Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014572.1 Kokia drynarioides strain JFW-HI SEQ_129611, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 46920
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:350 original size:10 final size:11
Alignment explanation
Indices: 329--361 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
319 AATCTCCCCA
329 TTCCTCTTCTC
1 TTCCTCTTCTC
340 TTCCT-TTCTC
1 TTCCTCTTCTC
350 TT-CTCTTCTC
1 TTCCTCTTCTC
360 TT
1 TT
362 TTCTATGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.10
10 14 0.67
11 5 0.24
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (11 bp):
TTCCTCTTCTC
Found at i:350 original size:15 final size:16
Alignment explanation
Indices: 332--362 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
322 CTCCCCATTC
332 CTCTTCTCTTC-CTTT
1 CTCTTCTCTTCTCTTT
347 CTCTTCTCTTCTCTTT
1 CTCTTCTCTTCTCTTT
363 TCTATGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
CTCTTCTCTTCTCTTT
Found at i:5033 original size:23 final size:23
Alignment explanation
Indices: 5007--5124 Score: 123
Period size: 23 Copynumber: 5.0 Consensus size: 23
4997 CGCTTACTGA
*
5007 TTAGCACTGTGTGTGCTCTCTGT
1 TTAGCACTGTGTGTGCCCTCTGT
* *
5030 TTAGCAC-GTTTCGTGCCCTCTGA
1 TTAGCACTGTGT-GTGCCCTCTGT
* *
5053 TCAGCACTTTGTGTGCCCTCTGTT
1 TTAGCACTGTGTGTGCCCTCTG-T
*
5077 ATTAGCACT-TCGTGTGCCCTCTGA
1 -TTAGCACTGT-GTGTGCCCTCTGT
*
5101 TTAGCACTTTGTGTGCCCTCTGT
1 TTAGCACTGTGTGTGCCCTCTGT
5124 T
1 T
5125 ACCCAGCACT
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
22 3 0.04
23 53 0.67
24 4 0.05
25 19 0.24
ACGTcount: A:0.11, C:0.27, G:0.22, T:0.40
Consensus pattern (23 bp):
TTAGCACTGTGTGTGCCCTCTGT
Found at i:5141 original size:48 final size:45
Alignment explanation
Indices: 5003--5150 Score: 174
Period size: 48 Copynumber: 3.2 Consensus size: 45
4993 AGTGCGCTTA
* *
5003 CTGATTAGCACTGTGTGTGCTCTCTGTT-TAGCACGTTTCGTGCCCT
1 CTGATTAGCACTTTGTGTGCCCTCTGTTATAGCAC-TTT-GTGCCCT
*
5049 CTGATCAGCACTTTGTGTGCCCTCTGTTATTAGCACTTCGTGTGCCCT
1 CTGATTAGCACTTTGTGTGCCCTCTGTTA-TAGCACTT--TGTGCCCT
*
5097 CTGATTAGCACTTTGTGTGCCCTCTGTTACCCAGCACTTATGTGCCCT
1 CTGATTAGCACTTTGTGTGCCCTCTGTTA--TAGCACTT-TGTGCCCT
5145 CT-ATTA
1 CTGATTA
5151 AGTACTTCAG
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
46 25 0.28
47 6 0.07
48 51 0.57
49 8 0.09
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.38
Consensus pattern (45 bp):
CTGATTAGCACTTTGTGTGCCCTCTGTTATAGCACTTTGTGCCCT
Found at i:5145 original size:25 final size:24
Alignment explanation
Indices: 5009--5146 Score: 117
Period size: 23 Copynumber: 5.8 Consensus size: 24
4999 CTTACTGATT
* * *
5009 AGCACTGTGTGTGCTCTCTGTT-T
1 AGCACTTTGTGTGCCCTCTGTTAC
* *
5032 AGCACGTTT-CGTGCCCTCTGAT-C
1 AGCAC-TTTGTGTGCCCTCTGTTAC
*
5055 AGCACTTTGTGTGCCCTCTGTTATT
1 AGCACTTTGTGTGCCCTCTGTTA-C
*
5080 AGCACTTCGTGTGCCCTCTGATT--
1 AGCACTTTGTGTGCCCTCTG-TTAC
5103 AGCACTTTGTGTGCCCTCTGTTACCC
1 AGCACTTTGTGTGCCCTCTGTTA--C
*
5129 AGCAC-TTATGTGCCCTCT
1 AGCACTTTGTGTGCCCTCT
5147 ATTAAGTACT
Statistics
Matches: 95, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
22 5 0.05
23 50 0.53
24 2 0.02
25 31 0.33
26 7 0.07
ACGTcount: A:0.12, C:0.30, G:0.21, T:0.37
Consensus pattern (24 bp):
AGCACTTTGTGTGCCCTCTGTTAC
Found at i:6333 original size:41 final size:41
Alignment explanation
Indices: 6276--6357 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
6266 GAAAAAATAA
6276 AATTGCATATTAGTCCTCGACGTCTTGGTTGTTGCTATTTT
1 AATTGCATATTAGTCCTCGACGTCTTGGTTGTTGCTATTTT
6317 AATTGCATATTAGTCCTCGACGTCTTGGTTGTTGCTATTTT
1 AATTGCATATTAGTCCTCGACGTCTTGGTTGTTGCTATTTT
6358 TGCTAAGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (41 bp):
AATTGCATATTAGTCCTCGACGTCTTGGTTGTTGCTATTTT
Found at i:6819 original size:72 final size:72
Alignment explanation
Indices: 6722--6858 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 72
6712 GATCCAGCAA
* * * * *
6722 GTGTTGTGGATTCTCTGAAGCTTGTGTGAGCAGCATC-AAGTCATTATTTATCGATGGCTTGAGA
1 GTGTTGCGAATTCTCCGAAGCTTGTGTGAACAGCATCGAA-TCATTATTTATCGATGGCTTAAGA
6786 TTTAGATC
65 TTTAGATC
* * *
6794 GTGTTGCGAATTCTCCGAAGTTTGTGTGAACAGCATCGAATCATTCTTTATTGATGGCTTAAGAT
1 GTGTTGCGAATTCTCCGAAGCTTGTGTGAACAGCATCGAATCATTATTTATCGATGGCTTAAGAT
6859 CTAACACATG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 54 0.96
73 2 0.04
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (72 bp):
GTGTTGCGAATTCTCCGAAGCTTGTGTGAACAGCATCGAATCATTATTTATCGATGGCTTAAGAT
TTAGATC
Found at i:6871 original size:72 final size:72
Alignment explanation
Indices: 6730--6886 Score: 185
Period size: 72 Copynumber: 2.2 Consensus size: 72
6720 AAGTGTTGTG
* * * * *
6730 GATTCTCTGAAGCTTGTGTGAGCAGCATCAAGTCATTATTTATCGATGGCTTGAGATTTAGATCG
1 GATTCTCTGAAGCTTGTGTGAACAGCATCAAGTCATTATTTATCGATGGCTTAAGATCTAGAACA
6795 TGTTGC-
66 TGTTGCA
* * * *
6801 GAATTCTCCGAAGTTTGTGTGAACAGCATCGAA-TCATTCTTTATTGATGGCTTAAGATCTA-AC
1 G-ATTCTCTGAAGCTTGTGTGAACAGCATC-AAGTCATTATTTATCGATGGCTTAAGATCTAGA-
6864 ACATGTTGCA
63 ACATGTTGCA
6874 GATTCTCTGAAGC
1 GATTCTCTGAAGC
6887 AGATTCTCTG
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
71 2 0.03
72 66 0.93
73 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (72 bp):
GATTCTCTGAAGCTTGTGTGAACAGCATCAAGTCATTATTTATCGATGGCTTAAGATCTAGAACA
TGTTGCA
Found at i:6890 original size:14 final size:14
Alignment explanation
Indices: 6871--6900 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6861 AACACATGTT
6871 GCAGATTCTCTGAA
1 GCAGATTCTCTGAA
6885 GCAGATTCTCTGAA
1 GCAGATTCTCTGAA
6899 GC
1 GC
6901 TTGTGTGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (14 bp):
GCAGATTCTCTGAA
Found at i:8557 original size:3 final size:3
Alignment explanation
Indices: 8549--8583 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
8539 AAAACCTGAA
8549 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
8584 ATCACCGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9347 original size:6 final size:6
Alignment explanation
Indices: 9338--9384 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
9328 TTAAATTTGT
* *
9338 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
9384 T
1 T
9385 AAAAATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:9353 original size:34 final size:34
Alignment explanation
Indices: 9310--9384 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
9300 CCCGACTCCT
* *
9310 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAA
*
9344 TTTAAATTTAATTTAAGTTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAA
9378 TTTAAAT
1 TTTAAAT
9385 AAAAATAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTTAAA
Found at i:9356 original size:11 final size:11
Alignment explanation
Indices: 9328--9382 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
9318 TATTTTAAGA
**
9328 TTAAATTTGTT
1 TTAAATTTAAT
9339 TTAAATTTAAAT
1 TTAAATTT-AAT
9351 TT-AATTTAAGT
1 TTAAATTTAA-T
*
9362 TTAAATTTATT
1 TTAAATTTAAT
9373 TTAAATTTAA
1 TTAAATTTAA
9383 ATAAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 2 0.05
11 26 0.70
12 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:9381 original size:17 final size:17
Alignment explanation
Indices: 9310--9384 Score: 107
Period size: 17 Copynumber: 4.4 Consensus size: 17
9300 CCCGACTCCT
9310 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
9328 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
* *
9344 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
9361 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
9378 TTTAAAT
1 TTTAAAT
9385 AAAAATAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
16 1 0.02
17 49 0.98
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:10004 original size:3 final size:3
Alignment explanation
Indices: 9998--10046 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
9988 AAAAAACGAT
* * * *
9998 TAA TAA TAA TAA TAA TAA TAA TAAA TAG CAT TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
10044 TAA
1 TAA
10047 CAAAAAGAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:11217 original size:30 final size:28
Alignment explanation
Indices: 11152--11255 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 28
11142 TTGACAGTCA
* * *
11152 TAACTTTTCTAAAATCACATTTTAACCTC
1 TAAC-TTTCAAAAATTATATTTTAACCTC
*
11181 AAAACTTCTCAAAAATTATATTTTGAACCT-
1 -TAACTT-TCAAAAATTATATTTT-AACCTC
*
11211 TGAACTTTCTAAAAATTATATTTTTACCTC
1 T-AACTTTC-AAAAATTATATTTTAACCTC
11241 TAACTTTCAAAAATT
1 TAACTTTCAAAAATT
11256 CCATTTTTGA
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
28 7 0.11
29 15 0.24
30 36 0.57
31 5 0.08
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.41
Consensus pattern (28 bp):
TAACTTTCAAAAATTATATTTTAACCTC
Found at i:11245 original size:29 final size:29
Alignment explanation
Indices: 11152--11527 Score: 181
Period size: 29 Copynumber: 12.8 Consensus size: 29
11142 TTGACAGTCA
* * * *
11152 TAACTTTTCTAAAATCACATTTTAACCTC
1 TAACTTTCCAAAAATTACATTTTTACCTC
* * *
11181 AAAAC-TTCTCAAAAATTATATTTTGAACCT-
1 -TAACTTTC-CAAAAATTACATTTT-TACCTC
* *
11211 TGAACTTTCTAAAAATTATATTTTTACCTC
1 T-AACTTTCCAAAAATTACATTTTTACCTC
*
11241 TAACTTT-CAAAAATTCCATTTTTGACC-C
1 TAACTTTCCAAAAATTACATTTTT-ACCTC
*
11269 TAATTTTTCCAAAAATTACATTTTTACC-C
1 TAA-CTTTCCAAAAATTACATTTTTACCTC
* *
11298 ATAAAC-TTCCTAAAATTCCATTTTTTACCT-
1 -T-AACTTTCCAAAAATTACA-TTTTTACCTC
* *
11328 TAATTTTCCAAAAATTACCA-TTTTACCCC
1 TAACTTTCCAAAAATTA-CATTTTTACCTC
* *
11357 TAAAC-ATCCAAAAATTACATTTTTACCCCC
1 T-AACTTTCCAAAAATTACATTTTTA-CCTC
* **
11387 AAAC-TTCCAAAAATTGTATTTTTGACCT-
1 TAACTTTCCAAAAATTACATTTTT-ACCTC
**
11415 TGATTTTTCC-AAAATTACCA-TTTTATCCT-
1 T-AACTTTCCAAAAATTA-CATTTTTA-CCTC
** * *
11444 TAAAC-TTCCATCAATTACATTTTTATCAC
1 T-AACTTTCCAAAAATTACATTTTTACCTC
*
11473 TGAAC-TTCCAAAAATTCCATTTTTTGACCTC
1 T-AACTTTCCAAAAATTACA-TTTTT-ACCTC
* * *
11504 GAATTTTCCCAAAATTACCATTTT
1 TAACTTTCCAAAAATTA-CATTTT
11528 ACCCCCAAAC
Statistics
Matches: 267, Mismatches: 49, Indels: 59
0.71 0.13 0.16
Matches are distributed among these distances:
28 36 0.13
29 124 0.46
30 78 0.29
31 27 0.10
32 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (29 bp):
TAACTTTCCAAAAATTACATTTTTACCTC
Found at i:11283 original size:58 final size:56
Alignment explanation
Indices: 11162--11556 Score: 233
Period size: 58 Copynumber: 6.8 Consensus size: 56
11152 TAACTTTTCT
* * * ** * * * *
11162 AAAATCACATTTTAACCTCAAAACTTCTCAAAAATTATATTTTGAACCTTGAACTTTCTA
1 AAAATTACATTTTTACC-CTAAACTTC-CAAAAATTCCATTTT-TACCCT-AATTTTCCA
* *
11222 AAAATTATATTTTTACCTCT-AACTTTCAAAAATTCCATTTTTGACCCTAATTTTTCCA
1 AAAATTACATTTTTACC-CTAAACTTCCAAAAATTCCATTTTT-ACCCTAA-TTTTCCA
* *
11280 AAAATTACATTTTTACCCATAAACTTCCTAAAATTCCATTTTTTACCTTAATTTTCCA
1 AAAATTACATTTTTACCC-TAAACTTCCAAAAATTCCA-TTTTTACCCTAATTTTCCA
* * * **
11338 AAAATTACCA-TTTTACCCCTAAACATCCAAAAATTACATTTTTACCCCCAAACTTCCA
1 AAAATTA-CATTTTTA-CCCTAAACTTCCAAAAATTCCATTTTTA-CCCTAATTTTCCA
** * *** * **
11396 AAAATTGTATTTTTGACCTTGATTTTTCC-AAAATTACCA-TTTTATCCTTAAACTTCCA
1 AAAATTACATTTTT-ACCCT-AAACTTCCAAAAATT-CCATTTTTA-CCCTAATTTTCCA
** * * * *
11454 TCAATTACATTTTTATCACTGAACTTCCAAAAATTCCATTTTTTGACCTCGAATTTTCCC
1 AAAATTACATTTTTA-CCCTAAACTTCCAAAAATTCCA-TTTTT-ACC-CTAATTTTCCA
* * *
11514 AAAATTACCA-TTTTACCCCCAAACTTCTAAAAATTTCATTTTT
1 AAAATTA-CATTTTTA-CCCTAAACTTCCAAAAATTCCATTTTT
11557 GATCTCGATT
Statistics
Matches: 260, Mismatches: 56, Indels: 39
0.73 0.16 0.11
Matches are distributed among these distances:
57 18 0.07
58 136 0.52
59 49 0.19
60 55 0.21
61 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (56 bp):
AAAATTACATTTTTACCCTAAACTTCCAAAAATTCCATTTTTACCCTAATTTTCCA
Found at i:11382 original size:87 final size:86
Alignment explanation
Indices: 11156--11556 Score: 346
Period size: 87 Copynumber: 4.6 Consensus size: 86
11146 CAGTCATAAC
* * * * * * * * *
11156 TTTTCTAAAATCA-CATTTTAACCTCAAAACTTCTCAAAAATTATATTTTGAACCTTGAACTTTC
1 TTTTCCAAAATTACCATTTT-ACCCCTAAACTTC-CAAAAATTACATTTTTACCCATAAAC-TTC
*
11220 TAAAAATT--ATATTTTTACCTCTAA
63 CAAAAATTCCAT-TTTTTACCT-TAA
* * **
11244 CTTTCAAAAATT-CCATTTTTGA-CCCTAATTTTTCCAAAAATTACATTTTTACCCATAAACTTC
1 TTTTCCAAAATTACCA-TTTT-ACCCCTAA-ACTTCCAAAAATTACATTTTTACCCATAAACTTC
*
11307 CTAAAATTCCATTTTTTACCTTAA
63 CAAAAATTCCATTTTTTACCTTAA
* **
11331 TTTTCCAAAAATTACCATTTTACCCCTAAACATCCAAAAATTACATTTTTACCCCCAAACTTCCA
1 TTTTCC-AAAATTACCATTTTACCCCTAAACTTCCAAAAATTACATTTTTACCCATAAACTTCCA
** * *
11396 AAAATTGTATTTTTGACCTTGAT
65 AAAATTCCATTTTTTACCTT-AA
* * ** * *
11419 TTTTCCAAAATTACCATTTTATCCTTAAACTTCCATCAATTACATTTTTA-TCACTGAACTTCCA
1 TTTTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATTACATTTTTACCCA-TAAACTTCCA
*
11483 AAAATTCCATTTTTTGACCTCGAA
65 AAAATTCCATTTTTT-ACCT-TAA
* * *
11507 TTTTCCCAAAATTACCATTTTACCCCCAAACTTCTAAAAATTTCATTTTT
1 TTTT-CCAAAATTACCATTTTACCCCTAAACTTCCAAAAATTACATTTTT
11557 GATCTCGATT
Statistics
Matches: 252, Mismatches: 48, Indels: 25
0.78 0.15 0.08
Matches are distributed among these distances:
86 1 0.00
87 123 0.49
88 77 0.31
89 51 0.20
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (86 bp):
TTTTCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATTACATTTTTACCCATAAACTTCCAA
AAATTCCATTTTTTACCTTAA
Found at i:11641 original size:58 final size:59
Alignment explanation
Indices: 11475--11644 Score: 184
Period size: 59 Copynumber: 2.9 Consensus size: 59
11465 TTTATCACTG
* * *
11475 AACTTCCAAAAATTCCATTTTTTGACCTCGAATTTTCCCAAAATTACCATTTTACCCCCA
1 AACTTCTAAAAATTTCA-TTTTTGACCTCGAATTTTCACAAAATTACCATTTTACCCCCA
* * * **
11535 AACTTCTAAAAATTTCATTTTTGATCTCGATTTTTCAAAAAATTACCATTTTACCCCTG
1 AACTTCTAAAAATTTCATTTTTGACCTCGAATTTTCACAAAATTACCATTTTACCCCCA
* * * *
11594 AA-TGTCT--AAAGTTCTATTTTTAACCTCGAACTTTCTCAAAATTACCATTTT
1 AACT-TCTAAAAATTTC-ATTTTTGACCTCGAATTTTCACAAAATTACCATTTT
11645 CCCATCGAGT
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
57 6 0.06
58 31 0.33
59 41 0.44
60 15 0.16
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.40
Consensus pattern (59 bp):
AACTTCTAAAAATTTCATTTTTGACCTCGAATTTTCACAAAATTACCATTTTACCCCCA
Found at i:11691 original size:30 final size:29
Alignment explanation
Indices: 11631--11694 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
11621 GAACTTTCTC
*
11631 AAAATTACCATTTTCCCATCGAGTGACCA
1 AAAATTACCATTTTCCCACCGAGTGACCA
*
11660 AAAATTACCATTTTACCCCCCGAGT-ATCCA
1 AAAATTACCATTTT-CCCACCGAGTGA-CCA
11690 AAAAT
1 AAAAT
11695 CATATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.27
Consensus pattern (29 bp):
AAAATTACCATTTTCCCACCGAGTGACCA
Found at i:11692 original size:29 final size:28
Alignment explanation
Indices: 11630--11692 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
11620 CGAACTTTCT
*
11630 CAAAATTACCATTTTCCCATCGAGTGAC
1 CAAAATTACCATTTTCCCACCGAGTGAC
*
11658 CAAAAATTACCATTTTACCCCCCGAGT-ATC
1 C-AAAATTACCATTTT-CCCACCGAGTGA-C
11688 CAAAA
1 CAAAA
11693 ATCATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 1 0.03
29 19 0.63
30 10 0.33
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25
Consensus pattern (28 bp):
CAAAATTACCATTTTCCCACCGAGTGAC
Found at i:11738 original size:33 final size:33
Alignment explanation
Indices: 11699--11771 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
11689 AAAAATCATA
11699 TTTAAACGTAACTCATGCGTTCAAGGATTGTAT
1 TTTAAACGTAACTCATGCGTTCAAGGATTGTAT
11732 TTTAAACGTAACTCATGCGTTCAAGGATTGTAT
1 TTTAAACGTAACTCATGCGTTCAAGGATTGTAT
11765 TTTAAAC
1 TTTAAAC
11772 TTTATTCAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
TTTAAACGTAACTCATGCGTTCAAGGATTGTAT
Found at i:21351 original size:18 final size:18
Alignment explanation
Indices: 21328--21363 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21318 GCATCTAATA
*
21328 TTGTTCCTTGTAATTATT
1 TTGTTCCTTGTAAATATT
21346 TTGTTCCTTGTAAATATT
1 TTGTTCCTTGTAAATATT
21364 CGGCATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.58
Consensus pattern (18 bp):
TTGTTCCTTGTAAATATT
Found at i:21878 original size:49 final size:48
Alignment explanation
Indices: 21805--22178 Score: 165
Period size: 49 Copynumber: 7.6 Consensus size: 48
21795 ACCATGAAAC
* *
21805 ATAAAGGGAAAGATTTAAGTCGCAACGGCAGATCCAGTACTGCAAAGAT
1 ATAAAGGGAAAGGTTCAAGTCGCAACGGCAGATCCAGTACT-CAAAGAT
* * * *
21854 TTAAAGGGAAAGGTTCAAGTCGCAATGGC-GAACCTAGTACCTCAGAAGAC
1 ATAAAGGGAAAGGTTCAAGTCGCAACGGCAGATCC-AGTA-CTCA-AAGAT
* * * *
21904 ATGAAGGGAAA-GATCTAAG-CTGCAACGACAGATCCAGTACCACAAAGAT
1 ATAAAGGGAAAGGTTC-AAGTC-GCAACGGCAGATCCAGTA-CTCAAAGAT
* * * * * *
21953 ACAAAGGGAAGGGTTTAAGTCGCAACGGC-GAACCTCTA-TAC-CACAGAA
1 ATAAAGGGAAAGGTTCAAGTCGCAACGGCAG-A--TCCAGTACTCAAAGAT
* * * * * *
22001 ACACGACGGGAAA-GATCTAAGATCGCAACGGTAAATCCAGTAC-CGTAAAGAC
1 ATA--AAGGGAAAGGTTC-AAG-TCGCAACGGCAGATCCAGTACTC--AAAGAT
* * * * *
22053 ACAAAGGGAAAGGTTTAAGTCGCAATGGC-GAACCTAGTAACTCAGAAGAC
1 ATAAAGGGAAAGGTTCAAGTCGCAACGGCAGATCC-AGT-ACTCA-AAGAT
* * * * * *
22103 ATGAAGGGAAA-GATCTAAGCCGCAACGACGGATCCAGTACCACAAAGAT
1 ATAAAGGGAAAGGTTC-AAGTCGCAACGGCAGATCCAGTA-CTCAAAGAT
* * *
22152 ACAAAGGGAAGGGTTTAAGTCGCAACG
1 ATAAAGGGAAAGGTTCAAGTCGCAACG
22179 ACGAACCCTA
Statistics
Matches: 242, Mismatches: 55, Indels: 56
0.69 0.16 0.16
Matches are distributed among these distances:
48 16 0.07
49 101 0.42
50 94 0.39
51 24 0.10
52 7 0.03
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (48 bp):
ATAAAGGGAAAGGTTCAAGTCGCAACGGCAGATCCAGTACTCAAAGAT
Found at i:21983 original size:99 final size:99
Alignment explanation
Indices: 21803--22582 Score: 899
Period size: 99 Copynumber: 7.9 Consensus size: 99
21793 GTACCATGAA
* * * * *** *
21803 ACATAAAGGGAAAGATTTAAGTCGCAACGGCAGATCCAGTACTGCAAAGATTTAAAGGGAAAGGT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAGGGT
*
21868 TCAAGTCGCAATGGCGAACCTAGTACCTCAGAAG
66 TTAAGTCGCAATGGCGAACCTAGTACCTCAGAAG
* * * *
21902 ACATGAAGGGAAAGATCTAAGCTGCAACGACAGATCCAGTACCACAAAGATACAAAGGGAAGGGT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAGGGT
* *
21967 TTAAGTCGCAACGGCGAACCTCTA-TACCACAGAA-
66 TTAAGTCGCAATGGCGAA-C-CTAGTACCTCAGAAG
* * * * * * *
22001 ACACGACGGGAAAGATCTAAGATCGCAACGGTAAATCCAGTACCGTAAAGACACAAAGGGAAAGG
1 ACATGAAGGGAAAGATCTAAG-CCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAGGG
*
22066 TTTAAGTCGCAATGGCGAACCTAGTAACTCAGAAG
65 TTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAG
* * * *
22101 ACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCACAAAGATACAAAGGGAAGGGT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAGGGT
* * *
22166 TTAAGTCGCAACGACGAACCCTA-TACCACAGAA-
66 TTAAGTCGCAATGGCGAA-CCTAGTACCTCAGAAG
* * * * * *
22199 ACACGACGAGAAAGATCTAAGACCGCAACGGTAGATCCAGTACCGCAAAGACACAAAAGGAAAGG
1 ACATGAAGGGAAAGATCTAAG-CCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAGGG
*
22264 TTTAAGTCGTAATGGCGAACCTAGTACCTCAGAAG
65 TTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAG
* * * * *
22299 AAATGAAGGGAAAGATCTAAGCCGCAACGGTAGATCCAGTACCACAAAGATACAAAAGGAAGGGT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAGGGT
* * *
22364 TTAAGTCGCAATGACGAACTCT-TTACCACAGAA-
66 TTAAGTCGCAATGGCGAAC-CTAGTACCTCAGAAG
* * * * * *
22397 ACACGACGGGAAAGATCTAAAACCGCAATGGCAGATCCAATACCGTAAAGACACAAAGGGAAGGG
1 ACATGAAGGGAAAGATCT-AAGCCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAGGG
*
22462 TTTAAGTCGCAATAGCGAACCTAGTACCTCAGAAG
65 TTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAG
* * * * * **
22497 ACATAAAGGGAAAGATTTAAGCCGTAATGAC-GAATCCAGTACCGCAAAGACACAAAGGGAAGAA
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCAG-ATCCAGTACCGCAAAGACACAAAGGGAAGGG
*
22561 TTTAAGTCGTAATGGCGAACCT
65 TTTAAGTCGCAATGGCGAACCT
22583 TTACCCTAGA
Statistics
Matches: 572, Mismatches: 95, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
98 43 0.08
99 408 0.71
100 118 0.21
101 3 0.01
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (99 bp):
ACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAGGGT
TTAAGTCGCAATGGCGAACCTAGTACCTCAGAAG
Found at i:22297 original size:198 final size:198
Alignment explanation
Indices: 21810--22569 Score: 1128
Period size: 198 Copynumber: 3.8 Consensus size: 198
21800 GAAACATAAA
* * * *** *
21810 GGGAAAGATTTAAG-TCGCAACGGCAGATCCAGTACTGCAAAGATTTAAAGGGAAAGGTTCAAGT
1 GGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAAGGTTTAAGT
*
21874 CGCAATGGCGAACCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGCTGCAACGACAGATCC
66 CGCAATGGCGAACCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGCCGCAACGACAGATCC
*
21939 AGTACCACAAAGATACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCTCTATACCACAGAAACA
131 AGTACCACAAAGATACAAAGGGAAGGGTTTAAGTCGCAACGACGAACC-CTATACCACAGAAACA
22004 CGAC
195 CGAC
* * * *
22008 GGGAAAGATCTAAGATCGCAACGGTAAATCCAGTACCGTAAAGACACAAAGGGAAAGGTTTAAGT
1 GGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAAGGTTTAAGT
* *
22073 CGCAATGGCGAACCTAGTAACTCAGAAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCC
66 CGCAATGGCGAACCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGCCGCAACGACAGATCC
22138 AGTACCACAAAGATACAAAGGGAAGGGTTTAAGTCGCAACGACGAACCCTATACCACAGAAACAC
131 AGTACCACAAAGATACAAAGGGAAGGGTTTAAGTCGCAACGACGAACCCTATACCACAGAAACAC
22203 GAC
196 GAC
* * *
22206 GAGAAAGATCTAAGACCGCAACGGTAGATCCAGTACCGCAAAGACACAAAAGGAAAGGTTTAAGT
1 GGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAAGGTTTAAGT
* * **
22271 CGTAATGGCGAACCTAGTACCTCAGAAGAAATGAAGGGAAAGATCTAAGCCGCAACGGTAGATCC
66 CGCAATGGCGAACCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGCCGCAACGACAGATCC
* * * *
22336 AGTACCACAAAGATACAAAAGGAAGGGTTTAAGTCGCAATGACGAACTCTTTACCACAGAAACAC
131 AGTACCACAAAGATACAAAGGGAAGGGTTTAAGTCGCAACGACGAACCCTATACCACAGAAACAC
22401 GAC
196 GAC
* * * * *
22404 GGGAAAGATCTAAAACCGCAATGGCAGATCCAATACCGTAAAGACACAAAGGGAAGGGTTTAAGT
1 GGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAAGGTTTAAGT
* * * * *
22469 CGCAATAGCGAACCTAGTACCTCAGAAGACATAAAGGGAAAGATTTAAGCCGTAATGAC-GAATC
66 CGCAATGGCGAACCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGCCGCAACGACAG-ATC
* * **
22533 CAGTACCGCAAAGACACAAAGGGAAGAATTTAAGTCG
130 CAGTACCACAAAGATACAAAGGGAAGGGTTTAAGTCG
22570 TAATGGCGAA
Statistics
Matches: 510, Mismatches: 50, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
197 1 0.00
198 358 0.70
199 151 0.30
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (198 bp):
GGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCGCAAAGACACAAAGGGAAAGGTTTAAGT
CGCAATGGCGAACCTAGTACCTCAGAAGACATGAAGGGAAAGATCTAAGCCGCAACGACAGATCC
AGTACCACAAAGATACAAAGGGAAGGGTTTAAGTCGCAACGACGAACCCTATACCACAGAAACAC
GAC
Found at i:22572 original size:49 final size:49
Alignment explanation
Indices: 22431--22579 Score: 160
Period size: 49 Copynumber: 3.0 Consensus size: 49
22421 GCAATGGCAG
* * ** *
22431 ATCCAATACCGTAAAGACACAAAGGGAAGGGTTTAAGTCGCAAT-AGCGA
1 ATCCAGTACCGCAAAGACACAAAGGGAAGAATTTAAGTCGTAATGA-CGA
* * *
22480 A-CCTAGTACCTCAGAAGACATAAAGGGAA-AGATTTAAGCCGTAATGACGA
1 ATCC-AGTACCGCA-AAGACACAAAGGGAAGA-ATTTAAGTCGTAATGACGA
*
22530 ATCCAGTACCGCAAAGACACAAAGGGAAGAATTTAAGTCGTAATGGCGA
1 ATCCAGTACCGCAAAGACACAAAGGGAAGAATTTAAGTCGTAATGACGA
22579 A
1 A
22580 CCTTTACCCT
Statistics
Matches: 82, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
48 2 0.02
49 39 0.48
50 38 0.46
51 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (49 bp):
ATCCAGTACCGCAAAGACACAAAGGGAAGAATTTAAGTCGTAATGACGA
Found at i:23277 original size:17 final size:17
Alignment explanation
Indices: 23254--23351 Score: 99
Period size: 17 Copynumber: 5.4 Consensus size: 17
23244 CCGGGTTCCT
23254 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
23272 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
23288 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
23305 TTTAAATTTAAATTTAATTTAAG
1 TTTAAATTT--A--T--TTTAAA
23328 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
23345 TTTAAAT
1 TTTAAAT
23352 AAAAAATGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
16 1 0.01
17 48 0.72
19 2 0.03
21 2 0.03
23 14 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:23291 original size:6 final size:6
Alignment explanation
Indices: 23282--23351 Score: 83
Period size: 6 Copynumber: 12.2 Consensus size: 6
23272 TTAAATTTGT
* * *
23282 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTTAAA TTT-AA TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
23328 TTTAAA TTT-AT TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
23352 AAAAAATGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
5 12 0.23
6 41 0.77
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:23302 original size:11 final size:11
Alignment explanation
Indices: 23272--23348 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
23262 TATTTTAAGA
*
23272 TTAAATTTGTT
1 TTAAATTTATT
*
23283 TTAAATTTAGAT
1 TTAAATTTA-TT
* *
23295 TT-ATTTTAAAT
1 TTAAATTT-ATT
*
23306 TTAAATTTAAAT
1 TTAAATTT-ATT
*
23318 TT-AATTTAAGT
1 TTAAATTT-ATT
23329 TTAAATTTATT
1 TTAAATTTATT
23340 TTAAATTTA
1 TTAAATTTA
23349 AATAAAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
11 37 0.66
12 19 0.34
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:23308 original size:23 final size:23
Alignment explanation
Indices: 23282--23351 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
23272 TTAAATTTGT
* *
23282 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAAATTTAATTTAAA
*
23305 TTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTAAATTTAATTTAAA
*
23328 TTTAAATTT-ATTTTAAATTTAAA
1 TTTAAATTTAAATTT-AATTTAAA
23351 T
1 T
23352 AAAAAATGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
22 4 0.10
23 37 0.90
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATTTAAA
Found at i:23976 original size:3 final size:3
Alignment explanation
Indices: 23961--24034 Score: 94
Period size: 3 Copynumber: 24.3 Consensus size: 3
23951 AAAACTATTC
*
23961 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
** * *
24010 ATA GCA TTA ATA ATA TTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
24035 CAAAAAGAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:25168 original size:30 final size:30
Alignment explanation
Indices: 25099--25199 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
25089 CTCAGAAGGT
* * * *
25099 CCCTAAACTGTCCAAAAATCATATTTTGA-
1 CCCTAAACTTTTCTAAAATCATATTTTAAC
*
25128 CCCTCAAACTTTTCTAAAATCACATTTTAAC
1 CCCT-AAACTTTTCTAAAATCATATTTTAAC
* * *
25159 CCCTAAACTTCTT-TAAAGTTATATTTTTAC
1 CCCTAAACTT-TTCTAAAATCATATTTTAAC
25189 CCCTAAACTTT
1 CCCTAAACTTT
25200 CCAAAATTCC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
29 5 0.08
30 49 0.82
31 6 0.10
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTTTCTAAAATCATATTTTAAC
Found at i:25229 original size:29 final size:29
Alignment explanation
Indices: 25197--25302 Score: 99
Period size: 30 Copynumber: 3.6 Consensus size: 29
25187 ACCCCTAAAC
*
25197 TTTCCAAAATTCCATTTTTGAACACAATT
1 TTTCCAAAATTCCATTTTTGACCACAATT
* * *
25226 TTTCCAAAAATTACATTTTT-ACCCCCAA-A
1 TTTCC-AAAATTCCATTTTTGA-CCACAATT
** * *
25255 CATCCAAAATTCCATTTTTGACCTCGATT
1 TTTCCAAAATTCCATTTTTGACCACAATT
25284 TTTCCAAAATTACCATTTT
1 TTTCCAAAATT-CCATTTT
25303 ACCCCTAAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
28 17 0.28
29 19 0.32
30 24 0.40
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.40
Consensus pattern (29 bp):
TTTCCAAAATTCCATTTTTGACCACAATT
Found at i:25271 original size:28 final size:28
Alignment explanation
Indices: 25099--25446 Score: 177
Period size: 29 Copynumber: 11.9 Consensus size: 28
25089 CTCAGAAGGT
*
25099 CCCTAAACTGTCCAAAAAT-CATATTTTGA-
1 CCCTAAACT-TCCAAAATTACAT-TTTT-AC
* * *
25128 CCCTCAAACTTTTCTAAAATCACATTTTAAC
1 CCCT-AAAC--TTCCAAAATTACATTTTTAC
* * *
25159 CCCTAAACTTCTTTAAAGTTATATTTTTAC
1 CCCTAAACTTC--CAAAATTACATTTTTAC
* *
25189 CCCTAAACTTTCCAAAATTCCATTTTTGAA
1 CCCTAAAC-TTCCAAAATTACATTTTT-AC
* **
25219 CAC-AATTTTTCCAAAAATTACATTTTTAC
1 CCCTAA-ACTTCC-AAAATTACATTTTTAC
* * *
25248 CCCCAAACATCCAAAATTCCATTTTTGAC
1 CCCTAAACTTCCAAAATTACATTTTT-AC
* * ***
25277 CTCGATTTTTCCAAAATTACCA-TTTTAC
1 CCCTAAACTTCCAAAATTA-CATTTTTAC
* *
25305 CCCTAAACTTCTAAAAATTACACTTTTAC
1 CCCTAAACTTC-CAAAATTACATTTTTAC
* *
25334 CCCTAAACTTCCAAAAAATT-TATTTTTAA
1 CCCTAAACTTCC--AAAATTACATTTTTAC
** * *
25363 CCC-AATTTTTTCAAAATTACAATTTTAC
1 CCCTAA-ACTTCCAAAATTACATTTTTAC
** *
25391 CCCTGCACTTCCAAAAATTACATTTTTAT
1 CCCTAAACTTCC-AAAATTACATTTTTAC
* *
25420 CCCTGAACTTCCAAAAATTCCATTTTT
1 CCCTAAACTTCC-AAAATTACATTTTT
25447 TACTCCGATT
Statistics
Matches: 242, Mismatches: 55, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
27 6 0.02
28 40 0.17
29 120 0.50
30 56 0.23
31 16 0.07
32 4 0.02
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (28 bp):
CCCTAAACTTCCAAAATTACATTTTTAC
Found at i:25321 original size:29 final size:29
Alignment explanation
Indices: 25227--25542 Score: 138
Period size: 29 Copynumber: 10.9 Consensus size: 29
25217 AACACAATTT
*
25227 TTCCAAAAATTA-CATTTTTACCCCCAAAC
1 TTCCAAAAATTACCA-TTTTACCCCTAAAC
* * * ***
25256 ATCC-AAAATT-CCATTTTTGACCTCGATTT
1 TTCCAAAAATTACCA-TTTT-ACCCCTAAAC
25285 TTCC-AAAATTACCATTTTACCCCTAAAC
1 TTCCAAAAATTACCATTTTACCCCTAAAC
*
25313 TTCTAAAAATTA-CACTTTTACCCCTAAAC
1 TTCCAAAAATTACCA-TTTTACCCCTAAAC
* * **
25342 TTCCAAAAAATTTA--TTTTTAACCC-AATTT
1 TTCC-AAAAA-TTACCATTTTACCCCTAA-AC
* * **
25371 TTTC-AAAATTACAATTTTACCCCTGCAC
1 TTCCAAAAATTACCATTTTACCCCTAAAC
* *
25399 TTCCAAAAATTA-CATTTTTATCCCTGAAC
1 TTCCAAAAATTACCA-TTTTACCCCTAAAC
* * ***
25428 TTCCAAAAATT-CCATTTTTTACTCCGATTTT
1 TTCCAAAAATTACCA--TTTTACCCCTA-AAC
**
25459 TTCTTAAAATTACCATTTTA-CCCTCAAAC
1 TTCCAAAAATTACCATTTTACCCCT-AAAC
* **
25488 TTCCAAAAATT-CCATTTTTGATCCC-AATT
1 TTCCAAAAATTACCA-TTTT-ACCCCTAAAC
* *
25517 TTTCAAAAATTACCATTTTAACCCTA
1 TTCCAAAAATTACCATTTTACCCCTA
25543 GGTATCCAAA
Statistics
Matches: 215, Mismatches: 49, Indels: 46
0.69 0.16 0.15
Matches are distributed among these distances:
26 3 0.01
27 4 0.02
28 44 0.20
29 120 0.56
30 26 0.12
31 15 0.07
32 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.39
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCCTAAAC
Found at i:25322 original size:58 final size:58
Alignment explanation
Indices: 25183--25542 Score: 229
Period size: 58 Copynumber: 6.2 Consensus size: 58
25173 AAAGTTATAT
* * * *
25183 TTTTACCCCTAAACTT-TCCAAAATTCCATTTTTGAACACAATTTTTCCAAAAATTACA
1 TTTTACCCCTAAACTTCT-AAAAATTCCATTTTTGACCCCGATTTTTCCAAAAATTACA
* * * *
25241 TTTTTACCCCCAAACATC-CAAAATTCCATTTTTGACCTCGATTTTTCC-AAAATTACCA
1 -TTTTACCCCTAAACTTCTAAAAATTCCATTTTTGACCCCGATTTTTCCAAAAATTA-CA
* * * *** *
25299 TTTTACCCCTAAACTTCTAAAAATTACACTTTT-ACCCCTAAACTTCCAAAAAATTTA-T
1 TTTTACCCCTAAACTTCTAAAAATTCCATTTTTGACCCCGATTTTTCC-AAAAA-TTACA
* ** * * * * *
25357 TTTTAACCC-AATTTTTTCAAAATTACAATTTT-ACCCCTGCA--CTTCCAAAAATTACA
1 TTTTACCCCTAAACTTCTAAAAATTCCATTTTTGACCCC-G-ATTTTTCCAAAAATTACA
* * * * * **
25413 TTTTTATCCCTGAACTTCCAAAAATTCCATTTTTTACTCCGATTTTTTCTTAAAATTACCA
1 -TTTTACCCCTAAACTTCTAAAAATTCCATTTTTGACCCCGA-TTTTTCCAAAAATTA-CA
* * *
25474 TTTTA-CCCTCAAACTTCCAAAAATTCCATTTTTGATCCCAATTTTT-CAAAAATTACCA
1 TTTTACCCCT-AAACTTCTAAAAATTCCATTTTTGACCCCGATTTTTCCAAAAATTA-CA
*
25532 TTTTAACCCTA
1 TTTTACCCCTA
25543 GGTATCCAAA
Statistics
Matches: 239, Mismatches: 44, Indels: 37
0.75 0.14 0.12
Matches are distributed among these distances:
55 3 0.01
56 5 0.02
57 68 0.28
58 81 0.34
59 36 0.15
60 44 0.18
61 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.39
Consensus pattern (58 bp):
TTTTACCCCTAAACTTCTAAAAATTCCATTTTTGACCCCGATTTTTCCAAAAATTACA
Found at i:25334 original size:86 final size:87
Alignment explanation
Indices: 25227--25506 Score: 336
Period size: 86 Copynumber: 3.2 Consensus size: 87
25217 AACACAATTT
* * *
25227 TTCCAAAAATTACATTTTTACCCCCAAACATCC-AAAATTCCATTTTTGACCTCGATTTTTCCAA
1 TTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCGATTTTTCCAA
25291 AATTACCATTTTACCCCTAAAC
66 AATTACCATTTTACCCCTAAAC
* * * * *
25313 TTCTAAAAATTACACTTTTACCCCTAAACTTCCAAAAAATT-TATTTTTAACC-CAATTTTTTCA
1 TTCCAAAAATTACATTTTTACCCCTAAACTTCC-AAAAATTCCATTTTTAACCTCGATTTTTCCA
* **
25376 AAATTACAATTTTACCCCTGCAC
65 AAATTACCATTTTACCCCTAAAC
* * *
25399 TTCCAAAAATTACATTTTTATCCCTGAACTTCCAAAAATTCCATTTTTTA-CTCCGATTTTTTCT
1 TTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCT-CGA-TTTTTC-
*
25463 TAAAATTACCATTTTA-CCCTCAAAC
63 CAAAATTACCATTTTACCCCT-AAAC
*
25488 TTCCAAAAATTCCATTTTT
1 TTCCAAAAATTACATTTTT
25507 GATCCCAATT
Statistics
Matches: 162, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
85 8 0.05
86 94 0.58
87 11 0.07
88 15 0.09
89 34 0.21
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.39
Consensus pattern (87 bp):
TTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCGATTTTTCCAA
AATTACCATTTTACCCCTAAAC
Found at i:25445 original size:57 final size:56
Alignment explanation
Indices: 25181--25446 Score: 157
Period size: 57 Copynumber: 4.6 Consensus size: 56
25171 TTAAAGTTAT
* ** **
25181 ATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGAACACAAT-TTTTCCAAAAATTAC
1 ATTTTTACCCCTAAAC-TTCCAAAATTCCACTTTT--AC-CCCTGACTTCCAAAAATTAC
* * * * *
25240 ATTTTTACCCCCAAACATCCAAAATTCCATTTTTGACCTC-GATTTTTCC-AAAATTACC
1 ATTTTTACCCCTAAACTTCCAAAATTCCACTTTT-ACCCCTGA--CTTCCAAAAATTA-C
* * * *
25298 A-TTTTACCCCTAAACTTCTAAAAATTACACTTTTACCCCTAAACTTCCAAAAAATT-T
1 ATTTTTACCCCTAAACTTC-CAAAATTCCACTTTTACCCCT-GACTTCC-AAAAATTAC
* ** * * *
25355 ATTTTTAACCC-AATTTTTTCAAAATTACAATTTTACCCCTGCACTTCCAAAAATTAC
1 ATTTTTACCCCTAA-ACTTCCAAAATTCCACTTTTACCCCTG-ACTTCCAAAAATTAC
* * *
25412 ATTTTTATCCCTGAACTTCCAAAAATTCCATTTTT
1 ATTTTTACCCCTAAACTTCC-AAAATTCCACTTTT
25447 TACTCCGATT
Statistics
Matches: 162, Mismatches: 30, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
56 8 0.05
57 73 0.45
58 59 0.36
59 22 0.14
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (56 bp):
ATTTTTACCCCTAAACTTCCAAAATTCCACTTTTACCCCTGACTTCCAAAAATTAC
Found at i:25478 original size:60 final size:58
Alignment explanation
Indices: 25402--25541 Score: 176
Period size: 60 Copynumber: 2.4 Consensus size: 58
25392 CCTGCACTTC
* * * *
25402 CAAAAATTA-CATTTTTATCCCT-GAACTTCCAAAAATTCCATTTTTTACTCCGATTTTTT
1 CAAAAATTACCA-TTTTA-CCCTCAAACTTCCAAAAATTCCATTTTTGA-TCCCAATTTTT
*
25461 CTTAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATCCCAATTTTT
1 C-AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATCCCAATTTTT
25520 CAAAAATTACCATTTTAACCCT
1 CAAAAATTACCATTTT-ACCCT
25542 AGGTATCCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
58 14 0.20
59 20 0.28
60 35 0.49
61 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATCCCAATTTTT
Found at i:33452 original size:17 final size:17
Alignment explanation
Indices: 33430--33471 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
33420 CCATACTATT
33430 GAACTTACTAAGTTATA
1 GAACTTACTAAGTTATA
33447 GAACTTACTAAGTTATA
1 GAACTTACTAAGTTATA
*
33464 AAACTTAC
1 GAACTTAC
33472 CACAGTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (17 bp):
GAACTTACTAAGTTATA
Found at i:42077 original size:49 final size:49
Alignment explanation
Indices: 41935--42086 Score: 128
Period size: 49 Copynumber: 3.1 Consensus size: 49
41925 CTTAAATATC
* * *
41935 TCCCTTCATGGTTCTGAGGTACAAGGTTCGCCATTGCGGCTTAAACATTT
1 TCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAAC-CTT
** * * * ** *
41985 TCCCTTCATTGTCGCCT-TGGTAC-TGGATTCACCGCTACGACTTAAACCTT
1 TCCCTTCA-TG-CTTCTGAGGTACAAGG-TTCGCCATTGCGACTTAAACCTT
* * *
42035 TCCCTTCATGCTTCTGAGGTACAAGGTTCGCCTTTGTGACTTAAATCTT
1 TCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT
42084 TCC
1 TCC
42087 GTTTATATCT
Statistics
Matches: 76, Mismatches: 21, Indels: 11
0.70 0.19 0.10
Matches are distributed among these distances:
48 3 0.04
49 27 0.36
50 22 0.29
51 22 0.29
52 2 0.03
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (49 bp):
TCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT
Found at i:42079 original size:100 final size:100
Alignment explanation
Indices: 41832--42066 Score: 292
Period size: 100 Copynumber: 2.4 Consensus size: 100
41822 TGGCTTAGAT
* * * * * *
41832 CTTTCGCTTCGTGCTT-TCGAGGTACAAGGTTCACCGTGGCGGCATAAAAATTTTCCCTTCATTA
1 CTTTCCCTTCATGCTTCT-GAGGTACAAGGTTCGCCATTGCGGCTTAAAAATTTTCCCTTCATTA
* * * * * *
41896 TCGTCATGGTACTGGATTTACCGTTGCGGCTTAAAT
65 TCGCCATGGTACTGGATTCACCGCTACGACTTAAAC
* * * * *
41932 ATCTCCCTTCATGGTTCTGAGGTACAAGGTTCGCCATTGCGGCTTAAACATTTTCCCTTCATTGT
1 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGGCTTAAAAATTTTCCCTTCATTAT
*
41997 CGCCTTGGTACTGGATTCACCGCTACGACTTAAAC
66 CGCCATGGTACTGGATTCACCGCTACGACTTAAAC
42032 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCC
1 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCC
42067 TTTGTGACTT
Statistics
Matches: 113, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
100 112 0.99
101 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.34
Consensus pattern (100 bp):
CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGGCTTAAAAATTTTCCCTTCATTAT
CGCCATGGTACTGGATTCACCGCTACGACTTAAAC
Found at i:45307 original size:18 final size:18
Alignment explanation
Indices: 45284--45319 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
45274 TTCTCGGTTA
45284 ATTGTGAGATAAACCGAG
1 ATTGTGAGATAAACCGAG
45302 ATTGTGAGATAAACCGAG
1 ATTGTGAGATAAACCGAG
45320 CGATATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
ATTGTGAGATAAACCGAG
Done.