Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009591.1 Hibiscus syriacus cultivar Beakdansim tig00116970_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: 2451160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:987889 original size:23 final size:22
Alignment explanation
Indices: 987847--987905 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
987837 ATAGGGCAGA
* *
987847 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
987869 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
*
987892 GGGAACTGATTCCC
1 GGGAACCGATTCCC
987906 TCTAGGGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:992061 original size:22 final size:22
Alignment explanation
Indices: 992031--992072 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
992021 TCAGCTGTTA
* *
992031 TAACTCCTGAAATTATATCATG
1 TAACCCCTGAAATTAAATCATG
*
992053 TAACCCCTGTAATTAAATCA
1 TAACCCCTGAAATTAAATCA
992073 AATAACTCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (22 bp):
TAACCCCTGAAATTAAATCATG
Found at i:992078 original size:22 final size:22
Alignment explanation
Indices: 992030--992078 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
992020 TTCAGCTGTT
* * *
992030 ATAACTCCTGAAATTATATCAT
1 ATAACCCCTGAAATTAAATCAA
* *
992052 GTAACCCCTGTAATTAAATCAA
1 ATAACCCCTGAAATTAAATCAA
992074 ATAAC
1 ATAAC
992079 TCCTATAACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (22 bp):
ATAACCCCTGAAATTAAATCAA
Found at i:992401 original size:20 final size:20
Alignment explanation
Indices: 992378--992428 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
992368 CACGAGCCGA
992378 GTCGAGCCGAGCAGAGCCAT
1 GTCGAGCCGAGCAGAGCCAT
* * * * *
992398 GTCGTGCCGTGCCGTGCCGT
1 GTCGAGCCGAGCAGAGCCAT
992418 GTCGAGCCGAG
1 GTCGAGCCGAG
992429 ACGAGACGGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.31, G:0.39, T:0.16
Consensus pattern (20 bp):
GTCGAGCCGAGCAGAGCCAT
Found at i:996386 original size:23 final size:23
Alignment explanation
Indices: 996337--996399 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
996327 GTGTTATATT
* **
996337 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
996360 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
996383 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
996400 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:996427 original size:19 final size:20
Alignment explanation
Indices: 996375--996427 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
996365 TTAAATATCT
996375 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
996394 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
996415 TTATTAAATATAT
1 TTATTAAATATAT
996428 AAATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:996439 original size:28 final size:27
Alignment explanation
Indices: 996384--996448 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
996374 TTTATTAAAA
996384 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
* *
996412 TCATTATTAAATATATAAATATTTTTAT
1 T-ATTATTAAATATATAAATAATATTAT
996440 TATATATTA
1 TAT-TATTA
996449 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 27 0.82
29 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:996842 original size:42 final size:43
Alignment explanation
Indices: 996741--996855 Score: 173
Period size: 43 Copynumber: 2.7 Consensus size: 43
996731 TACGTTCAGG
* *
996741 AAAACCAATTACGTGAAACAAACACTGAAAAATATTTTCCGCA
1 AAAACGAATTACGTGAAACAAACACTGAAAAACATTTTCCGCA
*
996784 AAAACGAATTACGTGAAACAAACAC-GAGAAAACATTTTTCG-A
1 AAAACGAATTACGTGAAACAAACACTGA-AAAACATTTTCCGCA
996826 AAAACGAATTACGTGAAACAAACA-TGAAAA
1 AAAACGAATTACGTGAAACAAACACTGAAAA
996856 TTCGAGAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
41 3 0.04
42 29 0.43
43 35 0.52
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.18
Consensus pattern (43 bp):
AAAACGAATTACGTGAAACAAACACTGAAAAACATTTTCCGCA
Found at i:1006634 original size:21 final size:20
Alignment explanation
Indices: 1006608--1006705 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
1006598 ATCAGTTTCC
1006608 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
1006629 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
1006648 ACAAATTCGCATTGCGATTTTCT
1 A-AAA-TCGCAACGCGATTTT-G
* *
1006671 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
1006691 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1006706 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 38 0.61
22 3 0.05
23 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:1006734 original size:20 final size:20
Alignment explanation
Indices: 1006672--1006925 Score: 305
Period size: 20 Copynumber: 12.7 Consensus size: 20
1006662 CGATTTTCTA
* ** *
1006672 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1006692 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
1006712 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1006732 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1006752 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
1006772 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1006792 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1006812 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1006832 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1006852 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1006872 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1006892 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1006913 AAATCGCAACGCG
1 AAATCGCAACGCG
1006926 ATATTTAAAG
Statistics
Matches: 200, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.01
20 180 0.90
21 17 0.09
22 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1007347 original size:33 final size:33
Alignment explanation
Indices: 1007308--1007378 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1007298 TTCACTTAGA
*
1007308 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1007341 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1007374 TTTCA
1 TTTCA
1007379 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1007515 original size:41 final size:41
Alignment explanation
Indices: 1007457--1007534 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1007447 TTGCAGAAGA
*
1007457 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1007498 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1007535 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1007531 original size:21 final size:21
Alignment explanation
Indices: 1007458--1007533 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1007448 TGCAGAAGAG
*
1007458 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
1007479 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
1007499 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
1007520 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1007534 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1007575 original size:19 final size:19
Alignment explanation
Indices: 1007553--1007650 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1007543 GAAACCAAAA
*
1007553 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1007572 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1007586 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1007605 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1007619 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
*
1007638 TCACGTTGCGATT
1 TCGCGTTGCGATT
1007651 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1007594 original size:14 final size:14
Alignment explanation
Indices: 1007575--1007664 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1007565 TTTCATTTCG
1007575 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1007589 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1007608 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1007622 CGTTGCGATTGTCATTTCA
1 CGTTGCGA-T-TC---TCT
1007641 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1007655 CGTTGCGATT
1 CGTTGCGATT
1007665 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1007600 original size:33 final size:33
Alignment explanation
Indices: 1007558--1007672 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1007548 CAAAATCGCA
1007558 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1007591 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1007624 TTGCGATTGTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1007657 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1007673 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1009720 original size:92 final size:93
Alignment explanation
Indices: 1009363--1009737 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
1009353 TAGATTGCTT
*
1009363 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1009428 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1009456 AGTAAATTTGTTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1009521 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1009549 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1009614 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1009642 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1009706 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1009733 AGTAA
1 AGTAA
1009738 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
91 6 0.02
92 77 0.28
93 196 0.70
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1009825 original size:19 final size:19
Alignment explanation
Indices: 1009785--1009912 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1009775 TAGTTTACTT
* *
1009785 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1009805 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1009824 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1009843 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1009857 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1009876 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1009890 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
1009908 TCGCA
1 TCGCA
1009913 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 9 0.10
19 38 0.43
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1009864 original size:33 final size:32
Alignment explanation
Indices: 1009821--1009912 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1009811 CGCGAAACCA
**
1009821 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1009853 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1009886 AAGATCGCAACGCGAAACC-AAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1009913 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 10 0.18
33 46 0.82
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1009935 original size:19 final size:19
Alignment explanation
Indices: 1009908--1010042 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
1009898 CGAAACCAAA
*
1009908 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1009927 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
*
1009943 T--CGTTGCGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
* *
1009960 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1009976 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
1009993 TCTCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1010012 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1010032 TCGTGTTGCGA
1 TCGCGTTGCGA
1010043 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 45 0.48
20 12 0.13
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1009949 original size:14 final size:14
Alignment explanation
Indices: 1009930--1009986 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1009920 TTTCATTTCG
1009930 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1009944 CGTTGCGATTTTCTTTT
1 CGTTGCGA--TTC-TTT
*
1009961 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1009977 CGTTGCGATT
1 CGTTGCGATT
1009987 TTCATTTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1009955 original size:33 final size:33
Alignment explanation
Indices: 1009913--1010005 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1009903 CCAAATCGCA
*
1009913 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* *
1009946 TTGCGATTTTCTTTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1009979 TTGCGATTTTCATTTCTCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1010006 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1011984 original size:14 final size:14
Alignment explanation
Indices: 1011965--1012000 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1011955 ATTGTTTAAT
1011965 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1011979 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1011993 TGATTTGT
1 TGATTTGT
1012001 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1012123 original size:19 final size:19
Alignment explanation
Indices: 1012107--1012204 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1012097 AAAAATGACT
1012107 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1012126 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1012145 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1012159 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1012178 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1012198 ATCGCAA
1 ATCGCAA
1012205 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1012236 original size:53 final size:53
Alignment explanation
Indices: 1012107--1012222 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
1012097 AAAAATGACT
1012107 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1012159 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1012212 ATCGCAATGCG
1 ATCGCAATGCG
1012223 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1012266 original size:33 final size:33
Alignment explanation
Indices: 1012229--1012381 Score: 150
Period size: 33 Copynumber: 4.5 Consensus size: 33
1012219 TGCGTTTATA
1012229 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
1012262 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
1012302 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
*
1012333 ATTTCGCATTGCGATTCTATCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1012366 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
1012382 TTCATTTCGC
Statistics
Matches: 96, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 51 0.53
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:1012275 original size:19 final size:19
Alignment explanation
Indices: 1012251--1012467 Score: 249
Period size: 19 Copynumber: 12.4 Consensus size: 19
1012241 GATTCTCTCG
1012251 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1012270 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1012289 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1012303 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1012322 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1012341 TTGCGA--TTC-TATCG--
1 TTGCGATTTTCATTTCGCA
1012355 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1012374 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1012393 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1012407 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1012427 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1012441 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1012460 TTGCGATT
1 TTGCGATT
1012468 CTCTCGTTGC
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 82 0.49
20 12 0.07
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1012286 original size:52 final size:52
Alignment explanation
Indices: 1012229--1012439 Score: 404
Period size: 52 Copynumber: 4.0 Consensus size: 52
1012219 TGCGTTTATA
1012229 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1012281 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1012333 ATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1012385 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1012438 AT
1 AT
1012440 GTTGGGATTT
Statistics
Matches: 156, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 139 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1012411 original size:33 final size:33
Alignment explanation
Indices: 1012270--1012489 Score: 241
Period size: 33 Copynumber: 6.5 Consensus size: 33
1012260 TCATTTCGCA
1012270 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1012303 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1012339 CATTGCGATTCTATCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1012374 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1012407 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1012441 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1012474 TTGCGATTTTAATTTC
1 TTGCGATTTTCATTTC
1012490 CGTGTTGCGA
Statistics
Matches: 156, Mismatches: 17, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 80 0.51
34 29 0.19
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1014997 original size:24 final size:24
Alignment explanation
Indices: 1014963--1015009 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1014953 CTGAAACATC
1014963 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1014987 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1015010 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1015720 original size:20 final size:20
Alignment explanation
Indices: 1015692--1015921 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
1015682 AAATTTCAGT
* * *
1015692 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1015712 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1015732 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1015752 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1015772 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1015792 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1015812 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1015832 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1015852 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1015872 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1015892 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1015912 GTTGCGATTT
1 GTTGCGATTT
1015922 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1015938 original size:21 final size:21
Alignment explanation
Indices: 1015908--1015990 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1015898 ATTTTCATAT
*
1015908 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1015929 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1015950 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1015971 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1015991 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1015981 original size:42 final size:43
Alignment explanation
Indices: 1015888--1015986 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1015878 ATTTATGTGT
* *
1015888 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1015929 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1015971 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1015987 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1020773 original size:32 final size:31
Alignment explanation
Indices: 1020719--1020779 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
1020709 TTAATATATT
* *
1020719 GTTAAAAAAAGTAGTATCGATTTTGTTATAA
1 GTTAAAAAAAGCAGTATCGATTTTATTATAA
* *
1020750 GTTAAAAAAAGGCGGTATTGATTTTATTAT
1 GTTAAAAAAA-GCAGTATCGATTTTATTAT
1020780 TATTGTGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (31 bp):
GTTAAAAAAAGCAGTATCGATTTTATTATAA
Found at i:1021260 original size:14 final size:15
Alignment explanation
Indices: 1021241--1021270 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1021231 TATTAGAATA
1021241 ATTTATTT-AATATT
1 ATTTATTTCAATATT
1021255 ATTTATTTCAATATT
1 ATTTATTTCAATATT
1021270 A
1 A
1021271 CTATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTTCAATATT
Found at i:1021356 original size:31 final size:31
Alignment explanation
Indices: 1021293--1021361 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
1021283 TATATCTATA
*
1021293 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
1021323 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
1021354 A-TTTATTA
1 ATTTTATTA
1021362 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:1021782 original size:200 final size:199
Alignment explanation
Indices: 1021462--1021898 Score: 526
Period size: 200 Copynumber: 2.2 Consensus size: 199
1021452 CACATATGTT
* * ** * *
1021462 ACATCGAAATCGATAATTATAATGTAATAGATAACTTTTTAATATAACCGGTATAAATATACTGA
1 ACATCGAAACCGATAATTATAATGTAATAGATAAATTTACAATATAACAGGTATAAATATACCGA
1021527 TTTTATGAAAGAATAGGTTAACATAATGTATCAACACAAATTTAAAAAATGTCGATACATTTTGT
66 TTTTATGAAAGAATAGGTTAACATAATGTATCAACACAAATTTAAAAAATGTCGATACATTTTGT
* * *
1021592 CCAGAATGAATGTCAAACGAGGTGCACACATAAAGTGTCGATACATTTATTAAA-AGTATCGATC
131 CCAGAATAAATGCCAAACGAGGTGCACACATAAAGTGTCGATACATTTA--AAATAGTATAGATC
1021656 CCAAAA
194 CCAAAA
*
1021662 ACATCGAAACCGATAATTACAATGTAATACG-TAAATTTACAATAT-ACTAGGTATAAATATACC
1 ACATCGAAACCGATAATTATAATGTAATA-GATAAATTTACAATATAAC-AGGTATAAATATACC
* * * * **** *
1021725 GGTTTTATGAGAA-AATAGGTCT-ACATAATGTATCGATAC-ATTTTAAGTTTGTGTCGATACTT
64 GATTTTATGA-AAGAATAGGT-TAACATAATGTATCAACACAAATTTAA-AAAATGTCGATACAT
* * * * * **
1021787 TTTTTCCATAATAAATGCCCAACGAGGTGCACGCATAAAGTGTTGATACATTTAAAATTTTATAG
126 TTTGTCCAGAATAAATGCCAAACGAGGTGCACACATAAAGTGTCGATACATTTAAAATAGTATAG
1021852 ATCCCAAAA
191 ATCCCAAAA
*
1021861 ATATCGAAACCGATAATTATAATGTAATAGATAAATTT
1 ACATCGAAACCGATAATTATAATGTAATAGATAAATTT
1021899 GTAATGTTTA
Statistics
Matches: 202, Mismatches: 28, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
198 4 0.02
199 55 0.27
200 139 0.69
201 4 0.02
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (199 bp):
ACATCGAAACCGATAATTATAATGTAATAGATAAATTTACAATATAACAGGTATAAATATACCGA
TTTTATGAAAGAATAGGTTAACATAATGTATCAACACAAATTTAAAAAATGTCGATACATTTTGT
CCAGAATAAATGCCAAACGAGGTGCACACATAAAGTGTCGATACATTTAAAATAGTATAGATCCC
AAAA
Found at i:1022445 original size:21 final size:21
Alignment explanation
Indices: 1022419--1022472 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1022409 GTTTCCAGAT
* *
1022419 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTAGACTA
1022440 TCGCAATGCGAACTTAGACTA
1 TCGCAATGCGAACTTAGACTA
1022461 TCGCAATGCGAA
1 TCGCAATGCGAA
1022473 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTAGACTA
Found at i:1023010 original size:6 final size:6
Alignment explanation
Indices: 1022983--1023060 Score: 135
Period size: 6 Copynumber: 13.5 Consensus size: 6
1022973 TCTCGTCTCG
1022983 GGTCGT -GTCGT -GTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1023028 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1023061 AATACGTGTC
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.21
6 56 0.79
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.35
Consensus pattern (6 bp):
GGTCGT
Found at i:1023206 original size:20 final size:21
Alignment explanation
Indices: 1023181--1023235 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
1023171 ACTTCGACTA
1023181 TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATATTACA-AGT
*
1023201 TCGCATTGCGATAGTTCCAAGT
1 TCGCATTGCGATA-TTACAAGT
1023223 TCGCATTGCGATA
1 TCGCATTGCGATA
1023236 ATCGAATCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 12 0.39
21 1 0.03
22 18 0.58
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATATTACAAGT
Found at i:1023633 original size:23 final size:23
Alignment explanation
Indices: 1023607--1023657 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1023597 TAAGTAATTA
**
1023607 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
1023630 ACCTATTACGTTATATAAGCGTT
1 ACCTATTACATTATATAAGCGCT
1023653 ACCTA
1 ACCTA
1023658 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:1023665 original size:23 final size:23
Alignment explanation
Indices: 1023617--1023666 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1023607 ACCTATTTTA
*
1023617 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
1023640 TTATATAAGCGTTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
1023663 TTAT
1 TTAT
1023667 TGTGTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:1023720 original size:23 final size:23
Alignment explanation
Indices: 1023694--1023744 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1023684 CCAGTAATTA
** *
1023694 ACCTATTTTATTATATAAGTGTT
1 ACCTATTACATTATATAAGTGGT
1023717 ACCTATTACATTATATAAGTGGT
1 ACCTATTACATTATATAAGTGGT
1023740 ACCTA
1 ACCTA
1023745 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (23 bp):
ACCTATTACATTATATAAGTGGT
Found at i:1023732 original size:87 final size:87
Alignment explanation
Indices: 1023599--1023831 Score: 376
Period size: 87 Copynumber: 2.7 Consensus size: 87
1023589 TAACAAATTA
* *
1023599 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGTTACCTAATATGT
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGT
*
1023664 TATTGTGTTTAATAATATTTCC
66 TATTGTGCTTAATAATATTTCC
* * * *
1023686 AGTAATTAACCTATTTTATTATATAAGTGTTACCTATTACATTATATAAGTGGTACCTAATATGT
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGT
*
1023751 TATTGTGCTTAATAATGTTTCC
66 TATTGTGCTTAATAATATTTCC
**
1023773 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTTTATTATATAAGCGCTACCTA
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTA
1023832 TTACATTATA
Statistics
Matches: 133, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 133 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (87 bp):
AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGT
TATTGTGCTTAATAATATTTCC
Found at i:1023808 original size:110 final size:110
Alignment explanation
Indices: 1023694--1023950 Score: 388
Period size: 110 Copynumber: 2.3 Consensus size: 110
1023684 CCAGTAATTA
* * *
1023694 ACCTATTTTATTATATAAGTGTTACCTATTACATTATATAAGTGGTACCTAATATGTTATTGTGC
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGC
*
1023759 TTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCT
66 TTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGAT
* *
1023804 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGC
* * *
1023869 TTGATAATGTTTCCAGTAATTAATCTATTTTATTATATAAGTGAT
66 TTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGAT
** * * *
1023914 ACCTATTACATTATATAAGCGGTACCTAATATATTAT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTAT
1023951 TGTGCTTGAT
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 133 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (110 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGC
TTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGAT
Found at i:1023811 original size:23 final size:23
Alignment explanation
Indices: 1023781--1023854 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
1023771 CCAGTAATTA
1023781 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
1023804 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
** *
1023827 ACCTATTACATTATATAAGCGTT
1 ACCTATTTTATTATATAAGCGCT
1023850 ACCTA
1 ACCTA
1023855 ATATGTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (23 bp):
ACCTATTTTATTATATAAGCGCT
Found at i:1023863 original size:23 final size:23
Alignment explanation
Indices: 1023781--1023863 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 23
1023771 CCAGTAATTA
*
1023781 ACCTATTTTATTATATAAGCGCT
1 ACCTATTATATTATATAAGCGCT
*
1023804 ACCTATTTTATTATATAAGCGCT
1 ACCTATTATATTATATAAGCGCT
* *
1023827 ACCTATTACATTATATAAGCGTT
1 ACCTATTATATTATATAAGCGCT
* *
1023850 ACCTAATATGTTAT
1 ACCTATTATATTAT
1023864 TGTGTTTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (23 bp):
ACCTATTATATTATATAAGCGCT
Found at i:1023897 original size:87 final size:86
Alignment explanation
Indices: 1023806--1024050 Score: 391
Period size: 87 Copynumber: 2.8 Consensus size: 86
1023796 TAAGCGCTAC
* *
1023806 CTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTGTTT
1 CTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTT
1023871 GATAATGTTTCCAGTAATTAA
66 GATAATGTTTCCAGTAATTAA
* * *
1023892 TCTATTTTATTATATAAGTGATACCTATTACATTATATAAGCGGTACCTAATATATTATTGTGCT
1 -CTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCT
1023957 TGATAATGTTTCCAGTAATTAA
65 TGATAATGTTTCCAGTAATTAA
* * *
1023979 CTTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGGTACTTAATATGTTATTGTACT
1 C-TATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCT
*
1024044 TGGTAAT
65 TGATAAT
1024051 ATTTTCGGTT
Statistics
Matches: 145, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
86 1 0.01
87 144 0.99
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (86 bp):
CTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTT
GATAATGTTTCCAGTAATTAA
Found at i:1023926 original size:23 final size:23
Alignment explanation
Indices: 1023900--1023950 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1023890 AATCTATTTT
* *
1023900 ATTATATAAGTGATACCTATTAC
1 ATTATATAAGCGATACCTAATAC
* *
1023923 ATTATATAAGCGGTACCTAATAT
1 ATTATATAAGCGATACCTAATAC
1023946 ATTAT
1 ATTAT
1023951 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (23 bp):
ATTATATAAGCGATACCTAATAC
Found at i:1023942 original size:197 final size:197
Alignment explanation
Indices: 1023607--1024018 Score: 725
Period size: 197 Copynumber: 2.1 Consensus size: 197
1023597 TAAGTAATTA
*
1023607 ACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGTTACCTAATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTGT
* *
1023672 TTAATAATATTTCCAGTAATTAACCTATTTTATTATATAAGTGTTACCTATTACATTATATAAGT
66 TTAATAATATTTCCAGTAATTAACCTATTTTATTATATAAGTGATACCTATTACATTATATAAGC
*
1023737 GGTACCTAATATGTTATTGTGCTTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCG
131 GGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCG
1023802 CT
196 CT
1023804 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTGT
* * *
1023869 TTGATAATGTTTCCAGTAATTAATCTATTTTATTATATAAGTGATACCTATTACATTATATAAGC
66 TTAATAATATTTCCAGTAATTAACCTATTTTATTATATAAGTGATACCTATTACATTATATAAGC
* *
1023934 GGTACCTAATATATTATTGTGCTTGATAATGTTTCCAGTAATTAACTTATTTTATTATATAAGCG
131 GGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCG
1023999 CT
196 CT
**
1024001 ACCTATTACATTATATAA
1 ACCTATTTTATTATATAA
1024019 ACGGTACTTA
Statistics
Matches: 204, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
197 204 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (197 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTGT
TTAATAATATTTCCAGTAATTAACCTATTTTATTATATAAGTGATACCTATTACATTATATAAGC
GGTACCTAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCG
CT
Found at i:1025798 original size:39 final size:41
Alignment explanation
Indices: 1025733--1025833 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 41
1025723 TTTTTTATTT
* *
1025733 TATTA-AAATATATT-TCTTAATTATTTAAAAAAT-A-AAA
1 TATTATAAATATATTATTTTAATCATTTAAAAAATAATAAA
* *
1025770 TATTATAAATGTATTATTTTAATCATTTAAAATATAATAAA
1 TATTATAAATATATTATTTTAATCATTTAAAAAATAATAAA
1025811 TAATTATAAATATATTATTTTAA
1 T-ATTATAAATATATTATTTTAA
1025834 AATATTAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
37 5 0.09
38 8 0.15
39 16 0.30
40 1 0.02
41 4 0.07
42 20 0.37
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (41 bp):
TATTATAAATATATTATTTTAATCATTTAAAAAATAATAAA
Found at i:1028862 original size:10 final size:10
Alignment explanation
Indices: 1028844--1028892 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
1028834 TCATCACACA
1028844 AAATTCTCTC
1 AAATTCTCTC
*
1028854 AATTTCTCTC
1 AAATTCTCTC
1028864 AAATTCTCTC
1 AAATTCTCTC
* *
1028874 AAATACTCTT
1 AAATTCTCTC
*
1028884 ATATTCTCT
1 AAATTCTCT
1028893 GTTTAATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.45
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:1028943 original size:23 final size:22
Alignment explanation
Indices: 1028917--1028961 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1028907 TTATTATATT
1028917 TTTAA-TATTTTATATTTAATTTA
1 TTTAAGTATTTTA-ATTT-ATTTA
1028940 TTTAAGTATTTTAATTTATTTA
1 TTTAAGTATTTTAATTTATTTA
1028962 ATATTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTAAGTATTTTAATTTATTTA
Found at i:1028966 original size:17 final size:17
Alignment explanation
Indices: 1028922--1028969 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
1028912 ATATTTTTAA
*
1028922 TATTTTATA-TTTAATT
1 TATTTAATATTTTAATT
1028938 TATTTAAGTATTTTAATT
1 TATTTAA-TATTTTAATT
1028956 TATTTAATATTTTA
1 TATTTAATATTTTA
1028970 CTTATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
18 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTTAATATTTTAATT
Found at i:1040783 original size:29 final size:29
Alignment explanation
Indices: 1040632--1040834 Score: 126
Period size: 29 Copynumber: 6.8 Consensus size: 29
1040622 ATTTAAAAAA
* *
1040632 AAAATAAAAATAACATATATTTGTTAAAGTT
1 AAAATAAGAATAATATATATTT-TT-AAGTT
* * ** *
1040663 AAGATAAGAATAAAATATAGTTAATAATTT
1 AAAATAAGAATAATATATA-TTTTTAAGTT
* * *
1040693 AAGATAAAAACAA-ATATATTATTTAAGTT
1 AAAATAAGAATAATATATATT-TTTAAGTT
** * *
1040722 -ACTTAAGACTGAAATATATATTTTTTAACTT
1 AAAATAAGAAT--AATATATA-TTTTTAAGTT
*
1040753 AAAATAAGAATAATATATAATTTTAAGTT
1 AAAATAAGAATAATATATATTTTTAAGTT
* *
1040782 AAAGATAA-AATAAAATATATTTTTAAATT
1 AAA-ATAAGAATAATATATATTTTTAAGTT
* *
1040811 ACAATGAA-AATAATTTATATTTTT
1 AAAAT-AAGAATAATATATATTTTT
1040835 TGAAAATTAA
Statistics
Matches: 135, Mismatches: 28, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
28 9 0.07
29 57 0.42
30 29 0.21
31 29 0.21
32 11 0.08
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (29 bp):
AAAATAAGAATAATATATATTTTTAAGTT
Found at i:1040787 original size:90 final size:90
Alignment explanation
Indices: 1040646--1040812 Score: 214
Period size: 90 Copynumber: 1.9 Consensus size: 90
1040636 TAAAAATAAC
* * * *
1040646 ATATATTTGTTAAAGTTAAGATAAGAATAAAATATAGTTAATAATTTAAGATAAAA-ACAAATAT
1 ATATATTTGTTAAACTTAAAATAAGAATAAAATATAATTAATAATTAAAGATAAAATA-AAATAT
*
1040710 ATTATTTAAGTTACTTAAGACTGAAAT
65 ATT-TTTAAATTACTTAAGACTGAAAT
* * *
1040737 ATATATTT-TTTAACTTAAAATAAGAATAATATATAATT-TTAAGTTAAAGATAAAATAAAATAT
1 ATATATTTGTTAAACTTAAAATAAGAATAAAATATAATTAATAA-TTAAAGATAAAATAAAATAT
1040800 ATTTTTAAATTAC
65 ATTTTTAAATTAC
1040813 AATGAAAATA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
89 12 0.18
90 45 0.68
91 9 0.14
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (90 bp):
ATATATTTGTTAAACTTAAAATAAGAATAAAATATAATTAATAATTAAAGATAAAATAAAATATA
TTTTTAAATTACTTAAGACTGAAAT
Found at i:1052496 original size:17 final size:17
Alignment explanation
Indices: 1052476--1052513 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1052466 TAACGAGTTA
1052476 TATAA-AATATATTTTAT
1 TATAATAATATATTTT-T
*
1052493 TATAATTATATATTTTT
1 TATAATAATATATTTTT
1052510 TATA
1 TATA
1052514 TTTTGTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATAATAATATATTTTT
Found at i:1071739 original size:16 final size:16
Alignment explanation
Indices: 1071718--1071756 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1071708 AAGATAACAA
1071718 TCACATCCGACATTTG
1 TCACATCCGACATTTG
1071734 TCACATCCGACATTTG
1 TCACATCCGACATTTG
1071750 TCACATC
1 TCACATC
1071757 ATATGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (16 bp):
TCACATCCGACATTTG
Found at i:1073909 original size:24 final size:26
Alignment explanation
Indices: 1073877--1073925 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
1073867 AATAAGAAGA
* *
1073877 AATATTTTTTTATA-ATA-ATATATC
1 AATAATTTTATATATATATATATATC
1073901 AATAATTTTATATATATATATATAT
1 AATAATTTTATATATATATATATAT
1073926 ATATATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 3 0.14
26 6 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
AATAATTTTATATATATATATATATC
Found at i:1075664 original size:31 final size:31
Alignment explanation
Indices: 1075628--1075687 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1075618 AACTTAAAAG
* *
1075628 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1075659 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1075688 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1076173 original size:20 final size:20
Alignment explanation
Indices: 1076137--1076196 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
1076127 AATATTATAT
*
1076137 TTAAAATTAAAT-CAAAATAA
1 TTAAAA-TAAATATAAAATAA
1076157 TTAAAATAAATATAAAAT-A
1 TTAAAATAAATATAAAATAA
*
1076176 TT--AATAATATATACAATAA
1 TTAAAATAA-ATATAAAATAA
1076195 TT
1 TT
1076197 TATATGATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 5 0.14
18 8 0.23
19 11 0.31
20 11 0.31
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAAATAAATATAAAATAA
Found at i:1076244 original size:27 final size:24
Alignment explanation
Indices: 1076207--1076261 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
1076197 TATATGATAT
1076207 AAAATTAAATATCTATAATATAATATTA
1 AAAATTAAATAT-T-TAATAT-AT-TTA
1076235 AAAATT-AATATTTAATATATTTA
1 AAAATTAAATATTTAATATATTTA
1076258 AAAA
1 AAAA
1076262 AATAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.26
24 2 0.07
25 6 0.22
26 1 0.04
27 5 0.19
28 6 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATTAAATATTTAATATATTTA
Found at i:1076245 original size:13 final size:13
Alignment explanation
Indices: 1076227--1076309 Score: 68
Period size: 13 Copynumber: 6.5 Consensus size: 13
1076217 ATCTATAATA
1076227 TAATATTAAAAAT
1 TAATATTAAAAAT
* *
1076240 TAATATTTAATA-
1 TAATATTAAAAAT
*
1076252 T-AT-TTAAAAAAA
1 TAATATT-AAAAAT
1076264 TAATATT-AAAAT
1 TAATATTAAAAAT
*
1076276 TAATA-TATATAAT
1 TAATATTA-AAAAT
1076289 ATAATATTAAAAAT
1 -TAATATTAAAAAT
1076303 TAATATT
1 TAATATT
1076310 TTATTTATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
10 2 0.04
11 6 0.11
12 11 0.20
13 23 0.42
14 11 0.20
15 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATATTAAAAAT
Found at i:1076279 original size:29 final size:30
Alignment explanation
Indices: 1076246--1076312 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 30
1076236 AAATTAATAT
1076246 TTAATATATTTAAAAAAATAATATT-AAAA
1 TTAATATATTTAAAAAAATAATATTAAAAA
* *
1076275 TTAATATA--T-ATAATATAATATTAAAAA
1 TTAATATATTTAAAAAAATAATATTAAAAA
1076302 TTAATAT-TTTA
1 TTAATATATTTA
1076313 TTTATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
26 11 0.34
27 12 0.38
28 1 0.03
29 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAATATATTTAAAAAAATAATATTAAAAA
Found at i:1076281 original size:63 final size:62
Alignment explanation
Indices: 1076206--1076363 Score: 216
Period size: 63 Copynumber: 2.6 Consensus size: 62
1076196 TTATATGATA
1076206 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATATATTTAAAAAAATAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAATTAATATTTAATATATTT-AAAAAATAATAT
* * * **
1076270 TAAAATTAATATATATAATATAATATTAAAAATTAATATTTTATTTATTTAAAATGTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATATATTTAAAAAATAATAT
*
1076332 TAAAATTAAAATC-A-AATATAATA-T-AAAATTAA
1 TAAAATTAATATCTATAATATAATATTAAAAATTAA
1076364 ATATAAAACT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
58 8 0.09
59 1 0.01
60 9 0.10
61 1 0.01
62 21 0.24
63 40 0.46
64 7 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (62 bp):
TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATATATTTAAAAAATAATAT
Found at i:1076289 original size:21 final size:21
Alignment explanation
Indices: 1076193--1076298 Score: 57
Period size: 21 Copynumber: 5.3 Consensus size: 21
1076183 TATATACAAT
* *
1076193 AATTTATATGATATAAAATTAA
1 AATTAATAT-ATATAATATTAA
**
1076215 ATATCTATA-ATATAATATTAAA
1 A-ATTAATATATATAATATT-AA
1076237 AATTAATAT-T-TAATA-T--
1 AATTAATATATATAATATTAA
* * *
1076253 ATTTAA-AAAAATAATATTAA
1 AATTAATATATATAATATTAA
1076273 AATTAATATATATAATA-TAA
1 AATTAATATATATAATATTAA
*
1076293 TATTAA
1 AATTAA
1076299 AAATTAATAT
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 1 0.02
20 18 0.28
21 23 0.36
22 4 0.06
23 6 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (21 bp):
AATTAATATATATAATATTAA
Found at i:1085360 original size:8 final size:9
Alignment explanation
Indices: 1085329--1085358 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1085319 TAAAGAAACT
1085329 AAAATGAAA
1 AAAATGAAA
1085338 AAAATGAAA
1 AAAATGAAA
1085347 AAAATGAAA
1 AAAATGAAA
1085356 AAA
1 AAA
1085359 TGTAGAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAATGAAA
Found at i:1086280 original size:2 final size:2
Alignment explanation
Indices: 1086273--1086337 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1086263 GAGTTCGGCT
1086273 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
1086315 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1086338 GTTTTCTTGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1088435 original size:36 final size:36
Alignment explanation
Indices: 1088351--1088491 Score: 205
Period size: 35 Copynumber: 4.0 Consensus size: 36
1088341 TGAATAAGAA
1088351 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT-
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGTC
1088386 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGTC
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGTC
* * *
1088422 GAACGGAATGAAGCATCGGCACTTTCGATTCAAGTC
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGTC
* * * *
1088458 GAACGGAAGGAGGCGTC-GCACTTTCCATTCAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
1088492 GTTCATCTTT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
35 51 0.52
36 47 0.48
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.21
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGTC
Found at i:1088444 original size:71 final size:71
Alignment explanation
Indices: 1088351--1088491 Score: 203
Period size: 71 Copynumber: 2.0 Consensus size: 71
1088341 TGAATAAGAA
*
1088351 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT-GAACGAAAGGAAGCATCAGCACTTTCGAT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGTCGAACGAAAGGAAGCATC-GCACTTTCCAT
1088415 TCAAGTC
65 TCAAGTC
* * * * * *
1088422 GAACGGAATGAAGCATCGGCACTTTCGATTCAAGTCGAACGGAAGGAGGCGTCGCACTTTCCATT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGTCGAACGAAAGGAAGCATCGCACTTTCCATT
1088487 CAAGT
66 CAAGT
1088492 GTTCATCTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 48 0.77
72 14 0.23
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.21
Consensus pattern (71 bp):
GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGTCGAACGAAAGGAAGCATCGCACTTTCCATT
CAAGTC
Found at i:1093257 original size:2 final size:2
Alignment explanation
Indices: 1093250--1093279 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1093240 TAATTAAGTC
1093250 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
1093280 GATTAAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1094488 original size:83 final size:83
Alignment explanation
Indices: 1094371--1094592 Score: 266
Period size: 83 Copynumber: 2.7 Consensus size: 83
1094361 CGTTTTTAGA
* * * * * ** *
1094371 AAAACGCCGCAATAGGGTGCTAAATTAGCGGCGTTTATATCACAAACGCTTCAATAGATTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCAGCGTTTATACCACAAACGCCACAATAGAGTATAAA
*
1094436 TTTTACGGCGATTTAGCC
66 TTTTACGGCGATTGAGCC
* * *
1094454 AAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTTACCACAAACGCCACAATAGAGTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCAGCGTTTATACCACAAACGCCACAATAGAGTATAAA
* *
1094519 TTTTGCGGCGATTGAGTC
66 TTTTACGGCGATTGAGCC
* * * *
1094537 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCATTT-TGACCAAAAACGCCGCAATA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCAGCGTTTAT-ACCACAAACGCCACAATA
1094593 TATTACACAT
Statistics
Matches: 118, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
82 1 0.01
83 117 0.99
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (83 bp):
AAAACGCCGCAATAGAGTGGTAAATTGGCAGCGTTTATACCACAAACGCCACAATAGAGTATAAA
TTTTACGGCGATTGAGCC
Found at i:1094502 original size:42 final size:42
Alignment explanation
Indices: 1094357--1094592 Score: 148
Period size: 42 Copynumber: 5.7 Consensus size: 42
1094347 TTGACATATA
* * * * *
1094357 GCGGCGTTTTTAG-AAAAACGCCGCAATAGGGTGCTAAATTA
1 GCGGCGTTTTGAGCCAAAACGCCGCAATAGAGTGGTAAATTG
* ** ** *
1094398 GCGGCGTTTAT-A-TCACAAACGCTTCAATAGA-TTATAAATTTT
1 GCGGCGTTT-TGAGCCA-AAACGCCGCAATAGAGTGGTAAA-TTG
* * * *
1094440 ACGGCGATTT-AGCCAAAACGCCGCAATATAGTGGTAAACTG
1 GCGGCGTTTTGAGCCAAAACGCCGCAATAGAGTGGTAAATTG
* * * * *
1094481 GCAGCGTTTTTA-CCACAAACGCCACAATAGAGT-ATAAATTTT
1 GCGGCGTTTTGAGCCA-AAACGCCGCAATAGAGTGGTAAA-TTG
* *
1094523 GCGGCG-ATTGAGTCAAAACGCCGCAATAGAGTGGTAAATTG
1 GCGGCGTTTTGAGCCAAAACGCCGCAATAGAGTGGTAAATTG
*
1094564 GCGGCATTTTGA-CCAAAAACGCCGCAATA
1 GCGGCGTTTTGAGCC-AAAACGCCGCAATA
1094593 TATTACACAT
Statistics
Matches: 147, Mismatches: 35, Indels: 25
0.71 0.17 0.12
Matches are distributed among these distances:
41 72 0.49
42 75 0.51
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (42 bp):
GCGGCGTTTTGAGCCAAAACGCCGCAATAGAGTGGTAAATTG
Found at i:1095358 original size:23 final size:21
Alignment explanation
Indices: 1095311--1095350 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1095301 CGAGCAATTA
1095311 GTTTTTTACTGAACACGAAAT
1 GTTTTTTACTGAACACGAAAT
1095332 GTTTTTTACTGAACACGAA
1 GTTTTTTACTGAACACGAA
1095351 TGATGTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
GTTTTTTACTGAACACGAAAT
Found at i:1096599 original size:12 final size:12
Alignment explanation
Indices: 1096582--1096607 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1096572 TTTAGTTCAT
1096582 CATTTCATCACC
1 CATTTCATCACC
1096594 CATTTCATCACC
1 CATTTCATCACC
1096606 CA
1 CA
1096608 CTAAAACTCA
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:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (12 bp):
CATTTCATCACC
Found at i:1098311 original size:21 final size:21
Alignment explanation
Indices: 1098285--1098369 Score: 109
Period size: 21 Copynumber: 4.0 Consensus size: 21
1098275 GCAAATAAAT
*
1098285 GCAGCGGAAGCAGAGAGAGAA
1 GCAGCGGAAGCACAGAGAGAA
*
1098306 GCAGCGGCAGCACAGAGAGAA
1 GCAGCGGAAGCACAGAGAGAA
*
1098327 GCAGC-GACAGCACAGAGAGAG
1 GCAGCGGA-AGCACAGAGAGAA
* *
1098348 GCAGCGGCAGGACAGAGAGAA
1 GCAGCGGAAGCACAGAGAGAA
1098369 G
1 G
1098370 TAATATATCA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.02
21 53 0.96
22 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.41, T:0.00
Consensus pattern (21 bp):
GCAGCGGAAGCACAGAGAGAA
Found at i:1098344 original size:42 final size:42
Alignment explanation
Indices: 1098285--1098369 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
1098275 GCAAATAAAT
*
1098285 GCAGCGGAAGCAGAGAGAGAAGCAGCGGCAGCACAGAGAGAA
1 GCAGCGGAAGCACAGAGAGAAGCAGCGGCAGCACAGAGAGAA
* *
1098327 GCAGC-GACAGCACAGAGAGAGGCAGCGGCAGGACAGAGAGAA
1 GCAGCGGA-AGCACAGAGAGAAGCAGCGGCAGCACAGAGAGAA
1098369 G
1 G
1098370 TAATATATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.39, C:0.20, G:0.41, T:0.00
Consensus pattern (42 bp):
GCAGCGGAAGCACAGAGAGAAGCAGCGGCAGCACAGAGAGAA
Found at i:1098943 original size:43 final size:41
Alignment explanation
Indices: 1098707--1098972 Score: 153
Period size: 43 Copynumber: 6.2 Consensus size: 41
1098697 CATACAGTTA
* * * * *
1098707 GCGGCGTTTTTGATAAAAACGCCGCAAAATCTCAAGACATATTCT
1 GCGGCG-TTTT-ATGAAAACGCCGCTAAATATCAACACCTA-T-T
* * * * * * *
1098752 GCGGCGTTTGTAGGAAAACGCCGGTAAAAATAAAAATCTACT
1 GCGGCGTTT-TATGAAAACGCCGCTAAATATCAACACCTATT
* *
1098794 GCGGCGTTTT-CGAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTTATGAAAACGCCGCTAAATATCAAC-ACCTATT
* * * **
1098834 GCGGCGTTTGTCTGCCAAATGCCATTAAATATCAACACCTATT
1 GCGGCGTTT-TATG-AAAACGCCGCTAAATATCAACACCTATT
* *
1098877 GCGGCGTTTTAATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTT-ATGA-AAACGCCGCTAAATATCAACACCTATT
* * **
1098920 GCGGCGTTTGT-TGAACAATCGCCGCTATATGTTGTA-ACCTATT
1 GCGGCGTTT-TATGAA-AA-CGCCGCTAAAT-ATCAACACCTATT
1098963 GCGGCGTTTT
1 GCGGCGTTTT
1098973 TTTGTTGAAA
Statistics
Matches: 174, Mismatches: 35, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
40 31 0.18
41 4 0.02
42 19 0.11
43 88 0.51
44 25 0.14
45 7 0.04
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTTATGAAAACGCCGCTAAATATCAACACCTATT
Found at i:1100690 original size:17 final size:17
Alignment explanation
Indices: 1100656--1100690 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1100646 GAATATTGAA
*
1100656 AAAAATATTAATCATTT
1 AAAAATATTAACCATTT
*
1100673 AAAAATATTAACCGTTT
1 AAAAATATTAACCATTT
1100690 A
1 A
1100691 TCGAGTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (17 bp):
AAAAATATTAACCATTT
Found at i:1100765 original size:35 final size:35
Alignment explanation
Indices: 1100725--1100793 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
1100715 TCGATCAATT
*
1100725 AATTCAGTTAAAATCGAATAATAAACACCCCTAAG
1 AATTCAGTTAAAACCGAATAATAAACACCCCTAAG
* * *
1100760 AATTCAGTTAAAACCGAATAGTGAACACCTCTAA
1 AATTCAGTTAAAACCGAATAATAAACACCCCTAA
1100794 TTATAAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.23
Consensus pattern (35 bp):
AATTCAGTTAAAACCGAATAATAAACACCCCTAAG
Found at i:1112507 original size:2 final size:2
Alignment explanation
Indices: 1112502--1112529 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1112492 GTTTTAAATA
1112502 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1112530 ATTTTCTGAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1126963 original size:19 final size:17
Alignment explanation
Indices: 1126922--1126957 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1126912 TAAAGCATCT
1126922 CCTCTCGACTATAAATA
1 CCTCTCGACTATAAATA
1126939 CCTCTCGACTATAAATA
1 CCTCTCGACTATAAATA
1126956 CC
1 CC
1126958 CCTCTCCCCC
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:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (17 bp):
CCTCTCGACTATAAATA
Found at i:1130606 original size:35 final size:35
Alignment explanation
Indices: 1130531--1130608 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
1130521 TTAAATACAT
*
1130531 CAAACTTACAATAAGTATTAAATGGTAAATAATAA
1 CAAAATTACAATAAGTATTAAATGGTAAATAATAA
*
1130566 TAAAATTACAATAACTGATATTAAATGGT-AAT-A-AA
1 CAAAATTACAATAA--G-TATTAAATGGTAAATAATAA
1130601 CAAAATTA
1 CAAAATTA
1130609 ACAAAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 21 0.57
36 1 0.03
37 4 0.11
38 11 0.30
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (35 bp):
CAAAATTACAATAAGTATTAAATGGTAAATAATAA
Found at i:1130656 original size:13 final size:13
Alignment explanation
Indices: 1130603--1130627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1130593 GTAATAAACA
1130603 AAATTAACAAAAT
1 AAATTAACAAAAT
1130616 AAATTAACAAAA
1 AAATTAACAAAA
1130628 AGTCCAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAACAAAAT
Found at i:1132768 original size:24 final size:24
Alignment explanation
Indices: 1132741--1132816 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 24
1132731 TAACTGCAAA
1132741 AAAAAATTAATTAAATAAAATATT
1 AAAAAATTAATTAAATAAAATATT
1132765 AAAAAATTTAAAAAGTTAAATAAAATATT
1 AAAAAA-TT---AA-TTAAATAAAATATT
*
1132794 AACAAAA-AAATTAAATAAAATAT
1 AA-AAAATTAATTAAATAAAATAT
1132817 GAGAGAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
24 19 0.42
25 4 0.09
28 2 0.04
29 16 0.36
30 4 0.09
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (24 bp):
AAAAAATTAATTAAATAAAATATT
Found at i:1132814 original size:29 final size:28
Alignment explanation
Indices: 1132738--1132815 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
1132728 TTATAACTGC
1132738 AAAAAAAAATT-AATTAAATAAAATATT
1 AAAAAAAAATTAAATTAAATAAAATATT
*
1132765 AAAAAATTTAAA--AAGTTAAATAAAATATT
1 AAAAAA---AAATTAAATTAAATAAAATATT
*
1132794 AACAAAAAAATTAAATAAAATA
1 AA-AAAAAAATTAAATTAAATA
1132816 TGAGAGAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
27 9 0.22
29 25 0.61
30 7 0.17
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (28 bp):
AAAAAAAAATTAAATTAAATAAAATATT
Found at i:1133121 original size:51 final size:51
Alignment explanation
Indices: 1133051--1133160 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
1133041 ACCCATGCAC
* * * *
1133051 CGCGCCTTATCCAGCGTGTCGCCATG-TCAGTATAAGGCGTAGTGTAT-GGG
1 CGCGCCTTAGCCAACGTGTCACCA-GATCAGTATAAGGCGCAGTGTATGGGG
* * *
1133101 CAGCGCCTTAGCCAATGTGTCACCAGATCAGTGTAAGGCGCGGTGTATGGGG
1 C-GCGCCTTAGCCAACGTGTCACCAGATCAGTATAAGGCGCAGTGTATGGGG
1133153 CGCGCCTT
1 CGCGCCTT
1133161 CCTGCAAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
50 2 0.04
51 44 0.88
52 4 0.08
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24
Consensus pattern (51 bp):
CGCGCCTTAGCCAACGTGTCACCAGATCAGTATAAGGCGCAGTGTATGGGG
Found at i:1135921 original size:110 final size:107
Alignment explanation
Indices: 1135732--1135989 Score: 344
Period size: 110 Copynumber: 2.4 Consensus size: 107
1135722 ATATTGTTCC
* * * *
1135732 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG--GAACTGGGAAATTGTTTGTTGAC
1 GAGTTCAATATCCTTCGT-GTAAAGTTGAAATTGGCTCTGAAGAACTGGGAAATTGTTTCTTGAC
*
1135795 AGCCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTT
65 AACCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTT
*
1135838 GAGTTCAATATCCTTCGCTGTAAAGTTGAAATTGACTCTGAATGAAACT-GGAAATTTGTTTCTT
1 GAGTTCAATATCCTTCG-TGTAAAGTTGAAATTGGCTCTGAA-G-AACTGGGAAA-TTGTTTCTT
* *
1135902 GACAATCAGTCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTGTCTT
62 GACAACCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTT
*
1135948 GAGTTCAATATCCCTCGATGTGAAA-TTGAAATTGGCTCTGAA
1 GAGTTCAATATCCTTCG-TGT-AAAGTTGAAATTGGCTCTGAA
1135990 ACTGGAAAGC
Statistics
Matches: 134, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
106 34 0.25
107 1 0.01
109 6 0.04
110 90 0.67
111 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (107 bp):
GAGTTCAATATCCTTCGTGTAAAGTTGAAATTGGCTCTGAAGAACTGGGAAATTGTTTCTTGACA
ACCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:1136978 original size:10 final size:11
Alignment explanation
Indices: 1136953--1136978 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1136943 ATATCAATTA
1136953 AAAAAGTTTTG
1 AAAAAGTTTTG
1136964 AAAAAGTTTTG
1 AAAAAGTTTTG
1136975 AAAA
1 AAAA
1136979 TATTGCCCCT
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (11 bp):
AAAAAGTTTTG
Found at i:1137817 original size:69 final size:69
Alignment explanation
Indices: 1137697--1137840 Score: 243
Period size: 69 Copynumber: 2.1 Consensus size: 69
1137687 CTCGTATGTG
* * *
1137697 TCTCTTTTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGA
1 TCTCATTTGATGCTCTATAATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGA
1137762 TCAA
66 TCAA
* *
1137766 TCTCATTTGATGCTCTATAATCTTCGAGTGAAGTGGTTCAGTGATTTAGAAATGATTGTGCTTGA
1 TCTCATTTGATGCTCTATAATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGA
1137831 TCAA
66 TCAA
1137835 TCTCAT
1 TCTCAT
1137841 AGTTTGAATC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (69 bp):
TCTCATTTGATGCTCTATAATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGA
TCAA
Found at i:1137962 original size:13 final size:12
Alignment explanation
Indices: 1137931--1137959 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1137921 TTTCTCTTTG
1137931 CTTTTGTTTTCT
1 CTTTTGTTTTCT
1137943 CTTTTGTTTTCT
1 CTTTTGTTTTCT
1137955 CTTTT
1 CTTTT
1137960 TGTCCTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (12 bp):
CTTTTGTTTTCT
Found at i:1141180 original size:22 final size:23
Alignment explanation
Indices: 1141146--1141207 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1141136 AAAGAAAAAT
1141146 AAATAAATAAAATTAAAG-ACATA
1 AAATAAATAAAA-TAAAGTACATA
*
1141169 AAATAAAT-AAATAAAGTCCATA
1 AAATAAATAAAATAAAGTACATA
* *
1141191 AAAGCAAATGAAATAAA
1 AAA-TAAATAAAATAAA
1141208 TAAAATACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 5 0.15
22 10 0.29
23 12 0.35
24 7 0.21
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (23 bp):
AAATAAATAAAATAAAGTACATA
Found at i:1141386 original size:40 final size:41
Alignment explanation
Indices: 1141342--1141434 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
1141332 ATATATATAT
1141342 ATATATATATATAATAAATAAAA-ACATAA-AAAAATAGTAA-
1 ATATATATATATAATAAATAAAACACATAATAAAAAT--TAAC
* * *
1141382 ATATATATATA-AATTAATAAAACAGATAATGAAAATTAAC
1 ATATATATATATAATAAATAAAACACATAATAAAAATTAAC
1141422 ATATATATATATA
1 ATATATATATATA
1141435 TATATATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
39 13 0.28
40 27 0.59
41 6 0.13
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (41 bp):
ATATATATATATAATAAATAAAACACATAATAAAAATTAAC
Found at i:1150927 original size:18 final size:18
Alignment explanation
Indices: 1150895--1150929 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1150885 TCGATTCTTC
*
1150895 CGACCGGTCGGACCAGTT
1 CGACCGGTCGAACCAGTT
*
1150913 CGACCGGTTGAACCAGT
1 CGACCGGTCGAACCAGT
1150930 GAACCGGTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (18 bp):
CGACCGGTCGAACCAGTT
Found at i:1155631 original size:206 final size:207
Alignment explanation
Indices: 1155277--1155689 Score: 819
Period size: 206 Copynumber: 2.0 Consensus size: 207
1155267 TTGAATTGGT
1155277 TAACAAAGATTGAAAGTTGGAAGGGCATAATGGTCTTTATACAATGAATGAATTAAAAATTCGCT
1 TAACAAAGATTGAAAGTTGGAAGGGCATAATGGTCTTTATACAATGAATGAATTAAAAATTCGCT
1155342 ATTGGATATTATATATCCACGTATAAAAGGGAAAAAGAGAGAATGGAAATCCAGAATTTTCTTCA
66 ATTGGATATTATATATCCACGTATAAAAGGGAAAAAGAGAGAATGGAAATCCAGAATTTTCTTCA
1155407 TCTTTCTTCCTTCTCCCACCGTGAGCTCCATAGTTAAGGTAAG-ATTCTTCTAGTTGGTTAGTTC
131 TCTTTCTTCCTTCTCCCACCGTGAGCTCCATAGTTAAGGTAAGAATTCTTCTAGTTGGTTAGTTC
1155471 TAGCAAATTATG
196 TAGCAAATTATG
1155483 TAACAAAGATTGAAAGTTGGAAGGGCATAATGGTCTTTATACAATGAATGAATTAAAAATTCGCT
1 TAACAAAGATTGAAAGTTGGAAGGGCATAATGGTCTTTATACAATGAATGAATTAAAAATTCGCT
1155548 ATTGGATATTATATATCCACGTATAAAAGGGAAAAAGAGAGAATGGAAATCCAGAATTTTCTTCA
66 ATTGGATATTATATATCCACGTATAAAAGGGAAAAAGAGAGAATGGAAATCCAGAATTTTCTTCA
1155613 TCTTTCTTCCTTCTCCCACCGTGAGCTCCATAGTTAAGGTAAGAATTCTTCTAGTTGGTTAGTTC
131 TCTTTCTTCCTTCTCCCACCGTGAGCTCCATAGTTAAGGTAAGAATTCTTCTAGTTGGTTAGTTC
1155678 TAGCAAATTATG
196 TAGCAAATTATG
1155690 AGTGGTTTTG
Statistics
Matches: 206, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
206 173 0.84
207 33 0.16
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (207 bp):
TAACAAAGATTGAAAGTTGGAAGGGCATAATGGTCTTTATACAATGAATGAATTAAAAATTCGCT
ATTGGATATTATATATCCACGTATAAAAGGGAAAAAGAGAGAATGGAAATCCAGAATTTTCTTCA
TCTTTCTTCCTTCTCCCACCGTGAGCTCCATAGTTAAGGTAAGAATTCTTCTAGTTGGTTAGTTC
TAGCAAATTATG
Found at i:1155995 original size:20 final size:19
Alignment explanation
Indices: 1155968--1156005 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1155958 ATGAGTTAAA
1155968 GTGATATAAGTTG-GTTTGG
1 GTGATAT-AGTTGAGTTTGG
1155987 GTGAGTATAGTTGAGTTTG
1 GTGA-TATAGTTGAGTTTG
1156006 AAGTACTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (19 bp):
GTGATATAGTTGAGTTTGG
Found at i:1156814 original size:14 final size:15
Alignment explanation
Indices: 1156795--1156829 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1156785 CTATATGAAA
1156795 ATGTGAC-ATGAGCT
1 ATGTGACAATGAGCT
*
1156809 ATGTGACAATGAGTT
1 ATGTGACAATGAGCT
1156824 ATGTGA
1 ATGTGA
1156830 TTACATGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (15 bp):
ATGTGACAATGAGCT
Found at i:1156970 original size:23 final size:23
Alignment explanation
Indices: 1156944--1157037 Score: 89
Period size: 23 Copynumber: 4.1 Consensus size: 23
1156934 GGTTCTACGC
1156944 GGTCCTTCGGGACAATTCTACAT
1 GGTCCTTCGGGACAATTCTACAT
* *
1156967 GGTCCTTCGGGACATTTCTACTT
1 GGTCCTTCGGGACAATTCTACAT
* * * * ***
1156990 TGTCCATCAGGACAATACTGTGT
1 GGTCCTTCGGGACAATTCTACAT
* *
1157013 GGTCCTTCGGGACATTTCTATAT
1 GGTCCTTCGGGACAATTCTACAT
1157036 GG
1 GG
1157038 CACTTTTGTG
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACAT
Found at i:1158343 original size:22 final size:22
Alignment explanation
Indices: 1158318--1158378 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
1158308 GGCATATGAA
*
1158318 ATTTGTCCCGAAAGACCTA-TGT
1 ATTTGTCCCGAAGGACC-ACTGT
1158340 ATTTGTCCCGAAGGACCACTGT
1 ATTTGTCCCGAAGGACCACTGT
*
1158362 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
1158379 GCGTAGACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCACTGT
Found at i:1160029 original size:16 final size:15
Alignment explanation
Indices: 1160004--1160035 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1159994 TTCAACTATC
1160004 TTTTAAAAGTCAATG
1 TTTTAAAAGTCAATG
1160019 TTTTGAAAAGTCAATG
1 TTTT-AAAAGTCAATG
1160035 T
1 T
1160036 GGCACATCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (15 bp):
TTTTAAAAGTCAATG
Found at i:1191590 original size:117 final size:117
Alignment explanation
Indices: 1191415--1191705 Score: 424
Period size: 117 Copynumber: 2.5 Consensus size: 117
1191405 TTCCCGAAAT
** *
1191415 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACGA-AGCTGAGGAGCCTGCAGTAAT
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAGCAAATGAGCCTGCAGTAAT
* * * * *
1191479 AACGTCTCCATCCAGTCGCTTTCA-TCACTACAATGTGTAGGTTCCTCAGAACC
65 AACGTCCCCAACCAGTCAC-TCCACTCACTACAATGTGTAGGTTCCCCAGAACC
* *
1191532 ATACACCCACCTGCACACCAGTAAAGACTTACCCTAAGCACACAGCAAATGAGTCTGCAGTAATA
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAATGAGCCTGCAGTAATA
*
1191597 ACTTCCCCAACCAGTCACTCCACTCACTACAATGTGTAGGTTCCCCAGAACC
66 ACGTCCCCAACCAGTCACTCCACTCACTACAATGTGTAGGTTCCCCAGAACC
* * *
1191649 ATACACCCACCTGCACACCAATAAGGACTTACCCTGAGCACACAACAAATGAGCCTG
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAATGAGCCTG
1191706 AAATACTTTC
Statistics
Matches: 156, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
116 4 0.03
117 152 0.97
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.19
Consensus pattern (117 bp):
ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAATGAGCCTGCAGTAATA
ACGTCCCCAACCAGTCACTCCACTCACTACAATGTGTAGGTTCCCCAGAACC
Found at i:1192673 original size:28 final size:29
Alignment explanation
Indices: 1192625--1192773 Score: 122
Period size: 29 Copynumber: 5.2 Consensus size: 29
1192615 CATTTTACAT
* * *
1192625 AAATAGCACCCTTTTCAAATTAATTCCCA
1 AAATAGCACTCATTTCGAATTAATTCCCA
*
1192654 AAATAGCA-TCATTTCGAATTAATTCTCA
1 AAATAGCACTCATTTCGAATTAATTCCCA
* * * * ** * *
1192682 TAATATCACGCTTTTCGAAAAAAATACCA
1 AAATAGCACTCATTTCGAATTAATTCCCA
*
1192711 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACTCATTTCGAATTAATTCCCA
* * *
1192740 GAATAGCACTAAAATT-GAATTAATTCCCA
1 AAATAGCACT-CATTTCGAATTAATTCCCA
*
1192769 GAATA
1 AAATA
1192774 TCACCGGTCA
Statistics
Matches: 93, Mismatches: 25, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
28 22 0.24
29 68 0.73
30 3 0.03
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (29 bp):
AAATAGCACTCATTTCGAATTAATTCCCA
Found at i:1192684 original size:58 final size:58
Alignment explanation
Indices: 1192626--1192748 Score: 151
Period size: 58 Copynumber: 2.1 Consensus size: 58
1192616 ATTTTACATA
* * * *
1192626 AATAGCACCCTTTTC-AAATTAATTCCCAAAATAGCA-TCATTTCGAATTAATTCTCAT
1 AATAGCACCCTTTTCGAAA-AAAATACCAAAATAGCACCCATTTCGAATTAATTCTCAT
* * * *
1192683 AATATCACGCTTTTCGAAAAAAATACCAAAATAGCACCCATTTCGAATTAATTCCCAG
1 AATAGCACCCTTTTCGAAAAAAATACCAAAATAGCACCCATTTCGAATTAATTCTCAT
1192741 AATAGCAC
1 AATAGCAC
1192749 TAAAATTGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
57 27 0.49
58 28 0.51
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (58 bp):
AATAGCACCCTTTTCGAAAAAAATACCAAAATAGCACCCATTTCGAATTAATTCTCAT
Found at i:1192810 original size:17 final size:17
Alignment explanation
Indices: 1192788--1192823 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1192778 CGGTCAACGA
*
1192788 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCAGG
1192805 TCAACGGTCGGGTCAGG
1 TCAACGGTCGGGTCAGG
1192822 TC
1 TC
1192824 GGGTCGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.25, G:0.42, T:0.19
Consensus pattern (17 bp):
TCAACGGTCGGGTCAGG
Found at i:1199076 original size:117 final size:117
Alignment explanation
Indices: 1198901--1199191 Score: 433
Period size: 117 Copynumber: 2.5 Consensus size: 117
1198891 TTCCCGAAAT
* **
1198901 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACGA-AGCTGAGGAGCCTGCAGTAAT
1 ATACACCCACCTGCACACCAATAAGGACTTACCCTAAGCAC-ACAGCAAAGGAGCCTGCAGTAAT
* * * * *
1198965 AACGTCTCCATCCAGTCGCTTTCA-TCACTACAATGTGTAGGTTCCTCAGAACC
65 AACGTCCCCAACCAGTCAC-TCCACTCACTACAATGTGTAGGTTCCCCAGAACC
* *
1199018 ATACACCCACCTGCACACCAATAAAGACTTACCCTAAGCACACAGCAAAGGAGTCTGCAGTAATA
1 ATACACCCACCTGCACACCAATAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAATA
*
1199083 ACTTCCCCAACCAGTCACTCCACTCACTACAATGTGTAGGTTCCCCAGAACC
66 ACGTCCCCAACCAGTCACTCCACTCACTACAATGTGTAGGTTCCCCAGAACC
* *
1199135 ATACACCCACCTGCACACCAATAAGGACTTACCCTGAGCACACAGCAAATGAGCCTG
1 ATACACCCACCTGCACACCAATAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTG
1199192 AAATACTTTC
Statistics
Matches: 157, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
116 4 0.03
117 153 0.97
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.19
Consensus pattern (117 bp):
ATACACCCACCTGCACACCAATAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAATA
ACGTCCCCAACCAGTCACTCCACTCACTACAATGTGTAGGTTCCCCAGAACC
Found at i:1200158 original size:29 final size:29
Alignment explanation
Indices: 1200118--1200193 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
1200108 AATATTTTTA
1200118 CATAATTAGCACCCTTTTTAAAATAATAAC
1 CATAA-TAGCACCCTTTTTAAAATAATAAC
* * * *
1200148 CATAATAGCACACTTTTCAAATTAATTAC
1 CATAATAGCACCCTTTTTAAAATAATAAC
*
1200177 CAAAATAGCA-CCTTTTT
1 CATAATAGCACCCTTTTT
1200194 GAATTAATTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 5 0.13
29 29 0.74
30 5 0.13
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (29 bp):
CATAATAGCACCCTTTTTAAAATAATAAC
Found at i:1200191 original size:28 final size:28
Alignment explanation
Indices: 1200124--1200305 Score: 112
Period size: 28 Copynumber: 6.2 Consensus size: 28
1200114 TTTACATAAT
* * * *
1200124 TAGCACCCTTTTTAAAATAATAACCATAA
1 TAGCA-CCTTTTCAAATTAATTACCAAAA
1200153 TAGCACACTTTTCAAATTAATTACCAAAA
1 TAGCAC-CTTTTCAAATTAATTACCAAAA
** *
1200182 TAGCACCTTTTTGAATTAATTCCCAAAA
1 TAGCACCTTTTCAAATTAATTACCAAAA
* * * * * *
1200210 TAACATCATTTCGAATTAATTCCCAGAA
1 TAGCACCTTTTCAAATTAATTACCAAAA
* **
1200238 TATCACCTTTTTTTCGAAAAAAATTACCAAAA
1 TAGCACC---TTTTC-AAATTAATTACCAAAA
* ** * *
1200270 TAGCACCCATTTCGGATTAATTCCCAGAA
1 TAGCA-CCTTTTCAAATTAATTACCAAAA
1200299 TAGCACC
1 TAGCACC
1200306 AAAATCGAAT
Statistics
Matches: 119, Mismatches: 28, Indels: 13
0.74 0.17 0.08
Matches are distributed among these distances:
28 50 0.42
29 44 0.37
30 4 0.03
31 4 0.03
32 15 0.13
33 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.31
Consensus pattern (28 bp):
TAGCACCTTTTCAAATTAATTACCAAAA
Found at i:1200300 original size:29 final size:29
Alignment explanation
Indices: 1200151--1200329 Score: 128
Period size: 28 Copynumber: 6.1 Consensus size: 29
1200141 TAATAACCAT
* * * *
1200151 AATAGCACACTTTTCAAATTAATTACCAA
1 AATAGCACCCATTTCGAATTAATTCCCAA
* *
1200180 AATAGCA-CCTTTTTGAATTAATTCCCAA
1 AATAGCACCCATTTCGAATTAATTCCCAA
* * *
1200208 AATAACA-TCATTTCGAATTAATTCCCAG
1 AATAGCACCCATTTCGAATTAATTCCCAA
* ** ** *
1200236 AATATCACCTTTTTTTCGAAAAAAATTACCAA
1 AATAGCACC--CATTTCG-AATTAATTCCCAA
* *
1200268 AATAGCACCCATTTCGGATTAATTCCCAG
1 AATAGCACCCATTTCGAATTAATTCCCAA
* ** *
1200297 AATAGCACCAAAATCGAATTAATTCCCAG
1 AATAGCACCCATTTCGAATTAATTCCCAA
1200326 AATA
1 AATA
1200330 TCATCGGTCA
Statistics
Matches: 117, Mismatches: 29, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
28 46 0.39
29 44 0.38
30 5 0.04
31 5 0.04
32 17 0.15
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (29 bp):
AATAGCACCCATTTCGAATTAATTCCCAA
Found at i:1200400 original size:19 final size:19
Alignment explanation
Indices: 1200376--1200424 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1200366 GTCAGGTCAG
*
1200376 GTCGGACTGGTTCAGACCA
1 GTCGGACCGGTTCAGACCA
*
1200395 GTCGGACCGGTTCAGACCG
1 GTCGGACCGGTTCAGACCA
*
1200414 GTTGGACCGGT
1 GTCGGACCGGT
1200425 CAAAACCGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.16, C:0.27, G:0.37, T:0.20
Consensus pattern (19 bp):
GTCGGACCGGTTCAGACCA
Found at i:1203960 original size:15 final size:15
Alignment explanation
Indices: 1203940--1203973 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1203930 CACCTCAAAC
*
1203940 CTTCACCTTCTCCTT
1 CTTCACCGTCTCCTT
1203955 CTTCACCGTCTCCTT
1 CTTCACCGTCTCCTT
1203970 CTTC
1 CTTC
1203974 GCCCTGTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.47, G:0.03, T:0.44
Consensus pattern (15 bp):
CTTCACCGTCTCCTT
Found at i:1206282 original size:34 final size:34
Alignment explanation
Indices: 1206239--1206308 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1206229 ACCACTACTG
1206239 CACATTGATTGAATCATTGACCTAATCTTTATCA
1 CACATTGATTGAATCATTGACCTAATCTTTATCA
1206273 CACATTGATTGAATCATTGACCTAATCTTTATCA
1 CACATTGATTGAATCATTGACCTAATCTTTATCA
1206307 CA
1 CA
1206309 AAACGGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (34 bp):
CACATTGATTGAATCATTGACCTAATCTTTATCA
Found at i:1211184 original size:30 final size:30
Alignment explanation
Indices: 1211150--1211212 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1211140 AGATGATTTT
* *
1211150 AATAAAA-TAAATAAATAAGATAATGATAAA
1 AATAAAATTAAATAAA-AAAATAATCATAAA
*
1211180 AATAAAATTAAATAAAAAAATAATCATCAA
1 AATAAAATTAAATAAAAAAATAATCATAAA
1211210 AAT
1 AAT
1211213 TTTTAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (30 bp):
AATAAAATTAAATAAAAAAATAATCATAAA
Found at i:1211481 original size:21 final size:21
Alignment explanation
Indices: 1211456--1211520 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1211446 TCAGATTCGT
*
1211456 AATGCGATTTTGGACTATCGC
1 AATGCGAATTTGGACTATCGC
* * *
1211477 AATGCGAATATGTA-AATCGC
1 AATGCGAATTTGGACTATCGC
*
1211497 AATGCGAACTTGGACTATCGC
1 AATGCGAATTTGGACTATCGC
1211518 AAT
1 AAT
1211521 ACTATGTGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (21 bp):
AATGCGAATTTGGACTATCGC
Found at i:1213496 original size:21 final size:20
Alignment explanation
Indices: 1213472--1213711 Score: 150
Period size: 21 Copynumber: 11.6 Consensus size: 20
1213462 CATATTCGCA
1213472 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTAGTCCAAGTT--CG
*
1213493 TTGCGA-TAGTCGAAGTTCACG
1 TTGCGATTAGTCCAAGTT--CG
* *
1213514 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTAGTCCAAGTTCG
* *
1213535 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTAGTCCAAGTTCG
* * *
1213556 ATGCGATTTATTCCAAATTCG
1 TTGCGA-TTAGTCCAAGTTCG
* * *
1213577 TTGCGATTTATTCCAAATTCA
1 TTGCGA-TTAGTCCAAGTTCG
1213598 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTAGTCCAAGTT--CG
*
1213619 TTGCGATTTATTCCAAGTTCG
1 TTGCGA-TTAGTCCAAGTTCG
* *
1213640 TTGTGA-TAGTCGAAGTTCGTG
1 TTGCGATTAGTCCAAGTTC--G
* * *
1213661 TTGCGATTTATTCCAAATTTG
1 TTGCGA-TTAGTCCAAGTTCG
*
1213682 CTGCGA-TAGTCCAAGTTCG
1 TTGCGATTAGTCCAAGTTCG
1213701 TTGCGA-TAGTC
1 TTGCGATTAGTC
1213712 GAACGTGTCG
Statistics
Matches: 184, Mismatches: 25, Indels: 22
0.80 0.11 0.10
Matches are distributed among these distances:
19 39 0.21
21 119 0.65
23 26 0.14
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTAGTCCAAGTTCG
Found at i:1213584 original size:42 final size:40
Alignment explanation
Indices: 1213525--1213707 Score: 215
Period size: 42 Copynumber: 4.4 Consensus size: 40
1213515 TGCGATTTAT
* *
1213525 TCCAAATTCGTTGCGATTTATTCCAAATTCGATGCGATTTAT
1 TCCAAGTTCGTTGCGATTTATTCCAAATTCGATGCGA--TAG
*
1213567 TCCAAATTCGTTGCGATTTATTCCAAATTC-ATTGCGATAG
1 TCCAAGTTCGTTGCGATTTATTCCAAATTCGA-TGCGATAG
* * *
1213607 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGTGATAG
1 TCCAAGTT--CGTTGCGATTTATTCCAAATTCGATGCGATAG
* * *
1213649 TCGAAGTTCGTGTTGCGATTTATTCCAAATTTGCTGCGATAG
1 TCCAAGTTC--GTTGCGATTTATTCCAAATTCGATGCGATAG
1213691 TCCAAGTTCGTTGCGAT
1 TCCAAGTTCGTTGCGAT
1213708 AGTCGAACGT
Statistics
Matches: 124, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
40 18 0.15
41 1 0.01
42 105 0.85
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (40 bp):
TCCAAGTTCGTTGCGATTTATTCCAAATTCGATGCGATAG
Found at i:1213624 original size:63 final size:63
Alignment explanation
Indices: 1213470--1213642 Score: 219
Period size: 63 Copynumber: 2.7 Consensus size: 63
1213460 TACATATTCG
* *
1213470 CATTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCACGTTGCGATTTATTCCAAATT
1 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATTTATTCCAAATT
* * * * *
1213533 CGTTGCGATTTATTCCAAATT--CGATGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 CATTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATT
1213596 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTG
1 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTG
1213643 TGATAGTCGA
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
61 9 0.10
63 66 0.72
65 17 0.18
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (63 bp):
CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATT
Found at i:1214241 original size:6 final size:6
Alignment explanation
Indices: 1214232--1214286 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
1214222 CGCCGTCGTC
1214232 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1214280 TCGTGG T
1 TCGTGG T
1214287 AATACGTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:1214411 original size:21 final size:20
Alignment explanation
Indices: 1214385--1214494 Score: 91
Period size: 21 Copynumber: 5.3 Consensus size: 20
1214375 TTTGGAATAA
1214385 ATCGCAACGCAAACTTCGACT
1 ATCGCAACGC-AACTTCGACT
* * *
1214406 ATCGCAACG-AATTTGGAAT
1 ATCGCAACGCAACTTCGACT
1214425 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGC-AACTTCGACT
* * *
1214448 ATCGCAACG-AATTTGGA-A
1 ATCGCAACGCAACTTCGACT
1214466 ACTCGCAACGCGAACTTCGACT
1 A-TCGCAACGC-AACTTCGACT
1214488 ATCGCAA
1 ATCGCAA
1214495 TACGAACTTG
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.01
19 21 0.30
21 39 0.57
22 1 0.01
23 7 0.10
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCAACTTCGACT
Found at i:1214500 original size:21 final size:20
Alignment explanation
Indices: 1214396--1214515 Score: 75
Period size: 21 Copynumber: 5.8 Consensus size: 20
1214386 TCGCAACGCA
1214396 AACTTCGACTATCGC-AACG
1 AACTTCGACTATCGCAAACG
* * * *
1214415 AATTTGGAATAAATCGCAACGCG
1 AACTTCGACT--ATCGCAA-ACG
1214438 AACTTCGACTATCGC-AACG
1 AACTTCGACTATCGCAAACG
* * * *
1214457 AATTTGGA-AACTCGCAACGCG
1 AACTTCGACTA-TCGCAA-ACG
1214478 AACTTCGACTATCGCAATACG
1 AACTTCGACTATCGCAA-ACG
* *
1214499 AACTTGGATTATCGCAA
1 AACTTCGACTATCGCAA
1214516 TGCGAATTAT
Statistics
Matches: 74, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
18 1 0.01
19 19 0.26
20 2 0.03
21 41 0.55
22 2 0.03
23 9 0.12
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
AACTTCGACTATCGCAAACG
Found at i:1214500 original size:42 final size:42
Alignment explanation
Indices: 1214371--1214494 Score: 216
Period size: 42 Copynumber: 3.0 Consensus size: 42
1214361 CCAGTCGTTG
*
1214371 CGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1214413 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
*
1214455 CGAATTTGG-A-AACTCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1214495 TACGAACTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
40 29 0.36
41 1 0.01
42 50 0.62
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
Done.