Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008088.1 Hibiscus syriacus cultivar Beakdansim tig00110598_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: 89828
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:235 original size:92 final size:93
Alignment explanation
Indices: 1--291 Score: 505
Period size: 92 Copynumber: 3.2 Consensus size: 93
1 GTCTTTT-GTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--TGTATTC-TTAAC
1 GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
62 AC--TG-AA-A-TATTTGTCTTTGTTTT
66 ACTGTGAAATAGTATTTGTCTTTGTTTT
85 GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
1 GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
150 ACTGTGAAATAGTATTTGTCTTTGTTTT
66 ACTGTGAAATAGTATTTGTCTTTGTTTT
178 GTCTTTTGGTTGAAAGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
1 GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
242 ACTGTGAAATAGTA-TTGTCTTTGTTTT
66 ACTGTGAAATAGTATTTGTCTTTGTTTT
269 GTCTTTTGGTTGAAAGTAAATTT
1 GTCTTTTGGTTGAAAGTAAATTT
292 ATCCATTCAA
Statistics
Matches: 197, Mismatches: 0, Indels: 12
0.94 0.00 0.06
Matches are distributed among these distances:
84 7 0.04
85 42 0.21
87 7 0.04
88 7 0.04
90 2 0.01
91 35 0.18
92 61 0.31
93 36 0.18
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
GTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAAC
ACTGTGAAATAGTATTTGTCTTTGTTTT
Found at i:375 original size:19 final size:19
Alignment explanation
Indices: 335--462 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
325 TAGTTTACTT
* *
335 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
355 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
374 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
393 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
407 TCGCAACGCG-AACCAAAA
1 TCGCAACGCGAAACCAAAA
*
425 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
439 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
458 TCGCA
1 TCGCA
463 TTGCGATTTC
Statistics
Matches: 90, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 6 0.07
17 3 0.03
18 11 0.12
19 36 0.40
20 13 0.14
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:410 original size:14 final size:13
Alignment explanation
Indices: 390--446 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 13
380 CGCGAAATGA
390 AAATCGCAACGAC
1 AAATCGCAACGAC
403 AGAATCGCAACGCGAACC
1 A-AATCGCAA--CG-A-C
421 AAAATCGCAACGAC
1 -AAATCGCAACGAC
435 AAGATCGCAACG
1 AA-ATCGCAACG
447 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.08
14 18 0.49
15 1 0.03
16 4 0.11
17 1 0.03
18 9 0.24
19 1 0.03
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (13 bp):
AAATCGCAACGAC
Found at i:430 original size:32 final size:32
Alignment explanation
Indices: 371--462 Score: 141
Period size: 32 Copynumber: 2.8 Consensus size: 32
361 CGCGAAACCA
**
371 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
403 AGAATCGCAACGCG-AACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
435 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
463 TTGCGATTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 29 0.53
33 25 0.45
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:498 original size:14 final size:14
Alignment explanation
Indices: 479--535 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
469 TTTCATTTCG
479 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
493 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
510 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
526 CGTTGCGATT
1 CGTTGCGATT
536 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:510 original size:33 final size:33
Alignment explanation
Indices: 463--554 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
453 CAAAATCGCA
*
463 TTGCGA-TTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
495 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
528 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
555 TTGGTTTCGC
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 6 0.10
33 52 0.90
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:517 original size:19 final size:19
Alignment explanation
Indices: 458--591 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
448 GAAACCAAAA
*
458 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
476 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
492 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
509 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
525 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
542 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
561 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
581 TCGTGTTGCGA
1 TCGCGTTGCGA
592 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 10 0.10
19 37 0.38
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2418 original size:38 final size:38
Alignment explanation
Indices: 2376--2448 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
2366 TAATTGATTG
*
2376 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
2414 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
2449 TGTAAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:2435 original size:19 final size:19
Alignment explanation
Indices: 2372--2435 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
2362 TAGTTAATTG
2372 ATTG-TTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
2390 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
2408 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
2428 ATTGATTT
1 ATTGATTT
2436 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 12, Indels: 5
0.65 0.25 0.10
Matches are distributed among these distances:
18 9 0.29
19 17 0.55
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:2455 original size:13 final size:14
Alignment explanation
Indices: 2430--2464 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2420 ATTGTTTAAT
2430 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2444 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
2457 TGATTTGT
1 TGATTTGT
2465 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2644 original size:20 final size:19
Alignment explanation
Indices: 2570--2670 Score: 126
Period size: 20 Copynumber: 5.6 Consensus size: 19
2560 AAAAATGACT
2570 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
2588 ATCGCAATGC-AAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2606 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2620 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCG-AAATGAAA
2640 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2660 ATCGCAATGCG
1 ATCGCAATGCG
2671 TTTATAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 17
0.79 0.02 0.19
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 3 0.04
17 5 0.07
18 19 0.26
19 2 0.03
20 31 0.43
21 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2723 original size:19 final size:19
Alignment explanation
Indices: 2699--3024 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
2689 GATTATCTCG
2699 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2718 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2737 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2751 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2770 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2789 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
2808 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
2827 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2846 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2860 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2879 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2898 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2912 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2931 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2950 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2964 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2984 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2998 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3017 TTGCGATT
1 TTGCGATT
3025 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2739 original size:52 final size:52
Alignment explanation
Indices: 2677--2996 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
2667 TGCGTTTATA
*
2677 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2729 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
2781 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
2838 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2890 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2942 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2995 AT
1 AT
2997 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2774 original size:71 final size:72
Alignment explanation
Indices: 2699--3024 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
2689 GATTATCTCG
2699 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
2763 TTTCGCA
66 TTTCGCA
* *
2770 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
2835 TTCATTTCGCA
62 TTCATTTCGCA
*
2846 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
2904 TTC-TCTCG--
62 TTCATTTCGCA
*
2912 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
2976 TTTCCGCA
66 TTT-CGCA
* *
2984 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
3025 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:2942 original size:161 final size:157
Alignment explanation
Indices: 2677--2996 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
2667 TGCGTTTATA
2677 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
2742 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
2807 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
2838 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
2903 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
2968 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
2995 AT
1 AT
2997 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:2968 original size:33 final size:33
Alignment explanation
Indices: 2718--3024 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
2708 TCATTTCGCA
*
2718 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2751 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
2787 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
2825 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2860 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
2896 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
2931 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2964 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
2998 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
3025 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:5002 original size:12 final size:12
Alignment explanation
Indices: 4985--5009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4975 TTCTTCGGGA
4985 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4997 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5009 C
1 C
5010 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5215 original size:22 final size:24
Alignment explanation
Indices: 5183--5227 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5173 CTGAAACATC
5183 ATCAAAATCC-G-TATTGACCAAT
1 ATCAAAATCCGGATATTGACCAAT
*
5205 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5228 GACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:5926 original size:20 final size:20
Alignment explanation
Indices: 5898--6306 Score: 486
Period size: 20 Copynumber: 20.4 Consensus size: 20
5888 AAATTTCAGT
* * * *
5898 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5918 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
5938 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5958 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
5978 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5998 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6018 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6038 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6058 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6078 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6098 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6118 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
6138 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6158 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6178 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
6198 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
6218 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
6238 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
6258 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
6278 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
6298 GTTGCGATT
1 GTTGCGATT
6307 ATGGAAAATC
Statistics
Matches: 343, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.02
20 331 0.97
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:9287 original size:18 final size:18
Alignment explanation
Indices: 9266--9307 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
9256 ATCTAAAACT
9266 GGTATCGATACCGGAAGG
1 GGTATCGATACCGGAAGG
*
9284 GGTATCGGTACCGGAAGG
1 GGTATCGATACCGGAAGG
9302 GGTATC
1 GGTATC
9308 AGTACCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.40, T:0.19
Consensus pattern (18 bp):
GGTATCGATACCGGAAGG
Found at i:9312 original size:18 final size:18
Alignment explanation
Indices: 9274--9313 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
9264 CTGGTATCGA
*
9274 TACCGGAAGGGGTATCGG
1 TACCGGAAGGGGTATCAG
9292 TACCGGAAGGGGTATCAG
1 TACCGGAAGGGGTATCAG
9310 TACC
1 TACC
9314 ATAGTATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.38, T:0.17
Consensus pattern (18 bp):
TACCGGAAGGGGTATCAG
Found at i:9718 original size:2 final size:2
Alignment explanation
Indices: 9713--9778 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
9703 AAGAGGAAGA
9713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
9755 AT AT AT AC AC AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
9779 TTATGTTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11145 original size:21 final size:21
Alignment explanation
Indices: 11120--11163 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
11110 AATATAAATT
*
11120 GTGTATCGATGCACTACTACA
1 GTGTACCGATGCACTACTACA
*
11141 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTACTACA
11162 GT
1 GT
11164 AACTTCAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
GTGTACCGATGCACTACTACA
Found at i:11719 original size:23 final size:23
Alignment explanation
Indices: 11693--11756 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
11683 AGCTCGTATA
11693 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
11716 AATTGCACCGAAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
11739 AATTGCATCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
11757 TATAAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:17214 original size:12 final size:12
Alignment explanation
Indices: 17173--17205 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
17163 ACATATCAAT
17173 TCATTATTCTTA
1 TCATTATTCTTA
*
17185 TTATTATTCTTA
1 TCATTATTCTTA
17197 TCATTATTC
1 TCATTATTC
17206 ATATGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTATTCTTA
Found at i:17902 original size:12 final size:12
Alignment explanation
Indices: 17885--17927 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
17875 ATATCATTTC
17885 ATTATTCTTAGT-
1 ATTATTCTTA-TA
* *
17897 ATTATTCTTCTC
1 ATTATTCTTATA
17909 ATTATTCTTATA
1 ATTATTCTTATA
17921 ATTATTC
1 ATTATTC
17928 ATATGATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 1 0.04
12 26 0.96
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.58
Consensus pattern (12 bp):
ATTATTCTTATA
Found at i:17936 original size:24 final size:24
Alignment explanation
Indices: 17878--17936 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
17868 CACATACATA
*
17878 TCATTTCATTATTCTTAGTATTAT
1 TCATATCATTATTCTTAGTATTAT
* *
17902 TCTTCTCATTATTCTTA-TAATTAT
1 TCATATCATTATTCTTAGT-ATTAT
*
17926 TCATATGATTA
1 TCATATCATTA
17937 ACAATCATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.56
Consensus pattern (24 bp):
TCATATCATTATTCTTAGTATTAT
Found at i:19956 original size:26 final size:25
Alignment explanation
Indices: 19922--20144 Score: 137
Period size: 26 Copynumber: 9.6 Consensus size: 25
19912 AATTAGATTG
*
19922 GCATGAAAGGATGTCATAAATAAAAT
1 GCATGAAAGGATGCCAT-AATAAAAT
* * *
19948 GCATAAAAGGA-GGCAT--T--AAG
1 GCATGAAAGGATGCCATAATAAAAT
19968 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCAT-AATAAAAT
* *
19994 GCATGAAAGGATG---T-AT-TAAG
1 GCATGAAAGGATGCCATAATAAAAT
*
20014 GCGTGAAAGGATGCCATCAATAAAAT
1 GCATGAAAGGATGCCAT-AATAAAAT
*
20040 GCATGAAAGGATG-CAT--T--AAG
1 GCATGAAAGGATGCCATAATAAAAT
20060 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCAT-AATAAAAT
* *
20086 GCATGAAAAGATG-CAT--T--AAG
1 GCATGAAAGGATGCCATAATAAAAT
*
20106 GCATGGAA-GATGCCATAAATAAAAT
1 GCATGAAAGGATGCCAT-AATAAAAT
* *
20131 GTATGAAATGATGC
1 GCATGAAAGGATGC
20145 ATTAAGGCAT
Statistics
Matches: 152, Mismatches: 20, Indels: 50
0.68 0.09 0.23
Matches are distributed among these distances:
19 4 0.03
20 53 0.35
21 9 0.06
22 3 0.02
23 3 0.02
24 2 0.01
25 20 0.13
26 58 0.38
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (25 bp):
GCATGAAAGGATGCCATAATAAAAT
Found at i:19988 original size:46 final size:46
Alignment explanation
Indices: 19921--20220 Score: 382
Period size: 46 Copynumber: 6.6 Consensus size: 46
19911 TAATTAGATT
* *
19921 GGCATGAAAGGATGTCATAAATAAAATGCATAAAAGGAGGCATTAA
1 GGCATGAAAGGATGCCATAAATAAAATGCATAAAAGGATGCATTAA
* *
19967 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGTATTAA
1 GGCATGAAAGGATGCCATAAATAAAATGCATAAAAGGATGCATTAA
* * *
20013 GGCGTGAAAGGATGCCATCAATAAAATGCATGAAAGGATGCATTAA
1 GGCATGAAAGGATGCCATAAATAAAATGCATAAAAGGATGCATTAA
20059 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAA-GATGCATTAA
1 GGCATGAAAGGATGCCATAAATAAAATGCAT-AAAAGGATGCATTAA
* * * *
20105 GGCATGGAA-GATGCCATAAATAAAATGTATGAAATGATGCATTAA
1 GGCATGAAAGGATGCCATAAATAAAATGCATAAAAGGATGCATTAA
* *
20150 GGCATGAAAGGATG-CAT---T--AAGGCATGAAAGTATGATGCATTAA
1 GGCATGAAAGGATGCCATAAATAAAATGCAT-AAA--AGGATGCATTAA
*
20193 GGCATGAAAGTATGCCATAAATAAAATG
1 GGCATGAAAGGATGCCATAAATAAAATG
20221 AAATTTAAAG
Statistics
Matches: 223, Mismatches: 19, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
40 5 0.02
41 2 0.01
42 1 0.00
43 25 0.11
44 6 0.03
45 41 0.18
46 136 0.61
47 4 0.02
49 3 0.01
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATAAAATGCATAAAAGGATGCATTAA
Found at i:20071 original size:20 final size:20
Alignment explanation
Indices: 19948--20207 Score: 153
Period size: 20 Copynumber: 11.7 Consensus size: 20
19938 TAAATAAAAT
* *
19948 GCATAAAAGGAGGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
19968 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
19994 GCATGAAAGGATGTATTAAG
1 GCATGAAAGGATGCATTAAG
* *
20014 GCGTGAAAGGATGCCATCAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
20040 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
20060 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
20086 GCATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
20106 GCATGGAA-GATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
20131 GTATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
20151 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
20171 GCATGAAAGTATGATGCATTAAG
1 GCATGAAAG---GATGCATTAAG
*
20194 GCATGAAAGTATGC
1 GCATGAAAGGATGC
20208 CATAAATAAA
Statistics
Matches: 191, Mismatches: 21, Indels: 56
0.71 0.08 0.21
Matches are distributed among these distances:
19 4 0.02
20 85 0.45
21 8 0.04
22 4 0.02
23 21 0.11
24 3 0.02
25 19 0.10
26 47 0.25
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:20190 original size:23 final size:23
Alignment explanation
Indices: 20138--20206 Score: 117
Period size: 23 Copynumber: 3.1 Consensus size: 23
20128 AATGTATGAA
20138 ATGATGCATTAAGGCATGAAAG-
1 ATGATGCATTAAGGCATGAAAGT
20160 --GATGCATTAAGGCATGAAAGT
1 ATGATGCATTAAGGCATGAAAGT
20181 ATGATGCATTAAGGCATGAAAGT
1 ATGATGCATTAAGGCATGAAAGT
20204 ATG
1 ATG
20207 CCATAAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
20 20 0.45
23 24 0.55
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.25
Consensus pattern (23 bp):
ATGATGCATTAAGGCATGAAAGT
Found at i:20681 original size:68 final size:68
Alignment explanation
Indices: 20586--20769 Score: 262
Period size: 68 Copynumber: 2.7 Consensus size: 68
20576 GATTAATTGT
* * * * *
20586 CTAACTGAGCAATTGGCAGAAAGGTGTCAATTATACTAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGAGCGATTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
20651 GGC
66 GGC
* ** *
20654 CTAACTGTGC-ATTTGACGCAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CTAACTGAGCGA-TTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
20718 AGGC
65 AGGC
*
20722 CTAACTGAGCGATTGGCAAAAAGGTGTCAATTATGCCAGTTAGATGAA
1 CTAACTGAGCGATTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAA
20770 CGGTGAAACA
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
67 1 0.01
68 100 0.98
69 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (68 bp):
CTAACTGAGCGATTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:20796 original size:29 final size:29
Alignment explanation
Indices: 20763--20823 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
20753 TATGCCAGTT
20763 AGATGAACGGTGAAACACTGTTGAGTAAA
1 AGATGAACGGTGAAACACTGTTGAGTAAA
*
20792 AGATGAACGGTTAAACACTGTTGAGTAAA
1 AGATGAACGGTGAAACACTGTTGAGTAAA
20821 AGA
1 AGA
20824 ATAATGTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (29 bp):
AGATGAACGGTGAAACACTGTTGAGTAAA
Found at i:22565 original size:16 final size:16
Alignment explanation
Indices: 22540--22574 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22530 AGTTTGCTCG
22540 TCGTTAGTGGTACTCA
1 TCGTTAGTGGTACTCA
* *
22556 TCGTTTGTGGTACTTA
1 TCGTTAGTGGTACTCA
22572 TCG
1 TCG
22575 CTGCTCGTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (16 bp):
TCGTTAGTGGTACTCA
Found at i:24585 original size:15 final size:15
Alignment explanation
Indices: 24565--24620 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
24555 AACCGGGTAT
24565 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
** *
24580 CGGGTACCCGTAAAAT
1 CGGGTACCCG-ATTAC
* *
24596 CTGGTACCCAATTAC
1 CGGGTACCCGATTAC
24611 CGGGTACCCG
1 CGGGTACCCG
24621 TAACATCCGG
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
15 20 0.67
16 10 0.33
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.20
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:25549 original size:25 final size:26
Alignment explanation
Indices: 25521--25573 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
25511 TGACCAACAA
*
25521 AATCGCAATGCGAA-AT-AAAGATCGC
1 AATCGCAACGCGAATATGAAA-ATCGC
25546 AATCGCAACGCGAATATGAAAATCGC
1 AATCGCAACGCGAATATGAAAATCGC
25572 AA
1 AA
25574 CGCGAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 13 0.52
26 9 0.36
27 3 0.12
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (26 bp):
AATCGCAACGCGAATATGAAAATCGC
Found at i:25571 original size:20 final size:20
Alignment explanation
Indices: 25546--25801 Score: 153
Period size: 20 Copynumber: 12.7 Consensus size: 20
25536 TAAAGATCGC
*
25546 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
25566 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* * * *
25586 AATCGCAAAGTG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
25606 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
25627 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
25647 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* *
25668 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
25688 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
25708 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
25728 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
25748 AATCACAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
25769 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
25789 AATCGCAACGCGA
1 AATCGCAACGCGA
25802 TTTTTAAAGC
Statistics
Matches: 184, Mismatches: 39, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
19 3 0.02
20 126 0.68
21 55 0.30
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:25652 original size:41 final size:40
Alignment explanation
Indices: 25607--25801 Score: 241
Period size: 41 Copynumber: 4.8 Consensus size: 40
25597 GATTCTGACT
* * *
25607 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGCGAATACGTAA
* * *
25648 ATCGCAACGAC-AATACGTAAAATCGCAACGAGAATACGTAA
1 ATCGCAACG-CGTATCCGT-AAATCGCAACGCGAATACGTAA
* *
25689 ATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAA
* *
25729 ATCGCAATGCGTATCCGTAAATCACAACGAC-AATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACG-CGAATACGT-AA
25770 ATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGA
25802 TTTTTAAAGC
Statistics
Matches: 134, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
40 57 0.43
41 77 0.57
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAA
Found at i:25716 original size:61 final size:61
Alignment explanation
Indices: 25607--25735 Score: 206
Period size: 61 Copynumber: 2.1 Consensus size: 61
25597 GATTCTGACT
* *
25607 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT-AA
* *
25669 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
25729 ATCGCAA
1 ATCGCAA
25736 TGCGTATCCG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 9 0.14
61 38 0.60
62 16 0.25
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (61 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
Found at i:25767 original size:101 final size:102
Alignment explanation
Indices: 25607--25800 Score: 318
Period size: 101 Copynumber: 1.9 Consensus size: 102
25597 GATTCTGACT
* * *
25607 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGACAATACGTAAAATC
25672 GCAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
66 GCAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
*
25709 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCACAACGACAATACGTAAAATC
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGACAATACGTAAAATC
* * *
25773 GCAACGCGTATCCGTAAATCGCAACGCG
66 GCAACGAGAATACGTAAATCGCAACGCG
25801 ATTTTTAAAG
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 69 0.81
102 16 0.19
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (102 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGACAATACGTAAAATC
GCAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
Found at i:26419 original size:21 final size:21
Alignment explanation
Indices: 26358--26436 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
26348 TTCTAAACTT
26358 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
26378 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
26398 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
26419 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
26437 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:26454 original size:33 final size:33
Alignment explanation
Indices: 26413--26493 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
26403 CGCAACGAGA
26413 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
26446 GAAATGAAAATCGTAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
26479 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
26494 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:26511 original size:19 final size:19
Alignment explanation
Indices: 26489--26634 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
26479 GAAACCAAAA
*
26489 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
26508 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
26527 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
26541 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
26560 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
26574 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
* **
26594 TCGCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
26613 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
26633 TC
1 TC
26635 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 19 0.19
16 5 0.05
17 5 0.05
19 41 0.41
20 30 0.30
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:26554 original size:33 final size:33
Alignment explanation
Indices: 26512--26585 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
26502 TTCATTTCGC
26512 GTTGCGATTTTAATTTCGCGTTGCGATTCTCTA
1 GTTGCGATTTTAATTTCGCGTTGCGATTCTCTA
* *
26545 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTAATTTCGCGTTGCGATTCTCTA
26578 GTTGCGAT
1 GTTGCGAT
26586 AGTCATTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (33 bp):
GTTGCGATTTTAATTTCGCGTTGCGATTCTCTA
Found at i:26592 original size:33 final size:33
Alignment explanation
Indices: 26524--26605 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
26514 TGCGATTTTA
**
26524 ATTTCGCGTTGCGATTCTCTAGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTAGTTGCGATAGTC
*
26557 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTAGTTGCGATAGTC
*
26590 ATTTTCGCATTGCGAT
1 A-TTTCGCGTTGCGAT
26606 AGTCATTCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 31 0.70
34 13 0.30
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTAGTTGCGATAGTC
Found at i:26622 original size:20 final size:20
Alignment explanation
Indices: 26570--26625 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
26560 TCGCGTTGCG
26570 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
* * *
26590 ATTTTCGCATTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
26610 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
26626 TTTCATTTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:28484 original size:94 final size:93
Alignment explanation
Indices: 28323--28702 Score: 609
Period size: 94 Copynumber: 4.1 Consensus size: 93
28313 TAGATTGCTT
* * *
28323 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACCGTGAAGTTAGT
28388 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
28417 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACCGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACCGTGAAGTTAGT
28482 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
28511 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACCGTGAAGTTAGT
*
28576 ATTTGTCTTTGTTTTGTCTTTTGGTTAAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTT-GA
* ** *
28605 AGTAAATTTGTTCGGTTGCTGCCAATTCTATTAAACTGTGTATTCTTTAATACTC-TGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC-CGTGAAGTTAG
*
28669 TATTTGTCTTTGTTTTATCTTTTGGTTGA
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGA
28698 AGTAA
1 AGTAA
28703 TGCAATCCAT
Statistics
Matches: 269, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
93 26 0.10
94 243 0.90
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACCGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:28830 original size:19 final size:19
Alignment explanation
Indices: 28806--28873 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
28796 ACGCGAAATG
*
28806 AATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAACCAA
28825 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
28839 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
*
28858 AATCACAACGCGAAAC
1 AATCGCAACGCGAAAC
28874 TATAATCGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 1 0.02
18 1 0.02
19 26 0.62
ACGTcount: A:0.50, C:0.29, G:0.15, T:0.06
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:28841 original size:14 final size:14
Alignment explanation
Indices: 28822--28848 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28812 AACGAGAAAC
28822 CAAAATCGCAACGA
1 CAAAATCGCAACGA
28836 CAAAATCGCAACG
1 CAAAATCGCAACG
28849 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:28942 original size:20 final size:20
Alignment explanation
Indices: 28917--29003 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
28907 GATTCTCTCG
*
28917 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-ATTTTCGCA
28937 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
28957 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
28977 TTGCGATAATCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
28997 TTGCGAT
1 TTGCGAT
29004 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 4 0.06
20 59 0.94
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:29578 original size:21 final size:21
Alignment explanation
Indices: 29510--29590 Score: 63
Period size: 21 Copynumber: 3.9 Consensus size: 21
29500 GGCCTCCCCT
*
29510 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCACTATC
** * * **
29531 ATCCCTCAAGAGTCCCCTCCC
1 ATCGTTCAAGAGGCCACTATC
* *
29552 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCACTATC
* *
29573 ATCGTTGAAGAGGTCACT
1 ATCGTTCAAGAGGCCACT
29591 CCCAACATTC
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCACTATC
Found at i:30852 original size:3 final size:3
Alignment explanation
Indices: 30844--30927 Score: 105
Period size: 3 Copynumber: 28.0 Consensus size: 3
30834 CCATATTAAT
* * * * * *
30844 TTA TTA TTA TTA TAA TTA TAA TTA TCA TTA TTA TAA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
30892 TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30928 AATACATTAA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:30947 original size:9 final size:9
Alignment explanation
Indices: 30872--30949 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
30862 TAATTATCAT
*
30872 TATTATAAT
1 TATTATAAA
30881 TATTATAAA
1 TATTATAAA
30890 TATTATAATTA
1 TATTATAA--A
* *
30901 TTATTATTAT
1 -TATTATAAA
* *
30911 TATTATTAT
1 TATTATAAA
30920 TATTATTAAA
1 TATTA-TAAA
*
30930 TA-CATTAAA
1 TATTA-TAAA
30939 TATTATAAA
1 TATTATAAA
30948 TA
1 TA
30950 ATAATAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
9 44 0.77
10 5 0.09
11 1 0.02
12 7 0.12
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (9 bp):
TATTATAAA
Found at i:31285 original size:19 final size:17
Alignment explanation
Indices: 31237--31299 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
31227 CAATAAAAGA
* *
31237 AAAAACACAGAGAG-AC
1 AAAAACACAGAAAGAAG
* *
31253 AAAGACAAAGAAAGACAG
1 AAAAACACAGAAAGA-AG
31271 AAAATACACAGAAAGAAG
1 AAAA-ACACAGAAAGAAG
*
31289 AGAAACACAGA
1 AAAAACACAGA
31300 GAAATCAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 11 0.30
17 7 0.19
18 9 0.24
19 10 0.27
ACGTcount: A:0.65, C:0.14, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAAACACAGAAAGAAG
Found at i:31302 original size:19 final size:19
Alignment explanation
Indices: 31234--31303 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
31224 CTGCAATAAA
* *
31234 AGAAAAAACACAGAGAGAC
1 AGAAAACACACAGAAAGAC
*
31253 A-AAGACA-A-AGAAAGAC
1 AGAAAACACACAGAAAGAC
*
31269 AGAAAATACACAGAAAGA-
1 AGAAAACACACAGAAAGAC
*
31287 AGAGAAACACAGAGAAA
1 AGA-AAACACACAGAAA
31304 TCAAATACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
16 8 0.20
17 5 0.12
18 8 0.20
19 19 0.47
ACGTcount: A:0.66, C:0.13, G:0.20, T:0.01
Consensus pattern (19 bp):
AGAAAACACACAGAAAGAC
Found at i:43621 original size:1 final size:1
Alignment explanation
Indices: 43617--43688 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
43607 GAGAAGAAAG
* * * * * * * * *
43617 AAAAAAGAAAGAAAAAAAAGAAAAAGAAAAAAAAGAGAGAAAAAAGAAAAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43682 AAAAAAA
1 AAAAAAA
43689 GGGGGGGTCA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:43645 original size:44 final size:43
Alignment explanation
Indices: 43596--43688 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
43586 ATTATGCTTG
* *
43596 AAGAAAAAAAAGAGAAGAAAGAAA-AAAGAAAGAAAAAAAAGAAA
1 AAGAAAAAAAAGAG-AGAAA-AAAGAAAAAAAAAAAAAAAAGAAA
43640 AAGAAAAAAAAGAGAGAAAAAAGAAAAAAAAAAAAAAAAGAAA
1 AAGAAAAAAAAGAGAGAAAAAAGAAAAAAAAAAAAAAAAGAAA
43683 AA-AAAA
1 AAGAAAA
43689 GGGGGGGTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 7 0.15
43 25 0.54
44 14 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (43 bp):
AAGAAAAAAAAGAGAGAAAAAAGAAAAAAAAAAAAAAAAGAAA
Found at i:43685 original size:9 final size:9
Alignment explanation
Indices: 43596--43687 Score: 107
Period size: 9 Copynumber: 10.2 Consensus size: 9
43586 ATTATGCTTG
43596 AAGAAAAAA
1 AAGAAAAAA
* *
43605 AAGAGAAGA
1 AAGAAAAAA
43614 AAGAAAAAAGA
1 AAG-AAAAA-A
43625 AAGAAAAAA
1 AAGAAAAAA
*
43634 AAGAAAAAG
1 AAGAAAAAA
43643 AA-AAAAAA
1 AAGAAAAAA
* *
43651 GAGAGAAAA
1 AAGAAAAAA
43660 AAGAAAAAA
1 AAGAAAAAA
43669 AA-AAAAAA
1 AAGAAAAAA
43677 AAGAAAAAA
1 AAGAAAAAA
43686 AA
1 AA
43688 AGGGGGGGTC
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
8 14 0.20
9 43 0.62
10 8 0.12
11 4 0.06
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:43685 original size:26 final size:26
Alignment explanation
Indices: 43596--43687 Score: 121
Period size: 26 Copynumber: 3.4 Consensus size: 26
43586 ATTATGCTTG
*
43596 AAGAAAAAAAAGAGAAGAAAGAAAAAAGA
1 AAGAAAAAAAAGA-AA-AAA-AAAAAAAA
*
43625 AAGAAAAAAAAGAAAAAGAAAAAAAA
1 AAGAAAAAAAAGAAAAAAAAAAAAAA
* *
43651 GAGAGAAAAAAGAAAAAAAAAAAAAA
1 AAGAAAAAAAAGAAAAAAAAAAAAAA
43677 AAGAAAAAAAA
1 AAGAAAAAAAA
43688 AGGGGGGGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
26 39 0.70
27 2 0.04
28 2 0.04
29 13 0.23
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAAAGAAAAAAAAAAAAAA
Found at i:43688 original size:39 final size:41
Alignment explanation
Indices: 43600--43688 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 41
43590 TGCTTGAAGA
43600 AAAAAAAGAGAAGAAAGAAAAAAGAAAGAAAAAAAAGAAAAAG
1 AAAAAAA-A-AAGAAAGAAAAAAGAAAGAAAAAAAAGAAAAAG
*
43643 --AAAAAAAAGAGAGAAAAAAGAAA-AAAAAAAA-AAAAAG
1 AAAAAAAAAAGAAAGAAAAAAGAAAGAAAAAAAAGAAAAAG
43680 AAAAAAAAA
1 AAAAAAAAA
43689 GGGGGGGTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
37 6 0.14
38 8 0.19
39 23 0.53
40 1 0.02
41 5 0.12
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (41 bp):
AAAAAAAAAAGAAAGAAAAAAGAAAGAAAAAAAAGAAAAAG
Found at i:44964 original size:83 final size:83
Alignment explanation
Indices: 44840--45715 Score: 1614
Period size: 83 Copynumber: 10.6 Consensus size: 83
44830 GAATTTGCCA
44840 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
44905 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
44923 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
44988 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
45006 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
* *
45071 TAGAAGATGAATTTG-CC
66 TAGAAGATGAATGTGTTC
45088 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
45153 TTAGAAGATGAATGTGTTC
65 TTAGAAGATGAATGTGTTC
45172 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
* *
45237 TAGAAGATGAATTTG-CC
66 TAGAAGATGAATGTGTTC
45254 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
45319 TTAGAAGATGAATGTGTTC
65 TTAGAAGATGAATGTGTTC
45338 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
45403 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
45421 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
45486 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
45504 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
45569 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
* *
45587 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCTGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
* * *
45652 TAAAAGATGAATTTG-CC
66 TAGAAGATGAATGTGTTC
*
45669 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGG
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
45716 TAAGAACTAC
Statistics
Matches: 773, Mismatches: 15, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
82 3 0.00
83 768 0.99
84 2 0.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
TAGAAGATGAATGTGTTC
Found at i:46605 original size:113 final size:112
Alignment explanation
Indices: 46418--46947 Score: 728
Period size: 113 Copynumber: 4.6 Consensus size: 112
46408 TGGATTGACA
* * *
46418 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGGAAGAAGAAATTCATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
46483 AGAATTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTAC-TGAATTCATCAATTGATGGATCAGCT
46531 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
46596 AGAGCTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTACT-GAATTCATCAATTGATGGATCAGCT
46644 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
46708 AGAACTTGTTCAACCTTTTACTGAATTCATCAATTGATGGATCAGCA
66 AGAACTTGTTCAACCTTTTACTGAATTCATCAATTGATGGATCAGCT
*
46755 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
46819 AGAACTTGTTCAA-CTTTTTCAT-AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
66 AGAACTTGTTCAACCTTTTAC-TGAATTC-AT--C------A-ATTGA-T-GGATCAG-CT
* * *
46878 TTTCTAGAGAAAGTTCATAATGAGAAGAACTCATC-AAAGAAGGATGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
46942 AGAACT
66 AGAACT
46948 CATCAAAAGC
Statistics
Matches: 376, Mismatches: 24, Indels: 24
0.89 0.06 0.06
Matches are distributed among these distances:
110 41 0.11
111 69 0.18
112 45 0.12
113 143 0.38
119 1 0.00
120 4 0.01
121 1 0.00
122 6 0.02
123 41 0.11
124 25 0.07
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (112 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTACTGAATTCATCAATTGATGGATCAGCT
Found at i:46806 original size:226 final size:223
Alignment explanation
Indices: 46390--46947 Score: 775
Period size: 223 Copynumber: 2.4 Consensus size: 223
46380 TTAGCAAAGA
* *
46390 TTCAAATCTATCATTTGATGGAT-TGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
1 TTCAAATCTATCATTTGATGGATCAGACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
* * *
46454 GAAGGAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTACATGAATTCATCAATT
66 GAA-GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATGAATTCATCAATT
*
46519 GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
130 GATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
46584 TTCATAATGAGAAGAGCTTGTTCAACCTTT
195 TTCATAATAAGAAGAACTTGTTCAA-CTTT
*
46614 TGCTCAAATCCATCATTTGATGGATCAG-CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCAT
1 T--TCAAATCTATCATTTGATGGATCAGACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCAT
46678 CTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-TGAATTCATCAAT
64 CTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATGAATTCATCAAT
46742 TGATGGATCAGCATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
129 TGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
46806 GTTCATAATAAGAAGAACTTGTTCAACTTT
194 GTTCATAATAAGAAGAACTTGTTCAACTTT
* * * * *
46836 TTCATAATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTTCTAGAGAAAGTTCATAATGA
1 TTCA-AA-TCTAT--C------A-TTTGA-T-GGATCAGACTTTTCCAGAGAAAGTTCATAATGA
* *
46901 GAAGAACTCATC-AAAGAAGGATGAAGAAGTTCATAATGAGAAGAACT
53 GAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACT
46948 CATCAAAAGC
Statistics
Matches: 300, Mismatches: 16, Indels: 26
0.88 0.05 0.08
Matches are distributed among these distances:
220 3 0.01
221 2 0.01
222 9 0.03
223 66 0.22
224 36 0.12
225 43 0.14
226 61 0.20
227 1 0.00
230 1 0.00
231 3 0.01
232 1 0.00
233 9 0.03
234 65 0.22
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (223 bp):
TTCAAATCTATCATTTGATGGATCAGACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
GAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATGAATTCATCAATTG
ATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATAAGAAGAACTTGTTCAACTTT
Found at i:46975 original size:42 final size:40
Alignment explanation
Indices: 46888--46995 Score: 191
Period size: 42 Copynumber: 2.7 Consensus size: 40
46878 TTTCTAGAGA
46888 AAGTTCATAATGAGAAGAACTCATC-AAAGAAGGATGAAG
1 AAGTTCATAATGAGAAGAACTCATCAAAAGAAGGATGAAG
46927 AAGTTCATAATGAGAAGAACTCATCAAAAGCGAAGGATGAAG
1 AAGTTCATAATGAGAAGAACTCATCAAAA--GAAGGATGAAG
46969 AAGTTCATAATGAGAAGAACTCATCAA
1 AAGTTCATAATGAGAAGAACTCATCAA
46996 GAGCTTATTC
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
39 25 0.38
40 3 0.05
42 38 0.58
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCAAAAGAAGGATGAAG
Found at i:47249 original size:3 final size:3
Alignment explanation
Indices: 47236--47313 Score: 86
Period size: 3 Copynumber: 25.7 Consensus size: 3
47226 ATTTTACCCA
* * *
47236 TAT TAAT TAT TAT TAT TAT TAT TAT AAT TAT AAT TAT CAT TAT TA-
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
47281 TAT TAT TAT AAA TAT TAT TAT TATT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TA
47314 ATACATTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 54 0.87
4 6 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:49157 original size:14 final size:14
Alignment explanation
Indices: 49125--49158 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
49115 TATTGTTTAA
49125 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
49139 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
49153 TTGATT
1 TTGATT
49159 ATAATATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:49324 original size:19 final size:19
Alignment explanation
Indices: 49300--49344 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
49290 AAATGTGAAA
49300 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
*
49319 TGCGATTTTCATTTCGTAT
1 TGCGATTTTCATTTCGCAT
49338 TGCGATT
1 TGCGATT
49345 CTCTCGTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCAT
Found at i:49374 original size:20 final size:20
Alignment explanation
Indices: 49349--49441 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
49339 GCGATTCTCT
49349 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
49369 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
49389 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
49409 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
49429 CGTTGCGATAGTC
1 CGTTGCGATAGTC
49442 GAATGAATGT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 64 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:50933 original size:25 final size:26
Alignment explanation
Indices: 50888--50950 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
50878 AGGAAAGCTT
*
50888 AAGTTATCTTAAGATTGAAAGATAAA-G
1 AAGTTAT-TAAAGATTGAAAGA-AAATG
50915 AAGTTATTAAAGATT-AAAGAAAATG
1 AAGTTATTAAAGATTGAAAGAAAATG
*
50940 -AGTTTTTAAAG
1 AAGTTATTAAAG
50951 GAAATTCTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 13 0.39
25 6 0.18
26 7 0.21
27 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (26 bp):
AAGTTATTAAAGATTGAAAGAAAATG
Found at i:51347 original size:64 final size:63
Alignment explanation
Indices: 51239--51475 Score: 194
Period size: 64 Copynumber: 3.6 Consensus size: 63
51229 TTCTGGACAA
* * *
51239 GATGCATCGATGCACATTCATAAGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCC
1 GATGCATCGATGCATA-GC-TAA-TGCATCGATGCA-TCCTTTTAAAAGAA-AACATCGAATGCA
51303 TTT
61 TTT
* *
51306 GATGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAATAATACTAACATCGAATGCAA
1 GATGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAA-GA-A--AACATCGAATGCAT
*
51371 TC
62 TT
* * * *
51373 AATGCATCGATGCATAAGGT-ATGCATCGATGCAT-CTCATTAATAAGGAAACATCGAATGCATT
1 GATGCATCGATGCAT-AGCTAATGCATCGATGCATCCT-TTTAA-AAGAAAACATCGAATGCATT
51436 T
63 T
* * * *
51437 TATGCACCGATGCACAAG-TAGTGCATCGATGCATACCTT
1 GATGCATCGATGCA-TAGCTAATGCATCGATGCAT-CCTT
51476 CATTGAAAGA
Statistics
Matches: 140, Mismatches: 19, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
63 4 0.03
64 60 0.43
65 4 0.03
66 7 0.05
67 60 0.43
68 5 0.04
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (63 bp):
GATGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAAGAAAACATCGAATGCATTT
Found at i:51976 original size:14 final size:16
Alignment explanation
Indices: 51959--51990 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
51949 ATTTACGTGA
51959 ATACATGT-ATAT-AT
1 ATACATGTGATATGAT
51973 ATACATGTGATATGAT
1 ATACATGTGATATGAT
51989 AT
1 AT
51991 GAGATATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (16 bp):
ATACATGTGATATGAT
Found at i:52183 original size:30 final size:30
Alignment explanation
Indices: 52147--52210 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
52137 AAGGAACATA
* *
52147 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
52177 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
52207 TGGA
1 TGGA
52211 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:55566 original size:64 final size:63
Alignment explanation
Indices: 55482--55694 Score: 173
Period size: 64 Copynumber: 3.3 Consensus size: 63
55472 CATTCATAAG
* * *
55482 TGCATCAATGCATTCC-TTTAA-AAGAAGAACATCGAATGCCTTTGATGCATCGATGCATAGCTA
1 TGCATCGATGCA-TCCTTTTAATAAGAA-AACATCGAATGCATTTAATGCATCGATGCATAG-TA
55545 A
63 A
* * * *
55546 TGCATCGATGCATCCTTTTAAAATAATAATAACATCGAATGCAATCAATGTATCGATGCATAAGG
1 TGCATCGATGCATCCTTTT--AATAAGAA-AACATCGAATGCATTTAATGCATCGATGCAT-A-G
55611 T-A
61 TAA
* * * * * * *
55613 TGCATCGATGCAT-CTCATTAATAAGGAAACATCGAATGTATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCT-TTTAATAAGAAAACATCGAATGCATTTAATGCATCGATGCA-TAGTAA
55677 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
55695 CATTGAAAGA
Statistics
Matches: 118, Mismatches: 20, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
63 5 0.04
64 52 0.44
65 6 0.05
66 6 0.05
67 46 0.39
68 2 0.02
69 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (63 bp):
TGCATCGATGCATCCTTTTAATAAGAAAACATCGAATGCATTTAATGCATCGATGCATAGTAA
Found at i:56402 original size:30 final size:30
Alignment explanation
Indices: 56368--56431 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
56358 AAGGAACATA
*
56368 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
56398 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
56428 TGGA
1 TGGA
56432 CAGGTCCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:58554 original size:24 final size:24
Alignment explanation
Indices: 58520--58573 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
58510 CTGAAAAATC
58520 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
58544 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
58568 ATCAAA
1 ATCAAA
58574 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:58587 original size:24 final size:24
Alignment explanation
Indices: 58520--58587 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
58510 CTGAAAAATC
* * *
58520 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
58544 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
58568 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
58588 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:59524 original size:39 final size:40
Alignment explanation
Indices: 59425--59525 Score: 136
Period size: 40 Copynumber: 2.5 Consensus size: 40
59415 TTGTGATAGT
* *
59425 CAGAATCTCGTTGCGATTTACAGATTCACATTGCGATTTA
1 CAGAATCGCATTGCGATTTACAGATTCACATTGCGATTTA
*
59465 CAGATTCGCATTGCGATTTAC-GTATTCACATTGCGA-TTA
1 CAGAATCGCATTGCGATTTACAG-ATTCACATTGCGATTTA
59504 C-GTAATCGCATTGCGATTTACA
1 CAG-AATCGCATTGCGATTTACA
59526 TAATCGCGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
38 1 0.02
39 22 0.41
40 31 0.57
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (40 bp):
CAGAATCGCATTGCGATTTACAGATTCACATTGCGATTTA
Found at i:59529 original size:20 final size:20
Alignment explanation
Indices: 59435--59539 Score: 122
Period size: 20 Copynumber: 5.3 Consensus size: 20
59425 CAGAATCTCG
* *
59435 TTGCGATTTACAGATTCACA
1 TTGCGATTTACATATTCGCA
*
59455 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACATATTCGCA
* *
59475 TTGCGATTTACGTATTCACA
1 TTGCGATTTACATATTCGCA
* *
59495 TTGCGA-TTACGTAATCGCA
1 TTGCGATTTACATATTCGCA
* *
59514 TTGCGATTTACATAATCGCG
1 TTGCGATTTACATATTCGCA
59534 TTGCGA
1 TTGCGA
59540 ATTAGGAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
19 17 0.22
20 59 0.78
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Found at i:59560 original size:21 final size:21
Alignment explanation
Indices: 59536--59581 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
59526 TAATCGCGTT
59536 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
59557 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
59578 GCGA
1 GCGA
59582 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:59676 original size:20 final size:20
Alignment explanation
Indices: 59651--59865 Score: 209
Period size: 20 Copynumber: 10.6 Consensus size: 20
59641 AATTATCGAT
59651 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
59671 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
59691 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
59712 CGCATTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* * *
59732 CTCATTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
59752 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
59772 CTCGTTGCGATTTACGGACA
1 CGCGTTGCGATTTACGGATA
*
59792 CGCGTTGCGATTTTTACGTAT-
1 CGCGTTGCGA--TTTACGGATA
* *
59813 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
59834 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
59855 CTCGTTGCGAT
1 CGCGTTGCGAT
59866 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 31, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
20 104 0.67
21 38 0.24
22 14 0.09
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:59740 original size:40 final size:41
Alignment explanation
Indices: 59653--59865 Score: 313
Period size: 40 Copynumber: 5.2 Consensus size: 41
59643 TTATCGATCG
*
59653 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
59694 CGTTGCGATTTACGGATACGCATTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
59734 CATTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
59774 CGTTGCGATTTACGGACACGCGTTGCGATTTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTTACGTATTCT
* * *
59816 CATTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
59857 CGTTGCGAT
1 CGTTGCGAT
59866 AGTCAGAATC
Statistics
Matches: 153, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
40 72 0.47
41 44 0.29
42 37 0.24
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:59897 original size:20 final size:20
Alignment explanation
Indices: 59874--59926 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
59864 ATAGTCAGAA
*
59874 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
59894 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
59914 TCGCGTTGCGATT
1 TCGCGTTGCGATT
59927 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:59987 original size:42 final size:42
Alignment explanation
Indices: 59894--59987 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
59884 ATTTATATGT
* *
59894 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
59935 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
59977 TCGCGTTGCGA
1 TCGCGTTGCGA
59988 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:60025 original size:20 final size:19
Alignment explanation
Indices: 59976--60029 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
59966 ATTCTTCATA
59976 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
59995 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
60016 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
60030 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:62557 original size:9 final size:9
Alignment explanation
Indices: 62540--62570 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
62530 ATTTGATCAT
62540 TTTGG-AAG
1 TTTGGAAAG
62548 TTTGGAAAG
1 TTTGGAAAG
62557 TTTGGAAAG
1 TTTGGAAAG
62566 TTTGG
1 TTTGG
62571 TGATTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (9 bp):
TTTGGAAAG
Found at i:63443 original size:61 final size:61
Alignment explanation
Indices: 63318--63435 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
63308 AAGGACACTA
* * *
63318 AGTGTAGGTGGTGGACATGACCTTATGTGTCATATATGGATTAACACTAGAGTGTAAACCT
1 AGTGTAGGTGGTGGACACGACCATATGTGTCATATACGGATTAACACTAGAGTGTAAACCT
** * *
63379 AGTGTAGGTGGTGGGTACGACCATATGTGTCATATCCGGATTAGCACTAGAGTGTAA
1 AGTGTAGGTGGTGGACACGACCATATGTGTCATATACGGATTAACACTAGAGTGTAA
63436 GCTTAGTGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (61 bp):
AGTGTAGGTGGTGGACACGACCATATGTGTCATATACGGATTAACACTAGAGTGTAAACCT
Found at i:65512 original size:25 final size:25
Alignment explanation
Indices: 65480--65530 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
65470 ATTATTCTCC
65480 TTTTATTTTATTCATTTCCTTAATT
1 TTTTATTTTATTCATTTCCTTAATT
65505 TTTTATTTTATTCATTTCCTTAATT
1 TTTTATTTTATTCATTTCCTTAATT
65530 T
1 T
65531 ATTACATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATTTTATTCATTTCCTTAATT
Found at i:67285 original size:21 final size:20
Alignment explanation
Indices: 67243--67285 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
67233 CATTGAAAAA
* * *
67243 AAACAATGGCAAAAACCCGT
1 AAACAATGACAAAAAACAGT
67263 AAACAATGACAAAAAAACAGT
1 AAACAATGAC-AAAAAACAGT
67284 AA
1 AA
67286 GCTACTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.60, C:0.19, G:0.12, T:0.09
Consensus pattern (20 bp):
AAACAATGACAAAAAACAGT
Found at i:67331 original size:23 final size:23
Alignment explanation
Indices: 67298--67363 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
67288 TACTATAAGG
*
67298 TAGAGAAAAACATGCCACAAAGA
1 TAGAGATAAACATGCCACAAAGA
* * *
67321 TAGAGATAAACGTGTCA-TAA-A
1 TAGAGATAAACATGCCACAAAGA
67342 T-GTAGAT-AACATGCCACAAAGA
1 TAG-AGATAAACATGCCACAAAGA
67364 CATAATTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
20 8 0.24
21 8 0.24
22 3 0.09
23 14 0.42
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (23 bp):
TAGAGATAAACATGCCACAAAGA
Found at i:67995 original size:33 final size:32
Alignment explanation
Indices: 67958--68028 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
67948 AAAGATTGAT
* * *
67958 AAATTTAATGTTATTTTTTTAATAATTTTAATA
1 AAATTTAATGATAATTTTATAATAA-TTTAATA
*
67991 AAATTTAATGATAATTTTATAATAATTTGATA
1 AAATTTAATGATAATTTTATAATAATTTAATA
68023 AAATTT
1 AAATTT
68029 CGTTATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.35
33 22 0.65
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (32 bp):
AAATTTAATGATAATTTTATAATAATTTAATA
Found at i:74284 original size:54 final size:52
Alignment explanation
Indices: 74196--74308 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 52
74186 TAGTTTTTTT
* *
74196 TATTTATTGTATAAAATAGAAAATTATTATAAAAATAGAGAGATGACATTATAA
1 TATTTATTCTATAAAATAGAAAATAATTATAAAAATAGAGAG--GACATTATAA
* *
74250 TATTTATTCTGTAAAATAGAAAATAATT-TAAAAAATATAGAGGACATTATAA
1 TATTTATTCTATAAAATAGAAAATAATTAT-AAAAATAGAGAGGACATTATAA
*
74302 TAATTAT
1 TATTTAT
74309 CCCTAAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
52 16 0.30
53 1 0.02
54 36 0.68
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (52 bp):
TATTTATTCTATAAAATAGAAAATAATTATAAAAATAGAGAGGACATTATAA
Found at i:75709 original size:75 final size:75
Alignment explanation
Indices: 75620--75777 Score: 289
Period size: 75 Copynumber: 2.1 Consensus size: 75
75610 GCCCTCCATA
75620 AAAATGCTTCTACTCTGAAAGGGCCAATTCCCAACCAAACATCTCCCCTCCAATTAAAACCAATC
1 AAAATGCTTCTACTCTGAAAGGGCCAATTCCCAACCAAACATCTCCCCTCCAATTAAAACCAATC
75685 TGCTCCCTGT
66 TGCTCCCTGT
* *
75695 AAAATGCTTCTACTCTGAAAGGGCCAATTCCCAACCAACCATTTCCCCTCCAATTAAAACCAATC
1 AAAATGCTTCTACTCTGAAAGGGCCAATTCCCAACCAAACATCTCCCCTCCAATTAAAACCAATC
75760 TGCTCCCTGT
66 TGCTCCCTGT
*
75770 CAAATGCT
1 AAAATGCT
75778 AAATTCGACG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.32, C:0.34, G:0.09, T:0.25
Consensus pattern (75 bp):
AAAATGCTTCTACTCTGAAAGGGCCAATTCCCAACCAAACATCTCCCCTCCAATTAAAACCAATC
TGCTCCCTGT
Found at i:85640 original size:2 final size:2
Alignment explanation
Indices: 85633--85695 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
85623 AAATTCATGA
85633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85675 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
85696 GAGAGAGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85700 original size:2 final size:2
Alignment explanation
Indices: 85695--85738 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
85685 ATATATATAT
85695 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
85737 AG
1 AG
85739 TACAATATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:86044 original size:2 final size:2
Alignment explanation
Indices: 86037--86069 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
86027 ATTGGAGTAT
86037 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
86070 GAAAAGATAC
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:86395 original size:20 final size:20
Alignment explanation
Indices: 86365--86414 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
86355 AAACATTTTT
*
86365 TATAT-ATTATA-TATTATAA
1 TATATAATTATATTAATA-AA
86384 TATATAATTATATTAATAAA
1 TATATAATTATATTAATAAA
*
86404 AATATAATTAT
1 TATATAATTAT
86415 TAATTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 18 0.67
21 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATAATTATATTAATAAA
Done.