Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012839.1 Corchorus capsularis cultivar CVL-1 contig12860, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35449
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:1997 original size:167 final size:166
Alignment explanation
Indices: 1608--2050 Score: 600
Period size: 167 Copynumber: 2.7 Consensus size: 166
1598 TGAGTCATTT
* * * * *
1608 TCAATTGAGAAATGACCAAAAAGTTTATTTATTTGATTCTCTCAAGAATTAAAAGTTAGGACATT
1 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACATT
* * * * ** * *
1673 TAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTATCTCATCATCAATCCTTAA
66 TAAATAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTAA
* * * *
1738 TGGGGATCTTTTATTAATTCCACTACTCTATTCAAG
131 TAGGGATCATTTAGTAATTCCACTACTCTATTAAAG
* * *
1774 TCCATTGAGAAATAACCAAAAAGATT-GCTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACAT
1 TCAATTGAGAAATGACCAAAAAGTTTAG-TTATTTAATCCCCTCAAGAATAAAAAGTTAGGACAT
* *
1838 TTAAATAATCTGTCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTT
65 TTAAATAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAAGCAAGCCTT
**
1903 GGTAGGGATCATTTAGTAATTCCACTACTCTATTAAAG
129 AATAGGGATCATTTAGTAATTCCACTACTCTATTAAAG
* * *
1941 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCGAGAATCAAAAGTTAGGATATT
1 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACATT
* *
2006 TAATTAATCTGCCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCT
66 TAAATAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT
2051 CGCTCCTCAT
Statistics
Matches: 240, Mismatches: 34, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
166 99 0.41
167 140 0.58
168 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (166 bp):
TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACATT
TAAATAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTAA
TAGGGATCATTTAGTAATTCCACTACTCTATTAAAG
Found at i:2665 original size:45 final size:45
Alignment explanation
Indices: 2614--2702 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
2604 ATTACTTCTT
*
2614 CAGCTCATCATTAATATGTGGTAGAGATCTTTCAGTAATTCCACC
1 CAGCTCATCATTAATATGGGGTAGAGATCTTTCAGTAATTCCACC
* * *
2659 CAGCTCATCATTAATTTGGGGTAGGGATCTTTTAGTAATTCCAC
1 CAGCTCATCATTAATATGGGGTAGAGATCTTTCAGTAATTCCAC
2703 TACTCTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (45 bp):
CAGCTCATCATTAATATGGGGTAGAGATCTTTCAGTAATTCCACC
Found at i:3065 original size:17 final size:17
Alignment explanation
Indices: 3039--3088 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
3029 ATACTTATGT
3039 GTGATTAGTGATTT-TA
1 GTGATTAGTGATTTATA
3055 GTGATTTAGTGATTTATA
1 GTGA-TTAGTGATTTATA
*
3073 GTCTGATTAATGATTT
1 G--TGATTAGTGATTT
3089 TATTTAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.14
17 10 0.34
18 3 0.10
19 9 0.31
20 3 0.10
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (17 bp):
GTGATTAGTGATTTATA
Found at i:3495 original size:24 final size:25
Alignment explanation
Indices: 3463--3511 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3453 TTGAATGATT
* *
3463 GAGATTTG-AAAGTTTGAAGGTTGA
1 GAGAATTGAAAAGTTTAAAGGTTGA
*
3487 GAGAATTGAAAAGTTTAAAGTTTGA
1 GAGAATTGAAAAGTTTAAAGGTTGA
3512 TGGAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.33
Consensus pattern (25 bp):
GAGAATTGAAAAGTTTAAAGGTTGA
Found at i:4950 original size:2 final size:2
Alignment explanation
Indices: 4943--4970 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4933 CCGAGAATCG
4943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4971 TTGGTACCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5766 original size:47 final size:47
Alignment explanation
Indices: 5713--5814 Score: 159
Period size: 47 Copynumber: 2.2 Consensus size: 47
5703 TCTCCGTGTT
* * * * *
5713 AATTGGGTTTCTGCTTTTCTTGGATTGGTTTTGCTTTGTTTTCTTTG
1 AATTGGGTTTCTGCTTTTCTTAGATTAGCTTTGCTTTGCTTTCTCTG
5760 AATTGGGTTTCTGCTTTTCTTAGATTAGCTTTGCTTTGCTTTCTCTG
1 AATTGGGTTTCTGCTTTTCTTAGATTAGCTTTGCTTTGCTTTCTCTG
5807 AATTGGGT
1 AATTGGGT
5815 ATTTTTTTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (47 bp):
AATTGGGTTTCTGCTTTTCTTAGATTAGCTTTGCTTTGCTTTCTCTG
Found at i:5897 original size:29 final size:29
Alignment explanation
Indices: 5832--5907 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
5822 TGTTTTCTCA
*
5832 TGTATTGATTATTTTCTTATTATGGTAGT
1 TGTATTGATTATTTTCTTATTATGCTAGT
*
5861 CG-ATTTGATTATTTTCTTGGATT-TGCT-GT
1 TGTA-TTGATTATTTTCTT--ATTATGCTAGT
5890 TGTATTGATTATTTTCTT
1 TGTATTGATTATTTTCTT
5908 CACTTTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 1 0.03
29 32 0.80
30 4 0.10
31 3 0.08
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (29 bp):
TGTATTGATTATTTTCTTATTATGCTAGT
Found at i:7214 original size:87 final size:87
Alignment explanation
Indices: 7121--7306 Score: 270
Period size: 86 Copynumber: 2.1 Consensus size: 87
7111 TTAAGAAATA
7121 AATTAAAAAAAATTCTAATATATCTAAGTTTTGT-AATTAAAATAGTAAAAATGGTAAAAATAAA
1 AATTAAAAAAAATTCTAATATATCTAAGTTTTGTAAATTAAAATAGT-AAAATGGTAAAAATAAA
*
7185 ATAGTTATAAAGAGATTAGATTT
65 ATAATTATAAAGAGATTAGATTT
* * * * *
7208 AATT--AAAAAATTTTAATATATCTAAGTTTTTTAAAATTAAAATAGTAAAATGTTAGAGATAAA
1 AATTAAAAAAAATTCTAATATATCTAAGTTTTGT-AAATTAAAATAGTAAAATGGTAAAAATAAA
7271 ATAATTATAAAGAGATTAGATTT
65 ATAATTATAAAGAGATTAGATTT
*
7294 AATTAATAAAAAT
1 AATTAAAAAAAAT
7307 AGAGTTTTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
85 26 0.30
86 40 0.45
87 16 0.18
88 6 0.07
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (87 bp):
AATTAAAAAAAATTCTAATATATCTAAGTTTTGTAAATTAAAATAGTAAAATGGTAAAAATAAAA
TAATTATAAAGAGATTAGATTT
Found at i:7273 original size:153 final size:151
Alignment explanation
Indices: 6839--7281 Score: 364
Period size: 145 Copynumber: 3.0 Consensus size: 151
6829 TTAAAAAGTA
*
6839 TAATATATCTAAGTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAGATT
1 TAATATATCTAAGTTTTGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAGATT
* * * ** * *
6904 AGATTTAATTAAATAATTCTAATATATCAAAGTTTTTTTTAATTAAAATAGTAAAATGATAAAAA
66 AGATTTAATTAAAAAATTTTAATATATCTAAGTTTTTTAAAATTAAAATAGTAAAATG-TTAAGA
* * *
6969 TAAAAT-AGTTATAAAGAGATC
130 TAAAATAAATTATAAAAAAATC
* * * * * * * *
6990 AAAAAGTCTCCAA---TT-T-CTTAAAAT--TAAAATGGTAAAAATAAAATATTTATAAAAATAT
1 TAATA-TATCTAAGTTTTGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAGAT
* * ** *** * * **
7048 T-GAATTTATAAATAAAAAATAGTTT-GTAGTAGAATAA-AACTGTAAAAGTTTAAAA-AATATC
65 TAG-A-TT-TAATTAAAAAAT--TTTAATA-TA-TCTAAGTTTTTTAAAA--TTAAAATAGTAAA
7109 AT-TTAAG---AAATAAATTA-AAAAAAATTC
121 ATGTTAAGATAAAATAAATTATAAAAAAA-TC
7136 TAATATATCTAAGTTTTGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAAGAGAT
1 TAATATATCTAAGTTTTGTAATTAAAATAGT-AAAATGGTAAAAATAAAATAGTTATAAAGAGAT
7201 TAGATTTAATTAAAAAATTTTAATATATCTAAGTTTTTTAAAATTAAAATAGTAAAATGTTAGAG
65 TAGATTTAATTAAAAAATTTTAATATATCTAAGTTTTTTAAAATTAAAATAGTAAAATGTTA-AG
7266 ATAAAAT-AATTATAAA
129 ATAAAATAAATTATAAA
7282 GAGATTAGAT
Statistics
Matches: 213, Mismatches: 49, Indels: 58
0.67 0.15 0.18
Matches are distributed among these distances:
144 1 0.00
145 47 0.22
146 11 0.05
147 23 0.11
148 15 0.07
149 25 0.12
150 18 0.08
151 20 0.09
152 13 0.06
153 39 0.18
154 1 0.00
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (151 bp):
TAATATATCTAAGTTTTGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAGATT
AGATTTAATTAAAAAATTTTAATATATCTAAGTTTTTTAAAATTAAAATAGTAAAATGTTAAGAT
AAAATAAATTATAAAAAAATC
Found at i:7335 original size:86 final size:87
Alignment explanation
Indices: 7155--7330 Score: 207
Period size: 86 Copynumber: 2.1 Consensus size: 87
7145 TAAGTTTTGT
* *
7155 AATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAAGAGATTAGATTTAATTAAAAAATT
1 AATTAAAATAGTAAAAATGGTAAAAATAAAATAATTATAAAGAGATTAGATTTAATTAAAAAAAT
** ***
7220 TTAATATATCTAAGTTTTTTAA
66 AGAATATATCTAAGTTGAATAA
* * *
7242 AATTAAAATAGT-AAAATGTTAGAGATAAAATAATTATAAAGAGATTAGATTTAATTAATAAAAA
1 AATTAAAATAGTAAAAATGGTAAAAATAAAATAATTATAAAGAGATTAGATTTAATTAA-AAAAA
* *
7306 TAGAGT-T-T-TTAGTTGAATAA
65 TAGAATATATCTAAGTTGAATAA
7326 AATTA
1 AATTA
7331 TAAAAGTTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
84 13 0.17
85 1 0.01
86 43 0.57
87 19 0.25
ACGTcount: A:0.53, C:0.01, G:0.11, T:0.36
Consensus pattern (87 bp):
AATTAAAATAGTAAAAATGGTAAAAATAAAATAATTATAAAGAGATTAGATTTAATTAAAAAAAT
AGAATATATCTAAGTTGAATAA
Found at i:7468 original size:6 final size:6
Alignment explanation
Indices: 7457--7484 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7447 ATTTTGGTGG
7457 ATGAGT ATGAGT ATGAGT ATGAGT ATGA
1 ATGAGT ATGAGT ATGAGT ATGAGT ATGA
7485 CGAAGAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (6 bp):
ATGAGT
Found at i:8917 original size:2 final size:2
Alignment explanation
Indices: 8910--8946 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8900 GAAAGAAAAC
8910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8947 AAAGTAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11765 original size:74 final size:74
Alignment explanation
Indices: 11644--11794 Score: 207
Period size: 74 Copynumber: 2.0 Consensus size: 74
11634 ACAAATTGTA
* * * * *
11644 AACTAAACTCACATTTCGTAGGACTTGAATTCAGGATCTCACAGTTTAGATACGGTGCATCTACT
1 AACTAAACTCACATTTCGTAAGACTTGAATTCAGAACCTCACAGTTTAGATAAGATGCATCTACT
11709 AGTTGAGCT
66 AGTTGAGCT
* *
11718 AACTAAACTCACA-TTCTGTAAGACTTGAA-TCTAGAACCTCACAGTTTAGGTAAGATGCATTTA
1 AACTAAACTCACATTTC-GTAAGACTTGAATTC-AGAACCTCACAGTTTAGATAAGATGCATCTA
11781 CTAGTTGAGCT
64 CTAGTTGAGCT
11792 AAC
1 AAC
11795 AACTCGATGC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
73 5 0.07
74 63 0.93
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (74 bp):
AACTAAACTCACATTTCGTAAGACTTGAATTCAGAACCTCACAGTTTAGATAAGATGCATCTACT
AGTTGAGCT
Found at i:14149 original size:35 final size:35
Alignment explanation
Indices: 14110--14177 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
14100 GCCCATTACC
14110 ACCTTTTTTTTTTTGCCACAAACACTTTACGAATA
1 ACCTTTTTTTTTTTGCCACAAACACTTTACGAATA
*
14145 ACCTTTTTTTTTTTGCCACAAATACTTTACGAA
1 ACCTTTTTTTTTTTGCCACAAACACTTTACGAA
14178 AAACGAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (35 bp):
ACCTTTTTTTTTTTGCCACAAACACTTTACGAATA
Found at i:15914 original size:82 final size:84
Alignment explanation
Indices: 15817--15977 Score: 263
Period size: 84 Copynumber: 1.9 Consensus size: 84
15807 TCTATTTTTA
*
15817 TTTAATTAAATCTAAT-TCCTTATAACTATTTTATTTTTACCA-TTTTACTATTTTAATTAAAAA
1 TTTAATTAAACCTAATCTCCTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAA
15880 ACTTAGATATATTAGAATT
66 ACTTAGATATATTAGAATT
* * *
15899 TTTAATTAAACCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACATA
1 TTTAATTAAACCTAATCTCCTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAA
*
15964 ACTTATATATATTA
66 ACTTAGATATATTA
15978 TTATAGTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
82 15 0.21
83 25 0.35
84 32 0.44
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.52
Consensus pattern (84 bp):
TTTAATTAAACCTAATCTCCTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAA
ACTTAGATATATTAGAATT
Found at i:16133 original size:35 final size:35
Alignment explanation
Indices: 16087--16154 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
16077 TTTATAAATA
* *
16087 TTTTATTTTTACCATTTTAATTTTAATAAATTGTT
1 TTTTAATTTTACCATTTTAATTTTAAAAAATTGTT
16122 TTTTAATTTTACCATTTTAATTTTAAAAAATTG
1 TTTTAATTTTACCATTTTAATTTTAAAAAATTG
16155 GAGACTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (35 bp):
TTTTAATTTTACCATTTTAATTTTAAAAAATTGTT
Found at i:21766 original size:156 final size:154
Alignment explanation
Indices: 21512--21857 Score: 358
Period size: 156 Copynumber: 2.2 Consensus size: 154
21502 AGACTTCGTA
** * * * *
21512 TGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAATTTGGGGTGTCAAACCTACTTCACTATGCT
1 TGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAACATGGGGAGACAAACCTACTTCACCATGCA
* * * * *
21577 AGAGAGGTAGGTTCTACTTATAATTTTTCCCATAGCTTCATGGGGATAATCTAAGTCTACTGGTG
66 AGAGAGCTAGATTCTACTTATAATTTTTCCCATAGCTTCATGGAGAGAATATAAGTC-ACT--TG
* *
21642 GAAAA-TCAGCTTCGTT-GGACTT-AGAG
128 GAAAATTCAGC-TCATTCAGACTTAAG-G
* * *
21668 TGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACATGGGGAGAGAAACCTAGTTCACCAT-CA
1 TGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAACATGGGGAGACAAACCTACTTCACCATGCA
* ** * * * ** *
21732 AGGGGAGCTCTATTTTACTTATAATTTTTTCCATAGTTTTGTGGAGAGAATATAAGTCCCTTGGA
66 A-GAGAGCTAGATTCTACTTATAATTTTTCCCATAGCTTCATGGAGAGAATATAAGTCACTTGGA
*
21797 AAAGTTTCAGCTCATTCAGAGTTAAGG
130 AAA--TTCAGCTCATTCAGACTTAAGG
21824 TGAAAAACTTATGCTAGTTTTTCAGTTAAGGACA
1 TGAAAAACTTATGCTAGTTTTTCAGTTAAGGACA
21858 GTTTGAGGTA
Statistics
Matches: 157, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
153 7 0.04
155 8 0.05
156 140 0.89
157 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (154 bp):
TGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAACATGGGGAGACAAACCTACTTCACCATGCA
AGAGAGCTAGATTCTACTTATAATTTTTCCCATAGCTTCATGGAGAGAATATAAGTCACTTGGAA
AATTCAGCTCATTCAGACTTAAGG
Found at i:26923 original size:4 final size:4
Alignment explanation
Indices: 26914--26940 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
26904 TGGATATATT
26914 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
26941 ATAAAATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:29092 original size:331 final size:329
Alignment explanation
Indices: 27761--31104 Score: 2584
Period size: 331 Copynumber: 10.2 Consensus size: 329
27751 ATACTTTACA
* * *
27761 TCATCTAACCAAATCTCAGCAACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGC-ACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
27826 TTCGATTTAATTAGAAACTAAATTC-GAAAAAATAAGAAAATACGATATTAAAAGCGT-CAAAAG
65 TTCGATTTAATTAGAAAAT-AATTCAGAAAAAATATGAAAA-ACGATATTAAAAGCGTGAAAAAC
* * * *
27889 CCTCCAATCTTTTTGGCGTTGAA-T-TACATTTTTATAAGTATTTTAGCCAAAACTTGA-GAAGA
128 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAA-A
* *** * * * * *
27951 AATCTTTCGTACCAATTTTTGCAAAATTTTGGCTGAAATCATGTACTAACAAACCATCACGGTTT
192 TATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAC--ATCA-CACGGTTT
* * * * *
28016 TTGGCTAAAAAGGAGTTCCGGGAACCCGGCTCAATTTTGCATGATTTTTGG-GTCCGAGACTACT
254 TTGGCTAAAAACGCGTTCCGGG--CCCGGCTCAGTTTTGCATGATTTTTGGCG-CCAAGACTCCT
28080 TGAAATATCTATAT
316 TGAAATATCTATAT
* * * *
28094 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAGATTTATTTTTACGAGCATTTGAATCTTGT
1 TCATCTAATCAAATCTCAG-CACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * * * *
28159 TTCGATTTAATTAGAAATTAATT-TGGAAAGATAGGAAAATA--ATAATAGAAA-TGTCAAAAGC
65 TTCGATTTAATTAGAAAATAATTCAGAAAAAATATGAAAA-ACGATATTA-AAAGCGTGAAAAAC
* * * *
28220 CCTTCAATCTTTTTGGCATTGAATTATACATTTTTTATGACTATTTTAGCTAAAAATTGA-GAAT
128 CCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAA-
* * *
28284 ATATTTTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACTATCACA--ATTT
191 ATA-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAC-ATCACACGGTTT
* * * ** * *
28347 TTAGCTAAAAAAGCG-TCATGGAGCCCAACTCAGTTTTCCATGATTTTTGGCCCCAAGACTCCTT
254 TTGGCTAAAAACGCGTTC-CGG-GCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
* *
28411 GAGATATCCATAT
317 GAAATATCTATAT
* * **
28424 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAG-CACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * ***
28489 TTCGATTTAATTGGAAATTAATTCAG-AAAAATATGAAAAATGATATTAAAAGCGGGAAAAGTTC
65 TTCGATTTAATTAGAAAATAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAACCC
* * * * * *
28553 TCCAATTTTTTTGGAGTTAAATTTAGATATTTGTTATGAATATTTT-GTCCAAAAATTGAGGAAA
130 TTCAATCTTTTTGGCGTTGAA-TTATATATTT-TTATGAGTATTTTAG-CCAAAAATTGAGGAAA
* * * * * * *
28617 AATTTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCATGTACTAAC--CATCATGGTTTTT
192 TATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCA-CACGGTTTTT
* * * * * * * * * *
28680 GGTTAAAAACGCATTTCGAGGCCAGGGATCAGTTTTCCATGACTTTAGGCGCCGACACTCCTTGA
256 GGCTAAAAACGCGTTCCG-GGCC-CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
28745 AATATCTATAT
319 AATATCTATAT
* ** * * *
28756 TCATCTAATAAAATCTTTGCTACATTACATTTAAGGATTTGTTTTTACGAGCATCTGATTCTTAT
1 TCATCTAATCAAATCTCAGC-ACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * *
28821 TTCGATTTTATTAAAAAATAATTCAGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAACCC
65 TTCGATTTAATTAGAAAATAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAACCC
* * * * * *
28886 TTCATTCTTTTTGGCGTTGAATTATATATTTTCATCAGTATTATGGCTAAAAATTGAGGAAATAT
130 TTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATAT
* * *
28951 CTTTCGGGTCAATTTTTGGAAAATTTTAGCCGACATCGTGTAATAATCATCACACGATTTTTGGC
195 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA-CATCACACGGTTTTTGGC
* * * * * ** * *
29016 TAAAAACGCGTTCCGGGTCTGGTTCAATTTTGAACAATTTTTGGCACCGAGACTCCTTGAAATAT
259 TAAAAACGCGTTCCGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT
29081 CTATAT
324 CTATAT
* * *
29087 TCATCTAA-CTAAA--TC--C-CA--GC-------CA-TTGTTTTTACAAGCATCTGAATCATGT
1 TCATCTAATC-AAATCTCAGCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
29136 TTTGTTTTTTAATTAG-AAATCAAGTT-TGAAAAAAGATAGGAAGAACGATATTAAAAACGTGAA
65 TTCG--ATTTAATTAGAAAAT-AA-TTCAG-AAAAA-ATATGAAAAACGATATTAAAAGCGTGAA
* * * * * * *
29199 AAGCCCTTCAATATTTTTGGCATTGAATTCTATATTTTTTTATGAGTATTGTGGCTAAAAATTGA
124 AAACCCTTCAATCTTTTTGGCGTTGAA-T-TATATATTTTTATGAGTATTTTAGCCAAAAATTGA
* * ***
29264 GGGAAAGTAT-TTT-GGGTCAATTTTTGCAAAATATTAGCCGAAAT--TGT-GTAACATCA-TTT
187 -GGAAA-TATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCACACG
* * * * * * ** *
29323 TTTTTTGTCAAAAAACGCGTTCTGGGGCCCCGGGAT-AGTTTTGCAAGATTTTAAGTGCCAAGAC
250 GTTTTTGGCTAAAAACGCGTTC-CGGG-CCC-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
* *
29387 TCCCTAAAATATCTATAT
312 TCCTTGAAATATCTATAT
* *
29405 TCATCTAATCAAATCTCAGGCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCA-GCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
29470 TTTGATTTAATTAG-AAATCAATTCAGAAAAAATAGGAAAGACGATAATAAAAGCGT-AAAATAC
65 TTCGATTTAATTAGAAAAT-AATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA-AC
* * *
29533 CTTTCAATATTTTTGGAGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAT
128 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAT
*
29598 ATCTTTCCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT-A-ATCATCACGGTTTTTT
193 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCA-CACGG--TTTT
* * * * * * *
29661 TTGCTAAAAACGCTTTCCAAGGCCCCAGG-TCTGTTTTTCATTATTTTTGGCGCTAAGACTCCTT
255 TGGCTAAAAACGCGTTCC--GGGCCC-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
* *
29725 GAGATATCCATAT
317 GAAATATCTATAT
* * * * * *
29738 TCATGTAATCAAATCTCAGGCACATTACATTTAATGATTT-TTTTTACGAGCAGCTGGATCTTAT
1 TCATCTAATCAAATCTCA-GCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
29802 TTCGATTTAATTAGAAATTAATTCATAAAAAATATGAAAAAC--T-TGAAAA--GT-------CG
65 TTCGATTTAATTAGAAAATAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAACCC
* * * *
29855 TTCAATCTTTTTGTC-TTGAATTATATATATTTTATGACTATTTTAGCTAAAAATTGA-TAAATA
130 TTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAATA
* ** * * *
29918 TCTTTCGGATCAATTTTAACAAAATTTTAGTCGAAATCGTGTAATAACTATCACA--ATTTTTAG
194 TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAC-ATCACACGGTTTTTGG
* * * * ** * ** * * *
29981 CAAAAAAGGCGTTCTAGGTCCCCAACTCAGTTTTCCATGATTTTTGGCAACAATACTCCTCGAGA
258 CTAAAAACGCGTTC-CGG-GCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
*
30046 TATCCATAT
321 TATCTATAT
* * * ** * * *
30055 TCATCTAATCAAATCTCAACCACATTGGATTTAAGAATTTGTTTTTAAAAGCATCCGAATTTTGC
1 TCATCTAATCAAATCTC-AGCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * ***
30120 TTCGATTTAATTGGAAATTAATTCAGAAAAAA-ATGAAAAACGATATTAAAAGCGGGAAAAGTTC
65 TTCGATTTAATTAGAAAATAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAACCC
* * * * ** *
30184 TCCAATCTTTTTGGAGTTAAATTAGATATTTGTTATGAGTATTTTTTCCAAAAATTGAGGAAAAA
130 TTCAATCTTTTTGGCGTTGAATTATATATTT-TTATGAGTATTTTAGCCAAAAATTGAGGAAATA
* * * * * *
30249 TTTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCATGTACTAAC--CATCATGGTTTTTGG
194 TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCA-CACGGTTTTTGG
* * * ** * *
30312 ATAAAAACGCATTTCGAGGTCAGGGCTCAGTTTT-CGATGATTTTAGGCGCCAACACTCCTTGAA
258 CTAAAAACGCGTTCCG-GG-CCCGGCTCAGTTTTGC-ATGATTTTTGGCGCCAAGACTCCTTGAA
30376 ATATCTATAT
320 ATATCTATAT
** * *
30386 TCATCTAA-CAAAATCTTTGCTACA-TGACATTTAAGGATTTGTTTTTACGAGCATTTGATTCTT
1 TCATCTAATC-AAATCTCAGC-ACATTG-CATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
* * **
30449 GTTTCGATTTTGA-TA-AAATATAATTCAGAAATAATATGAAAAATTATATTAAAAGCGTGAATT
63 GTTTCGA-TTTAATTAGAAA-ATAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAA--
* * * * * *
30512 ATATATTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCATCAGTATTATGGCCAAAAATTT
124 A-A-A-CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTG
*
30577 AGGAAATACCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACACG
186 AGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA-CATCACACG
* * * * * * *
30642 GTTTTTGGCTAAAAACGTGTTCCGGGCCCGGTTCAATTTTGAATAATTTTTGGCACCGAGACTCC
250 GTTTTTGGCTAAAAACGCGTTCCGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
30707 TTGAAATATCTATAT
315 TTGAAATATCTATAT
* * * *
30722 TCATCTAACCAAA--TC--C-CA--GC-------CA-TTGTTTTTACAAGCATCTGAATCATGTT
1 TCATCTAATCAAATCTCAGCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG-T
** * * * *
30772 TTGCTTTTTAGTTAG-AAATGAATTCTGAAAAAAGATAGGAAAAACGATATTAAAAGGGTGAAAA
65 TT-CGATTTAATTAGAAAAT-AATTCAG-AAAAA-ATATGAAAAACGATATTAAAAGCGTGAAAA
* * * *
30836 ACCCTTCAATATTTTT-GCGTTGAATTATATATATATATATTTTTTAATGAGTATTGTGGCTAAA
126 ACCCTTCAATCTTTTTGGCGTTG------A-AT-TATATA-TTTTT-ATGAGTATTTTAGCCAAA
*
30900 AATTGAGGAAAAGTAT-TTT-GGGTCAATTTTTGCAAAATATTAGCCGAAAT--TGT--TAACAT
181 AATTGAGG-AAA-TATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACAT
* * * * *
30959 --CATGGTTTTTTTTTTGTGCAAAAAACGCGTTCTGGGGACCCGGGAT-AGTTTTCCATGATTTT
244 CACACGG-----TTTTTG-GCTAAAAACGCGTTC-CGGG-CCC-GGCTCAGTTTTGCATGATTTT
* * *
31021 TAGTGCCAAGACTCCCTGAAATATCTATAT
300 TGGCGCCAAGACTCCTTGAAATATCTATAT
*
31051 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
1 TCATCTAATCAAATCTCAG-CACATTGCATTTAAGGATTTGTTTTTACGAGCAT
31105 TTAAATCTAA
Statistics
Matches: 2400, Mismatches: 444, Indels: 322
0.76 0.14 0.10
Matches are distributed among these distances:
315 26 0.01
316 26 0.01
317 120 0.05
318 110 0.05
319 126 0.05
320 71 0.03
321 75 0.03
322 25 0.01
323 12 0.00
324 30 0.01
325 4 0.00
326 19 0.01
327 28 0.01
328 120 0.05
329 92 0.04
330 244 0.10
331 431 0.18
332 280 0.12
333 254 0.11
334 69 0.03
335 42 0.02
336 121 0.05
337 34 0.01
338 23 0.01
339 2 0.00
344 1 0.00
345 15 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (329 bp):
TCATCTAATCAAATCTCAGCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
TCGATTTAATTAGAAAATAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAACCCT
TCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATC
TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCACACGGTTTTTGGCTA
AAAACGCGTTCCGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT
ATAT
Found at i:29460 original size:649 final size:648
Alignment explanation
Indices: 27796--30397 Score: 1686
Period size: 649 Copynumber: 4.0 Consensus size: 648
27786 TGGATTTAAG
** * * * *
27796 AATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAACTAAATTCGAAAAAATAA
1 AATTTGTTTTTAAAAGCATCTGAATCATGTTTCGATTTAATTAGAAA-TCAATTCAAAAAAATAG
* ** * * * *
27861 GAAAATACGATATTAAAAGCGTCAAAAG-CCTCCAATCTTTTTGGCGTTGAA-TT--ACATTT-T
65 GAAAA-ACGATATTAAAAACGGGAAAAGCCCTCCAATATTTTTGGAGTTAAATTTAGATATTTGT
* * * * *** * *
27921 TAT-AAGTATTTTAGCCAAAACTTGA-GAAGAAATCTTTCGTACCAATTTTTGCAAAATTTTGGC
129 TATGAA-TATTGTGGCCAAAAATTGAGGAA-AAATTTTTCGGGTCAATTTTTGCAAAATATTAGC
** * * * *
27984 TGAAATCATGTACTAACAAACCATCACGGTTTTTGGCT-AAAAA-GGAGTTCCG-GGAACC-CGG
192 CAAAAT-ATGTACT----AACCATCATGGTTTTTGG-TAAAAAACGCA-TTTCGAGG--CCAGGG
* * * * ** * * * * * *
28045 CTCAATTTTGCATGA-TTTTTGGGTCCGAGACTACTTGAAATATCTATATTCATCTAATCAAATC
248 ATCAGTTTTCCAAGACTTTAAGCG-CCAACACTCCCTAAAATATCTATATTCATCTAATCAAATC
* * * * *
28109 TCAGCCACATTGGATTTAAAGATTTATTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGA
312 TCAGGCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAA
* * * * * * * *
28174 AATTAATT-TGGAAAGATAGGAAAATAATAATAGAAA-TGTCAAAAGCCCTTCAATCTTTTTGGC
377 AAATAATTCAGAAAAAATAGAAAAATGATAATA-AAAGCGT-AAAAACCCTTCAATCTTTTTGGC
* * * *
28237 ATTGAATTATACATTTTTTATGACTATTTTAGCTAAAAATTGA-GAATATATTTTTTCGGGTCAA
440 GTTGAATTATATA-TTTTTATGAGTATTTTAGCTAAAAATTGAGGAA-ATA-TCTTTCGGGTCAA
* *
28301 TTTTTACAAAATTTTAGCCGAAATCGTGTAATAA-CTATCACA-ATTTTTAGCTAAAAAAGCG-T
502 TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATC-ATCACAGATTTTTAGCTAAAAACGCGTT
* * * ** * *
28363 CATGGAGCCCAACTCAGTTTTCCATGATTTTTGGCCCCAAGACTCCTTGAGATATCCATATTCAT
566 C-CGGAGCCCAACTCAATTTTCAACAATTTTTGGCACCAAGACTCCTTGAAATATCCATATTCAT
*
28428 CTAATCAAATCTCAGCCAC
630 CTAATCAAATCCCAGCCAC
* * *
28447 ATTGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTCGATTTAATTGGAAATTAATT
1 ------------AATTTGTTTTTAAAAGCATCTGAATCATGTTTCGATTTAATTAGAAATCAATT
* * * * ** *
28512 CAGAAAAATATGAAAAATGATATTAAAAGCGGGAAAAGTTCTCCAATTTTTTTGGAGTTAAATTT
54 CAAAAAAATAGGAAAAACGATATTAAAAACGGGAAAAGCCCTCCAATATTTTTGGAGTTAAATTT
* * *
28577 AGATATTTGTTATGAATATTTTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTTGCAAA
119 AGATATTTGTTATGAATATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCAAA
* *
28642 ATTTTAGCCAAAATCATGTACTAACCATCATGGTTTTTGGTTAAAAACGCATTTCGAGGCCAGGG
184 ATATTAGCCAAAAT-ATGTACTAACCATCATGGTTTTTGGTAAAAAACGCATTTCGAGGCCAGGG
* * * * * *
28707 ATCAGTTTTCCATGACTTTAGGCGCCGACACTCCTTGAAATATCTATATTCATCTAATAAAATCT
248 ATCAGTTTTCCAAGACTTTAAGCGCCAACACTCCCTAAAATATCTATATTCATCTAATCAAATCT
** ** * * *
28772 -TTGCTACATTACATTTAAGGATTTGTTTTTACGAGCATCTGATTCTTATTTCGATTTTATTAAA
313 CAGGC-ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAA
* *
28836 AAATAATTCAGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAACCCTTCATTCTTTTTGGC
377 AAATAATTCAGAAAAAATA-GAAAAATGATAATAAAAGCGT-AAAAACCCTTCAATCTTTTTGGC
* * * *
28901 GTTGAATTATATATTTTCATCAGTATTATGGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTT
440 GTTGAATTATATATTTTTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTT
* * *
28966 TTGGAAAATTTTAGCCGACATCGTGTAATAATCATCACACGATTTTTGGCTAAAAACGCGTTCCG
505 TTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACA-GATTTTTAGCTAAAAACGCGTTCCG
* **** * * *
29031 G-GTCTGGTTCAATTTTGAACAATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAA
569 GAGCCCAACTCAATTTTCAACAATTTTTGGCACCAAGACTCCTTGAAATATCCATATTCATCTAA
29095 -CTAAATCCCAG-C-C
634 TC-AAATCCCAGCCAC
* * * *
29108 -A-TTGTTTTTACAAGCATCTGAATCATGTTTTGTTTTTTAATTAGAAATCAAGTTTGAAAAAAG
1 AATTTGTTTTTAAAAGCATCTGAATCATGTTTCG--ATTTAATTAGAAATCAA--TTCAAAAAA-
* * * * *
29171 ATAGGAAGAACGATATTAAAAACGTGAAAAGCCCTTCAATATTTTTGGCA-TTGAATTCTATAT-
61 ATAGGAAAAACGATATTAAAAACGGGAAAAGCCCTCCAATATTTTTGG-AGTTAAATT-TAGATA
* * * * *
29234 TTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAAGTATTTT-GGGTCAATTTTTGCAAAATAT
124 TTTGTTATGAATATTGTGGCCAAAAATTGAGGAAAAAT-TTTTCGGGTCAATTTTTGCAAAATAT
* * ** * * * *
29298 TAGCCGAAAT-TGT-GTAA-CATCATTTTTTTTTGTCAAAAAACGC-GTTCTGGGGCCCCGGGAT
188 TAGCCAAAATATGTACTAACCATCATGGTTTTTGGT-AAAAAACGCATTTC-GAGG-CCAGGGAT
* * * *
29359 -AGTTTTGCAAGATTTTAAGTGCCAAGACTCCCTAAAATATCTATATTCATCTAATCAAATCTCA
250 CAGTTTTCCAAGACTTTAAGCGCCAACACTCCCTAAAATATCTATATTCATCTAATCAAATCTCA
* * *
29423 GGCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGATTTAATT-AGAAA
315 GGCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAAA
* * * * *
29487 TCAATTCAGAAAAAATAGGAAAGACGATAATAAAAGCGTAAAATACCTTTCAATATTTTTGGAGT
380 T-AATTCAGAAAAAATA-GAAAAATGATAATAAAAGCGTAAAA-ACCCTTCAATCTTTTTGGCGT
* *
29552 TGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCCGGTCAATTTTT
442 TGAATTATATATTTTTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTT
* * * *
29617 GCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTTTTGCTAAAAACGCTTTCCAAG
507 GCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAG-ATTTTTAGCTAAAAACGCGTTCC--G
* ** ** ** * * * *
29682 G-CCCCAGGTCTGTTTTTC-ATTATTTTTGGCGCTAAGACTCCTTGAGATATCCATATTCATGTA
569 GAGCCCAACTC-AATTTTCAACAATTTTTGGCACCAAGACTCCTTGAAATATCCATATTCATCTA
*
29745 ATCAAATCTCAGGCACATTAC
633 ATCAAATCCCA-GC-C---AC
* ** * * * * *
29766 ATTTAATGATTTTTTTTACGAGCAGCTGGATCTTATTTCGATTTAATTAGAAATTAATTCATAAA
1 ----AAT--TTGTTTTTAAAAGCATCTGAATCATGTTTCGATTTAATTAGAAATCAATTCA-AAA
* * * * * ** * *
29831 AAATATGAAAAAC----TT--------GAAAAGTCGTTCAATCTTTTT-GTCTTGAA-TTATATA
59 AAATAGGAAAAACGATATTAAAAACGGGAAAAGCCCTCCAATATTTTTGGAGTTAAATTTAGATA
* * * * * * * * ** *
29882 TATT-TTATGACTATTTTAGCTAAAAATTGA-TAAATATCTTTCGGATCAATTTTAACAAAATTT
124 T-TTGTTATGAATATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATAT
* * * * * *** * * * * * ***
29945 TAGTCGAAATCGTGTAATAACTATCACAATTTTTAGCAAAAAAGGC-GTTCTAGGTCC-CCAACT
188 TAGCCAAAAT-ATGTACTAACCATCATGGTTTTTGGTAAAAAACGCATTTCGAGG-CCAGGGA-T
* * ** ** * * * *
30008 CAGTTTTCCATGATTTTTGGCAACAATACT-CCTCGAGATATCCATATTCATCTAATCAAATCTC
250 CAGTTTTCCAAGACTTTAAGCGCCAACACTCCCT-AAAATATCTATATTCATCTAATCAAATCTC
** * ** * * * **
30072 AACCACATTGGATTTAAGAATTTGTTTTTAAAAGCATCCGAATTTTGCTTCGATTTAATTGGAAA
314 AGGCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAA
* * * * *** * *
30137 TTAATTCAGAAAAAA-ATGAAAAACGATATTAAAAGCGGGAAAAGTTCTCCAATCTTTTTGGAGT
379 ATAATTCAGAAAAAATA-GAAAAATGATAATAAAAGC-GTAAAAACCCTTCAATCTTTTTGGCGT
* * ** * * * *
30201 TAAATTAGATATTTGTTATGAGTATTTTTTCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTT
442 TGAATTATATATTT-TTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTT
* * * * * * * * * *
30266 TGCAAAATTTTAGCCAAAATCATGTACTAACCATCA-TGGTTTTTGGATAAAAACGCATTTC-GA
506 TGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACAGATTTTTAGCTAAAAACGCGTTCCGGA
** * * * ** * * * *
30329 GGTCAGGGCTCAGTTTTCGATGATTTTAGGCGCCAACACTCCTTGAAATATCTATATTCATCTAA
571 GCCCA--ACTCAATTTTCAACAATTTTTGGCACCAAGACTCCTTGAAATATCCATATTCATCTAA
30394 -CAAA
634 TCAAA
30398 ATCTTTGCTA
Statistics
Matches: 1571, Mismatches: 293, Indels: 166
0.77 0.14 0.08
Matches are distributed among these distances:
645 1 0.00
646 5 0.00
647 71 0.05
648 113 0.07
649 357 0.23
650 237 0.15
651 71 0.05
652 110 0.07
653 9 0.01
654 1 0.00
658 3 0.00
661 24 0.02
662 235 0.15
663 156 0.10
664 82 0.05
665 7 0.00
666 84 0.05
667 5 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (648 bp):
AATTTGTTTTTAAAAGCATCTGAATCATGTTTCGATTTAATTAGAAATCAATTCAAAAAAATAGG
AAAAACGATATTAAAAACGGGAAAAGCCCTCCAATATTTTTGGAGTTAAATTTAGATATTTGTTA
TGAATATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATATTAGCCAAA
ATATGTACTAACCATCATGGTTTTTGGTAAAAAACGCATTTCGAGGCCAGGGATCAGTTTTCCAA
GACTTTAAGCGCCAACACTCCCTAAAATATCTATATTCATCTAATCAAATCTCAGGCACATTGGA
TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAAATAATTCAGAAA
AAATAGAAAAATGATAATAAAAGCGTAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTT
TTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC
GAAATCGTGTAATAATCATCACAGATTTTTAGCTAAAAACGCGTTCCGGAGCCCAACTCAATTTT
CAACAATTTTTGGCACCAAGACTCCTTGAAATATCCATATTCATCTAATCAAATCCCAGCCAC
Found at i:30320 original size:981 final size:975
Alignment explanation
Indices: 27789--30658 Score: 2511
Period size: 981 Copynumber: 2.9 Consensus size: 975
27779 GCAACATTGG
* * * * * *
27789 ATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAACTAAATTC-GA
1 ATTTAAGGATTTGTTTTTACGAGCAGCTGATTCTTATTTCGATTTAATTAAAAAAT-AATTCAGA
* * * *
27853 AAAAATAAGAAAATACGATATTAAAAGCGTCAAAAGCCTCCAATCTTTTTGGCGTTGAATTACAT
65 AAAAATATGAAAA-A-GATATGAAAA-CGT----A-CCTTCAATCTTTTTGGCGTTGAATTATAT
* * * * * * * * **
27918 -TTTT-ATAAGTATTTTAGCCAAAACTTGA-GAAGAAATCTTTCGTACCAATTTTTGCAAAATTT
122 ATTTTCATCACTATTATAGCTAAAAATTGAGGAA-ATATCTTTCGGATCAATTTTAACAAAATTT
* * * * * * * * * * * * *
27980 TGGCTGAAATCATGTACTAA-CAAACCATCACGGTTTTTGGCTAAAAAGGAGTTCCGGGAACCCG
186 TAGCCGAAATCGTGTAATAATC--ATCA-CAC-ATTTTTAGCAAAAAACGCGTTCCAGG--TCCA
* ** *** * * *
28044 GCTCAATTTTGC-ATGATTTTTGGGTCCGAGACTACTTGAAATATCTATATTCATCTAATCAAAT
245 ACTCAATTTT-CAACAATTTTTGGCAACAAGACTCCTCGAAATATCTATATTCATCTAATCAAAT
* * ** *
28108 CTCAGCCACATTGGATTTAAAGATTTATTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAG
309 CTCAACCACATTGGATTTAAA-ATTTGTTTTTAAAAGCA--TGAATTTTG-TTCGATTTAATTAG
* * * * * * *
28173 AAATTAATTTGGAAAGATAGGAAAATA--ATAATAGAAATGTCAAAAGCCCTTCAATCTTTTTGG
370 AAATTAA-TTAGAAAAAAATGAAAA-ACGATATTA-AAACGTGAAAAGCCCTTCAATCTTTTTGG
* * *
28236 CATTGAATTATACATTTTTTATGACTATTTTAGCTAAAAATTGA-GAATATATTTTTTCGGGTCA
432 CATTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAA-A-AATTTTTCGGGTCA
* * * *
28300 ATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACTATCACAATTTTTAGCTAAAAAAGCG-TC
495 ATTTTTGCAAAATTTTAGCCGAAATC-TGTAATAACCATCATAATTTTTAG-TAAAAACGCGTTC
* * * * * *
28364 ATGGAGCCC--AACTCAGTTTTCCATGATTTTTGGCCCCAAGACTCCTTGAGATATCCATATTCA
558 -TGGGGCCCGGGA-TCAGTTTT-CATGATTTTAGGCGCCAAGACTCCTTGAAATATCTATATTCA
* * **
28427 TCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTAAAAGCATCTGAATCTTGTTTC
620 TCTAATCAAATCTCAGGCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
* * * *
28492 GATTTAATTGGAAATTAATTCAG-AAAAATATGAAAAATGATATTAAAAGCGGGAAAAGT-TCTC
685 GATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAATGATATTAAAAGC-GTAAAA-TACCTT
* * * * *
28555 CAATTTTTTTGGAGTTAAATTTAGATATTTGTTATGAATATTTTGTCCAAAAATTGAGGAAAAAT
748 CAATATTTTTGGAGTTGAA-TTATATATTT-TTATGAGTATTTTG-CCAAAAATTGAGGAAATAT
* * * * * * * *
28620 TTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCATGTACTAACCATCATGG--TTTTTGGT
810 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTTTGGC
* *
28683 TAAAAACGCATTTCGAGGCCAGGGATCAGTTTTCCATGACTTTAGGCGCCGACACTCCTTGAAAT
875 TAAAAACGCATTTCAAGGCCAGGGATCAGTTTTCCATGACTTTAGGCGCCAACACTCCTTGAAAT
* **
28748 ATCTATATTCATCTAATAAAATCTTTGCTACATTAC
940 ATCCATATTCATCTAATAAAATCTAGGCTACATTAC
* *
28784 ATTTAAGGATTTGTTTTTACGAGCATCTGATTCTTATTTCGATTTTATTAAAAAATAATTCAGAA
1 ATTTAAGGATTTGTTTTTACGAGCAGCTGATTCTTATTTCGATTTAATTAAAAAATAATTCAGAA
* *
28849 AAAATATGAAAAATGATATTAAAAGCGTGAAAAACCCTTCATTCTTTTTGGCGTTGAATTATATA
66 AAAATATGAAAAA-GATATGAAAA-CGT-----A-CCTTCAATCTTTTTGGCGTTGAATTATATA
* * * ***
28914 TTTTCATCAGTATTATGGCTAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGGAAAATTTTA
123 TTTTCATCACTATTATAGCTAAAAATTGAGGAAATATCTTTCGGATCAATTTTAACAAAATTTTA
* * * * ****
28979 GCCGACATCGTGTAATAATCATCACACGATTTTTGGCTAAAAACGCGTTCCGGGTCTGGTTCAAT
188 GCCGAAATCGTGTAATAATCATCACAC-ATTTTTAGCAAAAAACGCGTTCCAGGTCCAACTCAAT
* * * * * *
29044 TTTGAACAATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTAA-CTAAATC-CCAGC
252 TTTCAACAATTTTTGGCAACAAGACTCCTCGAAATATCTATATTCATCTAATC-AAATCTCAACC
** * ** * * * * * *
29107 -CATTGTTTTTACAA---GCATCT-GAATCATG--TTTTGTT--TTTTAATTAGAAATCAAGTTT
316 ACATTGGATTTAAAATTTGTTTTTAAAAGCATGAATTTTGTTCGATTTAATTAGAAATTAA-TTA
* *
29163 GAAAAAAGATAGGAAGAACGATATTAAAAACGTGAAAAGCCCTTCAATATTTTTGGCATTGAATT
380 GAAAAAA-AT--GAAAAACGATATT-AAAACGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATT
* * * * *
29228 CTATATTTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAAGTATTTT-GGGTCAATTTTTGCA
441 ATATA-TTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAAT-TTTTCGGGTCAATTTTTGCA
* * ** *
29292 AAATATTAGCCGAAAT-TGT-GTAA-CATCATTTTTTTTTGTCAAAAAACGCGTTCTGGGGCCCC
504 AAATTTTAGCCGAAATCTGTAATAACCATCATAATTTTTAGT--AAAAACGCGTTCTGGGG-CCC
* * * * *
29354 GGGAT-AGTTTTGCAAGATTTTAAGTGCCAAGACTCCCTAAAATATCTATATTCATCTAATCAAA
566 GGGATCAGTTTT-CATGATTTTAGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
* *
29418 TCTCAGGCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGATTTAATTA
630 TCTCAGGCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* * * * *
29483 GAAATCAATTCAGAAAAAATAGGAAAGACGATAATAAAAGCGTAAAATACCTTTCAATATTTTTG
695 GAAATTAATTCAGAAAAAATATGAAAAATGATATTAAAAGCGTAAAATACC-TTCAATATTTTTG
*
29548 GAGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCCGGTCAAT
759 GAGTTGAATTATATATTTTTATGAGTATTTT-GCCAAAAATTGAGGAAATATCTTTCGGGTCAAT
*
29613 TTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTTTTGCTAAAAACGC-TTT
823 TTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTTTGGCTAAAAACGCATTT
* * * * * * * *
29677 CCAAGGCCCCA-GG-TCTGTTTTTCATTATTTTTGGCGCTAAGACTCCTTGAGATATCCATATTC
888 -CAAGG--CCAGGGATCAGTTTTCCATGACTTTAGGCGCCAACACTCCTTGAAATATCCATATTC
* *
29740 ATGTAATCAAATCTCAGGC-ACATTAC
950 ATCTAATAAAATCT-AGGCTACATTAC
* * * *
29766 ATTTAATGATTT-TTTTTACGAGCAGCTGGA-TCTTATTTCGATTTAATTAGAAATTAATTCATA
1 ATTTAAGGATTTGTTTTTACGAGCAGCT-GATTCTTATTTCGATTTAATTAAAAAATAATTCAGA
* * * *
29829 AAAAATATGAAAAA-CT-TGAAAA-GT-CGTTCAATCTTTTTGTC-TTGAATTATATATATTTTA
65 AAAAATATGAAAAAGATATGAAAACGTACCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTCA
* * * *
29889 TGACTATTTTAGCTAAAAATTGA-TAAATATCTTTCGGATCAATTTTAACAAAATTTTAGTCGAA
129 TCACTATTATAGCTAAAAATTGAGGAAATATCTTTCGGATCAATTTTAACAAAATTTTAGCCGAA
* * *
29953 ATCGTGTAATAA-CTATCACA-ATTTTTAGCAAAAAAGGCGTTCTAGGTCCCCAACTCAGTTTTC
194 ATCGTGTAATAATC-ATCACACATTTTTAGCAAAAAACGCGTTCCAGGT--CCAACTCAATTTTC
* ** * * *
30016 CATGATTTTTGGCAACAATACTCCTCGAGATATCCATATTCATCTAATCAAATCTCAACCACATT
256 AACAATTTTTGGCAACAAGACTCCTCGAAATATCTATATTCATCTAATCAAATCTCAACCACATT
*
30081 GGATTTAAGAATTTGTTTTTAAAAGCATCCGAATTTTGCTTCGATTTAATTGGAAATTAATTCAG
321 GGATTTAA-AATTTGTTTTTAAAAGCAT--GAATTTTG-TTCGATTTAATTAGAAATTAATT-AG
* ** * * *
30146 AAAAAAATGAAAAACGATATTAAAAGCGGGAAAAGTTCTCCAATCTTTTTGG-AGTTAAATTAGA
381 AAAAAAATGAAAAACGATATTAAAA-CGTGAAAAGCCCTTCAATCTTTTTGGCA-TTGAATTATA
* ** * *
30210 TATTTGTTATGAGTATTTTTTCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTTGCAAAATT
444 TATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATT
* * ** * * * * * *
30275 TTAGCCAAAATCATGTACTAACCATCATGGTTTTTGGATAAAAACGCATT-TCGAGGTCAGGGCT
509 TTAGCCGAAATC-TGTAATAACCATCATAATTTTTAG-TAAAAACGCGTTCT-GGGGCCCGGGAT
*
30339 CAGTTTTCGATGATTTTAGGCGCCAACACTCCTTGAAATATCTATATTCATCTAA-CAAAATCT-
571 CAGTTTTC-ATGATTTTAGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATC-AAATCTC
** * * * *
30402 TTGCTACA-TGACATTTAAGGATTTGTTTTTACGAGCATTTGATTCTTGTTTCGATTTTGA-TA-
634 AGGC-ACATTG-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAG
* * *
30464 AAATATAATTCAGAAATAATATGAAAAATTATATTAAAAGCGTGAATTATATATTCCTTCAATCT
696 AAAT-TAATTCAGAAAAAATATGAAAAATGATATTAAAAGCGT-AA--A-ATA--CCTTCAATAT
* * * * * *
30529 TTTTGGCGTTGAATTATATATTTTCATCAGTATTATGGCCAAAAATTTAGGAAATACCTTTCGGG
754 TTTTGGAGTTGAATTATATATTTTTATGAGTATT-TTGCCAAAAATTGAGGAAATATCTTTCGGG
30594 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACACGG--TTTTTGGCTAAAAA
818 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCAT--CACGGTTTTTTTGGCTAAAAA
30657 CG
881 CG
30659 TGTTCCGGGC
Statistics
Matches: 1541, Mismatches: 255, Indels: 167
0.79 0.13 0.09
Matches are distributed among these distances:
966 22 0.01
967 1 0.00
968 116 0.08
969 41 0.03
970 9 0.01
971 2 0.00
974 3 0.00
975 5 0.00
976 2 0.00
977 5 0.00
978 70 0.05
979 80 0.05
980 115 0.07
981 352 0.23
982 180 0.12
983 79 0.05
984 39 0.03
985 5 0.00
986 123 0.08
987 5 0.00
988 5 0.00
990 1 0.00
991 10 0.01
992 3 0.00
993 57 0.04
994 20 0.01
995 121 0.08
996 7 0.00
997 59 0.04
998 4 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (975 bp):
ATTTAAGGATTTGTTTTTACGAGCAGCTGATTCTTATTTCGATTTAATTAAAAAATAATTCAGAA
AAAATATGAAAAAGATATGAAAACGTACCTTCAATCTTTTTGGCGTTGAATTATATATTTTCATC
ACTATTATAGCTAAAAATTGAGGAAATATCTTTCGGATCAATTTTAACAAAATTTTAGCCGAAAT
CGTGTAATAATCATCACACATTTTTAGCAAAAAACGCGTTCCAGGTCCAACTCAATTTTCAACAA
TTTTTGGCAACAAGACTCCTCGAAATATCTATATTCATCTAATCAAATCTCAACCACATTGGATT
TAAAATTTGTTTTTAAAAGCATGAATTTTGTTCGATTTAATTAGAAATTAATTAGAAAAAAATGA
AAAACGATATTAAAACGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGA
GTATTTTAGCTAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
TGTAATAACCATCATAATTTTTAGTAAAAACGCGTTCTGGGGCCCGGGATCAGTTTTCATGATTT
TAGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGGCACATTGGATTTAA
GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATA
TGAAAAATGATATTAAAAGCGTAAAATACCTTCAATATTTTTGGAGTTGAATTATATATTTTTAT
GAGTATTTTGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
CGTGTAATAATCATCACGGTTTTTTTGGCTAAAAACGCATTTCAAGGCCAGGGATCAGTTTTCCA
TGACTTTAGGCGCCAACACTCCTTGAAATATCCATATTCATCTAATAAAATCTAGGCTACATTAC
Found at i:33167 original size:330 final size:330
Alignment explanation
Indices: 32423--35448 Score: 2516
Period size: 331 Copynumber: 9.2 Consensus size: 330
32413 TTATGTTCCG
* * *
32423 GGGCCCCGGGTCAGTTTTCCATGATTTTTAGTG-CAAGACTCCTTGAAATATCTATATTCATCTA
1 GGGCCCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTA
* * *
32487 ATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTTA--AGCATCTAAATCCTGTTTCGAT
66 ATAAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * * * *
32550 TTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAACGATATTAAAAGCGT-AAAATACCGTTCAT
130 TTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA-GCCCTTCAA
* * * * * *
32614 TATTTTTGGCGTTAAATTGTATATTTTTTATGAGTATTTTAGCCAATAATTGAGGAAATATCTTT
194 TCTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTTT
** * *
32679 CCGGTCAATTTTTTCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGTTAAAAA
259 TGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAA-CATCACGGTTTTTGGCTAAAAA
* *
32744 CGCGTTCCA
323 AGCGTT-CT
* * * * ** * *
32753 GGGCCCTGGGTCAGTTTTGCATTATTTTTGGCGGTAAGACTCCTTGAGATATCCATATTCATCTA
1 GGGCCCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTA
* * * * * *
32818 ATCAAATCTCAGACACATTGCATTTAATGATTT-TTTTTACGAGCATCTGTATCTTGTTGCGATT
66 ATAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
* ** *
32882 TAATTAGAAATTAATTCATAAAAAATATGAAAAACGATAAGAAAAGCTTGAAAAGCCCTTCAATC
131 TAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATC
* * * *
32947 TTTTTGGCTTTGAATTATATATATT-TTATGACTATTTTAG-TAAAAATTGA-TAGATTATCTTT
196 TTTTTGGCGTTGAATTATATAT-TTGTTATGAGTATTTTAGCTAAAAATTGAGGA-AATATCTTT
* * * *** *
33009 TGGGTCAATTTTTACAAAATTTTAGCCGAAATCGAGTAAGTTATATCATAATTTTTAGCTAAAAA
259 TGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAA-TAACATCACGGTTTTTGGCTAAAAA
33074 AGCGTTCT
323 AGCGTTCT
* * * *
33082 GGGACCCCGACTCTGTTTTCCATGACTTTTGGCGCCAAGACTCCTTGAGATATCTATATTCATCT
1 GGG-CCCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT
* * ** *
33147 AATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTAAAAGCATCCGAATCTTGTTTCGAT
65 AATAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
** *
33212 TTAATT-GAAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTTCTCCAA
130 TTAATTAG-AAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAA
* * * * * *
33275 TTTTTTTGGCATTAAATTATATATTTGTTATGAGTATTTT-GCCCAAAAATTCAGGAAAAAT-TT
194 TCTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTTTAG-CTAAAAATTGAGGAAATATCTT
* * * * * * *
33338 TTCGGGTCATTTTTTGCAAAATTCTAGCCAAAATCATGTACTTACCATCACGGTTTTTGGCTAAA
258 TT-GGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTA-ATAACATCACGGTTTTTGGCTAAA
*
33403 AACA-CATT-T
321 AA-AGCGTTCT
* ** * * **
33412 CGAGACCAGGGCTTAGTTTTCCATGATTTTTGGCGCCGACTCTCCTTGAAATATCTATATTCATC
1 -G-GGCCCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATC
** * * * *
33477 TAATAAAATCTTTGCTAC-TTGATATTTAAGGATTTGATTTTACGAGCATCTGATTCTTGTTTCG
64 TAATAAAATCTCAGCCACATTG-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
* * *
33541 ATTTTATTAGAAATTAATTCATAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGCCCTTCA
128 ATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
* * * * * **
33606 ATATTTTTGGCGTTGAATTATATATATTTTTTATGATTATTGTGGCTAAATGTTGAGGAAA-AGT
193 ATCTTTTTGGCGTTGAA-T-TATATATTTGTTATGAGTATTTTAGCTAAAAATTGAGGAAATA-T
* * * * * ***** *
33670 GTTTTGGGTCAATTTTTGCAAAATATTAGCCGAAATTGTGTAACATCACAGATTTTTTTTTTTTT
255 CTTTTGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGT-A-AT-A-ACA-TCACGGTTTTTG
*
33735 GC-AAAAAACGCGTTCCG
315 GCTAAAAAA-GCGTT-CT
* * * *
33752 GGGCCCTGTG-TCAGTTTTGCATGATTTTTTGTG-CAAGACTCCTTGAAATATCTATATTCATCT
1 GGGCCCCG-GCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT
* * ** * *
33815 AAGAAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTTTGAGCATCTAAATCTTTTTTCGAT
65 AATAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * * * *
33880 TTAAATAGAAATTAATTCGGAAAAAGTA-GGAAAACTGATATTAAAAGCGT-AAAATACCCTTAA
130 TTAATTAGAAATTAATTCAGAAAAAATATGAAAAAC-GATATTAAAAGCGTGAAAA-GCCCTTCA
* * * * *
33943 ATATTTTTGGCGTTGAATTATATATTTCTTATAAGTATTTTAGCCAATAATTGAGGAAATATCTT
193 ATCTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTT
** * ** * * *
34008 TCCGGTCAATTTTCACAAAATTCCAGCTGAAATTGTGCAATAAACATCACGGTTTTTGGCTAAAA
258 TTGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAAT-AACATCACGGTTTTTGGCTAAAA
* *
34073 ACGCGTTCCA
322 AAGCGTT-CT
* * * * * * * * * *
34083 GGGCCCCGGGTCAGTTTTGCAT-TTTTTTCTGTGCTAATACTCCTTGAGATATCCATATTCATCC
1 GGGCCCCGGCTCAGTTTTCCATGATTTTT-GGCGCCAAGACTCCTTGAAATATCTATATTCATCT
* * * * * * * *
34147 AATAAAATCTCAGGCACGTTGCATTTGATGATTT-TTATCTACGAGCATCTGGATCTTGTTTAGA
65 AATAAAATCTCAGCCACATTGGATTTAAGGATTTGTT-TTTACGAGCATCTGAATCTTGTTTCGA
* * * * * *
34211 TTTAATTCGAAATTAATTCATAAAAAATATGAAAAACGATATGAAAAGCTTGAAAAGTCATTCAA
129 TTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAA
* * *
34276 TCTTTTTGGCATTGAATTATATATTTGTTATGACTATTTTAGCTAAAAATTGAGAAAATATCTTT
194 TCTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTTT
* ** **
34341 CGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACTATCACAATTTTTATCTAAAAA
259 TGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAAC-ATCACGGTTTTTGGCTAAAAA
*
34406 AGCGTTAT
323 AGCGTTCT
* * *
34414 GGGACCCCGACTCTGTTTTCCATGATTTTT-G-G-C--G-----TTG--ATATCCATATTCATCT
1 GGG-CCCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT
* * * * * * ** **
34467 AATCAGATATCAGCTACATTGGATTTAAGAATTTGATTTTAAAAGCATCCAAATCTTGTTTCGAT
65 AATAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * * ** *
34532 TTAATTGGAAATTAATGCA-AAAAAACACGAAAAACGATATTAAAAGCGTGAAAAGTTCTCCAAT
130 TTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAAT
* * * * * * * *
34596 CTTTTTGGAGTTAAATTAGATATTTGTTATAAGTATTTCATCCAAAAATTGAGGAAAAAT-TTTT
195 CTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTTTT
* * * * * * * *
34660 CGGATCATTTTTTGCAAAATTTTAGCCAAAATCATGTACTAGCCATCATGGTTTTTTGGCTAAAA
260 -GGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATA-ACATCACGG-TTTTTGGCTAAAA
* *
34725 ACGCATT-T
322 AAGCGTTCT
** * * *
34733 CGAGGCCAGGGCTCAGTTTTCCATGATTTTAGGCGCCGACACTCCTTGAAATATCTATATTCATC
1 -G-GGCCCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATC
** * * * *
34798 TAATAAAATCTTTGCTACA-TGACATTTAAGGATATGTTTTTACGAGCATCTGATTCTTGTTTCG
64 TAATAAAATCTCAGCCACATTG-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
* * * *
34862 ATTTTATTAAAAAATAATTCAGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAA-CCCTTCA
128 ATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
* * ** *
34926 ATCTTTTTGGCGTTGAATTATATATTT-TCATCAGTATGATGGCTAAAAATAT-AGGAAATATCT
193 ATCTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTTTAGCTAAAAAT-TGAGGAAATATCT
* *
34989 TTTGGGT---TTTGT--AAAATTTTAGCCGAAATCGTGTAATAATCATCACACCGTTTTTGGCTA
257 TTTGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAA-CAT--CACGGTTTTTGGCTA
* *
35049 AAAACGCGTTCC
319 AAAAAGCGTTCT
* * ** * * *
35061 GGG-CCCGGTTCAATTTTGAATAATTTTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTA
1 GGGCCCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTA
** * * * *
35125 ACCAAATCCCAG-C-C-------------A-TTGTTTTTACAAGCATCTGAATCATGTTTTGTTT
66 ATAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG---
* * ** * *
35174 TTTTAATTAGAAATCAATTTTGAAAAAAGATAGGAAAAACGATATTAAAAGCGTGAAAAACCCTT
128 ATTTAATTAGAAATTAATTCAG-AAAAA-ATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTT
* * * * * * * *
35239 CAATATTTTTGGCATTGAATTATATTTTTTTTATGAGTATTGTGGTTGAAAATTGAGGGAAAGTA
191 CAATCTTTTTGGCGTTGAATTATATATTTGTTATGAGTATTTTAGCTAAAAATTGA-GGAAA-TA
* * * ** ***** *
35304 --TTTTGGGTCAATTTTTGCAAAATATTAGCCGAAATTGTGTAACAGTAATGTTTTTTTTTTTTG
254 TCTTTTGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGT-A-A-TAACATCACGGTTTTTGG
*
35367 C-AAAAAACGCGTTCC
316 CTAAAAAA-GCGTTCT
* * * *
35382 GGGCTCCAGG-TCAGTTTTACATGATTTTTAGAGCCAAGACTCCTTGAAATATCTATATTCATCT
1 GGGC-CCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT
35446 AAT
65 AAT
35449 C
Statistics
Matches: 2157, Mismatches: 442, Indels: 202
0.77 0.16 0.07
Matches are distributed among these distances:
309 26 0.01
310 1 0.00
312 15 0.01
313 5 0.00
314 28 0.01
315 32 0.01
316 26 0.01
317 5 0.00
318 5 0.00
319 130 0.06
320 121 0.06
321 41 0.02
322 53 0.02
323 8 0.00
324 3 0.00
325 58 0.03
326 28 0.01
327 20 0.01
328 7 0.00
329 14 0.01
330 270 0.13
331 459 0.21
332 420 0.19
333 52 0.02
334 64 0.03
335 72 0.03
336 13 0.01
337 142 0.07
338 37 0.02
339 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (330 bp):
GGGCCCCGGCTCAGTTTTCCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTA
ATAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
TAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATC
TTTTTGGCGTTGAATTATATATTTGTTATGAGTATTTTAGCTAAAAATTGAGGAAATATCTTTTG
GGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACATCACGGTTTTTGGCTAAAAAAGC
GTTCT
Done.