Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000397.1 Hibiscus syriacus cultivar Beakdansim tig00000730_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: 136917
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4880 original size:15 final size:15
Alignment explanation
Indices: 4860--4893 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4850 AAAATACAAC
4860 ATTCCCAGTAATCCT
1 ATTCCCAGTAATCCT
* *
4875 ATTCCCTGTAATCTT
1 ATTCCCAGTAATCCT
4890 ATTC
1 ATTC
4894 TCACTGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (15 bp):
ATTCCCAGTAATCCT
Found at i:5582 original size:25 final size:26
Alignment explanation
Indices: 5528--5582 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 26
5518 TAAACTACAC
* *
5528 TTTTATACAATAATTTTAAAAATTCG
1 TTTTATACAATAATTTTAAAAAGTCA
*
5554 TTTT-TACAAT-ATTTTTAAAAGTCAA
1 TTTTATACAATAATTTTAAAAAGTC-A
5579 TTTT
1 TTTT
5583 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 11 0.44
25 10 0.40
26 4 0.16
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (26 bp):
TTTTATACAATAATTTTAAAAAGTCA
Found at i:8485 original size:15 final size:15
Alignment explanation
Indices: 8447--8477 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8437 GAGGTTCACG
8447 ACAGCTTGAAGGAGA
1 ACAGCTTGAAGGAGA
8462 ACAGCTTGAAGGAGA
1 ACAGCTTGAAGGAGA
8477 A
1 A
8478 AGAGTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.32, T:0.13
Consensus pattern (15 bp):
ACAGCTTGAAGGAGA
Found at i:10547 original size:12 final size:12
Alignment explanation
Indices: 10511--10541 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
10501 TATATATATA
10511 TTCTTTTGTTTT
1 TTCTTTTGTTTT
10523 TTCTTTTGTTTT
1 TTCTTTTGTTTT
10535 TTCTTTT
1 TTCTTTT
10542 TATTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTCTTTTGTTTT
Found at i:10668 original size:15 final size:14
Alignment explanation
Indices: 10648--10734 Score: 61
Period size: 14 Copynumber: 5.9 Consensus size: 14
10638 TGTTTTTTCC
10648 TTTTGTTTTATTTAA
1 TTTTGTTTTATTT-A
10663 TTTTGTTTTATTTA
1 TTTTGTTTTATTTA
* *
10677 TTTTATTAATTTAATTCA
1 TTTT-GT--TTT-ATTTA
*
10695 TTTTGTTATATTTCA
1 TTTTGTTTTATTT-A
*
10710 -TTT-ATTTATTTA
1 TTTTGTTTTATTTA
*
10722 TTTTATTTTATTT
1 TTTTGTTTTATTT
10735 TTATCTCTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
12 1 0.02
13 9 0.16
14 18 0.32
15 17 0.30
17 4 0.07
18 8 0.14
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTGTTTTATTTA
Found at i:10682 original size:9 final size:9
Alignment explanation
Indices: 10654--10757 Score: 84
Period size: 9 Copynumber: 11.0 Consensus size: 9
10644 TTCCTTTTGT
*
10654 TTTATTTAA
1 TTTATTTTA
*
10663 TTTTGTTTTA
1 -TTTATTTTA
10673 TTTATTTTA
1 TTTATTTTA
* *
10682 TTAATTTAA
1 TTTATTTTA
* *
10691 TTCATTTTG
1 TTTATTTTA
*
10700 TTATATTTCA
1 TT-TATTTTA
10710 TTTA-TTTA
1 TTTATTTTA
10718 TTTATTTTA
1 TTTATTTTA
10727 TTTTATTTTTA
1 -TTTA-TTTTA
10738 TCTCTATTTTA
1 T-T-TATTTTA
10749 TTTATTTTA
1 TTTATTTTA
10758 ATATTTTCCT
Statistics
Matches: 76, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
8 7 0.09
9 36 0.47
10 19 0.25
11 12 0.16
12 2 0.03
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTATTTTA
Found at i:10771 original size:35 final size:34
Alignment explanation
Indices: 10710--10800 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 34
10700 TTATATTTCA
*
10710 TTTATTTATTTATTTTATTTTATTTTTATCTCTAT
1 TTTATTTATTT-TTATATTTTATTTTTATCTCTAT
* * * *
10745 TTTATTTATTTTAATATTTTCCTTTTTATTTTTAT
1 TTTATTTATTTTTATATTTT-ATTTTTATCTCTAT
*
10780 TCT-TTTATTTTTATCATTTTA
1 TTTATTTATTTTTAT-ATTTTA
10801 ATTATTTAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
34 17 0.37
35 29 0.63
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (34 bp):
TTTATTTATTTTTATATTTTATTTTTATCTCTAT
Found at i:10776 original size:5 final size:5
Alignment explanation
Indices: 10648--10757 Score: 63
Period size: 5 Copynumber: 23.0 Consensus size: 5
10638 TGTTTTTTCC
* * * * * *
10648 TTTTG TTTTA TTTAA TTTTG TTTTA -TTTA TTTTA --TTA ATTTA ATTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * * *
10695 TTTTG TTATA TTTCA -TTTA -TTTA -TTTA TTTTA TTTTA TTTTTA TCTCTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA T-TTTA
10744 TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA
10758 ATATTTTCCT
Statistics
Matches: 82, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
3 3 0.04
4 19 0.23
5 51 0.62
6 9 0.11
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:10969 original size:12 final size:11
Alignment explanation
Indices: 10947--10972 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10937 TCGATTGTCC
10947 TTTTGTTTTTT
1 TTTTGTTTTTT
10958 TTTTGTTTTTT
1 TTTTGTTTTTT
10969 TTTT
1 TTTT
10973 ATTCCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:15065 original size:99 final size:99
Alignment explanation
Indices: 14882--15083 Score: 314
Period size: 99 Copynumber: 2.0 Consensus size: 99
14872 TTATAATATT
* * *
14882 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTAGTTAAATGCCCTGGTTTTATAG
1 ATATATATACAATAAAGCATGAGATGTCCCTCTAAAGCAATTAGTTAAATGCCCTGGCTTTATAG
* * *
14947 ATAAGATTTAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAACTAACCTGATAAAGGTGATTATA
* * * *
14981 ATATCTATATAATAAAGCATGAGATGTCCCTCTAAAGCAATTGGTTAAATGCCCTGGCTTTATGG
1 ATATATATACAATAAAGCATGAGATGTCCCTCTAAAGCAATTAGTTAAATGCCCTGGCTTTATAG
15046 ATAAGATTCAACTAACCTGATAAAGGTGATTATA
66 ATAAGATTCAACTAACCTGATAAAGGTGATTATA
15080 ATAT
1 ATAT
15084 TGAGTTGTCC
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (99 bp):
ATATATATACAATAAAGCATGAGATGTCCCTCTAAAGCAATTAGTTAAATGCCCTGGCTTTATAG
ATAAGATTCAACTAACCTGATAAAGGTGATTATA
Found at i:16568 original size:85 final size:85
Alignment explanation
Indices: 16394--16964 Score: 627
Period size: 85 Copynumber: 6.7 Consensus size: 85
16384 TGTTTATAGT
* * * *
16394 ATAGATCAAGGCGAGAAGGGTTATCTGCCAAC-AA-ACCTTTGAGTTCGATTTCATTCAGCTCAA
1 ATAGCTCAAGACGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTTCATTCAGCTCAA
*
16457 GGGCAATATCAAATTTACAGC
66 AGGC-ATATCAAATTTACAGC
* * * *
16478 ATAGCTCAAGACGAGAAGGAG-TATCCGTCAATAAAGACCTTCGAGTTCAATTTCATTCAGTTCA
1 ATAGCTCAAGACGAGAAGG-GTTATCTGTCAACAAAGACCTTCGAGTTCGATTTCATTCAGCTCA
16542 AAGGCATATCAAATTTACAGC
65 AAGGCATATCAAATTTACAGC
* *
16563 ATAGCTCAAGGA-GAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACTCA
1 ATAGCTCAA-GACGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTTCATTCAGCTCA
*
16627 AAGGCATATCAAACTTACAGC
65 AAGGCATATCAAATTTACAGC
* *
16648 ATAGCTCAAGGA-AAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCA
1 ATAGCTCAA-GACGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTTCATTCAGCTCA
*
16712 AGGGCATATCAAATTTACAGC
65 AAGGCATATCAAATTTACAGC
* * * * * * * *
16733 ATAGCTTAAGGCGAGAAGGGCTAGCTGCCAACAAATACCTTCGAGTTCAATTCCATTCAGCTCAA
1 ATAGCTCAAGACGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTTCATTCAGCTCAA
* * *
16798 GGGTATGTCAAATTTACAGC
66 AGGCATATCAAATTTACAGC
* * * ** * * * * *
16818 ATAACTTAAGTCGAGAAAAGCTATCTGTCAATAAAAAACCTTCGAGTTCGATTCCATTCAGGTC-
1 ATAGCTCAAGACGAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTTCATTCAGCTCA
* *
16882 AAGGATATATCAAATTT-CAGT
65 AAGG-CATATCAAATTTACAGC
* * * * * *
16903 ATAACTCAAGGCGAAAAGGGTTATCTGTCAATGAAA-ACTTTTGAGTTCGATTTCATTCAGCT
1 ATAGCTCAAGACGAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTTCATTCAGCT
16965 TGAGGGCCTA
Statistics
Matches: 424, Mismatches: 55, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
84 49 0.12
85 305 0.72
86 70 0.17
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (85 bp):
ATAGCTCAAGACGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTTCATTCAGCTCAA
AGGCATATCAAATTTACAGC
Found at i:16913 original size:255 final size:255
Alignment explanation
Indices: 16399--16978 Score: 715
Period size: 255 Copynumber: 2.3 Consensus size: 255
16389 ATAGTATAGA
* *
16399 TCAAGGC-GAGAAGGGTTATCTGCCAAC-AAACCTTTGAGTTCGATTTCATTCAGCTCAAGGGCA
1 TCAAGGCAAAGAAGGGTTATCTGTCAACAAAACCTTTGAGTTCGATTTCATTCAGCTCAAGGGC-
* * *
16462 ATATCAAATTTACAGCATAGCTCAAGACGAGAAGGAGTATCCGTCAATAAAGACCTTCGAGTTCA
65 ATATCAAATTTACAGCATAGCTCAAGACGAGAAGGAGTAGCCGCCAACAAAGACCTTCGAGTTCA
* * * ** *
16527 ATTTCATTCAGTTCAAAGGCATATCAAATTTACAGCATAGCTCAAGGAGAGAAGGGTTATCTGTC
130 ATTCCATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGAGAGAAAAGCTATCTGTC
* * *
16592 AACAAAGACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAAACTTACAGCATAGC
195 AAAAAAAACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAAACTTACAGCATAAC
* *
16653 TCAAGG-AAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
1 TCAAGGCAAAGAAGGGTTATCTGTCAACAAA-ACCTTTGAGTTCGATTTCATTCAGCTCAAGGGC
* * * *
16717 ATATCAAATTTACAGCATAGCTTAAGGCGAGAAGG-GCTAGCTGCCAACAAATACCTTCGAGTTC
65 ATATCAAATTTACAGCATAGCTCAAGACGAGAAGGAG-TAGCCGCCAACAAAGACCTTCGAGTTC
* * * * **
16781 AATTCCATTCAGCTCAAGGGTATGTCAAATTTACAGCATAACTTAAGTCGAGAAAAGCTATCTGT
129 AATTCCATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGAGAGAAAAGCTATCTGT
* ** * * *
16846 CAATAAAAAACCTTCGAGTTCGATTCCATTCAGGTC-AAGGATATATCAAA-TTTCAGTATAAC
194 CAA-AAAAAACCTTCGAGTTCGATTACATTCAACTCAAAGG-CATATCAAACTTACAGCATAAC
* * * **
16908 TCAAGGCGAA-AAGGGTTATCTGTCAATGAAAACTTTTGAGTTCGATTTCATTCAGCTTGAGGGC
1 TCAAGGCAAAGAAGGGTTATCTGTCAA-CAAAACCTTTGAGTTCGATTTCATTCAGCTCAAGGGC
*
16972 CTATCAA
65 ATATCAA
16979 CCATATGATA
Statistics
Matches: 278, Mismatches: 40, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
254 25 0.09
255 182 0.65
256 71 0.26
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (255 bp):
TCAAGGCAAAGAAGGGTTATCTGTCAACAAAACCTTTGAGTTCGATTTCATTCAGCTCAAGGGCA
TATCAAATTTACAGCATAGCTCAAGACGAGAAGGAGTAGCCGCCAACAAAGACCTTCGAGTTCAA
TTCCATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGAGAGAAAAGCTATCTGTCA
AAAAAAACCTTCGAGTTCGATTACATTCAACTCAAAGGCATATCAAACTTACAGCATAAC
Found at i:18472 original size:2 final size:2
Alignment explanation
Indices: 18461--18491 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18451 TTTATTACTA
18461 AT AT -T 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
18492 TTCTTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:18514 original size:18 final size:17
Alignment explanation
Indices: 18491--18526 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18481 TATATATATA
*
18491 TTTCTTTTCTTTTTTATT
1 TTTCTTTT-TATTTTATT
18509 TTTCTTTTTATTTTATT
1 TTTCTTTTTATTTTATT
18526 T
1 T
18527 ATTAATACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTCTTTTTATTTTATT
Found at i:18626 original size:5 final size:5
Alignment explanation
Indices: 18602--18707 Score: 110
Period size: 5 Copynumber: 21.0 Consensus size: 5
18592 CGTTTTTTCC
* * * * *
18602 TTTTA ATTTA TTCTTG TTTTA TTTTA TTTAA TTTTA -TTAA TTTTG TTTTA
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
18652 TTTTA TTTT- TATTTA TTTTA TTTTA TTTTA TTTTTA TCTTTA TTTTA
1 TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA -TTTTA T-TTTA TTTTA
18699 -TTTA TTTTA
1 TTTTA TTTTA
18708 ATTGTTTCCT
Statistics
Matches: 84, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
4 8 0.10
5 61 0.73
6 15 0.18
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:18704 original size:9 final size:9
Alignment explanation
Indices: 18619--18744 Score: 91
Period size: 9 Copynumber: 13.8 Consensus size: 9
18609 TTATTCTTGT
18619 TTTATTTTA
1 TTTATTTTA
18628 TTTAATTTTA
1 TTT-ATTTTA
* *
18638 TTAATTTTGT
1 TTTATTTT-A
18648 TTTATTTTA
1 TTTATTTTA
18657 --T-TTTTA
1 TTTATTTTA
18663 TTTATTTTA
1 TTTATTTTA
18672 TTTTATTTTA
1 -TTTATTTTA
* *
18682 TTT-TTATC
1 TTTATTTTA
18690 TTTATTTTA
1 TTTATTTTA
18699 TTTATTTTA
1 TTTATTTTA
* * *
18708 ATTGTTTCCTT
1 TTTATTT--TA
18719 TTTATCTTT-
1 TTTAT-TTTA
18728 TATTATTTTA
1 T-TTATTTTA
18738 TTTATTT
1 TTTATTT
18745 ATCAATTTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
6 5 0.05
7 1 0.01
8 7 0.08
9 43 0.47
10 30 0.33
11 4 0.04
12 2 0.02
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:21125 original size:23 final size:23
Alignment explanation
Indices: 21081--21126 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
21071 TATATTTATT
* *
21081 TTTTTATATTTTAAATTTAAATA
1 TTTTTATATTTTAAAATCAAATA
21104 TTTTTAT-TTTTAAAAATCAAATA
1 TTTTTATATTTT-AAAATCAAATA
21127 AGCCCTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTATATTTTAAAATCAAATA
Found at i:21172 original size:27 final size:28
Alignment explanation
Indices: 21130--21182 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
21120 TCAAATAAGC
**
21130 CCTTGAACTTTTAAAAACT-AATTTACT
1 CCTTGAACTTGAAAAAACTAAATTTACT
*
21157 CCTTGAACTTGAAAAAAGTAAATTTA
1 CCTTGAACTTGAAAAAACTAAATTTA
21183 ATCCATCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.36
Consensus pattern (28 bp):
CCTTGAACTTGAAAAAACTAAATTTACT
Found at i:24605 original size:28 final size:29
Alignment explanation
Indices: 24569--24626 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
24559 CCACTGTTAC
* *
24569 TTTCAAAGCATTGGCTC-ACCAGCATAATG
1 TTTCAAAGCAATGGCTCGA-CAACATAATG
24598 TTTC-AAGCAATGGCTCGACAACATAATG
1 TTTCAAAGCAATGGCTCGACAACATAATG
24626 T
1 T
24627 AAACATAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (29 bp):
TTTCAAAGCAATGGCTCGACAACATAATG
Found at i:25587 original size:30 final size:31
Alignment explanation
Indices: 25511--25579 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
25501 CAATAGTTAC
*
25511 GTTG-GGGACCATATTGCAAATGAACTAAAT
1 GTTGAGGGACCATATTGCAAACGAACTAAAT
*
25541 GTTGAGGGACCATATTGCAAACGGACT-AAT
1 GTTGAGGGACCATATTGCAAACGAACTAAAT
25571 GTTGAGGGA
1 GTTGAGGGA
25580 TTGTATTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (31 bp):
GTTGAGGGACCATATTGCAAACGAACTAAAT
Found at i:25667 original size:3 final size:3
Alignment explanation
Indices: 25659--25688 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25649 TACTTTACCC
25659 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25689 GGGTAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27575 original size:31 final size:31
Alignment explanation
Indices: 27540--27609 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
27530 CTTTTAAAAC
*
27540 TTGCAATACAATCCCTCAACATTTAGTCCGT
1 TTGCAATACAATCCCCCAACATTTAGTCCGT
*** *
27571 TTGCAATATGGTCCCCCAACATTTAGTCTGT
1 TTGCAATACAATCCCCCAACATTTAGTCCGT
*
27602 TTTCAATA
1 TTGCAATA
27610 TGGTCCCCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (31 bp):
TTGCAATACAATCCCCCAACATTTAGTCCGT
Found at i:27610 original size:31 final size:31
Alignment explanation
Indices: 27551--27617 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
27541 TGCAATACAA
*
27551 TCCCTCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
* *
27582 TCCCCCAACATTTAGTCTGTTTTCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
27613 TCCCC
1 TCCCC
27618 GACGTAACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTGCAATATGG
Found at i:33844 original size:20 final size:20
Alignment explanation
Indices: 33819--33871 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
33809 TTGAGATCAA
*
33819 TGGTCTCTATACCGAACGAC
1 TGGTCTCTATACCGAAAGAC
* *
33839 TGGTCTCCATACCTAAAGAC
1 TGGTCTCTATACCGAAAGAC
*
33859 TGGTCTTTATACC
1 TGGTCTCTATACC
33872 AAAAAATTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (20 bp):
TGGTCTCTATACCGAAAGAC
Found at i:35793 original size:15 final size:15
Alignment explanation
Indices: 35756--35787 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35746 ATTATTGTGA
*
35756 CAAATTTAATTTTGT
1 CAAAATTAATTTTGT
35771 CAAAATTAATTTTGT
1 CAAAATTAATTTTGT
35786 CA
1 CA
35788 CTATTAGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (15 bp):
CAAAATTAATTTTGT
Found at i:37624 original size:45 final size:43
Alignment explanation
Indices: 37554--37885 Score: 252
Period size: 45 Copynumber: 8.1 Consensus size: 43
37544 CTGTATGTGT
37554 ATTATTGGCATGAAAGTATGTCATAGCTGAAATGCATATGGGTGC
1 ATTATTGGCATGAAAG-ATG-CATAGCTGAAATGCATATGGGTGC
37599 ATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGC
1 ATTATTGGCATGAAA-GATG-CATAGCTGAAATGCATATGGGTGC
***
37644 ATTATCAACAT-AAA-A-G-A-A--T--AATGCATATGGGTGC
1 ATTATTGGCATGAAAGATGCATAGCTGAAATGCATATGGGTGC
37678 ATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGC
1 ATTATTGGCATGAAA-GATG-CATAGCTGAAATGCATATGGGTGC
** * *
37723 ATTATCAGCAT-TAA-A-G-A-A--T--AATGCATATAGGTGC
1 ATTATTGGCATGAAAGATGCATAGCTGAAATGCATATGGGTGC
*
37757 ATTATTGGCATGAAAGAATGTCATAGCTGAAATGCATACT-GGTGT
1 ATTATTGGCATGAAAG-ATG-CATAGCTGAAATGCATA-TGGGTGC
** *
37802 ATTATCAGCAT-AAA-A-G-A-A--T--AATACATATGGGTGC
1 ATTATTGGCATGAAAGATGCATAGCTGAAATGCATATGGGTGC
* *
37836 ATTATTGACATGAAAGGATGCCATAGCTGAAATGCATATGGGTGT
1 ATTATTGGCATGAAA-GATG-CATAGCTGAAATGCATATGGGTGC
37881 ATTAT
1 ATTAT
37886 CAACATAAAA
Statistics
Matches: 227, Mismatches: 24, Indels: 72
0.70 0.07 0.22
Matches are distributed among these distances:
33 1 0.00
34 65 0.29
35 8 0.04
36 3 0.01
37 3 0.01
38 6 0.03
39 3 0.01
40 3 0.01
41 6 0.03
42 3 0.01
43 3 0.01
44 8 0.04
45 113 0.50
46 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (43 bp):
ATTATTGGCATGAAAGATGCATAGCTGAAATGCATATGGGTGC
Found at i:37715 original size:79 final size:79
Alignment explanation
Indices: 37584--37977 Score: 607
Period size: 79 Copynumber: 5.0 Consensus size: 79
37574 TCATAGCTGA
37584 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
37649 CAACATAAAAGAAT
66 CAACATAAAAGAAT
*
37663 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
* *
37728 CAGCATTAAAGAAT
66 CAACATAAAAGAAT
* * * *
37742 AATGCATATAGGTGCATTATTGGCATGAAAGAATGTCATAGCTGAAATGCATACT-GGTGTATTA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATA-TGGGTGCATTA
*
37806 TCAGCATAAAAGAAT
65 TCAACATAAAAGAAT
* * *
37821 AATACATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGAAATGCATATGGGTGTATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
37886 CAACATAAAA-AAT
66 CAACATAAAAGAAT
* *
37899 AATGCATATGGGTGCATTATTGGCATGACAGGATGCCA-A-CATTGAAATGCATATGGGTGCGTT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGC--TGAAATGCATATGGGTGCATT
*
37962 ATCAACCTAAAAGAAT
64 ATCAACATAAAAGAAT
37978 GCTATAATTG
Statistics
Matches: 291, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
76 1 0.00
77 1 0.00
78 69 0.24
79 219 0.75
80 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
CAACATAAAAGAAT
Found at i:37746 original size:34 final size:34
Alignment explanation
Indices: 37708--37775 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
37698 TCATAGCTGA
* *
37708 AATGCATATGGGTGCATTATCAGCATTAAAGAAT
1 AATGCATATAGGTGCATTATCAGCATGAAAGAAT
**
37742 AATGCATATAGGTGCATTATTGGCATGAAAGAAT
1 AATGCATATAGGTGCATTATCAGCATGAAAGAAT
37776 GTCATAGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (34 bp):
AATGCATATAGGTGCATTATCAGCATGAAAGAAT
Found at i:38316 original size:30 final size:30
Alignment explanation
Indices: 38272--38344 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
38262 TATGCCAGTT
*
38272 AGAT-AAATGGTTAAAAAAATATTGGGTAAA
1 AGATGAAA-GGTTAAAAAAATATTGAGTAAA
* *
38302 AGATGAAAGGTT-AAATAATGTTGAGTAAA
1 AGATGAAAGGTTAAAAAAATATTGAGTAAA
38331 AGATGAAAGGTTAA
1 AGATGAAAGGTTAA
38345 GAACTGTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 26 0.68
30 9 0.24
31 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (30 bp):
AGATGAAAGGTTAAAAAAATATTGAGTAAA
Found at i:38332 original size:29 final size:29
Alignment explanation
Indices: 38288--38360 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
38278 ATGGTTAAAA
* *
38288 AAATATTGGGTAAAAGATGAAAGGTTAA-
1 AAATGTTGAGTAAAAGATGAAAGGTTAAG
38316 ATAATGTTGAGTAAAAGATGAAAGGTTAAG
1 A-AATGTTGAGTAAAAGATGAAAGGTTAAG
*
38346 AACTGTTGAGTAAAA
1 AAATGTTGAGTAAAA
38361 AGAATAATGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 38 0.95
30 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.25, T:0.26
Consensus pattern (29 bp):
AAATGTTGAGTAAAAGATGAAAGGTTAAG
Found at i:40478 original size:65 final size:64
Alignment explanation
Indices: 40362--40519 Score: 194
Period size: 65 Copynumber: 2.4 Consensus size: 64
40352 TGGAACTCTT
* *
40362 AGTGCATCGGTGCACTTAAATGCATTCGATGTTTCAAACAAGCCTAGAGTGCATCAATGCATGGT
1 AGTGCATCGATGCA-TAAAATGCATTCGATGTTTCAAACAAGCCTAGAGTGCATCAATGCATGG-
*
40427 T
64 A
* * * *
40428 TGTGCATCGATGCATAAAATACATTCGATGTTTCCATAA-AATCCTA-AGTGCATCGATGCATGG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTT-CA-AACAAGCCTAGAGTGCATCAATGCATGG
40491 A
64 A
*
40492 AGTGCATTGATGCATAAAATGCATTCGA
1 AGTGCATCGATGCATAAAATGCATTCGA
40520 AATGGGGTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
64 25 0.31
65 33 0.41
66 20 0.25
67 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTAGAGTGCATCAATGCATGGA
Found at i:43207 original size:21 final size:21
Alignment explanation
Indices: 43089--43210 Score: 68
Period size: 21 Copynumber: 5.6 Consensus size: 21
43079 ATCCCGACGG
*
43089 GTGTATCGATGCA-CTGC-TGA
1 GTGTATCGATGCACCTTCAT-A
* * *
43109 GTGCATCGATGCACATTCAAGGA
1 GTGTATCGATGCACCTTC-A-TA
* * *
43132 GTGTATTGGTGCACCTTCATT
1 GTGTATCGATGCACCTTCATA
* * * *
43153 TTGCATCGATGTACATTCATA
1 GTGTATCGATGCACCTTCATA
*
43174 GGGATGAATCGATGCACCTTCATA
1 --G-TGTATCGATGCACCTTCATA
43198 GTGTATCGATGCA
1 GTGTATCGATGCA
43211 TTGTGCACAA
Statistics
Matches: 73, Mismatches: 22, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
20 12 0.16
21 27 0.37
22 2 0.03
23 15 0.21
24 17 0.23
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (21 bp):
GTGTATCGATGCACCTTCATA
Found at i:48556 original size:46 final size:46
Alignment explanation
Indices: 48489--48594 Score: 162
Period size: 46 Copynumber: 2.3 Consensus size: 46
48479 TGCAGTAAGG
*
48489 GTGCATCGATGCATAAAATGCATTCGATGTTT-CA-AACAAGCCTGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-AAGCC-CGA
*
48535 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAATCCCGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCCGA
48581 GTGCATCGATGCAT
1 GTGCATCGATGCAT
48595 GGAAGTTCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
46 48 0.86
47 6 0.11
48 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCCGA
Found at i:49075 original size:139 final size:137
Alignment explanation
Indices: 48916--49169 Score: 368
Period size: 139 Copynumber: 1.8 Consensus size: 137
48906 ATTTTCAACA
**
48916 TAATAAAATTCAAGTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTAT-AAAA
1 TAATAAAATTCAAGAATTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAA
* *
48980 TATTATACTATTAGAACCA-TTTCTCCCTATTTTTTAGTGTCAAAAATGTTATATATTAACAAAA
66 T-TTATACTATCAGAAACATTTTC-CCCTATTTTTT-GTG-CAAAAATGTTATATATTAACAAAA
49044 TATATTGTAAT
127 TATATTGTAAT
* * * *
49055 TAATAAAATTTAAGAATTTTGTAATTAATTATTTTTGTAGTTATATATTTTAATCGTTATGAAAA
1 TAATAAAATTCAAGAATTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAA
* *
49120 TTTATACTATCATAAATATTTTCCCCTATTTTTTGTGCAAAAATGTTATA
66 TTTATACTATCAGAAACATTTTCCCCTATTTTTTGTGCAAAAATGTTATA
49170 GTGACAAGTT
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
137 13 0.13
138 3 0.03
139 78 0.76
140 9 0.09
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.48
Consensus pattern (137 bp):
TAATAAAATTCAAGAATTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAA
TTTATACTATCAGAAACATTTTCCCCTATTTTTTGTGCAAAAATGTTATATATTAACAAAATATA
TTGTAAT
Found at i:49284 original size:21 final size:23
Alignment explanation
Indices: 49226--49285 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
49216 TTATCACAAC
*
49226 AAAAATTATATTTTTTATTTAAT
1 AAAAATTATGTTTTTTATTTAAT
*
49249 AAAAGATTCAAGTTTTTTA-TTAA-
1 AAAA-ATT-ATGTTTTTTATTTAAT
49272 AAAAATTATGTTTT
1 AAAAATTATGTTTT
49286 CAGTTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 6 0.19
22 3 0.09
23 8 0.25
24 7 0.22
25 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (23 bp):
AAAAATTATGTTTTTTATTTAAT
Found at i:53383 original size:20 final size:20
Alignment explanation
Indices: 53358--53407 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
53348 TTTATTTGGA
*
53358 AAAAATTTGGTTTGGGGTTT
1 AAAAATTTGGTCTGGGGTTT
**
53378 AAAAATCCGGTCTGGGGTTT
1 AAAAATTTGGTCTGGGGTTT
*
53398 AAAAAATTGG
1 AAAAATTTGG
53408 ATGACTGGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (20 bp):
AAAAATTTGGTCTGGGGTTT
Found at i:60265 original size:77 final size:77
Alignment explanation
Indices: 60138--60294 Score: 296
Period size: 77 Copynumber: 2.0 Consensus size: 77
60128 CACAATCTTA
* *
60138 CCTTTCTCTATCACCGGAAAGAATGAATTTGGAATGAATTTTCTAAATGTTTTTCCTATTCCAAA
1 CCTTTCTCTATCACCGGAAAGAACGAATTTGGAATGAATTTTCTAAATGTTTTTCATATTCCAAA
60203 GTTCTAAACTAG
66 GTTCTAAACTAG
60215 CCTTTCTCTATCACCGGAAAGAACGAATTTGGAATGAATTTTCTAAATGTTTTTCATATTCCAAA
1 CCTTTCTCTATCACCGGAAAGAACGAATTTGGAATGAATTTTCTAAATGTTTTTCATATTCCAAA
60280 GTTCTAAACTAG
66 GTTCTAAACTAG
60292 CCT
1 CCT
60295 ATATATAGGG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (77 bp):
CCTTTCTCTATCACCGGAAAGAACGAATTTGGAATGAATTTTCTAAATGTTTTTCATATTCCAAA
GTTCTAAACTAG
Found at i:64061 original size:24 final size:24
Alignment explanation
Indices: 64007--64062 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
63997 TGAACGTTTG
** *
64007 GTTATGTTCGTTTATGTTTGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
*
64031 GTAATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
64055 TTTATGTT
1 GTTATGTT
64063 TAACCCAATC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.09, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:64482 original size:10 final size:10
Alignment explanation
Indices: 64467--64509 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
64457 GGGTCTCCAA
64467 CGTTTATGTT
1 CGTTTATGTT
64477 CGTTTATGTT
1 CGTTTATGTT
64487 CG----TGTT
1 CGTTTATGTT
64493 CGTTTATGTT
1 CGTTTATGTT
64503 CGTTTAT
1 CGTTTAT
64510 TTATTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 23 0.79
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:64494 original size:16 final size:16
Alignment explanation
Indices: 64473--64505 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
64463 CCAACGTTTA
64473 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
64489 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
64505 T
1 T
64506 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:64599 original size:16 final size:16
Alignment explanation
Indices: 64574--64614 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
64564 AAAAAAAATT
64574 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
64590 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
64606 T-TT-ATTTAT
1 TGTTCATTTAT
64615 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:65448 original size:2 final size:2
Alignment explanation
Indices: 65441--65466 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65431 TAAATGGGAA
65441 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
65467 TAGAGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65695 original size:31 final size:31
Alignment explanation
Indices: 65638--65709 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
65628 CATAAATAAA
*
65638 TACTT-AAAT-TATATTTTTTTTCATTTAAG
1 TACTTAAAATATATATCTTTTTTCATTTAAG
*
65667 TACTTAAAATATATCATCTTTTTT-ATTTAGG
1 TACTTAAAATATAT-ATCTTTTTTCATTTAAG
65698 TA-TCTAAAATAT
1 TACT-TAAAATAT
65710 TTTTTAATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 5 0.14
30 5 0.14
31 19 0.51
32 8 0.22
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (31 bp):
TACTTAAAATATATATCTTTTTTCATTTAAG
Found at i:70808 original size:7 final size:7
Alignment explanation
Indices: 70796--70832 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
70786 GTCAAAGAAA
70796 GTCAACG
1 GTCAACG
70803 GTCAACG
1 GTCAACG
*
70810 GT-ACCG
1 GTCAACG
70816 GTCAACG
1 GTCAACG
70823 GTCAACG
1 GTCAACG
70830 GTC
1 GTC
70833 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:70861 original size:19 final size:18
Alignment explanation
Indices: 70839--70917 Score: 86
Period size: 19 Copynumber: 4.2 Consensus size: 18
70829 GGTCGGGTCG
* *
70839 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGG-TCAAACC
70858 GGTCAAACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
*
70876 GGTTCGAACCGGTCAAACC
1 GG-TCAAACCGGTCAAACC
*
70895 GGTTCAAAACTGGTCAAACC
1 GG-TC-AAACCGGTCAAACC
70915 GGT
1 GGT
70918 TTTCCAGCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
18 8 0.15
19 31 0.58
20 14 0.26
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.16
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:70869 original size:9 final size:9
Alignment explanation
Indices: 70839--70917 Score: 86
Period size: 9 Copynumber: 8.3 Consensus size: 9
70829 GGTCGGGTCG
*
70839 GGTCAACCC
1 GGTCAAACC
*
70848 GGTTCAGACC
1 GG-TCAAACC
70858 GGTCAAACC
1 GGTCAAACC
70867 GGTCAAACC
1 GGTCAAACC
*
70876 GGTTCGAACC
1 GG-TCAAACC
70886 GGTCAAACC
1 GGTCAAACC
*
70895 GGTTCAAAACT
1 GG-TC-AAACC
70906 GGTCAAACC
1 GGTCAAACC
70915 GGT
1 GGT
70918 TTTCCAGCAG
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 34 0.58
10 19 0.32
11 6 0.10
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:70871 original size:28 final size:28
Alignment explanation
Indices: 70839--70902 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 28
70829 GGTCGGGTCG
*
70839 GGTCAACCCGGTTC-AGACCGGTCAAACC
1 GGTCAAACCGGTTCGA-ACCGGTCAAACC
70867 GGTCAAACCGGTTCGAACCGGTCAAACC
1 GGTCAAACCGGTTCGAACCGGTCAAACC
70895 GGTTCAAA
1 GG-TCAAA
70903 ACTGGTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 27 0.82
29 6 0.18
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (28 bp):
GGTCAAACCGGTTCGAACCGGTCAAACC
Found at i:73770 original size:17 final size:18
Alignment explanation
Indices: 73739--73772 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
73729 ATTTATTTTG
*
73739 TTTGTATTATTATATTAC
1 TTTGTATTATAATATTAC
73757 TTTGTA-TATAATATTA
1 TTTGTATTATAATATTA
73773 TAGCATGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTGTATTATAATATTAC
Found at i:82315 original size:14 final size:14
Alignment explanation
Indices: 82296--82322 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
82286 TACATTTTCA
82296 TTCTTCATTCTTTG
1 TTCTTCATTCTTTG
82310 TTCTTCATTCTTT
1 TTCTTCATTCTTT
82323 ACATTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (14 bp):
TTCTTCATTCTTTG
Found at i:87157 original size:136 final size:134
Alignment explanation
Indices: 86830--87327 Score: 547
Period size: 136 Copynumber: 3.7 Consensus size: 134
86820 AAGGAGGTGA
* * * *
86830 ATCAACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCCAACAAAAGGAGAAGAAGTTCAT
1 ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCAT
**
86894 AATGAGAAGAACTTGTTCAACCT-TAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCT
66 AATGAGAAGAACTTGTTCAACCTATA-CTCGATTCATAACAT-T----TTGAATCAACAACACCT
86958 CACTTGAGGG
125 CACTTGAGGG
* *
86968 ATCAACACTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCA
1 ATCAACATTTC-AATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCA
* * * * *** *
87033 TAATGAGAAGAGCTTGTTCGACCTATCACTTGATTCATTACATTTTGAATCAGTGACGCCTCACT
65 TAATGAGAAGAACTTGTTCAACCTAT-ACTCGATTCATAACATTTTGAATCAACAACACCTCACT
87098 TGAGGG
129 TGAGGG
* * *
87104 AAT-GACATTTCATATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTC
1 -ATCAACATTTCA-ATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTC
* * * * * * * *
87168 ATAATGAGAAGAGCTTGTTCGACCTATTGCTCGATTCACAACACTTCGAATCAACAATACCTCGC
64 ATAATGAGAAGAACTTGTTCAACCTA-TACTCGATTCATAACATTTTGAATCAACAACACCTCAC
*
87233 TTGAAGG
128 TTGAGGG
* * **
87240 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTTATCCGA-TGAGAGGA-AAGAAGTTC
1 ATCAACA-TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAG-GGAGAAGAAGTTC
*
87303 GTAATGAGAAGAACTTGTTCAACCT
64 ATAATGAGAAGAACTTGTTCAACCT
87328 TAACTTGTTT
Statistics
Matches: 309, Mismatches: 41, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
135 37 0.12
136 170 0.55
137 8 0.03
138 10 0.03
139 1 0.00
140 69 0.22
141 13 0.04
142 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (134 bp):
ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTATACTCGATTCATAACATTTTGAATCAACAACACCTCACTTG
AGGG
Found at i:88955 original size:24 final size:25
Alignment explanation
Indices: 88905--88958 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
88895 GTTTTATGTT
* * * *
88905 TTATATATTTATTTTGTTTGTATTA
1 TTATATATTTACTTTGTATATAATA
88930 TTATATA-TTACTTTGTATATAATA
1 TTATATATTTACTTTGTATATAATA
88954 TTATA
1 TTATA
88959 GCATGATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
TTATATATTTACTTTGTATATAATA
Found at i:92135 original size:17 final size:17
Alignment explanation
Indices: 92113--92170 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
92103 ACCGGTCAAC
92113 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
92130 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* *
92147 GGTCAACAGTTGGGTCG
1 GGTCAACGGTCGGGTCG
92164 GGTCAAC
1 GGTCAAC
92171 CCGATTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.16, C:0.22, G:0.43, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:92140 original size:7 final size:7
Alignment explanation
Indices: 92087--92123 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
92077 GTCAAATAAA
92087 GTCAACG
1 GTCAACG
92094 GTCAACG
1 GTCAACG
*
92101 GT-ACCG
1 GTCAACG
92107 GTCAACG
1 GTCAACG
92114 GTCAACG
1 GTCAACG
92121 GTC
1 GTC
92124 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:92188 original size:19 final size:19
Alignment explanation
Indices: 92164--92253 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
92154 AGTTGGGTCG
* *
92164 GGTCAACCCGATTCAGACC
1 GGTCAAACCGGTTCAGACC
92183 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
92202 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
92221 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
92241 GGTCAAACCGGTT
1 GGTCAAACCGGTT
92254 TTCCAGCAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.02
19 48 0.75
20 15 0.23
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:92194 original size:9 final size:9
Alignment explanation
Indices: 92180--92252 Score: 83
Period size: 9 Copynumber: 7.7 Consensus size: 9
92170 CCCGATTCAG
92180 ACCGGTCAA
1 ACCGGTCAA
*
92189 ACCGGTTCAG
1 ACCGG-TCAA
92199 ACCGGTCAA
1 ACCGGTCAA
*
92208 ACCGGTTCGA
1 ACCGG-TCAA
92218 ACCGGTCAA
1 ACCGGTCAA
92227 ACCGGTTCAAA
1 ACCGG-TC-AA
*
92238 ACTGGTCAA
1 ACCGGTCAA
92247 ACCGGT
1 ACCGGT
92253 TTTCCAGCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 28 0.52
10 20 0.37
11 6 0.11
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:98047 original size:20 final size:20
Alignment explanation
Indices: 98024--98061 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
98014 ATATTTTGCA
*
98024 ATATTAAAATTTATTAATAT
1 ATATTAAAATTTAATAATAT
*
98044 ATATTTAAATTTAATAAT
1 ATATTAAAATTTAATAAT
98062 TTGTTATATG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTAAAATTTAATAATAT
Found at i:101260 original size:2 final size:2
Alignment explanation
Indices: 101253--101286 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
101243 GCAAGGTGAT
*
101253 GA GA GA GA TA GA GA GA GA GA GA GA GA GA GA -A GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
101287 TAAGAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:102244 original size:3 final size:3
Alignment explanation
Indices: 102236--102312 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
102226 GACCCTATGG
102236 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
102284 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
102313 ATCAAAAGAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:102790 original size:13 final size:13
Alignment explanation
Indices: 102774--102806 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
102764 AATACCTTTT
102774 AAAATAATTTTAA
1 AAAATAATTTTAA
102787 AAAATAATTTTAA
1 AAAATAATTTTAA
*
102800 AAGATAA
1 AAAATAA
102807 AAAAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:103832 original size:27 final size:26
Alignment explanation
Indices: 103802--103966 Score: 98
Period size: 20 Copynumber: 6.9 Consensus size: 26
103792 ATGCCTTAAT
103802 GCATCCTTTCATGCATTTTAAATTATG
1 GCATCCTTTCATGCATTTT-AATTATG
* *
103829 GCAT-CTGTTCATGC---CT--TTGT-
1 GCATCCT-TTCATGCATTTTAATTATG
103849 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTT-AATTATG
* *
103876 GCATCCGTTCATGC---CT--TTAT-
1 GCATCCTTTCATGCATTTTAATTATG
103896 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTT-AATTATG
* *
103923 GCATCCGTTCATGC---CT--TTAT-
1 GCATCCTTTCATGCATTTTAATTATG
103943 GCATCCTTTCATGCATTTTCAATT
1 GCATCCTTTCATGCATTTT-AATT
103967 TTGAAATCGA
Statistics
Matches: 104, Mismatches: 12, Indels: 45
0.65 0.07 0.28
Matches are distributed among these distances:
20 37 0.36
21 13 0.12
23 3 0.03
24 3 0.03
26 11 0.11
27 37 0.36
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAATTATG
Found at i:103844 original size:47 final size:47
Alignment explanation
Indices: 103791--103966 Score: 316
Period size: 47 Copynumber: 3.7 Consensus size: 47
103781 AATTATGGCA
* * *
103791 CATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGCATCTGTT
1 CATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCATCCGTT
*
103838 CATGCCTTTGTGCATCCTTTCATGCATTTTCAATTATGGCATCCGTT
1 CATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCATCCGTT
103885 CATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCATCCGTT
1 CATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCATCCGTT
103932 CATGCCTTTATGCATCCTTTCATGCATTTTCAATT
1 CATGCCTTTATGCATCCTTTCATGCATTTTCAATT
103967 TTGAAATCGA
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 124 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.43
Consensus pattern (47 bp):
CATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCATCCGTT
Found at i:104482 original size:34 final size:34
Alignment explanation
Indices: 104402--104482 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
104392 ACCCTATTAG
* * * *
104402 GGTATCGATACCAAAATTAACTTCGATGTAGCCT
1 GGTATCGATACCCAAATTAAATTCAATGTAGACT
* **
104436 GGTATCGATACCCAATTTAAATTCAATGTTTACT
1 GGTATCGATACCCAAATTAAATTCAATGTAGACT
104470 GGTATCGATACCC
1 GGTATCGATACCC
104483 TTACCATGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (34 bp):
GGTATCGATACCCAAATTAAATTCAATGTAGACT
Found at i:105819 original size:34 final size:34
Alignment explanation
Indices: 105739--105819 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
105729 ACCCTATTAG
* * * *
105739 GGTATCGATACCAAAATTAACTTCGATGTAGCCT
1 GGTATCGATACCCAAATTAAATTCAATGTAGACT
* **
105773 GGTATCGATACCCAATTTAAATTCAATGTTTACT
1 GGTATCGATACCCAAATTAAATTCAATGTAGACT
105807 GGTATCGATACCC
1 GGTATCGATACCC
105820 TTACCATGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (34 bp):
GGTATCGATACCCAAATTAAATTCAATGTAGACT
Found at i:108543 original size:82 final size:79
Alignment explanation
Indices: 108374--108543 Score: 198
Period size: 82 Copynumber: 2.1 Consensus size: 79
108364 TCTAGAGCAA
* * * *
108374 ATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCTGAAGGAAGACGGGTCTTCTCTACT
1 ATCAGACTTAATATGTTCCTCTTTTTCGGGTAGTCAGA-CTGAAGGAAGACGAGTCTGCTCCACT
* *
108439 CTTCTTTCAGGGGAG
65 ATTCTTTAAGGGGAG
* * *
108454 ATCAGACTTAATTTGTTCCTCTTTTTTGGGTAGTCAG-CTTAATTTTGGAAGACGAGTCTGCTCC
1 ATCAGACTTAATATGTTCCTCTTTTTCGGGTAGTCAGACTGAA----GGAAGACGAGTCTGCTCC
*
108518 ACTATTTTTTAAGGGGAG
62 ACTATTCTTTAAGGGGAG
108536 ATCAGACT
1 ATCAGACT
108544 CAAGGTTGAT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
78 4 0.05
80 34 0.45
82 38 0.50
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (79 bp):
ATCAGACTTAATATGTTCCTCTTTTTCGGGTAGTCAGACTGAAGGAAGACGAGTCTGCTCCACTA
TTCTTTAAGGGGAG
Found at i:108632 original size:89 final size:89
Alignment explanation
Indices: 108510--109170 Score: 806
Period size: 89 Copynumber: 7.4 Consensus size: 89
108500 GGAAGACGAG
* * * * * * *
108510 TCTGCTCCACTATTTTTTAAGGGGAGATCAGACTCAAGGTTGATTTTCTTCGCTTCTTCTTTAGG
1 TCTGCTCCACTACTCTTT-CGGGGAGATCAGACTCGAGATTGATTTTCTTCGCTGCTTCTTCAGG
* * *
108575 AAGGCAAAATCTGAAACAAGAAGAA
65 AAGACCAAATCTGAAATAAGAAGAA
* * * *
108600 TATGCTCCACTACTCTTTTGGGGATATCAGACTTGAGATTGATTTTCTTCGCTGCTTCTTCAGGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTTCTTCGCTGCTTCTTCAGGA
108665 AGACCAAATCTGAAATAAGAAGAA
66 AGACCAAATCTGAAATAAGAAGAA
** * * * *
108689 TCTGCTCTGCTACTCTTTCAGGGATATCAGACTCGAGATTGATTTGCTTAC-CAGCTTCTTCAGG
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTTCTT-CGCTGCTTCTTCAGG
*
108753 AAGACCAAATTTGAAATATA-AAGAA
65 AAGACCAAATCTGAAATA-AGAAGAA
* * * * *
108778 TCTGCTTCACTACTCTTTCGAGGAGATCAGACTCGAGATTGATTTGCTTCGATACTTCTTCAGGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTTCTTCGCTGCTTCTTCAGGA
*
108843 AAACCAAATCTGAAATAAGAAGAA
66 AGACCAAATCTGAAATAAGAAGAA
* * * * *
108867 TATACTCCACTACTCTTCCGGGGAGATCAGACTCAAGATTGATTTTCTTCGCTGCTTCTTTAGGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTTCTTCGCTGCTTCTTCAGGA
* *
108932 ATACCAAATATGAAATAAGAAGAA
66 AGACCAAATCTGAAATAAGAAGAA
* ** * *
108956 TATGCTCTGCTACTCTTTCGGGGAGATCAGACTCAAGATTGATTTTCTTCACTGCTTCTTCAGGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTTCTTCGCTGCTTCTTCAGGA
*
109021 AGACCAAATCTGAAACAAGAAGAA
66 AGACCAAATCTGAAATAAGAAGAA
* * * * * * *
109045 TCTGCTTCACTACTCTTCCGGGGAGATCAAACTCGAGATTGATTTGCTTCGATACTTCTTCATGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTTCTTCGCTGCTTCTTCAGGA
**
109110 AGATAAAATCTGAAATAAGAAGAA
66 AGACCAAATCTGAAATAAGAAGAA
* *
109134 TCTGCTCCATTACTC-TTCTAGGGAGATCAGACTCGAG
1 TCTGCTCCACTACTCTTTC-GGGGAGATCAGACTCGAG
109171 GAATCTTTTA
Statistics
Matches: 492, Mismatches: 74, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
88 4 0.01
89 471 0.96
90 17 0.03
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (89 bp):
TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTTCTTCGCTGCTTCTTCAGGA
AGACCAAATCTGAAATAAGAAGAA
Found at i:108880 original size:267 final size:267
Alignment explanation
Indices: 108532--109167 Score: 925
Period size: 267 Copynumber: 2.4 Consensus size: 267
108522 TTTTTTAAGG
* * * * * * * *
108532 GGAGATCAGACTCAAGGTTGATTTTCTTCGCTTCTTCTTTAGGAAGGCAAAATCTGAAACAAGAA
1 GGAGATCAGACTCGAGATTGATTTGCTTCGATACTTCTTCAGGAAGACAAAATCTGAAATAAGAA
* * **
108597 GAATATGCTCCACTACTCTTTTGGGGATATCAGACTTGAGATTGATTTTCTTCGCTGCTTCTTCA
66 GAATATGCTCCACTACTCTTCTGGGGAGATCAGACTCAAGATTGATTTTCTTCGCTGCTTCTTCA
* * * *
108662 GGAAGACCAAATCTGAAATAAGAAGAATCTGCTCTGCTACTCTTTCAGGGATATCAGACTCGAGA
131 GGAAGACCAAATATGAAATAAGAAGAATATGCTCTGCTACTCTTTCAGGGAGATCAGACTCAAGA
* *
108727 TTGATTTGCTT-ACCAGCTTCTTCAGGAAGACCAAATTTGAAATATA-AAGAATCTGCTTCACTA
196 TTGATTTGCTTCA-CAGCTTCTTCAGGAAGACCAAATCTGAAACA-AGAAGAATCTGCTTCACTA
*
108790 CTCTTTCGA
259 CTCTTCCGA
* *
108799 GGAGATCAGACTCGAGATTGATTTGCTTCGATACTTCTTCAGGAAAACCAAATCTGAAATAAGAA
1 GGAGATCAGACTCGAGATTGATTTGCTTCGATACTTCTTCAGGAAGACAAAATCTGAAATAAGAA
* * *
108864 GAATATACTCCACTACTCTTCCGGGGAGATCAGACTCAAGATTGATTTTCTTCGCTGCTTCTTTA
66 GAATATGCTCCACTACTCTTCTGGGGAGATCAGACTCAAGATTGATTTTCTTCGCTGCTTCTTCA
* *
108929 GGAATACCAAATATGAAATAAGAAGAATATGCTCTGCTACTCTTTCGGGGAGATCAGACTCAAGA
131 GGAAGACCAAATATGAAATAAGAAGAATATGCTCTGCTACTCTTTCAGGGAGATCAGACTCAAGA
* *
108994 TTGATTTTCTTCACTGCTTCTTCAGGAAGACCAAATCTGAAACAAGAAGAATCTGCTTCACTACT
196 TTGATTTGCTTCACAGCTTCTTCAGGAAGACCAAATCTGAAACAAGAAGAATCTGCTTCACTACT
*
109059 CTTCCGG
261 CTTCCGA
* * *
109066 GGAGATCAAACTCGAGATTGATTTGCTTCGATACTTCTTCATGAAGATAAAATCTGAAATAAGAA
1 GGAGATCAGACTCGAGATTGATTTGCTTCGATACTTCTTCAGGAAGACAAAATCTGAAATAAGAA
* * *
109131 GAATCTGCTCCATTACTCTTCTAGGGAGATCAGACTC
66 GAATATGCTCCACTACTCTTCTGGGGAGATCAGACTC
109168 GAGGAATCTT
Statistics
Matches: 328, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
266 1 0.00
267 326 0.99
268 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (267 bp):
GGAGATCAGACTCGAGATTGATTTGCTTCGATACTTCTTCAGGAAGACAAAATCTGAAATAAGAA
GAATATGCTCCACTACTCTTCTGGGGAGATCAGACTCAAGATTGATTTTCTTCGCTGCTTCTTCA
GGAAGACCAAATATGAAATAAGAAGAATATGCTCTGCTACTCTTTCAGGGAGATCAGACTCAAGA
TTGATTTGCTTCACAGCTTCTTCAGGAAGACCAAATCTGAAACAAGAAGAATCTGCTTCACTACT
CTTCCGA
Found at i:114377 original size:16 final size:16
Alignment explanation
Indices: 114352--114382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
114342 CATGGACATG
*
114352 ATTATGTGTGATTATA
1 ATTATATGTGATTATA
114368 ATTATATGTGATTAT
1 ATTATATGTGATTAT
114383 CTGTATTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (16 bp):
ATTATATGTGATTATA
Found at i:115651 original size:149 final size:149
Alignment explanation
Indices: 115464--115778 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
115454 GAGTCGAGGG
* *
115464 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
115529 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
115594 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
115613 TCTACGTGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
115678 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
115743 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
115762 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
115779 TGCAATTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:115779 original size:23 final size:23
Alignment explanation
Indices: 115746--115790 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
115736 ATTATTATAT
*
115746 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
115769 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
115791 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:118626 original size:63 final size:64
Alignment explanation
Indices: 118491--118648 Score: 216
Period size: 63 Copynumber: 2.5 Consensus size: 64
118481 TGCAGTAAGA
* * *
118491 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATA-CCTGAGTGCATCGATGCATGTCAT
*
118555 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-CTGAGTGCATTGATGCATGGT-A
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCTGAGTGCATCGATGCAT-GTCA
118617 T
64 T
*
118618 GTGCATCGATGCATAAAATACATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
118649 CAATTTATTC
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
63 48 0.56
64 29 0.34
65 6 0.07
66 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCTGAGTGCATCGATGCATGTCAT
Found at i:121415 original size:44 final size:42
Alignment explanation
Indices: 121300--121422 Score: 108
Period size: 44 Copynumber: 2.8 Consensus size: 42
121290 AAAACCCGAC
* *
121300 GGATGCATCGATGCA-TGGCTT-GGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACT-G-TTAAGTGTATCGATGCACATTCAA
* * * *
121342 GGAGTGCATTGGTGCATCT-TCATGATGTATCGATGCACATTCAAA
1 GGA-TGCATCGATGCA-CTGTTAAG-TGTATCGATGCACATTC-AA
121387 GGGATGCATCGATGCACTGTTAAGTGTATCGATGCA
1 -GGATGCATCGATGCACTGTTAAGTGTATCGATGCA
121423 TTAAGCACAA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
42 4 0.06
43 11 0.17
44 30 0.47
45 16 0.25
46 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTTAAGTGTATCGATGCACATTCAA
Found at i:127340 original size:65 final size:65
Alignment explanation
Indices: 127203--127362 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
127193 TGCAGTAAGA
* * * *
127203 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGTATCGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGTCAT
* * *
127267 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTGAGTGCATCGATGTATGGT-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATGCAT-GTC
127330 AT
64 AT
*
127332 GTGTATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
127363 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 27 0.32
65 53 0.62
66 5 0.06
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGTCAT
Found at i:129727 original size:10 final size:10
Alignment explanation
Indices: 129712--129736 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
129702 TTTTTGCCAA
129712 ATCTTTCCAT
1 ATCTTTCCAT
129722 ATCTTTCCAT
1 ATCTTTCCAT
129732 ATCTT
1 ATCTT
129737 GATATGAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.52
Consensus pattern (10 bp):
ATCTTTCCAT
Found at i:134327 original size:17 final size:16
Alignment explanation
Indices: 134286--134327 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
134276 AAATACCTTT
134286 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
134302 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
134319 TAAAA-AATT
1 TAAAATAATT
134328 GATTTGCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:135376 original size:20 final size:20
Alignment explanation
Indices: 135333--135378 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
135323 TCTGGCAATG
* * *
135333 AACCGGTTGAAAACCGGTAG
1 AACCGGCTGAAAACCGGCAA
*
135353 AACCGGCTGAAAATCGGCAA
1 AACCGGCTGAAAACCGGCAA
135373 AACCGG
1 AACCGG
135379 GGTGAGCCGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.28, T:0.11
Consensus pattern (20 bp):
AACCGGCTGAAAACCGGCAA
Done.