Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013856.1 Kokia drynarioides strain JFW-HI SEQ_128884, 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: 42688
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:720 original size:23 final size:22
Alignment explanation
Indices: 682--725 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
672 TAAATACACT
* *
682 TTAAAAATATTGATATTCTTAAA
1 TTAAAAATAATAATATT-TTAAA
705 TTAAAAATAATAATATTTTAA
1 TTAAAAATAATAATATTTTAA
726 TAGGTGTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAAAAATAATAATATTTTAAA
Found at i:5486 original size:15 final size:15
Alignment explanation
Indices: 5466--5500 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
5456 AGTTGAAATT
5466 AAGTTTAATTAATAC
1 AAGTTTAATTAATAC
5481 AAGTTTAATTAATAC
1 AAGTTTAATTAATAC
5496 AAGTT
1 AAGTT
5501 GAAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (15 bp):
AAGTTTAATTAATAC
Found at i:5494 original size:64 final size:67
Alignment explanation
Indices: 5426--5554 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 67
5416 TTCAAAATTA
* *
5426 TAATACAAGTTCAAATTTAATTTAAATT-TAA-G-TTGAAA-TTAAGTTTAATTAATACAAGTTT
1 TAATACAAGTTCAAATTAAATTTAAATTGAAATGATT-AAATTTAAGTTTAATTAATACAAGTTT
5487 AAT
65 AAT
*
5490 TAATACAAGTTGAAATTAAATTTAAATTGAAATGACATTAAATTTAAGTTTAATTAATACAAGTT
1 TAATACAAGTTCAAATTAAATTTAAATTGAAATG--ATTAAATTTAAGTTTAATTAATACAAGTT
5555 GAAGTTAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
64 26 0.46
65 2 0.04
66 1 0.02
68 3 0.05
69 24 0.43
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (67 bp):
TAATACAAGTTCAAATTAAATTTAAATTGAAATGATTAAATTTAAGTTTAATTAATACAAGTTTA
AT
Found at i:5556 original size:54 final size:54
Alignment explanation
Indices: 5481--5608 Score: 213
Period size: 54 Copynumber: 2.4 Consensus size: 54
5471 TAATTAATAC
* *
5481 AAGTTTAATTAATACAAGTTGAAATTAAATTTAAA-TTGAAATGACATTAAATTT
1 AAGTTTAATTAATACAAGTTGAAATTAAATTTAAACTT-AAATGAAATGAAATTT
*
5535 AAGTTTAATTAATACAAGTTGAAGTTAAATTTAAACTTAAATGAAATGAAATTT
1 AAGTTTAATTAATACAAGTTGAAATTAAATTTAAACTTAAATGAAATGAAATTT
5589 AAGTTTAATTAATACAAGTT
1 AAGTTTAATTAATACAAGTT
5609 TGTCGAAACC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
54 68 0.97
55 2 0.03
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (54 bp):
AAGTTTAATTAATACAAGTTGAAATTAAATTTAAACTTAAATGAAATGAAATTT
Found at i:6256 original size:97 final size:97
Alignment explanation
Indices: 6063--6256 Score: 214
Period size: 97 Copynumber: 2.0 Consensus size: 97
6053 CACTTTTGAA
* *
6063 AAGGATGTTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTGTAGGTACAAATTTTC
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTGTAGGCACAAATTTTC
* * * * *
6128 AGAATCCGAGATGAGAAACATTGCCTTGATTT
66 AAAATCCGAAATAAAAAACATTGCCTCGATTT
* **
6160 AAGGATATTCGATTAT-TCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGT-TAAGGCACAAATTT
1 AAGGATATTCGATTATCT-CGATTTAAAGAAAAAGTCGCACCTAGTAAGTGT-AGGCACAAATTT
** * *
6222 TCAAAATTTGAAATAAAAAAATATTGTCTCGATTT
64 TCAAAATCCGAAAT-AAAAAACATTGCCTCGATTT
6257 TAAAGTTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
95 1 0.01
96 35 0.44
97 44 0.55
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTGTAGGCACAAATTTTC
AAAATCCGAAATAAAAAACATTGCCTCGATTT
Found at i:6791 original size:30 final size:30
Alignment explanation
Indices: 6647--6833 Score: 135
Period size: 30 Copynumber: 6.3 Consensus size: 30
6637 GTAAAAGGGT
** * *
6647 AATTTTT-GAAAGTTTTTAGGTTAAAAATGG
1 AATTTTTGGAAAG-TTTGGGGTCAAAAATGA
*
6677 AA-TTTTGG-AAGTTTGGGG--ATAAAATAGT
1 AATTTTTGGAAAGTTTGGGGTCA-AAAAT-GA
* *
6705 AATTTTAGG-AAGTTTTGGGGTCAAAAATGG
1 AATTTTTGGAAAG-TTTGGGGTCAAAAATGA
*
6735 AATTTTTGGAAAGTTCGAGGGT-AAAAATGA
1 AATTTTTGGAAAGTTTG-GGGTCAAAAATGA
6765 AATTTTTGGAAAGTTTGGGGTCAAAAAT-A
1 AATTTTTGGAAAGTTTGGGGTCAAAAATGA
**
6794 TAA-TTTTGGAGAAGTCGGGGGTC-AAAAT-A
1 -AATTTTTGGA-AAGTTTGGGGTCAAAAATGA
6823 TAATTTTTGGA
1 -AATTTTTGGA
6834 CAGTGTAGAG
Statistics
Matches: 133, Mismatches: 11, Indels: 26
0.78 0.06 0.15
Matches are distributed among these distances:
26 1 0.01
27 5 0.04
28 8 0.06
29 36 0.27
30 70 0.53
31 12 0.09
32 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTGGGGTCAAAAATGA
Found at i:8771 original size:6 final size:6
Alignment explanation
Indices: 8743--8846 Score: 83
Period size: 6 Copynumber: 18.0 Consensus size: 6
8733 CATTATTTAT
* * * *
8743 TTTAAA TTTATAA --TAAT TTTAAA TATAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
8789 -TTAAA TTCAAA TTTAAA ATTAAT TTTAAA TTTAAA TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
8835 TCTAAA TTTAAA
1 TTTAAA TTTAAA
8847 ACAAATTTAA
Statistics
Matches: 78, Mismatches: 14, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
4 1 0.01
5 16 0.21
6 59 0.76
7 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:8788 original size:12 final size:11
Alignment explanation
Indices: 8761--8874 Score: 79
Period size: 11 Copynumber: 10.0 Consensus size: 11
8751 TATAATAATT
*
8761 TTAAATATAAA
1 TTAAATTTAAA
*
8772 ATAAATTTAAA
1 TTAAATTTAAA
8783 CTTAAA-TTAAA
1 -TTAAATTTAAA
8794 TTCAAATTTAAAA
1 TT-AAATTT-AAA
*
8807 TTAATTTTAAA
1 TTAAATTTAAA
8818 TTTAAATTTAAA
1 -TTAAATTTAAA
* *
8830 ATAAATCTAAA
1 TTAAATTTAAA
**
8841 TTTAAA-ACAAA
1 -TTAAATTTAAA
*
8852 TTTAATCTTAAA
1 TTAAAT-TTAAA
*
8864 ATAAATTTAAA
1 TTAAATTTAAA
8875 GGGGCCCGGT
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
10 6 0.08
11 37 0.46
12 32 0.40
13 5 0.06
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:8834 original size:17 final size:17
Alignment explanation
Indices: 8743--8874 Score: 113
Period size: 17 Copynumber: 7.4 Consensus size: 17
8733 CATTATTTAT
* *
8743 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
*
8760 TTTAAATATAAAATAAA
1 TTTAAATTTAAAATAAA
* *
8777 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
*
8794 TTCAAATTTAAAATTAATTTTAAA
1 TTTAAATTT--AA--AA---TAAA
8818 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
8835 TCTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
8852 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
8869 TTTAAA
1 TTTAAA
8875 GGGGCCCGGT
Statistics
Matches: 92, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.03
17 68 0.74
18 2 0.02
19 2 0.02
20 2 0.02
21 1 0.01
22 2 0.02
24 12 0.13
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:8853 original size:58 final size:58
Alignment explanation
Indices: 8760--8871 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
8750 TTATAATAAT
* ** *
8760 TTTAAATATAAAATAAATTTAAACTTAAATTAAATTCAAAT-TTAAAATTAATTTTAAA
1 TTTAAATATAAAATAAATCTAAACTTAAAACAAATT-AAATCTTAAAATAAATTTTAAA
* * *
8818 TTTAAATTTAAAATAAATCTAAATTTAAAACAAATTTAATCTTAAAATAAATTT
1 TTTAAATATAAAATAAATCTAAACTTAAAACAAATTAAATCTTAAAATAAATTT
8872 AAAGGGGCCC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
57 3 0.07
58 43 0.93
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (58 bp):
TTTAAATATAAAATAAATCTAAACTTAAAACAAATTAAATCTTAAAATAAATTTTAAA
Found at i:8854 original size:41 final size:41
Alignment explanation
Indices: 8773--8854 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
8763 AAATATAAAA
* **
8773 TAAATTTAAACTTAAATTAAATTCAAATTTAAAATTAATTT
1 TAAATTTAAACTTAAAATAAATTCAAATTTAAAACAAATTT
*
8814 TAAATTTAAATTTAAAATAAA-TCTAAATTTAAAACAAATTT
1 TAAATTTAAACTTAAAATAAATTC-AAATTTAAAACAAATTT
8855 AATCTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 2 0.06
41 34 0.94
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (41 bp):
TAAATTTAAACTTAAAATAAATTCAAATTTAAAACAAATTT
Found at i:9595 original size:96 final size:97
Alignment explanation
Indices: 9405--9597 Score: 241
Period size: 96 Copynumber: 2.0 Consensus size: 97
9395 GAATTTTGGA
* ** * *
9405 AAAGGATATTTGATTATCTCGATTTAAAGAAAGGTTGCACCTAGTAAGTTAAGGCTCAAATTTTT
1 AAAGGATATTCGATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTG
*
9470 AGAATCGAAGATAAGAAAACATTGTCTCGATT
66 AGAATCGAAGATAAGAAAACATTGCCTCGATT
* *
9502 AAAGG-TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTT
1 AAAGGATATTCGATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCAC-AAATTTT
* *
9566 GA-AACTCGAA-ATGAA-AGAATATTGCCTCGATT
65 GAGAA-TCGAAGAT-AAGAAAACATTGCCTCGATT
9598 TTAAAGCTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
96 63 0.76
97 20 0.24
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (97 bp):
AAAGGATATTCGATTATCTCGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTG
AGAATCGAAGATAAGAAAACATTGCCTCGATT
Found at i:9956 original size:59 final size:59
Alignment explanation
Indices: 9862--10029 Score: 191
Period size: 59 Copynumber: 2.9 Consensus size: 59
9852 AATTAGGGTT
* * *
9862 AAAAAT-GACATTTTAG-ACATTTGAGGGTAAGATGGTAATTTTTGAAAGTTTTAAGGTC
1 AAAAATGGA-ATTTTTGAACATTTGAGGGTAAAATGGTAATTTTTGAAAGTTTTAAGGAC
* * * *
9920 AAAATTGGAGTTTTTGAACATTTGAGGGTAAAATGGTAATTTTTGAAAGATTTAGGGAC
1 AAAAATGGAATTTTTGAACATTTGAGGGTAAAATGGTAATTTTTGAAAGTTTTAAGGAC
* * *
9979 AAAAATGGAATTTTTGAA-ATTTCGAGGGAAAAAATTG-AATTTTTGTAAGTT
1 AAAAATGGAATTTTTGAACATTT-GAGGG-TAAAATGGTAATTTTTGAAAGTT
10030 CGAGGGTAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 14 0.15
59 73 0.78
60 6 0.06
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (59 bp):
AAAAATGGAATTTTTGAACATTTGAGGGTAAAATGGTAATTTTTGAAAGTTTTAAGGAC
Found at i:10050 original size:88 final size:88
Alignment explanation
Indices: 9943--10196 Score: 279
Period size: 88 Copynumber: 2.9 Consensus size: 88
9933 TTGAACATTT
* * *
9943 GAGGGT-AAAATGGTAATTTTTGAAAGATTTAGGGACAAAAATGGAATTTTTGAAATTTCGAGGG
1 GAGGGTAAAAAT-GTAATTTTTGAAAGATTTGGGGTCAAAAATGGAATTTTTGAAGTTTCGAGGG
***
10007 AAAAAAT-TGAATTTTTGTAAGTTC
65 AAAAAATGT-AATTTTCAAAAGTTC
* * *
10031 GAGGGTAAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGAAATTTTTGGAAGTTTAG-GGG
1 GAGGGTAAAAATGTAATTTTTGAAAGATTTGGGGTCAAAAATGGAATTTTT-GAAGTTTCGAGGG
* *
10095 TAAAAATGTAATTTTCAAAAGTTT
65 AAAAAATGTAATTTTCAAAAGTTC
* *
10119 GAGGTTAAAAATGTAATTTTTTGGAAA-A-TTGGGGTTAAAAATGGAATTTTGTG-AGTTTCGA-
1 GAGGGTAAAAATGTAA-TTTTT-GAAAGATTTGGGGTCAAAAATGGAATTTT-TGAAGTTTCGAG
*
10180 GGTAAAAATGTAATTTT
63 GGAAAAAATGTAATTTT
10197 TAGGATAATC
Statistics
Matches: 143, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
87 23 0.16
88 97 0.68
89 19 0.13
90 4 0.03
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (88 bp):
GAGGGTAAAAATGTAATTTTTGAAAGATTTGGGGTCAAAAATGGAATTTTTGAAGTTTCGAGGGA
AAAAATGTAATTTTCAAAAGTTC
Found at i:10057 original size:29 final size:29
Alignment explanation
Indices: 9896--10287 Score: 222
Period size: 29 Copynumber: 13.3 Consensus size: 29
9886 GGGTAAGATG
** * *
9896 GTAATTTTTGAAAGTTTTAAGGTCAAAATT
1 GTAATTTTTGAAAGTTCGAGGGT-AAAAAT
* * *
9926 GGAGTTTTTGAACA-TTTGAGGGT-AAAAT
1 GTAATTTTTGAA-AGTTCGAGGGTAAAAAT
* *
9954 GGTAATTTTTGAAAGATT-TAGGGACAAAAAT
1 -GTAATTTTTGAAAG-TTCGAGGG-TAAAAAT
* * *
9985 GGAATTTTTGAAATTTCGAGGGAAAAAAT
1 GTAATTTTTGAAAGTTCGAGGGTAAAAAT
*
10014 -TGAATTTTTGTAAGTTCGAGGGTAAAAAT
1 GT-AATTTTTGAAAGTTCGAGGGTAAAAAT
*
10043 GTAATTTTTGAAAGTTTTG-GGGTCAAAAAT
1 GTAATTTTTGAAAG-TTCGAGGGT-AAAAAT
* * *
10073 GAAATTTTTGGAAGTT-TAGGGGTAAAAAT
1 GTAATTTTTGAAAGTTCGA-GGGTAAAAAT
** * *
10102 GTAATTTTCAAAAGTTTGAGGTTAAAAAT
1 GTAATTTTTGAAAGTTCGAGGGTAAAAAT
*
10131 GTAATTTTTTGGAAAATT-G-GGGTTAAAAAT
1 GTAA-TTTTT-GAAAGTTCGAGGG-TAAAAAT
*
10161 GGAATTTTGTG--AGTTTCGA-GGTAAAAAT
1 GTAATTTT-TGAAAG-TTCGAGGGTAAAAAT
10189 GTAATTTTTAGGATAA--TCG-GGGTCAAAAAT
1 GTAATTTTT--GA-AAGTTCGAGGGT-AAAAAT
* *
10219 GGAA-TTTTGAAAAGTTCAAGGGTAAAAAT
1 GTAATTTTTG-AAAGTTCGAGGGTAAAAAT
* * *
10248 GTAATTTTGGAGAAGTT-TAGGGGTCAAAAT
1 GTAATTTTTGA-AAGTTCGA-GGGTAAAAAT
*
10278 GTGATTTTTG
1 GTAATTTTTG
10288 GACAGTTTAA
Statistics
Matches: 284, Mismatches: 43, Indels: 70
0.72 0.11 0.18
Matches are distributed among these distances:
27 5 0.02
28 22 0.08
29 128 0.45
30 117 0.41
31 11 0.04
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
GTAATTTTTGAAAGTTCGAGGGTAAAAAT
Found at i:10079 original size:59 final size:58
Alignment explanation
Indices: 9979--10287 Score: 183
Period size: 59 Copynumber: 5.3 Consensus size: 58
9969 ATTTAGGGAC
* * *
9979 AAAAATGGAATTTTTGAAA-TTTCGAGGG-AAAAAATTGAATTTTTGTAAGTTCGA-GGGT
1 AAAAATGTAATTTTTGAAAGTTTTG-GGGTAAAAAA-TGAATTTTTGGAAGTT-GAGGGGT
* *
10037 AAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGAAATTTTTGGAAGTTTAGGGGT
1 AAAAATGTAATTTTTGAAAGTTTTGGGGTAAAAAATG-AATTTTTGGAAGTTGAGGGGT
** * * * *
10096 AAAAATGTAATTTTCAAAAG-TTTGAGGTTAAAAATGTAATTTTTTGGAAAATTG-GGGTT
1 AAAAATGTAATTTTTGAAAGTTTTGGGGTAAAAAATG-AA-TTTTTGG-AAGTTGAGGGGT
* * * * *
10155 AAAAATGGAATTTTGTG--AGTTTCGAGGT-AAAAATGTAATTTTTAGGATA-AT-CGGGGT
1 AAAAATGTAATTTT-TGAAAGTTTTGGGGTAAAAAATG-AATTTTT-GGA-AGTTGAGGGGT
* *** * *
10212 CAAAAATGGAA-TTTTGAAAAGTTCAAGGGT-AAAAATGTAATTTTGGAGAAGTTTAGGGGT
1 -AAAAATGTAATTTTTG-AAAGTTTTGGGGTAAAAAATG-AATTTTTG-GAAGTTGAGGGGT
* *
10272 CAAAATGTGATTTTTG
1 AAAAATGTAATTTTTG
10288 GACAGTTTAA
Statistics
Matches: 203, Mismatches: 29, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
56 2 0.01
57 14 0.07
58 67 0.33
59 106 0.52
60 14 0.07
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (58 bp):
AAAAATGTAATTTTTGAAAGTTTTGGGGTAAAAAATGAATTTTTGGAAGTTGAGGGGT
Found at i:10277 original size:30 final size:29
Alignment explanation
Indices: 10033--10285 Score: 178
Period size: 30 Copynumber: 8.6 Consensus size: 29
10023 GTAAGTTCGA
*
10033 GGGTAAAAATGTAATTTTTGA-AAGTTTTG
1 GGGTAAAAATGTAA-TTTTGAGAAGTTTAG
*
10062 GGGTCAAAAATGAAATTTTTG-GAAGTTTAG
1 GGGT-AAAAATGTAA-TTTTGAGAAGTTTAG
* *
10092 GGGTAAAAATGTAATTTTCAAAAGTTT-G
1 GGGTAAAAATGTAATTTTGAGAAGTTTAG
* **
10120 AGGTTAAAAATGTAATTTTTTG-GAAAATT-G
1 -GGGTAAAAATGTAA--TTTTGAGAAGTTTAG
* * *
10150 GGGTTAAAAATGGAATTTTGTG-AGTTTCG
1 GGG-TAAAAATGTAATTTTGAGAAGTTTAG
* * * * *
10179 AGGTAAAAATGTAATTTTTAGGA-TAATCG
1 GGGTAAAAATGTAATTTTGAGAAGT-TTAG
* * * *
10208 GGGTCAAAAATGGAATTTTGAAAAGTTCAA
1 GGGT-AAAAATGTAATTTTGAGAAGTTTAG
10238 GGGTAAAAATGTAATTTTGGAGAAGTTTAG
1 GGGTAAAAATGTAATTTT-GAGAAGTTTAG
* *
10268 GGGTCAAAATGTGATTTT
1 GGGTAAAAATGTAATTTT
10286 TGGACAGTTT
Statistics
Matches: 176, Mismatches: 34, Indels: 27
0.74 0.14 0.11
Matches are distributed among these distances:
28 29 0.16
29 58 0.33
30 84 0.48
31 5 0.03
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTGAGAAGTTTAG
Found at i:11621 original size:260 final size:260
Alignment explanation
Indices: 11160--11693 Score: 1014
Period size: 260 Copynumber: 2.1 Consensus size: 260
11150 TTGAAACCTC
*
11160 ATTATCAAAATTAAACCCTTTGATTTTCTTTTCTTTGCATATATGGAGATTGTGCCCTGATTTGC
1 ATTATCAAAATTAAACCCTTTGATTTTCTTTTCTTTGCATATATGGAGATTATGCCCTGATTTGC
*
11225 TAAATTTGAATCCATAGAGAGGAAGCCTGGGGACGTACGATCGGTGGTGGCGGGGTTCAGAGAAA
66 TAAATTTGAATCCATAGAGAGGAAGCCTGGGGACGTACGATCGGTGGTGGCGGGGTTCAAAGAAA
*
11290 ACTCCAGCGTGAAGCTCCGGTAACGGTGGGCATATAAGTCCTTTCGAATCCTTTTCTTTAATAAA
131 ACTCCAGCGTGAAGCTCCGGTAACGATGGGCATATAAGTCCTTTCGAATCCTTTTCTTTAATAAA
11355 TGTTATTATTATTATTATTATTAATAAAAATAATTATTAAGGTTATTAATGTTATCAGCATCATA
196 TGTTATTATTATTATTATTATTAATAAAAATAATTATTAAGGTTATTAATGTTATCAGCATCATA
11420 ATTATCAAAATTAAACCCTTTGATTTTCTTTTCTTTGCATATATGGAGATTATGCCCTGATTTGC
1 ATTATCAAAATTAAACCCTTTGATTTTCTTTTCTTTGCATATATGGAGATTATGCCCTGATTTGC
11485 TAAATTTGAATCCATAGAGAGGAAGCCTGGGGACGTACGATCGGTGGTGGCGGGGTTCAAAGAAA
66 TAAATTTGAATCCATAGAGAGGAAGCCTGGGGACGTACGATCGGTGGTGGCGGGGTTCAAAGAAA
11550 ACTCCAGCGTGAAGCTCCGGTAACGATGGGCATATAAGTCCTTTCGAATCCTTTTCTTTAATAAA
131 ACTCCAGCGTGAAGCTCCGGTAACGATGGGCATATAAGTCCTTTCGAATCCTTTTCTTTAATAAA
11615 TGTTATTATTATTATTATTATTAATAAAAATAATTATTAAGGTTATTAATGTTATCAGCATCATA
196 TGTTATTATTATTATTATTATTAATAAAAATAATTATTAAGGTTATTAATGTTATCAGCATCATA
* * *
11680 TTTATTATAATTAA
1 ATTATCAAAATTAA
11694 TACTATTATT
Statistics
Matches: 268, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
260 268 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (260 bp):
ATTATCAAAATTAAACCCTTTGATTTTCTTTTCTTTGCATATATGGAGATTATGCCCTGATTTGC
TAAATTTGAATCCATAGAGAGGAAGCCTGGGGACGTACGATCGGTGGTGGCGGGGTTCAAAGAAA
ACTCCAGCGTGAAGCTCCGGTAACGATGGGCATATAAGTCCTTTCGAATCCTTTTCTTTAATAAA
TGTTATTATTATTATTATTATTAATAAAAATAATTATTAAGGTTATTAATGTTATCAGCATCATA
Found at i:12352 original size:17 final size:17
Alignment explanation
Indices: 12322--12408 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
12312 TTTTAATATT
* * *
12322 AATAATTTTTAATTCAA
1 AATAAATTTAAATTTAA
*
12339 AATAAATTCAAATTTAA
1 AATAAATTTAAATTTAA
* *
12356 AATAAATTTAAACTCAA
1 AATAAATTTAAATTTAA
* *
12373 CATGAATTTAAATTTAA
1 AATAAATTTAAATTTAA
* *
12390 AAAAAATTAAAATTTAA
1 AATAAATTTAAATTTAA
12407 AA
1 AA
12409 ATTAAAAGTT
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:13130 original size:206 final size:208
Alignment explanation
Indices: 12753--13192 Score: 563
Period size: 206 Copynumber: 2.1 Consensus size: 208
12743 TGAGTCGGTA
* * ** * * *
12753 TACTTCTCTGTATCTTC-TCAGGAAGGCGACCGCATCGCTTGTTTTGATCCACTTCTTTGTGTTT
1 TACTTCTCAGTATC-TCATCAGGAAGACGACCGCATCGCTTGTTTCAATCCACTTCTCTGTATCT
* * * **
12817 CATTAAGAAGATGGATTTGGTTCACTTCTTCGTATCTCATCAGGAAGCTAACCATTTTATTCCTT
65 CATTAAGAAGACGAATTTGGTCCACTTCTTCAAATCTCATCAGGAAGCTAACCATTTTATTCCTT
*
12882 CGACCTGCTTCTCAGTATCTCATTGGAAAGCTGGGATTCGAAGATTTGCTC-ATATCGAG-CATG
130 CGACCTGCTTCTCAGTATCTCATAGGAAAGCTGGGATTCGAAGATTTGCTCGAT-TCGAGCCATG
12945 TGT-TTGATTTGGTC
194 TGTATTGATTTGGTC
* * *
12959 TTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAAT-CAGTTTCTCTGTATCT
1 TACTTCTCAGTATCTCATCAGGAAGACGACCGCATCGCTTGTTTCAATCCA-CTTCTCTGTATCT
*
13023 CA-TAAGGAAGACGAATTTGGTCCACTTC-TCAAAATCTCATCAGGAAGCTAACCATTTTATTGC
65 CATTAA-GAAGACGAATTTGGTCCACTTCTTC-AAATCTCATCAGGAAGCTAACCATTTTATTCC
* * * *
13086 TTCGACCTGCTTCTCAGTATCTCATCAGG-AAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCCT
128 TTCGACCTGCTTCTCAGTATCTCAT-AGGAAAGCTGGGATTCGAAGATTTGCTCGATTCGAGCCA
*
13150 TGTTTCATTGATTTGGTC
192 TGTGT-ATTGATTTGGTC
13168 TACTTCTCAGTATCTCATCAGGAAG
1 TACTTCTCAGTATCTCATCAGGAAG
13193 CTAACAATTT
Statistics
Matches: 202, Mismatches: 23, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
205 9 0.04
206 150 0.74
207 8 0.04
209 35 0.17
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (208 bp):
TACTTCTCAGTATCTCATCAGGAAGACGACCGCATCGCTTGTTTCAATCCACTTCTCTGTATCTC
ATTAAGAAGACGAATTTGGTCCACTTCTTCAAATCTCATCAGGAAGCTAACCATTTTATTCCTTC
GACCTGCTTCTCAGTATCTCATAGGAAAGCTGGGATTCGAAGATTTGCTCGATTCGAGCCATGTG
TATTGATTTGGTC
Found at i:13259 original size:123 final size:123
Alignment explanation
Indices: 13037--13315 Score: 477
Period size: 123 Copynumber: 2.3 Consensus size: 123
13027 AGGAAGACGA
* ** * *
13037 ATTTGGTCCACTTCTCAAAATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACAATTTTATTGCTTCGACCTACTTCTCA
*
13102 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCCTTGTTTCATTG
66 GTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCTTTGAGCCTTGTTTCATTG
*
13160 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACAATTTTATTGCTTCGACCTACTTCTTA
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACAATTTTATTGCTTCGACCTACTTCTCA
* *
13225 GTATCTCATCAGGAAGCTGGGATTCGAAGTTTTGCTCGCTTTGAGTCTTGTTTCATTG
66 GTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCTTTGAGCCTTGTTTCATTG
13283 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAG
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAG
13316 ATGATCGCAT
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 147 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (123 bp):
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACAATTTTATTGCTTCGACCTACTTCTCA
GTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCTTTGAGCCTTGTTTCATTG
Found at i:13384 original size:332 final size:329
Alignment explanation
Indices: 12830--13799 Score: 1482
Period size: 332 Copynumber: 2.9 Consensus size: 329
12820 TAAGAAGATG
*
12830 GATTTGGT-TCACTTCTTC-GTATCTCATCAGGAAGCTAACCATTTTATTCCTTCGACCTGCTTC
1 GATTTGGTCT-ACTTC-TCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTC
* * * *
12893 TCAGTATCTCAT-TGGAAAGCTGGGATTCGAAGATTTGCTC-ATATCGAGCATGTGTTTGATTTG
64 TCAGTATCTCATCAGG-AAGCTGGGATTCGAAGATTTGCTCGCT-TTGAGCTTGTGTTTGATTTG
* *
12956 GTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCAGTTTCTCTGTAT
127 GTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTAT
* *
13021 CTCATAAGGAAGACGAATTTGGTCCACTTCTCAAAATCTCATCAGGAAGCTAACCATTTTATTGC
192 CTCATCAGGAAGACGAATTTGGTCCACTTCTCAGAATCTCATCAGGAAGCTAACCATTTTATTGC
*
13086 TTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCCTT
257 TTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTAAGCCTT
13151 GTTTCATT
322 GTTTCATT
* * *
13159 GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACAATTTTATTGCTTCGACCTACTTCTT
1 GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTC
* *
13224 AGTATCTCATCAGGAAGCTGGGATTCGAAGTTTTGCTCGCTTTGAGTCTTGTTTCATTGATTTGG
66 AGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCTTTGAG-CTTGTGT--TTGATTTGG
* * * *
13289 TCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATTGCTTGTTTCAATCCGCTTCTCAGTATC
128 TCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATC
13354 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGAATCTCATCAGGAAGCTAACCATTTTATTGCT
193 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGAATCTCATCAGGAAGCTAACCATTTTATTGCT
* *
13419 TCGACCTGCTTCTCAGTATCTCATTAGAAAGCTGGGGTTCGAAGATTTGCTCGCTTTAAGCCTTG
258 TCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTAAGCCTTG
13484 TTTCATT
323 TTTCATT
*
13491 GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGACCTGCTTCTC
1 GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTC
* * ** * *
13556 AGTATTTCATCAGGAAGCTGGGGTTAAAAGATTTGCTTGCTTTGAGCCTAG-GTTTGATTTGGTC
66 AGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCTTTGAG-CTTGTGTTTGATTTGGTC
* * ** ** *
13620 TTCTTCTCTGTATCTCATTAGGAAGATGACCGTGTCATTTGTTTCAATCCACTTCTCTGTATCTC
130 TTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTC
*
13685 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
195 ATCAGGAAGACGAATTTGGTCCACTTCTCAGAATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * *
13750 AACTTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTC
260 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
13800 ACATCGAGCC
Statistics
Matches: 583, Mismatches: 51, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
328 2 0.00
329 267 0.46
330 9 0.02
331 1 0.00
332 304 0.52
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (329 bp):
GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTC
AGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCTTTGAGCTTGTGTTTGATTTGGTCT
TCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCA
TCAGGAAGACGAATTTGGTCCACTTCTCAGAATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTAAGCCTTGTTT
CATT
Found at i:13588 original size:123 final size:120
Alignment explanation
Indices: 13369--13644 Score: 390
Period size: 123 Copynumber: 2.3 Consensus size: 120
13359 AGGAAGACGA
* *
13369 ATTTGGTCCACTTCTCAGAATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
* ** * *
13434 GTATCTCATTAGAAAGCTGGGGTTCGAAGATTTGCTCGCTTTAAGCCTTGTTTCATTG
66 GTATCTCATCAGAAAGCTGGGGTTAAAAGATTTGCTCGCTTTAAGCCTAG-GT--TTG
*
13492 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGACCTGCTTCTCA
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
* * * *
13557 GTATTTCATCAGGAAGCTGGGGTTAAAAGATTTGCTTGCTTTGAGCCTAGGTTTG
66 GTATCTCATCAGAAAGCTGGGGTTAAAAGATTTGCTCGCTTTAAGCCTAGGTTTG
* * *
13612 ATTTGGTCTTCTTCTCTGTATCTCATTAGGAAG
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAG
13645 ATGACCGTGT
Statistics
Matches: 138, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
120 33 0.24
122 1 0.01
123 104 0.75
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (120 bp):
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
GTATCTCATCAGAAAGCTGGGGTTAAAAGATTTGCTCGCTTTAAGCCTAGGTTTG
Found at i:14329 original size:49 final size:50
Alignment explanation
Indices: 14223--14329 Score: 144
Period size: 50 Copynumber: 2.2 Consensus size: 50
14213 ATGTTTCTAA
* **
14223 GGTACTGGGTTCGCCATTGCGACTTAAACCTTTCCCCTTCAAATCTTTGT
1 GGTACTGGATTCGCCATTGCGACTTAAACCTTTCCCCTTCAAATCTTCAT
* * **
14273 GGTACTGGATTCGCCATTGCGGCTTAAATCTTT-CCCTTCATGTCTTCAT
1 GGTACTGGATTCGCCATTGCGACTTAAACCTTTCCCCTTCAAATCTTCAT
14322 GGTACTGG
1 GGTACTGG
14330 GACCTGTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 20 0.40
50 30 0.60
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (50 bp):
GGTACTGGATTCGCCATTGCGACTTAAACCTTTCCCCTTCAAATCTTCAT
Found at i:23159 original size:29 final size:28
Alignment explanation
Indices: 23085--23354 Score: 202
Period size: 30 Copynumber: 9.3 Consensus size: 28
23075 GGACATCCAA
* *
23085 GGTAAATTGGTAATTTTTGAATGTTTCGGG
1 GGTAAAATGG-AATTTTTGAAAG-TTCGGG
* * *
23115 GTTAAAATGGAGTTTTTAGACA-TTCGGG
1 GGTAAAATGGAATTTTT-GAAAGTTCGGG
***
23143 GGTAAAATGGTAATTTTTGAAAGTTTTAG
1 GGTAAAATGG-AATTTTTGAAAGTTCGGG
* *
23172 TGTCAAAAATGGAATTTTTGAAACTTCGGG
1 GGT--AAAATGGAATTTTTGAAAGTTCGGG
* * * *
23202 GGTAAAATGGTAAATTTTAGAAAATTTGAG
1 GGTAAAATGG--AATTTTTGAAAGTTCGGG
* * *
23232 GTTAAAATGGAATTTTTGGAAGTTCGGA
1 GGTAAAATGGAATTTTTGAAAGTTCGGG
* * *
23260 GGTAAAAATGTAATTTTTGGAAGTTTCGAG
1 GGT-AAAATGGAATTTTTGAAAG-TTCGGG
** *
23290 CTTAAAAATGGAATTTTTGGAAGTTCGGG
1 GGT-AAAATGGAATTTTTGAAAGTTCGGG
*
23319 GGTAAAAATGTAATTTTTGAAAGTTCGGG
1 GGT-AAAATGGAATTTTTGAAAGTTCGGG
23348 GG-AAAAT
1 GGTAAAAT
23355 AAGGGTCAAA
Statistics
Matches: 191, Mismatches: 40, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
27 5 0.03
28 39 0.20
29 67 0.35
30 73 0.38
31 7 0.04
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
GGTAAAATGGAATTTTTGAAAGTTCGGG
Found at i:23202 original size:59 final size:58
Alignment explanation
Indices: 23085--23343 Score: 260
Period size: 59 Copynumber: 4.4 Consensus size: 58
23075 GGACATCCAA
* * * * * *
23085 GGTAAATTGGTAATTTTTGAATGTTTCG-GGGTTAAAATGGAGTTTTT-AGACATTCGGG
1 GGTAAAATGGTAATTTTTGAAAGTTT-GAGTGTAAAAATGGAATTTTTGAAAC-TTCGGG
*
23143 GGTAAAATGGTAATTTTTGAAAGTTTTAGTGTCAAAAATGGAATTTTTGAAACTTCGGG
1 GGTAAAATGGTAATTTTTGAAAGTTTGAGTGT-AAAAATGGAATTTTTGAAACTTCGGG
* * * * * *
23202 GGTAAAATGGTAAATTTTAGAAAATTTGAG-GTTAAAATGGAATTTTTGGAAGTTCGGA
1 GGTAAAATGGT-AATTTTTGAAAGTTTGAGTGTAAAAATGGAATTTTTGAAACTTCGGG
* * *
23260 GGTAAAAAT-GTAATTTTTGGAAGTTTCGAGCT-TAAAAATGGAATTTTTGGAAGTTCGGG
1 GGT-AAAATGGTAATTTTTGAAAGTTT-GAG-TGTAAAAATGGAATTTTTGAAACTTCGGG
23319 GGTAAAAAT-GTAATTTTTGAAAGTT
1 GGT-AAAATGGTAATTTTTGAAAGTT
23344 CGGGGGAAAA
Statistics
Matches: 173, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
57 12 0.07
58 57 0.33
59 86 0.50
60 18 0.10
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTTGAAAGTTTGAGTGTAAAAATGGAATTTTTGAAACTTCGGG
Found at i:23258 original size:117 final size:117
Alignment explanation
Indices: 23114--23325 Score: 297
Period size: 117 Copynumber: 1.8 Consensus size: 117
23104 AATGTTTCGG
* * *
23114 GGTTAAAATGGAGTTTTTAGACATTCGGGGGT-AAAATGGTAATTTTTGAAAGTTT-TAG-TGTC
1 GGTTAAAATGGAATTTTTAGACATTCGGAGGTAAAAAT-GTAATTTTTGAAAGTTTCGAGCT-T-
23176 AAAAATGGAATTTTTGAAACTTCGGGGGTAAAATGGTAAATTTTAGAAAATTTGA
63 AAAAATGGAATTTTTGAAACTTCGGGGGTAAAATGGTAAATTTTAGAAAATTTGA
* *
23231 GGTTAAAATGGAATTTTTGGA-AGTTCGGAGGTAAAAATGTAATTTTTGGAAGTTTCGAGCTTAA
1 GGTTAAAATGGAATTTTTAGACA-TTCGGAGGTAAAAATGTAATTTTTGAAAGTTTCGAGCTTAA
* *
23295 AAATGGAATTTTTGGAAGTTCGGGGGTAAAA
65 AAATGGAATTTTTGAAACTTCGGGGGTAAAA
23326 ATGTAATTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
116 1 0.01
117 74 0.88
118 8 0.10
119 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (117 bp):
GGTTAAAATGGAATTTTTAGACATTCGGAGGTAAAAATGTAATTTTTGAAAGTTTCGAGCTTAAA
AATGGAATTTTTGAAACTTCGGGGGTAAAATGGTAAATTTTAGAAAATTTGA
Found at i:23454 original size:29 final size:29
Alignment explanation
Indices: 23356--23463 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 29
23346 GGGGAAAATA
* * *
23356 AGGGTCAAAAATAGAATTTTGGGAAGTTCA
1 AGGGT-AAAAATGGAATTTTGGAAAGTTCG
* *
23386 AGGGGTAAAAATGTAATTTTTGGGAAA-ATCG
1 A-GGGTAAAAATGGAA-TTTT-GGAAAGTTCG
*
23417 A-GGTCAAAATGGAATTTTGGAAAGTTCG
1 AGGGTAAAAATGGAATTTTGGAAAGTTCG
*
23445 AGGGTAAAAATGTAATTTT
1 AGGGTAAAAATGGAATTTT
23464 AAAGAAGTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
27 5 0.08
28 8 0.13
29 26 0.41
30 9 0.14
31 11 0.17
32 4 0.06
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.30
Consensus pattern (29 bp):
AGGGTAAAAATGGAATTTTGGAAAGTTCG
Found at i:23481 original size:59 final size:59
Alignment explanation
Indices: 23349--23499 Score: 160
Period size: 59 Copynumber: 2.5 Consensus size: 59
23339 AAGTTCGGGG
* * * ***
23349 GAAAATAAGGGTCAAAAATAGAATTTTGGGAAGTTCAAGGGGTAAAAATGTAATTTTTGG
1 GAAAATAGGGGTC-AAAATGGAATTTTGGAAAGTTCAAGGGGTAAAAATGTAATTTTAAA
* * *
23409 GAAAATCGAGGTCAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAAATGTAATTTTAAA
1 GAAAATAGGGGTCAAAATGGAATTTTGGAAAGTTCAAGGGGTAAAAATGTAATTTTAAA
** *
23467 GAAGTTTAGGGGTCAAAATGTGATTTTTGGAAA
1 GAA-AATAGGGGTCAAAATG-GAATTTTGGAAA
23500 ATTTAAGGAC
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 21 0.28
59 33 0.44
60 21 0.28
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.29
Consensus pattern (59 bp):
GAAAATAGGGGTCAAAATGGAATTTTGGAAAGTTCAAGGGGTAAAAATGTAATTTTAAA
Found at i:24336 original size:21 final size:19
Alignment explanation
Indices: 24307--24355 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
24297 TTCCCAAATC
*
24307 TTTTCAAAAACATCTTGATCT
1 TTTTTAAAAACATCTT--TCT
*
24328 TTTTTAAAAACATCTTTTT
1 TTTTTAAAAACATCTTTCT
24347 TTTTTAAAA
1 TTTTTAAAA
24356 CCCCATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 11 0.42
21 15 0.58
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTTAAAAACATCTTTCT
Found at i:25296 original size:17 final size:17
Alignment explanation
Indices: 25276--25352 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
25266 AATAATTTTT
*
25276 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
25293 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* * * * *
25310 AACTCAACATGAATTTA
1 AATTTAAAATAAATTCA
25327 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
25344 AATTTAAAA
1 AATTTAAAA
25353 ATTAAAAGTT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:26977 original size:106 final size:110
Alignment explanation
Indices: 26702--26979 Score: 282
Period size: 110 Copynumber: 2.6 Consensus size: 110
26692 CATTGATTAC
* * * ** ***
26702 CAAACATCAAAAAA-AATATTTTTTATTCGTGTTTTATGGGTGTTGGTTATTAGTTGAAAAAGTG
1 CAAACACCAAAAAATAA-ATTTTTTATTTGTGTTTTATGGATGCCGACCATTAGTTGAAAAAGTG
** *
26766 AAAAAAATTTTGGATGTTAGGAAAGGTGATGTCAGCCATTAGTTGT
65 AAAAAAAAATTCGATGTTAGGAAAGGTGATGTCAGCCATTAGTTGT
* *
26812 CAAACACCAAAAAATAAATTTTTTATTTGTGTTTTATGGATGCCGGCCATTTGTTGAAAAAGTGA
1 CAAACACCAAAAAATAAATTTTTTATTTGTGTTTTATGGATGCCGACCATTAGTTGAAAAAGTGA
* * *
26877 AAAAAAAATTCGAGTGTTGGGAAAGGTG-T-T-TGTCATTAGTTG-
66 AAAAAAAATTCGA-TGTTAGGAAAGGTGATGTCAGCCATTAGTTGT
* * * * * *
26919 CAAACTCCCAAAAA-AAA-TTTTTATTTGTATTTTTTTGGATGTCGACCATTAATTGAAAAAG
1 CAAACACCAAAAAATAAATTTTTTATTTGT-GTTTTATGGATGCCGACCATTAGTTGAAAAAG
26980 AACCAAAAAA
Statistics
Matches: 143, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
105 11 0.08
106 29 0.20
107 12 0.08
108 10 0.07
109 1 0.01
110 65 0.45
111 15 0.10
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.36
Consensus pattern (110 bp):
CAAACACCAAAAAATAAATTTTTTATTTGTGTTTTATGGATGCCGACCATTAGTTGAAAAAGTGA
AAAAAAAATTCGATGTTAGGAAAGGTGATGTCAGCCATTAGTTGT
Found at i:28924 original size:3 final size:3
Alignment explanation
Indices: 28898--28950 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
28888 TAGATCTTTG
* * *
28898 ATT ATG ATT ATG ATT ATG ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28946 ATT AT
1 ATT AT
28951 ACCTTTTGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:29644 original size:5 final size:5
Alignment explanation
Indices: 29634--29671 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
29624 AGTTACTACT
*
29634 AATAA AATAA AATAA AATTA AATAA AATAA AATTAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA-TAA AA
29672 ATAACCAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:29658 original size:15 final size:15
Alignment explanation
Indices: 29638--29670 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
29628 ACTACTAATA
29638 AAATAAAATAAAATT
1 AAATAAAATAAAATT
29653 AAATAAAATAAAATT
1 AAATAAAATAAAATT
29668 AAA
1 AAA
29671 AATAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAATAAAATT
Found at i:30056 original size:4 final size:4
Alignment explanation
Indices: 30037--30086 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
30027 ATATTTTCTA
* * * *
30037 CTTT CTTT CCTCT CTTT CTTT TTTT TTTT TTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
30086 C
1 C
30087 CTCTCTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 38 0.93
5 3 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:34204 original size:19 final size:19
Alignment explanation
Indices: 34182--34218 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34172 ACTGTCACCC
* *
34182 ATCGTAATTAAAGTTGTTT
1 ATCGTAATCAAAATTGTTT
34201 ATCGTAATCAAAATTGTT
1 ATCGTAATCAAAATTGTT
34219 ATTGGAGCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (19 bp):
ATCGTAATCAAAATTGTTT
Found at i:35895 original size:30 final size:29
Alignment explanation
Indices: 35862--36193 Score: 236
Period size: 30 Copynumber: 11.3 Consensus size: 29
35852 TAAAAATATT
*
35862 ATTTTGACTCCTAAACTTCTCAAAAATTAT
1 ATTTTGAC-CCTAAACTTCTCAAAAATTAC
*
35892 ATTTTGATTCCTAAACTTCTCAAAAATTAC
1 ATTTTGA-CCCTAAACTTCTCAAAAATTAC
* *
35922 ATTTTGACCCCTAAACTTCTTAAAATTTAC
1 ATTTTGA-CCCTAAACTTCTCAAAAATTAC
* * *
35952 ATTTTGACCTTAAAATTTTCCAAAAATTAC
1 ATTTTGACCCTAAACTTCT-CAAAAATTAC
35982 A-TTTGACCCCTAAACTTCTCAAAAATTAC
1 ATTTTGA-CCCTAAACTTCTCAAAAATTAC
* * **
36011 ATTTTGGCCCCAAACACCT-AAAAATTATC
1 ATTTTGACCCTAAACTTCTCAAAAATTA-C
**
36040 ATTTTG-CCCTTAAAGATC-C-AAAATTATC
1 ATTTTGACCC-TAAACTTCTCAAAAATTA-C
* *
36068 ATTTTGACCCTAAACTTTTCCAAAATTACC
1 ATTTTGACCCTAAACTTCTCAAAAATTA-C
*
36098 ATTTT-ACCAC-AGAACATC-CAAAAATTACC
1 ATTTTGACC-CTA-AACTTCTCAAAAATTA-C
* * * * *
36127 ATTTGGCCCCTGAGCAT-TCAAAAATTACC
1 ATTTTGACCCTAAACTTCTCAAAAATTA-C
* * *
36156 ATTTTG-CCCTCAAATTTC-CAAAAGTCAC
1 ATTTTGACCCT-AAACTTCTCAAAAATTAC
36184 ATTTTCGACC
1 ATTTT-GACC
36194 TCAAATTTTC
Statistics
Matches: 244, Mismatches: 39, Indels: 38
0.76 0.12 0.12
Matches are distributed among these distances:
28 41 0.17
29 99 0.41
30 104 0.43
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (29 bp):
ATTTTGACCCTAAACTTCTCAAAAATTAC
Found at i:35995 original size:59 final size:59
Alignment explanation
Indices: 35862--36102 Score: 217
Period size: 59 Copynumber: 4.1 Consensus size: 59
35852 TAAAAATATT
* * *
35862 ATTTTGACTCCTAAACTTCTCAAAAATTATATTTTGATTCCTAAACTTCTCAAAAATTAC
1 ATTTTGACCCCTAAACTTCTCAAAAATTACATTTTGA-TCCTAAAATTCTCAAAAATTAC
* * *
35922 ATTTTGACCCCTAAACTTCTTAAAATTTACATTTTGA-CCTTAAAATTTTCCAAAAATTAC
1 ATTTTGACCCCTAAACTTCTCAAAAATTACATTTTGATCC-TAAAATTCT-CAAAAATTAC
** * *
35982 A-TTTGACCCCTAAACTTCTCAAAAATTACATTTTGGCCCCAAACA-CCT-AAAAATTATC
1 ATTTTGACCCCTAAACTTCTCAAAAATTACATTTTGATCCTAAA-ATTCTCAAAAATTA-C
* ** * * * *
36040 ATTTTG-CCCTTAAAGATC-C-AAAATTATCATTTTGACCCTAAACTTTTCCAAAATTACC
1 ATTTTGACCCCTAAACTTCTCAAAAATTA-CATTTTGATCCTAAAATTCTCAAAAATTA-C
36098 ATTTT
1 ATTTT
36103 ACCACAGAAC
Statistics
Matches: 150, Mismatches: 22, Indels: 20
0.78 0.11 0.10
Matches are distributed among these distances:
56 7 0.05
57 23 0.15
58 26 0.17
59 47 0.31
60 47 0.31
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.37
Consensus pattern (59 bp):
ATTTTGACCCCTAAACTTCTCAAAAATTACATTTTGATCCTAAAATTCTCAAAAATTAC
Found at i:36176 original size:58 final size:59
Alignment explanation
Indices: 35901--36178 Score: 143
Period size: 59 Copynumber: 4.8 Consensus size: 59
35891 TATTTTGATT
* * * *
35901 CCTAAACT-TCTCAAAAATTA-CATTTTGACCC-CTAAACTTCTTAAAATTTA-CATTTTGAC
1 CCTAAACTAT-TCAAAAATTACCATTTTG-CCCTC-AAACATC-CAAAAATTACCATTTGGAC
* * * *
35960 CTTAAAATTTTCCAAAAATTA-CA-TTTGACCC-CTAAACTTCTCAAAAATTA-CATTTTGG-C
1 CCTAAACTATT-CAAAAATTACCATTTTG-CCCTC-AAACATC-CAAAAATTACCA-TTTGGAC
* * * * * * *
36019 CCCAAAC-A-CCTAAAAATTATCATTTTGCCCTTAAAGATCC-AAAATTATCATTTTGAC
1 CCTAAACTATTC-AAAAATTACCATTTTGCCCTCAAACATCCAAAAATTACCATTTGGAC
* * * * *
36076 CCTAAACTTTTCCAAAATTACCATTTT-ACCACAGAACATCCAAAAATTACCATTTGGCC
1 CCTAAACTATTCAAAAATTACCATTTTGCCCTCA-AACATCCAAAAATTACCATTTGGAC
* * **
36135 CCTGAGC-ATTCAAAAATTACCATTTTGCCCTCAAATTTCCAAAA
1 CCTAAACTATTCAAAAATTACCATTTTGCCCTCAAACATCCAAAA
36179 GTCACATTTT
Statistics
Matches: 171, Mismatches: 34, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
56 12 0.07
57 21 0.12
58 55 0.32
59 67 0.39
60 16 0.09
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (59 bp):
CCTAAACTATTCAAAAATTACCATTTTGCCCTCAAACATCCAAAAATTACCATTTGGAC
Found at i:36176 original size:116 final size:114
Alignment explanation
Indices: 35911--36203 Score: 276
Period size: 116 Copynumber: 2.5 Consensus size: 114
35901 CCTAAACTTC
* *
35911 TCAAAAATTACATTTTGACCC-CTAAACTTCTTAAAATTTACATTTTGACCTTAAAATTTTCCAA
1 TCAAAAATTACATTTTG-CCCTC-AAACTTC-CAAAATTTACATTTTGACCCTAAAATTTTCCAA
* *
35975 AAATTACATTTGACCCCTAAACTTCTCAAAAATTACATTTTGGCCCCAAACA
63 AAATTACATTTGACCACTAAACATCTCAAAAATTACATTTTGGCCCCAAACA
* * ** *
36027 CCTAAAAATTATCATTTTGCCCTTAAAGATCCAAAA-TTATCATTTTGACCCTAAACTTTTCC-A
1 TC-AAAAATTA-CATTTTGCCCTCAAACTTCCAAAATTTA-CATTTTGACCCTAAAATTTTCCAA
* * *
36090 AAATTACCATTTTACCAC-AGAACATC-CAAAAATTACCA-TTTGGCCCCTGAGCA
63 AAATTA-CATTTGACCACTA-AACATCTCAAAAATTA-CATTTTGGCCCC-AAACA
* * * *
36143 TTCAAAAATTACCATTTTGCCCTCAAATTTCCAAAAGTCACATTTTCGA-CCTCAAATTTTC
1 -TCAAAAATTA-CATTTTGCCCTCAAACTTCCAAAATTTACATTTT-GACCCTAAAATTTTC
36204 TACAAGTTTG
Statistics
Matches: 146, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
115 29 0.20
116 89 0.61
117 21 0.14
118 7 0.05
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (114 bp):
TCAAAAATTACATTTTGCCCTCAAACTTCCAAAATTTACATTTTGACCCTAAAATTTTCCAAAAA
TTACATTTGACCACTAAACATCTCAAAAATTACATTTTGGCCCCAAACA
Found at i:36227 original size:29 final size:31
Alignment explanation
Indices: 36195--36260 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
36185 TTTTCGACCT
*
36195 CAAATTTTCTACAAGTTT-GATTTTAAT-CC
1 CAAATTTTCTACAAATTTCGATTTTAATCCC
* *
36224 CAAATTTTCTAGAAATTTCGATTTTGATCCC
1 CAAATTTTCTACAAATTTCGATTTTAATCCC
36255 CAAATT
1 CAAATT
36261 CCTCGAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 16 0.50
30 8 0.25
31 8 0.25
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (31 bp):
CAAATTTTCTACAAATTTCGATTTTAATCCC
Done.