Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_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: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 15
Found at i:15723 original size:17 final size:18
Alignment explanation
Indices: 15701--15741 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
15691 AAATTATATT
15701 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
*
15718 AGTAAAATACTTAACTAA
1 AGTAAAATACTTAAATAA
*
15736 ATTAAA
1 AGTAAA
15742 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:17888 original size:68 final size:69
Alignment explanation
Indices: 17809--17972 Score: 185
Period size: 70 Copynumber: 2.4 Consensus size: 69
17799 TGAAAAAGAT
17809 CTAAGAAGTATTTAGACCAAAAAATGTA-GGTCAA-GCTTAATTTGCCT-GATTTCAAAA-TAAA
1 CTAAGAAGTATTTAGACCAAAAAATG-AGGGTCAATGCTTAATTTGCCTAG-TTTCAAAACT-AA
*
17870 TAGGGAC
63 GAGGGAC
* * **
17877 CTAAGTAGTATTTAAACCAGAAAAATGAGGGTCAATGCTTAATTTTTCTAGTTTCAAAACTAAGA
1 CTAAGAAGTATTTAGACCA-AAAAATGAGGGTCAATGCTTAATTTGCCTAGTTTCAAAACTAAGA
17942 GGGAC
65 GGGAC
*
17947 CTTAA-AAGTATTTGGACCCAAAAAAT
1 C-TAAGAAGTATTTAGA-CCAAAAAAT
17973 TTGTTGTGGG
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
68 18 0.22
69 13 0.16
70 42 0.52
71 8 0.10
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (69 bp):
CTAAGAAGTATTTAGACCAAAAAATGAGGGTCAATGCTTAATTTGCCTAGTTTCAAAACTAAGAG
GGAC
Found at i:26920 original size:29 final size:29
Alignment explanation
Indices: 26878--27151 Score: 548
Period size: 29 Copynumber: 9.4 Consensus size: 29
26868 AGACCATAAC
26878 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
26907 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
26936 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
26965 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
26994 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
27023 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
27052 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
27081 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
27110 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
27139 AGAAGTTCGGTGA
1 AGAAGTTCGGTGA
27152 CATACTCAAA
Statistics
Matches: 245, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 245 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (29 bp):
AGAAGTTCGGTGATTAAAACGTAAGCTTT
Found at i:27673 original size:21 final size:21
Alignment explanation
Indices: 27648--27689 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27638 TTTTTTTAAT
*
27648 TTTTTC-CATCTAAATGTATTA
1 TTTTTCACAT-TAAATATATTA
27669 TTTTTCACATTAAATATATTA
1 TTTTTCACATTAAATATATTA
27690 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTTTCACATTAAATATATTA
Found at i:28446 original size:60 final size:59
Alignment explanation
Indices: 28335--28509 Score: 165
Period size: 60 Copynumber: 2.9 Consensus size: 59
28325 CCATAAGCCT
* * * * **
28335 CATTTTAAATTAGTCCTTAAAATTTTAAATATTTCAAATTAATCCTTAAACTATGA-CTA
1 CATTCTAAATTAGTCC-TAAAATTTTGAACATTTCAATTTAATCCCCAAACTATGACCTA
* *
28394 CTATTCTAAATTAGTCCTCAAAATTTTGAACATTTCAATTTCATCCCCAAACTATGACCTT
1 C-ATTCTAAATTAGTCCT-AAAATTTTGAACATTTCAATTTAATCCCCAAACTATGACCTA
* * * * *
28455 CATTCTAAATTGGTACATAAACTTTTTTGAACATTCCAATTTTAT-CCCAAACTAT
1 CATTCTAAATTAGT-CCTAAA--ATTTTGAACATTTCAATTTAATCCCCAAACTAT
28510 ACATAAATAC
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.02
60 61 0.63
61 15 0.15
62 19 0.20
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (59 bp):
CATTCTAAATTAGTCCTAAAATTTTGAACATTTCAATTTAATCCCCAAACTATGACCTA
Found at i:28815 original size:60 final size:58
Alignment explanation
Indices: 28635--28820 Score: 210
Period size: 60 Copynumber: 3.1 Consensus size: 58
28625 TTTGGATGAA
* * * * * * *
28635 TTTGAGGATGAAATTGGAAGATTCAAAAATTTAGGGACCAATTTAGAAAGAGGGTCATAA
1 TTTG-GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA-AATGAGGGTCATAG
* * *
28695 TTTAGGGATGAAATTAGAATATTCACAAGTTTAAGGACTAATTTAAAATGAGAGACATAG
1 TTT-GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTT-AAATGAGGGTCATAG
* *
28755 TTTGGAGATGAAATTAGAATATTCAAAAGTTTAAGGAATAATTTAAAGTGAGGGTTATAG
1 TTTGG-GATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAA-TGAGGGTCATAG
28815 TTTGGG
1 TTTGGG
28821 GCATATGATA
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
59 6 0.06
60 99 0.93
61 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.31
Consensus pattern (58 bp):
TTTGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAATGAGGGTCATAG
Found at i:29260 original size:112 final size:113
Alignment explanation
Indices: 29068--29526 Score: 729
Period size: 112 Copynumber: 4.1 Consensus size: 113
29058 TTGTCGGTTT
29068 GTGTCGATACTTTATAAAAA---A---ATCCATAACAATATAACAAGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAAATGACAAAAC
29127 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
29175 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACATGT-AAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAAATGACAAAAC
** *
29239 CGGTCTATAAATGACAAAACAGGTAAAGCATTACCGAATATATTGAAA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
29287 GTGTCTATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAAATGACAAAAC
* *
29351 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
29399 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAAGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAAATGACAAAAC
* * *
29464 CGGTCTATAAATGACAAAACAGGTAAAGTG-TAACCGGATATGTTGATA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCT-ACCGGATATATTGAAA
29512 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
29527 TATAAGTATC
Statistics
Matches: 328, Mismatches: 16, Indels: 10
0.93 0.05 0.03
Matches are distributed among these distances:
107 20 0.06
110 1 0.00
112 211 0.64
113 96 0.29
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (113 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAAATGACAAAAC
CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:29706 original size:182 final size:182
Alignment explanation
Indices: 29398--29852 Score: 707
Period size: 182 Copynumber: 2.5 Consensus size: 182
29388 ATATGTTGAT
* *
29398 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAAGTAAAAAAAATGACAAAA
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGT-AAAAATATGACAAAA
** * *
29463 CCGGTCTATAAATGACAAAACAGGTAAAGTGTAACCGGATATGTTGATAGTGTCGATACTTTATT
65 CCGGTCTCGAAATGACAAAACCGGTAAAGAGTAACCGGATATGTTGATAGTGTCGATACTTTATT
* * * * *
29528 ATAAGTATCGACACTTTTGGAATTTAAAAGAGAATACGT-TATAGCGCTAATAA
130 ATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGA-ATATATAGCGCCAATAA
*
29581 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAC
*
29646 CGGTCTCGAAATGATAAAACCGGTAAAGAGCT-ACCGGATATGTTGATAGTGTCGATACTTTATT
66 CGGTCTCGAAATGACAAAACCGGTAAAGAG-TAACCGGATATGTTGATAGTGTCGATACTTTATT
29710 ATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAATATATAGCGCCAATAA
130 ATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAATATATAGCGCCAATAA
* * *
29763 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAAGTAAAAATATGAAAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAC
* *
29828 CGATATCGAAATGACAAAACCGGTA
66 CGGTCTCGAAATGACAAAACCGGTA
29853 GTAAAAAAGT
Statistics
Matches: 250, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
181 1 0.00
182 201 0.80
183 48 0.19
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAC
CGGTCTCGAAATGACAAAACCGGTAAAGAGTAACCGGATATGTTGATAGTGTCGATACTTTATTA
TAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAATATATAGCGCCAATAA
Found at i:30500 original size:23 final size:23
Alignment explanation
Indices: 30471--30518 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
30461 AAATAGGTCC
*
30471 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
30494 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATATATT
30517 AT
1 AT
30519 CGTACTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:43556 original size:33 final size:30
Alignment explanation
Indices: 43496--43556 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 30
43486 GTTGTATTCG
* *
43496 TATTCGTTTATTTATTTTTTAATATGTTCA
1 TATTCGTTTATTTATTTTTAAAAATGTTCA
43526 TATTCGTTTATTTATTATTGTCAAAAATGTT
1 TATTCGTTTATTTATT-TT-T-AAAAATGTT
43557 TGTTTGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 2 0.08
32 1 0.04
33 7 0.27
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (30 bp):
TATTCGTTTATTTATTTTTAAAAATGTTCA
Found at i:52472 original size:24 final size:24
Alignment explanation
Indices: 52440--52489 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
52430 ATAGTAGGCT
52440 GCCCCCAACGCCAGGTTGAGAGCA
1 GCCCCCAACGCCAGGTTGAGAGCA
52464 GCCCCCAACGCCAGGTTGAGAGCA
1 GCCCCCAACGCCAGGTTGAGAGCA
52488 GC
1 GC
52490 TTCCGTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.38, G:0.30, T:0.08
Consensus pattern (24 bp):
GCCCCCAACGCCAGGTTGAGAGCA
Found at i:53937 original size:31 final size:31
Alignment explanation
Indices: 53901--53960 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
53891 TCATTTTGTT
*
53901 TGAATAAGTTGTTTTTAGTCATTACATTGAA
1 TGAATAAATTGTTTTTAGTCATTACATTGAA
53932 TGAATAAATTGTTTTTAGTCATTACATTG
1 TGAATAAATTGTTTTTAGTCATTACATTG
53961 GAAATAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (31 bp):
TGAATAAATTGTTTTTAGTCATTACATTGAA
Found at i:55889 original size:16 final size:16
Alignment explanation
Indices: 55868--55900 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55858 TAATAAATAA
55868 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
55884 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
55900 A
1 A
55901 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:55992 original size:16 final size:16
Alignment explanation
Indices: 55971--56031 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
55961 TAATAAATAA
55971 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
55987 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
56003 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
56019 ACGAACATAAACG
1 ACGAACATAAACG
56032 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:56888 original size:13 final size:13
Alignment explanation
Indices: 56872--56897 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56862 TGCACTATAA
56872 TATAACTTGTTTT
1 TATAACTTGTTTT
56885 TATAACTTGTTTT
1 TATAACTTGTTTT
56898 GAATCTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TATAACTTGTTTT
Found at i:57148 original size:10 final size:10
Alignment explanation
Indices: 57133--57180 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
57123 ATAAAAGAAT
57133 GAACATAAAC
1 GAACATAAAC
57143 GAACATAATCGAAC
1 GAACAT-A---AAC
57157 GAACATAAAC
1 GAACATAAAC
*
57167 GAACATAACC
1 GAACATAAAC
57177 GAAC
1 GAAC
57181 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:57148 original size:24 final size:24
Alignment explanation
Indices: 57120--57174 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
57110 GATTGTGTTA
*
57120 AACATAAAAGAATGAACATAAACG
1 AACATAAAAGAACGAACATAAACG
**
57144 AACATAATCGAACGAACATAAACG
1 AACATAAAAGAACGAACATAAACG
57168 AACATAA
1 AACATAA
57175 CCGAACGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAAAAGAACGAACATAAACG
Found at i:57157 original size:14 final size:14
Alignment explanation
Indices: 57140--57170 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
57130 AATGAACATA
*
57140 AACGAACATAATCG
1 AACGAACATAAACG
57154 AACGAACATAAACG
1 AACGAACATAAACG
57168 AAC
1 AAC
57171 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:57179 original size:24 final size:24
Alignment explanation
Indices: 57133--57181 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
57123 ATAAAAGAAT
*
57133 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
57157 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
57181 G
1 G
57182 TTCACGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.22, G:0.14, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:59021 original size:20 final size:20
Alignment explanation
Indices: 58952--59013 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
58942 GAAATTTAAA
*
58952 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATAAATTACAT
58972 TTCTGGAAAATAAATTACAT
1 TTCTGGAAAATAAATTACAT
58992 TTCTGGAAAATAAATTACAT
1 TTCTGGAAAATAAATTACAT
59012 TT
1 TT
59014 TTTAAAAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATAAATTACAT
Found at i:59385 original size:29 final size:30
Alignment explanation
Indices: 59350--59421 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 30
59340 CTTTACTAAA
*
59350 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTATTTAAATATATAAAAAATTATTAT
59379 -TCATTA-TTAAATATATAAAAAATTATTAT
1 AT-ATTATTTAAATATATAAAAAATTATTAT
*
59408 ATATTATTAAAATA
1 ATATTATTTAAATA
59422 AAAATATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 16 0.43
29 14 0.38
30 7 0.19
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (30 bp):
ATATTATTTAAATATATAAAAAATTATTAT
Found at i:59403 original size:26 final size:27
Alignment explanation
Indices: 59351--59517 Score: 94
Period size: 29 Copynumber: 5.9 Consensus size: 27
59341 TTTACTAAAA
59351 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
*
59379 TCATTATTAAATATATAAAAAATTATTAT
1 T-ATTATTAAATATATAAATAA-TATTAT
*
59408 ATATTATTAAA-ATAAAAATATAATATCT-T
1 -TATTATTAAATAT-ATAA-ATAATAT-TAT
** * *
59437 ATATTATTATAATATAATTGATTATTTTAT
1 -TATTATTA-AATAT-ATAAATAATATTAT
* * *
59467 ATAATATTAAAAATAT-AATATTA-TAT
1 -TATTATTAAATATATAAATAATATTAT
59493 TATTA-TAAATATTAATAAAT-ATATT
1 TATTATTAAATA-T-ATAAATAATATT
59518 TTAAATATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
24 5 0.05
25 5 0.05
26 7 0.06
27 7 0.06
28 20 0.18
29 40 0.37
30 21 0.19
31 4 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:59491 original size:22 final size:23
Alignment explanation
Indices: 59466--59509 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
59456 GATTATTTTA
59466 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
59488 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
59510 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:59514 original size:22 final size:22
Alignment explanation
Indices: 59470--59526 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
59460 ATTTTATATA
* *
59470 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
59491 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
59513 ATATTTTAAATATT
1 ATATTATAAATATT
59527 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:59525 original size:52 final size:51
Alignment explanation
Indices: 59406--59526 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
59396 AAAAATTATT
**
59406 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
59457 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
59511 ATATATTTTAAATATT
1 ATATATTTTAAATATT
59527 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:59773 original size:41 final size:42
Alignment explanation
Indices: 59716--59833 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
59706 ATGAATTACA
* *
59716 TTCCGGAAAATGAATTACGTAAAACAAACACGA-AAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAGAAAACATT
* *
59757 TTCCGGAAAACAAATTACGTGAAATAAACACGAGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAGAAAACATT
* * *
59799 TTACAGAAAACGAATTACATGAAACAAACACGAGA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAGA
59834 TTTCAAAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 29 0.43
42 38 0.57
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGAGAAAACATT
Found at i:62055 original size:3 final size:3
Alignment explanation
Indices: 62047--62101 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
62037 TCTTTTTTAA
*
62047 ATT ATT ATT ATT AATT ATT ATT TTT A-T ATT -TAT ATT ATT ATT -TT
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
*
62091 ATT AAT ATT AT
1 ATT ATT ATT AT
62102 ATTTTTACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 5 0.12
3 34 0.79
4 4 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:62079 original size:28 final size:28
Alignment explanation
Indices: 62052--62105 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
62042 TTTAAATTAT
62052 TATTATTA-ATTATTATTTTTATATTTA
1 TATTATTATATTATTATTTTTATATTTA
* * *
62079 TATTATTATTTTATTAATATTATATTT
1 TATTATTATATTATTATTTTTATATTT
62106 TTACATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TATTATTATATTATTATTTTTATATTTA
Found at i:62084 original size:17 final size:16
Alignment explanation
Indices: 62054--62108 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
62044 TAAATTATTA
62054 TTATTAATTATTATTTT
1 TTATTAA-TATTATTTT
*
62071 TATATTTATATTATTATT
1 T-TATTAATATTATT-TT
62089 TTATTAATATTATATTT
1 TTATTAATATTAT-TTT
62106 TTA
1 TTA
62109 CATATTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 24 0.73
18 9 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTAATATTATTTT
Found at i:62104 original size:19 final size:19
Alignment explanation
Indices: 62047--62104 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 19
62037 TCTTTTTTAA
62047 ATTATTATTATTAATTATTAT
1 ATTATT-TTATTAA-TATTAT
* *
62068 -TT-TTATATTTATA-T-T
1 ATTATTTTATTAATATTAT
62083 ATTATTTTATTAATATTAT
1 ATTATTTTATTAATATTAT
62102 ATT
1 ATT
62105 TTTACATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 11 0.38
18 6 0.21
19 6 0.21
20 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTATTTTATTAATATTAT
Found at i:62629 original size:9 final size:10
Alignment explanation
Indices: 62614--62638 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
62604 AAAAGAGGAG
62614 AAAAAAAAAC
1 AAAAAAAAAC
62624 AAAAAAAAAC
1 AAAAAAAAAC
62634 AAAAA
1 AAAAA
62639 CCACAACCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:69148 original size:16 final size:16
Alignment explanation
Indices: 69129--69176 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
69119 AGATTGAGAA
69129 ACATACATCAACTCAT
1 ACATACATCAACTCAT
*
69145 ACATACAT--A-T-AG
1 ACATACATCAACTCAT
*
69157 ACATACATCAACACAT
1 ACATACATCAACTCAT
69173 ACAT
1 ACAT
69177 GCATGTTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
14 2 0.08
16 13 0.52
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (16 bp):
ACATACATCAACTCAT
Found at i:69767 original size:105 final size:105
Alignment explanation
Indices: 69606--69905 Score: 372
Period size: 105 Copynumber: 2.9 Consensus size: 105
69596 TCTTCAAAAA
* * * * *
69606 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTGGATATACAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCAAATTTGTTTCACA
* * * *
69671 TTAAGCAAAGTTAATATCACTTGAGATTGTTGTTTCTTTT
66 TTAAACAAAATTAATATCACTTGAGATTGTTGTTTATTTC
* * *
69711 AAAACAAACTTCGTCTCGCTTGAGATATTTTTCCTTTGAGATACAAATTTCAAATTTGCTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCAAATTTGTTTCACA
* *
69776 TGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTC
66 TTAAACAAAATTAATATCACTTGAGATTGTTGTTTATTTC
* * * * * *
69816 GAAACAAATTTCATTTCGCTTGAGACATTTTTTTCTCTGGGATACAAATTT-AAATTTGTTGT-A
1 AAAACAAATTTCGTCTCGCTTGAGACA-TTTTTCCTTTGAGATACAAATTTCAAATTTGTT-TCA
69879 C-TTGAAACAAAATTAATATCACTTGAG
64 CATT-AAACAAAATTAATATCACTTGAG
69906 TTTTTCAAAA
Statistics
Matches: 167, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
104 1 0.01
105 145 0.87
106 21 0.13
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (105 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCAAATTTGTTTCACA
TTAAACAAAATTAATATCACTTGAGATTGTTGTTTATTTC
Found at i:70094 original size:29 final size:29
Alignment explanation
Indices: 70057--70128 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
70047 CTCTTGAGAT
70057 AAATCTTTGAGTCTGTTCCTTTTGAATA-A
1 AAATCTTTGAGTCTGTTCCTTTTGAA-ACA
*
70086 AAATCTTTGAGT-TGTTTCTTTTGAAACA
1 AAATCTTTGAGTCTGTTCCTTTTGAAACA
70114 AATATCTTTGAGTCT
1 AA-ATCTTTGAGTCT
70129 ATTTCTGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 1 0.03
28 15 0.38
29 22 0.56
30 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (29 bp):
AAATCTTTGAGTCTGTTCCTTTTGAAACA
Found at i:70143 original size:30 final size:29
Alignment explanation
Indices: 70088--70145 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
70078 TTGAATAAAA
* * *
70088 ATCTTTGAGTTGTTTCTTTTGAAACAAAT
1 ATCTTTGAGTTATTTCTGTTAAAACAAAT
70117 ATCTTTGAGTCTATTTCTGTTAAAACAAA
1 ATCTTTGAGT-TATTTCTGTTAAAACAAA
70146 GTTTTGTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (29 bp):
ATCTTTGAGTTATTTCTGTTAAAACAAAT
Found at i:70236 original size:64 final size:65
Alignment explanation
Indices: 70120--70244 Score: 198
Period size: 64 Copynumber: 1.9 Consensus size: 65
70110 AACAAATATC
*
70120 TTTGAGTCTATTTCTGTTAAAACAAAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAAAAAAATA
1 TTTGAGTCTATTTATGTTAAAACAAAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAAAAAAATA
* * * *
70185 TTTGAGTCTATTTATTTTGAAACAAAG-TTTGTCTCTCTTGAGACAATTTCGTGAAAAAAA
1 TTTGAGTCTATTTATGTTAAAACAAAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAAAAA
70245 TCTTTGAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 31 0.56
65 24 0.44
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (65 bp):
TTTGAGTCTATTTATGTTAAAACAAAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAAAAAAATA
Found at i:70302 original size:29 final size:28
Alignment explanation
Indices: 70237--70307 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
70227 ACAATTTCGT
*
70237 GAAAAAAATCTTTGAGTTGTTTCTTTTG
1 GAAAAAAATCTTTGAGTTGTTTCTCTTG
*
70265 AAAAAAAAATCTTTGAGTCTGTTTC-CTTG
1 -GAAAAAAATCTTTGAGT-TGTTTCTCTTG
70294 GAAACAAAAT-TTTG
1 GAAA-AAAATCTTTG
70308 TCTCTCTTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.19
29 24 0.65
30 6 0.16
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (28 bp):
GAAAAAAATCTTTGAGTTGTTTCTCTTG
Found at i:70362 original size:91 final size:89
Alignment explanation
Indices: 70175--70371 Score: 218
Period size: 92 Copynumber: 2.2 Consensus size: 89
70165 AATTTCGTAA
* *
70175 AAAAAAAATATTTGAGTCTATTTATTTTGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAA
1 AAAAAAAATATTTGAGTCTATTTACTTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAA
*
70240 AAAAATCTTTGAGTTGTTTCTTTT
66 AAAAATCTTTGAGTTATTTCTTTT
* * * * *
70264 GAAAAAAAAATCTTTGAGTCTGTTTCCTTGGAAACAAAATTTTGTCTCTCTTGGGACAATTTCTT
1 --AAAAAAAATATTTGAGTCTATTTACTTGGAAAC-AAAGTTTGTCTCTCTTGAGACAATTTC--
* **
70329 TTGAAAATCATCTTTGAGTATATTTC-TTT
61 GTGAAAAAAATCTTTGAGT-TATTTCTTTT
70358 AAAAACAAAT-TTTG
1 AAAAA-AAATATTTG
70372 CCTCTCTTGA
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
91 28 0.31
92 34 0.38
93 4 0.04
94 19 0.21
95 5 0.06
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (89 bp):
AAAAAAAATATTTGAGTCTATTTACTTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAA
AAAAATCTTTGAGTTATTTCTTTT
Found at i:70362 original size:92 final size:89
Alignment explanation
Indices: 70174--70371 Score: 227
Period size: 91 Copynumber: 2.2 Consensus size: 89
70164 CAATTTCGTA
* *
70174 AAAAAAAAATATTTGAGTCTATTTATTTTGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGA
1 AAAAAAAAAT-TTTGAGTCTATTTACTTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGA
*
70239 AAAAAATCTTTGAGTTGTTTCTTTT
65 AAAAAATCTTTGAGTTATTTCTTTT
* * * *
70264 GAAAAAAAAATCTTTGAGTCTGTTTCCTTGGAAACAAAATTTTGTCTCTCTTGGGACAATTTCTT
1 -AAAAAAAAAT-TTTGAGTCTATTTACTTGGAAAC-AAAGTTTGTCTCTCTTGAGACAATTTC--
* **
70329 TTGAAAATCATCTTTGAGTATATTTC-TTT
61 GTGAAAAAAATCTTTGAGT-TATTTCTTTT
*
70358 AAAAACAAATTTTG
1 AAAAAAAAATTTTG
70372 CCTCTCTTGA
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
91 29 0.32
92 29 0.32
93 9 0.10
94 19 0.21
95 5 0.05
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (89 bp):
AAAAAAAAATTTTGAGTCTATTTACTTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAA
AAAAATCTTTGAGTTATTTCTTTT
Found at i:70377 original size:156 final size:157
Alignment explanation
Indices: 70079--70383 Score: 400
Period size: 156 Copynumber: 1.9 Consensus size: 157
70069 CTGTTCCTTT
* * *
70079 TGAATAAAAATCTTTGAGTTGTTTCTTTTGAAACAAATATCTTTGAGTCTATTTCTGTTAAAACA
1 TGAATAAAAATCTTTGAGTTGTTTCTTTTGAAAAAAAAATCTTTGAGTCTATTTCTGTGAAAACA
* * **
70144 AAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAAAAAAATATTTGAGTCTATTTATTTTGAAACA
66 AAATTTTGTCTCTCTGGAGACAATTTCGTAAAAAAAAAATATTTGAGTATATTTATTTAAAAACA
*
70209 AAGTTTGTCTCTCTTGAGACAATTTCG
131 AAGTTTGCCTCTCTTGAGACAATTTCG
* *
70236 TGAA-AAAAATCTTTGAGTTGTTTCTTTTGAAAAAAAAATCTTTGAGTCTGTTTCCT-TGGAAAC
1 TGAATAAAAATCTTTGAGTTGTTTCTTTTGAAAAAAAAATCTTTGAGTCTATTT-CTGTGAAAAC
* *** ** * *
70299 AAAATTTTGTCTCTCTTGG-GACAATTTCTTTTGAAAATCATCTTTGAGTATATTTCTTTAAAAA
65 AAAATTTTGTCTCTC-TGGAGACAATTTCGTAAAAAAAAAATATTTGAGTATATTTATTTAAAAA
*
70363 CAAATTTTGCCTCTCTTGAGA
129 CAAAGTTTGCCTCTCTTGAGA
70384 TAGTTTCTAA
Statistics
Matches: 127, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
156 118 0.93
157 9 0.07
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (157 bp):
TGAATAAAAATCTTTGAGTTGTTTCTTTTGAAAAAAAAATCTTTGAGTCTATTTCTGTGAAAACA
AAATTTTGTCTCTCTGGAGACAATTTCGTAAAAAAAAAATATTTGAGTATATTTATTTAAAAACA
AAGTTTGCCTCTCTTGAGACAATTTCG
Found at i:71180 original size:28 final size:28
Alignment explanation
Indices: 71134--71229 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 28
71124 GAGACAGTTG
71134 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
71165 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
* *
71193 CTTTTGAAACAAATCTTTGAATCGGTTT
1 CTTTTGAAACAAATCTTTGAGTCTGTTT
*
71221 CTCTTGAAA
1 CTTTTGAAA
71230 TCATAACTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
28 45 0.76
29 3 0.05
30 3 0.05
31 8 0.14
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:71577 original size:174 final size:171
Alignment explanation
Indices: 71339--71675 Score: 577
Period size: 174 Copynumber: 1.9 Consensus size: 171
71329 TAACCAGCCG
*
71339 TCCTCATCAAGTAGGAACCGAGTTATCACCCTTAGATGGCCAAAAACTCTTCATCACGTATGAGC
1 TCCTCATCAAGTAGGAACCGAG-T-TCACCCTTAGATGGCCAAAAACTCTTCATCACATATGAGC
*
71404 AGTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAA
64 AGTGTCATACCCTGACCAGATTTCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCC--AAA
71469 AAAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATT
127 AAAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATT
*
71514 TCCTCATCACGTAGGAACCGAG-TCACCCTTAGATGGCCAAAAAAACTCTTCATCACATATGAGC
1 TCCTCATCAAGTAGGAACCGAGTTCACCCTTAGATGGCC--AAAAACTCTTCATCACATATGAGC
71578 AGTGTCATACCCTGACCAGATTTCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAA
64 AGTGTCATACCCTGACCAGATTTCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAA
*
71643 AACTCTTCATCACGTATGAGCAGTGTCGTCCCC
129 AACTCTTCATCACGTATGAGCAGTGTCATCCCC
71676 ACCAACACAC
Statistics
Matches: 156, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
172 53 0.34
174 82 0.53
175 21 0.13
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (171 bp):
TCCTCATCAAGTAGGAACCGAGTTCACCCTTAGATGGCCAAAAACTCTTCATCACATATGAGCAG
TGTCATACCCTGACCAGATTTCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAA
CTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATT
Found at i:71611 original size:86 final size:86
Alignment explanation
Indices: 71339--71675 Score: 579
Period size: 86 Copynumber: 3.9 Consensus size: 86
71329 TAACCAGCCG
*
71339 TCCTCATCAAGTAGGAACCGAGTTATCACCCTTAGATGGCC--AAAAACTCTTCATCACGTATGA
1 TCCTCATCACGTAGGAACCGAG---TCACCCTTAGATGGCCAAAAAAACTCTTCATCACGTATGA
71402 GCAGTGTCATCCCCTGACCAGATT
63 GCAGTGTCATCCCCTGACCAGATT
71426 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAAAACTCTTCATCACGTATGAG
1 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCC--AAAAAAACTCTTCATCACGTATGAG
71491 CAGTGTCATCCCCTGACCAGATT
64 CAGTGTCATCCCCTGACCAGATT
*
71514 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAACTCTTCATCACATATGAGCA
1 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAACTCTTCATCACGTATGAGCA
*
71579 GTGTCATACCCTGACCAGATT
66 GTGTCATCCCCTGACCAGATT
71600 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAACTCTTCATCACGTATGAGCA
1 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAACTCTTCATCACGTATGAGCA
*
71665 GTGTCGTCCCC
66 GTGTCATCCCC
71676 ACCAACACAC
Statistics
Matches: 240, Mismatches: 6, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
84 16 0.07
86 119 0.50
87 21 0.09
88 84 0.35
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (86 bp):
TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAACTCTTCATCACGTATGAGCA
GTGTCATCCCCTGACCAGATT
Found at i:71831 original size:3 final size:3
Alignment explanation
Indices: 71823--71877 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
71813 TCTTTTTTAA
*
71823 ATT ATT ATT ATT AATT ATT ATT TTT A-T ATT -TAT ATT ATT ATT -TT
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
*
71867 ATT AAT ATT AT
1 ATT ATT ATT AT
71878 ATTTTTACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 5 0.12
3 34 0.79
4 4 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:71855 original size:28 final size:28
Alignment explanation
Indices: 71828--71881 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
71818 TTTAAATTAT
71828 TATTATTA-ATTATTATTTTTATATTTA
1 TATTATTATATTATTATTTTTATATTTA
* * *
71855 TATTATTATTTTATTAATATTATATTT
1 TATTATTATATTATTATTTTTATATTT
71882 TTACATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TATTATTATATTATTATTTTTATATTTA
Found at i:71860 original size:17 final size:16
Alignment explanation
Indices: 71830--71884 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
71820 TAAATTATTA
71830 TTATTAATTATTATTTT
1 TTATTAA-TATTATTTT
*
71847 TATATTTATATTATTATT
1 T-TATTAATATTATT-TT
71865 TTATTAATATTATATTT
1 TTATTAATATTAT-TTT
71882 TTA
1 TTA
71885 CATATTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 24 0.73
18 9 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTAATATTATTTT
Found at i:71880 original size:19 final size:19
Alignment explanation
Indices: 71823--71880 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 19
71813 TCTTTTTTAA
71823 ATTATTATTATTAATTATTAT
1 ATTATT-TTATTAA-TATTAT
* *
71844 -TT-TTATATTTATA-T-T
1 ATTATTTTATTAATATTAT
71859 ATTATTTTATTAATATTAT
1 ATTATTTTATTAATATTAT
71878 ATT
1 ATT
71881 TTTACATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 11 0.38
18 6 0.21
19 6 0.21
20 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTATTTTATTAATATTAT
Found at i:73352 original size:29 final size:29
Alignment explanation
Indices: 73306--73395 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
73296 GCCCTTTAAG
*
73306 TTTCTGTTTTTCCATTTTAGTCCTCTAAC
1 TTTCTGTTTTACCATTTTAGTCCTCTAAC
* * * * **
73335 TTTCTGTTTTAGCTTTTTAGTTCTTTATG
1 TTTCTGTTTTACCATTTTAGTCCTCTAAC
** * *
73364 TTTCTGTTTTATTATTTTGGTCCTGTAAC
1 TTTCTGTTTTACCATTTTAGTCCTCTAAC
73393 TTT
1 TTT
73396 TTTATTTATT
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (29 bp):
TTTCTGTTTTACCATTTTAGTCCTCTAAC
Found at i:76665 original size:21 final size:21
Alignment explanation
Indices: 76639--76678 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
76629 TCTGCTGAAA
* *
76639 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
76660 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
76679 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Found at i:87081 original size:59 final size:59
Alignment explanation
Indices: 86989--87100 Score: 152
Period size: 59 Copynumber: 1.9 Consensus size: 59
86979 TACAGCAGCA
* * * * * * *
86989 GCTTTCAATGTACATGGTGTTATTTGTGAGCCTCTATAGGTTTATAATTCAACTAAATC
1 GCTTTCAATGTACATGATATGAATAGTGAGCCTCCATAGGTTCATAATTCAACTAAATC
*
87048 GCTTTCAATGTACATGATATGAATAGTGAGCCTCCGTAGGTTCATAATTCAAC
1 GCTTTCAATGTACATGATATGAATAGTGAGCCTCCATAGGTTCATAATTCAAC
87101 AATATCGATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (59 bp):
GCTTTCAATGTACATGATATGAATAGTGAGCCTCCATAGGTTCATAATTCAACTAAATC
Found at i:88469 original size:22 final size:21
Alignment explanation
Indices: 88427--88468 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
88417 TATATGTATT
*
88427 TGAAGAAAACAAATATGAAAA
1 TGAAGAAAACAAATATAAAAA
88448 TGAAGAGAAACAAAT-TAAAAA
1 TGAAGA-AAACAAATATAAAAA
88469 AAACAACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.67, C:0.05, G:0.14, T:0.14
Consensus pattern (21 bp):
TGAAGAAAACAAATATAAAAA
Found at i:88470 original size:23 final size:21
Alignment explanation
Indices: 88427--88470 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
88417 TATATGTATT
**
88427 TGAAGAAAACAAATATGAAAA
1 TGAAGAAAACAAATAAAAAAA
88448 TGAAGAGAAACAAATTAAAAAAA
1 TGAAGA-AAACAAA-TAAAAAAA
88471 ACAACCCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (21 bp):
TGAAGAAAACAAATAAAAAAA
Found at i:98083 original size:15 final size:15
Alignment explanation
Indices: 98063--98095 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
98053 CTGTTAACCA
98063 CCTTTTGTTCAAGTC
1 CCTTTTGTTCAAGTC
98078 CCTTTTGTTCAAGTC
1 CCTTTTGTTCAAGTC
98093 CCT
1 CCT
98096 AACTTGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.30, G:0.12, T:0.45
Consensus pattern (15 bp):
CCTTTTGTTCAAGTC
Found at i:102863 original size:40 final size:40
Alignment explanation
Indices: 102803--102931 Score: 177
Period size: 40 Copynumber: 3.2 Consensus size: 40
102793 TTATGAACAT
*
102803 TTTAGATATTCGAAACTCATACTTGAATCCGAGTAACGTG
1 TTTAGATATCCGAAACTCATACTTGAATCCGAGTAACGTG
* ** *
102843 TTTAGATATCCGAAAGTCATACTTGAATTTGAGTAACATG
1 TTTAGATATCCGAAACTCATACTTGAATCCGAGTAACGTG
* * * *
102883 CTCAGATATCCGAAACTCATATTTGAATCCGAATAACGTG
1 TTTAGATATCCGAAACTCATACTTGAATCCGAGTAACGTG
102923 TTTAGATAT
1 TTTAGATAT
102932 AAACGAGGTC
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (40 bp):
TTTAGATATCCGAAACTCATACTTGAATCCGAGTAACGTG
Found at i:123136 original size:23 final size:23
Alignment explanation
Indices: 123110--123233 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
123100 CACCACAACT
*
123110 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
* *
123133 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGTAGTGCCA
*
123156 CGTATAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
* *
123179 TATAATAATTGCACCG-AGTGCCG
1 CAT-ATAATTGCACCGTAGTGCCA
* * *
123202 CTTAGAATTACACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
*
123225 TATAATAAT
1 CAT-ATAAT
123234 GTCCATAAGG
Statistics
Matches: 82, Mismatches: 16, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
22 10 0.12
23 56 0.68
24 16 0.20
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGTAGTGCCA
Found at i:123198 original size:46 final size:47
Alignment explanation
Indices: 123112--123233 Score: 185
Period size: 46 Copynumber: 2.6 Consensus size: 47
123102 CCACAACTCA
* *
123112 TATAATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCG
*
123158 TATAATTGCACCGTAGTGCCATATAATAATTGCACC-GAGTGCCGCT
1 TATAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCG
* *
123204 TAGAATTACACCGTAGTGCCATATAATAAT
1 TATAATTGCACCGTAGTGCCATATAATAAT
123234 GTCCATAAGG
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
46 59 0.84
47 11 0.16
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (47 bp):
TATAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCG
Found at i:123411 original size:103 final size:103
Alignment explanation
Indices: 123240--123560 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
123230 TAATGTCCAT
* * * *
123240 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
123305 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
123343 AAGGACCACATATCATTCTTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
123408 GACTTCACATATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
123446 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAATTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
123511 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
123549 AAGAACCACATA
1 AAGGACCACATA
123561 GACCCTCGAC
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:129060 original size:23 final size:23
Alignment explanation
Indices: 129034--129158 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
129024 CACCACAACT
* *
129034 CATATAATTGCACCGAATTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
129057 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* * *
129080 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* *
129103 TATAATAATTGCACCGGAGTGCCG
1 CAT-ATAATTGCACCGGAGTGCCA
* * *
129127 CTTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
129150 TATAATAAT
1 CAT-ATAAT
129159 GTCCATAATG
Statistics
Matches: 80, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
23 58 0.73
24 22 0.28
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:129121 original size:47 final size:47
Alignment explanation
Indices: 129039--129158 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
129029 CAACTCATAT
* * *
129039 AATTGCACCGAATTGCCACAT-ATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
*
129085 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCTTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
129132 AATTGCACCGTAGTGCCATATAATAAT
1 AATTGCACCGTAGTGCCATATAATAAT
129159 GTCCATAATG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
46 18 0.26
47 51 0.74
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (47 bp):
AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
Found at i:129299 original size:103 final size:103
Alignment explanation
Indices: 129168--129484 Score: 555
Period size: 103 Copynumber: 3.1 Consensus size: 103
129158 TGTCCATAAT
* * * *
129168 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
129233 TTCACACATGTTCCAAAGAATACATATATGTTCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
129271 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
129336 TTCACATATGTTCCAAAGAATACATATATGTCCCGAA-
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
*
129373 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAAAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
129438 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
*
129476 AACCACATA
1 GACCACATA
129485 GACCCTCGAC
Statistics
Matches: 204, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
102 100 0.49
103 104 0.51
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:139822 original size:24 final size:23
Alignment explanation
Indices: 139789--139840 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
139779 TTTTTGATTC
139789 GTTTAATGTTC-ACAAACATATTT
1 GTTTAATGTTCGACAAA-ATATTT
* *
139812 GTTTATATGTTCGTCAAAATGTTT
1 GTTTA-ATGTTCGACAAAATATTT
139836 GTTTA
1 GTTTA
139841 GTGGTAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 4 0.16
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (23 bp):
GTTTAATGTTCGACAAAATATTT
Found at i:140523 original size:24 final size:24
Alignment explanation
Indices: 140479--140541 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
140469 TAATTTTAGG
*
140479 TTCGTTTA-ACGTTCACAAACATA
1 TTCGTTTATATGTTCACAAACATA
*
140502 TTCGTTTATATGTTCATC-AACATG
1 TTCGTTTATATGTTCA-CAAACATA
* *
140526 TTTGTTTATGTGTTCA
1 TTCGTTTATATGTTCA
140542 GGAATGAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.24
24 25 0.74
25 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (24 bp):
TTCGTTTATATGTTCACAAACATA
Found at i:169172 original size:21 final size:21
Alignment explanation
Indices: 169124--169173 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
169114 ATTTCCAGAT
*
169124 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
169145 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
169166 TCGCAATG
1 TCGCAATG
169174 TGATTTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:169215 original size:21 final size:21
Alignment explanation
Indices: 169184--169364 Score: 144
Period size: 21 Copynumber: 8.7 Consensus size: 21
169174 TGATTTACAT
* *
169184 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATATTCCAA
* * *
169205 GTTCGCGTTGCGATAGTCGAA
1 ATTCGCGTTGCGATATTCCAA
* *
169226 GTTCGCGTTGCGATTTTCCAA
1 ATTCGCGTTGCGATATTCCAA
*
169247 ATT--CGTTGCGATATTCGAA
1 ATTCGCGTTGCGATATTCCAA
*
169266 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TATTCCAA
*
169289 ATT--TGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TATTCCAA
*
169310 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATATTCCAA
*
169329 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TATTCCAA
169352 ATT--CGTTGCGATA
1 ATTCGCGTTGCGATA
169365 GTCAAAAATC
Statistics
Matches: 134, Mismatches: 18, Indels: 18
0.79 0.11 0.11
Matches are distributed among these distances:
19 27 0.20
21 89 0.66
23 18 0.13
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (21 bp):
ATTCGCGTTGCGATATTCCAA
Found at i:169265 original size:40 final size:42
Alignment explanation
Indices: 169210--169300 Score: 150
Period size: 40 Copynumber: 2.2 Consensus size: 42
169200 TCCAAGTTCG
169210 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
169250 CGTTGCGATATTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
169292 TGTTGCGAT
1 CGTTGCGAT
169301 TTATTCCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 28 0.60
41 2 0.04
42 17 0.36
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:169333 original size:63 final size:62
Alignment explanation
Indices: 169191--169363 Score: 244
Period size: 63 Copynumber: 2.8 Consensus size: 62
169181 CATATTCGCA
* * *
169191 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGA-TTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATTTTTCCAAATTCG
* * *
169252 TTGCGATATTCGAAGTTCGCGTTGCGATTTATTCCAAATTTGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTT-TTCCAAATTCG
169315 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
169364 AGTCAAAAAT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
61 32 0.32
62 2 0.02
63 65 0.66
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (62 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTTTCCAAATTCG
Found at i:169473 original size:6 final size:6
Alignment explanation
Indices: 169462--169491 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
169452 CACGTATTAT
169462 CACGAC CACGAC CACGAC CACGA- CACGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC C
169492 CTATCCAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:170146 original size:21 final size:21
Alignment explanation
Indices: 170120--170273 Score: 117
Period size: 21 Copynumber: 7.4 Consensus size: 21
170110 ATTTTGGACT
*
170120 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
170141 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
170162 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
170183 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
170204 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
170225 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
170246 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAACTTGGAATAA
170265 ATCGCAACG
1 ATCGCAACG
170274 CGAACTTCGA
Statistics
Matches: 105, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
19 35 0.33
21 42 0.40
23 28 0.27
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:170289 original size:21 final size:21
Alignment explanation
Indices: 170141--170318 Score: 179
Period size: 21 Copynumber: 8.6 Consensus size: 21
170131 TTTGGAATAA
170141 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
170162 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
170181 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * *
170204 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
170223 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * **
170246 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
170265 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
170286 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
170307 ATCGCAATGCGA
1 ATCGCAACGCGA
170319 CTATGTAAAT
Statistics
Matches: 127, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
19 34 0.27
21 74 0.58
23 19 0.15
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:170304 original size:42 final size:42
Alignment explanation
Indices: 170116--170294 Score: 335
Period size: 42 Copynumber: 4.3 Consensus size: 42
170106 TGCGATTTTG
170116 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
170158 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
170200 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
170242 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
170282 GACTATCGCAACG
1 GACTATCGCAACG
170295 CGAACTTGGA
Statistics
Matches: 135, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
40 32 0.24
41 1 0.01
42 102 0.76
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:170687 original size:2 final size:2
Alignment explanation
Indices: 170680--170725 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
170670 AAAGTATAAA
* *
170680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT CT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
170723 AT A
1 AT A
170726 GTTGTAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:173089 original size:91 final size:91
Alignment explanation
Indices: 172934--173111 Score: 338
Period size: 91 Copynumber: 2.0 Consensus size: 91
172924 GAGATGAGCG
*
172934 GATAAATAGGGTGTACGTCAGAACTCCCAATTTTTCTACTATTATCCTTTCGGCTGCGGCACCCA
1 GATAAATAGGGTGTACGTCAGAACTCCCAATTTTTCAACTATTATCCTTTCGGCTGCGGCACCCA
172999 CCATGCATTCATCTATTTATTTAGCA
66 CCATGCATTCATCTATTTATTTAGCA
*
173025 GATAAATAGGGTGTATGTCAGAACTCCCAATTTTTCAACTATTATCCTTTCGGCTGCGGCACCCA
1 GATAAATAGGGTGTACGTCAGAACTCCCAATTTTTCAACTATTATCCTTTCGGCTGCGGCACCCA
173090 CCATGCATTCATCTATTTATTT
66 CCATGCATTCATCTATTTATTT
173112 TTCAACCAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (91 bp):
GATAAATAGGGTGTACGTCAGAACTCCCAATTTTTCAACTATTATCCTTTCGGCTGCGGCACCCA
CCATGCATTCATCTATTTATTTAGCA
Found at i:174224 original size:15 final size:16
Alignment explanation
Indices: 174192--174228 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
174182 GGGCAGTAGT
174192 TGGAGGTAGGAGCTGG
1 TGGAGGTAGGAGCTGG
174208 TGGAGGT-GGAGAC-GG
1 TGGAGGTAGGAG-CTGG
174223 TGGAGG
1 TGGAGG
174229 CGGCGATGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.19, C:0.05, G:0.59, T:0.16
Consensus pattern (16 bp):
TGGAGGTAGGAGCTGG
Found at i:175979 original size:10 final size:10
Alignment explanation
Indices: 175944--175981 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
175934 ATGCTCACCA
175944 CATTATTTTT
1 CATTATTTTT
175954 CATT-TTTTT
1 CATTATTTTT
*
175963 C-TCATTTTT
1 CATTATTTTT
175972 CATTATTTTT
1 CATTATTTTT
175982 TTAGAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 1 0.04
9 12 0.50
10 11 0.46
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (10 bp):
CATTATTTTT
Found at i:176675 original size:35 final size:35
Alignment explanation
Indices: 176629--176740 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
176619 AAAACAGTCC
*
176629 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAATAAT
*
176664 TCAATTTCATTCTAAACCCTAAATTT-CAAAATAAT
1 TCAATTTCATTCTAAACCC-CAATTTCCAAAATAAT
** * * *
176699 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAATTTCCAAAATAAT
176734 TCAATTT
1 TCAATTT
176741 AAGGTTTAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 4 0.06
35 57 0.86
36 5 0.08
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAATTTCCAAAATAAT
Found at i:178566 original size:36 final size:35
Alignment explanation
Indices: 178510--178622 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
178500 TCTAAACCTT
* * * *
178510 AAATTGAAGTATTTTAGAATTTGGGGTTTATAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
178545 TAATTGAATTATTTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTA-TTTTGGAATTTGGGGTTTAGAATG
* * *
178581 AAATTGAATTACTTTGGAAATTGGGATTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
178616 AAATTGA
1 AAATTGA
178623 GGATTGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
35 36 0.55
36 30 0.45
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:183751 original size:18 final size:19
Alignment explanation
Indices: 183721--183757 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
183711 TAATATAGTA
*
183721 TTTAATATGTAAACTTAAT
1 TTTAATATGTAAAATTAAT
183740 TTTAATAT-TAAAATTAAT
1 TTTAATATGTAAAATTAAT
183758 ACTTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTAATATGTAAAATTAAT
Found at i:184145 original size:21 final size:21
Alignment explanation
Indices: 184121--184229 Score: 125
Period size: 21 Copynumber: 5.2 Consensus size: 21
184111 TATTCGCTAC
184121 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
184142 GCGAACTTGGATTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
184163 CCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
* *
184184 GCGAA-TATGTA-AATCGCAAT
1 GCGAACT-TGGACTATCGCAAT
* *
184204 GCGATA-GTCGACTATCGCAAT
1 GCGA-ACTTGGACTATCGCAAT
184225 GCGAA
1 GCGAA
184230 TATGTAAATC
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
20 16 0.21
21 59 0.79
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAT
Found at i:184201 original size:20 final size:20
Alignment explanation
Indices: 184176--184248 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
184166 AACTTGGACT
184176 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
184196 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
184217 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
184237 ATCGCAATGCGA
1 ATCGCAATGCGA
184249 TAGTCGACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 3 0.07
20 24 0.52
21 12 0.26
22 3 0.07
23 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:184217 original size:41 final size:41
Alignment explanation
Indices: 184172--184263 Score: 184
Period size: 41 Copynumber: 2.2 Consensus size: 41
184162 TCCGAACTTG
184172 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
184213 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
184254 GACTATCGCA
1 GACTATCGCA
184264 TTTCGATAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
Found at i:184263 original size:21 final size:21
Alignment explanation
Indices: 184172--184274 Score: 92
Period size: 21 Copynumber: 5.0 Consensus size: 21
184162 TCCGAACTTG
184172 GACTATCGCAATGCGAATA-T-
1 GACTATCGCAATGCG-ATAGTC
*
184192 GTA-AATCGCAATGCGATAGTC
1 G-ACTATCGCAATGCGATAGTC
184213 GACTATCGCAATGCGAATA-T-
1 GACTATCGCAATGCG-ATAGTC
*
184233 GTA-AATCGCAATGCGATAGTC
1 G-ACTATCGCAATGCGATAGTC
* *
184254 GACTATCGCATTTCGATAGTC
1 GACTATCGCAATGCGATAGTC
184275 CAAAATCGCA
Statistics
Matches: 68, Mismatches: 6, Indels: 17
0.75 0.07 0.19
Matches are distributed among these distances:
19 6 0.09
20 28 0.41
21 31 0.46
22 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (21 bp):
GACTATCGCAATGCGATAGTC
Found at i:184282 original size:21 final size:21
Alignment explanation
Indices: 184194--184285 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
184184 GCGAATATGT
*
184194 AAATCGCAATGCGATAGTCGA
1 AAATCGCAATGCGATAGTCCA
**
184215 CTATCGCAATGCGAATATGT---
1 AAATCGCAATGCG-ATA-GTCCA
*
184235 AAATCGCAATGCGATAGTCGA
1 AAATCGCAATGCGATAGTCCA
** * *
184256 CTATCGCATTTCGATAGTCCA
1 AAATCGCAATGCGATAGTCCA
184277 AAATCGCAA
1 AAATCGCAA
184286 CGACTGGTGG
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
18 2 0.04
19 3 0.06
20 11 0.20
21 33 0.61
22 3 0.06
23 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AAATCGCAATGCGATAGTCCA
Found at i:195122 original size:118 final size:117
Alignment explanation
Indices: 194908--195451 Score: 497
Period size: 118 Copynumber: 4.7 Consensus size: 117
194898 AGTGCTCGTT
* * * *
194908 TATAAACCACCATGCAAAATTAAATAATAGGACACTATTTCTCTTTGAGTC-TCTCTCACTATTC
1 TATAAACCACCATGCAAAATTAAACAAT-GGACACTATTTATCTTTGAG-CATCTCTCATTGTTC
* *** * *
194972 ATTATTTTATTCGGTTCATCATCTTATA-TTTGACACCAATACCAAAAACTTATA
64 ATTATCTTATTCAAATCATCATCTTA-AGTTTGACACCAACACCAAAAACTCATA
* * *
195026 TATAAACCACCGTGCATAATTAAACAATAGGACACTATTTATGTTTGAGCATCTCTCATTGTTCA
1 TATAAACCACCATGCAAAATTAAACAAT-GGACACTATTTATCTTTGAGCATCTCTCATTGTTCA
* * *
195091 TTATCTTATTCATATCATCACCTTAAGTTTGACACCAACACCAATAACTCATA
65 TTATCTTATTCAAATCATCATCTTAAGTTTGACACCAACACCAAAAACTCATA
* * * * * * *
195144 TATAAACCACCATACAGAATTAAGCAATGGGACATTATTTCTCTTCGAGCATCTTTCATTGTTCA
1 TATAAACCACCATGCAAAATTAAACAAT-GGACACTATTTATCTTTGAGCATCTCTCATTGTTCA
* * * * * * * *
195209 TTATCTTAATCAAAAT-ATCATCTTAGGTATGACACAAATACCAAGAGCTCGTA
65 TTATCTTATTC-AAATCATCATCTTAAGTTTGACACCAACACCAAAAACTCATA
* * *
195262 T-TAAACCATCATGCATAATTAAACAAT-G-----A--GATCTTT-AGCATCTCTCATTGTTCAT
1 TATAAACCACCATGCAAAATTAAACAATGGACACTATTTATCTTTGAGCATCTCTCATTGTTCAT
* * * * * **
195317 TATCTTATTCAAATCATCATCTTATGTCTAACATCAACA-CAAAATATTTGTA
66 TATCTTATTCAAATCATCATCTTAAGTTTGACACCAACACCAAAA-ACTCATA
* * * * *
195369 TATAAACCACCATACAAAATTAAACAATGAAACACTATTTTTCTTTGAGCCTCTCTCATTGTT-G
1 TATAAACCACCATGCAAAATTAAACAATG-GACACTATTTATCTTTGAGCATCTCTCATTGTTCA
195433 TTATCTTATTCAAATCATC
65 TTATCTTATTCAAATCATC
195452 TATTCTCTAT
Statistics
Matches: 348, Mismatches: 62, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
106 8 0.02
107 50 0.14
108 27 0.08
110 1 0.00
115 2 0.01
117 48 0.14
118 209 0.60
119 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (117 bp):
TATAAACCACCATGCAAAATTAAACAATGGACACTATTTATCTTTGAGCATCTCTCATTGTTCAT
TATCTTATTCAAATCATCATCTTAAGTTTGACACCAACACCAAAAACTCATA
Found at i:196564 original size:22 final size:23
Alignment explanation
Indices: 196538--196587 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
196528 AATTTTAAGA
196538 AAAATGAAAAAAAT-AAATTATT
1 AAAATGAAAAAAATAAAATTATT
* ** *
196560 TAAATTTAAAATATAAAATTATT
1 AAAATGAAAAAAATAAAATTATT
196583 AAAAT
1 AAAAT
196588 TTAAAAAGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAATGAAAAAAATAAAATTATT
Found at i:196603 original size:23 final size:22
Alignment explanation
Indices: 196546--196594 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
196536 GAAAAATGAA
*
196546 AAAAAT-AAATTATTTAAATTT
1 AAAAATAAAATTATTAAAATTT
196567 AAAATATAAAATTATTAAAATTT
1 AAAA-ATAAAATTATTAAAATTT
196590 AAAAA
1 AAAAA
196595 GTATCATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 3 0.12
23 18 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATAAAATTATTAAAATTT
Found at i:198628 original size:26 final size:25
Alignment explanation
Indices: 198614--198675 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
198604 TAAACATATT
*
198614 TTAAATTTTAAAATAAATTTAAATAG
1 TTAAATTTTAAAAT-AATTAAAATAG
*
198640 TTAAATTTTAAAATAAATTTAAATAG
1 TTAAATTTTAAAAT-AATTAAAATAG
198666 TTAAATTTTA
1 TTAAATTTTA
198676 CAAAATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
TTAAATTTTAAAATAATTAAAATAG
Found at i:198632 original size:12 final size:12
Alignment explanation
Indices: 198615--198659 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
198605 AAACATATTT
198615 TAAATTTTAAAA
1 TAAATTTTAAAA
198627 TAAA-TTTAAATA
1 TAAATTTTAAA-A
198639 GTTAAATTTTAAAA
1 --TAAATTTTAAAA
198653 TAAATTT
1 TAAATTT
198660 AAATAGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 6 0.21
12 12 0.41
14 5 0.17
15 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
TAAATTTTAAAA
Found at i:198646 original size:14 final size:14
Alignment explanation
Indices: 198627--198673 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
198617 AATTTTAAAA
198627 TAAATTTAAATAGT
1 TAAATTTAAATAGT
198641 TAAATTTTAAA-A--
1 TAAA-TTTAAATAGT
198653 TAAATTTAAATAGT
1 TAAATTTAAATAGT
198667 TAAATTT
1 TAAATTT
198674 TACAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 6 0.21
12 5 0.17
14 12 0.41
15 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (14 bp):
TAAATTTAAATAGT
Found at i:198799 original size:16 final size:15
Alignment explanation
Indices: 198780--198821 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
198770 CCTATATTAC
198780 ATTTTATTAAAAAAAT
1 ATTTTA-TAAAAAAAT
198796 A-TTTATAAAAAAAT
1 ATTTTATAAAAAAAT
198810 ATATTTAATAAA
1 AT-TTT-ATAAA
198822 TAAGTATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 4 0.17
17 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTTATAAAAAAAT
Found at i:198806 original size:14 final size:15
Alignment explanation
Indices: 198782--198811 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
198772 TATATTACAT
198782 TTTATTAAAAAAATA
1 TTTATTAAAAAAATA
198797 TTTA-TAAAAAAATA
1 TTTATTAAAAAAATA
198811 T
1 T
198812 ATTTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTATTAAAAAAATA
Found at i:198806 original size:15 final size:16
Alignment explanation
Indices: 198782--198821 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
198772 TATATTACAT
*
198782 TTTATTAAAAAA-ATA
1 TTTATAAAAAAATATA
198797 TTTATAAAAAAATATA
1 TTTATAAAAAAATATA
198813 TTTAATAAA
1 TTT-ATAAA
198822 TAAGTATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 6 0.27
17 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTATAAAAAAATATA
Found at i:200288 original size:23 final size:23
Alignment explanation
Indices: 200253--200300 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
200243 ATCAAGTACA
*
200253 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
200276 ATAATGTAATAGGTAGCGGTTAT
1 ATAATATAATAGGTAGCGCTTAT
200299 AT
1 AT
200301 TGACATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:201327 original size:182 final size:181
Alignment explanation
Indices: 200941--201572 Score: 901
Period size: 182 Copynumber: 3.5 Consensus size: 181
200931 TTTACTATCA
* * * ** *
200941 GTTTTGTTATTTCGAGATCGATTTTATCATATTTTTATATGTTATATT-ATTATGGATCGATATA
1 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGA-TATGGATCGATACA
* *
201005 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTTTTTTCTTTTAAA-TTCAAAAGTGTC
65 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTC
* * * *
201069 AATATTTATAATAAATTATCGACACTTTCAACATATCCGGCAGCTCTTTACC
130 GATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACC
* * *
201121 GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGATATAGATCGATATA
1 -GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGATATGGATCGATACA
* * *
201186 TTTTTATAAAGTATCGACACTTTATTGGCACTATAAATTCTTCTCTTTTAAATTTCAAAAGTGTC
65 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTC
* *
201251 GATACTTATAATAAAGTATCAATACTTTCAACATATCCGGTAGCTCTTTACC
130 GATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACC
* *
201303 GATTTTATCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1 G-TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGATATGGATCGATACA
* *
201368 TTTTTATAAAGCATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
65 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTC
* * **
201433 GATACTTAAAATAAAGTATCGACACTATCAACATATCCAATAGCGT-TTTACC
130 GATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGC-TCTTTACC
** * * *
201485 TGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACA
1 -GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGATATGGATCGATACA
201550 TTTTTATAAAGTATCGACACTTT
65 TTTTTATAAAGTATCGACACTTT
201573 CAATATATCC
Statistics
Matches: 407, Mismatches: 39, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
181 104 0.26
182 301 0.74
183 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (181 bp):
GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGATATGGATCGATACAT
TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCG
ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACC
Found at i:201640 original size:112 final size:112
Alignment explanation
Indices: 201443--201790 Score: 588
Period size: 112 Copynumber: 3.1 Consensus size: 112
201433 GATACTTAAA
* * * *
201443 ATAAAGTATCGACACTATCAACATATCCAATAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCAATAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
201508 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATATATTTTT
* * *
201555 ATAAAGTATCGACACTTTCAATATATCCAACAACGCTTTACTTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCAATAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
201620 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATATATTTTT
*
201667 ATAAAGTATCGACACTTTCAATATATCCAGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCAATAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
**
201732 TTTGTCATTTTTTTACCTGTTATATTATTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATATATTTTT
201779 ATAAAGTATCGA
1 ATAAAGTATCGA
201791 TACAAACCGA
Statistics
Matches: 221, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 221 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCAATAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATATATTTTT
Found at i:208442 original size:15 final size:16
Alignment explanation
Indices: 208404--208444 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
208394 ATATAGCCTA
208404 TGAATCATTCAACATT
1 TGAATCATTCAACATT
* *
208420 TGAATCATTCAGCGTT
1 TGAATCATTCAACATT
208436 T-AATCATTC
1 TGAATCATTC
208445 TGAAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:213632 original size:31 final size:31
Alignment explanation
Indices: 213597--213656 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
213587 TATAATATTA
*
213597 GATCATTTTCATTTTCATTTCATTAAAATAT
1 GATCATTTTCATTTTCATTTAATTAAAATAT
* *
213628 GATCATTTTCGTTTTTATTTAATTAAAAT
1 GATCATTTTCATTTTCATTTAATTAAAAT
213657 GTGGTCACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (31 bp):
GATCATTTTCATTTTCATTTAATTAAAATAT
Found at i:220888 original size:490 final size:491
Alignment explanation
Indices: 219962--220946 Score: 1864
Period size: 490 Copynumber: 2.0 Consensus size: 491
219952 TCACGATATC
* *
219962 AAGCAACGTGCTTGATTGGGGGGCTAAAGCCATTCAAATTCATCAACGCTTGGTTATTAAAGGAA
1 AAGCAACGTGCTTGATTAGGGGGCCAAAGCCATTCAAATTCATCAACGCTTGGTTATTAAAGGAA
*
220027 GGGTGTATAGATTTTTTTCGTGTGGGACGAACACAAAAAATAAAATTTCAGGATCGCATAGAATA
66 GGGTGTATAGATTTTTTTCGTGTGGGACGAACACAAAAAATAAAATTTCAGGATCGCATAAAATA
220092 GACATTTACCTTAAAAAAATTTGAATTTTAAGGTGCGCAAATCGAAAAAAAGGACACCCAAGCTC
131 GACATTTACCTTAAAAAAATTTGAATTTTAAGGTGCGCAAATCGAAAAAAAGGACACCCAAGCTC
*
220157 TTGCTAAAGAAAAGGTAGTGGGAGACTTCAAGTAAACGCACTTTGTACATCTCATATTTCCTGAG
196 TTGCTAAAGAAAAGGTAGTGGGAAACTTCAAGTAAACGCACTTTGTACATCTCATATTTCCTGAG
220222 GATGATGAGTGAACAAATTAAGAAAATTTGAGTGGATCATTAAGTAGCAATATTAAAAGAAATTA
261 GATGATGAGTGAACAAATTAAGAAAATTTGAGTGGATCATTAAGTAGCAATATTAAAAGAAATTA
220287 TACAGTAGACATGCAACCATGTTGAACAATGTTTCTGAGCTGGTTATGATGCTAAGACAAACTAC
326 TACAGTAGACATGCAACCATGTTGAACAATGTTTCTGAGCTGGTTATGATGCTAAGACAAACTAC
220352 ACTGACAAATTAGTGGTCGATAAATGGAACAACTCCATGTTTGTTTTCTTTCTTAGTGCAGAATG
391 ACTGACAAATTAGTGGTCGATAAATGGAACAACTCCATGTTTGTTTTCTTTCTTAGTGCAGAATG
220417 TAAACAAAACAGAACAACTAGCACTTCTCCAAACCT
456 TAAACAAAACAGAACAACTAGCACTTCTCCAAACCT
*
220453 AAGCGACGTGCTTGATTAGGGGGCCAAAGCCATTCAAATTCATCAACGCTTGGTTATTAAAGGAA
1 AAGCAACGTGCTTGATTAGGGGGCCAAAGCCATTCAAATTCATCAACGCTTGGTTATTAAAGGAA
* *
220518 GGGTGTATAGA-TTTTTTCGTGTGGGACGAACACAAAAAATAAAATTTCAGGATCGTATAAAATT
66 GGGTGTATAGATTTTTTTCGTGTGGGACGAACACAAAAAATAAAATTTCAGGATCGCATAAAATA
* *
220582 GACATTTACCTTAAAAAGATTTGAATTTTAAGGTGCGCAAATCGAAAAAAATGACACCCAAGCTC
131 GACATTTACCTTAAAAAAATTTGAATTTTAAGGTGCGCAAATCGAAAAAAAGGACACCCAAGCTC
*
220647 TTGTTAAAGAAAAGGTAGTGGGAAACTTCAAGTAAACGCACTTTGTACATCTCATATTTCCTGAG
196 TTGCTAAAGAAAAGGTAGTGGGAAACTTCAAGTAAACGCACTTTGTACATCTCATATTTCCTGAG
220712 GATGATGAGTGAACAAATTAAGAAAATTTGAGTGGATCATTAAGTAGCAATATTAAAAGAAATTA
261 GATGATGAGTGAACAAATTAAGAAAATTTGAGTGGATCATTAAGTAGCAATATTAAAAGAAATTA
220777 TACAGTAGACATGCAACCATGTTGAACAATGTTTCTGAGCTGGTTATGATGCTAAGACAAACTAC
326 TACAGTAGACATGCAACCATGTTGAACAATGTTTCTGAGCTGGTTATGATGCTAAGACAAACTAC
*
220842 ACTGACAAATTAGTGGTCGATAAATGGAACAACTCCATGTTTGTTTTCTTTCTTAGTGTAGAATG
391 ACTGACAAATTAGTGGTCGATAAATGGAACAACTCCATGTTTGTTTTCTTTCTTAGTGCAGAATG
220907 TAAACAAAACAGAACAACTAGCACTTCTCCAAACCT
456 TAAACAAAACAGAACAACTAGCACTTCTCCAAACCT
220943 AAGC
1 AAGC
220947 CTCTCAAGTT
Statistics
Matches: 483, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
490 410 0.85
491 73 0.15
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (491 bp):
AAGCAACGTGCTTGATTAGGGGGCCAAAGCCATTCAAATTCATCAACGCTTGGTTATTAAAGGAA
GGGTGTATAGATTTTTTTCGTGTGGGACGAACACAAAAAATAAAATTTCAGGATCGCATAAAATA
GACATTTACCTTAAAAAAATTTGAATTTTAAGGTGCGCAAATCGAAAAAAAGGACACCCAAGCTC
TTGCTAAAGAAAAGGTAGTGGGAAACTTCAAGTAAACGCACTTTGTACATCTCATATTTCCTGAG
GATGATGAGTGAACAAATTAAGAAAATTTGAGTGGATCATTAAGTAGCAATATTAAAAGAAATTA
TACAGTAGACATGCAACCATGTTGAACAATGTTTCTGAGCTGGTTATGATGCTAAGACAAACTAC
ACTGACAAATTAGTGGTCGATAAATGGAACAACTCCATGTTTGTTTTCTTTCTTAGTGCAGAATG
TAAACAAAACAGAACAACTAGCACTTCTCCAAACCT
Found at i:222228 original size:29 final size:29
Alignment explanation
Indices: 222186--222244 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
222176 ATTTTCACCT
*
222186 AACTAAATTGATGTAAGAAATGTCATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
*
222215 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
222244 A
1 A
222245 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGAAATGACATCAA
Found at i:225621 original size:64 final size:64
Alignment explanation
Indices: 225551--225692 Score: 153
Period size: 63 Copynumber: 2.2 Consensus size: 64
225541 ATGCACATGA
* ** **
225551 AGTGCATCGATGCACTCTTTTAAAATACAAACATCAAATGCCATCGATGCATCGATGCATAAG-G
1 AGTGCATCGATGCACCCCATT-AAATACAAACATCAAATAACATCGATGCATCGATGCAT-AGTG
225615 -
64 T
* * * ** *
225615 AGTGCATCAATGCACCCCATTAAATACAAACATCGAATAAGATTTATGCATCGATGCATGGTGT
1 AGTGCATCGATGCACCCCATTAAATACAAACATCAAATAACATCGATGCATCGATGCATAGTGT
225679 AGTGCATCGATGCA
1 AGTGCATCGATGCA
225693 TACCTCCATT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
62 1 0.02
63 33 0.52
64 30 0.47
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (64 bp):
AGTGCATCGATGCACCCCATTAAATACAAACATCAAATAACATCGATGCATCGATGCATAGTGT
Found at i:226072 original size:30 final size:30
Alignment explanation
Indices: 226036--226104 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
226026 TTATATCAGT
*
226036 TATGTGATAAAGGTAT-AGAAATGATATGTC
1 TATGTGATAAAGGTATGA-AAATAATATGTC
226066 TATGTGATAAAGGTATGAAAATAATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
226096 TACGTGATA
1 TATGTGATA
226105 CAAATTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:226390 original size:23 final size:23
Alignment explanation
Indices: 226330--226398 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
226320 CATTATTATA
*
226330 TGGCACTAT-GGTGCAATTCTACA
1 TGGCACT-TCGGTGCAATTCTACG
* * **
226353 CGGCACTCCAATGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
226376 TGGCACTTCGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTCTACG
226399 AGCTGTAGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:231990 original size:23 final size:22
Alignment explanation
Indices: 231964--232032 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 22
231954 CATTATTATA
231964 TGGCACCATGGTGCAATTCTACG
1 TGGCACC-TGGTGCAATTCTACG
231987 TGGCACTCTGGTGCAATTCTACG
1 TGGCAC-CTGGTGCAATTCTACG
* *
232010 TGGCACTTCGGTGCAATTATACG
1 TGGCACCT-GGTGCAATTCTACG
232033 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (22 bp):
TGGCACCTGGTGCAATTCTACG
Found at i:234777 original size:29 final size:29
Alignment explanation
Indices: 234728--234786 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
234718 ATTTTCACCT
234728 AACTAAATTGATATAACCAATGACATCAA
1 AACTAAATTGATATAACCAATGACATCAA
* *
234757 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATATAACCAATGACATCAA
234786 A
1 A
234787 TGAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATATAACCAATGACATCAA
Found at i:238799 original size:22 final size:21
Alignment explanation
Indices: 238743--238799 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
238733 AAATTAGTAC
* *
238743 TAATTATTAATTAAGTATATTT
1 TAATTATTAATT-AGTAAATTG
*
238765 TTATTATCT-ATTAGTAAATTAG
1 TAATTAT-TAATTAGTAAATT-G
238787 TAATTATTAATTA
1 TAATTATTAATTA
238800 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
TAATTATTAATTAGTAAATTG
Found at i:239824 original size:26 final size:26
Alignment explanation
Indices: 239793--239845 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
239783 AAAACATAAC
239793 AAGGCATCATATATCATAAAAATTAT
1 AAGGCATCATATATCATAAAAATTAT
239819 AAGGCATCATATATCATAAAAATTAT
1 AAGGCATCATATATCATAAAAATTAT
239845 A
1 A
239846 TAGCTCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (26 bp):
AAGGCATCATATATCATAAAAATTAT
Found at i:243069 original size:2 final size:2
Alignment explanation
Indices: 243062--243092 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
243052 TTGTTCCAAC
243062 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 T
243093 TTGTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:243322 original size:35 final size:35
Alignment explanation
Indices: 243283--243349 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
243273 ATGATGCGGA
*
243283 CAAAATGACGTCATTTTGGCGCAACTATTGATTTC
1 CAAAACGACGTCATTTTGGCGCAACTATTGATTTC
* * *
243318 CAAAACGACGTCGTTTTGGTGCACCTATTGAT
1 CAAAACGACGTCATTTTGGCGCAACTATTGAT
243350 GCCCATAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (35 bp):
CAAAACGACGTCATTTTGGCGCAACTATTGATTTC
Found at i:243369 original size:35 final size:35
Alignment explanation
Indices: 243330--243404 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
243320 AAACGACGTC
243330 GTTTTGGTGCACCTATTGATGCCCATA-ATGACATT
1 GTTTTGGTGCACCTATTGATGCCCA-AGATGACATT
* * *
243365 GTTTTGGTGCAGCTATTGATGCTCAAGATGATATT
1 GTTTTGGTGCACCTATTGATGCCCAAGATGACATT
243400 GTTTT
1 GTTTT
243405 AGGCACTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (35 bp):
GTTTTGGTGCACCTATTGATGCCCAAGATGACATT
Found at i:253700 original size:3 final size:3
Alignment explanation
Indices: 253692--253748 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
253682 TCTTATGTTA
*
253692 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
253740 ATT ATT ATT
1 ATT ATT ATT
253749 TCATATATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:257299 original size:131 final size:131
Alignment explanation
Indices: 257123--257372 Score: 324
Period size: 131 Copynumber: 1.9 Consensus size: 131
257113 CAATTAGAGT
* * * *
257123 AATAAATGATTGCTTTAAGGCATGAGAGGTAATTTATTCTTGATTGAAAATTATTAGATATTA-T
1 AATAAATGACTGCTTTAAGGCATGAGAGGTAATTTATGCTCGATTGAAAATCATTAGATATTACT
** *
257187 CGTTTTCTTTCAAATCAATATTGATTTTTAAGAAAG-AATAGTGATATATCTTCATCTCGATTGG
66 -GTTTTCACTCAAATCAATATTGAATTTTAA-AAAGAAATAGTGATATATCTTCATCTCGATTGG
257251 AGC
129 AGC
* * * *
257254 AATAAATGACTGCTTTAGGGTATGAGAGGTCATTTATGCTCGATTGGAAATCATTAGATATTACT
1 AATAAATGACTGCTTTAAGGCATGAGAGGTAATTTATGCTCGATTGAAAATCATTAGATATTACT
* * * * *
257319 GTTTTCACTCGAATCGATATTGAATTTTAATACGAAATAGTGATATCTCTTCAT
66 GTTTTCACTCAAATCAATATTGAATTTTAAAAAGAAATAGTGATATATCTTCAT
257373 TTAGATTAGA
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
130 2 0.02
131 98 0.97
132 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (131 bp):
AATAAATGACTGCTTTAAGGCATGAGAGGTAATTTATGCTCGATTGAAAATCATTAGATATTACT
GTTTTCACTCAAATCAATATTGAATTTTAAAAAGAAATAGTGATATATCTTCATCTCGATTGGAG
C
Found at i:258298 original size:14 final size:14
Alignment explanation
Indices: 258279--258305 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
258269 CTTGAACCCA
258279 CAAGAAGAAGAAAG
1 CAAGAAGAAGAAAG
258293 CAAGAAGAAGAAA
1 CAAGAAGAAGAAA
258306 TAAAGCTTCC
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:0.67, C:0.07, G:0.26, T:0.00
Consensus pattern (14 bp):
CAAGAAGAAGAAAG
Found at i:261991 original size:21 final size:20
Alignment explanation
Indices: 261965--262083 Score: 114
Period size: 21 Copynumber: 5.8 Consensus size: 20
261955 ATCAGTTTCC
261965 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
261986 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
262007 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
262026 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTTT-G
* *
262049 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
262069 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
262084 ACACATAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
19 1 0.01
20 19 0.23
21 59 0.71
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:262022 original size:42 final size:41
Alignment explanation
Indices: 261960--262083 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 41
261950 CGCAAATCAG
261960 TTTCCAAAATCGCAACGCGATTCTTGAAAATCGCAACGCGAT
1 TTTCCAAAATCGCAACGCGATT-TTGAAAATCGCAACGCGAT
* * ** **
262002 TCTT-GAAAATCGCAATGCGATAGT-ACAAATTCGCATTGCGAT
1 T-TTCCAAAATCGCAACGCGATTTTGA-AAA-TCGCAACGCGAT
* *
262044 TTTCCAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 TTTCCAAAATCGCAACGCGATTTTGAAAATCGCAACGCGA
262084 ACACATAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
40 1 0.02
41 15 0.23
42 45 0.70
43 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
TTTCCAAAATCGCAACGCGATTTTGAAAATCGCAACGCGAT
Found at i:262074 original size:20 final size:20
Alignment explanation
Indices: 261965--262102 Score: 84
Period size: 21 Copynumber: 6.7 Consensus size: 20
261955 ATCAGTTTCC
* *
261965 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
* *
261986 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
*
262007 AAAATCGCAATGCG-ATA-G
1 AAAATCGCAACGCGAATATG
** * * *
262025 TACAAATTCGCATTGCGATTTTCC
1 -A-AAA-TCGCAACGCGAATAT-G
262049 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
* *
262069 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATG
262088 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
262103 TATCCGTAAA
Statistics
Matches: 96, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 34 0.35
21 54 0.56
22 4 0.04
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:262112 original size:20 final size:20
Alignment explanation
Indices: 262050--262339 Score: 284
Period size: 20 Copynumber: 14.5 Consensus size: 20
262040 CGATTTTCCA
* ** *
262050 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
262070 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
262090 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
262110 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
262130 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
262150 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
262170 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
262190 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
262210 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
262230 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
262250 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
262270 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
262290 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
262310 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
262330 AAATCACAAC
1 AAATCGCAAC
262340 ACTGAAATTT
Statistics
Matches: 230, Mismatches: 32, Indels: 16
0.83 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 226 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:262136 original size:60 final size:60
Alignment explanation
Indices: 262070--262339 Score: 321
Period size: 60 Copynumber: 4.5 Consensus size: 60
262060 GCGAATATGA
* * * * *
262070 AAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGAGAATCCGTAAATCGCAACGAT-AATCCGT
* * * * * * * *
262130 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTATATCGCAACGCGT-ATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* *
262190 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
262250 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
262310 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
262340 ACTGAAATTT
Statistics
Matches: 188, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
59 1 0.01
60 185 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:263061 original size:24 final size:24
Alignment explanation
Indices: 263022--263068 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
263012 AAATTTGGTC
263022 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
263046 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
263069 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:265549 original size:33 final size:34
Alignment explanation
Indices: 265494--265658 Score: 174
Period size: 33 Copynumber: 4.7 Consensus size: 34
265484 CGAAAATTAC
* *
265494 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
265527 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
265561 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* * *
265599 AATCGCAACGA-GAGAATCGCAATACGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
265632 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
265659 CGAGAGAATC
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
32 1 0.01
33 49 0.44
34 16 0.14
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:265577 original size:19 final size:19
Alignment explanation
Indices: 265508--265696 Score: 210
Period size: 19 Copynumber: 10.7 Consensus size: 19
265498 GCAACGAGAG
265508 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
265527 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
265541 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
265561 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
265580 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
265599 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
265613 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
265632 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
265651 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
265665 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
265684 AATCGCATTGCGA
1 AATCGCAATGCGA
265697 TTCTCCCGTT
Statistics
Matches: 145, Mismatches: 9, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 83 0.57
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:265639 original size:52 final size:52
Alignment explanation
Indices: 265494--265696 Score: 272
Period size: 52 Copynumber: 3.9 Consensus size: 52
265484 CGAAAATTAC
*
265494 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
265541 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
265599 AATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
265651 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
265697 TTCTCCCGTT
Statistics
Matches: 138, Mismatches: 7, Indels: 17
0.85 0.04 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 83 0.60
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Done.