Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 86 of 343
Found at i:28563944 original size:18 final size:18
Alignment explanation
Indices: 28563921--28563962 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28563911 CTAAATCGTC
*
28563921 GAGATGCCATCGTCAGTT
1 GAGATGCCAACGTCAGTT
**
28563939 GAGATGGGAACGTCAGTT
1 GAGATGCCAACGTCAGTT
28563957 GAGATG
1 GAGATG
28563963 GGAAGAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (18 bp):
GAGATGCCAACGTCAGTT
Found at i:28563963 original size:18 final size:18
Alignment explanation
Indices: 28563931--28563966 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28563921 GAGATGCCAT
28563931 CGTCAGTTGAGATGGGAA
1 CGTCAGTTGAGATGGGAA
28563949 CGTCAGTTGAGATGGGAA
1 CGTCAGTTGAGATGGGAA
28563967 GAGAAGCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.39, T:0.22
Consensus pattern (18 bp):
CGTCAGTTGAGATGGGAA
Found at i:28564224 original size:63 final size:62
Alignment explanation
Indices: 28564150--28564275 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 62
28564140 TGACCAATCA
28564150 TTTCTTCGGTGGGTGGGTGTAACGACACTCTTTTCTTTACTAATTATCATCAACACATTTTTT
1 TTTCTTCGGTGGGTGGGTGTAACGACACTCTTTTCTTTACTAATTATCATCAACAC-TTTTTT
*
28564213 TTTCTTCGGTGGGTGGGTGTAATGACACTCTTTTCTTTACTAATTATCATCAACACTTTTTT
1 TTTCTTCGGTGGGTGGGTGTAACGACACTCTTTTCTTTACTAATTATCATCAACACTTTTTT
28564275 T
1 T
28564276 ACTTTAAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 7 0.11
63 55 0.89
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (62 bp):
TTTCTTCGGTGGGTGGGTGTAACGACACTCTTTTCTTTACTAATTATCATCAACACTTTTTT
Found at i:28568179 original size:18 final size:21
Alignment explanation
Indices: 28568137--28568179 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 21
28568127 AAATTGCCAT
*
28568137 GATGTCATGACACTAGAATTA
1 GATGTCATGACACTAGAACTA
28568158 GATGTCA-GACACT-G-ACTA
1 GATGTCATGACACTAGAACTA
28568176 GATG
1 GATG
28568180 CTGCAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 6 0.29
21 7 0.33
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (21 bp):
GATGTCATGACACTAGAACTA
Found at i:28573924 original size:29 final size:30
Alignment explanation
Indices: 28573870--28573929 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
28573860 ACCCTAAGTA
28573870 TAAATACAAATTTTTATTGTATTTTTCAGC
1 TAAATACAAATTTTTATTGTATTTTTCAGC
*
28573900 TAAATACAATTTTTTATTGTATTTTTCAGC
1 TAAATACAAATTTTTATTGTATTTTTCAGC
28573930 CTTTAATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.52
Consensus pattern (30 bp):
TAAATACAAATTTTTATTGTATTTTTCAGC
Found at i:28573974 original size:33 final size:33
Alignment explanation
Indices: 28573935--28574000 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
28573925 TCAGCCTTTA
28573935 ATTCAATTTTCCCCTACCTTAGTCGTTCACCCT
1 ATTCAATTTTCCCCTACCTTAGTCGTTCACCCT
28573968 ATTCAATTTTCCCCTACCTTAGTCGTTCACCCT
1 ATTCAATTTTCCCCTACCTTAGTCGTTCACCCT
28574001 CTTCCTCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.36, G:0.06, T:0.39
Consensus pattern (33 bp):
ATTCAATTTTCCCCTACCTTAGTCGTTCACCCT
Found at i:28575735 original size:40 final size:40
Alignment explanation
Indices: 28575681--28575874 Score: 318
Period size: 40 Copynumber: 4.9 Consensus size: 40
28575671 GATATAGCTT
*
28575681 CTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
28575721 CTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* * *
28575761 CTCCCACAATTGCCTTCGGGACTTGGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
28575801 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
28575841 CTCGCACAAATGCCTTCGAG-CTTAGCCCGGTTAT
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
28575875 CAATCCGAAT
Statistics
Matches: 144, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 13 0.09
40 131 0.91
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
Found at i:28579782 original size:30 final size:29
Alignment explanation
Indices: 28579732--28579788 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
28579722 GCCTTAAGTA
28579732 GCCGAAGCTAGTTAAATCGCACACTTACT
1 GCCGAAGCTAGTTAAATCGCACACTTACT
*
28579761 GCCGAAGCTAGTTTGAATCGCACACTTA
1 GCCGAAGCTAG-TTAAATCGCACACTTA
28579789 GTACCAAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (29 bp):
GCCGAAGCTAGTTAAATCGCACACTTACT
Found at i:28579799 original size:30 final size:29
Alignment explanation
Indices: 28579736--28579799 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
28579726 TAAGTAGCCG
* *
28579736 AAGCTAGTTAAATCGCACACTTACTGCCG
1 AAGCTAGTTAAATCGCACACTTACTACCA
* *
28579765 AAGCTAGTTTGAATCGCACACTTAGTACCA
1 AAGCTAG-TTAAATCGCACACTTACTACCA
28579795 AAGCT
1 AAGCT
28579800 TCTGATTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTACTACCA
Found at i:28580814 original size:13 final size:13
Alignment explanation
Indices: 28580796--28580821 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28580786 ACAAGCAGTT
28580796 AAATTTTCACACA
1 AAATTTTCACACA
28580809 AAATTTTCACACA
1 AAATTTTCACACA
28580822 TGTCAATTCA
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:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTTTCACACA
Found at i:28594517 original size:20 final size:20
Alignment explanation
Indices: 28594494--28594532 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28594484 ATGAATGACA
28594494 CATGAGCTAAGAA-AATGAAT
1 CATG-GCTAAGAAGAATGAAT
*
28594514 CATGGCTAATAAGAATGAA
1 CATGGCTAAGAAGAATGAA
28594533 CAAAGCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.21
Consensus pattern (20 bp):
CATGGCTAAGAAGAATGAAT
Found at i:28595990 original size:8 final size:8
Alignment explanation
Indices: 28595977--28596007 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
28595967 ATCGGCAAAA
28595977 GCCGAAAT
1 GCCGAAAT
28595985 GCCGAAAT
1 GCCGAAAT
28595993 GCCGAAAT
1 GCCGAAAT
28596001 GCCGAAA
1 GCCGAAA
28596008 AGTCGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.26, G:0.26, T:0.10
Consensus pattern (8 bp):
GCCGAAAT
Found at i:28596014 original size:16 final size:16
Alignment explanation
Indices: 28595973--28596015 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
28595963 ATGAATCGGC
28595973 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCG
*
28595989 AAATGCCGAAATGCCG
1 AAAAGCCGAAATGCCG
*
28596005 AAAAGTCGAAA
1 AAAAGCCGAAA
28596016 GGTTGAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.09
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:28596160 original size:19 final size:18
Alignment explanation
Indices: 28596138--28596174 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
28596128 AGAATTGGCC
28596138 AAATGGGCCGGAATGGGCT
1 AAATGGGCCGG-ATGGGCT
*
28596157 AAATGGGCCTGATGGGCT
1 AAATGGGCCGGATGGGCT
28596175 GTTGGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.19
Consensus pattern (18 bp):
AAATGGGCCGGATGGGCT
Found at i:28596297 original size:29 final size:29
Alignment explanation
Indices: 28596255--28596366 Score: 113
Period size: 29 Copynumber: 3.9 Consensus size: 29
28596245 ATAATATGAT
* *
28596255 TTGGGCCTAATGGTCCATATGAATGTGAA
1 TTGGGCCTAGTGGGCCATATGAATGTGAA
* * *
28596284 TTGGGCCTAGTGGTCCATAAGAATATGAA
1 TTGGGCCTAGTGGGCCATATGAATGTGAA
*
28596313 CTGGGCC-AGATGGGCCATATGAA--TGACA
1 TTGGGCCTAG-TGGGCCATATGAATGTGA-A
* *
28596341 TTGGGCCCAGTGGGCCATATGCATGT
1 TTGGGCCTAGTGGGCCATATGAATGT
28596367 ATGTAGGGGT
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
27 3 0.04
28 21 0.30
29 45 0.64
30 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (29 bp):
TTGGGCCTAGTGGGCCATATGAATGTGAA
Found at i:28596335 original size:58 final size:57
Alignment explanation
Indices: 28596247--28596359 Score: 140
Period size: 58 Copynumber: 2.0 Consensus size: 57
28596237 GCATGAGAAT
** * * *
28596247 AATATGATTTGGGCCTAATGGTCCATATGAATGTGA-ATTGGGCCTAGTGGTCCATAAG
1 AATATGAACTGGGCCTAATGGGCCATATGAA--TGACATTGGGCCCAGTGGGCCATAAG
28596305 AATATGAACTGGGCC-AGATGGGCCATATGAATGACATTGGGCCCAGTGGGCCATA
1 AATATGAACTGGGCCTA-ATGGGCCATATGAATGACATTGGGCCCAGTGGGCCATA
28596360 TGCATGTATG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
56 3 0.06
57 19 0.40
58 26 0.54
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (57 bp):
AATATGAACTGGGCCTAATGGGCCATATGAATGACATTGGGCCCAGTGGGCCATAAG
Found at i:28599923 original size:14 final size:15
Alignment explanation
Indices: 28599887--28599927 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
28599877 GTGCCAAAAC
28599887 ATACCACAATTCAAA
1 ATACCACAATTCAAA
* *
28599902 ATA-TACAATTC-GA
1 ATACCACAATTCAAA
28599915 ATACCACAATTCA
1 ATACCACAATTCA
28599928 TAATCAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 4 0.19
14 14 0.67
15 3 0.14
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (15 bp):
ATACCACAATTCAAA
Found at i:28602573 original size:68 final size:67
Alignment explanation
Indices: 28602501--28602650 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
28602491 CATCATGTGT
* * * *
28602501 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
28602563 ATGTAG
62 ATGTAG
** * *
28602569 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
28602634 AG
66 AG
28602636 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
28602651 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:28602606 original size:64 final size:64
Alignment explanation
Indices: 28602525--28602708 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
28602515 AGACATTATG
* *
28602525 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
28602589 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28602654 AA
63 AA
* * * * *
28602656 ACTG--GCTAGGTCACATGGGTGGTAGTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
28602709 CGAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 21 0.22
65 7 0.07
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28604655 original size:45 final size:45
Alignment explanation
Indices: 28604606--28604697 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
28604596 CGACAAATCC
*
28604606 CCATAGTGTCTTTCAAATACGGTCTTATTCATTTTCGTCATGTTG
1 CCATAGCGTCTTTCAAATACGGTCTTATTCATTTTCGTCATGTTG
* ** * * *
28604651 CCATAGCGTCTTTTAGCTATGGTCTTATTCGTTTTTGTCATGTTG
1 CCATAGCGTCTTTCAAATACGGTCTTATTCATTTTCGTCATGTTG
28604696 CC
1 CC
28604698 TTAACTGTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (45 bp):
CCATAGCGTCTTTCAAATACGGTCTTATTCATTTTCGTCATGTTG
Found at i:28605543 original size:180 final size:180
Alignment explanation
Indices: 28605262--28605618 Score: 493
Period size: 180 Copynumber: 2.0 Consensus size: 180
28605252 GAGCTACAGA
* * * *
28605262 ACTCCAAATTAAGATCCGTTAATTTTTCCAAAAACTAGACTCACATATATTATTATCACAAAATT
1 ACTCCAAATTAAGAACCGCTAATTTTTCCAAAAACTAGACTCACATATACTATTACCACAAAATT
* * * * * *
28605327 TTCAGAATTTTTTGTTTACCAAATTAGTACAGTTTATTCATTAAAGTTACTCCTATTCCACTATC
66 TTCAGAATTTTTAGTTTACCAAATCAGCAAAGTTTATTCATTAAAGATACCCCTATTCCACTATC
28605392 TAACAATTCCGACCTCTATTCACTAAAAATTATTTATCTCATGGTACGGG
131 TAACAATTCCGACCTCTATTCACTAAAAATTATTTATCTCATGGTACGGG
* *
28605442 ACTCCAAATTAAGAACCGCTAATTTTAT-CAAAAACTAGACTCACATATACTCTTACCATAAAAT
1 ACTCCAAATTAAGAACCGCTAATTTT-TCCAAAAACTAGACTCACATATACTATTACCACAAAAT
* * *
28605506 TTTCAGAATTTTTAGTTTATCC-AATCAGCAAAGTTTATTCATTAGAGATACCCCTATTTCACTG
65 TTTCAGAATTTTTAGTTTA-CCAAATCAGCAAAGTTTATTCATTAAAGATACCCCTATTCCACTA
* * * * * *
28605570 TCTGACAGTTCTGATCTTTTTTCACTAAAAATTATTTATCTCATGGTAC
129 TCTAACAATTCCGACCTCTATTCACTAAAAATTATTTATCTCATGGTAC
28605619 AGGTCTCAGA
Statistics
Matches: 154, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
180 151 0.98
181 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (180 bp):
ACTCCAAATTAAGAACCGCTAATTTTTCCAAAAACTAGACTCACATATACTATTACCACAAAATT
TTCAGAATTTTTAGTTTACCAAATCAGCAAAGTTTATTCATTAAAGATACCCCTATTCCACTATC
TAACAATTCCGACCTCTATTCACTAAAAATTATTTATCTCATGGTACGGG
Found at i:28609820 original size:179 final size:181
Alignment explanation
Indices: 28609542--28609875 Score: 494
Period size: 179 Copynumber: 1.9 Consensus size: 181
28609532 GATCCGTTAA
* * *
28609542 TTTTTCTAGAAATTATACTCACATATATTCTTACCATAAAATTTTAATAATTTTTGGTTTAGCCA
1 TTTTTCTAGAAACTAGACTCACATATATTCTTACCATAAAATTTTAATAATTTTTAGTTTAGCCA
* * ** * * *
28609607 TTTAGTACAGTTTATTCATTAAAGTTACCCCTATTTCACTATCCAATAGTTCCGACCTCTCTTCA
66 ATTAGTAAAGTTTATTCATTAAAAATACCCCTATTTCACTATCCAACAATTCCAACCTCTCTTCA
28609672 CT-AAAATTATTTATCTCATGGTACGAGACTCCAAATTGAGAATCCCTAGT
131 CTAAAAATTATTTATCTCATGGTACGAGACTCCAAATTGAGAATCCCTAGT
* *
28609722 TTTTTC-AGAAACTAGACTCATATATATTCTTACCATAAAATTTTCAA-AATTTTTAGTTTATCC
1 TTTTTCTAGAAACTAGACTCACATATATTCTTACCATAAAATTTT-AATAATTTTTAGTTTAGCC
* * * *
28609785 AATTAGTAAATTTTATTCATTAAAAATACCCCTATTTCACTATCTAACAATTCCAATCTTTCTTC
65 AATTAGTAAAGTTTATTCATTAAAAATACCCCTATTTCACTATCCAACAATTCCAACCTCTCTTC
28609850 ACTAAAAATTATTTATCTCATGGTAC
130 ACTAAAAATTATTTATCTCATGGTAC
28609876 AGATCTCTGA
Statistics
Matches: 136, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
179 106 0.78
180 30 0.22
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (181 bp):
TTTTTCTAGAAACTAGACTCACATATATTCTTACCATAAAATTTTAATAATTTTTAGTTTAGCCA
ATTAGTAAAGTTTATTCATTAAAAATACCCCTATTTCACTATCCAACAATTCCAACCTCTCTTCA
CTAAAAATTATTTATCTCATGGTACGAGACTCCAAATTGAGAATCCCTAGT
Found at i:28610519 original size:50 final size:50
Alignment explanation
Indices: 28610445--28610782 Score: 324
Period size: 50 Copynumber: 6.7 Consensus size: 50
28610435 TTGGTACGCA
* *
28610445 TAGTAGTCTGCACTTAGTACTACACATGTGACCTATCAATCTGGA-ACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCT-GATACACG
* * * * * *
28610495 TAGTAGGCTGTACTTAGTACTACACATGTGACTTATCCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACG
* * * * *
28610545 TAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTTAA-CGGGT--ACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA--CAATCTGATACACG
* * *
28610594 TAAAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 T--AGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACG
** * * ** * * * * *
28610646 TAGTAGCCTGCACTTAGTACGGCAGACGTGATCAAAACTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCTAACAATCTGATACACG
*
28610697 TAGTAGCCTGCTCTTAGTACTACACATGTGACCTAACAATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACG
**
28610747 TAGTAGCCTGCACTTAGTACTACACACATGACCTAA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
28610783 AACTATCTTA
Statistics
Matches: 229, Mismatches: 50, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
49 6 0.03
50 146 0.64
51 72 0.31
52 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACG
Found at i:28610636 original size:101 final size:101
Alignment explanation
Indices: 28610506--28610787 Score: 393
Period size: 101 Copynumber: 2.8 Consensus size: 101
28610496 AGTAGGCTGT
* * *
28610506 ACTTAGTACTACACATGTGACTTATCCATCTGATACATGTAGTAGCCTGCACTTAGTACTACACA
1 ACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACA
* ** *
28610571 TGTGATCAAAGTTAACGGGTACGTAAAGTAGCCTAC
66 CGTGATCAAAACTAACGGGTACGCAAAGTAGCCTAC
* ** *
28610607 ACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACGGCAGA
1 ACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACA
* * *
28610672 CGTGATCAAAACTATCGGGTACGCATAGTAGCCTGC
66 CGTGATCAAAACTAACGGGTACGCAAAGTAGCCTAC
* *
28610708 TCTTAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACTACACA
1 ACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACA
* *
28610773 CATGACCTAAAACTA
66 CGTGATC-AAAACTA
28610788 TCTTAAACAC
Statistics
Matches: 158, Mismatches: 22, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 151 0.96
102 7 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (101 bp):
ACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACA
CGTGATCAAAACTAACGGGTACGCAAAGTAGCCTAC
Found at i:28610838 original size:102 final size:100
Alignment explanation
Indices: 28610509--28610828 Score: 291
Period size: 101 Copynumber: 3.2 Consensus size: 100
28610499 AGGCTGTACT
* * * * * **
28610509 TAGTACTACACATGTGACTTATCCATCTGATACATGTAGTAGCCTGCACTTAGTACTACACATGT
1 TAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACGACACACAT
* ** * ** ** * * * *
28610574 GATCAAAGTTAACGGGTACGTAAAGTAGCCTACAC
66 GACCAAAACTATCGGAAACACATAGTAGCATGCTC
* * * * *
28610609 TTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACGGCAGACG
1 -TAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACGACACACA
* ** * *
28610674 TGATCAAAACTATCGGGTACGCATAGTAGCCTGCTC
65 TGACCAAAACTATCGGAAACACATAGTAGCATGCTC
*
28610710 TTAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACA
1 -TAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACGACACACA
**
28610775 TGACCTAAAACTATCTTAAACACATAGTAGCATGCATAC
65 TGACC-AAAACTATCGGAAACACATAGTAGCATGC-T-C
*
28610814 -AGTACTACAGATGTG
1 TAGTACTACACATGTG
28610829 TTCTCACAAT
Statistics
Matches: 187, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
101 148 0.79
102 37 0.20
103 1 0.01
104 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (100 bp):
TAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCCTGCACTTAGTACGACACACAT
GACCAAAACTATCGGAAACACATAGTAGCATGCTC
Found at i:28613514 original size:30 final size:30
Alignment explanation
Indices: 28613478--28613542 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
28613468 TAGGGGACAT
28613478 ACGGCCATATAACATAACCGTGTGTCACAC
1 ACGGCCATATAACATAACCGTGTGTCACAC
28613508 ACGGCCATATAACATAACCGTGTGTCACAC
1 ACGGCCATATAACATAACCGTGTGTCACAC
28613538 ACGGC
1 ACGGC
28613543 TGAGACTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.18
Consensus pattern (30 bp):
ACGGCCATATAACATAACCGTGTGTCACAC
Found at i:28618637 original size:39 final size:39
Alignment explanation
Indices: 28618583--28618708 Score: 198
Period size: 39 Copynumber: 3.2 Consensus size: 39
28618573 TTCAGTGATG
28618583 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
28618622 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * * * *
28618661 TATATCCGGACTTAAGGTTCACAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
28618700 TATGTCCGG
1 TATATCCGG
28618709 GCTAAAGTCC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:28618725 original size:39 final size:39
Alignment explanation
Indices: 28618583--28618778 Score: 193
Period size: 39 Copynumber: 5.0 Consensus size: 39
28618573 TTCAGTGATG
*
28618583 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
28618622 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * *
28618661 TATATCCGGACTTAAGGTTCACAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * * *
28618700 TATGTCCGGGC-TAAAGTCCCGCAGGCT-TAGAGCTGGTAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTAT-GTGCTGGAAT
** **
28618739 TATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGGCAAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTATGTGCTGG-AAT
28618778 T
1 T
28618779 GGTTTCAAGT
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
38 16 0.12
39 118 0.88
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:28622447 original size:12 final size:12
Alignment explanation
Indices: 28622426--28622460 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28622416 CAAACATCTA
*
28622426 ATACAATTTCAC
1 ATACATTTTCAC
*
28622438 ATACATTTTCTC
1 ATACATTTTCAC
28622450 ATACATTTTCA
1 ATACATTTTCA
28622461 ATTTCATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (12 bp):
ATACATTTTCAC
Found at i:28625006 original size:24 final size:24
Alignment explanation
Indices: 28624931--28625007 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
28624921 TGGGATTTTC
*
28624931 ATGTTTGTTGAATCATCATCGAAT
1 ATGTTTGTTGAATCATCATCAAAT
* * ** **
28624955 ATGTTTTTTGAA-C-CCAGGATTTT
1 ATGTTTGTTGAATCATCATCA-AAT
28624978 CATGTTTGTTGAATCATCATCAAAT
1 -ATGTTTGTTGAATCATCATCAAAT
28625003 ATGTT
1 ATGTT
28625008 CTTAGTCTTG
Statistics
Matches: 36, Mismatches: 13, Indels: 8
0.63 0.23 0.14
Matches are distributed among these distances:
22 2 0.06
23 2 0.06
24 27 0.75
25 2 0.06
26 3 0.08
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (24 bp):
ATGTTTGTTGAATCATCATCAAAT
Found at i:28640348 original size:80 final size:79
Alignment explanation
Indices: 28640118--28640374 Score: 285
Period size: 80 Copynumber: 3.3 Consensus size: 79
28640108 TTGAATGATG
* * * * *
28640118 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
28640181 TTGTGCGAGATACTA-A
64 TTGTGCGAG-TACTATA
* *
28640197 TTCCGGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTCTCGAAGGCAT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCAT
28640259 TTGTGCGAGTTACTATA
64 TTGTGCGAG-TACTATA
* *
28640276 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
**
28640341 GAACGAGTAGCTATA
66 GTGCGAGTA-CTATA
* *
28640356 TCC-GGTTAAATCCCGAAGG
1 TCCGGGCTAAGTCCCGAAGG
28640375 TACGTGATTT
Statistics
Matches: 152, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
77 2 0.01
78 55 0.36
79 24 0.16
80 69 0.45
81 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTACTATA
Found at i:28640355 original size:40 final size:40
Alignment explanation
Indices: 28640119--28640341 Score: 278
Period size: 40 Copynumber: 5.6 Consensus size: 40
28640109 TGAATGATGT
* * * *
28640119 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28640159 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28640199 CCGGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
28640236 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
28640277 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28640317 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28640342 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 34 0.21
39 1 0.01
40 118 0.72
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28647579 original size:38 final size:38
Alignment explanation
Indices: 28647527--28647610 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
28647517 ACAAGGTATT
*
28647527 ACATGTAGGTGCATCACTTATTTGAAGAACAAATCTGCA
1 ACATG-AGGTGCATCACTTATTTGAAGAACAAATCTACA
28647566 ACATGAGGTGCATCACTTATTTGAAGAACAAATCTACA
1 ACATGAGGTGCATCACTTATTTGAAGAACAAATCTACA
28647604 ACATGAG
1 ACATGAG
28647611 TAGCGTCATT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 39 0.89
39 5 0.11
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (38 bp):
ACATGAGGTGCATCACTTATTTGAAGAACAAATCTACA
Found at i:28648673 original size:35 final size:36
Alignment explanation
Indices: 28648622--28648735 Score: 108
Period size: 35 Copynumber: 3.2 Consensus size: 36
28648612 GATGAAATTC
*
28648622 ATCTCTATTTCATGTTTATT-TCTCAGATGGACTTT
1 ATCTCTATTTCGTGTTTATTATCTCAGATGGACTTT
* * * * *
28648657 ATCTTTGTTTTGTGTTTATTATCCCA-ATGGATTTT
1 ATCTCTATTTCGTGTTTATTATCTCAGATGGACTTT
* ** *
28648692 AACTCTATTTCGTGTTTATTGCCTC-GATAGACTTT
1 ATCTCTATTTCGTGTTTATTATCTCAGATGGACTTT
*
28648727 ATCGCTATT
1 ATCTCTATT
28648736 GATGTAACAC
Statistics
Matches: 60, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
35 56 0.93
36 4 0.07
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (36 bp):
ATCTCTATTTCGTGTTTATTATCTCAGATGGACTTT
Found at i:28650901 original size:20 final size:20
Alignment explanation
Indices: 28650876--28650915 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28650866 ATTAAATTCA
28650876 ATAACTTTTCTCAATAACCT
1 ATAACTTTTCTCAATAACCT
*
28650896 ATAACTTTTCTTAATAACCT
1 ATAACTTTTCTCAATAACCT
28650916 TACATCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAACTTTTCTCAATAACCT
Found at i:28652675 original size:27 final size:27
Alignment explanation
Indices: 28652626--28652709 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
28652616 AGGCTATCCC
* *
28652626 TTCATAATTCATCATACAA-GCTTTTCT
1 TTCATATTTCATCACA-AAGGCTTTTCT
28652653 TTCATATTTCATCACAAAGGCTTTGT-T
1 TTCATATTTCATCACAAAGGCTTT-TCT
* *** *
28652680 TTCATGTTTTGCCACAAAGGTTTTTCT
1 TTCATATTTCATCACAAAGGCTTTTCT
28652707 TTC
1 TTC
28652710 CTAACGTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
26 3 0.06
27 43 0.91
28 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (27 bp):
TTCATATTTCATCACAAAGGCTTTTCT
Found at i:28654207 original size:51 final size:51
Alignment explanation
Indices: 28654142--28654259 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
28654132 TATTTCATCT
* * *
28654142 ATGGGCTTACGCCATATGCCTTATACCAGACTACCATAGCCTCCTTCAACC
1 ATGGTCTTATGCCATATGCCTTATACCAGACTACCATAGCCTACTTCAACC
* * * * *
28654193 ATGGTCTTATGCCATATGCCTTATACTAGACTACCATTGCCTATTTCATCT
1 ATGGTCTTATGCCATATGCCTTATACCAGACTACCATAGCCTACTTCAACC
*
28654244 ATGATCTTATGCCATA
1 ATGGTCTTATGCCATA
28654260 AACCATCGTC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (51 bp):
ATGGTCTTATGCCATATGCCTTATACCAGACTACCATAGCCTACTTCAACC
Found at i:28656174 original size:29 final size:29
Alignment explanation
Indices: 28656142--28656245 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 29
28656132 TGACTAGACA
*
28656142 AAAAATTTGTATAAAAAATTAAAAATATT
1 AAAAATATGTATAAAAAATTAAAAATATT
* * * *
28656171 AAAAAAATATTTAAAAATATATAAGAAT-TGT
1 AAAAATATGTATAAAAA-AT-TAAAAATAT-T
**
28656202 AAAAATAT-T-TAAATTATTAAAAATATT
1 AAAAATATGTATAAAAAATTAAAAATATT
*
28656229 AAAAAT-TGTAAAAAAAA
1 AAAAATATGTATAAAAAA
28656246 ATTATTGTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
26 1 0.02
27 14 0.25
28 7 0.12
29 17 0.30
30 4 0.07
31 14 0.25
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATATGTATAAAAAATTAAAAATATT
Found at i:28656241 original size:17 final size:17
Alignment explanation
Indices: 28656184--28656294 Score: 50
Period size: 19 Copynumber: 6.2 Consensus size: 17
28656174 AAAATATTTA
*
28656184 AAAATATATAAGAATTGT
1 AAAATAT-TAAAAATTGT
* *
28656202 AAAAATATTTAAATTATT-A
1 -AAAATA-TTAAA-AATTGT
28656221 AAAATATTAAAAATTGT
1 AAAATATTAAAAATTGT
28656238 AAAA-A--AAAATTATTGT
1 AAAATATTAAAA--ATTGT
* * *
28656254 AAAAAAATAAATATTGT
1 AAAATATTAAAAATTGT
*
28656271 AAATAACTATTAAAAAATGT
1 -AA-AA-TATTAAAAATTGT
28656291 AAAA
1 AAAA
28656295 AGAATGTAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 23
0.68 0.10 0.22
Matches are distributed among these distances:
14 4 0.06
16 13 0.18
17 15 0.21
18 10 0.14
19 16 0.23
20 13 0.18
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATATTAAAAATTGT
Found at i:28656242 original size:9 final size:9
Alignment explanation
Indices: 28656153--28656234 Score: 78
Period size: 9 Copynumber: 8.8 Consensus size: 9
28656143 AAAATTTGTA
28656153 TAAAAA-AT
1 TAAAAATAT
28656161 TAAAAATAT
1 TAAAAATAT
28656170 TAAAAAAATATT
1 T--AAAAATA-T
28656182 TAAAAATAT
1 TAAAAATAT
*
28656191 ATAAGAAT-T
1 -TAAAAATAT
28656200 GTAAAAATAT
1 -TAAAAATAT
* *
28656210 TTAAATTAT
1 TAAAAATAT
28656219 TAAAAATAT
1 TAAAAATAT
28656228 TAAAAAT
1 TAAAAAT
28656235 TGTAAAAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
8 6 0.10
9 32 0.52
10 14 0.23
11 7 0.11
12 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
TAAAAATAT
Found at i:28656254 original size:16 final size:17
Alignment explanation
Indices: 28656228--28656273 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
28656218 TTAAAAATAT
*
28656228 TAAAAATTGTAAAAAAA
1 TAAATATTGTAAAAAAA
*
28656245 -AATTATTGTAAAAAAA
1 TAAATATTGTAAAAAAA
28656261 TAAATATTGTAAA
1 TAAATATTGTAAA
28656274 TAACTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (17 bp):
TAAATATTGTAAAAAAA
Found at i:28656517 original size:20 final size:20
Alignment explanation
Indices: 28656489--28656603 Score: 76
Period size: 20 Copynumber: 5.7 Consensus size: 20
28656479 GAGGATTTGA
*
28656489 TTTATTAATTATTTACAATT
1 TTTAATAATTATTTACAATT
* *
28656509 TTTAATAATT-TTTAAAGAAT
1 TTTAATAATTATTTACA-ATT
* * *
28656529 TTAAAT-ATTGTTTTATAATT
1 TTTAATAATT-ATTTACAATT
*
28656549 TTTAATAACTTCTTTACAA-T
1 TTTAATAA-TTATTTACAATT
* *
28656569 TTTAA-AATATTTTTAACAATA
1 TTTAATAAT-TATTT-ACAATT
28656590 TTTAATAATTATTT
1 TTTAATAATTATTT
28656604 CTTTTACAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
18 1 0.01
19 14 0.19
20 33 0.45
21 21 0.28
22 5 0.07
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTAATAATTATTTACAATT
Found at i:28656518 original size:10 final size:10
Alignment explanation
Indices: 28656505--28656599 Score: 54
Period size: 10 Copynumber: 9.4 Consensus size: 10
28656495 AATTATTTAC
28656505 AATTTTTAAT
1 AATTTTTAAT
28656515 AATTTTTAA-
1 AATTTTTAAT
* *
28656524 AGAATTTAAAT
1 A-ATTTTTAAT
*
28656535 -ATTGTTTTAT
1 AATT-TTTAAT
28656545 AATTTTTAAT
1 AATTTTTAAT
*
28656555 AACTTCTTT-AC
1 AA-TT-TTTAAT
*
28656566 AA-TTTTAAA
1 AATTTTTAAT
*
28656575 ATATTTTTAAC
1 A-ATTTTTAAT
*
28656586 AATATTTAAT
1 AATTTTTAAT
28656596 AATT
1 AATT
28656600 ATTTCTTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
8 3 0.05
9 6 0.09
10 37 0.58
11 15 0.23
12 3 0.05
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:28656549 original size:40 final size:40
Alignment explanation
Indices: 28656500--28656599 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 40
28656490 TTATTAATTA
28656500 TTTACAATTTTTAATAATT-TTTAAAGAATTT-AAATATTGT
1 TTTACAATTTTTAATAATTCTTTAAA-AATTTAAAATATT-T
* * *
28656540 TTTATAATTTTTAATAACTTCTTTACAATTTTAAAATATTT
1 TTTACAATTTTTAATAA-TTCTTTAAAAATTTAAAATATTT
* *
28656581 TTAACAATATTTAATAATT
1 TTTACAATTTTTAATAATT
28656600 ATTTCTTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
40 18 0.35
41 21 0.41
42 12 0.24
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (40 bp):
TTTACAATTTTTAATAATTCTTTAAAAATTTAAAATATTT
Found at i:28659228 original size:17 final size:17
Alignment explanation
Indices: 28659206--28659245 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28659196 TTTTCTTATT
*
28659206 TAAAATTTTA-AAAATAA
1 TAAAATTGTATAAAA-AA
28659223 TAAAATTGTATAAAAAA
1 TAAAATTGTATAAAAAA
28659240 TAAAAT
1 TAAAAT
28659246 CAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATTGTATAAAAAA
Found at i:28659847 original size:247 final size:246
Alignment explanation
Indices: 28659493--28660507 Score: 1107
Period size: 247 Copynumber: 4.1 Consensus size: 246
28659483 ATCTATTCTA
* * * * **
28659493 TTTAATTTTTTTTAAATAATGTATGCACGTGTTCG-ATAAAAAACTATTCTATTATGTTTAACTT
1 TTTAA-TTTATTT-AATAATGTTTGCATGT-TTCGCA-AAAAATC-ATTCTACCATGTTTAACTT
* * * * *
28659557 TTCTTTTAACAATATCTACATGTGGCTAACAAAAATTCATTCAATTATATTACCGTTATGATCGA
61 TTCTTTTAACAATATCTGCACGTGTCTAACAAAAATTCATTCAATTATATTGCAGTTATGATCGA
* * * * * * *
28659622 TATTGAATTACTTCTTTATATGATGTGTTTATGTTTCTAAATATGTCCTAATCATATTTGGTTCA
126 CATTGAACTACTTCTTTACATGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCA
* * *
28659687 CATTTA-ATTTTTTCGCAATGTCTGTGTGTGTCTGACAAAGATTTATTTTGTTCG-G
191 CATTTACATTTTTTCACAATGTCTGCGCGTGTCTGACAAAGATTTATTTTGTT-GTG
*
28659742 TTTAATTTATTTAATAATGTTTGCATGTATTCTGCAAAAAATCATTTTACCATGTTTAACTTTTC
1 TTTAATTTATTTAATAATGTTTGCATGT-TTC-GCAAAAAATCATTCTACCATGTTTAACTTTTC
* * * * *
28659807 ATTTAACAATATCCGCACGTGTCTAACAAAAATTCATTCAATTGTATTGCAGTTATAATTGACAT
64 TTTTAACAATATCTGCACGTGTCTAACAAAAATTCATTCAATTATATTGCAGTTATGATCGACAT
* * * *
28659872 TGAACTACTGCTTTATATGATGTGTTTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACGT
129 TGAACTACTTCTTTACATGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACAT
* * * ** * *
28659937 TTACAGTTTTTCACAATGTCTGTGTGTGTCCAACAAATATTTATTTTGTTTTG
194 TTACATTTTTTCACAATGTCTGCGCGTGTCTGACAAAGATTTATTTTGTTGTG
* * * *
28659990 TTTAATTTGTTTAATAATGTTTAAACATG-CTCGATAAAAAATCATTCTACCATGTTTAACTTTT
1 TTTAATTTATTTAATAATGTTT--GCATGTTTCG-CAAAAAATCATTCTACCATGTTTAACTTTT
* * ** * *
28660054 CTTTTAATAATATCTGCACGTGCCCGACAAAAATTCATTCAATTGA-ATTGTAGTTATGATCGGC
63 CTTTTAACAATATCTGCACGTGTCTAACAAAAATTCATTCAATT-ATATTGCAGTTATGATCGAC
* *
28660118 ATTGAACTACTTCTTTACATTACT-TGTCTGTGTTTCTAAATATGTCTTAATCATATTTTGTCCA
127 ATTGAACTACTTCTTTACATGA-TGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCA
* * * *
28660182 CACTTA-ATTTTTTCACAATTTTTGCGCGTGTCAGACAAAGATTTATTTTGTTGTG
191 CATTTACATTTTTTCACAATGTCTGCGCGTGTCTGACAAAGATTTATTTTGTTGTG
* * * * ** *
28660237 TTTAATTTTTTTAAAAATGTTTGCAGGTGTCCGGCAAAAAATCATTCTAATATGTTCAACTTTTC
1 TTTAATTTATTTAATAATGTTTGCATGT-TTC-GCAAAAAATCATTCTACCATGTTTAACTTTTC
* * * * * * *
28660302 TTTTAACAATATATGCATGTGT-TCGACAAAATTTCATTCAATTGTATTTCAGTTATGATCAACA
64 TTTTAACAATATCTGCACGTGTCT-AACAAAAATTCATTCAATTATATTGCAGTTATGATCGACA
* * * *
28660366 TTGAACTACTTCTTTACATGATATGTCTGTGATTCTAAATATGTCATAATCATATTTTGTCCACG
128 TTGAACTACTTCTTTACATGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACA
* * *
28660431 TTTACA-TTTTTCACAATGTCTGCGCGTGTTCT-ACAAAAATCTATTATGTTGTG
193 TTTACATTTTTTCACAATGTCTGCGCGTG-TCTGACAAAGATTTATTTTGTTGTG
28660484 TTT-ATTTATTTATAATAATGTTTG
1 TTTAATTTA-TT-TAATAATGTTTG
28660508 TAAGTGTCCA
Statistics
Matches: 650, Mismatches: 97, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
245 3 0.00
246 5 0.01
247 397 0.61
248 234 0.36
249 7 0.01
250 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (246 bp):
TTTAATTTATTTAATAATGTTTGCATGTTTCGCAAAAAATCATTCTACCATGTTTAACTTTTCTT
TTAACAATATCTGCACGTGTCTAACAAAAATTCATTCAATTATATTGCAGTTATGATCGACATTG
AACTACTTCTTTACATGATGTGTCTGTGTTTCTAAATATGTCCTAATCATATTTTGTCCACATTT
ACATTTTTTCACAATGTCTGCGCGTGTCTGACAAAGATTTATTTTGTTGTG
Found at i:28660502 original size:495 final size:495
Alignment explanation
Indices: 28659525--28660506 Score: 1285
Period size: 495 Copynumber: 2.0 Consensus size: 495
28659515 ATGCACGTGT
** * * *
28659525 TCGATAAAAAACTATTCTATTATGTTTAACTTTTCTTTTAACAATATCTACATGTGGCTAACAAA
1 TCGATAAAAAACTATTCTACCATGTTTAACTTTTCTTTTAACAATATCTACACGTGCCCAACAAA
* * * * *
28659590 AATTCATTCAATTATATTACCGTTATGATCGATATTGAATTACTTCTTTATATGATGTGTTTATG
66 AATTCATTCAATTATATTACAGTTATGATCGACATTGAACTACTTCTTTACATGATGTGTCTATG
* * * * * *
28659655 TTTCTAAATATGTCCTAATCATATTTGGTTCACATTTAATTTTTTCGCAATGTCTGTGTGTGTCT
131 TTTCTAAATATGTCCTAATCATATTTGGTCCACACTTAATTTTTTCACAATGTCTGCGCGTGTCA
* * * *
28659720 GACAAAGATTTATTTTGTTCGGTTTAATTTATTTAATAATGTTTGCATGTATTCTGCAAAAAATC
196 GACAAAGATTTATTTTGTTCGGTTTAATTTATTTAAAAATGTTTGCAGGTATCCGGCAAAAAATC
* * * *
28659785 ATTTTACCATGTTTAACTTTTCATTTAACAATATCCGCACGTGTCTAACAAAAATTCATTCAATT
261 ATTCTAACATGTTCAACTTTTCATTTAACAATATACGCACGTGTCTAACAAAAATTCATTCAATT
** * * * *
28659850 GTATTGCAGTTATAATTGACATTGAACTACTGCTTTATATGATGTGTTTGTGTTTCTAAATATGT
326 GTATTGCAGTTATAATCAACATTGAACTACTGCTTTACATGATATGTCTGTGATTCTAAATATGT
* * * * *
28659915 CCTAATCATATTTTGTCCACGTTTACAGTTTTTCACAATGTCTGTGTGTGTCCAACAAATATTTA
391 CATAATCATATTTTGTCCACGTTTACAGTTTTTCACAATGTCTGCGCGTGTCCAACAAAAATCTA
* *
28659980 TTTTGTTTTGTTTAATTTGTTTAATAATGTTTAAACATGC
456 TTATGTTGTGTTTAATTTGTTTAATAATGTTTAAACATGC
* * *
28660020 TCGATAAAAAA-TCATTCTACCATGTTTAACTTTTCTTTTAATAATATCTGCACGTGCCCGACAA
1 TCGATAAAAAACT-ATTCTACCATGTTTAACTTTTCTTTTAACAATATCTACACGTGCCCAACAA
** * *
28660084 AAATTCATTCAATTGA-ATTGTAGTTATGATCGGCATTGAACTACTTCTTTACATTACT-TGTCT
65 AAATTCATTCAATT-ATATTACAGTTATGATCGACATTGAACTACTTCTTTACATGA-TGTGTCT
* * * * *
28660147 GTGTTTCTAAATATGTCTTAATCATATTTTGTCCACACTTAATTTTTTCACAATTTTTGCGCGTG
128 ATGTTTCTAAATATGTCCTAATCATATTTGGTCCACACTTAATTTTTTCACAATGTCTGCGCGTG
* *
28660212 TCAGACAAAGATTTATTTTGTT-GTGTTTAATTTTTTTAAAAATGTTTGCAGGTGTCCGGCAAAA
193 TCAGACAAAGATTTATTTTGTTCG-GTTTAATTTATTTAAAAATGTTTGCAGGTATCCGGCAAAA
* * * * * *
28660276 AATCATTCTAATATGTTCAACTTTTCTTTTAACAATATATGCATGTGT-TCGACAAAATTTCATT
257 AATCATTCTAACATGTTCAACTTTTCATTTAACAATATACGCACGTGTCT-AACAAAAATTCATT
* * *
28660340 CAATTGTATTTCAGTTATGATCAACATTGAACTACTTCTTTACATGATATGTCTGTGATTCTAAA
321 CAATTGTATTGCAGTTATAATCAACATTGAACTACTGCTTTACATGATATGTCTGTGATTCTAAA
* *
28660405 TATGTCATAATCATATTTTGTCCACGTTTACA-TTTTTCACAATGTCTGCGCGTGTTCTACAAAA
386 TATGTCATAATCATATTTTGTCCACGTTTACAGTTTTTCACAATGTCTGCGCGTGTCCAACAAAA
*
28660469 ATCTATTATGTTGTGTTT-ATTTATTTATAATAATGTTT
451 ATCTATTATGTTGTGTTTAATTT-GTT-TAATAATGTTT
28660507 GTAAGTGTCC
Statistics
Matches: 417, Mismatches: 63, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
493 4 0.01
494 47 0.11
495 364 0.87
496 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (495 bp):
TCGATAAAAAACTATTCTACCATGTTTAACTTTTCTTTTAACAATATCTACACGTGCCCAACAAA
AATTCATTCAATTATATTACAGTTATGATCGACATTGAACTACTTCTTTACATGATGTGTCTATG
TTTCTAAATATGTCCTAATCATATTTGGTCCACACTTAATTTTTTCACAATGTCTGCGCGTGTCA
GACAAAGATTTATTTTGTTCGGTTTAATTTATTTAAAAATGTTTGCAGGTATCCGGCAAAAAATC
ATTCTAACATGTTCAACTTTTCATTTAACAATATACGCACGTGTCTAACAAAAATTCATTCAATT
GTATTGCAGTTATAATCAACATTGAACTACTGCTTTACATGATATGTCTGTGATTCTAAATATGT
CATAATCATATTTTGTCCACGTTTACAGTTTTTCACAATGTCTGCGCGTGTCCAACAAAAATCTA
TTATGTTGTGTTTAATTTGTTTAATAATGTTTAAACATGC
Found at i:28661089 original size:62 final size:63
Alignment explanation
Indices: 28660992--28661109 Score: 184
Period size: 62 Copynumber: 1.9 Consensus size: 63
28660982 AAAAAGAGTA
* * * *
28660992 AACATTGTTAATGAAACATAACTCAGTTGATAAATTTACCAAAA-ACAAATCAAATTGAAGTT
1 AACATTGTCAATAAAACATAACTCAATTGATAAATTTACCAAAACAAAAATCAAATTGAAGTT
*
28661054 AACATTGTCAATAAAACATAATTCAATTGATAAATTTACCAAAACAAAAATCAAAT
1 AACATTGTCAATAAAACATAACTCAATTGATAAATTTACCAAAACAAAAATCAAAT
28661110 GGAATTTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 40 0.80
63 10 0.20
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (63 bp):
AACATTGTCAATAAAACATAACTCAATTGATAAATTTACCAAAACAAAAATCAAATTGAAGTT
Found at i:28661098 original size:28 final size:27
Alignment explanation
Indices: 28661005--28661099 Score: 66
Period size: 28 Copynumber: 3.2 Consensus size: 27
28660995 ATTGTTAATG
*
28661005 AAACATAACTCAGTTGATAAATTTACCAA
1 AAACATAA-TCAATTGATAAATTTACC-A
**
28661034 AAACA-AATCAAATTGAAGTTAACATTGTCAATA
1 AAACATAATC-AATTG-A--TAA-ATT-T-ACCA
28661067 AAACATAATTCAATTGATAAATTTACCA
1 AAACATAA-TCAATTGATAAATTTACCA
28661095 AAACA
1 AAACA
28661100 AAAATCAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 19
0.68 0.07 0.25
Matches are distributed among these distances:
27 2 0.04
28 13 0.25
29 7 0.13
30 3 0.06
31 6 0.12
32 3 0.06
33 8 0.15
34 8 0.15
35 2 0.04
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (27 bp):
AAACATAATCAATTGATAAATTTACCA
Found at i:28661496 original size:3 final size:3
Alignment explanation
Indices: 28661488--28661540 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
28661478 TCAGCCCTAC
28661488 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28661536 T-T TAT
1 TAT TAT
28661541 GAGAATTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28678199 original size:45 final size:42
Alignment explanation
Indices: 28678115--28678231 Score: 103
Period size: 48 Copynumber: 2.6 Consensus size: 42
28678105 AGGTTATTGT
*
28678115 GAGCTAGTGTAAGACATGTCTGGGATGCATCAGCCACATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGATGCATCA--CACATTATGA
28678159 GAGCCAGTGTAAGACCATGTCTGGGGCATGGCATCA-ACATTGA-GA
1 GAGCCAGTGTAAGA-CATGTCT-GGG-AT-GCATCACACATT-ATGA
* *
28678204 CGAGTGCTAGTGTAAGACATGTTTGGGA
1 -GA--GCCAGTGTAAGACATGTCTGGGA
28678232 CATGCATCGG
Statistics
Matches: 62, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
44 13 0.21
45 15 0.24
46 9 0.15
47 8 0.13
48 17 0.27
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (42 bp):
GAGCCAGTGTAAGACATGTCTGGGATGCATCACACATTATGA
Found at i:28678248 original size:46 final size:45
Alignment explanation
Indices: 28678163--28678335 Score: 154
Period size: 46 Copynumber: 3.7 Consensus size: 45
28678153 TTATGAGAGC
* **
28678163 CAGTGTAAGACCATGTCTGGGGCATGGCATCAACATTGAGACG-AGT
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACGAAGT
* *
28678209 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCTTGAGACGTAAGT
1 -C-AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACG-AAGT
* * * **
28678257 CAATGTAAGACATGTCTGGGACATGCATCGGC-TACGAGATG-TTT
1 CAGTGTAAGACATGTCTGGGACATGCATCGGCAT-TGAGACGAAGT
*
28678301 CAGTATAAGACCATGTCTGGGACATAGCATCGGCA
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
28678336 CAGATATGCT
Statistics
Matches: 106, Mismatches: 13, Indels: 14
0.80 0.10 0.11
Matches are distributed among these distances:
44 9 0.08
45 15 0.14
46 56 0.53
47 14 0.13
48 12 0.11
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (45 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAAGT
Found at i:28679400 original size:41 final size:41
Alignment explanation
Indices: 28679342--28679443 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
28679332 AGGTTTTTGC
* *
28679342 ACACGGGCTA-GGACACGGGCATGTCATAGCCGTGTGAAGA
1 ACACGGGCCAGGGACACGGGCATGTCATAGCCGTGTAAAGA
** *
28679382 ACACGGGCCAGGGACACGGGTGTGTCATAGCCGTGTAAAGG
1 ACACGGGCCAGGGACACGGGCATGTCATAGCCGTGTAAAGA
28679423 ACACGGGCCAGGGACACGGGC
1 ACACGGGCCAGGGACACGGGC
28679444 GTGTGCTTGG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
40 9 0.16
41 46 0.84
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (41 bp):
ACACGGGCCAGGGACACGGGCATGTCATAGCCGTGTAAAGA
Found at i:28682888 original size:26 final size:26
Alignment explanation
Indices: 28682838--28682910 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
28682828 TTTGCCACAT
* *
28682838 ATACTGATACTGGCAGCTCAT-CTGTG
1 ATACTGTTACTGGCAGCT-TTGCTGTG
*
28682864 TTACTGTTACTGGCAGCTTTGCTGTG
1 ATACTGTTACTGGCAGCTTTGCTGTG
* * *
28682890 ATATTATTATTGGCAGCTTTG
1 ATACTGTTACTGGCAGCTTTG
28682911 TTGCGATATT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 1 0.03
26 38 0.97
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGTG
Found at i:28683846 original size:16 final size:17
Alignment explanation
Indices: 28683825--28683856 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28683815 TGGTTAGAGT
28683825 AAACTG-AAACTGTAGG
1 AAACTGAAAACTGTAGG
28683841 AAACTGAAAACTGTAG
1 AAACTGAAAACTGTAG
28683857 TGAGACCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (17 bp):
AAACTGAAAACTGTAGG
Found at i:28687193 original size:14 final size:14
Alignment explanation
Indices: 28687176--28687203 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28687166 AAAATAGTTT
28687176 TAAAAAGATAAAAA
1 TAAAAAGATAAAAA
28687190 TAAAAAGATAAAAA
1 TAAAAAGATAAAAA
28687204 GGAATTAACC
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:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
TAAAAAGATAAAAA
Found at i:28697817 original size:28 final size:28
Alignment explanation
Indices: 28697786--28697869 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
28697776 AACTTCGATC
28697786 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
28697814 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
28697836 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
*
28697864 CCGTGT
1 ACGTGT
28697870 ACCAGATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.20
23 2 0.05
24 3 0.07
25 6 0.15
26 3 0.07
27 2 0.05
28 13 0.32
29 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:28697859 original size:50 final size:49
Alignment explanation
Indices: 28697686--28697913 Score: 278
Period size: 49 Copynumber: 4.6 Consensus size: 49
28697676 TTGTGAGGTT
* * *
28697686 ACGTGTGTAGCACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTT
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTC
* * * * *
28697735 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTC-GATAACTTCGATC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATAA-TT-GGTC
* **
28697786 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTC
* *
28697836 ACGTGTGTAGTACTAAGTGCAGGCTACTCCGTGTACCAGATTATTGGTC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTC
* *
28697885 GCATGTGTAGTACTAAGTGCAGGCTACTA
1 ACGTGTGTAGTACTAAGTGCAGGCTACTA
28697914 TGCGTACTAG
Statistics
Matches: 152, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
49 66 0.43
50 50 0.33
51 36 0.24
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (49 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTC
Found at i:28700002 original size:31 final size:31
Alignment explanation
Indices: 28699964--28700026 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
28699954 CTTTTCACAC
28699964 TTCATATTTCATAACACTGGGCCGAAGCCTT
1 TTCATATTTCATAACACTGGGCCGAAGCCTT
**
28699995 TTCATATTTCATATTACTGGGCCGAAGCCTT
1 TTCATATTTCATAACACTGGGCCGAAGCCTT
28700026 T
1 T
28700027 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTCATATTTCATAACACTGGGCCGAAGCCTT
Found at i:28700327 original size:25 final size:24
Alignment explanation
Indices: 28700221--28700341 Score: 183
Period size: 24 Copynumber: 5.0 Consensus size: 24
28700211 CTTTTATCAT
*
28700221 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
28700246 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28700269 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
28700293 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
28700318 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28700342 CACTTCCTCC
Statistics
Matches: 90, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.20
24 41 0.46
25 31 0.34
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28700335 original size:49 final size:47
Alignment explanation
Indices: 28700221--28700341 Score: 181
Period size: 49 Copynumber: 2.5 Consensus size: 47
28700211 CTTTTATCAT
*
28700221 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAGCCCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAGCCCTTTTA
*
28700269 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCA-AAGCCCTTT-TA
28700318 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
28700342 CACTTCCTCC
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
47 22 0.32
48 21 0.31
49 25 0.37
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAGCCCTTTTA
Found at i:28700438 original size:25 final size:25
Alignment explanation
Indices: 28700409--28700464 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
28700399 ATATCATACA
* *
28700409 TCATTTTTACCTAGGGGCATAATGG
1 TCATTTTTACCTAGGGGCAAAACGG
28700434 TCATTTTTACCTAGGGGCAAAACGG
1 TCATTTTTACCTAGGGGCAAAACGG
28700459 TCATTT
1 TCATTT
28700465 CCATATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (25 bp):
TCATTTTTACCTAGGGGCAAAACGG
Found at i:28707073 original size:42 final size:43
Alignment explanation
Indices: 28706973--28707075 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
28706963 CAATGCCAAC
* * ***
28706973 GTCCCAGACGTGGTCTTACATGTAACTCAATATCGATGCCTTT
1 GTCCCAGACATGGTCTTACATGGAACTCAATATCGATGCCGAG
* *
28707016 GTCCCAGACAGGGTCTTACATGGAA-TCAGATAT-GATGTCGAG
1 GTCCCAGACATGGTCTTACATGGAACTCA-ATATCGATGCCGAG
28707058 GTCCCAGACATGGTCTTA
1 GTCCCAGACATGGTCTTA
28707076 TACGTAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 25 0.49
43 26 0.51
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGGAACTCAATATCGATGCCGAG
Found at i:28708913 original size:56 final size:56
Alignment explanation
Indices: 28708822--28708944 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
28708812 GAGATTGGCG
* * *
28708822 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
28708879 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
28708934 CTGAGTGTGCG
1 CTAAGTGTGCG
28708945 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:28708931 original size:27 final size:28
Alignment explanation
Indices: 28708822--28708944 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
28708812 GAGATTGGCG
* * * *
28708822 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
28708851 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
28708879 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
28708907 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
28708934 CTGAGTGTGCG
1 CTAAGTGTGCG
28708945 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:28708955 original size:27 final size:27
Alignment explanation
Indices: 28708847--28708957 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
28708837 TAAATTGTAC
* * *
28708847 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
28708875 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
28708903 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
28708930 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
28708957 A
1 A
28708958 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:28717045 original size:27 final size:27
Alignment explanation
Indices: 28717007--28717100 Score: 156
Period size: 27 Copynumber: 3.6 Consensus size: 27
28716997 TAAATTGTAC
*
28717007 AGCACTAAGTGTGCGAGTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGATTATAT
28717034 AGCACTAAGTGT--GAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATAT
28717059 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATAT
*
28717086 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28717101 GACTTAATAT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
25 24 0.38
27 39 0.62
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATAT
Found at i:28717111 original size:27 final size:27
Alignment explanation
Indices: 28717007--28717113 Score: 112
Period size: 27 Copynumber: 4.0 Consensus size: 27
28716997 TAAATTGTAC
* * *
28717007 AGCACTAAGTGTGCGAGTTGATTATGT
1 AGCACTAAGTGTGCGACTTGAATATAT
* *
28717034 AGCACTAAGTGT--GAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
* *
28717059 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
28717086 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
28717113 A
1 A
28717114 CTTTTGAATC
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
25 24 0.33
27 45 0.62
28 4 0.05
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:28723770 original size:46 final size:45
Alignment explanation
Indices: 28723717--28723892 Score: 167
Period size: 46 Copynumber: 3.8 Consensus size: 45
28723707 TATTTGGGCA
* *
28723717 TCCGAACTCGTTGATTTCAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
28723763 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
28723810 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * * *
28723856 CCCGAGCTTGTTGAGTTGATTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28723893 GCGAGTTACA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 64 0.60
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:28723872 original size:93 final size:93
Alignment explanation
Indices: 28723713--28723884 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
28723703 AGGATATTTG
* * *
28723713 GGCATCCGAACTCGTTGATTTCAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
28723778 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
28723806 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTTGTTGAG
1 GGCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
* *
28723871 TTGATTCTGAGTTC
66 TTGAGTCCGAGTTC
28723885 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:28727575 original size:30 final size:30
Alignment explanation
Indices: 28727541--28727601 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
28727531 TTCCCGAGCC
*
28727541 TAGGGGCAAAAGT-GTAAATATGCAAAAGTT
1 TAGGGACAAAA-TCGTAAATATGCAAAAGTT
* *
28727571 TAGGGACAAAATCGTAATTTTGCAAAAGTT
1 TAGGGACAAAATCGTAAATATGCAAAAGTT
28727601 T
1 T
28727602 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (30 bp):
TAGGGACAAAATCGTAAATATGCAAAAGTT
Found at i:28741946 original size:40 final size:40
Alignment explanation
Indices: 28741886--28742069 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 40
28741876 TATTCGAATG
*
28741886 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
28741926 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * *
28741966 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
* *
28742006 ATATCTGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
28742046 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
28742070 CTTGTGCGAG
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 118 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:28742019 original size:80 final size:80
Alignment explanation
Indices: 28741886--28742069 Score: 246
Period size: 80 Copynumber: 2.3 Consensus size: 80
28741876 TATTCGAATG
* * *
28741886 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
28741950 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* * * *
28741966 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCTGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
28742031 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
28742046 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
28742070 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 3 0.03
80 89 0.97
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:28744317 original size:41 final size:42
Alignment explanation
Indices: 28744260--28744338 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
28744250 GTGTGAATTT
* *
28744260 GTGTAAGACCATGTCTGGGACATTGGCATTG-TATATGTCTC
1 GTGTAAGACCATGTCTGGGACAGTGGCATCGATATATGTCTC
*
28744301 GTGTAAGACCCTGTCTGGGACAGTGGCATCGATATATG
1 GTGTAAGACCATGTCTGGGACAGTGGCATCGATATATG
28744339 ATAACATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 28 0.82
42 6 0.18
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACAGTGGCATCGATATATGTCTC
Found at i:28748239 original size:46 final size:46
Alignment explanation
Indices: 28748177--28748431 Score: 359
Period size: 46 Copynumber: 5.5 Consensus size: 46
28748167 GATGCCATAA
* * * * * *
28748177 TATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACAC-ATTTCATATCAGGTTGCCATGG
** *** * * *
28748223 TATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTACCATGA
1 TATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGG
28748270 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
28748316 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
28748362 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
28748408 TATCTTTCAACCATGGTCTTACAC
1 TATCTTTCAACCATGGTCTTACAC
28748432 CCATGGTTTT
Statistics
Matches: 192, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
46 156 0.81
47 36 0.19
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
Found at i:28748392 original size:92 final size:93
Alignment explanation
Indices: 28748171--28748503 Score: 364
Period size: 92 Copynumber: 3.5 Consensus size: 93
28748161 CGACATGATG
* * * * * * *
28748171 CCATAATATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAACC
1 CCATGATATCTTTCAACCATGGTCTTACAC-ATTTCATATCAGGTTGCCATGGTATCTTTCAACC
** * * *
28748235 ATGGTCTTATTCATTTTCCCGTCATGTTA
65 ATGGTCTTACACATTTTCACATCAGGTTA
28748264 CCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
1 CCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
* *
28748329 TGGTCTTACACA-TTTCATATCAGGTTG
66 TGGTCTTACACATTTTCACATCAGGTTA
*
28748356 CCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
1 CCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
*
28748421 TGGTCTTACACCCATGGTTTTACACATTTCATATCAGGTTG
66 TGGTCTTACA--CA---TTTT---CA---C--ATCAGGTTA
* *
28748462 CCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 CCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAG
28748504 AGAGCACACT
Statistics
Matches: 208, Mismatches: 17, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
92 88 0.42
93 63 0.30
94 2 0.01
98 3 0.01
101 2 0.01
106 50 0.24
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (93 bp):
CCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCA
TGGTCTTACACATTTTCACATCAGGTTA
Found at i:28748451 original size:60 final size:60
Alignment explanation
Indices: 28748372--28748491 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
28748362 TATCTTTCAA
28748372 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
*
28748432 CCATGGTTTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
28748492 ATTTCATTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (60 bp):
CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:28767460 original size:38 final size:37
Alignment explanation
Indices: 28767409--28767483 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 37
28767399 ACATAACATC
* *
28767409 ATTAACAACATTAATAATCTAATGCTATGGAAATTAA
1 ATTAACAAAATTAACAATCTAATGCTATGGAAATTAA
*
28767446 ATTAACAAAAATTAACAATCTAATTCTATGGAAATTAA
1 ATTAAC-AAAATTAACAATCTAATGCTATGGAAATTAA
28767484 CTTATTCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 6 0.18
38 28 0.82
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.32
Consensus pattern (37 bp):
ATTAACAAAATTAACAATCTAATGCTATGGAAATTAA
Found at i:28772737 original size:63 final size:63
Alignment explanation
Indices: 28772635--28772758 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
28772625 TCGATGTGTG
*
28772635 CACACGTGCTAGGAAAACGAGCATGTGTCCAGGCCATGTAACTCACTATTTGCAAATTAGAGC
1 CACACGTGCTAGGAAAAAGAGCATGTGTCCAGGCCATGTAACTCACTATTTGCAAATTAGAGC
* * **
28772698 CACACGTGCTAGGAAAAAGAGCATGTGTCCTGGCTATGTAACTCACTATTTGTGAATTAGA
1 CACACGTGCTAGGAAAAAGAGCATGTGTCCAGGCCATGTAACTCACTATTTGCAAATTAGA
28772759 ATCACATGGG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (63 bp):
CACACGTGCTAGGAAAAAGAGCATGTGTCCAGGCCATGTAACTCACTATTTGCAAATTAGAGC
Found at i:28779232 original size:23 final size:22
Alignment explanation
Indices: 28779199--28779269 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
28779189 CCTGAGCTAA
* *
28779199 TGAACGATAAGCTCTAT-TGAGC
1 TGAACGGTAAGCTC-ATGCGAGC
28779221 TGAAACGGTAAGCTCATGCGAGC
1 TG-AACGGTAAGCTCATGCGAGC
* *
28779244 TGAACAGTAAGCTCATACGAGC
1 TGAACGGTAAGCTCATGCGAGC
28779266 TGAA
1 TGAA
28779270 TCAATAAGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 26 0.60
23 17 0.40
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (22 bp):
TGAACGGTAAGCTCATGCGAGC
Found at i:28779256 original size:22 final size:22
Alignment explanation
Indices: 28779217--28779280 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
28779207 AAGCTCTATT
* *
28779217 GAGCTGAAACGGTAAGCTCATGC
1 GAGCTG-AACAGTAAGCTCATAC
28779240 GAGCTGAACAGTAAGCTCATAC
1 GAGCTGAACAGTAAGCTCATAC
*
28779262 GAGCTGAATCAATAAGCTC
1 GAGCTGAA-CAGTAAGCTC
28779281 TAATAATCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 22 0.59
23 15 0.41
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (22 bp):
GAGCTGAACAGTAAGCTCATAC
Found at i:28787933 original size:44 final size:40
Alignment explanation
Indices: 28787862--28788023 Score: 128
Period size: 42 Copynumber: 3.8 Consensus size: 40
28787852 TGTCTTATCG
* * *
28787862 TGTAAGACCACGTCTGGGGC-TTGGGCATCAATTTGTTATTTACA
1 TGTAAGACCATGTCT-GGACATT-GGCATCAATATG--ATTT-CA
*
28787906 TGTAAGACCATGTCTGGTACATTGGCATCGTATATGATTTCA
1 TGTAAGACCATGTCTGG-ACATTGGCATC-AATATGATTTCA
* * *
28787948 TGTAAGACCCTGTCTAGGACAGTGGCATCATATATGATTTCG
1 TGTAAGACCATGTCT-GGACATTGGCATCA-ATATGATTTCA
* * * *
28787990 TATAAGACCTTGTCTGGGACAGTGGCATCGATAT
1 TGTAAGACCATGTCT-GGACATTGGCATCAATAT
28788024 TTGATTACTT
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
41 4 0.04
42 62 0.61
43 8 0.08
44 21 0.21
45 6 0.06
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (40 bp):
TGTAAGACCATGTCTGGACATTGGCATCAATATGATTTCA
Found at i:28787962 original size:42 final size:41
Alignment explanation
Indices: 28787899--28788029 Score: 154
Period size: 42 Copynumber: 3.1 Consensus size: 41
28787889 TCAATTTGTT
*
28787899 ATTTACATGTAAGACCATGTCTGGTACATTGGCATCGTATATG
1 ATTT-CATGTAAGACCATGTCTGG-ACAGTGGCATCGTATATG
* *
28787942 ATTTCATGTAAGACCCTGTCTAGGACAGTGGCATCATATATG
1 ATTTCATGTAAGACCATGTCT-GGACAGTGGCATCGTATATG
* * * *
28787984 ATTTCGTATAAGACCTTGTCTGGGACAGTGGCATCGATATTTG
1 ATTTCATGTAAGACCATGTCT-GGACAGTGGCATCG-TATATG
28788027 ATT
1 ATT
28788030 ACTTATAAGG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 63 0.82
43 14 0.18
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (41 bp):
ATTTCATGTAAGACCATGTCTGGACAGTGGCATCGTATATG
Found at i:28788050 original size:43 final size:42
Alignment explanation
Indices: 28787908--28788060 Score: 110
Period size: 42 Copynumber: 3.6 Consensus size: 42
28787898 TATTTACATG
* * * * * * * *
28787908 TAAGACCATGTCTGGTACATTGGCATCGTATATGATTTCATG
1 TAAGACCACGCCTGGGACAGTGGCATCATATATGATTACGTA
* * *
28787950 TAAGACC-CTGTCTAGGACAGTGGCATCATATATGATTTCGTA
1 TAAGACCAC-GCCTGGGACAGTGGCATCATATATGATTACGTA
** * * *
28787992 TAAGACCTTGTCTGGGACAGTGGCATCGATATTTGATTACTTA
1 TAAGACCACGCCTGGGACAGTGGCATC-ATATATGATTACGTA
* * *
28788035 TAAGGCCACGCCTGGGATATTGGCAT
1 TAAGACCACGCCTGGGACAGTGGCAT
28788061 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
42 58 0.64
43 32 0.36
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
TAAGACCACGCCTGGGACAGTGGCATCATATATGATTACGTA
Found at i:28793227 original size:16 final size:16
Alignment explanation
Indices: 28793206--28793240 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28793196 CATGCCGAAG
*
28793206 TTTCAGCTTTTCGGCT
1 TTTCAGCTTTCCGGCT
28793222 TTTCAGCTTTCCGGCT
1 TTTCAGCTTTCCGGCT
28793238 TTT
1 TTT
28793241 AACAAGTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.26, G:0.17, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTCCGGCT
Found at i:28814583 original size:30 final size:30
Alignment explanation
Indices: 28814549--28814609 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28814539 TCCTTAACTC
28814549 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
28814579 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
28814609 A
1 A
28814610 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:28816441 original size:28 final size:28
Alignment explanation
Indices: 28816401--28816502 Score: 159
Period size: 28 Copynumber: 3.6 Consensus size: 28
28816391 GAATCATTCG
* *
28816401 ATATTTTGAACACTAAGTGTCATTCTCA
1 ATATTTCGTACACTAAGTGTCATTCTCA
* *
28816429 ATATCTCGCACACTAAGTGTCATTCTCA
1 ATATTTCGTACACTAAGTGTCATTCTCA
*
28816457 ATATTTCGTACACTAAGTGCCATTCTCA
1 ATATTTCGTACACTAAGTGTCATTCTCA
28816485 ATATTTCGTACACTAAGT
1 ATATTTCGTACACTAAGT
28816503 ACCATATTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (28 bp):
ATATTTCGTACACTAAGTGTCATTCTCA
Found at i:28821505 original size:28 final size:28
Alignment explanation
Indices: 28821471--28821626 Score: 150
Period size: 28 Copynumber: 5.5 Consensus size: 28
28821461 AACCGATCTT
* *
28821471 GCACACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
28821499 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
* *
28821528 GCACACACAATGCTCGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* * * * *
28821556 GCACACACATTGCCTCAATAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
*
28821585 GCACAAACAGTGCTCGATTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
*
28821613 ACACACACAGTGCT
1 GCACACACAGTGCT
28821627 TATGTTCACT
Statistics
Matches: 98, Mismatches: 28, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
28 57 0.58
29 41 0.42
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (28 bp):
GCACACACAGTGCTCGATTACGGAACTC
Found at i:28821511 original size:57 final size:57
Alignment explanation
Indices: 28821441--28821625 Score: 271
Period size: 57 Copynumber: 3.2 Consensus size: 57
28821431 GATCTCATTT
* * *
28821441 CACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
*
28821500 CACACACAGTGCCTCAACAACCGATCTCGCACACACAATGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * * * *
28821557 CACACACATTGCCTCAATAACCGATCTCGCACAAACAGTGCTCGATTACGGAACTCA
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
28821614 CACACACAGTGC
1 CACACACAGTGC
28821626 TTATGTTCAC
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
57 108 0.94
59 7 0.06
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.18
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
Found at i:28823640 original size:28 final size:28
Alignment explanation
Indices: 28823602--28823708 Score: 160
Period size: 28 Copynumber: 3.8 Consensus size: 28
28823592 GAATCATTCG
* *
28823602 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
*
28823630 ATATCTCGCACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
*
28823658 ATATTTCGTACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* *
28823686 ATATTTCGTACACTAAGTACCAT
1 ATATTTCGCACACTAAGTGCCAT
28823709 ATTTGATTGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:28829427 original size:30 final size:30
Alignment explanation
Indices: 28829393--28829453 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28829383 TCCTTAACTC
28829393 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
28829423 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
28829453 A
1 A
28829454 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:28833557 original size:28 final size:28
Alignment explanation
Indices: 28833525--28833594 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
28833515 AATGAGATTG
*
28833525 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
28833553 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
28833581 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28833595 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:28837351 original size:11 final size:11
Alignment explanation
Indices: 28837335--28837363 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
28837325 TCGTCAGTTG
28837335 AATAAAGTAAC
1 AATAAAGTAAC
28837346 AATAAAGTAAC
1 AATAAAGTAAC
28837357 AATAAAG
1 AATAAAG
28837364 AATAAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.07, G:0.10, T:0.17
Consensus pattern (11 bp):
AATAAAGTAAC
Found at i:28839700 original size:46 final size:46
Alignment explanation
Indices: 28839644--28839813 Score: 159
Period size: 46 Copynumber: 3.7 Consensus size: 46
28839634 TGGTTGAGCA
28839644 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * * * *
28839690 TCTGAACTCGTTGAGTTGAGTTCGAGTT--CGTA-AGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAA-T--G
** **
28839735 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAGCG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * *
28839783 CCCGAGCTCATTGAGTTGAGTCCGAGTTCAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
28839814 TTAGGGGCGA
Statistics
Matches: 98, Mismatches: 17, Indels: 18
0.74 0.13 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 3 0.03
45 1 0.01
46 53 0.54
47 26 0.27
48 1 0.01
49 2 0.02
50 4 0.04
51 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:28839800 original size:93 final size:93
Alignment explanation
Indices: 28839641--28839811 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
28839631 GGATGGTTGA
* * * *
28839641 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
*
28839706 TGAGTTCGAGTTCGTAAGATGTAACTAG
66 TGAGTCCGAGTTCGTAAGATGTAACTAG
** * *
28839734 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAGCGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
28839799 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28839812 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTAAGATGTAACTAG
Found at i:28840077 original size:19 final size:20
Alignment explanation
Indices: 28840040--28840077 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28840030 ATAAGGTGGT
28840040 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28840060 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28840078 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28844787 original size:19 final size:20
Alignment explanation
Indices: 28844750--28844787 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28844740 ATAAGGTGGT
28844750 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28844770 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28844788 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28850328 original size:20 final size:20
Alignment explanation
Indices: 28850303--28850367 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
28850293 ATGAATACAC
28850303 CATGTGCATATCATACATAT
1 CATGTGCATATCATACATAT
*
28850323 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAT
*
28850343 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAT
28850363 CATGT
1 CATGT
28850368 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (20 bp):
CATGTGCATATCATACATAT
Found at i:28850334 original size:11 final size:11
Alignment explanation
Indices: 28850303--28850356 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
28850293 ATGAATACAC
28850303 CATGTGCATAT
1 CATGTGCATAT
*
28850314 CA--TACATAT
1 CATGTGCATAT
28850323 CATGTGCATAT
1 CATGTGCATAT
* *
28850334 CA--TACATGT
1 CATGTGCATAT
28850343 CATGTGCATAT
1 CATGTGCATAT
28850354 CAT
1 CAT
28850357 ACATACCATG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 15 0.45
11 18 0.55
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (11 bp):
CATGTGCATAT
Found at i:28850446 original size:25 final size:25
Alignment explanation
Indices: 28850404--28850451 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28850394 ATATTTAAAC
* * *
28850404 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
28850429 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28850452 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:28855083 original size:9 final size:9
Alignment explanation
Indices: 28855069--28855121 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
28855059 ACACCATGTG
28855069 CATATCATA
1 CATATCATA
*
28855078 CATATCATGTG
1 CATATCA--TA
28855089 CATATCATA
1 CATATCATA
*
28855098 CATATCATGTG
1 CATATCA--TA
28855109 CATATCATA
1 CATATCATA
28855118 CATA
1 CATA
28855122 CCATGTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 20 0.56
11 16 0.44
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (9 bp):
CATATCATA
Found at i:28855088 original size:20 final size:20
Alignment explanation
Indices: 28855063--28855127 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
28855053 ATGAATACAC
28855063 CATGTGCATATCATACATAT
1 CATGTGCATATCATACATAT
28855083 CATGTGCATATCATACATAT
1 CATGTGCATATCATACATAT
*
28855103 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAT
28855123 CATGT
1 CATGT
28855128 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.34
Consensus pattern (20 bp):
CATGTGCATATCATACATAT
Found at i:28855094 original size:11 final size:11
Alignment explanation
Indices: 28855063--28855116 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
28855053 ATGAATACAC
28855063 CATGTGCATAT
1 CATGTGCATAT
*
28855074 CA--TACATAT
1 CATGTGCATAT
28855083 CATGTGCATAT
1 CATGTGCATAT
*
28855094 CA--TACATAT
1 CATGTGCATAT
28855103 CATGTGCATAT
1 CATGTGCATAT
28855114 CAT
1 CAT
28855117 ACATACCATG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 16 0.46
11 19 0.54
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (11 bp):
CATGTGCATAT
Found at i:28855203 original size:25 final size:25
Alignment explanation
Indices: 28855164--28855211 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28855154 ATATTTAAAC
* *
28855164 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
28855189 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
28855212 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:28860419 original size:39 final size:39
Alignment explanation
Indices: 28860372--28860505 Score: 223
Period size: 39 Copynumber: 3.4 Consensus size: 39
28860362 TGTGTGAGAT
*
28860372 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCTCGAAGGCATTCATGCTGGTG
*
28860411 TTATATCCGGGCTAAGTCCCGAAGGCATTCATGCTGGTG
1 TTATATCCGGGCTAAGTCTCGAAGGCATTCATGCTGGTG
*
28860450 TTATATCCGGGCTAAATCTCGAAGGCATTCATGCTGGTG
1 TTATATCCGGGCTAAGTCTCGAAGGCATTCATGCTGGTG
**
28860489 TTATATCTAGGCTAAGT
1 TTATATCCGGGCTAAGT
28860506 TTCAAAGGGA
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCTCGAAGGCATTCATGCTGGTG
Found at i:28868337 original size:39 final size:39
Alignment explanation
Indices: 28868293--28868426 Score: 214
Period size: 39 Copynumber: 3.4 Consensus size: 39
28868283 TGTGTGAGAT
* *
28868293 TTATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGAG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
28868332 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
28868371 TTATATCCGGGCTAAATCCCAAAGGCATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
28868410 TTATATCCGGGCAAAGT
1 TTATATCCGGGCTAAGT
28868427 TTCAAAGGCA
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:28891213 original size:28 final size:28
Alignment explanation
Indices: 28891173--28891251 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
28891163 GCAATCAAAT
* * *
28891173 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
28891201 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
28891229 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
28891252 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:28893972 original size:29 final size:28
Alignment explanation
Indices: 28893926--28893982 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
28893916 CTTTTGAGTC
*
28893926 CATTTAATTTTTAGTTAGTTTTTATTTT
1 CATTTAATTTTTAGTTAGTATTTATTTT
* * *
28893954 CATTTTATTTTTATTTTAGTATTTCTTTT
1 CATTTAATTTTTA-GTTAGTATTTATTTT
28893983 TTTCTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (28 bp):
CATTTAATTTTTAGTTAGTATTTATTTT
Found at i:28900213 original size:17 final size:16
Alignment explanation
Indices: 28900191--28900224 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28900181 GGGGATGGTG
28900191 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
28900208 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
28900224 T
1 T
28900225 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:28902114 original size:40 final size:40
Alignment explanation
Indices: 28902059--28902262 Score: 254
Period size: 40 Copynumber: 5.1 Consensus size: 40
28902049 CGGAATTTAA
* ** *
28902059 CCGGATATAGCAACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28902099 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28902139 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28902178 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
28902218 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28902258 CCGGA
1 CCGGA
28902263 CATCATTCGA
Statistics
Matches: 142, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 96 0.68
41 12 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28902189 original size:79 final size:80
Alignment explanation
Indices: 28902045--28902262 Score: 248
Period size: 79 Copynumber: 2.7 Consensus size: 80
28902035 GAATCACGTA
* * * ** * * *
28902045 CCTTCGGAATTTAACCGGATATAGCAACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAG
1 CCTTCGGGACTTAACCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAATATAG
28902109 TAACTCGCACAAATG
66 TAACTCGCACAAATG
*
28902124 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT-TA
1 CCTTCGGGACTTAA-CCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAATATA
28902187 GTAACTCGCACAAATG
65 GTAACTCGCACAAATG
* * * *
28902203 CCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATATAGTAAC-TCGCACCAATGCCTTCGGGACTTAGCCCGGA
28902263 CATCATTCGA
Statistics
Matches: 119, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 72 0.61
80 44 0.37
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CCTTCGGGACTTAACCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAATATAG
TAACTCGCACAAATG
Found at i:28910240 original size:79 final size:81
Alignment explanation
Indices: 28910131--28910313 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
28910121 CACTCGTTCA
* *
28910131 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
28910194 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
28910211 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
28910274 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
28910290 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28910314 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:28910313 original size:40 final size:40
Alignment explanation
Indices: 28910111--28910313 Score: 245
Period size: 40 Copynumber: 5.1 Consensus size: 40
28910101 TCGAATTTAA
* ** *
28910111 CCGGATATAG-CACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28910150 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28910190 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28910229 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
28910269 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28910309 CCGGA
1 CCGGA
28910314 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 41 0.29
40 86 0.61
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28917713 original size:27 final size:27
Alignment explanation
Indices: 28917683--28917860 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28917673 ATATTAAGTC
* * *
28917683 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
28917710 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
28917738 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
28917765 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
28917792 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
28917819 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
28917846 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28917861 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:28917767 original size:55 final size:54
Alignment explanation
Indices: 28917683--28917860 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
28917673 ATATTAAGTC
* * *
28917683 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
28917738 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
28917792 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
28917846 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28917861 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:28917849 original size:81 final size:82
Alignment explanation
Indices: 28917704--28917859 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
28917694 TGCTATATAA
* *
28917704 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
28917769 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
28917786 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
28917849 ACACTTAGTGC
65 ACACTTAGTGC
28917860 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:28925969 original size:40 final size:40
Alignment explanation
Indices: 28925897--28926126 Score: 242
Period size: 40 Copynumber: 5.9 Consensus size: 40
28925887 ATAGCCGTTT
* *
28925897 ATAACTCACAC-AATGCCTTCGGGACATAAACCCGGATTTA
1 ATAACTCGCACGAATGCCTTCGGGAC-TTAACCCGGATTTA
* *
28925937 ACAACTCGCACGACTGCCTTCGGGACTTAACCCGGATTT-
1 ATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
28925976 ATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 ATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
* *
28926016 ATAACTCGCACGAATGCCTTCGGAACCTAA-CCGGATTTA
1 ATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
* * * * *
28926055 GTATCTCGCAC-AA-GGC-TC-GGACTTAATCCGGATATA
1 ATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
* * * * *
28926091 TTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 ATAAC-TCGCACGAATGCCTTCGGGACTTAACCCGGA
28926127 CAGCATTCAT
Statistics
Matches: 162, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
35 6 0.04
36 12 0.07
37 9 0.06
38 4 0.02
39 57 0.35
40 61 0.38
41 13 0.08
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
ATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
Found at i:28926008 original size:79 final size:78
Alignment explanation
Indices: 28925894--28926067 Score: 251
Period size: 79 Copynumber: 2.2 Consensus size: 78
28925884 GACATAGCCG
* *
28925894 TTTATAACTCACACAATGCCTTCGGGACATAAACCCGGATTTAACAACTCGCACGACTGCCTTCG
1 TTTATAACTCGCACAATGCCTTCGGGACATAAACCCGGATTTAACAACTCGCACGAATGCCTTCG
* *
28925959 GGACTTAACCCGGA
66 GAACCTAA-CCGGA
* *
28925973 TTTATAACTCGCACGAATGCCTTCGGGAC-TTAACCCGGATTTAATAACTCGCACGAATGCCTTC
1 TTTATAACTCGCAC-AATGCCTTCGGGACATAAACCCGGATTTAACAACTCGCACGAATGCCTTC
28926037 GGAACCTAACCGGA
65 GGAACCTAACCGGA
*
28926051 TTTAGTATCTCGCACAA
1 TTTA-TAACTCGCACAA
28926068 GGCTCGGACT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 11 0.13
79 61 0.71
80 14 0.16
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (78 bp):
TTTATAACTCGCACAATGCCTTCGGGACATAAACCCGGATTTAACAACTCGCACGAATGCCTTCG
GAACCTAACCGGA
Found at i:28926112 original size:75 final size:79
Alignment explanation
Indices: 28925894--28926113 Score: 211
Period size: 79 Copynumber: 2.8 Consensus size: 79
28925884 GACATAGCCG
* * * * * **
28925894 TTTATAACTCACAC-AATGCCTTCGGGACATAAACCCGGATTTAACAACTCGCACGACTGCCTTC
1 TTTATAACTCGCACGAATGCCTTCGGGAC-TTAACCCGGATATAATAACTAGCACGAAAGCCTTC
* *
28925958 GGGACTTAACCCGGA
65 GGAACCTAACCCGGA
* * *
28925973 TTTATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCG
1 TTTATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATATAATAACTAGCACGAAAGCCTTCG
28926038 GAACCTAA-CCGGA
66 GAACCTAACCCGGA
* * * * *
28926051 TTTAGTATCTCGCAC-AA-GGC-TC-GGACTTAATCCGGATATATTCACTTAGCAC-AAAGCCTT
1 TTTA-TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATATAATAAC-TAGCACGAAAGCCTT
28926111 CGG
64 CGG
28926114 GACTTAGCCC
Statistics
Matches: 124, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
75 29 0.23
76 7 0.06
77 2 0.02
78 11 0.09
79 61 0.49
80 14 0.11
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (79 bp):
TTTATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATATAATAACTAGCACGAAAGCCTTCG
GAACCTAACCCGGA
Found at i:28928301 original size:27 final size:27
Alignment explanation
Indices: 28928271--28928448 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
28928261 ATATTAAGTC
* * *
28928271 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
28928298 CGCACACTTAGTGCCACATAATCAAATCT
1 CGCACACTTAGTGCTACATAGTC-AA-CT
28928327 C-CACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
28928353 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
28928380 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
28928407 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
28928434 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28928449 GTACATTTAA
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.02
27 101 0.78
28 22 0.17
29 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Done.