Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006402.1 Hibiscus syriacus cultivar Beakdansim tig00015435_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: 116101
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:2293 original size:12 final size:12
Alignment explanation
Indices: 2276--2334 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
2266 CACATAAGCA
2276 AATGTTATATTT
1 AATGTTATATTT
2288 AATGTTATATTT
1 AATGTTATATTT
*
2300 GAA--TTATCTTT
1 -AATGTTATATTT
**
2311 --TCATATATTT
1 AATGTTATATTT
2321 AATGTTATATTT
1 AATGTTATATTT
2333 AA
1 AA
2335 ATTAACATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
10 6 0.16
11 7 0.19
12 22 0.59
13 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (12 bp):
AATGTTATATTT
Found at i:2439 original size:16 final size:16
Alignment explanation
Indices: 2418--2449 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2408 AAAAAAATGT
*
2418 GTTTTGCATAATGCAC
1 GTTTTGCATAAAGCAC
2434 GTTTTGCATAAAGCAC
1 GTTTTGCATAAAGCAC
2450 CTTTGCTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (16 bp):
GTTTTGCATAAAGCAC
Found at i:15929 original size:21 final size:21
Alignment explanation
Indices: 15904--15951 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
15894 GAATTATTTA
15904 CAGGTTTAATCAATTACAAGT
1 CAGGTTTAATCAATTACAAGT
15925 CAGGTTTAATCAATTACAAGT
1 CAGGTTTAATCAATTACAAGT
15946 CAGGTT
1 CAGGTT
15952 GAGTAATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
CAGGTTTAATCAATTACAAGT
Found at i:19157 original size:28 final size:28
Alignment explanation
Indices: 19125--19202 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
19115 TTTTTAAACT
*
19125 TTAAATTAAACCATAAAACCCTCTAATC
1 TTAAATCAAACCATAAAACCCTCTAATC
* * *
19153 TTAAATCATACCCTATAACCCTCTAATC
1 TTAAATCAAACCATAAAACCCTCTAATC
* * *
19181 TTAAATCATACCCTATAACCCT
1 TTAAATCAAACCATAAAACCCT
19203 TATGTCCGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (28 bp):
TTAAATCAAACCATAAAACCCTCTAATC
Found at i:19510 original size:27 final size:27
Alignment explanation
Indices: 19473--19529 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
19463 ATCAAAATAA
* * *
19473 AAATAAAAAAATTAAATTTTAATGATT
1 AAATAAAAAAAATAAACTTTAATGACT
* *
19500 AAATTAAAAAAATAGACTTTAATGACT
1 AAATAAAAAAAATAAACTTTAATGACT
19527 AAA
1 AAA
19530 ATAAGAGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (27 bp):
AAATAAAAAAAATAAACTTTAATGACT
Found at i:19531 original size:28 final size:28
Alignment explanation
Indices: 19469--19531 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
19459 AGTGATCAAA
* *
19469 ATAAAAATAAAAAAATTAAATTTTAATG
1 ATAAAATTAAAAAAATTAAACTTTAATG
* *
19497 ATTAAATTAAAAAAA-TAGACTTTAATG
1 ATAAAATTAAAAAAATTAAACTTTAATG
19524 ACTAAAAT
1 A-TAAAAT
19532 AAGAGTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (28 bp):
ATAAAATTAAAAAAATTAAACTTTAATG
Found at i:27042 original size:29 final size:25
Alignment explanation
Indices: 26986--27036 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
26976 AAGTTCTTTA
*
26986 TTTACTTTTACAGCATGTTTCTATC
1 TTTACTGTTACAGCATGTTTCTATC
27011 TTTACTGTTACAGCATGTTTCTATC
1 TTTACTGTTACAGCATGTTTCTATC
27036 T
1 T
27037 ATCTTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (25 bp):
TTTACTGTTACAGCATGTTTCTATC
Found at i:33328 original size:43 final size:43
Alignment explanation
Indices: 33281--33365 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
33271 TTGTGATTTA
* * *
33281 TAGTGGTGTTTTTATCTACAAATGCCGCTAATTATCTTGTCTT
1 TAGTGGCGTTTTTAGCCACAAATGCCGCTAATTATCTTGTCTT
* * *
33324 TAGTGGCGTTTTTGGCCACAAATGCTGCTAATTCTCTTGTCT
1 TAGTGGCGTTTTTAGCCACAAATGCCGCTAATTATCTTGTCT
33366 ATAATGACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (43 bp):
TAGTGGCGTTTTTAGCCACAAATGCCGCTAATTATCTTGTCTT
Found at i:33398 original size:42 final size:43
Alignment explanation
Indices: 33296--33398 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
33286 GTGTTTTTAT
* * *
33296 CTACAAATGCCGCTAATTATCTTGTCTTTAGTGGCGTTTTTGG
1 CTACAAATGCCGCTAATTATCTTGTCTATAATGACGTTTTTGG
* * * *
33339 CCACAAATGCTGCTAATTCTCTTGTCTATAATGAC-TTTTTTG
1 CTACAAATGCCGCTAATTATCTTGTCTATAATGACGTTTTTGG
* *
33381 CTACAAACGCCGTTAATT
1 CTACAAATGCCGCTAATT
33399 GTATTATTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 20 0.41
43 29 0.59
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (43 bp):
CTACAAATGCCGCTAATTATCTTGTCTATAATGACGTTTTTGG
Found at i:35505 original size:20 final size:20
Alignment explanation
Indices: 35482--35533 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
35472 AACGCGATCC
35482 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
35502 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
35522 CCAAAATCGCAA
1 CCAGAATCGCAA
35534 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:35672 original size:60 final size:60
Alignment explanation
Indices: 35589--35782 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
35579 GATTTTCCAT
* ** * *
35589 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
35649 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
35709 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT--AAATCGCAACGCGTATCCGTA
35771 AATCGCAACGCG
1 AATCGCAACGCG
35783 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
62 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:35683 original size:20 final size:20
Alignment explanation
Indices: 35589--35782 Score: 212
Period size: 20 Copynumber: 9.6 Consensus size: 20
35579 GATTTTCCAT
* ** *
35589 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
35609 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
35629 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
35649 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
35669 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
35689 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
35709 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
35729 AATCGCAACG-ATAATACATAAA
1 AATCGCAACGCGT-ATCCGT--A
35751 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
35771 AATCGCAACGCG
1 AATCGCAACGCG
35783 ATATTTAAAG
Statistics
Matches: 145, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
19 2 0.01
20 125 0.86
21 2 0.01
22 15 0.10
23 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:36202 original size:33 final size:33
Alignment explanation
Indices: 36163--36233 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
36153 TTCACTTAGA
*
36163 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
36196 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
36229 TTTCA
1 TTTCA
36234 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:36396 original size:14 final size:14
Alignment explanation
Indices: 36377--36466 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
36367 TTTGGTTTCG
36377 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36391 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
36410 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36424 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
36441 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
36457 CGTTGCGATT
1 CGTTGCGATT
36467 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36402 original size:33 final size:33
Alignment explanation
Indices: 36360--36474 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
36350 ACTGTCGCAA
**
36360 TTGCGATTTTGGTTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36393 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
36426 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36459 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
36475 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:38369 original size:87 final size:92
Alignment explanation
Indices: 38161--38525 Score: 596
Period size: 88 Copynumber: 4.1 Consensus size: 92
38151 TAGATTGCTT
*
38161 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-A-ACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
38224 -TT-TCTTTG-TTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38249 AGTAAATTTG-TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAA-A-TAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAATAGTAT
38311 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
38338 AGTAAATTTGTTCGGTTGCTGCCAA-T-T-CTAAACTGTGTATTCTTTAACACTG-AAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAATAGTAT
38399 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
38426 AGTAAATTTGTTCGGTTGCTGCCAATTCTG--AAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
38489 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38517 AGTAAATTT
1 AGTAAATTT
38526 ATCCATTCAA
Statistics
Matches: 261, Mismatches: 3, Indels: 23
0.91 0.01 0.08
Matches are distributed among these distances:
86 4 0.02
87 66 0.25
88 74 0.28
89 58 0.22
90 15 0.06
91 44 0.17
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:38609 original size:19 final size:19
Alignment explanation
Indices: 38569--38697 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
38559 TAGTTTACTT
* *
38569 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
38589 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
38608 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
38627 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
38641 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
38660 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
38674 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
38693 TCGCA
1 TCGCA
38698 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:38648 original size:33 final size:32
Alignment explanation
Indices: 38605--38697 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
38595 CGCGAAACCA
**
38605 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
38637 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
38670 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
38698 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:38695 original size:52 final size:52
Alignment explanation
Indices: 38569--38697 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
38559 TAGTTTACTT
**
38569 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
38621 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
38674 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
38698 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:38715 original size:19 final size:19
Alignment explanation
Indices: 38693--38827 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
38683 GAAACCAAAA
*
38693 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
38712 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
38728 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
38745 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
38761 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
38778 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
38797 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
38817 TCGTGTTGCGA
1 TCGCGTTGCGA
38828 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:38734 original size:14 final size:14
Alignment explanation
Indices: 38715--38771 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38705 TTTCATTTCG
38715 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
38729 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
38746 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
38762 CGTTGCGATT
1 CGTTGCGATT
38772 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:38740 original size:33 final size:33
Alignment explanation
Indices: 38698--38790 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
38688 CAAAATCGCA
*
38698 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
38731 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
38764 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
38791 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:40880 original size:19 final size:19
Alignment explanation
Indices: 40864--40964 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
40854 AAAAATGACT
40864 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40883 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40902 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
40916 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40935 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
40954 ATCGCAATGCG
1 ATCGCAATGCG
40965 TTTATAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 51 0.69
20 6 0.08
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:41067 original size:19 final size:19
Alignment explanation
Indices: 40993--41295 Score: 340
Period size: 19 Copynumber: 17.4 Consensus size: 19
40983 GATTATCTCG
40993 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41012 -TGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41029 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
41043 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41062 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41081 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41100 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41119 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
41133 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41152 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41171 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41185 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41203 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41222 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41236 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
41255 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
41269 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
41288 TTGCGATT
1 TTGCGATT
41296 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 10, Indels: 54
0.79 0.03 0.17
Matches are distributed among these distances:
14 35 0.14
15 6 0.02
16 31 0.13
17 35 0.14
18 17 0.07
19 118 0.48
20 5 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:41137 original size:52 final size:51
Alignment explanation
Indices: 40993--41267 Score: 371
Period size: 52 Copynumber: 5.3 Consensus size: 51
40983 GATTATCTCG
*
40993 TTGCGATTTTCATTTCGCA-TGCGATTTCATTTCGCATTGCGA-TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTCATTTCGCA
*
41043 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGA-TTTCATTTCGCA
* *
41100 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCA
41152 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCA
41203 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTT-CGCA
41255 TTGCGATTTTCAT
1 TTGCGATTTTCAT
41268 GTTGGGATTT
Statistics
Matches: 213, Mismatches: 4, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
50 19 0.09
51 64 0.30
52 91 0.43
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (51 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCA
Found at i:41144 original size:90 final size:87
Alignment explanation
Indices: 40971--41267 Score: 357
Period size: 90 Copynumber: 3.4 Consensus size: 87
40961 TGCGTTTATA
*
40971 ATTTCGCATTGCGA-TT-ATCTCG--TTGCGATTTTCATTTCGCA-TGCGATTTCATTTCGCATT
1 ATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATT
41031 GCGATTCTTTCGTTGCGATTTTC
66 GCGATTC-TTCGTTGCGATTTTC
*
41054 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCA
1 ATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCA
41119 TTGCGATTCTGTCGTTGCGATTTTC
64 TTGCGATTCT-TCGTTGCGATTTTC
*
41144 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTCATTTCGCAT
1 ATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCAT
* * *
41204 TGCGATT-TTCATTTCGCA-TTGC
65 TGCGATTCTTCGTTGCG-ATTTTC
* *
41226 GATTCTCTCGTTGCGATTTCATTTCCGCATTGCGATTTTCAT
1 -ATT-TCGCATTGCGATTTCATTT-CGCATTGCGATTTTCAT
41268 GTTGGGATTT
Statistics
Matches: 190, Mismatches: 9, Indels: 26
0.84 0.04 0.12
Matches are distributed among these distances:
82 9 0.05
83 27 0.14
84 38 0.20
85 8 0.04
86 8 0.04
87 5 0.03
88 22 0.12
89 6 0.03
90 67 0.35
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (87 bp):
ATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATT
GCGATTCTTCGTTGCGATTTTC
Found at i:41243 original size:33 final size:33
Alignment explanation
Indices: 40971--41295 Score: 231
Period size: 33 Copynumber: 9.5 Consensus size: 33
40961 TGCGTTTATA
*
40971 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
41004 ATTTCGCA-TGCGATTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTC
*
41038 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
* *
41073 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
*
41111 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
41144 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
41184 GTTGCG-ATTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
41214 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
41246 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
*
41280 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
41296 GTATTTTCCG
Statistics
Matches: 248, Mismatches: 20, Indels: 48
0.78 0.06 0.15
Matches are distributed among these distances:
30 6 0.02
31 5 0.02
32 29 0.12
33 97 0.39
34 18 0.07
35 10 0.04
36 20 0.08
38 52 0.21
39 5 0.02
40 6 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:43590 original size:189 final size:183
Alignment explanation
Indices: 43277--43649 Score: 649
Period size: 189 Copynumber: 2.0 Consensus size: 183
43267 CTCTTTGCAA
43277 TCATACGCCACGTACAGTTTTGTCAATCATACACCTTGTTTCGAAACGATCTTGCTGATTTGTTA
1 TCATACGCCACGTACAGTTTTGTCAATCATACACCTTGTTTCGAAACGATCTTGCTGATTTGTTA
*
43342 ACTTTAGTTGATAGCCTCTTCCACATTTCGTATATAAGCTATCTTCAAGTCTTCCTTTGTATCAA
66 ACTTTAGTTGATAGCCTCTTCCACATTTCGTATAAAAGCTATCTTCAAGTCTTCCTTTGTATCAA
43407 AACAAT-ATCTTTCTTGATACGAATAACTTTGTGTAACAATCAAATGCTTTCT
131 AACAATCATCTTTCTTGATACGAATAACTTTGTGTAACAATCAAATGCTTTCT
*
43459 TCATACGCCACGTACATTTTTTGTCAATCATACACCTTGTTTCGAAACGATCTTTGCTTGATTTG
1 TCATACGCCACGTACA-GTTTTGTCAATCATACACCTTGTTTCGAAACGATC-TTGC-TGATTTG
43524 TTAACTTTTAGTTGATAGCCATCTTCCACACATTTCGTATAAAAGCTATCTTCAAGTCTTCCTTT
63 TTAAC-TTTAGTTGATAGCC-TCTT-C-CACATTTCGTATAAAAGCTATCTTCAAGTCTTCCTTT
*
43589 GTATCAAAACAATCATCTTTCTTGATACGAATAACTTTGTGTAACAATCAACTGCTTTCT
124 GTATCAAAACAATCATCTTTCTTGATACGAATAACTTTGTGTAACAATCAAATGCTTTCT
43649 T
1 T
43650 TATCAACTCT
Statistics
Matches: 180, Mismatches: 3, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
182 16 0.09
183 34 0.19
184 4 0.02
185 12 0.07
186 14 0.08
187 4 0.02
188 1 0.01
189 49 0.27
190 46 0.26
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (183 bp):
TCATACGCCACGTACAGTTTTGTCAATCATACACCTTGTTTCGAAACGATCTTGCTGATTTGTTA
ACTTTAGTTGATAGCCTCTTCCACATTTCGTATAAAAGCTATCTTCAAGTCTTCCTTTGTATCAA
AACAATCATCTTTCTTGATACGAATAACTTTGTGTAACAATCAAATGCTTTCT
Found at i:43959 original size:24 final size:24
Alignment explanation
Indices: 43925--43971 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43915 CTGAAACATC
43925 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
43949 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
43972 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:44585 original size:20 final size:20
Alignment explanation
Indices: 44560--44868 Score: 281
Period size: 20 Copynumber: 16.2 Consensus size: 20
44550 AACGGATTGT
*
44560 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCTCGTTGC
*
44580 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCTCGTTGC
*
44600 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCTCGTTGC
*
44620 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCTCGTTGC
*
44640 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCTCGTTGC
*
44660 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCTCGTTGC
44680 GATTTAC-G-----CGTTGC
1 GATTTACGGATTCTCGTTGC
*
44694 GATTTACGGATTATCG-TGC
1 GATTTACGGATTCTCGTTGC
* *
44713 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCTCGTTGC
* *
44733 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCTCGTTGC
* *
44753 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCTCGTTGC
* * *
44773 GA-TTACGGATACGCATTGC
1 GATTTACGGATTCTCGTTGC
* *
44792 GATTT----A--C-C-ATAC
1 GATTTACGGATTCTCGTTGC
* *
44804 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCTCGTTGC
* *
44824 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCTCGTTGC
* *
44844 GATTTATAGGATTCGCGTTGC
1 GATTTA-CGGATTCTCGTTGC
44865 GATT
1 GATT
44869 AATACGCGTG
Statistics
Matches: 252, Mismatches: 20, Indels: 33
0.83 0.07 0.11
Matches are distributed among these distances:
12 7 0.03
13 1 0.00
14 14 0.06
15 1 0.00
16 2 0.01
18 1 0.00
19 36 0.14
20 174 0.69
21 16 0.06
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
GATTTACGGATTCTCGTTGC
Found at i:44615 original size:40 final size:40
Alignment explanation
Indices: 44560--44798 Score: 311
Period size: 40 Copynumber: 6.2 Consensus size: 40
44550 AACGGATTGT
44560 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGC
1 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGC
44600 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGC
1 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGC
44640 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGC
1 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGC
44680 GATTTAC-G-----CGTTGCGATTTACGGATTATCG-TGC
1 GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGC
* * * *
44713 GATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGC
1 GATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGC
* * *
44753 GATTTACGGATACGCGTTGCGA-TTACGGA-TA-CGCATTGC
1 GATTTACAGATTCTCGTTGCGATTTACGGATTATCG--TTGC
44792 GATTTAC
1 GATTTAC
44799 CATACGATTT
Statistics
Matches: 188, Mismatches: 1, Indels: 21
0.90 0.00 0.10
Matches are distributed among these distances:
33 10 0.05
34 23 0.12
37 2 0.01
38 2 0.01
39 39 0.21
40 112 0.60
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (40 bp):
GATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGC
Found at i:44693 original size:14 final size:14
Alignment explanation
Indices: 44674--44701 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44664 TACGGATTAT
44674 CGTTGCGATTTACG
1 CGTTGCGATTTACG
44688 CGTTGCGATTTACG
1 CGTTGCGATTTACG
44702 GATTATCGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (14 bp):
CGTTGCGATTTACG
Found at i:44893 original size:11 final size:12
Alignment explanation
Indices: 44877--44905 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
44867 TTAATACGCG
44877 TGCGATTTGTA-
1 TGCGATTTGTAC
44888 TGCGATTTGTAC
1 TGCGATTTGTAC
44900 TGCGAT
1 TGCGAT
44906 CGCGATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (12 bp):
TGCGATTTGTAC
Found at i:44989 original size:20 final size:20
Alignment explanation
Indices: 44956--45006 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
44946 TGCGATTGCG
44956 TTGCGATT-TGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
44975 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
44995 TTGCGATTCTGG
1 TTGCGATTCTGG
45007 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:46774 original size:23 final size:23
Alignment explanation
Indices: 46748--46792 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
46738 CACCACAGCT
*
46748 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
46771 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
46793 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:47030 original size:149 final size:149
Alignment explanation
Indices: 46768--47072 Score: 556
Period size: 149 Copynumber: 2.0 Consensus size: 149
46758 CACCGAAGTG
*
46768 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
* *
46833 GATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
46898 ATATATATATCCCGAAAGA
131 ATACATATATCCCGAAAGA
46917 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
46982 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
* *
47047 ATACATATGTCCCGAAGGA
131 ATACATATATCCCGAAAGA
47066 CCGCGTA
1 CCGCGTA
47073 AACCCTCTAC
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
ATACATATATCCCGAAAGA
Found at i:47662 original size:64 final size:63
Alignment explanation
Indices: 47529--47685 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
47519 TAATGAGGGT
* * * ** *
47529 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
47593 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
47655 G
63 G
*
47656 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
47686 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:49034 original size:2 final size:2
Alignment explanation
Indices: 49029--49067 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
49019 ACACGTGTAT
*
49029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49068 CAACCTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:49138 original size:32 final size:32
Alignment explanation
Indices: 49076--49138 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
49066 ATCAACCTAT
* *
49076 ATGATTCTTTAAGAAAGTTCAAATACATTAAA
1 ATGATTCTTTAAGAAAATTCAAATAAATTAAA
* *
49108 ATGATTGTTTTAGAAAATT-AAATGAAATTAA
1 ATGATTCTTTAAGAAAATTCAAAT-AAATTAA
49139 TTCAAAGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.37
Consensus pattern (32 bp):
ATGATTCTTTAAGAAAATTCAAATAAATTAAA
Found at i:69487 original size:2 final size:2
Alignment explanation
Indices: 69480--69511 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
69470 AATAAAAATA
69480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69512 TTGAGTGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69743 original size:23 final size:23
Alignment explanation
Indices: 69685--69744 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
69675 CTTGGACCCC
*
69685 TATAAATATATATAAAATTTACT
1 TATATATATATATAAAATTTACT
* * * *
69708 AATGT-TCTAATATAAAATTTATT
1 TATATATAT-ATATAAAATTTACT
69731 TATATATATATATA
1 TATATATATATATA
69745 TATATAAAAG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATATATATATAAAATTTACT
Found at i:72994 original size:12 final size:12
Alignment explanation
Indices: 72977--73021 Score: 90
Period size: 12 Copynumber: 3.8 Consensus size: 12
72967 TATACTGCTT
72977 ATGTTTGAATTA
1 ATGTTTGAATTA
72989 ATGTTTGAATTA
1 ATGTTTGAATTA
73001 ATGTTTGAATTA
1 ATGTTTGAATTA
73013 ATGTTTGAA
1 ATGTTTGAA
73022 AATGTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (12 bp):
ATGTTTGAATTA
Found at i:75157 original size:23 final size:23
Alignment explanation
Indices: 75131--75179 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
75121 ATAACTTAAA
* * *
75131 AAATAATTTTAAAATTTAAGATG
1 AAATAATTTGAAAATTAAAAATG
75154 AAATAATTTGAAAATTAAAAATG
1 AAATAATTTGAAAATTAAAAATG
75177 AAA
1 AAA
75180 GTCTTAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (23 bp):
AAATAATTTGAAAATTAAAAATG
Found at i:76500 original size:58 final size:59
Alignment explanation
Indices: 76356--76503 Score: 144
Period size: 59 Copynumber: 2.5 Consensus size: 59
76346 AAAAGTTTTG
* * * *
76356 GGACCAATTTAGAATGAGGA-TCATAGTGTTG-GTATGAAATTGGAATGTTAAAAAATTGAA
1 GGACTAATTTAGAATGA-GATTCATAGT-TTGTG-GTGAAATTAGAATATTAAAAAATTGAA
* * *
76416 GGACTAATTTAGAATGAGATTCATAGTTTGTGGTGAAATTAGAATATTCAAAATTTTAA
1 GGACTAATTTAGAATGAGATTCATAGTTTGTGGTGAAATTAGAATATTAAAAAATTGAA
*
76475 GGA-TCAATTT-GAATGA-AGTTGATAGTTTG
1 GGACT-AATTTAGAATGAGA-TTCATAGTTTG
76504 GGGACATATG
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
57 1 0.01
58 17 0.22
59 34 0.45
60 24 0.32
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (59 bp):
GGACTAATTTAGAATGAGATTCATAGTTTGTGGTGAAATTAGAATATTAAAAAATTGAA
Found at i:80555 original size:2 final size:2
Alignment explanation
Indices: 80548--80572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
80538 CGTGAAAGGA
80548 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
80573 ATGGTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86750 original size:23 final size:23
Alignment explanation
Indices: 86720--86765 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
86710 TGCATCCGTA
86720 TCCTTGGCCTACACCTGATGGTG
1 TCCTTGGCCTACACCTGATGGTG
86743 TCCTTGGCCTACACCTGATGGTG
1 TCCTTGGCCTACACCTGATGGTG
86766 GTCTTACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.30, G:0.26, T:0.30
Consensus pattern (23 bp):
TCCTTGGCCTACACCTGATGGTG
Found at i:90150 original size:12 final size:12
Alignment explanation
Indices: 90133--90187 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
90123 GACAAGCACA
90133 AGGTGGTAGAGG
1 AGGTGGTAGAGG
90145 AGGTGGTAGAGG
1 AGGTGGTAGAGG
* *
90157 AGGAGGCAGAGG
1 AGGTGGTAGAGG
*
90169 TGGTGGTAGAGG
1 AGGTGGTAGAGG
*
90181 TGGTGGT
1 AGGTGGT
90188 GGATTTCGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.22, C:0.02, G:0.58, T:0.18
Consensus pattern (12 bp):
AGGTGGTAGAGG
Found at i:93821 original size:29 final size:29
Alignment explanation
Indices: 93779--93872 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
93769 GAATTCTACA
93779 GCGACCTTGGAGGTCGCCATGGCATCCGG
1 GCGACCTTGGAGGTCGCCATGGCATCCGG
93808 GCGACCTTGGAGGTCGCCATGGCATCCGG
1 GCGACCTTGGAGGTCGCCATGGCATCCGG
*
93837 GCGACCTTGGAGGTCGCCATGGCATCCGA
1 GCGACCTTGGAGGTCGCCATGGCATCCGG
93866 GCGACCT
1 GCGACCT
93873 GTGTGGTGTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.15, C:0.32, G:0.36, T:0.17
Consensus pattern (29 bp):
GCGACCTTGGAGGTCGCCATGGCATCCGG
Found at i:93968 original size:20 final size:20
Alignment explanation
Indices: 93943--93980 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
93933 GTATTGGAGC
*
93943 ATGCATGGGGGAGTTGTGGG
1 ATGCATGGGGGAGCTGTGGG
*
93963 ATGCATGTGGGAGCTGTG
1 ATGCATGGGGGAGCTGTG
93981 CATGGGACGT
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:0.16, C:0.08, G:0.50, T:0.26
Consensus pattern (20 bp):
ATGCATGGGGGAGCTGTGGG
Found at i:93992 original size:20 final size:20
Alignment explanation
Indices: 93969--94006 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
93959 TGGGATGCAT
*
93969 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
93989 GTGGGAACTGTGCATGGG
1 GTGGGAACTGTGCATGGG
94007 CCATGCACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.50, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:94561 original size:21 final size:21
Alignment explanation
Indices: 94536--94579 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
94526 AATCTAGTTA
94536 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
94557 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
94578 AT
1 AT
94580 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:94589 original size:28 final size:28
Alignment explanation
Indices: 94556--94616 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
94546 TAGTATAAAT
*
94556 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
94584 TATTAGTTTATTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
94612 TATTA
1 TATTA
94617 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (28 bp):
TATTAGTTTATTAGTTTAAGTTATATTA
Found at i:94675 original size:41 final size:45
Alignment explanation
Indices: 94578--94687 Score: 129
Period size: 48 Copynumber: 2.4 Consensus size: 45
94568 AGTTTAAGTT
94578 ATATTATATTAGTTTATTAGTTTAAGTTATATTATATTATATAAAAA
1 ATATTA-ATTAGTTTATTAGTTTAAGTTATATTATA-TATATAAAAA
*
94625 ATTAGTTAATTAGTTTCTTAGTTTAAG-T-TATTA-A-ATATAAAAA
1 A-TA-TTAATTAGTTTATTAGTTTAAGTTATATTATATATATAAAAA
* *
94668 ATATTAATTAATTTGTTAGT
1 ATATTAATTAGTTTATTAGT
94688 GTCTTTAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
41 15 0.26
42 2 0.03
43 10 0.17
45 1 0.02
46 5 0.09
47 2 0.03
48 20 0.34
49 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (45 bp):
ATATTAATTAGTTTATTAGTTTAAGTTATATTATATATATAAAAA
Found at i:95164 original size:20 final size:21
Alignment explanation
Indices: 95120--95164 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
95110 AAATATTGTG
**
95120 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
95141 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
95161 TTTA
1 TTTA
95165 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:95454 original size:26 final size:25
Alignment explanation
Indices: 95425--95483 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
95415 AAATCATATT
*
95425 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
95451 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
95477 ATTATTA
1 ATTATTA
95484 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:98386 original size:26 final size:26
Alignment explanation
Indices: 98312--98826 Score: 357
Period size: 26 Copynumber: 20.6 Consensus size: 26
98302 ATGTATTTAT
* *
98312 TAATCATTATAAAAATGATTTAATAA
1 TAATCATTATAATAATGATTTGATAA
* *
98338 TGAT--TTAAATATTTAATGATTTGATAA
1 TAATCATT--ATA-ATAATGATTTGATAA
*
98365 TAATCATTATAGTAATGATTTGATAA
1 TAATCATTATAATAATGATTTGATAA
98391 TAATCATTATAATAATGATTT-AGTAA
1 TAATCATTATAATAATGATTTGA-TAA
* *
98417 TAATCATTATAAAAATGATTTAATAA
1 TAATCATTATAATAATGATTTGATAA
* * * * *
98443 TGAT--TTA-AATATTTA-ATGAT-T
1 TAATCATTATAATAATGATTTGATAA
* * *
98464 TGATGATT-TAGTAATGATTTGATAA
1 TAATCATTATAATAATGATTTGATAA
*
98489 TAATCATTATAGTAATGATTTGATAA
1 TAATCATTATAATAATGATTTGATAA
98515 TAATCATTATAATAATGATTT-AGTAA
1 TAATCATTATAATAATGATTTGA-TAA
* *
98541 TAATCATTATAAAAATGATTTAATAA
1 TAATCATTATAATAATGATTTGATAA
* * * * *
98567 TGAT--TTA-AATATTTA-ATGAT-T
1 TAATCATTATAATAATGATTTGATAA
* * *
98588 TGATGATT-TAGTAATGATTTGATAA
1 TAATCATTATAATAATGATTTGATAA
*
98613 TAATCATTATAGTAATGATTTGATAA
1 TAATCATTATAATAATGATTTGATAA
98639 TAATCATTATAATAATGATTT-AGTAA
1 TAATCATTATAATAATGATTTGA-TAA
* *
98665 TAATCATTATAAAAATGATTTAATAA
1 TAATCATTATAATAATGATTTGATAA
* * * *
98691 TAAT--TTA-AATATTTA-ATGAT-T
1 TAATCATTATAATAATGATTTGATAA
* * *
98712 TGATGATT-TAGTAATGATTTGATAA
1 TAATCATTATAATAATGATTTGATAA
* *
98737 TAATTATTATAATAATGATTTTATAA
1 TAATCATTATAATAATGATTTGATAA
* * * *
98763 TAATTATT-TAGTTATTATTT-AGTAA
1 TAATCATTATAATAATGATTTGA-TAA
* * *
98788 TTAT--TTATAATAATGATTTAATAC
1 TAATCATTATAATAATGATTTGATAA
*
98812 TAATGATT-TAATAAT
1 TAATCATTATAATAAT
98827 TATTACTAAT
Statistics
Matches: 390, Mismatches: 65, Indels: 69
0.74 0.12 0.13
Matches are distributed among these distances:
21 11 0.03
22 9 0.02
23 38 0.10
24 38 0.10
25 44 0.11
26 227 0.58
27 21 0.05
29 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATCATTATAATAATGATTTGATAA
Found at i:98489 original size:124 final size:124
Alignment explanation
Indices: 98351--98810 Score: 809
Period size: 124 Copynumber: 3.7 Consensus size: 124
98341 TTTAAATATT
98351 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
1 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
98416 ATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAG
66 ATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAG
98475 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
1 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
98540 ATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAG
66 ATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAG
98599 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
1 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
*
98664 ATAATCATTATAAAAATGATTTAATAATAATTTAAATATTTAATGATTTGATGATTTAG
66 ATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAG
* * * * * * *
98723 TAATGATTTGATAATAATTATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTA
1 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
* *
98787 ATTAT--TTATAATAATGATTTAATA
66 ATAATCATTATAAAAATGATTTAATA
98811 CTAATGATTT
Statistics
Matches: 326, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
121 18 0.06
123 17 0.05
124 291 0.89
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
ATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAG
Found at i:98524 original size:150 final size:145
Alignment explanation
Indices: 98351--98694 Score: 412
Period size: 150 Copynumber: 2.3 Consensus size: 145
98341 TTTAAATATT
* *
98351 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
1 TAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGA-TT--TA
* * *
98416 ATAATCATTATAAAAATGATTTAAT-A-ATGATTTA-AAT-ATTTAATGATTTGATGATT-TAGT
62 ATAATCATT-T--AAAT-ATTTAATGATATGATTTAGAATGATTTAAT-A-ATAATCATTATAGT
*
98476 AATGATTTGATAATAATCATTATAG
121 AATGATTTGATAATAATCATTATAA
98501 TAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTAATA
1 TAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTAATA
* *
98566 ATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGA
65 ATCATTTAAATATTTAATGA--T-ATGATTTAG-AATGATTTAATAATAATCATTATAGTAATGA
98631 TTTGATAATAATCATTATAA
126 TTTGATAATAATCATTATAA
*
98651 TAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAATAAT
1 TAATGATTTGA-TAATAATCATTATAATAATGATTT-ATAATAAT
98695 TTAAATATTT
Statistics
Matches: 173, Mismatches: 9, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
143 7 0.04
144 5 0.03
146 1 0.01
147 10 0.06
148 8 0.05
149 10 0.06
150 125 0.72
151 7 0.04
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (145 bp):
TAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAATAA
TCATTTAAATATTTAATGATATGATTTAGAATGATTTAATAATAATCATTATAGTAATGATTTGA
TAATAATCATTATAA
Found at i:98525 original size:98 final size:100
Alignment explanation
Indices: 98312--98541 Score: 349
Period size: 98 Copynumber: 2.3 Consensus size: 100
98302 ATGTATTTAT
98312 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATAATAATCATTATAG
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTG-----AATCATTATAG
98377 TAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
61 TAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
98417 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTG-ATGATT-TAGTAATG
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGAATCATTATAGTAATG
*
98480 ATTTGATAATAATCATTATAGTAATGATTT-GATAA
66 ATTTGATAATAATCATTATAATAATGATTTAG-TAA
* *
98515 TAATCATTATAATAATGATTTAGTAAT
1 TAATCATTATAAAAATGATTTAATAAT
98542 AATCATTATA
Statistics
Matches: 120, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
97 1 0.01
98 65 0.54
99 5 0.04
105 49 0.41
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (100 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGAATCATTATAGTAATG
ATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:98797 original size:35 final size:37
Alignment explanation
Indices: 98756--98842 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
98746 TAATAATGAT
* * *
98756 TTTATAATAATTATTTAGT-T-ATTATTTAGTAATTA
1 TTTATAATAATTATTTAATATAATGATTTAATAATTA
*
98791 TTTATAATAATGATTTAATACTAATGATTTAATAATTA
1 TTTATAATAATTATTTAATA-TAATGATTTAATAATTA
98829 -TTACTAATAATTAT
1 TTTA-TAATAATTAT
98843 AGAATACTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (37 bp):
TTTATAATAATTATTTAATATAATGATTTAATAATTA
Found at i:98849 original size:38 final size:38
Alignment explanation
Indices: 98779--98852 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
98769 TTTAGTTATT
* **
98779 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
98817 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
98853 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:99058 original size:17 final size:17
Alignment explanation
Indices: 99033--99065 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
99023 ACTAAATATT
*
99033 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
99050 TAATGATTTGATACTA
1 TAATGATTTGATACTA
99066 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:99058 original size:25 final size:23
Alignment explanation
Indices: 98979--99058 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
98969 GATTTATTGT
98979 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
99000 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
99027 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
99049 GTAATGATTT
1 -TAAT-ATTT
99059 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:101241 original size:15 final size:14
Alignment explanation
Indices: 101218--101248 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
101208 TACAACACTA
101218 AACTTTAATATAAT
1 AACTTTAATATAAT
101232 AACTTATAATATAAT
1 AACTT-TAATATAAT
101247 AA
1 AA
101249 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:101256 original size:16 final size:16
Alignment explanation
Indices: 101223--101269 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
101213 CACTAAACTT
*
101223 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
101238 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
101254 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
101270 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:101390 original size:32 final size:34
Alignment explanation
Indices: 101310--101391 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
101300 TTAAACCCTT
*
101310 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
101343 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
101376 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
101392 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:101590 original size:41 final size:40
Alignment explanation
Indices: 101502--101590 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
101492 TTAACAAAAC
* *
101502 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
101543 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
101584 AAACTAA
1 AAACTAA
101591 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:102122 original size:29 final size:29
Alignment explanation
Indices: 102090--102164 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
102080 TCGTGAGCTA
** *
102090 GGACTACATGGCGACCTACTCGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCC
*
102119 GGACTACATGGCAACCTACAAGGTCGCCC
1 GGACTACATGGCGACCTACAAGGTCGCCC
* *
102148 AGACTGCATGGCGACCT
1 GGACTACATGGCGACCT
102165 CTCCATTGGC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.16
Consensus pattern (29 bp):
GGACTACATGGCGACCTACAAGGTCGCCC
Found at i:109634 original size:2 final size:2
Alignment explanation
Indices: 109627--109654 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
109617 CCATATGTTC
109627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
109655 TTGAATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109838 original size:32 final size:33
Alignment explanation
Indices: 109803--109871 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 33
109793 CCCAAAATAT
*
109803 TTTTTGATTAAAATAAGTATCTAAA--TTT-AT
1 TTTTTGATCAAAATAAGTATCTAAAGTTTTCAT
* *
109833 CTTTTTGGTCAAAATAGGTATCTAAAGTTTTCAT
1 -TTTTTGATCAAAATAAGTATCTAAAGTTTTCAT
109867 TTTTT
1 TTTTT
109872 TTCATCTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 22 0.69
33 8 0.25
34 2 0.06
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (33 bp):
TTTTTGATCAAAATAAGTATCTAAAGTTTTCAT
Found at i:110020 original size:30 final size:31
Alignment explanation
Indices: 109952--110060 Score: 103
Period size: 32 Copynumber: 3.5 Consensus size: 31
109942 AACTGATTAT
* * *
109952 TTTAGGTACCTATTTTGACTAAAAAATATAAA
1 TTTAGATACTTATTTTGACTAAAAAATAT-AC
*
109984 TTTAGATACTTATTTTGATTAAAAAA-ATAC
1 TTTAGATACTTATTTTGACTAAAAAATATAC
* ** **
110014 TTTAGATATTTAGATTGAGAAAAATAATATAC
1 TTTAGATACTTATTTTGACTAAAA-AATATAC
*
110046 TTTAGGTACTTATTT
1 TTTAGATACTTATTT
110061 ATAACATAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
30 20 0.32
31 4 0.06
32 38 0.61
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.42
Consensus pattern (31 bp):
TTTAGATACTTATTTTGACTAAAAAATATAC
Found at i:111028 original size:2 final size:2
Alignment explanation
Indices: 111021--111088 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
111011 CCAACTAAGC
111021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111063 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
111089 TTTAATGATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115231 original size:20 final size:20
Alignment explanation
Indices: 115206--115250 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
115196 GTCATCCAAT
115206 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCATACCGGA
115226 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCATACCGGA
115246 TTTTT
1 TTTTT
115251 TTCCGGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCATACCGGA
Done.