Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014385.1 Corchorus capsularis cultivar CVL-1 contig14406, 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: 47148
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:5349 original size:31 final size:31
Alignment explanation
Indices: 5314--5379 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
5304 AATTTTATGT
*
5314 TTTCCGATTGTA-CCTTTATTTTTAAAACATA
1 TTTCCAATTGTATCCTTT-TTTTTAAAACATA
5345 TTTCCAATTGTATCCTTTTTTTTAAAACATA
1 TTTCCAATTGTATCCTTTTTTTTAAAACATA
5376 TTTC
1 TTTC
5380 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTCCAATTGTATCCTTTTTTTTAAAACATA
Found at i:5386 original size:32 final size:31
Alignment explanation
Indices: 5320--5386 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
5310 ATGTTTTCCG
*
5320 ATTGTACCTTTATTTTTAAAACATATTTCCA
1 ATTGTACCTTTATTTTTAAAACATATTTCAA
5351 ATTGTATCCTTT-TTTTTAAAACATATTTCTAA
1 ATTGTA-CCTTTATTTTTAAAACATATTTC-AA
5383 ATTG
1 ATTG
5387 CCATTACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.51
Consensus pattern (31 bp):
ATTGTACCTTTATTTTTAAAACATATTTCAA
Found at i:5504 original size:22 final size:21
Alignment explanation
Indices: 5479--5557 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 21
5469 TGGTTATTAT
*
5479 AATTCCATGAGGAGGTTACCAA
1 AATTTCAT-AGGAGGTTACCAA
*
5501 AATTTCATAGAGTGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
*
5523 AATTTCATAGGATCAAGTTACCAA
1 AATTTCATAGG---AGGTTACCAA
5547 AATTTCATAGG
1 AATTTCATAGG
5558 TTGGTTATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.06
22 27 0.55
24 19 0.39
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (21 bp):
AATTTCATAGGAGGTTACCAA
Found at i:5547 original size:24 final size:23
Alignment explanation
Indices: 5493--5557 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 23
5483 CCATGAGGAG
*
5493 GTTACCAAAATTTCATA-GAGTG
1 GTTACCAAAATTTCATAGGAGTA
5515 GTTACCAAAATTTCATAGGA-TCAA
1 GTTACCAAAATTTCATAGGAGT--A
5539 GTTACCAAAATTTCATAGG
1 GTTACCAAAATTTCATAGG
5558 TTGGTTATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 18 0.46
23 2 0.05
24 19 0.49
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (23 bp):
GTTACCAAAATTTCATAGGAGTA
Found at i:5754 original size:22 final size:22
Alignment explanation
Indices: 5705--5760 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
5695 ACTTCATCGG
5705 GAGGTTATCAAAATTTTATAGT
1 GAGGTTATCAAAATTTTATAGT
*
5727 GTGGTTATCAAAATTTTATA-T
1 GAGGTTATCAAAATTTTATAGT
5748 GAAGGTTAT-AAAA
1 G-AGGTTATCAAAA
5761 GTCTCAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (22 bp):
GAGGTTATCAAAATTTTATAGT
Found at i:5835 original size:22 final size:22
Alignment explanation
Indices: 5766--6037 Score: 143
Period size: 22 Copynumber: 12.5 Consensus size: 22
5756 TAAAAGTCTC
* *
5766 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
* *
5786 AATTTGATAGA-AGATTATC-A
1 AATTTCATAGAGTGATTATCAA
* *
5806 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
*
5828 AATTTCATAAAGATATGATTATCAA
1 AATTTCAT--AGA-GTGATTATCAA
*
5853 AATTT-ATATGA-AGATTATCAA
1 AATTTCATA-GAGTGATTATCAA
*
5874 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
* * * *
5896 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
5918 AGTTACATA-ATGTGATTATCAA
1 AATTTCATAGA-GTGATTATCAA
* * * *
5940 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* *
5962 AATTTTATAAAGATG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
* * *
5984 AAATTCATAAAGAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
6006 ATTTTCA-AAATCTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
6028 AATTTCATAG
1 AATTTCATAG
6038 TGGTATTTTT
Statistics
Matches: 192, Mismatches: 41, Indels: 35
0.72 0.15 0.13
Matches are distributed among these distances:
20 18 0.09
21 34 0.18
22 115 0.60
23 6 0.03
24 5 0.03
25 14 0.07
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:5863 original size:18 final size:19
Alignment explanation
Indices: 5840--5878 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
5830 TTTCATAAAG
5840 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
5858 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
5879 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:5980 original size:66 final size:66
Alignment explanation
Indices: 5864--6012 Score: 158
Period size: 66 Copynumber: 2.3 Consensus size: 66
5854 ATTTATATGA
* ** * * * *
5864 AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTATC-AAAGTTACATAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAAATT-CATAA
*
5928 TG
65 AG
* * *
5930 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAA-AGATGTTATCAAAAATTCATAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCA-AAGAGAGGTTATCAAAAATTCATAA
5994 AG
65 AG
*
5996 AGATTATCAAATTTTCA
1 AGATTATCAAAATTTCA
6013 AAATCTGATT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
66 61 0.90
67 7 0.10
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAAATTCATAAA
G
Found at i:6145 original size:20 final size:20
Alignment explanation
Indices: 6120--6185 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 20
6110 ATGTAGTAAT
*
6120 CAAAATTTTAAGGAGGATAC
1 CAAAATTTCAAGGAGGATAC
*
6140 CAAAA-TTCAGGGAGGATAC
1 CAAAATTTCAAGGAGGATAC
*
6159 CAAAA-TTC-AGTGAGGATAT
1 CAAAATTTCAAG-GAGGATAC
6178 CAAAATTT
1 CAAAATTT
6186 AATATGAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 32 0.80
20 7 0.17
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (20 bp):
CAAAATTTCAAGGAGGATAC
Found at i:6155 original size:19 final size:19
Alignment explanation
Indices: 6131--6184 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
6121 AAAATTTTAA
6131 GGAGGATACCAAAATTCAG
1 GGAGGATACCAAAATTCAG
6150 GGAGGATACCAAAATTCAG
1 GGAGGATACCAAAATTCAG
* *
6169 TGAGGATATCAAAATT
1 GGAGGATACCAAAATT
6185 TAATATGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (19 bp):
GGAGGATACCAAAATTCAG
Found at i:6203 original size:22 final size:22
Alignment explanation
Indices: 6175--6648 Score: 142
Period size: 22 Copynumber: 21.7 Consensus size: 22
6165 TCAGTGAGGA
*
6175 TATCAAAATTTAATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
6197 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
6219 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
6241 TATCAAAATTTCATA-GCATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
6262 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
6285 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
6307 TATCAAAAAATCATAAGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
6329 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
6345 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
6367 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * * ** *
6390 TATTAAACTTTTATAAAAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
6413 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
6435 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
6457 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
6479 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
6501 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
6523 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
6545 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
6568 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
6590 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
6612 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
*
6634 TAACAAAATTTCATA
1 TATCAAAATTTCATA
6649 AGAAAGTTTA
Statistics
Matches: 331, Mismatches: 86, Indels: 70
0.68 0.18 0.14
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 8 0.02
21 17 0.05
22 224 0.68
23 64 0.19
24 6 0.02
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:6592 original size:45 final size:45
Alignment explanation
Indices: 6519--6604 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
6509 TTTTATAAAG
* * *
6519 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
6564 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
6605 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:7170 original size:19 final size:19
Alignment explanation
Indices: 7146--7183 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
7136 CTATTATATT
7146 TTTTTAA-TTTAATATTTTA
1 TTTTTAATTTTAAT-TTTTA
7165 TTTTTAATTTTAATTTTTA
1 TTTTTAATTTTAATTTTTA
7184 AATGTCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTAATTTTAATTTTTA
Found at i:7381 original size:22 final size:22
Alignment explanation
Indices: 7353--7459 Score: 78
Period size: 22 Copynumber: 4.9 Consensus size: 22
7343 TGTCTTTATG
7353 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
7375 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
7398 -GGTTATCAAAATTCCA-CAGTA
1 TGGTTATCAAAATTTCATAAG-A
* *
7419 TTGTTACCAAAATTTCA-AATGGA
1 TGGTTATCAAAATTTCATAA--GA
*
7442 -AGTTATCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
7460 GTGTGATTAT
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 57 0.88
23 5 0.08
24 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:7531 original size:22 final size:22
Alignment explanation
Indices: 7478--7543 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
7468 ATTGGTTACC
* *
7478 AAAATTTCATAGGATCAAGTTATT
1 AAAATTTCATAGGGT--GGTTATT
* *
7502 AAAATTTCTTAGGTTGGTTATT
1 AAAATTTCATAGGGTGGTTATT
* *
7524 GAAGTTTCATAGGGTGGTTA
1 AAAATTTCATAGGGTGGTTA
7544 ATTATCACAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 22 0.63
24 13 0.37
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (22 bp):
AAAATTTCATAGGGTGGTTATT
Found at i:7741 original size:21 final size:22
Alignment explanation
Indices: 7716--7819 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 22
7706 TCATAAGGAG
*
7716 TATCAAAATTTGATAGA-AGAT
1 TATCAAAATTTCATAGACAGAT
* **
7737 TATC-AAATCTCATAGAGTGAT
1 TATCAAAATTTCATAGACAGAT
***
7758 TATTGGAATTTCATAGAGATCAGAT
1 TATCAAAATTTCAT--AGA-CAGAT
*
7783 TATCAAAATTT-ATTGGA-AGAT
1 TATCAAAATTTCA-TAGACAGAT
7804 TATCAAAATTTCATAG
1 TATCAAAATTTCATAG
7820 TGTTGTTATC
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
20 10 0.16
21 27 0.43
22 8 0.13
23 2 0.03
24 4 0.06
25 12 0.19
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGACAGAT
Found at i:7831 original size:22 final size:22
Alignment explanation
Indices: 7764--7948 Score: 115
Period size: 22 Copynumber: 8.3 Consensus size: 22
7754 TGATTATTGG
*
7764 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATAGTGAT--G-TTATCAA
* *
7789 AATTT-ATTG-GAAGATTATCAA
1 AATTTCATAGTGATG-TTATCAA
*
7810 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAGTGATGTTATCAA
* *
7832 AATTTCAAAGTGAAGTTATCAA
1 AATTTCATAGTGATGTTATCAA
* * *
7854 AATTACATAATG-TGATTATCAG
1 AATTTCATAGTGATG-TTATCAA
* ** * *
7876 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGTGATGTTATCAA
* **
7898 AATTTTATAAAGATGTTATCAA
1 AATTTCATAGTGATGTTATCAA
** *
7920 AATTTCATAAAGATGTCATCAA
1 AATTTCATAGTGATGTTATCAA
*
7942 ATTTTCA
1 AATTTCA
7949 AAATGTGATT
Statistics
Matches: 127, Mismatches: 29, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
21 15 0.12
22 99 0.78
23 5 0.04
24 3 0.02
25 5 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
AATTTCATAGTGATGTTATCAA
Found at i:7899 original size:66 final size:66
Alignment explanation
Indices: 7801--7929 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
7791 TTTATTGGAA
* ** * * *
7801 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGTGAAGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAAGTTATCAAAATTACATAAT
7865 GT
65 GT
* * * *
7867 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAA
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAAGTTATCAAAATTACATAA
7930 AGATGTCATC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAAGTTATCAAAATTACATAATG
T
Found at i:8102 original size:19 final size:20
Alignment explanation
Indices: 8054--8104 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
8044 TTATGGAGTA
*
8054 ATCAAAATTTCAGAGAGGAT
1 ATCAAAATTTCAGAGACGAT
*
8074 ATCAAAATTTCAGGGACGAT
1 ATCAAAATTTCAGAGACGAT
8094 ATC-AAATTTCA
1 ATCAAAATTTCA
8105 TAGTTTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAGAGACGAT
Found at i:8303 original size:23 final size:23
Alignment explanation
Indices: 8241--8344 Score: 106
Period size: 23 Copynumber: 4.6 Consensus size: 23
8231 ATTTGTAGTT
* *
8241 ATTTATCAAAATTTTACAGGGAG
1 ATTTATCAAAATTTTATAGGAAG
*
8264 GTTTATCAAAATTTTATAGGAAG
1 ATTTATCAAAATTTTATAGGAAG
*
8287 ATTTATCAAAATTTTATA-G-CG
1 ATTTATCAAAATTTTATAGGAAG
* * * *
8308 ATGTTATCACAATTTCATAGTATG
1 AT-TTATCAAAATTTTATAGGAAG
8332 A-TTATCAAAATTT
1 ATTTATCAAAATTT
8345 CAGAGTGTGA
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
21 3 0.04
22 26 0.38
23 37 0.54
24 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (23 bp):
ATTTATCAAAATTTTATAGGAAG
Found at i:8336 original size:22 final size:22
Alignment explanation
Indices: 8054--8346 Score: 105
Period size: 22 Copynumber: 13.5 Consensus size: 22
8044 TTATGGAGTA
* *
8054 ATCAAAATTTCAGA-GAGGA-T
1 ATCAAAATTTCATAGGATGATT
* *
8074 ATCAAAATTTCA-GGGACGA-T
1 ATCAAAATTTCATAGGATGATT
* *
8094 ATC-AAATTTCATA-GTTTAGTT
1 ATCAAAATTTCATAGGATGA-TT
* * * *
8115 TTCAAATTTTCATAAG-TGGGTT
1 ATCAAAATTTCATAGGAT-GATT
* * *
8137 GTCAAAATTTCATAGTAT-ATAG
1 ATCAAAATTTCATAGGATGAT-T
8159 ATCAAAATTTCATAGGGA-GATT
1 ATCAAAATTTCATA-GGATGATT
* *
8181 AACAAACTTTCATA--ATGAGGTT
1 ATCAAAATTTCATAGGATGA--TT
** *
8203 ATCAAAAAATCATAGGGA-GGTT
1 ATCAAAATTTCATA-GGATGATT
* * *
8225 AACAAAATTT-GTA-G-TTATTT
1 ATCAAAATTTCATAGGATGA-TT
* * * *
8245 ATCAAAATTTTACAGGGAGGTTT
1 ATCAAAATTTCATA-GGATGATT
* *
8268 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGATGA-TT
*
8291 ATCAAAATTTTATAGCGATG-TT
1 ATCAAAATTTCATAG-GATGATT
* *
8313 ATCACAATTTCATAGTATGATT
1 ATCAAAATTTCATAGGATGATT
8335 ATCAAAATTTCA
1 ATCAAAATTTCA
8347 GAGTGTGATT
Statistics
Matches: 201, Mismatches: 46, Indels: 50
0.68 0.15 0.17
Matches are distributed among these distances:
19 12 0.06
20 33 0.16
21 10 0.05
22 102 0.51
23 39 0.19
24 4 0.02
25 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGATGATT
Found at i:8433 original size:17 final size:17
Alignment explanation
Indices: 8411--8444 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8401 ATCAATATAT
8411 CATATGGAGGTTATCAA
1 CATATGGAGGTTATCAA
**
8428 CATATGTTGGTTATCAA
1 CATATGGAGGTTATCAA
8445 AATTTCATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (17 bp):
CATATGGAGGTTATCAA
Found at i:8511 original size:22 final size:21
Alignment explanation
Indices: 8486--8541 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
8476 TTGAGGTCTT
*
8486 CAAAATTCCTTAAGGAGGTTAA
1 CAAAATT-CATAAGGAGGTTAA
8508 CAAAGATTCATAAGGAGGTTAA
1 CAAA-ATTCATAAGGAGGTTAA
*
8530 CAAAATTTATAA
1 CAAAATTCATAA
8542 AAAAGTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 7 0.23
22 21 0.68
23 3 0.10
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (21 bp):
CAAAATTCATAAGGAGGTTAA
Found at i:9675 original size:2 final size:2
Alignment explanation
Indices: 9668--9696 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9658 TGTAAATTTC
9668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9697 TGAAATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13078 original size:2 final size:2
Alignment explanation
Indices: 13071--13143 Score: 58
Period size: 2 Copynumber: 41.5 Consensus size: 2
13061 CCGTTTAGTA
*
13071 AT AT AT AT A- AT -T AA AT AT AT -T AT AT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
13108 CT A- AT AT AT AT A- AT -T AT AT AT AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13144 ATTATTAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
1 10 0.18
2 47 0.82
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13096 original size:19 final size:19
Alignment explanation
Indices: 13072--13130 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
13062 CGTTTAGTAA
13072 TATATATAATTAAATATAT
1 TATATATAATTAAATATAT
* * *
13091 TATATATATAATAATATCTAA
1 TATATATA-ATTAA-ATATAT
*
13112 TATATATAATTATATATAT
1 TATATATAATTAAATATAT
13131 AATAATATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 12 0.39
20 7 0.23
21 12 0.39
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATATAATTAAATATAT
Found at i:13129 original size:40 final size:40
Alignment explanation
Indices: 13069--13145 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
13059 AACCGTTTAG
*
13069 TAATATATATAATTAAATATATTAT-ATATATAATAATATC
1 TAATATATATAATTAAATATATAATAATATAT-ATAATATC
*
13109 TAATATATATAATTATATATATAATAATATATATAAT
1 TAATATATATAATTAAATATATAATAATATATATAAT
13146 TATTAAACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 28 0.82
41 6 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (40 bp):
TAATATATATAATTAAATATATAATAATATATATAATATC
Found at i:13892 original size:2 final size:2
Alignment explanation
Indices: 13885--13913 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13875 TAATATGTAG
13885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13914 TTAGTGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16313 original size:135 final size:135
Alignment explanation
Indices: 16127--16535 Score: 737
Period size: 135 Copynumber: 3.0 Consensus size: 135
16117 TATTTTGAGT
16127 TAATGGTTTGGTTTTATAACTCTTTTAATTAAGTGTTAATTAATGGTTTGTAAAAAATTACTAAA
1 TAATGGTTTGGTTTTATAACTCTTTTAATTAAGTGTTAATTAATGGTTTGTAAAAAATTACTAAA
*
16192 ACGGGGCGATAAGGTCTCACCAGATTAAAAGTTGGAAGGACTGTTAAGTAATTTCACGTTGCTAC
66 ACGGGGTGATAAGGTCTCACCAGATTAAAAGTTGGAAGGACTGTTAAGTAATTTCACGTTGCTAC
16257 AAAAA
131 AAAAA
16262 TAATGGTTTGGTTTTATAACTCTTTTAATTAAGTGTTAATTAATGGTTTGTAAAAAATTACTAAA
1 TAATGGTTTGGTTTTATAACTCTTTTAATTAAGTGTTAATTAATGGTTTGTAAAAAATTACTAAA
*
16327 ACGGGGTGATAAGGTCTCACCAGATTAAAAGTTGGAATGACTGTTAAGTAATTTCACGTTGCTAC
66 ACGGGGTGATAAGGTCTCACCAGATTAAAAGTTGGAAGGACTGTTAAGTAATTTCACGTTGCTAC
16392 AAAAA
131 AAAAA
* *
16397 TAATGGTTTGATTCTATAACTCTTTTAATTAAGTGTTAATTAATGGTTTGTAAAAAATTACTAAA
1 TAATGGTTTGGTTTTATAACTCTTTTAATTAAGTGTTAATTAATGGTTTGTAAAAAATTACTAAA
* * * * *
16462 ACGGGTTGATAAGATCTCACTAGATTAAAAATTGGAAGGACTGTTAAGTAAGTTCACGTTGCTAC
66 ACGGGGTGATAAGGTCTCACCAGATTAAAAGTTGGAAGGACTGTTAAGTAATTTCACGTTGCTAC
16527 AAAAA
131 AAAAA
16532 TAAT
1 TAAT
16536 ATGTAGTATA
Statistics
Matches: 264, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 264 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (135 bp):
TAATGGTTTGGTTTTATAACTCTTTTAATTAAGTGTTAATTAATGGTTTGTAAAAAATTACTAAA
ACGGGGTGATAAGGTCTCACCAGATTAAAAGTTGGAAGGACTGTTAAGTAATTTCACGTTGCTAC
AAAAA
Found at i:16717 original size:2 final size:2
Alignment explanation
Indices: 16710--16734 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16700 AAACTACTAA
16710 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 A
16735 ACTTAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17322 original size:13 final size:12
Alignment explanation
Indices: 17286--17332 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
17276 TCAATCTTTA
*
17286 TATATATTGATAA
1 TATATATT-ATAT
*
17299 TA-ATGTTATAT
1 TATATATTATAT
17310 TATATTATTATAT
1 TATA-TATTATAT
17323 TATATATTAT
1 TATATATTAT
17333 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:17522 original size:16 final size:16
Alignment explanation
Indices: 17471--17558 Score: 65
Period size: 15 Copynumber: 5.6 Consensus size: 16
17461 CCGAACCCGA
17471 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
** * **
17487 ATTCGAAGCCG-ACTT
1 ACCCGAACCCGAAAAT
17502 AACCCGAACCCGAAAAT
1 -ACCCGAACCCGAAAAT
* * *
17519 ACCCAAATCC-AAAAA
1 ACCCGAACCCGAAAAT
17534 ACCCGAACCCG-AAAT
1 ACCCGAACCCGAAAAT
*
17549 ACCCTAACCC
1 ACCCGAACCC
17559 TAACAGTACT
Statistics
Matches: 52, Mismatches: 17, Indels: 7
0.68 0.22 0.09
Matches are distributed among these distances:
15 26 0.50
16 24 0.46
17 2 0.04
ACGTcount: A:0.42, C:0.38, G:0.10, T:0.10
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:18585 original size:181 final size:181
Alignment explanation
Indices: 18281--18644 Score: 719
Period size: 181 Copynumber: 2.0 Consensus size: 181
18271 TGCTTTCGTG
18281 ATTATTAAATCCGGTATGGTTATTAAAACCATGATGATTATAATTCTAACCACGACCAAATACTG
1 ATTATTAAATCCGGTATGGTTATTAAAACCATGATGATTATAATTCTAACCACGACCAAATACTG
18346 AGTTGGAAAAGTCAAATGCTTCATAGCGATAGATAATCTATAAGTGCAATTGAATCAAGAAAGAG
66 AGTTGGAAAAGTCAAATGCTTCATAGCGATAGATAATCTATAAGTGCAATTGAATCAAGAAAGAG
18411 AATGTACCTAACCTCGAAATTAACTACGACCAAACTAATTAAGGGAGACAA
131 AATGTACCTAACCTCGAAATTAACTACGACCAAACTAATTAAGGGAGACAA
18462 ATTATTAAATCCGGTATGGTTATTAAAACCATGATGATTATAATTCTAACCACGACCAAATACTG
1 ATTATTAAATCCGGTATGGTTATTAAAACCATGATGATTATAATTCTAACCACGACCAAATACTG
18527 AGTTGGAAAAGTCAAATGCTTCATAGCGATAGATAATCTATAAGTGCAATTGAATCAAGAAAGAG
66 AGTTGGAAAAGTCAAATGCTTCATAGCGATAGATAATCTATAAGTGCAATTGAATCAAGAAAGAG
*
18592 AATGTACCTAACCTCGAAATTAACTACGACCAATCTAATTAAGGGAGACAA
131 AATGTACCTAACCTCGAAATTAACTACGACCAAACTAATTAAGGGAGACAA
18643 AT
1 AT
18645 ATACCTATTT
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 182 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (181 bp):
ATTATTAAATCCGGTATGGTTATTAAAACCATGATGATTATAATTCTAACCACGACCAAATACTG
AGTTGGAAAAGTCAAATGCTTCATAGCGATAGATAATCTATAAGTGCAATTGAATCAAGAAAGAG
AATGTACCTAACCTCGAAATTAACTACGACCAAACTAATTAAGGGAGACAA
Found at i:19664 original size:17 final size:16
Alignment explanation
Indices: 19644--19709 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
19634 CGGGGTATTT
19644 TCGGGTTCGGGCTTGAA
1 TCGGGTTCGGG-TTGAA
19661 TCGGGTTCGGGTTGAA
1 TCGGGTTCGGGTTGAA
** *
19677 T-TTGTGTCAGGTT-AA
1 TCGGGT-TCGGGTTGAA
19692 TTCGGGTTCGGGTTGAA
1 -TCGGGTTCGGGTTGAA
19709 T
1 T
19710 TTGGGTCAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 4 0.10
16 20 0.51
17 15 0.38
ACGTcount: A:0.14, C:0.12, G:0.38, T:0.36
Consensus pattern (16 bp):
TCGGGTTCGGGTTGAA
Found at i:19699 original size:32 final size:32
Alignment explanation
Indices: 19661--19747 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
19651 CGGGCTTGAA
* * *
19661 TCGGGTTCGGGTTGAATTTGTGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGATCAAT
19693 TCGGGTTCGGGTTGAATTTGGGTCAGATCAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGATCAAT
* *
19725 TCGGGTTCGGGTTCAGTTTGGGT
1 TCGGGTTCGGGTTGAATTTGGGT
19748 TTTGGCCAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGATCAAT
Found at i:19715 original size:17 final size:17
Alignment explanation
Indices: 19643--19737 Score: 83
Period size: 17 Copynumber: 5.8 Consensus size: 17
19633 TCGGGGTATT
19643 TTCGGGTTCGGGCTTGAA
1 TTCGGGTTCGGG-TTGAA
19661 -TCGGGTTCGGGTTGAA
1 TTCGGGTTCGGGTTGAA
* * *
19677 TTTGTG-TCAGGTT-AA
1 TTCGGGTTCGGGTTGAA
19692 TTCGGGTTCGGGTTGAA
1 TTCGGGTTCGGGTTGAA
* * * *
19709 TTTGGG-TC-AGATCAA
1 TTCGGGTTCGGGTTGAA
19724 TTCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
19738 CAGTTTGGGT
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
15 15 0.25
16 21 0.36
17 23 0.39
ACGTcount: A:0.14, C:0.13, G:0.37, T:0.37
Consensus pattern (17 bp):
TTCGGGTTCGGGTTGAA
Found at i:19903 original size:16 final size:16
Alignment explanation
Indices: 19884--19944 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
19874 TTTTCATAAA
*
19884 TTTTCGGATTCAGGTT
1 TTTTCGGGTTCAGGTT
* *
19900 TTTTCGGGTT-TGAGCT
1 TTTTCGGGTTCAG-GTT
*
19916 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCAGGTT
19932 TTTTCGGGTTCAG
1 TTTTCGGGTTCAG
19945 ATTCAGGCGG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
15 1 0.03
16 35 0.95
17 1 0.03
ACGTcount: A:0.07, C:0.13, G:0.31, T:0.49
Consensus pattern (16 bp):
TTTTCGGGTTCAGGTT
Found at i:20264 original size:185 final size:186
Alignment explanation
Indices: 19946--20318 Score: 669
Period size: 185 Copynumber: 2.0 Consensus size: 186
19936 CGGGTTCAGA
* *
19946 TTCAGGCGGGTTCTGATAGTTGACTTTTTCTAGTCAATCGGGTTCGGGTTTTCGGGCGGGTTTTT
1 TTCAAGCGGGTTCTGATAGTTGACTTTTTCTAGTCAATCGGGTTCGGGTTTTCGGGCAGGTTTTT
*
20011 TTCAGGTCGGGTTCACTTTGCCACCTCTAGCTAGTAGTACCAAAAACGGAAAGTCATCAACATTC
66 TTCAGGTCGGGTTCACTTTGCCACATCTAGCTAGTAGTACCAAAAACGGAAAGTCATCAACATTC
*
20076 CGTGCAGTTATAATTCTAACAACAAAATAATTAGGTAAGTTGGTAAAGTCAAATGC
131 CGTGCAGTTATAATTCTAACAACAAAATAATTAGGTAAGTTAGTAAAGTCAAATGC
*
20132 TTCAAGCGGGTTCTGATAGTTGACTTTTTCTAGTCAATCGGGTTCGGGTTTTCGGGTAGG-TTTT
1 TTCAAGCGGGTTCTGATAGTTGACTTTTTCTAGTCAATCGGGTTCGGGTTTTCGGGCAGGTTTTT
*
20196 TTC-GGATCGGGTTCACTTTGTCACATCTAGCTAGTAGTACCAAAAACGGAAAGTCATCAACATT
66 TTCAGG-TCGGGTTCACTTTGCCACATCTAGCTAGTAGTACCAAAAACGGAAAGTCATCAACATT
20260 CCGTGCAGTTATAATTCTAACAACAAAATAATTAGGTAAGTTAGTAAAGTCAAATGC
130 CCGTGCAGTTATAATTCTAACAACAAAATAATTAGGTAAGTTAGTAAAGTCAAATGC
20317 TT
1 TT
20319 GGTAGAGATA
Statistics
Matches: 180, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
184 2 0.01
185 121 0.67
186 57 0.32
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (186 bp):
TTCAAGCGGGTTCTGATAGTTGACTTTTTCTAGTCAATCGGGTTCGGGTTTTCGGGCAGGTTTTT
TTCAGGTCGGGTTCACTTTGCCACATCTAGCTAGTAGTACCAAAAACGGAAAGTCATCAACATTC
CGTGCAGTTATAATTCTAACAACAAAATAATTAGGTAAGTTAGTAAAGTCAAATGC
Found at i:21284 original size:60 final size:59
Alignment explanation
Indices: 21164--21284 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 59
21154 GAGGTGGATT
* * * *
21164 TCTTTTACAACACATCATGACACTATGATTATTTCCCTATCAATAATTAATTATACAATA
1 TCTTTCACAACACACCATGACACTATGATAATTTCCCTATCAATAATTAA-TATAAAATA
*
21224 TCTTTCACAGCACACCATGACACTATGATAATTTCCCTATCAATAATTTCAA-ATAAAATA
1 TCTTTCACAACACACCATGACACTATGATAATTTCCCTATCAATAA-TT-AATATAAAATA
21284 T
1 T
21285 TCCTTAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 50 0.93
61 2 0.04
62 2 0.04
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (59 bp):
TCTTTCACAACACACCATGACACTATGATAATTTCCCTATCAATAATTAATATAAAATA
Found at i:21674 original size:22 final size:22
Alignment explanation
Indices: 21649--21809 Score: 106
Period size: 22 Copynumber: 7.4 Consensus size: 22
21639 TATATTTTCG
*
21649 TAACTACACTATGAAATTTTAA
1 TAACTACACTATGAAATTTTGA
* *
21671 TAACTAGCCCTATGAATTTTTTG-
1 TAACTA-CACTATGAA-ATTTTGA
21694 TAATCATAC-C-ATGAAATTTTGA
1 TAA-C-TACACTATGAAATTTTGA
* *
21716 TAACCACA-T-TGAAATTGTGA
1 TAACTACACTATGAAATTTTGA
**
21736 T-AC-ATCGTTATGAAATTTTGA
1 TAACTA-CACTATGAAATTTTGA
* * *
21757 TAACAACATTATGAAATTTCGA
1 TAACTACACTATGAAATTTTGA
21779 TAACCT-CA-TAATGAAATTTTGA
1 TAA-CTACACT-ATGAAATTTTGA
21801 TAACTACAC
1 TAACTACAC
21810 GGAGACAACA
Statistics
Matches: 111, Mismatches: 12, Indels: 31
0.72 0.08 0.20
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 14 0.13
21 20 0.18
22 51 0.46
23 14 0.13
24 6 0.05
25 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (22 bp):
TAACTACACTATGAAATTTTGA
Found at i:21758 original size:41 final size:44
Alignment explanation
Indices: 21704--21804 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
21694 TAATCATACC
* * *
21704 ATGAAATTTTGATAACCACA-T-TGAAATTGT-GAT-ACATCGTT
1 ATGAAATTTTGATAACAACATTATGAAATT-TCGATAACATCATA
*
21745 ATGAAATTTTGATAACAACATTATGAAATTTCGATAACCTCATA
1 ATGAAATTTTGATAACAACATTATGAAATTTCGATAACATCATA
21789 ATGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
21805 TACACGGAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
41 19 0.37
42 2 0.04
43 10 0.19
44 21 0.40
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (44 bp):
ATGAAATTTTGATAACAACATTATGAAATTTCGATAACATCATA
Found at i:23367 original size:27 final size:25
Alignment explanation
Indices: 23305--23370 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
23295 TATAGATAGG
*
23305 AATTAAAATTATATTTTAATAATGGA
1 AATTATAA-TATATTTTAATAATGGA
*
23331 AATT-TTATATATTTTAATAATGGCA
1 AATTATAATATATTTTAATAATGG-A
23356 TAATTATAATATATT
1 -AATTATAATATATT
23371 GGAAGTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 16 0.47
25 2 0.06
26 8 0.24
27 8 0.24
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
AATTATAATATATTTTAATAATGGA
Found at i:23374 original size:43 final size:43
Alignment explanation
Indices: 23327--23456 Score: 197
Period size: 43 Copynumber: 3.0 Consensus size: 43
23317 ATTTTAATAA
*
23327 TGGAAATTTTATATATTTTAATAATGGCATAATTATAATATAT
1 TGGAAATTTTATATATTTTAATAATGGCATAATTAAAATATAT
* * * *
23370 TGGAAGTTTTATAGATTTCAATAATGACATAATTAAAATATAT
1 TGGAAATTTTATATATTTTAATAATGGCATAATTAAAATATAT
* *
23413 TGGTAATTTTATATATTTTAGTAATGGCATAATTAAAATATAT
1 TGGAAATTTTATATATTTTAATAATGGCATAATTAAAATATAT
23456 T
1 T
23457 TTGATAATGA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (43 bp):
TGGAAATTTTATATATTTTAATAATGGCATAATTAAAATATAT
Found at i:23909 original size:16 final size:15
Alignment explanation
Indices: 23875--24014 Score: 102
Period size: 16 Copynumber: 8.8 Consensus size: 15
23865 AAAACTAAAC
***
23875 GACCCGAACCCGTCC
1 GACCCGAACCCGGAT
23890 GACCCGAGACCCGGAT
1 GACCCGA-ACCCGGAT
*
23906 GACCCGCAACCCAGAT
1 GACCCG-AACCCGGAT
*
23922 GACCCGAGACCCGAAT
1 GACCCGA-ACCCGGAT
*
23938 GACCCGTAACCCAGAT
1 GACCCG-AACCCGGAT
* *
23954 GACCCGAAACTCGAAT
1 GACCCG-AACCCGGAT
23970 GACCCGTAACCC-GAGT
1 GACCCG-AACCCGGA-T
**
23986 GACCCGAGACCCATAT
1 GACCCGA-ACCCGGAT
24002 GACCCGAAACCCG
1 GACCCG-AACCCG
24015 AATAACCCTA
Statistics
Matches: 100, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
15 10 0.10
16 86 0.86
17 4 0.04
ACGTcount: A:0.29, C:0.40, G:0.22, T:0.09
Consensus pattern (15 bp):
GACCCGAACCCGGAT
Found at i:23926 original size:32 final size:32
Alignment explanation
Indices: 23890--24013 Score: 171
Period size: 32 Copynumber: 3.9 Consensus size: 32
23880 GAACCCGTCC
* *
23890 GACCCGAGACCCGGATGACCCGCAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
23922 GACCCGAGACCCGAATGACCCGTAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
* *
23954 GACCCGAAACTCGAATGACCCGTAACCC-GAGT
1 GACCCGAGACCCGAATGACCCGTAACCCAGA-T
*
23986 GACCCGAGACCC-ATATGACCCGAAACCC
1 GACCCGAGACCCGA-ATGACCCGTAACCC
24014 GAATAACCCT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
31 3 0.04
32 80 0.96
ACGTcount: A:0.31, C:0.39, G:0.22, T:0.09
Consensus pattern (32 bp):
GACCCGAGACCCGAATGACCCGTAACCCAGAT
Found at i:23934 original size:48 final size:47
Alignment explanation
Indices: 23875--24022 Score: 165
Period size: 48 Copynumber: 3.1 Consensus size: 47
23865 AAAACTAAAC
*** * *
23875 GACCCGAACCCGTCCGACCCGAGACCCGGATGACCCGCAACCC-AGAT
1 GACCCGAACCCGAATGACCCGAGACCCAGATGACCCGAAACCCGA-AT
*
23922 GACCCGAGACCCGAATGACCCGTA-ACCCAGATGACCCGAAACTCGAAT
1 GACCCGA-ACCCGAATGACCCG-AGACCCAGATGACCCGAAACCCGAAT
* *
23970 GACCCGTAACCCGAGTGACCCGAGACCCATATGACCCGAAACCCGAAT
1 GACCCG-AACCCGAATGACCCGAGACCCAGATGACCCGAAACCCGAAT
*
24018 AACCC
1 GACCC
24023 TAGAAGTTAA
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
47 8 0.09
48 75 0.87
49 3 0.03
ACGTcount: A:0.30, C:0.40, G:0.21, T:0.09
Consensus pattern (47 bp):
GACCCGAACCCGAATGACCCGAGACCCAGATGACCCGAAACCCGAAT
Found at i:23958 original size:9 final size:8
Alignment explanation
Indices: 23890--24008 Score: 65
Period size: 9 Copynumber: 14.9 Consensus size: 8
23880 GAACCCGTCC
23890 GACCCGA-
1 GACCCGAT
23897 GACCCGGAT
1 GACCC-GAT
23906 GACCCGCA-
1 GACCCG-AT
23914 -ACCCAGAT
1 GACCC-GAT
23922 GACCCGA-
1 GACCCGAT
23929 GACCCGAAT
1 GACCCG-AT
23938 GACCCG-T
1 GACCCGAT
*
23945 AACCCAGAT
1 GACCC-GAT
23954 GACCCGA-
1 GACCCGAT
* *
23961 AACTCGAAT
1 GACCCG-AT
23970 GACCCG-T
1 GACCCGAT
*
23977 AACCCGAGT
1 GACCCGA-T
23986 GACCCGA-
1 GACCCGAT
*
23993 GACCCATAT
1 GACCC-GAT
24002 GACCCGA
1 GACCCGA
24009 AACCCGAATA
Statistics
Matches: 86, Mismatches: 10, Indels: 31
0.68 0.08 0.24
Matches are distributed among these distances:
7 36 0.42
8 13 0.15
9 37 0.43
ACGTcount: A:0.30, C:0.38, G:0.23, T:0.09
Consensus pattern (8 bp):
GACCCGAT
Found at i:24022 original size:16 final size:16
Alignment explanation
Indices: 23890--24022 Score: 128
Period size: 16 Copynumber: 8.3 Consensus size: 16
23880 GAACCCGTCC
* *
23890 GACCCGAGACCCGGAT
1 GACCCGAAACCCGAAT
*
23906 GACCCGCAACCC-AGAT
1 GACCCGAAACCCGA-AT
*
23922 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
*
23938 GACCCGTAACCC-AGAT
1 GACCCGAAACCCGA-AT
*
23954 GACCCGAAACTCGAAT
1 GACCCGAAACCCGAAT
* *
23970 GACCCGTAACCCGAGT
1 GACCCGAAACCCGAAT
*
23986 GACCCGAGACCC-ATAT
1 GACCCGAAACCCGA-AT
24002 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
*
24018 AACCC
1 GACCC
24023 TAGAAGTTAA
Statistics
Matches: 94, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.02
16 89 0.95
17 3 0.03
ACGTcount: A:0.32, C:0.38, G:0.21, T:0.09
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:24599 original size:42 final size:42
Alignment explanation
Indices: 24535--24616 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
24525 TGTTGACACA
* * *
24535 TACCCCACCTGATAATTAATTATGTGTTTAATATTCAAAACC
1 TACCCCACCTGATAATCAATTATGTATTTAATATGCAAAACC
*
24577 TACCTCACCTGATAATCAATTATGTATTTAATATGCAAAA
1 TACCCCACCTGATAATCAATTATGTATTTAATATGCAAAA
24617 TTAATATCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (42 bp):
TACCCCACCTGATAATCAATTATGTATTTAATATGCAAAACC
Found at i:24868 original size:23 final size:23
Alignment explanation
Indices: 24842--24893 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
24832 AACCCGCCCA
24842 ACCCGACACCCGAAACCCGTATG
1 ACCCGACACCCGAAACCCGTATG
* **
24865 ACCCGAGACCCGAAATTCGTATG
1 ACCCGACACCCGAAACCCGTATG
24888 ACCCGA
1 ACCCGA
24894 AACTCGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.38, G:0.19, T:0.12
Consensus pattern (23 bp):
ACCCGACACCCGAAACCCGTATG
Found at i:24890 original size:16 final size:16
Alignment explanation
Indices: 24871--24940 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
24861 TATGACCCGA
* *
24871 GACCCGAAATTCGTAT
1 GACCCGAAACTCGAAT
24887 GACCCGAAACTCGAAT
1 GACCCGAAACTCGAAT
* *
24903 AACCCG-AA-TCCAGAT
1 GACCCGAAACTCGA-AT
* *
24918 GACCCAAAACCCGAAT
1 GACCCGAAACTCGAAT
24934 GACCCGA
1 GACCCGA
24941 GAAAACTGTC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
14 3 0.07
15 8 0.19
16 29 0.69
17 2 0.05
ACGTcount: A:0.37, C:0.33, G:0.17, T:0.13
Consensus pattern (16 bp):
GACCCGAAACTCGAAT
Found at i:25921 original size:4 final size:4
Alignment explanation
Indices: 25912--25946 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
25902 ATTTTGACCT
25912 TTTA TTTA TTTA TTTA TTTA TTTA TTTA CTTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TT
25947 AAATTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:31400 original size:16 final size:16
Alignment explanation
Indices: 31350--31417 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 16
31340 AGACAGTTTC
*
31350 TTCGGGTTATTCGGGT
1 TTCGGGTCATTCGGGT
*
31366 TTCAGGTCA-TCTGGG-
1 TTCGGGTCATTC-GGGT
* *
31381 TTCGGGTTATTTGGGT
1 TTCGGGTCATTCGGGT
*
31397 TTCGGGTCATACGGGT
1 TTCGGGTCATTCGGGT
31413 TTCGG
1 TTCGG
31418 TCTCGATTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
15 12 0.29
16 29 0.71
ACGTcount: A:0.09, C:0.15, G:0.37, T:0.40
Consensus pattern (16 bp):
TTCGGGTCATTCGGGT
Found at i:31714 original size:42 final size:42
Alignment explanation
Indices: 31651--31732 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
31641 TAGATATTAA
* *
31651 TTTTGAATAATAAATATATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATAATAAATACATAATTAATTATCAGGTGAGGTAGG
* *
31693 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATAATAAATACATAATTAATTATCAGGTGAGGTA
31733 TGTGTCAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATAATAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:32581 original size:16 final size:15
Alignment explanation
Indices: 32562--32653 Score: 87
Period size: 16 Copynumber: 5.7 Consensus size: 15
32552 TCGGGTCACA
32562 GGTCACTTGGGTTACG
1 GGTCA-TTGGGTTACG
* *
32578 GGTCATTCGGGTTTCC
1 GGTCATT-GGGTTACG
32594 GGTCATCTGGGTTACG
1 GGTCAT-TGGGTTACG
32610 GGTCATTTGGGTCT-CG
1 GGTCA-TTGGGT-TACG
*
32626 GGTCATCTGGGTTGCG
1 GGTCAT-TGGGTTACG
32642 GGTCATTCGGGT
1 GGTCATT-GGGT
32654 CTCGGGTCGA
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
15 5 0.08
16 57 0.88
17 3 0.05
ACGTcount: A:0.09, C:0.20, G:0.38, T:0.34
Consensus pattern (15 bp):
GGTCATTGGGTTACG
Found at i:32660 original size:48 final size:47
Alignment explanation
Indices: 32548--32661 Score: 110
Period size: 48 Copynumber: 2.4 Consensus size: 47
32538 GGGTCATAAG
* * *
32548 GGTC-TCGGGTCACAGGTCACTTGGGTTACGGGTCATTCGGGTTTCC
1 GGTCATCGGGTCTCGGGTCACTTGGGTTACGGGTCATTCGGGTTGCC
* *
32594 GGTCATCTGGGT-TACGGGTCATTTGGGTCT-CGGGTCA-TCTGGGTTGCG
1 GGTCATC-GGGTCT-CGGGTCACTTGGGT-TACGGGTCATTC-GGGTTGCC
32642 GGTCATTCGGGTCTCGGGTC
1 GGTCA-TCGGGTCTCGGGTC
32662 GAGTGGGTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
46 4 0.07
47 4 0.07
48 44 0.79
49 4 0.07
ACGTcount: A:0.09, C:0.22, G:0.38, T:0.32
Consensus pattern (47 bp):
GGTCATCGGGTCTCGGGTCACTTGGGTTACGGGTCATTCGGGTTGCC
Found at i:32670 original size:32 final size:32
Alignment explanation
Indices: 32552--32661 Score: 150
Period size: 32 Copynumber: 3.4 Consensus size: 32
32542 CATAAGGGTC
* *
32552 TCGGGTCACAGGTCA-CTTGGGTTACGGGTCAT
1 TCGGGTCTCGGGTCATC-TGGGTTACGGGTCAT
* *
32584 TCGGGTTTCCGGTCATCTGGGTTACGGGTCAT
1 TCGGGTCTCGGGTCATCTGGGTTACGGGTCAT
* *
32616 TTGGGTCTCGGGTCATCTGGGTTGCGGGTCAT
1 TCGGGTCTCGGGTCATCTGGGTTACGGGTCAT
32648 TCGGGTCTCGGGTC
1 TCGGGTCTCGGGTC
32662 GAGTGGGTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 68 0.99
33 1 0.01
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.32
Consensus pattern (32 bp):
TCGGGTCTCGGGTCATCTGGGTTACGGGTCAT
Found at i:32717 original size:15 final size:16
Alignment explanation
Indices: 32697--32728 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
32687 TCTGGTCAAA
32697 TCGGGTT-GGGCGGGT
1 TCGGGTTCGGGCGGGT
32712 TCGGGTTCGGGCGGGT
1 TCGGGTTCGGGCGGGT
32728 T
1 T
32729 TTCGGATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.00, C:0.16, G:0.56, T:0.28
Consensus pattern (16 bp):
TCGGGTTCGGGCGGGT
Found at i:33648 original size:2 final size:2
Alignment explanation
Indices: 33641--33667 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33631 GACTTTATGT
33641 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
33668 TATGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35593 original size:23 final size:24
Alignment explanation
Indices: 35566--35614 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
35556 TTCTCTTCCT
35566 TTTAGTAC-TTTTGGG-TTCTGGGC
1 TTTAGTACATTTTGGGCTT-TGGGC
*
35589 TTTAGTCCATTTTGGGCTTTGGGC
1 TTTAGTACATTTTGGGCTTTGGGC
35613 TT
1 TT
35615 ATGCCTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 14 0.61
25 2 0.09
ACGTcount: A:0.08, C:0.14, G:0.29, T:0.49
Consensus pattern (24 bp):
TTTAGTACATTTTGGGCTTTGGGC
Done.