Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015016.1 Kokia drynarioides strain JFW-HI SEQ_130060, 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: 243239
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 550 characters in sequence are not A, C, G, or T
Found at i:468 original size:105 final size:105
Alignment explanation
Indices: 286--709 Score: 830
Period size: 105 Copynumber: 4.0 Consensus size: 105
276 AAACTAGTTT
286 TTTAGTTGGCTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
1 TTTAGTTGGCTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
351 AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
66 AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
*
391 TTTAGTTGGYTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
1 TTTAGTTGGCTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
456 AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
66 AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
496 TTTAGTTGGCTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
1 TTTAGTTGGCTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
561 AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
66 AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
*
601 TTTAGTTGGTTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
1 TTTAGTTGGCTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
666 AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
66 AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
706 TTTA
1 TTTA
710 CAGTTGTAAT
Statistics
Matches: 316, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 316 1.00
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (105 bp):
TTTAGTTGGCTGTCGTCTTGCTAATACAATTTTCTCTGTACATAATTTTGTTGTTGAATGTAATT
AATATTGGATCTAGAGCCCTAAGTATAGTATTTTCGTCTA
Found at i:6346 original size:3 final size:3
Alignment explanation
Indices: 6340--6364 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6330 GTATTTTCAG
6340 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
6365 GTTCAAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:7165 original size:27 final size:27
Alignment explanation
Indices: 7112--7167 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
7102 CGATTACATA
* *
7112 AATAAAAAAAAATCATTTATTTAAATT
1 AATAAAAAAAAATCATTAAATTAAATT
*
7139 AATAAAATAAAATACATTAAATT-AATT
1 AATAAAAAAAAAT-CATTAAATTAAATT
7166 AA
1 AA
7168 AATAAAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
AATAAAAAAAAATCATTAAATTAAATT
Found at i:7451 original size:30 final size:30
Alignment explanation
Indices: 7410--7470 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
7400 AAAAAGATTA
* *
7410 AGTATCAAATTAAGAAGAAGTGTCAAGTTC
1 AGTACCAAATTAAGAAAAAGTGTCAAGTTC
7440 AGTACCAAATTAAGAAAAAGTGTCAAGTTC
1 AGTACCAAATTAAGAAAAAGTGTCAAGTTC
7470 A
1 A
7471 AACATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (30 bp):
AGTACCAAATTAAGAAAAAGTGTCAAGTTC
Found at i:8217 original size:60 final size:60
Alignment explanation
Indices: 8052--8397 Score: 301
Period size: 60 Copynumber: 5.7 Consensus size: 60
8042 TTTGTCAAAT
* *
8052 AAAAATTTAAATTTTTTTGTGTTGGTCATTGCATGGCCGACACCCCCCTTTTTTTATCTAG-TAA
1 AAAAATTCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACA-CCCCC--TTTTTATC-AGAT-A
** * ** * * *
8116 AAAAATT-ATTTTTTTTTGTGTTGGCCAGTATATGACTGACACCCCCTTTTTGTCAGATA
1 AAAAATTCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACCCCCTTTTTATCAGATA
* * * * * *
8175 AAAAATTTAAATTTTTTGGTGTTGGTCATTGCATGGCCGACA--CCATGTTCTATCTGATA
1 AAAAATTCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACCCCCT-TTTTATCAGATA
* * * * * *
8234 AAAAATTCAAATTTTTTTGGTATTGGTCA-TGCATTGGTCGACA-CCACTTATTATCTGATA
1 AAAAATTCAAATTTTTTT-GTGTTGGCCATTGCA-TGGCCGACACCCCCTTTTTATCAGATA
* * * *
8294 AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACCACCTTTCTATCTGATAA
1 AAAAATTCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACCCCCTTTTTATCAGAT-A
*
8355 AAAAATTCAAATATTTTTTGTGTTGACCA-TGCATTGGCCGACA
1 AAAAATTCAAAT-TTTTTTGTGTTGGCCATTGCA-TGGCCGACA
8398 TAAACTTTCC
Statistics
Matches: 231, Mismatches: 40, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
58 3 0.01
59 55 0.24
60 93 0.40
61 18 0.08
62 29 0.13
63 26 0.11
64 7 0.03
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (60 bp):
AAAAATTCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACCCCCTTTTTATCAGATA
Found at i:8316 original size:119 final size:120
Alignment explanation
Indices: 8171--8397 Score: 334
Period size: 119 Copynumber: 1.9 Consensus size: 120
8161 CTTTTTGTCA
* * *
8171 GATAAAAAATTTAAATTTTTTGGTGTTGGTCATTGCATGGCCGACACCA-TGTTCTATCTGAT-A
1 GATAAAAAAATCAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACCACT-TTCTATCTGATAA
** *
8234 AAAAATTCAAAT-TTTTTTGGTATTGGTCATGCATTGGTCGACACCACTTATTATCT
65 AAAAATTCAAATATTTTTT-GTATTGACCATGCATTGGCCGACACCACTTATTATCT
*
8290 GATAAAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACCACCTTTCTATCTGATAA
1 GATAAAAAAATCAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACCA-CTTTCTATCTGATAA
*
8355 AAAAATTCAAATATTTTTTGTGTTGACCATGCATTGGCCGACA
65 AAAAATTCAAATATTTTTTGTATTGACCATGCATTGGCCGACA
8398 TAAACTTTCC
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
119 45 0.47
120 11 0.11
121 34 0.35
122 6 0.06
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (120 bp):
GATAAAAAAATCAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACCACTTTCTATCTGATAAA
AAAATTCAAATATTTTTTGTATTGACCATGCATTGGCCGACACCACTTATTATCT
Found at i:13936 original size:97 final size:97
Alignment explanation
Indices: 13815--14253 Score: 676
Period size: 97 Copynumber: 4.6 Consensus size: 97
13805 ATTACATTTA
* *
13815 AAATTATGTTTAAATTATTTAAATAAAAAACTATTATTATATTATAATTTTTATCAAATAATGTA
1 AAATTATGTTTAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTG
* * *
13880 TTGACTTGACAACACATTATTCACTAATTTTT
66 TTGATTTGACAATACATTATTTACTAATTTTT
* * *
13912 AAATTATGTTAAAACTATTAAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTG
1 AAATTATGTTTAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTG
13977 TTGATTTGACAATACATTATTTACTAATTTTT
66 TTGATTTGACAATACATTATTTACTAATTTTT
* *
14009 AAATTATGTTAAAATTATTTAAATAAAAAACTATTATTATATTATAATTTTTATCAAATAATGTG
1 AAATTATGTTTAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTG
**
14074 TTGATTTGACAATACATTATTTACCCATTTTT
66 TTGATTTGACAATACATTATTTACTAATTTTT
* *
14106 AAA--AT-TTTAAATTATTTAAAT-AAAAACTATTATTATTTTACAATTTTTATCAAATAATGCG
1 AAATTATGTTTAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTG
* *
14167 TTGATTTGATAATACATTATTTACAAATTTTT
66 TTGATTTGACAATACATTATTTACTAATTTTT
*
14199 AAA--AT-TTTAAATTATTTAAATAAAAAACTATTATTATTTTACAATTTTTATCAAA
1 AAATTATGTTTAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAA
14254 ATTTATATTT
Statistics
Matches: 321, Mismatches: 20, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
93 87 0.27
94 48 0.15
95 2 0.01
97 184 0.57
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (97 bp):
AAATTATGTTTAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTG
TTGATTTGACAATACATTATTTACTAATTTTT
Found at i:14375 original size:22 final size:22
Alignment explanation
Indices: 14347--14406 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
14337 TGGACCACCC
*
14347 AAATTCCAGCTCACCTAAACCG
1 AAATTCCAGCTCACCAAAACCG
*
14369 AAATTCCAGCTCATCAAAACCG
1 AAATTCCAGCTCACCAAAACCG
*
14391 AAATTCCAGTTCACCA
1 AAATTCCAGCTCACCA
14407 CCACCCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.33, G:0.08, T:0.20
Consensus pattern (22 bp):
AAATTCCAGCTCACCAAAACCG
Found at i:14416 original size:22 final size:22
Alignment explanation
Indices: 14343--14417 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
14333 GCATTGGACC
14343 ACCCAAATTCCAGCTCACCTA-A
1 ACCCAAATTCCAGCTCACC-ACA
* * *
14365 ACCGAAATTCCAGCTCATCAAA
1 ACCCAAATTCCAGCTCACCACA
* * *
14387 ACCGAAATTCCAGTTCACCACC
1 ACCCAAATTCCAGCTCACCACA
14409 ACCCAAATT
1 ACCCAAATT
14418 TCGTTGTTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 1 0.02
22 44 0.98
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.19
Consensus pattern (22 bp):
ACCCAAATTCCAGCTCACCACA
Found at i:14467 original size:20 final size:20
Alignment explanation
Indices: 14419--14460 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
14409 ACCCAAATTT
14419 CGTTGTTGATTGCAGTTGAC
1 CGTTGTTGATTGCAGTTGAC
14439 CGTTGTTGATTGCCA-TTGAC
1 CGTTGTTGATTG-CAGTTGAC
14459 CG
1 CG
14461 ATTTTGACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.14, C:0.19, G:0.29, T:0.38
Consensus pattern (20 bp):
CGTTGTTGATTGCAGTTGAC
Found at i:16817 original size:23 final size:23
Alignment explanation
Indices: 16791--16835 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16781 CCATTTATTT
*
16791 TTTA-AATTTAATTTGTAATTTCG
1 TTTATAATTTAAATT-TAATTTCG
*
16814 TTTATATTTTAAATTTAATTTC
1 TTTATAATTTAAATTTAATTTC
16836 TAATTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTATAATTTAAATTTAATTTCG
Found at i:16824 original size:30 final size:30
Alignment explanation
Indices: 16784--16840 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
16774 ATTTTTTCCA
* *
16784 TTTATTTTTTAAATTTAATTTGTAATTTCG
1 TTTATATTTTAAATTTAATTTCTAATTTCG
16814 TTTATATTTTAAATTTAATTTCTAATT
1 TTTATATTTTAAATTTAATTTCTAATT
16841 ATTATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTATATTTTAAATTTAATTTCTAATTTCG
Found at i:17806 original size:60 final size:60
Alignment explanation
Indices: 17676--18018 Score: 291
Period size: 61 Copynumber: 5.7 Consensus size: 60
17666 GAAATGAGGG
* * ** * * * *
17676 AAAGTTGGTGTCGGCCAAGCAATGACCAATACAACAAAATTTGAATTTTTTTATTAGATA
1 AAAGGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAATTTGAAATTTTTTATCAGATA
* ** ***
17736 GGAAGGTGGTGTCGGCCATGCAATGGTCAACACCCAAAAATTTGTTTTTTTTTATCAGATA
1 -AAAGGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAATTTGAAATTTTTTATCAGATA
** * *
17797 ATTGGTGGTGTCGGCCAATGC-ATGGCCAACACAAAAAAAATTTGAAAATTTTTTATTAGATA
1 AAAGGTGGTGTCGGCC-ATGCAATGGTCAACAC-AAAAAAATTTG-AAATTTTTTATCAGATA
* *** * * *
17859 AAATGTGGTGTCAATCATACAATGGTCAACACAAAAAAATTTG-AATTTTTTATCTGTTA
1 AAAGGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAATTTGAAATTTTTTATCAGATA
* * * *
17918 AAAGG-GATGTCAGCCATGCAATGGTCAACACAAAAAAATTT-AAATTTTTTATCTGACAA
1 AAAGGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAATTTGAAATTTTTTATCAGA-TA
* * * **
17977 AAAGGGGGTGTCGACCATACAATGG-CTAACACCCAAAAATTT
1 AAAGGTGGTGTCGGCCATGCAATGGTC-AACACAAAAAAATTT
18019 TTTTTTATCA
Statistics
Matches: 228, Mismatches: 46, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
58 45 0.20
59 24 0.11
60 51 0.22
61 75 0.33
62 33 0.14
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (60 bp):
AAAGGTGGTGTCGGCCATGCAATGGTCAACACAAAAAAATTTGAAATTTTTTATCAGATA
Found at i:18107 original size:59 final size:59
Alignment explanation
Indices: 18034--18393 Score: 313
Period size: 59 Copynumber: 6.3 Consensus size: 59
18024 TATCAAATAC
* * * * * *
18034 ATGGCCGACACCAAAAAATTTAAGTTTTTTATCTGACAAAACGAGGTGTCGGTCATGCA
1 ATGGCCAACACCAAAAAATTTAAATTTTTTATCAGACAAAAAGGGGTGTCGGCCATGCA
* * *
18093 ATGGCCAACACCAAAAAATTTAAATTTTTTATCTGACAAAAAGGGGGTGTCCGCCATACA
1 ATGGCCAACACCAAAAAATTTAAATTTTTTATCAGACAAAAA-GGGGTGTCGGCCATGCA
* *
18153 ATGGCCAACACC--AAAATTT---TTTTTTACCAGATAAAAAAAGGGGTGTCGGCCATGCA
1 ATGGCCAACACCAAAAAATTTAAATTTTTTATCAG--ACAAAAAGGGGTGTCGGCCATGCA
* *
18209 ATGGTCAACACCAAAAAATTTAAATTTTTTATCAGACAAAAAGGGGTGTTGGCCATGCA
1 ATGGCCAACACCAAAAAATTTAAATTTTTTATCAGACAAAAAGGGGTGTCGGCCATGCA
* * * * ** *
18268 ATAGCCAACACC---AAATTT--TTTTTTTATCTGATAAAAAATACTGGTGTTGGCCAATGC-
1 ATGGCCAACACCAAAAAATTTAAATTTTTTATC--AGACAAAA-AGGGGTGTCGGCC-ATGCA
* * *
18325 ATGGCCAACACTAAAAAGA---AAATTTATT-T--GACAAAAAGGGGTGTCGACCATGCA
1 ATGGCCAACACCAAAAA-ATTTAAATTTTTTATCAGACAAAAAGGGGTGTCGGCCATGCA
*
18379 ATGACCAACACCAAA
1 ATGGCCAACACCAAA
18394 TTTTTTTTTT
Statistics
Matches: 247, Mismatches: 35, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
53 4 0.02
54 31 0.13
55 14 0.06
56 38 0.15
57 27 0.11
58 18 0.07
59 72 0.29
60 32 0.13
61 11 0.04
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (59 bp):
ATGGCCAACACCAAAAAATTTAAATTTTTTATCAGACAAAAAGGGGTGTCGGCCATGCA
Found at i:18139 original size:155 final size:152
Alignment explanation
Indices: 17887--18178 Score: 437
Period size: 155 Copynumber: 1.9 Consensus size: 152
17877 ACAATGGTCA
** *
17887 ACACAAAAAAATTTGAATTTTTTATCTGTTAAAAGGGATGTCAGCCATGCAATGGTCAACACAAA
1 ACACAAAAAAATTTGAATTTTTTATCTGACAAAAGGGATGTCAGCCATGCAATGGCCAACACAAA
*
17952 AAAATTTAAATTTTTTATCTGACAAAAAGGGGGTGT-CGACCATACAATGGCTAACACCCAAAAA
66 AAAATTTAAATTTTTTATCTGACAAAAAGGGGGTGTCCG-CCATACAATGGCCAACA-CC-AAAA
18016 TTTTTTTTTATCAAATACATGGCCG
128 TTTTTTTTTATCAAATACATGGCCG
* * *
18041 ACACCAAAAAATTT-AAGTTTTTTATCTGACAAAACGAGG-TGTCGGTCATGCAATGGCCAACAC
1 ACACAAAAAAATTTGAA-TTTTTTATCTGACAAAA-G-GGATGTCAGCCATGCAATGGCCAACAC
*
18104 CAAAAAATTTAAATTTTTTATCTGACAAAAAGGGGGTGTCCGCCATACAATGGCCAACACCAAAA
63 AAAAAAATTTAAATTTTTTATCTGACAAAAAGGGGGTGTCCGCCATACAATGGCCAACACCAAAA
18169 TTTTTTTTTA
128 TTTTTTTTTA
18179 CCAGATAAAA
Statistics
Matches: 126, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
153 16 0.13
154 30 0.24
155 76 0.60
156 4 0.03
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (152 bp):
ACACAAAAAAATTTGAATTTTTTATCTGACAAAAGGGATGTCAGCCATGCAATGGCCAACACAAA
AAAATTTAAATTTTTTATCTGACAAAAAGGGGGTGTCCGCCATACAATGGCCAACACCAAAATTT
TTTTTTATCAAATACATGGCCG
Found at i:18218 original size:116 final size:115
Alignment explanation
Indices: 18078--18403 Score: 407
Period size: 116 Copynumber: 2.9 Consensus size: 115
18068 GACAAAACGA
*
18078 GGTGTCGGTCATGCAATGGCCAACACCAAAAAATTTAAATTTTTTATCTGACAAAAAGGGGGTGT
1 GGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTAAATTTTTTATCTGACAAAAA-GGGGTGT
* * *
18143 CCGCCATACAATGGCCAACACCAAAATTTTTTTTTACCAGATAAAAAA-AGG
65 -CGCCATGCAATGGCCAACACCAAATTTTTTTTTTACCAGATAAAAAATACG
* *
18194 GGTGTCGGCCATGCAATGGTCAACACCAAAAAATTTAAATTTTTTATCAGACAAAAAGGGGTGTT
1 GGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTAAATTTTTTATCTGACAAAAAGGGGTG-T
* * * * *
18259 GGCCATGCAATAGCCAACACCAAATTTTTTTTTTATCTGATAAAAAATACT
65 CGCCATGCAATGGCCAACACCAAATTTTTTTTTTACCAGATAAAAAATACG
* * *
18310 GGTGTTGGCCAATGC-ATGGCCAACACTAAAAAGA---AAA---TTTATTTGACAAAAAGGGGTG
1 GGTGTCGGCC-ATGCAATGGCCAACACCAAAAA-ATTTAAATTTTTTATCTGACAAAAAGGGGTG
*
18368 TCGACCATGCAATGACCAACACCAAATTTTTTTTTT
64 TCG-CCATGCAATGGCCAACACCAAATTTTTTTTTT
18404 CAAATTATTA
Statistics
Matches: 186, Mismatches: 19, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
110 2 0.01
111 49 0.26
114 3 0.02
115 47 0.25
116 80 0.43
117 5 0.03
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (115 bp):
GGTGTCGGCCATGCAATGGCCAACACCAAAAAATTTAAATTTTTTATCTGACAAAAAGGGGTGTC
GCCATGCAATGGCCAACACCAAATTTTTTTTTTACCAGATAAAAAATACG
Found at i:18332 original size:57 final size:55
Alignment explanation
Indices: 18078--18335 Score: 198
Period size: 56 Copynumber: 4.5 Consensus size: 55
18068 GACAAAACGA
* * * * *
18078 GGTGTCGGTCATGCAATGGCCAACACCAAAAAATTTAAATTTTTTATCTGA-CAAAAAGGG
1 GGTGTTGGCCATGCAATGGCCAACACC---AAATTT--TTTTTTTATC-GATAAAAAAAGG
** * * *
18138 GGTGTCCGCCATACAATGGCCAACACCAAAATTTTTTTTTACCAGATAAAAAAAGG
1 GGTGTTGGCCATGCAATGGCCAACACCAAATTTTTTTTTTATC-GATAAAAAAAGG
* * * * *
18194 GGTGTCGGCCATGCAATGGTCAACACCAAAAAATTTAAATTTTTTATC-AGACAAAAAGG
1 GGTGTTGGCCATGCAATGGCCAACACC---AAATTT--TTTTTTTATCGATAAAAAAAGG
* **
18253 GGTGTTGGCCATGCAATAGCCAACACCAAATTTTTTTTTTATCTGATAAAAAATACT
1 GGTGTTGGCCATGCAATGGCCAACACCAAATTTTTTTTTTATC-GATAAAAAA-AGG
18310 GGTGTTGGCCAATGC-ATGGCCAACAC
1 GGTGTTGGCC-ATGCAATGGCCAACAC
18336 TAAAAAGAAA
Statistics
Matches: 162, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
54 9 0.06
55 10 0.06
56 43 0.27
57 26 0.16
58 4 0.02
59 38 0.23
60 24 0.15
61 8 0.05
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (55 bp):
GGTGTTGGCCATGCAATGGCCAACACCAAATTTTTTTTTTATCGATAAAAAAAGG
Found at i:25381 original size:17 final size:17
Alignment explanation
Indices: 25359--25393 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25349 AACAAATAAT
*
25359 TTAAAAATTATAAAAAA
1 TTAAAAATTAAAAAAAA
*
25376 TTAAAATTTAAAAAAAA
1 TTAAAAATTAAAAAAAA
25393 T
1 T
25394 ATATAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAAATTAAAAAAAA
Found at i:27273 original size:57 final size:57
Alignment explanation
Indices: 27199--27434 Score: 355
Period size: 57 Copynumber: 4.1 Consensus size: 57
27189 TGAAGGTGAA
* * * *
27199 GAAAGTGGTGAAGATGCATATTATGATGATTGGAGGTCTAAACTTTGTAGCAACCATG
1 GAAA-TGGTGAAGATGCATATTTTGATGATAGGAGGTCTAAACTTGGTGGCAACCATG
*
27257 GAAATGGTGAAGATGCATATTTTGATGATAGGAGGTCTAAGCTTGGTGGCAACCATG
1 GAAATGGTGAAGATGCATATTTTGATGATAGGAGGTCTAAACTTGGTGGCAACCATG
* **
27314 GAAATGGTGAAGATGCATATTTTGATGATACGAGGTCTATGCTTGGTGGCAACCATG
1 GAAATGGTGAAGATGCATATTTTGATGATAGGAGGTCTAAACTTGGTGGCAACCATG
* * * *
27371 GAAATGGTGGAGATGCATATTTTGATGATTGGAGGTCTAAACTTAGTGGCAACAATG
1 GAAATGGTGAAGATGCATATTTTGATGATAGGAGGTCTAAACTTGGTGGCAACCATG
27428 GAAATGG
1 GAAATGG
27435 GTTTAGTGGC
Statistics
Matches: 164, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
57 160 0.98
58 4 0.02
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.29
Consensus pattern (57 bp):
GAAATGGTGAAGATGCATATTTTGATGATAGGAGGTCTAAACTTGGTGGCAACCATG
Found at i:27440 original size:24 final size:24
Alignment explanation
Indices: 27413--27458 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
27403 AGGTCTAAAC
27413 TTAGTGGCAACAATGGAAATGGGT
1 TTAGTGGCAACAATGGAAATGGGT
*
27437 TTAGTGGCAACCATGGAAATGG
1 TTAGTGGCAACAATGGAAATGG
27459 TGAAGATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.24
Consensus pattern (24 bp):
TTAGTGGCAACAATGGAAATGGGT
Found at i:27497 original size:81 final size:81
Alignment explanation
Indices: 27359--27512 Score: 256
Period size: 81 Copynumber: 1.9 Consensus size: 81
27349 TCTATGCTTG
* * *
27359 GTGGCAACCATGGAAATGGTGGAGATGCATATTTTGATGATTGGAGGTCTAAACTTAGTGGCAA-
1 GTGGCAACCATGGAAATGGTGAAGATGCATATGTTGATGATTGGAGGTCTAAACTTAGTAGCAAG
27423 CAATGGAAATGGGTTTA
66 C-ATGGAAATGGGTTTA
*
27440 GTGGCAACCATGGAAATGGTGAAGATGCATATGTTGATGATTGGAGGTCTAAGCTTAGTAGCAAG
1 GTGGCAACCATGGAAATGGTGAAGATGCATATGTTGATGATTGGAGGTCTAAACTTAGTAGCAAG
27505 CATGGAAA
66 CATGGAAA
27513 CGAAGAATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
81 67 0.99
82 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (81 bp):
GTGGCAACCATGGAAATGGTGAAGATGCATATGTTGATGATTGGAGGTCTAAACTTAGTAGCAAG
CATGGAAATGGGTTTA
Found at i:40723 original size:31 final size:31
Alignment explanation
Indices: 40687--40826 Score: 94
Period size: 31 Copynumber: 4.6 Consensus size: 31
40677 AAAAGATTAG
*
40687 GTACCAAATTAGGAAAAAGAGTCAAGTTTAT
1 GTACCAAATTAGGAAAAAGAGTCAAGTTTAA
**
40718 GTACCAAATT-GGACCCCAA-A---AAGTTTAA
1 GTACCAAATTAGGA--AAAAGAGTCAAGTTTAA
* * ** * *
40746 ATACCAACTTAAAAAGAAAGTGTCAAGTTTAG
1 GTACCAAATTAGGAA-AAAGAGTCAAGTTTAA
* *
40778 GTACCAAATTAGAAAAAAGTGTCAAGTTTAA
1 GTACCAAATTAGGAAAAAGAGTCAAGTTTAA
*
40809 GTATCAAATT-GGACAAAA
1 GTACCAAATTAGGA-AAAA
40827 AATTAGGTAC
Statistics
Matches: 83, Mismatches: 17, Indels: 18
0.70 0.14 0.15
Matches are distributed among these distances:
28 17 0.20
29 1 0.01
30 5 0.06
31 39 0.47
32 21 0.25
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.24
Consensus pattern (31 bp):
GTACCAAATTAGGAAAAAGAGTCAAGTTTAA
Found at i:40775 original size:32 final size:31
Alignment explanation
Indices: 40738--40818 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
40728 GGACCCCAAA
*
40738 AAGTTTAAATACCAACTTAAAAAGAAAGTGTC
1 AAGTTTAAATACCAAATTAAAAA-AAAGTGTC
** *
40770 AAGTTTAGGTACCAAATTAGAAAAAAGTGTC
1 AAGTTTAAATACCAAATTAAAAAAAAGTGTC
* *
40801 AAGTTTAAGTATCAAATT
1 AAGTTTAAATACCAAATT
40819 GGACAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 24 0.56
32 19 0.44
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (31 bp):
AAGTTTAAATACCAAATTAAAAAAAAGTGTC
Found at i:55199 original size:16 final size:16
Alignment explanation
Indices: 55178--55241 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
55168 ATAAATAACA
*
55178 TTAATAGTAATAATAG
1 TTAATAATAATAATAG
*
55194 TTAATAATAATAATAA
1 TTAATAATAATAATAG
* *
55210 CTATTTAATAAATAATA-
1 TTA-ATAAT-AATAATAG
*
55227 TTAATATTAATAATA
1 TTAATAATAATAATA
55242 AATAGTAGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 7 0.18
16 19 0.49
17 6 0.15
18 7 0.18
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (16 bp):
TTAATAATAATAATAG
Found at i:55201 original size:3 final size:3
Alignment explanation
Indices: 55179--55302 Score: 52
Period size: 3 Copynumber: 39.0 Consensus size: 3
55169 TAAATAACAT
* * * *
55179 TAA TAG TAA TAA TAGT TAA TAA TAA TAA TAA CTATT TAA TAAA TAA TAT
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA -TA-A TAA T-AA TAA TAA
* * * * * * *
55228 TAA TAT TAA TAA TAAA TAG TAG TAA TAAA TAG CAT TAA TAAA TAT TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA
* *
55276 TAA AAA TAT TAA TAA TAA -AA TGAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA
55303 AAAAGGGAAA
Statistics
Matches: 89, Mismatches: 23, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
2 2 0.02
3 66 0.74
4 21 0.24
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55220 original size:14 final size:12
Alignment explanation
Indices: 55185--55293 Score: 65
Period size: 13 Copynumber: 8.5 Consensus size: 12
55175 ACATTAATAG
55185 TAATAATAGTTAA
1 TAATAATA-TTAA
*
55198 TAATAATAATAA
1 TAATAATATTAA
* *
55210 CTATTTAATAAATAA
1 -TA-ATAAT-ATTAA
*
55225 TATTAATATTAA
1 TAATAATATTAA
* *
55237 TAATAAATAGTAG
1 TAAT-AATATTAA
** *
55250 TAATAAATAGCAT
1 TAAT-AATATTAA
55263 TAATAAATATTAA
1 TAAT-AATATTAA
*
55276 TAAAAATATTAA
1 TAATAATATTAA
55288 TAATAA
1 TAATAA
55294 AATGAATAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
12 23 0.29
13 45 0.57
14 6 0.08
15 5 0.06
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:56662 original size:88 final size:86
Alignment explanation
Indices: 56414--56801 Score: 428
Period size: 88 Copynumber: 4.4 Consensus size: 86
56404 AATATTTTGT
* * * * *
56414 TTTTACCCTCGAACTTCCAAAAA-TCCATTTTTAACACCGAATCTTCC-AAAAATTCCATTTTTA
1 TTTTACCCCCAAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAAATTCCATTTTTA
*
56477 CCCCAAACTTCCAAAAATTCCA
65 CCCGAAACTTCCAAAAATTCCA
* **
56499 TTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACCCCCCGAACTTCCAAAAAA-TCCAATTTT
1 -TTTTACCCCCAAACTTCCAAAAATTCCATTTTTA-CCCCAAAACTTCCAAAAAATTCC-ATTTT
* *
56563 GACCCTAAAACTTCCAAAAATTCCA
63 TACCC-GAAACTTCCAAAAATTCCA
* *
56588 TTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAAATT-CATTTTTG
1 TTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAAATTCCATTTTT-
56652 ACCTCGAAACTTCCAAAAATTCCA
64 ACC-CGAAACTTCCAAAAATTCCA
* ** *
56676 TTTTACCCCCAAACTTCAAAAAATTTAATTTTTGACCCCAAAAC-TCCCAAAAATTCCATTTTTA
1 TTTTACCCCCAAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAAATTCCATTTTTA
* *
56740 CCCTCG-GACTTCCAAAAAATCCCA
65 -CC-CGAAACTTCC-AAAAATTCCA
* * *
56764 TTTTACCCCCGAACCTCCAAAAATTCCATTTTTGCCCC
1 TTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCC
56802 CGGATGTCCA
Statistics
Matches: 260, Mismatches: 29, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
86 22 0.08
87 71 0.27
88 119 0.46
89 48 0.18
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (86 bp):
TTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAAATTCCATTTTTAC
CCGAAACTTCCAAAAATTCCA
Found at i:56802 original size:29 final size:29
Alignment explanation
Indices: 56413--56824 Score: 431
Period size: 29 Copynumber: 14.1 Consensus size: 29
56403 AAATATTTTG
* *
56413 TTTTTACCCTCGAACTTCCAAAAA-TCCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
* * *
56441 TTTTTAACACCGAATCTTCCAAAAATTCCA
1 TTTTT-ACCCCCAAACTTCCAAAAATTCCA
56471 TTTTTA-CCCCAAACTTCCAAAAATTCCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
*
56499 TTTTTACCCCCAAACTTCCAAAAATCCCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
* *
56528 TTTTTACCCCCCGAACTTCCAAAAAATCCAA
1 TTTTTA-CCCCCAAACTTCCAAAAATTCC-A
* **
56559 TTTTGACCCTAAAACTTCCAAAAATTCCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
* *
56588 TTTTGACCCCAAAACTTCCAAAAATTCCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
*
56617 TTTTTACCCCTAAACTTCCAAAAAATT-CA
1 TTTTTACCCCCAAACTTCC-AAAAATTCCA
* *
56646 TTTTTGACCTCGAAACTTCCAAAAATTCCA
1 TTTTT-ACCCCCAAACTTCCAAAAATTCCA
* **
56676 -TTTTACCCCCAAACTTCAAAAAATTTAA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
* *
56704 TTTTTGACCCCAAAACTCCCAAAAATTCCA
1 TTTTT-ACCCCCAAACTTCCAAAAATTCCA
* ** *
56734 TTTTTACCCTCGGACTTCCAAAAAATCCCA
1 TTTTTACCCCCAAACTTCC-AAAAATTCCA
* *
56764 -TTTTACCCCCGAACCTCCAAAAATTCCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
* ** *
56792 TTTTTGCCCCCGGA-TGTCCAAAAACTCCA
1 TTTTTACCCCCAAACT-TCCAAAAATTCCA
56821 TTTT
1 TTTT
56825 CAACCTCCAA
Statistics
Matches: 325, Mismatches: 46, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
28 58 0.18
29 161 0.50
30 100 0.31
31 6 0.02
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
TTTTTACCCCCAAACTTCCAAAAATTCCA
Found at i:56901 original size:27 final size:28
Alignment explanation
Indices: 56869--56930 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
56859 CCGAATTTTC
*
56869 CCAAAATCACCATTTT-GCCCCGAGAAT
1 CCAAAATCACCATTTTACCCCCGAGAAT
* * *
56896 CCAAAATTATCATTTTACCCCCGAGCAT
1 CCAAAATCACCATTTTACCCCCGAGAAT
56924 CCGAAAA
1 CC-AAAA
56931 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 14 0.48
28 11 0.38
29 4 0.14
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (28 bp):
CCAAAATCACCATTTTACCCCCGAGAAT
Found at i:56940 original size:29 final size:28
Alignment explanation
Indices: 56886--56940 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
56876 CACCATTTTG
*
56886 CCCCGAGAATCCAAAATTATCATTTTAC
1 CCCCGAGAATCCAAAAGTATCATTTTAC
* *
56914 CCCCGAGCATCCGAAAAGTCTCATTTT
1 CCCCGAGAATCC-AAAAGTATCATTTT
56941 CAAACCCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.27
Consensus pattern (28 bp):
CCCCGAGAATCCAAAAGTATCATTTTAC
Found at i:62466 original size:24 final size:23
Alignment explanation
Indices: 62416--62466 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
62406 TAGTCCATTT
**
62416 ATTTTTATTTTTAGGAATTTAGT
1 ATTTTTATTTTTAGGAATTTAAA
* *
62439 ATTTTTATTTTTTTGGATTTTAAA
1 ATTTTTA-TTTTTAGGAATTTAAA
62463 ATTT
1 ATTT
62467 AGATACAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (23 bp):
ATTTTTATTTTTAGGAATTTAAA
Found at i:65205 original size:75 final size:74
Alignment explanation
Indices: 65118--65345 Score: 264
Period size: 75 Copynumber: 3.1 Consensus size: 74
65108 AACCGGATTG
* * **
65118 GGTT-CTACAACAGGGGACATAGCTGGAGCCAGCGAAGAAACCGAATCCTCACTGGTTTTTACAG
1 GGTTGCTAAAACAGGGGACATTGC-GGAGCCAGCGAAGAAACCGAATCCTCACCCGTTTTTACA-
*
65182 CA-GAATCATT
64 AAGGAATCATT
* * *
65192 GGTTGCTAAAACAGGGGACATTGCCGGAACCGGCGAAGAAACCGAATCCTCACCCTTTTTTACAA
1 GGTTGCTAAAACAGGGGACATTG-CGGAGCCAGCGAAGAAACCGAATCCTCACCCGTTTTTACAA
65257 AGGAATCATT
65 AGGAATCATT
* * * *
65267 GGTTGCTAAAGCAGGGGGA-ATTGACGGAGCCAGCGAAGAAACCAAATCCTCACCAGTTTTAACA
1 GGTTGCTAAAACA-GGGGACATTG-CGGAGCCAGCGAAGAAACCGAATCCTCACCCGTTTTTACA
* *
65331 ATGGAATCATC
64 AAGGAATCATT
65342 GGTT
1 GGTT
65346 TCAGTAATGG
Statistics
Matches: 132, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
74 5 0.04
75 121 0.92
76 6 0.05
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (74 bp):
GGTTGCTAAAACAGGGGACATTGCGGAGCCAGCGAAGAAACCGAATCCTCACCCGTTTTTACAAA
GGAATCATT
Found at i:65915 original size:21 final size:22
Alignment explanation
Indices: 65891--65933 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
65881 ACCAGATGCT
65891 GTGTTTGG-AAGA-AGGAAAATG
1 GTGTTTGGCAAGAGA-GAAAATG
65912 GTGTTTGGCAAGAGAGAAAATG
1 GTGTTTGGCAAGAGAGAAAATG
65934 AGAGGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 11 0.55
23 1 0.05
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.23
Consensus pattern (22 bp):
GTGTTTGGCAAGAGAGAAAATG
Found at i:65930 original size:22 final size:21
Alignment explanation
Indices: 65891--65933 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
65881 ACCAGATGCT
65891 GTGTTTGGAAGAAGGAAAATG
1 GTGTTTGGAAGAAGGAAAATG
65912 GTGTTTGGCAAG-AGAGAAAATG
1 GTGTTTGG-AAGAAG-GAAAATG
65934 AGAGGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.23
Consensus pattern (21 bp):
GTGTTTGGAAGAAGGAAAATG
Found at i:69136 original size:15 final size:16
Alignment explanation
Indices: 69106--69150 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
69096 TATTGTAATT
69106 AACAATATACATATGGTA
1 AACAATAT--ATATGGTA
69124 AAC-ATATATATGGTA
1 AACAATATATATGGTA
*
69139 ACCAATATATAT
1 AACAATATATAT
69151 ATATAAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 10 0.40
16 8 0.32
17 4 0.16
18 3 0.12
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (16 bp):
AACAATATATATGGTA
Found at i:69323 original size:23 final size:24
Alignment explanation
Indices: 69271--69323 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
69261 TTAGGGAGCG
*
69271 AAATT-AAATTATAATATTTACAA
1 AAATTAAAAATATAATATTTACAA
* *
69294 TAA-TAAAAATATAATTTTTA-AA
1 AAATTAAAAATATAATATTTACAA
69316 AAATTAAA
1 AAATTAAA
69324 TCAAGATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATTAAAAATATAATATTTACAA
Found at i:73855 original size:8 final size:8
Alignment explanation
Indices: 73846--73878 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
73836 GAAAATGATT
*
73846 TATTTTTT
1 TATTTTTA
73854 TATTTTTA
1 TATTTTTA
73862 TATTTTTA
1 TATTTTTA
73870 TATTTTTA
1 TATTTTTA
73878 T
1 T
73879 GGGTTCTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TATTTTTA
Found at i:89751 original size:5 final size:5
Alignment explanation
Indices: 89741--89765 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
89731 TTAGCGTAAT
89741 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
89766 AGTGAGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:92262 original size:29 final size:31
Alignment explanation
Indices: 92190--92264 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
92180 ATCATACTCA
* *
92190 TGGTCACTCAATTATCGATAAATTTATATTT
1 TGGTCACTCAATTATCGATAAAGTTATAATT
* *
92221 TGATCACTAAATTAT-GA-AAAGTTATAATT
1 TGGTCACTCAATTATCGATAAAGTTATAATT
*
92250 TGGTCATTCAATTAT
1 TGGTCACTCAATTAT
92265 TTAGAACGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 22 0.59
30 2 0.05
31 13 0.35
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (31 bp):
TGGTCACTCAATTATCGATAAAGTTATAATT
Found at i:92683 original size:29 final size:31
Alignment explanation
Indices: 92642--92710 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
92632 AACGATCTCG
*
92642 AATAATTAAATGA-TCAAAT-TATAATTT-TT
1 AATAATTAAATGATTAAAATGTA-AATTTATT
92671 AATAATTAAATGATTAAAATGTAAATTTATT
1 AATAATTAAATGATTAAAATGTAAATTTATT
92702 AATAATTAA
1 AATAATTAA
92711 TTAACCATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 13 0.36
30 10 0.28
31 13 0.36
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (31 bp):
AATAATTAAATGATTAAAATGTAAATTTATT
Found at i:92712 original size:15 final size:15
Alignment explanation
Indices: 92663--92712 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
92653 GATCAAATTA
92663 TAATTT-TTAATAAT
1 TAATTTATTAATAAT
* *
92677 TAAATGATTAA-AAT
1 TAATTTATTAATAAT
92691 GTAAATTTATTAATAAT
1 -T-AATTTATTAATAAT
92708 TAATT
1 TAATT
92713 AACCATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 9 0.32
17 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (15 bp):
TAATTTATTAATAAT
Found at i:94390 original size:86 final size:85
Alignment explanation
Indices: 94275--94444 Score: 286
Period size: 86 Copynumber: 2.0 Consensus size: 85
94265 TGAAGTTTCG
* *
94275 AGACTTAAAAAGTCAATTCAAAAAGTATAAAAATTAAAATTGATAAAATCAATATACAGCATAAA
1 AGACTTAAAAAGTCAATTCAAAAAGTATAAAAATTAAAATTGATAAAATCAATAAACAACATAAA
*
94340 GACTACATCTATAACTTACA
66 GACTAAATCTATAACTTACA
* *
94360 AGACTTAAAAAGTCAAATTCAAAAAGTATAAAAATTTAAATTGATCAAATCAATAAACAACATAA
1 AGACTTAAAAAGTC-AATTCAAAAAGTATAAAAATTAAAATTGATAAAATCAATAAACAACATAA
94425 AGACTAAATCTATAACTTAC
65 AGACTAAATCTATAACTTAC
94445 TCGGAATATA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 14 0.18
86 65 0.82
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (85 bp):
AGACTTAAAAAGTCAATTCAAAAAGTATAAAAATTAAAATTGATAAAATCAATAAACAACATAAA
GACTAAATCTATAACTTACA
Found at i:95874 original size:36 final size:36
Alignment explanation
Indices: 95827--95903 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
95817 TACCCAAGTC
*
95827 CTATGCATATTTGAAAGTATGTACCGAGATAAGACT
1 CTATGCATATTTGAAAGTATGTACCAAGATAAGACT
* * **
95863 CTATGCATATTTGGACGTATGTACCAAGATCTGACT
1 CTATGCATATTTGAAAGTATGTACCAAGATAAGACT
95899 CTATG
1 CTATG
95904 AGGACTCTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (36 bp):
CTATGCATATTTGAAAGTATGTACCAAGATAAGACT
Found at i:112597 original size:8 final size:8
Alignment explanation
Indices: 112584--112617 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
112574 ACATTCACAA
112584 TTTAAAAT
1 TTTAAAAT
112592 TTTAAAAT
1 TTTAAAAT
112600 TTTAAAAT
1 TTTAAAAT
112608 TTTAATAAT
1 TTTAA-AAT
112617 T
1 T
112618 AAATATCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 21 0.84
9 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:112988 original size:14 final size:14
Alignment explanation
Indices: 112966--113000 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
112956 TCGATTTTTT
112966 TAATATTAATACAA
1 TAATATTAATACAA
* *
112980 TAATCTTAATATAA
1 TAATATTAATACAA
112994 TAATATT
1 TAATATT
113001 CATAATACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAATACAA
Found at i:120774 original size:24 final size:24
Alignment explanation
Indices: 120742--120793 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
120732 TCATCCAGTC
120742 CACAACTTCCAAGACAAGTACAAT
1 CACAACTTCCAAGACAAGTACAAT
120766 CACAACTTCCAAGACAAGTACAAT
1 CACAACTTCCAAGACAAGTACAAT
120790 CACA
1 CACA
120794 GCCATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (24 bp):
CACAACTTCCAAGACAAGTACAAT
Found at i:123024 original size:4 final size:4
Alignment explanation
Indices: 123015--123041 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
123005 TGACTTGTAC
123015 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
123042 CAAATATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:125057 original size:2 final size:2
Alignment explanation
Indices: 125050--125090 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
125040 ATGAATATTA
125050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
125091 AACCCTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:131790 original size:12 final size:14
Alignment explanation
Indices: 131761--131797 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
131751 CCTTAAGCCA
131761 TGAACCCTAAACCT
1 TGAACCCTAAACCT
131775 TGAACCC-AAA-CT
1 TGAACCCTAAACCT
*
131787 TGAACCATAAA
1 TGAACCCTAAA
131798 GCCCGAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 8 0.38
13 6 0.29
14 7 0.33
ACGTcount: A:0.43, C:0.30, G:0.08, T:0.19
Consensus pattern (14 bp):
TGAACCCTAAACCT
Found at i:132152 original size:75 final size:75
Alignment explanation
Indices: 132029--132178 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
132019 ATGAAAAAAA
132029 TTTCTGAAATGTCATTAAATAATTGAAGAGGGAACATGAATGATGTGCTGGGAAGGACTCATAAA
1 TTTCTGAAATGTCATTAAATAATTGAAGAGGGAACATGAATGATGTGCTGGGAAGGACTCATAAA
132094 ATAACTTCTC
66 ATAACTTCTC
132104 TTTCTGAAATGTCATTAAATAATTGAAGAGGGAACATGAATGATGTGCTGGGAAGGACTCATAAA
1 TTTCTGAAATGTCATTAAATAATTGAAGAGGGAACATGAATGATGTGCTGGGAAGGACTCATAAA
132169 ATAACTTCTC
66 ATAACTTCTC
132179 CTATGTTAAG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (75 bp):
TTTCTGAAATGTCATTAAATAATTGAAGAGGGAACATGAATGATGTGCTGGGAAGGACTCATAAA
ATAACTTCTC
Found at i:135097 original size:12 final size:12
Alignment explanation
Indices: 135076--135169 Score: 56
Period size: 12 Copynumber: 8.2 Consensus size: 12
135066 CGTTTGTTTA
*
135076 ATGTTTACGAAC
1 ATGTTCACGAAC
135088 ATGTTCACGAA-
1 ATGTTCACGAAC
* *
135099 A-ATTAATCGAAC
1 ATGTTCA-CGAAC
135111 ATGTTCACG-A-
1 ATGTTCACGAAC
*
135121 ATATT-ATCGAAC
1 ATGTTCA-CGAAC
*
135133 ATGTTCACGAAA
1 ATGTTCACGAAC
**
135145 AT-TAAACGAAC
1 ATGTTCACGAAC
*
135156 ATGTTCATGAAC
1 ATGTTCACGAAC
135168 AT
1 AT
135170 ATAATTGAAC
Statistics
Matches: 60, Mismatches: 14, Indels: 16
0.67 0.16 0.18
Matches are distributed among these distances:
9 1 0.02
10 9 0.15
11 15 0.25
12 31 0.52
13 4 0.07
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (12 bp):
ATGTTCACGAAC
Found at i:135113 original size:23 final size:23
Alignment explanation
Indices: 135083--135190 Score: 146
Period size: 23 Copynumber: 4.7 Consensus size: 23
135073 TTAATGTTTA
135083 CGAACATGTTCACGAAAATTAAT
1 CGAACATGTTCACGAAAATTAAT
*
135106 CGAACATGTTCACGAATATT-AT
1 CGAACATGTTCACGAAAATTAAT
*
135128 CGAACATGTTCACGAAAATTAAA
1 CGAACATGTTCACGAAAATTAAT
* *
135151 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAAAAT-TAAT
* *
135175 TGAACACGTTCACGAA
1 CGAACATGTTCACGAA
135191 CAATGTTAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
22 21 0.28
23 37 0.50
24 16 0.22
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (23 bp):
CGAACATGTTCACGAAAATTAAT
Found at i:135147 original size:45 final size:47
Alignment explanation
Indices: 135083--135190 Score: 157
Period size: 45 Copynumber: 2.3 Consensus size: 47
135073 TTAATGTTTA
* *
135083 CGAACATGTTCACGAAAATTAATCGAACATGTTCACG-A-ATATTAT
1 CGAACATGTTCACGAAAATTAAACGAACATGTTCACGAACATATAAT
*
135128 CGAACATGTTCACGAAAATTAAACGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAAAATTAAACGAACATGTTCACGAACATATAAT
* *
135175 TGAACACGTTCACGAA
1 CGAACATGTTCACGAA
135191 CAATGTTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 35 0.62
46 1 0.02
47 20 0.36
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (47 bp):
CGAACATGTTCACGAAAATTAAACGAACATGTTCACGAACATATAAT
Found at i:145975 original size:10 final size:10
Alignment explanation
Indices: 145935--146188 Score: 62
Period size: 10 Copynumber: 25.8 Consensus size: 10
145925 TAAAATAATT
*
145935 AAAAATCATA
1 AAAAATTATA
*
145945 AAGAAATCAT-
1 AA-AAATTATA
* *
145955 ACAAATCATA
1 AAAAATTATA
145965 AAAAATTATAA
1 AAAAATTAT-A
** *
145976 AAAAAAAATT
1 AAAAATTATA
* *
145986 AAAAACTATT
1 AAAAATTATA
145996 AAAAATTA-A
1 AAAAATTATA
** *
146005 AATTATTATT
1 AAAAATTATA
*
146015 AAAACTTAT-
1 AAAAATTATA
*
146024 ATAAATTAT-
1 AAAAATTATA
*
146033 AAAACTTAT-
1 AAAAATTATA
**
146042 AAATGTTAT-
1 AAAAATTATA
146051 AAAAATATATA
1 AAAAAT-TATA
** *
146062 TTAAATTTTA
1 AAAAATTATA
*
146072 ATAAATTAT-
1 AAAAATTATA
*
146081 AAAAATTTTA
1 AAAAATTATA
*
146091 TAAAATTAATA
1 AAAAATT-ATA
*
146102 AACATATT-TA
1 AA-AAATTATA
** *
146112 AAATTTTGTA
1 AAAAATTATA
* **
146122 GAAACGTATA
1 AAAAATTATA
146132 AAAAATCT-TA
1 AAAAAT-TATA
* *
146142 AAAACTGAT-
1 AAAAATTATA
*
146151 AAAAATTATT
1 AAAAATTATA
*
146161 AAGAATTATA
1 AAAAATTATA
146171 AAAGAATTA-A
1 AAA-AATTATA
146181 AAAAATTA
1 AAAAATTA
146189 AAATTGATAT
Statistics
Matches: 179, Mismatches: 51, Indels: 29
0.69 0.20 0.11
Matches are distributed among these distances:
9 61 0.34
10 86 0.48
11 28 0.16
12 4 0.02
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAAATTATA
Found at i:146035 original size:18 final size:18
Alignment explanation
Indices: 146009--146103 Score: 68
Period size: 18 Copynumber: 5.1 Consensus size: 18
145999 AATTAAAATT
*
146009 ATTATTAAAACTTATATAA
1 ATTA-TAAAAATTATATAA
*
146028 ATTATAAAACTTATA-AA
1 ATTATAAAAATTATATAA
*
146045 TGTTATAAAAATATATATTAA
1 -ATTATAAAAAT-TATA-TAA
* *
146066 ATTTTAATAAATTATAAAA
1 ATTATAA-AAATTATATAA
*
146085 ATTTTATAAAATTA-ATAA
1 ATTATA-AAAATTATATAA
146103 A
1 A
146104 CATATTTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.03
18 24 0.38
19 22 0.34
20 10 0.16
21 6 0.09
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (18 bp):
ATTATAAAAATTATATAA
Found at i:146036 original size:37 final size:38
Alignment explanation
Indices: 145995--146083 Score: 94
Period size: 37 Copynumber: 2.3 Consensus size: 38
145985 TAAAAACTAT
*
145995 TAAAAATTA-AAATTATTATTAAAACT-TATA-TAAATTA
1 TAAAAATTATAAA-TATTA-TAAAAATATATATTAAATTA
* * *
146032 TAAAACTTATAAATGTTATAAAAATATATATTAAATTT
1 TAAAAATTATAAATATTATAAAAATATATATTAAATTA
146070 TAATAAATTATAAA
1 TAA-AAATTATAAA
146084 AATTTTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 6 0.14
37 16 0.37
38 12 0.28
39 9 0.21
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (38 bp):
TAAAAATTATAAATATTATAAAAATATATATTAAATTA
Found at i:146096 original size:19 final size:19
Alignment explanation
Indices: 146003--146116 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 19
145993 ATTAAAAATT
146003 AAAATTATTATTAAAACTTATA
1 AAAATT-TTA-TAAAA-TTATA
*
146025 TAAA--TTATAAAACTTAT-
1 AAAATTTTATAAAA-TTATA
*
146042 -AAATGTTATAAAAATATATA
1 AAAATTTTAT-AAAAT-TATA
*
146062 TTAAATTTTA-ATAAATTATA
1 -AAAATTTTATA-AAATTATA
146082 AAAATTTTATAAAATTAATA
1 AAAATTTTATAAAATT-ATA
* *
146102 AACATATT-TAAAATT
1 AAAATTTTATAAAATT
146117 TTGTAGAAAC
Statistics
Matches: 77, Mismatches: 5, Indels: 23
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.04
18 15 0.19
19 30 0.39
20 15 0.19
21 4 0.05
22 10 0.13
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (19 bp):
AAAATTTTATAAAATTATA
Found at i:153724 original size:26 final size:25
Alignment explanation
Indices: 153695--153748 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
153685 TTAGTGTTTC
153695 TTTCTTGT-GGAACATTTCCTTTGATT
1 TTTCTT-TAGGAACATTTCCTTT-ATT
*
153721 TTTCTTTAAGGAATATTTCCTTTATT
1 TTTCTTT-AGGAACATTTCCTTTATT
153747 TT
1 TT
153749 CTATCATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 1 0.04
26 11 0.44
27 13 0.52
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (25 bp):
TTTCTTTAGGAACATTTCCTTTATT
Found at i:155371 original size:23 final size:22
Alignment explanation
Indices: 155291--155371 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
155281 GCTGGGGAAA
* **
155291 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAAAGCAAT
* *
155313 CCAATAGGCACACACAATGCAAT
1 -CAGTAGGCACACACAAAGCAAT
** *
155336 CAGTAGGTGCACATAAAGCAAAT
1 CAGTAGGCACACACAAAGC-AAT
155359 CAGTAGGCACACA
1 CAGTAGGCACACA
155372 AGGTGCGAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
22 14 0.30
23 33 0.70
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAAAGCAAT
Found at i:155400 original size:23 final size:23
Alignment explanation
Indices: 155359--155437 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
155349 TAAAGCAAAT
*
155359 CAGTAGGCACAC-AAGGTGCGAAA
1 CAGTAAGCACACGAA-GTGCGAAA
* * *
155382 TAGTAAGCGCATGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
155405 CAGTAAGCACACGAAGTGAGAAAAA
1 CAGTAAGCACACGAAGTGCG--AAA
155430 CAGTAAGC
1 CAGTAAGC
155438 GCGCTTGCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 32 0.71
24 2 0.04
25 11 0.24
ACGTcount: A:0.43, C:0.18, G:0.28, T:0.11
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:157427 original size:29 final size:30
Alignment explanation
Indices: 157384--157460 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
157374 AGGATCAAAC
*
157384 CAAAATTTCAGATATAAAAT-CACACAAAAT
1 CAAAATTT-ATATATAAAATGCACACAAAAT
* **
157414 CAAAATTTATATATACAATTGCACATTAAAT
1 CAAAATTTATATATA-AAATGCACACAAAAT
* *
157445 CAAAGTTCATATATAA
1 CAAAATTTATATATAA
157461 TTTTGAGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 6 0.15
30 12 0.31
31 21 0.54
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (30 bp):
CAAAATTTATATATAAAATGCACACAAAAT
Found at i:157641 original size:29 final size:29
Alignment explanation
Indices: 157591--157647 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
157581 AAATTATATA
*
157591 ATTTTTAAAAGGCTAAATTATGAATTTTT
1 ATTTTTAAAAGGATAAATTATGAATTTTT
*
157620 ATTTTTAGAAGGATCAAA-TATGAATTTT
1 ATTTTTAAAAGGAT-AAATTATGAATTTT
157648 AAATTTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.46
Consensus pattern (29 bp):
ATTTTTAAAAGGATAAATTATGAATTTTT
Found at i:158250 original size:24 final size:23
Alignment explanation
Indices: 158223--158290 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
158213 TTTAAAACCC
158223 AAAATAATAAAAATATAAATTATT
1 AAAATAATAAAAATATAAATTA-T
* *
158247 AAAATAATAAAACTAT-ATTTAT
1 AAAATAATAAAAATATAAATTAT
* *
158269 AATATTATAAAAATATATAATT
1 AAAATAATAAAAATATA-AATT
158291 TAATTTCGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 14 0.39
23 4 0.11
24 18 0.50
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAATAATAAAAATATAAATTAT
Found at i:158285 original size:22 final size:23
Alignment explanation
Indices: 158223--158286 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
158213 TTTAAAACCC
*
158223 AAAATAATAAAAATATAAATTATT
1 AAAATAATAAAAATAT-ATTTATT
*
158247 AAAATAATAAAACTATATTTA-T
1 AAAATAATAAAAATATATTTATT
* *
158269 AATATTATAAAAATATAT
1 AAAATAATAAAAATATAT
158287 AATTTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 16 0.46
23 4 0.11
24 15 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAATAAAAATATATTTATT
Found at i:180756 original size:22 final size:22
Alignment explanation
Indices: 180708--180763 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
180698 ATATCCAAAC
*
180708 AATAACAATAAAATAATAGCAA
1 AATAATAATAAAATAATAGCAA
* * *
180730 CATAATAATAAAATGATAGTAA
1 AATAATAATAAAATAATAGCAA
180752 AATAATAA-AAAA
1 AATAATAATAAAA
180764 GCAATAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (22 bp):
AATAATAATAAAATAATAGCAA
Found at i:180798 original size:21 final size:22
Alignment explanation
Indices: 180761--180801 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
180751 AAATAATAAA
*
180761 AAAGCAATAAGAAAATAACATT
1 AAAGCAACAAGAAAATAACATT
180783 AAAGCAACAA-AAAATAACA
1 AAAGCAACAAGAAAATAACA
180802 AGAAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAGCAACAAGAAAATAACATT
Found at i:195836 original size:29 final size:30
Alignment explanation
Indices: 195804--195862 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
195794 TTTAGTTTAA
*
195804 TGTGCAATTCTATACATG-TATTTTGATTT
1 TGTGCAATTCTATACATGAAATTTTGATTT
* *
195833 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTCTATACATGAAATTTTGATTT
195863 GATCCGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGCAATTCTATACATGAAATTTTGATTT
Found at i:196536 original size:16 final size:16
Alignment explanation
Indices: 196489--196536 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
196479 AGCAATTTAA
*
196489 TTTTTTCTTTTATGTTC
1 TTTTTTC-TTTATTTTC
**
196506 TTTTAACTTTA-TTTC
1 TTTTTTCTTTATTTTC
196521 TTTTTTCTTTATTTTC
1 TTTTTTCTTTATTTTC
196537 ATTCTCTTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 12 0.48
16 8 0.32
17 5 0.20
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTTTCTTTATTTTC
Found at i:207286 original size:20 final size:20
Alignment explanation
Indices: 207258--207300 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
207248 GATTTATTTT
207258 TTTAATTTA-TGTAATTATAC
1 TTTAATTTATTGTAATTAT-C
* *
207278 TTTATTTTATTTTAATTATC
1 TTTAATTTATTGTAATTATC
207298 TTT
1 TTT
207301 TATACTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTAATTTATTGTAATTATC
Found at i:218202 original size:17 final size:17
Alignment explanation
Indices: 218180--218231 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
218170 CCAAACCCAA
*
218180 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
218197 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
218214 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
218231 A
1 A
218232 ATTAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:218225 original size:23 final size:23
Alignment explanation
Indices: 218182--218232 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
218172 AAACCCAAAT
* *
218182 TTTAAATTTTAATTTATTTTAAG
1 TTTAAATTTTAATTTAATTTAAA
*
218205 TTTAAA-TTTATTTTAAATTTAAA
1 TTTAAATTTTAATTT-AATTTAAA
218228 TTTAA
1 TTTAA
218233 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTAAATTTTAATTTAATTTAAA
Found at i:218477 original size:14 final size:15
Alignment explanation
Indices: 218448--218495 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
218438 TTATTTCAGG
*
218448 TTAATAAATGTATAA
1 TTAATAAATATATAA
*
218463 TTAATAATATATAATAT
1 TTAATAA-ATAT-ATAA
*
218480 TTATTAAATATATAA
1 TTAATAAATATATAA
218495 T
1 T
218496 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 11 0.41
16 7 0.26
17 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAATAAATATATAA
Found at i:218508 original size:20 final size:18
Alignment explanation
Indices: 218468--218506 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
218458 TATAATTAAT
**
218468 AATATATAATATTTATTA
1 AATATATAATATTTAAAA
218486 AATATATAATATTTTAAAA
1 AATATATAATA-TTTAAAA
218505 AA
1 AA
218507 ATTAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATATAATATTTAAAA
Found at i:219172 original size:30 final size:30
Alignment explanation
Indices: 219136--219303 Score: 137
Period size: 30 Copynumber: 5.6 Consensus size: 30
219126 CCCAAAAGGT
* **
219136 CCCTAAATTTTCAAAAAATCACGTTTTGAC
1 CCCTAAATTTTCCAAAAATCATATTTTGAC
* * *
219166 CCCTAAACTTTT-TAGAAATCATATTTTAAC
1 CCCTAAA-TTTTCCAAAAATCATATTTTGAC
** *
219196 CTATAAATTTTCCAAAAATCATATTTTAACC
1 CCCTAAATTTTCCAAAAATCATATTTTGA-C
*
219227 CCCTAAACTTTTCC-ATAATCATATTTTGAC
1 CCCTAAA-TTTTCCAAAAATCATATTTTGAC
* ** * *
219257 CCCTAAACTTT-GTAAAATTACATTTTG-C
1 CCCTAAATTTTCCAAAAATCATATTTTGAC
*
219285 CCCCAAATTTTCCAAAAAT
1 CCCTAAATTTTCCAAAAAT
219304 TACATTTTTA
Statistics
Matches: 110, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
28 10 0.09
29 23 0.21
30 48 0.44
31 23 0.21
32 6 0.05
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
CCCTAAATTTTCCAAAAATCATATTTTGAC
Found at i:219247 original size:61 final size:60
Alignment explanation
Indices: 219139--219253 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 60
219129 AAAAGGTCCC
* * *
219139 TAAATTTTCAAAAAATCACGTTTTGACCCCTAAACTTTTTAGAAATCATATTTTAACCTA
1 TAAATTTTCAAAAAATCACATTTTAACCCCTAAACTTTTCAGAAATCATATTTTAACCTA
* * *
219199 TAAATTTTCCAAAAATCATATTTTAACCCCCTAAACTTTTCCA-TAATCATATTTT
1 TAAATTTTCAAAAAATCACATTTTAA-CCCCTAAACTTTT-CAGAAATCATATTTT
219254 GACCCCTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 22 0.47
61 24 0.51
62 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (60 bp):
TAAATTTTCAAAAAATCACATTTTAACCCCTAAACTTTTCAGAAATCATATTTTAACCTA
Found at i:219390 original size:59 final size:59
Alignment explanation
Indices: 219298--219638 Score: 205
Period size: 59 Copynumber: 5.8 Consensus size: 59
219288 CAAATTTTCC
* * * *
219298 AAAAATTACATTTTTACA-TCGAACTTCCAAAAATTAGCATTTTACCCTC-AAACTTCTAA
1 AAAAATCACATTTTTGCACCCGAACTTCCAAAAATTACCATTTTACCCTCTAAA-TTC-AA
* *
219357 AAAAATCACATTTTTGCACCCGAACTTCC-AAAATTACCATTTTA-CCTCTGAATATC-C
1 AAAAATCACATTTTTGCACCCGAACTTCCAAAAATTACCATTTTACCCTCTAAAT-TCAA
* ** *
219414 AAAAATTACAAGTTTG-ACCCTAAACTTCCAAAAATTACCATTTTACCC-CTAAATTTCAA
1 AAAAATCACATTTTTGCACCC-GAACTTCCAAAAATTACCATTTTACCCTCTAAA-TTCAA
* * * *
219473 AAAAATTCACA-TTTTGC-CCTGAACTTTCC-AAAATTACTATTTTACCC-CCAAATGTC-C
1 AAAAA-TCACATTTTTGCACCCGAAC-TTCCAAAAATTACCATTTTACCCTCTAAAT-TCAA
* * * * * * * *
219530 AAAAATTACATTTTTG-ATCTCGAACTTTCTAAAAGTTATCATTTTTCCCTCGAACA-TC-C
1 AAAAATCACATTTTTGCA-CCCGAAC-TTCCAAAAATTACCATTTTACCCTCTAA-ATTCAA
* * *
219589 AAAAATTACCA-TTTTGC-CCTCG-AGTGTCCAAAAATTACCACTTTACCCTC
1 AAAAATCA-CATTTTTGCACC-CGAACT-TCCAAAAATTACCATTTTACCCTC
219639 GAACCTAAAA
Statistics
Matches: 225, Mismatches: 35, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
56 8 0.04
57 32 0.14
58 82 0.36
59 84 0.37
60 18 0.08
61 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (59 bp):
AAAAATCACATTTTTGCACCCGAACTTCCAAAAATTACCATTTTACCCTCTAAATTCAA
Found at i:219544 original size:29 final size:27
Alignment explanation
Indices: 219270--219543 Score: 140
Period size: 28 Copynumber: 9.5 Consensus size: 27
219260 TAAACTTTGT
*
219270 AAAATTACATTTTGCCCCCAAATTTTCCA
1 AAAATTACATTTTACCCCCAAA--TTCCA
** * *
219299 AAAATTACATTTTTACATCGAACTTCCA
1 AAAATTACA-TTTTACCCCCAAATTCCA
* *
219327 AAAATTAGCATTTTACCCTCAAACTTCTAAA
1 AAAATTA-CATTTTACCCCCAAA-TTC--CA
* * * *
219358 AAAATCACATTTTTGCACCCGAACTTCC-
1 AAAATTACA-TTTTAC-CCCCAAATTCCA
* **
219386 AAAATTACCATTTTACCTCTGAATATCCA
1 AAAATTA-CATTTTACCCCCAAAT-TCCA
* *
219415 AAAATTACAAGTTTGA-CCCTAAACTTCCA
1 AAAATTAC-A-TTTTACCCCCAAA-TTCCA
* *
219444 AAAATTACCATTTTACCCCTAAATTTCAAA
1 AAAATTA-CATTTTACCCCCAAA-TTC-CA
* ** *
219474 AAAATTCACATTTTGCCCTGAACTTTCC-
1 AAAATT-ACATTTTACCCCCAA-ATTCCA
219502 AAAATTACTATTTTACCCCCAAATGTCCA
1 AAAATTAC-ATTTTACCCCCAAAT-TCCA
219531 AAAATTACATTTT
1 AAAATTACATTTT
219544 TGATCTCGAA
Statistics
Matches: 186, Mismatches: 38, Indels: 43
0.70 0.14 0.16
Matches are distributed among these distances:
27 7 0.04
28 63 0.34
29 59 0.32
30 37 0.20
31 16 0.09
32 4 0.02
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (27 bp):
AAAATTACATTTTACCCCCAAATTCCA
Found at i:219556 original size:116 final size:115
Alignment explanation
Indices: 219270--219580 Score: 344
Period size: 116 Copynumber: 2.7 Consensus size: 115
219260 TAAACTTTGT
* *
219270 AAAATTACATTTTGCCCCCAAATTTTCCAAAAATTACATTTTT-ACATCGAACTTCCAAAAATTA
1 AAAATTACATTTTACCCCCAAA-TATCCAAAAATTACATTTTTGAC-TCGAACTTCCAAAAATTA
*
219334 GCATTTTACCCTCAAACTTCTAAAAAAATCACATTTTTGCACCCGAACTTCC
64 CCATTTTACCCTCAAACTTCTAAAAAAATCACATTTTTGCACCCGAACTTCC
* ** ** * *
219386 AAAATTACCATTTTACCTCTGAATATCCAAAAATTACAAGTTTGACCCTAAACTTCCAAAAATTA
1 AAAATTA-CATTTTACCCCCAAATATCCAAAAATTACATTTTTGACTC-GAACTTCCAAAAATTA
* *
219451 CCATTTTACCC-CTAAATTTC-AAAAAAATTCACA-TTTTGC-CCTGAACTTTCC
64 CCATTTTACCCTC-AAACTTCTAAAAAAA-TCACATTTTTGCACCCGAAC-TTCC
* * *
219502 AAAATTACTATTTTACCCCCAAATGTCCAAAAATTACATTTTTGATCTCGAACTTTCTAAAAGTT
1 AAAATTAC-ATTTTACCCCCAAATATCCAAAAATTACATTTTTGA-CTCGAAC-TTCCAAAAATT
* *
219567 ATCATTTTTCCCTC
63 ACCATTTTACCCTC
219581 GAACATCCAA
Statistics
Matches: 161, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
115 7 0.04
116 83 0.52
117 70 0.43
118 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (115 bp):
AAAATTACATTTTACCCCCAAATATCCAAAAATTACATTTTTGACTCGAACTTCCAAAAATTACC
ATTTTACCCTCAAACTTCTAAAAAAATCACATTTTTGCACCCGAACTTCC
Found at i:219601 original size:29 final size:29
Alignment explanation
Indices: 219294--219681 Score: 241
Period size: 29 Copynumber: 13.3 Consensus size: 29
219284 CCCCCAAATT
*
219294 TTCCAAAAATTA-CATTTTTA-CATCGAAC
1 TTCCAAAAATTACCA-TTTTACCCTCGAAC
* *
219322 TTCCAAAAATTAGCATTTTACCCTCAAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
* * *
219351 TTCTAAAAA-AATCACATTTTTGCACC-CGAAC
1 TTCCAAAAATTA-C-CA-TTTTAC-CCTCGAAC
219382 TTCC-AAAATTACCATTTTA-CCTCTGAA-
1 TTCCAAAAATTACCATTTTACCCTC-GAAC
* * *
219409 TATCCAAAAATTACAAGTTTGACCCT-AAAC
1 T-TCCAAAAATTACCA-TTTTACCCTCGAAC
* *
219439 TTCCAAAAATTACCATTTTACCC-CTAAAT
1 TTCCAAAAATTACCATTTTACCCTC-GAAC
* *
219468 TTCAAAAAAATT-CACATTTTGCCCT-GAAC
1 TTC-CAAAAATTAC-CATTTTACCCTCGAAC
* * *
219497 TTTCC-AAAATTACTATTTTACCC-CCAAA
1 -TTCCAAAAATTACCATTTTACCCTCGAAC
*
219525 TGTCCAAAAATTA-CATTTTTGA-TCTCGAAC
1 T-TCCAAAAATTACCA-TTTT-ACCCTCGAAC
* * * *
219555 TTTCTAAAAGTTATCATTTTTCCCTCGAAC
1 -TTCCAAAAATTACCATTTTACCCTCGAAC
* * *
219585 ATCCAAAAATTACCATTTTGCCCTCG-AG
1 TTCCAAAAATTACCATTTTACCCTCGAAC
*
219613 TGTCCAAAAATTACCACTTTACCCTCGAAC
1 T-TCCAAAAATTACCATTTTACCCTCGAAC
* ** *
219643 CTAAAAAAATTACCATTTTACCCTCGAGC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
*
219672 ATCCAAAAAT
1 TTCCAAAAAT
219682 CGCATTTTTG
Statistics
Matches: 277, Mismatches: 51, Indels: 63
0.71 0.13 0.16
Matches are distributed among these distances:
26 2 0.01
27 3 0.01
28 56 0.20
29 139 0.50
30 56 0.20
31 19 0.07
32 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCTCGAAC
Found at i:221876 original size:17 final size:18
Alignment explanation
Indices: 221851--221887 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
221841 TCATTTAAAA
221851 ATTATAAATACAT-AAATT
1 ATTATAAATA-ATAAAATT
221869 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
221886 AT
1 AT
221888 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 12 0.67
18 4 0.22
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:224831 original size:22 final size:20
Alignment explanation
Indices: 224795--224835 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
224785 AGATGGTGTA
224795 ATATATATACACATGTATAC
1 ATATATATACACATGTATAC
224815 ATATATATACATGCATGTATA
1 ATATATATACA--CATGTATA
224836 GTTTTACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (20 bp):
ATATATATACACATGTATAC
Found at i:229413 original size:14 final size:16
Alignment explanation
Indices: 229396--229427 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
229386 GACATATACC
229396 TTTTTT-AATAT-TTA
1 TTTTTTAAATATATTA
229410 TTTTTTAAATATATTA
1 TTTTTTAAATATATTA
229426 TT
1 TT
229428 ATTTGTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTTAAATATATTA
Found at i:233757 original size:20 final size:21
Alignment explanation
Indices: 233711--233757 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
233701 TTTACAAATT
* *
233711 TAAATTAAATAATAAAAATAG
1 TAAATAAAATAATAAAAACAG
*
233732 T-TATAAAATAA-AAAAACAG
1 TAAATAAAATAATAAAAACAG
233751 TAAATAA
1 TAAATAA
233758 CAAAGAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 8 0.38
20 12 0.57
21 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (21 bp):
TAAATAAAATAATAAAAACAG
Done.