Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010891.1 Corchorus capsularis cultivar CVL-1 contig10912, 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: 107657
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:423 original size:2 final size:2
Alignment explanation
Indices: 418--466 Score: 73
Period size: 2 Copynumber: 24.0 Consensus size: 2
408 ATATGCCATA
418 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT ACT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
461 AT AT AT
1 AT AT AT
467 TATTTTTGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.02
2 39 0.89
3 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:442 original size:15 final size:15
Alignment explanation
Indices: 418--466 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
408 ATATGCCATA
418 ATAT-ATATATATAT
1 ATATAATATATATAT
432 ATATAATATATATAT
1 ATATAATATATATAT
*
447 ATATACTATATACTAT
1 ATATAATATATA-TAT
463 ATAT
1 ATAT
467 TATTTTTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 4 0.12
15 21 0.66
16 7 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAATATATATAT
Found at i:770 original size:15 final size:14
Alignment explanation
Indices: 732--761 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
722 TCATTTTCCC
732 TTTTT-AGTCCATT
1 TTTTTCAGTCCATT
745 TTTTTCAGTCCATT
1 TTTTTCAGTCCATT
759 TTT
1 TTT
762 GTTGGGTCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTTCAGTCCATT
Found at i:2836 original size:11 final size:12
Alignment explanation
Indices: 2816--2859 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
2806 TTGACAACGC
2816 AACA-AAAACAA
1 AACAGAAAACAA
2827 AAC-GAAAACAA
1 AACAGAAAACAA
*
2838 AACAGAAATAAAA
1 AACAGAAA-ACAA
2851 AACAGAAAA
1 AACAGAAAA
2860 ACGAAAACGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 13 0.45
12 5 0.17
13 11 0.38
ACGTcount: A:0.77, C:0.14, G:0.07, T:0.02
Consensus pattern (12 bp):
AACAGAAAACAA
Found at i:6243 original size:31 final size:31
Alignment explanation
Indices: 6082--6244 Score: 137
Period size: 31 Copynumber: 5.3 Consensus size: 31
6072 TGGCATGCAT
* * *
6082 GCCACGTGGATCAAAAAGTAACACGTGGCAC
1 GCCACGTGTACCAAAAAGTGACACGTGGCAC
* * * * * * *
6113 ACCACGTGGATCAAAAAGTGATATGTTGCAT
1 GCCACGTGTACCAAAAAGTGACACGTGGCAC
* * * *
6144 GTCATGTGTGCCAAAAAGTGACACGTGACAC
1 GCCACGTGTACCAAAAAGTGACACGTGGCAC
* * * *
6175 GTCACATGTACCAAAAAGTGATACGTGACAC
1 GCCACGTGTACCAAAAAGTGACACGTGGCAC
** *
6206 ATCACGTGTACCAAAAAGTGACACGTGGCAT
1 GCCACGTGTACCAAAAAGTGACACGTGGCAC
6237 GCCACGTG
1 GCCACGTG
6245 CACTAAAGGA
Statistics
Matches: 104, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGTGACACGTGGCAC
Found at i:11961 original size:64 final size:64
Alignment explanation
Indices: 11882--12009 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
11872 TTTCTATTGA
11882 ACTTTGAAGAATGAATTTAAAATTAAAGTAGCAATGACATTTTTCTTGTTTACAAAATGGTCAC
1 ACTTTGAAGAATGAATTTAAAATTAAAGTAGCAATGACATTTTTCTTGTTTACAAAATGGTCAC
11946 ACTTTGAAGAATGAATTTAAAATTAAAGTAGCAATGACATTTTTCTTGTTTACAAAATGGTCAC
1 ACTTTGAAGAATGAATTTAAAATTAAAGTAGCAATGACATTTTTCTTGTTTACAAAATGGTCAC
12010 TGAAAGAGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (64 bp):
ACTTTGAAGAATGAATTTAAAATTAAAGTAGCAATGACATTTTTCTTGTTTACAAAATGGTCAC
Found at i:14443 original size:17 final size:17
Alignment explanation
Indices: 14421--14454 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
14411 GTAAGCAATA
14421 TTCCATCAGTATCATTT
1 TTCCATCAGTATCATTT
*
14438 TTCCATCAGTATTATTT
1 TTCCATCAGTATCATTT
14455 GCTAGGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.50
Consensus pattern (17 bp):
TTCCATCAGTATCATTT
Found at i:15035 original size:2 final size:2
Alignment explanation
Indices: 15028--15058 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15018 TAAGTTCTTA
15028 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
15059 GTTTATACTT
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:15977 original size:14 final size:14
Alignment explanation
Indices: 15958--15990 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
15948 CCTAGCCGCT
15958 CCTCTCCCCTTCTC
1 CCTCTCCCCTTCTC
15972 CCTCTCCCCTTCTC
1 CCTCTCCCCTTCTC
*
15986 TCTCT
1 CCTCT
15991 TTAGTTCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (14 bp):
CCTCTCCCCTTCTC
Found at i:16158 original size:26 final size:26
Alignment explanation
Indices: 16119--16169 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
16109 TTTATTTGAG
*
16119 GTTTTTTTTTAGTCGGTTT-GAGTCA
1 GTTTTTTTTTAGTCAGTTTCGAGTCA
16144 GTTTGTTTTTTAGTCAGTTTCGAGTC
1 GTTT-TTTTTTAGTCAGTTTCGAGTC
16170 TAGTCTCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 14 0.61
27 5 0.22
ACGTcount: A:0.12, C:0.10, G:0.24, T:0.55
Consensus pattern (26 bp):
GTTTTTTTTTAGTCAGTTTCGAGTCA
Found at i:16635 original size:31 final size:31
Alignment explanation
Indices: 16600--16665 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
16590 AATTTTATGT
* *
16600 TTTCCGATTGTA-CCTTTATTTTTAAAACATA
1 TTTCCAATTGTACCCCTT-TTTTTAAAACATA
16631 TTTCCAATTGTACCCCTTTTTTTAAAACATA
1 TTTCCAATTGTACCCCTTTTTTTAAAACATA
16662 TTTC
1 TTTC
16666 TTAATTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCCTTTTTTTAAAACATA
Found at i:16962 original size:22 final size:23
Alignment explanation
Indices: 16934--16991 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
16924 TGTTTCTATG
*
16934 TGGTTATCAAAATTTTAT-AAGA
1 TGGTTATCAAAATTTCATGAAGA
* * *
16956 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCATGAAGA
16979 -GGTTATCAAAATT
1 TGGTTATCAAAATT
16992 CCATAGTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.41
Consensus pattern (23 bp):
TGGTTATCAAAATTTCATGAAGA
Found at i:17004 original size:22 final size:22
Alignment explanation
Indices: 16979--17107 Score: 177
Period size: 22 Copynumber: 5.9 Consensus size: 22
16969 TTCATGAGGA
*
16979 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTCCATAGTGT
*
17001 GGTTACCAAAATTCTATAGTGT
1 GGTTACCAAAATTCCATAGTGT
*
17023 GGTTAGCAAAATTCCATAGTGT
1 GGTTACCAAAATTCCATAGTGT
*
17045 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTCCATAGTGT
* * * *
17067 AGTTACTAAAATTTCATAGAGT
1 GGTTACCAAAATTCCATAGTGT
*
17089 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTCCATAG
17108 GATCATGTTA
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 96 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (22 bp):
GGTTACCAAAATTCCATAGTGT
Found at i:17329 original size:22 final size:22
Alignment explanation
Indices: 17238--17523 Score: 78
Period size: 22 Copynumber: 12.8 Consensus size: 22
17228 TTTATAGTGT
*
17238 GGTTAACAAAATTTCAT-TAGAA
1 GGTTATCAAAATTTCATAT-GAA
* * *
17260 GGTTA-CTAATACTTCAT-CGAGA
1 GGTTATC-AAAATTTCATATGA-A
* **
17282 GGTTATCAAAATTTGAT-TGTGT
1 GGTTATCAAAATTTCATATG-AA
17304 GGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATATGAA
*
17326 GGTTAT-AAAAGTCTCAATTTCAT-AA
1 GGTTATCAAAA-TTTC-A--T-ATGAA
* * * *
17351 GGAGTACCCAAATTTGATA-GAA
1 GG-TTATCAAAATTTCATATGAA
*
17373 GGTTATC-AAATCTCATA-G-A
1 GGTTATCAAAATTTCATATGAA
*
17392 GTGATTATCAAAATTTCATAAAGATA
1 G-G-TTATCAAAATTTCAT-ATGA-A
*
17418 GGATTATCAAAATTT-ATATAAA
1 GG-TTATCAAAATTTCATATGAA
** *
17440 AATTATCAAAATTTCATAGTG-T
1 GGTTATCAAAATTTCATA-TGAA
* * * * *
17462 TGTTATGAAAATTACA-AAGCGA
1 GGTTATCAAAATTTCATATG-AA
* *
17484 GGTTATCAAAATTGCATAATG-T
1 GGTTATCAAAATTTCAT-ATGAA
*
17506 GATTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
17524 AAGGGGTCAA
Statistics
Matches: 196, Mismatches: 42, Indels: 53
0.67 0.14 0.18
Matches are distributed among these distances:
19 2 0.01
20 11 0.06
21 29 0.15
22 109 0.56
23 9 0.05
24 5 0.03
25 20 0.10
26 8 0.04
27 3 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATGAA
Found at i:17524 original size:22 final size:22
Alignment explanation
Indices: 17375--17611 Score: 127
Period size: 22 Copynumber: 10.7 Consensus size: 22
17365 TGATAGAAGG
* *
17375 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAAAGTGA
17396 TTATCAAAATTTCATAAAGATAGGA
1 TTATCAAAATTTCATAAAG-T--GA
**
17421 TTATCAAAATTT-ATATAA-AAA
1 TTATCAAAATTTCATA-AAGTGA
**
17442 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAAAG-TGA
* * *
17464 TTATGAAAA-TT-ACAAAGCGA
1 TTATCAAAATTTCATAAAGTGA
* *
17484 GGTTATCAAAATTGCATAATGTGA
1 --TTATCAAAATTTCATAAAGTGA
* *
17508 TTATCAAAATTTCATAAAGGGG
1 TTATCAAAATTTCATAAAGTGA
* * *
17530 TCAACAAAATTTTATAAAGATG-
1 TTATCAAAATTTCATAAAG-TGA
*
17552 TTATCAAAATTTCATAAAG-AA
1 TTATCAAAATTTCATAAAGTGA
*
17573 TTTATCAAATTTTCA-AATTA-TGA
1 -TTATCAAAATTTCATAA--AGTGA
17596 TTA-CAAAAATTTCATA
1 TTATC-AAAATTTCATA
17612 GTGGTATTTC
Statistics
Matches: 162, Mismatches: 33, Indels: 40
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.01
20 3 0.02
21 23 0.14
22 104 0.64
23 6 0.04
24 9 0.06
25 16 0.10
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGTGA
Found at i:17584 original size:21 final size:22
Alignment explanation
Indices: 17374--17587 Score: 136
Period size: 22 Copynumber: 9.7 Consensus size: 22
17364 TTGATAGAAG
* *
17374 GTTATC-AAATCTCATAGAG-T
1 GTTATCAAAATTTCATAAAGAT
17394 GATTATCAAAATTTCATAAAGAT
1 G-TTATCAAAATTTCATAAAGAT
*
17417 AGGATTATCAAAATTT-ATATAA-AA
1 --G-TTATCAAAATTTCATA-AAGAT
* ** *
17441 ATTATCAAAATTTCATAGTGTT
1 GTTATCAAAATTTCATAAAGAT
* * * *
17463 GTTATGAAAATTACA-AAGCGAG
1 GTTATCAAAATTTCATAA-AGAT
* *
17485 GTTATCAAAATTGCATAATG-T
1 GTTATCAAAATTTCATAAAGAT
**
17506 GATTATCAAAATTTCATAAAGGG
1 G-TTATCAAAATTTCATAAAGAT
* * *
17529 GTCAACAAAATTTTATAAAGAT
1 GTTATCAAAATTTCATAAAGAT
17551 GTTATCAAAATTTCATAAAGAAT
1 GTTATCAAAATTTCATAAAG-AT
*
17574 -TTATCAAATTTTCA
1 GTTATCAAAATTTCA
17588 AATTATGATT
Statistics
Matches: 150, Mismatches: 31, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 19 0.13
22 104 0.69
23 6 0.04
24 4 0.03
25 16 0.11
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAAGAT
Found at i:17728 original size:19 final size:19
Alignment explanation
Indices: 17692--17758 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
17682 ATATGGAGTA
17692 ATCAAAATTTCAGAGAGGAT
1 ATCAAAA-TTCAGAGAGGAT
* *
17712 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGAGAGGAT
* *
17731 ATCGAAATTCAGTGAGGAT
1 ATCAAAATTCAGAGAGGAT
17750 ATCAAAATT
1 ATCAAAATT
17759 TCATATGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 35 0.85
20 6 0.15
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGAGAGGAT
Found at i:17775 original size:22 final size:22
Alignment explanation
Indices: 17749--18226 Score: 107
Period size: 22 Copynumber: 21.7 Consensus size: 22
17739 TCAGTGAGGA
17749 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
17771 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* *
17793 TTTCAAAATTTCATA-AAAGGGT
1 TATCAAAATTTCATATGAA-GGT
* *
17815 TATCAAAATTTCAT-TGTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
17836 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
17859 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * ** * * *
17881 AACCAAAAAATCATAGGGAGCTTAAT
1 TATCAAAATTTCATATGAAG----GT
*
17907 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
17923 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
17945 TATCAAAATTTTATAGGGAGGCT
1 TATCAAAATTTCATATGAAGG-T
* * * *
17968 TATTAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
17991 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
** * *
18013 TATCACGATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
18035 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
18057 TA-CTAACAA-TTCATATGAAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
18079 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* *
18101 TATCAATATATCATATGGAA-GT
1 TATCAAAATTTCATAT-GAAGGT
* * * **
18123 TATTAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
18146 TATCAAAATTTCAT-TAGAAAGT
1 TATCAAAATTTCATAT-GAAGGT
18168 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
18190 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
*
18212 TAACAAAATTTCATA
1 TATCAAAATTTCATA
18227 AGAAAGTTTA
Statistics
Matches: 329, Mismatches: 86, Indels: 82
0.66 0.17 0.16
Matches are distributed among these distances:
16 8 0.02
18 1 0.00
20 9 0.03
21 17 0.05
22 214 0.65
23 65 0.20
24 6 0.02
25 2 0.01
26 7 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:17975 original size:23 final size:22
Alignment explanation
Indices: 17943--18047 Score: 93
Period size: 23 Copynumber: 4.7 Consensus size: 22
17933 TCATAAGAAA
17943 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTTATAGGGAG
* *
17965 GCTTATTAAAATTTTATAGGAAG
1 G-TTATCAAAATTTTATAGGGAG
* * *
17988 ATTTATCAAAATTTCATAGCGAG
1 -GTTATCAAAATTTTATAGGGAG
** * * *
18011 GTTATCACGATTTCATAGTGTG
1 GTTATCAAAATTTTATAGGGAG
*
18033 ATTATCAAAATTTTA
1 GTTATCAAAATTTTA
18048 AAGTGTGATT
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
22 29 0.45
23 36 0.55
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTTATAGGGAG
Found at i:18182 original size:45 final size:44
Alignment explanation
Indices: 17749--18226 Score: 169
Period size: 44 Copynumber: 10.8 Consensus size: 44
17739 TCAGTGAGGA
* * * *
17749 TATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAGT
1 TATCAAAATTTCATATGAAAGTTATCAAAATTTCATAGTGTGGT
* * *
17793 TTTCAAAATTTCATA--AAAGGGTTATCAAAATTTCATTGTAT-GT
1 TATCAAAATTTCATATGAAA--GTTATCAAAATTTCATAGTGTGGT
* ** * * *
17836 AGATCAAAATTTCATA-GGGAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATATGAAAG-TTATCAAAATTTCATAGTGTGGT
* * ** * *
17881 AACCAAAAAATCATAGGGAGCTTAA-TTATCAAAA--T--T--TGTAGT
1 TATCAAAATTTCATA-TGA----AAGTTATCAAAATTTCATAGTGTGGT
* * * * *
17923 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGCT
1 TATCAAAATTTCATATGAAAGTTATCAAAATTTCATAGTGTGG-T
* * * * * *
17968 TATTAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATATGAA-AGTTATCAAAATTTCATAGTGTGGT
** ** * * *
18013 TATCACGATTTCATAGTGTGA-TTATCAAAATTTTAAAGTGTGAT
1 TATCAAAATTTCATA-TGAAAGTTATCAAAATTTCATAGTGTGGT
* * * * * **
18057 TA-CTAACAA-TTCATATGAAGGTTTTTAAATTTTTATAAAGTGGT
1 TATC-AA-AATTTCATATGAAAGTTATCAAAATTTCATAGTGTGGT
* * * * * *
18101 TATCAATATATCATATGGAAGTTATTAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATATGAAAGTTATCAAAATTTCATAGTG-TGGT
* *
18146 TATCAAAATTTCAT-TAGAAAGTTATCAAAATTTCATATTGAGGT
1 TATCAAAATTTCATAT-GAAAGTTATCAAAATTTCATAGTGTGGT
* * * * * *
18190 CT-TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATA
1 -TATCAAAATTTCATATGAAAGTTATCAAAATTTCATA
18227 AGAAAGTTTA
Statistics
Matches: 315, Mismatches: 88, Indels: 62
0.68 0.19 0.13
Matches are distributed among these distances:
37 2 0.01
38 9 0.03
40 1 0.00
41 2 0.01
42 17 0.05
43 7 0.02
44 174 0.55
45 70 0.22
46 24 0.08
48 8 0.03
50 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (44 bp):
TATCAAAATTTCATATGAAAGTTATCAAAATTTCATAGTGTGGT
Found at i:22040 original size:36 final size:36
Alignment explanation
Indices: 22000--22216 Score: 150
Period size: 36 Copynumber: 5.4 Consensus size: 36
21990 AAAAAGAAAC
*
22000 AGTAAAAACAGAGGAGATTGCATACCTATAAGTTTG
1 AGTAAAAACAGAGGAGATTTCATACCTATAAGTTTG
* *
22036 AGTAAAAACAGAGGAAAAACAGAGGAGATTGCATCCCTATAAGTTTG
1 AGT--------A--AAAA-CAGAGGAGATTTCATACCTATAAGTTTG
22083 AGTAAAAACAGAGGAAAAACAGAGGATATTTCATACC-ATTAAGTTTG
1 AGTAAAAACAGA-G-------GA-GAT-T-TCATACCTA-TAAGTTTG
* *
22130 AGTAAAAACAGAGGACATTTCATACATATAAGTTTG
1 AGTAAAAACAGAGGAGATTTCATACCTATAAGTTTG
*
22166 AGTAAAAACAGAGGACATTTCATACC-ATTAAGTTTG
1 AGTAAAAACAGAGGAGATTTCATACCTA-TAAGTTTG
22202 AGTAAAAACAGAGGA
1 AGTAAAAACAGAGGA
22217 AAAAACAGAG
Statistics
Matches: 150, Mismatches: 6, Indels: 50
0.73 0.03 0.24
Matches are distributed among these distances:
35 1 0.01
36 69 0.46
37 7 0.05
38 2 0.01
39 3 0.02
44 3 0.02
45 3 0.02
46 7 0.05
47 55 0.37
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (36 bp):
AGTAAAAACAGAGGAGATTTCATACCTATAAGTTTG
Found at i:22060 original size:47 final size:47
Alignment explanation
Indices: 22003--22265 Score: 268
Period size: 47 Copynumber: 6.0 Consensus size: 47
21993 AAGAAACAGT
*
22003 AAAAACAGAGGAGATTGCATACCTATAAGTTTGAGTAAAAACAGAGG
1 AAAAACAGAGGAGATTTCATACCTATAAGTTTGAGTAAAAACAGAGG
* *
22050 AAAAACAGAGGAGATTGCATCCCTATAAGTTTGAGTAAAAACAGAGG
1 AAAAACAGAGGAGATTTCATACCTATAAGTTTGAGTAAAAACAGAGG
*
22097 AAAAACAGAGGATATTTCATACC-ATTAAGTTTGAGTAAAAACAGAGG
1 AAAAACAGAGGAGATTTCATACCTA-TAAGTTTGAGTAAAAACAGAGG
*
22144 ----AC-------ATTTCATACATATAAGTTTGAGTAAAAACAGAGG
1 AAAAACAGAGGAGATTTCATACCTATAAGTTTGAGTAAAAACAGAGG
22180 ----AC-------ATTTCATACC-ATTAAGTTTGAGTAAAAACAGAGG
1 AAAAACAGAGGAGATTTCATACCTA-TAAGTTTGAGTAAAAACAGAGG
*
22216 AAAAAACAGAGGAGATTTCATACCTATAAGTTTGAGTAAAGAAGAGAGG
1 -AAAAACAGAGGAGATTTCATACCTATAAGTTTGAGTAAA-AACAGAGG
22265 A
1 A
22266 TACTTACGAA
Statistics
Matches: 192, Mismatches: 7, Indels: 33
0.83 0.03 0.14
Matches are distributed among these distances:
35 1 0.01
36 64 0.33
37 1 0.01
41 2 0.01
43 2 0.01
46 1 0.01
47 88 0.46
48 25 0.13
49 8 0.04
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (47 bp):
AAAAACAGAGGAGATTTCATACCTATAAGTTTGAGTAAAAACAGAGG
Found at i:22220 original size:83 final size:83
Alignment explanation
Indices: 22000--22265 Score: 268
Period size: 83 Copynumber: 3.2 Consensus size: 83
21990 AAAAAGAAAC
* *
22000 AGTAAAAACAGAGGAGATTGCATACC-TATAAGTTTGAGTAAAAACAGAGGAAAAACAGAGGAGA
1 AGTAAAAACAGAGGACATTTCATACCAT-TAAGTTTGAGTAAAAACAGAGGAAAAACAGAGGAGA
* *
22064 TTGCATCCCTATAAGTTTG
65 TTTCATACCTATAAGTTTG
22083 AGTAAAAACAGAGGAAAAACAGAGGATATTTCATACCATTAAGTTTGAGTAAAAACAGAGG----
1 AGTAAAAACAGAGG----AC-------ATTTCATACCATTAAGTTTGAGTAAAAACAGAGGAAAA
*
22144 AC-------ATTTCATACATATAAGTTTG
55 ACAGAGGAGATTTCATACCTATAAGTTTG
22166 AGTAAAAACAGAGGACATTTCATACCATTAAGTTTGAGTAAAAACAGAGGAAAAAACAGAGGAGA
1 AGTAAAAACAGAGGACATTTCATACCATTAAGTTTGAGTAAAAACAGAGG-AAAAACAGAGGAGA
22231 TTTCATACCTATAAGTTTG
65 TTTCATACCTATAAGTTTG
*
22250 AGTAAAGAAGAGAGGA
1 AGTAAA-AACAGAGGA
22266 TACTTACGAA
Statistics
Matches: 151, Mismatches: 7, Indels: 48
0.73 0.03 0.23
Matches are distributed among these distances:
72 34 0.23
77 2 0.01
79 2 0.01
83 45 0.30
84 25 0.17
85 8 0.05
87 1 0.01
90 2 0.01
94 31 0.21
95 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (83 bp):
AGTAAAAACAGAGGACATTTCATACCATTAAGTTTGAGTAAAAACAGAGGAAAAACAGAGGAGAT
TTCATACCTATAAGTTTG
Found at i:22239 original size:48 final size:49
Alignment explanation
Indices: 22169--22265 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 49
22159 AAGTTTGAGT
22169 AAAAACAGAGGACATTTCATACC-ATTAAGTTTGAGTAAA-AACAGAGGA
1 AAAAACAGAGGACATTTCATACCTA-TAAGTTTGAGTAAAGAACAGAGGA
* *
22217 AAAAACAGAGGAGATTTCATACCTATAAGTTTGAGTAAAGAAGAGAGGA
1 AAAAACAGAGGACATTTCATACCTATAAGTTTGAGTAAAGAACAGAGGA
22266 TACTTACGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 36 0.80
49 9 0.20
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.21
Consensus pattern (49 bp):
AAAAACAGAGGACATTTCATACCTATAAGTTTGAGTAAAGAACAGAGGA
Found at i:31839 original size:51 final size:51
Alignment explanation
Indices: 31772--31881 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 51
31762 GCCTCCGCCA
* *
31772 CCACCTCCAGCACCAGTACCAGCAGTGAAGCAGGTTGCACCCCTGCCTCCT
1 CCACCTCCAGCACCAGTACCAGCAGTGAAGCAAGTTGCACCCCCGCCTCCT
* * *
31823 CCACCTCCAGCACCAGTAGCTGCAGTGAATCAAGTTGCACCCCCGCCTCCT
1 CCACCTCCAGCACCAGTACCAGCAGTGAAGCAAGTTGCACCCCCGCCTCCT
*
31874 CCTCCTCC
1 CCACCTCC
31882 TCCTCCTCCG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.20, C:0.45, G:0.17, T:0.17
Consensus pattern (51 bp):
CCACCTCCAGCACCAGTACCAGCAGTGAAGCAAGTTGCACCCCCGCCTCCT
Found at i:40654 original size:2 final size:2
Alignment explanation
Indices: 40621--40645 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40611 AGTGAGAGGC
40621 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
40646 AACAGAGAGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47919 original size:8 final size:8
Alignment explanation
Indices: 47906--47931 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
47896 AGAAGGTGAG
47906 GAAACAGA
1 GAAACAGA
47914 GAAACAGA
1 GAAACAGA
47922 GAAACAGA
1 GAAACAGA
47930 GA
1 GA
47932 CAGTGTTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.27, T:0.00
Consensus pattern (8 bp):
GAAACAGA
Found at i:58256 original size:16 final size:19
Alignment explanation
Indices: 58221--58260 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
58211 TTTCCCCTGT
58221 ATTAGAATAACAACGCAAG
1 ATTAGAATAACAACGCAAG
58240 ATTA-AATAA-AA-GCAAG
1 ATTAGAATAACAACGCAAG
58256 ATTAG
1 ATTAG
58261 GCCCCACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.45
17 2 0.10
18 5 0.25
19 4 0.20
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.20
Consensus pattern (19 bp):
ATTAGAATAACAACGCAAG
Found at i:61452 original size:14 final size:14
Alignment explanation
Indices: 61433--61460 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61423 AATATGAATA
61433 ATTTTTTTTTTTGG
1 ATTTTTTTTTTTGG
61447 ATTTTTTTTTTTGG
1 ATTTTTTTTTTTGG
61461 TTAAACTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.14, T:0.79
Consensus pattern (14 bp):
ATTTTTTTTTTTGG
Found at i:62711 original size:167 final size:165
Alignment explanation
Indices: 62436--62919 Score: 639
Period size: 167 Copynumber: 2.9 Consensus size: 165
62426 AACATATGGA
* * ** * *
62436 AATTACTAAAAGATCACCACCCCGGATTAATGAGGAGCTAGAGAA-TAAATTTTTTTCGTCTTTT
1 AATTAATAAAAGATCGCCACCAAGGATTGATGATGAGCTAGAGAACT-AATTTTTTTCGTCTTTT
* * * *
62500 CCAACTTGATAGATTACTTAAATGTCCTAACTTTTAATTCTTGAGGGGATTAAATAACTAGACTT
65 CCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACTA-ACTT
*
62565 TTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGG
129 TTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * * ** * *
62602 AATTACTAAAAGATC-CCTACCAAGGCTTGCTTTTGGAGTTAGAGAACTTATTTTTTTCGTCTTT
1 AATTAATAAAAGATCGCC-ACCAAGGATTGATGAT-GAGCTAGAGAACTAATTTTTTTCGTCTTT
* * *
62666 TCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAAGTAATTT
64 TCCTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACTAA-CT
*
62731 TTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGG
128 TTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * *
62769 AATTAATAAAAGATCGCCATCAAGGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTAC
1 AATTAATAAAAGATCGCCACCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTTC
* **
62834 CTACTCGACAGATTACTTAAAATGTCCTATTTTTTGATTCTTGAGGAGATTAAATAACTAAACTT
66 CTACTTGACAGATTACTT-AAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACT-AACTT
62899 TTTGGTCATTTCTCAATTGAC
129 TTTGGTCATTTCTCAATTGAC
62920 AAATGACTCA
Statistics
Matches: 275, Mismatches: 36, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
165 2 0.01
166 67 0.24
167 201 0.73
168 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (165 bp):
AATTAATAAAAGATCGCCACCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTTC
CTACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACTAACTTTT
TGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
Found at i:64957 original size:22 final size:22
Alignment explanation
Indices: 64910--64962 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
64900 ATTGATAGCG
* **
64910 AAACAAAAATAAAACGAAAACG
1 AAACAAAAATAAAACAAAAAAA
64932 AAACAAAAATAAAA-AAACAAAA
1 AAACAAAAATAAAACAAA-AAAA
*
64954 AAACGAAAA
1 AAACAAAAA
64963 CGATACCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.79, C:0.11, G:0.06, T:0.04
Consensus pattern (22 bp):
AAACAAAAATAAAACAAAAAAA
Found at i:69639 original size:23 final size:23
Alignment explanation
Indices: 69613--69658 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
69603 GCACTATATT
69613 TTTAAATTTTAATCAACATGTAA
1 TTTAAATTTTAATCAACATGTAA
69636 TTTAAATTTTAATCAACATGTAA
1 TTTAAATTTTAATCAACATGTAA
69659 CTAACTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (23 bp):
TTTAAATTTTAATCAACATGTAA
Found at i:76528 original size:105 final size:105
Alignment explanation
Indices: 76346--76544 Score: 344
Period size: 105 Copynumber: 1.9 Consensus size: 105
76336 CAGCAGAGGC
*
76346 ATGGATCACTTCCTTCCCTTCATCAACATTTACATTTGAATTCTCATAGCCCTTGACACCAGCAT
1 ATGGATCACTTCCTTCCCTTCATCAACATTTACATTTGAATTCTCATAGACCTTGACACCAGCAT
76411 TTTGCACTGGAGATGACTTAAGCTCTTTTGCAGAAGAAGA
66 TTTGCACTGGAGATGACTTAAGCTCTTTTGCAGAAGAAGA
* * * *
76451 ATGGATCAGTTCCTTCTCTTCATCAACATTTACTTTTGAATTCTCATAGACTTTGACACCAGCAT
1 ATGGATCACTTCCTTCCCTTCATCAACATTTACATTTGAATTCTCATAGACCTTGACACCAGCAT
*
76516 TTTGCACTGGAGATGACTTGAGCTCTTTT
66 TTTGCACTGGAGATGACTTAAGCTCTTTT
76545 TCCGAATCAG
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.36
Consensus pattern (105 bp):
ATGGATCACTTCCTTCCCTTCATCAACATTTACATTTGAATTCTCATAGACCTTGACACCAGCAT
TTTGCACTGGAGATGACTTAAGCTCTTTTGCAGAAGAAGA
Found at i:79896 original size:22 final size:23
Alignment explanation
Indices: 79853--79898 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
79843 TCCCATAATC
*
79853 TGCAATAATAATTACATCCCAAT
1 TGCAATAAGAATTACATCCCAAT
* *
79876 TGCAA-AAGAATTGCATTCCAAT
1 TGCAATAAGAATTACATCCCAAT
79898 T
1 T
79899 TTGAAAACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (23 bp):
TGCAATAAGAATTACATCCCAAT
Found at i:87929 original size:29 final size:29
Alignment explanation
Indices: 87864--87931 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
87854 TTACCCCCTG
*
87864 AACGTCCAAAATTGAGAGTTTATGTACAA
1 AACGTCCAAAATTGAGAGTTTATGAACAA
**
87893 AATATCCAAAATTGA-AGTTTA-GAAAACAA
1 AACGTCCAAAATTGAGAGTTTATG--AACAA
87922 AACGTCCAAA
1 AACGTCCAAA
87932 CTCTACAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.03
28 6 0.19
29 25 0.78
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.24
Consensus pattern (29 bp):
AACGTCCAAAATTGAGAGTTTATGAACAA
Found at i:90492 original size:16 final size:16
Alignment explanation
Indices: 90467--90500 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
90457 ATGCACCGGT
*
90467 AAAGGGTGGTAAGTAA
1 AAAGGCTGGTAAGTAA
90483 AAAGGCTGGTAAGTAA
1 AAAGGCTGGTAAGTAA
90499 AA
1 AA
90501 GAGGTTGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.32, T:0.18
Consensus pattern (16 bp):
AAAGGCTGGTAAGTAA
Found at i:91401 original size:19 final size:19
Alignment explanation
Indices: 91377--91420 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
91367 TATTGACTAT
*
91377 GAGAGAGTAAGTGGGAGGA
1 GAGAGACTAAGTGGGAGGA
* *
91396 GAGAGACTTAGTGGGGGGA
1 GAGAGACTAAGTGGGAGGA
91415 GAGAGA
1 GAGAGA
91421 AGAGGGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.02, G:0.52, T:0.11
Consensus pattern (19 bp):
GAGAGACTAAGTGGGAGGA
Found at i:99020 original size:16 final size:16
Alignment explanation
Indices: 98999--99031 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
98989 TGCTGTCTGT
98999 CCAAAGGGGATGGGGC
1 CCAAAGGGGATGGGGC
99015 CCAAAGGGGATGGGGC
1 CCAAAGGGGATGGGGC
99031 C
1 C
99032 TTCTGTGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.48, T:0.06
Consensus pattern (16 bp):
CCAAAGGGGATGGGGC
Done.