Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022934.1 Corchorus olitorius cultivar O-4 contig22967, 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: 71886
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3340 original size:105 final size:106
Alignment explanation
Indices: 3158--3418 Score: 395
Period size: 106 Copynumber: 2.5 Consensus size: 106
3148 AATTTTTCTA
* ** *
3158 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGTTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
3221 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
3261 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
3326 TTTCTAAAATCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
*
3368 TCCC-TAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
3419 AGGCTAAACT
Statistics
Matches: 144, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 27 0.19
104 14 0.10
105 36 0.25
106 47 0.33
107 20 0.14
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:3915 original size:2 final size:2
Alignment explanation
Indices: 3908--3947 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3898 CTATTTTGGC
3908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3948 AAAGTATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9064 original size:16 final size:16
Alignment explanation
Indices: 9038--9070 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9028 TAAAAAAATT
9038 AAATAAAAAATATATTA
1 AAATAAAAAATAT-TTA
9055 AAAT-AAAAATATTTA
1 AAATAAAAAATATTTA
9070 A
1 A
9071 TTTTTATGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAATATTTA
Found at i:9342 original size:2 final size:2
Alignment explanation
Indices: 9335--9385 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
9325 CAGAACTTTG
9335 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9375 AT AT AT AT AT A
1 AT AT AT AT AT A
9386 CTAGTTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9468 original size:22 final size:22
Alignment explanation
Indices: 9443--9517 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
9433 TTGAATATTT
*
9443 TTATGAAATTTTAATAACTACC
1 TTATGAAATTTTGATAACTACC
* * *
9465 TTATTAAATTTTGATAACCACG
1 TTATGAAATTTTGATAACTACC
* *
9487 TTATGGAATTTTGATAATTTACC
1 TTATGAAATTTTGATAA-CTACC
9510 -TATGAAAT
1 TTATGAAAT
9518 ATGAAACTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
22 40 0.95
23 2 0.05
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:9610 original size:21 final size:23
Alignment explanation
Indices: 9538--9595 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
9528 GATAACCTAA
9538 CTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
*
9561 CTATAAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
9584 CTATGAAATTTT
1 CTATGAAATTTT
9596 GTAATCTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.41
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Found at i:11166 original size:27 final size:26
Alignment explanation
Indices: 11111--11172 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
11101 TCTAAACTTT
11111 TATTATTTTAATAATGAAATAATTAAAA
1 TATTA-TTTAATAATGAAAT-ATTAAAA
11139 TATTATTTAATAATGGAAAT-TTAGAAA
1 TATTATTTAATAAT-GAAATATTA-AAA
11166 TA-TATTT
1 TATTATTT
11173 GCAAAAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.25
27 14 0.44
28 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
TATTATTTAATAATGAAATATTAAAA
Found at i:11232 original size:2 final size:2
Alignment explanation
Indices: 11225--11274 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
11215 TTCGTACTTT
*
11225 TA TA TA TA GTA TA AA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11267 TA CA TA TA
1 TA TA TA TA
11275 CTAGTTTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:11249 original size:19 final size:19
Alignment explanation
Indices: 11225--11268 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
11215 TTCGTACTTT
11225 TATATATAGTATAAATATA
1 TATATATAGTATAAATATA
* *
11244 TATATATATTATATATATA
1 TATATATAGTATAAATATA
11263 TATATA
1 TATATA
11269 CATATACTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATATATAGTATAAATATA
Found at i:14024 original size:33 final size:33
Alignment explanation
Indices: 13952--14027 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
13942 GAACTATCAA
* *
13952 CCAAAACAGAATTGTTTTCATCACAATGAGCAT
1 CCAAAACAGAATTGTTTTCATCACAATCAACAT
13985 CCAAAACAGAATT-TGTTTCATCACAATCAACA-
1 CCAAAACAGAATTGT-TTTCATCACAATCAACAT
14017 CCTAAAACAGA
1 CC-AAAACAGA
14028 TTTAGTGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 3 0.08
33 36 0.92
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (33 bp):
CCAAAACAGAATTGTTTTCATCACAATCAACAT
Found at i:14039 original size:33 final size:33
Alignment explanation
Indices: 13987--14116 Score: 120
Period size: 33 Copynumber: 3.9 Consensus size: 33
13977 ATGAGCATCC
* *
13987 AAAACAGAATTT-GTTTCATCACAATCAACACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT
* *
14020 AAAACAGATTTAGTGTCATCGCAAACAATA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * *
14052 CAAATTAGGTTTAGTATCATCACTAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
* *
14086 AAAACAGATTTCGTGTCATTACAAACAACAC
1 AAAACAGATTTAGTGTCATCACAAACAACAC
14117 TCAAATTAGG
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
32 6 0.08
33 67 0.89
34 2 0.03
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:14072 original size:66 final size:66
Alignment explanation
Indices: 14002--14128 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
13992 AGAATTTGTT
* *
14002 TCATCAC-AATCAACACCTAAAACAGATTTAGTGTCATCGCAAACAATACTCAAATTAGGTTTAG
1 TCATCACTAA-CAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAG
14066 TA
65 TA
* * *
14068 TCATCACTAACAACATCTAAAACAGATTTCGTGTCATTACAAACAACACTCAAATTAGGTT
1 TCATCACTAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTT
14129 CAGAATTACT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 53 0.96
67 2 0.04
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (66 bp):
TCATCACTAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAGT
A
Found at i:15824 original size:21 final size:21
Alignment explanation
Indices: 15768--15894 Score: 80
Period size: 22 Copynumber: 5.9 Consensus size: 21
15758 TTGGCGCATC
*
15768 AACTACCCTATTAAATTTTGAT
1 AACTA-CCTATGAAATTTTGAT
* **
15790 AACCATGTTATGAAATTTTGAT
1 AACTA-CCTATGAAATTTTGAT
* * *
15812 AATTACCTATGAAATTGTAAT
1 AACTACCTATGAAATTTTGAT
*
15833 AAACT-CCATATGAAACTTTGAT
1 -AACTACC-TATGAAATTTTGAT
*
15855 AACCTAACTATGAAA-TTTG-T
1 AA-CTACCTATGAAATTTTGAT
* *
15875 AACCTCCCTATGAGATTTTG
1 AA-CTACCTATGAAATTTTG
15895 TTAATCTCCC
Statistics
Matches: 81, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
20 13 0.16
21 24 0.30
22 43 0.53
23 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (21 bp):
AACTACCTATGAAATTTTGAT
Found at i:15906 original size:22 final size:20
Alignment explanation
Indices: 15817--15907 Score: 65
Period size: 22 Copynumber: 4.2 Consensus size: 20
15807 TTGATAATTA
* *
15817 CCTATGAAATTGTAATAAACTC
1 CCTATGAAATT-T-GTAACCTC
* *
15839 CATATGAAACTTTGATAACCTA
1 CCTATGAAA-TTTG-TAACCTC
*
15861 ACTATGAAATTTGTAACCTC
1 CCTATGAAATTTGTAACCTC
* *
15881 CCTATGAGATTTTGTTAATCTC
1 CCTATGA-AATTTG-TAACCTC
15903 CCTAT
1 CCTAT
15908 AATTTTTTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
20 12 0.22
21 9 0.16
22 32 0.58
23 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
CCTATGAAATTTGTAACCTC
Found at i:20958 original size:49 final size:49
Alignment explanation
Indices: 20883--20979 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
20873 TTTGACCGAC
*
20883 TGATTTGTATTTTCATTTCTCGTATATAACATTTATACATTTGTATTTG
1 TGATTTGTATTTTCATTTCTCGTATATAAAATTTATACATTTGTATTTG
20932 TGATTTGTATTTTCATTTCTTC-TATATAAAATTTATACATTTGTATTT
1 TGATTTGTATTTTCATTTC-TCGTATATAAAATTTATACATTTGTATTT
20980 TGTAAAATGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 44 0.96
50 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.57
Consensus pattern (49 bp):
TGATTTGTATTTTCATTTCTCGTATATAAAATTTATACATTTGTATTTG
Found at i:33610 original size:11 final size:12
Alignment explanation
Indices: 33586--33619 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
33576 CTTTAAGAAG
33586 ATATATATATCT
1 ATATATATATCT
33598 ATATATA-ATCT
1 ATATATATATCT
33609 ATATACTATAT
1 ATATA-TATAT
33620 ATAAAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 9 0.45
13 2 0.10
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATATCT
Found at i:34600 original size:20 final size:20
Alignment explanation
Indices: 34563--34601 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34553 TGCTATTATT
34563 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
34583 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
34602 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:35076 original size:22 final size:22
Alignment explanation
Indices: 35048--35258 Score: 171
Period size: 22 Copynumber: 9.5 Consensus size: 22
35038 TGTCTCTGTG
*
35048 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
35070 TGGTTATTATAATTTTATGTGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
35093 -GGTTATCAAATTTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
35114 CGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
35137 -AGTTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
*
35158 AGGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
35180 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
35202 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* * **
35226 AGGTTGTTGAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
35248 TGGTTATCAAA
1 TGGTTATCAAA
35259 GAGATTATCA
Statistics
Matches: 150, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.03
22 122 0.81
23 5 0.03
24 18 0.12
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:35126 original size:66 final size:66
Alignment explanation
Indices: 35049--35876 Score: 252
Period size: 66 Copynumber: 12.9 Consensus size: 66
35039 GTCTCTGTGT
* * * * * *
35049 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTTAT-GTGGAGGTTATCAAATTTTCATAGT
1 GGTTACCAAAATTTCATAGGATGGTTATTAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGT
35113 GC
65 GC
* *
35115 GGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGT
1 GGTTACCAAAATTTCATA-GGATGGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATAGT
*
35179 GT
65 GC
* * **
35181 GGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGTTGTTGAAATTTCATAG
1 GGTTACCAAAATTTCATAGGAT--GGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATAG
*
35246 TGT
64 TGC
* * * *
35249 GGTT------A--TCA-AAGA-GATTATCAAAATGTCATAGCG-AGGTTAT-AAGAATTTCATA-
1 GGTTACCAAAATTTCATAGGATGGTTATTAAAATTTCATAG-GAAGGTTATCAA-AATTTCATAG
35301 T--
64 TGC
* * * * *
35302 GGTTAACAAAATTTCATAAGGA-GGTTACTAATATTTCATTGGGAGGTTATCAAAATTTCATA-T
1 GGTTACCAAAATTTCAT-AGGATGGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATAGT
*
35365 GAA
65 G-C
** ** * *
35368 GGTTATAAAAGTCTCAATTTCATAAGGA--G-TACCAAAATTTGATA-GAAGGTTATC-AAATCT
1 GGTTA-CCAA-----AATTTCAT-AGGATGGTTATTAAAATTTCATAGGAAGGTTATCAAAATTT
* *
35428 CATAGAGT
59 CATAGTGC
*** * ** * *
35436 GGTTATTGAAATTTCACAAATATCGGATTATCAAAATTT-ATAGGAAGATTAT-AAAATTTTCAT
1 GGTTACCAAAATTTCA-TAGGAT-GG-TTATTAAAATTTCATAGGAAGGTTATCAAAA-TTTCAT
* *
35499 AGAGT
62 AGTGC
* * * * * *
35504 TGTTATCAAAATTTCAAAGCGA-GGTTATGAAAATTACATA--ATGTGATTATCAAAATTTCATA
1 GGTTACCAAAATTTCATAG-GATGGTTATTAAAATTTCATAGGAAG-G-TTATCAAAATTTCATA
* *
35566 GAGG
63 GTGC
* * * * * * * *
35570 GGTCAACAAAATTTTATAGAGA-GGTTATCAAAATTTCATA-AAGAGGTTATCAAATTTTCAAAA
1 GGTTACCAAAATTTCATAG-GATGGTTATTAAAATTTCATAGGA-AGGTTATCAAAATTTCATAG
*
35633 TGT
64 TGC
*
35636 GATTACCAAAATTTCATA-G-TGG----T---ATTTC-T-GGAGAGGTTATCAAAATTTCATAGT
1 GGTTACCAAAATTTCATAGGATGGTTATTAAAATTTCATAGGA-AGGTTATCAAAATTTCATAGT
**
35690 AT
65 GC
* * * * *
35692 AGTTACC-AAA--T--TAGGATGATTATTAAACTTTTATTATGG-A-GTAATCAAAATTTC--AG
1 GGTTACCAAAATTTCATAGGATGGTTATTAAAATTTCA-TA-GGAAGGTTATCAAAATTTCATAG
* *
35748 GGA
64 TGC
* * * * * ** *
35751 GGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAAG
1 GGTTACCAAAATTTCATAGGATGGTTATTAAAATTTCATAG-GAAGGTTATCAAAATTTCAT-AG
*
35815 AG-
64 TGC
* * * *
35817 GGTTATCAAAATTTCATAGAAT-GTAGATCAAAATTTCATAGGGAGAGGTTATCAAAATTT
1 GGTTACCAAAATTTCATAGGATGGT-TATTAAAATTTCATA-GGA-AGGTTATCAAAATTT
35877 GTAGTTATCA
Statistics
Matches: 577, Mismatches: 111, Indels: 146
0.69 0.13 0.18
Matches are distributed among these distances:
51 2 0.00
52 1 0.00
53 7 0.01
55 5 0.01
56 57 0.10
57 7 0.01
59 10 0.02
60 9 0.02
61 16 0.03
62 15 0.03
63 35 0.06
64 38 0.07
65 16 0.03
66 190 0.33
67 41 0.07
68 93 0.16
69 10 0.02
70 11 0.02
71 1 0.00
72 13 0.02
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (66 bp):
GGTTACCAAAATTTCATAGGATGGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTG
C
Found at i:35200 original size:44 final size:44
Alignment explanation
Indices: 35045--36143 Score: 234
Period size: 44 Copynumber: 25.1 Consensus size: 44
35035 TCTTGTCTCT
* * * * *
35045 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTTAT-
1 GTGTGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
* * * *
35088 GTGGAGGTTATCAAATTTTCATAGTG-CGGTTACCAAAATTTCATA
1 GT-GTGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATA
35133 -TG-GAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 GTGTG--GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
* * *
35177 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTA
1 GTGTGGTTATCAAAATTTCATAGGA--AGGTTATCAAAATTTCATA
* * ** *
35223 G-GAAGGTTGTTGAAATTTCATAGTGTGGTTATCAAAGAGATTATCAAAATGTCATA
1 GTG-TGGTTATCAAAATTTCATA----GG------AAG-G-TTATCAAAATTTCATA
* * * *
35279 GCGAGGTTAT-AAGAATTTCAT---ATGGTTAACAAAATTTCATAA
1 GTGTGGTTATCAA-AATTTCATAGGAAGGTTATCAAAATTTCAT-A
* * * *
35321 G-GAGGTTA-CTAATATTTCATTGGGAGGTTATCAAAATTTCATA
1 GTGTGGTTATC-AAAATTTCATAGGAAGGTTATCAAAATTTCATA
* * * *
35364 -TGAAGGTTATAAAAGTCTCAATTTCATAAGG-A-G-TACCAAAATTTGATA
1 GTG-TGGTTAT-CAA-----AATTTCAT-AGGAAGGTTATCAAAATTTCATA
** * * ** *
35412 G-AAGGTTATC-AAATCTCATA-GAGTGGTTATTGAAATTTCACAA
1 GTGTGGTTATCAAAATTTCATAGGA-AGGTTATCAAAATTTCA-TA
* * *
35455 ATATCGGATTATCAAAATTT-ATAGGAAGATTAT-AAAATTTTCATA
1 GTGT-GG-TTATCAAAATTTCATAGGAAGGTTATCAAAA-TTTCATA
* * * * *
35500 GAGTTGTTATCAAAATTTCAAAGCG-AGGTTATGAAAATTACATA
1 GTGTGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATA
* * * * * *
35544 ATGTGATTATCAAAATTTCATA-GAGGGGTCAACAAAATTTTATA
1 GTGTGGTTATCAAAATTTCATAGGA-AGGTTATCAAAATTTCATA
* * * * *
35588 GAGAGGTTATCAAAATTTCATA-AAGAGGTTATCAAATTTTCAAA
1 GTGTGGTTATCAAAATTTCATAGGA-AGGTTATCAAAATTTCATA
* * * * *
35632 ATGTGATTACCAAAATTTCATA-G-TGG---T----ATTTC-TG
1 GTGTGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
* * * *
35666 GAGAGGTTATCAAAATTTCATAGTATA-GTTA-CCAAA--T--TA
1 GTGTGGTTATCAAAATTTCATAGGA-AGGTTATCAAAATTTCATA
* * * * *
35705 G-GATGATTATTAAACTTTTATTATGG-A-GTAATCAAAATTTC--A
1 GTG-TGGTTATCAAAATTTCA-TA-GGAAGGTTATCAAAATTTCATA
* * * *
35747 GGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
* * * * *
35791 GTTTAGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
*
35835 GAATGTAG--ATCAAAATTTCATAGGGAGAGGTTATCAAAA--T--T-
1 G--TGTGGTTATCAAAATTTCATA-GGA-AGGTTATCAAAATTTCATA
* * *
35876 -TGTAGTTATCAAGATTTCATAAGG-AGGTTATCAAAATTTTATA
1 GTGTGGTTATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCATA
* * * * * * * *
35919 GGGAGGTTTATGAAATTTTTATAGGTAGGTTTATCAAAATCTAATTA
1 GTGTGG-TTATCAAAATTTCATAGGAAGG-TTATCAAAATTTCA-TA
* * * * * * * *
35966 -CGAGATTATTACAATTTCATAGTG-TGATTATCAAAATTTCAGA
1 GTGTGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATA
* * * * *
36009 GGGTGATTA-CTAACAA-TTCATATGGAA-GTTTTTAAATTTTCATA
1 GTGTGGTTATC-AA-AATTTCATA-GGAAGGTTATCAAAATTTCATA
* * * * * *
36053 ATGTGGTTATCAATAA-ATCATATGTAA-GTTATTAACATCTCATA
1 GTGTGGTTATCAA-AATTTCATA-GGAAGGTTATCAAAATTTCATA
** *
36097 GAT-CAGTTATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATA
1 G-TGTGGTTATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATA
36141 GTG
1 GTG
36144 AGATCTTTAA
Statistics
Matches: 771, Mismatches: 177, Indels: 215
0.66 0.15 0.18
Matches are distributed among these distances:
34 17 0.02
35 4 0.01
36 1 0.00
38 19 0.02
39 20 0.03
40 30 0.04
41 33 0.04
42 48 0.06
43 26 0.03
44 360 0.47
45 55 0.07
46 82 0.11
47 16 0.02
48 13 0.02
49 1 0.00
50 10 0.01
51 2 0.00
54 2 0.00
55 2 0.00
56 29 0.04
57 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (44 bp):
GTGTGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
Found at i:35337 original size:22 final size:22
Alignment explanation
Indices: 35263--35653 Score: 154
Period size: 22 Copynumber: 17.7 Consensus size: 22
35253 ATCAAAGAGA
*
35263 TTATCAAAATGTCAT-AGCGAGG
1 TTATCAAAATTTCATAAG-GAGG
*
35285 TTAT-AAGAATTTCAT-A--TGG
1 TTATCAA-AATTTCATAAGGAGG
*
35304 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
* **
35326 TTA-CTAATATTTCATTGGGAGG
1 TTATC-AAAATTTCATAAGGAGG
* *
35348 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAAGGAGG
*
35370 TTATAAAAGTCTCAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATAAGGAGG
* * *
35397 -TACCAAAATTTGAT-AGAAGG
1 TTATCAAAATTTCATAAGGAGG
* *
35417 TTATC-AAATCTCAT-AGAGTGG
1 TTATCAAAATTTCATAAG-GAGG
** * **
35438 TTATTGAAATTTCACAAATATCGG
1 TTATCAAAATTTCATAAGGA--GG
*
35462 ATTATCAAAATTT-AT-AGGAAGA
1 -TTATCAAAATTTCATAAGG-AGG
35484 TTAT-AAAATTTTCAT-A-GAGTTG
1 TTATCAAAA-TTTCATAAGGAG--G
35506 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAAG-GAGG
* * * * *
35528 TTATGAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAGGAGG
35550 TTATCAAAATTTCATAGAGG-GG
1 TTATCAAAATTTCATA-AGGAGG
* * *
35572 TCAACAAAATTTTAT-AGAGAGG
1 TTATCAAAATTTCATAAG-GAGG
*
35594 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAGGAGG
* * * * *
35616 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAAGGAGG
*
35638 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
35654 GTGGTATTTC
Statistics
Matches: 274, Mismatches: 60, Indels: 70
0.68 0.15 0.17
Matches are distributed among these distances:
19 16 0.06
20 28 0.10
21 21 0.08
22 162 0.59
23 14 0.05
24 7 0.03
25 12 0.04
26 2 0.01
27 1 0.00
28 11 0.04
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGG
Found at i:35898 original size:84 final size:86
Alignment explanation
Indices: 35755--35919 Score: 214
Period size: 84 Copynumber: 1.9 Consensus size: 86
35745 CAGGGAGGAT
* *
35755 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAA-GAGGG
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTT-ATAG-TTAGTTATCAAAATTTCATAAGGA-GG
35819 TTATCAAAATTTCATAGAATGTAG
63 TTATCAAAATTTCATAGAATGTAG
*
35843 ATCAAAATTTCATAGGGAGAGGTTATCAAAA-TT-T-G-TAGTTATCAAGATTTCATAAGGAGGT
1 ATCAAAATTTCATA-GGA-AGGTTATCAAAATTTATAGTTAGTTATCAAAATTTCATAAGGAGGT
*
35904 TATCAAAATTTTATAG
64 TATCAAAATTTCATAG
35920 GGAGGTTTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
84 36 0.51
85 2 0.03
86 1 0.01
87 1 0.01
88 14 0.20
89 4 0.06
90 12 0.17
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (86 bp):
ATCAAAATTTCATAGGAAGGTTATCAAAATTTATAGTTAGTTATCAAAATTTCATAAGGAGGTTA
TCAAAATTTCATAGAATGTAG
Found at i:35908 original size:22 final size:22
Alignment explanation
Indices: 35735--36286 Score: 128
Period size: 22 Copynumber: 25.3 Consensus size: 22
35725 TTATGGAGTA
* *
35735 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
* *
35755 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
35777 ATCAAAATTTCAT-AGTTTA-GTT
1 ATCAAAATTTCATAAG--GAGGTT
*
35799 TTCAAAATTTCATAA-GAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * *
35821 ATCAAAATTTCAT-AGAATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
*
35843 ATCAAAATTTCATAGGGAGAGGTT
1 ATCAAAATTTCATA-AG-GAGGTT
*
35867 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
*
35883 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
35905 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAAGGAGG-TT
* * *
35928 ATGAAATTTTTAT-AGGTAGGTTT
1 ATCAAAATTTCATAAGG-AGG-TT
* * * * *
35951 ATCAAAATCTAATTACGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
35973 ATTACAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
* * * *
35995 ATCAAAATTTCAGAGGGTGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
36017 A-CTAACAA-TTCATATGGAAGTT
1 ATC-AA-AATTTCATAAGGAGGTT
* * * * *
36039 TTTAAATTTTCATAATGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
36061 ATCAATAA-ATCATATGTAAGTT
1 ATCAA-AATTTCATAAGGAGGTT
* * * **
36083 ATTAACATCTCATAGATCA-GTT
1 ATCAAAATTTCATA-AGGAGGTT
** *
36105 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAAGGAGGTT
*
36127 ATCAAAATTTCAT-AGTGAGATCT
1 ATCAAAATTTCATAAG-GAGGT-T
* * **
36150 -TTAAAA-TTCTTTATTGAGGTT
1 ATCAAAATTTC-ATAAGGAGGTT
* * *
36171 AACAAAATTTCATAAGAAGGATA
1 ATCAAAATTTCATAAGGAGG-TT
** * * * *
36194 AAAAAAAATT-ATAA-AAAGAT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
36214 CTCGAAATTTCAT-AGTATCGTT
1 ATCAAAATTTCATAAGGA-GGTT
*
36236 ATTAAAATTTCAT-AGGAAGGTT
1 ATCAAAATTTCATAAGG-AGGTT
*
36258 ATCAAAATTTCATAAGGAGGTC
1 ATCAAAATTTCATAAGGAGGTT
36280 ATCAAAA
1 ATCAAAA
36287 ATAGCGTAAT
Statistics
Matches: 380, Mismatches: 109, Indels: 84
0.66 0.19 0.15
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 1 0.00
20 18 0.05
21 23 0.06
22 256 0.67
23 56 0.15
24 10 0.03
25 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:35938 original size:23 final size:23
Alignment explanation
Indices: 35881--35958 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
35871 AAATTTGTAG
* * *
35881 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
35903 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
35926 TTATGAAATTTTTATAGGTAGGT
1 TTATCAAAATTTTATAGGGAGGT
35949 TTATCAAAAT
1 TTATCAAAAT
35959 CTAATTACGA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 19 0.40
23 28 0.60
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:37444 original size:20 final size:20
Alignment explanation
Indices: 37407--37445 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
37397 TACTATTATT
37407 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
37427 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
37446 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:37639 original size:22 final size:22
Alignment explanation
Indices: 37611--37821 Score: 134
Period size: 22 Copynumber: 9.5 Consensus size: 22
37601 TGTCTTTGTG
37611 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
37633 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
37656 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
37677 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
*
37700 -AGTTATCAAAATTTCATGGAA-A
1 TGGTTATCAAAATTTCAT--AAGA
*
37722 -GGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
37743 TGGTTACCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
*
37765 TTAGGTTAT-AGAAATTTCAT-AGTG
1 -T-GGTTATCA-AAATTTCATAAG-A
* *
37789 TGGTTATCACAATTTTAT-AGAA
1 TGGTTATCAAAATTTCATAAG-A
*
37811 AGGTTATCAAA
1 TGGTTATCAAA
37822 GAGATTATCA
Statistics
Matches: 146, Mismatches: 27, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
22 117 0.80
23 11 0.08
24 16 0.11
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:37714 original size:66 final size:66
Alignment explanation
Indices: 37608--37784 Score: 225
Period size: 66 Copynumber: 2.7 Consensus size: 66
37598 TCTTGTCTTT
* * * * *
37608 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCAT-GAGGAGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGA-AAGGTTATCAAAATTCCA
37672 TA
65 TA
* *
37674 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATGGAAAGGTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGGAAAGGTTATCAAAATTCCA
37738 TA
65 TA
37740 GTGTGGTTACCAAAATTTCATAAGATTAGGTTAT-AGAAATTTCAT
1 GTGTGGTTACCAAAATTTCATAAGA-TA-GTTATCA-AAATTTCAT
37785 AGTGTGGTTA
Statistics
Matches: 97, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
65 2 0.02
66 75 0.77
67 6 0.06
68 14 0.14
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGAAAGGTTATCAAAATTCCAT
A
Found at i:37847 original size:22 final size:21
Alignment explanation
Indices: 37826--38239 Score: 153
Period size: 22 Copynumber: 18.7 Consensus size: 21
37816 ATCAAAGAGA
* *
37826 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATAG-GAGG
*
37848 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
37870 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
37892 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATA-GGAGG
*
37914 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
** * *
37936 TTATTTAAATTT-TTAAGTGTGG
1 TTATCAAAATTTCAT-AG-GAGG
*
37958 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
37980 TTATAAAAGTCTTAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
38005 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
38027 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
*
38047 ATTATCGAAATTTCATAGAGATTGG
1 -TTATCAAAATTTCATAG-GA--GG
* *
38072 ATTATCAGAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATAGG-AGG
***
38094 TTATCAAAATTTCATAGTGTTC
1 TTATCAAAATTTCATAG-GAGG
*
38116 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* ** **
38138 TTATCAAAATTACATAATTAAA
1 TTATCAAAATTTCAT-AGGAGG
* *
38160 ATATCAAAAAATTTCAGAGG-GG
1 TTATC--AAAATTTCATAGGAGG
* * *
38182 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAG-GAGG
**
38204 TTATCAAAATTTCATAAACAGG
1 TTATCAAAATTTCAT-AGGAGG
*
38226 TTATCAAATTTTCA
1 TTATCAAAATTTCA
38240 AAATGTGATT
Statistics
Matches: 293, Mismatches: 64, Indels: 70
0.69 0.15 0.16
Matches are distributed among these distances:
19 2 0.01
20 27 0.09
21 26 0.09
22 180 0.61
23 14 0.05
24 15 0.05
25 17 0.06
26 3 0.01
28 9 0.03
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:37960 original size:66 final size:65
Alignment explanation
Indices: 37826--37987 Score: 175
Period size: 66 Copynumber: 2.5 Consensus size: 65
37816 ATCAAAGAGA
* * *
37826 TTATCAAAATGTCATAGCGAGATTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
1 TTATCAAAATTTCATAGGGAGGTTATAA-AATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
37891 G
65 G
* *** *
37892 TTA-CTAATATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATTTAAATTT-TTAAGTG
1 TTATC-AAAATTTCATAGGGAGGTTAT-AAAATTTCATAGTGTGGTTAACAAAATTTCATAAG-G
*
37955 TGG
63 AGG
* *
37958 TTATCAAAATTTCATATGAAGGTTATAAAA
1 TTATCAAAATTTCATAGGGAGGTTATAAAA
37988 GTCTTAATTT
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
65 9 0.11
66 68 0.85
67 3 0.04
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (65 bp):
TTATCAAAATTTCATAGGGAGGTTATAAAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAGG
Found at i:38458 original size:22 final size:22
Alignment explanation
Indices: 38345--38770 Score: 174
Period size: 22 Copynumber: 19.6 Consensus size: 22
38335 CTATAGAGTA
* *
38345 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
*
38365 ATCAAAATTTCAT-AGTTTA-GTT
1 ATCAAAATTTCATAAG--GAGGTT
*
38387 TTC-AAATATTCATAA-GAGGGTT
1 ATCAAAAT-TTCATAAGGA-GGTT
* * *
38409 ATCAAAATTTCAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
*
38431 ATCAAAATTTCATAAGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
38453 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
** *
38475 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
38497 ATCAAAATTT-GT-A--A--TT
1 ATCAAAATTTCATAAGGAGGTT
* * *
38513 ATCAAGATTTCATAAAGAGGCT
1 ATCAAAATTTCATAAGGAGGTT
* *
38535 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAAGGAGG-TT
*
38558 ATCAAAATTTTAT-AGCGAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* * *
38580 ATCACAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
* *
38602 ATCAAAATTTCA-GAGTGTA-ATT
1 ATCAAAATTTCATAAG-G-AGGTT
*
38624 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAAGGAGGTT
* * * * * *
38646 TTTAAATTTTCTTAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
38668 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
38690 ATCAACATCTCAT-AGTGTTGGTT
1 ATCAAAATTTCATAAG-G-AGGTT
*
38713 ATCAAAATTTCAT-AGTAAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* * * *
38735 TTCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
38757 AACAAAATTTCATA
1 ATCAAAATTTCATA
38771 TGAAAGTTAA
Statistics
Matches: 298, Mismatches: 77, Indels: 60
0.69 0.18 0.14
Matches are distributed among these distances:
16 11 0.04
17 1 0.00
18 2 0.01
20 13 0.04
21 13 0.04
22 208 0.70
23 50 0.17
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:38552 original size:60 final size:61
Alignment explanation
Indices: 38450--38567 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 61
38440 TCATAAGGAG
* *
38450 ATTAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGG-TTATCAAAATTTGTA
1 ATTAACAAAATTTCATAAAGAGGCTATCAAAAAATCATAGGGAGGTTTATCAAAATTTGTA
* * ** *
38510 ATTATCAAGATTTCATAAAGAGGCTATCAAAATTTTATAGGGAGGTTTATCAAAATTT
1 ATTAACAAAATTTCATAAAGAGGCTATCAAAAAATCATAGGGAGGTTTATCAAAATTT
38568 TATAGCGAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 38 0.76
61 12 0.24
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (61 bp):
ATTAACAAAATTTCATAAAGAGGCTATCAAAAAATCATAGGGAGGTTTATCAAAATTTGTA
Found at i:38555 original size:82 final size:83
Alignment explanation
Indices: 38431--38589 Score: 194
Period size: 82 Copynumber: 1.9 Consensus size: 83
38421 TAGTATGTAG
* * * *
38431 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAATGAGG-TTATCAAAAAATCATAGGGAGG
1 ATCAAAATTTCATAAAGAGACTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
38495 TTATCAAAATTTGTAATT
66 TTATCAAAATTTGTAATT
* * * * * ** *
38513 ATCAAGATTTCATAAAGAGGCTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGCGAGG
1 ATCAAAATTTCATAAAGAGACTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
*
38578 TTATCACAATTT
66 TTATCAAAATTT
38590 CATAGTGTGA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
82 34 0.54
83 29 0.46
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (83 bp):
ATCAAAATTTCATAAAGAGACTAACAAAATTTCATAAGGAGGTTTATCAAAAAATCATAGCGAGG
TTATCAAAATTTGTAATT
Found at i:38583 original size:45 final size:44
Alignment explanation
Indices: 38510--38613 Score: 109
Period size: 45 Copynumber: 2.3 Consensus size: 44
38500 AAAATTTGTA
* *
38510 ATTATCAAGATTTCATAAAGAGGCTATCAAAATTTTATAGGGAGG
1 ATTATCAAAATTTCATAAAGAGGCTATCAAAATTTCATAGGG-GG
* * ** * * * *
38555 TTTATCAAAATTTTATAGCGAGGTTATCACAATTTCATAGTGTG
1 ATTATCAAAATTTCATAAAGAGGCTATCAAAATTTCATAGGGGG
38599 ATTATCAAAATTTCA
1 ATTATCAAAATTTCA
38614 GAGTGTAATT
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
44 14 0.30
45 33 0.70
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (44 bp):
ATTATCAAAATTTCATAAAGAGGCTATCAAAATTTCATAGGGGG
Found at i:38716 original size:23 final size:23
Alignment explanation
Indices: 38662--38728 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
38652 TTTTCTTAAC
*
38662 GTGGTTATCAATATATCATA-TG
1 GTGGTTATCAAAATATCATAGTG
* * *
38684 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAAAATATCATAGTG
* *
38707 TTGGTTATCAAAATTTCATAGT
1 GTGGTTATCAAAATATCATAGT
38729 AAGGTTTTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (23 bp):
GTGGTTATCAAAATATCATAGTG
Found at i:41507 original size:5 final size:5
Alignment explanation
Indices: 41499--41537 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
41489 AATCAAATCA
41499 ATCCC ATCCC ATCCC ATCCC ATCCC ATCCC ATCCC ATCC
1 ATCCC ATCCC ATCCC ATCCC ATCCC ATCCC ATCCC ATCC
41538 TCCTCATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
ATCCC
Found at i:45110 original size:3 final size:3
Alignment explanation
Indices: 45102--45127 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45092 ACACACACAA
45102 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
45128 AGCAGAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:48461 original size:49 final size:48
Alignment explanation
Indices: 48368--48461 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 48
48358 GTAGCTACAT
* *
48368 ATTAAGCTGCAATGTATTCATAATACAACCATCTCTATTCTTCATGCC
1 ATTAAGCTGCAATATATTCATAATACAACCATCTATATTCTTCATGCC
* * * * *
48416 ATTAAGGTGCAAATATATTCCTAATACAACTATGTATATTTTTCAT
1 ATTAAGCTGC-AATATATTCATAATACAACCATCTATATTCTTCAT
48462 ACTTTGAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 9 0.24
49 29 0.76
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (48 bp):
ATTAAGCTGCAATATATTCATAATACAACCATCTATATTCTTCATGCC
Found at i:51711 original size:29 final size:29
Alignment explanation
Indices: 51666--51737 Score: 119
Period size: 28 Copynumber: 2.5 Consensus size: 29
51656 TGTTATAATG
51666 AATCCAAATGGGTTTTTTTCTAAAAAAAA
1 AATCCAAATGGGTTTTTTTCTAAAAAAAA
**
51695 AAT-CAAATGGGTTTTTTTCTTTAAAAAA
1 AATCCAAATGGGTTTTTTTCTAAAAAAAA
51723 AATCCAAATGGGTTT
1 AATCCAAATGGGTTT
51738 CGTCCAACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 26 0.65
29 14 0.35
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (29 bp):
AATCCAAATGGGTTTTTTTCTAAAAAAAA
Found at i:53059 original size:127 final size:130
Alignment explanation
Indices: 52863--53122 Score: 400
Period size: 127 Copynumber: 2.0 Consensus size: 130
52853 GTCATTTAAG
* * * *
52863 AAATATATTTTAAAATTTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
1 AAATATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
*
52928 AAATAGGTATAAGGATATTAGATTTAATTAAATAAA-AAAGAGTTTTTAGTTGAGTAAAACTATA
66 AAATAAGTATAAGGATATTAGATTTAATTAAATAAAGAAAGAGTTTTTAGTTGAGTAAAACTATA
* *
52992 AAATATA-TTTAAAAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATGGTAAAAATT
1 AAATATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
* * * *
53055 AAATAATTATGAGGATATTATATTTAATTAAATAAAGATAGAGTTTTTAGTTGAGTAAAACTATA
66 AAATAAGTATAAGGATATTAGATTTAATTAAATAAAGAAAGAGTTTTTAGTTGAGTAAAACTATA
53120 AAA
1 AAA
53123 GTCTAATGGC
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
127 60 0.50
128 52 0.44
129 7 0.06
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (130 bp):
AAATATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
AAATAAGTATAAGGATATTAGATTTAATTAAATAAAGAAAGAGTTTTTAGTTGAGTAAAACTATA
Found at i:60365 original size:13 final size:14
Alignment explanation
Indices: 60347--60381 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
60337 GTCGGGTTTT
60347 AGTCAGTTTGTT-G
1 AGTCAGTTTGTTCG
*
60360 AGTCAGTTTTTTCG
1 AGTCAGTTTGTTCG
60374 AGTCAGTT
1 AGTCAGTT
60382 AGTGTTAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (14 bp):
AGTCAGTTTGTTCG
Found at i:61272 original size:18 final size:18
Alignment explanation
Indices: 61249--61283 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61239 ACAAAAACTG
61249 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
61267 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
61284 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:61423 original size:18 final size:17
Alignment explanation
Indices: 61402--61441 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
61392 ATATTATTTT
*
61402 TATAATTTTTATTAATAA
1 TATAATTATTATTAA-AA
61420 TATAATTATTATTAAAA
1 TATAATTATTATTAAAA
61437 TATAA
1 TATAA
61442 ATAATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATTATTATTAAAA
Found at i:61448 original size:18 final size:18
Alignment explanation
Indices: 61410--61456 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
61400 TTTATAATTT
*
61410 TTATTAATAATATAATTA
1 TTATTAATAATATAATAA
61428 TTATTAA-AATATAAATAA
1 TTATTAATAATAT-AATAA
61446 TTATATAATAA
1 TTAT-TAATAA
61457 ACGAACGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 3 0.12
20 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATTAATAATATAATAA
Found at i:61528 original size:35 final size:35
Alignment explanation
Indices: 61483--61578 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
61473 TATATAAACG
* *
61483 ACAATAAACGAGTCTGTTTGTGAACACTTAAATGA
1 ACAATAAACGAGCCTGTTCGTGAACACTTAAATGA
* *
61518 ATAATAAACGAACCTGTTCGTGAACACTTAAATGA
1 ACAATAAACGAGCCTGTTCGTGAACACTTAAATGA
61553 ACAATAAACGAGCCTGTTCGTGAACA
1 ACAATAAACGAGCCTGTTCGTGAACA
61579 TAAACGAACT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.25
Consensus pattern (35 bp):
ACAATAAACGAGCCTGTTCGTGAACACTTAAATGA
Found at i:70194 original size:22 final size:22
Alignment explanation
Indices: 70169--70348 Score: 71
Period size: 22 Copynumber: 7.9 Consensus size: 22
70159 TTGAATGTTT
70169 TTATGAAATTTTGATAACCATC
1 TTATGAAATTTTGATAACCATC
* *
70191 TTATTAAATTTT-ACTAACCATG
1 TTATGAAATTTTGA-TAACCATC
* * **
70213 TTATGGAATTTTGTTAATTTATC
1 TTATGAAATTTTGATAA-CCATC
* *
70236 TATGAAATATGAAACTTTGATAACC-TAA
1 --T----TATGAAATTTTGATAACCAT-C
* **
70264 TTATGAAATTTTAATAAAGATTC
1 TTATGAAATTTTGATAACCA-TC
* * *
70287 CTATGAAATTTTAATAAACCTTC
1 TTATGAAATTTTGAT-AACCATC
* * *
70310 CTATGAAATTTTG-TAATCTTC
1 TTATGAAATTTTGATAACCATC
*
70331 TTATG-ATTTTTGATAACC
1 TTATGAAATTTTGATAACC
70349 TCTCTGTGAT
Statistics
Matches: 116, Mismatches: 28, Indels: 29
0.67 0.16 0.17
Matches are distributed among these distances:
20 6 0.05
21 15 0.13
22 46 0.40
23 30 0.26
24 3 0.03
25 1 0.01
26 1 0.01
27 1 0.01
29 13 0.11
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCATC
Found at i:70336 original size:21 final size:23
Alignment explanation
Indices: 70265--70321 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
70255 ATAACCTAAT
**
70265 TATGAAATTTTAATAAAGATTCC
1 TATGAAATTTTAATAAACCTTCC
70288 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTAATAAACCTTCC
70311 TATGAAATTTT
1 TATGAAATTTT
70322 GTAATCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTAATAAACCTTCC
Found at i:70363 original size:22 final size:21
Alignment explanation
Indices: 70332--70389 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
70322 GTAATCTTCT
70332 TATGATTTTTGATAACCTCTC
1 TATGATTTTTGATAACCTCTC
* * *
70353 TGTGATATTTTGTTAATCTCTC
1 TATGAT-TTTTGATAACCTCTC
*
70375 TATAATTTTTTGATA
1 TATGA-TTTTTGATA
70390 CTATAGTACG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 5 0.17
22 23 0.79
23 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
TATGATTTTTGATAACCTCTC
Found at i:71856 original size:27 final size:28
Alignment explanation
Indices: 71812--71867 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
71802 GAAATTTATT
*
71812 TTTAAAAAATATAAAAATTGTTATTTTC
1 TTTAAAAAATATAAAAATAGTTATTTTC
** *
71840 TTTAAAAAAT-TTGAAATAGTTTTTTTC
1 TTTAAAAAATATAAAAATAGTTATTTTC
71867 T
1 T
71868 CCTACAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (28 bp):
TTTAAAAAATATAAAAATAGTTATTTTC
Done.