Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001991.1 Hibiscus syriacus cultivar Beakdansim tig00004072_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: 2373627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:382962 original size:42 final size:41
Alignment explanation
Indices: 382877--382999 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
382867 GTGAATCGGG
* * * * *
382877 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
382919 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * * *
382961 CTCTTCAACGATAGGAGTGGAATCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
383000 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:385083 original size:33 final size:33
Alignment explanation
Indices: 385026--385124 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
385016 ACGAGATAAT
*
385026 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
385060 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
385093 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
385125 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:385118 original size:19 final size:19
Alignment explanation
Indices: 385001--385166 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
384991 TCTTTTGGTT
*
385001 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
385020 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
385040 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
385058 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
385074 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
385092 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
385107 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
385127 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
385146 GAAATGAAAATTGCAATGC
1 GAAATGAAAATCGCAACGC
385165 GA
1 GA
385167 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 42 0.36
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:385184 original size:19 final size:19
Alignment explanation
Indices: 385162--385206 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
385152 AAAATTGCAA
*
385162 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
385181 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
385200 TGCGATT
1 TGCGATT
385207 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:385845 original size:20 final size:20
Alignment explanation
Indices: 385752--385845 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
385742 CGCTATGTAA
*
385752 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
385772 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
385792 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
385813 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
385833 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
385846 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:385864 original size:41 final size:41
Alignment explanation
Indices: 385773--385907 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
385763 AAAGTCAGTA
* * * ** *
385773 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
385813 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
385855 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
385896 TCGCGTTGCGAT
1 TCGCGTTGCGAT
385908 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:385878 original size:20 final size:20
Alignment explanation
Indices: 385834--385926 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
385824 ATAGTCAGTA
* **
385834 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
385855 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
385875 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
385896 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
385916 TCGCATTGCGA
1 TCGCATTGCGA
385927 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:385908 original size:41 final size:41
Alignment explanation
Indices: 385834--385929 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
385824 ATAGTCAGTA
*
385834 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
385875 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
385916 TCGCATTGCGAATT
1 TCGCATTGCGAATT
385930 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:394250 original size:104 final size:104
Alignment explanation
Indices: 394126--394334 Score: 332
Period size: 104 Copynumber: 2.0 Consensus size: 104
394116 TGTAACCCAA
394126 TAAAAATACTCCATTTATTTAATTTAATCATT-A-ATATATATAAATTTATATTTTTAATCATTT
1 TAAAAATACTCCATTTATTTAATTTAATCATTAATATATATATAAATTTATATTTTTAATCATTT
* * *
394189 AGTTGTCAAAAAAAGTTACTCCTTCTGCCTTATTAATTTTG
66 AATTGTCAAAAAAA--TACTCCTTCAGCCTTATCAATTTTG
*
394230 TAAAAATACTTCATTTATTTAATTTAATCATTAATATATATATAAATTTATATTTTTAATCATTT
1 TAAAAATACTCCATTTATTTAATTTAATCATTAATATATATATAAATTTATATTTTTAATCATTT
* *
394295 AATTGTCAATAAAATACTCCTTCAGCCTTATCATTTTTG
66 AATTGTCAAAAAAATACTCCTTCAGCCTTATCAATTTTG
394334 T
1 T
394335 CCCATTTTTA
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
104 54 0.56
105 1 0.01
106 42 0.43
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (104 bp):
TAAAAATACTCCATTTATTTAATTTAATCATTAATATATATATAAATTTATATTTTTAATCATTT
AATTGTCAAAAAAATACTCCTTCAGCCTTATCAATTTTG
Found at i:396668 original size:63 final size:63
Alignment explanation
Indices: 396565--396685 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
396555 ACGTGTGATT
* * * * *
396565 AAGTGATGATGTGGCATATGTTACATCATTCAAATTATGATATGATATATATTATATCACTTA
1 AAGTGATGATGTGACATATATTACATCATTCAAATAATGATATGACATATATCATATCACTTA
* *
396628 AAGTGATGATGTGACATATATTATATTA-TCAAAATAATGATATGACATATATCATATC
1 AAGTGATGATGTGACATATATTACATCATTC-AAATAATGATATGACATATATCATATC
396686 GCTAAAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (63 bp):
AAGTGATGATGTGACATATATTACATCATTCAAATAATGATATGACATATATCATATCACTTA
Found at i:396674 original size:31 final size:32
Alignment explanation
Indices: 396570--396708 Score: 113
Period size: 31 Copynumber: 4.4 Consensus size: 32
396560 TGATTAAGTG
* * * * * *
396570 ATGATGTGGCATATGTTACATCATTC-AAATT
1 ATGATATGACATATATTATATCACTCAAAATA
* * * *
396601 ATGATATGATATATATTATATCACTTAAAGTG
1 ATGATATGACATATATTATATCACTCAAAATA
* *
396633 ATGATGTGACATATATTATATTA-TCAAAATA
1 ATGATATGACATATATTATATCACTCAAAATA
* *
396664 ATGATATGACATATATCATATCGCT-AAAATA
1 ATGATATGACATATATTATATCACTCAAAATA
* *
396695 ATGACATGATATAT
1 ATGATATGACATAT
396709 TTTAGGTTAA
Statistics
Matches: 85, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
31 61 0.72
32 24 0.28
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (32 bp):
ATGATATGACATATATTATATCACTCAAAATA
Found at i:403157 original size:19 final size:19
Alignment explanation
Indices: 403129--403177 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
403119 GGTCGGGTCG
*
403129 GGTCAGACCGATTCAAACC
1 GGTCAAACCGATTCAAACC
* *
403148 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGATTCAAACC
*
403167 AGTCGAAACCG
1 GGTC-AAACCG
403178 GTTTTCAGCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (19 bp):
GGTCAAACCGATTCAAACC
Found at i:403852 original size:10 final size:10
Alignment explanation
Indices: 403837--403863 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
403827 AATTTAATCC
403837 CCAAATTTCA
1 CCAAATTTCA
403847 CCAAATTTCA
1 CCAAATTTCA
403857 CCAAATT
1 CCAAATT
403864 ACATCGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (10 bp):
CCAAATTTCA
Found at i:404780 original size:13 final size:13
Alignment explanation
Indices: 404762--404787 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
404752 GTAGCGCCTT
404762 CCAAAATCTCGAA
1 CCAAAATCTCGAA
404775 CCAAAATCTCGAA
1 CCAAAATCTCGAA
404788 GTAAATCTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (13 bp):
CCAAAATCTCGAA
Found at i:428082 original size:50 final size:50
Alignment explanation
Indices: 428006--428132 Score: 148
Period size: 50 Copynumber: 2.5 Consensus size: 50
427996 GTAGCAGTAA
* * *
428006 AGCGCGCCCCCCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTAT
1 AGCGCG-CCCCCTGACCCGCGATATACGCTGATCTGGCACCACGTGGGTAT
* * **
428057 AGCGCGCGCCCTG-CCCTGCGATATACGGTGATCTGGCGTCACGTGGGTAT
1 AGCGCGCCCCCTGACCC-GCGATATACGCTGATCTGGCACCACGTGGGTAT
* *
428107 AGTGCGCCCCCTGATCCGCGATATAC
1 AGCGCGCCCCCTGACCCGCGATATAC
428133 CTGGGTATCT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.03
50 54 0.84
51 8 0.12
ACGTcount: A:0.17, C:0.34, G:0.29, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCCCTGACCCGCGATATACGCTGATCTGGCACCACGTGGGTAT
Found at i:428270 original size:10 final size:10
Alignment explanation
Indices: 428255--428294 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
428245 TTTATCACAC
428255 CAAATTCTCT
1 CAAATTCTCT
428265 CAAATTCTCT
1 CAAATTCTCT
428275 -AAATTTCTCT
1 CAAA-TTCTCT
*
428285 CAAATACTCT
1 CAAATTCTCT
428295 ATATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:428284 original size:20 final size:20
Alignment explanation
Indices: 428259--428300 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
428249 TCACACCAAA
*
428259 TTCTCTCAAATTCTCTAAAT
1 TTCTCTCAAATACTCTAAAT
*
428279 TTCTCTCAAATACTCTATAT
1 TTCTCTCAAATACTCTAAAT
428299 TT
1 TT
428301 TTAAGGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.48
Consensus pattern (20 bp):
TTCTCTCAAATACTCTAAAT
Found at i:428617 original size:112 final size:111
Alignment explanation
Indices: 428421--428640 Score: 377
Period size: 112 Copynumber: 2.0 Consensus size: 111
428411 TGGAAATCAT
* *
428421 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTAATTTAATTTAAATTATTAGTAAT
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTAATTTAATTTAAATTATTAGTAAT
* *
428486 ATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTTTA
66 AATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTTTA
*
428532 ATATCTCGAGACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACG-TTTAATTTAATTTAAATTATTAGTAA
*
428597 TAATTAGTTGATTTATTTAATTCATGATTATTAGAGTAAGAATT
65 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATT
428641 AATTTTTGTA
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
111 35 0.34
112 67 0.66
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTAATTTAATTTAAATTATTAGTAAT
AATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTTTA
Found at i:430175 original size:18 final size:18
Alignment explanation
Indices: 430149--430183 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
430139 CAGCAGCCAC
*
430149 CACAGCCATATATGATGT
1 CACAACCATATATGATGT
430167 CACAACCATATATGATG
1 CACAACCATATATGATG
430184 CCGCCATCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (18 bp):
CACAACCATATATGATGT
Found at i:430543 original size:12 final size:12
Alignment explanation
Indices: 430523--430561 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
430513 TGCTCAGGAC
430523 GACGACGACGAT
1 GACGACGACGAT
** *
430535 GGTGACGACGAC
1 GACGACGACGAT
430547 GACGACGACGAT
1 GACGACGACGAT
430559 GAC
1 GAC
430562 AGCGAGGAGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.36, T:0.08
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:431934 original size:21 final size:21
Alignment explanation
Indices: 431908--431949 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
431898 AAAAATGTAT
*
431908 AACTTACTAACTTGCTTTCAC
1 AACTTACTAACTTACTTTCAC
431929 AACTTACTAACTTACTTTCAC
1 AACTTACTAACTTACTTTCAC
431950 TTACTCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.02, T:0.38
Consensus pattern (21 bp):
AACTTACTAACTTACTTTCAC
Found at i:434519 original size:51 final size:51
Alignment explanation
Indices: 434453--434567 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
434443 TATTGCAGAG
* * *
434453 CAGGGGGCGCTCTATACCCCACGTGTAAC-CC-AGTCAGCGTATAGCGCGGTA
1 CAGGGGGCGCGCTATACCCCACGTG--ACGCCAAATCAGCATATAGCGCGGTA
* *
434504 CAGGGGGCGCGCTATACTCCACGTGACGCCAAATCAGCATATAGCGCGGTT
1 CAGGGGGCGCGCTATACCCCACGTGACGCCAAATCAGCATATAGCGCGGTA
*
434555 CAGGGGGTGCGCT
1 CAGGGGGCGCGCT
434568 TTACTGCTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 2 0.04
50 2 0.04
51 52 0.93
ACGTcount: A:0.21, C:0.30, G:0.32, T:0.17
Consensus pattern (51 bp):
CAGGGGGCGCGCTATACCCCACGTGACGCCAAATCAGCATATAGCGCGGTA
Found at i:434798 original size:17 final size:17
Alignment explanation
Indices: 434764--434800 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
434754 TTTCACCTGT
**
434764 TAAATTTAAATATTTAA
1 TAAATTTAAATAGATAA
434781 TAAATTTAAATAGATAA
1 TAAATTTAAATAGATAA
434798 TAA
1 TAA
434801 TGTTCAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATAGATAA
Found at i:438198 original size:21 final size:20
Alignment explanation
Indices: 438157--438194 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
438147 TCACATTACC
438157 TAATTATTAAAATATTTAATT
1 TAATTATT-AAATATTTAATT
438178 TAATTATT-AATATTTAA
1 TAATTATTAAATATTTAA
438195 AATTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTATTAAATATTTAATT
Found at i:438202 original size:19 final size:18
Alignment explanation
Indices: 438158--438204 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
438148 CACATTACCT
*
438158 AATTATTA-AAATATTTA
1 AATTATTATTAATATTTA
*
438175 ATTTAATTATTAATATTTAA
1 AATT-ATTATTAATATTT-A
438195 AATTATTATT
1 AATTATTATT
438205 TTTAAACACT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.12
18 4 0.17
19 13 0.54
20 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATTATTAATATTTA
Found at i:441138 original size:21 final size:21
Alignment explanation
Indices: 441104--441145 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
441094 TAACAAGAAT
*
441104 AATTTAAAACAAAATTAAAAA
1 AATTTAAAACAAAACTAAAAA
441125 AATTGTAAAA-AAAACTAAAAA
1 AATT-TAAAACAAAACTAAAAA
441146 CGATGAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (21 bp):
AATTTAAAACAAAACTAAAAA
Found at i:445754 original size:23 final size:23
Alignment explanation
Indices: 445717--445777 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
445707 CAGCTCGTAT
445717 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * *
445740 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
445763 AAATGCACCGAAGTG
1 AAATGCACCGAAGTG
445778 TAGGGATGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:449705 original size:16 final size:16
Alignment explanation
Indices: 449683--449724 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
449673 ATTCAAAGTT
449683 GGCTGCAAATTGGGGCA
1 GGCTGCAAATTGGGG-A
449700 -GCTGCAAATTGGGGA
1 GGCTGCAAATTGGGGA
449715 GGCTGCAAAT
1 GGCTGCAAAT
449725 GTTCAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.26, C:0.17, G:0.38, T:0.19
Consensus pattern (16 bp):
GGCTGCAAATTGGGGA
Found at i:452295 original size:45 final size:45
Alignment explanation
Indices: 452237--452327 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
452227 AACGATAGTG
* * *
452237 ATTCTTCGTTTATATCAAAAGGGATGAATCGTCATCGACCGATAC
1 ATTCTCCGTTTATATCAAAAGGAATGAATCGTCATCAACCGATAC
452282 ATTCTCCGTTTATATCAAAAGGAATGAATCGTCATCAACCGATAC
1 ATTCTCCGTTTATATCAAAAGGAATGAATCGTCATCAACCGATAC
452327 A
1 A
452328 ATCATCTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (45 bp):
ATTCTCCGTTTATATCAAAAGGAATGAATCGTCATCAACCGATAC
Found at i:463432 original size:15 final size:15
Alignment explanation
Indices: 463412--463442 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
463402 TTGATCTAAT
*
463412 TATTATTAAAAATAA
1 TATTATAAAAAATAA
463427 TATTATAAAAAATAA
1 TATTATAAAAAATAA
463442 T
1 T
463443 GTGATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTATAAAAAATAA
Found at i:465891 original size:19 final size:21
Alignment explanation
Indices: 465867--465914 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
465857 TTAGTTTCCA
465867 CCATGTCTG-AAA-CTAACAG
1 CCATGTCTGTAAAGCTAACAG
465886 CCATGTCTGTTCAAAGCTAACAG
1 CCATGTCTG-T-AAAGCTAACAG
465909 CCATGT
1 CCATGT
465915 TAACGGGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (21 bp):
CCATGTCTGTAAAGCTAACAG
Found at i:471301 original size:2 final size:2
Alignment explanation
Indices: 471294--471325 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
471284 ATATGAAGAA
471294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
471326 CGTTATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:478410 original size:19 final size:19
Alignment explanation
Indices: 478346--478410 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
478336 TATTTTTAAG
* * *
478346 ATTATAATCAAAATGAATT
1 ATTATAATTATAATTAATT
* *
478365 AGTATAATATATAAATTCATAT
1 ATTATAAT-TAT-AATTAAT-T
478387 ATTATAATTATAATTAATT
1 ATTATAATTATAATTAATT
478406 ATTAT
1 ATTAT
478411 GCTTTATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
19 13 0.36
20 7 0.19
21 8 0.22
22 8 0.22
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTATAATTATAATTAATT
Found at i:478441 original size:14 final size:14
Alignment explanation
Indices: 478417--478449 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
478407 TTATGCTTTA
478417 TAAATAAATAT-CT
1 TAAATAAATATACT
478430 TAAATAAAATATACT
1 TAAAT-AAATATACT
478445 TAAAT
1 TAAAT
478450 TTAAACTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 6 0.33
15 7 0.39
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATAAATATACT
Found at i:479547 original size:2 final size:2
Alignment explanation
Indices: 479540--479571 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
479530 TCTGAATTCA
479540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
479572 GAATCAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:483407 original size:49 final size:49
Alignment explanation
Indices: 483348--483475 Score: 195
Period size: 48 Copynumber: 2.6 Consensus size: 49
483338 AATTGCTCTA
483348 TAATGAAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* * *
483397 TAATGCAAGTTAAATGCATAATAGTGCA-TTTTGGCAGAAATGTGCCAC
1 TAATGAAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* * *
483445 TAATGAAAGTTAAATGTATAACGGTGTATTT
1 TAATGAAAGTTAAATGCATAATGGTGCATTT
483476 CGGCATAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
48 42 0.60
49 28 0.40
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (49 bp):
TAATGAAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
Found at i:487447 original size:2 final size:2
Alignment explanation
Indices: 487440--487490 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
487430 ATTTTAATTG
487440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
487482 AT AT AT AT A
1 AT AT AT AT A
487491 AAATAAATTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:488428 original size:19 final size:19
Alignment explanation
Indices: 488400--488449 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
488390 GATATAGTTG
*
488400 ACCGGCTTGACCGGTCCAA
1 ACCGGTTTGACCGGTCCAA
* *
488419 ACCGGTTTGACCGTTCCGA
1 ACCGGTTTGACCGGTCCAA
*
488438 ACCGGTCTGACC
1 ACCGGTTTGACC
488450 CGACCCGGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.18, C:0.36, G:0.26, T:0.20
Consensus pattern (19 bp):
ACCGGTTTGACCGGTCCAA
Found at i:488489 original size:18 final size:18
Alignment explanation
Indices: 488444--488495 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
488434 CCGAACCGGT
* *
488444 CTGACCCGACCCGGCCCG
1 CTGACCTGACCCGACCCG
488462 CTGA-CTGACCCGACCCG
1 CTGACCTGACCCGACCCG
* *
488479 TTGACCTGACCTGACCC
1 CTGACCTGACCCGACCC
488496 AGTGACTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.15, C:0.48, G:0.23, T:0.13
Consensus pattern (18 bp):
CTGACCTGACCCGACCCG
Found at i:488501 original size:18 final size:18
Alignment explanation
Indices: 488445--488495 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
488435 CGAACCGGTC
* * *
488445 TGACCCGACCCGGCCCGC
1 TGACCTGACCCGACCCGT
488463 TGA-CTGACCCGACCCGT
1 TGACCTGACCCGACCCGT
*
488480 TGACCTGACCTGACCC
1 TGACCTGACCCGACCC
488496 AGTGACTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.16, C:0.47, G:0.24, T:0.14
Consensus pattern (18 bp):
TGACCTGACCCGACCCGT
Found at i:488558 original size:29 final size:29
Alignment explanation
Indices: 488497--488575 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
488487 ACCTGACCCA
* *
488497 GTGACTTTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* *
488526 GTGACATTTTGGGAATTA-TTTGTAACACG
1 GTGACATTTTGGGAATTATTTTG-AAAAAG
* *
488555 GTGATATTTTGGTAATTATTT
1 GTGACATTTTGGGAATTATTT
488576 AAAAAAAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.10
29 36 0.86
30 2 0.05
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.46
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:490352 original size:21 final size:21
Alignment explanation
Indices: 490326--490367 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
490316 CACGATATGT
*
490326 GGAGTAATGGTCGCATAGTAA
1 GGAGTAACGGTCGCATAGTAA
*
490347 GGAGTAACGGTCGCATCGTAA
1 GGAGTAACGGTCGCATAGTAA
490368 CGTTACGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.21
Consensus pattern (21 bp):
GGAGTAACGGTCGCATAGTAA
Found at i:490927 original size:21 final size:21
Alignment explanation
Indices: 490903--490956 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
490893 ATTACGGTGA
*
490903 TGACGTGACAGTTCACAGTAT
1 TGACGTGACAGTTCACAATAT
* *
490924 TGACATGACAGTTTACAATAT
1 TGACGTGACAGTTCACAATAT
*
490945 TGATGTGACAGT
1 TGACGTGACAGT
490957 CTACTATAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (21 bp):
TGACGTGACAGTTCACAATAT
Found at i:491509 original size:14 final size:14
Alignment explanation
Indices: 491490--491569 Score: 60
Period size: 14 Copynumber: 6.0 Consensus size: 14
491480 TCGATAATCT
491490 GTTCGTTTATATTC
1 GTTCGTTTATATTC
*
491504 GTTCGTTTATGTTC
1 GTTCGTTTATATTC
*
491518 GTTC-ATT-TA-T-
1 GTTCGTTTATATTC
* * *
491528 GTTCATTTATGTTT
1 GTTCGTTTATATTC
* *
491542 GTTCGTTTATGTTT
1 GTTCGTTTATATTC
*
491556 GTTTGTTTATATTC
1 GTTCGTTTATATTC
491570 AACTCAATCT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
10 4 0.08
11 3 0.06
12 2 0.04
13 3 0.06
14 41 0.77
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.61
Consensus pattern (14 bp):
GTTCGTTTATATTC
Found at i:491531 original size:24 final size:24
Alignment explanation
Indices: 491504--491559 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
491494 GTTTATATTC
491504 GTTCGTTTATGTTCGTTCATTTAT
1 GTTCGTTTATGTTCGTTCATTTAT
* * *
491528 GTTCATTTATGTTTGTTCGTTTAT
1 GTTCGTTTATGTTCGTTCATTTAT
*
491552 GTTTGTTT
1 GTTCGTTT
491560 GTTTATATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.62
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCATTTAT
Found at i:491660 original size:16 final size:17
Alignment explanation
Indices: 491635--491667 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
491625 ATCGATTAAT
*
491635 ATTTTAAAACCTAAATA
1 ATTTTAAAACCCAAATA
491652 ATTTT-AAACCCAAATA
1 ATTTTAAAACCCAAATA
491668 GATATACTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTTTAAAACCCAAATA
Found at i:491774 original size:10 final size:10
Alignment explanation
Indices: 491759--491786 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
491749 ATTTTATGTT
491759 TGTTCGTTTA
1 TGTTCGTTTA
491769 TGTTCGTTTA
1 TGTTCGTTTA
491779 TGTTCGTT
1 TGTTCGTT
491787 CATTTGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.11, G:0.21, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:491778 original size:24 final size:24
Alignment explanation
Indices: 491751--491827 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
491741 CCCAATTAAT
* *
491751 TTTATGTTTGTTCGTTTATGTTCG
1 TTTATGTTCGTTCATTTATGTTCG
* *
491775 TTTATGTTCGTTCATTTGTGTTCA
1 TTTATGTTCGTTCATTTATGTTCG
* * *
491799 TTTACGTTCATTTATTTATGTTCG
1 TTTATGTTCGTTCATTTATGTTCG
491823 TTTAT
1 TTTAT
491828 CATTTTACCA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.61
Consensus pattern (24 bp):
TTTATGTTCGTTCATTTATGTTCG
Found at i:492909 original size:7 final size:7
Alignment explanation
Indices: 492891--492924 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
492881 CCATTTGAAT
492891 ACATTCAA
1 ACATT-AA
492899 ACATTAA
1 ACATTAA
492906 ACATTAA
1 ACATTAA
492913 ACATTAA
1 ACATTAA
492920 ACATT
1 ACATT
492925 TTTTGGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (7 bp):
ACATTAA
Found at i:493575 original size:7 final size:7
Alignment explanation
Indices: 493565--493599 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
493555 TTCTTATATA
493565 TGGCTGC
1 TGGCTGC
493572 TGGCTGC
1 TGGCTGC
*
493579 TGGCTGT
1 TGGCTGC
*
493586 TGGCTGT
1 TGGCTGC
493593 TGGCTGC
1 TGGCTGC
493600 AATTGTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.43, T:0.34
Consensus pattern (7 bp):
TGGCTGC
Found at i:495527 original size:2 final size:2
Alignment explanation
Indices: 495520--495560 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
495510 AGTAATTAGT
495520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
495561 TTGAAAGATG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:506564 original size:45 final size:45
Alignment explanation
Indices: 506498--506596 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 45
506488 GCACTACTTG
* * **
506498 TGCATCGGTGCATAAAATGCATTCGATG-TTTTATTATTAATGGAA
1 TGCATCGATGCATAAAATGCATTCAATGTTTTTATT-TTAAAAGAA
* *
506543 TGCATCGATGCACT-AATTGCATTCAATGTTTTTATTTTAAAAGAG
1 TGCATCGATGCA-TAAAATGCATTCAATGTTTTTATTTTAAAAGAA
506588 TGCATCGAT
1 TGCATCGAT
506597 ACACCTTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 38 0.83
46 8 0.17
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (45 bp):
TGCATCGATGCATAAAATGCATTCAATGTTTTTATTTTAAAAGAA
Found at i:513390 original size:64 final size:64
Alignment explanation
Indices: 513321--513477 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
513311 TAATGAAGGT
* **
513321 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAAAAG
513384 A
64 A
* * *
513385 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAGA
* **
513449 GTGCATCGATGCACTACCCGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
513478 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 68 0.87
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAGA
Found at i:517565 original size:31 final size:31
Alignment explanation
Indices: 517488--517568 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
517478 TATTTATGTT
*
517488 AAGTGAT-CATGTCTTAATTAAAATAAAACAA
1 AAGTGATACA-GTATTAATTAAAATAAAACAA
* * *
517519 AATTGATAGAGTATTAATTAAAATAAAATAA
1 AAGTGATACAGTATTAATTAAAATAAAACAA
517550 AAGTGATCACA-TATTAATT
1 AAGTGAT-ACAGTATTAATT
517569 TTTTTAGATC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
31 39 0.93
32 3 0.07
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (31 bp):
AAGTGATACAGTATTAATTAAAATAAAACAA
Found at i:527013 original size:7 final size:7
Alignment explanation
Indices: 526964--527039 Score: 57
Period size: 7 Copynumber: 10.7 Consensus size: 7
526954 TTGATTATTT
526964 TAATAATA
1 TAAT-ATA
526972 TAATATAA
1 TAATAT-A
* *
526980 TATTTTA
1 TAATATA
*
526987 TTAT-TA
1 TAATATA
526993 TAAT-TA
1 TAATATA
526999 TAATATA
1 TAATATA
*
527006 TAACATA
1 TAATATA
527013 TAATATA
1 TAATATA
* *
527020 TATTTTAA
1 TAATAT-A
527028 TAATATA
1 TAATATA
527035 TAATA
1 TAATA
527040 AATTACTAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
6 11 0.20
7 29 0.54
8 14 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (7 bp):
TAATATA
Found at i:527199 original size:28 final size:27
Alignment explanation
Indices: 527168--527251 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 27
527158 TTTTTATATT
527168 TTAATAGTATTATTATTTTAATAAATAA
1 TTAATA-TATTATTATTTTAATAAATAA
* * *
527196 TTAATATA--ATTA--ATAATATATTA
1 TTAATATATTATTATTTTAATAAATAA
527219 TT-AT-TATTATTATTTTAATAAATAA
1 TTAATATATTATTATTTTAATAAATAA
*
527244 TTACTATA
1 TTAATATA
527252 ATTCATAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 14 0.33
25 14 0.33
26 1 0.02
27 4 0.09
28 6 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TTAATATATTATTATTTTAATAAATAA
Found at i:527227 original size:20 final size:20
Alignment explanation
Indices: 527169--527227 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
527159 TTTTATATTT
527169 TAATAGTATTATTATT-TTAA
1 TAATA-TATTATTATTATTAA
* *
527189 TAA-ATAATTAATATAATTAA
1 TAATAT-ATTATTATTATTAA
527209 TAATATATTATTATTATTA
1 TAATATATTATTATTATTA
527228 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.03
19 8 0.25
20 21 0.66
21 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATATATTATTATTATTAA
Found at i:527235 original size:48 final size:46
Alignment explanation
Indices: 527175--527269 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 46
527165 ATTTTAATAG
527175 TATTATTATTTTAATAAATAATTAATATAATTAATAATATATTATTAT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATA-ATT-TTAT
* *
527223 TATTATTATTTTAATAAATAATTACTATAATTCATAATAATTTTAT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATAATTTTAT
527269 T
1 T
527270 TAAATAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 5 0.11
47 3 0.07
48 37 0.82
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (46 bp):
TATTATTATTTTAATAAATAATTAATATAATTAATAATAATTTTAT
Found at i:527276 original size:33 final size:31
Alignment explanation
Indices: 527237--527328 Score: 93
Period size: 33 Copynumber: 2.9 Consensus size: 31
527227 ATTATTTTAA
527237 TAAATAATTACTATAATTCATAATAATTTTATT
1 TAAATAATTA-TATAA-TCATAATAATTTTATT
* *
527270 TAAATAAAATATATTAATCATAATATTTTTATT
1 TAAAT-AATTATA-TAATCATAATAATTTTATT
527303 TATAA-AATTATAT-AT-ATAAT-ATTTTA
1 TA-AATAATTATATAATCATAATAATTTTA
527329 ATAATTATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
28 5 0.10
29 5 0.10
30 2 0.04
31 1 0.02
32 6 0.12
33 24 0.46
34 9 0.17
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
TAAATAATTATATAATCATAATAATTTTATT
Found at i:527534 original size:16 final size:15
Alignment explanation
Indices: 527495--527534 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
527485 TCAAACAACG
527495 TAAAATAATTTTTAA
1 TAAAATAATTTTTAA
527510 -AAAATAATTTTTAA
1 TAAAATAATTTTTAA
527524 TAAATATAATT
1 TAAA-ATAATT
527535 CATTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATAATTTTTAA
Found at i:528420 original size:60 final size:60
Alignment explanation
Indices: 528351--528463 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
528341 TAGTGACATT
* * * * ** *
528351 TTTAGAATAAGGATCATAGTTTGGGAATAATGTTGGAATATTTAAAAGTTTGAAGATTAG
1 TTTAAAATAAGAACCATAATTTGGGAATAAAATTGAAATATTTAAAAGTTTGAAGATTAG
* *
528411 TTTAAAATAAGAACCATAATTTGGGGATAAAATTGAAATATTTAAAATTTTGA
1 TTTAAAATAAGAACCATAATTTGGGAATAAAATTGAAATATTTAAAAGTTTGA
528464 GGGCAAACTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (60 bp):
TTTAAAATAAGAACCATAATTTGGGAATAAAATTGAAATATTTAAAAGTTTGAAGATTAG
Found at i:528723 original size:15 final size:15
Alignment explanation
Indices: 528703--528732 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
528693 GAGCAATAAC
*
528703 AATTTAATTTTTAAA
1 AATTTAAATTTTAAA
528718 AATTTAAATTTTAAA
1 AATTTAAATTTTAAA
528733 GGACTCAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTAAATTTTAAA
Found at i:528930 original size:21 final size:21
Alignment explanation
Indices: 528900--528945 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
528890 ATACATTCAA
528900 TTAA-CCACTTGGGTTAATAT
1 TTAACCCACTTGGGTTAATAT
528920 TTAACCCACTTGGGTTAATAT
1 TTAACCCACTTGGGTTAATAT
528941 TTAAC
1 TTAAC
528946 GGAGAAGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (21 bp):
TTAACCCACTTGGGTTAATAT
Found at i:529723 original size:21 final size:21
Alignment explanation
Indices: 529698--529738 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
529688 TAATGAACAG
*
529698 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCACCGATGCAT
529719 TGCTACAGTGCACCGATGCA
1 TGCTACAGTGCACCGATGCA
529739 CAAAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCTACAGTGCACCGATGCAT
Found at i:533119 original size:26 final size:21
Alignment explanation
Indices: 533061--533158 Score: 169
Period size: 21 Copynumber: 4.6 Consensus size: 21
533051 TTTTTTACTT
*
533061 TTTTAATGATGATATGACATTA
1 TTTT-ATGATGACATGACATTA
*
533083 CTTTATGATGACATGACATTA
1 TTTTATGATGACATGACATTA
533104 TTTTATGATGACATGACATTA
1 TTTTATGATGACATGACATTA
533125 TTTTATGATGACATGACATTA
1 TTTTATGATGACATGACATTA
533146 TTTTATGATGACA
1 TTTTATGATGACA
533159 CATCATCATT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
21 70 0.96
22 3 0.04
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (21 bp):
TTTTATGATGACATGACATTA
Found at i:537442 original size:31 final size:31
Alignment explanation
Indices: 537400--537652 Score: 436
Period size: 31 Copynumber: 8.2 Consensus size: 31
537390 GGTCACAATA
*
537400 TAAACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
537431 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
537462 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
537493 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
537524 TAAA-TCGTTCATATGTGCCTTTAAACATATG
1 TAAACT-GTTCATATGTGCCTTTAAACATATG
*
537555 TAAACCGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
537586 TAAACCGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
537617 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
537648 TAAAC
1 TAAAC
537653 CCTCGACTCT
Statistics
Matches: 211, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
30 1 0.00
31 210 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:538340 original size:45 final size:45
Alignment explanation
Indices: 538245--538348 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 45
538235 TGCACTCCTT
* *
538245 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
* *
538290 ATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
538334 AGTGCATCGATGCAC
1 A-TGCATCGATGCAC
538349 TACCAATGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
44 2 0.04
45 46 0.87
46 5 0.09
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (45 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:538906 original size:15 final size:15
Alignment explanation
Indices: 538886--538919 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
538876 TGGAGATACG
*
538886 GAAGGAGAGGAAGAA
1 GAAGGAGAAGAAGAA
*
538901 GAAGGAGAAGAAGGA
1 GAAGGAGAAGAAGAA
538916 GAAG
1 GAAG
538920 AAGTTCTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
GAAGGAGAAGAAGAA
Found at i:538909 original size:9 final size:9
Alignment explanation
Indices: 538897--538922 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
538887 AAGGAGAGGA
538897 AGAAGAAGG
1 AGAAGAAGG
538906 AGAAGAAGG
1 AGAAGAAGG
538915 AGAAGAAG
1 AGAAGAAG
538923 TTCTGAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:545619 original size:14 final size:14
Alignment explanation
Indices: 545600--545626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
545590 GTTAATCGGA
545600 TTGCTTCTCATAAT
1 TTGCTTCTCATAAT
545614 TTGCTTCTCATAA
1 TTGCTTCTCATAA
545627 GTTTCTGTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (14 bp):
TTGCTTCTCATAAT
Found at i:551157 original size:36 final size:38
Alignment explanation
Indices: 551092--551167 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
551082 AATATAAATA
*
551092 TATATATATATATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACCAAAGTATTAATAAAATAGAA-AAGC
551130 TATATATATATACCAAA-TACTT-A-AAAATAGAAAAGC
1 TATATATATATACCAAAGTA-TTAATAAAATAGAAAAGC
551166 TA
1 TA
551168 CCCTCCCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 12 0.34
37 5 0.14
38 18 0.51
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (38 bp):
TATATATATATACCAAAGTATTAATAAAATAGAAAAGC
Found at i:551629 original size:18 final size:17
Alignment explanation
Indices: 551606--551648 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
551596 ATATATACAT
551606 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
551624 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
551641 ATAA-AATA
1 ATAATAATA
551649 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:552056 original size:37 final size:37
Alignment explanation
Indices: 552006--552110 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
551996 GTGCTTGTGG
* * * *
552006 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
552043 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
552080 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
552111 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:552955 original size:105 final size:103
Alignment explanation
Indices: 552650--553063 Score: 531
Period size: 105 Copynumber: 4.0 Consensus size: 103
552640 AGCATTGTTC
* * * * *
552650 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA-TGAGAAGTTG-TTGTTGACA
* * *
552715 ACCGGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
63 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
552756 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA-AA-TT-TTGTTGACAAGC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAGAAGTTGTTGTTGACAACC
* *
552818 AGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCT
66 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
552856 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AA-TGAGAAGTTGTTGTTGACAA
* *
552921 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
64 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
552961 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG--C----TGAGAAGTTATTTGTTGACAAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAGAAGTT-GTTGTTGACAAC
* *
553020 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
553059 CGAGT
1 CGAGT
553064 GTCACGATAT
Statistics
Matches: 280, Mismatches: 22, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
97 9 0.03
98 50 0.18
100 82 0.29
101 2 0.01
102 5 0.02
103 5 0.02
104 3 0.01
105 88 0.31
106 36 0.13
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (103 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAGAAGTTGTTGTTGACAACC
AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:553310 original size:36 final size:36
Alignment explanation
Indices: 553263--553338 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
553253 TGTTTGGAGA
* * *
553263 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
553299 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
553335 GAAA
1 GAAA
553339 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:553459 original size:105 final size:104
Alignment explanation
Indices: 553238--553556 Score: 518
Period size: 105 Copynumber: 3.1 Consensus size: 104
553228 TTCATTAAAT
* ** *
553238 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
553300 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
*
553339 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTTGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
553404 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
553444 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
553509 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
553548 TGTTTTCAA
1 TGTTTTCAA
553557 GAGAAACTAT
Statistics
Matches: 202, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
101 46 0.23
103 3 0.01
104 53 0.26
105 100 0.50
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:553513 original size:39 final size:39
Alignment explanation
Indices: 553459--553533 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
553449 TCAATGTTTA
* *
553459 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
553498 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
553534 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:555250 original size:183 final size:183
Alignment explanation
Indices: 554936--555472 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
554926 ATCAGGTTTA
*
554936 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
** *
555001 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTTGAGT
66 GCCAAGTGTCCGAGCAATGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
555065 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTTGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
555119 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAATGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * * *
555184 GCTAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATTTATTCATAAAGCCAGAGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
555249 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTTAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
555302 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGAAAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
555367 GCCAAGTGTCCGAGCATTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
555432 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
555473 CATATTTAAT
Statistics
Matches: 335, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 334 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:556567 original size:14 final size:14
Alignment explanation
Indices: 556548--556579 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
556538 AATTGCCACC
556548 AGGTGCCCGAAGTA
1 AGGTGCCCGAAGTA
556562 AGGTGCCCGAAGTA
1 AGGTGCCCGAAGTA
556576 AGGT
1 AGGT
556580 TCCTTCAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.38, T:0.16
Consensus pattern (14 bp):
AGGTGCCCGAAGTA
Found at i:559997 original size:45 final size:45
Alignment explanation
Indices: 559904--559994 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
559894 AGATAATTAC
* * ** * *
559904 AATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGA
1 AATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAAGA
559949 AATATATATATAATAATAATA-AAATAT-AGTAAAAAAATAAATGA
1 AATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAA-GA
559993 AA
1 AA
559995 ATAATTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 12 0.31
44 8 0.21
45 19 0.49
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (45 bp):
AATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAAGA
Found at i:560044 original size:18 final size:17
Alignment explanation
Indices: 560021--560063 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
560011 ATATATACAT
560021 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
560039 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
560056 ATAA-AATA
1 ATAATAATA
560064 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:560503 original size:37 final size:37
Alignment explanation
Indices: 560421--560522 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
560411 GTGCTTGTGG
* * * * * *
560421 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
560458 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
560495 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
560523 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:563482 original size:43 final size:44
Alignment explanation
Indices: 563319--563502 Score: 169
Period size: 43 Copynumber: 4.2 Consensus size: 44
563309 TTTTTGTTAC
* *
563319 AAACGCCGTTATATACC-AACCTTTACCGACGTTTGTATACT-A
1 AAACGCCGCTATATACCAAACCTTTAGCGACGTTTGTATACTAA
* * * * * *
563361 AAATGCCACTATATACCATACCATCAGCGGCGTTTGTATACTAA
1 AAACGCCGCTATATACCAAACCTTTAGCGACGTTTGTATACTAA
** * * * *
563405 AAACGCCATTATATACCAGATCTTTATCTG-CGTTT-TATCCTAA
1 AAACGCCGCTATATACCAAACCTTTAGC-GACGTTTGTATACTAA
** *
563448 AAACGCCGCTATATACCAAATTTTTAGCGACGTTTGTACACTAA
1 AAACGCCGCTATATACCAAACCTTTAGCGACGTTTGTATACTAA
*
563492 AAAAGCCGCTA
1 AAACGCCGCTA
563503 AATGTCAAAA
Statistics
Matches: 113, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
42 15 0.13
43 54 0.48
44 43 0.38
45 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (44 bp):
AAACGCCGCTATATACCAAACCTTTAGCGACGTTTGTATACTAA
Found at i:565276 original size:22 final size:24
Alignment explanation
Indices: 565230--565276 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
565220 TTTACCCTAT
*
565230 TTTTATAACTTCATCCCTCTAAAA
1 TTTTATAAATTCATCCCTCTAAAA
565254 TTTTATAAATTC-TCCC-CTAAAA
1 TTTTATAAATTCATCCCTCTAAAA
565276 T
1 T
565277 AAAATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTATAAATTCATCCCTCTAAAA
Found at i:575785 original size:393 final size:393
Alignment explanation
Indices: 575060--575847 Score: 1549
Period size: 393 Copynumber: 2.0 Consensus size: 393
575050 ATCTTGGTAA
575060 TAGAAATTAATCTGTTACCATCTCAAAGTGCGTTGAAAAGCCTCCATCCAAAAGTGTCGAGATAT
1 TAGAAATTAATCTGTTACCATCTCAAAGTGCGTTGAAAAGCCTCCATCCAAAAGTGTCGAGATAT
575125 CTCTGCTTGAGCTCATACTGGGAAAGAATTGTCTCGCATTCTAGCTGCCACAACTCTATGGGTTT
66 CTCTGCTTGAGCTCATACTGGGAAAGAATTGTCTCGCATTCTAGCTGCCACAACTCTATGGGTTT
575190 ATCTAAGAGTGTCGGATGCCTCCACTCAGTAGCTGGACTTCCTCCGCTGCTACTAAAAGCGTAGA
131 ATCTAAGAGTGTCGGATGCCTCCACTCAGTAGCTGGACTTCCTCCGCTGCTACTAAAAGCGTAGA
*
575255 GATTCATTTGTCCTAGTTAGGGGAAGATAGATACCTTCCCATATCTCCTACTTTTATAAAGAAGC
196 GATTCATTTGTCCTAGTTAGGGGAAGAGAGATACCTTCCCATATCTCCTACTTTTATAAAGAAGC
575320 CTTCATTTCTCAATCAAACTTTTTCGAGGGTGTTGAGTTGCCTTCTCTATCATCTGAAAATATTA
261 CTTCATTTCTCAATCAAACTTTTTCGAGGGTGTTGAGTTGCCTTCTCTATCATCTGAAAATATTA
*
575385 GAATCATTTTAACTCTCTTGTGACACCCTAATACAATCCAAAATAAGTTAATATGCATCTATCTT
326 GAATCATTTTAACTCTCTTGTGACACCCTAATACAATCCAAAATAAGTTAATATGCATCCATCTT
575450 TGG
391 TGG
575453 TAGAAATTAATCTGTTACCATCTCAAAGTGCGTTGAAAAGCCTCCATCCAAAAGTGTCGAGATAT
1 TAGAAATTAATCTGTTACCATCTCAAAGTGCGTTGAAAAGCCTCCATCCAAAAGTGTCGAGATAT
575518 CTCTGCTTGAGCTCATACTGGGAAAGAATTGTCTCGCATTCTAGCTGCCACAACTCTATGGGTTT
66 CTCTGCTTGAGCTCATACTGGGAAAGAATTGTCTCGCATTCTAGCTGCCACAACTCTATGGGTTT
*
575583 ATCTAAGAGTGTCGGATGCCTCCACTCAGTAGCTGGACTTCCTCCGCTGCTACTTAAAGCGTAGA
131 ATCTAAGAGTGTCGGATGCCTCCACTCAGTAGCTGGACTTCCTCCGCTGCTACTAAAAGCGTAGA
575648 GATTCATTTGTCCTAGTTAGGGGAAGAGAGATACCTTCCCATATCTCCTACTTTTATAAAGAAGC
196 GATTCATTTGTCCTAGTTAGGGGAAGAGAGATACCTTCCCATATCTCCTACTTTTATAAAGAAGC
575713 CTTCATTTCTCAATCAAACTTTTTCGAGGGTGTTGAGTTGCCTTCTCTATCATCTGAAAATATTA
261 CTTCATTTCTCAATCAAACTTTTTCGAGGGTGTTGAGTTGCCTTCTCTATCATCTGAAAATATTA
575778 GAATCATTTTAACTCTCTTGTGACACCCTAATACAATCCAAAATAAGTTAATATGCATCCATCTT
326 GAATCATTTTAACTCTCTTGTGACACCCTAATACAATCCAAAATAAGTTAATATGCATCCATCTT
575843 TGG
391 TGG
575846 TA
1 TA
575848 ATATGAGTAA
Statistics
Matches: 392, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
393 392 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (393 bp):
TAGAAATTAATCTGTTACCATCTCAAAGTGCGTTGAAAAGCCTCCATCCAAAAGTGTCGAGATAT
CTCTGCTTGAGCTCATACTGGGAAAGAATTGTCTCGCATTCTAGCTGCCACAACTCTATGGGTTT
ATCTAAGAGTGTCGGATGCCTCCACTCAGTAGCTGGACTTCCTCCGCTGCTACTAAAAGCGTAGA
GATTCATTTGTCCTAGTTAGGGGAAGAGAGATACCTTCCCATATCTCCTACTTTTATAAAGAAGC
CTTCATTTCTCAATCAAACTTTTTCGAGGGTGTTGAGTTGCCTTCTCTATCATCTGAAAATATTA
GAATCATTTTAACTCTCTTGTGACACCCTAATACAATCCAAAATAAGTTAATATGCATCCATCTT
TGG
Found at i:584061 original size:26 final size:25
Alignment explanation
Indices: 584017--584080 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
584007 TTATTTAATA
584017 TTAAAAAATAAATAAATAT-TATTAT
1 TTAAAAAATAAATAAATATATA-TAT
* *
584042 TTAAACAAATATATATATATATATAT
1 TTAAA-AAATAAATAAATATATATAT
584068 TTATATAAAATAA
1 TTA-A-AAAATAA
584081 TAATTAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 5 0.16
26 18 0.56
27 8 0.25
28 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
TTAAAAAATAAATAAATATATATAT
Found at i:585496 original size:17 final size:17
Alignment explanation
Indices: 585474--585511 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
585464 CTATAATATG
* *
585474 TAATAATAATAAATTAA
1 TAATAAAAATAAAATAA
585491 TAATAAAAATAAAATAA
1 TAATAAAAATAAAATAA
585508 TAAT
1 TAAT
585512 TATTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAATAAAAATAAAATAA
Found at i:585506 original size:11 final size:14
Alignment explanation
Indices: 585474--585510 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
585464 CTATAATATG
585474 TAATAATAATAAAT
1 TAATAATAATAAAT
585488 TAATAATAA-AAA-
1 TAATAATAATAAAT
585500 TAA-AATAATAA
1 TAATAATAATAA
585511 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 5 0.23
13 3 0.14
14 9 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:586033 original size:123 final size:123
Alignment explanation
Indices: 585879--586332 Score: 687
Period size: 123 Copynumber: 3.7 Consensus size: 123
585869 GAATTAAGGC
* * * *
585879 AAGGTTGAATAAGTTCTTCTCATTATAAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTCTTTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
** * * * * * *
585944 GAACTCTAACTGAAAATGATGATGCTGATCTATCTCTTTTTGCGATAGTGTCAAGCAA
66 GAACTCTCTCTGAAAATGTTGGTGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
* *
586002 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
586067 GAACTTTCTCTGAAAATTTTGGTACTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
66 GAACTCTCTCTGAAAATGTTGGTGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
*
586125 AAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
586190 GAACTTTCTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
66 GAACTCTCTCTGAAAATGTTGGTGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
* *
586248 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
586313 GAACTCT-TCT-AGAAATGTTG
66 GAACTCTCTCTGA-AAATGTTG
586333 AAAACATTCT
Statistics
Matches: 302, Mismatches: 28, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
122 11 0.04
123 291 0.96
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTCTCTGAAAATGTTGGTGCTGATCTATCTCCTTCTGCGATAGAGTCATGCAA
Found at i:586529 original size:76 final size:74
Alignment explanation
Indices: 586378--586548 Score: 261
Period size: 76 Copynumber: 2.3 Consensus size: 74
586368 GAGGTCTTAT
* * * ** *
586378 CATCTTGCAGTGTAGGTCTTACAGATGACCCTGAGGCTTTAATTATCAAAAATCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAACATCAAAAAGCTCCCGAAGGCT
586443 TTTTGAAAA
66 TTTTGAAAA
*
586452 CATCATGTACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAAAACATCAAAAAGCTCCCGAAGG
1 CATCATGCACTGTAGGTCTTACAGATGACCCGGAGGCTTT--AAACATCAAAAAGCTCCCGAAGG
586517 CTTTTTGAAAA
64 CTTTTTGAAAA
586528 CATCATGCACTGTAGGTCTTA
1 CATCATGCACTGTAGGTCTTA
586549 TGGATGTGGG
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 36 0.41
76 51 0.59
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (74 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAACATCAAAAAGCTCCCGAAGGCT
TTTTGAAAA
Found at i:587248 original size:22 final size:22
Alignment explanation
Indices: 587214--587315 Score: 118
Period size: 22 Copynumber: 4.6 Consensus size: 22
587204 AATAAGGCTT
*
587214 TCATCTTT-AAAAAGAGAATCTA
1 TCATCTTTGAAGAAGA-AATCTA
*
587236 TCATTTTTGAA-AAGAGAATCTA
1 TCATCTTTGAAGAAGA-AATCTA
* *
587258 TCATCTTTGAAGAATATATCTA
1 TCATCTTTGAAGAAGAAATCTA
* *
587280 TCATCTTTGAAGAATATATCTA
1 TCATCTTTGAAGAAGAAATCTA
587302 TCATCTTTGAAGAA
1 TCATCTTTGAAGAA
587316 TGTAGATGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
22 69 0.93
23 5 0.07
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAGAAGAAATCTA
Found at i:587316 original size:22 final size:22
Alignment explanation
Indices: 587231--587316 Score: 129
Period size: 22 Copynumber: 3.9 Consensus size: 22
587221 TAAAAAGAGA
* * *
587231 ATCTATCATTTTTGAA-AAGAGA
1 ATCTATCATCTTTGAAGAATA-T
587253 ATCTATCATCTTTGAAGAATAT
1 ATCTATCATCTTTGAAGAATAT
587275 ATCTATCATCTTTGAAGAATAT
1 ATCTATCATCTTTGAAGAATAT
587297 ATCTATCATCTTTGAAGAAT
1 ATCTATCATCTTTGAAGAAT
587317 GTAGATGTAG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 57 0.95
23 3 0.05
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (22 bp):
ATCTATCATCTTTGAAGAATAT
Found at i:589937 original size:22 final size:22
Alignment explanation
Indices: 589912--589971 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
589902 GTTCCGAAGG
589912 ACCACTGGATATGTCCCAAAGA
1 ACCACTGGATATGTCCCAAAGA
* *
589934 ACCACTGGATATGTCCCGAAGG
1 ACCACTGGATATGTCCCAAAGA
*
589956 ACCACTGGATACGTCC
1 ACCACTGGATATGTCC
589972 TGAATGACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (22 bp):
ACCACTGGATATGTCCCAAAGA
Found at i:596779 original size:18 final size:18
Alignment explanation
Indices: 596756--596812 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
596746 GTTCAGTATT
*
596756 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
596774 TGTCCCGTAGGACCACTGGA
1 TGTCCCGAAGGACCACT--A
596794 TACGTCCCGAAGGACCACT
1 T--GTCCCGAAGGACCACT
596813 GGATACGTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 15 0.47
20 2 0.06
22 15 0.47
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:596807 original size:22 final size:22
Alignment explanation
Indices: 596775--596827 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
596765 TGACCACTAT
*
596775 GTCCCGTAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
596797 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
596819 GTCCTGAAG
1 GTCCCGAAG
596828 TACTAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:602522 original size:42 final size:42
Alignment explanation
Indices: 602462--602545 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
602452 TTAGTTTTTT
* * * * * *
602462 CATTTGCTCTTTTTAATCATCTTGGAATTTTTTTGCTTGATC
1 CATTTGCTCATTTGAATCAGCCTGGAACTTTTTTACTTGATC
*
602504 CATTTGTTCATTTGAATCAGCCTGGAACTTTTTTACTTGATC
1 CATTTGCTCATTTGAATCAGCCTGGAACTTTTTTACTTGATC
602546 AATCATCTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.50
Consensus pattern (42 bp):
CATTTGCTCATTTGAATCAGCCTGGAACTTTTTTACTTGATC
Found at i:604453 original size:26 final size:28
Alignment explanation
Indices: 604423--604479 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
604413 AATAAAATAA
604423 AAATATTAAAAAAATAAT-A-TACATAT
1 AAATATTAAAAAAATAATAAGTACATAT
**
604449 AAATATTATGAAAATAATAAGTACATAT
1 AAATATTAAAAAAATAATAAGTACATAT
604477 AAA
1 AAA
604480 AAATTTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 16 0.59
27 1 0.04
28 10 0.37
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (28 bp):
AAATATTAAAAAAATAATAAGTACATAT
Found at i:604488 original size:28 final size:26
Alignment explanation
Indices: 604433--604490 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
604423 AAATATTAAA
*
604433 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
604459 AAAATAATAAGTACATATAAAAAATT-TG
1 AAAATAAT-A-TACATAT-AAAAATTATG
604487 AAAA
1 AAAA
604491 GAAAGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 8 0.29
27 1 0.04
28 13 0.46
29 6 0.21
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.29
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:605006 original size:18 final size:18
Alignment explanation
Indices: 604984--605027 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
604974 ATTTTAAGAA
*
604984 AATATATTCATATATATAT
1 AATATATT-ATATATAAAT
*
605003 -ATATATTATTTATAAAT
1 AATATATTATATATAAAT
605020 AATATATT
1 AATATATT
605028 TATTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATATTATATATAAAT
Found at i:605025 original size:24 final size:23
Alignment explanation
Indices: 604997--605043 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
604987 ATATTCATAT
* *
604997 ATATATATATATTATTTATAAATA
1 ATATATATAT-TTACTTAGAAATA
*
605021 ATATATTTATTTACTTAGAAATA
1 ATATATATATTTACTTAGAAATA
605044 TCATAAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATATATATTTACTTAGAAATA
Found at i:606629 original size:3 final size:3
Alignment explanation
Indices: 606621--606673 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
606611 CTATAATATG
* * *
606621 TAA TAA TAA TAA -AT TAA TAA TAA AAA TAA -AA TAA TTA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
606668 TAA TAA
1 TAA TAA
606674 AACCGTGACA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:606640 original size:14 final size:13
Alignment explanation
Indices: 606621--606673 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 13
606611 CTATAATATG
606621 TAATAATAATAAA
1 TAATAATAATAAA
606634 T--TAATAATAAA
1 TAATAATAATAAA
606645 -AATAA-AAT-AA
1 TAATAATAATAAA
*
606655 TTATAATAATAAA
1 TAATAATAATAAA
606668 TAATAA
1 TAATAA
606674 AACCGTGACA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
10 2 0.06
11 17 0.52
12 6 0.18
13 8 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:606643 original size:17 final size:16
Alignment explanation
Indices: 606621--606673 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
606611 CTATAATATG
606621 TAATAATAATAAATTAA
1 TAATAATAATAAA-TAA
*
606638 TAATAAAAATAAAATAA
1 TAATAATAAT-AAATAA
*
606655 TTATAATAATAAATAA
1 TAATAATAATAAATAA
606671 TAA
1 TAA
606674 AACCGTGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 8 0.26
17 20 0.65
18 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:609591 original size:19 final size:19
Alignment explanation
Indices: 609567--609611 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
609557 TCACTTATTG
609567 GCCACATGCCTTTCAAACA
1 GCCACATGCCTTTCAAACA
609586 GCCACATGCCTTTCAAACA
1 GCCACATGCCTTTCAAACA
609605 GCCACAT
1 GCCACAT
609612 ATCTTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.38, G:0.11, T:0.20
Consensus pattern (19 bp):
GCCACATGCCTTTCAAACA
Found at i:616212 original size:8 final size:8
Alignment explanation
Indices: 616199--616230 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
616189 ATTCGTCAAA
616199 TAGGCTTC
1 TAGGCTTC
*
616207 TAGGCTTT
1 TAGGCTTC
616215 TAGGCTTC
1 TAGGCTTC
616223 TAGGCTTC
1 TAGGCTTC
616231 GTTGAGGGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.41
Consensus pattern (8 bp):
TAGGCTTC
Found at i:616220 original size:16 final size:16
Alignment explanation
Indices: 616199--616229 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
616189 ATTCGTCAAA
616199 TAGGCTTCTAGGCTTT
1 TAGGCTTCTAGGCTTT
616215 TAGGCTTCTAGGCTT
1 TAGGCTTCTAGGCTT
616230 CGTTGAGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.42
Consensus pattern (16 bp):
TAGGCTTCTAGGCTTT
Found at i:616845 original size:13 final size:13
Alignment explanation
Indices: 616817--616862 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
616807 TAACCAAAAT
*
616817 TATTAAATGTTATA
1 TATTAAAT-ATATA
*
616831 TATTATATATATA
1 TATTAAATATATA
616844 TATTAAATATATA
1 TATTAAATATATA
*
616857 TTTTAA
1 TATTAA
616863 GCTCAAACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TATTAAATATATA
Found at i:617095 original size:25 final size:26
Alignment explanation
Indices: 617051--617101 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
617041 CAAACTTTAT
* * *
617051 TCGGTTCGGTTAATATTTAAA-AAAA
1 TCGGTTCGGTAAACAGTTAAAGAAAA
617076 TCGGTTCGGTAAACAGTTAAAGAAAA
1 TCGGTTCGGTAAACAGTTAAAGAAAA
617102 AAGTTCGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (26 bp):
TCGGTTCGGTAAACAGTTAAAGAAAA
Found at i:618139 original size:18 final size:18
Alignment explanation
Indices: 618100--618138 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
618090 TAATATAAAC
*
618100 AAAACTTAAGAAATTATT
1 AAAACTTAAGAAAGTATT
*
618118 AAAATTTAA-AAAGTATT
1 AAAACTTAAGAAAGTATT
618135 AAAA
1 AAAA
618139 AAATATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (18 bp):
AAAACTTAAGAAAGTATT
Found at i:620676 original size:30 final size:30
Alignment explanation
Indices: 620635--620702 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
620625 GAAACAGAAA
* * * *
620635 TCAGAATGGAGAATTTATCCCTTGCAGATG
1 TCAGAACGGAGAATATATCCCATGAAGATG
*
620665 TCAGAACGGAGAATATATCTCATGAAGATG
1 TCAGAACGGAGAATATATCCCATGAAGATG
*
620695 TTAGAACG
1 TCAGAACG
620703 AGGCTGAGCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (30 bp):
TCAGAACGGAGAATATATCCCATGAAGATG
Found at i:622358 original size:14 final size:14
Alignment explanation
Indices: 622339--622366 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
622329 CCTAACTTCT
622339 GTGTTTTTTCCAGA
1 GTGTTTTTTCCAGA
622353 GTGTTTTTTCCAGA
1 GTGTTTTTTCCAGA
622367 CCATGTACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (14 bp):
GTGTTTTTTCCAGA
Found at i:630733 original size:35 final size:35
Alignment explanation
Indices: 630687--630827 Score: 239
Period size: 35 Copynumber: 4.0 Consensus size: 35
630677 TAAGAAGAAA
630687 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
*
630722 GAAAGGAAGCATCAGCACTTTCGATTCAA-TAAGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAGT--GAAC
630758 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
*
630793 AAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
1 GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
630828 ATCGGCACTT
Statistics
Matches: 100, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
34 1 0.01
35 66 0.66
36 32 0.32
37 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (35 bp):
GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAAC
Found at i:630798 original size:71 final size:71
Alignment explanation
Indices: 630681--630821 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 71
630671 GGTGAATAAG
*
630681 AAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCAGCACTTTCGA
1 AAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAGCACTTTCGA
630746 TTCAAT
66 TTCAAT
* *
630752 AAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCGGCACTTTCGA
1 AAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAGCACTTTCGA
630817 TTCAA
66 TTCAA
630822 GTGAACATCG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (71 bp):
AAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAGCACTTTCGA
TTCAAT
Found at i:634068 original size:36 final size:36
Alignment explanation
Indices: 633997--634069 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
633987 GTTGGAAAAT
* *
633997 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATACTTTCTTTAAAAAATTAAAATCATAAA
*
634033 ATTTATATAACTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ACTTTCTTTAAAAAATT-AAAATCATAAA
634069 A
1 A
634070 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 24 0.75
37 8 0.25
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (36 bp):
ATTTATATACTTTCTTTAAAAAATTAAAATCATAAA
Found at i:637153 original size:17 final size:18
Alignment explanation
Indices: 637119--637167 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
637109 ACTTAATGTG
*
637119 ATATTTATATTTT-GAAA
1 ATATTTATATTTTATAAA
637136 ATATTTAT-TTTTATAAA
1 ATATTTATATTTTATAAA
*
637153 A-ATTCATATTTTATA
1 ATATTTATATTTTATA
637168 TGTATTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATTTATATTTTATAAA
Found at i:638660 original size:18 final size:21
Alignment explanation
Indices: 638628--638665 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
638618 ATTATATATA
638628 TATATATATATTAAT-TTTTG
1 TATATATATATTAATATTTTG
638648 TATATAT-TA-TAATATTTT
1 TATATATATATTAATATTTT
638666 ATTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (21 bp):
TATATATATATTAATATTTTG
Found at i:638664 original size:20 final size:22
Alignment explanation
Indices: 638626--638665 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
638616 TTATTATATA
*
638626 TATATATATATATTAATTTTTG
1 TATATATATATAATAATTTTTG
638648 TATATAT-TATAAT-ATTTT
1 TATATATATATAATAATTTT
638666 ATTTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (22 bp):
TATATATATATAATAATTTTTG
Found at i:638671 original size:26 final size:28
Alignment explanation
Indices: 638610--638671 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
638600 TTTAATTAAG
638610 TTAATTTTAT-TATATATATATATATATA
1 TTAATTTT-TGTATATATATATATATATA
638638 TTAATTTTTGTATATAT-TATA-ATAT-
1 TTAATTTTTGTATATATATATATATATA
*
638663 TTTATTTTT
1 TTAATTTTT
638672 ATAAGTACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 8 0.25
26 4 0.12
27 5 0.16
28 15 0.47
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TTAATTTTTGTATATATATATATATATA
Found at i:647575 original size:27 final size:27
Alignment explanation
Indices: 647544--647596 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
647534 GATCCAGGCA
647544 GATTTCTCGGTCATGATCAGAGATCCG
1 GATTTCTCGGTCATGATCAGAGATCCG
647571 GATTTCTCGGTCATGATCAGAGATCC
1 GATTTCTCGGTCATGATCAGAGATCC
647597 CGTGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (27 bp):
GATTTCTCGGTCATGATCAGAGATCCG
Found at i:647866 original size:20 final size:20
Alignment explanation
Indices: 647829--647871 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
647819 ATTCCACCTC
* *
647829 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
647849 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
647869 ATG
1 ATG
647872 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Done.