Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014191.1 Kokia drynarioides strain JFW-HI SEQ_129224, 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: 218677
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:1384 original size:41 final size:41
Alignment explanation
Indices: 1310--1393 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
1300 GTTAAAATCC
** *
1310 ACCTTTAGCGACGTTTATGAGAAAGTGTCGCTAATGCTCTG
1 ACCTTTAGCGACGTTTATGAGAAAGTCACGCTAATGATCTG
*
1351 ACCTTTAGCGGCGTTTATGAGAAAG-CACAGCTAATGATCTG
1 ACCTTTAGCGACGTTTATGAGAAAGTCAC-GCTAATGATCTG
1392 AC
1 AC
1394 TGCACTGACC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
ACCTTTAGCGACGTTTATGAGAAAGTCACGCTAATGATCTG
Found at i:1515 original size:40 final size:41
Alignment explanation
Indices: 1398--1576 Score: 218
Period size: 41 Copynumber: 4.4 Consensus size: 41
1388 TCTGACTGCA
* * *
1398 CTGACCTTTAGTGGCGCTTTGCCC-TAACCGCCGCTAATGCT
1 CTGACCTTTAGCGGCGCTTT-CCCACAAGCGCCGCTAATGCT
* *
1439 CTGACTTTTAGCGGCGCTTTCCCACAAGCGTCGCTAATGCT
1 CTGACCTTTAGCGGCGCTTTCCCACAAGCGCCGCTAATGCT
* ** * *
1480 CTGACCTTTCGCATCGCTTT-CCACAAGTGCCGCTAATGCA
1 CTGACCTTTAGCGGCGCTTTCCCACAAGCGCCGCTAATGCT
* *
1520 CTGACCTTTAGTGGCGCTTTCCCACAAGCGCCTCTAATGCT
1 CTGACCTTTAGCGGCGCTTTCCCACAAGCGCCGCTAATGCT
*
1561 CTGACCTTTTGCGGCG
1 CTGACCTTTAGCGGCG
1577 TTTATGAAGA
Statistics
Matches: 115, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
40 36 0.31
41 79 0.69
ACGTcount: A:0.16, C:0.34, G:0.21, T:0.29
Consensus pattern (41 bp):
CTGACCTTTAGCGGCGCTTTCCCACAAGCGCCGCTAATGCT
Found at i:7078 original size:11 final size:11
Alignment explanation
Indices: 7064--7156 Score: 64
Period size: 11 Copynumber: 8.1 Consensus size: 11
7054 GTCTAAACTC
7064 ATTTTAAATTT
1 ATTTTAAATTT
*
7075 ATTTTAAGATTA
1 ATTTTAA-ATTT
* **
7087 AATTT-GTTTT
1 ATTTTAAATTT
7097 AAATTTTAAATTT
1 -A-TTTTAAATTT
7110 ATTTTAAATTT
1 ATTTTAAATTT
*
7121 AAATTT-AATTT
1 -ATTTTAAATTT
*
7132 AAGTTTAAATTT
1 -ATTTTAAATTT
7144 ATTTTCAAATTT
1 ATTTT-AAATTT
7156 A
1 A
7157 AAATTATTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
10 2 0.03
11 32 0.50
12 27 0.42
13 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:7089 original size:17 final size:17
Alignment explanation
Indices: 7066--7176 Score: 134
Period size: 17 Copynumber: 6.4 Consensus size: 17
7056 CTAAACTCAT
7066 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
7084 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
7100 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
* *
7118 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
7135 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
7153 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
*
7170 TTAAAAT
1 TTTAAAT
7177 AAATAAGGTT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
16 1 0.01
17 50 0.62
18 29 0.36
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:7103 original size:35 final size:34
Alignment explanation
Indices: 7064--7158 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 34
7054 GTCTAAACTC
**
7064 ATTTTAAATTTATTTTAAGA-TTAAATTTGTTTTAA
1 ATTTTAAATTTATTTTAA-ATTTAAATTTAATTT-A
7099 ATTTTAAATTTATTTTAAATTTAAATTTAATTTA
1 ATTTTAAATTTATTTTAAATTTAAATTTAATTTA
*
7133 AGTTTAAATTTATTTTCAAATTTAAA
1 ATTTTAAATTTATTTT-AAATTTAAA
7159 ATTATTATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
34 17 0.31
35 38 0.69
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (34 bp):
ATTTTAAATTTATTTTAAATTTAAATTTAATTTA
Found at i:7121 original size:6 final size:6
Alignment explanation
Indices: 7094--7158 Score: 64
Period size: 6 Copynumber: 11.0 Consensus size: 6
7084 TTAAATTTGT
* *
7094 TTTAAA TTTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
7141 TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA
7159 ATTATTATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
5 13 0.27
6 25 0.52
7 10 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:7127 original size:52 final size:52
Alignment explanation
Indices: 7066--7176 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 52
7056 CTAAACTCAT
* * * *
7066 TTTAAATTTATTTTAAGATTAAATTTGTTTT-AAATTTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTCAAA-TTTAAAATTATTATAAA
*
7118 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTCAAATTTAAAATTATTATAAA
*
7170 TTAAAAT
1 TTTAAAT
7177 AAATAAGGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 49 0.94
53 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTTCAAATTTAAAATTATTATAAA
Found at i:7691 original size:42 final size:42
Alignment explanation
Indices: 7643--7726 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
7633 ATAAGAAGAG
7643 ACAAATAGCAAACAAAGAATAGATTGAAGGGTTTCAAAGTCT
1 ACAAATAGCAAACAAAGAATAGATTGAAGGGTTTCAAAGTCT
7685 ACAAATAGCAAACAAAGAATAGATTGAAGGGTTTCAAAGTCT
1 ACAAATAGCAAACAAAGAATAGATTGAAGGGTTTCAAAGTCT
7727 GCAAGCATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (42 bp):
ACAAATAGCAAACAAAGAATAGATTGAAGGGTTTCAAAGTCT
Found at i:9058 original size:30 final size:30
Alignment explanation
Indices: 8991--9455 Score: 345
Period size: 30 Copynumber: 15.9 Consensus size: 30
8981 AAACTATCTG
**
8991 AAAATTCCATTTTACACCT--AAACTTCC-
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
* *
9018 AAAATCCCATTTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
* *
9048 AAAATTCCA-TTTT-ACCCCCAAACTTCCA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
* * * * *
9076 ATAATCCCATTTTCGAACC-CAAAACTTTCG
1 AAAATTCCATTTTTG-ACCTCAAAACTTCCA
* *
9106 AAAATTCCATTTTT-ACCCCCAAACTTCCA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
* * *
9135 AAAA-TCCCTTTTTAACCTCAAAACTTCTA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
* *
9164 AAAATCCCATTTTTAACC-CTAAAACTTCCA
1 AAAATTCCATTTTTGACCTC-AAAACTTCCA
* * *
9194 AAAATTCCA-TTTTCA-CTCCCAAACTTCAA
1 AAAATTCCATTTTTGACCT-CAAAACTTCCA
* * * **
9223 AAAATTCCATTTTCGACCTCGAAGCAACCA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
**
9253 AAAATTCCATTTTTGATCC-CGTAACTTCCA
1 AAAATTCCATTTTTGA-CCTCAAAACTTCCA
* * * *
9283 AAAATTCCA-TTTTCACCCCCACACTTCCA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
* * *
9312 AAAATTTCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
* * *
9342 AAAATTCCATTTTTTACCCCTAAACTTCCA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
* *
9372 AAAATTCCA-TTTTAATCTC-AAACTTCCA
1 AAAATTCCATTTTTGACCTCAAAACTTCCA
*** *
9400 AAAATTACCA-TTTTG-CCTCTGGA-TGTCAA
1 AAAATT-CCATTTTTGACCTCAAAACT-TCCA
9429 AAAATTCCATTTTTTGACCTCAAAACT
1 AAAATTCCA-TTTTTGACCTCAAAACT
9456 CTCAAAATTA
Statistics
Matches: 351, Mismatches: 63, Indels: 43
0.77 0.14 0.09
Matches are distributed among these distances:
27 16 0.05
28 56 0.16
29 111 0.32
30 155 0.44
31 12 0.03
32 1 0.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCTCAAAACTTCCA
Found at i:9189 original size:59 final size:58
Alignment explanation
Indices: 8991--9413 Score: 353
Period size: 59 Copynumber: 7.2 Consensus size: 58
8981 AAACTATCTG
* *
8991 AAAATTCCA-TTTTACACCT-AAACTTCC-AAAATCCCATTTTTGACCTCGAAACTTCCA
1 AAAATTCCATTTTTAC-CCTCAAACTTCCAAAAATCCC-TTTTTAACCTCAAAACTTCCA
* * * * *
9048 AAAATTCCA-TTTTACCCCCAAACTTCCAATAATCCCATTTTCGAACC-CAAAACTTTCG
1 AAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCC-TTTT-TAACCTCAAAACTTCCA
* *
9106 AAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCTTTTTAACCTCAAAACTTCTA
1 AAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCTTTTTAACCTCAAAACTTCCA
* * * * * * *
9164 AAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTCA-CTCCCAAACTTCAA
1 AAAATTCCATTTTT-ACCCTCAAACTTCCAAAAATCCCTTTTTAACCT-CAAAACTTCCA
* * ** * * **
9223 AAAATTCCATTTTCGA-CCTCGAAGCAACCAAAAATTCCATTTTTGATCC-CGTAACTTCCA
1 AAAATTCCATTTT-TACCCTC-AAACTTCCAAAAA-TCCCTTTTT-AACCTCAAAACTTCCA
* * * * * *
9283 AAAATTCCATTTTCACCCCCACACTTCCAAAAATTTCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTTACCCTCAAACTTCCAAAAA-TCCCTTTTTAACCTCAAAACTTCCA
* * *
9342 AAAATTCCATTTTTTACCC-CTAAACTTCCAAAAATTCCATTTTAATCTC-AAACTTCCA
1 AAAATTCCA-TTTTTACCCTC-AAACTTCCAAAAATCCCTTTTTAACCTCAAAACTTCCA
9400 AAAATTACCATTTT
1 AAAATT-CCATTTT
9414 GCCTCTGGAT
Statistics
Matches: 299, Mismatches: 50, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
56 2 0.01
57 27 0.09
58 81 0.27
59 138 0.46
60 50 0.17
62 1 0.00
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (58 bp):
AAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCTTTTTAACCTCAAAACTTCCA
Found at i:9284 original size:89 final size:87
Alignment explanation
Indices: 8991--9413 Score: 419
Period size: 89 Copynumber: 4.8 Consensus size: 87
8981 AAACTATCTG
* * * *
8991 AAAATTCCA-TTTTACACCTAAACTTCC-AAAATCCCATTTTTGACCTCGAAACTTCCAAAAATT
1 AAAATTCCATTTTTAC-CCTAAACTTCCAAAAATTCCA-TTTTCACCCCCAAACTTCCAAAAATT
* *
9054 CCA-TTTT-ACCCCCAAACTTCCA
64 CCATTTTTAACCTCAAAACTTCCA
* * * * * * *
9076 ATAATCCCATTTTCGAACCCAAAACTTTCGAAAATTCCATTTTTACCCCCAAACTTCCAAAAA-T
1 AAAATTCCATTTT--TACCCTAAACTTCCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATT
* *
9140 CCCTTTTTAACCTCAAAACTTCTA
64 CCATTTTTAACCTCAAAACTTCCA
* * *
9164 AAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTCACTCCCAAACTTCAAAAAATT
1 AAAATTCCATTTTT-ACCCT-AAACTTCCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATT
** * * **
9229 CCATTTTCGACCTCGAAGCAACCA
64 CCATTTTTAACCTCAAAACTTCCA
*
9253 AAAATTCCATTTTTGATCCCGT-AACTTCCAAAAATTCCATTTTCACCCCCACACTTCCAAAAAT
1 AAAATTCCATTTTT-A-CCC-TAAACTTCCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAAT
* *
9317 TTCATTTTTAACCCCAAAACTTCCA
63 TCCATTTTTAACCTCAAAACTTCCA
** *
9342 AAAATTCCATTTTTTACCCCTAAACTTCCAAAAATTCCATTTT-AATCTCAAACTTCCAAAAATT
1 AAAATTCCA-TTTTTA-CCCTAAACTTCCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATT
9406 ACCATTTT
64 -CCATTTT
9414 GCCTCTGGAT
Statistics
Matches: 276, Mismatches: 48, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
85 7 0.03
86 6 0.02
87 38 0.14
88 89 0.32
89 127 0.46
90 8 0.03
91 1 0.00
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (87 bp):
AAAATTCCATTTTTACCCTAAACTTCCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATTCC
ATTTTTAACCTCAAAACTTCCA
Found at i:9914 original size:96 final size:96
Alignment explanation
Indices: 9797--9988 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
9787 AAGACTTTAA
* **
9797 AATCGAGGTAATATTCTTTTAT-TTCGAGTT-TCGAAA-ATTTGTGCCTTAACTTACTAGGTGAA
1 AATCGAGGCAATATTCTTTTATCTTCGA-TTCT-GAAATA-TTGCACCTTAACTTACTAGGTGAA
** **
9859 ATTTTTCTTCAAATTTAAATAATCGAATACCCTT
63 ACATTTCTTCAAATCGAAATAATCGAATACCCTT
* *
9893 AATCGAGGCAATGTT-TCTTTATCTTCGATTCTGAAATATTGCACCTTAACTTACTAGGTGCAAC
1 AATCGAGGCAATATTCT-TTTATCTTCGATTCTGAAATATTGCACCTTAACTTACTAGGTGAAAC
* *
9957 ATTTCTTCAAATCGAGATAATCGAATATCCTT
65 ATTTCTTCAAATCGAAATAATCGAATACCCTT
9989 TTCCCAAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 1 0.01
96 73 0.90
97 7 0.09
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATCTTCGATTCTGAAATATTGCACCTTAACTTACTAGGTGAAACA
TTTCTTCAAATCGAAATAATCGAATACCCTT
Found at i:16424 original size:20 final size:21
Alignment explanation
Indices: 16399--16437 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16389 CCAAGAAAGG
16399 AAAAAAGAA-AAAGAAAAGCA
1 AAAAAAGAAGAAAGAAAAGCA
*
16419 AAAAAAGAAGAAGGAAAAG
1 AAAAAAGAAGAAAGAAAAG
16438 TCAAGATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAGAAAGAAAAGCA
Found at i:17159 original size:16 final size:16
Alignment explanation
Indices: 17135--17165 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17125 TTTTGCCTAC
17135 AAAAGGATTTCCAAAG
1 AAAAGGATTTCCAAAG
*
17151 AAAATGATTTCCAAA
1 AAAAGGATTTCCAAA
17166 TTAGATTGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (16 bp):
AAAAGGATTTCCAAAG
Found at i:17309 original size:11 final size:10
Alignment explanation
Indices: 17289--17355 Score: 70
Period size: 10 Copynumber: 6.9 Consensus size: 10
17279 CATTTTACCC
17289 AAAA-AAAAG
1 AAAAGAAAAG
*
17298 AGAGAGAAAAG
1 A-AAAGAAAAG
17309 AAAAGAAAAG
1 AAAAGAAAAG
*
17319 AAAA-AGAA-
1 AAAAGAAAAG
17327 AAAAGAAAA-
1 AAAAGAAAAG
17336 AAAAGAAGAAG
1 AAAAGAA-AAG
17347 AAAAGAAAA
1 AAAAGAAAA
17356 AGGAAAGGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
8 4 0.08
9 14 0.29
10 18 0.37
11 13 0.27
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:17312 original size:16 final size:14
Alignment explanation
Indices: 17289--17355 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 14
17279 CATTTTACCC
17289 AAAAAAAAGAGAGAG
1 AAAAAAAAGA-AGAG
*
17304 AAAAGAAAAGAAAAG
1 AAAA-AAAAGAAGAG
17319 AAAAAGAAA-AA-AG
1 AAAAA-AAAGAAGAG
17332 AAAAAAAAGAAGAAG
1 AAAAAAAAGAAG-AG
17347 AAAAGAAAA
1 AAAA-AAAA
17356 AGGAAAGGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
12 3 0.07
13 9 0.20
14 3 0.07
15 20 0.44
16 10 0.22
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAGAG
Found at i:17325 original size:6 final size:6
Alignment explanation
Indices: 17304--17357 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 6
17294 AAAGAGAGAG
* *
17304 AAAAG- AAAAG- AAAAGA AAAAGA AAAA-A GAAA-A AAAAGA AGAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
17347 AAAAGA AAAAG
1 AAAAGA AAAAG
17358 GAAAGGTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
5 22 0.52
6 20 0.48
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:17351 original size:27 final size:28
Alignment explanation
Indices: 17302--17361 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
17292 AAAAAGAGAG
17302 AGAAAAGAAAAGAAAAGAAAAAGAAAAA
1 AGAAAAGAAAAGAAAAGAAAAAGAAAAA
17330 AGAAAA-AAAAGAAGAAG-AAAAGAAAAA
1 AGAAAAGAAAAGAA-AAGAAAAAGAAAAA
*
17357 GGAAA
1 AGAAA
17362 GGTCAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (28 bp):
AGAAAAGAAAAGAAAAGAAAAAGAAAAA
Found at i:17362 original size:11 final size:11
Alignment explanation
Indices: 17289--17362 Score: 73
Period size: 11 Copynumber: 6.9 Consensus size: 11
17279 CATTTTACCC
17289 AAAA-AAAAGA
1 AAAAGAAAAGA
* *
17299 GAGAGAAAAG-
1 AAAAGAAAAGA
17309 AAAAGAAAAGA
1 AAAAGAAAAGA
17320 AAAAGAAAA-A
1 AAAAGAAAAGA
*
17330 AGAAAAAAAAGA
1 A-AAAGAAAAGA
*
17342 AGAAGAAAAGA
1 AAAAGAAAAGA
*
17353 AAAAGGAAAG
1 AAAAGAAAAG
17363 GTCAAAGATG
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
10 12 0.24
11 37 0.73
12 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:18366 original size:49 final size:48
Alignment explanation
Indices: 18208--18367 Score: 153
Period size: 49 Copynumber: 3.3 Consensus size: 48
18198 AGACAAGATG
* * ** * * *
18208 GGAAAGATTGAAGCCACAATGATGAATCTTGTACCATAG-GAATGTGAA
1 GGAAAGATTGAAGCCGCAACGGCGAAACTTATACCTTAGAG-ATGTGAA
* * *
18256 GGAAGAGATTAAAGCTGCAATGGCGAAACTTATACCTTAGAGATGTGACA
1 GGAA-AGATTGAAGCCGCAACGGCGAAACTTATACCTTAGAGATGTGA-A
* *
18306 GGAAAGGTTGAAGCCGCAACGGC-AAACCTTATACCTTAGTGATGTGAA
1 GGAAAGATTGAAGCCGCAACGGCGAAA-CTTATACCTTAGAGATGTGAA
18354 GGGAAAGATTGAAG
1 -GGAAAGATTGAAG
18368 TCATAACGGT
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
48 8 0.09
49 79 0.85
50 6 0.06
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (48 bp):
GGAAAGATTGAAGCCGCAACGGCGAAACTTATACCTTAGAGATGTGAA
Found at i:18449 original size:47 final size:47
Alignment explanation
Indices: 18380--18500 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
18370 ATAACGGTGA
*
18380 ATCTTCCTGATGAGATACAGAGAAGTTAATCAAACAACGAAACGATC
1 ATCTTCCTGATGAGATACAGAGAAGTGAATCAAACAACGAAACGATC
* * * * *
18427 ATCTTCCTGATGAGATATAGAGAAATGGATCAAACAATGAAGCGATC
1 ATCTTCCTGATGAGATACAGAGAAGTGAATCAAACAACGAAACGATC
18474 ATCTTCCTGATGAGATACAGAGAAGTG
1 ATCTTCCTGATGAGATACAGAGAAGTG
18501 GACCAAAACA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (47 bp):
ATCTTCCTGATGAGATACAGAGAAGTGAATCAAACAACGAAACGATC
Found at i:20225 original size:31 final size:29
Alignment explanation
Indices: 20167--20247 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
20157 TTAAAAATGG
* *
20167 TGTTTTAACCCCTAAACTTTCTAAAATTTA
1 TGTTTTAACCCTTAAACTTTC-AAAAATTA
* *
20197 TGTTTTGACCCTTAAATTTTTCAAAAATTA
1 TGTTTTAACCCTTAAA-CTTTCAAAAATTA
* *
20227 TATTTTAACCCTCAAACTTTC
1 TGTTTTAACCCTTAAACTTTC
20248 CTGAAATTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 4 0.10
30 34 0.81
31 4 0.10
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (29 bp):
TGTTTTAACCCTTAAACTTTCAAAAATTA
Found at i:21439 original size:28 final size:28
Alignment explanation
Indices: 21394--21453 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
21384 GTTTCGACAG
21394 TATTATTTTGCACATTGGTGCTTATCGT
1 TATTATTTTGCACATTGGTGCTTATCGT
* *
21422 TATTATTTTGTACTTTGGTGCTTATCGT
1 TATTATTTTGCACATTGGTGCTTATCGT
21450 TATT
1 TATT
21454 TTCACTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.55
Consensus pattern (28 bp):
TATTATTTTGCACATTGGTGCTTATCGT
Found at i:22392 original size:20 final size:21
Alignment explanation
Indices: 22367--22411 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
22357 CAATGTTATA
22367 GATACC-TTTAATGAAGTATC
1 GATACCGTTTAATGAAGTATC
** *
22387 GATACCGTTTGTTTAAGTATC
1 GATACCGTTTAATGAAGTATC
22408 GATA
1 GATA
22412 TTTTGCCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (21 bp):
GATACCGTTTAATGAAGTATC
Found at i:31173 original size:53 final size:52
Alignment explanation
Indices: 31111--31218 Score: 207
Period size: 53 Copynumber: 2.1 Consensus size: 52
31101 TTATCCTTTA
31111 GTATTTGGAAAAATTGCTTTTTATTTCTCCCTACCAAATTAGGCAAACCAAG
1 GTATTTGGAAAAATTGCTTTTTATTTCTCCCTACCAAATTAGGCAAACCAAG
31163 GTATATTGGAAAAATTGCTTTTTATTTCTCCCTACCAAATTAGGCAAACCAAG
1 GTAT-TTGGAAAAATTGCTTTTTATTTCTCCCTACCAAATTAGGCAAACCAAG
31216 GTA
1 GTA
31219 CGTTTCTAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 4 0.07
53 51 0.93
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (52 bp):
GTATTTGGAAAAATTGCTTTTTATTTCTCCCTACCAAATTAGGCAAACCAAG
Found at i:36041 original size:3 final size:3
Alignment explanation
Indices: 36033--36058 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36023 ATTTGATCTT
36033 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
36059 TAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:37778 original size:18 final size:18
Alignment explanation
Indices: 37755--37792 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
37745 TAATATAGTT
37755 TTATTTG-GTTTATTCGAA
1 TTATTTGAG-TTATTCGAA
37773 TTATTTGAGTTATTCGAA
1 TTATTTGAGTTATTCGAA
37791 TT
1 TT
37793 CGAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (18 bp):
TTATTTGAGTTATTCGAA
Found at i:38342 original size:51 final size:49
Alignment explanation
Indices: 38287--38445 Score: 144
Period size: 51 Copynumber: 3.1 Consensus size: 49
38277 AAAATTTTTT
* *
38287 AAAAAATCTTTATTTTTCTTAAAAATCAAAACTTTTATTTTAAAATAGTT-
1 AAAAAATATTTATTTTT-TTAAAAATCTAAACTTTTATTTTAAAA-AGTTA
*** * *
38337 AAAAAATAAAAACTTTATTTAAAAAATTTAAACTTTT-TCCTTTAAAAAGATTA
1 AAAAAATATTTA-TTT-TTTTAAAAATCTAAACTTTTAT--TTTAAAAAG-TTA
38390 AAAAACATATTT-TTATTTTTAAAAATCTAAACTTTTATTTTAAAACAGTTA
1 AAAAA-ATATTTATT-TTTTTAAAAATCTAAACTTTTATTTTAAAA-AGTTA
38441 AAAAA
1 AAAAA
38446 TCAAAATTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
50 9 0.10
51 35 0.40
52 33 0.38
53 7 0.08
54 3 0.03
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (49 bp):
AAAAAATATTTATTTTTTTAAAAATCTAAACTTTTATTTTAAAAAGTTA
Found at i:38422 original size:103 final size:104
Alignment explanation
Indices: 38305--38524 Score: 336
Period size: 103 Copynumber: 2.1 Consensus size: 104
38295 TTTATTTTTC
* *
38305 TTAAAAATCAAAACTTTTATTTTAAAATAGTTAAAAAATAAAAACTTTATTTAAAAAATTTAAAC
1 TTAAAAATCTAAACTTTTATTTTAAAACAGTTAAAAAATAAAAACTTTATTTAAAAAATTTAAAC
* *
38370 TTTTTCCTTTAAAAAGATTAAAAAACATATTTTTAT-TT
66 TTTTTCCTTTAAAAAGATTAAAAAACAAATTTTTATAAT
* * * *
38408 TTAAAAATCTAAACTTTTATTTTAAAACAGTTAAAAAATCAAAATTTTGTTTAAAAATTTTAAAC
1 TTAAAAATCTAAACTTTTATTTTAAAACAGTTAAAAAATAAAAACTTTATTTAAAAAATTTAAAC
* *
38473 TTTTTCCTTTAAAATGATTAAAACACAAATTTTTATAAT
66 TTTTTCCTTTAAAAAGATTAAAAAACAAATTTTTATAAT
38512 TTAAAAA-CTAAAC
1 TTAAAAATCTAAAC
38525 ATTCTTTTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 98 0.92
104 8 0.08
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (104 bp):
TTAAAAATCTAAACTTTTATTTTAAAACAGTTAAAAAATAAAAACTTTATTTAAAAAATTTAAAC
TTTTTCCTTTAAAAAGATTAAAAAACAAATTTTTATAAT
Found at i:38472 original size:51 final size:49
Alignment explanation
Indices: 38305--38476 Score: 177
Period size: 51 Copynumber: 3.4 Consensus size: 49
38295 TTTATTTTTC
** * *
38305 TTAAAAATCAAAACTTTTATTTTAAAATAGTTAAAAAATAAAAACTTTAT
1 TTAAAAATTTAAACTTTTATTTTAAAA-AGTTAAAAAATCAAAATTTTAT
* *
38355 TTAAAAAATTTAAACTTTT-TCCTTTAAAAAGATTAAAAAA-CATATTTTTATTT
1 TT-AAAAATTTAAACTTTTAT--TTTAAAAAG-TTAAAAAATCAAAATTTTA--T
* *
38408 TTAAAAATCTAAACTTTTATTTTAAAACAGTTAAAAAATCAAAATTTTGT
1 TTAAAAATTTAAACTTTTATTTTAAAA-AGTTAAAAAATCAAAATTTTAT
38458 TTAAAAATTTTAAACTTTT
1 TTAAAAA-TTTAAACTTTT
38477 TCCTTTAAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
50 11 0.11
51 47 0.47
52 39 0.39
53 4 0.04
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (49 bp):
TTAAAAATTTAAACTTTTATTTTAAAAAGTTAAAAAATCAAAATTTTAT
Found at i:38524 original size:52 final size:51
Alignment explanation
Indices: 38305--38524 Score: 168
Period size: 52 Copynumber: 4.3 Consensus size: 51
38295 TTTATTTTTC
* * * **
38305 TTAAAAATCAAAACTTTTAT--TTTAAAATAGTTAAAAAATAAAAACTTTAT-T
1 TTAAAAATCTAAACTTTT-TCCTTTAAAAGA-TTAAAAAA-CAAATTTTTATAT
* * * *
38356 TAAAAAATTTAAACTTTTTCCTTTAAAAAGATTAAAAAACATATTTTTATTT
1 TTAAAAATCTAAACTTTTTCCTTT-AAAAGATTAAAAAACAAATTTTTATAT
* * *
38408 TTAAAAATCTAAACTTTTAT--TTTAAAACAGTTAAAAAATCAAA-ATTT-TGT
1 TTAAAAATCTAAACTTTT-TCCTTTAAAAGA-TTAAAAAA-CAAATTTTTATAT
* *
38458 TTAAAAATTTTAAACTTTTTCCTTTAAAATGATTAAAACACAAATTTTTATAAT
1 TTAAAAA-TCTAAACTTTTTCCTTTAAAA-GATTAAAAAACAAATTTTTAT-AT
38512 TTAAAAA-CTAAAC
1 TTAAAAATCTAAAC
38525 ATTCTTTTTT
Statistics
Matches: 135, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
50 16 0.12
51 50 0.37
52 53 0.39
53 8 0.06
54 8 0.06
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (51 bp):
TTAAAAATCTAAACTTTTTCCTTTAAAAGATTAAAAAACAAATTTTTATAT
Found at i:38561 original size:20 final size:20
Alignment explanation
Indices: 38524--38561 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38514 AAAAACTAAA
*
38524 CATTCTTTTTTTACAAAAAT
1 CATTCTTTTCTTACAAAAAT
38544 CATTACTTTTCTTA-AAAA
1 CATT-CTTTTCTTACAAAA
38562 TCAAAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (20 bp):
CATTCTTTTCTTACAAAAAT
Found at i:50782 original size:6 final size:6
Alignment explanation
Indices: 50771--50815 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
50761 TGATCAAAAT
* * *
50771 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
50816 TATGAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:58858 original size:21 final size:21
Alignment explanation
Indices: 58832--58874 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
58822 CTTAGTTCTT
58832 AAATAAAAAGTACCAACTATC
1 AAATAAAAAGTACCAACTATC
58853 AAATAAAAAGTACCAACTATC
1 AAATAAAAAGTACCAACTATC
58874 A
1 A
58875 TAGGTAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (21 bp):
AAATAAAAAGTACCAACTATC
Found at i:60975 original size:24 final size:23
Alignment explanation
Indices: 60948--60998 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
60938 GTTTTGGCGC
60948 TTTTTTT-TACTGTTTTG-GTTGAT
1 TTTTTTTCTA-TGTTTTGAGTTG-T
*
60971 TTTTTTTCTATTTTTTGAGTTGT
1 TTTTTTTCTATGTTTTGAGTTGT
60994 TTTTT
1 TTTTT
60999 ATTGTTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.08, C:0.04, G:0.14, T:0.75
Consensus pattern (23 bp):
TTTTTTTCTATGTTTTGAGTTGT
Found at i:60976 original size:22 final size:22
Alignment explanation
Indices: 60948--61007 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
60938 GTTTTGGCGC
60948 TTTTTTTTACTGTTTTGGTTGA-
1 TTTTTTTTACTGTTTT-GTTGAG
*
60970 TTTTTTTT-CTATTTT-TTGAG
1 TTTTTTTTACTGTTTTGTTGAG
*
60990 TTGTTTTTTATTGTTTTG
1 TT-TTTTTTACTGTTTTG
61008 ATTGTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 4 0.13
20 2 0.06
21 12 0.39
22 13 0.42
ACGTcount: A:0.08, C:0.03, G:0.15, T:0.73
Consensus pattern (22 bp):
TTTTTTTTACTGTTTTGTTGAG
Found at i:61018 original size:22 final size:22
Alignment explanation
Indices: 60950--61018 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 22
60940 TTTGGCGCTT
* * *
60950 TTTTTTACTGTTTTGGTTGATTT
1 TTTTTTATTGTTTTGATTG-TTA
*
60973 TTTTTCTATT-TTTTGA--GTTG
1 TTTTT-TATTGTTTTGATTGTTA
60993 TTTTTTATTGTTTTGATTGTTA
1 TTTTTTATTGTTTTGATTGTTA
61015 TTTT
1 TTTT
61019 CGTGTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
19 4 0.11
20 13 0.34
21 1 0.03
22 7 0.18
23 10 0.26
24 3 0.08
ACGTcount: A:0.10, C:0.03, G:0.14, T:0.72
Consensus pattern (22 bp):
TTTTTTATTGTTTTGATTGTTA
Found at i:61024 original size:20 final size:20
Alignment explanation
Indices: 60983--61024 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
60973 TTTTTCTATT
*
60983 TTTTGAGTTGTTTTTTATTG
1 TTTTGAGTTGTTTTTTAGTG
*
61003 TTTTGA-TTGTTATTTTCGTG
1 TTTTGAGTTGTT-TTTTAGTG
61023 TT
1 TT
61025 ATTTTTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.10, C:0.02, G:0.19, T:0.69
Consensus pattern (20 bp):
TTTTGAGTTGTTTTTTAGTG
Found at i:61030 original size:12 final size:12
Alignment explanation
Indices: 61010--61128 Score: 86
Period size: 12 Copynumber: 10.3 Consensus size: 12
61000 TTGTTTTGAT
*
61010 TGTTATTTTCG-
1 TGTTATTTTTGC
61021 TGTTATTTTTGC
1 TGTTATTTTTGC
*
61033 TGTTATTTTTGT
1 TGTTATTTTTGC
* *
61045 TATTGTTTTTGC
1 TGTTATTTTTGC
61057 TGTTA-TTTT--
1 TGTTATTTTTGC
* **
61066 TGTTGTTTTTAA
1 TGTTATTTTTGC
* *
61078 TGTT-GTTTTAC
1 TGTTATTTTTGC
61089 TGTTATTTTTGC
1 TGTTATTTTTGC
* * *
61101 TGCTATTTTGGT
1 TGTTATTTTTGC
*
61113 TGTTATTTTTGT
1 TGTTATTTTTGC
61125 TGTT
1 TGTT
61129 TGGATGTTAT
Statistics
Matches: 86, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
9 4 0.05
10 4 0.05
11 23 0.27
12 55 0.64
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:61031 original size:24 final size:23
Alignment explanation
Indices: 61010--61128 Score: 100
Period size: 24 Copynumber: 5.2 Consensus size: 23
61000 TTGTTTTGAT
61010 TGTTATTTTCGTGTTATTTTTGC
1 TGTTATTTTCGTGTTATTTTTGC
* * *
61033 TGTTATTTTTGTTATTGTTTTTGC
1 TGTTATTTTCG-TGTTATTTTTGC
* **
61057 TGTTATTTT--TGTTGTTTTTAA
1 TGTTATTTTCGTGTTATTTTTGC
*
61078 TGTTGTTTTAC-TGTTATTTTTGC
1 TGTTATTTT-CGTGTTATTTTTGC
* * *
61101 TGCTATTTTGGTTGTTATTTTTGT
1 TGTTATTTTCG-TGTTATTTTTGC
61125 TGTT
1 TGTT
61129 TGGATGTTAT
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
21 17 0.22
23 26 0.34
24 33 0.43
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (23 bp):
TGTTATTTTCGTGTTATTTTTGC
Found at i:61066 original size:68 final size:68
Alignment explanation
Indices: 60994--61128 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 68
60984 TTTGAGTTGT
* * * *
60994 TTTTTATTGTTTTGATTGTTATTTT-CGTGTTATTTTTGCTGTTATTTTTGTTATTGTTTTTGCT
1 TTTTTATTGTTTTGAATGTTATTTTAC-TGTTATTTTTGCTGCTATTTTGGTTATTATTTTTGCT
61058 GTTA
65 GTTA
* * * * *
61062 TTTTTGTTGTTTTTAATGTTGTTTTACTGTTATTTTTGCTGCTATTTTGGTTGTTATTTTTGTTG
1 TTTTTATTGTTTTGAATGTTATTTTACTGTTATTTTTGCTGCTATTTTGGTTATTATTTTTGCTG
61127 TT
66 TT
61129 TGGATGTTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 56 0.98
69 1 0.02
ACGTcount: A:0.10, C:0.04, G:0.17, T:0.69
Consensus pattern (68 bp):
TTTTTATTGTTTTGAATGTTATTTTACTGTTATTTTTGCTGCTATTTTGGTTATTATTTTTGCTG
TTA
Found at i:61115 original size:44 final size:44
Alignment explanation
Indices: 61050--61142 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
61040 TTTGTTATTG
* * *
61050 TTTTTGCTGTTATTTTTGTTGTT-TTTAATGTTGTTT-TACTGTTA
1 TTTTTGCTGCTATTTTGGTTGTTATTT-ATGTTGTTTGGA-TGTTA
*
61094 TTTTTGCTGCTATTTTGGTTGTTATTTTTGTTGTTTGGATGTTA
1 TTTTTGCTGCTATTTTGGTTGTTATTTATGTTGTTTGGATGTTA
61138 TTTTT
1 TTTTT
61143 TATGCGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 39 0.91
45 4 0.09
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.68
Consensus pattern (44 bp):
TTTTTGCTGCTATTTTGGTTGTTATTTATGTTGTTTGGATGTTA
Found at i:64703 original size:29 final size:29
Alignment explanation
Indices: 64670--64741 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
64660 TTCTTTTTGG
* *
64670 TTACTCAATTGTGAAAAGTTACAAAATGA
1 TTACTCAACTATGAAAAGTTACAAAATGA
* *
64699 TTACTCAACTATGAAAAGTTACAGAATGG
1 TTACTCAACTATGAAAAGTTACAAAATGA
* *
64728 TCACCCAACTATGA
1 TTACTCAACTATGA
64742 TTTTTTTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (29 bp):
TTACTCAACTATGAAAAGTTACAAAATGA
Found at i:64797 original size:59 final size:60
Alignment explanation
Indices: 64704--64822 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 60
64694 AATGATTACT
* * * * *
64704 CAACTATGAAAAGTTACAGAATGGTCACCCAACTA-TGATTTTTTTTCTCTTTTGGTCACC
1 CAACTATGAAAAGTTACAAAATGATCACCAAACTATTCA-ATTTTTTCTCTTTTGGTCACC
* *
64764 CAACTATG-AAAGTTACAAAATGATCATCAAACTATTCAATTTTTTCTTTTTTGGTCACC
1 CAACTATGAAAAGTTACAAAATGATCACCAAACTATTCAATTTTTTCTCTTTTGGTCACC
64823 AGTTAGCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 41 0.80
60 10 0.20
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (60 bp):
CAACTATGAAAAGTTACAAAATGATCACCAAACTATTCAATTTTTTCTCTTTTGGTCACC
Found at i:64797 original size:88 final size:88
Alignment explanation
Indices: 64638--64798 Score: 218
Period size: 88 Copynumber: 1.8 Consensus size: 88
64628 CTATAATAAA
* * * * * * *
64638 GGTCACCCAATTATGGTTATTTTTCTTTTTGGTTACTCAATTGTGAAAAGTTACAAAATGATTAC
1 GGTCACCCAACTATGATTATTTTTCTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGATCAC
64703 TCAACTATGAAAAGTTACAGAAT
66 TCAACTATGAAAAGTTACAGAAT
*
64726 GGTCACCCAACTATGATTTTTTTTCTCTTTTGGTCACCCAACTATG-AAAGTTACAAAATGATCA
1 GGTCACCCAACTATGATTATTTTTCT-TTTTGGTCACCCAACTATGAAAAGTTACAAAATGATCA
64790 -TCAAACTAT
65 CTC-AACTAT
64799 TCAATTTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 2 0.03
88 46 0.73
89 15 0.24
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (88 bp):
GGTCACCCAACTATGATTATTTTTCTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGATCAC
TCAACTATGAAAAGTTACAGAAT
Found at i:65025 original size:56 final size:58
Alignment explanation
Indices: 64863--65025 Score: 170
Period size: 59 Copynumber: 2.8 Consensus size: 58
64853 AAATTCTAAT
*** ** **
64863 ATAGTTGGGTGACCAAAAAAGACAAAATTGAATAGTTGATTGATCATTTTGTAACTTTTC
1 ATAGTTGGGTGACCAAAAAAGA-AAAAACCAA-AGTTGGGTGGCCATTTTGTAACTTTTC
*
64923 ATAGTTGGGTGACCAAAAAAATAAAAAACCAAAGTTGGGTGGCCATTTTGTAACTTTTC
1 ATAGTTGGGTGACC-AAAAAAGAAAAAACCAAAGTTGGGTGGCCATTTTGTAACTTTTC
* **
64982 ATAGTT-GGTGATC-AAAAAGAAAAAATTATAA-TTGGGTGGCCATT
1 ATAGTTGGGTGACCAAAAAAGAAAAAACCA-AAGTTGGGTGGCCATT
65026 AATGTAGTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
56 25 0.28
57 2 0.02
58 6 0.07
59 29 0.33
60 20 0.22
61 7 0.08
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.31
Consensus pattern (58 bp):
ATAGTTGGGTGACCAAAAAAGAAAAAACCAAAGTTGGGTGGCCATTTTGTAACTTTTC
Found at i:70459 original size:21 final size:21
Alignment explanation
Indices: 70433--70479 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
70423 CGTTTAAAGT
* *
70433 TTTAAGGTCTAAAGTCTCAAG
1 TTTAAGATCTAAAGTCTCAAA
70454 TTTAAGATCTAAAGTCTCAAA
1 TTTAAGATCTAAAGTCTCAAA
70475 TTTAA
1 TTTAA
70480 AGTTTTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (21 bp):
TTTAAGATCTAAAGTCTCAAA
Found at i:74187 original size:15 final size:16
Alignment explanation
Indices: 74157--74189 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
74147 TATCTCTTTC
74157 TTTTTTAAAATATTTA
1 TTTTTTAAAATATTTA
*
74173 TTTTTTAATAT-TTTA
1 TTTTTTAAAATATTTA
74188 TT
1 TT
74190 ATACTATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTAAAATATTTA
Found at i:74358 original size:13 final size:14
Alignment explanation
Indices: 74329--74374 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
74319 TAAGTGTATT
*
74329 ATAAAATAAAATAAA
1 ATAAAAT-ATATAAA
74344 ATAAAATAT-TAAA
1 ATAAAATATATAAA
74357 AT-AAATATATAAA
1 ATAAAATATATAAA
74370 A-AAAA
1 ATAAAA
74375 AACATCTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 6 0.21
13 14 0.50
14 1 0.04
15 7 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAAAATATATAAA
Found at i:75731 original size:19 final size:19
Alignment explanation
Indices: 75689--75732 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
75679 TTTTCTTTTA
*
75689 AAATTTTATGGTATTTAAT
1 AAATTTTATAGTATTTAAT
*
75708 AAATTTTATAG-ATTTCAT
1 AAATTTTATAGTATTTAAT
75726 ATAATTT
1 A-AATTT
75733 AAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (19 bp):
AAATTTTATAGTATTTAAT
Found at i:84244 original size:28 final size:28
Alignment explanation
Indices: 84200--84254 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
84190 AAATGAGCAT
* *
84200 CATGACCTTTGGATCAACAGGGAGTAAG
1 CATGACCTTCGGATCAACAAGGAGTAAG
84228 CATGACCTTC-GAGTCAACAAGGAGTAA
1 CATGACCTTCGGA-TCAACAAGGAGTAA
84255 ATCAAATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (28 bp):
CATGACCTTCGGATCAACAAGGAGTAAG
Found at i:84993 original size:21 final size:21
Alignment explanation
Indices: 84964--85015 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
84954 GGAGTTTTTA
84964 GTATCGGTAGAAG-CATGACAT
1 GTATCGGTAGAAGTCAT-ACAT
* *
84985 GTTTCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
85006 GTATCGGTAG
1 GTATCGGTAG
85016 TATTGTCCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:89815 original size:15 final size:17
Alignment explanation
Indices: 89780--89815 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
89770 TTTAAATTTT
89780 TTGAATTTTTTTATTGA
1 TTGAATTTTTTTATTGA
89797 -TGAA-TTTTTTATT-A
1 TTGAATTTTTTTATTGA
89811 TTGAA
1 TTGAA
89816 AAAATTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.06
15 13 0.72
16 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (17 bp):
TTGAATTTTTTTATTGA
Found at i:92893 original size:21 final size:21
Alignment explanation
Indices: 92868--92913 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
92858 AAATTGTAGT
*
92868 TAAAATT-TTAAATTAAAAAAA
1 TAAAATTCTTAAAAT-AAAAAA
92889 TAAAATTCTTAAAATAAAAAA
1 TAAAATTCTTAAAATAAAAAA
92910 TAAA
1 TAAA
92914 TTTAAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAATTCTTAAAATAAAAAA
Found at i:93232 original size:31 final size:30
Alignment explanation
Indices: 93172--93236 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
93162 TCCTCTATAT
* *
93172 ATATTTTTATCATTTTAATCATTTTTGTTA
1 ATATTTTTATCATTTTAATCACTTGTGTTA
** *
93202 CATATTTTTATCATTTTGGTCGCTTGTGTTA
1 -ATATTTTTATCATTTTAATCACTTGTGTTA
93233 ATAT
1 ATAT
93237 CATTACATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (30 bp):
ATATTTTTATCATTTTAATCACTTGTGTTA
Found at i:93851 original size:21 final size:22
Alignment explanation
Indices: 93827--93868 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
93817 ACAATCGATC
93827 CCAA-TATTTTTTTTGTTTTGA
1 CCAATTATTTTTTTTGTTTTGA
93848 CCAATTTATTTTTTTTGTTTT
1 CCAA-TTATTTTTTTTGTTTT
93869 ATGTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
23 15 0.79
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (22 bp):
CCAATTATTTTTTTTGTTTTGA
Found at i:95838 original size:2 final size:2
Alignment explanation
Indices: 95831--95872 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
95821 GATCCTGCAC
95831 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
95873 TACTTTCACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:98469 original size:17 final size:18
Alignment explanation
Indices: 98422--98461 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
98412 AAAAAATAAA
98422 ATTT-AAAATAATTATAC
1 ATTTAAAAATAATTATAC
98439 ATTTAAAAATAATTATA-
1 ATTTAAAAATAATTATAC
98456 ATTTAA
1 ATTTAA
98462 TAGAAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAAAATAATTATAC
Found at i:101991 original size:49 final size:49
Alignment explanation
Indices: 101938--102414 Score: 258
Period size: 49 Copynumber: 9.7 Consensus size: 49
101928 TGAACTTTAG
* * * *
101938 GGTATAAGATTCGCCATTGCAGCTTCAATCTTTCCCATCACATCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCTAA
* ** * * * *
101987 GGTATAAGGTTCGCCGTTATGGCTTCAACCTTTCCCTTTATATCTCCAT
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCTAA
* * ** * * ** * * *
102036 GGTACAGGATTCATCGTTACGGCCTCAATATTTCCCATTATTTTTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCTAA
* * * *
102085 GGTATAAGGTTTGCCGTTTCGGCTTCAACCTTT-CCATCCATATCT-TCAT
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCAT-CATATCTCT-AA
** * * * * ** *
102134 GGTATCGGATTCGCCATTACGGCTTCAATCTTTCTCATCACGTCTCTAG
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCTAA
** * ** * * *
102183 GGTACGAGGTTCGCCGTTGCGGCTTTGACCTTTCCCTTAATATCT-TCAT
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCT-AA
* * * ** * * *
102232 GGTATAGGATTTGCTGTTGCTACTTCAATCTTTCCCATTATTTCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCTAA
* * * * * * * *
102281 GGCATACGGTTTGTCGTTGCGGCTTCAACCTTTCCCTTCATATCTCCAT
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCTAA
* * * * * ** * *
102330 GGTACAGGATTTGCCATTGCGGCCTCAGTCTTTCCCATTATCTCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCTAA
* * * *
102379 GGTACAAGATTCACCTTTGTGGCTTCAACCTTTCCC
1 GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCC
102415 TCCAAACCTG
Statistics
Matches: 307, Mismatches: 115, Indels: 12
0.71 0.26 0.03
Matches are distributed among these distances:
48 6 0.02
49 296 0.96
50 5 0.02
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (49 bp):
GGTATAAGATTCGCCGTTGCGGCTTCAACCTTTCCCATCATATCTCTAA
Found at i:102070 original size:98 final size:98
Alignment explanation
Indices: 101945--102415 Score: 444
Period size: 98 Copynumber: 4.8 Consensus size: 98
101935 TAGGGTATAA
* * * * * *
101945 GATTCGCCATTGCAGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCGTTATGGC
1 GATTCGCCATTACGGCCTCAATCTTTCCCATTACTTCTCTAAGGTATAAGGTTCGCCGTTGTGGC
*
102010 TTCAACCTTTCCCTTTATATCTCCATGGTACAG
66 TTCAACCTTTCCCTTCATATCTCCATGGTACAG
** * * * * *
102043 GATTCATCGTTACGGCCTCAATATTTCCCATTATTTTTCTAAGGTATAAGGTTTGCCGTT-TCGG
1 GATTCGCCATTACGGCCTCAATCTTTCCCATTACTTCTCTAAGGTATAAGGTTCGCCGTTGT-GG
* * *
102107 CTTCAACCTTTCCATCCATATCTTCATGGTATC-G
65 CTTCAACCTTTCCCTTCATATCTCCATGGTA-CAG
* * * * * ** *
102141 GATTCGCCATTACGGCTTCAATCTTTCTCATCACGTCTCTAGGGTACGAGGTTCGCCGTTGCGGC
1 GATTCGCCATTACGGCCTCAATCTTTCCCATTACTTCTCTAAGGTATAAGGTTCGCCGTTGTGGC
** * * *
102206 TTTGACCTTTCCCTTAATATCTTCATGGTATAG
66 TTCAACCTTTCCCTTCATATCTCCATGGTACAG
* ** * ** * * * * * * *
102239 GATTTGCTGTTGCTACTTCAATCTTTCCCATTATTTCTCTAAGGCATACGGTTTGTCGTTGCGGC
1 GATTCGCCATTACGGCCTCAATCTTTCCCATTACTTCTCTAAGGTATAAGGTTCGCCGTTGTGGC
102304 TTCAACCTTTCCCTTCATATCTCCATGGTACAG
66 TTCAACCTTTCCCTTCATATCTCCATGGTACAG
* * * * * * *
102337 GATTTGCCATTGCGGCCTCAGTCTTTCCCATTA-TCTCTCTAAGGTACAAGATTCACCTTTGTGG
1 GATTCGCCATTACGGCCTCAATCTTTCCCATTACT-TCTCTAAGGTATAAGGTTCGCCGTTGTGG
102401 CTTCAACCTTTCCCT
65 CTTCAACCTTTCCCT
102416 CCAAACCTGT
Statistics
Matches: 294, Mismatches: 74, Indels: 10
0.78 0.20 0.03
Matches are distributed among these distances:
97 2 0.01
98 291 0.99
99 1 0.00
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (98 bp):
GATTCGCCATTACGGCCTCAATCTTTCCCATTACTTCTCTAAGGTATAAGGTTCGCCGTTGTGGC
TTCAACCTTTCCCTTCATATCTCCATGGTACAG
Found at i:102235 original size:196 final size:196
Alignment explanation
Indices: 101945--102415 Score: 554
Period size: 196 Copynumber: 2.4 Consensus size: 196
101935 TAGGGTATAA
* * *
101945 GATTCGCCATTGCAGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCGTTATGGC
1 GATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTACGGC
* *
102010 TTCAACCTTTCCCTTTATATCTCCATGGTACAGGA-TT-CATCGTTACGGCCTCAATATTTCCCA
66 TTCAACCTTTCCCTTAATATCTCCATGGTACAGGATTTGC-T-GTTACGACCTCAATATTTCCCA
* * * *
102073 TTATTTTTCTAAGGTATAAGGTTTGCCGTTTCGGCTTCAACCTTTCCATCCATATCTTCATGGTA
129 TTATTTCTCTAAGGCATAAGGTTTGCCGTTGCGGCTTCAACCTTTCCATCCATATCTCCATGGTA
102138 TC-G
194 -CAG
* * * * * *
102141 GATTCGCCATTACGGCTTCAATCTTTCTCATCACGTCTCTAGGGTACGAGGTTCGCCGTTGCGGC
1 GATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTACGGC
** * * * * * *
102206 TTTGACCTTTCCCTTAATATCTTCATGGTATAGGATTTGCTGTTGCTACTTCAATCTTTCCCATT
66 TTCAACCTTTCCCTTAATATCTCCATGGTACAGGATTTGCTGTTACGACCTCAATATTTCCCATT
* * * *
102271 ATTTCTCTAAGGCATACGGTTTGTCGTTGCGGCTTCAACCTTTCCCTTCATATCTCCATGGTACA
131 ATTTCTCTAAGGCATAAGGTTTGCCGTTGCGGCTTCAACCTTTCCATCCATATCTCCATGGTACA
102336 G
196 G
* * * * * * * **
102337 GATTTGCCATTGCGGCCTCAGTCTTTCCCATTATC-TCTCTAAGGTACAAGATTCACCTTTGTGG
1 GATTCGCCATTGCGGCTTCAATCTTTCCCATCA-CATCTCTAAGGTACAAGGTTCGCCGTTACGG
102401 CTTCAACCTTTCCCT
65 CTTCAACCTTTCCCT
102416 CCAAACCTGT
Statistics
Matches: 230, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
195 1 0.00
196 224 0.97
197 4 0.02
198 1 0.00
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (196 bp):
GATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTACGGC
TTCAACCTTTCCCTTAATATCTCCATGGTACAGGATTTGCTGTTACGACCTCAATATTTCCCATT
ATTTCTCTAAGGCATAAGGTTTGCCGTTGCGGCTTCAACCTTTCCATCCATATCTCCATGGTACA
G
Found at i:111625 original size:13 final size:13
Alignment explanation
Indices: 111607--111631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111597 TCAAGTTAGG
111607 ATTTAGTTTTATA
1 ATTTAGTTTTATA
111620 ATTTAGTTTTAT
1 ATTTAGTTTTAT
111632 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
ATTTAGTTTTATA
Found at i:133016 original size:46 final size:46
Alignment explanation
Indices: 132961--133048 Score: 176
Period size: 46 Copynumber: 1.9 Consensus size: 46
132951 GAAGTTGTGG
132961 TTGATTTTCAAGTCCCACAAAGATTTGTACTCAACTCGATGAGTGA
1 TTGATTTTCAAGTCCCACAAAGATTTGTACTCAACTCGATGAGTGA
133007 TTGATTTTCAAGTCCCACAAAGATTTGTACTCAACTCGATGA
1 TTGATTTTCAAGTCCCACAAAGATTTGTACTCAACTCGATGA
133049 AGGAAGATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (46 bp):
TTGATTTTCAAGTCCCACAAAGATTTGTACTCAACTCGATGAGTGA
Found at i:151048 original size:6 final size:6
Alignment explanation
Indices: 151037--151068 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
151027 GCTACTTTGG
151037 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
151069 GGGCGGTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:164763 original size:226 final size:226
Alignment explanation
Indices: 164369--164822 Score: 800
Period size: 226 Copynumber: 2.0 Consensus size: 226
164359 TGAAGTGCGT
*
164369 ATCTACTACAAGAGTAGCAATGTTGGTAAATAGGTCGGCGATGAATGAATTCAAAATGGGTAAAG
1 ATCTACTACAAGAGTAGCAATGTTGGTAAATAGGTCGGCAATGAATGAATTCAAAATGGGTAAAG
**
164434 GTCTTTGTCAATGTGATCCACTATCGCCTTTTCTATTTATACTGGTTACAAAAGTATTGCATCTG
66 GTCTTCATCAATGTGATCCACTATCGCCTTTTCTATTTATACTGGTTACAAAAGTATTGCATCTG
* * *
164499 ATGTTGGTGAAAGCGGAAGGGTTGGTGCTAATCGGTGGGATTCAAGATGTCATAATGTATAGATC
131 ATGTTAGTGAAAGCGGAAGGGCTGGTGCTAATCGGTGGGATTCAAGATGTCATAACGTATAGATC
164564 ATTTTCCCATTTACAGTTTGCGGACGATACA
196 ATTTTCCCATTTACAGTTTGCGGACGATACA
* *
164595 ATCTACTACAAGAGTAGCAATGTTGGTAAATGGGTCGGCAATGAATGAATTCAGAATGGGTAAAG
1 ATCTACTACAAGAGTAGCAATGTTGGTAAATAGGTCGGCAATGAATGAATTCAAAATGGGTAAAG
* *
164660 GTCTTCATCAGTGTGATCCATTATCGCCTTTTCTATTTATACTGGTTACAAAAGTATTGCATCTG
66 GTCTTCATCAATGTGATCCACTATCGCCTTTTCTATTTATACTGGTTACAAAAGTATTGCATCTG
*
164725 ATGTTAGTGAAAGCGGAAGGGCTGGTGCTGATCGGTGGGATTCAAGATGTCATAACGTATAGATC
131 ATGTTAGTGAAAGCGGAAGGGCTGGTGCTAATCGGTGGGATTCAAGATGTCATAACGTATAGATC
*
164790 ATTTTCCCATTTACAGTTTGCGGATGATACA
196 ATTTTCCCATTTACAGTTTGCGGACGATACA
164821 AT
1 AT
164823 TTTGTTTTTG
Statistics
Matches: 216, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
226 216 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (226 bp):
ATCTACTACAAGAGTAGCAATGTTGGTAAATAGGTCGGCAATGAATGAATTCAAAATGGGTAAAG
GTCTTCATCAATGTGATCCACTATCGCCTTTTCTATTTATACTGGTTACAAAAGTATTGCATCTG
ATGTTAGTGAAAGCGGAAGGGCTGGTGCTAATCGGTGGGATTCAAGATGTCATAACGTATAGATC
ATTTTCCCATTTACAGTTTGCGGACGATACA
Found at i:168278 original size:42 final size:42
Alignment explanation
Indices: 168183--168319 Score: 145
Period size: 42 Copynumber: 3.2 Consensus size: 42
168173 GATGTATAAA
* * * * * * *
168183 AAGGAAGACTAATGTCTCAGGTTGAGCATAAGAATTTG-TATA
1 AAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGAT-TT
*
168225 AATGGAAGACTCATGTCTCGGGATGGGAATGA-AATTATGA-TT
1 AA-GGAAGACTCATGTCTCGGGATGAGAATGAGAA-TATGATTT
168267 AGAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATTT
1 A-AGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATTT
168310 AAGGAAGACT
1 AAGGAAGACT
168320 TATGAGTCGA
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
42 48 0.60
43 32 0.40
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.26
Consensus pattern (42 bp):
AAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATTT
Found at i:173825 original size:23 final size:23
Alignment explanation
Indices: 173793--173842 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
173783 TTCATAAAAA
* *
173793 GTTTTTTCTCTGCCTGTTAGCAC
1 GTTTTCTCTCTACCTGTTAGCAC
*
173816 GTTTTCTCTCTACTTGTTAGCAC
1 GTTTTCTCTCTACCTGTTAGCAC
173839 GTTT
1 GTTT
173843 GTTTAATCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.16, T:0.50
Consensus pattern (23 bp):
GTTTTCTCTCTACCTGTTAGCAC
Found at i:179907 original size:11 final size:11
Alignment explanation
Indices: 179883--179915 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
179873 TAAATGAACA
179883 GAAC-GTTCGAT
1 GAACTGTTCG-T
179894 GAACTGTTCGT
1 GAACTGTTCGT
179905 GAACTGTTCGT
1 GAACTGTTCGT
179916 TTAACATTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.33
Consensus pattern (11 bp):
GAACTGTTCGT
Found at i:180262 original size:23 final size:23
Alignment explanation
Indices: 180219--180262 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
180209 CAATGTTCGT
*
180219 GAACATATTCATTTAACTTAATC
1 GAACATATTCATTGAACTTAATC
*
180242 GAACATGTTCA-TGAACATTAA
1 GAACATATTCATTGAAC-TTAA
180263 ACAAACAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (23 bp):
GAACATATTCATTGAACTTAATC
Found at i:187266 original size:25 final size:24
Alignment explanation
Indices: 187225--187276 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
187215 GACCTTCCTA
* *
187225 AGAAAAATCTCCACTAACTAAAATC
1 AGAAAAATATCCACTAA-AAAAATC
187250 AGAAAAATAT-CACCTAAAAAAATC
1 AGAAAAATATCCA-CTAAAAAAATC
187274 AGA
1 AGA
187277 TTTGACCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.17
Consensus pattern (24 bp):
AGAAAAATATCCACTAAAAAAATC
Found at i:188345 original size:67 final size:67
Alignment explanation
Indices: 188237--188373 Score: 256
Period size: 67 Copynumber: 2.0 Consensus size: 67
188227 GACAATTATA
* *
188237 GCACAATAAAACATGCAGAAATAGTAGTTACAATCTGGGGACTTTGGTATGCTCGTAATAAACTA
1 GCACAATAAAACATGCAGAAATAGCAGTTACAATCTAGGGACTTTGGTATGCTCGTAATAAACTA
188302 AT
66 AT
188304 GCACAATAAAACATGCAGAAATAGCAGTTACAATCTAGGGACTTTGGTATGCTCGTAATAAACTA
1 GCACAATAAAACATGCAGAAATAGCAGTTACAATCTAGGGACTTTGGTATGCTCGTAATAAACTA
188369 AT
66 AT
188371 GCA
1 GCA
188374 TGAAGGTATT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (67 bp):
GCACAATAAAACATGCAGAAATAGCAGTTACAATCTAGGGACTTTGGTATGCTCGTAATAAACTA
AT
Found at i:189179 original size:25 final size:25
Alignment explanation
Indices: 189151--189206 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
189141 ATGTTTATTT
**
189151 TGGTTTCTTGATTTTGTGGGTTTGA
1 TGGTTTCTTGATTTTGTGGGTAGGA
189176 TGGTTTCTTGATTTTGTGGGTAGGA
1 TGGTTTCTTGATTTTGTGGGTAGGA
189201 TGGTTT
1 TGGTTT
189207 GTGGGTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.09, C:0.04, G:0.34, T:0.54
Consensus pattern (25 bp):
TGGTTTCTTGATTTTGTGGGTAGGA
Found at i:196659 original size:18 final size:18
Alignment explanation
Indices: 196632--196667 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
196622 ATGGATGTCC
196632 ATCAACATCAAGATAAAG
1 ATCAACATCAAGATAAAG
*
196650 ATCAAGATCAAGATAAAG
1 ATCAACATCAAGATAAAG
196668 TTTAGTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.17
Consensus pattern (18 bp):
ATCAACATCAAGATAAAG
Found at i:203465 original size:4 final size:4
Alignment explanation
Indices: 203456--203496 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
203446 GAAGAAGAAG
203456 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG- AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
203497 CGACCAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:203947 original size:27 final size:27
Alignment explanation
Indices: 203879--203934 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
203869 TATTTAAAGA
203879 AATATATAAAAAAATGACTTACAATTT
1 AATATATAAAAAAATGACTTACAATTT
203906 AATATATAAAAAAATGACTTACAATTT
1 AATATATAAAAAAATGACTTACAATTT
203933 AA
1 AA
203935 AGTTAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (27 bp):
AATATATAAAAAAATGACTTACAATTT
Found at i:204690 original size:16 final size:16
Alignment explanation
Indices: 204669--204702 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
204659 AAATTACTTA
204669 AATTTACTTATT-AATT
1 AATTTA-TTATTAAATT
204685 AATTTATTATTAAATT
1 AATTTATTATTAAATT
204701 AA
1 AA
204703 AGTTTTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTATTATTAAATT
Found at i:208349 original size:21 final size:21
Alignment explanation
Indices: 208322--208373 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
208312 ATAGTGTAGA
*
208322 CTTCTACCGATACGTA-TGACG
1 CTTCTACCGATACG-AGTGAAG
* *
208343 GTTCTACTGATACGAGTGAAG
1 CTTCTACCGATACGAGTGAAG
208364 CTTCTACCGA
1 CTTCTACCGA
208374 AACAAATGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (21 bp):
CTTCTACCGATACGAGTGAAG
Found at i:217338 original size:34 final size:34
Alignment explanation
Indices: 217299--217364 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
217289 CAAAATATCA
*
217299 TTATTTTAACAAAGTAATGAATAATT-ATTTAATC
1 TTATTTTAACAAAGTAATAAAT-ATTAATTTAATC
**
217333 TTATTTTAGTAAAGTAATAAATATTAATTTAA
1 TTATTTTAACAAAGTAATAAATATTAATTTAA
217365 GGGTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (34 bp):
TTATTTTAACAAAGTAATAAATATTAATTTAATC
Found at i:218322 original size:18 final size:18
Alignment explanation
Indices: 218299--218335 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
218289 TAATAAAGTG
218299 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
218317 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
218335 T
1 T
218336 AAAACTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Done.