Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 8 of 322
Found at i:1954444 original size:18 final size:19
Alignment explanation
Indices: 1954423--1954458 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1954413 ATTATTTATC
1954423 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
1954441 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
1954459 TATACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:1957802 original size:10 final size:10
Alignment explanation
Indices: 1957784--1957861 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 10
1957774 CCAAATTTTC
1957784 CTTTTTCTTT
1 CTTTTTCTTT
1957794 -TTCTTTCTTT
1 CTT-TTTCTTT
*
1957804 CTTTTTCCTT
1 CTTTTTCTTT
*
1957814 C-TTTCCTTT
1 CTTTTTCTTT
*
1957823 CTCTGTTTCGTT
1 CT-T-TTTCTTT
*
1957835 CTACTTCTCTGTT
1 CT--TTTTCT-TT
1957848 CTTTTTCTTT
1 CTTTTTCTTT
1957858 CTTT
1 CTTT
1957862 ATTTCATTGT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
9 9 0.17
10 20 0.38
11 8 0.15
12 10 0.19
13 6 0.11
ACGTcount: A:0.01, C:0.26, G:0.04, T:0.69
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:1957808 original size:13 final size:14
Alignment explanation
Indices: 1957787--1957861 Score: 62
Period size: 14 Copynumber: 5.2 Consensus size: 14
1957777 AATTTTCCTT
1957787 TTTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
*
1957801 TTTCTTTTTCCTTC
1 TTTCTTTTTCTTTC
* * *
1957815 TTTC-CTTTCTCTG
1 TTTCTTTTTCTTTC
* *
1957828 TTTCGTTCTACTTCTC
1 TTTC-TTTTTCTT-TC
1957844 TGTTCTTTTTCTTTC
1 T-TTCTTTTTCTTTC
1957859 TTT
1 TTT
1957862 ATTTCATTGT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
13 9 0.20
14 19 0.42
15 6 0.13
16 8 0.18
17 3 0.07
ACGTcount: A:0.01, C:0.25, G:0.04, T:0.69
Consensus pattern (14 bp):
TTTCTTTTTCTTTC
Found at i:1957831 original size:27 final size:27
Alignment explanation
Indices: 1957779--1957831 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1957769 GACAACCAAA
* *
1957779 TTTTCCTTTTTCTTTTTCTTTCTTTCT
1 TTTTCCTTTTTCTCTTTCTCTCTTTCT
*
1957806 TTTTCCTTCTTTC-CTTTCTCTGTTTC
1 TTTTCCTT-TTTCTCTTTCTCTCTTTC
1957832 GTTCTACTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTTCCTTTTTCTCTTTCTCTCTTTCT
Found at i:1958078 original size:18 final size:19
Alignment explanation
Indices: 1958057--1958092 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1958047 ATTATTTATC
1958057 TAATAAATATCT-TTTAAA
1 TAATAAATATCTGTTTAAA
1958075 TAATAAATATCTGTTTAA
1 TAATAAATATCTGTTTAA
1958093 TATACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTGTTTAAA
Found at i:1958977 original size:17 final size:17
Alignment explanation
Indices: 1958955--1958989 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1958945 TTCGAATAGC
* *
1958955 TGTTTCTTTTCTTCTTT
1 TGTTTCATTTATTCTTT
1958972 TGTTTCATTTATTCTTT
1 TGTTTCATTTATTCTTT
1958989 T
1 T
1958990 ATTTTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCATTTATTCTTT
Found at i:1962203 original size:30 final size:30
Alignment explanation
Indices: 1962167--1962226 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1962157 CAATATGATC
1962167 CTATTTTATCTCATGGTAACCATTAAATCT
1 CTATTTTATCTCATGGTAACCATTAAATCT
1962197 CTATTTTATCTCATGGTAACCATTAAATCT
1 CTATTTTATCTCATGGTAACCATTAAATCT
1962227 TTCTTCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (30 bp):
CTATTTTATCTCATGGTAACCATTAAATCT
Found at i:1964746 original size:18 final size:18
Alignment explanation
Indices: 1964725--1964775 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
1964715 CTATTTTTGT
*
1964725 TATGATTTTCTGTTGAGA
1 TATGATTTTCTATTGAGA
*
1964743 TATGATTTCCTATTGAGA
1 TATGATTTTCTATTGAGA
1964761 TATGATTTTCTATTG
1 TATGATTTTCTATTG
1964776 GGATTTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.51
Consensus pattern (18 bp):
TATGATTTTCTATTGAGA
Found at i:1969029 original size:18 final size:18
Alignment explanation
Indices: 1969008--1969062 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
1968998 CTATTTTTGT
1969008 TATGATTTTCTGTTGAGA
1 TATGATTTTCTGTTGAGA
*
1969026 TATGATTTCCTGTTGAGA
1 TATGATTTTCTGTTGAGA
*
1969044 TATGATTTTCTATTGAGA
1 TATGATTTTCTGTTGAGA
1969062 T
1 T
1969063 TTGTTGCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (18 bp):
TATGATTTTCTGTTGAGA
Found at i:1969418 original size:17 final size:17
Alignment explanation
Indices: 1969380--1969428 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
1969370 TTAGCTATAA
1969380 ATATTTTTAT-AT-TTT
1 ATATTTTTATAATATTT
1969395 ATATTTTATATAA-ATTT
1 ATATTTT-TATAATATTT
*
1969412 ATTTTTTTATAATATTT
1 ATATTTTTATAATATTT
1969429 TAATTAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
17 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTTTTATAATATTT
Found at i:1969430 original size:18 final size:19
Alignment explanation
Indices: 1969388--1969430 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 19
1969378 AAATATTTTT
1969388 ATATTTTATATTTTATATA
1 ATATTTTATATTTTATATA
*
1969407 A-A-TTTAT-TTTTTTATA
1 ATATTTTATATTTTATATA
1969423 ATATTTTA
1 ATATTTTA
1969431 ATTAATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 5 0.24
19 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTTTATATTTTATATA
Found at i:1974811 original size:92 final size:92
Alignment explanation
Indices: 1974654--1974837 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
1974644 TTAATTCAGG
1974654 ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
1 ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
1974719 ACCGGAATGGGTCATTTTCCCCGAAAT
66 ACCGGAATGGGTCATTTTCCCCGAAAT
1974746 ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
1 ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
1974811 ACCGGAATGGGTCATTTTCCCCGAAAT
66 ACCGGAATGGGTCATTTTCCCCGAAAT
1974838 CACGTCCACG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (92 bp):
ACAAATTACACATAAAAGTCCTATTTTTTAAATTTTACCGAAATGGGTTCGGTATTTTATTATTT
ACCGGAATGGGTCATTTTCCCCGAAAT
Found at i:1981118 original size:25 final size:25
Alignment explanation
Indices: 1981074--1981164 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
1981064 CTCTTTTATG
*
1981074 AGCTTCCCGATAT-TGGCTCACATA
1 AGCTTCCCGTTATATGGCTCACATA
** *
1981098 ATTTTCCCGTTATATGGCTCACATG
1 AGCTTCCCGTTATATGGCTCACATA
*
1981123 AGCTTCTCGTTATATGGCTCGA-A-A
1 AGCTTCCCGTTATATGGCTC-ACATA
1981147 GAGCTTCCCGTTTATATG
1 -AGCTTCCCG-TTATATG
1981165 CTTGTATGAG
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
24 10 0.19
25 36 0.67
26 8 0.15
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCACATA
Found at i:1981175 original size:25 final size:25
Alignment explanation
Indices: 1981071--1981182 Score: 88
Period size: 25 Copynumber: 4.5 Consensus size: 25
1981061 AGGCTCTTTT
*
1981071 ATGAGCTTCCCGATAT-TGGCTC-A
1 ATGAGCTTCCCGTTATATGGCTCGA
* **
1981094 CATAATTTTCCCGTTATATGGCTC-A
1 -ATGAGCTTCCCGTTATATGGCTCGA
*
1981119 CATGAGCTTCTCGTTATATGGCTCGA
1 -ATGAGCTTCCCGTTATATGGCTCGA
* * *
1981145 AAGAGCTTCCCGTTTATAT-GCTTGT
1 ATGAGCTTCCCG-TTATATGGCTCGA
1981170 ATGAGCATTCCCG
1 ATGAGC-TTCCCG
1981183 AATATGAATT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
24 12 0.17
25 46 0.65
26 13 0.18
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGCTCGA
Found at i:1981853 original size:14 final size:15
Alignment explanation
Indices: 1981821--1981853 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1981811 TATGATAATG
*
1981821 TATGATTTGAGATAA
1 TATGATTGGAGATAA
1981836 TATGATTGGAGA-AA
1 TATGATTGGAGATAA
1981850 TATG
1 TATG
1981854 CATATAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (15 bp):
TATGATTGGAGATAA
Found at i:1988508 original size:13 final size:13
Alignment explanation
Indices: 1988490--1988514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1988480 GTGAATATTT
1988490 CTGTGATTTTGAC
1 CTGTGATTTTGAC
1988503 CTGTGATTTTGA
1 CTGTGATTTTGA
1988515 GTATATTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (13 bp):
CTGTGATTTTGAC
Found at i:1993357 original size:25 final size:23
Alignment explanation
Indices: 1993327--1993378 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1993317 GAAATTATTG
1993327 ATTTAATCTACTTAAATAAAATTAA
1 ATTTAATCTA-TTAAAT-AAATTAA
* *
1993352 ATTTAATCTATTATATAAATTGA
1 ATTTAATCTATTAAATAAATTAA
1993375 ATTT
1 ATTT
1993379 CGGAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 5 0.20
25 10 0.40
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAATCTATTAAATAAATTAA
Found at i:2013011 original size:17 final size:19
Alignment explanation
Indices: 2012984--2013019 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2012974 CAATTTAAAG
2012984 TTAAGAATTCCA-AACAAT
1 TTAAGAATTCCATAACAAT
2013002 TTAA-AATTCCATAACAAT
1 TTAAGAATTCCATAACAAT
2013020 CTGAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.31
Consensus pattern (19 bp):
TTAAGAATTCCATAACAAT
Found at i:2013353 original size:147 final size:147
Alignment explanation
Indices: 2013059--2013343 Score: 326
Period size: 147 Copynumber: 1.9 Consensus size: 147
2013049 AATTTGTACA
* * **
2013059 TATTATAATTTACCATAAAGTCAGTTACACATTTAAGGTTTAAGGTTATGTATCATTAATATAAA
1 TATTATAATTTACCATAAAGTCAATTACACATTTAAGGTTTAAGCTTACATATCATTAATAT-AA
* ** * *
2013124 AAAATGTACATTATAATGTCATAATTGTAGATAAGGTGACATATAATTAATAATCTATCTTAACT
65 AAAATATACATTATAATAACATAATTGTA-ATAAGGTGACATATAATTAATAATCTACCTAAACT
2013189 ATATAATGGTAACTGTATG
129 ATATAATGGTAACTGTATG
* * ** *
2013208 TATTATAATTTGA-CATAAAGTTAATTGCATGTTTAGGGTTTAAGCTTACATATCATTAATAT-A
1 TATTATAATTT-ACCATAAAGTCAATTACACATTTAAGGTTTAAGCTTACATATCATTAATATAA
* * *
2013271 AAAATATACATTATAATAACATAGTTGT-AT-AGAGTGATACATATCATTAATTATCTACCTAAA
65 AAAATATACATTATAATAACATAATTGTAATAAG-GTG--ACATATAATTAATAATCTACCTAAA
*
2013334 TTATATAATG
127 CTATATAATG
2013344 TCAATTGTAT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
144 2 0.02
145 5 0.04
147 55 0.48
149 51 0.45
150 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (147 bp):
TATTATAATTTACCATAAAGTCAATTACACATTTAAGGTTTAAGCTTACATATCATTAATATAAA
AAATATACATTATAATAACATAATTGTAATAAGGTGACATATAATTAATAATCTACCTAAACTAT
ATAATGGTAACTGTATG
Found at i:2018772 original size:15 final size:16
Alignment explanation
Indices: 2018752--2018785 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2018742 AATTATTGTT
2018752 TAAATAAATTTTTA-A
1 TAAATAAATTTTTACA
*
2018767 TAAATATATTTTTACA
1 TAAATAAATTTTTACA
2018783 TAA
1 TAA
2018786 TTTTTTCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATAAATTTTTACA
Found at i:2024472 original size:16 final size:17
Alignment explanation
Indices: 2024451--2024483 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2024441 ATCAATCTAA
2024451 TATTTAT-TTAAAATAT
1 TATTTATATTAAAATAT
*
2024467 TATTTATATTAACATAT
1 TATTTATATTAAAATAT
2024484 ATGAAAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTATATTAAAATAT
Found at i:2025360 original size:14 final size:14
Alignment explanation
Indices: 2025338--2025367 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2025328 TCTCTACCGA
*
2025338 AAAATTTTGTACCC
1 AAAACTTTGTACCC
2025352 AAAACTTTGTACCC
1 AAAACTTTGTACCC
2025366 AA
1 AA
2025368 CGGTTGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAACTTTGTACCC
Found at i:2043147 original size:16 final size:17
Alignment explanation
Indices: 2043126--2043160 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2043116 TAAATTTTAA
2043126 ATTTTTTTA-AAATAAT
1 ATTTTTTTAGAAATAAT
*
2043142 ATTTTTTTAGAATTAAT
1 ATTTTTTTAGAAATAAT
2043159 AT
1 AT
2043161 CTACTCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTTTTAGAAATAAT
Found at i:2043158 original size:17 final size:16
Alignment explanation
Indices: 2043122--2043160 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2043112 ATACTAAATT
2043122 TTAA-ATTTTTTTAAA
1 TTAATATTTTTTTAAA
*
2043137 ATAATATTTTTTTAGAA
1 TTAATATTTTTTTA-AA
2043154 TTAATAT
1 TTAATAT
2043161 CTACTCATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 3 0.15
16 9 0.45
17 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAATATTTTTTTAAA
Found at i:2046541 original size:32 final size:32
Alignment explanation
Indices: 2046481--2046541 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2046471 TGTATAATTA
2046481 TATTAAATTATTTAAATATTATCTAAAATATT
1 TATTAAATTATTTAAATATTATCTAAAATATT
*
2046513 TATTTAATT-TTT-AATATTATGTCTAAAAT
1 TATTAAATTATTTAAATATTA--TCTAAAAT
2046542 GAACATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
31 3 0.12
32 16 0.62
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (32 bp):
TATTAAATTATTTAAATATTATCTAAAATATT
Found at i:2052712 original size:18 final size:18
Alignment explanation
Indices: 2052686--2052728 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2052676 AAAAGCTGTT
*
2052686 TTTACATATATCAATAAA
1 TTTATATATATCAATAAA
*
2052704 TTTATATATATTAATAAA
1 TTTATATATATCAATAAA
2052722 TTTATAT
1 TTTATAT
2052729 TTTAAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATATATATCAATAAA
Found at i:2053993 original size:32 final size:32
Alignment explanation
Indices: 2053952--2054012 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
2053942 TGTCAGTCAT
2053952 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
2053984 TTCAATATCCAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
2054013 CAATATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:2054019 original size:27 final size:30
Alignment explanation
Indices: 2053952--2054025 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 30
2053942 TGTCAGTCAT
2053952 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
2053984 TTCAATATCCAACAAGCTTAAAAC-AT-AA
1 TTCAATATCCAACAAGCTTAAAACAATAAA
*
2054012 -TCAATATCTAACAA
1 TTCAATATCCAACAA
2054026 ATTCAAGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 13 0.32
28 2 0.05
29 2 0.05
32 24 0.59
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (30 bp):
TTCAATATCCAACAAGCTTAAAACAATAAA
Found at i:2057031 original size:154 final size:154
Alignment explanation
Indices: 2056751--2057059 Score: 600
Period size: 154 Copynumber: 2.0 Consensus size: 154
2056741 TTATAACTTA
*
2056751 AGATAACCAAGACTACTTAACTGGCTGAACTCAATGTGATCTCAAATGGGGGATACTTATGGATC
1 AGATAACCAAGACTACTTAACTGGCTGAACTCAATATGATCTCAAATGGGGGATACTTATGGATC
2056816 ATAGTATTCAGTAAGAAAGCATTCCTATTTGAATTATTCCCTAATCGTTGCTCTTGTGTTCCTAG
66 ATAGTATTCAGTAAGAAAGCATTCCTATTTGAATTATTCCCTAATCGTTGCTCTTGTGTTCCTAG
2056881 CATTTTTTACCATGGCACAAGGAT
131 CATTTTTTACCATGGCACAAGGAT
*
2056905 AGATAACCAAGACTACTTAATTGGCTGAACTCAATATGATCTCAAATGGGGGATACTTATGGATC
1 AGATAACCAAGACTACTTAACTGGCTGAACTCAATATGATCTCAAATGGGGGATACTTATGGATC
2056970 ATAGTATTCAGTAAGAAAGCATTCCTATTTGAATTATTCCCTAATCGTTGCTCTTGTGTTCCTAG
66 ATAGTATTCAGTAAGAAAGCATTCCTATTTGAATTATTCCCTAATCGTTGCTCTTGTGTTCCTAG
2057035 CATTTTTTACCATGGCACAAGGAT
131 CATTTTTTACCATGGCACAAGGAT
2057059 A
1 A
2057060 CGAATAATTG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (154 bp):
AGATAACCAAGACTACTTAACTGGCTGAACTCAATATGATCTCAAATGGGGGATACTTATGGATC
ATAGTATTCAGTAAGAAAGCATTCCTATTTGAATTATTCCCTAATCGTTGCTCTTGTGTTCCTAG
CATTTTTTACCATGGCACAAGGAT
Found at i:2057661 original size:17 final size:17
Alignment explanation
Indices: 2057639--2057691 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
2057629 TCTTCAACAG
2057639 ACAGATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
*
2057656 ACAGAT--TAAA--CAA
1 ACAGATGCAAAATCCAA
*
2057669 ACATATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
2057686 ACAGAT
1 ACAGAT
2057692 TCTTCAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 8 0.29
15 6 0.21
17 14 0.50
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.15
Consensus pattern (17 bp):
ACAGATGCAAAATCCAA
Found at i:2057677 original size:30 final size:30
Alignment explanation
Indices: 2057634--2057692 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2057624 AAGATTCTTC
*
2057634 AACAGACAGATGCAAAATCCAAACAGATTA
1 AACAAACAGATGCAAAATCCAAACAGATTA
*
2057664 AACAAACATATGCAAAATCCAAACAGATT
1 AACAAACAGATGCAAAATCCAAACAGATT
2057693 CTTCAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.20, G:0.10, T:0.15
Consensus pattern (30 bp):
AACAAACAGATGCAAAATCCAAACAGATTA
Found at i:2063509 original size:31 final size:32
Alignment explanation
Indices: 2063437--2063513 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
2063427 ACTGAGCTCT
* * * * * *
2063437 CAAAAATTTTGAAAAATTTTCATTAGGCTCTT
1 CAAAATTTTTGGAAAATCTTCATTAAGCCCTC
2063469 CAAAATTTTTGGAAAATCTT-ATTAAGCCCTC
1 CAAAATTTTTGGAAAATCTTCATTAAGCCCTC
2063500 CAAAATTTTTGGAA
1 CAAAATTTTTGGAA
2063514 TATTCTCATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 22 0.56
32 17 0.44
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (32 bp):
CAAAATTTTTGGAAAATCTTCATTAAGCCCTC
Found at i:2064386 original size:2 final size:2
Alignment explanation
Indices: 2064379--2064416 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2064369 AAAAAGAAAA
2064379 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2064417 CACCTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2079689 original size:11 final size:9
Alignment explanation
Indices: 2079651--2079713 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
2079641 CTAATAAAAA
2079651 TTTTATAA-
1 TTTTATAAT
2079659 -TTT-TAAT
1 TTTTATAAT
2079666 TTTTATAAT
1 TTTTATAAT
*
2079675 TTTTATGAT
1 TTTTATAAT
2079684 ATTTT-TAAT
1 -TTTTATAAT
*
2079693 ATTTTAAAAT
1 -TTTTATAAT
*
2079703 TTTTAAAAT
1 TTTTATAAT
2079712 TT
1 TT
2079714 ATTACTAAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
8 3 0.06
9 31 0.66
10 7 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2085989 original size:30 final size:31
Alignment explanation
Indices: 2085927--2086026 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
2085917 AAGTCAAGAG
* *
2085927 TTTCAAGTC-AGGTCATCTCGGATTT-AGGTCA
1 TTTCAAGTCTAGGTCAT-TTGG-TTTCGGGTCA
* *
2085958 TTTCACGTTTA-GTCATTTGGGTTT-GGGTCA
1 TTTCAAGTCTAGGTCATTT-GGTTTCGGGTCA
* *
2085988 TTCCAAGTCTAGGTCATTTGGTTTCGAGTCA
1 TTTCAAGTCTAGGTCATTTGGTTTCGGGTCA
*
2086019 TTTTAAGT
1 TTTCAAGT
2086027 TTGTTAGGTA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
30 22 0.40
31 32 0.58
32 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (31 bp):
TTTCAAGTCTAGGTCATTTGGTTTCGGGTCA
Found at i:2086006 original size:31 final size:31
Alignment explanation
Indices: 2085930--2086008 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 31
2085920 TCAAGAGTTT
* *
2085930 CAAGTC-AGGTCATCTCGGATTTAGGTCATTT
1 CAAGTCTAGGTCAT-TTGGATTTAGGTCATTC
* * * *
2085961 CACGTTTA-GTCATTTGGGTTTGGGTCATTC
1 CAAGTCTAGGTCATTTGGATTTAGGTCATTC
2085991 CAAGTCTAGGTCATTTGG
1 CAAGTCTAGGTCATTTGG
2086009 TTTCGAGTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
30 19 0.50
31 18 0.47
32 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (31 bp):
CAAGTCTAGGTCATTTGGATTTAGGTCATTC
Found at i:2091557 original size:22 final size:23
Alignment explanation
Indices: 2091516--2091561 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
2091506 AAACCCGCCC
2091516 ATATTATTATTTTTTAAATATTT
1 ATATTATTATTTTTTAAATATTT
2091539 ATATTA-TATTATTTT-AATATTT
1 ATATTATTATT-TTTTAAATATTT
2091561 A
1 A
2091562 ATAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTATTATTTTTTAAATATTT
Found at i:2095321 original size:33 final size:34
Alignment explanation
Indices: 2095218--2095322 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
2095208 AAACTCATGT
* * * *
2095218 TAAGCAAGTTTATTGCTACTGTAATGATTTGTTA
1 TAAGCATGATTATTGCTACCGTATTGATTTGTTA
* * *
2095252 TAAGCATGATGATT-CTTACCATATTGATTTGCTA
1 TAAGCATGATTATTGC-TACCGTATTGATTTGTTA
*
2095286 TAAGCATG-TTATTGCTACCGTATTGATCTGTTA
1 TAAGCATGATTATTGCTACCGTATTGATTTGTTA
2095319 TAAG
1 TAAG
2095323 TATGTCATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
33 24 0.41
34 34 0.59
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (34 bp):
TAAGCATGATTATTGCTACCGTATTGATTTGTTA
Found at i:2100354 original size:23 final size:23
Alignment explanation
Indices: 2100310--2100356 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2100300 CCCATTGAAA
2100310 GTTAATAAAAATTTCCATTATGT
1 GTTAATAAAAATTTCCATTATGT
*
2100333 GTTAATAAAAATTTTCATTATGT
1 GTTAATAAAAATTTCCATTATGT
2100356 G
1 G
2100357 CACTTGGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (23 bp):
GTTAATAAAAATTTCCATTATGT
Found at i:2104636 original size:14 final size:14
Alignment explanation
Indices: 2104617--2104644 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2104607 CATTAAAGAT
2104617 GCCACTTAGGAACC
1 GCCACTTAGGAACC
2104631 GCCACTTAGGAACC
1 GCCACTTAGGAACC
2104645 CGAAGAGATG
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:0.29, C:0.36, G:0.21, T:0.14
Consensus pattern (14 bp):
GCCACTTAGGAACC
Found at i:2106029 original size:34 final size:34
Alignment explanation
Indices: 2105990--2106055 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
2105980 AGTATGAAAG
*
2105990 TATAAATAAAACATATGTACGATATATGAATACA
1 TATAAATAAAACATATGGACGATATATGAATACA
** *
2106024 TATAAATAAAATGTATGGATGATATATGAATA
1 TATAAATAAAACATATGGACGATATATGAATA
2106056 AATGTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.32
Consensus pattern (34 bp):
TATAAATAAAACATATGGACGATATATGAATACA
Found at i:2108879 original size:41 final size:40
Alignment explanation
Indices: 2108829--2108908 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
2108819 AAACTAGCAG
**
2108829 TTTAACAATTTATATGCAAGGAACTAGCAAAAAATCAACAA
1 TTTAACAATTTATATGCAACAAACTAGC-AAAAATCAACAA
* *
2108870 TTTAGCAATTTATATGCAACAAATTAGCAAAAATCAACA
1 TTTAACAATTTATATGCAACAAACTAGCAAAAATCAACA
2108909 CGAAATAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 11 0.31
41 24 0.69
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (40 bp):
TTTAACAATTTATATGCAACAAACTAGCAAAAATCAACAA
Found at i:2111205 original size:15 final size:15
Alignment explanation
Indices: 2111185--2111221 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2111175 GAAGTAAATG
2111185 TGATAACATTAGGAT
1 TGATAACATTAGGAT
2111200 TGATAACATTAGGAT
1 TGATAACATTAGGAT
2111215 TGATAAC
1 TGATAAC
2111222 GACACATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (15 bp):
TGATAACATTAGGAT
Found at i:2121766 original size:22 final size:22
Alignment explanation
Indices: 2121740--2121807 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
2121730 ATATCTAAAC
*
2121740 AATAACAACAAAATAGTAGCTA
1 AATAACAACAAAATAGTAGCAA
* * * *
2121762 TATAATAGCAAAATGGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* *
2121784 AACAACAACAAAATAGTAGAAA
1 AATAACAACAAAATAGTAGCAA
2121806 AA
1 AA
2121808 AATTTAGACA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:2125178 original size:4 final size:4
Alignment explanation
Indices: 2125161--2125191 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2125151 GAAGATGAAA
*
2125161 GAGG GAGT GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG
2125192 AACGTGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.71, T:0.03
Consensus pattern (4 bp):
GAGG
Found at i:2128467 original size:11 final size:10
Alignment explanation
Indices: 2128428--2128486 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
2128418 AATTCGATTT
2128428 ATTTAAATTCG
1 ATTTAAATT-G
2128439 AGTTTAAATTG
1 A-TTTAAATTG
2128450 ATTTAAATTG
1 ATTTAAATTG
***
2128460 ATTTTAAAACA
1 A-TTTAAATTG
*
2128471 ATTTAAATTT
1 ATTTAAATTG
2128481 ATTTAA
1 ATTTAA
2128487 GATAAAATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 22 0.55
11 10 0.25
12 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (10 bp):
ATTTAAATTG
Found at i:2130247 original size:24 final size:24
Alignment explanation
Indices: 2130219--2130265 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2130209 ATGAAATAAT
*
2130219 TAAAATTTTAAAAATTATTAAAAA
1 TAAAATATTAAAAATTATTAAAAA
* *
2130243 TAAAATATTGATAATTATTAAAA
1 TAAAATATTAAAAATTATTAAAA
2130266 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAATATTAAAAATTATTAAAAA
Found at i:2130249 original size:33 final size:33
Alignment explanation
Indices: 2130212--2130275 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
2130202 AAAATGTATG
2130212 AAATAATT-AAAATT-TTAAAAATTATTAAAAATA
1 AAAT-ATTGAAAATTATT-AAAATTATTAAAAATA
* *
2130245 AAATATTGATAATTATTAAAATTATTTAAAA
1 AAATATTGAAAATTATTAAAATTATTAAAAA
2130276 CATATACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.11
33 22 0.81
34 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (33 bp):
AAATATTGAAAATTATTAAAATTATTAAAAATA
Found at i:2131566 original size:32 final size:31
Alignment explanation
Indices: 2131530--2131638 Score: 102
Period size: 32 Copynumber: 3.6 Consensus size: 31
2131520 TATGATTCAC
2131530 ATTTATTAAATTTTATAAATATCGAGAGTTAA
1 ATTTATTAAATTTT-TAAATATCGAGAGTTAA
*
2131562 ATTTATTAAATTTTTAGAAT-CCGA-A-TTAA
1 ATTTATTAAATTTTTA-AATATCGAGAGTTAA
* ** *
2131591 ATTGA-T-AATTTTATAAATATTAAGGGTTAA
1 ATTTATTAAATTTT-TAAATATCGAGAGTTAA
*
2131621 ATTTATTGAATTTTTAAA
1 ATTTATTAAATTTTTAAA
2131639 ATTCGAATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
27 9 0.14
28 4 0.06
29 8 0.13
30 9 0.14
31 10 0.16
32 23 0.37
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (31 bp):
ATTTATTAAATTTTTAAATATCGAGAGTTAA
Found at i:2131608 original size:59 final size:60
Alignment explanation
Indices: 2131538--2131667 Score: 181
Period size: 59 Copynumber: 2.2 Consensus size: 60
2131528 ACATTTATTA
* * *
2131538 AATTTTATAAATATCGAGAGTTAAATTTATTAAATTTTTAGAATCCGAATTAAATTGA-T
1 AATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATT
* * * *
2131597 AATTTTATAAATATTAAGGGTTAAATTTATTGAATTTTTAAAATTCGAATTAAAATGATT
1 AATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATT
*
2131657 AATTTTGTAAA
1 AATTTTATAAA
2131668 CATTGAGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
59 51 0.82
60 11 0.18
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (60 bp):
AATTTTATAAATATCAAGAGTTAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATT
Found at i:2131681 original size:59 final size:59
Alignment explanation
Indices: 2131559--2131683 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
2131549 TATCGAGAGT
* * * **
2131559 TAAATTTATTAAATTTTTAGAATCCGAATTAAATTGATAATTTTATAAATATTAAGGGT
1 TAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATAATTTTATAAACATTAAGGAA
* * * *
2131618 TAAATTTATTGAATTTTTAAAATTCGAATTAAAATGATTAATTTTGTAAACATTGA-GAA
1 TAAATTTATTAAATTTTTAAAATCCGAATTAAAATGA-TAATTTTATAAACATTAAGGAA
2131677 TAAATTT
1 TAAATTT
2131684 GTTGTTTTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 41 0.73
60 15 0.27
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (59 bp):
TAAATTTATTAAATTTTTAAAATCCGAATTAAAATGATAATTTTATAAACATTAAGGAA
Found at i:2138623 original size:23 final size:23
Alignment explanation
Indices: 2138568--2138612 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2138558 AAGCGTGTTC
* * *
2138568 ATATTATTTTTTATTTTTTTAAA
1 ATATTATATTATATTATTTTAAA
2138591 ATATTATATTATATTATTTTAA
1 ATATTATATTATATTATTTTAA
2138613 TATTTGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATTATATTATATTATTTTAAA
Found at i:2138636 original size:26 final size:29
Alignment explanation
Indices: 2138599--2138659 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 29
2138589 AAATATTATA
*
2138599 TTATAT-TATTTTAATAT-TTGATA-TTT
1 TTATATATATTTTAATATATTGAAATTTT
* *
2138625 TTATATAT-TTTTTATTTATTGAAATTTT
1 TTATATATATTTTAATATATTGAAATTTT
2138653 TTATATA
1 TTATATA
2138660 GTCATCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 13 0.45
27 6 0.21
28 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (29 bp):
TTATATATATTTTAATATATTGAAATTTT
Found at i:2138644 original size:28 final size:28
Alignment explanation
Indices: 2138572--2138659 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
2138562 GTGTTCATAT
* * *
2138572 TATTTTTTATTTTTTTAAAATATTATATTA
1 TATTTTTTATTTATTTGAAAT-TTTTA-TA
* *
2138602 TATTATTTTA-ATATTTGATATTTTTATA
1 TATT-TTTTATTTATTTGAAATTTTTATA
2138630 TATTTTTTATTTA-TTGAAATTTTTTATA
1 TATTTTTTATTTATTTGAAA-TTTTTATA
2138658 TA
1 TA
2138660 GTCATCTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
27 10 0.21
28 18 0.38
29 4 0.08
30 11 0.23
31 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TATTTTTTATTTATTTGAAATTTTTATA
Found at i:2138917 original size:6 final size:6
Alignment explanation
Indices: 2138906--2138932 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2138896 CAATACATCT
2138906 AATTCA AATTCA AATTCA AATTCA AAT
1 AATTCA AATTCA AATTCA AATTCA AAT
2138933 CGATTGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCA
Found at i:2141559 original size:17 final size:18
Alignment explanation
Indices: 2141526--2141559 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2141516 TCATAACAGT
*
2141526 TTTTATAATTTTTAAAAC
1 TTTTATAATTTTAAAAAC
2141544 TTTTA-AATTTTAAAAA
1 TTTTATAATTTTAAAAA
2141560 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTATAATTTTAAAAAC
Found at i:2148724 original size:14 final size:14
Alignment explanation
Indices: 2148691--2148723 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2148681 CGTTGATTAA
*
2148691 AATTTTATTAAATT
1 AATTTTAATAAATT
2148705 AATTTTAATAAATT
1 AATTTTAATAAATT
2148719 -ATTTT
1 AATTTT
2148724 TTTTTGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTTAATAAATT
Found at i:2171357 original size:92 final size:95
Alignment explanation
Indices: 2171113--2171381 Score: 257
Period size: 92 Copynumber: 2.9 Consensus size: 95
2171103 GATCCAACAG
* ** ** * * *
2171113 AAATCTATCATAGTAAATATTATTTCCCTAAAGTTGTAGTTGAGCAGATTGAAGCTA-AAAATCC
1 AAATCTACCATAGCGAATATTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTCC
2171177 TATACCCTTGAAGTTGCAGTAGGTCAGATT
66 TATACCCTTGAAGTTGCAGTAGGTCAGATT
* * * *
2171207 AAATCTACCATAGCGAATCTTATCCCCCTGAAGTTGCAGTGGAGCAAGA-TAAAACTACAAATTC
1 AAATCTACCATAGCGAATATTATCCCCCTAAAGTTGCAGTGGAGC-AGATTGAAGCTACAAATTC
* * *
2171271 C-ATTCCC-TGAAGTTGCAGTGGGT-TGATT
65 CTATACCCTTGAAGTTGCAGTAGGTCAGATT
** * * *
2171299 GAAA-CTACGGTGGTGAATATTATCCCCCTAAAGTTACAGTGGAGCAGATTGAAGCTACAAA-TC
1 -AAATCTACCATAGCGAATATTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTC
* *
2171362 TTAT-CTCCTTAAAGTTGCAG
65 CTATAC-CCTTGAAGTTGCAG
2171382 GGGAGCAAAT
Statistics
Matches: 142, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
91 6 0.04
92 52 0.37
93 28 0.20
94 47 0.33
95 9 0.06
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (95 bp):
AAATCTACCATAGCGAATATTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATTCC
TATACCCTTGAAGTTGCAGTAGGTCAGATT
Found at i:2171539 original size:44 final size:44
Alignment explanation
Indices: 2171319--2171561 Score: 193
Period size: 44 Copynumber: 5.5 Consensus size: 44
2171309 TGGTGAATAT
* * * *
2171319 TATCCCCCTAAAGTTACAGTGGAGC-AGATTGAAGCTACAAATCT
1 TATCCCCCTGAAGTTGCAGTGGAACAAGA-TGAAGCTACAAATCC
* * * * * * * *
2171363 TATCTCCTTAAAGTTGCAGGGGAGCAA-ATTAAAGCTACAAGTCT
1 TATCCCCCTGAAGTTGCAGTGGAACAAGA-TGAAGCTACAAATCC
* * * **
2171407 TATCTCCTTGAAGTTGCAGTGGAACAAGATGAAGCTACAAGTTT
1 TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACAAATCC
**
2171451 TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACTGATCC
1 TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACAAATCC
* * * * * *
2171495 TATGCCCCTGAGGTTGCAGTGGAGCAAGACGAGGATACAAATCC
1 TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACAAATCC
** * *
2171539 TATATCCTTGAAGTTACAGTGGA
1 TATCCCCCTGAAGTTGCAGTGGA
2171562 TTGGATTGAA
Statistics
Matches: 166, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
44 164 0.99
45 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
TATCCCCCTGAAGTTGCAGTGGAACAAGATGAAGCTACAAATCC
Found at i:2171963 original size:22 final size:22
Alignment explanation
Indices: 2171936--2171977 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2171926 CCCACTTGCT
2171936 AAACCTAATA-CCCAATAACCCG
1 AAACCTAATAGCCC-ATAACCCG
2171958 AAACCTAATAGCCCATAACC
1 AAACCTAATAGCCCATAACC
2171978 TAAACTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.45, C:0.36, G:0.05, T:0.14
Consensus pattern (22 bp):
AAACCTAATAGCCCATAACCCG
Found at i:2173320 original size:3 final size:3
Alignment explanation
Indices: 2173275--2173302 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2173265 TTGCCTTTAC
2173275 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2173303 TATCTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2180963 original size:29 final size:30
Alignment explanation
Indices: 2180900--2181013 Score: 114
Period size: 28 Copynumber: 4.0 Consensus size: 30
2180890 TACATACATG
* *
2180900 CATATAGCCCA-CTAGGCCCAA-TCTTATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
* *
2180928 CAAATGGCCGATCT-GGCCCAATTCATATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
* *
2180957 CTTATGGCCCA-CTAGGCCCAATTCA-CTT
1 CATATGGCCCATCTAGGCCCAATTCATATT
* *
2180985 CATATGGCCTAT-TAGGCCCAAATCATATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
2181014 ATACTCATAC
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
28 40 0.58
29 29 0.42
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (30 bp):
CATATGGCCCATCTAGGCCCAATTCATATT
Found at i:2181003 original size:57 final size:57
Alignment explanation
Indices: 2180906--2181013 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
2180896 CATGCATATA
* *
2180906 GCCCACTAGGCCCAATCTTATTCAAATGGCCGATCTGGCCCAATTCATATTCTTATG
1 GCCCACTAGGCCCAATCTCATTCAAATGGCCGATCTGGCCCAAATCATATTCTTATG
* *
2180963 GCCCACTAGGCCCAAT-TCACTTCATATGGCCTAT-TAGGCCCAAATCATATT
1 GCCCACTAGGCCCAATCTCA-TTCAAATGGCCGATCT-GGCCCAAATCATATT
2181014 ATACTCATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
56 3 0.07
57 42 0.93
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.29
Consensus pattern (57 bp):
GCCCACTAGGCCCAATCTCATTCAAATGGCCGATCTGGCCCAAATCATATTCTTATG
Found at i:2181109 original size:18 final size:19
Alignment explanation
Indices: 2181086--2181131 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2181076 TAGGCCCAAC
*
2181086 AGCCCA-TCAGTCCCATTT
1 AGCCCATTCAGGCCCATTT
*
2181104 AGCCCATTCTGGCCCATTT
1 AGCCCATTCAGGCCCATTT
*
2181123 AGCCAATTC
1 AGCCCATTC
2181132 TCAACCCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.22, C:0.37, G:0.13, T:0.28
Consensus pattern (19 bp):
AGCCCATTCAGGCCCATTT
Found at i:2181272 original size:8 final size:8
Alignment explanation
Indices: 2181229--2181275 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
2181219 GTAGCCCAAC
2181229 TTTCGGCT
1 TTTCGGCT
*
2181237 TTTTGGCAT
1 TTTCGGC-T
2181246 TTT-GGCT
1 TTTCGGCT
*
2181253 TTTCAGCT
1 TTTCGGCT
*
2181261 TTTCGGCA
1 TTTCGGCT
2181269 TTTCGGC
1 TTTCGGC
2181276 CTTTGTCGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 4 0.12
8 25 0.76
9 4 0.12
ACGTcount: A:0.06, C:0.21, G:0.23, T:0.49
Consensus pattern (8 bp):
TTTCGGCT
Found at i:2187161 original size:23 final size:25
Alignment explanation
Indices: 2187142--2187212 Score: 70
Period size: 27 Copynumber: 2.8 Consensus size: 25
2187132 TCTTGTACAT
*
2187142 GTATGCTCATACGAGCTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATTG
* * *
2187167 GTATGCTCACACGAACTATGAAAATAG
1 GTATGCTCACACGAGC--TGTAAATTG
**
2187194 GCCTGCTCACACGAGCTGT
1 GTATGCTCACACGAGCTGT
2187213 GGGTCAGAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
25 16 0.44
27 20 0.56
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATTG
Found at i:2190615 original size:71 final size:71
Alignment explanation
Indices: 2190499--2190728 Score: 433
Period size: 71 Copynumber: 3.2 Consensus size: 71
2190489 GGCCTTGGTA
2190499 AAGTGGCAAGGTGGCACCACTAAGTTCCTAAAAAAGATGGCGTCTAGGAAGGAATTAAAGGTCCA
1 AAGTGGCAAGGTGGCACCACTAAGTTCCTAAAAAAGATGGCGTCTAGGAAGGAATTAAAGGTCCA
2190564 GGGTTC
66 GGGTTC
2190570 AAGTGGCAAGGTGGCACCACTAAGTTCCTAAAAAAGATGGCGTCTAGGAAGGAATTAAAGGTCCA
1 AAGTGGCAAGGTGGCACCACTAAGTTCCTAAAAAAGATGGCGTCTAGGAAGGAATTAAAGGTCCA
2190635 GGGTTC
66 GGGTTC
*
2190641 AAGTGGCAAGGTGGCACCACTAAGTTCCTAAAAAAGATGGCGTCTAGGAAGGAATTAAAGGTTCA
1 AAGTGGCAAGGTGGCACCACTAAGTTCCTAAAAAAGATGGCGTCTAGGAAGGAATTAAAGGTCCA
2190706 GGGTTC
66 GGGTTC
*
2190712 AAGTTGCAAGGTAGGCA
1 AAGTGGCAAGGT-GGCA
2190729 TATGGTTACT
Statistics
Matches: 156, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
71 152 0.97
72 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (71 bp):
AAGTGGCAAGGTGGCACCACTAAGTTCCTAAAAAAGATGGCGTCTAGGAAGGAATTAAAGGTCCA
GGGTTC
Found at i:2191568 original size:40 final size:38
Alignment explanation
Indices: 2191523--2191605 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 38
2191513 ATATCGGAGC
* *
2191523 AGCTATGCTGCAACTATGGAGTGTAGGGATGGGTGGGTTG
1 AGCTATGC-CCAACT-TGGAGTGTAGGGATAGGTGGGTTG
* * *
2191563 AGCTATTCCCCACTTGGAGTGTAGGGCTAGGTGGGTTG
1 AGCTATGCCCAACTTGGAGTGTAGGGATAGGTGGGTTG
2191601 AGCTA
1 AGCTA
2191606 CCTGAATGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 27 0.71
39 4 0.11
40 7 0.18
ACGTcount: A:0.19, C:0.14, G:0.39, T:0.28
Consensus pattern (38 bp):
AGCTATGCCCAACTTGGAGTGTAGGGATAGGTGGGTTG
Found at i:2203637 original size:30 final size:30
Alignment explanation
Indices: 2203603--2203662 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2203593 CTTTAATACG
2203603 AACTTTGGAAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGAAAAATTACAC-TTTTGCCCCTA
* * *
2203633 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
2203663 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:2205741 original size:15 final size:15
Alignment explanation
Indices: 2205712--2205750 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
2205702 AACAGAGAAG
2205712 CCAAGAATAAAGAAAT
1 CCAAG-ATAAAGAAAT
2205728 CCAAGATAAAGAAAT
1 CCAAGATAAAGAAAT
*
2205743 CCATGATA
1 CCAAGATA
2205751 CGAGAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:2208572 original size:49 final size:49
Alignment explanation
Indices: 2208495--2208739 Score: 285
Period size: 49 Copynumber: 4.9 Consensus size: 49
2208485 TAGCCGAAGC
* * *
2208495 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * *
2208544 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC-AAT
* * ** *
2208594 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACATGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T
** * * *
2208645 TAT-TAGGTATGCATAGTAGCCTCCACTTAGTACTACACATGCGACCAAT
1 TATCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* *
2208694 TATCTGGTACACGTAGTAGCCCGCACTTAGTACTACACACGTGACC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC
2208740 TCACAATAGC
Statistics
Matches: 162, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
49 79 0.49
50 49 0.30
51 34 0.21
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:2208682 original size:101 final size:98
Alignment explanation
Indices: 2208508--2208733 Score: 281
Period size: 100 Copynumber: 2.3 Consensus size: 98
2208498 CTGGTACGCA
** * * *
2208508 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCAGGTACACATAGTAGCCTCCACTTA
*
2208573 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACC-AACCATCTGATACACG
* * * **
2208607 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTATTAGGTATGCATAGTAGCCTCCACT
1 TAGTAGCCTGCACTTAGTACTACACACACGA-CCAA-TTATCAGGTACACATAGTAGCCTCCACT
* ** *
2208672 TAGTACTACACATGCGACCAATTATCTGGTACACG
64 TAGTACTACACACGCGACCAACCATCTGATACACG
*
2208707 TAGTAGCCCGCACTTAGTACTACACAC
1 TAGTAGCCTGCACTTAGTACTACACAC
2208734 GTGACCTCAC
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
99 28 0.26
100 42 0.39
101 39 0.36
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCAGGTACACATAGTAGCCTCCACTTA
GTACTACACACGCGACCAACCATCTGATACACG
Found at i:2209421 original size:30 final size:30
Alignment explanation
Indices: 2209387--2209446 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2209377 CTTTAATACG
2209387 AACTTTGGAAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGAAAAATTACAC-TTTTGCCCCTA
* * *
2209417 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
2209447 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:2211407 original size:43 final size:42
Alignment explanation
Indices: 2211341--2211455 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 42
2211331 AGCATATGCA
* * * *
2211341 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAACCAAACA-CG
* * * ***
2211384 ATGCCATTGTCCCAGACAAGGTCTTACACGAAACCAGGTACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAACCAAACACG
2211426 ATGCCAATGTCCCAGACATGGTCTTACATG
1 ATGCCAATGTCCCAGACATGGTCTTACATG
2211456 CAAAACAGAA
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 29 0.49
43 30 0.51
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAAACCAAACACG
Found at i:2212393 original size:26 final size:26
Alignment explanation
Indices: 2212355--2212405 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2212345 ATGATGATTT
* * *
2212355 TTAATTTGGTTTTAACTAATATAACA
1 TTAATATGCTTTTAACCAATATAACA
*
2212381 TTAATATGCTTTTTACCAATATAAC
1 TTAATATGCTTTTAACCAATATAAC
2212406 CTTATTATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (26 bp):
TTAATATGCTTTTAACCAATATAACA
Found at i:2214124 original size:27 final size:27
Alignment explanation
Indices: 2214083--2214160 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
2214073 GAATACTTTA
* * *
2214083 GTTTACCAAAA-TACTGAAATGCCCTTG
1 GTTTA-CAAAATTACTAAAATACCCTCG
2214110 GTTTACAAAATTACTAAAATACCCTCG
1 GTTTACAAAATTACTAAAATACCCTCG
* * *
2214137 ATTAACAAAATTACCAAAATACCC
1 GTTTACAAAATTACTAAAATACCC
2214161 CTAGTTTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.11
27 39 0.89
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (27 bp):
GTTTACAAAATTACTAAAATACCCTCG
Found at i:2214202 original size:27 final size:27
Alignment explanation
Indices: 2214111--2214203 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 27
2214101 ATGCCCTTGG
* *
2214111 TTTACAAAATTACTAAAATACCCTCGA
1 TTTACAAAATTACCAAAATACCCCCGA
* *
2214138 TTAACAAAATTACCAAAATA-CCCCTA
1 TTTACAAAATTACCAAAATACCCCCGA
** *
2214164 GTTTGTAAAATTACCAAAGTACCCCCGA
1 -TTTACAAAATTACCAAAATACCCCCGA
*
2214192 TTTACAGAATTA
1 TTTACAAAATTA
2214204 TCGTTTTACC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
26 4 0.08
27 43 0.83
28 5 0.10
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCCCGA
Found at i:2214256 original size:27 final size:27
Alignment explanation
Indices: 2214226--2214528 Score: 360
Period size: 27 Copynumber: 11.2 Consensus size: 27
2214216 CAATTTAAAA
*
2214226 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
2214253 AATTACTAAAATACTCTTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
2214280 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
2214307 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
2214334 AATTA-TCGAAATACCCCTATAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* * *
2214361 AATTATTAAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
2214388 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
2214415 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
2214442 AATTA-TCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* * * *
2214469 AATTACTAAAATACCTCTATAGGCTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
2214496 AATTACCGAGATA-CCCTCGTGGGGTAA
1 AATTACTGAAATACCCCT-GTAGGGTAG
2214523 AATTAC
1 AATTAC
2214529 AATTTTGCCC
Statistics
Matches: 233, Mismatches: 38, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
26 5 0.02
27 226 0.97
28 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:2214284 original size:54 final size:54
Alignment explanation
Indices: 2214226--2214528 Score: 432
Period size: 54 Copynumber: 5.6 Consensus size: 54
2214216 CAATTTAAAA
* * *
2214226 AATTATTGAAATACCCCTGTAGGGTAGAATTACTAAAATACTCTTGTAAGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
*
2214280 AATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
* *
2214334 AATTATCGAAATACCCCTATAGGGTAGAATTATTAAAATACCCCTGTAAGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
* *
2214388 AATTA-CTGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
1 AATTATC-GAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
* *
2214442 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCTCTAT-AGGCTAG
1 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGG-TAG
* * * *
2214496 AATTACCGAGATA-CCCTCGTGGGGTAAAATTAC
1 AATTATCGAAATACCCCT-GTAGGGTAGAATTAC
2214529 AATTTTGCCC
Statistics
Matches: 226, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
53 8 0.04
54 217 0.96
55 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (54 bp):
AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
Found at i:2215122 original size:27 final size:26
Alignment explanation
Indices: 2215099--2215199 Score: 121
Period size: 27 Copynumber: 3.8 Consensus size: 26
2215089 TAAGTGGTTT
*
2215099 TGCCACATTATTTGATTCTGGTGGCTA
1 TGCCACAATATTTG-TTCTGGTGGCTA
* *
2215126 TGCCACAAATATCTGTTCTGGTGGCTC
1 TGCCAC-AATATTTGTTCTGGTGGCTA
* *
2215153 TGCCACAATATTTGTATCTGGTGACTC
1 TGCCACAATATTTGT-TCTGGTGGCTA
*
2215180 TGTCACAATATTTGTTCTGG
1 TGCCACAATATTTGTTCTGG
2215200 CAGCCATGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 13 0.20
27 47 0.71
28 6 0.09
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (26 bp):
TGCCACAATATTTGTTCTGGTGGCTA
Found at i:2215326 original size:6 final size:6
Alignment explanation
Indices: 2215317--2215401 Score: 66
Period size: 6 Copynumber: 13.8 Consensus size: 6
2215307 TTGCATTTAC
* * * *
2215317 ATTCTG ATTCTG ATTCTG -TTACCTA ATACTG ATTCTG ATTCT- ATCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* *
2215367 ATACTA ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
2215402 CATTTTGGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
5 4 0.06
6 54 0.83
7 4 0.06
8 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (6 bp):
ATTCTG
Found at i:2215348 original size:25 final size:25
Alignment explanation
Indices: 2215320--2215384 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
2215310 CATTTACATT
*
2215320 CTGATTCTGATTCTGTTACCTAATA
1 CTGATTCTGATTCTGTCACCTAATA
*
2215345 CTGATTCTGATTCTATCACCTAATA
1 CTGATTCTGATTCTGTCACCTAATA
*
2215370 CTAATTCTGATTCTG
1 CTGATTCTGATTCTG
2215385 ATTCTGATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.43
Consensus pattern (25 bp):
CTGATTCTGATTCTGTCACCTAATA
Found at i:2215352 original size:31 final size:29
Alignment explanation
Indices: 2215317--2215391 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 29
2215307 TTGCATTTAC
*
2215317 ATTCTGATTCTGATTCTGTTACCTAATACTG
1 ATTCTGATTCTGATTCTG--ACCTAATACTA
2215348 ATTCTGATTCT-A-TC--ACCTAATACTA
1 ATTCTGATTCTGATTCTGACCTAATACTA
2215373 ATTCTGATTCTGATTCTGA
1 ATTCTGATTCTGATTCTGA
2215392 TTCTGATTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 21 0.54
26 1 0.03
27 2 0.05
29 3 0.08
30 1 0.03
31 11 0.28
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (29 bp):
ATTCTGATTCTGATTCTGACCTAATACTA
Found at i:2217989 original size:25 final size:27
Alignment explanation
Indices: 2217961--2218019 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
2217951 CTATTCACCA
* *
2217961 AATTCATA-AAGATA-GCATGTCTAAG
1 AATTCATATAAGAAAGGCATATCTAAG
*
2217986 AATTCA-ATCAGAAAGGCATATCTAAG
1 AATTCATATAAGAAAGGCATATCTAAG
2218012 AATTCATA
1 AATTCATA
2218020 GTGACCATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.04
25 10 0.36
26 16 0.57
27 1 0.04
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (27 bp):
AATTCATATAAGAAAGGCATATCTAAG
Found at i:2221756 original size:43 final size:42
Alignment explanation
Indices: 2221708--2221814 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
2221698 CAATGCGAAC
* *
2221708 GTCCCAGACATGGTCTTACATGTAATCAAACATCGATGCCACT
1 GTCCCAGACATGGTCTTACATGAAATCAAACA-CGATGCCAAT
* ** * *
2221751 GTCCCAGACAGGGTCTTACACAAAATCAGATACGATGCCAAT
1 GTCCCAGACATGGTCTTACATGAAATCAAACACGATGCCAAT
2221793 GTCCCAGACATGGTCTTACATG
1 GTCCCAGACATGGTCTTACATG
2221815 CAAAACAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 28 0.52
43 26 0.48
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACATGAAATCAAACACGATGCCAAT
Found at i:2223555 original size:48 final size:46
Alignment explanation
Indices: 2223480--2223650 Score: 200
Period size: 48 Copynumber: 3.6 Consensus size: 46
2223470 GTAAATTGCT
*
2223480 GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATAATAT-GCC
* * * *
2223528 GATGCCATGTCCCAGACATGGTTTTACACTAGCATACAT-ATCAATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TTCATAAT--ATGCC
* *
2223576 GATGCCATGTCCAAGACATGGTCTTACACTGGCTTTCATAATGTAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TTCATAATAT-GCC
*
2223624 GATGCTATGTCCCAGACATGGTCTTAC
1 GATGCCATGTCCCAGACATGGTCTTAC
2223651 GCTAGCACAC
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
47 3 0.03
48 96 0.92
49 5 0.05
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATAATATGCC
Found at i:2223644 original size:96 final size:96
Alignment explanation
Indices: 2223480--2223666 Score: 293
Period size: 96 Copynumber: 1.9 Consensus size: 96
2223470 GTAAATTGCT
* *
2223480 GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCCGATGCCATGTCCCAGAC
1 GATGCCATGCCCAAGACATGGTCTTACACTGGCTCTCATAATATAGCCGATGCCATGTCCCAGAC
* *
2223545 ATGGTTTTACACTAGCATACATATCAATGTC
66 ATGGTCTTACACTAGCACACATATCAATGTC
* * * *
2223576 GATGCCATGTCCAAGACATGGTCTTACACTGGCTTTCATAATGTAGCCGATGCTATGTCCCAGAC
1 GATGCCATGCCCAAGACATGGTCTTACACTGGCTCTCATAATATAGCCGATGCCATGTCCCAGAC
*
2223641 ATGGTCTTACGCTAGCACACATATCA
66 ATGGTCTTACACTAGCACACATATCA
2223667 CCCAAATGTC
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (96 bp):
GATGCCATGCCCAAGACATGGTCTTACACTGGCTCTCATAATATAGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTAGCACACATATCAATGTC
Found at i:2229458 original size:47 final size:48
Alignment explanation
Indices: 2229366--2229548 Score: 208
Period size: 48 Copynumber: 3.8 Consensus size: 48
2229356 GGTGAATTGT
* *
2229366 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTTTCATAATGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGC
*
2229414 CGATGCCATGTCCCAGACATGG-CTTACACTGGCTCTCGTAATGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGC
* * * * * * ****
2229461 TGATGCCATATCCCACACATGGTCTTACACTAGCACACAT-ATCAACAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGC
* *
2229509 CGATGCCATGTCCCAGACATGGTCTCACACTTGCTCTCAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT
2229549 TGTAACAGTC
Statistics
Matches: 112, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
47 44 0.39
48 68 0.61
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGC
Found at i:2230638 original size:41 final size:43
Alignment explanation
Indices: 2230593--2230691 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 43
2230583 GCAATTTAAA
* *
2230593 CTAGCTTCGACT-ATAT-GA-GGCAGTAAGTGTAG-GGAATTGTT
1 CTAGCTTCGACTAAT-TGGATGGCACTAAGTGT-GCGGAATTATT
*
2230634 CTAGCTTCGGCTAATTGGGATGGCACTAAGTGTGCGGAATTATT
1 CTAGCTTCGACTAATT-GGATGGCACTAAGTGTGCGGAATTATT
*
2230678 CTAGCTTCGGCTAA
1 CTAGCTTCGACTAA
2230692 CTGTTGCAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
41 12 0.24
42 2 0.04
43 3 0.06
44 33 0.66
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.31
Consensus pattern (43 bp):
CTAGCTTCGACTAATTGGATGGCACTAAGTGTGCGGAATTATT
Found at i:2243177 original size:25 final size:24
Alignment explanation
Indices: 2243144--2243192 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2243134 AACAATTCAA
* *
2243144 TAAATATATATAAAAATAATAAATT
1 TAAAAATATAT-AAAATAAAAAATT
2243169 TAAAAATATATAAAATAAAAAATT
1 TAAAAATATATAAAATAAAAAATT
2243193 ATTGTTGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAATATATAAAATAAAAAATT
Found at i:2243187 original size:15 final size:15
Alignment explanation
Indices: 2243146--2243189 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2243136 CAATTCAATA
*
2243146 AATATATATAAAAAT
1 AATAAATATAAAAAT
*
2243161 AATAAATTTAAAAAT
1 AATAAATATAAAAAT
2243176 ATATAAA-ATAAAAA
1 A-ATAAATATAAAAA
2243190 ATTATTGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAATATAAAAAT
Found at i:2245440 original size:11 final size:11
Alignment explanation
Indices: 2245413--2245455 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2245403 TGACCTTTCC
2245413 AAGGTATGGG-
1 AAGGTATGGGA
*
2245423 TAGGTATGGGA
1 AAGGTATGGGA
*
2245434 AAGGTATGGGC
1 AAGGTATGGGA
2245445 AAGGTATGGGA
1 AAGGTATGGGA
2245456 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:2245452 original size:22 final size:21
Alignment explanation
Indices: 2245413--2245455 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2245403 TGACCTTTCC
*
2245413 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
2245434 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
2245456 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:2246602 original size:26 final size:24
Alignment explanation
Indices: 2246573--2246620 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
2246563 TCACAATCTT
*
2246573 AAATATTAAGATGTTTATTAAATATA
1 AAATATTAA-ATGTGT-TTAAATATA
2246599 AAATATTAAATGTGTTTAAATA
1 AAATATTAAATGTGTTTAAATA
2246621 ATTAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (24 bp):
AAATATTAAATGTGTTTAAATATA
Found at i:2251333 original size:21 final size:21
Alignment explanation
Indices: 2251307--2251347 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2251297 AGACGAGCAA
* *
2251307 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2251328 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2251348 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2254474 original size:76 final size:76
Alignment explanation
Indices: 2254348--2254499 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
2254338 TTCGATCTTA
*
2254348 TTTTATCTAATGATAACTATTATATCTTGCTTTATGAAAAGACAATTACTAACAAATGGTAATTA
1 TTTTATCTAATGATAACTATTATATCTTGCTTCATGAAAAGACAATTACTAACAAATGGTAATTA
2254413 AGCCATTTATC
66 AGCCATTTATC
2254424 TTTTATCTAATGATAACTATTATATCTTGCTTCATGAAAAGACAATTACTAACAAATGGTAATTA
1 TTTTATCTAATGATAACTATTATATCTTGCTTCATGAAAAGACAATTACTAACAAATGGTAATTA
2254489 AGCCATTTATC
66 AGCCATTTATC
2254500 ACTAAGACAA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (76 bp):
TTTTATCTAATGATAACTATTATATCTTGCTTCATGAAAAGACAATTACTAACAAATGGTAATTA
AGCCATTTATC
Found at i:2256273 original size:32 final size:31
Alignment explanation
Indices: 2256224--2256309 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
2256214 TCACTATTGA
* * * *
2256224 TGTTATTATTTATTATTATTTTATTTCTACTTT
1 TGTTATCA-TTATTATTATATTATAT-TACTAT
*
2256257 TGTTATCATTATTATTACTATTGTATTACTAT
1 TGTTATCATTATTATTA-TATTATATTACTAT
*
2256289 TGTTATCAGTATTATTATATT
1 TGTTATCATTATTATTATATT
2256310 TTCTTTTCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 4 0.09
32 30 0.65
33 12 0.26
ACGTcount: A:0.26, C:0.07, G:0.06, T:0.62
Consensus pattern (31 bp):
TGTTATCATTATTATTATATTATATTACTAT
Found at i:2256849 original size:15 final size:14
Alignment explanation
Indices: 2256809--2256850 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
2256799 TATCATCATC
2256809 ATTA-TTTTTATTA
1 ATTATTTTTTATTA
2256822 ATTATTTTATTATTA
1 ATTATTTT-TTATTA
2256837 ATTATTTATTTATT
1 ATTATTT-TTTATT
2256851 CATACCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.15
14 3 0.12
15 18 0.69
16 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTATTTTTTATTA
Found at i:2256897 original size:3 final size:3
Alignment explanation
Indices: 2256877--2256919 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
2256867 CAAGCTTTCG
*
2256877 ATT ATTT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2256920 GTTCACATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2261240 original size:16 final size:16
Alignment explanation
Indices: 2261219--2261254 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2261209 TAACTCAGGA
2261219 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
2261235 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
2261251 GCTG
1 GCTG
2261255 TGATTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.19
Consensus pattern (16 bp):
GCTGCAGGAGTACATG
Found at i:2262097 original size:120 final size:120
Alignment explanation
Indices: 2261971--2262260 Score: 485
Period size: 120 Copynumber: 2.4 Consensus size: 120
2261961 AATTATTTTA
* *
2261971 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTT-TCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTTATATTT
* *
2262035 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
2262091 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATT-ATTATTTTAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTAAATTTATATTT
2262155 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
2262211 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT
2262261 GTTTAAATAT
Statistics
Matches: 159, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
119 7 0.04
120 149 0.94
121 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:2262153 original size:15 final size:14
Alignment explanation
Indices: 2262101--2262156 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
2262091 AATTTTATTA
2262101 AATTATA-TATTTT
1 AATTATATTATTTT
*
2262114 AATTATAATATATTT
1 AATTATATTAT-TTT
*
2262129 AATAATTATTATTTT
1 AATTA-TATTATTTT
2262144 AATT-TA-TATTTT
1 AATTATATTATTTT
2262156 A
1 A
2262157 CAGTATCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.19
13 9 0.24
14 3 0.08
15 13 0.35
16 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATATTATTTT
Found at i:2262217 original size:61 final size:61
Alignment explanation
Indices: 2262032--2262218 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
2262022 TCAAATTTTC
*
2262032 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
* * * * * * *
2262093 TTTTATTA-AATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATTATT-ATT-TTAATTTA
1 TTTTA-TAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAA-TATTAATTATTAA--GA
2262150 TA
61 -A
*
2262152 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
2262213 TTTTAT
1 TTTTAT
2262219 TAAATTATAT
Statistics
Matches: 95, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
56 4 0.04
57 12 0.13
58 8 0.08
59 16 0.17
60 8 0.08
61 21 0.22
62 9 0.09
63 13 0.14
64 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (61 bp):
TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
Found at i:2262240 original size:18 final size:17
Alignment explanation
Indices: 2262212--2262246 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2262202 ATTATTAAGA
*
2262212 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2262229 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2262247 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2262360 original size:147 final size:149
Alignment explanation
Indices: 2262200--2262474 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
2262190 ATAAGAATAT
*
2262200 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
2262265 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
2262328 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
2262347 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
2262412 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
2262475 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:2262387 original size:18 final size:17
Alignment explanation
Indices: 2262359--2262393 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2262349 ATTATTAAGA
*
2262359 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2262376 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2262394 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2262604 original size:44 final size:45
Alignment explanation
Indices: 2262555--2262649 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
2262545 TTACACCTCT
* * *
2262555 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
** *
2262599 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
2262644 ATTACA
1 ATTACA
2262650 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:2262649 original size:16 final size:16
Alignment explanation
Indices: 2262630--2262681 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
2262620 GATTTGCTAT
* * *
2262630 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
2262646 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2262662 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2262678 TACA
1 TACA
2262682 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2263466 original size:4 final size:4
Alignment explanation
Indices: 2263420--2263555 Score: 64
Period size: 4 Copynumber: 33.8 Consensus size: 4
2263410 TTAAGTCCTT
* * * * *
2263420 TTTA TTTTA ATTA TTTTA TTCA TTTA TTTA CTTA TTCA CTTA TTTA TTTA
1 TTTA -TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * * *
2263470 TTCA -TTA TTCCT- TTTA TGTTA TTCA TTTA TTTA CTCA TATA CTTA TCTA
1 TTTA TTTA TT--TA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
2263519 TTTA TATA -TTA TTCA CTTA TTTA TTTA TTT- TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2263556 TAATCCTTGT
Statistics
Matches: 93, Mismatches: 30, Indels: 17
0.66 0.21 0.12
Matches are distributed among these distances:
3 8 0.09
4 71 0.76
5 13 0.14
6 1 0.01
ACGTcount: A:0.25, C:0.10, G:0.01, T:0.64
Consensus pattern (4 bp):
TTTA
Found at i:2263493 original size:53 final size:53
Alignment explanation
Indices: 2263430--2263532 Score: 147
Period size: 53 Copynumber: 1.9 Consensus size: 53
2263420 TTTATTTTAA
* * *
2263430 TTATTTTATTCATTTATTTACTTAT-TCACTTATTTATTTAT-TCATTATTCCTT
1 TTATGTTATTCATTTATTTACTCATAT-ACTTATCTATTTATAT-ATTATTCCTT
2263483 TTATGTTATTCATTTATTTACTCATATACTTATCTATTTATATATTATTC
1 TTATGTTATTCATTTATTTACTCATATACTTATCTATTTATATATTATTC
2263533 ACTTATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
53 43 0.96
54 2 0.04
ACGTcount: A:0.25, C:0.13, G:0.01, T:0.61
Consensus pattern (53 bp):
TTATGTTATTCATTTATTTACTCATATACTTATCTATTTATATATTATTCCTT
Found at i:2263719 original size:14 final size:15
Alignment explanation
Indices: 2263686--2263717 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2263676 TACTTATCCA
2263686 TTTATCTATTTATTT
1 TTTATCTATTTATTT
*
2263701 TTTATCTCTTTATTT
1 TTTATCTATTTATTT
2263716 TT
1 TT
2263718 ATACATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATCTATTTATTT
Found at i:2263954 original size:29 final size:30
Alignment explanation
Indices: 2263916--2263979 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
2263906 ATTTATTTAT
2263916 TATTACTATAA-TATG-ATTATTAATATTAA
1 TATTACTATAATTATGCATTATTAATA-TAA
* *
2263945 TATTATTATAATTATGTCATTATTATTATAA
1 TATTACTATAATTATG-CATTATTAATATAA
2263976 TATT
1 TATT
2263980 CCTTTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.33
30 4 0.13
31 7 0.23
32 9 0.30
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (30 bp):
TATTACTATAATTATGCATTATTAATATAA
Found at i:2272489 original size:24 final size:24
Alignment explanation
Indices: 2272437--2272489 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2272427 TTTGAAGGAG
* * *
2272437 ATTTAGTATTTATTAGTACAATAT
1 ATTTGGTATTTATTAGCACAAAAT
*
2272461 ATTTGGTATTTATTAGCATAAAAT
1 ATTTGGTATTTATTAGCACAAAAT
*
2272485 CTTTG
1 ATTTG
2272490 TTCTTTCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (24 bp):
ATTTGGTATTTATTAGCACAAAAT
Found at i:2276603 original size:28 final size:28
Alignment explanation
Indices: 2276571--2276626 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2276561 CCAAGGCTGA
2276571 CTTTT-ATCT-CTTGATTTCAATTTCAATC
1 CTTTTAATCTACTTG-TTT-AATTTCAATC
*
2276599 CTTTTAATTTACTTGTTTAATTTCAATC
1 CTTTTAATCTACTTGTTTAATTTCAATC
2276627 ATTTACTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 15 0.60
29 6 0.24
30 4 0.16
ACGTcount: A:0.23, C:0.18, G:0.04, T:0.55
Consensus pattern (28 bp):
CTTTTAATCTACTTGTTTAATTTCAATC
Found at i:2285768 original size:13 final size:12
Alignment explanation
Indices: 2285740--2285774 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2285730 AAATCAACCT
* *
2285740 TTTTTACTTCTC
1 TTTTTGCTTTTC
2285752 TTTTTGCTTTTC
1 TTTTTGCTTTTC
2285764 TTTTTGCTTTT
1 TTTTTGCTTTT
2285775 TGATTACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTGCTTTTC
Found at i:2285909 original size:18 final size:17
Alignment explanation
Indices: 2285886--2285931 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
2285876 TGTTTTTTTG
2285886 TTTTTGTTTTCTGCCTCT
1 TTTTTGTTTTCTGCC-CT
*
2285904 TTTTTGTTTT-TTCCCT
1 TTTTTGTTTTCTGCCCT
*
2285920 TCTTTGTTTTCT
1 TTTTTGTTTTCT
2285932 TGTATCTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.44
17 4 0.16
18 10 0.40
ACGTcount: A:0.00, C:0.20, G:0.09, T:0.72
Consensus pattern (17 bp):
TTTTTGTTTTCTGCCCT
Found at i:2285923 original size:19 final size:18
Alignment explanation
Indices: 2285886--2285924 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2285876 TGTTTTTTTG
*
2285886 TTTTTGTTTTCTGCCTCT
1 TTTTTGTTTTCTCCCTCT
*
2285904 TTTTTGTTTTTTCCCTTCT
1 TTTTTGTTTTCTCCC-TCT
2285923 TT
1 TT
2285925 GTTTTCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.72
Consensus pattern (18 bp):
TTTTTGTTTTCTCCCTCT
Found at i:2286877 original size:12 final size:12
Alignment explanation
Indices: 2286852--2286886 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2286842 AAATCAATTT
* *
2286852 TTTTTACTTCTC
1 TTTTTGCTTTTC
2286864 TTTTTGCTTTTC
1 TTTTTGCTTTTC
2286876 TTTTTGCTTTT
1 TTTTTGCTTTT
2286887 TGATTACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTGCTTTTC
Found at i:2287035 original size:19 final size:18
Alignment explanation
Indices: 2286998--2287036 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2286988 TGTTTTTTTG
*
2286998 TTTTTGTTTTCTGCCTCT
1 TTTTTGTTTTCTCCCTCT
*
2287016 TTTTTGTTTTTTCCCTTCT
1 TTTTTGTTTTCTCCC-TCT
2287035 TT
1 TT
2287037 ATTTTCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.72
Consensus pattern (18 bp):
TTTTTGTTTTCTCCCTCT
Found at i:2287988 original size:12 final size:12
Alignment explanation
Indices: 2287963--2287997 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2287953 AAATCAATTT
* *
2287963 TTTTTACTTCTC
1 TTTTTGCTTTTC
2287975 TTTTTGCTTTTC
1 TTTTTGCTTTTC
2287987 TTTTTGCTTTT
1 TTTTTGCTTTT
2287998 TGATTACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTGCTTTTC
Done.