Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015016.1 Corchorus capsularis cultivar CVL-1 contig15037, 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: 58804
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:34 original size:2 final size:2
Alignment explanation
Indices: 27--66 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17 CTAAAACTAG
27 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67 ATGTCTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8472 original size:1 final size:1
Alignment explanation
Indices: 8466--8495 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
8456 CGCACAGCTG
*
8466 TTTTTTTTTTTTTTTTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8496 AAGGGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:21533 original size:20 final size:20
Alignment explanation
Indices: 21508--21549 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
21498 TTTTGATAAG
21508 TCAGATTTCTTCTTACAATT
1 TCAGATTTCTTCTTACAATT
*
21528 TCAGATTTTTTCTTACAATT
1 TCAGATTTCTTCTTACAATT
21548 TC
1 TC
21550 TAAAATCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (20 bp):
TCAGATTTCTTCTTACAATT
Found at i:27018 original size:20 final size:20
Alignment explanation
Indices: 26993--27030 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26983 CATGGCATGC
26993 CATGTCAACAATTATTGAGT
1 CATGTCAACAATTATTGAGT
* *
27013 CATGTCAATAATTTTTGA
1 CATGTCAACAATTATTGA
27031 CAGTTGAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
CATGTCAACAATTATTGAGT
Found at i:28848 original size:29 final size:31
Alignment explanation
Indices: 28816--28910 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 31
28806 GTTGAGGACG
*
28816 TTTGCCTCC-TAAACTT-CAAA-TCTGGACAT
1 TTTGCC-CCTTAAACTTCCAAATTCAGGACAT
*
28845 TTTGCCCCTTAAATTTCCAAATTCAGGACAT
1 TTTGCCCCTTAAACTTCCAAATTCAGGACAT
** * * **
28876 TTAACCTCTTTAACTTTCCAAATTCAAAACAT
1 TTTGCCCCTTAAAC-TTCCAAATTCAGGACAT
28908 TTT
1 TTT
28911 ACCCATGACA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 2 0.04
29 12 0.23
30 4 0.08
31 17 0.33
32 17 0.33
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (31 bp):
TTTGCCCCTTAAACTTCCAAATTCAGGACAT
Found at i:28877 original size:31 final size:32
Alignment explanation
Indices: 28839--28913 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
28829 CTTCAAATCT
*
28839 GGACATTTTGCC-CCTTAAATTTCCAAATTCA
1 GGACATTTTACCTCCTTAAATTTCCAAATTCA
* * *
28870 GGACATTTAACCTCTTTAACTTTCCAAATTCA
1 GGACATTTTACCTCCTTAAATTTCCAAATTCA
**
28902 AAACATTTTACC
1 GGACATTTTACC
28914 CATGACAGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 10 0.28
32 26 0.72
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (32 bp):
GGACATTTTACCTCCTTAAATTTCCAAATTCA
Found at i:31476 original size:8 final size:8
Alignment explanation
Indices: 31463--31487 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31453 TCTAAACTAA
31463 TGGTTTCT
1 TGGTTTCT
31471 TGGTTTCT
1 TGGTTTCT
31479 TGGTTTCT
1 TGGTTTCT
31487 T
1 T
31488 CAGATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.24, T:0.64
Consensus pattern (8 bp):
TGGTTTCT
Found at i:32516 original size:26 final size:26
Alignment explanation
Indices: 32471--32522 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
32461 TTTTTATTTG
*
32471 AGTTTGTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTGAGTCAGTTTCGAGTC
*
32496 AGTTTGTTTTTTAGTCAGTTTCGAGTC
1 AGTTTG-TTTTGAGTCAGTTTCGAGTC
32523 TAGTCTCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.13, C:0.10, G:0.27, T:0.50
Consensus pattern (26 bp):
AGTTTGTTTTGAGTCAGTTTCGAGTC
Found at i:35660 original size:4 final size:4
Alignment explanation
Indices: 35651--35682 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
35641 ATCACATCAC
35651 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
35683 TTTTTGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:39889 original size:2 final size:2
Alignment explanation
Indices: 39882--39916 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
39872 AAGCTATGAG
39882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39917 TTAGATNTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40563 original size:14 final size:14
Alignment explanation
Indices: 40517--40575 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
40507 TTACTATATC
40517 TATACTATACTATA
1 TATACTATACTATA
* *
40531 TATATATATAC-ACA
1 TATA-CTATACTATA
40545 CTATACTATACTATA
1 -TATACTATACTATA
40560 TATA-TACTACTATA
1 TATACTA-TACTATA
40574 TA
1 TA
40576 AAATCACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.05
14 24 0.65
15 11 0.30
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
TATACTATACTATA
Found at i:40571 original size:24 final size:23
Alignment explanation
Indices: 40511--40573 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
40501 CTTATCTTAC
*
40511 TATATCTA-TACTATACTATATA
1 TATATATACTACTATACTATATA
*
40533 TATATATACACACTATACTATACTA
1 TATATATAC-TACTATACTATA-TA
40558 TATATATACTACTATA
1 TATATATACTACTATA
40574 TAAAATCACC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.20
24 17 0.49
25 11 0.31
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (23 bp):
TATATATACTACTATACTATATA
Found at i:40879 original size:15 final size:16
Alignment explanation
Indices: 40854--40883 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40844 AATAATTATT
40854 TTTATATTATAATATA
1 TTTATATTATAATATA
40870 TTTA-ATTATAATAT
1 TTTATATTATAATAT
40884 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTATATTATAATATA
Found at i:41755 original size:331 final size:329
Alignment explanation
Indices: 41142--44557 Score: 2496
Period size: 331 Copynumber: 10.5 Consensus size: 329
41132 TATGAGTATT
* * *
41142 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACAATATTAAAAGCG
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAATATGAAAAACGATATTAGAAGCG
* * * * * *
41207 TGAAAAGCCCTTCAATTTTTTTGACGTTGAATTGTATATTTTTTATGAGTACTATGGCTAAAAAT
65 TGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCTAAAAAT
* * * *
41272 TGA-GAAAAATATTTCGGGTAAATTTTTGCAAAATATTAGCCGAAATC--GTATAA-CATCATGG
129 TGAGGAAAAATATTTCCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGG
* * * *** * * * *
41333 TTTTTTTTTTAGTTAAAATCTTGTTCC-GGGGCCCAAGG-TCGGTTTTACATGATTTTT-GTCGT
194 -----TTTTTGGCTAAAAACGCATTCCAGGGTCCC--GGCTCAGTTTTGCATGATTTTTGGT-GC
* * *
41395 CAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCCGCCACATTGGATTTAAGGATTTA
251 CAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTG
*
41460 TTTTTACGAGTATC
316 TTTTTACGAGCATC
* * *
41474 TAAATCTTATTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAGAAGCGT
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATATGAAAAACGATATTAGAAGCGT
* * * * * * *
41539 AAAAAACACTTCAATATTTTTTGCATTGAATTATATATTTGTTATGAGTATTTTAGCTAAAATTT
66 GAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTT-TTATGAGTATTTTAGCTAAAAATT
* * * *
41604 GAGGAAATATATTTCCGGTCAATTTTTACGAAATTTTAGTCGAAATCGTGTAATAACCATCACGG
130 GAGGAAAAATATTTCCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ATAACCATCACGG
* *
41669 TTTTTGGCTAATAAA-GCATTCCAGGG-CCTCGGATCAGTTTTGCATTATTTTTGGTGCCAAGAC
194 TTTTTGGCTAA-AAACGCATTCCAGGGTCC-CGGCTCAGTTTTGCATGATTTTTGGTGCCAAGAC
* * * * * * *
41732 TCCTTGAGATGTTTACT-TTCATCTAATCAAATTTCAACCACATTGCATTTAAGGATTTATTTTT
257 TCCTTGAAATATCTA-TATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTT
41796 ACGAGCATC
321 ACGAGCATC
* * * * *
41805 TAAATCTTATTTTGGATTTAATTAGAAATTAATTC-AGAAAAATATG-AAAACGATATGAAAAGC
1 TGAATCTT-GTTTCGATTTAATTAGAAATTAATTCGA-AAAAATATGAAAAACGATATTAGAAGC
* * * * * *
41868 GTGAAAAGTCCTCCAATCTTTTTGGTGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAA
64 GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCTAAAAA
* ** * * *
41933 TTGA-GACAAAATTTTTGTGGTCATTTTTTGCAAAAATTTTAGTCTAAATCGTGTATAACCATCA
128 TTGAGGA-AAAATATTTCCGGTCAATTTTTGC-AAAATTTTAGCCGAAATCGTGTATAACCATCA
** * * * * * * * * * *
41997 CGGTTTTTTACTAAAAACACAATT-CGGGGTCCTGACTTAGATTTGCATAATTTTTGGCGTCGAG
191 CGGTTTTTGGCTAAAAACGC-ATTCCAGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAG
* * * *
42061 ACTTCTTGAAATATCTACATTCATCAAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTT
255 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTT
42126 TACGAGCATC
320 TACGAGCATC
* * * *
42136 TGAATCTTGTTTCGATTTAATT-GTAAATTGAGTC-AGAAAAATATAAAAAACGATATTAAAAGC
1 TGAATCTTGTTTCGATTTAATTAG-AAATTAATTCGA-AAAAATATGAAAAACGATATTAGAAGC
** *
42199 GTGAAAAGTACTTCAATCTTTTTTGGAGTTG-A--ATA-A----TAT-A-TA-TTTAGAC-AAAA
64 GTGAAAAGCCCTTCAATC-TTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAG-CTAAAA
* * * * * *
42252 ATTGTGGGAAAATATTTCTGGTCAA-TTTTGCAAAATATTAGCCGAAATAGTGTACGTTAGTCAA
127 ATTGAGGAAAAATATTTCCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA---TA---AC
* * * * * * * *
42316 AATCACGGTTTTTGACTCAAAACGCGTTCCAGGGTCCCGGTTCAGTGTTGCATGATTGTTGGCGC
186 CATCACGGTTTTTGGCTAAAAACGCATTCCAGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTGC
** * * ** *
42381 CCCGACTCCTTTAAATATCTAAATTCATCTAATCAAATCTCAGTGACATTGGATTTAAGGATTTG
251 CAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTG
*** * *
42446 -TAAAACAAGCATT
316 TTTTTACGAGCATC
* * * * * *
42459 TGAATCATATTTCGATTTAATTAGAAATTAATTCAGAAAATAATAGGGAAAACAATATTAGAAGT
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAA-AATATGAAAAACGATATTAGAAGC
* * ** *
42524 ATGAAAAGCCCTTCAATATTTTTGGTATTTAATTATATAATTTTTATGAGTATTATT-GCTAAAA
64 GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTATGAGTATT-TTAGCTAAAA
* * * * *
42588 ATTGAGGAAATAA-CTTT-CGAATCAATTTTTGCAAAATTCTAGCCTAAATCGTGTAATAATCAT
127 ATTGAGGAAA-AATATTTCCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ATAACCAT
* * * * * * * *
42651 CATAGTTTTTTTTTTTTGCTAAAAACGCGTTGCAGGGTCCCGGCTAAGTTTTGTATGATTTTTTG
189 CA-CG-----GTTTTTGGCTAAAAACGCATTCCAGGGTCCCGGCTCAGTTTTGCATGATTTTTGG
* ** * * * * * *
42716 CGCCAAGACTTTTTGATATATCCATATTCATCTATTCAAAACTCAG---C--T--A-TAAAGAAT
248 TGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGAT
42773 TTGTTTTTACGAGCATC
313 TTGTTTTTACGAGCATC
*
42790 TGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAATATGAAAAAGGATATTAAGAA-C
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGA-AAAAATATGAAAAACGATATT-AGAAGC
* * * * *
42853 GTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATACTTTATGAGTATTTTTAGCTAAAA
64 GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTA-TTTTAGCTAAAA
* ** *
42918 ATTTGAAGG-AAAATTTTTTGGGT-TATTTTCTGCAAAATTTGT-GCCGAAATCGTGTATTAACC
127 A-TTG-AGGAAAAATATTTCCGGTCAATTTT-TGCAAAATTT-TAGCCGAAATCGTGTA-TAACC
* * ** * * * * **
42980 ATCACGGTTTTTAGCTAAAAATGCATT-TTGGGGCCATGGCTTAGTTTTGCATGATCTTTGGCAC
187 ATCACGGTTTTTGGCTAAAAACGCATTCCAGGGTCC-CGGCTCAGTTTTGCATGATTTTTGGTGC
* * * * * * *
43044 CGAGAATCCTTAAAATATCTATATTCATCAAATCAAATCTCAGTCACATTAAATTTAAGGATTTA
251 CAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTG
***
43109 TTTTTATTTGCATC
316 TTTTTACGAGCATC
* * * *
43123 TGAATCTTATTTCCATTTAATTAGAAATTAATTC-AGAAAAATATGAAAAACGATATTAAAAGCA
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGA-AAAAATATGAAAAACGATATTAGAAGCG
* ** * * ** ** *
43187 TCAAAAGTGCTCCTATCTTTTTGGCGTTGAATTATATATATTTTATGACCATTGAAGCTAAAATT
65 TGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCTAAAAAT
* *
43252 TGAGGAAAAATATTT-CGAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTG--T-ACCATCGCT
129 TGAGGAAAAATATTTCCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCAC-
* ** * * * ** *
43313 GTTTTTTGGCTAAAAACGTGTTTCAGGGTCCCGAG-TCAGTTTTTCATGATTTTTTGTGGAAAAA
192 GGTTTTTGGCTAAAAACGCATTCCAGGGTCCCG-GCTCAGTTTTGCATGATTTTTGGTGCCAAGA
*
43377 CTCCTTGAAATATC--TA-T-A--T--T--AATCT-A---A-A--AAATTTAAGGA-TT-TTTTT
256 CTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTT
*
43423 ACGAGCATT
321 ACGAGCATC
* * * * * *
43432 TGAATCATATTTCGATTTAATTAGAAATTAATTTGAAAAAAGAAAAAGAAAAACGATGTTAGAAG
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCG--AAAA-AATATGAAAAACGATATTAGAAG
* * *
43497 CGTGAGAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCTAAAA
63 CGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCTAAAA
* * * *
43562 ATTGA-GAAAAATATTT-CGCGTCAATTTTTACAAAATTTTAGCAG-AAT-TTGTGT-ACCATCA
127 ATTGAGGAAAAATATTTCCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCA
* * * *
43622 TGGTTTTTTGGCTAAAAACGCGTTCC-GGGACCCTGTG-TCAGTTTTGCATGATTTTTGGTGTCA
191 CGG-TTTTTGGCTAAAAACGCATTCCAGGGTCCC-G-GCTCAGTTTTGCATGATTTTTGGTGCCA
* * * *
43685 AGACTCCTTAAAATATATTTATATTCATCTAATCAAATCTCAGCCACATTGTATTTAAGAATTTG
253 AGACTCCTT-GAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTG
** *
43750 TTTTTACGAGTTTT
316 TTTTTACGAGCATC
* * * * * * * *
43764 TAAATCATGTTTCGATTTAATCAGAAACTATTTTGGAAATAAACTAGGAAAAACGATATTAGAAA
1 TGAATCTTGTTTCGATTTAATTAGAAATTA-ATTCGAAA-AAA-TATGAAAAACGATATTAGAAG
* * * * *
43829 CGTGAAAAAGGCTTTCAA-CTTTTTTGGCGTTGAATTATATATTTTTTACGAGTATTTTCGCTAG
63 CGTG-AAAAGCCCTTCAATC-TTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCTAA
* * * * * *
43893 AAATCAT-AAGAAGAATCTTTCGGGTCAATTTTTGTAAAATTTTA-CC-ATCA-CG-GT-T----
125 AAAT--TGAGGAAAAATATTTCCGGTCAATTTTTGCAAAATTTTAGCCGA-AATCGTGTATAACC
* ** * * * * * * * *
43948 -T-TC-G-CCTCGGCTAAAAACACGTTAC-GGGGCCCAGCTCAGTTTTGCATGATTTTTGATGGC
187 ATCACGGTTTTTGGCTAAAAACGCATTCCAGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTGCC
* * *
44008 AAGATTCCTTGAAATATCTATATTCATCTAACCAAAAATCTCAGCCACATTAAATTTAAGGATTT
252 AAGACTCCTTGAAATATCTATATTCATCTAATC--AAATCTCAGCCACATTGAATTTAAGGATTT
44073 GTTTTTACGAGCATC
315 GTTTTTACGAGCATC
* * ** * * **
44088 TAAATCTTGTCTCGATTTAATTAGAAATTAATTAAAAAAAAATCTGAAAAACAATATTAGAAATG
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATT-CGAAAAAATATGAAAAACGATATTAGAAGCG
* ** * * *
44153 TTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGTATTCTAGCAAAAAAT
65 TGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCTAAAAAT
* * * *
44218 TGAGGAAATATCTTT-CGAGTCAACTTTTGCAAGATTTTAG-C-----C--G-A-AA-C-T----
129 TGAGGAAAAATATTTCCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACG
* * * * * *
44266 GTTTTTGGCTAAAAACACGTTTCA-GGACCACGGCTCTGTTTTGCATGATATTTGGTGCCGAA-A
193 GTTTTTGGCTAAAAACGCATTCCAGGGTCC-CGGCTCAGTTTTGCATGATTTTTGGTGCC-AAGA
* * *
44329 CTCCTTAAAATATCTTTATTCATCTAATCAAAT-TCCAGTCACATTGAATTTAAGGATTTGTTTT
256 CTCCTTGAAATATCTATATTCATCTAATCAAATCT-CAGCCACATTGAATTTAAGGATTTGTTTT
* *
44393 TATGTGCATC
320 TACGAGCATC
* * * *
44403 TGAATCTTGTTTCGATTTAATTAAAAATTAAATC-AAAAAATATGAAAAACAATATTAAAAGCGT
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATATGAAAAACGATATTAGAAGCGT
* * * *
44467 GAAAAGTCCTCCAATCTTTTTTGCGTTGAATTATATATATTTTATGAGTATTTTTA-CCAAAAAT
66 GAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTA-TTTTAGCTAAAAAT
* *
44531 TGGGGAAAAATATTTCGGGTC-ATTTTT
129 TGAGGAAAAATATTTCCGGTCAATTTTT
44558 ACCATTATGG
Statistics
Matches: 2472, Mismatches: 459, Indels: 326
0.76 0.14 0.10
Matches are distributed among these distances:
309 43 0.02
310 12 0.00
311 108 0.04
312 82 0.03
313 95 0.04
314 7 0.00
315 72 0.03
316 23 0.01
317 53 0.02
318 26 0.01
319 9 0.00
320 57 0.02
321 58 0.02
322 40 0.02
323 53 0.02
324 224 0.09
325 129 0.05
326 2 0.00
327 12 0.00
328 55 0.02
329 71 0.03
330 89 0.04
331 549 0.22
332 237 0.10
333 180 0.07
334 7 0.00
335 41 0.02
336 29 0.01
337 28 0.01
338 81 0.03
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (329 bp):
TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATATGAAAAACGATATTAGAAGCGT
GAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCTAAAAATTG
AGGAAAAATATTTCCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGGTT
TTTGGCTAAAAACGCATTCCAGGGTCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCT
TGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAG
CATC
Found at i:43102 original size:987 final size:981
Alignment explanation
Indices: 41398--43229 Score: 2306
Period size: 987 Copynumber: 1.9 Consensus size: 981
41388 TTGTCGTCAA
* * * *
41398 GACTCCTTGAAATATCTATATTCATCTAATCAAATCTCCGCCACATTGGATTTAAGGATTTATTT
1 GACTCCTTGAAATATCTAAATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTAGTA
** * * * *
41463 TTACGAGTATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGAT
66 AAACAAGCATCTAAATCATATTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACAAT
* *
41528 ATTAGAAGCGTAAAAAACACTTCAATATTTTTTGCATTGAATTATATATTTGTTATGAGTATTTT
131 ATTAGAAGCATAAAAAACACTTCAATATTTTTGGCATTGAATTATATATTTGTTATGAGTATTTT
* * * * *
41593 AGCTAAAATTTGAGGAAATATATTTCCGGTCAATTTTTACGAAATTTTAGTCGAAATCGTGTAAT
196 AGCTAAAAATTGAGGAAATATATTTCCGATCAATTTTTACAAAATTCTAGCCGAAATCGTGTAAT
* * *
41658 AACCATCACGGTTTTTGGCTAATAAAGCATTCCAGGGCCTCGGATCAGTTTTGCATTATTTTTGG
261 AACCATCAAGGTTTTTGGCTAATAAAGCATTCCAGGGCCTCGGATAAGTTTTGCATGATTTTTGG
* * ** * *
41723 TGCCAAGACTCCTTGAGATGTTTACTTTCATCTAATCAAATTTCAACCACATTGCATTTAAGGAT
326 CGCCAAGACTCCTTGAGATATCCACTTTCATCTAATCAAA--T-AACCACA-TGCATTAAAGAAT
* *
41788 TTATTTTTACGAGCATCTAAATCTTATTTTGGATTTAATTAGAAATTAATTCAGAAAAATATGAA
387 TTATTTTTACGAGCATCTAAATCTTAGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAA
* *
41853 AACGATATGAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTAAATTATATATATTTCATGAG
452 AACGATATGAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATTTCATGAG
* * *
41918 TATTTTAGCCAAAAATTGAGACAAAATTTTTGTGGTCATTTTTTGCAAAAATTTTAGTCTAAATC
517 TATTTTAGCCAAAAATTGAGACAAAATTTTTGTGGTCATTTTCTGCAAAAATTTTAGCCGAAATC
41983 GTGTATAACCATCACGGTTTTTTACTAAAAACACAATTCGGGGTCCTGACTTAGATTTGCATAAT
582 GTGTATAACCATCACGGTTTTTTACTAAAAACACAATTCGGGGTCCTGACTTAGATTTGCATAAT
* ** * * * **
42048 TTTTGGCGTCGAGACTTCTTGAAATATCTACATTCATCAAATCAAATCTCAGCCACATTGCATTT
647 CTTTGGCACCGAGAATCCTTAAAATATCTACATTCATCAAATCAAATCTCAGCCACATTAAATTT
* * * *
42113 AAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT-GTAAATTGAGTCAGAAAAA
712 AAGGATTTATTTTTACGAGCATCTGAATCTTATTTCCATTTAATTAG-AAATTAAGTCAGAAAAA
* * *
42177 TATAAAAAACGATATTAAAAGCGTGAAAAGTACTTCAATCTTTTTTGGAGTTGAATAATATATAT
776 TATAAAAAACGATATTAAAAGCATCAAAAGTACTCCAATC-TTTTTGGAGTTGAATAATATATAT
42242 TTAGACAAAAATTGTGGGAAAATATTTCTGGTCAATTTTGCAAAATATTAGCCGAAATAGTGTAC
840 TTAGACAAAAATTGTGGGAAAATATTTCTGGTCAATTTTGCAAAATATTAGCCGAAATAGTGTAC
42307 GTTAGTCAAAATCACGGTTTTTGACTCAAAACGCGTTCCAGGGTCCCGGTTCAGTGTTGCATGAT
905 GTTAGTCAAAATCACGGTTTTTGACTCAAAACGCGTTCCAGGGTCCCGGTTCAGTGTTGCATGAT
42372 TGTTGGCGCCCC
970 TGTTGGCGCCCC
* **
42384 GACTCCTTTAAATATCTAAATTCATCTAATCAAATCTCAGTGACATTGGATTTAAGGATTT-GTA
1 GACTCCTTGAAATATCTAAATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTAGTA
* * *
42448 AAACAAGCATTTGAATCATATTTCGATTTAATTAGAAATTAATTCAGAAAATAATAGGGAAAACA
66 AAACAAGCATCTAAATCATATTTCGATTTAATTAGAAATTAATTC-GAAAA-AATAGGAAAAACA
* * * * * *
42513 ATATTAGAAGTATGAAAAGCCCTTCAATATTTTTGGTATTTAATTATATAATTT-TTATGAGTAT
129 ATATTAGAAGCATAAAAAACACTTCAATATTTTTGGCATTGAATTATAT-ATTTGTTATGAGTAT
* *
42577 TATT-GCTAAAAATTGAGGAAATA-ACTTT-CGAATCAATTTTTGCAAAATTCTAGCCTAAATCG
193 T-TTAGCTAAAAATTGAGGAAATATA-TTTCCG-ATCAATTTTTACAAAATTCTAGCCGAAATCG
* * * * * *
42639 TGTAATAATCATCATAGTTTTTTTTTTTTGCTAA-AAACGCGTTGCAGGGTCC-CGGCTAAGTTT
255 TGTAATAACCATCA-AG-----GTTTTTGGCTAATAAA-GCATTCCAGGG-CCTCGGATAAGTTT
* * ** * * *
42702 TGTATGATTTTTTGCGCCAAGACTTTTTGATATATCCA-TATTCATCTATTC-AA-AA-CTCA-G
312 TGCATGATTTTTGGCGCCAAGACTCCTTGAGATATCCACT-TTCATCTAATCAAATAACCACATG
* *
42762 C-TATAAAGAATTTGTTTTTACGAGCATCTGAATCTT-GTTTCGATTTAATTAGAAATTAATTCA
376 CAT-TAAAGAATTTATTTTTACGAGCATCTAAATCTTAGTTTCGATTTAATTAGAAATTAATTCA
* *
42825 GAAAAATATGAAAAAGGATATTAAGAA-CGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTAT
440 GAAAAATATG-AAAACGATATGAA-AAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTAT
* * *
42889 ATATACTTT-ATGAGTATTTTTAGCTAAAAATTTGA-AGGAAAATTTTT-TGGGTTATTTTCTGC
503 ATATA-TTTCATGAGTA-TTTTAGCCAAAAA-TTGAGA-CAAAATTTTTGT-GGTCATTTTCTGC
** * *
42951 -AAAATTTGT-GCCGAAATCGTGTATTAACCATCACGG-TTTTTAGCTAAAAATGCATTTTGGGG
563 AAAAATTT-TAGCCGAAATCGTGTA-TAACCATCACGGTTTTTTA-CTAAAAACACAATTCGGGG
* * * *
43013 -CCATGGCTTAGTTTTGCATGATCTTTGGCACCGAGAATCCTTAAAATATCTATATTCATCAAAT
625 TCC-TGACTTAGATTTGCATAATCTTTGGCACCGAGAATCCTTAAAATATCTACATTCATCAAAT
* ***
43077 CAAATCTCAGTCACATTAAATTTAAGGATTTATTTTTATTTGCATCTGAATCTTATTTCCATTTA
689 CAAATCTCAGCCACATTAAATTTAAGGATTTATTTTTACGAGCATCTGAATCTTATTTCCATTTA
* * * *
43142 ATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCATCAAAAGTGCTCCTATCTTT
754 ATTAGAAATTAAGTCAGAAAAATATAAAAAACGATATTAAAAGCATCAAAAGTACTCCAATCTTT
* *
43207 TTGGCGTTGAATTATATATATTT
819 TTGGAGTTGAATAATATATATTT
43230 TATGACCATT
Statistics
Matches: 718, Mismatches: 100, Indels: 56
0.82 0.11 0.06
Matches are distributed among these distances:
984 36 0.05
985 128 0.18
986 134 0.19
987 336 0.47
988 10 0.01
992 6 0.01
993 66 0.09
994 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (981 bp):
GACTCCTTGAAATATCTAAATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTAGTA
AAACAAGCATCTAAATCATATTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACAAT
ATTAGAAGCATAAAAAACACTTCAATATTTTTGGCATTGAATTATATATTTGTTATGAGTATTTT
AGCTAAAAATTGAGGAAATATATTTCCGATCAATTTTTACAAAATTCTAGCCGAAATCGTGTAAT
AACCATCAAGGTTTTTGGCTAATAAAGCATTCCAGGGCCTCGGATAAGTTTTGCATGATTTTTGG
CGCCAAGACTCCTTGAGATATCCACTTTCATCTAATCAAATAACCACATGCATTAAAGAATTTAT
TTTTACGAGCATCTAAATCTTAGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAACG
ATATGAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCGTTAAATTATATATATTTCATGAGTATT
TTAGCCAAAAATTGAGACAAAATTTTTGTGGTCATTTTCTGCAAAAATTTTAGCCGAAATCGTGT
ATAACCATCACGGTTTTTTACTAAAAACACAATTCGGGGTCCTGACTTAGATTTGCATAATCTTT
GGCACCGAGAATCCTTAAAATATCTACATTCATCAAATCAAATCTCAGCCACATTAAATTTAAGG
ATTTATTTTTACGAGCATCTGAATCTTATTTCCATTTAATTAGAAATTAAGTCAGAAAAATATAA
AAAACGATATTAAAAGCATCAAAAGTACTCCAATCTTTTTGGAGTTGAATAATATATATTTAGAC
AAAAATTGTGGGAAAATATTTCTGGTCAATTTTGCAAAATATTAGCCGAAATAGTGTACGTTAGT
CAAAATCACGGTTTTTGACTCAAAACGCGTTCCAGGGTCCCGGTTCAGTGTTGCATGATTGTTGG
CGCCCC
Found at i:47629 original size:32 final size:33
Alignment explanation
Indices: 47593--47661 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
47583 GCTCTTACAC
* *
47593 ACAATGAAGTT-GCGGGCCTTCATTACGCCGTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
*
47625 ACAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
47658 ACAA
1 ACAA
47662 GTTGAGCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 11 0.33
33 22 0.67
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (33 bp):
ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
Found at i:48891 original size:24 final size:24
Alignment explanation
Indices: 48859--48904 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
48849 GTAGGCTCGC
48859 CGAGCCTAATCGAGTCCCCTCTGA
1 CGAGCCTAATCGAGTCCCCTCTGA
* *
48883 CGAGTCTAATCGAGTCTCCTCT
1 CGAGCCTAATCGAGTCCCCTCT
48905 AATATTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.26
Consensus pattern (24 bp):
CGAGCCTAATCGAGTCCCCTCTGA
Found at i:53276 original size:15 final size:16
Alignment explanation
Indices: 53256--53286 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53246 TCTGCTTTTA
53256 TAATTT-AATTGCTTT
1 TAATTTAAATTGCTTT
53271 TAATTTAAATTGCTTT
1 TAATTTAAATTGCTTT
53287 GATCACTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TAATTTAAATTGCTTT
Found at i:57912 original size:126 final size:126
Alignment explanation
Indices: 57687--58150 Score: 578
Period size: 126 Copynumber: 3.7 Consensus size: 126
57677 ATATATATAT
* * *
57687 TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTTGACGTATTCCGATA
1 TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACATATTCCGACA
*
57752 TTTGTAAGTGTCGGTATAGATATTATATCGTGACATTTTCTAAACATCGCTAAAAAAATAC
66 TTTGTAAGCGTCGGTATAGATATTATATCGTGACATTTTCTAAACATCGCTAAAAAAATAC
* * ** **
57813 TATACCGACGTTTGCAAATGTCGGAATAAGTTTTTCACATCATTTGATTTCGTTATATTTTGACA
1 TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACATATTCCGACA
* * * * *
57878 TTTGTAAGTGTCGATATAGATATTGTATCGTGACATTTGCTAAACATCGTTAAAAAAATAC
66 TTTGTAAGCGTCGGTATAGATATTATATCGTGACATTTTCTAAACATCGCTAAAAAAATAC
* * * * *
57939 TATACCGACGTTTGCAAATGTCGGAATAAG-TTTTCACATCATTTGATTTCGACGTATTTCGATA
1 TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACATATTCCGACA
* * ** *
58003 -TTGTAAGCGTTGGTATAGATATTATATTGTGACATTTAT-TAAATGTCGCT-AAAAAATAA
66 TTTGTAAGCGTCGGTATAGATATTATATCGTGACATTT-TCTAAACATCGCTAAAAAAATAC
** * ** **
58062 TATACCGACGTTTACAAATGTCATAACAA-TTTCTTCACATCATTTGTTTTTTATGTATTCCGAC
1 TATACCGACGTTTACAAATGTCGGAACAAGTTT-TTCACATCATTTGATTTCGACATATTCCGAC
*
58126 ATTTGTAAGCGTTGGTATAGATATT
65 ATTTGTAAGCGTCGGTATAGATATT
58151 CGTGACATTT
Statistics
Matches: 296, Mismatches: 38, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
123 35 0.12
124 66 0.22
125 52 0.18
126 143 0.48
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (126 bp):
TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACATATTCCGACA
TTTGTAAGCGTCGGTATAGATATTATATCGTGACATTTTCTAAACATCGCTAAAAAAATAC
Found at i:58129 original size:249 final size:252
Alignment explanation
Indices: 57687--58150 Score: 663
Period size: 249 Copynumber: 1.9 Consensus size: 252
57677 ATATATATAT
*
57687 TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTTGACGTATTCCGATA
1 TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGATA
* *
57752 TTTGTAAGTGTCGGTATAGATATTATATCGTGACATTTTCTAAACATCGCTAAAAAAATACTATA
66 TTTGTAAGCGTCGGTATAGATATTATATCGTGACATTTTCTAAACATCGCTAAAAAAATAATATA
* * * **
57817 CCGACGTTTGCAAATGTCGGAATAAGTTTTTCACATCATTTGATTTCGTTATATTTTGACATTTG
131 CCGACGTTTACAAATGTCAGAACAAGTTTTTCACATCATTTGATTTCGTTATATTCCGACATTTG
*
57882 TAAGTGTCGATATAGATATTGTATCGTGACATTTGCTAAACATCGTTAAAAAAATAC
196 TAAGCGTCGATATAGATATTGTATCGTGACATTTGCTAAACATCGTTAAAAAAATAC
* * *
57939 TATACCGACGTTTGCAAATGTCGGAATAAG-TTTTCACATCATTTGATTTCGACGTATTTCGATA
1 TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGATA
* * **
58003 -TTGTAAGCGTTGGTATAGATATTATATTGTGACATTTAT-TAAATGTCGCT-AAAAAATAATAT
66 TTTGTAAGCGTCGGTATAGATATTATATCGTGACATTT-TCTAAACATCGCTAAAAAAATAATAT
* *
58065 ACCGACGTTTACAAATGTCATAACAA-TTTCTTCACATCATTTG-TTT-TTTATGTATTCCGACA
130 ACCGACGTTTACAAATGTCAGAACAAGTTT-TTCACATCATTTGATTTCGTTA--TATTCCGACA
* *
58127 TTTGTAAGCGTTGGTATAGATATT
192 TTTGTAAGCGTCGATATAGATATT
58151 CGTGACATTT
Statistics
Matches: 188, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
247 3 0.02
248 6 0.03
249 75 0.40
250 43 0.23
251 33 0.18
252 28 0.15
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (252 bp):
TATACCGACGTTTACAAATGTCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGATA
TTTGTAAGCGTCGGTATAGATATTATATCGTGACATTTTCTAAACATCGCTAAAAAAATAATATA
CCGACGTTTACAAATGTCAGAACAAGTTTTTCACATCATTTGATTTCGTTATATTCCGACATTTG
TAAGCGTCGATATAGATATTGTATCGTGACATTTGCTAAACATCGTTAAAAAAATAC
Done.