Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006066.1 Hibiscus syriacus cultivar Beakdansim tig00014345_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: 70120
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2574 original size:35 final size:35
Alignment explanation
Indices: 2494--2609 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
2484 CAAAATCATC
*
2494 ATTTCCAATACTAGTGGGATAACCTAATTTGAGCAT
1 ATTTCCAATACTAGTGGGAAAACCTAATTT-AGCAT
*
2530 ATTTGCAATACTAGTGGGAAAACCTAATTTAGCAT
1 ATTTCCAATACTAGTGGGAAAACCTAATTTAGCAT
* *
2565 ATTTCCAATACTAATGGGAAAACCTAATTTATCAT
1 ATTTCCAATACTAGTGGGAAAACCTAATTTAGCAT
2600 ATTTCCAATA
1 ATTTCCAATA
2610 TTGAGCATTA
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 47 0.63
36 28 0.37
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (35 bp):
ATTTCCAATACTAGTGGGAAAACCTAATTTAGCAT
Found at i:5500 original size:216 final size:216
Alignment explanation
Indices: 5126--5545 Score: 657
Period size: 216 Copynumber: 1.9 Consensus size: 216
5116 GTGAGAAAGT
5126 AAAAAAGGTGAGATGAATTGTTGTAAAAGATAAAATAATATATATTATTTTAATCAATATTTTTT
1 AAAAAAGGTGAGATGAATTGTTGTAAAAGATAAAATAATATATATTATTTTAATCAATATTTTTT
*
5191 TTAATTTAAAAATTTAGAATAAAAGTTGACATTGGTTTCTTACCCACGTCAAAGAGCACAAAACT
66 TTAATTTAAAAATTTAGAATAAAAGTTGACATTGGCTTCTTACCCACGTCAAAGAGCACAAAACT
*
5256 CAAAAAATAGATGTACAGAAGTTTTAACTCTTAATATAATATATTAAATATT-GATACTTTTTTA
131 CAAAAAATAGATGTACAGAAGTTTTAACTCTTAATAAAATATATTAAATATTAG-TACTTTTTTA
*
5320 AGGAAAATGGGAGAAAGTAAAA
195 AGAAAAATGGGAGAAAGTAAAA
* **
5342 AAAAAAGGTGAGATGAATTGTTGTAAAAGGTAAAATGGTATATATTATTTTAATCAATA-TTTTT
1 AAAAAAGGTGAGATGAATTGTTGTAAAAGATAAAATAATATATATTATTTTAATCAATATTTTTT
** * *
5406 TTAATTTAAAAATTTAGAATAAAAGGTTGACATTGGCTTCTTACTTACGTCAAAGAGTACAAAGC
66 TTAATTTAAAAATTTAGAATAAAA-GTTGACATTGGCTTCTTACCCACGTCAAAGAGCACAAAAC
* * * * *
5471 TCAAGAAATA-AGTGTGCATAATTTTTAACTCTTAATAAAATATATTAAATGTTAGTACTTTTTT
130 TCAAAAAATAGA-TGTACAGAAGTTTTAACTCTTAATAAAATATATTAAATATTAGTACTTTTTT
5535 AAGAAAAATGG
194 AAGAAAAATGG
5546 ATATGCATTT
Statistics
Matches: 186, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
215 30 0.16
216 155 0.83
217 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (216 bp):
AAAAAAGGTGAGATGAATTGTTGTAAAAGATAAAATAATATATATTATTTTAATCAATATTTTTT
TTAATTTAAAAATTTAGAATAAAAGTTGACATTGGCTTCTTACCCACGTCAAAGAGCACAAAACT
CAAAAAATAGATGTACAGAAGTTTTAACTCTTAATAAAATATATTAAATATTAGTACTTTTTTAA
GAAAAATGGGAGAAAGTAAAA
Found at i:6560 original size:26 final size:25
Alignment explanation
Indices: 6510--6564 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
6500 ATGCAATTTG
* *
6510 AAAGTTGGATGATAAAATAAAAAATT
1 AAAGTTGAATGATAAAACAAAAAA-T
* *
6536 AAAGTTGAATGATAAAACCAGAAAT
1 AAAGTTGAATGATAAAACAAAAAAT
6561 AAAG
1 AAAG
6565 ACAAAATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (25 bp):
AAAGTTGAATGATAAAACAAAAAAT
Found at i:7126 original size:37 final size:38
Alignment explanation
Indices: 7048--7132 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 38
7038 ATTTAAATGA
* * *
7048 TAAACGAACACAAATAAAAGAACATAAACAAACGGATG
1 TAAACGAACACAAATAAAAGAACAGAAACAAACAGACG
* *
7086 TAAACGAACAC-AATAAATGAACAGAAACGAACTAG-CG
1 TAAACGAACACAAATAAAAGAACAGAAACAAAC-AGACG
7123 TAAACGAACA
1 TAAACGAACA
7133 TAAACAAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 29 0.71
38 12 0.29
ACGTcount: A:0.58, C:0.18, G:0.14, T:0.11
Consensus pattern (38 bp):
TAAACGAACACAAATAAAAGAACAGAAACAAACAGACG
Found at i:7175 original size:23 final size:23
Alignment explanation
Indices: 7149--7197 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
7139 AACCTGTACA
* *
7149 AACATAACAAATGAACATAATCG
1 AACACAACAAATGAACATAAACG
* *
7172 AACACAATAAATGAACGTAAACG
1 AACACAACAAATGAACATAAACG
7195 AAC
1 AAC
7198 GTAAACAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (23 bp):
AACACAACAAATGAACATAAACG
Found at i:7433 original size:34 final size:34
Alignment explanation
Indices: 7390--7472 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
7380 AAATGAAAGG
*
7390 ACATTAACGAACATACACAGACATAAATAAACGA
1 ACATAAACGAACATACACAGACATAAATAAACGA
* * *
7424 ACATAAACGATCACACACCGACATAAATAAACGA
1 ACATAAACGAACATACACAGACATAAATAAACGA
* *
7458 ATATAAATGAACATA
1 ACATAAACGAACATA
7473 AATGAACGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.55, C:0.20, G:0.08, T:0.16
Consensus pattern (34 bp):
ACATAAACGAACATACACAGACATAAATAAACGA
Found at i:8987 original size:20 final size:20
Alignment explanation
Indices: 8962--9003 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
8952 TAAATTAACA
8962 AATAGACATAGATAAGATTT
1 AATAGACATAGATAAGATTT
8982 AATAGACATAGATAAGATTT
1 AATAGACATAGATAAGATTT
9002 AA
1 AA
9004 AAGAAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (20 bp):
AATAGACATAGATAAGATTT
Found at i:9767 original size:28 final size:27
Alignment explanation
Indices: 9726--9804 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
9716 ATAAATAATT
*
9726 AAAAAT-TAAAAATAAAGAAAAAGAAGA
1 AAAAATATATAAATAAAGAAAAA-AAGA
*
9753 AAAAATATATAAATAAA-ACAAATAAATA
1 AAAAATATATAAATAAAGA-AAA-AAAGA
9781 AAATAATA-ATAAA-AAAGAAAAAAA
1 AAA-AATATATAAATAAAGAAAAAAA
9805 ATAATATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 3 0.07
27 13 0.29
28 24 0.53
29 5 0.11
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (27 bp):
AAAAATATATAAATAAAGAAAAAAAGA
Found at i:9770 original size:24 final size:23
Alignment explanation
Indices: 9737--9812 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 23
9727 AAAATTAAAA
*
9737 ATAAAGAAAAAGAAGAAAAAATAT
1 ATAAATAAAAAGAA-AAAAAATAT
*
9761 ATAAATAAAACAAATAAATAAAATA-
1 ATAAATAAAA-AGA-AAA-AAAATAT
9786 AT-AATAAAAAAGAAAAAAAATAAT
1 ATAAAT-AAAAAGAAAAAAAAT-AT
9810 ATA
1 ATA
9813 TATATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
22 5 0.12
23 4 0.10
24 16 0.38
25 10 0.24
26 7 0.17
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.17
Consensus pattern (23 bp):
ATAAATAAAAAGAAAAAAAATAT
Found at i:9831 original size:55 final size:54
Alignment explanation
Indices: 9712--9833 Score: 138
Period size: 55 Copynumber: 2.2 Consensus size: 54
9702 AAATAGTGAG
* * *
9712 TAAAATAAATAATTAAAAATTAAAAATAAAGAAAAAGAAGAAAAAATATATAAA
1 TAAAATAAATAAATAAAAAATAAAAATAAAGAAAAAAAAGAAAAAATATATAAA
* * * * *
9766 TAAAACAAATAAATAAAATAATAATAAA-AAAGAAAAAAAATAATATATATATATA
1 TAAAATAAATAAATAAAA-AATAA-AAATAAAGAAAAAAAAGAAAAAATATATAAA
*
9821 TATAATAAATAAA
1 TAAAATAAATAAA
9834 AACATAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
54 16 0.29
55 37 0.66
56 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (54 bp):
TAAAATAAATAAATAAAAAATAAAAATAAAGAAAAAAAAGAAAAAATATATAAA
Found at i:9921 original size:46 final size:45
Alignment explanation
Indices: 9774--9925 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 45
9764 AATAAAACAA
* * *
9774 ATAAATAAAATAATAATAAAAA-AGAAAAAA-AAT-AATATATATAT
1 ATAAATTAAA-AA-AATAAAAACATAAAAAATAGTAAATATATATAT
* *
9818 ATATA-T-AATAAATAAAAACATAAAAAATAGTAAATATATATAT
1 ATAAATTAAAAAAATAAAAACATAAAAAATAGTAAATATATATAT
* * *
9861 ATAAATTAATAAAATAAATA-ATAAAAACATA-TATATATATATAT
1 ATAAATTAAAAAAATAAAAACATAAAAA-ATAGTAAATATATATAT
*
9905 ATGTAATCTAAAAAAATAAAA
1 AT-AAAT-TAAAAAAATAAAA
9926 TATATATTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
40 8 0.09
41 8 0.09
42 4 0.05
43 15 0.17
44 26 0.30
45 15 0.17
46 11 0.13
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (45 bp):
ATAAATTAAAAAAATAAAAACATAAAAAATAGTAAATATATATAT
Found at i:10541 original size:36 final size:37
Alignment explanation
Indices: 10450--10560 Score: 154
Period size: 37 Copynumber: 3.0 Consensus size: 37
10440 ACGCTTGTGG
* *
10450 ATCCTATTTTTAGGAGTTTGAA-TCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATTC-TAGTAAAATTCT
10487 ATCCTATTTTTAGGAGTTTGAATTCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATTCTAGTAAAATTCT
* * *
10524 ATCCTA-TTTTAAGAGTTTGAATCCTAGTAAACTTCT
1 ATCCTATTTTTAGGAGTTTGAATTCTAGTAAAATTCT
10560 A
1 A
10561 ACGTTATGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
36 28 0.41
37 38 0.56
38 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATTCTAGTAAAATTCT
Found at i:11191 original size:34 final size:34
Alignment explanation
Indices: 11153--11265 Score: 201
Period size: 34 Copynumber: 3.3 Consensus size: 34
11143 GGTCTTGGGA
*
11153 TTCAAGAGAAACATTTTCAAAGGTTTTTTTGTGT
1 TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
11187 TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
1 TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
11221 TTCAAGAGAAACAATTTCAAAGGATTTTTTT-TGT
1 TTCAAGAGAAACAATTTCAAAGG-TTTTTTTGTGT
11255 TTCAAGAGAAA
1 TTCAAGAGAAA
11266 TTGTCTCAAG
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
34 70 0.91
35 7 0.09
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.40
Consensus pattern (34 bp):
TTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
Found at i:11299 original size:37 final size:36
Alignment explanation
Indices: 11250--11554 Score: 315
Period size: 37 Copynumber: 8.4 Consensus size: 36
11240 AAGGATTTTT
* * *
11250 TTTGTTTCAAGAGAAATTGTCTCAAGGGAGGCAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
11286 TTTTGTTTCAAGAGAAACATAT-TC---AGAG-----A
1 -TTTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAA
*
11315 TTGGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA
1 TT--TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
11353 CTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
11390 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAG----A--CAAAA
11432 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
11468 CTTAGTTCCAAAAGAAATTGTCTCAATG-GAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAA
* *
11505 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
11541 TTTGTTTCAAGAGA
1 TTTGTTTCAAGAGA
11555 GACAAAACTT
Statistics
Matches: 228, Mismatches: 18, Indels: 45
0.78 0.06 0.15
Matches are distributed among these distances:
28 2 0.01
29 3 0.01
30 17 0.07
33 4 0.02
34 3 0.01
35 1 0.00
36 75 0.33
37 80 0.35
38 5 0.02
39 2 0.01
40 1 0.00
42 35 0.15
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:11406 original size:36 final size:36
Alignment explanation
Indices: 11319--11554 Score: 312
Period size: 36 Copynumber: 6.3 Consensus size: 36
11309 CAGAGATTGG
*
11319 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
11356 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
11392 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG----A--CAAAATT
11434 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
11471 AGTTCCAAAAGAAATTGTCTCAATG-GAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAATT
* *
11507 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
11543 TGTTTCAAGAGA
1 TGTTTCAAGAGA
11555 GACAAAACTT
Statistics
Matches: 176, Mismatches: 14, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
35 1 0.01
36 75 0.43
37 62 0.35
38 2 0.01
40 1 0.01
42 35 0.20
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:11412 original size:73 final size:72
Alignment explanation
Indices: 11319--11554 Score: 319
Period size: 73 Copynumber: 3.2 Consensus size: 72
11309 CAGAGATTGG
11319 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAG
11384 ACAAAATT
65 ACAAAATT
* *
11392 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAATTTGTTTCAAGAGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA-A-AG----AGACAAAATTTGTTTCAAGGGAAACTGTCTCAA
11457 GAGAGACAAAACTT
60 GAGAGACAAAA-TT
* * * * **
11471 AGTTCCAAAAGAAATTGTCTCAATGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
11536 TAAAATT
66 CAAAATT
11543 TGTTTCAAGAGA
1 TGTTTCAAGAGA
11555 GACAAAACTT
Statistics
Matches: 142, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
72 11 0.08
73 64 0.45
74 1 0.01
75 2 0.01
77 1 0.01
78 35 0.25
79 28 0.20
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (72 bp):
TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
CAAAATT
Found at i:11447 original size:115 final size:115
Alignment explanation
Indices: 11319--11535 Score: 355
Period size: 115 Copynumber: 1.9 Consensus size: 115
11309 CAGAGATTGG
* * **
11319 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAA-GAGA
1 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAATG-GA
11383 GACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAATT
65 GACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAATT
* *
11434 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAATGGAG
1 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAATGGAG
*
11499 ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
66 ACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
11536 TAAAATTTGT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
115 93 0.99
116 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (115 bp):
TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAATGGAG
ACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGGCAAAATT
Found at i:11552 original size:21 final size:22
Alignment explanation
Indices: 11526--11569 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
11516 GGAAACTGTC
*
11526 TCAAGAGAGATAAAA-TTTGTT
1 TCAAGAGAGACAAAACTTTGTT
11547 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAACTTTGTT
11569 T
1 T
11570 TGAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (22 bp):
TCAAGAGAGACAAAACTTTGTT
Found at i:11569 original size:22 final size:21
Alignment explanation
Indices: 11496--11569 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
11486 TGTCTCAATG
11496 GAGACAAAATTTGTTTCAAG-
1 GAGACAAAATTTGTTTCAAGA
* *
11516 G-G---AAA-CTGTCTCAAGA
1 GAGACAAAATTTGTTTCAAGA
*
11532 GAGATAAAATTTGTTTCAAGA
1 GAGACAAAATTTGTTTCAAGA
11553 GAGACAAAACTTTGTTT
1 GAGACAAAA-TTTGTTT
11570 TGAGTAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
15 8 0.19
16 4 0.10
17 1 0.02
19 1 0.02
20 4 0.10
21 17 0.40
22 7 0.17
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (21 bp):
GAGACAAAATTTGTTTCAAGA
Found at i:11863 original size:116 final size:116
Alignment explanation
Indices: 11658--11887 Score: 381
Period size: 116 Copynumber: 2.0 Consensus size: 116
11648 CCTGAAGATA
* *
11658 AATGTTGCTAGTGAGTATGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGT
1 AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGT
*
11723 GAAGTTAAGCCTTGAATTGGATATCCTTCGCCGTGAAGTTGAAATCCAATT
66 GAAGTTAAGCCTTGAATTGAATATCCTTCGCCGTGAAGTTGAAATCCAATT
* *
11774 AATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGT
1 AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGT
* *
11839 GAAGTTGAGCCTT-AACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
66 GAAGTTAAGCCTTGAA-TTGAATATCCTTCGCCGTGAAGTTGAAATCCAA
11888 GCTTATATTG
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 2 0.02
116 104 0.98
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (116 bp):
AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGT
GAAGTTAAGCCTTGAATTGAATATCCTTCGCCGTGAAGTTGAAATCCAATT
Found at i:16312 original size:4 final size:4
Alignment explanation
Indices: 16303--16363 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
16293 ATAGTGAGTA
* * * * * *
16303 AAAT AAAT AAAT AAAT AAAT AAAA AGAAG AAAA AAAT ATAG AAAT AAAAC
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT -AAAT
16353 AAAT AAAT AAA
1 AAAT AAAT AAA
16364 ATAATAATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
4 39 0.87
5 6 0.13
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (4 bp):
AAAT
Found at i:16325 original size:21 final size:21
Alignment explanation
Indices: 16216--16374 Score: 60
Period size: 21 Copynumber: 7.3 Consensus size: 21
16206 AAAAGGTAAG
16216 AAATAAATAAATAAATAAAATTA
1 AAATAAATAAATAAAT-AAA-TA
* * * *
16239 AAATGAAGAAA-AAACAAATT
1 AAATAAATAAATAAATAAATA
* *
16259 AAATAAA-AGATAAGATAAAGA
1 AAATAAATAAATAA-ATAAATA
* * * *
16280 AAGTAAAGATAAA-ATAGTGAGTA
1 AAAT-AA-ATAAATA-AATAAATA
16303 AAATAAATAAATAAATAAATA
1 AAATAAATAAATAAATAAATA
* *
16324 AAA-AGAAGAAA-AAA-ATATA
1 AAATA-AATAAATAAATAAATA
*
16343 GAAATAAAACAAATAAATAAAATA
1 -AAAT-AAATAAATAAAT-AAATA
16367 ATAATAAA
1 A-AATAAA
16375 AAAGTTAAAA
Statistics
Matches: 98, Mismatches: 23, Indels: 30
0.65 0.15 0.20
Matches are distributed among these distances:
19 6 0.06
20 16 0.16
21 33 0.34
22 12 0.12
23 21 0.21
24 10 0.10
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.19
Consensus pattern (21 bp):
AAATAAATAAATAAATAAATA
Found at i:16392 original size:2 final size:2
Alignment explanation
Indices: 16387--16451 Score: 51
Period size: 2 Copynumber: 32.5 Consensus size: 2
16377 AGTTAAAATA
* * * * * * *
16387 AT AT AT AT AT AT AT AT AT AT A- AT AA AT AA AA AC AT AA AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16428 AT AGT AT AT AT AT AT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT A
16452 AATTTATAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
1 1 0.02
2 51 0.94
3 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (2 bp):
AT
Found at i:16436 original size:44 final size:47
Alignment explanation
Indices: 16381--16492 Score: 142
Period size: 44 Copynumber: 2.5 Consensus size: 47
16371 TAAAAAAGTT
* *
16381 AAAATAATATATATATATATATATAT-AATAAATAAAA-ACATAA-A
1 AAAATAGTATATATATATATATATATAAATAAATAAAACAAATAATA
**
16425 AAAATAGTATATATATATATATATATAAATTTATAAAACAAATAATA
1 AAAATAGTATATATATATATATATATAAATAAATAAAACAAATAATA
* *
16472 AAAA-AGAACATATATATATAT
1 AAAATAGTATATATATATATAT
16493 GTAATCTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
44 25 0.42
45 9 0.15
46 20 0.34
47 5 0.08
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (47 bp):
AAAATAGTATATATATATATATATATAAATAAATAAAACAAATAATA
Found at i:17107 original size:37 final size:35
Alignment explanation
Indices: 17057--17160 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 35
17047 TTGTGGATCT
17057 TATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCC
1 TATTTTTAGGAGTTTGAATC-TAGTA-AACTCTATCC
17094 TATTTTTAGGAGTTTGAATTCTAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAA-TCTAGT-AAACTCTATCC
*
17131 TATGTTTAGGAGTTTGAATCCTAGTAAACT
1 TATTTTTAGGAGTTTGAAT-CTAGTAAACT
17161 TCTAACGTTA
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
36 6 0.10
37 54 0.86
38 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.41
Consensus pattern (35 bp):
TATTTTTAGGAGTTTGAATCTAGTAAACTCTATCC
Found at i:17828 original size:35 final size:36
Alignment explanation
Indices: 17756--17838 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
17746 GGTCTTGGAA
* *
17756 TTCAAGAGAAACATTTTCAAAGCTTTTTTTTTGTGT
1 TTCAAGAGAAATAATTTCAAAGCTTTTTTTTTGTGT
*
17792 TTCAAGAGAAATAATTTCAAAGGTTTTTTTTT-TGT
1 TTCAAGAGAAATAATTTCAAAGCTTTTTTTTTGTGT
17827 TTCAAGAGAAAT
1 TTCAAGAGAAAT
17839 TGTCTCATGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 15 0.34
36 29 0.66
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (36 bp):
TTCAAGAGAAATAATTTCAAAGCTTTTTTTTTGTGT
Found at i:17979 original size:36 final size:36
Alignment explanation
Indices: 17892--18155 Score: 253
Period size: 37 Copynumber: 7.3 Consensus size: 36
17882 CAGAGATTGG
17892 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
17929 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
17965 TGTTTCAAGAGAAACTGTCTCAACAGAGACAAAGGCAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC--A---AAA-TT
18007 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
18044 AGTTCCAAAAGAAATTGTCTCAATG-GAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAATT
* * *
18080 TGTTT-AATGTA-AAAATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAACTGTCTCAAGAGAGACAAAATT
* *
18108 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
18144 TGTTTCAAGAGA
1 TGTTTCAAGAGA
18156 GACAAAACTT
Statistics
Matches: 187, Mismatches: 20, Indels: 41
0.75 0.08 0.17
Matches are distributed among these distances:
28 14 0.07
29 4 0.02
30 1 0.01
31 1 0.01
32 4 0.02
34 1 0.01
35 4 0.02
36 54 0.29
37 67 0.36
38 2 0.01
40 1 0.01
41 3 0.02
42 31 0.17
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:18153 original size:21 final size:22
Alignment explanation
Indices: 18127--18170 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
18117 GGAAACTGTC
*
18127 TCAAGAGAGATAAAA-TTTGTT
1 TCAAGAGAGACAAAACTTTGTT
18148 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAACTTTGTT
18170 T
1 T
18171 TGAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (22 bp):
TCAAGAGAGACAAAACTTTGTT
Found at i:18464 original size:116 final size:116
Alignment explanation
Indices: 18259--18488 Score: 318
Period size: 116 Copynumber: 2.0 Consensus size: 116
18249 CCTGAAGATA
* * * *
18259 AATGTTGCTAGTGGGTACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCATTGT
1 AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGACCCATTCATTGT
* *
18324 GAAGTTCAGCCTTGAATTGGATATCCTTCGCCGTGAAGTTGAAATCCAATG
66 GAAGTTCAGCCTTGAATTGAATATCCTTCGCCGTAAAGTTGAAATCCAATG
* *** *
18375 AATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGGTTCATTCGTTGT
1 AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGACCCATTCATTGT
* **
18440 GAAGTTGAGCCTT-AACTTGAATATCCTTCGTTGTAAAGTTGAAATCCAA
66 GAAGTTCAGCCTTGAA-TTGAATATCCTTCGCCGTAAAGTTGAAATCCAA
18489 GCTTATATTG
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
115 2 0.02
116 97 0.98
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (116 bp):
AATGTTGCTAGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGACCCATTCATTGT
GAAGTTCAGCCTTGAATTGAATATCCTTCGCCGTAAAGTTGAAATCCAATG
Found at i:23374 original size:3 final size:3
Alignment explanation
Indices: 23366--23394 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23356 AAAACAAATA
23366 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23395 AGTAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23424 original size:32 final size:29
Alignment explanation
Indices: 23341--23471 Score: 88
Period size: 28 Copynumber: 4.3 Consensus size: 29
23331 AAAAAAGAAG
* * *
23341 AAAAAATATATAAATAAAACAAATAAATA
1 AAAAAATATATATATAATATAAATAAATA
*
23370 ATAATAATA-ATA-ATAATA-ATAATAAAGTA
1 A-AAAAATATATATATAATATA-AATAAA-TA
*
23399 AAAAAATATATATATATATATATAATAAAAA
1 AAAAAATATATATATA-ATATA-AATAAATA
* *
23430 CATAAAAATAGTAAATATATATATAAATTAATA
1 -A-AAAAATA-TATATATA-ATATAAATAAATA
23463 AAACAAATA
1 AAA-AAATA
23472 ATAAAAAATA
Statistics
Matches: 84, Mismatches: 7, Indels: 19
0.76 0.06 0.17
Matches are distributed among these distances:
27 1 0.01
28 17 0.20
29 10 0.12
30 9 0.11
31 6 0.07
32 15 0.18
33 13 0.15
34 13 0.15
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (29 bp):
AAAAAATATATATATAATATAAATAAATA
Found at i:23446 original size:40 final size:38
Alignment explanation
Indices: 23352--23520 Score: 129
Period size: 40 Copynumber: 4.3 Consensus size: 38
23342 AAAAATATAT
*
23352 AAATAAAACA-AATAAATA-ATA-ATA-ATAATAATAATA
1 AAATAAAA-ATAATAAATATATATATATATATTAATAA-A
23388 ATAATAAAGTAA-AA-AAATATATATATATATATATAATAAA
1 A-AATAAA--AATAATAAATATATATATATATAT-TAATAAA
*
23428 AACATAAAAATAGTAAATATATATATA-A-ATTAATAAAA
1 AA-ATAAAAATAATAAATATATATATATATATTAAT-AAA
*
23466 CAAATAATAAAAAATAACATATATATATATATATGTAATCTAAA
1 -AAATAA-AAATAATAA-ATATATATATATATAT-TAA--TAAA
23510 AAATAAAAATA
1 AAATAAAAATA
23521 TATACTAAAG
Statistics
Matches: 109, Mismatches: 5, Indels: 32
0.75 0.03 0.22
Matches are distributed among these distances:
36 1 0.01
37 15 0.14
38 17 0.16
39 16 0.15
40 34 0.31
41 7 0.06
42 6 0.06
43 9 0.08
44 3 0.03
45 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (38 bp):
AAATAAAAATAATAAATATATATATATATATTAATAAA
Found at i:23551 original size:74 final size:75
Alignment explanation
Indices: 23399--23543 Score: 165
Period size: 72 Copynumber: 2.0 Consensus size: 75
23389 TAATAAAGTA
* * *
23399 AAAAAATATATATATATATATATAATAAAAACATAAAAATAGTAAATATATATATAAATTAATAA
1 AAAAAATACATATATATATATATAATAAAAACATAAAAATAGTAAAAATATATATAAAGTAATAA
*
23464 AACAAATAAT
66 AAAAAATAAT
** *
23474 AAAAAATAACATATATATATATAT-ATGTAATC-TAAAAA-A-TAAAAATATATACTAAAGTAA-
1 AAAAAAT-ACATATATATATATATAATAAAAACATAAAAATAGTAAAAATATATA-TAAAGTAAT
23534 AAAAGAAAAT
64 AAAA-AAAAT
23544 GCATAAAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
72 15 0.25
73 12 0.20
74 6 0.10
75 12 0.20
76 15 0.25
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (75 bp):
AAAAAATACATATATATATATATAATAAAAACATAAAAATAGTAAAAATATATATAAAGTAATAA
AAAAAATAAT
Found at i:24105 original size:37 final size:37
Alignment explanation
Indices: 24064--24194 Score: 199
Period size: 37 Copynumber: 3.5 Consensus size: 37
24054 CTTGTGGATT
24064 CTATTTTTAGGAGTTTGAATTATAGTAGAACTCTATC
1 CTATTTTTAGGAGTTTGAATTATAGTAGAACTCTATC
*
24101 CTATTTTTAGGAGTTTGAATTATAGTAGAATTCTATC
1 CTATTTTTAGGAGTTTGAATTATAGTAGAACTCTATC
* * * * * *
24138 CTATTTTTAAGAGTTTGAATTCTAATAAAACTATATT
1 CTATTTTTAGGAGTTTGAATTATAGTAGAACTCTATC
24175 CTATTTTTAGGAGTTTGAAT
1 CTATTTTTAGGAGTTTGAAT
24195 CCTAGTAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 85 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTGAATTATAGTAGAACTCTATC
Found at i:24204 original size:37 final size:37
Alignment explanation
Indices: 24064--24209 Score: 193
Period size: 37 Copynumber: 3.9 Consensus size: 37
24054 CTTGTGGATT
*
24064 CTATTTTTAGGAGTTTGAATTATAGTAGAACTCTATC
1 CTATTTTTAGGAGTTTGAATTATAGTAAAACTCTATC
* *
24101 CTATTTTTAGGAGTTTGAATTATAGTAGAATTCTATC
1 CTATTTTTAGGAGTTTGAATTATAGTAAAACTCTATC
* * * * *
24138 CTATTTTTAAGAGTTTGAATTCTAATAAAACTATATT
1 CTATTTTTAGGAGTTTGAATTATAGTAAAACTCTATC
** *
24175 CTATTTTTAGGAGTTTGAATCCTAGTAAAATTCTA
1 CTATTTTTAGGAGTTTGAATTATAGTAAAACTCTA
24210 ACGTTATGTT
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTGAATTATAGTAAAACTCTATC
Found at i:27844 original size:13 final size:13
Alignment explanation
Indices: 27826--27873 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
27816 AACGGTCAAT
27826 GGGTCGGGTAAAC
1 GGGTCGGGTAAAC
*
27839 GGGTCGGGTCAAC
1 GGGTCGGGTAAAC
* * *
27852 AGGACAGGTAAAC
1 GGGTCGGGTAAAC
27865 GGGTCGGGT
1 GGGTCGGGT
27874 CGGGTTATGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.46, T:0.15
Consensus pattern (13 bp):
GGGTCGGGTAAAC
Found at i:29096 original size:31 final size:31
Alignment explanation
Indices: 29060--29118 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
29050 ATACACAATT
29060 ACTTTCGTTTTTATTTAATTAAGATATGATC
1 ACTTTCGTTTTTATTTAATTAAGATATGATC
29091 ACTTTCGTTTTTATTTAATTAAGATATG
1 ACTTTCGTTTTTATTTAATTAAGATATG
29119 GTCATCACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
ACTTTCGTTTTTATTTAATTAAGATATGATC
Found at i:29340 original size:31 final size:30
Alignment explanation
Indices: 29295--29435 Score: 107
Period size: 31 Copynumber: 4.8 Consensus size: 30
29285 GTGACACTAT
*
29295 ATATACTTTGAAAAGTTAAAATAATAATAAA
1 ATATA-TTTTAAAAGTTAAAATAATAATAAA
* * * *
29326 ATATATTTTCAAAAGTTTAGATAAGAAGGAAA
1 ATATATTTT-AAAAGTTAAAATAATAA-TAAA
* *
29358 ATATATTTTTAAA-TTAAAATAA-AA-ATA
1 ATATATTTTAAAAGTTAAAATAATAATAAA
* *
29385 AT-T-TTTTTAAA-TTAAATTAATAATAAA
1 ATATATTTTAAAAGTTAAAATAATAATAAA
*
29412 ATATA-TTTAATAAGTTAATATAAT
1 ATATATTTTAA-AAGTTAAAATAAT
29436 TTTTTCTTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
25 16 0.18
26 3 0.03
27 8 0.09
28 5 0.06
29 4 0.05
30 18 0.20
31 22 0.25
32 12 0.14
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (30 bp):
ATATATTTTAAAAGTTAAAATAATAATAAA
Found at i:29397 original size:25 final size:25
Alignment explanation
Indices: 29355--29410 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
29345 GATAAGAAGG
29355 AAAAT-ATATTTTTAAATTAAAATA
1 AAAATAATATTTTTAAATTAAAATA
* *
29379 AAAATAATTTTTTTAAATTAAATTA
1 AAAATAATATTTTTAAATTAAAATA
*
29404 ATAATAA
1 AAAATAA
29411 AATATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAATAATATTTTTAAATTAAAATA
Found at i:30155 original size:22 final size:21
Alignment explanation
Indices: 30129--30172 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
30119 ATCGCTGTTG
30129 TCGTTG-TCGATATCATTTGTCA
1 TCGTTGATCGA-ATC-TTTGTCA
*
30151 TCGTTGATTGAATCTTTGTCA
1 TCGTTGATCGAATCTTTGTCA
30172 T
1 T
30173 TTATCCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 9 0.45
23 3 0.15
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (21 bp):
TCGTTGATCGAATCTTTGTCA
Found at i:31498 original size:2 final size:2
Alignment explanation
Indices: 31491--31535 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
31481 AACAATTTCT
31491 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31533 TC T
1 TC T
31536 TTCAGAATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:34377 original size:11 final size:11
Alignment explanation
Indices: 34361--34417 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
34351 TTACATTATA
34361 AAAAATATATT
1 AAAAATATATT
34372 AAAAATATATT
1 AAAAATATATT
***
34383 ATTGATA-ATT
1 AAAAATATATT
34393 ATAAAAT-T-TT
1 A-AAAATATATT
34403 AAAAATATATT
1 AAAAATATATT
34414 AAAA
1 AAAA
34418 TTTCTATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
9 5 0.14
10 8 0.22
11 23 0.64
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATATT
Found at i:34950 original size:7 final size:7
Alignment explanation
Indices: 34940--35007 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
34930 AAACTAAGAT
34940 TTAAACC
1 TTAAACC
34947 TTAAACC
1 TTAAACC
*
34954 TTAAATC
1 TTAAACC
* *
34961 GTAAATAC
1 TTAAA-CC
*
34969 -TAAATC
1 TTAAACC
34975 TTAAACC
1 TTAAACC
34982 TTAAACAC
1 TTAAAC-C
*
34990 -TAAATC
1 TTAAACC
34996 TTAAACC
1 TTAAACC
*
35003 ATAAA
1 TTAAA
35008 ACCTGACCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 2 0.04
7 45 0.92
8 2 0.04
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.29
Consensus pattern (7 bp):
TTAAACC
Found at i:34958 original size:28 final size:28
Alignment explanation
Indices: 34915--35007 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 28
34905 CTTTGTAATG
* *
34915 AACCCTAAACCCTAAAAACTAAGAT-TTA
1 AACCTTAAACCTTAAAAACTAA-ATATTA
* *
34943 AACCTTAAACCTT-AAATCGTAAATACTA
1 AACCTTAAACCTTAAAAAC-TAAATATTA
* * *
34971 AATCTTAAACCTTAAACACTAAATCTTA
1 AACCTTAAACCTTAAAAACTAAATATTA
*
34999 AACCATAAA
1 AACCTTAAA
35008 ACCTGACCAC
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
27 6 0.12
28 42 0.82
29 3 0.06
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26
Consensus pattern (28 bp):
AACCTTAAACCTTAAAAACTAAATATTA
Found at i:34972 original size:21 final size:21
Alignment explanation
Indices: 34948--35007 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
34938 ATTTAAACCT
* * *
34948 TAAACCTTAAATCGTAAATAC
1 TAAATCTTAAACCGTAAACAC
*
34969 TAAATCTTAAACCTTAAACAC
1 TAAATCTTAAACCGTAAACAC
*
34990 TAAATCTTAAACCATAAA
1 TAAATCTTAAACCGTAAA
35008 ACCTGACCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (21 bp):
TAAATCTTAAACCGTAAACAC
Found at i:38523 original size:17 final size:16
Alignment explanation
Indices: 38501--38546 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
38491 GGCTCGTTAA
38501 AAATTCGAGTCGAGCT
1 AAATTCGAGTCGAGCT
*
38517 CAAATTCGAGTTGAGCT
1 -AAATTCGAGTCGAGCT
* *
38534 GAGTTCGAGTCGA
1 AAATTCGAGTCGA
38547 TTCCATTCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (16 bp):
AAATTCGAGTCGAGCT
Found at i:40177 original size:37 final size:36
Alignment explanation
Indices: 40134--40235 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
40124 ATAGTATAAC
40134 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
40171 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
40205 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
40236 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:41081 original size:105 final size:105
Alignment explanation
Indices: 40783--41548 Score: 1069
Period size: 105 Copynumber: 7.3 Consensus size: 105
40773 CATTGTTCCA
* * * * ** * * *
40783 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
40848 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ***
40889 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTTAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
40949 AGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
40989 AATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
41054 AACGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
41094 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
41159 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
41199 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
41264 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
41304 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
41369 AGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
41409 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
41474 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
41515 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
41549 CGCAGATGGC
Statistics
Matches: 597, Mismatches: 52, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
99 1 0.00
100 78 0.13
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.01
105 402 0.67
106 79 0.13
107 4 0.01
109 21 0.04
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:42285 original size:67 final size:65
Alignment explanation
Indices: 42152--42545 Score: 247
Period size: 65 Copynumber: 5.8 Consensus size: 65
42142 AAGATATCTG
* * * **
42152 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
42217 TT
64 TT
* * *
42219 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
42284 T
65 T
* ** * *
42285 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA-----T--A-A-A
** *
42349 GACAAA-ACT
56 TTCAAAGATT
* * * * * * * * * *
42358 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * *
42423 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA-T-
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T-AA-ATTC
* *
42486 AGACGAAAT
59 A-AAG-ATT
* * *
42495 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
42546 CTATCTCAAG
Statistics
Matches: 254, Mismatches: 51, Indels: 39
0.74 0.15 0.11
Matches are distributed among these distances:
64 5 0.02
65 81 0.32
66 8 0.03
67 24 0.09
68 31 0.12
70 2 0.01
71 3 0.01
72 55 0.22
73 40 0.16
74 5 0.02
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.29
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:42336 original size:36 final size:35
Alignment explanation
Indices: 42285--42565 Score: 265
Period size: 36 Copynumber: 8.0 Consensus size: 35
42275 TTCAAAGATT
* *
42285 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
42321 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
42356 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
42394 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
42423 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
42458 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
42495 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
42530 TTTGTTTCAA-AGGAAACTATCTCAAGAGAGACAAAA
1 -TTGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAA
42566 CTCTTCTAGT
Statistics
Matches: 204, Mismatches: 24, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 11 0.05
36 132 0.65
37 33 0.16
38 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:42395 original size:138 final size:137
Alignment explanation
Indices: 42236--42546 Score: 435
Period size: 138 Copynumber: 2.3 Consensus size: 137
42226 CAAGAGTAAT
* ** * *
42236 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* *
42301 TGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
66 TGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCC
42365 AAAAGAAAC
129 AAAAGAAAC
* * *
42374 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * * * *
42439 TGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAA
66 TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAA
*
42504 GAGAAAC
131 AAGAAAC
* *
42511 TGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAAC
42547 TATCTCAAGA
Statistics
Matches: 153, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
137 51 0.33
138 102 0.67
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
TGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAA
AAGAAAC
Found at i:42445 original size:102 final size:102
Alignment explanation
Indices: 42321--42509 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
42311 TAGACGAAAA
*
42321 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGA
42386 GACGAAATTTGTTTCAA-AGAAAACATATTCAAATATT
65 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * ** *
42423 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
42488 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAAGAGAAA
42510 CTGTCTCAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 37 0.47
102 42 0.53
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:42606 original size:71 final size:72
Alignment explanation
Indices: 42427--42607 Score: 215
Period size: 72 Copynumber: 2.5 Consensus size: 72
42417 AATATTTTGT
* * * * *
42427 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTATCTCAAGAGAGACGA
** *
42492 AATTTGT
66 AAACTGC
42499 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTATCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTATCTCAAGAGAGACGA
42563 AAACT-C
66 AAACTGC
* * * *
42569 TTCTAGTGAAAACGGTCTCAAGCGAGAC-AAATCTTGTTT
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAAT-TTGTTT
42608 TAAGAAAAAC
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
70 10 0.11
71 27 0.28
72 58 0.61
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (72 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTATCTCAAGAGAGACGA
AAACTGC
Found at i:43069 original size:18 final size:18
Alignment explanation
Indices: 43046--43081 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43036 TGTTGAATCC
43046 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
43064 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
43082 TTGATGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.33, G:0.06, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:43543 original size:22 final size:22
Alignment explanation
Indices: 43518--43561 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
43508 CATTTTTGTT
43518 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
43540 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
43562 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:44179 original size:13 final size:12
Alignment explanation
Indices: 44162--44225 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 12
44152 TTTTTGTCCC
44162 TTTTTCTTTTTT
1 TTTTTCTTTTTT
*
44174 CTTTTTGTTCTTTT
1 -TTTTTCTT-TTTT
*
44188 TTTTGCTTTTGTT
1 TTTTTCTTTT-TT
*
44201 TTTTGCTTCTTCTT
1 TTTTTCTT-TT-TT
44215 TTTTTCTTTTT
1 TTTTTCTTTTT
44226 GCCCTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 3 0.07
13 25 0.58
14 15 0.35
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:44204 original size:26 final size:26
Alignment explanation
Indices: 44162--44225 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 26
44152 TTTTTGTCCC
44162 TTTTTCTTTTTTCTTTTTG-TTCTT-T
1 TTTTTC-TTTTTCTTTTTGCTTCTTCT
44187 TTTTTGCTTTTGT-TTTTTGCTTCTTCTT
1 TTTTT-CTTTT-TCTTTTTGCTTCTTC-T
44215 TTTTTCTTTTT
1 TTTTTCTTTTT
44226 GCCCTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
25 15 0.44
26 8 0.24
27 5 0.15
28 6 0.18
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (26 bp):
TTTTTCTTTTTCTTTTTGCTTCTTCT
Found at i:45391 original size:15 final size:16
Alignment explanation
Indices: 45360--45398 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
45350 AATGTAGATG
45360 AAAATGCAAATAGGCA
1 AAAATGCAAATAGGCA
*
45376 AAAATGCAAA-ATGCA
1 AAAATGCAAATAGGCA
*
45391 AGAATGCA
1 AAAATGCA
45399 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.56, C:0.13, G:0.18, T:0.13
Consensus pattern (16 bp):
AAAATGCAAATAGGCA
Found at i:46735 original size:5 final size:5
Alignment explanation
Indices: 46725--46753 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
46715 GCAAGTGATG
46725 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
46754 GAAAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:48475 original size:18 final size:17
Alignment explanation
Indices: 48454--48496 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
48444 ATATATACAT
48454 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
48472 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
48489 ATAA-AATA
1 ATAATAATA
48497 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:48963 original size:34 final size:34
Alignment explanation
Indices: 48886--48986 Score: 139
Period size: 34 Copynumber: 2.9 Consensus size: 34
48876 ATAGTATAAC
*
48886 TCTATCCTATTTTTAGGAGTTTGAATCATAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAAT
* *
48923 TTTATCCTATTTTTAAGAGTTTGAATCCTAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAT
*
48957 TCTATCCTATTATTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
48987 GTAGGACGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 32 0.55
37 26 0.45
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (34 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAT
Found at i:50230 original size:21 final size:22
Alignment explanation
Indices: 50189--50237 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
50179 TATTTCACTG
** *
50189 TAATTAAAAAATTGGA-TTAAA
1 TAATTAAAAAATAAGACTAAAA
50210 TAATTAAAAAATAAGACTAAAA
1 TAATTAAAAAATAAGACTAAAA
50232 TAATTA
1 TAATTA
50238 TTGAGTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (22 bp):
TAATTAAAAAATAAGACTAAAA
Found at i:55522 original size:31 final size:31
Alignment explanation
Indices: 55461--55525 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
55451 TTATGTATCC
*
55461 AAAGTGATGATATAATACATATCATATGTTT
1 AAAGTGATGATATAATACATATAATATGTTT
* * *
55492 AAAGTGATGATATAATATATGTAATGTGTTT
1 AAAGTGATGATATAATACATATAATATGTTT
55523 AAA
1 AAA
55526 ATAATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.38
Consensus pattern (31 bp):
AAAGTGATGATATAATACATATAATATGTTT
Found at i:58139 original size:3 final size:3
Alignment explanation
Indices: 58131--58171 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
58121 ATTTGCTTAT
58131 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
58172 TAGGTTACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61217 original size:18 final size:18
Alignment explanation
Indices: 61190--61287 Score: 151
Period size: 18 Copynumber: 5.4 Consensus size: 18
61180 GAGGGTCTAC
61190 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
61208 GTGATCCTTCAGGACATA
1 GTGGTCCTTCGGGACATA
*
61226 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGACATA
* *
61244 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
61262 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
61280 GTGGTCCT
1 GTGGTCCT
61288 ACAGGAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.18, C:0.22, G:0.31, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:61524 original size:2 final size:2
Alignment explanation
Indices: 61519--61552 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61509 ATATATGTTA
61519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61553 GAATGAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61635 original size:16 final size:16
Alignment explanation
Indices: 61614--61655 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
61604 AGAATATGAA
61614 AATAAGAGATCATATG
1 AATAAGAGATCATATG
61630 AATAAGAGATCATATG
1 AATAAGAGATCATATG
61646 AATAAGAGAT
1 AATAAGAGAT
61656 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (16 bp):
AATAAGAGATCATATG
Found at i:66844 original size:3 final size:3
Alignment explanation
Indices: 66838--66930 Score: 116
Period size: 3 Copynumber: 30.7 Consensus size: 3
66828 TTCATTTAAA
66838 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
66883 AAT TAC TAA TAT TAT TATT TAT TAT TAA TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
66929 TA
1 TA
66931 CAAGCCCAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.01
3 73 0.94
4 4 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:67329 original size:18 final size:19
Alignment explanation
Indices: 67308--67345 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
67298 AGAAAAGAAG
67308 AGAGACAGA-GAATACAAC
1 AGAGACAGAGGAATACAAC
* *
67326 AGAGACGGAGGAATCCAAC
1 AGAGACAGAGGAATACAAC
67345 A
1 A
67346 AAAAAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.18, G:0.26, T:0.05
Consensus pattern (19 bp):
AGAGACAGAGGAATACAAC
Done.