Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 18 of 29
Found at i:2705480 original size:14 final size:14
Alignment explanation
Indices: 2705463--2705531 Score: 72
Period size: 14 Copynumber: 4.9 Consensus size: 14
2705453 AGTCATAAGT
*
2705463 AAAAACACAAAAA-
1 AAAAAAACAAAAAG
*
2705476 AAAAAAAGAAAAAG
1 AAAAAAACAAAAAG
2705490 AAAGAAAA-AAAAAG
1 AAA-AAAACAAAAAG
2705504 AAAAAAGACAAAAA-
1 AAAAAA-ACAAAAAG
2705518 AACAAAAACAAAAA
1 AA-AAAAACAAAAA
2705532 CACACACACA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
13 14 0.29
14 22 0.45
15 13 0.27
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAG
Found at i:2705487 original size:10 final size:10
Alignment explanation
Indices: 2705474--2705509 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
2705464 AAAACACAAA
2705474 AAAAAAAAAG
1 AAAAAAAAAG
*
2705484 AAAAAGAAAG
1 AAAAAAAAAG
2705494 AAAAAAAAAG
1 AAAAAAAAAG
2705504 AAAAAA
1 AAAAAA
2705510 GACAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2705517 original size:10 final size:9
Alignment explanation
Indices: 2705471--2705525 Score: 60
Period size: 10 Copynumber: 6.1 Consensus size: 9
2705461 GTAAAAACAC
2705471 AAAA-AAAA
1 AAAAGAAAA
2705479 AAAAGAAAA
1 AAAAGAAAA
2705488 AGAAAGAAAA
1 A-AAAGAAAA
*
2705498 AAAA-AGAA
1 AAAAGAAAA
2705506 AAAAGACAAA
1 AAAAGA-AAA
*
2705516 AAAACAAAA
1 AAAAGAAAA
2705525 A
1 A
2705526 CAAAAACACA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
8 11 0.28
9 13 0.32
10 16 0.40
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:2706892 original size:27 final size:26
Alignment explanation
Indices: 2706861--2706913 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
2706851 TTCTTTCCAA
*
2706861 AGTCCACAACTCTGTGGCACTCTTTTT
1 AGTCCACAACTCCGTGGCAC-CTTTTT
2706888 AGTCCACAACTCCGTGGCACCTTTTT
1 AGTCCACAACTCCGTGGCACCTTTTT
2706914 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.34
Consensus pattern (26 bp):
AGTCCACAACTCCGTGGCACCTTTTT
Found at i:2706928 original size:35 final size:32
Alignment explanation
Indices: 2706763--2707043 Score: 272
Period size: 32 Copynumber: 8.7 Consensus size: 32
2706753 TCTCTTTTCC
* * * *
2706763 AAGTCCACGACTCAGTGGCATCTTTTC-TTCA
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTA
* * *
2706794 AAGTCCACGACTCAGTGGCA--TTTTTTTCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTCTT-TT-A
* *
2706826 AAGTCCACAACTTCGTGGCACCTTTTTCTTTCCA
1 AAGTCCACAACTCCGTGGCACC-TTTTCTTT-TA
*
2706860 AAGTCCACAACTCTGTGGCA-C---TCTTTT-
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTA
* *
2706887 TAGTCCACAACTCCGTGGCACCTTTTTTTTTTTAA
1 AAGTCCACAACTCCGTGGCACC--TTTTCTTTT-A
*
2706922 AAGTCCACAACTCCGTGGCACCTTTTCTTTTC
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTA
2706954 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAA
1 AAGTCCACAACTCCGTGGCACC-TTTTC-TTTT-A
* *
2706989 AAGTCCACAACTCCAGTGGCACCTTTTCCTTTC
1 AAGTCCACAACTCC-GTGGCACCTTTTCTTTTA
2707022 AAGTCCACAACTCCGTGGCACC
1 AAGTCCACAACTCCGTGGCACC
2707044 CCCTTTTAAA
Statistics
Matches: 212, Mismatches: 19, Indels: 37
0.79 0.07 0.14
Matches are distributed among these distances:
27 18 0.08
28 1 0.00
29 9 0.04
30 1 0.00
31 21 0.10
32 48 0.23
33 33 0.16
34 27 0.13
35 46 0.22
36 8 0.04
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.34
Consensus pattern (32 bp):
AAGTCCACAACTCCGTGGCACCTTTTCTTTTA
Found at i:2706972 original size:67 final size:66
Alignment explanation
Indices: 2706793--2707043 Score: 316
Period size: 67 Copynumber: 3.8 Consensus size: 66
2706783 TCTTTTCTTC
* * * * *
2706793 AAAGTCCACGACTCAGTGGCA-TTTTTTTCTTCAAAGTCCACAACTTCGTGGCACC-TTTTTCTT
1 AAAGTCCACAACTCCGTGGCACTTTTCTT-TTC-AAGTCCACAACTCCGTGGCACCTTTTTTTTT
**
2706856 TCC
64 TTA
* *
2706859 AAAGTCCACAACTCTGTGGCAC---TCTTTT-TAGTCCACAACTCCGTGGCACCTTTTTTTTTTT
1 AAAGTCCACAACTCCGTGGCACTTTTCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTTTTTTT
2706920 A
66 A
*
2706921 AAAGTCCACAACTCCGTGGCACCTTTTCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
1 AAAGTCCACAACTCCGTGGCA-CTTTTCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTTTTTT
2706986 TA
65 TA
*
2706988 AAAGTCCACAACTCCAGTGGCACCTTTTCCTTTCAAGTCCACAACTCCGTGGCACC
1 AAAGTCCACAACTCC-GTGGCA-CTTTTCTTTTCAAGTCCACAACTCCGTGGCACC
2707044 CCCTTTTAAA
Statistics
Matches: 165, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
61 20 0.12
62 28 0.17
63 3 0.02
64 3 0.02
66 25 0.15
67 47 0.28
68 39 0.24
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (66 bp):
AAAGTCCACAACTCCGTGGCACTTTTCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTTTTTTT
A
Found at i:2707050 original size:35 final size:34
Alignment explanation
Indices: 2706888--2707044 Score: 205
Period size: 35 Copynumber: 4.6 Consensus size: 34
2706878 CACTCTTTTT
* *
2706888 AGTCCACAACTCCGTGGCACCTTTTTTTTTTTAAA
1 AGTCCACAACTCCGTGGCACC-CTTTTCTTTTAAA
*
2706923 AGTCCACAACTCCGTGGCA-CCTTTTCTTTT-CA
1 AGTCCACAACTCCGTGGCACCCTTTTCTTTTAAA
*
2706955 AGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAA
1 AGTCCACAACTCCGTGGCACCCTTTTC-TTTTAAA
* *
2706990 AGTCCACAACTCCAGTGGCA-CCTTTTCCTTT-CA
1 AGTCCACAACTCC-GTGGCACCCTTTTCTTTTAAA
2707023 AGTCCACAACTCCGTGGCACCC
1 AGTCCACAACTCCGTGGCACCC
2707045 CCTTTTAAAG
Statistics
Matches: 109, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
32 26 0.24
33 30 0.28
34 8 0.07
35 39 0.36
36 6 0.06
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.32
Consensus pattern (34 bp):
AGTCCACAACTCCGTGGCACCCTTTTCTTTTAAA
Found at i:2707171 original size:49 final size:48
Alignment explanation
Indices: 2707115--2707577 Score: 481
Period size: 49 Copynumber: 9.8 Consensus size: 48
2707105 CAACCTTTCC
*
2707115 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTT
* *
2707164 AAGTCCAATGTAGCTGGCCTTGAGTCAGCATATTGGCA-C----CTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTT
*
2707207 AAGTCCAATATTA-CTGGCCTTAAATCAGCATATTGGCACCTTTATCTTT
1 AAGTCCAATA-TAGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTT
* * *
2707256 AAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCA-C----CTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTT
* * * *
2707299 AAGTCCAATATCGCTAGCCTTGAATCAGTAAATTGGCACCTTTATCTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTT
* * *
2707348 AAGTCCATTGTAGCTGGCCTTGAATCAGCACATTGGCA-C----CTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTT
*
2707391 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTT
* * * * * * * *
2707440 AAGTCCAATGTAGTTGGTCTTGAATTAGCACATTGGCATCGTCACCTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTATCTTT
* *
2707489 AAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCGTCTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTATC-T-TT
* * *
2707540 GAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
2707578 TAAGCCCAAT
Statistics
Matches: 341, Mismatches: 49, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
43 110 0.32
44 5 0.01
48 6 0.02
49 182 0.53
50 2 0.01
51 36 0.11
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (48 bp):
AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTT
Found at i:2707211 original size:22 final size:22
Alignment explanation
Indices: 2707186--2707250 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
2707176 GCTGGCCTTG
2707186 AGTCAGCATATTGGCACCTTTA
1 AGTCAGCATATTGGCACCTTTA
** *
2707208 AGTCCAATATTACTGG--CC-TTA
1 AGT-CAGCA-TATTGGCACCTTTA
*
2707229 AATCAGCATATTGGCACCTTTA
1 AGTCAGCATATTGGCACCTTTA
2707251 TCTTTAAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
19 5 0.16
20 3 0.10
21 7 0.23
22 8 0.26
23 3 0.10
24 5 0.16
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (22 bp):
AGTCAGCATATTGGCACCTTTA
Found at i:2707272 original size:92 final size:92
Alignment explanation
Indices: 2707115--2707711 Score: 773
Period size: 92 Copynumber: 6.5 Consensus size: 92
2707105 CAACCTTTCC
2707115 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTG
* *
2707180 GCCTTGAGTCAGCATATTGGCACCTTT
66 GCCTTGAATCAGCACATTGGCACCTTT
** *
2707207 AAGTCCAATATTACTGGCCTTAAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTG
*
2707272 GCCTTGAATTAGCACATTGGCACCTTT
66 GCCTTGAATCAGCACATTGGCACCTTT
* * * *
2707299 AAGTCCAATATCGCTAGCCTTGAATCAGTAAATTGGCACCTTTATCTTTAAGTCCATTGTAGCTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTG
2707364 GCCTTGAATCAGCACATTGGCACCTTT
66 GCCTTGAATCAGCACATTGGCACCTTT
*
2707391 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGTTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTG
* *
2707456 GTCTTGAATTAGCACATTGGCATCGTCACCTTT
66 GCCTTGAATCAGCACATT-G----G-CACCTTT
* * *
2707489 AAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCGTCTTGAGTCCAATGTAGC
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC-T-TTAAGTCCAATGTAGC
2707554 TGGCCTTGAATCAGCACATTGGCA----T
64 TGGCCTTGAATCAGCACATTGGCACCTTT
* * * ** * * *
2707579 AAGCCCAATATCGCTGGCCTTGAGTTAGCATATTGGCACC-TCGTCTTTAAGACCAATGTCGATG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTG
* *
2707643 GTCTTGAATCAGCACATTAGCA-C---
66 GCCTTGAATCAGCACATTGGCACCTTT
* * * *
2707666 AAG-CCTAATATCGTTGGCCGTGAATCAGCATATTGGTATCTTTATC
1 AAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
2707712 ACTTTTCTCA
Statistics
Matches: 447, Mismatches: 47, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
86 2 0.00
87 65 0.15
88 4 0.01
89 3 0.01
90 37 0.08
92 246 0.55
93 1 0.00
94 2 0.00
95 1 0.00
97 1 0.00
98 51 0.11
99 2 0.00
100 32 0.07
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (92 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTG
GCCTTGAATCAGCACATTGGCACCTTT
Found at i:2707623 original size:141 final size:139
Alignment explanation
Indices: 2707200--2707665 Score: 418
Period size: 141 Copynumber: 3.3 Consensus size: 139
2707190 AGCATATTGG
* * *
2707200 CACCTTTAAGTCCAATATTACTGGCCTTAAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTT-TCTTTAAGTCCAAT
* * * *
2707265 GTAGCTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGTAA
65 GTAGCTGGCCTTGAATCAGCACATTGGCA---TTAAGTCCAATATCGCTGGCCTTGAATTAGCAA
2707330 ATTGGCACCT--T
127 ATTGGCACCTCGT
* * * * * *
2707341 TATCTTTAAGTCCATTGTAGCTGGCCTTGAATCAGCACATTGGCA-C----CTTTAAGTCCAATA
1 CACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTTTCTTTAAGTCCAATG
* * * * * *
2707401 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGTTGGTCTTGAATT
66 TAGCTGGCCTTGAATCAGCACATTGG---C---A---TTAAGTCCAATATCGCTGGCCTTGAATT
*
2707466 AGCACATTGGCA--TCGT
122 AGCAAATTGGCACCTCGT
* *
2707482 CACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCGTCTTGAGTCCA
1 CACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACC-TTTTC-T-TTAAGTCCA
* * *
2707547 ATGTAGCTGGCCTTGAATCAGCACATTGGCA-TAAGCCCAATATCGCTGGCCTTGAGTTAGCATA
63 ATGTAGCTGGCCTTGAATCAGCACATTGGCATTAAGTCCAATATCGCTGGCCTTGAATTAGCAAA
2707611 TTGGCACCTCGT
128 TTGGCACCTCGT
* * * * * *
2707623 ---CTTTAAGACCAATGTCGATGGTCTTGAATCAGCACATTAGCAC
1 CACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCAC
2707666 AAGCCTAATA
Statistics
Matches: 262, Mismatches: 45, Indels: 39
0.76 0.13 0.11
Matches are distributed among these distances:
135 36 0.14
138 37 0.14
139 33 0.13
140 1 0.00
141 116 0.44
142 1 0.00
143 1 0.00
146 1 0.00
147 1 0.00
148 1 0.00
149 34 0.13
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (139 bp):
CACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTTTCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGCATTAAGTCCAATATCGCTGGCCTTGAATTAGCAAATTG
GCACCTCGT
Found at i:2707676 original size:87 final size:87
Alignment explanation
Indices: 2707493--2707701 Score: 258
Period size: 87 Copynumber: 2.4 Consensus size: 87
2707483 ACCTTTAAGT
* * * *
2707493 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCGTCTTGAGTCCAATGTAGCTGGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC---TTCGTCTTAAGACCAATGTAGATGGC
* *
2707558 CTTGAATCAGCACATTGGCATAAGC
63 CTTGAATCAGCACATTAGCACAAGC
* * * *
2707583 CCAATATCGCTGGCCTTGAGTTAGCATATTGGCACC-TCGTCTTTAAGACCAATGTCGATGGTCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTC-TTAAGACCAATGTAGATGGCCT
2707647 TGAATCAGCACATTAGCACAAGC
65 TGAATCAGCACATTAGCACAAGC
* * *
2707670 CTAATATCGTTGGCCGTGAATCAGCATATTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGG
2707702 TATCTTTATC
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
86 5 0.05
87 65 0.63
90 33 0.32
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCTTAAGACCAATGTAGATGGCCTT
GAATCAGCACATTAGCACAAGC
Found at i:2708577 original size:13 final size:13
Alignment explanation
Indices: 2708559--2708583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2708549 TTCAACAATT
2708559 TGTATCGATACAA
1 TGTATCGATACAA
2708572 TGTATCGATACA
1 TGTATCGATACA
2708584 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2708652 original size:13 final size:13
Alignment explanation
Indices: 2708634--2708658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2708624 GCTAAGGAAA
2708634 TGTATCGATACAC
1 TGTATCGATACAC
2708647 TGTATCGATACA
1 TGTATCGATACA
2708659 TGGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:2715398 original size:22 final size:21
Alignment explanation
Indices: 2715357--2715398 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
2715347 TTTAAATATG
2715357 ATTAAATTTATTTTTGTTATA
1 ATTAAATTTATTTTTGTTATA
2715378 ATTAAGATATTATTTTT-TTAT
1 ATTAA-AT-TTATTTTTGTTAT
2715399 TTATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTAAATTTATTTTTGTTATA
Found at i:2715480 original size:26 final size:26
Alignment explanation
Indices: 2715451--2715502 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2715441 ACTTTATAAT
*
2715451 TTATGAAATTATTTACGATATTGTTA
1 TTATGAAATTATTTACGATAATGTTA
*
2715477 TTATGAAATTATTTATGATAATGTTA
1 TTATGAAATTATTTACGATAATGTTA
2715503 GCTCGGTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.50
Consensus pattern (26 bp):
TTATGAAATTATTTACGATAATGTTA
Found at i:2716088 original size:13 final size:14
Alignment explanation
Indices: 2716070--2716103 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2716060 TTATAGGTTC
*
2716070 TTTTAAATTTTAT-
1 TTTTAAATTATATA
2716083 TTTTAAATTATATA
1 TTTTAAATTATATA
2716097 TTTTAAA
1 TTTTAAA
2716104 AAATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAAATTATATA
Found at i:2716244 original size:17 final size:17
Alignment explanation
Indices: 2716211--2716255 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
2716201 AATACATAAA
**
2716211 TTAATTTAAATTTTTAT
1 TTAATTTAAATAATTAT
2716228 TTAATTTAAATAATTAT
1 TTAATTTAAATAATTAT
2716245 TATAAATTTAA
1 T-T-AATTTAA
2716256 TTTAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 16 0.67
18 1 0.04
19 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTAAATAATTAT
Found at i:2716274 original size:23 final size:24
Alignment explanation
Indices: 2716226--2716279 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
2716216 TTAAATTTTT
** *
2716226 ATTTAATTTAAATAATTATTATAA
1 ATTTAATTTAAATAATTAACAAAA
2716250 ATTTAATTT-AATAATTAACAAAA
1 ATTTAATTTAAATAATTAACAAAA
*
2716273 ATATAAT
1 ATTTAAT
2716280 ATGTTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAATTTAAATAATTAACAAAA
Found at i:2716340 original size:15 final size:15
Alignment explanation
Indices: 2716322--2716352 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2716312 TAAATAATAA
2716322 TAATTTAAAATTATT
1 TAATTTAAAATTATT
*
2716337 TAATTTAACATTATT
1 TAATTTAAAATTATT
2716352 T
1 T
2716353 TATAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTAAAATTATT
Found at i:2717423 original size:36 final size:34
Alignment explanation
Indices: 2717377--2717464 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
2717367 TTTTTATATT
**
2717377 TATATTAATTTTTAATTATAATCATAAA-ATATTAAA
1 TATA-TAATTTTTAAAAATAAT-ATAAATAT-TTAAA
*
2717413 TATATAAATTTTAAAAAATAATATAAATATTTAAA
1 TATAT-AATTTTTAAAAATAATATAAATATTTAAA
*
2717448 TAAATAATTTATTAAAA
1 TATATAATTT-TTAAAA
2717465 TTTATATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 20 0.45
36 19 0.43
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
TATATAATTTTTAAAAATAATATAAATATTTAAA
Found at i:2717436 original size:21 final size:23
Alignment explanation
Indices: 2717411--2717468 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 23
2717401 TAAAATATTA
2717411 AATATATAAAT-TTTAAA-AAAT
1 AATATATAAATATTTAAATAAAT
2717432 -A-ATATAAATATTTAAATAAAT
1 AATATATAAATATTTAAATAAAT
*
2717453 AATTTATTAAA-ATTTA
1 AATATA-TAAATATTTA
2717469 TATGAAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
21 4 0.13
22 1 0.03
23 7 0.23
24 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATATAAATATTTAAATAAAT
Found at i:2717438 original size:19 final size:21
Alignment explanation
Indices: 2717409--2717455 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
2717399 CATAAAATAT
2717409 TAAAT-ATATAAAT-TTTAAA
1 TAAATAATATAAATATTTAAA
2717428 -AAATAATATAAATATTTAAA
1 TAAATAATATAAATATTTAAA
2717448 TAAATAAT
1 TAAATAAT
2717456 TTATTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 6 0.24
21 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATAATATAAATATTTAAA
Found at i:2717439 original size:35 final size:37
Alignment explanation
Indices: 2717394--2717464 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
2717384 ATTTTTAATT
*
2717394 ATAATCATAAA-ATATTAAATATATAAATT-TTAAAAA
1 ATAATCATAAATAT-TTAAATAAATAAATTATTAAAAA
*
2717430 ATAAT-ATAAATATTTAAATAAATAATTTATTAAAA
1 ATAATCATAAATATTTAAATAAATAAATTATTAAAA
2717465 TTTATATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 18 0.58
36 13 0.42
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (37 bp):
ATAATCATAAATATTTAAATAAATAAATTATTAAAAA
Found at i:2717610 original size:22 final size:21
Alignment explanation
Indices: 2717585--2717633 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
2717575 AAAATTAATT
*
2717585 TTAAAATTTAATA-AATATATTA
1 TTAAAA-TTAATATAA-ATATAA
2717607 TTAAAA-TAATATAAATATAA
1 TTAAAATTAATATAAATATAA
2717627 TTAAAAT
1 TTAAAAT
2717634 GTATAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 16 0.67
21 2 0.08
22 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAATTAATATAAATATAA
Found at i:2718688 original size:2 final size:2
Alignment explanation
Indices: 2718681--2718711 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2718671 CATTCTCCCT
2718681 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2718712 TGGGTATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2722751 original size:2 final size:2
Alignment explanation
Indices: 2722744--2722773 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2722734 TTAAGCAGTG
2722744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2722774 GGAACCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2731302 original size:3 final size:3
Alignment explanation
Indices: 2731294--2731325 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2731284 AAATTAATTA
2731294 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2731326 GACACTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2735469 original size:32 final size:34
Alignment explanation
Indices: 2735433--2735553 Score: 158
Period size: 36 Copynumber: 3.5 Consensus size: 34
2735423 TCATTCAAGT
**
2735433 CTAAGATAGAAACCTC-CT-TATC-TTTTCACGGG
1 CTAAGATAG-AACCTCTCTCTATCTTTTTCAAAGG
2735465 CTAAGATAGAACCTCTCTCCCTATCTTTTTCAAAGG
1 CTAAGATAGAACCTCTCT--CTATCTTTTTCAAAGG
2735501 CTAAGATAGAACCTCTCTCCCTATCTTTTTCAAAGG
1 CTAAGATAGAACCTCTCT--CTATCTTTTTCAAAGG
2735537 CTAAGATAGAACCTCTC
1 CTAAGATAGAACCTCTC
2735554 AATCACTTAG
Statistics
Matches: 82, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
31 6 0.07
32 11 0.13
35 4 0.05
36 61 0.74
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (34 bp):
CTAAGATAGAACCTCTCTCTATCTTTTTCAAAGG
Found at i:2735503 original size:36 final size:36
Alignment explanation
Indices: 2735446--2735553 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
2735436 AGATAGAAAC
* **
2735446 CTCCTTATC-TTTTCACGGGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
2735481 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
2735517 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
2735553 C
1 C
2735554 AATCACTTAG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 8 0.12
36 61 0.88
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (36 bp):
CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
Found at i:2736052 original size:24 final size:24
Alignment explanation
Indices: 2736020--2736090 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
2736010 CAATGTATCA
2736020 ATACATGAACAGTGATAAACAGTG
1 ATACATGAACAGTGATAAACAGTG
* * *
2736044 ATACATGAACAATGATGAATAGTG
1 ATACATGAACAGTGATAAACAGTG
* *
2736068 ATATATAAACAGTGATAAACAGT
1 ATACATGAACAGTGATAAACAGT
2736091 AATGTATCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (24 bp):
ATACATGAACAGTGATAAACAGTG
Found at i:2740255 original size:19 final size:18
Alignment explanation
Indices: 2740231--2740328 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
2740221 TAGCTTACAT
2740231 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
2740250 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
2740263 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
2740282 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
2740295 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
2740315 TGTATCGATACAAA
1 TGTATCGATACAAA
2740329 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:2740267 original size:32 final size:32
Alignment explanation
Indices: 2740226--2740326 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
2740216 GGCAGTAGCT
*
2740226 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
2740258 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
2740290 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
2740323 TACA
1 TACA
2740327 AATCGTTGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 52 0.78
33 15 0.22
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:2740268 original size:13 final size:13
Alignment explanation
Indices: 2740250--2740306 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2740240 ACAAAACTTA
2740250 TGTATCGATACAT
1 TGTATCGATACAT
2740263 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
2740281 ATGTATCGATACAT
1 -TGTATCGATACAT
2740295 TGTATCGATACA
1 TGTATCGATACA
2740307 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2740714 original size:58 final size:57
Alignment explanation
Indices: 2740652--2740888 Score: 162
Period size: 58 Copynumber: 4.1 Consensus size: 57
2740642 TAAAAAAGTT
*
2740652 CCTAAAACATGAAAAATGACTAAAATGATCTTAAAATGTAGGAAATCGCATAAAAATC
1 CCTAAAACATGAAAAATGACTAAAATGATCTTAAAATGTAAGAAAT-GCATAAAAATC
* * * * *
2740710 CCTAAAACATTG-CAAATGACCT-AAATGGTTTTAAAATGCAAGAAATTAG-AT-AAAAGC
1 CCTAAAACA-TGAAAAATGA-CTAAAATGATCTTAAAATGTAAGAAA-T-GCATAAAAATC
* * * * ** * **
2740767 CCTTAAAACATGAGAAATTACTAAAATGACCCTAAAATGTGTGAAATTGAATAAATGGT-
1 CC-TAAAACATGAAAAATGACTAAAATGATCTTAAAATGTAAGAAA-TGCATAAA-AATC
* ** * *
2740826 CCTAAATCATGGTAAATTACTAAAATGATGCAT-AAATGTAAGAAATGACATAAAAATC
1 CCTAAAACATGAAAAATGACTAAAATGAT-CTTAAAATGTAAGAAATG-CATAAAAATC
2740884 CCTAA
1 CCTAA
2740889 GTCATGGAAA
Statistics
Matches: 138, Mismatches: 29, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
57 15 0.11
58 111 0.80
59 12 0.09
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.25
Consensus pattern (57 bp):
CCTAAAACATGAAAAATGACTAAAATGATCTTAAAATGTAAGAAATGCATAAAAATC
Found at i:2740802 original size:29 final size:28
Alignment explanation
Indices: 2740770--2740853 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
2740760 TAAAAGCCCT
2740770 TAAAACATGAGAAATTACTAAAATGACCC
1 TAAAACATG-GAAATTACTAAAATGACCC
** * **
2740799 TAAAATGTGTGAAATTGAAT-AAATGGTCC
1 TAAAACATG-GAAATT-ACTAAAATGACCC
*
2740828 TAAATCATGGTAAATTACTAAAATGA
1 TAAAACATGG-AAATTACTAAAATGA
2740854 TGCATAAATG
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
28 3 0.07
29 36 0.88
30 2 0.05
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (28 bp):
TAAAACATGGAAATTACTAAAATGACCC
Found at i:2740894 original size:58 final size:57
Alignment explanation
Indices: 2740826--2740999 Score: 147
Period size: 58 Copynumber: 3.0 Consensus size: 57
2740816 AATAAATGGT
* * *
2740826 CCTAAATCATGGTAAATTACTAAAATGATGCATAAATGTAAGAAATGACATAAAAATC
1 CCTAAGTCATGG-AAATCACTAAAATGATGCATAAATGTAAGAAATAACATAAAAATC
*
2740884 CCTAAGTCATGGAAATCATTAAAATGA--CATAAAAATGTATA-AAATAACATAAAAATC
1 CCTAAGTCATGGAAATCACTAAAATGATGCAT--AAATGTA-AGAAATAACATAAAAATC
** * * * * * * * * *
2740941 TTTAGGTTATGAAAAATGACTAAAATAATGTAAAAATGTATGAAATAACACAAAAATC
1 CCTAAGTCATG-GAAATCACTAAAATGATGCATAAATGTAAGAAATAACATAAAAATC
2740999 C
1 C
2741000 ATAATATGCA
Statistics
Matches: 92, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
55 3 0.03
57 42 0.46
58 46 0.50
60 1 0.01
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (57 bp):
CCTAAGTCATGGAAATCACTAAAATGATGCATAAATGTAAGAAATAACATAAAAATC
Found at i:2747708 original size:4 final size:4
Alignment explanation
Indices: 2747699--2747728 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2747689 CAATAAATCC
2747699 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
2747729 CTAAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:2750139 original size:15 final size:14
Alignment explanation
Indices: 2750104--2750150 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2750094 TGATACTAAA
2750104 AATATTTTATATAT
1 AATATTTTATATAT
*
2750118 AAGATTTTACTATAT
1 AATATTTTA-TATAT
* *
2750133 TATA-TTTATAAAT
1 AATATTTTATATAT
2750146 AATAT
1 AATAT
2750151 AATAATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 7 0.27
14 12 0.46
15 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
AATATTTTATATAT
Found at i:2750229 original size:30 final size:29
Alignment explanation
Indices: 2750131--2750231 Score: 85
Period size: 36 Copynumber: 3.1 Consensus size: 29
2750121 ATTTTACTAT
2750131 ATTATATTTATAAATAATATAATAATAATTAAA
1 ATTATATTTA-AAAT-ATATAAT-AT-ATTAAA
* *
2750164 TATTTTATATTTAATAATATTAAAAATATACTAAA
1 -A--TTATATTTAA-AATA-T-ATAATATATTAAA
2750199 ATTATATTTAAAAGTATATAATATATTAAA
1 ATTATATTTAAAA-TATATAATATATTAAA
2750229 ATT
1 ATT
2750232 TTAGTTTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
30 14 0.25
31 3 0.05
32 12 0.21
34 2 0.04
35 7 0.12
36 15 0.26
37 4 0.07
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTATATTTAAAATATATAATATATTAAA
Found at i:2750748 original size:30 final size:31
Alignment explanation
Indices: 2750694--2750766 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
2750684 ATTAAAGTTT
* * *
2750694 AAAATATACATATTTTTAATATTTAAATTAT-
1 AAAAT-TATATATATTTAATATTTAAATGATA
* * *
2750725 AATATTATATATATTTATTATTTATATGATA
1 AAAATTATATATATTTAATATTTAAATGATA
2750756 AAAATTATATA
1 AAAATTATATA
2750767 ATATATATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
AAAATTATATATATTTAATATTTAAATGATA
Found at i:2750789 original size:42 final size:42
Alignment explanation
Indices: 2750722--2750803 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 42
2750712 ATATTTAAAT
* * *
2750722 TATAATATTATATATATTTATTATTTATATGA-TAAAAATTA
1 TATAATATTATATATACTAATTATTTATATAATTAAAAATTA
2750763 TATAATA-TATATATAACTAATATATTTATATAATTAAAAAT
1 TATAATATTATATAT-ACTAAT-TATTTATATAATTAAAAAT
2750804 ATGTTAAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 7 0.20
41 11 0.31
42 10 0.29
43 7 0.20
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (42 bp):
TATAATATTATATATACTAATTATTTATATAATTAAAAATTA
Found at i:2750881 original size:19 final size:18
Alignment explanation
Indices: 2750857--2750898 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
2750847 AATTTGATTA
2750857 TTTTTTAAATAAATTTAAT
1 TTTTTTAAATAAATTT-AT
**
2750876 TTTTTTATTTAAATTTAT
1 TTTTTTAAATAAATTTAT
2750894 TTTTT
1 TTTTT
2750899 GAGTATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTAAATAAATTTAT
Found at i:2752598 original size:13 final size:13
Alignment explanation
Indices: 2752578--2752602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2752568 ATTTTATCAT
2752578 TTAAATAGTAATA
1 TTAAATAGTAATA
2752591 TTAAATAGTAAT
1 TTAAATAGTAAT
2752603 TGGCAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
TTAAATAGTAATA
Found at i:2753379 original size:31 final size:32
Alignment explanation
Indices: 2753344--2753403 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
2753334 AAAAATATTA
2753344 AAATAA-AATTAATAATTAAAGT-TTTTTAAAT
1 AAATAATAATTAA-AATTAAAGTATTTTTAAAT
* *
2753375 AAATAATTATTAAAATTAAATTATTTTTA
1 AAATAATAATTAAAATTAAAGTATTTTTA
2753404 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (32 bp):
AAATAATAATTAAAATTAAAGTATTTTTAAAT
Found at i:2753517 original size:15 final size:16
Alignment explanation
Indices: 2753499--2753532 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2753489 GCTTAATTTC
2753499 TTTT-AATTTAAATAA
1 TTTTAAATTTAAATAA
*
2753514 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATAA
2753530 TTT
1 TTT
2753533 CATATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAATTTAAATAA
Found at i:2754541 original size:16 final size:17
Alignment explanation
Indices: 2754488--2754543 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 17
2754478 AATTATTAAC
*
2754488 ATAT-TAAAATTATATA
1 ATATATAAATTTATATA
*
2754504 ATATATAATACTTTAAATA
1 ATATATAA-A-TTTATATA
2754523 ATATATAAATTTATA-A
1 ATATATAAATTTATATA
2754539 ATATA
1 ATATA
2754544 ATATGATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 10 0.29
17 8 0.24
18 2 0.06
19 14 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAAATTTATATA
Found at i:2754928 original size:12 final size:12
Alignment explanation
Indices: 2754900--2754932 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2754890 ATCGATCTAA
*
2754900 ATTTTATTTTTT
1 ATTTAATTTTTT
2754912 A-TTAATTTTTT
1 ATTTAATTTTTT
2754923 ATTTAATTTT
1 ATTTAATTTT
2754933 AAAAAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTAATTTTTT
Found at i:2755405 original size:16 final size:15
Alignment explanation
Indices: 2755372--2755406 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2755362 ATATTAATAT
*
2755372 TTATAATTTTTTATA
1 TTATAATTTTTTAAA
2755387 TTATAATTTTTTAAAA
1 TTATAATTTTTT-AAA
2755403 TTAT
1 TTAT
2755407 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATAATTTTTTAAA
Found at i:2755520 original size:14 final size:15
Alignment explanation
Indices: 2755501--2755530 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2755491 GGTGTTGATG
2755501 TTTTTATT-GAAAAT
1 TTTTTATTAGAAAAT
2755515 TTTTTATTAGAAAAT
1 TTTTTATTAGAAAAT
2755530 T
1 T
2755531 GTGTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTTTATTAGAAAAT
Found at i:2756017 original size:110 final size:107
Alignment explanation
Indices: 2755792--2756017 Score: 283
Period size: 110 Copynumber: 2.1 Consensus size: 107
2755782 ACATTAAATT
* * * *
2755792 ATTTTATTTTTAACATTTTAATTTTTCTTTATCCTTAAAAATGTAAATAAATTTATTTCATATAA
1 ATTTTACTTTTAACATTTTAATTTTTCATTAACCTTAAAAATGTAAATAAATTTATTTCAAATAA
* * *
2755857 AATAGTTAAAACTTACATTAAGTTTATTTATTGATATTTTTA
66 AAAAGTTAAAACTCACATTAAATTTATTTATTGATATTTTTA
**
2755899 ATTTTTTTACTTTTAACATTTTAATTTTTCATTAACCTTAAAAA-GTAAATAGGTTTATTTCAAA
1 A---TTTTACTTTTAACATTTTAATTTTTCATTAACCTTAAAAATGTAAATAAATTTATTTCAAA
**
2755963 TAAAAAAGTGTTAAAACTCACATTAAATTTATTTATCTTTTTATTTTTA
63 TAAAAAA--GTTAAAACTCACATTAAATTTATTTA--TTGATATTTTTA
2756012 ATTTTA
1 ATTTTA
2756018 TATTAAAATT
Statistics
Matches: 101, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
107 1 0.01
109 23 0.23
110 42 0.42
111 24 0.24
113 11 0.11
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (107 bp):
ATTTTACTTTTAACATTTTAATTTTTCATTAACCTTAAAAATGTAAATAAATTTATTTCAAATAA
AAAAGTTAAAACTCACATTAAATTTATTTATTGATATTTTTA
Found at i:2759419 original size:20 final size:21
Alignment explanation
Indices: 2759385--2759429 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
2759375 TGCAAACAAT
2759385 TTAAAAGGATAAATTACTTAA
1 TTAAAAGGATAAATTACTTAA
*
2759406 TTAAAAGG-TAAATTATTTAA
1 TTAAAAGGATAAATTACTTAA
2759426 TTAA
1 TTAA
2759430 TAATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (21 bp):
TTAAAAGGATAAATTACTTAA
Found at i:2759428 original size:28 final size:27
Alignment explanation
Indices: 2759396--2759479 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 27
2759386 TAAAAGGATA
2759396 AATTACTTAATTAAAAGGTAAATTATTT
1 AATTA-TTAATTAAAAGGTAAATTATTT
*
2759424 AATTAATAATTTTAAAA-GTAAATTATTT
1 AATTATTAA--TTAAAAGGTAAATTATTT
* * *
2759452 AACTAATGATTTAAAAGGTAAATTATTT
1 AA-TTATTAATTAAAAGGTAAATTATTT
2759480 GATTTTGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
27 9 0.19
28 29 0.62
29 9 0.19
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (27 bp):
AATTATTAATTAAAAGGTAAATTATTT
Found at i:2759630 original size:93 final size:95
Alignment explanation
Indices: 2759512--2759696 Score: 284
Period size: 93 Copynumber: 2.0 Consensus size: 95
2759502 ACAGGGTAAC
* *
2759512 TTATTCATTTCCCACAACACCATATAATTATACGTCCATGTTTTACACAATTAATTT-AAACCAC
1 TTATTCATTTCCCACAACACCATATAATTATACATCCATATTTTACACAATTAATTTAAAACCAC
*
2759576 AAAATTATTATAGTTTATAAAA-AAATAAA
66 AAAATTATTATAATTTATAAAATAAATAAA
* * * * *
2759605 TTATTCATTTCCCACAACACTATATAATTATACATGCATATTTTACATAATTAATTTAAAACTAT
1 TTATTCATTTCCCACAACACCATATAATTATACATCCATATTTTACACAATTAATTTAAAACCAC
2759670 AAAATTATTATAATTTATAAAATAAAT
66 AAAATTATTATAATTTATAAAATAAAT
2759697 TAACTTACTT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 52 0.63
94 26 0.32
95 4 0.05
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (95 bp):
TTATTCATTTCCCACAACACCATATAATTATACATCCATATTTTACACAATTAATTTAAAACCAC
AAAATTATTATAATTTATAAAATAAATAAA
Found at i:2760136 original size:36 final size:36
Alignment explanation
Indices: 2760076--2760146 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
2760066 AAAACTTGCA
* *
2760076 AAAATATGAACAAATTAAATAAAACACTATAAAATC
1 AAAATATGAACAAAATAAATAAAACACTAAAAAATC
* *
2760112 AAAATATTAACAAAAATAAA-AAAACCCTAAAAAAT
1 AAAATATGAAC-AAAATAAATAAAACACTAAAAAAT
2760147 AGCTTAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 23 0.77
37 7 0.23
ACGTcount: A:0.68, C:0.11, G:0.01, T:0.20
Consensus pattern (36 bp):
AAAATATGAACAAAATAAATAAAACACTAAAAAATC
Found at i:2760612 original size:14 final size:14
Alignment explanation
Indices: 2760577--2760614 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2760567 ATGTATATGA
2760577 ATATATAAATTATT
1 ATATATAAATTATT
*
2760591 ATACATAAATTATT
1 ATATATAAATTATT
*
2760605 ATTTATAAAT
1 ATATATAAAT
2760615 ACACAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATAAATTATT
Found at i:2761517 original size:2 final size:2
Alignment explanation
Indices: 2761512--2761550 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2761502 TGTTATTTTC
*
2761512 AT AT AT AA 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
2761551 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2761555 original size:2 final size:2
Alignment explanation
Indices: 2761550--2761576 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2761540 ATATATATAT
2761550 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2761577 ATGTTAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2771313 original size:97 final size:96
Alignment explanation
Indices: 2771139--2771382 Score: 364
Period size: 97 Copynumber: 2.5 Consensus size: 96
2771129 TTTTATTCAT
2771139 CGGGGATACTCCAACCCCATTATTCCGAGGGGATACTCCAACCCCGTTTTTTAAACTTGTCAAGA
1 CGGGGATACTCCAACCCCATTATTCCGAGGGGATACTCCAACCCCGTTTTTTAAACTTGTCAAGA
2771204 TCATTCTTATTTTTACCTAAACTATTATTGA
66 TCATTCTTATTTTTACCTAAACTATTATTGA
* * * **
2771235 CGGGGACAGTCCAACTCCATTATTCCGAGGGGATACTCCAACCTTGTTTTTTTAAACTTGTCAAG
1 CGGGGATACTCCAACCCCATTATTCCGAGGGGATACTCCAACCCCG-TTTTTTAAACTTGTCAAG
*
2771300 ATCATTCTTATTTTTACCTAAACTATTATTGT
65 ATCATTCTTATTTTTACCTAAACTATTATTGA
* ** * *
2771332 CGGGGATACTCCAACCGCATCCCTT-CGAGGAGATACTCCAACCCCATTTTT
1 CGGGGATACTCCAACCCCAT-TATTCCGAGGGGATACTCCAACCCCGTTTTT
2771383 CAACAAAAAA
Statistics
Matches: 130, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
96 46 0.35
97 82 0.63
98 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (96 bp):
CGGGGATACTCCAACCCCATTATTCCGAGGGGATACTCCAACCCCGTTTTTTAAACTTGTCAAGA
TCATTCTTATTTTTACCTAAACTATTATTGA
Found at i:2775409 original size:22 final size:22
Alignment explanation
Indices: 2775384--2775431 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2775374 TAGAAGATTA
* *
2775384 AAATATTA-TTTTTATATATCAT
1 AAATATAATTTTTTAAAT-TCAT
*
2775406 AAATGTAATTTTTTAAATTCAT
1 AAATATAATTTTTTAAATTCAT
2775428 AAAT
1 AAAT
2775432 TAAAATTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
AAATATAATTTTTTAAATTCAT
Found at i:2775418 original size:23 final size:23
Alignment explanation
Indices: 2775392--2775448 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2775382 TAAAATATTA
2775392 TTTTTATATATCATAAATGT-AAT
1 TTTTTATATATCATAAAT-TAAAT
*
2775415 TTTTTAAAT-TCATAAATTAAAAT
1 TTTTTATATATCATAAATT-AAAT
*
2775438 TTGTTATATAT
1 TTTTTATATAT
2775449 ATTATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 8 0.29
23 18 0.64
24 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTTATATATCATAAATTAAAT
Found at i:2776765 original size:24 final size:23
Alignment explanation
Indices: 2776727--2776772 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2776717 CTAAAATTTT
* *
2776727 AAATAATAATAATTAATCAATTG
1 AAATAAAAATAATTAATAAATTG
2776750 AAATAAAAATATATTAATAAATT
1 AAATAAAAATA-ATTAATAAATT
2776773 CATTTCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATAAAAATAATTAATAAATTG
Found at i:2778101 original size:16 final size:15
Alignment explanation
Indices: 2778062--2778104 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
2778052 CTAAACAAGT
2778062 TTGTATCAATATAAA
1 TTGTATCAATATAAA
*
2778077 TTG-ATCAATATAGA
1 TTGTATCAATATAAA
2778091 TTAGTATCAATATA
1 TT-GTATCAATATA
2778105 CACATTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 12 0.48
15 4 0.16
16 9 0.36
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (15 bp):
TTGTATCAATATAAA
Found at i:2778228 original size:19 final size:21
Alignment explanation
Indices: 2778185--2778229 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2778175 ACTAATTTTT
* *
2778185 TATTTTTTTCTTAATCATTTT
1 TATTTTTTTCATAATCATTTA
2778206 TATTTTTTTCAT-AT-ATTTA
1 TATTTTTTTCATAATCATTTA
2778225 TATTT
1 TATTT
2778230 AAATAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 2 0.09
21 11 0.50
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTTTTTCATAATCATTTA
Found at i:2778713 original size:39 final size:37
Alignment explanation
Indices: 2778670--2778807 Score: 127
Period size: 38 Copynumber: 3.6 Consensus size: 37
2778660 TTAAGGACTC
2778670 TATTTTAATATAGAAATTATTAAATTGATTTTATGAATA
1 TATTTTAATATA-AAATTATTAAATTGATTTTAT-AATA
* * * * *
2778709 TATTTTAATATCAAAGTGTT-AATATGATTTTAAAAATT
1 TATTTTAATATAAAATTATTAAAT-TGATTTT-ATAATA
2778747 TATTTTAATATAAAATTATTAAAATT-ATCTTTATAGATA
1 TATTTTAATATAAAATTATT-AAATTGAT-TTTATA-ATA
* * *
2778786 TGTATTAATATAAAAATATTAA
1 TATTTTAATATAAAATTATTAA
2778808 TGTGATCTTG
Statistics
Matches: 80, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
37 3 0.04
38 39 0.49
39 35 0.44
40 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (37 bp):
TATTTTAATATAAAATTATTAAATTGATTTTATAATA
Found at i:2778715 original size:78 final size:77
Alignment explanation
Indices: 2778611--2778771 Score: 200
Period size: 78 Copynumber: 2.1 Consensus size: 77
2778601 TAAAGTTTAC
* * * * *
2778611 TAAAATGATTTTAATGAATATATTTTAATTTGAGAA-TGTTGATAAAATTTTAAGGACTCTATTT
1 TAAAATGATTTTAATGAATATATTTTAATATCA-AAGTGTTAATAAAATTTTAA-AAATCTATTT
2778675 TAATATAGAAATTAT
64 TAATATA-AAATTAT
* ** *
2778690 TAAATTGATTTT-ATGAATATATTTTAATATCAAAGTGTTAATATGATTTTAAAAATTTATTTTA
1 TAAAATGATTTTAATGAATATATTTTAATATCAAAGTGTTAATAAAATTTTAAAAATCTATTTTA
2778754 ATATAAAATTAT
66 ATATAAAATTAT
2778766 TAAAAT
1 TAAAAT
2778772 TATCTTTATA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
76 12 0.17
77 16 0.23
78 32 0.45
79 11 0.15
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (77 bp):
TAAAATGATTTTAATGAATATATTTTAATATCAAAGTGTTAATAAAATTTTAAAAATCTATTTTA
ATATAAAATTAT
Found at i:2778794 original size:77 final size:78
Alignment explanation
Indices: 2778670--2778832 Score: 190
Period size: 77 Copynumber: 2.1 Consensus size: 78
2778660 TTAAGGACTC
* * * *
2778670 TATTTTAATATAGAAATTATTAAATTGATTTTATGAATATATTTTAATATCAAAGTGTTAATATG
1 TATTTTAATATAGAAATTATTAAATTGATTTTATGAATATATATTAATATAAAAATATTAATATG
*
2778735 AT-TTTAAAAATT
66 ATCTTGAAAAATT
*
2778747 TATTTTAATATA-AAATTATTAAAATT-ATCTTTAT-AGATATGTATTAATATAAAAATATTAAT
1 TATTTTAATATAGAAATTATT-AAATTGAT-TTTATGA-ATATATATTAATATAAAAATATTAAT
* *
2778809 GTGATCTTGAAAACTT
63 ATGATCTTGAAAAATT
*
2778825 GATTTTAA
1 TATTTTAA
2778833 AGCAAAAATA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
76 11 0.15
77 47 0.64
78 15 0.21
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (78 bp):
TATTTTAATATAGAAATTATTAAATTGATTTTATGAATATATATTAATATAAAAATATTAATATG
ATCTTGAAAAATT
Found at i:2779208 original size:2 final size:2
Alignment explanation
Indices: 2779201--2779237 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2779191 TGAGTATAAG
*
2779201 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2779238 GAGATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2782995 original size:52 final size:51
Alignment explanation
Indices: 2782863--2783051 Score: 202
Period size: 52 Copynumber: 3.7 Consensus size: 51
2782853 ATTTAACTGG
* * * ** *
2782863 ATGTATCGATACATTGAAGAATGTATCGATACATTTATGTCAAAACCTAGA
1 ATGTATCGATACAATAAAAAATGTATCGATACATTTGGGTCAAAACCCAGA
* * * * *
2782914 ATGTATCGATAAAATGAATAATATATCGATACATTTGGGTCAAAAACCCAAA
1 ATGTATCGATACAATAAAAAATGTATCGATACATTTGGGTC-AAAACCCAGA
* * * *
2782966 ATTTATCGATACAATAAAAAATGTGTCGATACATTTGGAT-TAAA-CCAGA
1 ATGTATCGATACAATAAAAAATGTATCGATACATTTGGGTCAAAACCCAGA
*
2783015 ATGTATCAATACAATAAAAAAATGTATCGATACATTT
1 ATGTATCGATACAAT-AAAAAATGTATCGATACATTT
2783052 TCTTTCTAGA
Statistics
Matches: 116, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
49 17 0.15
50 23 0.20
51 35 0.30
52 41 0.35
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACAATAAAAAATGTATCGATACATTTGGGTCAAAACCCAGA
Found at i:2783155 original size:21 final size:20
Alignment explanation
Indices: 2783088--2783161 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
2783078 GACATGGCCC
* *
2783088 TGTATCGATACATTTCAAACA
1 TGTATCGATACA-TTCACATA
2783109 TGTATCGATACATTCACATA
1 TGTATCGATACATTCACATA
* *
2783129 TGTATCGATACATTCACTTGT
1 TGTATCGATACATTCACAT-A
2783150 TGTATCGATACA
1 TGTATCGATACA
2783162 AATTGTAGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 24 0.50
21 24 0.50
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTCACATA
Found at i:2786771 original size:20 final size:21
Alignment explanation
Indices: 2786746--2786799 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
2786736 TTTTTCCTGC
2786746 ATGTATCGATACAATTCA-TA
1 ATGTATCGATACAATTCAGTA
* * *
2786766 ATGTATCAATACATTTGAGTA
1 ATGTATCGATACAATTCAGTA
2786787 ATGTATCGATACA
1 ATGTATCGATACA
2786800 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTCAGTA
Found at i:2786790 original size:21 final size:20
Alignment explanation
Indices: 2786746--2786803 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
2786736 TTTTTCCTGC
*
2786746 ATGTATCGATACAATTCATA
1 ATGTATCGATACATTTCATA
* *
2786766 ATGTATCAATACATTTGAGTA
1 ATGTATCGATACATTTCA-TA
2786787 ATGTATCGATACATTTC
1 ATGTATCGATACATTTC
2786804 CTTGGCAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTCATA
Found at i:2788010 original size:33 final size:33
Alignment explanation
Indices: 2787968--2788032 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2787958 TACCACTATT
*
2787968 TTTACCGATACATGGT-ACATTGTATCGATACAA
1 TTTACCGATACATGATGA-ATTGTATCGATACAA
*
2788001 TTTATCGATACATGATGAATTGTATCGATACA
1 TTTACCGATACATGATGAATTGTATCGATACA
2788033 TTACTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
TTTACCGATACATGATGAATTGTATCGATACAA
Found at i:2789620 original size:3 final size:3
Alignment explanation
Indices: 2789612--2789647 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2789602 TCAACGATCA
* *
2789612 ATG ATG ATG AAG ATG ATA ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
2789648 GTGACTCAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:2794683 original size:20 final size:20
Alignment explanation
Indices: 2794642--2794680 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2794632 CCTAGGCAGC
* *
2794642 CACTGCCAGGTCGCGATCGG
1 CACTCCCAGGTCGCGAACGG
2794662 CACTCCCAGGTCGC-AACGG
1 CACTCCCAGGTCGCGAACGG
2794681 GCAGCTCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.38, G:0.31, T:0.13
Consensus pattern (20 bp):
CACTCCCAGGTCGCGAACGG
Found at i:2796730 original size:13 final size:13
Alignment explanation
Indices: 2796712--2796736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2796702 CATCATGCTT
2796712 TGTATCGATATAG
1 TGTATCGATATAG
2796725 TGTATCGATATA
1 TGTATCGATATA
2796737 TGTTCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TGTATCGATATAG
Found at i:2797696 original size:54 final size:55
Alignment explanation
Indices: 2797592--2797705 Score: 133
Period size: 55 Copynumber: 2.1 Consensus size: 55
2797582 AGATTGGATT
* * * * * *
2797592 AAAATTTCATGTGTAAAAAGTTAAATTAAAATTTTTTATTTAAAGAATCTAGTGA
1 AAAATTTCATGTATAAAAAGTTAAATCAAAATTGTATATTAAAAGAATCTAATGA
* *
2797647 AAAATTTCATGTAT-GAAAGTTTAATCAAGAATTGTATATTAAAAG-ATCTAATGA
1 AAAATTTCATGTATAAAAAGTTAAATCAA-AATTGTATATTAAAAGAATCTAATGA
2797701 AAAAT
1 AAAAT
2797706 CCCATATGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
54 24 0.48
55 26 0.52
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.37
Consensus pattern (55 bp):
AAAATTTCATGTATAAAAAGTTAAATCAAAATTGTATATTAAAAGAATCTAATGA
Found at i:2799791 original size:16 final size:16
Alignment explanation
Indices: 2799766--2799797 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2799756 TGAAACTAAT
*
2799766 AAATATATTTTTAAAA
1 AAATAAATTTTTAAAA
2799782 AAATAAATTTTTAAAA
1 AAATAAATTTTTAAAA
2799798 GTTGACTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAAATTTTTAAAA
Found at i:2801388 original size:8 final size:8
Alignment explanation
Indices: 2801370--2801449 Score: 54
Period size: 8 Copynumber: 9.6 Consensus size: 8
2801360 TAAAAATTAT
2801370 TATTAAATA
1 TATT-AATA
2801379 TATTAATA
1 TATTAATA
**
2801387 TAAGAATA
1 TATTAATA
*
2801395 TATTGATA
1 TATTAATA
*
2801403 AATT-ATA
1 TATTAATA
*
2801410 TTTTAATAA
1 TATTAAT-A
2801419 TATTTAATA
1 TA-TTAATA
*
2801428 TTTTAATA
1 TATTAATA
*
2801436 TATATTATA
1 TAT-TAATA
2801445 TATTA
1 TATTA
2801450 TTTTAATTAT
Statistics
Matches: 54, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
7 5 0.09
8 29 0.54
9 15 0.28
10 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (8 bp):
TATTAATA
Found at i:2801430 original size:18 final size:21
Alignment explanation
Indices: 2801406--2801456 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 21
2801396 ATTGATAAAT
2801406 TATATTTTAATA-ATATT-TA
1 TATATTTTAATATATATTATA
2801425 -ATATTTTAATATATATTATA
1 TATATTTTAATATATATTATA
2801445 TATTATTTTAAT
1 TA-TATTTTAAT
2801457 TATTTAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.39
19 5 0.18
20 2 0.07
21 1 0.04
22 9 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATTTTAATATATATTATA
Found at i:2801907 original size:23 final size:20
Alignment explanation
Indices: 2801870--2801911 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
2801860 ATTTTTATAT
2801870 TTTATTTTTAATTATTTATC
1 TTTATTTTTAATTATTTATC
2801890 TTTATTTTATTAACTTATTTAT
1 TTTA-TTT-TTAA-TTATTTAT
2801912 ATATATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 4 0.21
23 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTTTAATTATTTATC
Found at i:2801934 original size:37 final size:40
Alignment explanation
Indices: 2801904--2802001 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
2801894 TTTTATTAAC
2801904 TTATTT-ATATATATA-AT-ATTTTAATAATTTTTAATTA
1 TTATTTAATATATATATATAATTTTAATAATTTTTAATTA
* * **
2801941 TTATTTAATATATATATATAATTTTAATCACTTTTAACAGA
1 TTATTTAATATATATATATAATTTTAATAATTTTTAA-TTA
2801982 TTA-TTATATATATATATATA
1 TTATTTA-ATATATATATATA
2802002 CAATTCAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
37 6 0.12
38 9 0.17
39 2 0.04
40 18 0.35
41 17 0.33
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (40 bp):
TTATTTAATATATATATATAATTTTAATAATTTTTAATTA
Found at i:2801997 original size:41 final size:39
Alignment explanation
Indices: 2801904--2802001 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 39
2801894 TTTTATTAAC
* **
2801904 TTATTTATATATATA-AT-ATTTTAATAATTTTTAATTA
1 TTATTTATATATATATATAATTTTAATAACTTTTAAAGA
*
2801941 TTATTTAATATATATATATAATTTTAATCACTTTTAACAGA
1 TTATTT-ATATATATATATAATTTTAATAACTTTTAA-AGA
2801982 TTATTATATATATATATATA
1 TTATT-TATATATATATATA
2802002 CAATTCAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
37 6 0.12
38 9 0.17
39 2 0.04
40 15 0.29
41 19 0.37
42 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (39 bp):
TTATTTATATATATATATAATTTTAATAACTTTTAAAGA
Found at i:2802091 original size:20 final size:20
Alignment explanation
Indices: 2802066--2802110 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2802056 AATATACTTC
* *
2802066 ATAATTTTAATTTTATTATT
1 ATAATTTAAATTATATTATT
2802086 ATAATTTAAATTATATTATT
1 ATAATTTAAATTATATTATT
2802106 ATAAT
1 ATAAT
2802111 AATTAATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATAATTTAAATTATATTATT
Found at i:2803217 original size:15 final size:15
Alignment explanation
Indices: 2803199--2803229 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2803189 ACAAAAAATT
2803199 TAATATTTTAAAAAA
1 TAATATTTTAAAAAA
2803214 TAATATTTTAAAAAA
1 TAATATTTTAAAAAA
2803229 T
1 T
2803230 TTAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATATTTTAAAAAA
Found at i:2805154 original size:20 final size:20
Alignment explanation
Indices: 2805131--2805189 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
2805121 CATTTTATGG
2805131 TGTATCGATACTTAGCAATT
1 TGTATCGATACTTAGCAATT
2805151 TGTATCG--A--TA-CAA--
1 TGTATCGATACTTAGCAATT
2805164 TGTATCGATACTTAGCAATT
1 TGTATCGATACTTAGCAATT
2805184 TGTATC
1 TGTATC
2805190 AATATATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
13 7 0.22
15 4 0.12
16 2 0.06
17 2 0.06
18 4 0.12
20 13 0.41
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (20 bp):
TGTATCGATACTTAGCAATT
Found at i:2805327 original size:22 final size:22
Alignment explanation
Indices: 2805293--2805335 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2805283 TACATTAAGT
2805293 ATTTTTACTTTGAAAAACATTG
1 ATTTTTACTTTGAAAAACATTG
2805315 ATTTATTAC-TTGAAAAACATT
1 ATTT-TTACTTTGAAAAACATT
2805336 TAAACTTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTTTTACTTTGAAAAACATTG
Found at i:2817118 original size:16 final size:17
Alignment explanation
Indices: 2817094--2817134 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2817084 AAAAATTAAA
*
2817094 AATTATTTTTA-TTTTT
1 AATTATTTTAATTTTTT
*
2817110 AATTTTTTTAATTTTTT
1 AATTATTTTAATTTTTT
2817127 AATTATTT
1 AATTATTT
2817135 ATTTAAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
AATTATTTTAATTTTTT
Found at i:2817874 original size:11 final size:11
Alignment explanation
Indices: 2817838--2817875 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
2817828 AAAAAATAAA
2817838 TTTATTTTATT
1 TTTATTTTATT
2817849 TTT-TATTTATAT
1 TTTAT-TTTAT-T
2817861 TTTATTTTATT
1 TTTATTTTATT
2817872 TTTA
1 TTTA
2817876 AATGATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.04
11 13 0.54
12 9 0.38
13 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:2821790 original size:52 final size:52
Alignment explanation
Indices: 2821642--2821770 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2821632 CGAAATATGA
*
2821642 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
2821694 AAATTTGCCTGCATGTATTGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
2821746 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2821771 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2821883 original size:13 final size:13
Alignment explanation
Indices: 2821865--2821922 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
2821855 ACAACACTTA
2821865 TGTATCGATACAT
1 TGTATCGATACAT
2821878 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
2821897 ATGTATCGATACAT
1 -TGTATCGATACAT
2821911 TGTATCGATACA
1 TGTATCGATACA
2821923 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2821903 original size:20 final size:19
Alignment explanation
Indices: 2821846--2821943 Score: 94
Period size: 20 Copynumber: 5.7 Consensus size: 19
2821836 TAGCTTACAT
2821846 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
2821865 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
2821878 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
2821898 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
2821911 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
2821931 TGTATCGATACAA
1 TGTATCGATACAA
2821944 ATCGTTGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 27
0.71 0.00 0.29
Matches are distributed among these distances:
13 18 0.28
14 2 0.03
16 9 0.14
17 3 0.05
19 11 0.17
20 22 0.34
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:2821904 original size:33 final size:33
Alignment explanation
Indices: 2821841--2821942 Score: 197
Period size: 33 Copynumber: 3.1 Consensus size: 33
2821831 GGCAGTAGCT
2821841 TACATTGTATCGATACAACAC-TTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
2821873 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
2821906 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
2821939 TACA
1 TACA
2821943 AATCGTTGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
32 21 0.30
33 48 0.70
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (33 bp):
TACATTGTATCGATACAACACTTTATGTATCGA
Found at i:2822818 original size:38 final size:38
Alignment explanation
Indices: 2822776--2822848 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
2822766 GAATTTTAAA
* *
2822776 ATTATTATCTA-AAATTTAAATTTTAAATTTAAATTCTG
1 ATTA-TATCTAGAAATTTAAAATCTAAATTTAAATTCTG
**
2822814 ATTATATCTAGATTTTTAAAATCTAAATTTAAATT
1 ATTATATCTAGAAATTTAAAATCTAAATTTAAATT
2822849 TTAAGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 6 0.20
38 24 0.80
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (38 bp):
ATTATATCTAGAAATTTAAAATCTAAATTTAAATTCTG
Found at i:2823682 original size:8 final size:8
Alignment explanation
Indices: 2823651--2823683 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
2823641 CAATATTTTA
*
2823651 TATATATA
1 TATATATT
2823659 TATATATT
1 TATATATT
2823667 TATATATT
1 TATATATT
2823675 TATATATT
1 TATATATT
2823683 T
1 T
2823684 GATTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATATATT
Found at i:2823839 original size:6 final size:6
Alignment explanation
Indices: 2823828--2823856 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2823818 TATTCTTTAT
2823828 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
2823857 TCAAGTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:2825232 original size:21 final size:22
Alignment explanation
Indices: 2825184--2825235 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2825174 TTAATATATT
* *
2825184 TATTAAGTATGTTAGGTAAATA
1 TATTAGGTGTGTTAGGTAAATA
*
2825206 TATTAGGTGTGTTAGGT-GATA
1 TATTAGGTGTGTTAGGTAAATA
*
2825227 TGTTAGGTG
1 TATTAGGTG
2825236 AGCAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (22 bp):
TATTAGGTGTGTTAGGTAAATA
Found at i:2825253 original size:37 final size:34
Alignment explanation
Indices: 2825191--2825295 Score: 138
Period size: 37 Copynumber: 3.0 Consensus size: 34
2825181 ATTTATTAAG
2825191 TATGTTAGGTAAATATATTAGGTGTGTTAGGTGA
1 TATGTTAGGTAAATATATTAGGTGTGTTAGGTGA
* *
2825225 TATGTTAGGTGAGCAATATATTAAGTGTGTTAGGTGG
1 TATGTTAGGT-A--AATATATTAGGTGTGTTAGGTGA
* * *
2825262 TGTGTTAGGTAAACATATTAGGTGTGTTCGGTGA
1 TATGTTAGGTAAATATATTAGGTGTGTTAGGTGA
2825296 ACATATCTCG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
34 29 0.48
35 1 0.02
36 1 0.02
37 30 0.49
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.39
Consensus pattern (34 bp):
TATGTTAGGTAAATATATTAGGTGTGTTAGGTGA
Found at i:2825288 original size:22 final size:22
Alignment explanation
Indices: 2825260--2825301 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2825250 TGTGTTAGGT
2825260 GGTGTGTTAGGTAAACATATTA
1 GGTGTGTTAGGTAAACATATTA
* *
2825282 GGTGTGTTCGGTGAACATAT
1 GGTGTGTTAGGTAAACATAT
2825302 CTCGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.07, G:0.31, T:0.36
Consensus pattern (22 bp):
GGTGTGTTAGGTAAACATATTA
Found at i:2829999 original size:34 final size:34
Alignment explanation
Indices: 2829907--2830006 Score: 137
Period size: 37 Copynumber: 2.9 Consensus size: 34
2829897 ATTAACTGTA
2829907 TTAGGTAAACATATTAAGTGTGTTAGGTGGTATG
1 TTAGGTAAACATATTAAGTGTGTTAGGTGGTATG
* *
2829941 TTAGGTAGGCAATATATTAAGTGTGTTAGGTGGTGTG
1 TTAGGTA---AACATATTAAGTGTGTTAGGTGGTATG
* *
2829978 TTAGGTAAACATATTAGGTGTGCTAGGTG
1 TTAGGTAAACATATTAAGTGTGTTAGGTG
2830007 AACATATCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 26 0.45
37 32 0.55
ACGTcount: A:0.27, C:0.04, G:0.32, T:0.37
Consensus pattern (34 bp):
TTAGGTAAACATATTAAGTGTGTTAGGTGGTATG
Found at i:2830004 original size:22 final size:22
Alignment explanation
Indices: 2829972--2830013 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2829962 TGTGTTAGGT
*
2829972 GGTGTGTTAGGTAAACATATTA
1 GGTGTGCTAGGTAAACATATTA
*
2829994 GGTGTGCTAGGTGAACATAT
1 GGTGTGCTAGGTAAACATAT
2830014 CTTGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (22 bp):
GGTGTGCTAGGTAAACATATTA
Found at i:2834682 original size:20 final size:21
Alignment explanation
Indices: 2834644--2834684 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2834634 AATATAAATT
2834644 TATTTTATATTAATATTTTTA
1 TATTTTATATTAATATTTTTA
2834665 TATTTT-TA-TAATTATTTTTA
1 TATTTTATATTAA-TATTTTTA
2834685 AATAAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 10 0.53
21 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTATATTAATATTTTTA
Found at i:2838133 original size:13 final size:13
Alignment explanation
Indices: 2838112--2838154 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
2838102 AATTTAATAA
2838112 AATAA-TACATTT
1 AATAACTACATTT
2838124 AACT-ACTACATTT
1 AA-TAACTACATTT
2838137 AATAACTACATTT
1 AATAACTACATTT
2838150 AATAA
1 AATAA
2838155 AATAATATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.14
13 24 0.86
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
AATAACTACATTT
Found at i:2839507 original size:21 final size:21
Alignment explanation
Indices: 2839464--2839507 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2839454 ATTTAAAATA
* *
2839464 ATTGTTTCAATTTTTGTATGT
1 ATTGTTTCAATTTTAGTAAGT
2839485 ATTGTTTCCAA-TTTAGTAAGT
1 ATTGTTT-CAATTTTAGTAAGT
2839506 AT
1 AT
2839508 CTTGGGGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTGTTTCAATTTTAGTAAGT
Found at i:2846642 original size:13 final size:13
Alignment explanation
Indices: 2846624--2846648 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2846614 ATTACTCAAA
2846624 TGTATCGATACAT
1 TGTATCGATACAT
2846637 TGTATCGATACA
1 TGTATCGATACA
2846649 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2846750 original size:52 final size:52
Alignment explanation
Indices: 2846657--2846780 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
2846647 CACTGATCTT
*
2846657 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2846708 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2846760 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2846781 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2847774 original size:21 final size:21
Alignment explanation
Indices: 2847741--2847781 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2847731 CTAAGTAAAA
2847741 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2847762 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2847782 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2847846 original size:20 final size:20
Alignment explanation
Indices: 2847817--2847891 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
2847807 CAAAACCCTG
2847817 AAAA-GTATCGATACACATT
1 AAAATGTATCGATACACATT
* *
2847836 TAAATGTATCGATACAAATT
1 AAAATGTATCGATACACATT
* * *
2847856 GCACA-GTATCGATACACA-C
1 -AAAATGTATCGATACACATT
2847875 AAATATGTATCGATACA
1 AAA-ATGTATCGATACA
2847892 GGTCATTGGC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
18 1 0.02
19 4 0.09
20 37 0.84
21 2 0.05
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (20 bp):
AAAATGTATCGATACACATT
Found at i:2848010 original size:21 final size:22
Alignment explanation
Indices: 2847976--2848030 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
2847966 TTTCACTATT
2847976 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2847998 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2848019 CATCACTGTTCA
1 CATCACTGTTCA
2848031 CACTGTTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:2848118 original size:13 final size:13
Alignment explanation
Indices: 2848100--2848125 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2848090 ACATATTTGT
2848100 GTGTATCGATACA
1 GTGTATCGATACA
2848113 GTGTATCGATACA
1 GTGTATCGATACA
2848126 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:2856422 original size:31 final size:31
Alignment explanation
Indices: 2856384--2856498 Score: 171
Period size: 31 Copynumber: 3.7 Consensus size: 31
2856374 TAAAAAAAAA
2856384 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
2856415 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
2856446 AAAGTCCACGACGCAGTGGC-ATC-CTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
2856475 TTTAAAGTCCACGACTCAGTGGCA
1 ---AAAGTCCACGACTCAGTGGCA
2856499 TTTTGTCTCA
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
29 5 0.07
30 3 0.04
31 49 0.64
32 19 0.25
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.23
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:2856578 original size:27 final size:27
Alignment explanation
Indices: 2856540--2856591 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2856530 TTTTTTCATC
*
2856540 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
*
2856567 TTTAAGCCCACAACTCTGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
2856592 TTCTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:2856613 original size:34 final size:33
Alignment explanation
Indices: 2856570--2856729 Score: 230
Period size: 33 Copynumber: 4.7 Consensus size: 33
2856560 GCACCCGTTT
2856570 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCA
1 AAGCCCACAACTCTGTGGCACCTTCTTCTTTT-A
*
2856604 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTA
1 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTA
* *
2856637 AAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTCA
1 AAGCCCACAACTCTGTGGCAC-C-TTCTT-CTTTT-A
* *
2856674 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTA
1 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTA
2856707 AAGCCCACAACTCTGTGGCACCT
1 AAGCCCACAACTCTGTGGCACCT
2856730 ACAACTTTGT
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
33 43 0.37
34 37 0.32
35 9 0.08
36 6 0.05
37 20 0.17
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.32
Consensus pattern (33 bp):
AAGCCCACAACTCTGTGGCACCTTCTTCTTTTA
Found at i:2856645 original size:33 final size:33
Alignment explanation
Indices: 2856508--2856729 Score: 233
Period size: 34 Copynumber: 6.7 Consensus size: 33
2856498 ATTTTGTCTC
* * *
2856508 AAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTCTTC-T-TTT
* *
2856543 -AAGTCCACAACTCCGTGGCA-C--C--CGTTT
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
*
2856570 -AAGCCCACAACTCTGTGGCACCTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
2856602 CAAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
** *
2856636 AAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTCTT-CTTTT
*
2856672 CAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
*
2856706 AAAGCCCACAACTCTGTGGCACCT
1 AAAGCCCACAACTCCGTGGCACCT
2856730 ACAACTTTGT
Statistics
Matches: 161, Mismatches: 15, Indels: 24
0.81 0.08 0.12
Matches are distributed among these distances:
27 21 0.13
28 1 0.01
29 1 0.01
30 1 0.01
32 4 0.02
33 43 0.27
34 55 0.34
35 9 0.06
36 6 0.04
37 20 0.12
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.32
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
Found at i:2856686 original size:70 final size:70
Alignment explanation
Indices: 2856508--2856924 Score: 398
Period size: 70 Copynumber: 5.9 Consensus size: 70
2856498 ATTTTGTCTC
* * * *
2856508 AAAGCCCACAATTCCGTGGCA--CTTTTTTCATCTTT--AAGTCCACAACTCCGTGGCACC----
1 AAAGCCCACAACTCTGTGGCACTCTTTTTTCCT-TTTCAAAGCCCACAACTCCGTGGCACCTTTT
*
2856565 -CGTTT
65 TCTTTT
* *
2856570 -AAGCCCACAACTCTGTGGCAC-C-TTCTT-CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
2856631 CTTTT
66 CTTTT
*
2856636 AAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
2856701 CTTTT
66 CTTTT
* *
2856706 AAAGCCCACAACTCTGTGGCACCTACAACTTTGTGGCACTCTCTTTCCCTTTTTAAAGCCTACAA
1 AAAGCCCACAACTCTGTGGCA-CT----C----T-----T-T-TTT-CCTTTTCAAAGCCCACAA
2856771 CTCCGTGGCACCTTTTTCTGTTT
49 CTCCGTGGCACCTTTTTCT-TTT
* *
2856794 AAAGCCCACAACTCCGTGGCACTC-TTTTTCCGTTTTCAAAGCCCACAACTCCGTGGCACTTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTTCC-TTTTCAAAGCCCACAACTCCGTGGCACCTTTT
2856858 TCTTTT
65 TCTTTT
* * * *
2856864 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT--AAGTCCACAACTCCGTGGCATCTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTT
2856925 CTCCCTTCCT
Statistics
Matches: 303, Mismatches: 20, Indels: 58
0.80 0.05 0.15
Matches are distributed among these distances:
59 3 0.01
60 1 0.00
61 43 0.14
62 1 0.00
66 4 0.01
67 20 0.07
68 23 0.08
69 4 0.01
70 91 0.30
71 43 0.14
72 1 0.00
73 1 0.00
75 1 0.00
79 1 0.00
83 1 0.00
84 1 0.00
85 1 0.00
86 3 0.01
87 37 0.12
88 23 0.08
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (70 bp):
AAAGCCCACAACTCTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
CTTTT
Found at i:2856789 original size:87 final size:88
Alignment explanation
Indices: 2856643--2856815 Score: 294
Period size: 87 Copynumber: 2.0 Consensus size: 88
2856633 TTTAAAGCCC
* *
2856643 ACAACTTTGTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTA
1 ACAACTTTGTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
*
2856707 AAGCCCACAACTCTGTGGCACCT
66 AAGCCCACAACTCCGTGGCACCT
* *
2856730 ACAACTTTGTGGCACTCTCTTTCCCTTTTTAAAGCCTACAACTCCGTGGCACCTTTTTCTGTTTA
1 ACAACTTTGTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
2856795 AAGCCCACAACTCCGTGGCAC
66 AAGCCCACAACTCCGTGGCAC
2856816 TCTTTTTCCG
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 56 0.70
88 24 0.30
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (88 bp):
ACAACTTTGTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
AAGCCCACAACTCCGTGGCACCT
Found at i:2856805 original size:34 final size:34
Alignment explanation
Indices: 2856757--2856944 Score: 225
Period size: 35 Copynumber: 5.4 Consensus size: 34
2856747 TCTTTCCCTT
* *
2856757 TTTAAAGCCTACAACTCCGTGGCACCTTTTTCTG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCG
2856791 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCG
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCG
* *
2856826 TTTTCAAAGCCCACAACTCCGTGGCA-CTTTTTTCT
1 -TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCG
*
2856861 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCG
* * * * *
2856896 TTTTAAGTCCACAACTCCGTGGCATCTTTCTCCC
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCG
2856930 TTCCTAAAGCCCACA
1 TT--TAAAGCCCACA
2856945 CAAGTCGGTG
Statistics
Matches: 135, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
33 21 0.16
34 37 0.27
35 44 0.33
36 12 0.09
37 21 0.16
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCG
Found at i:2856821 original size:158 final size:157
Alignment explanation
Indices: 2856597--2856885 Score: 490
Period size: 158 Copynumber: 1.8 Consensus size: 157
2856587 GCACCTTCTT
**
2856597 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACTC-T
*
2856662 TTTTCC-TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGC
65 TTTTCCGTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
2856726 ACCTACAACTTTGTGGCACTCTCTTTCC
130 ACCTACAACTTTGTGGCACTCTCTTTCC
* * *
2856754 CTTTTTAAAGCCTACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCT-TTTAAAGCCCACAACTCCGTGGCACTCT
*
2856819 TTTTCCGTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGC
65 TTTTCCGTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
2856884 AC
130 AC
2856886 TCTTTTTCCC
Statistics
Matches: 123, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
157 40 0.33
158 83 0.67
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (157 bp):
CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
TTTCCGTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCA
CCTACAACTTTGTGGCACTCTCTTTCC
Found at i:2856856 original size:35 final size:35
Alignment explanation
Indices: 2856738--2856944 Score: 244
Period size: 34 Copynumber: 5.9 Consensus size: 35
2856728 CTACAACTTT
* *
2856738 GTGGCACTCTCTTTCCCTTTTTAAAGCCTACAACTCC
1 GTGGCAC-CTTTTTCCC-TTTTAAAGCCCACAACTCC
2856775 GTGGCACCTTTTT--CTGTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCCCT-TTTAAAGCCCACAACTCC
*
2856809 GTGGCACTCTTTTTCCGTTTTCAAAGCCCACAACTCC
1 GTGGCAC-CTTTTTCCCTTTT-AAAGCCCACAACTCC
*
2856846 GTGGCA-CTTTTT-TCTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCCCTTTTAAAGCCCACAACTCC
*
2856879 GTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCC
1 GTGGCAC-CTTTTTCCCTTTTAAAGCCCACAACTCC
* * *
2856914 GTGGCATCTTTCTCCCTTCCTAAAGCCCACA
1 GTGGCACCTTTTTCCCTT-TTAAAGCCCACA
2856945 CAAGTCGGTG
Statistics
Matches: 149, Mismatches: 11, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
33 22 0.15
34 39 0.26
35 38 0.26
36 21 0.14
37 29 0.19
ACGTcount: A:0.19, C:0.34, G:0.13, T:0.34
Consensus pattern (35 bp):
GTGGCACCTTTTTCCCTTTTAAAGCCCACAACTCC
Found at i:2856965 original size:104 final size:102
Alignment explanation
Indices: 2856756--2856944 Score: 247
Period size: 104 Copynumber: 1.8 Consensus size: 102
2856746 CTCTTTCCCT
* **
2856756 TTTTAAAGCCTACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTT
* * * *
2856821 TTCCGTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
66 CTCCCTTCTCAAAGCCCACAACTCCGTGGCAC--TCTTC
* *
2856860 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA-TCTT
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTT
2856924 TCTCCCTTC-CTAAAGCCCACA
65 TCTCCCTTCTC-AAAGCCCACA
2856945 CAAGTCGGTG
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
103 1 0.01
104 45 0.60
105 29 0.39
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (102 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTT
CTCCCTTCTCAAAGCCCACAACTCCGTGGCACTCTTC
Done.