Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005024.1 Hibiscus syriacus cultivar Beakdansim tig00011277_pilon, 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: 902903
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 3 of 3
Found at i:452174 original size:21 final size:21
Alignment explanation
Indices: 452148--452195 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
452138 GTCCCATATA
*
452148 GATACTTTGAGGGTAGTTATG
1 GATACTTTGAGGGTAGTTATC
452169 GATACTTTGAGGGTAGTTATC
1 GATACTTTGAGGGTAGTTATC
452190 GATACT
1 GATACT
452196 AGAGTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (21 bp):
GATACTTTGAGGGTAGTTATC
Found at i:457171 original size:19 final size:17
Alignment explanation
Indices: 457135--457168 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
457125 TTTTGCCAGA
457135 GCATTTTATTTTGTTTT
1 GCATTTTATTTTGTTTT
457152 GCATATTTATTTT-TTTT
1 GCAT-TTTATTTTGTTTT
457169 TTGTATAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.71
Consensus pattern (17 bp):
GCATTTTATTTTGTTTT
Found at i:467332 original size:20 final size:20
Alignment explanation
Indices: 467298--467350 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
467288 CCCAATGGGG
*
467298 GTATCGATACGAAGGGACCA
1 GTATCGATACCAAGGGACCA
*
467318 GTA-CTGATACCAAGGGTCCA
1 GTATC-GATACCAAGGGACCA
467338 GTATCGATACCAA
1 GTATCGATACCAA
467351 TGTACGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.19
Consensus pattern (20 bp):
GTATCGATACCAAGGGACCA
Found at i:476372 original size:133 final size:132
Alignment explanation
Indices: 476134--476387 Score: 402
Period size: 133 Copynumber: 1.9 Consensus size: 132
476124 TTTAAGGTGG
* * *
476134 TACCACTGATTATGCAATTACAATAATGCCTATCATATTGAAAATTCTAAAATACAACTTATACT
1 TACCACTGATTATGCAATTACAATAATCCCTATCAGATTGAAAATACTAAAATACAACTTATACT
* * *
476199 AAAAATAAGTAGAAATTAAGTACGACAAAGATATTTTATAAAAAACTTTAATATATTAGCTGGGG
66 AAAAATAAGTAGAAATAAAGTACGACAAAGATATATTAT-AAAAACTGTAATATATTAGCTGGGG
476264 CTC
130 CTC
* * *
476267 TACCATTGATTCTGCACTTACAATAATCCCTATCAGATTGAAAATACTAAAATACAACTTATACT
1 TACCACTGATTATGCAATTACAATAATCCCTATCAGATTGAAAATACTAAAATACAACTTATACT
476332 AAAAATAAGTAGAAATAAAGTACGACAAA-AGTATATTATAAAAACTGTAATATATT
66 AAAAATAAGTAGAAATAAAGTACGACAAAGA-TATATTATAAAAACTGTAATATATT
476388 TGGTTGATAA
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
132 17 0.15
133 94 0.85
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (132 bp):
TACCACTGATTATGCAATTACAATAATCCCTATCAGATTGAAAATACTAAAATACAACTTATACT
AAAAATAAGTAGAAATAAAGTACGACAAAGATATATTATAAAAACTGTAATATATTAGCTGGGGC
TC
Found at i:482694 original size:24 final size:24
Alignment explanation
Indices: 482662--482718 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
482652 TTATCTACAA
*
482662 CTGAAGCTGAATACATGGCAGTGG
1 CTGAAGCTGAATACATGGCAGCGG
*
482686 CTGAAGCTGAATAGATGGCAGCGG
1 CTGAAGCTGAATACATGGCAGCGG
482710 CTGAAGCTG
1 CTGAAGCTG
482719 CAAAAGAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.19
Consensus pattern (24 bp):
CTGAAGCTGAATACATGGCAGCGG
Found at i:484347 original size:12 final size:12
Alignment explanation
Indices: 484330--484430 Score: 76
Period size: 13 Copynumber: 7.9 Consensus size: 12
484320 CGATTTCGAT
484330 CTTTTAGGTTTA
1 CTTTTAGGTTTA
484342 CTTTTAGGTTTA
1 CTTTTAGGTTTA
* * *
484354 CGTTTTTGTGGTTG
1 C-TTTTAG-GTTTA
*
484368 TTTTTAGGTTTTA
1 CTTTTAGG-TTTA
484381 CTTTTAGGTTTA
1 CTTTTAGGTTTA
* * *
484393 CGTTTTTGTGGTTG
1 C-TTTTAG-GTTTA
*
484407 TTTTTAGGTTTTA
1 CTTTTAGG-TTTA
484420 CTTTTAGGTTT
1 CTTTTAGGTTT
484431 GCGTTCCCAA
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
12 23 0.34
13 38 0.57
14 6 0.09
ACGTcount: A:0.11, C:0.06, G:0.22, T:0.61
Consensus pattern (12 bp):
CTTTTAGGTTTA
Found at i:484378 original size:20 final size:20
Alignment explanation
Indices: 484350--484418 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
484340 TACTTTTAGG
484350 TTTACGTTTTTGTGGTTGTT
1 TTTACGTTTTTGTGGTTGTT
* ** * *
484370 TTTAGGTTTTACT-TTTAG-G
1 TTTACGTTTTTGTGGTT-GTT
484389 TTTACGTTTTTGTGGTTGTT
1 TTTACGTTTTTGTGGTTGTT
*
484409 TTTAGGTTTT
1 TTTACGTTTT
484419 ACTTTTAGGT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.09, C:0.04, G:0.23, T:0.64
Consensus pattern (20 bp):
TTTACGTTTTTGTGGTTGTT
Found at i:484386 original size:39 final size:39
Alignment explanation
Indices: 484331--484435 Score: 194
Period size: 39 Copynumber: 2.7 Consensus size: 39
484321 GATTTCGATC
484331 TTTTAGG-TTTACTTTTAGGTTTACGTTTTTGTGGTTGT
1 TTTTAGGTTTTACTTTTAGGTTTACGTTTTTGTGGTTGT
484369 TTTTAGGTTTTACTTTTAGGTTTACGTTTTTGTGGTTGT
1 TTTTAGGTTTTACTTTTAGGTTTACGTTTTTGTGGTTGT
*
484408 TTTTAGGTTTTACTTTTAGGTTTGCGTT
1 TTTTAGGTTTTACTTTTAGGTTTACGTT
484436 CCCAATTGTT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
38 7 0.11
39 58 0.89
ACGTcount: A:0.10, C:0.06, G:0.23, T:0.61
Consensus pattern (39 bp):
TTTTAGGTTTTACTTTTAGGTTTACGTTTTTGTGGTTGT
Found at i:487778 original size:6 final size:6
Alignment explanation
Indices: 487769--487799 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
487759 TCGTCCTTCG
487769 ATCTTT ATCTTT ATCTTT ATCTTT -TCTTT AT
1 ATCTTT ATCTTT ATCTTT ATCTTT ATCTTT AT
487800 TTCCTTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
ATCTTT
Found at i:490540 original size:3 final size:3
Alignment explanation
Indices: 490529--490576 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
490519 TCCTGAAAAA
* * *
490529 AAT ATT AAT AAT AAT TAT AAT AAT ACT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
490575 AA
1 AA
490577 AATGTTTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:490939 original size:37 final size:36
Alignment explanation
Indices: 490897--490992 Score: 135
Period size: 34 Copynumber: 2.7 Consensus size: 36
490887 GTCTTTTTGC
490897 TTCAAGAGAAAC-ATTTTCAAAGGTTTTTTTTTTGTGT
1 TTCAAGAGAAACGA-TTTCAAAGG-TTTTTTTTTGTGT
*
490934 TTCAAGAAAAACGATTTCAAAGG--TTTTTTTGTGT
1 TTCAAGAGAAACGATTTCAAAGGTTTTTTTTTGTGT
*
490968 TTCAAAAGAAACGATTTCAAAGGTT
1 TTCAAGAGAAACGATTTCAAAGGTT
490993 GGTGTTTCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
34 32 0.60
37 20 0.38
38 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (36 bp):
TTCAAGAGAAACGATTTCAAAGGTTTTTTTTTGTGT
Found at i:491000 original size:30 final size:31
Alignment explanation
Indices: 490930--491009 Score: 92
Period size: 34 Copynumber: 2.5 Consensus size: 31
490920 TTTTTTTTTT
*
490930 GTGTTTCAAGAA-AAACGATTTCAAAGGTTTTTTT
1 GTGTTTCAA-AAGAAACGATTTCAAAGG---TTTG
490964 GTGTTTCAAAAGAAACGATTTCAAAGG-TTG
1 GTGTTTCAAAAGAAACGATTTCAAAGGTTTG
*
490994 GTGTTTCAAGAGAAAC
1 GTGTTTCAAAAGAAAC
491010 TGTCTCAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 17 0.40
33 2 0.05
34 24 0.56
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (31 bp):
GTGTTTCAAAAGAAACGATTTCAAAGGTTTG
Found at i:491087 original size:36 final size:36
Alignment explanation
Indices: 490995--491419 Score: 404
Period size: 36 Copynumber: 12.1 Consensus size: 36
490985 CAAAGGTTGG
*
490995 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
491032 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** *
491068 TGTTTCAATAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* * ** * * * *
491105 AGTTCCAAAAGAAACTATCTCAAGGGATACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
491141 TGTTTCAA-GGAACACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAA-AC-TGTCTCAAGAGAGACAAAATT
491170 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*** * *
491206 TGTTT-AAAAAAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
491241 TGTTTCAA-GGAACACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAA-AC-TGTCTCAAGAGAGACAAAATT
* *
491270 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAGAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
491306 TGTTTCAAGGGAAACTGTCTCAAGAGAGGCAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
491342 TGTTTCAATGGG-AACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAA-GGGAAACTGTCTCAAGAGAGACAAAATT
* *
491378 TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
491415 TGTTT
1 TGTTT
491420 TGAGTAAAGT
Statistics
Matches: 322, Mismatches: 39, Indels: 54
0.78 0.09 0.13
Matches are distributed among these distances:
28 3 0.01
29 30 0.09
30 10 0.03
31 2 0.01
32 4 0.01
33 3 0.01
35 39 0.12
36 155 0.48
37 76 0.24
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:491241 original size:100 final size:100
Alignment explanation
Indices: 491066--491349 Score: 406
Period size: 100 Copynumber: 2.8 Consensus size: 100
491056 AGAGACAAAA
** * * * *
491066 TTTGTTTCAATAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TAAAAGAAACTGTCTCAAGGG
*
491131 ATACGAAATTTGTTTCAAGGAACACATATTCAAAGAT
64 AGACGAAATTTGTTTCAAGGAACACATATTCAAAGAT
*
491168 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAAAAAACTGTCTCAAGGGAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAAGAAACTGTCTCAAGGGAG
491233 ACGAAATTTGTTTCAAGGAACACATATTCAAAGAT
66 ACGAAATTTGTTTCAAGGAACACATATTCAAAGAT
* * ** *
491268 TTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAGAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT-AAAAGAAACTGTCTCAAGGGA
* *
491333 GGCAAAATTTGTTTCAA
65 GACGAAATTTGTTTCAA
491350 TGGGAACTGT
Statistics
Matches: 165, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
100 95 0.58
101 37 0.22
102 33 0.20
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (100 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAAGAAACTGTCTCAAGGGAG
ACGAAATTTGTTTCAAGGAACACATATTCAAAGAT
Found at i:491280 original size:50 final size:50
Alignment explanation
Indices: 491124--491281 Score: 121
Period size: 50 Copynumber: 3.2 Consensus size: 50
491114 AGAAACTATC
*
491124 TCAAGGGATACGAAATTTGTTTCAAGGAACACATATTCAAAGATTTTGTT
1 TCAAGGGAGACGAAATTTGTTTCAAGGAACACATATTCAAAGATTTTGTT
* * * * * * *** *
491174 TCAA--G-G--GAAA-CTGTCTCAAGAGAGACAAAATTTGTTTAAAAAAAACTGTC
1 TCAAGGGAGACGAAATTTGTTTCAAG-GA-AC-ACA--T-ATTCAAAGATTTTGTT
491224 TCAAGGGAGACGAAATTTGTTTCAAGGAACACATATTCAAAGATTTTGTT
1 TCAAGGGAGACGAAATTTGTTTCAAGGAACACATATTCAAAGATTTTGTT
491274 TCAAGGGA
1 TCAAGGGA
491282 AACAGTCTCA
Statistics
Matches: 75, Mismatches: 21, Indels: 24
0.62 0.17 0.20
Matches are distributed among these distances:
44 8 0.11
45 6 0.08
46 2 0.03
47 2 0.03
48 1 0.01
49 1 0.01
50 34 0.45
51 1 0.01
52 1 0.01
53 3 0.04
54 2 0.03
55 6 0.08
56 8 0.11
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (50 bp):
TCAAGGGAGACGAAATTTGTTTCAAGGAACACATATTCAAAGATTTTGTT
Found at i:491821 original size:124 final size:124
Alignment explanation
Indices: 491608--491946 Score: 412
Period size: 124 Copynumber: 2.7 Consensus size: 124
491598 GGCACGATAT
* * ** * ** * *
491608 CCTTCTTCGTGAAGTTAAAATTGTGGATGGCTCCTTCACTGTGAAATTGAGCCTTGAATTAGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * * * * *
491673 TCATTCATTGTGAAGTTAAAATCCACA-C-AGAAGATGAATGTTGCTGGTGGGTACGATTC
66 TCATTCGTCGTGAAGTTGAAATCCA-ATCTA-AAGATGAATGTTGCTGGAGAGAACGATTC
* **
491732 CCTTCGTCGTGAAGTTGAAACCGTGGATAGCCCCTTCGTTGTGAAGTTGAGCCTCAAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
491797 TCATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGAGAGAACGATTC
66 TCATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGAGAGAACGATTC
* * * * * *
491856 CCTTCGTCGTGAAATTGAAACCGTAGATGGCCCATTCGTTGTGAAGTTAAGCCTTGACTTGAATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* *
491921 TCCTTTGTCGTGAAGTTGAAATCCAA
66 TCATTCGTCGTGAAGTTGAAATCCAA
491947 GCTTGTATTG
Statistics
Matches: 184, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
123 1 0.01
124 182 0.99
125 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (124 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
TCATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGAGAGAACGATTC
Found at i:492220 original size:34 final size:34
Alignment explanation
Indices: 492181--492260 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
492171 GACCTATTCG
492181 TCGTGAAGTTGAGCCTTGACTTGAATATCCTTCA
1 TCGTGAAGTTGAGCCTTGACTTGAATATCCTTCA
*
492215 TCGTGAAGTTGAGCCTTGACTTGAATATCCTTCG
1 TCGTGAAGTTGAGCCTTGACTTGAATATCCTTCA
492249 TCGTGAAGTTGA
1 TCGTGAAGTTGA
492261 AATCCAAGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (34 bp):
TCGTGAAGTTGAGCCTTGACTTGAATATCCTTCA
Found at i:492622 original size:32 final size:31
Alignment explanation
Indices: 492581--492669 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
492571 TTCACATCTG
*
492581 GATGTTGAATCCCTAAAGATGCCCCAATATTC
1 GATGTTGAATCCCTAAA-ATGCCCCAACATTC
* * * *
492613 GATGTTGAATCTCCGAAAATACCTCAACATTT
1 GATGTTGAATC-CCTAAAATGCCCCAACATTC
**
492645 GATGTTGAATCTTTAAATATGCCCC
1 GATGTTGAATCCCTAAA-ATGCCCC
492670 CATTGTTCCT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
31 3 0.07
32 37 0.82
33 5 0.11
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (31 bp):
GATGTTGAATCCCTAAAATGCCCCAACATTC
Found at i:493758 original size:29 final size:30
Alignment explanation
Indices: 493726--493801 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
493716 TCTTGTCTTC
*
493726 TTCTTTCTTCACTTTTC-CTTTG-TTTTTGT
1 TTCTTT-TTCACTTTTCTCTTTGCTTTTTCT
*
493755 TTCTTTTTTTA-TTTTCTCTTTGCTTTTTCT
1 TTC-TTTTTCACTTTTCTCTTTGCTTTTTCT
* *
493785 TTGTTTTTCTCTTTTCT
1 TTCTTTTTCACTTTTCT
493802 TTTTTGTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 5 0.13
29 16 0.42
30 17 0.45
ACGTcount: A:0.03, C:0.18, G:0.05, T:0.74
Consensus pattern (30 bp):
TTCTTTTTCACTTTTCTCTTTGCTTTTTCT
Found at i:493776 original size:23 final size:22
Alignment explanation
Indices: 493750--493806 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
493740 TTCCTTTGTT
493750 TTTGTTTCTTTTTTTATTTTCTC
1 TTTGTTTCTTTTTTTATTTT-TC
* * *
493773 TTTGCTT-TTTCTTTGTTTTTC
1 TTTGTTTCTTTTTTTATTTTTC
*
493794 TCT-TTTCTTTTTT
1 TTTGTTTCTTTTTT
493807 GTTATGATTG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.07
21 9 0.33
22 10 0.37
23 6 0.22
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (22 bp):
TTTGTTTCTTTTTTTATTTTTC
Found at i:493781 original size:12 final size:12
Alignment explanation
Indices: 493766--493804 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
493756 TCTTTTTTTA
493766 TTTTCTCTTTGC
1 TTTTCTCTTTGC
*
493778 TTTT-TCTTTGT
1 TTTTCTCTTTGC
*
493789 TTTTCTCTTTTC
1 TTTTCTCTTTGC
493801 TTTT
1 TTTT
493805 TTGTTATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTCTCTTTGC
Found at i:495763 original size:19 final size:20
Alignment explanation
Indices: 495727--495764 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
495717 GCAAATGATA
495727 AAAATAAAATGAAAGAAAAC
1 AAAATAAAATGAAAGAAAAC
495747 AAAA-AAAAT-AAAGGAAAA
1 AAAATAAAATGAAA-GAAAA
495765 AGTTAGTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 10 0.59
20 4 0.24
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.08
Consensus pattern (20 bp):
AAAATAAAATGAAAGAAAAC
Found at i:498182 original size:22 final size:22
Alignment explanation
Indices: 498154--498197 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
498144 ATGGTTTCGT
*
498154 GCTATGGCCGAGAGTCCATAGC
1 GCTATGGCCAAGAGTCCATAGC
498176 GCTATGGCCAAGAGTCCATAGC
1 GCTATGGCCAAGAGTCCATAGC
498198 ACCTCTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.18
Consensus pattern (22 bp):
GCTATGGCCAAGAGTCCATAGC
Found at i:499198 original size:15 final size:15
Alignment explanation
Indices: 499178--499220 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
499168 AATCGAATCG
499178 AATCGAATTAATCAT
1 AATCGAATTAATCAT
*
499193 AATCGAATTGATCAT
1 AATCGAATTAATCAT
* *
499208 AACCAAATTAATC
1 AATCGAATTAATC
499221 GAACTTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (15 bp):
AATCGAATTAATCAT
Found at i:499591 original size:187 final size:186
Alignment explanation
Indices: 499361--499734 Score: 651
Period size: 187 Copynumber: 2.0 Consensus size: 186
499351 AAATTAAATA
* * *
499361 TTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAAAAATATATAATTATAAAATAAAAATTTTA
1 TTTTTAATTAAAAAAAAAATTTACAATTAATTTAAAAAATATATAATTATAAAATAAAAATTTTA
499426 GATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
66 GATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
*
499491 TGGGTTTTAAATGGTTTGAGCTTAA-CCCATATGTTATATATAATATATTTAATATT
131 TGGGTTTTAAATGGTTTGAGC-TAAGCCCATATATTATATATAATATATTTAATATT
*
499547 TTTTTAATTAAAAAAAACAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTT
1 TTTTTAATTAAAAAAAA-AATTTACAATTAATTTAAAAAATATATAATTATAAAATAAAAATTTT
* *
499612 ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
65 AGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
*
499677 TTGGGTTTTAAATGGTTTGGGCTAAGCCCATATATTATATATAATATATTTAATATT
130 TTGGGTTTTAAATGGTTTGAGCTAAGCCCATATATTATATATAATATATTTAATATT
499734 T
1 T
499735 AAAATTTAAT
Statistics
Matches: 178, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
186 19 0.11
187 159 0.89
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (186 bp):
TTTTTAATTAAAAAAAAAATTTACAATTAATTTAAAAAATATATAATTATAAAATAAAAATTTTA
GATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
TGGGTTTTAAATGGTTTGAGCTAAGCCCATATATTATATATAATATATTTAATATT
Found at i:502373 original size:64 final size:63
Alignment explanation
Indices: 502301--502421 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 63
502291 ATTGTTCAAG
* * * *
502301 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCAAATGCCATCA
* * *
502365 GTGTATCGATGCACAAGTAGTGCATCGATGTACCCCCTTAAATACAAACATCAAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCAAATG
502422 GGATTTACAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 16 0.32
64 34 0.68
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCAAATGCCATCA
Found at i:503195 original size:23 final size:23
Alignment explanation
Indices: 503115--503187 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
503105 GGAACTACTA
*
503115 TGCAATTCTACGCGGCACTACGG
1 TGCAATTCTACGCGGCACTTCGG
* *
503138 TGCAATTCTATGCGGCACTTCGA
1 TGCAATTCTACGCGGCACTTCGG
503161 TGCAATTCTACGCGGCACTTCGG
1 TGCAATTCTACGCGGCACTTCGG
503184 TGCA
1 TGCA
503188 TTTATACGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.26
Consensus pattern (23 bp):
TGCAATTCTACGCGGCACTTCGG
Found at i:510104 original size:23 final size:23
Alignment explanation
Indices: 510078--510136 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
510068 ATCTTATATG
*
510078 GCACTACGGTGCAATTCTACGCT-
1 GCACTTCGGTGCAATTCTACG-TA
*
510101 GCACTTCGGTGCAATTCTATGTA
1 GCACTTCGGTGCAATTCTACGTA
510124 GCACTTCGGTGCA
1 GCACTTCGGTGCA
510137 TTTATACGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGTA
Found at i:536487 original size:59 final size:59
Alignment explanation
Indices: 536339--536583 Score: 354
Period size: 59 Copynumber: 4.2 Consensus size: 59
536329 ATACAATCAA
*
536339 TATGATTTTCTT-CCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACA-CTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACCTAG
* *
536396 TA-GATTTTCTTACCATTTTAGCACACAGAGTGCCCTATCTGGAAATTCATACACCTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACCTAG
* * *
536454 TATGATTTCCTTACCATTTTAGCACATAAAGTGCCCTATCT-GAAATTTCATACACTTAA
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAA-TTCATACACCTAG
* * * **
536513 TATGATTTCCTTATCATTTTAGCACAAAAAGTGCCCTATCTGGAATTTCATACAATTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACCTAG
536572 TATGATTTCCTT
1 TATGATTTCCTT
536584 TATCTCTCCT
Statistics
Matches: 172, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
56 9 0.05
57 42 0.24
58 10 0.06
59 108 0.63
60 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (59 bp):
TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACCTAG
Found at i:539054 original size:26 final size:24
Alignment explanation
Indices: 539013--539062 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
539003 TTTCATTTTT
*
539013 ATAAAAATATTTAACTTACATAAA
1 ATAAAAATATTTAACTTAAATAAA
539037 ATAAAACATATCTTAACTTAAATAAA
1 ATAAAA-ATAT-TTAACTTAAATAAA
539063 CAACAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.26
25 4 0.17
26 13 0.57
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAAAAATATTTAACTTAAATAAA
Found at i:539542 original size:59 final size:59
Alignment explanation
Indices: 539450--539800 Score: 513
Period size: 59 Copynumber: 5.9 Consensus size: 59
539440 TAAATTCAAT
* * * *
539450 TGGAATTTCATACAATTAATATGATTTTCTTACCATTTTAGCACAAAAAGTGCCCTATC
1 TGGAATTTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * * *
539509 TGGAAATCCATACACCTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATA
1 TGGAATTTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
539568 TGGAAATTCATACACCTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGTCCTATC
1 TGGAATTTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
** * *
539627 TATAATTTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCATATC
1 TGGAATTTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * * *
539686 TGGAATTTCATACAATTAGTATGATTTTCTTATCATTTTAGCGCACAAAGTGCCCTATC
1 TGGAATTTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
539745 TGGAATTTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACAAAGTGCCCT
1 TGGAATTTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
539801 TTGGTAATTT
Statistics
Matches: 264, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 264 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (59 bp):
TGGAATTTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:540268 original size:53 final size:53
Alignment explanation
Indices: 540207--540323 Score: 171
Period size: 53 Copynumber: 2.2 Consensus size: 53
540197 CCTTCAGAAG
* * *
540207 GGTATCGATACACTACTAGGATATCGGTACCCAATTTAAATTCGATATTTATA
1 GGTATCGATACACTACTAGGATATCGGTACCCAAATTAAATTCGATATTCACA
* * * *
540260 GGTATCGATACACTACTGGGGTATCGGTACCCAAATTAAATTTGATATTCGCA
1 GGTATCGATACACTACTAGGATATCGGTACCCAAATTAAATTCGATATTCACA
540313 GGTATCGATAC
1 GGTATCGATAC
540324 CTCTTAAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (53 bp):
GGTATCGATACACTACTAGGATATCGGTACCCAAATTAAATTCGATATTCACA
Found at i:547058 original size:3 final size:3
Alignment explanation
Indices: 547050--547075 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
547040 AAAGTAAAAC
547050 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
547076 TATTATTATT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:547080 original size:3 final size:3
Alignment explanation
Indices: 547074--547102 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
547064 AATAATAATA
547074 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
547103 AAAACATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:549898 original size:20 final size:20
Alignment explanation
Indices: 549873--549939 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
549863 TCTTGACTTG
*
549873 GAAGAGAAGAGGATGAAGAC
1 GAAGAGAAGAGGATGAAGAA
*
549893 GAAGAGAAGAGGATAAAGAA
1 GAAGAGAAGAGGATGAAGAA
549913 GAAGAGAAGAGGATGAAGAA
1 GAAGAGAAGAGGATGAAGAA
549933 GAAGAGA
1 GAAGAGA
549940 GAAAGAGAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.55, C:0.01, G:0.39, T:0.04
Consensus pattern (20 bp):
GAAGAGAAGAGGATGAAGAA
Found at i:583065 original size:43 final size:42
Alignment explanation
Indices: 582964--583115 Score: 153
Period size: 44 Copynumber: 3.5 Consensus size: 42
582954 ACGAAAAGCT
*
582964 GTAAGGTCTTACCCCTACACAAAGCAGATGAGCCTGCAGAAAA-G
1 GTAAGGTCTTA-CCCTACACAAAGCAGAAGAGCCT-CA-AAAATG
* * *
583008 GTAAGGTCTTACCCTGGCACATAGCAGAAGAGCCTCACAAATG
1 GTAAGGTCTTACCCT-ACACAAAGCAGAAGAGCCTCAAAAATG
* * * * *
583051 GTAAGGTCTCACCCTTCCACACAGTAGAGGAGCCTTCAAAAATG
1 GTAAGGTCTTACCC-TACACAAAGCAGAAGAGCC-TCAAAAATG
583095 GTAAGGTCTTACCCATACACA
1 GTAAGGTCTTACCC-TACACA
583116 TAGAAAATGA
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 3 0.03
43 34 0.37
44 54 0.59
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (42 bp):
GTAAGGTCTTACCCTACACAAAGCAGAAGAGCCTCAAAAATG
Found at i:583131 original size:44 final size:43
Alignment explanation
Indices: 582964--583132 Score: 137
Period size: 44 Copynumber: 3.9 Consensus size: 43
582954 ACGAAAAGCT
* * * *
582964 GTAAGGTCTTACCCCTACACAAAGCAGATGAGCCTGCAGAAAA-G
1 GTAAGGTCTTA-CCCTACACATAGAAAATGAGCCTTCA-AAAATG
* * *
583008 GTAAGGTCTTACCCTGGCACATAGCAGAA-GAGCC-TCACAAATG
1 GTAAGGTCTTACCCT-ACACATAG-AAAATGAGCCTTCAAAAATG
* * * * * *
583051 GTAAGGTCTCACCCTTCCACACAGTAGAGGAGCCTTCAAAAATG
1 GTAAGGTCTTACCC-TACACATAGAAAATGAGCCTTCAAAAATG
*
583095 GTAAGGTCTTACCCATACACATAGAAAATGATCCTTCA
1 GTAAGGTCTTACCC-TACACATAGAAAATGAGCCTTCA
583133 GAAACTTCCT
Statistics
Matches: 97, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
42 4 0.04
43 31 0.32
44 61 0.63
45 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (43 bp):
GTAAGGTCTTACCCTACACATAGAAAATGAGCCTTCAAAAATG
Found at i:588860 original size:44 final size:44
Alignment explanation
Indices: 588796--588951 Score: 204
Period size: 44 Copynumber: 3.5 Consensus size: 44
588786 CGAAAAATTT
* *
588796 GTAAGGTCTTACCGTTGCACATAGCAGAGGAGCCTGCAGAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* * * * *
588840 GTATGGTCTTACCCTGGCACATAGTAAAGGAGCCTTCAAAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* * * * *
588884 GTAAGGTCTCACCCTTGCACACAACAGATGAGCCTTTAGAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
588928 GTAAGGTCTTACCCTTGCACATAG
1 GTAAGGTCTTACCCTTGCACATAG
588952 TAAATGATCA
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 92 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (44 bp):
GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
Found at i:588969 original size:44 final size:44
Alignment explanation
Indices: 588796--588969 Score: 195
Period size: 44 Copynumber: 4.0 Consensus size: 44
588786 CGAAAAATTT
* * *
588796 GTAAGGTCTTACCGTTGCACATAGCAGAGGAGCCTGCAGAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAATG
* * * *
588840 GTATGGTCTTACCCTGGCACATAGTAAAGGAGCCTTCAAAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAATG
* * * * * *
588884 GTAAGGTCTCACCCTTGCACACAACAGATGAGCCTTTAGAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAATG
* * * *
588928 GTAAGGTCTTACCCTTGCACATAGTAAATGATCATTCAGAAA
1 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAA
588970 CTTCCTCCAA
Statistics
Matches: 105, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 105 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (44 bp):
GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAATG
Found at i:596048 original size:42 final size:42
Alignment explanation
Indices: 595975--596069 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
595965 AGTGTGTTTG
* * *
595975 GGATCAATCCCTCAAGTAAAATGATCGATCCCTTCACC-AAAA
1 GGATCGATCCCTCAAGTAAAAGGATAGATCCCTTC-CCTAAAA
* *
596017 GGATCGATCCTTCAA-TGAAAAGGATAGATCCCTTCCCTTAAA
1 GGATCGATCCCTCAAGT-AAAAGGATAGATCCCTTCCCTAAAA
596059 GGATCGATCCC
1 GGATCGATCCC
596070 CTTGTTACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.07
42 42 0.93
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (42 bp):
GGATCGATCCCTCAAGTAAAAGGATAGATCCCTTCCCTAAAA
Found at i:596069 original size:21 final size:21
Alignment explanation
Indices: 595991--596069 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
595981 ATCCCTCAAG
*
595991 TAAAATGATCGATCCCTTCACC
1 TAAAAGGATCGATCCCTTC-CC
**
596013 -AAAAGGATCGAT-CCTTCAA
1 TAAAAGGATCGATCCCTTCCC
*
596032 TGAAAAGGATAGATCCCTTCCC
1 T-AAAAGGATCGATCCCTTCCC
*
596054 TTAAAGGATCGATCCC
1 TAAAAGGATCGATCCC
596070 CTTGTTACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
20 5 0.11
21 35 0.76
22 6 0.13
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (21 bp):
TAAAAGGATCGATCCCTTCCC
Found at i:599184 original size:31 final size:30
Alignment explanation
Indices: 599116--599188 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
599106 TCTATAAGCC
* **
599116 TTAGAAAATTTTGGGGACCATCATGTAATT
1 TTAGAAAATTTAGGGGACCATCATACAATT
*
599146 TTTGAAAATTTAGGGGACCAAATCA-ACAATT
1 TTAGAAAATTTAGGGGACC--ATCATACAATT
599177 TTAGAAAATTTA
1 TTAGAAAATTTA
599189 TGGATTATTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 17 0.47
31 15 0.42
32 4 0.11
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (30 bp):
TTAGAAAATTTAGGGGACCATCATACAATT
Found at i:602302 original size:202 final size:201
Alignment explanation
Indices: 601929--602528 Score: 1075
Period size: 202 Copynumber: 3.0 Consensus size: 201
601919 ACGCCAAGGG
* *
601929 AAGAGTCTCGTCAGAATCATT-CTTTTTCCTTTGTTTGATTTTAGATTTTTTAGTTAATGTTTAA
1 AAGAGTCTCGTCGGAATCGTTCCTTTTTCCTTTGTTTGATTTTAGATTTTTTAGTTAATGTTTAA
*
601993 GGGAAAAAAGATCATTGATTGCTAAAATACAAAAAAAATCAACCAAAACCCTAGATTGTTCATTT
66 GGGAAAAAAGATCATGGATTGCTAAAATACAAAAAAAATCAACCAAAACCCTAGATTGTTCATTT
602058 TCCCGCCATAAATTACCCATATGTTTAATGGCTACTCTTTTTTCCTAATTGTTTGTCATTTTAAG
131 TCCCGCCATAAATTACCCATATGTTTAATGGCTACTCTTTTTTCCTAATTGTTTGTCATTTTAAG
602123 CCCCTT
196 CCCCTT
602129 AAGAGTCTCGTCGGAATCGTTCCTTTTTCCTTTGTTTGATTTTAGATTTTTTAGTTAATGTTTAA
1 AAGAGTCTCGTCGGAATCGTTCCTTTTTCCTTTGTTTGATTTTAGATTTTTTAGTTAATGTTTAA
* *
602194 GGGAAAAAAGATCATGGATTTCTAAAATACAAAAAAAAATCAACCAAAACCTTAGATTGTTCATT
66 GGGAAAAAAGATCATGGATTGCTAAAATAC-AAAAAAAATCAACCAAAACCCTAGATTGTTCATT
*
602259 TTCCCGCCATAAATTACCCATATGTTTAATGGCTACCCTTTTTTCCTAATTGTTTGTCATTTTAA
130 TTCCCGCCATAAATTACCCATATGTTTAATGGCTACTCTTTTTTCCTAATTGTTTGTCATTTTAA
602324 GCCCCTT
195 GCCCCTT
602331 AAGAGTCTCGTCGGAATCGTTCCTTTTTCCTTTGTTTGATTTTAGATTTTTTAGTTAATGTTTAA
1 AAGAGTCTCGTCGGAATCGTTCCTTTTTCCTTTGTTTGATTTTAGATTTTTTAGTTAATGTTTAA
* *
602396 TGGAAAAAATATCATGGATTGCTAAAATACAAAAAAAATCAACCAAAACCCT--A--GTTCATTT
66 GGGAAAAAAGATCATGGATTGCTAAAATACAAAAAAAATCAACCAAAACCCTAGATTGTTCATTT
*
602457 TCCCGCCATAAATTACCCATATGTTTATTGGCTACTCTTTTTTCCTAATTGTTTGTCATTTTAAG
131 TCCCGCCATAAATTACCCATATGTTTAATGGCTACTCTTTTTTCCTAATTGTTTGTCATTTTAAG
602522 CCCCTT
196 CCCCTT
602528 A
1 A
602529 TCTTTTTTTT
Statistics
Matches: 386, Mismatches: 12, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
197 78 0.20
199 1 0.00
200 19 0.05
201 92 0.24
202 196 0.51
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (201 bp):
AAGAGTCTCGTCGGAATCGTTCCTTTTTCCTTTGTTTGATTTTAGATTTTTTAGTTAATGTTTAA
GGGAAAAAAGATCATGGATTGCTAAAATACAAAAAAAATCAACCAAAACCCTAGATTGTTCATTT
TCCCGCCATAAATTACCCATATGTTTAATGGCTACTCTTTTTTCCTAATTGTTTGTCATTTTAAG
CCCCTT
Found at i:606171 original size:27 final size:27
Alignment explanation
Indices: 606117--606171 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
606107 TTCAGAAAAA
* *
606117 ATAAAATAAAATAAAATTAAGCATATG
1 ATAAAATAAAATAAAATAAAGCAAATG
*
606144 ATAAAATAAAATAGAATAAATG-AAATG
1 ATAAAATAAAATAAAATAAA-GCAAATG
606171 A
1 A
606172 AATAAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (27 bp):
ATAAAATAAAATAAAATAAAGCAAATG
Found at i:611520 original size:12 final size:12
Alignment explanation
Indices: 611503--611528 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
611493 CTTTATTCAC
611503 TCTCTTTTTTTT
1 TCTCTTTTTTTT
611515 TCTCTTTTTTTT
1 TCTCTTTTTTTT
611527 TC
1 TC
611529 CTGCTCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TCTCTTTTTTTT
Found at i:615698 original size:65 final size:64
Alignment explanation
Indices: 615580--615724 Score: 163
Period size: 65 Copynumber: 2.2 Consensus size: 64
615570 TATTCAAAGG
*
615580 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATTGAACATCGAATGCATT
1 CATGCACCGATGCACTCA-TCCATGCATCGATGCATC-ATGAATTAATTAAACATCGAATGCATT
615644 C
64 C
*
615645 CATGCACCGATGCACTC-TCCATGCATCGATGCATTC-TGAA-TATTTTCAAAACATCGAATGCA
1 CATGCACCGATGCACTCATCCATGCATCGATGCA-TCATGAATTA-ATT--AAACATCGAATGCA
*
615707 TTT
62 TTC
* *
615710 GATGCATCGATGCAC
1 CATGCACCGATGCAC
615725 AAGACATGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
62 2 0.03
63 6 0.09
64 16 0.23
65 44 0.63
66 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCACCGATGCACTCATCCATGCATCGATGCATCATGAATTAATTAAACATCGAATGCATTC
Found at i:615733 original size:65 final size:64
Alignment explanation
Indices: 615629--615787 Score: 176
Period size: 65 Copynumber: 2.5 Consensus size: 64
615619 GAATTAATTG
* * **** * *
615629 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCATTCTGAATA-TTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCA-CCAGAATATTTTTC-
615693 A
64 A
* * **
615694 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATGTACCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACCAGAATATTTTTCA
*
615758 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
615788 TCCTTAGTGC
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 34 0.43
65 46 0.57
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACCAGAATATTTTTCA
Found at i:617869 original size:20 final size:21
Alignment explanation
Indices: 617836--617875 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
617826 TTTTAACGTA
617836 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
617856 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
617876 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Found at i:617883 original size:22 final size:20
Alignment explanation
Indices: 617835--617879 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
617825 ATTTTAACGT
617835 AATTGATATTCATTTTAAAC
1 AATTGATATTCATTTTAAAC
*
617855 CATTGATA-TCAATTTTCAAAC
1 AATTGATATTC-ATTTT-AAAC
617876 AATT
1 AATT
617880 TGATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTGATATTCATTTTAAAC
Found at i:618653 original size:20 final size:20
Alignment explanation
Indices: 618628--618716 Score: 90
Period size: 20 Copynumber: 4.4 Consensus size: 20
618618 CCAGGTTGTA
*
618628 AATATTATATTATAATTATT
1 AATATTATATTATAACTATT
618648 AATATTATATTATAACTATT
1 AATATTATATTATAACTATT
* *
618668 -ATTTTATTATTATAACAATT
1 AATATTA-TATTATAACTATT
* * *
618688 AAAATTATAATTATTATTATT
1 AATATTAT-ATTATAACTATT
*
618709 ATTATTAT
1 AATATTAT
618717 TAATATTGCT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
19 5 0.09
20 32 0.57
21 19 0.34
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTATATTATAACTATT
Found at i:618677 original size:3 final size:3
Alignment explanation
Indices: 618630--618723 Score: 68
Period size: 3 Copynumber: 32.3 Consensus size: 3
618620 AGGTTGTAAA
* * * *
618630 TAT TA- TAT TAT AAT TAT TAA TAT TA- TAT TAT AAC TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
618675 TAT TAT AAC AAT TAA AAT TAT AAT TAT TAT TAT TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
618723 T
1 T
618724 GCTTATGTTT
Statistics
Matches: 68, Mismatches: 20, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
2 6 0.09
3 62 0.91
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:620016 original size:14 final size:14
Alignment explanation
Indices: 619997--620026 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
619987 ATCATTTTTA
619997 ATATGTATATATAT
1 ATATGTATATATAT
620011 ATATGTATATATAT
1 ATATGTATATATAT
620025 AT
1 AT
620027 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:627126 original size:18 final size:18
Alignment explanation
Indices: 627084--627129 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
627074 TAGTTTGATT
*
627084 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
627102 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
627120 AATGAACTAA
1 AATGAACTAA
627130 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:627205 original size:17 final size:17
Alignment explanation
Indices: 627185--627226 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
627175 ACTACTTCCC
627185 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
627202 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
627219 TTAATGAA
1 TAAATGAA
627227 CAACATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:630556 original size:42 final size:42
Alignment explanation
Indices: 630497--630582 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
630487 AAGTCTTTCA
* *
630497 GGCCATCAATAAGTCTTTCA-AGCATGATGCTTAAATCCTTAG
1 GGCCATCAATAAGTCTTT-AGAGCATAATGATTAAATCCTTAG
* *
630539 GGCCATTAGTAAGTCTTTAGAGCATAATGATTAAATCCTTAG
1 GGCCATCAATAAGTCTTTAGAGCATAATGATTAAATCCTTAG
630581 GG
1 GG
630583 TAATTTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (42 bp):
GGCCATCAATAAGTCTTTAGAGCATAATGATTAAATCCTTAG
Found at i:630593 original size:42 final size:42
Alignment explanation
Indices: 630506--630593 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
630496 AGGCCATCAA
* * *
630506 TAAGTCTTTCAAGCATGATGCTTAAATCCTTAGGGCCATTAG
1 TAAGTCTTTCAAGCATAATGATTAAATCCTTAGGGCAATTAG
* *
630548 TAAGTCTTT-AGAGCATAATGATTAAATCCTTAGGGTAATTTG
1 TAAGTCTTTCA-AGCATAATGATTAAATCCTTAGGGCAATTAG
630590 TAAG
1 TAAG
630594 CCTTCACGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (42 bp):
TAAGTCTTTCAAGCATAATGATTAAATCCTTAGGGCAATTAG
Found at i:630674 original size:80 final size:79
Alignment explanation
Indices: 630541--630753 Score: 302
Period size: 80 Copynumber: 2.7 Consensus size: 79
630531 ATCCTTAGGG
* * * *
630541 CCATTAGTAAGTCTTTAGAGCATAATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCA-CGGAA
1 CCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTT-CGGTAATTTGTAAGCCTTCATC-AAA
630605 GAGTAGTGAAGCAAAC
64 GAGTAGTGAAGCAAAC
630621 CCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGCTAATTTGTAAGCCTTCATCAAAG
1 CCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG-TAATTTGTAAGCCTTCATCAAAG
*
630686 AGTAGTGAAGCAAAT
65 AGTAGTGAAGCAAAC
* * * *
630701 TCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGTGTCATTTGTAAG
1 CCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCG-GTAATTTGTAAG
630754 TCTTTCGAAC
Statistics
Matches: 121, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
79 2 0.02
80 117 0.97
81 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (79 bp):
CCATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGTAATTTGTAAGCCTTCATCAAAGA
GTAGTGAAGCAAAC
Found at i:631230 original size:14 final size:15
Alignment explanation
Indices: 631211--631244 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
631201 TTTATCCGGG
631211 TTATAAATATT-ATA
1 TTATAAATATTAATA
*
631225 TTATAATTATTAATA
1 TTATAAATATTAATA
631240 TTATA
1 TTATA
631245 TTATAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAAATATTAATA
Found at i:631239 original size:20 final size:20
Alignment explanation
Indices: 631211--631256 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
631201 TTTATCCGGG
*
631211 TTATAAATATTATATTATAA
1 TTATTAATATTATATTATAA
631231 TTATTAATATTATATTATAA
1 TTATTAATATTATATTATAA
*
631251 CTATTA
1 TTATTA
631257 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATTAATATTATATTATAA
Found at i:631263 original size:20 final size:20
Alignment explanation
Indices: 631216--631290 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
631206 CCGGGTTATA
*
631216 AATATTATATTATAATTATT
1 AATATTATATTATAACTATT
631236 AATATTATATTATAACTATT
1 AATATTATATTATAACTATT
* * * *
631256 ATTGTTATTATTTTAACAATT
1 AATATTA-TATTATAACTATT
*
631277 AAAATTATAATTAT
1 AATATTAT-ATTAT
631291 TATTAGTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 25 0.57
21 19 0.43
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (20 bp):
AATATTATATTATAACTATT
Found at i:631266 original size:3 final size:3
Alignment explanation
Indices: 631218--631312 Score: 52
Period size: 3 Copynumber: 32.3 Consensus size: 3
631208 GGGTTATAAA
* * * * *
631218 TAT TA- TAT TAT AAT TAT TAA TAT TA- TAT TAT AAC TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
631264 TAT T-T TAAC AAT TAA AAT TAT AAT TAT TAT TAG TAT TAT TAT TAA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
631309 TAT T
1 TAT T
631313 GCTTATGTTT
Statistics
Matches: 64, Mismatches: 24, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
2 6 0.09
3 58 0.91
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:632599 original size:2 final size:2
Alignment explanation
Indices: 632587--632620 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
632577 GTCATTTTTA
* *
632587 AT AT GT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
632621 CCTCATGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:633639 original size:11 final size:13
Alignment explanation
Indices: 633603--633633 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
633593 TGCACACCCC
633603 TAGTTTACATATA
1 TAGTTTACATATA
*
633616 TAGTTTATATATA
1 TAGTTTACATATA
633629 TAGTT
1 TAGTT
633634 CATATAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (13 bp):
TAGTTTACATATA
Found at i:633706 original size:17 final size:18
Alignment explanation
Indices: 633672--633707 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
633662 TACAATAATT
633672 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
633690 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
633707 A
1 A
633708 CTTATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:635331 original size:178 final size:178
Alignment explanation
Indices: 635028--635384 Score: 653
Period size: 178 Copynumber: 2.0 Consensus size: 178
635018 AATATGCATC
*
635028 AAACCGACCTGAGTGAGCAGGTAGCCCCAGAAGAAAGAGGACTGAATCAAACCGACTGTTGCACT
1 AAACCGACCTGAGTGAGCAGGTAGCCCCAGAAGAAAGACGACTGAATCAAACCGACTGTTGCACT
* * *
635093 GTTCCAGTTAAACTCTTTTGACATGGGAGTATTGCAATGCACATCTTGACCTGCAAAAGGCATGG
66 GTTCAAGTTAAACTCTTTTGACATGGGAGTATTGCAATGCACATCTTGACCTGAAAAAGGCATAG
635158 ATAGAGTGCAGCTCAGCCAGCAAA-CAAGTAGAAATTTATTGTAGTGCT
131 ATAGAGTGCAGCTCAGCCAG-AAAGCAAGTAGAAATTTATTGTAGTGCT
635206 AAACCGACCTGAGTGAGCAGGTAGCCCCAGAAGAAAGACGACTGAATCAAACCGACTGTTGCACT
1 AAACCGACCTGAGTGAGCAGGTAGCCCCAGAAGAAAGACGACTGAATCAAACCGACTGTTGCACT
*
635271 GTTCAAGTTAAACTCTTTTGACATGGGAGTATTGCAATGCTCATCTTGACCTGAAAAAGGCATAG
66 GTTCAAGTTAAACTCTTTTGACATGGGAGTATTGCAATGCACATCTTGACCTGAAAAAGGCATAG
635336 ATAGAGTGCAGCTCAGCCAGAAAGCAAGTAGAAATTTATTGTAGTGCT
131 ATAGAGTGCAGCTCAGCCAGAAAGCAAGTAGAAATTTATTGTAGTGCT
635384 A
1 A
635385 TTGTTCACAA
Statistics
Matches: 173, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
177 3 0.02
178 170 0.98
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (178 bp):
AAACCGACCTGAGTGAGCAGGTAGCCCCAGAAGAAAGACGACTGAATCAAACCGACTGTTGCACT
GTTCAAGTTAAACTCTTTTGACATGGGAGTATTGCAATGCACATCTTGACCTGAAAAAGGCATAG
ATAGAGTGCAGCTCAGCCAGAAAGCAAGTAGAAATTTATTGTAGTGCT
Found at i:657805 original size:17 final size:18
Alignment explanation
Indices: 657771--657811 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
657761 TTATGACTTT
657771 ATTTTTGAGAAAATTGAG
1 ATTTTTGAGAAAATTGAG
657789 ATTTTTGATG-AAA-TGAG
1 ATTTTTGA-GAAAATTGAG
657806 ATTTTT
1 ATTTTT
657812 AATTTGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 11 0.50
19 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (18 bp):
ATTTTTGAGAAAATTGAG
Found at i:659257 original size:18 final size:20
Alignment explanation
Indices: 659221--659260 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
659211 TCAACATTTG
659221 AATAAACAAAACAGTAGAAA
1 AATAAACAAAACAGTAGAAA
*
659241 AATAAA-AAAATAG-AGAAA
1 AATAAACAAAACAGTAGAAA
659259 AA
1 AA
659261 AGGTTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.75, C:0.05, G:0.10, T:0.10
Consensus pattern (20 bp):
AATAAACAAAACAGTAGAAA
Found at i:664041 original size:54 final size:54
Alignment explanation
Indices: 663982--664231 Score: 306
Period size: 54 Copynumber: 4.6 Consensus size: 54
663972 TTGACATATT
* *
663982 TTCATAATGAGTTTGTGAATTACCGTGTCGACACTATGTGTGCAACCCACATAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACAGAA
** *
664036 TTCATAATGTA-TTTGTGAATTATTGTATCGACACTATGTGTGTAACCCACAGAA
1 TTCATAATG-AGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACAGAA
* * * * *
664090 TTCATAATGAGTTTGTGAATTACCGTATCGGCAATATGTGTGCAATCCATAAAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACAGAA
* ** **
664144 TTCA-AATGAGTTTGTGAATTACCGTATTGGTACTATGTGTGCAACCCATGGAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACAGAA
* * * *
664197 TTTATAATGAGTTTGTAAATTTCCATATCGACACT
1 TTCATAATGAGTTTGTGAATTACCGTATCGACACT
664232 TAGGTGCAAA
Statistics
Matches: 167, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 47 0.28
54 119 0.71
55 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (54 bp):
TTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACAGAA
Found at i:664210 original size:107 final size:108
Alignment explanation
Indices: 663982--664229 Score: 311
Period size: 107 Copynumber: 2.3 Consensus size: 108
663972 TTGACATATT
* * *
663982 TTCATAATGAGTTTGTGAATTACCGTGTCGACACTATGTGTGCAACCCACATAATTCATAATGTA
1 TTCATAATGAGTTTGTGAATTACCGTATCGACAATATGTGTGCAACCCACAAAATTCATAATGTA
** *
664047 TTTGTGAATTATTGTATCGACACTATGTGTGTAACCCACAGAA
66 TTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACAGAA
* * *
664090 TTCATAATGAGTTTGTGAATTACCGTATCGGCAATATGTGTGCAATCCATAAAATTCA-AATG-A
1 TTCATAATGAGTTTGTGAATTACCGTATCGACAATATGTGTGCAACCCACAAAATTCATAATGTA
* ** **
664153 GTTTGTGAATTACCGTATTGGTACTATGTGTGCAACCCATGGAA
66 -TTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACAGAA
* * * *
664197 TTTATAATGAGTTTGTAAATTTCCATATCGACA
1 TTCATAATGAGTTTGTGAATTACCGTATCGACA
664230 CTTAGGTGCA
Statistics
Matches: 120, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
106 1 0.01
107 67 0.56
108 52 0.43
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (108 bp):
TTCATAATGAGTTTGTGAATTACCGTATCGACAATATGTGTGCAACCCACAAAATTCATAATGTA
TTTGTGAATTACCGTATCGACACTATGTGTGCAACCCACAGAA
Found at i:671114 original size:53 final size:54
Alignment explanation
Indices: 670961--671151 Score: 258
Period size: 54 Copynumber: 3.6 Consensus size: 54
670951 TTGACATATT
** * *
670961 TTCATAATGAGTTTGTGAATTATAGTATCGACACTATGTGTGCAAACCACGGAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGGAA
* * * ***
671015 TTCATAATGAGTTTGTGAATTACCATATCAGCACTATGTGTACAACCCATAAAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGGAA
671069 TTCATAATGAGTTTGTG-ATTACCGTATCGGCACTATGTGTGCAACCCACGGAA
1 TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGGAA
* * *
671122 TTCATAATGAGTTTGGGAATTGCCATATCG
1 TTCATAATGAGTTTGTGAATTACCGTATCG
671152 ACGCTTAGGT
Statistics
Matches: 117, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
53 46 0.39
54 71 0.61
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
TTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGGAA
Found at i:676851 original size:42 final size:42
Alignment explanation
Indices: 676792--676874 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
676782 AGACTAATTA
676792 TCTGGTTGATGCATTACCTAGAGGAGGAGGCAATCATCATTG
1 TCTGGTTGATGCATTACCTAGAGGAGGAGGCAATCATCATTG
* * *
676834 TCTGGTTGATGCATTACCTGGAGGAGGAGTCAGTCATCATT
1 TCTGGTTGATGCATTACCTAGAGGAGGAGGCAATCATCATT
676875 CATAGTGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (42 bp):
TCTGGTTGATGCATTACCTAGAGGAGGAGGCAATCATCATTG
Found at i:679907 original size:18 final size:19
Alignment explanation
Indices: 679870--679907 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
679860 CATTCATGGG
*
679870 GTATCGATACCTGGAGGGTA
1 GTATCGATACC-GAAGGGTA
679890 GTATCGATACC-AAGGGTA
1 GTATCGATACCGAAGGGTA
679908 CTGATACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (19 bp):
GTATCGATACCGAAGGGTA
Found at i:681755 original size:12 final size:12
Alignment explanation
Indices: 681738--681762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
681728 TTCATGGTTA
681738 TTGTTTTTTTTT
1 TTGTTTTTTTTT
681750 TTGTTTTTTTTT
1 TTGTTTTTTTTT
681762 T
1 T
681763 GATTGGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:689729 original size:35 final size:35
Alignment explanation
Indices: 689668--689805 Score: 222
Period size: 35 Copynumber: 3.9 Consensus size: 35
689658 TGATCTAATC
*
689668 TTGCTTCATTACTCTTTTTGTGAAGGCTTGATTGCA
1 TTGCTTCACTACTC-TTTTGTGAAGGCTTGATTGCA
* * *
689704 TTACTTCAGTACTCTTTTGTAAAGGCTTGATTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGCA
*
689739 TTGCTTCACTGCTCTTTTGTGAAGGCTTGATTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGCA
689774 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
689806 CAAATGACTT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 82 0.87
36 12 0.13
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (35 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGCA
Found at i:694103 original size:2 final size:2
Alignment explanation
Indices: 694096--694120 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
694086 ATAAACAAGA
694096 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 A
694121 ATCATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:700625 original size:17 final size:18
Alignment explanation
Indices: 700605--700638 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
700595 AAAATTAAAG
700605 AAAAAACTA-AATTTTAA
1 AAAAAACTATAATTTTAA
*
700622 AAAAAATTATAATTTTA
1 AAAAAACTATAATTTTA
700639 TTGCAACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAAACTATAATTTTAA
Found at i:710044 original size:24 final size:25
Alignment explanation
Indices: 709992--710044 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
709982 ATATATATTT
*
709992 AAAATTTCCATCAAAATATTAATAA
1 AAAATTTCCATCAAAATATAAATAA
*
710017 AAAA-TTCCTTCAAAATA-AAATAA
1 AAAATTTCCATCAAAATATAAATAA
710040 CAAAA
1 -AAAA
710045 ATATGATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 4 0.16
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAATTTCCATCAAAATATAAATAA
Found at i:710827 original size:52 final size:52
Alignment explanation
Indices: 710749--710857 Score: 218
Period size: 52 Copynumber: 2.1 Consensus size: 52
710739 TGTTGAGGAA
710749 AATGTGAAACCAATTGTTGGTTCATAAATGTGCAGACGTACACAATGTGGGT
1 AATGTGAAACCAATTGTTGGTTCATAAATGTGCAGACGTACACAATGTGGGT
710801 AATGTGAAACCAATTGTTGGTTCATAAATGTGCAGACGTACACAATGTGGGT
1 AATGTGAAACCAATTGTTGGTTCATAAATGTGCAGACGTACACAATGTGGGT
710853 AATGT
1 AATGT
710858 TAATGTCCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
AATGTGAAACCAATTGTTGGTTCATAAATGTGCAGACGTACACAATGTGGGT
Found at i:716854 original size:29 final size:29
Alignment explanation
Indices: 716809--716867 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
716799 CCAGATAGTA
*
716809 CCTACTTACAACTTTGGTGTTTTCGATGT
1 CCTACTTACAACATTGGTGTTTTCGATGT
716838 CCTACTTACAACATTGGTGTTTTCGATGT
1 CCTACTTACAACATTGGTGTTTTCGATGT
716867 C
1 C
716868 TTAGAGTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (29 bp):
CCTACTTACAACATTGGTGTTTTCGATGT
Found at i:719882 original size:20 final size:20
Alignment explanation
Indices: 719859--719963 Score: 119
Period size: 19 Copynumber: 5.5 Consensus size: 20
719849 TCTGAAACTT
*
719859 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
719879 AAAATCGCAACTCGAAAATG
1 AAAATCGCAACGCGAAAATG
**
719899 ATTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
* *
719918 -AAATCGCAAGGCGAAACT-
1 AAAATCGCAACGCGAAAATG
*
719936 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
719955 AAAATCGCA
1 AAAATCGCA
719964 TTGTGATTCT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.14
19 34 0.46
20 30 0.41
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:720357 original size:22 final size:22
Alignment explanation
Indices: 720330--720371 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
720320 GAGATAGACG
720330 GATTTCACCGGAGATGGGGACT
1 GATTTCACCGGAGATGGGGACT
*
720352 GATTTCATCGGAGATGGGGA
1 GATTTCACCGGAGATGGGGA
720372 TAGATGTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.14, G:0.38, T:0.24
Consensus pattern (22 bp):
GATTTCACCGGAGATGGGGACT
Found at i:720578 original size:20 final size:20
Alignment explanation
Indices: 720548--720641 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
720538 GCGCTTTGAA
*
720548 AATCACGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
720568 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
720588 AATCGCGTTGCGATATTCAG
1 AATCGCGTTGCGATAGTCAG
*
720608 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
720628 AATCGCATTGCGAT
1 AATCGCGTTGCGAT
720642 TTACATATTC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:720648 original size:20 final size:20
Alignment explanation
Indices: 720555--720662 Score: 92
Period size: 20 Copynumber: 5.4 Consensus size: 20
720545 GAAAATCACG
* ** *
720555 TTGCGATAGTCAGCATCGCG
1 TTGCGATATTCATAATCGCA
* * *
720575 TTGCGATAGTCAGAATCGCG
1 TTGCGATATTCATAATCGCA
* *
720595 TTGCGATATTCAGAATCGCG
1 TTGCGATATTCATAATCGCA
*
720615 TTGCGATAGTCATAATCGCA
1 TTGCGATATTCATAATCGCA
*
720635 TTGCGAT-TTACATATTCGCA
1 TTGCGATATT-CATAATCGCA
*
720655 TTACGATA
1 TTGCGATA
720663 GTCGGAAAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
19 1 0.01
20 77 0.99
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (20 bp):
TTGCGATATTCATAATCGCA
Found at i:720662 original size:40 final size:40
Alignment explanation
Indices: 720555--720723 Score: 117
Period size: 40 Copynumber: 4.2 Consensus size: 40
720545 GAAAATCACG
* * * * *
720555 TTGCGATAGTCAGCATCGCGTTGCGATAGTCAGAATCGCG
1 TTGCGATATTCAGAATCGCATTACGATAGTCAGAATCGCA
* * *
720595 TTGCGATATTCAGAATCGCGTTGCGATAGTCATAATCGCA
1 TTGCGATATTCAGAATCGCATTACGATAGTCAGAATCGCA
* * *
720635 TTGCGAT-TTACATATTCGCATTACGATAGTCGGAAAATCGCA
1 TTGCGATATT-CAGAATCGCATTACGATAGTC--AGAATCGCA
** * * * * *
720677 ACGCGA-ATTTGGAAAATCGCAATGCGATAGTCAGAATCGCG
1 TTGCGATA-TT-CAGAATCGCATTACGATAGTCAGAATCGCA
720718 TTGCGA
1 TTGCGA
720724 ATCTGGCAAC
Statistics
Matches: 103, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
39 2 0.02
40 60 0.58
41 11 0.11
42 12 0.12
43 18 0.17
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (40 bp):
TTGCGATATTCAGAATCGCATTACGATAGTCAGAATCGCA
Found at i:723695 original size:17 final size:17
Alignment explanation
Indices: 723675--723718 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
723665 TTAATCAGAA
723675 TTTTCTTTTTCTTTAAT
1 TTTTCTTTTTCTTTAAT
** *
723692 TTTTCGCTTTCTTTACT
1 TTTTCTTTTTCTTTAAT
723709 TTTTGCTTTT
1 TTTT-CTTTT
723719 ACTGTTTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.07, C:0.16, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTCTTTTTCTTTAAT
Found at i:726380 original size:16 final size:14
Alignment explanation
Indices: 726362--726411 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 14
726352 TAATTAAATT
726362 AAAAAATAACAATAA
1 AAAAAATAA-AATAA
*
726377 TAAAAAATAAAAACAA
1 -AAAAAAT-AAAATAA
726393 AATAAAATAAAATAA
1 AA-AAAATAAAATAA
726408 AAAA
1 AAAA
726412 TAATCACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 2 0.07
15 10 0.33
16 16 0.53
17 2 0.07
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAATAAAATAA
Found at i:727912 original size:19 final size:19
Alignment explanation
Indices: 727870--727914 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
727860 GGTAAGGGTT
*
727870 TGGGTTTTAATTTTTAAAA
1 TGGGTTTTAATGTTTAAAA
*
727889 GGGGTTTT-ATGTTTAAATA
1 TGGGTTTTAATGTTTAAA-A
727908 TGGGTTT
1 TGGGTTT
727915 AGGTTTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (19 bp):
TGGGTTTTAATGTTTAAAA
Found at i:759616 original size:35 final size:37
Alignment explanation
Indices: 759555--759627 Score: 132
Period size: 35 Copynumber: 2.0 Consensus size: 37
759545 TGATCTAATC
759555 TTGCTTCACTACTCTTTTTGTGAAGGCTTGATT-AAA
1 TTGCTTCACTACTCTTTTTGTGAAGGCTTGATTCAAA
759591 TTGCTTCACTACTC-TTTTGTGAAGGCTTGATTCAAA
1 TTGCTTCACTACTCTTTTTGTGAAGGCTTGATTCAAA
759627 T
1 T
759628 GACTTGCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 18 0.50
36 18 0.50
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (37 bp):
TTGCTTCACTACTCTTTTTGTGAAGGCTTGATTCAAA
Found at i:759647 original size:41 final size:36
Alignment explanation
Indices: 759544--759647 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 36
759534 GATAAAACTT
*
759544 TTGATCTAATCTTGCTTCACTACTCTTTTTGTGAAGGC
1 TTGAT-TAAACTTGCTTCACTACTC-TTTTGTGAAGGC
759582 TTGATTAAA-TTGCTTCACTACTCTTTTGTGAAGGC
1 TTGATTAAACTTGCTTCACTACTCTTTTGTGAAGGC
759617 TTGATTCAAATGACTTGCTTCCACTACTCTT
1 TTGATT--AA--ACTTGCTT-CACTACTCTT
759648 CCGTTAAGAT
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
35 18 0.31
36 14 0.24
37 5 0.08
38 5 0.08
39 1 0.02
40 6 0.10
41 10 0.17
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (36 bp):
TTGATTAAACTTGCTTCACTACTCTTTTGTGAAGGC
Found at i:767422 original size:30 final size:31
Alignment explanation
Indices: 767375--767438 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
767365 AGTAGGCCGA
*
767375 CCACCCTTAGGAAGCTCCAACCGCCCTT-CGG
1 CCACCCTTAGCAAGCTCCAACCG-CCTTCCGG
*
767406 CCACCC-TAGCAAGCTCCAGCCGCCTTCCGG
1 CCACCCTTAGCAAGCTCCAACCGCCTTCCGG
767436 CCA
1 CCA
767439 TCGTGCGGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 4 0.13
30 20 0.67
31 6 0.20
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.14
Consensus pattern (31 bp):
CCACCCTTAGCAAGCTCCAACCGCCTTCCGG
Found at i:770318 original size:3 final size:3
Alignment explanation
Indices: 770303--770348 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
770293 TTGTAACCAA
* *
770303 AAT AAT AAA AAT AAT AAT -AT AAT AA- AAT TAT AAT AAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
770347 AA
1 AA
770349 AACTCGAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:770334 original size:11 final size:10
Alignment explanation
Indices: 770304--770350 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
770294 TGTAACCAAA
770304 ATAATAAAA-
1 ATAATAAAAT
770313 ATAAT--AAT
1 ATAATAAAAT
770321 ATAATAAAATT
1 ATAATAAAA-T
*
770332 ATAATAATAT
1 ATAATAAAAT
770342 ATAATAAAA
1 ATAATAAAA
770351 CTCGAACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
7 2 0.06
8 5 0.16
9 5 0.16
10 11 0.34
11 9 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:770337 original size:19 final size:17
Alignment explanation
Indices: 770304--770342 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
770294 TGTAACCAAA
770304 ATAATAAAAATAATAAT
1 ATAATAAAAATAATAAT
770321 ATAATAAAATTATAATAAT
1 ATAATAAAA--ATAATAAT
770340 ATA
1 ATA
770343 TAATAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAAAAATAATAAT
Found at i:778662 original size:31 final size:32
Alignment explanation
Indices: 778612--778677 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
778602 AGTAGGCCGA
*
778612 CCACCCCTTAGGAAGCTCCAACCGCCTTCCGG
1 CCACCCCTTAGCAAGCTCCAACCGCCTTCCGG
*
778644 CCACCCC-TAGCAAGCTCCAGCCGCCTTCCGG
1 CCACCCCTTAGCAAGCTCCAACCGCCTTCCGG
778675 CCA
1 CCA
778678 TCGTGCGGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 25 0.78
32 7 0.22
ACGTcount: A:0.18, C:0.50, G:0.18, T:0.14
Consensus pattern (32 bp):
CCACCCCTTAGCAAGCTCCAACCGCCTTCCGG
Found at i:786189 original size:24 final size:25
Alignment explanation
Indices: 786137--786189 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
786127 ATATATATTT
*
786137 AAAATTTCCTTCAAAATATTAATAA
1 AAAATTTCCTTCAAAATATAAATAA
786162 AAAA-TTCCTTCAAAAT-TAAATAA
1 AAAATTTCCTTCAAAATATAAATAA
786185 CAAAA
1 -AAAA
786190 ATATTATACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.23
24 16 0.62
25 4 0.15
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAATTTCCTTCAAAATATAAATAA
Found at i:806332 original size:15 final size:17
Alignment explanation
Indices: 806312--806343 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
806302 ATTTTGCTTT
806312 AAATTA-ATT-TAAAAA
1 AAATTATATTATAAAAA
806327 AAATTATATTATAAAAA
1 AAATTATATTATAAAAA
806344 TTAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTATATTATAAAAA
Found at i:806388 original size:13 final size:13
Alignment explanation
Indices: 806365--806398 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
806355 AATAAAAATG
806365 AAATTTAATTCAT
1 AAATTTAATTCAT
* *
806378 ATATTTTATTCAT
1 AAATTTAATTCAT
806391 AAATTTAA
1 AAATTTAA
806399 AAATTAAATA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTTAATTCAT
Found at i:807389 original size:4 final size:4
Alignment explanation
Indices: 807380--807407 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
807370 CAATGCATGT
807380 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
807408 TACATAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:810889 original size:24 final size:24
Alignment explanation
Indices: 810857--810904 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
810847 TCGTTATTGT
*
810857 ATCCTGGGAGACAGACAACCAATG
1 ATCCTGGGAGACAGACAAACAATG
810881 ATCCTGGGAGACAGACAAACAATG
1 ATCCTGGGAGACAGACAAACAATG
810905 CTCTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (24 bp):
ATCCTGGGAGACAGACAAACAATG
Found at i:817662 original size:35 final size:35
Alignment explanation
Indices: 817601--817738 Score: 231
Period size: 35 Copynumber: 3.9 Consensus size: 35
817591 TGATCTAATC
*
817601 TTGCTTCACTACTCTTTTTGTGAAGGCTTGATTGTA
1 TTGCTTCACTACTC-TTTTGTGAAGGCTTGATTGAA
*
817637 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGAA
* *
817672 TTGCTTCACTACTCTTTTGTGAAAGCTTGATTAAA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGAA
817707 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
817739 CAAATGACTT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 83 0.86
36 14 0.14
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (35 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGAA
Found at i:830631 original size:25 final size:25
Alignment explanation
Indices: 830603--830656 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
830593 GCCTGTAACC
830603 AAAATAATAAAAATA-ATAATATAAT
1 AAAATAATAAAAATATAT-ATATAAT
* * *
830628 AAAATTATAATAATATATTTATAAT
1 AAAATAATAAAAATATATATATAAT
830653 AAAA
1 AAAA
830657 CTTTTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATAATAAAAATATATATATAAT
Found at i:830639 original size:19 final size:17
Alignment explanation
Indices: 830606--830644 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
830596 TGTAACCAAA
830606 ATAATAAAAATAATAAT
1 ATAATAAAAATAATAAT
830623 ATAATAAAATTATAATAAT
1 ATAATAAAA--ATAATAAT
830642 ATA
1 ATA
830645 TTTATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAAAAATAATAAT
Found at i:834577 original size:21 final size:19
Alignment explanation
Indices: 834544--834599 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
834534 GAAAGAACCC
*
834544 AAAA-AAAGGGAAAAAGAAA
1 AAAATAAAGAGAAAAA-AAA
834563 AAAATAAATGAGAAATAAAAA
1 AAAATAAA-GAGAAA-AAAAA
834584 AAAATAAAGA-AAAAAA
1 AAAATAAAGAGAAAAAA
834600 TATTTGATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 5 0.15
21 16 0.48
22 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAATAAAGAGAAAAAAAA
Found at i:835610 original size:16 final size:17
Alignment explanation
Indices: 835581--835616 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
835571 AAGTTTTCTT
*
835581 TTTCTTTCATTTTTCGC
1 TTTCTTTCACTTTTCGC
835598 TTTCTTT-ACTTTTCGC
1 TTTCTTTCACTTTTCGC
835614 TTT
1 TTT
835617 TATTGTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.06, C:0.22, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTCTTTCACTTTTCGC
Found at i:838449 original size:21 final size:22
Alignment explanation
Indices: 838416--838485 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
838406 AACAATTAAT
*
838416 AAAC-ATAATTAAATTAA-AAAA
1 AAACAATAA-TAAATAAATAAAA
*
838437 TAACAATAATAAA-AAATAAAA
1 AAACAATAATAAATAAATAAAA
838458 AAACAATAA-AAATGAAATAAAA
1 AAACAATAATAAAT-AAATAAAA
838480 TAAACA
1 -AAACA
838486 CTAGTACAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.12
21 19 0.46
22 12 0.29
23 5 0.12
ACGTcount: A:0.74, C:0.06, G:0.01, T:0.19
Consensus pattern (22 bp):
AAACAATAATAAATAAATAAAA
Found at i:839203 original size:31 final size:32
Alignment explanation
Indices: 839156--839225 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
839146 ACAATAGGCT
839156 GGCCACCCCTTAGCAAGCTCCAACCGCCTTCC
1 GGCCACCCCTTAGCAAGCTCCAACCGCCTTCC
* *
839188 GGCCACCTC-TAGCAAGCTCCAGCCGCCTTCC
1 GGCCACCCCTTAGCAAGCTCCAACCGCCTTCC
839219 GGCCACC
1 GGCCACC
839226 GTGCGGTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 28 0.78
32 8 0.22
ACGTcount: A:0.17, C:0.50, G:0.19, T:0.14
Consensus pattern (32 bp):
GGCCACCCCTTAGCAAGCTCCAACCGCCTTCC
Found at i:846702 original size:24 final size:24
Alignment explanation
Indices: 846650--846702 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
846640 CCAAAATTAT
*
846650 AAAAATTCCTTCAAAATATTAATA
1 AAAAATTCCTTCAAAATATAAATA
846674 AAAAATTCCTTCAAAATA-AAATA
1 AAAAATTCCTTCAAAATATAAATA
846697 ACAAAA
1 A-AAAA
846703 AGATGATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAAATTCCTTCAAAATATAAATA
Found at i:850090 original size:22 final size:22
Alignment explanation
Indices: 850050--850093 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
850040 AGTCGAGGGT
* **
850050 TACATAGGTCCTTTGGGACATA
1 TACATAGGTCATTAAGGACATA
850072 TACATAGGTCATTAAGGACATA
1 TACATAGGTCATTAAGGACATA
850094 GATTTCACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (22 bp):
TACATAGGTCATTAAGGACATA
Found at i:860798 original size:29 final size:28
Alignment explanation
Indices: 860731--860811 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
860721 ATTACTCTTT
*
860731 TATATATAAAAAACTAATATTATAAAACAAG
1 TATA-ATAAAAAA-TAA-ATTATAAAACAAA
* *
860762 TGTCATAAAAAATTAAATTATAAAA-ATAA
1 TATAATAAAAAA-TAAATTATAAAACA-AA
860791 TATAATAAAAAATAAA-TATAA
1 TATAATAAAAAATAAATTATAA
860812 TTAATACGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 5 0.12
28 5 0.12
29 20 0.47
30 11 0.26
31 2 0.05
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (28 bp):
TATAATAAAAAATAAATTATAAAACAAA
Found at i:860808 original size:16 final size:16
Alignment explanation
Indices: 860766--860812 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
860756 AACAAGTGTC
860766 ATAAAAAATTAAAT-T-
1 ATAAAAAA-TAAATATA
860781 AT-AAAAAT-AATATA
1 ATAAAAAATAAATATA
860795 ATAAAAAATAAATATA
1 ATAAAAAATAAATATA
860811 AT
1 AT
860813 TAATACGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.11
13 2 0.07
14 7 0.25
15 8 0.29
16 8 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAAATAAATATA
Found at i:866923 original size:15 final size:15
Alignment explanation
Indices: 866903--866939 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
866893 TGAGACATTA
*
866903 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
866918 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
*
866933 CCTGCCC
1 CCCGCCC
866940 AGCTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.68, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:876712 original size:32 final size:31
Alignment explanation
Indices: 876667--876732 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
876657 AACAACAAAC
* *
876667 AAGAGGAAAAAATCTAAAATATAAAGAAAAA
1 AAGAGGAAAAAATCAAAAAAATAAAGAAAAA
* *
876698 AAGAGAGAAGAAATCAAAAAAATAGAGAAAAA
1 AAGAG-GAAAAAATCAAAAAAATAAAGAAAAA
876730 AAG
1 AAG
876733 TTTTGATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 5 0.17
32 25 0.83
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.09
Consensus pattern (31 bp):
AAGAGGAAAAAATCAAAAAAATAAAGAAAAA
Found at i:889026 original size:22 final size:23
Alignment explanation
Indices: 888993--889054 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
888983 ATTAATAGTC
* *
888993 CTAATATAATATTTAATATTAAA
1 CTAATATTATATTTAATAATAAA
* * *
889016 CT-ATATTATATATAAAAATATA
1 CTAATATTATATTTAATAATAAA
*
889038 CTAATATTATAATTAAT
1 CTAATATTATATTTAAT
889055 CTTATAATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
CTAATATTATATTTAATAATAAA
Found at i:890760 original size:70 final size:71
Alignment explanation
Indices: 890628--890761 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 71
890618 CTAATCTTTC
* *
890628 TTCACTACTCTTTTTGTGAAGGCTTGATTACATTGCTTCACTACTCTTTTGTAAACGTTTGATTG
1 TTCACTACTCTTTTTGTGAAGGATTGATTACATTGCTTCACTACTCTTTTGTAAACGCTTGATTG
890693 TATTTA
66 TATTTA
* *
890699 TTCACTACTC-TTTTGTGAAGGATTGATTACATTGCTTCACTACTCTTTTGTGAAGGCTTGATT
1 TTCACTACTCTTTTTGTGAAGGATTGATTACATTGCTTCACTACTCTTTTGTAAACGCTTGATT
890762 CAAATGACTT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
70 49 0.83
71 10 0.17
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (71 bp):
TTCACTACTCTTTTTGTGAAGGATTGATTACATTGCTTCACTACTCTTTTGTAAACGCTTGATTG
TATTTA
Found at i:890786 original size:41 final size:35
Alignment explanation
Indices: 890627--890761 Score: 180
Period size: 35 Copynumber: 3.8 Consensus size: 35
890617 TCTAATCTTT
*
890627 CTTCACTACTCTTTTTGTGAAGGCTTGATTACATTG
1 CTTCACTACTC-TTTTGTGAAGGATTGATTACATTG
* * * ** *
890663 CTTCACTACTCTTTTGTAAACGTTTGATTGTATTT
1 CTTCACTACTCTTTTGTGAAGGATTGATTACATTG
*
890698 ATTCACTACTCTTTTGTGAAGGATTGATTACATTG
1 CTTCACTACTCTTTTGTGAAGGATTGATTACATTG
*
890733 CTTCACTACTCTTTTGTGAAGGCTTGATT
1 CTTCACTACTCTTTTGTGAAGGATTGATT
890762 CAAATGACTT
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 73 0.87
36 11 0.13
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (35 bp):
CTTCACTACTCTTTTGTGAAGGATTGATTACATTG
Done.