Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012618.1 Kokia drynarioides strain JFW-HI SEQ_127627, 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: 97296
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:4138 original size:17 final size:17
Alignment explanation
Indices: 4116--4149 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4106 CTAAGAATTT
4116 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
4133 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
4150 GTATTAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:4815 original size:43 final size:43
Alignment explanation
Indices: 4645--4815 Score: 191
Period size: 43 Copynumber: 4.0 Consensus size: 43
4635 GAAAAATACC
* * * * * *
4645 GCTATAGAACATGGTCTTTAGCGGCGCTTTTTGCACAAACACC
1 GCTAAAGACCATGGTCTTTAGCGGCACTTTTCGCACAAACGCT
* * * * *
4688 CCTAAA-AGCCATGGTCTTAAGCGGCGCTTTTTGCACAAACGAT
1 GCTAAAGA-CCATGGTCTTTAGCGGCACTTTTCGCACAAACGCT
* *
4731 GCTAAAGACCATGGTCTTTAGCGGCACTTATCTCACAAACGCT
1 GCTAAAGACCATGGTCTTTAGCGGCACTTTTCGCACAAACGCT
* *
4774 GCTAAAGATCATGGTCTTTAGCGGCACTTTTCCCACAAACGC
1 GCTAAAGACCATGGTCTTTAGCGGCACTTTTCGCACAAACGC
4816 CACTAACATT
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.01
43 107 0.98
44 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (43 bp):
GCTAAAGACCATGGTCTTTAGCGGCACTTTTCGCACAAACGCT
Found at i:9064 original size:28 final size:28
Alignment explanation
Indices: 9033--9094 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
9023 AAAATGAGAT
* * *
9033 TTTTGGATACCCGGGGGCAAAATGGTAA
1 TTTTGGACACCCGAGGGAAAAATGGTAA
*
9061 TTTTGGACACTCGAGGGAAAAATGGTAA
1 TTTTGGACACCCGAGGGAAAAATGGTAA
9089 TTTTGG
1 TTTTGG
9095 GAAGGTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (28 bp):
TTTTGGACACCCGAGGGAAAAATGGTAA
Found at i:9170 original size:29 final size:28
Alignment explanation
Indices: 9138--9327 Score: 89
Period size: 29 Copynumber: 6.5 Consensus size: 28
9128 ATTTGGGGAT
9138 AAAATGGTAATTTTGGAGAAATTGAAGTAA
1 AAAAT-GTAATTTTGGAGAAATTGAAGT-A
** **
9168 AAAATAG-AATTTTGGAGAGTTTAGGGGTA
1 AAAAT-GTAATTTTGGAGAAATT-GAAGTA
* * * * **
9197 AAAAAGTAATTTGTGTAAAAATCGGGGTTA
1 AAAATGTAATTT-TGGAGAAATTGAAG-TA
* ** *
9227 AAAATGGAATTTTGGAGAGTTTAAGAGTA
1 AAAATGTAATTTTGGAGAAATTGA-AGTA
*
9256 AAAATGTAATTTTTGGA-AAATTCGATGTAA
1 AAAATGTAA-TTTTGGAGAAATT-GAAGT-A
* * *
9286 AAAATGAAATTTTGGA-AAGTTTAAGGGTA
1 AAAATGTAATTTTGGAGAAATTGAA--GTA
9315 AAAATGTAATTTT
1 AAAATGTAATTTT
9328 TTTAAAATAA
Statistics
Matches: 119, Mismatches: 31, Indels: 21
0.70 0.18 0.12
Matches are distributed among these distances:
28 2 0.02
29 71 0.60
30 46 0.39
ACGTcount: A:0.43, C:0.01, G:0.23, T:0.33
Consensus pattern (28 bp):
AAAATGTAATTTTGGAGAAATTGAAGTA
Found at i:9272 original size:30 final size:29
Alignment explanation
Indices: 9225--9328 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
9215 AAATCGGGGT
*
9225 TAAAAATGGAA-TTTTGGAGAGTTTAAGAG
1 TAAAAATGTAATTTTTGGA-AGTTTAAGAG
** *
9254 TAAAAATGTAATTTTTGGAAAATT-CGATG
1 TAAAAATGTAATTTTTGGAAGTTTAAGA-G
* *
9283 TAAAAAATG-AAATTTTGGAAAGTTTAAGGG
1 T-AAAAATGTAATTTTTGG-AAGTTTAAGAG
9313 TAAAAATGTAATTTTT
1 TAAAAATGTAATTTTT
9329 TTAAAATAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
28 2 0.03
29 30 0.51
30 26 0.44
31 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.20, T:0.36
Consensus pattern (29 bp):
TAAAAATGTAATTTTTGGAAGTTTAAGAG
Found at i:9314 original size:118 final size:116
Alignment explanation
Indices: 9138--9384 Score: 302
Period size: 118 Copynumber: 2.1 Consensus size: 116
9128 ATTTGGGGAT
* *
9138 AAAATGGTAA-TTTTGGAGAAATTGAAGTAAAAAATAGAATTTTGGAGAGTTTAGGGGTAAAAAA
1 AAAAT-GTAATTTTTGGAGAAATTGAAGTAAAAAATAGAATTTTGGAAAGTTTAAGGGTAAAAAA
** * * *
9202 GTAATTTGTGTAAAAATCGGGGTTAAAAATGGAATTTTGGAGAGTTTAAGAGTA
65 GTAATTT-TGTAAAAAT-AAGGTCAAAAATGGAATTTTAGAAAGTTTAAGAGTA
*
9256 AAAATGTAATTTTTGGA-AAATTCGATGTAAAAAAT-GAAATTTTGGAAAGTTTAAGGGTAAAAA
1 AAAATGTAATTTTTGGAGAAATT-GAAGTAAAAAATAG-AATTTTGGAAAGTTTAAGGGTAAAAA
* * * * *
9319 TGTAATTTTTTTAAAATAAGGTCAAAAATGGAATTTTAGAAAGTTTTAGGGTA
64 AGTAATTTTGTAAAAATAAGGTCAAAAATGGAATTTTAGAAAGTTTAAGAGTA
*
9372 AAAAAGTAATTTT
1 AAAATGTAATTTT
9385 AAAAAATTTA
Statistics
Matches: 112, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
116 41 0.37
117 17 0.15
118 54 0.48
ACGTcount: A:0.44, C:0.01, G:0.22, T:0.33
Consensus pattern (116 bp):
AAAATGTAATTTTTGGAGAAATTGAAGTAAAAAATAGAATTTTGGAAAGTTTAAGGGTAAAAAAG
TAATTTTGTAAAAATAAGGTCAAAAATGGAATTTTAGAAAGTTTAAGAGTA
Found at i:9374 original size:28 final size:30
Alignment explanation
Indices: 9342--9417 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 30
9332 AAATAAGGTC
**
9342 AAAAATGGAATTTTAGAAAGTTTTAGGG-T
1 AAAAATGGAATTTTAGAAAAATTTAGGGTT
* *
9371 AAAAAAGTAATTTTA-AAAAATTTAGGGTT
1 AAAAATGGAATTTTAGAAAAATTTAGGGTT
*
9400 -AAAATGGAATTTTGGAAA
1 AAAAATGGAATTTTAGAAA
9418 TTCGAGGACC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (30 bp):
AAAAATGGAATTTTAGAAAAATTTAGGGTT
Found at i:9404 original size:57 final size:58
Alignment explanation
Indices: 9164--9417 Score: 253
Period size: 59 Copynumber: 4.4 Consensus size: 58
9154 AGAAATTGAA
* * * * **
9164 GTAAAAAATAGAATTTTGGAGAGTTTAGGGGTAAAAAAGTAATTTGTGTAAAAATCGGG
1 GTAAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAAAGTAATTT-TTTAAAAATTAGG
* * * * ** * *
9223 GTTAAAAATGGAATTTTGGAGAGTTTAAGAGTAAAAATGTAATTTTTGGAAAATTCGAT
1 GTAAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAAAGTAATTTTTTAAAAATTAG-G
* * * *
9282 GTAAAAAATGAAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTTTAAAA-TAAG
1 GTAAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAAAGTAATTTTTTAAAAATTAGG
* * * *
9339 GTCAAAAATGGAATTTTAGAAAGTTTTAGGGTAAAAAAGTAA-TTTTAAAAAATTTAGG
1 GTAAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAAAGTAATTTTTTAAAAA-TTAGG
*
9397 GT-TAAAATGGAATTTTGGAAA
1 GTAAAAAATGGAATTTTGGAAA
9418 TTCGAGGACC
Statistics
Matches: 162, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
56 8 0.05
57 54 0.33
58 13 0.08
59 87 0.54
ACGTcount: A:0.44, C:0.01, G:0.22, T:0.33
Consensus pattern (58 bp):
GTAAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAAAGTAATTTTTTAAAAATTAGG
Found at i:10414 original size:3 final size:3
Alignment explanation
Indices: 10402--10468 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
10392 TTTCAAATTC
* * *
10402 TAT T-T TAT TAT TAT TAT TAT TAT TAA AAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10449 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
10469 ATGCTATTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:11159 original size:17 final size:17
Alignment explanation
Indices: 11101--11180 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
11091 TAAATAAATT
* *
11101 TAAACTTAATATTTATAA
1 TAAATTTAA-ATTTAAAA
**
11119 TAAATTTAAATTCCAAA
1 TAAATTTAAATTTAAAA
** *
11136 TGGATTTAAATTTAATA
1 TAAATTTAAATTTAAAA
*
11153 TATATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
11170 TAAATTTAAAT
1 TAAATTTAAAT
11181 CTGTTGGGCC
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
17 41 0.84
18 8 0.16
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:11730 original size:49 final size:49
Alignment explanation
Indices: 11668--12352 Score: 260
Period size: 49 Copynumber: 14.0 Consensus size: 49
11658 TTCCCCTTGT
* *
11668 GTCTTCGTGGTACTAGATTTGCCGTTGCGGCTTAAATCTTTCCTTTTATC
1 GTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCA-C
* * * *
11718 -TCTTGGTTGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCAC
1 GTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAC
* * *
11766 GTCTTCGTGGTACTAGATTCACCGTTGCAGCTTAAATCTTTCACTTT-AT
1 GTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTC-CTTTCAC
* * * * **
11815 G-CTTC-TGACGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTT-GT
1 GTCTTCGTG--GTACTAGATTCGCCGTTGCGGCTTAAATCTTT-CCTTTCAC
* * * * * * * * *
11864 GTCTTGGCGGTATTGGATTCACCGTTACAGG-TTAAGTCTTTCCCTTCAT
1 GTCTTCGTGGTACTAGATTCGCCGTTGC-GGCTTAAATCTTTCCTTTCAC
* * ** *
11913 GTCTTTGTGGTACTAGATTCACCGTTATGGCTTAAATCTTTCCCTTT-AT
1 GTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTT-CCTTTCAC
* * * * * *
11962 G-CTTCTGAGGTA-TAAGGTTCGCCGTTGCGACTTAAACCTTT-CTCCTCAT
1 GTCTTC-GTGGTACT-AGATTCGCCGTTGCGGCTTAAATCTTTCCT-TTCAC
* * * * * *
12011 GTCTTTGCGGTACTGGATTCGTCGTTGCAGCTTAAATCTTTCCCTTT-AT
1 GTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTT-CCTTTCAC
* * * ** * *
12060 GTC-TCTGAGGTACTAGGTTCGCCATTGCAACTTAAACCTTTCCCTTT-AT
1 GTCTTC-GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTT-CCTTTCAC
* * * * * *
12109 G-CTTCTGAGGTA-TAAGGTTCACCGTTGCGACTTAAACCTTTTTGCTTGT---
1 GTCTTC-GTGGTACT-AGATTCGCCGTTGCGGCTTAAA--TCTTTCCTT-TCAC
* * * * * *
12158 GTCTTTGTGGTACTGGATTCGCCGTTGCAGATTAAATCTTTCCCTTCAT
1 GTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAC
* * * ** * * * * *
12207 GTC-TCTGAGGTACTAGGTTTGCCACTGTGACTTAAACCTTTCCTTTTAT
1 GTCTTC-GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAC
* * * * * * * *
12256 G-CTTCTGAGGTACGCAG-TTCGTCGTTGCGACTTAAACCTTTCCCTCCAT
1 GTCTTC-GTGGTAC-TAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAC
* * * * * * * *
12305 ATCTTCATGGTACTGGATTCACCGTTACGACTTAGATCTTTCCCTTCA
1 GTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCA
12353 TGCTTCGAAG
Statistics
Matches: 483, Mismatches: 117, Indels: 71
0.72 0.17 0.11
Matches are distributed among these distances:
46 1 0.00
47 10 0.02
48 22 0.05
49 413 0.86
50 30 0.06
51 7 0.01
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.39
Consensus pattern (49 bp):
GTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCAC
Found at i:11760 original size:98 final size:98
Alignment explanation
Indices: 11643--12348 Score: 391
Period size: 98 Copynumber: 7.2 Consensus size: 98
11633 AGGTTCGCTA
* * * *
11643 TTGCGACTTAAACCCTTCCCCTTGTGTCTTCGTGGTACTAGATTTGCCGTTGCGGCTTAAATCTT
1 TTGCGACTTAAACCTTTCCCCTTATGTCTTCGTGGTACTAGATTCGCCGTTGCAGCTTAAATCTT
* * *
11708 TCCTTTTATCTCTTGGTTGTACTAGATTCGTCG
66 TCCCTTTATCTCTTGGTGGTACTAGATTCGCCG
* * * *
11741 TTGCGGCTTAAATCTTT-CCCTTCACGTCTTCGTGGTACTAGATTCACCGTTGCAGCTTAAATCT
1 TTGCGACTTAAACCTTTCCCCTT-ATGTCTTCGTGGTACTAGATTCGCCGTTGCAGCTTAAATCT
* ** * *
11805 TTCACTTTATGCT-TCT-GACGTACTAGGTTCGCCA
65 TTCCCTTTAT-CTCT-TGGTGGTACTAGATTCGCCG
* * * * * * * * * *
11839 TTGCGACTTAAACCTTTCCCTTTGTGTCTTGGCGGTATTGGATTCACCGTTACAGGTTAAGTCTT
1 TTGCGACTTAAACCTTTCCCCTTATGTCTTCGTGGTACTAGATTCGCCGTTGCAGCTTAAATCTT
* * * *
11904 TCCCTTCATGTCTTTGTGGTACTAGATTCACCG
66 TCCCTTTATCTCTTGGTGGTACTAGATTCGCCG
** * * * * * *
11937 TTATGGCTTAAATCTTTCCCTTTATG-CTTCTGAGGTA-TAAGGTTCGCCGTTGC-GACTTAAAC
1 TTGCGACTTAAACCTTTCCCCTTATGTCTTC-GTGGTACT-AGATTCGCCGTTGCAG-CTTAAAT
* * * * * *
11999 CTTTCTCC-TCATGTCTTTGCGGTACTGGATTCGTCG
63 CTTTC-CCTTTATCTCTTGGTGGTACTAGATTCGCCG
* * * * * * *
12035 TTGC-AGCTTAAATCTTTCCCTTTATGTC-TCTGAGGTACTAGGTTCGCCATTGCAACTTAAACC
1 TTGCGA-CTTAAACCTTTCCCCTTATGTCTTC-GTGGTACTAGATTCGCCGTTGCAGCTTAAATC
* * *
12098 TTTCCCTTTATGCT-TCT-GAGGTA-TAAGGTTCACCG
64 TTTCCCTTTAT-CTCT-TGGTGGTACT-AGATTCGCCG
*** * * * *
12133 TTGCGACTTAAACCTTTTTGCTTGTGTCTTTGTGGTACTGGATTCGCCGTTGCAGATTAAATCTT
1 TTGCGACTTAAACCTTTCCCCTTATGTCTTCGTGGTACTAGATTCGCCGTTGCAGCTTAAATCTT
* * * * * *
12198 TCCCTTCATGTCTCT-GAGGTACTAGGTTTGCCA
66 TCCCTTTATCTCT-TGGTGGTACTAGATTCGCCG
* * ** * * * *
12231 CTGTGACTTAAACCTTTCCTTTTATG-CTTCTGAGGTACGCAG-TTCGTCGTTGC-GACTTAAAC
1 TTGCGACTTAAACCTTTCCCCTTATGTCTTC-GTGGTAC-TAGATTCGCCGTTGCAG-CTTAAAT
** * ** * *
12293 CTTTCCCTCCATATCTTCATGGTACTGGATTCACCG
63 CTTTCCCTTTATCTCTTGGTGGTACTAGATTCGCCG
* * *
12329 TTACGACTTAGATCTTTCCC
1 TTGCGACTTAAACCTTTCCC
12349 TTCATGCTTC
Statistics
Matches: 469, Mismatches: 113, Indels: 52
0.74 0.18 0.08
Matches are distributed among these distances:
97 21 0.04
98 431 0.92
99 17 0.04
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (98 bp):
TTGCGACTTAAACCTTTCCCCTTATGTCTTCGTGGTACTAGATTCGCCGTTGCAGCTTAAATCTT
TCCCTTTATCTCTTGGTGGTACTAGATTCGCCG
Found at i:11856 original size:147 final size:147
Alignment explanation
Indices: 11649--12354 Score: 662
Period size: 147 Copynumber: 4.8 Consensus size: 147
11639 GCTATTGCGA
* * * * * * * *
11649 CTTAAACCCTTCCCCTTGTGTCTTC-GTGGTACTAGATTTGCCGTTGCGGCTTAAATCTTTCCTT
1 CTTAAACCTTTCCCTTTATG-CTTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCCTT
* ** * * * * *
11713 TTATCTCTTGGTTGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCACGTCT-TCGTGGT
65 TTATGTCTTGGCGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCT-GAGGT
11777 ACTAGATTCACCGTTGCAG
129 ACTAGATTCACCGTTGCAG
* * * * *
11796 CTTAAATCTTTCACTTTATGCTTCTGACGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAACCTTTCCCTTTATGCTTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCCTTT
* * * * * * * *
11861 TGTGTCTTGGCGGTATTGGATTCACCGTTACAGGTTAAGTCTTTCCCTTCATGTCTTTGTGGTAC
66 TATGTCTTGGCGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAC
***
11926 TAGATTCACCGTTATGG
131 TAGATTCACCGTTGCAG
*
11943 CTTAAATCTTTCCCTTTATGCTTCTGAGGTA-TAAGGTTCGCCGTTGCGACTTAAACCTTT-CTC
1 CTTAAACCTTTCCCTTTATGCTTCTGAGGTACT-AGGTTCGCCGTTGCGACTTAAACCTTTCCT-
* * * * *
12006 CTCATGTCTTTGCGGTACTGGATTCGTCGTTGCAGCTTAAATCTTTCCCTTTATGTCTCTGAGGT
64 TTTATGTCTTGGCGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGT
* * * *
12071 ACTAGGTTCGCCATTGCAA
129 ACTAGATTCACCGTTGCAG
*
12090 CTTAAACCTTTCCCTTTATGCTTCTGAGGTA-TAAGGTTCACCGTTGCGACTTAAACCTTT--TT
1 CTTAAACCTTTCCCTTTATGCTTCTGAGGTACT-AGGTTCGCCGTTGCGACTTAAACCTTTCCTT
* * * *
12152 GCTTGTGTCTTTGTGGTACTGGATTCGCCGTTGCAGATTAAATCTTTCCCTTCATGTCTCTGAGG
65 --TTATGTCTTGGCGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGG
* *
12217 TACTAGGTTTGCCACTG-TG-A-
128 TACTA-GATT--CACCGTTGCAG
* * * *
12237 CTTAAACCTTTCCTTTTATGCTTCTGAGGTACGCA-GTTCGTCGTTGCGACTTAAACCTTTCCCT
1 CTTAAACCTTTCCCTTTATGCTTCTGAGGTAC-TAGGTTCGCCGTTGCGACTTAAACCTTTCCTT
** * *** * * *
12301 CCATATCTTCATGGTACTGGATTCACCGTTAC-GACTTAGATCTTTCCCTTCATG
65 TTATGTCTTGGCGGTACTGGATTCGCCGTTGCAG-CTTAAATCTTTCCCTTCATG
12355 CTTCGAAGTA
Statistics
Matches: 464, Mismatches: 81, Indels: 28
0.81 0.14 0.05
Matches are distributed among these distances:
146 8 0.02
147 445 0.96
148 6 0.01
149 3 0.01
150 2 0.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (147 bp):
CTTAAACCTTTCCCTTTATGCTTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCCTTT
TATGTCTTGGCGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAC
TAGATTCACCGTTGCAG
Found at i:21835 original size:28 final size:28
Alignment explanation
Indices: 21804--21863 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
21794 AAAATGAGAT
* *
21804 TTTTGGATACGAGGGGGTAAAATGGTAA
1 TTTTGGACACGAGGGGGCAAAATGGTAA
**
21832 TTTTGGACACTCGGGGGCAAAATGGTAA
1 TTTTGGACACGAGGGGGCAAAATGGTAA
21860 TTTT
1 TTTT
21864 TTGAAAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (28 bp):
TTTTGGACACGAGGGGGCAAAATGGTAA
Found at i:21969 original size:29 final size:28
Alignment explanation
Indices: 21938--22037 Score: 71
Period size: 28 Copynumber: 3.5 Consensus size: 28
21928 ATTAGAGTCA
21938 AAAATGGAATTTTAGGAAGTTCGAAGGT
1 AAAATGGAATTTTAGGAAGTTCGAAGGT
* ** * *
21966 AAAATAGTAACTTTTGAAAAAATT--TAGGTT
1 AAAAT-GGAA-TTTT-AGGAAGTTCGAAGG-T
21996 AAAAATGGAATTTT-GGAAAGTTCGAAGGT
1 -AAAATGGAATTTTAGG-AAGTTCGAAGGT
*
22025 AAAATGGTATTTT
1 AAAATGGAATTTT
22038 TTGGAAAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
28 21 0.40
29 11 0.21
30 11 0.21
31 10 0.19
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTAGGAAGTTCGAAGGT
Found at i:22004 original size:59 final size:59
Alignment explanation
Indices: 21906--22101 Score: 217
Period size: 59 Copynumber: 3.4 Consensus size: 59
21896 GACATCCAGG
* *
21906 GGTAAAATGGTAA--TTTGGAAAAA-TTAGAGTCAAAAATGGAATTTTAGGAAGTTCGAA
1 GGTAAAATGGTAATTTTTGAAAAAATTTAG-GTTAAAAATGGAATTTTAGGAAGTTCGAA
* *
21963 GGTAAAATAGTAACTTTTGAAAAAATTTAGGTTAAAAATGGAATTTT-GGAAAGTTCGAA
1 GGTAAAATGGTAATTTTTGAAAAAATTTAGGTTAAAAATGGAATTTTAGG-AAGTTCGAA
* * ** * * *
22022 GGTAAAATGGTATTTTTTGGAAAAATTGGGGTT-AAAATGGAATTTTAGAAAGTGC-AGG
1 GGTAAAATGGTAATTTTTGAAAAAATTTAGGTTAAAAATGGAATTTTAGGAAGTTCGA-A
22080 GGTAAAAT-GTAATTTTTGAAAA
1 GGTAAAATGGTAATTTTTGAAAA
22102 GTTCGGGGTC
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
57 25 0.21
58 28 0.24
59 62 0.52
60 4 0.03
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.32
Consensus pattern (59 bp):
GGTAAAATGGTAATTTTTGAAAAAATTTAGGTTAAAAATGGAATTTTAGGAAGTTCGAA
Found at i:22082 original size:29 final size:28
Alignment explanation
Indices: 22049--22129 Score: 101
Period size: 29 Copynumber: 2.9 Consensus size: 28
22039 TGGAAAAATT
22049 GGGGTTAAAATGGAATTTTAGAAAGTGC
1 GGGGTTAAAATGGAATTTTAGAAAGTGC
* * *
22077 AGGGG-TAAAATGTAATTTTTGAAAAGTTC
1 -GGGGTTAAAATGGAATTTTAG-AAAGTGC
*
22106 GGGGTCAAAATGGAATTTTAGAAA
1 GGGGTTAAAATGGAATTTTAGAAA
22130 TTCGAGGACC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 21 0.48
29 23 0.52
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (28 bp):
GGGGTTAAAATGGAATTTTAGAAAGTGC
Found at i:23866 original size:17 final size:17
Alignment explanation
Indices: 23794--23870 Score: 52
Period size: 17 Copynumber: 4.5 Consensus size: 17
23784 TTTGGACATT
* *
23794 AATTTAAA-TAAATTTA
1 AATTTAAATTTAATATA
*
23810 AACTTAATATTT-ATAGTA
1 AATTTAA-ATTTAATA-TA
* *
23828 AATTTAAATTCCAA-ATG
1 AATTTAAATT-TAATATA
*
23845 GATTTAAATTTAATATA
1 AATTTAAATTTAATATA
23862 AATTTAAAT
1 AATTTAAAT
23871 ATGTTGGGCC
Statistics
Matches: 45, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
16 8 0.18
17 26 0.58
18 10 0.22
19 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAATATA
Found at i:27092 original size:41 final size:41
Alignment explanation
Indices: 27047--27257 Score: 298
Period size: 41 Copynumber: 5.2 Consensus size: 41
27037 TTTAAATAAA
* * * *
27047 TTAGCAGCACTTTCCCATAAGCACCGCTATTGCTTTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
*
27088 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACTT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * *
27129 TTAGCGGCACTTGCCCATAAGTGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* *
27170 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGTTCTGACTT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* *
27211 TTAGCGGCGCTTTCCCTTAAGCGCCGCTATTACTCT-ACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
*
27251 TTTGCGG
1 TTAGCGG
27258 TGTTTATATA
Statistics
Matches: 151, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 9 0.06
41 142 0.94
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
Found at i:27884 original size:23 final size:23
Alignment explanation
Indices: 27830--27887 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
27820 CGTTCATCCT
* * *
27830 TGCTGACTAGACCTTTTAGAAGT
1 TGCTGACTGGACCTTCTAGAAGC
27853 TGCTGACTGGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
27876 TGCTGACTGGAC
1 TGCTGACTGGAC
27888 GCCACGTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
TGCTGACTGGACCTTCTAGAAGC
Found at i:28162 original size:17 final size:17
Alignment explanation
Indices: 28142--28186 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
28132 AGCGCATAAT
*
28142 TAAAATATAATTAAAAA
1 TAAAATATAAATAAAAA
*
28159 TAAAATA-AAATAAAAC
1 TAAAATATAAATAAAAA
28175 TAAAA-ATAAATA
1 TAAAATATAAATA
28187 TACTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 17 0.68
17 7 0.28
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAATATAAATAAAAA
Found at i:28167 original size:22 final size:22
Alignment explanation
Indices: 28142--28184 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28132 AGCGCATAAT
* *
28142 TAAAATATAATTAAAAATAAAA
1 TAAAATAAAACTAAAAATAAAA
28164 TAAAATAAAACTAAAAATAAA
1 TAAAATAAAACTAAAAATAAA
28185 TATACTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
TAAAATAAAACTAAAAATAAAA
Found at i:28254 original size:11 final size:11
Alignment explanation
Indices: 28215--28253 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
28205 TTTTCAATTT
28215 TTTTTTTCAAAA
1 TTTTTTTC-AAA
28227 TTTTTTT-AAA
1 TTTTTTTCAAA
28237 TTTTTTTC-AA
1 TTTTTTTCAAA
28247 TTTTTTT
1 TTTTTTT
28254 TAAAAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 19 0.73
12 7 0.27
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:33496 original size:30 final size:29
Alignment explanation
Indices: 33414--33893 Score: 369
Period size: 30 Copynumber: 16.1 Consensus size: 29
33404 AAAAATTTTG
33414 TTTTAATCCCCGAACTTCCAAAAA-TCCAT
1 TTTTAA-CCCCGAACTTCCAAAAATTCCAT
* * *
33443 TCTTGACCACGACACTTCCAAAAATTCCAT
1 TTTTAACCCCGA-ACTTCCAAAAATTCCAT
* *
33473 TTTTAACCCCGAACTTCTAAAAAATCCAT
1 TTTTAACCCCGAACTTCCAAAAATTCCAT
* * *
33502 TTTTAACCCCAAAACTTCTAAATATTCCAT
1 TTTTAACCCC-GAACTTCCAAAAATTCCAT
* * *
33532 TTTTACCACCCGAACTTCCAAAAATGCTAT
1 TTTTAAC-CCCGAACTTCCAAAAATTCCAT
*
33562 TTTTAACCCCAAAACTTCCAAAAA-TCTCATT
1 TTTTAACCCC-GAACTTCCAAAAATTC-CA-T
* * *
33593 TTTTACCCCCAAACTTCTAAAAA-TCCTAT
1 TTTTAACCCCGAACTTCCAAAAATTCC-AT
*** *
33622 TTTTAACCTTAAAACTTCCAAAAATTCTAT
1 TTTTAACC-CCGAACTTCCAAAAATTCCAT
* * *
33652 TTTTACCCCCGGACTTCCAAAAATGCCAT
1 TTTTAACCCCGAACTTCCAAAAATTCCAT
** *
33681 TTTTAACCTCAAAACTTCCAAAAATTCTAT
1 TTTTAACC-CCGAACTTCCAAAAATTCCAT
* *
33711 TTTT-ACCCTCGAACTTCTAAAAATGCCAT
1 TTTTAACCC-CGAACTTCCAAAAATTCCAT
*
33740 TTTTAACCTCGAAACTTCCAAAAATTCCAT
1 TTTTAACCCCG-AACTTCCAAAAATTCCAT
* *
33770 TTTT-ACCCCTGAACATCCAAAAATGCCAT
1 TTTTAACCCC-GAACTTCCAAAAATTCCAT
* ** * *
33799 TTTTTACCCTAAAATTTCCAAAAATTTCATT
1 TTTTAACCC-CGAACTTCCAAAAATTCCA-T
** * *
33830 TTTTTCCCCCGAA-TGTCTAGAAATTCCAT
1 TTTTAACCCCGAACT-TCCAAAAATTCCAT
* * *
33859 TTTTAAACCTCGAATTTTCCCAAAATTACCAT
1 TTTT-AACCCCGAA-CTTCCAAAAATT-CCAT
33891 TTT
1 TTT
33894 GTCCCCAGGT
Statistics
Matches: 358, Mismatches: 70, Indels: 43
0.76 0.15 0.09
Matches are distributed among these distances:
28 6 0.02
29 129 0.36
30 184 0.51
31 31 0.09
32 8 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTTAACCCCGAACTTCCAAAAATTCCAT
Found at i:33496 original size:59 final size:59
Alignment explanation
Indices: 33414--33832 Score: 474
Period size: 59 Copynumber: 7.1 Consensus size: 59
33404 AAAAATTTTG
* * * * *
33414 TTTTAATCCCCGAACTTCCAAAAAT-CCATTCTTGACCACGACACTTCCAAAAATTCCAT
1 TTTTAA-CCCCGAACTTCCAAAAATGCCATTTTTAACCTCAAAACTTCCAAAAATTCCAT
* * * *
33473 TTTTAACCCCGAACTTCTAAAAAAT-CCATTTTTAACCCCAAAACTTCTAAATATTCCAT
1 TTTTAACCCCGAACTTC-CAAAAATGCCATTTTTAACCTCAAAACTTCCAAAAATTCCAT
* * *
33532 TTTTACCACCCGAACTTCCAAAAATGCTATTTTTAACCCCAAAACTTCCAAAAA-TCTCATT
1 TTTTAAC-CCCGAACTTCCAAAAATGCCATTTTTAACCTCAAAACTTCCAAAAATTC-CA-T
* * * * *
33593 TTTTACCCCCAAACTTCTAAAAAT-CCTATTTTTAACCTTAAAACTTCCAAAAATTCTAT
1 TTTTAACCCCGAACTTCCAAAAATGCC-ATTTTTAACCTCAAAACTTCCAAAAATTCCAT
* * *
33652 TTTTACCCCCGGACTTCCAAAAATGCCATTTTTAACCTCAAAACTTCCAAAAATTCTAT
1 TTTTAACCCCGAACTTCCAAAAATGCCATTTTTAACCTCAAAACTTCCAAAAATTCCAT
* *
33711 TTTT-ACCCTCGAACTTCTAAAAATGCCATTTTTAACCTCGAAACTTCCAAAAATTCCAT
1 TTTTAACCC-CGAACTTCCAAAAATGCCATTTTTAACCTCAAAACTTCCAAAAATTCCAT
* * * *
33770 TTTT-ACCCCTGAACATCCAAAAATGCCATTTTTTACC-CTAAAATTTCCAAAAATTTCAT
1 TTTTAACCCC-GAACTTCCAAAAATGCCATTTTTAACCTC-AAAACTTCCAAAAATTCCAT
33829 TTTT
1 TTTT
33833 TTCCCCCGAA
Statistics
Matches: 315, Mismatches: 34, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
58 16 0.05
59 210 0.67
60 79 0.25
61 10 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
TTTTAACCCCGAACTTCCAAAAATGCCATTTTTAACCTCAAAACTTCCAAAAATTCCAT
Found at i:33822 original size:89 final size:88
Alignment explanation
Indices: 33426--33864 Score: 395
Period size: 89 Copynumber: 4.9 Consensus size: 88
33416 TTAATCCCCG
* * *
33426 AACTTCCAAAAA-TCCATTCTTGACCAC-GACACTTCCAAAAATTCCATTTTTAACCCCGAACTT
1 AACTTCCAAAAATTCCATT-TTTACC-CTAAAACTTCCAAAAATTCCATTTTTAACCCCGAACTT
* *
33489 CTAAAAAATCCATTTTTAACCCCAA
64 CCAAAAATTCCATTTTTAACCCCAA
* * *** * * *
33514 AACTTCTAAATATTCCATTTTTACCACCCGAACTTCCAAAAATGCTATTTTTAACCCCAAAACTT
1 AACTTCCAAAAATTCCATTTTTACC-CTAAAACTTCCAAAAATTCCATTTTTAACCCC-GAACTT
* *
33579 CCAAAAA-TCTCATTTTTTACCCCCA
64 CCAAAAATTC-CATTTTTAACCCCAA
* * * * *
33604 AACTTCTAAAAA-TCCTATTTTTAACCTTAAAACTTCCAAAAATTCTATTTTTACCCCCGGACTT
1 AACTTCCAAAAATTCC-ATTTTT-ACCCTAAAACTTCCAAAAATTCCATTTTTAACCCCGAACTT
* *
33668 CCAAAAATGCCATTTTTAACCTCAA
64 CCAAAAATTCCATTTTTAACCCCAA
* ** * * *
33693 AACTTCCAAAAATTCTATTTTTACCCTCGAACTTCTAAAAATGCCATTTTTAACCTCGAAACTTC
1 AACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTTAACCCCG-AACTTC
**
33758 CAAAAATTCCATTTTT-ACCCCTG
65 CAAAAATTCCATTTTTAACCCCAA
* * * * **
33781 AACATCCAAAAATGCCATTTTTTACCCTAAAATTTCCAAAAATTTCATTTTTTTCCCCCGAA-TG
1 AACTTCCAAAAATTCCA-TTTTTACCCTAAAACTTCCAAAAATTCCA-TTTTTAACCCCGAACT-
* *
33845 TCTAGAAATTCCATTTTTAA
63 TCCAAAAATTCCATTTTTAA
33865 ACCTCGAATT
Statistics
Matches: 284, Mismatches: 54, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
88 64 0.23
89 137 0.48
90 80 0.28
91 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (88 bp):
AACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTTAACCCCGAACTTCC
AAAAATTCCATTTTTAACCCCAA
Found at i:55867 original size:204 final size:204
Alignment explanation
Indices: 55388--56134 Score: 885
Period size: 204 Copynumber: 3.7 Consensus size: 204
55378 AACGGCGTGA
* * *
55388 TCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCGACGCTCGATGTGAGCAAATCT
1 TCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCGCGA--TGAACAAATCT
* * * * * *
55453 TTGAATCCC-AACTTCCTGATGAGACACCGAGAAG-TAGATCAAAGCAATAAACGATTAACTTCC
64 TCGAA-CCCTAGCTTCCTGATGAGACACCGAGAAGCAAGATCGAAGCAATAAACGGTTAGCTTCC
* *
55516 TGAAGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAA
128 TGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAA
*
55581 CAAACGACGCGG
193 CAAACAACGCGG
* **
55593 CCATCTTCCTGATG-G-------GAAGAAGACCAAATCAAACCCACGCATGATGAACAAATCTTC
1 TCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCGCGATGAACAAATCTTC
* * ** * * *
55650 GAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAG-TCGAAGTAATAAAATGGTTAGCTTCCGG
66 GAACCCTAGCTTCCTGATGAGACACCGAGAAGCAAGATCGAAGCAAT-AAACGGTTAGCTTCCTG
* * * * * *
55714 ATGAGATACTGAGAAGTGAACTAAATTCGTCTTCTTGATGAAATACAGAGAAGTGGATTGAAACA
130 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACA
55779 AACAACGCGG
195 AACAACGCGG
* *
55789 TCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCGATGAACAAATCTTC
1 TCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCGCGATGAACAAATCTTC
* * * * *
55854 GAACCCTAGCTTCCTGATGAAATACTGAGAAGC-AGGTCGAAGCAATAAACGGTTAGCTTCTTGA
66 GAACCCTAGCTTCCTGATGAGACACCGAGAAGCAAGATCGAAGCAATAAACGGTTAGCTTCCTGA
*
55918 TAAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAA
131 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAA
* * *
55983 ATAAATGCGA
196 A-CAACGCGG
* * *
55993 TCATCTTCCTGATGAGGTACTAAGAAGAAGACCAAATCAAACTCACGCTTGACG-TGAGCAAATC
1 TCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGC--G-CGATGAACAAATC
* * * * *
56057 TTCGAA-TCTCAGCTTCCTTATAAGACACCGAGAAGC-AGTTCGAAGCAATAAACGGTTAGTTTC
63 TTCGAACCCT-AGCTTCCTGATGAGACACCGAGAAGCAAGATCGAAGCAATAAACGGTTAGCTTC
56120 CTGATGAGATACTGA
127 CTGATGAGATACTGA
56135 AAAGAAGGTC
Statistics
Matches: 463, Mismatches: 62, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
194 3 0.01
195 43 0.09
196 93 0.20
197 27 0.06
203 76 0.16
204 129 0.28
205 15 0.03
206 75 0.16
207 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (204 bp):
TCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCGCGATGAACAAATCTTC
GAACCCTAGCTTCCTGATGAGACACCGAGAAGCAAGATCGAAGCAATAAACGGTTAGCTTCCTGA
TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAA
ACAACGCGG
Found at i:56485 original size:23 final size:24
Alignment explanation
Indices: 56459--56510 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
56449 GCCCAACAGG
*
56459 ATTTAAATTAATTTTAAAA-TTAA
1 ATTTAAATTAAGTTTAAAATTTAA
**
56482 ATTTATTTTAAGTTTAAAATTTAA
1 ATTTAAATTAAGTTTAAAATTTAA
56506 ATTTA
1 ATTTA
56511 TTATAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTAAATTAAGTTTAAAATTTAA
Found at i:56498 original size:17 final size:17
Alignment explanation
Indices: 56459--56533 Score: 64
Period size: 17 Copynumber: 4.3 Consensus size: 17
56449 GCCCAACAGG
*
56459 ATTTAAATTAATTTTAA
1 ATTTAAATTTATTTTAA
*
56476 AATTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
56493 GTTTAAAATTTAAATTT--
1 ATTT-AAATTT-ATTTTAA
56510 ATTATAAATTTAATTTTAA
1 ATT-TAAATTT-ATTTTAA
56529 ATTTA
1 ATTTA
56534 TTTAAATCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
17 30 0.65
18 9 0.20
19 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:56507 original size:6 final size:6
Alignment explanation
Indices: 56459--56533 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
56449 GCCCAACAGG
* * * *
56459 ATTTAA A-TTAA TTTTAA AATTAA ATTT-A TTTTAA GTTTAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
56506 ATTT-- ATTATAA ATTTAA TTTTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTAA ATTTA
56534 TTTAAATCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
4 3 0.06
5 9 0.17
6 34 0.63
7 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:56510 original size:24 final size:24
Alignment explanation
Indices: 56466--56540 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 24
56456 AGGATTTAAA
*
56466 TTAATTTTAAAA-TTAAATTTATT
1 TTAAATTTAAAATTTAAATTTATT
*
56489 TTAAGTTTAAAATTTAAATTTATT
1 TTAAATTTAAAATTTAAATTTATT
* *
56513 ATAAATTT-AATTTTAAATTTA-T
1 TTAAATTTAAAATTTAAATTTATT
56535 TTAAAT
1 TTAAAT
56541 CAAAAGTCCC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 6 0.13
23 23 0.50
24 17 0.37
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (24 bp):
TTAAATTTAAAATTTAAATTTATT
Found at i:56588 original size:23 final size:25
Alignment explanation
Indices: 56535--56586 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
56525 TTAAATTTAT
56535 TTAAATCAAAAGTCCCAATTACAAA
1 TTAAATCAAAAGTCCCAATTACAAA
56560 TTAAATC-AAAGT-CCAATTAC-AA
1 TTAAATCAAAAGTCCCAATTACAAA
56582 TTAAA
1 TTAAA
56587 ATGTCCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 5 0.19
25 7 0.26
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (25 bp):
TTAAATCAAAAGTCCCAATTACAAA
Found at i:57355 original size:12 final size:12
Alignment explanation
Indices: 57346--57371 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57336 AATAATAACT
57346 ATGCTAATAATA
1 ATGCTAATAATA
57358 ATGCTAATAATA
1 ATGCTAATAATA
57370 AT
1 AT
57372 AATATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (12 bp):
ATGCTAATAATA
Found at i:57356 original size:3 final size:3
Alignment explanation
Indices: 57350--57438 Score: 61
Period size: 3 Copynumber: 29.0 Consensus size: 3
57340 ATAACTATGC
** * * *
57350 TAA TAA TAA TGC TAA TAA TAA TAA TAT TAT TAA TAAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
** ** * *
57396 TTG TTT TAA TAA TAA AAA TAA TAA TAT TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
57439 AAAGGAAGAC
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
3 61 0.91
4 6 0.09
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:57393 original size:22 final size:21
Alignment explanation
Indices: 57362--57438 Score: 84
Period size: 22 Copynumber: 3.6 Consensus size: 21
57352 ATAATAATGC
57362 TAATAATAATAATATTATTAA
1 TAATAATAATAATATTATTAA
* *
57383 TAAATGATAATAAT-TGTTTTAA
1 T-AATAATAATAATAT-TATTAA
* *
57405 TAATAAAAATAATAATATTAA
1 TAATAATAATAATATTATTAA
57426 TTAATAATAATAA
1 -TAATAATAATAA
57439 AAAGGAAGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 17 0.38
22 28 0.62
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TAATAATAATAATATTATTAA
Found at i:57429 original size:25 final size:25
Alignment explanation
Indices: 57362--57435 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
57352 ATAATAATGC
* *
57362 TAATAATAATAATATTATTAATAAA
1 TAATAATAATATTATTAATAATAAA
* *
57387 TGATAATAAT-TGTTTTAATAATAAA
1 TAATAATAATAT-TATTAATAATAAA
57412 -AATAATAATATTAATTAATAATAA
1 TAATAATAATATT-ATTAATAATAA
57436 TAAAAAGGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
24 9 0.22
25 31 0.77
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
TAATAATAATATTATTAATAATAAA
Found at i:58495 original size:30 final size:29
Alignment explanation
Indices: 58463--58772 Score: 331
Period size: 30 Copynumber: 10.5 Consensus size: 29
58453 GATCTGTCCA
* * *
58463 AAAAATTTCGTTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
* *
58492 AAAAA-TCCATTCTTGACCC-CAAAAATTCC
1 AAAAATTCCATT-TTTACCCTC-AAACTTCC
*
58521 AAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
* *
58550 AAAAATTTCATTTTTAACCCTAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTCAAACTTCC
* * * *
58580 AAAAATCCCATTTTTTACCCCCGAACTTCT
1 AAAAATTCCA-TTTTTACCCTCAAACTTCC
* *
58610 AAAAATCCCATTTTTAACTCC-AAAACTTCC
1 AAAAATTCCATTTTT-AC-CCTCAAACTTCC
58640 AAAAATTCCATTTTTACCCTCAAACTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
* *
58669 AAAAATGCCATTTTTAACCTCGAAACTTCC
1 AAAAATTCCATTTTTACCCTC-AAACTTCC
*
58699 AAAAATTCCAATTTTACCCTCAAACTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC
* * *
58728 AAAAATGCCATTTTTTATCCC-AAAATTTCC
1 AAAAATTCCA-TTTTTA-CCCTCAAACTTCC
58758 AAAAATTCCATTTTT
1 AAAAATTCCATTTTT
58773 GCCCCCGAAT
Statistics
Matches: 237, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
28 7 0.03
29 104 0.44
30 116 0.49
31 10 0.04
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCAAACTTCC
Found at i:58814 original size:59 final size:58
Alignment explanation
Indices: 58463--58781 Score: 406
Period size: 59 Copynumber: 5.4 Consensus size: 58
58453 GATCTGTCCA
* * * * *
58463 AAAAATTTCGTTTTTACCCTCGAACTTCCAAAAAT-CCATTCTTGACCCCAAAAATTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATGCCATT-TTTAACCCAAAACTTCC
**
58521 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTTCATTTTTAACCCTAAAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATGCCATTTTTAACCC-AAAACTTCC
* * * *
58580 AAAAATCCCATTTTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACTCCAAAACTTCC
1 AAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAATGCCATTTTTAAC-CCAAAACTTCC
* *
58640 AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATGCCATTTTTAACCTCGAAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATGCCATTTTTAACC-CAAAACTTCC
* * * *
58699 AAAAATTCCAATTTTACCCTCAAACTTCCAAAAATGCCATTTTTTATCCCAAAATTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATGCCA-TTTTTAACCCAAAACTTCC
* *
58758 AAAAATTCCATTTTTGCCCCCGAA
1 AAAAATTCCATTTTTACCCTCGAA
58782 TGTCTAAAAC
Statistics
Matches: 230, Mismatches: 25, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
58 40 0.17
59 129 0.56
60 59 0.26
61 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (58 bp):
AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATGCCATTTTTAACCCAAAACTTCC
Found at i:61787 original size:144 final size:144
Alignment explanation
Indices: 61592--61937 Score: 559
Period size: 144 Copynumber: 2.4 Consensus size: 144
61582 CTCAAACAAC
* * * *
61592 AGGCTTGTTGGACCAATCCCATCTTCCGTCAGCAGCTTAACCAATCTTGCCTCGTTGTACCTTCA
1 AGGCTTGTTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCCTTGTACCTTCA
*
61657 AAGCAACCAACTTGATGGTTCCATTCCAGAAGATATTGGGAGACTAAAGAATTTGGTTATATTGG
66 AAGCAACCAACTTGATGGTTCCATTCCAGAAGATATTGGGAGACTAAAGAATTTGGTTAGATTGG
61722 AACTATCCTCCAAT
131 AACTATCCTCCAAT
* *
61736 AGGCTTGTTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCCTTGTTCCTTCC
1 AGGCTTGTTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCCTTGTACCTTCA
* *
61801 AAGCAACCAACTTGATGGTTCCATTCCAGAAGATATTGGGAGACTAAGGAATTTGGTTGGATTGG
66 AAGCAACCAACTTGATGGTTCCATTCCAGAAGATATTGGGAGACTAAAGAATTTGGTTAGATTGG
*
61866 ATCTATCCTCCAAT
131 AACTATCCTCCAAT
* * *
61880 AGGCTTGTCGGTCCAATCCCATCATT-TGTCAGCAACTTAACCAAGCTTGCCTTCTTGT
1 AGGCTTGTTGGTCCAATCCCATC-TTCTGTCAGCAACTTAACCAATCTTGCCTCCTTGT
61938 TTCCAGAAGA
Statistics
Matches: 188, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
144 186 0.99
145 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (144 bp):
AGGCTTGTTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCCTTGTACCTTCA
AAGCAACCAACTTGATGGTTCCATTCCAGAAGATATTGGGAGACTAAAGAATTTGGTTAGATTGG
AACTATCCTCCAAT
Found at i:61954 original size:114 final size:114
Alignment explanation
Indices: 61824--62052 Score: 343
Period size: 114 Copynumber: 2.0 Consensus size: 114
61814 GATGGTTCCA
* ** **
61824 TTCCAGAAGATATTGGGAGACTAAGGAATTTGGTTGGATTGGATCTATCCTCCAATAGGCTTGTC
1 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTAAATTGGATCTATCCGACAATAGGCTTGTC
* *
61889 GGTCCAATCCCATCATT-TGTCAGCAACTTAACCAAGCTTGCCTTCTTGT
66 GGTCCAATCCCATC-TTCTGTCAGCAACTAAACAAAGCTTGCCTTCTTGT
*
61938 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTAAATTGGATCTATCCGACAATAGGCTTGTT
1 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTAAATTGGATCTATCCGACAATAGGCTTGTC
* * *
62003 GGTCCAATCCCATCTTCTGTCTGCAACTAAACAAATCTTGCCTTGTTGT
66 GGTCCAATCCCATCTTCTGTCAGCAACTAAACAAAGCTTGCCTTCTTGT
62052 T
1 T
62053 CCTTCGAGGC
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 2 0.02
114 101 0.98
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (114 bp):
TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTAAATTGGATCTATCCGACAATAGGCTTGTC
GGTCCAATCCCATCTTCTGTCAGCAACTAAACAAAGCTTGCCTTCTTGT
Found at i:62140 original size:258 final size:258
Alignment explanation
Indices: 61680--62189 Score: 797
Period size: 258 Copynumber: 2.0 Consensus size: 258
61670 GATGGTTCCA
* **
61680 TTCCAGAAGATATTGGGAGACTAAAGAATTTGGTTATATTGGAACTATCCTCCAATAGGCTTGTT
1 TTCCAGAAGATATTGGGAGACTAAAGAATTTGGTTAAATTGGAACTATCCGACAATAGGCTTGTT
* *
61745 GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCCTTGTTCCTTCCAAGCAACCA
66 GGTCCAATCCCATCTTCTGTCAGCAACTAAACAAATCTTGCCTCCTTGTTCCTTCCAAGCAACCA
* * * * * *
61810 ACTTGATGGTTCCATTCCAGAAGATATTGGGAGACTAAGGAATTTGGTTGGATTGGATCTATCCT
131 ACTTAATGGATCCATTCCACAAGAAATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCT
61875 CCAATAGGCTTGTCGGTCCAATCCCATCATT-TGTCAGCAACTTAACCAAGCTTGCCTTCTTGT
196 CCAATAGGCTTGTCGGTCCAATCCCATC-TTCTGTCAGCAACTTAACCAAGCTTGCCTTCTTGT
* *
61938 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTAAATTGGATCTATCCGACAATAGGCTTGTT
1 TTCCAGAAGATATTGGGAGACTAAAGAATTTGGTTAAATTGGAACTATCCGACAATAGGCTTGTT
* ** * *
62003 GGTCCAATCCCATCTTCTGTCTGCAACTAAACAAATCTTGCCTTGTTGTTCCTTCGAGGCAACCA
66 GGTCCAATCCCATCTTCTGTCAGCAACTAAACAAATCTTGCCTCCTTGTTCCTTCCAAGCAACCA
*
62068 ACTTAATGGATCCATTCCACAAGAAATTTGGAGACTAACGAATTTGGTTGAATTGGATCTATCCT
131 ACTTAATGGATCCATTCCACAAGAAATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCT
* * * *
62133 TCAATAGGCTTGTTGGTCCAATCCCATCTTCTGTCGGCAACTTAACCAATCTTGCCT
196 CCAATAGGCTTGTCGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAAGCTTGCCT
62190 CGTTGTTCCT
Statistics
Matches: 228, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
257 2 0.01
258 226 0.99
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (258 bp):
TTCCAGAAGATATTGGGAGACTAAAGAATTTGGTTAAATTGGAACTATCCGACAATAGGCTTGTT
GGTCCAATCCCATCTTCTGTCAGCAACTAAACAAATCTTGCCTCCTTGTTCCTTCCAAGCAACCA
ACTTAATGGATCCATTCCACAAGAAATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCT
CCAATAGGCTTGTCGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAAGCTTGCCTTCTTGT
Found at i:62733 original size:144 final size:144
Alignment explanation
Indices: 61938--62719 Score: 1167
Period size: 144 Copynumber: 5.4 Consensus size: 144
61928 GCCTTCTTGT
* **
61938 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTAAATTGGATCTATCCGACAATAGGCTTGTT
1 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTGTT
* * * * *
62003 GGTCCAATCCCATCTTCTGTCTGCAACTAAACAAATCTTGCCTTGTTGTTCCTTCGAGGCAACCA
66 GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTTCTTGTTCCTTCGAAGCAACCA
* *
62068 ACTTAATGGATCCA
131 ACTTGATGGTTCCA
* * * *
62082 TTCCACAAGAAATTTGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTTCAATAGGCTTGTT
1 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTGTT
* *
62147 GGTCCAATCCCATCTTCTGTCGGCAACTTAACCAATCTTGCC-TCGTTGTTCCTTCGAAGAAACC
66 GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTTC-TTGTTCCTTCGAAGCAACC
62211 AACTTGATGGTTCCA
130 AACTTGATGGTTCCA
* * * *
62226 TTCCAAAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGCTCTATCCTTCAATAAGCTT-TC
1 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTGT-
* * * *
62290 AGGT-CACATCCCATCATCTGTCAGCAACTTAACCAAGCTTGCCTTCTTGTTCCTTCAAAGCAAC
65 TGGTCCA-ATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTTCTTGTTCCTTCGAAGCAAC
62354 CAACTTGATGGTTCCA
129 CAACTTGATGGTTCCA
* * * *
62370 TTCCAGAAGATATTGGGAGACTGAGGAATTTGGTTGCATTGGATCTATCCTCCAATAGGTTTGTT
1 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTGTT
* *
62435 GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTG-ATTCCTTGTTCCTTCAAAGCAACC
66 GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTT-CTTGTTCCTTCGAAGCAACC
*
62499 GACTTGATGGTTCCA
130 AACTTGATGGTTCCA
* * *
62514 TTCCAGAAAATATTGGGAGACTAAGGAATTTGGTTGGATTGGATCTATCCTCCAATAGGCTTGTT
1 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTGTT
* * *
62579 GGTCCAATCCCATCATCTGTCAGCAACTTAACCAAGCTTGCCTTCTTGTTCCTTGGAAGCAACCA
66 GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTTCTTGTTCCTTCGAAGCAACCA
62644 ACTTGATGGTTCCA
131 ACTTGATGGTTCCA
62658 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTT
1 TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTT
62720 TCAGGTCACA
Statistics
Matches: 579, Mismatches: 51, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
143 6 0.01
144 566 0.98
145 7 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (144 bp):
TTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTGTT
GGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTTCTTGTTCCTTCGAAGCAACCA
ACTTGATGGTTCCA
Found at i:75381 original size:31 final size:32
Alignment explanation
Indices: 75345--75409 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
75335 TCTTTCCAAG
* *
75345 AACAAATATTGTTCCCAT-CCCCCATAGACCA
1 AACAAATACTATTCCCATCCCCCCATAGACCA
*
75376 AACAAATACTATTCCTATCCCCCCATAGACCA
1 AACAAATACTATTCCCATCCCCCCATAGACCA
75408 AA
1 AA
75410 GAAAATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.22
Consensus pattern (32 bp):
AACAAATACTATTCCCATCCCCCCATAGACCA
Found at i:78930 original size:23 final size:22
Alignment explanation
Indices: 78900--79044 Score: 125
Period size: 23 Copynumber: 6.4 Consensus size: 22
78890 ACGCTAGCGC
78900 GCTTACTG-TTCAGCACTATGTGT
1 GCTTACTGATTC-GCACT-TGTGT
*
78923 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGATTCGCACTT-GTGT
*
78946 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGATTCGCACTT-GTGT
* * * *
78969 GCCTACTGATTTGCGCTATGTGC
1 GCTTACTGATTCGCACT-TGTGT
*
78992 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGATTCGCACT-TGTGT
*
79014 GCATACTGGATT-GCACTGTGTGT
1 GCTTACT-GATTCGCACT-TGTGT
79037 GCTTACTG
1 GCTTACTG
79045 TTTCCCCAGC
Statistics
Matches: 108, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
22 16 0.15
23 88 0.81
24 4 0.04
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (22 bp):
GCTTACTGATTCGCACTTGTGT
Found at i:79030 original size:68 final size:69
Alignment explanation
Indices: 78915--79044 Score: 151
Period size: 68 Copynumber: 1.9 Consensus size: 69
78905 CTGTTCAGCA
* * * * *
78915 CTATGTGTGCTTACTGTTTCGCACTTCGTGTGCTTACTGTTTCGCACT-TCGTGTGCCTACTGAT
1 CTATGTGCGCCTACTGATTCGCACTTCGTGTGCATACTGATTCGCACTGT-GTGTGCCTACTGAT
78979 TTGCG
65 TTGCG
*
78984 CTATGTGCGCCTACTGATT-GCACTGT-GTGTGCATACTGGATT-GCACTGTGTGTGCTTACTG
1 CTATGTGCGCCTACTGATTCGCACT-TCGTGTGCATACT-GATTCGCACTGTGTGTGCCTACTG
79045 TTTCCCCAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
68 31 0.60
69 21 0.40
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.39
Consensus pattern (69 bp):
CTATGTGCGCCTACTGATTCGCACTTCGTGTGCATACTGATTCGCACTGTGTGTGCCTACTGATT
TGCG
Found at i:81645 original size:39 final size:39
Alignment explanation
Indices: 81601--81684 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
81591 TGGGACAAGT
*
81601 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTATCATCCAATATG-AAAGGATTGTGA
* * * *
81640 CTCTT-CAATAGGTGTCCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCCAAGAGGTAT-CATCCAATATGAAAGGATTGTGA
81679 CTCTTC
1 CTCTTC
81685 GAAAGGTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
38 8 0.22
39 21 0.57
40 8 0.22
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (39 bp):
CTCTTCCAAGAGGTATCATCCAATATGAAAGGATTGTGA
Found at i:81692 original size:39 final size:40
Alignment explanation
Indices: 81618--81697 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
81608 AAGAGGTATG
81618 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
* *
81658 TCCAATTTG-AAAGGGTTGTGACTCTTCGAA-AGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTC-AATAGGTGTCCA
81697 T
1 T
81698 TGAGTGCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 27 0.73
40 10 0.27
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
Found at i:91079 original size:144 final size:144
Alignment explanation
Indices: 90916--91210 Score: 475
Period size: 144 Copynumber: 2.0 Consensus size: 144
90906 TATTGAATCG
* *
90916 ACAAGTCTATTGTTGGAGAGATTC-AAATAAGTCAAATTTCTCAAATATCCAAGTTCCAATGGGA
1 ACAATTCTATTGTTGGAGAGACTCAAAAT-AGTCAAATTTCTCAAATATCCAAGTTCCAATGGGA
* * *
90980 TAGATCCATTGCTTTGGTTCCTCCAAAGGATCAGATATTGGAGACTGGTTAATTGACCCAAAGCA
65 TAGATCCATTGATTTGGTTCCCCCAAAGGATCAGAGATTGGAGACTGGTTAATTGACCCAAAGCA
91045 GAAGGGATTGGACCA
130 GAAGGGATTGGACCA
* * *
91060 ACAATTCTATTGTTGGAGAGACTCAAAATAGTCAAATTTCTCAAGTATCCAATTTCTAATGGGAT
1 ACAATTCTATTGTTGGAGAGACTCAAAATAGTCAAATTTCTCAAATATCCAAGTTCCAATGGGAT
* *
91125 AGATCCATTGATTTGGTTCCCCCAAAGGATCAGAGATTGGAGATTGGTTAATTGATCCAAAGCAG
66 AGATCCATTGATTTGGTTCCCCCAAAGGATCAGAGATTGGAGACTGGTTAATTGACCCAAAGCAG
*
91190 AAGGGATTGGATCA
131 AAGGGATTGGACCA
91204 ACAATTC
1 ACAATTC
91211 CACATTGATG
Statistics
Matches: 139, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
144 135 0.97
145 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (144 bp):
ACAATTCTATTGTTGGAGAGACTCAAAATAGTCAAATTTCTCAAATATCCAAGTTCCAATGGGAT
AGATCCATTGATTTGGTTCCCCCAAAGGATCAGAGATTGGAGACTGGTTAATTGACCCAAAGCAG
AAGGGATTGGACCA
Found at i:91711 original size:58 final size:58
Alignment explanation
Indices: 91558--91735 Score: 243
Period size: 59 Copynumber: 3.0 Consensus size: 58
91548 AAGAAATTTG
91558 GGTGTTGGTCATGCAATGGTCGACACCCCTTTTTAAT-ATGATAAAAAAATCAAATTTTT
1 GGTGTTGGTCATGCAATGGTCGACACCCCTTTTT-ATCA-GATAAAAAAATCAAATTTTT
*
91617 GGTGTTGGTCATGCAATGGTCGACACCCCTTTTTTATCAGAT-AAAAAATACAATTTTTT
1 GGTGTTGGTCATGCAATGGTCGACACCCC-TTTTTATCAGATAAAAAAAT-CAAATTTTT
* * ** * *
91676 TGTGTTGGTCATACAATGACCGACACCCCTATTTATCTGATAAAAAAATCAAATTTTT
1 GGTGTTGGTCATGCAATGGTCGACACCCCTTTTTATCAGATAAAAAAATCAAATTTTT
91734 GG
1 GG
91736 CCATCACCCC
Statistics
Matches: 106, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
58 26 0.25
59 74 0.70
60 6 0.06
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (58 bp):
GGTGTTGGTCATGCAATGGTCGACACCCCTTTTTATCAGATAAAAAAATCAAATTTTT
Found at i:91818 original size:101 final size:103
Alignment explanation
Indices: 91642--91837 Score: 315
Period size: 101 Copynumber: 1.9 Consensus size: 103
91632 ATGGTCGACA
* *
91642 CCCCTTTTTTATCAGATAAAAAATACAATTTTTTTGTGTTGGTCATACAATGACCGACACCCCTA
1 CCCCTTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGGCCATACAATGACCGACACCCCTA
91707 TTTATCTGAT-AAAAAAATCAAA-TTTTTGGCCATCAC
66 TTTATCTGATAAAAAAAATCAAACTTTTTGGCCATCAC
** * *
91743 CCCCTTTTTTATCAGATAAAAAATTTAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTA
1 CCCCTTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGGCCATACAATGACCGACACCCCTA
*
91808 TTTATTTGATAAAAAAAATCAAACTTTTTG
66 TTTATCTGATAAAAAAAATCAAACTTTTTG
91838 AGTGTTGGTC
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 68 0.79
102 12 0.14
103 6 0.07
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (103 bp):
CCCCTTTTTTATCAGATAAAAAATACAATTTTTTGGTGTTGGCCATACAATGACCGACACCCCTA
TTTATCTGATAAAAAAAATCAAACTTTTTGGCCATCAC
Found at i:91905 original size:62 final size:60
Alignment explanation
Indices: 91753--91909 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
91743 CCCCTTTTTT
* * *
91753 ATCAGAT-AAAAAATTT-AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTATTT
1 ATCAGATAAAAAAATTTAAATTTTTTGGTGTTGGTCAGGCAATGGCCGACACCCCTATTC
** * * * *
91811 ATTTGATAAAAAAAATCAAACTTTTTGAGTGTTGGTCAGGCAATGGCCGACACCCCCTCTTC
1 ATCAGATAAAAAAATTTAAATTTTTTG-GTGTTGGTCAGGCAATGGCCGACA-CCCCTATTC
91873 A-CAGATAAAAAAATTTAAAATTTTTTTGGTGTTGGTC
1 ATCAGATAAAAAAATTT-AAA-TTTTTTGGTGTTGGTC
91910 GACACCCCAT
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
58 5 0.06
59 7 0.09
60 8 0.10
61 33 0.42
62 20 0.25
63 6 0.08
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (60 bp):
ATCAGATAAAAAAATTTAAATTTTTTGGTGTTGGTCAGGCAATGGCCGACACCCCTATTC
Found at i:94307 original size:12 final size:11
Alignment explanation
Indices: 94291--94341 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
94281 AAAATTCTAC
94291 ATTAAATTTAA
1 ATTAAATTTAA
94302 AGTTAAAATTTAA
1 A-TT-AAATTTAA
*
94315 ATTACATTTAAA
1 ATTAAATTT-AA
94327 ATT-AATTTAA
1 ATTAAATTTAA
94337 CATTA
1 -ATTA
94342 TTTAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 2 0.06
11 13 0.39
12 9 0.27
13 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:94323 original size:24 final size:25
Alignment explanation
Indices: 94279--94331 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
94269 AAGTTTGAAT
* *
94279 TTAAAATTCTACATTAAATTTAAAG
1 TTAAAATTCTAAATTAAATTTAAAA
*
94304 TTAAAATT-TAAATTACATTTAAAA
1 TTAAAATTCTAAATTAAATTTAAAA
94328 TTAA
1 TTAA
94332 TTTAACATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
TTAAAATTCTAAATTAAATTTAAAA
Found at i:94339 original size:18 final size:19
Alignment explanation
Indices: 94295--94340 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
94285 TTCTACATTA
*
94295 AATTTAA-AGTTAAAATTT
1 AATTTAACATTTAAAATTT
*
94313 AAATT-ACATTTAAAA-TT
1 AATTTAACATTTAAAATTT
94330 AATTTAACATT
1 AATTTAACATT
94341 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTTAACATTTAAAATTT
Found at i:94660 original size:84 final size:83
Alignment explanation
Indices: 94362--94814 Score: 570
Period size: 84 Copynumber: 5.3 Consensus size: 83
94352 AAAGATTATT
* * * * *
94362 ATTATTATTATATTACAATTTATATCAAATATTGTGTTCATTTGACAATACATTATTTATTAAAT
1 ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAATAAATTATTTATT-AAT
*
94427 TTT-CATATTTAAAGTACAA
65 TTTAAATATTTAAA-TACAA
* *
94446 ATTATTATTATTATACTACAATTTTTATCAAATAACGTGTTGATTTAACAATAAATTATTTACTA
1 ATTATTATTA-TAT--TACAATTTTTATCAAATAATGTGTTGATTTAACAATAAATTATTTATTA
* *
94511 AATTTAAATATTTAAATAAAAA
63 ATTTTAAATATTTAAAT-ACAA
* *
94533 ATGTTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATTAA
1 A--TTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAATAAATTATTTATTAA
94598 TTTTAAATATTTAAAGTACAA
64 TTTTAAATATTTAAA-TACAA
* * *
94619 ATTATTATTATAATACAATTTTTAT-ACAATAATGTGTTGATTTAACAATAAATTATTTACTAAA
1 ATTATTATTATATTACAATTTTTATCA-AATAATGTGTTGATTTAACAATAAATTATTTATTAAT
*
94683 TTTAAATATTTAAATAAAAAA
65 TTTAAATATTTAAAT--ACAA
* * * *
94704 ATTATTATTATATTATAATTTTTATCAGATAATGTGTTGATTTAATAATATATTATTTATTAATT
1 ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAATAAATTATTTATTAATT
94769 TTAAATATTTAAAT-CAACA
66 TTAAATATTTAAATAC-A-A
*
94788 ATTATTATTATACTACAATTTTTATCA
1 ATTATTATTATATTACAATTTTTATCA
94815 GATTTAAATT
Statistics
Matches: 323, Mismatches: 32, Indels: 28
0.84 0.08 0.07
Matches are distributed among these distances:
83 3 0.01
84 106 0.33
85 76 0.24
86 71 0.22
87 55 0.17
88 3 0.01
89 9 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (83 bp):
ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAATAAATTATTTATTAATT
TTAAATATTTAAATACAA
Found at i:94793 original size:169 final size:171
Alignment explanation
Indices: 94361--94814 Score: 697
Period size: 169 Copynumber: 2.7 Consensus size: 171
94351 AAAAGATTAT
* * * *
94361 TATTATTATTATATTACAATTTATATCAAATATTGTGTTCATTTGACAATACATTATTTATTAAA
1 TATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATT-AA
*
94426 TTTT-CATATTTAAAGTACAA-ATTATTATTATTATACTACAATTTTTATCAAATAACGTGTTGA
65 TTTTAAATATTTAAAGT-CAACA--ATTATTATTATACTACAATTTTTATCAAATAACGTGTTGA
94489 TTTAACAATAAATTATTTACTAAATTTAAATATTTAAATAAAAAA
127 TTTAACAATAAATTATTTACTAAATTTAAATATTTAAATAAAAAA
*
94534 TGTTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATTAAT
1 TATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATTAAT
* *
94599 TTTAAATATTTAAAGT--ACAAATTATTATTATAATACAATTTTTAT-ACAATAATGTGTTGATT
66 TTTAAATATTTAAAGTCAAC-AATTATTATTATACTACAATTTTTATCA-AATAACGTGTTGATT
94661 TAACAATAAATTATTTACTAAATTTAAATATTTAAATAAAAAA
129 TAACAATAAATTATTTACTAAATTTAAATATTTAAATAAAAAA
* * * *
94704 -ATTATTATTATATTATAATTTTTATCAGATAATGTGTTGATTTAATAATATATTATTTATTAAT
1 TATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATTAAT
94768 TTTAAATATTTAAA-TCAACAATTATTATTATACTACAATTTTTATCA
66 TTTAAATATTTAAAGTCAACAATTATTATTATACTACAATTTTTATCA
94815 GATTTAAATT
Statistics
Matches: 260, Mismatches: 14, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
168 1 0.00
169 99 0.38
170 85 0.33
172 7 0.03
173 68 0.26
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (171 bp):
TATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATTAAT
TTTAAATATTTAAAGTCAACAATTATTATTATACTACAATTTTTATCAAATAACGTGTTGATTTA
ACAATAAATTATTTACTAAATTTAAATATTTAAATAAAAAA
Found at i:97280 original size:23 final size:24
Alignment explanation
Indices: 97249--97294 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
97239 TCCGTTTACT
*
97249 TTTTATA-TTTAATTTGTAATTTCG
1 TTTTATATTTTAAATT-TAATTTCG
97273 TTTT-TATTTTAAATTTAATTTC
1 TTTTATATTTTAAATTTAATTTC
97295 TA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTATATTTTAAATTTAATTTCG
Done.