Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003883.1 Hibiscus syriacus cultivar Beakdansim tig00008374_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: 195228
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:4933 original size:2 final size:2
Alignment explanation
Indices: 4926--4990 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
4916 TTATAAATAA
4926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4968 AT AT AT AT AT AT AT -T AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4991 ATAAATAAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 59 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6725 original size:3 final size:3
Alignment explanation
Indices: 6717--6849 Score: 152
Period size: 3 Copynumber: 45.0 Consensus size: 3
6707 TTTGGGCATG
* * *
6717 TAA TAA TAA T-T TAA TTAA TAA TAA TAA T-T TAA TTAA TAA T-T TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
*
6761 TTAA TAA TAA TAA TAA TAAA TAA TAA -AA TAA TAA TAA -AA TAA TAG
1 -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6806 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6850 ACCAAATGAA
Statistics
Matches: 112, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
2 9 0.08
3 91 0.81
4 12 0.11
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:7346 original size:122 final size:121
Alignment explanation
Indices: 7220--7656 Score: 503
Period size: 122 Copynumber: 3.7 Consensus size: 121
7210 TTAAGGCAAT
*
7220 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
*
7285 CACT-TCTGGAAATGTTGATGCTGATCTTTCTCCTTTTGTGATAGAGTCATGCAAAAG
66 CTCTCTCTGGAAA-GTTGATG-TGATCTTTCTCCTTTTGTGATAGAGTCATGCAAAAG
* * * * *
7342 GTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTATTCAGATAAGTTCTTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
7407 CTTTCTCTGGAAAGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATACAAAAAG
66 CTCTCTCTGGAAAGTTGATG-TGATCTTTCTCCTTTTGTGATAGAGTCATGC-AAAAG
*
7465 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG---TTCTCATTATGAA
1 GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * * *
7527 CTTTCTCTAGCAA--TG-T-TGA--TTTAT-C--TAGTGAT-GAATTCAAGCAAAAG
66 CTCTCTCTGGAAAGTTGATGTGATCTTTCTCCTTTTGTGATAG-AGTCATGCAAAAG
* *
7574 GTT-AAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAAA-AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGA
7638 ACTCT-T-TGGAAAAGTTGAT
65 ACTCTCTCTGG-AAAGTTGAT
7657 CCATCGAGTG
Statistics
Matches: 273, Mismatches: 31, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
108 2 0.01
109 49 0.18
110 12 0.04
111 3 0.01
112 17 0.06
113 5 0.02
114 1 0.00
115 3 0.01
117 1 0.00
118 2 0.01
120 24 0.09
122 96 0.35
123 58 0.21
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (121 bp):
GTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTCTCTGGAAAGTTGATGTGATCTTTCTCCTTTTGTGATAGAGTCATGCAAAAG
Found at i:8521 original size:54 final size:53
Alignment explanation
Indices: 8434--8594 Score: 216
Period size: 54 Copynumber: 3.0 Consensus size: 53
8424 ATAATTACTG
* * *
8434 GTTCATAAAACATTTGACAACACATTTATCCTTTCTTGTGGCTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTC-TGTGGATTCTGCACAGAT
* *
8488 GTTCGTAAAACATTTGACAACACATTCATCCTTTC-CTGGATTCATGCACATAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTGTGGATTC-TGCACAGAT
* * *
8541 GTTCGTAAAACATTTGACAACGCATTCATCCTTTCCTGTGGTTTTTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTT-CTGTGGATTCTGCACAGAT
8595 TTTTTCTCTG
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
52 6 0.06
53 41 0.44
54 42 0.45
55 5 0.05
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTGTGGATTCTGCACAGAT
Found at i:8559 original size:53 final size:52
Alignment explanation
Indices: 8434--8578 Score: 209
Period size: 53 Copynumber: 2.7 Consensus size: 52
8424 ATAATTACTG
* * * *
8434 GTTCATAAAACATTTGACAACACATTTATCCTTTCTTGTGGCTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTC--CTGGATTCTGCACAGAT
*
8488 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGGATTCATGCACATAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGGATTC-TGCACAGAT
*
8541 GTTCGTAAAACATTTGACAACGCATTCATCCTTTCCTG
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTG
8579 TGGTTTTTGC
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
52 6 0.07
53 45 0.54
54 33 0.39
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGGATTCTGCACAGAT
Found at i:20462 original size:17 final size:18
Alignment explanation
Indices: 20429--20464 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20419 ATTTTAAGAA
20429 AAATATATTAAATTTTAT
1 AAATATATTAAATTTTAT
*
20447 AAATATA-TATATTTTAT
1 AAATATATTAAATTTTAT
20464 A
1 A
20465 TTTTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATATATTAAATTTTAT
Found at i:20467 original size:24 final size:24
Alignment explanation
Indices: 20431--20499 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
20421 TTTAAGAAAA
* * *
20431 ATATATTAAATTTTATAAATATAT
1 ATATTTTATATTTTATAAATATAG
20455 ATATTTTATATTTTATAAATA-AG
1 ATATTTTATATTTTATAAATATAG
20478 ATA-TTTAT-TTACTTATAAATAT
1 ATATTTTATATT--TTATAAATAT
20500 CAGAAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.05
22 5 0.13
23 13 0.33
24 19 0.49
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
ATATTTTATATTTTATAAATATAG
Found at i:22210 original size:3 final size:3
Alignment explanation
Indices: 22202--22294 Score: 97
Period size: 3 Copynumber: 32.0 Consensus size: 3
22192 TTTGTACCTG
* * *
22202 TAA TAA TAA T-T TAA TTAT TAA TAA TAA TAA -AA AAA TATA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
*
22247 TAA -AA -AA TAA TAG TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
22292 TAA
1 TAA
22295 ACCAAATGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
2 9 0.12
3 63 0.82
4 5 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:22243 original size:18 final size:17
Alignment explanation
Indices: 22220--22294 Score: 89
Period size: 17 Copynumber: 4.4 Consensus size: 17
22210 ATTTAATTAT
22220 TAATAATAATAAAAAAA
1 TAATAATAATAAAAAAA
22237 TATATAATAAT-AAAAAA
1 TA-ATAATAATAAAAAAA
* * *
22254 TAATAGTAATATAATAA
1 TAATAATAATAAAAAAA
*
22271 TAATAATAATAATAATAA
1 TAATAATAATAA-AAAAA
22289 TAATAA
1 TAATAA
22295 ACCAAATGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.14
17 24 0.48
18 19 0.38
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (17 bp):
TAATAATAATAAAAAAA
Found at i:23138 original size:14 final size:15
Alignment explanation
Indices: 23107--23140 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23097 GATTTAATAG
*
23107 AAAAAGTCCAATTAA
1 AAAAAATCCAATTAA
*
23122 AAAAAATCCAATCAA
1 AAAAAATCCAATTAA
23137 AAAA
1 AAAA
23141 CGTATGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAAAATCCAATTAA
Found at i:23632 original size:12 final size:13
Alignment explanation
Indices: 23610--23638 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
23600 AATTAAAAAT
23610 AAAATGTTTTTTA
1 AAAATGTTTTTTA
23623 AAAATGTTTTTTA
1 AAAATGTTTTTTA
23636 AAA
1 AAA
23639 TCTAAATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
AAAATGTTTTTTA
Found at i:27518 original size:466 final size:465
Alignment explanation
Indices: 26540--27683 Score: 1862
Period size: 466 Copynumber: 2.5 Consensus size: 465
26530 ACAAGTAAGA
** * ** ** *
26540 TAAAGCCTTTGCTCGAAGTACATTTTACAAAAAATACTGAAACAAAAAGAAATAAAACACAAACT
1 TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAA-AAAGGGAAATGCAATACAAACT
* * * * * *
26605 TCAAAGCCAAAAACGGAGCTCTATTTGTTAACAATAGAACAGAGCAACTTGTCCTCTG-TTTTAA
65 TCAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTTTGTTTTTAA
* *
26669 ACAACAAAGTACATTTTAAAATCAACCATAAAGGATAAAAGAACTAAAAGAAGAAAAAATAGTAG
130 ACAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAG
* *
26734 AATAGATAGAGACTCAAGGAAAAAAAGTGAAGGCGACAGCGTTAAGGTTTAAAGAGAGTGCGAAG
195 AATAGAT--AGACTCAAGGAAAAAAAGTAAAGGCGACAGCGTTAAGATTTAAAGAGAGTGCGAAG
*
26799 GTGAGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGGGATAGCTTATTTTTA
258 GTGAGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGAGATAGCTTATTTTTA
*
26864 GTCAGTGTTGTCAAGGGCACCAGGTGCACTAGAGGCGCTAAGACCTCTAAATAGCCTGAGGCATA
323 GTCAGTGTTGTCAAGGGCAACAGGTGCACTAGAGGCGCTAAGACCTCTAAATAGCCTGAGGCATA
*
26929 TGGAGCAAAAAAGCACGTGCCCGGTTGAAATAAGGTGCATGCATATAAAAATATTTATAATGCAT
388 TGGAGCAAAAAAGCACGTGCCCGGTTGAAATAAGGTGCATACATATAAAAATATTTATAATGCAT
26994 GTAGACGTAAAAT
453 GTAGACGTAAAAT
*
27007 TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGGAAAGGCAATACAAACTT
1 TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGGAAATGCAATACAAACTT
* **
27072 CAAAGCCAAAAACCGAGCTCTATTTTTTAACGCTAAAACAGAAAAACTTCTCCTTTGTTTTTTAA
66 CAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTTTG-TTTTTAA
27137 ACAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAG
130 ACAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAG
* *
27202 AATAGATAGACTCAAGGAAAAAAAAAGTAAAGGTGACAGCGTTAAGATTTAAAGAGGGTGCGAAG
195 AATAGATAGACTCAAGG--AAAAAAAGTAAAGGCGACAGCGTTAAGATTTAAAGAGAGTGCGAAG
27267 GTGAGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGAGATAGCTTA-TTTTA
258 GTGAGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGAGATAGCTTATTTTTA
* ** *
27331 GTCCGTGTTGTCAAGGGCAACAGGTGCACTAGAGGCGCTAAGAGTTCTATATAGCCTGAGGCATA
323 GTCAGTGTTGTCAAGGGCAACAGGTGCACTAGAGGCGCTAAGACCTCTAAATAGCCTGAGGCATA
* * *
27396 TGG-TCAAAAAAGCGCTTGCCCGGTTGAAATAAGGTGCATACATATAAAAATATTTATAATGCAT
388 TGGAGCAAAAAAGCACGTGCCCGGTTGAAATAAGGTGCATACATATAAAAATATTTATAATGCAT
27460 GTAGACGTAAAAT
453 GTAGACGTAAAAT
* *
27473 TAAAGTCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGTAAATGCAATACAAACTT
1 TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGGAAATGCAATACAAACTT
*
27538 CAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAATAGAGCAACTTCTCCTTTGTTTTTAAA
66 CAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTTTGTTTTTAAA
*
27603 CAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAATTAGTAGA
131 CAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAGA
*
27668 ATAGGTAGACTCAAGG
196 ATAGATAGACTCAAGG
27684 GGGAAAAAGT
Statistics
Matches: 630, Mismatches: 43, Indels: 10
0.92 0.06 0.01
Matches are distributed among these distances:
465 87 0.14
466 260 0.41
467 107 0.17
468 176 0.28
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (465 bp):
TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGGAAATGCAATACAAACTT
CAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTTTGTTTTTAAA
CAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAGA
ATAGATAGACTCAAGGAAAAAAAGTAAAGGCGACAGCGTTAAGATTTAAAGAGAGTGCGAAGGTG
AGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGAGATAGCTTATTTTTAGTC
AGTGTTGTCAAGGGCAACAGGTGCACTAGAGGCGCTAAGACCTCTAAATAGCCTGAGGCATATGG
AGCAAAAAAGCACGTGCCCGGTTGAAATAAGGTGCATACATATAAAAATATTTATAATGCATGTA
GACGTAAAAT
Found at i:32102 original size:15 final size:15
Alignment explanation
Indices: 32059--32095 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
32049 TTTTTTAATA
32059 ATAAAAAAATTATTT
1 ATAAAAAAATTATTT
32074 -TAAAAAAATTATTT
1 ATAAAAAAATTATTT
32088 ATAAAAAA
1 ATAAAAAA
32096 CTAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAAAAAATTATTT
Found at i:33729 original size:20 final size:20
Alignment explanation
Indices: 33704--33761 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
33694 ATCATATTCC
33704 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
33724 CTGGTAATCTTACATTCACA
1 CTGGTAATCTTACATTCCCA
*
33744 CTGGTAATCTCACATTCC
1 CTGGTAATCTTACATTCC
33762 GTGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.34
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:35650 original size:5 final size:5
Alignment explanation
Indices: 35637--35693 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
35627 TTGGGCCTGG
* * *
35637 AAAAG AAAAT AAAATT AAAATT AAAAT AAATT AAAA- AAAAT AAATT AAAA-
1 AAAAT AAAAT AAAA-T AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
35687 AAAAT AA
1 AAAAT AA
35694 CCATAATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 8 0.18
5 25 0.57
6 11 0.25
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:35686 original size:13 final size:14
Alignment explanation
Indices: 35637--35693 Score: 78
Period size: 14 Copynumber: 3.8 Consensus size: 14
35627 TTGGGCCTGG
35637 AAAAGAAAATAAAATT
1 AAAA-AAAAT-AAATT
35653 AAAATTAAAATAAATT
1 AAAA--AAAATAAATT
35669 AAAAAAAATAAATT
1 AAAAAAAATAAATT
35683 AAAAAAAATAA
1 AAAAAAAATAA
35694 CCATAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
14 21 0.54
16 13 0.33
17 5 0.13
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAAAAAATAAATT
Found at i:35788 original size:25 final size:28
Alignment explanation
Indices: 35754--35819 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 28
35744 ACCTATATAA
35754 TATATA-TTTTCAAAAAAAATT-AAAAT
1 TATATAGTTTTCAAAAAAAATTCAAAAT
*
35780 TAT-T--TTTT--TAAAAAATTCAAAAT
1 TATATAGTTTTCAAAAAAAATTCAAAAT
35803 TATATAGTTTTCAAAAA
1 TATATAGTTTTCAAAAA
35820 TGTTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
22 8 0.25
23 8 0.25
24 5 0.16
25 1 0.03
26 7 0.22
28 3 0.09
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (28 bp):
TATATAGTTTTCAAAAAAAATTCAAAAT
Found at i:35874 original size:2 final size:2
Alignment explanation
Indices: 35869--35896 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35859 TTAAAAACTA
35869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35897 TCAAAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35878 original size:36 final size:35
Alignment explanation
Indices: 35803--35882 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 35
35793 AATTCAAAAT
35803 TATATAGTTTTCAAAAATGTTTT-AAAACTATATAT-
1 TATATA-TTTTC-AAAATGTTTTAAAAACTATATATA
*
35838 TATATGTTTTCAAAATGTTTTTTAAAAACTAATATATA
1 TATATATTTTCAAAATG--TTTTAAAAACT-ATATATA
35876 TATATAT
1 TATATAT
35883 ATATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
33 6 0.16
34 5 0.13
35 9 0.24
36 6 0.16
37 6 0.16
38 6 0.16
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (35 bp):
TATATATTTTCAAAATGTTTTAAAAACTATATATA
Found at i:35900 original size:84 final size:83
Alignment explanation
Indices: 35803--36036 Score: 255
Period size: 72 Copynumber: 2.9 Consensus size: 83
35793 AATTCAAAAT
* *
35803 TATATAGTTTTCAAAAATGTTTT-AAAACTATATA-T-TATATGTTTTCAAAATGTTTTTTAAAA
1 TATATAGTATTC-AAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATG--TTTTAAAA
35865 ACTAATATATATATATATATATA
63 ACT-ATATAT-TATATATATATA
*
35888 TATATA-TATTCAAAATGTTTTAAAAACTATATATTATATATATTTTTAAAATGTTTTAAAAAC-
1 TATATAGTATTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGTTTTAAAAACT
35951 --------TATATAT-TA
66 ATATATTATATATATATA
* *
35960 TATATACT-TTCAAAATGTTTTAAAAACTATATAATATATATATGTTTTCAAAATGTTTTAAAAA
1 TATATAGTATTCAAAATGTTTTAAAAACTATAT-AT-TATATATATTTTCAAAATGTTTTAAAAA
36024 CTATATATTATAT
64 CTATATATTATAT
36037 TTTTTTAAAT
Statistics
Matches: 129, Mismatches: 5, Indels: 32
0.78 0.03 0.19
Matches are distributed among these distances:
72 32 0.25
73 10 0.08
74 27 0.21
83 13 0.10
84 25 0.19
85 7 0.05
86 15 0.12
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (83 bp):
TATATAGTATTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGTTTTAAAAACT
ATATATTATATATATATA
Found at i:35904 original size:50 final size:45
Alignment explanation
Indices: 35831--36036 Score: 156
Period size: 36 Copynumber: 5.0 Consensus size: 45
35821 GTTTTAAAAC
* *
35831 TATATATTATATGTTTTCAAAATGTTTTTTAAAAACTAATATATATATA
1 TATATATTATATATATTCAAAATG--TTTTAAAAACT-ATATAT-TATA
35880 TATATATATATATATATTCAAAATGTTTTAAAAAC--TATA-TAT-
1 TATATAT-TATATATATTCAAAATGTTTTAAAAACTATATATTATA
35922 TATATA-TAT-T-T-TT-AAAATGTTTTAAAAAC--TATA---TA
1 TATATATTATATATATTCAAAATGTTTTAAAAACTATATATTATA
*
35957 T-TATA-TATA-CT-TTCAAAATGTTTTAAAAAC--TATA-TA-A
1 TATATATTATATATATTCAAAATGTTTTAAAAACTATATATTATA
*
35994 TATATA-TATGT-T-TTCAAAATGTTTTAAAAACTATATATTATA
1 TATATATTATATATATTCAAAATGTTTTAAAAACTATATATTATA
36036 T
1 T
36037 TTTTTTAAAT
Statistics
Matches: 141, Mismatches: 3, Indels: 33
0.80 0.02 0.19
Matches are distributed among these distances:
34 8 0.06
35 4 0.03
36 40 0.28
37 4 0.03
38 28 0.20
39 1 0.01
40 7 0.05
41 2 0.01
42 8 0.06
43 3 0.02
45 4 0.03
48 10 0.07
49 7 0.05
50 15 0.11
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (45 bp):
TATATATTATATATATTCAAAATGTTTTAAAAACTATATATTATA
Found at i:35928 original size:36 final size:36
Alignment explanation
Indices: 35878--36122 Score: 334
Period size: 36 Copynumber: 6.7 Consensus size: 36
35868 AATATATATA
*
35878 TATATATATATATATATATTCAAAATGTTTTAAAAAC
1 TATATAT-TATATATATTTTCAAAATGTTTTAAAAAC
*
35915 TATATATTATATATATTTTTAAAATGTTTTAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTAAAAAC
*
35951 TATATATTATATATACTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTAAAAAC
*
35987 TATATAATATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATAT-AT-TATATATATTTTCAAAATGTTTTAAAAAC
* * *
36025 TATATATTATAT-T-TTTT-TAAATTTGTTTATAAAC
1 TATATATTATATATATTTTCAAAATGT-TTTAAAAAC
36059 TATATATTATATATATTTTCAAAATGTTTTAAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTT-AAAAAC
36096 TATATAATATATATATATATTTCAAAA
1 TATAT-AT-TATATATAT-TTTCAAAA
36123 ATCATTTGCA
Statistics
Matches: 186, Mismatches: 12, Indels: 17
0.87 0.06 0.08
Matches are distributed among these distances:
33 5 0.03
34 24 0.13
35 2 0.01
36 78 0.42
37 26 0.14
38 34 0.18
39 9 0.05
40 8 0.04
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATATTATATATATTTTCAAAATGTTTTAAAAAC
Found at i:36714 original size:80 final size:80
Alignment explanation
Indices: 36587--37776 Score: 1515
Period size: 80 Copynumber: 14.8 Consensus size: 80
36577 TGGCCTTGAA
* * ** * *
36587 TGTAATCGAACTCGAATGTATTTGTTGACAGATAGTCCTTCTCGCCTTGAGCTATGCTGTAAATG
1 TGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATG
36652 ATGTGCCTTTGAGCTGAG
63 ATGTGCCTTTGAGCTGAG
* * *
36670 TGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATAATG
1 TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
36735 TGCCTTTGAGCTGAG
66 TGCCTTTGAGCTGAG
*
36750 TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTAAGCTATGCTGCAAATGATG
1 TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
* * *
36815 TGTCTCTAAGCTGAG
66 TGCCTTTGAGCTGAG
* *
36830 TGTTAATCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGAT
1 TG-TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
* *
36895 ATGCC--T---C--AA
65 GTGCCTTTGAGCTGAG
* * * * * *
36904 TGTAATCGAACTCGAATGTCTTTGGCAGATAACCCTTATTTCCTTAAGTTATGCTGTAAATGTAT
1 TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATG-AT
*
36969 -TGTCTTTGAGCTGAG
65 GTGCCTTTGAGCTGAG
* * * * * *
36984 TGTAATCAAACTCGAAGGTCTTTGGTAGGTAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATG
1 TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
*
37049 TGCCTTTAAGCTGAG
66 TGCCTTTGAGCTGAG
*
37064 TGTAATCGAACTC-AATGGTCTTTGGCAGATAACCCATCTTGCCTTGAGCTATGCTGCAAATGAT
1 TGTAATCGAACTCGAA-GGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
*
37128 GTGCCTCTGAGCTGAG
65 GTGCCTTTGAGCTGAG
* * * *
37144 TGTTAATCGAACTTGAAGGTCTTTGGCAGATAACCCTTCTTGCATTGAGCTATGTTGCAAATAAT
1 TG-TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
*
37209 GTGCCTTTGAGCTAAG
65 GTGCCTTTGAGCTGAG
* * * * *
37225 TGTAATCAAACTCGAAGGTCTTTGGTAGATAACCCTTATTGCCTTGGGTTATGCTGCAAATGATG
1 TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
* *
37290 TACCTTTGAGCTAAG
66 TGCCTTTGAGCTGAG
*
37305 -GTAATCGAACTCGAAGGTCTTTGGCATG-TAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGCA-GATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGAT
*
37368 GTACCTTTGAGCTGAG
65 GTGCCTTTGAGCTGAG
* * * *
37384 TGTAATCGAACTTGAAGGTCTTTGGCAGATAACCCTTATTTCCTTGAGTTATGCTGCAAATGATG
1 TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
*
37449 TACCTTTGAGCTGAG
66 TGCCTTTGAGCTGAG
* * * * *
37464 TATAATCGAACTCGAAGGTCTTTGGTAGATAGCCCTTATTGCCTTGAGCTATTCTGCAAATGATG
1 TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
*
37529 TGCATTTGAGCTGAG
66 TGCCTTTGAGCTGAG
* * *
37544 TGTAATCGAACTCGAAGGTCTTTGTTGTCAGATAACCCTT-TTAGCCTTGAGTTATGATGTAAAT
1 TGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTT-GCCTTGAGCTATGCTGCAAAT
37608 GATGTGCCTTTGAGCTGAG
62 GATGTGCCTTTGAGCTGAG
*
37627 TGTAATCGAACTCGAAGGTCTTTTGTTGGCA-ATATAGCCTTTCTTGCCTTGAGCTATGCTGCAA
1 TGTAATCGAACTCGAAGGTC---T-TTGGCAGATA-A-CCCTTCTTGCCTTGAGCTATGCTGCAA
*
37691 ATGAGGTGCCTTTGAGCTGAG
60 ATGATGTGCCTTTGAGCTGAG
*
37712 TGTAATCGAACTCGAATGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAAT
1 TGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAAT
37777 AGAAAAAAAA
Statistics
Matches: 975, Mismatches: 104, Indels: 55
0.86 0.09 0.05
Matches are distributed among these distances:
73 55 0.06
74 5 0.01
75 1 0.00
76 1 0.00
78 1 0.00
79 76 0.08
80 496 0.51
81 133 0.14
82 5 0.01
83 90 0.09
84 31 0.03
85 72 0.07
86 6 0.01
87 3 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (80 bp):
TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
TGCCTTTGAGCTGAG
Found at i:38635 original size:13 final size:13
Alignment explanation
Indices: 38602--38637 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
38592 AATATGATTA
38602 TTTTAAAAATAAT
1 TTTTAAAAATAAT
*
38615 TTAT-AAAATAAT
1 TTTTAAAAATAAT
38627 TTTTAAAAATA
1 TTTTAAAAATA
38638 GGATTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTAAAAATAAT
Found at i:39049 original size:15 final size:15
Alignment explanation
Indices: 39029--39057 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39019 GCTATTTATG
39029 ATTAAAATCATAATT
1 ATTAAAATCATAATT
39044 ATTAAAATCATAAT
1 ATTAAAATCATAAT
39058 GGCTAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAATCATAATT
Found at i:40135 original size:3 final size:3
Alignment explanation
Indices: 40127--40194 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
40117 TATTTTTTAT
*
40127 TAA TAA TAA TAA TAA TAA -AA TAA TAA TAG TAA TAAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
40171 TAA TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
40195 CAAATGGATG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:40556 original size:20 final size:20
Alignment explanation
Indices: 40531--40595 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
40521 AAATTAAGGT
40531 TGAACAAGTTCTTCTCATTA
1 TGAACAAGTTCTTCTCATTA
** *
40551 TGAACATCTTCTTCTTCTTTA
1 TGAACAAGTTCTTC-TCATTA
**
40572 -G-ATGAGTTCTTCTCATTA
1 TGAACAAGTTCTTCTCATTA
40590 TGAACA
1 TGAACA
40596 TCTCTGGAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 5 0.16
19 8 0.25
20 14 0.44
21 5 0.16
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (20 bp):
TGAACAAGTTCTTCTCATTA
Found at i:40651 original size:121 final size:112
Alignment explanation
Indices: 40526--41173 Score: 781
Period size: 113 Copynumber: 5.6 Consensus size: 112
40516 GAATCAAATT
* * *
40526 AAGGTTGAACAAGTTCTTCTCATTATGAACATCTTCTTCTTCTTTAGATGAGTTCTTCTCATTAT
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * *
40591 GAACAT-CTCTGGAAATGTTGATGCCGATCTATATCCTTCTGTGATAGAA-TCAAAC-A
66 GAACTTCCTCTGGAAAAGTTGAT-CC-ATC--GA-------GTGAT-GAATTCAAACAA
* * * *
40647 AAGGTTGAACAAGTTCTTCTCATTAAGAACTTCTTCTTCCTCTTCAGATGATTTCTTCTCATTAT
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
40712 GAACAT-CTATGGAAATGTTGATGCTGATCTATCTCATTCTGTGATAGAA-TCAAAC-A
66 GAACTTCCTCTGGAAAAGTTGAT-C----C-ATC-GA----GTGAT-GAATTCAAACAA
* * * *
40768 AAGGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTCTTCAGATGAGTTCTTATCATTAT
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
*
40833 GAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAA
66 GAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
*
40880 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* *
40945 TGAACTTCCTCTGGAAGAGTTGATCCATCGAGTGATGAATTCAAGCAA
65 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
*
40993 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
*
41058 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAA
65 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
*
41106 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTC--CTTCTTTAGATGAGTTCTTCTCATTAT
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
41169 GAACT
66 GAACT
41174 CTACATGGCA
Statistics
Matches: 492, Mismatches: 27, Indels: 27
0.90 0.05 0.05
Matches are distributed among these distances:
110 33 0.07
111 10 0.02
112 37 0.08
113 218 0.44
115 1 0.00
116 3 0.01
117 1 0.00
121 170 0.35
122 14 0.03
124 1 0.00
125 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
Found at i:42399 original size:18 final size:18
Alignment explanation
Indices: 42362--42399 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
42352 TATGTGAAAG
*
42362 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCAAA
42380 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
42398 AA
1 AA
42400 GATAATCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:42807 original size:12 final size:12
Alignment explanation
Indices: 42792--42831 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
42782 TTCTTTTCAT
42792 TTCATTTTTTTC
1 TTCATTTTTTTC
42804 TTCATTTTTTTC
1 TTCATTTTTTTC
*
42816 TTCTTTTTTCTTC
1 TTCATTTTT-TTC
42829 TTC
1 TTC
42832 TTCAAGCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (12 bp):
TTCATTTTTTTC
Found at i:42829 original size:10 final size:10
Alignment explanation
Indices: 42797--42830 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
42787 TTCATTTCAT
42797 TTTTTTCTTC
1 TTTTTTCTTC
42807 ATTTTTTTCTTC
1 --TTTTTTCTTC
42819 TTTTTTCTTC
1 TTTTTTCTTC
42829 TT
1 TT
42831 CTTCAAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
12 10 0.45
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:53549 original size:27 final size:25
Alignment explanation
Indices: 53493--53550 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
53483 AAAACATTAA
*
53493 TAAAAAATAATATATATAAATATAT
1 TAAAAAATAATATATATAAAAATAT
* *
53518 GAAAATAATAAGTATATATAAAAATTT
1 TAAAA-AATAA-TATATATAAAAATAT
53545 TAAAAA
1 TAAAAA
53551 GAATTATAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 17 0.63
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (25 bp):
TAAAAAATAATATATATAAAAATAT
Found at i:55433 original size:3 final size:3
Alignment explanation
Indices: 55427--55497 Score: 65
Period size: 3 Copynumber: 24.0 Consensus size: 3
55417 AGTTTTTTTT
* * * * * *
55427 TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA -AA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55474 TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA
55498 AAACAAACTG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 4 0.07
3 54 0.89
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:56644 original size:95 final size:96
Alignment explanation
Indices: 56459--56717 Score: 357
Period size: 95 Copynumber: 2.7 Consensus size: 96
56449 AGCTGGATCT
* * *
56459 ATAAAG-TCGGGGAGTTTAACCAATTGCTTTAGAGGGACAACTTAA--TATCATTGTATAGATAT
1 ATAAAGCT-GGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCT-TTATTGTAT--AT-T
*
56521 TATAATCGCTTTTATCAGGCTAGCTGAATATTATCC
61 TATAATCACTTTTATCAGGCTAGCTGAATATTATCC
*
56557 ATAAAGCTGGGGCGTTTAACCAATTTCTCTT-GAGGGACAACTCAAGCTTTATTGTAT-TTTATA
1 ATAAAGCTGGGGCGTTTAACCAATTGCT-TTAGAGGGACAACTCAAGCTTTATTGTATATTTATA
*
56620 ATCACTTTTATCAGGCTAGCTGAATCTTATCC
65 ATCACTTTTATCAGGCTAGCTGAATATTATCC
* *
56652 ATAAAGTTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATATATAA
1 ATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTTATAA
56717 T
66 T
56718 ATTATAATCT
Statistics
Matches: 146, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
94 2 0.01
95 87 0.60
96 8 0.05
98 37 0.25
99 11 0.08
100 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (96 bp):
ATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTTATAA
TCACTTTTATCAGGCTAGCTGAATATTATCC
Found at i:59357 original size:8 final size:8
Alignment explanation
Indices: 59344--59370 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
59334 AATTATTAAA
59344 AAAAATAC
1 AAAAATAC
59352 AAAAATAC
1 AAAAATAC
59360 AAAAATAC
1 AAAAATAC
59368 AAA
1 AAA
59371 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAC
Found at i:60846 original size:5 final size:5
Alignment explanation
Indices: 60826--60882 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
60816 GTTGGACCTG
* *
60826 TAAAA GAAAA TGAAAA TAAAA TAAAA T-AAA TAAAAA TAAAA AATAAA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TA-AAA
60873 TAAAAA TAAA
1 T-AAAA TAAA
60883 TAACCATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.09
5 22 0.51
6 16 0.37
7 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:60853 original size:10 final size:10
Alignment explanation
Indices: 60826--60882 Score: 53
Period size: 11 Copynumber: 5.4 Consensus size: 10
60816 GTTGGACCTG
*
60826 TAAAAGAAAA
1 TAAAATAAAA
60836 TGAAAATAAAA
1 T-AAAATAAAA
60847 TAAAAT-AAA
1 TAAAATAAAA
60856 TAAAAATAAAA
1 T-AAAATAAAA
*
60867 AATAAATAAAAA
1 TA-AAAT-AAAA
60879 TAAA
1 TAAA
60883 TAACCATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 4 0.10
10 12 0.31
11 18 0.46
12 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:60870 original size:17 final size:17
Alignment explanation
Indices: 60848--60882 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
60838 AAAATAAAAT
60848 AAAATAAATAAAAATAA
1 AAAATAAATAAAAATAA
60865 AAAATAAATAAAAATAA
1 AAAATAAATAAAAATAA
60882 A
1 A
60883 TAACCATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATAAATAAAAATAA
Found at i:60891 original size:10 final size:10
Alignment explanation
Indices: 60833--60885 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
60823 CTGTAAAAGA
*
60833 AAATGAAAAT
1 AAATAAAAAT
60843 AAA-ATAAAAT
1 AAATA-AAAAT
60853 AAATAAAAAT
1 AAATAAAAAT
60863 --A-AAAAAT
1 AAATAAAAAT
60870 AAATAAAAAT
1 AAATAAAAAT
60880 AAATAA
1 AAATAA
60886 CCATAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
7 6 0.16
8 1 0.03
9 1 0.03
10 28 0.76
11 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:60891 original size:27 final size:28
Alignment explanation
Indices: 60838--60900 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
60828 AAAGAAAATG
60838 AAAATAAAATAAAATAAATAAAAATAA-
1 AAAATAAAATAAAATAAATAAAAATAAT
**
60865 AAAAT-AAATAAAAATAAATAACCATAAT
1 AAAATAAAAT-AAAATAAATAAAAATAAT
60893 AATAATAA
1 AA-AATAA
60901 TATTATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.13
27 20 0.67
28 2 0.07
29 3 0.10
30 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (28 bp):
AAAATAAAATAAAATAAATAAAAATAAT
Found at i:60970 original size:26 final size:26
Alignment explanation
Indices: 60941--61030 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 26
60931 AAACCTATAT
60941 AATATATATTTTTAAAAATATTTAAA
1 AATATATATTTTTAAAAATATTTAAA
60967 AATAT-T-TTTCTTAAAAA-ATTTTCAAA
1 AATATATATTT-TTAAAAATA-TTT-AAA
* * *
60993 ATTATATAGTTTTCAAAAATGTTTTAAA
1 AATATATA-TTTTTAAAAAT-ATTTAAA
*
61021 ACTATATATT
1 AATATATATT
61031 ATATGTTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
24 4 0.08
25 11 0.21
26 12 0.23
27 3 0.06
28 16 0.31
29 6 0.12
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
AATATATATTTTTAAAAATATTTAAA
Found at i:61050 original size:33 final size:36
Alignment explanation
Indices: 60993--61319 Score: 190
Period size: 36 Copynumber: 8.5 Consensus size: 36
60983 AATTTTCAAA
60993 ATTATATAGTTTTCAAAAATG-TTTT-AAAACTAT-AT
1 ATTATAT-GTTTTC-AAAATGTTTTTAAAAACTATAAT
61028 ATTATATGTTTTCAAAATGTTTTTTTAAAAACTATAAT
1 ATTATATGTTTTCAAAATG--TTTTTAAAAACTATAAT
*
61066 ATATATATGTTTTCATATATATTTTTAAAATGTTTTAAAAACTATATAAT
1 AT-TATATGTTTTCA-A-A-A----T---GT-TTTTAAAAAC--TATAAT
* * *
61116 AATATATATATGTTTTCAAAAATG-TTTTAAAAACTAT-AT
1 -AT-TATATGTTTTC---AAAATGTTTTTAAAAACTATAAT
*
61155 ATTATGTATATTTTCAAAATG-TTTTAAAAACTAT-AT
1 ATTA--TATGTTTTCAAAATGTTTTTAAAAACTATAAT
61191 AATATATATGTTTTCAAAATG-TTTTAAAAACTAT-AT
1 -AT-TATATGTTTTCAAAATGTTTTTAAAAACTATAAT
*
61227 ATTATATATTTTCAAAATG-TTTTAAAAACTAT-AT
1 ATTATATGTTTTCAAAATGTTTTTAAAAACTATAAT
* * *
61261 ATTATATATATTTTCAAAATATTTTAAAAAACTATATAAT
1 A-T-TATATGTTTTCAAAATGTTTTTAAAAAC--TATAAT
* *
61301 ATATATATATTTCCAAAAT
1 AT-TATATGTTTTCAAAAT
61320 CATTTCCAAA
Statistics
Matches: 247, Mismatches: 12, Indels: 62
0.77 0.04 0.19
Matches are distributed among these distances:
33 6 0.02
34 38 0.15
35 10 0.04
36 70 0.28
37 21 0.09
38 8 0.03
39 41 0.17
40 7 0.03
41 1 0.00
42 11 0.04
46 1 0.00
47 2 0.01
48 10 0.04
50 6 0.02
51 12 0.05
52 1 0.00
53 1 0.00
54 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
ATTATATGTTTTCAAAATGTTTTTAAAAACTATAAT
Found at i:61176 original size:36 final size:36
Alignment explanation
Indices: 61080--61348 Score: 335
Period size: 36 Copynumber: 7.2 Consensus size: 36
61070 ATATGTTTTC
*
61080 ATATATATTTTTAAAATGTTTTAAAAACTATATAATAAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATAT-AT--T
61119 ATATATATGTTTTCAAAAATGTTTTAAAAACTATATATT
1 ATATATA--TTTTC-AAAATGTTTTAAAAACTATATATT
* *
61158 ATGTATATTTTCAAAATGTTTTAAAAACTATATAAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
*
61194 ATATATGTTTTCAAAATGTTTTAAAAACTATATA-T
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
61229 -TATATATTTTCAAAATGTTTTAAAAACTATATATT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
*
61264 ATATATATTTTCAAAATATTTTAAAAAACTATATAATAT
1 ATATATATTTTCAAAATGTTTT-AAAAACTATAT-AT-T
* ** **
61303 ATATATATTTCCAAAATCATTTCCAAACTATAATATAT
1 ATATATATTTTCAAAATGTTTTAAAAACTAT-ATAT-T
61341 ATATATAT
1 ATATATAT
61349 ACATAAATAA
Statistics
Matches: 209, Mismatches: 12, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
34 32 0.15
35 2 0.01
36 75 0.36
37 16 0.08
38 21 0.10
39 36 0.17
41 6 0.03
42 21 0.10
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATATATTTTCAAAATGTTTTAAAAACTATATATT
Found at i:61244 original size:70 final size:70
Alignment explanation
Indices: 61081--61306 Score: 326
Period size: 70 Copynumber: 3.1 Consensus size: 70
61071 TATGTTTTCA
*
61081 TATATATTTTTAAAATGTTTTAAAAACTATATAATAATATATATATGTTTTCAAAAATGTTTTAA
1 TATATATTTTCAAAATGTTTTAAAAAC--TAT-AT-A-ATATATATGTTTTC-AAAATGTTTTAA
61146 AAACTATATAT
60 AAACTATATAT
61157 TATGTATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAAC
1 TA--TATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAAC
61222 TATATAT
64 TATATAT
* * *
61229 TATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATATTTTAAAAAACT
1 TATATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTTT-AAAAACT
*
61294 ATATAA
65 ATATAT
61300 TATATAT
1 TATATAT
61307 ATATTTCCAA
Statistics
Matches: 142, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
70 52 0.37
71 19 0.13
72 25 0.18
73 14 0.10
74 1 0.01
75 2 0.01
76 5 0.04
78 24 0.17
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (70 bp):
TATATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAACTA
TATAT
Found at i:66476 original size:24 final size:24
Alignment explanation
Indices: 66405--66476 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
66395 GCTTATGACA
66405 TGATAATAT-TTAAATATTGTTTC
1 TGATAATATATTAAATATTGTTTC
* **
66428 TGTTTGTGATATTAAAATATTGTTT-
1 TGATAAT-ATATT-AAATATTGTTTC
66453 TGATAATATATTAAATATTAGTTT
1 TGATAATATATTAAATATT-GTTT
66477 AAATTTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
23 11 0.28
24 11 0.28
25 6 0.15
26 11 0.28
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (24 bp):
TGATAATATATTAAATATTGTTTC
Found at i:67710 original size:36 final size:36
Alignment explanation
Indices: 67670--67743 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
67660 TTTACAGTTA
*
67670 TACTTATAAATCTTTGTTGTAATTATGAATATTTTC
1 TACTTATAAATCTTTATTGTAATTATGAATATTTTC
*
67706 TACTTGTAAATCTTTATTGTAATTATGAATATTTTC
1 TACTTATAAATCTTTATTGTAATTATGAATATTTTC
67742 TA
1 TA
67744 TTTTTAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (36 bp):
TACTTATAAATCTTTATTGTAATTATGAATATTTTC
Found at i:75722 original size:36 final size:36
Alignment explanation
Indices: 75682--75755 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
75672 TTTACAGTTA
*
75682 TACTTATAAATCTTTGTTGTAATTATGAATATTTTC
1 TACTTATAAATCTTTATTGTAATTATGAATATTTTC
*
75718 TACTTGTAAATCTTTATTGTAATTATGAATATTTTC
1 TACTTATAAATCTTTATTGTAATTATGAATATTTTC
75754 TA
1 TA
75756 TTTTTAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (36 bp):
TACTTATAAATCTTTATTGTAATTATGAATATTTTC
Found at i:82465 original size:22 final size:23
Alignment explanation
Indices: 82403--82473 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 23
82393 GCTTATGACA
*
82403 TGATAATATTTAAATATTGTTTC
1 TGATAATATATAAATATTGTTTC
* **
82426 TGTTTGTGATATTAAAATATTGTTT-
1 TGATAAT-ATA-T-AAATATTGTTTC
82451 TGATAATATATAAATATTAGTTT
1 TGATAATATATAAATATT-GTTT
82474 AAATTTAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
22 7 0.19
23 9 0.24
24 5 0.14
25 5 0.14
26 11 0.30
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.52
Consensus pattern (23 bp):
TGATAATATATAAATATTGTTTC
Found at i:83679 original size:36 final size:36
Alignment explanation
Indices: 83639--83712 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
83629 TTTACAGTTA
*
83639 TACTTATAAATCTTTGTTGTAATTATGAATATTTTC
1 TACTTATAAATCTTTATTGTAATTATGAATATTTTC
*
83675 TACTTGTAAATCTTTATTGTAATTATGAATATTTTC
1 TACTTATAAATCTTTATTGTAATTATGAATATTTTC
83711 TA
1 TA
83713 TTTTTAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (36 bp):
TACTTATAAATCTTTATTGTAATTATGAATATTTTC
Found at i:87617 original size:16 final size:16
Alignment explanation
Indices: 87596--87636 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
87586 ACAATTTATA
*
87596 TTAAAATTTAAAAAAT
1 TTAAAATTAAAAAAAT
87612 TTAAAATTAAAAAAAT
1 TTAAAATTAAAAAAAT
87628 TT-AAATTAA
1 TTAAAATTAA
87637 TCAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAATTAAAAAAAT
Found at i:87642 original size:15 final size:15
Alignment explanation
Indices: 87599--87649 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 15
87589 ATTTATATTA
*
87599 AAATTTAAAAAATTT
1 AAATTAAAAAAATTT
87614 AAAATTAAAAAAATTT
1 -AAATTAAAAAAATTT
**
87630 AAATTAATCAAA-TT
1 AAATTAAAAAAATTT
87644 AAATTA
1 AAATTA
87650 CATATATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 8 0.25
15 10 0.31
16 14 0.44
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATTAAAAAAATTT
Found at i:88272 original size:33 final size:34
Alignment explanation
Indices: 88231--88303 Score: 121
Period size: 33 Copynumber: 2.1 Consensus size: 34
88221 TACCCTAATT
88231 TTTTATGATATTATTAACAAAA-TGTGTTTATTA
1 TTTTATGATATTATTAACAAAATTGTGTTTATTA
*
88264 TTTTATGATATTATTAACAAAATTTTGTTTATTA
1 TTTTATGATATTATTAACAAAATTGTGTTTATTA
88298 TATTTA
1 T-TTTA
88304 ATTGAGTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
33 22 0.59
34 11 0.30
35 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.55
Consensus pattern (34 bp):
TTTTATGATATTATTAACAAAATTGTGTTTATTA
Found at i:96711 original size:22 final size:24
Alignment explanation
Indices: 96672--96715 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
96662 TCCCATATTA
*
96672 TTTAAATATATATGTTTTTAAAAG
1 TTTAAATATATATCTTTTTAAAAG
96696 TTTAAATATA-A-CTTTTTAAA
1 TTTAAATATATATCTTTTTAAA
96716 CATGAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (24 bp):
TTTAAATATATATCTTTTTAAAAG
Found at i:102094 original size:11 final size:11
Alignment explanation
Indices: 102078--102113 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
102068 AAATGATCAT
102078 TAATGTTTGAG
1 TAATGTTTGAG
102089 TAATGTTTGAG
1 TAATGTTTGAG
*
102100 TAATGTTTAAG
1 TAATGTTTGAG
102111 TAA
1 TAA
102114 ATTTTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (11 bp):
TAATGTTTGAG
Found at i:106248 original size:32 final size:32
Alignment explanation
Indices: 106186--106248 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
106176 GGCAGAAACA
* * *
106186 CCGCAATAGGTTTGATATTTATAGGTGTTTTC
1 CCGCAACAGGTTTGATATTTAGAGGCGTTTTC
* *
106218 CCGCAACAGGTTTGCTATTTAGCGGCGTTTT
1 CCGCAACAGGTTTGATATTTAGAGGCGTTTT
106249 TAGTCACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (32 bp):
CCGCAACAGGTTTGATATTTAGAGGCGTTTTC
Found at i:109584 original size:75 final size:76
Alignment explanation
Indices: 109407--109613 Score: 276
Period size: 75 Copynumber: 2.7 Consensus size: 76
109397 CAAAGCCAAA
* * **
109407 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGG
1 AATTCCAGAATGCTCAGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATT-CCCCCTAAACAG
109472 TTTTGGCCCCGAG
64 TTTTGGCCCCGAG
*
109485 ATTTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
109550 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * * *
109560 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTATCGATTCCCCC
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
109614 CTTCTACAAC
Statistics
Matches: 117, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
73 16 0.14
74 8 0.07
75 31 0.26
76 14 0.12
77 22 0.19
78 26 0.22
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:115279 original size:22 final size:22
Alignment explanation
Indices: 115238--115304 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
115228 CTCGTATAAA
115238 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
115261 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
115283 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
115305 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:115957 original size:2 final size:2
Alignment explanation
Indices: 115950--116001 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
115940 TCTCTTAAAC
115950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
115992 AT AT AT AT AT
1 AT AT AT AT AT
116002 CACATGTTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117042 original size:21 final size:21
Alignment explanation
Indices: 117018--117062 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
117008 TCTTGTTCGT
* *
117018 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
117039 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
117060 TTG
1 TTG
117063 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:120238 original size:22 final size:22
Alignment explanation
Indices: 120197--120263 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
120187 CTCGTATAAA
120197 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
120220 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
120242 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
120264 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:120913 original size:2 final size:2
Alignment explanation
Indices: 120906--120957 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
120896 TCTCTTAAAC
120906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120948 AT AT AT AT AT
1 AT AT AT AT AT
120958 TCACATGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121994 original size:21 final size:21
Alignment explanation
Indices: 121970--122014 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
121960 TCTTGTTCGT
* *
121970 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
121991 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
122012 TTG
1 TTG
122015 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:123551 original size:23 final size:21
Alignment explanation
Indices: 123497--123578 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
123487 TTTTGGTGCA
123497 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAATCGATTCCCCCCCT
* **
123517 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCCT
*
123538 GAAGGGGAATCGATTCCCCCCACA
1 G-A-GGGAATCGATTCCCCCC-CT
*
123562 G-GGGAATCGATACCCCC
1 GAGGGAATCGATTCCCCC
123579 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 10 0.20
21 23 0.46
22 1 0.02
23 15 0.30
24 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCCT
Found at i:125542 original size:9 final size:8
Alignment explanation
Indices: 125520--125570 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
125510 TGTTTCAACA
125520 TTTTGGAT
1 TTTTGGAT
125528 ATTTTGGAT
1 -TTTTGGAT
125537 TGTTT-GAT
1 T-TTTGGAT
125545 TTTGTGGAT
1 TTT-TGGAT
*
125554 TGTTGGA-
1 TTTTGGAT
125561 TTTTGGAT
1 TTTTGGAT
125569 TT
1 TT
125571 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:125554 original size:17 final size:17
Alignment explanation
Indices: 125522--125565 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
125512 TTTCAACATT
125522 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
125539 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
125556 TTGGATTTTG
1 TTGGATTTTG
125566 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:126329 original size:76 final size:77
Alignment explanation
Indices: 126161--126363 Score: 288
Period size: 77 Copynumber: 2.7 Consensus size: 77
126151 CCAAAAATTA
* * **
126161 CAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGGTTTTG
1 CAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTG
126226 GCCCCGAGATTTC
65 GCCCCGAGATTTC
126239 CAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-G
1 CAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGG
*
126303 CTCCGAGAATTT-
66 CCCCGAG-ATTTC
* * *
126315 CAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCC
1 CAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
126364 TTGTACAACG
Statistics
Matches: 116, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
74 17 0.15
75 8 0.07
76 28 0.24
77 41 0.35
78 22 0.19
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (77 bp):
CAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGG
CCCCGAGATTTC
Found at i:128847 original size:42 final size:41
Alignment explanation
Indices: 128748--128851 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 41
128738 TTTTATCTTT
128748 GTATTTTAGTTTAAATAGGTTTCTATTTCAATTAGGATTTAG
1 GTATTTTAGTTTAAATA-GTTTCTATTTCAATTAGGATTTAG
* * * * *
128790 G-ATTTTATTTTAAATAGTATTTTATTTTATATT-TGTTTTAG
1 GTATTTTAGTTTAAATAGT-TTCTATTTCA-ATTAGGATTTAG
128831 GTATTTTAGTTTAAATAGTTT
1 GTATTTTAGTTTAAATAGTTT
128852 TAAGAGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.04
41 31 0.58
42 20 0.38
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (41 bp):
GTATTTTAGTTTAAATAGTTTCTATTTCAATTAGGATTTAG
Found at i:129515 original size:17 final size:17
Alignment explanation
Indices: 129490--129523 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
129480 CTTTATCCCA
*
129490 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
129507 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
129524 GTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:129615 original size:18 final size:19
Alignment explanation
Indices: 129594--129634 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
129584 TATTTATTAT
*
129594 TTTATTATT-TCCCTTTTA
1 TTTATTATTATCCATTTTA
*
129612 TTTATTATTATCTATTTTA
1 TTTATTATTATCCATTTTA
129631 TTTA
1 TTTA
129635 ATTAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTATTATCCATTTTA
Found at i:131970 original size:15 final size:17
Alignment explanation
Indices: 131944--131977 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
131934 ACATGATACG
131944 TGTGATTACATG-TATA
1 TGTGATTACATGTTATA
131960 TGTGA-TACATGTTATA
1 TGTGATTACATGTTATA
131976 TG
1 TG
131978 ATATGAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (17 bp):
TGTGATTACATGTTATA
Found at i:132141 original size:30 final size:30
Alignment explanation
Indices: 132105--132162 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
132095 AGAGTCGAGG
*
132105 GTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTACCTATGTTCTCTCGA-ACATATGGACA
*
132135 GTTACCTATGTTCTCTGGAACATATGGA
1 GTTACCTATGTTCTCTCGAACATATGGA
132163 TAGGTCCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (30 bp):
GTTACCTATGTTCTCTCGAACATATGGACA
Found at i:132970 original size:2 final size:2
Alignment explanation
Indices: 132965--133019 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
132955 TATATATATA
132965 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
133007 TG TG TG TG TG TG T
1 TG TG TG TG TG TG T
133020 CAATGTATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:134069 original size:30 final size:30
Alignment explanation
Indices: 134033--134090 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
134023 AGAGTCGAGG
* *
134033 GTTACCTATG-TCTTTTGAGACATATGGACA
1 GTTACCTATGTTCTCTAGA-ACATATGGACA
134063 GTTACCTATGTTCTCTAGAACATATGGA
1 GTTACCTATGTTCTCTAGAACATATGGA
134091 TAGGTCCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (30 bp):
GTTACCTATGTTCTCTAGAACATATGGACA
Found at i:134246 original size:8 final size:8
Alignment explanation
Indices: 134235--134262 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
134225 ATGTAAAGAG
134235 TGTTTACA
1 TGTTTACA
134243 TGTTTACA
1 TGTTTACA
134251 TGTTTACA
1 TGTTTACA
134259 TGTT
1 TGTT
134263 AATATGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54
Consensus pattern (8 bp):
TGTTTACA
Found at i:134269 original size:16 final size:16
Alignment explanation
Indices: 134235--134270 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
134225 ATGTAAAGAG
*
134235 TGTTTACATGTTTACA
1 TGTTTACATGTTAACA
*
134251 TGTTTACATGTTAATA
1 TGTTTACATGTTAACA
134267 TGTT
1 TGTT
134271 ATTGTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (16 bp):
TGTTTACATGTTAACA
Found at i:135854 original size:23 final size:23
Alignment explanation
Indices: 135828--135896 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
135818 CACCACAGCT
*
135828 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
135851 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
135874 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
135897 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:136142 original size:30 final size:30
Alignment explanation
Indices: 136099--136176 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
136089 TCACAATTCA
* * *
136099 CATAATTTGTATCACATAGACATATTATTTT
1 CATAACTT-TATCACATAGACATATCATTTC
136130 CATAACTTTATCACATAGACATATCATTTC
1 CATAACTTTATCACATAGACATATCATTTC
*
136160 CATACCTTTATCACATA
1 CATAACTTTATCACATA
136177 ACTCATATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 36 0.84
31 7 0.16
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.40
Consensus pattern (30 bp):
CATAACTTTATCACATAGACATATCATTTC
Found at i:138860 original size:19 final size:19
Alignment explanation
Indices: 138836--138873 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
138826 TTAAGGTAAA
*
138836 TATATTTTATGAATAGTAT
1 TATATTGTATGAATAGTAT
138855 TATATTGTATGAATAGTAT
1 TATATTGTATGAATAGTAT
138874 CGATACTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (19 bp):
TATATTGTATGAATAGTAT
Found at i:138939 original size:21 final size:21
Alignment explanation
Indices: 138913--138954 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
138903 TAATGAATAG
*
138913 TGCTACAGTGTATCGATGCAC
1 TGCTACAGTGTATCAATGCAC
138934 TGCTACAGTGTATCAATGCAC
1 TGCTACAGTGTATCAATGCAC
138955 AAAAACATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGTATCAATGCAC
Found at i:139556 original size:23 final size:23
Alignment explanation
Indices: 139530--139617 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
139520 AGCTCGTATA
*
139530 AATTGCATCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
139553 AATT-TATCTCGAAAG-ACCGCGTAG
1 AATTGCA-C-CG-AAGTGCCACGTAG
*
139577 AGTTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
139600 AAATGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
139618 TATAAGATTT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
22 4 0.08
23 28 0.57
24 13 0.27
25 4 0.08
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:146117 original size:21 final size:21
Alignment explanation
Indices: 146092--146140 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
146082 TAATGAACAT
*
146092 TGCTACAGTGTATCGATGCAC
1 TGCTACAGTGTACCGATGCAC
146113 TGCTACAGTGTACCGATGCAC
1 TGCTACAGTGTACCGATGCAC
146134 TGCTACA
1 TGCTACA
146141 ATAAATTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAC
Found at i:148646 original size:12 final size:12
Alignment explanation
Indices: 148629--148658 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
148619 GATCTGAAGA
148629 AAAGCCTATGAG
1 AAAGCCTATGAG
148641 AAAGCCTATGAG
1 AAAGCCTATGAG
148653 AAAGCC
1 AAAGCC
148659 AAAATCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (12 bp):
AAAGCCTATGAG
Found at i:148927 original size:15 final size:14
Alignment explanation
Indices: 148877--148928 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
148867 TTTAGCGAAC
* *
148877 TTTATTTCATTCTA
1 TTTATTTTATTTTA
148891 TTTATTTTATTTTGA
1 TTTATTTTATTTT-A
* *
148906 GTAATTTTATTTTA
1 TTTATTTTATTTTA
148920 TTTTATTTT
1 -TTTATTTT
148929 TCTCTGAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:150972 original size:41 final size:41
Alignment explanation
Indices: 150917--151021 Score: 124
Period size: 41 Copynumber: 2.5 Consensus size: 41
150907 TTTTATCTTT
*
150917 GTATTTTAGTTTAAATAGGTTTTTATTTCA-ATTAGGTTTTAG
1 GTATATTAGTTTAAATA-GTTTTTATTTCATATT-GGTTTTAG
* * *
150959 G-ATATTATTTTAAATAGTATTTTATTTTATATTTGTTTTAG
1 GTATATTAGTTTAAATAGT-TTTTATTTCATATTGGTTTTAG
*
151000 GTATTTTAGTTTAAATAGTTTT
1 GTATATTAGTTTAAATAGTTTT
151022 AAGAGTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
40 2 0.04
41 33 0.61
42 19 0.35
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (41 bp):
GTATATTAGTTTAAATAGTTTTTATTTCATATTGGTTTTAG
Found at i:151687 original size:17 final size:17
Alignment explanation
Indices: 151662--151695 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
151652 TTTTATCCCA
*
151662 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
151679 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
151696 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:151771 original size:8 final size:9
Alignment explanation
Indices: 151743--151813 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 9
151733 TTTTTTATAT
151743 TTATATTTA
1 TTATATTTA
151752 TTACTATTTA
1 TTA-TATTTA
151762 TTAT-TTTA
1 TTATATTTA
**
151770 TTAT-TTCCC
1 TTATATT-TA
*
151779 TTTTATTTA
1 TTATATTTA
151788 TTATTATTTA
1 TTA-TATTTA
*
151798 TTTTATTTTA
1 TTATA-TTTA
151808 TTATAT
1 TTATAT
151814 CTTTTTAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 10 0.20
9 12 0.24
10 27 0.55
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATATTTA
Found at i:151818 original size:36 final size:34
Alignment explanation
Indices: 151733--151818 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 34
151723 TTAAAACCCC
*
151733 TTTT-TTATAT-TTATATTTATTACTATTTATTA
1 TTTTATTATATCTTTTATTTATTACTATTTATTA
* *
151765 TTTTATTATTTCCCTTTTATTTATTATTATTTATTTTA
1 TTTTATTATAT--CTTTTATTTATTACTATTTA--TTA
151803 TTTTATTATATCTTTT
1 TTTTATTATATCTTTT
151819 TAACTTCACC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 4 0.09
33 5 0.11
36 22 0.50
38 13 0.30
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (34 bp):
TTTTATTATATCTTTTATTTATTACTATTTATTA
Found at i:154953 original size:21 final size:21
Alignment explanation
Indices: 154927--154966 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
154917 TAAAGCACCC
154927 AATAATAACATTTCCGGTAGA
1 AATAATAACATTTCCGGTAGA
*
154948 AATAATAATATTTCCGGTA
1 AATAATAACATTTCCGGTA
154967 ATTTTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
AATAATAACATTTCCGGTAGA
Found at i:158195 original size:14 final size:14
Alignment explanation
Indices: 158178--158213 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
158168 ATTTTATGGC
*
158178 TTAAGGTTTAGGAT
1 TTAAGATTTAGGAT
158192 TTAAGATTTAGGAT
1 TTAAGATTTAGGAT
*
158206 TTGAGATT
1 TTAAGATT
158214 GAGGTAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTAAGATTTAGGAT
Found at i:166669 original size:15 final size:15
Alignment explanation
Indices: 166649--166677 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
166639 GCCATAAACC
166649 TCATCGTCATCGTCT
1 TCATCGTCATCGTCT
166664 TCATCGTCATCGTC
1 TCATCGTCATCGTC
166678 GGCCAAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.14, T:0.38
Consensus pattern (15 bp):
TCATCGTCATCGTCT
Found at i:167590 original size:13 final size:13
Alignment explanation
Indices: 167574--167600 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
167564 GACATATTAT
167574 ATAAAATTATTTA
1 ATAAAATTATTTA
167587 ATAAAATTATTTA
1 ATAAAATTATTTA
167600 A
1 A
167601 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:167610 original size:15 final size:14
Alignment explanation
Indices: 167574--167616 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
167564 GACATATTAT
167574 ATAAAATTATTT-A
1 ATAAAATTATTTAA
167587 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
167601 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
167616 A
1 A
167617 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:168009 original size:13 final size:13
Alignment explanation
Indices: 167991--168035 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
167981 TAATTTACTT
167991 TATATAGTTTATA
1 TATATAGTTTATA
*
168004 TATATATATGTTATA
1 TATATA-GT-TTATA
168019 TATATAGTTTATA
1 TATATAGTTTATA
168032 TATA
1 TATA
168036 CTATACATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 15 0.54
14 2 0.07
15 11 0.39
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:168011 original size:15 final size:15
Alignment explanation
Indices: 167991--168040 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
167981 TAATTTACTT
167991 TATATAGTTTATATA
1 TATATAGTTTATATA
*
168006 TATATA-TGT-TATA
1 TATATAGTTTATATA
168019 TATATAGTTTATATA
1 TATATAGTTTATATA
168034 TACTATA
1 TA-TATA
168041 CATGATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 10 0.33
14 4 0.13
15 12 0.40
16 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:168066 original size:15 final size:17
Alignment explanation
Indices: 168030--168066 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
168020 ATATAGTTTA
168030 TATATACTATACATGAT
1 TATATACTATACATGAT
168047 T-TATAC-ATACAT-AT
1 TATATACTATACATGAT
168061 TATATA
1 TATATA
168067 AAATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 10 0.53
16 5 0.26
17 1 0.05
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (17 bp):
TATATACTATACATGAT
Found at i:168425 original size:14 final size:14
Alignment explanation
Indices: 168398--168469 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
168388 TCTATTTATA
* *
168398 TTAGGGTTTGTGGT
1 TTAGGATTTATGGT
168412 TTAGGATTTATGGT
1 TTAGGATTTATGGT
*
168426 TTAGTG-TTTATGAT
1 TTAG-GATTTATGGT
* *
168440 TTAGGGTTTAGGGT
1 TTAGGATTTATGGT
* *
168454 TTATGATTTAGGGT
1 TTAGGATTTATGGT
168468 TT
1 TT
168470 CTATAAACTG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
13 1 0.02
14 47 0.96
15 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (14 bp):
TTAGGATTTATGGT
Found at i:168426 original size:21 final size:22
Alignment explanation
Indices: 168398--168469 Score: 105
Period size: 21 Copynumber: 3.4 Consensus size: 22
168388 TCTATTTATA
*
168398 TTAGGGTTT-GTGGTTTAGGAT
1 TTAGGGTTTAGTGGTTTATGAT
*
168419 TTATGGTTTAGT-GTTTATGAT
1 TTAGGGTTTAGTGGTTTATGAT
168440 TTAGGGTTTAG-GGTTTATGAT
1 TTAGGGTTTAGTGGTTTATGAT
168461 TTAGGGTTT
1 TTAGGGTTT
168470 CTATAAACTG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
21 44 0.96
22 2 0.04
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (22 bp):
TTAGGGTTTAGTGGTTTATGAT
Found at i:168557 original size:2 final size:2
Alignment explanation
Indices: 168552--168591 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
168542 TTTATATAGT
*
168552 TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
168592 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 31 0.91
3 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:168567 original size:20 final size:20
Alignment explanation
Indices: 168558--168630 Score: 58
Period size: 22 Copynumber: 3.5 Consensus size: 20
168548 TAGTTATATA
168558 TATATATATATATATATAGT
1 TATATATATATATATATAGT
* *
168578 T-TATATATACTATACATGGTT
1 TATATATATA-TATATATAG-T
* *
168599 TATACATATATGTACTATAAGT
1 TATATATATATATA-TAT-AGT
*
168621 TACATATATA
1 TATATATATA
168631 ATTTAGGGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
19 8 0.20
20 8 0.20
21 5 0.12
22 18 0.45
23 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
TATATATATATATATATAGT
Found at i:168745 original size:2 final size:2
Alignment explanation
Indices: 168738--168892 Score: 57
Period size: 2 Copynumber: 82.0 Consensus size: 2
168728 ATAGTGTTTC
* *
168738 TA TA TA TA TA TA TA TA TA TA -A TC TA TA GA T- TA -A T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
168776 T- TA GT- TA TA CA TA CA TA TA TA TA CA -A TA T- TA -A TA TA AA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
168814 T- TA TA AA T- TA TA AA CTA TA TA T- TT TA TA TA GTT 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
* * * *
168855 TA TA GT- TA TA TA CA TA CA TA CA TA CA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
168893 ATTAAAAGTA
Statistics
Matches: 110, Mismatches: 26, Indels: 34
0.65 0.15 0.20
Matches are distributed among these distances:
1 13 0.12
2 93 0.85
3 4 0.04
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:168811 original size:68 final size:68
Alignment explanation
Indices: 168739--168892 Score: 147
Period size: 68 Copynumber: 2.2 Consensus size: 68
168729 TAGTGTTTCT
*
168739 ATATATATATATATATATAATCTATAGATTAATTATATTAG-TTATACATACATA-TATATACAA
1 ATATATATATATATATATAAACTATAGATT--TTATA-TAGTTTATACATACATAGTATATAC-A
*
168802 TA-TTA-
62 TACATAC
* * * * *
168807 ATATAAAT-TATAAATTATAAACTATATATTTTATATAGTTTATATATATATAGTTATATACATA
1 ATATATATATATATA-TATAAACTATAGATTTTATATAGTTTATACATACATAG-TATATACATA
168871 CATAC
64 CATAC
*
168876 ATACATATATATATATA
1 ATATATATATATATATA
168893 ATTAAAAGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
65 3 0.04
66 16 0.23
67 8 0.12
68 29 0.42
69 8 0.12
70 5 0.07
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (68 bp):
ATATATATATATATATATAAACTATAGATTTTATATAGTTTATACATACATAGTATATACATACA
TAC
Found at i:169247 original size:2 final size:2
Alignment explanation
Indices: 169240--169383 Score: 229
Period size: 2 Copynumber: 72.5 Consensus size: 2
169230 ACTTTGAATA
* * *
169240 AT AT AT AT AT AT A- AA AGT AT AT AC AT AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
169282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
169324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
169366 A- AT AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
169384 CATAAGTGAC
Statistics
Matches: 132, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
1 2 0.02
2 129 0.98
3 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:169762 original size:22 final size:22
Alignment explanation
Indices: 169704--169763 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
169694 CTCAAAAAAT
*
169704 TTCCCACCTCTAAATTTGCCAA
1 TTCCCACCTTTAAATTTGCCAA
*** ** *
169726 TTATAAGATTAAAATTTGCCAA
1 TTCCCACCTTTAAATTTGCCAA
169748 TTCCCACCTTTAAATT
1 TTCCCACCTTTAAATT
169764 CCTACCACTC
Statistics
Matches: 25, Mismatches: 13, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (22 bp):
TTCCCACCTTTAAATTTGCCAA
Found at i:169879 original size:15 final size:15
Alignment explanation
Indices: 169856--169982 Score: 62
Period size: 15 Copynumber: 8.1 Consensus size: 15
169846 TTAAATTTTT
169856 TATAATTTATACATA
1 TATAATTTATACATA
* *
169871 TATAGTTTATATATA
1 TATAATTTATACATA
169886 TATATATATTA-ACATA
1 TATA-AT-TTATACATA
* *
169902 AATTAAAGTTTATAAACTA
1 TA-T-AA-TTTATACA-TA
* * *
169921 TATAATTTTTATAGTT
1 TATAATTTATACA-TA
* *
169937 TAT-ATATATATATA
1 TATAATTTATACATA
*
169951 TATATAGTT-TACATA
1 TATA-ATTTATACATA
*
169966 TATAATTTATATATA
1 TATAATTTATACATA
169981 TA
1 TA
169983 GTTCATATAA
Statistics
Matches: 83, Mismatches: 19, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
14 7 0.08
15 40 0.48
16 18 0.22
17 10 0.12
18 5 0.06
19 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
TATAATTTATACATA
Found at i:169968 original size:13 final size:13
Alignment explanation
Indices: 169930--169991 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
169920 ATATAATTTT
169930 TATAGTTTATATA
1 TATAGTTTATATA
169943 TATA---TATATA
1 TATAGTTTATATA
*
169953 TATAGTTTACATA
1 TATAGTTTATATA
*
169966 TATAATTTATATA
1 TATAGTTTATATA
*
169979 TATAGTTCATATA
1 TATAGTTTATATA
169992 AACATAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
10 10 0.24
13 31 0.76
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:171211 original size:18 final size:18
Alignment explanation
Indices: 171167--171234 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
171157 GCCCATAATT
*
171167 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
171185 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
* *
171203 TATAAATATA-TATATATA
1 TATATATATAGTTTATA-A
171221 TATATATATTAGTT
1 TATATATA-TAGTT
171235 GTTTTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 6 0.15
18 30 0.75
19 3 0.08
20 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:171756 original size:216 final size:215
Alignment explanation
Indices: 171314--172010 Score: 1202
Period size: 216 Copynumber: 3.2 Consensus size: 215
171304 TCCCTTCGTA
* * *
171314 TTGTTTAATTTACTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAAATGT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
171379 ATTTGCATCTAAAATTGACCCATACTT-TTACTTATTTCTATTTTTTAATT-GACCCATAACTTT
66 ATTTGCATCTAAAATTGA-CCATACTTATTACTTATTTCTATTTTTTAATTGGA-CCATAACTTT
*
171442 TTAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAGTTATTTCGA
129 TTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGA
171506 TTTGATCCCTCATCAATGTGTG
194 TTTGATCCCTCATCAATGTGTG
171528 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
* * *
171593 ATTTGCATCTGAAATTGACCTATACTTATTATTTATTTCTATTTTTAAATTGGACCATAACTTTT
66 ATTTGCATCTAAAATTGACC-ATACTTATTACTTATTTCTATTTTTTAATTGGACCATAACTTTT
*
171658 TAAATGGATATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
130 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
*
171723 TTGACCCCTCATCAATGTGTG
195 TTGATCCCTCATCAATGTGTG
* * *
171744 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAAGTTAATCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
*
171809 ATTTGCATCTAAAATTGACACATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGAC-CATACTTATTACTTATTTCTATTTTTTAATTGGACCATAACTTTT
171874 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
130 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
171939 TTGATCCCTCATCAATGTGTG
195 TTGATCCCTCATCAATGTGTG
* *
171960 TTGTTTAATTTATTTAAATTTTTATTTGTAACTCCATATTTGTTCAATTTA
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
172011 ATTCTTAAAT
Statistics
Matches: 456, Mismatches: 22, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
213 2 0.00
214 85 0.19
215 52 0.11
216 316 0.69
217 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (215 bp):
TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
ATTTGCATCTAAAATTGACCATACTTATTACTTATTTCTATTTTTTAATTGGACCATAACTTTTT
AAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATT
TGATCCCTCATCAATGTGTG
Found at i:173408 original size:2 final size:2
Alignment explanation
Indices: 173401--173430 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
173391 AATGTCATTA
173401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173431 TTAAGGCCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190675 original size:20 final size:20
Alignment explanation
Indices: 190611--190683 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
190601 CAACTCAATT
190611 TCGAATTCGCAACAC-GAAAG
1 TCGAATTCGCAACACAG-AAG
* **
190631 -CTAATTTCGCAACACAG-TT
1 TCGAA-TTCGCAACACAGAAG
190650 TCCGAATTCGCAACACAGAAG
1 T-CGAATTCGCAACACAGAAG
190671 TCGAATTCGCAAC
1 TCGAATTCGCAAC
190684 TCGAAATTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 3 0.07
20 34 0.81
21 5 0.12
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (20 bp):
TCGAATTCGCAACACAGAAG
Found at i:190680 original size:40 final size:38
Alignment explanation
Indices: 190596--190683 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 38
190586 ATAACCAACA
* *
190596 AATT-GCAACTCAATTTCGAATTCGCAACACGAAAGCT
1 AATTCGCAACACAATTTCGAATTCGCAACACGAAAGCG
*
190633 AATTTCGCAACACAGTTTCCGAATTCGCAACAC-AGAAGTCG
1 AA-TTCGCAACACAATTT-CGAATTCGCAACACGA-AAG-CG
190674 AATTCGCAAC
1 AATTCGCAAC
190684 TCGAAATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 2 0.05
38 2 0.05
39 11 0.26
40 25 0.58
41 3 0.07
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (38 bp):
AATTCGCAACACAATTTCGAATTCGCAACACGAAAGCG
Found at i:190704 original size:22 final size:21
Alignment explanation
Indices: 190676--190729 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
190666 AGAAGTCGAA
190676 TTCGCAACTCGAAATTGACATT
1 TTCGCAACTCGAAATT-ACATT
* * *
190698 TTCGCAACACG-AATTTCTTT
1 TTCGCAACTCGAAATTACATT
190718 TTCGCAACTCGA
1 TTCGCAACTCGA
190730 TTTTTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 13 0.48
21 4 0.15
22 10 0.37
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (21 bp):
TTCGCAACTCGAAATTACATT
Found at i:190749 original size:40 final size:39
Alignment explanation
Indices: 190698--190825 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
190688 AATTGACATT
* *
190698 TTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTAAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTTT-AA
* *
190738 TTCGCAACACGAGTTTAATTTTCACAACTCGATTTTCTAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTT-TAA
* * * * * *
190778 TTCGTAACGCGAGTTTCGTTTTCGCAACGCAAATTTTGAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTC-GATTTTTAA
190818 TTCGCAAC
1 TTCGCAAC
190826 CCATCCTGCT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
40 67 0.92
41 6 0.08
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (39 bp):
TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTTTAA
Found at i:190807 original size:20 final size:20
Alignment explanation
Indices: 190694--190805 Score: 73
Period size: 20 Copynumber: 5.6 Consensus size: 20
190684 TCGAAATTGA
*
190694 CATTTTCGCAACACGAATTT
1 CATTTTCGCAACACGAGTTT
* * *
190714 CTTTTTCGCAACTCGATTTT
1 CATTTTCGCAACACGAGTTT
* **
190734 TAAATTCGCAACACGAGTTT
1 CATTTTCGCAACACGAGTTT
* * * *
190754 AATTTTCACAACTCGATTTT
1 CATTTTCGCAACACGAGTTT
* * *
190774 C-TAATTCGTAACGCGAGTTT
1 CAT-TTTCGCAACACGAGTTT
*
190794 CGTTTTCGCAAC
1 CATTTTCGCAAC
190806 GCAAATTTTG
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
19 1 0.01
20 65 0.97
21 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.38
Consensus pattern (20 bp):
CATTTTCGCAACACGAGTTT
Found at i:191276 original size:17 final size:17
Alignment explanation
Indices: 191245--191295 Score: 93
Period size: 17 Copynumber: 2.9 Consensus size: 17
191235 GCTTTATGAT
191245 TCTTCTCTCTCTCTTTTG
1 TCTTCTCT-TCTCTTTTG
191263 TCTTCTCTTCTCTTTTG
1 TCTTCTCTTCTCTTTTG
191280 TCTTCTCTTCTCTTTT
1 TCTTCTCTTCTCTTTT
191296 TCATTGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 25 0.76
18 8 0.24
ACGTcount: A:0.00, C:0.31, G:0.04, T:0.65
Consensus pattern (17 bp):
TCTTCTCTTCTCTTTTG
Found at i:191458 original size:42 final size:41
Alignment explanation
Indices: 191384--191479 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 41
191374 ACATATCAGG
* * * *
191384 ATTCGCGTTACGAA-TTCAAAAATCGAGTTGCGAAAACGAA
1 ATTCGTGTTGCGAATTTAAAAAATCGAGTTGCGAAAAAGAA
191424 ACTT-GTGTTGCGAATTTAAAAATATCGAGTTGCGAAAAAGAA
1 A-TTCGTGTTGCGAATTTAAAAA-ATCGAGTTGCGAAAAAGAA
191466 ATTCGTGTTGCGAA
1 ATTCGTGTTGCGAA
191480 AATGTCAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 9 0.19
41 10 0.21
42 29 0.60
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (41 bp):
ATTCGTGTTGCGAATTTAAAAAATCGAGTTGCGAAAAAGAA
Found at i:191492 original size:22 final size:20
Alignment explanation
Indices: 191406--191497 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 20
191396 AATTCAAAAA
*
191406 TCGAGTTGCGAAAACGAAACT
1 TCGAGTTGCGAAAAAGAAA-T
* *
191427 T-GTGTTGCGAATTTAA-AAAT
1 TCGAGTTGCGAA--AAAGAAAT
191447 ATCGAGTTGCGAAAAAGAAAT
1 -TCGAGTTGCGAAAAAGAAAT
* *
191468 TCGTGTTGCGAAAATGTCAAAT
1 TCGAGTTGCGAAAAAG--AAAT
191490 TCGAGTTG
1 TCGAGTTG
191498 TGAATTCGAC
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
20 26 0.46
21 9 0.16
22 21 0.38
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (20 bp):
TCGAGTTGCGAAAAAGAAAT
Done.