Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011983.1 Kokia drynarioides strain JFW-HI SEQ_126981, 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: 94486
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:42 original size:26 final size:26
Alignment explanation
Indices: 23--72 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
13 TAAACAAAGC
23 TTTTAAAAAGTGTTGTTAAAAAATGA
1 TTTTAAAAAGTGTTGTTAAAAAATGA
* * *
49 TTTTGACAAGTGTTTTTAAAAAAT
1 TTTTAAAAAGTGTTGTTAAAAAAT
73 TAGACATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (26 bp):
TTTTAAAAAGTGTTGTTAAAAAATGA
Found at i:4654 original size:16 final size:16
Alignment explanation
Indices: 4629--4672 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
4619 TATCATTACT
*
4629 AATTTAAAATTTTATA
1 AATTAAAAATTTTATA
* * *
4645 AATTATAAATTGTCTA
1 AATTAAAAATTTTATA
4661 AATTAAAAATTT
1 AATTAAAAATTT
4673 ATCATTTTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
AATTAAAAATTTTATA
Found at i:5636 original size:21 final size:20
Alignment explanation
Indices: 5608--5647 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5598 CATCCTTTCT
5608 TTTTAAAAAAATTAAAACTA
1 TTTTAAAAAAATTAAAACTA
5628 TTTTAAAAAAATTAAAACTA
1 TTTTAAAAAAATTAAAACTA
5648 ATTAAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TTTTAAAAAAATTAAAACTA
Found at i:5652 original size:10 final size:10
Alignment explanation
Indices: 5617--5658 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
5607 TTTTTAAAAA
5617 AATTAAAACT
1 AATTAAAACT
* *
5627 ATTTTAAAA-A
1 A-ATTAAAACT
5637 AATTAAAACT
1 AATTAAAACT
5647 AATTAAAACT
1 AATTAAAACT
5657 AA
1 AA
5659 AAATATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 6 0.23
10 14 0.54
11 6 0.23
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (10 bp):
AATTAAAACT
Found at i:5652 original size:19 final size:20
Alignment explanation
Indices: 5610--5654 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
5600 TCCTTTCTTT
*
5610 TTAAAAAAATTAAAACTATT
1 TTAAAAAAATTAAAACTATA
5630 TTAAAAAAATTAAAACTA-A
1 TTAAAAAAATTAAAACTATA
5649 TTAAAA
1 TTAAAA
5655 CTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAAAAAATTAAAACTATA
Found at i:16956 original size:56 final size:56
Alignment explanation
Indices: 16898--17033 Score: 186
Period size: 56 Copynumber: 2.4 Consensus size: 56
16888 AAACACATTA
16898 AAAATAACATTCAAACAATAAAAATAACAACAAAAACAGCAACAAAAATAACA-GT
1 AAAATAACATTCAAACAATAAAAATAACAACAAAAACAGCAACAAAAATAACACGT
* * * *
16953 AAAACAACATTAAAAACAATAAAAATAGCAACAAAAACAGTAACAAAAATAACACG-
1 AAAATAACATT-CAAACAATAAAAATAACAACAAAAACAGCAACAAAAATAACACGT
* *
17009 AAAATAACAATCAAAACAGTAAAAA
1 AAAATAACATTC-AAACAATAAAAA
17034 AAATCGATTA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
55 10 0.14
56 59 0.84
57 1 0.01
ACGTcount: A:0.68, C:0.15, G:0.04, T:0.12
Consensus pattern (56 bp):
AAAATAACATTCAAACAATAAAAATAACAACAAAAACAGCAACAAAAATAACACGT
Found at i:16958 original size:44 final size:44
Alignment explanation
Indices: 16897--16989 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
16887 AAAACACATT
* * *
16897 AAAAATAACATTCAAACAATA-AAAATAACAACAAAAACAGCAAC
1 AAAAATAACAGTAAAACAACATAAAA-AACAACAAAAACAGCAAC
* * *
16941 AAAAATAACAGTAAAACAACATTAAAAACAATAAAAATAGCAAC
1 AAAAATAACAGTAAAACAACATAAAAAACAACAAAAACAGCAAC
16985 AAAAA
1 AAAAA
16990 CAGTAACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 39 0.93
45 3 0.07
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (44 bp):
AAAAATAACAGTAAAACAACATAAAAAACAACAAAAACAGCAAC
Found at i:17790 original size:5 final size:5
Alignment explanation
Indices: 17782--17811 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
17772 ACAATAAATT
*
17782 TTAAA TTAAA TTAAA TTAAA TTAAT TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
17812 ATGTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:17902 original size:19 final size:21
Alignment explanation
Indices: 17859--17905 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
17849 ATTACAATCA
*
17859 AACCCAATACCTTAAAAATCT
1 AACCCAATACCTTAAAAACCT
17880 -ACCCAA-ACCTT-AAAACCT
1 AACCCAATACCTTAAAAACCT
17898 AACCCAAT
1 AACCCAAT
17906 GCCTAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 6 0.26
19 11 0.48
20 6 0.26
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCAATACCTTAAAAACCT
Found at i:18503 original size:26 final size:29
Alignment explanation
Indices: 18474--18533 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
18464 AGTTGAAGAA
*
18474 GGAAAGAATGTGTT-T-T-ATTTTTTAAT
1 GGAAAGAATGGGTTATGTCATTTTTTAAT
*
18500 GGAAAGAATGGGTTATGTCTTTTTTTAAT
1 GGAAAGAATGGGTTATGTCATTTTTTAAT
18529 GGAAA
1 GGAAA
18534 TAATCAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 13 0.45
27 1 0.03
28 1 0.03
29 14 0.48
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (29 bp):
GGAAAGAATGGGTTATGTCATTTTTTAAT
Found at i:18939 original size:30 final size:30
Alignment explanation
Indices: 18815--18940 Score: 155
Period size: 30 Copynumber: 4.2 Consensus size: 30
18805 ATCATTTTTA
* *
18815 ACCCCCAAAGTTTTCAAAAATTCATATTTG
1 ACCCCTAAAGTTTTCAAAAATTCAAATTTG
*
18845 ACCCTTAAA-TTTTCTAAAAATTCAAATTTG
1 ACCCCTAAAGTTTTC-AAAAATTCAAATTTG
* * * * *
18875 ACTCCTAAAATTTCCAAAAATTCAAGTTTA
1 ACCCCTAAAGTTTTCAAAAATTCAAATTTG
*
18905 ACCCCTAAAGTTTTCAAAAATTAAAATTTG
1 ACCCCTAAAGTTTTCAAAAATTCAAATTTG
18935 ACCCCT
1 ACCCCT
18941 TTTTAATGTA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 5 0.06
30 71 0.89
31 4 0.05
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (30 bp):
ACCCCTAAAGTTTTCAAAAATTCAAATTTG
Found at i:21634 original size:18 final size:18
Alignment explanation
Indices: 21611--21647 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21601 CGATTGAATC
* *
21611 ATTTTTATTTATTTATTT
1 ATTTTTAATAATTTATTT
21629 ATTTTTAATAATTTATTT
1 ATTTTTAATAATTTATTT
21647 A
1 A
21648 ATTGAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTAATAATTTATTT
Found at i:22972 original size:25 final size:25
Alignment explanation
Indices: 22925--22972 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
22915 TAGGTTAATT
**
22925 AGAGTTTAACTGAGAAACTAAAAAC
1 AGAGTTTAACTGAGAAAAGAAAAAC
22950 AGAGTTTAACTCGA-AAAAGAAAA
1 AGAGTTTAACT-GAGAAAAGAAAA
22973 GTTGAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.19
Consensus pattern (25 bp):
AGAGTTTAACTGAGAAAAGAAAAAC
Found at i:23856 original size:204 final size:206
Alignment explanation
Indices: 23506--23913 Score: 604
Period size: 204 Copynumber: 2.0 Consensus size: 206
23496 TAAATCTCTT
* *
23506 GCATAATCAGAATCAACATATCCGACTAAACCTTTTTGAGTTCTTCCAAACTCTAACCACATGTT
1 GCATAATCAAAATCAACATATCCAACTAAACCTTTTTGAGTTCTTCCAAACTCTAACCACATGTT
* * **
23571 AGAAGTACCTCGTAAATATATAAAAATCTACTTAATCGCATGTCAGTGTAACTCACCAGGATTTG
66 AGAAGTACCTCGTAAATATATAAAAATCCACTTAACCAAATGTCAGTGTAACTCACCAGGATTTG
** * * *
23636 CCATTTATCAACTAAC-ACTAAC-ACATGTGAAATATCAGAACTAGTGTATACCATTGCATACAT
131 CCACGTATCAACTAACAACTAACAACATGTGAAATATCAGAACGAGTGCATACCATTGCATAAAT
23699 CAAACTTAACC
196 CAAACTTAACC
* * * *
23710 GCATAATCAAAATCAACATATCCAACTAGACTTTTTTGAGTTCTTCCAAACTCTAAGCACGTGTT
1 GCATAATCAAAATCAACATATCCAACTAAACCTTTTTGAGTTCTTCCAAACTCTAACCACATGTT
* * *
23775 AGAAGTACCTTGTAAATATATAAAAATCCACTTAACCAAATGTCAGTGTAACTTACTAGGATTTG
66 AGAAGTACCTCGTAAATATATAAAAATCCACTTAACCAAATGTCAGTGTAACTCACCAGGATTTG
* *
23840 CCACGTATCGACTAACAAAACTAACAACATGTGTAATATCAGAACGAGTGCATACCATTGCATAA
131 CCACGTATCAACTAAC--AACTAACAACATGTGAAATATCAGAACGAGTGCATACCATTGCATAA
23905 ATCAAACTT
194 ATCAAACTT
23914 CTAACTACGC
Statistics
Matches: 180, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
204 130 0.72
207 6 0.03
208 44 0.24
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (206 bp):
GCATAATCAAAATCAACATATCCAACTAAACCTTTTTGAGTTCTTCCAAACTCTAACCACATGTT
AGAAGTACCTCGTAAATATATAAAAATCCACTTAACCAAATGTCAGTGTAACTCACCAGGATTTG
CCACGTATCAACTAACAACTAACAACATGTGAAATATCAGAACGAGTGCATACCATTGCATAAAT
CAAACTTAACC
Found at i:29041 original size:96 final size:96
Alignment explanation
Indices: 28852--29043 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
28842 ACTTTTGCAA
** *
28852 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* *
28917 GAATCGAAGATAAGGAAACATTGTCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * *
28948 AAGGGTATTTGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
*
29012 -GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
29044 TTTTAAAGCT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 3 0.04
96 75 0.90
97 5 0.06
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (96 bp):
AAGGATATTTGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:29356 original size:30 final size:30
Alignment explanation
Indices: 29321--29555 Score: 142
Period size: 30 Copynumber: 8.0 Consensus size: 30
29311 GTGAAATAGT
* *
29321 AATTTTGGGAAAATTCGGGGTTAAAAATGG
1 AATTTTTGGAAATTTCGGGGTTAAAAATGG
* * * *
29351 AATTTTTAGACA-TTCGGGGGT-AAAAGGG
1 AATTTTTGGAAATTTCGGGGTTAAAAATGG
** * * * **
29379 TAATTTTAAG-AGTTTTGAGGTCGAAAATGG
1 -AATTTTTGGAAATTTCGGGGTTAAAAATGG
* * *
29409 GATTTTTGGAAATTTAGGGG-TAAAAATTG
1 AATTTTTGGAAATTTCGGGGTTAAAAATGG
* *
29438 AATTTTTGGAAGTTTCGAGGG-TAAAAATAG
1 AATTTTTGGAAATTTCG-GGGTTAAAAATGG
* * *
29468 AATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTTGGAAATTTCGGGGTTAAAAATGG
* * * *
29498 GA-TTTTGGGAAGTTCGAGGG-TAAAAAGGG
1 AATTTTTGGAAATTTCG-GGGTTAAAAATGG
* * *
29527 AATTTTTGGAAGTTTCGAGGTCAAAAATG
1 AATTTTTGGAAATTTCGGGGTTAAAAATG
29556 AGATTTTGGG
Statistics
Matches: 153, Mismatches: 43, Indels: 18
0.71 0.20 0.08
Matches are distributed among these distances:
28 6 0.04
29 70 0.46
30 77 0.50
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (30 bp):
AATTTTTGGAAATTTCGGGGTTAAAAATGG
Found at i:29434 original size:29 final size:29
Alignment explanation
Indices: 29402--29575 Score: 183
Period size: 30 Copynumber: 5.9 Consensus size: 29
29392 TTTGAGGTCG
* *
29402 AAAATGGGATTTTTGGAAATTTAGGGGTA
1 AAAATGGGATTTTTGGAAGTTTCGGGGTA
* *
29431 AAAATTGAATTTTTGGAAGTTTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTTCG-GGGTA
* * *
29461 AAAATAGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGGATTTTTGGAAGTTTCGGGGT-A
*
29491 AAAATGGGATTTTGGGAAG-TTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTTCG-GGGTA
*
29520 AAAA-GGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGG-ATTTTTGGAAGTTTCGGGGT-A
* *
29550 AAAATGAGATTTTGGGAAG-TTCGGGG
1 AAAATGGGATTTTTGGAAGTTTCGGGG
29576 ACCTCCAGGG
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
28 3 0.02
29 51 0.41
30 67 0.54
31 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGTTTCGGGGTA
Found at i:29502 original size:89 final size:89
Alignment explanation
Indices: 29389--29570 Score: 244
Period size: 89 Copynumber: 2.0 Consensus size: 89
29379 TAATTTTAAG
* * * **
29389 AGTTTTGAGGTCGAAAATGGGATTTTTGGAAATTTAG-GGGTAAAAATTGAATTTTTGGAAGTTT
1 AGTTTCGAGGTCAAAAATGGGA-TTTTGGAAAGTTAGAGGGTAAAAAGGGAATTTTTGGAAGTTT
*
29453 CGAGGGT-AAAAAT-AGAATTTTTGGA
65 CGA-GGTCAAAAATGAG-ATTTTGGGA
* *
29478 AGTTTCGAGGTCAAAAATGGGATTTTGGGAAGTTCGAGGGTAAAAAGGGAATTTTTGGAAGTTTC
1 AGTTTCGAGGTCAAAAATGGGATTTTGGAAAGTTAGAGGGTAAAAAGGGAATTTTTGGAAGTTTC
29543 GAGGTCAAAAATGAGATTTTGGGA
66 GAGGTCAAAAATGAGATTTTGGGA
29567 AGTT
1 AGTT
29571 CGGGGACCTC
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
88 14 0.17
89 66 0.80
90 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (89 bp):
AGTTTCGAGGTCAAAAATGGGATTTTGGAAAGTTAGAGGGTAAAAAGGGAATTTTTGGAAGTTTC
GAGGTCAAAAATGAGATTTTGGGA
Found at i:29571 original size:59 final size:59
Alignment explanation
Indices: 29402--29572 Score: 231
Period size: 59 Copynumber: 2.9 Consensus size: 59
29392 TTTGAGGTCG
* * * * *
29402 AAAATGGG-ATTTTTGGAAATTTAGGGGT-AAAAATTGA-ATTTTTGGAAGTTTCGAGGGT
1 AAAAAGGGAATTTTTGGAAGTTTCGAGGTCAAAAA-TGAGATTTTGGGAAG-TTCGAGGGT
** *
29460 AAAAATAGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTGGGAAGTTCGAGGGT
1 AAAAAGGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTGGGAAGTTCGAGGGT
29519 AAAAAGGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTGGGAAGTTCG
1 AAAAAGGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTGGGAAGTTCG
29573 GGGACCTCCA
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
58 5 0.05
59 79 0.80
60 15 0.15
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (59 bp):
AAAAAGGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTGGGAAGTTCGAGGGT
Found at i:30335 original size:79 final size:78
Alignment explanation
Indices: 30198--30375 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 78
30188 GTCGCGAGTT
* * * ** * * *
30198 CGTAGCCACGCGCCGCTGCGTGTCTCCGCCATGGCAACATCTGATCGTACGCGGGCCCCCACATC
1 CGTAGCCACGCGCCGTTGCGCGTTTCCGCGGTGGCAACATCCGATCGTACACGCG-CCCCACATC
30263 TCAGGTCACC-GATC
65 TCAGGTCACCAG-TC
* * * *
30277 CGTAGTCATGCGCCGTTGCGCGTTTCCGCGGTGGCAACGTCCGATCGTCCACGCGCCCCACATCT
1 CGTAGCCACGCGCCGTTGCGCGTTTCCGCGGTGGCAACATCCGATCGTACACGCGCCCCACATCT
**
30342 TTGGTCACCAGTC
66 CAGGTCACCAGTC
30355 CGTAGCCACGCGCCGTTGCGC
1 CGTAGCCACGCGCCGTTGCGC
30376 CTCTCCGCCA
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
78 38 0.46
79 44 0.54
ACGTcount: A:0.14, C:0.39, G:0.27, T:0.20
Consensus pattern (78 bp):
CGTAGCCACGCGCCGTTGCGCGTTTCCGCGGTGGCAACATCCGATCGTACACGCGCCCCACATCT
CAGGTCACCAGTC
Found at i:30396 original size:78 final size:78
Alignment explanation
Indices: 30198--30430 Score: 234
Period size: 78 Copynumber: 3.0 Consensus size: 78
30188 GTCGCGAGTT
* * * * * * *
30198 CGTAGCCACGCGCCGCTGCGTGTCTCCGCCATGGCAACATCTGATCGTACGCGGGCCCCCACATC
1 CGTAGCCACGCGCCGTTGCGCGTCTCCGCCATGGCAACGTCCGATCGTCCACGCG-CCCCACATC
30263 TCAGGTCACCGATC
65 TCAGGTCACCGATC
* * * **
30277 CGTAGTCATGCGCCGTTGCGCGTTTCCGCGGTGGCAACGTCCGATCGTCCACGCGCCCCACATCT
1 CGTAGCCACGCGCCGTTGCGCGTCTCCGCCATGGCAACGTCCGATCGTCCACGCGCCCCACATCT
**
30342 TTGGTCACC-AGTC
66 CAGGTCACCGA-TC
* * * * * * *
30355 CGTAGCCACGCGCCGTTGCGCCTCTCCGCCATAGCACCGTCCAATCGTCCATGCTCCCCATATCT
1 CGTAGCCACGCGCCGTTGCGCGTCTCCGCCATGGCAACGTCCGATCGTCCACGCGCCCCACATCT
* *
30420 CCGATCACCGA
66 CAGGTCACCGA
30431 GGAGTTCAAA
Statistics
Matches: 123, Mismatches: 29, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
77 1 0.01
78 78 0.63
79 44 0.36
ACGTcount: A:0.15, C:0.41, G:0.24, T:0.20
Consensus pattern (78 bp):
CGTAGCCACGCGCCGTTGCGCGTCTCCGCCATGGCAACGTCCGATCGTCCACGCGCCCCACATCT
CAGGTCACCGATC
Found at i:31407 original size:6 final size:6
Alignment explanation
Indices: 31391--31479 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
31381 ACATTTAAAA
*
31391 TAAATTT TAAATT TAAATT TATAA-- TAAATT TAAATT TAAA-C TAAATT
1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* * * *
31438 TAAATT TAGAA-- TAAACT TAATTT TAAA-A TAAATT TAAGTT TA
1 TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT TA
31480 TTGGTCCCAG
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
4 4 0.06
5 12 0.18
6 42 0.64
7 8 0.12
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:31410 original size:24 final size:23
Alignment explanation
Indices: 31383--31479 Score: 79
Period size: 23 Copynumber: 4.0 Consensus size: 23
31373 GACCTTGGAC
31383 ATTTAAAATAAATTTTAAATTTAA
1 ATTTAAAATAAA-TTTAAATTTAA
*
31407 ATTTATAATAAATTTAAATTTAA
1 ATTTAAAATAAATTTAAATTTAA
* *
31430 A-CTAAATTTAAATTTAGAATAAACTTAA
1 ATTTAAA-ATAAATTTA-AAT----TTAA
* *
31458 TTTTAAAATAAATTTAAGTTTA
1 ATTTAAAATAAATTTAAATTTA
31480 TTGGTCCCAG
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
22 3 0.05
23 23 0.40
24 14 0.24
27 2 0.03
28 12 0.21
29 4 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTAAAATAAATTTAAATTTAA
Found at i:31418 original size:17 final size:17
Alignment explanation
Indices: 31398--31480 Score: 105
Period size: 17 Copynumber: 4.9 Consensus size: 17
31388 AAATAAATTT
31398 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
31415 TAAATTTAAATTTA-AA
1 TAAATTTAAATTTATAA
*
31431 CTAAATTTAAATTTAGAA
1 -TAAATTTAAATTTATAA
* * *
31449 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
31466 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
31481 TGGTCCCAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
16 2 0.03
17 54 0.93
18 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:31438 original size:34 final size:34
Alignment explanation
Indices: 31398--31480 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
31388 AAATAAATTT
* *
31398 TAAATTTAAATTTATAATAAATTTAAATTTAAAC
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
* *
31432 TAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
31466 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
31481 TGGTCCCAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAATTTAAAA
Found at i:32303 original size:218 final size:218
Alignment explanation
Indices: 31908--32452 Score: 658
Period size: 218 Copynumber: 2.6 Consensus size: 218
31898 CTCATCAGGG
* * *
31908 AGCTAACCACTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGAT
1 AGCTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
*
31973 TTGCTCACATCGGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGC
66 TTGCTCACATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGC
* * **
32038 GTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCTGGAAAACGAATTTGGTCCACTTCTCCTTA
131 GTCATTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTA
*
32103 TCTCGTCAGGAAGATGGTCAAGA
196 TCTCATCAGGAAGATGGTCAAGA
** * *
32126 AGCTAACCGTTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGAT
1 AGCTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
* * * *
32191 TTGCTCACGTCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCTTCAGGAAGATGACTGC
66 TTGCTCACATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGC
* * * * *
32256 GTCATTTGTTTCAATTCGCTTGTTTGTATTTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTA
131 GTCATTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTA
32321 TCTCATC------A--G----GA
196 TCTCATCAGGAAGATGGTCAAGA
* * * ** * * *
32332 AGCTAACC-TTTTATTGCTTTGACCTTATTCTCAATGTCTCATCAGGAAGTTGGGGTTCGAAGAT
1 AGCTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
* * *
32396 TTGCTCACATCGAGCGT--G---GATTTGGTTTTTCTTCTCAGTGTCTCATCAAGAAGATGA
66 TTGCTCACATCGAGCGTGAGTTTGATTTGG-TCTTCTTCTCAGTATCTCATCAGGAAGATGA
32453 TCGCATCGCT
Statistics
Matches: 289, Mismatches: 37, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
200 6 0.02
201 27 0.09
203 1 0.00
205 63 0.22
206 10 0.03
210 1 0.00
212 1 0.00
218 180 0.62
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (218 bp):
AGCTAACCACTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
TTGCTCACATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGC
GTCATTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCAGTA
TCTCATCAGGAAGATGGTCAAGA
Found at i:32970 original size:28 final size:28
Alignment explanation
Indices: 32938--32999 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
32928 TCAAATATTC
* *
32938 TATTAAAGAAGATGATCAAAGGAAACAA
1 TATTAAAAAAGAGGATCAAAGGAAACAA
*
32966 TATTAAAAAAGAGGATCAAAGGAAATAA
1 TATTAAAAAAGAGGATCAAAGGAAACAA
32994 TCATTA
1 T-ATTA
33000 GTTGAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.21
Consensus pattern (28 bp):
TATTAAAAAAGAGGATCAAAGGAAACAA
Found at i:34911 original size:29 final size:28
Alignment explanation
Indices: 34863--35331 Score: 266
Period size: 29 Copynumber: 16.1 Consensus size: 28
34853 ACCCCGAAGG
*
34863 ACCCTAAACTATCCAAAAATTACCATTTT
1 ACCCTGAACT-TCCAAAAATTACCATTTT
* *
34892 ACACCTGAACTTCTAAAAA-TCCCATTTTT
1 AC-CCTGAACTTCCAAAAATTACCA-TTTT
**
34921 GACCCCCAAACTTCCAAAAA-T-CCATTTTT
1 -A-CCCTGAACTTCCAAAAATTACCA-TTTT
** *
34950 GACCCAAAAACTTCCAAAAATTACCATTTC
1 -ACCC-TGAACTTCCAAAAATTACCATTTT
* *
34980 ACCCCCGAACTTCCAAAAA-TCCCATTTTTT
1 A-CCCTGAACTTCCAAAAATTACCA--TTTT
* *
35010 A-CTTCGAAACTTCTAAAAATTACCATTTT
1 ACCCT-G-AACTTCCAAAAATTACCATTTT
35039 ACCCCTGAACTTCCAAAAATT-CCATTTTT
1 A-CCCTGAACTTCCAAAAATTACCA-TTTT
* * *
35068 GACCCTAAAACTTCCAAAAAATACCATTTC
1 -ACCCT-GAACTTCCAAAAATTACCATTTT
* **
35098 ACCCCCGAACTTTAAAAAATCTA--ATTTTT
1 A-CCCTGAACTTCCAAAAAT-TACCA-TTTT
** *
35127 AACCCAAAAACTTCCAAAAATTACCATTTC
1 -ACCC-TGAACTTCCAAAAATTACCATTTT
* *
35157 ACCCTCGAACTTCCAAGAA-TCCCATTTTT
1 ACCCT-GAACTTCCAAAAATTACCA-TTTT
35186 GA-CCTCGAAACTTCCAAAAATTACCATTTT
1 -ACCCT-G-AACTTCCAAAAATTACCATTTT
*
35216 ACCCTTGAACTTCCAAAAA-TCCCATTTTT
1 ACCC-TGAACTTCCAAAAATTACCA-TTTT
** *
35245 GATCCCAAAATTTCC-AAAATTACCATTTT
1 -A-CCCTGAACTTCCAAAAATTACCATTTT
*
35274 ACCCTCGAACTTCTAAAAA-T-CTCATTTT
1 ACCCT-GAACTTCCAAAAATTAC-CATTTT
*
35302 GACCCCGAACTTCC-AAAATTACCATTTT
1 -ACCCTGAACTTCCAAAAATTACCATTTT
35330 AC
1 AC
35332 TCCCGGATGT
Statistics
Matches: 347, Mismatches: 50, Indels: 88
0.72 0.10 0.18
Matches are distributed among these distances:
27 10 0.03
28 51 0.15
29 152 0.44
30 112 0.32
31 22 0.06
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (28 bp):
ACCCTGAACTTCCAAAAATTACCATTTT
Found at i:34938 original size:59 final size:56
Alignment explanation
Indices: 34868--35331 Score: 251
Period size: 59 Copynumber: 7.9 Consensus size: 56
34858 GAAGGACCCT
*
34868 AAACTATCCAAAAATTACCATTTTACACCTGAACTTCTAAAAA-TCCCATTTTTGACCCCC
1 AAACT-TCCAAAAA-T-CCATTTTACACCTGAACTTCTAAAAATTACCA-TTTT-ACCCCC
** * *
34928 AAACTTCCAAAAATCCATTTTTGAC-CCAAAAACTTCCAAAAATTACCATTTCACCCCC
1 AAACTTCCAAAAATCCA-TTTT-ACACC-TGAACTTCTAAAAATTACCATTTTACCCCC
* ** * *
34986 GAACTTCCAAAAATCCCATTTTTTACTTCGAAACTTCTAAAAATTACCATTTTACCCCT
1 AAACTTCCAAAAAT-CCATTTTACACCT-G-AACTTCTAAAAATTACCATTTTACCCCC
* * * * *
35045 GAACTTCCAAAAATTCCATTTTTGAC-CCTAAAACTTCCAAAAAATACCATTTCACCCCC
1 AAACTTCCAAAAA-TCCA-TTTT-ACACCT-GAACTTCTAAAAATTACCATTTTACCCCC
* ** * ** * * *
35104 GAACTTTAAAAAATCTAATTTTTA-ACCCAAAAACTTCCAAAAATTACCATTTCACCCTC
1 AAACTTCCAAAAATC-CA-TTTTACA-CC-TGAACTTCTAAAAATTACCATTTTACCCCC
* * ** * **
35163 GAACTTCCAAGAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTACCCTT
1 AAACTTCCAAAAAT-CCATTTTACACCT-G-AACTTCTAAAAATTACCATTTTACCCCC
* ** * * *
35222 GAACTTCCAAAAATCCCATTTTTGATC-CCAAAATTTC-CAAAATTACCATTTTACCCTC
1 AAACTTCCAAAAAT-CCA-TTTT-A-CACCTGAACTTCTAAAAATTACCATTTTACCCCC
* * * *
35280 GAACTTCTAAAAATCTCATTTTGAC-CCCGAACTTC-CAAAATTACCATTTTAC
1 AAACTTCCAAAAATC-CATTTT-ACACCTGAACTTCTAAAAATTACCATTTTAC
35332 TCCCGGATGT
Statistics
Matches: 331, Mismatches: 50, Indels: 50
0.77 0.12 0.12
Matches are distributed among these distances:
56 25 0.08
57 10 0.03
58 74 0.22
59 199 0.60
60 21 0.06
61 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (56 bp):
AAACTTCCAAAAATCCATTTTACACCTGAACTTCTAAAAATTACCATTTTACCCCC
Found at i:35066 original size:118 final size:116
Alignment explanation
Indices: 34899--35328 Score: 496
Period size: 118 Copynumber: 3.7 Consensus size: 116
34889 TTTACACCTG
* * *
34899 AACTTCTAAAAA-TCCCATTTTTGACCCCCAAACTTCCAAAAATCCATTTTTGACCCAAAAACTT
1 AACTTCTAAAAATTACCA-TTTT-ACCCTCGAACTTCCAAAAATCCATTTTTGACCC-AAAACTT
* * *
34963 CCAAAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTTACTTCGA
63 CCAAAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTAACTCCAA
35017 AACTTCTAAAAATTACCATTTTACCC-CTGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTT
1 AACTTCTAAAAATTACCATTTTACCCTC-GAACTTCCAAAAA-TCCATTTTTGACCC-AAAACTT
* ** **
35081 CCAAAAAATACCATTTCACCCCCGAACTTTAAAAAATCTAATTTTTAAC-CCAAA
63 CCAAAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTAACTCC-AA
* * * *
35135 AACTTCCAAAAATTACCATTTCACCCTCGAACTTCCAAGAATCCCATTTTTGACCTCGAAACTTC
1 AACTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAAT-CCATTTTTGACC-CAAAACTTC
* ** *
35200 CAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA-TCCCAA
64 CAAAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTAACT-CCAA
* * * **
35253 AATTTC-CAAAATTACCATTTTACCCTCGAACTTCTAAAAATCTCA-TTTTGACCCCGAACTTCC
1 AACTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATC-CATTTTTGACCCAAAACTTCC
35316 -AAAATTACCATTT
65 AAAAATTACCATTT
35329 TACTCCCGGA
Statistics
Matches: 271, Mismatches: 31, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
114 13 0.05
115 8 0.03
116 10 0.04
117 51 0.19
118 181 0.67
119 8 0.03
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (116 bp):
AACTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCATTTTTGACCCAAAACTTCCA
AAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTAACTCCAA
Found at i:35169 original size:177 final size:175
Alignment explanation
Indices: 34899--35328 Score: 582
Period size: 177 Copynumber: 2.4 Consensus size: 175
34889 TTTACACCTG
* * * * *
34899 AACTTCTAAAAATCCCATTTTTGACCCCCAAACTTCCAAAAATC-CATTTTTGACCCAAAAACTT
1 AACTTCCAAAAATACCA--TTTCACCCCCGAACTT-TAAAAATCTCATTTTTGACCCAAAAACTT
* * *
34963 CCAAAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTTACTTCGAAACTTCTAAAA
63 CCAAAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAA
*
35028 ATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGA-CCCTAA
128 ATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGATCCC-AA
* *
35076 AACTTCCAAAAAATACCATTTCACCCCCGAACTTTAAAAAATCTAATTTTTAACCCAAAAACTTC
1 AACTTCC-AAAAATACCATTTCACCCCCGAACTTT-AAAAATCTCATTTTTGACCCAAAAACTTC
* *
35141 CAAAAATTACCATTTCACCCTCGAACTTCCAAGAATCCCATTTTTGACCTCGAAACTTCCAAAAA
64 CAAAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAA
*
35206 TTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGATCCCAA
129 TTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGATCCCAA
* * * * **
35253 AATTTCCAAAATTACCATTTTACCCTCGAACTTCTAAAAATCTCA-TTTTGACCC-CGAACTTCC
1 AACTTCCAAAAATACCATTTCACCCCCGAACTT-TAAAAATCTCATTTTTGACCCAAAAACTTCC
35316 -AAAATTACCATTT
65 AAAAATTACCATTT
35329 TACTCCCGGA
Statistics
Matches: 226, Mismatches: 22, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
173 13 0.06
174 7 0.03
175 8 0.04
176 53 0.23
177 133 0.59
178 12 0.05
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (175 bp):
AACTTCCAAAAATACCATTTCACCCCCGAACTTTAAAAATCTCATTTTTGACCCAAAAACTTCCA
AAAATTACCATTTCACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATT
ACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGATCCCAA
Found at i:35758 original size:97 final size:96
Alignment explanation
Indices: 35656--35848 Score: 239
Period size: 97 Copynumber: 2.0 Consensus size: 96
35646 AAACTTTAAA
* * * *
35656 AATCGAGGCAATG-TTCTTTTAT-TTCGAGTTTTGAAA-ATTCGTGCCTTAACTCACTAGGTGTA
1 AATCGAGGCAATGTTTC-CTTATCTTCGA-TTCTGAAATATT-GGGCCTTAACTCACTAGGTGCA
**
35718 ATTTTTTCTTCAAATCAAAATAATCGAATACCCTT
63 A-CCTTTCTTCAAATCAAAATAATCGAATACCCTT
*
35753 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAATATTGGGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAATATTGGGCCTTAACTCACTAGGTGCAACC
* * *
35818 TTTCTTCAAATCGAGATAATCGAATATCCTT
66 TTTCTTCAAATCAAAATAATCGAATACCCTT
35849 TTGCAAAAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
96 28 0.34
97 44 0.53
98 11 0.13
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAATATTGGGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCAAAATAATCGAATACCCTT
Found at i:52998 original size:23 final size:22
Alignment explanation
Indices: 52972--53024 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
52962 ATATAAATTT
52972 TAAATATTT-TAAAATAATTAATA
1 TAAATATTTATAAAAT--TTAATA
*
52995 TAAATGATTTATAAAATTTAATT
1 TAAAT-ATTTATAAAATTTAATA
53018 TAAATAT
1 TAAATAT
53025 AAAAACTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 15 0.56
24 4 0.15
25 6 0.22
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TAAATATTTATAAAATTTAATA
Found at i:53388 original size:31 final size:31
Alignment explanation
Indices: 53338--53398 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
53328 AACAATCCAA
* * **
53338 TGACTTGAATAAAAACTTTCGCATAATTCAG
1 TGACTTAAACAAAAACTTTCAAATAATTCAG
*
53369 TGACTTAAACAAAAGCTTTCAAATAATTCA
1 TGACTTAAACAAAAACTTTCAAATAATTCA
53399 ATGATCATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (31 bp):
TGACTTAAACAAAAACTTTCAAATAATTCAG
Found at i:54632 original size:32 final size:32
Alignment explanation
Indices: 54577--54639 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
54567 ATTAATCAAT
* *
54577 ATGAGTTATCAAATAAAATTAATTTATTTATC
1 ATGAGTTATCAAATAAAAGTAATTAATTTATC
* **
54609 ATGAGTTATTAAATTCAAGTAATTAATTTAT
1 ATGAGTTATCAAATAAAAGTAATTAATTTAT
54640 AAGTTTATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (32 bp):
ATGAGTTATCAAATAAAAGTAATTAATTTATC
Found at i:56962 original size:29 final size:29
Alignment explanation
Indices: 56930--56995 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
56920 ATTCATCCAT
*
56930 AAAGGCTCACATATAACAAAGTTAGTCAC
1 AAAGGCTCACATATAACAAAGTTAGCCAC
*
56959 AAAGGCTCACATATAACAGAGTTAGCCAC
1 AAAGGCTCACATATAACAAAGTTAGCCAC
56988 AAAGGCTC
1 AAAGGCTC
56996 TTTTTCAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (29 bp):
AAAGGCTCACATATAACAAAGTTAGCCAC
Found at i:62549 original size:128 final size:129
Alignment explanation
Indices: 62378--62628 Score: 310
Period size: 128 Copynumber: 2.0 Consensus size: 129
62368 TGTCCGATTC
* * * *
62378 ATTTATGTTTATGAATAAACTCATTTATTTATCTATTCGTTTATTGACTCATTTATT-TGAAAAT
1 ATTTATATTTATGAAGAAACTCATTTATTTATCTATTCGTTTATAGACTCATTTATTCAG-AAAT
* *
62442 GATATTTTCCAATAAAAAATAC-TAAATAATATA-TCCCTCTATTTTTATATTTAAATTCGGTTT
65 GATATTTTCCAATAAAAAATACTTAAATAATATATTCCATCTATTTCTATATTTAAATTCGGTTT
* * * * *
62505 ATTTATATTTATGAAGAAGCTCGTTTTTTTTATCTATTTGTTTATAGACTCGTTTATTCAGAAAT
1 ATTTATATTTATGAAGAAACTC-ATTTATTTATCTATTCGTTTATAGACTCATTTATTCAGAAAT
* * * * * *
62570 TATATTTTCCTATGACAAATACTTAGATAATATATTCCATCTATTTCTATATTTGAATT
65 GATATTTTCCAATAAAAAATACTTAAATAATATATTCCATCTATTTCTATATTTAAATT
62629 TGGACTCTTT
Statistics
Matches: 103, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
127 19 0.18
128 52 0.50
129 11 0.11
130 21 0.20
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.49
Consensus pattern (129 bp):
ATTTATATTTATGAAGAAACTCATTTATTTATCTATTCGTTTATAGACTCATTTATTCAGAAATG
ATATTTTCCAATAAAAAATACTTAAATAATATATTCCATCTATTTCTATATTTAAATTCGGTTT
Found at i:66758 original size:10 final size:10
Alignment explanation
Indices: 66743--66773 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
66733 GGAGCATCAT
66743 AAAAACAAAA
1 AAAAACAAAA
66753 AAAAACAAAA
1 AAAAACAAAA
66763 AAAACACAAAA
1 AAAA-ACAAAA
66774 TGGTTGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:75451 original size:31 final size:31
Alignment explanation
Indices: 75400--75491 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
75390 TCTAAAATTA
* *
75400 ATAATACATAAAATAT-TTTAAA-ATTTTAAAT
1 ATAATA-ATAAATTATATTTAAATAATTT-AAT
75431 ATAATAATAAATTATATTTAAATAATTTAAT
1 ATAATAATAAATTATATTTAAATAATTTAAT
* ** * *
75462 ATAGTGGTAAATAATATTTAAATGATTTAA
1 ATAATAATAAATTATATTTAAATAATTTAA
75492 AATAGTGCTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 8 0.15
31 40 0.77
32 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (31 bp):
ATAATAATAAATTATATTTAAATAATTTAAT
Found at i:75497 original size:31 final size:31
Alignment explanation
Indices: 75438--75498 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
75428 AATATAATAA
* *
75438 TAAATTATATTTAAATAATTTAATATAGTGG
1 TAAATAATATTTAAATAATTTAAAATAGTGG
*
75469 TAAATAATATTTAAATGATTTAAAATAGTG
1 TAAATAATATTTAAATAATTTAAAATAGTG
75499 CTGCATAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (31 bp):
TAAATAATATTTAAATAATTTAAAATAGTGG
Found at i:78528 original size:104 final size:104
Alignment explanation
Indices: 78340--78652 Score: 590
Period size: 104 Copynumber: 3.0 Consensus size: 104
78330 GGGTACTGAA
78340 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
1 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
*
78405 AAGCTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
66 AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
* *
78444 AATAACCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTGTCCATTTGTGAAAGTGAG
1 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
*
78509 AAGTTCAGGTTGATCGTGTCAATAGGAAGCAATTTCAGT
66 AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
78548 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
1 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
78613 AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
66 AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
78652 A
1 A
78653 GTAGTATTAG
Statistics
Matches: 202, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 202 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (104 bp):
AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
Found at i:85462 original size:5 final size:5
Alignment explanation
Indices: 85452--85477 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
85442 AGTTGCTAAC
85452 TGTGT TGTGT TGTGT TGTGT TGTGT T
1 TGTGT TGTGT TGTGT TGTGT TGTGT T
85478 TAGGTCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (5 bp):
TGTGT
Found at i:86650 original size:9 final size:9
Alignment explanation
Indices: 86612--86777 Score: 56
Period size: 10 Copynumber: 17.9 Consensus size: 9
86602 GACATGTGAA
86612 AAAAATTAT
1 AAAAATTAT
*
86621 GAAAA--AT
1 AAAAATTAT
*
86628 AAAATTTAAT
1 AAAAATT-AT
*
86638 AAAAGTTAT
1 AAAAATTAT
86647 AAAAATTATT
1 AAAAATTA-T
**
86657 AAATTTTAAT
1 AAAAATT-AT
86667 AAAAA-TAT
1 AAAAATTAT
*
86675 AAAAATATTT
1 AAAAAT-TAT
*
86685 AAAATTTATT
1 AAAAATTA-T
* *
86695 ATAAAATAGAA
1 A-AAAAT-TAT
86706 AAAAATATAT
1 AAAAAT-TAT
* *
86716 AAATAGTA-
1 AAAAATTAT
*
86724 AAAAATATAA
1 AAAAAT-TAT
*
86734 AAAAATTGT
1 AAAAATTAT
*
86743 AAAATTTTAT
1 AAAA-ATTAT
*
86753 AAAAATCAT
1 AAAAATTAT
86762 -AAAA-TAT
1 AAAAATTAT
86769 AAAATATTA
1 AAAA-ATTA
86778 AAATTTTATA
Statistics
Matches: 113, Mismatches: 28, Indels: 31
0.66 0.16 0.18
Matches are distributed among these distances:
7 7 0.06
8 18 0.16
9 28 0.25
10 53 0.47
11 6 0.05
12 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:86686 original size:28 final size:27
Alignment explanation
Indices: 86629--86765 Score: 98
Period size: 28 Copynumber: 4.8 Consensus size: 27
86619 ATGAAAAATA
* *
86629 AAATTTAATAAAAGTTATAAAAAT-TATT
1 AAATTTTATAAAA-ATATAAAAATAT-TT
86657 AAATTTTAATAAAAATATAAAAATATTT
1 AAATTTT-ATAAAAATATAAAAATATTT
* * *
86685 AAAATTTATTATAAAATAGAAAAAAATATAT
1 -AAA-TT-TTATAAAA-ATATAAAAATATTT
** *
86716 AAATAGTA-AAAAATATAAAAAAATTGT
1 AAATTTTATAAAAATATAAAAATATT-T
86743 AAAATTTTATAAAAATCATAAAA
1 -AAATTTTATAAAAAT-ATAAAA
86766 TATAAAATAT
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
26 9 0.10
27 5 0.06
28 25 0.29
29 17 0.20
30 17 0.20
31 13 0.15
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
AAATTTTATAAAAATATAAAAATATTT
Found at i:87027 original size:10 final size:9
Alignment explanation
Indices: 87012--87090 Score: 54
Period size: 10 Copynumber: 8.6 Consensus size: 9
87002 TAAAGAACAT
87012 TTTTTATGCA
1 TTTTTATG-A
*
87022 TTTTTATAA
1 TTTTTATGA
87031 TTTTTAATGA
1 TTTTT-ATGA
*
87041 TTTTTATAAA
1 TTTTTAT-GA
* **
87051 ATTTTACAA
1 TTTTTATGA
87060 TTTTTTAT-A
1 -TTTTTATGA
87069 TTTTTATGA
1 TTTTTATGA
*
87078 -TTTTATAA
1 TTTTTATGA
87086 TTTTT
1 TTTTT
87091 TTTCTAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
8 14 0.25
9 16 0.29
10 26 0.46
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTATGA
Found at i:87036 original size:19 final size:18
Alignment explanation
Indices: 87012--87090 Score: 81
Period size: 19 Copynumber: 4.3 Consensus size: 18
87002 TAAAGAACAT
87012 TTTTTATGCATTTTTATAA
1 TTTTTATG-ATTTTTATAA
87031 TTTTTAATGATTTTTATAAA
1 TTTTT-ATGATTTTTAT-AA
* **
87051 ATTTTACAATTTTT-TATA
1 TTTTTATGATTTTTATA-A
87069 TTTTTATGA-TTTTATAA
1 TTTTTATGATTTTTATAA
87086 TTTTT
1 TTTTT
87091 TTTCTAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 11 0.22
18 10 0.20
19 20 0.40
20 9 0.18
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTTTATGATTTTTATAA
Found at i:87091 original size:10 final size:9
Alignment explanation
Indices: 87021--87090 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
87011 TTTTTTATGC
87021 ATTTTTATA
1 ATTTTTATA
*
87030 ATTTTTAATG
1 ATTTTT-ATA
87040 ATTTTTATAA
1 ATTTTTAT-A
* *
87050 AATTTTACA
1 ATTTTTATA
87059 ATTTTT-TA
1 ATTTTTATA
*
87067 TATTTTTATG
1 -ATTTTTATA
87077 A-TTTTATA
1 ATTTTTATA
87085 ATTTTT
1 ATTTTT
87091 TTTCTAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 8 0.17
9 25 0.52
10 15 0.31
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:87137 original size:27 final size:29
Alignment explanation
Indices: 87089--87144 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
87079 TTTATAATTT
* *
87089 TTTTTCTAATTTTTAATAAAATTTAAATA
1 TTTTTCTAATTTTCAATAAAATATAAATA
87118 TTTTT-TAATTTTCAA-AAAATATAAATA
1 TTTTTCTAATTTTCAATAAAATATAAATA
87145 CTTAAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTTCTAATTTTCAATAAAATATAAATA
Found at i:87968 original size:23 final size:24
Alignment explanation
Indices: 87913--87972 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
87903 TCATTAACAT
* * *
87913 TGTTCGTGAATATGTTTAATTATA
1 TGTTAGTGAACATGTTCAATTATA
*
87937 TGTTAGTGAACATGTTCATTTA-A
1 TGTTAGTGAACATGTTCAATTATA
*
87960 TGTTTGTGAACAT
1 TGTTAGTGAACAT
87973 ATTTGATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (24 bp):
TGTTAGTGAACATGTTCAATTATA
Found at i:88031 original size:21 final size:21
Alignment explanation
Indices: 88007--88046 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
87997 TTCGTGAACA
88007 TTAAACAAACGAACATGAATT
1 TTAAACAAACGAACATGAATT
* *
88028 TTAAATAAACGAATATGAA
1 TTAAACAAACGAACATGAA
88047 CAAAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (21 bp):
TTAAACAAACGAACATGAATT
Found at i:90149 original size:60 final size:60
Alignment explanation
Indices: 89998--90149 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 60
89988 TCTAAAAAAA
* *
89998 AAAAAAAGCTTAGGTGCCAAATTAGAAAAAAAATGTCAAGTTCAGGTATCAAATTGTGTCC
1 AAAAAAAGCTTAGGTGCCAAATTA-AAAAAAAATGTCAAGTTCAAGTATCAAATTGTATCC
** * * * *
90059 AAAAAAAATTTAGGTGTCAAATCAAGAAAAAGTGTCAAGTTCAAGTATCAAATTAG-AT-C
1 AAAAAAAGCTTAGGTGCCAAATTAAAAAAAAATGTCAAGTTCAAGTATCAAATT-GTATCC
* * *
90118 AAAAAAGGCTTAAGTACCAAATTAAAAAAAAA
1 AAAAAAAGCTTAGGTGCCAAATTAAAAAAAAA
90150 AAAAATTCAA
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
59 24 0.33
60 28 0.38
61 21 0.29
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (60 bp):
AAAAAAAGCTTAGGTGCCAAATTAAAAAAAAATGTCAAGTTCAAGTATCAAATTGTATCC
Done.