Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014522.1 Kokia drynarioides strain JFW-HI SEQ_129561, 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: 96360
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 107 characters in sequence are not A, C, G, or T
Found at i:2490 original size:20 final size:20
Alignment explanation
Indices: 2465--2506 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2455 CAAACACTAG
2465 AAAAT-ATTAACTTTTCCAGA
1 AAAATAATTAA-TTTTCCAGA
*
2485 AAAATAATTCATTTTCCAGA
1 AAAATAATTAATTTTCCAGA
2505 AA
1 AA
2507 TCATTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATAATTAATTTTCCAGA
Found at i:3403 original size:2 final size:2
Alignment explanation
Indices: 3396--3420 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3386 CCACATCCTT
3396 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 T
3421 TAGAATTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4738 original size:23 final size:23
Alignment explanation
Indices: 4706--4749 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4696 ACTACCATTT
4706 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
4729 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
4750 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:4742 original size:13 final size:11
Alignment explanation
Indices: 4710--4752 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
4700 CCATTTTCTA
*
4710 AATAAAATAAT
1 AATAAAATATT
4721 AAT-AAATATCT
1 AATAAAATAT-T
4732 AAGTAAAATATT
1 AA-TAAAATATT
4744 AATAAAATA
1 AATAAAATA
4753 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:20608 original size:2 final size:2
Alignment explanation
Indices: 20601--20641 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20591 TTACAAATTA
20601 AT AT AT AT AT 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 AT AT AT AT AT A
20642 AATGGTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25546 original size:22 final size:23
Alignment explanation
Indices: 25521--25589 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 23
25511 ATACAAAACA
*
25521 AAATGGAGAGTAC-CAAAGTATT
1 AAATGGAGAGCACACAAAGTATT
*
25543 AAATGGAGAGCACACAAAGTACTAG
1 AAATGGAGAGCACACAAAGTA-T-T
25568 ATAATGGAGAGCACACAAAGTA
1 A-AATGGAGAGCACACAAAGTA
25590 CTAGATAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.29
23 7 0.17
24 1 0.02
25 1 0.02
26 20 0.49
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGGAGAGCACACAAAGTATT
Found at i:25576 original size:26 final size:26
Alignment explanation
Indices: 25544--25614 Score: 124
Period size: 26 Copynumber: 2.7 Consensus size: 26
25534 CAAAGTATTA
25544 AATGGAGAGCACACAAAGTACTAGAT
1 AATGGAGAGCACACAAAGTACTAGAT
25570 AATGGAGAGCACACAAAGTACTAGAT
1 AATGGAGAGCACACAAAGTACTAGAT
**
25596 AACAGAGAGCACACAAAGT
1 AATGGAGAGCACACAAAGT
25615 GCTAAATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (26 bp):
AATGGAGAGCACACAAAGTACTAGAT
Found at i:25648 original size:23 final size:23
Alignment explanation
Indices: 25548--25649 Score: 80
Period size: 26 Copynumber: 4.2 Consensus size: 23
25538 GTATTAAATG
* *
25548 GAGAGCACACAAAGTACTAGATAA
1 GAGAACACACAAAGTACTA-ATCA
*
25572 TGGAGAGCACACAAAGTACTAGATAACA
1 --GAGAACACACAAAGTACTA-AT--CA
* *
25600 GAGAGCACACAAAGTGCTAAAT-A
1 GAGAACACACAAAGTACT-AATCA
*
25623 GAGAATACACAAAGTACTAATCA
1 GAGAACACACAAAGTACTAATCA
25646 GAGA
1 GAGA
25650 GCACGAAACG
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
22 3 0.04
23 21 0.31
26 41 0.61
27 1 0.01
28 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.14
Consensus pattern (23 bp):
GAGAACACACAAAGTACTAATCA
Found at i:25686 original size:23 final size:23
Alignment explanation
Indices: 25548--25697 Score: 126
Period size: 23 Copynumber: 6.3 Consensus size: 23
25538 GTATTAAATG
*
25548 GAGAGCACACAAAGTACTAGATA-A
1 GAGAGCACACAAAGTGCTA-A-ACA
*
25572 TGGAGAGCACACAAAGTACTAGATAACA
1 --GAGAGCACACAAAGTGCT--A-AACA
*
25600 GAGAGCACACAAAGTGCTAAATA
1 GAGAGCACACAAAGTGCTAAACA
** * *
25623 GAGAATACACAAAGTACTAATCA
1 GAGAGCACACAAAGTGCTAAACA
*
25646 GAGAGCACGA-AACGTGCTAAACA
1 GAGAGCAC-ACAAAGTGCTAAACA
25669 GAGAGCACACACAA-TGCTAAACA
1 GAGAGCACACA-AAGTGCTAAACA
25692 GAGAGC
1 GAGAGC
25698 GCGCTAAAGT
Statistics
Matches: 104, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.01
23 61 0.59
24 3 0.03
26 35 0.34
27 1 0.01
28 3 0.03
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (23 bp):
GAGAGCACACAAAGTGCTAAACA
Found at i:27886 original size:28 final size:28
Alignment explanation
Indices: 27855--27912 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
27845 AAAAGGTTTC
*
27855 TAGTTGAACCACAAAAATGAAAGGGTCT
1 TAGTTGAACCACAAAAATGAAAGGGGCT
* * *
27883 TAGTTTAGCCACAAAAATGAGAGGGGCT
1 TAGTTGAACCACAAAAATGAAAGGGGCT
27911 TA
1 TA
27913 CTTTTCCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (28 bp):
TAGTTGAACCACAAAAATGAAAGGGGCT
Found at i:32918 original size:33 final size:33
Alignment explanation
Indices: 32876--33106 Score: 250
Period size: 33 Copynumber: 7.0 Consensus size: 33
32866 ACCATGTATT
* * *
32876 TTATACGAGCCTGTATGTATGTGAACCTTAGGA
1 TTATGCGAGCCTGTATGTATGCGAACCCTAGGA
* *
32909 TTATGCGAGCCTATATGTATGCGAACCCTAGGC
1 TTATGCGAGCCTGTATGTATGCGAACCCTAGGA
* * * * *
32942 TTATGTGAGCCTCTATGTTTACGAACTCTAGGA
1 TTATGCGAGCCTGTATGTATGCGAACCCTAGGA
* *
32975 TTATGCGAGCTTGTATGTATGCGAACCCTAAGA
1 TTATGCGAGCCTGTATGTATGCGAACCCTAGGA
*
33008 TTATG-GAAGCCTGTATGTATGTC-AACCCTAGGC
1 TTATGCG-AGCCTGTATGTATG-CGAACCCTAGGA
* * *
33041 TTATGCGAGCATGTATGTATGCAAACCCTAGGG
1 TTATGCGAGCCTGTATGTATGCGAACCCTAGGA
* * * *
33074 TTATGCGAACCTATATGCATGCGAACTCTAGGA
1 TTATGCGAGCCTGTATGTATGCGAACCCTAGGA
33107 ACATGCAAGC
Statistics
Matches: 164, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
32 2 0.01
33 160 0.98
34 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (33 bp):
TTATGCGAGCCTGTATGTATGCGAACCCTAGGA
Found at i:40680 original size:7 final size:7
Alignment explanation
Indices: 40668--40694 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40658 TCAAATAAAA
40668 AAATCCT
1 AAATCCT
40675 AAATCCT
1 AAATCCT
40682 AAATCCT
1 AAATCCT
40689 AAATCC
1 AAATCC
40695 CAAACACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATCCT
Found at i:43835 original size:39 final size:39
Alignment explanation
Indices: 43786--43865 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
43776 ATTATCTCTT
*
43786 TAACGGTAATCCTATGTGGCAGTCCAACTAGATTTTAAG
1 TAACGATAATCCTATGTGGCAGTCCAACTAGATTTTAAG
*
43825 TAACGATAATCCTATGTGGTAGTCCAACTAGATTTTAAG
1 TAACGATAATCCTATGTGGCAGTCCAACTAGATTTTAAG
43864 TA
1 TA
43866 TCAACTTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (39 bp):
TAACGATAATCCTATGTGGCAGTCCAACTAGATTTTAAG
Found at i:51745 original size:18 final size:18
Alignment explanation
Indices: 51724--51759 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
51714 AAAACATGAG
*
51724 AATTTTTTCTAAACAACA
1 AATTTTTTATAAACAACA
*
51742 AATTTTTTATTAACAACA
1 AATTTTTTATAAACAACA
51760 CAAGAGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTTTTATAAACAACA
Found at i:58443 original size:26 final size:25
Alignment explanation
Indices: 58410--58476 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
58400 TAAAAATTAT
*
58410 TTTAAATTTAAATTTATGTTTTAAA
1 TTTAAATTTAAATTTATGTTCTAAA
*
58435 TTTAAAATTTGAAATAT-TGTTCTAAA
1 TTT-AAATTT-AAATTTATGTTCTAAA
* *
58461 CTTAATTTTAAATTTA
1 TTTAAATTTAAATTTA
58477 AAATACAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 5 0.15
25 8 0.24
26 16 0.47
27 5 0.15
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTAAATTTAAATTTATGTTCTAAA
Found at i:59189 original size:3 final size:3
Alignment explanation
Indices: 59181--59230 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
59171 AGTAATAAAT
* *
59181 ATA ATA ATA ATA ATA ATA ACT- TTA ATA TTAA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA ATA ATA
59227 ATA A
1 ATA A
59231 AAGAAATTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 36 0.90
4 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:60443 original size:57 final size:57
Alignment explanation
Indices: 60346--60626 Score: 250
Period size: 60 Copynumber: 4.8 Consensus size: 57
60336 AACGTTTTGA
* * *
60346 CCCTAAACTTTCTAAAAATTATATTTTAACCCTCAAACTTCCAAAAATTACCATTTT-C
1 CCCTAAACTTTC-AAAAATCACATTTTTACCCT-AAACTTCCAAAAATTACCATTTTAC
* *
60404 CCTTGAACTTTCAAAAATCACATTTTTACCTCTAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAACTTTCAAAAATCACATTTTTACC-CTAAACTTCCAAAAATTACCATTTTAC
* *
60462 CCCTAAACTTAC-AAAATCACATTTTTGCCCCTAAACTTTCCAAAAATTA-CATTTTTTAC
1 CCCTAAACTTTCAAAAATCACATTTTT-ACCCTAAAC-TTCCAAAAATTACCA--TTTTAC
* * ** *
60521 CCCTAAACTTCCAAAAATTACCA-TTTTACCACCGAACTTTCCAAAAATCA-CATTTTTACC
1 CCCTAAACTTTCAAAAATCA-CATTTTTACC-CTAAAC-TTCCAAAAATTACCA-TTTTA-C
* * * *
60581 CCCTAAACTTCCAAAAATTACCA-TTTTACCTCTGAACTTACAAAAA
1 CCCTAAACTTTCAAAAATCA-CATTTTTACC-CTAAACTTCCAAAAA
60627 AATCATATTT
Statistics
Matches: 195, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
57 60 0.31
58 36 0.18
59 33 0.17
60 64 0.33
61 2 0.01
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.33
Consensus pattern (57 bp):
CCCTAAACTTTCAAAAATCACATTTTTACCCTAAACTTCCAAAAATTACCATTTTAC
Found at i:60568 original size:60 final size:58
Alignment explanation
Indices: 60346--60671 Score: 249
Period size: 60 Copynumber: 5.6 Consensus size: 58
60336 AACGTTTTGA
* * *
60346 CCCTAAACTTTCTAAAAATTA-TATTTTAACCCTCAAAC-TTCCAAAAATTACCA-TTTT-C
1 CCCTAAAC-TTCCAAAAATTACCATTTT-ACCC-CGAACTTTCCAAAAATTA-CATTTTTAC
* * * * **
60404 CCTTGAACTTTCAAAAATCA-CATTTTTACCTCTAAAC-TTCCAAAAATTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATTACCA-TTTTACC-CCGAACTTTCCAAAAATTA-CATTTTTAC
* * * *
60462 CCCTAAACTTAC-AAAATCA-CATTTTTGCCCCTAAACTTTCCAAAAATTACATTTTTTAC
1 CCCTAAACTTCCAAAAATTACCA-TTTTACCCC-GAACTTTCCAAAAATTACA-TTTTTAC
*
60521 CCCTAAACTTCCAAAAATTACCATTTTACCACCGAACTTTCCAAAAATCACATTTTTACC
1 CCCTAAACTTCCAAAAATTACCATTTTACC-CCGAACTTTCCAAAAATTACATTTTTA-C
* * * * **
60581 CCCTAAACTTCCAAAAATTACCATTTTACCTCTGAACTTACAAAAAAAT-CATATTTTTG
1 CCCTAAACTTCCAAAAATTACCATTTTACC-CCGAACTTTCCAAAAATTACAT-TTTTAC
* * *
60640 CCCAAAACCTCTAAAAATTACCATTTTACCCC
1 CCCTAAACTTCCAAAAATTACCATTTTACCCC
60672 CAGTCATCCA
Statistics
Matches: 227, Mismatches: 29, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
56 1 0.00
57 58 0.26
58 34 0.15
59 53 0.23
60 77 0.34
61 4 0.02
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATTACCATTTTACCCCGAACTTTCCAAAAATTACATTTTTAC
Found at i:60608 original size:30 final size:28
Alignment explanation
Indices: 60346--60671 Score: 262
Period size: 29 Copynumber: 11.1 Consensus size: 28
60336 AACGTTTTGA
* * *
60346 CCCTAAACTTTCTAAAAATTATATTTTAA
1 CCCTAAAC-TTCCAAAAATTACATTTTAC
60375 CCCTCAAACTTCCAAAAATTACCATTTT-C
1 CCCT-AAACTTCCAAAAATTA-CATTTTAC
* * * *
60404 CCTTGAACTTTCAAAAATCACATTTTTAC
1 CCCTAAACTTCCAAAAATTACA-TTTTAC
*
60433 CTCTAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTAC
* * *
60462 CCCTAAACTTAC-AAAATCACATTTTTGC
1 CCCTAAACTTCCAAAAATTACA-TTTTAC
60490 CCCTAAACTTTCCAAAAATTACATTTTTTAC
1 CCCTAAAC-TTCCAAAAATTACA--TTTTAC
60521 CCCTAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTAC
* *
60550 CACC-GAACTTTCCAAAAATCACATTTTTACC
1 C-CCTAAAC-TTCCAAAAATTACA-TTTTA-C
60581 CCCTAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTAC
* * * * * **
60610 CTCTGAACTTACAAAAAAATCATATTTTTG
1 CCCTAAACTT-C-CAAAAATTACATTTTAC
* * *
60640 CCCAAAACCTCTAAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTAC
60669 CCC
1 CCC
60672 CAGTCATCCA
Statistics
Matches: 239, Mismatches: 39, Indels: 38
0.76 0.12 0.12
Matches are distributed among these distances:
27 4 0.02
28 43 0.18
29 83 0.35
30 79 0.33
31 30 0.13
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTACATTTTAC
Found at i:60624 original size:29 final size:29
Alignment explanation
Indices: 60346--60626 Score: 263
Period size: 29 Copynumber: 9.6 Consensus size: 29
60336 AACGTTTTGA
* * *
60346 CCCTAAACTTTCTAAAAATTATA-TTTTAA
1 CCCTAAAC-TTCCAAAAATTACATTTTTAC
60375 CCCTCAAACTTCCAAAAATTACCA-TTTT-C
1 CCCT-AAACTTCCAAAAATTA-CATTTTTAC
* * * *
60404 CCTTGAACTTTCAAAAATCACATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
*
60433 CTCTAAACTTCCAAAAATTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTTAC
* * *
60462 CCCTAAACTTAC-AAAATCACATTTTTGC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
60490 CCCTAAACTTTCCAAAAATTACATTTTTTAC
1 CCCTAAAC-TTCCAAAAATTACA-TTTTTAC
60521 CCCTAAACTTCCAAAAATTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTTAC
* *
60550 CACC-GAACTTTCCAAAAATCACATTTTTACC
1 C-CCTAAAC-TTCCAAAAATTACATTTTTA-C
60581 CCCTAAACTTCCAAAAATTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTTAC
* * *
60610 CTCTGAACTTACAAAAA
1 CCCTAAACTTCCAAAAA
60627 AATCATATTT
Statistics
Matches: 210, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.02
28 36 0.17
29 80 0.38
30 67 0.32
31 23 0.11
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:65330 original size:3 final size:3
Alignment explanation
Indices: 65322--65374 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
65312 CACATCGTAA
* *
65322 AAG AAG AAG AAG AAG AAG AAG AAT AAG AAG AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
65370 AAG AA
1 AAG AA
65375 AGAGTGAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:65936 original size:12 final size:11
Alignment explanation
Indices: 65919--65994 Score: 55
Period size: 13 Copynumber: 6.5 Consensus size: 11
65909 ATAGAGAAGG
65919 AAAAGAAAGAA
1 AAAAGAAAGAA
*
65930 TAAAAGAATAAAA
1 -AAAAGAA-AGAA
65943 AAAAGGAAAGGAA
1 AAAA-GAAA-GAA
65956 AAAAGAAAAAGAA
1 AAAAG--AAAGAA
*
65969 AATAGAAA-AA
1 AAAAGAAAGAA
* *
65979 AAGAGAAACAA
1 AAAAGAAAGAA
65990 AAAAG
1 AAAAG
65995 GAGAGGTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
10 9 0.17
11 9 0.17
12 13 0.25
13 19 0.36
14 3 0.06
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.04
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:65940 original size:36 final size:33
Alignment explanation
Indices: 65889--65994 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 33
65879 GGATTTAATG
65889 AAGAAAAA-ATAAATAAAAAAATAGAGAAGGAAAAGA
1 AAGAAAAAGA-AAATAAAAAAA-AGAGAAGG-AAA-A
*
65925 AAGAATAAA-AGAATAAAAAAAAG-GAAAGGAAAA
1 AAGAA-AAAGAAAATAAAAAAAAGAG-AAGGAAAA
**
65958 AAGAAAAAGAAAATAGAAAAAAAGAGAAACAAAA
1 AAGAAAAAGAAAATA-AAAAAAAGAGAAGGAAAA
65992 AAG
1 AAG
65995 GAGAGGTCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
32 3 0.05
33 11 0.18
34 21 0.34
35 7 0.11
36 15 0.25
37 4 0.07
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (33 bp):
AAGAAAAAGAAAATAAAAAAAAGAGAAGGAAAA
Found at i:65951 original size:25 final size:23
Alignment explanation
Indices: 65919--65994 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 23
65909 ATAGAGAAGG
65919 AAAAGAAA-GAATAAAAGAATAAAA
1 AAAAGAAAGGAA-AAAAGAA-AAAA
65943 AAAAGGAAAGGAAAAAAGAAAAAGA
1 AAAA-GAAAGGAAAAAAGAAAAA-A
* *
65968 AAATAGAAA--AAAAGAGAAACAA
1 AAA-AGAAAGGAAAAAAGAAAAAA
65990 AAAAG
1 AAAAG
65995 GAGAGGTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.04
22 4 0.09
23 10 0.22
24 7 0.15
25 19 0.41
26 4 0.09
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.04
Consensus pattern (23 bp):
AAAAGAAAGGAAAAAAGAAAAAA
Found at i:65959 original size:13 final size:13
Alignment explanation
Indices: 65924--65978 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
65914 GAAGGAAAAG
65924 AAAGAATAAAAGAA
1 AAAGAA-AAAAGAA
* *
65938 TAA-AAAAAAGGA
1 AAAGAAAAAAGAA
*
65950 AAGGAAAAAAGAA
1 AAAGAAAAAAGAA
*
65963 AAAGAAAATAGAA
1 AAAGAAAAAAGAA
65976 AAA
1 AAA
65979 AAGAGAAACA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
12 7 0.21
13 24 0.73
14 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:67049 original size:50 final size:50
Alignment explanation
Indices: 66931--67192 Score: 214
Period size: 50 Copynumber: 5.3 Consensus size: 50
66921 GGATTGAAAC
* * * * *
66931 CGCAATGGCAAATCCGGTACCTTAGAAGATGTGACA-AGAAAGGTTGAGGC
1 CGCAATGGCGAACCCGGTACCTCAGAAGATGTGA-AGGGAAAGGTTGAGGT
* * * * * *
66981 CGTAACGGTGAACCCGGTACCTCAGAAGATGGGATGGGAAAGATTGAGGT
1 CGCAATGGCGAACCCGGTACCTCAGAAGATGTGAAGGGAAAGGTTGAGGT
** *
67031 CGCAATGGCGAATTCGGTA-C-CATGAA-ATGT-AATGAGAAAGGTTGAGGT
1 CGCAATGGCGAACCCGGTACCTCA-GAAGATGTGAA-GGGAAAGGTTGAGGT
* * * * ** *
67079 TGCAATGGCGAACCCGATA-C-CATGAAGATTTTAAGGGAAAGACTGAGGC
1 CGCAATGGCGAACCCGGTACCTCA-GAAGATGTGAAGGGAAAGGTTGAGGT
* * * *
67128 CGCAATGACGAACCTGGTACCTTAGAAGATATGAAGGGAAAGGTTGAGGT
1 CGCAATGGCGAACCCGGTACCTCAGAAGATGTGAAGGGAAAGGTTGAGGT
67178 CGCAATGGCGAACCC
1 CGCAATGGCGAACCC
67193 AGTTCCATGA
Statistics
Matches: 164, Mismatches: 41, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
47 1 0.01
48 40 0.24
49 33 0.20
50 89 0.54
51 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (50 bp):
CGCAATGGCGAACCCGGTACCTCAGAAGATGTGAAGGGAAAGGTTGAGGT
Found at i:67140 original size:49 final size:49
Alignment explanation
Indices: 67016--67218 Score: 160
Period size: 49 Copynumber: 4.1 Consensus size: 49
67006 AAGATGGGAT
* * ** * *
67016 GGGAAAGATTGAGGTCGCAATGGCGAATTCGGTACCATGAA-A-TGTAA
1 GGGAAAGACTGAGGCCGCAATGGCGAACCCGATACCATGAAGATTTTAA
* ** **
67063 TGAGAAAGGTTGAGGTTGCAATGGCGAACCCGATACCATGAAGATTTTAA
1 -GGGAAAGACTGAGGCCGCAATGGCGAACCCGATACCATGAAGATTTTAA
* * * * * *
67113 GGGAAAGACTGAGGCCGCAATGACGAACCTGGTACCTTAGAAGATATGAA
1 GGGAAAGACTGAGGCCGCAATGGCGAACCCGATACCAT-GAAGATTTTAA
** * *
67163 GGGAAAGGTTGAGGTCGCAATGGCGAACCC-AGTTCCATGAAGATTTTAA
1 GGGAAAGACTGAGGCCGCAATGGCGAACCCGA-TACCATGAAGATTTTAA
*
67212 AGGAAAG
1 GGGAAAG
67219 GTTGAAGCCG
Statistics
Matches: 122, Mismatches: 29, Indels: 7
0.77 0.18 0.04
Matches are distributed among these distances:
48 35 0.29
49 45 0.37
50 42 0.34
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (49 bp):
GGGAAAGACTGAGGCCGCAATGGCGAACCCGATACCATGAAGATTTTAA
Found at i:67248 original size:99 final size:99
Alignment explanation
Indices: 67066--67253 Score: 243
Period size: 99 Copynumber: 1.9 Consensus size: 99
67056 AATGTAATGA
* * *
67066 GAAAGGTTGAGGTTGCAATGGCGAACCCGATACCATGAAGATTTTAAGGGAAAGACTGAGGCCGC
1 GAAAGGTTGAGGTCGCAATGGCGAACCCGATACCATGAAGATTTTAAAGGAAAGACTGAAGCCGC
* ***
67131 AATGACGAACCTGGTACCTTAGAAGATATGAAGG
66 AACGACGAACCCAATACCTTAGAAGATATGAAGG
* **
67165 GAAAGGTTGAGGTCGCAATGGCGAACCC-AGTTCCATGAAGATTTTAAAGGAAAGGTTGAAGCCG
1 GAAAGGTTGAGGTCGCAATGGCGAACCCGA-TACCATGAAGATTTTAAAGGAAAGACTGAAGCCG
* **
67229 TAACGGTGAACCCAATACCTTAGAA
65 CAACGACGAACCCAATACCTTAGAA
67254 AAAAAGATGG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
98 1 0.01
99 74 0.99
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.20
Consensus pattern (99 bp):
GAAAGGTTGAGGTCGCAATGGCGAACCCGATACCATGAAGATTTTAAAGGAAAGACTGAAGCCGC
AACGACGAACCCAATACCTTAGAAGATATGAAGG
Found at i:67470 original size:41 final size:41
Alignment explanation
Indices: 67413--67503 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
67403 TATCATTCAG
* * *
67413 TCTTTTACCCTTAATCAAGAAGGGCAGATTGAAGATACCAA
1 TCTTTTACCATTAATCAAGAAGGACAGAATGAAGATACCAA
* **
67454 TCTTTTACCATTAATCAAGAAGGACAGAATGAAGATTCTGA
1 TCTTTTACCATTAATCAAGAAGGACAGAATGAAGATACCAA
67495 TCTTTTACC
1 TCTTTTACC
67504 CTGAGCCCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (41 bp):
TCTTTTACCATTAATCAAGAAGGACAGAATGAAGATACCAA
Found at i:67557 original size:39 final size:39
Alignment explanation
Indices: 67514--67620 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 39
67504 CTGAGCCCGA
67514 GGTAGATCAACATCAGCCAATCTCTTACCCCGAACCTAG
1 GGTAGATCAACATCAGCCAATCTCTTACCCCGAACCTAG
* * * * * * *
67553 GGTAGAT-TACAGCCATCCGATCTCTTACCCCGAGCTTGG
1 GGTAGATCAACA-TCAGCCAATCTCTTACCCCGAACCTAG
*
67592 GGTAGATCACCATCAGCCAATCTCTTACC
1 GGTAGATCAACATCAGCCAATCTCTTACC
67621 TCAAGACTAG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
38 3 0.06
39 49 0.91
40 2 0.04
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (39 bp):
GGTAGATCAACATCAGCCAATCTCTTACCCCGAACCTAG
Found at i:67596 original size:78 final size:78
Alignment explanation
Indices: 67514--67671 Score: 228
Period size: 78 Copynumber: 2.0 Consensus size: 78
67504 CTGAGCCCGA
* * *
67514 GGTAGATCAACATCAGCCAATCTCTTACCCCGAA-CCTAGGGTAGATTACAGCCATCCGATCTCT
1 GGTAGATCAACATCAGCCAATCTCTTACCCC-AAGACTAGGGCAAATTACAGCCATCCGATCTCT
67578 TACCCCGAGCTTGG
65 TACCCCGAGCTTGG
* * * *
67592 GGTAGATCACCATCAGCCAATCTCTTACCTCAAGACTAGGGCAAATTGCAGCCATCCGATCTTTT
1 GGTAGATCAACATCAGCCAATCTCTTACCCCAAGACTAGGGCAAATTACAGCCATCCGATCTCTT
*
67657 ACCTCGAGCTTGG
66 ACCCCGAGCTTGG
67670 GG
1 GG
67672 CATATTGCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 2 0.03
78 69 0.97
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.24
Consensus pattern (78 bp):
GGTAGATCAACATCAGCCAATCTCTTACCCCAAGACTAGGGCAAATTACAGCCATCCGATCTCTT
ACCCCGAGCTTGG
Found at i:67673 original size:39 final size:39
Alignment explanation
Indices: 67562--67680 Score: 102
Period size: 39 Copynumber: 3.1 Consensus size: 39
67552 GGGTAGATTA
* * *
67562 CAGCCATCCGATCTCTTACCCCGAGCTTGGGGTAGA-T-
1 CAGCCATCCGATCTCTTACCTCGAGCTTGGGGCAAATTG
* * *
67599 CA-CCATCAGCCAATCTCTTACCTCAAGAC-TAGGGCAAATTG
1 CAGCCAT---CCGATCTCTTACCTCGAG-CTTGGGGCAAATTG
* *
67640 CAGCCATCCGATCTTTTACCTCGAGCTTGGGGCATATTG
1 CAGCCATCCGATCTCTTACCTCGAGCTTGGGGCAAATTG
67679 CA
1 CA
67681 ATCATTCGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
36 4 0.06
37 2 0.03
38 1 0.02
39 48 0.76
40 2 0.03
41 2 0.03
42 4 0.06
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (39 bp):
CAGCCATCCGATCTCTTACCTCGAGCTTGGGGCAAATTG
Found at i:67732 original size:77 final size:78
Alignment explanation
Indices: 67650--67797 Score: 192
Period size: 77 Copynumber: 1.9 Consensus size: 78
67640 CAGCCATCCG
* * * * *
67650 ATCTTTTACCTCGAGCTTGGGGCATATTGCAATCATTCGAT-TTTTACCCCGA-CACTGGGGCAG
1 ATCTTTTACCCCGAGCCTAGGACAGATTGCAATCATTCGATCTTTTACCCCGAGC-CTGGGGCAG
67713 ATCACCAGTAGCCA
65 ATCACCAGTAGCCA
* * * *
67727 ATCTTTTACCCCGAGCCTATGACAGATTGCAGTCATTCGATCTTTTACCCCGAGCTTGGGGTAGA
1 ATCTTTTACCCCGAGCCTAGGACAGATTGCAATCATTCGATCTTTTACCCCGAGCCTGGGGCAGA
67792 TCACCA
66 TCACCA
67798 TCAACCTATT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
77 34 0.57
78 25 0.42
79 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (78 bp):
ATCTTTTACCCCGAGCCTAGGACAGATTGCAATCATTCGATCTTTTACCCCGAGCCTGGGGCAGA
TCACCAGTAGCCA
Found at i:67813 original size:116 final size:116
Alignment explanation
Indices: 67569--67816 Score: 266
Period size: 116 Copynumber: 2.1 Consensus size: 116
67559 TTACAGCCAT
* * * *
67569 CCGATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAGCCAATCTCTTACCTCAAGACTAGGGC
1 CCGAT-TCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGACTAGGAC
* * ** *
67634 AAATTGCAGCCATCCGATCTTTTACCTCGAGCTTGGGGCATATTGCAATCAT
65 AAATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGATCACAATCAA
* * * * * *
67686 TCGATTTTTACCCCGA-CACTGGGGCAGATCACCAGT-AGCCAATCTTTTACCCCGAGCCTATGA
1 CCGATTCTTACCCCGAGC-CTGGGGCAGATCACCA-TCAGCCAATCTCTTACCCCAAGACTAGGA
* * * * *
67749 CAGATTGCAGTCATTCGATCTTTTACCCCGAGCTTGGGGTAGATCACCATCAA
64 CAAATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGATCACAATCAA
*
67802 CCTATTCTTACCCCG
1 CCGATTCTTACCCCG
67817 CGATAGGGGT
Statistics
Matches: 106, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
115 1 0.01
116 100 0.94
117 5 0.05
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (116 bp):
CCGATTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCAAGACTAGGACA
AATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGATCACAATCAA
Found at i:68100 original size:37 final size:37
Alignment explanation
Indices: 68059--68131 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
68049 AATAAAGCGG
*
68059 TCGTCTTCTTGATGAGATACAGAGAAGTGGACCAAAT
1 TCGTCTTCTTGATGAGATACAGAAAAGTGGACCAAAT
*
68096 TCGTCTTCTTGATGAGATACAGAAAAGTGGATCAAA
1 TCGTCTTCTTGATGAGATACAGAAAAGTGGACCAAA
68132 ATAAGTGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (37 bp):
TCGTCTTCTTGATGAGATACAGAAAAGTGGACCAAAT
Found at i:68294 original size:209 final size:207
Alignment explanation
Indices: 67919--69349 Score: 1444
Period size: 209 Copynumber: 6.9 Consensus size: 207
67909 TGCAGTTATC
* * *
67919 CAAAACAAATGAGGTGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGACACAA
1 CAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
* *
67984 AGCTCGAA-GTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAG
66 AGCTC-AATGTGAGGAAA-CTTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* * *
68048 CAATAAAGCGGTC-GTCTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCTTGATGAG
128 CAATAAAACGGTCAG-CTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAG
*
68112 ATACAGAAAAGTGGAT
192 ATACAGAAAAGCGGAT
* * * *
68128 CAAAATAAGTGATGCGGTCATCTTCTTGATGAGGTACTGAGAAGTAGACCAAAACAATGAAACCA
1 CAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAA-CA
* * * *
68193 AAGCTCGATGTGAGAAAAATTTCGAACCCAGCTTCTTGATGAGATACTGAGAAAG-AGGTCGAAG
65 AAGCTCAATGTGAG-GAAACTTCGAACCCAGCTTCCTGATGAGATACTGAG-AAGCAGGTCGAAG
* * * * * * *
68257 TAATAAAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATTTGTCTTCCTGATGAGA
128 CAATAAAACGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* *
68322 TACAGAGAAGTGGAT
193 TACAGAAAAGCGGAT
* ** * * * * * *
68337 CAAAATAA-CAAGG-TGACATCTTCCTGATAAGATACTAAGAAGTAGACCAAATCAATGAAACCA
1 CAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
* * * * * ***
68400 AGCTCAACGTGAACGAAACTTCGAACCCCGCTTCCTGATGAGATATTAAGAAATGGGTCGAAGCA
66 AGCTCAATGTG-AGGAAACTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * * * * *
68465 ATAAAGCGGTTA-CTTTCCTGATGAGATACAGAGAAGTGAACCAGATTCTTTTTCCTAATGAGAT
130 ATAAAACGGTCAGC-TTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
*
68529 ACAGAGAAA-TGGAT
194 ACAGA-AAAGCGGAT
** * * * * *
68543 CAAAACAA-CAAGACAGTCATCTTCTTGATGAGATATTGAGAAGTAGACCAAATCAATAAAACCA
1 CAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
* * * * * * *
68607 GGCTCAAAGTGAGCAAATCTTCGAACCCTAACTTCCTGATGAGATACTAAGAAGCAAGTCGAAAC
66 AGCTCAATGTGAGGAAA-CTTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * ** *
68672 AATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTAATCTTTCTGATGAGAT
129 AATAAAACGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
*
68737 ACAGAGAAGCGGAT
194 ACAGAAAAGCGGAT
** * * *
68751 TGAAACAAGTGAGGCAGTCATCTTCTTGATGAGATACTGAGAAGTATACCAAATCAATGAAATAA
1 CAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
* * * * *
68816 AGCTCAATGTGAGCGAAACTTCGAACTCAATCTTCCTGATAAGATACTTAGAAGCAGGTGGAAGC
66 AGCTCAATGTGAG-GAAACTTCGAAC-CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * *
68881 AATAAAATGGTCAGCTTCCTGATGAGATATAGAGAAGTGGACCAAATTCGTCTTCCTGGTGAGAT
129 AATAAAACGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
68946 ACAGAGAAA-CGGAT
194 ACAGA-AAAGCGGAT
** * * * * ** * * *
68960 TGAAACAAGCGAGGCAGTCATCTTCCTAATGAGATACAAAGAAGTATACCAACTCAATGGAACAA
1 CAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
* * * *
69025 AGCTCAATGCGAGCGAAACTTCGAACCTTAGCTTCTTGATGAGATACTGAGAAGCAGGTTGAAGC
66 AGCTCAATGTGAG-GAAACTTCGAACC-CAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * * * *
69090 AATAAAATGGTCAGCTTCTTGATGAGATACTGAGAAGTGGCCCAAATTCGTCTTCTTGATGAGAT
129 AATAAAACGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* * *
69155 ATAGATAAGCAGAT
194 ACAGAAAAGCGGAT
* * * * * * *
69169 TAAAACAAGTGAGGCGGTCATCTTCCTAATGAGATACGGAAAAGTATACCAAATCAATAAAACAA
1 CAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
* * * * * **
69234 AGCAT-AATGTGAGCGAAACTTC-AAGCATCATCTTCTTGATGAGATGCTGAGAAGTAGACCGAA
66 AGC-TCAATGTGAG-GAAACTTCGAA-C-CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
* * * * * * *
69297 GCAATAAAATGGTCATCTTCCTGACGATATGCAGAAAAGTGTACCAAATTCGT
127 GCAATAAAACGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGT
69350 ATTTCTAGTA
Statistics
Matches: 1039, Mismatches: 160, Indels: 46
0.83 0.13 0.04
Matches are distributed among these distances:
205 3 0.00
206 133 0.13
207 107 0.10
208 102 0.10
209 659 0.63
210 32 0.03
211 3 0.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (207 bp):
CAAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
AGCTCAATGTGAGGAAACTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
TAAAACGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
AGAAAAGCGGAT
Found at i:70187 original size:59 final size:58
Alignment explanation
Indices: 70083--70303 Score: 227
Period size: 58 Copynumber: 3.8 Consensus size: 58
70073 ACGTTTTGAC
* * * *
70083 CCCTAAA-TTTTCCAAAATTATATTTTAACCCTTAAACTTT-TAAAAATTACCATTTTA
1 CCCTAAACTTTTCAAAAATCATATTTT-ACCCTCAAACTTTCCAAAAATTACCATTTTA
* * * *
70140 CACCTAAACTTTTCAAAAATTATAATTTTACCCCCAAA-TTTCCAAAAATTATCATTTTG
1 C-CCTAAACTTTTCAAAAATCAT-ATTTTACCCTCAAACTTTCCAAAAATTACCATTTTA
* * **
70199 CCTCTAAAC-TTCCAAAAATCACATTTTTACCCTTGAAC-TTCCAAAAATTACCATTTTA
1 CC-CTAAACTTTTCAAAAATCATA-TTTTACCCTCAAACTTTCCAAAAATTACCATTTTA
* *
70257 CCCTCAAACTTCTAAAAAATCATATTTTACCCTCAAACTTTCCAAAA
1 CCCT-AAACTTTTCAAAAATCATATTTTACCCTCAAACTTTCCAAAA
70304 CATTTTACCC
Statistics
Matches: 134, Mismatches: 20, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
57 4 0.03
58 66 0.49
59 59 0.44
60 5 0.04
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.36
Consensus pattern (58 bp):
CCCTAAACTTTTCAAAAATCATATTTTACCCTCAAACTTTCCAAAAATTACCATTTTA
Found at i:70216 original size:29 final size:28
Alignment explanation
Indices: 70083--70336 Score: 186
Period size: 29 Copynumber: 8.9 Consensus size: 28
70073 ACGTTTTGAC
*
70083 CCCTAAATTTTCC-AAAATTAT-ATTTTAA
1 CCCTAAA-CTTCCAAAAATTATCATTTT-A
** *
70111 CCCTTAAACTTTTAAAAATTACCATTTTA
1 CCC-TAAACTTCCAAAAATTATCATTTTA
* *
70140 CACCTAAACTTTTCAAAAATTATAATTTTA
1 C-CCTAAAC-TTCCAAAAATTATCATTTTA
* * *
70170 CCCCCAAATTTCCAAAAATTATCATTTTG
1 -CCCTAAACTTCCAAAAATTATCATTTTA
*
70199 CCTCTAAACTTCCAAAAATCA-CATTTTTA
1 CC-CTAAACTTCCAAAAATTATCA-TTTTA
* *
70228 CCCTTGAACTTCCAAAAATTACCATTTTA
1 CCC-TAAACTTCCAAAAATTATCATTTTA
* *
70257 CCCTCAAACTTCTAAAAAATCAT-ATTTTA
1 CCCT-AAACTTC-CAAAAATTATCATTTTA
70286 CCCTCAAACTTTCC--AAA--A-CATTTTA
1 CCCT-AAAC-TTCCAAAAATTATCATTTTA
70311 CCCCT-AACTTCCAAAAATTATCATTT
1 -CCCTAAACTTCCAAAAATTATCATTT
70337 GCCCTTGAAC
Statistics
Matches: 183, Mismatches: 23, Indels: 40
0.74 0.09 0.16
Matches are distributed among these distances:
23 4 0.02
24 3 0.02
25 10 0.05
26 4 0.02
27 4 0.02
28 16 0.09
29 100 0.55
30 41 0.22
31 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.37
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTATCATTTTA
Found at i:75029 original size:18 final size:17
Alignment explanation
Indices: 74974--75029 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
74964 TTATAAATAA
74974 TTATTTCAATTATTAAT
1 TTATTTCAATTATTAAT
* *
74991 ATTATATT-GATTAATTTAT
1 -TTAT-TTCAATT-ATTAAT
75010 TTATTTCAAATTATTAAT
1 TTATTTC-AATTATTAAT
75028 TT
1 TT
75030 TTTTAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
17 2 0.07
18 18 0.60
19 10 0.33
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
TTATTTCAATTATTAAT
Found at i:75476 original size:18 final size:18
Alignment explanation
Indices: 75453--75502 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
75443 ATGCTTTTCC
*
75453 TCTGCCTTGTGGCACGCT
1 TCTGCCTTGTGACACGCT
75471 TCTGCCTTGTGACACGCT
1 TCTGCCTTGTGACACGCT
*
75489 TCTGCCTTATGACA
1 TCTGCCTTGTGACA
75503 TGTTTTCATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.12, C:0.32, G:0.22, T:0.34
Consensus pattern (18 bp):
TCTGCCTTGTGACACGCT
Found at i:75828 original size:10 final size:10
Alignment explanation
Indices: 75813--75844 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
75803 TGACGTTTTA
75813 TTTTTTAATT
1 TTTTTTAATT
*
75823 TTTTTTATTT
1 TTTTTTAATT
75833 TTTTTTAATT
1 TTTTTTAATT
75843 TT
1 TT
75845 CTTTGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:75853 original size:20 final size:20
Alignment explanation
Indices: 75813--75853 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
75803 TGACGTTTTA
*
75813 TTTTTTAATTTTTTTTATTT
1 TTTTTTAATTTTCTTTATTT
*
75833 TTTTTTAATTTTCTTTGTTT
1 TTTTTTAATTTTCTTTATTT
75853 T
1 T
75854 ATTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTTAATTTTCTTTATTT
Found at i:86264 original size:31 final size:31
Alignment explanation
Indices: 86228--86295 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
86218 CTTAAGAATC
*
86228 CAGTGACTTAAATAAAAACCTTTGAATAATT
1 CAGTGACTTAAATAAAAACCTTAGAATAATT
* * * *
86259 TAGTGACTTAAATGAAAACGTTAGATTAATT
1 CAGTGACTTAAATAAAAACCTTAGAATAATT
86290 CAGTGA
1 CAGTGA
86296 TTATTTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACCTTAGAATAATT
Done.