Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012803.1 Corchorus capsularis cultivar CVL-1 contig12824, 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: 150847
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5887 original size:41 final size:40
Alignment explanation
Indices: 5823--5907 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 40
5813 CAACTCATCA
* * *
5823 ATTTTCTAAAACTCTATCTCAATAATATCTCAAATTTGGG
1 ATTTTCTAAAACCCCATCCCAATAATATCTCAAATTTGGG
5863 TATTTTCTAAAACCCCATCCCAATAATATCTCAAATTTGGG
1 -ATTTTCTAAAACCCCATCCCAATAATATCTCAAATTTGGG
5904 ATTT
1 ATTT
5908 ACCCTTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 4 0.10
41 37 0.90
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (40 bp):
ATTTTCTAAAACCCCATCCCAATAATATCTCAAATTTGGG
Found at i:6539 original size:256 final size:256
Alignment explanation
Indices: 6084--6596 Score: 855
Period size: 256 Copynumber: 2.0 Consensus size: 256
6074 ATCTAAAAGG
*
6084 AGAAATTATTAGGTGGGACGGACCCACCACGTCATCAATGGGACTAACCAATAGAATTTTGCCAT
1 AGAAATTATTAGGTGGGACGGACCCACCACGTCATCAATGGGACTAACCAATAGAATCTTGCCAT
* *
6149 GTCAAATTAACTCCTTAAATTTAGGCACGATTTTACCCCAAGGTTTAACCCCCCTTTAAAACAAA
66 GTCAAATGAACTCCTTAAATTTAGGCACGATTTTACCCCAAGATTTAACCCCCCTTTAAAACAAA
* ** *
6214 CCCTATATAAAGGGTAAGTCCCCAAATTTGAGATTTTATTGGGATAAGGTTTTAGAAAATTGATG
131 CCATATATAAACAGTAAGTCCCCAAATTTGAGATATTATTGGGATAAGGTTTTAGAAAATTGATG
* *
6279 AGTTGTCTTCATATTATTGGTTGGTACCATAGATGACGTGGTGGGTCCGTCCCACCTAATA
196 AGTTGTCTTAATATCATTGGTTGGTACCATAGATGACGTGGTGGGTCCGTCCCACCTAATA
* *
6340 AGAAATTATTAGGTGGGACGGACCCACCACGTCATCCATGGGACTAACCAATGGAATCTTGCCAT
1 AGAAATTATTAGGTGGGACGGACCCACCACGTCATCAATGGGACTAACCAATAGAATCTTGCCAT
* * * * *
6405 GTCAAATGACCTCCTTAAATTTAGGCACGATTTTAGCCCAAGATTTAGCCCCCTTTTAAAATAAA
66 GTCAAATGAACTCCTTAAATTTAGGCACGATTTTACCCCAAGATTTAACCCCCCTTTAAAACAAA
* *
6470 TCATCTATAAACAGTAAGTCCCCAAATTTGAGATATTATTGGGATAAGGTTTTAGAAAATTGATG
131 CCATATATAAACAGTAAGTCCCCAAATTTGAGATATTATTGGGATAAGGTTTTAGAAAATTGATG
*
6535 AGTTGTCTTAATATCATTGGTTGGTCCCATAGATGACGTGGTGGGTCCGTCCCACCTAATA
196 AGTTGTCTTAATATCATTGGTTGGTACCATAGATGACGTGGTGGGTCCGTCCCACCTAATA
6596 A
1 A
6597 TTTCTCGATC
Statistics
Matches: 238, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
256 238 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (256 bp):
AGAAATTATTAGGTGGGACGGACCCACCACGTCATCAATGGGACTAACCAATAGAATCTTGCCAT
GTCAAATGAACTCCTTAAATTTAGGCACGATTTTACCCCAAGATTTAACCCCCCTTTAAAACAAA
CCATATATAAACAGTAAGTCCCCAAATTTGAGATATTATTGGGATAAGGTTTTAGAAAATTGATG
AGTTGTCTTAATATCATTGGTTGGTACCATAGATGACGTGGTGGGTCCGTCCCACCTAATA
Found at i:6718 original size:25 final size:26
Alignment explanation
Indices: 6680--6735 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
6670 GTAAGCCACA
6680 AACTTTCTTATTTGTCAAATAACG-T
1 AACTTTCTTATTTGTCAAATAACGTT
* *
6705 AACTTTCTTCTTTGTCAAGTAACGTT
1 AACTTTCTTATTTGTCAAATAACGTT
6731 AACTT
1 AACTT
6736 ACCGGCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.45
Consensus pattern (26 bp):
AACTTTCTTATTTGTCAAATAACGTT
Found at i:12146 original size:19 final size:20
Alignment explanation
Indices: 12119--12156 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12109 TACTATTATT
12119 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
12139 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
12157 AATGTCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:12401 original size:44 final size:43
Alignment explanation
Indices: 12322--12408 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
12312 GTCTCTATGT
* ** *
12322 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCAT-AGGA
12366 GGTTATCAAAATTCCAT-AGTATGGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTCCATAAG-ATGGTTACCAAAATTTCATAGGA
12409 TCAGGTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCATAGGA
Found at i:12458 original size:22 final size:22
Alignment explanation
Indices: 12320--12460 Score: 97
Period size: 22 Copynumber: 6.3 Consensus size: 22
12310 TTGTCTCTAT
*
12320 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATCAAAATTTCATAGG
* * *
12342 ATGGTTATTATAATTTCAT-GAG
1 GTGGTTATCAAAATTTCATAG-G
* * *
12364 GAGGTTATCAAAATTCCATAGT
1 GTGGTTATCAAAATTTCATAGG
* *
12386 ATGGTTACCAAAATTTCATAGG
1 GTGGTTATCAAAATTTCATAGG
* * * *
12408 ATCAGGTTATTAAAATCTC-TTGG
1 GT--GGTTATCAAAATTTCATAGG
**
12431 GTTGGTTATTGAAATTTCATAGG
1 G-TGGTTATCAAAATTTCATAGG
12454 GTGGTTA
1 GTGGTTA
12461 ATTATCACAA
Statistics
Matches: 90, Mismatches: 23, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
22 69 0.77
23 8 0.09
24 13 0.14
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAAAATTTCATAGG
Found at i:12619 original size:22 final size:21
Alignment explanation
Indices: 12560--12877 Score: 132
Period size: 22 Copynumber: 14.3 Consensus size: 21
12550 TTCATTAAAT
*
12560 ATTTCATGGAGAGGTTATCAAA
1 ATTTCATAGA-AGGTTATCAAA
* *
12582 ATTTTATA-ACGTGGTTATCAAA
1 ATTTCATAGA--AGGTTATCAAA
*
12604 ATTTCATATGAAGGTTATAAAAGTCTAA
1 ATTTCATA-GAAGG-T-T---A-TCAAA
* *
12632 ATTTCAT--AAGGAGTACCAAA
1 ATTTCATAGAAGG-TTATCAAA
*
12652 ATTTGATAGAAGGTTATC-AA
1 ATTTCATAGAAGGTTATCAAA
* *
12672 ATCTCATA-AAGTGATTATCGAA
1 ATTTCATAGAAG-G-TTATCAAA
12694 ATTTCATAGAGATCGGATTATCAAA
1 ATTTCATAGA-A--GG-TTATCAAA
*
12719 ATTT-ATAGAAAGATTATCAAA
1 ATTTCATAG-AAGGTTATCAAA
*
12740 ATTTCATAG-TGTTGTTATCAAA
1 ATTTCATAGAAG--GTTATCAAA
* *
12762 ATTTCAAAGCGAGGTTATCAAA
1 ATTTCATAG-AAGGTTATCAAA
* * *
12784 ATTACATA-ATGTGATTATCAGA
1 ATTTCATAGAAG-G-TTATCAAA
* * *
12806 ATTTCATAGAGGGGTCAACAAA
1 ATTTCATAGA-AGGTTATCAAA
*
12828 ATATT-ATAAAGAGGTTATCAAA
1 AT-TTCATAGA-AGGTTATCAAA
*
12850 ATTTCATAAAGAGGTTATCAAA
1 ATTTCATAGA-AGGTTATCAAA
*
12872 TTTTCA
1 ATTTCA
12878 AAATATGATT
Statistics
Matches: 229, Mismatches: 37, Indels: 60
0.70 0.11 0.18
Matches are distributed among these distances:
19 3 0.01
20 20 0.09
21 25 0.11
22 133 0.58
23 6 0.03
24 11 0.05
25 18 0.08
26 1 0.00
27 1 0.00
28 11 0.05
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (21 bp):
ATTTCATAGAAGGTTATCAAA
Found at i:12802 original size:44 final size:44
Alignment explanation
Indices: 12709--12899 Score: 140
Period size: 44 Copynumber: 4.4 Consensus size: 44
12699 ATAGAGATCG
* * * * *
12709 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTACATAATG-T
*
12753 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTACATAATGT
* * * * * * * *
12796 GATTATCAGAATTTCATAGAGGGGTCAACAAAA-TATTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTA-CATAATGT
* * * * *
12840 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATAT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTACATAATGT
12884 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
12900 TAGTGGTAAT
Statistics
Matches: 112, Mismatches: 29, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
43 17 0.15
44 93 0.83
45 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTACATAATGT
Found at i:13139 original size:44 final size:44
Alignment explanation
Indices: 12983--13453 Score: 200
Period size: 44 Copynumber: 10.8 Consensus size: 44
12973 TTATGGAATA
* * * *
12983 ATCAAAATTTC--AGGGAGGATATCAAAATTTCATATGAAGATT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * * *
13025 ATGAAAATTTCATTGTTTA-GTTTTCAAAATTTTATAAGAGG-G-TT
1 ATCAAAATTTCATAG-TGAGGTTATCAAAATTTCAT-AG-GGAGATT
* * * *
13069 ATCAAAATTTCACAGT-ATGTAGATCAAAATTTTATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGATT
* * **
13113 AACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGA-ACTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA-TT
* * * *
13157 ATCAAAATTT--T--T-A-GTTATCAAGATTTCATAAGAAAATT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * * * *
13195 ATCAAAATTTTACAGGGATGTTTATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGTGA-GGTTATCAAAATTTCATAGGGAGA-TT
* * * * *
13241 ATCAAAATTTCATAGCGAGGCTATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * ** *
13285 ATCAAAATTTCAGAGTGTGATTA-CTAACAA-TTCATATAGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATC-AA-AATTTCATAGGGAGATT
* * * ** * * * * *
13329 TTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
* * * ** *
13373 ATCAACATCTCATAGTGTTGGTTATCAAAATTTCATATCGAGGTCT
1 ATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATAGGGAGAT-T
* * * * *
13419 -TCAAAATTCCTTAGGGAGGTTAACCAAATTTCATA
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
13454 AGAAGGTTAA
Statistics
Matches: 320, Mismatches: 83, Indels: 50
0.71 0.18 0.11
Matches are distributed among these distances:
38 28 0.09
39 2 0.01
40 1 0.00
42 14 0.04
43 10 0.03
44 168 0.52
45 78 0.24
46 19 0.06
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGATT
Found at i:13140 original size:22 final size:22
Alignment explanation
Indices: 12997--13542 Score: 105
Period size: 22 Copynumber: 25.0 Consensus size: 22
12987 AAATTTCAGG
*
12997 GAGGATATCAAAATTTCAT-AT
1 GAGGTTATCAAAATTTCATAAT
* * **
13018 GAAGATTATGAAAATTTCATTGTT
1 G-AGGTTATCAAAATTTCA-TAAT
* * *
13042 TA-GTTTTCAAAATTTTATAA-
1 GAGGTTATCAAAATTTCATAAT
* *
13062 GAGGGTTATCAAAATTTCACAGT
1 GA-GGTTATCAAAATTTCATAAT
* * * **
13085 -ATGTAGATCAAAATTTTATAGG
1 GAGGT-TATCAAAATTTCATAAT
* *
13107 GAGATTAACAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAAT
** **
13129 GAGGTTATCAAAAAATCATAGG
1 GAGGTTATCAAAATTTCATAAT
**
13151 GAACTTATCAAAATTT--T--T
1 GAGGTTATCAAAATTTCATAAT
*
13169 -A-GTTATCAAGATTTCATAA-
1 GAGGTTATCAAAATTTCATAAT
** * * **
13188 GAAAATTATCAAAATTTTACAGG
1 G-AGGTTATCAAAATTTCATAAT
* * *
13211 GATGTTTATCAAAATTTTAT-AG
1 GA-GGTTATCAAAATTTCATAAT
* **
13233 GAAGATTTATCAAAATTTCATAGC
1 G-AG-GTTATCAAAATTTCATAAT
* * *
13257 GAGGCTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATAAT
* * * *
13279 GTGATTATCAAAATTTCAGAGT
1 GAGGTTATCAAAATTTCATAAT
* *
13301 GTGATTA-CTAACAA-TTCAT-AT
1 GAGGTTATC-AA-AATTTCATAAT
* * * *
13322 AGAGGTTTTTAAATTTTCATAAC
1 -GAGGTTATCAAAATTTCATAAT
* * *
13345 GTGGTTATCAATATATCAT-AT
1 GAGGTTATCAAAATTTCATAAT
* * *
13366 GGAGGTTATCAACATCTCATAGT
1 -GAGGTTATCAAAATTTCATAAT
*
13389 GTTGGTTATCAAAATTTCAT-AT
1 G-AGGTTATCAAAATTTCATAAT
* * **
13411 CGAGGTCT-TCAAAATTCCTTAGG
1 -GAGGT-TATCAAAATTTCATAAT
* *
13434 GAGGTTAACCAAATTTCATAA-
1 GAGGTTATCAAAATTTCATAAT
* *
13455 GAAGGTTA-AAAAATTT-ATAAA
1 G-AGGTTATCAAAATTTCATAAT
* * * * *
13476 AAGATTCTCGAAATTCCATACTAT
1 GAGGTTATCAAAATTTCATA--AT
* *
13500 CA--TTATCAAAATTTCAT-AG
1 GAGGTTATCAAAATTTCATAAT
*
13519 GAAGTTTATCAAAATTTCATAAT
1 G-AGGTTATCAAAATTTCATAAT
13542 G
1 G
13543 GGATCATAAA
Statistics
Matches: 371, Mismatches: 111, Indels: 84
0.66 0.20 0.15
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 1 0.00
19 1 0.00
20 11 0.03
21 22 0.06
22 260 0.70
23 60 0.16
24 4 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAT
Found at i:13221 original size:23 final size:23
Alignment explanation
Indices: 13193--13250 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
13183 CATAAGAAAA
*
13193 TTATCAAAATTTTACAGGGATG-T
1 TTATCAAAATTTTACA-GGAAGAT
*
13216 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTACAGGAAGAT
13239 TTATCAAAATTT
1 TTATCAAAATTT
13251 CATAGCGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTACAGGAAGAT
Found at i:15816 original size:11 final size:11
Alignment explanation
Indices: 15800--15825 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
15790 AAAAATTAGC
15800 TCAAATATTTA
1 TCAAATATTTA
15811 TCAAATATTTA
1 TCAAATATTTA
15822 TCAA
1 TCAA
15826 TTTGCAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
TCAAATATTTA
Found at i:16967 original size:13 final size:13
Alignment explanation
Indices: 16916--16974 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
16906 GTCTGTTTTG
16916 AAGAAGAAAAGAA
1 AAGAAGAAAAGAA
*
16929 AAGGA-AAAAGAA
1 AAGAAGAAAAGAA
* * *
16941 AATATA-CAAGGAA
1 AAGA-AGAAAAGAA
16954 AAGAAGAAAAGAA
1 AAGAAGAAAAGAA
16967 AAGGAAGA
1 AA-GAAGA
16975 GAAAAAGAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
12 10 0.29
13 20 0.57
14 5 0.14
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.03
Consensus pattern (13 bp):
AAGAAGAAAAGAA
Found at i:24301 original size:98 final size:98
Alignment explanation
Indices: 24132--24319 Score: 376
Period size: 98 Copynumber: 1.9 Consensus size: 98
24122 GGTTCAATTT
24132 GCTTTCATTCTTCTTTTGAAATTCCTAGTTTCCTCTTGTTCTATAAAATGGAAATCACATTTCCT
1 GCTTTCATTCTTCTTTTGAAATTCCTAGTTTCCTCTTGTTCTATAAAATGGAAATCACATTTCCT
24197 ATTTGCAGGTCTTGGTGCCACATTGCAACATCA
66 ATTTGCAGGTCTTGGTGCCACATTGCAACATCA
24230 GCTTTCATTCTTCTTTTGAAATTCCTAGTTTCCTCTTGTTCTATAAAATGGAAATCACATTTCCT
1 GCTTTCATTCTTCTTTTGAAATTCCTAGTTTCCTCTTGTTCTATAAAATGGAAATCACATTTCCT
24295 ATTTGCAGGTCTTGGTGCCACATTG
66 ATTTGCAGGTCTTGGTGCCACATTG
24320 AATGTTGCAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (98 bp):
GCTTTCATTCTTCTTTTGAAATTCCTAGTTTCCTCTTGTTCTATAAAATGGAAATCACATTTCCT
ATTTGCAGGTCTTGGTGCCACATTGCAACATCA
Found at i:27358 original size:17 final size:17
Alignment explanation
Indices: 27336--27370 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
27326 TTTGGATTGT
27336 TTCTTTTTGGATGGCGG
1 TTCTTTTTGGATGGCGG
27353 TTCTTTTTGGATGGCGG
1 TTCTTTTTGGATGGCGG
27370 T
1 T
27371 GGTTGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.11, G:0.34, T:0.49
Consensus pattern (17 bp):
TTCTTTTTGGATGGCGG
Found at i:34386 original size:137 final size:135
Alignment explanation
Indices: 34142--34386 Score: 420
Period size: 137 Copynumber: 1.8 Consensus size: 135
34132 CAACTAAACT
34142 TCATTCACTATACAGAGCATTGCCTACAAAAGGCCTTTTTTTTTTTTTTGCACTGGCCTACAAAG
1 TCATTCACTATACAGAGCATTGCCTACAAAAGGCCTTTTTTTTTTTTTTGCACTGGCCTACAAAG
* *
34207 TCCTTTTGTCAAGACCATGTAAAATTAAGGGTGATCTCCATTCACCAGTAGATCAAACTAATTTT
66 TACTTTTGTCAAGACCATGTAAAATTAAGGATGATCTCCATTCACCAGTAGATCAAACTAATTTT
34272 TCACC
131 TCACC
*
34277 TCATTCACTATACAGAGCATTGCCTAC-AAAGGCCTTTTTTTTTTTTTTTTTGCACTTGCCTACA
1 TCATTCACTATACAGAGCATTGCCTACAAAAGGCC---TTTTTTTTTTTTTTGCACTGGCCTACA
*
34341 AAGTACTTTTGTCGAGACCATGTAAAATTAAGGATGATCTCCATTC
63 AAGTACTTTTGTCAAGACCATGTAAAATTAAGGATGATCTCCATTC
34387 CTCTTTGTTC
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
134 7 0.07
135 27 0.26
137 69 0.67
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (135 bp):
TCATTCACTATACAGAGCATTGCCTACAAAAGGCCTTTTTTTTTTTTTTGCACTGGCCTACAAAG
TACTTTTGTCAAGACCATGTAAAATTAAGGATGATCTCCATTCACCAGTAGATCAAACTAATTTT
TCACC
Found at i:36333 original size:32 final size:32
Alignment explanation
Indices: 36287--36351 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
36277 AAAATGGAAA
*
36287 TAAAAAAAAATGTTT-AGACCCAGTAAGTAGTC
1 TAAAAAAAAATGTTTAAG-CCCAATAAGTAGTC
** *
36319 TAAAAAAAGTTGTTTAAGCCCAATGAGTAGTC
1 TAAAAAAAAATGTTTAAGCCCAATAAGTAGTC
36351 T
1 T
36352 TTTTTTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (32 bp):
TAAAAAAAAATGTTTAAGCCCAATAAGTAGTC
Found at i:38155 original size:20 final size:19
Alignment explanation
Indices: 38126--38167 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
38116 GTAAGAATTT
38126 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
*
38145 TATTATTAATATGTAATATA
1 TATT-TTAATATATAATATA
38165 TAT
1 TAT
38168 ATGTGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Found at i:38165 original size:22 final size:21
Alignment explanation
Indices: 38044--38169 Score: 65
Period size: 20 Copynumber: 6.1 Consensus size: 21
38034 AAAATCATTT
38044 TATT-TTAATATGTAAA-ATA
1 TATTATTAATATGTAAATATA
* *
38063 TTTTATTAA-AT-AAGAATATA
1 TATTATTAATATGTA-AATATA
38083 TA-TA-TATATATGTAAATA-A
1 TATTATTA-ATATGTAAATATA
* * *
38102 GAATATATATATATGTAAGA-ATTT
1 TATTAT-TA-ATATGTAA-ATA-TA
*
38126 TATT-TTAATATAT-AATATA
1 TATTATTAATATGTAAATATA
38145 TATTATTAATATGTAATATATA
1 TATTATTAATATGTAA-ATATA
38167 TAT
1 TAT
38170 GTGTAATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 29
0.67 0.09 0.24
Matches are distributed among these distances:
18 3 0.04
19 18 0.22
20 26 0.32
21 7 0.09
22 22 0.28
23 2 0.03
24 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.47
Consensus pattern (21 bp):
TATTATTAATATGTAAATATA
Found at i:44812 original size:6 final size:6
Alignment explanation
Indices: 44801--44827 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
44791 GTTTATATTT
44801 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
44828 ATTCGAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:48248 original size:7 final size:7
Alignment explanation
Indices: 48236--48261 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48226 AAACTTACAC
48236 TCTTTTG
1 TCTTTTG
48243 TCTTTTG
1 TCTTTTG
48250 TCTTTTG
1 TCTTTTG
48257 TCTTT
1 TCTTT
48262 AACTTGACGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.12, T:0.73
Consensus pattern (7 bp):
TCTTTTG
Found at i:48811 original size:36 final size:31
Alignment explanation
Indices: 48713--48904 Score: 163
Period size: 31 Copynumber: 6.5 Consensus size: 31
48703 GGCGCCCGAC
48713 GTGGCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
*
48744 GTGCCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
*
48775 GTGGCACGCCACATGTACCAAAAAGT--C--
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
*
48802 GTGTCA---CA--TGTACCAAAAAGTGATACAT
1 GTGGCACGCCACGTGTACCAAAAAGTG--ACAT
* *
48830 GT--CACGCCACGTATACCAAAAAGTGACAC
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
* * * ** * * *
48859 ATGGCATGCCACATGTTTCAAAAAATGGCAC
1 GTGGCACGCCACGTGTACCAAAAAGTGACAT
*
48890 GTGGCATGCCACGTG
1 GTGGCACGCCACGTG
48905 CACAAAAGGA
Statistics
Matches: 132, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
22 13 0.10
24 2 0.02
26 3 0.02
27 5 0.04
28 2 0.02
29 7 0.05
31 100 0.76
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.18
Consensus pattern (31 bp):
GTGGCACGCCACGTGTACCAAAAAGTGACAT
Found at i:71609 original size:23 final size:22
Alignment explanation
Indices: 71583--71634 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
71573 TGAAATTTTA
*
71583 ATAACCAACACTATGAGATGTTG
1 ATAACCAACA-TATGAGATATTG
** *
71606 ATAACCTCCATATGATATATTG
1 ATAACCAACATATGAGATATTG
71628 ATAACCA
1 ATAACCA
71635 CGTTATGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (22 bp):
ATAACCAACATATGAGATATTG
Found at i:71765 original size:22 final size:23
Alignment explanation
Indices: 71707--71979 Score: 130
Period size: 22 Copynumber: 12.9 Consensus size: 23
71697 GATTATCACA
*
71707 CTATGAAATTTTGATAAATCTTC
1 CTATGAAATTTTGATAACTCTTC
*
71730 CTATAAAATTTTGATAACT-TTC
1 CTATGAAATTTTGATAACTCTTC
* *
71752 TTATGAAATCTTGATAA------
1 CTATGAAATTTTGATAACTCTTC
*
71769 CTA-CAAATTTTGATAACCTC--C
1 CTATGAAATTTTGATAA-CTCTTC
*
71790 CTATG-ATTTTTGATAA-TC-TC
1 CTATGAAATTTTGATAACTCTTC
* * *
71810 ATTATGAAATTTTGTTAA-TCTCC
1 -CTATGAAATTTTGATAACTCTTC
* *
71833 CTATGAAATTTTGAT--CTACATA
1 CTATGAAATTTTGATAACT-CTTC
*
71855 CTATGAAATTTTGATAAC-CCTC
1 CTATGAAATTTTGATAACTCTTC
* * * ***
71877 TTATGACATTTTGAAAACT-AAA
1 CTATGAAATTTTGATAACTCTTC
71899 CTATGAAATTTTGATAAC-CTTC
1 CTATGAAATTTTGATAACTCTTC
* *
71921 ATATGAAATTTTGAT-A-TCCTC
1 CTATGAAATTTTGATAACTCTTC
* *
71942 C-CTG-AATTTTGAT-A-TCCTC
1 CTATGAAATTTTGATAACTCTTC
*
71961 CT-TGAAATTTTGATTACTC
1 CTATGAAATTTTGATAACTC
71980 CATAATAAAA
Statistics
Matches: 192, Mismatches: 37, Indels: 43
0.71 0.14 0.16
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
19 20 0.10
20 12 0.06
21 23 0.12
22 105 0.55
23 18 0.09
24 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (23 bp):
CTATGAAATTTTGATAACTCTTC
Found at i:71980 original size:19 final size:20
Alignment explanation
Indices: 71924--71974 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
71914 AACCTTCATA
71924 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
71944 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
71963 TGAAATTTTGAT
1 TGAAATTTTGAT
71975 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:72218 original size:88 final size:88
Alignment explanation
Indices: 72055--72220 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 88
72045 AGAAATACCA
* * ***
72055 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTT
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTTGATAACAAC
**
72120 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* * *
72143 CTATG-AATTTCTGATAATCACATTATGTAATTTTGATAACCTAGTTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCT-CTTTATGAAATTTTGATAACA
*
72206 ACACTATGAAATTTT
64 ACACTATAAAATTTT
72221 AATCTTTCTA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 7 0.11
88 55 0.85
89 3 0.05
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:72261 original size:25 final size:22
Alignment explanation
Indices: 72055--72441 Score: 114
Period size: 22 Copynumber: 17.5 Consensus size: 22
72045 AGAAATACCA
72055 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
72078 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * **
72099 TTATGAAATTTTGATAACCTTT
1 CTATGAAATTTTGATAATCACT
* * * * * *
72121 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
72143 CTATG-AATTTCTGATAATCACAT
1 CTATGAAATTT-TGATAATCAC-T
* * *
72166 -TATGTAATTTTGATAACCTAGT
1 CTATGAAATTTTGATAATC-ACT
* *
72188 -TTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
**
72209 CTATGAAA-TTT--TAATCTTT
1 CTATGAAATTTTGATAATCACT
72228 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAAT-C-A-CT
*
72252 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
72274 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
* * *
72294 CTATCAAATTTTGGTACTC-CT
1 CTATGAAATTTTGATAATCACT
*
72315 -TATGAAAATGAGACTTTTATAA-C-CTT
1 CTATG-AAAT-----TTTGATAATCAC-T
*
72341 CATATGAAATTTTGATAATCACA
1 C-TATGAAATTTTGATAATCACT
* * * *
72364 CTATAAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAATCACT
*
72386 CCATGAAATATTTG-TAA-C-CT
1 CTATGAAAT-TTTGATAATCACT
* *
72406 CCTGATGAAATTTTGTTAACCA-T
1 -CT-ATGAAATTTTGATAATCACT
72429 ACTATGAAATTTT
1 -CTATGAAATTTT
72442 TAGTACCTCG
Statistics
Matches: 276, Mismatches: 53, Indels: 71
0.69 0.13 0.18
Matches are distributed among these distances:
18 3 0.01
19 11 0.04
20 13 0.05
21 43 0.16
22 153 0.55
23 18 0.07
24 7 0.03
25 14 0.05
26 6 0.02
27 4 0.01
28 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:72417 original size:44 final size:44
Alignment explanation
Indices: 72364--72468 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
72354 GATAATCACA
* *
72364 CTATAAAATTTTGATAACC-TCCCCATGAAATATTT-GTAACCTC-
1 CTATGAAATTTTGATAACCAT-ACCATGAAATATTTAGT-ACCTCG
* * *
72407 CTGATGAAATTTTGTTAACCATACTATGAAATTTTTAGTACCTCG
1 CT-ATGAAATTTTGATAACCATACCATGAAATATTTAGTACCTCG
*
72452 CTATGACATTTTGATAA
1 CTATGAAATTTTGATAA
72469 TCTCTTTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
43 2 0.04
44 44 0.86
45 5 0.10
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCATACCATGAAATATTTAGTACCTCG
Found at i:72565 original size:24 final size:22
Alignment explanation
Indices: 72504--72569 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
72494 TTGTGATAAT
* * *
72504 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTAAGAAATTTTAA
72526 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTAAGAAATTTTAA
*
72548 TAACCTGATCCTAAGAAATTTT
1 TAACC--AACCTAAGAAATTTT
72570 GGTAACCACA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 24 0.63
24 14 0.37
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTTAA
Found at i:72588 original size:46 final size:46
Alignment explanation
Indices: 72538--72643 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 46
72528 ACCAACCTAA
* *
72538 GAAATTTTAATAACCTGATCC-TAAGA-AATTTTGGTAACCACAGTA-T
1 GAAATTTTGATAACCT--TCCATAAGAGAA-TTTGGTAACCACACTATT
*
72584 GAAATTTTGATAA-CTTCCATATGAGAATTTGGTAACCACACTATT
1 GAAATTTTGATAACCTTCCATAAGAGAATTTGGTAACCACACTATT
72629 G-AATTTTGATAACCT
1 GAAATTTTGATAACCT
72644 CCTCATGAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
43 3 0.06
44 30 0.57
45 8 0.15
46 12 0.23
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (46 bp):
GAAATTTTGATAACCTTCCATAAGAGAATTTGGTAACCACACTATT
Found at i:72590 original size:22 final size:21
Alignment explanation
Indices: 72562--72691 Score: 95
Period size: 22 Copynumber: 6.0 Consensus size: 21
72552 CTGATCCTAA
*
72562 GAAATTTTGGTAACCACAGTAT
1 GAAATTTTGATAACCACA-TAT
72584 GAAATTTTGATAACTTC-CATAT
1 GAAATTTTGATAAC--CACATAT
*
72606 GAGAA-TTTGGTAACCACACTATT
1 GA-AATTTTGATAACCACA-TA-T
* *
72629 G-AATTTTGATAACCTCCTCAT
1 GAAATTTTGATAACCACAT-AT
** * *
72650 GAAATCATAATAACCATCTTAT
1 GAAATTTTGATAACCA-CATAT
72672 GAAATTTTGATAACCACATA
1 GAAATTTTGATAACCACATA
72692 GAGATAAAAA
Statistics
Matches: 84, Mismatches: 14, Indels: 21
0.71 0.12 0.18
Matches are distributed among these distances:
20 1 0.01
21 10 0.12
22 64 0.76
23 8 0.10
24 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (21 bp):
GAAATTTTGATAACCACATAT
Found at i:73129 original size:31 final size:30
Alignment explanation
Indices: 73064--73134 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
73054 ATGGCAATTT
* *
73064 AGAAATATATATTTAAAAAAAGGTATAATC
1 AGAAATATATATTTAAAAAAAGGTACAATA
73094 AGAAATATAT-TTTAAAAAAATGGGTACAATA
1 AGAAATATATATTTAAAAAAA--GGTACAATA
73125 AGAAA-ATATA
1 AGAAATATATA
73135 AAGTTTCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 10 0.28
30 14 0.39
31 12 0.33
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.28
Consensus pattern (30 bp):
AGAAATATATATTTAAAAAAAGGTACAATA
Found at i:73569 original size:15 final size:17
Alignment explanation
Indices: 73532--73572 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
73522 TCGGAACCAT
*
73532 ATGACCCGAAACTGAAA
1 ATGACCCGAAACTCAAA
*
73549 AAGACCC-AAAC-CAAA
1 ATGACCCGAAACTCAAA
73564 ATGACCCGA
1 ATGACCCGA
73573 CATTTGAGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 9 0.45
16 5 0.25
17 6 0.30
ACGTcount: A:0.49, C:0.29, G:0.15, T:0.07
Consensus pattern (17 bp):
ATGACCCGAAACTCAAA
Found at i:74001 original size:22 final size:21
Alignment explanation
Indices: 73951--74001 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
73941 TAAAATAATT
73951 ATAAAATATTGAATTTAATTAA
1 ATAAAATA-TGAATTTAATTAA
*
73973 ATGAAAATA-GAATTTTTATTAGA
1 AT-AAAATATGAA-TTTAATTA-A
73996 ATAAAA
1 ATAAAA
74002 CTGTATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 3 0.12
22 13 0.52
23 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (21 bp):
ATAAAATATGAATTTAATTAA
Found at i:75277 original size:109 final size:109
Alignment explanation
Indices: 75066--75361 Score: 432
Period size: 109 Copynumber: 2.7 Consensus size: 109
75056 TAAATTAAAA
** *
75066 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
*
75130 AGAATAAAGTTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
75177 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
* *
75242 ATAAAATTGTATATTAGAAAAATTTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* * *
75286 TGGTAAAAAGAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
75351 GTAGAATAAAA
61 GTAGAATAAAA
75362 CTATAATAGT
Statistics
Matches: 170, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
109 118 0.69
110 13 0.08
111 11 0.06
114 28 0.16
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:96417 original size:5 final size:5
Alignment explanation
Indices: 96407--96443 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
96397 ATTGTAATTG
* *
96407 TGTCA TGTCA TGTCA TGTCA TGCCA TGCCA TGTCA TG
1 TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA TGTCA TG
96444 ATTAGTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (5 bp):
TGTCA
Found at i:100937 original size:23 final size:23
Alignment explanation
Indices: 100917--100963 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
100907 TATCTATCGA
*
100917 ATATCGGAGTGATCATATATCAT
1 ATATCAGAGTGATCATATATCAT
*
100940 ATATCAGATTGATCATATATCAT
1 ATATCAGAGTGATCATATATCAT
100963 A
1 A
100964 ATTAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (23 bp):
ATATCAGAGTGATCATATATCAT
Found at i:102712 original size:2 final size:2
Alignment explanation
Indices: 102705--102744 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
102695 AACATATAAG
102705 TA TA TA TA TA TA TA TA TA TA TA TA TA 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
102745 AATGCTTGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107946 original size:7 final size:7
Alignment explanation
Indices: 107931--107962 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
107921 GATAAAAACT
*
107931 TGGAGCA
1 TGGAACA
107938 TGGAACA
1 TGGAACA
107945 TGGAACA
1 TGGAACA
107952 TGGAACA
1 TGGAACA
107959 TGGA
1 TGGA
107963 GTATCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.34, T:0.16
Consensus pattern (7 bp):
TGGAACA
Found at i:108764 original size:32 final size:32
Alignment explanation
Indices: 108721--108781 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
108711 AGAAGACATT
*
108721 ATGAAGAATTATTGTAATATTAATATCGAACA
1 ATGAAGAATTATTGTAATATCAATATCGAACA
*
108753 ATGAAGGATTATTGTAATATCAATATCGA
1 ATGAAGAATTATTGTAATATCAATATCGA
108782 GTTTGTTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (32 bp):
ATGAAGAATTATTGTAATATCAATATCGAACA
Found at i:123650 original size:23 final size:23
Alignment explanation
Indices: 123627--123669 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
123617 ATTATTGAAT
*
123627 TTCTTTGTTTCA-TTTTTTTTAA
1 TTCTTTGTTTAAGTTTTTTTTAA
*
123649 TTGTTTGTTTAAGTTTTTTTT
1 TTCTTTGTTTAAGTTTTTTTT
123670 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.74
Consensus pattern (23 bp):
TTCTTTGTTTAAGTTTTTTTTAA
Found at i:125345 original size:7 final size:7
Alignment explanation
Indices: 125333--125359 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
125323 GATAAGCAAA
125333 GCATATT
1 GCATATT
125340 GCATATT
1 GCATATT
125347 GCATATT
1 GCATATT
125354 GCATAT
1 GCATAT
125360 ATATGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (7 bp):
GCATATT
Found at i:126100 original size:22 final size:22
Alignment explanation
Indices: 126072--126119 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
126062 TTGTATTATT
126072 TTATGTGGATTTGGTTAGATTG
1 TTATGTGGATTTGGTTAGATTG
126094 TTATGTGGATTTGGTTAGATTG
1 TTATGTGGATTTGGTTAGATTG
126116 TTAT
1 TTAT
126120 TTTATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (22 bp):
TTATGTGGATTTGGTTAGATTG
Found at i:146470 original size:33 final size:33
Alignment explanation
Indices: 146400--146516 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 33
146390 GATCATGTGG
* * **
146400 CCGGTTATGGCCGGGCATGGCCGA-GTCATGTGA
1 CCGGTTGTGGCCGGGCATGGTC-ATGTCGCGTGA
*
146433 CCGGTTGTGGCCGGGCATGGTCATGTCGCGTGG
1 CCGGTTGTGGCCGGGCATGGTCATGTCGCGTGA
* *
146466 CCGGTTGTGGCCGGACATGGTCATGTCGCGTAA
1 CCGGTTGTGGCCGGGCATGGTCATGTCGCGTGA
146499 CCGG-TGTTGGCCGGGCAT
1 CCGGTTG-TGGCCGGGCAT
146517 CTCCAAGTCG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 3 0.04
33 70 0.96
ACGTcount: A:0.11, C:0.25, G:0.41, T:0.23
Consensus pattern (33 bp):
CCGGTTGTGGCCGGGCATGGTCATGTCGCGTGA
Found at i:146527 original size:66 final size:66
Alignment explanation
Indices: 146396--146536 Score: 153
Period size: 66 Copynumber: 2.1 Consensus size: 66
146386 AAAGGATCAT
* * * * *
146396 GTGGCCGGTTATGGCCGGGCATGGCCGAGTCATGTGACCGGTTGTGGCCGGGCATGGTCATGTCG
1 GTGGCCGGTTATGGCCGGACATGGCCGAGTCACGTAACCGGTTGTGGCCGGGCATGCTCAAGTCG
146461 C
66 C
* * *
146462 GTGGCCGGTTGTGGCCGGACATGGTC-ATGTCGCGTAACCGG-TGTTGGCCGGGCAT-CTCCAAG
1 GTGGCCGGTTATGGCCGGACATGGCCGA-GTCACGTAACCGGTTG-TGGCCGGGCATGCT-CAAG
146524 TCGC
63 TCGC
*
146528 ATGGCCGGT
1 GTGGCCGGT
146537 CACTTGTGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
65 4 0.06
66 59 0.94
ACGTcount: A:0.11, C:0.26, G:0.40, T:0.23
Consensus pattern (66 bp):
GTGGCCGGTTATGGCCGGACATGGCCGAGTCACGTAACCGGTTGTGGCCGGGCATGCTCAAGTCG
C
Found at i:147303 original size:155 final size:156
Alignment explanation
Indices: 147062--147469 Score: 459
Period size: 155 Copynumber: 2.6 Consensus size: 156
147052 GAGCCTCTCT
* * * * * * * *
147062 TCATAGTAAACTAGACGTCTCACCTTAAACTGTCCTTAAATGAAAAACTAGCATAAATTTTTCAC
1 TCATAGTGAAGTAGACTTCTCACCTCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCAT
** * ** * *
147127 CTTAAGTCTGAATGAGCTGAAACTTTTCCAATG-GACTTATACTATCTCCATAAGAC-TATGGAA
66 CTTAAGTCTGTTTGAGATGAAACTTCGCCAA-GAGACTTAGACTATCTCCA-AAAACTTATGGAA
* *
147190 AAAGTTCTAAGTAAAACCGAGCTTCCCT-
129 AAAATTCTAAGTAAAACCGAAC-TCCCTA
** * *
147218 TGGTAGTGAA-TAGACTTCTCACCTCAAATTGTCCTTAACTGAAAAACTTGCACAAGTTTTTCAT
1 TCATAGTGAAGTAGACTTCTCACCTCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCAT
*
147282 -TCTAAGTCTGTTTGAGATGAAACTTCGCCAAGAGACTTAGATTATCTCCAAAAACTTATGGAAA
66 CT-TAAGTCTGTTTGAGATGAAACTTCGCCAAGAGACTTAGACTATCTCCAAAAACTTATGGAAA
*
147346 AAATTCTAAGTAAAATCGAACTCCCTA
130 AAATTCTAAGTAAAACCGAACTCCCTA
* ** * * *
147373 TCATGGTGAAGT-GGTTTCTCACCCCAAGCTGTCCTTAACTGAAAAATTTGCATAAGTTTTTCAT
1 TCATAGTGAAGTAGACTTCTCACCTCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCAT
* *
147437 CTTAAGTCCGTTTGAGATGAAACTTAGCCAAGA
66 CTTAAGTCTGTTTGAGATGAAACTTCGCCAAGA
147470 TGGTCCACAT
Statistics
Matches: 212, Mismatches: 34, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
154 11 0.05
155 192 0.91
156 9 0.04
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (156 bp):
TCATAGTGAAGTAGACTTCTCACCTCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCAT
CTTAAGTCTGTTTGAGATGAAACTTCGCCAAGAGACTTAGACTATCTCCAAAAACTTATGGAAAA
AATTCTAAGTAAAACCGAACTCCCTA
Found at i:150740 original size:60 final size:62
Alignment explanation
Indices: 150540--150805 Score: 389
Period size: 62 Copynumber: 4.3 Consensus size: 62
150530 AATTTTTTTA
* * *
150540 AAATTATATATAGCGGCGTCTAGACGCCGCTATATTTAAAGGTTTTTTTTATAAAAAATCTC
1 AAATTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAGGGTTTTTTTTATAAAAAATCTC
* *
150602 AAATTAAATATAGCAGCGTTTAGACGCCGCTAAATTTAAGGGTTTTTTTTATAAAAAATCTC
1 AAATTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAGGGTTTTTTTTATAAAAAATCTC
* *
150664 AAATTAAATATAGCGGCGTTTAGACGCCGCTAT-TTTGAAGAG-TTTTTTTA-AAAAAATCTT
1 AAATTAAATATAGCGGCGTTTAGACGCCGCTATATTT-AAGGGTTTTTTTTATAAAAAATCTC
* *
150724 AAATTAAATATTGCGGCGTTTAGACGCCGCTATATTTAAGGG--TTTTTTAAAAATAAATCTC
1 AAATTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAGGGTTTTTTTTATAAA-AAATCTC
*
150785 AAATTAAATATAACGGCGTTT
1 AAATTAAATATAGCGGCGTTT
150806 CTGTAGGGAA
Statistics
Matches: 186, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
59 7 0.04
60 48 0.26
61 39 0.21
62 92 0.49
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (62 bp):
AAATTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAGGGTTTTTTTTATAAAAAATCTC
Found at i:150746 original size:122 final size:123
Alignment explanation
Indices: 150540--150805 Score: 396
Period size: 122 Copynumber: 2.2 Consensus size: 123
150530 AATTTTTTTA
* *
150540 AAATTATATATAGCGGCGTCTAGACGCCGCTATATTTAAAGGTTTTTTTTATAAAAAATCTCAAA
1 AAATTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAAGGTTTTTTTTATAAAAAATCTCAAA
*
150605 TTAAATATAGCAGCGTTTAGACGCCGCTAAATTTAAGGGTTTTTTTTATAAA-AAATCTC
66 TTAAATATAGCAGCGTTTAGACGCCGCTAAATTTAAGGG--TTTTTTAAAAATAAATCTC
* *
150664 AAATTAAATATAGCGGCGTTTAGACGCCGCTAT-TTTGAAGAG-TTTTTTTA-AAAAAATCTTAA
1 AAATTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAAG-GTTTTTTTTATAAAAAATCTCAA
* * *
150726 ATTAAATATTGCGGCGTTTAGACGCCGCTATATTTAAGGGTTTTTTAAAAATAAATCTC
65 ATTAAATATAGCAGCGTTTAGACGCCGCTAAATTTAAGGGTTTTTTAAAAATAAATCTC
*
150785 AAATTAAATATAACGGCGTTT
1 AAATTAAATATAGCGGCGTTT
150806 CTGTAGGGAA
Statistics
Matches: 131, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
120 10 0.08
121 27 0.21
122 48 0.37
123 14 0.11
124 32 0.24
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (123 bp):
AAATTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAAGGTTTTTTTTATAAAAAATCTCAAA
TTAAATATAGCAGCGTTTAGACGCCGCTAAATTTAAGGGTTTTTTAAAAATAAATCTC
Done.