Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold662
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: 43477
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:3329 original size:21 final size:21
Alignment explanation
Indices: 3300--3344 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3290 AAGTTTTCAT
*
3300 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3320 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3342 TTT
1 TTT
3345 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:5578 original size:13 final size:13
Alignment explanation
Indices: 5560--5585 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5550 CAATTTTTTG
5560 TGTATCGATACAT
1 TGTATCGATACAT
5573 TGTATCGATACAT
1 TGTATCGATACAT
5586 ACTTAGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5600 original size:32 final size:33
Alignment explanation
Indices: 5540--5603 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
5530 TACAAGCCAA
** *
5540 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTAGTGTATCGATACAT
5573 TGTATCGATAC-ATACTTAGTGTATCGATACA
1 TGTATCGATACAATACTTAGTGTATCGATACA
5604 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTAGTGTATCGATACAT
Found at i:6771 original size:51 final size:51
Alignment explanation
Indices: 6670--6787 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
6660 AAGAGATGGT
* * *
6670 AGGGTTGGAGTATCCCCAAAGATAAAGAATTCGATATTGTGGAAGTAAAAA-
1 AGGGTTAGAGTAT-CCCAAAGATAAAGAATTCAATATTGTGAAAGTAAAAAC
* *
6721 ATGGGGTTAGAGTATCCCAAAGATAAA-AATTCAATGTTTTGAAAGTAAAAAC
1 A--GGGTTAGAGTATCCCAAAGATAAAGAATTCAATATTGTGAAAGTAAAAAC
*
6773 AAGGTTAGAGTATCC
1 AGGGTTAGAGTATCC
6788 TTTCAGAGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
50 13 0.22
51 21 0.36
52 13 0.22
53 11 0.19
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (51 bp):
AGGGTTAGAGTATCCCAAAGATAAAGAATTCAATATTGTGAAAGTAAAAAC
Found at i:6980 original size:78 final size:78
Alignment explanation
Indices: 6783--6991 Score: 192
Period size: 80 Copynumber: 2.7 Consensus size: 78
6773 AAGGTTAGAG
* * * * * *
6783 TATCCTTTCAGAGATGGTAAGG-TTGGAGTATCCCTAGAGATAAAAAATTTGATGTTTTAGATTT
1 TATCCCTTCAGAGATGGT-GGGATCGAAGTATCCCTAGAGATGAAAAATTTGACGTTTTAGA--T
* *
6847 AAAAATAGGGTTGGAG
63 AAAAATAGAGTTGGAC
* * *
6863 TATCCCTTCAGAGATGGTGGGATTGGAGTAT-CCTCAGAGATGAAAAATTTGACGTTTTGGA-AA
1 TATCCCTTCAGAGATGGTGGGATCGAAGTATCCCT-AGAGATGAAAAATTTGACGTTTTAGATAA
* *
6926 TAGATAGAGTTGTAC
65 -AAATAGAGTTGGAC
* * *
6941 TATCTCCTT-GGAGATGGTGGGGTCGAAGTATCCCTAGAGATGAAAATTTTG
1 TATC-CCTTCAGAGATGGTGGGATCGAAGTATCCCTAGAGATGAAAAATTTG
6992 GTGTTTTAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
77 2 0.02
78 47 0.43
79 12 0.11
80 49 0.45
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.32
Consensus pattern (78 bp):
TATCCCTTCAGAGATGGTGGGATCGAAGTATCCCTAGAGATGAAAAATTTGACGTTTTAGATAAA
AATAGAGTTGGAC
Found at i:7065 original size:79 final size:76
Alignment explanation
Indices: 6808--7338 Score: 263
Period size: 79 Copynumber: 6.7 Consensus size: 76
6798 GGTAAGGTTG
* * * ** *
6808 GAGTATCCCTAGAGATAAAAAATTTGATGTTTTAGATTTAAAAATAGGGTTGGAGTATCCCTTCA
1 GAGTATCCC-AGAGATGAAAATTTTGATGTTTTAAAAGT-AAAATAGGGTTGGAGTACCCCTT--
* *
6873 GAGATGGTGG-GATTG
62 GAGATGTTGGAG-TTA
* * * * * * * *
6888 GAGTATCCTCAGAGATGAAAAATTTGACGTTTTGGAAA-T-AGATAGAGTTGTACTATCTCCTTG
1 GAGTATCC-CAGAGATGAAAATTTTGATGTTTT-AAAAGTAAAATAGGGTTGGAGTA-CCCCTT-
* * *
6951 GAGATGGTGG-GGTC
62 GAGATGTTGGAGTTA
* * *
6965 GAAGTATCCCTAGAGATGAAAATTTTGGTGTTTTAAAAGTGAAAATGGGGGTTAGAGTACCCCTT
1 G-AGTATCCC-AGAGATGAAAATTTTGATGTTTTAAAAGT-AAAAT-AGGGTTGGAGTACCCCTT
** * *
7030 TTGATGTTAGAGTTG
62 GAGATGTTGGAGTTA
* ** * * * *
7045 GAGTATTCCCAGAGATGAAAAATTTGATGTTTTGGAAGTAAAATTAGGGTTGGAGCATCTCTCGG
1 GAGTA-TCCCAGAGATGAAAATTTTGATGTTTTAAAAGTAAAA-TAGGGTTGGAGTACCCCT-TG
*
7110 AGATAG-TGGAATTA
63 AGAT-GTTGGAGTTA
* * * *
7124 GAGTATCCCCGGAGATGAAAAATTTT-ACGTTTT-GAAGTAGAAATGGGGTTGGAGTATCCCCTT
1 GAGTAT-CCCAGAGATG-AAAATTTTGATGTTTTAAAAGTA-AAATAGGGTTGGAGTA-CCCCTT
* * *
7187 AGAGATGGTGGGGTTG
62 -GAGATGTTGGAGTTA
*
7203 GAGTATCCTC-GAAGATGAAAATTTT-AGTGTTTTAAAAGTGAAAATAAGGGTTGGAGTACCTCT
1 GAGTATCC-CAG-AGATGAAAATTTTGA-TGTTTTAAAAGT-AAAAT-AGGGTTGGAGTACCCCT
** *
7266 TTTGATGTTGGGGTTA
61 TGAGATGTTGGAGTTA
* * ** **
7282 GAGTATCCCTAGAGATAAAAAATTCAATGTTTTGGAAGTAGAAA-AGAGGTTGGAGTA
1 GAGTATCCC-AGAGATGAAAATTTTGATGTTTTAAAAGTA-AAATAG-GGTTGGAGTA
7339 TCCTCGAAGA
Statistics
Matches: 350, Mismatches: 70, Indels: 64
0.72 0.14 0.13
Matches are distributed among these distances:
77 8 0.02
78 110 0.31
79 143 0.41
80 68 0.19
81 21 0.06
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.31
Consensus pattern (76 bp):
GAGTATCCCAGAGATGAAAATTTTGATGTTTTAAAAGTAAAATAGGGTTGGAGTACCCCTTGAGA
TGTTGGAGTTA
Found at i:7194 original size:237 final size:237
Alignment explanation
Indices: 6804--7341 Score: 672
Period size: 237 Copynumber: 2.3 Consensus size: 237
6794 AGATGGTAAG
* ** *
6804 GTTGGAGTATCCCTAGAGATAAAAAATTTGATGTTTTAGATTTAAAAATAGGGTTGGAGTATCCC
1 GTTGGAGTATCCCTAGAGATAAAAAATTTGATGTTTTGGAAGTAAAAATAGGGTTGGAGCATCCC
* * * *
6869 TTCAGAGATGGTGGGATTGGAGTATCCTCAGAGATGAAAAATTTGACGTTTTGGAAATAGATAGA
66 TTCAGAGATAGTGGAATTAGAGTATCCCCAGAGATGAAAAATTTGACGTTTTGGAAATAGATAGA
* * * *
6934 GTTGTACTATCTCCTTGGAGATGGTGGGGTCGAAGTATCCCTAG-AGATGAAAATTTTGGTGTTT
131 GTTGGACTATCCCCTTAGAGATGGTGGGGTCGAAGTAT-CCTAGAAGATGAAAATTTTAGTGTTT
**
6998 TAAAAGTGAAAATGGGGGTTAGAGTACCCCTTTTGATGTTAGA
195 TAAAAGTGAAAATAAGGGTTAGAGTACCCCTTTTGATGTTAGA
* * *
7041 GTTGGAGTATTCCC-AGAGATGAAAAATTTGATGTTTTGGAAGTAAAATTAGGGTTGGAGCATCT
1 GTTGGAGTA-TCCCTAGAGATAAAAAATTTGATGTTTTGGAAGTAAAAATAGGGTTGGAGCATCC
* * * *
7105 C-TCGGAGATAGTGGAATTAGAGTATCCCCGGAGATGAAAAATTTTACGTTTT-GAAGTAGAAAT
65 CTTCAGAGATAGTGGAATTAGAGTATCCCCAGAGATGAAAAATTTGACGTTTTGGAAATAG--AT
* * * * * *
7168 GGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCTCGAAGATGAAAATTTTAGTGT
128 AGAGTTGGACTATCCCCTTAGAGATGGTGGGGTCGAAGTATCCTAGAAGATGAAAATTTTAGTGT
* * * *
7233 TTTAAAAGTGAAAATAAGGGTTGGAGTACCTCTTTTGATGTTGGG
193 TTTAAAAGTGAAAATAAGGGTTAGAGTACCCCTTTTGATGTTAGA
* ** * *
7278 GTTAGAGTATCCCTAGAGATAAAAAATTCAATGTTTTGGAAGTAGAAA-AGAGGTTGGAGTATCC
1 GTTGGAGTATCCCTAGAGATAAAAAATTTGATGTTTTGGAAGTAAAAATAG-GGTTGGAGCATCC
7342 TCGAAGATGA
Statistics
Matches: 256, Mismatches: 39, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
235 6 0.02
236 54 0.21
237 192 0.75
238 4 0.02
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (237 bp):
GTTGGAGTATCCCTAGAGATAAAAAATTTGATGTTTTGGAAGTAAAAATAGGGTTGGAGCATCCC
TTCAGAGATAGTGGAATTAGAGTATCCCCAGAGATGAAAAATTTGACGTTTTGGAAATAGATAGA
GTTGGACTATCCCCTTAGAGATGGTGGGGTCGAAGTATCCTAGAAGATGAAAATTTTAGTGTTTT
AAAAGTGAAAATAAGGGTTAGAGTACCCCTTTTGATGTTAGA
Found at i:7219 original size:158 final size:160
Alignment explanation
Indices: 6808--7341 Score: 447
Period size: 158 Copynumber: 3.4 Consensus size: 160
6798 GGTAAGGTTG
* * ** * *
6808 GAGTATCCCTAGAGATAAAAAATTTGATGTTTTAGATTTAAAAATAGGGTTGGAGTAT-CCCTTC
1 GAGTATCCCTAGAGATGAAAAATTTTATGTTTTAGAAGTAGAAATGGGGTTGGAGTATCCCCTT-
* * * * *
6872 AGAGATGGTGGGATTGGAGTATCCTCAGAGATGAAAAATTTGACGTTTTGGAAAT-AGA-TAGAG
65 AGAGATGGTGGGGTTGGAGTATCCTCAGAGATGAAAAATTTGATGTTTTGGAAGTAAAATTAGGG
* * * * *
6935 TTGTA-CTATCTCCTTGGAGATGGTGGGGTC
130 TTGGAGCTATCTCCTCGGAGATAGTGGAGTA
* * *
6965 GAAGTATCCCTAGAGATG-AAAATTTTGGTGTTTTAAAAGT-GAAAATGGGGGTTAGAGTA-CCC
1 G-AGTATCCCTAGAGATGAAAAATTTT-ATGTTTTAGAAGTAG-AAAT-GGGGTTGGAGTATCCC
** * * *
7027 CTT-TTGATGTTAGAGTTGGAGTATTCC-CAGAGATGAAAAATTTGATGTTTTGGAAGTAAAATT
62 CTTAGAGATGGTGGGGTTGGAGTA-TCCTCAGAGATGAAAAATTTGATGTTTTGGAAGTAAAATT
*
7090 AGGGTTGGAGC-ATCT-CTCGGAGATAGTGGAATTA
126 AGGGTTGGAGCTATCTCCTCGGAGATAGTGG-AGTA
** *
7124 GAGTATCCCCGGAGATGAAAAATTTTACGTTTT-GAAGTAGAAATGGGGTTGGAGTATCCCCTTA
1 GAGTATCCCTAGAGATGAAAAATTTTATGTTTTAGAAGTAGAAATGGGGTTGGAGTATCCCCTTA
* ** *
7188 GAGATGGTGGGGTTGGAGTATCCTC-GAAGATG-AAAATTTTAGTGTTTTAAAAGTGAAAATAAG
66 GAGATGGTGGGGTTGGAGTATCCTCAG-AGATGAAAAATTTGA-TGTTTTGGAAGT-AAAATTAG
* *** *
7251 GGTTGGAG-TACCT-CT-TTTGAT-GTTGGGGTTA
128 GGTTGGAGCTATCTCCTCGGAGATAG-TGGAG-TA
* ** * * *
7282 GAGTATCCCTAGAGATAAAAAATTCAATGTTTTGGAAGTAGAAAAGAGGTTGGAGTATCC
1 GAGTATCCCTAGAGATGAAAAATTTTATGTTTTAGAAGTAGAAATGGGGTTGGAGTATCC
7342 TCGAAGATGA
Statistics
Matches: 301, Mismatches: 54, Indels: 42
0.76 0.14 0.11
Matches are distributed among these distances:
156 11 0.04
157 77 0.26
158 131 0.44
159 81 0.27
160 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (160 bp):
GAGTATCCCTAGAGATGAAAAATTTTATGTTTTAGAAGTAGAAATGGGGTTGGAGTATCCCCTTA
GAGATGGTGGGGTTGGAGTATCCTCAGAGATGAAAAATTTGATGTTTTGGAAGTAAAATTAGGGT
TGGAGCTATCTCCTCGGAGATAGTGGAGTA
Found at i:7644 original size:22 final size:22
Alignment explanation
Indices: 7592--7646 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
7582 TTCGTGAGAG
*
7592 AAATTTGAAAACACGAAAACTA
1 AAATTTGAGAACACGAAAACTA
7614 AAATTTGAGAACACGAAAACTA
1 AAATTTGAGAACACGAAAACTA
7636 AAATTTGAGAA
1 AAATTTGAGAA
7647 AAATATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.56, C:0.11, G:0.13, T:0.20
Consensus pattern (22 bp):
AAATTTGAGAACACGAAAACTA
Found at i:8183 original size:43 final size:41
Alignment explanation
Indices: 8122--8203 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 41
8112 AGGATTTGTA
* * * *
8122 GCCACCTAATTGACTTAGGTGGCATTGCATTGCATTGCATGTT
1 GCCACCTAAATCAATTAGGTGGCAATGCA-TGCATT-CATGTT
8165 GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATG
1 GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATG
8204 CATGAAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.11
42 6 0.17
43 25 0.71
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (41 bp):
GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGTT
Found at i:8488 original size:20 final size:21
Alignment explanation
Indices: 8458--8496 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
8448 GCTGCTGCAA
8458 AAAATATAATAATAAATAAAT
1 AAAATATAATAATAAATAAAT
8479 AAAA-ATAATAATAAATAA
1 AAAATATAATAATAAATAA
8497 CGGACAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATATAATAATAAATAAAT
Found at i:8951 original size:30 final size:31
Alignment explanation
Indices: 8885--8952 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
8875 CAACCACCGG
* * * *
8885 CAGCCCCCACAGCTCCCACAGTAACTTTCAG
1 CAGCTCCCACAGCTCCCACAGCAACTTCCAA
*
8916 TAGCTCCCACAGCT-CCACAGCAACTTCCAA
1 CAGCTCCCACAGCTCCCACAGCAACTTCCAA
8946 CAGCTCC
1 CAGCTCC
8953 AGCAGAGCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.26, C:0.46, G:0.12, T:0.16
Consensus pattern (31 bp):
CAGCTCCCACAGCTCCCACAGCAACTTCCAA
Found at i:9065 original size:22 final size:22
Alignment explanation
Indices: 9034--9089 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
9024 CTTCCAGCAG
* * *
9034 CTCCAGCAGCTTCCACGATAGC
1 CTCCAGCAGCTCCCACGACAAC
*
9056 CTCCAACAGCTCCCACGACAAC
1 CTCCAGCAGCTCCCACGACAAC
9078 CTCCAGCAGCTC
1 CTCCAGCAGCTC
9090 AGCAGCCTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.46, G:0.14, T:0.14
Consensus pattern (22 bp):
CTCCAGCAGCTCCCACGACAAC
Found at i:9442 original size:5 final size:5
Alignment explanation
Indices: 9432--9460 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9422 TTTTTTTTAA
9432 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
9461 ACAAAAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:14538 original size:22 final size:23
Alignment explanation
Indices: 14494--14538 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
14484 ATATTCATGG
*
14494 CATTCATTCAACATTTTCATAAT
1 CATTCATTCAACATTTGCATAAT
* *
14517 CATTCA-TCAATATTTGCTTAAT
1 CATTCATTCAACATTTGCATAAT
14539 TAATAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (23 bp):
CATTCATTCAACATTTGCATAAT
Found at i:22789 original size:42 final size:42
Alignment explanation
Indices: 22729--23652 Score: 611
Period size: 42 Copynumber: 21.9 Consensus size: 42
22719 AAACTTTTGA
*
22729 AGACTTTCCTTCCATTAGTCTGCCTGTCGGCTTTGACCCTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * *
22771 AGACTTTCCTTCCCTTAGTTTGCTTGTCGACTTTGACCCTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
** * * * *
22813 AGACTTTTTTTCCTTTAGTCTGCCTGTCGGCTTTGATCTTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * * *
22855 AGACTTTCCTTTCCTAAGTCTG-CTTTCGGCTTTGATCTTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * * * *
22896 AGACTTTTCTACCCTTAGTCTACCTATCAGCTTTGA-CTTTG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * *
22937 AAGACTTTCCTGCCCTTAGTTTGCCTATCAGCTTTGACCTTAG
1 -AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * ** *
22980 AGACTTTCTTTCCCTTAGTTTGCCTGTCGATTTTGACCCTAA
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * *
23022 AGACTTTCCTACCCTTCAGTCTGCTTGTCGGCTTTGGCCTTAG
1 AGACTTTCCTTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTAG
* * * * * * *
23065 AAAC--TACTTCATCTAAAGTTTGCTTGTCGGCTTTAACCCTAG
1 AGACTTTCCTTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTAG
* ** * *
23107 AGACTTTCCTATCCCTCAGTCTGCCTGTCAACTTTGACCTTGG
1 AGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *** * *
23150 AGACTTTCCTAT-CCTCAGTCTACCTGTCAAATTTGACTCTGG
1 AGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
23192 AGACTTTCCTT-CCTTCAATCTGCCTGTCAGCTTTGACTCTAG
1 AGACTTTCCTTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTAG
* ** *
23234 AGACTTTCCTTCCCTTAGTCTGTCTGTCGATTTTGACCCTTG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * * * *
23276 AGACTTTCCTACCCTTTAGTTTGCTTATTGACTTTGACCCTGG
1 AGACTTTCCTTCCC-TTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * * *
23319 AGAC-TACCTTACCTAAAGTTTGCCTATCGACTTTGACCCTAG
1 AGACTTTCCTTCCCT-TAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * * *
23361 AGATTTTTCTAT-CCTCAATCTGCCTGTCGGCTTTGATCCTGG
1 AGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
*
23403 AGACTTTCCTAT-CCTCAGTCTGCCTGTCGGCTTTGACCCT-G
1 AGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * *
23444 AAGACTTTCCTATGCTTTAGTCTGCCTGTTGGCTTTGACCTTAG
1 -AGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* ** * * ** *
23488 AGAC-TACCTTATCTAAAGTTTATCTGTCGGCTTTGACCCTGG
1 AGACTTTCCTTCCCT-TAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
23530 AGAC-TACC-TCATCTAAAGTCTGCCTGTCGGCTTTGACCCTAG
1 AGACTTTCCTTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
23572 AGACTTTCCTAT-CCTCAGTCTGCCTGTCAGCTTTGACTCT-G
1 AGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
23613 AAGACTTTCCTAT-CCTTCAATCTGTCTGTCGGATTTGACC
1 -AGACTTTCCT-TCCCTT-AGTCTGCCTGTCGGCTTTGACC
23653 TTGGTGACTA
Statistics
Matches: 711, Mismatches: 146, Indels: 49
0.78 0.16 0.05
Matches are distributed among these distances:
41 53 0.07
42 506 0.71
43 142 0.20
44 7 0.01
45 3 0.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (42 bp):
AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
Found at i:23322 original size:169 final size:169
Alignment explanation
Indices: 22729--23695 Score: 635
Period size: 169 Copynumber: 5.7 Consensus size: 169
22719 AAACTTTTGA
* * * *
22729 AGACTTTCCTTCCATTAGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTTCCTTCCCTTAGTTTG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGACTTTGACCCTTGAAGACTTTCCTACCCTTAGTTTG
* * * * * * * * * *
22793 CTTGTCGACTTTGACCCTGGAGACTTT-TTTTCCTTTAGTCTGCCTGTCGGCTTTGATCTTGGAG
66 CCTGTTGACTTTGACCTTGGAGACTTTCCTATCC-TAAGTTTGCCTGTCGACTTTGACCCTGGAG
* *
22857 ACTTTCCTTTCC-T-AAGTCTG-CTTTCGGCTTTGA-TCTTGG
130 ACTTTCC-TTCCTTCAA-TCTGCCTGTCGGCTTTGACTC-TAG
* * * * * *
22896 AGACTTTTCTACCCTTAGTCTACCTATC-AGCTTTGA-CTTTGAAGACTTTCCTGCCCTTAGTTT
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGA-CTTTGACCCTTGAAGACTTTCCTACCCTTAGTTT
* * * * * * **
22959 GCCT-ATCAGCTTTGACCTTAGAGACTTT-CTTTCCCTTAGTTTGCCTGTCGATTTTGACCCTAA
65 GCCTGTTGA-CTTTGACCTTGGAGACTTTCCTAT-CCTAAGTTTGCCTGTCGACTTTGACCCTGG
* * * *
23022 AGACTTTCCTACCCTTCAGTCTGCTTGTCGGCTTTGGC-CTTAG
128 AGACTTTCCT-TCCTTCAATCTGCCTGTCGGCTTTGACTC-TAG
* * * * * * * * * *
23065 AAAC--TACTTCATCTAAAGTTTGCTTGTCGGCTTTAACCCTAG-AGACTTTCCTATCCCTCAGT
1 AGACTTTCCTTC-CCT-TAGTCTGCCTGTCGACTTTGACCCTTGAAGACTTTCCTA-CCCTTAGT
* ** * * * * * *
23127 CTGCCTGTCAACTTTGACCTTGGAGACTTTCCTATCCTCAGTCTACCTGTCAAATTTGACTCTGG
63 TTGCCTGTTGACTTTGACCTTGGAGACTTTCCTATCCTAAGTTTGCCTGTCGACTTTGACCCTGG
*
23192 AGACTTTCCTTCCTTCAATCTGCCTGTCAGCTTTGACTCTAG
128 AGACTTTCCTTCCTTCAATCTGCCTGTCGGCTTTGACTCTAG
* *
23234 AGACTTTCCTTCCCTTAGTCTGTCTGTCGATTTTGACCCTTG-AGACTTTCCTACCCTTTAGTTT
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGACTTTGACCCTTGAAGACTTTCCTACCC-TTAGTTT
* * * * * *
23298 GCTTATTGACTTTGACCCTGGAGAC-TACCT-TACCTAAAGTTTGCCTATCGACTTTGACCCTAG
65 GCCTGTTGACTTTGACCTTGGAGACTTTCCTAT-CCT-AAGTTTGCCTGTCGACTTTGACCCTGG
* * *
23361 AGATTTTTCTATCC-TCAATCTGCCTGTCGGCTTTGA-TCCTGG
128 AGACTTTCCT-TCCTTCAATCTGCCTGTCGGCTTTGACT-CTAG
* * * * *
23403 AGACTTTCCTAT-CCTCAGTCTGCCTGTCGGCTTTGACCC-TGAAGACTTTCCTATGCTTTAGTC
1 AGACTTTCCT-TCCCTTAGTCTGCCTGTCGACTTTGACCCTTGAAGACTTTCCTA-CCCTTAGTT
* * * ** *
23466 TGCCTGTTGGCTTTGACCTTAGAGAC-TACCTTAT-CTAAAGTTTATCTGTCGGCTTTGACCCTG
64 TGCCTGTTGACTTTGACCTTGGAGACTTTCC-TATCCT-AAGTTTGCCTGTCGACTTTGACCCTG
* * * *
23529 GAGAC-TACC-TCATCTAAAGTCTGCCTGTCGGCTTTGACCCTAG
127 GAGACTTTCCTTCCT-TCAA-TCTGCCTGTCGGCTTTGACTCTAG
* * * *
23572 AGACTTTCCTAT-CCTCAGTCTGCCTGTC-AGCTTTGACTC-TGAAGACTTTCCTATCCTTCAAT
1 AGACTTTCCT-TCCCTTAGTCTGCCTGTCGA-CTTTGACCCTTGAAGACTTTCCTACCCTT-AGT
* * * * * * * *
23634 CTGTCTGTCGGA-TTTGACCTTGGTGAC-TACCATATCCTTCAGTTTGCTTGTCGGCTTTGACC
63 TTGCCTGT-TGACTTTGACCTTGGAGACTTTCC-TATCC-TAAGTTTGCCTGTCGACTTTGACC
23696 TAAGAGAATC
Statistics
Matches: 629, Mismatches: 133, Indels: 73
0.75 0.16 0.09
Matches are distributed among these distances:
166 7 0.01
167 109 0.17
168 30 0.05
169 377 0.60
170 95 0.15
171 11 0.02
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (169 bp):
AGACTTTCCTTCCCTTAGTCTGCCTGTCGACTTTGACCCTTGAAGACTTTCCTACCCTTAGTTTG
CCTGTTGACTTTGACCTTGGAGACTTTCCTATCCTAAGTTTGCCTGTCGACTTTGACCCTGGAGA
CTTTCCTTCCTTCAATCTGCCTGTCGGCTTTGACTCTAG
Found at i:23427 original size:211 final size:212
Alignment explanation
Indices: 22729--23652 Score: 676
Period size: 211 Copynumber: 4.4 Consensus size: 212
22719 AAACTTTTGA
* * * * * *
22729 AGACTTTCCT-TCCATTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT-TCCCTT-AGTT
1 AGACTTTCCTATCC-TCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTTTCCTAT-CCTTCAATC
* * * * * * * * *
22791 TGCTTGTCGACTTTGACCCTGGAGACTTT-TTTTCCTTTAGTCTGCCTGTCGGCTTTGATCTTGG
64 TGCCTGTCGGCTTTGACCCTGAAGACTTTCCTATCCCTTAGTCTGCCTGTCGACTTTGACCTTAG
* * * * * * * * ** *
22855 AGACTTTCCTTTCCT-AAGTCT-GCTTTCGGCTTTGATCTTGGAGACT-TTTCTACCCT-TAGTC
129 AGAC-TACCTTACCTAAAGTTTATCTATCGACTTTGACCCTGGAGACTACCTC-A-CCTAAAGTC
* * * *
22916 TACCTATC-AGCTTTGA-CTTTG
191 TGCCTGTCGA-CTTTGACCCTAG
** * * * * * *
22937 AAGACTTTCCTGCCCTTAGTTTGCCTATCAGCTTTGAC-CTTAGAGACTTT-CTTTCCCTT-AGT
1 -AGACTTTCCTATCCTCAGTCTGCCTGTCAGCTTTGACTC-TGGAGACTTTCCTAT-CCTTCAAT
* ** * * * *
22999 TTGCCTGTCGATTTTGACCCTAAAGACTTTCCTA-CCCTTCAGTCTGCTTGTCGGCTTTGGCCTT
63 CTGCCTGTCGGCTTTGACCCTGAAGACTTTCCTATCCCTT-AGTCTGCCTGTCGACTTTGACCTT
* * * * * * * * *
23063 AGAAACTA-CTTCATCTAAAGTTT-GCTTGTCGGCTTTAACCCTAGAGACTTTCCT-ATCCCT-C
127 AGAGACTACCTT-ACCTAAAGTTTATC-TATCGACTTTGACCCTGGAGAC-TACCTCA--CCTAA
* * *
23124 AGTCTGCCTGTCAACTTTGACCTTGG
187 AGTCTGCCTGTCGACTTTGACCCTAG
* **
23150 AGACTTTCCTATCCTCAGTCTACCTGTCAAATTTGACTCTGGAGACTTTCCT-TCCTTCAATCTG
1 AGACTTTCCTATCCTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTTTCCTATCCTTCAATCTG
* * * *
23214 CCTGTCAGCTTTGACTCT-AGAGACTTTCCT-TCCCTTAGTCTGTCTGTCGATTTTGACCCTT-G
66 CCTGTCGGCTTTGACCCTGA-AGACTTTCCTATCCCTTAGTCTGCCTGTCGACTTTGA-CCTTAG
* ** * * * *
23276 AGACTTTCC-TACCCTTTAGTTT-GCTTATTGACTTTGACCCTGGAGACTACCTTACCTAAAGTT
129 AGAC-TACCTTA-CCTAAAGTTTATC-TATCGACTTTGACCCTGGAGACTACCTCACCTAAAGTC
*
23339 TGCCTATCGACTTTGACCCTAG
191 TGCCTGTCGACTTTGACCCTAG
* * * * *
23361 AGATTTTTCTATCCTCAATCTGCCTGTCGGCTTTGA-TCCTGGAGACTTTCCTATCC-TCAGTCT
1 AGACTTTCCTATCCTCAGTCTGCCTGTCAGCTTTGACT-CTGGAGACTTTCCTATCCTTCAATCT
* * * *
23424 GCCTGTCGGCTTTGACCCTGAAGACTTTCCTATGCTTTAGTCTGCCTGTTGGCTTTGACCTTAGA
65 GCCTGTCGGCTTTGACCCTGAAGACTTTCCTATCCCTTAGTCTGCCTGTCGACTTTGACCTTAGA
* * * *
23489 GACTACCTTATCTAAAGTTTATCTGTCGGCTTTGACCCTGGAGACTACCTCATCTAAAGTCTGCC
130 GACTACCTTACCTAAAGTTTATCTATCGACTTTGACCCTGGAGACTACCTCACCTAAAGTCTGCC
*
23554 TGTCGGCTTTGACCCTAG
195 TGTCGACTTTGACCCTAG
*
23572 AGACTTTCCTATCCTCAGTCTGCCTGTCAGCTTTGACTCTGAAGACTTTCCTATCCTTCAATCTG
1 AGACTTTCCTATCCTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTTTCCTATCCTTCAATCTG
* *
23637 TCTGTCGGATTTGACC
66 CCTGTCGGCTTTGACC
23653 TTGGTGACTA
Statistics
Matches: 577, Mismatches: 105, Indels: 63
0.77 0.14 0.08
Matches are distributed among these distances:
208 6 0.01
209 82 0.14
210 39 0.07
211 259 0.45
212 181 0.31
213 10 0.02
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (212 bp):
AGACTTTCCTATCCTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTTTCCTATCCTTCAATCTG
CCTGTCGGCTTTGACCCTGAAGACTTTCCTATCCCTTAGTCTGCCTGTCGACTTTGACCTTAGAG
ACTACCTTACCTAAAGTTTATCTATCGACTTTGACCCTGGAGACTACCTCACCTAAAGTCTGCCT
GTCGACTTTGACCCTAG
Found at i:23470 original size:127 final size:126
Alignment explanation
Indices: 22729--23695 Score: 608
Period size: 127 Copynumber: 7.6 Consensus size: 126
22719 AAACTTTTGA
* * * * *
22729 AGACTTTCCT-TCCATTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT-TCCCTTAGTTT
1 AGACTTTCCTATCC-TCAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT-CCTCAGTCT
* * * ** * * * *
22792 GCTTGTCGACTTTGACCCTGGAGACTTTTTTTCCTTTAGTCTGCCTGTCGGCTTTGATCTTGG
64 GCCTGTCGGCTTTGACCCTGAAGACTTTCCTTCCTTTAGTCTGCCTGTCGACTTTGACCCTAG
* * * * * * * *
22855 AGACTTTCCTTTCCT-AAGTCTG-CTTTCGGCTTTGATCTTGGAGACTTTTCTACCCTTAGTCTA
1 AGACTTTCCTATCCTCAA-TCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCTCAGTCTG
* * ** * * * * *
22918 CCTATCAGCTTTGACTTTGAAGACTTTCCTGCCCTTAGTTTGCCTATC-AGCTTTGACCTTAG
65 CCTGTCGGCTTTGACCCTGAAGACTTTCCTTCCTTTAGTCTGCCTGTCGA-CTTTGACCCTAG
* * * * ** ** *
22980 AGACTTT-CTTTCCCTTAGTTTGCCTGTCGATTTTGACCCTAAAGACTTTCCTACCCTTCAGTCT
1 AGACTTTCCTAT-CCTCAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCC-TCAGTCT
* * * * ** * * * *
23044 GCTTGTCGGCTTTGGCCTTAGAA-AC--TACTTCATCTAAAGTTTGCTTGTCGGCTTTAACCCTA
64 GCCTGTCGGCTTTGACCCT-GAAGACTTTCCTTC--CTTTAGTCTGCCTGTCGACTTTGACCCTA
23106 G
126 G
* ** * *
23107 AGACTTTCCTATCCCTCAGTCTGCCTGTCAACTTTGACCTTGGAGACTTTCCTATCCTCAGTCTA
1 AGACTTTCCTAT-CCTCAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCTCAGTCTG
*** * * * * *
23172 CCTGTCAAATTTGACTCTGGAGACTTTCCTTCCTTCAATCTGCCTGTC-AGCTTTGACTCTAG
65 CCTGTCGGCTTTGACCCTGAAGACTTTCCTTCCTTTAGTCTGCCTGTCGA-CTTTGACCCTAG
* * * ** * * * *
23234 AGACTTTCCT-TCCCTTAGTCTGTCTGTCGATTTTGACCCTTGAGACTTTCCTACCCTTTAGTTT
1 AGACTTTCCTAT-CCTCAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCC-TCAGTCT
* * * * * * ** * *
23298 GCTTATTGACTTTGACCCTGGAGAC-TACCTTACCTAAAGTTTGCCTATCGACTTTGACCCTAG
64 GCCTGTCGGCTTTGACCCTGAAGACTTTCCTT-CCTTTAGTCTGCCTGTCGACTTTGACCCTAG
* * *
23361 AGATTTTTCTATCCTCAATCTGCCTGTCGGCTTTGATCCTGGAGACTTTCCTATCCTCAGTCTGC
1 AGACTTTCCTATCCTCAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCTCAGTCTGC
* * * *
23426 CTGTCGGCTTTGACCCTGAAGACTTTCCTATGCTTTAGTCTGCCTGTTGGCTTTGACCTTAG
66 CTGTCGGCTTTGACCCTGAAGACTTTCCT-TCCTTTAGTCTGCCTGTCGACTTTGACCCTAG
* * * ** * *
23488 AGAC-TACCTTAT-CTAAAGTTTATCTGTCGGCTTTGACCCTGGAGAC-TACCTCAT-CTAAAGT
1 AGACTTTCC-TATCCTCAA-TCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-ATCCT-CAGT
* *
23549 CTGCCTGTCGGCTTTGACCCT-AGAGACTTTCCTATCC-TCAGTCTGCCTGTC-AGCTTTGACTC
62 CTGCCTGTCGGCTTTGACCCTGA-AGACTTTCCT-TCCTTTAGTCTGCCTGTCGA-CTTTGACCC
23611 T-G
124 TAG
* * * * *
23613 AAGACTTTCCTATCCTTCAATCTGTCTGTCGGATTTGACCTTGGTGAC-TACCATATCCTTCAGT
1 -AGACTTTCCTATCC-TCAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC-TATCC-TCAGT
* *
23677 TTGCTTGTCGGCTTTGACC
62 CTGCCTGTCGGCTTTGACC
23696 TAAGAGAATC
Statistics
Matches: 651, Mismatches: 154, Indels: 70
0.74 0.18 0.08
Matches are distributed among these distances:
124 4 0.01
125 96 0.15
126 152 0.23
127 322 0.49
128 71 0.11
129 6 0.01
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (126 bp):
AGACTTTCCTATCCTCAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCTCAGTCTGC
CTGTCGGCTTTGACCCTGAAGACTTTCCTTCCTTTAGTCTGCCTGTCGACTTTGACCCTAG
Found at i:23516 original size:254 final size:250
Alignment explanation
Indices: 22760--23650 Score: 821
Period size: 254 Copynumber: 3.5 Consensus size: 250
22750 GCCTGTCGGC
* ** *
22760 TTTGACCCTAGAGACTTTCCTTCCC-TTAGTTTGCTTGTCGACTTTGACCCTGGAGACTTTTTTT
1 TTTGACCCTAGAGACTTTCCTACCCTTTAGTTTGCTTGTCGACTTTGACCCTGGAGAC-TACTTA
** * * * * * *
22824 CCTTTAGTCTGCCTGTCGGCTTTGATCTTGGAGACTTTCCTTTCCT-AAGTCTG-CTTTCGGCTT
65 CCTAAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCTCAA-TCTGCCTGTCGGCTT
* * * * * *
22887 TGATCTTGGAGACTTTTCTACCCTTAGTCTACCTATCAGCTTTGACTTTGAAGACTTTCC-TGCC
129 TGATCCTGGAGACTTTCCTATCCTCAGTCTACCTGTCAGCTTTGACTCTGAAGACTTTCCTTG-C
* * * * *
22951 CTTAGTTTGCCTATCAGCTTTGACCTTAGAGACTTTCTTTCCCTTAGTTTGCCTGTCGAT
193 TTTAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTT--CTTAGTTTGTCTGTCGAT
* * * * * * * *
23011 TTTGACCCTAAAGACTTTCCTACCCTTCAGTCTGCTTGTCGGCTTTGGCCTTAGAAACTACTTCA
1 TTTGACCCTAGAGACTTTCCTACCCTTTAGTTTGCTTGTCGACTTTGACCCTGGAGACTACTT-A
* * * * **
23076 TCTAAAGTTTGCTTGTCGGCTTTAACCCTAGAGACTTTCCTATCCCTCAGTCTGCCTGTCAACTT
65 CCTAAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTAT-CCTCAATCTGCCTGTCGGCTT
** * *
23141 TGA-CCTTGGAGACTTTCCTATCCTCAGTCTACCTGTCAAATTTGACTCTGGAGACTTTCCTTCC
129 TGATCC-TGGAGACTTTCCTATCCTCAGTCTACCTGTCAGCTTTGACTCTGAAGACTTTCCTTGC
* * * *
23205 TTCAATCTGCCTGTCAGCTTTGA-CTCTAGAGACTTTCCTTCCCTTAGTCTGTCTGTCGAT
193 TTTAGTCTGCCTGTCAGCTTTGACCT-TAGAGAC-TTCCTT-TCTTAGTTTGTCTGTCGAT
* * *
23265 TTTGACCCTTGAGACTTTCCTACCCTTTAGTTTGCTTATTGACTTTGACCCTGGAGACTACCTTA
1 TTTGACCCTAGAGACTTTCCTACCCTTTAGTTTGCTTGTCGACTTTGACCCTGGAGACTA-CTTA
* * * *
23330 CCTAAAGTTTGCCTATCGACTTTGACCCTAGAGATTTTTCTATCCTCAATCTGCCTGTCGGCTTT
65 CCTAAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCTCAATCTGCCTGTCGGCTTT
* * *
23395 GATCCTGGAGACTTTCCTATCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCCTATGCT
130 GATCCTGGAGACTTTCCTATCCTCAGTCTACCTGTCAGCTTTGACTCTGAAGACTTTCCT-TGCT
** * * * **
23460 TTAGTCTGCCTGTTGGCTTTGACCTTAGAGACTACCTTATCTAAAGTTTATCTGTCGGC
194 TTAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTT-TCT-TAGTTTGTCTGTCGAT
* * * ** * * * * * *
23519 TTTGACCCTGGAGAC-TACCT-CATCTAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT
1 TTTGACCCTAGAGACTTTCCTAC-CCTTTAGTTTGCTTGTCGACTTTGACCCTGGAGAC-TACTT
* * * * *
23582 ATCCT-CAGTCTGCCTGTCAGCTTTGACTCT-GAAGACTTTCCTATCCTTCAATCTGTCTGTCGG
64 A-CCTAAAGTTTGCCTGTCGGCTTTGACCCTAG-AGACTTTCCTATCC-TCAATCTGCCTGTCGG
*
23645 ATTTGA
126 CTTTGA
23651 CCTTGGTGAC
Statistics
Matches: 512, Mismatches: 108, Indels: 37
0.78 0.16 0.06
Matches are distributed among these distances:
251 26 0.05
252 60 0.12
253 151 0.29
254 264 0.52
255 11 0.02
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.38
Consensus pattern (250 bp):
TTTGACCCTAGAGACTTTCCTACCCTTTAGTTTGCTTGTCGACTTTGACCCTGGAGACTACTTAC
CTAAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCTCAATCTGCCTGTCGGCTTTG
ATCCTGGAGACTTTCCTATCCTCAGTCTACCTGTCAGCTTTGACTCTGAAGACTTTCCTTGCTTT
AGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTTCTTAGTTTGTCTGTCGAT
Found at i:24229 original size:25 final size:24
Alignment explanation
Indices: 24158--24232 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
24148 TATTCAATGT
* *
24158 AAAATATAATAATAAGTAAAAATAAA
1 AAAATATAAAAATAA--AAAAATTAA
**
24184 AAAATATCAAAAA-AATCAAATTAA
1 AAAATAT-AAAAATAAAAAAATTAA
24208 AAAATAATAAAAATAAAAAAATTAA
1 AAAAT-ATAAAAATAAAAAAATTAA
24233 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
24 16 0.40
25 11 0.28
26 9 0.22
27 4 0.10
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (24 bp):
AAAATATAAAAATAAAAAAATTAA
Found at i:24334 original size:43 final size:41
Alignment explanation
Indices: 24273--24355 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 41
24263 AGGATTTGTA
* * * *
24273 GCCACCTAATTGACTTAGGTGGCATTGCATTGCATTGCATGCT
1 GCCACCTAAATCAATTAGGTGGCAATGC-TTGCATT-CATGCT
24316 GCCACCTAAATCAATTAGGTGGCAATGCTTGCATTCATGC
1 GCCACCTAAATCAATTAGGTGGCAATGCTTGCATTCATGC
24356 ATGAAATTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 5 0.14
42 7 0.19
43 24 0.67
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (41 bp):
GCCACCTAAATCAATTAGGTGGCAATGCTTGCATTCATGCT
Found at i:24638 original size:18 final size:17
Alignment explanation
Indices: 24612--24648 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
24602 CTGCTACAAA
24612 AAAATATAATAATAAAT
1 AAAATATAATAATAAAT
24629 AAAATAATAATAATAAAT
1 AAAAT-ATAATAATAAAT
24647 AA
1 AA
24649 CAGACAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATATAATAATAAAT
Found at i:25002 original size:22 final size:19
Alignment explanation
Indices: 24951--25020 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 19
24941 CATGGCAGCC
24951 TCCAGCAGCT-CAACAACT
1 TCCAGCAGCTCCAACAACT
24969 TCCAGCAGCTCCAACAACT
1 TCCAGCAGCTCCAACAACT
*
24988 TCCATGGCAGCCTCCAGCAAC-
1 TCCA--GCAG-CTCCAACAACT
25009 TCCAGCAGCTCC
1 TCCAGCAGCTCC
25021 CACGACAGCC
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
18 14 0.30
19 16 0.34
21 8 0.17
22 9 0.19
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (19 bp):
TCCAGCAGCTCCAACAACT
Found at i:25217 original size:22 final size:22
Alignment explanation
Indices: 25192--25247 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
25182 CTTCTAGTAG
*
25192 CTCCAGCAGCTTCCACGGCAGC
1 CTCCAGCAGCTCCCACGGCAGC
*
25214 CTCCAGCAGCTCCCACGGTAGC
1 CTCCAGCAGCTCCCACGGCAGC
*
25236 CTCCAGTAGCTC
1 CTCCAGCAGCTC
25248 AGTAGCCTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (22 bp):
CTCCAGCAGCTCCCACGGCAGC
Found at i:25236 original size:101 final size:104
Alignment explanation
Indices: 25008--25249 Score: 269
Period size: 101 Copynumber: 2.3 Consensus size: 104
24998 CCTCCAGCAA
* *
25008 CTCCAGCAGCTCCCACGACAGCCTCTAATAGCTCAGCAACCACGAGCAGCCCCCACAGATCCCAC
1 CTCCAGCAGCTCCCACGATAGCCTCCAATAGCTCAGCAACCACGAGCAGCCCCCACAGATCCCAC
** * *
25073 AGTAACTTCTAGCAGCTCCCACAGCAACTTCCGCAATAGC
66 AACAACTTCTAGCAGCT-CCACAGCAACTTCCACAACAGC
* ** * *
25113 CTCCAGCAGCTCTCACGATAGCCTCCACCAGCTCAGCAATCC-C-AGTAGCTCCCACA-ACTCCC
1 CTCCAGCAGCTCCCACGATAGCCTCCAATAGCTCAGCAA-CCACGAGCAGCCCCCACAGA-TCCC
* * **
25175 ACAACAACTTCTAGTAGCT-C-CAGCAGCTTCCACGGCAGC
64 ACAACAACTTCTAGCAGCTCCACAGCAACTTCCACAACAGC
* *
25214 CTCCAGCAGCTCCCACGGTAGCCTCCAGTAGCTCAG
1 CTCCAGCAGCTCCCACGATAGCCTCCAATAGCTCAG
25250 TAGCCTCCAG
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
101 46 0.40
102 1 0.01
103 1 0.01
104 31 0.27
105 35 0.30
106 2 0.02
ACGTcount: A:0.26, C:0.42, G:0.16, T:0.16
Consensus pattern (104 bp):
CTCCAGCAGCTCCCACGATAGCCTCCAATAGCTCAGCAACCACGAGCAGCCCCCACAGATCCCAC
AACAACTTCTAGCAGCTCCACAGCAACTTCCACAACAGC
Found at i:29764 original size:20 final size:21
Alignment explanation
Indices: 29739--29793 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
29729 CATTACAAGC
* * *
29739 ATGTATCGATACATTCA-TTT
1 ATGTATCGATACAATAACTTA
*
29759 ATGTATTGATACAATAACTTA
1 ATGTATCGATACAATAACTTA
29780 ATGTATCGATACAA
1 ATGTATCGATACAA
29794 ATTATAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (21 bp):
ATGTATCGATACAATAACTTA
Found at i:31405 original size:20 final size:20
Alignment explanation
Indices: 31382--31454 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
31372 ACAATTCAAA
31382 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
31402 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
31423 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
31443 GTATCGATACAT
1 GTATCGATACAT
31455 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:31426 original size:21 final size:21
Alignment explanation
Indices: 31400--31475 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
31390 ACATGTTGCA
31400 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
31421 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
31441 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
31462 ATGTATCGATACAT
1 ATGTATCGATACAT
31476 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:31433 original size:41 final size:41
Alignment explanation
Indices: 31382--31475 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
31372 ACAATTCAAA
*
31382 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
31423 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
31464 GTATCGATACAT
1 GTATCGATACAT
31476 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:31532 original size:13 final size:13
Alignment explanation
Indices: 31514--31539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31504 TACAGCAAGT
31514 ATGTATCGATACA
1 ATGTATCGATACA
31527 ATGTATCGATACA
1 ATGTATCGATACA
31540 CAAAAAATTG
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:37725 original size:20 final size:21
Alignment explanation
Indices: 37647--37724 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
37637 ATGTCCAAAA
*
37647 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
37667 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
37691 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
37712 TGTATCGATACAT
1 TGTATCGATACAT
37725 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:37729 original size:13 final size:13
Alignment explanation
Indices: 37711--37749 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
37701 ACATTTTTTG
37711 TTGTATCGATACA
1 TTGTATCGATACA
37724 TTGTATCGATACA
1 TTGTATCGATACA
*
37737 CTGTATCGATACA
1 TTGTATCGATACA
37750 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:39699 original size:92 final size:92
Alignment explanation
Indices: 39542--39725 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
39532 GCAAATAAAT
39542 TTTGATATGAATTACTTGATTAAGGGGGAGATTTATTAATAAACGGGGGAGATAAATGAGAGAAT
1 TTTGATATGAATTACTTGATTAAGGGGGAGATTTATTAATAAACGGGGGAGATAAATGAGAGAAT
39607 GCGTGAATTACCTTATTAAGGGGGAGA
66 GCGTGAATTACCTTATTAAGGGGGAGA
39634 TTTGATATGAATTACTTGATTAAGGGGGAGATTTATTAATAAACGGGGGAGATAAATGAGAGAAT
1 TTTGATATGAATTACTTGATTAAGGGGGAGATTTATTAATAAACGGGGGAGATAAATGAGAGAAT
39699 GCGTGAATTACCTTATTAAGGGGGAGA
66 GCGTGAATTACCTTATTAAGGGGGAGA
39726 ATATACAAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.29
Consensus pattern (92 bp):
TTTGATATGAATTACTTGATTAAGGGGGAGATTTATTAATAAACGGGGGAGATAAATGAGAGAAT
GCGTGAATTACCTTATTAAGGGGGAGA
Found at i:40313 original size:20 final size:20
Alignment explanation
Indices: 40290--40362 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
40280 ACAATTCAAA
40290 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
40310 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
40331 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
40351 GTATCGATACAT
1 GTATCGATACAT
40363 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:40334 original size:21 final size:21
Alignment explanation
Indices: 40308--40383 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
40298 ACATGTTGCA
40308 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
40329 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
40349 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
40370 ATGTATCGATACAT
1 ATGTATCGATACAT
40384 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:40341 original size:41 final size:41
Alignment explanation
Indices: 40290--40383 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
40280 ACAATTCAAA
*
40290 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
40331 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
40372 GTATCGATACAT
1 GTATCGATACAT
40384 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:40440 original size:13 final size:13
Alignment explanation
Indices: 40422--40447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40412 TACAGCAAGT
40422 ATGTATCGATACA
1 ATGTATCGATACA
40435 ATGTATCGATACA
1 ATGTATCGATACA
40448 CAAAAAATTG
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:41384 original size:99 final size:98
Alignment explanation
Indices: 41212--41411 Score: 348
Period size: 99 Copynumber: 2.0 Consensus size: 98
41202 TATATATCAG
41212 CATGTATGTTCATCATGTTTTCAAGTTTATTTAATTATGTGAAGAAGGAATGTGATTTGTTAGCT
1 CATGTATGTTCATCATGTTTTCAAGTTTATTTAATTATGTGAAGAAGGAATGTGATTTGTTAGCT
*
41277 TATATATGGTGTTAGTTACCTTTTTTTTTTATTAT
66 TATATATGGTGTTAGTT-CC-ATTTTTTTTATTAT
41312 CATGTATGTTCATCATG-TTTCAAGTTTATTTAATTATGTGAAGAAGGAATGTGATTTGTTAGCT
1 CATGTATGTTCATCATGTTTTCAAGTTTATTTAATTATGTGAAGAAGGAATGTGATTTGTTAGCT
* *
41376 TGTATATGGTGTTAGTTTCATTTTTTTTATTAT
66 TATATATGGTGTTAGTTCCATTTTTTTTATTAT
41409 CAT
1 CAT
41412 TTTTTGCCCT
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
97 16 0.16
98 1 0.01
99 63 0.65
100 17 0.18
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.51
Consensus pattern (98 bp):
CATGTATGTTCATCATGTTTTCAAGTTTATTTAATTATGTGAAGAAGGAATGTGATTTGTTAGCT
TATATATGGTGTTAGTTCCATTTTTTTTATTAT
Found at i:42370 original size:150 final size:149
Alignment explanation
Indices: 42089--42369 Score: 340
Period size: 150 Copynumber: 1.9 Consensus size: 149
42079 TTTTTATATC
* *
42089 CACTCAAGTCATGCTTTCATATTCCCATGGTTTTCCGTAAGGGTATGAAAATTTTTAACACCTTT
1 CACTCAAGTCATGCTTTCATATTCCCATAGTTTTCCGTAAGGGTATGAAAAATTTTAACACCTTT
* * * * *
42154 TGCATCTCTTGGTTTTTCCGTTAGGTGCGAAACGTAACTTTTGAAAATAGAAGTTAAATTTTAAA
66 T-CATCTCCTGGTTTTTCCGTCAGGTACAAAACATAACTTTTGAAAATAGAAGTTAAATTTTAAA
42219 AAAACATGGTCGGCTATGCT
130 AAAACATGGTCGGCTATGCT
* * * * *
42239 CACTCGAGTCATGTTTTCATATTCCTATAGTTTTCTGT-AGGGCTATGAAAAATTTTAATACCTT
1 CACTCAAGTCATGCTTTCATATTCCCATAGTTTTCCGTAAGGG-TATGAAAAATTTTAACACCTT
* * *
42303 TAT-ATC-CCTGG-TTTTCCGTCAGGTACAAAACATAA-TTTTTATAACTTTGAAGTT-AATTTT
65 T-TCATCTCCTGGTTTTTCCGTCAGGTACAAAACATAACTTTTGA-AA-ATAGAAGTTAAATTTT
42363 AAAAAAA
127 AAAAAAA
42370 ATCAAATTTC
Statistics
Matches: 112, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
146 5 0.04
147 35 0.31
148 11 0.10
149 7 0.06
150 53 0.47
151 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (149 bp):
CACTCAAGTCATGCTTTCATATTCCCATAGTTTTCCGTAAGGGTATGAAAAATTTTAACACCTTT
TCATCTCCTGGTTTTTCCGTCAGGTACAAAACATAACTTTTGAAAATAGAAGTTAAATTTTAAAA
AAACATGGTCGGCTATGCT
Done.