Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005053.1 Hibiscus syriacus cultivar Beakdansim tig00011345_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: 97356
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1535 original size:64 final size:64
Alignment explanation
Indices: 1404--1689 Score: 404
Period size: 64 Copynumber: 4.5 Consensus size: 64
1394 TGCAGCTTTT
** * *
1404 AGAGTCAATTTCAACTTCACAGCAAAGG--A-T--ACTCTACAAACAACTTTCCTGTTTCATTC
1 AGAGTCAATTTCAACTTCACAATAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
1463 AGAGTCAATTTCAAATTCACAATGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATC
1 AGAGTCAATTTCAACTTCACAATAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
1527 AGAATCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAATAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
1591 AGAGTCAATTTCAGCTTCACAACAAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAATAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1655 AGAGTCAATTTCAACTTCAC-ATCAAAGGATATTGG
1 AGAGTCAATTTCAACTTCACAAT-AAAGGATATTGG
1690 CTCGAAGCGA
Statistics
Matches: 202, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
59 24 0.12
61 1 0.00
62 1 0.00
63 1 0.00
64 175 0.87
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAATAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:1959 original size:109 final size:109
Alignment explanation
Indices: 1768--1990 Score: 358
Period size: 109 Copynumber: 2.0 Consensus size: 109
1758 AATTTGGTGA
1768 AACAACCCTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAATGAA
1 AACAACCCTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAATGAA
* *
1833 TGAGCCATCTACGATTTCAACTTCACAATGAAGGATATCGTGCC
66 TGAGCCATCCACGATTTCAACTTCACAACGAAGGATATCGTGCC
* ** *
1877 AACAATCCTTGGATTTCAACTTCATGACGAAGGATATCCAATTCCAAGCTCAACTTCACAACT-A
1 AACAACCCTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAA-TGA
*
1941 ATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
65 ATGAGCCATCCACGATTTCAACTTCACAACGAAGGATATCGTGCC
*
1986 CACAA
1 AACAA
1991 ACAACATCCA
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
109 104 0.99
110 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (109 bp):
AACAACCCTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAATGAA
TGAGCCATCCACGATTTCAACTTCACAACGAAGGATATCGTGCC
Found at i:3253 original size:36 final size:36
Alignment explanation
Indices: 3185--3253 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
3175 TGTTTTTATT
* **
3185 TTAATATTACATTTTTATATATTATTTTCTTTAGTA
1 TTAATATTACATTTATATATATTATTCCCTTTAGTA
* * *
3221 TTAATATTATATTTATATATTTTCTTCCCTTTA
1 TTAATATTACATTTATATATATTATTCCCTTTA
3254 TTTATTTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.01, T:0.61
Consensus pattern (36 bp):
TTAATATTACATTTATATATATTATTCCCTTTAGTA
Found at i:3316 original size:5 final size:5
Alignment explanation
Indices: 3306--3499 Score: 61
Period size: 5 Copynumber: 39.2 Consensus size: 5
3296 TATATTTTTA
* * *
3306 TTATT TTATT TTCTT TATATT TT-TT TTTTGCT TTA-T TTATTT ATTATA
1 TTATT TTATT TTATT T-TATT TTATT TTAT--T TTATT TTA-TT -TTATT
** * *
3354 TTATT TTATT ATT-TT TTATT TTA-T TTGCT TTATT TTTTCT TTTTCT
1 TTATT TTATT -TTATT TTATT TTATT TTATT TTATT TTAT-T TTAT-T
* * * * * * *
3400 TTATT TTTTT TTTTT TTATT TT-TT AT-TT TTACT TT-CT TTATT GT-GT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
* * *
3446 TTATT TT-TT ATTTTT TTATT TT-TG TT-CT TTATT TTCATT TTA-T TTATT
1 TTATT TTATT -TTATT TTATT TTATT TTATT TTATT TT-ATT TTATT TTATT
3494 TTATT T
1 TTATT T
3500 ACTTTTTTCT
Statistics
Matches: 145, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
4 36 0.25
5 78 0.54
6 25 0.17
7 6 0.04
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:3359 original size:32 final size:30
Alignment explanation
Indices: 3310--3462 Score: 96
Period size: 33 Copynumber: 4.8 Consensus size: 30
3300 TTTTTATTAT
*
3310 TTTATTTTCTTTA-TATTTTTTTTTTGCTTTA
1 TTTA-TTTATTTATTATTTTTTTTTT-CTTTA
*
3341 TTTATTTATTATATTATTTTATTATTT-TTTA
1 TTTATTTATT-TATTATTTT-TTTTTTCTTTA
* *
3372 TTTTATTTGCTTTATT-TTTTCTTTTTCTTTA
1 -TTTATTT-ATTTATTATTTTTTTTTTCTTTA
* * * *
3403 TTTTTTTTTTTTTTATTTTTTATTTTTACTTTC
1 TTTATTTATTTATTA-TTTTT-TTTTT-CTTTA
* *
3436 TTTATTGTGTTTATTTTTTATTTTTTT
1 TTTATT-TATTTATTATTT-TTTTTTT
3463 ATTTTTGTTC
Statistics
Matches: 96, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
29 5 0.05
30 15 0.16
31 22 0.23
32 22 0.23
33 24 0.25
34 8 0.08
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.79
Consensus pattern (30 bp):
TTTATTTATTTATTATTTTTTTTTTCTTTA
Found at i:3371 original size:27 final size:26
Alignment explanation
Indices: 3292--3426 Score: 74
Period size: 29 Copynumber: 5.2 Consensus size: 26
3282 TATATATATA
3292 TATATATATTTTTATTATTTTATT-TTCTT
1 TATAT-TA-TTTTATTATTTT-TTATT-TT
* * *
3321 TATATTTTTTTTTTGCTTTATTTATTTAT
1 TATATTATTTTATT-ATTT-TTTATTT-T
3350 TATATTATTTTATTATTTTTTA-TTT
1 TATATTATTTTATTATTTTTTATTTT
**
3375 TAT-TTGCTTTATT-TTTTCTT-TTTCT
1 TATATTATTTTATTATTTT-TTATTT-T
3400 T-TATT-TTTT-TT-TTTTTTATTTT
1 TATATTATTTTATTATTTTTTATTTT
3422 T-TATT
1 TATATT
3427 TTTACTTTCT
Statistics
Matches: 88, Mismatches: 9, Indels: 25
0.72 0.07 0.20
Matches are distributed among these distances:
22 8 0.09
23 13 0.15
24 16 0.18
25 8 0.09
26 2 0.02
27 10 0.11
28 10 0.11
29 21 0.24
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (26 bp):
TATATTATTTTATTATTTTTTATTTT
Found at i:3385 original size:63 final size:60
Alignment explanation
Indices: 3301--3468 Score: 173
Period size: 63 Copynumber: 2.7 Consensus size: 60
3291 ATATATATAT
*
3301 TTTTATTATTTTATTTTCTTTATATTTTT-TTTTTGCTTTATTTATTTATTATATTATTTTATTA
1 TTTT-TTATTTTATTTGCTTTAT-TTTTTCTTTTT-CTTTATTT-TTTATTATATTATTTT-TTA
* * *
3365 TTTTTTATTTTATTTGCTTTATTTTTTCTTTTTCTTTATTTTTTTTTTTTTTATTTTTTA
1 TTTTTTATTTTATTTGCTTTATTTTTTCTTTTTCTTTATTTTTTATTATATTATTTTTTA
* *
3425 TTTTTACTTTCTTTATTGTG-TTTATTTTTT-ATTTT-TTTATTTTT
1 TTTTT--TAT-TTTATT-TGCTTTATTTTTTCTTTTTCTTTATTTTT
3469 GTTCTTTATT
Statistics
Matches: 93, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
60 8 0.09
61 22 0.24
62 19 0.20
63 38 0.41
64 6 0.06
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.79
Consensus pattern (60 bp):
TTTTTTATTTTATTTGCTTTATTTTTTCTTTTTCTTTATTTTTTATTATATTATTTTTTA
Found at i:3403 original size:26 final size:22
Alignment explanation
Indices: 3399--3468 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
3389 TTTCTTTTTC
3399 TTTATTTTTTTTTTTTTTATTT
1 TTTATTTTTTTTTTTTTTATTT
** *
3421 TTTATTTTTACTTTCTTTATTGT
1 TTTATTTTTTTTTTTTTTATT-T
*
3444 GTTTATTTTTTATTTTTTTATTT
1 -TTTATTTTTTTTTTTTTTATTT
3467 TT
1 TT
3469 GTTCTTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 20 0.50
23 2 0.05
24 18 0.45
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (22 bp):
TTTATTTTTTTTTTTTTTATTT
Found at i:3453 original size:39 final size:37
Alignment explanation
Indices: 3300--3468 Score: 116
Period size: 39 Copynumber: 4.3 Consensus size: 37
3290 TATATATATA
**
3300 TTTTTATTATTTTA-TTTTCTTTATATTTTT-TTTTTGCT
1 TTTTTA-T-TTTTACTTTTCTTTAT-TTTTTATTTTTTAT
3338 TTATTTATTTATTA-TATTAT-TTTATTATTTT-TTATTTTAT
1 TT-TTTATTT-TTACT-TT-TCTTTATT-TTTTATT-TTTTAT
* *
3378 TTGCTTTATTTTTTCTTTTTCTTTATTTTTTTTTTTTTTAT
1 TT--TTTATTTTTAC-TTTTCTTTA-TTTTTTATTTTTTAT
3419 TTTTTATTTTTAC-TTTCTTTATTGTGTTTATTTTTTATT
1 TTTTTATTTTTACTTTTCTTTATT-T-TTTATTTTTTA-T
3458 TTTTTATTTTT
1 TTTTTATTTTT
3469 GTTCTTTATT
Statistics
Matches: 110, Mismatches: 6, Indels: 29
0.76 0.04 0.20
Matches are distributed among these distances:
36 2 0.02
37 11 0.10
38 18 0.16
39 39 0.35
40 10 0.09
41 25 0.23
42 5 0.05
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.79
Consensus pattern (37 bp):
TTTTTATTTTTACTTTTCTTTATTTTTTATTTTTTAT
Found at i:3468 original size:9 final size:9
Alignment explanation
Indices: 3300--3621 Score: 104
Period size: 9 Copynumber: 34.0 Consensus size: 9
3290 TATATATATA
3300 TTTTTA-TT
1 TTTTTATTT
*
3308 ATTTTATTT
1 TTTTTATTT
*
3317 TCTTTATATT
1 TTTTTAT-TT
3327 TTTTT-TTT
1 TTTTTATTT
**
3335 GCTTTATTT
1 TTTTTATTT
3344 ATTTATTATATT
1 -TTT-TTAT-TT
*
3356 ATTTTATTAT
1 TTTTTATT-T
3366 TTTTTATTT
1 TTTTTATTT
3375 TATTTGCT-TTAT
1 T-TTT--TATT-T
*
3387 TTTTTCTTT
1 TTTTTATTT
3396 TTCTTTATTT
1 TT-TTTATTT
3406 TTTTT-TTT
1 TTTTTATTT
*
3414 TTTATTTTTT
1 TTT-TTATTT
*
3424 ATTTTTACTT
1 -TTTTTATTT
* *
3434 TCTTTATTG
1 TTTTTATTT
*
3443 TGTTTA--T
1 TTTTTATTT
3450 TTTTTA-TT
1 TTTTTATTT
3458 TTTTTATTT
1 TTTTTATTT
* *
3467 TTGTTCTTT
1 TTTTTATTT
*
3476 ATTTTCATTT
1 -TTTTTATTT
*
3486 TATTTATTT
1 TTTTTATTT
* *
3495 TATTTA-CT
1 TTTTTATTT
*
3503 TTTTTCTTT
1 TTTTTATTT
** * *
3512 ACTTTGTCT
1 TTTTTATTT
3521 TTTTTATTT
1 TTTTTATTT
3530 CTTCTTTATCTT
1 -TT-TTTAT-TT
*
3542 TCTTTACTTCCT
1 TTTTTA-TT--T
3554 TTATTT-TCTCT
1 TT-TTTAT-T-T
3565 TTTTTATTT
1 TTTTTATTT
** *
3574 CATTTGTTT
1 TTTTTATTT
3583 TTTTTCATTT
1 TTTTT-ATTT
*
3593 TATTTATTT
1 TTTTTATTT
*
3602 TTATTACCTTT
1 TTTTTA--TTT
3613 TTTTTATTT
1 TTTTTATTT
3622 AACAAGTATC
Statistics
Matches: 232, Mismatches: 50, Indels: 63
0.67 0.14 0.18
Matches are distributed among these distances:
7 5 0.02
8 28 0.12
9 88 0.38
10 63 0.27
11 35 0.15
12 10 0.04
13 3 0.01
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTTATTT
Found at i:3516 original size:5 final size:4
Alignment explanation
Indices: 3337--3500 Score: 65
Period size: 4 Copynumber: 40.0 Consensus size: 4
3327 TTTTTTTTGC
*
3337 TTTA TTTA TTTA -TTA TATTA TTT- TATTA TTT- TTTA TTTTA TTTGC
1 TTTA TTTA TTTA TTTA T-TTA TTTA T-TTA TTTA TTTA -TTTA TTT-A
* * * * *
3382 TTTA TTTT TTCTT TTTC TTTA TTT- TTTT TTTT TTTA TTT- TTTA -TT-
1 TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
3427 TTTA CTTTC TTTA TTGTG TTTA TTT- TTTA TTTT TTTA TTTT TGTTC TTTA
1 TTTA -TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
3477 TTTTCA TTTTA TTTA TTTTA TTTA
1 -TTT-A -TTTA TTTA -TTTA TTTA
3501 CTTTTTTCTT
Statistics
Matches: 126, Mismatches: 15, Indels: 38
0.70 0.08 0.21
Matches are distributed among these distances:
3 20 0.16
4 68 0.54
5 33 0.26
6 5 0.04
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3586 original size:19 final size:19
Alignment explanation
Indices: 3564--3603 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3554 TTATTTTCTC
*
3564 TTTTTT-ATTTCATTTGTT
1 TTTTTTCATTTCATTTATT
*
3582 TTTTTTCATTTTATTTATT
1 TTTTTTCATTTCATTTATT
3601 TTT
1 TTT
3604 ATTACCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTTTTCATTTCATTTATT
Found at i:11510 original size:62 final size:62
Alignment explanation
Indices: 11434--11554 Score: 233
Period size: 62 Copynumber: 2.0 Consensus size: 62
11424 GAAAACAGGG
*
11434 AATTATGGCTTAAAAGTATTATTAGGGGTGGTGAAGGTTTTGTATTCTAAAAAATAGATACA
1 AATTATGGCTTAAAAGTATTATTAGGGGTGGTGAAAGTTTTGTATTCTAAAAAATAGATACA
11496 AATTATGGCTTAAAAGTATTATTAGGGGTGGTGAAAGTTTTGTATTCTAAAAAATAGAT
1 AATTATGGCTTAAAAGTATTATTAGGGGTGGTGAAAGTTTTGTATTCTAAAAAATAGAT
11555 GCATTGCAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (62 bp):
AATTATGGCTTAAAAGTATTATTAGGGGTGGTGAAAGTTTTGTATTCTAAAAAATAGATACA
Found at i:19391 original size:24 final size:24
Alignment explanation
Indices: 19359--19404 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
19349 TTTTCTGATG
*
19359 ATGTATAAAACATTTATGTACATT
1 ATGTATAAAACATCTATGTACATT
19383 ATGTATAAAACATCTATGTACA
1 ATGTATAAAACATCTATGTACA
19405 ATGTCATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (24 bp):
ATGTATAAAACATCTATGTACATT
Found at i:19755 original size:31 final size:31
Alignment explanation
Indices: 19715--19779 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
19705 TACAATATAA
*
19715 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGAAATATGG
* * *
19746 TCCCTCAACATTTAGTTCGTTTGAAATGTGG
1 TCCCCCAACATTTAGTCCGTTTGAAATATGG
19777 TCC
1 TCC
19780 TTGATGTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTGAAATATGG
Found at i:21819 original size:31 final size:32
Alignment explanation
Indices: 21784--21857 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
21774 TAAAATTTAT
*
21784 AATATAATCCCCT-AACATTTAGTTCGTTTGC
1 AATATAATCCCCTCAACATTTAGTCCGTTTGC
*
21815 AATATAGT-CCCTCAACATTTAGTCCGTTTGC
1 AATATAATCCCCTCAACATTTAGTCCGTTTGC
* *
21846 AACATGATCCCC
1 AATATAATCCCC
21858 GACGTAACTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 4 0.11
31 29 0.81
32 3 0.08
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (32 bp):
AATATAATCCCCTCAACATTTAGTCCGTTTGC
Found at i:22802 original size:15 final size:17
Alignment explanation
Indices: 22765--22810 Score: 69
Period size: 15 Copynumber: 2.8 Consensus size: 17
22755 TGTTTCTGAG
22765 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
22783 GGAATTGGAAT-TGT-A
1 GGAATTGGAATCTGTAA
22798 GGAATTGGAATCT
1 GGAATTGGAATCT
22811 AAATCTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
17 3 0.11
18 11 0.41
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:23427 original size:33 final size:32
Alignment explanation
Indices: 23379--23465 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 32
23369 TTTTCACCCT
23379 AAACCCGAACCCGACCCGAATATCACAA-TTAAAA
1 AAACCCG-ACCCGACCCGAATATCA-AACTT-AAA
*
23413 AAACCCGACCCGACCCAAATATCAAACTTAAA
1 AAACCCGACCCGACCCGAATATCAAACTTAAA
23445 AAACCCTGACCCGATCCCGAA
1 AAACCC-GACCCGA-CCCGAA
23466 ATTTTTTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
32 11 0.23
33 25 0.52
34 12 0.25
ACGTcount: A:0.44, C:0.36, G:0.09, T:0.11
Consensus pattern (32 bp):
AAACCCGACCCGACCCGAATATCAAACTTAAA
Found at i:23503 original size:110 final size:110
Alignment explanation
Indices: 23381--23582 Score: 316
Period size: 110 Copynumber: 1.8 Consensus size: 110
23371 TTCACCCTAA
23381 ACCCGAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACCCAAATATCAAAC-TTAAA
1 ACCCGAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACCCAAATATCAAACTTTAAA
*
23445 AAACCCTGACCCGATCCCGAAATTTTTTGAAAAACAACTTGACTCG
66 AAACCC-GACCCGAACCCGAAATTTTTTGAAAAACAACTTGACTCG
* * * * * *
23491 ACCCGAGCCCGACCCGAATTTCACACTTACAAAAACCCGACTCGACCCGAATATCAAACTTTAAA
1 ACCCGAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACCCAAATATCAAACTTTAAA
*
23556 AAACCCGACCCGAACCCGAATTTTTTT
66 AAACCCGACCCGAACCCGAAATTTTTT
23583 ATAAAAAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
110 72 0.87
111 11 0.13
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.18
Consensus pattern (110 bp):
ACCCGAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACCCAAATATCAAACTTTAAA
AAACCCGACCCGAACCCGAAATTTTTTGAAAAACAACTTGACTCG
Found at i:23538 original size:33 final size:33
Alignment explanation
Indices: 23491--23578 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 33
23481 ACTTGACTCG
*
23491 ACCCGAGCCCGACCCGAATTTCACAC-TTACAAAA
1 ACCCGA-CCCGACCCGAATTTCAAACTTTA-AAAA
* *
23525 ACCCGACTCGACCCGAATATCAAACTTTAAAAA
1 ACCCGACCCGACCCGAATTTCAAACTTTAAAAA
23558 ACCCGACCCGAACCCGAATTT
1 ACCCGACCCG-ACCCGAATTT
23579 TTTTATAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 29 0.62
34 18 0.38
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.16
Consensus pattern (33 bp):
ACCCGACCCGACCCGAATTTCAAACTTTAAAAA
Found at i:23590 original size:33 final size:30
Alignment explanation
Indices: 23553--23620 Score: 73
Period size: 33 Copynumber: 2.2 Consensus size: 30
23543 ATCAAACTTT
*
23553 AAAAAACCCGACCCGAACCCGAATTTTTTTATA
1 AAAAAACCCGA-CCGAACCCGAA-ATTTTTA-A
* * *
23586 AAAAAATCCGATCGATCCCGAAATTTTTAA
1 AAAAAACCCGACCGAACCCGAAATTTTTAA
23616 AAAAA
1 AAAAA
23621 TTCGACCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 6 0.19
31 6 0.19
32 9 0.29
33 10 0.32
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (30 bp):
AAAAAACCCGACCGAACCCGAAATTTTTAA
Found at i:23606 original size:110 final size:110
Alignment explanation
Indices: 23381--23607 Score: 300
Period size: 110 Copynumber: 2.1 Consensus size: 110
23371 TTCACCCTAA
23381 ACCCGAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACCCAAATATCAAACTTAAAA
1 ACCCGAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACCCAAATATCAAACTTAAAA
* * *
23446 AACCCTGACCCGATCCCGAAATTTTTTGAAAAACAACTTGACTCG
66 AACCCTGACCCGAACCCGAAATTTTTTGAAAAAAAACTCGACTCG
* * * * * *
23491 ACCCGAGCCCGACCCGAATTTCACACTTACAAAAACCCGACTCGACCCGAATATCAAACTTTAAA
1 ACCCGAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACCCAAATATCAAAC-TTAAA
*
23556 AAACCC-GACCCGAACCCG-AATTTTTTTATAAAAAAA-TCCGA-TCG
65 AAACCCTGACCCGAACCCGAAATTTTTTGA-AAAAAAACT-CGACTCG
23600 ATCCCGAA
1 A-CCCGAA
23608 ATTTTTAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
109 14 0.14
110 77 0.75
111 11 0.11
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.18
Consensus pattern (110 bp):
ACCCGAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGACCCAAATATCAAACTTAAAA
AACCCTGACCCGAACCCGAAATTTTTTGAAAAAAAACTCGACTCG
Found at i:23880 original size:26 final size:26
Alignment explanation
Indices: 23851--23907 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
23841 ACGCCACCTT
23851 AGATTTGGGATCTTTGAATTCAAGCA
1 AGATTTGGGATCTTTGAATTCAAGCA
23877 AGATTTGGGATCTTTGAATTCAAGCA
1 AGATTTGGGATCTTTGAATTCAAGCA
23903 AGATT
1 AGATT
23908 AGCTAGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.35
Consensus pattern (26 bp):
AGATTTGGGATCTTTGAATTCAAGCA
Found at i:24778 original size:38 final size:38
Alignment explanation
Indices: 24695--24856 Score: 199
Period size: 38 Copynumber: 4.3 Consensus size: 38
24685 TCAAAGATTG
* *
24695 TATATACTATATACGTTTTCAAAAATG--TTTT-CAAAAC
1 TATATA-T-TATACGTTTTCAAAACTGTTTTTTAAAAAAC
*
24732 CATATATTATACGTTTTCAAAACTGTTTTTTAAAAAAC
1 TATATATTATACGTTTTCAAAACTGTTTTTTAAAAAAC
* * *
24770 TATATATTATACGTTTTCGAAACCGTTTTTAAAAAAAC
1 TATATATTATACGTTTTCAAAACTGTTTTTTAAAAAAC
24808 TATATATTATACGTTTTCAAAACAT-TTTTTTAAAAAA-
1 TATATATTATACGTTTTCAAAAC-TGTTTTTTAAAAAAC
24845 TACTATATTATA
1 TA-TATATTATA
24857 TATGTTTTCA
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
35 17 0.15
36 1 0.01
37 11 0.10
38 81 0.74
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.43
Consensus pattern (38 bp):
TATATATTATACGTTTTCAAAACTGTTTTTTAAAAAAC
Found at i:25641 original size:15 final size:15
Alignment explanation
Indices: 25621--25676 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
25611 ACCATGTAGA
25621 GGGAATCTGTACCCG
1 GGGAATCTGTACCCG
25636 GGGAATC-GATACCCCTGGG
1 GGGAATCTG-TA-CCC---G
*
25655 GGGAATCTGTTCCCG
1 GGGAATCTGTACCCG
25670 GGGAATC
1 GGGAATC
25677 GATACCCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
14 1 0.03
15 17 0.50
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.36, T:0.20
Consensus pattern (15 bp):
GGGAATCTGTACCCG
Found at i:25693 original size:35 final size:34
Alignment explanation
Indices: 25621--25703 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
25611 ACCATGTAGA
*
25621 GGGAATCTGTACCCGGGGAATCGATACCCCTGGG
1 GGGAATCTGTTCCCGGGGAATCGATACCCCTGGG
25655 GGGAATCTGTTCCCGGGGAATCGATACCCCCTGGG
1 GGGAATCTGTTCCCGGGGAATCGATA-CCCCTGGG
25690 GGGAATCTGTTCCC
1 GGGAATCTGTTCCC
25704 CCTAGGGGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 25 0.53
35 22 0.47
ACGTcount: A:0.18, C:0.28, G:0.34, T:0.20
Consensus pattern (34 bp):
GGGAATCTGTTCCCGGGGAATCGATACCCCTGGG
Found at i:25711 original size:21 final size:20
Alignment explanation
Indices: 25635--25729 Score: 89
Period size: 21 Copynumber: 5.0 Consensus size: 20
25625 ATCTGTACCC
25635 GGGGAATC-GATA-CCCCTGG
1 GGGGAATCTG-TACCCCCTGG
*
25654 GGGGAATCTGT--TCCC---
1 GGGGAATCTGTACCCCCTGG
25669 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
*
25689 GGGGAATCTGTTCCCCCTAGG
1 GGGGAATCTGTACCCCCT-GG
25710 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
25730 ACAATCTGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
14 1 0.02
15 9 0.14
17 3 0.05
18 3 0.05
19 9 0.14
20 18 0.29
21 20 0.32
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:28759 original size:34 final size:32
Alignment explanation
Indices: 28706--28775 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
28696 CCTTACAAAC
* *
28706 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
28738 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
28772 TCCC
1 TCCC
28776 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:29086 original size:21 final size:21
Alignment explanation
Indices: 29060--29101 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29050 CCAGAATGGG
*
29060 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
29081 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
29102 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:29292 original size:35 final size:34
Alignment explanation
Indices: 29217--29298 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
29207 CATGCAGGGA
*
29217 GGAATCTGTACCCGGGGAATCGATACCCCTGGGG
1 GGAATCTGTTCCCGGGGAATCGATACCCCTGGGG
*
29251 GAAATCTGTTCCCGGGGAATCGATACCCCCTGGGG
1 GGAATCTGTTCCCGGGGAATCGATA-CCCCTGGGG
29286 GGAATCTGTTCCC
1 GGAATCTGTTCCC
29299 CCCCAGGGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 23 0.52
35 21 0.48
ACGTcount: A:0.20, C:0.28, G:0.32, T:0.21
Consensus pattern (34 bp):
GGAATCTGTTCCCGGGGAATCGATACCCCTGGGG
Found at i:31066 original size:50 final size:51
Alignment explanation
Indices: 30988--31092 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 51
30978 TCATAGCAAC
* * *
30988 AGTAGTAGAATACTTGGAATCACTAATGCATCATGTATTATAGATAACAAT
1 AGTAATAGAATACTTGGAATCACTAATGCATCATGTAATATAAATAACAAT
* *
31039 AGTAATAGATTACTTGGAA-CACTAATGCATCATGTAATATAAATAGCAAT
1 AGTAATAGAATACTTGGAATCACTAATGCATCATGTAATATAAATAACAAT
31089 AGTA
1 AGTA
31093 CTTGGAATCG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 32 0.65
51 17 0.35
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (51 bp):
AGTAATAGAATACTTGGAATCACTAATGCATCATGTAATATAAATAACAAT
Found at i:32946 original size:2 final size:2
Alignment explanation
Indices: 32939--32969 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32929 ATATCATAAA
32939 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
32970 GAATCAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:34614 original size:20 final size:20
Alignment explanation
Indices: 34577--34614 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34567 GGTCGTTTCT
*
34577 AGCCATTGGAGATGATTTGG
1 AGCCATTGGAGATAATTTGG
*
34597 AGCCATTGGGGATAATTT
1 AGCCATTGGAGATAATTT
34615 TTCTGTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (20 bp):
AGCCATTGGAGATAATTTGG
Found at i:35011 original size:20 final size:20
Alignment explanation
Indices: 34986--35024 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34976 GCTCAAATTC
34986 TATTTTAATAG-ACTTTGAAT
1 TATTTT-ATAGAACTTTGAAT
*
35006 TATTTTTTAGAACTTTGAA
1 TATTTTATAGAACTTTGAA
35025 CAAATTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (20 bp):
TATTTTATAGAACTTTGAAT
Found at i:36042 original size:26 final size:26
Alignment explanation
Indices: 35973--36035 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
35963 AAGATTGTAA
35973 AATATTTTATTGTGTTATAATAAATT
1 AATATTTTATTGTGTTATAATAAATT
35999 AATATTTTATTGTGTTATAATAAATT
1 AATATTTTATTGTGTTATAATAAATT
*
36025 AATAATTTATT
1 AATATTTTATT
36036 ATTTTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (26 bp):
AATATTTTATTGTGTTATAATAAATT
Found at i:36058 original size:15 final size:16
Alignment explanation
Indices: 36028--36070 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
36018 ATAAATTAAT
*
36028 AATTTATTATTTTATTA
1 AATTT-TTATTATATTA
36045 AA-TTTTATTATATTA
1 AATTTTTATTATATTA
36060 AATTTTTATTA
1 AATTTTTATTA
36071 ATTTTTGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 12 0.50
16 10 0.42
17 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTTTATTATATTA
Found at i:37005 original size:21 final size:20
Alignment explanation
Indices: 36981--37028 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
36971 TACAATATTG
**
36981 ATTTCATATATTAATAATTTT
1 ATTTCATATA-TAATAAAATT
37002 ATTT-AGTATATAATAAAATT
1 ATTTCA-TATATAATAAAATT
37022 ATTTCAT
1 ATTTCAT
37029 TGAATAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTCATATATAATAAAATT
Found at i:43753 original size:6 final size:6
Alignment explanation
Indices: 43728--43772 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
43718 GTTGAGGATG
* * * *
43728 TGGGTA CGGGTA TGGATA TTGGTA TTGGTA TGGGTA TGGGTA TGG
1 TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGG
43773 TGGCATGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.02, G:0.44, T:0.36
Consensus pattern (6 bp):
TGGGTA
Found at i:44557 original size:15 final size:15
Alignment explanation
Indices: 44537--44599 Score: 67
Period size: 15 Copynumber: 4.0 Consensus size: 15
44527 ACTCATCTGT
44537 ATCATCATAATCATC
1 ATCATCATAATCATC
44552 ATCATCA-AGATCA-C
1 ATCATCATA-ATCATC
44566 AATCATCATCCAAGTCATC
1 -ATCATCAT--AA-TCATC
44585 ATCATCATAATCATC
1 ATCATCATAATCATC
44600 GTCACTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.05
15 23 0.56
16 2 0.05
17 1 0.02
18 12 0.29
19 1 0.02
ACGTcount: A:0.40, C:0.29, G:0.03, T:0.29
Consensus pattern (15 bp):
ATCATCATAATCATC
Found at i:46912 original size:19 final size:20
Alignment explanation
Indices: 46888--46938 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
46878 AATGACCAAT
46888 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
46907 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
46927 AAAATCGCAACG
1 AAAATCGCAACG
46939 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:46932 original size:20 final size:20
Alignment explanation
Indices: 46888--47145 Score: 115
Period size: 20 Copynumber: 12.6 Consensus size: 20
46878 AATGACCAAT
* *
46888 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
46907 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
46927 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
***
46947 AAAATCGCAACG-GACAAAAG
1 AAAATCGCAACGCGA-TTTAG
* * **
46967 AAAATCGCAACACGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
46988 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
47011 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
47031 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
47051 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
47071 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
47091 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * *
47114 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
47134 AGAATCGCAACG
1 AAAATCGCAACG
47146 TTAAAAAGAA
Statistics
Matches: 187, Mismatches: 43, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
19 18 0.10
20 125 0.67
21 15 0.08
22 1 0.01
23 28 0.15
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:47159 original size:20 final size:20
Alignment explanation
Indices: 47136--47175 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
47126 CGATTGAGAG
*
47136 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
47156 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
47176 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:47162 original size:83 final size:83
Alignment explanation
Indices: 46992--47165 Score: 222
Period size: 83 Copynumber: 2.1 Consensus size: 83
46982 GCTTCCAAGT
* ** * *
46992 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
* *** * *
47057 GCAATGCGATTGAGAGAG
66 GCAACGCGAAAAAGAAAA
*
47075 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
**
47140 GCAACGTTAAAAAGAAAA
66 GCAACGCGAAAAAGAAAA
47158 TCGCAACG
1 TCGCAACG
47166 GTCAAAAGAA
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
GCAACGCGAAAAAGAAAA
Found at i:47254 original size:6 final size:6
Alignment explanation
Indices: 47243--47286 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
47233 GACACGTATT
47243 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
47287 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:47984 original size:6 final size:6
Alignment explanation
Indices: 47969--48030 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
47959 TCTCGTCTCG
*
47969 GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
*
48016 GGTCGT GATCGT GGT
1 GGTCGT GGTCGT GGT
48031 AATACGTGTC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 5 0.09
6 48 0.91
ACGTcount: A:0.02, C:0.16, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:48133 original size:20 final size:20
Alignment explanation
Indices: 48108--48151 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
48098 TTTTTAACTA
*
48108 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
48128 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
48148 TTCT
1 TTCT
48152 CAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:48161 original size:20 final size:20
Alignment explanation
Indices: 48138--48380 Score: 82
Period size: 20 Copynumber: 11.6 Consensus size: 20
48128 TTCTTTTTAA
48138 CGTTGCGATTTTCTCAATCG
1 CGTTGCGATTTTCTCAATCG
*
48158 CGTTGCGATATTGCGATTCTCTCAGTCG
1 CGTTGCG--A-T----TT-TCTCAATCG
* *
48186 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTCAATCG
* * * *
48206 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTCAATCG
* ***
48226 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTCAATCG
*
48246 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTTTC-TC--AATCG
** **
48269 CGTTGCGAACTT-GGAAGCTCG
1 CGTTGCGATTTTCTCAA--TCG
* *
48290 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTCAATCG
*** **
48308 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTCAATCG
*
48330 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTCAATCG
*
48350 CGTTGCGA-TTT-TGATATCG
1 CGTTGCGATTTTCTCA-ATCG
48369 CGTTGCGATTTT
1 CGTTGCGATTTT
48381 ATTGGTCATT
Statistics
Matches: 172, Mismatches: 31, Indels: 40
0.71 0.13 0.16
Matches are distributed among these distances:
18 4 0.02
19 17 0.10
20 99 0.58
21 16 0.09
22 3 0.02
23 15 0.09
26 1 0.01
27 2 0.01
28 15 0.09
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTCAATCG
Found at i:48180 original size:28 final size:28
Alignment explanation
Indices: 48140--48193 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
48130 CTTTTTAACG
*
48140 TTGCGATTTTCTCAATCGCGTTGCGATA
1 TTGCGATTCTCTCAATCGCGTTGCGATA
*
48168 TTGCGATTCTCTCAGTCGCGTTGCGA
1 TTGCGATTCTCTCAATCGCGTTGCGA
48194 CTCTCTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (28 bp):
TTGCGATTCTCTCAATCGCGTTGCGATA
Found at i:48232 original size:40 final size:40
Alignment explanation
Indices: 48167--48255 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
48157 GCGTTGCGAT
* * * * **
48167 ATTGCGATTCTCTCAGTCGCGTTGCGACTCTCTCAATCGC
1 ATTGCGATTCTATAAATCGCATTGCGACTCAATCAATCGC
*
48207 ATTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGC
1 ATTGCGATTCTATAAATCGCATTGCGACTCAATCAATCGC
48247 ATTGCGATT
1 ATTGCGATT
48256 TTCTTCTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (40 bp):
ATTGCGATTCTATAAATCGCATTGCGACTCAATCAATCGC
Found at i:48370 original size:19 final size:20
Alignment explanation
Indices: 48330--48380 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
48320 TTCTTTTTAA
*
48330 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
48350 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
48369 CGTTGCGATTTT
1 CGTTGCGATTTT
48381 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:49101 original size:13 final size:14
Alignment explanation
Indices: 49078--49106 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49068 CTAATAATAT
49078 TAAATTATATTAAA
1 TAAATTATATTAAA
49092 TAAA-TATATTAAA
1 TAAATTATATTAAA
49105 TA
1 TA
49107 TATTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATTATATTAAA
Found at i:52547 original size:126 final size:126
Alignment explanation
Indices: 52166--52640 Score: 832
Period size: 126 Copynumber: 3.8 Consensus size: 126
52156 CTATAATCGG
** *
52166 TTCACTATTCACGTGAAGGCGCGCCCCCGGGAACGCGCCTTCCATTATTTCGTCAGAGAAT-TTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
52230 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
52291 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAG-A-A-TA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
52353 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
52414 TTCACTATTCATGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
52479 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
52540 TTAACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
52605 TAATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
52641 ATAACTTAAA
Statistics
Matches: 335, Mismatches: 11, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
123 118 0.35
124 2 0.01
125 56 0.17
126 159 0.47
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:53087 original size:33 final size:34
Alignment explanation
Indices: 53026--53125 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
53016 GAAATTAATG
*
53026 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
53060 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
53093 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
53126 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:53710 original size:21 final size:21
Alignment explanation
Indices: 53622--53715 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
53612 TATGGTATAA
*
53622 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
53643 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
53664 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
53685 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
53706 AACCCTGCGG
1 AACCCTGCGG
53716 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:53745 original size:21 final size:21
Alignment explanation
Indices: 53719--53766 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
53709 CCTGCGGAGA
*
53719 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
53740 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
53761 GGGCAT
1 TGGCAT
53767 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:55469 original size:19 final size:17
Alignment explanation
Indices: 55447--55488 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
55437 GACAAACAAT
55447 ATAATTAGCAAAAAAATTA
1 ATAATTA-CAAAAAAA-TA
*
55466 ATAATT-CTAAAAAATA
1 ATAATTACAAAAAAATA
55482 ATAATTA
1 ATAATTA
55489 TATAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.38
17 7 0.33
19 6 0.29
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAATTACAAAAAAATA
Found at i:55515 original size:33 final size:31
Alignment explanation
Indices: 55473--55549 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 31
55463 TTAATAATTC
* *
55473 TAAAAAATAATAATTATATAATATTATTTTAATA
1 TAAAAAATAATAATTACATAA-A-TA-TATAATA
*
55507 -AAAAAATAATATTTACATAAATATATAATA
1 TAAAAAATAATAATTACATAAATATATAATA
55537 TAAAAAATAATAA
1 TAAAAAATAATAA
55550 CTATTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 6 0.16
31 13 0.34
32 1 0.03
33 18 0.47
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (31 bp):
TAAAAAATAATAATTACATAAATATATAATA
Found at i:55526 original size:19 final size:18
Alignment explanation
Indices: 55500--55562 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
55490 ATAATATTAT
55500 TTTAATAAAAAAATAATA
1 TTTAATAAAAAAATAATA
* *
55518 TTTACATAAATATATAATA
1 TTTA-ATAAAAAAATAATA
*
55537 --TAA-AAAATAATAACTA
1 TTTAATAAAAAAATAA-TA
55553 TTTAA-AAAAA
1 TTTAATAAAAA
55563 TACTAACATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 7 0.20
16 3 0.09
17 2 0.06
18 11 0.31
19 12 0.34
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAATAAAAAAATAATA
Found at i:55574 original size:34 final size:33
Alignment explanation
Indices: 55506--55580 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
55496 TTATTTTAAT
* *
55506 AAAAAAATAATATTTACATAAATATATAATATA
1 AAAAAAATAATATTTACATAAAAATATAACATA
55539 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAA-AATAA-TATTTACATAAAAATA-TAACATA
*
55573 AAATAAAT
1 AAAAAAAT
55581 TTCTTACCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 14 0.39
34 16 0.44
35 6 0.17
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (33 bp):
AAAAAAATAATATTTACATAAAAATATAACATA
Found at i:56577 original size:60 final size:60
Alignment explanation
Indices: 56512--56628 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
56502 TGAATTGATT
* * ** * * *
56512 TTTAAACGTTTAAATATTTTAATTTCATCCCCAAACTAT-GGCTTTCATTCTAAATTAATC
1 TTTAAAAGTTTAAACATTCCAATTTCAACCCCAAACTATAGCCCTTC-TTCTAAATTAATC
*
56572 TTTAAAATTTTAAACATTCCAATTTCAACCCCAAACTATAGCCCTTCTTCTAAATTA
1 TTTAAAAGTTTAAACATTCCAATTTCAACCCCAAACTATAGCCCTTCTTCTAAATTA
56629 GTCCCCAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 43 0.90
61 5 0.10
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.40
Consensus pattern (60 bp):
TTTAAAAGTTTAAACATTCCAATTTCAACCCCAAACTATAGCCCTTCTTCTAAATTAATC
Found at i:58055 original size:60 final size:60
Alignment explanation
Indices: 57934--58056 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
57924 AGTCCACAAT
* * * * ** * *
57934 TATAGGGTATTTCCTTGTTGAGTCTCTCAACTATTAAAAGTTATAAAATTGTCATTTGAC
1 TATAGGGTATTGCCTTGTTGAGTCCCTCAACTATTAAAAATTACAAAACAGTCACTCGAC
*
57994 TATAGGGTGTTGCCTTGTTGAGTCCCTCAACTATTAAAAATTACAAAACAGTCACTCGAC
1 TATAGGGTATTGCCTTGTTGAGTCCCTCAACTATTAAAAATTACAAAACAGTCACTCGAC
58054 TAT
1 TAT
58057 TCATATGTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (60 bp):
TATAGGGTATTGCCTTGTTGAGTCCCTCAACTATTAAAAATTACAAAACAGTCACTCGAC
Found at i:58962 original size:37 final size:36
Alignment explanation
Indices: 58890--58963 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 36
58880 GTTGAAAAAT
*
58890 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
*
58926 ATTTATATATATATT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATT-AAAATCATAAA
58963 A
1 A
58964 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 10 0.30
37 17 0.52
38 6 0.18
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:62486 original size:40 final size:41
Alignment explanation
Indices: 62419--62559 Score: 232
Period size: 40 Copynumber: 3.5 Consensus size: 41
62409 AATGACCAAC
*
62419 AAATTCGCAACGCG-AATTCAAATTTCGCAACCCAGGTTCT
1 AAATTCGCAACGCGAAAGTCAAATTTCGCAACCCAGGTTCT
* *
62459 AAATTCGCAACGCTAAAGTCAAA-TTCGCAATCCAGGTTCT
1 AAATTCGCAACGCGAAAGTCAAATTTCGCAACCCAGGTTCT
*
62499 AAATTCGCAACGCGAAAGTCAAATTTCGCAACCCAGGTTCC
1 AAATTCGCAACGCGAAAGTCAAATTTCGCAACCCAGGTTCT
62540 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
62560 CAAAATCGCA
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
40 51 0.55
41 42 0.45
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (41 bp):
AAATTCGCAACGCGAAAGTCAAATTTCGCAACCCAGGTTCT
Found at i:62597 original size:21 final size:21
Alignment explanation
Indices: 62499--62631 Score: 107
Period size: 21 Copynumber: 6.5 Consensus size: 21
62489 TCCAGGTTCT
*
62499 AAATTCGCAACGCGAAAGT-C
1 AAATTCGCAACGCGATAGTCC
* *
62519 AAATTTCGCAAC-CCA-GGTTCC
1 AAA-TTCGCAACGCGATAG-TCC
*
62540 AAATTCGCAACGCGAAAGTCC
1 AAATTCGCAACGCGATAGTCC
* *
62561 AAAATCGCAACGCGATAGTCG
1 AAATTCGCAACGCGATAGTCC
* *
62582 AAATTCACAACGCGAT--T-T
1 AAATTCGCAACGCGATAGTCC
*
62600 AAGATTCGCAACGCGATACTCC
1 AA-ATTCGCAACGCGATAGTCC
*
62622 AAAATCGCAA
1 AAATTCGCAA
62632 TGCATTTGTT
Statistics
Matches: 91, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.02
19 15 0.16
20 14 0.15
21 57 0.63
22 3 0.03
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (21 bp):
AAATTCGCAACGCGATAGTCC
Found at i:63595 original size:21 final size:21
Alignment explanation
Indices: 63568--63626 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
63558 GTCCGAGTTA
63568 CCCGCGACGGCCGCAATAACG
1 CCCGCGACGGCCGCAATAACG
* ** **
63589 TCCGCGATAGCCGCAATAGTG
1 CCCGCGACGGCCGCAATAACG
63610 CCCGCGACGGCCGCAAT
1 CCCGCGACGGCCGCAAT
63627 CACGGTAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.39, G:0.29, T:0.10
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAACG
Found at i:63768 original size:21 final size:21
Alignment explanation
Indices: 63744--63784 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
63734 TACGATTTTG
*
63744 GACTATCGCGTTGCGAATTTC
1 GACTATCACGTTGCGAATTTC
*
63765 GACTTTCACGTTGCGAATTT
1 GACTATCACGTTGCGAATTT
63785 GAAACCTGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (21 bp):
GACTATCACGTTGCGAATTTC
Found at i:63825 original size:19 final size:19
Alignment explanation
Indices: 63814--63863 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
63804 TTGAATTTGT
63814 GTTGCGAATTTGAGATCGA
1 GTTGCGAATTTGAGATCGA
*
63833 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCGA
63852 GTTGCGAATTTG
1 GTTGCGAATTTG
63864 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCGA
Found at i:74857 original size:35 final size:35
Alignment explanation
Indices: 74810--74902 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
74800 AACACAATCA
*
74810 TCAATTACATTCTAAACCCCAAAATCCAAAATGCT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* * *
74845 TCAATTATATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* *
74880 TTAATTACATGCCT-AACCCCAAA
1 TCAATTACAT-TCTAAACCCCAAA
74903 TTCATAATCC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 47 0.96
36 2 0.04
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:75087 original size:46 final size:46
Alignment explanation
Indices: 75020--75115 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
75010 CAATAAGTGA
**
75020 TTATGTTGGGTTTTGGGTTATGTTGGACCTAAATACTCAATTCAAT
1 TTATGTTGGGTTTAAGGTTATGTTGGACCTAAATACTCAATTCAAT
*
75066 TTATGTTGGGTTTAAGGTTATGTTGGACCTAAATACTCAATTTAAT
1 TTATGTTGGGTTTAAGGTTATGTTGGACCTAAATACTCAATTCAAT
75112 TTAT
1 TTAT
75116 AAAATAGTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (46 bp):
TTATGTTGGGTTTAAGGTTATGTTGGACCTAAATACTCAATTCAAT
Found at i:75278 original size:145 final size:147
Alignment explanation
Indices: 75102--75395 Score: 468
Period size: 148 Copynumber: 2.0 Consensus size: 147
75092 ACCTAAATAC
* * *
75102 TCAATTTAATTTATAAAATAGTTGACACGAATTTTTTTCGATTT-G-TTATAAAATTTAAATCAA
1 TCAATTCAATTTATAAAATAGTTAACACGAATTTTTTTCGATTTAGTTTATAAAACTTAAATCAA
* * *
75165 GTTTG-ATTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATA
66 G-TCGAATTGAATTAAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATACTATA
75229 ATATTATTTGATTCTAAT
130 ATATTATTTGATTCTAAT
*
75247 TCAATTCAATTTATAAAATAGTTAACTCGAATTTTTTTCGATTTGAGTTTATAAAACTTAAATCA
1 TCAATTCAATTTATAAAATAGTTAACACGAATTTTTTTCGATTT-AGTTTATAAAACTTAAATCA
* *
75312 AGTCGAATTGAATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTATTATACTATA
65 AGTCGAATTGAATTAAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATACTATA
75377 ATATTATTTGATTCTAAT
130 ATATTATTTGATTCTAAT
75395 T
1 T
75396 TAAATAGTTT
Statistics
Matches: 136, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
145 41 0.30
147 3 0.02
148 92 0.68
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.49
Consensus pattern (147 bp):
TCAATTCAATTTATAAAATAGTTAACACGAATTTTTTTCGATTTAGTTTATAAAACTTAAATCAA
GTCGAATTGAATTAAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATACTATAA
TATTATTTGATTCTAAT
Found at i:75995 original size:103 final size:103
Alignment explanation
Indices: 75816--76033 Score: 323
Period size: 103 Copynumber: 2.1 Consensus size: 103
75806 AGAGTTATGT
*
75816 TTTGAGGGTTTAGGGTTGTTACTTCAAGTTCAATTTGTTATGACATATTTTAAGAATGGATTATG
1 TTTGAGGGTTTAGGGTTGTTACTTCAAGTTCAATTTGTTATGACAGATTTTAAGAATGGATTATG
* * *
75881 AATTTGGGGTTGAGCATGTAACTGGAGTATTTTTGGAA
66 AATTTGGGGTTGAGCATATAACTGAAGTATTTTTAGAA
* * ** *
75919 TTTGAGGGTTTAGGGTTGCTT-CTTCAAGTTTAGTTTGTTATGGTAGATTTTGAGAATGGATTAT
1 TTTGAGGGTTTAGGGTTG-TTACTTCAAGTTCAATTTGTTATGACAGATTTTAAGAATGGATTAT
*
75983 GAATTTGGGGTTGAGCATATAATTGAAGTATTTTTAGAA
65 GAATTTGGGGTTGAGCATATAACTGAAGTATTTTTAGAA
76022 TTTGA-GGTTTAG
1 TTTGAGGGTTTAG
76034 AATGTAATTG
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
102 7 0.07
103 95 0.91
104 2 0.02
ACGTcount: A:0.25, C:0.05, G:0.27, T:0.43
Consensus pattern (103 bp):
TTTGAGGGTTTAGGGTTGTTACTTCAAGTTCAATTTGTTATGACAGATTTTAAGAATGGATTATG
AATTTGGGGTTGAGCATATAACTGAAGTATTTTTAGAA
Found at i:76042 original size:36 final size:36
Alignment explanation
Indices: 75983--76115 Score: 180
Period size: 36 Copynumber: 3.7 Consensus size: 36
75973 AATGGATTAT
* * * * *
75983 GAATTTGGGGTTGAGCATATAATTGAAGTATTTTTA
1 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTTG
76019 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTTG
1 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTTG
**
76055 GAATTTGAGGTTTAGAATGTAATTGAAACA-TTTTG
1 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTTG
76090 GAATTT-AGGGTTTAGAATGTAATTGA
1 GAATTTGA-GGTTTAGAATGTAATTGA
76116 TGATTGTGTT
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
34 1 0.01
35 29 0.33
36 59 0.66
ACGTcount: A:0.32, C:0.02, G:0.25, T:0.41
Consensus pattern (36 bp):
GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTTG
Found at i:81209 original size:21 final size:21
Alignment explanation
Indices: 81183--81227 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
81173 GATTTCTGGG
* *
81183 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
81204 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
81225 CAA
1 CAA
81228 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:81908 original size:24 final size:24
Alignment explanation
Indices: 81860--81906 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
81850 ATATGGCATG
*
81860 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
81884 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
81907 ATAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:82160 original size:31 final size:31
Alignment explanation
Indices: 82122--82277 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
82112 AGGGTCGAGG
82122 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
82153 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
82184 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
82215 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
82246 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
82277 G
1 G
82278 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:85433 original size:21 final size:21
Alignment explanation
Indices: 85407--85451 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
85397 GATTTCTGGG
* *
85407 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
85428 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
85449 CAA
1 CAA
85452 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:86133 original size:24 final size:24
Alignment explanation
Indices: 86085--86131 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
86075 ATATGGCATG
*
86085 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
86109 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
86132 ATAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:86384 original size:31 final size:31
Alignment explanation
Indices: 86346--86500 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
86336 AGGGTCGAGG
86346 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
86377 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
86408 GTTTACCTAT-TTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
86438 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
86469 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
86500 G
1 G
86501 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 28 0.25
31 84 0.74
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:86431 original size:61 final size:61
Alignment explanation
Indices: 86346--86500 Score: 231
Period size: 61 Copynumber: 2.5 Consensus size: 61
86336 AGGGTCGAGG
* *
86346 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTAT-TTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACT
*
86408 GTTTACCTATTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACT
* *
86469 GATTACCTAGGTTCTTCGGAATC-TATGGACTG
1 GTTTACCTA-TTTCTTCGGAA-CATATGGACTG
86501 GTCCTTCGGG
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
61 56 0.66
62 28 0.33
63 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (61 bp):
GTTTACCTATTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACT
Found at i:93878 original size:155 final size:158
Alignment explanation
Indices: 93566--94037 Score: 871
Period size: 155 Copynumber: 3.0 Consensus size: 158
93556 GCTGGAAGAT
* *
93566 AGCCTGCGC-AGTCTCTGGTAAGCAAAAACAAGAAACTGGACATGGATGCTGGGGAATGTGAGTG
1 AGCCTGCTCAAGTCTCTGGTAAGAAAAAACAAGAAACTGGACATGGATGCTGGGGAATGTGAGTG
*
93630 GTTAAACTCAAGGAGTGATATCGATGCAATAGGTAAGGAGATCGAGAGATTGTTGGTAGATGAAC
66 GTTAAACTCGAGGAGTGATATCGATGCAATAGGTAAGGAGATCGAGAGATTGTTGGTAGATGAAC
93695 TAATAGCTGAGGTAGTGCATGGCTAGTA
131 TAATAGCTGAGGTAGTGCATGGCTAGTA
93723 AGCCTGCTCAAGTCTCTGGTAAG-AAAAA-AAGAAACTGGACATGGATGCTGGGGAATGTGAGTG
1 AGCCTGCTCAAGTCTCTGGTAAGAAAAAACAAGAAACTGGACATGGATGCTGGGGAATGTGAGTG
93786 GTT-AACTCGAGGAGTGATATCGATGCAATAGGTAAGGAGATCGAGAGATTGTTGGTAGATGAAC
66 GTTAAACTCGAGGAGTGATATCGATGCAATAGGTAAGGAGATCGAGAGATTGTTGGTAGATGAAC
93850 TAATAGCTGAGGTAGTGCATGGCTAGTA
131 TAATAGCTGAGGTAGTGCATGGCTAGTA
*
93878 AGCCTGCTCAAGTCTCTGGTAAGAAAAAACAAGAAACTGGACATGGATGCCGGGGAATGTGAGTG
1 AGCCTGCTCAAGTCTCTGGTAAGAAAAAACAAGAAACTGGACATGGATGCTGGGGAATGTGAGTG
*
93943 GTTAAACTCGAGGAGTGATATTGATGCAATAGGTAAGGAGATCGAGAGATTGTTGGTAGATGAAC
66 GTTAAACTCGAGGAGTGATATCGATGCAATAGGTAAGGAGATCGAGAGATTGTTGGTAGATGAAC
94008 TAATAGCTGAGGTAGTGCATGGCTAGTA
131 TAATAGCTGAGGTAGTGCATGGCTAGTA
94036 AG
1 AG
94038 ATGATAGTTT
Statistics
Matches: 307, Mismatches: 4, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
155 111 0.36
156 43 0.14
157 50 0.16
158 103 0.34
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (158 bp):
AGCCTGCTCAAGTCTCTGGTAAGAAAAAACAAGAAACTGGACATGGATGCTGGGGAATGTGAGTG
GTTAAACTCGAGGAGTGATATCGATGCAATAGGTAAGGAGATCGAGAGATTGTTGGTAGATGAAC
TAATAGCTGAGGTAGTGCATGGCTAGTA
Done.