Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001912.1 Kokia drynarioides strain JFW-HI SEQ_113705, 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: 17952
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:672 original size:26 final size:26
Alignment explanation
Indices: 638--692 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
628 TAAGTCTCAA
638 TTTGAGGTTAAACTAATCC-AAATTAT
1 TTTGAGGTTAAACTAA-CCTAAATTAT
664 TTTGAGGTTAAACTAACCTAAATTAT
1 TTTGAGGTTAAACTAACCTAAATTAT
690 TTT
1 TTT
693 TAGTGAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (26 bp):
TTTGAGGTTAAACTAACCTAAATTAT
Found at i:3905 original size:97 final size:97
Alignment explanation
Indices: 3720--3905 Score: 252
Period size: 97 Copynumber: 1.9 Consensus size: 97
3710 AAAAGGATAG
* *
3720 TCGATTATCTCGATTTGAAGAAAAATCGCGCCTACTAAGTTAAGGCACAAATTTTCAGAATCGGA
1 TCGATTATCTCGATTTGAAAAAAAATCGCGCCTACTAAGTTAAGGCACAAATTTTCAAAATCGGA
* * *
3785 GATAAAGAAACATTGTCTTGATTTAAGGGTAT
66 AATAAAGAAACATTGCCTCGATTTAAGGGTAT
*
3817 TCGATTAT-TCCGATTTGAAAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACTC-
1 TCGATTATCT-CGATTTGAAAAAAAATCGCGCCTACTAAGTTAAGGCACAAATTTTCAAAA-TCG
**
3880 GAAATAAA-AGAATTTTGCCTCGATTT
64 GAAATAAAGA-AACATTGCCTCGATTT
3906 TAAAGGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
96 2 0.03
97 74 0.95
98 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (97 bp):
TCGATTATCTCGATTTGAAAAAAAATCGCGCCTACTAAGTTAAGGCACAAATTTTCAAAATCGGA
AATAAAGAAACATTGCCTCGATTTAAGGGTAT
Found at i:4257 original size:31 final size:31
Alignment explanation
Indices: 4222--4362 Score: 104
Period size: 28 Copynumber: 4.8 Consensus size: 31
4212 TTTAGACATC
*
4222 CGAGGGCAAAATAGTAAATTTTGGAAATTTT
1 CGAGGGCAAAATAGTAATTTTTGGAAATTTT
* *
4253 CGAGGTCAAAAATAG-AATTTTTGGACA--TT
1 CGAGGGC-AAAATAGTAATTTTTGGAAATTTT
* * *
4282 CG-GGGTAAAATGGTAATTTTTGGAAGTTTT
1 CGAGGGCAAAATAGTAATTTTTGGAAATTTT
* *
4312 -G-GGGTCAAAAT-GGAATTTTT-GACA--TT
1 CGAGGG-CAAAATAGTAATTTTTGGAAATTTT
* *
4338 CGAGGGTAAAATGGTAATTTTTGGA
1 CGAGGGCAAAATAGTAATTTTTGGA
4363 TGTTTCTAGG
Statistics
Matches: 87, Mismatches: 14, Indels: 20
0.72 0.12 0.17
Matches are distributed among these distances:
26 2 0.02
27 12 0.14
28 25 0.29
29 18 0.21
30 7 0.08
31 16 0.18
32 7 0.08
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.34
Consensus pattern (31 bp):
CGAGGGCAAAATAGTAATTTTTGGAAATTTT
Found at i:4416 original size:59 final size:59
Alignment explanation
Indices: 4370--4543 Score: 194
Period size: 59 Copynumber: 3.0 Consensus size: 59
4360 GGATGTTTCT
**
4370 AGGTCAAAAAATGAAATTTTGGAAAGTTT-GGGGGAAAAATGTAATTTTTGAAAAGTTTA
1 AGGTC-AAAAATGAAATTTTGGAAAGTTTAGGGACAAAAATGTAATTTTTGAAAAGTTTA
* * **
4429 AGGTCAAAAATGGAATTTTGGAAAGTTTAGGGACAAAAATGTAATTTTT-ATGAAGTTCG
1 AGGTCAAAAATGAAATTTTGGAAAGTTTAGGGACAAAAATGTAATTTTTGA-AAAGTTTA
* ** * *
4488 AGGTC-AAAATGGAATTTTTGGAAAAATTAGGGTCAAAAATGGAA-TTTTGAAAAGTT
1 AGGTCAAAAAT-GAAATTTTGGAAAGTTTAGGGACAAAAATGTAATTTTTGAAAAGTT
4544 CGAGGGTAAA
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
58 37 0.38
59 61 0.62
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (59 bp):
AGGTCAAAAATGAAATTTTGGAAAGTTTAGGGACAAAAATGTAATTTTTGAAAAGTTTA
Found at i:4448 original size:116 final size:116
Alignment explanation
Indices: 4150--4448 Score: 306
Period size: 117 Copynumber: 2.6 Consensus size: 116
4140 GTAAAACGGT
* * * * *
4150 AATTTTGGACACTTCGGGGGAAAAATAATAATTTTT-AGAGGTTCGAGGTTAAAAATGGAATCTT
1 AATTTTGGACA-TTTGGGGGAAAAATAGTAATTTTTGAGAAGTTTGAGGTCAAAAATGGAAT-TT
4214 TAGACATCCGAGGGCAAAATAGTAAATTTTGGAAATTTTCGAGGTCAAAAATAGA
64 T-GACATCCGAGGGCAAAATAGTAAATTTTGG-AATTTTCGAGGTCAAAAATAGA
* * * * *
4269 ATTTTTGGACA-TTCGGGGTAAAATGGTAATTTTTG-GAAGTTTTGGGGTC-AAAATGGAATTTT
1 AATTTTGGACATTTGGGGGAAAAATAGTAATTTTTGAGAAG-TTTGAGGTCAAAAATGGAA-TTT
* * * * *
4331 TGACATTCGAGGGTAAAATGGTAATTTTTGG-ATGTTTCTAGGTCAAAAA-ATGA
64 TGACATCCGAGGGCAAAATAGTAAATTTTGGAAT-TTTCGAGGTCAAAAATA-GA
* * *
4384 AATTTTGGAAAGTTTGGGGGAAAAAT-GTAATTTTTGAAAAGTTTAAGGTCAAAAATGGAATTTT
1 AATTTTGGACA-TTTGGGGGAAAAATAGTAATTTTTGAGAAGTTTGAGGTCAAAAATGGAATTTT
4448 G
65 G
4449 GAAAGTTTAG
Statistics
Matches: 149, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
114 3 0.02
115 25 0.17
116 48 0.32
117 56 0.38
118 7 0.05
119 10 0.07
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (116 bp):
AATTTTGGACATTTGGGGGAAAAATAGTAATTTTTGAGAAGTTTGAGGTCAAAAATGGAATTTTG
ACATCCGAGGGCAAAATAGTAAATTTTGGAATTTTCGAGGTCAAAAATAGA
Found at i:4529 original size:30 final size:29
Alignment explanation
Indices: 4238--4584 Score: 144
Period size: 29 Copynumber: 11.9 Consensus size: 29
4228 CAAAATAGTA
* * * *
4238 AATTTTGGAAATTTTCGAGGTCAAAAATAG
1 AATTTTTGAAAATTTAG-GGTCAAAAATGG
* * **
4268 AATTTTTGGACATTCGGGGT--AAAATGG
1 AATTTTTGAAAATTTAGGGTCAAAAATGG
** *
4295 TAATTTTTGGAAGTTTTGGGGTC-AAAATGG
1 -AATTTTT-GAAAATTTAGGGTCAAAAATGG
* *
4325 AATTTTTG-ACATTCGAGGGT--AAAATGG
1 AATTTTTGAAAATT-TAGGGTCAAAAATGG
*** *
4352 TAATTTTTGGATGTTTCTA-GGTCAAAAAATGA
1 -AATTTTT-GAAAATT-TAGGGTC-AAAAATGG
* * ** *
4384 AATTTTGGAAAGTTT-GGGGGAAAAATGT
1 AATTTTTGAAAATTTAGGGTCAAAAATGG
*
4412 AATTTTTGAAAAGTTTAAGGTCAAAAATGG
1 AATTTTTGAAAA-TTTAGGGTCAAAAATGG
* * * *
4442 AATTTTGGAAAGTTTAGGGACAAAAATGT
1 AATTTTTGAAAATTTAGGGTCAAAAATGG
* * *
4471 AATTTTT-ATGAAGTTCGAGGTC-AAAATGG
1 AATTTTTGA-AAATTTAG-GGTCAAAAATGG
*
4500 AATTTTTGGAAAAATTAGGGTCAAAAATGG
1 AATTTTT-GAAAATTTAGGGTCAAAAATGG
* *
4530 AA-TTTTGAAAAGTTCGAGGGTAAAAACAT--
1 AATTTTTGAAAA-TT-TAGGGTCAAAA-ATGG
* *
4559 AATTTTCGAAAAGTTCAGGGTCAAAA
1 AATTTTTGAAAA-TTTAGGGTCAAAA
4585 TATGATTTTT
Statistics
Matches: 241, Mismatches: 54, Indels: 45
0.71 0.16 0.13
Matches are distributed among these distances:
27 16 0.07
28 42 0.17
29 86 0.36
30 82 0.34
31 9 0.04
32 6 0.02
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.33
Consensus pattern (29 bp):
AATTTTTGAAAATTTAGGGTCAAAAATGG
Found at i:4563 original size:59 final size:58
Alignment explanation
Indices: 4404--4584 Score: 150
Period size: 59 Copynumber: 3.1 Consensus size: 58
4394 AGTTTGGGGG
* ** ** ** *
4404 AAAAATGTAATTTTTGA-AAAGTTTAAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGAC
1 AAAAATGGAA-TTTTGATAAAGTTCGAGGT-AAAAACAGAATTTTGGAAAAATTAGGGTC
* * * * **
4463 AAAAATGTAATTTTTATGAAGTTCGAGGTCAAAATGGAATTTTTGGAAAAATTAGGGTC
1 AAAAATGGAATTTTGATAAAGTTCGAGGTAAAAACAGAA-TTTTGGAAAAATTAGGGTC
* * *
4522 AAAAATGGAATTTTGA-AAAGTTCGAGGGTAAAAACATAATTTTCGAAAAGTTCAGGGTC
1 AAAAATGGAATTTTGATAAAGTTCGA-GGTAAAAACAGAATTTTGGAAAAATT-AGGGTC
4581 AAAA
1 AAAA
4585 TATGATTTTT
Statistics
Matches: 101, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
58 33 0.33
59 68 0.67
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.30
Consensus pattern (58 bp):
AAAAATGGAATTTTGATAAAGTTCGAGGTAAAAACAGAATTTTGGAAAAATTAGGGTC
Found at i:4597 original size:88 final size:89
Alignment explanation
Indices: 4405--4585 Score: 210
Period size: 88 Copynumber: 2.1 Consensus size: 89
4395 GTTTGGGGGA
* * * * *
4405 AAAATGTAATTTTT-GAAAAGTTTAAGGTCAAAAATGGAATTTTGGAAAGTTTAGGGACAAAAAT
1 AAAATGGAATTTTTGGAAAAGATTAAGGTCAAAAATGGAATTTTGAAAAGTTGAGGGACAAAAAC
* * *
4469 GTAATTTTTATGAAGTTCGAGGTC
66 ATAATTTTGATAAAGTTCGAGGTC
* *
4493 AAAATGGAATTTTTGGAAAA-ATTAGGGTCAAAAATGGAATTTTGAAAAGTTCGAGGG-TAAAAA
1 AAAATGGAATTTTTGGAAAAGATTAAGGTCAAAAATGGAATTTTGAAAAGTT-GAGGGACAAAAA
4556 CATAATTTTCGA-AAAGTTC-AGGGTC
65 CATAATTTT-GATAAAGTTCGA-GGTC
4581 AAAAT
1 AAAAT
4586 ATGATTTTTG
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
87 1 0.01
88 68 0.86
89 10 0.13
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (89 bp):
AAAATGGAATTTTTGGAAAAGATTAAGGTCAAAAATGGAATTTTGAAAAGTTGAGGGACAAAAAC
ATAATTTTGATAAAGTTCGAGGTC
Found at i:5488 original size:22 final size:23
Alignment explanation
Indices: 5458--5500 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
5448 TTAGACTTTC
*
5458 AAAGTTTAAATTTAATTTAAAAT
1 AAAGTTTAAATTTAAATTAAAAT
5481 AAAG-TTAAATTTAAATTAAA
1 AAAGTTTAAATTTAAATTAAA
5501 CCCAAACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
AAAGTTTAAATTTAAATTAAAAT
Found at i:5493 original size:17 final size:17
Alignment explanation
Indices: 5464--5562 Score: 94
Period size: 17 Copynumber: 5.9 Consensus size: 17
5454 TTTCAAAGTT
5464 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
* *
5480 TAAAGTTAAATTTAAAT
1 TAAATTTAAATTTAAAA
*** * *
5497 TAAACCCAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
5514 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
*
5531 TAAATTCAAATTT-AAA
1 TAAATTTAAATTTAAAA
*
5547 TAAATTTAGATTTAAA
1 TAAATTTAAATTTAAA
5563 TTTTAAAAAT
Statistics
Matches: 63, Mismatches: 18, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
16 19 0.30
17 44 0.70
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5499 original size:5 final size:6
Alignment explanation
Indices: 5462--5565 Score: 60
Period size: 6 Copynumber: 18.5 Consensus size: 6
5452 ACTTTCAAAG
* * ***
5462 TTTAAA TTT-AA TTTAAA -ATAAA GTTAAA TTTAAA -TTAAA CCCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
5507 CTCAAA -ATAAA TTTAAA TTTAAA -GTAAA TTCAAA TTTAAA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
5551 TTTAGA TTTAAA TTT
1 TTTAAA TTTAAA TTT
5566 TAAAAATGGG
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
4 4 0.05
5 21 0.28
6 51 0.67
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (6 bp):
TTTAAA
Found at i:6100 original size:39 final size:36
Alignment explanation
Indices: 6006--6124 Score: 107
Period size: 39 Copynumber: 3.2 Consensus size: 36
5996 AAAAGGTCGG
* * *
6006 ATGGTTGCAATCTGCCCCAGGCTTAGGGTAAGAGAT
1 ATGGTTGCAATTTGCCCTAGGCTTGGGGTAAGAGAT
*
6042 -TGGTTGACAATGATCTGCCCTAGGCTTGGGGTAAAAGAT
1 ATGGTTG-CAAT--T-TGCCCTAGGCTTGGGGTAAGAGAT
* *
6081 CAAATGGTTGCAATTTGCCCTAGACTCGGGGTAAGAGAT
1 ---ATGGTTGCAATTTGCCCTAGGCTTGGGGTAAGAGAT
6120 -TGGTT
1 ATGGTT
6125 AATGACGATC
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
39 42 0.62
40 1 0.01
42 4 0.06
43 6 0.09
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (36 bp):
ATGGTTGCAATTTGCCCTAGGCTTGGGGTAAGAGAT
Found at i:6100 original size:78 final size:77
Alignment explanation
Indices: 6006--6203 Score: 243
Period size: 78 Copynumber: 2.6 Consensus size: 77
5996 AAAAGGTCGG
** * * *
6006 ATGGTTGCAATCTGCCCCAGGCTTAGGGTAAGAGATTGGTTGACAATGATCTGCCCTAGGCTTGG
1 ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGACAACGATCTGCCCCAGGCTCGG
6071 GGTAAAAGATCAA
66 GGT-AAAGATCAA
* * * * **
6084 ATGGTTGCAATTTGCCCTAGACTCGGGGTAAGAGATTGGTTAATGACGATCTGCCCCAGGCTCGG
1 ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGACAACGATCTGCCCCAGGCTCGG
*
6149 GGTAAAGATCCA
66 GGTAAAGATCAA
* * * *
6161 ATGGTTTCAATCTGCCTCAAGCTCGGGGTAAAAGATTGGTTGA
1 ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGA
6204 TGATGTAACT
Statistics
Matches: 100, Mismatches: 20, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
77 43 0.43
78 57 0.57
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (77 bp):
ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGACAACGATCTGCCCCAGGCTCGG
GGTAAAGATCAA
Found at i:6570 original size:98 final size:98
Alignment explanation
Indices: 6468--6650 Score: 242
Period size: 98 Copynumber: 1.9 Consensus size: 98
6458 TTACGGTCGT
* *
6468 AACCTTTCCCTTCAAATCTTCAAGGTACTAGATTCACCATTACGGCTTAAATATTTCCTTTCGTG
1 AACCTTTCCCTTCAAATCTTCAAGGTACTAGATTCACCATTACGGCTTAAATATTTCCCTTCATG
* *
6533 -TTTCTGAGGTACAAGGTTCGTCCTTGCGACTTA
66 CTTCCT-AAGTACAAGGTTCGTCCTTGCGACTTA
* ** *** * *
6566 AACCTTTCCCTTTAAATCTTCGTGGTACTAGATTTTTCGTTACGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTCAAATCTTCAAGGTACTAGATTCACCATTACGGCTTAAATATTTCCCTTCATG
6631 CTTCCTAAGTACAAGGTTCG
66 CTTCCTAAGTACAAGGTTCG
6651 CGGTTTTGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 68 0.94
99 4 0.06
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (98 bp):
AACCTTTCCCTTCAAATCTTCAAGGTACTAGATTCACCATTACGGCTTAAATATTTCCCTTCATG
CTTCCTAAGTACAAGGTTCGTCCTTGCGACTTA
Found at i:6593 original size:49 final size:48
Alignment explanation
Indices: 6540--7174 Score: 300
Period size: 49 Copynumber: 12.8 Consensus size: 48
6530 GTGTTTCTGA
*
6540 GGTACAAGGTTCGTCCTTGCGACTTAAACCTTTCCCTTTAAAT-CTTCGT
1 GGTACAAGGTTCG-CCTTGCGACTTAAACCTTTCCCTTT-CATGCTTCGT
* * ** * * * * *
6589 GGTACTAGATTTTTCGTTACGGCTTAAATCTTTCCC-TTCATGCTTCCT
1 GGTACAAG-GTTCGCCTTGCGACTTAAACCTTTCCCTTTCATGCTTCGT
* * * *
6637 AAGTACAAGGTTCGCGGTTTTGTTGTTGCGGCTTAAATCTTTCCC-TTCATGCTTC-T
1 -GGTACAAGGTTCGC---------CTTGCGACTTAAACCTTTCCCTTTCATGCTTCGT
* *
6693 GAGATACAAGGTTCGCTGTTGTGACTTAAACCTTTCCCTCCTT-AT-CTTCGT
1 G-G-TACAAGGTTCGC-CTTGCGACTTAAACCTTTCCCT--TTCATGCTTCGT
* * * *
6744 GGTAC-TGGATTCACCGTTGC-AGCTTAAATCTTTCCC-TTCATGCTTCCT
1 GGTACAAGG-TTCGCC-TTGCGA-CTTAAACCTTTCCCTTTCATGCTTCGT
*
6792 AGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTT-ATGCTTCCT
1 -GGTACAAGGTTCGCC-TTGCGACTTAAACCTTTCCCTTTCATGCTTCGT
** * *
6841 AGGTACAAGGTTTACCGTTGCGACTTAAACCTTT-CCTTTTATTTCCTT-GT
1 -GGTACAAGGTTCGCC-TTGCGACTTAAACCTTTCCCTTTCA--TGCTTCGT
* * * * * * * *
6891 GGTAC-TGTATTTGCTGTTGCGGCTTAAATCTTTCCC-TTCATGCTTTTGA
1 GGTACAAG-GTTCGC-CTTGCGACTTAAACCTTTCCCTTTCATGC-TTCGT
* ** *
6940 GGTACAAGGTTTGCCGTTATGACTTAAACCTTTCCCTATTTAT-CTTCGT
1 GGTACAAGGTTCGCC-TTGCGACTTAAACCTTTCCCT-TTCATGCTTCGT
* * * *
6989 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCC-TCCATGTCTTTGT
1 GGTACAAGGTTCGCC-TTGCGACTTAAACCTTTCCCTTTCATG-CTTCGT
* * * * ** *
7038 GGTAC-TGGATTTGTCGTTGCGGCTTAAGTCTTTCCC-TTCATGCTTCCT
1 GGTACAAGG-TTCG-CCTTGCGACTTAAACCTTTCCCTTTCATGCTTCGT
* * * *
7086 CGGTACAAGGTTCGCCGTTACGACTTAAA-CTTTTCCTTTTATGCTTCCT
1 -GGTACAAGGTTCGCC-TTGCGACTTAAACCTTTCCCTTTCATGCTTCGT
*
7135 AGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTT
1 -GGTACAAGGTTCG-CCTTGCGACTTAAACCTTTCCCTTT
7175 ATTTTCTTGT
Statistics
Matches: 453, Mismatches: 84, Indels: 97
0.71 0.13 0.15
Matches are distributed among these distances:
46 2 0.00
47 9 0.02
48 38 0.08
49 316 0.70
50 30 0.07
51 12 0.03
52 2 0.00
56 2 0.00
57 42 0.09
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (48 bp):
GGTACAAGGTTCGCCTTGCGACTTAAACCTTTCCCTTTCATGCTTCGT
Found at i:6893 original size:147 final size:146
Alignment explanation
Indices: 6539--7226 Score: 742
Period size: 147 Copynumber: 4.6 Consensus size: 146
6529 CGTGTTTCTG
** * **
6539 AGGTACAAGGTTCGTCC-TTGCGACTTAAACCTTTCCCTTTAAATCTTCGTGGTACTAGATTTTT
1 AGGTACAAGGTTCG-CCGTTGCGACTTAAACCTTTCCCTTTATTTCTT-GTGGTACTGGATTTAC
* * * * *
6603 CGTTACGGCTTAAATCTTTCCCTTCATGCTTCCTAAGTACAAGGTTCGCGGTTTTGTTGTTGCGG
64 CGTTGCGGCTTAAATCTTTCCCTTCATGCTTCCTAGGTACAAGGTTCGC--------CGTTACGA
* *
6668 CTTAAATCTTTCCCTTCATGCTT-CT
121 CTTAAACCTTTCCCTTTATGCTTCCT
* * * *
6693 GAGATACAAGGTTCGCTGTTGTGACTTAAACCTTTCCCTCCTTA--TCTTCGTGGTACTGGATTC
1 -AGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT--TTATTTCTT-GTGGTACTGGATTT
* * *
6756 ACCGTTGCAGCTTAAATCTTTCCCTTCATGCTTCCTAGGTACAAGGTTCGCCATTGCGACTTAAA
62 ACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCCTAGGTACAAGGTTCGCCGTTACGACTTAAA
6821 CCTTTCCCTTTATGCTTCCT
127 CCTTTCCCTTTATGCTTCCT
** * * * *
6841 AGGTACAAGGTTTACCGTTGCGACTTAAACCTTTCCTTTTATTTCCTTGTGGTACTGTATTTGCT
1 AGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTATTT-CTTGTGGTACTGGATTTACC
* * *
6906 GTTGCGGCTTAAATCTTTCCCTTCATGCTT-TTGAGGTACAAGGTTTGCCGTTATGACTTAAACC
65 GTTGCGGCTTAAATCTTTCCCTTCATGCTTCCT-AGGTACAAGGTTCGCCGTTACGACTTAAACC
*
6970 TTTCCCTATTTAT-CTTCGT
129 TTTCCC--TTTATGCTTCCT
* * ** * **
6989 -GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTCCATGTCTTTGTGGTACTGGATTTGTC
1 AGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTATTTC-TTGTGGTACTGGATTTACC
* * *
7053 GTTGCGGCTTAAGTCTTTCCCTTCATGCTTCCTCGGTACAAGGTTCGCCGTTACGACTTAAACTT
65 GTTGCGGCTTAAATCTTTCCCTTCATGCTTCCTAGGTACAAGGTTCGCCGTTACGACTTAAACCT
*
7118 TTCCTTTTATGCTTCCT
130 TTCCCTTTATGCTTCCT
* * *
7135 AGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTATTTTCTTGTGGTATTGGATTCACC
1 AGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTA-TTTCTTGTGGTACTGGATTTACC
* *
7200 GTTACGACTTAAATCTTTCCCTTCATG
65 GTTGCGGCTTAAATCTTTCCCTTCATG
7227 GTATTAGATT
Statistics
Matches: 454, Mismatches: 64, Indels: 38
0.82 0.12 0.07
Matches are distributed among these distances:
145 8 0.02
146 7 0.02
147 320 0.70
148 14 0.03
149 5 0.01
154 1 0.00
155 96 0.21
157 3 0.01
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.40
Consensus pattern (146 bp):
AGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTATTTCTTGTGGTACTGGATTTACCG
TTGCGGCTTAAATCTTTCCCTTCATGCTTCCTAGGTACAAGGTTCGCCGTTACGACTTAAACCTT
TCCCTTTATGCTTCCT
Found at i:7176 original size:49 final size:49
Alignment explanation
Indices: 6661--7176 Score: 410
Period size: 49 Copynumber: 10.5 Consensus size: 49
6651 CGGTTTTGTT
* * * * *
6661 GTTGCGGCTTAAATCTTTCCCTTCATGCTT-CTGAGATACAAGGTTCGCT
1 GTTGCGACTTAAACCTTTCCCTTTATGCTTCCT-AGGTACAAGGTTCGCC
* * * *
6710 GTTGTGACTTAAACCTTTCCCTCCTTAT-CTTCGT-GGTAC-TGGATTCACC
1 GTTGCGACTTAAACCTTTCCCT--TTATGCTTCCTAGGTACAAGG-TTCGCC
* *
6759 GTTGC-AGCTTAAATCTTTCCCTTCATGCTTCCTAGGTACAAGGTTCGCC
1 GTTGCGA-CTTAAACCTTTCCCTTTATGCTTCCTAGGTACAAGGTTCGCC
* **
6808 ATTGCGACTTAAACCTTTCCCTTTATGCTTCCTAGGTACAAGGTTTACC
1 GTTGCGACTTAAACCTTTCCCTTTATGCTTCCTAGGTACAAGGTTCGCC
* * * * * *
6857 GTTGCGACTTAAACCTTTCCTTTTAT--TTCCTTGTGGTAC-TGTATTTGCT
1 GTTGCGACTTAAACCTTTCCCTTTATGCTTCC-T-AGGTACAAG-GTTCGCC
* * * * *
6906 GTTGCGGCTTAAATCTTTCCCTTCATGCTT-TTGAGGTACAAGGTTTGCC
1 GTTGCGACTTAAACCTTTCCCTTTATGCTTCCT-AGGTACAAGGTTCGCC
** * * *
6955 GTTATGACTTAAACCTTTCCCTATTTAT-CTTCGT-GGTACTAGATTCGCC
1 GTTGCGACTTAAACCTTTCCC--TTTATGCTTCCTAGGTACAAGGTTCGCC
** ** * * *
7004 GTTGCGACTTAAACCTTTCCCTCCATGTCTTTGT-GGTAC-TGGATTTGTC
1 GTTGCGACTTAAACCTTTCCCTTTATG-CTTCCTAGGTACAAGG-TTCGCC
* ** * *
7053 GTTGCGGCTTAAGTCTTTCCCTTCATGCTTCCTCGGTACAAGGTTCGCC
1 GTTGCGACTTAAACCTTTCCCTTTATGCTTCCTAGGTACAAGGTTCGCC
* * * *
7102 GTTACGACTTAAACTTTTCCTTTTATGCTTCCTAGGTACAAGGTTCGTC
1 GTTGCGACTTAAACCTTTCCCTTTATGCTTCCTAGGTACAAGGTTCGCC
7151 GTTGCGACTTAAACCTTTCCCTTTAT
1 GTTGCGACTTAAACCTTTCCCTTTAT
7177 TTTCTTGTGG
Statistics
Matches: 369, Mismatches: 75, Indels: 46
0.75 0.15 0.09
Matches are distributed among these distances:
47 10 0.03
48 15 0.04
49 321 0.87
50 12 0.03
51 11 0.03
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (49 bp):
GTTGCGACTTAAACCTTTCCCTTTATGCTTCCTAGGTACAAGGTTCGCC
Found at i:7202 original size:98 final size:98
Alignment explanation
Indices: 6802--7226 Score: 373
Period size: 98 Copynumber: 4.3 Consensus size: 98
6792 AGGTACAAGG
* * * * *
6802 TTCGCCATTGCGACTTAAACCTTTCCCTTTATGCTTCCTAGGTACAAGGTTTACCGTTGCGACTT
1 TTCGCCGTTACGACTTAAACTTTTCCCTTCATGCTTCCTAGGTACAAGGTTTGCCGTTGCGACTT
* * *
6867 AAACCTTTCCTTTTATTTCCTTGTGGTACTGTA
66 AAACCTTTCCCTTTATTTTCTTGTGGTACTGGA
* * * * * **
6900 TTTGCTGTTGCGGCTTAAA-TCTTTCCCTTCATGCTT-TTGAGGTACAAGGTTTGCCGTTATGAC
1 TTCGCCGTTACGACTTAAACT-TTTCCCTTCATGCTTCCT-AGGTACAAGGTTTGCCGTTGCGAC
*
6963 TTAAACCTTTCCC--TATTTATCTTCGTGGTACTAGA
64 TTAAACCTTTCCCTTTATTT-TCTT-GTGGTACTGGA
* * * ** * * *
6998 TTCGCCGTTGCGACTTAAACCTTTCCCTCCATGTCTTTGT-GGTAC-TGGATTTGTCGTTGCGGC
1 TTCGCCGTTACGACTTAAACTTTTCCCTTCATG-CTTCCTAGGTACAAGG-TTTGCCGTTGCGAC
** * * * * *
7061 TTAAGTCTTTCCCTTCATGCTTCCT-CGGTACAAGG-
64 TTAAACCTTTCCCTTTAT-TTTCTTGTGGTAC-TGGA
* * * *
7096 TTCGCCGTTACGACTTAAACTTTTCCTTTTATGCTTCCTAGGTACAAGGTTCGTCGTTGCGACTT
1 TTCGCCGTTACGACTTAAACTTTTCCCTTCATGCTTCCTAGGTACAAGGTTTGCCGTTGCGACTT
*
7161 AAACCTTTCCCTTTATTTTCTTGTGGTATTGGA
66 AAACCTTTCCCTTTATTTTCTTGTGGTACTGGA
*
7194 TTCACCGTTACGACTTAAA-TCTTTCCCTTCATG
1 TTCGCCGTTACGACTTAAACT-TTTCCCTTCATG
7227 GTATTAGATT
Statistics
Matches: 256, Mismatches: 54, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
96 5 0.02
97 17 0.07
98 221 0.86
99 6 0.02
100 6 0.02
101 1 0.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (98 bp):
TTCGCCGTTACGACTTAAACTTTTCCCTTCATGCTTCCTAGGTACAAGGTTTGCCGTTGCGACTT
AAACCTTTCCCTTTATTTTCTTGTGGTACTGGA
Found at i:13409 original size:29 final size:29
Alignment explanation
Indices: 13372--13464 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 29
13362 TTGAAGGTTT
*
13372 AGGGTTAAAAATGGAATCTTTGGACATCCG
1 AGGGTTAAAAAT-GAATTTTTGGACATCCG
* * *
13402 AGGGTAAAATAAT-AATTTTTGGAAATTTTCG
1 AGGGTTAAA-AATGAATTTTTGGACA--TCCG
13433 -GGGTTAAAAATAGAATTTTTGGACATCCG
1 AGGGTTAAAAAT-GAATTTTTGGACATCCG
13462 AGG
1 AGG
13465 TAAAATGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
29 16 0.32
30 17 0.34
31 17 0.34
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (29 bp):
AGGGTTAAAAATGAATTTTTGGACATCCG
Found at i:13567 original size:57 final size:56
Alignment explanation
Indices: 13356--13569 Score: 193
Period size: 57 Copynumber: 3.7 Consensus size: 56
13346 GGAAAAATAG
* * * * *
13356 TAATTTTTGAAGGTTTAGGGTT-AAAAATGGAATCTTTGGACATCCGAGGGTAAAATAA
1 TAATTTTGGAA-GTTTCGAGTTCAAAAATGAAAT-TTTGGACATCCGA-GGTAAAATGA
* * *
13414 TAATTTTTGGAAATTTTCGGGGTT-AAAAATAGAATTTTTGGACATCCGAGGTAAAATGA
1 TAA-TTTTGG-AAGTTTC-GAGTTCAAAAAT-GAAATTTTGGACATCCGAGGTAAAATGA
* * *
13473 TAATTGTTGGAAGTTTC-AGGATC-AAAATGAAATTTTTGGACATCCGTGGATAAAATGG
1 TAATT-TTGGAAGTTTCGA-GTTCAAAAATGAAA-TTTTGGACATCCGAGG-TAAAATGA
*
13531 CAATTTTGGAAGTTTCGAGTTCAAAAATGAAATTTTGGA
1 TAATTTTGGAAGTTTCGAGTTCAAAAATGAAATTTTGGA
13570 ATGTTCGAGG
Statistics
Matches: 131, Mismatches: 14, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
56 3 0.02
57 43 0.33
58 32 0.24
59 24 0.18
60 26 0.20
61 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (56 bp):
TAATTTTGGAAGTTTCGAGTTCAAAAATGAAATTTTGGACATCCGAGGTAAAATGA
Found at i:13614 original size:59 final size:58
Alignment explanation
Indices: 13320--13794 Score: 243
Period size: 58 Copynumber: 8.1 Consensus size: 58
13310 AACGGGGAGT
** * * * *
13320 AAAATGATAATTTTGGACTCTTCAAGGGAAAAATAGTAATTTTT-GAAGGTT-TAGGGTTA
1 AAAATGA-AATTTTGGA-AGTTCGAGGGTAAAATAGTAATTTTTGGAAAGTTCT-GGGTCA
* * * * * *
13379 AAAATGGAATCTTTGGACA-TCCGAGGGTAAAATAATAATTTTTGGAAATTTTCGGGGTTA
1 AAAATGAAAT-TTTGGA-AGTTCGAGGGTAAAATAGTAATTTTTGGAAA-GTTCTGGGTCA
* * * * *
13439 AAAATAGAATTTTTGGACA-TCCGA-GGTAAAAT-GATAATTGTTGG-AAGTTTCAGGATC-
1 AAAAT-GAAATTTTGGA-AGTTCGAGGGTAAAATAG-TAATTTTTGGAAAG-TTCTGGGTCA
* * * * * *
13496 AAAATGAAATTTTTGGACA-TCCGTGGATAAAATGGCAA-TTTTGG-AAGTT-TCGAGTTCA
1 AAAATGAAA-TTTTGGA-AGTTCGAGGGTAAAATAGTAATTTTTGGAAAGTTCT-G-GGTCA
13554 AAAATGAAATTTTGGAATGTTCGAGGGTAAAA-ATGTAATTTTTGGAAAGTTCTGGGTCA
1 AAAATGAAATTTTGGAA-GTTCGAGGGTAAAATA-GTAATTTTTGGAAAGTTCTGGGTCA
* * * *
13613 AAAATGGAATTTTAGAAAGTTCGAGGGCAAAAT-GTAATTTTTGGAAAATT-TGGG--A
1 AAAATGAAATTTT-GGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAAGTTCTGGGTCA
* ** **
13668 AAAATGTAATTTTTGTGAAGTTCG-GGGTCAAAATAG-AATTTTTGGAAAAATCAAGGTCA
1 AAAATG-AAATTTTG-GAAGTTCGAGGGT-AAAATAGTAATTTTTGGAAAGTTCTGGGTCA
* * * * * * *
13727 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAAATA-TATTTTTTTGAAAAGTTCGGGGTTA
1 AAAATGAAATTTTGG-AAGTTCGAGGGT-AAAATAGTA-ATTTTTGGAAAGTTCTGGGTCA
13787 AAATATGA
1 AAA-ATGA
13795 TTTCTGGACA
Statistics
Matches: 330, Mismatches: 53, Indels: 64
0.74 0.12 0.14
Matches are distributed among these distances:
55 11 0.03
56 38 0.12
57 44 0.13
58 90 0.27
59 87 0.26
60 53 0.16
61 7 0.02
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (58 bp):
AAAATGAAATTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAAGTTCTGGGTCA
Found at i:13729 original size:85 final size:87
Alignment explanation
Indices: 13552--13791 Score: 240
Period size: 85 Copynumber: 2.8 Consensus size: 87
13542 GTTTCGAGTT
* ** * *
13552 CAAAAATGAAATTTTGGAATGTTCGAGGGTAAAAATGTAATTTTTG-GAAAGTTCTGGGTCAAAA
1 CAAAAATGGAATTTTGGAAAATTTG-GGGTAAAAATGTAATTTTTGTGAAAGTTCGGGGTC-AAA
* ** *
13616 ATGGAATTTTAGAAAGTTCGAGGG
64 ATAGAATTTTAGAAAAATCAAGGG
*
13640 C-AAAATGTAATTTTTGGAAAATTT-GGG-AAAAATGTAATTTTTGTG-AAGTTCGGGGTCAAAA
1 CAAAAATGGAA-TTTTGGAAAATTTGGGGTAAAAATGTAATTTTTGTGAAAGTTCGGGGTCAAAA
* *
13701 TAGAATTTTTGGAAAAATCAAGGT
65 TAGAA-TTTTAGAAAAATCAAGGG
* * * *
13725 CAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAATAT-ATTTTTTTGAAAAGTTCGGGGTTAAA
1 CAAAAATGGAATTTTGGAAAATTT-GGGGTAAAAATGTAATTTTTGTG-AAAGTTCGGGGTCAAA
13789 ATA
64 ATA
13792 TGATTTCTGG
Statistics
Matches: 127, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
84 8 0.06
85 53 0.42
86 12 0.09
87 19 0.15
88 18 0.14
89 17 0.13
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (87 bp):
CAAAAATGGAATTTTGGAAAATTTGGGGTAAAAATGTAATTTTTGTGAAAGTTCGGGGTCAAAAT
AGAATTTTAGAAAAATCAAGGG
Found at i:13758 original size:29 final size:30
Alignment explanation
Indices: 13344--13760 Score: 133
Period size: 29 Copynumber: 14.4 Consensus size: 30
13334 GGACTCTTCA
* *
13344 AGGG-AAAAATAGTAATTTTT-GAAGGTTT-
1 AGGGTAAAAAT-GGAATTTTTGGAAAGTTTC
* * *
13372 AGGGTTAAAAATGGAATCTTTGGACA--TCC
1 AGGG-TAAAAATGGAATTTTTGGAAAGTTTC
*
13401 GAGGGTAAAATAAT--AATTTTTGGAAATTTTC
1 -AGGGT-AAA-AATGGAATTTTTGGAAAGTTTC
* * *
13432 GGGGTTAAAAATAGAATTTTTGGACA---TC
1 AGGG-TAAAAATGGAATTTTTGGAAAGTTTC
* * *
13460 CGAGGT-AAAATGATAATTGTTGG-AAGTTTC
1 AG-GGTAAAAATG-GAATTTTTGGAAAGTTTC
* * * *
13490 AGGATCAAAATGAAATTTTTGGACA---TC
1 AGGGTAAAAATGGAATTTTTGGAAAGTTTC
*
13517 CGTGG-ATAAAATGGCAA-TTTTGG-AAGTTTC
1 AG-GGTA-AAAATGG-AATTTTTGGAAAGTTTC
* * *
13547 -GAGTTCAAAAAT-GAAATTTTGGAATG-TTC
1 AG-GGT-AAAAATGGAATTTTTGGAAAGTTTC
*
13576 GAGGGTAAAAATGTAATTTTTGGAAAG-TTC
1 -AGGGTAAAAATGGAATTTTTGGAAAGTTTC
* *
13606 TGGGTCAAAAATGGAA-TTTTAGAAAG-TTC
1 AGGGT-AAAAATGGAATTTTTGGAAAGTTTC
* * *
13635 GAGGG-CAAAATGTAATTTTTGGAAAATTT-
1 -AGGGTAAAAATGGAATTTTTGGAAAGTTTC
*
13664 -GGG-AAAAATGTAATTTTTGTG-AAG-TTC
1 AGGGTAAAAATGGAATTTTTG-GAAAGTTTC
* * * **
13691 GGGGTCAAAATAGAATTTTTGGAAA-AATC
1 AGGGTAAAAATGGAATTTTTGGAAAGTTTC
* *
13720 AAGGTCAAAAATGGAA-TTTTGGAAAGTTTG
1 AGGGT-AAAAATGGAATTTTTGGAAAGTTTC
*
13750 GGGGTAAAAAT
1 AGGGTAAAAAT
13761 ATATTTTTTT
Statistics
Matches: 290, Mismatches: 55, Indels: 87
0.67 0.13 0.20
Matches are distributed among these distances:
26 2 0.01
27 30 0.10
28 45 0.16
29 112 0.39
30 82 0.28
31 19 0.07
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (30 bp):
AGGGTAAAAATGGAATTTTTGGAAAGTTTC
Found at i:13767 original size:114 final size:114
Alignment explanation
Indices: 13553--13775 Score: 272
Period size: 114 Copynumber: 1.9 Consensus size: 114
13543 TTTCGAGTTC
** **
13553 AAAAATGAAATTTTGGAATGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTCTGGGTCAAAAAT
1 AAAAATGAAATTTTGGAATGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAAT
* *
13618 GGAATTTTAGAAAGTTCGAGGGCAAAATGTAATTTTTGGAAAATTTGGG
66 GGAATTTTAGAAAGTTCGAGGGAAAAATATAATTTTTGGAAAATTTGGG
* *
13667 AAAAATGTAATTTTTGTGAA-GTTCG-GGGTCAAAATAG-AATTTTTGGAAAAATCAAGGTCAAA
1 AAAAATG-AAATTTTG-GAATGTTCGAGGGTAAAAAT-GTAATTTTTGGAAAAATCAAGGTCAAA
* * * * *
13729 AATGGAATTTTGGAAAGTTTGGGGGTAAAAATATATTTTTTTGAAAA
63 AATGGAATTTTAGAAAGTTCGAGGG-AAAAATATAATTTTTGGAAAA
13776 GTTCGGGGTT
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
114 59 0.64
115 30 0.33
116 3 0.03
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (114 bp):
AAAAATGAAATTTTGGAATGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAAT
GGAATTTTAGAAAGTTCGAGGGAAAAATATAATTTTTGGAAAATTTGGG
Found at i:13790 original size:30 final size:32
Alignment explanation
Indices: 13736--13797 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
13726 AAAAATGGAA
* *
13736 TTTTGGAAAGTTTGGGGGTAAAAATAT-ATTT
1 TTTTGAAAAGTTTCGGGGTAAAAATATGATTT
*
13767 TTTTGAAAAG-TTCGGGGTTAAAATATGATTT
1 TTTTGAAAAGTTTCGGGGTAAAAATATGATTT
13798 CTGGACAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.42
Consensus pattern (32 bp):
TTTTGAAAAGTTTCGGGGTAAAAATATGATTT
Found at i:14940 original size:22 final size:20
Alignment explanation
Indices: 14907--14957 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
14897 CTTTTTATTA
*
14907 TTATTATTATTAACATTCAT
1 TTATCATTATTAACATTCAT
**
14927 TCATATCATTATTATTATTCAT
1 T--TATCATTATTAACATTCAT
14949 TTATCATTA
1 TTATCATTA
14958 ATGTCGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.35
22 17 0.65
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATCATTATTAACATTCAT
Found at i:15628 original size:11 final size:11
Alignment explanation
Indices: 15612--15650 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15602 ACTTTCAAAG
15612 TTTAAATTTAA
1 TTTAAATTTAA
* *
15623 TTTAAAATAAA
1 TTTAAATTTAA
15634 TTTAAATTTAA
1 TTTAAATTTAA
*
15645 ATTAAA
1 TTTAAA
15651 CCCAAACTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:15643 original size:17 final size:17
Alignment explanation
Indices: 15614--15712 Score: 85
Period size: 17 Copynumber: 5.9 Consensus size: 17
15604 TTTCAAAGTT
15614 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
*
15630 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAA
*** * *
15647 TAAACCCAAACTCAAAA
1 TAAATTTAAATTTAAAA
* * *
15664 TAAGTTTAGATTTAAAG
1 TAAATTTAAATTTAAAA
*
15681 TAAATTCAAATTT-AAA
1 TAAATTTAAATTTAAAA
*
15697 TAAATTTAGATTTAAA
1 TAAATTTAAATTTAAA
15713 TTTTAAAAAT
Statistics
Matches: 60, Mismatches: 21, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
16 20 0.33
17 40 0.67
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:15649 original size:5 final size:6
Alignment explanation
Indices: 15612--15715 Score: 51
Period size: 6 Copynumber: 18.5 Consensus size: 6
15602 ACTTTCAAAG
* ***
15612 TTTAAA TTT-AA TTTAAA -ATAAA TTTAAA TTTAAA -TTAAA CCCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * * *
15657 CTCAAA -ATAAG TTTAGA TTTAAA -GTAAA TTCAAA TTTAAA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
15701 TTTAGA TTTAAA TTT
1 TTTAAA TTTAAA TTT
15716 TAAAAATGGG
Statistics
Matches: 73, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
4 4 0.05
5 20 0.27
6 49 0.67
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:15664 original size:34 final size:33
Alignment explanation
Indices: 15626--15714 Score: 106
Period size: 34 Copynumber: 2.7 Consensus size: 33
15616 AATTTAATTT
*
15626 AAAATAAATTTAAATTTAAATTAAACCCAAACTC
1 AAAATAAATTTAGATTTAAATTAAACCCAAA-TC
* * ** *
15660 AAAATAAGTTTAGATTTAAAGTAAATTCAAATT
1 AAAATAAATTTAGATTTAAATTAAACCCAAATC
*
15693 TAAATAAATTTAGATTTAAATT
1 AAAATAAATTTAGATTTAAATT
15715 TTAAAAATGG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 20 0.43
34 26 0.57
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (33 bp):
AAAATAAATTTAGATTTAAATTAAACCCAAATC
Found at i:15713 original size:16 final size:16
Alignment explanation
Indices: 15661--15713 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
15651 CCCAAACTCA
*
15661 AAATAAGTTTAGATTT
1 AAATAAATTTAGATTT
* *
15677 AAAGTAAATTCAAATTT
1 AAA-TAAATTTAGATTT
15694 AAATAAATTTAGATTT
1 AAATAAATTTAGATTT
15710 AAAT
1 AAAT
15714 TTTAAAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 18 0.58
17 13 0.42
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (16 bp):
AAATAAATTTAGATTT
Found at i:16878 original size:16 final size:16
Alignment explanation
Indices: 16840--16884 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
16830 CTTGTCGAAC
* *
16840 CTAAATTTAAATTGAT
1 CTAAATTTAAAATAAT
* *
16856 TTGAATTTAAAATAAT
1 CTAAATTTAAAATAAT
16872 CTAAATTTAAAAT
1 CTAAATTTAAAAT
16885 GATCAAACAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (16 bp):
CTAAATTTAAAATAAT
Done.