Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009011.1 Corchorus capsularis cultivar CVL-1 contig09032, whole genome shotgun sequence
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: 144078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:16642 original size:28 final size:29
Alignment explanation
Indices: 16597--16668 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
16587 ACTTGTAGCG
*
16597 TTTGGACATTTCGCCCC-TGAACTTCAAT
1 TTTGGACATTTTGCCCCTTGAACTTCAAT
* *
16625 TTTGGACATTTTGTCCCTTGAACTTCATT
1 TTTGGACATTTTGCCCCTTGAACTTCAAT
16654 TTTGAGACATTTTGC
1 TTTG-GACATTTTGC
16669 TATTTCAGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 15 0.39
29 14 0.37
30 9 0.24
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.43
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCTTGAACTTCAAT
Found at i:16665 original size:30 final size:28
Alignment explanation
Indices: 16597--16668 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
16587 ACTTGTAGCG
*
16597 TTTGGACATTTCGCCCCTGAACTTCAAT
1 TTTGGACATTTTGCCCCTGAACTTCAAT
* *
16625 TTTGGACATTTTGTCCCTTGAACTTCATT
1 TTTGGACATTTTG-CCCCTGAACTTCAAT
16654 TTTGAGACATTTTGC
1 TTTG-GACATTTTGC
16669 TATTTCAGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 12 0.31
29 18 0.46
30 9 0.23
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.43
Consensus pattern (28 bp):
TTTGGACATTTTGCCCCTGAACTTCAAT
Found at i:16839 original size:29 final size:29
Alignment explanation
Indices: 16792--16863 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
16782 CCTGATGGGG
* * *
16792 CAAAACTTCCTAAAGTTGAAGTTCAGGGGA
1 CAAAACGTCC-AAAATTGAAGTTCAGAGGA
*
16822 CAAAATGTCCAAAATTGAAGTTCAGAGGA
1 CAAAACGTCCAAAATTGAAGTTCAGAGGA
16851 CAAAACGTCCAAA
1 CAAAACGTCCAAA
16864 TGCTACAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 29 0.78
30 8 0.22
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (29 bp):
CAAAACGTCCAAAATTGAAGTTCAGAGGA
Found at i:20762 original size:2 final size:2
Alignment explanation
Indices: 20757--20781 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20747 TCTTGTGAGG
20757 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20782 CGTAATCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20951 original size:29 final size:29
Alignment explanation
Indices: 20892--20956 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
20882 ACCGAACCAT
*****
20892 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAAGC
*
20921 CAAATAAGCCCCTGAACTCTTAAAAAAGC
1 CAAATAAGCCCCTGAACTATTAAAAAAGC
20950 CAAATAA
1 CAAATAA
20957 ACCCTATTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAAGC
Found at i:29096 original size:27 final size:27
Alignment explanation
Indices: 29056--29111 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
29046 CGAGAGCGAA
*
29056 GAGGTGTCGTACGTGCTAGAAACTTAT
1 GAGGTGTCGCACGTGCTAGAAACTTAT
29083 GAGGTGTCGCACGTGCTAGAAACTTAT
1 GAGGTGTCGCACGTGCTAGAAACTTAT
29110 GA
1 GA
29112 AGAAGATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (27 bp):
GAGGTGTCGCACGTGCTAGAAACTTAT
Found at i:33011 original size:6 final size:6
Alignment explanation
Indices: 33002--33036 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
32992 TTAAAATCAC
*
33002 AATAAC AATAAA AATAAA AATAAA AATAAA AATAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAA
33037 GAGGGTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:43118 original size:60 final size:61
Alignment explanation
Indices: 43040--43160 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 61
43030 CTCTTCAAAG
43040 GACACAGTTTTTATTTTTA-T-TATCTCTGTTATTATGTGGTGTGCTTCTTTTGTCTGATA
1 GACACAGTTTTTATTTTTATTATATCTCTGTTATTATGTGGTGTGCTTCTTTTGTCTGATA
43099 GACACAGTTTTTTATTTTTATTATATCTCTGTTATTATGTGGTGTGCTTCTTTTGTCTGATA
1 GACACAG-TTTTTATTTTTATTATATCTCTGTTATTATGTGGTGTGCTTCTTTTGTCTGATA
43161 CTTATTACTT
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
59 7 0.12
60 12 0.20
61 1 0.02
62 39 0.66
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.55
Consensus pattern (61 bp):
GACACAGTTTTTATTTTTATTATATCTCTGTTATTATGTGGTGTGCTTCTTTTGTCTGATA
Found at i:48620 original size:17 final size:17
Alignment explanation
Indices: 48600--48633 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
48590 GTTTTTAGTC
48600 ACTTAACTTTTTAACTT
1 ACTTAACTTTTTAACTT
*
48617 ACTTAAGTTTTTAACTT
1 ACTTAACTTTTTAACTT
48634 TATGTGAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.53
Consensus pattern (17 bp):
ACTTAACTTTTTAACTT
Found at i:62292 original size:2 final size:2
Alignment explanation
Indices: 62287--62315 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62277 ATAAAAAATA
62287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62316 ATAAAAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68018 original size:15 final size:15
Alignment explanation
Indices: 67998--68027 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
67988 TGTTGGGAAT
*
67998 AATCATTGGGTGTAG
1 AATCATTGAGTGTAG
68013 AATCATTGAGTGTAG
1 AATCATTGAGTGTAG
68028 GTCTTTGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (15 bp):
AATCATTGAGTGTAG
Found at i:69919 original size:9 final size:9
Alignment explanation
Indices: 69905--69930 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
69895 TTGCCCATGC
69905 TCTTCTTCA
1 TCTTCTTCA
69914 TCTTCTTCA
1 TCTTCTTCA
69923 TCTTCTTC
1 TCTTCTTC
69931 CTCCTCTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.58
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:72581 original size:6 final size:6
Alignment explanation
Indices: 72565--72609 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
72555 AAGACACGGC
72565 TATTATT TATTTT TA-TTT TATTTT TATTTT TATTTT TATTTT TAT
1 TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TAT
72610 GCAGAATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
5 5 0.14
6 28 0.76
7 4 0.11
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:72586 original size:11 final size:11
Alignment explanation
Indices: 72570--72606 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
72560 ACGGCTATTA
72570 TTTATTTTTAT
1 TTTATTTTTAT
72581 TTTATTTTTATT
1 TTTATTTTTA-T
72593 TTTATTTTTAT
1 TTTATTTTTAT
72604 TTT
1 TTT
72607 TATGCAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:76797 original size:29 final size:29
Alignment explanation
Indices: 76734--76800 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
76724 ACACCGAACC
* ***
76734 GTCAAATAAGCCTCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTATAAAA
* *
76763 GCCAAATAAGCCCCTGAACTCTTATAAAA
1 GTCAAATAAGCCCCTGAACTATTATAAAA
76792 GTCAAATAA
1 GTCAAATAA
76801 ACCCTGTTAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.27
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTATAAAA
Found at i:77895 original size:48 final size:48
Alignment explanation
Indices: 77839--77935 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
77829 GTCAGTTTAA
77839 GGACTTCTTTACTTGAAATTACTATTGCATTAACTCCCAAACATATAT
1 GGACTTCTTTACTTGAAATTACTATTGCATTAACTCCCAAACATATAT
77887 GGACTTCTTTACTTGAAATTACTATTGCATTAACTCCCAAACATATAT
1 GGACTTCTTTACTTGAAATTACTATTGCATTAACTCCCAAACATATAT
77935 G
1 G
77936 TATGTACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (48 bp):
GGACTTCTTTACTTGAAATTACTATTGCATTAACTCCCAAACATATAT
Found at i:84904 original size:18 final size:18
Alignment explanation
Indices: 84883--84919 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
84873 ATTCACACCC
84883 TTCTCAAATGAAATTGTG
1 TTCTCAAATGAAATTGTG
*
84901 TTCTCAGATGAAATTGTG
1 TTCTCAAATGAAATTGTG
84919 T
1 T
84920 ATGAAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (18 bp):
TTCTCAAATGAAATTGTG
Found at i:96125 original size:54 final size:54
Alignment explanation
Indices: 95959--96126 Score: 138
Period size: 54 Copynumber: 3.1 Consensus size: 54
95949 ATTCAATTAA
95959 ATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAA-TTTGGATAT
1 ATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTTGGATAT
* * * * * *
96012 ACT-AA---AAT-T-TTTCTAATATACAATTT-TATTCTACTAAAAACTCTATTTT-CATTT
1 ATTAAATCTAATATCTTTATAAT-TAC--TTTAT-TTTTACCAAAAA----ATTTTGGATAT
96066 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTTGGATAT
1 -ATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTTGGATAT
96121 ATTAAA
1 ATTAAA
96127 ATTTTTTCTA
Statistics
Matches: 85, Mismatches: 12, Indels: 35
0.64 0.09 0.27
Matches are distributed among these distances:
47 7 0.08
48 4 0.05
49 4 0.05
50 13 0.15
52 2 0.02
53 2 0.02
54 15 0.18
55 8 0.09
56 2 0.02
58 13 0.15
59 4 0.05
60 4 0.05
61 7 0.08
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (54 bp):
ATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTTGGATAT
Found at i:96176 original size:110 final size:108
Alignment explanation
Indices: 95922--96217 Score: 441
Period size: 110 Copynumber: 2.7 Consensus size: 108
95912 ACTATTATAG
* *
95922 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
95987 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
96035 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
96100 TTACCAAAAAATTTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAA-TTTGGATATACTAAAA-TTTTTCTAATATACAA
* **
96145 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTAA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAATTACTTT-A
96209 TTTTTACCA
63 TTTTTACCA
96218 TTTTAATTTA
Statistics
Matches: 172, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
108 48 0.28
109 19 0.11
110 64 0.37
111 10 0.06
112 10 0.06
113 21 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (108 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
Found at i:103718 original size:6 final size:6
Alignment explanation
Indices: 103707--103733 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
103697 AAAGACATAT
103707 ATTCAA ATTCAA ATTCAA ATTCAA ATT
1 ATTCAA ATTCAA ATTCAA ATTCAA ATT
103734 ATTATAACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTCAA
Found at i:105053 original size:2 final size:2
Alignment explanation
Indices: 105046--105071 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
105036 AATGCATTTG
105046 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
105072 TTCTCGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105957 original size:21 final size:21
Alignment explanation
Indices: 105922--105963 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
105912 TATGGGTGTG
*
105922 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
105944 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
105964 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:109770 original size:74 final size:74
Alignment explanation
Indices: 109692--109848 Score: 271
Period size: 74 Copynumber: 2.1 Consensus size: 74
109682 TGGTCTTTTC
* *
109692 ACACTTTTC-GAGTGACTAAAAAGCCCCTTTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTT
1 ACACTTTTCGGA-TGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTT
109756 TTTCGTAATT
65 TTTCGTAATT
109766 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
109831 TTCGTAATT
66 TTCGTAATT
*
109840 ACACATTTC
1 ACACTTTTC
109849 CCTTCCTTAA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
74 77 0.97
75 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.40
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:112328 original size:26 final size:26
Alignment explanation
Indices: 112298--112350 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
112288 AGTGTAAAAA
112298 ATTAAAAATGGACATGCTCGGAATAG
1 ATTAAAAATGGACATGCTCGGAATAG
112324 ATTAAAAATGGACATGCTCGGAATAG
1 ATTAAAAATGGACATGCTCGGAATAG
112350 A
1 A
112351 ATAATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (26 bp):
ATTAAAAATGGACATGCTCGGAATAG
Found at i:116085 original size:9 final size:9
Alignment explanation
Indices: 116071--116098 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
116061 TTCTATATAA
116071 CTCTCAAGC
1 CTCTCAAGC
116080 CTCTCAAGC
1 CTCTCAAGC
116089 CTCTCAAGC
1 CTCTCAAGC
116098 C
1 C
116099 CCGACCTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.46, G:0.11, T:0.21
Consensus pattern (9 bp):
CTCTCAAGC
Found at i:118191 original size:60 final size:60
Alignment explanation
Indices: 118065--118184 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
118055 ATGTTCAAGT
* ** * *
118065 CTTATTTAACCAAATTAAAAGCATGAACCCTAAATTGAGGATTTTCACATACGTTAGGAC
1 CTTATTTAACCAAATTAAAAGCATGAACCATAAATTGAACATTTTCAAATACGTTAAGAC
* * * *
118125 CTTATTTAACCAAATTAAAAGTATGAGCCATAAATTGAACATTTTGAAATATGTTTAAGA
1 CTTATTTAACCAAATTAAAAGCATGAACCATAAATTGAACATTTTCAAATACG-TTAAGA
118185 GCTATTTTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 45 0.90
61 5 0.10
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (60 bp):
CTTATTTAACCAAATTAAAAGCATGAACCATAAATTGAACATTTTCAAATACGTTAAGAC
Found at i:119155 original size:78 final size:78
Alignment explanation
Indices: 119026--119178 Score: 288
Period size: 78 Copynumber: 2.0 Consensus size: 78
119016 AGCCTGACAG
119026 CTTCAGCACTAAAAAGACACCTCCTTTCCTCTCCAAAGCTACAACCCGACGCGAAACCAACGAAA
1 CTTCAGCACTAAAAAGACACCTCCTTTCCTCTCCAAAGCTACAACCCGACGCGAAACCAACGAAA
119091 AAGACTCAAACAC
66 AAGACTCAAACAC
**
119104 CTTCAGCACTAAAAAGATGCCTCCTTTCCTCTCCAAAGCTACAACCCGACGCGAAACCAACGAAA
1 CTTCAGCACTAAAAAGACACCTCCTTTCCTCTCCAAAGCTACAACCCGACGCGAAACCAACGAAA
119169 AAGACTCAAA
66 AAGACTCAAA
119179 TGAAGATCCT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.39, C:0.35, G:0.11, T:0.15
Consensus pattern (78 bp):
CTTCAGCACTAAAAAGACACCTCCTTTCCTCTCCAAAGCTACAACCCGACGCGAAACCAACGAAA
AAGACTCAAACAC
Found at i:120642 original size:3 final size:3
Alignment explanation
Indices: 120636--120697 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
120626 AAAGAGAAAT
120636 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
120684 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
120698 TTTATTATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:126592 original size:3 final size:3
Alignment explanation
Indices: 126571--126620 Score: 75
Period size: 3 Copynumber: 16.3 Consensus size: 3
126561 GAAGAGAAAT
126571 ATA AT- ATA TATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
126617 ATA A
1 ATA A
126621 GAGAATTAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 36 0.80
4 7 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:128422 original size:60 final size:60
Alignment explanation
Indices: 128342--128482 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 60
128332 AGCCTTTTTG
* * * *
128342 CATACGTTAAAGTCTTATTTAACCAAATTAAAAGCATGAATCC-TAAATTGAGGATTTTCA
1 CATACGTTAAAGCCTTATTTAACCAAAGTAAAAGCATG-AGCCATAAATTGAGCATTTTCA
*
128402 CATACGTTAGAA-CCTTATTTAACCAAAGTAAAAGCATGAGCCATAAATTGAGCATTTTGA
1 CATACGTTA-AAGCCTTATTTAACCAAAGTAAAAGCATGAGCCATAAATTGAGCATTTTCA
* *
128462 CATATGTTAAAGAGCTTATTT
1 CATACGTTAAAG-CCTTATTT
128483 TGAGCAATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
59 5 0.07
60 56 0.80
61 9 0.13
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (60 bp):
CATACGTTAAAGCCTTATTTAACCAAAGTAAAAGCATGAGCCATAAATTGAGCATTTTCA
Found at i:129678 original size:1 final size:1
Alignment explanation
Indices: 129672--129698 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
129662 TATTCTTGAG
129672 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
129699 GAGATAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:130376 original size:30 final size:30
Alignment explanation
Indices: 130342--130443 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 30
130332 TTTTGGACAC
130342 TTGAGGCTTGATTCGCCGCCTCCTCTTCTT
1 TTGAGGCTTGATTCGCCGCCTCCTCTTCTT
*
130372 TTGAGCCTTGATT---CGCCTCCTCTTCTT
1 TTGAGGCTTGATTCGCCGCCTCCTCTTCTT
* * *
130399 TCGAGGCTTGATCATTCGCCTCCT-CTTTATCTT
1 TTGAGGCTTG---ATTCGCCGCCTCCTCT-TCTT
130432 TTGAGGCTTGAT
1 TTGAGGCTTGAT
130444 CATTGGCCTC
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
27 22 0.37
30 17 0.29
32 3 0.05
33 17 0.29
ACGTcount: A:0.10, C:0.29, G:0.19, T:0.42
Consensus pattern (30 bp):
TTGAGGCTTGATTCGCCGCCTCCTCTTCTT
Found at i:130396 original size:27 final size:28
Alignment explanation
Indices: 130358--130461 Score: 111
Period size: 33 Copynumber: 3.5 Consensus size: 28
130348 CTTGATTCGC
*
130358 CGCCTCCTCTTCTTTTGAGCCTTG-ATT
1 CGCCTCCTCTTCTTTTGAGGCTTGAATT
*
130385 CGCCTCCTCTTCTTTCGAGGCTTGATCATT
1 CGCCTCCTCTTCTTTTGAGGCTTGA--ATT
130415 CGCCTCCTCTTTATCTTTTGAGGCTTGATCATT
1 CGCCTCCTC--T-TCTTTTGAGGCTTGA--ATT
*
130448 GGCCTCCTCTTCTT
1 CGCCTCCTCTTCTT
130462 GTGGGACTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
27 22 0.33
30 16 0.24
31 1 0.01
32 1 0.01
33 27 0.40
ACGTcount: A:0.09, C:0.33, G:0.15, T:0.43
Consensus pattern (28 bp):
CGCCTCCTCTTCTTTTGAGGCTTGAATT
Found at i:130438 original size:33 final size:32
Alignment explanation
Indices: 130382--130458 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 32
130372 TTGAGCCTTG
130382 ATTCGCCTCCTC--TTCTTTCGAGGCTTGATC
1 ATTCGCCTCCTCTTTTCTTTCGAGGCTTGATC
*
130412 ATTCGCCTCCTCTTTATCTTTTGAGGCTTGATC
1 ATTCGCCTCCTCTTT-TCTTTCGAGGCTTGATC
*
130445 ATTGGCCTCCTCTT
1 ATTCGCCTCCTCTT
130459 CTTGTGGGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
30 12 0.29
32 1 0.02
33 29 0.69
ACGTcount: A:0.10, C:0.31, G:0.16, T:0.43
Consensus pattern (32 bp):
ATTCGCCTCCTCTTTTCTTTCGAGGCTTGATC
Found at i:131194 original size:21 final size:21
Alignment explanation
Indices: 131169--131212 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
131159 CAGCATGCCA
131169 CGAAACTTTGA-GTGGTCAGGC
1 CGAAA-TTTGAGGTGGTCAGGC
* *
131190 CGAAATTTTAGGTGGTCGGGC
1 CGAAATTTGAGGTGGTCAGGC
131211 CG
1 CG
131213 CTTCTTATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.25
Consensus pattern (21 bp):
CGAAATTTGAGGTGGTCAGGC
Found at i:131329 original size:6 final size:6
Alignment explanation
Indices: 131320--131359 Score: 53
Period size: 6 Copynumber: 6.2 Consensus size: 6
131310 TCGGGCTGCC
131320 GCTGGG GCTGGG GCTGGG GCTGCAGG CGCTGGG GCTGGG G
1 GCTGGG GCTGGG GCTGGG GCTG--GG -GCTGGG GCTGGG G
131360 AGGAGTTCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 23 0.74
7 2 0.06
8 2 0.06
9 4 0.13
ACGTcount: A:0.03, C:0.20, G:0.62, T:0.15
Consensus pattern (6 bp):
GCTGGG
Found at i:136293 original size:55 final size:56
Alignment explanation
Indices: 136211--136363 Score: 218
Period size: 55 Copynumber: 2.7 Consensus size: 56
136201 AACTTAATAT
136211 ATAAAATAAAATTACAATTGGTTGTTAGAAATGTTGATGTCGGGTTAACTAAGA-A
1 ATAAAATAAAATTACAATTGGTTGTTAGAAATGTTGATGTCGGGTTAACTAAGATA
** * * *
136266 ATACTATAAAATTACAATTGGTTGTTAGAAATATTCATGTCGGGTTAACTAAGATT
1 ATAAAATAAAATTACAATTGGTTGTTAGAAATGTTGATGTCGGGTTAACTAAGATA
* *
136322 ATAAAATTAAAATTACGAATTGGTGGTTAGAGATGTTGATGT
1 ATAAAA-TAAAATTAC-AATTGGTTGTTAGAAATGTTGATGT
136364 ATTGGATTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
55 50 0.60
56 4 0.05
57 9 0.11
58 21 0.25
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (56 bp):
ATAAAATAAAATTACAATTGGTTGTTAGAAATGTTGATGTCGGGTTAACTAAGATA
Found at i:139963 original size:22 final size:22
Alignment explanation
Indices: 139938--140150 Score: 71
Period size: 22 Copynumber: 9.7 Consensus size: 22
139928 ATGATCCCAT
139938 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * ** *
139960 TATGAAATTTTAACAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
139982 TATGGAATTTTGAGAACTTTTT
1 TATGAAATTTTGATAACCTTCC
**
140004 TAT--AATTTTTTTAACCTT-C
1 TATGAAATTTTGATAACCTTCC
* * *
140023 TCATGAAATTTTGTTAATCTCCC
1 T-ATGAAATTTTGATAACCTTCC
* * *
140046 TA-AAGAATTTTGA-AGATC-TCAA
1 TATGA-AATTTTGATA-ACCTTC-C
*
140068 TATAAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
140090 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * * *
140113 TATGAGATGTTGATAACCTGCA
1 TATGAAATTTTGATAACCTTCC
* *
140135 TATGATATATTGATAA
1 TATGAAATTTTGATAA
140151 TCACGTTATG
Statistics
Matches: 141, Mismatches: 37, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.01
20 13 0.09
21 4 0.03
22 99 0.70
23 24 0.17
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:140309 original size:22 final size:22
Alignment explanation
Indices: 140278--140319 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
140268 GATAAACATC
*
140278 CTTATAAAATTTTAATAACTTT
1 CTTATAAAATCTTAATAACTTT
* *
140300 CTTATGAAATCTTGATAACT
1 CTTATAAAATCTTAATAACT
140320 ACAAATTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (22 bp):
CTTATAAAATCTTAATAACTTT
Found at i:140351 original size:22 final size:22
Alignment explanation
Indices: 140322--140438 Score: 103
Period size: 22 Copynumber: 5.3 Consensus size: 22
140312 TGATAACTAC
140322 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
140344 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* *
140366 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
* * * *
140388 AAATTTTGATCTACAT-ACTGTG
1 AAATTTTGAT-AACCTCCCTATG
*
140410 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
140432 AAATTTT
1 AAATTTT
140439 AAAAACTAAA
Statistics
Matches: 71, Mismatches: 21, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
21 2 0.03
22 67 0.94
23 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:140595 original size:44 final size:44
Alignment explanation
Indices: 140545--140674 Score: 122
Period size: 44 Copynumber: 3.0 Consensus size: 44
140535 GAAATACCAC
*
140545 TATGAAATTTTTGTAATCACATTTTGAAAATTGGATAACCTCTT
1 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTT
* * * *
140589 TATGAAA-TTTTGATAATCTC-TTTAT-AAAATTTTGTTGACCCCTT
1 TATGAAATTTTTG-TAATCACATTT-TGAAAA-TTTGATAACCTCTT
* * * * *
140633 TATGAAATTCTTATAATCACATTATGTAATTTTGATAACCTC
1 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTC
140675 ACTTTGAAAT
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
43 12 0.18
44 47 0.71
45 7 0.11
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (44 bp):
TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTT
Found at i:140685 original size:22 final size:21
Alignment explanation
Indices: 140569--141161 Score: 147
Period size: 22 Copynumber: 26.8 Consensus size: 21
140559 AATCACATTT
* * *
140569 TGAAAATTGGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
* *
140591 TGAAATTTTGATAATCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
* * *
140613 TAAAATTTTGTTGACC-CCTTTA
1 TGAAATTTTGATAACCTCC--TA
* * *
140635 TGAAATTCTT-ATAATCACATTA
1 TGAAATT-TTGATAACCTC-CTA
* *
140657 TGTAATTTTGATAACCTCACTT
1 TGAAATTTTGATAACCTC-CTA
* * **
140679 TGAAATTATAATAACAACGCTA
1 TGAAATTTTGATAACCTC-CTA
*
140701 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAA-CCTCCTA
140723 T-AAATTTTGATAACCCGATCTCTA
1 TGAAATTTTGATAA-CC--TC-CTA
* *
140747 TAAAATTTCGATAATCACT-CTA
1 TGAAATTTTGATAA-C-CTCCTA
* * *
140769 TGAGA-TTGGATAACCTTCTA
1 TGAAATTTTGATAACCTCCTA
* * *
140789 TCAAATTTTGGTAATCCT-TTA
1 TGAAATTTTGATAA-CCTCCTA
* *
140810 TGAAATTGAGACTTTTATAACCTTCATA
1 TGAAA-T-----TTTGATAACC-TCCTA
*
140838 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCT-CCTA
*
140860 TGAAATATT-AGTAACCTCCTAA
1 TGAAATTTTGA-TAACCTCCT-A
* **
140882 TGAAATTTTGTTAACGACACTA
1 TGAAATTTTGATAACCTC-CTA
*
140904 TGAAATTCTTAATTATAACCTCGCTA
1 TGAAA-T-TT--TGATAACCTC-CTA
** *
140930 TGTCATTTTGATAACCT-CTT
1 TGAAATTTTGATAACCTCCTA
** *
140950 TGATAACATTTCT-ATAAAAT--TG
1 TG--AA-ATTT-TGATAACCTCCTA
* *
140972 TGATAA--TT-A-ATCATCCTA
1 TGA-AATTTTGATAACCTCCTA
** *
140990 TGAAATTTCAATAACCAACCTA
1 TGAAATTTTGATAACC-TCCTA
* *
141012 AGAAATTTTAATAACCTGATCCTA
1 TGAAATTTTGATAACC---TCCTA
* *
141036 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
141058 TGAAATTTTGATAACTTCCATA
1 TGAAATTTTGATAACCTCC-TA
*
141080 TGAAATTTT-AGTAACCACACTA
1 TGAAATTTTGA-TAACCTC-CTA
* *
141102 TGGAATTCTGATAACCTCCTCA
1 TGAAATTTTGATAACCTCCT-A
* * *
141124 TGAAATTATAATAACCATCTTA
1 TGAAATTTTGATAACC-TCCTA
141146 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
141162 ACATAGAGAC
Statistics
Matches: 422, Mismatches: 96, Indels: 106
0.68 0.15 0.17
Matches are distributed among these distances:
16 3 0.01
17 4 0.01
18 5 0.01
19 3 0.01
20 14 0.03
21 47 0.11
22 251 0.59
23 24 0.06
24 28 0.07
25 13 0.03
26 15 0.04
27 8 0.02
28 7 0.02
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:141051 original size:46 final size:45
Alignment explanation
Indices: 140984--141101 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 45
140974 ATAATTAATC
* *
140984 ATCCTATGAAATTTCAATAACCAAC-CTAAGAAATTTTAATAACCT
1 ATCCTATGAAATTTTAGTAACCAACACTAAGAAATTTTAATAA-CT
* * *
141029 GATCCTATGAAATTTTGGTAACC-ACACTATGAAATTTTGATAACT
1 -ATCCTATGAAATTTTAGTAACCAACACTAAGAAATTTTAATAACT
141074 -TCCATATGAAATTTTAGTAACC-ACACTA
1 ATCC-TATGAAATTTTAGTAACCAACACTA
141102 TGGAATTCTG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 3 0.05
44 23 0.36
45 4 0.06
46 34 0.53
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (45 bp):
ATCCTATGAAATTTTAGTAACCAACACTAAGAAATTTTAATAACT
Found at i:141097 original size:44 final size:43
Alignment explanation
Indices: 140985--141160 Score: 176
Period size: 44 Copynumber: 4.0 Consensus size: 43
140975 TAATTAATCA
* * *
140985 TCCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCT
1 TCCTATGAAATTTTAATAACCACA-CTATGAAATTTTGATAA-CT
**
141029 GATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACT
1 --TCCTATGAAATTTTAATAACCACACTATGAAATTTTGATAACT
* * * *
141074 TCCATATGAAATTTTAGTAACCACACTATGGAATTCTGATAACC
1 TCC-TATGAAATTTTAATAACCACACTATGAAATTTTGATAACT
* *
141118 TCCTCATGAAATTATAATAACCATC-TTATGAAATTTTGATAAC
1 TCCT-ATGAAATTTTAATAACCA-CACTATGAAATTTTGATAAC
141161 CACATAGAGA
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
43 4 0.04
44 70 0.62
45 3 0.03
46 34 0.30
47 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (43 bp):
TCCTATGAAATTTTAATAACCACACTATGAAATTTTGATAACT
Found at i:141162 original size:22 final size:22
Alignment explanation
Indices: 140983--141162 Score: 154
Period size: 22 Copynumber: 8.1 Consensus size: 22
140973 GATAATTAAT
**
140983 CATCCTATGAAATTTCAATAAC
1 CATCCTATGAAATTTTGATAAC
* * *
141005 CAACCTAAGAAATTTTAATAAC
1 CATCCTATGAAATTTTGATAAC
*
141027 CTGATCCTATGAAATTTTGGTAAC
1 C--ATCCTATGAAATTTTGATAAC
141051 CA-CACTATGAAATTTTGATAA-
1 CATC-CTATGAAATTTTGATAAC
*
141072 CTTCCATATGAAATTTT-AGTAAC
1 CATCC-TATGAAATTTTGA-TAAC
* *
141095 CA-CACTATGGAATTCTGATAAC
1 CATC-CTATGAAATTTTGATAAC
* *
141117 C-TCCTCATGAAATTATAATAAC
1 CATCCT-ATGAAATTTTGATAAC
*
141139 CATCTTATGAAATTTTGATAAC
1 CATCCTATGAAATTTTGATAAC
141161 CA
1 CA
141163 CATAGAGACA
Statistics
Matches: 128, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
21 6 0.05
22 98 0.77
23 6 0.05
24 18 0.14
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
CATCCTATGAAATTTTGATAAC
Found at i:141251 original size:20 final size:18
Alignment explanation
Indices: 141234--141289 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
141224 TAAAAAAATT
141234 AATAAGGAATGATTAAAA
1 AATAAGGAATGATTAAAA
***
141252 AATAATTTATGATTAAAAA
1 AATAAGGAATGATT-AAAA
*
141271 AATAATGGAATAATTAAAA
1 AATAA-GGAATGATTAAAA
141290 TATTATTTAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 11 0.38
19 13 0.45
20 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AATAAGGAATGATTAAAA
Found at i:141298 original size:38 final size:40
Alignment explanation
Indices: 141222--141298 Score: 104
Period size: 38 Copynumber: 1.9 Consensus size: 40
141212 TTAAAAAATA
*
141222 ATTAAAAAAATTAATAAGGAATGATTAAAAAATAATTTATG
1 ATTAAAAAAATTAAT-AGGAATAATTAAAAAATAATTTATG
* *
141263 ATTAAAAAAA-TAAT-GGAATAATTAAAATATTATTTA
1 ATTAAAAAAATTAATAGGAATAATTAAAAAATAATTTA
141299 GTAATGACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 19 0.58
40 4 0.12
41 10 0.30
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (40 bp):
ATTAAAAAAATTAATAGGAATAATTAAAAAATAATTTATG
Found at i:141379 original size:31 final size:32
Alignment explanation
Indices: 141313--141379 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
141303 TGACAATTTA
* * *
141313 GAAATATGTTGTTTAAAAAAAGGGTATAATTG
1 GAAATATGTTGTTAAAAAAAAGGGTACAATCG
141345 GAAATAT-TT-TTAAAAAATAAGGGTACAATCG
1 GAAATATGTTGTTAAAAAA-AAGGGTACAATCG
141376 GAAA
1 GAAA
141380 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 17 0.55
32 7 0.23
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.30
Consensus pattern (32 bp):
GAAATATGTTGTTAAAAAAAAGGGTACAATCG
Found at i:142138 original size:18 final size:19
Alignment explanation
Indices: 142115--142153 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
142105 ATTATTATTT
142115 TTTTTTTTTGCACA-AAAA
1 TTTTTTTTTGCACACAAAA
142133 TTTTTTTTTGCACACAAAA
1 TTTTTTTTTGCACACAAAA
142152 TT
1 TT
142154 ATTCTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTTTTTTTGCACACAAAA
Found at i:142456 original size:61 final size:61
Alignment explanation
Indices: 142361--142482 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
142351 AAAATCCACA
142361 TAGGATTCAACATGGGGCCACCTTGCTACACAATCTATCCACATAGGCAGCTCAAAAAGCC
1 TAGGATTCAACATGGGGCCACCTTGCTACACAATCTATCCACATAGGCAGCTCAAAAAGCC
142422 TAGGATTCAACATGGGGCCACCTTGCTACACAATCTATCCACATAGGCAGCTCAAAAAGCC
1 TAGGATTCAACATGGGGCCACCTTGCTACACAATCTATCCACATAGGCAGCTCAAAAAGCC
142483 ATGTAAGATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.20
Consensus pattern (61 bp):
TAGGATTCAACATGGGGCCACCTTGCTACACAATCTATCCACATAGGCAGCTCAAAAAGCC
Found at i:143646 original size:60 final size:60
Alignment explanation
Indices: 143567--143689 Score: 142
Period size: 60 Copynumber: 2.0 Consensus size: 60
143557 AGCCTTTTTG
* * *
143567 CATACGTTCAAGTCTTATTTAACTAAATGAAAAGCATGAACCCTAAATTGAGA-ATTTTCA
1 CATACGTTCAAGCCTTATTTAACCAAATGAAAAGCATGAACCATAAATTGA-ACATTTTCA
* * * **
143627 CATACG-TCAGAGCCTTATTTGACCAAATTAAAAGTATGGGCCATAAATTGAACATTTTCA
1 CATACGTTCA-AGCCTTATTTAACCAAATGAAAAGCATGAACCATAAATTGAACATTTTCA
143687 CAT
1 CAT
143690 TTTCACATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 4 0.08
60 49 0.92
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (60 bp):
CATACGTTCAAGCCTTATTTAACCAAATGAAAAGCATGAACCATAAATTGAACATTTTCA
Found at i:144047 original size:2 final size:2
Alignment explanation
Indices: 144040--144078 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
144030 TATATCAATA
144040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.