Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014052.1 Kokia drynarioides strain JFW-HI SEQ_129083, 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: 99011
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:870 original size:29 final size:28
Alignment explanation
Indices: 828--957 Score: 102
Period size: 29 Copynumber: 4.5 Consensus size: 28
818 AAACTGATCG
*
828 AAAATTACCATTTTACCCCTGAACTTCC
1 AAAAATACCATTTTACCCCTGAACTTCC
*
856 AAAAAT-CCTATTTTTGACCTC-GAAACTTCC
1 AAAAATACC-A-TTTT-ACCCCTG-AACTTCC
* * * *
886 AAAAATTACCACTTAACCCCTAAACTTCT
1 AAAAA-TACCATTTTACCCCTGAACTTCC
* * *
915 AATAATTACCATTTTACCCCCGGACTTCC
1 AA-AAATACCATTTTACCCCTGAACTTCC
*
944 AAAAATCCCATTTT
1 AAAAATACCATTTT
958 TACTCCCGGA
Statistics
Matches: 78, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
27 2 0.03
28 16 0.21
29 36 0.46
30 20 0.26
31 2 0.03
32 2 0.03
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAATACCATTTTACCCCTGAACTTCC
Found at i:1853 original size:15 final size:16
Alignment explanation
Indices: 1822--1854 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1812 AATACCTACA
*
1822 TTTTTTCAAAACGATT
1 TTTTTTAAAAACGATT
1838 TTTTTTAAAAAC-ATT
1 TTTTTTAAAAACGATT
1853 TT
1 TT
1855 GTGGTGATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTTTAAAAACGATT
Found at i:5658 original size:195 final size:194
Alignment explanation
Indices: 5319--5764 Score: 571
Period size: 195 Copynumber: 2.3 Consensus size: 194
5309 ATATCGACGT
* *
5319 GATGGTTGAGGTACCGA-ATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCA
1 GATGGCTGAGGTACC-ACATATGTTGCGAGTCCTCGATAGCTCATGTGAGCAGCATCGTGAGTCA
*
5383 GGAAATGAGAAATAAATCTAAGAATGGATTACAGGCCCTACGATGGTTGGGATTTATGCATAAGT
65 GGAAAAGAGAAATAAATCTAAGAATGGATTACAGGCCCTACGATGGTTGGGATTTATGCATAAGT
*** * *
5448 GCATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGGAAACAATTATATGCACAGATACCGTA
130 GCATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGG-AACAATT-TACAAACAGACACCATA
*
5513 TC
193 CC
*
5515 GATGGCTGAGGTATCACATATGTTGCGAGTCCTCTG-TAGCTCATGTGAGCAGCATCGTGAGTCA
1 GATGGCTGAGGTACCACATATGTTGCGAGTCCTC-GATAGCTCATGTGAGCAGCATCGTGAGTCA
* * * * *
5579 -TAAAAGAGATATAAAATCCT-A-AATGGATTATAGGTCCTACGATGGTTGGGATTTATGCTTCA
65 GGAAAAGAGAAAT-AAAT-CTAAGAATGGATTACAGGCCCTACGATGGTTGGGATTTATGCAT-A
** * * *
5641 A-TGCATATTCTCGACAGCTCGTGTGAGCAGTATCGTTAGGGGACAGTTTACAAACAGACACCAT
127 AGTGCATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGGAACAATTTACAAACAGACACCAT
5705 ACC
192 ACC
* * * *
5708 GATGGCTGGGGTACCGCATATGTTGCTAGTCCTCGATAGCTCATATGAGCAGCATCG
1 GATGGCTGAGGTACCACATATGTTGCGAGTCCTCGATAGCTCATGTGAGCAGCATCG
5765 GATACTGGTA
Statistics
Matches: 219, Mismatches: 25, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
192 1 0.00
193 63 0.29
194 5 0.02
195 83 0.38
196 64 0.29
197 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (194 bp):
GATGGCTGAGGTACCACATATGTTGCGAGTCCTCGATAGCTCATGTGAGCAGCATCGTGAGTCAG
GAAAAGAGAAATAAATCTAAGAATGGATTACAGGCCCTACGATGGTTGGGATTTATGCATAAGTG
CATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGGAACAATTTACAAACAGACACCATACC
Found at i:8209 original size:22 final size:22
Alignment explanation
Indices: 8181--8238 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
8171 CATAAAATAT
*
8181 TCAATTATAATGGCGCAATCAA
1 TCAATTATATTGGCGCAATCAA
*
8203 TCAATTATATTGGAGCAATCAA
1 TCAATTATATTGGCGCAATCAA
*
8225 TCTATTATATTGGC
1 TCAATTATATTGGC
8239 ATAATACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (22 bp):
TCAATTATATTGGCGCAATCAA
Found at i:10034 original size:18 final size:20
Alignment explanation
Indices: 10008--10046 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
9998 TTAAACTCCA
10008 ATTTAACCCAA-AA-TATTT
1 ATTTAACCCAATAATTATTT
*
10026 ATTTTACCCAATAATTATTT
1 ATTTAACCCAATAATTATTT
10046 A
1 A
10047 AAACCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAACCCAATAATTATTT
Found at i:10551 original size:24 final size:24
Alignment explanation
Indices: 10501--10551 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
10491 TTTAGTTTAG
** *
10501 TTTAGTTTTTTTTCTTTTTTAGGT
1 TTTAGTTTTTTCCCTTTTTTAGCT
10525 TTTAGTTTATTTCCCTTTTTTA-CT
1 TTTAGTTT-TTTCCCTTTTTTAGCT
10549 TTT
1 TTT
10552 CTTCATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.73
Consensus pattern (24 bp):
TTTAGTTTTTTCCCTTTTTTAGCT
Found at i:13064 original size:18 final size:22
Alignment explanation
Indices: 13041--13083 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
13031 ATTTTTTTAG
13041 TTTA-TTAAA-AA-ATTAAA-T
1 TTTATTTAAAGAACATTAAACT
13059 TTTATTTAAAGAACATTAAACT
1 TTTATTTAAAGAACATTAAACT
13081 TTT
1 TTT
13084 TATCAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 2 0.10
21 6 0.29
22 4 0.19
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTATTTAAAGAACATTAAACT
Found at i:19090 original size:43 final size:42
Alignment explanation
Indices: 19028--19216 Score: 222
Period size: 43 Copynumber: 4.4 Consensus size: 42
19018 CTTGCTGTAC
*
19028 AAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATGTTTT
1 AAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATG-TTT
19071 AAAGGAAGACTCAT-ATCTCGAGATGAGCATGAGATTTATGTTT
1 AAAGGAAGACTCATGA-CTCGAGATGAGCATGAGA-TTATGTTT
* * * *
19114 AAAAATGAAGACTCGTGACTCG-GAAGGAGCATGAGA-TGTGTTT
1 --AAAGGAAGACTCATGACTCGAG-ATGAGCATGAGATTATGTTT
* *
19157 AAAGGAAGACTCGTGACTCGGGATGAGCATGAGATTATGTTT
1 AAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATGTTT
* *
19199 AATGGAAGACTTATGACT
1 AAAGGAAGACTCATGACT
19217 TGATTGTGAT
Statistics
Matches: 127, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
41 30 0.24
42 22 0.17
43 41 0.32
44 6 0.05
45 27 0.21
46 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.28
Consensus pattern (42 bp):
AAAGGAAGACTCATGACTCGAGATGAGCATGAGATTATGTTT
Found at i:20721 original size:34 final size:34
Alignment explanation
Indices: 20678--20747 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
20668 TAACTGCAGG
20678 GAGAAGAAGAAACCATCTCCTAAGGAAGAGAATA
1 GAGAAGAAGAAACCATCTCCTAAGGAAGAGAATA
20712 GAGAAGAAGAAACCATCTCCTAAGGAAGAGAATA
1 GAGAAGAAGAAACCATCTCCTAAGGAAGAGAATA
20746 GA
1 GA
20748 TTTAAAACTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.50, C:0.14, G:0.24, T:0.11
Consensus pattern (34 bp):
GAGAAGAAGAAACCATCTCCTAAGGAAGAGAATA
Found at i:34680 original size:25 final size:25
Alignment explanation
Indices: 34652--34738 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
34642 ATTCTGTTTA
34652 GCTCGTAAGAGTGATATTCTATCTG
1 GCTCGTAAGAGTGATATTCTATCTG
* * *
34677 GCTCGTGAGAGCGATATTCTATCTT
1 GCTCGTAAGAGTGATATTCTATCTG
* * *
34702 ACTCGTAAAAGT-ACTACTCTATCTGG
1 GCTCGTAAGAGTGA-TATTCTATCT-G
*
34728 GCTCATAAGAG
1 GCTCGTAAGAG
34739 CTAAACTCTT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
24 1 0.02
25 39 0.81
26 8 0.17
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (25 bp):
GCTCGTAAGAGTGATATTCTATCTG
Found at i:35472 original size:24 final size:24
Alignment explanation
Indices: 35434--35493 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
35424 TATTTTGAGA
* *
35434 TGACACATGGTCTAGCCCAAGGTT
1 TGACACACGGGCTAGCCCAAGGTT
35458 TGACACACGGGCTAGCCCAAGGTT
1 TGACACACGGGCTAGCCCAAGGTT
35482 TGACACACGGGC
1 TGACACACGGGC
35494 ATGTGGGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (24 bp):
TGACACACGGGCTAGCCCAAGGTT
Found at i:40403 original size:11 final size:11
Alignment explanation
Indices: 40384--40416 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
40374 TTAGGATATT
40384 ATTTATATTTA
1 ATTTATATTTA
*
40395 ATTTGTATTTA
1 ATTTATATTTA
40406 ATTTATATTTA
1 ATTTATATTTA
40417 CCATTTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:46967 original size:21 final size:21
Alignment explanation
Indices: 46921--46967 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
46911 CATCTTTAAT
46921 CTCT-AACCCTAAGTCATAAC
1 CTCTAAACCCTAAGTCATAAC
* *
46941 CCCTAAACCCTAAGCTC-TAAG
1 CTCTAAACCCTAAG-TCATAAC
46962 CTCTAA
1 CTCTAA
46968 GCCTTAAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 17 0.77
22 2 0.09
ACGTcount: A:0.34, C:0.36, G:0.06, T:0.23
Consensus pattern (21 bp):
CTCTAAACCCTAAGTCATAAC
Found at i:47050 original size:6 final size:6
Alignment explanation
Indices: 47041--47106 Score: 62
Period size: 7 Copynumber: 10.5 Consensus size: 6
47031 TTAAAACCCT
* * *
47041 AACCTA AACCTAA AACCTA ATCCTA AACCTAA AACCTA ACCCT- AACCAA
1 AACCTA AACCT-A AACCTA AACCTA AACCT-A AACCTA AACCTA AACCTA
47090 AACCCTA AACCCTA AAC
1 AA-CCTA AA-CCTA AAC
47107 ATTAATGATA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 3 0.06
6 23 0.46
7 24 0.48
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCTA
Found at i:47056 original size:19 final size:19
Alignment explanation
Indices: 47025--47106 Score: 98
Period size: 19 Copynumber: 4.3 Consensus size: 19
47015 CACACACACA
47025 TAAACCTTAAAACCCTAA-CC
1 TAAACC-TAAAA-CCTAACCC
*
47045 TAAACCTAAAACCTAATCC
1 TAAACCTAAAACCTAACCC
47064 TAAACCTAAAACCTAACCC
1 TAAACCTAAAACCTAACCC
47083 T-AACC-AAAACCCTAAACCC
1 TAAACCTAAAA-CCT-AACCC
47102 TAAAC
1 TAAAC
47107 ATTAATGATA
Statistics
Matches: 57, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
17 4 0.07
18 12 0.21
19 32 0.56
20 9 0.16
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (19 bp):
TAAACCTAAAACCTAACCC
Found at i:47057 original size:13 final size:13
Alignment explanation
Indices: 47041--47105 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
47031 TTAAAACCCT
47041 AACCTAAACCTAA
1 AACCTAAACCTAA
*
47054 AACCTAATCCT-A
1 AACCTAAACCTAA
47066 AACCTAAAACCT-A
1 AACCT-AAACCTAA
*
47079 ACCCT-AACC-AA
1 AACCTAAACCTAA
47090 AACCCTAAACCCTAA
1 AA-CCTAAA-CCTAA
47105 A
1 A
47106 CATTAATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 6 0.14
12 9 0.21
13 22 0.52
14 2 0.05
15 3 0.07
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.15
Consensus pattern (13 bp):
AACCTAAACCTAA
Found at i:48792 original size:77 final size:80
Alignment explanation
Indices: 48624--48798 Score: 243
Period size: 77 Copynumber: 2.2 Consensus size: 80
48614 CAATGAATGA
*
48624 AGATCTGAAAACTAAAATAGAGATGAAAACTTGTTCTAAAGATAAAAACAAAAAACCCACAAAAA
1 AGATCTGAAAACTAAAACAGAGATGAAAACTTGTTCTAAAGAT--AAACAAAAAACCCACAAAAA
48689 TAAAAGAAGATAACCAT
64 TAAAAGAAGATAACCAT
* * * *
48706 AGATTTGAAAACTAAAACAGAGATGAAAACTT-TTCTAAAGAT-GA-AAAAAACCCATAGAAATA
1 AGATCTGAAAACTAAAACAGAGATGAAAACTTGTTCTAAAGATAAACAAAAAACCCACAAAAATA
48768 AAAGAAGATAACCA-
66 AAAGAAGATAACCAT
48782 AGGATCTG-AAACTAAAA
1 A-GATCTGAAAACTAAAA
48799 AAAGACATGA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
76 10 0.12
77 35 0.41
78 1 0.01
81 10 0.12
82 30 0.35
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.18
Consensus pattern (80 bp):
AGATCTGAAAACTAAAACAGAGATGAAAACTTGTTCTAAAGATAAACAAAAAACCCACAAAAATA
AAAGAAGATAACCAT
Found at i:51037 original size:30 final size:30
Alignment explanation
Indices: 50975--51039 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
50965 ACTTATTTTA
* *
50975 TTGTTAATTTTATTATTATTTTAGAAATAT
1 TTGTTAATTTTATTACTATTTTAGAAACAT
* **
51005 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTATTACTATTTTAGAAACAT
51035 TTGTT
1 TTGTT
51040 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTACTATTTTAGAAACAT
Found at i:51530 original size:23 final size:24
Alignment explanation
Indices: 51498--51543 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
51488 TTAGTATGAT
51498 AAAAATATA-TTCTCATGATTTATC
1 AAAAATATAGTTCTCATG-TTTATC
51522 AAAAA-ATATGTTCTCATGTTTA
1 AAAAATATA-GTTCTCATGTTTA
51544 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 9 0.45
25 8 0.40
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (24 bp):
AAAAATATAGTTCTCATGTTTATC
Found at i:51551 original size:25 final size:26
Alignment explanation
Indices: 51496--51552 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
51486 TATTAGTATG
**
51496 ATAAAAATATATTCTCATGATTTATC
1 ATAAAAATATATTCTCATGATTTAAA
*
51522 A-AAAAATATGTTCTCATG-TTTAAA
1 ATAAAAATATATTCTCATGATTTAAA
51546 ATAAAAA
1 ATAAAAA
51553 AGTAATTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.19
25 21 0.78
26 1 0.04
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (26 bp):
ATAAAAATATATTCTCATGATTTAAA
Found at i:56421 original size:40 final size:39
Alignment explanation
Indices: 56377--56504 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 39
56367 TGTTAAGCCA
56377 TAGCTTGAATTTTAACACCGGCTCGTAGCCTGCTATGCTG
1 TAGCTTGAATTTTAACACCGGCTCGTAGCCTGCTATGC-G
* * * *
56417 TAGCTT-AGATTTTAATACC-G-TC-TCGCCTTCTAAAT-CC
1 TAGCTTGA-ATTTTAACACCGGCTCGTAGCCTGCT--ATGCG
* *
56454 TAG-TTGCATTTTAACACCGGCTCGTAGCCTGCTAAGCCG
1 TAGCTTGAATTTTAACACCGGCTCGTAGCCTGCTATG-CG
56493 TAGCTTGAATTT
1 TAGCTTGAATTT
56505 ATTCGAACAA
Statistics
Matches: 67, Mismatches: 11, Indels: 20
0.68 0.11 0.20
Matches are distributed among these distances:
36 12 0.18
37 12 0.18
38 5 0.07
39 15 0.22
40 23 0.34
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (39 bp):
TAGCTTGAATTTTAACACCGGCTCGTAGCCTGCTATGCG
Found at i:66649 original size:23 final size:23
Alignment explanation
Indices: 66625--66766 Score: 85
Period size: 23 Copynumber: 6.1 Consensus size: 23
66615 CTAGCGTTCT
*
66625 CTCTGATTAGCATTGTGTGTGCT
1 CTCTGATTAGCATTGTGTGTGCC
* * *
66648 CTCCG-TTCAGCATTTTGCGTGCC
1 CTCTGATT-AGCATTGTGTGTGCC
** * * *
66671 CTCTTTTTAGCA-CGTTTCATGCC
1 CTCTGATTAGCATTGTGT-GTGCC
* *
66694 CTCTGTTTAGCACTGTGTGTGCC
1 CTCTGATTAGCATTGTGTGTGCC
* *
66717 CTCTATTATTAGCACTT-CGTGTGCC
1 CTC--TGATTAGCA-TTGTGTGTGCC
66742 CTCTGATTAGCACTT-TGTGTGCC
1 CTCTGATTAGCA-TTGTGTGTGCC
66765 CT
1 CT
66767 TTGTTACCCA
Statistics
Matches: 91, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
22 3 0.03
23 65 0.71
24 5 0.05
25 17 0.19
26 1 0.01
ACGTcount: A:0.12, C:0.27, G:0.20, T:0.40
Consensus pattern (23 bp):
CTCTGATTAGCATTGTGTGTGCC
Found at i:66732 original size:25 final size:24
Alignment explanation
Indices: 66700--66797 Score: 92
Period size: 25 Copynumber: 4.0 Consensus size: 24
66690 TGCCCTCTGT
66700 TTAGCACTGTGTGTGCCCTCTATTA
1 TTAGCACT-TGTGTGCCCTCTATTA
*
66725 TTAGCACTTCGTGTGCCCTC--TGA
1 TTAGCACTT-GTGTGCCCTCTATTA
* *
66748 TTAGCACTTTGTGTGCCCTTTGTTA
1 TTAGCAC-TTGTGTGCCCTCTATTA
** *
66773 CCCAGCACTTATGTGCCCTCTATTA
1 -TTAGCACTTGTGTGCCCTCTATTA
66798 AGTACTTCAG
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
23 18 0.30
24 3 0.05
25 34 0.57
26 5 0.08
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.39
Consensus pattern (24 bp):
TTAGCACTTGTGTGCCCTCTATTA
Found at i:66788 original size:48 final size:48
Alignment explanation
Indices: 66690--66797 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
66680 GCACGTTTCA
* ** *
66690 TGCCCTCTGTTTAGCACTGTGTGTGCCCTCTATTATTAGCACTTCGTG
1 TGCCCTCTGATTAGCACTGTGTGTGCCCTCTATTACCAGCACTTCATG
* * *
66738 TGCCCTCTGATTAGCACTTTGTGTGCCCTTTGTTACCCAGCACTT-ATG
1 TGCCCTCTGATTAGCACTGTGTGTGCCCTCTATTA-CCAGCACTTCATG
66786 TGCCCTCT-ATTA
1 TGCCCTCTGATTA
66798 AGTACTTCAG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 4 0.08
48 41 0.79
49 7 0.13
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.39
Consensus pattern (48 bp):
TGCCCTCTGATTAGCACTGTGTGTGCCCTCTATTACCAGCACTTCATG
Found at i:69761 original size:13 final size:13
Alignment explanation
Indices: 69743--69789 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
69733 TTAAATGGTA
69743 AAATGAAATGTTT
1 AAATGAAATGTTT
*
69756 AGATGAAAT-TGTT
1 AAATGAAATGT-TT
*
69769 ATATGAAATGTTT
1 AAATGAAATGTTT
69782 AAATGAAA
1 AAATGAAA
69790 ATAGATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 1 0.03
13 27 0.93
14 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (13 bp):
AAATGAAATGTTT
Found at i:69799 original size:27 final size:26
Alignment explanation
Indices: 69745--69800 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
69735 AAATGGTAAA
* * *
69745 ATGAAATGTTTAGATGAAATTGTTAT
1 ATGAAATGTTTAAATGAAATAGATAT
69771 ATGAAATGTTTAAATGAAAATAGATAT
1 ATGAAATGTTTAAATG-AAATAGATAT
69798 ATG
1 ATG
69801 TAATTGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.38
Consensus pattern (26 bp):
ATGAAATGTTTAAATGAAATAGATAT
Found at i:72518 original size:10 final size:10
Alignment explanation
Indices: 72485--72520 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
72475 ATTTCTTTTT
72485 TTTTTCTTTTC
1 TTTTTC-TTTC
*
72496 TTCTTCTTTC
1 TTTTTCTTTC
72506 TTTTTCTTTC
1 TTTTTCTTTC
72516 TTTTT
1 TTTTT
72521 GTGAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:74922 original size:96 final size:96
Alignment explanation
Indices: 74727--74919 Score: 248
Period size: 98 Copynumber: 2.0 Consensus size: 96
74717 AAACCTTGAA
* * * * *
74727 AAGGGTATTCGATTATCCCGGTTAGAAGAAAAGTCGCGTCTAGTAAGTTAAGGTACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCG-CTAATAAGTCAAGGCACAAATTTTCA
*
74792 AAACCCGAGATAAAAAGAATATTGCCTCGATTT
65 AAA-CCGAGATAAAAAGAATATTGCCTCAATTT
** *
74825 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATCGC-CTAATAAGTCAAGGCACAAATTTTCAA
1 AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCGCTAATAAGTCAAGGCACAAATTTTCAA
74889 AA-CGAGA-AATAAAGGAATATTGCCTCAATTT
66 AACCGAGATAA-AAA-GAATATTGCCTCAATTT
74920 TAAATATTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
93 2 0.02
94 8 0.10
95 16 0.19
96 26 0.31
98 32 0.38
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (96 bp):
AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCGCTAATAAGTCAAGGCACAAATTTTCAA
AACCGAGATAAAAAGAATATTGCCTCAATTT
Found at i:76362 original size:29 final size:32
Alignment explanation
Indices: 76302--76362 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 32
76292 CGACTGCCTT
* *
76302 TTTATTATTTTTTAATATATTTATTTATTAAA
1 TTTATTATTTATTAATATATTTATTTACTAAA
*
76334 TTTA-TATTTATTAAT-TA-TTATTTCCTAAA
1 TTTATTATTTATTAATATATTTATTTACTAAA
76363 AAACGTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 10 0.38
30 2 0.08
31 10 0.38
32 4 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTATTATTTATTAATATATTTATTTACTAAA
Found at i:76542 original size:121 final size:121
Alignment explanation
Indices: 76328--76569 Score: 376
Period size: 121 Copynumber: 2.0 Consensus size: 121
76318 ATATTTATTT
* **
76328 ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAACGTTTCATAATAAATGGTCATATCAGG
1 ATTAAATTTATATTTATTAATTATAATTTCCTAAAAAACGTTTCATAATAAATGGTCATAAAAGG
* *
76393 TTATAATAATGGAATAAATTAATGCATTAATGTACAATAAAACGTTATGAAATTCA
66 TTATAATAATGGAATAAATTAATGCATTAATGAACAATAAAACATTATGAAATTCA
* *
76449 ATTAAATTTATATTTATTAATTATAATTTCTTTAAAAACGTTTCATAATAAATGGTCATAAAAGG
1 ATTAAATTTATATTTATTAATTATAATTTCCTAAAAAACGTTTCATAATAAATGGTCATAAAAGG
** * * *
76514 TTATAATAATGGAATAAATTGGTGCATTAATGAATATTAAAACATTTTGAAATTCA
66 TTATAATAATGGAATAAATTAATGCATTAATGAACAATAAAACATTATGAAATTCA
76570 TATAATAAAC
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 109 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (121 bp):
ATTAAATTTATATTTATTAATTATAATTTCCTAAAAAACGTTTCATAATAAATGGTCATAAAAGG
TTATAATAATGGAATAAATTAATGCATTAATGAACAATAAAACATTATGAAATTCA
Found at i:77134 original size:23 final size:22
Alignment explanation
Indices: 77107--77198 Score: 69
Period size: 23 Copynumber: 4.0 Consensus size: 22
77097 ATTTTGGACT
77107 TTTAAACTAAATTTAAAATTAAG
1 TTTAAA-TAAATTTAAAATTAAG
* *
77130 TTTAAA-ACCATTTCAAAATTTAAA
1 TTTAAATA-AATTT-AAAA-TTAAG
*
77154 TTTAAAATAAATTTAAACTTAAG
1 TTT-AAATAAATTTAAAATTAAG
* * *
77177 CTTCAAATAATTTTAAATTTAA
1 -TTTAAATAAATTTAAAATTAA
77199 AACCAATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
21 1 0.02
22 4 0.07
23 30 0.55
24 12 0.22
25 7 0.13
26 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTAAATAAATTTAAAATTAAG
Found at i:77152 original size:24 final size:22
Alignment explanation
Indices: 77117--77160 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
77107 TTTAAACTAA
*
77117 ATTTAAAATTAAGTTTAAAACC
1 ATTTAAAATTAAATTTAAAACC
77139 ATTTCAAAATTTAAATTTAAAA
1 ATTT-AAAA-TTAAATTTAAAA
77161 TAAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 4 0.21
24 11 0.58
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTTAAAATTAAATTTAAAACC
Found at i:77167 original size:17 final size:17
Alignment explanation
Indices: 77145--77234 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 17
77135 AACCATTTCA
77145 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
*
77162 AAATTTAAACTTAAGCTTCAAAT
1 AAATTTAAA--T----TTAAAAT
* *
77185 AATTTTAAATTTAAAAC
1 AAATTTAAATTTAAAAT
* *
77202 CAATTTAAACTTAAAAT
1 AAATTTAAATTTAAAAT
* *
77219 AATTTTAAAATTAAAA
1 AAATTTAAATTTAAAA
77235 GTTTGATTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
17 40 0.71
19 1 0.02
21 1 0.02
23 14 0.25
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:77767 original size:49 final size:49
Alignment explanation
Indices: 77708--77821 Score: 147
Period size: 49 Copynumber: 2.3 Consensus size: 49
77698 CGTCGTTTAA
* * * ** *
77708 GGCCTTAACCTTTTCCTTTGTATCTTCGTGGTTTCGGGTTTACCATTGC
1 GGCCTCAACCTTTCCCTTTGTATCTTCGGGGTACCGAGTTTACCATTGC
* * *
77757 GGCCTCAACCTTTCCCTTTGTATGTTCGGGGTACCGAGTTTGCCATTTC
1 GGCCTCAACCTTTCCCTTTGTATCTTCGGGGTACCGAGTTTACCATTGC
77806 GGCCTCAACCTTTCCC
1 GGCCTCAACCTTTCCC
77822 ATTACATCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.11, C:0.30, G:0.20, T:0.39
Consensus pattern (49 bp):
GGCCTCAACCTTTCCCTTTGTATCTTCGGGGTACCGAGTTTACCATTGC
Found at i:78052 original size:50 final size:50
Alignment explanation
Indices: 77798--78508 Score: 347
Period size: 50 Copynumber: 14.3 Consensus size: 50
77788 TACCGAGTTT
* * * * * * *
77798 GCCATTTCGGCCTCAACCTTTCCCATT-ACATCTTCTAAAGTACCAGGCTC
1 GCCATTGCGACCTCAACCTTTCCC-TTCACCTCTTCTTAGGTATCAGGTTC
* * *** * ** *
77848 GCCATTG-TAGTCTCAACCTTTCCCTTTGTCTCTTCGT-GGTATTGGGTTA
1 GCCATTGCGA-CCTCAACCTTTCCCTTCACCTCTTCTTAGGTATCAGGTTC
* * *** * *
77897 GCCGTTGC-AGCCTCAACCTTTCCCATCGTATTTTCTAAGGTATC-GGATTC
1 GCCATTGCGA-CCTCAACCTTTCCCTTCACCTCTTCTTAGGTATCAGG-TTC
* * * * * *
77947 GCCGTCGCGGCCTCGATCC-TTCCCTTCATCTCTTCAT-GGTA-CTAGGTTC
1 GCCATTGCGACCTC-AACCTTTCCCTTCACCTCTTCTTAGGTATC-AGGTTC
* ** * *
77996 ACCATTGCGATTTCAACCTTTCCCATCACCTCTTCTTAGGTATCGGGTTC
1 GCCATTGCGACCTCAACCTTTCCCTTCACCTCTTCTTAGGTATCAGGTTC
* * * * *
78046 GCCATTGCGGCCTCAACCTTTCCCTTCACATCTT-TTAAGT-TACCGAATTC
1 GCCATTGCGACCTCAACCTTTCCCTTCACCTCTTCTTAGGTAT-CAG-GTTC
* * * *
78096 GCCGTTGC-AGCCTCAATCC-TTCCTTTCATCTCTTCAT-GGTA-CTAGGTTC
1 GCCATTGCGA-CCTCAA-CCTTTCCCTTCACCTCTTCTTAGGTATC-AGGTTC
* * * *
78145 GCCATTAC-AGCTTCAACCTTTCCCATCACCTCTTCTTAGGTA-CCGAGTTC
1 GCCATTGCGA-CCTCAACCTTTCCCTTCACCTCTTCTTAGGTATCAG-GTTC
* * * * * * *
78195 GCCATTACGGCCTCGACCTTTCCCTTCACATCTT-TTAAG-ATACTAGATTA
1 GCCATTGCGACCTCAACCTTTCCCTTCACCTCTTCTTAGGTAT-C-AGGTTC
* * ** *
78245 GCCATTGCGACCTCAATCGTTCCCTTCGTCTCTTCAT-GGTA-CTAGGTTC
1 GCCATTGCGACCTCAACCTTTCCCTTCACCTCTTCTTAGGTATC-AGGTTC
* * *
78294 GCCATTGC-AGCTTCAACCTTTCCCATCACCTCTTTTTAGGTATCAGGTTC
1 GCCATTGCGA-CCTCAACCTTTCCCTTCACCTCTTCTTAGGTATCAGGTTC
* ** * *
78344 GCCATTACGGTCTCAACCTTTCCCTTCACATCTT-TTAAGGTATCAGATTC
1 GCCATTGCGACCTCAACCTTTCCCTTCACCTCTTCTT-AGGTATCAGGTTC
* ** * * *
78394 GCCATTGCGGCCTCAATCC-TTCCCTTCGTCTCTTCAT-GGTACCGGGTTC
1 GCCATTGCGACCTCAA-CCTTTCCCTTCACCTCTTCTTAGGTATCAGGTTC
* * * * *
78443 ACCATTACGACCTCAACCTTTCCCTTCACATCTT-TTATGGTACCAGATTC
1 GCCATTGCGACCTCAACCTTTCCCTTCACCTCTTCTTA-GGTATCAGGTTC
* *
78493 ACCGTTGCGACCTCAA
1 GCCATTGCGACCTCAA
78509 TGTCAAACCT
Statistics
Matches: 496, Mismatches: 127, Indels: 76
0.71 0.18 0.11
Matches are distributed among these distances:
48 12 0.02
49 180 0.36
50 290 0.58
51 14 0.03
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.34
Consensus pattern (50 bp):
GCCATTGCGACCTCAACCTTTCCCTTCACCTCTTCTTAGGTATCAGGTTC
Found at i:78066 original size:149 final size:149
Alignment explanation
Indices: 77906--78484 Score: 747
Period size: 149 Copynumber: 3.9 Consensus size: 149
77896 AGCCGTTGCA
* ** * * * *
77906 GCCTCAACCTTTCCCATCGTAT-TTTCTAAGGTATCGGATTCGCCGTCGCGGCCTCGATCCTTCC
1 GCCTCAACCTTTCCCTTCACATCTTT-TAAGGTATCAGATTCGCCATTGCGGCCTCAATCCTTCC
* *
77970 CTTCATCTCTTCATGGTACTAGGTTCACCATTGC-GATTTCAACCTTTCCCATCACCTCTTCTTA
65 CTTCATCTCTTCATGGTACTAGGTTCACCATTACAG-CTTCAACCTTTCCCATCACCTCTTCTTA
*
78034 GGTATCGGGTTCGCCATTGCG
129 GGTATCGGGTTCGCCATTACG
* * * *
78055 GCCTCAACCTTTCCCTTCACATCTTTTAAGTTA-CCGAATTCGCCGTTGCAGCCTCAATCCTTCC
1 GCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAG-ATTCGCCATTGCGGCCTCAATCCTTCC
* *
78119 TTTCATCTCTTCATGGTACTAGGTTCGCCATTACAGCTTCAACCTTTCCCATCACCTCTTCTTAG
65 CTTCATCTCTTCATGGTACTAGGTTCACCATTACAGCTTCAACCTTTCCCATCACCTCTTCTTAG
* *
78184 GTACCGAGTTCGCCATTACG
130 GTATCGGGTTCGCCATTACG
* * * * *
78204 GCCTCGACCTTTCCCTTCACATCTTTTAAGATA-CTAGATTAGCCATTGCGACCTCAATCGTTCC
1 GCCTCAACCTTTCCCTTCACATCTTTTAAGGTATC-AGATTCGCCATTGCGGCCTCAATCCTTCC
* * * *
78268 CTTCGTCTCTTCATGGTACTAGGTTCGCCATTGCAGCTTCAACCTTTCCCATCACCTCTTTTTAG
65 CTTCATCTCTTCATGGTACTAGGTTCACCATTACAGCTTCAACCTTTCCCATCACCTCTTCTTAG
*
78333 GTATCAGGTTCGCCATTACG
130 GTATCGGGTTCGCCATTACG
*
78353 GTCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGATTCGCCATTGCGGCCTCAATCCTTCCC
1 GCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGATTCGCCATTGCGGCCTCAATCCTTCCC
* ** * * *
78418 TTCGTCTCTTCATGGTACCGGGTTCACCATTAC-GACCTCAACCTTTCCCTTCACATCTT-TTAT
66 TTCATCTCTTCATGGTACTAGGTTCACCATTACAG-CTTCAACCTTTCCCATCACCTCTTCTTA-
78481 GGTA
129 GGTA
78485 CCAGATTCAC
Statistics
Matches: 380, Mismatches: 43, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
148 6 0.02
149 368 0.97
150 6 0.02
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.35
Consensus pattern (149 bp):
GCCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGATTCGCCATTGCGGCCTCAATCCTTCCC
TTCATCTCTTCATGGTACTAGGTTCACCATTACAGCTTCAACCTTTCCCATCACCTCTTCTTAGG
TATCGGGTTCGCCATTACG
Found at i:78144 original size:99 final size:100
Alignment explanation
Indices: 78041--78509 Score: 404
Period size: 99 Copynumber: 4.7 Consensus size: 100
78031 TTAGGTATCG
* * *
78041 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGTTACC-GAATTCGCCGTTGCA
1 GGTTCGCCATTACGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAG-ATTCGCCATTGCA
*
78105 GCCTCAATCC-TTCCTTTCATCTCTTCATGGTACTA
65 GCCTCAATCCTTTCCCTTCATCTCTTCATGGTACTA
* * * * *
78140 GGTTCGCCATTACAGCTTCAACCTTTCCCATCACCTCTTCTT-AGGTACC-GAGTTCGCCATTAC
1 GGTTCGCCATTACGGCCTCAACCTTTCCCTTCACATCTT-TTAAGGTACCAGA-TTCGCCATTGC
* * * * *
78203 GGCCTCGA-CCTTTCCCTTCA-CATCTTTTAAGATACTA
64 AGCCTCAATCCTTTCCCTTCATC-TC-TTCATGGTACTA
* * * * * * * * * * *
78240 GATTAGCCATTGCGACCTCAATCGTTCCCTT--CGTCTCTTCATGGTACTAGGTTCGCCATTGCA
1 GGTTCGCCATTACGGCCTCAACCTTTCCCTTCACATCT-TTTAAGGTACCAGATTCGCCATTGCA
* * * **
78303 GCTTCAA-CCTTTCCCATCACCTCTTTTTAGGTA-TCA
65 GCCTCAATCCTTTCCCTTCATCTCTTCAT-GGTACT-A
* * *
78339 GGTTCGCCATTACGGTCTCAACCTTTCCCTTCACATCTTTTAAGGTATCAGATTCGCCATTGCGG
1 GGTTCGCCATTACGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAGATTCGCCATTGCAG
* **
78404 CCTCAATCC-TTCCCTTCGTCTCTTCATGGTACCG
66 CCTCAATCCTTTCCCTTCATCTCTTCATGGTACTA
* * * * *
78438 GGTTCACCATTACGACCTCAACCTTTCCCTTCACATCTTTTATGGTACCAGATTCACCGTTGC-G
1 GGTTCGCCATTACGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAGATTCGCCATTGCAG
78502 ACCTCAAT
66 -CCTCAAT
78510 GTCAAACCTG
Statistics
Matches: 289, Mismatches: 65, Indels: 32
0.75 0.17 0.08
Matches are distributed among these distances:
98 14 0.05
99 195 0.67
100 74 0.26
101 6 0.02
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.34
Consensus pattern (100 bp):
GGTTCGCCATTACGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTACCAGATTCGCCATTGCAG
CCTCAATCCTTTCCCTTCATCTCTTCATGGTACTA
Found at i:86879 original size:30 final size:30
Alignment explanation
Indices: 86768--87015 Score: 167
Period size: 29 Copynumber: 8.5 Consensus size: 30
86758 TTTTAGGTCG
* * * *
86768 AAAATGTGACTTTTGGAAGTTTG-GGAGCA
1 AAAATGTAATTTTTGGAAGTTTGAGGGGTA
* * *
86797 AAAATGGTAACTTTTGGATGTTCGA-GGGT-
1 AAAAT-GTAATTTTTGGAAGTTTGAGGGGTA
* *
86826 AAAATGGTAA-TTTTAG-AGATTCGAGGGGTA
1 AAAAT-GTAATTTTTGGAAG-TTTGAGGGGTA
* * *
86856 AAAATGTGATTTTTGGAAGTTCGAGGGCT-
1 AAAATGTAATTTTTGGAAGTTTGAGGGGTA
* *
86885 AAAATGTAATTTTTTGAAAGTTTGA-GGAT-
1 AAAATGTAA-TTTTTGGAAGTTTGAGGGGTA
* * *
86914 AAAATGCAATTTTTAGAAGTTT-AGGGGTC
1 AAAATGTAATTTTTGGAAGTTTGAGGGGTA
* * *
86943 AAAATGAAATTTTTAGAAGTTTGA-TGGTA
1 AAAATGTAATTTTTGGAAGTTTGAGGGGTA
* *
86972 AAAATGTAATTTTTGAAAAGTTTGAGGGCT-
1 AAAATGTAATTTTTG-GAAGTTTGAGGGGTA
*
87002 AAAATATAATTTTT
1 AAAATGTAATTTTT
87016 AGAAAGTGTA
Statistics
Matches: 179, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
27 2 0.01
28 24 0.13
29 78 0.44
30 71 0.40
31 4 0.02
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAGTTTGAGGGGTA
Found at i:86918 original size:58 final size:59
Alignment explanation
Indices: 86796--87022 Score: 223
Period size: 58 Copynumber: 3.9 Consensus size: 59
86786 GTTTGGGAGC
* * * *
86796 AAAAATGGTAACTTTTGGATGTTCGAGGG-TAAAATGGTAA-TTTTAGAGA-TTCGAGGGGT
1 AAAAAT-GTAATTTTTGGAAGTTCGAGGGCTAAAAT-GTAATTTTTAGAAAGTTTGA-GGGT
* * *
86855 AAAAATGTGATTTTTGGAAGTTCGAGGGCTAAAATGTAATTTTTTGAAAGTTTGAGGAT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGCTAAAATGTAATTTTTAGAAAGTTTGAGGGT
* * * * * *
86914 -AAAATGCAATTTTTAGAAGTT-TAGGGGTCAAAATGAAATTTTTAG-AAGTTTGATGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGCT-AAAATGTAATTTTTAGAAAGTTTGAGGGT
* * *
86971 AAAAATGTAATTTTTGAAAAGTTTGAGGGCTAAAATATAATTTTTAGAAAGT
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGCTAAAATGTAATTTTTAGAAAGT
87023 GTAGGGACCT
Statistics
Matches: 137, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
57 15 0.11
58 68 0.50
59 41 0.30
60 13 0.09
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (59 bp):
AAAAATGTAATTTTTGGAAGTTCGAGGGCTAAAATGTAATTTTTAGAAAGTTTGAGGGT
Found at i:86976 original size:87 final size:89
Alignment explanation
Indices: 86849--87028 Score: 224
Period size: 87 Copynumber: 2.0 Consensus size: 89
86839 TAGAGATTCG
** *
86849 AGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGCTAAAATGTAATTTTTTG-AAAGTTTGA-GG
1 AGGGGTAAAAATGAAATTTTTAGAAGTTCGAGGGCTAAAATGTAA-TTTTTGAAAAGTTTGAGGG
* *
86912 ATAAAATGCAATTTTTAG-AAGTTT
65 ATAAAATACAATTTTTAGAAAGTGT
* * *
86936 AGGGGTCAAAATGAAATTTTTAGAAGTTTGATGG-TAAAAATGTAATTTTTGAAAAGTTTGAGGG
1 AGGGGTAAAAATGAAATTTTTAGAAGTTCGAGGGCT-AAAATGTAATTTTTGAAAAGTTTGAGGG
* *
87000 CTAAAATATAATTTTTAGAAAGTGT
65 ATAAAATACAATTTTTAGAAAGTGT
87025 AGGG
1 AGGG
87029 ACCTTTTGAG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
86 7 0.09
87 46 0.58
88 17 0.22
89 9 0.11
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (89 bp):
AGGGGTAAAAATGAAATTTTTAGAAGTTCGAGGGCTAAAATGTAATTTTTGAAAAGTTTGAGGGA
TAAAATACAATTTTTAGAAAGTGT
Found at i:87022 original size:30 final size:30
Alignment explanation
Indices: 86820--87022 Score: 174
Period size: 29 Copynumber: 6.9 Consensus size: 30
86810 TTGGATGTTC
* *
86820 GAGGG-TAAAATGGTAA-TTTTAGAGA-TTC
1 GAGGGCTAAAAT-GTAATTTTTAGAAAGTTT
* * * *
86848 GAGGGGTAAAAATGTGATTTTT-GGAAGTTC
1 GAGGGCT-AAAATGTAATTTTTAGAAAGTTT
*
86878 GAGGGCTAAAATGTAATTTTTTGAAAGTTT
1 GAGGGCTAAAATGTAATTTTTAGAAAGTTT
* *
86908 GA-GGATAAAATGCAATTTTTAG-AAGTTT
1 GAGGGCTAAAATGTAATTTTTAGAAAGTTT
* *
86936 -AGGGGTCAAAATGAAATTTTTAG-AAGTTT
1 GAGGGCT-AAAATGTAATTTTTAGAAAGTTT
*
86965 GATGG-TAAAAATGTAATTTTT-GAAAAGTTT
1 GAGGGCT-AAAATGTAATTTTTAG-AAAGTTT
*
86995 GAGGGCTAAAATATAATTTTTAGAAAGT
1 GAGGGCTAAAATGTAATTTTTAGAAAGT
87023 GTAGGGACCT
Statistics
Matches: 146, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.01
28 15 0.10
29 71 0.49
30 57 0.39
31 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
GAGGGCTAAAATGTAATTTTTAGAAAGTTT
Found at i:88111 original size:29 final size:32
Alignment explanation
Indices: 88051--88111 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 32
88041 CGACTGCCTT
* *
88051 TTTATTATTTTTTAATATATTTATTTATTAAA
1 TTTATTATTTATTAATATATTTATTTACTAAA
*
88083 TTTA-TATTTATTAAT-TA-TTATTTCCTAAA
1 TTTATTATTTATTAATATATTTATTTACTAAA
88112 AAAACGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 10 0.38
30 2 0.08
31 10 0.38
32 4 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTATTATTTATTAATATATTTATTTACTAAA
Found at i:88913 original size:17 final size:17
Alignment explanation
Indices: 88893--88956 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
88883 CATTCCAAAT
88893 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
**
88910 TTTAAATTTAAAACCAA
1 TTTAAATTTAAAATAAA
*
88927 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
88944 TTTAAAATTAAAA
1 TTTAAATTTAAAA
88957 GTTAGATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:88916 original size:24 final size:24
Alignment explanation
Indices: 88852--88918 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
88842 ATTTTGGACT
* * *
88852 TTTAAACTAAATTTAAA-ATTAAG
1 TTTAAAATAAATTTAAATTTTAAA
* *
88875 TTTAAAAT-CATTCCAAATTTTAAA
1 TTTAAAATAAATT-TAAATTTTAAA
88899 TTTAAAATAAATTTAAATTT
1 TTTAAAATAAATTTAAATTT
88919 AAAACCAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 3 0.09
23 10 0.29
24 18 0.53
25 3 0.09
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (24 bp):
TTTAAAATAAATTTAAATTTTAAA
Found at i:88929 original size:28 final size:28
Alignment explanation
Indices: 88897--88950 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
88887 CCAAATTTTA
*
88897 AATTTAAA-ATAAATTTAAATTTAAAACC
1 AATTTAAACATAAA-ATAAATTTAAAACC
*
88925 AATTTAAACTTAAAATAAATTTAAAA
1 AATTTAAACATAAAATAAATTTAAAA
88951 TTAAAAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (28 bp):
AATTTAAACATAAAATAAATTTAAAACC
Found at i:98068 original size:31 final size:31
Alignment explanation
Indices: 98033--98108 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
98023 AATTGATGTA
*
98033 TTTATATATATAATTGACA-TAAAATCAAAAT
1 TTTATATATATAATTGAAACTAAAAT-AAAAT
* * *
98064 TTTATATATA-CATTTAAACTATAATAAAAT
1 TTTATATATATAATTGAAACTAAAATAAAAT
*
98094 TTCATATATATAATT
1 TTTATATATATAATT
98109 ACTCCAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (31 bp):
TTTATATATATAATTGAAACTAAAATAAAAT
Done.