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 57 of 206
Found at i:16162093 original size:17 final size:17
Alignment explanation
Indices: 16162021--16162115 Score: 66
Period size: 17 Copynumber: 5.5 Consensus size: 17
16162011 CTTAAGCATG
*
16162021 TTTTAAAATTAAAG-AAA
1 TTTTAAACTT-AAGTAAA
** *
16162038 TTTTAGGCTTAAGTGAAT
1 TTTTAAACTTAAGT-AAA
* **
16162056 TTTTGAACTTAAGTATG
1 TTTTAAACTTAAGTAAA
16162073 TTTTAAACTTAAGTAAA
1 TTTTAAACTTAAGTAAA
* * *
16162090 TTTTTAATTTGAGTAAA
1 TTTTAAACTTAAGTAAA
*
16162107 TTTCAAACT
1 TTTTAAACT
16162116 GTTTTCTCTA
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
16 3 0.05
17 42 0.72
18 13 0.22
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTTAAACTTAAGTAAA
Found at i:16162556 original size:124 final size:127
Alignment explanation
Indices: 16162275--16162562 Score: 377
Period size: 124 Copynumber: 2.3 Consensus size: 127
16162265 TTTAGAGTTG
* * * **
16162275 TTTTTAGAGGTTGCGATCATAAACCGACAAACCTTTATAACATTAGCTGGGAGCGTAGGTCTGCT
1 TTTTTAGAGGTTGCGATCATAAACTGAAAAACCTTTATAACATTAGCTGAGAGCGTAGGTCCACT
* * ** *
16162340 AACTGTGTTGGAGATGCGAGCAAGCTCTTAGAATATCATCTGGGAACATAGGTTTGCTAGCTG
66 AACTGTGTT-GAGATGCGAGCAAGCTCTTAGAATATCAGCTGAGAACATAGGTCCGCTAGCTA
* *
16162403 TTTTTAGAGGTTGCGATCATAAA-TCGAAAAACCTTTATTACATTAGTTGAGAGCGTAGGTCCAC
1 TTTTTAGAGGTTGCGATCATAAACT-GAAAAACCTTTATAACATTAGCTGAGAGCGTAGGTCCAC
* * * *
16162467 TAGCTGTGTT-AGA-GC-TGCGAGCTCTTAGAATATCAGCTGAGAATATAGGTCCGCTAGCTA
65 TAACTGTGTTGAGATGCGAGCAAGCTCTTAGAATATCAGCTGAGAACATAGGTCCGCTAGCTA
*
16162527 TTTTTGGAGGTTGCGATCATAAACTGAAAAACCTTT
1 TTTTTAGAGGTTGCGATCATAAACTGAAAAACCTTT
16162563 GAATAATACT
Statistics
Matches: 141, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
124 70 0.50
125 3 0.02
126 3 0.02
128 65 0.46
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (127 bp):
TTTTTAGAGGTTGCGATCATAAACTGAAAAACCTTTATAACATTAGCTGAGAGCGTAGGTCCACT
AACTGTGTTGAGATGCGAGCAAGCTCTTAGAATATCAGCTGAGAACATAGGTCCGCTAGCTA
Found at i:16166495 original size:10 final size:10
Alignment explanation
Indices: 16166468--16166512 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
16166458 GACACACATC
16166468 AATCACATAT
1 AATCACATAT
*
16166478 AAGCACATAT
1 AATCACATAT
* *
16166488 AATTACATAC
1 AATCACATAT
*
16166498 AATCACATTT
1 AATCACATAT
16166508 AATCA
1 AATCA
16166513 AAGTGTATGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (10 bp):
AATCACATAT
Found at i:16166955 original size:8 final size:8
Alignment explanation
Indices: 16166944--16166984 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
16166934 TATGTTCATG
16166944 ATTTCACA
1 ATTTCACA
16166952 ATTTCACA
1 ATTTCACA
16166960 ATTTCACA
1 ATTTCACA
*
16166968 AATTCACA
1 ATTTCACA
*
16166976 AATTCACA
1 ATTTCACA
16166984 A
1 A
16166985 ACAAACATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (8 bp):
ATTTCACA
Found at i:16174835 original size:196 final size:196
Alignment explanation
Indices: 16174496--16174867 Score: 600
Period size: 196 Copynumber: 1.9 Consensus size: 196
16174486 TTCCACAAGC
*
16174496 TCATTAAACAACTCTGTATTTTGGGCCACTAAATAAACCTGAATCTCACGATTGTGCCCAAAGCG
1 TCATCAAACAACTCTGTATTTTGGGCCACTAAATAAACCTGAATCTCACGATTGTGCCCAAAGCG
* ** * *
16174561 GAACCTTTTACAATGATCCTTCTAAGTCAAAACCATCTCAGGAGCATACTGACAAAGGTGCACAA
66 GAACCTCTTACAATGATCCTTCTAAGTCAAAACCATCTCAAAAGAATACTGACAAAGGCGCACAA
*
16174626 ACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAGGATCTAAAAATTCCCACCATAAG
131 ACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATCTAAAAATTCCCACCATAAG
16174691 T
196 T
**
16174692 TCATCAAACAACTCTGTATTTTTTGCCACTAAATAAACCTGAATCTCACGATTGTGCCCAAAGCG
1 TCATCAAACAACTCTGTATTTTGGGCCACTAAATAAACCTGAATCTCACGATTGTGCCCAAAGCG
* * * * *
16174757 GAACCTCTTACAATGATCCTTCTCAGTCAAAACTATCTTAAAAGAATACTGACTAAGGCGCATAA
66 GAACCTCTTACAATGATCCTTCTAAGTCAAAACCATCTCAAAAGAATACTGACAAAGGCGCACAA
* *
16174822 ACTCTGCCTCATAGTTAGCCACAGACAAGCTACCTTGCACAAGATC
131 ACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATC
16174868 CATATACTGC
Statistics
Matches: 160, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
196 160 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (196 bp):
TCATCAAACAACTCTGTATTTTGGGCCACTAAATAAACCTGAATCTCACGATTGTGCCCAAAGCG
GAACCTCTTACAATGATCCTTCTAAGTCAAAACCATCTCAAAAGAATACTGACAAAGGCGCACAA
ACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATCTAAAAATTCCCACCATAAG
T
Found at i:16175925 original size:20 final size:22
Alignment explanation
Indices: 16175900--16175952 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
16175890 GTGTTATGTA
16175900 GGTATCGATACTGCCTTT-A-T
1 GGTATCGATACTGCCTTTAATT
* *
16175920 GGTATCGATATTTCCTTTAATT
1 GGTATCGATACTGCCTTTAATT
*
16175942 GGTATCTATAC
1 GGTATCGATAC
16175953 CACTTGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.59
21 1 0.04
22 10 0.37
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (22 bp):
GGTATCGATACTGCCTTTAATT
Found at i:16180743 original size:5 final size:5
Alignment explanation
Indices: 16180733--16180765 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
16180723 AAAACTCATA
16180733 AAAAT AAAAT AAAAT AAAAT AAAAT AAATAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
16180766 CTAATCATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:16181543 original size:15 final size:15
Alignment explanation
Indices: 16181523--16181571 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 15
16181513 TATATATTAT
16181523 AATATTAATTAATAA
1 AATATTAATTAATAA
*
16181538 AATATTATTACTTATTAA
1 AATATTA--A-TTAATAA
16181556 AATATT-ATTAATAA
1 AATATTAATTAATAA
16181570 AA
1 AA
16181572 ATATCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 8 0.28
15 8 0.28
17 1 0.03
18 12 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATTAATTAATAA
Found at i:16181546 original size:18 final size:18
Alignment explanation
Indices: 16181525--16181567 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
16181515 TATATTATAA
16181525 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
16181543 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
16181561 TATTAAT
1 TATTAAT
16181568 AAAAATATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:16190237 original size:39 final size:39
Alignment explanation
Indices: 16190194--16190287 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
16190184 CATGTTTTTA
* *
16190194 AGTATTGTGATATATGCTTGAATATTATGTGATTATATG
1 AGTATTGTGATATATGCTTAAATATTAAGTGATTATATG
*
16190233 AGTATTGTGATATATGCTTAAATGTTAAGTGATTATATG
1 AGTATTGTGATATATGCTTAAATATTAAGTGATTATATG
* * *
16190272 TGAAATGTGATATATG
1 AGTATTGTGATATATG
16190288 TTTACCTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTAAATATTAAGTGATTATATG
Found at i:16192542 original size:22 final size:22
Alignment explanation
Indices: 16192501--16192550 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
16192491 CTCATCTTTA
*
16192501 GTGTTATTGTTTCTTTATTTTT
1 GTGTTATTGTTTCTTAATTTTT
*
16192523 GTGTTAGTTGTTT-TTAATTTAT
1 GTGTTA-TTGTTTCTTAATTTTT
16192545 GT-TTAT
1 GTGTTAT
16192551 CAAGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 15 0.60
23 6 0.24
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.68
Consensus pattern (22 bp):
GTGTTATTGTTTCTTAATTTTT
Found at i:16195675 original size:28 final size:28
Alignment explanation
Indices: 16195643--16195767 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
16195633 CATGGCATAT
16195643 TCAAGTAAGAGTCAGCATGGACTATCTA
1 TCAAGTAAGAGTCAGCATGGACTATCTA
16195671 TCAAGTAAGAGTCAGCATGGACTATCTA
1 TCAAGTAAGAGTCAGCATGGACTATCTA
*
16195699 TCAAGTAAGAGTCCGCATGGACTATC-A
1 TCAAGTAAGAGTCAGCATGGACTATCTA
* * *
16195726 TTCAAGAAAGAGTTC-GCAAGGACTATCTT
1 -TCAAGTAAGAG-TCAGCATGGACTATCTA
16195755 TCAAGTAAGAGTC
1 TCAAGTAAGAGTC
16195768 CACAATGATT
Statistics
Matches: 89, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
27 3 0.03
28 84 0.94
29 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (28 bp):
TCAAGTAAGAGTCAGCATGGACTATCTA
Found at i:16195786 original size:56 final size:56
Alignment explanation
Indices: 16195643--16195806 Score: 176
Period size: 56 Copynumber: 2.9 Consensus size: 56
16195633 CATGGCATAT
* *
16195643 TCAAGTAAGAGT-CAGCATGGACTATC-TATCAAGTAAGAG-TCAGCATGGACTATCTA
1 TCAAGTAAGAGTCCA-CATGGACTATCAT-TCAAGAAAGAGTTC-GCAAGGACTATCTA
* *
16195699 TCAAGTAAGAGTCCGCATGGACTATCATTCAAGAAAGAGTTCGCAAGGACTATCTT
1 TCAAGTAAGAGTCCACATGGACTATCATTCAAGAAAGAGTTCGCAAGGACTATCTA
* * * *
16195755 TCAAGTAAGAGTCCACAAT-GATTGTTC-TTCAAGAAGGAGTCCGCAAGGACTA
1 TCAAGTAAGAGTCCAC-ATGGACT-ATCATTCAAGAAAGAGTTCGCAAGGACTA
16195807 ACTAATGAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
56 86 0.91
57 8 0.09
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (56 bp):
TCAAGTAAGAGTCCACATGGACTATCATTCAAGAAAGAGTTCGCAAGGACTATCTA
Found at i:16195787 original size:84 final size:84
Alignment explanation
Indices: 16195641--16195806 Score: 198
Period size: 84 Copynumber: 2.0 Consensus size: 84
16195631 GCCATGGCAT
* *
16195641 ATTCAAGTAAGAGTCAGCATGGACTATCTATCAAGTAAGAGTCAGCATGGACTATCTATCAAGTA
1 ATTCAAGAAAGAGTCAGCAAGGACTATCTATCAAGTAAGAGTCAGCATGGACTATCTATCAAG-A
*
16195706 A-GAGTCCGCATGGACTATC
65 AGGAGTCCGCAAGGACTATC
* * *
16195725 ATTCAAGAAAGAGTTC-GCAAGGACTATCTTTCAAGTAAGAGTCCA-CAAT-GATTGTTCT-TCA
1 ATTCAAGAAAGAG-TCAGCAAGGACTATCTATCAAGTAAGAGT-CAGC-ATGGACT-ATCTATCA
16195786 AGAAGGAGTCCGCAAGGACTA
62 AGAAGGAGTCCGCAAGGACTA
16195807 ACTAATGAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
83 2 0.03
84 60 0.85
85 9 0.13
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (84 bp):
ATTCAAGAAAGAGTCAGCAAGGACTATCTATCAAGTAAGAGTCAGCATGGACTATCTATCAAGAA
GGAGTCCGCAAGGACTATC
Found at i:16209081 original size:32 final size:32
Alignment explanation
Indices: 16209035--16209103 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
16209025 GGTGAGACGA
*
16209035 CTTACTTCTATTATATAAAAACCTAGTTAACT
1 CTTAATTCTATTATATAAAAACCTAGTTAACT
16209067 CTTAATTCTATTATATAAAAACCTAGTTAACT
1 CTTAATTCTATTATATAAAAACCTAGTTAACT
16209099 CTTAA
1 CTTAA
16209104 AAGCAATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (32 bp):
CTTAATTCTATTATATAAAAACCTAGTTAACT
Found at i:16219438 original size:5 final size:5
Alignment explanation
Indices: 16219428--16219452 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16219418 TATGTTAGGT
16219428 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
16219453 ACTTTTTTTA
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:16220084 original size:51 final size:53
Alignment explanation
Indices: 16220019--16220127 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 53
16220009 TAGCAATTAA
16220019 CAAATCAACCGACCATTATTTTATCA-TTACATTGTCTAAAGCAATAGGGAAG
1 CAAATCAACCGACCATTATTTTATCATTTACATTGTCTAAAGCAATAGGGAAG
* * * *
16220071 -AAATCAACTGACCATTGTTTTATCATTTATATTGTCTAAAGTAATAGGGAAG
1 CAAATCAACCGACCATTATTTTATCATTTACATTGTCTAAAGCAATAGGGAAG
16220123 CAAAT
1 CAAAT
16220128 TAGATTAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
51 23 0.45
52 24 0.47
53 4 0.08
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (53 bp):
CAAATCAACCGACCATTATTTTATCATTTACATTGTCTAAAGCAATAGGGAAG
Found at i:16221207 original size:37 final size:37
Alignment explanation
Indices: 16221108--16221194 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
16221098 AAAATGAATA
* *
16221108 ATTCCCTGGCAAAAGAAGATAG-AGATGAACAGGAGTG
1 ATTCCCTGCCAAAAGAA-ATCGAAGATGAACAGGAGTG
* *
16221145 ATTCTCTGCCAAAAGAAATCGAAGATGAACATGAGTG
1 ATTCCCTGCCAAAAGAAATCGAAGATGAACAGGAGTG
16221182 ATTCCCTGCCAAA
1 ATTCCCTGCCAAA
16221195 TGCGGACGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 3 0.07
37 41 0.93
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (37 bp):
ATTCCCTGCCAAAAGAAATCGAAGATGAACAGGAGTG
Found at i:16221434 original size:22 final size:23
Alignment explanation
Indices: 16221403--16221454 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
16221393 CACATCGACC
16221403 AACAAATCAAATTTAA-ATTCAA
1 AACAAATCAAATTTAACATTCAA
* *
16221425 AACAATTCAAATTTAACTTTCAA
1 AACAAATCAAATTTAACATTCAA
*
16221448 AAAAAAT
1 AACAAAT
16221455 AATTTTCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (23 bp):
AACAAATCAAATTTAACATTCAA
Found at i:16221500 original size:37 final size:37
Alignment explanation
Indices: 16221425--16221504 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
16221415 TTAAATTCAA
* *
16221425 AACAATTCAAATTTAACTTTCAAAAAAAATAATTTTC
1 AACAAATCAAATTTAACTTTCAAAAAAAATAATGTTC
* ** **
16221462 AACAAATCAAATTTAATTTTTTAAAAATTTAATGTTC
1 AACAAATCAAATTTAACTTTCAAAAAAAATAATGTTC
16221499 AA-AAAT
1 AACAAAT
16221505 TTTCTTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 4 0.11
37 32 0.89
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (37 bp):
AACAAATCAAATTTAACTTTCAAAAAAAATAATGTTC
Found at i:16222095 original size:29 final size:28
Alignment explanation
Indices: 16222063--16222124 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
16222053 AAAAGCCTTT
16222063 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
16222092 TTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
16222120 TTTTT
1 TTTTT
16222125 CGAGAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:16222665 original size:125 final size:126
Alignment explanation
Indices: 16222343--16222681 Score: 626
Period size: 126 Copynumber: 2.7 Consensus size: 126
16222333 CGTCTCTGGT
* *
16222343 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
16222408 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTTCGATTTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCTCGATATTTCTGAG
16222469 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
16222534 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCT-GATATTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCTCGATATTTCTGAG
*
16222594 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGTGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
16222659 TGGACGCGATTTTGCTACAGTAG
66 TGGACGCGATTTTGCTACAGTAG
16222682 AAAGTTTAGG
Statistics
Matches: 208, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
125 98 0.47
126 110 0.53
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (126 bp):
CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCTCGATATTTCTGAG
Found at i:16226152 original size:29 final size:29
Alignment explanation
Indices: 16226110--16226489 Score: 516
Period size: 29 Copynumber: 13.2 Consensus size: 29
16226100 NNNNNNNNNN
*
16226110 TTTAGGTTAGGTTTAGGGTTTTTAGTTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
* *
16226139 TTTAGGTTAGGTTTAGGGTTGTAAATTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
* *
16226168 TTTAGGTTA-GATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
16226196 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
* *
16226225 TTTTAGGTTAGGGTTAGGGTTTTAAATTAA
1 -TTTAGGTTAGGTTTAGGGTTTTTAATTAA
*
16226255 TTTAGGTTAGGTTTAGGGTTTTTAGTTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
16226284 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
* * * *
16226313 TTTATGTTA-GATTAAGGTTTTTAGTTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
*
16226341 TTTAGGTTAGCTTTAGGGTTTTTAATTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
* *
16226370 TTTAGGTTA-GATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
* *
16226398 CTTAGGTTAGGTTTAAGGTTTTTAATTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
** * ***
16226427 TTTCTGTTA-GATTAGGGTTTTTAGCCAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
16226455 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA
16226484 TTTAGG
1 TTTAGG
16226490 GTTTTTATTT
Statistics
Matches: 301, Mismatches: 45, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
28 93 0.31
29 181 0.60
30 27 0.09
ACGTcount: A:0.24, C:0.01, G:0.24, T:0.50
Consensus pattern (29 bp):
TTTAGGTTAGGTTTAGGGTTTTTAATTAA
Found at i:16226199 original size:57 final size:57
Alignment explanation
Indices: 16226110--16226489 Score: 528
Period size: 57 Copynumber: 6.6 Consensus size: 57
16226100 NNNNNNNNNN
* * * * *
16226110 TTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTGTAAATTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAGTTAA
* * * *
16226168 TTTAGGTTA-GATTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAATTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAGTTAA
* * *
16226225 TTTTAGGTTAGGGTTAGGGTTTTAAATTAATTTAGGTTAGGTTTAGGGTTTTTAGTTAA
1 -TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAGTTAA
* *
16226284 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTATGTTAGATTAAGGTTTTTAGTTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAA
*
16226341 TTTAGGTTAGCTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAA
* * ** **
16226398 CTTAGGTTAGGTTTAAGGTTTTTAATTAATTTCTGTTAGATTAGGGTTTTTAGCCAA
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAA
16226455 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGG
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGG
16226490 GTTTTTATTT
Statistics
Matches: 294, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
57 197 0.67
58 53 0.18
59 44 0.15
ACGTcount: A:0.24, C:0.01, G:0.24, T:0.50
Consensus pattern (57 bp):
TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAA
Found at i:16226414 original size:86 final size:86
Alignment explanation
Indices: 16226110--16226489 Score: 539
Period size: 86 Copynumber: 4.4 Consensus size: 86
16226100 NNNNNNNNNN
* * *
16226110 TTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTGTAAATTAATTTAGGT
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAAGGTTTTAAATTAATTTAGGT
16226175 TAGATTAGGGTTTTTAGTTAA
66 TAGATTAGGGTTTTTAGTTAA
* *
16226196 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTTAGGTTAGGGTTAGGGTTTTAAATTAATTTAGG
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAA-TTTAGGTTAGGTTTAAGGTTTTAAATTAATTTAGG
*
16226261 TTAGGTTTAGGGTTTTTAGTTAA
65 TTA-GATTAGGGTTTTTAGTTAA
* * * *
16226284 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTATGTTA-GATTAAGGTTTTTAGTTAATTTAGGT
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAAGGTTTTAAATTAATTTAGGT
* *
16226348 TAGCTTTAGGGTTTTTAATTAA
66 TAG-ATTAGGGTTTTTAGTTAA
* * * * **
16226370 TTTAGGTTA-GATTAGGGTTTTTAGTTAACTTAGGTTAGGTTTAAGGTTTTTAATTAATTTCTGT
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAAGGTTTTAAATTAATTTAGGT
**
16226434 TAGATTAGGGTTTTTAGCCAA
66 TAGATTAGGGTTTTTAGTTAA
16226455 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGG
1 TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGG
16226490 GTTTTTATTT
Statistics
Matches: 264, Mismatches: 25, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
85 48 0.18
86 125 0.47
87 44 0.17
88 47 0.18
ACGTcount: A:0.24, C:0.01, G:0.24, T:0.50
Consensus pattern (86 bp):
TTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAAGGTTTTAAATTAATTTAGGT
TAGATTAGGGTTTTTAGTTAA
Found at i:16226568 original size:26 final size:25
Alignment explanation
Indices: 16226533--16226585 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
16226523 TTTTCTTAAA
16226533 AAATTTCTATGCGTATTACATCAAAT
1 AAATTTCTAT-CGTATTACATCAAAT
**
16226559 AAATTTCTATTTTATTACATCAAAT
1 AAATTTCTATCGTATTACATCAAAT
16226584 AA
1 AA
16226586 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.42
Consensus pattern (25 bp):
AAATTTCTATCGTATTACATCAAAT
Found at i:16226726 original size:24 final size:24
Alignment explanation
Indices: 16226699--16226751 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
16226689 AGCGGTTGTT
16226699 CTTCCTCTGGTGCTGATTGTGGTC
1 CTTCCTCTGGTGCTGATTGTGGTC
* * *
16226723 CTTCCTCTGGTGGTGGTTGTGGTT
1 CTTCCTCTGGTGCTGATTGTGGTC
16226747 CTTCC
1 CTTCC
16226752 AGTTCAGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.02, C:0.25, G:0.30, T:0.43
Consensus pattern (24 bp):
CTTCCTCTGGTGCTGATTGTGGTC
Found at i:16227050 original size:18 final size:18
Alignment explanation
Indices: 16227006--16227051 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
16226996 TATTCGGAAA
* *
16227006 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
16227024 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
16227042 AGGAAACATA
1 AGGATACATA
16227052 CCTGGCATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:16227706 original size:7 final size:7
Alignment explanation
Indices: 16227696--16227720 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16227686 TTATATACAT
16227696 AATACTA
1 AATACTA
16227703 AATACTA
1 AATACTA
16227710 AATACTA
1 AATACTA
16227717 AATA
1 AATA
16227721 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:16228855 original size:30 final size:30
Alignment explanation
Indices: 16228802--16228866 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
16228792 TCCATTGATG
*
16228802 AAAATATAAAAAAATTTAAAATTATTTTTAA
1 AAAATATAAAAAAATTTAAAATTA-CTTTAA
*
16228833 AAAATATAAAAAAA-TTATAATTACTTTAA
1 AAAATATAAAAAAATTTAAAATTACTTTAA
16228862 AAAAT
1 AAAAT
16228867 GGATTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 10 0.31
30 8 0.25
31 14 0.44
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTACTTTAA
Found at i:16228936 original size:22 final size:22
Alignment explanation
Indices: 16228911--16228961 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
16228901 AAATATGAGT
*
16228911 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAACGAAA
16228933 TTGAGAGAATTTTGGAACGAAA
1 TTGAGAGAATTTTGGAACGAAA
16228955 TTGAGAG
1 TTGAGAG
16228962 GATTAGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.39, C:0.02, G:0.31, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAACGAAA
Found at i:16230142 original size:58 final size:58
Alignment explanation
Indices: 16230080--16230205 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
16230070 TTTTAATAAG
* *
16230080 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
16230138 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
16230196 ATTATTATTA
1 ATTATTATTA
16230206 TATGAATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.36
58 39 0.64
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:16230226 original size:58 final size:56
Alignment explanation
Indices: 16230080--16230233 Score: 168
Period size: 58 Copynumber: 2.7 Consensus size: 56
16230070 TTTTAATAAG
* * * *
16230080 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATTTTAACATA
1 ATTATTATT-AATATAATTTAA-AAAAATAATATATAATTTAACAAAATTTTAACATA
* * *
16230138 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATT-AATATAATTTAAAAAAATAATATATAATTTAACAAAATT-TTAACATA
16230196 ATTATTATT-ATATGAA-TTAAAAAATCATAATATATAAT
1 ATTATTATTAATAT-AATTTAAAAAA--ATAATATATAAT
16230234 ACTATCAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
56 11 0.13
57 24 0.29
58 49 0.58
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (56 bp):
ATTATTATTAATATAATTTAAAAAAATAATATATAATTTAACAAAATTTTAACATA
Found at i:16234193 original size:47 final size:47
Alignment explanation
Indices: 16234142--16234237 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
16234132 TTTTGTAATG
*
16234142 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAACATTGT
1 TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAACATTGT
*
16234189 TTAATTATAATTTTCAATCAAACAATATAAGTAATATACAACATTGT
1 TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAACATTGT
16234236 TT
1 TT
16234238 GAAGATCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (47 bp):
TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAACATTGT
Found at i:16236198 original size:16 final size:18
Alignment explanation
Indices: 16236165--16236202 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
16236155 ATCATTATTT
16236165 AAATAAAATATAATAGTA
1 AAATAAAATATAATAGTA
16236183 AAATAAAATA-AA-AGTA
1 AAATAAAATATAATAGTA
16236199 AAAT
1 AAAT
16236203 CCATATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAATATAATAGTA
Found at i:16240501 original size:20 final size:20
Alignment explanation
Indices: 16240476--16240542 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
16240466 GGAGCACCAA
*
16240476 ACCAAAATTTATGAGAGAAT
1 ACCAAAAATTATGAGAGAAT
*
16240496 ACCAAAAAAATATGAGA-AAGT
1 ACC-AAAAATTATGAGAGAA-T
* * *
16240517 ACCAAAAATCATAAAAGAAT
1 ACCAAAAATTATGAGAGAAT
16240537 ACCAAA
1 ACCAAA
16240543 CCAAAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.60, C:0.13, G:0.10, T:0.16
Consensus pattern (20 bp):
ACCAAAAATTATGAGAGAAT
Found at i:16240509 original size:21 final size:21
Alignment explanation
Indices: 16240485--16240524 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
16240475 AACCAAAATT
16240485 TATGAGAGAA-TACCAAAAAAA
1 TATGAGA-AAGTACCAAAAAAA
16240506 TATGAGAAAGTACCAAAAA
1 TATGAGAAAGTACCAAAAA
16240525 TCATAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (21 bp):
TATGAGAAAGTACCAAAAAAA
Found at i:16248753 original size:25 final size:25
Alignment explanation
Indices: 16248719--16248768 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
16248709 GAAGAAAGAA
16248719 AGTTTTACTTTCTTTACAATTTAGT
1 AGTTTTACTTTCTTTACAATTTAGT
16248744 AGTTTTACTTTCTTTACAATTTAGT
1 AGTTTTACTTTCTTTACAATTTAGT
16248769 CCTTCCACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (25 bp):
AGTTTTACTTTCTTTACAATTTAGT
Found at i:16250599 original size:20 final size:20
Alignment explanation
Indices: 16250576--16250614 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16250566 AATAAATACC
*
16250576 AAAAAATTATTTTAAAAATT
1 AAAAAAGTATTTTAAAAATT
16250596 AAAAAAGTATTTTAAAAAT
1 AAAAAAGTATTTTAAAAAT
16250615 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAAAAGTATTTTAAAAATT
Found at i:16251604 original size:24 final size:25
Alignment explanation
Indices: 16251562--16251611 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
16251552 TCTTACTTTC
16251562 AATTATTCACATAAAATCATCCACCA
1 AATTATT-ACATAAAATCATCCACCA
* *
16251588 AATTATT-CATAATATCATTCACCA
1 AATTATTACATAAAATCATCCACCA
16251612 TTCACTTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (25 bp):
AATTATTACATAAAATCATCCACCA
Found at i:16253452 original size:16 final size:15
Alignment explanation
Indices: 16253421--16253466 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
16253411 TAAACACTTC
*
16253421 AATTTTAATTAATAAT
1 AATTTTAA-AAATAAT
16253437 AAATTTTAAAAATAAT
1 -AATTTTAAAAATAAT
16253453 AATTTTAAATAATA
1 AATTTTAAA-AATA
16253467 TTCATCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.33
16 10 0.37
17 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTTAAAAATAAT
Found at i:16255027 original size:2 final size:2
Alignment explanation
Indices: 16255020--16255046 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16255010 TTTAATTCAG
16255020 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16255047 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16257968 original size:87 final size:87
Alignment explanation
Indices: 16257822--16258003 Score: 330
Period size: 87 Copynumber: 2.1 Consensus size: 87
16257812 ATAGGTTCAA
*
16257822 GTTCTATTGGACGCAATTTAGTACTGATTTCTCTATATTCCATTAAGTTAGAATTTTCTATTTAT
1 GTTCTATTGGACGCAATTTAGTACTGATTTCTCTATATTCCATCAAGTTAGAATTTTCTATTTAT
16257887 AATTGTTCTTGAAGTTGAA-ATT
66 AATTGTTCTTGAAGTTGAAGA-T
*
16257909 GTTCTATTGGACGCAATTTAGTATTGATTTCTCTATATTCCATCAAGTTAGAATTTTCTATTTAT
1 GTTCTATTGGACGCAATTTAGTACTGATTTCTCTATATTCCATCAAGTTAGAATTTTCTATTTAT
16257974 AATTGTTCTTGAAGTTGAAGAT
66 AATTGTTCTTGAAGTTGAAGAT
16257996 GTTCTATT
1 GTTCTATT
16258004 TGGTCTTGAA
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
87 91 0.99
88 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (87 bp):
GTTCTATTGGACGCAATTTAGTACTGATTTCTCTATATTCCATCAAGTTAGAATTTTCTATTTAT
AATTGTTCTTGAAGTTGAAGAT
Found at i:16259722 original size:2 final size:2
Alignment explanation
Indices: 16259715--16259745 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
16259705 TGAAAATGAA
*
16259715 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16259746 AACGTGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16260141 original size:2 final size:2
Alignment explanation
Indices: 16260134--16260168 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16260124 AACATAGAAG
16260134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16260169 AAAAATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16261123 original size:16 final size:14
Alignment explanation
Indices: 16261102--16261140 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
16261092 TAACCGAAAG
16261102 AAAAGAATAACAAAA
1 AAAAGAA-AACAAAA
*
16261117 TAAAAGAAAAGAAAA
1 -AAAAGAAAACAAAA
16261132 AAAAGAAAA
1 AAAAGAAAA
16261141 TCCCCCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 6 0.27
16 7 0.32
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (14 bp):
AAAAGAAAACAAAA
Found at i:16261140 original size:6 final size:5
Alignment explanation
Indices: 16261098--16261140 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
16261088 GTTTTAACCG
* *
16261098 AAAGA AAAGA ATAACA AAATA AAAGA AAAGA AAA-A AAAGA AAA
1 AAAGA AAAGA A-AAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
16261141 TCCCCCCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 4 0.12
5 25 0.76
6 4 0.12
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:16262143 original size:3 final size:3
Alignment explanation
Indices: 16262137--16262189 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
16262127 GTATTATTTG
* *
16262137 TTA TTA TTA TTA TTA TAA TTA TTA TAA TTA -TA TTA TATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA
16262183 TTA TTA T
1 TTA TTA T
16262190 ACCTACATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:16262343 original size:26 final size:28
Alignment explanation
Indices: 16262314--16262375 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 28
16262304 TTTTTTTTAC
*
16262314 ATATATATATAC-ATTT-ATATTTTATA
1 ATATATATATACGATTTCATATGTTATA
*
16262340 ATAT-T-TATACGTTTTCATATGTTATA
1 ATATATATATACGATTTCATATGTTATA
*
16262366 ATTTATATAT
1 ATATATATAT
16262376 GTTTATACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 5 0.17
25 4 0.14
26 16 0.55
27 1 0.03
28 3 0.10
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (28 bp):
ATATATATATACGATTTCATATGTTATA
Found at i:16262529 original size:4 final size:4
Alignment explanation
Indices: 16262507--16262546 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
16262497 ACTTATGCTT
*
16262507 TTTA TTTA TGTA TTT- TTTA TTTA TTTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA
16262547 GATATCTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 25 0.78
5 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:16268529 original size:27 final size:26
Alignment explanation
Indices: 16268484--16268571 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 26
16268474 AAAAATAATA
*
16268484 AAAATTATTTTTATAATTTTTACTTTTT
1 AAAA-TATTTTTAT-ATTTTTAATTTTT
*
16268512 -AAATGATTTTAATGA-TTTTAATTTTT
1 AAAAT-ATTTTTAT-ATTTTTAATTTTT
16268538 AAAATATTTTTATATTTTTTTGAATTTTT
1 AAAATATTTTTATA--TTTTT-AATTTTT
16268567 AAAAT
1 AAAAT
16268572 TTAATTGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.02
26 18 0.36
27 15 0.30
28 4 0.08
29 12 0.24
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.60
Consensus pattern (26 bp):
AAAATATTTTTATATTTTTAATTTTT
Found at i:16270692 original size:24 final size:24
Alignment explanation
Indices: 16270658--16270709 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16270648 TTTCTATAAG
* *
16270658 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
16270682 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
16270706 ATTT
1 ATTT
16270710 GACCTGCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:16276093 original size:18 final size:17
Alignment explanation
Indices: 16276060--16276098 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
16276050 TTGTATAAAT
16276060 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
16276078 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
16276095 TGTG
1 TGTG
16276099 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:16276337 original size:23 final size:23
Alignment explanation
Indices: 16276310--16276385 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
16276300 AGTGTTATTG
16276310 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
16276333 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16276356 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16276379 ATCAGTG
1 ATCAGTG
16276386 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16280620 original size:18 final size:17
Alignment explanation
Indices: 16280587--16280625 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
16280577 TTGTATAAAT
16280587 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
16280605 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
16280622 TGTG
1 TGTG
16280626 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:16280743 original size:8 final size:8
Alignment explanation
Indices: 16280730--16280758 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
16280720 CACTAGAGAC
16280730 CAGTGTTA
1 CAGTGTTA
16280738 CAGTGTTA
1 CAGTGTTA
16280746 CAGTGTTA
1 CAGTGTTA
16280754 CAGTG
1 CAGTG
16280759 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:16280872 original size:23 final size:23
Alignment explanation
Indices: 16280845--16280920 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
16280835 AGTGTTATTG
16280845 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
16280868 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16280891 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16280914 ATCAGTG
1 ATCAGTG
16280921 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16282718 original size:13 final size:11
Alignment explanation
Indices: 16282690--16282732 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
16282680 AGTTAAAAAT
16282690 TATTTTATTAA
1 TATTTTATTAA
16282701 TATTTTAGTTAGA
1 TATTTTA-TTA-A
*
16282714 TA-TTTATTAT
1 TATTTTATTAA
16282724 TATTTTATT
1 TATTTTATT
16282733 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:16282719 original size:23 final size:23
Alignment explanation
Indices: 16282693--16282736 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
16282683 TAAAAATTAT
16282693 TTTATTAATATTTTAGTTAGATA
1 TTTATTAATATTTTAGTTAGATA
* *
16282716 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTAGTTAGA
16282737 AAATGGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTAGTTAGATA
Found at i:16285419 original size:560 final size:560
Alignment explanation
Indices: 16284359--16285484 Score: 2148
Period size: 560 Copynumber: 2.0 Consensus size: 560
16284349 AGTAGGATTC
16284359 AATCACCTGCTCTAAATCGTTGTCCCTACTGATCTAAAAAATGGAATATCTTACGAGGTCCAGTG
1 AATCACCTGCTCTAAATCGTTGTCCCTACTGATCTAAAAAATGGAATATCTTACGAGGTCCAGTG
* *
16284424 ACGAAAGATATATACATTTGATGCTCGAATTTCTTCTCTAGACCTCCACTTTTCCCTTAATCCTT
66 ACGAAAGATATATACATTTGATGCTCGAATTTCTTCTCCAGACCTCCACTTTTCCCCTAATCCTT
16284489 GTCCAAAGCTTTTTAACATAATGGTCTGGTTGAATGCCAAATCTTTAGATTGTGCTGCTACAAAA
131 GTCCAAAGCTTTTTAACATAATGGTCTGGTTGAATGCCAAATCTTTAGATTGTGCTGCTACAAAA
16284554 ATAGACTCAATTTCGGTCTCACAAATTTGCCTATTGTAATGGATAACAGCTCTGACTCGTCTGTT
196 ATAGACTCAATTTCGGTCTCACAAATTTGCCTATTGTAATGGATAACAGCTCTGACTCGTCTGTT
16284619 TATCTTCAACCAAATATCCTATTCCACATGTTTAAAACCGAGAAAATATTAAAAAATATAGTTAT
261 TATCTTCAACCAAATATCCTATTCCACATGTTTAAAACCGAGAAAATATTAAAAAATATAGTTAT
16284684 CATCACCCAAAACGCTAAATCTACATGTAATTTAACGAATTACCTTTGCTTCGACAATAGCGTAA
326 CATCACCCAAAACGCTAAATCTACATGTAATTTAACGAATTACCTTTGCTTCGACAATAGCGTAA
16284749 GAATGAAATTCAAGTTTTCACGACAACGTCGATTACTCGTAATGCCAAGATGTTCAGATCAAAAA
391 GAATGAAATTCAAGTTTTCACGACAACGTCGATTACTCGTAATGCCAAGATGTTCAGATCAAAAA
*
16284814 TCTGCTTCGAAGATCGGTATGGAAAATTACGGGCCTGTGCTGAGTTCTTTCTATAGAGCTCATTT
456 TCTGCTTCGAAGATCGGTATGGAAAATTACGGGCCTGTACTGAGTTCTTTCTATAGAGCTCATTT
16284879 GTGAGGGAGAAAATACTCCCCCATAGTGGCTTTTTTAGGG
521 GTGAGGGAGAAAATACTCCCCCATAGTGGCTTTTTTAGGG
16284919 AATCACCTGCTCTAAATCGTTGTCCCTACTGATCTAAAAAATGGAATATCTTACGAGGTCCAGTG
1 AATCACCTGCTCTAAATCGTTGTCCCTACTGATCTAAAAAATGGAATATCTTACGAGGTCCAGTG
16284984 ACGAAAGATATATACATTTGATGCTCGAATTTCTTCTCCAGATCC-CCACTTTTCCCCTAATCCT
66 ACGAAAGATATATACATTTGATGCTCGAATTTCTTCTCCAGA-CCTCCACTTTTCCCCTAATCCT
16285048 TGTCCAAAGCTTTTTAACATAATGGTCTGGTTGAATGCCAAATCTTTAGATTGTGCTGCTACAAA
130 TGTCCAAAGCTTTTTAACATAATGGTCTGGTTGAATGCCAAATCTTTAGATTGTGCTGCTACAAA
16285113 AATAGACTCAATTTCGGTCTCACAAATTTGCCTATTGTAATGGATAACAGCTCTGACTCGTCTGT
195 AATAGACTCAATTTCGGTCTCACAAATTTGCCTATTGTAATGGATAACAGCTCTGACTCGTCTGT
* *
16285178 TTATCTTCAACCAAATATCTTATTCCACATGTTTAAAACCGAGAAAATATTAAAAAATATAGTTC
260 TTATCTTCAACCAAATATCCTATTCCACATGTTTAAAACCGAGAAAATATTAAAAAATATAGTTA
16285243 TCATCACCCAAAACGCTAAATCTACATGTAATTTAACGAATTACCTTTGCTTCGACAATAGCGTA
325 TCATCACCCAAAACGCTAAATCTACATGTAATTTAACGAATTACCTTTGCTTCGACAATAGCGTA
*
16285308 AGAATGAAATTCAAGTTTTCACGACAACGTCGATTACTTGTAATGCCAAGATGTTCAGATCAAAA
390 AGAATGAAATTCAAGTTTTCACGACAACGTCGATTACTCGTAATGCCAAGATGTTCAGATCAAAA
*
16285373 ATCTGCTTCGAAGATTGGTATGGAAAATTACGGGCCCT-TACTGAGTTCTTTCTATAGAGCTCAT
455 ATCTGCTTCGAAGATCGGTATGGAAAATTACGGG-CCTGTACTGAGTTCTTTCTATAGAGCTCAT
*
16285437 TTGTGAGGGAGAAAATACTCCCCCGTAGTGGCTTTTTTAGGG
519 TTGTGAGGGAGAAAATACTCCCCCATAGTGGCTTTTTTAGGG
16285479 AATCAC
1 AATCAC
16285485 GAAACTTTTA
Statistics
Matches: 556, Mismatches: 8, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
560 551 0.99
561 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (560 bp):
AATCACCTGCTCTAAATCGTTGTCCCTACTGATCTAAAAAATGGAATATCTTACGAGGTCCAGTG
ACGAAAGATATATACATTTGATGCTCGAATTTCTTCTCCAGACCTCCACTTTTCCCCTAATCCTT
GTCCAAAGCTTTTTAACATAATGGTCTGGTTGAATGCCAAATCTTTAGATTGTGCTGCTACAAAA
ATAGACTCAATTTCGGTCTCACAAATTTGCCTATTGTAATGGATAACAGCTCTGACTCGTCTGTT
TATCTTCAACCAAATATCCTATTCCACATGTTTAAAACCGAGAAAATATTAAAAAATATAGTTAT
CATCACCCAAAACGCTAAATCTACATGTAATTTAACGAATTACCTTTGCTTCGACAATAGCGTAA
GAATGAAATTCAAGTTTTCACGACAACGTCGATTACTCGTAATGCCAAGATGTTCAGATCAAAAA
TCTGCTTCGAAGATCGGTATGGAAAATTACGGGCCTGTACTGAGTTCTTTCTATAGAGCTCATTT
GTGAGGGAGAAAATACTCCCCCATAGTGGCTTTTTTAGGG
Found at i:16286710 original size:19 final size:19
Alignment explanation
Indices: 16286686--16286724 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
16286676 AATAAATTAC
*
16286686 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
16286705 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
16286724 T
1 T
16286725 GCTGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:16286778 original size:19 final size:19
Alignment explanation
Indices: 16286740--16286823 Score: 52
Period size: 19 Copynumber: 4.6 Consensus size: 19
16286730 AATAAATTAC
* * *
16286740 TCATCTTGGTTACTTGAGT
1 TCATCTTAGTTAATTAAGT
16286759 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
* * *
16286778 T--GC-TAGAATAAATT-A-C
1 TCATCTTAG--TTAATTAAGT
16286794 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
16286813 TCAACTTAGTT
1 TCATCTTAGTT
16286824 CACTTAGTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
16 4 0.08
17 7 0.15
18 7 0.15
19 30 0.62
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:16286833 original size:54 final size:54
Alignment explanation
Indices: 16286667--16286823 Score: 269
Period size: 54 Copynumber: 2.9 Consensus size: 54
16286657 ATAAGTATTT
16286667 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
* *
16286721 AGTTGCTGGAATAAATTACTCATCTTGGTTACTTGAGTTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
* * *
16286775 AGTTGCTAGAATAAATTACTCATCTTAGTTAATTAAGTTCAACTTAGTT
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTT
16286824 CACTTAGTTG
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
Found at i:16290701 original size:18 final size:17
Alignment explanation
Indices: 16290672--16290714 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
16290662 TCTCTCAATT
*
16290672 CTTTCT-AATCTCTTAA
1 CTTTCTCAATCTCTAAA
16290688 CTTTCTCAACTCTCTAAA
1 CTTTCTCAA-TCTCTAAA
*
16290706 TTTTCTCAA
1 CTTTCTCAA
16290715 GTTTTTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 15 0.65
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.47
Consensus pattern (17 bp):
CTTTCTCAATCTCTAAA
Found at i:16292722 original size:9 final size:9
Alignment explanation
Indices: 16292708--16292760 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
16292698 AAAAATAATA
16292708 TAATAATTT
1 TAATAATTT
16292717 TAATAATTT
1 TAATAATTT
16292726 T-AT-ATTT
1 TAATAATTT
* *
16292733 CAA-AA-AT
1 TAATAATTT
16292740 TAATAATTT
1 TAATAATTT
*
16292749 TAATAGTTT
1 TAATAATTT
16292758 TAA
1 TAA
16292761 AATCATTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
7 7 0.20
8 6 0.17
9 22 0.63
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (9 bp):
TAATAATTT
Found at i:16292747 original size:32 final size:35
Alignment explanation
Indices: 16292677--16292759 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 35
16292667 ATCATATGCA
16292677 TTTAATAATTTTATATTTCAAAAAAATAATATAATAAT
1 TTTAATAATTTTATATTTC---AAAATAATATAATAAT
16292715 TTTAATAATTTTATATTTC-AAA-AAT-TAATAAT
1 TTTAATAATTTTATATTTCAAAATAATATAATAAT
*
16292747 TTTAATAGTTTTA
1 TTTAATAATTTTA
16292760 AAATCATTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 19 0.43
33 3 0.07
34 3 0.07
38 19 0.43
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (35 bp):
TTTAATAATTTTATATTTCAAAATAATATAATAAT
Found at i:16298816 original size:43 final size:43
Alignment explanation
Indices: 16298755--16298842 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
16298745 TTTCAATAGG
16298755 AACAAATGGAAACATCATCCAAGCCCCGTACTAAGAGATAATT
1 AACAAATGGAAACATCATCCAAGCCCCGTACTAAGAGATAATT
*
16298798 AACAAATGGAAACATCATCCAAGCCTCGTACTAAGAGATAATT
1 AACAAATGGAAACATCATCCAAGCCCCGTACTAAGAGATAATT
16298841 AA
1 AA
16298843 TTTTTAGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (43 bp):
AACAAATGGAAACATCATCCAAGCCCCGTACTAAGAGATAATT
Found at i:16306033 original size:21 final size:22
Alignment explanation
Indices: 16305996--16306036 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
16305986 AAATAGGGAG
*
16305996 AAAACAACATGAAAATAGCATT
1 AAAACAACATAAAAATAGCATT
16306018 AAAACAACA-AAAAATAGCA
1 AAAACAACATAAAAATAGCA
16306037 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.66, C:0.15, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAACAACATAAAAATAGCATT
Found at i:16311977 original size:38 final size:39
Alignment explanation
Indices: 16311904--16311978 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
16311894 ATATAATTCT
* *
16311904 TATTATTTATTTTGGGTTTTGTTGAATGATGGATTGTTA
1 TATTATTTATTTTAGGTTTTGTTGAATGATAGATTGTTA
*
16311943 TATTGTTTATTTTAGG-TTTGTTGAA-GTATAGATTGT
1 TATTATTTATTTTAGGTTTTGTTGAATG-ATAGATTGT
16311979 ATTTTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.03
38 17 0.53
39 14 0.44
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.56
Consensus pattern (39 bp):
TATTATTTATTTTAGGTTTTGTTGAATGATAGATTGTTA
Found at i:16316526 original size:15 final size:15
Alignment explanation
Indices: 16316502--16316531 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16316492 GGGTTAACTT
16316502 CCTTTCTATAAACCA
1 CCTTTCTATAAACCA
*
16316517 CCTTTGTATAAACCA
1 CCTTTCTATAAACCA
16316532 ATCACAATGA
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:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (15 bp):
CCTTTCTATAAACCA
Found at i:16318003 original size:49 final size:49
Alignment explanation
Indices: 16317946--16318049 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
16317936 TCATGTGTTA
* *
16317946 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTGACCTTTTGATTCATGATATTAAACTTAATTT
* *
16317995 TAATTTTATAAAGTGTTTACCTTTTGATTCGTGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTGACCTTTTGATTCATGATATTAAACTTAATTT
16318044 TAATTT
1 TAATTT
16318050 GTTTTTTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTGACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:16319475 original size:21 final size:21
Alignment explanation
Indices: 16319434--16319476 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16319424 AATTAAGTAG
*
16319434 ATTATATATAATTTTTATAGT
1 ATTATATATAATATTTATAGT
*
16319455 ATTATATATTATGATTT-TAGT
1 ATTATATATAAT-ATTTATAGT
16319476 A
1 A
16319477 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATATATAATATTTATAGT
Found at i:16319549 original size:16 final size:16
Alignment explanation
Indices: 16319513--16319551 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16319503 GAATTTCATT
**
16319513 AAATTATATTTTTTAA
1 AAATTATATTTAATAA
16319529 AAATTATATTTAATAA
1 AAATTATATTTAATAA
*
16319545 TAATTAT
1 AAATTAT
16319552 GTTAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTATATTTAATAA
Found at i:16319786 original size:45 final size:44
Alignment explanation
Indices: 16319697--16319789 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
16319687 ATTACAACAT
* * *
16319697 CATTTCATTCAACCAAACACAAGAATACTATTATAGTTATATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTATATTC
* *
16319741 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGCTATATTC
16319786 CATT
1 CATT
16319790 ACAGCGAACC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.50
45 20 0.48
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTATATTC
Found at i:16322461 original size:18 final size:18
Alignment explanation
Indices: 16322440--16322489 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
16322430 TCGTTCATGT
*
16322440 CCACGTCCTCGACCGTGA
1 CCACGTCCTCGACCGCGA
* * *
16322458 CCACGACCACGACCGCGG
1 CCACGTCCTCGACCGCGA
*
16322476 CCATGTCCTCGACC
1 CCACGTCCTCGACC
16322490 ACAACTACTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.48, G:0.22, T:0.12
Consensus pattern (18 bp):
CCACGTCCTCGACCGCGA
Found at i:16323674 original size:24 final size:25
Alignment explanation
Indices: 16323640--16323692 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
16323630 ATAGGAAAGT
* *
16323640 GGTTACAAGAAGATGAAAGGTTAAA
1 GGTTACAAGAAGATGAAAAGTGAAA
16323665 GGTTA-AAGAAGATGAAAAGTGAAA
1 GGTTACAAGAAGATGAAAAGTGAAA
16323689 GGTT
1 GGTT
16323693 GAACATCCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.30, T:0.21
Consensus pattern (25 bp):
GGTTACAAGAAGATGAAAAGTGAAA
Found at i:16329178 original size:31 final size:29
Alignment explanation
Indices: 16329105--16329178 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
16329095 GGCTCAGATT
*
16329105 ACATTTTAGTCACTTATGTTTAAAATGTT
1 ACATTTTAGTCACTTATGTTTAAAATGTA
* * ***
16329134 ACGTTTTAATCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-T-AAAATGTA
16329165 ACATTTTAGTCACT
1 ACATTTTAGTCACT
16329179 GAGCCGTTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 18 0.51
30 1 0.03
31 16 0.46
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTAAAATGTA
Found at i:16336588 original size:20 final size:19
Alignment explanation
Indices: 16336563--16336602 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
16336553 TTCAAATAAT
*
16336563 TTAATTTGATATAATAAAAA
1 TTAATTTGAAAT-ATAAAAA
*
16336583 TTAATTTTAAATATAAAAA
1 TTAATTTGAAATATAAAAA
16336602 T
1 T
16336603 CTTGTACGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAATTTGAAATATAAAAA
Found at i:16337851 original size:24 final size:24
Alignment explanation
Indices: 16337824--16337873 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
16337814 TTAAGGTTAT
*
16337824 TAAATATAAAAATATGTAAATATG
1 TAAATATAAAAATATATAAATATG
* * *
16337848 TAAATATATATATATATATATATG
1 TAAATATAAAAATATATAAATATG
16337872 TA
1 TA
16337874 TTTAAAGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
TAAATATAAAAATATATAAATATG
Found at i:16338039 original size:3 final size:3
Alignment explanation
Indices: 16338031--16338064 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
16338021 GATAGGAGTA
*
16338031 AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16338065 GTACTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16338232 original size:8 final size:8
Alignment explanation
Indices: 16338219--16338253 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
16338209 AATATAAAGA
16338219 AAAATAAT
1 AAAATAAT
16338227 AAAATAAT
1 AAAATAAT
16338235 AAAATAAT
1 AAAATAAT
16338243 AATAATAAT
1 AA-AATAAT
16338252 AA
1 AA
16338254 CAGGACTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATAAT
Found at i:16338235 original size:3 final size:3
Alignment explanation
Indices: 16338221--16338253 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
16338211 TATAAAGAAA
16338221 AAT AAT AA- AAT AAT AA- AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16338254 CAGGACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:16338243 original size:11 final size:12
Alignment explanation
Indices: 16338221--16338253 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
16338211 TATAAAGAAA
16338221 AATAATAA-AAT
1 AATAATAATAAT
16338232 AATAA-AATAAT
1 AATAATAATAAT
16338243 AATAATAATAA
1 AATAATAATAA
16338254 CAGGACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.10
11 13 0.65
12 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:16339714 original size:44 final size:44
Alignment explanation
Indices: 16339666--16339771 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
16339656 CTTCTTCGCA
* **
16339666 GCAACTTCAGGGGGA-AGAGA-TTCGTGGTTTTAGTCTGCTCCACT
1 GCAACTTCAGGGAGATA-AGACTT-GTGGTTTTAACCTGCTCCACT
* * *
16339710 GCAACGTCAAGGAGATAAGACTTGTTGTTTTAACCTGCTCCACT
1 GCAACTTCAGGGAGATAAGACTTGTGGTTTTAACCTGCTCCACT
*
16339754 GCGACTTCAGGGAGATAA
1 GCAACTTCAGGGAGATAA
16339772 TGTTTGATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
44 48 0.94
45 3 0.06
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (44 bp):
GCAACTTCAGGGAGATAAGACTTGTGGTTTTAACCTGCTCCACT
Found at i:16339920 original size:44 final size:44
Alignment explanation
Indices: 16339873--16341265 Score: 386
Period size: 44 Copynumber: 31.8 Consensus size: 44
16339863 AAATTCGCTA
* *
16339873 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * *
16339917 TCTTCAA-CATACTCCACTGCTGCTCAGGGAGATAAGGATGGT---G
1 TCTTCAATC-TGCTCCACTACTGCTTAGGGAGATAA-GAT-CTACAG
* * * * * *
16339960 TC-TAAATCTGCTTCC-CTACTACATTGGGGAAATAAGAT-TCGCCG
1 TCTTCAATCTGC-TCCACTACTGC-TTAGGGAGATAAGATCT-ACAG
* * *
16340004 TTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * * ***
16340048 TCTTCGACCTACTCCACTGCTGCTCAGGGAGATAGGAT-TGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * *
16340091 GCTTAAATCTGCTTCC-CTACTACCTTGGGGAAGATAAGAT-TCGCCG
1 TCTTCAATCTGC-TCCACTACT-GCTTAGGG-AGATAAGATCT-ACAG
* * * * *
16340137 TCGTCGATCTGCTCCACTACTGTTTAGGGGGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * * * **
16340181 TTTTCAACCTACTCCACTGCTGCTCAGGGAAATAAG-GCTAGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * *
16340224 GCTTAAATATGCTTCC-CTTACTACATT-GGGAATATAAGAT-TCACCA-
1 TCTTCAATCTGC-TCCAC-TACTGC-TTAGGG-AGATAAGATCT-A-CAG
** * * * *
16340270 TCTTTGATCTGCTCCACTGCTGCTTAGGGAGATAAAATTTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * * *
16340314 TCTTCAACCTACTCCACTGCTACTCAGGGAGATAAG-GCTAGTAG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA-CAG
* * *
16340358 -CTTAAATCTGCT-TACTAC--CTTAGGGAAGATAAGAT-TCACCG
1 TCTTCAATCTGCTCCACTACTGCTTAGGG-AGATAAGATCT-ACAG
* * * * *
16340399 TCTTCGATTTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * * ***
16340443 TCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGA-CTGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * *
16340486 GCTTAAATCTACTTCC-CTACTACCTT-GGGAAGATAAGAT-TCGCCG
1 TCTTCAATCTGC-TCCACTACT-GCTTAGGG-AGATAAGATCT-ACAG
** * *
16340531 TCTTTGATCTGCTCCATTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * * * ***
16340575 TCTTCGACCTACTCCATTACTACTCAGGGAGATAGGA-CTGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * ** * * * *
16340618 GCTTAAATCTGTTTCC-CTACAACCTTAGGAATATAAGAT-TCGCCG
1 TCTTCAATCTG-CTCCACTAC-TGCTTAGGGAGATAAGATCT-ACAG
* * * *
16340663 TCTTCGATCTGCTCCACTACTGCTTAGGAAGATAGGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * *
16340707 TCTTCAA-CTTACTCCACTGCTGCTCAGGGAGATAGGA-C--CGG
1 TCTTCAATC-TGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * *
16340748 TGGCTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCGCCG
1 T--CTTCAATCTGC-TCCACTACT-GCTTAGGG-AGATAAGATCT-ACAG
** *
16340795 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * * * ***
16340839 TATTCGACCTACTCCACTACTACTCAGGGAGATAGGA-CTGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * * * *
16340882 GCTTAAATATGCTTC-CTACT-ATATCGGGAAGATAAGAT-TCGCCG
1 TCTTCAATCTGCTCCACTACTGCT-TAGGG-AGATAAGATCT-ACAG
* * * *
16340926 TCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTGCAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * * *
16340970 TCTTCAACCTACTCCATTGCTGCTCAGGGAGATAGGA-CTGA-TG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ACAG
* * * *
16341013 GCTTAAATCTGCTTCCTACTA-T-C-TCGGGAAGATAAGAT-TCACCG
1 TCTTCAATCTGC-TCC-ACTACTGCTTAGGG-AGATAAGATCT-ACAG
* * *
16341057 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * ***
16341101 TCTTCAACCTACTCCACTGCTGCTTAGGGAGATAGGA-CTGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * * * *
16341144 GCTTAAATCTACTTCCTACTA-T-C-TCGGGAAGATAAGAT-TCGCTG
1 TCTTCAATCTGC-TCC-ACTACTGCTTAGGG-AGATAAGATCT-ACAG
* * * *
16341188 TCTTCAATCTGTTCCACTACTGCTTAGGGAGACAAGATCTGCAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
* * * *
16341232 TCTTCAACCTACTCCACCATTG-TTCAGGGAGATA
1 TCTTCAATCTGCTCCACTACTGCTT-AGGGAGATA
16341266 TGATTTGATA
Statistics
Matches: 957, Mismatches: 298, Indels: 188
0.66 0.21 0.13
Matches are distributed among these distances:
40 7 0.01
41 12 0.01
42 50 0.05
43 168 0.18
44 552 0.58
45 138 0.14
46 27 0.03
47 3 0.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAG
Found at i:16341265 original size:131 final size:132
Alignment explanation
Indices: 16339855--16341248 Score: 1977
Period size: 131 Copynumber: 10.6 Consensus size: 132
16339845 TGTAACTTTA
* **
16339855 GGGAA-ATAAAATTCGCTATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
1 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
* *
16339919 TTCAACATACTCCACTGCTGCTCAGGGAGATAAGGA-TGGTGTC-TAAATCTGCTTCCCTACTAC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCCTACTAC
*
16339982 ATT
130 CTT
*
16339985 GGGGAA-ATAAGATTCGCCGTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT
1 -GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT
* *
16340049 CTTCGACCTACTCCACTGCTGCTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTAC
65 CTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTAC
16340114 CTT
130 CTT
* * *
16340117 GGGGAAGATAAGATTCGCCGTCGTCGATCTGCTCCACTACTGTTTAGGGGGATAAGATCTACAAT
1 -GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT
* * * *
16340182 TTTCAACCTACTCCACTGCTGCTCAGGGAAATAAGG-CTAGTGGCTTAAATATGCTTCCCTTACT
65 CTTCAACCTACTCCACTGCTGCTCAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCC-TACT
*
16340246 ACATT
128 ACCTT
* * * * * * *
16340251 GGGAATATAAGATTCACCATCTTTGATCTGCTCCACTGCTGCTTAGGGAGATAAAATTTACAATC
1 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
* * *
16340316 TTCAACCTACTCCACTGCTACTCAGGGAGATAAGG-CTAGTAGCTTAAATCTGC-T---TACTAC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCCTACTAC
16340376 CTT
130 CTT
* * * *
16340379 AGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTACTGCTTAGGGAGACAGGATCTACAAT
1 -GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT
* *
16340444 CTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTGGTGGCTTAAATCTACTTCCCTACTAC
65 CTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTAC
16340509 CTT
130 CTT
* *
16340512 GGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCATTACTGCTTAGGGAGATAAGATCTACAATC
1 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
* * * * * *
16340577 TTCGACCTACTCCATTACTACTCAGGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACAACC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
16340642 TT
131 TT
* * * *
16340644 AGGAATATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGAAGATAGGATCTACAATC
1 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
* *
16340709 TTCAACTTACTCCACTGCTGCTCAGGGAGATAGGACCGGTGGCTTAAATCTGCTTCCCTACTACC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
16340774 TT
131 TT
* *
16340776 GGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATA
1 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
* * * * **
16340841 TTCGACCTACTCCACTACTACTCAGGGAGATAGGACTGGTGGCTTAAATATGCTT-CCTACTATA
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
*
16340905 TC
131 TT
* *
16340907 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTGCAATC
1 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
* * *
16340972 TTCAACCTACTCCATTGCTGCTCAGGGAGATAGGACTGATGGCTTAAATCTGCTT-CCTACTATC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
*
16341036 TC
131 TT
* *
16341038 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATC
1 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
* * *
16341103 TTCAACCTACTCCACTGCTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTT-CCTACTATC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
*
16341167 TC
131 TT
* * * * *
16341169 GGGAAGATAAGATTCGCTGTCTTCAATCTGTTCCACTACTGCTTAGGGAGACAAGATCTGCAATC
1 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
16341234 TTCAACCTACTCCAC
66 TTCAACCTACTCCAC
16341249 CATTGTTCAG
Statistics
Matches: 1138, Mismatches: 114, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
128 11 0.01
129 100 0.09
130 5 0.00
131 423 0.37
132 373 0.33
133 215 0.19
134 11 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC
TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
TT
Found at i:16341969 original size:108 final size:108
Alignment explanation
Indices: 16341758--16341977 Score: 250
Period size: 108 Copynumber: 2.0 Consensus size: 108
16341748 AAAAAACGCT
* * * *
16341758 TGAAAAAGATTATCAAAATGGACAAGATGAAATTTTGTTGAGAACAAAGCTCTAAATAAATGAAT
1 TGAAAAAGATTATCAAAATGGACAACATGAAATATTATTGAGAACAAAGCTCAAAATAAATGAAT
* *
16341823 CAATCAAGATAGTAAACTTTGCAAAGATACAAACTGAATAAAA
66 CAATCAAGATAGCAAACTTTGCAAAGATACAAAATGAATAAAA
* * * *
16341866 TGAAACAA-ATTATCACAATGGATAACATGAAATATTATTGAGAACAAAGGTCAAAATGAA-GAA
1 TGAAA-AAGATTATCAAAATGGACAACATGAAATATTATTGAGAACAAAGCTCAAAATAAATG-A
* * * *
16341929 ATTAATCAAGATAGCAAATTTTG-ATAATATA-AGAAATGAATAAGA
64 ATCAATCAAGATAGCAAACTTTGCA-AAGATACA-AAATGAATAAAA
16341974 TGAA
1 TGAA
16341978 GACAGGTGCC
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
107 3 0.03
108 89 0.95
109 2 0.02
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.25
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAACATGAAATATTATTGAGAACAAAGCTCAAAATAAATGAAT
CAATCAAGATAGCAAACTTTGCAAAGATACAAAATGAATAAAA
Found at i:16351595 original size:29 final size:30
Alignment explanation
Indices: 16351536--16351593 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
16351526 TCCGGGCCTT
*
16351536 GGGGCAAAAATGTAATTATTCAAAAGTTTA
1 GGGGCAAAAATGTAATTATTAAAAAGTTTA
16351566 GGGGC-AAAATCGTAATT-TTGAAAAAGTT
1 GGGGCAAAAAT-GTAATTATT-AAAAAGTT
16351594 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATTAAAAAGTTTA
Found at i:16352045 original size:50 final size:50
Alignment explanation
Indices: 16351931--16352122 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
16351921 ATTTGGGTCA
*
16351931 AGAGGTCCCATGTAAGACCATGTCTAGGACAT-GCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
16351980 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
16352030 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
16352080 AGAACATCCCATGTAAGACCATGTCTGAGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16352123 TGTTATGATC
Statistics
Matches: 125, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
49 30 0.24
50 62 0.50
51 33 0.26
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:16352121 original size:101 final size:99
Alignment explanation
Indices: 16351931--16352122 Score: 276
Period size: 101 Copynumber: 1.9 Consensus size: 99
16351921 ATTTGGGTCA
* * ** *
16351931 AGAGGTCCCATGTAAGACCATGTCTAGGACATGCATTGGCACCGAGATGAGAGGTCTCATGTAAG
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGCATGGGCACCGAGATGAGACATCCCATGTAAG
*
16351996 ACCATGTCTGGGACATGGCGTTGGCACCGAGATG
66 ACCATGTCTGAGACATGGCGTTGGCACCGAGATG
* * *
16352030 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGTA
1 AGAGGTCCCACGTAAGACCATGTCTAGGACAT-GCATGGGCACCGAGATGAG-ACATCCCATGTA
*
16352095 AGACCATGTCTGAGACATGGCTTTGGCA
64 AGACCATGTCTGAGACATGGCGTTGGCA
16352123 TGTTATGATC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 29 0.36
100 17 0.21
101 35 0.43
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.21
Consensus pattern (99 bp):
AGAGGTCCCACGTAAGACCATGTCTAGGACATGCATGGGCACCGAGATGAGACATCCCATGTAAG
ACCATGTCTGAGACATGGCGTTGGCACCGAGATG
Found at i:16355338 original size:12 final size:11
Alignment explanation
Indices: 16355314--16355365 Score: 65
Period size: 10 Copynumber: 4.9 Consensus size: 11
16355304 CTTCTTTTAT
*
16355314 TTTATTTTAT-
1 TTTATTTTTTC
16355324 TTTATTTTTTC
1 TTTATTTTTTC
16355335 TTTTATTTTTTC
1 -TTTATTTTTTC
16355347 -TT-TTTTTTC
1 TTTATTTTTTC
16355356 TTTATTTTTT
1 TTTATTTTTT
16355366 TTAACATTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
9 7 0.19
10 13 0.35
11 6 0.16
12 11 0.30
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTATTTTTTC
Found at i:16355366 original size:12 final size:11
Alignment explanation
Indices: 16355293--16355366 Score: 55
Period size: 12 Copynumber: 6.5 Consensus size: 11
16355283 TGGCCTCTCA
16355293 TTTTTCTTTTT
1 TTTTTCTTTTT
16355304 CTTCTTT-TATTTT
1 -TT-TTTCT-TTTT
* *
16355317 ATTTTATTTTAT
1 TTTTTCTTTT-T
16355329 TTTTTCTTTTAT
1 TTTTTCTTTT-T
16355341 TTTTTC--TTT
1 TTTTTCTTTTT
16355350 TTTTTCTTTATT
1 TTTTTCTTT-TT
16355362 TTTTT
1 TTTTT
16355367 TAACATTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
9 7 0.13
10 2 0.04
11 7 0.13
12 29 0.56
13 7 0.13
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:16360837 original size:3 final size:3
Alignment explanation
Indices: 16360829--16360862 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
16360819 GATAGAAGTA
*
16360829 AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16360863 GTGCTAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16378174 original size:5 final size:5
Alignment explanation
Indices: 16378164--16378189 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16378154 TGTTTGGAGT
16378164 GAAGA GAAGA GAAGA GAAGA GAAGA G
1 GAAGA GAAGA GAAGA GAAGA GAAGA G
16378190 TGAGTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:16387598 original size:9 final size:9
Alignment explanation
Indices: 16387584--16387614 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
16387574 TCGAGTTGAT
16387584 TCGAATAAC
1 TCGAATAAC
16387593 TCGAATAAC
1 TCGAATAAC
16387602 TCGAATAAC
1 TCGAATAAC
16387611 TCGA
1 TCGA
16387615 TTCGTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (9 bp):
TCGAATAAC
Found at i:16388109 original size:85 final size:85
Alignment explanation
Indices: 16388009--16388245 Score: 298
Period size: 85 Copynumber: 2.8 Consensus size: 85
16387999 CACTTACAGA
** * *
16388009 AAAAAACGTTGCTAAAGGTCATGTTCTTTAGCGGTGCTTAGGAAAAAAACGCCGCT-AATGATCA
1 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGTGCTTAGGAAAAAAACGCCGCTAAAAG-TAA
*
16388073 TGTTCTTTAGCGGCGCTTGGG
65 TGTTCTATAGCGGCGCTTGGG
* *
16388094 AAAAAACGCCGCTAAAGATCATATTCTTTAGCGGTGCTTAGGAAAAAAACGCCGCTAAAAGTAAT
1 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGTGCTTAGGAAAAAAACGCCGCTAAAAGTAAT
*
16388159 GTTCTATAGCGGCGCTTGGT
66 GTTCTATAGCGGCGCTTGGG
* * * * * * * * *
16388179 AAAAGACACCGCTAAAAGTAATGTTCTATAGCAGCGCTT-GGTAGAAAACGCCGCTAAAAGTAAT
1 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGTGCTTAGGAAAAAAACGCCGCTAAAAGTAAT
16388243 GTT
66 GTT
16388246 TGAAGCGCCG
Statistics
Matches: 132, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 26 0.20
85 103 0.78
86 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (85 bp):
AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGTGCTTAGGAAAAAAACGCCGCTAAAAGTAAT
GTTCTATAGCGGCGCTTGGG
Found at i:16388114 original size:42 final size:42
Alignment explanation
Indices: 16388007--16388236 Score: 248
Period size: 42 Copynumber: 5.4 Consensus size: 42
16387997 GGCACTTACA
** * *
16388007 GAAAAAAACGTTGCTAAAGGTCATGTTCTTTAGCGGTGCTTAG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-G
*
16388050 GAAAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
* * *
16388092 GGAAAAAACGCCGCTAAAGATCATATTCTTTAGCGGTGCTTAG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-G
* *
16388135 GAAAAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTG
1 GAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTG
* * * * * *
16388177 GTAAAAGACACCGCTAAA-AGTAATGTTCTATAGCAGCGCTTG
1 GAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTG
* *
16388219 GTAGAAAACGCCGCTAAA
1 GAAAAAAACGCCGCTAAA
16388237 AGTAATGTTT
Statistics
Matches: 164, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
42 93 0.57
43 71 0.43
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (42 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
Found at i:16394401 original size:7 final size:7
Alignment explanation
Indices: 16394391--16394436 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
16394381 TGATATATTT
16394391 TTATGTA
1 TTATGTA
16394398 TTATGTAA
1 TTATGT-A
16394406 GTTATGTAA
1 -TTATGT-A
16394415 GTTATGTA
1 -TTATGTA
16394423 TTATGTA
1 TTATGTA
16394430 TTATGTA
1 TTATGTA
16394437 AGTACTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.54
8 2 0.05
9 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (7 bp):
TTATGTA
Found at i:16394412 original size:9 final size:9
Alignment explanation
Indices: 16394398--16394857 Score: 354
Period size: 9 Copynumber: 52.4 Consensus size: 9
16394388 TTTTTATGTA
16394398 TTATGTAAG
1 TTATGTAAG
16394407 TTATGTAAG
1 TTATGTAAG
16394416 TTATGT-A-
1 TTATGTAAG
16394423 TTATGT-A-
1 TTATGTAAG
16394430 TTATGTAAG
1 TTATGTAAG
*
16394439 -TACTATAAG
1 TTA-TGTAAG
16394448 TTATGTAAG
1 TTATGTAAG
*
16394457 TAATGT-A-
1 TTATGTAAG
16394464 TTATGTAAG
1 TTATGTAAG
*
16394473 TTGTGTATA-
1 TTATGTA-AG
*
16394482 ATAT-TAA-
1 TTATGTAAG
*
16394489 TTATGTGAG
1 TTATGTAAG
*
16394498 TTGTGT-A-
1 TTATGTAAG
* *
16394505 TAATGTCAG
1 TTATGTAAG
*
16394514 TTAAG-AAGG
1 TTATGTAA-G
16394523 TTATGT-A-
1 TTATGTAAG
*
16394530 TAATGTAAG
1 TTATGTAAG
**
16394539 TTATGCCAG
1 TTATGTAAG
* *
16394548 TTATTTAAT
1 TTATGTAAG
16394557 TTATGTAAG
1 TTATGTAAG
16394566 TTATGTAAG
1 TTATGTAAG
* *
16394575 TTATTTAAT
1 TTATGTAAG
16394584 TTATGTAAG
1 TTATGTAAG
16394593 TTATGTAAG
1 TTATGTAAG
* *
16394602 TTATTTAAT
1 TTATGTAAG
*
16394611 TTTTGTAAG
1 TTATGTAAG
16394620 TTATGTAAG
1 TTATGTAAG
* *
16394629 TTATTTAAT
1 TTATGTAAG
*
16394638 TTTTGTAAG
1 TTATGTAAG
16394647 TTATGTAAG
1 TTATGTAAG
*
16394656 TTACT-TAAT
1 TTA-TGTAAG
16394665 TTATGTAA-
1 TTATGTAAG
16394673 TTAATGTAAG
1 TT-ATGTAAG
*
16394683 TTACT-TAAT
1 TTA-TGTAAG
16394692 TTATGTAA-
1 TTATGTAAG
16394700 TTAATGTAAG
1 TT-ATGTAAG
*
16394710 TTACT-TAAT
1 TTA-TGTAAG
16394719 TTATGTAAG
1 TTATGTAAG
16394728 TTATGTAAG
1 TTATGTAAG
*
16394737 TTACT-TAAT
1 TTA-TGTAAG
16394746 TTATGTAAG
1 TTATGTAAG
*
16394755 TTACGTAAG
1 TTATGTAAG
* *
16394764 TTATTTAAT
1 TTATGTAAG
16394773 TTATGTAAG
1 TTATGTAAG
16394782 TTATGTAAG
1 TTATGTAAG
*
16394791 TTACT-TAAT
1 TTA-TGTAAG
16394800 TTATGTAAG
1 TTATGTAAG
16394809 TTATGTAAG
1 TTATGTAAG
* *
16394818 TTATTTAAT
1 TTATGTAAG
*
16394827 TTTTGTAAG
1 TTATGTAAG
*
16394836 TTGTGTAA-
1 TTATGTAAG
16394844 TTAATGTAAG
1 TT-ATGTAAG
16394854 TTAT
1 TTAT
16394858 TTAATTTGTG
Statistics
Matches: 357, Mismatches: 63, Indels: 62
0.74 0.13 0.13
Matches are distributed among these distances:
7 31 0.09
8 25 0.07
9 287 0.80
10 14 0.04
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:16394566 original size:27 final size:27
Alignment explanation
Indices: 16394532--16394843 Score: 484
Period size: 27 Copynumber: 11.6 Consensus size: 27
16394522 GTTATGTATA
**
16394532 ATGTAAGTTATGCCAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
16394559 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
16394586 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
*
16394613 TTGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
* *
16394640 TTGTAAGTTATGTAAGTTACTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
*
16394667 ATGTAA-TTAATGTAAGTTACTTAATTT
1 ATGTAAGTT-ATGTAAGTTATTTAATTT
*
16394694 ATGTAA-TTAATGTAAGTTACTTAATTT
1 ATGTAAGTT-ATGTAAGTTATTTAATTT
*
16394721 ATGTAAGTTATGTAAGTTACTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
*
16394748 ATGTAAGTTACGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
*
16394775 ATGTAAGTTATGTAAGTTACTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
16394802 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
* *
16394829 TTGTAAGTTGTGTAA
1 ATGTAAGTTATGTAA
16394844 TTAATGTAAG
Statistics
Matches: 271, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
26 2 0.01
27 267 0.99
28 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.50
Consensus pattern (27 bp):
ATGTAAGTTATGTAAGTTATTTAATTT
Found at i:16398659 original size:113 final size:112
Alignment explanation
Indices: 16398478--16398827 Score: 443
Period size: 113 Copynumber: 3.1 Consensus size: 112
16398468 TTCCCACAAC
* * *
16398478 GCGCCGCTAATAATATGTTTTAGCGGCGTTTTACCATAAGCGCCAC-AACTGCTAATATACATCA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTA-AATAAGCGCCACTAA-TGCTAATATACATCA
*
16398542 AGACCAAAGCGCTGCATTTTGGTTAATATTTTGCGGCGCTTTACAATAA
64 AGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAA
* * *
16398591 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAAATAAGCGCCACTAATCCTAATGTACCTCAA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTT-AAATAAGCGCCACTAATGCTAATATACATCAA
* * * * * *
16398656 GACCAAA-CACTGCGTTTTGGTTAAGAAATATTGCGGCGCTTTTCAGTAC
65 GACCAAAGCGCTGCGTTTTGGTT-A-ATATTTTGCGGCGCTTTACAATAA
* * * *
16398705 TCGCCGCTAATACTATACTTTAGCGGCGTTTTAATATAAGCGTCACTAATGCTACTATACATCAA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTAA-ATAAGCGCCACTAATGCTAATATACATCAA
* * *
16398770 GACCAAAGCGCTGCGTTTTGGTTAATCTTTTGCGGCGTTTTCCAATAA
65 GACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAA
*
16398818 GCGCCACTAA
1 GCGCCGCTAA
16398828 GCCTAATATA
Statistics
Matches: 201, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
112 13 0.06
113 89 0.44
114 85 0.42
115 14 0.07
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (112 bp):
GCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAATAAGCGCCACTAATGCTAATATACATCAAG
ACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAA
Found at i:16398848 original size:74 final size:73
Alignment explanation
Indices: 16398722--16398867 Score: 179
Period size: 74 Copynumber: 2.0 Consensus size: 73
16398712 TAATACTATA
* * *
16398722 CTTTAGCGGCGTTTTAATATAAGCGTCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTT
1 CTTTAGCGGCGTTTTAATATAAGCGCCACTAATGCTAATATACAGCAAGACCAAA-CGCTGCGTT
16398787 TTGGTTAAT
65 TTGGTTAAT
* * * * *
16398796 CTTTTGCGGCGTTTTCCA-ATAAGCGCCACTAA-GCCTAATATACCGCAAGACCAAACTCTGTGT
1 CTTTAGCGGCGTTTT-AATATAAGCGCCACTAATG-CTAATATACAGCAAGACCAAACGCTGCGT
16398859 TTTGGTTAA
64 TTTGGTTAA
16398868 GAAATCTTGC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
73 16 0.26
74 45 0.73
75 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (73 bp):
CTTTAGCGGCGTTTTAATATAAGCGCCACTAATGCTAATATACAGCAAGACCAAACGCTGCGTTT
TGGTTAAT
Found at i:16398933 original size:188 final size:187
Alignment explanation
Indices: 16398608--16398981 Score: 586
Period size: 188 Copynumber: 2.0 Consensus size: 187
16398598 TAATACTATG
* * *
16398608 CTTTAGCGGCGTTTTCAAATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACACTGCGTTT
1 CTTTAGCGGCGTTTTCAAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACACTGCGTTT
*
16398673 TGGTTAAGAAATATTGCGGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTA
66 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTA
*
16398738 ATATAAGCGTCACTAATGCTACTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
131 ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAA-CGCTGCGTTTTGGTTAAT
* * * *
16398796 CTTTTGCGGCGTTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGTGTTT
1 CTTTAGCGGCGTTTTCAAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACACTGCGTTT
* * *
16398861 TGGTTAAGAAATCTTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCGGCGTTTTT
66 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTA
* * * * *
16398926 GTATAAGCGCCACTAATGCTAGTGTACCTCAAGACCAAACTCTGCGTTTTGGTTAA
131 ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAACGCTGCGTTTTGGTTAA
16398982 GATGTATTGC
Statistics
Matches: 169, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
187 16 0.09
188 153 0.91
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (187 bp):
CTTTAGCGGCGTTTTCAAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACACTGCGTTT
TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTA
ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAACGCTGCGTTTTGGTTAAT
Found at i:16398995 original size:114 final size:114
Alignment explanation
Indices: 16398795--16399052 Score: 329
Period size: 114 Copynumber: 2.3 Consensus size: 114
16398785 TTTTGGTTAA
* ** *
16398795 TCTTTTGCGGCGTTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGTGTT
1 TCTTTAGCGGCGTTTTTAAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTT
* *
16398860 TTGGTTAAGAAATCTTGCGGCGCTTTTCACTACTCGCCGCTAATACTAT
66 TTGGTTAAGAAATATTGCGGCGCTTTTCACGACTCGCCGCTAATACTAT
** * * *
16398909 TCTTTAGCGGCGTTTTTGTATAAGCGCCACTAATG-CTAGTGTACCTCAAGACCAAACTCTGCGT
1 TCTTTAGCGGCGTTTTTAAATAAGCGCCACTAA-GCCTAATATACCGCAAGACCAAACTCTGCGT
** ** * *
16398973 TTTGGTTAAGATGTATTGCGGCGCTTTTTGCGGCTCGCCGCTAATTCTAT
65 TTTGGTTAAGAAATATTGCGGCGCTTTTCACGACTCGCCGCTAATACTAT
* *
16399023 GCTTTAGCGGCGATTTTAAATAAGCGCCAC
1 TCTTTAGCGGCGTTTTTAAATAAGCGCCAC
16399053 GAATTATATA
Statistics
Matches: 123, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
114 122 0.99
115 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (114 bp):
TCTTTAGCGGCGTTTTTAAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTT
TTGGTTAAGAAATATTGCGGCGCTTTTCACGACTCGCCGCTAATACTAT
Found at i:16399048 original size:302 final size:302
Alignment explanation
Indices: 16398495--16399098 Score: 776
Period size: 302 Copynumber: 2.0 Consensus size: 302
16398485 TAATAATATG
*
16398495 TTTTAGCGGCGTTTTACCATAAGCGCCACAACTGCTAATATACATCAAGACCAAAGCGCTGCATT
1 TTTTAGCGGCGTTTTACCATAAGCGCCACAAC-GCTAATATACAGCAAGACCAAAGCGCTGCATT
* *
16398560 TTGGTTAATATTTTGCGGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCA
65 TTGGTTAAAATCTTGCGGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCA
16398625 AATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACACTGCGTTTTGGTTAAGAAATATTGC
130 AATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACACTGCGTTTTGGTTAAGAAATATTGC
* *
16398690 GGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAATATAAGCGTCACTAAT
195 GGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAATATAAGCGCCACGAAT
* *
16398755 GCTACTA-T-ACATCAAGACCAAAGCGCTGCGTTTTGGTTAATC
260 GATA-TAGTAACATCAAGACCAAAACGCTGCGTTTTGGTTAATC
* * **
16398797 TTTT-GCGGCGTTTT-CCAATAAGCGCCACTAA-GCCTAATATACCGCAAGACCAAA-CTCTGTG
1 TTTTAGCGGCGTTTTACC-ATAAGCGCCAC-AACG-CTAATATACAGCAAGACCAAAGCGCTGCA
* * ** *
16398858 TTTTGGTTAAGAAATCTTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCGGCGTT
63 TTTTGGTT-A-AAATCTTGCGGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTT
*** * * * **
16398923 TTTGTATAAGCGCCACTAATGCTAGTGTACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATGTA
126 TTCAAATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACACTGCGTTTTGGTTAAGAAATA
* * *
16398988 TTGCGGCGCTTTTTGC-G-GCTCGCCGCTAATTCTATGCTTTAGCGGCGATTTTAA-ATAAGCGC
191 TTGCGGCGC-TTTT-CAGTACTCGCCGCTAATACTATACTTTAGCGGCG-TTTTAATATAAGCGC
* * *
16399050 CACGAATTATATAGTACACATCTAGTCCAAAACGCTGCGTTTTGGTTAA
253 CACGAATGATATAGTA-ACATCAAGACCAAAACGCTGCGTTTTGGTTAA
16399099 GAGCTTTTGC
Statistics
Matches: 261, Mismatches: 30, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
300 15 0.06
301 43 0.16
302 162 0.62
303 11 0.04
304 30 0.11
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (302 bp):
TTTTAGCGGCGTTTTACCATAAGCGCCACAACGCTAATATACAGCAAGACCAAAGCGCTGCATTT
TGGTTAAAATCTTGCGGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAA
ATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACACTGCGTTTTGGTTAAGAAATATTGCG
GCGCTTTTCAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAATATAAGCGCCACGAATG
ATATAGTAACATCAAGACCAAAACGCTGCGTTTTGGTTAATC
Found at i:16402235 original size:19 final size:19
Alignment explanation
Indices: 16402185--16402247 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
16402175 GAACAAAAAA
16402185 TTATAAAATAATCAAAATAAT
1 TTATAAAATAATCAAAAT--T
*
16402206 CT-TAAAA-AATCAAAATT
1 TTATAAAATAATCAAAATT
*
16402223 TTATAAAATAATCTTAAATT
1 TTATAAAATAATC-AAAATT
16402243 TTATA
1 TTATA
16402248 TAAAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 13 0.36
20 15 0.42
21 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
TTATAAAATAATCAAAATT
Found at i:16406778 original size:48 final size:48
Alignment explanation
Indices: 16406707--16406804 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
16406697 ACATTGTCAA
16406707 AATAACACACATCAACAAGGCATCAAAAGTACCAAGGTTACATCAACC
1 AATAACACACATCAACAAGGCATCAAAAGTACCAAGGTTACATCAACC
*
16406755 AATAACACACATCAACAAGGCATCCAAAGTACCAAGGTTACATCAACC
1 AATAACACACATCAACAAGGCATCAAAAGTACCAAGGTTACATCAACC
16406803 AA
1 AA
16406805 AATGACATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.48, C:0.28, G:0.10, T:0.14
Consensus pattern (48 bp):
AATAACACACATCAACAAGGCATCAAAAGTACCAAGGTTACATCAACC
Found at i:16410137 original size:33 final size:33
Alignment explanation
Indices: 16410100--16410257 Score: 124
Period size: 33 Copynumber: 4.7 Consensus size: 33
16410090 ACATTCGTAG
* *
16410100 TGTCATAACCCAATTATGGTCTTATCATCAGAA
1 TGTCATAGCCCAACTATGGTCTTATCATCAGAA
* *
16410133 TGTCATAGCCCAACTATGGTCTTAT-ATATAAATA
1 TGTCATAGCCCAACTATGGTCTTATCAT-CAGA-A
* * * * * *
16410167 CTGCCATGGTCCAACCATGGTCTTA-CGTTCATG-G
1 -TGTCATAGCCCAACTATGGTCTTATC-ATCA-GAA
* * **
16410201 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGTCATAGCCCAACTATGGTCTTATCATCAGAA
16410234 TGTCATAGCCCAACTATGGTCTTA
1 TGTCATAGCCCAACTATGGTCTTA
16410258 CATATAAACA
Statistics
Matches: 93, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
32 3 0.03
33 66 0.71
34 2 0.02
35 21 0.23
36 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (33 bp):
TGTCATAGCCCAACTATGGTCTTATCATCAGAA
Found at i:16410278 original size:101 final size:101
Alignment explanation
Indices: 16410103--16410327 Score: 387
Period size: 101 Copynumber: 2.2 Consensus size: 101
16410093 TTCGTAGTGT
* *
16410103 CATAACCCAATTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGTCTTATATATAAATAC
1 CATAACCCAATTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGTCTTACATATAAACAC
* *
16410168 TGCCATGGTCCAACCATGGTCTTACGTTCATGGTGC
66 TGCCATGGTCCAACCATGGTCTTACGTTCATAGTAC
*
16410204 CATAACCCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGTCTTACATATAAACAC
1 CATAACCCAATTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGTCTTACATATAAACAC
* *
16410269 TGTCATGGTCCAACCATGGTCTTCCGTTCATAGTAC
66 TGCCATGGTCCAACCATGGTCTTACGTTCATAGTAC
16410305 CATAACCCAATTATGGTCTTATC
1 CATAACCCAATTATGGTCTTATC
16410328 CGTCAATTCA
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 116 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (101 bp):
CATAACCCAATTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGTCTTACATATAAACAC
TGCCATGGTCCAACCATGGTCTTACGTTCATAGTAC
Found at i:16412836 original size:320 final size:320
Alignment explanation
Indices: 16412254--16412893 Score: 1154
Period size: 320 Copynumber: 2.0 Consensus size: 320
16412244 AAAATATCTC
*
16412254 ATTAAAATATTAATAAAATAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCTC
1 ATTAAAATATTAATAAAATAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCAC
16412319 TAATATCATCATTGCCTTCTAAAGTTCTCTCTCTTTCTAATTGACCATTTTGCCCTTTATGATCT
66 TAATATCATCATTGCCTTCTAAAGTTCTCTCTCTTTCTAATTGACCATTTTGCCCTTTATGATCT
* * * *
16412384 TTTAAAACTCCATCCTTGAGTCATCACTTAATTTGGTAAATTTGTGATTTAGTCCCTTATAATTC
131 TTTAAAACTCCATCCTTGAGTCATAACTTAATTTGGAAAAATTGTGATTTAGTCCCTCATAATTC
16412449 TTCACCTATTCAATTTGGTCCTAATTCATCCATTTTACTTAGTTTCTAGATCATTCCACCCTTAA
196 TTCACCTATTCAATTTGGTCCTAATTCATCCATTTTACTTAGTTTCTAGATCATTCCACCCTTAA
16412514 AATATTTGCACTATTGGTCCTTCAAATTTTTCATATTTACACTTTAACCCCTCAAATTTT
261 AATATTTGCACTATTGGTCCTTCAAATTTTTCATATTTACACTTTAACCCCTCAAATTTT
16412574 ATTAAAATATTAATAAAATAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCAC
1 ATTAAAATATTAATAAAATAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCAC
*
16412639 TAATATCATCATTGCCTTCTAGAGTTCTCTCTCTTTCTAATTGACCATTTTGCCCTTTATGATCT
66 TAATATCATCATTGCCTTCTAAAGTTCTCTCTCTTTCTAATTGACCATTTTGCCCTTTATGATCT
* *
16412704 TTTAAAATTTCATCCTTGAGTCATAACTTAATTTGGAAAAATTGTGATTTAGTCCCTCATAATTC
131 TTTAAAACTCCATCCTTGAGTCATAACTTAATTTGGAAAAATTGTGATTTAGTCCCTCATAATTC
* * *
16412769 TTCACCTATTCAATTTGGTCTTAGTTCATCCATTTTCCTTAGTTTCTAGATCATTCCACCCTTAA
196 TTCACCTATTCAATTTGGTCCTAATTCATCCATTTTACTTAGTTTCTAGATCATTCCACCCTTAA
* * *
16412834 AATATTTTCACTATTTGTCCTTTAAATTTTTCATATTTACACTTTAACCCCTCAAATTTT
261 AATATTTGCACTATTGGTCCTTCAAATTTTTCATATTTACACTTTAACCCCTCAAATTTT
16412894 GAGTATTTAC
Statistics
Matches: 306, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
320 306 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.43
Consensus pattern (320 bp):
ATTAAAATATTAATAAAATAATATTTATCTAATTAAATAATTATAAAATATCATCAAAATATCAC
TAATATCATCATTGCCTTCTAAAGTTCTCTCTCTTTCTAATTGACCATTTTGCCCTTTATGATCT
TTTAAAACTCCATCCTTGAGTCATAACTTAATTTGGAAAAATTGTGATTTAGTCCCTCATAATTC
TTCACCTATTCAATTTGGTCCTAATTCATCCATTTTACTTAGTTTCTAGATCATTCCACCCTTAA
AATATTTGCACTATTGGTCCTTCAAATTTTTCATATTTACACTTTAACCCCTCAAATTTT
Found at i:16412860 original size:24 final size:22
Alignment explanation
Indices: 16412828--16412871 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
16412818 ATCATTCCAC
16412828 CCTTAAAATATTTTCACTATTTGT
1 CCTTAAAAT-TTTTCA-TATTTGT
*
16412852 CCTTTAAATTTTTCATATTT
1 CCTTAAAATTTTTCATATTT
16412872 ACACTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.27, C:0.16, G:0.02, T:0.55
Consensus pattern (22 bp):
CCTTAAAATTTTTCATATTTGT
Found at i:16413217 original size:24 final size:24
Alignment explanation
Indices: 16413190--16413295 Score: 74
Period size: 24 Copynumber: 4.4 Consensus size: 24
16413180 ATGGCTCTCT
16413190 TGAGCTTCCTGATATTAGCTCGCA
1 TGAGCTTCCTGATATTAGCTCGCA
* * * *
16413214 TGAGCTTCCT-AAATTTGGCTCTCT
1 TGAGCTTCCTGATA-TTAGCTCGCA
* *
16413238 TAAGCTTCCTG-T-TTATGGCTCGTA
1 TGAGCTTCCTGATATTA--GCTCGCA
* *
16413262 TGAGCTTCCCGATAATTGGCTCGCA
1 TGAGCTTCCTGAT-ATTAGCTCGCA
*
16413287 AGAGCTTCC
1 TGAGCTTCC
16413296 CGTTGCATAG
Statistics
Matches: 60, Mismatches: 15, Indels: 13
0.68 0.17 0.15
Matches are distributed among these distances:
22 2 0.03
23 2 0.03
24 39 0.65
25 15 0.25
27 2 0.03
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (24 bp):
TGAGCTTCCTGATATTAGCTCGCA
Found at i:16415285 original size:50 final size:51
Alignment explanation
Indices: 16415223--16415332 Score: 168
Period size: 50 Copynumber: 2.2 Consensus size: 51
16415213 CCATTTCAAT
*
16415223 CCTTTTCATAATTTCATGACATAGGTCATTTGAATACATACCTTTCCTTTC
1 CCTTTTCATAATTTCATGACATAGGTCATTTGAATACATACATTTCCTTTC
* * *
16415274 CCTTTT-ATAATTTCATGACATAGTTTATTTGAATGCATACATTTCCTTTC
1 CCTTTTCATAATTTCATGACATAGGTCATTTGAATACATACATTTCCTTTC
*
16415324 CTTTTTCAT
1 CCTTTTCAT
16415333 GCTTGTTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
50 45 0.85
51 8 0.15
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (51 bp):
CCTTTTCATAATTTCATGACATAGGTCATTTGAATACATACATTTCCTTTC
Found at i:16427120 original size:17 final size:17
Alignment explanation
Indices: 16427098--16427133 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16427088 AAAGATAGAT
16427098 TTTTAGTCTAAATATTA
1 TTTTAGTCTAAATATTA
* *
16427115 TTTTAGTTTAAATTTTA
1 TTTTAGTCTAAATATTA
16427132 TT
1 TT
16427134 ATTTGATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTAGTCTAAATATTA
Found at i:16427695 original size:16 final size:16
Alignment explanation
Indices: 16427674--16427709 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16427664 TTTTCACTCC
* *
16427674 CTCCCTCCCTCCTTCA
1 CTCCCTCACACCTTCA
16427690 CTCCCTCACACCTTCA
1 CTCCCTCACACCTTCA
16427706 CTCC
1 CTCC
16427710 ACAAAACGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.61, G:0.00, T:0.28
Consensus pattern (16 bp):
CTCCCTCACACCTTCA
Found at i:16433347 original size:24 final size:24
Alignment explanation
Indices: 16433315--16433362 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16433305 CTTTACGATT
16433315 CTACTTAACCAGCCTCTATTCTAA
1 CTACTTAACCAGCCTCTATTCTAA
16433339 CTACTTAACCAGCCTCTATTCTAA
1 CTACTTAACCAGCCTCTATTCTAA
16433363 GGCATGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.33
Consensus pattern (24 bp):
CTACTTAACCAGCCTCTATTCTAA
Found at i:16436253 original size:3 final size:3
Alignment explanation
Indices: 16436247--16436277 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16436237 TTATTATTAT
16436247 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
16436278 TATTTGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:16441843 original size:35 final size:35
Alignment explanation
Indices: 16441804--16441872 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
16441794 TTACCTCAAA
* * *
16441804 GCCTTTTTAGTTGAACTTCTTATCATGAATATTTT
1 GCCTTTCTAATTGAACTCCTTATCATGAATATTTT
16441839 GCCTTTCTAATTGAACTCCTTATCATGAATATTT
1 GCCTTTCTAATTGAACTCCTTATCATGAATATTT
16441873 CAGAATTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (35 bp):
GCCTTTCTAATTGAACTCCTTATCATGAATATTTT
Found at i:16444980 original size:21 final size:21
Alignment explanation
Indices: 16444954--16444993 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16444944 TATATTTATT
*
16444954 CATAACATAGGTAAGTTCAAC
1 CATAACATACGTAAGTTCAAC
*
16444975 CATAACATACGTAATTTCA
1 CATAACATACGTAAGTTCA
16444994 CAAATATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (21 bp):
CATAACATACGTAAGTTCAAC
Found at i:16445501 original size:176 final size:176
Alignment explanation
Indices: 16445207--16445560 Score: 672
Period size: 176 Copynumber: 2.0 Consensus size: 176
16445197 ATAAACCATT
*
16445207 TTATAAGAAATTACACTTTTTGAATCTTACCACCTTTTCATGAACGTAAGTATATTTCCATTTGG
1 TTATAAGAAATTACACTTTTTGAATCTTACCACCTTTTCATGAACATAAGTATATTTCCATTTGG
*
16445272 CCAAATACCATTTCAATGTATATCATTAATATTAAACATGATCTAATGCAACCAAAAGCTCAACA
66 CCAAATACCATTTCAATGAATATCATTAATATTAAACATGATCTAATGCAACCAAAAGCTCAACA
*
16445337 CAAACCTAAGCATCATCCACAATCTCAATCGATGAATTCATTTATG
131 CAAACCTAAGCATCATCCACAATCTCAATCAATGAATTCATTTATG
16445383 TTATAAGAAATTACACTTTTTGAATCTTACCACCTTTTCATGAACATAAGTATATTTCCATTTGG
1 TTATAAGAAATTACACTTTTTGAATCTTACCACCTTTTCATGAACATAAGTATATTTCCATTTGG
*
16445448 CCAATTACCATTTCAATGAATATCATTAATATTAAACATGATCTAATGCAACCAAAAGCTCAACA
66 CCAAATACCATTTCAATGAATATCATTAATATTAAACATGATCTAATGCAACCAAAAGCTCAACA
16445513 CAAACCTAAGCATCATCCACAATCTCAATCAATGAATTCATTTATG
131 CAAACCTAAGCATCATCCACAATCTCAATCAATGAATTCATTTATG
16445559 TT
1 TT
16445561 CAAGTCAGTA
Statistics
Matches: 174, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
176 174 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (176 bp):
TTATAAGAAATTACACTTTTTGAATCTTACCACCTTTTCATGAACATAAGTATATTTCCATTTGG
CCAAATACCATTTCAATGAATATCATTAATATTAAACATGATCTAATGCAACCAAAAGCTCAACA
CAAACCTAAGCATCATCCACAATCTCAATCAATGAATTCATTTATG
Done.