Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007615.1 Hibiscus syriacus cultivar Beakdansim tig00022706_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: 95037
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3443 original size:2 final size:2
Alignment explanation
Indices: 3436--3476 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3426 AGAATTACGA
3436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
3477 TAATATTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5120 original size:27 final size:27
Alignment explanation
Indices: 5090--5144 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5080 GGATGAAACT
* *
5090 ATGATAGGGAGAGCACAGGTGAAGGGA
1 ATGACAGGGAGAGCACAGGCGAAGGGA
* *
5117 ATGACGGGGAGAGCACCGGCGAAGGGA
1 ATGACAGGGAGAGCACAGGCGAAGGGA
5144 A
1 A
5145 AGGGTAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.45, T:0.07
Consensus pattern (27 bp):
ATGACAGGGAGAGCACAGGCGAAGGGA
Found at i:6778 original size:10 final size:10
Alignment explanation
Indices: 6760--6790 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6750 TTTTTACGAG
6760 ATTACTATTC
1 ATTACTATTC
*
6770 ATTAATATTC
1 ATTACTATTC
6780 ATTACTATTC
1 ATTACTATTC
6790 A
1 A
6791 CGTGAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTACTATTC
Found at i:11917 original size:15 final size:15
Alignment explanation
Indices: 11897--11931 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11887 GGTCGGGTCA
11897 TTCGGATCGAATCAT
1 TTCGGATCGAATCAT
**
11912 TTCGGATCGGGTCAT
1 TTCGGATCGAATCAT
11927 TTCGG
1 TTCGG
11932 GCTAGGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (15 bp):
TTCGGATCGAATCAT
Found at i:13386 original size:15 final size:15
Alignment explanation
Indices: 13360--13408 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
13350 CACATTTTTC
13360 ACAAAGATAAAATAAA
1 ACAAA-ATAAAATAAA
*
13376 ATAAAATAAAATAAA
1 ACAAAATAAAATAAA
13391 ACAAAATGAAAATGAAA
1 ACAAAAT-AAAAT-AAA
13408 A
1 A
13409 GAGGTGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 16 0.55
16 9 0.31
17 4 0.14
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (15 bp):
ACAAAATAAAATAAA
Found at i:13404 original size:6 final size:5
Alignment explanation
Indices: 13366--13408 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
13356 TTTCACAAAG
*
13366 ATAAA ATAAA ATAAA ATAAA ATAAA ACAAA ATGAAA ATGAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA AT-AAA A
13409 GAGGTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 25 0.71
6 10 0.29
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:19385 original size:33 final size:35
Alignment explanation
Indices: 19319--19406 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 35
19309 ATCTCAATGG
* *
19319 TTTTGTGTTTCAAAAGAAACATTTTCAATGG-T-T
1 TTTTGTGTTTCAAGAGAAACAATTTCAATGGTTCT
19352 TTTTGTGTTTCAAGAGAAACAATTTCAGA-GGTTTCT
1 TTTTGTGTTTCAAGAGAAACAATTTCA-ATGG-TTCT
*
19388 TTTTGTATTTCAAGAGAAA
1 TTTTGTGTTTCAAGAGAAA
19407 ATTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
33 27 0.56
34 1 0.02
35 1 0.02
36 19 0.40
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (35 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAATGGTTCT
Found at i:19399 original size:36 final size:33
Alignment explanation
Indices: 19294--19406 Score: 106
Period size: 33 Copynumber: 3.4 Consensus size: 33
19284 GACAGAACTC
* ** *
19294 GTTTCAAGGGAAATGATCTCAATGG--TTTTGT
1 GTTTCAAGAGAAACAATTTCAATGGTTTTTTGT
* *
19325 GTTTCAAAAGAAACATTTTCAATGGTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAATGGTTTTTTGT
19358 GTTTCAAGAGAAACAATTTCAGA-GGTTTCTTTTTGT
1 GTTTCAAGAGAAACAATTTCA-ATGG--T-TTTTTGT
*
19394 ATTTCAAGAGAAA
1 GTTTCAAGAGAAA
19407 ATTTTGTTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 19 0.28
33 27 0.40
34 1 0.01
35 1 0.01
36 19 0.28
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (33 bp):
GTTTCAAGAGAAACAATTTCAATGGTTTTTTGT
Found at i:19501 original size:37 final size:37
Alignment explanation
Indices: 19451--19885 Score: 178
Period size: 37 Copynumber: 12.7 Consensus size: 37
19441 TTTTTCGAGA
*
19451 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
*
19488 GAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
*
19525 GAAAACAGAT-TC-A-A-AG-----ATTTTGTTTCAAGG
1 G-AAACTG-TCTCAAGAGAGACAAAATTTTGTTTCAAGG
* * **
19555 GAAACTGTCTCAAGAGAAACGAAA-TTCATTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
* * * * *
19591 GAAA-TGTTTTC-A-A-TG-----TTTTTCTTTCAAAG
1 GAAACTG-TCTCAAGAGAGACAAAATTTTGTTTCAAGG
*
19620 GAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
* ** *
19657 GAAACTATCTCAAGAGAGACAAAA-TTCATTTAAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
* ** * * *
19693 GAGA-TGT-T-------TTCAATATTAATGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATT-TTGTTTCAAGG
* *
19722 GAAA-TCGTCTCAAGGGAGATAAAATTTTG-TTCAAGG
1 GAAACT-GTCTCAAGAGAGACAAAATTTTGTTTCAAGG
* * * * ** *
19758 GAAACTATCTCAAGCGATATAAAA-TTCATTTCGAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
** * *
19794 GAAA-TGT-T-----TTG--AATATTTATGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTT-TGTTTCAAGG
*
19823 GAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
* *
19860 GAACCTATCTCAAGAGAGACAAAATT
1 GAAACTGTCTCAAGAGAGACAAAATT
19886 CAGTTCAATT
Statistics
Matches: 287, Mismatches: 65, Indels: 92
0.65 0.15 0.21
Matches are distributed among these distances:
27 7 0.02
28 4 0.01
29 43 0.15
30 24 0.08
31 3 0.01
32 2 0.01
34 3 0.01
35 11 0.04
36 65 0.23
37 106 0.37
38 18 0.06
39 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (37 bp):
GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
Found at i:19518 original size:104 final size:103
Alignment explanation
Indices: 19404--19594 Score: 260
Period size: 104 Copynumber: 1.8 Consensus size: 103
19394 ATTTCAAGAG
* * *
19404 AAAATTTTGTTTCAA-GAAAAACATATTCAAATATTGGTT-TTTCGAGAGAAACTGTCTCAAGAG
1 AAAATTTTGTTTCAAGGAAAAACAGATTCAAAGATT--TTGTTTCAAGAGAAACTGTCTCAAGAG
* **
19467 AGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
64 AAACAAAA-TTCATTTCAAGGGAAACTGTCTCAAGGGAGAC
* *
19508 AAAATTTTGTTTCAAGGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAA
1 AAAATTTTGTTTCAAGGAAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAA
*
19573 ACGAAATTCATTTCAAGGGAAA
66 ACAAAATTCATTTCAAGGGAAA
19595 TGTTTTCAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
103 16 0.21
104 43 0.57
105 17 0.22
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (103 bp):
AAAATTTTGTTTCAAGGAAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAA
ACAAAATTCATTTCAAGGGAAACTGTCTCAAGGGAGAC
Found at i:19645 original size:65 final size:66
Alignment explanation
Indices: 19480--19661 Score: 233
Period size: 65 Copynumber: 2.8 Consensus size: 66
19470 CAAAACTTTG
19480 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAACAGATTCAAAGATTT
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGG-AAACAGATTCAAAGATTT
*
19545 TG
65 TC
* * * ** * * * *
19547 TTTCAAGGGAAACTGTCTCAAGAGAAACGAAA-TTCATTTCAAGGGAAA-TGTTTTCAATGTTTT
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAG-ATTCAAAGATTT
19610 TC
65 TC
*
19612 TTTCAAAGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC
1 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC
19662 TATCTCAAGA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
64 1 0.01
65 41 0.43
66 25 0.26
67 29 0.30
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (66 bp):
TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAGATTCAAAGATTTT
C
Found at i:19795 original size:36 final size:36
Alignment explanation
Indices: 19729--19797 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
19719 AGAGAAATCG
* *
19729 TCTCAAGGGAGATAAAATTTTGTTCAAGGGAAACTA
1 TCTCAAGCGAGATAAAATTATGTTCAAGGGAAACTA
* *
19765 TCTCAAGCGATATAAAATTCAT-TTCGAGGGAAA
1 TCTCAAGCGAGATAAAATT-ATGTTCAAGGGAAA
19798 TGTTTTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 27 0.96
37 1 0.04
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TCTCAAGCGAGATAAAATTATGTTCAAGGGAAACTA
Found at i:19801 original size:101 final size:102
Alignment explanation
Indices: 19536--19939 Score: 536
Period size: 102 Copynumber: 4.0 Consensus size: 102
19526 AAAACAGATT
* * *
19536 CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAAACGAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * *
19601 CAATGTTTTTCTTTCAA-AGGAAACTGTCTCAAGGGAGA
65 CAATATTTATGTTTCAAGA-GAAACTGTCTCAAGGGAGA
* *
19639 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTAAAGGGAGATGTTTTC
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
*
19704 AATATTAATGTTTCAAGAGAAA-TCGTCTCAAGGGAGA
66 AATATTTATGTTTCAAGAGAAACT-GTCTCAAGGGAGA
* * * * * *
19741 TAAAATTTTG-TTCAAGGGAAACTATCTCAAGCGATATAAAATTCATTTCGAGGGAAATGTTTTG
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
19805 AATATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
66 AATATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
* * * *
19842 CAAAATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCAGTTC-----AATTTTTTTC
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
* *
19902 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
66 AATATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
19939 C
1 C
19940 GAAACTTAGT
Statistics
Matches: 268, Mismatches: 29, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
97 43 0.16
101 91 0.34
102 129 0.48
103 5 0.02
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (102 bp):
CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
AATATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
Found at i:19990 original size:97 final size:97
Alignment explanation
Indices: 19597--19982 Score: 276
Period size: 101 Copynumber: 3.9 Consensus size: 97
19587 AAGGGAAATG
* * * * * * **
19597 TTTTCAATGTTTTTCTTTCAA-AGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TTTTCAATATTTATGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAA
* * * * *
19661 CTATCTCAAGAGAGACAAAATTCATTTAAAGGGAGATG
65 ATATCTCAAGAGAGACAAAATTCAGTT-CA---A-TTT
* * * * * **
19699 TTTTCAATATTAATGTTTCAAGAGAAA-TCGTCTCAAGGGAGATAAAATTTTG-TTCAAGGGAAA
1 TTTTCAATATTTATGTTTCAAGAGAAACT-GTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAA
* * * * * * *
19762 CTATCTCAAGCGATATAAAATTCATTTCGAGGGAAATG
65 ATATCTCAAGAGAGACAAAATTCAGTTC-----AATTT
* * * * ** **
19800 TTTTGAATATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACC
1 TTTTCAATATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAA
19865 TATCTCAAGAGAGACAAAATTCAGTTCAATTT
66 TATCTCAAGAGAGACAAAATTCAGTTCAATTT
* *
19897 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAACTTAG-TTCTAAAAGAAA
1 TTTTCAATATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTC-AAAAGAAA
* *
19961 ATGTCTCAAGGGAGACAAAATT
65 ATATCTCAAGAGAGACAAAATT
19983 TGTTTCAAGA
Statistics
Matches: 243, Mismatches: 31, Indels: 25
0.81 0.10 0.08
Matches are distributed among these distances:
96 3 0.01
97 73 0.30
101 86 0.35
102 79 0.33
103 1 0.00
105 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (97 bp):
TTTTCAATATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAA
TATCTCAAGAGAGACAAAATTCAGTTCAATTT
Found at i:19994 original size:19 final size:21
Alignment explanation
Indices: 19966--20013 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
19956 AGAAAATGTC
*
19966 TCAAGGGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
19987 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
20008 TCAAGA
1 TCAAGA
20014 AAAAAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:20471 original size:18 final size:18
Alignment explanation
Indices: 20444--20479 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20434 TGTTGAATCC
*
20444 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
*
20462 CCAAAAATGCCCTAATAT
1 CCAAAAATGCCCCAATAT
20480 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:20905 original size:22 final size:22
Alignment explanation
Indices: 20879--20933 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
20869 TTGTGTTTGG
*
20879 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
20901 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
20923 TCAAAGGTTTG
1 TCAAAGGTTTG
20934 ATGGGGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:21587 original size:15 final size:13
Alignment explanation
Indices: 21567--21606 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
21557 TTGTCACTTT
21567 TTCTTTCGATTTTTG
1 TTCTTTCG--TTTTG
21582 TTCTTTCGTTTTG
1 TTCTTTCGTTTTG
*
21595 TTCTTTTGTTTT
1 TTCTTTCGTTTT
21607 TTTCCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 16 0.67
15 8 0.33
ACGTcount: A:0.03, C:0.12, G:0.12, T:0.72
Consensus pattern (13 bp):
TTCTTTCGTTTTG
Found at i:21614 original size:14 final size:13
Alignment explanation
Indices: 21577--21638 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
21567 TTCTTTCGAT
*
21577 TTTTGTTCTTTCG
1 TTTTGTTCTTTTG
21590 TTTTGTTCTTTTG
1 TTTTGTTCTTTTG
* *
21603 TTTTTTTC-CTT-
1 TTTTGTTCTTTTG
*
21614 TTTTGCTTCTTTTC
1 TTTTG-TTCTTTTG
21628 TTTT-TTCTTTT
1 TTTTGTTCTTTT
21639 TACCCTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
11 4 0.10
12 12 0.29
13 21 0.51
14 4 0.10
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTTGTTCTTTTG
Found at i:21631 original size:24 final size:23
Alignment explanation
Indices: 21590--21639 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
21580 TGTTCTTTCG
*
21590 TTTTGTTCTTTTGTTTTTTTCCTT
1 TTTTGTTCTTTTGCTTTTTT-CTT
21614 TTTTGCTTCTTTT-CTTTTTTCTT
1 TTTTG-TTCTTTTGCTTTTTTCTT
21637 TTT
1 TTT
21640 ACCCTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 11 0.46
25 7 0.29
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (23 bp):
TTTTGTTCTTTTGCTTTTTTCTT
Found at i:21638 original size:22 final size:22
Alignment explanation
Indices: 21577--21639 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 22
21567 TTCTTTCGAT
* *
21577 TTTTG-TTCTTTCGTTTTGTTC
1 TTTTGCTTTTTTCTTTTTGTTC
*
21598 TTTTGTTTTTTTCCTTTTTTGCTTC
1 TTTTGCTTTTTT-C-TTTTTG-TTC
21623 TTTT-CTTTTTTCTTTTT
1 TTTTGCTTTTTTCTTTTT
21640 ACCCTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 5 0.14
22 10 0.29
23 2 0.06
24 11 0.31
25 7 0.20
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (22 bp):
TTTTGCTTTTTTCTTTTTGTTC
Found at i:24605 original size:21 final size:23
Alignment explanation
Indices: 24575--24616 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
24565 TAATAAATAT
24575 TAAATAAATTA-AAGAAAAAACA
1 TAAATAAATTATAAGAAAAAACA
*
24597 TAAA-AAATTATAATAAAAAA
1 TAAATAAATTATAAGAAAAAA
24617 TTATAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (23 bp):
TAAATAAATTATAAGAAAAAACA
Found at i:24627 original size:23 final size:23
Alignment explanation
Indices: 24564--24627 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 23
24554 AAAATATTAG
*
24564 ATAAT-AAATATTA-AATAAATT
1 ATAATAAAAAATTATAATAAATT
* * *
24585 A-AAGAAAAAA-CATAAAAAATT
1 ATAATAAAAAATTATAATAAATT
24606 ATAATAAAAAATTATAATAAAT
1 ATAATAAAAAATTATAATAAAT
24628 AAAATGGAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
20 3 0.09
21 13 0.41
22 8 0.25
23 8 0.25
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAATAAAAAATTATAATAAATT
Found at i:24631 original size:16 final size:13
Alignment explanation
Indices: 24596--24626 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
24586 AAGAAAAAAC
24596 ATAAAAAATTATA
1 ATAAAAAATTATA
24609 ATAAAAAATTATA
1 ATAAAAAATTATA
24622 ATAAA
1 ATAAA
24627 TAAAATGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAAAATTATA
Found at i:25765 original size:2 final size:2
Alignment explanation
Indices: 25760--25822 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
25750 GTAAATACAC
*
25760 AT AT AT AT -T AT -T AA AT A- 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
25799 AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
25823 ATTTGGAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50079 original size:6 final size:6
Alignment explanation
Indices: 50068--50113 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
50058 AGACACGTAT
50068 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
50114 CGAGACGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:50824 original size:21 final size:21
Alignment explanation
Indices: 50784--50824 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
50774 AATTTGGAAA
** *
50784 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
50805 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
50825 GCGAATTAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:53025 original size:111 final size:110
Alignment explanation
Indices: 52827--53120 Score: 419
Period size: 111 Copynumber: 2.6 Consensus size: 110
52817 AACTTTCAAA
* * ** *
52827 AAAGTATCGATCCTTTTTATAAAAAGTATTTATACTTTCAACATATCAGGTAAATTTTACCGGTT
1 AAAGTATCGATCATTTTTAT-AAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACC-GTT
* *
52892 TTGTAATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTGT
64 TTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTAT
* * * *
52939 AAAGTATCTATCTTTTTTATAAAAGGATCGATATTTTCAACATATAAGGTAAATTTTATCGTTTT
1 AAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCG-TTT
* *
53004 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTAT
65 TGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTAT
*
53050 AAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATCAA-GCAAATTTTACCGTTT
1 AAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATAT-AAGGTAAATTTTACCGTTT
53114 TGTCATA
65 TGTCATA
53121 TTTTTACTTG
Statistics
Matches: 163, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
110 11 0.07
111 132 0.81
112 20 0.12
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (110 bp):
AAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGTTTT
GTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTAT
Found at i:53866 original size:111 final size:111
Alignment explanation
Indices: 53672--53959 Score: 438
Period size: 111 Copynumber: 2.6 Consensus size: 111
53662 ATTTTACCGG
* *
53672 TTTTGTCATATTTTTACCTGTTTTATTGTAAAGTATCTATATTTTTTATAAAAGGATCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATACTTTTTATAAAAGGATCGATACTT
53737 TCAACATATAAGGTAAATTTTACCCTTTTTATCATAATGAAACTGA
66 TCAACATATAAGGTAAATTTTACCCTTTTTATCATAATGAAACTGA
* * *
53783 TTTTGTCATATTTTTACCTGGTATATTGTAAAGTATTTATCCTTTTTATAAAAGGATCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATACTTTTTATAAAAGGATCGATACTT
* *
53848 TCAACATATTAA-GTAAATTTTACCCTTTTTGTCATAATGAAACTGG
66 TCAACATA-TAAGGTAAATTTTACCCTTTTTATCATAATGAAACTGA
* * *
53894 TTTTGTCATATTTTTACCTGTTATATTGTATAA-TATCGATACATTTTTAT-AAAGTATTGATAC
1 TTTTGTCATATTTTTACCTGTTATATTGTA-AAGTATCTATAC-TTTTTATAAAAGGATCGATAC
53957 TTT
64 TTT
53960 ATATACGCTA
Statistics
Matches: 161, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
111 149 0.93
112 12 0.07
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.47
Consensus pattern (111 bp):
TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATACTTTTTATAAAAGGATCGATACTT
TCAACATATAAGGTAAATTTTACCCTTTTTATCATAATGAAACTGA
Found at i:54007 original size:782 final size:765
Alignment explanation
Indices: 52503--54650 Score: 3185
Period size: 782 Copynumber: 2.7 Consensus size: 765
52493 TGTTCATACT
* *
52503 TATTTCACTGTGAACAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAATATATTAATTTAG
1 TATTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
*
52568 TAATTATACGC-TTCTAATGATTTATTTTTTATGTTATGGTATATATTATTATTAAATTAAAAAC
66 TAATTATACGCGTT-TAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAAC
* * *
52632 AATAAACATATATATTACATATTTATCATTATCTTTGGTTAAAATTGTTAAATTTAAATTTTAAA
130 AATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAA
*
52697 TAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATAAAATTATTAAATTAAT
195 TAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAAT
52762 ATTGTAGGTGGAAAACATGAAACACTATT-AAAAATTGTTGAAACATAAATTACATAACTTTCAA
260 ATTGTAGGTGGAAAACATGAAACACTATTAAAAAATT-TTGAAACATAAATTACATAACTTTCAA
*
52826 AAAAGTATCGATCCTTTTTATAAAAAGTATTTATACTTTCAACATATCAGGTAAATTTTACCGGT
324 AAAAGTATCGATCCTTTTTATAAAAAGTATTTATACTTTCAACATATCAGATAAATTTTACC---
*
52891 TTTGTAATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTGTAAAGTATCTATCTTTTT
386 ----------TG--A--GATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCTTTTT
* *
52956 TATAAAAGGATCGATATTTTCAACATATAAGGTAAATTTTATCGTTTTTGTCATAATGAAACTGG
437 TATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGG
*
53021 TTTTGTCATATTTTTACCTGTTATATTATAAAGTATCGATCATTTTTATAAAAGGATCGATACTT
502 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAGGATCGATACTT
*
53086 TCAACATATCAAGCAAATTTTACCGTTTTGTCATATTTTTACTTGTTATATTGTAAAATATCGAT
567 TCAACATATCAAGCAAATTTTACCGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGAT
**
53151 ACATTTTTATAAAGTATCGATACTTTATAGGTGCTATTACTCCTTTTCTTTTAAATTCCAAAAGT
632 ACATTTTTATAAAGTATCGATACTTTATAGACGCTATTACTCCTTTTCTTTTAAATTCCAAAAGT
* *
53216 GTCGATACTTATTTAAATGGAATCGATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGG
697 GTCGATACTTATTTAAATGGAATCAATACTTTCAACATATCCGGTAGGTAGTTTAATGTAATAGG
*
53281 TAAG
762 CAAG
* *
53285 TATTTCACTGTGAAAAATATTAATTTAAGGTTATCTTTTGAGTGATATTTAAGATATTAATTTAG
1 TATTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
53350 TAATTATACGCGTTTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
66 TAATTATACGCGTTTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
*
53415 ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTATTAAATTTAAATTCTAAAT
131 ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
*
53480 AATATTTTATAAAATATCAAAACAATCAAATAATTTGTTGTGTAAATGAAATTATTAAATTAATA
196 AATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA
* *
53545 TTGTATGTGGAAAACATGAAACACTATTAAAAAATTTTGAAACTTAAATTACATAACTTTCAAAA
261 TTGTAGGTGGAAAACATGAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAAAA
* * *
53610 AAATATCGATCCTTTTTATAAAAAATATTTATACTTTCAATATATCAGATAAATTTTACC-G-G-
326 AAGTATCGATCCTTTTTATAAAAAGTATTTATACTTTCAACATATCAGATAAATTTTACCTGAGA
* *
53672 TTTTGTCATATTTTTACCTGTTTTATTGTAAAGTATCTATATTTTTTATAAAAGGATCGATACTT
391 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCTTTTTTATAAAAGGATCGATACTT
* * *
53737 TCAACATATAAGGTAAATTTTACCCTTTTTATCATAATGAAACTGATTTTGTCATATTTTTACCT
456 TCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCT
* ** * * *
53802 GGTATATTGTAAAGTATTTATCCTTTTTATAAAAGGATCGATACTTTCAACATATTAAGTAAATT
521 GTTATATTGTAAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATCAAGCAAATT
*
53867 TTACCCTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTATAATATCG
586 TTA----------C---------C--GTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCG
* * *
53932 ATACATTTTTATAAAGTATTGATACTTTATATACGCTATTACTGCTTTT-TTTTAAATTCCAAAA
630 ATACATTTTTATAAAGTATCGATACTTTATAGACGCTATTACTCCTTTTCTTTTAAATTCCAAAA
*
53996 GTGTTGATACTTATTTAAATGGAATCAATACTTTCAACATATCCGGTAGGTAGTTTAATGTAATA
695 GTGTCGATACTTATTTAAATGGAATCAATACTTTCAACATATCCGGTAGGTAGTTTAATGTAATA
54061 GGCAAG
760 GGCAAG
*
54067 TATTTCACTGTGAAAAACATTAATTTATGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
1 TATTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
* * * *
54132 TAATTATACGTGTCTAATGATTTATTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACA
66 TAATTATACGCGTTTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
*
54197 ATAAACATAGATATTACATATTTATTATTATCTTTTGTTAAAATTGTTAAATTTAAATTCTAAAT
131 ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
*
54262 AATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA
196 AATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA
*
54327 TTGTAGGTGGAAAACATGAAACACTATTAAAAAATTTTAAAACATAAATTACATAACTTTCAAAA
261 TTGTAGGTGGAAAACATGAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAAAA
* *
54392 AAGTATCGATCTTTTTTATAAAAAGTATCTATACTTTCAACATATCAGATAAATTTTACCGGTTT
326 AAGTATCGATCCTTTTTATAAAAAGTATTTATACTTTCAACATATCAGATAAATTTTA-C-----
* *
54457 TATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTTA
385 ---C----TG--A--GATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCTTTTTTA
* *
54522 TAAAAGGATCGATACTTTCAACATATAAGTTAAATTTTACTGTTTTTGTCATAATGAAACTGGTT
439 TAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTT
* * *
54587 TTGTCATATTTTTACTTGTTATATTGTAAAATATCGATACATTTTTAT-AAAGTATCGATACTTT
504 TTGTCATATTTTTACCTGTTATATTGTAAAGTATCGAT-CATTTTTATAAAAGGATCGATACTTT
54651 ATAGGCACTA
Statistics
Matches: 1244, Mismatches: 78, Indels: 68
0.89 0.06 0.05
Matches are distributed among these distances:
762 183 0.15
763 1 0.00
768 1 0.00
772 1 0.00
781 1 0.00
782 803 0.65
783 91 0.07
791 1 0.00
796 1 0.00
801 1 0.00
802 152 0.12
803 8 0.01
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (765 bp):
TATTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
TAATTATACGCGTTTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
AATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA
TTGTAGGTGGAAAACATGAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAAAA
AAGTATCGATCCTTTTTATAAAAAGTATTTATACTTTCAACATATCAGATAAATTTTACCTGAGA
TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCTTTTTTATAAAAGGATCGATACTT
TCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCT
GTTATATTGTAAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATCAAGCAAATT
TTACCGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCG
ATACTTTATAGACGCTATTACTCCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATG
GAATCAATACTTTCAACATATCCGGTAGGTAGTTTAATGTAATAGGCAAG
Found at i:54556 original size:111 final size:112
Alignment explanation
Indices: 54390--54650 Score: 357
Period size: 111 Copynumber: 2.3 Consensus size: 112
54380 TAACTTTCAA
* * *
54390 AAAAGTATCGAT-CTTTTTTATAAAAAGTATCTATACTTTCAACATATCAGATAAATTTTACCGG
1 AAAA-TATCGATACATTTTTAT-AAAAGTATCGATACTTTCAACATATAAGATAAATTTTACCGG
54454 TTTTATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
64 TTTTATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
* * * * * * * *
54503 AAAGTTTCTAT-CCTTTTTATAAAAGGATCGATACTTTCAACATATAAGTTAAATTTTACTGTTT
1 AAAATATCGATACATTTTTATAAAAGTATCGATACTTTCAACATATAAGATAAATTTTACCGGTT
* * *
54567 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACTTGTTATATTGT
66 TTATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
54614 AAAATATCGATACATTTTTAT-AAAGTATCGATACTTT
1 AAAATATCGATACATTTTTATAAAAGTATCGATACTTT
54651 ATAGGCACTA
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
111 105 0.81
112 21 0.16
113 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.45
Consensus pattern (112 bp):
AAAATATCGATACATTTTTATAAAAGTATCGATACTTTCAACATATAAGATAAATTTTACCGGTT
TTATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
Found at i:54622 original size:691 final size:688
Alignment explanation
Indices: 53701--55321 Score: 2595
Period size: 692 Copynumber: 2.4 Consensus size: 688
53691 GTTTTATTGT
* * * * *
53701 AAAGTATCTATATTTTTTAT-AAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCCTTT
1 AAAGTATCGATCTTTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTA-CC-TT
*
53765 TTATCATAATGAAACTGATTTTGTCATATTTTTACCTGGTATATTGTAAAGTATT-TATCCTTTT
64 TTATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGT-TTCTATCCTTTT
*
53829 TATAAAAGGATCGATACTTTCAACATATTAAGTAAATTTTACCCTTTTTGTCATAATGAAACTGG
128 TATAAAAGGATCGATACTTTCAACATA-TAAGTAAATTTTACCGTTTTTGTCATAATGAAACTGG
* * *
53894 TTTTGTCATATTTTTACCTGTTATATTGTATAATATCGATACATTTTTATAAAGTATTGATACTT
192 TTTTGTCATATTTTTACATGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTT
* * * *
53959 TATATACGCTATTACTGCTTTT-TTTTAAATTCCAAAAGTGTTGATACTTATTTAAATGGAATCA
257 TATAGACACTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCA
*
54023 ATACTTTCAACATATCCGGTAGGTAGTTTAATGTAATAGGCAAGTATTTCACTGTGAAAAACATT
322 ATACTTTCAACATATCCGGTAGGTAGTTTAATGTAATAGGCAAGTATTTCACTGTAAAAAACATT
* *
54088 AATTTATGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAGTAATTATACGTGTCTAATGAT
387 AATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAGTAATTATACGCGTCTAATGAT
54153 TTATTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATAT
452 TTATTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATAT
* * * *
54218 TTATTATTATCTTTTGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATAAAA
517 TTATTATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATAAAA
54283 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
582 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGG-AAACATGAAA
54348 CACTATTAAAAAATTTT-AAAACATAAATTACATAACTTTCAAA
646 CACTATTAAAAAATTTTGAAAA-ATAAATTACATAACTTTCAAA
*
54391 AAAGTATCGATCTTTTTTATAAAAAGTATCTATACTTTCAACATATCAGATAAATTTTACCGGTT
1 AAAGTATCGATCTTTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACC--TT
54456 TTATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTT
64 TTATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTT
*
54521 ATAAAAGGATCGATACTTTCAACATATAAGTTAAATTTTACTGTTTTTGTCATAATGAAACTGGT
129 ATAAAAGGATCGATACTTTCAACATATAAG-TAAATTTTACCGTTTTTGTCATAATGAAACTGGT
*
54586 TTTGTCATATTTTTACTTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTT
193 TTTGTCATATTTTTACATGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTT
* *
54651 ATAGGCACTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCGA
258 ATAGACACTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCAA
* * *
54716 TACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAATATTA
323 TACTTTCAACATATCCGGTAGGTAGTTTAATGTAATAGGCAAGTATTTCACTGTAAAAAACATTA
* * * *
54781 ATTTAAGGTTATCTTTTTAGTGATATTTAAGATATTATTTTAGTAATTATATGCGTCTAATGATT
388 ATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAGTAATTATACGCGTCTAATGATT
*
54846 TATTTTTTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATATT
453 TATTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATATT
*
54911 TATTATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATCAAAA
518 TATTATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATAAAAA
54976 CAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAACATGAAACA
583 CAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAACATGAAACA
*
55041 CTATTAAAAATTTTTGAAAAATAAATTACATAACTTTCAAA
648 CTATTAAAAAATTTTGAAAAATAAATTACATAACTTTCAAA
*
55082 AAAGTATCGATCCTTTTTATAAAAAGTATCTATACTTTCAACATATCAGGT-AA----A--TTTT
1 AAAGTATCGATCTTTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCTTTT
*
55140 ATC-----G-----G-TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTAT
66 ATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTTAT
*
55194 AAAATGATCGATACTTTCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTT
131 AAAAGGATCGATACTTTCAACATATAA-GTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTT
* * * *
55259 TATCATATTTTTACATGTTATATTGTAAAATATCTAT-CCTTTTTATAAAAGGATCGATACTTT
195 TGTCATATTTTTACATGTTATATTGTAAAATATCGATACATTTTTAT-AAAGTATCGATACTTT
55322 CAACATATCA
Statistics
Matches: 877, Mismatches: 46, Indels: 35
0.92 0.05 0.04
Matches are distributed among these distances:
670 8 0.01
671 158 0.18
672 2 0.00
677 1 0.00
682 7 0.01
686 1 0.00
690 28 0.03
691 331 0.38
692 341 0.39
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (688 bp):
AAAGTATCGATCTTTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCTTTT
ATCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTTAT
AAAAGGATCGATACTTTCAACATATAAGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTT
GTCATATTTTTACATGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTTATA
GACACTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCAATAC
TTTCAACATATCCGGTAGGTAGTTTAATGTAATAGGCAAGTATTTCACTGTAAAAAACATTAATT
TAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAGTAATTATACGCGTCTAATGATTTAT
TTTGTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATATTTAT
TATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATAAAAACAA
TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAACATGAAACACTA
TTAAAAAATTTTGAAAAATAAATTACATAACTTTCAAA
Found at i:55337 original size:111 final size:111
Alignment explanation
Indices: 55143--55419 Score: 473
Period size: 111 Copynumber: 2.5 Consensus size: 111
55133 AAATTTTATC
* *
55143 GGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAATGATCGATAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCCTTTTTATAAAAGGATCGATAC
*
55208 TTTCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACT
66 TTTCAACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACT
* *
55254 GGTTTTATCATATTTTTACATGTTATATTGTAAAATATCTATCCTTTTTATAAAAGGATCGATAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCCTTTTTATAAAAGGATCGATAC
*
55319 TTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAACT
66 TTTCAACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACT
* *
55365 GGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAA
1 GGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTAT-CCTTTTTATAAA
55420 GTACTGATAC
Statistics
Matches: 155, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
111 144 0.93
112 11 0.07
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (111 bp):
GGTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCCTTTTTATAAAAGGATCGATAC
TTTCAACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACT
Found at i:56909 original size:220 final size:220
Alignment explanation
Indices: 56559--57390 Score: 1279
Period size: 220 Copynumber: 3.8 Consensus size: 220
56549 GAGAAAATTG
* * * * * *
56559 GGTCAATCTGGAAAAAACTTGGTTTTGAAGACGACTCTGCTCATCCGTGTTGAATAGATATGGTC
1 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
* * * * * * *
56624 GCTTTCAAATAAATTGTTTGTTGGAGATGACATTGTTCCCTCTCGTTGAGGAAGTCAGGTCAATC
66 TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTCTCGTTGAGGAAGTCGGGTCAATC
* * *
56689 TGGAGATAATTTGGAGACAACACGGTTCCTTCGCATTGAGGAAGTCTGATTGTCTGAGGATGACA
131 TGGAGATAATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
56754 CTGCTCCTTCGTGTTGAGGAGATCA
196 CTGCTCCTTCGTGTTGAGGAGATCA
*
56779 GGTCAATCTGGAGACAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
1 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
*
56844 GT-TTTCAGATAAATTGTTTGTTGGAGATGACGTTGTTTCTTCTCGTTGAGGAAGTCGGGTCAAT
66 -TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTCTCGTTGAGGAAGTCGGGTCAAT
* * *
56908 CTGGAGATAATTTGGAGACAACATGATTTCTTCGCGTTGAGGAAGTTTGATTGTCTGATGATGAC
130 CTGGAGATAATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGAC
* * *
56973 ACTACTCCTTCATGTTGAGGAGATTA
195 ACTGCTCCTTCGTGTTGAGGAGATCA
* * * * *
56999 GGTCAATCTAGAGATAATTTGTTGTTGAAGATGACTCTGCTCATCCGTGTTGAAGAGATCTGGTC
1 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
* * *
57064 TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTTCGTTGAGGAAGTCGAGTCAATT
66 TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTCTCGTTGAGGAAGTCGGGTCAATC
*
57129 TGGAGATAATTTAGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
131 TGGAGATAATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
57194 CTGCTCCTTCGTGTTGAGGAGATCA
196 CTGCTCCTTCGTGTTGAGGAGATCA
* * **
57219 GGTCAATCTGGAGATAATTTGGTGTTGAAGACAACTATACTCATATGTGTTGAAGAGATATGGTC
1 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
* * *
57284 TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTTCATTGAGGAAGTCGGGTCAATA
66 TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTCTCGTTGAGGAAGTCGGGTCAATC
*
57349 TGGAGATAATTTGGAGACAACATGATTCCTTCGTGTTGAGGA
131 TGGAGATAATTTGGAGACAACATGATTCCTTCGCGTTGAGGA
57391 GATAGGGTCA
Statistics
Matches: 558, Mismatches: 52, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
219 1 0.00
220 557 1.00
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (220 bp):
GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTCTCGTTGAGGAAGTCGGGTCAATC
TGGAGATAATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
CTGCTCCTTCGTGTTGAGGAGATCA
Found at i:57908 original size:103 final size:103
Alignment explanation
Indices: 57768--57997 Score: 234
Period size: 103 Copynumber: 2.3 Consensus size: 103
57758 GGTGAGATAA
* *
57768 AATTTTGTTTCGAGTGAAAC-ATTT-CAAAATTTATGTTTCAAGGGAAAACTATCTCAA-TCGGG
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTATGTTTCAAGGGAAAACTATCTCAAGT-GAG
* * *
57830 AAGAAATTTGCTTTTAAGAAAAACAATCTCAAATGTCATC
65 AAGAAATTAGCTTTTAAGAAAAA-AATCTCAAACGACATC
*** * ** * *
57870 -ATTTTGTTTCAAGTGAAACAATTTCCAGTTTTTGTGTTTTGAGGGAAAATTGTCTCAAGTGAGA
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTATGTTTCAAGGGAAAACTATCTCAAGTGAGA
* * * * * *
57934 CGAAATTAGTTTTTAGGAAAAATATCTCAAGCGAGATC
66 AGAAATTAGCTTTTAAGAAAAAAATCTCAAACGACATC
*
57972 AATTTTGTTTCAAGTGAATCAATTTC
1 AATTTTGTTTCAAGTGAAACAATTTC
57998 AAATTTTGAG
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
101 18 0.17
102 15 0.14
103 70 0.67
104 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (103 bp):
AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTATGTTTCAAGGGAAAACTATCTCAAGTGAGA
AGAAATTAGCTTTTAAGAAAAAAATCTCAAACGACATC
Found at i:58177 original size:37 final size:36
Alignment explanation
Indices: 58065--58180 Score: 106
Period size: 37 Copynumber: 3.2 Consensus size: 36
58055 CAAGGATTTG
* *
58065 TGTTTCAAGAGAAATTGTCTCAAGCGAGAAAAAATT
1 TGTTTCAAGAAAAATTGTCTCAAGCGAGATAAAATT
** *** * * *
58101 TGTTTTTAGAAGAAACAATCTCAAGTGAGATTAATTT
1 TGTTTCAAGAA-AAATTGTCTCAAGCGAGATAAAATT
* *
58138 TGTTTCAAGAAAAATTGTCTCAAACGAGATGAAACTT
1 TGTTTCAAGAAAAATTGTCTCAAGCGAGAT-AAAATT
58175 TGTTTC
1 TGTTTC
58181 GGGATAAACA
Statistics
Matches: 59, Mismatches: 19, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
36 22 0.37
37 37 0.63
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (36 bp):
TGTTTCAAGAAAAATTGTCTCAAGCGAGATAAAATT
Found at i:65655 original size:5 final size:5
Alignment explanation
Indices: 65645--65675 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
65635 TTTCACAAAG
*
65645 ATAAA ATAAA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
65676 GTGAAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:69316 original size:10 final size:10
Alignment explanation
Indices: 69298--69328 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
69288 TTTTTACGAG
69298 ATTACTATTC
1 ATTACTATTC
*
69308 ATTAATATTC
1 ATTACTATTC
69318 ATTACTATTC
1 ATTACTATTC
69328 A
1 A
69329 CGTGAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTACTATTC
Found at i:74476 original size:15 final size:15
Alignment explanation
Indices: 74456--74490 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
74446 GGTCGGGTCA
74456 TTCGGATCGAATCAT
1 TTCGGATCGAATCAT
**
74471 TTCGGATCGGGTCAT
1 TTCGGATCGAATCAT
74486 TTCGG
1 TTCGG
74491 GCTAGGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (15 bp):
TTCGGATCGAATCAT
Found at i:77835 original size:43 final size:43
Alignment explanation
Indices: 77787--77875 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
77777 ACTATATTTA
* *
77787 TTACTTGTATGAGAGCTCTTTATTTAATATTTGTATTTAAAAT
1 TTACTTGAATGAGAGCTCTTTATTTAATACTTGTATTTAAAAT
*
77830 TTACTTGAATGAGAGCTCTTTATTTAATGCTTGTATTTAAAAT
1 TTACTTGAATGAGAGCTCTTTATTTAATACTTGTATTTAAAAT
77873 TTA
1 TTA
77876 TTTTCTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.49
Consensus pattern (43 bp):
TTACTTGAATGAGAGCTCTTTATTTAATACTTGTATTTAAAAT
Found at i:81249 original size:2 final size:2
Alignment explanation
Indices: 81244--81294 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
81234 GTAAATACAC
*
81244 AT AT AT AT -T AT -T AA AT A- 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
81283 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
81295 ATTTAGAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:81918 original size:36 final size:33
Alignment explanation
Indices: 81814--81926 Score: 124
Period size: 33 Copynumber: 3.4 Consensus size: 33
81804 GACAGAACTC
* * *
81814 GTTTCAAGGGAAACGATCTCAATGG--TTTTGT
1 GTTTCAAGAGAAACAATTTCAATGGTTTTTTGT
* *
81845 GTTTCAAAAGAAACATTTTCAATGGTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAATGGTTTTTTGT
81878 GTTTCAAGAGAAACAATTTCAGA-GGTTTCTTTTTGT
1 GTTTCAAGAGAAACAATTTCA-ATGG--T-TTTTTGT
81914 GTTTCAAGAGAAA
1 GTTTCAAGAGAAA
81927 ATTTTGTTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
31 20 0.29
33 27 0.39
34 1 0.01
35 1 0.01
36 20 0.29
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (33 bp):
GTTTCAAGAGAAACAATTTCAATGGTTTTTTGT
Found at i:82012 original size:37 final size:37
Alignment explanation
Indices: 81961--82114 Score: 148
Period size: 37 Copynumber: 4.4 Consensus size: 37
81951 CAAATATTGG
* * *
81961 TGTTTCGAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
81998 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
82035 TGTTTCAAGGGAAAACAGAT-TC-A-A-AG-----ATTT
1 TGTTTCAAGGG-AAACTG-TCTCAAGAGAGACAAAATTT
*
82065 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
**
82101 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
82115 TGTTTTCAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
28 1 0.01
29 7 0.07
30 16 0.16
31 1 0.01
32 2 0.02
35 2 0.02
36 14 0.14
37 46 0.47
38 7 0.07
39 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:82039 original size:104 final size:103
Alignment explanation
Indices: 81924--82114 Score: 276
Period size: 104 Copynumber: 1.8 Consensus size: 103
81914 GTTTCAAGAG
* * *
81924 AAAATTTTGTTTCAA-GAAAAACATATTCAAATATTGGTGTTTCGAGAGAAACTGTCTCAAGAGA
1 AAAATTTTGTTTCAAGGAAAAACAGATTCAAAGATT-GTGTTTCAAGAGAAACTGTCTCAAGAGA
**
81988 GACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
65 GACAAAA-TTCATTTCAAGGGAAACTGTCTCAAGGGAGAC
* * *
82028 AAAATTTTGTTTCAAGGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 AAAATTTTGTTTCAAGGAAAAACAGATTCAAAGATTGTGTTTCAAGAGAAACTGTCTCAAGAGAG
*
82093 ACGAAATTCATTTCAAGGGAAA
66 ACAAAATTCATTTCAAGGGAAA
82115 TGTTTTCAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
103 14 0.18
104 46 0.60
105 17 0.22
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (103 bp):
AAAATTTTGTTTCAAGGAAAAACAGATTCAAAGATTGTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAACTGTCTCAAGGGAGAC
Found at i:82159 original size:65 final size:66
Alignment explanation
Indices: 82000--82181 Score: 217
Period size: 65 Copynumber: 2.8 Consensus size: 66
81990 CAAAACTTTG
*
82000 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAACAGATTCAAAGATTT
1 TTTCAAAGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGG-AAACAGATTCAAAGATTT
*
82065 TG
65 TC
* * * ** * * *
82067 TTTCAAGGGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA-TGTTTTCAATG-TGT
1 TTTCAAAGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAG-ATTCAAAGAT-T
82129 TTC
64 TTC
*
82132 TTTCAAATGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC
1 TTTCAAAGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC
82182 TATCTCAAGA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
64 2 0.02
65 40 0.41
66 25 0.26
67 30 0.31
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (66 bp):
TTTCAAAGGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACAGATTCAAAGATTTT
C
Found at i:82282 original size:203 final size:198
Alignment explanation
Indices: 82056--82511 Score: 556
Period size: 203 Copynumber: 2.3 Consensus size: 198
82046 AAAACAGATT
82056 CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTTTGTTT-AAGGGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTT
*
82121 CAATGTGTT-TCTTTCAA-ATGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTA
64 CAATAT-TTATCTTTCAAGA-GAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTA
*
82184 TCTCAAGAGAGACAAAATTCATTTAAAGGGAGATGTTTTCAATATTAATGTTTCAAGAGAAACCG
127 TCTCAAGAGAGACAAAATTCAGTT-AA---A-ATGTTTTCAATATTAATGTTTCAAGAGAAACCG
*
82249 TCTCAAGGGAGA
187 TCTCAAGAGAGA
* * * ** * *
82261 CAAAATTTTGTTTAAGGGAAACTATCTCAAGCGATATAAAATTCATTTCGAGGGAAATGTTTTGA
1 CAAAATTTTGTTTAAGGGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCA
* *
82326 ATATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCTC
66 ATATTTATCTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTC
* * * * * **
82391 AAGAGAGACAAAATTCAGTTCAATTTTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGAG
131 AAGAGAGACAAAATTCAGTTAAAATGTTTTCAATATTAATGTTTCAAGAGAAACCGTCTCAAGAG
82456 AGA
196 AGA
* * * ** * * **
82459 CGAAACTTAGTTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAG
1 CAAAATTTTGTT-TAAGGGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAG
82512 AGAGACAAAA
Statistics
Matches: 215, Mismatches: 33, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
198 47 0.22
199 30 0.14
202 3 0.01
203 121 0.56
204 10 0.05
205 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (198 bp):
CAAAATTTTGTTTAAGGGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCA
ATATTTATCTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTC
AAGAGAGACAAAATTCAGTTAAAATGTTTTCAATATTAATGTTTCAAGAGAAACCGTCTCAAGAG
AGA
Found at i:82329 original size:101 final size:101
Alignment explanation
Indices: 82056--82459 Score: 525
Period size: 102 Copynumber: 4.0 Consensus size: 101
82046 AAAACAGATT
* *
82056 CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * *
82121 CAATGTGTTTCTTTCAA-ATGAAACTGTCTCAAGGGAGA
65 CAATAT-TATGTTTCAAGA-GAAACTGTCTCAAGGGAGA
* *
82159 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTAAAGGGAGATGTTTTC
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
*
82224 AATATTAATGTTTCAAGAGAAACCGTCTCAAGGGAGA
66 AATATT-ATGTTTCAAGAGAAACTGTCTCAAGGGAGA
* * * * *
82261 CAAAATTTTGTTT-AAGGGAAACTATCTCAAGCGATATAAAATTCATTTCGAGGGAAATGTTTTG
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
82325 AATATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
66 AATA-TTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
* * * *
82362 CAAAATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCAGTTC-----AATTTTTTTC
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
* * *
82422 AATGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGA
66 AAT-ATTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
82459 C
1 C
82460 GAAACTTAGT
Statistics
Matches: 269, Mismatches: 27, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
97 41 0.15
101 91 0.34
102 132 0.49
103 5 0.02
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.31
Consensus pattern (101 bp):
CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
AATATTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
Found at i:82510 original size:97 final size:97
Alignment explanation
Indices: 82132--82502 Score: 271
Period size: 101 Copynumber: 3.7 Consensus size: 97
82122 AATGTGTTTC
* * * ** *
82132 TTTCAA-ATGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 TTTCAAGA-GAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAATATCTCAAGAGAGA
* * * * *
82196 CAAAATTCATTTAAAGGGAGATGTTTTCAATATTAATG
65 CAAAATTCAGTT-CA---A-TTTTTTTCAATATTTATG
* * * * ** * * * *
82234 TTTCAAGAGAAACCGTCTCAAGGGAGACAAAATTTTGTTT-AAGGGAAACTATCTCAAGCGATAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAATATCTCAAGAGAGAC
* * * *
82298 AAAATTCATTTCGAGGGAAATGTTTTGAATATTTATG
66 AAAATTCAGTTC-----AATTTTTTTCAATATTTATG
* * * ** **
82335 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAATATCTCAAGAGAGAC
*
82400 AAAATTCAGTTCAATTTTTTTCAATGTTTATG
66 AAAATTCAGTTCAATTTTTTTCAATATTTATG
* * * *
82432 TTTCAAGAGAAATTGTCTCAAGAGAGACGAAACTTAG-TTCTAAAAGAAAATGTCTCAAGGGAGA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTC-AAAAGAAAATATCTCAAGAGAGA
*
82496 CGAAATT
65 CAAAATT
82503 TGTTTCAAGA
Statistics
Matches: 232, Mismatches: 29, Indels: 21
0.82 0.10 0.07
Matches are distributed among these distances:
96 3 0.01
97 71 0.31
101 87 0.38
102 69 0.30
103 1 0.00
105 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (97 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAATATCTCAAGAGAGAC
AAAATTCAGTTCAATTTTTTTCAATATTTATG
Found at i:82514 original size:19 final size:21
Alignment explanation
Indices: 82486--82533 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
82476 AGAAAATGTC
* *
82486 TCAAGGGAGACGAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
82507 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
82528 TCAAGA
1 TCAAGA
82534 AAAACAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:82540 original size:21 final size:21
Alignment explanation
Indices: 82498--82540 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
82488 AAGGGAGACG
* *
82498 AAATTTGTTTCAAGAGAGACA
1 AAATTTGTTTCAAGAAAAACA
82519 AAATTTGTTTCAAGAAAAACA
1 AAATTTGTTTCAAGAAAAACA
82540 A
1 A
82541 CCTTGAGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (21 bp):
AAATTTGTTTCAAGAAAAACA
Found at i:83422 original size:22 final size:22
Alignment explanation
Indices: 83396--83450 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
83386 TTGTGTTTGG
*
83396 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
*
83418 TCAAAAGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
83440 TCAAAGGTTTG
1 TCAAAGGTTTG
83451 ATGGGATAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:84123 original size:13 final size:13
Alignment explanation
Indices: 84095--84158 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
84085 TTCTTTCGAT
*
84095 TTTTGTTCTTTCG
1 TTTTGTTCTTTTG
84108 TTTTGTTCTTTTG
1 TTTTGTTCTTTTG
84121 TTTT-TT-TTCCTT-
1 TTTTGTTCTT--TTG
*
84133 TTTTGCTTCTTTTC
1 TTTTG-TTCTTTTG
*
84147 TTTTTTTCTTTT
1 TTTTGTTCTTTT
84159 TACCCTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
11 2 0.05
12 6 0.14
13 27 0.63
14 6 0.14
15 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (13 bp):
TTTTGTTCTTTTG
Found at i:84125 original size:39 final size:39
Alignment explanation
Indices: 84082--84158 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
84072 TTTTTGTCAT
*
84082 TTTTTCTTTCGATTTTTG-TTC-TTTCGTTTTGTTCTTTTG
1 TTTTT-TTTCCATTTTTGCTTCTTTTC-TTTTGTTCTTTTG
* *
84121 TTTTTTTTCCTTTTTTGCTTCTTTTCTTTTTTTCTTTT
1 TTTTTTTTCCATTTTTGCTTCTTTTCTTTTGTTCTTTT
84159 TACCCTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 10 0.30
39 19 0.58
40 4 0.12
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (39 bp):
TTTTTTTTCCATTTTTGCTTCTTTTCTTTTGTTCTTTTG
Found at i:84126 original size:15 final size:14
Alignment explanation
Indices: 84081--84125 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
84071 TTTTTTGTCA
84081 TTTT-TTCTTTCGAT
1 TTTTGTTCTTTCG-T
84095 TTTTGTTCTTTCG-
1 TTTTGTTCTTTCGT
*
84108 TTTTGTTCTTTTGT
1 TTTTGTTCTTTCGT
84122 TTTT
1 TTTT
84126 TTTCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 12 0.43
14 8 0.29
15 8 0.29
ACGTcount: A:0.02, C:0.11, G:0.11, T:0.76
Consensus pattern (14 bp):
TTTTGTTCTTTCGT
Found at i:84136 original size:17 final size:17
Alignment explanation
Indices: 84116--84171 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
84106 CGTTTTGTTC
84116 TTTTGTTTTTTTTCCTT
1 TTTTGTTTTTTTTCCTT
* *
84133 TTTTGCTTCTTTT-CTT
1 TTTTGTTTTTTTTCCTT
* * *
84149 TTTT-TCTTTTTACCCT
1 TTTTGTTTTTTTTCCTT
84165 TTTTGTT
1 TTTTGTT
84172 CTGATTGAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
15 4 0.14
16 13 0.45
17 12 0.41
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTTGTTTTTTTTCCTT
Found at i:84150 original size:25 final size:24
Alignment explanation
Indices: 84108--84159 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
84098 TGTTCTTTCG
*
84108 TTTTGTTCTTTTGTTTTTTTTCCTT
1 TTTTGTTCTTTTGCTTTTTTT-CTT
84133 TTTTGCTTCTTTT-CTTTTTTTCTT
1 TTTTG-TTCTTTTGCTTTTTTTCTT
84157 TTT
1 TTT
84160 ACCCTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 12 0.48
26 7 0.28
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (24 bp):
TTTTGTTCTTTTGCTTTTTTTCTT
Found at i:84159 original size:31 final size:31
Alignment explanation
Indices: 84113--84173 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
84103 TTTCGTTTTG
*
84113 TTCTTTTGTTTTTTTT-CCTTTTTTGCTTCTT
1 TTCTTTTGTTTTTTTTACCCTTTTTG-TTCTT
84144 TTCTTTT-TTTCTTTTTACCCTTTTTGTTCT
1 TTCTTTTGTTT-TTTTTACCCTTTTTGTTCT
84174 GATTGAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 3 0.11
31 16 0.59
32 8 0.30
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (31 bp):
TTCTTTTGTTTTTTTTACCCTTTTTGTTCTT
Found at i:87136 original size:13 final size:13
Alignment explanation
Indices: 87120--87147 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
87110 TAAAAAACAT
87120 AAAAATTATAATA
1 AAAAATTATAATA
87133 AAAAATTATAATA
1 AAAAATTATAATA
87146 AA
1 AA
87148 TAAAATGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAATTATAATA
Found at i:88290 original size:2 final size:2
Alignment explanation
Indices: 88285--88347 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
88275 GTAAATACAC
*
88285 AT AT AT AT -T AT -T AA AT A- 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
88324 AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
88348 ATTTGGAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.