Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 177 of 211
Found at i:54936914 original size:98 final size:98
Alignment explanation
Indices: 54936497--54936964 Score: 386
Period size: 98 Copynumber: 4.7 Consensus size: 98
54936487 GTTTAACGTC
* * * * * * *
54936497 GTAGCTTCAATCTGTTGCGCTACATCG-CTTGAGAAGTAAGATTCGCCGTTATGGCCTAAATCTT
1 GTAGCTTCAATCTGTTCCGCTGCAACGCCTCGA-AA-TAAGATTTGCCGTTGTGGCCTCAATCTT
* *** * *
54936561 TTAATTGCAATGTCGGGGAAGCGTGATTCGCCGAT
64 TTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTT
* ** ** * * ** * * *
54936596 GTAGCCTCAATCTGTTCCATTGCATTGCCTGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCGCTGCAACGCCT-CGAAATAAGATTTGCCGTTGTGGCCTCAATCTTT
* *
54936661 TAATTGTAATGTCAGGGAAGTAAGATCCGCTGTT
65 TAATTGCAATGTCAGGGAAGTAAGATCCGCCGTT
* * * *** * * * * *
54936695 GTAGCTTCAATCT-TT-TGATTGCAATGTCAGGGAAGTAAGATCCT-CTGTTGTAGCTTCAATCT
1 GTAGCTTCAATCTGTTCCG-CTGCAACG-CCTCGAAATAAGAT-TTGCCGTTGTGGCCTCAATCT
* * *
54936757 TTTAATTGCAATATCATGGAAGTAAGATCCGCTGTT
63 TTTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTT
* *
54936793 GTAGCTTCAATCTGTTCCACTGCAAAGCCTCGAAATAAGATTTGCCGTTGTGGCCTCAATCTTTT
1 GTAGCTTCAATCTGTTCCGCTGCAACGCCTCGAAATAAGATTTGCCGTTGTGGCCTCAATCTTTT
* * **
54936858 GATTGCAATGTCAGGGAAGTGAGATTTGCCGTT
66 AATTGCAATGTCAGGGAAGTAAGATCCGCCGTT
* * * *
54936891 GTAGCTTCAATCTGTTCCGCTGCACCGCTTCGAAATAAGATTTGCCATTGTGACCTCAATCTTTT
1 GTAGCTTCAATCTGTTCCGCTGCAACGCCTCGAAATAAGATTTGCCGTTGTGGCCTCAATCTTTT
54936956 AAATTGCAA
66 -AATTGCAA
54936965 ACTATGGTTA
Statistics
Matches: 302, Mismatches: 58, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
97 1 0.00
98 197 0.65
99 99 0.33
100 3 0.01
101 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (98 bp):
GTAGCTTCAATCTGTTCCGCTGCAACGCCTCGAAATAAGATTTGCCGTTGTGGCCTCAATCTTTT
AATTGCAATGTCAGGGAAGTAAGATCCGCCGTT
Found at i:54936931 original size:147 final size:147
Alignment explanation
Indices: 54936533--54936908 Score: 407
Period size: 147 Copynumber: 2.6 Consensus size: 147
54936523 GCTTGAGAAG
* * * * * * * *
54936533 TAAGATTCGCCGTTATGGCCTAAATCTTTTAATTGCAATGTCGGGGAAGCGTGATTCGCCGATGT
1 TAAGATTCGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCAGGGAAGTGAGATTTGCCGTTGT
* * * *
54936598 AGCCTCAATCTGTTCCATTGCATTGCCTGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTA
66 AGCTTCAATCTGTTCCATTGCATAG-CTTGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTCA
* * * * *
54936663 ATTGTAATGTCAGGGAAG
130 ACTGCAAAGTCAGCGAAA
* * * * * * *
54936681 TAAGATCCGCTGTTGTAGCTTCAATCTTTTGATTGCAATGTCAGGGAAGTAAGATCCT-CTGTTG
1 TAAGATTCGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCAGGGAAGTGAGAT-TTGCCGTTG
** * *
54936745 TAGCTTCAATCT-TTTAATTGCAATATCATGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTT
65 TAGCTTCAATCTGTTCCATTGC-ATAGCTTGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TT
* **
54936809 CCACTGCAAAG-CCTCGAAA
128 CAACTGCAAAGTCAGCGAAA
*
54936828 TAAGATTTGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCAGGGAAGTGAGATTTGCCGTTGT
1 TAAGATTCGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCAGGGAAGTGAGATTTGCCGTTGT
54936893 AGCTTCAATCTGTTCC
66 AGCTTCAATCTGTTCC
54936909 GCTGCACCGC
Statistics
Matches: 182, Mismatches: 41, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
146 1 0.01
147 110 0.60
148 71 0.39
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (147 bp):
TAAGATTCGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCAGGGAAGTGAGATTTGCCGTTGT
AGCTTCAATCTGTTCCATTGCATAGCTTGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTCAA
CTGCAAAGTCAGCGAAA
Found at i:54936932 original size:49 final size:49
Alignment explanation
Indices: 54936790--54936941 Score: 137
Period size: 49 Copynumber: 3.1 Consensus size: 49
54936780 AAGATCCGCT
* *
54936790 GTTGTAGCTTCAATCTGTTCCACTGCAAAGCCTCGAAATAAGATTTGCC
1 GTTGTAGCTTCAATCTGTTCCGCTGCAAAGCATCGAAATAAGATTTGCC
* * * * * ** * *
54936839 GTTGTGGCCTCAATCT-TT-TGATTGCAATGTCAGGGAAGTGAGATTTGCC
1 GTTGTAGCTTCAATCTGTTCCG-CTGCAAAG-CATCGAAATAAGATTTGCC
** *
54936888 GTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTCGAAATAAGATTTGCC
1 GTTGTAGCTTCAATCTGTTCCGCTGCAAAGCATCGAAATAAGATTTGCC
*
54936937 ATTGT
1 GTTGT
54936942 GACCTCAATC
Statistics
Matches: 76, Mismatches: 23, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
48 8 0.11
49 60 0.79
50 7 0.09
51 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (49 bp):
GTTGTAGCTTCAATCTGTTCCGCTGCAAAGCATCGAAATAAGATTTGCC
Found at i:54954806 original size:21 final size:21
Alignment explanation
Indices: 54954745--54954854 Score: 87
Period size: 23 Copynumber: 5.1 Consensus size: 21
54954735 CCTGATTAGT
54954745 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* * ** * *
54954765 AAACGACCCACGAGGTCCCTG
1 ATACGACACATAAAGTGCCTG
*
54954786 ATACGACACATAAAGTACCTGAG
1 ATACGACACATAAAGTGCCT--G
* *
54954809 ATACGACACATAAACTGTCTG
1 ATACGACACATAAAGTGCCTG
*
54954830 ATGTACGACACATAAAGTGTCTG
1 A--TACGACACATAAAGTGCCTG
54954853 AT
1 AT
54954855 CGGCAAAGCC
Statistics
Matches: 70, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
20 8 0.11
21 24 0.34
23 38 0.54
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:54954850 original size:23 final size:24
Alignment explanation
Indices: 54954784--54954854 Score: 101
Period size: 23 Copynumber: 3.0 Consensus size: 24
54954774 ACGAGGTCCC
**
54954784 TGATACGACACATAAAGTACCTGA
1 TGATACGACACATAAAGTGTCTGA
*
54954808 -GATACGACACATAAACTGTCTGA
1 TGATACGACACATAAAGTGTCTGA
54954831 TG-TACGACACATAAAGTGTCTGA
1 TGATACGACACATAAAGTGTCTGA
54954854 T
1 T
54954855 CGGCAAAGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 41 0.98
24 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
TGATACGACACATAAAGTGTCTGA
Found at i:54955883 original size:18 final size:18
Alignment explanation
Indices: 54955862--54955903 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
54955852 AATGCCTCTG
*
54955862 TTCTTTCTTTCT-TTTTGT
1 TTCTTTCTTT-TGTTTTCT
54955880 TTCTTTCTTTTGTTTTCT
1 TTCTTTCTTTTGTTTTCT
54955898 TTCTTT
1 TTCTTT
54955904 TGTTCACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (18 bp):
TTCTTTCTTTTGTTTTCT
Found at i:54955905 original size:14 final size:14
Alignment explanation
Indices: 54955865--54955907 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
54955855 GCCTCTGTTC
54955865 TTTCTTTCTTTT-T
1 TTTCTTTCTTTTGT
54955878 GTTTCTTTCTTTTGT
1 -TTTCTTTCTTTTGT
54955893 TTTCTTTCTTTTGT
1 TTTCTTTCTTTTGT
54955907 T
1 T
54955908 CACTAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 27 0.96
15 1 0.04
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTCTTTCTTTTGT
Found at i:54956074 original size:28 final size:28
Alignment explanation
Indices: 54956043--54956096 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
54956033 TAATTTATTT
54956043 TTTAATAAAATA-TTTATAATATAATTAA
1 TTTAATAAAATACTTTATAAT-TAATTAA
*
54956071 TTTAATAATATACTTTATAATTAATT
1 TTTAATAAAATACTTTATAATTAATT
54956097 TATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTAATAAAATACTTTATAATTAATTAA
Found at i:54956100 original size:11 final size:11
Alignment explanation
Indices: 54956062--54956100 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
54956052 ATATTTATAA
54956062 TATAATTAATT
1 TATAATTAATT
*
54956073 TAATAATATACTT
1 T-ATAAT-TAATT
54956086 TATAATTAATT
1 TATAATTAATT
54956097 TATA
1 TATA
54956101 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:54956122 original size:21 final size:20
Alignment explanation
Indices: 54956074--54956123 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
54956064 TAATTAATTT
*
54956074 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* * *
54956094 ATTTATATATTTATATAAATA
1 AATAATATACTT-TATAAATA
54956115 AATAATATA
1 AATAATATA
54956124 AAAATCTAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:54964595 original size:23 final size:23
Alignment explanation
Indices: 54964569--54964692 Score: 82
Period size: 23 Copynumber: 5.4 Consensus size: 23
54964559 ATTATAATCA
*
54964569 TATGTATTAGTGTTAAATTTCAT
1 TATGTATTAGTTTTAAATTTCAT
*
54964592 TATGTATTATTTTTAAA--TCAAT
1 TATGTATTAGTTTTAAATTTC-AT
*
54964614 ATAT-TATTAGTATCATAAATTTTCAT
1 -TATGTATTAGT-T-TTAAA-TTTCAT
* *
54964640 GTAT-TATTAG-CTTAGATTT-AT
1 -TATGTATTAGTTTTAAATTTCAT
*
54964661 TATGTATTTGTTTTTAAA-TTCAT
1 TATGTATTAG-TTTTAAATTTCAT
54964684 TATGTATTA
1 TATGTATTA
54964693 TCATTTCGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
20 3 0.04
21 9 0.12
22 13 0.17
23 36 0.46
24 4 0.05
26 11 0.14
27 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (23 bp):
TATGTATTAGTTTTAAATTTCAT
Found at i:54966224 original size:25 final size:25
Alignment explanation
Indices: 54966195--54966259 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
54966185 ATTAGCTCTC
54966195 ATGAGCTTCCCGTTATATGGTTCTT
1 ATGAGCTTCCCGTTATATGGTTCTT
54966220 ATGAGCTTCCCGTTATATGGTTCTT
1 ATGAGCTTCCCGTTATATGGTTCTT
**
54966245 GCGAGCTTCCCGTTA
1 ATGAGCTTCCCGTTA
54966260 ATAGCTCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.40
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGTTCTT
Found at i:54966355 original size:25 final size:25
Alignment explanation
Indices: 54966327--54966411 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
54966317 TAGCTCTTAT
*
54966327 GAGCATCCCGA-TATATGGCTCTTCG
1 GAGCTTCCCGATTA-ATGGCTCTTCG
* * *
54966352 GAGCTTCCTGATTTAAAGGCTCTTTCAT
1 GAGCTTCCCGA-TTAATGGCTC-TTC-G
*
54966380 GAGCTTCCCGATTAATGGCTCTCCG
1 GAGCTTCCCGATTAATGGCTCTTCG
54966405 GAGCTTC
1 GAGCTTC
54966412 TCGACATTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
25 16 0.33
26 8 0.17
27 14 0.29
28 10 0.21
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCTTCG
Found at i:54966472 original size:25 final size:25
Alignment explanation
Indices: 54966444--54966499 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
54966434 TTCTCAATAT
54966444 TGGCTCGTATA-AGCTTCCCATTACA
1 TGGCTC-TATAGAGCTTCCCATTACA
* *
54966469 TGGCTCTCTAGAGCTTCCCATTATA
1 TGGCTCTATAGAGCTTCCCATTACA
54966494 TGGCTC
1 TGGCTC
54966500 AAAAGAAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 3 0.11
25 25 0.89
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.34
Consensus pattern (25 bp):
TGGCTCTATAGAGCTTCCCATTACA
Found at i:54971496 original size:22 final size:22
Alignment explanation
Indices: 54971463--54971544 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
54971453 ACATAATGTG
54971463 AATTCTAATTTTAAAAAATTATT
1 AATT-TAATTTTAAAAAATTATT
* *
54971486 AATTTAATTTTAAATAAAATACTA
1 AATTTAATTTTAAA-AAATTA-TT
* *
54971510 AAATT-ATTTTATAAAATTATT
1 AATTTAATTTTAAAAAATTATT
*
54971531 AATTTAAGTTTAAA
1 AATTTAATTTTAAA
54971545 TAAAAGTGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.11
22 21 0.45
23 16 0.34
24 5 0.11
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (22 bp):
AATTTAATTTTAAAAAATTATT
Found at i:54971547 original size:24 final size:23
Alignment explanation
Indices: 54971463--54971549 Score: 74
Period size: 23 Copynumber: 3.8 Consensus size: 23
54971453 ACATAATGTG
*
54971463 AATTCTAATTTTAA-AAAATTATT
1 AATT-TAATTTAAATAAAATTATT
*
54971486 AATTTAATTTTAAATAAAA-TACTA
1 AATTTAA-TTTAAATAAAATTA-TT
* *
54971510 AAATT-ATTT-TATAAAATTATT
1 AATTTAATTTAAATAAAATTATT
54971531 AATTTAAGTTTAAATAAAA
1 AATTTAA-TTTAAATAAAA
54971550 GTGATTAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
21 11 0.22
22 9 0.18
23 15 0.30
24 15 0.30
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (23 bp):
AATTTAATTTAAATAAAATTATT
Found at i:54972682 original size:29 final size:29
Alignment explanation
Indices: 54972648--54972710 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
54972638 TCAAACATGG
54972648 ATTAATAATCTAAAAATATCAAATCAAGA
1 ATTAATAATCTAAAAATATCAAATCAAGA
*
54972677 ATTAATAATCTAGAAATATCAAATCAAGA
1 ATTAATAATCTAAAAATATCAAATCAAGA
54972706 ATTAA
1 ATTAA
54972711 GTACACATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (29 bp):
ATTAATAATCTAAAAATATCAAATCAAGA
Found at i:54972706 original size:15 final size:15
Alignment explanation
Indices: 54972661--54972706 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
54972651 AATAATCTAA
54972661 AAATATCAAATCAAG
1 AAATATCAAATCAAG
* *
54972676 -AAT-TAATAATCTAG
1 AAATATCA-AATCAAG
54972690 AAATATCAAATCAAG
1 AAATATCAAATCAAG
54972705 AA
1 AA
54972707 TTAAGTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.24
Consensus pattern (15 bp):
AAATATCAAATCAAG
Found at i:54974903 original size:9 final size:9
Alignment explanation
Indices: 54974886--54974922 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54974876 TGAGTTTTCG
54974886 AATTCGAAT
1 AATTCGAAT
*
54974895 AACTCGAAT
1 AATTCGAAT
54974904 AATTCGAAT
1 AATTCGAAT
54974913 AATTCGAAT
1 AATTCGAAT
54974922 A
1 A
54974923 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:54975176 original size:30 final size:31
Alignment explanation
Indices: 54975135--54975194 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
54975125 AAACCTTTTA
* *
54975135 TTTTTCCCTAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
*
54975165 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
54975195 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:54981308 original size:21 final size:21
Alignment explanation
Indices: 54981282--54981322 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54981272 AGACGAGCAA
* *
54981282 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
54981303 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
54981323 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:54988104 original size:12 final size:11
Alignment explanation
Indices: 54988087--54988143 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
54988077 AACAAATCCT
54988087 CTCTCATATTTC
1 CTCTCA-ATTTC
54988099 CTCTCAA-TTC
1 CTCTCAATTTC
54988109 CTCTCAATTTC
1 CTCTCAATTTC
*
54988120 CTAC-CAAAATT-
1 CT-CTC-AATTTC
54988131 CTCTCAATTTC
1 CTCTCAATTTC
54988142 CT
1 CT
54988144 TCCAAAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 15 0.39
11 12 0.32
12 11 0.29
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:54988134 original size:22 final size:22
Alignment explanation
Indices: 54988104--54988159 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
54988094 ATTTCCTCTC
54988104 AATTCCTCTCAATTTCCTACCAA
1 AATT-CTCTCAATTTCCTACCAA
*
54988127 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTACCAA
54988149 AATTCTCTCAA
1 AATTCTCTCAA
54988160 ATCCATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTACCAA
Found at i:54989348 original size:7 final size:7
Alignment explanation
Indices: 54989336--54989360 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54989326 ATTTGATTGA
54989336 TATTTAG
1 TATTTAG
54989343 TATTTAG
1 TATTTAG
54989350 TATTTAG
1 TATTTAG
54989357 TATT
1 TATT
54989361 ATGTATATAA
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:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:54989580 original size:29 final size:29
Alignment explanation
Indices: 54989504--54990019 Score: 499
Period size: 29 Copynumber: 19.1 Consensus size: 29
54989494 TCAACTACGC
54989504 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* * *
54989533 AACCCCTAACTTAAATTAATTACAAACCCT
1 AA-CCCTAACCTAATTTAATTAAAAACCCT
*
54989563 AACTCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
54989592 AACCCTAATCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
54989621 -A----AACC---TTTAACTTAAAAACCCT
1 AACCCTAACCTAATTTAA-TTAAAAACCCT
* *
54989643 AACCTTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
54989672 AACCCTAACCTAATTTAATTAAAAACTCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
54989701 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
54989730 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
54989759 AACTCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
54989788 AA----ATCC----TTAACTTAAAAACCCT
1 AACCCTAACCTAATTTAA-TTAAAAACCCT
* *
54989810 AACCTTAACCTAAATTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
54989833 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
54989862 -A----AA-CT--CTTAACTTAAAAACCCT
1 AACCCTAACCTAATTTAA-TTAAAAACCCT
** * *
54989884 AACATTAACCTAAATTAATTAAATACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
54989913 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
54989942 AAACCCT----T-A---ACTTAAAAACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
*
54989964 AACCTTAACCTAATTTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
54989987 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
54990016 AACC
1 AACC
54990020 TAAGTTAACA
Statistics
Matches: 405, Mismatches: 33, Indels: 98
0.76 0.06 0.18
Matches are distributed among these distances:
21 17 0.04
22 47 0.12
23 41 0.10
24 5 0.01
25 11 0.03
26 5 0.01
27 12 0.03
28 4 0.01
29 219 0.54
30 44 0.11
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:54989635 original size:22 final size:20
Alignment explanation
Indices: 54989601--54989656 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
54989591 TAACCCTAAT
54989601 CTAA-CTTAA-TTAAAAACC
1 CTAACCTTAACTTAAAAACC
54989619 CTAAACCTTTAACTTAAAAACC
1 CT-AACC-TTAACTTAAAAACC
*
54989641 CTAACCTTAACCTAAA
1 CTAACCTTAACTTAAA
54989657 TTAATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 10 0.30
21 8 0.24
22 11 0.33
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
CTAACCTTAACTTAAAAACC
Found at i:54989652 original size:80 final size:80
Alignment explanation
Indices: 54989548--54990017 Score: 614
Period size: 80 Copynumber: 6.0 Consensus size: 80
54989538 CTAACTTAAA
* * * *
54989548 TTAA-TTACAAACCCTAA-CTCTAACCTAATTTAATTAAAAACCCTAACCCTAATCTAACTTAAT
1 TTAACTTAAAAACCCTAACCT-TAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAAT
54989611 TAAAAACCCTAAACCT
65 TAAAAACCCTAAACCT
54989627 TTAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATT
1 TTAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATT
*
54989692 AAAAACTCTAACCCTAACCTAAT
66 AAAAACCCT-A----AACC---T
* * *
54989715 TTAA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACTCTAACCTAATTTAATT
1 TTAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATT
54989779 AAAAACCCTAAATCC-
66 AAAAACCCTAAA-CCT
54989794 TTAACTTAAAAACCCTAACCTTAACCTAAATTAATT--AAA----AACCCTAACCTAATTTAATT
1 TTAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATT
54989853 AAAAACCCTAAA-CT
66 AAAAACCCTAAACCT
* *
54989867 CTTAACTTAAAAACCCTAACATTAACCTAAATTAATTAAATACCCTAACCCTAACCTAATTTAAT
1 -TTAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAAT
*
54989932 TAAAAACCCTAAACCC
65 TAAAAACCCTAAACCT
*
54989948 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATT--AAA----AACCCTAACCTAATTTAATT
1 TTAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATT
54990007 AAAAACCCTAA
66 AAAAACCCTAA
54990018 CCTAAGTTAA
Statistics
Matches: 352, Mismatches: 18, Indels: 47
0.84 0.04 0.11
Matches are distributed among these distances:
72 1 0.00
74 97 0.28
76 2 0.01
78 5 0.01
79 8 0.02
80 156 0.44
81 4 0.01
82 2 0.01
83 2 0.01
85 4 0.01
86 1 0.00
87 65 0.18
88 5 0.01
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (80 bp):
TTAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATT
AAAAACCCTAAACCT
Found at i:54989708 original size:109 final size:109
Alignment explanation
Indices: 54989516--54990019 Score: 529
Period size: 109 Copynumber: 4.7 Consensus size: 109
54989506 CCCTAACCTA
* * * *
54989516 ATTTAATTAAAAACCCTAACCCCTAACTTAAATTAATTACAAACCCTAACTCTAACCTAATTTAA
1 ATTTAATTAAAAACCCTAA-CCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAA
* *
54989581 TTAAAAACCCTAACCCTAATCTAACTTAATTAAAAACCCTAAACC
65 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
54989626 -TTTAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAA
1 ATTTAA-TTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAA
*
54989690 TTAAAAACTCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACC
65 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-A----AACC
* *
54989740 TAATTTAATTAAAAACCCTAA-CTCTAACCTAATTTAATTAAAAACCCTAA----ATCC----TT
1 --ATTTAATTAAAAACCCTAACCT-TAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTT
* *
54989796 AACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCT-AACC
63 AA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
* ** *
54989843 TAATTTAATTAAAAACCCT-A----AA-CT--CTTAACTTAAAAACCCTAACATTAACCTAAATT
1 --ATTTAATTAAAAACCCTAACCTTAACCTAAATTAA-TTAAAAACCCTAACCCTAACCTAATTT
*
54989900 AATTAAATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
63 AATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
* *
54989947 -CTTAACTTAAAAACCCTAACCTTAACCTAATTTAATT--AAA----AACCCTAACCTAATTTAA
1 ATTTAA-TTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAA
54990005 TTAAAAACCCTAACC
65 TTAAAAACCCTAACC
54990020 TAAGTTAACA
Statistics
Matches: 341, Mismatches: 23, Indels: 67
0.79 0.05 0.16
Matches are distributed among these distances:
95 4 0.01
96 13 0.04
97 2 0.01
98 2 0.01
100 3 0.01
101 4 0.01
102 12 0.04
103 90 0.26
104 8 0.02
107 5 0.01
108 6 0.02
109 122 0.36
110 18 0.05
112 3 0.01
114 4 0.01
115 2 0.01
116 38 0.11
117 5 0.01
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (109 bp):
ATTTAATTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAAT
TAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC
Found at i:54989817 original size:20 final size:22
Alignment explanation
Indices: 54989773--54989823 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
54989763 CTAACCTAAT
54989773 TTAA-TTAAAAACCCTAAATCC
1 TTAACTTAAAAACCCTAAATCC
54989794 TTAACTTAAAAACCCT-AA-CC
1 TTAACTTAAAAACCCTAAATCC
*
54989814 TTAACCTAAA
1 TTAACTTAAA
54989824 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 11 0.39
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAACTTAAAAACCCTAAATCC
Found at i:54989897 original size:20 final size:22
Alignment explanation
Indices: 54989829--54989897 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 22
54989819 CTAAATTAAT
* *
54989829 TAAAAACCCTAACCTAATTTAA-T
1 TAAAAACCCTAAACT-A-TTAACC
* *
54989852 TAAAAACCCTAAACTCTTAACT
1 TAAAAACCCTAAACTATTAACC
54989874 TAAAAACCCT-AAC-ATTAACC
1 TAAAAACCCTAAACTATTAACC
54989894 TAAA
1 TAAA
54989898 TTAATTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 9 0.22
21 7 0.17
22 11 0.27
23 14 0.34
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAAAACCCTAAACTATTAACC
Found at i:54990017 original size:18 final size:20
Alignment explanation
Indices: 54989971--54990013 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
54989961 CCTAACCTTA
54989971 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
54989992 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
54990014 CTAACCTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:54990169 original size:116 final size:116
Alignment explanation
Indices: 54990024--54990261 Score: 422
Period size: 116 Copynumber: 2.1 Consensus size: 116
54990014 CTAACCTAAG
* *
54990024 TTAACAATGTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTAGTACTAACAAATAA
1 TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTAGTACTAACAAATAA
54990089 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* * *
54990140 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTAGTACTAACAAATAA
*
54990205 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
54990256 TTAATA
1 TTAATA
54990262 CAATTTATCA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (116 bp):
TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTAGTACTAACAAATAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:54990278 original size:17 final size:18
Alignment explanation
Indices: 54990237--54990278 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
54990227 TTTACTAACC
* *
54990237 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
54990255 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
54990272 ATTAATA
1 ATTAATA
54990279 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:54993501 original size:126 final size:124
Alignment explanation
Indices: 54993153--54993489 Score: 494
Period size: 126 Copynumber: 2.7 Consensus size: 124
54993143 CCCAAATATG
* * * * * *
54993153 CTACTGTAGCAAAAGAGCGTCCACGATGGCACAATTTCATAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * * *
54993218 TAGAAGCAATTTTATATTATTTGCTCAGAAACGTCAAAAAAACTTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATTATTTCTTACATGAC
* ** * *
54993277 TTACTGTAGCAAAAGCGCACTGACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
54993342 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATC-AAAAAA-AATTATTTCTTACATGAC
54993403 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
54993468 TAGAAACGATTTTATACTATTT
66 TAGAAGCGATTTTATACTATTT
54993490 TATTAGAAAC
Statistics
Matches: 188, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
124 86 0.46
125 6 0.03
126 96 0.51
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATTATTTCTTACATGAC
Found at i:55001587 original size:18 final size:20
Alignment explanation
Indices: 55001544--55001588 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
55001534 AACTTCTCAA
55001544 AAATATTTATGAAAATAGATT
1 AAAT-TTTATGAAAATAGATT
*
55001565 -GATTTTATGAAAA-AG-TT
1 AAATTTTATGAAAATAGATT
55001582 AAATTTT
1 AAATTTT
55001589 TTTGGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
17 2 0.10
18 7 0.33
19 10 0.48
20 2 0.10
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
AAATTTTATGAAAATAGATT
Found at i:55002090 original size:11 final size:11
Alignment explanation
Indices: 55002076--55002100 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55002066 AATATATAAA
55002076 AAATATTTTTT
1 AAATATTTTTT
55002087 AAATATTTTTT
1 AAATATTTTTT
55002098 AAA
1 AAA
55002101 CAATTAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:55011292 original size:30 final size:30
Alignment explanation
Indices: 55011256--55011318 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
55011246 ACTTAATAAG
* *
55011256 CAAATGTCTCTAAAATCATAATAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
55011286 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
55011316 CAA
1 CAA
55011319 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:55013270 original size:31 final size:31
Alignment explanation
Indices: 55013235--55013307 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
55013225 ATTTTCATAT
* *
55013235 TTTTTTTAATTGAGTTGATAAAATATGAAA-A
1 TTTTTTTAATCGAGTTG-TAAAATACGAAATA
*
55013266 TTTTTTTAACCGAGTTGTAAAATACGAAATA
1 TTTTTTTAATCGAGTTGTAAAATACGAAATA
55013297 TTTTTTTAATC
1 TTTTTTTAATC
55013308 AAATTAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (31 bp):
TTTTTTTAATCGAGTTGTAAAATACGAAATA
Found at i:55030173 original size:26 final size:24
Alignment explanation
Indices: 55030058--55030174 Score: 85
Period size: 24 Copynumber: 4.7 Consensus size: 24
55030048 CTATGACCGA
* * *
55030058 TAAGCTCTTTCTGAGCTAATGAATAG
1 TAAGCTCTTAC-GAGCTGA-GAACAG
* *
55030084 TAAGCTC-TATCGAGCT-AGAAATAA
1 TAAGCTCTTA-CGAGCTGAG-AACAG
55030108 TAAGCTCTTACGAGCTGAGAACAG
1 TAAGCTCTTACGAGCTGAGAACAG
* *
55030132 TAAGCTCTTACAAGCTGATATATCAG
1 TAAGCTCTTACGAGCTGAGA-A-CAG
* *
55030158 TAAGCTCATGCGAGCTG
1 TAAGCTCTTACGAGCTG
55030175 TGGTGAGTCC
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
23 1 0.01
24 39 0.51
25 11 0.14
26 25 0.33
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
TAAGCTCTTACGAGCTGAGAACAG
Found at i:55034183 original size:31 final size:31
Alignment explanation
Indices: 55034145--55034203 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
55034135 ATGGCAAGTA
* *
55034145 AAAAGTGGTAGCTTCGGTTACTTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
55034176 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
55034204 TCGGCTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:55034215 original size:46 final size:46
Alignment explanation
Indices: 55034158--55034249 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
55034148 AGTGGTAGCT
* * *
55034158 TCGGTTACTTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACTTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* *
55034204 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACTTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
55034250 GTGAATAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (46 bp):
TCGGCTACTTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:55034253 original size:31 final size:31
Alignment explanation
Indices: 55034205--55034273 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
55034195 ACCTGATCAT
* * *
55034205 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
55034236 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
55034267 CGGCTAC
1 CGGCTAC
55034274 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:55036201 original size:88 final size:87
Alignment explanation
Indices: 55036052--55036227 Score: 316
Period size: 88 Copynumber: 2.0 Consensus size: 87
55036042 CTAAACCAGA
*
55036052 TTTCCCCACAATGGGTTTCTAAGGTCATGGTCCTATCCCACCATGACATATGAAATGTATGTGTA
1 TTTCCCCACAATGGGTTTCTAAGGTCATAGTCCTATCCCACCATGACATATGAAATGTATGTGTA
* *
55036117 TTAAGATGTGTTATCACATCTCC
66 TTAAGACGCGTTATCACAT-TCC
55036140 TTTCCCCACAATGGGTTTCTAAGGTCATAGTCCTATCCCACCATGACATATGAAATGTATGTGTA
1 TTTCCCCACAATGGGTTTCTAAGGTCATAGTCCTATCCCACCATGACATATGAAATGTATGTGTA
55036205 TTAAGACGCGTTATCACATTCC
66 TTAAGACGCGTTATCACATTCC
55036227 T
1 T
55036228 GACCCCTCAA
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
87 4 0.05
88 81 0.95
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (87 bp):
TTTCCCCACAATGGGTTTCTAAGGTCATAGTCCTATCCCACCATGACATATGAAATGTATGTGTA
TTAAGACGCGTTATCACATTCC
Found at i:55036982 original size:29 final size:30
Alignment explanation
Indices: 55036915--55036983 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
55036905 ATTTGATATT
* * *
55036915 ATTTAATTCTTTTTAATAATACAATGACTA
1 ATTTAATTCTATTTAATAATAAAAAGACTA
* * *
55036945 AATTGATTC-ATTTAATAGTAAAAAGACTA
1 ATTTAATTCTATTTAATAATAAAAAGACTA
55036974 ATTTAATTCT
1 ATTTAATTCT
55036984 TTTTTTATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (30 bp):
ATTTAATTCTATTTAATAATAAAAAGACTA
Found at i:55037373 original size:43 final size:43
Alignment explanation
Indices: 55037308--55037391 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
55037298 TTAATGAATG
55037308 AATGAATCTCAAGTTATAATCTATTGATTAAGTGTTCACTTTA
1 AATGAATCTCAAGTTATAATCTATTGATTAAGTGTTCACTTTA
* *
55037351 AATGAATCTCAAGTTTTGATCTATTGATTAAGTGTTCACTT
1 AATGAATCTCAAGTTATAATCTATTGATTAAGTGTTCACTT
55037392 ACTCAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (43 bp):
AATGAATCTCAAGTTATAATCTATTGATTAAGTGTTCACTTTA
Found at i:55040237 original size:37 final size:37
Alignment explanation
Indices: 55040195--55040265 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
55040185 TTGTGCACAT
55040195 TGATCACGTTGGATTTGTTTACAAATATTTTTTTCAG
1 TGATCACGTTGGATTTGTTTACAAATATTTTTTTCAG
55040232 TGATCACGTTGGATTTGTTTACAAATATTTTTTT
1 TGATCACGTTGGATTTGTTTACAAATATTTTTTT
55040266 TTCCGATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (37 bp):
TGATCACGTTGGATTTGTTTACAAATATTTTTTTCAG
Found at i:55043707 original size:46 final size:46
Alignment explanation
Indices: 55043638--55043729 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
55043628 AAAGATTTAT
* *
55043638 GATACTACATTTTAACAAAATATTTATTGGATTGTCCATTCTAAAG
1 GATACTACATTTTAACAAAATATTTATTGAATTGTCCACTCTAAAG
*
55043684 GATACTACATTTTAACAAGATATTTATTGAATTGTCCACTCTAAAG
1 GATACTACATTTTAACAAAATATTTATTGAATTGTCCACTCTAAAG
55043730 ATTAGGTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (46 bp):
GATACTACATTTTAACAAAATATTTATTGAATTGTCCACTCTAAAG
Found at i:55048356 original size:4 final size:4
Alignment explanation
Indices: 55048349--55048373 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55048339 TAATTAAACC
55048349 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
55048374 TATGGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:55058627 original size:40 final size:40
Alignment explanation
Indices: 55058555--55058633 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
55058545 TGGTACTTTA
* * * *
55058555 TGGTGTGTAGGGTTGGATGGGTTGATTCTATCCCTATATT
1 TGGTGTGCAGGGTGGGATGGGTCGATTCTATCCCCATATT
*
55058595 TGGTGTGCAGGGATGGGA-GGGTCGATTTTATCCCCATAT
1 TGGTGTGCAGGG-TGGGATGGGTCGATTCTATCCCCATAT
55058634 GGTGTGTTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.16, C:0.13, G:0.34, T:0.37
Consensus pattern (40 bp):
TGGTGTGCAGGGTGGGATGGGTCGATTCTATCCCCATATT
Found at i:55062219 original size:146 final size:147
Alignment explanation
Indices: 55062024--55062350 Score: 385
Period size: 146 Copynumber: 2.2 Consensus size: 147
55062014 ATTGAATCTG
* * * * * *
55062024 TAACTAATTTTATGGTAGATTATAAAATATA-TAGTTAATATTATATAATTAAGGTAGATTATTA
1 TAACTAA-CTTATGGTAGATTATAATATATACAAGTAAACATTATATAATTAAGATAGATTATTA
* * * * * *
55062088 ATAATATGTATAT-CTATGTATAGCTATGCTATTATAATATATATTTTTATATTAATGAGATGTA
65 ATAATATGTA-ATCCTATATAAAACTATGATATTATAATATATATTTTTATATTAATGAGACGCA
*
55062152 AGC-TTAAACCCTAAATGTA
129 A-CATTAAACCCTAAACGTA
55062171 TAACTAACTGTATGGTAGATTATAATATATACAAG-AAACA-TATATAATTAAGATAGATTATTA
1 TAACTAACT-TATGGTAGATTATAATATATACAAGTAAACATTATATAATTAAGATAGATTATTA
* * * *
55062234 ATAATATGTAATCCTATATAAAATTATGATATTTTAATGTATATTTTTATATTAATGATACGCAA
65 ATAATATGTAATCCTATATAAAACTATGATATTATAATATATATTTTTATATTAATGAGACGCAA
* *
55062299 CATTAAACTCTAAACGTG
130 CATTAAACCCTAAACGTA
* *
55062317 TAATTAACTTCATAGTAGATTATAATATATACAA
1 TAACTAACTT-ATGGTAGATTATAATATATACAA
55062351 TTAGCATGGA
Statistics
Matches: 154, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
145 4 0.03
146 118 0.77
147 30 0.19
148 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (147 bp):
TAACTAACTTATGGTAGATTATAATATATACAAGTAAACATTATATAATTAAGATAGATTATTAA
TAATATGTAATCCTATATAAAACTATGATATTATAATATATATTTTTATATTAATGAGACGCAAC
ATTAAACCCTAAACGTA
Found at i:55066681 original size:17 final size:17
Alignment explanation
Indices: 55066661--55066713 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
55066651 TTCATAAACA
55066661 TATATCATTCATTTCAT-
1 TATATCATT-ATTTCATG
*
55066678 TATATCAATATTTCATG
1 TATATCATTATTTCATG
55066695 TACTATCA-T-TTTCATG
1 TA-TATCATTATTTCATG
55066711 TAT
1 TAT
55066714 TTCAGGTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.03
16 16 0.48
17 11 0.33
18 5 0.15
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (17 bp):
TATATCATTATTTCATG
Found at i:55066972 original size:33 final size:33
Alignment explanation
Indices: 55066926--55067054 Score: 100
Period size: 33 Copynumber: 3.8 Consensus size: 33
55066916 GTTTTCTTTA
*
55066926 TGCCATAGTCCAACTATGGTCTTACACTTGTAT
1 TGCCATAGCCCAACTATGGTCTTACACTTGTAT
* * * * ** *
55066959 TGCCATGGCCCAACCATGGCCTTACTCACGTAG
1 TGCCATAGCCCAACTATGGTCTTACACTTGTAT
* *
55066992 TGCCATATCCCAGA-TATGGTCTTATCATCTT-CAT
1 TGCCATAGCCCA-ACTATGGTCTTA-CA-CTTGTAT
*
55067026 GATGCCATAGCCCAGCTATGGTCTTACAC
1 --TGCCATAGCCCAACTATGGTCTTACAC
55067055 ATGCACATAT
Statistics
Matches: 71, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
33 43 0.61
34 4 0.06
35 3 0.04
36 21 0.30
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.30
Consensus pattern (33 bp):
TGCCATAGCCCAACTATGGTCTTACACTTGTAT
Found at i:55067112 original size:108 final size:105
Alignment explanation
Indices: 55066960--55067158 Score: 249
Period size: 108 Copynumber: 1.9 Consensus size: 105
55066950 CACTTGTATT
* **
55066960 GCCATGGCCCAACCATGGCCTTACTCACGTAGTGCCATATCCCAGATATGGTCTTATCATCTTCA
1 GCCATGGCCCAACCATGGCCTTACTCACGTAGTGCCATAACCCAGATATGGTCTTATCA-CTGAA
*
55067025 TGATGCCATAGCCCAGCTATGGTCTTACACATGCACATATACC
65 T--TGCCATAGCCCAACTATGGTCTTACACATGCACATATACC
* * ** * *
55067068 GCCATGGTCCAACCATGGTCTTACGTTCACG-A-TGTTATAACCCAGTTATGGTCTTTTCACTGA
1 GCCATGGCCCAACCATGGCCTTAC--TCACGTAGTGCCATAACCCAGATATGGTCTTATCACTGA
55067131 ATTGCCATAGCCCAACTATGGTCTTACA
64 ATTGCCATAGCCCAACTATGGTCTTACA
55067159 TTTACACACT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
105 25 0.32
107 4 0.05
108 44 0.56
109 1 0.01
110 5 0.06
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (105 bp):
GCCATGGCCCAACCATGGCCTTACTCACGTAGTGCCATAACCCAGATATGGTCTTATCACTGAAT
TGCCATAGCCCAACTATGGTCTTACACATGCACATATACC
Found at i:55077294 original size:15 final size:15
Alignment explanation
Indices: 55077274--55077303 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55077264 AAATAAATTA
*
55077274 AAAATTTGAAATTTT
1 AAAATTTAAAATTTT
55077289 AAAATTTAAAATTTT
1 AAAATTTAAAATTTT
55077304 TTAAAATAAT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAAATTTAAAATTTT
Found at i:55079258 original size:20 final size:20
Alignment explanation
Indices: 55079221--55079258 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55079211 ATTTTTAAAA
*
55079221 AATATATAATATAATATATT
1 AATATATAATAAAATATATT
55079241 AATATATAA-AAAAGTATA
1 AATATATAATAAAA-TATA
55079259 CAAGATGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AATATATAATAAAATATATT
Found at i:55080030 original size:15 final size:15
Alignment explanation
Indices: 55080007--55080037 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55079997 GAGTAACAAA
55080007 AATGGAATTTTGATT
1 AATGGAATTTTGATT
*
55080022 AATGTAATTTTGATT
1 AATGGAATTTTGATT
55080037 A
1 A
55080038 GGGAAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (15 bp):
AATGGAATTTTGATT
Found at i:55081294 original size:84 final size:84
Alignment explanation
Indices: 55081150--55081333 Score: 255
Period size: 84 Copynumber: 2.2 Consensus size: 84
55081140 AAAAAGAGCA
* * *
55081150 TATGGAAAATAAAGAATCAAATATGGGAAATGAAAGAGAATAGCGTATATGAAAAATAGAGATAT
1 TATGGAAAATAGAGAATCAAATATGGGAAATGAAAGAGAATAACGAATATGAAAAATAGAGATAT
*
55081215 GAAAGGAAATTTAATATTT
66 GAAAGGAAATTGAATATTT
* * *
55081234 TATGGAAAATAGATAATCAAATATGGGAAA-GAAAAGAGAATAAC-AACTATGTAAAGTAGAGAT
1 TATGGAAAATAGAGAATCAAATATGGGAAATG-AAAGAGAATAACGAA-TATGAAAAATAGAGAT
*
55081297 ATGAAAGGGAATTGAATATTT
64 ATGAAAGGAAATTGAATATTT
*
55081318 TATGAAAAATAGAGAA
1 TATGGAAAATAGAGAA
55081334 ATTAATTATT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
83 2 0.02
84 86 0.98
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.24
Consensus pattern (84 bp):
TATGGAAAATAGAGAATCAAATATGGGAAATGAAAGAGAATAACGAATATGAAAAATAGAGATAT
GAAAGGAAATTGAATATTT
Found at i:55082676 original size:20 final size:21
Alignment explanation
Indices: 55082643--55082683 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
55082633 ACAGACAACG
55082643 CATTCATGTATTAAAATATAA
1 CATTCATGTATTAAAATATAA
*
55082664 CATTCAT-TATTAATATATAA
1 CATTCATGTATTAAAATATAA
55082684 ATTTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (21 bp):
CATTCATGTATTAAAATATAA
Found at i:55094638 original size:13 final size:13
Alignment explanation
Indices: 55094620--55094652 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
55094610 GATCCTTTAA
55094620 AAAAAATCAAAAT
1 AAAAAATCAAAAT
55094633 AAAAAATCAAAAT
1 AAAAAATCAAAAT
55094646 AAAAAAT
1 AAAAAAT
55094653 GAGAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATCAAAAT
Found at i:55097172 original size:128 final size:127
Alignment explanation
Indices: 55096799--55097177 Score: 544
Period size: 128 Copynumber: 3.0 Consensus size: 127
55096789 TAGCCTTATC
* * ** * * *
55096799 TCCCTGAGCAGCAGTGGAGTAGGTGGGAAACTGCAGATCTTGTCTCTCTAAGCAGTAGTGGAGCA
1 TCCCTGACCAGCAGTGGAATAGGTTAGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
* *
55096864 GATCGAAGATGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCAAAAGTCCTATG
66 GATCGAAGA-CGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
* * * *
55096927 TCCCTGACCAGCAGTAGAATAGGTTAAAAATTACAGATATTGT-TCCCCTAAGCAGTAGCGGAGC
1 TCCCTGACCAGCAGTGGAATAGGTTAGAAATTGCAGATCTTGTCT-CCCTAAGCAGTAGCGGAGC
*
55096991 AGATCGAAGACGACAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
65 AGATCGAAGACG-CGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
* *
55097055 TCCCTGACCAGCAATGGAATAGGTTAGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCAGAGCA
1 TCCCTGACCAGCAGTGGAATAGGTTAGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
* * *
55097120 GATCGACGACAGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAGTC
66 GATCGAAGAC-GCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTC
55097178 ATTTCTCTCT
Statistics
Matches: 223, Mismatches: 24, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
127 2 0.01
128 219 0.98
129 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (127 bp):
TCCCTGACCAGCAGTGGAATAGGTTAGAAATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
GATCGAAGACGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
Found at i:55101681 original size:11 final size:11
Alignment explanation
Indices: 55101654--55101714 Score: 70
Period size: 11 Copynumber: 5.6 Consensus size: 11
55101644 AAATAAATCC
55101654 TTTCTCT-AAT
1 TTTCTCTCAAT
*
55101664 ATTCTCTCAAT
1 TTTCTCTCAAT
55101675 TTTCTCTCAAT
1 TTTCTCTCAAT
*
55101686 TTCCTCTCAAT
1 TTTCTCTCAAT
* * *
55101697 TTCCTCTAAAA
1 TTTCTCTCAAT
55101708 TTTCTCT
1 TTTCTCT
55101715 TAAATCCCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
10 6 0.14
11 38 0.86
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTCTCTCAAT
Found at i:55102906 original size:7 final size:7
Alignment explanation
Indices: 55102896--55102920 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55102886 TTGGTATTTA
55102896 GTATTAT
1 GTATTAT
55102903 GTATTAT
1 GTATTAT
55102910 GTATTAT
1 GTATTAT
55102917 GTAT
1 GTAT
55102921 ATAACTAATA
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:55103590 original size:18 final size:18
Alignment explanation
Indices: 55103553--55103596 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
55103543 ATGCCAAGTG
* *
55103553 TGTATCCTAGCCCTTTTA
1 TGTATCCTAACCCTTATA
*
55103571 TGTATCCTAACTCTTATA
1 TGTATCCTAACCCTTATA
*
55103589 TGTTTCCT
1 TGTATCCT
55103597 TTTTCAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:55103876 original size:21 final size:21
Alignment explanation
Indices: 55103852--55103895 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55103842 AAATACCCTA
* * *
55103852 CCGGAGGAACCATAATCCCCG
1 CCGGAGCAACCACAACCCCCG
55103873 CCGGAGCAACCACAACCCCCG
1 CCGGAGCAACCACAACCCCCG
55103894 CC
1 CC
55103896 AAAAGATGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.48, G:0.20, T:0.05
Consensus pattern (21 bp):
CCGGAGCAACCACAACCCCCG
Found at i:55107371 original size:126 final size:126
Alignment explanation
Indices: 55107214--55107483 Score: 450
Period size: 126 Copynumber: 2.1 Consensus size: 126
55107204 TATGCGCCAC
* *
55107214 GTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCTGCTTAA
1 GTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAACATCCTGCTTAA
* *
55107279 AGCGTTTTTGACACTATTTTCTAAAAAATGTCTACTCGAAATTATTTTTTCAGGAGCTACT
66 AGCGTTTTTGACACTATTTGCTAAAAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACT
*
55107340 GTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCTGTACTTCTGCTGACAAAACATCCTGCTTAA
1 GTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAACATCCTGCTTAA
* * * * *
55107405 AGTGTTTTTGACATTGTTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACT
66 AGCGTTTTTGACACTATTTGCTAAAAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACT
55107466 GTAGCAAAAGCGCGTCCA
1 GTAGCAAAAGCGCGTCCA
55107484 ACCCTAATCT
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 134 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (126 bp):
GTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAACATCCTGCTTAA
AGCGTTTTTGACACTATTTGCTAAAAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACT
Found at i:55108686 original size:12 final size:12
Alignment explanation
Indices: 55108669--55108693 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55108659 GGTGTTCATT
55108669 CGGTTAACCGAC
1 CGGTTAACCGAC
55108681 CGGTTAACCGAC
1 CGGTTAACCGAC
55108693 C
1 C
55108694 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:55108873 original size:9 final size:9
Alignment explanation
Indices: 55108855--55108948 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
55108845 TTTGGTTAAA
55108855 AATTAACCG
1 AATTAACCG
*
55108864 AATTACCCG
1 AATTAACCG
55108873 AATTAACCG
1 AATTAACCG
*
55108882 AATTACCCG
1 AATTAACCG
*
55108891 AATTACCCG
1 AATTAACCG
*
55108900 AATTAACTG
1 AATTAACCG
*
55108909 AATTACCCG
1 AATTAACCG
55108918 AATTAACCG
1 AATTAACCG
*
55108927 AATTAACCA
1 AATTAACCG
*
55108936 AATTAACCA
1 AATTAACCG
55108945 AATT
1 AATT
55108949 GAATCACTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:55109078 original size:18 final size:18
Alignment explanation
Indices: 55109055--55109089 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
55109045 TAATTTTATG
55109055 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
55109073 ATTGGGTTGGGTTGGGT
1 ATTGGGTTGGGTTGGGT
55109090 TGAATACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.51, T:0.40
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:55109100 original size:23 final size:23
Alignment explanation
Indices: 55109056--55109103 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
55109046 AATTTTATGA
**
55109056 TTGGGTTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTTGAATAATTGGG
*
55109079 TTGGGTTGGGTTGAATACTTGGG
1 TTGGGTTGGGTTGAATAATTGGG
55109102 TT
1 TT
55109104 TAGATTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.10, C:0.02, G:0.46, T:0.42
Consensus pattern (23 bp):
TTGGGTTGGGTTGAATAATTGGG
Found at i:55110687 original size:18 final size:17
Alignment explanation
Indices: 55110664--55110707 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
55110654 CTTATTTATA
**
55110664 TATATACATATATGTTTT
1 TATATACATATAT-AATT
55110682 TATATACAT-TATAATT
1 TATATACATATATAATT
55110698 TATATACATA
1 TATATACATA
55110708 ACGATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 11 0.48
17 3 0.13
18 9 0.39
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (17 bp):
TATATACATATATAATT
Found at i:55110845 original size:10 final size:10
Alignment explanation
Indices: 55110832--55110887 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
55110822 TTCATATACA
55110832 TATATATTTT
1 TATATATTTT
55110842 TATATATATTT
1 TATATAT-TTT
* *
55110853 TACA-ATTTA
1 TATATATTTT
***
55110862 TATATATACA
1 TATATATTTT
55110872 TATATATTTT
1 TATATATTTT
55110882 TATATA
1 TATATA
55110888 CTTTATAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 5 0.14
10 25 0.69
11 6 0.17
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATTTT
Found at i:55110875 original size:38 final size:38
Alignment explanation
Indices: 55110795--55110917 Score: 130
Period size: 38 Copynumber: 3.3 Consensus size: 38
55110785 ATACCCTTTT
*
55110795 TACATATATATTTTCT-TAT-TTTTATAATTCATATACA
1 TACATATATATTTT-TATATATTTTATAATTTATATACA
* *
55110832 T--ATATAT-TTTTATATATATTTTACAATTTATATATA
1 TACATATATATTTT-TATATATTTTATAATTTATATACA
* *
55110868 TACATATATATTTTTATATACTTTATAATTTCCATATGCA
1 TACATATATATTTTTATATATTTTATAATTT--ATATACA
55110908 TACATATATA
1 TACATATATA
55110918 CATATTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.07
35 9 0.13
36 16 0.23
37 1 0.01
38 21 0.30
39 4 0.06
40 15 0.21
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (38 bp):
TACATATATATTTTTATATATTTTATAATTTATATACA
Found at i:55110911 original size:40 final size:40
Alignment explanation
Indices: 55110827--55110917 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
55110817 TATAATTCAT
* *
55110827 ATACATATATATTTTTATATATATTTTACAATTTATATAT
1 ATACATATATATTTTTATATATACTTTACAATTTATATAC
* *
55110867 ATACATATATA-TTTT-TATATACTTTATAATTTCCATATGC
1 ATACATATATATTTTTATATATACTTTACAATTT--ATATAC
55110907 ATACATATATA
1 ATACATATATA
55110918 CATATTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
38 15 0.33
39 4 0.09
40 26 0.58
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.51
Consensus pattern (40 bp):
ATACATATATATTTTTATATATACTTTACAATTTATATAC
Found at i:55124877 original size:6 final size:6
Alignment explanation
Indices: 55124866--55124890 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55124856 ATTGAGAATA
55124866 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
55124891 AAATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:55125011 original size:16 final size:16
Alignment explanation
Indices: 55124989--55125025 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
55124979 ATATTTCATT
55124989 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
55125006 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
55125021 TAATA
1 TAATA
55125026 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:55130990 original size:27 final size:28
Alignment explanation
Indices: 55130947--55131013 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
55130937 AAACACCATT
*
55130947 AAAA-ATAATAGAAAATATAAATT-T-TA
1 AAAATATAATATAAAATA-AAATTATATA
*
55130973 AAAATATAATATATAATAAAATTATATA
1 AAAATATAATATAAAATAAAATTATATA
*
55131001 AATAATTTAATAT
1 AA-AATATAATAT
55131014 TTGTAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.26
27 12 0.35
28 4 0.12
29 9 0.26
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAATATAATATAAAATAAAATTATATA
Found at i:55131162 original size:97 final size:97
Alignment explanation
Indices: 55131048--55131245 Score: 387
Period size: 97 Copynumber: 2.0 Consensus size: 97
55131038 ACTAGCATAA
*
55131048 TTAATTTTAAAGGAAAAATAGAGAAAATTGGTTTAATCATCAATTCAATGAATTTTTTAGTCCGA
1 TTAATTTTAAAGAAAAAATAGAGAAAATTGGTTTAATCATCAATTCAATGAATTTTTTAGTCCGA
55131113 ATAAGTACCCAATAGGTTCTAGATCCAACTTG
66 ATAAGTACCCAATAGGTTCTAGATCCAACTTG
55131145 TTAATTTTAAAGAAAAAATAGAGAAAATTGGTTTAATCATCAATTCAATGAATTTTTTAGTCCGA
1 TTAATTTTAAAGAAAAAATAGAGAAAATTGGTTTAATCATCAATTCAATGAATTTTTTAGTCCGA
55131210 ATAAGTACCCAATAGGTTCTAGATCCAACTTG
66 ATAAGTACCCAATAGGTTCTAGATCCAACTTG
55131242 TTAA
1 TTAA
55131246 AACATATTTC
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (97 bp):
TTAATTTTAAAGAAAAAATAGAGAAAATTGGTTTAATCATCAATTCAATGAATTTTTTAGTCCGA
ATAAGTACCCAATAGGTTCTAGATCCAACTTG
Found at i:55133200 original size:22 final size:22
Alignment explanation
Indices: 55133157--55133201 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
55133147 TTAGATATAG
* *
55133157 ATTTTAATTATGTATAATTTTT
1 ATTTTAATTATGTAGAAGTTTT
* *
55133179 ATTTTTATTATTTAGAAGTTTT
1 ATTTTAATTATGTAGAAGTTTT
55133201 A
1 A
55133202 AGCTTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
ATTTTAATTATGTAGAAGTTTT
Found at i:55136661 original size:21 final size:19
Alignment explanation
Indices: 55136605--55136663 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 19
55136595 ATTGTTCTAG
55136605 AATTTTTTTT-AATTTTTT
1 AATTTTTTTTAAATTTTTT
* *
55136623 AACTTTCTTTATATATTTTTT
1 AA-TTT-TTTTTAAATTTTTT
55136644 AGATTTTTTTTAGAATTTTT
1 A-ATTTTTTTTA-AATTTTT
55136664 ATAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 9 0.28
21 17 0.53
22 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
AATTTTTTTTAAATTTTTT
Found at i:55136721 original size:20 final size:20
Alignment explanation
Indices: 55136683--55136720 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55136673 TAAAAATTTA
*
55136683 AAAATTAGTTTGAACTTTTG
1 AAAATTAGTTTAAACTTTTG
*
55136703 AAAATTATTTTAAA-TTTT
1 AAAATTAGTTTAAACTTTT
55136721 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
AAAATTAGTTTAAACTTTTG
Found at i:55138506 original size:79 final size:79
Alignment explanation
Indices: 55138388--55138539 Score: 268
Period size: 79 Copynumber: 1.9 Consensus size: 79
55138378 ACTCTCACTG
*
55138388 TATAAAGATAAATATTAGATTAAATTTAATATTAAAATAATTAAGTTTAATCATAGTTGAACGCT
1 TATAAAGATAAATATTAGATTAAATTTAATATTAAAATAATTAAGTTTAATCATAGTTCAACGCT
55138453 CTAAACTCCCCCTA
66 CTAAACTCCCCCTA
* * *
55138467 TATAAGGATAAATATTAGATTAAATTTAATATTAAAATAATTAAGTTTAATTATAGTTCAACTCT
1 TATAAAGATAAATATTAGATTAAATTTAATATTAAAATAATTAAGTTTAATCATAGTTCAACGCT
55138532 CTAAACTC
66 CTAAACTC
55138540 ATTGTGAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (79 bp):
TATAAAGATAAATATTAGATTAAATTTAATATTAAAATAATTAAGTTTAATCATAGTTCAACGCT
CTAAACTCCCCCTA
Found at i:55145676 original size:66 final size:67
Alignment explanation
Indices: 55145561--55145765 Score: 295
Period size: 66 Copynumber: 3.0 Consensus size: 67
55145551 ATAAAGATAA
* *
55145561 ATATTAGATTAAATTTAACATTAAAGCAATTAAATTTAATCATAGTTGAACTCTCTAAACTCTCT
1 ATATTAGATTAAATTTAATATTAAAGCAATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCT
55145626 AT
66 AT
* * *
55145628 ATATTAGATTAAATTTAATATTTAA-CAATTAAGTTTAATCATAATTGAACTCTCTAAACTCTCC
1 ATATTAGATTAAATTTAATATTAAAGCAATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCT
55145692 AT
66 AT
* * * * *
55145694 ATATAAACATTAAATTTAATATTAAAGTAATTAAGTTTAATTATAGTTGAACTCTCTAAACTCAC
1 ATAT-TAGATTAAATTTAATATTAAAGCAATTAAGTTTAATCATAGTTGAACTCTCTAAACTC-T
55145759 CTAT
64 CTAT
55145763 ATA
1 ATA
55145766 AAGAGTCTTG
Statistics
Matches: 122, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
66 42 0.34
67 41 0.34
68 33 0.27
69 6 0.05
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (67 bp):
ATATTAGATTAAATTTAATATTAAAGCAATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCT
AT
Found at i:55159631 original size:22 final size:22
Alignment explanation
Indices: 55159603--55159650 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
55159593 CTCTCTAATC
55159603 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
55159625 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
55159647 CTCT
1 CTCT
55159651 GAAACCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:55159681 original size:51 final size:51
Alignment explanation
Indices: 55159625--55159737 Score: 181
Period size: 51 Copynumber: 2.2 Consensus size: 51
55159615 TTCCAAAATT
*
55159625 CTCTCAATTTCCTTCCAAAATTCTCTGAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
* * *
55159676 CTCTCAATTTCCTTCGAAATTTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
55159727 CCCTCAATTTC
1 CTCTCAATTTC
55159738 ATTTTTTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.27, C:0.28, G:0.02, T:0.42
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
Found at i:55159872 original size:18 final size:19
Alignment explanation
Indices: 55159849--55159907 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
55159839 TAAGTATTAA
55159849 ATTTA-ATTTTTAATTATT
1 ATTTAGATTTTTAATTATT
*
55159867 ATTTAAGATTTTT-TTTATT
1 ATTT-AGATTTTTAATTATT
* *
55159886 -TATATATTTTTATATTATT
1 ATTTAGATTTTTA-ATTATT
55159905 ATT
1 ATT
55159908 AATTTATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 7 0.23
18 6 0.19
19 11 0.35
20 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTAGATTTTTAATTATT
Found at i:55160867 original size:7 final size:7
Alignment explanation
Indices: 55160855--55160879 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55160845 AGTCGATTGA
55160855 TATTTAG
1 TATTTAG
55160862 TATTTAG
1 TATTTAG
55160869 TATTTAG
1 TATTTAG
55160876 TATT
1 TATT
55160880 ATGTATATAA
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:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:55161556 original size:18 final size:18
Alignment explanation
Indices: 55161530--55161564 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55161520 AGGTGTGTTT
* *
55161530 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
55161548 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
55161565 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:55161802 original size:132 final size:132
Alignment explanation
Indices: 55161565--55161807 Score: 398
Period size: 132 Copynumber: 1.8 Consensus size: 132
55161555 CTTACATGTA
* * *
55161565 TCCTTTTCCGAATACTATGGCAGGTTGGAGCCAAATGCCCGATTCAGCTCCATTTCCTGTGATGC
1 TCCTTTTCCGAATACTATGGCAAGTTGGAGCCAAATGCCAGATTCAACTCCATTTCCTGTGATGC
** * *
55161630 CGAGCGGGCCGTCGATATCTAGGCCAGCGGCGCAGGAGGGATCGCAAGGGGGGCCGTCGGAGAGC
66 CGAGCGAACCGTCCATATCTAGGCCAACGGCGCAGGAGGGATCGCAAGGGGGGCCGTCGGAGAGC
55161695 TC
131 TC
*
55161697 TCCTTTTCCGAATACTATGGCAAGTTGGAGCCAAATGCCTAG-TTCAACTCCATTTCCTGTTATG
1 TCCTTTTCCGAATACTATGGCAAGTTGGAGCCAAATGCC-AGATTCAACTCCATTTCCTGTGATG
55161761 CCGAGCGAACCGTCCATATCTAGGCCAACGGCGCAGGAGGGATCGCA
65 CCGAGCGAACCGTCCATATCTAGGCCAACGGCGCAGGAGGGATCGCA
55161808 CATACCTTCG
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
132 101 0.99
133 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (132 bp):
TCCTTTTCCGAATACTATGGCAAGTTGGAGCCAAATGCCAGATTCAACTCCATTTCCTGTGATGC
CGAGCGAACCGTCCATATCTAGGCCAACGGCGCAGGAGGGATCGCAAGGGGGGCCGTCGGAGAGC
TC
Found at i:55167207 original size:138 final size:137
Alignment explanation
Indices: 55167049--55167472 Score: 627
Period size: 138 Copynumber: 3.1 Consensus size: 137
55167039 ACATAGATAA
* *
55167049 AATTAATATATTAATTTGATTCATACAAGATATTAATTGTATATATTTTAATGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAATGAATTTATTAATA
* * *
55167114 TAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTACTATTATTTTGAA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTG-A
55167179 AAGAATAT
130 AAGAATAT
* ***
55167187 AATTAATATATGAATTTGATTCATACAAAATATTAATTTTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAATGAATTTATTAATA
* * *
55167252 TAAACAGTTGTATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGAA
55167317 AGAAATAT
131 AG-AATAT
55167325 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTT-ATCGAATTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAAT-GAATTTATTAAT
* * *
55167389 ATAAATAAATTTATTAATTAATTAATTTCGGTCAAAATATAAAAGATATGGAAATTAATATTCTT
65 AT-AA-ACAGTTA-T-ATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
55167454 TTGGAAA-AATAT
126 TT-GAAAGAATAT
55167466 AATTAAT
1 AATTAAT
55167473 TTGTTCTAAC
Statistics
Matches: 257, Mismatches: 22, Indels: 11
0.89 0.08 0.04
Matches are distributed among these distances:
137 3 0.01
138 183 0.71
139 2 0.01
140 4 0.02
141 13 0.05
142 49 0.19
143 3 0.01
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (137 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAATGAATTTATTAATA
TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGAA
AGAATAT
Found at i:55167529 original size:75 final size:75
Alignment explanation
Indices: 55167446--55167591 Score: 249
Period size: 75 Copynumber: 1.9 Consensus size: 75
55167436 ATGGAAATTA
*
55167446 ATATTCTTTTGGAAA-AATATAATTAATTTGTTCTAACTTTCCATTTGTCTTCTCTATTAATAAG
1 ATATTCTTTTGGAAAGAATATAATT-ATTTGTTCTAACTTTCAATTTGTCTTCTCTATTAATAAG
55167510 GGAATAATGAT
65 GGAATAATGAT
* *
55167521 ATATTCTTTTGGAAAGAATATAATTCTTTTTTCTAACTTTCAATTTGTCTTCTCTATTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTATTTGTTCTAACTTTCAATTTGTCTTCTCTATTAATAAGG
55167586 GAATAA
66 GAATAA
55167592 ACCTGGTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
75 58 0.87
76 9 0.13
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATATAATTATTTGTTCTAACTTTCAATTTGTCTTCTCTATTAATAAGG
GAATAATGAT
Found at i:55186407 original size:26 final size:27
Alignment explanation
Indices: 55186378--55186434 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
55186368 AATTATGTGT
55186378 TAATTTC-AAGACTTATGTAATGTTTG
1 TAATTTCAAAGACTTATGTAATGTTTG
* *
55186404 TAA-TTCAAATACTTATGTAATGTTTT
1 TAATTTCAAAGACTTATGTAATGTTTG
55186430 TAATT
1 TAATT
55186435 ATGTAGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 3 0.11
26 23 0.85
27 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (27 bp):
TAATTTCAAAGACTTATGTAATGTTTG
Found at i:55200306 original size:12 final size:12
Alignment explanation
Indices: 55200289--55200315 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55200279 ACGATTTTTT
55200289 TTTGTTTATTTA
1 TTTGTTTATTTA
55200301 TTTGTTTATTTA
1 TTTGTTTATTTA
55200313 TTT
1 TTT
55200316 TTTTCTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTGTTTATTTA
Found at i:55201210 original size:24 final size:25
Alignment explanation
Indices: 55201155--55201210 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
55201145 TCATATCTTT
* * *
55201155 GAAGTTATTGTGTATTATTATTCTA
1 GAAGTTATTATGCATTATTACTCTA
*
55201180 -AAATTATTATGCATTATTACT-TA
1 GAAGTTATTATGCATTATTACTCTA
55201203 GAAGTTAT
1 GAAGTTAT
55201211 GCTGTATTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (25 bp):
GAAGTTATTATGCATTATTACTCTA
Found at i:55202775 original size:9 final size:9
Alignment explanation
Indices: 55202751--55202787 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55202741 TGAGTTTTCG
*
55202751 AATTCAAAT
1 AATTCGAAT
*
55202760 AACTCGAAT
1 AATTCGAAT
55202769 AATTCGAAT
1 AATTCGAAT
55202778 AATTCGAAT
1 AATTCGAAT
55202787 A
1 A
55202788 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55212462 original size:27 final size:26
Alignment explanation
Indices: 55212414--55212464 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
55212404 TAGAATTAAT
*
55212414 TTGTTATTCATCATTTGCTTTGTATA
1 TTGTTAATCATCATTTGCTTTGTATA
55212440 TTGTTAATCAATCATGTTG-TTTGTA
1 TTGTTAATC-ATCAT-TTGCTTTGTA
55212465 AGAATATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.55
Consensus pattern (26 bp):
TTGTTAATCATCATTTGCTTTGTATA
Found at i:55222240 original size:19 final size:19
Alignment explanation
Indices: 55222216--55222253 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
55222206 ATAAAAGAAT
55222216 AAAAA-TTTAAAAAACTATA
1 AAAAATTTTAAAAAA-TATA
55222235 AAAAATTTTAAAAAATATA
1 AAAAATTTTAAAAAATATA
55222254 TATCCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTTTAAAAAATATA
Found at i:55222857 original size:25 final size:26
Alignment explanation
Indices: 55222820--55222874 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
55222810 TTCCTTTCTC
* *
55222820 TTTTATGA-TTTTTATTTTT-TTATAT
1 TTTTATAACTTTTAATTTTTATT-TAT
55222845 TTTTATAACTTTTGAATTTTTATTTAT
1 TTTTATAACTTTT-AATTTTTATTTAT
55222872 TTT
1 TTT
55222875 CAAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 12 0.48
28 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTATAACTTTTAATTTTTATTTAT
Found at i:55222874 original size:17 final size:17
Alignment explanation
Indices: 55222820--55222874 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
55222810 TTCCTTTCTC
55222820 TTTTATGATTTTTATTT-
1 TTTTAT-ATTTTTATTTA
*
55222837 TTTTATATTTTTA-TAA
1 TTTTATATTTTTATTTA
55222853 CTTTTGA-ATTTTTATTTA
1 -TTTT-ATATTTTTATTTA
55222871 TTTT
1 TTTT
55222875 CAAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 1 0.03
16 7 0.22
17 21 0.66
18 3 0.09
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (17 bp):
TTTTATATTTTTATTTA
Found at i:55233937 original size:18 final size:18
Alignment explanation
Indices: 55233856--55233929 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
55233846 CCTAAAGCTC
*
55233856 TCATGCATTCTTCTCCCT
1 TCATCCATTCTTCTCCCT
*
55233874 TCATCCGTTCTTCTCCCT
1 TCATCCATTCTTCTCCCT
* ***
55233892 TCATCCAGTAAGCTCCCT
1 TCATCCATTCTTCTCCCT
55233910 TCATCCATTCTTCTCCCT
1 TCATCCATTCTTCTCCCT
55233928 TC
1 TC
55233930 CTTCATTCCT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.12, C:0.42, G:0.05, T:0.41
Consensus pattern (18 bp):
TCATCCATTCTTCTCCCT
Found at i:55236072 original size:13 final size:13
Alignment explanation
Indices: 55236054--55236081 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55236044 CTTGTACAAG
55236054 TAAACTTCATAAA
1 TAAACTTCATAAA
55236067 TAAACTTCATAAA
1 TAAACTTCATAAA
55236080 TA
1 TA
55236082 GAGAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTTCATAAA
Found at i:55236521 original size:14 final size:15
Alignment explanation
Indices: 55236499--55236575 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
55236489 AATCAAAACA
55236499 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
55236513 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
55236528 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
55236548 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
55236562 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
55236576 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:55236540 original size:20 final size:20
Alignment explanation
Indices: 55236515--55236554 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55236505 AATATTTTCC
*
55236515 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55236535 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55236555 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55236560 original size:34 final size:35
Alignment explanation
Indices: 55236503--55236569 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
55236493 AAAACACCAG
*
55236503 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
55236538 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55236570 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55236576 original size:14 final size:14
Alignment explanation
Indices: 55236538--55236577 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55236528 ACAGAAAAGT
*
55236538 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
55236552 AAATCATTTTACGG
1 AAAACATTTTACAG
55236566 AAAACATTTTAC
1 AAAACATTTTAC
55236578 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:55237893 original size:25 final size:25
Alignment explanation
Indices: 55237860--55237907 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
55237850 GACCACTAAG
55237860 TTTTCTATTCGTGTGCACCTATAAT
1 TTTTCTATTCGTGTGCACCTATAAT
*
55237885 TTTTCTATTCGTGTGGACCTATA
1 TTTTCTATTCGTGTGCACCTATA
55237908 TAAAGCCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (25 bp):
TTTTCTATTCGTGTGCACCTATAAT
Found at i:55240119 original size:42 final size:42
Alignment explanation
Indices: 55240072--55240236 Score: 152
Period size: 42 Copynumber: 3.9 Consensus size: 42
55240062 GAGTTTAAGA
* * *
55240072 TTAACCCTTCTGGGTTTCAGTTTAGCTCTTTTGAGCTTCAGT
1 TTAACCCTTATGGGTTTCAGCTTAGCTCTTATGAGCTTCAGT
* ** * * * *
55240114 TTAACCCTAATAAGTTTTAGCTTAGCTCTTCTAAGCTTCAGA
1 TTAACCCTTATGGGTTTCAGCTTAGCTCTTATGAGCTTCAGT
* * *
55240156 TTAACCCTTATGGGTTTCCGCTTAGTTCCTATGAGCTTCCA-T
1 TTAACCCTTATGGGTTTCAGCTTAGCTCTTATGAGCTT-CAGT
* * * * *
55240198 TTAACCCTTACGGGTTTCCGTTTAGCACTTATGTGCTTC
1 TTAACCCTTATGGGTTTCAGCTTAGCTCTTATGAGCTTC
55240237 TGTGCAGTCT
Statistics
Matches: 97, Mismatches: 25, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
41 1 0.01
42 94 0.97
43 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (42 bp):
TTAACCCTTATGGGTTTCAGCTTAGCTCTTATGAGCTTCAGT
Found at i:55244393 original size:16 final size:16
Alignment explanation
Indices: 55244372--55244415 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
55244362 AAATAGGGTC
55244372 GTATGACCGTGACAGA
1 GTATGACCGTGACAGA
*
55244388 GTATGACCGTGATAGA
1 GTATGACCGTGACAGA
*
55244404 GTATGAACGTGA
1 GTATGACCGTGA
55244416 GTTCGTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.23
Consensus pattern (16 bp):
GTATGACCGTGACAGA
Found at i:55252607 original size:17 final size:17
Alignment explanation
Indices: 55252585--55252620 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55252575 AATTTTTTTC
55252585 TATTTTTTTATAGAAAA
1 TATTTTTTTATAGAAAA
*
55252602 TATTTTTTTATGGAAAA
1 TATTTTTTTATAGAAAA
55252619 TA
1 TA
55252621 AAAAAAGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (17 bp):
TATTTTTTTATAGAAAA
Found at i:55253300 original size:25 final size:24
Alignment explanation
Indices: 55253272--55253330 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
55253262 CGTACTTAAT
* *
55253272 TAAAAAAATAGATTATTTTTATAAA
1 TAAAAAAATAGAATATTTTGAT-AA
*
55253297 TAAAAAAATTGAATATTTTGATAA
1 TAAAAAAATAGAATATTTTGATAA
55253321 TAAAAAAATA
1 TAAAAAAATA
55253331 TATGGTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (24 bp):
TAAAAAAATAGAATATTTTGATAA
Found at i:55253315 original size:24 final size:25
Alignment explanation
Indices: 55253272--55253330 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
55253262 CGTACTTAAT
*
55253272 TAAAAAAATAGATTATTTTT-ATAAA
1 TAAAAAAATAGAATATTTTTGAT-AA
*
55253297 TAAAAAAATTGAATA-TTTTGATAA
1 TAAAAAAATAGAATATTTTTGATAA
55253321 TAAAAAAATA
1 TAAAAAAATA
55253331 TATGGTTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.50
25 15 0.50
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (25 bp):
TAAAAAAATAGAATATTTTTGATAA
Found at i:55257930 original size:46 final size:46
Alignment explanation
Indices: 55257863--55258093 Score: 356
Period size: 46 Copynumber: 5.0 Consensus size: 46
55257853 CATGGCAAAG
* *
55257863 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* * *
55257909 TGTGAAAAGTATGTATGGTATTTCGGTAAAGAAAACCATGCTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* *
55257955 TGTGAAAAGTAGGTATGGTATTTCGGT-AAAAAAACCATAATGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
* *
55258000 TGTGAAAAGTAGGTATGATGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
*
55258046 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAG-AAAACCATACTGAGT
55258093 T
1 T
55258094 ATAGCAATGT
Statistics
Matches: 167, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
45 40 0.24
46 111 0.66
47 16 0.10
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGT
Found at i:55258016 original size:91 final size:92
Alignment explanation
Indices: 55257863--55258093 Score: 356
Period size: 91 Copynumber: 2.5 Consensus size: 92
55257853 CATGGCAAAG
* * * *
55257863 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAAGTATGTATGGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAAAAAACCATACTGAGTTGTGAAAAGTAGGTATGAT
*
55257928 ATTTCGGTAAAGAAAACCATGCTGAGT
66 ATTTCGGTAAAGAAAACCATACTGAGT
* *
55257955 TGTGAAAAGTAGGTATGGTATTTCGGT-AAAAAAACCATAATGAGTTGTGAAAAGTAGGTATGAT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAAAAAACCATACTGAGTTGTGAAAAGTAGGTATGAT
* *
55258019 GTTTCGGTGAAGAAAACCATACTGAGT
66 ATTTCGGTAAAGAAAACCATACTGAGT
*
55258046 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAAACCATACTGAGTT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAA-AAAAACCATACTGAGTT
55258094 ATAGCAATGT
Statistics
Matches: 126, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
91 83 0.66
92 27 0.21
93 16 0.13
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (92 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAAAAAACCATACTGAGTTGTGAAAAGTAGGTATGAT
ATTTCGGTAAAGAAAACCATACTGAGT
Found at i:55263085 original size:23 final size:23
Alignment explanation
Indices: 55263059--55263133 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
55263049 AATAGTGCCA
55263059 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55263082 CACTGA-ATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55263104 CACTGAGATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55263127 CACTGAT
1 CACTGAT
55263134 CAATAATACT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 21 0.44
23 27 0.56
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:55271905 original size:20 final size:20
Alignment explanation
Indices: 55271864--55271912 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
55271854 ATATACATAT
*
55271864 ATATAAAT-AGATAAATAAA
1 ATATAAATAACATAAATAAA
* *
55271883 ATATAAATAACATAATTACA
1 ATATAAATAACATAAATAAA
*
55271903 ATATCAATAA
1 ATATAAATAA
55271913 GGCTAGTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAAATAACATAAATAAA
Found at i:55279133 original size:23 final size:23
Alignment explanation
Indices: 55279107--55279153 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
55279097 ACTGCCAATA
55279107 TATTAGTTATTGGTTTCTCTCTT
1 TATTAGTTATTGGTTTCTCTCTT
55279130 TATTAGTTATTGGTTTCTCTCTT
1 TATTAGTTATTGGTTTCTCTCTT
55279153 T
1 T
55279154 CTTGAGTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.62
Consensus pattern (23 bp):
TATTAGTTATTGGTTTCTCTCTT
Found at i:55285894 original size:19 final size:19
Alignment explanation
Indices: 55285870--55285942 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
55285860 AATCTTCAGG
55285870 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55285889 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
55285908 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55285927 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
55285943 AGATATGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55285968 original size:22 final size:21
Alignment explanation
Indices: 55285870--55285968 Score: 93
Period size: 19 Copynumber: 4.9 Consensus size: 21
55285860 AATCTTCAGG
*
55285870 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
55285889 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
55285908 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
55285927 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
55285949 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
55285969 TTAATTTGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
19 47 0.67
22 12 0.17
23 11 0.16
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.38
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:55288850 original size:24 final size:24
Alignment explanation
Indices: 55288823--55288868 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
55288813 AGAACAATCC
* *
55288823 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
55288847 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
55288869 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:55290596 original size:210 final size:210
Alignment explanation
Indices: 55290234--55290657 Score: 848
Period size: 210 Copynumber: 2.0 Consensus size: 210
55290224 CACATTTGAT
55290234 AATGGAGGTGAATGGGATGTATGAAGAAATGTTGAGAGGCGTTCACATCAATGCCATTTTTGAAG
1 AATGGAGGTGAATGGGATGTATGAAGAAATGTTGAGAGGCGTTCACATCAATGCCATTTTTGAAG
55290299 ACACAATTTGCAAGGGTCCTTGAAGATATTCGCCCTTATCAACTTAGAAGTGTTCTAAGTAATTG
66 ACACAATTTGCAAGGGTCCTTGAAGATATTCGCCCTTATCAACTTAGAAGTGTTCTAAGTAATTG
55290364 AACTGCGGAAGAAATATCTGTAGTTTTTTAGAGCTTATTTAGAGTAATGTTCAGAACAATTTTGT
131 AACTGCGGAAGAAATATCTGTAGTTTTTTAGAGCTTATTTAGAGTAATGTTCAGAACAATTTTGT
55290429 TATTTTTAGCCTAAA
196 TATTTTTAGCCTAAA
55290444 AATGGAGGTGAATGGGATGTATGAAGAAATGTTGAGAGGCGTTCACATCAATGCCATTTTTGAAG
1 AATGGAGGTGAATGGGATGTATGAAGAAATGTTGAGAGGCGTTCACATCAATGCCATTTTTGAAG
55290509 ACACAATTTGCAAGGGTCCTTGAAGATATTCGCCCTTATCAACTTAGAAGTGTTCTAAGTAATTG
66 ACACAATTTGCAAGGGTCCTTGAAGATATTCGCCCTTATCAACTTAGAAGTGTTCTAAGTAATTG
55290574 AACTGCGGAAGAAATATCTGTAGTTTTTTAGAGCTTATTTAGAGTAATGTTCAGAACAATTTTGT
131 AACTGCGGAAGAAATATCTGTAGTTTTTTAGAGCTTATTTAGAGTAATGTTCAGAACAATTTTGT
55290639 TATTTTTAGCCTAAA
196 TATTTTTAGCCTAAA
55290654 AATG
1 AATG
55290658 ATAAAAATTC
Statistics
Matches: 214, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 214 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (210 bp):
AATGGAGGTGAATGGGATGTATGAAGAAATGTTGAGAGGCGTTCACATCAATGCCATTTTTGAAG
ACACAATTTGCAAGGGTCCTTGAAGATATTCGCCCTTATCAACTTAGAAGTGTTCTAAGTAATTG
AACTGCGGAAGAAATATCTGTAGTTTTTTAGAGCTTATTTAGAGTAATGTTCAGAACAATTTTGT
TATTTTTAGCCTAAA
Found at i:55291331 original size:6 final size:6
Alignment explanation
Indices: 55291314--55291348 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
55291304 AAAAGGGATG
*
55291314 ACAAAA AAAAAA ACAAAA ACAAAA A-AAAA ACAAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA
55291349 TCTACCAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Done.