Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold295
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: 1524207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:274185 original size:154 final size:151
Alignment explanation
Indices: 273999--274427 Score: 510
Period size: 152 Copynumber: 2.8 Consensus size: 151
273989 TTTTCTATTC
* * *
273999 CGTAAATTT-TTCGATAGGATTTTTCTAAGTTTATAATTTTCAAAATTCTTCAAATATTATTGTT
1 CGTAAATTTCTTCGGTATGATTTTTCTAGGTTTATAATTTTCAAAATTCTTCAAATATTATTGTT
* * * *
274063 TAATTCATATTAAATCAGTTTTGAAAAAATCAATTTATTTTATGAGTTTTAGGATTTTTTCTATT
66 TAATTCATATTAAATCAGTTTTGAAAAATTTAATTTATTTTATGAGTTTTAGAATTTTTT-GA-T
*
274128 ATCAAGATACAGA-GATTTTTACTT
129 ACCAAGATACA-ACGATTTTTAC-T
*
274152 CGTAAATTTCTCCGGTATGATTTTTCTAGGTTTATAATTTTCAAAATTCTTCAAATATTATTGTT
1 CGTAAATTTCTTCGGTATGATTTTTCTAGGTTTATAATTTTCAAAATTCTTCAAATATTATTGTT
*
274217 TAACTCATATTAAATCAGTTTTGAAAAATTTAATTTATTTTATGAGTTTTAGAATTTTTTGATAC
66 TAATTCATATTAAATCAGTTTTGAAAAATTTAATTTATTTTATGAGTTTTAGAATTTTTTGATAC
* *
274282 CAAGATGCAACGCTTTTTACT
131 CAAGATACAACGATTTTTACT
* * * * ** *
274303 CTGTAAATTTCTTCGGT-TAGATTTTTCTCGATTTA-AGATTTTTAAAACTAATCAAATATTTTT
1 C-GTAAATTTCTTCGGTAT-GATTTTTCTAGGTTTATA-ATTTTCAAAATTCTTCAAATATTATT
* * * * * * *
274366 ATTAAATTAATATTAAATCAATTTATG-ATAATTTAATTTATTTTATAAGTTTT-GCATTTTTT
63 GTTTAATTCATATTAAATCAGTTT-TGAAAAATTTAATTTATTTTATGAGTTTTAGAATTTTTT
274428 TATAAAACAC
Statistics
Matches: 242, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
151 13 0.05
152 110 0.45
153 12 0.05
154 107 0.44
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (151 bp):
CGTAAATTTCTTCGGTATGATTTTTCTAGGTTTATAATTTTCAAAATTCTTCAAATATTATTGTT
TAATTCATATTAAATCAGTTTTGAAAAATTTAATTTATTTTATGAGTTTTAGAATTTTTTGATAC
CAAGATACAACGATTTTTACT
Found at i:276210 original size:18 final size:18
Alignment explanation
Indices: 276183--276220 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
276173 ATATTCCTTC
276183 TACTTATTACTCATCTAA
1 TACTTATTACTCATCTAA
* *
276201 TACTTGTTACTCATTTAA
1 TACTTATTACTCATCTAA
276219 TA
1 TA
276221 AATATGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (18 bp):
TACTTATTACTCATCTAA
Found at i:277735 original size:19 final size:19
Alignment explanation
Indices: 277710--277768 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
277700 TTGTATCGAT
*
277710 ACATTGTATTGATACATGT
1 ACATTGTATTGATACATGA
* *
277729 TCATTGTATCGATACATGA
1 ACATTGTATTGATACATGA
*
277748 ACAAATGTATTGATACATGA
1 AC-ATTGTATTGATACATGA
277768 A
1 A
277769 ATTAGCAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (19 bp):
ACATTGTATTGATACATGA
Found at i:277762 original size:20 final size:19
Alignment explanation
Indices: 277714--277768 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
277704 ATCGATACAT
** *
277714 TGTATTGATACATGTTCAT
1 TGTATTGATACATGAACAA
*
277733 TGTATCGATACATGAACAAA
1 TGTATTGATACATGAAC-AA
277753 TGTATTGATACATGAA
1 TGTATTGATACATGAA
277769 ATTAGCAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
TGTATTGATACATGAACAA
Found at i:277834 original size:13 final size:13
Alignment explanation
Indices: 277816--277840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277806 CATGACACAT
277816 TGTATCGATACAA
1 TGTATCGATACAA
277829 TGTATCGATACA
1 TGTATCGATACA
277841 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:277838 original size:33 final size:33
Alignment explanation
Indices: 277796--277860 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
277786 TACCACTATT
*
277796 TGTATCGATACATGACA-CATTGTATCGATACAA
1 TGTATCGATACATGA-AGAATTGTATCGATACAA
277829 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCGATACATGAAGAATTGTATCGATACA
277861 TTGTCCCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATGAAGAATTGTATCGATACAA
Found at i:283746 original size:13 final size:13
Alignment explanation
Indices: 283728--283754 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
283718 ATATTATGCT
283728 TTGTATCGATACA
1 TTGTATCGATACA
283741 TTGTATCGATACA
1 TTGTATCGATACA
283754 T
1 T
283755 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:283763 original size:19 final size:19
Alignment explanation
Indices: 283739--283795 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
283729 TGTATCGATA
*
283739 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGAT
*
283758 CATTGTATCGATATATGGAT
1 CATTGTATCGATACAT-GAT
* *
283778 AATTGTATCGACACATGA
1 CATTGTATCGATACATGA
283796 AATTGGCAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:283784 original size:20 final size:19
Alignment explanation
Indices: 283735--283800 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
283725 GCTTTGTATC
283735 GATACATTGTATCGATACAT
1 GATA-ATTGTATCGATACAT
* * *
283755 GTTCATTGTATCGATATAT
1 GATAATTGTATCGATACAT
*
283774 GGATAATTGTATCGACACAT
1 -GATAATTGTATCGATACAT
283794 GA-AATTG
1 GATAATTG
283801 GCAGTAGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 5 0.13
19 16 0.42
20 17 0.45
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
GATAATTGTATCGATACAT
Found at i:283862 original size:13 final size:13
Alignment explanation
Indices: 283846--283891 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
283836 TGGTACAATA
283846 TATCGATACATTG
1 TATCGATACATTG
283859 TATCGATACA-TG
1 TATCGATACATTG
283871 -AT-G--A-ATTG
1 TATCGATACATTG
283879 TATCGATACATTG
1 TATCGATACATTG
283892 CTTATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
7 1 0.04
8 3 0.11
9 2 0.07
10 2 0.07
11 2 0.07
12 3 0.11
13 14 0.52
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:283883 original size:33 final size:33
Alignment explanation
Indices: 283823--283891 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
283813 CTACCACTGT
*
283823 TTGTATCGATACATGGTACAATATATCGATACA
1 TTGTATCGATACATGATACAATATATCGATACA
* *
283856 TTGTATCGATACATGATGA-ATTGTATCGATACA
1 TTGTATCGATACATGAT-ACAATATATCGATACA
283889 TTG
1 TTG
283892 CTTATAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATATATCGATACA
Found at i:289230 original size:20 final size:21
Alignment explanation
Indices: 289188--289230 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
289178 TATTAAAAAG
*
289188 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAATGAA
289209 TTAGCTAA-GAAAAACAAT-AA
1 TTAGCTAATG-AAAACAATGAA
289229 TT
1 TT
289231 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (21 bp):
TTAGCTAATGAAAACAATGAA
Found at i:293155 original size:13 final size:13
Alignment explanation
Indices: 293134--293173 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
293124 ACAACATTCC
293134 TTATATCGATACA
1 TTATATCGATACA
*
293147 TTGTATCGATACA
1 TTATATCGATACA
293160 TTATATCGATACA
1 TTATATCGATACA
293173 T
1 T
293174 GGGTTACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (13 bp):
TTATATCGATACA
Found at i:295065 original size:22 final size:22
Alignment explanation
Indices: 295040--295081 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
295030 TTTTTTAAGA
295040 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGGGAGAAATGC
*
295062 TTTGATAAAGGGGGAGAAAT
1 TTTGACAAAGGGGGAGAAAT
295082 ATGTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (22 bp):
TTTGACAAAGGGGGAGAAATGC
Found at i:295690 original size:13 final size:13
Alignment explanation
Indices: 295672--295698 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
295662 ACATTATGCT
295672 TTGTATCGATACA
1 TTGTATCGATACA
295685 TTGTATCGATACA
1 TTGTATCGATACA
295698 T
1 T
295699 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:295695 original size:33 final size:32
Alignment explanation
Indices: 295653--295716 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
295643 CTCACCCAAA
*
295653 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
295686 TGTATCGATACATGTTCATTGTATCGATACA
1 TGTATCGATACATGTTCATTGTATCGATACA
295717 CGGACAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:295707 original size:19 final size:19
Alignment explanation
Indices: 295682--295738 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
295672 TTGTATCGAT
*
295682 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
295701 TCATTGTATCGATACACGG
1 ACATTGTATCGATACATGG
295720 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
295739 AAATTGGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:295815 original size:33 final size:33
Alignment explanation
Indices: 295768--295836 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
295758 CTACCACTGT
*
295768 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
* *
295801 TTGTGTCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
295834 TTG
1 TTG
295837 CCTATAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:299479 original size:33 final size:33
Alignment explanation
Indices: 299426--299494 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
299416 AGTTGATCAC
* * *
299426 TTCACTTTCGCAGCGTATGGATAAGCATTTTAG
1 TTCACTTTCGCAGCGCATGGATAAGAACTTTAG
* * *
299459 TTCATTTTCGCAGTGCATGGATGAGAACTTTAG
1 TTCACTTTCGCAGCGCATGGATAAGAACTTTAG
299492 TTC
1 TTC
299495 TCTTAACCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (33 bp):
TTCACTTTCGCAGCGCATGGATAAGAACTTTAG
Found at i:300279 original size:21 final size:22
Alignment explanation
Indices: 300255--300304 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
300245 TTTCAATAAG
*
300255 TGTTTTTGAG-TTATGAA-CAAA
1 TGTTTTTGAGCTT-TAAATCAAA
*
300276 TGTTTTCGAGCTTTAAATCAAA
1 TGTTTTTGAGCTTTAAATCAAA
300298 TGTTTTT
1 TGTTTTT
300305 AAGTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (22 bp):
TGTTTTTGAGCTTTAAATCAAA
Found at i:300566 original size:13 final size:13
Alignment explanation
Indices: 300548--300572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
300538 CATGACACAT
300548 TGTATCGATACAA
1 TGTATCGATACAA
300561 TGTATCGATACA
1 TGTATCGATACA
300573 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:303277 original size:222 final size:222
Alignment explanation
Indices: 302891--303334 Score: 879
Period size: 222 Copynumber: 2.0 Consensus size: 222
302881 ATCATTAGTA
302891 AAGATATAATGATTATAGGATTTTACAATGCCTCCGATGAAAAATTGTTGTCAAAGAAGCTAAAT
1 AAGATATAATGATTATAGGATTTTACAATGCCTCCGATGAAAAATTGTTGTCAAAGAAGCTAAAT
302956 ATTAATACTCAATGACTCATCTTTGATAGTTTTTGGTCAATAGCTTCATAGCAATCTTGGATCAC
66 ATTAATACTCAATGACTCATCTTTGATAGTTTTTGGTCAATAGCTTCATAGCAATCTTGGATCAC
303021 TAGAAAACAAAAAAACAATATCCCATTAGTTAAAGCTATTTTAAAAATTTGAGTATCATTTTAAA
131 TAGAAAACAAAAAAACAATATCCCATTAGTTAAAGCTATTTTAAAAATTTGAGTATCATTTTAAA
303086 TTATTATATATTTGTCTATTCAATATC
196 TTATTATATATTTGTCTATTCAATATC
303113 AAGATATAATGATTATAGGATTTTACAATGCCTCCGATGAAAAATTGTTGTCAAAGAAGCTAAAT
1 AAGATATAATGATTATAGGATTTTACAATGCCTCCGATGAAAAATTGTTGTCAAAGAAGCTAAAT
303178 ATTAATACTCAATGACTCATCTTTGATAGTTTTTGGTCAATAGCTTCATAGCAATCTTGGATCAC
66 ATTAATACTCAATGACTCATCTTTGATAGTTTTTGGTCAATAGCTTCATAGCAATCTTGGATCAC
303243 TAGAAAACAAAAAAACAATATCCCATTAGTTAAAGCTATTTTAAAAATTTGAGTATCATTTTAAA
131 TAGAAAACAAAAAAACAATATCCCATTAGTTAAAGCTATTTTAAAAATTTGAGTATCATTTTAAA
*
303308 TTATTATATATTTGTGTATTCAATATC
196 TTATTATATATTTGTCTATTCAATATC
303335 CTTATTAAAC
Statistics
Matches: 221, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 221 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (222 bp):
AAGATATAATGATTATAGGATTTTACAATGCCTCCGATGAAAAATTGTTGTCAAAGAAGCTAAAT
ATTAATACTCAATGACTCATCTTTGATAGTTTTTGGTCAATAGCTTCATAGCAATCTTGGATCAC
TAGAAAACAAAAAAACAATATCCCATTAGTTAAAGCTATTTTAAAAATTTGAGTATCATTTTAAA
TTATTATATATTTGTCTATTCAATATC
Found at i:305848 original size:20 final size:20
Alignment explanation
Indices: 305823--305874 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
305813 TCACAATTTG
* * *
305823 TATCGACACATTCTTCATTA
1 TATCGATACATTCCTCAATA
*
305843 TATCGATACATTCCTCAATG
1 TATCGATACATTCCTCAATA
305863 TATCGATACATT
1 TATCGATACATT
305875 TAGGCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (20 bp):
TATCGATACATTCCTCAATA
Found at i:308298 original size:79 final size:78
Alignment explanation
Indices: 308207--308900 Score: 639
Period size: 79 Copynumber: 8.8 Consensus size: 78
308197 TTTATTTCCA
* * * * *
308207 AGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGAGGATACTCTAG
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAA
308272 CCCCGTTATTTCTG
66 CCCCGTTATTT-TG
* * * * * * * *
308286 AGAGGATACTCCAATCCTGATTTTAATTCCAAAACATTAATTTTTCATAATCGAGAATACTCTAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAA
*
308351 CCCCGTTATTTTCA
66 CCCCGTTATTTT-G
* * * * *
308365 AGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACCAATTTTCCACAATCGAGAATACTCCAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAA
308430 CCCCGTTATTTTTG
66 CCCCGTTA-TTTTG
* * * ** *
308444 AGGGGATA-TGCCAACCTCGGTTTTATTTCCAAAACACCAAAATTTCACAACCGAGGATACTCCA
1 AGGGGATACT-CCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCA
308508 ACCCCGTTATTTTTG
65 ACCCCGTTA-TTTTG
* * * * * *
308523 AAGGGATACTCAAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAA
308588 CCCCGTTATTTTCG
66 CCCCGTTATTTT-G
* * * * * *
308602 AGGGGATACTCCAACTCTGGTTTTATTTCTAAAACA-TCGATTTTTCACAA-CTGGGGATACTCC
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACT-AATTTTTCACAATC-GAGGATACTCC
*
308665 AACCCTGTTATTTTCG
64 AACCCCGTTATTTT-G
* * * * * *
308681 AGGGAATACTCCAACCTCGATTTTATTTTCAAAACACTGATTTTTTACAATC-AGGGATACTCTA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGA-GGATACTCCA
**
308745 ACCCCGTTATTTCCA
65 ACCCCGTTATTT-TG
* * ** *
308760 AGGGAATATTTTAACCCCGATTTTATTTCCAAAACACTAA-TTTTCTACAATTG-GGAATACTCC
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTC-ACAATCGAGG-ATACTCC
* *
308823 AACCCCTTTATTTCCG
64 AACCCCGTTATTT-TG
* ** * * * * *
308839 AGGGGATAC-CCTAATCTTGACTTTATTTCTAAAACA-TCAATTTTCCATAATCGGGGATACTC
1 AGGGGATACTCC-AACCCCGATTTTATTTCCAAAACACT-AATTTTTCACAATCGAGGATACTC
308901 TAACTCCGGT
Statistics
Matches: 515, Mismatches: 82, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
78 14 0.03
79 488 0.95
80 13 0.03
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (78 bp):
AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAA
CCCCGTTATTTTG
Found at i:308468 original size:158 final size:158
Alignment explanation
Indices: 308198--308900 Score: 713
Period size: 158 Copynumber: 4.4 Consensus size: 158
308188 ATTCTTGTTT
* * * * *
308198 TTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGAGG
1 TTATTTTCAAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGG
* * * * * **
308263 ATACTCTAGCCCCGTTATTTCTGAGAGGATACTCCAATCCT-GATTTTAATTCCAAAACATTAAT
66 ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCTCGATTTTATTTCCAAAACACCAAT
* *
308327 TTTTCATAATCGAGAATACTCTAACCCCG
130 TTTTCACAATCGAGAATACTCCAACCCCG
* * * *
308356 TTATTTTCAAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACCAATTTTCCACAATCGAGA
1 TTATTTTCAAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGG
** * *
308421 ATACTCCAACCCCGTTATTTTTGAGGGGATA-TGCCAACCTCGGTTTTATTTCCAAAACACCAAA
66 ATACTCCAACCCCGTTATTTCCGAGGGGATACT-CCAACCTCGATTTTATTTCCAAAACACCAAT
* * *
308485 ATTTCACAACCGAGGATACTCCAACCCCG
130 TTTTCACAATCGAGAATACTCCAACCCCG
* * *
308514 TTATTTTTGAA-GGGATACTCAAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGG
1 TTA-TTTTCAAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAG
* * * * *
308578 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CTCTGGTTTTATTTCTAAAACATCGA
65 GATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTC-GATTTTATTTCCAAAACACCAA
* * *
308642 TTTTTCACAA-CTGGGGATACTCCAACCCTG
129 TTTTTCACAATC-GAGAATACTCCAACCCCG
* * ** *
308672 TTATTTTCGAGGGAATACTCCAACCTCGATTTTATTTTCAAAACACTGATTTTTTACAATC-AGG
1 TTATTTTCAAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGA-G
* * * * ** * *
308736 GATACTCTAACCCCGTTATTTCCAAGGGAATATTTTAACCCCGATTTTATTTCCAAAACACTAA-
65 GATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAAT
* * *
308800 TTTTCTACAATTGGGAATACTCCAACCCCT
130 TTTTC-ACAATCGAGAATACTCCAACCCCG
* * * * * * * * *
308830 TTATTTCCGAGGGGATAC-CCTAATCTTGACTTTA-TTTCTAAAACATCAATTTTCCATAATCGG
1 TTATTTTCAAGGGGATACTCC-AACCTCGATTTTATTTTC-AAAACACCAATTTTTCACAATCGA
308893 GGATACTC
64 GGATACTC
308901 TAACTCCGGT
Statistics
Matches: 458, Mismatches: 73, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
157 24 0.05
158 425 0.93
159 9 0.02
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (158 bp):
TTATTTTCAAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGG
ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATT
TTTCACAATCGAGAATACTCCAACCCCG
Found at i:308592 original size:237 final size:236
Alignment explanation
Indices: 308198--308900 Score: 828
Period size: 237 Copynumber: 3.0 Consensus size: 236
308188 ATTCTTGTTT
* * * *
308198 TTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGAGG
1 TTATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACTAATTTTTCACAATCGAGG
* * * * *
308263 ATACTCTAGCCCCGTTATTTCTG-AGAGGATACTCCAATCCT-GATTTTAATTCCAAAACATTAA
66 ATACTCTAACCCCGTTATTTTTGAAG-GGATACT-CAAACCTCGATTTTATTTCCAAAACACTAA
* * * *
308326 TTTTTCATAATCGAGAATACTCTAACCCCGTTATTTTCAAGGGGATACTCCAACCTCGGTTTTAT
129 TTTTTCACAATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CTCGGTTTTAT
* * * *
308391 TTCCAAAACACCAATTTTCCACAATCGAGAATACTCCAACCCCG
193 TTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCCCG
* * * ** *
308435 TTATTTTTGAGGGGATA-TGCCAACCTCGGTTTTATTTCCAAAACACCAAAATTTCACAACCGAG
1 TTATTTTCGAGGGGATACT-CCAACCTCGGTTTTATTTTCAAAACACTAATTTTTCACAATCGAG
* * *
308499 GATACTCCAACCCCGTTATTTTTGAAGGGATACTCAAACCTCGATTTTATTTTCAAAACACCAAT
65 GATACTCTAACCCCGTTATTTTTGAAGGGATACTCAAACCTCGATTTTATTTCCAAAACACTAAT
*
308564 TTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTCTGGTTTTATT
130 TTTTCACAATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTC-GGTTTTATT
* * *
308629 TCTAAAACATCGATTTTTCACAA-CTGGGGATACTCCAACCCTG
194 TCTAAAACATCAATTTTCCACAATC-GGGGATACTCCAACCCCG
* * * *
308672 TTATTTTCGAGGGAATACTCCAACCTCGATTTTATTTTCAAAACACTGATTTTTTACAATC-AGG
1 TTATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACTAATTTTTCACAATCGA-G
** * ** *
308736 GATACTCTAACCCCGTTA-TTTCCAAGGGAATATTTTAACCCCGATTTTATTTCCAAAACACTAA
65 GATACTCTAACCCCGTTATTTTTGAAGGG-ATACTCAAACCTCGATTTTATTTCCAAAACACTAA
* * * * **
308800 -TTTTCTACAATTGGGAATACTCCAACCCCTTTATTTCCGAGGGGATAC-CCTAATCTTGACTTT
129 TTTTTC-ACAATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGATACTCC-AA-CTCGGTTTT
*
308863 ATTTCTAAAACATCAATTTTCCATAATCGGGGATACTC
191 ATTTCTAAAACATCAATTTTCCACAATCGGGGATACTC
308901 TAACTCCGGT
Statistics
Matches: 395, Mismatches: 59, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
236 27 0.07
237 362 0.92
238 6 0.02
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (236 bp):
TTATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACTAATTTTTCACAATCGAGG
ATACTCTAACCCCGTTATTTTTGAAGGGATACTCAAACCTCGATTTTATTTCCAAAACACTAATT
TTTCACAATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTCGGTTTTATTTC
TAAAACATCAATTTTCCACAATCGGGGATACTCCAACCCCG
Found at i:308924 original size:130 final size:130
Alignment explanation
Indices: 308771--309030 Score: 346
Period size: 130 Copynumber: 2.0 Consensus size: 130
308761 GGGAATATTT
* * *
308771 TAACCCCGATTTTATTTCCAAAACA-CTAATTTTCTACAATTGGGAATACTCCAACCCCTTTATT
1 TAACCCCGATTTTATTTCCAAAACATCGAATTTTC-ACAATCGGGAATACTCCAACCCCATTATT
* * *
308835 TCCGA-GGGGATAC-CCTAATCTTGACTTTATTTCTAAAACATCAATTTTCCATAATCGGGGATA
65 TCC-ATGGGGATACTCC-AACCTCGACTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATA
308898 CTC
128 CTC
* * * *
308901 TAACTCCGGTTTTATTTCCAAAACATCGAATTTTCACCATCGGGGATACTCCAACCCCATTATTT
1 TAACCCCGATTTTATTTCCAAAACATCGAATTTTCACAATCGGGAATACTCCAACCCCATTATTT
** * *
308966 CCATGGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTC
66 CCATGGGGATACTCCAACCTCGACTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTC
309031 CAATCCCGTT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
129 1 0.01
130 102 0.90
131 10 0.09
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (130 bp):
TAACCCCGATTTTATTTCCAAAACATCGAATTTTCACAATCGGGAATACTCCAACCCCATTATTT
CCATGGGGATACTCCAACCTCGACTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTC
Found at i:308974 original size:79 final size:79
Alignment explanation
Indices: 308891--309063 Score: 253
Period size: 79 Copynumber: 2.2 Consensus size: 79
308881 TTCCATAATC
*
308891 GGGGATACTCTAA-CTCCGGTTTTATTTCCAAAACATCGAATTTT-CACCATCGGGGATACTCCA
1 GGGGATACTCCAACCT-CGGTTTTATTTCCAAAACATCG-ATTTTCCACCATCGGGGATACTCCA
308954 ACCCCATTATTTC-CA
64 ACCCCATTATTTCTCA
*
308969 TGGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAA
1 -GGGGATACTCCAACCTCGGTTTTATTTCCAAAACATCGATTTTCCACCATCGGGGATACTCCAA
* * *
309034 TCCCGTTATTTCTGA
65 CCCCATTATTTCTCA
309049 GGGGATACTCCAACC
1 GGGGATACTCCAACC
309064 CTATTTTTTA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
78 5 0.06
79 78 0.91
80 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCTCGGTTTTATTTCCAAAACATCGATTTTCCACCATCGGGGATACTCCAAC
CCCATTATTTCTCA
Found at i:310418 original size:24 final size:20
Alignment explanation
Indices: 310401--310474 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
310391 TTTTACCTAG
310401 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*** *
310421 ATGTATCGATACATAGATGA
1 ATGTATCGATACATTTTTCA
*
310441 ATGTATTGATACATTCTTT-A
1 ATGTATCGATACATT-TTTCA
310461 ATGTATCGATACAT
1 ATGTATCGATACAT
310475 CTAGTTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:316153 original size:13 final size:13
Alignment explanation
Indices: 316112--316164 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
316102 CCGTTAAAAG
316112 CAATGTATCGATA
1 CAATGTATCGATA
316125 CAA--T-TC-AT-
1 CAATGTATCGATA
316133 C-ATGTATCGATA
1 CAATGTATCGATA
*
316145 CATTGTATCGATA
1 CAATGTATCGATA
316158 CAATGTA
1 CAATGTA
316165 CCATGTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:316157 original size:33 final size:33
Alignment explanation
Indices: 316115--316179 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
316105 TTAAAAGCAA
*
316115 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
316148 TGTATCGATACAATGTACCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
316180 AACAGTAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:316253 original size:19 final size:19
Alignment explanation
Indices: 316209--316264 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
316199 CTGCCAGTTT
**
316209 CATGTATCGATACAACTGTC
1 CATGTATCGATACAA-TGAA
316229 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
316248 CATGTATCGATACAATG
1 CATGTATCGATACAATG
316265 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:316267 original size:13 final size:13
Alignment explanation
Indices: 316249--316275 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
316239 TACAATGAAC
316249 ATGTATCGATACA
1 ATGTATCGATACA
316262 ATGTATCGATACA
1 ATGTATCGATACA
316275 A
1 A
316276 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:318660 original size:22 final size:23
Alignment explanation
Indices: 318622--318665 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
318612 ATAATTTTGA
*
318622 TGAAAAGTGAAGTATTT-TAAAG
1 TGAAAAGTGAAGAATTTGTAAAG
318644 TGAAAA-TGAAGAAATTTGTAAA
1 TGAAAAGTGAAG-AATTTGTAAA
318666 AGATTTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (23 bp):
TGAAAAGTGAAGAATTTGTAAAG
Found at i:320166 original size:13 final size:13
Alignment explanation
Indices: 320148--320173 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320138 CATTTTGGGA
320148 TGTATCGATACAT
1 TGTATCGATACAT
320161 TGTATCGATACAT
1 TGTATCGATACAT
320174 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:320170 original size:33 final size:32
Alignment explanation
Indices: 320128--320191 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
320118 TACAAGCCAA
*
320128 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
320161 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
320192 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:320291 original size:13 final size:13
Alignment explanation
Indices: 320273--320297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320263 ACATTTGGTC
320273 ATGTATCGATACA
1 ATGTATCGATACA
320286 ATGTATCGATAC
1 ATGTATCGATAC
320298 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:324181 original size:20 final size:20
Alignment explanation
Indices: 324135--324189 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
324125 GTATCGATAC
* **
324135 ATTGTATCGATACTTGTTCA
1 ATTGTATCGATACATGGACA
324155 A-TGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
324174 ATTGTATCGATACATG
1 ATTGTATCGATACATG
324190 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:324236 original size:13 final size:13
Alignment explanation
Indices: 324218--324266 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
324208 CTACCACTGT
324218 TTGTATCGATACA
1 TTGTATCGATACA
324231 TTGTATCGATACA
1 TTGTATCGATACA
324244 -TG-AT-G--A-A
1 TTGTATCGATACA
324251 TTGTATCGATACA
1 TTGTATCGATACA
324264 TTG
1 TTG
324267 CTTGTAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 1 0.03
8 3 0.10
9 2 0.07
10 2 0.07
11 2 0.07
12 3 0.10
13 17 0.57
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:330021 original size:13 final size:13
Alignment explanation
Indices: 330003--330028 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329993 CAACATTCCC
330003 TGTATCGATACAT
1 TGTATCGATACAT
330016 TGTATCGATACAT
1 TGTATCGATACAT
330029 AGGTAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:331983 original size:29 final size:29
Alignment explanation
Indices: 331915--331975 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
331905 TGAAAAATAA
* * *
331915 AATAAATTTTTGCTTTGATTAAGGGGGGG
1 AATAAATTTTTACTTTGATTAAGAGGGAG
331944 AATAAATTTTTACTTTGATTAAGAGGGAG
1 AATAAATTTTTACTTTGATTAAGAGGGAG
331973 AAT
1 AAT
331976 TTTTTTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (29 bp):
AATAAATTTTTACTTTGATTAAGAGGGAG
Found at i:332490 original size:20 final size:20
Alignment explanation
Indices: 332465--332531 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
332455 TACTTCAAAG
332465 TACATAGACAATTGTATCAA
1 TACATAGACAATTGTATCAA
** *
332485 TACATAGGTATTTGTATCAA
1 TACATAGACAATTGTATCAA
* * *
332505 TACAATTGTCCA-TGTATCAA
1 TAC-ATAGACAATTGTATCAA
332525 TACATAG
1 TACATAG
332532 GTATTTGTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.08
20 31 0.84
21 3 0.08
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (20 bp):
TACATAGACAATTGTATCAA
Found at i:332540 original size:20 final size:20
Alignment explanation
Indices: 332476--332549 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
332466 ACATAGACAA
332476 TTGTATCAATACATAGGTAT
1 TTGTATCAATACATAGGTAT
* **
332496 TTGTATCAATACA-ATTGTCC
1 TTGTATCAATACATA-GGTAT
*
332516 ATGTATCAATACATAGGTAT
1 TTGTATCAATACATAGGTAT
*
332536 TTGTATCGATACAT
1 TTGTATCAATACAT
332550 TATGGTTGAC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
TTGTATCAATACATAGGTAT
Found at i:332735 original size:13 final size:13
Alignment explanation
Indices: 332717--332769 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
332707 CGGTACATGG
332717 TACATTGTATCGA
1 TACATTGTATCGA
332730 TACATTGTATCGA
1 TACATTGTATCGA
332743 TACA-TG-AT-G-
1 TACATTGTATCGA
332752 -A-ATTGTATCGA
1 TACATTGTATCGA
332763 TACATTG
1 TACATTG
332770 CCTGTAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:332747 original size:33 final size:33
Alignment explanation
Indices: 332701--332769 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
332691 CTACCACTGT
* *
332701 TTGTATCGGTACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
332734 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
332767 TTG
1 TTG
332770 CCTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:333555 original size:12 final size:12
Alignment explanation
Indices: 333538--333564 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
333528 TCCGAGTCAC
333538 CATTATCATCAT
1 CATTATCATCAT
333550 CATTATCATCAT
1 CATTATCATCAT
333562 CAT
1 CAT
333565 CGTCATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (12 bp):
CATTATCATCAT
Found at i:334266 original size:13 final size:13
Alignment explanation
Indices: 334248--334273 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
334238 CATTTTTCTG
334248 TGTATCGATACAT
1 TGTATCGATACAT
334261 TGTATCGATACAT
1 TGTATCGATACAT
334274 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:334270 original size:33 final size:33
Alignment explanation
Indices: 334228--334293 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
334218 GCCAAGGAAA
***
334228 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATCGATCTGTGTATCGATACAT
*
334261 TGTATCGATACATCGATCTTTGTATCGATACAT
1 TGTATCGATACATCGATCTGTGTATCGATACAT
334294 CTAGGAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATCGATCTGTGTATCGATACAT
Found at i:336809 original size:28 final size:28
Alignment explanation
Indices: 336770--336844 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
336760 TTTTTTTATA
336770 ATCGAGGG-TACTCCAACCCT-GTTATTT
1 ATCG-GGGATACTCCAACCCTCGTTATTT
*
336797 CATCGGGGATACTCCAA-TCTCGTTATTT
1 -ATCGGGGATACTCCAACCCTCGTTATTT
336825 -TCGAGGGGATACTCCAACCC
1 ATC--GGGGATACTCCAACCC
336845 CAATTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 2 0.05
27 5 0.12
28 32 0.80
29 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCTCGTTATTT
Found at i:336890 original size:51 final size:51
Alignment explanation
Indices: 336829--337016 Score: 238
Period size: 51 Copynumber: 3.7 Consensus size: 51
336819 TTATTTTCGA
*
336829 GGGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATC
* * * * *
336880 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTCTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATC
*
336931 GGGGATACTCCAACCCCGATTTTATTT-TCAAAATACCAA-TTTTCTATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAATACCAATTTTTC-ACAATC
* * *
336982 GGGGATACTCCAGCCCCG-TTGTTATCTCCAAAATA
1 GGGGATACTCCAACCCCGATT-TTATTTCTAAAATA
337017 TTAAATTTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
50 6 0.05
51 112 0.95
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATC
Found at i:337012 original size:102 final size:102
Alignment explanation
Indices: 336829--337014 Score: 279
Period size: 102 Copynumber: 1.8 Consensus size: 102
336819 TTATTTTCGA
336829 GGGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
* *
336894 TCCGATTTTATTTCCAAAACACAAATTTCTCACAATC
66 CCCGATTTTATCTCCAAAACACAAATTTCTCACAATC
* *
336931 GGGGATACTCCAACCCCGATTTTATTT-TCAAAATACCAA-TTTTCTATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCAATTTTATTTCT-AAAATACCAATTTTTC-ACAATCGGGGATACTCCA
*
336994 GCCCCG-TTGTTATCTCCAAAA
64 ACCCCGATT-TTATCTCCAAAA
337015 TATTAAATTT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
101 8 0.11
102 68 0.89
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31
Consensus pattern (102 bp):
GGGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGATTTTATCTCCAAAACACAAATTTCTCACAATC
Found at i:342373 original size:49 final size:50
Alignment explanation
Indices: 342280--342379 Score: 148
Period size: 49 Copynumber: 2.0 Consensus size: 50
342270 TCCAGTCCTA
* * * *
342280 AAAGAGCTGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
1 AAAGAGCAGGACGCCTTCTCCTTTTCAAAGCCCACACAAATTGGTGGCAC
*
342330 AAAGAGCAGGATGCCTTCTCCTTTT-AAAGCCCACACAAATTGGTGGCAC
1 AAAGAGCAGGACGCCTTCTCCTTTTCAAAGCCCACACAAATTGGTGGCAC
342379 A
1 A
342380 TCACAGTCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 24 0.53
50 21 0.47
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (50 bp):
AAAGAGCAGGACGCCTTCTCCTTTTCAAAGCCCACACAAATTGGTGGCAC
Found at i:342407 original size:61 final size:60
Alignment explanation
Indices: 342329--342584 Score: 277
Period size: 61 Copynumber: 4.4 Consensus size: 60
342319 GTTGGTGGCA
* * * *
342329 CAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAATTGGTGGCACATCACAGTCCT
1 CAAAGAGCAGGACGCCTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCT
*
342390 CAAAGAGCAGAACG-----CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T-AGTCCT
1 CAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCT
* * *
342444 CAAATAGCAGGACGCCTTT-C----AAAACCCACACGAGTTGGTGGCACTTCTCAGTCCT
1 CAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCT
* *
342499 CAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTC-CTAGTCCT
1 CAAAGAGCAGGACGCC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTC-AGTCCT
*
342560 CAAAGAGCAGGACGCTCTCTCCTTT
1 CAAAGAGCAGGACGC-CTTTCCTTT
342585 CACCCTTTAG
Statistics
Matches: 163, Mismatches: 16, Indels: 32
0.77 0.08 0.15
Matches are distributed among these distances:
53 3 0.02
54 40 0.25
55 48 0.29
56 5 0.03
57 1 0.01
58 1 0.01
60 1 0.01
61 63 0.39
62 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (60 bp):
CAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCT
Found at i:342433 original size:55 final size:55
Alignment explanation
Indices: 342349--342574 Score: 251
Period size: 54 Copynumber: 4.0 Consensus size: 55
342339 GATGCCTTCT
* * *
342349 CCTTTTAAAGCCCACACAAATTGGTGGCACATCACAGTCCTCAAAGAGCAGAACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGAACG
* *
342404 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T-AGTCCTCAAATAGCAGGACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCTCAAAGAGCAGAACG
* * * * *
342458 CCTTTCAAAACCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCA-GA--AC---G
* *
342519 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTC-CTAGTCCTCAAAGAGCAGGACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTC-AGTCCTCAAAGAGCAGAACG
342574 C
1 C
342575 TCTCTCCTTT
Statistics
Matches: 142, Mismatches: 19, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
53 3 0.02
54 45 0.32
55 43 0.30
56 3 0.02
58 2 0.01
60 2 0.01
61 44 0.31
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (55 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGAACG
Found at i:342496 original size:109 final size:112
Alignment explanation
Indices: 342349--342574 Score: 289
Period size: 109 Copynumber: 2.0 Consensus size: 112
342339 GATGCCTTCT
* *
342349 CCTTTTAAAGCCCACACAAATTGGTGGCACATCACAGTCCTCAAAGAGCA-GA-AC-GCCTTTTA
1 CCTTTCAAAACCCACACAAATTGGTGGCACATCACAGTCCTCAAAGAGCAGGAGACTGCCTTTTA
*
342411 AAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAATAGCAGGACG
66 AAGCCCACACAAGTTGGTGGCA-CTTCTAGTCCTCAAAGAGCAGGACG
* * * * * *
342458 CCTTTCAAAACCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTT
1 CCTTTCAAAACCCACACAAATTGGTGGCACATCACAGTCCTCAAAGAGCAGGA-GAC--TGCCTT
*
342523 TTAAAGCCCACACAAGTTGGTGGCATTTCCTAGTCCTCAAAGAGCAGGACG
63 TTAAAGCCCACACAAGTTGGTGGCACTT-CTAGTCCTCAAAGAGCAGGACG
342574 C
1 C
342575 TCTCTCCTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
109 44 0.44
110 2 0.02
112 1 0.01
114 2 0.02
115 29 0.29
116 21 0.21
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (112 bp):
CCTTTCAAAACCCACACAAATTGGTGGCACATCACAGTCCTCAAAGAGCAGGAGACTGCCTTTTA
AAGCCCACACAAGTTGGTGGCACTTCTAGTCCTCAAAGAGCAGGACG
Found at i:342666 original size:100 final size:95
Alignment explanation
Indices: 342493--342770 Score: 357
Period size: 100 Copynumber: 2.8 Consensus size: 95
342483 GGCACTTCTC
* *
342493 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTCCTAGTC
1 AGTCCTCAAAGAGCAGGA---C-GTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTC
342558 CTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTT
62 CTCAAAGAGCAGGACGC-CTCTCCTTTCACCCTTT
*
342593 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC
1 AGTCCTCAAAGAGCAGGACG---T-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTC
* *
342658 CTCAAAGAGTAGGATGCCCCTCTCCTTTCACCCTTT
62 CTCAAAGAGCAGGA--CGCCTCTCCTTTCACCCTTT
* *
342694 AGTCCTCAAAGAGCAAGACG--CCTTTTAAAGCCCAAACAAGTTGGTGGCACCTT--TAGTCCTC
1 AGTCCTCAAAGAGCAGGACGTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTC
342755 AAAGAGCAGGACGCCT
65 AAAGAGCAGGACGCCT
342771 TTCAAAGCCC
Statistics
Matches: 161, Mismatches: 10, Indels: 22
0.83 0.05 0.11
Matches are distributed among these distances:
92 4 0.02
94 17 0.11
95 28 0.17
96 3 0.02
97 1 0.01
99 1 0.01
100 69 0.43
101 36 0.22
102 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (95 bp):
AGTCCTCAAAGAGCAGGACGTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCA
AAGAGCAGGACGCCTCTCCTTTCACCCTTT
Found at i:342771 original size:54 final size:54
Alignment explanation
Indices: 342693--342877 Score: 228
Period size: 54 Copynumber: 3.3 Consensus size: 54
342683 TTTCACCCTT
* *
342693 TAGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCAAACAAGTTGGTGGCACCTT-
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTC
* *
342747 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTAGGTGGCACTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTT-GGTGGCACTTC
*
342802 TCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 T-AGTCCTCAAAGAGCAGGA---C---GCCTTTTAAAGCCCACACAAGTTGGTGGCACTT-C
342864 TAGTCCTCAAAGAG
1 TAGTCCTCAAAGAG
342878 TAGGGCGCTC
Statistics
Matches: 114, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
54 42 0.37
55 8 0.07
56 18 0.16
59 1 0.01
61 23 0.20
62 22 0.19
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (54 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTC
Found at i:342840 original size:211 final size:212
Alignment explanation
Indices: 342593--343050 Score: 701
Period size: 211 Copynumber: 2.1 Consensus size: 212
342583 TTCACCCTTT
342593 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC
342658 CTCAAAGAGTAGGATGC-CCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTTAA
66 CTCAAAGAGTAGG--GCGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTTAA
*
342722 AGCCCAAACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACGCCTT-T-C-AAAGCCCAC
129 AGCCCAAACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTAAAGCCCAC
* *
342783 ACGAGTTAGGTGGCACTTCTC
193 ACAAGTT-GGTGGCACTTCCC
* * *
342804 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC
* *
342869 CTCAAAGAGTAGGGCGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAG
66 CTCAAAGAGTAGGGCGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTTAAAG
* *
342934 CCCACACAAGTTTGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCA
131 CCCAAACAAGTTGGTGGCACTT-CCAGTCCTCAAAGAGCAGGACGCCTTCTCC---TAAAGCCCA
342999 CACAAGTTGGTGGCACTTCCC
192 CACAAGTTGGTGGCACTTCCC
* *
343020 AATCCTCAAAGAGCAGGACGCCCTCTCCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
343051 CACCCTTTAG
Statistics
Matches: 224, Mismatches: 14, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
209 5 0.02
210 64 0.29
211 99 0.44
212 1 0.00
213 1 0.00
216 39 0.17
217 15 0.07
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (212 bp):
AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC
CTCAAAGAGTAGGGCGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTTAAAG
CCCAAACAAGTTGGTGGCACTTCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTAAAGCCCACACA
AGTTGGTGGCACTTCCC
Found at i:342877 original size:61 final size:59
Alignment explanation
Indices: 342714--342895 Score: 214
Period size: 61 Copynumber: 3.1 Consensus size: 59
342704 GAGCAAGACG
*
342714 CCTTTTAAAGCCCAAACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACGCCTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTAGTCCTCAAAGAGCAGGACGCCTTT
* *
342773 -C----AAAGCCCACACGAGTTAGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTT-GGTGGCACTTCT-AGTCCTCAAAGAGCAGGACGCC-TTT
* * *
342830 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGGCGCTCTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTT-CTAGTCCTCAAAGAGCAGGACGC-CTTT
342891 CCTTT
1 CCTTT
342896 CACCCTTTAG
Statistics
Matches: 104, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
54 17 0.16
55 8 0.08
56 21 0.20
57 3 0.03
58 2 0.02
61 35 0.34
62 18 0.17
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.26
Consensus pattern (59 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:343019 original size:61 final size:61
Alignment explanation
Indices: 342924--343050 Score: 227
Period size: 61 Copynumber: 2.1 Consensus size: 61
342914 GAGCAGGACG
* * *
342924 CCTTTTAAAGCCCACACAAGTTTGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCCCTCT
342985 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCCCTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCCCTCT
343046 CCTTT
1 CCTTT
343051 CACCCTTTAG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCCCTCT
Found at i:343026 original size:155 final size:153
Alignment explanation
Indices: 342433--343185 Score: 763
Period size: 155 Copynumber: 4.9 Consensus size: 153
342423 GTTGGTGGCA
* * * *
342433 CCTTTAGTCCTCAAATAGCAGGACGCCTTTCAAAACCCACACGAGTTGGTGGCACTTCTCAGTCC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTC-CAGTCC
* * *
342498 TCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTCCTAGTCCTCAA
65 TCAAAGAGCAGGACGCC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
* *
342563 AGAGCAGGACGCTCTCTCCTTTCAC
129 AGAGTAGGACGCCCTCTCCTTTCAC
342588 CCTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 CCTTTAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCACTT-C
* * * ** * * * *** **
342653 CAGTCCTCAAAGAGTAGGATGCCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGC-CT
59 CAGTCCTCAAAGAGCAGGA--CGCCTTTCCTTT-----TAAAGCCCACACA-AGTTGGTGGCAC-
*** * ** **
342717 TTTAAAG-CC-C-AA-A-CA--A-G---T-TGGTGGCA-
115 TTCCCAGTCCTCAAAGAGTAGGACGCCCTCTCCTTTCAC
* *
342743 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTAGGTGGCACTTCTCAGTC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTT-GGTGGCACTTC-CAGTC
* *
342808 CTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCA
64 CTCAAAGAGCAGGACGCC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCA
* *
342873 AAGAGTAGGGCGCTCTCTCCTTTCAC
128 AAGAGTAGGACGCCCTCTCCTTTCAC
*
342899 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTTGTGGCACTTCCCAGTCC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTT-CCAGTCC
*
342964 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAA
65 TCAAAGAGCAGGACGCCTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAA
*
343029 AGAGCAGGACGCCCTCTCCTTTCAC
129 AGAGTAGGACGCCCTCTCCTTTCAC
*
343054 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCC
* * *
343118 TCAAAGAGCAGGACGCCTTT-C----AAAGCTCACACGAGTTGGTGGCACTTCTCAGTCCTCAAA
65 TCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAA
343178 GAGTAGGA
130 GAGTAGGA
343186 TGCCTTTTCC
Statistics
Matches: 495, Mismatches: 67, Indels: 79
0.77 0.10 0.12
Matches are distributed among these distances:
143 9 0.02
144 11 0.02
145 1 0.00
146 2 0.00
147 1 0.00
148 45 0.09
149 28 0.06
150 28 0.06
151 1 0.00
152 1 0.00
153 1 0.00
154 27 0.05
155 202 0.41
156 53 0.11
157 1 0.00
160 1 0.00
161 48 0.10
162 8 0.02
163 4 0.01
164 1 0.00
165 2 0.00
166 1 0.00
167 10 0.02
168 9 0.02
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (153 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCT
CAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAG
AGTAGGACGCCCTCTCCTTTCAC
Found at i:343060 original size:311 final size:301
Alignment explanation
Indices: 342390--343185 Score: 927
Period size: 311 Copynumber: 2.6 Consensus size: 301
342380 TCACAGTCCT
** * ** *
342390 CAAAGAGC-AGAACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAATAGCAG
1 CAAAGAGCAAG-ACGCCTTCCAAAGCCCAAACAAGTTCCTGGCACCTTTAGTCCTCAAAGAGCAG
*
342454 GACGCCTTTCAAAACCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTT
65 GACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTT
* *
342519 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
130 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCTCTCTCCTT
342584 TCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
195 TCACCCTTTAGTCCTCAAAGAGCAGGACG----C-CCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * ** * *
342649 TTCCCAGTCCTCAAAGAGTAGGATGCCCCTCTCCTTTCACCCTTTAGTCCT
255 TTCCCAGTCCTCAAAGAGCAGGACGCCCCTCTCCTTT----CTAAAGCCCA
** **
342700 CAAAGAGCAAGACGCCTTTTAAAGCCCAAACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGG
1 CAAAGAGCAAGACGCCTTCCAAAGCCCAAACAAGTTCCTGGCACCTTTAGTCCTCAAAGAGCAGG
342765 ACGCCTTTCAAAGCCCACACGAGTTAGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTT
66 ACGCCTTTCAAAGCCCACACGAGTT-GGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTT
*
342830 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGGCGCTCTCTCCTT
130 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCTCTCTCCTT
*
342895 TCACCCTTTAGTCCTCAAAGAGCAGGACG-CCTTTTAAAGCCCACACAAGTTTGTGGCACTTCCC
195 TCACCCTTTAGTCCTCAAAGAGCAGGACGCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
*
342959 AGTCCTCAAAGAGCAGGACG-CCTTCTCCTTT-TAAAGCCCA
260 AGTCCTCAAAGAGCAGGACGCCCCTCTCCTTTCTAAAGCCCA
* *** ** * * **
342999 CACA-AGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCCCTCTCCTTTCACCCTTTAGTC
1 CAAAGAGCAAGACGC-CTTCCAAAGCC-C-AA-A-CA--A-G---T-TCCTGGCA-CCTTTAGTC
* *
343063 CTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T-AGTCCTCAAAGAG
53 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA-CTTCTCAGTCCTCAAAGAG
* * *
343126 CAGGACGCC-TTT-C----AAAGCTCACACGAGTTGGTGGCACTT-CTCAGTCCTCAAAGAGTAG
117 CAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCT-AGTCCTCAAAGAGTAG
343184 GA
181 GA
343186 TGCCTTTTCC
Statistics
Matches: 435, Mismatches: 34, Indels: 41
0.85 0.07 0.08
Matches are distributed among these distances:
298 5 0.01
299 15 0.03
300 1 0.00
301 2 0.00
302 3 0.01
303 43 0.10
304 10 0.02
305 53 0.12
306 1 0.00
307 1 0.00
308 3 0.01
309 22 0.05
310 96 0.22
311 180 0.41
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (301 bp):
CAAAGAGCAAGACGCCTTCCAAAGCCCAAACAAGTTCCTGGCACCTTTAGTCCTCAAAGAGCAGG
ACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTC
CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGACGCTCTCTCCTTT
CACCCTTTAGTCCTCAAAGAGCAGGACGCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCA
GTCCTCAAAGAGCAGGACGCCCCTCTCCTTTCTAAAGCCCA
Found at i:343136 original size:25 final size:25
Alignment explanation
Indices: 343054--343137 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
343044 CTCCTTTCAC
343054 CCTTTAGTCCTCAAAGAGCAGGACG
1 CCTTTAGTCCTCAAAGAGCAGGACG
* * * ** *
343079 CCTTTTAAAGCCCACACAAGTTGGTGG-CA
1 CC-TTT--AGTCCTCA-AAG-AGCAGGACG
343108 CCTTTAGTCCTCAAAGAGCAGGACG
1 CCTTTAGTCCTCAAAGAGCAGGACG
343133 CCTTT
1 CCTTT
343138 CAAAGCTCAC
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
24 3 0.07
25 11 0.27
26 9 0.22
28 9 0.22
29 6 0.15
30 3 0.07
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (25 bp):
CCTTTAGTCCTCAAAGAGCAGGACG
Found at i:343136 original size:54 final size:55
Alignment explanation
Indices: 343054--343249 Score: 263
Period size: 54 Copynumber: 3.5 Consensus size: 55
343044 CTCCTTTCAC
343054 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
343108 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCTCACACGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
343162 -CTTCTCAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCT-AGTCCTCAAAGAGCAGGA---C---GCCTTTTAAAGCCCACACAAGTTGGTGGCA
343223 CCTTCTAGTCCTCAAAGAGCAGGACGC
1 CCTTCTAGTCCTCAAAGAGCAGGACGC
343250 TCTCTCCTTT
Statistics
Matches: 123, Mismatches: 10, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
53 3 0.02
54 52 0.42
55 18 0.15
58 2 0.02
61 43 0.35
62 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (55 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:343162 original size:209 final size:209
Alignment explanation
Indices: 342899--343409 Score: 837
Period size: 209 Copynumber: 2.4 Consensus size: 209
342889 CTCCTTTCAC
* *
342899 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTTGTGGCACTTCCCAGTCC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACTTCCCAGTCC
*
342964 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAATCCTCA
66 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAATCCTCA
*
343028 AAGAGCAGGACGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCA
130 AAGAGCAGGACGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCA
343093 CACAAGTTGGTGGCA
195 CACAAGTTGGTGGCA
* * *
343108 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCTCACACGAGTTGGTGGCACTTCTCAGTCC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACTTCCCAGTCC
* * * *
343173 TCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAA
66 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAATCCTCAA
*
343238 AGAGCAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
131 AGAGCAGGACGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
343303 ACAAGTTGGTGGCA
196 ACAAGTTGGTGGCA
* * *
343317 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACGAGTTGGTAGCACCTT-CCAAT
1 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCA-CTTCCCAGT
*
343381 CTTCAAAGAGCAGGACGCCTTTTCCTTTT
64 CCTCAAAGAGCAGGACGCCTTTTCCTTTT
343410 CTCCTTTGTC
Statistics
Matches: 278, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
209 198 0.71
210 77 0.28
211 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (209 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACTTCCCAGTCC
TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAATCCTCAA
AGAGCAGGACGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
ACAAGTTGGTGGCA
Found at i:343275 original size:364 final size:365
Alignment explanation
Indices: 342593--343430 Score: 1376
Period size: 364 Copynumber: 2.3 Consensus size: 365
342583 TTCACCCTTT
*
342593 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATC
* *
342658 CTCAAAGAGTAGGATGCCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTTAAA
66 CTCAAAGAGCAGGACG-CCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTTAAA
342723 GCCCAAACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAG
130 GCCCAAACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAG
342788 TTAGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTG
195 TTAGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTG
* *
342853 GTGGCACTTCCTAGTCCTCAAAGAGTAGGGCGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGC
260 GTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGC
* *
342918 AGGACGCCTTTTAAAGCCCACACAAGTTTGTGGCA-CTTCCC
325 AGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CC
342959 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATC
*
343024 CTCAAAGAGCAGGACGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAG
66 CTCAAAGAGCAGGACGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTTAAAG
* *
343089 CCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCTCACACGAGT
131 CCCAAACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGT
*
343154 T-GGTGGCACTTCTCAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGG
196 TAGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGG
343218 TGGCACCTT-CTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGC
261 TGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGC
*
343282 AGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
325 AGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCC
* * *
343323 AGTCCTCAAAGAGCAGGA-----T-GCCTTTTAAAGCCCACACGAGTTGGTAGCACCTT-CCAAT
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAAT
* * * *
343381 CTTCAAAGAGCAGGACGCCTTTTCCTTTTC-TCCTTT-GTCCTCAAAGAGCA
65 CCTCAAAGAGCAGGACGCCCTCTCC-TTTCACCCTTTAGTCCTCAAAGAGCA
343431 TCACACACTT
Statistics
Matches: 449, Mismatches: 19, Indels: 17
0.93 0.04 0.04
Matches are distributed among these distances:
357 14 0.03
358 59 0.13
359 8 0.02
364 172 0.38
365 118 0.26
366 78 0.17
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (365 bp):
AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAATC
CTCAAAGAGCAGGACGCCCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAAGACGCCTTTTAAAG
CCCAAACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGT
TAGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGG
TGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCA
GGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCC
Found at i:343297 original size:155 final size:149
Alignment explanation
Indices: 343108--343430 Score: 447
Period size: 155 Copynumber: 2.1 Consensus size: 149
343098 GTTGGTGGCA
* *
343108 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCTCACACGAGTTGGTGGCA-CTTCTCAGTC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTC
* * * *
343172 CTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCA
65 CTCAAAGAGCAGGATG------CCTTTTAAAGCCCACACAAGTTGGTAGCACCTTCCAATCCTCA
343237 AAGAGCAGGACG-CTCTCTCC-TTTCAC
124 AAGAGCAGGACGCCT-TCTCCTTTTC-C
343263 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* *
343328 TCAAAGAGCAGGATGCCTTTTAAAGCCCACACGAGTTGGTAGCACCTTCCAATCTTCAAAGAGCA
66 TCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTAGCACCTTCCAATCCTCAAAGAGCA
* *
343393 GGACGCCTTTTCCTTTTCT
131 GGACGCCTTCTCCTTTTCC
343412 CCTTT-GTCCTCAAAGAGCA
1 CCTTTAGTCCTCAAAGAGCA
343431 TCACACACTT
Statistics
Matches: 155, Mismatches: 10, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
148 14 0.09
149 59 0.38
150 6 0.04
155 73 0.47
156 3 0.02
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (149 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
TCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTAGCACCTTCCAATCCTCAAAGAGCA
GGACGCCTTCTCCTTTTCC
Found at i:343328 original size:55 final size:55
Alignment explanation
Indices: 343263--343402 Score: 210
Period size: 55 Copynumber: 2.6 Consensus size: 55
343253 CTCCTTTCAC
*
343263 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCA
* * *
343317 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACGAGTTGGTAGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCA
* * *
343372 CCTTCCAATCTTCAAAGAGCAGGACGCCTTT
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTT
343403 TCCTTTTCTC
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 5 0.06
55 72 0.94
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCA
Found at i:343485 original size:45 final size:45
Alignment explanation
Indices: 343407--343610 Score: 179
Period size: 45 Copynumber: 4.6 Consensus size: 45
343397 GCCTTTTCCT
* * ** * * *
343407 TTTCTCCTTTGTCCTCAAAGAGCATCACACACTTCA-TTCCCTTC
1 TTTCTCTTTTATCCTCAAAGAGCAGGACGCACTTTAGTTTCCTTC
*
343451 TTTCCTCTTTTATCCTCAAAGAGCAGGACGCACTTTATTTTCC-TC
1 TTT-CTCTTTTATCCTCAAAGAGCAGGACGCACTTTAGTTTCCTTC
* * * *
343496 -TT-TCTTTTGTCCTCAAAGAGTATGACGCA-TTTAGTTTTCTT-
1 TTTCTCTTTTATCCTCAAAGAGCAGGACGCACTTTAGTTTCCTTC
* * *
343537 TTTCTCCTTTGTCCTCAAAGAGCAGGACGCTCTTTA-TTTCCTTC
1 TTTCTCTTTTATCCTCAAAGAGCAGGACGCACTTTAGTTTCCTTC
* *
343581 TTTTCCCTTCTAGTCCTCAAAGAGCAGGAC
1 -TTTCTCTTTTA-TCCTCAAAGAGCAGGAC
343611 ACATTTCGTC
Statistics
Matches: 130, Mismatches: 21, Indels: 16
0.78 0.13 0.10
Matches are distributed among these distances:
41 8 0.06
42 27 0.21
43 29 0.22
44 9 0.07
45 36 0.28
46 21 0.16
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (45 bp):
TTTCTCTTTTATCCTCAAAGAGCAGGACGCACTTTAGTTTCCTTC
Found at i:343515 original size:42 final size:42
Alignment explanation
Indices: 343456--343610 Score: 163
Period size: 42 Copynumber: 3.6 Consensus size: 42
343446 CCTTCTTTCC
*
343456 TCTTTTATCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTT
1 TCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTT
* * *
343498 TCTTTTGTCCTCAAAGAGTATGACGCA-TTTAGTTTT-CTTTT
1 TCTTTTGTCCTCAAAGAGCAGGACGCACTTTA-TTTTCCTCTT
*
343539 TCTCCTTTGTCCTCAAAGAGCAGGACGCTCTTTA-TTTCCTTCTTT
1 TCT--TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC-TC-TT
*
343584 TCCCTTCTAGTCCTCAAAGAGCAGGAC
1 T--CTT-TTGTCCTCAAAGAGCAGGAC
343611 ACATTTCGTC
Statistics
Matches: 94, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
41 11 0.12
42 31 0.33
43 22 0.23
44 5 0.05
45 4 0.04
46 19 0.20
47 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (42 bp):
TCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTT
Found at i:343563 original size:85 final size:89
Alignment explanation
Indices: 343383--343655 Score: 234
Period size: 85 Copynumber: 3.2 Consensus size: 89
343373 CTTCCAATCT
* **
343383 TCAAAGAGCAGGACGC-C--T-TTTCCTT-TTCTCCTT-T-GTCCTCAAAGAGCATCACACACTT
1 TCAAAGAGCAGGACGCACTTTATTTCCTTCTTTTCCTTCTAGTCCTCAAAGAGCAGGACACA-TT
* * * *
343441 CA-T-TCCCTTCTTTCCTCTTTTATCC
65 TAGTCTTCCTT-TTT-CTCCTTTGTCC
* * * *
343466 TCAAAGAGCAGGACGCACTTTATTTTCC-TC-TTT-CTT-TTGTCCTCAAAGAGTATGACGCATT
1 TCAAAGAGCAGGACGCACTTTA-TTTCCTTCTTTTCCTTCTAGTCCTCAAAGAGCAGGACACATT
*
343527 TAGT-TTTCTTTTTCTCCTTTGTCC
65 TAGTCTTCCTTTTTCTCCTTTGTCC
*
343551 TCAAAGAGCAGGACGCTCTTTATTTCCTTCTTTTCCCTTCTAGTCCTCAAAGAGCAGGACACATT
1 TCAAAGAGCAGGACGCACTTTATTTCCTTCTTTT-CCTTCTAGTCCTCAAAGAGCAGGACACATT
* * *
343616 TCGTCTTCCTTTTTTTCCTTTTTCC
65 TAGTCTTCCTTTTTCTCCTTTGTCC
*
343641 TCGAAA-AGTAGGACG
1 TC-AAAGAGCAGGACG
343656 TACTCTTTTT
Statistics
Matches: 156, Mismatches: 19, Indels: 23
0.79 0.10 0.12
Matches are distributed among these distances:
83 16 0.10
84 6 0.04
85 32 0.21
86 14 0.09
87 26 0.17
88 8 0.05
89 24 0.15
90 27 0.17
91 3 0.02
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.39
Consensus pattern (89 bp):
TCAAAGAGCAGGACGCACTTTATTTCCTTCTTTTCCTTCTAGTCCTCAAAGAGCAGGACACATTT
AGTCTTCCTTTTTCTCCTTTGTCC
Found at i:347062 original size:28 final size:26
Alignment explanation
Indices: 347029--347102 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 26
347019 TTTTTTTATA
*
347029 ATCGGGGGTACTCCAACCATGTTATTT
1 ATCGGGGGTACTCCAACC-CGTTATTT
*
347056 CATCGGGGATACTCCAATCCCGTTATTT
1 -ATCGGGGGTACTCCAA-CCCGTTATTT
347084 -TCGAGGGGATACTCCAACC
1 ATCG-GGGG-TACTCCAACC
347103 TCGATTTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 3 0.08
27 5 0.12
28 30 0.75
29 2 0.05
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (26 bp):
ATCGGGGGTACTCCAACCCGTTATTT
Found at i:347148 original size:51 final size:52
Alignment explanation
Indices: 347088--347204 Score: 168
Period size: 51 Copynumber: 2.3 Consensus size: 52
347078 TTATTTTCGA
* * *
347088 GGGGATACTCCAACCT-CGATTTT-GTTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCTCCGATTTTATTTTC-AAAACACCAATTTCTCACAATC
*
347139 GGGGATACTCCAA-CTCCGATTTTATTTTCAAAACACTAATTTCTCACAATC
1 GGGGATACTCCAACCTCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
347190 GGGGATACTCCAACC
1 GGGGATACTCCAACC
347205 CCGTTATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
50 2 0.03
51 52 0.88
52 5 0.08
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCTCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
Found at i:347221 original size:79 final size:79
Alignment explanation
Indices: 347138--347288 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
347128 TTTTCACAAT
* * * *
347138 CGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTCTCACAATCGGGGATACTCCA
1 CGGGGATACTCAAACCCCGATTTTATTTTCAAAACACCAATTTTCT-ACAATCGAGGATACTCCA
347202 ACCCCGTTATTTTCA
65 ACCCCGTTATTTTCA
* * * *
347217 CGGGGATACTCAAACCCCGATTTTATTTTCAAAATACCAATTTTCTATAATCGAGGATACTCTAG
1 CGGGGATACTCAAACCCCGATTTTATTTTCAAAACACCAATTTTCTACAATCGAGGATACTCCAA
347282 CCCCGTT
66 CCCCGTT
347289 GTTATCTCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 58 0.92
80 5 0.08
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (79 bp):
CGGGGATACTCAAACCCCGATTTTATTTTCAAAACACCAATTTTCTACAATCGAGGATACTCCAA
CCCCGTTATTTTCA
Found at i:347301 original size:130 final size:130
Alignment explanation
Indices: 347057--347301 Score: 327
Period size: 130 Copynumber: 1.9 Consensus size: 130
347047 ATGTTATTTC
* * *
347057 ATCGGGGATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTGTTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGATTTTGTTTCTAAAAT
* * * *
347122 ACCAATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTCTCACA
66 ACCAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATCTCCAAAACACTAATTTCTCACA
*
347187 ATCGGGGATACTCCAACCCCGTTATTTTC-ACGGGGATACTCAAACCCCGATTTTATTT-TCAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGA-GGGGATACTCAAACCCCGATTTTGTTTCT-AAA
* * *
347250 ATACCAA-TTTTCTATAATCGAGGATACTCTAGCCCCG-TTGTTATCTCCAAAA
64 ATACCAATTTTTC-ACAATCGAGGATACTCCAACCCCGATT-TTATCTCCAAAA
347302 TATTAAATTT
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
129 9 0.09
130 91 0.91
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (130 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGATTTTGTTTCTAAAAT
ACCAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATCTCCAAAACACTAATTTCTCACA
Found at i:347548 original size:22 final size:22
Alignment explanation
Indices: 347523--347567 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
347513 TCGTCCTTCC
347523 TTTCTATGTTTTTTTATGCATT
1 TTTCTATGTTTTTTTATGCATT
347545 TTTCTATGTTTTTTTATGCATT
1 TTTCTATGTTTTTTTATGCATT
347567 T
1 T
347568 ATTTTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (22 bp):
TTTCTATGTTTTTTTATGCATT
Found at i:349607 original size:33 final size:33
Alignment explanation
Indices: 349552--349614 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
349542 TTAGAAGCAA
* * *
349552 TGTATTGATACAATTCATCATGTATTAATATAT
1 TGTATCGATACAATTCACCATGTATCAATATAT
349585 TGTATCGATACAATGT-ACCATGTATCAATA
1 TGTATCGATACAAT-TCACCATGTATCAATA
349615 CAAACAGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (33 bp):
TGTATCGATACAATTCACCATGTATCAATATAT
Found at i:349685 original size:13 final size:13
Alignment explanation
Indices: 349667--349693 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
349657 ACAATTGTCC
349667 ATGTATCGATACA
1 ATGTATCGATACA
349680 ATGTATCGATACA
1 ATGTATCGATACA
349693 A
1 A
349694 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:352530 original size:20 final size:21
Alignment explanation
Indices: 352486--352558 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 21
352476 TTTTATAATT
*
352486 TGTATCGATACAAT-AG-GCAA
1 TGTATCGATAC-ATGAGTGAAA
*
352506 GGTATCGATACATGAGTG-AA
1 TGTATCGATACATGAGTGAAA
* * **
352526 TGTATCAATACTTGCCTGAAA
1 TGTATCGATACATGAGTGAAA
352547 TGTATCGATACA
1 TGTATCGATACA
352559 AAACCACTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.05
20 27 0.64
21 13 0.31
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAGTGAAA
Found at i:352625 original size:20 final size:21
Alignment explanation
Indices: 352583--352639 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
352573 TCTGGAAGGG
352583 AAATGTATCGATACATAAGT-
1 AAATGTATCGATACATAAGTA
* ***
352603 AAATGTATTGATACATGCTTA
1 AAATGTATCGATACATAAGTA
*
352624 AAATATATCGATACAT
1 AAATGTATCGATACAT
352640 TCTGAGTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (21 bp):
AAATGTATCGATACATAAGTA
Found at i:353772 original size:13 final size:13
Alignment explanation
Indices: 353754--353843 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
353744 TTCAACAATT
353754 TGTATCGATACAA
1 TGTATCGATACAA
353767 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
353782 GTGTTGTATCGATATAA
1 ----TGTATCGATACAA
353799 TGTATCGATACATAA
1 TGTATCGATAC--AA
353814 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
353831 TGTATCGCTACAA
1 TGTATCGATACAA
353844 AGCTACTGCC
Statistics
Matches: 62, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
13 33 0.53
15 4 0.06
17 4 0.06
19 21 0.34
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:353791 original size:19 final size:18
Alignment explanation
Indices: 353767--353829 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
353757 ATCGATACAA
353767 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
353786 TGTATCGAT--ATAA---
1 TGTATCGATACATAAGTT
353799 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
353818 TGTATCGATACA
1 TGTATCGATACA
353830 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
15 4 0.11
17 4 0.11
19 21 0.55
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:353794 original size:32 final size:32
Alignment explanation
Indices: 353753--353842 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
353743 TTTCAACAAT
353753 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
353785 TTGTATCGATATAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
353817 TTGTATCGATACAATGTATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
353843 AAGCTACTGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:356136 original size:27 final size:27
Alignment explanation
Indices: 356106--356176 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
356096 TTTATTCATT
356106 GGGGACACTCCAACCCCATTCCTCCGA
1 GGGGACACTCCAACCCCATTCCTCCGA
*
356133 GGGGACACTCCAACCCCATTCTTCCGA
1 GGGGACACTCCAACCCCATTCCTCCGA
356160 GGGGACACTCCAACCCC
1 GGGGACACTCCAACCCC
356177 GTTTTCAACC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.23, C:0.44, G:0.20, T:0.14
Consensus pattern (27 bp):
GGGGACACTCCAACCCCATTCCTCCGA
Found at i:358689 original size:28 final size:27
Alignment explanation
Indices: 358657--358733 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
358647 TTATCTCGAA
* *
358657 ATACTCCAACCCTATTATTT-TCGAGAGG
1 ATACTCCAACCC-ATT-TTTATCGAAAAG
*
358685 ATACTCTAATCCCATTTTTATCGAAAAG
1 ATACTCCAA-CCCATTTTTATCGAAAAG
358713 ATACTCCAACGCCATTTTTAT
1 ATACTCCAAC-CCATTTTTAT
358734 TTTCGAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
27 4 0.10
28 35 0.83
29 3 0.07
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (27 bp):
ATACTCCAACCCATTTTTATCGAAAAG
Found at i:358798 original size:79 final size:78
Alignment explanation
Indices: 358712--358934 Score: 297
Period size: 79 Copynumber: 2.8 Consensus size: 78
358702 TTATCGAAAA
358712 GATACTCCAACGCCATTTTTATTTTCGAAATATTAAATTTTTCATCTCAAAGATATTCCAACCCT
1 GATACTCCAAC-CCATTTTTATTTTCGAAATATTAAATTTTTCATCTCAAAGATATTCCAACCCT
358777 GTTATTTTTAA-AGG
65 GTTATTTTTAAGA-G
* * * *
358791 GATACTCCAACCCCATTTTTATTTTTGAAATATTAAAATTTTCATCTCAGAGATACTCCAACCCT
1 GATACTCCAA-CCCATTTTTATTTTCGAAATATTAAATTTTTCATCTCAAAGATATTCCAACCCT
*
358856 GTTATTTTTGAGAG
65 GTTATTTTTAAGAG
* * * *
358870 GATACTCCAACCTCGTTTTTA-TTTCTAAAATATTAAATTTTTCATCATCAAGGGTATTCCAACC
1 GATACTCCAACC-CATTTTTATTTTC-GAAATATTAAATTTTTCATC-TCAAAGATATTCCAACC
358934 C
63 C
358935 CATATTCAGA
Statistics
Matches: 126, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
78 5 0.04
79 105 0.83
80 16 0.13
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (78 bp):
GATACTCCAACCCATTTTTATTTTCGAAATATTAAATTTTTCATCTCAAAGATATTCCAACCCTG
TTATTTTTAAGAG
Found at i:358806 original size:107 final size:105
Alignment explanation
Indices: 358614--358812 Score: 283
Period size: 107 Copynumber: 1.9 Consensus size: 105
358604 GGGAATATTT
* * *
358614 CAACCCCATTTTTATTTTTGAAATATTAAATTTTTATCTCGAAATACTCCAACCCTATTATTTTC
1 CAACCCCATTTTTATTTTCGAAATATTAAATTTTTATCTCAAAATACTCCAACCCTATTATTTTA
* * *
358679 GAGAGGATACTCTAATCCCATTTTTATCGAAAAGATACTC
66 AAGAGGATACTCCAACCCCATTTTTATCGAAAAGATACTC
* * *
358719 CAACGCCATTTTTATTTTCGAAATATTAAATTTTTCATCTCAAAGATATTCCAACCCTGTTATTT
1 CAACCCCATTTTTATTTTCGAAATATTAAATTTTT-ATCTCAAA-ATACTCCAACCCTATTA-TT
358784 TTAAAG-GGATACTCCAACCCCATTTTTAT
63 TTAAAGAGGATACTCCAACCCCATTTTTAT
358813 TTTTGAAATA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
105 33 0.40
106 7 0.09
107 36 0.44
108 6 0.07
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.40
Consensus pattern (105 bp):
CAACCCCATTTTTATTTTCGAAATATTAAATTTTTATCTCAAAATACTCCAACCCTATTATTTTA
AAGAGGATACTCCAACCCCATTTTTATCGAAAAGATACTC
Found at i:360395 original size:20 final size:19
Alignment explanation
Indices: 360370--360478 Score: 104
Period size: 20 Copynumber: 5.8 Consensus size: 19
360360 CTGCCAAGGA
360370 AATGTATCGATACATTATTC
1 AATGTATCGATACATT-TTC
*
360390 AATGTATTGATACA---T-
1 AATGTATCGATACATTTTC
360405 --TGTATCGATACATTTTGC
1 AATGTATCGATACATTTT-C
* *
360423 ATTGTATCGATACATTGCTC
1 AATGTATCGATACATT-TTC
*
360443 ATTGTATCGATACATTTTAC
1 AATGTATCGATACATTTT-C
360463 AATGTATCGATACATT
1 AATGTATCGATACATT
360479 CAGGCATTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
13 11 0.15
16 2 0.03
19 1 0.01
20 60 0.80
21 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (19 bp):
AATGTATCGATACATTTTC
Found at i:360457 original size:40 final size:40
Alignment explanation
Indices: 360402--360478 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
360392 TGTATTGATA
* *
360402 CATTGTATCGATACATTTTGCATTGTATCGATACATTGCT
1 CATTGTATCGATACATTTTACAATGTATCGATACATTGCT
360442 CATTGTATCGATACATTTTACAATGTATCGATACATT
1 CATTGTATCGATACATTTTACAATGTATCGATACATT
360479 CAGGCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (40 bp):
CATTGTATCGATACATTTTACAATGTATCGATACATTGCT
Found at i:362835 original size:51 final size:51
Alignment explanation
Indices: 362770--362938 Score: 178
Period size: 51 Copynumber: 3.3 Consensus size: 51
362760 ATTTTTCATC
* * * * * *
362770 TCGGGAATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTCCATAA
* *
362821 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
* * * * * *
362872 CCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCGACTTTACACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
* *
362923 TTGGGGATATTCCAAC
1 TCGGGGATACTCCAAC
362939 CCCGTTATTT
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 98 0.99
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
Found at i:364524 original size:19 final size:19
Alignment explanation
Indices: 364500--364554 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
364490 AATTCAACGA
364500 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
364519 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
364538 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
364555 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:367032 original size:51 final size:53
Alignment explanation
Indices: 366963--367304 Score: 199
Period size: 52 Copynumber: 6.5 Consensus size: 53
366953 AGTTTATCAA
* * * * *
366963 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
367014 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
367068 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAAT
** *** * * *
367121 CCCGTT-ATTTTCGAGGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 TTC-TTCACAATC--GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * *
367175 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* * * *
367228 TTCCTT--TAATCGGGGACACTCCAACTCCGATTTTATTTTCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
367280 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
367305 CTCGTTATTT
Statistics
Matches: 221, Mismatches: 46, Indels: 47
0.70 0.15 0.15
Matches are distributed among these distances:
50 4 0.02
51 35 0.16
52 80 0.36
53 38 0.17
54 39 0.18
55 22 0.10
57 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:367190 original size:107 final size:106
Alignment explanation
Indices: 367026--367443 Score: 323
Period size: 107 Copynumber: 3.9 Consensus size: 106
367016 TTCTATAATC
*
367026 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
367091 AACCCCGTTAATCATCGGGGATACTCCAATCCCGTTATTTTCGA
63 AACCCCGTTAATCATCGGGGATACTCCAATCCCGTTATTTTCGA
* * *
367135 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
** * ** * * * * **
367199 ATCCTGGTTTTATTTTC---AAAACGCCAATTTTCC-TT-TAATC--
64 A-CCCCG-TTAATCATCGGGGATACTCCAA--TCCCGTTATTTTCGA
* * * *
367239 GGGGACACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* * * * *
367304 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCGTTA-ATCATCGGGGATACTCCAATCCCGTTATTTTCGA
* ** * * *** * * *
367347 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
**
367412 CCCGTT-ATTTTCGAAGGGATACTCCAATCCCG
66 CCCGTTAATCATCG--GGGATACTCCAATCCCG
367444 ATTTTTTTTC
Statistics
Matches: 237, Mismatches: 54, Indels: 38
0.72 0.16 0.12
Matches are distributed among these distances:
102 2 0.01
103 7 0.03
104 43 0.18
105 20 0.08
106 21 0.09
107 89 0.38
108 27 0.11
109 28 0.12
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (106 bp):
GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAATCCCGTTATTTTCGA
Found at i:367288 original size:104 final size:103
Alignment explanation
Indices: 366968--367303 Score: 288
Period size: 104 Copynumber: 3.2 Consensus size: 103
366958 ATCAATTCTC
* * * *
366968 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGAGGATACTCCAA-TCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
367032 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * * ** * * * * **
367073 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--TCCCGTTATTTTCGA
1 CACAATCGAGGATACTCCAATCCGGTTTTATTTTC---AAAACACCAATTTTCC-TT-TAATC--
* * *
367135 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
* *
367179 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
* * *
367244 CACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
367284 CACAATCGAGGATACTCCAA
1 CACAATCGAGGATACTCCAA
367304 CCTCGTTATT
Statistics
Matches: 177, Mismatches: 38, Indels: 33
0.71 0.15 0.13
Matches are distributed among these distances:
103 6 0.03
104 44 0.25
105 33 0.19
106 20 0.11
107 41 0.23
108 5 0.03
109 28 0.16
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGAGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:367324 original size:28 final size:28
Alignment explanation
Indices: 367288--367364 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
367278 ATTTTTCACA
* * *
367288 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
367316 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
367344 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
367365 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:367339 original size:212 final size:212
Alignment explanation
Indices: 366966--367371 Score: 602
Period size: 212 Copynumber: 1.9 Consensus size: 212
366956 TTATCAATTC
* *
366966 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
367031 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 CACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * * *
367096 CGTTAATCATCGGGGATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
367161 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
367178 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
367242 GACACTCCAACTCCGATTTTATTTTC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GACACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
367305 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
367370 AT
193 AT
367372 TCCCAAAATA
Statistics
Matches: 173, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 31 0.18
212 109 0.63
213 33 0.19
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
CACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:367497 original size:78 final size:79
Alignment explanation
Indices: 367318--367519 Score: 230
Period size: 78 Copynumber: 2.6 Consensus size: 79
367308 GTTATTTCAT
* * * *
367318 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
* * *
367383 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * ** *
367397 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCC-GATTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAAT-A
367460 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
367475 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
367520 TGTTATTATC
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 8 0.08
78 55 0.53
79 41 0.39
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:369880 original size:17 final size:16
Alignment explanation
Indices: 369852--369898 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
369842 ATAATAGCAT
369852 TACAAATTAATAAGAA
1 TACAAATTAATAAGAA
*
369868 TACAAATTTAATAAAAAA
1 TACAAA-TTAAT-AAGAA
369886 TA-AAATTAATAAG
1 TACAAATTAATAAG
369899 GATATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 8 0.30
18 6 0.22
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (16 bp):
TACAAATTAATAAGAA
Found at i:369935 original size:14 final size:14
Alignment explanation
Indices: 369912--369953 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
369902 ATATTTTTAG
369912 AAAATATAATAACTA
1 AAAAT-TAATAACTA
*
369927 AAAATTAATAAATA
1 AAAATTAATAACTA
369941 AAATATT-ATAACT
1 AAA-ATTAATAACT
369954 TTATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATTAATAACTA
Found at i:370202 original size:23 final size:23
Alignment explanation
Indices: 370176--370232 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
370166 TTTTGAAAAT
370176 TAATTAACATT-TATTTATTAATA
1 TAATTAAC-TTATATTTATTAATA
*
370199 TAATT-ACTTAATATTTATTAGTA
1 TAATTAACTT-ATATTTATTAATA
370222 TAATTAA-TTAT
1 TAATTAACTTAT
370233 TAATATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.07
22 4 0.13
23 23 0.77
24 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATTAACTTATATTTATTAATA
Found at i:370211 original size:13 final size:12
Alignment explanation
Indices: 370190--370248 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 12
370180 TAACATTTAT
370190 TTATTAATATAA
1 TTATTAATATAA
*
370202 TTACTTAATATTTA
1 TTA-TTAATA-TAA
370216 TTAGTATAAT-TAA
1 TTA-T-TAATATAA
370229 TTATTAATATAA
1 TTATTAATATAA
370241 TTAATTAA
1 TT-ATTAA
370249 AATTTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.10
12 9 0.23
13 16 0.41
14 6 0.15
15 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
TTATTAATATAA
Found at i:370234 original size:16 final size:16
Alignment explanation
Indices: 370213--370247 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
370203 TACTTAATAT
*
370213 TTATTAGTATAATTAA
1 TTATTAATATAATTAA
370229 TTATTAATATAATTAA
1 TTATTAATATAATTAA
370245 TTA
1 TTA
370248 AAATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTATTAATATAATTAA
Found at i:371417 original size:20 final size:20
Alignment explanation
Indices: 371389--371433 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
371379 TTAATCTGAA
*
371389 TTCATCACACATTGGC-AAAG
1 TTCAACACAC-TTGGCTAAAG
*
371409 TTCAACACACTTTGCTAAAG
1 TTCAACACACTTGGCTAAAG
371429 TTCAA
1 TTCAA
371434 GTTCAGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (20 bp):
TTCAACACACTTGGCTAAAG
Found at i:374509 original size:3 final size:3
Alignment explanation
Indices: 374501--374528 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
374491 AGGATATTGT
374501 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
374529 GGTGGAAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:374797 original size:16 final size:16
Alignment explanation
Indices: 374778--374830 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
374768 ATCGGATCAG
*
374778 TTTTAAATTTGAATTA
1 TTTTAAATTTTAATTA
374794 TTTT--ATTTTAAGTTA
1 TTTTAAATTTTAA-TTA
*
374809 TTTTAAATTTTAGTTA
1 TTTTAAATTTTAATTA
374825 TTTTAA
1 TTTTAA
374831 GTTATTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 13 0.41
17 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTTAAATTTTAATTA
Found at i:374811 original size:10 final size:10
Alignment explanation
Indices: 374796--374836 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
374786 TTGAATTATT
374796 TTATTTTAAG
1 TTATTTTAAG
374806 TTATTTTAA-
1 TTATTTTAAG
374815 --ATTTT-AG
1 TTATTTTAAG
374822 TTATTTTAAG
1 TTATTTTAAG
374832 TTATT
1 TTATT
374837 GTTTAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
6 1 0.04
7 5 0.19
9 5 0.19
10 16 0.59
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (10 bp):
TTATTTTAAG
Found at i:376269 original size:23 final size:23
Alignment explanation
Indices: 376226--376269 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
376216 TTAAAATAAA
* *
376226 AAAATTATTTATAATGTATATTT
1 AAAATTAATTATAATGAATATTT
376249 AAAATTCAATTATAAT-AATAT
1 AAAATT-AATTATAATGAATAT
376270 AAGTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AAAATTAATTATAATGAATATTT
Found at i:378030 original size:24 final size:24
Alignment explanation
Indices: 377995--378049 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
377985 ATGACAATGA
377995 ATTT-TAACCTAAAGTTTTAATTT
1 ATTTATAACCTAAAGTTTTAATTT
*
378018 ATTTATAATCTAAAGTTTTAATTT
1 ATTTATAACCTAAAGTTTTAATTT
378042 ATTTATAA
1 ATTTATAA
378050 GTATCTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTTATAACCTAAAGTTTTAATTT
Found at i:393968 original size:42 final size:42
Alignment explanation
Indices: 393853--395735 Score: 1255
Period size: 42 Copynumber: 44.7 Consensus size: 42
393843 TTTTTTTGCT
* * *
393853 TTCCCTTAGTCTGCCTGTTGGCTTTGACCCTAGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * *
393895 TACCCTTTAGTTTGTCTGTCGACTTTAACCCTTGAGACTTTTC
1 TTCCC-TTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
393938 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * * *
393980 TACTCTTCGGTCTGCCTATCGGCTTCGTCCCTGGAGAC--TGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * ** *
394021 CTCATCTAAAGTCTGTTTGTCGGCTTTGACCCTAGAGACTTTTC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* ** * * *
394065 ATCCCTTAGTCTGCCTGTC-AATTTAATCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
394106 TACCCTTCAGTCTGCCTATCGGCTTCGTCCCTGGAGAC--TGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * *
394147 CTCATCTAAAGTCTGTCTGTCGACTTTGACCCTGGAGACTTTCC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
394191 TT-CCTTCAGTCTGCCTATCGGCTTTGACCTTGGATAC--TGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* ** * * * * * *
394231 CTCATTTAAAGTCTGCCTGTCGACTTTGATCTTAGATAC--TGC
1 TTCCCTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* ** * * ** *
394273 CTCATTTAAAGTTTGCCTGTCAGCTTTGACTTTGAAGACTTTTC
1 TTCCCTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
394317 TACCCTTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCC-TTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * **
394360 TTCCCTTAATCTGCCTATCGGCTTTGACCCTTAAGA-TTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTT-C
* * * * *
394402 TACCCTTCAGTCTGCCTGTCAGCTTCGTCCCTGGAGAC--TGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
394443 CTCATCTAAAGTCTGTCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
394487 ATCCCTTAGTCTG-CTGTTGGCTTTGACCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* ** * * *
394528 TACTTTTCAGTCTGCCTGTCGGCTTCGTCCCTGGAGA--TTAC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * ** * *
394569 CTCATCTAAAGTCTGCCGGTCAACTTTGACCTTGGAGACTTTCC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** *
394613 TT-CCTTCAGTCTGCCTGTTAGCTTTGACCCCGGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * * *
394655 AACCCTTAGTCTTCCTATTGGCTTTGACCTTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
394697 AT-CCTTGAGTCTGTCTGTCGGCTTTGACCATGGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * *
394739 AACCCTCAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
394781 TACCCTTCAGTCTGCCTGTCGGCTTCGTCCCTAGAGA--TTGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
394822 CTCACCTAAAGTTTGCCTGTCGGCTTTGACCTTGAAGACTTTTC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
394866 ATCCCTTAGTCAGCCTGTCGG-TTTGACCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
394907 TACCCTTCAGTCTGCCTGTCGGCTTCGTCCCTGGAGAC--TGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * *
394948 CTCATCTAAAGTCTGCCTGTCGGCTTAGACCCTAGAGACTTTCC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
394992 TT-CCTTCAGTCTGCCTATTGGCTTTGACCTTAGAGAC--TGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* ** * * *
395032 CTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGAAGACTTTTT
1 TTCCCTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
395076 TTCCCTTAATCTACCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * * ** *
395118 AACCCTCAGTCTGCCAGTCGG-TTTCGTCCCTAAAGAC--TGC
1 TTCCCTTAGTCTGCCTGTCGGCTTT-GACCCTGGAGACTTTTC
* * * * *
395158 CTCATCTAAATTCTGCCTGTCGGCTTTGACCTTGGAGAC-TTTC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
395201 TTTCCCTCAGTCTGCCTGTCGGCTTTGACCCAGAAAACTTTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * * * *
395244 AACCCTCAGTCTTCCTATTGGCTTTGACCGTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
395286 AT-CCTTGAGTCTGTCTATCGACTTTGACCCTGGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * * * * *
395328 AACTCTCAGTCTGCTTGTCGGCTTTGACCTTTGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
395370 TTCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTT-
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
395411 TAACCCTTAGTCTGCTTGTCGGCTTTGACCCTGGAGAC-TTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
395453 TTTCCCTCAATCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
395495 TTTCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
395537 TTTCCCTCAGTCTGCCTGTCGGCTTTGACCCCGAAGACTTTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
395580 ATCCCTTAGTTTGCCTGTCGG-TTTAACCCTAGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
395621 TTCCCTCAGTCTGCATGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * ** * *
395663 ATCCCTTAGTTTGCCTGTCAGCTTTGTTCCTAGAGATTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
395705 TTTCCCTAAGTCTGCCCGTTGGTTTTGACCC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCC
395736 GGAAGATTTT
Statistics
Matches: 1430, Mismatches: 345, Indels: 131
0.75 0.18 0.07
Matches are distributed among these distances:
40 9 0.01
41 147 0.10
42 1002 0.70
43 237 0.17
44 33 0.02
45 2 0.00
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.36
Consensus pattern (42 bp):
TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
Found at i:395839 original size:15 final size:17
Alignment explanation
Indices: 395819--395850 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
395809 AACTGTGTGG
395819 TCCTGC-TT-TTGTTTT
1 TCCTGCATTCTTGTTTT
395834 TCCTGCATTCTTGTTTT
1 TCCTGCATTCTTGTTTT
395851 ATTCTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.03, C:0.22, G:0.12, T:0.62
Consensus pattern (17 bp):
TCCTGCATTCTTGTTTT
Found at i:396257 original size:33 final size:33
Alignment explanation
Indices: 396192--396277 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
396182 AAAAATCAAA
*
396192 AAAAATTAA-AAATAATAATATTCAATATAATAAT
1 AAAAATCAAGAAATAA-AA-ATTCAATATAATAAT
*
396226 AAAAATCAAGAAATAAAAATTTAATATAATAAT
1 AAAAATCAAGAAATAAAAATTCAATATAATAAT
396259 AAAAATCAAGAAATAAAAA
1 AAAAATCAAGAAATAAAAA
396278 AAATTCAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
33 33 0.67
34 10 0.20
35 6 0.12
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (33 bp):
AAAAATCAAGAAATAAAAATTCAATATAATAAT
Found at i:396304 original size:23 final size:20
Alignment explanation
Indices: 396259--396315 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
396249 ATATAATAAT
*
396259 AAAAATCAAGAAATAAA--A
1 AAAAATCAAAAAATAAAGTA
*
396277 AAAATTCAAACAAAATAAAGTA
1 AAAAATC-AA-AAAATAAAGTA
396299 AAAAATCAAAAAATAAA
1 AAAAATCAAAAAATAAA
396316 AAATGACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 6 0.19
19 2 0.06
20 15 0.47
21 2 0.06
22 7 0.22
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (20 bp):
AAAAATCAAAAAATAAAGTA
Found at i:397607 original size:14 final size:14
Alignment explanation
Indices: 397590--397644 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
397580 TTTTTGAATT
397590 TTTTTATTTCTTGA
1 TTTTTATTTCTTGA
*
397604 TTTTTATTATTATATTGAA
1 --TTT-TTATT-TCTTG-A
397623 TTTTTATTTCTTGA
1 TTTTTATTTCTTGA
397637 TTTTTATT
1 TTTTTATT
397645 ATTATATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 9 0.26
15 4 0.12
16 8 0.24
17 8 0.24
18 4 0.12
19 1 0.03
ACGTcount: A:0.20, C:0.04, G:0.05, T:0.71
Consensus pattern (14 bp):
TTTTTATTTCTTGA
Found at i:397610 original size:33 final size:34
Alignment explanation
Indices: 397583--397675 Score: 136
Period size: 33 Copynumber: 2.7 Consensus size: 34
397573 TTTATTTTTT
397583 TTGAATTTTTTTATTTCTTGATTTTTATTATTATA
1 TTGAA-TTTTTTATTTCTTGATTTTTATTATTATA
397618 TTGAA-TTTTTATTTCTTGATTTTTATTATTATA
1 TTGAATTTTTTATTTCTTGATTTTTATTATTATA
* *
397651 TTGAATATTATTATTT-TTAATTTTT
1 TTGAAT-TTTTTATTTCTTGATTTTT
397676 TTTGATTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
33 33 0.61
34 8 0.15
35 13 0.24
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (34 bp):
TTGAATTTTTTATTTCTTGATTTTTATTATTATA
Found at i:400917 original size:3 final size:3
Alignment explanation
Indices: 400909--400942 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
400899 GAGAATTGCA
400909 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
400943 GGAAAAACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:402424 original size:20 final size:21
Alignment explanation
Indices: 402399--402451 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
402389 TTACAAGCCA
402399 ATGTATCGATACAAT-TTGGG
1 ATGTATCGATACAATCTTGGG
*
402419 ATGTATCGATAC-ATCTTGTG
1 ATGTATCGATACAATCTTGGG
402439 -TGTATCGATACAA
1 ATGTATCGATACAA
402452 ACAATTACGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGTATCGATACAATCTTGGG
Found at i:402539 original size:20 final size:21
Alignment explanation
Indices: 402492--402544 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
402482 GCCAATCACT
*
402492 TGTATCGATACATTCTTTGTA
1 TGTATCGATACATTCTTGGTA
*
402513 AGTATCGATACA-T-TTGGTCA
1 TGTATCGATACATTCTTGGT-A
402533 TGTATCGATACA
1 TGTATCGATACA
402545 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 11 0.39
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTTGGTA
Found at i:402550 original size:13 final size:13
Alignment explanation
Indices: 402532--402556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
402522 ACATTTGGTC
402532 ATGTATCGATACA
1 ATGTATCGATACA
402545 ATGTATCGATAC
1 ATGTATCGATAC
402557 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:402589 original size:20 final size:20
Alignment explanation
Indices: 402566--402606 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
402556 CTGTGCATTA
*
402566 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTTAAAGG
402586 TGTATCGATACATTTAAAGG
1 TGTATCGATACATTTAAAGG
402606 T
1 T
402607 ATTAACCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTTAAAGG
Found at i:405042 original size:13 final size:13
Alignment explanation
Indices: 405024--405055 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
405014 ATAAACCCTT
*
405024 TGTATCGATACAC
1 TGTATCGATACAA
405037 TGTATCGATACAA
1 TGTATCGATACAA
405050 TGTATC
1 TGTATC
405056 TGTCGCGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Done.