Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015258.1 Kokia drynarioides strain JFW-HI SEQ_130303, 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: 342652
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 809 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:11393 original size:27 final size:27
Alignment explanation
Indices: 11326--11389 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 27
11316 TGAGGAGTAA
*
11326 TCTGATTCTAGCTCAAAAGAGCGTTAT
1 TCTGATTCTGGCTCAAAAGAGCGTTAT
*
11353 TCTGATTTTGGCTC-AAAGAGCGTTAT
1 TCTGATTCTGGCTCAAAAGAGCGTTAT
11379 TCTGATTCTGG
1 TCTGATTCTGG
11390 GCTCGTAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 22 0.65
27 12 0.35
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (27 bp):
TCTGATTCTGGCTCAAAAGAGCGTTAT
Found at i:11416 original size:24 final size:25
Alignment explanation
Indices: 11383--11444 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
11373 CGTTATTCTG
* *
11383 ATTCTGGGCTCGTAAG-AGCTAACT
1 ATTCTAGGCTCGTAAGCAGCTAACC
* *
11407 GTTCTAGGCTCAT-AGCAGCTAACC
1 ATTCTAGGCTCGTAAGCAGCTAACC
11431 ATTCTAGGCTCGTA
1 ATTCTAGGCTCGTA
11445 TGAACTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (25 bp):
ATTCTAGGCTCGTAAGCAGCTAACC
Found at i:16399 original size:20 final size:20
Alignment explanation
Indices: 16374--16440 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
16364 TTAGGTATTG
* *
16374 TTTGGTAAATCCTTAGATAT
1 TTTGGTAAATCCTTACAAAT
*
16394 TTTGGTATAA-CCTTATAAAT
1 TTTGGTA-AATCCTTACAAAT
** *
16414 TTTAATAAATCTTTACAAAT
1 TTTGGTAAATCCTTACAAAT
16434 TTTGGTA
1 TTTGGTA
16441 TGTCAAAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTGGTAAATCCTTACAAAT
Found at i:16504 original size:20 final size:20
Alignment explanation
Indices: 16479--16584 Score: 92
Period size: 20 Copynumber: 5.2 Consensus size: 20
16469 GAGATCAAGA
16479 AAATCTTTAAAATTATTGGT
1 AAATCTTTAAAATTATTGGT
* *
16499 AAATCTTTAGAAGTATTGGT
1 AAATCTTTAAAATTATTGGT
* *
16519 AAATCTTTAGAAATTTTTGAT
1 AAATCTTTA-AAATTATTGGT
*
16540 AAATAC-TTAGATATT-TTGGT
1 AAAT-CTTTA-AAATTATTGGT
* *
16560 AAATCCCTCAAAA-TATTGGT
1 AAAT-CTTTAAAATTATTGGT
16580 AAATC
1 AAATC
16585 AATAGAAATA
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.03
20 47 0.66
21 21 0.30
22 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (20 bp):
AAATCTTTAAAATTATTGGT
Found at i:16543 original size:41 final size:40
Alignment explanation
Indices: 16479--16564 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 40
16469 GAGATCAAGA
*
16479 AAATCTTTAAAATTATTGGTAAAT-CTTTAGA-AGTATTGGT
1 AAATCTTTAAAATTATTGATAAATAC-TTAGATA-TATTGGT
* *
16519 AAATCTTTAGAAATTTTTGATAAATACTTAGATATTTTGGT
1 AAATCTTTA-AAATTATTGATAAATACTTAGATATATTGGT
16560 AAATC
1 AAATC
16565 CCTCAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
40 9 0.22
41 29 0.73
42 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (40 bp):
AAATCTTTAAAATTATTGATAAATACTTAGATATATTGGT
Found at i:16593 original size:20 final size:20
Alignment explanation
Indices: 16479--16600 Score: 88
Period size: 20 Copynumber: 6.0 Consensus size: 20
16469 GAGATCAAGA
*
16479 AAATCTTTA-AAATTATTGGT
1 AAATCATTAGAAA-TATTGGT
* *
16499 AAATCTTTAGAAGTATTGGT
1 AAATCATTAGAAATATTGGT
* * *
16519 AAATCTTTAGAAATTTTTGAT
1 AAATCATTAGAAA-TATTGGT
* *
16540 AAAT-ACTTAGATATTTTGGT
1 AAATCA-TTAGAAATATTGGT
* *
16560 AAATCCCTCA-AAATATTGGT
1 AAAT-CATTAGAAATATTGGT
*
16580 AAATCAATAGAAATATTGGT
1 AAATCATTAGAAATATTGGT
16600 A
1 A
16601 TGCAAAATTG
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.02
20 61 0.74
21 19 0.23
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (20 bp):
AAATCATTAGAAATATTGGT
Found at i:16703 original size:20 final size:19
Alignment explanation
Indices: 16674--16753 Score: 106
Period size: 19 Copynumber: 4.2 Consensus size: 19
16664 ATTTTCGTAT
16674 AATCTTAAAAATTTCGATA
1 AATCTTAAAAATTTCGATA
*
16693 AATCTTAAAAATTTCAATA
1 AATCTTAAAAATTTCGATA
* *
16712 AATTCTTAAATATTTTGATA
1 AA-TCTTAAAAATTTCGATA
* *
16732 AATCTTAAAAAATTCAATA
1 AATCTTAAAAATTTCGATA
16751 AAT
1 AAT
16754 TCTTGAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 36 0.69
20 16 0.31
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.39
Consensus pattern (19 bp):
AATCTTAAAAATTTCGATA
Found at i:16763 original size:39 final size:39
Alignment explanation
Indices: 16676--16782 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 39
16666 TTTCGTATAA
* * *
16676 TCTTAAAAATTTCGATAAATCTTAAAAATTTCAATAAAT
1 TCTTAAATATTTTGATAAATCTTAAAAAATTCAATAAAT
16715 TCTTAAATATTTTGATAAATCTTAAAAAATTCAATAAAT
1 TCTTAAATATTTTGATAAATCTTAAAAAATTCAATAAAT
* * *
16754 TCTTGAATATTTTAATAAATTATTAAAAA
1 TCTTAAATATTTTGATAAA-TCTTAAAAA
16783 TATTGATAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 53 0.87
40 8 0.13
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (39 bp):
TCTTAAATATTTTGATAAATCTTAAAAAATTCAATAAAT
Found at i:16791 original size:20 final size:20
Alignment explanation
Indices: 16676--16783 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
16666 TTTCGTATAA
*
16676 TCTTAAAAATTTCGATAAA-
1 TCTTAAAAATTTCAATAAAT
16695 TCTTAAAAATTTCAATAAAT
1 TCTTAAAAATTTCAATAAAT
* **
16715 TCTTAAATATTTTGATAAA-
1 TCTTAAAAATTTCAATAAAT
*
16734 TCTTAAAAAATTCAATAAAT
1 TCTTAAAAATTTCAATAAAT
* * *
16754 TCTTGAATATTTTAATAAAT
1 TCTTAAAAATTTCAATAAAT
*
16774 TATTAAAAAT
1 TCTTAAAAAT
16784 ATTGATAACT
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
19 33 0.46
20 39 0.54
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (20 bp):
TCTTAAAAATTTCAATAAAT
Found at i:18573 original size:88 final size:88
Alignment explanation
Indices: 18415--18579 Score: 233
Period size: 88 Copynumber: 1.9 Consensus size: 88
18405 GCACTGCCTG
* * *
18415 GTGTGATATTTGTATGTGTTTCATGGAAGCATTGAGAGAACAGGAAGGTTACTTGTCCAAAGAGA
1 GTGTGATATTTGGATGTGTTTCATGGAAACACTGAGAGAACAGGAAGGTTACTTGTCCAAAGAGA
*
18480 AAAGAGAGAAGGGTTACTGTCCA
66 AAAGAGAAAAGGGTTACTGTCCA
* * * *
18503 GTGTGATATTTGGATGTGTTTCATTGAAACACTGAGTGAACAGGAAGGTTAGTTGTCCTCAA-AG
1 GTGTGATATTTGGATGTGTTTCATGGAAACACTGAGAGAACAGGAAGGTTACTTGTCC-AAAGAG
*
18567 ACAAGAGAAAAGG
65 AAAAGAGAAAAGG
18580 AAGGTTATAG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 65 0.97
89 2 0.03
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (88 bp):
GTGTGATATTTGGATGTGTTTCATGGAAACACTGAGAGAACAGGAAGGTTACTTGTCCAAAGAGA
AAAGAGAAAAGGGTTACTGTCCA
Found at i:23492 original size:31 final size:31
Alignment explanation
Indices: 23457--23519 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
23447 AGTACGTAGC
*
23457 ATCATTCCACAATAGGGGAATTCTTAGCCTG
1 ATCATTCCACAATAGGGCAATTCTTAGCCTG
23488 ATCATTCCACAATAGGGCAATTCTTAGCCTG
1 ATCATTCCACAATAGGGCAATTCTTAGCCTG
23519 A
1 A
23520 CTAATGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (31 bp):
ATCATTCCACAATAGGGCAATTCTTAGCCTG
Found at i:26821 original size:21 final size:21
Alignment explanation
Indices: 26797--26876 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
26787 TAGAAGTAAG
* *
26797 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCAGTAGAAGAGTC
26818 ACTTGTATCAGTAGAAGAGTC
1 ACTTGTATCAGTAGAAGAGTC
**
26839 ACTTGTATCAGTAGAACTGTC
1 ACTTGTATCAGTAGAAGAGTC
*
26860 A-TAGGTATCAGTAGAAG
1 ACT-TGTATCAGTAGAAG
26877 CCTGTATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 1 0.02
21 51 0.98
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (21 bp):
ACTTGTATCAGTAGAAGAGTC
Found at i:28021 original size:35 final size:34
Alignment explanation
Indices: 27965--28059 Score: 118
Period size: 35 Copynumber: 2.7 Consensus size: 34
27955 GGTTTAACAC
*
27965 AATGACATGTTTAACATGCGAATCAGAAACAGAAT
1 AATGGCATG-TTAACATGCGAATCAGAAACAGAAT
* **
28000 AATGGCATGCTTAACATGCGAATCATAGTCAGAAT
1 AATGGCATG-TTAACATGCGAATCAGAAACAGAAT
*
28035 AATAGCATGTCTAACATGCGAATCA
1 AATGGCATGT-TAACATGCGAATCA
28060 TAATTAGAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 1 0.02
35 52 0.98
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (34 bp):
AATGGCATGTTAACATGCGAATCAGAAACAGAAT
Found at i:28060 original size:35 final size:34
Alignment explanation
Indices: 27976--28091 Score: 135
Period size: 35 Copynumber: 3.4 Consensus size: 34
27966 ATGACATGTT
* * *
27976 TAACATGCGAATCAGAAACAGAATAATGGCATGC
1 TAACATGCGAATCATAATCAGAATAATAGCATGC
*
28010 TTAACATGCGAATCATAGTCAGAATAATAGCATGTC
1 -TAACATGCGAATCATAATCAGAATAATAGCATG-C
* *
28046 TAACATGCGAATCATAATTAGAATATTA-CATGC
1 TAACATGCGAATCATAATCAGAATAATAGCATGC
* *
28079 TCACATGTGAATC
1 TAACATGCGAATC
28092 GGAATATCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
33 12 0.17
34 4 0.06
35 54 0.76
36 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (34 bp):
TAACATGCGAATCATAATCAGAATAATAGCATGC
Found at i:28291 original size:35 final size:35
Alignment explanation
Indices: 28247--28360 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 35
28237 TTTTAACGAG
28247 CATGCGAATCAGAAAT-AGAATAAT-GACATGCTTAA
1 CATGCGAATCA-AAATCAGAATAATAG-CATGCTTAA
* * * *
28282 CATGTGAATCATAGTCAGAATAATAGCATGTTTAA
1 CATGCGAATCAAAATCAGAATAATAGCATGCTTAA
* * * *
28317 CATGCGAATCATAATCAAAATATTA-CATGC-TCA
1 CATGCGAATCAAAATCAGAATAATAGCATGCTTAA
28350 CATGCGAATCA
1 CATGCGAATCA
28361 GAATATCAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
33 13 0.19
34 6 0.09
35 47 0.70
36 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (35 bp):
CATGCGAATCAAAATCAGAATAATAGCATGCTTAA
Found at i:34378 original size:16 final size:17
Alignment explanation
Indices: 34344--34383 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34334 ACATGCATGG
*
34344 CATAAATTTAATGATTA
1 CATAAATTTAATAATTA
34361 CATAAATTTAA-AATTA
1 CATAAATTTAATAATTA
*
34377 CAAAAAT
1 CATAAAT
34384 AAAATTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (17 bp):
CATAAATTTAATAATTA
Found at i:46386 original size:17 final size:17
Alignment explanation
Indices: 46364--46398 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
46354 CACTAACATT
*
46364 AAAATGCAATGACAATG
1 AAAATGCAACGACAATG
46381 AAAATGCAACGACAATG
1 AAAATGCAACGACAATG
46398 A
1 A
46399 TTACTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.14
Consensus pattern (17 bp):
AAAATGCAACGACAATG
Found at i:47733 original size:38 final size:38
Alignment explanation
Indices: 47644--47718 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
47634 ACATTTCTAA
* * *
47644 ACATCGTCATGCAGTGACAAGTTTGGGCGCAATTTTGG
1 ACATAGTCATGCAGTGACAAGTTTGGACGCAATTCTGG
* *
47682 ACATTGTCATGCAGTGACAATTTTGGACGCAATTCTG
1 ACATAGTCATGCAGTGACAAGTTTGGACGCAATTCTG
47719 AATAGATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (38 bp):
ACATAGTCATGCAGTGACAAGTTTGGACGCAATTCTGG
Found at i:55087 original size:28 final size:29
Alignment explanation
Indices: 55033--55087 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
55023 TTTTACAGTT
*
55033 TTTTTTTTAAATTTATATACTTGTTTTAA
1 TTTTTTTTAAATTTATATACTTATTTTAA
* *
55062 TTTTTTTTAATTTTCTATA-TTATTTT
1 TTTTTTTTAAATTTATATACTTATTTT
55088 GACATTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTTTTTTAAATTTATATACTTATTTTAA
Found at i:59518 original size:20 final size:20
Alignment explanation
Indices: 59493--59538 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
59483 CTCATTTATT
59493 TATATAAATACATTAAT-AAA
1 TATATAAATACA-TAATAAAA
*
59513 TATATAAATATATAATAAAA
1 TATATAAATACATAATAAAA
59533 TATATA
1 TATATA
59539 TTATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TATATAAATACATAATAAAA
Found at i:59940 original size:2 final size:2
Alignment explanation
Indices: 59935--59973 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
59925 TAAAAAAAAA
59935 AT AT AT AT 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 AT AT AT AT A
59974 AATTAATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60645 original size:126 final size:126
Alignment explanation
Indices: 60385--61004 Score: 690
Period size: 126 Copynumber: 4.8 Consensus size: 126
60375 TTTTGGTCTA
* * ** *
60385 ACACTTTCCTAAGTGTTGGGATAGAGTTGTCGACATACATTTTGGCCAACTCTTTTGTATAAAGG
1 ACACTTTCCTAAGTGTTGGGATAGATTTGCCGACATACGCTTTGGCCAACTC-TTTGTATAAGGG
*
60450 TTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCAGCTTTGTCCAACA-TAT-TCCG
65 TTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTATGT-CG
* *
60511 ACACTTTCCTAAGTGTTGGGATAGATTTGCCGACATACGCTTTAGTCAACTCTTTGTATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGATTTGCCGACATACGCTTTGGCCAACTCTTTGTATAAGGGT
* * * *
60576 TGGGATATGCATGCTTAAGGTAACGCTTAAATAATAGTCGGCTTTGTCCAACACTATGTTG
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTATGTCG
* * **
60637 ACACTTTCCCAAGTGTT-GGTTAGAGTTT-CTAACATACGCTTTGGCCAACTCTTTGTATAAGGG
1 ACACTTTCCTAAGTGTTGGGATAGA-TTTGCCGACATACGCTTTGGCCAACTCTTTGTATAAGGG
*** * *
60700 TTGGGATATGCATGCCTAATATAACGCTTAAATAAAAGTCGGCTTTGTTCAACACTATGCCGGCA
65 TTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTAT----G--
60765 CCTTTAGGCCG
124 ----T----CG
* * * * * * *** *
60776 ACAATTTCCTAAGTGTTGGGATAGATTTGTCGGCACAAGTTTTGAATAACTTTTTGTATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGATTTGCCGACATACGCTTTGGCCAACTCTTTGTATAAGGGT
* *
60841 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAATCGGTTTTGTCCAACACTATGTCG
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTATGTCG
* * *** *
60902 ACACTTTCCTAAGTGTTGAGATAGACTTGGTAACATACGCTTCGGCCAACTCTTTGTATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGATTTGCCGACATACGCTTTGGCCAACTCTTTGTATAAGGGT
* *
60967 TGTGATATGCATGCCTAAGGCAACACTTAAATAAGAGT
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
61005 TGGCAAATTA
Statistics
Matches: 412, Mismatches: 63, Indels: 38
0.80 0.12 0.07
Matches are distributed among these distances:
125 151 0.37
126 156 0.38
127 1 0.00
129 1 0.00
130 1 0.00
135 1 0.00
136 1 0.00
139 19 0.05
140 81 0.20
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (126 bp):
ACACTTTCCTAAGTGTTGGGATAGATTTGCCGACATACGCTTTGGCCAACTCTTTGTATAAGGGT
TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAACACTATGTCG
Found at i:60998 original size:391 final size:391
Alignment explanation
Indices: 60276--61000 Score: 1037
Period size: 391 Copynumber: 1.9 Consensus size: 391
60266 TATACTTGCC
* *
60276 AACATACGCTTTAATCAACTCTTTGTATAAGGGTTGGGATATGCATGCCCTAGACAATGCTTAAA
1 AACATACGCTTTAACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCCTAGACAACGCTTAAA
* * * *
60341 TAAAAGTTGACTTTGTCCAACACTACGCCGACACTTTTGGTCTAACACTTTCCTAAGTGTTGGGA
66 TAAAAGTCGACTTTGTCCAACACTACGCCGACACTTTAGGTCCAACAATTTCCTAAGTGTTGGGA
* **
60406 TAGAGTTGTCGACATACATTTTGGCCAACTCTTTTGTATAAAGGTTGGGATATGCATGCCTAAGG
131 TAGAGTTGTCGACACACATTTTGAACAACTCTTTTGTATAAAGGTTGGGATATGCATGCCTAAGG
* *
60471 CAACGCTTAAATAAGAGTCAGCTTTGTCCAACATATTCCGACACTTTCCTAAGTGTTGGGATAGA
196 CAACGCTTAAATAAGAATCAGCTTTGTCCAACATATTCCGACACTTTCCTAAGTGTTGAGATAGA
* * * * * * *
60536 TTTGCCGACATACGCTTTAGTCAACTCTTTGTATAAGGGTTGGGATATGCATGCTTAAGGTAACG
261 CTTGCCAACATACGCTTCAGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACA
60601 CTTAAATAATAGTCGGCTTTGTCCAACACTATGTTGACACTTTCCCAAGTGTTGGTTAGAGTTTC
326 CTTAAATAATAGTCGGCTTTGTCCAACACTATGTTGACACTTTCCCAAGTGTTGGTTAGAGTTTC
60666 T
391 T
** * *
60667 AACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATG-CCTAATATAACGCTTAA
1 AACATACGCTTTAACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCCT-AGACAACGCTTAA
* * * * *
60731 ATAAAAGTCGGCTTTGTTCAACACTATGCCGGCACCTTTAGG-CCGACAATTTCCTAAGTGTTGG
65 ATAAAAGTCGACTTTGTCCAACACTACGCCGACA-CTTTAGGTCCAACAATTTCCTAAGTGTTGG
* * * *
60795 GATAGATTTGTCGGCACA-AGTTTTGAATAACT-TTTTGTATAAGGGTTGGGATATGCATGCCTA
129 GATAGAGTTGTCGACACACA-TTTTGAACAACTCTTTTGTATAAAGGTTGGGATATGCATGCCTA
* *
60858 AGGCAACGCTTAAATAAGAATCGGTTTTGTCCAACACTATGT-CGACACTTTCCTAAGTGTTGAG
193 AGGCAACGCTTAAATAAGAATCAGCTTTGTCCAACA-TAT-TCCGACACTTTCCTAAGTGTTGAG
** * *
60922 ATAGACTTGGTAACATACGCTTCGGCCAACTCTTTGTATAAGGGTTGTGATATGCATGCCTAAGG
256 ATAGACTTGCCAACATACGCTTCAGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGG
60987 CAACACTTAAATAA
321 CAACACTTAAATAA
61001 GAGTTGGCAA
Statistics
Matches: 292, Mismatches: 37, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
390 67 0.23
391 218 0.75
392 7 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (391 bp):
AACATACGCTTTAACCAACTCTTTGTATAAGGGTTGGGATATGCATGCCCTAGACAACGCTTAAA
TAAAAGTCGACTTTGTCCAACACTACGCCGACACTTTAGGTCCAACAATTTCCTAAGTGTTGGGA
TAGAGTTGTCGACACACATTTTGAACAACTCTTTTGTATAAAGGTTGGGATATGCATGCCTAAGG
CAACGCTTAAATAAGAATCAGCTTTGTCCAACATATTCCGACACTTTCCTAAGTGTTGAGATAGA
CTTGCCAACATACGCTTCAGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACA
CTTAAATAATAGTCGGCTTTGTCCAACACTATGTTGACACTTTCCCAAGTGTTGGTTAGAGTTTC
T
Found at i:61325 original size:21 final size:21
Alignment explanation
Indices: 61301--61351 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
61291 TTTTATATTG
* * *
61301 AACCTTGAATTTAGAAACCTA
1 AACCTTAAACTTAGAAACCCA
*
61322 AACCTTAAACTTAGAATCCCA
1 AACCTTAAACTTAGAAACCCA
*
61343 AACCATAAA
1 AACCTTAAA
61352 ACTATAGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (21 bp):
AACCTTAAACTTAGAAACCCA
Found at i:71921 original size:17 final size:17
Alignment explanation
Indices: 71889--71922 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
71879 AAATTGCCCC
* *
71889 TTTAATTTATTTCTTTT
1 TTTAATTTAGTCCTTTT
71906 TTTAATTTAGTCCTTTT
1 TTTAATTTAGTCCTTTT
71923 ACCTTTGGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTAATTTAGTCCTTTT
Found at i:72042 original size:30 final size:30
Alignment explanation
Indices: 72006--72134 Score: 179
Period size: 30 Copynumber: 4.3 Consensus size: 30
71996 TTAAAAAATG
**
72006 CATTTTGACTCCTAAACTTTTTTAAAATTA
1 CATTTTGACTCCTAAACTTTCCTAAAATTA
72036 CATTTTGACT-CTCAAACTTTCCTAAAATTA
1 CATTTTGACTCCT-AAACTTTCCTAAAATTA
* * *
72066 CATTTTGACCCCTTAACTTTCCCAAAATTA
1 CATTTTGACTCCTAAACTTTCCTAAAATTA
*
72096 CATTTTGACTCTTAAACTTTCCTAAAATTA
1 CATTTTGACTCCTAAACTTTCCTAAAATTA
*
72126 TATTTTGAC
1 CATTTTGAC
72135 CCCCAAAATT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 2 0.02
30 83 0.95
31 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.43
Consensus pattern (30 bp):
CATTTTGACTCCTAAACTTTCCTAAAATTA
Found at i:72070 original size:60 final size:60
Alignment explanation
Indices: 72006--72165 Score: 205
Period size: 60 Copynumber: 2.6 Consensus size: 60
71996 TTAAAAAATG
*
72006 CATTTTGACTCCTAAACTTTTTTAAAATTACATTTTGACTCTCAAACTTTCCTAAAATTA
1 CATTTTGACCCCTAAACTTTTTTAAAATTACATTTTGACTCTCAAACTTTCCTAAAATTA
* *** *
72066 CATTTTGACCCCTTAACTTTCCCAAAATTACATTTTGACTCTTAAACTTTCCTAAAATTA
1 CATTTTGACCCCTAAACTTTTTTAAAATTACATTTTGACTCTCAAACTTTCCTAAAATTA
* * * *
72126 TATTTTGACCCCCAAAATTCTTTAAAACTT-CAATTTTGAC
1 CATTTTGACCCCTAAACTTTTTTAAAA-TTAC-ATTTTGAC
72166 CTTGTTTTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
60 74 0.88
61 10 0.12
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.41
Consensus pattern (60 bp):
CATTTTGACCCCTAAACTTTTTTAAAATTACATTTTGACTCTCAAACTTTCCTAAAATTA
Found at i:75028 original size:38 final size:38
Alignment explanation
Indices: 74953--75029 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 38
74943 TATTACACAC
*
74953 ATATAACATACAATAAATAATTAAAATATGTGTTTTAA
1 ATATAACATACAATAAATAATTAAAATATGTGGTTTAA
*
74991 ATATAACATATAATAAATAA-TAAAA-ATGTAAGGTTTAA
1 ATATAACATACAATAAATAATTAAAATATGT--GGTTTAA
75029 A
1 A
75030 ATTAATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 4 0.11
37 5 0.14
38 26 0.74
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (38 bp):
ATATAACATACAATAAATAATTAAAATATGTGGTTTAA
Found at i:77715 original size:237 final size:240
Alignment explanation
Indices: 77293--77770 Score: 811
Period size: 237 Copynumber: 2.0 Consensus size: 240
77283 TAAAGGTTGT
* *
77293 TTTTTGTGTGTGTGTTTTTATACTTTTCCAATGTTTTGGCTGCTATTGGGTTTTTTTGCTTTGTA
1 TTTTTGTGTGTGTGTTTTTATACTTTTCCAATGCTTTGGCTGCCATTGGGTTTTTTTGCTTTGTA
* *
77358 GAACTTCTCTTTATGTTTAGAATAATAGCATGAAAGTTTTTCTTATAGAAAGGAACTTTTGTATG
66 GAACTTCTCTTTATGTTTAGAATAATAGCATGAAACTTTTTCTTATAGAAAGGAACGTTTGTATG
*
77423 TATATCTTATTATCTTGATCAGTTTATTCCAATTTGGTAAAAGCAAAATGAAACTTGACTGTT-T
131 TATATCTTATTATCTTGATCAGTTTATTCCAATTTGGTAAAAGCAAAATGAAACTTGACTGTTAA
*
77487 ATTTCAATCAAATAATTATATTTACAAGCTTCACTAAAAAAACAA
196 ATTTCAATCAAATAATTATATTAACAAGCTTCACTAAAAAAACAA
*
77532 TTTTT-TGTGTGT-TTTTTATACTTTTCCAATGCTTTGGCTGCCATTTGG-TTTTTTGCTTTGTA
1 TTTTTGTGTGTGTGTTTTTATACTTTTCCAATGCTTTGGCTGCCATTGGGTTTTTTTGCTTTGTA
* *
77594 GAACTTCTCTTTATGTTTAGAATAATAGCATTTACACTTTTTCTTATAGAAAGGAACGTTTGTAT
66 GAACTTCTCTTTATGTTTAGAATAATAGCA-TGAAACTTTTTCTTATAGAAAGGAACGTTTGTAT
* *
77659 GTATTTCTTATTATCTTGATCAGTTTATTCCAATTTGGTAAAAGCAAATTGAAACTTGACTGTTA
130 GTATATCTTATTATCTTGATCAGTTTATTCCAATTTGGTAAAAGCAAAATGAAACTTGACTGTTA
*
77724 AATTTCAATCAAATAATTATATTAACAAGCTTCACTACAAAAACAA
195 AATTTCAATCAAATAATTATATTAACAAGCTTCACTAAAAAAACAA
77770 T
1 T
77771 GCAGGGATTA
Statistics
Matches: 225, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
236 44 0.20
237 125 0.56
238 51 0.23
239 5 0.02
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (240 bp):
TTTTTGTGTGTGTGTTTTTATACTTTTCCAATGCTTTGGCTGCCATTGGGTTTTTTTGCTTTGTA
GAACTTCTCTTTATGTTTAGAATAATAGCATGAAACTTTTTCTTATAGAAAGGAACGTTTGTATG
TATATCTTATTATCTTGATCAGTTTATTCCAATTTGGTAAAAGCAAAATGAAACTTGACTGTTAA
ATTTCAATCAAATAATTATATTAACAAGCTTCACTAAAAAAACAA
Found at i:82745 original size:275 final size:266
Alignment explanation
Indices: 82263--82774 Score: 745
Period size: 275 Copynumber: 1.9 Consensus size: 266
82253 AATGAGCTAC
* **
82263 TTACAGAATCACGTCTACCTAAAGAAGTAACACAACATACTTTTGATAATGTTGACCTTGCCAAG
1 TTACAGAATCACGTCTACCTAAAGAAGCAACACAACATACTTTTGATAATGTTGACAATGCCAAG
* * *
82328 CATGATGCGGGTGAGTTCCATGATGCCAATTCTGATCAGCAATGGCGACAAGTATTTGAATACAA
66 CATGATGCAGGTAAGTTCAATGATGCCAATTCTGATCAGCAATGGCGACAAGTATTTGAATACAA
*** *
82393 CAGTGAAGATGGTGAGTTATCAAAGCTTGAAGAAAACTCTTCATGGTTCTCCGGATATGATAGTT
131 CAGTGAAGATCACGAGTTATCAAAGCTTGAAGAAAACTCGTCATGGTTCTCCGGATATGATAGTT
82458 GCAATATTTAGATCACATCTAACTGCAGAATCATGTATGTATTATTAGTAACAGTTTCTCTCACG
196 GCAATATTTAGATCACATCTAACTGCAGAATCATGTATGTATTATTAGTAACAGTTTCTCTCACG
82523 TTTAAT
261 TTTAAT
* *
82529 TTACAGAATCATGTCTACCTAAAGAAGCAATACAACATACTTTTGATAATGTTGACAATGCCAAG
1 TTACAGAATCACGTCTACCTAAAGAAGCAACACAACATACTTTTGATAATGTTGACAATGCCAAG
* *
82594 CATGATGCAGGTAAGTTCAATGATGTCAATGATACTTATCAGCAATGGCGACAAGTATTTGAACC
66 CATGATGCAGGTAAGTTCAATGATGCCAAT--T-CTGATCAGCAATGGCGACAAGTATTTG-A--
* ** **
82659 ATTCTATAGTGGTGAAGATCACGAGTTATCAAAGCTTGAAGAAAACTCGTCATGGTTCTTTGGAT
125 ATAC-A-A-CAGTGAAGATCACGAGTTATCAAAGCTTGAAGAAAACTCGTCATGGTTCTCCGGAT
* * *
82724 ATGATCGTTGCAATATTTAGATCACGTTTAACTGCAGAATCATGTATGTAT
187 ATGATAGTTGCAATATTTAGATCACATCTAACTGCAGAATCATGTATGTAT
82775 ACTAACAGTT
Statistics
Matches: 215, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
266 86 0.40
268 1 0.00
269 26 0.12
270 1 0.00
272 3 0.01
273 1 0.00
274 1 0.00
275 96 0.45
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (266 bp):
TTACAGAATCACGTCTACCTAAAGAAGCAACACAACATACTTTTGATAATGTTGACAATGCCAAG
CATGATGCAGGTAAGTTCAATGATGCCAATTCTGATCAGCAATGGCGACAAGTATTTGAATACAA
CAGTGAAGATCACGAGTTATCAAAGCTTGAAGAAAACTCGTCATGGTTCTCCGGATATGATAGTT
GCAATATTTAGATCACATCTAACTGCAGAATCATGTATGTATTATTAGTAACAGTTTCTCTCACG
TTTAAT
Found at i:91304 original size:42 final size:42
Alignment explanation
Indices: 91258--91353 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
91248 AATTAAAAAT
*
91258 AATATGAGTGGGCTTAAAATGAGCTTGAGTTAATCTTTTGCA
1 AATATGAGTGGGCTTAAAATAAGCTTGAGTTAATCTTTTGCA
* *
91300 AATATGGGTGGGCTTAAAATAAGCTTGAGTTAGTCTTTTGCA
1 AATATGAGTGGGCTTAAAATAAGCTTGAGTTAATCTTTTGCA
91342 AATATGAGTGGG
1 AATATGAGTGGG
91354 TTTGAGCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.34
Consensus pattern (42 bp):
AATATGAGTGGGCTTAAAATAAGCTTGAGTTAATCTTTTGCA
Found at i:96326 original size:27 final size:27
Alignment explanation
Indices: 96256--96328 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
96246 TGTTGTAAAT
* * *
96256 GTGGGAAGTCTGCAAAGATTATCTAAT
1 GTGGGAAGTCTGCAAGGACTATCTAAC
* *
96283 GTGGGAAGTCCGTAAGGACTATCTAAC
1 GTGGGAAGTCTGCAAGGACTATCTAAC
96310 GTGGGAAGTCTGCAAGGAC
1 GTGGGAAGTCTGCAAGGAC
96329 CTTGTAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (27 bp):
GTGGGAAGTCTGCAAGGACTATCTAAC
Found at i:98345 original size:51 final size:51
Alignment explanation
Indices: 98285--98471 Score: 232
Period size: 51 Copynumber: 3.6 Consensus size: 51
98275 CTATAAACGA
* * *
98285 AAAGGTCCGATGACTAAGTGTCATCGTGAATAAATGAATGCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * *
98336 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * * * **
98387 AAAGGTCTGATGACTTAGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTATGGATT
98439 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
98472 TTAAATGAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
51 80 0.69
52 9 0.08
53 26 0.22
54 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
Found at i:103534 original size:32 final size:31
Alignment explanation
Indices: 103506--103568 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 31
103496 TTAAAATTTG
103506 TTTAAAAAAATCATAAAAATTATAAAAATATAAA
1 TTTAAAAAAATC--AAAAATTATAAAAAT-TAAA
*
103540 TTTAAAAAAATCAAAATTTATAAAAATTA
1 TTTAAAAAAATCAAAAATTATAAAAATTA
103569 TTACGAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 2 0.07
32 14 0.50
34 12 0.43
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (31 bp):
TTTAAAAAAATCAAAAATTATAAAAATTAAA
Found at i:103550 original size:16 final size:17
Alignment explanation
Indices: 103506--103566 Score: 72
Period size: 16 Copynumber: 3.6 Consensus size: 17
103496 TTAAAATTTG
103506 TTTAAAAAAATCATAAAA
1 TTTAAAAAAATCAT-AAA
* *
103524 ATTATAAAAAT-ATAAA
1 TTTAAAAAAATCATAAA
103540 TTTAAAAAAATCA-AAA
1 TTTAAAAAAATCATAAA
*
103556 TTTATAAAAAT
1 TTTAAAAAAAT
103567 TATTACGAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 25 0.68
17 3 0.08
18 9 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TTTAAAAAAATCATAAA
Found at i:105263 original size:12 final size:12
Alignment explanation
Indices: 105243--105286 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
105233 GAAAAACTTC
105243 ATATGTATCTAT
1 ATATGTATCTAT
* * *
105255 TTCTGTATCCAT
1 ATATGTATCTAT
105267 ATATGTATCTAT
1 ATATGTATCTAT
*
105279 ATTTGTAT
1 ATATGTAT
105287 GTGAATCAGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.52
Consensus pattern (12 bp):
ATATGTATCTAT
Found at i:109051 original size:8 final size:8
Alignment explanation
Indices: 109038--109084 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
109028 ATTGTGCTTT
109038 TATACATA
1 TATACATA
109046 TATAC--A
1 TATACATA
109052 TATACATA
1 TATACATA
*
109060 TATATATA
1 TATACATA
* *
109068 TACATATA
1 TATACATA
109076 TATACATA
1 TATACATA
109084 T
1 T
109085 TTTTTCTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 6 0.18
8 27 0.82
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (8 bp):
TATACATA
Found at i:109074 original size:10 final size:10
Alignment explanation
Indices: 109043--109084 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
109033 GCTTTTATAC
109043 ATATATACAT
1 ATATATACAT
* *
109053 ATACATATAT
1 ATATATACAT
109063 ATATATACAT
1 ATATATACAT
109073 ATATATACAT
1 ATATATACAT
109083 AT
1 AT
109085 TTTTTCTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATACAT
Found at i:109078 original size:14 final size:14
Alignment explanation
Indices: 109038--109079 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
109028 ATTGTGCTTT
*
109038 TATACATATATACA
1 TATACATATATATA
109052 TATACATATATATA
1 TATACATATATATA
109066 TATACATATATATA
1 TATACATATATATA
109080 CATATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
TATACATATATATA
Found at i:114017 original size:18 final size:18
Alignment explanation
Indices: 113979--114017 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
113969 TGTATCTGTC
*
113979 TCTATATCCGTATATGCA
1 TCTATATCCGTATATGAA
* *
113997 TCTATATCTGTATGTGAA
1 TCTATATCCGTATATGAA
114015 TCT
1 TCT
114018 GTTTATCTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (18 bp):
TCTATATCCGTATATGAA
Found at i:114504 original size:40 final size:40
Alignment explanation
Indices: 114460--114593 Score: 118
Period size: 40 Copynumber: 3.4 Consensus size: 40
114450 AATCTTTATT
*
114460 GTGTCATTGCTAGTT-TGATAGTAATATCGCAATGTTTACA
1 GTGTCATTGCTAGTTATGATAGTAATAT-GTAATGTTTACA
114500 GTGTCATTG-TCAGTTCAATGATAGT-AT-TGTAATGTTTACA
1 GTGTCATTGCT-AGTT--ATGATAGTAATATGTAATGTTTACA
* * * * * *
114540 GTGTCACTGCCAGTTCTG-TAATAATATTGTAGTGTTTATA
1 GTGTCATTGCTAGTTATGATAGTAATA-TGTAATGTTTACA
114580 GTGTCATTGC-AGTT
1 GTGTCATTGCTAGTT
114594 CGGTTGTAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 17
0.76 0.08 0.17
Matches are distributed among these distances:
37 3 0.04
38 4 0.05
39 5 0.06
40 56 0.72
41 1 0.01
42 2 0.03
43 7 0.09
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (40 bp):
GTGTCATTGCTAGTTATGATAGTAATATGTAATGTTTACA
Found at i:114622 original size:39 final size:40
Alignment explanation
Indices: 114421--114627 Score: 110
Period size: 40 Copynumber: 5.2 Consensus size: 40
114411 ATGTTTTCAA
* * * * * * **
114421 TGTCACGGCTAGTTCAGTAATAATATTACAATCTTTATTG
1 TGTCACTGCCAGTTCGGTAATAATATTGCAGTATTTACAG
* * * * * * * *
114461 TGTCATTGCTAGTTTGATAGTAATATCGCAATGTTTACAG
1 TGTCACTGCCAGTTCGGTAATAATATTGCAGTATTTACAG
* * ** * * * * *
114501 TGTCATTGTCAGTTCAATGATAGTATTGTAATGTTTACAG
1 TGTCACTGCCAGTTCGGTAATAATATTGCAGTATTTACAG
* * * *
114541 TGTCACTGCCAGTTCTGTAATAATATTGTAGTGTTTATAG
1 TGTCACTGCCAGTTCGGTAATAATATTGCAGTATTTACAG
* ** *
114581 TGTCATTG-CAGTTCGGTTGTAATCTTGCAGTATTTACAG
1 TGTCACTGCCAGTTCGGTAATAATATTGCAGTATTTACAG
114620 TGTCACTG
1 TGTCACTG
114628 TCAATTCTGT
Statistics
Matches: 130, Mismatches: 37, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
39 31 0.24
40 99 0.76
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (40 bp):
TGTCACTGCCAGTTCGGTAATAATATTGCAGTATTTACAG
Found at i:116954 original size:17 final size:16
Alignment explanation
Indices: 116934--116998 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
116924 ATTGTTCACT
116934 TTTTATATATTTTTAAA
1 TTTTATATATTTTT-AA
*
116951 TTTTATA-AATTTTAA
1 TTTTATATATTTTTAA
*
116966 TATTTGTAT-TTTTTAA
1 T-TTTATATATTTTTAA
*
116982 TAATTATAATATTTTTA
1 T-TTTAT-ATATTTTTA
116999 TAATTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.08
16 21 0.54
17 9 0.23
18 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTATATATTTTTAA
Found at i:116968 original size:25 final size:26
Alignment explanation
Indices: 116934--117015 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 26
116924 ATTGTTCACT
116934 TTTTATATATTTTTAAATTTTATA-AA
1 TTTTA-ATATTTTTAAATTTTATATAA
* **
116960 TTTTAATATTTGTATTTTTTA-ATAA
1 TTTTAATATTTTTAAATTTTATATAA
* *
116985 TTATAATATTTTTATAATTTTTTATAA
1 TTTTAATATTTTTA-AATTTTATATAA
117012 TTTT
1 TTTT
117016 TTATAATTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
24 1 0.02
25 27 0.61
26 9 0.20
27 7 0.16
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTAATATTTTTAAATTTTATATAA
Found at i:117004 original size:9 final size:9
Alignment explanation
Indices: 116933--117024 Score: 61
Period size: 10 Copynumber: 10.3 Consensus size: 9
116923 TATTGTTCAC
116933 TTTTTATATA
1 TTTTTATA-A
116943 TTTTTA-AA
1 TTTTTATAA
116951 -TTTTATAA
1 TTTTTATAA
*
116959 ATTTTA-ATA
1 TTTTTATA-A
*
116968 TTTGTAT--
1 TTTTTATAA
116975 TTTTTAATAA
1 TTTTT-ATAA
* *
116985 TTATAAT-A
1 TTTTTATAA
116993 TTTTTATAA
1 TTTTTATAA
117002 TTTTTTATAA
1 -TTTTTATAA
117012 TTTTTTATAA
1 -TTTTTATAA
117022 TTT
1 TTT
117025 AACCACGTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 19
0.72 0.08 0.21
Matches are distributed among these distances:
7 9 0.14
8 12 0.18
9 17 0.26
10 28 0.42
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:117021 original size:10 final size:10
Alignment explanation
Indices: 116985--117024 Score: 71
Period size: 10 Copynumber: 3.9 Consensus size: 10
116975 TTTTTAATAA
116985 TTATAATATTT
1 TTATAAT-TTT
116996 TTATAATTTT
1 TTATAATTTT
117006 TTATAATTTT
1 TTATAATTTT
117016 TTATAATTT
1 TTATAATTT
117025 AACCACGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 22 0.76
11 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATAATTTT
Found at i:120113 original size:21 final size:19
Alignment explanation
Indices: 120057--120140 Score: 53
Period size: 21 Copynumber: 4.1 Consensus size: 19
120047 AATAATTGTG
*
120057 TTTTAATTACTTTTT-AAATA
1 TTTTAATT--TTTTTAAAATT
*
120077 TTTTAGTTTTTATTTAAAATT
1 TTTTA-ATTTT-TTTAAAATT
*
120098 TTCCTTTATTTTTTTAAATATT
1 TT--TTAATTTTTTTAAA-ATT
*
120120 ATTTTAATTATTTTAAAATT
1 -TTTTAATTTTTTTAAAATT
120140 T
1 T
120141 GTAATGTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
19 3 0.06
20 11 0.22
21 26 0.51
22 7 0.14
23 4 0.08
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTAATTTTTTTAAAATT
Found at i:120648 original size:18 final size:20
Alignment explanation
Indices: 120625--120667 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
120615 AAATTCAAAG
*
120625 AAATA-TAT-AAAAATATAA
1 AAATATTATCAAAAATAAAA
*
120643 AAATATTTTCAAAAATAAAA
1 AAATATTATCAAAAATAAAA
120663 AAATA
1 AAATA
120668 AATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 2 0.10
20 14 0.67
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATATTATCAAAAATAAAA
Found at i:120746 original size:12 final size:12
Alignment explanation
Indices: 120729--120759 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
120719 CTTCCCCTTT
120729 CCCTCCCTCTCC
1 CCCTCCCTCTCC
*
120741 CTCTCCCTCTCC
1 CCCTCCCTCTCC
120753 CCCTCCC
1 CCCTCCC
120760 CCCACTTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (12 bp):
CCCTCCCTCTCC
Found at i:121466 original size:6 final size:6
Alignment explanation
Indices: 121446--121488 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
121436 TAATATGAAT
*
121446 GGAT-G GGAT-G GGATGG GGATGG GGATGG GGACGG GGATGG GGA
1 GGATGG GGATGG GGATGG GGATGG GGATGG GGATGG GGATGG GGA
121489 CAGTTGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.19, C:0.02, G:0.65, T:0.14
Consensus pattern (6 bp):
GGATGG
Found at i:138406 original size:6 final size:6
Alignment explanation
Indices: 138385--138420 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
138375 TATCCCACAA
* *
138385 CCTTCC CTTTCC CCTTCT CCTTCC CCTTCC CCTTCC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC
138421 TTTCTCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
CCTTCC
Found at i:138408 original size:18 final size:18
Alignment explanation
Indices: 138385--138419 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
138375 TATCCCACAA
*
138385 CCTTCCCTTTCCCCTTCT
1 CCTTCCCCTTCCCCTTCT
138403 CCTTCCCCTTCCCCTTC
1 CCTTCCCCTTCCCCTTC
138420 CTTTCTCATT
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:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (18 bp):
CCTTCCCCTTCCCCTTCT
Found at i:140663 original size:99 final size:99
Alignment explanation
Indices: 140492--140690 Score: 362
Period size: 99 Copynumber: 2.0 Consensus size: 99
140482 TTGTAGAATT
140492 GACTAAACTGTAGCTTTGATACCTATCACACCCCAAGTCTAACGAGTTCAAGGTTTTGGCATATA
1 GACTAAACTGTAGCTTTGATACCTATCACACCCCAAGTCTAACGAGTTCAAGGTTTTGGCATATA
*
140557 ATGGTGAAATAAGTTGTTTGGCGAAGTGAAATCC
66 ATGGTGAAATAAGTTGTTTGGCAAAGTGAAATCC
*
140591 GACTAAACTGTAGCTTTGATACCTATCACACCCCAAGTCTAGCGAGTTCAAGGTTTTGGCATATA
1 GACTAAACTGTAGCTTTGATACCTATCACACCCCAAGTCTAACGAGTTCAAGGTTTTGGCATATA
* *
140656 GTGGTGAAATAAGTTGTTTGGCAAAGTGGAATCC
66 ATGGTGAAATAAGTTGTTTGGCAAAGTGAAATCC
140690 G
1 G
140691 CCCAATTGAA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (99 bp):
GACTAAACTGTAGCTTTGATACCTATCACACCCCAAGTCTAACGAGTTCAAGGTTTTGGCATATA
ATGGTGAAATAAGTTGTTTGGCAAAGTGAAATCC
Found at i:141531 original size:17 final size:16
Alignment explanation
Indices: 141508--141556 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
141498 TTTCATCATA
141508 AAAATTAAATTAAATT
1 AAAATTAAATTAAATT
* *
141524 ATAAATTAAATAAAAAT
1 A-AAATTAAATTAAATT
* *
141541 AAAATTTAATTTAATT
1 AAAATTAAATTAAATT
141557 TAGATAACCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTAAATT
Found at i:141952 original size:20 final size:20
Alignment explanation
Indices: 141927--141969 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
141917 TATAAGTTTG
141927 GTGTTATGAGTTTGATGGCA
1 GTGTTATGAGTTTGATGGCA
141947 GTGTTATGAGTTTGATGGCA
1 GTGTTATGAGTTTGATGGCA
141967 GTG
1 GTG
141970 AATTAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.05, G:0.37, T:0.40
Consensus pattern (20 bp):
GTGTTATGAGTTTGATGGCA
Found at i:148273 original size:18 final size:18
Alignment explanation
Indices: 148233--148275 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
148223 ATTCAATGTG
148233 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
148251 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
148269 TAATTAA
1 TAATTAA
148276 AAACCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:149181 original size:22 final size:22
Alignment explanation
Indices: 149155--149199 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
149145 TAGCAAATGA
*
149155 TTTT-AAAATTATTAAATTAATT
1 TTTTAAAAATT-TAAAATTAATT
149177 TTTTAAAAATTTAAAATTAATT
1 TTTTAAAAATTTAAAATTAATT
149199 T
1 T
149200 AAAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATTTAAAATTAATT
Found at i:149231 original size:29 final size:30
Alignment explanation
Indices: 149158--149239 Score: 105
Period size: 29 Copynumber: 2.7 Consensus size: 30
149148 CAAATGATTT
*
149158 TAAAATTATT-AAATTAATTTTTTAAAAATT
1 TAAAATTATTAAAATT-ATTTTTTAAAAATA
*
149188 TAAAATTAATTTAAAATTATTTTTT-ACAATA
1 TAAAATT-A-TTAAAATTATTTTTTAAAAATA
149219 TAAAATTATTAAAATTATTTT
1 TAAAATTATTAAAATTATTTT
149240 AATATTTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
29 13 0.28
30 8 0.17
31 12 0.26
32 9 0.19
33 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAAATA
Found at i:149464 original size:40 final size:39
Alignment explanation
Indices: 149406--149488 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
149396 GTTTTGGGCA
149406 AAATTGATTAAAAGAAAAAACTTTATTCCATTTCCCAGC
1 AAATTGATTAAAAGAAAAAACTTTATTCCATTTCCCAGC
149445 AAATTGATTAAAAGAAAAAACTTTATTCCATTTCCCAGC
1 AAATTGATTAAAAGAAAAAACTTTATTCCATTTCCCAGC
149484 AAATT
1 AAATT
149489 AAAATCATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (39 bp):
AAATTGATTAAAAGAAAAAACTTTATTCCATTTCCCAGC
Found at i:149960 original size:13 final size:13
Alignment explanation
Indices: 149942--149967 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
149932 AGAAGGGGAA
149942 TAGAAAAAAAACC
1 TAGAAAAAAAACC
149955 TAGAAAAAAAACC
1 TAGAAAAAAAACC
149968 CACCAAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.15, G:0.08, T:0.08
Consensus pattern (13 bp):
TAGAAAAAAAACC
Found at i:150190 original size:31 final size:30
Alignment explanation
Indices: 150154--150216 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
150144 TATTTTTAAA
*
150154 AATAATTCTAAATTAATTT-TAAAATAATTTT
1 AATAATTCTAAATT--TTTAAAAAATAATTTT
* *
150185 AATAATTTTATATTTTTAAAAAATAATTTT
1 AATAATTCTAAATTTTTAAAAAATAATTTT
150215 AA
1 AA
150217 AATCATTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.11
30 13 0.46
31 12 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
AATAATTCTAAATTTTTAAAAAATAATTTT
Found at i:150224 original size:11 final size:11
Alignment explanation
Indices: 150142--150224 Score: 59
Period size: 11 Copynumber: 7.7 Consensus size: 11
150132 AGGGGATGAT
*
150142 AATATTTTTAAA
1 AATAATTTT-AA
*
150154 AATAATTCTAA
1 AATAATTTTAA
*
150165 ATTAATTTTAA
1 AATAATTTTAA
150176 AATAATTTT--
1 AATAATTTTAA
150185 AATAATTTT--
1 AATAATTTTAA
*
150194 -ATATTTTTAAAA
1 AATAATTTT--AA
150206 AATAATTTTAA
1 AATAATTTTAA
*
150217 AATCATTT
1 AATAATTT
150225 GCTGACTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
8 7 0.12
9 9 0.16
11 28 0.48
12 7 0.12
13 7 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
AATAATTTTAA
Found at i:150618 original size:37 final size:37
Alignment explanation
Indices: 150578--150647 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
150568 ATTTTTTTGA
*
150578 AAAAATAACATA-TATTTATATATT-TA-AAATATATGT
1 AAAAATAAAATACTA-TTAT-TATTGTATAAATATATGT
150614 AAAAATAAAATACTATTATTATTGTATAAATATA
1 AAAAATAAAATACTATTATTATTGTATAAATATA
150648 ACGTTTAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 4 0.13
36 17 0.57
37 9 0.30
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (37 bp):
AAAAATAAAATACTATTATTATTGTATAAATATATGT
Found at i:151734 original size:29 final size:32
Alignment explanation
Indices: 151665--151747 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 32
151655 CAAAATTTAT
* *
151665 TTTAAAGACTAAATTAGAATTTTTTTTAGAAA
1 TTTAAGGACTAAATTAGAATTTTTTGTAGAAA
* * *
151697 CTTAGGGACTAAATT-GGATTTTTTGT-G-AA
1 TTTAAGGACTAAATTAGAATTTTTTGTAGAAA
* *
151726 TTTAAGGACTAATTTATAATTT
1 TTTAAGGACTAAATTAGAATTT
151748 CAGTGATGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
29 14 0.35
30 5 0.12
31 9 0.22
32 12 0.30
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (32 bp):
TTTAAGGACTAAATTAGAATTTTTTGTAGAAA
Found at i:151938 original size:75 final size:75
Alignment explanation
Indices: 151851--152002 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
151841 GTCTACTTGG
151851 AAAACTCTAGTTATTTTGAGGCCTTTTACGCAATTTACCCAATTTGTTTGGTTTAAAAACCCTTA
1 AAAACTCTAGTTATTTTGAGGCCTTTTACGCAATTTACCCAATTTGTTTGGTTTAAAAACCCTTA
151916 TTCTTCTTTC
66 TTCTTCTTTC
151926 AAAACTCTAGTTATTTTGAGGCCTTTTACGCAATTTACCCAATTTGTTTGGTTTAAAAACCCTTA
1 AAAACTCTAGTTATTTTGAGGCCTTTTACGCAATTTACCCAATTTGTTTGGTTTAAAAACCCTTA
151991 TTCTTCTTTC
66 TTCTTCTTTC
152001 AA
1 AA
152003 CAACCCCTTC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (75 bp):
AAAACTCTAGTTATTTTGAGGCCTTTTACGCAATTTACCCAATTTGTTTGGTTTAAAAACCCTTA
TTCTTCTTTC
Found at i:152652 original size:26 final size:24
Alignment explanation
Indices: 152596--152645 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
152586 TTGACCCACT
*
152596 ACCCGACTCGAACCCGTGAGCCTG
1 ACCCGACTCGAACCCATGAGCCTG
152620 ACCCGACTCGTGAACCCATGA-CCTG
1 ACCCGACTC--GAACCCATGAGCCTG
152645 A
1 A
152646 ATCCGACCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 5 0.22
26 9 0.39
ACGTcount: A:0.24, C:0.40, G:0.22, T:0.14
Consensus pattern (24 bp):
ACCCGACTCGAACCCATGAGCCTG
Found at i:154355 original size:30 final size:30
Alignment explanation
Indices: 154294--154370 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
154284 TTAGATTCTC
154294 AAGTTGAAAAAAAAAATTTTAAGTACATTAA
1 AAGTTGAAAAAAAAAATTTTAAG-ACATTAA
* * *
154325 AAGTTGATAAAAAAAATTTTGAA-CCCTTAA
1 AAGTTGAAAAAAAAAATTTT-AAGACATTAA
* *
154355 AAGCTAAAAAAAAAAA
1 AAGTTGAAAAAAAAAA
154371 AATTTGGGGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 18 0.46
31 19 0.49
32 2 0.05
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.25
Consensus pattern (30 bp):
AAGTTGAAAAAAAAAATTTTAAGACATTAA
Found at i:157749 original size:38 final size:39
Alignment explanation
Indices: 157685--157768 Score: 127
Period size: 38 Copynumber: 2.2 Consensus size: 39
157675 ATAAATGATT
157685 TTAAAATTATTAAAATTAATTATTTGAAATAAAAAATTA
1 TTAAAATTATTAAAATTAATTATTTGAAATAAAAAATTA
* *
157724 TTAAAATTATT-ATATT-ATTATTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATTAATTA-TTTGAAATAAAAAATTA
157762 TTAAAAT
1 TTAAAAT
157769 AGAACGTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
37 4 0.10
38 27 0.64
39 11 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (39 bp):
TTAAAATTATTAAAATTAATTATTTGAAATAAAAAATTA
Found at i:157779 original size:37 final size:37
Alignment explanation
Indices: 157685--157780 Score: 95
Period size: 38 Copynumber: 2.5 Consensus size: 37
157675 ATAAATGATT
* *
157685 TTAAAATTATTAAAATTAATTATTTGAAATAAAAAATTA
1 TTAAAATTA-GAACATT-ATTATTTGAAATAAAAAATTA
** * *
157724 TTAAAATTATTATATTATTATTTTGAAATATAAAATTA
1 TTAAAATTAGAACATTATTA-TTTGAAATAAAAAATTA
*
157762 TTAAAA-TAGAACGTTATTA
1 TTAAAATTAGAACATTATTA
157781 ATTCTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
37 13 0.27
38 27 0.55
39 9 0.18
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (37 bp):
TTAAAATTAGAACATTATTATTTGAAATAAAAAATTA
Found at i:158845 original size:28 final size:28
Alignment explanation
Indices: 158814--158867 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
158804 AAATATATTT
158814 TAATATAATAATTTTATATTTCAAAATA
1 TAATATAATAATTTTATATTTCAAAATA
158842 TAATATAATAATTTTATATTTCAAAA
1 TAATATAATAATTTTATATTTCAAAA
158868 AAAATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATATAATAATTTTATATTTCAAAATA
Found at i:158882 original size:31 final size:28
Alignment explanation
Indices: 158814--158888 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
158804 AAATATATTT
*
158814 TAATATAATAATTTTATATTTCAAAATA
1 TAATATAATAATTTTATATTTCAAAAAA
158842 TAATATAATAATTTTATATTTCAAAAAAAA
1 TAATATAATAATTTTATATTTC--AAAAAA
*
158872 TAATTTTAATAATTTTA
1 TAA-TATAATAATTTTA
158889 AAATTATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
28 22 0.52
30 8 0.19
31 12 0.29
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATATAATAATTTTATATTTCAAAAAA
Found at i:159175 original size:19 final size:19
Alignment explanation
Indices: 159138--159178 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
159128 GCTTAATTTT
* **
159138 TTTTATGTTTTATTTAATA
1 TTTTATGTATTATGAAATA
159157 TTTTATGTATTATGAAATA
1 TTTTATGTATTATGAAATA
159176 TTT
1 TTT
159179 AACTTCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTTATGTATTATGAAATA
Found at i:159522 original size:56 final size:58
Alignment explanation
Indices: 159450--159593 Score: 172
Period size: 56 Copynumber: 2.5 Consensus size: 58
159440 AATTTTTTAC
* * *
159450 AACTCTTTCATGTTTTACGAATTACTTAATATCT-TAGAAAC-TGTCATATTT-TAAAT
1 AACTCTTTTATATTTTACGAATTACTTAATATCTGTAAAAACGTGTCAT-TTTCTAAAT
* * * *
159506 AATTCTTTTATATTTTACGAATTACTTAAT-TTTGTAAAAACGTTTTCATTTTCTAAGT
1 AACTCTTTTATATTTTACGAATTACTTAATATCTGTAAAAACG-TGTCATTTTCTAAAT
159564 AACTCTTTTATATTTTACGAATTA-TTAATA
1 AACTCTTTTATATTTTACGAATTACTTAATA
159594 ATCCTTTCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
55 2 0.03
56 33 0.44
57 8 0.11
58 32 0.43
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (58 bp):
AACTCTTTTATATTTTACGAATTACTTAATATCTGTAAAAACGTGTCATTTTCTAAAT
Found at i:164390 original size:30 final size:28
Alignment explanation
Indices: 164357--164671 Score: 194
Period size: 29 Copynumber: 10.8 Consensus size: 28
164347 TTAGACATTC
164357 GAGGGTAAAATGGTAATTTTTGGAAATTT
1 GAGGGTAAAAT-GTAATTTTTGGAAATTT
* * * *
164386 CGA-GGTCAAAAATGAAAATTTTGGATATTC
1 -GAGGGT--AAAATGTAATTTTTGGAAATTT
* * *
164416 GAGGGTAAAATAATAATTTTCGAAAATTT
1 GAGGGTAAAAT-GTAATTTTTGGAAATTT
*
164445 GAGGGTAAAATGTATTTTTTGGAAAGTTT
1 GAGGGTAAAATGTAATTTTTGGAAA-TTT
* *
164474 AAGGGTAAAAATGTAATTTTTGGAAGTTT
1 GAGGGT-AAAATGTAATTTTTGGAAATTT
*
164503 -AGGGGTAAAAATGTAATTTTTGTAAAGTTT
1 GA-GGGT-AAAATGTAATTTTTGGAAA-TTT
* * *
164533 AAGGTTAAAAATGGAA-TTTTGGAAATTT
1 GAGGGT-AAAATGTAATTTTTGGAAATTT
* * *
164561 TAGGGGTAAAATGGTAA-TTTAGTATAATTT
1 GA-GGGTAAAAT-GTAATTTTTGGA-AATTT
* * * *
164591 -AGGTTAAAATGGAATTTTTAGAAGTTT
1 GAGGGTAAAATGTAATTTTTGGAAATTT
*
164618 -AGGGGTAAACATGTAA-TTTTGGAAAAGTTC
1 GA-GGGTAAA-ATGTAATTTTTGG-AAA-TTT
* *
164648 GAGGGTCAAAATATGATTTTTGGA
1 GAGGGT-AAAATGTAATTTTTGGA
164672 TAGTTTAGGG
Statistics
Matches: 224, Mismatches: 41, Indels: 40
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.04
28 48 0.21
29 86 0.38
30 66 0.29
31 16 0.07
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (28 bp):
GAGGGTAAAATGTAATTTTTGGAAATTT
Found at i:164443 original size:59 final size:59
Alignment explanation
Indices: 164304--164448 Score: 177
Period size: 59 Copynumber: 2.5 Consensus size: 59
164294 CTTTGGGGGC
* *
164304 AAAATAGTAATTTTC-AAAAGGTTCGAGGTTAAAAACAAAAATTTTAGACATTCGAGGGT
1 AAAATAGTAATTTTCGAAAA-TTTCGAGGTCAAAAACAAAAATTTTAGACATTCGAGGGT
* * * ** * *
164363 AAAATGGTAATTTTTGGAAATTTCGAGGTCAAAAATGAAAATTTTGGATATTCGAGGGT
1 AAAATAGTAATTTTCGAAAATTTCGAGGTCAAAAACAAAAATTTTAGACATTCGAGGGT
*
164422 AAAATAATAATTTTCGAAAATTT-GAGG
1 AAAATAGTAATTTTCGAAAATTTCGAGG
164449 GTAAAATGTA
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
58 4 0.06
59 65 0.90
60 3 0.04
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (59 bp):
AAAATAGTAATTTTCGAAAATTTCGAGGTCAAAAACAAAAATTTTAGACATTCGAGGGT
Found at i:164485 original size:59 final size:59
Alignment explanation
Indices: 164417--164580 Score: 174
Period size: 59 Copynumber: 2.8 Consensus size: 59
164407 TGGATATTCG
*
164417 AGGGT-AAAATAATAATTTTCGAAAATTT-GAGGGT-AAAATGTATTTTTTGGAAAGTTTA
1 AGGGTAAAAAT-ATAATTTTCGAAAATTTAG-GGGTAAAAATGTAATTTTTGGAAAGTTTA
* * * * *
164475 AGGGTAAAAATGTAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGTAAAGTTTA
1 AGGGTAAAAATATAATTTTCGAAAATTTAGGGGTAAAAATGTAATTTTTGGAAAGTTTA
* ** * *
164534 AGGTTAAAAATGGAATTTTGGAAATTTTAGGGGT-AAAATGGTAATTT
1 AGGGTAAAAATATAATTTTCGAAAATTTAGGGGTAAAAAT-GTAATTT
164581 AGTATAATTT
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
58 27 0.30
59 64 0.70
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (59 bp):
AGGGTAAAAATATAATTTTCGAAAATTTAGGGGTAAAAATGTAATTTTTGGAAAGTTTA
Found at i:165783 original size:3 final size:3
Alignment explanation
Indices: 165775--165851 Score: 66
Period size: 3 Copynumber: 24.7 Consensus size: 3
165765 TGTTTTCCCT
*** *
165775 TTA TTA TTA TTA TTA TTA CCG TTA TTA ATA TTA -TA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
165820 TTA TTA TTA TTTA TTAA ATA GTTA TTA TTA TT
1 TTA TTA TTA -TTA TT-A TTA -TTA TTA TTA TT
165852 TCAAAACAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
2 2 0.03
3 48 0.81
4 9 0.15
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:165830 original size:30 final size:30
Alignment explanation
Indices: 165778--165851 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
165768 TTTCCCTTTA
*
165778 TTATTATTATTATTACCGTTATTAATATT-ATAT
1 TTATTATTATTATTA-C-TTATT--TATTAATAG
165811 TTATTATTATTATTA-TTATTTATTAAATAG
1 TTATTATTATTATTACTTATTTATT-AATAG
165841 TTATTATTATT
1 TTATTATTATT
165852 TCAAAACAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 4 0.11
30 19 0.50
33 15 0.39
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (30 bp):
TTATTATTATTATTACTTATTTATTAATAG
Found at i:166424 original size:18 final size:19
Alignment explanation
Indices: 166387--166431 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
166377 CACAATTTAT
*
166387 TGGTGACGATGGTTGATGA
1 TGGTGACGAGGGTTGATGA
*
166406 TGGTGACG-GGGTTGTTGA
1 TGGTGACGAGGGTTGATGA
*
166424 TGCTGACG
1 TGGTGACG
166432 TGGCAGCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.16, C:0.09, G:0.44, T:0.31
Consensus pattern (19 bp):
TGGTGACGAGGGTTGATGA
Found at i:166629 original size:6 final size:6
Alignment explanation
Indices: 166618--166695 Score: 53
Period size: 6 Copynumber: 14.0 Consensus size: 6
166608 ATTATTTAAA
* *
166618 TAAATT TAAATT TAAATT T--A-T TAAATT T--ATGA TAAATT TAAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAAT-T TAAATT TAAATT
* * *
166662 TAAA-A TAAATT TAATTT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
166696 CTGTTGGGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
3 2 0.04
4 3 0.05
5 10 0.18
6 38 0.69
7 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:166669 original size:17 final size:17
Alignment explanation
Indices: 166649--166693 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
166639 TAAATTTATG
166649 ATAAATTTAAAATTAAA
1 ATAAATTTAAAATTAAA
**
166666 ATAAATTTAATTTTAAA
1 ATAAATTTAAAATTAAA
166683 ATAAATTTAAA
1 ATAAATTTAAA
166694 TTCTGTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATTTAAAATTAAA
Found at i:167191 original size:49 final size:49
Alignment explanation
Indices: 167114--167827 Score: 349
Period size: 49 Copynumber: 14.7 Consensus size: 49
167104 TGGTACTAAA
* * * *
167114 TTCGCTGTTGCGGCTTAAATTTTTCCTTTCATGCTTCTGAGGTATAAGG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
* * * *
167163 TTCGCCATTGCAACTTAAA-CTTTCCCTT--TG-TATCTTCATGGTACT-AGA
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCT-TC-TGA-GGTA-TAAGG
*
167211 TTCGCCGTTGC-AGCTTAAATCTTTCCCTTCATG-TCCCTGAGGTATAAGG
1 TTCGCCGTTGCGA-CTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGG
** * * * * * *
167260 TTCAACATTGTGACTTAAACCTTTCCCTCCATATCTTC--ATGGTACT-AGA
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GCTTCTGA-GGTA-TAAGG
* * * * * *
167309 TTCACCGTTGCGGCTTAAATCCTTCCCTTCATGCTTTTAAGGTACAAGG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
* * *
167358 TTCGCCGTCGCGACTTGAA-CATTTCCCTTCAAT-CTTC-GTGGTACT--GG
1 TTCGCCGTTGCGACTTAAATC-TTTCCCTTC-ATGCTTCTGAGGTA-TAAGG
* * * *
167405 ATTCGCCATTGTGGCTTAAATCTTT-CCTAT-AT-C-TCTAAGGTATAAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCT-TCATGCTTCTGAGGTATAAGG
* * * **
167452 TTCACCGTTACGACTTAAACCTTTCCCTTTGTGTCTTC--ATGGTACT--GG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATG-CTTCTGA-GGTA-TAAGG
*
167500 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-TCTCTGAGGTATAAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGG
** * * * ** *
167550 TTCGTTGTTACGACTTAAACCTTTCCTTTTGTGTCTTC-GTGGTACT--GG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATG-CTTCTGAGGTA-TAAGG
* *
167598 ATTCGCCATTGCGATTTAAATCTTTCCCTTCATG-TCTCTGAGGTATAAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGG
* * * * *
167648 TTCGTCGTTGCGACTTAAAGCTTTCCTTTCGTGTCTTC-GTGGTACT--GG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATG-CTTCTGAGGTA-TAAGG
** * * * *
167696 ATTCGCTTTTGCGGCTTAAAACTTTCCCTTCAAGCTTCTGAGGTACAAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
* * * * * * * *
167746 TTCGCTGTTGCAACTTAAACCTTTCCCTCCATATCTTC-GTGGTATTAGA
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GCTTCTGAGGTATAAGG
* * *
167795 TTCGTCATTGCGGCTTAAATCTTTCCCTTCATG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATG
167828 TTTCATGGTA
Statistics
Matches: 493, Mismatches: 117, Indels: 111
0.68 0.16 0.15
Matches are distributed among these distances:
45 4 0.01
46 30 0.06
47 16 0.03
48 74 0.15
49 334 0.68
50 28 0.06
51 7 0.01
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (49 bp):
TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
Found at i:167327 original size:98 final size:98
Alignment explanation
Indices: 167102--167828 Score: 786
Period size: 98 Copynumber: 7.5 Consensus size: 98
167092 CTTCAATCCG
* * * *
167102 CATGGTACTAAATTCGCTGTTGCGGCTTAAATTTTTCCTTTCATG-CTTCTGAGGTATAAGGTTC
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAGGTTC
* * *
167166 GCCATTGCAACTTAAA-CTTTCCCTTTGTATCTT
65 GCCGTTGCGACTTAAACCTTTCCCTTCGTATCTT
* * *
167199 CATGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCCCTGAGGTATAAGGTTCA
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
* * * * *
167264 ACATTGTGACTTAAACCTTTCCCTCCATATCTT
66 CCGTTGCGACTTAAACCTTTCCCTTCGTATCTT
* * * * *
167297 CATGGTACTAGATTCACCGTTGCGGCTTAAATCCTTCCCTTCATG-CTTTTAAGGTACAAGGTTC
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAGGTTC
* * * *
167361 GCCGTCGCGACTTGAACATTTCCCTTC-AATCTT
65 GCCGTTGCGACTTAAACCTTTCCCTTCGTATCTT
* * * * * * *
167394 CGTGGTACTGGATTCGCCATTGTGGCTTAAATCTTT-CC-T-ATATCTCTAAGGTATAAGGTTCA
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
* * *
167456 CCGTTACGACTTAAACCTTTCCCTTTGTGTCTT
66 CCGTTGCGACTTAAACCTTTCCCTTCGTATCTT
*
167489 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
** * * * *
167554 TTGTTACGACTTAAACCTTTCCTTTTGTGTCTT
66 CCGTTGCGACTTAAACCTTTCCCTTCGTATCTT
* * * **
167587 CGTGGTACTGGATTCGCCATTGCGATTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
* * * *
167652 TCGTTGCGACTTAAAGCTTTCCTTTCGTGTCTT
66 CCGTTGCGACTTAAACCTTTCCCTTCGTATCTT
* * ** * * *
167685 CGTGGTACTGGATTCGCTTTTGCGGCTTAAAACTTTCCCTTCAAG-CTTCTGAGGTACAAGGTTC
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAGGTTC
* * * *
167749 GCTGTTGCAACTTAAACCTTTCCCTCCATATCTT
65 GCCGTTGCGACTTAAACCTTTCCCTTCGTATCTT
* * * *
167783 CGTGGTATTAGATTCGTCATTGCGGCTTAAATCTTTCCCTTCATGT
1 CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGT
167829 TTCATGGTAC
Statistics
Matches: 535, Mismatches: 85, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
94 38 0.07
95 39 0.07
96 4 0.01
97 106 0.20
98 348 0.65
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (98 bp):
CATGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCG
CCGTTGCGACTTAAACCTTTCCCTTCGTATCTT
Found at i:168276 original size:18 final size:18
Alignment explanation
Indices: 168250--168284 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
168240 TTGGCTAAAG
*
168250 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
168268 AATAATTACAAGGAACA
1 AATAATTACAAGGAACA
168285 GTATTAAATG
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:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:179768 original size:29 final size:30
Alignment explanation
Indices: 179692--180122 Score: 187
Period size: 29 Copynumber: 14.7 Consensus size: 30
179682 CAGACGCTTC
* * * *
179692 GAGGGTAAAATAGTAATTTTCAAAAAGTTC
1 GAGGGTAAAATGGTAATTTTTAGAAAGTTT
* ** * *
179722 GAGGTTAAAAAT-AAAATTTTTAGACA-TCT
1 GAGGGT-AAAATGGTAATTTTTAGAAAGTTT
* *
179751 GAGGGTAAAATGGTAA-TTTTGGAAATTTT
1 GAGGGTAAAATGGTAATTTTTAGAAAGTTT
*
179780 GA-GGTCAAAAATGG-AATTTTTAGATA-TTT
1 GAGGGT--AAAATGGTAATTTTTAGAAAGTTT
*
179809 -AGGGGT-AAATGGTAATTTTT-GGAAGTTT
1 GA-GGGTAAAATGGTAATTTTTAGAAAGTTT
* *
179837 AAGGCTAAAAAT-GTAATTTTTAGAAAGTTT
1 GAGGGT-AAAATGGTAATTTTTAGAAAGTTT
* *
179867 GAGGGTAAAAAAT-GTAA-TTTTCGGAAGTTT
1 GAGGGT--AAAATGGTAATTTTTAGAAAGTTT
* *
179897 -AGGAGTAAAAAT-GTAATTTTT-GTGAAGTTC
1 GAGG-GT-AAAATGGTAATTTTTAG-AAAGTTT
* * *
179927 GA-GGTCAAAGATGG-AA-TTTTGGAAAGATC
1 GAGGGT-AAA-ATGGTAATTTTTAGAAAGTTT
* * *
179956 GAGGGTAAAAAT-GTAATTTTTGGAAAATTA
1 GAGGGT-AAAATGGTAATTTTTAGAAAGTTT
* * *
179986 GAGGTTAAAAATGG-AA-TTTTGGAAAGTTC
1 GAGGGT-AAAATGGTAATTTTTAGAAAGTTT
*
180015 GAGGGTAAAATGGTAA-TTTTAG-GAGTATT
1 GAGGGTAAAATGGTAATTTTTAGAAAGT-TT
* *
180044 CGAGGTTAAAAATGG-AATTTTTGGAAA-TTT
1 -GAGGGT-AAAATGGTAATTTTTAGAAAGTTT
* * *
180074 AAGGATAAAATTGTAATTTTTA-AAAGTTT
1 GAGGGTAAAATGGTAATTTTTAGAAAGTTT
**
180103 -AGGGGTAAAAAAGTAATTTT
1 GA-GGGTAAAATGGTAATTTT
180123 GGAAAAGTTT
Statistics
Matches: 317, Mismatches: 49, Indels: 71
0.73 0.11 0.16
Matches are distributed among these distances:
27 8 0.03
28 50 0.16
29 114 0.36
30 113 0.36
31 31 0.10
32 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
GAGGGTAAAATGGTAATTTTTAGAAAGTTT
Found at i:179793 original size:30 final size:30
Alignment explanation
Indices: 179757--180070 Score: 207
Period size: 30 Copynumber: 10.7 Consensus size: 30
179747 ATCTGAGGGT
* *
179757 AAAATGGTAA-TTTTGGAAATTTTGAGGTCA
1 AAAATGGTAATTTTTGGAAAGTTCGAGGT-A
* * * * *
179787 AAAATGG-AATTTTTAGATATTTAGGGGT-
1 AAAATGGTAATTTTTGGAAAGTTCGAGGTA
**
179815 -AAATGGTAATTTTTGG-AAGTTTAAGGCTA
1 AAAATGGTAATTTTTGGAAAGTTCGAGG-TA
* *
179844 AAAAT-GTAATTTTTAGAAAGTTTGAGGGTAA
1 AAAATGGTAATTTTTGGAAAGTTCGA-GGT-A
* *
179875 AAAAT-GTAATTTTCGG-AAGTT-TAGGAGTA
1 AAAATGGTAATTTTTGGAAAGTTCGA-G-GTA
179904 AAAAT-GTAATTTTTGTG-AAGTTCGAGGTCA
1 AAAATGGTAATTTTTG-GAAAGTTCGAGGT-A
* *
179934 AAGATGG-AA-TTTTGGAAAGATCGAGGGTA
1 AAAATGGTAATTTTTGGAAAGTTCGA-GGTA
* *
179963 AAAAT-GTAATTTTTGGAAAATTAGAGGTTA
1 AAAATGGTAATTTTTGGAAAGTTCGAGG-TA
179993 AAAATGG-AA-TTTTGGAAAGTTCGAGGGT-
1 AAAATGGTAATTTTTGGAAAGTTCGA-GGTA
* *
180021 AAAATGGTAATTTTAGGAGTA-TTCGAGGTTA
1 AAAATGGTAATTTTTGGA-AAGTTCGAGG-TA
180052 AAAATGG-AATTTTTGGAAA
1 AAAATGGTAATTTTTGGAAA
180071 TTTAAGGATA
Statistics
Matches: 230, Mismatches: 29, Indels: 51
0.74 0.09 0.16
Matches are distributed among these distances:
27 11 0.05
28 18 0.08
29 72 0.31
30 101 0.44
31 28 0.12
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAAGTTCGAGGTA
Found at i:179801 original size:58 final size:57
Alignment explanation
Indices: 179692--180018 Score: 199
Period size: 59 Copynumber: 5.6 Consensus size: 57
179682 CAGACGCTTC
* ** * * * *
179692 GAGGGTAAAATAGTAATTTTCAAAAAGTTCGAGGTTAAAAATAAAATTTTTAGACATCT
1 GAGGGTAAAATGGTAATTTT-GGAAAGTTTGAGGTCAAAAATGAAATTTTTAGAAAT-T
* * *
179751 GAGGGTAAAATGGTAATTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTAGATATT
1 GAGGGTAAAATGGTAATTTTGGAAAGTTTGAGGTCAAAAATGAAATTTTTAGAAATT
* * *
179808 TAGGGGT-AAATGGTAATTTTTGG-AAGTTTAAGG-CTAAAAATGTAATTTTTAGAAAGTTT
1 GA-GGGTAAAATGGTAA-TTTTGGAAAGTTTGAGGTC-AAAAATGAAATTTTTAGAAA--TT
* * *
179867 GAGGGTAAAAAAT-GTAATTTTCGG-AAGTTT-AGGAGT-AAAAATGTAATTTTTGTGAAGTT
1 GAGGGT--AAAATGGTAATTTT-GGAAAGTTTGA-G-GTCAAAAATGAAATTTTT-AGAAATT
* * * *
179926 CGA-GGTCAAAGATGG-AATTTTGGAAAGATCGAGGGT-AAAAATGTAATTTTTGGAAAATT
1 -GAGGGT-AAA-ATGGTAATTTTGGAAAGTTTGA-GGTCAAAAATGAAATTTTTAG-AAATT
* *
179985 AGAGGTTAAAAATGG-AATTTTGGAAAGTTCGAGG
1 -GAGGGT-AAAATGGTAATTTTGGAAAGTTTGAGG
180019 GTAAAATGGT
Statistics
Matches: 222, Mismatches: 26, Indels: 41
0.77 0.09 0.14
Matches are distributed among these distances:
56 1 0.00
57 37 0.17
58 50 0.23
59 87 0.39
60 39 0.18
61 8 0.04
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (57 bp):
GAGGGTAAAATGGTAATTTTGGAAAGTTTGAGGTCAAAAATGAAATTTTTAGAAATT
Found at i:179905 original size:88 final size:86
Alignment explanation
Indices: 179757--180165 Score: 243
Period size: 88 Copynumber: 4.6 Consensus size: 86
179747 ATCTGAGGGT
* * * *
179757 AAAATGGTAATTTTGGAAATTTTGA-GGTCAAAAATGGAATTTTTAGATATTTAGGGGT-AAATG
1 AAAAT-GTAATTTTGGAAAGTTTGAGGGT-AAAAATGTAATTTTTGGA-ATTTAGGAGTAAAAT-
*
179820 GTAATTTTTG-GAAGTTTAAGG-CTA
62 GTAATTTTTGTGAAGTTCAAGGTC-A
* *
179844 AAAATGTAATTTTTAGAAAGTTTGAGGGTAAAAAATGTAATTTTCGGAAGTTTAGGAGTAAAAAT
1 AAAATGTAA-TTTTGGAAAGTTTGAGGGT-AAAAATGTAATTTTTGGAA-TTTAGGAGT-AAAAT
*
179909 GTAATTTTTGTGAAGTTCGAGGTCA
62 GTAATTTTTGTGAAGTTCAAGGTCA
* * * * *
179934 AAGATGGAATTTTGGAAAGATCGAGGGTAAAAATGTAATTTTTGGAAAATTA-GAGGTTAAAAAT
1 AAAATGTAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGG-AATTTAGGA-G-T-AAAAT
* *
179998 GGAA-TTTTG-GAAAGTTCGAGGGT--
62 GTAATTTTTGTG-AAGTTC-AAGGTCA
* *
180021 AAAATGGTAATTTTAGG--AGTATTCGAGGTTAAAAATGGAATTTTTGGAAATTTAAGGA-TAAA
1 AAAAT-GTAATTTT-GGAAAGT-TT-GAGGGTAAAAATGTAATTTTTGG-AATTT-AGGAGTAAA
** * *
180083 ATTGTAATTTTT-AAAAGTTTAGGGGT-A
60 A-TGTAATTTTTGTGAAGTTCA-AGGTCA
* * ** * *
180110 AAAAAGTAATTTTGGAAAAGTTTAAGGGTTGAAATATGATTTTTGGATAGTTTAGG
1 AAAATGTAATTTTGG-AAAGTTTGAGGGTAAAAATGTAATTTTTGGA-A-TTTAGG
180166 GACCTCTATG
Statistics
Matches: 257, Mismatches: 37, Indels: 55
0.74 0.11 0.16
Matches are distributed among these distances:
86 4 0.02
87 36 0.14
88 107 0.42
89 82 0.32
90 25 0.10
91 3 0.01
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (86 bp):
AAAATGTAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAATTTAGGAGTAAAATGTAA
TTTTTGTGAAGTTCAAGGTCA
Found at i:180114 original size:59 final size:59
Alignment explanation
Indices: 179757--180136 Score: 261
Period size: 59 Copynumber: 6.4 Consensus size: 59
179747 ATCTGAGGGT
* * * * *
179757 AAAATGGTAATTTTGGAAATTTTGAGG-TCAAAAATGGAATTTTTAGATA-TTTAGGGGT--
1 AAAATGG-AATTTTGGAAAGTTTAAGGAT-AAAAATGTAATTTTTA-AAAGTTTAGAGGTAA
*
179815 -AAATGGTAATTTTTGG-AAGTTTAAGGCTAAAAATGTAATTTTTAGAAAGTTT-GAGGGTAA
1 AAAATGG-AA-TTTTGGAAAGTTTAAGGATAAAAATGTAATTTTTA-AAAGTTTAGA-GGTAA
* ** * *
179875 AAAATGTAATTTTCGG-AAGTTT-AGGAGTAAAAATGTAATTTTTGTGAAG-TTCGAGGTCA
1 AAAATGGAATTTT-GGAAAGTTTAAGGA-TAAAAATGTAATTTTT-AAAAGTTTAGAGGTAA
* * ** * *
179934 AAGATGGAATTTTGGAAAGATCGAGGGTAAAAATGTAATTTTTGGAAAA--TTAGAGGTTA
1 AAAATGGAATTTTGGAAAGTTTAAGGATAAAAATGTAATTTTT--AAAAGTTTAGAGGTAA
** * ** * *
179993 AAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATGGTAA-TTTTAGGAGTATTCGAGGTTA
1 AAAATGGAATTTTGGAAAGTTTAAGGATAAAAAT-GTAATTTTTAAAAGT-TTAGAGGTAA
* *
180052 AAAATGGAATTTTTGGAAA-TTTAAGGATAAAATTGTAATTTTTAAAAGTTTAGGGGTAA
1 AAAATGGAA-TTTTGGAAAGTTTAAGGATAAAAATGTAATTTTTAAAAGTTTAGAGGTAA
*
180111 AAAA-GTAATTTTGGAAAAGTTTAAGG
1 AAAATGGAATTTTGG-AAAGTTTAAGG
180137 GTTGAAATAT
Statistics
Matches: 265, Mismatches: 34, Indels: 45
0.77 0.10 0.13
Matches are distributed among these distances:
56 2 0.01
57 42 0.16
58 30 0.11
59 128 0.48
60 58 0.22
61 5 0.02
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAAGTTTAAGGATAAAAATGTAATTTTTAAAAGTTTAGAGGTAA
Found at i:180131 original size:30 final size:29
Alignment explanation
Indices: 179753--180166 Score: 198
Period size: 30 Copynumber: 14.1 Consensus size: 29
179743 AGACATCTGA
*
179753 GGGT-AAAATGGTAATTTTGGAAA-TTTTG
1 GGGTAAAAAT-GTAATTTTGGAAAGTTTAG
* * * *
179781 AGGTCAAAAATGGAATTTTTAGATA-TTTAG
1 GGGT-AAAAATGTAA-TTTTGGAAAGTTTAG
*
179811 GGGT--AAATGGTAATTTTTGG-AAGTTTAA
1 GGGTAAAAAT-GTAA-TTTTGGAAAGTTTAG
* *
179839 GGCTAAAAATGTAATTTTTAGAAAGTTT-G
1 GGGTAAAAATGTAA-TTTTGGAAAGTTTAG
179868 AGGGTAAAAAATGTAATTTTCGG-AAGTTTAG
1 -GGGT-AAAAATGTAATTTT-GGAAAGTTTAG
* *
179899 GAGTAAAAATGTAATTTTTGTG-AAG-TTCG
1 GGGTAAAAATGTAA-TTTTG-GAAAGTTTAG
* * * * *
179928 AGGTCAAAGATGGAATTTTGGAAAG-ATCG
1 GGGT-AAAAATGTAATTTTGGAAAGTTTAG
*
179957 AGGGTAAAAATGTAATTTTTGGAAA-ATTAG
1 -GGGTAAAAATGTAA-TTTTGGAAAGTTTAG
* * *
179987 AGGTTAAAAATGGAATTTTGGAAAG-TTCG
1 -GGGTAAAAATGTAATTTTGGAAAGTTTAG
*
180016 AGGGT-AAAATGGTAATTTTAGG--AGTATTCG
1 -GGGTAAAAAT-GTAATTTT-GGAAAGT-TTAG
* * *
180046 AGGTTAAAAATGGAATTTTTGGAAA-TTTAA
1 -GGGTAAAAATGTAA-TTTTGGAAAGTTTAG
* * **
180076 GGATAAAATTGTAATTTTTAAAAGTTTAG
1 GGGTAAAAATGTAATTTTGGAAAGTTTAG
*
180105 GGGTAAAAAAGTAATTTTGGAAAAGTTTAAG
1 GGGTAAAAATGTAATTTTGG-AAAGTTT-AG
* * * *
180136 GGTTGAAATATG-ATTTTTGGATAGTTTAG
1 GGGT-AAAAATGTAATTTTGGAAAGTTTAG
180165 GG
1 GG
180167 ACCTCTATGG
Statistics
Matches: 302, Mismatches: 52, Indels: 63
0.72 0.12 0.15
Matches are distributed among these distances:
27 5 0.02
28 34 0.11
29 105 0.35
30 118 0.39
31 34 0.11
32 6 0.02
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTGGAAAGTTTAG
Found at i:181260 original size:3 final size:3
Alignment explanation
Indices: 181252--181334 Score: 53
Period size: 3 Copynumber: 27.7 Consensus size: 3
181242 TGTTTTCCCT
*** *
181252 TTA TTA TTA TTA TTA TTA CCG TTA TTA ATA TTA -TA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
** * * *
181297 TTA ACA TTA TCA TTA TTTA TTA -AA TAA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
181335 TCAAAACAAT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
2 3 0.05
3 52 0.87
4 5 0.08
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:181312 original size:21 final size:19
Alignment explanation
Indices: 181273--181334 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 19
181263 ATTATTACCG
181273 TTATTAATATTATATTTATTA
1 TTATTAA-ATTATA-TTATTA
181294 TTATTAACATTATCATTA-T-
1 TTATTAA-ATTAT-ATTATTA
181313 TTATTAAA-TA-ATTATTA
1 TTATTAAATTATATTATTA
181330 TTATT
1 TTATT
181335 TCAAAACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 4 0.11
16 1 0.03
17 7 0.19
18 1 0.03
19 7 0.19
20 1 0.03
21 15 0.41
22 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTAAATTATATTATTA
Found at i:181313 original size:36 final size:35
Alignment explanation
Indices: 181251--181334 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
181241 TTGTTTTCCC
** *
181251 TTTATTATTATTATTATTACCGTTATTAATATT-ATA
1 TTTATTATTATTAACATTACCATTATT--TATTAATA
*
181287 TTTATTATTATTAACATTATCATTATTTATTAAATA
1 TTTATTATTATTAACATTACCATTATTTATT-AATA
*
181323 ATTATTATTATT
1 TTTATTATTATT
181335 TCAAAACAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 4 0.10
36 37 0.90
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTATTATTATTAACATTACCATTATTTATTAATA
Found at i:182142 original size:17 final size:17
Alignment explanation
Indices: 182120--182182 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
182110 TAAATAAATT
*
182120 TAAATTTAAATTTATGA
1 TAAATTTAAATTTATAA
182137 TAAATTTAAATTT-TCAA
1 TAAATTTAAATTTAT-AA
*
182154 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTATAA
*
182171 TAAATTCAAATT
1 TAAATTTAAATT
182183 CTATTGGGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
16 1 0.02
17 40 0.98
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:183182 original size:11 final size:11
Alignment explanation
Indices: 183166--183225 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
183156 CTTAATGGTT
183166 TTAATATTAAA
1 TTAATATTAAA
183177 TTAATA-TAATA
1 TTAATATTAA-A
*
183188 TT-AGATTAAA
1 TTAATATTAAA
*
183198 TTTAGTATTAAA
1 -TTAATATTAAA
*
183210 -TATTATTAAA
1 TTAATATTAAA
183220 TTAATA
1 TTAATA
183226 AAATATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
10 15 0.38
11 18 0.46
12 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:183286 original size:20 final size:19
Alignment explanation
Indices: 183261--183327 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
183251 TAAATTAATT
*
183261 TTAATATTAAAATAATCACA
1 TTAATATTAAAATAAT-AAA
*
183281 TTAATATTAAATTAATAAA
1 TTAATATTAAAATAATAAA
* * *
183300 TTACTATTAAGATAAT-TA
1 TTAATATTAAAATAATAAA
183318 TTAA-ATTAAA
1 TTAATATTAAA
183328 TTTTATAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
17 5 0.13
18 4 0.10
19 15 0.38
20 15 0.38
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (19 bp):
TTAATATTAAAATAATAAA
Found at i:202320 original size:21 final size:21
Alignment explanation
Indices: 202281--202322 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
202271 GTTTTTAAGC
*
202281 TTTAAATTATTCTAATTATAT
1 TTTAAATTATTCGAATTATAT
202302 TTTAAATTATT-GAATTTATAT
1 TTTAAATTATTCGAA-TTATAT
202323 CAATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAAATTATTCGAATTATAT
Found at i:205539 original size:13 final size:14
Alignment explanation
Indices: 205502--205539 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
205492 ATTTTATTTC
205502 TCAAAATCACTTTT
1 TCAAAATCACTTTT
*
205516 TCAAAGT-ACTTTT
1 TCAAAATCACTTTT
205529 T-AAAATCACTT
1 TCAAAATCACTT
205540 CTCAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 4 0.19
13 11 0.52
14 6 0.29
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (14 bp):
TCAAAATCACTTTT
Found at i:207047 original size:52 final size:52
Alignment explanation
Indices: 206969--207070 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
206959 GTAAACAATC
* *
206969 GTATAGTAGGCCTTGAGCCGGTGAATGATTAGCAGGCCTT-GAGCCGATGAAT
1 GTATAGCAGGCCTTGAGCCGGTGAATGATTAGCAAG-CTTCGAGCCGATGAAT
207021 GTATAGCAGGCCTTGAGCCGGTGAATGATTAGCAAGCTTCGAGCCGATGA
1 GTATAGCAGGCCTTGAGCCGGTGAATGATTAGCAAGCTTCGAGCCGATGA
207071 TTAAATAGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 3 0.06
52 44 0.94
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (52 bp):
GTATAGCAGGCCTTGAGCCGGTGAATGATTAGCAAGCTTCGAGCCGATGAAT
Found at i:207066 original size:26 final size:26
Alignment explanation
Indices: 206976--207054 Score: 133
Period size: 26 Copynumber: 3.0 Consensus size: 26
206966 ATCGTATAGT
206976 AGGCCTTGAGCCGGTGAATGATTAGC
1 AGGCCTTGAGCCGGTGAATGATTAGC
*
207002 AGGCCTTGAGCCGATGAATG-TATAGC
1 AGGCCTTGAGCCGGTGAATGAT-TAGC
207028 AGGCCTTGAGCCGGTGAATGATTAGC
1 AGGCCTTGAGCCGGTGAATGATTAGC
207054 A
1 A
207055 AGCTTCGAGC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.02
26 47 0.96
27 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (26 bp):
AGGCCTTGAGCCGGTGAATGATTAGC
Found at i:207095 original size:52 final size:52
Alignment explanation
Indices: 206971--207083 Score: 165
Period size: 52 Copynumber: 2.2 Consensus size: 52
206961 AAACAATCGT
* * **
206971 ATAGTAGGCCTTGAGCCGGTGAATGATTAGCAGGCCTTGAGCCGATGAATGT
1 ATAGCAGGCCTTGAGCCGGTGAATGATTAGCAAGCCTTGAGCCGATGAATAA
*
207023 ATAGCAGGCCTTGAGCCGGTGAATGATTAGCAAG-CTTCGAGCCGATGATTAA
1 ATAGCAGGCCTTGAGCCGGTGAATGATTAGCAAGCCTT-GAGCCGATGAATAA
207075 ATAGCAGGC
1 ATAGCAGGC
207084 TTCGTGCCGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 3 0.05
52 52 0.95
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (52 bp):
ATAGCAGGCCTTGAGCCGGTGAATGATTAGCAAGCCTTGAGCCGATGAATAA
Found at i:210039 original size:24 final size:24
Alignment explanation
Indices: 210002--210048 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
209992 CCAATTAGGG
210002 AATTATTGTTTAG-ACTTAATTTT
1 AATTATTGTTTAGAACTTAATTTT
* *
210025 AATTATCTTTTTAGAATTTAATTT
1 AATTAT-TGTTTAGAACTTAATTT
210049 AGATCCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (24 bp):
AATTATTGTTTAGAACTTAATTTT
Found at i:215954 original size:140 final size:140
Alignment explanation
Indices: 215702--215983 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
215692 ATTCTACGAC
215702 ATTTGCTTCACTGCAACCTCAAAAAGATAGGATTTAATGTTGTAGAATTATCCTGCTCCACTTCT
1 ATTTGCTTCACTGCAACCTCAAAAAGATAGGATTTAATGTTGTAGAATTATCCTGCTCCACTTCT
*
215767 ATCTTTAGGGAGATAAGATTCGCTAATGACTTTAATCCGACCCACTTCAACTTCAAGGGTATATG
66 ATCTTTAGGGAGATAAGATTCGCTAATGACTTTAATCCGACCCACTTCAACTTCAAGGGTATAAG
215832 ATTTGTTCTT
131 ATTTGTTCTT
* *
215842 ATTTGCTTCACTGCAACCTCAAGAAGATAGGATTTGATGTTGTAGAATTATCCTGCTCCACTTCT
1 ATTTGCTTCACTGCAACCTCAAAAAGATAGGATTTAATGTTGTAGAATTATCCTGCTCCACTTCT
215907 ATCTTTAGGGAGAT-AGAATTCGCTAATGACTTTAATCCGACCCACTTCAACTTCAAGGGTATAA
66 ATCTTTAGGGAGATAAG-ATTCGCTAATGACTTTAATCCGACCCACTTCAACTTCAAGGGTATAA
215971 GATTTGTTCTT
130 GATTTGTTCTT
215982 AT
1 AT
215984 AGCTTCATCC
Statistics
Matches: 138, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
139 2 0.01
140 136 0.99
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (140 bp):
ATTTGCTTCACTGCAACCTCAAAAAGATAGGATTTAATGTTGTAGAATTATCCTGCTCCACTTCT
ATCTTTAGGGAGATAAGATTCGCTAATGACTTTAATCCGACCCACTTCAACTTCAAGGGTATAAG
ATTTGTTCTT
Found at i:216269 original size:39 final size:39
Alignment explanation
Indices: 216238--216484 Score: 162
Period size: 39 Copynumber: 6.5 Consensus size: 39
216228 CAATTTGTCT
*
216238 TCTGGTTAGGGTAAAAGATTGAATTGCTTCAATTTG-CC
1 TCTGGTTAGGGTAAAAGATTGAATTGCTTCAATCTGCCC
* *
216276 TCATGGTTGGGGT--AAGA--G-A-----TCAATCTGCCT
1 TC-TGGTTAGGGTAAAAGATTGAATTGCTTCAATCTGCCC
* *
216306 TCTGGTTAGGGTAAAAAATTGGATTGCTTCAATCTGCCC
1 TCTGGTTAGGGTAAAAGATTGAATTGCTTCAATCTGCCC
** * * *
216345 -CATGGTCGGGGTAAAAGA-TCAGATGGTCTTCAATCTGTCC
1 TC-TGGTTAGGGTAAAAGATTGA-ATTG-CTTCAATCTGCCC
* * * *
216385 TCTAGTTAGGGTAAAATATTGGATTGCTTCAATCTGCCT
1 TCTGGTTAGGGTAAAAGATTGAATTGCTTCAATCTGCCC
* * * * *
216424 TATGGTTGGGGTAAGAGATCGAA-TGATCTTCAATTTGCCC
1 TCTGGTTAGGGTAAAAGATTGAATTG--CTTCAATCTGCCC
*
216464 TCTTGTTAGGGTAAAAGATTG
1 TCTGGTTAGGGTAAAAGATTG
216485 GAGGTTGTAA
Statistics
Matches: 154, Mismatches: 36, Indels: 36
0.68 0.16 0.16
Matches are distributed among these distances:
29 16 0.10
30 3 0.02
31 3 0.02
33 1 0.01
34 2 0.01
35 1 0.01
37 4 0.03
38 6 0.04
39 62 0.40
40 54 0.35
41 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (39 bp):
TCTGGTTAGGGTAAAAGATTGAATTGCTTCAATCTGCCC
Found at i:216281 original size:79 final size:79
Alignment explanation
Indices: 216163--216486 Score: 332
Period size: 79 Copynumber: 4.2 Consensus size: 79
216153 CTCTATAGTT
* * *
216163 TTAGGAGTAAACA-ATTGGATTGTTTCAATCTGCCCCATGGTCGGGATAAGGGATCAGATGGTCT
1 TTAGG-GTAAA-AGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCT
* * *
216227 TCAATTTGTCTTCTGG
64 TCAATCTGCCCTCTGG
* * * *
216243 TTAGGGTAAAAGATTGAATTGCTTCAATTTGCCTCATGGTTGGGGT-A-AG---AGA------TC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCTTC
*
216297 AATCTGCCTTCTGG
66 AATCTGCCCTCTGG
* *
216311 TTAGGGTAAAAAATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCAGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCTTC
* *
216376 AATCTGTCCTCTAG
66 AATCTGCCCTCTGG
* ** * *
216390 TTAGGGTAAAATATTGGATTGCTTCAATCTGCCTTATGGTTGGGGTAAGAGATC-GAATGATCTT
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAG-ATGGTCTT
* *
216454 CAATTTGCCCTCTTG
65 CAATCTGCCCTCTGG
216469 TTAGGGTAAAAGATTGGA
1 TTAGGGTAAAAGATTGGA
216487 GGTTGTAACT
Statistics
Matches: 204, Mismatches: 27, Indels: 27
0.79 0.10 0.10
Matches are distributed among these distances:
68 55 0.27
69 1 0.00
70 2 0.01
73 3 0.01
74 3 0.01
77 1 0.00
78 3 0.01
79 131 0.64
80 5 0.02
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (79 bp):
TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGGTCTTC
AATCTGCCCTCTGG
Found at i:216336 original size:68 final size:68
Alignment explanation
Indices: 216227--216443 Score: 229
Period size: 68 Copynumber: 3.0 Consensus size: 68
216217 CAGATGGTCT
* * * * *
216227 TCAATTTGTCTTCTGGTTAGGGTAAAAGATTGAATTGCTTCAATTTGCCTCATGGTTGGGGTAAG
1 TCAATCTGCCTTCTGGTTAGGGTAAAAAATTGGATTGCTTCAATCTGCCTCATGGTTGGGGTAAG
216292 AGA
66 AGA
* *
216295 TCAATCTGCCTTCTGGTTAGGGTAAAAAATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAA
1 TCAATCTGCCTTCTGGTTAGGGTAAAAAATTGGATTGCTTCAATCTGCCTCATGGTTGGGGT--A
216360 AGATCAGA
64 AG---AGA
* * *
216368 TGGTCTTCAATCTGTCC-TCTAGTTAGGGTAAAATATTGGATTGCTTCAATCTGCCTTATGGTTG
1 ------TCAATCTG-CCTTCTGGTTAGGGTAAAAAATTGGATTGCTTCAATCTGCCTCATGGTTG
216432 GGGTAAGAGA
59 GGGTAAGAGA
216442 TC
1 TC
216444 GAATGATCTT
Statistics
Matches: 125, Mismatches: 12, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
68 57 0.46
70 3 0.02
73 3 0.02
74 3 0.02
77 3 0.02
79 54 0.43
80 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (68 bp):
TCAATCTGCCTTCTGGTTAGGGTAAAAAATTGGATTGCTTCAATCTGCCTCATGGTTGGGGTAAG
AGA
Found at i:216436 original size:147 final size:148
Alignment explanation
Indices: 216163--216443 Score: 447
Period size: 147 Copynumber: 1.9 Consensus size: 148
216153 CTCTATAGTT
* * **
216163 TTAGGAGTAAACAATTGGATTGTTTCAATCTGCCCCATGGTCGGGATAAGGGATCAGATGGTCTT
1 TTAGGAGTAAAAAATTGGATTGCTTCAATCTGCCCCATGGTCGGGATAAAAGATCAGATGGTCTT
* * * *
216228 CAATTTGTCTTCTGGTTAGGGTAAAAGATTGAATTGCTTCAATTTGCCTCATGGTTGGGGTAAGA
66 CAATCTGTCCTCTAGTTAGGGTAAAAGATTGAATTGCTTCAATCTGCCTCATGGTTGGGGTAAGA
216293 GATCAATCTGCCTTCTGG
131 GATCAATCTGCCTTCTGG
*
216311 TTAGG-GTAAAAAATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATCAGATGGTCTT
1 TTAGGAGTAAAAAATTGGATTGCTTCAATCTGCCCCATGGTCGGGATAAAAGATCAGATGGTCTT
* * *
216375 CAATCTGTCCTCTAGTTAGGGTAAAATATTGGATTGCTTCAATCTGCCTTATGGTTGGGGTAAGA
66 CAATCTGTCCTCTAGTTAGGGTAAAAGATTGAATTGCTTCAATCTGCCTCATGGTTGGGGTAAGA
216440 GATC
131 GATC
216444 GAATGATCTT
Statistics
Matches: 121, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
147 116 0.96
148 5 0.04
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (148 bp):
TTAGGAGTAAAAAATTGGATTGCTTCAATCTGCCCCATGGTCGGGATAAAAGATCAGATGGTCTT
CAATCTGTCCTCTAGTTAGGGTAAAAGATTGAATTGCTTCAATCTGCCTCATGGTTGGGGTAAGA
GATCAATCTGCCTTCTGG
Found at i:217034 original size:96 final size:95
Alignment explanation
Indices: 216843--217046 Score: 214
Period size: 96 Copynumber: 2.1 Consensus size: 95
216833 GTTGCAACCC
* ** * *
216843 TAATCTTTCCCTTCACATCTTTAGGGTACATGGTTCCCCGTGCGGCTTCAACCTTTCCCTCCATA
1 TAATCTTTCCCATCACATCCCTAAGGTACAAGGTTCCCCGTGCGGCTTCAACCTTT--CTCCATA
*
216908 ACTTTAGGGTACAAGATTCACCGTTGCGACTT
64 ACTTTAGGGTACAAGATTCACCGTTACGACTT
* * *
216940 TAATCTTTCCCATCACGTCCCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTCTT-TTCAT-
1 TAATCTTTCCCATCACATCCCTAAGGTACAAGGTTCCCCG-TGCGGCTTCAACCT-TTCTCCATA
* ** *
217003 ATTTCTAGGGTATTAGATTTACCGTTACGACTT
64 ACTT-TAGGGTACAAGATTCACCGTTACGACTT
* *
217036 CAATGTTTCCC
1 TAATCTTTCCC
217047 TTTAAACCTG
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
95 3 0.03
96 37 0.42
97 33 0.37
98 14 0.16
99 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.35
Consensus pattern (95 bp):
TAATCTTTCCCATCACATCCCTAAGGTACAAGGTTCCCCGTGCGGCTTCAACCTTTCTCCATAAC
TTTAGGGTACAAGATTCACCGTTACGACTT
Found at i:217957 original size:22 final size:22
Alignment explanation
Indices: 217932--217987 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
217922 CTTGACCTTC
217932 CTTTTTTTCTTTTTC-TTTTCTT
1 CTTTTTTTCTTTTTCTTTTTC-T
*
217954 CTTTTTTTCCTTTTCTTTTTCT
1 CTTTTTTTCTTTTTCTTTTTCT
217976 CTTTTTTT-TTTT
1 CTTTTTTTCTTTT
217988 GAATTTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 3 0.10
22 23 0.74
23 5 0.16
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
CTTTTTTTCTTTTTCTTTTTCT
Found at i:217967 original size:28 final size:26
Alignment explanation
Indices: 217936--217987 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
217926 ACCTTCCTTT
*
217936 TTTTCTTTTTCTTTTCTTCTTTTTTTCC
1 TTTTCTTTTTCTCTT-TT-TTTTTTTCC
217964 TTTTCTTTTTCTCTTTTTTTTTTT
1 TTTTCTTTTTCTCTTTTTTTTTTT
217988 GAATTTCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 2 0.09
28 14 0.61
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTTCTTTTTCTCTTTTTTTTTTTCC
Found at i:217969 original size:14 final size:14
Alignment explanation
Indices: 217929--217987 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
217919 CACCTTGACC
*
217929 TTCCTTTTTTTCTTT
1 TTCCTTTTCTT-TTT
*
217944 TTCTTTTCTTCTTTTT
1 TTC-CTT-TTCTTTTT
217960 TTCCTTTTCTTTTT
1 TTCCTTTTCTTTTT
*
217974 CT-CTTTT-TTTTT
1 TTCCTTTTCTTTTT
217986 TT
1 TT
217988 GAATTTCTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 6 0.16
13 5 0.14
14 9 0.24
15 5 0.14
16 8 0.22
17 4 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCCTTTTCTTTTT
Found at i:223817 original size:28 final size:28
Alignment explanation
Indices: 223764--223850 Score: 122
Period size: 28 Copynumber: 3.0 Consensus size: 28
223754 ACGTTAAAAA
*
223764 TATATTTTAATATAATAATTTTAATAATTT
1 TATA-TTTAAAAT-ATAATTTTAATAATTT
223794 TATATTTCAAAATATAA-TTTAATAATTT
1 TATATTT-AAAATATAATTTTAATAATTT
*
223822 TATATTTAAAAAATAATTTTAATAATTT
1 TATATTTAAAATATAATTTTAATAATTT
223850 T
1 T
223851 TAAATTATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.15
28 30 0.57
29 7 0.13
30 8 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATTTAAAATATAATTTTAATAATTT
Found at i:223852 original size:29 final size:29
Alignment explanation
Indices: 223777--223850 Score: 125
Period size: 28 Copynumber: 2.6 Consensus size: 29
223767 ATTTTAATAT
223777 AATAATTTTAATAATTTTATATTTCAAAA
1 AATAATTTTAATAATTTTATATTTCAAAA
*
223806 TATAA-TTTAATAATTTTATATTT-AAAA
1 AATAATTTTAATAATTTTATATTTCAAAA
223833 AATAATTTTAATAATTTT
1 AATAATTTTAATAATTTT
223851 TAAATTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
27 8 0.19
28 30 0.71
29 4 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
AATAATTTTAATAATTTTATATTTCAAAA
Found at i:237495 original size:7 final size:7
Alignment explanation
Indices: 237483--237510 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
237473 ATTTTTTTTG
237483 TTTGGGA
1 TTTGGGA
237490 TTTGGGA
1 TTTGGGA
237497 TTTGGGA
1 TTTGGGA
237504 TTTGGGA
1 TTTGGGA
237511 ACAAGGCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
TTTGGGA
Found at i:248948 original size:2 final size:2
Alignment explanation
Indices: 248941--248969 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
248931 ATACATACAT
248941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
248970 CAATTGCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:251763 original size:24 final size:24
Alignment explanation
Indices: 251722--251771 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
251712 TACAAGAATA
* *
251722 TTAAAGGTTAAAGAAGATGGAAGG
1 TTAAAGGTCAAAGAAGATGAAAGG
* *
251746 TTAAAGGTCAAGGGAGATGAAAGG
1 TTAAAGGTCAAAGAAGATGAAAGG
251770 TT
1 TT
251772 GAACATCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.34, T:0.22
Consensus pattern (24 bp):
TTAAAGGTCAAAGAAGATGAAAGG
Found at i:256153 original size:96 final size:95
Alignment explanation
Indices: 255981--256171 Score: 219
Period size: 96 Copynumber: 2.0 Consensus size: 95
255971 AACTTTGGAA
* * * * * *
255981 AAGGATGTTCGATTATCTCGTTTTAAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTCCAGA
1 AAGGATATTCGATTATCTCGTTTGAAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTCCAAA
*
256046 ATCAGAGAT-AAAGAAACATTGCCTCGATTT
66 ATCAGAAATAAAAG-AACATTGCCTCGATTT
**
256076 AAGGATATTCGATTAT-TCGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAAATTT-C
1 AAGGATATTCGATTATCTCG-TTTGAA-AAAAATCGCACCTAGTAAGTTAAGGCAC-AAATTTCC
*
256139 AAAACTC-GAAATAAAAGAATATTGCCTCGATTT
63 AAAA-TCAGAAATAAAAGAACATTGCCTCGATTT
256172 TAAAGTTTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
94 3 0.04
95 20 0.25
96 46 0.57
97 12 0.15
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (95 bp):
AAGGATATTCGATTATCTCGTTTGAAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTCCAAA
ATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:256419 original size:28 final size:27
Alignment explanation
Indices: 256388--256507 Score: 93
Period size: 28 Copynumber: 4.3 Consensus size: 27
256378 AAAATGTGAT
256388 TTTTGGATACTCGAGGGTAAAATGGTAA
1 TTTTGGATACTC-AGGGTAAAATGGTAA
* **
256416 TTTTGGACACTCAGGGGGCAAATGGTAA
1 TTTTGGATACTCA-GGGTAAAATGGTAA
*
256444 TTTTGGGA-AGTTCAGGGTTTAAAATGG-AA
1 TTTT-GGATA-CTCAGGG--TAAAATGGTAA
**
256473 TTTTAGGCAT-CTGGGGGTAAAATGGTAA
1 TTTT-GG-ATACTCAGGGTAAAATGGTAA
256501 TTTTGGA
1 TTTTGGA
256508 AAAAAAAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
26 1 0.01
27 11 0.15
28 37 0.50
29 18 0.24
30 7 0.09
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (27 bp):
TTTTGGATACTCAGGGTAAAATGGTAA
Found at i:256551 original size:29 final size:29
Alignment explanation
Indices: 256510--256625 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
256500 ATTTTGGAAA
256510 AAAAAATAGGGGTCAAAAATGGAATTTTG
1 AAAAAATAGGGGTCAAAAATGGAATTTTG
* *
256539 AAAAAATAAGGGTCAAAAATGGAATTTTT
1 AAAAAATAGGGGTCAAAAATGGAATTTTG
** ** *
256568 TGAAGTTTGGGGT-AAAAATGGTAATTTTTG
1 AAAAAATAGGGGTCAAAAATGG-AA-TTTTG
* *
256598 AAAAAATCGAGGTCAAAAATGGAATTTT
1 AAAAAATAGGGGTCAAAAATGGAATTTT
256626 TGGAAGTTCG
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
28 8 0.12
29 40 0.58
30 13 0.19
31 8 0.12
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.29
Consensus pattern (29 bp):
AAAAAATAGGGGTCAAAAATGGAATTTTG
Found at i:256612 original size:59 final size:60
Alignment explanation
Indices: 256519--256715 Score: 237
Period size: 59 Copynumber: 3.4 Consensus size: 60
256509 AAAAAAATAG
* *
256519 GGGTCAAAAATGG-AA-TTTTGAAAAAAT-AAGGGTCAAAAATGGAATTTTTTGAAGTTTG-
1 GGGT-AAAAATGGTAATTTTTGAAAAAATCAA-GGTCAAAAATGGAATTTTTGGAAGTTCGA
*
256577 GGGTAAAAATGGTAATTTTTGAAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGA
1 GGGTAAAAATGGTAATTTTTGAAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGA
* *** * *
256637 GGGT-AAAATGGTAATTTTTGGAAGTTTCAAGGTCAAAAAT-GAAATTTTGGAAAGTTCGC
1 GGGTAAAAATGGTAATTTTTGAAAAAATCAAGGTCAAAAATGGAATTTTTGG-AAGTTCGA
256696 GGGTAAAAAT-GTAATTTTTG
1 GGGTAAAAATGGTAATTTTTG
256716 GATAGTTTAT
Statistics
Matches: 123, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
57 8 0.07
58 15 0.12
59 90 0.73
60 10 0.08
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (60 bp):
GGGTAAAAATGGTAATTTTTGAAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGA
Done.