTA
303712 TCAGTAGAAGTCTCACTTGTA
1 TCAGTAGAAGTCTCACTTGTA
*
303733 TCGGTAG
1 TCAGTAG
303740 TACGACTCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
19 5 0.14
20 1 0.03
21 24 0.67
22 1 0.03
23 5 0.14
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (21 bp):
TCAGTAGAAGTCTCACTTGTA
Found at i:303761 original size:41 final size:42
Alignment explanation
Indices: 303670--303765 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
303660 ATGACATGTT
*
303670 TCAGTAGAAGTCTCACTTGTATCAATAATACTGCCTCAAGTA
1 TCAGTAGAAGTCTCACTTGTATCAATAATACTGACTCAAGTA
** *
303712 TCAGTAGAAGTCTCACTTGTATCGGTAGTAC-GACTCAAGTA
1 TCAGTAGAAGTCTCACTTGTATCAATAATACTGACTCAAGTA
303753 T-AGGTAGAAGTCT
1 TCA-GTAGAAGTCT
303766 ACACCATTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.02
41 20 0.41
42 28 0.57
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
TCAGTAGAAGTCTCACTTGTATCAATAATACTGACTCAAGTA
Done.