Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010100.1 Corchorus capsularis cultivar CVL-1 contig10121, 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: 30186
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Found at i:1556 original size:204 final size:207
Alignment explanation
Indices: 1198--1612 Score: 674
Period size: 204 Copynumber: 2.0 Consensus size: 207
1188 CAAGATTGAT
* *
1198 GAGAGTGATTGGGACGAACATCTTGAAATTCAACTACCACATTTTTATGGTTTTGAAAAAAAAGA
1 GAGAATGATTGGGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAGA
* * *
1263 AATACCGAAGGGTAAGATGAAGTTCTCTTTTTCTTACAAGCATAATTTTGTGGGATACTTACGGA
66 AATACAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACAAGCATAATTTGGTGGGATACTTACGGA
* * * * *
1328 TTGTTATGTTTGTAGGCTATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACGGCTG
131 TTGCTATGTTTGGAGGATATCTACTTTGACAACTGATATGTCAGAAAAAGAGATAGTTACGGCTA
1393 GTTACTCCACAC
196 GTTACTCCACAC
1405 GAGAATGATTGGGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTG-AAAAAAA-A
1 GAGAATGATTGGGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAGA
*
1468 AA-ACAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGA
66 AATACAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACAAGCATAATTTGGTGGGATACTTACGGA
* **
1532 TTGCTATGTTTGGAGGATATCTACTTTGACAAGTGATATGTCAGAAACTGAGATAGTTACGGCTA
131 TTGCTATGTTTGGAGGATATCTACTTTGACAACTGATATGTCAGAAAAAGAGATAGTTACGGCTA
*
1597 GTTACTCCATAC
196 GTTACTCCACAC
1609 GAGA
1 GAGA
1613 TCCAGCGGGG
Statistics
Matches: 193, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
204 130 0.67
205 3 0.02
206 7 0.04
207 53 0.27
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (207 bp):
GAGAATGATTGGGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAGA
AATACAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACAAGCATAATTTGGTGGGATACTTACGGA
TTGCTATGTTTGGAGGATATCTACTTTGACAACTGATATGTCAGAAAAAGAGATAGTTACGGCTA
GTTACTCCACAC
Found at i:3849 original size:55 final size:55
Alignment explanation
Indices: 3751--3889 Score: 142
Period size: 55 Copynumber: 2.5 Consensus size: 55
3741 AATGATGATG
* * *
3751 ATCAAACCCCTAAGTTCAATAGTCAAACCACAAAAAACATCATTGTACATGCAT-
1 ATCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATCATTGTAAATGCATC
* * *
3805 AGTCAAAGCCCAAAGTTCGATAGTCAAA-C-GAAAAAACATTTCATTTTAAATGCATC
1 A-TCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACA--TCATTGTAAATGCATC
* *
3861 ATCAAACCCCGAAGTTTGATAAG-CAAACC
1 ATCAAACCCCAAAGTTCGAT-AGTCAAACC
3890 TCGAAGTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
53 8 0.11
54 2 0.03
55 56 0.80
56 4 0.06
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (55 bp):
ATCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATCATTGTAAATGCATC
Found at i:3889 original size:21 final size:21
Alignment explanation
Indices: 3862--3910 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
3852 AAATGCATCA
3862 TCAAACCCCGAAGTTTGATAAG
1 TCAAACCCCGAAGTTTGAT-AG
*
3884 -CAAACCTCGAAGTTTGATAG
1 TCAAACCCCGAAGTTTGATAG
3904 TCAAACC
1 TCAAACC
3911 ACAAAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.22
Consensus pattern (21 bp):
TCAAACCCCGAAGTTTGATAG
Found at i:3956 original size:76 final size:76
Alignment explanation
Indices: 3803--3965 Score: 172
Period size: 76 Copynumber: 2.1 Consensus size: 76
3793 TTGTACATGC
* * * *
3803 ATAGTCAAAGCC-CAAAGTTCGATAGTCAAACGAAAAAACATTTCATTTTAAATGCATCATCAAA
1 ATAGTCAAA-CCTCGAAGTTCGATAGTCAAACCAAAAAACATTTCAATGTAAATGCATCATCAAA
*
3867 CCCCGAAGTTTG
65 CCCCAAAGTTTG
* * * **
3879 ATAAG-CAAACCTCGAAGTTTGATAGTCAAACCACAAAAAACATTTTAATGTATATGCATGGTC-
1 AT-AGTCAAACCTCGAAGTTCGATAGTCAAA-C-CAAAAAACATTTCAATGTAAATGCATCATCA
3942 AACCCCAAAG-TTG
63 AACCCCAAAGTTTG
3955 ATAGTCAAACC
1 ATAGTCAAACC
3966 ACAAAAAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
75 4 0.06
76 33 0.46
77 12 0.17
78 23 0.32
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (76 bp):
ATAGTCAAACCTCGAAGTTCGATAGTCAAACCAAAAAACATTTCAATGTAAATGCATCATCAAAC
CCCAAAGTTTG
Found at i:4121 original size:95 final size:94
Alignment explanation
Indices: 3991--4265 Score: 414
Period size: 95 Copynumber: 2.9 Consensus size: 94
3981 TACATGTATG
* *
3991 AAGTACTAACTTTTTT-TTTGAAGTAAAAAACAAAAAATACTAACTTAAGAAAGTAGTGGGTCGA
1 AAGTACTAACTTTTTTGTTTGAAGT-AAAAA-AAAAAATACTAACTTAAGAAAGTAGTGGCTTGA
*
4055 TTATATGAAAAGATGGATAAATCTAAAGAAA
64 TTATATGAAGAGATGGATAAATCTAAAGAAA
* *
4086 AAGTACTAACTTTTTTGGTTTGAAGTAAAAAAAAAAATACTAAGTTAAAAAAGTAGTGGCTTGAT
1 AAGTACTAACTTTTTT-GTTTGAAGTAAAAAAAAAAATACTAACTTAAGAAAGTAGTGGCTTGAT
4151 TATATGAAGAGATGGATAAATCTAAAGAAA
65 TATATGAAGAGATGGATAAATCTAAAGAAA
* * *
4181 AAATAATAACTTTTTTTGTTTGAAGT--TAAAAAAAA-ACTAACTTAAGAAAGTAGTGGCTTGAT
1 AAGTACTAAC-TTTTTTGTTTGAAGTAAAAAAAAAAATACTAACTTAAGAAAGTAGTGGCTTGAT
4243 TATATGAAGAGATGGATAAATCT
65 TATATGAAGAGATGGATAAATCT
4266 TCTGGTTAGT
Statistics
Matches: 167, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
92 48 0.29
93 8 0.05
95 92 0.55
96 11 0.07
97 8 0.05
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.31
Consensus pattern (94 bp):
AAGTACTAACTTTTTTGTTTGAAGTAAAAAAAAAAATACTAACTTAAGAAAGTAGTGGCTTGATT
ATATGAAGAGATGGATAAATCTAAAGAAA
Found at i:5749 original size:144 final size:144
Alignment explanation
Indices: 5489--5776 Score: 576
Period size: 144 Copynumber: 2.0 Consensus size: 144
5479 ATGACTTGCA
5489 CCTTATTGCCAACAAGATCAAGAATTCATGCTTAAAGCCATCAAGAACAAAAAGGTCAAGATTGA
1 CCTTATTGCCAACAAGATCAAGAATTCATGCTTAAAGCCATCAAGAACAAAAAGGTCAAGATTGA
5554 TGAGAATGAGTGAGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAA
66 TGAGAATGAGTGAGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAA
5619 ACAGAAGGGTTAAG
131 ACAGAAGGGTTAAG
5633 CCTTATTGCCAACAAGATCAAGAATTCATGCTTAAAGCCATCAAGAACAAAAAGGTCAAGATTGA
1 CCTTATTGCCAACAAGATCAAGAATTCATGCTTAAAGCCATCAAGAACAAAAAGGTCAAGATTGA
5698 TGAGAATGAGTGAGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAA
66 TGAGAATGAGTGAGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAA
5763 ACAGAAGGGTTAAG
131 ACAGAAGGGTTAAG
5777 ATGAAGTTTT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (144 bp):
CCTTATTGCCAACAAGATCAAGAATTCATGCTTAAAGCCATCAAGAACAAAAAGGTCAAGATTGA
TGAGAATGAGTGAGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAA
ACAGAAGGGTTAAG
Found at i:6095 original size:203 final size:204
Alignment explanation
Indices: 5715--6109 Score: 634
Period size: 203 Copynumber: 1.9 Consensus size: 204
5705 GAGTGAGACG
*
5715 AACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAAACAGAAGGGTTAAGATG
1 AACATCTTGAAATTCAACTACCACATCTTTATAGTTTTGAAAAAAAAAACAGAAGGGTTAAGATG
* * * ** * *
5780 AAGTTTTCTTTTCTTACTAGCATAATTTAGTAGGATGTTTACGAATTGTTTGTGTTTGCAGGATA
66 AAGTTCTCTTTTCTTACTAGCATAATCTACTAGGATACTAACGAATTGTTTATGTTTGCAGGATA
*
5845 TCTACTTTGACAATTGATGTTTCAGAAAAAGAGATAGTTATGGCTGGTTACTCCACACGAGAATG
131 TCTACTTTGACAATTGATGTTTCAGAAAAAGAGATAGTTACGGCTGGTTACTCCACACGAGAATG
5910 ATTGGGATA
196 ATTGGGATA
5919 AACATCTTGAAATTCAACTACCACATCTTTATAGTTTTGGAAAAAAAAAACAGAAGGG-TAAGAT
1 AACATCTTGAAATTCAACTACCACATCTTTATAGTTTT-GAAAAAAAAAACAGAAGGGTTAAGAT
* *
5983 GAAGTTCTCTTTTTCTTCCTAGCATAATCTACT-GGATACTAACGGATTG-TTATGTTTGCAGGA
65 GAAGTTCTC-TTTTCTTACTAGCATAATCTACTAGGATACTAACGAATTGTTTATGTTTGCAGGA
* *
6046 TGTCTACTTTGACAATTGATGTTTCAGAAAAAGAGATAGTTACGGCTGGTTACTCCATACGAGA
129 TATCTACTTTGACAATTGATGTTTCAGAAAAAGAGATAGTTACGGCTGGTTACTCCACACGAGA
6110 TTCAGCGGGC
Statistics
Matches: 176, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
203 74 0.42
204 63 0.36
205 39 0.22
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (204 bp):
AACATCTTGAAATTCAACTACCACATCTTTATAGTTTTGAAAAAAAAAACAGAAGGGTTAAGATG
AAGTTCTCTTTTCTTACTAGCATAATCTACTAGGATACTAACGAATTGTTTATGTTTGCAGGATA
TCTACTTTGACAATTGATGTTTCAGAAAAAGAGATAGTTACGGCTGGTTACTCCACACGAGAATG
ATTGGGATA
Found at i:9871 original size:24 final size:24
Alignment explanation
Indices: 9837--9888 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
9827 ATCAAACTAC
* *
9837 TTCGCGTGTCTTCTTTTCAGGGTG
1 TTCGCGGGTCTTCTCTTCAGGGTG
9861 TTCGCGGGTCTTCTCTTCAGGGTG
1 TTCGCGGGTCTTCTCTTCAGGGTG
9885 TTCG
1 TTCG
9889 GTATAGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.04, C:0.23, G:0.31, T:0.42
Consensus pattern (24 bp):
TTCGCGGGTCTTCTCTTCAGGGTG
Found at i:10459 original size:63 final size:63
Alignment explanation
Indices: 10381--10499 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
10371 AGGACAATCT
10381 CCGGACTTGCGGGAGAAACTAAACAA-AAAGAGAGAGGCAGACGAGATAGATAAGCAGCTGGAA
1 CCGGACTTGCGGGAGAAACTAAACAAGAAA-AGAGAGGCAGACGAGATAGATAAGCAGCTGGAA
* * *
10444 CCGGACTTGCGGGAGAAACTAAATAAGAAAAGAGAGGCGGATGAGATAGATAAGCA
1 CCGGACTTGCGGGAGAAACTAAACAAGAAAAGAGAGGCAGACGAGATAGATAAGCA
10500 ATTGGAACAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
63 49 0.94
64 3 0.06
ACGTcount: A:0.43, C:0.14, G:0.32, T:0.11
Consensus pattern (63 bp):
CCGGACTTGCGGGAGAAACTAAACAAGAAAAGAGAGGCAGACGAGATAGATAAGCAGCTGGAA
Found at i:15999 original size:77 final size:77
Alignment explanation
Indices: 15903--16452 Score: 745
Period size: 77 Copynumber: 7.1 Consensus size: 77
15893 TTGGAAGTAC
*
15903 AAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGGAAGTAAGA
1 AAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGGAAGTAAAA
*
15968 ATTTCCAAGTCT
66 ATTTCCAAGTGT
*
15980 AAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACTAAAAAGAAATTTGGAAGTAAAA
1 AAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGGAAGTAAAA
*
16045 ATTTCCAAATGT
66 ATTTCCAAGTGT
* **
16057 TAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAAGTAAAAAGAAATTTGGAAGTAAAA
1 AAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGGAAGTAAAA
16122 ATTTCCAAGTGAT
66 ATTTCCAAGTG-T
*
16135 AAA-CATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACC-AAAAGAAATTTGGAAGTAAAA
1 AAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGGAAGTAAAA
16198 ATTTCCAAGTG-
66 ATTTCCAAGTGT
* *
16209 ATAATTATCTCCCTATAAGCGGAAGAGTTTCATGGGGAGGAACTAAAAAGAAATTTGGAAGTAAA
1 A-AATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGGAAGTAAA
*
16274 AATTTCCAAGTCT
65 AATTTCCAAGTGT
16287 AAATTATCTCCCTATGTGCGGATGTGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGG
1 AAATTATCTCCCTA--T---GA---GCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGG
*
16352 AAGTAGAAATTTCCAAGTGT
58 AAGTAAAAATTTCCAAGTGT
* * * * ** * *
16372 AAAATTA-GTCCCGATG-TCCGAATGAGTGACATAGGGA-GAA-AATAAAAGAAATTTGGAAGTA
1 -AAATTATCTCCCTATGAGCGGAA-GAGTTTCATGGGGAGGAACCA-AAAAGAAATTTGGAAGTA
*
16433 GAAATTTCCAAGTGT
63 AAAATTTCCAAGTGT
16448 AAATT
1 AAATT
16453 TCCCAATGTC
Statistics
Matches: 430, Mismatches: 27, Indels: 34
0.88 0.05 0.07
Matches are distributed among these distances:
74 1 0.00
75 8 0.02
76 108 0.25
77 237 0.55
78 4 0.01
79 1 0.00
80 1 0.00
82 1 0.00
83 1 0.00
85 62 0.14
86 6 0.01
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (77 bp):
AAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGGAAGTAAAA
ATTTCCAAGTGT
Found at i:16104 original size:154 final size:153
Alignment explanation
Indices: 15904--16452 Score: 755
Period size: 153 Copynumber: 3.5 Consensus size: 153
15894 TGGAAGTACA
* *
15904 AATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAAGAAATTTGGAAGTAAGAA
1 AATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACTAAAAAGAAATTTGGAAGTAAAAA
15969 TTTCCAAGTCTAAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACTAAAAAGAAATT
66 TTTCCAAGTCTAAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAAC-AAAAAGAAATT
*
16034 TGGAAGTAAAAATTTCCAAATGTT
130 TGGAAGTAAAAATTTCCAAGTGTT
*
16058 AATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAAGTAAAAAGAAATTTGGAAGTAAAAA
1 AATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACTAAAAAGAAATTTGGAAGTAAAAA
* * *
16123 TTTCCAAGTGATAAA-CATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACCAAAAGAAATT
66 TTTCCAAGT-CTAAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACAAAAAGAAATT
*
16187 TGGAAGTAAAAATTTCCAAGTGAT
130 TGGAAGTAAAAATTTCCAAGTGTT
*
16211 AATTATCTCCCTATAAGCGGAAGAGTTTCATGGGGAGGAACTAAAAAGAAATTTGGAAGTAAAAA
1 AATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACTAAAAAGAAATTTGGAAGTAAAAA
16276 TTTCCAAGTCTAAATTATCTCCCTATGTGCGGATGTGCGGAAGAGTTTCATGGGGAGGAACCAAA
66 TTTCCAAGTCTAAATTATCTCCCTA--T---GA---GCGGAAGAGTTTCATGGGGAGGAA-CAAA
* *
16341 AAGAAATTTGGAAGTAGAAATTTCCAAGTGTAA
122 AAGAAATTTGGAAGTAAAAATTTCCAAGTGT-T
* * * * ** * * * *
16374 AATTA-GTCCCGATG-TCCGAATGAGTGACATAGGGAGAAAAT-AAAAGAAATTTGGAAGTAGAA
1 AATTATCTCCCTATGAGCGGAA-GAGTTTCATGGGGAGGAACTAAAAAGAAATTTGGAAGTAAAA
*
16436 ATTTCCAAGTGTAAATT
65 ATTTCCAAGTCTAAATT
16453 TCCCAATGTC
Statistics
Matches: 354, Mismatches: 28, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
152 4 0.01
153 113 0.32
154 108 0.31
155 5 0.01
158 2 0.01
161 64 0.18
162 53 0.15
163 5 0.01
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (153 bp):
AATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACTAAAAAGAAATTTGGAAGTAAAAA
TTTCCAAGTCTAAATTATCTCCCTATGAGCGGAAGAGTTTCATGGGGAGGAACAAAAAGAAATTT
GGAAGTAAAAATTTCCAAGTGTT
Found at i:16514 original size:81 final size:82
Alignment explanation
Indices: 16254--16904 Score: 470
Period size: 89 Copynumber: 7.8 Consensus size: 82
16244 GGAGGAACTA
* * * * * * * *
16254 AAAAGAAATTTGGAAGTAAAAATTTCCAAGTCTAAATTATCTCCCTATGTGCGGATGTGC-GGAA
1 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAA-T-T-TCCCAATGTCCCGATGTCCTTGAT
** * *
16318 GAGTTTCATGGGGAGGAACCA-
63 GAGTGACATCGGGAAGAA--AT
* *
16339 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTGTAAAATT----A-GTCCCGATGTCC--GAATGA
1 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCCCGATGTCCTTG-ATGA
*
16397 GTGACATAGGG-AGAAAAT
65 GTGACATCGGGAAG-AAAT
* *
16415 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTGTAAATTTCCCAATGTCCCGATGTCC-GGATGAG
1 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCCCGATGTCCTTGATGAG
*
16479 TGACATAGGG-AGAAAAT
66 TGACATCGGGAAG-AAAT
*** *
16496 AAAAGAAATTTGGAAGTAGAAATTT--AAGAAAAAATTTCCCAATGTCCCAATGTCCTTATGACC
1 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCCCGATGTCC-T-TGA--
*
16559 TTGTATGCGACATCGGGAAGAAAT
62 -TG-A-GTGACATCGGGAAGAAAT
* * * * * ** * *
16583 TAAAGGAATTTGGAAGTAGAAATTTCAAAGTTTAAATCTCCCAACGTCCTTATGACCTTG-TGTG
1 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCCCGATGTCCTTGATGAG
*
16647 CGACATCGGGAAGAAAT
66 TGACATCGGGAAGAAAT
* * * * **
16664 TAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATCTCCCAACGTCCTTATGATCCTATGACC
1 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCCCGATG-TCCT-TGA--
*
16729 TTGTGTGCGACATCGGGAAGAAAT
62 -TGAGT--GACATCGGGAAGAAAT
* * * ** *
16753 TAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATCTCCCAATGTCCTTATGACCTTATGACC
1 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCCCGATGTCC-T-TGA--
*
16818 TTGTGTGCGACATCGGGAAGAAAT
62 -TGAGT--GACATCGGGAAGAAAT
* * * *
16842 TAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCTCAATGTCCTT-ATGA
1 AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCCCGATGTCCTTGATGA
16905 CCCCGTGTGT
Statistics
Matches: 496, Mismatches: 41, Indels: 60
0.83 0.07 0.10
Matches are distributed among these distances:
75 1 0.00
76 40 0.08
77 22 0.04
78 1 0.00
79 26 0.05
80 1 0.00
81 130 0.26
82 7 0.01
83 7 0.01
85 36 0.07
86 2 0.00
87 43 0.09
88 6 0.01
89 174 0.35
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (82 bp):
AAAAGAAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAATGTCCCGATGTCCTTGATGAG
TGACATCGGGAAGAAAT
Found at i:16761 original size:170 final size:170
Alignment explanation
Indices: 16411--16906 Score: 624
Period size: 170 Copynumber: 2.9 Consensus size: 170
16401 CATAGGGAGA
* * * * * ** * *
16411 AAATAAAAGAAATTTGGAAGTAGAAATTTCCAAGTGTAAATTTCCCAATGTCCCGATGTCC-GGA
1 AAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATCTCCCAACGTCCTTATGACCTTG-
* * * * * ***
16475 TGAGTGACATAGGG-AGAAAATAAAAGAAATTTGGAAGTAGAAATTT--AAGAAAAAATTTCCCA
65 TGTGCGACATCGGGAAG-AAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCA
*
16537 ATGTCCCAATGTCCTTATGACCTTGTATGCGACATCGGGAAG
129 ACGTCCCAATGTCCTTATGACCTTGTATGCGACATCGGGAAG
*
16579 AAATTAAAGGAATTTGGAAGTAGAAATTTCAAAGTTTAAATCTCCCAACGTCCTTATGACCTTGT
1 AAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATCTCCCAACGTCCTTATGACCTTGT
*
16644 GTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATCTCCCAAC
66 GTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAAC
** *
16709 GTCCTTATGATCC-TATGACCTTGTGTGCGACATCGGGAAG
131 GTCCCAATG-TCCTTATGACCTTGTATGCGACATCGGGAAG
*
16749 AAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATCTCCCAATGTCCTTATGACCTTAT
1 AAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATCTCCCAA----C----GTCCTTAT
16814 GACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAAT
58 GACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAAT
* *
16879 TTCCCAATGTCTCAATGTCCTTATGACC
123 TTCCCAACGTCCCAATGTCCTTATGACC
16907 CCGTGTGTGA
Statistics
Matches: 284, Mismatches: 30, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
168 90 0.32
169 3 0.01
170 93 0.33
171 3 0.01
174 1 0.00
177 3 0.01
178 91 0.32
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (170 bp):
AAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATCTCCCAACGTCCTTATGACCTTGT
GTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAAGTTTAAATTTCCCAAC
GTCCCAATGTCCTTATGACCTTGTATGCGACATCGGGAAG
Found at i:16932 original size:89 final size:89
Alignment explanation
Indices: 16628--16906 Score: 490
Period size: 89 Copynumber: 3.1 Consensus size: 89
16618 ATCTCCCAAC
16628 GTCCTTATGACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAA
1 GTCCTTATGACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAA
*
16693 GTTTAAATCTCCCAACGTCCTTAT
66 GTTTAAATCTCCCAATGTCCTTAT
16717 GATCC-TATGACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCA
1 G-TCCTTATGACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCA
16781 AGTTTAAATCTCCCAATGTCCTTAT
65 AGTTTAAATCTCCCAATGTCCTTAT
*
16806 GACCTTATGACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAA
1 GTCCTTATGACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAA
* *
16871 GTTTAAATTTCCCAATGT-CTCAAT
66 GTTTAAATCTCCCAATGTCCT-TAT
16895 GTCCTTATGACC
1 GTCCTTATGACC
16907 CCGTGTGTGA
Statistics
Matches: 182, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
88 4 0.02
89 175 0.96
90 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (89 bp):
GTCCTTATGACCTTGTGTGCGACATCGGGAAGAAATTAAAGGAATTTGGAAGTAGAAATTTCCAA
GTTTAAATCTCCCAATGTCCTTAT
Found at i:20490 original size:24 final size:24
Alignment explanation
Indices: 20456--20507 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
20446 ATCAAACTAC
*
20456 TTCGCGTGTCTTCTCTTCAGGGTG
1 TTCGCGGGTCTTCTCTTCAGGGTG
20480 TTCGCGGGTCTTCTCTTCAGGGTG
1 TTCGCGGGTCTTCTCTTCAGGGTG
20504 TTCG
1 TTCG
20508 GTATAGCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.04, C:0.25, G:0.31, T:0.40
Consensus pattern (24 bp):
TTCGCGGGTCTTCTCTTCAGGGTG
Found at i:26248 original size:13 final size:13
Alignment explanation
Indices: 26219--26256 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
26209 CTTGGAATGA
26219 AATTTTG-TTTTG
1 AATTTTGATTTTG
26231 AATTTTGAATTTTG
1 AATTTTG-ATTTTG
*
26245 ATTTTTGATTTT
1 AATTTTGATTTT
26257 TTTGGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 5 0.22
14 11 0.48
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (13 bp):
AATTTTGATTTTG
Done.