Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 13 of 28
Found at i:2035482 original size:51 final size:50
Alignment explanation
Indices: 2035253--2035487 Score: 240
Period size: 50 Copynumber: 4.7 Consensus size: 50
2035243 GTAAAGTGAT
* * *
2035253 TTGACTATTCTTCATCAA-CTTTGGATAATCGAGAGAGGTAGTCGTAATTA
1 TTGACTATTCTTCACCAACCTTT-GACAATCGAGAGAAGTAGTCGTAATTA
* * ** * *
2035303 TTGACTATTTTTCACCAAACTTTGACAATTAAGAGAAGT-GACCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAAGTAG-TCGTAATTA
* * *
2035353 TTGACTATTCTTCACCAACTTTTGACAATCTAGAGAAGTAGTCGAAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAAGTAGTCGTAATTA
* * * * * *
2035403 TTGACTATTATTCACCAATCTTTGACAATCGATAGAGGTGGCTTGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAAGTAG-TCGTAATTA
* * *
2035454 TTGACTATTCTTCATCAACCTTTAACAATAGAGA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGA
2035488 AAGGTGACCG
Statistics
Matches: 150, Mismatches: 31, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
49 1 0.01
50 109 0.73
51 40 0.27
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAAGTAGTCGTAATTA
Found at i:2036086 original size:50 final size:50
Alignment explanation
Indices: 2035984--2036094 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
2035974 AAGTAGTCGA
* * *
2035984 AATTATTGACTATTCTTCACCAACCTTTGACAATCAATAGAGGTAGCTGT
1 AATTATTGACTATTCTTCACCAACCTTTAACAATCAAGAAAGGTAGCTGT
*
2036034 AATTATTGACTATTCTTCACCAACCTTTAACAAT-AGAGAAAGGT-GATCGT
1 AATTATTGACTATTCTTCACCAACCTTTAACAATCA-AGAAAGGTAGCT-GT
*
2036084 AATTGTTGACT
1 AATTATTGACT
2036095 CTAAGTATCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
49 3 0.06
50 51 0.94
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (50 bp):
AATTATTGACTATTCTTCACCAACCTTTAACAATCAAGAAAGGTAGCTGT
Found at i:2036541 original size:585 final size:586
Alignment explanation
Indices: 2035377--2036543 Score: 2054
Period size: 585 Copynumber: 2.0 Consensus size: 586
2035367 CCAACTTTTG
* *
2035377 ACAATCTAGAGAAGTAGTCGAAATTATTGACTATTATTCACCAATCTTTGACAATCGATAGAGGT
1 ACAATCTAGAGAAGTAGTCGAAATTATTGACTATTATTCACCAACCTTTGACAATCAATAGAGGT
* *
2035442 GGCTTGTAATTATTGACTATTCTTCATCAACCTTTAACAATAGAGAAAGGTGACCGTAATTGTTG
66 AGCTTGTAATTATTGACTATTCTTCACCAACCTTTAACAATAGAGAAAGGTGACCGTAATTGTTG
*
2035507 ACTCTAAGTATCTCAAGTATGACTATAAATAGCCATTCAAGTTCATTCATTTAATGTATCCTAGA
131 ACTCTAAGTATCTCAAGTATGACTATAAATAGCCATTCAAGTTCATTCATTTAATGTATCCCAGA
2035572 ATTGAAAGAAATAAAATCCTCTGTCTTTGCCCGTAGACGTAGGCTTTACATCGAACCACATAACT
196 ATTGAAAGAAATAAAATCCTCTGTCTTTGCCCGTAGACGTAGGCTTTACATCGAACCACATAACT
* *
2035637 TTGTGTCTTCTATTGTGTGTGCTTGTTCTTCATTTTTCTAATTTCATTTTAGCTGTGGCCCTACT
261 TTGTGTCTTCTATTGTATGTGCTTGTTCTTCATTTTTCTAATTTCATTTTAGCTATGGCCCTACT
*
2035702 CTACCTATCAATGCACTAACAGTGGTATAAGAGCTATTGGTTGTTGAGGCACTGTTCACGTATAC
326 CTACCTATCAATGCACTAACAGTGGTATAAGAGCTATTGGTTGTCGAGGCACTGTTCACGTATAC
2035767 AGGCATTGTTCACACATATAATTACTGTGCACGTAAAACAGTGAAAGCAAATTCTGAATTCGTGG
391 AGGCATTGTTCACACATATAATTACTGTGCACGTAAAACAGTGAAAGCAAATTCTGAATTCGTGG
*
2035832 AGGAAAAACAATGGCGACAAATTACTGAAATTGAGAAGTTTAAGGGAAACAAATTCACATTGTGA
456 AGGAAAAACAATGGCGACAAATTACTGAAATTGAGAAGTTTAACGGAAACAAATTCACATTGTGA
*
2035897 AAAATAAAGATGAAAGCTGTTTTAAGAAAAAATAATTGCCTGGTAGTAATTGGAGAGAGGTCGAG
521 AAAATAAAGATGAAAGCTGTTTTAAGAAAAAATAATTGCCTGATAGTAATTGGAGAGAGGTCGAG
2035962 T
586 T
*
2035963 ACAATCTAGAGAAGTAGTCGAAATTATTGACTATTCTTCACCAACCTTTGACAATCAATAGAGGT
1 ACAATCTAGAGAAGTAGTCGAAATTATTGACTATTATTCACCAACCTTTGACAATCAATAGAGGT
*
2036028 AGC-TGTAATTATTGACTATTCTTCACCAACCTTTAACAATAGAGAAAGGTGATCGTAATTGTTG
66 AGCTTGTAATTATTGACTATTCTTCACCAACCTTTAACAATAGAGAAAGGTGACCGTAATTGTTG
**
2036092 ACTCTAAGTATCTCAAGTATGGTTATAAATAGCCATTCAAGTTCATTCATTTAATGTATCCCAGA
131 ACTCTAAGTATCTCAAGTATGACTATAAATAGCCATTCAAGTTCATTCATTTAATGTATCCCAGA
* * * * * *
2036157 ATTGAGAGAAATAAAATCTTCTGTCTTTGCCCGTGGACGTAGGCTTTACATCGAATCACTGTAAT
196 ATTGAAAGAAATAAAATCCTCTGTCTTTGCCCGTAGACGTAGGCTTTACATCGAACCAC-ATAAC
2036222 TTTGTGTCTTCTATTGTATGTGCTTGTTCTTCATTTTTCTAATTTCATTTTAGCTATGGCCCTAC
260 TTTGTGTCTTCTATTGTATGTGCTTGTTCTTCATTTTTCTAATTTCATTTTAGCTATGGCCCTAC
2036287 TCTA-CTCATCAATGCACTAACAGTGGTATAAGAGCTATTGGTTGTCGAGGCACTGTTCACGTAT
325 TCTACCT-ATCAATGCACTAACAGTGGTATAAGAGCTATTGGTTGTCGAGGCACTGTTCACGTAT
* *
2036351 ACAGGCATTGTTCACACATATAATTACTGTGTACGTAAAACAGT-AGAAGTAAATTCTGAATTCG
389 ACAGGCATTGTTCACACATATAATTACTGTGCACGTAAAACAGTGA-AAGCAAATTCTGAATTCG
* *
2036415 TGGTGGAAAAATAATGGCGACAAATTAC-GAAATTGAGAAGTTTAACGGAAACAAATTCACATTG
453 TGGAGGAAAAACAATGGCGACAAATTACTGAAATTGAGAAGTTTAACGGAAACAAATTCACATTG
*
2036479 TGAAAAATAAAGATGAAAGCTGTTTTAAGGAAAAATAATTGCCTGATAGTAATTGGAGAGAGGTC
518 TGAAAAATAAAGATGAAAGCTGTTTTAAGAAAAAATAATTGCCTGATAGTAATTGGAGAGAGGTC
2036544 AAGTGAGATA
Statistics
Matches: 553, Mismatches: 25, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
585 277 0.50
586 276 0.50
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (586 bp):
ACAATCTAGAGAAGTAGTCGAAATTATTGACTATTATTCACCAACCTTTGACAATCAATAGAGGT
AGCTTGTAATTATTGACTATTCTTCACCAACCTTTAACAATAGAGAAAGGTGACCGTAATTGTTG
ACTCTAAGTATCTCAAGTATGACTATAAATAGCCATTCAAGTTCATTCATTTAATGTATCCCAGA
ATTGAAAGAAATAAAATCCTCTGTCTTTGCCCGTAGACGTAGGCTTTACATCGAACCACATAACT
TTGTGTCTTCTATTGTATGTGCTTGTTCTTCATTTTTCTAATTTCATTTTAGCTATGGCCCTACT
CTACCTATCAATGCACTAACAGTGGTATAAGAGCTATTGGTTGTCGAGGCACTGTTCACGTATAC
AGGCATTGTTCACACATATAATTACTGTGCACGTAAAACAGTGAAAGCAAATTCTGAATTCGTGG
AGGAAAAACAATGGCGACAAATTACTGAAATTGAGAAGTTTAACGGAAACAAATTCACATTGTGA
AAAATAAAGATGAAAGCTGTTTTAAGAAAAAATAATTGCCTGATAGTAATTGGAGAGAGGTCGAG
T
Found at i:2042463 original size:9 final size:9
Alignment explanation
Indices: 2042449--2042480 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2042439 TAAAAAATAT
2042449 TTTTTTATC
1 TTTTTTATC
2042458 TTTTTTA--
1 TTTTTTATC
2042465 TTTTTTATC
1 TTTTTTATC
2042474 TTTTTTA
1 TTTTTTA
2042481 CTAAACATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTATC
Found at i:2042470 original size:16 final size:16
Alignment explanation
Indices: 2042449--2042480 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2042439 TAAAAAATAT
2042449 TTTTTTATCTTTTTTA
1 TTTTTTATCTTTTTTA
2042465 TTTTTTATCTTTTTTA
1 TTTTTTATCTTTTTTA
2042481 CTAAACATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTATCTTTTTTA
Found at i:2042524 original size:16 final size:17
Alignment explanation
Indices: 2042503--2042548 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
2042493 ATAAAAAATA
2042503 TTTTTT-ATCTTTTTA-C
1 TTTTTTAAT-TTTTTATC
2042519 TTTTTTAATTTTTTATC
1 TTTTTTAATTTTTTATC
*
2042536 -TTTTCAATTTTTT
1 TTTTTTAATTTTTT
2042549 TCTCTCCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 24 0.89
17 3 0.11
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTAATTTTTTATC
Found at i:2042529 original size:24 final size:24
Alignment explanation
Indices: 2042502--2042548 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2042492 AATAAAAAAT
* *
2042502 ATTTTTTATCTTTTTACTTTTTTA
1 ATTTTTTATCTTTTCAATTTTTTA
2042526 ATTTTTTATCTTTTCAATTTTTT
1 ATTTTTTATCTTTTCAATTTTTT
2042549 TCTCTCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (24 bp):
ATTTTTTATCTTTTCAATTTTTTA
Found at i:2043115 original size:24 final size:26
Alignment explanation
Indices: 2043083--2043136 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
2043073 ATTTAATTTA
*
2043083 ATATGTTA-TTTT-TAATTATATAAT
1 ATATATTATTTTTATAATTATATAAT
2043107 ATATATTATTTTTATAATTATATAAT
1 ATATATTATTTTTATAATTATATAAT
2043133 ATAT
1 ATAT
2043137 TATATAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.26
25 4 0.15
26 16 0.59
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
ATATATTATTTTTATAATTATATAAT
Found at i:2043137 original size:24 final size:23
Alignment explanation
Indices: 2043081--2043139 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
2043071 GGATTTAATT
*
2043081 TAATATGTTA-TTTTTAATTATA
1 TAATATATTATTTTTTAATTATA
2043103 TAATATATATTATTTTTATAATTATA
1 T-A-ATATATTATTTTT-TAATTATA
2043129 TAATATATTAT
1 TAATATATTAT
2043140 ATAATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.03
23 1 0.03
24 16 0.50
25 5 0.16
26 9 0.28
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TAATATATTATTTTTTAATTATA
Found at i:2043138 original size:12 final size:12
Alignment explanation
Indices: 2043123--2043166 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
2043113 TATTTTTATA
2043123 ATTATATAATAT
1 ATTATATAATAT
2043135 ATTATATAATAT
1 ATTATATAATAT
2043147 A-TATCATATATAAT
1 ATTAT-ATA-AT-AT
2043161 ATTATA
1 ATTATA
2043167 GTATAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.11
12 16 0.57
13 2 0.07
14 4 0.14
15 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTATATAATAT
Found at i:2043155 original size:9 final size:9
Alignment explanation
Indices: 2043095--2043171 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 9
2043085 ATGTTATTTT
2043095 TAAT-TATA
1 TAATATATA
2043103 TAATATATA
1 TAATATATA
* * *
2043112 TTATTTTTA
1 TAATATATA
2043121 TAAT-TATA
1 TAATATATA
2043129 TAATATAT-
1 TAATATATA
2043137 T-ATATAATA
1 TAATAT-ATA
2043146 TATATCATATA
1 TA-AT-ATATA
2043157 TAATAT-TA
1 TAATATATA
*
2043165 TAGTATA
1 TAATATA
2043172 AACATTTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
7 4 0.07
8 21 0.38
9 19 0.35
10 2 0.04
11 7 0.13
12 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (9 bp):
TAATATATA
Found at i:2046372 original size:15 final size:15
Alignment explanation
Indices: 2046352--2046380 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2046342 AGAATGGAAA
2046352 AAAAAATAAATAAAT
1 AAAAAATAAATAAAT
2046367 AAAAAATAAATAAA
1 AAAAAATAAATAAA
2046381 GAAGTGGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:2051746 original size:14 final size:14
Alignment explanation
Indices: 2051727--2051753 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2051717 TTATTTGTGT
2051727 AATTTCAGATTTAG
1 AATTTCAGATTTAG
2051741 AATTTCAGATTTA
1 AATTTCAGATTTA
2051754 AAATGGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (14 bp):
AATTTCAGATTTAG
Found at i:2051963 original size:19 final size:19
Alignment explanation
Indices: 2051900--2051963 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
2051890 CTCTTTTTCG
2051900 TTATTTTT-TTTAT--ATA
1 TTATTTTTATTTATAAATA
*
2051916 TTATTATTTA-ATATAAAT-
1 TTATT-TTTATTTATAAATA
*
2051934 TTAATTATTATTTATAAATA
1 TT-ATTTTTATTTATAAATA
2051954 TTATTTTTAT
1 TTATTTTTAT
2051964 AATTGATGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
16 5 0.14
17 6 0.16
18 5 0.14
19 19 0.51
20 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTTTATTTATAAATA
Found at i:2054389 original size:2 final size:2
Alignment explanation
Indices: 2054382--2054411 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2054372 ATCAAAAGAA
2054382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2054412 TCAAAGTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2056704 original size:24 final size:24
Alignment explanation
Indices: 2056677--2056722 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2056667 ACTGCCGACA
2056677 GTATTAAGA-GAAAAGAAAATGATT
1 GTATTAA-ATGAAAAGAAAATGATT
*
2056701 GTATTAAATGACAAGAAAATGA
1 GTATTAAATGAAAAGAAAATGA
2056723 ATTATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.54, C:0.02, G:0.20, T:0.24
Consensus pattern (24 bp):
GTATTAAATGAAAAGAAAATGATT
Found at i:2057205 original size:21 final size:21
Alignment explanation
Indices: 2057176--2057217 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2057166 TAATATAATC
2057176 ATCTCATGTCAAATATTGCCT
1 ATCTCATGTCAAATATTGCCT
* *
2057197 ATCTTATGTCTAATATTGCCT
1 ATCTCATGTCAAATATTGCCT
2057218 GTATAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (21 bp):
ATCTCATGTCAAATATTGCCT
Found at i:2062065 original size:13 final size:13
Alignment explanation
Indices: 2062033--2062104 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
2062023 TAACGTAACC
*
2062033 AATAAAGAT-ATA
1 AATAAATATAATA
2062045 TAATAAATATAATA
1 -AATAAATATAATA
2062059 AATAAAT-T-ATA
1 AATAAATATAATA
* *
2062070 AA-AAATTTAAAA
1 AATAAATATAATA
2062082 AATAAATA-AATA
1 AATAAATATAATA
*
2062094 CAAAAAATATA
1 -AATAAATATA
2062105 TAATTATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
10 4 0.08
11 6 0.12
12 8 0.17
13 26 0.54
14 4 0.08
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (13 bp):
AATAAATATAATA
Found at i:2062075 original size:23 final size:23
Alignment explanation
Indices: 2062043--2062088 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2062033 AATAAAGATA
* *
2062043 TATAATAAATATAATAAATAAAT
1 TATAAAAAATATAAAAAATAAAT
*
2062066 TATAAAAAATTTAAAAAATAAAT
1 TATAAAAAATATAAAAAATAAAT
2062089 AAATACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TATAAAAAATATAAAAAATAAAT
Found at i:2063122 original size:16 final size:15
Alignment explanation
Indices: 2063103--2063167 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 15
2063093 TTTAATTTTT
2063103 AATTTATATTTAAATA
1 AATTT-TATTTAAATA
* *
2063119 AATTTTTACTTAAATT
1 AA-TTTTATTTAAATA
*
2063135 AATTTTAATATAAATTA
1 AATTTT-ATTTAAA-TA
2063152 ATATTTTATTTAAATA
1 A-ATTTTATTTAAATA
2063168 TAAATTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.10
16 19 0.49
17 11 0.28
18 5 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTTATTTAAATA
Found at i:2063176 original size:34 final size:32
Alignment explanation
Indices: 2063103--2063182 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
2063093 TTTAATTTTT
*
2063103 AATTTATATTTAAATAAATTTTTACTTAAATTA
1 AATTTA-ATATAAATAAATTTTTACTTAAATTA
* * *
2063136 ATTTTAATATAAATTAATATTTTATTTAAATATA
1 AATTTAATATAAATAAAT-TTTTACTTAAAT-TA
*
2063170 AATTTAAAATAAA
1 AATTTAATATAAA
2063183 AATTATACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
32 10 0.26
33 16 0.41
34 13 0.33
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
AATTTAATATAAATAAATTTTTACTTAAATTA
Found at i:2063228 original size:22 final size:23
Alignment explanation
Indices: 2063202--2063245 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2063192 ATAAAATTTA
*
2063202 ATTTTATTGAAAT-TATATTAAT
1 ATTTTATTGAAATATAAATTAAT
*
2063224 ATTTTATTTAAATATAAATTAA
1 ATTTTATTGAAATATAAATTAA
2063246 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTTATTGAAATATAAATTAAT
Found at i:2063233 original size:70 final size:71
Alignment explanation
Indices: 2063148--2063297 Score: 230
Period size: 70 Copynumber: 2.1 Consensus size: 71
2063138 TTTAATATAA
* * *
2063148 ATTAATATTTTATTTAAATATAAATTTAAAATAAAAATTATACAATAAAATTTAATTTTATTGAA
1 ATTAATATTTTATTTAAATATAAATTAAAAATAAAAATTATACAATAAAATTCAATTTTATAGAA
2063213 ATTAT-
66 ATTATC
* *
2063218 ATTAATATTTTATTTAAATATAAATTAAAAATAAAAATTATACGATGAAATTCAATTTTATAGAA
1 ATTAATATTTTATTTAAATATAAATTAAAAATAAAAATTATACAATAAAATTCAATTTTATAGAA
*
2063283 GTTATC
66 ATTATC
*
2063289 ATTATTATT
1 ATTAATATT
2063298 CTAATATGAT
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 64 0.89
71 8 0.11
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (71 bp):
ATTAATATTTTATTTAAATATAAATTAAAAATAAAAATTATACAATAAAATTCAATTTTATAGAA
ATTATC
Found at i:2065036 original size:185 final size:185
Alignment explanation
Indices: 2064724--2065090 Score: 671
Period size: 185 Copynumber: 2.0 Consensus size: 185
2064714 TTGTATTTAT
*
2064724 AATATTTATTATTCTTGAGTATTTGTCTTTTCTTCTATACTTCATAATTATGATTATCATATTGA
1 AATATTTATTATTCTTGAGTATTTATCTTTTCTTCTATACTTCATAATTATGATTATCATATTGA
* * *
2064789 TTTAATGTTTGGTACCGCATTTGATTGGTAGGATAATCTATAGCTATTTAGAAAATCAAATCCGT
66 TTTAATATTTGGTACCGCATTTGATTGGTAAGATAATCTATAACTATTTAGAAAATCAAATCCGT
2064854 AATTTTTTGATCGTTCTAATAAAAATGGCAACTAACTTGATTAAGAAGAATTCAC
131 AATTTTTTGATCGTTCTAATAAAAATGGCAACTAACTTGATTAAGAAGAATTCAC
*
2064909 AATATTTATTATTTTTGAGTATTTATCTTTTCTTCTATACTTCATAATTATGATTATCATATTGA
1 AATATTTATTATTCTTGAGTATTTATCTTTTCTTCTATACTTCATAATTATGATTATCATATTGA
*
2064974 TTTAATATTTGGTACTGCATTTGATTGGTAAGATAATCTATAACTATTTAGAAAATCAAATCCGT
66 TTTAATATTTGGTACCGCATTTGATTGGTAAGATAATCTATAACTATTTAGAAAATCAAATCCGT
*
2065039 AATTTTTTGATCGTTCTAATAAAAATGGCTACTAACTTGATTAAGAAGAATT
131 AATTTTTTGATCGTTCTAATAAAAATGGCAACTAACTTGATTAAGAAGAATT
2065091 AATAATCTAA
Statistics
Matches: 175, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
185 175 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (185 bp):
AATATTTATTATTCTTGAGTATTTATCTTTTCTTCTATACTTCATAATTATGATTATCATATTGA
TTTAATATTTGGTACCGCATTTGATTGGTAAGATAATCTATAACTATTTAGAAAATCAAATCCGT
AATTTTTTGATCGTTCTAATAAAAATGGCAACTAACTTGATTAAGAAGAATTCAC
Found at i:2066027 original size:18 final size:19
Alignment explanation
Indices: 2065990--2066036 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
2065980 TTATAATTAA
*
2065990 ATTTAAATAAAAATATATT
1 ATTTAAATTAAAATATATT
*
2066009 ATTTTAATTAAAA-ATATT
1 ATTTAAATTAAAATATATT
2066027 ATTTAAATTA
1 ATTTAAATTA
2066037 GACATAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATTAAAATATATT
Found at i:2066714 original size:15 final size:14
Alignment explanation
Indices: 2066673--2066715 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2066663 CTAATAAATT
*
2066673 TTTAAATATTAAAA
1 TTTAAATATAAAAA
*
2066687 TTTCAA-ATAAAAA
1 TTTAAATATAAAAA
2066700 TTATAAATATAAAAA
1 TT-TAAATATAAAAA
2066715 T
1 T
2066716 GTTATTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAAATATAAAAA
Found at i:2066904 original size:13 final size:13
Alignment explanation
Indices: 2066866--2066961 Score: 71
Period size: 12 Copynumber: 7.5 Consensus size: 13
2066856 CTTTTTGATT
2066866 ATTTAAA-ATATT-
1 ATTTAAATA-ATTA
*
2066878 ATTTATAT-ATTA
1 ATTTAAATAATTA
*
2066890 ATATAAATAATTA
1 ATTTAAATAATTA
2066903 ATTTAAATAA-TA
1 ATTTAAATAATTA
2066915 ATTTAAATTTAATTA
1 ATTTAAA--TAATTA
*
2066930 AATTAAAT--TTAA
1 ATTTAAATAATT-A
2066942 ATTTAAAT-ATTA
1 ATTTAAATAATTA
2066954 TATTTAAA
1 -ATTTAAA
2066962 ATCTTATTCA
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
11 5 0.07
12 30 0.43
13 23 0.33
14 3 0.04
15 8 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAATAATTA
Found at i:2067436 original size:2 final size:2
Alignment explanation
Indices: 2067429--2067486 Score: 71
Period size: 2 Copynumber: 28.5 Consensus size: 2
2067419 TAAATAAATC
* * * *
2067429 AT AT AT AT AT AT AT AT AT AT AT AA AT AG AA AGT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
2067472 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2067487 AAGATTGGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2068114 original size:16 final size:16
Alignment explanation
Indices: 2068089--2068120 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2068079 TAATAATGTT
2068089 AATTAAAATAAAATAA
1 AATTAAAATAAAATAA
*
2068105 AATTATAATAAAATAA
1 AATTAAAATAAAATAA
2068121 TTATTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATTAAAATAAAATAA
Found at i:2068544 original size:23 final size:22
Alignment explanation
Indices: 2068513--2068558 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2068503 TTTAAAAATT
* *
2068513 ATTTTTAATTAATATTTATATAA
1 ATTTATAATTAA-ATTTAAATAA
2068536 ATTTATAATTAAATTTAAATAA
1 ATTTATAATTAAATTTAAATAA
2068558 A
1 A
2068559 AATATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTATAATTAAATTTAAATAA
Found at i:2069686 original size:12 final size:13
Alignment explanation
Indices: 2069641--2069687 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2069631 GTTACATATT
2069641 TATATAAATTTTGA
1 TATATAAATTTT-A
*
2069655 TATATTAATTTATA
1 TATATAAATTT-TA
2069669 TTATATAAATTTTA
1 -TATATAAATTTTA
2069683 -ATATA
1 TATATA
2069688 TTCATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 5 0.17
14 13 0.45
15 11 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TATATAAATTTTA
Found at i:2069689 original size:19 final size:20
Alignment explanation
Indices: 2069665--2069751 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 20
2069655 TATATTAATT
2069665 TATATTATATA-AATTTTAA
1 TATATTATATATAATTTTAA
*
2069684 TATATTCATATATTAATATTGTAC
1 TATATT-ATATA-TAAT-TT-TAA
* *
2069708 TCATATT-TATATTATTTT-T
1 T-ATATTATATATAATTTTAA
2069727 TATATTATATA-ATATTTTAA
1 TATATTATATATA-ATTTTAA
2069747 T-TATT
1 TATATT
2069752 TTATTACATC
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
18 5 0.09
19 20 0.37
20 7 0.13
21 2 0.04
22 6 0.11
23 6 0.11
24 3 0.06
25 5 0.09
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (20 bp):
TATATTATATATAATTTTAA
Found at i:2069695 original size:27 final size:27
Alignment explanation
Indices: 2069624--2069698 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 27
2069614 AATATTCATA
*
2069624 TTAATATGTTACATAT-TTATATAAATT
1 TTAATATATT-CATATATTATATAAATT
* *
2069651 TTGATATATTAATTTATATTATATAAATT
1 TTAATATATTCA--TATATTATATAAATT
2069680 TTAATATATTCATATATTA
1 TTAATATATTCATATATTA
2069699 ATATTGTACT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 1 0.03
27 15 0.38
28 3 0.08
29 21 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (27 bp):
TTAATATATTCATATATTATATAAATT
Found at i:2069745 original size:29 final size:30
Alignment explanation
Indices: 2069640--2069768 Score: 92
Period size: 29 Copynumber: 4.3 Consensus size: 30
2069630 TGTTACATAT
* *
2069640 TTATATAA-ATTTTGATATATTAAT-TTATA
1 TTATATAATATTTTAAT-TATTATTATTATA
2069669 TTATATAA-ATTTTAATATATTCATATATTAATA
1 TTATATAATATTTTAAT-TATT-AT-TATT-ATA
* *
2069702 TTGTACTCATA-TTTATATTATT-TT-TTATA
1 TTATA-TAATATTTTA-ATTATTATTATTATA
*
2069731 TTATATAATATTTTAATTATT-TTATTACA
1 TTATATAATATTTTAATTATTATTATTATA
*
2069760 TCATATAAT
1 TTATATAAT
2069769 TATATTATGT
Statistics
Matches: 83, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
28 12 0.14
29 43 0.52
30 3 0.04
31 2 0.02
32 3 0.04
33 7 0.08
34 10 0.12
35 3 0.04
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (30 bp):
TTATATAATATTTTAATTATTATTATTATA
Found at i:2070284 original size:19 final size:20
Alignment explanation
Indices: 2070240--2070303 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
2070230 GATTGATTCC
* *
2070240 AATTTAAATATATATTTTATT
1 AATTTGAATAT-TATTTGATT
2070261 AATTTGAAT-TTATTTGATT
1 AATTTGAATATTATTTGATT
* *
2070280 GATTTGAATCATTATTTGAAT
1 AATTTGAAT-ATTATTTGATT
2070301 AAT
1 AAT
2070304 ATAAAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.44
20 1 0.03
21 19 0.53
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (20 bp):
AATTTGAATATTATTTGATT
Found at i:2071480 original size:21 final size:22
Alignment explanation
Indices: 2071438--2071478 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2071428 TAAGTATTAA
*
2071438 ATATAATTAA-TTAATAAAAAT
1 ATATATTTAATTTAATAAAAAT
2071459 ATATATTTAATTTAATAAAA
1 ATATATTTAATTTAATAAAA
2071479 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATTTAATTTAATAAAAAT
Found at i:2072758 original size:32 final size:31
Alignment explanation
Indices: 2072722--2072813 Score: 73
Period size: 32 Copynumber: 2.8 Consensus size: 31
2072712 TTTACCACTT
2072722 TTTTTATTTTTATAATTTTCCTT-TTTTTAATA
1 TTTTTATTTTTATAATTTT--TTATTTTTAATA
* *
2072754 TTTTT-GTTTTAAAATATTTTTAATTTTTAATA
1 TTTTTATTTTTATAAT-TTTTT-ATTTTTAATA
2072786 TATTTTATTTATT-TAATTTCTTTTATTT
1 T-TTTTATTT-TTATAA-TT-TTTTATTT
2072814 AAAATGTTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
30 2 0.04
31 8 0.17
32 18 0.38
33 4 0.08
34 9 0.19
35 7 0.15
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (31 bp):
TTTTTATTTTTATAATTTTTTATTTTTAATA
Found at i:2072800 original size:18 final size:17
Alignment explanation
Indices: 2072747--2072814 Score: 59
Period size: 16 Copynumber: 4.0 Consensus size: 17
2072737 TTTTCCTTTT
*
2072747 TTTAATATTTTTGTTT-
1 TTTAATATTTTTATTTA
** *
2072763 TAAAATATTTTTAATT-
1 TTTAATATTTTTATTTA
2072779 TTTAATATATTTTATTTA
1 TTTAATAT-TTTTATTTA
*
2072797 TTTAATTTCTTTTATTTA
1 TTTAATAT-TTTTATTTA
2072815 AAATGTTGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
16 18 0.44
17 7 0.17
18 16 0.39
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (17 bp):
TTTAATATTTTTATTTA
Found at i:2073061 original size:23 final size:23
Alignment explanation
Indices: 2073035--2073104 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
2073025 TCAATATACA
*
2073035 TATTTTATTATTAATTTTAATTT
1 TATTATATTATTAATTTTAATTT
* *
2073058 TATTATAATAATAA--TTAATTT
1 TATTATATTATTAATTTTAATTT
* *
2073079 TATTATATTATTATTTTTAATCT
1 TATTATATTATTAATTTTAATTT
2073102 TAT
1 TAT
2073105 CAATGTCTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 18 0.47
23 20 0.53
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATATTATTAATTTTAATTT
Found at i:2073075 original size:21 final size:19
Alignment explanation
Indices: 2073036--2073086 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
2073026 CAATATACAT
*
2073036 ATTTTATTAT-TAATTTTA
1 ATTTTATTATATAATATTA
2073054 ATTTTATTATAATAATAATTA
1 ATTTTATTAT-ATAAT-ATTA
2073075 ATTTTATTATAT
1 ATTTTATTATAT
2073087 TATTATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 10 0.34
20 6 0.21
21 13 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATTATATAATATTA
Found at i:2076546 original size:36 final size:36
Alignment explanation
Indices: 2076471--2076547 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
2076461 GTGTAAATAA
* * * *
2076471 ATTTTTTTAATTTAATTCAATTTAATCTCAATAATT
1 ATTTTTTAAATTTAATTAAATTTAATATCAAGAATT
2076507 ATTTTTTAAATTTAATATAAATATTAATAT-AAGAA-T
1 ATTTTTTAAATTTAAT-TAAAT-TTAATATCAAGAATT
2076543 ATTTT
1 ATTTT
2076548 AATTTTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 21 0.60
37 8 0.23
38 6 0.17
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (36 bp):
ATTTTTTAAATTTAATTAAATTTAATATCAAGAATT
Found at i:2079735 original size:15 final size:16
Alignment explanation
Indices: 2079712--2079742 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2079702 ATTTTATTAA
2079712 TTATCTAAAAATTATT
1 TTATCTAAAAATTATT
2079728 TTAT-TAAAAATTATT
1 TTATCTAAAAATTATT
2079743 AAATTACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATCTAAAAATTATT
Found at i:2082153 original size:46 final size:47
Alignment explanation
Indices: 2082061--2082153 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
2082051 TGTTTTATTC
* *
2082061 TGTTACCAACAATAGAGGCATTATAAAAATATTATATTAAATTAATT
1 TGTTACCAACAACAGAGGCATCATAAAAATATTATATTAAATTAATT
*
2082108 TGTTACCAACAACAGAGGCATCAT-AAAATATTATATTAGATTAATT
1 TGTTACCAACAACAGAGGCATCATAAAAATATTATATTAAATTAATT
2082154 GTTCATGTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 21 0.49
47 22 0.51
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (47 bp):
TGTTACCAACAACAGAGGCATCATAAAAATATTATATTAAATTAATT
Found at i:2083427 original size:26 final size:26
Alignment explanation
Indices: 2083391--2083451 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
2083381 CATTCCTCAT
2083391 CTAAGCACATAATTGCTTTGTTGTAC
1 CTAAGCACATAATTGCTTTGTTGTAC
2083417 CTAAGCACATAATTGCTTTGTTGTAC
1 CTAAGCACATAATTGCTTTGTTGTAC
2083443 CTAAGCACA
1 CTAAGCACA
2083452 CTGCATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (26 bp):
CTAAGCACATAATTGCTTTGTTGTAC
Found at i:2084311 original size:2 final size:2
Alignment explanation
Indices: 2084304--2084337 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2084294 ACATACATAC
2084304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2084338 CCAGAAGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2087173 original size:20 final size:20
Alignment explanation
Indices: 2087148--2087188 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2087138 AATTTAATAT
2087148 TAATATTAATATTATTTATA
1 TAATATTAATATTATTTATA
*
2087168 TAATATTACTATTATTTATA
1 TAATATTAATATTATTTATA
2087188 T
1 T
2087189 TTATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATATTAATATTATTTATA
Found at i:2087304 original size:37 final size:43
Alignment explanation
Indices: 2087208--2087304 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 43
2087198 TTTAATTTAA
* *
2087208 ATAAAATATAATTTTTAAATTTTATTGAAATTTATTTATATTT
1 ATAAAATATAATTTTTAAATTATATTGAAATTAATTTATATTT
*
2087251 ATAAATATATAA--TTTAAA-TAT-TTG-TA-TAATTTAT-TTT
1 ATAAA-ATATAATTTTTAAATTATATTGAAATTAATTTATATTT
2087288 -TAAAATATAATTTTTAA
1 ATAAAATATAATTTTTAA
2087305 TAATTTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
35 6 0.12
36 4 0.08
37 8 0.17
38 7 0.15
39 1 0.02
40 3 0.06
41 2 0.04
42 6 0.12
43 5 0.10
44 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (43 bp):
ATAAAATATAATTTTTAAATTATATTGAAATTAATTTATATTT
Found at i:2088273 original size:2 final size:2
Alignment explanation
Indices: 2088266--2088301 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2088256 GATTAATTGT
2088266 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2088302 GAGTAAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2088501 original size:22 final size:24
Alignment explanation
Indices: 2088454--2088501 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
2088444 ATTATTTAAC
2088454 ATAATTTTAATTATTATTCATAAAT
1 ATAATTTTAATTA-TATTCATAAAT
*
2088479 ATAATTTTAA-TA-ATTTATAAAT
1 ATAATTTTAATTATATTCATAAAT
2088501 A
1 A
2088502 AATCTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
24 2 0.09
25 10 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAATTTTAATTATATTCATAAAT
Found at i:2088503 original size:26 final size:25
Alignment explanation
Indices: 2088454--2088504 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2088444 ATTATTTAAC
* **
2088454 ATAATTTTAATTATTATTCATAAAT
1 ATAATTTTAATAATTATAAATAAAT
2088479 ATAATTTTAATAATTTATAAATAAAT
1 ATAATTTTAATAA-TTATAAATAAAT
2088505 CTTATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
ATAATTTTAATAATTATAAATAAAT
Found at i:2088883 original size:18 final size:20
Alignment explanation
Indices: 2088860--2088939 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
2088850 TATATCGTGT
2088860 TTATATTTT-T-TATTATAA
1 TTATATTTTATATATTATAA
2088878 TTATATTTTATATATTAT-A
1 TTATATTTTATATATTATAA
* *
2088897 TATAAATTTAGATATATTAATAA
1 T-TATATTT-TATATATT-ATAA
* *
2088920 TT-TATATTATATATTTTAA
1 TTATATTTTATATATTATAA
2088939 T
1 T
2088940 ACAATCATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
18 9 0.18
19 7 0.14
20 19 0.38
21 10 0.20
22 3 0.06
23 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
TTATATTTTATATATTATAA
Found at i:2089703 original size:17 final size:17
Alignment explanation
Indices: 2089683--2089723 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2089673 TTTAAATTAA
*
2089683 TATTAT-TTTTATATCAT
1 TATTATATTTAATAT-AT
2089700 TATTATATTTAATATAT
1 TATTATATTTAATATAT
2089717 TATTATA
1 TATTATA
2089724 ACAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTATATTTAATATAT
Found at i:2094007 original size:29 final size:29
Alignment explanation
Indices: 2093974--2094029 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2093964 TACATTATAG
2093974 TAAATAAAATATTTTAATTTTTATATTAT
1 TAAATAAAATATTTTAATTTTTATATTAT
** *
2094003 TAAATTTAGTATTTTAATTTTTATATT
1 TAAATAAAATATTTTAATTTTTATATT
2094030 TTTTAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TAAATAAAATATTTTAATTTTTATATTAT
Found at i:2094010 original size:14 final size:14
Alignment explanation
Indices: 2093982--2094031 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
2093972 AGTAAATAAA
*
2093982 ATATTTTAATTTTT
1 ATATTTTAATATTT
2093996 ATATTATTAA-ATTT
1 ATATT-TTAATATTT
*
2094010 AGTATTTTAATTTTT
1 A-TATTTTAATATTT
2094025 ATATTTT
1 ATATTTT
2094032 TTAAATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
ATATTTTAATATTT
Found at i:2094032 original size:15 final size:15
Alignment explanation
Indices: 2093985--2094032 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2093975 AAATAAAATA
2093985 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
* *
2094000 TATTAA-ATTTAGTA-
1 TTTTAATTTTTA-TAT
2094014 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
2094029 TTTT
1 TTTT
2094033 TAAATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTAATTTTTATAT
Found at i:2095300 original size:4 final size:4
Alignment explanation
Indices: 2095291--2095322 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
2095281 GAAACAGAGC
*
2095291 TTAT TTAT TTAT TTAT TTAT TGAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
2095323 AGATTCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:2095308 original size:12 final size:12
Alignment explanation
Indices: 2095291--2095327 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2095281 GAAACAGAGC
*
2095291 TTATTTATTTAT
1 TTATTTATTGAT
2095303 TTATTTATTGAT
1 TTATTTATTGAT
*
2095315 TTATTTATAGAT
1 TTATTTATTGAT
2095327 T
1 T
2095328 CTAAATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:2096291 original size:20 final size:20
Alignment explanation
Indices: 2096266--2096304 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2096256 TGTAAAGTAA
2096266 TATTTATTT-TATTTATTTAT
1 TATTTATTTATATTT-TTTAT
2096286 TATTTATTTATATTTTTTA
1 TATTTATTTATATTTTTTA
2096305 CTATACCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTTATTTATATTTTTTAT
Found at i:2096574 original size:19 final size:19
Alignment explanation
Indices: 2096538--2096587 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2096528 TGATATCACG
* **
2096538 AATTAAATAATATTAAATT
1 AATTAAAAAATAAAAAATT
2096557 AATTAAAAAATAAAAAATT
1 AATTAAAAAATAAAAAATT
*
2096576 ATATTATAAAAT
1 A-ATTAAAAAAT
2096588 CTAAATAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTAAAAAATAAAAAATT
Found at i:2096760 original size:18 final size:17
Alignment explanation
Indices: 2096737--2096770 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2096727 TTTACCTGTA
*
2096737 TTTATTTATGTTTTATAT
1 TTTATTAAT-TTTTATAT
2096755 TTTATTAATTTTTATA
1 TTTATTAATTTTTATA
2096771 AATGTATCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTATTAATTTTTATAT
Found at i:2097931 original size:17 final size:17
Alignment explanation
Indices: 2097904--2097943 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2097894 TCATTGTGCT
*
2097904 TACATATATGAAAATGA
1 TACAAATATGAAAATGA
*
2097921 TCCAAATATGAAAATGA
1 TACAAATATGAAAATGA
2097938 TACAAA
1 TACAAA
2097944 GAACATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (17 bp):
TACAAATATGAAAATGA
Found at i:2100161 original size:19 final size:19
Alignment explanation
Indices: 2100139--2100177 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2100129 GATAATAAAT
* *
2100139 ATTAATTATTTTATTAGTA
1 ATTAATAATTTTATAAGTA
2100158 ATTAATAATTTTATAAGTA
1 ATTAATAATTTTATAAGTA
2100177 A
1 A
2100178 ACATCATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTAATAATTTTATAAGTA
Found at i:2100942 original size:20 final size:19
Alignment explanation
Indices: 2100905--2100943 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2100895 ATATATATTT
2100905 TTTAAAAATAAAAAATTAA
1 TTTAAAAATAAAAAATTAA
*
2100924 TTTATAAATAAATAAATTAA
1 TTTAAAAATAAA-AAATTAA
2100944 GTCATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTAAAAATAAAAAATTAA
Found at i:2105310 original size:17 final size:17
Alignment explanation
Indices: 2105290--2105323 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2105280 TTTAGTGTAG
2105290 GAAATGATGATTTTATA
1 GAAATGATGATTTTATA
2105307 GAAATGATGATTTTATA
1 GAAATGATGATTTTATA
2105324 TGAGGACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
GAAATGATGATTTTATA
Found at i:2107975 original size:17 final size:17
Alignment explanation
Indices: 2107939--2107971 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2107929 AATTTATATA
*
2107939 ATTTTTATATAATTAAT
1 ATTTTAATATAATTAAT
2107956 ATTTTAATA-AATTAAT
1 ATTTTAATATAATTAAT
2107972 TATTAGATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATATAATTAAT
Found at i:2110723 original size:17 final size:18
Alignment explanation
Indices: 2110686--2110725 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2110676 ATTATTATTG
*
2110686 AAAAGAATTTAGATTTGA
1 AAAAAAATTTAGATTTGA
*
2110704 AAAAAAATTTGGATTT-A
1 AAAAAAATTTAGATTTGA
2110721 AAAAA
1 AAAAA
2110726 GTTATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (18 bp):
AAAAAAATTTAGATTTGA
Found at i:2111450 original size:2 final size:2
Alignment explanation
Indices: 2111443--2111468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2111433 CAAACACAAC
2111443 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2111469 GTAGTTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2116053 original size:197 final size:195
Alignment explanation
Indices: 2115589--2116174 Score: 691
Period size: 197 Copynumber: 3.0 Consensus size: 195
2115579 AATATTATAG
* * *
2115589 AATACGTGAAAGTTGATAAACTCATTACAGTTTATAATATTCATAAATATAAAAATCGATAAGTA
1 AATACGTGTAAGTCGATAAACTCATTACAGTTTATAATATTCATAAATATAAAGATCGATAAGTA
* * * * *
2115654 CAGTAAACAATAACTTAATTCAATAA-ATATAAT-AGAATACGTGTACGTCGTTAAACTTATTAT
66 CAGTAAACGATAAATTAATTCAATAATATATAATGA-AATACGTGTA-ATCGATAAACTCATTAT
* * * * * *
2115717 AATTGTCAATAATAATAAATATGTAAACTAACAAATCTAAAAGT-A-ACA--AACTCAACAATAT
129 AATT-TTAATAATCATAAATATGTAAACTAACAAATATAAAAATAATAAATTAACTTAACAATAT
2115778 AGAA
193 A-AA
* * ** * ***
2115782 AACACGTGTAAGTCGATAAACTCATTATAACTTATGATATTCATAAATATGGTGATCGATAAGTA
1 AATACGTGTAAGTCGATAAACTCATTACAGTTTATAATATTCATAAATATAAAGATCGATAAGTA
* * * * ** *
2115847 CAATAAACGACAAATTAATTTAACAATATATAATGAAATACGTGTGAAAAGATAAACCCATTATA
66 CAGTAAACGATAAATTAATTCAATAATATATAATGAAATACGTGT-AATCGATAAACTCATTATA
2115912 ATATTTAATAATCATAAATATGTAAACTAACAAATATAAAAATAATAAATTAACTTAACAATATA
130 AT-TTTAATAATCATAAATATGTAAACTAACAAATATAAAAATAATAAATTAACTTAACAATATA
2115977 AA
194 AA
* * *
2115979 AATACGTGTAAGTCGATAAACTCAATACGGTTTATAATATTCATAAATATAAAGATCGATAAATA
1 AATACGTGTAAGTCGATAAACTCATTACAGTTTATAATATTCATAAATATAAAGATCGATAAGTA
**
2116044 CAGTAAACGATAAATTAATTCAATAATATATAATGAAATATATGTAAGTCGATAAACTCATTATA
66 CAGTAAACGATAAATTAATTCAATAATATATAATGAAATACGTGTAA-TCGATAAACTCATTATA
* * * * *
2116109 ATTTTTAATAA-CTATAAATATATAAACTGATAAATATACAAATAATAAATTAATTTAACAATAT
130 A-TTTTAATAATC-ATAAATATGTAAACTAACAAATATAAAAATAATAAATTAACTTAACAATAT
2116173 AA
193 AA
2116175 TGAAAGCACG
Statistics
Matches: 328, Mismatches: 54, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
193 74 0.23
194 65 0.20
195 4 0.01
196 5 0.02
197 166 0.51
198 14 0.04
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (195 bp):
AATACGTGTAAGTCGATAAACTCATTACAGTTTATAATATTCATAAATATAAAGATCGATAAGTA
CAGTAAACGATAAATTAATTCAATAATATATAATGAAATACGTGTAATCGATAAACTCATTATAA
TTTTAATAATCATAAATATGTAAACTAACAAATATAAAAATAATAAATTAACTTAACAATATAAA
Found at i:2116118 original size:101 final size:98
Alignment explanation
Indices: 2115589--2116179 Score: 312
Period size: 101 Copynumber: 6.0 Consensus size: 98
2115579 AATATTATAG
* * * * * *
2115589 AATACGTGAAAGTTGATAAACTCATTACAGTTTATAATATTCATAAATATAAAAATCGATAAGTA
1 AATACGTGTAAGTCGATAAACTCATTATAATTTATAATATTCATAAATATAAAGATCGATAAATA
* *
2115654 CAGTAAACAATAACTTAATTCAATAA-ATATAAT-A
66 CA-TAAACGATAAATTAATT-AA-AATATATAATGA
* * * * * * * * *
2115688 GAATACGTGTACGTCGTTAAACTTATTATAATTGT-CAATAATAATAAATATGTAA-A-CTAACA
1 -AATACGTGTAAGTCGATAAACTCATTATAATT-TATAATATTCATAAATAT-AAAGATC-GATA
* * *
2115750 AAT-C-TAAAAG-TAACA--AACTCAACA-ATAT-A-GAA
62 AATACATAAACGATAA-ATTAA-TTAAAATATATAATG-A
* * * *** *
2115782 AACACGTGTAAGTCGATAAACTCATTATAACTTATGATATTCATAAATATGGTGATCGATAAGTA
1 AATACGTGTAAGTCGATAAACTCATTATAATTTATAATATTCATAAATATAAAGATCGATAAATA
*
2115847 CAATAAACGACAAATTAATTTAACAATATATAATGA
66 C-ATAAACGATAAATTAA-TTAA-AATATATAATGA
** * * * * *
2115883 AATACGTGTGAA-AAGATAAACCCATTATAATATT-TAATAATCATAAATATGTAA-A-CTAACA
1 AATACGTGT-AAGTCGATAAACTCATTATAAT-TTATAATATTCATAAATAT-AAAGATC-GATA
* * ** *
2115944 AATATAAAAATAATAAATTAACTTAACA-ATATAA--A
62 AATACATAAACGATAAATTAA-TTAAAATATATAATGA
* ***
2115979 AATACGTGTAAGTCGATAAACTCAATACGGTTTATAATATTCATAAATATAAAGATCGATAAATA
1 AATACGTGTAAGTCGATAAACTCATTATAATTTATAATATTCATAAATATAAAGATCGATAAATA
2116044 CAGTAAACGATAAATTAATTCAATAATATATAATGA
66 CA-TAAACGATAAATTAATT-AA-AATATATAATGA
** * *
2116080 AATATATGTAAGTCGATAAACTCATTATAATTTTTAATA-ACTATAAATATATAA-A-CTGATAA
1 AATACGTGTAAGTCGATAAACTCATTATAATTTATAATATTC-ATAAATATA-AAGATC-GATAA
* * ** *
2116142 ATATACAAATAATAAATTAATTTAACA-ATATAATGA
63 ATACATAAACGATAAATTAA-TTAAAATATATAATGA
2116178 AA
1 AA
2116180 GCACGAATAA
Statistics
Matches: 365, Mismatches: 88, Indels: 78
0.69 0.17 0.15
Matches are distributed among these distances:
92 1 0.00
93 45 0.12
94 8 0.02
95 10 0.03
96 57 0.16
97 21 0.06
98 23 0.06
99 11 0.03
100 80 0.22
101 102 0.28
102 7 0.02
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (98 bp):
AATACGTGTAAGTCGATAAACTCATTATAATTTATAATATTCATAAATATAAAGATCGATAAATA
CATAAACGATAAATTAATTAAAATATATAATGA
Found at i:2116601 original size:16 final size:15
Alignment explanation
Indices: 2116580--2116618 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2116570 AATTTTAACT
*
2116580 TATTTTTTAAATATTA
1 TATTTTTTAAA-AATA
2116596 TATTTTTTAAAAATA
1 TATTTTTTAAAAATA
2116611 -ATTTTTTA
1 TATTTTTTA
2116619 TCGATAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 3 0.14
16 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTTTAAAAATA
Found at i:2117744 original size:1 final size:1
Alignment explanation
Indices: 2117738--2117769 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
2117728 AATTTGAGAG
*
2117738 TTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2117770 CAGTCGGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:2121835 original size:84 final size:84
Alignment explanation
Indices: 2121731--2121896 Score: 269
Period size: 84 Copynumber: 2.0 Consensus size: 84
2121721 TATAAGCCGG
* * *
2121731 TAAAGAGGAAAAAGATCTACATCAAAACATGCTTCACTAAAAACAACTCATGTAACTGACACCAA
1 TAAAGAGGAAAAACATCTACATCAAAACATGCTTCACTAAAAACAACTCATGTAACTAACAACAA
2121796 CTAATTGGGTGTCAATGTA
66 CTAATTGGGTGTCAATGTA
* * *
2121815 TAAAGAGGGAAAACATCTACATCAACACGTGCTTCACTAAAAACAACTCATGTAACTAACAACAA
1 TAAAGAGGAAAAACATCTACATCAAAACATGCTTCACTAAAAACAACTCATGTAACTAACAACAA
*
2121880 CTAATTTGGTGTCAATG
66 CTAATTGGGTGTCAATG
2121897 CTTGCATGAG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (84 bp):
TAAAGAGGAAAAACATCTACATCAAAACATGCTTCACTAAAAACAACTCATGTAACTAACAACAA
CTAATTGGGTGTCAATGTA
Found at i:2128583 original size:41 final size:41
Alignment explanation
Indices: 2128538--2128618 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
2128528 GTAGCTAGGC
* * *
2128538 TCAAATGTAGAGGCAAATCAAACTGTAAGATA-TTGGTAGAA
1 TCAAAGGTAGAAGCAAATCAAACTATAAGA-AGTTGGTAGAA
* *
2128579 TCAAAGGTGGAAGCAAATCAAATTATAAGAAGTTGGTAGA
1 TCAAAGGTAGAAGCAAATCAAACTATAAGAAGTTGGTAGA
2128619 CGAATGGTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.23
Consensus pattern (41 bp):
TCAAAGGTAGAAGCAAATCAAACTATAAGAAGTTGGTAGAA
Found at i:2129862 original size:2 final size:2
Alignment explanation
Indices: 2129857--2129885 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2129847 AGATAATATA
2129857 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2129886 ATACACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2132146 original size:32 final size:32
Alignment explanation
Indices: 2132081--2132152 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
2132071 CAAAGAAAAA
* *
2132081 TATATAA-GTTTTTAATTTTATTTTAAAATTT
1 TATATAATTTTTTTAATATTATTTTAAAATTT
*
2132112 TATTTAATTTTTTTAATATT-TTTTACTAAA-TT
1 TATATAATTTTTTTAATATTATTTTA--AAATTT
2132144 TATATAATT
1 TATATAATT
2132153 GTACTCATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
31 11 0.32
32 20 0.59
33 3 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (32 bp):
TATATAATTTTTTTAATATTATTTTAAAATTT
Found at i:2132402 original size:11 final size:11
Alignment explanation
Indices: 2132386--2132411 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2132376 TTTTGAGAAA
2132386 AAATTAAAAAT
1 AAATTAAAAAT
2132397 AAATTAAAAAT
1 AAATTAAAAAT
2132408 AAAT
1 AAAT
2132412 GAGTGTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATTAAAAAT
Found at i:2133562 original size:24 final size:25
Alignment explanation
Indices: 2133535--2133591 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
2133525 TTTAAATATC
2133535 AAATTATAAAATTACT-TA-TAATTT
1 AAATTATAAAATTA-TATATTAATTT
* *
2133559 AAA-TATCAATTTATATATTAATTT
1 AAATTATAAAATTATATATTAATTT
2133583 AAATTATAA
1 AAATTATAA
2133592 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.04
23 10 0.37
24 12 0.44
25 4 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTATAAAATTATATATTAATTT
Found at i:2134115 original size:23 final size:22
Alignment explanation
Indices: 2134071--2134118 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
2134061 TTTAAATAAT
*
2134071 AAATTTATTAAATTTAATTATA
1 AAATATATTAAATTTAATTATA
2134093 AAATATATATAAATATTAA-TATA
1 AAATATAT-TAAAT-TTAATTATA
2134116 AAA
1 AAA
2134119 ATTTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 12 0.52
24 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATATATTAAATTTAATTATA
Found at i:2134119 original size:24 final size:22
Alignment explanation
Indices: 2134060--2134120 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
2134050 TTGAATTATT
*
2134060 ATTTAA-ATAATAAATTTATTAA
1 ATTTAATATAA-AAATATATTAA
2134082 ATTTAAT-TATAAAATATATATAA
1 ATTTAATATA-AAAATATAT-TAA
2134105 ATATTAATATAAAAAT
1 AT-TTAATATAAAAAT
2134121 TTTATATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 15 0.45
23 6 0.18
24 10 0.30
25 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAATATAAAAATATATTAA
Found at i:2134140 original size:29 final size:29
Alignment explanation
Indices: 2134095--2134150 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
2134085 TAATTATAAA
2134095 ATATATATAAATATTAATATAA-AAATTTT
1 ATATATATAAATATTAA-ATAATAAATTTT
*
2134124 ATATATTTATAAT-TTAAATAATAAATT
1 ATATATATA-AATATTAAATAATAAATT
2134151 AGATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 17 0.71
30 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATATATAAATATTAAATAATAAATTTT
Found at i:2135461 original size:21 final size:20
Alignment explanation
Indices: 2135420--2135462 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2135410 ATTTAATACA
2135420 ATATTATTATTATAAATAGT
1 ATATTATTATTATAAATAGT
*
2135440 ATATTCATTAATTTTAAA-AGT
1 ATATT-ATT-ATTATAAATAGT
2135461 AT
1 AT
2135463 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 8 0.40
22 7 0.35
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
ATATTATTATTATAAATAGT
Found at i:2136021 original size:2 final size:2
Alignment explanation
Indices: 2136008--2136041 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2135998 AACACCTCAA
*
2136008 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2136042 GAATATTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2136123 original size:2 final size:2
Alignment explanation
Indices: 2136116--2136162 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2136106 TTTGATTATC
2136116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2136158 TA TA T
1 TA TA T
2136163 GAACATAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2137647 original size:21 final size:21
Alignment explanation
Indices: 2137627--2137665 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2137617 AATAAATATT
2137627 TTATTT-TTA-ATTTATAATA
1 TTATTTATTATATTTATAATA
2137646 TTATTTATTATATTTATAAT
1 TTATTTATTATATTTATAAT
2137666 TATAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTTATTATATTTATAATA
Found at i:2140219 original size:26 final size:24
Alignment explanation
Indices: 2140189--2140241 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 24
2140179 ATATTATATT
2140189 AATATTTATAATTATATTTAAATAA-A
1 AATATTT-TAA-T-TATTTAAATAATA
*
2140215 AATATTTTTATTATTTAAATAATA
1 AATATTTTAATTATTTAAATAATA
2140239 AAT
1 AAT
2140242 CAGAATGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 11 0.44
24 5 0.20
25 2 0.08
26 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATTTTAATTATTTAAATAATA
Found at i:2140882 original size:2 final size:2
Alignment explanation
Indices: 2140875--2140921 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2140865 GCAATAATTG
*
2140875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2140917 AT AT A
1 AT AT A
2140922 GTAAACACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2141633 original size:11 final size:11
Alignment explanation
Indices: 2141619--2141664 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
2141609 TATTATTAAA
2141619 ATATTAATTTT
1 ATATTAATTTT
2141630 ATATTAATATTT
1 ATATTAAT-TTT
2141642 ATA-T-ATTTT
1 ATATTAATTTT
2141651 ATAATTAAATTTT
1 AT-ATT-AATTTT
2141664 A
1 A
2141665 ATAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 10 0.33
12 6 0.20
13 6 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:2141636 original size:19 final size:21
Alignment explanation
Indices: 2141612--2141659 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
2141602 TTTATTATAT
2141612 TATTAAAATAT-TA-ATTTTA
1 TATTAAAATATATATATTTTA
* *
2141631 TATTAATATTTATATATTTTA
1 TATTAAAATATATATATTTTA
2141652 TAATTAAA
1 T-ATTAAA
2141660 TTTTAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 7 0.30
22 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTAAAATATATATATTTTA
Found at i:2142529 original size:2 final size:2
Alignment explanation
Indices: 2142522--2142556 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2142512 CAGCATAGTG
2142522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2142557 GTATTTATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2145439 original size:16 final size:17
Alignment explanation
Indices: 2145413--2145454 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2145403 GAATTAAATT
* *
2145413 TTATAAATTAATTTAAA
1 TTATTAATTAATATAAA
*
2145430 TT-TTAATTAATATACA
1 TTATTAATTAATATAAA
2145446 TTATTAATT
1 TTATTAATT
2145455 TTATTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATTAATTAATATAAA
Found at i:2148668 original size:2 final size:2
Alignment explanation
Indices: 2148661--2148702 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2148651 TTCATGTACA
2148661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2148703 TATCCCTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2149795 original size:23 final size:23
Alignment explanation
Indices: 2149751--2149798 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2149741 TTTATATTTA
* * *
2149751 ATATATTATTAGTGTATAAAATT
1 ATATATTATAAATGAATAAAATT
*
2149774 ATATATTATAAATGAATCAAATT
1 ATATATTATAAATGAATAAAATT
2149797 AT
1 AT
2149799 GAAATTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (23 bp):
ATATATTATAAATGAATAAAATT
Found at i:2150282 original size:2 final size:2
Alignment explanation
Indices: 2150275--2150301 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2150265 GGATGGCTTT
2150275 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2150302 CGCAAAGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2150564 original size:15 final size:15
Alignment explanation
Indices: 2150533--2150589 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
2150523 TTCATCATAA
* *
2150533 ATAAAATAATTAAAT
1 ATAAAATAAATATAT
2150548 ATAAAATAAATATAT
1 ATAAAATAAATATAT
*
2150563 ATTTAAA-AAAT-TAT
1 A-TAAAATAAATATAT
*
2150577 ATAATATAAATAT
1 ATAAAATAAATAT
2150590 TTTAAATATG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.09
14 8 0.24
15 19 0.56
16 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAATAAATATAT
Found at i:2153114 original size:9 final size:9
Alignment explanation
Indices: 2153100--2153134 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
2153090 ATTCAGTAAC
2153100 ATAATAATG
1 ATAATAATG
*
2153109 ATAATAATA
1 ATAATAATG
2153118 ATAATAATG
1 ATAATAATG
2153127 ATAATAAT
1 ATAATAAT
2153135 TTTTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (9 bp):
ATAATAATG
Found at i:2153145 original size:3 final size:3
Alignment explanation
Indices: 2153100--2153134 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2153090 ATTCAGTAAC
* *
2153100 ATA ATA ATG ATA ATA ATA ATA ATA ATG ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2153135 TTTTTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2154595 original size:19 final size:20
Alignment explanation
Indices: 2154540--2154600 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
2154530 TTAATTATTG
2154540 AATATAAATTCATATTTATTATA
1 AATAT-AATT-ATATTT-TTATA
* *
2154563 AATATATTTA-ATTTTTTTA
1 AATATAATTATATTTTTATA
2154582 AA-ATAATTATATTTTTATA
1 AATATAATTATATTTTTATA
2154601 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.18
19 14 0.42
20 4 0.12
21 1 0.03
22 3 0.09
23 5 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATAATTATATTTTTATA
Found at i:2157958 original size:23 final size:23
Alignment explanation
Indices: 2157892--2157950 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 23
2157882 AAATTATTAT
2157892 TTAATTA-ATAAAA-AT-TAAAT-
1 TTAATTATA-AAAATATATAAATA
2157912 TTAATTATAAAAATATATAAATA
1 TTAATTATAAAAATATATAAATA
2157935 TTAA-TATAAATAATAT
1 TTAATTATAAA-AATAT
2157951 TTTAATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 11 0.32
21 3 0.09
22 11 0.32
23 9 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAATTATAAAAATATATAAATA
Found at i:2159481 original size:13 final size:13
Alignment explanation
Indices: 2159459--2159488 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2159449 GAATAAAATA
2159459 TTTATATTTATTT
1 TTTATATTTATTT
*
2159472 TTTATTTTTATTT
1 TTTATATTTATTT
2159485 TTTA
1 TTTA
2159489 AATGATTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATATTTATTT
Found at i:2160761 original size:21 final size:19
Alignment explanation
Indices: 2160730--2160777 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
2160720 AAATAGTAGT
*
2160730 ATATGATAAATGATCAATAA
1 ATATAATAAATGATCAAT-A
*
2160750 ATAGTAATAAATGATTAATA
1 ATA-TAATAAATGATCAATA
2160770 ATATAATA
1 ATATAATA
2160778 GTAACTAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 7 0.28
21 13 0.52
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (19 bp):
ATATAATAAATGATCAATA
Found at i:2161751 original size:28 final size:27
Alignment explanation
Indices: 2161689--2161751 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
2161679 ATAATTCGTG
**
2161689 TATTTAT-ATTATATTTGTATATTTTA
1 TATTTATAATTATATTTAAATATTTTA
* *
2161715 TCATATATAATTATATTTAAAATTTTTTA
1 T-ATTTATAATTATATTT-AAATATTTTA
2161744 TATTTATA
1 TATTTATA
2161752 TAAATTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.03
27 5 0.17
28 15 0.52
29 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TATTTATAATTATATTTAAATATTTTA
Found at i:2165600 original size:4 final size:4
Alignment explanation
Indices: 2165591--2165649 Score: 55
Period size: 4 Copynumber: 14.8 Consensus size: 4
2165581 TCCTCTATTT
* * * * * *
2165591 TATA TATA TATA TATA TATA TATA TAAA TAGA TAGA TATG TTTA TATG
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
2165639 TATT TATA TAT
1 TATA TATA TAT
2165650 TAAAATAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:2165606 original size:10 final size:10
Alignment explanation
Indices: 2165591--2165649 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
2165581 TCCTCTATTT
2165591 TATATATATA
1 TATATATATA
2165601 TATATATATA
1 TATATATATA
*
2165611 TATATAAATA
1 TATATATATA
* * *
2165621 GATAGATATG
1 TATATATATA
* *
2165631 TTTATATGTA
1 TATATATATA
*
2165641 TTTATATAT
1 TATATATAT
2165650 TAAAATAATT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (10 bp):
TATATATATA
Found at i:2170187 original size:206 final size:205
Alignment explanation
Indices: 2169816--2170234 Score: 723
Period size: 206 Copynumber: 2.0 Consensus size: 205
2169806 GTAGCCTTGG
*
2169816 CTTCAAGAACCTCTCAATGGAATCAAGCATGTGTCATACAACACATCTTGTCTCTATTTTTTAAA
1 CTTCAAGAACCTCTCAATGGAATCAAGCATGTGTCATACAACACATCTTCTCTCTATTTTTTAAA
*
2169881 GTAGGTCATTATGGATAGCCTGCATCCATAGCCATGTACTGAAAGGAAGATCATTTTGGCTGATT
66 GTAGGTCATTATGGATAGCCTGCATCCACAGCCATGTACTGAAAGGAAGATCATTTTGGCTGATT
* *** *
2169946 GTTCCCGTGTAAGGAACCAGCTAGGCTTAGAAAAAAATATTGAAATTACGACATTTAGCTAGCCA
131 GCTCCCGCACAAGGAACCAGCTAGGCTTAGAAAAAAATATAGAAATTACGACATTTAGCTAGCCA
2170011 GTTCATTAGC
196 GTTCATTAGC
2170021 CTTCAAGAACCTCTCATCATGGAATCAAGCATGTGTCATACAACACATCTTCTCTCTA-TTTTTA
1 CTTCAAGAACCTCTCA--ATGGAATCAAGCATGTGTCATACAACACATCTTCTCTCTATTTTTTA
*
2170085 AAGTAGGTCATTATGGATAGCCTGCATCCACAGCTATGTACTGAAAGGAAGATCATTTTGGCTGA
64 AAGTAGGTCATTATGGATAGCCTGCATCCACAGCCATGTACTGAAAGGAAGATCATTTTGGCTGA
* *
2170150 TTGCTCCTGCACAAGGAACCAGCTAGGCTTAGAAAAAATTATAGAAATTACGACATTTAGCTAGC
129 TTGCTCCCGCACAAGGAACCAGCTAGGCTTAGAAAAAAATATAGAAATTACGACATTTAGCTAGC
2170215 CAGTTCATTAGC
194 CAGTTCATTAGC
2170227 CTTCAAGA
1 CTTCAAGA
2170235 TGGGAGGCAA
Statistics
Matches: 202, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
205 16 0.08
206 147 0.73
207 39 0.19
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (205 bp):
CTTCAAGAACCTCTCAATGGAATCAAGCATGTGTCATACAACACATCTTCTCTCTATTTTTTAAA
GTAGGTCATTATGGATAGCCTGCATCCACAGCCATGTACTGAAAGGAAGATCATTTTGGCTGATT
GCTCCCGCACAAGGAACCAGCTAGGCTTAGAAAAAAATATAGAAATTACGACATTTAGCTAGCCA
GTTCATTAGC
Found at i:2172219 original size:16 final size:16
Alignment explanation
Indices: 2172198--2172228 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2172188 TTTAATATTA
2172198 AATAAATATTAAATAT
1 AATAAATATTAAATAT
*
2172214 AATAAATATTTAATA
1 AATAAATATTAAATA
2172229 AAAATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATATTAAATAT
Found at i:2172226 original size:17 final size:17
Alignment explanation
Indices: 2172198--2172248 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
2172188 TTTAATATTA
2172198 AATAAATA-TTAAATAT
1 AATAAATATTTAAATAT
*
2172214 AATAAATATTT-AATAAA
1 AATAAATATTTAAAT-AT
* *
2172231 AATATATATTTAACTAT
1 AATAAATATTTAAATAT
2172248 A
1 A
2172249 TGGTATTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 11 0.39
17 15 0.54
18 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAAATATTTAAATAT
Found at i:2172368 original size:16 final size:16
Alignment explanation
Indices: 2172347--2172381 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2172337 TTTATTACTT
2172347 TTTAAA-AATTTATCAA
1 TTTAAATAATTT-TCAA
2172363 TTTAAATAATTTTCAA
1 TTTAAATAATTTTCAA
2172379 TTT
1 TTT
2172382 TATTATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATAATTTTCAA
Found at i:2172398 original size:18 final size:18
Alignment explanation
Indices: 2172372--2172423 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
2172362 ATTTAAATAA
*
2172372 TTTTCAATTTTATTATAT
1 TTTTTAATTTTATTATAT
* *
2172390 TTTTTAA-TTTA-AAAAT
1 TTTTTAATTTTATTATAT
*
2172406 CTTTTAATTTTATTATAT
1 TTTTTAATTTTATTATAT
2172424 GTATTAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 9 0.35
17 8 0.31
18 9 0.35
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAATTTTATTATAT
Found at i:2172401 original size:34 final size:34
Alignment explanation
Indices: 2172361--2172451 Score: 121
Period size: 34 Copynumber: 2.6 Consensus size: 34
2172351 AAAATTTATC
* * *
2172361 AATTTAAATAATTTTCAATTTTATTATATTTTTT
1 AATTTAAATAATTTTTAATTTTATTATATGTATT
2172395 AATTTAAA-AATCTTTTAATTTTATTATATGTATT
1 AATTTAAATAAT-TTTTAATTTTATTATATGTATT
*
2172429 AAATTAAATAAATTTTTAATTTT
1 AATTTAAAT-AATTTTTAATTTT
2172452 TAATTCAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
33 3 0.06
34 34 0.68
35 10 0.20
36 3 0.06
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (34 bp):
AATTTAAATAATTTTTAATTTTATTATATGTATT
Found at i:2173654 original size:16 final size:17
Alignment explanation
Indices: 2173631--2173675 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2173621 TTAATTATTA
2173631 TCAAATTAAAATATAAT
1 TCAAATTAAAATATAAT
* *
2173648 T-AAATTAAATTATCAT
1 TCAAATTAAAATATAAT
*
2173664 TCAAATAAAAAT
1 TCAAATTAAAAT
2173676 GTTAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (17 bp):
TCAAATTAAAATATAAT
Found at i:2173848 original size:24 final size:25
Alignment explanation
Indices: 2173820--2173866 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2173810 TTAAATTTAT
2173820 CTTTAAT-TTAAT-TATATATGTTGA
1 CTTTAATATTAATATAT-TATGTTGA
2173844 CTTTAATATTAATATATTATGTT
1 CTTTAATATTAATATATTATGTT
2173867 ATTTGTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.33
25 11 0.52
26 3 0.14
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (25 bp):
CTTTAATATTAATATATTATGTTGA
Found at i:2173864 original size:25 final size:24
Alignment explanation
Indices: 2173820--2173866 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
2173810 TTAAATTTAT
2173820 CTTTAATTTAATTATATATGTTGA
1 CTTTAATTTAATTATATATGTTGA
2173844 CTTTAATATTAA-TATATTATGTT
1 CTTTAAT-TTAATTATA-TATGTT
2173867 ATTTGTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (24 bp):
CTTTAATTTAATTATATATGTTGA
Found at i:2174085 original size:20 final size:22
Alignment explanation
Indices: 2174043--2174086 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2174033 TTATTAAATT
*
2174043 TTTAAATAATAATAATTAATTAA
1 TTTAAATAAAAATAATT-ATTAA
2174066 TTTAAATAAAAAT-ATT-TTAA
1 TTTAAATAAAAATAATTATTAA
2174086 T
1 T
2174087 AATTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAATAAAAATAATTATTAA
Found at i:2174190 original size:26 final size:27
Alignment explanation
Indices: 2174148--2174199 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2174138 TTTAACATAC
*
2174148 ATTTAAATATAACTTAATAATAATTTA
1 ATTTAAATATAACTTAAAAATAATTTA
2174175 ATTT-AATAATAA-TTAAAAATAATTT
1 ATTTAAAT-ATAACTTAAAAATAATTT
2174200 TAAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
ATTTAAATATAACTTAAAAATAATTTA
Found at i:2174194 original size:58 final size:55
Alignment explanation
Indices: 2174049--2174195 Score: 140
Period size: 58 Copynumber: 2.6 Consensus size: 55
2174039 AATTTTTAAA
* * * *
2174049 TAATAATAATTAATTAAT-TTAAATAAAAATATTTTAATAATTTTATTATATAAT
1 TAATAATAATTAATTAATAATAATTAAAAATATTTAAATAATTTTATAATATAAT
*
2174103 TAATAAATACATTAAATTAA-AATAAATTTAAAATATTTAACATACA-TTTA-AATATAACT
1 TAAT-AATA-ATT-AATTAATAAT-AATTAAAAATATTTAA-ATA-ATTTTATAATATAA-T
2174162 TAATAATAATTTAATTTAATAATAATTAAAAATA
1 TAATAATAA-TTAA-TTAATAATAATTAAAAATA
2174196 ATTTTAAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
54 4 0.05
55 4 0.05
56 3 0.04
57 10 0.13
58 39 0.51
59 15 0.20
60 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (55 bp):
TAATAATAATTAATTAATAATAATTAAAAATATTTAAATAATTTTATAATATAAT
Found at i:2174351 original size:26 final size:25
Alignment explanation
Indices: 2174316--2174393 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 25
2174306 TTAAAATAAT
*
2174316 AATTTCAAAATAAATATATTTTATTA
1 AATTTAAAAATAAATATATTTT-TTA
*
2174342 AATTTAAAAATAAATAAATATTTTTA
1 AATTTAAAAATAAATATAT-TTTTTA
*
2174368 AATATTAAAAATAATTATATTTTTTA
1 AAT-TTAAAAATAAATATATTTTTTA
2174394 TAAAAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 29 0.63
27 17 0.37
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTTAAAAATAAATATATTTTTTA
Found at i:2174875 original size:29 final size:29
Alignment explanation
Indices: 2174828--2174915 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
2174818 AATTTATATA
* *
2174828 AATTTAATATTTTAA-AAAATTTTAATTTT
1 AATTTAAT-TATTAATAAAATATTAATTTT
* *
2174857 AATTTAATTATTAATAAAA-ATAAATTTC
1 AATTTAATTATTAATAAAATATTAATTTT
* * *
2174885 AATATTAATTTCTTGATAAAATGTTAATTTT
1 AAT-TTAA-TTATTAATAAAATATTAATTTT
2174916 TTTATGTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 14 0.30
29 16 0.35
30 10 0.22
31 6 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
AATTTAATTATTAATAAAATATTAATTTT
Found at i:2175355 original size:10 final size:10
Alignment explanation
Indices: 2175342--2175384 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
2175332 ACAAAAAATT
2175342 TATAAATAAA
1 TATAAATAAA
*
2175352 TATAAA-AAT
1 TATAAATAAA
*
2175361 TAAAAATAAA
1 TATAAATAAA
2175371 TATAAATAAA
1 TATAAATAAA
2175381 TATA
1 TATA
2175385 TTTTTTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TATAAATAAA
Found at i:2175358 original size:19 final size:19
Alignment explanation
Indices: 2175335--2175376 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2175325 TAAAATCACA
*
2175335 AAAAATTTATAAATAAATAT
1 AAAAA-TTAAAAATAAATAT
2175355 AAAAATTAAAAATAAATAT
1 AAAAATTAAAAATAAATAT
2175374 AAA
1 AAA
2175377 TAAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTAAAAATAAATAT
Found at i:2175613 original size:23 final size:21
Alignment explanation
Indices: 2175587--2175631 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
2175577 TTTTTTATGT
2175587 AAATAATATAAATATAATATAAA
1 AAATAAT-TAAA-ATAATATAAA
*
2175610 AAATAATTAAAATATTATAAA
1 AAATAATTAAAATAATATAAA
2175631 A
1 A
2175632 CGACAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 4 0.19
23 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAATTAAAATAATATAAA
Done.