Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004657.1 Hibiscus syriacus cultivar Beakdansim tig00010440_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: 101312
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12406 original size:21 final size:21
Alignment explanation
Indices: 12382--12438 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
12372 GAGCCTTTTT
*
12382 GAGGATTTCATCAAATCCAAG
1 GAGGATATCATCAAATCCAAG
*
12403 GAGGGTATCATCAAATCCAAG
1 GAGGATATCATCAAATCCAAG
* *
12424 GAGGGTATCACCAAA
1 GAGGATATCATCAAA
12439 AAGAAAGTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
GAGGATATCATCAAATCCAAG
Found at i:15847 original size:3 final size:3
Alignment explanation
Indices: 15835--15917 Score: 150
Period size: 3 Copynumber: 27.7 Consensus size: 3
15825 ATTTACAATC
15835 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
15880 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
15918 GAACACCATA
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 73 0.94
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16291 original size:42 final size:41
Alignment explanation
Indices: 16198--16296 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
16188 GTCTTATGGG
* * * *
16198 TGGCCCGAAGGACTTATCATCTTGCTGGAAAGACTTATAGA
1 TGGCCTGAAGGACTTAGCATCATGCTAGAAAGACTTATAGA
* *
16239 T-GACTCGAAGGATTTAAGCATCATGCTAGAAAGACTTACT-GA
1 TGGCCT-GAAGGACTT-AGCATCATGCTAGAAAGACTTA-TAGA
16281 TGGCCTGAAGGACTTA
1 TGGCCTGAAGGACTTA
16297 CTCAACAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
40 2 0.04
41 10 0.22
42 30 0.65
43 4 0.09
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (41 bp):
TGGCCTGAAGGACTTAGCATCATGCTAGAAAGACTTATAGA
Found at i:16377 original size:58 final size:58
Alignment explanation
Indices: 16315--16498 Score: 185
Period size: 59 Copynumber: 3.2 Consensus size: 58
16305 GAAACCTTTG
* * * * *
16315 AAAATCATGCTCAGTTTC-TTAAAAACTATCGTT-TATAGTTATCATCAAGAAACCCCTA
1 AAAATCAGGCTCAGTTTCTTTAAAAAAT-TCATTGGA-AGTAATCATCAAGAAACCCCTA
* *
16373 AAAATTAGGCTTAGTTTCTTTAAAAAATTCATTGGAAGTAATCATCAAGAAACCCCTA
1 AAAATCAGGCTCAGTTTCTTTAAAAAATTCATTGGAAGTAATCATCAAGAAACCCCTA
* * * * * * *
16431 AAACGT-AGGCTTAACTTTTTTTAAAAAAATCATTAGAAGTAATCATCAAGAAACCCCTT
1 AAA-ATCAGGC-TCAGTTTCTTTAAAAAATTCATTGGAAGTAATCATCAAGAAACCCCTA
16490 AAAATCAGG
1 AAAATCAGG
16499 ATAGCTCTTT
Statistics
Matches: 106, Mismatches: 15, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
58 48 0.45
59 58 0.55
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (58 bp):
AAAATCAGGCTCAGTTTCTTTAAAAAATTCATTGGAAGTAATCATCAAGAAACCCCTA
Found at i:16483 original size:59 final size:58
Alignment explanation
Indices: 16355--16493 Score: 206
Period size: 59 Copynumber: 2.4 Consensus size: 58
16345 GTTTATAGTT
* * * *
16355 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAAAATTCATTGGAAGTA
1 ATCATCAAGAAACCCCTAAAAAGTAGGCTTACTTTCTTTAAAAAAATCATTAGAAGTA
* *
16413 ATCATCAAGAAACCCCTAAAACGTAGGCTTAACTTTTTTTAAAAAAATCATTAGAAGTA
1 ATCATCAAGAAACCCCTAAAAAGTAGGCTT-ACTTTCTTTAAAAAAATCATTAGAAGTA
*
16472 ATCATCAAGAAACCCCTTAAAA
1 ATCATCAAGAAACCCCTAAAAA
16494 TCAGGATAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 28 0.39
59 44 0.61
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (58 bp):
ATCATCAAGAAACCCCTAAAAAGTAGGCTTACTTTCTTTAAAAAAATCATTAGAAGTA
Found at i:16642 original size:54 final size:55
Alignment explanation
Indices: 16526--16769 Score: 295
Period size: 54 Copynumber: 4.6 Consensus size: 55
16516 TCATTATGTT
* * *
16526 AAGAAACCTCTAAAACTCAGACTTAATTTCTTTGAAAACTCATTTAAAAATCATC
1 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCATC
16581 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTT-AAAACTCATTTAAAAATCATC
1 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCATC
* *
16635 AAGAAACTTCTTAAAATCAGAC----TTTCTTTGAAAACTTATTT-AAAATCATC
1 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCATC
** * * * *
16685 AAGAAACTTCTAAAAATTGGAATTAGCTTCTTTCAAAACTCATTTGAAAAT-ATC
1 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCATC
* ** * *
16739 AAGAGACCCCTAAAAATTAGGCTTAGTTTCT
1 AAGAAACTTCTAAAAATCAGACTTAGTTTCT
16770 AAAATTTCTT
Statistics
Matches: 164, Mismatches: 19, Indels: 13
0.84 0.10 0.07
Matches are distributed among these distances:
50 34 0.21
51 10 0.06
54 85 0.52
55 35 0.21
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (55 bp):
AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCATC
Found at i:16716 original size:104 final size:105
Alignment explanation
Indices: 16552--16742 Score: 305
Period size: 104 Copynumber: 1.8 Consensus size: 105
16542 TCAGACTTAA
* *
16552 TTTCTTTGAAAACTCATTTAAAAATCATCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTT-AA
1 TTTCTTTGAAAACTCATTTAAAAATCATCAAGAAACTTCTAAAAATCAGAATTAGCTTCTTTCAA
16616 AACTCATTTAAAAATCATCAAGAAACTTCTTAAAATCAGAC
66 AACTCATTTAAAAAT-ATCAAGAAACTTCTTAAAATCAGAC
* **
16657 TTTCTTTGAAAACTTATTT-AAAATCATCAAGAAACTTCTAAAAATTGGAATTAGCTTCTTTCAA
1 TTTCTTTGAAAACTCATTTAAAAATCATCAAGAAACTTCTAAAAATCAGAATTAGCTTCTTTCAA
*
16721 AACTCATTTGAAAATATCAAGA
66 AACTCATTTAAAAATATCAAGA
16743 GACCCCTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
104 45 0.57
105 34 0.43
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (105 bp):
TTTCTTTGAAAACTCATTTAAAAATCATCAAGAAACTTCTAAAAATCAGAATTAGCTTCTTTCAA
AACTCATTTAAAAATATCAAGAAACTTCTTAAAATCAGAC
Found at i:16820 original size:52 final size:54
Alignment explanation
Indices: 16727--16839 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 54
16717 TCAAAACTCA
* * * *
16727 TTTGAAAATATCAAGAGACCCCTAAAAATTAGGCTTAGTTT-CTAAAAT-TTCT
1 TTTGAAAACATCAAGAAACCCATAAAAATCAGGCTTAGTTTCCTAAAATATTCT
* * * *
16779 TTTGAAAACATCAAGAAACCCATGACAATCAGGTTTCGTTTCCTAAAATATTCT
1 TTTGAAAACATCAAGAAACCCATAAAAATCAGGCTTAGTTTCCTAAAATATTCT
16833 TTTGAAA
1 TTTGAAA
16840 CACCATGTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 33 0.65
53 7 0.14
54 11 0.22
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (54 bp):
TTTGAAAACATCAAGAAACCCATAAAAATCAGGCTTAGTTTCCTAAAATATTCT
Found at i:29328 original size:28 final size:28
Alignment explanation
Indices: 29259--29328 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
29249 ATATTTCTTG
*
29259 ATACCATTGCAATATAGAAATGAAATAG
1 ATACCATTGCAATATAGAAATGAAATAA
**
29287 ATACTGTTGCAATATAGAAATGAAATAA
1 ATACCATTGCAATATAGAAATGAAATAA
*
29315 ATACCATTGGAATA
1 ATACCATTGCAATA
29329 CTTGTTCTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (28 bp):
ATACCATTGCAATATAGAAATGAAATAA
Found at i:34227 original size:30 final size:31
Alignment explanation
Indices: 34163--34228 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
34153 AGTTACATCA
* *
34163 GGGACCATATTGCAAATGGACTAAATATTTG
1 GGGACCATATTGCAAATAGACTAAATAGTTG
*
34194 GGGACCATATTGCAAATAGACTTAAT-GTTG
1 GGGACCATATTGCAAATAGACTAAATAGTTG
34224 GGGAC
1 GGGAC
34229 TGTTTTGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGACCATATTGCAAATAGACTAAATAGTTG
Found at i:34935 original size:31 final size:31
Alignment explanation
Indices: 34861--34938 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
34851 CAGTTACGTC
* * *
34861 GGGGACTATATTACAAACGGGCTAAATATTG
1 GGGGACTATATTGCAAACGGACTAAATATTA
* * *
34892 GGGGACCATATTGCAAATGGACTAAATGTTA
1 GGGGACTATATTGCAAACGGACTAAATATTA
*
34923 GGGGACTGTATTGCAA
1 GGGGACTATATTGCAA
34939 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (31 bp):
GGGGACTATATTGCAAACGGACTAAATATTA
Found at i:35675 original size:20 final size:20
Alignment explanation
Indices: 35650--35763 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
35640 AATTGGAAAA
35650 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
35670 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
35690 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
35711 ATCACAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
35731 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
35751 TTCGCAACGCGAT
1 ATCGCAATGCGAT
35764 TTACATAGCG
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.79
21 12 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:36362 original size:19 final size:19
Alignment explanation
Indices: 36318--36362 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
36308 GCAACGAGAG
*
36318 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
36337 AGA-CGCAACGCGAAACAAA
1 A-ATCGCAACGCGAAACAAA
36356 AATCGCA
1 AATCGCA
36363 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 21 0.91
20 1 0.04
ACGTcount: A:0.51, C:0.24, G:0.18, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:36380 original size:19 final size:19
Alignment explanation
Indices: 36358--36522 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
36348 GAAACAAAAA
*
36358 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36377 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
36396 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
36415 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
36429 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
36448 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
36462 TCTCGTTACGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
36481 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
36501 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
36521 TC
1 TC
36523 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
14 18 0.16
16 4 0.03
17 4 0.03
19 59 0.51
20 30 0.26
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:36438 original size:38 final size:38
Alignment explanation
Indices: 36358--36522 Score: 134
Period size: 33 Copynumber: 4.6 Consensus size: 38
36348 GAAACAAAAA
* * *
36358 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
*
36396 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
* **
36431 T--CGTCGCGATAGTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
* ** *
36464 T--CGTTACGATAGTCATTTCCGCGTTGCGATTCTCATTA
1 TCGCGTTGCGATTTTCATTT-CGCGTTGCGATTCTCA-TG
*
36502 TCTCGTTGCGATTTTCATTTC
1 TCGCGTTGCGATTTTCATTTC
36523 AACCAAAAGA
Statistics
Matches: 108, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
33 44 0.41
34 15 0.14
35 1 0.01
38 33 0.31
39 1 0.01
40 14 0.13
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
Found at i:36449 original size:33 final size:33
Alignment explanation
Indices: 36412--36497 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
36402 TGCGATTTTT
*
36412 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCACGATAGTC
*
36445 ATTTCGCGTTGCGATTCTCTCGTTACGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCACGATAGTC
36478 ATTTCCGCGTTGCGATTCTC
1 ATTT-CGCGTTGCGATTCTC
36498 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTCACGATAGTC
Found at i:36499 original size:20 final size:20
Alignment explanation
Indices: 36476--36522 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36466 GTTACGATAG
36476 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
36496 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
36516 TCATTTC
1 TCATTTC
36523 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:40022 original size:14 final size:14
Alignment explanation
Indices: 40003--40038 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39993 ATTGTTTAAT
40003 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
40017 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
40031 TGATTTGT
1 TGATTTGT
40039 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:40182 original size:14 final size:14
Alignment explanation
Indices: 40163--40219 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
40153 GCGAAATGAA
40163 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40177 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
40196 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40210 AATCGCAACG
1 AATCGCAACG
40220 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40190 original size:33 final size:33
Alignment explanation
Indices: 40145--40234 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
40135 AAAAAGTACT
*
40145 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
40178 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
40211 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
40235 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:40204 original size:19 final size:19
Alignment explanation
Indices: 40145--40205 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
40135 AAAAAGTACT
*
40145 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
40164 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
40178 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
40197 ATCGCAACG
1 ATCGCAACG
40206 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:40252 original size:19 final size:19
Alignment explanation
Indices: 40230--40380 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
40220 CGAAATTAAA
40230 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
40249 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
40264 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
40282 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
40296 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
40315 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
40330 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
40348 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
40367 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
40381 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:40276 original size:33 final size:32
Alignment explanation
Indices: 40234--40360 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
40224 ATTAAATTCG
40234 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
40267 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
40300 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
40333 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
40361 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:40312 original size:66 final size:66
Alignment explanation
Indices: 40227--40359 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
40217 ACGCGAAATT
*
40227 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
40292 G
66 G
*
40293 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
40358 G
66 G
40359 A
1 A
40360 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:44624 original size:20 final size:20
Alignment explanation
Indices: 44599--44647 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
44589 TGTTAAATTA
44599 AAATGCATATATGCATGAGG
1 AAATGCATATATGCATGAGG
44619 AAATGCATATATGCATGAGG
1 AAATGCATATATGCATGAGG
44639 AAATGCATA
1 AAATGCATA
44648 CCAAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (20 bp):
AAATGCATATATGCATGAGG
Found at i:47946 original size:350 final size:353
Alignment explanation
Indices: 47296--47989 Score: 979
Period size: 350 Copynumber: 2.0 Consensus size: 353
47286 TTTTTTCGAC
* * * * *
47296 GAGTAAAAAAATCAAGATCACGATTGACTGAAATAATTAAAATAAAATATAGATAAAAAATGAAA
1 GAGTAAAAAAATAAAGATCACGATTAACAGAAATAATGAAAATAAAATAAAGATAAAAAAT--AA
* * * *
47361 AAAAAAGATTGTCAGTTTTCACTGAGAAAACTCAAGAAAGACAAAATTTATTAAGATAGTCTTTT
64 AAAAAAGATTGACAGATTTCACTGAGAAAACTCAAGAAAGACAAAATTTATGAAGATAATCTTTT
* *
47426 TCCTTGTTCTTCGATTTTCTCTCCACCAATAAAAAAATTTTAAAGAAAAAAGAAGATAAAAATAT
129 TCCTTATTCTTCGATTTTCTCTCCACCAATAAAAAAATTTTAAAGAAAAAAGAAGAGAAAAATAT
* *
47491 CAAAATTGAACAAAATAAAAGAACGCACACAAAAAGGAATTACTTGTACTCAAAGGTTTTCTCTT
194 CAAAATTGAACAAAATAAAAGAACACACACAAAAAGGAATTACATGTACTCAAAGGTTTTCTCTT
* * *
47556 ATTGCTCCTATCTTTCAATTTACAATCCCCCTCCATTACAAAATAAGATTACCTATTTAT-GGCT
259 ATTGCTCATATCTTTCAAGTTACAATCCCCCTCCATTACAAAATAAAATTACCTATTTATAGGCT
47620 CCCAAAAAACCCTAAAAGCACTATCTTCGGG
324 CCCAAAAAA-CCTAAAAGCACTATCTTCGGG
**
47651 GAGT-AAAAAATAAAGATCGTGATTAACAGAAATAATGAAAATAAAATAAAGATAAAAAAT-AAA
1 GAGTAAAAAAATAAAGATCACGATTAACAGAAATAATGAAAATAAAATAAAGATAAAAAATAAAA
* * * *
47714 AAATGATTGACAGATTTCATTGAGAAACCTCGAGAAAGGA-AAAATTTATGAAGATAATCTTTTT
66 AAAAGATTGACAGATTTCACTGAGAAAACTCAAGAAA-GACAAAATTTATGAAGATAATCTTTTT
* *** * * *
47778 CTTTATTCTTC-AGTTTTCTCTCCACCAAT-AAATTTTCTTTTAAGAAAAGATAAGAGAAAAA-A
130 CCTTATTCTTCGA-TTTTCTCTCCACCAATAAAAAAAT-TTTAAAGAAAAAAGAAGAGAAAAATA
* * *
47840 TCGAAATTGAACAAAATAAAAGAACACACACAAAAAGGAATTACATGTAGTGAAAGGTTTTCTCT
193 TCAAAATTGAACAAAATAAAAGAACACACACAAAAAGGAATTACATGTACTCAAAGGTTTTCTCT
* *
47905 TATTGCTCATATCTTTCAAGTTACAATCCCCCTCCATTACAAAATAAAATTGCCTATTTATAGGT
258 TATTGCTCATATCTTTCAAGTTACAATCCCCCTCCATTACAAAATAAAATTACCTATTTATAGGC
47970 TCCCAAAAAACCTAAAAGCA
323 TCCCAAAAAACCTAAAAGCA
47990 AAAAAAATAA
Statistics
Matches: 301, Mismatches: 34, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
350 133 0.44
351 113 0.38
352 2 0.01
354 49 0.16
355 4 0.01
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (353 bp):
GAGTAAAAAAATAAAGATCACGATTAACAGAAATAATGAAAATAAAATAAAGATAAAAAATAAAA
AAAAGATTGACAGATTTCACTGAGAAAACTCAAGAAAGACAAAATTTATGAAGATAATCTTTTTC
CTTATTCTTCGATTTTCTCTCCACCAATAAAAAAATTTTAAAGAAAAAAGAAGAGAAAAATATCA
AAATTGAACAAAATAAAAGAACACACACAAAAAGGAATTACATGTACTCAAAGGTTTTCTCTTAT
TGCTCATATCTTTCAAGTTACAATCCCCCTCCATTACAAAATAAAATTACCTATTTATAGGCTCC
CAAAAAACCTAAAAGCACTATCTTCGGG
Found at i:49797 original size:21 final size:22
Alignment explanation
Indices: 49763--49807 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
49753 TTTTATGGTT
*
49763 AAATAGGCTCCAACCCAAACCA
1 AAATAAGCTCCAACCCAAACCA
* *
49785 AAATAAGC-CCAACTCAACCCA
1 AAATAAGCTCCAACCCAAACCA
49806 AA
1 AA
49808 GCTTGTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.49, C:0.36, G:0.07, T:0.09
Consensus pattern (22 bp):
AAATAAGCTCCAACCCAAACCA
Found at i:63153 original size:16 final size:17
Alignment explanation
Indices: 63132--63163 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
63122 TTTGCTTCAT
63132 TTGTGG-TTCGATGTTG
1 TTGTGGTTTCGATGTTG
63148 TTGTGGTTTCGATGTT
1 TTGTGGTTTCGATGTT
63164 TCGGCTCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.06, G:0.34, T:0.53
Consensus pattern (17 bp):
TTGTGGTTTCGATGTTG
Found at i:63598 original size:27 final size:25
Alignment explanation
Indices: 63566--63620 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
63556 AAAAGAAGGG
63566 AAAATATTAATAAAATAATAAATATAA
1 AAAATATTAATAAAA-AATAAA-ATAA
*
63593 AAAATATTAATATAAAATAAAATAA
1 AAAATATTAATAAAAAATAAAATAA
63618 AAA
1 AAA
63621 GCATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 7 0.26
26 6 0.22
27 14 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAATATTAATAAAAAATAAAATAA
Found at i:63604 original size:15 final size:15
Alignment explanation
Indices: 63566--63609 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
63556 AAAAGAAGGG
63566 AAAATATTAATA-AA
1 AAAATATTAATATAA
*
63580 ATAATA--AATATAA
1 AAAATATTAATATAA
63593 AAAATATTAATATAA
1 AAAATATTAATATAA
63608 AA
1 AA
63610 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 5 0.20
15 9 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATATTAATATAA
Found at i:63670 original size:37 final size:36
Alignment explanation
Indices: 63623--63907 Score: 265
Period size: 37 Copynumber: 7.8 Consensus size: 36
63613 AATAAAAAGC
* * **
63623 ATTTTTAAAACTATATATCATATATGTTTTTTTAAAT
1 ATTTTCAAAACTATATAT-ATATATATTTTTAAAAAT
* * *
63660 GTTTTCAAAACCATATAAAATATATATTTTTAAAAACT
1 ATTTTCAAAACTATAT-ATATATATATTTTTAAAAA-T
* * **
63698 GTTTTTAAAACTATATA-ATATATATTTTCCAAAAT
1 ATTTTCAAAACTATATATATATATATTTTTAAAAAT
* *
63733 ATTTT-AAAACTATATAT-TTTATATATTTCAAAAAT
1 ATTTTCAAAACTATATATATATATAT-TTTTAAAAAT
* *
63768 ATTTTCAAAACTATATAT-TATATATATTTTCAAGAT
1 ATTTTCAAAACTATATATATATATAT-TTTTAAAAAT
* *
63804 ATTTTTAAAAACTATATATTATATATATTTTCAAAAAT
1 A-TTTTCAAAACTATATA-TATATATATTTTTAAAAAT
* *
63842 ATTTTCAAAACTATATA-ATATATAAGTTTTCAAAAT
1 ATTTTCAAAACTATATATATATAT-ATTTTTAAAAAT
*
63878 GTTTTCAAAAACTATATATTATATATATTT
1 ATTTTC-AAAACTATATA-TATATATATTT
63908 CAAAAACCGA
Statistics
Matches: 208, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
34 17 0.08
35 25 0.12
36 56 0.27
37 69 0.33
38 28 0.13
39 13 0.06
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (36 bp):
ATTTTCAAAACTATATATATATATATTTTTAAAAAT
Found at i:63769 original size:11 final size:12
Alignment explanation
Indices: 63753--63851 Score: 60
Period size: 12 Copynumber: 8.0 Consensus size: 12
63743 TATATATTTT
63753 ATATATTTCAAAA
1 ATAT-TTTCAAAA
63766 ATATTTTCAAAA
1 ATATTTTCAAAA
* * *
63778 CTATATATT-ATAT
1 --ATATTTTCAAAA
*
63791 ATATTTTC-AAG
1 ATATTTTCAAAA
*
63802 ATATTTTTAAAA
1 ATATTTTCAAAA
* *
63814 ACTATATATT-ATAT
1 A-TAT-T-TTCAAAA
63828 ATATTTTCAAAA
1 ATATTTTCAAAA
63840 ATATTTTCAAAA
1 ATATTTTCAAAA
63852 CTATATAATA
Statistics
Matches: 66, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
11 16 0.24
12 26 0.39
13 12 0.18
14 10 0.15
15 2 0.03
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.45
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:63850 original size:74 final size:72
Alignment explanation
Indices: 63623--63913 Score: 322
Period size: 74 Copynumber: 4.0 Consensus size: 72
63613 AATAAAAAGC
* * ** * * * **
63623 ATTTTTAAAACTATATATCATATATGTTTTTTTAAAT-GTTTTCAAAACCATATAAAATATATAT
1 ATTTTCAAAACTATATAT-ATATAT-ATTTTCAAAATATTTTTAAAAACTATATATTATATATA-
*
63687 TTTTAAAAACT
63 TTTCAAAAA-T
* * *
63698 GTTTTTAAAACTATATA-ATATATATTTTCCAAAATA-TTTT-AAAACTATATATTTTATATATT
1 ATTTTCAAAACTATATATATATATATTTT-CAAAATATTTTTAAAAACTATATATTATATATATT
63760 TCAAAAAT
65 TCAAAAAT
*
63768 ATTTTCAAAACTATATATTATATATATTTTCAAGATATTTTTAAAAACTATATATTATATATATT
1 ATTTTCAAAACTATATA-TATATATATTTTCAAAATATTTTTAAAAACTATATATTATATATA-T
63833 TTCAAAAAT
64 TTCAAAAAT
* *
63842 ATTTTCAAAACTATATA-ATATATAAGTTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
1 ATTTTCAAAACTATATATATATAT-A-TTTTCAAAATATTTTTAAAAACTATATATTATATATAT
63906 TTCAAAAA
64 TTCAAAAA
63914 CCGATATTTT
Statistics
Matches: 191, Mismatches: 16, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
70 16 0.08
71 14 0.07
72 41 0.21
73 43 0.23
74 61 0.32
75 16 0.08
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (72 bp):
ATTTTCAAAACTATATATATATATATTTTCAAAATATTTTTAAAAACTATATATTATATATATTT
CAAAAAT
Found at i:64682 original size:85 final size:85
Alignment explanation
Indices: 64535--64945 Score: 572
Period size: 85 Copynumber: 4.8 Consensus size: 85
64525 CGCTGTCATC
* * * ** * *
64535 GAGCTGAATGGAATTGAACTTGAAGGTTTTTGTGGACAGATAGCAATTGTCGCCTTGTGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
64600 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * *
64620 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
64685 TGTAAATTTTGATAAGCCCTT
66 TGTAAA-TTTGATATGCCCTT
* * * * * *
64706 TAGCTGAATGGAATTGAACTCGAAGATTTTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* *
64771 TATAAATTTGATATGGCCTT
66 TGTAAATTTGATATGCCCTT
*
64791 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * *
64856 TTTAAATTTTATATGGCCTT
66 TGTAAATTTGATATGCCCTT
* *
64876 GAGCTGAATGGAATCGAACTCGAAGGTTGTTT-TTGACAGATAGCCCTTCTCTCCTTGAGCTATA
1 GAGCTGAATGGAATCGAACTCGAAGGTT-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
64940 CTGTAA
65 CTGTAA
64946 TACGCTTGGA
Statistics
Matches: 292, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
85 213 0.73
86 79 0.27
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCCTT
Found at i:64821 original size:171 final size:170
Alignment explanation
Indices: 64535--64938 Score: 585
Period size: 171 Copynumber: 2.4 Consensus size: 170
64525 CGCTGTCATC
* * ** * *
64535 GAGCTGAATGGAATTGAACTTGAAGGTTTTTGTGGACAGATAGCAATTGTCGCCTTGTGCTATGC
1 GAGCTGAATGGAATTGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* *
64600 TGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAACC
66 TATAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAAATAACC
64665 CTTCTCGCCTTAAGCTATGCTGTAAATTTTGATAAGCCCTT
131 CTTCTCGCCTTAAGCTATGCTGTAAATTTT-ATAAGCCCTT
* * * * *
64706 TAGCTGAATGGAATTGAACTCGAAGATTTTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGT
1 GAGCTGAATGGAATTGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * *
64771 TATAAATTTGATATGGCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAAATAGCC
66 TATAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAAATAACC
* * * *
64836 CTTCTCGCCTTGAGCTATGCTTTAAATTTTATATGGCCTT
131 CTTCTCGCCTTAAGCTATGCTGTAAATTTTATAAGCCCTT
* *
64876 GAGCTGAATGGAATCGAACTCGAAGGTTGTTT-TTGACAGATAGCCCTTCTCTCCTTGAGCTAT
1 GAGCTGAATGGAATTGAACTCGAAGGTT-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
64939 ACTGTAATAC
Statistics
Matches: 206, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
170 61 0.30
171 145 0.70
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (170 bp):
GAGCTGAATGGAATTGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TATAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAAATAACC
CTTCTCGCCTTAAGCTATGCTGTAAATTTTATAAGCCCTT
Found at i:68389 original size:75 final size:76
Alignment explanation
Indices: 68183--68391 Score: 269
Period size: 75 Copynumber: 2.8 Consensus size: 76
68173 CAAAGCCAAA
* * * **
68183 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
68248 TTGGCTCCGAG
66 TTGGCTCCGAG
* * *
68259 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
68323 TTTGTTCCGAG
66 TTGGCTCCGAG
* ** *
68334 AATTCCAGTATGCTCAGAGGGAACCGATTCCCCACCCCAGG-GGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCC-CCATAGGAGGAACCGATTCCCCCCT
68392 GTTCAACGGT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
75 66 0.57
76 44 0.38
77 5 0.04
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (76 bp):
AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:74188 original size:21 final size:21
Alignment explanation
Indices: 74162--74201 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
74152 CCCCCTTTGA
*
74162 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
74183 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
74202 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:76551 original size:47 final size:47
Alignment explanation
Indices: 76492--76588 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
76482 AGTGTTAAAG
76492 TAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAATCTTAAAATTAC
1 TAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAATCTTAAAATTAC
76539 TAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAATCTTAAAATTAC
1 TAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAATCTTAAAATTAC
76586 TAA
1 TAA
76589 AATGTTTTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (47 bp):
TAAGGGGGAGTAATTTCAAAACTTGATTTCAAAAATCTTAAAATTAC
Found at i:76998 original size:75 final size:75
Alignment explanation
Indices: 76848--77031 Score: 242
Period size: 75 Copynumber: 2.4 Consensus size: 75
76838 CAAAGCCAAA
* * * * **
76848 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
76913 TTGGCACCGAG
65 TTGGCACCGAG
* * *
76924 ATTTCCAGAATGCTCGGAGGGAACCTATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* **
76989 TTGTTCCGAG
66 TGGCACCGAG
*
76999 AATTCCAGTATGCTCGGAGGGAACCGATTCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCC
77032 ACCCCAGGGG
Statistics
Matches: 93, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 69 0.74
76 24 0.26
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCACCGAG
Found at i:79497 original size:319 final size:319
Alignment explanation
Indices: 78819--79779 Score: 1654
Period size: 321 Copynumber: 3.0 Consensus size: 319
78809 TCTATTACTC
*
78819 ACCATTGCAGGCTAAAAGAATTGTACCAGTGCATCTATCGAATTCAGTAAGGGAGCTCTTCCGGC
1 ACCATTGCAGGTTAAAAGAATTGTACCAGTGCATCTATCGAATTCAGTAAGGGAGCTCTTCCGGC
* * * * *
78884 GTAGTTTACAGTGTATGATATATGTGATTAGGGGTCATGTAATTATATTTTGTTTTATATATGAG
66 GTAGTTT-CAGAGTATGGTACATATGATTAGGGGGCATGTAATTATATTTTGTTTTATATATGAG
*
78949 TCTGAAAATCTGGTTTATTTCGAATACTAATAACTTTTATTTTGTACTCATAAATAATATTATGA
130 TCTGAAAATCTGGTTTATTTCGAATACTAATAACTTTTATTTTGTACTCATAAATAATTTTATGA
** *
79014 GTTTACAAGTTTTAAGAAAAAATTTAAATTTTCTGCTATTTTTACGGTGGGTCGCTCCAGTGGCC
195 GTTTACAAGTTTTAAGAAAAGTTTTAATTTTTC-GCTATTTTTACGGTGGGTCGCTCCAGTGGCC
* * *
79079 CTAATATGACACTCCAGATCGGATCAGGCTATCCGCATCAGTTTGAGGGGGTTACATTTAG
259 CTAATGTGACACTCCAGATCGGATCGGGCTATCCGCATCGGTTTGAGGGGGTTACATTTAG
* *
79140 ACCATTACAGGTTAAAAGAATTGTACCAATGCATCTATCGAATTCAGTAAGGGAGCTCTTCCGGC
1 ACCATTGCAGGTTAAAAGAATTGTACCAGTGCATCTATCGAATTCAGTAAGGGAGCTCTTCCGGC
79205 GTAGTTTGCAGAGTATGGTACATATGATTAGGGGGCATGTAATTATATTTTGTTTTATATATGAG
66 GTAGTTT-CAGAGTATGGTACATATGATTAGGGGGCATGTAATTATATTTTGTTTTATATATGAG
79270 TCTGAAAATCTGGTTTATTTCGAATACTAATAAC-TTTATTTTGTACTCATAAATAATTTTATGA
130 TCTGAAAATCTGGTTTATTTCGAATACTAATAACTTTTATTTTGTACTCATAAATAATTTTATGA
79334 GTTTACAAGTTTTAAGAAAAGTTTTAATTTTTCGCTATTTTTACGGTGGGTCGCTCCAGTGGCCC
195 GTTTACAAGTTTTAAGAAAAGTTTTAATTTTTCGCTATTTTTACGGTGGGTCGCTCCAGTGGCCC
*
79399 TAATGTGACACTCCAGATCGGATCGGGCTATCCTCATCGGTTTGAGGGGGTTACATTTAG
260 TAATGTGACACTCCAGATCGGATCGGGCTATCCGCATCGGTTTGAGGGGGTTACATTTAG
* *
79459 ACCATTGGAGGTTAAAAGAATTGTACCAGTGCATCTATCGAATTTAGTAAGGGAGCTCTTCCGGC
1 ACCATTGCAGGTTAAAAGAATTGTACCAGTGCATCTATCGAATTCAGTAAGGGAGCTCTTCCGGC
*
79524 GTAGTTTCTAGAGTATGGTACATATGATTAGGGGGAATGTAATTATATTTTGTTTTATATATGAG
66 GTAGTTTC-AGAGTATGGTACATATGATTAGGGGGCATGTAATTATATTTTGTTTTATATATGAG
79589 TCTGAAAATCTGGTTTATTTCGAATACTAATAACTTTTATTTTGTACTCATAAATAATTTTATGA
130 TCTGAAAATCTGGTTTATTTCGAATACTAATAACTTTTATTTTGTACTCATAAATAATTTTATGA
* * * *
79654 GTTTACAAGTTTTAAGAAAAGTTCTAAATTTTCCGCTATTTTTACGGTGGGTCACTCCGGTGGCC
195 GTTTACAAGTTTTAAGAAAAGTT-TTAATTTTTCGCTATTTTTACGGTGGGTCGCTCCAGTGGCC
*
79719 CTAATGTGACACTCCAGATCGGATCGGGCTATCCGCATCGATTTGAGGGGGTTACATTTAG
259 CTAATGTGACACTCCAGATCGGATCGGGCTATCCGCATCGGTTTGAGGGGGTTACATTTAG
79780 TGGTATCAGA
Statistics
Matches: 609, Mismatches: 28, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
318 1 0.00
319 245 0.40
320 112 0.18
321 251 0.41
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (319 bp):
ACCATTGCAGGTTAAAAGAATTGTACCAGTGCATCTATCGAATTCAGTAAGGGAGCTCTTCCGGC
GTAGTTTCAGAGTATGGTACATATGATTAGGGGGCATGTAATTATATTTTGTTTTATATATGAGT
CTGAAAATCTGGTTTATTTCGAATACTAATAACTTTTATTTTGTACTCATAAATAATTTTATGAG
TTTACAAGTTTTAAGAAAAGTTTTAATTTTTCGCTATTTTTACGGTGGGTCGCTCCAGTGGCCCT
AATGTGACACTCCAGATCGGATCGGGCTATCCGCATCGGTTTGAGGGGGTTACATTTAG
Found at i:83936 original size:85 final size:85
Alignment explanation
Indices: 83785--84037 Score: 380
Period size: 85 Copynumber: 3.0 Consensus size: 85
83775 GGATATGACA
* * * * *
83785 GTAAATTTGATATGCCCTTGAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTAACAAATAGCCC
1 GTAAATTTGATATGGCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCC
*
83850 TTCTCGCTTTGAGCTATGCT
66 TTCTCGCCTTGAGCTATGCT
*
83870 GTAAATTTGATATGGCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAACCC
1 GTAAATTTGATATGGCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCC
83935 TTCTCGCCTTGAGCTATGCT
66 TTCTCGCCTTGAGCTATGCT
* * * *
83955 TTAAATTTGATATGGCCTTGAGCTGAATGAAATTGAACTCGAAGGTTGTTTTTTGACAGATAACC
1 GTAAATTTGATATGGCCTTGAGCTGAATGGAATCGAACTCGAAGGTT-TTTGTTGACAGATAACC
* *
84020 CTTTTCTCCTTGAGCTAT
65 CTTCTCGCCTTGAGCTAT
84038 ATTGTAATAG
Statistics
Matches: 153, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 121 0.79
86 32 0.21
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (85 bp):
GTAAATTTGATATGGCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAACCC
TTCTCGCCTTGAGCTATGCT
Found at i:88179 original size:19 final size:20
Alignment explanation
Indices: 88136--88179 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
88126 AATAAAGTAT
* **
88136 TATTGAATTTTAAGATTTTA
1 TATTCAATTTTAAGATTAAA
88156 TATTCAATTTTAA-ATTAAA
1 TATTCAATTTTAAGATTAAA
88175 TATTC
1 TATTC
88180 GACTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (20 bp):
TATTCAATTTTAAGATTAAA
Found at i:95388 original size:21 final size:20
Alignment explanation
Indices: 95364--95420 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 20
95354 ATCCTCGCTA
95364 TGTATCGATACACTATGAATG
1 TGTATCGATACACT-TGAATG
*
95385 TGTA-CTGATACATTCTTTAATG
1 TGTATC-GATACA--CTTGAATG
*
95407 TGCATCGATACACT
1 TGTATCGATACACT
95421 CAAGAGTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
20 3 0.10
21 10 0.33
22 14 0.47
23 3 0.10
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTATCGATACACTTGAATG
Found at i:95776 original size:64 final size:64
Alignment explanation
Indices: 95699--95843 Score: 195
Period size: 64 Copynumber: 2.3 Consensus size: 64
95689 GCACCATCTA
** * *
95699 ATGCATCGATGCAC-CCTTGAATAAATTGAATTTCGAATGCATTTTGTGTACCGATGCACA-AGG
1 ATGCATCGATGCACTCC-TGAATAAATTGAACATCGAATGCATTTTATGTACCGATGCACAGA-C
95762 C
64 C
** *
95763 ATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGTATTTTATGTACCGATGCACAGACC
1 ATGCATCGATGCACTCCTGAATAAATTGAACATCGAATGCATTTTATGTACCGATGCACAGACC
95827 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
95844 AGGCTTATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 69 0.96
65 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTGAATAAATTGAACATCGAATGCATTTTATGTACCGATGCACAGACC
Found at i:95855 original size:64 final size:65
Alignment explanation
Indices: 95679--95886 Score: 183
Period size: 64 Copynumber: 3.2 Consensus size: 65
95669 TTTCAAAGTA
* * * * ** ** *
95679 GTGTACCGATGCACCATCTAATGCATCGATGCAC-CCTTGAATAAATTG-AATTTCGAATGCATT
1 GTGTACCGATGCACAAGC-CATGCATCGATGCACTCC-GGAATATTTTGAAACATCGAATGTATT
95742 TT
64 TT
* *
95744 GTGTACCGATGCACAAGGCATGCATCGATGCACTCCTGAATATTTTG-AACATCGAATGTATTTT
1 GTGTACCGATGCACAAGCCATGCATCGATGCACTCCGGAATATTTTGAAACATCGAATGTATTTT
* ** * *
95808 ATGTACCGATGCAC-AGACCATGCATCGATGCACTCCAGGCTTA-TTTGAAAGATCAAATGTATT
1 GTGTACCGATGCACAAG-CCATGCATCGATGCACTCC-GGAATATTTTGAAACATCGAATGTATT
95871 TT
64 TT
* *
95873 GCGTATCGATGCAC
1 GTGTACCGATGCAC
95887 CCTTAGTGTA
Statistics
Matches: 120, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.02
64 72 0.60
65 46 0.38
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (65 bp):
GTGTACCGATGCACAAGCCATGCATCGATGCACTCCGGAATATTTTGAAACATCGAATGTATTTT
Found at i:98845 original size:13 final size:12
Alignment explanation
Indices: 98825--98852 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
98815 GGGGAGTAAT
98825 TTTTAAAAATGA
1 TTTTAAAAATGA
98837 TTTTAAAAATGA
1 TTTTAAAAATGA
98849 TTTT
1 TTTT
98853 CAAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
TTTTAAAAATGA
Done.