Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008945.1 Hibiscus syriacus cultivar Beakdansim tig00112266_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: 308463
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:7994 original size:25 final size:25
Alignment explanation
Indices: 7942--7998 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
7932 TTTTCTTTTC
***
7942 TTTTTTTTAATTTTCGGAATTTGTT
1 TTTTTTTTAATTTTCGGAATTCCCT
7967 TTTTTTTTAATTTTCGGAATTCCCT
1 TTTTTTTTAATTTTCGGAATTCCCT
7992 TTTTTTT
1 TTTTTTT
7999 CAAGATGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (25 bp):
TTTTTTTTAATTTTCGGAATTCCCT
Found at i:9292 original size:28 final size:28
Alignment explanation
Indices: 9260--9313 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
9250 TGAATTAACT
9260 AAACAAATGATGAAAATGCTGTTATGCA
1 AAACAAATGATGAAAATGCTGTTATGCA
*
9288 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAAAATGCTGTTATG
9314 TGAATGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (28 bp):
AAACAAATGATGAAAATGCTGTTATGCA
Found at i:9372 original size:81 final size:80
Alignment explanation
Indices: 9233--9394 Score: 263
Period size: 81 Copynumber: 2.0 Consensus size: 80
9223 ATGATGTAAA
* * *
9233 GTGAATGTGGGTGCATGTGAATTAACTAAACAAATGATGAAAATGCTGTTATGCAAAACAAATGA
1 GTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATGAAAATGCTGTTATGCAAAACAAATGA
9298 TGAACATGCTGTTAT
66 TGAACATGCTGTTAT
*
9313 GTGAATGTGAGTGCACGTGAATTTAACAAAACAAATGAT-AAATATGCTGTTATTCAAAACAAAT
1 GTGAATGTGAGTGCACGTGAA-TTAACAAAACAAATGATGAAA-ATGCTGTTATGCAAAACAAAT
9377 GATGAACATGCTGTTAT
64 GATGAACATGCTGTTAT
9394 G
1 G
9395 AATCCCACGA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
80 22 0.29
81 54 0.71
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (80 bp):
GTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATGAAAATGCTGTTATGCAAAACAAATGA
TGAACATGCTGTTAT
Found at i:9379 original size:28 final size:28
Alignment explanation
Indices: 9339--9393 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
9329 GTGAATTTAA
*
9339 CAAAACAAATGATAAATATGCTGTTATT
1 CAAAACAAATGATAAACATGCTGTTATT
*
9367 CAAAACAAATGATGAACATGCTGTTAT
1 CAAAACAAATGATAAACATGCTGTTAT
9394 GAATCCCACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (28 bp):
CAAAACAAATGATAAACATGCTGTTATT
Found at i:14963 original size:25 final size:25
Alignment explanation
Indices: 14935--14989 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
14925 TTTTCTTTTC
**
14935 TTTTTTTTAATTTTCGGAATTTGTT
1 TTTTTTTTAATTTTCGGAATTCCTT
14960 TTTTTTTTAATTTTCGGAATTCCTT
1 TTTTTTTTAATTTTCGGAATTCCTT
14985 TTTTT
1 TTTTT
14990 CAAGATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.15, C:0.07, G:0.09, T:0.69
Consensus pattern (25 bp):
TTTTTTTTAATTTTCGGAATTCCTT
Found at i:16284 original size:28 final size:28
Alignment explanation
Indices: 16252--16305 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
16242 TGAATTAACT
16252 AAACAAATGATGAAAATGCTGTTATGCA
1 AAACAAATGATGAAAATGCTGTTATGCA
*
16280 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAAAATGCTGTTATG
16306 TGAATGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (28 bp):
AAACAAATGATGAAAATGCTGTTATGCA
Found at i:16374 original size:83 final size:80
Alignment explanation
Indices: 16225--16388 Score: 247
Period size: 83 Copynumber: 2.0 Consensus size: 80
16215 ATGATGTAAA
* * * * *
16225 GTGAATGTGGGTGCATGTGAATTAACTAAACAAATGATGAAAATGCTGTTATGCAAAACAAATGA
1 GTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATAAAAATACTGTTATGCAAAACAAATGA
16290 TGAACATGCTGTTAT
66 TGAACATGCTGTTAT
*
16305 GTGAATGTGAGTGCACGTGAATTTAACAAAACAAATGATAAATATATACTGTTATTCAAAACAAA
1 GTGAATGTGAGTGCACGTGAA-TTAACAAAACAAATGATAAA-A-ATACTGTTATGCAAAACAAA
16370 TGATGAACATGCTGTTAT
63 TGATGAACATGCTGTTAT
16388 G
1 G
16389 AATCCCACAA
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 19 0.25
81 18 0.24
82 1 0.01
83 37 0.49
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.29
Consensus pattern (80 bp):
GTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATAAAAATACTGTTATGCAAAACAAATGA
TGAACATGCTGTTAT
Found at i:22660 original size:23 final size:24
Alignment explanation
Indices: 22603--22661 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
22593 CTTTTCTTTA
*
22603 TTTCTTTTTCTTCTTTTCGAGTGC
1 TTTCATTTTCTTCTTTTCGAGTGC
**
22627 TTTCAACTTCTTCTTTT-GAGTGC
1 TTTCATTTTCTTCTTTTCGAGTGC
*
22650 TTTTATTTTCTT
1 TTTCATTTTCTT
22662 TGCTGATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.08, C:0.19, G:0.10, T:0.63
Consensus pattern (24 bp):
TTTCATTTTCTTCTTTTCGAGTGC
Found at i:26813 original size:497 final size:500
Alignment explanation
Indices: 25851--26838 Score: 1786
Period size: 497 Copynumber: 2.0 Consensus size: 500
25841 ACCTTGGATT
25851 GAAGTTGGCAACCTTGTTGTTTCCCGATCTAAGAGAGACACCAAATGCTACAACTTGGATTGAAA
1 GAAGTTGGCAACCTTGTTGTTTCCCGATCTAAGAGAGACACCAAATGCTACAACTTGGATTGAAA
* *
25916 GTAATCTGCACAAAAGAAGAAGAATTTATTAAGTAATATGATAATTAAGAAATGAAAAGTAAATG
66 GTAATATGCACAAAAGAAGAAGAATTGATTAAGTAATATGATAATTAAGAAATGAAAAGTAAATG
* * *
25981 GAAATGGAAAGAATTGAAAAGGAAAAGAAAGGAATGTTATCAAAGATGGGTTGCGGAAGTAATGT
131 GAAATGGAAAGAATTGAAAAGG---AGAAAGGAATGTTATCAAAGATAGGCTGCAGAAGTAATGT
26046 TGATTTATCCTTCAATGCAAGAGAATTCGGCCACCAATGATGTTGCTGATCGTATGCCTTAATGA
193 TGATTTATCCTTCAATGCAAGAGAATTCGGCCACCAATGATGTTGCTGATCGTATGCCTTAATGA
26111 TGAATGAAGGATGTTTTAATTGGTGATGAAGATGATATTGGAATGGTGATAGATTTGGCGTGAAG
258 TGAATGAAGGATGTTTTAATTGGTGATGAAGATGATATTGGAATGGTGATAGATTTGGCGTGAAG
*
26176 GTGATGGGATATGGAGATGGAAATAGTATCTTATAAAACTTAAAGGAACCAATGTTATAAAGAAC
323 GTGATGGGATATGGAGATGGAAATAGTATCTTATAAAACTAAAAGGAACCAATGTTATAAAGAAC
*
26241 AAAGACCCGTTTCTTATAAGTCTTATAAGGGATGGTAGTAAGGACTTTGACCTGCTAGTTATAAG
388 AAAGACCCGTTTCTTATAAGTCTTATAAGGGATGGTAGTAAGGACTTTGACCCGCTAGTTATAAG
26306 AACTAGGAACCAGAAGTATCAAGGGGAAGGAATGACGCCAATGATGGA
453 AACTAGGAACCAGAAGTATCAAGGGGAAGGAATGACGCCAATGATGGA
*
26354 GAAGTTGGCAACCTTGTTGTTT-CCGATCTAGGAGAGACACCAAATGCTACAACTTGGATTGAAA
1 GAAGTTGGCAACCTTGTTGTTTCCCGATCTAAGAGAGACACCAAATGCTACAACTTGGATTGAAA
26418 GTAATATGCACAAAAGAAGAAGAATTGATTAAGTAATATGATAATTAAGAAATGAAAAGTAAATG
66 GTAATATGCACAAAAGAAGAAGAATTGATTAAGTAATATGATAATTAAGAAATGAAAAGTAAATG
*
26483 GAAATGGAAAGAATTG-AAATG-GAAAGGAATGTTATCAAAGATAGGCTGCAGAAGTAATGTTGA
131 GAAATGGAAAGAATTGAAAAGGAGAAAGGAATGTTATCAAAGATAGGCTGCAGAAGTAATGTTGA
* *
26546 TTTATCCTTCAATGCAAGAGAATTCGGCTACCAATGATGTTGCTGGT-GTATGCCTTAATGATGA
196 TTTATCCTTCAATGCAAGAGAATTCGGCCACCAATGATGTTGCTGATCGTATGCCTTAATGATGA
* *
26610 ATGAAGGATGTTTTAATTGGTGATGAAGATGGTATTGGAATGGTGATAGATTTGGTGTGAAGGTG
261 ATGAAGGATGTTTTAATTGGTGATGAAGATGATATTGGAATGGTGATAGATTTGGCGTGAAGGTG
*
26675 ATGGGATATGGAGATGGAAATAGTATCTTATAAAACTAAGAATGAACCAATGTTATAAAGAACAA
326 ATGGGATATGGAGATGGAAATAGTATCTTATAAAACTAA-AAGGAACCAATGTTATAAAGAACAA
26740 AGACCCGTTTCTTATAAGTCTTATAAGGGATGGTAGTAAGGACTTTGACCCGCTAGTTATAAGAA
390 AGACCCGTTTCTTATAAGTCTTATAAGGGATGGTAGTAAGGACTTTGACCCGCTAGTTATAAGAA
26805 CTAGGAACCAGAAGTATCAAGGGGAAGGAATGAC
455 CTAGGAACCAGAAGTATCAAGGGGAAGGAATGAC
26839 ACCACAAACT
Statistics
Matches: 470, Mismatches: 14, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
496 118 0.25
497 206 0.44
501 4 0.01
502 120 0.26
503 22 0.05
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (500 bp):
GAAGTTGGCAACCTTGTTGTTTCCCGATCTAAGAGAGACACCAAATGCTACAACTTGGATTGAAA
GTAATATGCACAAAAGAAGAAGAATTGATTAAGTAATATGATAATTAAGAAATGAAAAGTAAATG
GAAATGGAAAGAATTGAAAAGGAGAAAGGAATGTTATCAAAGATAGGCTGCAGAAGTAATGTTGA
TTTATCCTTCAATGCAAGAGAATTCGGCCACCAATGATGTTGCTGATCGTATGCCTTAATGATGA
ATGAAGGATGTTTTAATTGGTGATGAAGATGATATTGGAATGGTGATAGATTTGGCGTGAAGGTG
ATGGGATATGGAGATGGAAATAGTATCTTATAAAACTAAAAGGAACCAATGTTATAAAGAACAAA
GACCCGTTTCTTATAAGTCTTATAAGGGATGGTAGTAAGGACTTTGACCCGCTAGTTATAAGAAC
TAGGAACCAGAAGTATCAAGGGGAAGGAATGACGCCAATGATGGA
Found at i:31040 original size:25 final size:25
Alignment explanation
Indices: 30992--31041 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
30982 TCTTTTTCTT
* *
30992 CTTTTGAGTGCTGTATTTTTTTTTC
1 CTTTTGAGTGCTGTACTTTGTTTTC
31017 CTTTTGAGTGCT-TCACTTTGTTTTC
1 CTTTTGAGTGCTGT-ACTTTGTTTTC
31042 TGATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (25 bp):
CTTTTGAGTGCTGTACTTTGTTTTC
Found at i:34805 original size:23 final size:22
Alignment explanation
Indices: 34762--34807 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34752 TTTTTCTTCT
* *
34762 TTTGAGTGCTGGATTTTTTTTC
1 TTTGAGTGCTGCATTTGTTTTC
*
34784 TTTGAGTGCTTCACTTTGTTTTC
1 TTTGAGTGCTGCA-TTTGTTTTC
34807 T
1 T
34808 GATTTTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.09, C:0.13, G:0.20, T:0.59
Consensus pattern (22 bp):
TTTGAGTGCTGCATTTGTTTTC
Found at i:37468 original size:20 final size:20
Alignment explanation
Indices: 37423--37470 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
37413 TGTGGGAGTC
37423 TTTTCTTTCTCTTTTTGTTT
1 TTTTCTTTCTCTTTTTGTTT
*
37443 TCTTCTTTCT-TTTTCT-TTT
1 TTTTCTTTCTCTTTT-TGTTT
37462 TGTTTCTTT
1 T-TTTCTTT
37471 TGTTGCAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTTCTTTCTCTTTTTGTTT
Found at i:39752 original size:19 final size:19
Alignment explanation
Indices: 39710--39749 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39700 TATCCTTTCT
*
39710 TTATTTCATTTCATTTTTA
1 TTATTTCATTTCATTCTTA
*
39729 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
39749 T
1 T
39750 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:42009 original size:16 final size:16
Alignment explanation
Indices: 41988--42020 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41978 TTGCAACAAA
41988 AAGAAAAA-AAAGAAAG
1 AAGAAAAACAAA-AAAG
42004 AAGAAAAACAAAAAAG
1 AAGAAAAACAAAAAAG
42020 A
1 A
42021 TAAAGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAAAAACAAAAAAG
Found at i:42016 original size:22 final size:22
Alignment explanation
Indices: 41985--42027 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41975 ATGTTGCAAC
*
41985 AAAAAGAAAAAAAAGAAAGAAG
1 AAAAACAAAAAAAAGAAAGAAG
* *
42007 AAAAACAAAAAAGATAAAGAA
1 AAAAACAAAAAAAAGAAAGAA
42028 AAGACTCCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAACAAAAAAAAGAAAGAAG
Found at i:49498 original size:19 final size:19
Alignment explanation
Indices: 49476--49526 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
49466 TTTTTTGAAA
*
49476 TTTTGGCTTTTTTGGCTTTT
1 TTTTGG-TTTTTTGCCTTTT
*
49496 TTTTTGTTTTTTGCCTTTT
1 TTTTGGTTTTTTGCCTTTT
*
49515 TTTTTGTTTTTT
1 TTTTGGTTTTTT
49527 TGAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (19 bp):
TTTTGGTTTTTTGCCTTTT
Found at i:49505 original size:18 final size:19
Alignment explanation
Indices: 49483--49526 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
49473 AAATTTTGGC
*
49483 TTTTTTGGCTTTTTTTTTG
1 TTTTTTGCCTTTTTTTTTG
49502 TTTTTTGCCTTTTTTTTTG
1 TTTTTTGCCTTTTTTTTTG
49521 TTTTTT
1 TTTTTT
49527 TGAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (19 bp):
TTTTTTGCCTTTTTTTTTG
Found at i:55909 original size:48 final size:48
Alignment explanation
Indices: 55817--55909 Score: 107
Period size: 48 Copynumber: 1.9 Consensus size: 48
55807 CACACTCCAA
* * * * * *
55817 TTTGCCTTTTCATCGCGACTAGAGGGTTGGTTAGAGCCATTTATCGTG
1 TTTGCCTTTTCATCGCGACTAGAGAGCTCGATAGAGACACTTATCGTG
*
55865 TTTGCCTTTTCATTGCGACTAGGAGAGCTCGATAG-GACACTTATC
1 TTTGCCTTTTCATCGCGACTA-GAGAGCTCGATAGAGACACTTATC
55910 CATCTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
48 28 0.76
49 9 0.24
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (48 bp):
TTTGCCTTTTCATCGCGACTAGAGAGCTCGATAGAGACACTTATCGTG
Found at i:56438 original size:12 final size:12
Alignment explanation
Indices: 56389--56420 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
56379 TTACGAAAAA
56389 CAAAAAAAAAGG
1 CAAAAAAAAAGG
*
56401 CAAAAACAAAGG
1 CAAAAAAAAAGG
56413 CAAAAAAA
1 CAAAAAAA
56421 CAAAAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAGG
Found at i:56444 original size:20 final size:21
Alignment explanation
Indices: 56393--56445 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
56383 GAAAAACAAA
* *
56393 AAAAAAGGCAAAAACAAAGGC
1 AAAAAAGACAAAAACAAAGCC
56414 AAAAAA-ACAAAAA-AAAGCC
1 AAAAAAGACAAAAACAAAGCC
*
56433 AAAAAAGCCAAAA
1 AAAAAAGACAAAA
56446 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.39
20 11 0.39
21 6 0.21
ACGTcount: A:0.74, C:0.15, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAAAGACAAAAACAAAGCC
Found at i:72405 original size:15 final size:15
Alignment explanation
Indices: 72369--72408 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
72359 ATAATTAAGA
*
72369 AAAGAAATGGAAATGG
1 AAAGAAAT-GAAAGGG
72385 AAAGAAATGAAAGGG
1 AAAGAAATGAAAGGG
*
72400 ATAGAAATG
1 AAAGAAATG
72409 TTATCAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.30, T:0.12
Consensus pattern (15 bp):
AAAGAAATGAAAGGG
Found at i:74831 original size:14 final size:14
Alignment explanation
Indices: 74812--74838 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
74802 ATTGGCGTGA
74812 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
74826 ATGGTGATGGAAA
1 ATGGTGATGGAAA
74839 TAGTATCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:77774 original size:22 final size:21
Alignment explanation
Indices: 77737--77777 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
77727 CCATCTCCAT
77737 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
77758 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
77778 ATTCCACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:78301 original size:10 final size:10
Alignment explanation
Indices: 78288--78331 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
78278 AGAAAAGACA
78288 AAAAAATAAG
1 AAAAAATAAG
78298 AAAAAATAAG
1 AAAAAATAAG
*
78308 AAAAAAAAAG
1 AAAAAATAAG
78318 -AAAAA-AAG
1 AAAAAATAAG
78326 AAAAAA
1 AAAAAA
78332 AAAATGAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 3 0.09
9 10 0.31
10 19 0.59
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (10 bp):
AAAAAATAAG
Found at i:78332 original size:10 final size:10
Alignment explanation
Indices: 78271--78334 Score: 64
Period size: 10 Copynumber: 6.8 Consensus size: 10
78261 AAATTGGAGT
78271 AAAAAAAAG-
1 AAAAAAAAGA
* *
78280 AAAAGACA-A
1 AAAAAAAAGA
*
78289 AAAAATAAGA
1 AAAAAAAAGA
*
78299 AAAAATAAGA
1 AAAAAAAAGA
78309 AAAAAAAAG-
1 AAAAAAAAGA
78318 -AAAAAAAGA
1 AAAAAAAAGA
78327 AAAAAAAA
1 AAAAAAAA
78335 ATGAGAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 8 0.18
9 11 0.24
10 26 0.58
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:78334 original size:18 final size:18
Alignment explanation
Indices: 78271--78334 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
78261 AAATTGGAGT
*
78271 AAAAAAAAGAAAAGACA-A
1 AAAAAAAAGAAAA-AAAGA
*
78289 AAAAATAAGAAAAAATAAGA
1 AAAAAAAAG-AAAAA-AAGA
78309 AAAAAAAAGAAAAAAAGA
1 AAAAAAAAGAAAAAAAGA
78327 AAAAAAAA
1 AAAAAAAA
78335 ATGAGAAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 21 0.52
19 10 0.25
20 9 0.22
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.03
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAGA
Found at i:79352 original size:22 final size:22
Alignment explanation
Indices: 79312--79354 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
79302 AAACACCTTG
79312 AAGAAAAACATTAAAACAATGA
1 AAGAAAAACATTAAAACAATGA
*
79334 AAGAACAAC-TTAAAGACAATG
1 AAGAAAAACATTAAA-ACAATG
79355 CAATTGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.14
Consensus pattern (22 bp):
AAGAAAAACATTAAAACAATGA
Found at i:81795 original size:77 final size:78
Alignment explanation
Indices: 81705--81862 Score: 300
Period size: 77 Copynumber: 2.0 Consensus size: 78
81695 ATCTTATCTC
*
81705 ATATATAAAATTACTCTTGTGAGCTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAAC
1 ATATAAAAAATTACTCTTGTGAGCTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAAC
81770 AAGTAT-ATTCCT
66 AAGTATAATTCCT
81782 ATATAAAAAATTACTCTTGTGAGCTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAAC
1 ATATAAAAAATTACTCTTGTGAGCTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAAC
81847 AAGTATAATTCCT
66 AAGTATAATTCCT
81860 ATA
1 ATA
81863 CTTGTGGCGT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
77 70 0.89
78 9 0.11
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (78 bp):
ATATAAAAAATTACTCTTGTGAGCTATTTCTCTTCAAAGTTCTTTGTGAACTTTATCGATTAAAC
AAGTATAATTCCT
Found at i:82069 original size:22 final size:21
Alignment explanation
Indices: 82032--82072 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
82022 CCATCTCCAT
82032 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
82053 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
82073 ATTCTGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:82592 original size:27 final size:27
Alignment explanation
Indices: 82562--82617 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
82552 AAATTGGAGT
82562 AAAAAAAAAAGAAAAAAAAAAAAAAAA
1 AAAAAAAAAAGAAAAAAAAAAAAAAAA
*** *
82589 AAAAAATTCAGAAAAGAAAAAAAAAAA
1 AAAAAAAAAAGAAAAAAAAAAAAAAAA
82616 AA
1 AA
82618 GCAAAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.89, C:0.02, G:0.05, T:0.04
Consensus pattern (27 bp):
AAAAAAAAAAGAAAAAAAAAAAAAAAA
Found at i:82624 original size:1 final size:1
Alignment explanation
Indices: 82562--82617 Score: 58
Period size: 1 Copynumber: 56.0 Consensus size: 1
82552 AAATTGGAGT
* *** * *
82562 AAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAATTCAGAAAAGAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
82618 GCAAAAAGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.02, G:0.05, T:0.04
Consensus pattern (1 bp):
A
Found at i:86680 original size:11 final size:11
Alignment explanation
Indices: 86666--86724 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
86656 AAATTAGAGT
86666 AAAAAAAAGAA
1 AAAAAAAAGAA
*
86677 AAAAAAAAAAA
1 AAAAAAAAGAA
86688 AAAAAAATTCAGAA
1 AAAAAAA---AGAA
86702 AAAAAAAAGAA
1 AAAAAAAAGAA
**
86713 AGTAAAAAGAA
1 AAAAAAAAGAA
86724 A
1 A
86725 GCAAGCCATG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 31 0.76
14 10 0.24
ACGTcount: A:0.85, C:0.02, G:0.08, T:0.05
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:90355 original size:22 final size:21
Alignment explanation
Indices: 90318--90358 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
90308 CCATCTCCAT
90318 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
90339 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
90359 ATTCTGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:91776 original size:8 final size:8
Alignment explanation
Indices: 91763--91818 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
91753 ATATTTTTTT
91763 CAAAAAAA
1 CAAAAAAA
91771 CAAAAAAAAA
1 C--AAAAAAA
*
91781 CAAAAAAGG
1 CAAAAAA-A
91790 CAAAAAAA
1 CAAAAAAA
91798 C--AAAAA
1 CAAAAAAA
91804 -AAAAAAA
1 CAAAAAAA
91811 CAAAAAAA
1 CAAAAAAA
91819 AGCTAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
6 5 0.12
7 5 0.12
8 15 0.38
9 7 0.17
10 8 0.20
ACGTcount: A:0.86, C:0.11, G:0.04, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:91827 original size:11 final size:10
Alignment explanation
Indices: 91764--91819 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
91754 TATTTTTTTC
91764 AAAAAAACAA
1 AAAAAAACAA
91774 AAAAAAAC-A
1 AAAAAAACAA
**
91783 AAAAAGGCAA
1 AAAAAAACAA
*
91793 AAAAACAAAAA
1 AAAAA-AACAA
91804 AAAAAAACAA
1 AAAAAAACAA
91814 AAAAAA
1 AAAAAA
91820 GCTAAAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
9 7 0.18
10 24 0.63
11 7 0.18
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:98508 original size:12 final size:12
Alignment explanation
Indices: 98493--98557 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 12
98483 AAATTGGAGT
98493 AAAAAAAAGAAA
1 AAAAAAAAGAAA
98505 AAAAAAAAGAAA
1 AAAAAAAAGAAA
98517 AAAATTCAGAAA-AGAA
1 AAAA---A-AAAGA-AA
98533 AAAAAAAAGAAA
1 AAAAAAAAGAAA
*
98545 AGTAAAAAAGAAA
1 A-AAAAAAAGAAA
98558 GCAAACTATG
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
12 22 0.49
13 12 0.27
15 2 0.04
16 9 0.20
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.05
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:98551 original size:17 final size:16
Alignment explanation
Indices: 98493--98558 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 16
98483 AAATTGGAGT
*
98493 AAAA-AAAAGAAAAAAA
1 AAAAGAAAA-AAAAAAG
**
98509 AAAAGAAAAAAATTCAG
1 AAAAGAAAAAAA-AAAG
98526 AAAAGAAAAAAAAAAG
1 AAAAGAAAAAAAAAAG
*
98542 AAAAGTAAAAAAGAAAG
1 AAAAG-AAAAAAAAAAG
98559 CAAACTATGG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
16 14 0.34
17 27 0.66
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAG
Found at i:105290 original size:5 final size:5
Alignment explanation
Indices: 105280--105310 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
105270 ACTCAAAAAG
105280 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
105311 GAAGTTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:110983 original size:24 final size:24
Alignment explanation
Indices: 110931--110983 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
110921 CTTTTCTTTG
**
110931 CTTTTCTTCTTTTTTAGTGCTGGA
1 CTTTTCTTCTTTTGGAGTGCTGGA
* *
110955 TTTTTCTTCTTTTGGAGTGCTTGA
1 CTTTTCTTCTTTTGGAGTGCTGGA
110979 CTTTT
1 CTTTT
110984 ATTTGCTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.15, G:0.17, T:0.60
Consensus pattern (24 bp):
CTTTTCTTCTTTTGGAGTGCTGGA
Found at i:115843 original size:35 final size:36
Alignment explanation
Indices: 115756--115843 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 36
115746 TACAATTTGT
* *
115756 TCATCACCATCTTCCATCACCATTATCATGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
115792 TCATCACCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
115827 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
115844 TTCCATTTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 27 0.57
36 20 0.43
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:131220 original size:20 final size:20
Alignment explanation
Indices: 131195--131236 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
131185 TTTTTTGAAA
131195 TTTTGGCTTTTTTGTTTTTT
1 TTTTGGCTTTTTTGTTTTTT
*
131215 TTTTGGTTTTTTTGTTTTTT
1 TTTTGGCTTTTTTGTTTTTT
131235 TT
1 TT
131237 AAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.83
Consensus pattern (20 bp):
TTTTGGCTTTTTTGTTTTTT
Found at i:136088 original size:22 final size:20
Alignment explanation
Indices: 136051--136095 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
136041 CCATCTCCAT
136051 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCA-C
*
136072 TTCATCCATCAAGACCATCAC
1 TTCAT-CATCAACACCATCAC
136093 TTC
1 TTC
136096 CGCATCCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.31, C:0.38, G:0.02, T:0.29
Consensus pattern (20 bp):
TTCATCATCAACACCATCAC
Found at i:138380 original size:19 final size:20
Alignment explanation
Indices: 138339--138389 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
138329 GAAACCCCTT
*
138339 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
138359 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
138378 TGAAGATACATG
1 TGAAAATACATG
138390 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:139323 original size:30 final size:31
Alignment explanation
Indices: 139282--139341 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
139272 ACATGCTGCC
139282 ATGATATCTAAATA-AAATGCAAACATAATAA
1 ATGATATCTAAA-ACAAATGCAAACATAATAA
* *
139313 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
139342 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 21 0.81
31 4 0.15
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:142060 original size:33 final size:33
Alignment explanation
Indices: 142023--142085 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
142013 GATGAAACAA
142023 TGCTAAGGAGCACAATCCCGGTCTTCACAAACT
1 TGCTAAGGAGCACAATCCCGGTCTTCACAAACT
* *
142056 TGCTAAGGAGCATAATCTCGGTCTTCACAA
1 TGCTAAGGAGCACAATCCCGGTCTTCACAA
142086 TGAACTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (33 bp):
TGCTAAGGAGCACAATCCCGGTCTTCACAAACT
Found at i:145883 original size:5 final size:5
Alignment explanation
Indices: 145873--145925 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
145863 TTGAACTTCT
* *
145873 TTTTC TTTTC TTTTC TGAATTTT TTTTC TTCTTT TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC T---TTTC TTTTC TT-TTC TTTTC TTTTC TTTTC
145922 TTTT
1 TTTT
145926 TGCACTCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
6 4 0.10
8 4 0.10
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:145891 original size:24 final size:23
Alignment explanation
Indices: 145853--145912 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
145843 CCTTGGCTTG
145853 CTTTCTCTTTT-TGAACTTCTTTTT
1 CTTT-TCTTTTCTGAA-TTCTTTTT
*
145877 CTTTTCTTTTCTGAATTTTTTTT
1 CTTTTCTTTTCTGAATTCTTTTT
*
145900 CTTCTTTTTTTCT
1 CTT-TTCTTTTCT
145913 TTTCTTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (23 bp):
CTTTTCTTTTCTGAATTCTTTTT
Found at i:146997 original size:16 final size:16
Alignment explanation
Indices: 146971--147013 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
146961 GGATGTAAAG
146971 GCATC-TTCATGGGCA
1 GCATCATTCATGGGCA
146986 GCATCATTCATGGGCA
1 GCATCATTCATGGGCA
147002 GCATCATTCATG
1 GCATCATTCATG
147014 AAAGGTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (16 bp):
GCATCATTCATGGGCA
Found at i:148893 original size:19 final size:19
Alignment explanation
Indices: 148869--148905 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
148859 TATATGATTT
148869 TTTTAATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
148888 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
148906 GTCTTGGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:154101 original size:19 final size:20
Alignment explanation
Indices: 154071--154110 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
154061 GTATAATAAC
154071 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
154091 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
154110 A
1 A
154111 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:156184 original size:33 final size:33
Alignment explanation
Indices: 156106--156206 Score: 91
Period size: 35 Copynumber: 3.1 Consensus size: 33
156096 ATACAATCTG
* * *
156106 TCCATCATCATATCACGCCTATATCATCA-CCATAT
1 TCCATCACCATATCACGCCAATAACATCATCC---T
156141 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
156174 TCCATTACCATTTCA-TCCATTAA-ATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
156205 TC
1 TC
156207 ATTCATCAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
31 10 0.17
32 6 0.10
33 14 0.24
35 26 0.45
36 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.32
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:160600 original size:35 final size:37
Alignment explanation
Indices: 160543--160612 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
160533 ATAAGATACA
* * *
160543 ATATGTCCATCATCATTATCACGCCTATATCATCACC
1 ATATGTCCATCACCATTATCACGCCAATAACATCACC
160580 ATAT-TCCATCACCA-TATCACGCCAATAACATCA
1 ATATGTCCATCACCATTATCACGCCAATAACATCA
160613 TCCTTCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 17 0.57
36 9 0.30
37 4 0.13
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGCCAATAACATCACC
Found at i:160627 original size:33 final size:33
Alignment explanation
Indices: 160583--160651 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
160573 CATCACCATA
*
160583 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
160616 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
160649 TTC
1 TTC
160652 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:164260 original size:19 final size:20
Alignment explanation
Indices: 164232--164271 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
164222 GGATAATAAT
164232 ATAAGTAATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
164252 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
164271 A
1 A
164272 GGATGGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAATGAAATA
Found at i:164725 original size:19 final size:21
Alignment explanation
Indices: 164682--164733 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
164672 GAAACTCCTT
164682 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
164703 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
164722 TGAAGATACATG
1 TGAAAATACATG
164734 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:174366 original size:16 final size:16
Alignment explanation
Indices: 174345--174378 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
174335 AAAAGACCTT
174345 ACCAGAATATACCCTC
1 ACCAGAATATACCCTC
174361 ACCAGAATATACCCTC
1 ACCAGAATATACCCTC
174377 AC
1 AC
174379 AATGCCTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.38, G:0.06, T:0.18
Consensus pattern (16 bp):
ACCAGAATATACCCTC
Found at i:179540 original size:19 final size:20
Alignment explanation
Indices: 179502--179549 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
179492 ACCCCTTTGG
**
179502 AAATACATGATTTTTGATGA
1 AAATACATGATTTTAAATGA
179522 AAATACATGA-TTTAAATGA
1 AAATACATGATTTTAAATGA
*
179541 AGATACATG
1 AAATACATG
179550 CTCTTGGACG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (20 bp):
AAATACATGATTTTAAATGA
Found at i:182496 original size:15 final size:16
Alignment explanation
Indices: 182446--182497 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 16
182436 TGATAGTGAA
182446 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
182463 A-ATA-AAAAATGAAATG
1 ATA-AGAAAAATGAAA-G
182479 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
182494 ATAA
1 ATAA
182498 CTTACAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 11 0.35
16 10 0.32
17 10 0.32
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:183530 original size:19 final size:20
Alignment explanation
Indices: 183483--183533 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
183473 GAAACCCCTT
**
183483 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
183503 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
183522 TGAAGATACATG
1 TGAAAATACATG
183534 CTCTTGGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:191991 original size:14 final size:14
Alignment explanation
Indices: 191972--192009 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
191962 TGCAACAACA
191972 ACAAAAAGAAAAAT
1 ACAAAAAGAAAAAT
191986 ACAAAAAGAAAAAT
1 ACAAAAAGAAAAAT
192000 ACAAAAAGAA
1 ACAAAAAGAA
192010 GTGCAAAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.79, C:0.08, G:0.08, T:0.05
Consensus pattern (14 bp):
ACAAAAAGAAAAAT
Found at i:192101 original size:15 final size:15
Alignment explanation
Indices: 192090--192118 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
192080 ACTCAAAAAG
192090 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
192105 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
192119 GTTGAAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:193510 original size:9 final size:9
Alignment explanation
Indices: 193496--193523 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
193486 TCCAGAGACA
193496 TCAAATGTT
1 TCAAATGTT
193505 TCAAATGTT
1 TCAAATGTT
193514 TCAAATGTT
1 TCAAATGTT
193523 T
1 T
193524 TGTTTTGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TCAAATGTT
Found at i:197923 original size:20 final size:19
Alignment explanation
Indices: 197900--197941 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
197890 CTTCTTTTAA
*
197900 TACCTTTGAATCTTTTTTTC
1 TACCTTTCAAT-TTTTTTTC
*
197920 TACCTTTCCATTTTTTTTC
1 TACCTTTCAATTTTTTTTC
197939 TAC
1 TAC
197942 TTTTTCTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (19 bp):
TACCTTTCAATTTTTTTTC
Found at i:206583 original size:34 final size:36
Alignment explanation
Indices: 206537--206603 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 36
206527 ATTTAGAAGT
*
206537 TGGTGATAATATAGG-TTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
206571 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
206604 CAGATTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 14 0.48
35 4 0.14
36 11 0.38
ACGTcount: A:0.30, C:0.01, G:0.36, T:0.33
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:210588 original size:13 final size:14
Alignment explanation
Indices: 210556--210597 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
210546 TTTCTTCACT
210556 TTTTCTTTGCTTTTTA
1 TTTTCTTT-C-TTTTA
*
210572 TTTTC-TTCTTTTC
1 TTTTCTTTCTTTTA
210585 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
210598 GCACTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 9 0.38
14 8 0.33
15 2 0.08
16 5 0.21
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTCTTTCTTTTA
Found at i:211079 original size:35 final size:36
Alignment explanation
Indices: 211032--211099 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
211022 ATTTAGAAGT
211032 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
211067 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
211100 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:214720 original size:20 final size:21
Alignment explanation
Indices: 214695--214738 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
214685 TTTGCTATTT
214695 AAAAAAAACAAAAAAA-AAAA
1 AAAAAAAACAAAAAAACAAAA
**
214715 AAAAAAGGCAAAAAAACAAAA
1 AAAAAAAACAAAAAAACAAAA
214736 AAA
1 AAA
214739 GCCAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.89, C:0.07, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAAAACAAAA
Found at i:214745 original size:17 final size:18
Alignment explanation
Indices: 214706--214746 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
214696 AAAAAAACAA
214706 AAAAAAAAAAAAAAAGGC
1 AAAAAAAAAAAAAAAGGC
* *
214724 AAAAAAACAAAAAAAGCC
1 AAAAAAAAAAAAAAAGGC
214742 AAAAA
1 AAAAA
214747 TTTCAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAGGC
Found at i:226434 original size:33 final size:33
Alignment explanation
Indices: 226356--226458 Score: 93
Period size: 33 Copynumber: 3.1 Consensus size: 33
226346 ATACAATCTG
* * *
226356 TCCATCATCATTATCACGCCTATATCATCA-CCATT
1 TCCATCACCA-TATCACGCCAATAACATCATCC--T
226391 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
226424 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
226457 TC
1 TC
226459 ATTCATCAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
33 24 0.41
34 24 0.41
35 11 0.19
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:229908 original size:20 final size:21
Alignment explanation
Indices: 229873--229913 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
229863 TTTGATAACA
*
229873 ATTATATTCCTTTCATTTCTT
1 ATTATATTCATTTCATTTCTT
229894 ATTAT-TTCATTTCATTTCTT
1 ATTATATTCATTTCATTTCTT
229914 TCTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTATATTCATTTCATTTCTT
Found at i:229933 original size:24 final size:24
Alignment explanation
Indices: 229877--229934 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
229867 ATAACAATTA
229877 TATTCC-TTTCATTTCTTATTATT
1 TATTCCATTTCATTTCTTATTATT
*
229900 TCATTTCATTTC-TTTCTTAATT-TAT
1 T-ATTCCATTTCATTTCTT-ATTAT-T
229925 TATTCCATTT
1 TATTCCATTT
229935 TAATCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 1 0.03
24 19 0.66
25 9 0.31
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTCCATTTCATTTCTTATTATT
Found at i:235676 original size:22 final size:21
Alignment explanation
Indices: 235651--235694 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
235641 TAATTATTCA
235651 ATTTAAAACAACATGTATTTCC
1 ATTTAAAA-AACATGTATTTCC
**
235673 ATTTAAAAGTCATGTATTTCC
1 ATTTAAAAAACATGTATTTCC
235694 A
1 A
235695 AATAGGGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTTAAAAAACATGTATTTCC
Found at i:236227 original size:22 final size:21
Alignment explanation
Indices: 236201--236244 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
236191 GGCTGTGGAA
*
236201 TTGATGGTCTTGATGGATGAAG
1 TTGATGATCTTGAT-GATGAAG
*
236223 TTGATGATGTTGATGATGAAG
1 TTGATGATCTTGATGATGAAG
236244 T
1 T
236245 GGAGATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.25, C:0.02, G:0.34, T:0.39
Consensus pattern (21 bp):
TTGATGATCTTGATGATGAAG
Found at i:239953 original size:16 final size:16
Alignment explanation
Indices: 239934--240002 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 16
239924 TTTTTTTGAA
239934 TTCTTTTTCTTTTCTT
1 TTCTTTTTCTTTTCTT
*
239950 TTCTTCTTT-TCTTCTT
1 TTCTT-TTTCTTTTCTT
239966 TTCTGATTTTTCTCTTT-TT
1 TTC---TTTTTCT-TTTCTT
239985 TATCTTTTTC-TTTCTT
1 T-TCTTTTTCTTTTCTT
240001 TT
1 TT
240003 TGCACTCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 17
0.69 0.03 0.27
Matches are distributed among these distances:
15 4 0.09
16 17 0.40
17 9 0.21
18 3 0.07
19 6 0.14
20 4 0.09
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (16 bp):
TTCTTTTTCTTTTCTT
Found at i:239958 original size:8 final size:8
Alignment explanation
Indices: 239945--239969 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
239935 TCTTTTTCTT
239945 TTCTTTTC
1 TTCTTTTC
239953 TTCTTTTC
1 TTCTTTTC
239961 TTCTTTTC
1 TTCTTTTC
239969 T
1 T
239970 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:240340 original size:22 final size:21
Alignment explanation
Indices: 240314--240357 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
240304 GGCTGCGGAA
*
240314 TTGATGGTCTTGATGGATGAAG
1 TTGATGATCTTGAT-GATGAAG
*
240336 TTGATGATGTTGATGATGAAG
1 TTGATGATCTTGATGATGAAG
240357 T
1 T
240358 GGAGATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.25, C:0.02, G:0.34, T:0.39
Consensus pattern (21 bp):
TTGATGATCTTGATGATGAAG
Found at i:242166 original size:6 final size:6
Alignment explanation
Indices: 242138--242180 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
242128 GTGTAGCAAC
* *
242138 AAAAAG CAAAAG AAAGAAG AAAAAT AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
242181 CTCCTATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:242169 original size:12 final size:12
Alignment explanation
Indices: 242138--242180 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
242128 GTGTAGCAAC
*
242138 AAAAAGCAAAAG
1 AAAAAGAAAAAG
*
242150 AAAGAAGAAAAAT
1 AAA-AAGAAAAAG
242163 AAAAAG-AAAAG
1 AAAAAGAAAAAG
242174 AAAAAGA
1 AAAAAGA
242181 CTCCTATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 10 0.38
12 6 0.23
13 10 0.38
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:242643 original size:22 final size:22
Alignment explanation
Indices: 242618--242660 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
242608 AAAAAAATTG
242618 AAAAG-AAGATTAGAAGA-AATGA
1 AAAAGCAA-ATTA-AAGACAATGA
242640 AAAAGCAAATTAAAGACAATG
1 AAAAGCAAATTAAAGACAATG
242661 CAACTGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.63, C:0.05, G:0.19, T:0.14
Consensus pattern (22 bp):
AAAAGCAAATTAAAGACAATGA
Found at i:243608 original size:19 final size:20
Alignment explanation
Indices: 243561--243611 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
243551 GAAACCCCTT
**
243561 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
243581 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
243600 TGAAGATACATG
1 TGAAAATACATG
243612 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:252108 original size:21 final size:21
Alignment explanation
Indices: 252069--252108 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
252059 AAGGAAGATT
*
252069 AATGAAATGATAAAGATAAGA
1 AATGAAATGATAAAAATAAGA
252090 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
252109 AGGATAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGA
Found at i:252156 original size:22 final size:21
Alignment explanation
Indices: 252131--252171 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
252121 GTTGTGGAAT
252131 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
252153 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
252172 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:258895 original size:35 final size:36
Alignment explanation
Indices: 258839--258906 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
258829 ATACAATCTG
*
258839 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTAAATCATCACCATAT
*
258875 TCCATCACCA-TATCACGCCTAAATTATCACCA
1 TCCATCACCATTATCACGCCTAAATCATCACCA
258907 ACTTCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTAAATCATCACCATAT
Found at i:263350 original size:22 final size:23
Alignment explanation
Indices: 263309--263361 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
263299 ACAATCTGTC
* *
263309 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACACCTAAAT
263332 CATCACCA-TATCACACCTAAAT
1 CATCACCATTATCACACCTAAAT
*
263354 TATCACCA
1 CATCACCA
263362 ACTTCTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (23 bp):
CATCACCATTATCACACCTAAAT
Found at i:265049 original size:14 final size:14
Alignment explanation
Indices: 265032--265059 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
265022 GTTAAGGATT
265032 GATGGTGATGGAAA
1 GATGGTGATGGAAA
265046 GATGGTGATGGAAA
1 GATGGTGATGGAAA
265060 TAGTATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:265434 original size:19 final size:20
Alignment explanation
Indices: 265393--265435 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
265383 GAAACCCCTT
*
265393 TGAAAACACATGATTTGTAA
1 TGAAAACACATAATTTGTAA
*
265413 TGAAAATACATAATTT-TAA
1 TGAAAACACATAATTTGTAA
265432 TGAA
1 TGAA
265436 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTGTAA
Found at i:270176 original size:22 final size:21
Alignment explanation
Indices: 270139--270179 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
270129 CCATCTCCAT
*
270139 TTCATCATCAACACCATCATC
1 TTCATCATCAAAACCATCATC
270160 TTCATCCATCAAAACCATCA
1 TTCAT-CATCAAAACCATCA
270180 ATTCCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (21 bp):
TTCATCATCAAAACCATCATC
Found at i:270538 original size:6 final size:6
Alignment explanation
Indices: 270515--270565 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
270505 AAAAATTCAG
** *
270515 AAAAGA ATAAATGA AAAAGA AAAAGA AAAA-A AAATCA AAAAGA GAAAGA
1 AAAAGA A-AAA-GA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
270564 AA
1 AA
270566 GCCAAGGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
5 4 0.11
6 24 0.65
7 6 0.16
8 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (6 bp):
AAAAGA
Found at i:270549 original size:23 final size:25
Alignment explanation
Indices: 270482--270565 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 25
270472 ATTAGAGTGC
*
270482 AAAAAGAAAAGAA-AAGA-CAAAAAA
1 AAAAAGAAAAGAATAA-ATCAAAAAG
*
270506 AAAATTCAGAAAAGAATAAATGAAAAAG
1 AAAA---AGAAAAGAATAAATCAAAAAG
270534 AAAAAGAAAA-AA-AAATCAAAAAG
1 AAAAAGAAAAGAATAAATCAAAAAG
*
270557 AGAAAGAAA
1 AAAAAGAAA
270566 GCCAAGGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 18 0.35
24 6 0.12
25 6 0.12
27 10 0.20
28 11 0.22
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (25 bp):
AAAAAGAAAAGAATAAATCAAAAAG
Found at i:279997 original size:21 final size:21
Alignment explanation
Indices: 279958--280001 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
279948 GCCATCTCTA
279958 TCCTTTCTTTATTTCATTTCAT
1 TCCTTTCTTTA-TTCATTTCAT
279980 TCCTTATCTTTA-TCATTTCAT
1 TCCTT-TCTTTATTCATTTCAT
280001 T
1 T
280002 AATCTTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (21 bp):
TCCTTTCTTTATTCATTTCAT
Found at i:280224 original size:14 final size:14
Alignment explanation
Indices: 280205--280234 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
280195 AGGATTCAGC
280205 CATGAAGATACATT
1 CATGAAGATACATT
*
280219 CATGAAGATATATT
1 CATGAAGATACATT
280233 CA
1 CA
280235 GTATATCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
CATGAAGATACATT
Found at i:283185 original size:19 final size:20
Alignment explanation
Indices: 283161--283211 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
283151 CAGCCAAGAG
* * *
283161 CATGTATATTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAC
283180 CATGTATTTTCATAAAAAAC
1 CATGTATTTTCATAAAAAAC
283200 CATGTATTTTCA
1 CATGTATTTTCA
283212 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAC
Found at i:284057 original size:5 final size:5
Alignment explanation
Indices: 284042--284093 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
284032 TTGGAGTGCA
* *
284042 AAAAG -AAAG AAAAG AAAAAG AAGAATC AAAAG AAAAG AAAAG AGAAG
1 AAAAG AAAAG AAAAG -AAAAG AA-AA-G AAAAG AAAAG AAAAG AAAAG
284089 AAAAG
1 AAAAG
284094 TTGCAAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.10
5 24 0.62
6 9 0.23
7 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:288953 original size:18 final size:17
Alignment explanation
Indices: 288912--288953 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
288902 GCAAAGGAAA
288912 AAGAAACACTCAAAAAG
1 AAGAAACACTCAAAAAG
*
288929 ATTGAAAGCACTCAAAAAG
1 A-AGAAA-CACTCAAAAAG
288948 AAGAAA
1 AAGAAA
288954 AAGAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 8 0.38
19 12 0.57
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (17 bp):
AAGAAACACTCAAAAAG
Found at i:291718 original size:13 final size:12
Alignment explanation
Indices: 291700--291729 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
291690 TGGCCAAAGA
291700 TGAAAAGGTATG
1 TGAAAAGGTATG
291712 TTGAAAAGGTATG
1 -TGAAAAGGTATG
291725 TGAAA
1 TGAAA
291730 GATGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAAAGGTATG
Found at i:294058 original size:19 final size:20
Alignment explanation
Indices: 294034--294084 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
294024 TGACCAAGAG
* *
294034 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
294053 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
294073 CATGTATTTTCA
1 CATGTATTTTCA
294085 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:294462 original size:17 final size:17
Alignment explanation
Indices: 294440--294480 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
294430 ACATCATCAA
294440 CTTCCATATCACGCCAT
1 CTTCCATATCACGCCAT
*
294457 CTTCCATATCATGCCAT
1 CTTCCATATCACGCCAT
294474 CTTCCAT
1 CTTCCAT
294481 CTCCATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.22, C:0.39, G:0.05, T:0.34
Consensus pattern (17 bp):
CTTCCATATCACGCCAT
Found at i:294954 original size:11 final size:11
Alignment explanation
Indices: 294938--294962 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
294928 AAGAAGAATC
294938 AAAAGAAAAGA
1 AAAAGAAAAGA
294949 AAAAGAAAAGA
1 AAAAGAAAAGA
294960 AAA
1 AAA
294963 GTTACAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:297183 original size:19 final size:20
Alignment explanation
Indices: 297145--297183 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
297135 ATCATTCACT
*
297145 TGCATACTATATGATTTTCA
1 TGCATAATATATGATTTTCA
297165 TGCATAATATATG-TTTTCA
1 TGCATAATATATGATTTTCA
297184 CATCTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (20 bp):
TGCATAATATATGATTTTCA
Found at i:298171 original size:19 final size:20
Alignment explanation
Indices: 298147--298197 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
298137 CGGCCAAGAG
* *
298147 CATGTATCTTCATTAAA-AT
1 CATGTATTTTCATCAAACAT
298166 CATGTATTTTCATCAAACAT
1 CATGTATTTTCATCAAACAT
298186 CATGTATTTTCA
1 CATGTATTTTCA
298198 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAACAT
Found at i:298571 original size:17 final size:17
Alignment explanation
Indices: 298549--298589 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
298539 ACATCACCAA
298549 CTTCCATATCACGCCAT
1 CTTCCATATCACGCCAT
*
298566 CTTCCATATCATGCCAT
1 CTTCCATATCACGCCAT
*
298583 ATTCCAT
1 CTTCCAT
298590 CTCCATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.37, G:0.05, T:0.34
Consensus pattern (17 bp):
CTTCCATATCACGCCAT
Found at i:298608 original size:24 final size:24
Alignment explanation
Indices: 298562--298608 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
298552 CCATATCACG
*
298562 CCATCTTCCATATCATGCCATATT
1 CCATCTTCCATATCACGCCATATT
*
298586 CCATC-TCCATTTCACGCCTATAT
1 CCATCTTCCATATCACGCC-ATAT
298609 AATCAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.36
Consensus pattern (24 bp):
CCATCTTCCATATCACGCCATATT
Done.