Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 25
Found at i:515600 original size:26 final size:25
Alignment explanation
Indices: 515548--515610 Score: 101
Period size: 25 Copynumber: 2.5 Consensus size: 25
515538 GATTTAACAA
515548 AAAGGGGGAGAAGTGTAAAAATGTT
1 AAAGGGGGAGAAGTGTAAAAATGTT
515573 AAAGGGGGAGAAGTGT-AAAATGTTTT
1 AAAGGGGGAGAAGTGTAAAAATG--TT
515599 AAAGGGGGAGAA
1 AAAGGGGGAGAA
515611 ATGTTATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.17
25 16 0.44
26 14 0.39
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.19
Consensus pattern (25 bp):
AAAGGGGGAGAAGTGTAAAAATGTT
Found at i:515614 original size:19 final size:20
Alignment explanation
Indices: 515590--515629 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
515580 GAGAAGTGTA
*
515590 AAATGTTTTA-AAGGGGGAG
1 AAATGTTATAGAAGGGGGAG
515609 AAATGTTATAGTAAGGGGGAG
1 AAATGTTATAG-AAGGGGGAG
515630 TAATTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (20 bp):
AAATGTTATAGAAGGGGGAG
Found at i:533111 original size:138 final size:138
Alignment explanation
Indices: 532863--533178 Score: 488
Period size: 138 Copynumber: 2.3 Consensus size: 138
532853 CATTTAGTGT
** * * *
532863 CGAAAATGCACTGTTATGTATTAAACAAATTCGATCAATAACTTATATACATAATTGTATACCAA
1 CGAAAATGCACCATTATGAATTAAACAAAATCGATCGATAACTTATATACATAATTGTATACCAA
*
532928 AATGGTAATTCAAAAACTTATTATGAATACCATGATTGTACATATAGTGCCAAAAGTACACATAG
66 AATGGTAATTCAAAAACTTATTATGAATACCATGATTGCACATATAGTGCCAAAAGTACACATAG
*
532993 TATTGATA
131 TACTGATA
* * * * *
533001 CGAAAATGCACCATTATGCATTAAACAAAATCAATCGATAACTTATATACATAATTTTATATCGA
1 CGAAAATGCACCATTATGAATTAAACAAAATCGATCGATAACTTATATACATAATTGTATACCAA
* * *
533066 AATGTTAATTCACAAACTTATTATGAATACCATGATTGCACATATAGTGCCAAAAGTATACATAG
66 AATGGTAATTCAAAAACTTATTATGAATACCATGATTGCACATATAGTGCCAAAAGTACACATAG
533131 TACTGATA
131 TACTGATA
*
533139 CAAAAATGCACCATTATGAATTAAACAAAATCGATCGATA
1 CGAAAATGCACCATTATGAATTAAACAAAATCGATCGATA
533179 CCATCATACA
Statistics
Matches: 161, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 161 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (138 bp):
CGAAAATGCACCATTATGAATTAAACAAAATCGATCGATAACTTATATACATAATTGTATACCAA
AATGGTAATTCAAAAACTTATTATGAATACCATGATTGCACATATAGTGCCAAAAGTACACATAG
TACTGATA
Found at i:537924 original size:34 final size:34
Alignment explanation
Indices: 537880--538063 Score: 124
Period size: 34 Copynumber: 5.5 Consensus size: 34
537870 TATAAAAGTT
537880 ATGTCTCTTCA-CAAATAGGTGCCTCCCAAAAATC
1 ATGTCTCTTCACCAAA-AGGTGCCTCCCAAAAATC
* ** * *
537914 GTGTCTCTTCACCAAAAGGTGTTTCCTAAAAGTC
1 ATGTCTCTTCACCAAAAGGTGCCTCCCAAAAATC
** ** * *
537948 ATGTCTCTTCACCAAAAGGTTTCTGTCAGAAGTC
1 ATGTCTCTTCACCAAAAGGTGCCTCCCAAAAATC
* * * ** *
537982 ATGACTCTTCACCTAGAGGTATCTCCCAAAAGTC
1 ATGTCTCTTCACCAAAAGGTGCCTCCCAAAAATC
* **
538016 A--TCTCTTCACC-AAAGGATGCCTCCCTAATGTC
1 ATGTCTCTTCACCAAAAGG-TGCCTCCCAAAAATC
* *
538048 ATGACTCTTCATCAAA
1 ATGTCTCTTCACCAAA
538064 GATTGTCTCT
Statistics
Matches: 118, Mismatches: 27, Indels: 9
0.77 0.18 0.06
Matches are distributed among these distances:
31 4 0.03
32 21 0.18
34 87 0.74
35 6 0.05
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (34 bp):
ATGTCTCTTCACCAAAAGGTGCCTCCCAAAAATC
Found at i:545327 original size:21 final size:21
Alignment explanation
Indices: 545301--545359 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
545291 ATTATCCAAT
545301 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
545322 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
545343 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
545360 TAATAAATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:555213 original size:20 final size:20
Alignment explanation
Indices: 555152--555199 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
555142 TCACTCAATC
*
555152 AAAACTTCATGATCACACCA
1 AAAACTTTATGATCACACCA
555172 AAAACTTTATGATCACACCA
1 AAAACTTTATGATCACACCA
555192 AAAACTTT
1 AAAACTTT
555200 GTATGACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAACTTTATGATCACACCA
Found at i:563182 original size:55 final size:55
Alignment explanation
Indices: 563092--563266 Score: 194
Period size: 56 Copynumber: 3.1 Consensus size: 55
563082 ATTATACTGG
* * *
563092 TATTAAAACTTCCATATTTT-ATAGTATCAAATTGGATAAGTTAAACATTACAACGT
1 TATTCAAACTTCCAT-TTTTAAT-GTAACAAATTGGATAAGTTAAACATTACTACGT
* * **
563148 TATTCAAACTTCTATTTTTAATGTAACAACTTGGATAAGTTAAGACATTA-TATTT
1 TATTCAAACTTCCATTTTTAATGTAACAAATTGGATAAGTTAA-ACATTACTACGT
* * *
563203 CTATTTAAACATCCATTTTTAATGTAA-AAATTTGGATAAGTTGAACATTACTACGT
1 -TATTCAAACTTCCATTTTTAATGTAACAAA-TTGGATAAGTTAAACATTACTACGT
563259 TATTCAAA
1 TATTCAAA
563267 TTTTGATCTT
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
55 40 0.40
56 59 0.60
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (55 bp):
TATTCAAACTTCCATTTTTAATGTAACAAATTGGATAAGTTAAACATTACTACGT
Found at i:563908 original size:25 final size:23
Alignment explanation
Indices: 563866--563911 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
563856 TGCAAGGGCC
*
563866 AAGGAGTTTCAAGAAGCCATGAA
1 AAGGAGTTTCAACAAGCCATGAA
563889 AAGGTAGTTTACAACAAGCCATG
1 AAGG-AGTTT-CAACAAGCCATG
563912 GACGTGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (23 bp):
AAGGAGTTTCAACAAGCCATGAA
Found at i:566310 original size:55 final size:56
Alignment explanation
Indices: 566232--566343 Score: 172
Period size: 55 Copynumber: 2.0 Consensus size: 56
566222 TTTTGCTAAG
* * *
566232 ACATTGCAATGCTATTCAAACTTCCATATTTTAATGTAACAATTTGGATAAGTTAA
1 ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAA
* *
566288 ACATTACAATGC-ATTCAAACTTCCATATTTGATTGTAACAACTTGGATGAGTTAA
1 ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAA
566343 A
1 A
566344 ATCTTTAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 40 0.78
56 11 0.22
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (56 bp):
ACATTACAATGCTATTCAAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAA
Found at i:575459 original size:24 final size:26
Alignment explanation
Indices: 575410--575462 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
575400 AACATGTGAA
575410 AATAATAATAAAAAATATTAATATAAT
1 AATAATAATAAAAAATA-TAATATAAT
*
575437 AATATTAATAAAAAATA-AA-ATAAT
1 AATAATAATAAAAAATATAATATAAT
575461 AA
1 AA
575463 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 2 0.08
27 16 0.64
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (26 bp):
AATAATAATAAAAAATATAATATAAT
Found at i:575879 original size:34 final size:34
Alignment explanation
Indices: 575841--575925 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 34
575831 TCCTACTTCA
* * *
575841 ACTCAAAATTC-TATAGTTTTAGTGTTTTAATATG
1 ACTCAAAATACGT-TAGTTTTAGTGTTTCAATAGG
*
575875 ACTC-AAATACGTTGGTTTTAGTGTTTCAATAGG
1 ACTCAAAATACGTTAGTTTTAGTGTTTCAATAGG
*
575908 ACTC-AAATACGTTGGTTT
1 ACTCAAAATACGTTAGTTT
575926 ATTTTCTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 41 0.89
34 5 0.11
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (34 bp):
ACTCAAAATACGTTAGTTTTAGTGTTTCAATAGG
Found at i:575896 original size:33 final size:33
Alignment explanation
Indices: 575856--575925 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
575846 AAATTCTATA
* *
575856 GTTTTAGTGTTTTAATATGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
575889 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
575922 GTTT
1 GTTT
575926 ATTTTCTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (33 bp):
GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
Found at i:576003 original size:25 final size:24
Alignment explanation
Indices: 575973--576041 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 24
575963 AAGGCTTGCA
575973 AAAATAATAAAAT-AAAAATATATT
1 AAAATAATAAAATAAAAAATATA-T
575997 AACAATAATAATAAATAAATAAATATAT
1 AA-AATAAT-A-AAATAAA-AAATATAT
* *
576025 AATATAATATAATAAAA
1 AAAATAATAAAATAAAA
576042 TGTTTTTGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
24 3 0.08
25 12 0.32
26 2 0.05
27 9 0.24
28 5 0.13
29 7 0.18
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAATAATAAAATAAAAAATATAT
Found at i:576692 original size:165 final size:163
Alignment explanation
Indices: 576383--576903 Score: 472
Period size: 169 Copynumber: 3.1 Consensus size: 163
576373 AACTGAATGG
* * * * *
576383 AATCGAACTCGAAGGTCTTTGGCAGATATCCCTTCTTGCCTTGAGCTATTCTGCAAATGATGGTG
1 AATCAAACTCGAAGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT-GTG
* * * * * *
576448 CCTTTGAGCTGAGTGGAGTCGAACTCGAAGGTCTTT-GTT-TACAGACAACCCTTCTAGCCTTGA
65 CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGA-AGATAACCCTTCTA-ACTTAA
* *
576511 GTTATG-TCGTAAATGATGTGCCCTCGAAGATGAGTGT
128 GTTATGCT-GCAAATGATGTG-CCTCGAAGATGAGCGT
* * * * * * * *
576548 AATCAAAGTCGAGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGT
1 AATCAAACTCGAAGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGC
* *
576613 CTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCAACTTAAGT
66 CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCT-AACTTAAGT
* * * *
576678 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
130 TATGCTGCAAATGATGTGCCTCGAAGATGAGCGT
* * * * * *
576712 AGTCGAACTCGAAGGTCTTTTGGTCATAAATAACCTTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 AATCAAACTCGAAGGTC-TTTGG---TAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT
* * * * * * * *
576777 GTACCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTTGACT
62 GT-GCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTC-TAACT
* * * * *
576842 TAAGTTATGCTACAAATGATGTTCCTTGGAGCTGAGCGT
125 TAAGTTATGCTGCAAATGATGTGCCTCGAAGATGAGCGT
* * *
576881 AGTCGAACTCGAAGGCCTTTGGT
1 AATCAAACTCGAAGGTCTTTGGT
576904 GGGCACGATT
Statistics
Matches: 293, Mismatches: 53, Indels: 20
0.80 0.14 0.05
Matches are distributed among these distances:
164 59 0.20
165 92 0.31
166 3 0.01
168 37 0.13
169 101 0.34
170 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (163 bp):
AATCAAACTCGAAGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGC
CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTAACTTAAGTT
ATGCTGCAAATGATGTGCCTCGAAGATGAGCGT
Found at i:576902 original size:84 final size:85
Alignment explanation
Indices: 576385--576908 Score: 441
Period size: 84 Copynumber: 6.3 Consensus size: 85
576375 CTGAATGGAA
* * * * * *
576385 TCGAACTCGAAGGTC--T--TTGGCAGATATCCCTTCTTGCCTTGAGCTATTCTGCAAATGATGG
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT-G
* * *
576446 TG-CCTTTGAGCTGAGTGGAG
65 TGCCCTTGGAGCTGAGCGTAG
** * * * *
576466 TCGAACTCGAAGGTCTTT-GTTTACAGACAACCCTTCTAGCCTTGAGTTATG-TCGTAAATGATG
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCT-GCAAATGATG
* * * * *
576529 TGCCCTCGAAGATGAGTGTAA
65 TGCCCTTGGAGCTGAGCGTAG
* * * * * * *
576550 TCAAAGTCGAGGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* *
576611 G-TCTTGGAGTTGAGCGTAG
66 GCCCTTGGAGCTGAGCGTAG
* *
576630 TCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCA-ACTTAAGTTATGCTGCAAATGATA
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT-AGACTTAAGTTATGCTGCAAATGATG
576694 TG-CCTTGGAGCTGAGCGTAG
65 TGCCCTTGGAGCTGAGCGTAG
*** * * * * *
576714 TCGAACTCGAAGGTCTTTTGG-TCATAAATAACCTTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * * *
576778 TACCCTCGAAGCTGAGTGTAA
65 TGCCCTTGGAGCTGAGCGTAG
* * * *
576799 TCAAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
576864 -TCCTTGGAGCTGAGCGTAG
66 GCCCTTGGAGCTGAGCGTAG
* *
576883 TCGAACTCGAAGGCCTTTGGTGGGCA
1 TCGAACTCGAAGGTCTTTGGTTGGCA
576909 CGATTCCCTT
Statistics
Matches: 351, Mismatches: 76, Indels: 29
0.77 0.17 0.06
Matches are distributed among these distances:
80 29 0.08
81 47 0.13
82 1 0.00
83 6 0.02
84 201 0.57
85 67 0.19
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (85 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
GCCCTTGGAGCTGAGCGTAG
Found at i:577208 original size:110 final size:110
Alignment explanation
Indices: 577026--577665 Score: 858
Period size: 110 Copynumber: 5.9 Consensus size: 110
577016 TGTTTCAAGG
* * * *
577026 CCAATATCCTTTGCCGTAAAGTTGAAATTGACTCT--A--AAACTGGAAAGTTGTTTATTGACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTGACAG
* *
577087 TCAGTCACCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* * * *
577132 CTAATATCATTCGCTGTGAAGTTGAAATCGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTGACAG
577197 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* * * * *
577242 CCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGATAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTGACAG
*
577307 TCAGTCGCCCTTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* * * * * * *
577352 CCAGTATCATTCGGTGTGAAATTGAAATTGACTCTGAATGAAAATGGAAAGTTGTTCATTGACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTGACAG
** * * *
577417 TCAACCGCCCCTTCGCTGTGTAGTTGAGTTTGTGTTGTCTTGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* * * *
577462 CCAATATCCTTCGCTATGAAGTTGAATTTGACTCTGAAT-AATACTAAAAAATTGTTTATTGACA
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAA-ACTGAAAAGTTGTTTATTGACA
* * *
577526 GTCAATCACCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
65 GTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* * * * *
577572 CCAATATCCTTCGCAGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAAGTTGTTTGTTGACCG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTGACAG
* *
577637 TCGGTCGCCCCTTCGCTGTAAAGTTGAGC
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGC
577666 AACCACCATC
Statistics
Matches: 463, Mismatches: 65, Indels: 8
0.86 0.12 0.01
Matches are distributed among these distances:
106 29 0.06
108 1 0.00
109 2 0.00
110 429 0.93
111 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (110 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTATTGACAG
TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
Found at i:579537 original size:18 final size:18
Alignment explanation
Indices: 579494--579531 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
579484 GTGAAGTATG
*
579494 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
579512 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
579530 AA
1 AA
579532 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:583512 original size:18 final size:18
Alignment explanation
Indices: 583491--583526 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
583481 CCTCTCATTA
583491 CACGGCATGCTCTAATTC
1 CACGGCATGCTCTAATTC
583509 CACGGCATGCTCTAATTC
1 CACGGCATGCTCTAATTC
583527 TTCCATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (18 bp):
CACGGCATGCTCTAATTC
Found at i:586443 original size:21 final size:21
Alignment explanation
Indices: 586402--586443 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
586392 ATATGCATCC
* * *
586402 ATATTAGCTCATAGACTTTAT
1 ATATTAGCTCACACACATTAT
586423 ATATTAGCTCACACACATTAT
1 ATATTAGCTCACACACATTAT
586444 GAGATGATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (21 bp):
ATATTAGCTCACACACATTAT
Found at i:586900 original size:25 final size:25
Alignment explanation
Indices: 586850--586900 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
586840 CTCCTTGCTA
*
586850 GCTAGCTAGCTACTCAAGCAGGCTT
1 GCTAGCTAGCTACTCAAGCAAGCTT
*
586875 GCTAGCTAGCTACTCAAGCAATCTT
1 GCTAGCTAGCTACTCAAGCAAGCTT
586900 G
1 G
586901 GAGGAAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (25 bp):
GCTAGCTAGCTACTCAAGCAAGCTT
Found at i:587827 original size:11 final size:11
Alignment explanation
Indices: 587811--587836 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
587801 ATACCAGAAA
587811 GAAGTGCAAGT
1 GAAGTGCAAGT
587822 GAAGTGCAAGT
1 GAAGTGCAAGT
587833 GAAG
1 GAAG
587837 AAATAAAAAA
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:0.38, C:0.08, G:0.38, T:0.15
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:587920 original size:18 final size:18
Alignment explanation
Indices: 587897--587932 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
587887 CAAGCACTCA
587897 AAAAGAAGA-AAAGAAAAG
1 AAAAGAA-ATAAAGAAAAG
587915 AAAAGAAATAAAGAAAAG
1 AAAAGAAATAAAGAAAAG
587933 TTGAAAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (18 bp):
AAAAGAAATAAAGAAAAG
Found at i:589270 original size:16 final size:16
Alignment explanation
Indices: 589249--589280 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
589239 TTAAACAAGT
589249 ATAGTTCCTATACTTG
1 ATAGTTCCTATACTTG
589265 ATAGTTCCTATACTTG
1 ATAGTTCCTATACTTG
589281 TGGCGTCATT
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:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (16 bp):
ATAGTTCCTATACTTG
Found at i:596893 original size:56 final size:56
Alignment explanation
Indices: 596773--597208 Score: 551
Period size: 56 Copynumber: 7.9 Consensus size: 56
596763 CCCACTAGCA
*
596773 ATACAGAAATTCATAAACAT-ATTATGAATTTCTTAG-TTTTGTACACAAAGTGCCC
1 ATACAGAAATTCATAAAC-TCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
** * * *
596828 ACGCGGAAATTCATAAACTCGTTATGAATTTCCTAGCTTTTGCACACAAAGTGCCC
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * * * *
596884 ATACAGAAATTCATAAACTTATTATGAAATTCTTAG-TTTTTCACAAAAAGTTCCC
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * *
596939 ATACAGAAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACATAAAATGTCC
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * * *
596994 ATACGGAAATTCATAAACTCATTGTGAATTTCTTAGCTTTTGCACACAAAGTTCTC
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * * *
597050 ATAC-GAAAATTCATAAAATCATTATAAATTTCTTAGCTTTTGCACACAAAGTGTCT
1 ATACAG-AAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * * *
597106 ATATAGAAATTCATAAACTCATTATGAATTTCTTAGCGTTGGCACACAAAGTGCCT
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * *
597162 ATACGGAAATTCATAAACTTATTATGAATTTCTTA-ATTTTGCACACA
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACA
597209 TTGTTCCATT
Statistics
Matches: 327, Mismatches: 49, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
54 1 0.00
55 137 0.42
56 188 0.57
57 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (56 bp):
ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
Found at i:596894 original size:111 final size:112
Alignment explanation
Indices: 596773--597208 Score: 576
Period size: 111 Copynumber: 3.9 Consensus size: 112
596763 CCCACTAGCA
* **
596773 ATACAGAAATTCATAAACAT-ATTATGAATTTCTTAG-TTTTGTACACAAAGTGCCCACGCGGAA
1 ATACAGAAATTCATAAAC-TCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAA
* * *
596836 ATTCATAAACTCGTTATGAATTTCCTAGCTTTTGCACACAAAGTGCCC
65 ATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGTCC
* * * * * *
596884 ATACAGAAATTCATAAACTTATTATGAAATTCTTAG-TTTTTCACAAAAAGTTCCCATACAGAAA
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAA
* *
596948 TTCATAAACTCATTATGAATTTCTTAG-TTTTGCACATAAAATGTCC
66 TTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGTCC
* * * * *
596994 ATACGGAAATTCATAAACTCATTGTGAATTTCTTAGCTTTTGCACACAAAGTTCTCATACGAAAA
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAA
* * *
597059 TTCATAAAATCATTATAAATTTCTTAGCTTTTGCACACAAAGTGTCT
66 TTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGTCC
* * * *
597106 ATATAGAAATTCATAAACTCATTATGAATTTCTTAGCGTTGGCACACAAAGTGCCTATACGGAAA
1 ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAA
* *
597171 TTCATAAACTTATTATGAATTTCTTA-ATTTTGCACACA
66 TTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACA
597209 TTGTTCCATT
Statistics
Matches: 282, Mismatches: 40, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
110 49 0.17
111 138 0.49
112 95 0.34
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (112 bp):
ATACAGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAA
TTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGTCC
Found at i:599055 original size:22 final size:21
Alignment explanation
Indices: 599029--599069 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
599019 GCTGCAGAAA
599029 TGATGGTCTTGATGGATGAAGT
1 TGATGGTCTTGAT-GATGAAGT
*
599051 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
599070 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGT
Found at i:603112 original size:31 final size:31
Alignment explanation
Indices: 603074--603132 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
603064 TTGATTAGTA
603074 TAAACCAAAACTTCCATCTCCTCACATTCTT
1 TAAACCAAAACTTCCATCTCCTCACATTCTT
*
603105 TAAACCAAAACTTCCTTCTCCTCACATT
1 TAAACCAAAACTTCCATCTCCTCACATT
603133 ATTTTCTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (31 bp):
TAAACCAAAACTTCCATCTCCTCACATTCTT
Found at i:603764 original size:35 final size:35
Alignment explanation
Indices: 603725--603837 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 35
603715 TAAGGGAATA
* *
603725 GTGATAATATAGGCGTGAAATGGTGATAGAAGATG
1 GTGATGATATAGGCGTGAAATGGTGATAGAATATG
* * *
603760 GTGATGATATAGGCATGCAATGGTGATGGAATATG
1 GTGATGATATAGGCGTGAAATGGTGATAGAATATG
*
603795 GTGATGATATAGGCGGGAAAATGGTGATAGAATATG
1 GTGATGATATAGGCGTG-AAATGGTGATAGAATATG
603831 GTGATGA
1 GTGATGA
603838 ACAAATAATA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 45 0.66
36 23 0.34
ACGTcount: A:0.35, C:0.04, G:0.35, T:0.27
Consensus pattern (35 bp):
GTGATGATATAGGCGTGAAATGGTGATAGAATATG
Found at i:603797 original size:13 final size:13
Alignment explanation
Indices: 603779--603836 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
603769 TAGGCATGCA
603779 ATGGTGATGGAAT
1 ATGGTGATGGAAT
603792 ATGGTGAT-G-AT
1 ATGGTGATGGAAT
* *
603803 ATAGGCG--GGAAA
1 AT-GGTGATGGAAT
*
603815 ATGGTGATAGAAT
1 ATGGTGATGGAAT
603828 ATGGTGATG
1 ATGGTGATG
603837 AACAAATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
11 8 0.24
12 7 0.21
13 19 0.56
ACGTcount: A:0.33, C:0.02, G:0.38, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAT
Found at i:608613 original size:19 final size:19
Alignment explanation
Indices: 608591--608631 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
608581 TTGAGTGTAT
608591 TTTGCAACTTT-TTCTTTTC
1 TTTG-AACTTTCTTCTTTTC
*
608610 TTTGAATTTTCTTCTTTTC
1 TTTGAACTTTCTTCTTTTC
608629 TTT
1 TTT
608632 TCTTTTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.10, C:0.17, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTGAACTTTCTTCTTTTC
Found at i:608689 original size:20 final size:21
Alignment explanation
Indices: 608664--608703 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
608654 TGTAGGAGTC
608664 TTTTCTTTT-TTTTTTGTTTT
1 TTTTCTTTTCTTTTTTGTTTT
608684 TTTTCTTTTGCTTTTTTGTT
1 TTTTCTTTT-CTTTTTTGTT
608704 GCATCACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTTGTTTT
Found at i:609110 original size:13 final size:13
Alignment explanation
Indices: 609092--609130 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
609082 ATGGGTGTGA
*
609092 ATGGTGATGGAGG
1 ATGGTGATGGAAG
609105 ATGGTGATGGAAAG
1 ATGGTGATGG-AAG
*
609119 ATAGTGATGGAA
1 ATGGTGATGGAA
609131 ATAGTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.23
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:609510 original size:19 final size:20
Alignment explanation
Indices: 609469--609511 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
609459 GAAACCCCTT
* *
609469 TGAAAATACGTGATTTTAGA
1 TGAAAATACATGATTTTAAA
609489 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
609508 TGAA
1 TGAA
609512 GTTACATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:619930 original size:90 final size:90
Alignment explanation
Indices: 619777--619954 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
619767 CCTAACACAC
* * *
619777 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
619842 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
619867 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
619932 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
619955 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:624133 original size:17 final size:17
Alignment explanation
Indices: 624093--624135 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
624083 TTAACACGTA
* *
624093 TAGTTCATTTAGTTATG
1 TAGTTCATTTAATTAAG
* *
624110 CACTTCATTTAATTAAG
1 TAGTTCATTTAATTAAG
624127 TAGTTCATT
1 TAGTTCATT
624136 GATGCATATG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.49
Consensus pattern (17 bp):
TAGTTCATTTAATTAAG
Found at i:624190 original size:17 final size:17
Alignment explanation
Indices: 624146--624198 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
624136 GATGCATATG
* *
624146 GTTCATTCAATAAACTTG
1 GTTCATTCATTAAAC-TA
*
624164 GTTTATTCATTAAACTA
1 GTTCATTCATTAAACTA
624181 GTTCATTCATTAAACTA
1 GTTCATTCATTAAACTA
624198 G
1 G
624199 CTCCTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (17 bp):
GTTCATTCATTAAACTA
Found at i:633744 original size:20 final size:21
Alignment explanation
Indices: 633720--633789 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
633710 ATATCTAGAG
*
633720 TTAATTAAATATATATTTTAA
1 TTAATTAAATATATATTTCAA
*
633741 -TAATCCTGAATATATAATTTCAA
1 TTAAT--TAAATATAT-ATTTCAA
*
633764 TTAATTAAATATAGATTT-AA
1 TTAATTAAATATATATTTCAA
633784 TTAATT
1 TTAATT
633790 TGAAACAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 12 0.29
21 4 0.10
22 15 0.37
23 6 0.15
24 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAATTAAATATATATTTCAA
Found at i:642645 original size:5 final size:5
Alignment explanation
Indices: 642635--642665 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
642625 GTGCTTTCAA
642635 CTTTT CTTTT C-TTT CTTTT CTTTT CTTTT CT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CT
642666 ACTTTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:642654 original size:14 final size:14
Alignment explanation
Indices: 642635--642662 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
642625 GTGCTTTCAA
642635 CTTTTCTTTTCTTT
1 CTTTTCTTTTCTTT
642649 CTTTTCTTTTCTTT
1 CTTTTCTTTTCTTT
642663 TCTACTTTTT
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:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTCTTT
Found at i:646947 original size:32 final size:32
Alignment explanation
Indices: 646911--646977 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
646901 TGAGTCCTTT
*
646911 AGGCTTGTGATGGTTCGGATAACCCTTCATGA
1 AGGCTTGTGATGGTTCAGATAACCCTTCATGA
*
646943 AGGCTTGTGATGGTTCAGCTAACCCTTCATGA
1 AGGCTTGTGATGGTTCAGATAACCCTTCATGA
646975 AGG
1 AGG
646978 GGCTTGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (32 bp):
AGGCTTGTGATGGTTCAGATAACCCTTCATGA
Found at i:646992 original size:32 final size:32
Alignment explanation
Indices: 646911--646996 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
646901 TGAGTCCTTT
** * *
646911 AGGCTTGTGATGGTTCGGATAACCCTTCATGA
1 AGGCTTGTGATAATTCAGCTAACCCTTCATGA
**
646943 AGGCTTGTGATGGTTCAGCTAACCCTTCATGA
1 AGGCTTGTGATAATTCAGCTAACCCTTCATGA
646975 AGGGGC-T-TGATAATTCAGCTAA
1 A--GGCTTGTGATAATTCAGCTAA
646997 GGATGGGAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 44 0.92
33 1 0.02
34 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (32 bp):
AGGCTTGTGATAATTCAGCTAACCCTTCATGA
Found at i:647808 original size:2 final size:2
Alignment explanation
Indices: 647801--647849 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
647791 TCATAATAAC
647801 TA TA TA TA -A 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
647842 TA TA TA TA
1 TA TA TA TA
647850 AAAAATAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:652389 original size:2 final size:2
Alignment explanation
Indices: 652372--652407 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
652362 TTATTATCAT
*
652372 TA TA AA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
652408 GAAAATAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:654510 original size:6 final size:6
Alignment explanation
Indices: 654500--654537 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
654490 AGCAACGTGC
*
654500 AACAAC AACAAA AACAAA AACAAA ATAC-AA AACAAA AA
1 AACAAA AACAAA AACAAA AACAAA A-ACAAA AACAAA AA
654538 AGAAGTGACG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 2 0.07
6 25 0.86
7 2 0.07
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (6 bp):
AACAAA
Found at i:657111 original size:16 final size:16
Alignment explanation
Indices: 657090--657120 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
657080 AAGATGCTTG
657090 TCTCCACTTAGCCATA
1 TCTCCACTTAGCCATA
657106 TCTCCACTTAGCCAT
1 TCTCCACTTAGCCAT
657121 CACTTTGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.39, G:0.06, T:0.32
Consensus pattern (16 bp):
TCTCCACTTAGCCATA
Found at i:662833 original size:15 final size:15
Alignment explanation
Indices: 662813--662858 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
662803 TTTGATATCA
662813 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
662828 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
662843 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
662859 TTATTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:670047 original size:56 final size:57
Alignment explanation
Indices: 669960--670081 Score: 144
Period size: 56 Copynumber: 2.2 Consensus size: 57
669950 TTGGAAAATC
* *
669960 AAAATGAAATGTTAAGAAAGGAGTTATAGCTTTCAAAAAT-AAACTCTGAAAACT-TTG
1 AAAAAGAAATGTTAAGAAAGGAGTTAGAGCTTTCAAAAATGAAA-TCTG-AAACTATTG
* * *
670017 AAAAAGAAAT-TTGAAG-AAGGATTTAGAGCTTTCAAAAATGAAATTTGAAAGTATTG
1 AAAAAGAAATGTT-AAGAAAGGAGTTAGAGCTTTCAAAAATGAAATCTGAAACTATTG
670073 AAAAAGAAA
1 AAAAAGAAA
670082 ATTTTGATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
55 4 0.07
56 38 0.67
57 15 0.26
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (57 bp):
AAAAAGAAATGTTAAGAAAGGAGTTAGAGCTTTCAAAAATGAAATCTGAAACTATTG
Found at i:680858 original size:22 final size:23
Alignment explanation
Indices: 680815--680858 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
680805 TTTTTCTTAA
680815 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTTC
*
680838 TTTTGAGTGC-TTCGATTTCTT
1 TTTTGAGTGCTTTCAATTTCTT
680859 TGCTGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTTC
Found at i:683165 original size:2 final size:2
Alignment explanation
Indices: 683158--683206 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
683148 ATATCACCAT
683158 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
683200 TA TA TA T
1 TA TA TA T
683207 GCTGCTTATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:686749 original size:2 final size:2
Alignment explanation
Indices: 686742--686766 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
686732 ATATGACCAT
686742 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 T
686767 TCCGATGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:691208 original size:22 final size:22
Alignment explanation
Indices: 691166--691208 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
691156 TCTTTGTAAT
* *
691166 TTCTTTTCTTTTATTCTTTTTG
1 TTCTCTTCTTTTATGCTTTTTG
691188 TTCTCTTCTTTTAGTGCTTTT
1 TTCTCTTCTTTTA-TGCTTTT
691209 ACTTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (22 bp):
TTCTCTTCTTTTATGCTTTTTG
Found at i:693076 original size:22 final size:21
Alignment explanation
Indices: 693051--693092 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
693041 GGGTGCATAA
*
693051 TTGATGGTCTTGATGGATGAAG
1 TTGATAGTCTTGAT-GATGAAG
*
693073 TTGATAGTGTTGATGATGAA
1 TTGATAGTCTTGATGATGAA
693093 ATGGAGATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.26, C:0.02, G:0.33, T:0.38
Consensus pattern (21 bp):
TTGATAGTCTTGATGATGAAG
Found at i:694359 original size:2 final size:2
Alignment explanation
Indices: 694348--694391 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
694338 TCATAATAAC
*
694348 TA TA TA -A TA TA TA TA TA TA TA TA TA TA GT- TT 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
694389 TA T
1 TA T
694392 GATAATAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.92
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:694768 original size:16 final size:16
Alignment explanation
Indices: 694747--694785 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
694737 CGAATACATT
694747 TGGCCTTGAACGTTTA
1 TGGCCTTGAACGTTTA
694763 TGGCCTTGAACGTTTA
1 TGGCCTTGAACGTTTA
*
694779 TGTCCTT
1 TGGCCTT
694786 TATCATTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (16 bp):
TGGCCTTGAACGTTTA
Found at i:703026 original size:25 final size:24
Alignment explanation
Indices: 702998--703055 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
702988 AAGAAAAATC
** *
702998 AGAAAAAAAATTGAAGCACTCCAAA
1 AGAAAAAAAATCCAA-CACTCAAAA
703023 AGAAATAAAAATCCAACACTCAAAA
1 AGAAA-AAAAATCCAACACTCAAAA
703048 AGAAAAAA
1 AGAAAAAA
703056 CAAAACAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.10
25 18 0.62
26 8 0.28
ACGTcount: A:0.66, C:0.16, G:0.09, T:0.10
Consensus pattern (24 bp):
AGAAAAAAAATCCAACACTCAAAA
Found at i:706921 original size:24 final size:24
Alignment explanation
Indices: 706891--706967 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 24
706881 AAAAATCAGA
* * *
706891 AAAGAAATTGAAACACTCCAAAAG
1 AAAGAAAATCAAACACTCAAAAAG
706915 AAAGAAAAATCAAACACTCAAAAAG
1 AAAG-AAAATCAAACACTCAAAAAG
* * *
706940 -AAGAAAA--AAACAATGAAAAAA
1 AAAGAAAATCAAACACTCAAAAAG
706961 AAAGAAA
1 AAAGAAA
706968 GTTGAAGCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 11 0.24
22 6 0.13
23 4 0.09
24 7 0.16
25 17 0.38
ACGTcount: A:0.70, C:0.12, G:0.10, T:0.08
Consensus pattern (24 bp):
AAAGAAAATCAAACACTCAAAAAG
Found at i:706948 original size:25 final size:25
Alignment explanation
Indices: 706901--706947 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
706891 AAAGAAATTG
*
706901 AAACACTCCAAAAGAAAGAAAAATC
1 AAACACTCAAAAAGAAAGAAAAATC
706926 AAACACTCAAAAAG-AAGAAAAA
1 AAACACTCAAAAAGAAAGAAAAA
706948 AACAATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.68, C:0.17, G:0.09, T:0.06
Consensus pattern (25 bp):
AAACACTCAAAAAGAAAGAAAAATC
Found at i:712481 original size:24 final size:24
Alignment explanation
Indices: 712454--712508 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
712444 TCTTTTTTCT
* *
712454 TTTTCTTCTTTTTAAGTGTTTGAC
1 TTTTCTTCTTTTGAAGTGCTTGAC
* *
712478 TTTTATTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGAAGTGCTTGAC
712502 TTTTCTT
1 TTTTCTT
712509 TGTTATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.11, C:0.13, G:0.15, T:0.62
Consensus pattern (24 bp):
TTTTCTTCTTTTGAAGTGCTTGAC
Found at i:712582 original size:12 final size:12
Alignment explanation
Indices: 712565--712590 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
712555 GTTGTTGTTA
712565 TTTTTGGCATTC
1 TTTTTGGCATTC
712577 TTTTTGGCATTC
1 TTTTTGGCATTC
712589 TT
1 TT
712591 CCACCAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTTTGGCATTC
Found at i:714620 original size:14 final size:13
Alignment explanation
Indices: 714596--714666 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
714586 GCTTGCTTTA
*
714596 TTTTTTACTTTTC
1 TTTTTTTCTTTTC
714609 TTCTTTTTCTTTTC
1 TT-TTTTTCTTTTC
**
714623 TTTTTTTCTGAAT-
1 TTTTTTTCT-TTTC
*
714636 TTTTCTTCTTTT-
1 TTTTTTTCTTTTC
*
714648 TGTCTTTTCTTTTC
1 T-TTTTTTCTTTTC
714662 TTTTT
1 TTTTT
714667 GTACTCCAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
12 2 0.04
13 29 0.64
14 14 0.31
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:714662 original size:18 final size:18
Alignment explanation
Indices: 714598--714668 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 18
714588 TTGCTTTATT
*
714598 TTTTACTTTTCTTCTTTTTC
1 TTTT-CTTTTCTT-TTTGTC
* **
714618 TTTTCTTTT-TTTCTGAA
1 TTTTCTTTTCTTTTTGTC
*
714635 TTTT-TCTTCTTTTTGTC
1 TTTTCTTTTCTTTTTGTC
714652 TTTTCTTTTCTTTTTGT
1 TTTTCTTTTCTTTTTGT
714669 ACTCCAATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
16 3 0.08
17 15 0.38
18 13 0.32
19 5 0.12
20 4 0.10
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGTC
Found at i:716300 original size:2 final size:2
Alignment explanation
Indices: 716293--716341 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
716283 TCATAATAGC
716293 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
716335 TA TA TA T
1 TA TA TA T
716342 GATTATAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:719262 original size:5 final size:5
Alignment explanation
Indices: 719242--719300 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
719232 TTCTTTTTGA
* *
719242 CTTTT CTTCT -TTTT CTTTT CTTTT -TTCTT -TTTT CTTGTT TTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTTTT CTT-TT CTTTT CTTTT
719291 CTTTT CTTTT
1 CTTTT CTTTT
719301 TGTACTCCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 7 0.15
5 35 0.76
6 4 0.09
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (5 bp):
CTTTT
Found at i:719269 original size:7 final size:7
Alignment explanation
Indices: 719230--719295 Score: 57
Period size: 7 Copynumber: 9.3 Consensus size: 7
719220 CCTTGGCTTG
719230 TTTTCTT
1 TTTTCTT
*
719237 TTTGACTT
1 TTT-TCTT
719245 TTCTTC-T
1 TT-TTCTT
719252 TTTTC--
1 TTTTCTT
719257 TTTTCTT
1 TTTTCTT
719264 TTTTCTT
1 TTTTCTT
719271 TTTTCTT
1 TTTTCTT
*
719278 GTTTTTTT
1 -TTTTCTT
719286 CTTTTCTT
1 -TTTTCTT
719294 TT
1 TT
719296 CTTTTTGTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
5 5 0.10
6 3 0.06
7 22 0.45
8 18 0.37
9 1 0.02
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:719271 original size:18 final size:18
Alignment explanation
Indices: 719242--719301 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 18
719232 TTCTTTTTGA
719242 CTTTTCTTCTTTTTCTTTT
1 CTTTT-TTCTTTTTCTTTT
*
719261 CTTTTTTCTTTTTTCTTGT
1 CTTTTTTC-TTTTTCTTTT
719280 -TTTTTTC-TTTTCTTTT
1 CTTTTTTCTTTTTCTTTT
719296 CTTTTT
1 CTTTTT
719302 GTACTCCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 8 0.22
17 5 0.14
18 10 0.27
19 14 0.38
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (18 bp):
CTTTTTTCTTTTTCTTTT
Found at i:723826 original size:50 final size:50
Alignment explanation
Indices: 723751--723848 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
723741 ACTCCACTCT
* *
723751 CAATAGTAAACCATCTATTCATGGAATAAAATTCTTTTTAGGGAATTAAG
1 CAATAGTAAACCATCTATTCATGGAATAAAATTCATTTTAGGAAATTAAG
723801 CAATAGTAAACCATCTATTCATGGAATAAAATTCATTTTAGGAAATTA
1 CAATAGTAAACCATCTATTCATGGAATAAAATTCATTTTAGGAAATTA
723849 TCACTTAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (50 bp):
CAATAGTAAACCATCTATTCATGGAATAAAATTCATTTTAGGAAATTAAG
Found at i:729003 original size:33 final size:33
Alignment explanation
Indices: 728961--729060 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
728951 ACCGTAGTGC
728961 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
*
728994 TAATTCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
* * *
729027 TAATCCGTATGACACAGAAGGTCATGTTCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
729060 T
1 T
729061 CTGTACTAGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCGTGTCCACCA
Found at i:729028 original size:17 final size:17
Alignment explanation
Indices: 728975--729029 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
728965 CCGTATGACA
728975 CATAAGGTCGTGTCCAC
1 CATAAGGTCGTGTCCAC
* * *
728992 CATAA-TTCGTAT-GAC
1 CATAAGGTCGTGTCCAC
729007 ACATAAGGTCGTGTCCAC
1 -CATAAGGTCGTGTCCAC
729025 CATAA
1 CATAA
729030 TCCGTATGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.07
16 10 0.34
17 15 0.52
18 2 0.07
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (17 bp):
CATAAGGTCGTGTCCAC
Found at i:735468 original size:33 final size:33
Alignment explanation
Indices: 735369--735468 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
735359 ACTGTAGTGC
* *
735369 TAATCCGTATGAAACATAAGATCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
* **
735402 CAATTTGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
*
735435 TAATCCATATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
735468 T
1 T
735469 CTGTACTAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCGTGTCCACCA
Found at i:738666 original size:27 final size:27
Alignment explanation
Indices: 738629--738686 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
738619 CTTTCTTTTT
*
738629 TTTTTTAAATTCTTCAT-TTTTTTTCTC
1 TTTTTGAAATT-TTCATCTTTTTTTCTC
**
738656 TTTTTGAAATTTTTTTCTTTTTTTCTC
1 TTTTTGAAATTTTCATCTTTTTTTCTC
738683 TTTT
1 TTTT
738687 CTTTCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTTTGAAATTTTCATCTTTTTTTCTC
Found at i:739023 original size:22 final size:21
Alignment explanation
Indices: 738995--739036 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
738985 GGCTACGGAA
738995 TTGATGGTCTTGATAGATGAAG
1 TTGATGGTCTTGAT-GATGAAG
*
739017 TTGATGGTGTTGATGATGAA
1 TTGATGGTCTTGATGATGAA
739037 ATGGAGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.26, C:0.02, G:0.33, T:0.38
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGAAG
Found at i:741408 original size:23 final size:22
Alignment explanation
Indices: 741371--741416 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
741361 AATTATAAAT
*
741371 GAAGATGTTGGTGGTCTTGATG
1 GAAGATGTTGATGGTCTTGATG
*
741393 GAAGATGGTTGATGGTGTTGATG
1 GAAGAT-GTTGATGGTCTTGATG
741416 G
1 G
741417 TGTATGGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.20, C:0.02, G:0.43, T:0.35
Consensus pattern (22 bp):
GAAGATGTTGATGGTCTTGATG
Found at i:747789 original size:16 final size:16
Alignment explanation
Indices: 747768--747799 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
747758 TCTTCCACTA
747768 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
747784 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
747800 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:751145 original size:19 final size:20
Alignment explanation
Indices: 751104--751154 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
751094 GAAACCCCTT
*
751104 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
751124 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
751143 TGAAGATACATG
1 TGAAAATACATG
751155 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:755475 original size:28 final size:28
Alignment explanation
Indices: 755415--755477 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 28
755405 TTTCTTTTCT
**
755415 TTTCTTTT-TCTTCTTTTGAGTGCTGGA
1 TTTCTTTTCTCTTCTTTTGAGTGCTCCA
755442 -TT-TTTTCT-TTCTTTTGAGTGCTCCA
1 TTTCTTTTCTCTTCTTTTGAGTGCTCCA
755467 CTTTCTTTTCT
1 -TTTCTTTTCT
755478 GATTTTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 19 0.63
26 3 0.10
27 2 0.07
28 6 0.20
ACGTcount: A:0.06, C:0.19, G:0.13, T:0.62
Consensus pattern (28 bp):
TTTCTTTTCTCTTCTTTTGAGTGCTCCA
Found at i:767236 original size:20 final size:22
Alignment explanation
Indices: 767207--767246 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
767197 AGGAGAGCTT
767207 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
767227 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
767247 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:778655 original size:24 final size:24
Alignment explanation
Indices: 778626--778675 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
778616 TGGTGGTTGA
*
778626 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
778650 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
778674 TT
1 TT
778676 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:779181 original size:17 final size:16
Alignment explanation
Indices: 779150--779183 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
779140 CACGTGAGGA
779150 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
779166 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
779183 T
1 T
779184 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:788892 original size:24 final size:24
Alignment explanation
Indices: 788863--788912 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
788853 TGGTGGTTGA
*
788863 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
788887 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
788911 TT
1 TT
788913 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:789418 original size:17 final size:16
Alignment explanation
Indices: 789387--789420 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
789377 CACGTGAGGA
789387 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
789403 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
789420 T
1 T
789421 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:797913 original size:19 final size:20
Alignment explanation
Indices: 797866--797916 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
797856 GAAACCCCTT
**
797866 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
797886 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
797905 TGAAGATACATG
1 TGAAAATACATG
797917 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:810463 original size:10 final size:10
Alignment explanation
Indices: 810445--810474 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
810435 GATGTCAAAG
*
810445 GTAGTTGAAT
1 GTAGCTGAAT
810455 GTAGCTGAAT
1 GTAGCTGAAT
810465 GTAGCTGAAT
1 GTAGCTGAAT
810475 ATAATGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (10 bp):
GTAGCTGAAT
Found at i:811587 original size:24 final size:23
Alignment explanation
Indices: 811529--811588 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
811519 AAAATCAGCA
811529 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
* **
811552 AACAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
811576 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
811589 AAAGAAAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.63, C:0.12, G:0.17, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:816550 original size:13 final size:13
Alignment explanation
Indices: 816534--816572 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
816524 GTGCTTTTAA
816534 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
816547 CTTTTCTTTTCTTT
1 CTTTTC-TTTCTTT
*
816561 -TTTTCCTTCTTT
1 CTTTTCTTTCTTT
816573 TTGAGAGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 6 0.25
13 11 0.46
14 7 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:824567 original size:26 final size:26
Alignment explanation
Indices: 824534--824603 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
824524 TCCCATCCTT
*
824534 ATTTCATTTCATTTCTTATATTTATC
1 ATTTCATTTCATTTCTTATATTAATC
*
824560 ATTTCATTTAATCTTCCTT-TATTAATC
1 ATTTCATTTCAT-TT-CTTATATTAATC
*
824587 ATTT-TTTTC-TTTCTTAT
1 ATTTCATTTCATTTCTTAT
824604 CTATGTTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 3 0.08
24 3 0.08
25 1 0.03
26 14 0.38
27 13 0.35
28 3 0.08
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTCATTTCATTTCTTATATTAATC
Found at i:824588 original size:27 final size:26
Alignment explanation
Indices: 824534--824590 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
824524 TCCCATCCTT
* *
824534 ATTTCATTTCATTTCTTATATTTATC
1 ATTTCATTTAATTTCTTATATTAATC
824560 ATTTCATTTAATCTTCCTT-TATTAATC
1 ATTTCATTTAAT-TT-CTTATATTAATC
824587 ATTT
1 ATTT
824591 TTTTCTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 13 0.48
28 3 0.11
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTCATTTAATTTCTTATATTAATC
Found at i:843853 original size:20 final size:21
Alignment explanation
Indices: 843809--843861 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
843799 TTGAACTTCT
843809 TTTTCTTTTCTTCTTTTATGA
1 TTTTCTTTTCTTCTTTTATGA
*
843830 TTTT-TTTTCTTCTTTTTAT-C
1 TTTTCTTTTCTTC-TTTTATGA
843850 TTTTCTTTTCTT
1 TTTTCTTTTCTT
843862 TTTGCACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCTTTTCTTCTTTTATGA
Found at i:845644 original size:27 final size:26
Alignment explanation
Indices: 845590--845646 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
845580 CACCATCTTT
* *
845590 ATTTCATTTCATTTCTTATATTTATC
1 ATTTCATTTAATTTCTTATATTAATC
845616 ATTTCATTTAATATTCCTT-TATTAATC
1 ATTTCATTTAAT-TT-CTTATATTAATC
845643 ATTT
1 ATTT
845647 TTTCTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 13 0.48
28 3 0.11
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTCATTTAATTTCTTATATTAATC
Found at i:853987 original size:22 final size:20
Alignment explanation
Indices: 853962--854001 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
853952 ATGTTTGTTT
853962 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
853984 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
854002 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:854235 original size:15 final size:15
Alignment explanation
Indices: 854212--854247 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
854202 ACTAATATTC
* *
854212 TTATCATAATATATA
1 TTATAATAACATATA
854227 TTATAATAACATATA
1 TTATAATAACATATA
854242 TTATAA
1 TTATAA
854248 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:858274 original size:22 final size:20
Alignment explanation
Indices: 858249--858288 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
858239 ATGTTTGTTT
858249 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
858271 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
858289 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:858522 original size:15 final size:15
Alignment explanation
Indices: 858499--858534 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
858489 ACTAATATTC
* *
858499 TTATCATAATATATA
1 TTATAATAACATATA
858514 TTATAATAACATATA
1 TTATAATAACATATA
858529 TTATAA
1 TTATAA
858535 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:860370 original size:16 final size:16
Alignment explanation
Indices: 860349--860391 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
860339 TGCGACCTTT
860349 CATGAATGATGCTGCC
1 CATGAATGATGCTGCC
860365 CATGAATGATGCTGCC
1 CATGAATGATGCTGCC
860381 CATGAA-GATGC
1 CATGAATGATGC
860392 CTTTTCATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (16 bp):
CATGAATGATGCTGCC
Found at i:861150 original size:19 final size:20
Alignment explanation
Indices: 861126--861165 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
861116 AATCCTTTCT
861126 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
861145 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
861165 T
1 T
861166 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:869340 original size:23 final size:23
Alignment explanation
Indices: 869314--869367 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
869304 CTAACTTTTC
869314 TTTCTTTTTTTTC-TTTTGAGTG
1 TTTCTTTTTTTTCTTTTTGAGTG
**
869336 TTTTCAATTTTTTCTTTTTGAGTG
1 -TTTCTTTTTTTTCTTTTTGAGTG
*
869360 CTTCTTTT
1 TTTCTTTT
869368 CTGATTTTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.70
Consensus pattern (23 bp):
TTTCTTTTTTTTCTTTTTGAGTG
Found at i:871035 original size:21 final size:22
Alignment explanation
Indices: 871009--871049 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
870999 ATCTTTAACC
871009 TATAGAT-GTT-TATTTCATAGT
1 TATAGATAGTTAT-TTTCATAGT
871030 TATAGATAGTTATTTTCATA
1 TATAGATAGTTATTTTCATA
871050 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 10 0.56
23 1 0.06
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (22 bp):
TATAGATAGTTATTTTCATAGT
Found at i:871055 original size:22 final size:21
Alignment explanation
Indices: 871009--871049 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
870999 ATCTTTAACC
871009 TATAGATGTTTATTTCATAGT
1 TATAGATGTTTATTTCATAGT
871030 TATAGATAG-TTATTTTCATA
1 TATAGAT-GTTTA-TTTCATA
871050 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (21 bp):
TATAGATGTTTATTTCATAGT
Found at i:878406 original size:8 final size:8
Alignment explanation
Indices: 878395--878456 Score: 67
Period size: 8 Copynumber: 8.0 Consensus size: 8
878385 TTTTTGGCTC
878395 TTTTTTTG
1 TTTTTTTG
878403 TTTTTTTG
1 TTTTTTTG
**
878411 -CCTTTT-
1 TTTTTTTG
878417 TTTTTTTG
1 TTTTTTTG
*
878425 CCTTTTTTG
1 -TTTTTTTG
878434 -TTTTTTG
1 TTTTTTTG
878441 TTTTTTTG
1 TTTTTTTG
878449 TTTTTTTG
1 TTTTTTTG
878457 AAAAAAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
7 15 0.33
8 23 0.51
9 7 0.16
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:878406 original size:19 final size:17
Alignment explanation
Indices: 878384--878440 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
878374 AAATTTTGGC
878384 TTTTTTGGCTCTTTTTTT
1 TTTTTTGGC-CTTTTTTT
*
878402 GTTTTTTTGCC--TTTTT
1 -TTTTTTGGCCTTTTTTT
*
878418 TTTTTT-GCCTTTTTTG
1 TTTTTTGGCCTTTTTTT
878434 TTTTTTG
1 TTTTTTG
878441 TTTTTTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 3 0.09
15 6 0.18
16 15 0.45
18 1 0.03
19 8 0.24
ACGTcount: A:0.00, C:0.11, G:0.12, T:0.77
Consensus pattern (17 bp):
TTTTTTGGCCTTTTTTT
Found at i:878420 original size:14 final size:14
Alignment explanation
Indices: 878398--878438 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
878388 TTGGCTCTTT
878398 TTTTGTTTTTTTGCC
1 TTTT-TTTTTTTGCC
878413 TTTTTTTTTTTGCC
1 TTTTTTTTTTTGCC
878427 TTTTTTGTTTTT
1 TTTTTT-TTTTT
878439 TGTTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTTTGCC
Found at i:878421 original size:20 final size:20
Alignment explanation
Indices: 878384--878420 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
878374 AAATTTTGGC
*
878384 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
878404 TTTTTTGCCT-TTTTTTT
1 TTTTTTGCCTCTTTTTTT
878421 TTTGCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:878437 original size:21 final size:20
Alignment explanation
Indices: 878395--878445 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
878385 TTTTTGGCTC
*
878395 TTTTTTTGTTTTTTTGCCTTTT
1 TTTTTTTGCTTTTTTG--TTTT
878417 TTTTTTTGCCTTTTTTGTTTT
1 TTTTTTTG-CTTTTTTGTTTT
878438 TTGTTTTT
1 TT-TTTTT
878446 TTGTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 6 0.23
22 13 0.50
23 7 0.27
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (20 bp):
TTTTTTTGCTTTTTTGTTTT
Found at i:878444 original size:14 final size:15
Alignment explanation
Indices: 878396--878454 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
878386 TTTTGGCTCT
878396 TTTTTTGTTTTTTTGC
1 TTTTTTG-TTTTTTGC
*
878412 CTTTTT-TTTTTTGCC
1 TTTTTTGTTTTTTG-C
*
878427 TTTTTTGTTTTTTGT
1 TTTTTTGTTTTTTGC
878442 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
878455 TGAAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
14 7 0.18
15 19 0.50
16 12 0.32
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (15 bp):
TTTTTTGTTTTTTGC
Found at i:895164 original size:22 final size:20
Alignment explanation
Indices: 895139--895178 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
895129 ATGTTTGTTT
895139 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
895161 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
895179 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:896532 original size:13 final size:13
Alignment explanation
Indices: 896510--896539 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
896500 ACTAAACACC
896510 TTTC-ACATACCT
1 TTTCAACATACCT
896522 TTTCAACATACCT
1 TTTCAACATACCT
896535 TTTCA
1 TTTCA
896540 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:900711 original size:22 final size:20
Alignment explanation
Indices: 900686--900725 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
900676 ATGTTTGTTT
900686 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
900708 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
900726 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:908704 original size:2 final size:2
Alignment explanation
Indices: 908697--908728 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
908687 ATTTATTTTC
908697 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
908729 CCTATAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:910067 original size:19 final size:20
Alignment explanation
Indices: 910043--910082 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
910033 TATCATTTCT
910043 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
910062 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
910082 T
1 T
910083 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:910085 original size:19 final size:18
Alignment explanation
Indices: 910039--910085 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
910029 TCTCTATCAT
910039 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
910056 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
910075 TTACTTATATT
1 TT-CTTATATT
910086 ATTACCCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:913494 original size:10 final size:9
Alignment explanation
Indices: 913462--913492 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
913452 TTTTTTGAAA
*
913462 TTTTAGCTT
1 TTTTGGCTT
913471 TTTTGGCTT
1 TTTTGGCTT
913480 TTTTGGCTT
1 TTTTGGCTT
913489 TTTT
1 TTTT
913493 TGTTTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.03, C:0.10, G:0.16, T:0.71
Consensus pattern (9 bp):
TTTTGGCTT
Found at i:915164 original size:2 final size:2
Alignment explanation
Indices: 915157--915194 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
915147 TGCTATAATC
*
915157 AT AT AT AT AT AA 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
915195 TATCTATAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:916923 original size:23 final size:22
Alignment explanation
Indices: 916896--916945 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
916886 CTCTATCTTT
*
916896 TTATTTA-TTTCATTTCATTATTA
1 TTATTTATTTTCATTAC-TTA-TA
916919 TTATTTATTTTCATTACTTATA
1 TTATTTATTTTCATTACTTATA
916941 TTATT
1 TTATT
916946 ACCCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 10 0.40
24 8 0.32
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTATTTTCATTACTTATA
Found at i:917229 original size:14 final size:13
Alignment explanation
Indices: 917212--917260 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
917202 GTGCAAAAAG
917212 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
917226 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
917239 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
917250 AAAGAAAAAGA
1 AAAGAAAAAGA
917261 TTTCAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:923394 original size:22 final size:20
Alignment explanation
Indices: 923369--923408 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
923359 ATGTTTGTTT
923369 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
923391 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
923409 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:923642 original size:15 final size:15
Alignment explanation
Indices: 923619--923654 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
923609 ACTAATATTC
* *
923619 TTATCATAATATATA
1 TTATAATAACATATA
923634 TTATAATAACATATA
1 TTATAATAACATATA
923649 TTATAA
1 TTATAA
923655 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:927669 original size:22 final size:20
Alignment explanation
Indices: 927644--927683 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
927634 ATGTTTGTTT
927644 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
927666 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
927684 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:927917 original size:15 final size:15
Alignment explanation
Indices: 927894--927929 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
927884 ACTAATATTC
* *
927894 TTATCATAATATATA
1 TTATAATAACATATA
927909 TTATAATAACATATA
1 TTATAATAACATATA
927924 TTATAA
1 TTATAA
927930 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:928387 original size:23 final size:22
Alignment explanation
Indices: 928360--928409 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
928350 CTCTATCTTT
*
928360 TTATTTA-TTTCATTTCATTATTA
1 TTATTTATTTTCATTAC-TTA-TA
928383 TTATTTATTTTCATTACTTATA
1 TTATTTATTTTCATTACTTATA
928405 TTATT
1 TTATT
928410 ACCCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 10 0.40
24 8 0.32
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTATTTTCATTACTTATA
Found at i:934336 original size:19 final size:19
Alignment explanation
Indices: 934312--934356 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
934302 CCTTGTTGAG
934312 GATGAAGGATAATTTCAAA
1 GATGAAGGATAATTTCAAA
934331 GATGAAGGATAATTTCAAA
1 GATGAAGGATAATTTCAAA
934350 GATGAAG
1 GATGAAG
934357 AAATGGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.24
Consensus pattern (19 bp):
GATGAAGGATAATTTCAAA
Found at i:938562 original size:24 final size:21
Alignment explanation
Indices: 938528--938570 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
938518 TCCACAAGAC
*
938528 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
938550 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
938571 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Done.