Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1333
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: 44072
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:115 original size:47 final size:43
Alignment explanation
Indices: 32--154 Score: 122
Period size: 47 Copynumber: 2.7 Consensus size: 43
22 TCGGGACTTA
* * * *
32 TCACATTTATACACTTATACACATCA-CACGTTGGCCACTCGGCCCT
1 TCACATATATACACTT-T-CACATCATCACATCGGCCA-TCAG-CCT
*
78 GTCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCT
1 -TCACATATATACACTTTCACA-TCATCACATCGGCCATCAGCCT
*
123 TCTCATTATATACACTTTCACATCATCACATC
1 TCACA-TATATACACTTTCACATCATCACATC
155 TCACATTCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
44 14 0.21
45 23 0.34
46 6 0.09
47 24 0.36
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.32
Consensus pattern (43 bp):
TCACATATATACACTTTCACATCATCACATCGGCCATCAGCCT
Found at i:161 original size:60 final size:60
Alignment explanation
Indices: 95--212 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
85 ATATACACTT
* **
95 TCACATTCATCACATCGGCCATTAGCCTTC-TCATTATATACACTTTCACA-TCATCACATC
1 TCACATTCATCACATCGGCCATGAG-C-TCATCACAATATACACTTTCACATTCATCACATC
155 TCACATTCATCACATCGGCCATGAGCTCATCACAATATACACTTTCACATTCATCACA
1 TCACATTCATCACATCGGCCATGAGCTCATCACAATATACACTTTCACATTCATCACA
213 CGGATATTAG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 2 0.04
59 19 0.36
60 32 0.60
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.31
Consensus pattern (60 bp):
TCACATTCATCACATCGGCCATGAGCTCATCACAATATACACTTTCACATTCATCACATC
Found at i:166 original size:16 final size:15
Alignment explanation
Indices: 140--170 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
130 ATATACACTT
140 TCACATCATCACATC
1 TCACATCATCACATC
155 TCACATTCATCACATC
1 TCACA-TCATCACATC
171 GGCCATGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (15 bp):
TCACATCATCACATC
Found at i:419 original size:48 final size:47
Alignment explanation
Indices: 155--573 Score: 507
Period size: 48 Copynumber: 9.1 Consensus size: 47
145 TCATCACATC
* *
155 TCACATTCATCACATCGGCCATGAG-CTCATCAC--A-ATATACACTT
1 TCACATTCATCACATC-GCCATTAGCCTTATCACATATATATACACTT
**
199 TCACATTCATCACA-CGGATATTAGCCTTA-CA-ATATAT-TACACTT
1 TCACATTCATCACATC-GCCATTAGCCTTATCACATATATATACACTT
*
243 TCACATTCATCACATGGCCATTAGCCTTATCACATATATATACACTT
1 TCACATTCATCACATCGCCATTAGCCTTATCACATATATATACACTT
*
290 TCACATTCAT--CATTGCCATT--CCTTATCACATATATATACACTT
1 TCACATTCATCACATCGCCATTAGCCTTATCACATATATATACACTT
* *
333 TCACATTCATCACATTGGCCATTCGCCTTATCAC--ATATATACACTT
1 TCACATTCATCACA-TCGCCATTAGCCTTATCACATATATATACACTT
379 TCACATTCATCACATCGCCATTAGGCCTTATCACATATATATACACTT
1 TCACATTCATCACATCGCCATTA-GCCTTATCACATATATATACACTT
* *
427 TCACATTCATCACATGGCCATTAGGCCTTATCACACATATATACACTT
1 TCACATTCATCACATCGCCATTA-GCCTTATCACATATATATACACTT
* *
475 TCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTT
1 TCACATTCATCACA-TCGCCATT-AGCCTTATCACATATATATACACTT
*
522 TCACATTCATCACATCGGCATTAGGCCTTATCA-ATAATATATACA--T
1 TCACATTCATCACATCGCCATTA-GCCTTATCACAT-ATATATACACTT
568 TCACAT
1 TCACAT
574 CACAATTATC
Statistics
Matches: 336, Mismatches: 17, Indels: 42
0.85 0.04 0.11
Matches are distributed among these distances:
43 42 0.12
44 50 0.15
45 22 0.07
46 71 0.21
47 43 0.13
48 90 0.27
49 18 0.05
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.33
Consensus pattern (47 bp):
TCACATTCATCACATCGCCATTAGCCTTATCACATATATATACACTT
Found at i:547 original size:143 final size:141
Alignment explanation
Indices: 155--573 Score: 591
Period size: 143 Copynumber: 3.0 Consensus size: 141
145 TCATCACATC
* * *
155 TCACATTCATCACATCGGCCATGAG-CTCAT--CACA-ATATACACTTTCACATTCATCACA-CG
1 TCACATTCATCACAT-GGCCATTAGCCTTATCACACATATATACACTTTCACATTCATCACATTG
** *
215 GATATTAGCCTTA-CA-ATATATTACACTTTCACATTCATCACAT-GGCCATTA-GCCTTATCAC
65 GCCATTCGCCTTATCACATATA-TACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCAC
276 ATATATATACACTT
128 ATATATATACACTT
* *
290 TCACATTCAT--CATTGCCATT--CCTTATCACATATATATACACTTTCACATTCATCACATTGG
1 TCACATTCATCACATGGCCATTAGCCTTATCACACATATATACACTTTCACATTCATCACATTGG
*
351 CCATTCGCCTTATCACATATATACACTTTCACATTCATCACATCGCCATTAGGCCTTATCACATA
66 CCATTCGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGCCTTATCACATA
416 TATATACACTT
131 TATATACACTT
427 TCACATTCATCACATGGCCATTAGGCCTTATCACACATATATACACTTTCACATTCATCACATTG
1 TCACATTCATCACATGGCCATTA-GCCTTATCACACATATATACACTTTCACATTCATCACATTG
492 GCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGCCTTATCA-A
65 GCCATTC-GCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGCCTTATCACA
556 TAATATATACA--T
129 T-ATATATACACTT
568 TCACAT
1 TCACAT
574 CACAATTATC
Statistics
Matches: 256, Mismatches: 12, Indels: 26
0.87 0.04 0.09
Matches are distributed among these distances:
131 4 0.02
132 5 0.02
133 6 0.02
134 24 0.09
135 21 0.08
136 29 0.11
137 40 0.16
139 9 0.04
141 7 0.03
142 48 0.19
143 63 0.25
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.33
Consensus pattern (141 bp):
TCACATTCATCACATGGCCATTAGCCTTATCACACATATATACACTTTCACATTCATCACATTGG
CCATTCGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGCCTTATCACATA
TATATACACTT
Found at i:609 original size:95 final size:94
Alignment explanation
Indices: 230--573 Score: 410
Period size: 95 Copynumber: 3.7 Consensus size: 94
220 TAGCCTTACA
*
230 ATATATTACACTTTCACATTCATCACATGGCCATTA-GCCTTATCACATATATATACACTTTCAC
1 ATATA-TACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACAAATATATACAC-TTCAC
*
294 ATTCAT--CATT-GCCATT---CCTTATCAC
64 ATTCATCACATTAGCCATTCGGCCATATCAC
*
319 ATATATATACACTTTCACATTCATCACATTGGCCATT-CGCCTTATCAC--ATATATACACTTTC
1 --ATATATACACTTTCACATTCATCACA-TGGCCATTAGGCCTTATCACAAATATATACAC-TTC
* * *
381 ACATTCATCACA-TCGCCATTAGGCCTTATCAC
62 ACATTCATCACATTAGCCATTCGGCCATATCAC
*
413 ATATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACACATATATACACTTTCA
1 --ATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACAAATATATACAC-TTCA
* *
478 CATTCATCACATTGGCCATTCGGCCTTATCAC
63 CATTCATCACATTAGCCATTCGGCCATATCAC
510 ATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCA-ATAATATATACA-TTCAC
1 ATATATACACTTTCACATTCATCACAT-GGCCATTAGGCCTTATCACA-AATATATACACTTCAC
572 AT
64 AT
574 CACAATTATC
Statistics
Matches: 235, Mismatches: 4, Indels: 26
0.89 0.02 0.10
Matches are distributed among these distances:
89 22 0.09
90 22 0.09
91 31 0.13
93 15 0.06
94 48 0.20
95 51 0.22
96 28 0.12
97 18 0.08
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (94 bp):
ATATATACACTTTCACATTCATCACATGGCCATTAGGCCTTATCACAAATATATACACTTCACAT
TCATCACATTAGCCATTCGGCCATATCAC
Found at i:4042 original size:39 final size:40
Alignment explanation
Indices: 3967--4310 Score: 545
Period size: 39 Copynumber: 8.7 Consensus size: 40
3957 CCAGCATGAT
* * * *
3967 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
4007 TGCTCTTCGGG-TTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
4046 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
4086 TGCTCTTCGGGACTTAG-CCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
4125 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
4165 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
4204 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
4243 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
4283 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
4311 GTCGAGACCT
Statistics
Matches: 287, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
39 153 0.53
40 134 0.47
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:4108 original size:79 final size:80
Alignment explanation
Indices: 3967--4310 Score: 545
Period size: 79 Copynumber: 4.4 Consensus size: 80
3957 CCAGCATGAT
* * * * * *
3967 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGG-TTTAGCACGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
*
4031 TATCACTAGCACGAA
66 CATCACTAGCACGAA
* *
4046 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAG-CCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
*
4110 CATCACTAGCATGAA
66 CATCACTAGCACGAA
4125 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTC-GGACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
*
4189 CATCACTAGCATGAA
66 CATCACTAGCACGAA
*
4204 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
4268 CATCACTAGCACGAA
66 CATCACTAGCACGAA
4283 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
4311 GTCGAGACCT
Statistics
Matches: 247, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
78 46 0.19
79 182 0.74
80 19 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
CATCACTAGCACGAA
Found at i:4201 original size:118 final size:119
Alignment explanation
Indices: 3954--4310 Score: 578
Period size: 118 Copynumber: 3.0 Consensus size: 119
3944 CGAATACACG
* * * * * * *
3954 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGG-
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
* * *
4018 TTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
66 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG-ACTTAGCCCGGATACA
4073 TCACTAGCATGAATGCTCTTCGGGACTTAG-CCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
4137 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACA
66 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACA
4191 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
4255 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT-CA
66 CTTAGCCCGGATACATCACTAGCACGAATGCTCTTC-GGACTTAGCCCGGATACA
4309 TC
1 TC
4311 GTCGAGACCT
Statistics
Matches: 225, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
117 8 0.04
118 140 0.62
119 77 0.34
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (119 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
CTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTTAGCCCGGATACA
Found at i:6916 original size:49 final size:47
Alignment explanation
Indices: 6531--7122 Score: 949
Period size: 47 Copynumber: 12.6 Consensus size: 47
6521 CCCTTCGGGA
* * * * * *
6531 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6578 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
6624 CTCATCACATATATACA-TTTCACATTCATCACATCAGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6670 CTTATCACATATATACA-TTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6716 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6763 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6810 CTTATCACATATATACACTTTCACATTCATCACAT-GGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6856 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6905 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6952 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7001 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7050 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7097 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
7123 CACAATTATC
Statistics
Matches: 513, Mismatches: 25, Indels: 14
0.93 0.05 0.03
Matches are distributed among these distances:
45 24 0.05
46 97 0.19
47 253 0.49
48 27 0.05
49 112 0.22
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:6987 original size:96 final size:94
Alignment explanation
Indices: 6531--7122 Score: 949
Period size: 96 Copynumber: 6.3 Consensus size: 94
6521 CCCTTCGGGA
* * * * * * * *
6531 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
6596 TTTCACATTCATCACATCGGCCATTA-GC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * *
6624 CTCATCACATATATACA-TTTCACATTCATCACATCAGCTATTAGGCCTTATCACATATATACA-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
6687 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
6716 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
6781 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
6810 CTTATCACATATATACACTTTCACATTCATCACAT-GGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
6874 ACTTTCACATTCATCACATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
6905 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
6970 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
7001 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
7066 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
7097 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
7123 CACAATTATC
Statistics
Matches: 469, Mismatches: 22, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
91 26 0.06
92 55 0.12
93 78 0.17
94 80 0.17
95 72 0.15
96 113 0.24
98 45 0.10
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:12583 original size:57 final size:57
Alignment explanation
Indices: 12501--12676 Score: 174
Period size: 57 Copynumber: 3.1 Consensus size: 57
12491 AAAAAAATTG
* * * * *
12501 GAAATCATTTGGAAGTG-ATACTGGTTTTCACTATAATGAAAATAAAAATGGAGAAAT
1 GAAAACATTTGGAAATGAATA-TGGTTTTCTCCAAAATGAAAATAAAAATGGAGAAAT
* * * * * *
12558 GAAAACATTTGGAAATTATTATGGTTTTCTCGAAAATGGAAATGAAAATGGAGATAT
1 GAAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAATAAAAATGGAGAAAT
* * * * * *
12615 GGAATCATTTGGAAATGAATGTGGTTTTTTCCAAAATGAAAATGAAAAATGAAAAAAT
1 GAAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAAT-AAAAATGGAGAAAT
12673 GAAA
1 GAAA
12677 TTGACCTGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
57 79 0.84
58 15 0.16
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.30
Consensus pattern (57 bp):
GAAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAATAAAAATGGAGAAAT
Found at i:16020 original size:47 final size:47
Alignment explanation
Indices: 15958--16048 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 47
15948 GGTAACCTAG
* *
15958 GATGGTAGCTTATATGTACATTGAGTCATCG-TTCCTAGGCAACCTGA
1 GATGGTAGATTATATGTACACTGAGTCATCGATTCC-AGGCAACCTGA
16005 GATGGTAGATTATATGTACACTGAGTCATCGATTCCAGGCAACC
1 GATGGTAGATTATATGTACACTGAGTCATCGATTCCAGGCAACC
16049 CAGGGTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 37 0.90
48 4 0.10
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (47 bp):
GATGGTAGATTATATGTACACTGAGTCATCGATTCCAGGCAACCTGA
Found at i:18642 original size:24 final size:24
Alignment explanation
Indices: 18580--18642 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
18570 ATTGTATAAG
* *
18580 ATAGTGAAATGCATAAATTAGTGC
1 ATAGTGAAATGCATATATTAGTGA
18604 ATAG-G-AATGTCATATATTAGCTGA
1 ATAGTGAAATG-CATATATTAG-TGA
18628 AT-GTGAAATGCATAT
1 ATAGTGAAATGCATAT
18643 GTTTGGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 4 0.12
23 11 0.33
24 14 0.42
25 4 0.12
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (24 bp):
ATAGTGAAATGCATATATTAGTGA
Found at i:20179 original size:37 final size:37
Alignment explanation
Indices: 20121--20191 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
20111 GCTCAGACGT
*
20121 AATCTCCACACAAAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACAAAGTCATCGGGTCTTACCCGGACAA
**
20158 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACAAAGTCATCGGGTCTTACCCGGA
20192 ATATATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
AATCTCCACACAAAGTCATCGGGTCTTACCCGGACAA
Found at i:20450 original size:48 final size:48
Alignment explanation
Indices: 20337--20521 Score: 289
Period size: 48 Copynumber: 3.8 Consensus size: 48
20327 GCACATCGCC
*
20337 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* * * * *
20385 TATATATATCTCACATTAACCATTCAGCTTTACCATATATGCATATCTCA
1 TACATAT-T-TCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
20435 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
20483 TACATATTTCACATTAGCCATTCGGATTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
20522 TGCATGTTCA
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
48 80 0.65
49 2 0.02
50 41 0.33
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:20520 original size:98 final size:98
Alignment explanation
Indices: 20337--20526 Score: 303
Period size: 98 Copynumber: 1.9 Consensus size: 98
20327 GCACATCGCC
*
20337 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATCTCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATATCTCACATT
*
20402 AACCATTCAGCTTTACCATATATGCATATCTCA
66 AACCATTCAGATTTACCATATATGCATATCTCA
*
20435 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT-T-TCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATATCTCACATT
* *
20498 AGCCATTCGGATTTACCACATATATGCAT
66 AACCATTCAGATTTA-C-CATATATGCAT
20527 GTTCATATTC
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
96 19 0.22
97 2 0.02
98 64 0.75
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (98 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATATCTCACATT
AACCATTCAGATTTACCATATATGCATATCTCA
Found at i:20565 original size:47 final size:47
Alignment explanation
Indices: 20491--20684 Score: 316
Period size: 47 Copynumber: 4.1 Consensus size: 47
20481 CATACATATT
* ** * *
20491 TCACATTAGCCATTCGGATTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
20538 CCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
20585 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
20632 TCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
20679 TCACAT
1 TCACAT
20685 AAAATCCTAA
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 137 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:20578 original size:25 final size:25
Alignment explanation
Indices: 20559--20685 Score: 85
Period size: 25 Copynumber: 5.3 Consensus size: 25
20549 ATTCAGCCTT
20559 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCATGTTCACATTC
* * *
20584 ATCACAT-T-GGCCA--TTCGGCCTT-
1 ATCACATATATG-CATGTTC-ACATTC
20606 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCATGTTCACATTC
* * *
20631 ATCACAT-T-GGCCA--TTCGGCCTT-
1 ATCACATATATG-CATGTTC-ACATTC
*
20653 ATCTCATATATGCATGTTCACATTC
1 ATCACATATATGCATGTTCACATTC
20678 ATCACATA
1 ATCACATA
20686 AAATCCTAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 28
0.64 0.12 0.24
Matches are distributed among these distances:
22 19 0.26
23 14 0.19
24 14 0.19
25 27 0.36
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.35
Consensus pattern (25 bp):
ATCACATATATGCATGTTCACATTC
Found at i:20716 original size:94 final size:91
Alignment explanation
Indices: 20517--20705 Score: 231
Period size: 94 Copynumber: 2.1 Consensus size: 91
20507 GATTTACCAC
*
20517 ATATATGCATGTTCATATTCACCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACAT
1 ATATATGCATGTTCACATTCACCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACAT
** * * *
20582 TCATCACATTGGCCATTCGGCCTTATCAC
66 TCATCACATT-GAAAAT--GCCTAATCAA
* * *
20611 ATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACAT
1 ATATATGCATGTTCACATTCACCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACAT
20676 TCATCACA-T-AAAAT-CCTAAATCAAA
66 TCATCACATTGAAAATGCCT-AATC-AA
20701 ATATA
1 ATATA
20706 AATTTTCATG
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
88 3 0.04
89 3 0.04
90 6 0.07
91 2 0.02
93 1 0.01
94 69 0.82
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (91 bp):
ATATATGCATGTTCACATTCACCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACAT
TCATCACATTGAAAATGCCTAATCAA
Found at i:25260 original size:51 final size:51
Alignment explanation
Indices: 25188--25567 Score: 294
Period size: 51 Copynumber: 7.5 Consensus size: 51
25178 TTAGGTCGCA
*
25188 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCAACAACTTCAATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAACAACTTCAATCACG
* * * ** *
25239 TGTGTAGTACTAAGTGGAGGCTACTACT-TGTA-TCAA-ATGGTT-AGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTA-TGCGTACCCAACA-ACTTCA-ATCACG
* * * * * * * * * *
25289 TGTGTAGTACTAAGAGCAGGCTAATACGTGTA-CTAGA-TAGTT-AGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCA-ACAACTTCA-ATCACG
* * *
25339 TGTATAGTACTAAGTGCAGGCTATTATGCGTACCCGACAACTTCAATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAACAACTTCAATCACG
* * *
25390 TGTGTAGTACTAAGCGCAGGCTATTATGCATACCCAACAACTTCAATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAACAACTTCAATCACG
* * * * * *
25441 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGA-TAGTT-AGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCA-ACAACTTCA-ATCACG
* ** *
25491 TGTGTAGTAATAAGTGCAGGCTACTATGCGTACCTGACAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAACAACTTCAATCACG
* * **
25542 TGTTTAGTACAAAGTATAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
25568 CGTGTGTCAG
Statistics
Matches: 259, Mismatches: 57, Indels: 26
0.76 0.17 0.08
Matches are distributed among these distances:
49 3 0.01
50 115 0.44
51 139 0.54
52 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (51 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAACAACTTCAATCACG
Found at i:25264 original size:101 final size:101
Alignment explanation
Indices: 25133--25614 Score: 522
Period size: 101 Copynumber: 4.8 Consensus size: 101
25123 TGATTTTAGG
* * *
25133 TCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
25198 TAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
66 TAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
* * * * *
25234 TCACGTGTGTAGTACTAAGTGGAGGCTACTACTTGTATCAAATGGTTAGGTCACGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
* * * ** * * * *
25299 TAAGAGCAGGCTAATACGTGTA-CTAGA-TAGTT-AGG
66 TAAGTGCAGGCTACTATGCATACCCA-ACAACTTCA-A
* * * * * * * * * *
25334 TCGCATGTATAGTACTAAGTGCAGGCTATTATGCGTACCCGACAACTTCA-ATCACGTGTGTAGT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAGTT-AGGTCACGTGTGTAGT
* *
25398 ACTAAGCGCAGGCTATTATGCATACCCAACAACTTCAA
64 ACTAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
* *
25436 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTAA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
* ** *
25501 TAAGTGCAGGCTACTATGCGTACCTGACAACTTCGA
66 TAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
* * ** ** *
25537 TCACGTGTTTAGTACAAAGTATAGGCTACTACGTGTGTCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
25602 TAAGTGCAGGCTA
66 TAAGTGCAGGCTA
25615 TTTCGTGTAC
Statistics
Matches: 305, Mismatches: 68, Indels: 16
0.78 0.17 0.04
Matches are distributed among these distances:
99 1 0.00
100 37 0.12
101 225 0.74
102 41 0.13
103 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
TAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
Found at i:25319 original size:151 final size:150
Alignment explanation
Indices: 25128--25674 Score: 708
Period size: 151 Copynumber: 3.6 Consensus size: 150
25118 TAAGATGATT
*
25128 TTAGGTCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
* * *
25193 AGTACTAAGTGCAGGCTACTATGCATACCCAACAACTTCAATCACGTGTGTAGTACTAAGTGGAG
66 AGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGTGCAG
25258 GCTACTACTTGTATCAAATGG
131 GCTACTAC-TGTATCAAATGG
* * * *
25279 TTAGGTCACGTGTGTAGTACTAAGAGCAGGCTAATACGTGTACTAGATAGTTAGGTCGCATGTAT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
* *
25344 AGTACTAAGTGCAGGCTATTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGCGCAG
66 AGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGTGCAG
* * **
25409 GCTATTA-TGCATACCCAACA-AC
131 GCTACTACTG--TA-TCAA-ATGG
* *
25431 TTCA-ATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTG
1 TT-AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTG
* * * * * **
25495 TAGTAATAAGTGCAGGCTACTATGCGTACCTGACAACTTCGATCACGTGTTTAGTACAAAGTATA
65 TAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGTGCA
* *
25560 GGCTACTACGTGTGTCAGATGG
130 GGCTACTAC-TGTATCAAATGG
* * * *
25582 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTATTTCGTGTACC-GA-ATTTTTGGTCGCATGTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA-GTTAGGTCGCATGTG
* *
25645 TAGCACTAAGTGCAGGCTACTATGAGTACC
65 TAGTACTAAGTGCAGGCTACTATGCGTACC
25675 AGATAGCTTC
Statistics
Matches: 342, Mismatches: 44, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
149 3 0.01
150 43 0.13
151 169 0.49
152 123 0.36
153 2 0.01
154 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (150 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
AGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGTGCAG
GCTACTACTGTATCAAATGG
Found at i:25593 original size:202 final size:201
Alignment explanation
Indices: 25128--25616 Score: 586
Period size: 202 Copynumber: 2.4 Consensus size: 201
25118 TAAGATGATT
* * * * *
25128 TTAGGTCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
1 TTAGATCACGTGTATAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGT
* *
25193 AGTACTAAGTGCAGGCTACTATGCATACCCAACAACTTCAATCACGTGTGTAGTACTAAGTGGAG
66 AGTACTAAGTGCAGGCTATTATGCATACCCAACAACTTCAATCACGTGTGTAGTACTAAGTGCAG
* * * * * *
25258 GCTACTACTTGTATCAAATGGTTAGGTCACGTGTGTAGTACTAAGAGCAGGCTAATACGTGTACT
131 GCTACTACGTGTACCAAATAGTTAGGTCACATGTGTAGTAATAAGAGCAGGCTAATACGCGTACT
* *
25323 AGATAG
196 AGAAAC
* * * * * * * * * *
25329 TTAGGTCGCATGTATAGTACTAAGTGCAGGCTATTATGCGTACCCGACAACTTCA-ATCACGTGT
1 TTAGATCACGTGTATAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAGTT-AGGTCACGTGT
*
25393 GTAGTACTAAGCGCAGGCTATTATGCATACCCAACAACTTCAATCACGTGTGTAGTACTAAGTGC
64 GTAGTACTAAGTGCAGGCTATTATGCATACCCAACAACTTCAATCACGTGTGTAGTACTAAGTGC
* * * *
25458 AGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTAATAAGTGCAGGCTACTATGCGTA
129 AGGCTACTACGTGTACCAAATAGTTAGGTCACATGTGTAGTAATAAGAGCAGGCTAATACGCGTA
25523 CCT-GACAAC
194 -CTAGA-AAC
* * * ** ** *
25532 TTCGATCACGTGTTTAGTACAAAGTATAGGCTACTACGTGTGTCAGATGGTTAGGTCACGTGTGT
1 TTAGATCACGTGTATAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGT
25597 AGTACTAAGTGCAGGCTATT
66 AGTACTAAGTGCAGGCTATT
25617 TCGTGTACCG
Statistics
Matches: 236, Mismatches: 47, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
201 40 0.17
202 159 0.67
203 37 0.16
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (201 bp):
TTAGATCACGTGTATAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGT
AGTACTAAGTGCAGGCTATTATGCATACCCAACAACTTCAATCACGTGTGTAGTACTAAGTGCAG
GCTACTACGTGTACCAAATAGTTAGGTCACATGTGTAGTAATAAGAGCAGGCTAATACGCGTACT
AGAAAC
Found at i:25899 original size:16 final size:15
Alignment explanation
Indices: 25878--25907 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25868 GAATGGAGTA
25878 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
25894 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
25908 AAAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:32205 original size:50 final size:50
Alignment explanation
Indices: 32143--32492 Score: 357
Period size: 50 Copynumber: 7.0 Consensus size: 50
32133 TAAGATGGTT
* *
32143 TTAGGTCACATGTGTAGTACTAAGTGTAGGGTACTACGTGTACCAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
** * * * * * *
32193 TTAGGTTGCATGTTTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAAC
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAG
* * * * * *
32244 TTCA-ATCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCGACAAC
1 TT-AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAG
* *
32295 TTCA-ATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
1 TT-AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * *
32345 TTAGGTCACATGTGTAGTACTAAGTCCAGGCTACTACGTGTATCAGATGG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
** * * * *
32395 TTAGGTCATGTGTGTAGTACTAAGTGCAAGCTATTACGTGTACCGGATTG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * *
32445 TT-GGTCGCATGTGTAGTACTAAGTGTAGGCTACTAGGCGTA-CAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
32493 CTTCTGTTAC
Statistics
Matches: 254, Mismatches: 43, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
48 5 0.02
49 32 0.13
50 127 0.50
51 89 0.35
52 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
Found at i:32268 original size:51 final size:51
Alignment explanation
Indices: 32207--32386 Score: 256
Period size: 51 Copynumber: 3.5 Consensus size: 51
32197 GTTGCATGTT
*
32207 TAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTG
1 TAGTACTAAGTGCAGGCTACTATGTGTACCCGACAACTTCAATCACGTGTG
32258 TAGTACTAAGTGCAGGCTACTATGTGTACCCGACAACTTCAATCACGTGTG
1 TAGTACTAAGTGCAGGCTACTATGTGTACCCGACAACTTCAATCACGTGTG
* * * * * *
32309 TAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAGTT-AGGTCACATGTG
1 TAGTACTAAGTGCAGGCTACTATGTGTACCCGACAACTTCA-ATCACGTGTG
* *
32359 TAGTACTAAGTCCAGGCTACTACGTGTA
1 TAGTACTAAGTGCAGGCTACTATGTGTA
32387 TCAGATGGTT
Statistics
Matches: 120, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
49 1 0.01
50 38 0.32
51 81 0.68
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (51 bp):
TAGTACTAAGTGCAGGCTACTATGTGTACCCGACAACTTCAATCACGTGTG
Found at i:32710 original size:16 final size:15
Alignment explanation
Indices: 32689--32718 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
32679 GAATGGAGTA
32689 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
32705 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
32719 TAAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:38598 original size:27 final size:25
Alignment explanation
Indices: 38561--38625 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
38551 GGAGAAGGCT
38561 TTCTGTGGCTCTACACAAACTATCTA
1 TTCTGTGGCTCTACACAAA-TATCTA
** *
38587 TTCTGGTGGCTCGCCACAAATATCTG
1 TTCT-GTGGCTCTACACAAATATCTA
38613 TTCTGTGGCTCTA
1 TTCTGTGGCTCTA
38626 TCCACAATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 7 0.21
26 13 0.39
27 13 0.39
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.35
Consensus pattern (25 bp):
TTCTGTGGCTCTACACAAATATCTA
Found at i:38634 original size:26 final size:26
Alignment explanation
Indices: 38561--38672 Score: 88
Period size: 27 Copynumber: 4.2 Consensus size: 26
38551 GGAGAAGGCT
*
38561 TTCTGTGGCTCTA-CACAAACTATCTA
1 TTCTGTGGCTCTATCACAAA-TATCTG
**
38587 TTCTGGTGGCTC-GCCACAAATATCTG
1 TTCT-GTGGCTCTATCACAAATATCTG
*
38613 TTCTGTGGCTCTATC-CACAATAGGCTG
1 TTCTGTGGCTCTATCACA-AATA-TCTG
*
38640 TATCTGGTGACTCTATCAC-AATATCTG
1 T-TCT-GTGGCTCTATCACAAATATCTG
38667 TCTCTG
1 T-TCTG
38673 GATAATGCTG
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
25 9 0.13
26 19 0.27
27 24 0.34
28 7 0.10
29 10 0.14
30 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (26 bp):
TTCTGTGGCTCTATCACAAATATCTG
Done.