Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2051
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: 64281
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3804 original size:28 final size:27
Alignment explanation
Indices: 3741--3809 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
3731 ATATTAAGTC
*
3741 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
3768 CGCACACTTAGTGCTATGTAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
3796 CGCACACTTAGTGC
1 CGCACACTTAGTGC
3810 CAATCTCATG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:5875 original size:46 final size:45
Alignment explanation
Indices: 5698--5955 Score: 191
Period size: 46 Copynumber: 5.5 Consensus size: 45
5688 TTTGTGCGCT
* * * *
5698 AGTGTAAGAAATGTCTGGGACATGCATTGGCCA-CATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CATGA-GATGAGAGCC
** * * * * *
5744 AGTGTAAGACATGTCTAAGACATGGCAACGACATTGTGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCA-TGAGATGAGAGCC
* * *
5791 AGTGTAAGACATGTATGGGGCATGCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCAT-GAGATG-AGAGCC
* *
5837 AGTGTAAGACATGTCTGGGACATGCATTGGCTATGAGAT--GAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-ATGAGATGAGAGCC
* * * *
5881 AGTGTAAGACCACGTTTGGGACATGACATCAGCACGGAGATGCGAGAGCC
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCA-TGAGAT--GAGAGCC
5931 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
5956 GCGTTAGACT
Statistics
Matches: 164, Mismatches: 34, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
44 12 0.07
45 15 0.09
46 78 0.48
47 32 0.20
50 27 0.16
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATGAGATGAGAGCC
Found at i:7548 original size:30 final size:30
Alignment explanation
Indices: 7512--7580 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
7502 ATGGGGCAGA
7512 CCGTGTGTCACACACGGCCTAGACACATGC
1 CCGTGTGTCACACACGGCCTAGACACATGC
* *
7542 CCGTGTGTCATACATGGCCTAGACACATGC
1 CCGTGTGTCACACACGGCCTAGACACATGC
7572 CCGTGTGTC
1 CCGTGTGTC
7581 CAACCTTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.22
Consensus pattern (30 bp):
CCGTGTGTCACACACGGCCTAGACACATGC
Found at i:8776 original size:45 final size:45
Alignment explanation
Indices: 8712--8798 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
8702 CCAAAACATG
8712 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
* * *
8757 TGTCACATATATCATGAACTCAGATCATAACTCAATGAGTTC
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTC
8799 AGATTACATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
Found at i:19833 original size:126 final size:125
Alignment explanation
Indices: 19608--20107 Score: 664
Period size: 125 Copynumber: 4.0 Consensus size: 125
19598 GGCCAATTAT
* * * * * *
19608 GAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTTTTTTAGACATTTTGCTGACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATA-ATTTTGCTGACAGTGCATC
* *
19673 CTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTGAAAATTATTTTTTCAA
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* **
19734 GAACTACTGTAGAAAAAGAACGTTTACGTAGGAGCTTTTTCCTATAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTT-CTATAATTTTGCTGACAGTGCATC
* * * * * *
19799 CTGCTTGAGGCATTTTTGACACTATTTGTTCAG-AACTTCTTCTCATAATTATCTTTTCAT
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* ** * *
19859 GAACTAATGTAGAAAAAGAGCGTCCACGT-GGTAGCTTTTTTCCCTAATTTTGCTGACAATACAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGG-AGC-TTTTTCTATAATTTTGCTGACAGTGCAT
* * *
19923 CCTGCTTGAAGCGTTTTTGGCACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTT-AG
64 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* * *
19984 GAACTACTGTAGAAAAAGAGCGTCAATGTAGGAGCTTTTTCTATATTTTTGCTGACAGTGCATCC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATAATTTTGCTGACAGTGCATCC
* * *
20049 TGCTTGAAGCGTTTTTGACACTATTTATTCAGAAACGTCTTATCAAAATTATTTTTTCA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCA
20108 GTGTAAAAAT
Statistics
Matches: 322, Mismatches: 46, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
124 79 0.25
125 130 0.40
126 110 0.34
127 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATAATTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
Found at i:20196 original size:28 final size:27
Alignment explanation
Indices: 20164--20245 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 27
20154 TTAAAAAAAA
20164 CTAAACCCTAATTTAATTAAATTTAACC
1 CTAAACCCTAATTTAATT-AATTTAACC
*
20192 CTAAACCCTAATTTAATTTATTTAAAACC
1 CTAAACCCTAATTTAATTAATTT--AACC
20221 CTAGAACCCTAATTTAATTAATTTA
1 CTA-AACCCTAATTTAATTAATTTA
20246 TTTAAAAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.08
28 19 0.39
29 7 0.14
30 19 0.39
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (27 bp):
CTAAACCCTAATTTAATTAATTTAACC
Found at i:20231 original size:58 final size:57
Alignment explanation
Indices: 20164--20346 Score: 190
Period size: 58 Copynumber: 3.1 Consensus size: 57
20154 TTAAAAAAAA
*
20164 CTAAACCCTAATTTAATTAAATTTAACCCTAAACCCTAATTTAATTTATTTAAAACC
1 CTAAACCCTAATTTAATTAAATTTAATCCTAAACCCTAATTTAATTTATTTAAAACC
* *
20221 CTAGAACCCTAATTTAATTAATTTATTTAAAAATCGTAAACCCCAATTTAATTTATTTAAAACC
1 CTA-AACCCTAATTTAATTAA---ATTT---AATCCTAAACCCTAATTTAATTTATTTAAAACC
* * * **
20285 CCAAACCTTAATTTACTT-AATTT-ATTTTAAAACCCTAAATTCTAATTTATTTAAAACC
1 CTAAACCCTAATTTAATTAAATTTAATCCT-AAACCCT-AATT-TAATTTATTTAAAACC
20343 CTAA
1 CTAA
20347 TTTAATTTAT
Statistics
Matches: 106, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
55 3 0.03
56 6 0.06
57 7 0.07
58 36 0.34
59 4 0.04
61 4 0.04
62 1 0.01
63 13 0.12
64 32 0.30
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (57 bp):
CTAAACCCTAATTTAATTAAATTTAATCCTAAACCCTAATTTAATTTATTTAAAACC
Found at i:20247 original size:34 final size:32
Alignment explanation
Indices: 20164--20335 Score: 150
Period size: 34 Copynumber: 5.5 Consensus size: 32
20154 TTAAAAAAAA
20164 CTAAACCCTAATTTAATTAA---ATTT--AACC
1 CTAAACCCTAATTT-ATTAATTTATTTAAAACC
20192 CTAAACCCTAA--T-TTAATTTATTTAAAACC
1 CTAAACCCTAATTTATTAATTTATTTAAAACC
*
20221 CTAGAACCCTAATTTAATTAATTTATTTAAAAATC
1 CTA-AACCCTAATTT-ATTAATTTATTT-AAAACC
* *
20256 GTAAACCCCAA--T-TTAATTTATTTAAAACC
1 CTAAACCCTAATTTATTAATTTATTTAAAACC
* *
20285 CCAAACCTTAATTTACTTAATTTATTTTAAAACC
1 CTAAACCCTAATTTA-TTAATTTA-TTTAAAACC
**
20319 CTAAATTCTAATTTATT
1 CTAAACCCTAATTTATT
20336 TAAAACCCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
24 4 0.03
26 1 0.01
27 4 0.03
28 11 0.09
29 19 0.16
30 19 0.16
31 1 0.01
32 2 0.02
33 10 0.09
34 38 0.33
35 7 0.06
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.40
Consensus pattern (32 bp):
CTAAACCCTAATTTATTAATTTATTTAAAACC
Found at i:20269 original size:64 final size:63
Alignment explanation
Indices: 20193--20316 Score: 194
Period size: 64 Copynumber: 2.0 Consensus size: 63
20183 AATTTAACCC
* *
20193 TAAACCCTAATTTAATTTATTTAAAACCCTAGAACCCTAATTTAATTAATTTATTTAAAAATCG
1 TAAACCCCAATTTAATTTATTTAAAACCCCA-AACCCTAATTTAATTAATTTATTTAAAAATCG
* * *
20257 TAAACCCCAATTTAATTTATTTAAAACCCCAAACCTTAATTTACTTAATTTATTTTAAAA
1 TAAACCCCAATTTAATTTATTTAAAACCCCAAACCCTAATTTAATTAATTTATTTAAAAA
20317 CCCTAAATTC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
63 26 0.47
64 29 0.53
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.40
Consensus pattern (63 bp):
TAAACCCCAATTTAATTTATTTAAAACCCCAAACCCTAATTTAATTAATTTATTTAAAAATCG
Found at i:20297 original size:29 final size:29
Alignment explanation
Indices: 20164--20416 Score: 147
Period size: 34 Copynumber: 8.6 Consensus size: 29
20154 TTAAAAAAAA
*
20164 CTAAACCCTAATTTAATTAAATTT--AACC
1 CTAAACCCTAATTTAATT-TATTTAAAACC
20192 CTAAACCCTAATTTAATTTATTTAAAACC
1 CTAAACCCTAATTTAATTTATTTAAAACC
*
20221 CTAGAACCCTAATTTAATTAATTTATTTAAAAATC
1 CTA-AACCCTAA--T--TTAATTTATTT-AAAACC
* *
20256 GTAAACCCCAATTTAATTTATTTAAAACC
1 CTAAACCCTAATTTAATTTATTTAAAACC
* *
20285 CCAAACCTTAATTTACTTAATTTATTTTAAAACC
1 CTAAACCCTAA--T--TTAATTTA-TTTAAAACC
*
20319 CTAAA---T--TCTAATTTATTTAAAACC
1 CTAAACCCTAATTTAATTTATTTAAAACC
20343 CT-------AATTTAATTTATTTAAAACC
1 CTAAACCCTAATTTAATTTATTTAAAACC
*
20365 TTAAAAACCCTAATTTACTTAATTTATTTAAAAACC
1 CT--AAACCCTAA--T--TTAATTTATTT-AAAACC
* *
20401 ATAAACCCTAAGTTAA
1 CTAAACCCTAATTTAA
20417 ATAATTTTTA
Statistics
Matches: 181, Mismatches: 15, Indels: 56
0.72 0.06 0.22
Matches are distributed among these distances:
22 18 0.10
24 11 0.06
25 7 0.04
27 5 0.03
28 18 0.10
29 19 0.10
30 23 0.13
31 4 0.02
32 2 0.01
33 9 0.05
34 40 0.22
35 18 0.10
36 7 0.04
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.38
Consensus pattern (29 bp):
CTAAACCCTAATTTAATTTATTTAAAACC
Found at i:20332 original size:63 final size:64
Alignment explanation
Indices: 20188--20337 Score: 205
Period size: 63 Copynumber: 2.4 Consensus size: 64
20178 AATTAAATTT
*
20188 AACCCTAAACCCTAATTTAATTTATTTAAAACCCTAGAACCCTAATTTAATTAATTTATTTAAA
1 AACCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTAATTAATTTATTTAAA
* * * * * *
20252 AATCGTAAACCCCAATTTAATTTATTTAAAACCCCA-AACCTTAATTTACTTAATTTATTTTAA
1 AACCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTAATTAATTTATTTAAA
**
20315 AACCCTAAATTCTAATTT-ATTTA
1 AACCCTAAACCCTAATTTAATTTA
20338 AAACCCTAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
62 5 0.07
63 37 0.50
64 32 0.43
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.39
Consensus pattern (64 bp):
AACCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTAATTAATTTATTTAAA
Found at i:20355 original size:22 final size:23
Alignment explanation
Indices: 20301--20369 Score: 104
Period size: 22 Copynumber: 3.0 Consensus size: 23
20291 CTTAATTTAC
20301 TTAATTTATTTTAAAACCCTAAAT
1 TTAATTTA-TTTAAAACCCTAAAT
20325 TCTAATTTATTTAAAACCCT-AAT
1 T-TAATTTATTTAAAACCCTAAAT
*
20348 TTAATTTATTTAAAACCTTAAA
1 TTAATTTATTTAAAACCCTAAA
20370 AACCCTAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
22 17 0.40
23 6 0.14
24 12 0.29
25 7 0.17
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATTTATTTAAAACCCTAAAT
Found at i:20422 original size:34 final size:35
Alignment explanation
Indices: 20349--20431 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 35
20339 AACCCTAATT
* **
20349 TAATTTATTT-AAAACCTTAAAAACCCTAATTTACT
1 TAATTTATTTAAAAACC-TAAAAACCCTAAGTTAAA
*
20384 TAATTTATTTAAAAACC-ATAAACCCTAAGTTAAA
1 TAATTTATTTAAAAACCTAAAAACCCTAAGTTAAA
20418 TAATTT-TTATAAAA
1 TAATTTATT-TAAAA
20432 TAAGACTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.05
34 24 0.57
35 10 0.24
36 6 0.14
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (35 bp):
TAATTTATTTAAAAACCTAAAAACCCTAAGTTAAA
Found at i:23241 original size:48 final size:48
Alignment explanation
Indices: 23189--23325 Score: 195
Period size: 48 Copynumber: 2.9 Consensus size: 48
23179 ATCGATATGT
* *
23189 GATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGACCTAC
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGACATAC
* **
23237 GATCCCATGTAAGACCATGT-TCGGGACATGGCATTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCT-GGGACATGGCATTGGCATCGACATAC
* *
23285 GATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
23326 CTACCATATG
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 1 0.01
48 78 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGACATAC
Found at i:25674 original size:37 final size:37
Alignment explanation
Indices: 25615--25790 Score: 307
Period size: 37 Copynumber: 4.8 Consensus size: 37
25605 AGCTCAGACG
* * *
25615 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
25652 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
25689 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
25726 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
25763 TAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
25791 TAGAGCTCGG
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 135 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:25996 original size:47 final size:47
Alignment explanation
Indices: 25909--26552 Score: 1063
Period size: 47 Copynumber: 13.6 Consensus size: 47
25899 CCCTTCGGGA
* * * * * *
25909 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
25956 CCTGTCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26003 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26050 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26099 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26146 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
26193 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26242 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26289 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
26336 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26385 CTTATCACATATATACATTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26432 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26479 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26526 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
26553 TATTCAAATA
Statistics
Matches: 559, Mismatches: 32, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
47 425 0.76
49 134 0.24
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:26178 original size:143 final size:143
Alignment explanation
Indices: 25909--26552 Score: 1116
Period size: 143 Copynumber: 4.5 Consensus size: 143
25899 CCCTTCGGGA
* * * * *
25909 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
25972 ACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
26037 TCGGCCATTAGGC
131 TCGGCCATTAGGC
* * *
26050 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
26115 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
26180 TCGGCTATTAGGC
131 TCGGCCATTAGGC
*
26193 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
26258 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
26323 TCGGCCATTAGGC
131 TCGGCCATTAGGC
26336 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
26401 ATTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
26466 TCGGCTATTAGGC
131 TCGGCCATTAGGC
* *
26479 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
26542 ACTTTCACATT
66 ACTTTCACATT
26553 TATTCAAATA
Statistics
Matches: 478, Mismatches: 23, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
141 73 0.15
142 1 0.00
143 404 0.85
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:26256 original size:190 final size:188
Alignment explanation
Indices: 25909--26552 Score: 1090
Period size: 190 Copynumber: 3.4 Consensus size: 188
25899 CCCTTCGGGA
* * * * * * * *
25909 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
25974 TTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
26039 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 GGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
26099 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
26164 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
* * *
26229 TTGGCCATTCGACCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
26289 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* * *
26354 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
26419 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
26479 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
26544 TTTCACATT
66 TTTCACATT
26553 TATTCAAATA
Statistics
Matches: 430, Mismatches: 20, Indels: 10
0.93 0.04 0.02
Matches are distributed among these distances:
188 19 0.04
190 323 0.75
192 88 0.20
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:29977 original size:41 final size:40
Alignment explanation
Indices: 29932--30089 Score: 178
Period size: 41 Copynumber: 3.9 Consensus size: 40
29922 GATTCTTAGT
29932 ACTGGCTCAAAAGCCCTTC-AAGACCAAGCTCGGATTAGACC
1 ACTGGCTCAAAAGCCCTTCGAA-ACCAAGCTCGGATTAGA-C
* * * *
29973 ACTGGCTCGAAGGCCCTTCGAAACTAAGTTCGG-TTATGAC
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTA-GAC
* * *
30013 ACTGGCTCTAAAGCCCTTCGAAACTAAGTTCGGTTATTAG-C
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGG--ATTAGAC
*
30054 ACTGGCTCAAAGGCCCTTCGAAACCAAGCTCGGATT
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATT
30090 TAAACCCTGA
Statistics
Matches: 102, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
39 3 0.03
40 35 0.34
41 58 0.57
42 3 0.03
43 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTAGAC
Found at i:30028 original size:81 final size:80
Alignment explanation
Indices: 29932--30086 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 80
29922 GATTCTTAGT
*
29932 ACTGGCTCAAAAGCCCTTC-AAGACCAAGCTCGG-ATTAGACCACTGGCTCGAAGGCCCTTCGAA
1 ACTGGCTCAAAAGCCCTTCGAA-ACCAAGCTCGGTATTAG--CACTGGCTCAAAGGCCCTTCGAA
* *
29995 ACTAAGTTCGGTTATGAC
63 ACCAAGCTCGGTTATGAC
* * *
30013 ACTGGCTCTAAAGCCCTTCGAAACTAAGTTCGGTTATTAGCACTGGCTCAAAGGCCCTTCGAAAC
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGG-TATTAGCACTGGCTCAAAGGCCCTTCGAAAC
30078 CAAGCTCGG
65 CAAGCTCGG
30087 ATTTAAACCC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
81 58 0.89
82 2 0.03
83 5 0.08
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (80 bp):
ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGTATTAGCACTGGCTCAAAGGCCCTTCGAAACC
AAGCTCGGTTATGAC
Found at i:41712 original size:49 final size:49
Alignment explanation
Indices: 41657--41988 Score: 182
Period size: 49 Copynumber: 6.7 Consensus size: 49
41647 ACTAATATGT
41657 TGATAAGGCCGTAATGGCCAAATGTGATG-ATGTGAACAAGCGTAT-GATG
1 TGATAAGGCCGTAATGGCC-AATGTGATGAATGTGAAC-AGCGTATAGATG
* * *
41706 TGATAAGGCC-TAAAT-G-CAATGTGAATGAATG-GAACCGTGTATATATG
1 TGATAAGGCCGT-AATGGCCAATGTG-ATGAATGTGAACAGCGTATAGATG
* *
41753 TGGATAGAGGCCGTAATGGCCGATGTGATGAATGTGAA-ATG-GTATATATG
1 T-GATA-AGGCCGTAATGGCCAATGTGATGAATGTGAACA-GCGTATAGATG
* * ** *
41803 AT-ATAAGG-CG-AATGCCCAATGTGATGAATGTGAACCTGTAATATATAGTGG
1 -TGATAAGGCCGTAATGGCCAATGTGATGAATGTGAA-CAG-CGTATAGA-T-G
* *
41854 TGATAAAGGCC-TAA-GGCCAGATGTGATGAATGTGAACATGTGT-TAGTTG
1 TGAT-AAGGCCGTAATGGCCA-ATGTGATGAATGTGAACA-GCGTATAGATG
** *
41903 TGATAAGG-CG--ATGGCCAGATGTGATGAAGGGTGTGAACAATG-A-ATATG
1 TGATAAGGCCGTAATGGCCA-ATGTGATGAA---TGTGAACAGCGTATAGATG
*
41951 ATGATAAGGTCG-AATGGCCAATAGTGAATGAATGTGAA
1 -TGATAAGGCCGTAATGGCCAAT-GTG-ATGAATGTGAA
41989 GTGAATTGCC
Statistics
Matches: 230, Mismatches: 18, Indels: 70
0.72 0.06 0.22
Matches are distributed among these distances:
46 34 0.15
47 32 0.14
48 19 0.08
49 51 0.22
50 33 0.14
51 26 0.11
52 15 0.07
53 20 0.09
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (49 bp):
TGATAAGGCCGTAATGGCCAATGTGATGAATGTGAACAGCGTATAGATG
Found at i:41782 original size:97 final size:96
Alignment explanation
Indices: 41651--41891 Score: 257
Period size: 97 Copynumber: 2.5 Consensus size: 96
41641 TGATGTACTA
* * *
41651 ATATGTTGATAAGGCCGTAATGGCCAAATGTGATG-ATGTGAACAAGCGTATGATGTG-ATAAGG
1 ATATGTGGATAAGGCCGTAATGGCCAGATGTGATGAATGTGAACAAG-GTAT-ATATGAATAAGG
41714 CCTAAATG-CAATGTGAATGAATG-GAACCGTGT-AT
64 -C-AAATGCCAATGTG-ATGAATGTGAACC-TGTAAT
*
41748 ATATGTGGATAGAGGCCGTAATGGCC-GATGTGATGAATGTGAA-ATGGTATATATGATATAAGG
1 ATATGTGGATA-AGGCCGTAATGGCCAGATGTGATGAATGTGAACAAGGTATATATGA-ATAAGG
*
41811 CGAATGCCCAATGTGATGAATGTGAACCTGTAAT
64 CAAATG-CCAATGTGATGAATGTGAACCTGTAAT
41845 ATATAGTGGTGATAAAGGCC-TAA-GGCCAGATGTGATGAATGTGAACA
1 ATAT-GT-G-GAT-AAGGCCGTAATGGCCAGATGTGATGAATGTGAACA
41892 TGTGTTAGTT
Statistics
Matches: 125, Mismatches: 5, Indels: 25
0.81 0.03 0.16
Matches are distributed among these distances:
95 8 0.06
96 15 0.12
97 44 0.35
98 27 0.22
99 21 0.17
100 9 0.07
101 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.27
Consensus pattern (96 bp):
ATATGTGGATAAGGCCGTAATGGCCAGATGTGATGAATGTGAACAAGGTATATATGAATAAGGCA
AATGCCAATGTGATGAATGTGAACCTGTAAT
Found at i:41925 original size:100 final size:96
Alignment explanation
Indices: 41651--41930 Score: 244
Period size: 97 Copynumber: 2.9 Consensus size: 96
41641 TGATGTACTA
* * * *
41651 ATATGTTGAT-AAGGCCGTAATGGCCAAATGTGATG-ATGTGAACAAGCGTAT-GATG-TGATAA
1 ATATGTGGATAAAGGCCGTAATGGCC-GATGTGATGAATGTGAA-ATG-GTATATATGAT-ATAA
*
41712 GGCCTAAATG--CAATGTGAATGAATGGAACCGTGTAT
62 GG-C-GAATGCCCAATGTG-ATGAATGGAACCGTGTAT
*
41748 ATATGTGGATAGAGGCCGTAATGGCCGATGTGATGAATGTGAAATGGTATATATGATATAAGGCG
1 ATATGTGGATAAAGGCCGTAATGGCCGATGTGATGAATGTGAAATGGTATATATGATATAAGGCG
41813 AATGCCCAATGTGATGAATGTGAACC-TGTAAT
66 AATGCCCAATGTGATGAATG-GAACCGTGT-AT
41845 ATATAGTGGTGATAAAGGCC-TAA-GGCCAGATGTGATGAATGTGAACATGTGT-TAGT-TG-TG
1 ATAT-GT-G-GATAAAGGCCGTAATGGCC-GATGTGATGAATGTGAA-ATG-GTATA-TATGAT-
*
41905 ATAAGGCG-ATGGCCAGATGTGATGAA
58 ATAAGGCGAATGCCCA-ATGTGATGAA
41931 GGGTGTGAAC
Statistics
Matches: 158, Mismatches: 8, Indels: 31
0.80 0.04 0.16
Matches are distributed among these distances:
95 4 0.03
96 15 0.09
97 46 0.29
98 28 0.18
99 28 0.18
100 34 0.22
101 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (96 bp):
ATATGTGGATAAAGGCCGTAATGGCCGATGTGATGAATGTGAAATGGTATATATGATATAAGGCG
AATGCCCAATGTGATGAATGGAACCGTGTAT
Found at i:42393 original size:34 final size:34
Alignment explanation
Indices: 42350--42460 Score: 117
Period size: 34 Copynumber: 3.3 Consensus size: 34
42340 ACGACTCTAA
42350 CCGATGACTACGTGTGGA-A-TATGTCGGGGTAA-AC
1 CCGATGACTACGT-TGGAGATTATGTC--GGTAAGAC
42384 CCGATGACTACGTTGGAGATTATGTCGGTAAGAC
1 CCGATGACTACGTTGGAGATTATGTCGGTAAGAC
*
42418 CC-ATGACTAC-TCGTGGAGATTTTGTCCGGTAAGA-
1 CCGATGACTACGT--TGGAGATTATGT-CGGTAAGAC
42452 CCGATGACT
1 CCGATGACT
42461 TAACGTTCAG
Statistics
Matches: 69, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
32 1 0.01
33 17 0.25
34 31 0.45
35 20 0.29
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (34 bp):
CCGATGACTACGTTGGAGATTATGTCGGTAAGAC
Found at i:42473 original size:35 final size:33
Alignment explanation
Indices: 42384--42474 Score: 94
Period size: 35 Copynumber: 2.7 Consensus size: 33
42374 CGGGGTAAAC
*
42384 CCGATGACT-ACGTTGGAGATTATGTCGGTAAGA
1 CCGATGACTAACGTT-GAGATTTTGTCGGTAAGA
* * *
42417 CCCATGACTACTCGTGGAGATTTTGTCCGGTAAGA
1 CCGATGACTA-ACGTTGAGATTTTGT-CGGTAAGA
*
42452 CCGATGACTTAACGTTCAGATTT
1 CCGATGAC-TAACGTTGAGATTT
42475 GTTGGGTAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
33 8 0.17
34 9 0.20
35 27 0.59
36 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (33 bp):
CCGATGACTAACGTTGAGATTTTGTCGGTAAGA
Found at i:43968 original size:39 final size:38
Alignment explanation
Indices: 43864--44159 Score: 319
Period size: 37 Copynumber: 7.8 Consensus size: 38
43854 TATTTGTAGC
43864 TTCGTGCTAGTGATTATCCGGGCTAAGTCCCGAGGAGCA
1 TTCGTGCTAGTGATTATCCGGGCTAAGT-CCGAGGAGCA
* *
43903 TGTCGTGATAGTGATATATCCGGGCTAAGTCCGAAGAGCA
1 T-TCGTGCTAGTGAT-TATCCGGGCTAAGTCCGAGGAGCA
43943 TTCGTGCTAGTGATGATATCC-GGCTAAGTCCGAGGAGCA
1 TTCGTGCTAGTGAT--TATCCGGGCTAAGTCCGAGGAGCA
43982 TTCGTGC-AGTGATGTATCCGGG--AAGTCCCGAGGAGCA
1 TTCGTGCTAGTGAT-TATCCGGGCTAAGT-CCGAGGAGCA
*
44019 TTCGTGCTAGTGATTATCCGGGCTAAGTCCGA-AAGCA
1 TTCGTGCTAGTGATTATCCGGGCTAAGTCCGAGGAGCA
44056 TTC--GCTAGTGATGTATCCGGGCTAAGTCCGAGGAGC-
1 TTCGTGCTAGTGAT-TATCCGGGCTAAGTCCGAGGAGCA
* * **
44092 TTCATGC-AGTGATATATCCCGTGCTAAACCCCGA--AGCA
1 TTCGTGCTAGTGAT-TAT-CCGGGCT-AAGTCCGAGGAGCA
* *
44130 TTCGTGCT-GTGTTATATCCGGGCTAGGTCC
1 TTCGTGCTAGTGAT-TATCCGGGCTAAGTCC
44160 CAAAGAGAAA
Statistics
Matches: 224, Mismatches: 17, Indels: 35
0.81 0.06 0.13
Matches are distributed among these distances:
35 9 0.04
36 28 0.12
37 58 0.26
38 40 0.18
39 47 0.21
40 28 0.12
41 14 0.06
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26
Consensus pattern (38 bp):
TTCGTGCTAGTGATTATCCGGGCTAAGTCCGAGGAGCA
Found at i:48267 original size:97 final size:96
Alignment explanation
Indices: 48114--48589 Score: 607
Period size: 97 Copynumber: 5.0 Consensus size: 96
48104 TTAGGATTTT
*
48114 ATGTGATG-ATGTGAACATGCGTATGTGTGATAAGGTTGAGAATGGCCAATGTGATGAATGTGAA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGG-CG-GAATGGCCAATGTGATGAATGTGAA
* *
48178 CCCGTAATATAGTGTGATAAGGCCGAATGGCTA
64 CCTGTAATATAGTGTGATAAGGCCGAATGGCCA
48211 ATGTGATGAATGTGAACATGCGTATGTGTTGATAAGGCGGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGATGAATGTGAACATGCGTATGTG-TGATAAGGCGGAATGGCCAATGTGATGAATGTGAAC
*
48276 CCGTATATATATGTGTGATAAGGCCGAATGGCC-
65 CTGTA-ATATA-GTGTGATAAGGCCGAATGGCCA
48309 ATGTGATGAATGTGAACATGCG-ATGTGTGATAAGGTC-GAATGGCCAATGTGATGAATTGTGAA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGG-CGGAATGGCCAATGTGATGAA-TGTGAA
*
48372 CCTGTATATATATATCCGTGATAAGGCCGAATGGCCA
64 CCTGTA-ATATA-GT--GTGATAAGGCCGAATGGCCA
* *
48409 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCAATGTGAT-AATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCGGAATGGCCAATGTGATGAATGTGAACC
** *
48473 TG-CGTAT-GTGTGATAAGGCTGAATGGCCA
66 TGTAATATAGTGTGATAAGGCCGAATGGCCA
* * * * * *
48502 ATGTGATGAA--TGAACATGCATATATGAGATAAGGCCGAAT-GCCAATATGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCGGAATGGCCAATGTGATGAATGTGAACC
* *
48564 TG-CATATA-TGTGGTAAGGCCGAATGG
66 TGTAATATAGTGTGATAAGGCCGAATGG
48590 GCTATTGCGA
Statistics
Matches: 349, Mismatches: 17, Indels: 32
0.88 0.04 0.08
Matches are distributed among these distances:
90 10 0.03
91 58 0.17
93 29 0.08
95 1 0.00
96 27 0.08
97 67 0.19
98 47 0.13
99 56 0.16
100 25 0.07
101 29 0.08
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (96 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCGGAATGGCCAATGTGATGAATGTGAACC
TGTAATATAGTGTGATAAGGCCGAATGGCCA
Found at i:48463 original size:22 final size:22
Alignment explanation
Indices: 48435--48508 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
48425 CATGCGTATG
48435 TGTGATAAGGCTGAATGGCCAA
1 TGTGATAAGGCTGAATGGCCAA
* * *
48457 TGTGATAATG-TGAACAT-GCGTATG
1 TGTGATAAGGCTG-A-ATGGC-CA-A
48481 TGTGATAAGGCTGAATGGCCAA
1 TGTGATAAGGCTGAATGGCCAA
48503 TGTGAT
1 TGTGAT
48509 GAATGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
21 2 0.05
22 18 0.45
23 6 0.15
24 12 0.30
25 2 0.05
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (22 bp):
TGTGATAAGGCTGAATGGCCAA
Found at i:48484 original size:46 final size:47
Alignment explanation
Indices: 48389--48589 Score: 293
Period size: 46 Copynumber: 4.4 Consensus size: 47
48379 ATATATATCC
*
48389 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGT
1 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGT
* *
48436 GTGATAAGGCTGAATGGCCAATGTGAT-AATGTGAACATGCGTATGT
1 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGT
* *
48482 GTGATAAGGCTGAATGGCCAATGTGATGAA--TGAACATGCATATAT
1 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGT
* * *
48527 GAGATAAGGCCGAAT-GCCAATATGATGAATGTGAACATGCATATAT
1 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGT
*
48573 GTGGTAAGGCCGAATGG
1 GTGATAAGGCCGAATGG
48590 GCTATTGCGA
Statistics
Matches: 142, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
44 13 0.09
45 26 0.18
46 74 0.52
47 29 0.20
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (47 bp):
GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGT
Found at i:48486 original size:24 final size:24
Alignment explanation
Indices: 48410--48488 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 24
48400 GAATGGCCAA
48410 TGTGATGAATGTGAACATGCGTATG
1 TGTGAT-AATGTGAACATGCGTATG
* * *
48435 TGTGATAAGGCTG-A-ATG-GCCA-A
1 TGTGATAATG-TGAACATGCG-TATG
48457 TGTGATAATGTGAACATGCGTATG
1 TGTGATAATGTGAACATGCGTATG
48481 TGTGATAA
1 TGTGATAA
48489 GGCTGAATGG
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
21 2 0.05
22 11 0.26
23 8 0.19
24 13 0.31
25 8 0.19
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (24 bp):
TGTGATAATGTGAACATGCGTATG
Found at i:48505 original size:24 final size:24
Alignment explanation
Indices: 48432--48506 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
48422 GAACATGCGT
48432 ATGTGTGATAAGGCTGAATGGCCA
1 ATGTGTGATAAGGCTGAATGGCCA
* **
48456 A--TGTGATAATG-TGAACAT-GCGT
1 ATGTGTGATAAGGCTG-A-ATGGCCA
48478 ATGTGTGATAAGGCTGAATGGCCA
1 ATGTGTGATAAGGCTGAATGGCCA
48502 ATGTG
1 ATGTG
48507 ATGAATGAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 2 0.05
22 13 0.33
23 4 0.10
24 18 0.46
25 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (24 bp):
ATGTGTGATAAGGCTGAATGGCCA
Found at i:48562 original size:91 final size:92
Alignment explanation
Indices: 48114--48589 Score: 402
Period size: 91 Copynumber: 5.0 Consensus size: 92
48104 TTAGGATTTT
* * * * ** *
48114 ATGTGATGATGTGAACATGCGTATGTGTGATAAGGTTGAGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGATGAAGTGAACATGCATATATGAGATAAGG--CCGAATGGCCAATATGAT-AATGTGAAC
** * *
48179 CCGTAATATAGTGTGATAAGGCCGAATGGCTA
63 ATG-CATATA-TGTGATAAGGCCGAATGGCCA
* * * * *
48211 ATGTGATGAATGTGAACATGCGTATGTGTTGATAAGGCGGAATGGCCAATGTGATGAATGTGAAC
1 ATGTGATGAA-GTGAACATGCATATATG-AGATAAGGCCGAATGGCCAATATGAT-AATGTGAA-
** *
48276 CCGTATATATATGTGTGATAAGGCCGAATGGCC-
62 -C--ATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
48309 ATGTGATGAATGTGAACATGC-GATGTGTGATAAGGTCGAATGGCCAATGTGATGAATTGTGAAC
1 ATGTGATGAA-GTGAACATGCATATATGAGATAAGGCCGAATGGCCAATATGAT-AA-TGTGAA-
**
48373 CTGTATATATATATCCGTGATAAGGCCGAATGGCCA
62 C---ATGCATATAT--GTGATAAGGCCGAATGGCCA
* * * * *
48409 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCAATGTGATAATGTGAACAT
1 ATGTGATGAA-GTGAACATGCATATATGAGATAAGGCCGAATGGCCAATATGATAATGTGAACAT
* * *
48474 GCGTATGTGTGATAAGGCTGAATGGCCA
65 GCATATATGTGATAAGGCCGAATGGCCA
48502 ATGTGATGAA-TGAACATGCATATATGAGATAAGGCCGAAT-GCCAATATGATGAATGTGAACAT
1 ATGTGATGAAGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATATGAT-AATGTGAACAT
*
48565 GCATATATGTGGTAAGGCCGAATGG
65 GCATATATGTGATAAGGCCGAATGG
48590 GCTATTGCGA
Statistics
Matches: 336, Mismatches: 30, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
90 10 0.03
91 58 0.17
93 29 0.09
95 6 0.02
96 29 0.09
97 56 0.17
98 39 0.12
99 53 0.16
100 27 0.08
101 29 0.09
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (92 bp):
ATGTGATGAAGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATATGATAATGTGAACATG
CATATATGTGATAAGGCCGAATGGCCA
Found at i:48955 original size:37 final size:37
Alignment explanation
Indices: 48805--48948 Score: 211
Period size: 37 Copynumber: 3.9 Consensus size: 37
48795 TTGGAATATT
48805 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
48842 TCCGGG-AAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
48878 TCCGAGTAAGACCCGATGACTAC-TCGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGT-GTGGAGATTATG
* * * *
48915 TCTGGGTAAGACCCGATAACTTCATGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
48949 TCGTCTGAGC
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
36 36 0.37
37 61 0.62
38 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:61064 original size:84 final size:86
Alignment explanation
Indices: 60967--61132 Score: 195
Period size: 85 Copynumber: 1.9 Consensus size: 86
60957 TGTAGATGTA
*
60967 TATTGTGATATAA-GCTAAATGGCCGTTGATGAG-T-GAAA-GTATA-TGTG-TAAGGGCCGAAA
1 TATTGTGA-ATAAGGCT-AATGGCCGATG-TGAGATGGAAATGTATATTGTGATAA-GGCC-AAA
61026 GGCCAATGTG-ATGAATGTGAAAACATG
61 -GCC-ATGTGAATGAATGTGAAAACATG
*
61053 TATTGTG-ATAAGGCTAATGGCCGATGTGAGATGGAAATGTATATTGTGATAAGGCCTAAGCCAT
1 TATTGTGAATAAGGCTAATGGCCGATGTGAGATGGAAATGTATATTGTGATAAGGCCAAAGCCAT
61117 GTGAATGAATGTGAAA
66 GTGAATGAATGTGAAA
61133 TGTAAATAGA
Statistics
Matches: 71, Mismatches: 2, Indels: 15
0.81 0.02 0.17
Matches are distributed among these distances:
83 4 0.06
84 20 0.28
85 22 0.31
86 14 0.20
87 8 0.11
88 3 0.04
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (86 bp):
TATTGTGAATAAGGCTAATGGCCGATGTGAGATGGAAATGTATATTGTGATAAGGCCAAAGCCAT
GTGAATGAATGTGAAAACATG
Found at i:61081 original size:45 final size:44
Alignment explanation
Indices: 60884--61395 Score: 171
Period size: 45 Copynumber: 11.7 Consensus size: 44
60874 ACTATGTGAT
*
60884 ATAAGGCCTAATGGCCGA-G-GATGAATGTGAAAATCGTGATATAATGTG
1 ATAAGG-CTAATGGCC-ATGTGATGAATGTGAAAAT-ATG-TAT--TGTG
* * * * *
60932 ATAAGGCTGAATAGCGATGTGA-GAATGT--AGATGTATATTGTG
1 ATAAGGCT-AATGGCCATGTGATGAATGTGAAAATATGTATTGTG
* * *
60974 ATATAAGCTAAATGGCCGT-TGATG-A-GTGAAAGTA--TA-TGTG
1 ATA-AGGCT-AATGGCCATGTGATGAATGTGAAAATATGTATTGTG
* * *
61014 -TAAGGGCCGAAAGGCCAATGTGATGAATGTGAAAACATGTATTGTG
1 ATAA-GG-CTAATGGCC-ATGTGATGAATGTGAAAATATGTATTGTG
* *
61060 ATAAGGCTAATGGCCGATGTGA-G-ATG-G-AAATGTATATTGTG
1 ATAAGGCTAATGGCC-ATGTGATGAATGTGAAAATATGTATTGTG
* *
61101 ATAAGGCCTAA--GCCATGTGAATGAATGTG--AA-ATGTAAAT-AG
1 ATAAGG-CTAATGGCCATGTG-ATGAATGTGAAAATATGT-ATTGTG
* * * ** *
61142 ATAAGGCGAATGGCCAAATGGTGATAAATGTG-AAA-GTGTAATAATA
1 ATAAGGCTAATGGCC--AT-GTGATGAATGTGAAAATATGT-ATTGTG
* * * *
61188 AGTGAAGGCCTAATAGCGATGTGATG-ATGTGATAGTATGTATATATGTG
1 A-T-AAGG-CTAATGGCCATGTGATGAATGTGAAAATATG--TAT-TGTG
* * *
61237 -TAAGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAGTATATGTG
1 ATAAGGCTAATGGCC-ATGTGATGAATGTGAAAATAT-GTAT-TGTG
*
61283 ATAAGGCTAAT-GCCAT-TGGATGAATGTGAAAATGATATATATG-G
1 ATAAGGCTAATGGCCATGT-GATGAATGTGAAAAT-ATGTAT-TGTG
*
61327 ATAAGGC-AA-GGCCATGTGATGAATGTG--AA-AGGTA-TGTG
1 ATAAGGCTAATGGCCATGTGATGAATGTGAAAATATGTATTGTG
* *
61365 -TAAAGGCCAAT-GCCATGCGATGAATGTGAAA
1 AT-AAGGCTAATGGCCATGTGATGAATGTGAAA
61396 TGTATATAGT
Statistics
Matches: 355, Mismatches: 57, Indels: 111
0.68 0.11 0.21
Matches are distributed among these distances:
37 3 0.01
38 7 0.02
39 35 0.10
40 13 0.04
41 39 0.11
42 27 0.08
43 41 0.12
44 24 0.07
45 61 0.17
46 39 0.11
47 31 0.09
48 25 0.07
49 10 0.03
ACGTcount: A:0.36, C:0.08, G:0.29, T:0.27
Consensus pattern (44 bp):
ATAAGGCTAATGGCCATGTGATGAATGTGAAAATATGTATTGTG
Found at i:61099 original size:41 final size:43
Alignment explanation
Indices: 60923--61107 Score: 129
Period size: 41 Copynumber: 4.4 Consensus size: 43
60913 AAAATCGTGA
* * * * *
60923 TATAATGTGATAAGGCTGAATAG-CGATGTGAGAATGTAGATG
1 TATATTGTGATAAGGCTAAATGGCCGATGTGAGAATGGAAATG
* *
60965 TATATTGTGATATAAGCTAAATGGCCG-T-TGATGAGT-GAAA-G
1 TATATTGTGATA-AGGCTAAATGGCCGATGTGA-GAATGGAAATG
* * **
61006 TATA-TGTG-TAAGGGCCGAAA-GGCCAATGTGATGAATGTGAAAACA
1 TATATTGTGATAA-GG-CTAAATGGCCGATGTGA-GAATG-G-AAATG
*
61051 TGTATTGTGATAAGGCT-AATGGCCGATGTGAG-ATGGAAATG
1 TATATTGTGATAAGGCTAAATGGCCGATGTGAGAATGGAAATG
61092 TATATTGTGATAAGGC
1 TATATTGTGATAAGGC
61108 CTAAGCCATG
Statistics
Matches: 111, Mismatches: 18, Indels: 29
0.70 0.11 0.18
Matches are distributed among these distances:
38 1 0.01
39 7 0.06
40 9 0.08
41 30 0.27
42 17 0.15
43 16 0.14
44 8 0.07
45 14 0.13
46 6 0.05
47 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.29
Consensus pattern (43 bp):
TATATTGTGATAAGGCTAAATGGCCGATGTGAGAATGGAAATG
Found at i:61341 original size:43 final size:45
Alignment explanation
Indices: 61024--61403 Score: 219
Period size: 45 Copynumber: 8.7 Consensus size: 45
61014 TAAGGGCCGA
**
61024 AAGGCCAATGTGATGAATGTGAAAACAT-GTAT-TGTGATAAGGCT
1 AAGGCC-ATGTGATGAATGTGAAAATGTAGTATATGTGATAAGGCT
61068 AATGGCCGATGTGA-G-ATG-G-AAATGTA-TAT-TGTGATAAGGCCT
1 AA-GGCC-ATGTGATGAATGTGAAAATGTAGTATATGTGATAAGG-CT
* *
61110 AA-GCCATGTGAATGAATGTG-AAATGTA--A-AT-AGATAAGGCG
1 AAGGCCATGTG-ATGAATGTGAAAATGTAGTATATGTGATAAGGCT
* * * *
61150 AATGGCCAAATGGTGATAAATGTGAAAGTGTAATAATAAGTG--AAGGCCT
1 AA-GGCC--AT-GTGATGAATGTGAAAATGTAGT-ATATGTGATAAGG-CT
* * * *
61199 AATAGCGATGTGATG-ATGTGATAGTATGTA-TATATGTG-TAAGCCT
1 AA-GGCCATGTGATGAATGTGA-A-AATGTAGTATATGTGATAAGGCT
*
61244 AATGGCCGATGTGATGAATGTGAAAGTGTAGTATATGTGATAAGGCT
1 AA-GGCC-ATGTGATGAATGTGAAAATGTAGTATATGTGATAAGGCT
*
61291 AATGCCAT-TGGATGAATGTGAAAATGATA-TATATG-GATAAGGC-
1 AAGGCCATGT-GATGAATGTGAAAATG-TAGTATATGTGATAAGGCT
* *
61334 AAGGCCATGTGATGAATGTG-AAA-G--GTATGTGT-A-AAGGCC
1 AAGGCCATGTGATGAATGTGAAAATGTAGTATATGTGATAAGGCT
* *
61373 AATGCCATGCGATGAATGTG-AAATGTA-TATA
1 AAGGCCATGTGATGAATGTGAAAATGTAGTATA
61404 GTACAGGGCC
Statistics
Matches: 271, Mismatches: 29, Indels: 75
0.72 0.08 0.20
Matches are distributed among these distances:
38 5 0.02
39 32 0.12
40 8 0.03
41 29 0.11
42 16 0.06
43 28 0.10
44 23 0.08
45 65 0.24
46 32 0.12
47 20 0.07
48 5 0.02
49 7 0.03
50 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (45 bp):
AAGGCCATGTGATGAATGTGAAAATGTAGTATATGTGATAAGGCT
Found at i:61395 original size:82 final size:85
Alignment explanation
Indices: 61059--61403 Score: 224
Period size: 92 Copynumber: 4.0 Consensus size: 85
61049 CATGTATTGT
*
61059 GATAAGGCTAATGGCCGATGTGA-G-ATG-GAAA--TGTATATTGTGATAAGGCCTAA-GCCATG
1 GATAAGGC-AA-GGCCGATGTGATGAATGTGAAAGGAGTATA-TGTGATAAGGCC-AATGCCAT-
* *
61118 TGAATGAATGTGAAATGTA-A-ATA
61 TGGATGAATGTGAAATGTATATATG
* * * *
61141 GATAAGGCGAATGGCCAAATGGTGATAAATGTGAAAGTGTAATAATAAGTG--AAGGCCTAATAG
1 GATAAGGC-AA-GGCC-GAT-GTGATGAATGTGAAAG-G-AGT-ATATGTGATAAGGCC-AAT-G
*
61204 CGA-TGTGATG-ATGTGATAGTATGTATATATG
57 CCATTG-GATGAATGTGA-A--ATGTATATATG
* *
61235 TG-TAAGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAGTATATGTGATAAGGCTAATGCCAT
1 -GATAAGGC-AA-GGCCGATGTGATGAATGTGAAAG-G-AGTATATGTGATAAGGCCAATGCCAT
61299 TGGATGAATGTGAAAATGATATATATG
61 TGGATGAATGTG-AAATG-TATATATG
*
61326 GATAAGGCAAGGCC-ATGTGATGAATGTGAAA-G-GTATGTGT-A-AAGGCCAATGCCA-TGCGA
1 GATAAGGCAAGGCCGATGTGATGAATGTGAAAGGAGTATATGTGATAAGGCCAATGCCATTG-GA
61385 TGAATGTGAAATGTATATA
65 TGAATGTGAAATGTATATA
61404 GTACAGGGCC
Statistics
Matches: 216, Mismatches: 20, Indels: 56
0.74 0.07 0.19
Matches are distributed among these distances:
80 6 0.03
81 7 0.03
82 37 0.17
83 3 0.01
84 11 0.05
86 4 0.02
87 4 0.02
88 17 0.08
89 21 0.10
90 10 0.05
91 33 0.15
92 39 0.18
93 9 0.04
94 14 0.06
95 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (85 bp):
GATAAGGCAAGGCCGATGTGATGAATGTGAAAGGAGTATATGTGATAAGGCCAATGCCATTGGAT
GAATGTGAAATGTATATATG
Found at i:61612 original size:37 final size:36
Alignment explanation
Indices: 61549--61721 Score: 219
Period size: 38 Copynumber: 4.8 Consensus size: 36
61539 TATGAGCTTA
*
61549 AAGA-CCGATGAATACGTGTGGAAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGG-AGATTATGT-CGGGT
61586 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGTGT
1 AAGACCCGATGACTACGTGTGGAGATTATGT-CGG-GT
*
61624 AAGACCCGATGACTATCGTGTGGAGATTTTGTC-GGT
1 AAGACCCGATGACTA-CGTGTGGAGATTATGTCGGGT
61660 AAGACTCCGATGACTAC-TGTGGAGATT-TGTCGGGT
1 AAGAC-CCGATGACTACGTGTGGAGATTATGTCGGGT
* * *
61695 AAGACCCGATAACTTCATGTGGAGATT
1 AAGACCCGATGACTACGTGTGGAGATT
61722 TCGTCTGAGC
Statistics
Matches: 126, Mismatches: 4, Indels: 14
0.88 0.03 0.10
Matches are distributed among these distances:
34 13 0.10
35 28 0.22
36 8 0.06
37 28 0.22
38 34 0.27
39 15 0.12
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (36 bp):
AAGACCCGATGACTACGTGTGGAGATTATGTCGGGT
Done.