Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018839.1 Corchorus olitorius cultivar O-4 contig18872, 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: 95524
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--54 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43 CT CT CT CT CT CT
1 CT CT CT CT CT CT
55 AATTCACTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3070 original size:22 final size:23
Alignment explanation
Indices: 3029--3073 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3019 AATGCTACTC
* *
3029 CAAGGTAGTGTAAAATAAAAGCA
1 CAAGGTAATGTAAAACAAAAGCA
3052 CAAGGTAAT-TAAAACAAAAGCA
1 CAAGGTAATGTAAAACAAAAGCA
3074 TAATCCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.56, C:0.11, G:0.18, T:0.16
Consensus pattern (23 bp):
CAAGGTAATGTAAAACAAAAGCA
Found at i:7031 original size:29 final size:28
Alignment explanation
Indices: 6953--7051 Score: 105
Period size: 29 Copynumber: 3.6 Consensus size: 28
6943 ATAGAAATAG
6953 TAAAAGCTGTTTAACACCACAAAC---C
1 TAAAAGCTGTTTAACACCACAAACAAAC
**** *
6978 TAAAAGCTGTTTAACACTTTGAACAAAAA
1 TAAAAGCTGTTTAACACCACAAAC-AAAC
*
7007 AAAAAGCTGTTTAACACCACAAACAAACC
1 TAAAAGCTGTTTAACACCACAAACAAA-C
7036 TAAAAGCTGTTTAACA
1 TAAAAGCTGTTTAACA
7052 TTCATCAAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
25 20 0.35
28 3 0.05
29 34 0.60
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.22
Consensus pattern (28 bp):
TAAAAGCTGTTTAACACCACAAACAAAC
Found at i:9447 original size:22 final size:22
Alignment explanation
Indices: 9422--9463 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9412 GGCAAATCCG
*
9422 TAACCTAAATGACCCAAGAAGT
1 TAACCCAAATGACCCAAGAAGT
*
9444 TAACCCGAATGACCCAAGAA
1 TAACCCAAATGACCCAAGAA
9464 TATTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.14
Consensus pattern (22 bp):
TAACCCAAATGACCCAAGAAGT
Found at i:10827 original size:130 final size:130
Alignment explanation
Indices: 10675--10928 Score: 370
Period size: 129 Copynumber: 2.0 Consensus size: 130
10665 GTCATTTAAG
* * *
10675 AAATATATTTTAAAAATTCTAATATATCTAAG-TTTTTTAATTAAATTAGTAAAATGGTAAAAAT
1 AAATATATTTAAAAAATTCTAATATA--TAAGTTTTTTTAATTAAAATAGTAAAATAGTAAAAAT
* * * * *
10739 AAAATAGGTATAAAGATATTAGATTTTA-TACAATAGAAATAGAGTTTTTAGTTGAGTAAAATTA
64 AAAATAAGTATAAAGATAGTAGATTTAATTA-AATAAAAATAGAGTTTTTAGTTAAGTAAAATTA
10803 TAA
128 TAA
10806 AAATATA-TTAAAAAATTCTAATATATAAGTTTTTTTAATTAAAATAGTAAAATAGTAAAAATAA
1 AAATATATTTAAAAAATTCTAATATATAAGTTTTTTTAATTAAAATAGTAAAATAGTAAAAATAA
* *
10870 AATAATTATAAGGATAGTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAA
66 AATAAGTATAAAGATAGTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAA
10929 CCATTGTTTT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
128 4 0.04
129 81 0.73
130 19 0.17
131 7 0.06
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.38
Consensus pattern (130 bp):
AAATATATTTAAAAAATTCTAATATATAAGTTTTTTTAATTAAAATAGTAAAATAGTAAAAATAA
AATAAGTATAAAGATAGTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAATTATAA
Found at i:23716 original size:10 final size:10
Alignment explanation
Indices: 23698--23771 Score: 54
Period size: 10 Copynumber: 8.0 Consensus size: 10
23688 TTTTGTTTTT
*
23698 TAATTATTAA
1 TAATAATTAA
*
23708 TTATAATTAA
1 TAATAATTAA
*
23718 TAATAA-CAA
1 TAATAATTAA
*
23727 T-TTAAATTAA
1 TAAT-AATTAA
23737 TAATAA-T--
1 TAATAATTAA
23744 TAATAATT-A
1 TAATAATTAA
23753 -AATAATTAA
1 TAATAATTAA
23762 TAATAATTAA
1 TAATAATTAA
23772 AAAAATAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
7 6 0.12
8 9 0.18
9 7 0.14
10 27 0.54
11 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATAATTAA
Found at i:23742 original size:29 final size:25
Alignment explanation
Indices: 23703--23771 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 25
23693 TTTTTTAATT
*
23703 ATTAATTATAATTAATAATAACAATTTAA
1 ATTAATAATAATTAATAATAA-AA--T-A
*
23732 ATTAATAATAATTAATAATTAAATA
1 ATTAATAATAATTAATAATAAAATA
23757 ATTAATAATAATTAA
1 ATTAATAATAATTAA
23772 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 16 0.42
26 1 0.03
28 2 0.05
29 19 0.50
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTAATAATAATTAATAATAAAATA
Found at i:23743 original size:22 final size:21
Alignment explanation
Indices: 23710--23767 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
23700 ATTATTAATT
23710 ATAATTAATAATAACAATTTAA
1 ATAATTAATAATAACAA-TTAA
*
23732 ATTAA-TAATAATTAATAATTAA
1 A-TAATTAATAA-TAACAATTAA
23754 ATAATTAATAATAA
1 ATAATTAATAATAA
23768 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.19
22 18 0.56
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTAATAATAACAATTAA
Found at i:23749 original size:7 final size:7
Alignment explanation
Indices: 23698--23765 Score: 61
Period size: 7 Copynumber: 9.6 Consensus size: 7
23688 TTTTGTTTTT
*
23698 TAATTAT
1 TAATTAA
23705 TAATT-A
1 TAATTAA
23711 TAATTAA
1 TAATTAA
23718 TAA-TAA
1 TAATTAA
*
23724 CAATTTAAA
1 TAA-TT-AA
23733 TTAA-TAA
1 -TAATTAA
23740 TAATTAA
1 TAATTAA
23747 TAATTAAA
1 TAATT-AA
23755 TAATTAA
1 TAATTAA
23762 TAAT
1 TAAT
23766 AATTAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
6 13 0.25
7 25 0.49
8 9 0.18
9 2 0.04
10 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATTAA
Found at i:23779 original size:15 final size:17
Alignment explanation
Indices: 23731--23772 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
23721 TAACAATTTA
23731 AATT-AATAATAATTAAT
1 AATTAAATAATAA-TAAT
23748 AATTAAATAATTAATAAT
1 AATTAAATAA-TAATAAT
23766 AATTAAA
1 AATTAAA
23773 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATAATAATAAT
Found at i:24877 original size:14 final size:15
Alignment explanation
Indices: 24845--24885 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
24835 ACAATAAATA
*
24845 TTTTTTCTTTCTTTC
1 TTTTTTCTTTGTTTC
24860 TTTTTTCTTTGTTT-
1 TTTTTTCTTTGTTTC
24874 TTTTTTCTTTGT
1 TTTTTTCTTTGT
24886 GAATATACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (15 bp):
TTTTTTCTTTGTTTC
Found at i:25035 original size:29 final size:30
Alignment explanation
Indices: 25003--25064 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
24993 ATTATAAATT
25003 AATTGGCAATAAAT-AATAAATTATTGTTA
1 AATTGGCAATAAATAAATAAATTATTGTTA
25032 AATTGGCAATAAATAAATAAATTATTGTTA
1 AATTGGCAATAAATAAATAAATTATTGTTA
25062 AAT
1 AAT
25065 CAAGGAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (30 bp):
AATTGGCAATAAATAAATAAATTATTGTTA
Found at i:35189 original size:2 final size:2
Alignment explanation
Indices: 35182--35224 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
35172 TAGTATTTAG
*
35182 TA TA TA TA TA TT TA GTA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35224 T
1 T
35225 GTTTGAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35193 original size:22 final size:22
Alignment explanation
Indices: 35182--35224 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
35172 TAGTATTTAG
35182 TATAT-ATATATTTAGTATATA
1 TATATAATATATTTAGTATATA
*
35203 TATATAATATATATA-TATATA
1 TATATAATATATTTAGTATATA
35224 T
1 T
35225 GTTTGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATAATATATTTAGTATATA
Found at i:35195 original size:15 final size:15
Alignment explanation
Indices: 35175--35222 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
35165 TACTATTTAG
35175 TATTTAGTATATATA
1 TATTTAGTATATATA
35190 TATTTAGTATATATA
1 TATTTAGTATATATA
*
35205 TATAATA-TATATATA
1 TAT-TTAGTATATATA
35220 TAT
1 TAT
35223 ATGTTTGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (15 bp):
TATTTAGTATATATA
Found at i:35202 original size:13 final size:13
Alignment explanation
Indices: 35183--35221 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
35173 AGTATTTAGT
*
35183 ATATATATATTTA
1 ATATATATATATA
*
35196 GTATATATATATA
1 ATATATATATATA
35209 ATATATATATATA
1 ATATATATATATA
35222 TATGTTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (13 bp):
ATATATATATATA
Found at i:50004 original size:18 final size:17
Alignment explanation
Indices: 49981--50014 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
49971 AAAGTTTAAC
49981 TTTTTTTCT-AAAAATAA
1 TTTTTTT-TGAAAAATAA
49998 TTTTTTTTGAAAAATAA
1 TTTTTTTTGAAAAATAA
50015 AAGTCAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTTTTTGAAAAATAA
Found at i:58179 original size:2 final size:2
Alignment explanation
Indices: 58132--58163 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
58122 ACTCGAGAGC
*
58132 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58164 TCAAATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58851 original size:29 final size:29
Alignment explanation
Indices: 58809--58885 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
58799 CAAAACGGTT
58809 AAATAAGCCCCTGAGCTCTAATTACAGCC
1 AAATAAGCCCCTGAGCTCTAATTACAGCC
*
58838 AAATAAGCTCCTGAGCTCTAATTACAGCC
1 AAATAAGCCCCTGAGCTCTAATTACAGCC
* *
58867 AAATAAGTCCCTGAACTCT
1 AAATAAGCCCCTGAGCTCT
58886 TTAAAAAGGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (29 bp):
AAATAAGCCCCTGAGCTCTAATTACAGCC
Found at i:59691 original size:79 final size:79
Alignment explanation
Indices: 59560--59717 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
59550 ATAAGGGGTT
*
59560 GACCAAAATGATAAATTAGGCTTGAATTGTTATTTGTGGTGGAAGACAGTTGGTTCGAGCCTTCA
1 GACCAAAATGATAAATTAGGCTTGAATTGTTATTTGTGGTGGAAAACAGTTGGTTCGAGCCTTCA
59625 CAAACCTCTAACGA
66 CAAACCTCTAACGA
59639 GACCAAAATGATAAATTAGGCTTGAATTGTTATTTGTGGTGGAAAACAGTTGGTTCGAGCCTTCA
1 GACCAAAATGATAAATTAGGCTTGAATTGTTATTTGTGGTGGAAAACAGTTGGTTCGAGCCTTCA
59704 CAAACCTCTAACGA
66 CAAACCTCTAACGA
59718 TAGATGATTT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (79 bp):
GACCAAAATGATAAATTAGGCTTGAATTGTTATTTGTGGTGGAAAACAGTTGGTTCGAGCCTTCA
CAAACCTCTAACGA
Found at i:62167 original size:14 final size:15
Alignment explanation
Indices: 62148--62176 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62138 ATATAACCCA
62148 ATATCA-CATATAAT
1 ATATCACCATATAAT
62162 ATATCACCATATAAT
1 ATATCACCATATAAT
62177 TTTGGTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATCACCATATAAT
Found at i:62733 original size:15 final size:15
Alignment explanation
Indices: 62713--62744 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
62703 ACTACATTAC
62713 TACTACAAGCTATAG
1 TACTACAAGCTATAG
62728 TACTACAAGCTATAG
1 TACTACAAGCTATAG
62743 TA
1 TA
62745 TTCTTTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (15 bp):
TACTACAAGCTATAG
Found at i:63484 original size:32 final size:33
Alignment explanation
Indices: 63443--63504 Score: 117
Period size: 32 Copynumber: 1.9 Consensus size: 33
63433 TTTGCCTTTC
63443 AAATGCTGAGGTTGCATTCTAGACA-GAAAAAA
1 AAATGCTGAGGTTGCATTCTAGACATGAAAAAA
63475 AAATGCTGAGGTTGCATTCTAGACATGAAA
1 AAATGCTGAGGTTGCATTCTAGACATGAAA
63505 CCTAAATGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (33 bp):
AAATGCTGAGGTTGCATTCTAGACATGAAAAAA
Found at i:70848 original size:31 final size:31
Alignment explanation
Indices: 70810--70869 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
70800 CTATTAGAGC
70810 TTTTTTTTT-GCCAGAGAACTATTAGAGTTTT
1 TTTTTTTTTGGCCAGA-AACTATTAGAGTTTT
* *
70841 TTTTTTTTTGGCCTGAAGCTATTAGAGTT
1 TTTTTTTTTGGCCAGAAACTATTAGAGTT
70870 CGAAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.20, C:0.10, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTTTTTTTGGCCAGAAACTATTAGAGTTTT
Found at i:74054 original size:16 final size:16
Alignment explanation
Indices: 74033--74063 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
74023 TTATTTGTGT
74033 GAAAAAAAAAAAGAAA
1 GAAAAAAAAAAAGAAA
*
74049 GAAAAAGAAAAAGAA
1 GAAAAAAAAAAAGAA
74064 TTGGCCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAAAGAAA
Found at i:79966 original size:81 final size:81
Alignment explanation
Indices: 79831--79990 Score: 320
Period size: 81 Copynumber: 2.0 Consensus size: 81
79821 CCCTCGCCAT
79831 GGAATCACCAGAACTTAAGAAGAAACGGCGGACTTAGAGCCCATGGAGTTGATGACATCCACCAA
1 GGAATCACCAGAACTTAAGAAGAAACGGCGGACTTAGAGCCCATGGAGTTGATGACATCCACCAA
79896 GAGACCTTTTTTTTGA
66 GAGACCTTTTTTTTGA
79912 GGAATCACCAGAACTTAAGAAGAAACGGCGGACTTAGAGCCCATGGAGTTGATGACATCCACCAA
1 GGAATCACCAGAACTTAAGAAGAAACGGCGGACTTAGAGCCCATGGAGTTGATGACATCCACCAA
79977 GAGACCTTTTTTTT
66 GAGACCTTTTTTTT
79991 TAGATAAGAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (81 bp):
GGAATCACCAGAACTTAAGAAGAAACGGCGGACTTAGAGCCCATGGAGTTGATGACATCCACCAA
GAGACCTTTTTTTTGA
Found at i:80387 original size:25 final size:26
Alignment explanation
Indices: 80345--80410 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
80335 TTTTTTTTTC
*
80345 AAATATATTTCTAAATTA-CCATTATCA
1 AAATATATTT-T-TATTAGCCATTATCA
* *
80372 AAATATATTTTTATTATGTCATTATTA
1 AAATATATTTTTATTA-GCCATTATCA
*
80399 AAATATAATTTT
1 AAATATATTTTT
80411 GTGTAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 28 0.85
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (26 bp):
AAATATATTTTTATTAGCCATTATCA
Found at i:80481 original size:126 final size:128
Alignment explanation
Indices: 80345--80599 Score: 406
Period size: 126 Copynumber: 2.0 Consensus size: 128
80335 TTTTTTTTTC
* *
80345 AAATATATTTCTAAATTACCATTATCAAAATATATTTTTATTATGTCATTATTAAAATATAATTT
1 AAATATATTTCTAAATTACCATTATCAAAATATATTTTAATTATGCCATTATTAAAATATAATTT
*
80410 TGTGTA-ATTTTTTTCAAGTATAACTCTAAATTGGCATTATT-AAATATAATTTTTACAAAAT
66 TGTGTACATTTTTTTCAAATATAACTCTAAATTGGCATTATTAAAATATAATTTTTACAAAAT
**
80471 AAATATATTTCTAAATTGTCATTATCAAAATATATTTTAATTATGCCATTATTAAAATATAATTT
1 AAATATATTTCTAAATTACCATTATCAAAATATATTTTAATTATGCCATTATTAAAATATAATTT
* ** **
80536 TGTGTACCTTTTTTTCAAATATATTTCTAAATTTTCATTATTAAAATATAATTTTTACAAAAT
66 TGTGTACATTTTTTTCAAATATAACTCTAAATTGGCATTATTAAAATATAATTTTTACAAAAT
80599 A
1 A
80600 TAATTTTATT
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
126 67 0.57
127 29 0.25
128 21 0.18
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.47
Consensus pattern (128 bp):
AAATATATTTCTAAATTACCATTATCAAAATATATTTTAATTATGCCATTATTAAAATATAATTT
TGTGTACATTTTTTTCAAATATAACTCTAAATTGGCATTATTAAAATATAATTTTTACAAAAT
Found at i:80501 original size:27 final size:27
Alignment explanation
Indices: 80471--80536 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
80461 TTTACAAAAT
*
80471 AAATATATTTCTAAAT-TGTCATTATCA
1 AAATATATTT-TAAATATGCCATTATCA
* *
80498 AAATATATTTTAATTATGCCATTATTA
1 AAATATATTTTAAATATGCCATTATCA
80525 AAATATAATTTT
1 AAATAT-ATTTT
80537 GTGTACCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.12
27 25 0.74
28 5 0.15
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (27 bp):
AAATATATTTTAAATATGCCATTATCA
Found at i:80582 original size:27 final size:27
Alignment explanation
Indices: 80471--80585 Score: 78
Period size: 27 Copynumber: 4.3 Consensus size: 27
80461 TTTACAAAAT
* *
80471 AAATATATTTCTAAATTGTCATTATCA
1 AAATATATTTCTAAATTTTCATTATTA
*
80498 AAATATATTT-T-AATTATGCCATTATTA
1 AAATATATTTCTAAATT-T-TCATTATTA
* * ** *
80525 AAATATAATTTTGTGTACCTTT--TT-TTC
1 AAATAT-A-TTTCT-AAATTTTCATTATTA
80552 AAATATATTTCTAAATTTTCATTATTA
1 AAATATATTTCTAAATTTTCATTATTA
80579 AAATATA
1 AAATATA
80586 ATTTTTACAA
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
24 4 0.06
25 8 0.12
26 4 0.06
27 40 0.61
28 3 0.05
29 3 0.05
30 1 0.02
31 1 0.02
32 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (27 bp):
AAATATATTTCTAAATTTTCATTATTA
Found at i:82493 original size:44 final size:44
Alignment explanation
Indices: 82430--82518 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
82420 TTCAAAGTTT
* *
82430 GTAGGTTTCTAATCTCAACTCCTATTTTCTATCTTATATAATTC
1 GTAGGTCTCTAATCTCAACTCCTATTTTCTATCATATATAATTC
** *
82474 GTAGGTCTCTAATCTCAACTTTTATTTTTTATCATATATAATTC
1 GTAGGTCTCTAATCTCAACTCCTATTTTCTATCATATATAATTC
82518 G
1 G
82519 ACAACAATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (44 bp):
GTAGGTCTCTAATCTCAACTCCTATTTTCTATCATATATAATTC
Found at i:85836 original size:11 final size:11
Alignment explanation
Indices: 85817--85846 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
85807 TTTGTTATTG
*
85817 AGGTAGCCCAT
1 AGGTCGCCCAT
85828 AGGTCGCCCAT
1 AGGTCGCCCAT
85839 AGGTCGCC
1 AGGTCGCC
85847 TATTGAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (11 bp):
AGGTCGCCCAT
Found at i:90138 original size:2 final size:2
Alignment explanation
Indices: 90131--90158 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
90121 TGAGAGTCGG
90131 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
90159 TATGGACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:94760 original size:12 final size:12
Alignment explanation
Indices: 94743--94768 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
94733 ACGTAAAAAA
94743 TTTTCAATAAAT
1 TTTTCAATAAAT
94755 TTTTCAATAAAT
1 TTTTCAATAAAT
94767 TT
1 TT
94769 GTATGTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTCAATAAAT
Found at i:94902 original size:22 final size:22
Alignment explanation
Indices: 94831--94892 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
94821 AATTTCGATA
** *
94831 ACCTATGAAAACTTGATAA-CC
1 ACCTATGAAATTTTGATAATCT
*
94852 ACTCTGTGAAATTTTGATAATCT
1 AC-CTATGAAATTTTGATAATCT
*
94875 TCCTATGAAATTTTGATA
1 ACCTATGAAATTTTGATA
94893 GTCACACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
ACCTATGAAATTTTGATAATCT
Found at i:94907 original size:22 final size:22
Alignment explanation
Indices: 94860--94908 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
94850 CCACTCTGTG
* *
94860 AAATTTTGATAATCTTCCTATG
1 AAATTTTGATAATCTACCTATA
*
94882 AAATTTTGATAGTC-ACACTATA
1 AAATTTTGATAATCTAC-CTATA
94904 AAATT
1 AAATT
94909 GGTAAGCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAATCTACCTATA
Found at i:95448 original size:2 final size:2
Alignment explanation
Indices: 95441--95471 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
95431 ATGCAAAATA
95441 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 A
95472 CACAAAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.