Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002492.1 Hibiscus syriacus cultivar Beakdansim tig00005082_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: 93611
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:777 original size:21 final size:21
Alignment explanation
Indices: 733--777 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
723 ATGATTTTAA
* * *
733 AAAATTGAAAGTTTAGGTATT
1 AAAACTGAAAGTTTAGATACT
*
754 AAAACTGATAGTTTAGATACT
1 AAAACTGAAAGTTTAGATACT
775 AAA
1 AAA
778 TCTGCAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (21 bp):
AAAACTGAAAGTTTAGATACT
Found at i:2249 original size:2 final size:2
Alignment explanation
Indices: 2242--2292 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
2232 AATTCAGTAT
2242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2283 TA TA TA -A TA T
1 TA TA TA TA TA T
2293 CATGGAGCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16312 original size:44 final size:44
Alignment explanation
Indices: 16249--16474 Score: 240
Period size: 44 Copynumber: 5.1 Consensus size: 44
16239 TAAAAGTGGC
* *
16249 TATCACTTGTCGCTTAGTTATATTTGGATCGGCTTAGAAGGGGA
1 TATCACTTGTCGTTTAGTTATATTTGGATCGGCTTAGATGGGGA
* * * * *
16293 TATCACGTGTTGTTTAGTTATATTTGGA-CAAG-TTCAGCTGGGTA
1 TATCACTTGTCGTTTAGTTATATTTGGATC-GGCTT-AGATGGGGA
* * * * **
16337 CATCACTTGTCGTTTAGTTATATATGGATTGTCTTAGATGGGTT
1 TATCACTTGTCGTTTAGTTATATTTGGATCGGCTTAGATGGGGA
* *
16381 TTTCACTTGTCGTTTAGTTATACTTGGATCGGCTTAGATGGGGA
1 TATCACTTGTCGTTTAGTTATATTTGGATCGGCTTAGATGGGGA
* * * *
16425 TATCACTTGTTGTTTAGATAATATTTGGATTGACTTAGATGGGGA
1 TATCACTTGTCGTTTAG-TTATATTTGGATCGGCTTAGATGGGGA
16470 TATCA
1 TATCA
16475 TTTTTTCAAT
Statistics
Matches: 147, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
43 3 0.02
44 114 0.78
45 30 0.20
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.41
Consensus pattern (44 bp):
TATCACTTGTCGTTTAGTTATATTTGGATCGGCTTAGATGGGGA
Found at i:22234 original size:20 final size:20
Alignment explanation
Indices: 22209--22253 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
22199 TTATCTGGAA
* *
22209 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGATCTGAGGTTT
22229 AAAAATCCGATCTGAGGTTT
1 AAAAATCCGATCTGAGGTTT
22249 AAAAA
1 AAAAA
22254 ATTAGATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (20 bp):
AAAAATCCGATCTGAGGTTT
Found at i:22455 original size:22 final size:21
Alignment explanation
Indices: 22416--22456 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
22406 AGTGAAAAAA
**
22416 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTAAATCCGAT
22437 CCGGATCGGATTTAAATCCG
1 CCGGATC-GATTTAAATCCG
22457 GCTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGAT
Found at i:25897 original size:32 final size:31
Alignment explanation
Indices: 25860--25933 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
25850 AAATTACGTA
* *
25860 TTTAGTACTCAAACTATTTATTTTTGGTTCGT
1 TTTAGTACTCAAACT-TTAATTTTTGGTTCAT
* *
25892 TTTAGTACGT-AAAGTTTAATTTTTGTTTCAT
1 TTTAGTAC-TCAAACTTTAATTTTTGGTTCAT
*
25923 TTTACTACTCA
1 TTTAGTACTCA
25934 TGGTTAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.03
31 21 0.60
32 12 0.34
33 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.53
Consensus pattern (31 bp):
TTTAGTACTCAAACTTTAATTTTTGGTTCAT
Found at i:26147 original size:21 final size:21
Alignment explanation
Indices: 26122--26166 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
26112 ATTTTTAGGA
*
26122 AAAATTAAAAATTTAGATACT
1 AAAATTAAAAATTTAAATACT
* *
26143 AAAATTAATAATTTAAATATT
1 AAAATTAAAAATTTAAATACT
26164 AAA
1 AAA
26167 CACGTAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATTAAAAATTTAAATACT
Found at i:27421 original size:18 final size:18
Alignment explanation
Indices: 27398--27442 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
27388 TCACGGAATG
*
27398 TAAGATTATCGGCGGGAA
1 TAAGATTACCGGCGGGAA
*
27416 TAAGATTACCGGTGGGAA
1 TAAGATTACCGGCGGGAA
27434 TAAGATTAC
1 TAAGATTAC
27443 TGGAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.24
Consensus pattern (18 bp):
TAAGATTACCGGCGGGAA
Found at i:28601 original size:20 final size:20
Alignment explanation
Indices: 28576--28613 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28566 TTAGAGATTG
28576 AAATTTAAG-TTTTCAAAAAA
1 AAATTT-AGTTTTTCAAAAAA
28596 AAATTTAGTTTTTCAAAA
1 AAATTTAGTTTTTCAAAA
28614 TTTTGAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
AAATTTAGTTTTTCAAAAAA
Found at i:31041 original size:116 final size:115
Alignment explanation
Indices: 30834--31175 Score: 535
Period size: 116 Copynumber: 2.9 Consensus size: 115
30824 CTGTGGGAAT
* * *
30834 CATGCTATTCAGAGGCAAGAATGACTGGAAACATCCCAATTCTCCAAAATTTCTGAAAAAAAAAA
1 CATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTG---AAACAAA
* *
30899 CAAAAGAAAACCATAATCAAGCTTCATTTTTTTTCAAATAAATCAATTTTGAC
63 CATAAGAAAACCATAATCAAGCTTCATTTTTTTTCAAATAAAACAATTTTGAC
* *
30952 CATGCTATTCAGAGGCTAGAATGATTGGAAAACAACCCAATTCTCCTAAATTTCTGAAACAAACA
1 CATGCTATTCAGAGGCAAGAATGATTGG-AAACATCCCAATTCTCCTAAATTTCTGAAACAAACA
31017 TAAGAAAACCATAATCAAGCTTCATTTTTTTTTCAAATAAAACAATTTTGAC
65 TAAGAAAACCATAATCAAGCTTCA-TTTTTTTTCAAATAAAACAATTTTGAC
*
31069 CATGCTATTCAGAGGCAAGAACGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACAT
1 CATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACAT
* *
31134 AAGAAAACCACAATCAAGCTTCA--TTTTTTCATATAAAACAAT
66 AAGAAAACCATAATCAAGCTTCATTTTTTTTCAAATAAAACAAT
31176 ATTGTCAACA
Statistics
Matches: 210, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
113 18 0.09
116 89 0.42
117 52 0.25
118 26 0.12
119 25 0.12
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (115 bp):
CATGCTATTCAGAGGCAAGAATGATTGGAAACATCCCAATTCTCCTAAATTTCTGAAACAAACAT
AAGAAAACCATAATCAAGCTTCATTTTTTTTCAAATAAAACAATTTTGAC
Found at i:32653 original size:51 final size:52
Alignment explanation
Indices: 32553--32655 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 52
32543 TCCATCGATG
***
32553 CACACAATCTCGTTTACATTTGTGGGAGATTATTGACTAATCTCATTAATTA
1 CACACAATCTCGTTTACATTTGTCCAAGATTATTGACTAATCTCATTAATTA
*
32605 CACACAATCTCGTTTACATTTG-CCAAGATTATTGACTAATCTCGTTAATTA
1 CACACAATCTCGTTTACATTTGTCCAAGATTATTGACTAATCTCATTAATTA
32656 ATTTGCCAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 25 0.53
52 22 0.47
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (52 bp):
CACACAATCTCGTTTACATTTGTCCAAGATTATTGACTAATCTCATTAATTA
Found at i:34560 original size:2 final size:2
Alignment explanation
Indices: 34553--34591 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
34543 AGTAAACTCT
34553 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34592 GTGCCCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34729 original size:23 final size:22
Alignment explanation
Indices: 34702--34764 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
34692 GTGAAAATTA
34702 TCCCGAAGGACCTCATGTACATG
1 TCCCGAAGGACCT-ATGTACATG
* *
34725 TCCCGAAGAACCTATGTATATG
1 TCCCGAAGGACCTATGTACATG
*
34747 TCCCGAATGACCTATGTA
1 TCCCGAAGGACCTATGTA
34765 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 24 0.67
23 12 0.33
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (22 bp):
TCCCGAAGGACCTATGTACATG
Found at i:35517 original size:21 final size:21
Alignment explanation
Indices: 35491--35544 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
35481 CGGTACCCTT
*
35491 GGTATCGATACTACCCTCTAG
1 GGTATCGATACTACCCCCTAG
35512 GGTATCGATACTACCCCCTAG
1 GGTATCGATACTACCCCCTAG
35533 GGTATCGATACT
1 GGTATCGATACT
35545 CCATAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (21 bp):
GGTATCGATACTACCCCCTAG
Found at i:37019 original size:20 final size:21
Alignment explanation
Indices: 36996--37035 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36986 TTTTTGGTTA
* *
36996 TTTTGAATT-ATTTAAATTAT
1 TTTTCAATTAATTCAAATTAT
37016 TTTTCAATTAATTCAAATTA
1 TTTTCAATTAATTCAAATTA
37036 AATATCCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTCAATTAATTCAAATTAT
Found at i:38031 original size:3 final size:3
Alignment explanation
Indices: 38023--38059 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
38013 AAGGATATTT
38023 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
38060 GTTATTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:43483 original size:52 final size:52
Alignment explanation
Indices: 43416--43514 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
43406 ATACCCAAAC
**
43416 TGACCCGACTTACTATATACTTGAATAAAATCGAAACCCAAAATGACTGACT
1 TGACCCGACTTACTATATACCCGAATAAAATCGAAACCCAAAATGACTGACT
* * * *
43468 TGACTCGACTTACTATATACCCGAATAAAATTGAACCCCGAAATGAC
1 TGACCCGACTTACTATATACCCGAATAAAATCGAAACCCAAAATGAC
43515 CTAATTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (52 bp):
TGACCCGACTTACTATATACCCGAATAAAATCGAAACCCAAAATGACTGACT
Found at i:43867 original size:12 final size:13
Alignment explanation
Indices: 43850--43878 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
43840 CTTAGTTGTG
43850 AAAATTAAAAT-T
1 AAAATTAAAATCT
43862 AAAATTAAAATCT
1 AAAATTAAAATCT
43875 AAAA
1 AAAA
43879 ATTCAATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATCT
Found at i:43987 original size:21 final size:19
Alignment explanation
Indices: 43953--43999 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
43943 TTAGATTGAA
*
43953 AAATAAAGATTAAATAAAT
1 AAATAAAGAATAAATAAAT
43972 CAAATAGAAGAATAAATAAAT
1 -AAATA-AAGAATAAATAAAT
43993 AAATAAA
1 AAATAAA
44000 TTGAGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
21 13 0.52
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (19 bp):
AAATAAAGAATAAATAAAT
Found at i:45985 original size:84 final size:82
Alignment explanation
Indices: 45883--46096 Score: 216
Period size: 84 Copynumber: 2.6 Consensus size: 82
45873 TTGTGTCTTT
* * *
45883 GAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATAC
1 GAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGTG-CAGATAACCCTTCTAGACTTAAGCTATAC
**
45948 TGTAAATGATATGCCCTC
65 TACAAATGATATGCCCTC
*** * *
45966 GAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-GCAGATAACCCTTCTCGACTTAAGCTATGC
1 G-AGCTGAGTGTAATCGAACTCAAAGGTCTTTGGTGCAGATAACCCTTCTAGACTTAAGCTATAC
* * * *
46029 TACAAATGATGTGTCGTT
65 TACAAATGATATGCCCTC
* * * *
46047 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTGTGTTGGCAGACAACCCTTC
1 GAGCTGAGTGTAATCGAACTCAAAGGTCTT-TGGT-GCAGATAACCCTTC
46097 GTCGTGAAGT
Statistics
Matches: 105, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
80 24 0.23
81 38 0.36
82 1 0.01
83 2 0.02
84 40 0.38
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (82 bp):
GAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGTGCAGATAACCCTTCTAGACTTAAGCTATACT
ACAAATGATATGCCCTC
Found at i:46506 original size:88 final size:88
Alignment explanation
Indices: 46387--46565 Score: 322
Period size: 88 Copynumber: 2.0 Consensus size: 88
46377 TGAAGTTGAA
*
46387 CTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
1 CTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAT
46452 TGTTTATTGACAACCAGCGGTCC
66 TGTTTATTGACAACCAGCGGTCC
* *
46475 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
1 CTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAT
*
46540 TGTTTGTTGACAACCAGCGGTCC
66 TGTTTATTGACAACCAGCGGTCC
46563 CTT
1 CTT
46566 CGTCGTGAAG
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (88 bp):
CTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAT
TGTTTATTGACAACCAGCGGTCC
Found at i:46660 original size:106 final size:106
Alignment explanation
Indices: 46475--47658 Score: 2082
Period size: 106 Copynumber: 11.2 Consensus size: 106
46465 CCAGCGGTCC
*
46475 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
46540 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
46581 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
46646 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
46687 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
46752 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
46793 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
46858 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* *
46899 CTTGCGTTGTCTTGAGTCCAATATCCTTCGCATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGC-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
*
46964 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
65 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* * * *
47006 CTTGCATTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
*
47071 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* * *
47112 CTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
*
47177 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
47218 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
47283 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* *
47324 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
*
47389 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* * * *
47430 CTTGCGTTGTCTTGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
*
47495 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
47536 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-AGGAAG
1 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAG
* * *
47600 TTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAA
65 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* *
47642 CTTGTGTTGTCTCGAGT
1 CTTGCGTTGTCTGGAGT
47659 GGCACGATAT
Statistics
Matches: 1050, Mismatches: 26, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
106 947 0.90
107 103 0.10
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
Found at i:51340 original size:12 final size:13
Alignment explanation
Indices: 51323--51351 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
51313 CTTAGTTGTG
51323 AAAATTAAAAT-T
1 AAAATTAAAATCT
51335 AAAATTAAAATCT
1 AAAATTAAAATCT
51348 AAAA
1 AAAA
51352 ATTCAATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATCT
Found at i:51460 original size:21 final size:19
Alignment explanation
Indices: 51426--51472 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
51416 TTAGATTGAA
*
51426 AAATAAAGATTAAATAAAT
1 AAATAAAGAATAAATAAAT
51445 CAAATAGAAGAATAAATAAAT
1 -AAATA-AAGAATAAATAAAT
51466 AAATAAA
1 AAATAAA
51473 TTGAGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
21 13 0.52
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (19 bp):
AAATAAAGAATAAATAAAT
Found at i:58416 original size:21 final size:20
Alignment explanation
Indices: 58330--58487 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
58320 AAATGACCAA
**
58330 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
58349 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
58369 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
58389 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
58410 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
58431 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
58451 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
58472 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
58488 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:58549 original size:20 final size:20
Alignment explanation
Indices: 58455--58683 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
58445 GATTTTCCAG
* ** *
58455 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
58475 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
58495 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
58515 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
58535 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
58555 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
58575 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
58595 AATCGCAACG-ATAATCCAAA
1 AATCGCAACGCGT-ATCCGTA
* * *
58615 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
58635 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
58655 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
58675 AATCACAAC
1 AATCGCAAC
58684 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:59415 original size:24 final size:24
Alignment explanation
Indices: 59376--59422 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
59366 AAATTTGGTC
59376 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
59400 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
59423 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:59614 original size:12 final size:12
Alignment explanation
Indices: 59597--59621 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59587 ATATAATCCC
59597 GAAGAAGAAAAA
1 GAAGAAGAAAAA
59609 GAAGAAGAAAAA
1 GAAGAAGAAAAA
59621 G
1 G
59622 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:64552 original size:21 final size:21
Alignment explanation
Indices: 64470--64553 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
64460 CAGAACCCCA
* *
64470 GGGGGGTATCGATTCCC-CTG
1 GGGGGGAATCGATTCCCTCAG
* *
64490 TGGGGGGAATCGGTTCCCCTTCAA
1 -GGGGGGAATCGATT-CCC-TCAG
* *
64514 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGATTCCCTCAG
64535 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
64554 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
21 32 0.62
22 6 0.12
23 13 0.25
24 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAG
Found at i:68400 original size:22 final size:21
Alignment explanation
Indices: 68358--68397 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
68348 GAGTTTGTTT
*
68358 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
68379 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
68398 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:71537 original size:33 final size:34
Alignment explanation
Indices: 71486--71684 Score: 140
Period size: 33 Copynumber: 5.7 Consensus size: 34
71476 CAGAAATTAC
* *
71486 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
71519 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * *
71553 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
* * *
71592 AAT-GCGGA-AACGAAAATCGCAATACGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* * *
71625 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
71658 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
71685 CGAGAGAATC
Statistics
Matches: 129, Mismatches: 19, Indels: 31
0.72 0.11 0.17
Matches are distributed among these distances:
32 2 0.02
33 55 0.43
34 33 0.26
35 1 0.01
36 1 0.01
37 1 0.01
38 14 0.11
39 21 0.16
40 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:71682 original size:52 final size:53
Alignment explanation
Indices: 71500--71722 Score: 353
Period size: 53 Copynumber: 4.2 Consensus size: 53
71490 GCAACGAGAG
* *
71500 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
*
71553 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAACGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
* *
71606 AATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
71658 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
71710 AATCGCATTGCGA
1 AATCGCAATGCGA
71723 TTCTCTCGTT
Statistics
Matches: 161, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
52 69 0.43
53 91 0.57
54 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:71695 original size:33 final size:33
Alignment explanation
Indices: 71553--71716 Score: 145
Period size: 33 Copynumber: 4.8 Consensus size: 33
71543 CGGAAATGAA
71553 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
71586 AATCGCAATGCGGAAACGAAAATCGCAATACGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGC-A-ACG--A-GAG
* * * * **
71625 AATCGCAACGAGAGAATCG-CAATGCGAAATTA-A-
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAG
71658 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
71691 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
71717 TTGCGATTCT
Statistics
Matches: 103, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
31 6 0.06
32 7 0.07
33 47 0.46
34 14 0.14
35 1 0.01
36 4 0.04
38 4 0.04
39 17 0.17
40 3 0.03
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:71825 original size:52 final size:53
Alignment explanation
Indices: 71712--71829 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
71702 GAAATTAAAA
71712 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTAATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTAATT
*
71765 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTAATT
71817 TCGCATTGCGATT
1 TCGCATTGCGATT
71830 TTCATTTCGC
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTAATT
Found at i:71855 original size:19 final size:19
Alignment explanation
Indices: 71731--71847 Score: 172
Period size: 19 Copynumber: 6.4 Consensus size: 19
71721 GATTCTCTCG
71731 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
71751 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
71770 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
71784 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
71803 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
71822 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
71841 TTGCGAT
1 TTGCGAT
71848 AGTCATTTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 6 0.07
19 55 0.62
20 14 0.16
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:71973 original size:14 final size:14
Alignment explanation
Indices: 71954--71990 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
71944 CATCAATTAC
71954 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
71968 ACAAATCATCTTTT
1 ACAAATCAACTTTT
71982 ACAAATCAA
1 ACAAATCAA
71991 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:72084 original size:43 final size:43
Alignment explanation
Indices: 72036--72139 Score: 199
Period size: 43 Copynumber: 2.4 Consensus size: 43
72026 CCGATCATCT
72036 ACTATTGAATCAACTTTTACAAATAAATTAAACAATCAATTAA
1 ACTATTGAATCAACTTTTACAAATAAATTAAACAATCAATTAA
*
72079 ACTATTGAATCAACTTTTACAAATCAATTAAACAATCAATTAA
1 ACTATTGAATCAACTTTTACAAATAAATTAAACAATCAATTAA
72122 ACTATTGAATCAACTTTT
1 ACTATTGAATCAACTTTT
72140 GCAGCCATAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (43 bp):
ACTATTGAATCAACTTTTACAAATAAATTAAACAATCAATTAA
Found at i:72417 original size:35 final size:35
Alignment explanation
Indices: 72371--72438 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
72361 TCGATTTAGC
72371 CATATAATAGTGACTTACATAAATTTAAAAAAAGA
1 CATATAATAGTGACTTACATAAATTTAAAAAAAGA
*
72406 CATATATTAGTGACTTACATAAATTTAAAAAAA
1 CATATAATAGTGACTTACATAAATTTAAAAAAA
72439 AAATTAATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (35 bp):
CATATAATAGTGACTTACATAAATTTAAAAAAAGA
Found at i:73358 original size:19 final size:19
Alignment explanation
Indices: 73316--73469 Score: 148
Period size: 19 Copynumber: 8.6 Consensus size: 19
73306 TAGTTTACTT
* *
73316 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
73336 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
73355 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
73374 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
73393 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
73407 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
73426 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
73440 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
73459 TCGCAATGCGA
1 TCGCAACGCGA
73470 TTTTGGTTTC
Statistics
Matches: 111, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
14 16 0.14
16 11 0.10
17 11 0.10
19 61 0.55
20 12 0.11
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:73410 original size:14 final size:14
Alignment explanation
Indices: 73391--73447 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
73381 GCGAAATGAA
*
73391 AATCGCAACGACAG
1 AATCGCAACGAAAG
73405 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
73422 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
73438 AATCGCAACG
1 AATCGCAACG
73448 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:73418 original size:33 final size:33
Alignment explanation
Indices: 73334--73464 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
73324 CGAAACTTAA
* *
73334 AATCGCAACGCGAAATGATAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
73372 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
73405 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
73438 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
73465 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
33 59 0.67
34 1 0.01
36 1 0.01
38 27 0.31
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:73500 original size:14 final size:14
Alignment explanation
Indices: 73481--73507 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
73471 TTTGGTTTCG
73481 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
73495 CGTTGCGATTTTG
1 CGTTGCGATTTTG
73508 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:73507 original size:33 final size:33
Alignment explanation
Indices: 73465--73559 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
73455 AAAATCGCAA
73465 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
73498 TGCGATTTTGGTTTCGCGTTGCGATTCTT-TTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTGTCGT
**
73531 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
73560 GTTTCGCGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.49
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:73519 original size:19 final size:19
Alignment explanation
Indices: 73465--73593 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
73455 AAAATCGCAA
73465 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
73484 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
73498 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
73517 TGCGATTCT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
**
73531 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
73550 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
73569 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
73589 TGCGA
1 TGCGA
73594 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 48 0.52
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:73774 original size:93 final size:93
Alignment explanation
Indices: 73638--73920 Score: 523
Period size: 93 Copynumber: 3.1 Consensus size: 93
73628 ATGGATTGCA
*
73638 TTACTTT-AACTAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
73702 TACCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
73730 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
73795 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
73823 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
73888 TAGCAGAATTGGCAGCAATCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
73916 TTACT
1 TTACT
73921 AAGCAATCTA
Statistics
Matches: 186, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 7 0.04
93 179 0.96
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:75652 original size:20 final size:20
Alignment explanation
Indices: 75621--75717 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
75611 TTTTGGTTGA
75621 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
75641 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
75661 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
75680 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
75695 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
75715 AAT
1 AAT
75718 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:75673 original size:21 final size:21
Alignment explanation
Indices: 75619--75683 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
75609 TCTTTTGGTT
75619 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
75640 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
75660 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
75681 GAA
1 GAA
75684 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:75687 original size:14 final size:14
Alignment explanation
Indices: 75668--75724 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
75658 GAGAAATGAA
75668 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
75682 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
75701 AATCGCAACGAGAG
1 AATCGCAACGAGAG
75715 AATCGCAACG
1 AATCGCAACG
75725 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:75700 original size:33 final size:33
Alignment explanation
Indices: 75619--75741 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
75609 TCTTTTGGTT
*
75619 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
75660 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
75693 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
75726 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
75742 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:75822 original size:41 final size:41
Alignment explanation
Indices: 75765--75842 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
75755 TCGCGTTGCG
*
75765 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
75806 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
75843 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:75827 original size:20 final size:21
Alignment explanation
Indices: 75766--75841 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
75756 CGCGTTGCGA
75766 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
75787 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
75807 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
75828 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
75842 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:75963 original size:33 final size:33
Alignment explanation
Indices: 75921--75991 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
75911 AATACTAACT
75921 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
75954 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
75987 TGAAA
1 TGAAA
75992 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:76397 original size:20 final size:20
Alignment explanation
Indices: 76370--76562 Score: 192
Period size: 20 Copynumber: 9.6 Consensus size: 20
76360 CTTTAAATAT
76370 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
76390 CACGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
76412 -TCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTACGGATA
*
76431 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
76451 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
76471 CGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
76491 CACGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
* * *
76511 TGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
76531 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
76551 CGCGTTGCGATT
1 CGCGTTGCGATT
76563 CTGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:79492 original size:30 final size:31
Alignment explanation
Indices: 79452--79535 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
79442 AGCTACTTTT
*
79452 CCCATATTAGTCTCTGAGTTTCTCTA-TTAC
1 CCCATATTAGTCCCTGAGTTTCTCTATTTAC
* * **
79482 CCCCTATTAGTCCCTGAGTTTCGCTATTTTT
1 CCCATATTAGTCCCTGAGTTTCTCTATTTAC
79513 CCCATATTAGTCCCTGAGTTTCT
1 CCCATATTAGTCCCTGAGTTTCT
79536 TTTCCCTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 23 0.50
31 23 0.50
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.43
Consensus pattern (31 bp):
CCCATATTAGTCCCTGAGTTTCTCTATTTAC
Found at i:79524 original size:31 final size:30
Alignment explanation
Indices: 79429--79534 Score: 131
Period size: 31 Copynumber: 3.5 Consensus size: 30
79419 TTAAAGATTC
* *
79429 AGTCCCTGATTTTAGCTACTTTTCCCATATT
1 AGTCCCTGAGTTTCGCTA-TTTTCCCATATT
* * ** *
79460 AGTCTCTGAGTTTCTCTATTACCCCCTATT
1 AGTCCCTGAGTTTCGCTATTTTCCCATATT
79490 AGTCCCTGAGTTTCGCTATTTTTCCCATATT
1 AGTCCCTGAGTTTCGCTA-TTTTCCCATATT
79521 AGTCCCTGAGTTTC
1 AGTCCCTGAGTTTC
79535 TTTTCCCTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
30 25 0.40
31 37 0.60
ACGTcount: A:0.17, C:0.27, G:0.12, T:0.43
Consensus pattern (30 bp):
AGTCCCTGAGTTTCGCTATTTTCCCATATT
Found at i:89430 original size:60 final size:58
Alignment explanation
Indices: 89333--89515 Score: 145
Period size: 58 Copynumber: 3.1 Consensus size: 58
89323 TATAGTCTTT
* ** * *
89333 ATTCTAAATTAGTTCATAAACTTTTAAAAACTCCAATTTAATTCTTAAACTA-TGGCTGTC
1 ATTCTAAATTAG-TCATAAACTCTTAAAAACTCCAATTTAA-TCCCAAACAATTAGCT-TC
* * * * *
89393 ATTCTAAATTAGTCATTAAACTCTTGAACATTTCAATTTCATCCCAAACAATTAGCTTC
1 ATTCTAAATTAGTCA-TAAACTCTTAAAAACTCCAATTTAATCCCAAACAATTAGCTTC
** *** * * *
89452 ATTCTAAATTAGTCCCAAACT-TTTTGAACATTCAATTTCATCACAAACAATTAGCTTC
1 ATTCTAAATTAGTCATAAACTCTTAAAAAC-TCCAATTTAATCCCAAACAATTAGCTTC
89510 ATTCTA
1 ATTCTA
89516 TGTATTTATT
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
57 3 0.03
58 38 0.37
59 26 0.25
60 35 0.34
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.38
Consensus pattern (58 bp):
ATTCTAAATTAGTCATAAACTCTTAAAAACTCCAATTTAATCCCAAACAATTAGCTTC
Found at i:89500 original size:58 final size:59
Alignment explanation
Indices: 89391--89515 Score: 191
Period size: 58 Copynumber: 2.1 Consensus size: 59
89381 ACTATGGCTG
** *
89391 TCATTCTAAATTAGTCATTAAACTCTTGAACATTTCAATTTCATCCCAAACAATTAGCT
1 TCATTCTAAATTAGTCACCAAACTCTTGAACATTTCAATTTCATCACAAACAATTAGCT
*
89450 TCATTCTAAATTAGTC-CCAAACTTTTTGAACA-TTCAATTTCATCACAAACAATTAGCT
1 TCATTCTAAATTAGTCACCAAAC-TCTTGAACATTTCAATTTCATCACAAACAATTAGCT
89508 TCATTCTA
1 TCATTCTA
89516 TGTATTTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
58 37 0.61
59 24 0.39
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (59 bp):
TCATTCTAAATTAGTCACCAAACTCTTGAACATTTCAATTTCATCACAAACAATTAGCT
Found at i:89512 original size:29 final size:29
Alignment explanation
Indices: 89424--89513 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
89414 TCTTGAACAT
89424 TTCAATTTCATCCCAAACAATTAGCTTCA
1 TTCAATTTCATCCCAAACAATTAGCTTCA
* ** * **
89453 TTCTAAATT-AGTCCCAAACTTTTTG-AACA
1 TTC-AATTTCA-TCCCAAACAATTAGCTTCA
*
89482 TTCAATTTCATCACAAACAATTAGCTTCA
1 TTCAATTTCATCCCAAACAATTAGCTTCA
89511 TTC
1 TTC
89514 TATGTATTTA
Statistics
Matches: 44, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
28 14 0.32
29 15 0.34
30 15 0.34
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.37
Consensus pattern (29 bp):
TTCAATTTCATCCCAAACAATTAGCTTCA
Done.