Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008311.1 Corchorus capsularis cultivar CVL-1 contig08332, 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: 58860
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:25 original size:2 final size:2
Alignment explanation
Indices: 13--89 Score: 91
Period size: 2 Copynumber: 38.0 Consensus size: 2
3 GTACTTTTAT
13 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA 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 TA TA
* * * * * *
56 TA TA TA CA CA CA CA CA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
90 GATTTATTTA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 70 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:721 original size:45 final size:45
Alignment explanation
Indices: 657--748 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
647 ATATAGTCTC
657 TCTCCCAATTGAGAACCAATATATATATGATAAACTAATTTAAGT
1 TCTCCCAATTGAGAACCAATATATATATGATAAACTAATTTAAGT
702 TCTCCCAATTGAGAACCAATATATATATGATAAACTAATTTAAGT
1 TCTCCCAATTGAGAACCAATATATATATGATAAACTAATTTAAGT
747 TC
1 TC
749 AATATATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (45 bp):
TCTCCCAATTGAGAACCAATATATATATGATAAACTAATTTAAGT
Found at i:1972 original size:49 final size:49
Alignment explanation
Indices: 1890--2400 Score: 491
Period size: 49 Copynumber: 10.7 Consensus size: 49
1880 AAATATGGTG
* * * * * * *
1890 CCTTCCGACCGGGAA-GCGTATTTTTGGAATAAGAGAAGAGAAGTGCGA
1 CCTTCCGACCGGGAAGGGGCATTTTAGGAATAAGACAAGAAAACTGTGA
* * *
1938 CCTTCAGACCGGGAATGGGCATTTTAGGAATAAGAAAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTAGGAATAAGACAAGAAAACTGTGA
* * * * *
1987 CCTTCGGACCGGGAAGGGGTATTTTTGGAATAACAGAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTAGGAATAAGACAAGAAAACTGTGA
* * *
2036 CCTTCTGACCGGGAAGGGGCATTTTA-AAATAAGACAAGAAATCTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTAGGAATAAGACAAGAAAACTGTGA
* *
2084 CCTTTCGACCGGGAAGGGGCATTTTTA-GAATAAGATAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCA-TTTTAGGAATAAGACAAGAAAACTGTGA
* *
2133 CCTTCCGACCGGGAAAGGGCCATTTTTA-GAATAAGACAAGAAAATTGTGA
1 CCTTCCGACCGGG-AAGGGGCA-TTTTAGGAATAAGACAAGAAAACTGTGA
* * * *
2183 CTTTTCGACCGGGAAGGGGCATTTTTGGAATAAG---AG--GA---TG-
1 CCTTCCGACCGGGAAGGGGCATTTTAGGAATAAGACAAGAAAACTGTGA
* * * **
2223 --TTCCGACTGGGAAGGGGCGTTTTTGGAATAAGTGAAGAAAA-TCGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTAGGAATAAGACAAGAAAACT-GTGA
* * *
2270 CCTTCCGACCGGGAAGGAGAATTTTTGGAATAAGACAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTAGGAATAAGACAAGAAAACTGTGA
* *
2319 CCTTCCAACCGGGAAGGGGTATTTTTA-GAATAAGACAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCA-TTTTAGGAATAAGACAAGAAAACTGTGA
** *
2368 CCTTCTTACCGGGAATGGGCATTTTTA-GAATAA
1 CCTTCCGACCGGGAAGGGGCA-TTTTAGGAATAA
2401 AAAAGTAAAC
Statistics
Matches: 393, Mismatches: 53, Indels: 33
0.82 0.11 0.07
Matches are distributed among these distances:
38 29 0.07
41 4 0.01
43 1 0.00
44 1 0.00
46 4 0.01
48 55 0.14
49 250 0.64
50 49 0.12
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (49 bp):
CCTTCCGACCGGGAAGGGGCATTTTAGGAATAAGACAAGAAAACTGTGA
Found at i:2058 original size:98 final size:96
Alignment explanation
Indices: 1890--2400 Score: 544
Period size: 98 Copynumber: 5.3 Consensus size: 96
1880 AAATATGGTG
* * * * * * *
1890 CCTTCCGACCGGGAA-GCGTATTTTTGGAATAAGAGAAGAGAAGTGCGACCTTCAGACCGGGAAT
1 CCTT-CGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAG
*
1954 GGGCATTTTAGGAATAAGAAAAGAAAACTGTGA
65 GGGCATTTTA-GAATAAGACAAGAAAACTGTGA
* * *
1987 CCTTCGGACCGGGAAGGGGTATTTTTGGAATAACAGAAGAAAACTGTGACCTTCTGACCGGGAAG
1 CCTTC-GACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAG
* *
2052 GGGCATTTTAAAATAAGACAAGAAATCTGTGA
65 GGGCATTTTAGAATAAGACAAGAAAACTGTGA
* *
2084 CCTTTCGACCGGGAAGGGGCATTTTTAGAATAAGATAAGAAAACTGTGACCTTCCGACCGGGAAA
1 CC-TTCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGG-AA
* *
2149 GGGCCATTTTTAGAATAAGACAAGAAAATTGTGA
64 GGGGCA-TTTTAGAATAAGACAAGAAAACTGTGA
* *
2183 CTTTTCGACCGGGAAGGGGCATTTTTGGAATAAGAG--G---A---TG---TTCCGACTGGGAAG
1 C-CTTCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAG
* * **
2237 GGGCGTTTTTGGAATAAGTGAAGAAAA-TCGTGA
65 GGGC-ATTTTAGAATAAGACAAGAAAACT-GTGA
* * * *
2270 CCTTCCGACCGGGAAGGAGAATTTTTGGAATAAGACAAGAAAACTGTGACCTTCCAACCGGGAAG
1 CCTT-CGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAG
*
2335 GGGTATTTTTAGAATAAGACAAGAAAACTGTGA
65 GGGCA-TTTTAGAATAAGACAAGAAAACTGTGA
* * *
2368 CCTTCTTACCGGGAATGGGCATTTTTAGAATAA
1 CCTTC-GACCGGGAAGGGGCATTTTTGGAATAA
2401 AAAAGTAAAC
Statistics
Matches: 347, Mismatches: 44, Indels: 45
0.80 0.10 0.10
Matches are distributed among these distances:
86 3 0.01
87 57 0.16
88 10 0.03
89 1 0.00
91 2 0.01
92 1 0.00
94 1 0.00
95 2 0.01
96 1 0.00
97 87 0.25
98 125 0.36
99 57 0.16
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (96 bp):
CCTTCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAGG
GGCATTTTAGAATAAGACAAGAAAACTGTGA
Found at i:2282 original size:87 final size:88
Alignment explanation
Indices: 2135--2304 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 88
2125 AACTGTGACC
* * *
2135 TTCCGACCGGGAAAGGGCCATTTTTAGAATAAGACAAGAAAATTGTGACTTTTCGACCGGGAAGG
1 TTCCGACCGGGAAAGGGCCATTTTTAGAATAAGACAAGAAAATCGTGACCTTCCGACCGGGAAGG
* *
2200 GGCATTTTTGGAATAAGAGGATG
66 AGAATTTTTGGAATAAGAGGATG
* * * * **
2223 TTCCGACTGGG-AAGGGGCGTTTTTGGAATAAGTGAAGAAAATCGTGACCTTCCGACCGGGAAGG
1 TTCCGACCGGGAAAGGGCCATTTTTAGAATAAGACAAGAAAATCGTGACCTTCCGACCGGGAAGG
2287 AGAATTTTTGGAATAAGA
66 AGAATTTTTGGAATAAGA
2305 CAAGAAAACT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
87 61 0.86
88 10 0.14
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (88 bp):
TTCCGACCGGGAAAGGGCCATTTTTAGAATAAGACAAGAAAATCGTGACCTTCCGACCGGGAAGG
AGAATTTTTGGAATAAGAGGATG
Found at i:2350 original size:136 final size:137
Alignment explanation
Indices: 2089--2353 Score: 376
Period size: 136 Copynumber: 1.9 Consensus size: 137
2079 TGTGACCTTT
*
2089 CGACCGGGAAGGGGCATTTTTAGAATAAGATAAGAAAACTGTGACCTTCCGACCGGGAAAGGGCC
1 CGACCGGGAAGGGGCATTTTTAGAATAAGATAAGAAAACTGTGACCTTCCGACCGGGAAAGGGCA
* * * * *
2154 ATTTTTAGAATAAGACAAGAAAATTGTGACTTTTCGACCGGGAAGGGGCATTTTTGGAATAAGAG
66 ATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCAACCGGGAAGGGGCATTTTTAGAATAAGAG
2219 GATGTTC
131 GATGTTC
* * *
2226 CGACTGGGAAGGGGCGTTTTTGGAATAAG-TGAAGAAAA-TCGTGACCTTCCGACCGGG-AAGGA
1 CGACCGGGAAGGGGCATTTTTAGAATAAGAT-AAGAAAACT-GTGACCTTCCGACCGGGAAAGG-
* *
2288 G-AATTTTTGGAATAAGACAAGAAAACTGTGACCTTCCAACCGGGAAGGGGTATTTTTAGAATAA
63 GCAATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCAACCGGGAAGGGGCATTTTTAGAATAA
2352 GA
128 GA
2354 CAAGAAAACT
Statistics
Matches: 114, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
136 63 0.55
137 51 0.45
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.23
Consensus pattern (137 bp):
CGACCGGGAAGGGGCATTTTTAGAATAAGATAAGAAAACTGTGACCTTCCGACCGGGAAAGGGCA
ATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCAACCGGGAAGGGGCATTTTTAGAATAAGAG
GATGTTC
Found at i:2625 original size:126 final size:127
Alignment explanation
Indices: 2401--2709 Score: 380
Period size: 126 Copynumber: 2.5 Consensus size: 127
2391 TTTAGAATAA
* * * *
2401 AAAAGTAAACAATACCTTCCGATGGGTAA--GCAAACTAGGAAAGTAAACAACACCTTTCGGTGG
1 AAAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAATGTAAACAACACCTTTCGGTGG
* * * * *
2464 GGAGGGGCAAAACAGGAAAGCAGACTTAAACAACACTTTCTGGTGAGGAAGGGCAAACTGGG
66 GGAGGAGCAAAACAGGAAAGCAGAATGAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG
* *
2526 -AAAGTAAACAACACCTTCCGGTGGGGAAGGGCCAACTAGGAATGTAAACGACACCTTTCGGTGG
1 AAAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAATGTAAACAACACCTTTCGGTGG
* * * * *
2590 GGATGAGCAAAACATGAATAG-A-AATAGAAACAACACCTTCCGGTGGGGAATGGCAGACTGGG
66 GGAGGAGCAAAACAGGAA-AGCAGAAT-GAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG
*
2652 AAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAAAC-AGGAATAG-AAACAACACCTT
1 AAAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTAGGAAT-GTAAACAACACCTT
2710 CAGATAAGGA
Statistics
Matches: 158, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
124 25 0.16
125 2 0.01
126 77 0.49
127 50 0.32
128 4 0.03
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (127 bp):
AAAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAATGTAAACAACACCTTTCGGTGG
GGAGGAGCAAAACAGGAAAGCAGAATGAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG
Found at i:2674 original size:41 final size:40
Alignment explanation
Indices: 2402--2730 Score: 236
Period size: 40 Copynumber: 8.0 Consensus size: 40
2392 TTAGAATAAA
* * * *
2402 AAAGTAAACAATACCTTCCGATGGGTAA--GCAAACTAGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG
* * * *
2440 AAAGTAAACAACACCTTTCGGTGGGGAGGGGCAAAACAGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGG
* * *
2481 AAGCAGACTTAAACAACACTTTCTGGTGAGGAAGGGCAAACTGGG
1 AA--AG---TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG
* *
2526 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCCAACTAGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG
* * * * * *
2566 AATGTAAACGACACCTTTCGGTGGGGATGAGCAAAACATGAATAG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAAC-TG---GG
* *
2611 AAA-TAGAAACAACACCTTCCGGTGGGGAATGGCAGACTGGG
1 AAAGT--AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG
* *
2652 AAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAAAC-AGG
1 -AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGG
* * **
2693 AATAG-AAACAACACCTTCAGATAAGGAAGGGCAAACTG
1 AA-AGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTG
2731 AGAATGAGAC
Statistics
Matches: 226, Mismatches: 45, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
38 23 0.10
39 4 0.02
40 85 0.38
41 40 0.18
42 7 0.03
43 5 0.02
44 3 0.01
45 14 0.06
46 45 0.20
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (40 bp):
AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG
Found at i:2687 original size:87 final size:86
Alignment explanation
Indices: 2531--2700 Score: 234
Period size: 87 Copynumber: 2.0 Consensus size: 86
2521 CTGGGAAAGT
** * * *
2531 AAACAACACCTTCCGGTGGGGAAGGGCCAACTAGGAATGTAAACGACACCTTTCGGTGGGGATGA
1 AAACAACACCTTCCGGTGGGGAAGGGCCAACTAGGAAACTAAACAACACCTTCCGGTGGGGAAGA
*
2596 GCAAAACATGAATAGAAATAG
66 GCAAAACAGGAATAGAAATAG
* *
2617 AAACAACACCTTCCGGTGGGGAATGG-CAGACTGGGAAAACTAAACAACACCTTCCGGTGGGGAA
1 AAACAACACCTTCCGGTGGGGAAGGGCCA-ACTAGG-AAACTAAACAACACCTTCCGGTGGGGAA
*
2681 GGGCAAAACAGGAATAGAAA
64 GAGCAAAACAGGAATAGAAA
2701 CAACACCTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
85 2 0.03
86 30 0.41
87 41 0.56
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.14
Consensus pattern (86 bp):
AAACAACACCTTCCGGTGGGGAAGGGCCAACTAGGAAACTAAACAACACCTTCCGGTGGGGAAGA
GCAAAACAGGAATAGAAATAG
Found at i:3432 original size:51 final size:50
Alignment explanation
Indices: 3323--3512 Score: 145
Period size: 51 Copynumber: 3.8 Consensus size: 50
3313 CAACTTAATC
* * * * * *
3323 AAAGGTCAATCTTTTAGTCCAAAATCTCACTTTTA-TCACAACTTAATTA
1 AAAGTTCAATCTCTTAGTCCAAGATTTCACTTTTATTTACAAATTAATTA
*
3372 AAAGTTCAATCTCTTAGTCCCAAGATTTCACATTTATTTACAAATTAATTA
1 AAAGTTCAATCTCTTAGT-CCAAGATTTCACTTTTATTTACAAATTAATTA
* * * * *
3423 CAATTTCAATC-CTTTAGTTCAAAGATCTT-ATTTTTATTTACAAATTAATCA
1 AAAGTTCAATCTC-TTAG-TCCAAGAT-TTCACTTTTATTTACAAATTAATTA
* * * * *
3474 TAAGTTCCATCAT-TTAGCTCAAAGATCTCATTTTTATTT
1 AAAGTTCAATC-TCTTAG-TCCAAGATTTCACTTTTATTT
3513 CACTTTAATA
Statistics
Matches: 115, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
49 16 0.14
50 16 0.14
51 80 0.70
52 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.42
Consensus pattern (50 bp):
AAAGTTCAATCTCTTAGTCCAAGATTTCACTTTTATTTACAAATTAATTA
Found at i:3649 original size:32 final size:32
Alignment explanation
Indices: 3587--3649 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
3577 TTTTCACCTT
*
3587 TTACATAAAAATTCAATCTTTATTTACAAAAA
1 TTACATAAAAATTCAATCTTTAATTACAAAAA
* *
3619 TTACTTAAAAGTTCAATCTTTTAATT-CAAAA
1 TTACATAAAAATTCAATC-TTTAATTACAAAA
3650 TTCAAACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.40
Consensus pattern (32 bp):
TTACATAAAAATTCAATCTTTAATTACAAAAA
Found at i:3695 original size:21 final size:20
Alignment explanation
Indices: 3671--3710 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3661 TTCACAAACT
3671 ACTTAAAAGATTTAATCTTTC
1 ACTTAAAA-ATTTAATCTTTC
*
3692 ACTTAAGAATTTAATCTTT
1 ACTTAAAAATTTAATCTTT
3711 ATTTACAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (20 bp):
ACTTAAAAATTTAATCTTTC
Found at i:3711 original size:51 final size:51
Alignment explanation
Indices: 3594--3770 Score: 198
Period size: 51 Copynumber: 3.5 Consensus size: 51
3584 CTTTTACATA
* * *
3594 AAAATTCAATCTTTATTTACAAAAATTACTTAAAAG-TTCAATCTTTTAATTC
1 AAAATTCAATCTTTA-TT-CACAAACTACTTAAAAGATTCAATCTTTCAATTC
* * *
3646 AAAATTCAAACTTTATTCACAAACTACTTAAAAGATTTAATCTTTCACTT-
1 AAAATTCAATCTTTATTCACAAACTACTTAAAAGATTCAATCTTTCAATTC
* * *
3696 AAGAATTTAATCTTTATTTACAAACTACTTAAAAGATTCAATCTTTTAA-TC
1 AA-AATTCAATCTTTATTCACAAACTACTTAAAAGATTCAATCTTTCAATTC
* *
3747 AAAAGCTCAATCTTTATTTACAAA
1 AAAA-TTCAATCTTTATTCACAAA
3771 TTAATCTAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
50 20 0.19
51 73 0.68
52 14 0.13
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (51 bp):
AAAATTCAATCTTTATTCACAAACTACTTAAAAGATTCAATCTTTCAATTC
Found at i:3799 original size:102 final size:101
Alignment explanation
Indices: 3596--3780 Score: 248
Period size: 102 Copynumber: 1.8 Consensus size: 101
3586 TTTACATAAA
* *
3596 AATTCAATCTTTATTTACAAAAATTACTTAAAAGTTCAATCTTTTAATTCAAAATTCAAACTTTA
1 AATTCAATCTTTATTTAC-AAAACTACTTAAAAGTTCAATCTTTTAATTCAAAACTCAAACTTTA
*
3661 TTCACAAACTACTTAAAAGATTTAATCTTTCACTTAAG
65 TTCACAAACTAATT-AAAGATTTAATCTTTCACTTAAG
* *
3699 AATTTAATCTTTATTTAC-AAACTACTTAAAAGATTCAATCTTTTAA-TCAAAAGCTCAATCTTT
1 AATTCAATCTTTATTTACAAAACTACTTAAAAG-TTCAATCTTTTAATTCAAAA-CTCAAACTTT
* *
3762 ATTTACAAATTAATCTAAA
64 ATTCACAAACTAAT-TAAA
3781 TTTCCAATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
101 19 0.26
102 35 0.49
103 18 0.25
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (101 bp):
AATTCAATCTTTATTTACAAAACTACTTAAAAGTTCAATCTTTTAATTCAAAACTCAAACTTTAT
TCACAAACTAATTAAAGATTTAATCTTTCACTTAAG
Found at i:4637 original size:49 final size:49
Alignment explanation
Indices: 4549--5090 Score: 585
Period size: 49 Copynumber: 11.5 Consensus size: 49
4539 AAATCTGGTG
* * * * *
4549 CCTTCCGACCGGGAA-GCGTATTTTTGGAATAAGAGAAGAAAAGTGCGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
* *
4597 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAAAAGAAAATTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
4646 CCTTCCGACCGGGAAGGGGCATTTTTGGAAT-----AAG---A--G-GA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
* * * *
4684 CCTTCCAACTGGGAAGGGGCATTTTTTGAATAAGTA-AAGAAAATTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAG-ACAAGAAAACTGTGA
* *
4733 CCTTCCAACCGGGAAGGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
* *
4782 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
* * * *
4831 TCTTCCGACCAGGAAGGGACATTTTTAGAATAAGACAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
* * *
4880 CCTTCCGACCCGAAAGGGGCATTTTTGGAATAAG---AG--GAC---G-
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
* * * *
4920 -C-TCTGACCAGGAAGGGGCTTTTTTGGAATAA-ATGAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGA-CAAGAAAACTGTGA
* ** *
4967 CCTTTCGACCGGGAATAGGCATTTTTGGAATAAGACAAGAAAATTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
*
5016 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGA
1 CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
* *
5065 CCTTTCTGACCGGGAATGGGCATTTT
1 CC-TTCCGACCGGGAAGGGGCATTTT
5091 CAGAATAAAA
Statistics
Matches: 421, Mismatches: 46, Indels: 52
0.81 0.09 0.10
Matches are distributed among these distances:
38 56 0.13
39 2 0.00
41 4 0.01
43 5 0.01
44 5 0.01
46 4 0.01
48 18 0.04
49 305 0.72
50 22 0.05
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (49 bp):
CCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGACAAGAAAACTGTGA
Found at i:4698 original size:38 final size:38
Alignment explanation
Indices: 4644--4717 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
4634 AGAAAATTGT
*
4644 GACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAG
1 GACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAGAG
* *
4682 GACCTTCCAACTGGGAAGGGGCATTTTTTGAATAAG
1 GACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAG
4718 TAAAGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (38 bp):
GACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAGAG
Found at i:4744 original size:87 final size:87
Alignment explanation
Indices: 4595--4865 Score: 292
Period size: 87 Copynumber: 3.0 Consensus size: 87
4585 AGAAAAGTGC
* *
4595 GACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAAAAGAAAATTGTGACCTTCCGACCGGGA
1 GACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAGAAAAGAAAATTGTGACCTTCCAACCGGGA
*
4660 AGGGGCATTTTTGGAATAAGAG
66 AGGAGCATTTTTGGAATAAGAG
* * *
4682 GACCTTCCAACTGGGAAGGGGCATTTTTTGAATAAGTAAAGAAAATTGTGACCTTCCAACCGGGA
1 GACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAGAAAAGAAAATTGTGACCTTCCAACCGGGA
4747 AGGAGCATTTTTGGAATAAGACAAGAAAACTG
66 AGGAGCATTTTTGGAAT-----AAG---A--G
* * * * * * * *
4779 TGACCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGATCTTCCGACCAGG
1 -GACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAGAAAAGAAAATTGTGACCTTCCAACCGGG
*
4844 AAGG-GACATTTTTAGAATAAGA
65 AAGGAG-CATTTTTGGAATAAGA
4866 CAAGAAAACT
Statistics
Matches: 155, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
87 76 0.49
90 1 0.01
92 3 0.02
93 3 0.02
95 1 0.01
97 2 0.01
98 69 0.45
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (87 bp):
GACCTTCCAACCGGGAAGGGGCATTTTTGGAATAAGAAAAGAAAATTGTGACCTTCCAACCGGGA
AGGAGCATTTTTGGAATAAGAG
Found at i:4744 original size:136 final size:136
Alignment explanation
Indices: 4568--4816 Score: 410
Period size: 136 Copynumber: 1.8 Consensus size: 136
4558 CGGGAAGCGT
* *
4568 ATTTTTGGAATAAGAGAAGAAAAGTGCGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAA
1 ATTTTTGGAATAAGAGAAGAAAAGTGCGACCTTCCAACCGGGAAGGAGCATTTTTGGAATAAGAA
* *
4633 AAGAAAATTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGAGGACCTTCCAACTGGGA
66 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGAGGACCTTCCAACTGGGA
4698 AGGGGC
131 AGGGGC
* * *
4704 ATTTTTTGAATAAGTA-AAGAAAATTGTGACCTTCCAACCGGGAAGGAGCATTTTTGGAATAAGA
1 ATTTTTGGAATAAG-AGAAGAAAAGTGCGACCTTCCAACCGGGAAGGAGCATTTTTGGAATAAGA
*
4768 CAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGA
65 AAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGA
4817 CAAGAAAACT
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
136 103 0.99
137 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (136 bp):
ATTTTTGGAATAAGAGAAGAAAAGTGCGACCTTCCAACCGGGAAGGAGCATTTTTGGAATAAGAA
AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGAGGACCTTCCAACTGGGA
AGGGGC
Found at i:4988 original size:87 final size:87
Alignment explanation
Indices: 4837--5001 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 87
4827 GGGATCTTCC
*
4837 GACCAGGAAGGGACATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCAT
1 GACCAGGAAGGGACATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGAGGCAT
4902 TTTTGGAATAAGAGGACGCTCT
66 TTTTGGAATAAGAGGACGCTCT
* * * * * * * *
4924 GACCAGGAAGGGGCTTTTTTGGAATAA-ATGAAGAAAACTGTGACCTTTCGACCGGGAATAGGCA
1 GACCAGGAAGGGACATTTTTAGAATAAGA-CAAGAAAACTGTGACCTTCCGACCCGAAAGAGGCA
4988 TTTTTGGAATAAGA
65 TTTTTGGAATAAGA
5002 CAAGAAAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
86 1 0.01
87 67 0.99
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (87 bp):
GACCAGGAAGGGACATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGAGGCAT
TTTTGGAATAAGAGGACGCTCT
Found at i:4991 original size:234 final size:233
Alignment explanation
Indices: 4549--5108 Score: 770
Period size: 234 Copynumber: 2.4 Consensus size: 233
4539 AAATCTGGTG
* * * * *
4549 CCTTCCGACCGGGAA-GCGTATTTTTGGAATAAGAGAAGAAAAGTGCGACCTTCCGACCGGGAAG
1 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGCGACCTTCCGACCGGGAA-
* * * *
4613 GGGCATTTTTGGAATAAGAAAAGAAAATTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATA
65 GGGCATTTTTAGAATAAGAAAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTGGAATA
** * *
4678 AGAGGACCTTCCAACTGGGAAGGGGCATTTTTTGAATAAGTAAAGAAAATTGTGACCTTCCAACC
130 AGAGGACCTTCCAACCAGGAAGGGGCATTTTTTGAATAAATAAAGAAAACTGTGACCTTCCAACC
*
4743 GGGAAGGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
195 GGGAAAGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
* * *
4782 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGATCTTCCGACCAGGAAG
1 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGCGACCTTCCGACCGGGAAG
*
4847 GGACATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTGGAATA
66 GG-CATTTTTAGAATAAGAAAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTGGAATA
** * * *
4912 AGAGGACGC-TCTGACCAGGAAGGGGC-TTTTTTGGAATAAATGAAGAAAACTGTGACCTTTCGA
130 AGAGGAC-CTTCCAACCAGGAAGGGGCATTTTTT-GAATAAATAAAGAAAACTGTGACCTTCCAA
*
4975 CCGGGAATAG-GCATTTTTGGAATAAGACAAGAAAATTGTGA
193 CCGGGAA-AGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
* *
5016 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGACCTTTCTGACCGGGAA
1 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGCGACC-TTCCGACCGGGAA
* *
5081 TGGGCATTTTCAGAATAA-AAAAGTAAAC
65 -GGGCATTTTTAGAATAAGAAAAGAAAAC
5109 AATACCTTCC
Statistics
Matches: 289, Mismatches: 31, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
233 24 0.08
234 236 0.82
235 26 0.09
236 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.23
Consensus pattern (233 bp):
CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGCGACCTTCCGACCGGGAAG
GGCATTTTTAGAATAAGAAAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTGGAATAA
GAGGACCTTCCAACCAGGAAGGGGCATTTTTTGAATAAATAAAGAAAACTGTGACCTTCCAACCG
GGAAAGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
Found at i:5037 original size:136 final size:136
Alignment explanation
Indices: 4788--5050 Score: 368
Period size: 136 Copynumber: 1.9 Consensus size: 136
4778 GTGACCTTCC
* * *
4788 GACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGATCTTCCGACCAGGAAGGGACAT
1 GACCAGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGACCTTCCGACCAGGAAAGGACAT
*
4853 TTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTGGAATAAGAGGA
66 TTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTAGAATAAGAGGA
4918 CGCTCT
131 CGCTCT
* * * * * *
4924 GACCAGGAAGGGGCTTTTTTGGAATAA-ATGAAGAAAACTGTGACCTTTCGACCGGGAATAGG-C
1 GACCAGGAAGGGGCATTTTTAGAATAAGA-CAAGAAAACTGGGACCTTCCGACCAGGAA-AGGAC
* * * *
4987 ATTTTTGGAATAAGACAAGAAAATTGTGACCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGA
64 ATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTAGAATAAGA
5051 CAAGAAAACT
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
135 1 0.01
136 108 0.97
137 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.22
Consensus pattern (136 bp):
GACCAGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGACCTTCCGACCAGGAAAGGACAT
TTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTAGAATAAGAGGA
CGCTCT
Found at i:5144 original size:40 final size:40
Alignment explanation
Indices: 5100--5405 Score: 221
Period size: 40 Copynumber: 7.5 Consensus size: 40
5090 TCAGAATAAA
* * *
5100 AAAGTAAACAATACCTTCCGATGGGGAATGGCAAACTAGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
* * *
5140 AAAGTAAACAACACCTTCCAGT-GGGAAGGGGCAAAACAACAAAGC
1 AAAGTAAACAACACCTTCCGGTGGGGAA-GGGC---A-AAC-TAGG
* * * * *
5185 AGACGTAAACAACACTTTCTGGTGAGGAAGGGCAAACTGGG
1 A-AAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
* * *
5226 AAAGTAAACAACCCCTTCCGGTGGGGAAGTGCCAACTAGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
* ** *
5266 AATGTAAACAACACCTTCCGGTGGGGACTGGCAAAACATGAATAG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAAC-T--A-GG
* * *
5311 AAATTGAAATAACACCTTCCAGT---GAAGGGCAAACT-GG
1 AAAGT-AAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
* *
5348 AAACTAAACAACACCTTCCGGTAGGGAAGGGCAAAAC-AGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTAGG
5388 AATAG-AAACAACACCTTC
1 AA-AGTAAACAACACCTTC
5406 AGATAAGGAA
Statistics
Matches: 206, Mismatches: 40, Indels: 40
0.72 0.14 0.14
Matches are distributed among these distances:
36 15 0.07
37 5 0.02
39 12 0.06
40 101 0.49
41 7 0.03
42 8 0.04
43 7 0.03
44 4 0.02
45 7 0.03
46 36 0.17
47 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (40 bp):
AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
Found at i:5169 original size:234 final size:234
Alignment explanation
Indices: 4549--5172 Score: 615
Period size: 234 Copynumber: 2.7 Consensus size: 234
4539 AAATCTGGTG
* * * * * * *
4549 CCTTCCGACCGGGAA-GCGTATTTTTGGAATAAGAGAAGAAAAGTGCGACCTTCCGACCGGGAAG
1 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGACCTTCCGACCAGGAAG
* ** *** * * *** *
4613 GGGCATTTTTGGAATAAGAAAAGAAAATTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATA
66 GGACATTTTCAGAATAAGAAAAGAAAACAATGACCTTCCGACCCGAAAGGGGCAAACTAGGAATA
** * *
4678 AG--AGGACCTTCCAACTGGGAAGGGGCATTTTTTGAATAAGTAAAGAAAATTGTGACCTTCCAA
131 AGACAACACCTTCC-A-TGGGAAGGGGCATTTTTTGAATAAATAAAGAAAACTGTGACCTTCCAA
*
4741 CCGGGAAGGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
194 CCGGGAAAGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
*
4782 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGATCTTCCGACCAGGAAG
1 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGACCTTCCGACCAGGAAG
* * ** *** *
4847 GGACATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCCGAAAGGGGCATTTTTGGAATA
66 GGACATTTTCAGAATAAGAAAAGAAAACAATGACCTTCCGACCCGAAAGGGGCAAACTAGGAATA
** * * * * *
4912 AGAGGACGCTCTGACCA--GGAAGGGGC-TTTTTTGGAATAAATGAAGAAAACTGTGACCTTTCG
131 AGACAACAC-CT-TCCATGGGAAGGGGCATTTTTT-GAATAAATAAAGAAAACTGTGACCTTCCA
*
4974 ACCGGGAATAG-GCATTTTTGGAATAAGACAAGAAAATTGTGA
193 ACCGGGAA-AGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
* * *
5016 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGACCTTTCTGACCGGGAA
1 CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGACC-TTCCGACCAGGAA
* *** * *
5081 TGGG-CATTTTCAGAATAA-AAAAGTAAACAAT-ACCTTCCGATGGGGAA-TGGCAAACTAGGAA
65 -GGGACATTTTCAGAATAAGAAAAGAAAACAATGACCTTCCGACCCGAAAGGGGCAAACTAGG-A
5142 AGTAA-ACAACACCTTCCAGTGGGAAGGGGCA
128 A-TAAGACAACACCTTCCA-TGGGAAGGGGCA
5173 AAACAACAAA
Statistics
Matches: 328, Mismatches: 48, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
231 3 0.01
232 9 0.03
233 39 0.12
234 243 0.74
235 25 0.08
236 4 0.01
237 3 0.01
238 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (234 bp):
CCTTCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGAAAACTGGGACCTTCCGACCAGGAAG
GGACATTTTCAGAATAAGAAAAGAAAACAATGACCTTCCGACCCGAAAGGGGCAAACTAGGAATA
AGACAACACCTTCCATGGGAAGGGGCATTTTTTGAATAAATAAAGAAAACTGTGACCTTCCAACC
GGGAAAGAGCATTTTTGGAATAAGACAAGAAAACTGTGA
Found at i:5325 original size:126 final size:122
Alignment explanation
Indices: 5100--5405 Score: 316
Period size: 126 Copynumber: 2.5 Consensus size: 122
5090 TCAGAATAAA
* * *
5100 AAAGTAAACAATACCTTCCGATGGGGAA-TGGCAAACTAGGAAAGTAAACAACACCTTCCAGTGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGT-GCAAACTAGGAATGTAAACAACACCTTCCAGTGG
* * * **
5164 GAAGGGGCAAAACAACAAAGCAGACGTAAACAACACTTTCTGGTGAGGAAGGGCAAACTGGG
65 GAACGGGCAAAACAACAAAGCAAACGTAAACAACACCTTCCAGT---GAAGGGCAAACT-GG
* * *
5226 AAAGTAAACAACCCCTTCCGGTGGGGAAGTGCCAACTAGGAATGTAAACAACACCTTCCGGTGGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGTGCAAACTAGGAATGTAAACAACACCTTCCAGTGGG
* * ** * *
5291 GACTGGCAAAACATGAATAG-AAA-TTGAAATAACACCTTCCAGTGAAGGGCAAACTGG
66 AACGGGCAAAACAACAA-AGCAAACGT-AAACAACACCTTCCAGTGAAGGGCAAACTGG
* * *
5348 AAACTAAACAACACCTTCCGGTAGGGAAGGGCAAAAC-AGGAATAG-AAACAACACCTTC
1 AAAGTAAACAACACCTTCCGGTGGGGAAGTGC-AAACTAGGAAT-GTAAACAACACCTTC
5406 AGATAAGGAA
Statistics
Matches: 153, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
122 49 0.32
123 16 0.10
125 1 0.01
126 84 0.55
127 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (122 bp):
AAAGTAAACAACACCTTCCGGTGGGGAAGTGCAAACTAGGAATGTAAACAACACCTTCCAGTGGG
AACGGGCAAAACAACAAAGCAAACGTAAACAACACCTTCCAGTGAAGGGCAAACTGG
Found at i:6126 original size:51 final size:50
Alignment explanation
Indices: 6017--6206 Score: 145
Period size: 51 Copynumber: 3.8 Consensus size: 50
6007 CAACTTAATC
* * * * * *
6017 AAAGGTCAATCTTTTAGTCCAAAATCTCACTTTTA-TCACAACTTAATTA
1 AAAGTTCAATCTCTTAGTCCAAGATTTCACTTTTATTTACAAATTAATTA
*
6066 AAAGTTCAATCTCTTAGTCCCAAGATTTCACATTTATTTACAAATTAATTA
1 AAAGTTCAATCTCTTAGT-CCAAGATTTCACTTTTATTTACAAATTAATTA
* * * * *
6117 CAATTTCAATC-CTTTAGTTCAAAGATCTT-ATTTTTATTTACAAATTAATCA
1 AAAGTTCAATCTC-TTAG-TCCAAGAT-TTCACTTTTATTTACAAATTAATTA
* * * * *
6168 TAAGTTCCATCAT-TTAGCTCAAAGATCTCATTTTTATTT
1 AAAGTTCAATC-TCTTAG-TCCAAGATTTCACTTTTATTT
6207 CACTTTAATA
Statistics
Matches: 115, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
49 16 0.14
50 16 0.14
51 80 0.70
52 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.42
Consensus pattern (50 bp):
AAAGTTCAATCTCTTAGTCCAAGATTTCACTTTTATTTACAAATTAATTA
Found at i:7392 original size:22 final size:22
Alignment explanation
Indices: 7364--7407 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
7354 GACAATTCCA
7364 AGATTAACTCTTAATGAAATGG
1 AGATTAACTCTTAATGAAATGG
7386 AGATTAACTCTTAATGAAATGG
1 AGATTAACTCTTAATGAAATGG
7408 CCTAAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (22 bp):
AGATTAACTCTTAATGAAATGG
Found at i:8824 original size:8 final size:8
Alignment explanation
Indices: 8811--8843 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
8801 TTTGTGTTTA
8811 TCTTTTTT
1 TCTTTTTT
8819 TCTTTTTT
1 TCTTTTTT
*
8827 T-TTTATT
1 TCTTTTTT
8834 TCTTTTTT
1 TCTTTTTT
8842 TC
1 TC
8844 ATCATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (8 bp):
TCTTTTTT
Found at i:8837 original size:15 final size:14
Alignment explanation
Indices: 8813--8842 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
8803 TGTGTTTATC
8813 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
8827 TTTTATTTCTTTTTT
1 TTTT-TTTCTTTTTT
8842 T
1 T
8843 CATCATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:8976 original size:20 final size:20
Alignment explanation
Indices: 8933--8976 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
8923 CAAAAATCCT
* *
8933 TTTTGAGAAAAACATTTTTC
1 TTTTGAGAAAAACATTTCTA
8953 TTTTGA-AAAAACAATTTCTA
1 TTTTGAGAAAAAC-ATTTCTA
8973 TTTT
1 TTTT
8977 AGGAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (20 bp):
TTTTGAGAAAAACATTTCTA
Found at i:13318 original size:35 final size:35
Alignment explanation
Indices: 13272--13684 Score: 666
Period size: 35 Copynumber: 11.8 Consensus size: 35
13262 GAATCCGTAA
* *
13272 TAATTAACTTAATTCAGGGTAATTAAGTAATTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
13307 TAATAAACTTAATTCAGGGTAATTAAGTGAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
13342 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
13377 TAATAAACTTAATTCAGGGTAATTAAGTGAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
13412 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAT
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
13447 TAATCAACTTAATTCAGGGTAATTGAGTGAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
13482 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
13517 TAGTCAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
13552 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
13587 TAATAAACTTAATTCAGGGTAATTAAGTAAGTCAT
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
13622 TAATCAACTTAATTCAGGATAATTAAGTGAGTTCA-
1 TAATCAACTTAATTCAGGGTAATTAAGTAAG-TCAG
* *
13657 TAGTTAACTTAATTCAGGGTAATTAAGT
1 TAATCAACTTAATTCAGGGTAATTAAGT
13685 TTAGTAAGAA
Statistics
Matches: 352, Mismatches: 25, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
35 349 0.99
36 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.33
Consensus pattern (35 bp):
TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
Found at i:15135 original size:49 final size:49
Alignment explanation
Indices: 15058--15700 Score: 710
Period size: 49 Copynumber: 13.6 Consensus size: 49
15048 TCTGGCGCCC
* * *
15058 TCCGACCGGGAA-GGGTATTTTTGGAATAAGAGAAGAAAAGTGCGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* * *
15106 TCCGACCGGGAAGAGGCATTTTTGGAATAAGA-AA-AAAAATGTGACTT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
** * *
15153 TTGGACCGGGAAGGGGCATTTTTGGAAAAACAGAAGAAAACTGTGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* *
15202 TCCGACCGGGAA-GGGCATTTTTGGAATAAGACAAGAAAACTATGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* * * * *
15250 TCCGACCGGGAATGGGTACTTTTAGAATAAGACAAGAAAACTGTGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* * *
15299 TCCGACCAGGAAAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGACCT
1 TCCGACC-GGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
15349 TCCGACCGGGAAGGGGCATTTTTGGAAT-----AAG---A---TGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* *
15387 TCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTATGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* *
15436 TCCGAACGAGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTAAGA-CT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGT--GACCT
* * *
15486 TCCGACCGGGAAGGGGGATTTTTGGAATAAGAAAAGAAAATTGTGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
*
15535 TCCGACCGGGAAGGGGAATTTTTGGAAT-----AAG---A--G-GACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* **
15573 TCTGACCAAGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* * * *
15622 TCCGACCGGGAAGGGGCATTTTTAGAATAAGACAAGATAATTGTGACCT
1 TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
* * ** *
15671 TCTGACTGGGAATAGGCATTTTTAGAATAA
1 TCCGACCGGGAAGGGGCATTTTTGGAATAA
15701 AAAAGTAAAC
Statistics
Matches: 511, Mismatches: 54, Indels: 59
0.82 0.09 0.09
Matches are distributed among these distances:
38 62 0.12
39 1 0.00
41 2 0.00
43 6 0.01
44 6 0.01
46 2 0.00
47 37 0.07
48 63 0.12
49 244 0.48
50 86 0.17
51 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (49 bp):
TCCGACCGGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCT
Found at i:15399 original size:38 final size:38
Alignment explanation
Indices: 15343--15418 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
15333 AAGAAAACTG
*
15343 TGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGA
1 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGA
15381 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGA
1 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGA
15419 GAAGAAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (38 bp):
TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGA
Found at i:15427 original size:186 final size:185
Alignment explanation
Indices: 15196--15710 Score: 739
Period size: 186 Copynumber: 2.8 Consensus size: 185
15186 AAGAAAACTG
* *
15196 TGACCTTCCGACCGGGAA-GGGCATTTTTGGAATAAGACAAGAAAACTATGACCTTCCGACCGGG
1 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTATGACCTTCCGACCGGG
* * *
15260 AATGGGTACTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCAGGAAAGGGGCATTTTTAG
66 AAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACC-GGAAAGGGGCATTTTTAG
* *
15325 AATAAGACAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGA
130 AATAAGAAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGA
* *
15381 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTATGACCTTCCGAACGAG
1 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTATGACCTTCCGACCGGG
* * * * *
15446 AAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTAAGA-CTTCCGACCGGGAAGGGGGATTTTTG
66 AAGGGGCATTTTTAGAATAAGACAAGAAAACTGT--GACCTTCCGACCGGAAAGGGGCATTTTTA
*
15510 GAATAAGAAAAGAAAATTGTGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGA
129 GAATAAGAAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGA
* * * *
15567 GGACCTTCTGACCAAGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGG
1 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTATGACCTTCCGACCGGG
* * * * * **
15632 AAGGGGCATTTTTAGAATAAGACAAGATAATTGTGACCTTCTGACTGGGAATAGGCATTTTTAGA
66 AAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCGGAAAGGGGCATTTTTAGA
*
15697 ATAA-AAAAGTAAAC
131 ATAAGAAAAGAAAAC
15711 AACACCTTTC
Statistics
Matches: 293, Mismatches: 33, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
184 10 0.03
185 43 0.15
186 229 0.78
187 9 0.03
188 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (185 bp):
TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTATGACCTTCCGACCGGG
AAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCGGAAAGGGGCATTTTTAGA
ATAAGAAAAGAAAACTGTGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGA
Found at i:15440 original size:87 final size:87
Alignment explanation
Indices: 15293--15653 Score: 470
Period size: 87 Copynumber: 4.0 Consensus size: 87
15283 AAGAAAACTG
* *
15293 TGACCTTCCGACCAGGAAAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCGG
1 TGACCTTCCGACCAGG-AAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGG
15358 GAAGGGGCATTTTTGGAATAAGA
65 GAAGGGGCATTTTTGGAATAAGA
* * *
15381 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTATGACCTTCCGAACGAG
1 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGG
15446 AAGGGGCATTTTTGGAATAAGAGAAGAAAA
66 AAGGGGCATTTTTGGAAT-----AAG---A
* * * * *
15476 CTGTAAGACTTCCGACCGGGAAGGGGGATTTTTGGAATAAGAAAAGAAAATTGTGACCTTCCGAC
1 -TG--A-CCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGAC
*
15541 CGGGAAGGGGAATTTTTGGAATAAGA
62 CGGGAAGGGGCATTTTTGGAATAAGA
* * *
15567 GGACCTTCTGACCAAGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGG
1 TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGG
*
15632 AAGGGGCATTTTTAGAATAAGA
66 AAGGGGCATTTTTGGAATAAGA
15654 CAAGATAATT
Statistics
Matches: 237, Mismatches: 24, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
87 137 0.58
88 17 0.07
90 1 0.00
91 1 0.00
92 3 0.01
94 3 0.01
95 1 0.00
96 2 0.01
98 1 0.00
99 71 0.30
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (87 bp):
TGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGG
AAGGGGCATTTTTGGAATAAGA
Found at i:15489 original size:137 final size:135
Alignment explanation
Indices: 15243--15653 Score: 457
Period size: 137 Copynumber: 3.0 Consensus size: 135
15233 CAAGAAAACT
* * * * * * *
15243 ATGACCTTCCGACCGGGAATGGGTACTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCAG
1 ATGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGAGAAGAAAACT-TGACCTTCCGAACAA
* *
15308 GAAAGGGGCATTTTTAGAATAAGACAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTG
65 G-AAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTG
15373 GAATAAG
129 GAATAAG
* * *
15380 ATGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTATGACCTTCCGAACGA
1 ATGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGAGAAGAAAACT-TGACCTTCCGAACAA
*
15445 GAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTAAGA-CTTCCGACCGGGAAGGGGGATTTTT
65 GAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGT--GACCTTCCGACCGGGAAGGGGCATTTTT
15509 GGAATAAGAAAAG
128 GGAAT-----AAG
*
15522 AAAATTGTGACCTTCCGACCGGGAAGGGGAATTTTTGGAAT-A-AG-AG-------GACCTTCTG
1 ---A---TGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGAGAAGAAAACTTGACCTTCCG
*
15577 ACCAAGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATT
60 AACAAGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATT
*
15642 TTTAGAATAAG
125 TTTGGAATAAG
15653 A
1 A
15654 CAAGATAATT
Statistics
Matches: 240, Mismatches: 20, Indels: 37
0.81 0.07 0.12
Matches are distributed among these distances:
128 1 0.00
131 3 0.01
135 2 0.01
136 60 0.25
137 131 0.55
138 2 0.01
142 3 0.01
145 3 0.01
146 2 0.01
147 1 0.00
148 32 0.13
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.22
Consensus pattern (135 bp):
ATGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGAGAAGAAAACTTGACCTTCCGAACAAG
AAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGA
ATAAG
Found at i:15572 original size:38 final size:38
Alignment explanation
Indices: 15530--15605 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
15520 AGAAAATTGT
**
15530 GACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGAG
1 GACCTTCCGACCAAGAAGGGGAATTTTTGGAATAAGAG
* *
15568 GACCTTCTGACCAAGAAGGGGCATTTTTGGAATAAGAG
1 GACCTTCCGACCAAGAAGGGGAATTTTTGGAATAAGAG
15606 AAGAAAACTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (38 bp):
GACCTTCCGACCAAGAAGGGGAATTTTTGGAATAAGAG
Found at i:15682 original size:136 final size:136
Alignment explanation
Indices: 15444--15700 Score: 399
Period size: 136 Copynumber: 1.9 Consensus size: 136
15434 CTTCCGAACG
*
15444 AGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTAAGACTTCCGACCGGGAAGGGGGATTTTT
1 AGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGT-AGACTTCCGACCGGGAAGGGGCATTTTT
* * *
15509 GGAATAAGAAAAGAAAATTGTGACCTTCCGACCGGGAAGGGGAATTTTTGGAATAAGAGGACCTT
65 AGAATAAGAAAAGAAAATTGTGACCTTCCGACCGGGAAGAGGAATTTTTAGAATAAGAGGACCTT
15574 CTGACCA
130 CTGACCA
15581 AGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGT-GACCTTCCGACCGGGAAGGGGCATTTTT
1 AGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTAGA-CTTCCGACCGGGAAGGGGCATTTTT
* * * * * *
15645 AGAATAAGACAAGATAATTGTGACCTTCTGACTGGGAATAGGCATTTTTAGAATAA
65 AGAATAAGAAAAGAAAATTGTGACCTTCCGACCGGGAAGAGGAATTTTTAGAATAA
15701 AAAAGTAAAC
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
135 2 0.02
136 71 0.65
137 36 0.33
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (136 bp):
AGAAGGGGCATTTTTGGAATAAGAGAAGAAAACTGTAGACTTCCGACCGGGAAGGGGCATTTTTA
GAATAAGAAAAGAAAATTGTGACCTTCCGACCGGGAAGAGGAATTTTTAGAATAAGAGGACCTTC
TGACCA
Found at i:15757 original size:40 final size:40
Alignment explanation
Indices: 15702--16097 Score: 307
Period size: 40 Copynumber: 9.4 Consensus size: 40
15692 TTAGAATAAA
* *
15702 AAAGTAAACAACACCTTTCGATGGGGAAGGGCAAACTAGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
* * * *
15742 AAAGTAGACAACACCTTCCGGTGGGGAAGGTCAAAATGGG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
* * * *
15782 AAAGCAGACTTAAACAACACCTTCTGATGAGGAAGCGCAAACT-GG
1 -AA--AG---TAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
* *
15827 AAAGTAAACAACACCTTCCGGTGGGGAAGCGCAAAACATGAAAGC
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAAC-T---AGG
* ** * *
15872 AGAGTTAAACAACACCTTATGGTGAGGAAGGGCAAACTTGG
1 AAAG-TAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
* * *
15913 AAAGTAAACAACACCTTCCAGTGGGGAAGGGCCAA-TAAAG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACT-AGG
* * * *
15953 AATGTAAACAACACCTTCCGTTGGGGACGGGCAAAAC-ATG
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTAGG
* *
15993 AATAGAAATAGAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGG
1 AA-AG---T--AAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
*
16039 AAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAAAC-AGG
1 -AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTAGG
16080 AATAG-AAACAACACCTTC
1 AA-AGTAAACAACACCTTC
16098 AGATAAGGAA
Statistics
Matches: 282, Mismatches: 48, Indels: 52
0.74 0.13 0.14
Matches are distributed among these distances:
39 26 0.09
40 112 0.40
41 40 0.14
42 5 0.02
43 3 0.01
44 4 0.01
45 13 0.05
46 77 0.27
47 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.14
Consensus pattern (40 bp):
AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG
Found at i:15816 original size:46 final size:44
Alignment explanation
Indices: 15749--16075 Score: 149
Period size: 46 Copynumber: 7.7 Consensus size: 44
15739 AGGAAAGTAG
*
15749 ACAACACCTTCCGGTGGGGAAG-GTCAAAATGGGAAAGCAGACTTAA
1 ACAACACCTTCCGGTGAGGAAGCG-CAAAAT-GGAAAGCAGA-TTAA
* * *
15795 ACAACACCTTCTGATGAGGAAGCGCAAACTGG-AA--AG--TAA
1 ACAACACCTTCCGGTGAGGAAGCGCAAAATGGAAAGCAGATTAA
*
15834 ACAACACCTTCCGGTGGGGAAGCGCAAAACAT-GAAAGCAGAGTTAA
1 ACAACACCTTCCGGTGAGGAAGCGC-AAA-ATGGAAAGCAGA-TTAA
** * *
15880 ACAACACCTTATGGTGAGGAAGGGCAAACTTGG-AA--AG--TAA
1 ACAACACCTTCCGGTGAGGAAGCGCAAA-ATGGAAAGCAGATTAA
* * * *
15920 ACAACACCTTCCAGTGGGGAAGGGC-CAAT--AAAG-A-ATGTAA
1 ACAACACCTTCCGGTGAGGAAGCGCAAAATGGAAAGCAGAT-TAA
* * * * * *
15960 ACAACACCTTCCGTTGGGGACGGGCAAAACAT-GAATAG-AAATAGAA
1 ACAACACCTTCCGGTGAGGAAGCGC-AAA-ATGGAA-AGCAGAT-TAA
* * * * * *
16006 ACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAA--A-ACTAA
1 ACAACACCTTCCGGTGAGGAAGCGCAAAATGGAAAGCAGATTAA
* *
16047 ACAACACCTTCCGGTGGGGAAGGGCAAAA
1 ACAACACCTTCCGGTGAGGAAGCGCAAAA
16076 CAGGAATAGA
Statistics
Matches: 225, Mismatches: 34, Indels: 49
0.73 0.11 0.16
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
39 26 0.12
40 53 0.24
41 32 0.14
42 4 0.02
43 7 0.03
44 6 0.03
45 16 0.07
46 76 0.34
47 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (44 bp):
ACAACACCTTCCGGTGAGGAAGCGCAAAATGGAAAGCAGATTAA
Found at i:15850 original size:85 final size:83
Alignment explanation
Indices: 15706--15942 Score: 330
Period size: 85 Copynumber: 2.8 Consensus size: 83
15696 AATAAAAAAG
* *
15706 TAAACAACACCTTTCGATGGGGAAGGGCAAACTAGGAAAGTAGACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTT-GATGAGGAAGGGCAAACT-GGAAAGTAAACAACACCTTCCGGTGGGGAAG
**
15771 GTCAAAATGGGAAAGCAGACT
64 G-CAAAACAGGAAAGCAGACT
*
15792 TAAACAACACCTTCTGATGAGGAAGCGCAAACTGGAAAGTAAACAACACCTTCCGGTGGGGAAGC
1 TAAACAACACCTT-TGATGAGGAAGGGCAAACTGGAAAGTAAACAACACCTTCCGGTGGGGAAG-
* *
15857 GCAAAACATGAAAGCAGAGT
64 GCAAAACAGGAAAGCAGACT
* *
15877 TAAACAACACCTTATGGTGAGGAAGGGCAAACTTGGAAAGTAAACAACACCTTCCAGTGGGGAAG
1 TAAACAACACCTT-TGATGAGGAAGGGCAAAC-TGGAAAGTAAACAACACCTTCCGGTGGGGAAG
15942 G
64 G
15943 GCCAATAAAG
Statistics
Matches: 137, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
85 75 0.55
86 61 0.45
87 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.15
Consensus pattern (83 bp):
TAAACAACACCTTTGATGAGGAAGGGCAAACTGGAAAGTAAACAACACCTTCCGGTGGGGAAGGC
AAAACAGGAAAGCAGACT
Found at i:15987 original size:126 final size:128
Alignment explanation
Indices: 15749--16097 Score: 358
Period size: 126 Copynumber: 2.7 Consensus size: 128
15739 AGGAAAGTAG
* * * * * *
15749 ACAACACCTTCCGGTGGGGAAGGTCAAAATGGGAAAGCAGACTTAAACAACACCTT-CTGATGAG
1 ACAACACCTTACGGTGAGGAAGGGCAAACTGGG-AA--A-AC-TAAACAACACCTTCCAG-TGGG
* *
15813 GAAGCGC-AAACTGGAA-AGTAAACAACACCTTCCGGTGGGGAAGCGCAAAACATGAA-AGCAGA
60 GAAGGGCAAAACAGGAATAGTAAACAACACCTTCCGGTGGGGAAGCGCAAAACATGAATAG-A-A
* *
15875 GT-TAA
123 ATAGAA
* * *
15880 ACAACACCTTATGGTGAGGAAGGGCAAACTTGG-AAAGTAAACAACACCTTCCAGTGGGGAAGGG
1 ACAACACCTTACGGTGAGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCAGTGGGGAAGGG
* * *
15944 CCAATAA-A-GAAT-GTAAACAACACCTTCCGTTGGGGACGGGCAAAACATGAATAGAAATAGAA
66 -CAA-AACAGGAATAGTAAACAACACCTTCCGGTGGGGAAGCGCAAAACATGAATAGAAATAGAA
* * * *
16006 ACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAAAACTAAACAACACCTTCCGGTGGGGAAGGG
1 ACAACACCTTACGGTGAGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCAGTGGGGAAGGG
16071 CAAAACAGGAATAG-AAACAACACCTTC
66 CAAAACAGGAATAGTAAACAACACCTTC
16098 AGATAAGGAA
Statistics
Matches: 184, Mismatches: 23, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
125 25 0.14
126 78 0.42
127 50 0.27
128 3 0.02
129 1 0.01
131 27 0.15
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (128 bp):
ACAACACCTTACGGTGAGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCAGTGGGGAAGGG
CAAAACAGGAATAGTAAACAACACCTTCCGGTGGGGAAGCGCAAAACATGAATAGAAATAGAA
Found at i:16933 original size:51 final size:50
Alignment explanation
Indices: 16687--16950 Score: 169
Period size: 51 Copynumber: 5.3 Consensus size: 50
16677 TTAAAAGGTT
* * * * *
16687 TCATTTTTATTCCAACTTAATC-AAAGGTCAATCTTTTAGTCCAAA-ATC
1 TCATTTTTATTTCAAATTAATCAAAAGTTCAATCATTTAGTTCAAAGATC
** ** * * * * * *
16735 TCACATTTATCACAACTTAATTAAAATTTCAATC-TCTTAGTCCCAAGATT
1 TCATTTTTATTTCAAATTAATCAAAAGTTCAATCAT-TTAGTTCAAAGATC
* * * * * *
16785 TCACTTTTATTTATAAATTAATGACAATTTCAATCCTTTAGTTCAAAGATC
1 TCATTTTTATTT-CAAATTAATCAAAAGTTCAATCATTTAGTTCAAAGATC
* * * *
16836 TTATTTTTATTTACAAATTAATCATAAGTTCCATCATTTAGCTCAAAGATC
1 TCATTTTTATTT-CAAATTAATCAAAAGTTCAATCATTTAGTTCAAAGATC
** * *
16887 TCATTTTTATTTCACTTTAATCAAAAAGTTTAATCTTTTCA-TTCAAAGAT-
1 TCATTTTTATTTCAAATTAATC-AAAAGTTCAATCATTT-AGTTCAAAGATC
*
16937 TCCATTTTCATTTC
1 T-CATTTTTATTTC
16951 TCATTATTCA
Statistics
Matches: 171, Mismatches: 37, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
48 18 0.11
49 18 0.11
50 20 0.12
51 113 0.66
52 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (50 bp):
TCATTTTTATTTCAAATTAATCAAAAGTTCAATCATTTAGTTCAAAGATC
Found at i:18242 original size:32 final size:32
Alignment explanation
Indices: 18203--18312 Score: 141
Period size: 32 Copynumber: 3.4 Consensus size: 32
18193 TCGACCCGAT
* * *
18203 ACCCGAATGACTCGCAACCCAGATGACCTGAG
1 ACCCGAATGACCCGTAACCCAGATGACCTGAA
* *
18235 ACTCGAATGACCCGTAACTCAGATGACCTGAA
1 ACCCGAATGACCCGTAACCCAGATGACCTGAA
*
18267 ACCCGAATGACCCGTAACCC-GAGTGACCCGAA
1 ACCCGAATGACCCGTAACCCAGA-TGACCTGAA
*
18299 ACCCGAATAACCCG
1 ACCCGAATGACCCG
18313 AGAAGTTAAC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 2 0.03
32 66 0.97
ACGTcount: A:0.33, C:0.35, G:0.20, T:0.13
Consensus pattern (32 bp):
ACCCGAATGACCCGTAACCCAGATGACCTGAA
Found at i:18285 original size:16 final size:16
Alignment explanation
Indices: 18195--18313 Score: 98
Period size: 16 Copynumber: 7.4 Consensus size: 16
18185 GAACCCGCTC
*
18195 GACCCGATACCCGAAT
1 GACCCGAAACCCGAAT
* *
18211 GACTCGCAACCC-AGAT
1 GACCCGAAACCCGA-AT
* * *
18227 GACCTGAGACTCGAAT
1 GACCCGAAACCCGAAT
* *
18243 GACCCGTAACTC-AGAT
1 GACCCGAAACCCGA-AT
*
18259 GACCTGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
18275 GACCCGTAACCCGAGT
1 GACCCGAAACCCGAAT
18291 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
*
18307 AACCCGA
1 GACCCGA
18314 GAAGTTAACC
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
15 2 0.03
16 75 0.95
17 2 0.03
ACGTcount: A:0.33, C:0.34, G:0.20, T:0.13
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:19115 original size:16 final size:16
Alignment explanation
Indices: 19096--19231 Score: 69
Period size: 16 Copynumber: 8.6 Consensus size: 16
19086 CTGACCTAAT
*
19096 TGACCCGAAACCCGAG
1 TGACCCGAAACCCGAA
**
19112 TGACCCG-AACCCGCC
1 TGACCCGAAACCCGAA
** * *
19127 CAACCCGAGACCC-AG
1 TGACCCGAAACCCGAA
** *
19142 TAGACCCGTGACCTGAA
1 T-GACCCGAAACCCGAA
* *
19159 TGACCCGGAATCCGAA
1 TGACCCGAAACCCGAA
* *
19175 TGACCCGAGACCCAAA
1 TGACCCGAAACCCGAA
* *
19191 TGACCCGAAACCTGTA
1 TGACCCGAAACCCGAA
* * * *
19207 TGATCCGAGACCTGAT
1 TGACCCGAAACCCGAA
19223 TGACCCGAA
1 TGACCCGAA
19232 TAACCCGAAC
Statistics
Matches: 87, Mismatches: 30, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
15 11 0.13
16 74 0.85
17 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.22, T:0.12
Consensus pattern (16 bp):
TGACCCGAAACCCGAA
Found at i:19230 original size:32 final size:31
Alignment explanation
Indices: 19144--19231 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 31
19134 AGACCCAGTA
* *
19144 GACCCGTGACCTGAATGACCCGGAATCCGAAT
1 GACCCGAGACCTGAATGACCC-GAAACCGAAT
** *
19176 GACCCGAGACCCAAATGACCCGAAACCTGTAT
1 GACCCGAGACCTGAATGACCCGAAACC-GAAT
* *
19208 GATCCGAGACCTGATTGACCCGAA
1 GACCCGAGACCTGAATGACCCGAA
19232 TAACCCGAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
31 5 0.11
32 41 0.89
ACGTcount: A:0.31, C:0.32, G:0.23, T:0.15
Consensus pattern (31 bp):
GACCCGAGACCTGAATGACCCGAAACCGAAT
Found at i:20758 original size:2 final size:2
Alignment explanation
Indices: 20751--20786 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20741 TATAGTCTAT
20751 TA TA TA TA TA TA TA TA TA TA TA TA 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
20787 GACGGATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21803 original size:21 final size:21
Alignment explanation
Indices: 21779--21821 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
21769 AAATGAACTT
21779 CACCTGGAAA-ATAAGAACAAC
1 CACCT-GAAAGATAAGAACAAC
21800 CACCTGAAAGATAAGAACAAC
1 CACCTGAAAGATAAGAACAAC
21821 C
1 C
21822 CACACTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.51, C:0.26, G:0.14, T:0.09
Consensus pattern (21 bp):
CACCTGAAAGATAAGAACAAC
Found at i:22538 original size:126 final size:119
Alignment explanation
Indices: 22315--22559 Score: 364
Period size: 126 Copynumber: 2.0 Consensus size: 119
22305 AAGACAAAAT
* *
22315 AGAGATGGGTTGAAGGGAGAGAGATGGGAGAATGATAAATTAAAAAAAATGGAGGAAGAATATGG
1 AGAGATGGGTTGAAGGGAGAGAGATGGAAGAATGATAAATTAAAAAAAATGGAGGAAGAAGATGG
* * *
22380 AGTAACGCAGGGAAGAAGGGAAGAATATATCTGGTAGGAAAATATTTTATGTTA
66 AGTAACGCAGGGAAGAAGGGAAGAATAGATCTGCTAGGAAAACATTTTATGTTA
*
22434 AGAGATGGGTTGAAGGGAGAGTGATGGAAGAATGATAAATTTAAAAAAAAAAGATTTGGAGGAAG
1 AGAGATGGGTTGAAGGGAGAGAGATGGAAGAATGATAAA-TT---AAAAAAA-A--TGGAGGAAG
*
22499 AAGATGGAGTAATGCAGGGAAGAAGGGAAGAATAGATCTGCTAGGAAAACATTTTATGTTA
59 AAGATGGAGTAACGCAGGGAAGAAGGGAAGAATAGATCTGCTAGGAAAACATTTTATGTTA
22560 TTTTAATTTT
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
119 37 0.33
120 2 0.02
123 7 0.06
124 1 0.01
126 65 0.58
ACGTcount: A:0.44, C:0.03, G:0.32, T:0.21
Consensus pattern (119 bp):
AGAGATGGGTTGAAGGGAGAGAGATGGAAGAATGATAAATTAAAAAAAATGGAGGAAGAAGATGG
AGTAACGCAGGGAAGAAGGGAAGAATAGATCTGCTAGGAAAACATTTTATGTTA
Found at i:22830 original size:30 final size:31
Alignment explanation
Indices: 22766--22839 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
22756 TATCAATTTT
* *
22766 TATCCTGAATTGACACAAAACGATAACGTTA
1 TATCCTCAATTGACACAAAACGATAACATTA
* * *
22797 TATCCTCAATTGACACAAGA-GGTAATATTA
1 TATCCTCAATTGACACAAAACGATAACATTA
22827 TATCC-CGAATTGA
1 TATCCTC-AATTGA
22840 GTATTTAGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.03
30 18 0.49
31 18 0.49
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (31 bp):
TATCCTCAATTGACACAAAACGATAACATTA
Found at i:31121 original size:23 final size:23
Alignment explanation
Indices: 31072--31134 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
31062 GTGGCCGGTT
*
31072 GTGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGGGCATGGCCGAGTCAC
*
31095 GTGGCCGGGCATGGCC-ATGTCGC
1 GTGGCCGGGCATGGCCGA-GTCAC
31118 GTGGCCGGTG-ATGGCCG
1 GTGGCCGG-GCATGGCCG
31135 GGCATCTCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 1 0.03
23 33 0.94
24 1 0.03
ACGTcount: A:0.10, C:0.27, G:0.46, T:0.17
Consensus pattern (23 bp):
GTGGCCGGGCATGGCCGAGTCAC
Found at i:31133 original size:33 final size:32
Alignment explanation
Indices: 31094--31192 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 32
31084 GGCCGAGTCA
**
31094 TGTGGCCGGGCATGGCCATGTCGCGTGGCCGG
1 TGTGGCCGGGCATCTCCATGTCGCGTGGCCGG
*
31126 TGATGGCCGGGCATCTCCATGTCGCATGGCCGG
1 TG-TGGCCGGGCATCTCCATGTCGCGTGGCCGG
* *
31159 TGTTGCGCGGGCATCTCCAAGTCGCGTGGCCGG
1 TGTGGC-CGGGCATCTCCATGTCGCGTGGCCGG
31192 T
1 T
31193 CACAAGTGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
32 5 0.08
33 54 0.92
ACGTcount: A:0.09, C:0.29, G:0.40, T:0.21
Consensus pattern (32 bp):
TGTGGCCGGGCATCTCCATGTCGCGTGGCCGG
Found at i:36472 original size:9 final size:9
Alignment explanation
Indices: 36431--36473 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
36421 AACAGCACAG
*
36431 ATTTTTTTG
1 ATTTTTTTT
36440 ATTTTTTTT
1 ATTTTTTTT
36449 ATTTTTTTT
1 ATTTTTTTT
36458 ATTTTTTTAT
1 ATTTTTTT-T
36468 ATTTTT
1 ATTTTT
36474 CGATATAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 25 0.78
10 7 0.22
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:37528 original size:33 final size:34
Alignment explanation
Indices: 37458--37598 Score: 123
Period size: 33 Copynumber: 4.3 Consensus size: 34
37448 AAAGGATCAT
* **
37458 GTGGCCGGTTG-TGGCCGGGCATGGCCGA-GTCAT
1 GTGGCCGGTTGATGGCCGGGCATCGCC-ATGTCGC
* *
37491 GTGGCCGGTTG-TGGTCGGGCATGGCCATGTCGC
1 GTGGCCGGTTGATGGCCGGGCATCGCCATGTCGC
* *
37524 GTGGCTGG-TGATGGCCGGGCATCTCCATGTCGC
1 GTGGCCGGTTGATGGCCGGGCATCGCCATGTCGC
* * * *
37557 ATGGCCGG-TG-TTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTTGATGGC-CGGGCATCGCCATGTCGC
37590 GTGGCCGGT
1 GTGGCCGGT
37599 CACAAGTGCT
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
32 6 0.07
33 86 0.93
ACGTcount: A:0.09, C:0.26, G:0.43, T:0.23
Consensus pattern (34 bp):
GTGGCCGGTTGATGGCCGGGCATCGCCATGTCGC
Found at i:37993 original size:96 final size:96
Alignment explanation
Indices: 37809--37986 Score: 293
Period size: 96 Copynumber: 1.9 Consensus size: 96
37799 ATAATCTGGC
* *
37809 GCCACGTTGTCTCCCTCTTCAATTCAATTCAGACCCGACCCGATTCTCCATTCCCCTGATTTTCT
1 GCCACGTCGTCTCCCTCTTCAATTCAATTCAGACCCAACCCGATTCTCCATTCCCCTGATTTTCT
*
37874 GCGATTCCCCTCTGCAGCAGATTCATTTGGT
66 ACGATTCCCCTCTGCAGCAGATTCATTTGGT
* * *
37905 GCCACGTCGTCTTCCTCTTGAATTCAATTCAGACCCAACCCGATTCTCCATTCCCTTGATTTTCT
1 GCCACGTCGTCTCCCTCTTCAATTCAATTCAGACCCAACCCGATTCTCCATTCCCCTGATTTTCT
*
37970 ACGATTCCCCTTTGCAG
66 ACGATTCCCCTCTGCAG
37987 TGGATTCGTT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 75 1.00
ACGTcount: A:0.17, C:0.35, G:0.13, T:0.34
Consensus pattern (96 bp):
GCCACGTCGTCTCCCTCTTCAATTCAATTCAGACCCAACCCGATTCTCCATTCCCCTGATTTTCT
ACGATTCCCCTCTGCAGCAGATTCATTTGGT
Found at i:38849 original size:2 final size:2
Alignment explanation
Indices: 38836--38865 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38826 TGGTTTTAGA
*
38836 AT AT AA 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
38866 TTGTGTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44197 original size:31 final size:30
Alignment explanation
Indices: 44159--44242 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
44149 TTAATGTCCT
* **
44159 TTTTGCCCCCTGAACTTGTATGATTTT-GATG
1 TTTTGCCCCATGAACTTGTA--ATTTTGGACA
*
44190 TTTTGCCCCATAAACTT-TAATTTTGGACA
1 TTTTGCCCCATGAACTTGTAATTTTGGACA
* *
44219 TTTTGCCCCTTGAACTTGCAATTT
1 TTTTGCCCCATGAACTTGTAATTT
44243 GAAGCCATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 5 0.11
29 17 0.39
30 7 0.16
31 15 0.34
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.44
Consensus pattern (30 bp):
TTTTGCCCCATGAACTTGTAATTTTGGACA
Found at i:44298 original size:13 final size:13
Alignment explanation
Indices: 44280--44331 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
44270 TATTACTGAT
44280 GTGGCATTGCCAC
1 GTGGCATTGCCAC
44293 GTGGCATTTTGGTCCAAC
1 GTGGCA--TT-G-CC-AC
*
44311 GTGGCTTTGCCAC
1 GTGGCATTGCCAC
44324 GTGGCATT
1 GTGGCATT
44332 TTTGATCCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 15 0.47
14 2 0.06
15 3 0.09
16 3 0.09
17 2 0.06
18 7 0.22
ACGTcount: A:0.13, C:0.25, G:0.31, T:0.31
Consensus pattern (13 bp):
GTGGCATTGCCAC
Found at i:44321 original size:31 final size:32
Alignment explanation
Indices: 44280--44354 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
44270 TATTACTGAT
*
44280 GTGGCATTGCCACGTGGCA-TTTTGGTCCAAC
1 GTGGCATTGCCACGTGGCATTTTTGATCCAAC
* *
44311 GTGGCTTTGCCACGTGGCATTTTTGATCCGAC
1 GTGGCATTGCCACGTGGCATTTTTGATCCAAC
44343 GTGGCATTGCCA
1 GTGGCATTGCCA
44355 AGTCAGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 18 0.46
32 21 0.54
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (32 bp):
GTGGCATTGCCACGTGGCATTTTTGATCCAAC
Found at i:46216 original size:2 final size:2
Alignment explanation
Indices: 46211--46241 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46201 ACCTAAAAAA
46211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46242 ATGATACAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52736 original size:107 final size:105
Alignment explanation
Indices: 52599--52883 Score: 439
Period size: 107 Copynumber: 2.7 Consensus size: 105
52589 TTATCACAGA
52599 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTA
*
52664 TTTTAAGGGTAAATTTCAAAATTAATAATTTATTATTATAGG
66 TTTTAAGGGTAAATTCCAAAATTAATAA--TATTATTATAGG
* * *
52706 GTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCTCAAATTAAAATTTTATTTTTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTA
* *
52771 TTTTAAGGGTAAATTCCATAATTAATAATATTGTTATAGG
66 TTTTAAGGGTAAATTCCAAAATTAATAATATTATTATAGG
* * * * *
52811 GTTTTAGAAATAAAATATATAACTAA-TTCATTAAGTTTAG-CCCAAATTAAAATTAAAATTTTG
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTA
52874 TTTTAAGGGT
66 TTTTAAGGGT
52884 TAGAAAAATT
Statistics
Matches: 164, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
103 28 0.17
104 13 0.08
105 35 0.21
107 88 0.54
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (105 bp):
GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTA
TTTTAAGGGTAAATTCCAAAATTAATAATATTATTATAGG
Found at i:53564 original size:6 final size:6
Alignment explanation
Indices: 53553--53591 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
53543 ATTCCCCGTC
* * *
53553 GGGGAT GGGGAT GGGGAC GGGGAC GGGGAT GGGGTT GGG
1 GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGG
53592 AAGTCGGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.13, C:0.05, G:0.69, T:0.13
Consensus pattern (6 bp):
GGGGAT
Found at i:53575 original size:18 final size:18
Alignment explanation
Indices: 53552--53586 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53542 CATTCCCCGT
*
53552 CGGGGATGGGGATGGGGA
1 CGGGGACGGGGATGGGGA
53570 CGGGGACGGGGATGGGG
1 CGGGGACGGGGATGGGG
53587 TTGGGAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.69, T:0.09
Consensus pattern (18 bp):
CGGGGACGGGGATGGGGA
Found at i:53742 original size:27 final size:27
Alignment explanation
Indices: 53699--53768 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
53689 GCCCAAGGGT
*
53699 ATTTTGATCATTTTTTGCA-TCTAGGGGC
1 ATTTTGGTCA-TTTTTGCACTC-AGGGGC
*
53727 ATTTTGGTCATTTTTGCACTCGGGGGC
1 ATTTTGGTCATTTTTGCACTCAGGGGC
*
53754 ATTTTAGTCATTTTT
1 ATTTTGGTCATTTTT
53769 AAGTTCATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 27 0.71
28 11 0.29
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.49
Consensus pattern (27 bp):
ATTTTGGTCATTTTTGCACTCAGGGGC
Found at i:57601 original size:38 final size:38
Alignment explanation
Indices: 57548--57851 Score: 445
Period size: 38 Copynumber: 8.1 Consensus size: 38
57538 ACCCCAATAA
* * *
57548 AATTAAG-GACCAAAGTAATAGTAACCGGTAAAATTCAT
1 AATTAAGAG-CCAAAGTAATAGTAATCAGTAAAATTGAT
* * *
57586 ACTTAAGAGTCAAAGTAATAGTAATCAGTAAAACTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
* **
57624 AATTAAGAGTC-AAGGGAT--TAATCAGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
* *
57659 AATTAAGAGGCAAAGTAATAGTAATCAGTAAGATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
*
57697 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
57735 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
57773 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
* *
57811 AATTAAGAGCAAAAGTAATAGCAATCAGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
57849 AAT
1 AAT
57852 CAAGGGTCAA
Statistics
Matches: 243, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
35 26 0.11
36 5 0.02
37 5 0.02
38 206 0.85
39 1 0.00
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (38 bp):
AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
Found at i:58016 original size:34 final size:33
Alignment explanation
Indices: 57946--58022 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
57936 AGTAAAAGAG
***
57946 TAATCAGTAATTAAGAAAGAAAATAAAAATTTT
1 TAATCAGTAATTAAGAAAGAAAATAAAAAGGAT
* *
57979 TAATCAGTAATTAAGAAAGGAAGTAAAAAAGGAT
1 TAATCAGTAATTAAGAAAGAAAAT-AAAAAGGAT
58013 TAATCAGTAA
1 TAATCAGTAA
58023 ATTAGTAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (33 bp):
TAATCAGTAATTAAGAAAGAAAATAAAAAGGAT
Found at i:58334 original size:19 final size:19
Alignment explanation
Indices: 58298--58337 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58288 TAAGAAGGTC
* *
58298 AAAAAATGGTGTGGAGTAA
1 AAAAAATGGTATGAAGTAA
*
58317 AAAAAATGGTATTAAGTAA
1 AAAAAATGGTATGAAGTAA
58336 AA
1 AA
58338 GAGTAAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (19 bp):
AAAAAATGGTATGAAGTAA
Found at i:58437 original size:16 final size:16
Alignment explanation
Indices: 58384--58437 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
58374 GTAAAAGGGT
**
58384 TAAAAATGGTATCCAG
1 TAAAAATGGTATTAAG
* *
58400 TAAGAGATGGTATTAAA
1 TAA-AAATGGTATTAAG
*
58417 CAAAAATGGTATTAAG
1 TAAAAATGGTATTAAG
58433 TAAAA
1 TAAAA
58438 GAGTAAGAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
TAAAAATGGTATTAAG
Done.