Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2300
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: 195119
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1836 original size:49 final size:50
Alignment explanation
Indices: 1716--1952 Score: 268
Period size: 49 Copynumber: 4.7 Consensus size: 50
1706 ATTTGGGTAA
* * * *
1716 AGAGATCCCATGTAAGACCATGTCT-GGACATGACATTGGCATCCTTAAGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGAC--G
*
1770 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1820 AGAGGT-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
1869 AGAGGTCCC-TATAAGACCATGTCTGGGACAT-GCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
1917 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
1953 TTTGGCATGT
Statistics
Matches: 160, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
47 1 0.01
48 13 0.08
49 71 0.44
50 30 0.19
51 2 0.01
52 4 0.03
54 25 0.16
55 14 0.09
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1929 original size:99 final size:102
Alignment explanation
Indices: 1720--1960 Score: 316
Period size: 99 Copynumber: 2.4 Consensus size: 102
1710 GGGTAAAGAG
* *
1720 ATCCCATGTAAGACCATGTCT-GGACATGACATTGGCATCCTTAAGACATGAGAGGTCCCCTGTA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGACATGAGAGGTCCCCTATA
* *
1784 AGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAG
63 AGACCATGTCTGGGACATGGCATGGGCACCGACACGAGAC
* * *
1824 GT-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAGATGAGAGGT-CCCTATAAGA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGACATGAGAGGTCCCCTATAAGA
1885 CCATGTCTGGGACAT-GCATGGGCACC-ATCACGAGAAC
66 CCATGTCTGGGACATGGCATGGGCACCGA-CACGAG-AC
*
1922 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1961 GTTATTATCA
Statistics
Matches: 123, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
96 1 0.01
97 16 0.13
98 26 0.21
99 45 0.37
103 20 0.16
104 15 0.12
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (102 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGACATGAGAGGTCCCCTATAAGA
CCATGTCTGGGACATGGCATGGGCACCGACACGAGAC
Found at i:8882 original size:50 final size:50
Alignment explanation
Indices: 8758--9006 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
8748 GATAATAACA
* * ** * *
8758 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
8809 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
8859 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
8909 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
8964 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
9007 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:8936 original size:100 final size:104
Alignment explanation
Indices: 8757--9006 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
8747 TGATAATAAC
**
8757 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
8822 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
8859 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
8922 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
8964 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
9007 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:9122 original size:13 final size:13
Alignment explanation
Indices: 9101--9132 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9091 GCTTGGATCA
*
9101 TCATCAAATAAAT
1 TCATAAAATAAAT
9114 TCATAAAATAAAT
1 TCATAAAATAAAT
9127 TCATAA
1 TCATAA
9133 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:9379 original size:30 final size:30
Alignment explanation
Indices: 9344--9401 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9334 CCTCGACTCT
*
9344 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
9374 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
9402 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:13043 original size:21 final size:20
Alignment explanation
Indices: 13001--13043 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
12991 TTTTTTTATT
**
13001 TTATAAAAAAATAAAATTAA
1 TTATAAAAAAATAAAAAAAA
*
13021 TTATAAATTAAATAAAAAAAA
1 TTATAAA-AAAATAAAAAAAA
13042 TT
1 TT
13044 TTGACTCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TTATAAAAAAATAAAAAAAA
Found at i:25021 original size:126 final size:126
Alignment explanation
Indices: 24787--25027 Score: 378
Period size: 126 Copynumber: 1.9 Consensus size: 126
24777 CTTTAAGAGG
* *
24787 ATATTCGAATATTCGAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCATTTGAA
1 ATATTCGAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATTTGAA
* *** *
24852 TTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTGAGAGTAAACCGGTAAAAGA
66 TTCTTTAAATACCGAACATTGCCTTTATTTTAAAAACAATTGAGAATAAACCGGTAAAAGA
24913 ATATTCTG-ATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATTTGA
1 ATATTC-GAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATTTGA
*
24977 ATTCTTTAAATACCGAACATT-TCTATTATTTTAAAAACAATTGAGAATAAA
65 ATTCTTTAAATACCGAACATTGCCT-TTATTTTAAAAACAATTGAGAATAAA
25028 TCTGTGAATA
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
125 2 0.02
126 102 0.97
127 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (126 bp):
ATATTCGAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATTTGAA
TTCTTTAAATACCGAACATTGCCTTTATTTTAAAAACAATTGAGAATAAACCGGTAAAAGA
Found at i:25667 original size:20 final size:21
Alignment explanation
Indices: 25642--25682 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25632 ACGAACTATT
*
25642 ATAATAGTAG-AATATAATAA
1 ATAATAGTAGTAATAAAATAA
*
25662 ATAATATTAGTAATAAAATAA
1 ATAATAGTAGTAATAAAATAA
25683 TATTAACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (21 bp):
ATAATAGTAGTAATAAAATAA
Found at i:25675 original size:16 final size:17
Alignment explanation
Indices: 25656--25687 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25646 TAGTAGAATA
25656 TAAT-AAATAATATTAG
1 TAATAAAATAATATTAG
25672 TAATAAAATAATATTA
1 TAATAAAATAATATTA
25688 ACTATTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAAAATAATATTAG
Found at i:25730 original size:15 final size:15
Alignment explanation
Indices: 25705--25747 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
25695 ACAGTAAAGT
*
25705 ATAAT-AAAATAGTA
1 ATAATAAAAATAATA
25719 ATAATAAAAATAATA
1 ATAATAAAAATAATA
*
25734 ATACTAAAAATAAT
1 ATAATAAAAATAAT
25748 CAATTTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
ATAATAAAAATAATA
Found at i:26789 original size:17 final size:15
Alignment explanation
Indices: 26756--26791 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
26746 TAGGTTTAGG
26756 TGGGTTTTGGGGTAT
1 TGGGTTTTGGGGTAT
26771 TGGGTTATTGGGTGTAT
1 TGGGTT-TTGGG-GTAT
26788 TGGG
1 TGGG
26792 CTTAGAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.44
Consensus pattern (15 bp):
TGGGTTTTGGGGTAT
Found at i:43084 original size:3 final size:3
Alignment explanation
Indices: 43076--43100 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43066 ATCTTATCTA
43076 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
43101 TGATGATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:45005 original size:3 final size:3
Alignment explanation
Indices: 44999--45030 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44989 TGGAAAGGAA
44999 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
45031 GAACAAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:56241 original size:28 final size:29
Alignment explanation
Indices: 56193--56262 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
56183 TATTTTTTTC
*
56193 AAAGTTAAATTTAATCCTTAA-TTAAAAA
1 AAAGTTAAATTTAATCATTAACTTAAAAA
* *
56221 AAAGTTAAATTTGA-CAATTAACCTTTTAAAA
1 AAAGTTAAATTTAATC-ATTAA-C-TTAAAAA
56252 AAAGTTAAATT
1 AAAGTTAAATT
56263 ATTAGTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.03
28 17 0.49
31 17 0.49
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAGTTAAATTTAATCATTAACTTAAAAA
Found at i:60564 original size:6 final size:6
Alignment explanation
Indices: 60553--60582 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
60543 GATGAGTCCA
60553 TGTAGG TGTAGG TGTAGG TGTAGG TGTAGG
1 TGTAGG TGTAGG TGTAGG TGTAGG TGTAGG
60583 GTCTTCGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGTAGG
Found at i:66668 original size:22 final size:22
Alignment explanation
Indices: 66643--66685 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
66633 GTTACTAATA
66643 TATTT-TTATAAATGTGTATATT
1 TATTTCTT-TAAATGTGTATATT
66665 TATTTCTTTAAATGTGTATAT
1 TATTTCTTTAAATGTGTATAT
66686 CTTAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (22 bp):
TATTTCTTTAAATGTGTATATT
Found at i:67063 original size:22 final size:23
Alignment explanation
Indices: 67038--67090 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
67028 ATTGATGAAG
67038 ATAATAAAT-TGT-ACATATTAAA
1 ATAA-AAATGTGTAACATATTAAA
67060 ATAAAAATGTGTAAAACATATTAAA
1 ATAAAAATGTGT--AACATATTAAA
67085 ATAAAA
1 ATAAAA
67091 CTTTAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.15
22 7 0.26
25 16 0.59
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAAAAATGTGTAACATATTAAA
Found at i:67430 original size:59 final size:60
Alignment explanation
Indices: 67338--67509 Score: 188
Period size: 59 Copynumber: 2.9 Consensus size: 60
67328 TTAATATAAC
* * * * * *
67338 ATTTGCTACCTGAACTTCACACTTTTTCCTAATTTTGTACCTTAA-CTTTTTTTGGCCCA
1 ATTTGATACCTCAACTTGACACTTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
* * * *
67397 ATTTGGTACCTCAACTTGACAGTTTTTCCTAATTTGGCACCTAAACCATTTTTTGGCCCA
1 ATTTGATACCTCAACTTGACACTTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
* * * *
67457 ATTTTATACGC-CAACTTGCCATTTTTTCCTAATTTAGTACCT-AAGCATTTTTT
1 ATTTGATAC-CTCAACTTGACACTTTTTCCTAATTTAGTACCTAAACCATTTTTT
67510 TAGGTTCATT
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
59 48 0.50
60 47 0.49
61 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.44
Consensus pattern (60 bp):
ATTTGATACCTCAACTTGACACTTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
Found at i:67510 original size:60 final size:59
Alignment explanation
Indices: 67338--67510 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 59
67328 TTAATATAAC
* * * * *
67338 ATTTGCTACCTGAACTTCACACTTTTTCCTAATTTTGTACCTTAAC-TTTTTTTGGCCCA
1 ATTTGATACCTCAACTTGACAGTTTTTCCTAATTTAGTACC-TAACATTTTTTTGGCCCA
* * *
67397 ATTTGGTACCTCAACTTGACAGTTTTTCCTAATTTGGCACCTAAACCA-TTTTTTGGCCCA
1 ATTTGATACCTCAACTTGACAGTTTTTCCTAATTTAGTACCT-AA-CATTTTTTTGGCCCA
* * *
67457 ATTTTATACGC-CAACTTGCCATTTTTTCCTAATTTAGTACCTAAGCATTTTTTT
1 ATTTGATAC-CTCAACTTGACAGTTTTTCCTAATTTAGTACCTAA-CATTTTTTT
67511 AGGTTCATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 1 0.01
59 41 0.43
60 53 0.55
61 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.44
Consensus pattern (59 bp):
ATTTGATACCTCAACTTGACAGTTTTTCCTAATTTAGTACCTAACATTTTTTTGGCCCA
Found at i:67998 original size:18 final size:19
Alignment explanation
Indices: 67972--68013 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
67962 AAGTACCAAC
*
67972 TTAAGAAAA-ATATCAAAT
1 TTAAAAAAATATATCAAAT
*
67990 TTAAAAAAATATATCTAAT
1 TTAAAAAAATATATCAAAT
68009 TTAAA
1 TTAAA
68014 TACGGAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
TTAAAAAAATATATCAAAT
Found at i:68548 original size:27 final size:26
Alignment explanation
Indices: 68489--68549 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
68479 CAATGTTTAT
*
68489 ATCTTTTTTATCAAATTTATTCCTTA
1 ATCTTTTTTATCAAATTTATTCCCTA
* * *
68515 TTCCTTTTTTAGTTAAATTTGTTCCCTA
1 AT-CTTTTTTA-TCAAATTTATTCCCTA
68543 ATCTTTT
1 ATCTTTT
68550 CAAAAACAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.04
27 13 0.46
28 14 0.50
ACGTcount: A:0.21, C:0.16, G:0.03, T:0.59
Consensus pattern (26 bp):
ATCTTTTTTATCAAATTTATTCCCTA
Found at i:68691 original size:31 final size:30
Alignment explanation
Indices: 68656--68713 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
68646 TATTCTAAAT
*
68656 TTTTGAAT-TTTTATGAACTTTTTAATTTCTA
1 TTTTGAATATTTTAT-AA-ATTTTAATTTCTA
68687 TTTTGAATATTTTATAAATTTTAATTT
1 TTTTGAATATTTTATAAATTTTAATTT
68714 ATTTGTTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 9 0.36
31 10 0.40
32 6 0.24
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTTGAATATTTTATAAATTTTAATTTCTA
Found at i:81566 original size:14 final size:14
Alignment explanation
Indices: 81547--81575 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
81537 ATGTTGAGAT
81547 AAGGTTATACCAAG
1 AAGGTTATACCAAG
81561 AAGGTTATACCAAG
1 AAGGTTATACCAAG
81575 A
1 A
81576 CAGCAAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AAGGTTATACCAAG
Found at i:92326 original size:45 final size:46
Alignment explanation
Indices: 92248--92428 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
92238 GCTCTCTCAT
* * *
92248 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
92294 ATGAAATGTGTAAGA-CATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
**
92339 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
92385 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
92429 TCAAAGATAA
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 41 0.34
46 80 0.66
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:106958 original size:53 final size:53
Alignment explanation
Indices: 106877--107027 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
106867 CTTACACGGT
* *
106877 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAACCCAG-CTATGGTCTTATACGGAATCACATTA
*
106932 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTA
** * * *
106985 TCACATTGCACCGATGCCATAGCCCAGCTACGGTCTTAAACGG
1 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGG
107028 GCACACTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:113991 original size:53 final size:53
Alignment explanation
Indices: 113910--114060 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
113900 CTTACACGGT
* *
113910 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
113965 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
114018 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
114061 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:115781 original size:42 final size:42
Alignment explanation
Indices: 115718--115844 Score: 145
Period size: 42 Copynumber: 3.0 Consensus size: 42
115708 CTTCGTTTTC
** *
115718 TCGATGCCATAGTTCAACTATGGTCTTACACATC-TTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACA-CATTCACAT-A
* *
115761 T-GATGCCATAGCCCGGCTATGGTCTTACACACATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACACATTCACATA
*
115802 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ACATTCACATA
115843 TC
1 TC
115845 TCACTGATGC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
41 11 0.15
42 60 0.82
43 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACACATTCACATA
Found at i:115979 original size:31 final size:31
Alignment explanation
Indices: 115944--116123 Score: 256
Period size: 31 Copynumber: 5.8 Consensus size: 31
115934 CTTGTCACTT
* *
115944 GTAGCCGAAGCTACCACTATTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
**
115975 GTAGCC-AGAGCTACCGTTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
116006 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
116037 GTAGCCAGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
* *
116068 GTAGCAGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
116099 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
116124 TGTCATTTGT
Statistics
Matches: 134, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
30 4 0.03
31 128 0.96
32 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:127640 original size:9 final size:9
Alignment explanation
Indices: 127626--127667 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
127616 AGAGATTTAA
127626 TTAAAATAT
1 TTAAAATAT
127635 TTAAAAT-T
1 TTAAAATAT
*
127643 TAAGAAATAAT
1 TTA-AAAT-AT
127654 TTAAAATAT
1 TTAAAATAT
127663 TTAAA
1 TTAAA
127668 TTATGTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 3 0.11
9 18 0.64
10 4 0.14
11 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
TTAAAATAT
Found at i:129198 original size:24 final size:24
Alignment explanation
Indices: 129170--129229 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
129160 TTAATATATT
*
129170 TATTT-AGTTTGAATATTAATTTGG
1 TATTTAAGTTT-AATATTAATTTAG
*
129194 TATTTAAGTTTAATTTTAATTTAG
1 TATTTAAGTTTAATATTAATTTAG
*
129218 TATTTGAGTTTA
1 TATTTAAGTTTA
129230 GTATCTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (24 bp):
TATTTAAGTTTAATATTAATTTAG
Found at i:146772 original size:24 final size:24
Alignment explanation
Indices: 146727--146773 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
146717 TTTGTTTGTT
*
146727 TAATTTTAAAATTCAGATATCAAA
1 TAATTTTAAAATTCAGAAATCAAA
*
146751 TAATTTTAACAATT-TGAAATCAA
1 TAATTTTAA-AATTCAGAAATCAA
146774 TCTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TAATTTTAAAATTCAGAAATCAAA
Found at i:146884 original size:21 final size:22
Alignment explanation
Indices: 146849--146891 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
146839 ATAACCACCT
*
146849 AATAATTTGAATAATTTTTTTA
1 AATAATTTGAATAATTATTTTA
146871 AATAATTT-AATAATTATTTTA
1 AATAATTTGAATAATTATTTTA
146892 TAACTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATAATTTGAATAATTATTTTA
Found at i:147342 original size:28 final size:28
Alignment explanation
Indices: 147284--147342 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
147274 ACATGAATCG
* *
147284 ATTATTTAATTAGTAAACGAAGTATAAA
1 ATTATTTAACTAATAAACGAAGTATAAA
147312 ATTATTTAACTACATAAAC-AA-TATAATA
1 ATTATTTAACTA-ATAAACGAAGTATAA-A
147340 ATT
1 ATT
147343 TTACCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 17 0.63
29 5 0.19
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (28 bp):
ATTATTTAACTAATAAACGAAGTATAAA
Found at i:150140 original size:9 final size:9
Alignment explanation
Indices: 150115--150144 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
150105 ATCATTAGCC
150115 TAAGTTAAT
1 TAAGTTAAT
150124 TAAGGTTAAT
1 TAA-GTTAAT
150134 TAAGTTAAT
1 TAAGTTAAT
150143 TA
1 TA
150145 TGATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (9 bp):
TAAGTTAAT
Found at i:150154 original size:19 final size:19
Alignment explanation
Indices: 150115--150154 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
150105 ATCATTAGCC
*
150115 TAAGTTAATTAAGGTTAAT
1 TAAGTTAATTAAGATTAAT
* *
150134 TAAGTTAATTATGATTTAT
1 TAAGTTAATTAAGATTAAT
150153 TA
1 TA
150155 TATATTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (19 bp):
TAAGTTAATTAAGATTAAT
Found at i:150693 original size:24 final size:24
Alignment explanation
Indices: 150664--150711 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
150654 AATGAAAAAG
150664 TTTAAGGAACATTTGAAAATTGAA
1 TTTAAGGAACATTTGAAAATTGAA
150688 TTTAAGGAACATTTGAAAATTGAA
1 TTTAAGGAACATTTGAAAATTGAA
150712 ATTGAACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTAAGGAACATTTGAAAATTGAA
Found at i:153768 original size:19 final size:17
Alignment explanation
Indices: 153733--153774 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
153723 CTTATTTTAA
153733 TATTTATATTAGAGTAG
1 TATTTATATTAGAGTAG
*
153750 TATTATATATTTAGTGTAG
1 TATT-TATA-TTAGAGTAG
153769 -ATTTAT
1 TATTTAT
153775 TTTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (17 bp):
TATTTATATTAGAGTAG
Found at i:157633 original size:6 final size:6
Alignment explanation
Indices: 157622--157649 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
157612 TCCCAATATC
157622 AGCCTT AGCCTT AGCCTT AGCCTT AGCC
1 AGCCTT AGCCTT AGCCTT AGCCTT AGCC
157650 ATTTCACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.29
Consensus pattern (6 bp):
AGCCTT
Found at i:159273 original size:38 final size:38
Alignment explanation
Indices: 159222--159298 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
159212 CAATTCGACA
* *
159222 ATCAATATAGTAGATTAATAGTCATTGATAAGTAGAAG
1 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
159260 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
1 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
159298 A
1 A
159299 ACATACCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (38 bp):
ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
Found at i:166323 original size:25 final size:26
Alignment explanation
Indices: 166285--166343 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
166275 TTAGAATCTA
*
166285 TTTTTAA-AATAATTAAA-T-TTAACT
1 TTTTTAATAAAAATTAAACTATTAA-T
166309 TTTTTAATAAAAATTAAACTATTAAT
1 TTTTTAATAAAAATTAAACTATTAAT
*
166335 TTTGTAATA
1 TTTTTAATA
166344 CATATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.23
25 9 0.30
26 10 0.33
27 4 0.13
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTAATAAAAATTAAACTATTAAT
Found at i:167658 original size:21 final size:23
Alignment explanation
Indices: 167628--167678 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
167618 TTTTTTAAGT
*
167628 TAAATTTAAAAT-A-AAAAAATA
1 TAAATATAAAATAAGAAAAAATA
*
167649 TAAATATAAATTAAGAAAAAATA
1 TAAATATAAAATAAGAAAAAATA
167672 TAAATAT
1 TAAATAT
167679 TAAGAACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 1 0.04
23 15 0.58
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAATATAAAATAAGAAAAAATA
Found at i:169752 original size:2 final size:2
Alignment explanation
Indices: 169745--169794 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
169735 CTTATCTAAA
169745 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
169787 TC TC TC TC
1 TC TC TC TC
169795 ATGCCATACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:172908 original size:15 final size:16
Alignment explanation
Indices: 172879--172924 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
172869 TAATAAAGTC
172879 TCATTCTTTTCATTTTA
1 TCATT-TTTTCATTTTA
172896 TCATTTTTT-ATTTTA
1 TCATTTTTTCATTTTA
*
172911 TTATTTTATTCATT
1 TCATTTT-TTCATT
172925 CAAAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 12 0.46
16 6 0.23
17 8 0.31
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (16 bp):
TCATTTTTTCATTTTA
Found at i:175807 original size:17 final size:17
Alignment explanation
Indices: 175785--175843 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
175775 AAAAAATATA
175785 AAATTAATAATGTTAAC
1 AAATTAATAATGTTAAC
175802 AAATTAATAATG--AATC
1 AAATTAATAATGTTAA-C
* *
175818 TAATTAA-AAT-TTAAA
1 AAATTAATAATGTTAAC
175833 AAATTAATAAT
1 AAATTAATAAT
175844 ATTTTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 11 0.31
16 12 0.34
17 12 0.34
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATTAATAATGTTAAC
Found at i:176934 original size:48 final size:48
Alignment explanation
Indices: 176873--176992 Score: 240
Period size: 48 Copynumber: 2.5 Consensus size: 48
176863 ATTACAAACA
176873 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
176921 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
176969 TCAATTATTTACCCTATTAACAAA
1 TCAATTATTTACCCTATTAACAAA
176993 GCTCGGACTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (48 bp):
TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
Found at i:178592 original size:5 final size:5
Alignment explanation
Indices: 178582--178606 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
178572 TTTCTTTTAT
178582 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
178607 CTTAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:181311 original size:31 final size:31
Alignment explanation
Indices: 181237--181297 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
181227 GTTAACACTC
*
181237 TTAAAATTACTTTATCAAATTCAGGTTCATA
1 TTAAAATTATTTTATCAAATTCAGGTTCATA
181268 TTAAAATTATTTTATCAAATTCAGGTTCAT
1 TTAAAATTATTTTATCAAATTCAGGTTCAT
181298 TATAGCATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (31 bp):
TTAAAATTATTTTATCAAATTCAGGTTCATA
Found at i:182614 original size:20 final size:20
Alignment explanation
Indices: 182577--182614 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
182567 AAAAGAAAAA
* *
182577 AAAATGTAATAAAAAAAAGT
1 AAAAGGTAAAAAAAAAAAGT
182597 AAAAGGTAAAAAAAAAAA
1 AAAAGGTAAAAAAAAAAA
182615 TTGCCGACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAAGGTAAAAAAAAAAAGT
Found at i:183179 original size:20 final size:20
Alignment explanation
Indices: 183154--183195 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
183144 TACTATTAAT
183154 ATTATTTTAATATTAATA-TA
1 ATTATTTTAA-ATTAATACTA
*
183174 ATTATTTTTAATTAATACTA
1 ATTATTTTAAATTAATACTA
183194 AT
1 AT
183196 ATAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATTTTAAATTAATACTA
Found at i:183188 original size:25 final size:25
Alignment explanation
Indices: 183160--183218 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 25
183150 TAATATTATT
183160 TTAATATTAATATAAT-TATTTTTAA
1 TTAATATTAATATAATAT-TTTTTAA
*
183185 TTAATACTAATATAATATTTTTTAA
1 TTAATATTAATATAATATTTTTTAA
183210 TTATATATT
1 TTA-ATATT
183219 GATTATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAATATTAATATAATATTTTTTAA
Found at i:184583 original size:141 final size:149
Alignment explanation
Indices: 184425--184726 Score: 406
Period size: 159 Copynumber: 2.0 Consensus size: 149
184415 ACATACACAT
* *
184425 AGATTGTCACATGGATAATATGTCATCACTTAATTAATTTTTAAAATTTT-A-AAAAATTCAAAA
1 AGATTGTCACATAGATAACATGTCATCACTTAATTAATTTTTAAAATTTTAATAAAAATTCAAAA
184488 AAATAT-AAAA-A-A-TAT-TTTTT-ATATTTTAAAAGAATTAATTAAATATTAAAATGCCATCC
66 AAATATAAAAATATATTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAAAATGCCATCC
184547 A-CCAAAATATCCACATGTA
131 ACCCAAAA-ATCCACATGTA
*
184566 AGATTGTCACATAGATAACATGTCATCACTTAATTAATTTTTTAAATTTTAAAAAATTCAAAAAT
1 AGATTGTCACATAGATAACATGTCATCACTTAATTAATTTTTAAAATTTT----AA-T-AAAAAT
184631 TCAAAAAAATATAAAAATATATTTTTTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAA
60 TCAAAAAAATATAAAAATATA----TTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAA
*
184696 AATGCCATCCACCCAACAATCCACATGTA
121 AATGCCATCCACCCAAAAATCCACATGTA
184725 AG
1 AG
184727 CCACATCAAC
Statistics
Matches: 138, Mismatches: 4, Indels: 20
0.85 0.02 0.12
Matches are distributed among these distances:
141 47 0.34
146 1 0.01
149 18 0.13
150 4 0.03
151 1 0.01
152 1 0.01
157 3 0.02
158 5 0.04
159 53 0.38
160 5 0.04
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.36
Consensus pattern (149 bp):
AGATTGTCACATAGATAACATGTCATCACTTAATTAATTTTTAAAATTTTAATAAAAATTCAAAA
AAATATAAAAATATATTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAAAATGCCATCC
ACCCAAAAATCCACATGTA
Done.