Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007734.1 Hibiscus syriacus cultivar Beakdansim tig00109991_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: 739340
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:309429 original size:7 final size:7
Alignment explanation
Indices: 309417--309449 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
309407 TTTTGAATTG
309417 AATTTTT
1 AATTTTT
309424 AATTTTT
1 AATTTTT
*
309431 AA-TTTA
1 AATTTTT
309437 AATTTTT
1 AATTTTT
309444 AATTTT
1 AATTTT
309450 CGCAATTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
AATTTTT
Found at i:309440 original size:13 final size:13
Alignment explanation
Indices: 309424--309448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
309414 TTGAATTTTT
309424 AATTTTTAATTTA
1 AATTTTTAATTTA
309437 AATTTTTAATTT
1 AATTTTTAATTT
309449 TCGCAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTAATTTA
Found at i:311040 original size:37 final size:37
Alignment explanation
Indices: 310994--311067 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
310984 GTTATTCAAC
310994 CGATGACAGACGAAGGCAGAAGACTAGTCAACATATT
1 CGATGACAGACGAAGGCAGAAGACTAGTCAACATATT
311031 CGATGACAGACGAAGGCAGAAGACTAGTCAACATATT
1 CGATGACAGACGAAGGCAGAAGACTAGTCAACATATT
311068 AGAAGCTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (37 bp):
CGATGACAGACGAAGGCAGAAGACTAGTCAACATATT
Found at i:313294 original size:106 final size:108
Alignment explanation
Indices: 313099--313302 Score: 268
Period size: 110 Copynumber: 1.9 Consensus size: 108
313089 TGGTAGTAGT
* * * * *
313099 TCAACTTCACAGCGAAGGGGCGGCTGATTGTCAACAAACAACTTTTCAATTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAAGTTC--TCAGAGCCAA
*
313164 TTTAAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGC
64 TTTAAACTTCACAGAGAAGGATATTAGACTCGAGACAGCACAAGC
* *
313209 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAATAA-TTTCCCAGTTC-CAGAGCCAATT
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAAGTTCTCAGAGCCAATT
* * * *
313272 TCAACTTCACGGAGGAGGATATTGGACTCGA
66 TAAACTTCACAGAGAAGGATATTAGACTCGA
313303 AACAATACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
106 36 0.44
109 8 0.10
110 38 0.46
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (108 bp):
TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAAGTTCTCAGAGCCAATT
TAAACTTCACAGAGAAGGATATTAGACTCGAGACAGCACAAGC
Found at i:314162 original size:124 final size:124
Alignment explanation
Indices: 313998--314466 Score: 654
Period size: 124 Copynumber: 3.8 Consensus size: 124
313988 ACTTACATTA
* * *
313998 GATTTCAACTCCACGACGAATGATATCCAATTTC-AGGCTCAACTTCACAATGAAGGGGCCATCC
1 GATTTCAACTTCACGACGAAGGATATCCAA-TTCAAGGCTCAACTTCACAACGAAGGGGCCATCC
*
314062 AC-AGTTTCAACTTCACGACGAAGGAAATCGTGCTCACTAGTAACATTCATCTTTAGATTG
65 ACGA-TTTCAACTTCACGACGAAGGAAATCGTGCTCACCAGTAACATTCATCTTTAGATTG
* ** * *
314122 GATTTCAACTTCACGACGAAGGATGTCCAATTCCCGGCTCAACTTCACAACGAAAGGGCCATCAA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
* * * * *
314187 CGGTTTCAACTTCACGATGAAGGGAATCGTGTTTACCAGTAACATTCATCTTTAGATTG
66 CGATTTCAACTTCACGACGAAGGAAATCGTGCTCACCAGTAACATTCATCTTTAGATTG
* * * *
314246 GATTTCAAATTCACGACGAATGATATCCAATTCACGGCTCAACTTCACAACGAAGGGGTCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
* * * *
314311 CGATTTCAACTTCACGACAAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGATTG
66 CGATTTCAACTTCACGACGAAGGAAATCGTGCTCACCAGTAACATTCATCTTTAGATTG
* * *
314370 GATTTCAACTTCACGACGAAGTATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
* * *
314435 CGATTTCAACTTAACGACGAAAGATATCGTGC
66 CGATTTCAACTTCACGACGAAGGAAATCGTGC
314467 CCAATGGATC
Statistics
Matches: 304, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
123 3 0.01
124 301 0.99
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (124 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
CGATTTCAACTTCACGACGAAGGAAATCGTGCTCACCAGTAACATTCATCTTTAGATTG
Found at i:314663 original size:14 final size:15
Alignment explanation
Indices: 314646--314697 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
314636 ATATATATAA
*
314646 TAATTATT-TATTAT
1 TAATTATTATAATAT
314660 TAATTATTATAATAT
1 TAATTATTATAATAT
*
314675 T-ATTATTAATACTAT
1 TAATTATT-ATAATAT
314690 TAA-TATTA
1 TAATTATTA
314698 CTTTTGTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 15 0.45
15 17 0.52
16 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTATTATAATAT
Found at i:314679 original size:21 final size:21
Alignment explanation
Indices: 314653--314697 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
314643 TAATAATTAT
*
314653 TTATTATTAATTATTA-TAATA
1 TTATTATTAA-TACTATTAATA
314674 TTATTATTAATACTATTAATA
1 TTATTATTAATACTATTAATA
314695 TTA
1 TTA
314698 CTTTTGTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTATTAATACTATTAATA
Found at i:317546 original size:19 final size:19
Alignment explanation
Indices: 317518--317560 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
317508 AAAGGTAATT
317518 ATTTTGAATTGAAT-TTTTA
1 ATTTTGAATT-AATATTTTA
* *
317537 ATTTTTAATTTATATTTTA
1 ATTTTGAATTAATATTTTA
317556 ATTTT
1 ATTTT
317561 CACAATTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATTTTGAATTAATATTTTA
Found at i:320205 original size:42 final size:41
Alignment explanation
Indices: 320127--320214 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 41
320117 ATAGCGTTAC
* * * *
320127 AATATGTTATTTAATTAATAAAATATAGTGAGTTATTATAA
1 AATATATTATTTAATAAATAAAATATAATGAATTATTATAA
*
320168 AATATATTATTTTAATAAATTAAAATATAAT-AATTATTTTAA
1 AATATATTA-TTTAATAAA-TAAAATATAATGAATTATTATAA
320210 AATAT
1 AATAT
320215 TAATATGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
41 8 0.20
42 22 0.55
43 10 0.25
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (41 bp):
AATATATTATTTAATAAATAAAATATAATGAATTATTATAA
Found at i:320219 original size:25 final size:27
Alignment explanation
Indices: 320160--320220 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
320150 TATAGTGAGT
*
320160 TATT-ATAAAATATATTATTTTAATAA
1 TATTAATATAATATATTATTTTAATAA
320186 -ATTAAAATATAATA-ATTATTTTAA-AA
1 TATT--AATATAATATATTATTTTAATAA
320212 TATTAATAT
1 TATTAATAT
320221 GTTTAGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
25 8 0.27
26 2 0.07
27 13 0.43
28 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TATTAATATAATATATTATTTTAATAA
Found at i:324070 original size:40 final size:38
Alignment explanation
Indices: 324008--324092 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 38
323998 AAACATCGTT
*
324008 AAATTTTGAATGAGGGTACTAAAATAAAACAAAAACTA
1 AAATTTTGAATGAGGATACTAAAATAAAACAAAAACTA
* * *
324046 AAATTTTTAATGGTAGGATACTAAAATGAAATAAAAACTA
1 AAATTTTGAAT-G-AGGATACTAAAATAAAACAAAAACTA
324086 AAATTTT
1 AAATTTT
324093 ACGTATGGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 10 0.24
39 1 0.02
40 30 0.73
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (38 bp):
AAATTTTGAATGAGGATACTAAAATAAAACAAAAACTA
Found at i:331769 original size:4 final size:4
Alignment explanation
Indices: 331762--331792 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
331752 ATTTCCTTCC
331762 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
331793 AGACAGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:332308 original size:2 final size:2
Alignment explanation
Indices: 332245--332290 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
332235 ACTATGCATG
332245 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
332287 AT AT
1 AT AT
332291 CACATATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:333434 original size:43 final size:42
Alignment explanation
Indices: 333386--333467 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 42
333376 CTCTCAAGAA
*
333386 TGATTGTAATATGTT-AGTTTAATGTATTTGTAGATTGTTACCT
1 TGATTGTAATATGTTGA-TTTAATGTA-TTGTAGATAGTTACCT
*
333429 TGATTGTAATATGTTGATTTAGTGTATTGTAGATAGTTA
1 TGATTGTAATATGTTGATTTAATGTATTGTAGATAGTTA
333468 ATATGAAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 12 0.33
43 23 0.64
44 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (42 bp):
TGATTGTAATATGTTGATTTAATGTATTGTAGATAGTTACCT
Found at i:333606 original size:29 final size:29
Alignment explanation
Indices: 333571--333666 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
333561 TCATTTAAGC
* *
333571 ACCTAAATTAGTTTTTGGTCAAAATAAGT
1 ACCTAAATTATTTTTTGGTCAAAATAAAT
** *
333600 ATTTAAACTTATTTTTTTAGTCAAAATAAAT
1 ACCTAAA-TTA-TTTTTTGGTCAAAATAAAT
* *
333631 ACCTAAAGTATTTTTTGGTCAAAATAGAT
1 ACCTAAATTATTTTTTGGTCAAAATAAAT
*
333660 ACATAAA
1 ACCTAAA
333667 GTATCCAATT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 28 0.52
30 5 0.09
31 21 0.39
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (29 bp):
ACCTAAATTATTTTTTGGTCAAAATAAAT
Found at i:333793 original size:28 final size:28
Alignment explanation
Indices: 333753--333858 Score: 115
Period size: 28 Copynumber: 3.6 Consensus size: 28
333743 GAAAAATTTG
*
333753 AATACTTTT-GGTACATATTTTGACCAAA
1 AATA-TTTTAGGTACTTATTTTGACCAAA
*
333781 AATATTTTAGGTACTTATTTTTACCAAA
1 AATATTTTAGGTACTTATTTTGACCAAA
*
333809 AATATAAGTTTAAGTACTTATTTTGACCAAAAA
1 AATAT---TTTAGGTACTTATTTTGACC--AAA
*
333842 AATACTTTAGGTACTTA
1 AATATTTTAGGTACTTA
333859 GACGAAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
27 4 0.06
28 26 0.39
30 11 0.17
31 18 0.27
33 7 0.11
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (28 bp):
AATATTTTAGGTACTTATTTTGACCAAA
Found at i:333858 original size:30 final size:30
Alignment explanation
Indices: 333753--333858 Score: 126
Period size: 31 Copynumber: 3.6 Consensus size: 30
333743 GAAAAATTTG
* *
333753 AATACTTTTGGTACATATTTTGACC--AAA
1 AATACTTTAGGTACTTATTTTGACCAAAAA
* *
333781 AATATTTTAGGTACTTATTTTTACCAAAAA
1 AATACTTTAGGTACTTATTTTGACCAAAAA
* * *
333811 TATAAGTTTAAGTACTTATTTTGACCAAAAA
1 AAT-ACTTTAGGTACTTATTTTGACCAAAAA
333842 AATACTTTAGGTACTTA
1 AATACTTTAGGTACTTA
333859 GACGAAAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 21 0.33
30 17 0.27
31 26 0.41
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (30 bp):
AATACTTTAGGTACTTATTTTGACCAAAAA
Found at i:337534 original size:30 final size:30
Alignment explanation
Indices: 337500--337566 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
337490 CAAAACACCT
337500 AACTTTTGGAAA-TCACAC-TTTT-GATCCCTA
1 AACTTTT-GAAATTCAC-CTTTTTCG-TCCCTA
*
337530 AACTTTTGAAATTTACCTTTTTCGTCCCTA
1 AACTTTTGAAATTCACCTTTTTCGTCCCTA
337560 AACTTTT
1 AACTTTT
337567 CTAAACTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 5 0.15
30 27 0.82
31 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTTTTGAAATTCACCTTTTTCGTCCCTA
Found at i:338879 original size:39 final size:39
Alignment explanation
Indices: 338822--338898 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
338812 GCGGTGTTTG
* *
338822 TAACAAAAATACCACTAAATAACTTGACTTTTTGCGACA
1 TAACAAAAATACCACTAAATAACCTAACTTTTTGCGACA
** *
338861 TAACAAAAATGTCGCTAAATAACCTAACTTTTTGCGAC
1 TAACAAAAATACCACTAAATAACCTAACTTTTTGCGAC
338899 GTTTGTTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.29
Consensus pattern (39 bp):
TAACAAAAATACCACTAAATAACCTAACTTTTTGCGACA
Found at i:346671 original size:20 final size:20
Alignment explanation
Indices: 346643--346701 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
346633 CACTGAATAT
346643 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
346663 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
346682 -TGCCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
346701 T
1 T
346702 AATCCCTCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
20 16 0.50
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:347673 original size:26 final size:26
Alignment explanation
Indices: 347637--347695 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
347627 TTTCAAATAT
347637 GAACTCTATTTCAAAATTCCATTCAA
1 GAACTCTATTTCAAAATTCCATTCAA
* *
347663 GAACTTTATTTTAAAATTCCATTCAA
1 GAACTCTATTTCAAAATTCCATTCAA
347689 GAACTCT
1 GAACTCT
347696 TAATCTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (26 bp):
GAACTCTATTTCAAAATTCCATTCAA
Found at i:348494 original size:21 final size:21
Alignment explanation
Indices: 348467--348518 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
348457 TATGTTTATT
* *
348467 AAAAAATATTATTTTATTCAA
1 AAAAAATATGATTTAATTCAA
* *
348488 TAAAAATAGGGATTTAATTCAA
1 AAAAAATA-TGATTTAATTCAA
348510 AAAAAATAT
1 AAAAAATAT
348519 ATATATAGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAAAATATGATTTAATTCAA
Found at i:350326 original size:44 final size:45
Alignment explanation
Indices: 350206--350327 Score: 167
Period size: 45 Copynumber: 2.8 Consensus size: 45
350196 ATAAATTTTT
* *
350206 TTACCATTTA-TCCATAAACTTGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * * *
350250 TTACCATTTGTTTCATAAGCTCGTAAGTTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
*
350295 TTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
350328 GCATGTTTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
44 33 0.49
45 34 0.51
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:352638 original size:23 final size:23
Alignment explanation
Indices: 352608--352652 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
352598 TTGGTCATTG
*
352608 TCTAAATTTTTTAGTATTACAAT
1 TCTAAATTTTTGAGTATTACAAT
*
352631 TCTAAATTTTTGGGTATTACAA
1 TCTAAATTTTTGAGTATTACAA
352653 ATCATTCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (23 bp):
TCTAAATTTTTGAGTATTACAAT
Found at i:358038 original size:13 final size:13
Alignment explanation
Indices: 358020--358047 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
358010 TGAACTCTCC
358020 CCTATTAATCCAA
1 CCTATTAATCCAA
358033 CCTATTAATCCAA
1 CCTATTAATCCAA
358046 CC
1 CC
358048 CAATATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (13 bp):
CCTATTAATCCAA
Found at i:364847 original size:24 final size:24
Alignment explanation
Indices: 364813--364866 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
364803 CTGAAAAATC
364813 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
364837 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
364861 ATCAAA
1 ATCAAA
364867 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:364880 original size:24 final size:24
Alignment explanation
Indices: 364813--364880 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
364803 CTGAAAAATC
* * *
364813 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
364837 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
364861 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
364881 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:365752 original size:20 final size:21
Alignment explanation
Indices: 365729--365976 Score: 196
Period size: 20 Copynumber: 12.3 Consensus size: 21
365719 AGAATCTCGT
365729 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
365749 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
365769 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * * *
365789 TGCGAATTAGGAAAATTGCAA
1 TGCGATTTACGTAAATCGCAA
365810 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* *
365830 TGCGA-TTACGT-ATTCGCAT
1 TGCGATTTACGTAAATCGCAA
* *
365849 TG-TATTTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* * *
365868 TGCGATTGT-CCTAATTCGCAT
1 TGCGATT-TACGTAAATCGCAA
* *
365889 TGCGATTTACGT-AATTGCAT
1 TGCGATTTACGTAAATCGCAA
* *
365909 TGCGATTTACGT-ATTCGCAT
1 TGCGATTTACGTAAATCGCAA
* * *
365929 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
** * *
365950 CACGAATTT-GGGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
365971 TGCGAT
1 TGCGAT
365977 AGTCAGAATC
Statistics
Matches: 190, Mismatches: 29, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.01
19 27 0.14
20 104 0.55
21 55 0.29
22 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:365820 original size:41 final size:41
Alignment explanation
Indices: 365729--365839 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
365719 AGAATCTCGT
*
365729 TGCGATTTAC-TAAATCGCAATGCG-ATTACGTAAATCGCAA
1 TGCGA-TTACGTAAATCGCAATGCGAATTACGAAAATCGCAA
* *
365769 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATTGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTACGAAAATCGCAA
365810 TGCGATTACGTAAATCGCAATGCG-ATTACG
1 TGCGATTACGTAAATCGCAATGCGAATTACG
365840 TATTCGCATT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
39 4 0.06
40 24 0.37
41 37 0.57
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (41 bp):
TGCGATTACGTAAATCGCAATGCGAATTACGAAAATCGCAA
Found at i:365948 original size:61 final size:58
Alignment explanation
Indices: 365732--365933 Score: 147
Period size: 61 Copynumber: 3.4 Consensus size: 58
365722 ATCTCGTTGC
* * ** * *
365732 GATTTAC-TAAATCGCAATGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATG
1 GATTTACGT-AATCGCATTGCGATTGCCAAAATCGCAATGCGATTACGT-ATTCGCATTG
* * * * * * **
365791 CGAATTAGGAAAATTGCAATGCGATTACGTAAATCGCAATGCGATTACGTATTCGCATTG
1 -GATTTACG-TAATCGCATTGCGATTGCCAAAATCGCAATGCGATTACGTATTCGCATTG
* * * *
365851 TATTTACGTAATCGCATTGCGATTGTCCTAATTCGCATTGCGATTTACGTAATT-GCATTG
1 GATTTACGTAATCGCATTGCGATTG-CCAAAATCGCAATGCGA-TTACGT-ATTCGCATTG
*
365911 CGATTTACGTATTCGCATTGCGA
1 -GATTTACGTAATCGCATTGCGA
365934 ATTAGGAAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
58 13 0.11
59 19 0.16
60 25 0.21
61 61 0.52
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (58 bp):
GATTTACGTAATCGCATTGCGATTGCCAAAATCGCAATGCGATTACGTATTCGCATTG
Found at i:365955 original size:21 final size:21
Alignment explanation
Indices: 365931--365970 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
365921 ATTCGCATTG
365931 CGAATTAGGAAAATCGCAACA
1 CGAATTAGGAAAATCGCAACA
* *
365952 CGAATTTGGGAAATCGCAA
1 CGAATTAGGAAAATCGCAA
365971 TGCGATAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACA
Found at i:367221 original size:60 final size:58
Alignment explanation
Indices: 367070--367237 Score: 153
Period size: 60 Copynumber: 2.8 Consensus size: 58
367060 AGTATATACA
* * *
367070 TATAGTTTCGGATGAAATTGAAATA-TTAAACAGTTTAGGA-TCAATTTAGAATGAATGT
1 TATAGTTTAGGATGAAATTGAAATATTTAAA-AGTTTAAGACT-AATTTAGAATCAATGT
* * * ** *
367128 CATAATTTGAGGGTGAAATTGAAACGTTCAAAAGTTTGAAGACTAATTTAGAATC-ATAGT
1 TATAGTTT-AGGATGAAATTGAAATATTTAAAAGTTT-AAGACTAATTTAGAATCAAT-GT
* *
367188 TATAGTTTAAGGATGAAATTAAAATATTTAAAAGCTTAAGAACTAATTTA
1 TATAGTTT-AGGATGAAATTGAAATATTTAAAAGTTTAAG-ACTAATTTA
367238 AAATAAAAAT
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
58 6 0.07
59 23 0.27
60 56 0.65
61 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (58 bp):
TATAGTTTAGGATGAAATTGAAATATTTAAAAGTTTAAGACTAATTTAGAATCAATGT
Found at i:371628 original size:17 final size:18
Alignment explanation
Indices: 371606--371640 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
371596 AATACAATTT
371606 TTATTTTT-TTTATATTA
1 TTATTTTTATTTATATTA
371623 TTATTTTTAATTTATATT
1 TTATTTTT-ATTTATATT
371641 TTTACTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTTATTTATATTA
Found at i:371629 original size:14 final size:14
Alignment explanation
Indices: 371606--371652 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
371596 AATACAATTT
*
371606 TTATTTTTTTTATA
1 TTATTATTTTTATA
371620 TTATTATTTTTA-A
1 TTATTATTTTTATA
371633 TT-TATATTTTTACTA
1 TTAT-TATTTTTA-TA
371648 TTATT
1 TTATT
371653 TTAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 1 0.04
13 11 0.39
14 11 0.39
15 4 0.14
16 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTATTTTTATA
Found at i:371655 original size:19 final size:19
Alignment explanation
Indices: 371613--371659 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
371603 TTTTTATTTT
* * *
371613 TTTTATATTATTATTTTTA
1 TTTTATATTTTTACTATTA
*
371632 ATTTATATTTTTACTATTA
1 TTTTATATTTTTACTATTA
371651 TTTTA-ATTT
1 TTTTATATTT
371660 AAAATTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATATTTTTACTATTA
Found at i:372547 original size:4 final size:4
Alignment explanation
Indices: 372538--372564 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
372528 AATATTCTCA
372538 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
372565 GAAAAGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:373117 original size:37 final size:36
Alignment explanation
Indices: 373076--373147 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
373066 CATAAAATGA
*
373076 GTTTGTTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATG
* *
373113 GTTTGCTTCACTACTCTTCCGTTAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
373148 TGACCTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATG
Found at i:373216 original size:2 final size:2
Alignment explanation
Indices: 373209--373242 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
373199 GTATGTTTAA
373209 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
373243 GAAAATTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:374131 original size:23 final size:23
Alignment explanation
Indices: 374078--374128 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
374068 GATAATTTAA
*
374078 AAATAATAATATTTCAAATAAGT
1 AAATAATAAGATTTCAAATAAGT
* *
374101 AAATAATAAGATTTTAAA-AATT
1 AAATAATAAGATTTCAAATAAGT
374123 AAATAA
1 AAATAA
374129 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATAATAAGATTTCAAATAAGT
Found at i:374139 original size:19 final size:19
Alignment explanation
Indices: 374054--374140 Score: 61
Period size: 19 Copynumber: 4.4 Consensus size: 19
374044 TATAATATTA
* *
374054 TTTAAAATTAAATAGATAA
1 TTTAAAATTAAATAAATAT
*
374073 TTTAAAAAT-AAT-AATAT
1 TTTAAAATTAAATAAATAT
* * *
374090 TTCAAATAAGTAAATAATAAGAT
1 TT-TAA-AATTAAAT-A-AATAT
374113 TTTAAAAATTAAATAAATAT
1 TTT-AAAATTAAATAAATAT
374133 TTTAAAAT
1 TTTAAAAT
374141 ATTTTCATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
17 5 0.10
18 5 0.10
19 16 0.31
20 10 0.19
21 1 0.02
22 7 0.13
23 8 0.15
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTAAAATTAAATAAATAT
Found at i:374210 original size:24 final size:23
Alignment explanation
Indices: 374141--374210 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
374131 ATTTTAAAAT
374141 ATTTTCATAATAT-TATAAATATAA
1 ATTTT-ATAATATATATAAATA-AA
* * *
374165 TTTTTAGAATA-ATTTAATATAAA
1 ATTTTATAATATATATAA-ATAAA
374188 ATTTTATAATTATATATAAATAA
1 ATTTTATAA-TATATATAAATAA
374211 TTATTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 18 0.50
24 13 0.36
25 5 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (23 bp):
ATTTTATAATATATATAAATAAA
Found at i:376162 original size:30 final size:30
Alignment explanation
Indices: 376108--376168 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
376098 GTAAACTATA
*
376108 AGTTTAGTAGTTAAACTATTATTTTTGTTCT
1 AGTTTAGTACTTAAACTATTATTTTT-TTCT
* *
376139 AGTTTGGTACTTAAA-TTTTATTTTTTTCT
1 AGTTTAGTACTTAAACTATTATTTTTTTCT
376168 A
1 A
376169 AAAGAATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 9 0.33
31 13 0.48
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (30 bp):
AGTTTAGTACTTAAACTATTATTTTTTTCT
Found at i:379100 original size:3 final size:3
Alignment explanation
Indices: 379092--379132 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
379082 TCGATTCCAA
379092 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
379133 ATAACAGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:383366 original size:59 final size:60
Alignment explanation
Indices: 383262--383375 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 60
383252 TGATCCCTAA
*
383262 ACTTTTAAATATTCTAATTTTATCCCGAAACTATGACTATTATTCTAAATTAGTCTTCAG
1 ACTTTTAAATATTCTAATTTCATCCCGAAACTATGACTATTATTCTAAATTAGTCTTCAG
* * *
383322 ACTTTTGAATATT-TCATTTCATCCCTAAACTATGAC-ATTCATTCTAAATTAGTC
1 ACTTTTAAATATTCTAATTTCATCCCGAAACTATGACTATT-ATTCTAAATTAGTC
383376 CCTAAACTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 3 0.06
59 34 0.69
60 12 0.24
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.43
Consensus pattern (60 bp):
ACTTTTAAATATTCTAATTTCATCCCGAAACTATGACTATTATTCTAAATTAGTCTTCAG
Found at i:383385 original size:59 final size:59
Alignment explanation
Indices: 383247--383410 Score: 174
Period size: 60 Copynumber: 2.7 Consensus size: 59
383237 ATACAAATTT
* * * *
383247 TAAATT-GATCCCTAAACTTTTAAATATTCTAATTTTATCCCGAAACTATGACTATTATTC
1 TAAATTAG-TCCCTAAACTTTTGAATATT-TCATTTCATCCCTAAACTATGACTATTATTC
* *
383307 TAAATTAGT-CTTCAGACTTTTGAATATTTCATTTCATCCCTAAACTATGAC-ATTCATTC
1 TAAATTAGTCCCT-AAACTTTTGAATATTTCATTTCATCCCTAAACTATGACTATT-ATTC
* *
383366 TAAATTAGTCCCTAAACTTTTTGAATACTCCAATTTCAT-CCTAAA
1 TAAATTAGTCCCTAAAC-TTTTGAATATTTC-ATTTCATCCCTAAA
383411 TTATATGTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
58 3 0.03
59 38 0.43
60 39 0.44
61 8 0.09
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (59 bp):
TAAATTAGTCCCTAAACTTTTGAATATTTCATTTCATCCCTAAACTATGACTATTATTC
Found at i:383673 original size:29 final size:29
Alignment explanation
Indices: 383597--383725 Score: 134
Period size: 29 Copynumber: 4.4 Consensus size: 29
383587 AGACGGTCTT
*
383597 AGTTTAAGGGTGAAATTAGAATAATCAAA
1 AGTTTAAGGATGAAATTAGAATAATCAAA
*
383626 AGTTTAAGGGTGAAATTAGAATAATCAAA
1 AGTTTAAGGATGAAATTAGAATAATCAAA
* * * *
383655 AGTTTAAGGATTAATTTAGAATGTGAGTC-AT
1 AGTTTAAGGATGAAATTAGAA--T-AATCAAA
* * * *
383686 ACTTTAGGGATAAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTAGAATAATCAAA
383715 AGTTTAAGGAT
1 AGTTTAAGGAT
383726 CAATTTAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.04
29 58 0.70
31 19 0.23
32 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTAGAATAATCAAA
Found at i:383714 original size:60 final size:60
Alignment explanation
Indices: 383638--383751 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
383628 TTTAAGGGTG
* * *
383638 AAATTAGAATAATCAAAAGTTTAAGGATTAATTTAGAATGTGAGTCATACTTTAGGGATA
1 AAATTAGAATAATCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATACTTTAGGGATA
* * *
383698 AAATTAGAATATTCAAAAGTTTAAGGATCAATTTAAAATGAGAGTTATAGTTTA
1 AAATTAGAATAATCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATACTTTA
383752 AGGAAATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (60 bp):
AAATTAGAATAATCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATACTTTAGGGATA
Found at i:384850 original size:40 final size:38
Alignment explanation
Indices: 384784--384888 Score: 111
Period size: 40 Copynumber: 2.7 Consensus size: 38
384774 TATTGAACAT
* * *
384784 AAAATATTAAGAAGAATATAATATTTTCGGTTGTCAACCG
1 AAAATATTAAGAACAATATAACATTTTCAG-T-TCAACCG
* *
384824 AAAATATTATGAACAATGTAACATTTTCAGTTCAACCG
1 AAAATATTAAGAACAATATAACATTTTCAGTTCAACCG
* *
384862 AAAATGTTGAAAAACAATGATAACATT
1 AAAATATT-AAGAACAAT-ATAACATT
384889 ATAAGTTTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 14 0.26
39 8 0.15
40 32 0.59
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (38 bp):
AAAATATTAAGAACAATATAACATTTTCAGTTCAACCG
Found at i:385172 original size:29 final size:28
Alignment explanation
Indices: 385113--385172 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
385103 TTTCATGTTT
*
385113 TATTACTATTATAGTTTTTTTGGAAAGAA
1 TATTACTATTATAGTTTTTTT-GAAAAAA
*
385142 TATTGCTATTATAGTTGATTTTT-AAAAAA
1 TATTACTATTATAGTT--TTTTTGAAAAAA
385171 TA
1 TA
385173 AAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 22 0.81
31 5 0.19
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (28 bp):
TATTACTATTATAGTTTTTTTGAAAAAA
Found at i:385297 original size:13 final size:13
Alignment explanation
Indices: 385279--385304 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
385269 TTTCAATTTC
385279 CTCATTGAACTTA
1 CTCATTGAACTTA
385292 CTCATTGAACTTA
1 CTCATTGAACTTA
385305 ATACATTGGG
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
CTCATTGAACTTA
Found at i:389115 original size:135 final size:136
Alignment explanation
Indices: 388870--389145 Score: 493
Period size: 135 Copynumber: 2.0 Consensus size: 136
388860 AGTGTATTTG
388870 CAACTAGCTTTCCAAATAATTTTAGTGAGGAGGAGGAGGAGGAGTTTTTTTTTTAATTTTTAATT
1 CAACTAGCTTTCCAAATAATTTTAGT--GGAGGAGGAGGAGGAGTTTTTTTTTTAATTTTTAATT
*
388935 GTCACATAACACTTTAACTAATGGAGTTAATGGTCGAGGGACCAAAATTAAACAGATTGATAATG
64 GTCACATAACACTTTAACTAATGGAGTTAACGGTCGAGGGACCAAAATTAAACAGATTGATAATG
389000 TAAGGGAC
129 TAAGGGAC
389008 CAACTAGCTTTCCAAATAATTTTAGT-GAGGAGGAGGAGGAGTTTTTATTTTT-ATTTTTAATTG
1 CAACTAGCTTTCCAAATAATTTTAGTGGAGGAGGAGGAGGAGTTTTT-TTTTTAATTTTTAATTG
*
389071 TCACGTAACACTTTAACTAATGGAGTTAACGGTCGAGGGACCAAAATTAAACAGATTGATAATGT
65 TCACATAACACTTTAACTAATGGAGTTAACGGTCGAGGGACCAAAATTAAACAGATTGATAATGT
389136 AAGGGAC
130 AAGGGAC
389143 CAA
1 CAA
389146 GCGCACTTAA
Statistics
Matches: 135, Mismatches: 2, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
135 104 0.77
136 5 0.04
138 26 0.19
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (136 bp):
CAACTAGCTTTCCAAATAATTTTAGTGGAGGAGGAGGAGGAGTTTTTTTTTTAATTTTTAATTGT
CACATAACACTTTAACTAATGGAGTTAACGGTCGAGGGACCAAAATTAAACAGATTGATAATGTA
AGGGAC
Found at i:391091 original size:31 final size:31
Alignment explanation
Indices: 391053--391159 Score: 171
Period size: 31 Copynumber: 3.5 Consensus size: 31
391043 GAGTCGAGGG
391053 TTACCTATGTTCTTTGGGACATATGGACTAT
1 TTACCTATGTTCTTTGGGACATATGGACTAT
*
391084 TTACCTATGTTCTTTGGGACATATGGACTGT
1 TTACCTATGTTCTTTGGGACATATGGACTAT
*
391115 TTACCTATGTTCTTCGGGACATATGGACTGA-
1 TTACCTATGTTCTTTGGGACATATGGACT-AT
*
391146 TTACCTAGGTTCTT
1 TTACCTATGTTCTT
391160 CGAGACCTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTTGGGACATATGGACTAT
Found at i:391160 original size:31 final size:31
Alignment explanation
Indices: 391053--391175 Score: 167
Period size: 31 Copynumber: 4.0 Consensus size: 31
391043 GAGTCGAGGG
*
391053 TTACCTATGTTCTTTGGGACATATGGACT-A
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* *
391083 TTTACCTATGTTCTTTGGGACATATGGACTGT
1 -TTACCTATGTTCTTCGGGACATATGGACTGA
391115 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* * * *
391146 TTACCTAGGTTCTTCGAGACCTATAGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
391176 GTCCTTCGGG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 84 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:391389 original size:31 final size:31
Alignment explanation
Indices: 391350--391450 Score: 148
Period size: 31 Copynumber: 3.3 Consensus size: 31
391340 TATATATGTT
391350 ACAGATTACCTATGTTCTTCGGGACATATGG
1 ACAGATTACCTATGTTCTTCGGGACATATGG
* * *
391381 ACAAATTACCTATGTTCTTTGGGACATATGA
1 ACAGATTACCTATGTTCTTCGGGACATATGG
* * *
391412 ACAGGTTACCTATGTTATTCGGGATATATGG
1 ACAGATTACCTATGTTCTTCGGGACATATGG
391443 ACAGATTA
1 ACAGATTA
391451 TTATATGAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (31 bp):
ACAGATTACCTATGTTCTTCGGGACATATGG
Found at i:394814 original size:45 final size:45
Alignment explanation
Indices: 394752--394839 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
394742 AAAACGGTTC
* *
394752 GGTTTTCGGTTCGGTTTAAAGTCTCAATTCTTTTGATTCGGTTTG
1 GGTTTTCCGTTCAGTTTAAAGTCTCAATTCTTTTGATTCGGTTTG
394797 GGTTTTCCGTTCAGTTTAAAGTCTCAATTCTTTTGATTCGGTT
1 GGTTTTCCGTTCAGTTTAAAGTCTCAATTCTTTTGATTCGGTT
394840 CGGTTCGGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (45 bp):
GGTTTTCCGTTCAGTTTAAAGTCTCAATTCTTTTGATTCGGTTTG
Found at i:395800 original size:40 final size:39
Alignment explanation
Indices: 395764--395837 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
395754 AAATCATACC
*
395764 TAAAA-TTTAGTTTGTGTTTCATTTTA-TATCTCATCAT
1 TAAAACTTGAGTTTGTGTTTCATTTTAGTATCTCATCAT
*
395801 TAAAAGCTTGAGTTTTTGTTTCATTTTAGTATCTCAT
1 TAAAA-CTTGAGTTTGTGTTTCATTTTAGTATCTCAT
395838 TGTTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 5 0.16
39 19 0.59
40 8 0.25
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (39 bp):
TAAAACTTGAGTTTGTGTTTCATTTTAGTATCTCATCAT
Found at i:395859 original size:21 final size:21
Alignment explanation
Indices: 395816--395859 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
395806 GCTTGAGTTT
* *
395816 TTGTTTCATTTTAGTATCTCA
1 TTGTTTCATTTTAGTACCCCA
395837 TTGTTTCATTTTAGTACCCCA
1 TTGTTTCATTTTAGTACCCCA
395858 TT
1 TT
395860 CAAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (21 bp):
TTGTTTCATTTTAGTACCCCA
Found at i:396967 original size:12 final size:12
Alignment explanation
Indices: 396950--396974 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
396940 AAAGAAAAGG
396950 AATATATCAATT
1 AATATATCAATT
396962 AATATATCAATT
1 AATATATCAATT
396974 A
1 A
396975 GTGTTTATTG
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AATATATCAATT
Found at i:405260 original size:29 final size:30
Alignment explanation
Indices: 405189--405261 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
405179 GATTTAACAA
405189 TTCAATGGTATAATTGAAACATAAATTAAAG
1 TTCAATGGTATAATTG-AACATAAATTAAAG
* * *
405220 TTCAGTGCTATAATTG-ATA-AAATTGAAAG
1 TTCAATGGTATAATTGAACATAAATT-AAAG
*
405249 TTTAATGGTATAA
1 TTCAATGGTATAA
405262 ACAATTTAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.14
29 16 0.46
31 14 0.40
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (30 bp):
TTCAATGGTATAATTGAACATAAATTAAAG
Found at i:405660 original size:15 final size:16
Alignment explanation
Indices: 405630--405660 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
405620 ATGAGAATAA
405630 AAGATTACTAGGGAAT
1 AAGATTACTAGGGAAT
405646 AAGATTACT-GGGAAT
1 AAGATTACTAGGGAAT
405661 GTTGTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGATTACTAGGGAAT
Found at i:405828 original size:38 final size:36
Alignment explanation
Indices: 405793--405862 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
405783 TAAAAATTGT
405793 AAAATATTTATAT-ATTTTCTTTAAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTT-AAAAAATTAAATTC
* *
405830 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAATTAAA
405863 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 10 0.33
37 15 0.50
38 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:406896 original size:31 final size:30
Alignment explanation
Indices: 406861--406930 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
406851 TTTTGCTAAC
* * *
406861 ATTTGTTCTTAAGGGCTCAATTTTTTTCAAT
1 ATTTGTTATGAAGGGCTCAA-TCTTTTCAAT
* *
406892 ATTTGTTATGAGGGGTTCAATCTTTTCAAT
1 ATTTGTTATGAAGGGCTCAATCTTTTCAAT
*
406922 ATTTTTTAT
1 ATTTGTTAT
406931 TAGGTGCATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.53
Consensus pattern (30 bp):
ATTTGTTATGAAGGGCTCAATCTTTTCAAT
Found at i:409030 original size:63 final size:63
Alignment explanation
Indices: 408936--409064 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
408926 TTGGTGGCAT
* * * **
408936 TGCAAATTCATCCCCTTCACGGTAGTCGTCAGGGCCTAAGTCGTAATCAGATTCCGGTGGAAG
1 TGCAAACTCATCCCCTCCACGGTAGTAGTCAGGGCCTAAGTCGTAATCAGAGACCGGTGGAAG
* * * *
408999 TGCAAACTCATCTCCTCCACGGTGGTAGTCAGGGCCTAGGTCGTAATCGGAGACCGGTGGAAG
1 TGCAAACTCATCCCCTCCACGGTAGTAGTCAGGGCCTAAGTCGTAATCAGAGACCGGTGGAAG
409062 TGC
1 TGC
409065 GAAATCCGCC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (63 bp):
TGCAAACTCATCCCCTCCACGGTAGTAGTCAGGGCCTAAGTCGTAATCAGAGACCGGTGGAAG
Found at i:409134 original size:87 final size:87
Alignment explanation
Indices: 408988--409174 Score: 216
Period size: 87 Copynumber: 2.1 Consensus size: 87
408978 GTAATCAGAT
* * ** * * * * *
408988 TCCGGTGGAAGTGCAAACTCATCTCCTCCACGGTGGTAGTCAGGGCCTAGGTCGTAATCGGAGAC
1 TCCGGTGGCACTGCAAACTCATCTCCTCCACCATCGTAGTCAGCGCCTAAGTCGAAATCGAAGAC
409053 CGGTGGAAGTGCGAAATCCGCC
66 CGGTGGAAGTGCGAAATCCGCC
* **
409075 TCCGGTGGCACTGCAAATTCATCTCCAT-CACCATCGTAGTCAGCGCCTAAGTCGAAATCGAATT
1 TCCGGTGGCACTGCAAACTCATCTCC-TCCACCATCGTAGTCAGCGCCTAAGTCGAAATCGAAGA
*
409139 CGGGTGGAAGTGCGAAATCCGCC
65 CCGGTGGAAGTGCGAAATCCGCC
*
409162 -CTTGGTGGCACTG
1 TC-CGGTGGCACTG
409175 TAATTGTATC
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
86 1 0.01
87 82 0.98
88 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.21
Consensus pattern (87 bp):
TCCGGTGGCACTGCAAACTCATCTCCTCCACCATCGTAGTCAGCGCCTAAGTCGAAATCGAAGAC
CGGTGGAAGTGCGAAATCCGCC
Found at i:410928 original size:16 final size:15
Alignment explanation
Indices: 410907--410967 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
410897 ACCCAACCTA
410907 TTTTCAACCTGATCTG
1 TTTTCAACCTGA-CTG
*
410923 TTTTCAACTTGACATG
1 TTTTCAACCTGAC-TG
* *
410939 TTTTTAATCTGACCTG
1 TTTTCAACCTGA-CTG
*
410955 TTTTTAACCTGAC
1 TTTTCAACCTGAC
410968 ATGTAAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
15 2 0.05
16 35 0.92
17 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (15 bp):
TTTTCAACCTGACTG
Found at i:413980 original size:16 final size:16
Alignment explanation
Indices: 413931--413985 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
413921 ACTCACTTTG
413931 AATAATATATATATATA
1 AATAA-ATATATATATA
* * *
413948 TATAAGTATATACATA
1 AATAAATATATATATA
413964 AATAAATATATATATA
1 AATAAATATATATATA
*
413980 ATTAAA
1 AATAAA
413986 CATAAGTGAC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AATAAATATATATATA
Found at i:414244 original size:30 final size:30
Alignment explanation
Indices: 414208--414272 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
414198 GATGTTACTG
*
414208 ATCCATGACTAAAGGTAACAACAAATTTCA
1 ATCCATGACTAAAGGTAACAACAAATTCCA
* *
414238 ATCCATGGCTAAAGGTACCAACAAATTCCA
1 ATCCATGACTAAAGGTAACAACAAATTCCA
414268 A-CCAT
1 ATCCAT
414273 TGGATCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.22
Consensus pattern (30 bp):
ATCCATGACTAAAGGTAACAACAAATTCCA
Found at i:414621 original size:12 final size:12
Alignment explanation
Indices: 414606--414643 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
414596 GTTATTTAAA
414606 CGGGTATTGGGC
1 CGGGTATTGGGC
*
414618 CGGGTATTGGGT
1 CGGGTATTGGGC
414630 CGGGTATTGGGC
1 CGGGTATTGGGC
414642 CG
1 CG
414644 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:414633 original size:24 final size:24
Alignment explanation
Indices: 414606--414660 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
414596 GTTATTTAAA
* * *
414606 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
414630 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
414654 CGGGTAT
1 CGGGTAT
414661 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:414744 original size:32 final size:32
Alignment explanation
Indices: 414659--414760 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
414649 CGGGTCGGGT
* *
414659 ATATATATATATATATTTAAATTAAATATATAA
1 ATAT-TATATATATATTTAAATTAAATTTATTA
* *
414692 ATA-TATATTTTTTATTTAAATTAAATTTATTA
1 ATATTATA-TATATATTTAAATTAAATTTATTA
*
414724 ATATTATATATATATATAAA-TAATTATTT-TTA
1 ATATTATATATATATTTAAATTAA--ATTTATTA
414756 ATATT
1 ATATT
414761 TATCGGGTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
31 7 0.12
32 40 0.69
33 11 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
ATATTATATATATATTTAAATTAAATTTATTA
Found at i:415148 original size:46 final size:47
Alignment explanation
Indices: 415048--415148 Score: 136
Period size: 46 Copynumber: 2.2 Consensus size: 47
415038 TTTTTATTTT
*
415048 ATTTGGGAATTTAGAGGGAAATTAGGAAATTTTGAGAATATAGAGAA
1 ATTTGGGAATTTAGAGGGAAATTAGGAAATTTAGAGAATATAGAGAA
* * *
415095 A-TGGGGAATTTAGAGGGCAATTGGGAAATTTAGAGAGA-ATAGA-AA
1 ATTTGGGAATTTAGAGGGAAATTAGGAAATTTAGAGA-ATATAGAGAA
415140 ATTTGGGAA
1 ATTTGGGAA
415149 GTTGGCCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 3 0.06
46 42 0.89
47 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.31, T:0.27
Consensus pattern (47 bp):
ATTTGGGAATTTAGAGGGAAATTAGGAAATTTAGAGAATATAGAGAA
Found at i:415392 original size:28 final size:28
Alignment explanation
Indices: 415360--415432 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
415350 ATAGTTTATA
* *
415360 TAAACCTTAAACCCTAAATCATAAATCT
1 TAAACCCTAAACCCTAAATCATAAATCC
* *
415388 TAAACCCTACACCCTAAATTATAAATCC
1 TAAACCCTAAACCCTAAATCATAAATCC
*
415416 TAAACCCTAAACACTAA
1 TAAACCCTAAACCCTAA
415433 TATATGTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAACCCTAAACCCTAAATCATAAATCC
Found at i:415405 original size:21 final size:21
Alignment explanation
Indices: 415360--415426 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
415350 ATAGTTTATA
* * *
415360 TAAACCTTAAACCCTAAATCA
1 TAAATCTTAAACCCTAAACCC
*
415381 TAAATCTTAAACCCTACACCC
1 TAAATCTTAAACCCTAAACCC
*
415402 TAAAT-TATAAATCCTAAACCC
1 TAAATCT-TAAACCCTAAACCC
415423 TAAA
1 TAAA
415427 CACTAATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 1 0.03
21 38 0.97
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAATCTTAAACCCTAAACCC
Found at i:415681 original size:26 final size:26
Alignment explanation
Indices: 415652--415720 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 26
415642 TAGTTTATAC
*
415652 ATATATAGTTTATATACATAATTTAT
1 ATATATAGTTTATAAACATAATTTAT
*
415678 ATATATAGTTCACATAAACATAATTTAT
1 ATATATAGTT--TATAAACATAATTTAT
*
415706 ATATATAGCTTATAA
1 ATATATAGTTTATAA
415721 TAATTATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 14 0.38
28 23 0.62
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (26 bp):
ATATATAGTTTATAAACATAATTTAT
Found at i:415747 original size:18 final size:18
Alignment explanation
Indices: 415703--415859 Score: 86
Period size: 18 Copynumber: 8.2 Consensus size: 18
415693 AAACATAATT
*
415703 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
415721 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
* *
415739 TATAAATATAATTTATAA
1 TATATATATAGTTTATAA
*
415757 TTTTATATACATAGTTTATATA
1 ---TATATATATAGTTTATA-A
* * * * *
415779 TACATTTCACATAAATATAATTTA
1 T--ATAT-ATAT-AGT-TTA-TAA
415803 TATATATATAGTTTATAA
1 TATATATATAGTTTATAA
*
415821 TA-ATTATATAGTTTATAT
1 TATA-TATATAGTTTATAA
*
415839 TATATATATAGTGTAT-A
1 TATATATATAGTTTATAA
415856 TATA
1 TATA
415860 ATTTTATATT
Statistics
Matches: 107, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
17 6 0.06
18 59 0.55
19 5 0.05
20 2 0.02
21 20 0.19
22 8 0.07
23 2 0.02
24 4 0.04
25 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:415753 original size:49 final size:49
Alignment explanation
Indices: 415691--415867 Score: 143
Period size: 49 Copynumber: 3.6 Consensus size: 49
415681 TATAGTTCAC
* *
415691 ATAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTATAAT
1 ATAAATATAATTTATATATATAGTTTATAATAATTATATAGTTTATAAT
* * *
415740 ATAAATATAATTTATA-AT-T--TTATATACATAGTTTATATA-TACATT-TCAC
1 ATAAATATAATTTATATATATAGTT-TATA-ATA-ATTATATAGT---TTATAAT
*
415789 ATAAATATAATTTATATATATATAGTTTATAATAATTATATAGTTTATATT
1 ATAAATATAA-TT-TATATATATAGTTTATAATAATTATATAGTTTATAAT
* * * *
415840 ATATATATAGTGTATATATA-ATTTTATA
1 ATAAATATAATTTATATATATAGTTTATA
415868 TTATATATAT
Statistics
Matches: 101, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
45 1 0.01
46 4 0.04
47 5 0.05
48 16 0.16
49 35 0.35
50 7 0.07
51 13 0.13
52 9 0.09
53 5 0.05
54 4 0.04
55 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (49 bp):
ATAAATATAATTTATATATATAGTTTATAATAATTATATAGTTTATAAT
Found at i:415778 original size:15 final size:15
Alignment explanation
Indices: 415638--415876 Score: 107
Period size: 15 Copynumber: 16.4 Consensus size: 15
415628 CTATATATTT
*
415638 TATATAGTTTATACA
1 TATATAGTTTATATA
415653 TATATAGTTTATATA
1 TATATAGTTTATATA
*
415668 CATA-A--TT-TATA
1 TATATAGTTTATATA
* *
415679 TATATAGTTCACATA
1 TATATAGTTTATATA
* * *
415694 AACATA-ATT-TATA
1 TATATAGTTTATATA
*
415707 TATATAGCTTATAATAA
1 TATATAGTTTAT-AT-A
415724 TTATATAGTTTATA-A
1 -TATATAGTTTATATA
*
415739 TATA-A--ATATA-A
1 TATATAGTTTATATA
* *
415750 TTTATAATTT-TATA
1 TATATAGTTTATATA
*
415764 TACATAGTTTATATA
1 TATATAGTTTATATA
* * *
415779 TACAT--TTCACATA
1 TATATAGTTTATATA
* *
415792 AATATAATTTATATA
1 TATATAGTTTATATA
415807 TATATAGTTTATAATAA
1 TATATAGTTTAT-AT-A
415824 TTATATAGTTTATATTATA
1 -TATATAG-TT-TA-TATA
*
415843 TATATAGTGTATATA
1 TATATAGTTTATATA
415858 TA-AT--TTTATATTA
1 TATATAGTTTATA-TA
415871 TATATA
1 TATATA
415877 TATATTATAT
Statistics
Matches: 169, Mismatches: 30, Indels: 50
0.68 0.12 0.20
Matches are distributed among these distances:
11 15 0.09
12 9 0.05
13 23 0.14
14 22 0.13
15 57 0.34
16 6 0.04
17 4 0.02
18 25 0.15
19 3 0.02
20 4 0.02
21 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:415779 original size:98 final size:100
Alignment explanation
Indices: 415660--415848 Score: 301
Period size: 100 Copynumber: 1.9 Consensus size: 100
415650 ACATATATAG
*
415660 TTTATATACATAATTTATATATATAGTTCACATAAACATAA-TT-TATATATATAGCTTATAATA
1 TTTATATACATAATTTATATATACAGTTCACATAAACATAATTTATATATATATAGCTTATAATA
415723 ATTATATAGTTTATAATATAAATATAATTTATAAT
66 ATTATATAGTTTATAATATAAATATAATTTATAAT
* * * *
415758 TTTATATACATAGTTTATATATACATTTCACATAAATATAATTTATATATATATAGTTTATAATA
1 TTTATATACATAATTTATATATACAGTTCACATAAACATAATTTATATATATATAGCTTATAATA
* *
415823 ATTATATAGTTTATATTATATATATA
66 ATTATATAGTTTATAATATAAATATA
415849 GTGTATATAT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 37 0.45
99 2 0.02
100 43 0.52
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (100 bp):
TTTATATACATAATTTATATATACAGTTCACATAAACATAATTTATATATATATAGCTTATAATA
ATTATATAGTTTATAATATAAATATAATTTATAAT
Found at i:415808 original size:2 final size:2
Alignment explanation
Indices: 415801--415886 Score: 53
Period size: 2 Copynumber: 45.5 Consensus size: 2
415791 AAATATAATT
* *
415801 TA TA TA TA TA TA GTT TA TA -A TA -A T- TA TA TA GTT TA TA T- TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
415841 TA TA TA TA GTG TA TA TA TA -A T- TT TA TA T- TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
415881 T- TA TA T
1 TA TA TA T
415887 TTTTTTCAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
1 8 0.12
2 55 0.83
3 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (2 bp):
TA
Found at i:415820 original size:28 final size:28
Alignment explanation
Indices: 415638--415820 Score: 83
Period size: 28 Copynumber: 6.5 Consensus size: 28
415628 CTATATATTT
415638 TATATAGTTTATACATATATAGTTTATATA
1 TATATAGTTTATA-A-ATATAGTTTATATA
* * * *
415668 CATA-A-TTTATATATATAGTTCACATA
1 TATATAGTTTATAAATATAGTTTATATA
* * * * *
415694 AACATAATTTATATATATAGCTTATAATAA
1 TATATAGTTTATAAATATAGTTTAT-AT-A
**
415724 TTATATAGTTTAT-AATATA-AATATA-A
1 -TATATAGTTTATAAATATAGTTTATATA
* * * *
415750 TTTATAATTTTATATACATAGTTTATATA
1 TATAT-AGTTTATAAATATAGTTTATATA
* * *
415779 TACAT--TTCACATAAATATAATTTATATA
1 TATATAGTT--TATAAATATAGTTTATATA
415807 TATATAGTTTATAA
1 TATATAGTTTATAA
415821 TAATTATATA
Statistics
Matches: 111, Mismatches: 29, Indels: 28
0.66 0.17 0.17
Matches are distributed among these distances:
25 4 0.04
26 23 0.21
27 5 0.05
28 49 0.44
29 10 0.09
30 11 0.10
31 9 0.08
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (28 bp):
TATATAGTTTATAAATATAGTTTATATA
Found at i:415876 original size:9 final size:9
Alignment explanation
Indices: 415793--415886 Score: 51
Period size: 9 Copynumber: 10.4 Consensus size: 9
415783 TTTCACATAA
415793 ATATA-ATT
1 ATATATATT
415801 -TATATA-T
1 ATATATATT
415808 ATATAGT-TT
1 ATATA-TATT
415817 ATA-ATAATT
1 ATATAT-ATT
415826 ATATAGT-TT
1 ATATA-TATT
415835 ATAT-TA-T
1 ATATATATT
415842 ATATATAGTGT
1 ATATATA-T-T
415853 ATATATAATT
1 ATATAT-ATT
*
415863 TTATATTATAT
1 ATATA-TAT-T
415874 ATATATATT
1 ATATATATT
415883 ATAT
1 ATAT
415887 TTTTTTCAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 31
0.67 0.02 0.31
Matches are distributed among these distances:
7 12 0.18
8 8 0.12
9 21 0.31
10 11 0.16
11 15 0.22
12 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (9 bp):
ATATATATT
Found at i:415877 original size:100 final size:96
Alignment explanation
Indices: 415647--415881 Score: 256
Period size: 100 Copynumber: 2.3 Consensus size: 96
415637 TTATATAGTT
* * * * *
415647 TATACATATATAGTTTATATACATAATTTATATATATAGTTCACATAAACATAATTTATATATAT
1 TATA-ATATATAATTT-TATATATAGTATATATATACAGTTCACATAAACATAATTTATATATAT
415712 AGCTTATAATAATTATATAGTTTATAATATAAA
64 AGCTTATAATAATTATATAGTTTATAATATAAA
* * * *
415745 TATAATTTATAATTTTATATACATAGTTTATATATACATTTCACATAAATATAATTTATATATAT
1 TATAATATATAATTTTATAT--ATAGTATATATATACAGTTCACATAAACATAA-TT-TATATAT
* *
415810 ATAGTTTATAATAATTATATAGTTTATATTATATATA
62 ATAGCTTATAATAATTATATAGTTTATA--ATATAAA
*
415847 TAGTGTATATATAATTTTATATTATA-TATATATAT
1 TA-T-AATATATAATTTTATA-TATAGTATATATAT
415882 TATATTTTTT
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
96 4 0.03
97 9 0.08
98 32 0.28
99 2 0.02
100 34 0.29
102 16 0.14
103 4 0.03
104 14 0.12
105 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (96 bp):
TATAATATATAATTTTATATATAGTATATATATACAGTTCACATAAACATAATTTATATATATAG
CTTATAATAATTATATAGTTTATAATATAAA
Found at i:415886 original size:18 final size:18
Alignment explanation
Indices: 415800--415887 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 18
415790 TAAATATAAT
415800 TTATATATATATAGTT-TA
1 TTATATATATATA-TTATA
*
415818 TAATA-AT-TATA-TAGT-
1 TTATATATATATATTA-TA
415833 TTATAT-TATATA-TATA
1 TTATATATATATATTATA
*
415849 GTGTATATATA-ATTTTATA
1 -T-TATATATATATATTATA
415868 TTATATATATATATTATA
1 TTATATATATATATTATA
415886 TT
1 TT
415888 TTTTTCAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
14 1 0.02
15 6 0.11
16 11 0.20
17 11 0.20
18 21 0.38
19 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATATATATATATTATA
Found at i:415892 original size:28 final size:30
Alignment explanation
Indices: 415793--415886 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 30
415783 TTTCACATAA
* *
415793 ATATAATTTATATATATATAGTTTATAATA-AT
1 ATATAATTT-TATAT-TATA-TATATAGTATAT
* *
415825 -TATATAGTTTATATTATATATATAGTGTAT
1 ATATA-ATTTTATATTATATATATAGTATAT
415855 ATATAATTTTATATTATATATATA-TAT-T
1 ATATAATTTTATATTATATATATAGTATAT
415883 ATAT
1 ATAT
415887 TTTTTTCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
28 5 0.09
29 8 0.15
30 24 0.45
31 13 0.25
32 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
ATATAATTTTATATTATATATATAGTATAT
Found at i:419240 original size:87 final size:87
Alignment explanation
Indices: 419003--419241 Score: 252
Period size: 87 Copynumber: 2.7 Consensus size: 87
418993 GGGAGACTTG
* * * * * * *
419003 GTAGTAGGCAGGGCCTAAGCCGTAATCGGAGTCCGGTGGAAGTGCGAAATCCACCATTGGTGGCA
1 GTAGTAGTCAGGGCCTAAGTCATAATAGAAGTCCGGTGGAAGTGCGAAATCCGCCCTTGGTGGCA
* *
419068 CTACAAATTCATCTCCTTCACG
66 ATACAAATTCATCTCCTTCACC
* * * * *
419090 GTAGTAGTCAGGGCCTAAGTCATAATCGGAGTCCGGCGGAAGAGCGAACTCCG--CTTCCGGTGG
1 GTAGTAGTCAGGGCCTAAGTCATAATAGAAGTCCGGTGGAAGTGCGAAATCCGCCCTT--GGTGG
*
419153 CAATGCAAATTCATCTCCTTCACC
64 CAATACAAATTCATCTCCTTCACC
* * *
419177 G-ACGTAGTCAGGGCCTAAGTCGA-AATAGAATTCGGGTGGAAGTGCGAAATCCGCCCTTAGTGG
1 GTA-GTAGTCAGGGCCTAAGTC-ATAATAGAAGTCCGGTGGAAGTGCGAAATCCGCCCTTGGTGG
419240 CA
64 CA
419242 CTGTAATTGT
Statistics
Matches: 127, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
85 2 0.02
86 1 0.01
87 120 0.94
88 1 0.01
89 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (87 bp):
GTAGTAGTCAGGGCCTAAGTCATAATAGAAGTCCGGTGGAAGTGCGAAATCCGCCCTTGGTGGCA
ATACAAATTCATCTCCTTCACC
Found at i:424255 original size:128 final size:127
Alignment explanation
Indices: 424087--424415 Score: 367
Period size: 128 Copynumber: 2.6 Consensus size: 127
424077 GTTTGAGAAC
* * * * *
424087 AAAAAACGCCGCAATAGGTCA-ATATATATTACGGCGTTTTTTGA-ACAAACGCCGCAAAAGGTC
1 AAAAAACGCTGCAAAAGGTCAGATCTATA--ACGGCGTTTTTAGACACAAACGCCGCAAAAGATC
* * * * * *
424150 GATATCTATAATGGCATTTTTGGAACAAACGCCGCAAAAAGTTATGATATATAGCGTCGTTTCTA
64 -AGACCTATAATGGCATTTTTAGAACAAACGCCGCAAAAAGTCA-GACATATAGCGGCGTTTCTA
424215 G
127 G
* * *
424216 AAAAAACGCTGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATCAG
1 AAAAAACGCTGCAAAAGGTCAGATCTATAACGGCGTTTTTAGACACAAACGCCGCAAAAGATCAG
* * * * * *
424281 ACCTATACTGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGG
66 ACCTATAATGGCATTTTTAGAACAAACGCCGCAAAAAGTCAGACATATAGCGGCGTTTCTAG
* * * *
424343 ACACAAACGCTGCAAAAGATCAGACCTATAACGGCGTTTTTAAACACAAACGCCGCAAAA-AGTC
1 A-AAAAACGCTGCAAAAGGTCAGATCTATAACGGCGTTTTTAGACACAAACGCCGCAAAAGA-TC
424407 AGACCTATA
64 AGACCTATA
424416 GCGGCGTTTT
Statistics
Matches: 171, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
127 18 0.11
128 110 0.64
129 37 0.22
130 6 0.04
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (127 bp):
AAAAAACGCTGCAAAAGGTCAGATCTATAACGGCGTTTTTAGACACAAACGCCGCAAAAGATCAG
ACCTATAATGGCATTTTTAGAACAAACGCCGCAAAAAGTCAGACATATAGCGGCGTTTCTAG
Found at i:424308 original size:85 final size:84
Alignment explanation
Indices: 424116--424441 Score: 395
Period size: 85 Copynumber: 3.8 Consensus size: 84
424106 CAATATATAT
* * * ** *
424116 TACGGCGTTTTTTGAACAAACGCCGCAAAAGGTCGATATCTATAATGGCATTTTTGGA-ACAAAC
1 TACGGCGTTTTTAGAACAAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGATACAAAC
* **
424180 GCCGCAAAA-AGTTATGATATA
65 GCCGCAAAAGA-TCA-GACCTA
* * * * *
424201 TAGCGTCGTTTCTAGAAAAAACGCTGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAAC
1 TA-CGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAAC
424266 GCCGCAAAAGATCAGACCTA
65 GCCGCAAAAGATCAGACCTA
*
424286 TACTGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAAC
1 TAC-GGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAAC
*
424351 GCTGCAAAAGATCAGACCTA
65 GCCGCAAAAGATCAGACCTA
* * *
424371 TAACGGCGTTTTTAAACACAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTCGGATACAAA
1 T-ACGGCGTTTTTAGA-ACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAA
*
424436 CACCGC
64 CGCCGC
424442 TAATTACCTT
Statistics
Matches: 210, Mismatches: 25, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
84 1 0.00
85 113 0.54
86 95 0.45
87 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (84 bp):
TACGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACG
CCGCAAAAGATCAGACCTA
Found at i:424435 original size:43 final size:42
Alignment explanation
Indices: 424118--424441 Score: 321
Period size: 43 Copynumber: 7.6 Consensus size: 42
424108 ATATATATTA
* * * * *
424118 CGGCGTTTTTTGAACAAACGCCGCAAAAGGTCGATATCTATAA
1 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTC-AGACCTATAG
* * * **
424161 TGGCATTTTTGGAACAAACGCCGCAAAAAGTTATGATATATAG
1 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTCA-GACCTATAG
* * * * * * *
424204 CGTCGTTTCTAGAAAAAACGCTGCAAAAGGTCAGATCTATAG
1 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTCAGACCTATAG
424246 CGGCGTTTTTGGATACAAACGCCGC-AAAAGATCAGACCTATA-
1 CGGCGTTTTTGGA-ACAAACGCCGCAAAAAG-TCAGACCTATAG
* *
424288 CTGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAG
1 C-GGCGTTTTTGGAACAAACGCCGCAAAAAGTCAGACCTATAG
* *
424331 CGGCGTTTTTGGACACAAACGCTGC-AAAAGATCAGACCTATAA
1 CGGCGTTTTTGGA-ACAAACGCCGCAAAAAG-TCAGACCTATAG
**
424374 CGGCGTTTTTAAACACAAACGCCGCAAAAAGTCAGACCTATAG
1 CGGCGTTTTTGGA-ACAAACGCCGCAAAAAGTCAGACCTATAG
* *
424417 CGGCGTTTTCGGATACAAACACCGC
1 CGGCGTTTTTGGA-ACAAACGCCGC
424442 TAATTACCTT
Statistics
Matches: 232, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
42 61 0.26
43 166 0.72
44 5 0.02
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (42 bp):
CGGCGTTTTTGGAACAAACGCCGCAAAAAGTCAGACCTATAG
Found at i:427900 original size:42 final size:42
Alignment explanation
Indices: 427849--428123 Score: 362
Period size: 41 Copynumber: 6.6 Consensus size: 42
427839 TATGACAATT
* *
427849 GCGGTGTTTGGTATTAAAACGCCACTAAAGTAAGAGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* *
427891 GCGGCGTTTGGT-TTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
*
427932 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTACGAATCTATA
1 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATA
427973 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* * *
428015 GCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* * * * * *
428057 GCGGCGTTT-GAATAAAAACGCCATTAAAATACTAGTTTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* *
428098 GCGGCGTTT-GTATAAAAATGCCACTA
1 GCGGCGTTTGGTATTAAAACGCCACTA
428124 CATTACGATT
Statistics
Matches: 206, Mismatches: 23, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
40 3 0.01
41 116 0.56
42 87 0.42
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (42 bp):
GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
Found at i:428141 original size:41 final size:41
Alignment explanation
Indices: 427849--428169 Score: 319
Period size: 41 Copynumber: 7.8 Consensus size: 41
427839 TATGACAATT
* * * *
427849 GCGGTGTTTGGTATTAAAACGCCACTAAAGTAAGAGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGATTCTATA
* *
427891 GCGGCGTTTGGT-TTAAAACGCCACAAAAGTACG-TGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAT-TCTATA
* *
427932 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGATTCTATA
* *
427973 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGATTCTATA
* * *
428015 GCGGCGTTTGGTATTAAAACGCCACAAAAGTATG-TGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAT-TCTATA
* * * *
428057 GCGGCGTTTGAATAAAAACGCCATTAAAATACTAGTT-TATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGA-TTCTATA
* * *
428098 GCGGCGTTTGTATAAAAATGCCACTACATTACGATTCGT-TA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGATTC-TATA
* * * *
428139 GCGGCATTTTTATACAAACGTCACTAAAGTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTA
428170 TAGTATTTTG
Statistics
Matches: 237, Mismatches: 33, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
40 4 0.02
41 143 0.60
42 89 0.38
43 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGATTCTATA
Found at i:428143 original size:166 final size:165
Alignment explanation
Indices: 427849--428169 Score: 416
Period size: 166 Copynumber: 1.9 Consensus size: 165
427839 TATGACAATT
* * ** *
427849 GCGGTGTTTGGTATTAAAACGCCACTAAAGTAAGAGTCTATAGCGGCGTTTGGTTTAAAACGCCA
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTAAGAGTCTATAGCGGCGTTTGAATAAAAACGCCA
* *
427914 CAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATAGCGGCG
66 CAAAAGTACGTGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAATCTATAGCGGCA
427979 TTTGGTATTA-AAACGCCACTAAAGTACGAGTCTATA
131 TTT-GTA-TACAAACGCCACTAAAGTACGAGTCTATA
* *
428015 GCGGCGTTTGGTATTAAAACGCCACAAAAGTATGTGTCTATAGCGGCGTTTGAATAAAAACGCCA
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTAAGAGTCTATAGCGGCGTTTGAATAAAAACGCCA
* * * * * *
428080 TTAAAA-TAC-TAGTTTATAGCGGCGTTTGTATAAAAATGCCACTACATTACGATTCGT-TAGCG
66 -CAAAAGTACGT-GTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAATC-TATAGCG
* *
428142 GCATTTTTATACAAACGTCACTAAAGTA
128 GCATTTGTATACAAACGCCACTAAAGTA
428170 TAGTATTTTG
Statistics
Matches: 134, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
164 2 0.01
165 18 0.13
166 109 0.81
167 5 0.04
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (165 bp):
GCGGCGTTTGGTATTAAAACGCCACAAAAGTAAGAGTCTATAGCGGCGTTTGAATAAAAACGCCA
CAAAAGTACGTGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAATCTATAGCGGCA
TTTGTATACAAACGCCACTAAAGTACGAGTCTATA
Found at i:439876 original size:2 final size:2
Alignment explanation
Indices: 439869--439893 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
439859 TTTGGATTCA
439869 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
439894 GATAACAAAA
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:443786 original size:15 final size:15
Alignment explanation
Indices: 443766--443795 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
443756 TAATTAAATT
443766 ATTTAAAAAAATTTA
1 ATTTAAAAAAATTTA
*
443781 ATTTAAAAACATTTA
1 ATTTAAAAAAATTTA
443796 TCACAATTAG
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:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAAAAAATTTA
Found at i:451022 original size:21 final size:21
Alignment explanation
Indices: 450978--451023 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
450968 CGAAGTACCG
* **
450978 CATATATCTTCCAAAGGATTA
1 CATATATCTCCCAAAGGACCA
*
450999 CATATATGTCCCAAAGGACCA
1 CATATATCTCCCAAAGGACCA
451020 CATA
1 CATA
451024 GAACCCTCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (21 bp):
CATATATCTCCCAAAGGACCA
Found at i:453278 original size:189 final size:188
Alignment explanation
Indices: 452932--453284 Score: 460
Period size: 189 Copynumber: 1.9 Consensus size: 188
452922 CATTTTTTTC
*
452932 ATTCAAACTTAAATATATATTATTTTAATTTGAAATATACAAAAATATATAATTATCTTTAATAT
1 ATTCAAACTTAAATAGATATTATTTTAATTTGAAATATACAAAAATATATAATTATCTTTAATAT
* ** * ***** * *
452997 TCAAAGTTAAAAAGGTAATAAATACCTTTTTAAATTGACTTATCCAAATAATAATTATCATACTA
66 TCAAAGATAAAAAAATAACAAATA-CAAAAGAAATTGACTTATCAAAAGAATAATTATCATACTA
*
453062 ATATTCAAATTAAATAATATATTTAATTTGCAATGGTGTAAAGGTAAACTCCTTTTATT
130 ATATTCAAATTAAATAATATATTTAATTTACAATGGTGTAAAGGTAAACTCCTTTTATT
* *
453121 ATTCAAACTTAAATAGATATTATTTTAATTTGAAATATACAAAATTATATAATTATATTTTAATA
1 ATTCAAACTTAAATAGATATTATTTTAATTTGAAATATACAAAAATATATAATTAT-CTTTAATA
* * * *
453186 TTCAAA-ATAAAAAAATAACAAATA-AAAAGAAAGTTGATTTATTAAAAGAGTAATTATCATATT
65 TTCAAAGATAAAAAAATAACAAATACAAAAGAAA-TTGACTTATCAAAAGAATAATTATCATACT
*
453249 AATATTTAAATTAAA-AATTATATTTTAATTTACAAT
129 AATATTCAAATTAAATAA-TATA-TTTAATTTACAAT
453285 AGTCAAAAGG
Statistics
Matches: 140, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
187 5 0.04
188 42 0.30
189 80 0.57
190 13 0.09
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (188 bp):
ATTCAAACTTAAATAGATATTATTTTAATTTGAAATATACAAAAATATATAATTATCTTTAATAT
TCAAAGATAAAAAAATAACAAATACAAAAGAAATTGACTTATCAAAAGAATAATTATCATACTAA
TATTCAAATTAAATAATATATTTAATTTACAATGGTGTAAAGGTAAACTCCTTTTATT
Found at i:455856 original size:21 final size:21
Alignment explanation
Indices: 455817--455860 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
455807 CAAATTTATT
455817 AAATTTTAAAGGAATAATAATA
1 AAATTTTAAAGGAATAAT-ATA
**
455839 AAATTTTAATTGAA-AATATA
1 AAATTTTAAAGGAATAATATA
455859 AA
1 AA
455861 TAAAATATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
22 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
AAATTTTAAAGGAATAATATA
Found at i:461194 original size:20 final size:20
Alignment explanation
Indices: 461171--461209 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
461161 TGTTGATATG
461171 GGCTATTTTTTATTGACATA
1 GGCTATTTTTTATTGACATA
461191 GGCTATTTTTTATTGACAT
1 GGCTATTTTTTATTGACAT
461210 GAAATTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (20 bp):
GGCTATTTTTTATTGACATA
Found at i:471499 original size:21 final size:21
Alignment explanation
Indices: 471469--471511 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
471459 TCAATATATC
*
471469 AAGTCGTCTTAACGATAAAAA
1 AAGTCATCTTAACGATAAAAA
471490 AAGTCATCTTAACGATAAAAA
1 AAGTCATCTTAACGATAAAAA
471511 A
1 A
471512 TATTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTCATCTTAACGATAAAAA
Found at i:472746 original size:21 final size:22
Alignment explanation
Indices: 472720--472773 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
472710 GCATGTCCAG
*
472720 TTTGAAAAT-TTAAAAGGATAA
1 TTTGAAAATATTAAAAGGACAA
* *
472741 TTTG-AAATATTAAATGGCCAA
1 TTTGAAAATATTAAAAGGACAA
472762 TTTGAAAA-ATTA
1 TTTGAAAATATTA
472774 GTGAGTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.14
21 21 0.75
22 3 0.11
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (22 bp):
TTTGAAAATATTAAAAGGACAA
Found at i:488053 original size:14 final size:15
Alignment explanation
Indices: 488031--488077 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
488021 TATAAGGTAA
*
488031 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
488045 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
488060 TATTTATTATGATTAT
1 T-TTTATTATAATTAT
488076 TT
1 TT
488078 GAAAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:493754 original size:17 final size:18
Alignment explanation
Indices: 493711--493751 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
493701 AATTTATATT
493711 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
493728 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
493746 ATTAAA
1 AGTAAA
493752 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:495404 original size:42 final size:42
Alignment explanation
Indices: 495342--495456 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 42
495332 AAAAGGTGAG
** * *
495342 TAAAGTAGAACGGAGGGAAGCATCGCACTTTTGATTATTGTC
1 TAAAGTAGAACGGAACGAAGCATCGCACTTTCGATTATCGTC
* * *
495384 TAAAGTAGAACGGAATGAAGCATCACACTTTCGATTCTCGTC
1 TAAAGTAGAACGGAACGAAGCATCGCACTTTCGATTATCGTC
* *
495426 T-ATGTAGAAC-GAACGAAAACATCGCACTTTC
1 TAAAGTAGAACGGAACG-AAGCATCGCACTTTC
495457 AATACTTAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
40 4 0.06
41 21 0.34
42 37 0.60
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (42 bp):
TAAAGTAGAACGGAACGAAGCATCGCACTTTCGATTATCGTC
Found at i:496563 original size:19 final size:20
Alignment explanation
Indices: 496531--496568 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
496521 TTCTCTCGTC
496531 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
496550 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
496569 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:497595 original size:22 final size:21
Alignment explanation
Indices: 497541--497604 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
497531 AGTCGAGGGT
497541 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
497562 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
497584 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
497605 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:498165 original size:22 final size:22
Alignment explanation
Indices: 498137--498182 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
498127 TGTAGCAGTA
498137 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
*
498159 CTGTAGCAGGGGAATTGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
498181 CT
1 CT
498183 ATTTGCATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.35, T:0.26
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGTTCC
Found at i:502666 original size:15 final size:15
Alignment explanation
Indices: 502648--502683 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
502638 AAAATATAAT
502648 AAATATATT-TTTATA
1 AAATATATTATTT-TA
502663 AAATATATTATTTTA
1 AAATATATTATTTTA
502678 AAATAT
1 AAATAT
502684 TAATATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATATATTATTTTA
Found at i:504035 original size:8 final size:10
Alignment explanation
Indices: 504011--504049 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
504001 CCACACCAAA
*
504011 TTCTCTCAAT
1 TTCTCTCAAC
504021 TTCTCTCAAC
1 TTCTCTCAAC
504031 TTCTCTCAAC
1 TTCTCTCAAC
504041 TTCTCTCAA
1 TTCTCTCAA
504050 ATACTCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (10 bp):
TTCTCTCAAC
Found at i:504056 original size:10 final size:10
Alignment explanation
Indices: 504007--504066 Score: 66
Period size: 10 Copynumber: 6.0 Consensus size: 10
503997 TTCACCACAC
504007 CAAATTCTCT
1 CAAATTCTCT
*
504017 CAATTTCTCT
1 CAAATTCTCT
*
504027 CAACTTCTCT
1 CAAATTCTCT
*
504037 CAACTTCTCT
1 CAAATTCTCT
*
504047 CAAATACTCT
1 CAAATTCTCT
* *
504057 TATATTCTCT
1 CAAATTCTCT
504067 GTTTAAGGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 43 1.00
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:504056 original size:20 final size:20
Alignment explanation
Indices: 504007--504056 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
503997 TTCACCACAC
*
504007 CAAATTCTCTCAATTTCTCT
1 CAAATTCTCTCAACTTCTCT
*
504027 CAACTTCTCTCAACTTCTCT
1 CAAATTCTCTCAACTTCTCT
*
504047 CAAATACTCT
1 CAAATTCTCT
504057 TATATTCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (20 bp):
CAAATTCTCTCAACTTCTCT
Found at i:504130 original size:23 final size:22
Alignment explanation
Indices: 504091--504135 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
504081 TTATTATATT
*
504091 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
504114 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
504136 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:504142 original size:17 final size:18
Alignment explanation
Indices: 504105--504143 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
504095 ATATTTTGTA
504105 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
504123 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
504140 TTTA
1 TTTA
504144 CTTAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:506022 original size:22 final size:22
Alignment explanation
Indices: 505997--506044 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
505987 ATATTAGTCA
505997 TTCGGGACGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
*
506019 TTCGGGACGTATCTAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
506041 TTCG
1 TTCG
506045 AAACAAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.31
Consensus pattern (22 bp):
TTCGGGACGTATCCAGTGGTCC
Found at i:512921 original size:22 final size:22
Alignment explanation
Indices: 512887--512984 Score: 142
Period size: 22 Copynumber: 4.5 Consensus size: 22
512877 GATGGTATAT
* *
512887 TAGTCTTTAGGGACGTATCCAG
1 TAGTCCTTCGGGACGTATCCAG
* *
512909 TGGTCCTTCGGGACATATCCAG
1 TAGTCCTTCGGGACGTATCCAG
*
512931 TGGTCCTTCGGGACGTATCCAG
1 TAGTCCTTCGGGACGTATCCAG
*
512953 TAGTCTTTCGGGACGTATCCAG
1 TAGTCCTTCGGGACGTATCCAG
512975 TAGTCCTTCG
1 TAGTCCTTCG
512985 AGACAAAGTG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 68 1.00
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (22 bp):
TAGTCCTTCGGGACGTATCCAG
Found at i:516791 original size:2 final size:2
Alignment explanation
Indices: 516784--516812 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
516774 CTTTTTAGAT
516784 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 T
516813 CAAATAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:519784 original size:31 final size:31
Alignment explanation
Indices: 519749--519845 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
519739 ATGGTATTCC
519749 GACTATAAGGTGTTATTTTATTGAGTCCTTA
1 GACTATAAGGTGTTATTTTATTGAGTCCTTA
** *** * * **
519780 GACTATTAA-AAGTTA-CAAAATG-GTCATCC
1 GACTA-TAAGGTGTTATTTTATTGAGTCCTTA
519809 GACTATAAGGTGTTATTTTATTGAGTCCTTA
1 GACTATAAGGTGTTATTTTATTGAGTCCTTA
519840 GACTAT
1 GACTAT
519846 TAAAAGTTAC
Statistics
Matches: 44, Mismatches: 18, Indels: 8
0.63 0.26 0.11
Matches are distributed among these distances:
28 3 0.07
29 13 0.30
30 6 0.14
31 19 0.43
32 3 0.07
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (31 bp):
GACTATAAGGTGTTATTTTATTGAGTCCTTA
Found at i:519814 original size:29 final size:29
Alignment explanation
Indices: 519780--519875 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
519770 TGAGTCCTTA
519780 GACTATTAAAAGTTACAAAATGGTCATCC
1 GACTATTAAAAGTTACAAAATGGTCATCC
** *** * * **
519809 GACTA-TAAGGTGTTATTTTATTGAGTCCTTA
1 GACTATTAA-AAGTTA-CAAAATG-GTCATCC
519840 GACTATTAAAAGTTACAAAATGGTCATCC
1 GACTATTAAAAGTTACAAAATGGTCATCC
519869 GACTATT
1 GACTATT
519876 CATTATGTTT
Statistics
Matches: 45, Mismatches: 18, Indels: 8
0.63 0.25 0.11
Matches are distributed among these distances:
28 3 0.07
29 20 0.44
30 6 0.13
31 13 0.29
32 3 0.07
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (29 bp):
GACTATTAAAAGTTACAAAATGGTCATCC
Found at i:519817 original size:60 final size:60
Alignment explanation
Indices: 519700--519874 Score: 291
Period size: 60 Copynumber: 2.9 Consensus size: 60
519690 CTATAAAATA
* *
519700 TTATTTT-TTCGAGTCCATCGACTATTAAAAAGTTACAAAATGGT-ATTCCGACTATAAGGTG
1 TTATTTTATT-GAGTCCTTAGACTATT-AAAAGTTACAAAATGGTCA-TCCGACTATAAGGTG
519761 TTATTTTATTGAGTCCTTAGACTATTAAAAGTTACAAAATGGTCATCCGACTATAAGGTG
1 TTATTTTATTGAGTCCTTAGACTATTAAAAGTTACAAAATGGTCATCCGACTATAAGGTG
519821 TTATTTTATTGAGTCCTTAGACTATTAAAAGTTACAAAATGGTCATCCGACTAT
1 TTATTTTATTGAGTCCTTAGACTATTAAAAGTTACAAAATGGTCATCCGACTAT
519875 TCATTATGTT
Statistics
Matches: 110, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
60 86 0.78
61 22 0.20
62 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (60 bp):
TTATTTTATTGAGTCCTTAGACTATTAAAAGTTACAAAATGGTCATCCGACTATAAGGTG
Found at i:521711 original size:15 final size:15
Alignment explanation
Indices: 521691--521728 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
521681 TTGTTCCCGT
521691 TCACCCCACCTCCAA
1 TCACCCCACCTCCAA
*
521706 TCACCCCACCTCCAG
1 TCACCCCACCTCCAA
521721 TCACCCCA
1 TCACCCCA
521729 ACTTCGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.61, G:0.03, T:0.13
Consensus pattern (15 bp):
TCACCCCACCTCCAA
Found at i:522743 original size:31 final size:31
Alignment explanation
Indices: 522676--522735 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
522666 CAATTTAAGG
*
522676 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
522707 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
522736 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:522827 original size:19 final size:19
Alignment explanation
Indices: 522800--522866 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
522790 AATGTTTTTA
* *
522800 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
522819 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
522838 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
522857 TGAACAGTAA
1 TGAACAGTAA
522867 CCCGATGCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Done.