Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009351.1 Corchorus capsularis cultivar CVL-1 contig09372, 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: 125485
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:1124 original size:2 final size:2
Alignment explanation
Indices: 1119--1149 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1109 CTATTAGCTC
1119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1150 AATTAAGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15705 original size:15 final size:15
Alignment explanation
Indices: 15685--15729 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
15675 AAATCCTCAG
15685 CAAGGACTCCTGGGA
1 CAAGGACTCCTGGGA
15700 CAAGGACTCCTGGGA
1 CAAGGACTCCTGGGA
*
15715 CAAGGACTTCTGGGA
1 CAAGGACTCCTGGGA
15730 AGTGGTACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.33, T:0.16
Consensus pattern (15 bp):
CAAGGACTCCTGGGA
Found at i:17662 original size:144 final size:144
Alignment explanation
Indices: 17402--17692 Score: 546
Period size: 144 Copynumber: 2.0 Consensus size: 144
17392 AACAAAAAGA
*
17402 GACAGTAACCTTTCAGTCTCCGATATTCAAGCTAATGAAGGACTTGATCATCAGGGTTGGCCAGA
1 GACAGTAACCTTTCAGTCTCCGATATTCAAGCTAATGAAGGACTTGATCATCAGGGTCGGCCAGA
**
17467 ATCAAAGCACAATTCTCTGATTAGGTTTGATGAACTTGACATTTGTCTCCCTGACGAGGACTTCC
66 ATCAAAGCACAATTCTCTGATTAGGTTTGATGAACTTGACATTTGTCTCCCTGACGAGGACAGCC
17532 TGATTACAGTTGAT
131 TGATTACAGTTGAT
17546 GACAGTAACCTTTCAGTCTCCGATATTCAAGCTAATGAAGGACTTGATCATCAGGGTCGGCCAGA
1 GACAGTAACCTTTCAGTCTCCGATATTCAAGCTAATGAAGGACTTGATCATCAGGGTCGGCCAGA
*
17611 ATCAAAGCACAATTCTCTGATTAGGTTTGATGAACTTGACATTTGTCTCCCTGATGAGGACAGCC
66 ATCAAAGCACAATTCTCTGATTAGGTTTGATGAACTTGACATTTGTCTCCCTGACGAGGACAGCC
17676 TGATTACAGTTGAT
131 TGATTACAGTTGAT
17690 GAC
1 GAC
17693 TACATATATC
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 143 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (144 bp):
GACAGTAACCTTTCAGTCTCCGATATTCAAGCTAATGAAGGACTTGATCATCAGGGTCGGCCAGA
ATCAAAGCACAATTCTCTGATTAGGTTTGATGAACTTGACATTTGTCTCCCTGACGAGGACAGCC
TGATTACAGTTGAT
Found at i:24423 original size:2 final size:2
Alignment explanation
Indices: 24416--24448 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
24406 CCAACTTTAA
24416 AT AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24449 AAACTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25950 original size:38 final size:38
Alignment explanation
Indices: 25903--25978 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
25893 TGTAGGATAG
25903 GGTGCAATTTAACATTAAAATCCTTTAATAGTTAGGAC
1 GGTGCAATTTAACATTAAAATCCTTTAATAGTTAGGAC
* *
25941 GGTGCAATTTAACATTAAAATCCTTTCATGGTTAGGAC
1 GGTGCAATTTAACATTAAAATCCTTTAATAGTTAGGAC
25979 TTTGAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (38 bp):
GGTGCAATTTAACATTAAAATCCTTTAATAGTTAGGAC
Found at i:26541 original size:17 final size:17
Alignment explanation
Indices: 26507--26542 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
26497 CCTGCTATGA
**
26507 AAAATTAATAATCTAAT
1 AAAATTAATAATAAAAT
26524 AAAATTAATAATAAAAT
1 AAAATTAATAATAAAAT
26541 AA
1 AA
26543 TTTATGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTAATAATAAAAT
Found at i:28158 original size:39 final size:38
Alignment explanation
Indices: 28109--28182 Score: 130
Period size: 39 Copynumber: 1.9 Consensus size: 38
28099 AGATCTATAC
*
28109 TACTATATATAAAAGTACGAATAAGGGGAAACTTTTCTA
1 TACTATATATAAAAGCACGAATAAGGGGAAA-TTTTCTA
28148 TACTATATATAAAAGCACGAATAAGGGGAAATTTT
1 TACTATATATAAAAGCACGAATAAGGGGAAATTTT
28183 ATGTTTTCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (38 bp):
TACTATATATAAAAGCACGAATAAGGGGAAATTTTCTA
Found at i:28222 original size:31 final size:29
Alignment explanation
Indices: 28187--28250 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
28177 AATTTTATGT
*
28187 TTTCCGATTGCACCCTTATTTTTAAAACATA
1 TTTCCAATTGCA-CCTT-TTTTTAAAACATA
* *
28218 TTTCCAATTGTACCTTTTTTTTAAACATA
1 TTTCCAATTGCACCTTTTTTTAAAACATA
28247 TTTC
1 TTTC
28251 TAAATTGCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (29 bp):
TTTCCAATTGCACCTTTTTTTAAAACATA
Found at i:28257 original size:30 final size:30
Alignment explanation
Indices: 28200--28257 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
28190 CCGATTGCAC
*
28200 CCTTATTTTTAAAACATATTTCCAATTGTA
1 CCTTATTTTTAAAACATATTTCAAATTGTA
*
28230 CCTT-TTTTTTAAACATATTTCTAAATTG
1 CCTTATTTTTAAAACATATTTC-AAATTG
28258 CCATTACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.31, C:0.16, G:0.03, T:0.50
Consensus pattern (30 bp):
CCTTATTTTTAAAACATATTTCAAATTGTA
Found at i:28385 original size:22 final size:22
Alignment explanation
Indices: 28360--28498 Score: 136
Period size: 22 Copynumber: 6.2 Consensus size: 22
28350 TCCATGAGGA
*
28360 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
28382 GGTTACCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * *
28404 AGTTACCAAAATTTCATAGAGT
1 GGTTATCAAAATTTCATAGTGT
* *
28426 GGTTACCAAAATTTCATAGGATCT
1 GGTTATCAAAATTTCATA-G-TGT
* *
28450 GGTTATTAAAATTTCTTAG-GTT
1 GGTTATCAAAATTTCATAGTG-T
** *
28472 GGTTATTGAAATTTCATAGGGT
1 GGTTATCAAAATTTCATAGTGT
28494 GGTTA
1 GGTTA
28499 ATTATCACAA
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
22 81 0.81
23 3 0.03
24 16 0.16
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:28460 original size:24 final size:23
Alignment explanation
Indices: 28336--28491 Score: 94
Period size: 22 Copynumber: 7.0 Consensus size: 23
28326 ATATTTTACT
* *
28336 TTGGTTATTATAATTCCATGAGGA
1 TTGGTTATTAAAATTTCAT-AGGA
* *
28360 --GGTTATCAAAATTCCATA-G-
1 TTGGTTATTAAAATTTCATAGGA
**
28379 TGTGGTTACCAAAATTTCATA-G-
1 T-TGGTTATTAAAATTTCATAGGA
* **
28401 TGTAGTTACCAAAATTTCATA-GA
1 T-TGGTTATTAAAATTTCATAGGA
* **
28424 GTGGTTACCAAAATTTCATAGGA
1 TTGGTTATTAAAATTTCATAGGA
*
28447 TCTGGTTATTAAAATTTCTTAGG-
1 T-TGGTTATTAAAATTTCATAGGA
*
28470 TTGGTTATTGAAATTTCATAGG
1 TTGGTTATTAAAATTTCATAGG
28492 GTGGTTAATT
Statistics
Matches: 113, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 90 0.80
23 3 0.03
24 18 0.16
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (23 bp):
TTGGTTATTAAAATTTCATAGGA
Found at i:28666 original size:22 final size:22
Alignment explanation
Indices: 28552--28924 Score: 109
Period size: 22 Copynumber: 16.8 Consensus size: 22
28542 TGCCATAGCG
28552 AGGTTAT-ACAAATTTCATAGTG-
1 AGGTTATCA-AAATTTCATA-TGA
* *
28574 TGGTTAACAAAATTTCAT-TAGA
1 AGGTTATCAAAATTTCATAT-GA
* * ** *
28596 AGGTTA-CTAATACTTCATCGGG
1 AGGTTATC-AAAATTTCATATGA
*
28618 AGGTTATCAAAATTTTATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
28640 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
28662 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* * * *
28687 AGGAGTACCAAAATTTGATA-AA
1 AGG-TTATCAAAATTTCATATGA
*
28709 AGGTTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* *
28728 AGTGATTATCGAAATTTCATAAAGA
1 AG-G-TTATCAAAATTTCAT-ATGA
*
28753 TATGATTATCAAAATTT-ATATGA
1 -A-GGTTATCAAAATTTCATATGA
**
28776 AAATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * *
28798 TTGTTATCAAAATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
*
28820 AGGTTATCAAAATTACATAATG-
1 AGGTTATCAAAATTTCAT-ATGA
* *
28842 TGATTATCAAAATTTCATA-GA
1 AGGTTATCAAAATTTCATATGA
* * * *
28863 GGGGTCAACAAAATTT--TATAA
1 -AGGTTATCAAAATTTCATATGA
*
28884 AGATGTTATCAAAATTTCATA-AA
1 AG--GTTATCAAAATTTCATATGA
*
28907 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
28925 AAATCTGATT
Statistics
Matches: 263, Mismatches: 50, Indels: 76
0.68 0.13 0.20
Matches are distributed among these distances:
19 2 0.01
20 15 0.06
21 32 0.12
22 163 0.62
23 13 0.05
24 9 0.03
25 17 0.06
26 7 0.03
27 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:28849 original size:44 final size:44
Alignment explanation
Indices: 28779--28924 Score: 161
Period size: 44 Copynumber: 3.3 Consensus size: 44
28769 TATATGAAAA
* * *
28779 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAATGATGTTATCAAAATTTCAAAGAGAGG
* * *
28823 TTATCAAAATTACATAATG-TGATTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGATG-TTATCAAAATTTCAAAGAGAGG
* * * *
28867 TCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCATAATGATGTTATCAAAATTTCA-AAGAGAGG
*
28911 TTATCAAATTTTCA
1 TTATCAAAATTTCA
28925 AAATCTGATT
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
43 2 0.02
44 78 0.94
45 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGATGTTATCAAAATTTCAAAGAGAGG
Found at i:28875 original size:66 final size:66
Alignment explanation
Indices: 28739--28924 Score: 162
Period size: 66 Copynumber: 2.8 Consensus size: 66
28729 GTGATTATCG
* * * * **
28739 AAATTTCATAAAGATATGATTATCAAAATTTATATGAA-A-ATTATCAAAATTTCATAGTGTTGT
1 AAATTTCATAAAG--A-GGTTATCAAAA-TTACATAAAGAGATTATCAAAATTTCATAGAGGGGT
* *
28802 TATCA
62 CAACA
* * *
28807 AAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAGGGGTCAA
1 AAATTTCATAA-AGAGGTTATCAAAATTACATAAAGAGATTATCAAAATTTCATAGAGGGGTCAA
28871 CA
65 CA
* * * * *
28873 AAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 AAATTTCATAAAGAGGTTATCAAAATTACATAAAGAGATTATCAAAATTTCA
28925 AAATCTGATT
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
64 6 0.06
65 10 0.11
66 66 0.69
67 4 0.04
68 9 0.09
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (66 bp):
AAATTTCATAAAGAGGTTATCAAAATTACATAAAGAGATTATCAAAATTTCATAGAGGGGTCAAC
A
Found at i:28877 original size:88 final size:88
Alignment explanation
Indices: 28783--28949 Score: 221
Period size: 88 Copynumber: 1.9 Consensus size: 88
28773 TGAAAATTAT
** * * * *
28783 CAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATCTGATT
28847 ATC-AAAATTTCATAGAGGGGTCAA
65 A-CAAAAATTTCATAGAGGGGTCAA
* * *
28871 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATCTGATTA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATCTGATTA
28936 CAAAAATTTCATAG
66 CAAAAATTTCATAG
28950 TGGTATTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 1 0.01
88 65 0.96
89 2 0.03
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (88 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATCTGATTA
CAAAAATTTCATAGAGGGGTCAA
Found at i:29057 original size:20 final size:20
Alignment explanation
Indices: 29032--29099 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 20
29022 ATGGAGTAAA
*
29032 CAAAATTTTAGGGAGGATAC
1 CAAAATTTCAGGGAGGATAC
*
29052 CAAAA-TTCAGGGAGGATAT
1 CAAAATTTCAGGGAGGATAC
* * *
29071 CAAAA-TTCAGTGAGAATAT
1 CAAAATTTCAGGGAGGATAC
29090 CAAAATTTCA
1 CAAAATTTCA
29100 TATGAAGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 34 0.79
20 9 0.21
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (20 bp):
CAAAATTTCAGGGAGGATAC
Found at i:29063 original size:19 final size:19
Alignment explanation
Indices: 29041--29096 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
29031 ACAAAATTTT
*
29041 AGGGAGGATACCAAAATTC
1 AGGGAGGATATCAAAATTC
29060 AGGGAGGATATCAAAATTC
1 AGGGAGGATATCAAAATTC
* *
29079 AGTGAGAATATCAAAATT
1 AGGGAGGATATCAAAATT
29097 TCATATGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (19 bp):
AGGGAGGATATCAAAATTC
Found at i:29115 original size:22 final size:22
Alignment explanation
Indices: 29087--29646 Score: 142
Period size: 22 Copynumber: 25.7 Consensus size: 22
29077 TCAGTGAGAA
29087 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
29109 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
29131 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
29153 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
29174 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
29197 TAACAAAATTTCATAATGAA-GT
1 TATCAAAATTTCAT-ATGAAGGT
** * * * *
29219 TATCAAAAAATCGTAAGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
29241 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
29257 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
29279 TATCAAAATTTTATACGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
29302 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
* *
29325 TATCAAAATTTCATA-GCGAGAT
1 TATCAAAATTTCATATG-AAGGT
* * * *
29347 TATCACAACTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * * *
29369 TATCAAAATTTTAAAGGATGAT
1 TATCAAAATTTCATATGAAGGT
*
29391 TAAT-AACAA-TTCATATGGAGGT
1 T-ATCAA-AATTTCATATGAAGGT
* * * * *
29413 TTTTAAATTTTTATA-AAATGGT
1 TATCAAAATTTCATATGAA-GGT
* * * *
29435 TATCAATATATCATATGGAGAT
1 TATCAAAATTTCATATGAAGGT
* * **
29457 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
29480 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
29502 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
29524 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
29546 TAACAAAATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
29568 T-TAAAAAAATT-ATA-AAAGGAT
1 TAT-CAAAATTTCATATGAAGG-T
* ** * **
29589 TCTTGAAATTCCATA-GTACCGT
1 TATCAAAATTTCATATG-AAGGT
*
29611 TATCAAAATTTCATA-GGAGGT
1 TATCAAAATTTCATATGAAGGT
29632 TATCAAAATTTCATA
1 TATCAAAATTTCATA
29647 ATGGGATCAT
Statistics
Matches: 387, Mismatches: 113, Indels: 77
0.67 0.20 0.13
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 5 0.01
21 42 0.11
22 259 0.67
23 67 0.17
24 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:29224 original size:44 final size:43
Alignment explanation
Indices: 29087--29561 Score: 158
Period size: 44 Copynumber: 10.9 Consensus size: 43
29077 TCAGTGAGAA
* * * * *
29087 TATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAGT
1 TATCAAAATTTCATAGGGA-GTTATCAAAATTTCATAATGTAGT
*
29131 TTTCAAAATTTCATAAGAGG-GTTATCAAAATTTCATAGTATGTAG-
1 TATCAAAATTTCAT-AG-GGAGTTATCAAAATTTCATA--ATGTAGT
* *
29176 -ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAAGT
1 TATCAAAATTTCATAGGGAG-TTATCAAAATTTCATAATGTAGT
** * *
29219 TATCAAAAAATCGTAAGGAGCTTATCAAAA--T--T--TGTAGT
1 TATCAAAATTTCATAGGGAG-TTATCAAAATTTCATAATGTAGT
* ** * * *
29257 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTAT-ACGGAGGTT
1 TATCAAAATTTCAT-AGGGAGTTATCAAAATTTCATAATGTA-G-T
* * * * **
29302 TATTAAAATTTTATAGAAAGATTTATCAAAATTTCATAGCG-AGAT
1 TATCAAAATTTCATAG--GGAGTTATCAAAATTTCATAATGTAG-T
* * * *
29347 TATCACAACTTCATAGTGTGA-TTATCAAAATTT--TAAAGGATGAT
1 TATCAAAATTTCATAG-G-GAGTTATCAAAATTTCATAATGTA-G-T
* * * * * ** *
29391 TAAT-AACAA-TTCATATGGAGGTTTTTAAATTTTTATAAAATGGT
1 T-ATCAA-AATTTCATAGGGA-GTTATCAAAATTTCATAATGTAGT
* * * * * * *
29435 TATCAATATATCATATGGAGATTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGGGAG-TTATCAAAATTTCATAATG-TAGT
* *
29480 TATCAAAATTTCATTGGGAAGTTATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATAGGG-AGTTATCAAAATTTCATAATGTA-GT
* * *
29524 CT-TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATAA
1 -TATCAAAATTTCATAGGGA-GTTATCAAAATTTCATAA
29562 GAAAGTTTAA
Statistics
Matches: 322, Mismatches: 73, Indels: 72
0.69 0.16 0.15
Matches are distributed among these distances:
38 24 0.07
39 3 0.01
40 2 0.01
42 14 0.04
43 12 0.04
44 168 0.52
45 69 0.21
46 28 0.09
47 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (43 bp):
TATCAAAATTTCATAGGGAGTTATCAAAATTTCATAATGTAGT
Found at i:29326 original size:23 final size:22
Alignment explanation
Indices: 29256--29340 Score: 73
Period size: 23 Copynumber: 3.8 Consensus size: 22
29246 AAATTTGTAG
* * *
29256 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTAT-AGAAGAT
* *
29278 TTATCAAAATTTTATACGGAGGT
1 TTATCAAAATTTTATA-GAAGAT
*
29301 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAG-AAGAT
*
29324 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
29341 CGAGATTATC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 1 0.02
22 16 0.32
23 33 0.66
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTTATAGAAGAT
Found at i:29505 original size:45 final size:45
Alignment explanation
Indices: 29431--29516 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
29421 TTTTATAAAA
* *
29431 TGGTTATCAATATATCATATGGAGATTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAGATTATCAAAATCTCATAGTGT
* *
29476 TGGTTATCAAAATTTCAT-TGG-GAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATATGGAG-A-TTATCAAAATCTCATA
29517 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 4 0.11
45 30 0.86
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAGATTATCAAAATCTCATAGTGT
Found at i:41090 original size:3 final size:3
Alignment explanation
Indices: 41082--41129 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
41072 ACAAATTACG
41082 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41130 ATATGAGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54529 original size:29 final size:29
Alignment explanation
Indices: 54487--54545 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
54477 AAGAAAAGAT
54487 AAAACCATGCCTACTGATAGTATTTCTTC
1 AAAACCATGCCTACTGATAGTATTTCTTC
54516 AAAACCATGCCTACTGATAGTATTTCTTC
1 AAAACCATGCCTACTGATAGTATTTCTTC
54545 A
1 A
54546 GATGAAGGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (29 bp):
AAAACCATGCCTACTGATAGTATTTCTTC
Found at i:63094 original size:20 final size:21
Alignment explanation
Indices: 63055--63098 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
63045 TGGAACTGGA
63055 TTGCTAAACACCACCCCCCTT
1 TTGCTAAACACCACCCCCCTT
* * *
63076 TTGCTAAATACCGCCCCCTTT
1 TTGCTAAACACCACCCCCCTT
63097 TT
1 TT
63099 ACACTTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.41, G:0.07, T:0.32
Consensus pattern (21 bp):
TTGCTAAACACCACCCCCCTT
Found at i:63240 original size:26 final size:26
Alignment explanation
Indices: 63211--63278 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
63201 TTCCTTCATT
63211 TTAATCATAAACTAATTA-AATACTAA
1 TTAATCATAAACTAATTAGAA-ACTAA
*
63237 TTAATAATAAACTAATTAGAAACTAA
1 TTAATCATAAACTAATTAGAAACTAA
* *
63263 TTAAACATAAAGTAAT
1 TTAATCATAAACTAAT
63279 AAACTAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 35 0.95
27 2 0.05
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAATCATAAACTAATTAGAAACTAA
Found at i:63241 original size:15 final size:15
Alignment explanation
Indices: 63211--63254 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
63201 TTCCTTCATT
*
63211 TTAATCATAAACTAA
1 TTAATAATAAACTAA
63226 TT-A-AAT--ACTAA
1 TTAATAATAAACTAA
63237 TTAATAATAAACTAA
1 TTAATAATAAACTAA
63252 TTA
1 TTA
63255 GAAACTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
11 7 0.29
12 1 0.04
13 5 0.21
14 1 0.04
15 10 0.42
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATAATAAACTAA
Found at i:64053 original size:85 final size:85
Alignment explanation
Indices: 63910--64078 Score: 329
Period size: 85 Copynumber: 2.0 Consensus size: 85
63900 AATATAGAGT
63910 ATATGCGATCTCGAAATTGAATGAGCATATGTGGGTTTGTGCCACTATGTGGACTTTGTAAGTTA
1 ATATGCGATCTCGAAATTGAATGAGCATATGTGGGTTTGTGCCACTATGTGGACTTTGTAAGTTA
63975 GTTATCTTCATTAAGATAGC
66 GTTATCTTCATTAAGATAGC
*
63995 ATATGCGATCTCGAAATTGAATGAGCATATGTGGGTTTGTGCCACTATGTGGGCTTTGTAAGTTA
1 ATATGCGATCTCGAAATTGAATGAGCATATGTGGGTTTGTGCCACTATGTGGACTTTGTAAGTTA
64060 GTTATCTTCATTAAGATAG
66 GTTATCTTCATTAAGATAG
64079 TGATTTGTCT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (85 bp):
ATATGCGATCTCGAAATTGAATGAGCATATGTGGGTTTGTGCCACTATGTGGACTTTGTAAGTTA
GTTATCTTCATTAAGATAGC
Found at i:66875 original size:129 final size:129
Alignment explanation
Indices: 66645--66884 Score: 453
Period size: 129 Copynumber: 1.9 Consensus size: 129
66635 TCCTTACCAT
*
66645 TTTGTAATATCTTAGTGCATTTGACAATAACAGCTAACATCGTAAGAATTTATACTAATCATTGA
1 TTTGTAATATCTTAGTGCATTTGACAATAACAGCTAACATCGTAAGAATTTATACCAATCATTGA
*
66710 TTTTCTGGCTACATGCTTTTCTTTTAATAATGGAATTTGTTTCTTAGTCAATTGCGATCTAACA
66 TTTTCTGGCTACATGCTTTTCTTTTAATAATGGAATTTGGTTCTTAGTCAATTGCGATCTAACA
*
66774 TTTGTAATATCTTAGTGCATTTGACAATAACAGTTAACATCGTAAGAATTTATACCAATCATTGA
1 TTTGTAATATCTTAGTGCATTTGACAATAACAGCTAACATCGTAAGAATTTATACCAATCATTGA
66839 TTTTCTGGCTACATGCTTTTCTTTTAATAATGGAATTTGGTTCTTA
66 TTTTCTGGCTACATGCTTTTCTTTTAATAATGGAATTTGGTTCTTA
66885 AAGTTAATTG
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 108 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (129 bp):
TTTGTAATATCTTAGTGCATTTGACAATAACAGCTAACATCGTAAGAATTTATACCAATCATTGA
TTTTCTGGCTACATGCTTTTCTTTTAATAATGGAATTTGGTTCTTAGTCAATTGCGATCTAACA
Found at i:77653 original size:10 final size:10
Alignment explanation
Indices: 77638--77690 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
77628 GCCCTATCGA
77638 TGGCCGGTTG
1 TGGCCGGTTG
77648 TGGCCGGTTGG
1 TGGCCGGTT-G
** *
77659 TGTGCCAATCG
1 TG-GCCGGTTG
77670 ATGGCCGGTTG
1 -TGGCCGGTTG
77681 TGGCCGGTTG
1 TGGCCGGTTG
77691 CCCCATGCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 19 0.56
11 9 0.26
12 6 0.18
ACGTcount: A:0.06, C:0.21, G:0.45, T:0.28
Consensus pattern (10 bp):
TGGCCGGTTG
Found at i:78575 original size:49 final size:51
Alignment explanation
Indices: 78472--78622 Score: 184
Period size: 50 Copynumber: 3.0 Consensus size: 51
78462 GATTCCTTTA
* * ** *
78472 GATCGATGTCACATT-TTTTTT-CTACCATATTCGGTACTAATCCGGATCC
1 GATCGATGACACATTATTTTTTGGTACCCCATCCGGTACTAATCCGGATCC
*
78521 GATCGATGATACA-TATTTTTTGGTACCCCATCCGGTACTAATCCGGATCC
1 GATCGATGACACATTATTTTTTGGTACCCCATCCGGTACTAATCCGGATCC
* ** *
78571 -ATCGATGACACATTTTTTTTTGGTACCCCATCCAATACTAATCTGGATCC
1 GATCGATGACACATTATTTTTTGGTACCCCATCCGGTACTAATCCGGATCC
78621 GA
1 GA
78623 CCTGCGTCAC
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
48 1 0.01
49 28 0.32
50 57 0.66
51 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (51 bp):
GATCGATGACACATTATTTTTTGGTACCCCATCCGGTACTAATCCGGATCC
Found at i:90132 original size:16 final size:15
Alignment explanation
Indices: 90111--90143 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
90101 TCGAACCCGA
90111 GAACCCGCCCGAACCC
1 GAACCCGCCC-AACCC
90127 GAACCCGCCCAACCC
1 GAACCCGCCCAACCC
90142 GA
1 GA
90144 TTTGACCAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.27, C:0.55, G:0.18, T:0.00
Consensus pattern (15 bp):
GAACCCGCCCAACCC
Found at i:90266 original size:32 final size:31
Alignment explanation
Indices: 90179--90278 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 31
90169 GAACCTGCCC
**
90179 GACCCGAGACCCGAATGACCCACAACCCGGAT
1 GACCCGAGACCCGAATGACCCGTAACCC-GAT
* *
90211 GACACGAGACCCAAATGACCCGTAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCC-GAT
* *
90243 GACCCGAAACCCGAATGAACCGTAACCCGAGT
1 GACCCGAGACCCGAATGACCCGTAACCCGA-T
90275 GACC
1 GACC
90279 TGTGACCTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 2 0.03
32 56 0.97
ACGTcount: A:0.34, C:0.37, G:0.21, T:0.08
Consensus pattern (31 bp):
GACCCGAGACCCGAATGACCCGTAACCCGAT
Found at i:90269 original size:16 final size:16
Alignment explanation
Indices: 90187--90278 Score: 80
Period size: 16 Copynumber: 5.8 Consensus size: 16
90177 CCGACCCGAG
**
90187 ACCCGAATGACCCACA
1 ACCCGAATGACCCGTA
* *
90203 ACCCGGATGACACG-A
1 ACCCGAATGACCCGTA
*
90218 GACCCAAATGACCCGTA
1 -ACCCGAATGACCCGTA
*
90235 ACCC-AGATGACCCGAA
1 ACCCGA-ATGACCCGTA
*
90251 ACCCGAATGAACCGTA
1 ACCCGAATGACCCGTA
*
90267 ACCCGAGTGACC
1 ACCCGAATGACC
90279 TGTGACCTGA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.03
16 57 0.93
17 2 0.03
ACGTcount: A:0.35, C:0.37, G:0.20, T:0.09
Consensus pattern (16 bp):
ACCCGAATGACCCGTA
Found at i:90865 original size:42 final size:42
Alignment explanation
Indices: 90818--90912 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
90808 AACGGTTTAA
* *
90818 AATATT-AACACATACCCCCACATGATAATTAATTATGTATTT
1 AATATTCAAAACATA-CCCCACATGATAATCAATTATGTATTT
* * *
90860 AATATTCAAAACCTACCTCACCTGATAATCAATTATGTATTT
1 AATATTCAAAACATACCCCACATGATAATCAATTATGTATTT
90902 AATATTCAAAA
1 AATATTCAAAA
90913 TTAATATCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 41 0.87
43 6 0.13
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (42 bp):
AATATTCAAAACATACCCCACATGATAATCAATTATGTATTT
Found at i:91131 original size:16 final size:16
Alignment explanation
Indices: 91112--91208 Score: 90
Period size: 16 Copynumber: 6.1 Consensus size: 16
91102 CCCGCCCAAT
**
91112 CCGAGACCCGGTTAAC
1 CCGAGACCCGAATAAC
*
91128 CCGAGACCCGAATGAC
1 CCGAGACCCGAATAAC
* * *
91144 CCGAAACCCGTATTAC
1 CCGAGACCCGAATAAC
91160 CCGAGACCCGAATAAC
1 CCGAGACCCGAATAAC
*
91176 CCGA-ACCC-AGATGAC
1 CCGAGACCCGA-ATAAC
* *
91191 CCGAAACCCGAATTAC
1 CCGAGACCCGAATAAC
91207 CC
1 CC
91209 AAGGAAACTG
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
14 1 0.01
15 12 0.18
16 53 0.79
17 1 0.01
ACGTcount: A:0.32, C:0.39, G:0.19, T:0.10
Consensus pattern (16 bp):
CCGAGACCCGAATAAC
Found at i:97169 original size:36 final size:36
Alignment explanation
Indices: 97122--97193 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
97112 GAATATCGTG
*
97122 AATAAAATGTGTCTTGGATTCACTCACTCCCACACT
1 AATAAAATGTGTCTTAGATTCACTCACTCCCACACT
97158 AATAAAATGTGTCTTAGATTCACTCACTCCCACACT
1 AATAAAATGTGTCTTAGATTCACTCACTCCCACACT
97194 TTCTCTAGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.31
Consensus pattern (36 bp):
AATAAAATGTGTCTTAGATTCACTCACTCCCACACT
Found at i:98768 original size:19 final size:20
Alignment explanation
Indices: 98732--98773 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
98722 TCAATTGGCC
* *
98732 AAAAAGAAAGAGAAAGAG-G
1 AAAAAAAAAAAGAAAGAGAG
*
98751 AAAAAAAAAAAGATAGAGAG
1 AAAAAAAAAAAGAAAGAGAG
98771 AAA
1 AAA
98774 CTACCTGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAGAAAGAGAG
Found at i:100589 original size:17 final size:16
Alignment explanation
Indices: 100570--100600 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
100560 GCTTCGGGTT
100570 TTTTTGGGTTCAGGTA
1 TTTTTGGGTTCAGGTA
100586 TTTTTGGGTTCAGGT
1 TTTTTGGGTTCAGGT
100601 TCGAGTCCGG
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:0.10, C:0.06, G:0.32, T:0.52
Consensus pattern (16 bp):
TTTTTGGGTTCAGGTA
Found at i:101325 original size:21 final size:21
Alignment explanation
Indices: 101301--101344 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
101291 AAAATTTTTA
101301 TTTTATAA-ATAATTCTTGATT
1 TTTTATAATATAATT-TTGATT
*
101322 TTTTATAATATTATTTTGATT
1 TTTTATAATATAATTTTGATT
101343 TT
1 TT
101345 GGGCTCGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTATAATATAATTTTGATT
Found at i:102562 original size:17 final size:16
Alignment explanation
Indices: 102521--102555 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
102511 AAAAAATCCG
*
102521 AACCCAAAAAAGCTCA
1 AACCCAAAAAAACTCA
102537 AACCCAAAAAAACTCA
1 AACCCAAAAAAACTCA
102553 AAC
1 AAC
102556 TCGAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.31, G:0.03, T:0.06
Consensus pattern (16 bp):
AACCCAAAAAAACTCA
Found at i:102611 original size:48 final size:48
Alignment explanation
Indices: 102508--102599 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
102498 GAACCTTAGT
* *
102508 TCGAAAAAATCCGAACCCAAAAAAGCTCAAACCCAAAAAAACTCAAAC
1 TCGAAAATATCCGAACCCAAAAAAGCTCAAACCCAAAAAAACCCAAAC
* *
102556 TCGAAAATATCCGAA-CCAGAAAAAGGTCAAATCCAAAAAAACCC
1 TCGAAAATATCCGAACCCA-AAAAAGCTCAAACCCAAAAAAACCC
102600 GAATCCGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 3 0.08
48 36 0.92
ACGTcount: A:0.54, C:0.27, G:0.09, T:0.10
Consensus pattern (48 bp):
TCGAAAATATCCGAACCCAAAAAAGCTCAAACCCAAAAAAACCCAAAC
Found at i:102793 original size:16 final size:15
Alignment explanation
Indices: 102765--102844 Score: 79
Period size: 15 Copynumber: 5.1 Consensus size: 15
102755 CAGAACCCGA
*
102765 ACCCGAATTAACCTG
1 ACCCAAATTAACCTG
*
102780 ACCCAAATTCAACCCG
1 ACCCAAATT-AACCTG
*
102796 AACCCAAATTAACCTA
1 -ACCCAAATTAACCTG
**
102812 ACCCAAATTAACTCAA
1 ACCCAAATTAAC-CTG
*
102828 ACCCGAATTAACCTG
1 ACCCAAATTAACCTG
102843 AC
1 AC
102845 ATAAATCCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
15 23 0.43
16 22 0.41
17 9 0.17
ACGTcount: A:0.41, C:0.35, G:0.06, T:0.17
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:102794 original size:32 final size:32
Alignment explanation
Indices: 102758--102863 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 32
102748 ACCCAAACAG
*
102758 AACCCGAACCCGAATTAACCTGACCCAAATTC
1 AACCCAAACCCGAATTAACCTGACCCAAATTC
* * *
102790 AACCCGAACCCAAATTAACCTAACCCAAATT-
1 AACCCAAACCCGAATTAACCTGACCCAAATTC
* ** *
102821 AACTCAAACCCGAATTAACCTGACATAAATCC
1 AACCCAAACCCGAATTAACCTGACCCAAATTC
102853 AACCCAAACCC
1 AACCCAAACCC
102864 AACTCAAACC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 24 0.38
32 39 0.62
ACGTcount: A:0.42, C:0.37, G:0.06, T:0.15
Consensus pattern (32 bp):
AACCCAAACCCGAATTAACCTGACCCAAATTC
Found at i:103807 original size:26 final size:26
Alignment explanation
Indices: 103778--103831 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
103768 ATTCGAATTA
103778 AATTGTTTGATACGTAGGAAATTTTG
1 AATTGTTTGATACGTAGGAAATTTTG
103804 AATTGTTTGATACGTAGGAAATTTTG
1 AATTGTTTGATACGTAGGAAATTTTG
103830 AA
1 AA
103832 AGTACTACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (26 bp):
AATTGTTTGATACGTAGGAAATTTTG
Found at i:125249 original size:41 final size:41
Alignment explanation
Indices: 125186--125270 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
125176 TATGAAACCC
*
125186 AAACCCTAACAAACAATATAAACCCTAAGTGAGATAA-AAG
1 AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAGAAG
* *
125226 AAACCCTCAAAAAACACAT-TAAACTCTAGGTGAGATAAGAAG
1 AAACCCT-AAAAAACA-ATATAAACCCTAAGTGAGATAAGAAG
125268 AAA
1 AAA
125271 AAACATGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 7 0.18
41 24 0.62
42 8 0.21
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (41 bp):
AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAGAAG
Done.