Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012268.1 Corchorus capsularis cultivar CVL-1 contig12289, 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: 98341
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6365 original size:6 final size:6
Alignment explanation
Indices: 6354--6387 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
6344 AAAGAAATCG
6354 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAA
6388 GGGTTAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:15899 original size:6 final size:6
Alignment explanation
Indices: 15888--15917 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
15878 CATTGCATGC
15888 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT
1 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT
15918 TCTATTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (6 bp):
ATTTGT
Found at i:23605 original size:154 final size:154
Alignment explanation
Indices: 23384--23912 Score: 519
Period size: 154 Copynumber: 3.4 Consensus size: 154
23374 CTTGGCTAAG
* *
23384 TTTCATCTCAAAC-GAACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAAGGATAGTTTGGG
1 TTTCATCTCAAACAG-ACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGAG
* * * *
23448 GTGAGAAACCACTTCACCATGATA-GCGAGTTCGGTTTTACTTAGAATTTTTT-CATAGTCTTGT
65 GTGAGAAACCAGTTCACCATCA-AGGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAGTCTTAT
*
23511 GGAGATAATCTAAGTCTGCTGGCCAAA
129 GGAGATAATCTAAGTCTACTGG-CAAA
**
23538 TTTCATCTCAAACAGACTT-AGAATGAAAAACTTATGCAAGTTTTTCGGTTAAGGACAGTTTGAG
1 TTTCATCTCAAACAGACTTAAG-ATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGAG
** * *
23602 GTGAGAAGTCAGTTCACTC-TCAAGGGGAGTTTGGTTTTACTTAG-TTTTTTTCCCATAG-CTTT
65 GTGAGAAACCAGTTCAC-CATCAAGGGGAGTTCGGTTTTACTTAGAATTTTTT-CCATAGTC-TT
* *
23664 ATGGAGATAATCTAAGCCTACTGGTGGAAA
127 ATGGAGATAATCTAAGTCTACT-G-GCAAA
* * *** *
23694 -ATCAGCTTC-ATTGGACTT-AGAATGAAAAAC-TATGCTAGTTTTTCATTTAAGGACAGTTT-A
1 TTTCATC-TCAAACAGACTTAAG-ATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGA
* * ** *
23754 GG-GAGGAACCAAGTTCACCATCAAGGGGAGCTCATTTTTACTTGGAATTTTTTCCATAGTCTTA
64 GGTGAGAAACC-AGTTCACCATCAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAGTCTTA
* *
23818 TGGAGAGAATCTAAGT-TCCTAGGCAAA
128 TGGAGATAATCTAAGTCTACT-GGCAAA
* * * * * * *
23845 GTTTCAACTCAATCAGACGTAAGGTGGAAAACTGATGCTAGTTTTTCATTTAAGGACAGTTTGAG
1 -TTTCATCTCAAACAGACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGAG
23910 GTG
65 GTG
23913 TGAAGTCTAG
Statistics
Matches: 309, Mismatches: 45, Indels: 40
0.78 0.11 0.10
Matches are distributed among these distances:
151 4 0.01
152 12 0.04
153 79 0.26
154 153 0.50
155 53 0.17
156 7 0.02
157 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (154 bp):
TTTCATCTCAAACAGACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAAGGACAGTTTGAGG
TGAGAAACCAGTTCACCATCAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAGTCTTATGG
AGATAATCTAAGTCTACTGGCAAA
Found at i:24261 original size:17 final size:17
Alignment explanation
Indices: 24239--24272 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24229 AGACTACAGT
24239 TCATGCTACCTAGTACC
1 TCATGCTACCTAGTACC
*
24256 TCATGCTACCTTGTACC
1 TCATGCTACCTAGTACC
24273 ATGAGGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (17 bp):
TCATGCTACCTAGTACC
Found at i:25174 original size:22 final size:21
Alignment explanation
Indices: 25149--25251 Score: 84
Period size: 22 Copynumber: 4.8 Consensus size: 21
25139 TGAATATTTT
25149 TATGAAATTTTGATAACTACC
1 TATGAAATTTTGATAACTACC
* *
25170 ATATGAAATTTTGATAATTATC
1 -TATGAAATTTTGATAACTACC
* *
25192 TATAAAATTGTGATAA--ACAC
1 TATGAAATTTTGATAACTAC-C
* *
25212 TATAAGAAACTTTGATAACCTAAC
1 TAT--GAAATTTTGATAA-CTACC
*
25236 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
25252 ACTCTCCTCT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 4 0.06
21 14 0.22
22 40 0.62
24 4 0.06
25 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:27775 original size:27 final size:26
Alignment explanation
Indices: 27745--27805 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
27735 AAATTTCCAT
27745 TATTTTAGTAATGG-AATAATTA-AAATA
1 TATTTTAG-AATGGCAAT--TTAGAAATA
27772 TATTTTGAGAATGGCAATTTAGAAATA
1 TATTTT-AGAATGGCAATTTAGAAATA
27799 TATTTTA
1 TATTTTA
27806 AAATAAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 4 0.13
27 22 0.71
28 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.43
Consensus pattern (26 bp):
TATTTTAGAATGGCAATTTAGAAATA
Found at i:27940 original size:31 final size:31
Alignment explanation
Indices: 27905--27971 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
27895 AACTTTATGT
* *
27905 TTTCCGATTATATCCTTATTTTT-AAAACATA
1 TTTCCAATTATACCCTT-TTTTTAAAAACATA
*
27936 TTTCCAATTGTACCCTTTTTTTAAAAAACATA
1 TTTCCAATTATACCCTTTTTTT-AAAAACATA
27968 TTTC
1 TTTC
27972 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 5 0.16
31 14 0.45
32 12 0.39
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCAATTATACCCTTTTTTTAAAAACATA
Found at i:28500 original size:110 final size:111
Alignment explanation
Indices: 28307--28535 Score: 433
Period size: 110 Copynumber: 2.1 Consensus size: 111
28297 TACTCTTAAT
28307 TTCAATTTTTAAATGTCAATAAAAAGATTAAACTAACACTAACACGTACAATACTATTGTTAGTG
1 TTCAATTTTTAAATGTCAATAAAAAGATTAAACTAACACTAACACGTACAATACTATTGTTAGTG
*
28372 AAGCTCCATCTATTCGTTATATAATGTTTTGCCGCATTCACT-TTG
66 AAACTCCATCTATTCGTTATATAATGTTTTGCCGCATTCACTATTG
28417 TTCAATTTTTAAATGTCAATAAAAAGATTAAACTAACACTAACACGTACAATACTATTGTTAGTG
1 TTCAATTTTTAAATGTCAATAAAAAGATTAAACTAACACTAACACGTACAATACTATTGTTAGTG
28482 AAACTCCATCTATTCGTTATATAATGTTTTGCCGCATTCACTATTG
66 AAACTCCATCTATTCGTTATATAATGTTTTGCCGCATTCACTATTG
*
28528 TTGAATTT
1 TTCAATTT
28536 AATATTTTAC
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 106 0.91
111 10 0.09
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (111 bp):
TTCAATTTTTAAATGTCAATAAAAAGATTAAACTAACACTAACACGTACAATACTATTGTTAGTG
AAACTCCATCTATTCGTTATATAATGTTTTGCCGCATTCACTATTG
Found at i:28748 original size:22 final size:22
Alignment explanation
Indices: 28719--28924 Score: 111
Period size: 22 Copynumber: 9.3 Consensus size: 22
28709 TTGTCTCTGT
*
28719 GTGGTTATAAAAATTTCATAAG
1 GTGGTTATCAAAATTTCATAAG
* * * *
28741 ATGGTTATTATAATTTCATCAG
1 GTGGTTATCAAAATTTCATAAG
*
28763 GGGGTTATCAAAA-TTC-TATAG
1 GTGGTTATCAAAATTTCATA-AG
* *
28784 TGTGGTTACCAAAATTTCATATG
1 -GTGGTTATCAAAATTTCATAAG
***
28807 AAAGTTATCAAAATTTCAT-AG
1 GTGGTTATCAAAATTTCATAAG
*
28828 TGTGGTTACCAAAATTTCAT-AG
1 -GTGGTTATCAAAATTTCATAAG
* *
28850 TGTGG-TACCAAAGTTTCAT-AG
1 -GTGGTTATCAAAATTTCATAAG
* * *
28871 GATCAGGTTATTAAAAATTC-TTAG
1 G-T--GGTTATCAAAATTTCATAAG
** *
28895 GTTGGTTATTGAAATTTCATAGG
1 G-TGGTTATCAAAATTTCATAAG
28918 GTGGTTA
1 GTGGTTA
28925 ATTATTACAG
Statistics
Matches: 142, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.01
21 22 0.15
22 94 0.66
23 10 0.07
24 14 0.10
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAAAATTTCATAAG
Found at i:28823 original size:66 final size:66
Alignment explanation
Indices: 28717--28869 Score: 177
Period size: 66 Copynumber: 2.3 Consensus size: 66
28707 TCTTGTCTCT
** ** * * *
28717 GTGTGGTTATAAAAATTTCATAAGATGGTTATTATAATTTCATCAG-GGGGTTATCAAAA-TTCT
1 GTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCAT-AGTGGGGTTACCAAAATTTC-
28780 ATA
64 ATA
* *
28783 GTGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGGGGTTACCAAAATTTCAT
28848 A
66 A
*
28849 GTGTGG-TACCAAAGTTTCATA
1 GTGTGGTTACCAAAATTTCATA
28870 GGATCAGGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
65 16 0.21
66 56 0.75
67 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGGGGTTACCAAAATTTCAT
A
Found at i:28860 original size:21 final size:22
Alignment explanation
Indices: 28717--28870 Score: 129
Period size: 22 Copynumber: 7.0 Consensus size: 22
28707 TCTTGTCTCT
**
28717 GTGTGGTTATAAAAATTTCATAA
1 GTGTGGTTACCAAAATTTCAT-A
* ** *
28740 G-ATGGTTATTATAATTTCATCA
1 GTGTGGTTACCAAAATTTCAT-A
* *
28762 G-GGGGTTATCAAAA-TTCTATA
1 GTGTGGTTACCAAAATTTC-ATA
28783 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTACCAAAATTTCATA
** *
28805 -TGAAAGTTATCAAAATTTCATA
1 GTG-TGGTTACCAAAATTTCATA
28827 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTACCAAAATTTCATA
*
28849 GTGTGG-TACCAAAGTTTCATA
1 GTGTGGTTACCAAAATTTCATA
28870 G
1 G
28871 GATCAGGTTA
Statistics
Matches: 109, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
21 22 0.20
22 81 0.74
23 6 0.06
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
GTGTGGTTACCAAAATTTCATA
Found at i:29174 original size:22 final size:24
Alignment explanation
Indices: 29139--29268 Score: 75
Period size: 22 Copynumber: 5.8 Consensus size: 24
29129 TGATAGAAGC
*
29139 TTATC-AAATCTCATAGAG-T-GA
1 TTATCAAAATTTCATAGAGATCGA
**
29160 TTATTGAAATTTCATAGAGATCGGA
1 TTATCAAAATTTCATAGAGATC-GA
* *
29185 TTATCAAAATTTCATAGTG-TTG-
1 TTATCAAAATTTCATAGAGATCGA
* *
29207 TTATCAAAATTTCA-A-AGCA-AGG
1 TTATCAAAATTTCATAGAG-ATCGA
* *
29229 TTATCAAAA--TCATATA-ATTGA
1 TTATCAAAATTTCATAGAGATCGA
*
29250 TTATCAGAATTTCATAGAG
1 TTATCAAAATTTCATAGAG
29269 GGGTCAACAA
Statistics
Matches: 84, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.06
21 16 0.19
22 36 0.43
23 8 0.10
24 1 0.01
25 18 0.21
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (24 bp):
TTATCAAAATTTCATAGAGATCGA
Found at i:29317 original size:22 final size:22
Alignment explanation
Indices: 29166--29329 Score: 111
Period size: 22 Copynumber: 7.4 Consensus size: 22
29156 GTGATTATTG
*
29166 AAATTTCATAGAGATCGGATTATCA
1 AAATTTCATAAAGA--GG-TTATCA
** **
29191 AAATTTCATAGTGTTGTTATCA
1 AAATTTCATAAAGAGGTTATCA
29213 AAATTTC--AAAGCAAGGTTATCA
1 AAATTTCATAAAG--AGGTTATCA
** *
29235 AAA--TCATATAATTGATTATCA
1 AAATTTCATA-AAGAGGTTATCA
* * * * *
29256 GAATTTCATAGAGGGGTCAACA
1 AAATTTCATAAAGAGGTTATCA
*
29278 AAATTTTATAAAGAGGTTATCA
1 AAATTTCATAAAGAGGTTATCA
29300 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAAAGAGGTTATCA
*
29322 AATTTTCA
1 AAATTTCA
29330 AAATATGATT
Statistics
Matches: 107, Mismatches: 25, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
20 4 0.04
21 9 0.08
22 74 0.69
23 8 0.07
25 12 0.11
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
AAATTTCATAAAGAGGTTATCA
Found at i:29486 original size:22 final size:22
Alignment explanation
Indices: 29369--29747 Score: 109
Period size: 22 Copynumber: 17.8 Consensus size: 22
29359 ATTTCTGGGG
*
29369 AGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
29391 TGGTTA-CCAAA--T--TAGGA
1 AGGTTATCAAAATTTCATAGGA
*
29408 AGGTTATTAAACATTT-ACTATGG-
1 AGGTTATCAAA-ATTTCA-TA-GGA
* * *
29431 A-GTAATTAAAATTTCAGA-G-
1 AGGTTATCAAAATTTCATAGGA
* * *
29450 AGGATATGAAAATTTCATATGA
1 AGGTTATCAAAATTTCATAGGA
**
29472 AGGTTATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG-GA
* *
29495 A-GTTTTCAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
* * *
29516 GGGTTACCAAAA-TTCATA-GT
1 AGGTTATCAAAATTTCATAGGA
* * * *
29536 ATGTAGATCAAAATTTTATAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * * * *
29559 AGATTAACAAACTTTCAAAATG-
1 AGGTTATCAAAATTTC-ATAGGA
** * *
29581 AGGTTATCAAAAAATCTTAGGG
1 AGGTTATCAAAATTTCATAGGA
*
29603 AGGTTATC-AAA-TT--T--GT
1 AGGTTATCAAAATTTCATAGGA
* * *
29619 A-GTTACCAAGATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
* * * *
29640 AAGTTATAAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGGA
*
29662 AGGTTTATCAAAATTTTATAGGA
1 AGG-TTATCAAAATTTCATAGGA
* *
29685 AGATTTATCAAAATTTCTTAGCG-
1 AG-GTTATCAAAATTTCATAG-GA
* *
29708 AGGTTAATCACAATTTCATAGTA
1 AGGTT-ATCAAAATTTCATAGGA
* *
29731 TGATTATCAAAATTTCA
1 AGGTTATCAAAATTTCA
29748 GAGTGTAATT
Statistics
Matches: 256, Mismatches: 71, Indels: 60
0.66 0.18 0.16
Matches are distributed among these distances:
15 5 0.02
16 4 0.02
17 11 0.04
18 3 0.01
19 5 0.02
20 17 0.07
21 30 0.12
22 116 0.45
23 62 0.24
24 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:29717 original size:23 final size:22
Alignment explanation
Indices: 29643--29745 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 22
29633 CATAAGAAAG
*
29643 TTATAAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATA-GGAGGT
*
29666 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGG-AGGT
29689 TTATCAAAATTTCT-TAGCGAGGT
1 TTATCAAAATTT-TATAG-GAGGT
* * * * * *
29712 TAATCACAATTTCATAGTATGA
1 TTATCAAAATTTTATAGGAGGT
29734 TTATCAAAATTT
1 TTATCAAAATTT
29746 CAGAGTGTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
22 14 0.22
23 49 0.75
24 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAGGT
Found at i:29746 original size:45 final size:47
Alignment explanation
Indices: 29629--29746 Score: 127
Period size: 46 Copynumber: 2.6 Consensus size: 47
29619 AGTTACCAAG
* * * * *
29629 ATTTCATAAGAA-AGTTATAAAAATTT-TATAGGGAGGTTTATCAAA
1 ATTTCATAGGAAGATTTATCAAAATTTCTATAGCGAGGTTAATCAAA
* *
29674 ATTTTATAGGAAGATTTATCAAAATTTCT-TAGCGAGGTTAATCACA
1 ATTTCATAGGAAGATTTATCAAAATTTCTATAGCGAGGTTAATCAAA
* *
29720 ATTTCATAGTATGA-TTATCAAAATTTC
1 ATTTCATAGGAAGATTTATCAAAATTTC
29747 AGAGTGTAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
45 23 0.38
46 37 0.61
47 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (47 bp):
ATTTCATAGGAAGATTTATCAAAATTTCTATAGCGAGGTTAATCAAA
Found at i:29758 original size:22 final size:22
Alignment explanation
Indices: 29714--29759 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
29704 AGCGAGGTTA
* * *
29714 ATCACAATTTCATAGTATGATT
1 ATCAAAATTTCAGAGTATAATT
*
29736 ATCAAAATTTCAGAGTGTAATT
1 ATCAAAATTTCAGAGTATAATT
29758 AT
1 AT
29760 TAACAATTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
ATCAAAATTTCAGAGTATAATT
Found at i:29892 original size:44 final size:42
Alignment explanation
Indices: 29829--30216 Score: 159
Period size: 44 Copynumber: 9.0 Consensus size: 42
29819 GTTATATGAA
* *
29829 GGTTATCAAAATTTCATAGTTTGGTTTTCAAAATTTCATAAGAG
1 GGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCAT-AG-G
*
29873 GGTTATCAAAATTTCATAGTAT-GTAGATCAAAATTTCATAGG
1 GGTTATCAAAATTTCATAGTATGGT-TATCAAAATTTCATAGG
* * **
29915 GAGATTAACAAAATTTCATAATGA-GGTTATCAAAAAATCATAGGG
1 G-G-TTATCAAAATTTCATAGT-ATGGTTATCAAAATTTCATA-GG
* * *
29960 AGGTTATCAAAA-TT--T-GTA--GTTACCAAGATTTCATACGAA
1 -GGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATA-G-G
* * * * * *
29999 AGTTATAAAAATTTTATAGGAAGGTTATCAAAATTTTATAGG
1 GGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGG
* * * *
30041 AAGATTTATCAAAATTTCATAGCGA-GGTTATCACAATTTCGTAGTG
1 --G-GTTATCAAAATTTCATAG-TATGGTTATCAAAATTTCATAG-G
* * * * **
30087 TGATTATCAAAATTTTAGAGTGTAATTA-CTAATAA-TTCATATGG
1 -GGTTATCAAAATTTCATAGTATGGTTATC-AA-AATTTCATA-GG
* * * ** * *
30131 AGGTTTTTAAATTTTCATAACATGGTTATCAATATATCATATGG
1 -GGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATA-GG
* * * *
30175 AGGTTATCAACATCTCATAGTGTTGGTTATCGAAATTTCATA
1 -GGTTATCAAAATTTCATAGT-ATGGTTATCAAAATTTCATA
30217 TTGAGGTCTT
Statistics
Matches: 253, Mismatches: 65, Indels: 51
0.69 0.18 0.14
Matches are distributed among these distances:
38 23 0.09
39 3 0.01
40 1 0.00
41 2 0.01
42 4 0.02
43 10 0.04
44 148 0.58
45 58 0.23
46 4 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (42 bp):
GGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGG
Found at i:29969 original size:66 final size:65
Alignment explanation
Indices: 29828--29974 Score: 161
Period size: 66 Copynumber: 2.2 Consensus size: 65
29818 GGTTATATGA
*** * ** ** *
29828 AGGTTATCAAAATTTCATAGTTTGGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAGAGGGTTATCAAAAAATCATAGG
* *
29893 ATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGA-GGTTATCAAAAAATCATA
1 AGGT-TATCAAAATTTCATAGGGAGATTAACAAAATTTCATAA-GAGGGTTATCAAAAAATCATA
29957 GGG
64 -GG
29960 AGGTTATCAAAATTT
1 AGGTTATCAAAATTT
29975 GTAGTTACCA
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
65 3 0.05
66 57 0.86
67 6 0.09
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (65 bp):
AGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAGAGGGTTATCAAAAAATCATAGG
Found at i:30049 original size:23 final size:22
Alignment explanation
Indices: 29820--30079 Score: 124
Period size: 22 Copynumber: 12.0 Consensus size: 22
29810 CATATGGAGG
*
29820 TTATATGAAGGTTATCAAAATT
1 TTATAGGAAGGTTATCAAAATT
* *** *
29842 TCATAGTTTGGTTTTCAAAATT
1 TTATAGGAAGGTTATCAAAATT
* * *
29864 TCATAAGAGGGTTATCAAAATT
1 TTATAGGAAGGTTATCAAAATT
* * * *
29886 TCATA-GTATGTAGATCAAAATT
1 TTATAGGAAGGT-TATCAAAATT
* * * *
29908 TCATAGGGAGATTAACAAAATT
1 TTATAGGAAGGTTATCAAAATT
* * **
29930 TCATAATG-AGGTTATCAAAAAA
1 TTAT-AGGAAGGTTATCAAAATT
* *
29952 TCATAGGGAGGTTATCAAAA--
1 TTATAGGAAGGTTATCAAAATT
* * *
29972 TT-T--GTA-GTTACCAAGATT
1 TTATAGGAAGGTTATCAAAATT
* * * *
29990 TCATACGAAAGTTATAAAAATT
1 TTATAGGAAGGTTATCAAAATT
30012 TTATAGGAAGGTTATCAAAATT
1 TTATAGGAAGGTTATCAAAATT
*
30034 TTATAGGAAGATTTATCAAAATT
1 TTATAGGAAG-GTTATCAAAATT
* *
30057 TCATAGCG-AGGTTATCACAATT
1 TTATAG-GAAGGTTATCAAAATT
30079 T
1 T
30080 CGTAGTGTGA
Statistics
Matches: 183, Mismatches: 43, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
16 8 0.04
17 2 0.01
18 1 0.01
19 2 0.01
20 1 0.01
21 7 0.04
22 138 0.75
23 23 0.13
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATAGGAAGGTTATCAAAATT
Found at i:30325 original size:22 final size:22
Alignment explanation
Indices: 30311--30370 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
30301 CATAGTATCA
*
30311 TTATTAAAATTTCATAGGAAAT
1 TTATCAAAATTTCATAGGAAAT
30333 TTATCAAAATTTCATAGGAAAT
1 TTATCAAAATTTCATAGGAAAT
30355 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
30371 ATGGGATCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAAAT
Found at i:30334 original size:12 final size:12
Alignment explanation
Indices: 30317--30356 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
30307 ATCATTATTA
30317 AAATTTCATAGG
1 AAATTTCATAGG
30329 AAATTT-ATCA--
1 AAATTTCAT-AGG
30339 AAATTTCATAGG
1 AAATTTCATAGG
30351 AAATTT
1 AAATTT
30357 ATCAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 7 0.29
11 4 0.17
12 13 0.54
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (12 bp):
AAATTTCATAGG
Found at i:30810 original size:17 final size:17
Alignment explanation
Indices: 30788--30820 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30778 ATCCAAAGGC
30788 TTTACTTTAGTGATTTA
1 TTTACTTTAGTGATTTA
*
30805 TTTACTTTATTGATTT
1 TTTACTTTAGTGATTT
30821 GTAATATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.64
Consensus pattern (17 bp):
TTTACTTTAGTGATTTA
Found at i:31707 original size:2 final size:2
Alignment explanation
Indices: 31702--31733 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
31692 CAATATATCT
31702 TA TA TA TA TA TA TA -A T- 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
31734 ATTTTACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31722 original size:16 final size:16
Alignment explanation
Indices: 31701--31731 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31691 GCAATATATC
31701 TTATATATATATATAA
1 TTATATATATATATAA
31717 TTATATATATATATA
1 TTATATATATATATA
31732 TAATTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATATATATATATAA
Found at i:31725 original size:18 final size:18
Alignment explanation
Indices: 31702--31736 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31692 CAATATATCT
31702 TATATATATATATAATTA
1 TATATATATATATAATTA
31720 TATATATATATATAATT
1 TATATATATATATAATT
31737 TTACTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATATATATATAATTA
Found at i:31948 original size:54 final size:53
Alignment explanation
Indices: 31885--31991 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 53
31875 TAGGCCTTTG
* * * * *
31885 TTTGATGAATTTCATTATTTAA-CACGTTCTTTTGATTACATGAATTTTTTTTAA
1 TTTGATGAATTTCATTATCTAACCA-ATTATTATGATTAAATG-ATTTTTTTTAA
*
31939 TTTGATGAATTTTATTATCTAACCAATTATTATGATTAAATGATTTTTTTTAA
1 TTTGATGAATTTCATTATCTAACCAATTATTATGATTAAATGATTTTTTTTAA
31992 AAAAAAGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 11 0.24
54 33 0.72
55 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.53
Consensus pattern (53 bp):
TTTGATGAATTTCATTATCTAACCAATTATTATGATTAAATGATTTTTTTTAA
Found at i:32937 original size:16 final size:16
Alignment explanation
Indices: 32918--32950 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32908 AATTAAAATT
*
32918 AAAAAAA-AAGAAGAA
1 AAAAAAAGAAAAAGAA
32933 AAAAAAAGAAAAAGAA
1 AAAAAAAGAAAAAGAA
32949 AA
1 AA
32951 GTTTCTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAGAA
Found at i:32950 original size:13 final size:13
Alignment explanation
Indices: 32918--32942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32908 AATTAAAATT
32918 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
32931 AAAAAAAAAGAA
1 AAAAAAAAAGAA
32943 AAAGAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:40727 original size:13 final size:13
Alignment explanation
Indices: 40709--40733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40699 ACATGCATTA
40709 AAAACGGACATGT
1 AAAACGGACATGT
40722 AAAACGGACATG
1 AAAACGGACATG
40734 AATATGATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.24, T:0.12
Consensus pattern (13 bp):
AAAACGGACATGT
Found at i:40929 original size:27 final size:27
Alignment explanation
Indices: 40899--40973 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
40889 AGTAGACTTA
* * *
40899 AAATGACTAGAATGCCGCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
*
40926 AAATGACCAAAATGCCCCTGAACTTGC
1 AAATGACCAAAATGCCCCTGAACATGC
40953 AAATGACCAAAATGCCCCTGA
1 AAATGACCAAAATGCCCCTGA
40974 CACCGAACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:53574 original size:99 final size:97
Alignment explanation
Indices: 53390--53582 Score: 307
Period size: 99 Copynumber: 2.0 Consensus size: 97
53380 AAAAATTGTC
53390 TTTGCAAAAGAAAAGTGTTTTCTCTCAAAAAGGTTTTTAGAGAAAATTGGTTTCAAAAGTTTTTC
1 TTTGCAAAAGAAAAGTGTTTTCTCTCAAAAAGGTTTTTAGAGAAAATTGGTTTCAAAAGTTTTTC
* *
53455 AAAGGCAAGCGCATATTGAAATAAAAGAACAGTT
66 AAAAGCAAGCGCATAGTGAAA-AAAA-AACAGTT
53489 TTTGCAAAAGAAAAGTGTTTT-TCTCAAAAAAGGTTTTTAGAGAAAATTGGTTTCAAAAGTTTTT
1 TTTGCAAAAGAAAAGTGTTTTCTCTC-AAAAAGGTTTTTAGAGAAAATTGGTTTCAAAAGTTTTT
* * *
53553 TAAAAGCAAGTGCATGGTGAAAAAAAAACA
65 CAAAAGCAAGCGCATAGTGAAAAAAAAACA
53583 AAAAAAATCT
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
97 4 0.05
98 8 0.09
99 76 0.86
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (97 bp):
TTTGCAAAAGAAAAGTGTTTTCTCTCAAAAAGGTTTTTAGAGAAAATTGGTTTCAAAAGTTTTTC
AAAAGCAAGCGCATAGTGAAAAAAAAACAGTT
Found at i:54445 original size:37 final size:37
Alignment explanation
Indices: 54395--54492 Score: 126
Period size: 37 Copynumber: 2.6 Consensus size: 37
54385 TCAACAATCA
* * *
54395 ACCACGGACTGGTCTCTTCTCGATTCTCAAGCAA-CTG
1 ACCACGGACTGGTCTCTTCTCAAATATCAA-CAAGCTG
* *
54432 ACCACGGATTGGTCTCTTCTCAAATATCAACAAGTTG
1 ACCACGGACTGGTCTCTTCTCAAATATCAACAAGCTG
*
54469 ACCACGTACTGGTCTCTTCTCAAA
1 ACCACGGACTGGTCTCTTCTCAAA
54493 CTCCAACAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
36 3 0.06
37 50 0.94
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.29
Consensus pattern (37 bp):
ACCACGGACTGGTCTCTTCTCAAATATCAACAAGCTG
Found at i:54500 original size:37 final size:35
Alignment explanation
Indices: 54395--54517 Score: 120
Period size: 37 Copynumber: 3.4 Consensus size: 35
54385 TCAACAATCA
* *
54395 ACCACGGACTGGTCTCTTCTCGATTCTCAAGCAACTG
1 ACCACGGACTGGTCTCTTCTCAAATC-CAA-CAACTG
* * *
54432 ACCACGGATTGGTCTCTTCTCAAATATCAACAAGTTG
1 ACCACGGACTGGTCTCTTCTCAAAT-CCAACAA-CTG
* *
54469 ACCACGTACTGGTCTCTTCTCAAACTCCAACAATTG
1 ACCACGGACTGGTCTCTTCTCAAA-TCCAACAACTG
* *
54505 GCCATGGACTGGT
1 ACCACGGACTGGT
54518 TACCTTTCAA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
36 16 0.22
37 55 0.76
38 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (35 bp):
ACCACGGACTGGTCTCTTCTCAAATCCAACAACTG
Found at i:54800 original size:38 final size:39
Alignment explanation
Indices: 54709--54814 Score: 169
Period size: 39 Copynumber: 2.7 Consensus size: 39
54699 AAAGTCATCG
*
54709 AAGTTGACTGGAAACAGGTCACCTTTCAACAATAATCAA
1 AAGTTGACTGGAAACAGGTCATCTTTCAACAATAATCAA
*
54748 AAGTTGACTGGAAACAGGTCATCTTTCAGCAATAATC-A
1 AAGTTGACTGGAAACAGGTCATCTTTCAACAATAATCAA
* *
54786 AAGTTGACTAGAAACATGTCATCTTTCAA
1 AAGTTGACTGGAAACAGGTCATCTTTCAA
54815 GTTATCAGAG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
38 27 0.44
39 35 0.56
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (39 bp):
AAGTTGACTGGAAACAGGTCATCTTTCAACAATAATCAA
Found at i:54889 original size:36 final size:36
Alignment explanation
Indices: 54849--54987 Score: 136
Period size: 36 Copynumber: 3.7 Consensus size: 36
54839 TATCAAAGTT
54849 GACTGGAAACAGGTCATCTTTCAGCAATTATCTTAC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCTTAC
* * * *
54885 GACTGGAAACAGGTCGTCTTTCAGCACTTATAAGGTT-T
1 GACTGGAAACAGGTCATCTTTCAGCAATTAT---CTTAC
* * **
54923 TACTGGAAACAGGTCATCTTTCAACAAGTTATCAAGATC
1 GACTGGAAACAGGTCATCTTTCAGCAA-TTATC-TTA-C
*
54962 GACTAGAAACAGGTCATCTTTCAGCA
1 GACTGGAAACAGGTCATCTTTCAGCA
54988 GTTTTCGGTT
Statistics
Matches: 81, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
36 29 0.36
38 23 0.28
39 29 0.36
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (36 bp):
GACTGGAAACAGGTCATCTTTCAGCAATTATCTTAC
Found at i:54975 original size:39 final size:38
Alignment explanation
Indices: 54836--54987 Score: 159
Period size: 38 Copynumber: 4.0 Consensus size: 38
54826 TCATCTTCCA
*
54836 AATTATCAA-AGTTGACTGGAAACAGGTCATCTTTCAGC
1 AATTATCAAGA-TCGACTGGAAACAGGTCATCTTTCAGC
** *
54874 AATTATC-TTA-CGACTGGAAACAGGTCGTCTTTCAGC
1 AATTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
* * ** *
54910 ACTTAT-AAGGTTTTACTGGAAACAGGTCATCTTTCAAC
1 AATTATCAA-GATCGACTGGAAACAGGTCATCTTTCAGC
*
54948 AAGTTATCAAGATCGACTAGAAACAGGTCATCTTTCAGC
1 AA-TTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
54987 A
1 A
54988 GTTTTCGGTT
Statistics
Matches: 91, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
36 29 0.32
38 31 0.34
39 29 0.32
40 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (38 bp):
AATTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
Found at i:55055 original size:23 final size:24
Alignment explanation
Indices: 55024--55073 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
55014 TTTCAACAAC
* *
55024 TTTTCAATTTACAACTTTTCGGCA
1 TTTTCAATTTACAACTTTACAGCA
55048 TTTT-AATTTACAACTTTACAGCA
1 TTTTCAATTTACAACTTTACAGCA
55071 TTT
1 TTT
55074 CAACAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (24 bp):
TTTTCAATTTACAACTTTACAGCA
Found at i:55112 original size:23 final size:23
Alignment explanation
Indices: 55082--55133 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
55072 TTCAACAACT
*
55082 TTTCAATTTACAAATTTTCAGCA
1 TTTCAATTTACAAATTTACAGCA
*
55105 TTTCAATTTACAACTTTACAGCA
1 TTTCAATTTACAAATTTACAGCA
55128 TTTCAA
1 TTTCAA
55134 CAACTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (23 bp):
TTTCAATTTACAAATTTACAGCA
Found at i:55169 original size:51 final size:51
Alignment explanation
Indices: 55010--55518 Score: 685
Period size: 51 Copynumber: 9.8 Consensus size: 51
55000 CCCCAAACGG
*
55010 AGCATTTCAACAACTTTTCAATTTACAACTTTTCGGCATTTTAATTTACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTT---CA---GAATTTACAACTTTAC
*
55067 AGCATTTCAACAACTTTTCAATTTACAAATTTTCAGCATTTCAATTTACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAG------AATTTACAACTTTAC
*
55124 AGCATTTCAACAACTTTTCAATTTGCAACTTTTCAGAATTTACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
*
55175 AGCATTTCAACAACTTTTCAATTTGCAACTTTTCAGAATTTACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
55226 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
*
55277 AGCATTTCAACAACTTTTCAATTTGCAACTTTTCAGAATTTACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
55328 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
*
55379 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGCATTTCAATTCACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAG------AATTTACAACTTTAC
* *
55436 GGCATTTCAACAACTTTTC-A---GC-A--TTTC--AATTTACAACTTTAC
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
** *
55478 AATATTTCAACAACTTTACAATTTACAACTTTTCAGCAATT
1 AGCATTTCAACAACTTTTCAATTTACAACTTTTCAG-AATT
55519 CAATTCTCAA
Statistics
Matches: 414, Mismatches: 16, Indels: 49
0.86 0.03 0.10
Matches are distributed among these distances:
42 29 0.07
43 1 0.00
46 1 0.00
47 1 0.00
49 4 0.01
50 4 0.01
51 252 0.61
52 5 0.01
53 1 0.00
54 2 0.00
56 1 0.00
57 113 0.27
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (51 bp):
AGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAACTTTAC
Found at i:55500 original size:34 final size:31
Alignment explanation
Indices: 55109--55509 Score: 193
Period size: 34 Copynumber: 11.9 Consensus size: 31
55099 TCAGCATTTC
*
55109 AATTTACAACTTTACAGCATTTCAACAACTTTTC-
1 AATTTACAACTTTACA--ATTT--ACAACTTTACA
* *
55143 AATTTGCAACTTTTCAGAATTTACAACTTTACA
1 AATTTACAAC-TTT-ACAATTTACAACTTTACA
* * * *
55176 GCATTTCAACAACTTTTCAATTTGCAACTTTTCA
1 -AATTT--ACAACTTTACAATTTACAACTTTACA
*
55210 GAATTTACAACTTTACAGCATTTCAACAACTTTTC-
1 -AATTTACAACTTTACA--ATTT--ACAACTTTACA
*
55245 AATTTACAACTTTTCAGAATTTACAACTTTACA
1 AATTTACAAC-TTT-ACAATTTACAACTTTACA
* * * *
55278 GCATTTCAACAACTTTTCAATTTGCAACTTTTCA
1 -AATTT--ACAACTTTACAATTTACAACTTTACA
*
55312 GAATTTACAACTTTACAGCATTTCAACAACTTTTC-
1 -AATTTACAACTTTACA--ATTT--ACAACTTTACA
*
55347 AATTTACAACTTTTCAGAATTTACAACTTTACA
1 AATTTACAAC-TTT-ACAATTTACAACTTTACA
* * *
55380 GCATTTCAACAACTTTTCAATTTACAACTTTTCA
1 -AATTT--ACAACTTTACAATTTACAACTTTACA
* * **
55414 GCATTT-CAA-TTCACAACTTTACGGCATTTCAACA
1 -AATTTACAACTTTACAA-TTTACAAC-TTT--ACA
* * *
55448 ACTTTTCAGCATTT-CAATTTACAACTTTACA
1 AATTTACAAC-TTTACAATTTACAACTTTACA
55479 ATATTTCAACAACTTTACAATTTACAACTTT
1 A-ATTT--ACAACTTTACAATTTACAACTTT
55510 TCAGCAATTC
Statistics
Matches: 288, Mismatches: 42, Indels: 74
0.71 0.10 0.18
Matches are distributed among these distances:
30 5 0.02
31 13 0.05
32 53 0.18
33 9 0.03
34 147 0.51
35 21 0.07
36 40 0.14
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.39
Consensus pattern (31 bp):
AATTTACAACTTTACAATTTACAACTTTACA
Found at i:55546 original size:57 final size:57
Alignment explanation
Indices: 55445--55554 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
55435 CGGCATTTCA
* * *
55445 ACAACTTTTCAGCATTTCAATTTACAACTTTACAATATTTCAACAACTTTACAATTT
1 ACAACTTTTCAGCAATTCAATTTACAACTTTACAACATTCCAACAACTTTACAATTT
** *
55502 ACAACTTTTCAGCAATTCAATTCT-CAACTTTTGAGCATTCCAACAACTTTACA
1 ACAACTTTTCAGCAATTCAATT-TACAACTTTACAACATTCCAACAACTTTACA
55555 GTTTTCGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 45 0.98
58 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (57 bp):
ACAACTTTTCAGCAATTCAATTTACAACTTTACAACATTCCAACAACTTTACAATTT
Found at i:59663 original size:21 final size:21
Alignment explanation
Indices: 59634--59684 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
59624 TTGAAAGGCA
*
59634 TGAAGGACGAAATAGGAATGC
1 TGAAGGACGAAAGAGGAATGC
* * *
59655 TGAATGACGGAGGAGGAATGC
1 TGAAGGACGAAAGAGGAATGC
59676 TGAAGGACG
1 TGAAGGACG
59685 GAGGATGAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.39, T:0.14
Consensus pattern (21 bp):
TGAAGGACGAAAGAGGAATGC
Found at i:59685 original size:21 final size:21
Alignment explanation
Indices: 59647--59689 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
59637 AGGACGAAAT
*
59647 AGGAATGCTGAATGACGGAGG
1 AGGAATGCTGAAGGACGGAGG
59668 AGGAATGCTGAAGGACGGAGG
1 AGGAATGCTGAAGGACGGAGG
59689 A
1 A
59690 TGAGGTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.44, T:0.12
Consensus pattern (21 bp):
AGGAATGCTGAAGGACGGAGG
Found at i:64868 original size:13 final size:13
Alignment explanation
Indices: 64849--64881 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
64839 AAATTTTAGA
64849 AAAAGAAGA-AAG
1 AAAAGAAGAGAAG
64861 AAACAGAAGAGAAG
1 AAA-AGAAGAGAAG
64875 AAAAGAA
1 AAAAGAA
64882 AGTTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 10 0.53
14 6 0.32
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAGAAG
Found at i:65082 original size:2 final size:2
Alignment explanation
Indices: 65077--65111 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
65067 TTTTTATTCG
*
65077 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65112 ACTAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:65383 original size:13 final size:13
Alignment explanation
Indices: 65365--65402 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
65355 TTGCATACAC
65365 AAAAGAAAAGC-AA
1 AAAAGAAAA-CAAA
65378 AAAAGAAAACAAA
1 AAAAGAAAACAAA
65391 AAAAGAAAACAA
1 AAAAGAAAACAA
65403 TGGAAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.04
13 23 0.96
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAGAAAACAAA
Found at i:67366 original size:32 final size:32
Alignment explanation
Indices: 67325--67385 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
67315 GTCATGTCGG
*
67325 GTTAAATTTGGGTCAAATTGATTTGGGTTCGA
1 GTTAAATTTGGGTCAAATTGATTCGGGTTCGA
* **
67357 GTTAAATTTGGTTCAGGTTGATTCGGGTT
1 GTTAAATTTGGGTCAAATTGATTCGGGTT
67386 TGGGTCAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.43
Consensus pattern (32 bp):
GTTAAATTTGGGTCAAATTGATTCGGGTTCGA
Found at i:67627 original size:22 final size:23
Alignment explanation
Indices: 67599--67641 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
67589 TAGTATTGAA
67599 TTCGGG-TTTTTTCAGGTTCGAG
1 TTCGGGTTTTTTTCAGGTTCGAG
*
67621 TTCGGGTTTTTTTCGGGTTCG
1 TTCGGGTTTTTTTCAGGTTCG
67642 GATTTTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.05, C:0.14, G:0.33, T:0.49
Consensus pattern (23 bp):
TTCGGGTTTTTTTCAGGTTCGAG
Found at i:67682 original size:16 final size:16
Alignment explanation
Indices: 67661--67718 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
67651 GAATTTCAGA
67661 TTTTTCGGGTTCTGGT
1 TTTTTCGGGTTCTGGT
*
67677 TTTTTCAGGTT-TGAGCT
1 TTTTTCGGGTTCTG-G-T
* *
67694 TCTTT-GGGTTCAGG-
1 TTTTTCGGGTTCTGGT
67708 TTTTTCGGGTT
1 TTTTTCGGGTT
67719 AGGGTTCGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 16 0.48
17 6 0.18
ACGTcount: A:0.05, C:0.12, G:0.29, T:0.53
Consensus pattern (16 bp):
TTTTTCGGGTTCTGGT
Found at i:87897 original size:6 final size:7
Alignment explanation
Indices: 87880--87910 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
87870 AAATCCTTAA
87880 AAAAAAT
1 AAAAAAT
87887 AAAAAAT
1 AAAAAAT
87894 AAAAAAT
1 AAAAAAT
87901 -AAAAAT
1 AAAAAAT
87907 AAAA
1 AAAA
87911 CAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:87899 original size:14 final size:13
Alignment explanation
Indices: 87880--87910 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
87870 AAATCCTTAA
87880 AAAAAATAAAAAAT
1 AAAAAAT-AAAAAT
87894 AAAAAATAAAAAT
1 AAAAAATAAAAAT
87907 AAAA
1 AAAA
87911 CAAAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:91731 original size:39 final size:37
Alignment explanation
Indices: 91678--91754 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 37
91668 AATCGCAAAA
* *
91678 TTTTTTTTTTAGAAAAATTGGAAAAAAGGAAAAACTTTT
1 TTTTTTTTTTAGAAAAAATGG-AAAAA-CAAAAACTTTT
91717 TTTTTTTTTTAGAAAAAATGGAAAAACAAAAACTTTT
1 TTTTTTTTTTAGAAAAAATGGAAAAACAAAAACTTTT
91754 T
1 T
91755 AAAGTAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 11 0.31
38 5 0.14
39 20 0.56
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (37 bp):
TTTTTTTTTTAGAAAAAATGGAAAAACAAAAACTTTT
Done.