Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009267.1 Hibiscus syriacus cultivar Beakdansim tig00112925_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: 1725308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:437159 original size:27 final size:29
Alignment explanation
Indices: 437098--437159 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 29
437088 GAAAAACTTG
* * *
437098 TGATAA-TTAAATTAATATTATTACTTTT
1 TGATAATTTAAAATAATATTATTACGTTA
437126 TGA-AATTTAAAATAA-ATTATTA-GTTA
1 TGATAATTTAAAATAATATTATTACGTTA
437152 TGATAATT
1 TGATAATT
437160 ACATTAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.17
27 13 0.45
28 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (29 bp):
TGATAATTTAAAATAATATTATTACGTTA
Found at i:441822 original size:20 final size:20
Alignment explanation
Indices: 441681--441810 Score: 199
Period size: 20 Copynumber: 6.5 Consensus size: 20
441671 ATTCATGGGT
441681 AACGCGATTCTGACTATCGC
1 AACGCGATTCTGACTATCGC
*
441701 AACGAGATTCTGACTATCGC
1 AACGCGATTCTGACTATCGC
441721 AACGCGATTCTGACTATCGC
1 AACGCGATTCTGACTATCGC
*
441741 AACGAGATTCTGACTATCGC
1 AACGCGATTCTGACTATCGC
**
441761 AACGCGATAAT-ACGTGATCGC
1 AACGCGATTCTGAC-T-ATCGC
441782 AACGCGATTCTGACTATCGC
1 AACGCGATTCTGACTATCGC
441802 AACGCGATT
1 AACGCGATT
441811 TTGAGTAACG
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
19 2 0.02
20 80 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (20 bp):
AACGCGATTCTGACTATCGC
Found at i:442694 original size:24 final size:24
Alignment explanation
Indices: 442643--442696 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
442633 GTATTCGAAA
*
442643 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
442667 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
442691 TTTGAT
1 TTTGAT
442697 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:445131 original size:20 final size:20
Alignment explanation
Indices: 445106--445312 Score: 221
Period size: 20 Copynumber: 10.7 Consensus size: 20
445096 CACATTCATT
445106 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
*
445126 TGACTATCGCAACGCGATTA
1 TGACTATCGCAACGCGAATA
* *
445146 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
445166 TGACTATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
445186 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
445206 TAATTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
445226 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
445243 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
** *
445259 TGACTATCGCAATACGAATT
1 TGACTATCGCAACGCGAATA
* * *
445279 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
445299 TGACTATCGCAACG
1 TGACTATCGCAACG
445313 AGAAAATCGC
Statistics
Matches: 155, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
14 7 0.05
16 5 0.03
17 4 0.03
18 2 0.01
19 11 0.07
20 126 0.81
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:445176 original size:60 final size:60
Alignment explanation
Indices: 445103--445312 Score: 247
Period size: 60 Copynumber: 3.6 Consensus size: 60
445093 TTACACATTC
*
445103 ATTTGACTATCGCAACGCGAATATGACTATCGCAACGCGATTATGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGAATATGACTATCGCAACGCGATTATGACTATCGCAACGCGA
* * * *
445163 ATTTGACTATCGCAATGCGAAAATGACTATCGCAACGCGAATT-TAATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATATGACTATCGCAACGCG-ATTATGACTATCGCAACGCGA
* * **
445223 ATTTGACTATCGCAA--CG-AGAT-A--ATCGCAACGCGA-AATGACTATCGCAATACGA
1 ATTTGACTATCGCAACGCGAATATGACTATCGCAACGCGATTATGACTATCGCAACGCGA
* * *
445276 ATTTGATTATCGCAACGGGAATTTGACTATCGCAACG
1 ATTTGACTATCGCAACGCGAATATGACTATCGCAACG
445313 AGAAAATCGC
Statistics
Matches: 127, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
53 28 0.22
54 11 0.09
55 1 0.01
56 3 0.02
57 4 0.03
58 2 0.02
59 9 0.07
60 66 0.52
61 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (60 bp):
ATTTGACTATCGCAACGCGAATATGACTATCGCAACGCGATTATGACTATCGCAACGCGA
Found at i:445487 original size:36 final size:34
Alignment explanation
Indices: 445447--445526 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 34
445437 TCAACTTTTA
*
445447 ATCAATTAAACAAGCACAAATAATAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
445483 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
*
445513 ATCAAATAAACAAA
1 ATCAATTAAACAAA
445527 TCAACTCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 26 0.68
32 2 0.05
34 3 0.08
36 7 0.18
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:445497 original size:30 final size:30
Alignment explanation
Indices: 445462--445527 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
445452 TTAAACAAGC
* *
445462 ACAAATAATAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAAATAA
445492 ACAAATAAGAATTATTTACACATCAAATAA
1 ACAAATAAGAATTATTTACACATCAAATAA
445522 ACAAAT
1 ACAAAT
445528 CAACTCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAAATAA
Found at i:447491 original size:20 final size:20
Alignment explanation
Indices: 447466--447509 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
447456 TATAGTTTCT
447466 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
447486 GAAACTTAAAATTGCAACAC
1 GAAACTTAAAATCGCAACAC
447506 GAAA
1 GAAA
447510 ATGATTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:447522 original size:20 final size:20
Alignment explanation
Indices: 447476--447543 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
447466 GAAACTTAAA
* * *
447476 ATCGCAACACGAAACTTAAA
1 ATCGCAACACGAAAATGAAT
* *
447496 ATTGCAACACGAAAATGATT
1 ATCGCAACACGAAAATGAAT
* ** *
447516 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGAAT
447536 ATCGCAAC
1 ATCGCAAC
447544 GAGATAATCG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.21
Consensus pattern (20 bp):
ATCGCAACACGAAAATGAAT
Found at i:447692 original size:74 final size:74
Alignment explanation
Indices: 447571--447728 Score: 262
Period size: 74 Copynumber: 2.1 Consensus size: 74
447561 AAACTAAATT
447571 CGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATAGTCAAATTCGCGTTGCGAT
1 CGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATAGTCAAATTCGCGTTGCGAT
*
447636 AGTCATTTC
66 AATCATTTC
* * *
447645 CGCGTTGCGATAGTCGTTTTCGCATTGCGATTATCCCGTTGTGATAGTCAAATTCGCGTTGCGAT
1 CGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATAGTCAAATTCGCGTTGCGAT
*
447710 AATCATTTT
66 AATCATTTC
*
447719 CGTGTTGCGA
1 CGCGTTGCGA
447729 CTATTCTTCT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (74 bp):
CGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCATTGCGATAGTCAAATTCGCGTTGCGAT
AATCATTTC
Found at i:447720 original size:20 final size:20
Alignment explanation
Indices: 447569--447728 Score: 110
Period size: 20 Copynumber: 8.6 Consensus size: 20
447559 CGAAACTAAA
447569 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
*
447589 TTCGCATTGCGAT--T-A--
1 TTCGCGTTGCGATAGTCATT
* * **
447604 -TCCCATTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCATT
447623 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
* *
447643 TCCGCGTTGCGATAGTCGTT
1 TTCGCGTTGCGATAGTCATT
*
447663 TTCGCATTGCGAT--T-A--
1 TTCGCGTTGCGATAGTCATT
* * **
447678 -TCCCGTTGTGATAGTCAAA
1 TTCGCGTTGCGATAGTCATT
*
447697 TTCGCGTTGCGATAATCATT
1 TTCGCGTTGCGATAGTCATT
*
447717 TTCGTGTTGCGA
1 TTCGCGTTGCGA
447729 CTATTCTTCT
Statistics
Matches: 108, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
14 20 0.19
16 2 0.02
17 3 0.03
18 2 0.02
20 81 0.75
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCATT
Found at i:449748 original size:20 final size:20
Alignment explanation
Indices: 449725--449792 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
449715 GAAACTTAAA
* *
449725 ATCGCAACACGAAAATGATT
1 ATCGCAACGCGAAAATGACT
**
449745 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
449765 ATCGCAACGCG-AAATGGCT
1 ATCGCAACGCGAAAATGACT
449784 ATCGCAACG
1 ATCGCAACG
449793 AGATAATCGC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 14 0.34
20 27 0.66
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:450178 original size:22 final size:22
Alignment explanation
Indices: 450151--450220 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
450141 GATGGAGATA
450151 GACGGATTTCGCAGGAGATGGG
1 GACGGATTTCGCAGGAGATGGG
* *
450173 GACGGATTTCGCCGGAAATGGG
1 GACGGATTTCGCAGGAGATGGG
450195 GACGGATTTCGTCA-GAGATGGG
1 GACGGATTTCG-CAGGAGATGGG
450217 GACG
1 GACG
450221 AATGTCGCCG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCAGGAGATGGG
Found at i:450395 original size:20 final size:20
Alignment explanation
Indices: 450372--450497 Score: 164
Period size: 20 Copynumber: 6.2 Consensus size: 20
450362 AAATCGCAAC
*
450372 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCGCGTT
*
450392 GCGATAGTCAGAATCGAGTT
1 GCGATAGTCAGAATCGCGTT
**
450412 GCGATCACGT-ATTATCGCGTT
1 GCGAT-A-GTCAGAATCGCGTT
*
450433 GCGATAGTCCGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
*
450453 GCGATAGTCAGAATCGCATT
1 GCGATAGTCAGAATCGCGTT
*
450473 GCGATAGTTAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
450493 GCGAT
1 GCGAT
450498 CACGTGTTAT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 73 0.80
21 14 0.15
22 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:450518 original size:61 final size:60
Alignment explanation
Indices: 450372--450497 Score: 168
Period size: 61 Copynumber: 2.1 Consensus size: 60
450362 AAATCGCAAC
* **
450372 GCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGAGTTGCGATCACGTATTATCGCGTT
1 GCGATAGTC-GAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATCACGTAGAATCGCGTT
450433 GCGATAGTCCGAATCGCGTTGCGATAGTCAGAATCGCA-TTGCGAT-A-GTTAGAATCGCGTT
1 GCGATAGT-CGAATCGCGTTGCGATAGTCAGAATCG-AGTTGCGATCACG-TAGAATCGCGTT
450493 GCGAT
1 GCGAT
450498 CACGTGTTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
59 1 0.02
60 16 0.27
61 40 0.68
62 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (60 bp):
GCGATAGTCGAATCGCGTTGCGATAGTCAGAATCGAGTTGCGATCACGTAGAATCGCGTT
Found at i:450538 original size:81 final size:81
Alignment explanation
Indices: 450363--450518 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
450353 GCGCTTTGAA
** * *
450363 AATCGCAACGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGAGTTGCGATCACGTATTATC
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATAGTCAGAATCGAGTTGCGATCACGTATTATC
*
450428 GCGTTGCGATAGTCCG
66 GCGTTGCGATAGTCAG
* * * *
450444 AATCGCGTTGCGATAGTCAGAATCGCATTGCGATAGTTAGAATCGCGTTGCGATCACGTGTTATC
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATAGTCAGAATCGAGTTGCGATCACGTATTATC
450509 GCGTTGCGAT
66 GCGTTGCGAT
450519 TTATATATTC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (81 bp):
AATCGCATTGCGATAGTCAGAATCGCATTGCGATAGTCAGAATCGAGTTGCGATCACGTATTATC
GCGTTGCGATAGTCAG
Found at i:450557 original size:21 final size:21
Alignment explanation
Indices: 450527--450599 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
450517 ATTTATATAT
* *
450527 TCGCATTGC-GATTATCTAAAA
1 TCGCAATGCGGATT-TCGAAAA
450548 TCGCAATGCGGATTTCGAAAA
1 TCGCAATGCGGATTTCGAAAA
450569 TCGCAATGCGGATTTCGAAAA
1 TCGCAATGCGGATTTCGAAAA
*
450590 TCGTAATGCG
1 TCGCAATGCG
450600 ATGGTCAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
21 44 0.92
22 4 0.08
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (21 bp):
TCGCAATGCGGATTTCGAAAA
Found at i:450671 original size:19 final size:19
Alignment explanation
Indices: 450646--450701 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
450636 TGCGATAATG
*
450646 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
* *
450665 TAGATCGTATTGCGATTTA
1 GAGATCGCATTGCGATTTA
450684 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
450702 TGTTGGTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:451570 original size:2 final size:2
Alignment explanation
Indices: 451565--451702 Score: 78
Period size: 2 Copynumber: 71.0 Consensus size: 2
451555 TTTTTTAGTT
*
451565 TA TA TA TA TA TA TA TA TA TA CT- TA TA T- TA TA TA GTT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* * * *
451606 TA TA TA TA TA TA TA TA TA -A AA GTA TA TA TT TA TA -A TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
451647 CA TA -A GTA TA -A TG TA CA T- TA TA TA TA CA TG TA TCA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
451688 TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA
451703 ATTGTTTCAA
Statistics
Matches: 103, Mismatches: 19, Indels: 28
0.69 0.13 0.19
Matches are distributed among these distances:
1 9 0.09
2 88 0.85
3 6 0.06
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:451677 original size:17 final size:18
Alignment explanation
Indices: 451613--451691 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 18
451603 TATTATATAT
*
451613 ATATATATATAAAAGTAT-
1 ATATATATAT-AATGTATC
451631 ATAT-T-TATAATGTATGC
1 ATATATATATAATGTAT-C
*
451648 ATA-A-GTATAATGTA-C
1 ATATATATATAATGTATC
451663 AT-TATATATACATGTATC
1 ATATATATATA-ATGTATC
451681 ATATATATATA
1 ATATATATATA
451692 TATATATTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
15 10 0.20
16 7 0.14
17 18 0.36
18 7 0.14
19 8 0.16
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
ATATATATATAATGTATC
Found at i:451788 original size:22 final size:22
Alignment explanation
Indices: 451760--451804 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
451750 CATTTTGTAA
451760 TTTTTTTATCACATTCTACAAT
1 TTTTTTTATCACATTCTACAAT
451782 TTTTTTTATCACATTCTACAAT
1 TTTTTTTATCACATTCTACAAT
451804 T
1 T
451805 ATTATGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTTTATCACATTCTACAAT
Found at i:452314 original size:2 final size:2
Alignment explanation
Indices: 452307--452343 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
452297 GAATGCGTTT
452307 TA 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 TA T
452344 GAGAATTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:454299 original size:167 final size:169
Alignment explanation
Indices: 454010--454345 Score: 658
Period size: 167 Copynumber: 2.0 Consensus size: 169
454000 GGAGACTAAG
454010 CCTTGCCCGACCAAAAAGTGTTACAGGCGGCCTTTTGCTTGGAGGAGACAAGGTCAAGAGATTTT
1 CCTTGCCCGACCAAAAAGTGTTACAGGCGGCCTTTTGCTTGGAGGAGACAAGGTCAAGAGATTTT
454075 TCTTGTAAGATGATATGATAATAGGCTGCAGTACAGGTTCTGCACAATTTTGAGTGAGCTCATTA
66 TCTTGTAAGATGATATGATAATAGGCTGCAGTACAGGTTCTGCACAATTTTGAGTGAGCTCATTA
454140 ACCTTGGGAGGACAAGCTACAGTTTTGACAGGTGAATTT
131 ACCTTGGGAGGACAAGCTACAGTTTTGACAGGTGAATTT
454179 CCTTGCCCGACC-AAAAGTGTTACAGGCGGCCTTTTGCTTGGAGGAGACAAGGTCAAGAGATTTT
1 CCTTGCCCGACCAAAAAGTGTTACAGGCGGCCTTTTGCTTGGAGGAGACAAGGTCAAGAGATTTT
454243 TC-TGTAAGATGATATGATAATAGGCTGCAGTACAGGTTCTGCACAATTTTGAGTGAGCTCATTA
66 TCTTGTAAGATGATATGATAATAGGCTGCAGTACAGGTTCTGCACAATTTTGAGTGAGCTCATTA
454307 ACCTTGGGAGGACAAGCTACAGTTTTGACAGGTGAATTT
131 ACCTTGGGAGGACAAGCTACAGTTTTGACAGGTGAATTT
454346 ACTGGTGGAC
Statistics
Matches: 167, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
167 101 0.60
168 54 0.32
169 12 0.07
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (169 bp):
CCTTGCCCGACCAAAAAGTGTTACAGGCGGCCTTTTGCTTGGAGGAGACAAGGTCAAGAGATTTT
TCTTGTAAGATGATATGATAATAGGCTGCAGTACAGGTTCTGCACAATTTTGAGTGAGCTCATTA
ACCTTGGGAGGACAAGCTACAGTTTTGACAGGTGAATTT
Found at i:459853 original size:87 final size:87
Alignment explanation
Indices: 459707--459880 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
459697 GTGATATTTG
459707 CAGACATCTTAATTTAAGAAGCGTGTCTCCGTACAAAGGCACAATATATGGCCCACACCGGGAGA
1 CAGACATCTTAATTTAAGAAGCGTGTCTCCGTACAAAGGCACAATATATGGCCCACACCGGGAGA
459772 CATACGCATAATTTTATTTTAA
66 CATACGCATAATTTTATTTTAA
459794 CAGACATCTTAATTTAAGAAGCGTGTCTCCGTACAAAGGCACAATATATGGCCCACACCGGGAGA
1 CAGACATCTTAATTTAAGAAGCGTGTCTCCGTACAAAGGCACAATATATGGCCCACACCGGGAGA
459859 CATACGCATAATTTTATTTTAA
66 CATACGCATAATTTTATTTTAA
459881 GAACGACGAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (87 bp):
CAGACATCTTAATTTAAGAAGCGTGTCTCCGTACAAAGGCACAATATATGGCCCACACCGGGAGA
CATACGCATAATTTTATTTTAA
Found at i:461134 original size:171 final size:171
Alignment explanation
Indices: 460849--461192 Score: 643
Period size: 171 Copynumber: 2.0 Consensus size: 171
460839 ATTATTTCTC
460849 TTCGACTGCATTTCTAATATAGGCTGCTCAAAGAGTTAAGATAAGAACAGGGATTTAGCTTAAAT
1 TTCGACTGCATTTCTAATATAGGCTGCTCAAAGAGTTAAGATAAGAACAGGGATTTAGCTTAAAT
*
460914 CCAGCTTTAGTTATAAGAAAACTTAAAGTACAAGATAATGGTTTAGAAATGTGAAAACAAATCTA
66 CCAGCTCTAGTTATAAGAAAACTTAAAGTACAAGATAATGGTTTAGAAATGTGAAAACAAATCTA
* *
460979 GCTCAAGTGTTGAGCATCGCTGTGAAAAGTGCTGCTATTTG
131 GCTCAAGTGTTGAGCATCGATGTGAAAAGTGCTGCTATCTG
461020 TTCGACTGCATTTCTAATATAGGCTGCTCAAAGAGTTAAGATAAGAACAGGGATTTAGCTTAAAT
1 TTCGACTGCATTTCTAATATAGGCTGCTCAAAGAGTTAAGATAAGAACAGGGATTTAGCTTAAAT
* *
461085 CCAGCTCTAGTTATAAGAAAACTTCAAGTATAAGATAATGGTTTAGAAATGTGAAAACAAATCTA
66 CCAGCTCTAGTTATAAGAAAACTTAAAGTACAAGATAATGGTTTAGAAATGTGAAAACAAATCTA
461150 GCTCAAGTGTTGAGCATCGATGTGAAAAGTGCTGCTATCTG
131 GCTCAAGTGTTGAGCATCGATGTGAAAAGTGCTGCTATCTG
461191 TT
1 TT
461193 GAATTAAAAT
Statistics
Matches: 168, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
171 168 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (171 bp):
TTCGACTGCATTTCTAATATAGGCTGCTCAAAGAGTTAAGATAAGAACAGGGATTTAGCTTAAAT
CCAGCTCTAGTTATAAGAAAACTTAAAGTACAAGATAATGGTTTAGAAATGTGAAAACAAATCTA
GCTCAAGTGTTGAGCATCGATGTGAAAAGTGCTGCTATCTG
Found at i:466415 original size:28 final size:29
Alignment explanation
Indices: 466345--466420 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
466335 ATCAAATACG
* * *
466345 CTGAATGCTAAACGGTTTAGCATTCAACA
1 CTGAATGATGAACGGTTCAGCATTCAACA
466374 CTGAATGATGAACGGTTCAGCATTC-ACA
1 CTGAATGATGAACGGTTCAGCATTCAACA
* *
466402 TTGAATGGTGAACGGTTCA
1 CTGAATGATGAACGGTTCA
466421 ACAATAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 20 0.48
29 22 0.52
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (29 bp):
CTGAATGATGAACGGTTCAGCATTCAACA
Found at i:474187 original size:81 final size:80
Alignment explanation
Indices: 474022--474188 Score: 217
Period size: 81 Copynumber: 2.1 Consensus size: 80
474012 CCTAACCGAA
** * *
474022 TTAATTAGAAAATTATTAACCAAACTGAATTAACTGCTTTTTGAAAATTATTAACCGAATTAATT
1 TTAATTAGAAAATTATTAACCAAACCAAATTAACAGCTTTTTGAAAATCATTAACCGAATTAATT
*
474087 GAAGTAAAAATTTGC
66 GAAGAAAAAATTTGC
* * ** **
474102 TTAATTTGAAAATTATTAATCAAACCAAATTAACAGCTTTTTTTTAAATCATTAATGGAATTAAT
1 TTAATTAGAAAATTATTAACCAAACCAAATTAACAGC-TTTTTGAAAATCATTAACCGAATTAAT
*
474167 TGAAGAAAAAATTTGG
65 TGAAGAAAAAATTTGC
474183 TTAATT
1 TTAATT
474189 CAGTTCAGTT
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
80 32 0.43
81 42 0.57
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (80 bp):
TTAATTAGAAAATTATTAACCAAACCAAATTAACAGCTTTTTGAAAATCATTAACCGAATTAATT
GAAGAAAAAATTTGC
Found at i:474279 original size:34 final size:29
Alignment explanation
Indices: 474213--474271 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
474203 AAACCAAACT
*
474213 ATTTGAAAATTATTAACCGAACTGAATTA
1 ATTTGAAAATTATTAACCGAACCGAATTA
474242 ATTTGAAAATTATTAACCGAACCGAATTA
1 ATTTGAAAATTATTAACCGAACCGAATTA
474271 A
1 A
474272 CCTAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (29 bp):
ATTTGAAAATTATTAACCGAACCGAATTA
Found at i:474481 original size:17 final size:17
Alignment explanation
Indices: 474434--474471 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
474424 AACAACTTAC
* *
474434 AATTAATTTAAA-TAAT
1 AATTTATTTAAACAAAT
474450 AATTTATTTAAACAAAT
1 AATTTATTTAAACAAAT
474467 AATTT
1 AATTT
474472 TTTTTGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTATTTAAACAAAT
Found at i:474898 original size:30 final size:29
Alignment explanation
Indices: 474859--474921 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
474849 TAACGGCCGA
*
474859 TGGT-TGATTGAATCAATTAAATAGTTGGG
1 TGGTCTGATTGAATCAATTAAA-AGTTCGG
*
474888 TGGTCTGATTGATTCAATTAAAAGTTCGG
1 TGGTCTGATTGAATCAATTAAAAGTTCGG
474917 TGGTC
1 TGGTC
474922 ATATTGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (29 bp):
TGGTCTGATTGAATCAATTAAAAGTTCGG
Found at i:474918 original size:29 final size:30
Alignment explanation
Indices: 474859--474930 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
474849 TAACGGCCGA
* *
474859 TGGT-TGATTGAATCAATTAAATAGTTGGG
1 TGGTCTGATTGATTCAATTAAATAGTTCGG
474888 TGGTCTGATTGATTCAATTAAA-AGTTCGG
1 TGGTCTGATTGATTCAATTAAATAGTTCGG
474917 TGGTCAT-ATTGATT
1 TGGTC-TGATTGATT
474931 TTTTATCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (30 bp):
TGGTCTGATTGATTCAATTAAATAGTTCGG
Found at i:475206 original size:20 final size:20
Alignment explanation
Indices: 475183--475300 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 20
475173 ATTCGCGTTG
475183 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
475203 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* **
475224 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * *
475244 CATTTCGCGTTGCTATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* **
475265 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
475285 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
475301 AGTTGAAATG
Statistics
Matches: 74, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 45 0.61
21 29 0.39
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:475233 original size:21 final size:21
Alignment explanation
Indices: 475207--475319 Score: 99
Period size: 20 Copynumber: 5.6 Consensus size: 21
475197 ATTTTCCATT
475207 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
475228 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
475248 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
475269 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
475289 TCGCGTTGCGATAGTTG-AAA
1 TCGCGTTGCGATAGTTGAAAA
475309 T-GCGTTGCGAT
1 TCGCGTTGCGAT
475320 TTTCCATTCG
Statistics
Matches: 69, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
19 10 0.14
20 31 0.45
21 28 0.41
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:475325 original size:39 final size:41
Alignment explanation
Indices: 475187--475384 Score: 270
Period size: 41 Copynumber: 5.0 Consensus size: 41
475177 GCGTTGCATT
475187 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
475228 TCGCGTTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
475269 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG-AAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
475309 T-GCGTTGCGATTTTCCA-TT--CGTTGCGATAGTCT-ACAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAA
* * *
475346 T-GTGTTGCGATTTTCCAAATT--CGTTGCGATAGTTAAAAA
1 TCGCGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTTGAAAA
475385 AAAGATTTTG
Statistics
Matches: 147, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
36 12 0.08
37 18 0.12
38 4 0.03
39 33 0.22
40 4 0.03
41 76 0.52
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:476125 original size:41 final size:40
Alignment explanation
Indices: 476080--476305 Score: 202
Period size: 41 Copynumber: 5.7 Consensus size: 40
476070 CAACGAATTT
476080 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAA-TTGGAAAATCGCAACGACAACTGTAGACTA
* * * * * * *
476121 TCGCATCGCGAACTGAAAAATTGCAACG-CGATTTTCA-ACTA
1 TCGCA--ACGAATTGGAAAATCGCAACGACAACTGT-AGACTA
* *
476162 TCGCAACGCGAAATGGAAAATCGCAACG-CGA-T-T----T-
1 TCGCAA--CGAATTGGAAAATCGCAACGACAACTGTAGACTA
476196 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAA-TTGGAAAATCGCAACGACAACTGTAGACTA
476237 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAA-TTGGAAAATCGCAACGACAACTGTAGACTA
*
476278 TCGCAACGCGAACTGGAAAATCGCAACG
1 TCGCAA--CGAATTGGAAAATCGCAACG
476306 CGAAATGGAA
Statistics
Matches: 155, Mismatches: 14, Indels: 31
0.77 0.07 0.16
Matches are distributed among these distances:
32 4 0.03
33 15 0.10
34 8 0.05
35 2 0.01
36 1 0.01
39 1 0.01
40 2 0.01
41 85 0.55
42 29 0.19
43 8 0.05
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (40 bp):
TCGCAACGAATTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:476220 original size:19 final size:19
Alignment explanation
Indices: 476196--476264 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
476186 AACGCGATTT
476196 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
476215 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
476237 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
476256 TCGCAACGA
1 TCGCAACGA
476265 CAACTGTAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 22 0.56
20 2 0.05
21 2 0.05
22 13 0.33
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:476242 original size:22 final size:22
Alignment explanation
Indices: 476214--476285 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
476204 AATTTGGAAA
476214 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
476236 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
476255 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
476277 ATCGCAACG
1 ATCGCAACG
476286 CGAACTGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:476278 original size:116 final size:115
Alignment explanation
Indices: 476076--476308 Score: 344
Period size: 116 Copynumber: 2.0 Consensus size: 115
476066 ATCACAACGA
*
476076 ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCATCGCGAACTGAAAAA
1 ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCA-CACGAACTGAAAAA
* * * *
476141 TTGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCG
65 TCGCAACGCAACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCG
* *
476192 ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCA-ACGAATTTGGAAAA
1 ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCACACGAA-CTGAAAAA
*
476256 TCGCAACGACAACTGT-AGACTATCGCAACGCGAACTGGAAAATCGCAACGCG
65 TCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCG
476308 A
1 A
476309 AATGGAAAAT
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
114 4 0.04
115 14 0.13
116 88 0.83
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (115 bp):
ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCACACGAACTGAAAAAT
CGCAACGCAACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCG
Found at i:476302 original size:20 final size:20
Alignment explanation
Indices: 476249--476328 Score: 99
Period size: 20 Copynumber: 3.9 Consensus size: 20
476239 GCAACGAATT
476249 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
476269 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
*
476291 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAC
476311 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
476329 TTTTCAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
20 35 0.67
21 1 0.02
22 16 0.31
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:476394 original size:68 final size:60
Alignment explanation
Indices: 476120--476418 Score: 199
Period size: 61 Copynumber: 4.9 Consensus size: 60
476110 ACTGTAGACT
* * * *
476120 ATCGCATCGCGAACTGAAAAATTGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAA-TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
** * ** * **
476181 ATCGCAACGCG-AT----TTTCGCAACG-AATTTGGAA-AATCGCAACGAC-AACTGTAGACT
1 ATCGCAACGCGAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACG-CGAACTG--GAAA
* * *
476236 ATCGCAA--CGAATTTGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAA--TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAACTGGAAA
476297 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGAATCGCAA
1 ATCGCAACGCG-AATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAACTG----G-AA
476362 A
60 A
* *
476363 ATCGCAACGCG-ATGGAAAATCTATCGCAACGCGATTTTCAATTATCGCAATGCGAA
1 ATCGCAACGCGAATGG-AAA---ATCGCAACGCGATTTTCAACTATCGCAACGCGAA
476419 ATGCAACGCG
Statistics
Matches: 186, Mismatches: 24, Indels: 49
0.72 0.09 0.19
Matches are distributed among these distances:
53 15 0.08
54 8 0.04
55 16 0.09
56 1 0.01
59 1 0.01
60 9 0.05
61 43 0.23
62 21 0.11
63 16 0.09
64 6 0.03
65 4 0.02
66 14 0.08
68 32 0.17
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (60 bp):
ATCGCAACGCGAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
Found at i:478072 original size:8 final size:9
Alignment explanation
Indices: 478059--478134 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
478049 ATATTAGAAG
478059 TTATAAA-T
1 TTATAAATT
478067 TTATAAAATT
1 TTAT-AAATT
*
478077 TTAAAAATT
1 TTATAAATT
*
478086 TTATAAAAT
1 TTATAAATT
**
478095 AAATAAAATT
1 TTAT-AAATT
*
478105 TTAAAAATT
1 TTATAAATT
*
478114 TTAAAAATT
1 TTATAAATT
*
478123 TTAAAAATT
1 TTATAAATT
478132 TTA
1 TTA
478135 AATTTTTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
8 4 0.07
9 43 0.77
10 9 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTATAAATT
Found at i:478077 original size:9 final size:8
Alignment explanation
Indices: 478063--478164 Score: 60
Period size: 9 Copynumber: 11.4 Consensus size: 8
478053 TAGAAGTTAT
478063 AAATTTATA
1 AAATTT-TA
478072 AAATTTTAA
1 AAATTTT-A
478081 AAATTTTATA
1 AAA-TTT-TA
**
478091 AAATAAATA
1 AAAT-TTTA
478100 AAATTTTAA
1 AAATTTT-A
478109 AAATTTTAA
1 AAATTTT-A
478118 AAATTTTAA
1 AAATTTT-A
478127 AAATTTTA
1 AAATTTTA
*
478135 AATTTTTTTA
1 AA--ATTTTA
**
478145 AAATAAATA
1 AAAT-TTTA
478154 AAATTTTA
1 AAATTTTA
478162 AAA
1 AAA
478165 GATAAAAATA
Statistics
Matches: 75, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
8 11 0.15
9 49 0.65
10 14 0.19
11 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAATTTTA
Found at i:478086 original size:18 final size:18
Alignment explanation
Indices: 478059--478164 Score: 85
Period size: 18 Copynumber: 5.9 Consensus size: 18
478049 ATATTAGAAG
*
478059 TTAT-AAATTTATAAAATT
1 TTATAAAATTT-TAAAAAT
478077 TTA-AAAATTTTATAAAAT
1 TTATAAAATTTTA-AAAAT
**
478095 AAATAAAATTTTAAAAAT
1 TTATAAAATTTTAAAAAT
478113 TT-TAAAAATTTTAAAAAT
1 TTAT-AAAATTTTAAAAAT
* *
478131 TT-TAAATTTTTTTAAAAT
1 TTATAAA-ATTTTAAAAAT
**
478149 AAATAAAATTTTAAAA
1 TTATAAAATTTTAAAA
478165 GATAAAAATA
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
17 6 0.08
18 52 0.73
19 13 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATAAAATTTTAAAAAT
Found at i:478090 original size:19 final size:18
Alignment explanation
Indices: 478066--478136 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
478056 AAGTTATAAA
478066 TTTATAAAATTTTAAAAAT
1 TTTA-AAAATTTTAAAAAT
**
478085 TTTATAAAA-TAAATAAAAT
1 TTTA-AAAATTTTA-AAAAT
478104 TTTAAAAATTTTAAAAAT
1 TTTAAAAATTTTAAAAAT
478122 TTTAAAAATTTTAAA
1 TTTAAAAATTTTAAA
478137 TTTTTTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 26 0.57
19 20 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAAAATTTTAAAAAT
Found at i:478100 original size:28 final size:28
Alignment explanation
Indices: 478069--478164 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
478059 TTATAAATTT
478069 ATAAAATTTTAAAAATTTTATAAAATAA
1 ATAAAATTTTAAAAATTTTATAAAATAA
*
478097 ATAAAATTTTAAAAATTTTA-AAAAT-T
1 ATAAAATTTTAAAAATTTTATAAAATAA
* * *
478123 TTAAAAATTTT-AAATTTTTTTAAAATAA
1 AT-AAAATTTTAAAAATTTTATAAAATAA
478151 ATAAAATTTTAAAA
1 ATAAAATTTTAAAA
478165 GATAAAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.14
27 26 0.45
28 24 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAAAATTTTAAAAATTTTATAAAATAA
Found at i:483389 original size:62 final size:62
Alignment explanation
Indices: 483292--483416 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
483282 TCATCGGGAG
483292 ACAATTAAACACATAGACTCCTATCAAAATTTCTTGAAGAACCAATAACATATGATCATTGC
1 ACAATTAAACACATAGACTCCTATCAAAATTTCTTGAAGAACCAATAACATATGATCATTGC
483354 ACAATTAAACACATAGACTCCTATCAAAATTTCTTGAAGAACCAATAACATATGATCATTGC
1 ACAATTAAACACATAGACTCCTATCAAAATTTCTTGAAGAACCAATAACATATGATCATTGC
483416 A
1 A
483417 TGTAGGGATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (62 bp):
ACAATTAAACACATAGACTCCTATCAAAATTTCTTGAAGAACCAATAACATATGATCATTGC
Found at i:487194 original size:31 final size:32
Alignment explanation
Indices: 487148--487207 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
487138 TGTTGGTTGC
487148 TGTTGTAGTTGTTGTTTT-TGGTTGTTATGTT
1 TGTTGTAGTTGTTGTTTTGTGGTTGTTATGTT
* *
487179 TGTTTTAGTTTTTGTTTTGTGGTTGTTAT
1 TGTTGTAGTTGTTGTTTTGTGGTTGTTAT
487208 TCTCTATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.07, C:0.00, G:0.27, T:0.67
Consensus pattern (32 bp):
TGTTGTAGTTGTTGTTTTGTGGTTGTTATGTT
Found at i:487850 original size:20 final size:19
Alignment explanation
Indices: 487808--487853 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
487798 TACTTATATT
*
487808 TATATTTGTTTTCAAACCA
1 TATATTTGTTTTCAAAACA
487827 TATATTATGTTTTCTAAAACTA
1 TATATT-TGTTTTC-AAAAC-A
487849 TATAT
1 TATAT
487854 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 7 0.30
21 4 0.17
22 6 0.26
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (19 bp):
TATATTTGTTTTCAAAACA
Found at i:487887 original size:22 final size:21
Alignment explanation
Indices: 487857--487934 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 21
487847 TATATATATA
487857 TATATATATATATTTCAAAAC
1 TATATATATATATTTCAAAAC
*
487878 TATATTATATATACGTTTTTTCAAAAT
1 TATA-TATATATA-----TTTCAAAAC
*
487905 TATATATTTAT-TTTCAAAAC
1 TATATATATATATTTCAAAAC
487925 TATATATATA
1 TATATATATA
487935 ACCAAAACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
20 17 0.36
21 4 0.09
22 8 0.17
26 6 0.13
27 12 0.26
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (21 bp):
TATATATATATATTTCAAAAC
Found at i:488593 original size:181 final size:181
Alignment explanation
Indices: 488160--488642 Score: 618
Period size: 181 Copynumber: 2.7 Consensus size: 181
488150 GTTAGATCTG
* * * * *
488160 AAAATTTTGATTCACTTTACTGTTCTTCAGGGAAAATTGAATC-AAGATTGATTTGTTTCACTGC
1 AAAATTTTGATACACTTT-CTGCTCTTCAGGGAAGATTGAATCGAACA-TGATTTGCTTCACTGC
* * * * * ** * * *
488224 TCTTCAGGAAGATCAAATATGGAAAG--TGACAATCTGCTCTACTACTCTTTAAGAGAGATTAGA
64 TCTTCAGGAAGACCAAAT-TGAAAAGAAAGAGAATATGCTCCGCTACTCTTTAGGGGAGATCAGA
* * *
488287 TCTAAGGGAAGACGGGTCTACTCCACTACTCTTTAGGGGAGATCAGACTCAAGA
128 TCTAAAGGAAAACGGGCCTACTCCACTACTCTTTAGGGGAGATCAGACTCAAGA
* * * *
488341 AAAATTTTGATATAC-TTCTGCTCTTCAGGGAAGATTGAATCGAACGTGATTTGCTTTACTGATC
1 AAAATTTTGATACACTTTCTGCTCTTCAGGGAAGATTGAATCGAACATGATTTGCTTCACTGCTC
* *
488405 TTCAGGAAGACCAAATTGAAAAGAAAGAGAATTTGCTCCGCTACTCTTCAGGGGAGATCAGATCT
66 TTCAGGAAGACCAAATTGAAAAGAAAGAGAATATGCTCCGCTACTCTTTAGGGGAGATCAGATCT
*
488470 AAAGGAAAAC-GGCCTGCTCCACTACTCTTTAGGGGAGATCAGACTCAAGA
131 AAAGGAAAACGGGCCTACTCCACTACTCTTTAGGGGAGATCAGACTCAAGA
* *
488520 AAAATTTTGATCCACTTTGCTGCTCTTCAGGGAAGATTGAATCGAACATGATTTGCTTCATTGCT
1 AAAATTTTGATACACTTT-CTGCTCTTCAGGGAAGATTGAATCGAACATGATTTGCTTCACTGCT
* *
488585 CTTCAGGAAGACCAAA-TCAGAAAGAAAGAGAATATGCTCCGCTACTATTTAGGGGAGA
65 CTTCAGGAAGACCAAATTGA-AAAGAAAGAGAATATGCTCCGCTACTCTTTAGGGGAGA
488643 CCAAACTCGA
Statistics
Matches: 262, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
178 6 0.02
179 103 0.39
180 47 0.18
181 106 0.40
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (181 bp):
AAAATTTTGATACACTTTCTGCTCTTCAGGGAAGATTGAATCGAACATGATTTGCTTCACTGCTC
TTCAGGAAGACCAAATTGAAAAGAAAGAGAATATGCTCCGCTACTCTTTAGGGGAGATCAGATCT
AAAGGAAAACGGGCCTACTCCACTACTCTTTAGGGGAGATCAGACTCAAGA
Found at i:491086 original size:21 final size:22
Alignment explanation
Indices: 491057--491097 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
491047 CATAGACTTA
* *
491057 ATTTCTTCTTCTAGTTGTTTCC
1 ATTTCTTCTTCAAATTGTTTCC
491079 ATTT-TTCTTCAAATTGTTT
1 ATTTCTTCTTCAAATTGTTT
491098 GCTTGACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.15, C:0.17, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTCTTCTTCAAATTGTTTCC
Found at i:500158 original size:14 final size:13
Alignment explanation
Indices: 500118--500160 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
500108 TCCTAATGGG
500118 CAAT-TTTGAAAA
1 CAATGTTTGAAAA
*
500130 CTATGTTTGAAAA
1 CAATGTTTGAAAA
500143 CAATGTTTGAAAAA
1 CAATGTTTG-AAAA
500157 CAAT
1 CAAT
500161 ATGTAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 3 0.11
13 16 0.59
14 8 0.30
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:500692 original size:44 final size:44
Alignment explanation
Indices: 500637--500738 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 44
500627 TGCACTGTAC
* *
500637 AGTGTATCGATGCACATTCAAGGAATGTATCGGTGCACCTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCAT
* * * *
500681 AGTGTATCGATGCACATTTACGGGATGCATCGGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCAT
500725 AGTGTATCGATGCA
1 AGTGTATCGATGCA
500739 TAGTGCACAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTTCAT
Found at i:508703 original size:23 final size:23
Alignment explanation
Indices: 508671--508729 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
508661 ATCTTATATA
*
508671 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* * *
508694 GCACTTCGGTGTAATTCTATGTG
1 GCACTTCGGTGCAATTCTACGCG
508717 GCACTTCGGTGCA
1 GCACTTCGGTGCA
508730 TTTATACGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:510907 original size:21 final size:21
Alignment explanation
Indices: 510881--510920 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
510871 TAACCGTTCC
510881 CCGACCGAACTAATTCGGTGG
1 CCGACCGAACTAATTCGGTGG
* *
510902 CCGACCGAATTAGTTCGGT
1 CCGACCGAACTAATTCGGT
510921 TCGGTCGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.23
Consensus pattern (21 bp):
CCGACCGAACTAATTCGGTGG
Found at i:511649 original size:38 final size:40
Alignment explanation
Indices: 511568--511672 Score: 101
Period size: 38 Copynumber: 2.7 Consensus size: 40
511558 CCTAATTCCC
* ** **
511568 AAATTATTTCACCTTAGCATTCTAAA-TTCCTAATTTCTT
1 AAATTATTTCACCCTAATATTCTAAATTTTTTAATTTCTT
* *
511607 AAATTGTTTCACCGT-A-ATTCTAAATTTTTTAATTT-TT
1 AAATTATTTCACCCTAATATTCTAAATTTTTTAATTTCTT
*
511644 AAAATTATTTTACCCTAATATTCTAAATT
1 -AAATTATTTCACCCTAATATTCTAAATT
511673 ATTTCTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
37 10 0.19
38 20 0.37
39 14 0.26
40 10 0.19
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (40 bp):
AAATTATTTCACCCTAATATTCTAAATTTTTTAATTTCTT
Found at i:512118 original size:36 final size:36
Alignment explanation
Indices: 512071--512142 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
512061 TAATATTTTA
512071 GGTACTCAATTTTGTACACCCCTACCATTTAGTTTG
1 GGTACTCAATTTTGTACACCCCTACCATTTAGTTTG
*
512107 GGTACTCAATTTTGTACACCCCTACCCTTTAGTTTG
1 GGTACTCAATTTTGTACACCCCTACCATTTAGTTTG
512143 TATTCTAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (36 bp):
GGTACTCAATTTTGTACACCCCTACCATTTAGTTTG
Found at i:519937 original size:11 final size:11
Alignment explanation
Indices: 519910--519958 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
519900 ATTGTTAGAA
*
519910 TGTTATTAATT
1 TGTTATTAGTT
*
519921 TATTATTAGTT
1 TGTTATTAGTT
*
519932 TGTTA-TGGTT
1 TGTTATTAGTT
519942 TGTTATTAGTT
1 TGTTATTAGTT
519953 TGTTAT
1 TGTTAT
519959 GGTTTGTTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.63
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:519944 original size:10 final size:10
Alignment explanation
Indices: 519929--519966 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
519919 TTTATTATTA
519929 GTTTGTTATG
1 GTTTGTTATG
*
519939 GTTTGTTATTA
1 GTTTGTTA-TG
519950 GTTTGTTATG
1 GTTTGTTATG
519960 GTTTGTT
1 GTTTGTT
519967 GGTTACTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.11, C:0.00, G:0.26, T:0.63
Consensus pattern (10 bp):
GTTTGTTATG
Found at i:519949 original size:21 final size:21
Alignment explanation
Indices: 519923--519966 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
519913 TATTAATTTA
519923 TTATTAGTTTGTTATGGTTTG
1 TTATTAGTTTGTTATGGTTTG
519944 TTATTAGTTTGTTATGGTTTG
1 TTATTAGTTTGTTATGGTTTG
519965 TT
1 TT
519967 GGTTACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.64
Consensus pattern (21 bp):
TTATTAGTTTGTTATGGTTTG
Found at i:522327 original size:63 final size:63
Alignment explanation
Indices: 522221--522344 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
522211 CCTTAAGGGA
* * ** *
522221 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
522284 ACATCTTAGGG-CTGTAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
522345 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 4 0.08
63 48 0.92
ACGTcount: A:0.26, C:0.27, G:0.28, T:0.19
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:523240 original size:17 final size:17
Alignment explanation
Indices: 523226--523282 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
523216 CAACGGTCCA
*
523226 GTCAACGGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
523243 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
523260 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
523277 GTCAAC
1 GTCAAC
523283 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.25, G:0.40, T:0.18
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGG
Found at i:523310 original size:10 final size:10
Alignment explanation
Indices: 523278--523327 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
523268 TCGGGTCGGG
*
523278 TCAACCCGGT
1 TCAAACCGGT
*
523288 TCAGACCGG-
1 TCAAACCGGT
523297 TCAAACCGGT
1 TCAAACCGGT
*
523307 TCAAAACTGG-
1 TC-AAACCGGT
523317 TCAAACCGGT
1 TCAAACCGGT
523327 T
1 T
523328 TTCCAATAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:523318 original size:20 final size:19
Alignment explanation
Indices: 523276--523327 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
523266 AGTCGGGTCG
* *
523276 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
523295 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
523315 GGTCAAACCGGTT
1 GGTCAAACCGGTT
523328 TTCCAATAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:529609 original size:32 final size:31
Alignment explanation
Indices: 529521--529645 Score: 81
Period size: 31 Copynumber: 4.0 Consensus size: 31
529511 ACCCTAAGGG
* *
529521 AACATCTTAGGGCCTG-AGAGCCTACCCAAGA
1 AACATCTCAGGGCC-GCAGAGCCTACCTAAGA
* * * * ** *
529552 TAGATTTCGGGGCCGTGGGGCCTACCTAAGA
1 AACATCTCAGGGCCGCAGAGCCTACCTAAGA
* * * **
529583 ACACATCTTAGGGCCGCAGGGTCTACCCGAGA
1 A-ACATCTCAGGGCCGCAGAGCCTACCTAAGA
**
529615 ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 AACATCTCAGGGCCGCAGAGCCTACCTAAGA
529646 GTCACATTAG
Statistics
Matches: 67, Mismatches: 25, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
30 1 0.01
31 44 0.66
32 22 0.33
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (31 bp):
AACATCTCAGGGCCGCAGAGCCTACCTAAGA
Found at i:529628 original size:63 final size:63
Alignment explanation
Indices: 529522--529645 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
529512 CCCTAAGGGA
* * ** *
529522 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* * *
529585 ACATCTTAGGGCC-GCAGGGTCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
529646 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:530554 original size:17 final size:17
Alignment explanation
Indices: 530534--530607 Score: 112
Period size: 17 Copynumber: 4.4 Consensus size: 17
530524 CAACGGTCCA
*
530534 GTCAACGGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
*
530551 GTCAACAGTCGGGTCAG
1 GTCAACAGTCGGGTCGG
530568 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
* *
530585 GTTAACAGTCGGGTCGA
1 GTCAACAGTCGGGTCGG
530602 GTCAAC
1 GTCAAC
530608 CCGGTTCAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.20, C:0.23, G:0.38, T:0.19
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGG
Found at i:530621 original size:10 final size:10
Alignment explanation
Indices: 530603--530652 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
530593 TCGGGTCGAG
*
530603 TCAACCCGGT
1 TCAAACCGGT
*
530613 TCAGACCGG-
1 TCAAACCGGT
530622 TCAAACCGGT
1 TCAAACCGGT
*
530632 TCAAAACTGG-
1 TC-AAACCGGT
530642 TCAAACCGGT
1 TCAAACCGGT
530652 T
1 T
530653 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:530643 original size:20 final size:19
Alignment explanation
Indices: 530602--530652 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
530592 GTCGGGTCGA
* *
530602 GTCAACCCGGTTCAGACCG
1 GTCAAACCGGTTCAAACCG
*
530621 GTCAAACCGGTTCAAAACTG
1 GTCAAACCGGTTC-AAACCG
530641 GTCAAACCGGTT
1 GTCAAACCGGTT
530653 TTCCAGCAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (19 bp):
GTCAAACCGGTTCAAACCG
Found at i:531593 original size:21 final size:22
Alignment explanation
Indices: 531568--531624 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
531558 AATGTTAGAG
*
531568 TGTTATTAGTTTGTTA-TGGTT
1 TGTTATTAGTTTGTTATTAGTT
*
531589 TGTTATTAGCTTGTTATTAGTT
1 TGTTATTAGTTTGTTATTAGTT
*
531611 TGTTA-TGGTTTGTT
1 TGTTATTAGTTTGTT
531625 GGTTACTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.14, C:0.02, G:0.23, T:0.61
Consensus pattern (22 bp):
TGTTATTAGTTTGTTATTAGTT
Found at i:531624 original size:10 final size:11
Alignment explanation
Indices: 531568--531616 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
531558 AATGTTAGAG
531568 TGTTATTAGTT
1 TGTTATTAGTT
*
531579 TGTTA-TGGTT
1 TGTTATTAGTT
*
531589 TGTTATTAGCT
1 TGTTATTAGTT
531600 TGTTATTAGTT
1 TGTTATTAGTT
531611 TGTTAT
1 TGTTAT
531617 GGTTTGTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.61
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:533871 original size:59 final size:59
Alignment explanation
Indices: 533779--533907 Score: 231
Period size: 59 Copynumber: 2.2 Consensus size: 59
533769 GATTGATTTT
* *
533779 AAAATAAAAACTGTTGGTGTAACCCATCACATCAAATCAAACCTAACTAGAAAATAGTA
1 AAAATAAAAACTGTTAGTGTAACCCATCACATCAAATCAAACCTAACTAAAAAATAGTA
*
533838 AAAATAAAAACTGTTAGTTTAACCCATCACATCAAATCAAACCTAACTAAAAAATAGTA
1 AAAATAAAAACTGTTAGTGTAACCCATCACATCAAATCAAACCTAACTAAAAAATAGTA
533897 AAAATAAAAAC
1 AAAATAAAAAC
533908 AGTTCGTGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 67 1.00
ACGTcount: A:0.53, C:0.18, G:0.07, T:0.22
Consensus pattern (59 bp):
AAAATAAAAACTGTTAGTGTAACCCATCACATCAAATCAAACCTAACTAAAAAATAGTA
Found at i:535965 original size:66 final size:66
Alignment explanation
Indices: 535859--535990 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
535849 AAATTGTTGT
535859 TTCCTTTGGGATGATGAACAGGGATTAGAGCCGGTGGTTTGCCCTGCAGGAGATAACATAGATAC
1 TTCCTTTGGGATGATGAACAGGGATTAGAGCCGGTGGTTTGCCCTGCAGGAGATAACATAGATAC
535924 C
66 C
*
535925 TTCCTTTGGGATGATGAACAGGGATTAGAGCCGGTGGTTTGCCCTGCGGGAGATAACATAGATAC
1 TTCCTTTGGGATGATGAACAGGGATTAGAGCCGGTGGTTTGCCCTGCAGGAGATAACATAGATAC
535990 C
66 C
535991 ACCATGGATC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (66 bp):
TTCCTTTGGGATGATGAACAGGGATTAGAGCCGGTGGTTTGCCCTGCAGGAGATAACATAGATAC
C
Found at i:538789 original size:21 final size:21
Alignment explanation
Indices: 538763--538807 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
538753 TAGGAAAGAT
538763 AGTAAATGTGGTCTGTCAGAA
1 AGTAAATGTGGTCTGTCAGAA
538784 AGTAAATGTGGTCTGTCAGAA
1 AGTAAATGTGGTCTGTCAGAA
538805 AGT
1 AGT
538808 CATACTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (21 bp):
AGTAAATGTGGTCTGTCAGAA
Found at i:545790 original size:2 final size:2
Alignment explanation
Indices: 545783--545810 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
545773 CAAGGATTCC
545783 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
545811 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548421 original size:26 final size:26
Alignment explanation
Indices: 548385--548445 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
548375 CCAGCCTCCA
548385 TTACACCTCTCAAACCCTTCCTTTAC
1 TTACACCTCTCAAACCCTTCCTTTAC
*
548411 TTACACCTCTCAAGCCCTTCCTTTAC
1 TTACACCTCTCAAACCCTTCCTTTAC
*
548437 TTGCACCTC
1 TTACACCTC
548446 CAACGCAGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.20, C:0.43, G:0.03, T:0.34
Consensus pattern (26 bp):
TTACACCTCTCAAACCCTTCCTTTAC
Found at i:551175 original size:25 final size:25
Alignment explanation
Indices: 551146--551195 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
551136 TTTGTGAATA
551146 GAGCAAACTAGATTGGGAAGGTCGC
1 GAGCAAACTAGATTGGGAAGGTCGC
551171 GAGCAAACTAGATTGGGAAGGTCGC
1 GAGCAAACTAGATTGGGAAGGTCGC
551196 CCTTGCCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (25 bp):
GAGCAAACTAGATTGGGAAGGTCGC
Found at i:551761 original size:5 final size:5
Alignment explanation
Indices: 551751--551922 Score: 251
Period size: 5 Copynumber: 33.4 Consensus size: 5
551741 TTTCTCTAAA
551751 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATATT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA-T
551802 ATATAT TATAT TATAT TATA- T-TAT TATAT TATAT TATAT ATATTAT
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TA-TAT
551848 TATAT TATAT TATATT ATATAT TATAT TATAT TATAT ATATAT TAT-T
1 TATAT TATAT TATA-T -TATAT TATAT TATAT TATAT -TATAT TATAT
551895 ATATAT TATAT TATAT TATAT TATAT TA
1 -TATAT TATAT TATAT TATAT TATAT TA
551923 GAAGATGAAA
Statistics
Matches: 156, Mismatches: 0, Indels: 22
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.01
4 3 0.02
5 126 0.81
6 14 0.09
7 11 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:552272 original size:2 final size:2
Alignment explanation
Indices: 552265--552304 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
552255 ATAATCTACC
552265 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
552305 GTATGTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:552309 original size:4 final size:4
Alignment explanation
Indices: 552302--552448 Score: 294
Period size: 4 Copynumber: 36.8 Consensus size: 4
552292 TATATATATA
552302 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
552350 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
552398 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
552446 TAT
1 TAT
552449 AATTACTTAC
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 143 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:554051 original size:16 final size:17
Alignment explanation
Indices: 554030--554062 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
554020 ACATTGATAT
554030 AATTTTAATATG-CATA
1 AATTTTAATATGACATA
*
554046 AATTTTGATATGACATA
1 AATTTTAATATGACATA
554063 TATATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (17 bp):
AATTTTAATATGACATA
Found at i:556150 original size:25 final size:23
Alignment explanation
Indices: 556121--556184 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
556111 TCAGATTTTA
556121 TTGTAATTGGGCCTTCGGGTCATCT
1 TTGTAATTGGGCCTT-GGGTCAT-T
* **
556146 TTGTAATATGGGTTCTTGGGTTGTT
1 TTGTAAT-TGGG-CCTTGGGTCATT
556171 TTGTAATTGGGCCT
1 TTGTAATTGGGCCT
556185 CAAGTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.06
24 4 0.12
25 15 0.45
26 9 0.27
27 3 0.09
ACGTcount: A:0.12, C:0.12, G:0.30, T:0.45
Consensus pattern (23 bp):
TTGTAATTGGGCCTTGGGTCATT
Found at i:556219 original size:3 final size:3
Alignment explanation
Indices: 556204--556282 Score: 149
Period size: 3 Copynumber: 26.3 Consensus size: 3
556194 GTTTGGGCCT
*
556204 ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
556252 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
556283 CTGGACAAAG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:559965 original size:24 final size:24
Alignment explanation
Indices: 559916--559965 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
559906 CTAATTTTAC
** *
559916 ATCCTTAAAATTTTATAACTTCAT
1 ATCCTTAAAATTTTATAAAATAAT
559940 ATCCATTAAAATTTT-TAAAATAAT
1 ATCC-TTAAAATTTTATAAAATAAT
559964 AT
1 AT
559966 TTTAAGTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (24 bp):
ATCCTTAAAATTTTATAAAATAAT
Found at i:562086 original size:3 final size:3
Alignment explanation
Indices: 562080--562225 Score: 283
Period size: 3 Copynumber: 48.7 Consensus size: 3
562070 AATAATAATA
562080 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
562128 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
562176 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ACG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
562224 AT
1 AT
562226 CGATTAATCC
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 141 1.00
ACGTcount: A:0.34, C:0.01, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:564141 original size:30 final size:29
Alignment explanation
Indices: 564091--564149 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
564081 TTTTTAAATT
564091 TTATAAATAGATTACATAAGTAATCAAAAA
1 TTATAAATAGATTACATAAGTAA-CAAAAA
* *
564121 TTATAAATAGA-TACCGTAAGTGACAAAAA
1 TTATAAATAGATTA-CATAAGTAACAAAAA
564150 CTTAACTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (29 bp):
TTATAAATAGATTACATAAGTAACAAAAA
Found at i:568056 original size:2 final size:2
Alignment explanation
Indices: 568051--568092 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
568041 AAAGAAACTC
568051 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
568093 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:568097 original size:2 final size:2
Alignment explanation
Indices: 568092--568118 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
568082 TCTCTCTCTC
568092 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 T
568119 CGTTATCTTT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:568328 original size:2 final size:2
Alignment explanation
Indices: 568323--568355 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
568313 TATTTTAATG
568323 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 T
568356 TGGCACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:575686 original size:44 final size:44
Alignment explanation
Indices: 575623--575707 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
575613 CTTCATGGAG
*
575623 GAATATGGTACGAAGATTTTGTATAACATCGCTCTAAATAATAT
1 GAATATGATACGAAGATTTTGTATAACATCGCTCTAAATAATAT
575667 GAATATGATACGAAGATTTTGTATAACATCGCTCTAAATAA
1 GAATATGATACGAAGATTTTGTATAACATCGCTCTAAATAA
575708 CCACACATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (44 bp):
GAATATGATACGAAGATTTTGTATAACATCGCTCTAAATAATAT
Found at i:577788 original size:50 final size:50
Alignment explanation
Indices: 577728--577834 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
577718 TCTAGAAGCT
* * *
577728 TGTGGAATCCTCTGAAATATTCTGTAGATGTGTAGAAGCTTGTGGAAGAG
1 TGTGGAATCCTCTGAAATATTCTGGAGATGTGTAGAACCTTATGGAAGAG
* * * *
577778 TGTGGTATCCTCTGGAATATTCTGGAGATGTGTGGAACCTTATGGAAAAG
1 TGTGGAATCCTCTGAAATATTCTGGAGATGTGTAGAACCTTATGGAAGAG
*
577828 TATGGAA
1 TGTGGAA
577835 GAATATGGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.32
Consensus pattern (50 bp):
TGTGGAATCCTCTGAAATATTCTGGAGATGTGTAGAACCTTATGGAAGAG
Found at i:580543 original size:19 final size:20
Alignment explanation
Indices: 580521--580560 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
580511 TAAACGTTTT
580521 TATGAATAATACT-ATATTG
1 TATGAATAATACTGATATTG
*
580540 TATGAATAGTACTGATATTG
1 TATGAATAATACTGATATTG
580560 T
1 T
580561 GCAAATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
TATGAATAATACTGATATTG
Found at i:580652 original size:21 final size:21
Alignment explanation
Indices: 580616--580688 Score: 119
Period size: 21 Copynumber: 3.4 Consensus size: 21
580606 AAATTCAGAA
*
580616 TGCTACAGGGGTATCGATACCC
1 TGCTACA-GTGTATCGATACCC
580638 TGCTACAGTGTATCGATACCC
1 TGCTACAGTGTATCGATACCC
*
580659 TGCTACAGTGTACCGATACCC
1 TGCTACAGTGTATCGATACCC
580680 TGCTACAGT
1 TGCTACAGT
580689 AATTTCGACC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 42 0.86
22 7 0.14
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (21 bp):
TGCTACAGTGTATCGATACCC
Found at i:581645 original size:32 final size:32
Alignment explanation
Indices: 581544--581664 Score: 144
Period size: 32 Copynumber: 3.9 Consensus size: 32
581534 GAAGGACCTA
* *
581544 TCCATATGTTCC-TAAGAACATAGGTAA-CTG
1 TCCATATGTCCCGAAAGAACATAGGTAATCTG
*
581574 TCCATATATCCCG-AAGAACATAGGTAATTCTG
1 TCCATATGTCCCGAAAGAACATAGGTAA-TCTG
581606 TCCATATGTCCCGAAAG-ACATAGGTAATCATG
1 TCCATATGTCCCGAAAGAACATAGGTAATC-TG
* *
581638 TCCATATGTCTCAAAAG-ACATAGGTAA
1 TCCATATGTCCCGAAAGAACATAGGTAA
581665 CCCTCGACTC
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
30 24 0.30
31 2 0.02
32 52 0.64
33 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGAACATAGGTAATCTG
Found at i:583587 original size:50 final size:50
Alignment explanation
Indices: 583510--583624 Score: 185
Period size: 50 Copynumber: 2.3 Consensus size: 50
583500 TAGAACTCTC
* *
583510 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
1 TAGAAGCTTGTGGAAGAGTGTGAAATCCTCTGGAATATTATGGAGATGTG
583560 TAGAAGCTTGTGGAAGAGTGTGAAATCCTCTGGAATATTATGGAGATGTG
1 TAGAAGCTTGTGGAAGAGTGTGAAATCCTCTGGAATATTATGGAGATGTG
* * *
583610 TGGAACCTTATGGAA
1 TAGAAGCTTGTGGAA
583625 AAGTACGGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.30
Consensus pattern (50 bp):
TAGAAGCTTGTGGAAGAGTGTGAAATCCTCTGGAATATTATGGAGATGTG
Found at i:585557 original size:20 final size:21
Alignment explanation
Indices: 585507--585557 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
585497 GGAAATATTC
* *
585507 ATTTTAGGTAGCGAAATTAAA
1 ATTTTAGGTAGCAAAAATAAA
**
585528 ATTTCCGGTAG-AAAAATAAA
1 ATTTTAGGTAGCAAAAATAAA
585548 ATTTTAGGTA
1 ATTTTAGGTA
585558 ACGTTCTACC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (21 bp):
ATTTTAGGTAGCAAAAATAAA
Found at i:595141 original size:3 final size:3
Alignment explanation
Indices: 595133--595170 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
595123 TGTCCGGATG
595133 TAT TAT TAT TAT TAT TA- TAT TAAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA
595171 ACATTTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:595179 original size:24 final size:24
Alignment explanation
Indices: 595133--595181 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
595123 TGTCCGGATG
**
595133 TATTATTATTATTATTATATTAAT
1 TATTATTATTATTAACATATTAAT
*
595157 TATTATTATTATTAACATTTTAAT
1 TATTATTATTATTAACATATTAAT
595181 T
1 T
595182 TACATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTATTATTATTAACATATTAAT
Found at i:596234 original size:17 final size:17
Alignment explanation
Indices: 596212--596247 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
596202 AAACGGGGAT
596212 GGGTTTAGTAATTGTTG
1 GGGTTTAGTAATTGTTG
596229 GGGTTTAGTAATTGTTG
1 GGGTTTAGTAATTGTTG
596246 GG
1 GG
596248 AGTAAGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (17 bp):
GGGTTTAGTAATTGTTG
Found at i:596877 original size:20 final size:21
Alignment explanation
Indices: 596852--596907 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
596842 TCGAAATGGA
*
596852 GTGCATGGATGCACTAC-ATG
1 GTGCATGGATGCACTACAAGG
* *
596872 GTGCATCGATGCACTGCAAGG
1 GTGCATGGATGCACTACAAGG
*
596893 GTGCATGGATACACT
1 GTGCATGGATGCACT
596908 TTAACACCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTACAAGG
Found at i:601260 original size:27 final size:24
Alignment explanation
Indices: 601225--601280 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
601215 ATAATAAGAC
* *
601225 TAGTAATATTTATGTTTAATATTATT
1 TAGTAATATCTAT-ATTAA-ATTATT
601251 TAGTAGATATCTATATTAAATTATT
1 TAGTA-ATATCTATATTAAATTATT
601276 T-GTAA
1 TAGTAA
601281 ACTAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 3 0.11
25 7 0.26
26 9 0.33
27 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (24 bp):
TAGTAATATCTATATTAAATTATT
Found at i:607568 original size:23 final size:23
Alignment explanation
Indices: 607542--607590 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
607532 TAAATTCTGC
*
607542 AAGAATGATAGATTTTCTTTTCA
1 AAGAATGATAGATTCTCTTTTCA
*
607565 AAG-ATGATAGATTCTCTTTTTA
1 AAGAATGATAGATTCTCTTTTCA
607587 AAGA
1 AAGA
607591 CGAAAGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (23 bp):
AAGAATGATAGATTCTCTTTTCA
Found at i:608703 original size:83 final size:82
Alignment explanation
Indices: 608552--608825 Score: 363
Period size: 83 Copynumber: 3.3 Consensus size: 82
608542 ATTTTTTTTT
* * * *
608552 AAATCTTCACGGAAGAGTAGTGAAGCAAAATTAAAATGC-GATCTCCACGAAAAAGTAGTGGAAT
1 AAATCTTCACGGAAGAGTAGTGAAGCAAAAGT-AAAT-CTGAACTCCACGAAAGAGTAGTGGAAA
*
608616 GATTTTTCAGCAAATTATG
64 GATTTTTCAGCAAAGTATG
* * *
608635 AAATCTTCATGGAAGAGTAGTGAAGAAAAAGTAAATCTGAACTCTACGAAAGAGTAGTGGAACAG
1 AAATCTTCACGGAAGAGTAGTGAAGCAAAAGTAAATCTGAACTCCACGAAAGAGTAGTGGAA-AG
608700 ATTTTTCAGCAAAGTATG
65 ATTTTTCAGCAAAGTATG
* *
608718 AAATCTTCACGGAAGAGTAGTGAAGCAAAAGCAAATCTGAACTCCACGAAAGAGTAGTGGAATGG
1 AAATCTTCACGGAAGAGTAGTGAAGCAAAAGTAAATCTGAACTCCACGAAAGAGTAGTGGAA-AG
608783 ATTTTTCAGCAAAGTAT-
65 ATTTTTCAGCAAAGTATG
* * * *
608800 AAAGCCTTCATGAAAGAGTAATGAAG
1 AAA-TCTTCACGGAAGAGTAGTGAAG
608826 TCATGAAAAT
Statistics
Matches: 170, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 28 0.16
83 141 0.83
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (82 bp):
AAATCTTCACGGAAGAGTAGTGAAGCAAAAGTAAATCTGAACTCCACGAAAGAGTAGTGGAAAGA
TTTTTCAGCAAAGTATG
Found at i:608772 original size:37 final size:37
Alignment explanation
Indices: 608647--608776 Score: 100
Period size: 37 Copynumber: 3.3 Consensus size: 37
608637 ATCTTCATGG
* * *
608647 AAGAGTAGTGAAGAAAAAGTAAATCTGAACTCTACGA
1 AAGAGTAGTGAAGCAAAAGCAAATCTGAACTCCACGA
* * * *
608684 AAGAGTAGTGGAA-CAGATTTTTCAGCAAAGTATGAAATCTTCACGG
1 AAGAGTAGT-GAAGCA-A-----AAGCAAA-TCTG-AA-CTCCACGA
608730 AAGAGTAGTGAAGCAAAAGCAAATCTGAACTCCACGA
1 AAGAGTAGTGAAGCAAAAGCAAATCTGAACTCCACGA
608767 AAGAGTAGTG
1 AAGAGTAGTG
608777 GAATGGATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
37 26 0.37
38 6 0.08
39 3 0.04
40 6 0.08
43 5 0.07
44 3 0.04
45 6 0.08
46 16 0.23
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (37 bp):
AAGAGTAGTGAAGCAAAAGCAAATCTGAACTCCACGA
Found at i:609115 original size:12 final size:12
Alignment explanation
Indices: 609084--609151 Score: 56
Period size: 11 Copynumber: 5.9 Consensus size: 12
609074 CCGAGTGATG
609084 ATAATTATAT-T
1 ATAATTATATAT
609095 AT-ATATATATAT
1 ATAAT-TATATAT
609107 ATAATTATATAT
1 ATAATTATATAT
*
609119 ATTAATAATAT-T
1 A-TAATTATATAT
*
609131 ATAAATAT-TAT
1 ATAATTATATAT
*
609142 -TATTTATATA
1 ATAATTATATA
609152 GCCCGAAGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
10 8 0.17
11 15 0.33
12 13 0.28
13 10 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATAATTATATAT
Found at i:609115 original size:18 final size:18
Alignment explanation
Indices: 609092--609151 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
609082 TGATAATTAT
609092 ATTATATATATATATATA
1 ATTATATATATATATATA
609110 ATTATATATAT-TA-ATA
1 ATTATATATATATATATA
*
609126 A-TAT-TATA-A-ATATT
1 ATTATATATATATATATA
*
609140 ATTATTTATATA
1 ATTATATATATA
609152 GCCCGAAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
13 1 0.03
14 7 0.19
15 6 0.17
16 8 0.22
17 3 0.08
18 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATATATATATATATA
Found at i:611162 original size:20 final size:20
Alignment explanation
Indices: 611137--611186 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
611127 ATGTGTTTCC
*
611137 TTTTTTAAAAAACATATATA
1 TTTTTTAAAAAACATATAAA
* ***
611157 TTTTTTTAATTTCATATAAA
1 TTTTTTAAAAAACATATAAA
611177 TTTTTTAAAA
1 TTTTTTAAAA
611187 TTATCATATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTTAAAAAACATATAAA
Found at i:611599 original size:21 final size:21
Alignment explanation
Indices: 611561--611605 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
611551 TTAAATGATT
** *
611561 TTAAAAACAAAATTAATACAA
1 TTAAAAACAAAAAAAATAAAA
*
611582 TTAAAAATAAAAAAAATAAAA
1 TTAAAAACAAAAAAAATAAAA
611603 TTA
1 TTA
611606 TTAATTTGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
TTAAAAACAAAAAAAATAAAA
Found at i:612688 original size:75 final size:74
Alignment explanation
Indices: 612497--612693 Score: 286
Period size: 75 Copynumber: 2.6 Consensus size: 74
612487 GTTAAATCCA
* * * *
612497 CTCTGCAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTATTGATAAGATTACTTGCCAGATT
1 CTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATAAGATTACTTGCAAGAGT
612562 TTGAATTGG
66 TTGAATTGG
* * *
612571 CTTTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATAATATTGCATTGCAAGAG
1 CTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATAAGATTAC-TTGCAAGAG
612636 TTTGAATTGG
65 TTTGAATTGG
* * * *
612646 CTCTGAAGCAGTCAAAGAATCCAATTCCAACTCAATATTCTACTGATA
1 CTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATA
612694 TCATTAATGA
Statistics
Matches: 110, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 50 0.45
75 60 0.55
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (74 bp):
CTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGATAAGATTACTTGCAAGAGT
TTGAATTGG
Found at i:616064 original size:3 final size:3
Alignment explanation
Indices: 616058--616106 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
616048 GATTTTTTTA
616058 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
616106 A
1 A
616107 TGATATAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:620445 original size:16 final size:16
Alignment explanation
Indices: 620403--620445 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
620393 AAAGAATATC
620403 AAATATG-TATTTTTAA
1 AAATATGTTA-TTTTAA
*
620419 AACTATGTTATTTTAA
1 AAATATGTTATTTTAA
*
620435 AAATATTTTAT
1 AAATATGTTAT
620446 ACTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (16 bp):
AAATATGTTATTTTAA
Found at i:633325 original size:10 final size:10
Alignment explanation
Indices: 633312--633337 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
633302 GGAAATTATG
633312 GAGAATTCTA
1 GAGAATTCTA
633322 GAGAATTCTA
1 GAGAATTCTA
633332 GAGAAT
1 GAGAAT
633338 CTCTCCCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (10 bp):
GAGAATTCTA
Found at i:644960 original size:16 final size:16
Alignment explanation
Indices: 644939--644972 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
644929 TTTTTTCATG
644939 AACCAAAA-TACTATTA
1 AACCAAAATTA-TATTA
644955 AACCAAAATTATATTA
1 AACCAAAATTATATTA
644971 AA
1 AA
644973 TATACAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AACCAAAATTATATTA
Found at i:645166 original size:131 final size:131
Alignment explanation
Indices: 644928--645191 Score: 343
Period size: 131 Copynumber: 2.0 Consensus size: 131
644918 TTAAATATTT
* * * * *
644928 ATTTTTTCATGAACCAAAATACTATTAAACCAAAATTATATTAAATATACAAATTTTAACAGGGG
1 ATTTTTACATAAACAAAAATACTATTAAACCAAAATTATATTAAAGATACAAATTTTAACAGGGA
* * * *
644993 CTGGGACCCTTTTGGGCCCTCAATAAGCTCCGCCCATAATTTTTGGCTATAAATAGATGGCTATA
66 CCGGGACCCTTTTAGGCCCTCAATAAGCTCCACCCATAATTTTTGGCTATAAATAGATGACTATA
645058 A
131 A
* *
645059 ATTTTTACATAAACAAAAATACTATTAGACTAAAATTATATTAAAGATACAAATTTTAACAGGGA
1 ATTTTTACATAAACAAAAATACTATTAAACCAAAATTATATTAAAGATACAAATTTTAACAGGGA
* * * * * *
645124 CCGATG-CCCTTTTAAGG-TCTCATTATGCTCCACCCATGATTTTTTGCTATAAATAGATGACTA
66 CCG-GGACCCTTTT-AGGCCCTCAATAAGCTCCACCCATAATTTTTGGCTATAAATAGATGACTA
645187 TAA
129 TAA
645190 AT
1 AT
645192 AAAAGGTATC
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
131 111 0.97
132 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (131 bp):
ATTTTTACATAAACAAAAATACTATTAAACCAAAATTATATTAAAGATACAAATTTTAACAGGGA
CCGGGACCCTTTTAGGCCCTCAATAAGCTCCACCCATAATTTTTGGCTATAAATAGATGACTATA
A
Found at i:645888 original size:13 final size:13
Alignment explanation
Indices: 645872--645898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
645862 TTTATACATA
645872 AATTTTAATTTTT
1 AATTTTAATTTTT
645885 AATTTTAATTTTT
1 AATTTTAATTTTT
645898 A
1 A
645899 TAAGACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATTTTAATTTTT
Found at i:646747 original size:43 final size:43
Alignment explanation
Indices: 646700--646781 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
646690 ATGAAAAAAA
646700 ATTAAAGAAAT-AAA-GAAATAATTATTAT-ATAATTATAAAAATC
1 ATTAAA-AAATAAAATGAAATAA-TATTATAAT-ATTATAAAAATC
* *
646743 ATTAAAAATTAAAATTAAATAATATTATAATATTATAAA
1 ATTAAAAAATAAAATGAAATAATATTATAATATTATAAA
646782 TATTTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 3 0.09
43 23 0.68
44 8 0.24
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (43 bp):
ATTAAAAAATAAAATGAAATAATATTATAATATTATAAAAATC
Found at i:647011 original size:19 final size:19
Alignment explanation
Indices: 646987--647026 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
646977 TCAATCATAA
646987 ATTATTCAGTTTA-TAAATT
1 ATTATT-AGTTTATTAAATT
*
647006 ATTATTATTTTATTAAATT
1 ATTATTAGTTTATTAAATT
647025 AT
1 AT
647027 ATAATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTATTAGTTTATTAAATT
Found at i:650847 original size:19 final size:19
Alignment explanation
Indices: 650823--650859 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
650813 AATCCTAATC
*
650823 ATTAGGCTATAATTTAGGA
1 ATTAGGCTATAACTTAGGA
650842 ATTAGGCTATAACTTAGG
1 ATTAGGCTATAACTTAGG
650860 CAACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTAGGCTATAACTTAGGA
Found at i:650920 original size:74 final size:74
Alignment explanation
Indices: 650836--650984 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
650826 AGGCTATAAT
650836 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
650901 ATTTTGTAA
66 ATTTTGTAA
650910 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
650975 ATTTTGTAA
66 ATTTTGTAA
650984 T
1 T
650985 CTATCACTCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (74 bp):
TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
ATTTTGTAA
Found at i:655353 original size:19 final size:19
Alignment explanation
Indices: 655329--655365 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
655319 AATCCTAATC
*
655329 ATTAGGCTATAATTTAGGA
1 ATTAGGCTATAACTTAGGA
655348 ATTAGGCTATAACTTAGG
1 ATTAGGCTATAACTTAGG
655366 CAACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTAGGCTATAACTTAGGA
Done.