Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1607
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: 65751
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:2836 original size:13 final size:13
Alignment explanation
Indices: 2818--2843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2808 TACACACAAG
2818 ATGTATCGATACA
1 ATGTATCGATACA
2831 ATGTATCGATACA
1 ATGTATCGATACA
2844 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2860 original size:33 final size:32
Alignment explanation
Indices: 2800--2863 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
2790 CTTAACTATT
*
2800 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
2832 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
2864 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:13654 original size:28 final size:28
Alignment explanation
Indices: 13582--13852 Score: 303
Period size: 28 Copynumber: 9.6 Consensus size: 28
13572 CAATACGAAT
*
13582 TCTTTTCAAAGCCCACAAGTCAGTGGCT
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
13610 TCCTTCTCAAAGCCCATAAATTAGTGGCA
1 T-CTTTTCAAAGCCCACAAGTCAGTGGCA
* *
13639 TCTTTTCAAAGCCCATAAATCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
13667 TCCTTTCAAAACCCACAAGTTAGTGGTAA
1 TCTTTTCAAAGCCCACAAGTCAGTGG-CA
*
13696 CCCTTTTCAAAGCCCACAAGTCAGTGGCA
1 -TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
13725 CCTTTTCAAAGCCCATAAGTTAGTGGTA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
13753 TCGTTTT-AAAGCCCACAAGTGAGTGGCA
1 TC-TTTTCAAAGCCCACAAGTCAGTGGCA
* *
13781 CCCTTTT-AAAGCCCACAAGTAAGTGGCA
1 -TCTTTTCAAAGCCCACAAGTCAGTGGCA
13809 TCTTTTCAAAGCCCACAAGTCAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
13837 TCCTTTCAAAGCCCAC
1 TCTTTTCAAAGCCCAC
13853 GCAAGTTGAT
Statistics
Matches: 207, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
27 5 0.02
28 150 0.72
29 30 0.14
30 22 0.11
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (28 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:13730 original size:86 final size:85
Alignment explanation
Indices: 13585--13852 Score: 351
Period size: 86 Copynumber: 3.2 Consensus size: 85
13575 TACGAATTCT
* * * * *
13585 TTTCAAAGCCCACAAGTCAGTGGCT-TCCTTCTCAAAGCCCATAAATTAGTGGCATCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGG-TACCCTTTTCAAAGCCCACAAGTAAGTGGCATCTTTTCAAA
*
13649 GCCCATAAATCAGTGGCATCC
65 GCCCATAAGTCAGTGGCATCC
* * * *
13670 TTTCAAAACCCACAAGTTAGTGGTAACCCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGT-ACCCTTTTCAAAGCCCACAAGTAAGTGGCATCTTTTCAAA
* * *
13735 GCCCATAAGTTAGTGGTATCG
65 GCCCATAAGTCAGTGGCATCC
* * *
13756 TTTTAAAGCCCACAAGTGAGTGGCACCCTTTT-AAAGCCCACAAGTAAGTGGCATCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGTACCCTTTTCAAAGCCCACAAGTAAGTGGCATCTTTTCAAAG
*
13820 CCCACAAGTCAGTGGCATCC
66 CCCATAAGTCAGTGGCATCC
13840 TTTCAAAGCCCAC
1 TTTCAAAGCCCAC
13853 GCAAGTTGAT
Statistics
Matches: 158, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
84 59 0.37
85 29 0.18
86 70 0.44
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (85 bp):
TTTCAAAGCCCACAAGTCAGTGGTACCCTTTTCAAAGCCCACAAGTAAGTGGCATCTTTTCAAAG
CCCATAAGTCAGTGGCATCC
Found at i:13782 original size:56 final size:57
Alignment explanation
Indices: 13582--13852 Score: 354
Period size: 56 Copynumber: 4.8 Consensus size: 57
13572 CAATACGAAT
* * * *
13582 TCTTTTCAAAGCCCACAAGTCAGTGGCTTCCTTCTCAAAGCCCATAAATTAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * *
13639 TCTTTTCAAAGCCCATAAATCAGTGGCATCC-TTTCAAAACCCACAAGTTAGTGGTAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGG-CA
* * *
13696 CCCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCATAAGTTAGTGGTA
1 -TCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGGCA
* * *
13753 TCGTTTT-AAAGCCCACAAGTGAGTGGCACCCTTTT-AAAGCCCACAAGTAAGTGGCA
1 TC-TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGGCA
13809 TCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCAC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCAC
13853 GCAAGTTGAT
Statistics
Matches: 186, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
55 7 0.04
56 91 0.49
57 42 0.23
58 46 0.25
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (57 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGGCA
Found at i:15102 original size:20 final size:20
Alignment explanation
Indices: 15077--15126 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
15067 GGTGGGGATG
* *
15077 AAGGAAGAAGAAGAAGAATA
1 AAGGAAAAAAAAGAAGAATA
15097 AAGGAAAAAAAAGAAG-A-A
1 AAGGAAAAAAAAGAAGAATA
15115 AAGGAAAAAAAA
1 AAGGAAAAAAAA
15127 AGAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.46
19 1 0.04
20 14 0.50
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AAGGAAAAAAAAGAAGAATA
Found at i:15135 original size:19 final size:18
Alignment explanation
Indices: 15077--15135 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
15067 GGTGGGGATG
* *
15077 AAGGAAGAAGAAGAAGAATA
1 AAGGAAAAAAAAGAA-AA-A
*
15097 AAGGAAAAAAAAGAAGAA
1 AAGGAAAAAAAAGAAAAA
15115 AAGGAAAAAAAAAGAAAAA
1 AAGG-AAAAAAAAGAAAAA
15134 AA
1 AA
15136 TATGAAATGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.15
19 16 0.47
20 13 0.38
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (18 bp):
AAGGAAAAAAAAGAAAAA
Found at i:16318 original size:315 final size:314
Alignment explanation
Indices: 15742--16368 Score: 1040
Period size: 315 Copynumber: 2.0 Consensus size: 314
15732 TTGTACCTTA
* *
15742 TTTTTGTGTTAAAACTTGAGTGGTATGATCAACGGGCTGTTTATCATCTTAAATTACTCCGAGAT
1 TTTTTGTGTTAAAACTTGAGTGGTATGATCAACGGGCTGTTTATCATCTCAAATTACTCAGAGAT
*
15807 TGTGTAAATGAGTTCTTGATGCTCATACCACTCTTCCCTTTCGGTCACAGACATTCGAATGTCCA
66 TGTGTAAATGAGTTCGTGATGCTCATACCACTCTTCCCTTTCGGTCACAGACATTCGAATGTCCA
*
15872 TAACTCAAGTTTAGACCCGTAAACACTAAGAAAACCAAAATTCTCCTTTGTTTTCCTCCATTCCT
131 TAACTCAAGTTTAGACCCGTAAACACTAAGAAAACCAAAATTATCCTTTGTTTTCCTCCATTCCT
* * *
15937 TTCTGGCAGCACCACTGTTGCCCATTGAAAAATCATTTTAAAATATTAAACCATTTTTCCTGATT
196 TGCTGGCAGCACCACTGTTGCACATTGAAAAATCATTTTAAAATATTAAACCATTTTTCATGATT
* * *
16002 TTTTTATAATTTTTCTTTCAAAGTGTGTTAAAATACCTTTCCAATGGTGTCTTG
261 TTTTTATAATTTTTCTTTCAAAGTGTGTCAAAATACCATTCCAATGGGGTCTTG
*
16056 TTTTTGTGTTAAAACTTGAGTGGTATGATCAACGGGTTGTTTCATCATCTCAAATTACTCTAG-G
1 TTTTTGTGTTAAAACTTGAGTGGTATGATCAACGGGCTGTTT-ATCATCTCAAATTACTC-AGAG
* * * *
16120 ATTGTGTAAATGAGTTCGTGATGCTCATACCACTCTTTCCTTTTGGTCACGGACGTTCGAATGTC
64 ATTGTGTAAATGAGTTCGTGATGCTCATACCACTCTTCCCTTTCGGTCACAGACATTCGAATGTC
* * * *
16185 CATGACTCGAGTTTAGACCCGTAAACACTAAGAAAACCAAAATTATCCTTTGTTTTCCTTCGTTC
129 CATAACTCAAGTTTAGACCCGTAAACACTAAGAAAACCAAAATTATCCTTTGTTTTCCTCCATTC
16250 CTTGCTGGCAGCACCACTGTTGCACATTGAAAAATCATTTTAAAATATTAAACCATTTTTCATGA
194 CTTGCTGGCAGCACCACTGTTGCACATTGAAAAATCATTTTAAAATATTAAACCATTTTTCATGA
* *
16315 TTTTTTTATAATTTTTCTTTGAAAGTGTGTCGAAATACCATTCCAATGGGGTCT
259 TTTTTTTATAATTTTTCTTTCAAAGTGTGTCAAAATACCATTCCAATGGGGTCT
16369 ATTAACCCTC
Statistics
Matches: 290, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
314 41 0.14
315 248 0.86
316 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (314 bp):
TTTTTGTGTTAAAACTTGAGTGGTATGATCAACGGGCTGTTTATCATCTCAAATTACTCAGAGAT
TGTGTAAATGAGTTCGTGATGCTCATACCACTCTTCCCTTTCGGTCACAGACATTCGAATGTCCA
TAACTCAAGTTTAGACCCGTAAACACTAAGAAAACCAAAATTATCCTTTGTTTTCCTCCATTCCT
TGCTGGCAGCACCACTGTTGCACATTGAAAAATCATTTTAAAATATTAAACCATTTTTCATGATT
TTTTTATAATTTTTCTTTCAAAGTGTGTCAAAATACCATTCCAATGGGGTCTTG
Found at i:23250 original size:13 final size:13
Alignment explanation
Indices: 23232--23256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23222 ACACAAAGTA
23232 TGTATCGATACAT
1 TGTATCGATACAT
23245 TGTATCGATACA
1 TGTATCGATACA
23257 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23253 original size:32 final size:33
Alignment explanation
Indices: 23212--23279 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
23202 GTAGCCAAAC
*
23212 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
23244 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
23277 TTG
1 TTG
23280 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:31998 original size:13 final size:13
Alignment explanation
Indices: 31980--32004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31970 ACACAAAGTA
31980 TGTATCGATACAT
1 TGTATCGATACAT
31993 TGTATCGATACA
1 TGTATCGATACA
32005 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:32001 original size:32 final size:33
Alignment explanation
Indices: 31960--32027 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
31950 GTAGCCAAAC
*
31960 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
31992 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
32025 TTG
1 TTG
32028 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:35673 original size:52 final size:52
Alignment explanation
Indices: 35525--35653 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
35515 CGAAATATGA
35525 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
35577 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
35629 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
35654 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:35772 original size:32 final size:33
Alignment explanation
Indices: 35727--35792 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
35717 AGTAGCTTAT
*
35727 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCAATACAAAACTTTATGTATCGATAC
*
35759 ATTGTATCAATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAACTTTATGTATCGATAC
35792 A
1 A
35793 AATCATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (33 bp):
ATTGTATCAATACAAAACTTTATGTATCGATAC
Found at i:45624 original size:20 final size:20
Alignment explanation
Indices: 45599--45675 Score: 118
Period size: 20 Copynumber: 3.8 Consensus size: 20
45589 TTTGCCTGCA
45599 TGTATCGATACATTTTATAG
1 TGTATCGATACATTTTATAG
45619 TGTATCGATACATTTTATAG
1 TGTATCGATACATTTTATAG
* * *
45639 TGTATCGATACATCTGAGTAA
1 TGTATCGATACATTTTA-TAG
45660 TGTATCGATACATTTT
1 TGTATCGATACATTTT
45676 TTGGCAGTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 35 0.69
21 16 0.31
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTTATAG
Found at i:45672 original size:41 final size:40
Alignment explanation
Indices: 45599--45675 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
45589 TTTGCCTGCA
* * *
45599 TGTATCGATACATTTTATAGTGTATCGATACATTTTATAG
1 TGTATCGATACATCTGATAATGTATCGATACATTTTATAG
45639 TGTATCGATACATCTGAGTAATGTATCGATACATTTT
1 TGTATCGATACATCTGA-TAATGTATCGATACATTTT
45676 TTGGCAGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 15 0.45
41 18 0.55
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.43
Consensus pattern (40 bp):
TGTATCGATACATCTGATAATGTATCGATACATTTTATAG
Found at i:45717 original size:19 final size:19
Alignment explanation
Indices: 45693--45822 Score: 89
Period size: 19 Copynumber: 7.7 Consensus size: 19
45683 TAGCTTATAT
45693 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
45712 TGTATCCATAC---A--T-
1 TGTATCGATACAAAACTTA
45725 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
45744 TGTATCCATAC---A--T-
1 TGTATCGATACAAAACTTA
45757 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
45776 TGTATCCATAC---A--T-
1 TGTATCGATACAAAACTTA
*
45789 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAC-TTA
45809 TGTATCGATACAAA
1 TGTATCGATACAAA
45823 TCGTTGAAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 37
0.66 0.05 0.29
Matches are distributed among these distances:
13 30 0.35
14 3 0.04
16 6 0.07
18 2 0.02
19 31 0.36
20 13 0.15
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:45732 original size:32 final size:32
Alignment explanation
Indices: 45691--45820 Score: 233
Period size: 32 Copynumber: 4.0 Consensus size: 32
45681 AGTAGCTTAT
45691 ATTGTATCGATACAAAACTTATGTATCCATAC
1 ATTGTATCGATACAAAACTTATGTATCCATAC
45723 ATTGTATCGATACAAAACTTATGTATCCATAC
1 ATTGTATCGATACAAAACTTATGTATCCATAC
45755 ATTGTATCGATACAAAACTTATGTATCCATAC
1 ATTGTATCGATACAAAACTTATGTATCCATAC
* *
45787 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAC-TTATGTATCCATAC
45820 A
1 A
45821 AATCGTTGAA
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 81 0.85
33 14 0.15
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCCATAC
Found at i:47045 original size:14 final size:15
Alignment explanation
Indices: 47026--47059 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
47016 TTTTTAGAAA
*
47026 AAAAACAAAA-AATG
1 AAAAACAAAACAAAG
47040 AAAAACAAAACAAAG
1 AAAAACAAAACAAAG
47055 AAAAA
1 AAAAA
47060 AAGAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.82, C:0.09, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAACAAAACAAAG
Found at i:47057 original size:15 final size:14
Alignment explanation
Indices: 47026--47073 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
47016 TTTTTAGAAA
*
47026 AAAAACAAAAAATG
1 AAAAACAAAAAAAG
47040 AAAAACAAAACAAAG
1 AAAAACAAAA-AAAG
47055 AAAAA-AAGAGAAAAG
1 AAAAACAA-A-AAAAG
47070 AAAA
1 AAAA
47074 GAACTTGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.40
15 17 0.57
16 1 0.03
ACGTcount: A:0.81, C:0.06, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAAACAAAAAAAG
Found at i:48313 original size:61 final size:61
Alignment explanation
Indices: 48132--49093 Score: 1098
Period size: 61 Copynumber: 16.0 Consensus size: 61
48122 CAACAGGACG
* *
48132 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAATCCTCAAAGAGCAGGACGCC-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
48192 -C----AAAGCCCACACAAGCTGGTGGCAC-TTTCAGTCTTGAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* *
48247 CCTTTTAAAGCCCACACAATTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
48308 ACTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGGACGCTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
48370 CCTTTCAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGAAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
48431 CCTTTTCAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAAAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTT
* * *
48493 CC-TTTAAAGCCCACACAATTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
48552 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
48612 -C----AAAGCCCACACAAGCTGGTGGCAC-CTTCAGTTCTCAAAGAGCAGGACGTCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * ** *
48667 CCTTTTAAAGCCCACACAAGGTGGTGGCACCTTCCAATCCTCAAAGAATAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTT-T
* * *
48728 CCTTTTAAAGCCCACACACGGTGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTTT-T
* * *
48789 CCTTTTAAAG-CCACACAAGTTGGTGGCAGTTTTCTAGTCCTCGAAGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
48850 CCTTTTAAAGCCCATACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTT-T
* * *
48911 CTTTTTAAAGCCCACACAAGTTGGTGACACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
48973 CCTTTTAAAACCCACACAAGTTGGTGGCAC-CTTCTAGTTCTCAAAGAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTT-T
** * ** * *
49034 CCTTGCAAAGCCCATACAAGTTGGTGGCAC-CCTCTAGTCCCCAAGGAGCAGGAC-CCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTT
49094 TATTCTCCTT
Statistics
Matches: 783, Mismatches: 87, Indels: 64
0.84 0.09 0.07
Matches are distributed among these distances:
54 41 0.05
55 55 0.07
56 2 0.00
59 33 0.04
60 106 0.14
61 389 0.50
62 153 0.20
63 4 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:48384 original size:123 final size:122
Alignment explanation
Indices: 48132--49093 Score: 1189
Period size: 123 Copynumber: 8.0 Consensus size: 122
48122 CAACAGGACG
* ** * *
48132 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACGCC-TTT-C--
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCCTTTTCCTT
* * *
48193 --AAAGCCCACACAAGCTGGTGGCAC-TTTC-AGTCTTGAAAGAGCAGGACGCCTTTT
65 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
48247 CCTTTTAAAGCCCACACAATTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTTACTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTT
* *
48312 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGGACGCTTTTT
65 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
48370 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGAAGGATGCCTTTTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGATGCCTTTTCCTT
* * * *
48435 TTCAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAAAGCAGGATGCCTTTT
65 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
*
48493 CC-TTTAAAGCCCACACAATTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
*
48557 TAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC-TTT
66 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
48612 -C----AAAGCCCACACAAGCTGGTGGCACCTTCAGTTCTCAAAGAGCAGGACGTCTTTTCCTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
* * * * ** *
48672 TAAAGCCCACACAAGGTGGTGGCAC-CTTCCAATCCTCAAAGAATAGGATG-CTTTCT
66 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTT-T
* * *
48728 CCTTTTAAAGCCCACACACGGTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATG-CTTTCTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGCCTTT-TCCT
* * *
48792 TTTAAAG-CCACACAAGTTGGTGGCAGTTTTCTAGTCCTCGAAGAGTAGGACGCCTTTT
64 TTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
48850 CCTTTTAAAGCCCATACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTCTCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCCTTT-TCCT
* *
48914 TTTAAAGCCCACACAAGTTGGTGACACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTT
64 TTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
48973 CCTTTTAAAACCCACACAAGTTGGTGGCACCTTCTAGTTCTCAAAGAGCAGGATG-CTTTCTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGATGCCTTT-TCCT
** * ** * *
49037 TGCAAAGCCCATACAAGTTGGTGGCAC-CCTCTAGTCCCCAAGGAGCAGGAC-CCTTTT
64 TTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
49094 TATTCTCCTT
Statistics
Matches: 746, Mismatches: 76, Indels: 44
0.86 0.09 0.05
Matches are distributed among these distances:
114 1 0.00
115 147 0.20
116 7 0.01
117 2 0.00
118 1 0.00
119 3 0.00
120 24 0.03
121 128 0.17
122 170 0.23
123 263 0.35
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (122 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:52568 original size:13 final size:13
Alignment explanation
Indices: 52550--52577 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52540 ATATAAAGAT
52550 CAATGTATCGATA
1 CAATGTATCGATA
52563 CAATGTATCGATA
1 CAATGTATCGATA
52576 CA
1 CA
52578 TTGAGTAATG
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:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:52653 original size:19 final size:19
Alignment explanation
Indices: 52629--52713 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
52619 AGCGATACAT
52629 TGTATCGATACAATACTTA
1 TGTATCGATACAATACTTA
52648 TGTATCGATAC---A-TTA
1 TGTATCGATACAATACTTA
*
52663 --TATCGATACAACACTTA
1 TGTATCGATACAATACTTA
* *
52680 TGTATCGATACAGTTACTGTT
1 TGTATCGATACA-ATACT-TA
52701 TGTATCGATACAA
1 TGTATCGATACAA
52714 ATTGTTGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
13 9 0.17
15 3 0.06
16 2 0.04
17 3 0.06
19 21 0.39
20 3 0.06
21 13 0.24
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAATACTTA
Found at i:52667 original size:32 final size:32
Alignment explanation
Indices: 52616--52691 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
52606 GCAGTAGCTT
* * *
52616 TGTAGCGATACATTGTATCGATACAATACTTA
1 TGTATCGATACATTATATCGATACAACACTTA
52648 TGTATCGATACATTATATCGATACAACACTTA
1 TGTATCGATACATTATATCGATACAACACTTA
52680 TGTATCGATACA
1 TGTATCGATACA
52692 GTTACTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTATATCGATACAACACTTA
Found at i:53643 original size:49 final size:50
Alignment explanation
Indices: 53550--53671 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 50
53540 TGTTAAAGAT
* * * * *
53550 GCCAATATGATCATTCAAGGCCAACGATATCGGACTTAAGGAT-GAAGGT
1 GCCAATATGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAGAAGGC
* * * **
53599 GCCAATGTGCTGATTGAAGGCCAACGACATTGGTTTTAAAGATGACGAAGGC
1 GCCAATATGCTGATTCAAGGCCAACGACATCGGACTTAAAGAT-A-GAAGGC
53651 GCCAATATGCTGATTCAAGGC
1 GCCAATATGCTGATTCAAGGC
53672 TAGTGATATT
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
49 34 0.59
52 24 0.41
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (50 bp):
GCCAATATGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAGAAGGC
Found at i:53790 original size:39 final size:39
Alignment explanation
Indices: 53736--53894 Score: 174
Period size: 39 Copynumber: 3.9 Consensus size: 39
53726 TAAAGACAAG
** * *
53736 GTGCCAATATGCTGATTCAATTCCAGCGATATTGGGCTT
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGGCTT
* *
53775 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGG-------GCTT
* *
53821 GTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGGCTT
*
53860 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGG
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGG
53895 TCTTAAAAGA
Statistics
Matches: 101, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
39 65 0.64
46 36 0.36
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (39 bp):
GTGCCAATATGCTGATTCAAGGCCAACGACATTGGGCTT
Found at i:53862 original size:85 final size:86
Alignment explanation
Indices: 53597--53950 Score: 404
Period size: 87 Copynumber: 4.0 Consensus size: 86
53587 AAGGATGAAG
* * *
53597 GTGCCAATGTGCTGATTGAAGGCCAACGACATTGGTTTTAAAGATGACGAAGGCGCCAATATGCT
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGAT-----AGGTGCCAATATGCT
* *
53662 GATTCAAGGCTAGTGATATTGGACTT
61 GATTCAAGGCCAGCGATATTGGACTT
* * ** * * *
53688 GTGCCAATGTGCTCATTCAAGGCCAGTGGCATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGA-TAGGTGCCAATATGCTGATT
** *
53753 CAATTCCAGCGATATTGGGCTT
65 CAAGGCCAGCGATATTGGACTT
53775 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGAT-GGTGCCAATATGCTGATTC
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGATAGGTGCCAATATGCTGATTC
*
53839 AAGGCCAACGATATTGGACTT
66 AAGGCCAGCGATATTGGACTT
* * *
53860 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAGATAAGAAAGGTGCCAATATAC
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGT-TTTAAAGAT-----AGGTGCCAATATGC
* *
53925 TGATTCAAGGCCAGCAATATTAGACT
60 TGATTCAAGGCCAGCGATATTGGACT
53951 CAAGAGGTTA
Statistics
Matches: 225, Mismatches: 30, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
85 71 0.32
86 8 0.04
87 73 0.32
91 38 0.17
92 35 0.16
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (86 bp):
GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGATAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTT
Found at i:54023 original size:43 final size:43
Alignment explanation
Indices: 53958--54098 Score: 158
Period size: 43 Copynumber: 3.1 Consensus size: 43
53948 ACTCAAGAGG
* *
53958 TTAAAGGTCCCAATATGTTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGGAC
* * *
54001 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTAGG-C
1 TTAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATT-GGAC
*
54044 TTAAAGATAAAGGTGCCAATATGTTGATTCAAGGCAAACGATATTGGAC
1 -T-----TAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGGAC
54093 TTAAAG
1 TTAAAG
54099 ACAAGGTGCC
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
43 40 0.49
44 3 0.04
48 3 0.04
49 35 0.43
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (43 bp):
TTAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGGAC
Found at i:54074 original size:49 final size:49
Alignment explanation
Indices: 53860--54109 Score: 237
Period size: 49 Copynumber: 5.1 Consensus size: 49
53850 TATTGGACTT
* *
53860 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAGATAAGAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGAT---AAAG
* * * * *
53913 GTGCCAATATACTGATTCAAGGCCAGCAATATTAGACTCAAGAGGTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA-A-GATAAAG
* *
53964 GTCCCAATATGTTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAG
* * *
54007 GTGCCAATGTGCTGATTCAAGGCCAACGACATTAGG-CTTAAAGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATAAAG
* * * *
54056 GTGCCAATATGTTGATTCAAGGCAAACGATATTGGACTTAAAGA-CAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAG
54104 GTGCCA
1 GTGCCA
54110 CGAAGTTGTG
Statistics
Matches: 164, Mismatches: 23, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
43 34 0.21
44 3 0.02
48 11 0.07
49 42 0.26
51 36 0.22
52 2 0.01
53 34 0.21
54 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (49 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAG
Found at i:54086 original size:92 final size:94
Alignment explanation
Indices: 53909--54098 Score: 267
Period size: 92 Copynumber: 2.0 Consensus size: 94
53899 AAAAGATAAG
* * *
53909 AAAGGTGCCAATATACTGATTCAAGGCCAGCAATATTAGACTCAAGAGGTTAAAGGTCCCAATAT
1 AAAGGTGCCAATATACTGATTCAAGGCCAACAACATTAGACTCAAGAGGATAAAGGTCCCAATAT
* *
53974 GTTGATTCAAGGCCAGCGATATTGGACTT
66 GTTGATTCAAGGCAAACGATATTGGACTT
* * * * * *
54003 AAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTAGGCTTAA-A-GATAAAGGTGCCAATAT
1 AAAGGTGCCAATATACTGATTCAAGGCCAACAACATTAGACTCAAGAGGATAAAGGTCCCAATAT
54066 GTTGATTCAAGGCAAACGATATTGGACTT
66 GTTGATTCAAGGCAAACGATATTGGACTT
54095 AAAG
1 AAAG
54099 ACAAGGTGCC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 46 0.54
93 1 0.01
94 38 0.45
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (94 bp):
AAAGGTGCCAATATACTGATTCAAGGCCAACAACATTAGACTCAAGAGGATAAAGGTCCCAATAT
GTTGATTCAAGGCAAACGATATTGGACTT
Found at i:54088 original size:143 final size:141
Alignment explanation
Indices: 53824--54093 Score: 366
Period size: 143 Copynumber: 1.9 Consensus size: 141
53814 AAAGATGGTG
*
53824 CCAATATGCTGATTCAAGGCCAACGATATTGGACTTGTGCCAATATGCTGATTCAAGGCCAGCGA
1 CCAATATGCTGATTCAAGGCCAACGATATTGGACTTGTGCCAATATGCTGATTCAAGGCCAACGA
* *
53889 CATTGGTCTTAAAAGATAAGAAAGGTGCCAATATACTGATTCAAGGCCAGCAATATTAGACTCAA
66 CATTGGTCTTAAAAGAT-A-AAAGGTGCCAATATACTGATTCAAGGCAAACAATATTAGACTCAA
53954 GAGGTTAAAGGTC
129 GAGGTTAAAGGTC
* * *
53967 CCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAACGATATTGGACTT----GTGCCAATATGCTGATTCAAGGCCA
** * *
54032 ACGACATTAGG-CTT-AAAGAT-AAAGGTGCCAATATGTTGATTCAAGGCAAACGATATTGGACT
62 ACGACATT-GGTCTTAAAAGATAAAAGGTGCCAATATACTGATTCAAGGCAAACAATATTAGACT
54094 TAAAGACAAG
Statistics
Matches: 112, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
143 70 0.62
146 6 0.05
147 34 0.30
148 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (141 bp):
CCAATATGCTGATTCAAGGCCAACGATATTGGACTTGTGCCAATATGCTGATTCAAGGCCAACGA
CATTGGTCTTAAAAGATAAAAGGTGCCAATATACTGATTCAAGGCAAACAATATTAGACTCAAGA
GGTTAAAGGTC
Found at i:54154 original size:34 final size:35
Alignment explanation
Indices: 54130--54281 Score: 183
Period size: 35 Copynumber: 4.5 Consensus size: 35
54120 GCCTTACAGA
54130 AAAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGG
1 AAAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGG
54165 AAAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGG
1 AAAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGG
* * * *
54200 GAAAAGGG-TGCCACGGA-GTCATGGACTTAAAAAG
1 AAAAAGGGATGCCACGGAGGT-GTGGGCTTAAAAGG
* *
54234 -AAAA-GG-TGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGG
*
54266 AACAA-GG-TGCCACGGA
1 AAAAAGGGATGCCACGGA
54282 ATTGTGGACT
Statistics
Matches: 106, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.22
33 21 0.20
34 20 0.19
35 42 0.40
ACGTcount: A:0.36, C:0.14, G:0.36, T:0.14
Consensus pattern (35 bp):
AAAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGG
Found at i:54176 original size:35 final size:34
Alignment explanation
Indices: 54103--54420 Score: 217
Period size: 34 Copynumber: 9.8 Consensus size: 34
54093 TTAAAGACAA
* * * * *
54103 GGTGCCACGAAGTTGTGGCCTT-ACAGAAAAAAG
1 GGTGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
*
54136 GGATGCCACGGAGGTGTGGGCTTAAAAGGAAAAAG
1 GG-TGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
* *
54171 GGATGCCACGGAGGTGTGGGCTTAAAAGGGAAAAG
1 GG-TGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
* *
54206 GGTGCCACGGA-GTCATGGACTTAAAAAG-AAAA-
1 GGTGCCACGGAGGT-GTGGACTTAAAAGGAAAAAG
* *
54238 GGTGCCACGGAGTTGTGGACTTAAAAGGAACAA-
1 GGTGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
** *
54271 GGTGCCACGGAATTGTGGACTT-------CAAAG
1 GGTGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
* * *
54298 GGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAA
1 GGTGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
* * * *
54332 AGTGCCACGGAGTTATGGA-TT------TAAAAG
1 GGTGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
* *
54359 GGTGCCACGGAGTTGTGGACTTAAAAGGAACAA-
1 GGTGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
* * *
54392 GGCGCCACAGAGTTGTGGACTTTAAAAGG
1 GGTGCCACGGAGGTGTGGAC-TTAAAAGG
54421 TTGCCAGGGA
Statistics
Matches: 233, Mismatches: 31, Indels: 41
0.76 0.10 0.13
Matches are distributed among these distances:
26 2 0.01
27 41 0.18
28 2 0.01
32 23 0.10
33 53 0.23
34 67 0.29
35 45 0.19
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.18
Consensus pattern (34 bp):
GGTGCCACGGAGGTGTGGACTTAAAAGGAAAAAG
Found at i:54306 original size:27 final size:27
Alignment explanation
Indices: 54201--54448 Score: 163
Period size: 27 Copynumber: 8.3 Consensus size: 27
54191 CTTAAAAGGG
**
54201 AAAAGGGTGCCACGGAGTCATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
54228 AAAAAGAAAAGGTGCCACGGAGTTGTGGACTT
1 -AAAAG----GGTGCCACGGAGTTGTGGACTT
*
54260 AAAAGGAACAAGGTGCCACGGAATTGTGGACTT
1 AAAA-G-----GGTGCCACGGAGTTGTGGACTT
* *
54293 CAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
54320 AAAAGGAAAAAAAGTGCCACGGAGTTATGGATTT
1 AAAAGG-------GTGCCACGGAGTTGTGGACTT
54354 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
54381 AAAAGGAACAAGGCGCCACAGAGTTGTGGACTTT
1 AAAA-G-----GGTGCCACGGAGTTGTGGAC-TT
* * *
54415 AAAAGGTTGCCAGGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
54442 AAAAGGG
1 AAAAGGG
54449 AAAAGAGTGC
Statistics
Matches: 179, Mismatches: 21, Indels: 41
0.74 0.09 0.17
Matches are distributed among these distances:
27 56 0.31
28 21 0.12
31 4 0.02
32 22 0.12
33 46 0.26
34 30 0.17
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:54342 original size:34 final size:33
Alignment explanation
Indices: 54299--54507 Score: 138
Period size: 34 Copynumber: 6.6 Consensus size: 33
54289 ACTTCAAAGG
*
54299 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAAA
1 GTGCCACGGAGTTGTGGACTTAAAAGG-AAAAAA
* *
54333 GTGCCACGGAGTTATGGATTTAAAAGG------
1 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAA
* *
54360 GTGCCACGGAGTTGTGGACTTAAAAGGAACAAG
1 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAA
* *
54393 GCGCCACAGAGTTGTGGACTTTAAAAGG------
1 GTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAA
* * * *
54421 TTGCCAGGGAGTTGTGGGCTTAAAAGGGAAAAGA
1 GTGCCACGGAGTTGTGGACTTAAAA-GGAAAAAA
* **
54455 GTGCCACGGAGTCGTGGACTTGGAA-GAAAAAA
1 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAA
* ** *
54487 ATGCCACTAAGTCGTGGACTT
1 GTGCCACGGAGTTGTGGACTT
54508 TGGAAAGAGA
Statistics
Matches: 139, Mismatches: 22, Indels: 30
0.73 0.12 0.16
Matches are distributed among these distances:
27 31 0.22
28 16 0.12
32 24 0.17
33 17 0.12
34 51 0.37
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (33 bp):
GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAA
Found at i:54367 original size:61 final size:61
Alignment explanation
Indices: 54166--54475 Score: 354
Period size: 61 Copynumber: 5.0 Consensus size: 61
54156 CTTAAAAGGA
* * * *
54166 AAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGGGAAAAGGGTGCCACGGAGTCATGGACTTA
1 AAAAGGG-TGCCACGGAGTTGTGGGCTTAAAA-GGAAAAAGGTGCCACGGAGTTATGGACTTT
* * * *
54229 AAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAATTGTGGAC-TT
1 AAAAG----GGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTATGGACTTT
* *
54293 CAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAAAGTGCCACGGAGTTATGGA-TTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAAAGGTGCCACGGAGTTATGGACTTT
* * * * *
54354 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGCGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTATGGACTTT
* * * **
54415 AAAAGGTTGCCAGGGAGTTGTGGGCTTAAAAGGGAAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTATGGACTT
54476 GGAAGAAAAA
Statistics
Matches: 210, Mismatches: 29, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
60 46 0.22
61 90 0.43
62 18 0.09
63 5 0.02
64 5 0.02
65 22 0.10
66 22 0.10
67 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.35, T:0.19
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTATGGACTTT
Found at i:54411 original size:121 final size:124
Alignment explanation
Indices: 54166--54475 Score: 446
Period size: 122 Copynumber: 2.5 Consensus size: 124
54156 CTTAAAAGGA
* *
54166 AAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGGGAAAAGGGTGCCACGGAGTCATGGACTTAAA
1 AAAAGGG-TGCCACGGAGTTGTGGGCTTAAAAGGGAAAAGAGTGCCACGGAGTCATGGACTTAAA
* *
54231 AAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAATTGTGGAC-TT
65 AAG---AGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGCGCCACAGAATTGTGGACTTT
* * * * *
54293 CAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAAAGTGCCACGGAGTTATGGA-TTTAAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAAGAGTGCCACGGAGTCATGGACTTAAAA
*
54357 AG-GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGCGCCACAGAGTTGTGGACTTT
66 AGAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGCGCCACAGAATTGTGGACTTT
* * *
54415 AAAAGGTTGCCAGGGAGTTGTGGGCTTAAAAGGGAAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAAGAGTGCCACGGAGTCATGGACTT
54476 GGAAGAAAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
121 50 0.30
122 53 0.32
123 2 0.01
125 7 0.04
126 46 0.28
127 6 0.04
ACGTcount: A:0.32, C:0.14, G:0.35, T:0.19
Consensus pattern (124 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAAGAGTGCCACGGAGTCATGGACTTAAAA
AGAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGCGCCACAGAATTGTGGACTTT
Found at i:54513 original size:62 final size:61
Alignment explanation
Indices: 54447--54736 Score: 341
Period size: 62 Copynumber: 4.7 Consensus size: 61
54437 GGCTTAAAAG
* * *
54447 GGAAAAGAG-TGCCACGGAGTCGTGGACTTGGAAGAAAAAAATGCCACTAAGTCGTGGACTTT
1 GGAAAAGAGATGCCACTGAGTCGTGGACTTTGAAG-AAAAGATGCCACTAAGTCGTGGAC-TT
* *
54509 GG-AAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCATGGACTTT
1 GGAAAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTGGAC-TT
* * * *
54570 GGGGAAAAAAGACGCCACTGAGTCATGAACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTT
1 --GGAAAAGAGATGCCACTGAGTCGTGGACTTTGAAG-AAAAGATGCCACTAAGTCGTGGACTT
* * * *
54634 AGAAAAGAGATGCTATTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTTGTGGACTT
1 GGAAAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTT
* * * * *
54695 GGAAGAAAAGAAGCCACTAAGTCATGGACTTTGAAGGAAAGA
1 GGAA-AAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGA
54737 GATTTGAAGA
Statistics
Matches: 195, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
61 58 0.30
62 83 0.43
63 2 0.01
64 30 0.15
65 22 0.11
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.21
Consensus pattern (61 bp):
GGAAAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTT
Found at i:54553 original size:31 final size:31
Alignment explanation
Indices: 54448--54736 Score: 307
Period size: 31 Copynumber: 9.2 Consensus size: 31
54438 GCTTAAAAGG
* *
54448 GAAAAGAGTGCCACGGAGTCGTGGACTTGGAA
1 GAAAAGA-TGCCACTGAGTCGTGGACTTTGAA
* *
54480 GAAAAAAATGCCACTAAGTCGTGGACTTTG--
1 G-AAAAGATGCCACTGAGTCGTGGACTTTGAA
54510 GAAAGAGATGCCACTGAGTCGTGGACTTTGAA
1 GAAA-AGATGCCACTGAGTCGTGGACTTTGAA
*
54542 GAAAAGATGCCACTGAGTCATGGACTTTGGGGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTT---GAA
* * *
54576 -AAAAGACGCCACTGAGTCATGAACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
* *
54606 GAAAAAGATGCCACTAAGTCGTGGACTTAGAA
1 G-AAAAGATGCCACTGAGTCGTGGACTTTGAA
* * *
54638 -AAGAGATGCTATTGAGTCGTGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
* * *
54668 GAAAAGATGCCACTAAGTTGTGGACTTGGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
* * *
54699 GAAAAGAAGCCACTAAGTCATGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
*
54730 GGAAAGA
1 GAAAAGA
54737 GATTTGAAGA
Statistics
Matches: 217, Mismatches: 30, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.01
30 52 0.24
31 80 0.37
32 49 0.23
33 30 0.14
34 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (31 bp):
GAAAAGATGCCACTGAGTCGTGGACTTTGAA
Found at i:54618 original size:126 final size:124
Alignment explanation
Indices: 54448--54739 Score: 388
Period size: 126 Copynumber: 2.3 Consensus size: 124
54438 GCTTAAAAGG
* * * * * * *
54448 GAAAAGAGTGCCACGGAGTCGTGGACTTGGAAGAAAAAAATGCCACTAAGTCGTGGACTTTGGAA
1 GAAAAGA-AGCCACTGAGTCATGGACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTTAGAAA
*
54513 AGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCATGGACTTTGGGGAA
65 AGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGAC-TT--GGAA
* *
54576 -AAAAGACGCCACTGAGTCATGAACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTTAGAAAA
1 GAAAAGAAGCCACTGAGTCATGGACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTTAGAAAA
* * **
54640 GAGATGCTATTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTTGTGGACTTGGAA
66 GAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGACTTGGAA
* *
54699 GAAAAGAAGCCACTAAGTCATGGACTTTGAAGGAAAGAGAT
1 GAAAAGAAGCCACTGAGTCATGGACTTTGAA-GAAAAAGAT
54740 TTGAAGAATT
Statistics
Matches: 145, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
123 4 0.03
124 27 0.19
125 10 0.07
126 98 0.68
127 6 0.04
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (124 bp):
GAAAAGAAGCCACTGAGTCATGGACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTTAGAAAA
GAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGACTTGGAA
Found at i:56028 original size:7 final size:7
Alignment explanation
Indices: 56016--56074 Score: 68
Period size: 7 Copynumber: 8.3 Consensus size: 7
56006 CCTTCGCACT
56016 TTTTTTG
1 TTTTTTG
56023 TTTTTT-
1 TTTTTTG
56029 TTTGTGTGTG
1 TTT-T-T-TG
*
56039 TTGTTT-
1 TTTTTTG
56045 TTTTTTG
1 TTTTTTG
56052 TTTTTTG
1 TTTTTTG
56059 TTTTTTG
1 TTTTTTG
56066 TTTTTTG
1 TTTTTTG
56073 TT
1 TT
56075 GTGTTTGTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
6 8 0.18
7 31 0.69
8 2 0.04
9 2 0.04
10 2 0.04
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (7 bp):
TTTTTTG
Found at i:56044 original size:19 final size:18
Alignment explanation
Indices: 56020--56076 Score: 66
Period size: 17 Copynumber: 3.2 Consensus size: 18
56010 CGCACTTTTT
56020 TTGTTTTTTTTTGTGTGTG
1 TTGTTTTTTTTTGT-TGTG
*
56039 TTGTTTTTTTTTGTT-TT
1 TTGTTTTTTTTTGTTGTG
56056 TTGTTTTTTGTTT-TT-TG
1 TTGTTTTTT-TTTGTTGTG
56073 TTGT
1 TTGT
56077 GTTTGTACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 17 0.49
18 4 0.11
19 14 0.40
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (18 bp):
TTGTTTTTTTTTGTTGTG
Found at i:56045 original size:24 final size:22
Alignment explanation
Indices: 56016--56079 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 22
56006 CCTTCGCACT
56016 TTTTTTGTTTTTTTTTGTGTGTG
1 TTTTTTGTTTTTTTTTGTGT-TG
*
56039 TTGTTTT-TTTTTGTTT-T-TTG
1 TT-TTTTGTTTTTTTTTGTGTTG
*
56059 TTTTTTGTTTTTTGTTGTGTT
1 TTTTTTGTTTTTTTTTGTGTT
56080 TGTACTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 4 0.12
20 11 0.32
21 2 0.06
22 3 0.09
23 10 0.29
24 4 0.12
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (22 bp):
TTTTTTGTTTTTTTTTGTGTTG
Found at i:62427 original size:22 final size:22
Alignment explanation
Indices: 62399--62475 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
62389 CTCATTCTCT
62399 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
* * *
62421 CATCACTGTTCAT-CA-CTATT
1 CATCACTGTTCATGTATCGATA
62441 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
62463 CATCACTGTTCAT
1 CATCACTGTTCAT
62476 CACTGTACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.34
21 2 0.04
22 29 0.62
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:62436 original size:10 final size:10
Alignment explanation
Indices: 62421--62481 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
62411 TGTATCGATA
62421 CATCACTGTT
1 CATCACTGTT
*
62431 CATCACTATT
1 CATCACTGTT
62441 CATCACTGTT
1 CATCACTGTT
* *
62451 CATGTA-TCGATA
1 CAT-CACT-G-TT
62463 CATCACTGTT
1 CATCACTGTT
62473 CATCACTGT
1 CATCACTGT
62482 ACATTGAGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
10 32 0.78
11 4 0.10
12 5 0.12
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (10 bp):
CATCACTGTT
Found at i:62457 original size:42 final size:42
Alignment explanation
Indices: 62398--62479 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
62388 TCTCATTCTC
62398 TCATCACTGTTCATGTATCGATACATCACTGTTCATCACTAT
1 TCATCACTGTTCATGTATCGATACATCACTGTTCATCACTAT
62440 TCATCACTGTTCATGTATCGATACATCACTGTTCATCACT
1 TCATCACTGTTCATGTATCGATACATCACTGTTCATCACT
62480 GTACATTGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.38
Consensus pattern (42 bp):
TCATCACTGTTCATGTATCGATACATCACTGTTCATCACTAT
Found at i:63046 original size:32 final size:33
Alignment explanation
Indices: 62986--63050 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 33
62976 CTAAGTGATT
62986 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGA
1 GAGAGGTTCTATCTTAGCCTTT-AAAAAGATAGA
63020 GAGAGGTTTCTATCTTAGCC-TT-AAAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTAAAAAGATAG
63051 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 9 0.30
34 8 0.27
35 13 0.43
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (33 bp):
GAGAGGTTCTATCTTAGCCTTTAAAAAGATAGA
Found at i:64311 original size:33 final size:33
Alignment explanation
Indices: 64251--64316 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
64241 AAATTCCCAG
* * *
64251 ATGTATCGATACAAAGATTAATTTATCGATACA
1 ATGTATCGACACAAAGAGTAATGTATCGATACA
**
64284 ATGTATCGACACATTGAGTAATGTATCGATACA
1 ATGTATCGACACAAAGAGTAATGTATCGATACA
64317 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (33 bp):
ATGTATCGACACAAAGAGTAATGTATCGATACA
Found at i:64388 original size:32 final size:32
Alignment explanation
Indices: 64342--64410 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
64332 CTTTGTAGCT
* *
64342 ATACATTATATCGATAGAACACTTATGTATCG
1 ATACATTATATCGATACAACACTTATGTATCA
* *
64374 ATACATTGTGTCGATACAACACTTATGTATCA
1 ATACATTATATCGATACAACACTTATGTATCA
64406 ATACA
1 ATACA
64411 GTTACTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
ATACATTATATCGATACAACACTTATGTATCA
Found at i:65473 original size:45 final size:45
Alignment explanation
Indices: 65409--65544 Score: 272
Period size: 45 Copynumber: 3.0 Consensus size: 45
65399 TTATTCTTTC
65409 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
1 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
65454 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
1 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
65499 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
1 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
65544 A
1 A
65545 GCCTTGTAGA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (45 bp):
AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
Done.