Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold792
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: 24561
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Found at i:9628 original size:1 final size:1
Alignment explanation
Indices: 9622--9732 Score: 96
Period size: 1 Copynumber: 111.0 Consensus size: 1
9612 AGCGTCCTCC
* * * ** ** *
9622 AAAAAAACAAAAAAAAAAAAAACAAAACAAAAAAAACGAAAAAAATGAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
9687 AAAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9733 GGGGGTCCGG
Statistics
Matches: 84, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.87, C:0.09, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:9666 original size:40 final size:37
Alignment explanation
Indices: 9622--9732 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 37
9612 AGCGTCCTCC
9622 AAAAAAACAAAAAAAAAAAAAACAAAACAAAAAAAACGA
1 AAAAAAACAAAAAAAAAAAAAACAAAACAAAAAAAA--A
**
9661 AAAAAATGAAAAAACAAAAAAAA-AAAA-AAAAAAAAA
1 AAAAAAACAAAAAA-AAAAAAAACAAAACAAAAAAAAA
* * *
9697 ACAAAAACAATAAAAAAACAAACAAAAACAAAAAAA
1 AAAAAAACAAAAAAAAAAAAAAC-AAAACAAAAAAA
9733 GGGGGTCCGG
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
35 7 0.11
36 11 0.18
37 4 0.07
38 15 0.25
39 16 0.26
40 8 0.13
ACGTcount: A:0.87, C:0.09, G:0.02, T:0.02
Consensus pattern (37 bp):
AAAAAAACAAAAAAAAAAAAAACAAAACAAAAAAAAA
Found at i:9678 original size:46 final size:44
Alignment explanation
Indices: 9622--9732 Score: 145
Period size: 46 Copynumber: 2.5 Consensus size: 44
9612 AGCGTCCTCC
*
9622 AAAAAAACAAAAAAAAAAAAAACAAAACAAA-AAAAACGAA-AAAA
1 AAAAAAACAAAAAAAAAAAAAA-AAAAAAAACAAAAAC-AATAAAA
9666 ATGAAAAAACAAAAAAAAAAAAAAAAAAAAAACAAAAACAATAAAA
1 A--AAAAAACAAAAAAAAAAAAAAAAAAAAAACAAAAACAATAAAA
* *
9712 AAACAAACAAAAACAAAAAAA
1 AAAAAAACAAAAAAAAAAAAA
9733 GGGGGTCCGG
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
44 19 0.32
45 9 0.15
46 32 0.53
ACGTcount: A:0.87, C:0.09, G:0.02, T:0.02
Consensus pattern (44 bp):
AAAAAAACAAAAAAAAAAAAAAAAAAAAAACAAAAACAATAAAA
Found at i:11478 original size:88 final size:87
Alignment explanation
Indices: 11170--11607 Score: 476
Period size: 88 Copynumber: 5.0 Consensus size: 87
11160 CATTCATCAC
* * * ** * **
11170 CCTTCAAAAGTCCACAAGTCAGTGGCA-TATTCTTCAAAGCCCACAAGTTAGTGGCATTTTTTTC
1 CCTTTAAAAGCCCACAAGTTAGTGGCACCCTT-TTCAAAGCCCACAAGTCAGTGGCATACTTTTC
11234 AAAAGCCCACAAGTCAGTGGCAA
65 AAAAGCCCACAAGTCAGTGGCAA
* * * *
11257 CC-TTCAAAGCCCACAAATTAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCAT-CTTTTC
1 CCTTTAAAAGCCCACAAGTTAGTGGCACCCTTTT-CAAAGCCCACAAGTCAGTGGCATACTTTTC
* * * * *
11320 CAAAGTCCACAACTCCGTGGCACT
65 AAAAGCCCACAAGTCAGTGGCA-A
**
11344 CTTTTTCTTTTGTAAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATA
1 C-----C-TTTAAAAGCCCACAAGTTAGTGGCACCCTTTTC-AAAGCCCACAAGTCAGTGGCATA
*
11409 GTTTTCAAAAGCCCACAAGTCAGTGGCAA
59 CTTTTCAAAAGCCCACAAGTCAGTGGCAA
*
11438 CCTTTAAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTC
1 CCTTTAAAAGCCCACAAGTTAGTGGCACCCTTTTC-AAAGCCCACAAGTCAGTGGCATACTTTTC
11503 AAAAGCCCACAAGTCAGTGGCAA
65 AAAAGCCCACAAGTCAGTGGCAA
* * * * * *
11526 CCTTTAAAAACCCACAAGTCAGTGGCAACC--TTCAAAGCCCACAAATCAGTGGCA-CCCTTT-A
1 CCTTTAAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATACTTTTCA
*
11587 AAAGCCCACAAGTCGGTGGCA
66 AAAGCCCACAAGTCAGTGGCA
11608 CATTTTCCAT
Statistics
Matches: 301, Mismatches: 38, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
83 21 0.07
84 3 0.01
85 20 0.07
86 47 0.16
87 25 0.08
88 110 0.37
89 1 0.00
92 1 0.00
93 1 0.00
94 49 0.16
95 23 0.08
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (87 bp):
CCTTTAAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATACTTTTCA
AAAGCCCACAAGTCAGTGGCAA
Found at i:11608 original size:28 final size:29
Alignment explanation
Indices: 11172--11607 Score: 379
Period size: 30 Copynumber: 14.9 Consensus size: 29
11162 TTCATCACCC
* *
11172 TTCAAAAGTCCACAAGTCAGTGGCATA-TT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCT
* ***
11201 CTTC-AAAGCCCACAAGTTAGTGGCATTTTT
1 -TTCAAAAGCCCACAAGTCAGTGGCA-ACCT
11231 TTCAAAAGCCCACAAGTCAGTGGCAACC-
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* * *
11259 TTC-AAAGCCCACAAATTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
** * * *
11288 TTCCGAAGCCCACAAGTCGGTGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* * * *
11317 TTCCAAAGTCCACAACTCCGTGGC-ACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-C--T
** * *
11348 TTCTTTTGTAAGCCCACAAGTTAGTGGCACCCTT
1 TTC----AAAAGCCCACAAGTCAGTGGCAACC-T
**
11382 TTCAAAAGCCCACAAGTCAGTGGCATAGTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCT
11412 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* *
11441 TT-AAAAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
**
11470 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCT
11500 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
*
11529 TT-AAAAACCCACAAGTCAGTGGCAACC-
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
* *
11556 TTC-AAAGCCCACAAATCAGTGGCACCCT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCT
*
11584 TT-AAAAGCCCACAAGTCGGTGGCA
1 TTCAAAAGCCCACAAGTCAGTGGCA
11608 CATTTTCCAT
Statistics
Matches: 335, Mismatches: 51, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
27 44 0.13
28 72 0.21
29 58 0.17
30 135 0.40
31 4 0.01
34 5 0.01
35 16 0.05
36 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (29 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:11667 original size:43 final size:43
Alignment explanation
Indices: 11618--11707 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
11608 CATTTTCCAT
* *
11618 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGATGACCTTGAATCAGCACATTGGCAC
* *
11661 CTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGATGACCTTGAATCAGCACATTGGCAC
11704 CTTT
1 CTTT
11708 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGATGACCTTGAATCAGCACATTGGCAC
Found at i:11739 original size:52 final size:53
Alignment explanation
Indices: 11661--11814 Score: 175
Period size: 52 Copynumber: 2.9 Consensus size: 53
11651 ACATTGGCAC
*
11661 CTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTTTCTCAG
* * * * *
11713 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAG
* * * * * *
11768 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTT
11815 ATCACTTTTC
Statistics
Matches: 83, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
52 37 0.45
53 5 0.06
54 6 0.07
55 35 0.42
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTTTCTCAG
Found at i:12593 original size:13 final size:13
Alignment explanation
Indices: 12575--12599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12565 CATAAAGTGT
12575 TGTATCGATACAA
1 TGTATCGATACAA
12588 TGTATCGATACA
1 TGTATCGATACA
12600 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12597 original size:33 final size:33
Alignment explanation
Indices: 12555--12621 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12545 TTCAACGATT
12555 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
12588 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
12621 T
1 T
12622 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:12724 original size:52 final size:52
Alignment explanation
Indices: 12682--12862 Score: 344
Period size: 52 Copynumber: 3.5 Consensus size: 52
12672 CACTGATCTT
12682 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
12734 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
12786 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
12838 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
12863 TCATATTTCG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 127 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:15746 original size:28 final size:28
Alignment explanation
Indices: 15713--15782 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
15703 TCATAATTGA
**
15713 AGATACTCTAACCCCGTTATTTCATCGG
1 AGATACTCTAACCCCGTTATTTCAGAGG
* * *
15741 AGATACTCCAACCTCGTTATTTCCGAGG
1 AGATACTCTAACCCCGTTATTTCAGAGG
*
15769 GGATACTCTAACCC
1 AGATACTCTAACCC
15783 TGGCTTTATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.29
Consensus pattern (28 bp):
AGATACTCTAACCCCGTTATTTCAGAGG
Found at i:15877 original size:28 final size:28
Alignment explanation
Indices: 15823--15891 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
15813 TAATCAAGGG
**
15823 TACTCCAACCCCGTTATGTCATCGAGGA
1 TACTCCAACCCCGTTATGTCAGAGAGGA
* * *
15851 TACTCCAATCCCGTTATTTCCGAGAGGA
1 TACTCCAACCCCGTTATGTCAGAGAGGA
*
15879 TACTCCGACCCCG
1 TACTCCAACCCCG
15892 ATTTTATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (28 bp):
TACTCCAACCCCGTTATGTCAGAGAGGA
Found at i:15916 original size:107 final size:107
Alignment explanation
Indices: 15666--15938 Score: 302
Period size: 107 Copynumber: 2.6 Consensus size: 107
15656 ACGTTACGAC
* * * * * *
15666 ACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCATAATTGAA-GATACTCTAACCCCGT
1 ACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAA-TCAAGGGTACTCCAACCCCGT
* *
15730 TATTTCATCGGAGATACTCCAACCTCGTTATTTCCGAGGGGAT
65 TATGTCATCGGAGATACTCCAACCTCGTTATTTCCGAGAGGAT
* * ** * ***
15773 ACTCTAACCCTGGCTTTATATCTAAAATATTGATTTTTCATAATCAAGGGTACTCCAACCCCGTT
1 ACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATCAAGGGTACTCCAACCCCGTT
15838 ATGTCATC-GAGGATACTCCAATCC-CGTTATTTCCGAGAGGAT
66 ATGTCATCGGA-GATACTCCAA-CCTCGTTATTTCCGAGAGGAT
* * * *
15880 ACTCCGACCCCGATTTTATTTTTAAAATACCAATTTTTCACAATC-GGGGATACTCCAAC
1 ACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATCAAGGG-TACTCCAAC
15939 TCTGATTTTA
Statistics
Matches: 134, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
106 8 0.06
107 124 0.93
108 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (107 bp):
ACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATCAAGGGTACTCCAACCCCGTT
ATGTCATCGGAGATACTCCAACCTCGTTATTTCCGAGAGGAT
Found at i:15946 original size:51 final size:51
Alignment explanation
Indices: 15876--16043 Score: 176
Period size: 51 Copynumber: 3.3 Consensus size: 51
15866 ATTTCCGAGA
* ** * *
15876 GGATACTCCGACCCCGATTTTATTTTTAAAATACCAATTTTTCACAATCGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGG
* * *
15927 GGATACTCCAACTCTGATTTTATTTCCAAAACACTAATTTCTCACAATCGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGG
*** * * * *
15978 GGATACTCCAAACCCCGGCCTTATTTCTAAAGCATCGATTTACT-ACAATCGG
1 GGATACTCC-AACCCCGATTTTATTTCCAAAACACCAATTT-CTCACAATCGG
16030 GGATACTCCAACCC
1 GGATACTCCAACCC
16044 TGTTATTTTT
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
51 57 0.59
52 38 0.39
53 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGG
Found at i:17192 original size:112 final size:110
Alignment explanation
Indices: 16995--17199 Score: 268
Period size: 112 Copynumber: 1.8 Consensus size: 110
16985 TTATACATTT
* * *
16995 TGATCCATTCGTGCCTAGGAAAATAGGGTATGTCTTCTATGGGTTTTGAAAATTTTAAGCCCAAC
1 TGATCCATTCATGCCTAGGAAAATAGGGTA-GCCTTCTATGAGTTTTGAAAATTTTAAGCCCAAC
* ** * *
17060 CACATCAAAGTTGTTTGATTTTCGAAAAATTCATATTTTATTTGATC
65 AACATCAAACCTGCTAGATTTTC-AAAAATTCATATTTTATTTGATC
* **
17107 TGATCCATTCATGCCTAGGAAAATGGGGTA-CCTATCGTATGAGTTTTGAAAATTTTGTGCCCAA
1 TGATCCATTCATGCCTAGGAAAATAGGGTAGCCT-TC-TATGAGTTTTGAAAATTTTAAGCCCAA
17171 CAACATCAAACCTGCTAGATTTTCAAAAA
64 CAACATCAAACCTGCTAGATTTTCAAAAA
17200 GATTGGGCGT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
110 2 0.03
111 7 0.09
112 71 0.89
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (110 bp):
TGATCCATTCATGCCTAGGAAAATAGGGTAGCCTTCTATGAGTTTTGAAAATTTTAAGCCCAACA
ACATCAAACCTGCTAGATTTTCAAAAATTCATATTTTATTTGATC
Found at i:17548 original size:20 final size:20
Alignment explanation
Indices: 17481--17553 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
17471 TAGACCGCAT
*
17481 TTACATTTGCATCATTTCA-
1 TTACATTTGCATCTTTTCAC
* * *
17500 TGTGCATTTGCTATATTGAT-AC
1 T-TACATTTGC-ATCTT-TTCAC
*
17522 TTGCATTTGCATCTTTTCAC
1 TTACATTTGCATCTTTTCAC
17542 TTACATTTGCAT
1 TTACATTTGCAT
17554 TGGTATTGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
19 2 0.05
20 25 0.60
21 13 0.31
22 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (20 bp):
TTACATTTGCATCTTTTCAC
Found at i:19932 original size:81 final size:80
Alignment explanation
Indices: 19758--20842 Score: 745
Period size: 81 Copynumber: 13.4 Consensus size: 80
19748 GGTTTTATTA
* * * * * * * * *
19758 GTTTCGCCCTTGTCAACCCTTTTTACCCATTGGC-TTATCAATTTCGCCTTGGCCAATCTTTGAA
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTAT-AGTTTCGCCCTGGCCAACCTTTTAA
* * * *
19822 GTAGTTGGCTTT-GCTG
65 TTGGTTGACTTTATC-G
* * * * * *
19838 GTTTCGTCCTAGTCAACCCTTTTAACCTATTGGCTTTACTAGTTTGGCCTTGGCCAACCTTCTAA
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTA-TAGTTTCGCCCTGGCCAACCTTTTAA
*
19903 TTGGTTGACTTTATTG
65 TTGGTTGACTTTATCG
*** * * * * *** *
19919 GTTTTGATTTAGTCAACCCTTCTAA-CTCATTGGTTTTATCGATTTTGGCC-AAACAACCTATTA
1 GTTTTGCCCTAGTCAACCCTTCTAACCT-ATTGGCTTTATAG-TTTCGCCCTGGCCAACCTTTTA
**
19982 ATTGGTTGACTTTATTA
64 ATTGGTTGACTTTATCG
* * * **
19999 GTTTCGCCCTAGTCAACCCTTTTAACCTATTGGTTTTATTAGTTTCATCCTGGCCAACCTTTTAA
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTA-TAGTTTCGCCCTGGCCAACCTTTTAA
*
20064 TTGGTTGACTTTATCA
65 TTGGTTGACTTTATCG
* * * * * * * * *
20080 ATTTAGCCATGGTTAACCCTTCTAACCCATTGGCTTTAATGGTTTTGCCCTGGCCAACCTTTGAA
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTT-ATAGTTTCGCCCTGGCCAACCTTTTAA
* *
20145 TTGGTTAACTTTATTG
65 TTGGTTGACTTTATCG
* * * * * *
20161 GTTTCGCCCTAATCAACCCTTCTAACCTTTTGGCTTTATTGATTTTGACCTGGCCAACC-TTTAA
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATAG-TTTCGCCCTGGCCAACCTTTTAA
20225 TTGGTTGACTTTATCG
65 TTGGTTGACTTTATCG
* * * * * * * * *
20241 GTTTTGTCGTGGTCTATACCGTTCTAACCCATTAGCTTTACTGGTTTCACCTTGGCCAACCTTTT
1 GTTTTGCCCTAGTC-A-ACCCTTCTAACCTATTGGCTTTA-TAGTTTCGCCCTGGCCAACCTTTT
20306 AATTGGTTGACTTTATCG
63 AATTGGTTGACTTTATCG
** * * * * * *
20324 GTTTCACCCTAATCAACCCTTCTAA-CTCATTGGTTTTATCGATTTTGCCCT-GACAACCTATTA
1 GTTTTGCCCTAGTCAACCCTTCTAACCT-ATTGGCTTTATAG-TTTCGCCCTGGCCAACCTTTTA
*
20387 ATTAGTTGAC-TTATCG
64 ATTGGTTGACTTTATCG
* * * * *
20403 ATTTTGCCCAAGTCAAACCATTCTAACAC-ATTGGCTTTATCGGTTTCGCCTTGGCCAACCTTTT
1 GTTTTGCCCTAGTC-AACCCTTCTAAC-CTATTGGCTTTAT-AGTTTCGCCCTGGCCAACCTTTT
*
20467 AATTAGTTGACTTTATCG
63 AATTGGTTGACTTTATCG
* * * * * *
20485 GTTTTACCGT-GATCAACCCTTCTAACCCATTGGCTTTATTGGTTTCACCCTCGCCAA-CTTTTA
1 GTTTTGCCCTAG-TCAACCCTTCTAACCTATTGGCTTTA-TAGTTTCGCCCTGGCCAACCTTTTA
*
20548 ATTGGTTGACTTTATCA
64 ATTGGTTGACTTTATCG
* * * * * ** * *
20565 ATTTCGTCTTAGTCAACCTTTCTAACAGATTGGCTTTATCGATTTTGCCCTGGCCAACCTTTTAA
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATAG-TTTCGCCCTGGCCAACCTTTTAA
*
20630 TTGGTTGACTTTATTG
65 TTGGTTGACTTTATCG
* * * * * * *
20646 GTTTCGCCCAAGTCAACCCTTCTAACATGTTGGCTTTATCAGTTTCGCCTTGGTCAACTTTTTAA
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTAT-AGTTTCGCCCTGGCCAACCTTTTAA
* **
20711 TTGGTTGACTTCATTA
65 TTGGTTGACTTTATCG
* * * * * * * * ** * *
20727 TTTTTGCCTTGGTCAACCTTTTTAACATGTTAGG-TTTATTGATTTTACCTTGGCCAACTTTTTA
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATT-GGCTTTATAG-TTTCGCCCTGGCCAACCTTTTA
* * *
20791 ATTAGTTGGCTTTATCA
64 ATTGGTTGACTTTATCG
* * * * *
20808 ATTTCGCCCTAGTCAATCCTTCTAACTTGTTGGCT
1 GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCT
20843 CATATGGTTT
Statistics
Matches: 796, Mismatches: 177, Indels: 63
0.77 0.17 0.06
Matches are distributed among these distances:
79 17 0.02
80 237 0.30
81 457 0.57
82 54 0.07
83 31 0.04
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (80 bp):
GTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATAGTTTCGCCCTGGCCAACCTTTTAAT
TGGTTGACTTTATCG
Found at i:20016 original size:40 final size:40
Alignment explanation
Indices: 19972--20077 Score: 106
Period size: 41 Copynumber: 2.6 Consensus size: 40
19962 TTTGGCCAAA
* * *
19972 CAACCTATTAATTGGTTGACTTTATTAGTTTCGCCCTAGT
1 CAACCTTTTAATTGGTTGACTTTATTAGTTTCACCCTAGC
* * ** * *
20012 CAACCCTTTTAACCT-ATTGGTTTTATTAGTTTCATCCTGGC
1 CAA-CCTTTTAA-TTGGTTGACTTTATTAGTTTCACCCTAGC
20053 CAACCTTTTAATTGGTTGACTTTAT
1 CAACCTTTTAATTGGTTGACTTTAT
20078 CAATTTAGCC
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
39 1 0.02
40 19 0.38
41 29 0.58
42 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (40 bp):
CAACCTTTTAATTGGTTGACTTTATTAGTTTCACCCTAGC
Found at i:20023 original size:161 final size:160
Alignment explanation
Indices: 19769--20842 Score: 825
Period size: 161 Copynumber: 6.7 Consensus size: 160
19759 TTTCGCCCTT
* * * * * * * * * *
19769 GTCAACCCTTTTTACCCATTGGC-TTATC-AATTTCGCCTTGGCCAATCTTTGAAGTAGTTGGCT
1 GTCAACCCTTCTAACACATTGGCTTTATCGATTTTGGCC-TGGCCAACCTTTTAATTGGTTGACT
** * * * *
19832 TTGCTGGTTTCGTCCTAGTCAACCCTTTTAACCTATTGGCTTTACTAGTTTGGCCTTGGCCAACC
65 TTATTGGTTTCGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATTAGTTTCGCC-TGGCCAACC
* * *
19897 TTCTAATTGGTTGACTTTATTGGTTTTGATTTA
129 TTTTAATTGGTTGACTTTATCGATTTTG-TTTA
* * *** *
19930 GTCAACCCTTCTAACTCATTGGTTTTATCGATTTTGGCC-AAACAACCTATTAATTGGTTGACTT
1 GTCAACCCTTCTAACACATTGGCTTTATCGATTTTGGCCTGGCCAACCTTTTAATTGGTTGACTT
* * * *
19994 TATTAGTTTCGCCCTAGTCAACCCTTTTAACCTATTGGTTTTATTAGTTTCATCCTGGCCAACCT
66 TATTGGTTTCGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATTAGTTTC-GCCTGGCCAACCT
* * ** *
20059 TTTAATTGGTTGACTTTATCAATTTAGCCATG
130 TTTAATTGGTTGACTTTATCGATTTTG-TTTA
* * * * * *
20091 GTTAACCCTTCTAACCCATTGGCTTTAAT-GGTTTTGCCCTGGCCAACCTTTGAATTGGTTAACT
1 GTCAACCCTTCTAACACATTGGCTTT-ATCGATTTTGGCCTGGCCAACCTTTTAATTGGTTGACT
* * *
20155 TTATTGGTTTCGCCCTAATCAACCCTTCTAACCTTTTGGCTTTATT-GATTTTGACCTGGCCAAC
65 TTATTGGTTTCGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATTAG-TTTCG-CCTGGCCAAC
* * *
20219 C-TTTAATTGGTTGACTTTATCGGTTTTGTCGTG
128 CTTTTAATTGGTTGACTTTATCGATTTTGT-TTA
* * * * **
20252 GTCTATACCGTTCTAACCCATTAGCTTTA-CTG-GTTTCACCTTGGCCAACCTTTTAATTGGTTG
1 GTC-A-ACCCTTCTAACACATTGGCTTTATC-GATTTTGGCC-TGGCCAACCTTTTAATTGGTTG
* * * * * * *
20315 ACTTTATCGGTTTCACCCTAATCAACCCTTCTAA-CTCATTGGTTTTA-TCGATTTTGCCCT-GA
62 ACTTTATTGGTTTCGCCCTAGTCAACCCTTCTAACCT-ATTGGCTTTATTAG-TTTCG-CCTGGC
* * ***
20377 CAACCTATTAATTAGTTGAC-TTATCGATTTTGCCCAA
124 CAACCTTTTAATTGGTTGACTTTATCGATTTTG-TTTA
* * * *
20414 GTCAAACCATTCTAACACATTGGCTTTATCG-GTTTCGCCTTGGCCAACCTTTTAATTAGTTGAC
1 GTC-AACCCTTCTAACACATTGGCTTTATCGATTTTGGCC-TGGCCAACCTTTTAATTGGTTGAC
* ** * * * * *
20478 TTTATCGGTTTTACCGT-GATCAACCCTTCTAACCCATTGGCTTTATTGGTTTCACCCTCGCCAA
64 TTTATTGGTTTCGCCCTAG-TCAACCCTTCTAACCTATTGGCTTTATTAGTTTC-GCCTGGCCAA
* *
20542 -CTTTTAATTGGTTGACTTTATCAATTTCGTCTTA
127 CCTTTTAATTGGTTGACTTTATCGATTTTGT-TTA
* * *
20576 GTCAACCTTTCTAACAGATTGGCTTTATCGATTTTGCCCTGGCCAACCTTTTAATTGGTTGACTT
1 GTCAACCCTTCTAACACATTGGCTTTATCGATTTTGGCCTGGCCAACCTTTTAATTGGTTGACTT
* * * * * *
20641 TATTGGTTTCGCCCAAGTCAACCCTTCTAACATGTTGGCTTTATCAGTTTCGCCTTGGTCAACTT
66 TATTGGTTTCGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATTAGTTTCGCC-TGGCCAACCT
* * * *
20706 TTTAATTGGTTGACTTCAT-TATTTTTGCCTTG
130 TTTAATTGGTTGACTTTATCGA-TTTTG-TTTA
* * ** * * * * *
20738 GTCAACCTTTTTAACATGTTAGG-TTTATTGATTTT-ACCTTGGCCAACTTTTTAATTAGTTGGC
1 GTCAACCCTTCTAACACATT-GGCTTTATCGATTTTGGCC-TGGCCAACCTTTTAATTGGTTGAC
*** * * *
20801 TTTATCAATTTCGCCCTAGTCAATCCTTCTAACTTGTTGGCT
64 TTTATTGGTTTCGCCCTAGTCAACCCTTCTAACCTATTGGCT
20843 CATATGGTTT
Statistics
Matches: 743, Mismatches: 137, Indels: 65
0.79 0.14 0.07
Matches are distributed among these distances:
160 2 0.00
161 378 0.51
162 251 0.34
163 112 0.15
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (160 bp):
GTCAACCCTTCTAACACATTGGCTTTATCGATTTTGGCCTGGCCAACCTTTTAATTGGTTGACTT
TATTGGTTTCGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATTAGTTTCGCCTGGCCAACCTT
TTAATTGGTTGACTTTATCGATTTTGTTTA
Found at i:20179 original size:242 final size:243
Alignment explanation
Indices: 19847--20833 Score: 957
Period size: 242 Copynumber: 4.1 Consensus size: 243
19837 GGTTTCGTCC
* * * * * *
19847 TAGTCAACCCTTTTAACCTATTGGCTTTACTAG-TTTGGCCTTGGCCAACCTTCTAATTGGTTGA
1 TAGTCAACCCTTCTAACCCATTGGCTTTAATCGATTTTGCCCTGGCCAACCTT-TAATTGGTTGA
* **** * * * ***
19911 CTTTATTGGTTTTGATTTAGTCAACCCTTCTAACTCATTGGTTTTATCGATTTTGGCC-AAACAA
65 CTTTATTGGTTTCGCCCAAGTCAACCCTTCTAACTCATTGGCTTTATCGAGTTTCGCCTGGCCAA
* * * * * * * * *
19975 CCTATTAATTGGTTGACTTTATTAGTTTCGCCCTAGTCAACCCTTTTAACCTATTGGTTTTATTA
130 CCTTTTAATTGGTTGACTTTATCAGTTTTGCCGTGGTCAACCCTTCTAACCCATTGGCTTTATTG
20040 GTTTCATCC-TGGCCAACCTTTTAATTGGTTGACTTTATCAATTTAGCCA
195 GTTTCA-CCTTGGCCAACCTTTTAATTGGTTGACTTTATCAATTTAGCCA
* * * *
20089 TGGTTAACCCTTCTAACCCATTGGCTTTAAT-GGTTTTGCCCTGGCCAACCTTTGAATTGGTTAA
1 TAGTCAACCCTTCTAACCCATTGGCTTTAATCGATTTTGCCCTGGCCAACCTTT-AATTGGTTGA
* * *
20153 CTTTATTGGTTTCGCCCTAA-TCAACCCTTCTAAC-CTTTTGGCTTTATTGA-TTTTGACCTGGC
65 CTTTATTGGTTTCGCCC-AAGTCAACCCTTCTAACTC-ATTGGCTTTATCGAGTTTCG-CCTGGC
* * * *
20215 CAACC-TTTAATTGGTTGACTTTATCGGTTTTGTCGTGGTCTATACCGTTCTAACCCATTAGCTT
127 CAACCTTTTAATTGGTTGACTTTATCAGTTTTGCCGTGGTC-A-ACCCTTCTAACCCATTGGCTT
* ** *
20279 TACTGGTTTCACCTTGGCCAACCTTTTAATTGGTTGACTTTATCGGTTTCA-CCC
190 TATTGGTTTCACCTTGGCCAACCTTTTAATTGGTTGACTTTATCAATTT-AGCCA
* * * * *
20333 TAATCAACCCTTCTAACTCATTGG-TTTTATCGATTTTGCCCT-GACAACCTATTAATTAGTTGA
1 TAGTCAACCCTTCTAACCCATTGGCTTTAATCGATTTTGCCCTGGCCAACCT-TTAATTGGTTGA
* * * * *
20396 C-TTATCGATTTTGCCCAAGTCAAACCATTCTAACACATTGGCTTTATCG-GTTTCGCCTTGGCC
65 CTTTATTGGTTTCGCCCAAGTC-AACCCTTCTAACTCATTGGCTTTATCGAGTTTCGCC-TGGCC
* * * *
20459 AACCTTTTAATTAGTTGACTTTATCGGTTTTACCGTGATCAACCCTTCTAACCCATTGGCTTTAT
128 AACCTTTTAATTGGTTGACTTTATCAGTTTTGCCGTGGTCAACCCTTCTAACCCATTGGCTTTAT
* * * * *
20524 TGGTTTCACCCTCGCCAA-CTTTTAATTGGTTGACTTTATCAATTTCGTCT
193 TGGTTTCACCTTGGCCAACCTTTTAATTGGTTGACTTTATCAATTTAGCCA
* **
20574 TAGTCAACCTTTCTAACAGATTGGCTTT-ATCGATTTTGCCCTGGCCAACCTTTTAATTGGTTGA
1 TAGTCAACCCTTCTAACCCATTGGCTTTAATCGATTTTGCCCTGGCCAACC-TTTAATTGGTTGA
* *
20638 CTTTATTGGTTTCGCCCAAGTCAACCCTTCTAACAT-GTTGGCTTTATC-AGTTTCGCCTTGGTC
65 CTTTATTGGTTTCGCCCAAGTCAACCCTTCTAAC-TCATTGGCTTTATCGAGTTTCGCC-TGGCC
* * * * * * * ***
20701 AACTTTTTAATTGGTTGACTTCATTATTTTTGCCTTGGTCAACCTTTTTAACATGTTAGG-TTTA
128 AACCTTTTAATTGGTTGACTTTATCAGTTTTGCCGTGGTCAACCCTTCTAACCCATT-GGCTTTA
* * * * * * *
20765 TTGATTTTACCTTGGCCAACTTTTTAATTAGTTGGCTTTATCAATTTCGCCC
192 TTGGTTTCACCTTGGCCAACCTTTTAATTGGTTGACTTTATCAATTTAGCCA
*
20817 TAGTCAATCCTTCTAAC
1 TAGTCAACCCTTCTAAC
20834 TTGTTGGCTC
Statistics
Matches: 613, Mismatches: 105, Indels: 53
0.80 0.14 0.07
Matches are distributed among these distances:
241 69 0.11
242 291 0.47
243 128 0.21
244 124 0.20
245 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (243 bp):
TAGTCAACCCTTCTAACCCATTGGCTTTAATCGATTTTGCCCTGGCCAACCTTTAATTGGTTGAC
TTTATTGGTTTCGCCCAAGTCAACCCTTCTAACTCATTGGCTTTATCGAGTTTCGCCTGGCCAAC
CTTTTAATTGGTTGACTTTATCAGTTTTGCCGTGGTCAACCCTTCTAACCCATTGGCTTTATTGG
TTTCACCTTGGCCAACCTTTTAATTGGTTGACTTTATCAATTTAGCCA
Found at i:20631 original size:405 final size:405
Alignment explanation
Indices: 19860--20649 Score: 1027
Period size: 405 Copynumber: 2.0 Consensus size: 405
19850 TCAACCCTTT
* * ** * *
19860 TAACCTATTGGCTTTACTAGTTTGGCCTTGGCCAACCTTCTAATTGGTTGACTTTATTGGTTTTG
1 TAACCCATTAGCTTTACTAGTTTCACCTTGGCCAACCTTCTAATTGGTTGACTTTATCGGTTTTC
** * * *
19925 ATTTAGTCAACCCTTCTAACTCATTGGTTTTATCGATTTTGGCCAAACAACCTATTAATTGGTTG
66 ACCTAATCAACCCTTCTAACTCATTGGTTTTATCGATTTTGCCCAAACAACCTATTAATTAGTTG
* * * * * * *
19990 ACTTTATTAGTTTCGCCCTAGTCAACCCTTTTAACCTATTGGTTTTATTAGTTTCATCCTGGCCA
131 ACTTTATGAGTTTCGCCCAAGTCAACCATTCTAACCTATTGGCTTTATCAGTTTCAGCCTGGCCA
* * *
20055 ACCTTTTAATTGGTTGACTTTATCAATTTAGCCATGGTTAACCCTTCTAACCCATTGGCTTTAAT
196 ACCTTTTAATTAGTTGACTTTATCAATTTAGCCATGATCAACCCTTCTAACCCATTGGCTTTAAT
** * ***
20120 GGTTTTGCCCTGGCCAACCTTTGAATTGGTTAACTTTATTGGTTTCGCCCTAATCAACCCTTCTA
261 GGTTTCACCCTCGCCAACCTTTGAATTGGTTAACTTTATCAATTTCGCCCTAATCAACCCTTCTA
*** *
20185 ACCTTTTGGCTTTATTGATTTTGACCTGGCCAACCTTTAATTGGTTGACTTTATCGGTTTTGTCG
326 ACAGATTGGCTTTATCGATTTTGACCTGGCCAACCTTTAATTGGTTGACTTTATCGGTTTTGTCG
20250 TGGTCTATACCGTTC
391 TGGTCTATACCGTTC
* *
20265 TAACCCATTAGCTTTACTGGTTTCACCTTGGCCAACCTTTTAATTGGTTGACTTTATCGG-TTTC
1 TAACCCATTAGCTTTACTAGTTTCACCTTGGCCAACCTTCTAATTGGTTGACTTTATCGGTTTTC
**
20329 ACCCTAATCAACCCTTCTAACTCATTGGTTTTATCGATTTTGCCCTGACAACCTATTAATTAGTT
66 A-CCTAATCAACCCTTCTAACTCATTGGTTTTATCGATTTTGCCCAAACAACCTATTAATTAGTT
* *
20394 GAC-TTATCGA-TTTTGCCCAAGTCAAACCATTCTAACAC-ATTGGCTTTATCGGTTTC-GCCTT
130 GACTTTAT-GAGTTTCGCCCAAGTC-AACCATTCTAAC-CTATTGGCTTTATCAGTTTCAGCC-T
** *
20455 GGCCAACCTTTTAATTAGTTGACTTTATCGGTTTTA-CCGTGATCAACCCTTCTAACCCATTGGC
191 GGCCAACCTTTTAATTAGTTGACTTTATC-AATTTAGCCATGATCAACCCTTCTAACCCATTGGC
* * * * * *
20519 TTTATTGGTTTCACCCTCGCCAA-CTTTTAATTGGTTGACTTTATCAATTTCGTCTTAGTCAACC
255 TTTAATGGTTTCACCCTCGCCAACCTTTGAATTGGTTAACTTTATCAATTTCGCCCTAATCAACC
* * *
20583 TTTCTAACAGATTGGCTTTATCGATTTTGCCCTGGCCAACCTTTTAATTGGTTGACTTTATTGGT
320 CTTCTAACAGATTGGCTTTATCGATTTTGACCTGGCCAACC-TTTAATTGGTTGACTTTATCGGT
20648 TT
384 TT
20650 CGCCCAAGTC
Statistics
Matches: 329, Mismatches: 49, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
404 89 0.27
405 235 0.71
406 5 0.02
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (405 bp):
TAACCCATTAGCTTTACTAGTTTCACCTTGGCCAACCTTCTAATTGGTTGACTTTATCGGTTTTC
ACCTAATCAACCCTTCTAACTCATTGGTTTTATCGATTTTGCCCAAACAACCTATTAATTAGTTG
ACTTTATGAGTTTCGCCCAAGTCAACCATTCTAACCTATTGGCTTTATCAGTTTCAGCCTGGCCA
ACCTTTTAATTAGTTGACTTTATCAATTTAGCCATGATCAACCCTTCTAACCCATTGGCTTTAAT
GGTTTCACCCTCGCCAACCTTTGAATTGGTTAACTTTATCAATTTCGCCCTAATCAACCCTTCTA
ACAGATTGGCTTTATCGATTTTGACCTGGCCAACCTTTAATTGGTTGACTTTATCGGTTTTGTCG
TGGTCTATACCGTTC
Found at i:20702 original size:41 final size:40
Alignment explanation
Indices: 20433--20842 Score: 138
Period size: 41 Copynumber: 10.2 Consensus size: 40
20423 TTCTAACACA
* * *
20433 TTGGCTTTATCGGTTTCGCCTTGGCCAACCTTTTAA-TTAG
1 TTGGCTTTATCAGTTTCGCCTTGGTCAACTTTTTAACTT-G
* * ** * * * * ***
20473 TTGACTTTATCGGTTTTACCGTGATCAACCCTTCTAACCCA
1 TTGGCTTTATCAGTTTCGCCTTGGTCAA-CTTTTTAACTTG
** * * * *
20514 TTGGCTTTATTGGTTTCACCCTCGCCAAC-TTTTAA-TTGG
1 TTGGCTTTATCAGTTTCGCCTTGGTCAACTTTTTAACTT-G
* * * * * *
20553 TTGACTTTATCAATTTCGTCTTAGTCAACCTTTCTAAC-AG
1 TTGGCTTTATCAGTTTCGCCTTGGTCAA-CTTTTTAACTTG
* * * *
20593 ATTGGCTTTATC-GATTTTGCCCTGGCCAACCTTTTAA-TTGG
1 -TTGGCTTTATCAG-TTTCGCCTTGGTCAACTTTTTAACTT-G
* ** *** * * *
20634 TTGACTTTATTGGTTTCGCCCAAGTCAACCCTTCTAACATG
1 TTGGCTTTATCAGTTTCGCCTTGGTCAA-CTTTTTAACTTG
20675 TTGGCTTTATCAGTTTCGCCTTGGTCAACTTTTTAA-TTGG
1 TTGGCTTTATCAGTTTCGCCTTGGTCAACTTTTTAACTT-G
* * * * * *
20715 TTGACTTCATTATTTTTGCCTTGGTCAACCTTTTTAACATG
1 TTGGCTTTATCAGTTTCGCCTTGGTCAA-CTTTTTAACTTG
* ** *
20756 TTAGG-TTTAT-TGATTTTACCTTGGCCAACTTTTTAA-TTAG
1 TT-GGCTTTATCAG-TTTCGCCTTGGTCAACTTTTTAACTT-G
* * * * *
20796 TTGGCTTTATCAATTTCGCCCTAGTCAATCCTTCTAACTTG
1 TTGGCTTTATCAGTTTCGCCTTGGTCAA-CTTTTTAACTTG
20837 TTGGCT
1 TTGGCT
20843 CATATGGTTT
Statistics
Matches: 266, Mismatches: 81, Indels: 45
0.68 0.21 0.11
Matches are distributed among these distances:
39 28 0.11
40 107 0.40
41 126 0.47
42 5 0.02
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (40 bp):
TTGGCTTTATCAGTTTCGCCTTGGTCAACTTTTTAACTTG
Found at i:20805 original size:40 final size:40
Alignment explanation
Indices: 20674--20805 Score: 117
Period size: 40 Copynumber: 3.3 Consensus size: 40
20664 CTTCTAACAT
* * ** *
20674 GTTGGCTTTATCAGTTTCGCCTTGGTCAACTTTTTAATTG
1 GTTGGCTTTATTATTTTTACCTTGGTCAACTTTTTAATTA
* * * *
20714 GTTGACTTCATTATTTTTGCCTTGGTCAACCTTTTTAA-CA
1 GTTGGCTTTATTATTTTTACCTTGGTCAA-CTTTTTAATTA
*
20754 TGTTAGG-TTTATTGA-TTTTACCTTGGCCAACTTTTTAATTA
1 -GTT-GGCTTTATT-ATTTTTACCTTGGTCAACTTTTTAATTA
20795 GTTGGCTTTAT
1 GTTGGCTTTAT
20806 CAATTTCGCC
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
39 2 0.03
40 40 0.54
41 30 0.41
42 2 0.03
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.49
Consensus pattern (40 bp):
GTTGGCTTTATTATTTTTACCTTGGTCAACTTTTTAATTA
Found at i:21032 original size:90 final size:91
Alignment explanation
Indices: 20831--21035 Score: 290
Period size: 90 Copynumber: 2.3 Consensus size: 91
20821 CAATCCTTCT
* * *
20831 AACTTGTTGGCTCATATGGTTTCGTCCCGGTCAATACCCATATAACTCGTTGGCACCTATGGTTT
1 AACTTGTTGGTTCGTATGGTTTCGTCCCGATCAATACCCATATAACTCGTTGGCACCTATGGTTT
*
20896 TGTCCCAGTCGACAACTTTCTAAACA
66 TGTCCCAGCCGACAACTTTCTAAACA
* * * *
20922 AACTTGTTAGTTTGTATGGTTTCGTCCCGATCAATACCCATCTAACTTG-TGGCACCTATGGTTT
1 AACTTGTTGGTTCGTATGGTTTCGTCCCGATCAATACCCATATAACTCGTTGGCACCTATGGTTT
20986 TGTCCCAGCCGAC-ACTTTTTCT-AACA
66 TGTCCCAGCCGACAAC--TTTCTAAACA
*
21012 AACTTGTTGGTTCGTGTGGTTTCG
1 AACTTGTTGGTTCGTATGGTTTCG
21036 CCCAAGTCAA
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
89 2 0.02
90 52 0.51
91 47 0.47
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.36
Consensus pattern (91 bp):
AACTTGTTGGTTCGTATGGTTTCGTCCCGATCAATACCCATATAACTCGTTGGCACCTATGGTTT
TGTCCCAGCCGACAACTTTCTAAACA
Done.