Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold55
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: 4293517
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.26
Warning! 910309 characters in sequence are not A, C, G, or T
File 2 of 21
Found at i:168336 original size:51 final size:50
Alignment explanation
Indices: 168174--168352 Score: 184
Period size: 51 Copynumber: 3.6 Consensus size: 50
168164 TAAATTTCTA
* * ***
168174 AATTTTTCAC-CTCGGGGATACTCCAAC-CCCAGTTCCGTTTCAAAACATC
1 AATTTTTCACAATCGGGGATACTCCAACTCCGA-TTTTATTTCAAAACATC
** *
168223 AATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAGCATC
1 AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC-AAAACATC
* ** *
168274 GATTTACCACAATCGGGGATACTTCAACTCCGATTTTATTTTCAAAACA-C
1 AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTA-TTTCAAAACATC
*
168324 TAATTTTTCACAATTGGGGATACTCCAAC
1 -AATTTTTCACAATCGGGGATACTCCAAC
168353 CCTGTTATTT
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
49 8 0.08
50 23 0.22
51 70 0.67
52 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (50 bp):
AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCAAAACATC
Found at i:168482 original size:28 final size:27
Alignment explanation
Indices: 168441--168516 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
168431 TTTTTTTATA
*
168441 ATCGGGG-TACTCCAACCCCGTTGTTT
1 ATCGGGGATACTCCAACCCCGTTATTT
*
168467 CATCGGGGATACTCCAATCCCGTTATTT
1 -ATCGGGGATACTCCAACCCCGTTATTT
* * *
168495 TTGAGGGGATACACCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
168517 ATTTTATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.20
28 33 0.80
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTATTT
Found at i:168569 original size:51 final size:51
Alignment explanation
Indices: 168499--168618 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
168489 TTATTTTTGA
* * *
168499 GGGGATACACCAACCCCGATTTTATTTCTAAAATACCAAGTTTC-CACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA-TTTCTCACAATC
* *
168550 GGGGATACTCTAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
168601 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
168619 TTATTTTTGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 4 0.07
51 57 0.93
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
Found at i:168632 original size:79 final size:78
Alignment explanation
Indices: 168549--168769 Score: 244
Period size: 79 Copynumber: 2.8 Consensus size: 78
168539 TTTCCACAAT
* * * * *
168549 CGGGGATACTCTAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAA
1 CGGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTT-TCATAATCGGGGATACTCCAA
* *
168614 CCCCGTTATTTTTG
65 CCCCATTATTTTCG
* * ** *
168628 CGGGGATACTCCAACCCCAATTTTATTTTTAAAATACCAATTTTCTATAATCAAGGATACTCTAA
1 CGGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTC-ATAATCGGGGATACTCCAA
**
168693 CCTTATTATTTTCG
65 CCCCATTATTTTCG
* * * *
168707 AGGGGATACTCCAACCCCAATTTTTATTTCTAGAACACTGATTTTTCATAATCGGGGATACTC
1 CGGGGATACTCCAACCCCAA-TTTTATTTCTAAAACAC-CAATTTTCATAATCGGGGATACTC
168770 TAGCCCAGTT
Statistics
Matches: 117, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
78 2 0.02
79 81 0.69
80 28 0.24
81 6 0.05
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTCATAATCGGGGATACTCCAAC
CCCATTATTTTCG
Found at i:170647 original size:32 final size:33
Alignment explanation
Indices: 170589--170652 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
170579 TACAAGCCAA
**
170589 TGTATCGATACAATTTTTTGTCTATCGATACAT
1 TGTATCGATACAATACTTTGTCTATCGATACAT
*
170622 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTCTATCGATACA
170653 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTCTATCGATACAT
Found at i:171407 original size:59 final size:59
Alignment explanation
Indices: 171315--171456 Score: 268
Period size: 59 Copynumber: 2.4 Consensus size: 59
171305 ATTGGTACAT
171315 TCTCCCCCTTAATAAGATAAATTTAGCAAATTTACGCATTCTCCCCTTTTATTAAAAAA
1 TCTCCCCCTTAATAAGATAAATTTAGCAAATTTACGCATTCTCCCCTTTTATTAAAAAA
171374 TCTCCCCCTTAATAAGATAAATTTAGCAAATTTACGCATTCTCCCCTTTTATTAAAAAA
1 TCTCCCCCTTAATAAGATAAATTTAGCAAATTTACGCATTCTCCCCTTTTATTAAAAAA
*
171433 TCTCCCCCTTAATAAGGT-AATTTA
1 TCTCCCCCTTAATAAGATAAATTTA
171457 TACACATATC
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
58 6 0.07
59 76 0.93
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.36
Consensus pattern (59 bp):
TCTCCCCCTTAATAAGATAAATTTAGCAAATTTACGCATTCTCCCCTTTTATTAAAAAA
Found at i:172605 original size:13 final size:13
Alignment explanation
Indices: 172587--172622 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
172577 AATCCCCCTG
172587 TATCGATACAGTA
1 TATCGATACAGTA
* *
172600 TATCGATACATTG
1 TATCGATACAGTA
172613 TATCGATACA
1 TATCGATACA
172623 AAGAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTA
Found at i:174703 original size:15 final size:15
Alignment explanation
Indices: 174683--174713 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
174673 ATTTCGTTTG
*
174683 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
174698 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
174713 G
1 G
174714 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:178797 original size:13 final size:13
Alignment explanation
Indices: 178779--178868 Score: 72
Period size: 13 Copynumber: 6.0 Consensus size: 13
178769 CAATTTTTTG
178779 TGTATCGATACAT
1 TGTATCGATACAT
178792 TGTATCGATACATACTTT
1 TGTATCGATAC--A---T
178810 GTGTATCGATACAT
1 -TGTATCGATACAT
178824 TGTATCGATACATACTTT
1 TGTATCGATAC--A---T
178842 GTGTATCGATACAT
1 -TGTATCGATACAT
178856 TGTATCGATACAT
1 TGTATCGATACAT
178869 ACTTTGTGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 35 0.54
14 2 0.03
15 2 0.03
17 2 0.03
18 2 0.03
19 22 0.34
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:178816 original size:19 final size:19
Alignment explanation
Indices: 178792--178886 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
178782 ATCGATACAT
178792 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
178811 TGTATCGATAC--A---T-
1 TGTATCGATACATACTTTG
178824 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
178843 TGTATCGATAC--A---T-
1 TGTATCGATACATACTTTG
178856 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
178875 TGTATCGATACA
1 TGTATCGATACA
178887 AGTTTGGCTA
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
15 2 0.03
17 2 0.03
18 2 0.03
19 34 0.53
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATACTTTG
Found at i:178816 original size:32 final size:32
Alignment explanation
Indices: 178759--178886 Score: 229
Period size: 32 Copynumber: 4.0 Consensus size: 32
178749 TACAAGCCAA
**
178759 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATAC-ATACTTTGTGTATCGATACAT
178792 TGTATCGATACATACTTTGTGTATCGATACAT
1 TGTATCGATACATACTTTGTGTATCGATACAT
178824 TGTATCGATACATACTTTGTGTATCGATACAT
1 TGTATCGATACATACTTTGTGTATCGATACAT
178856 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
178887 AGTTTGGCTA
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 82 0.88
33 11 0.12
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:183207 original size:13 final size:13
Alignment explanation
Indices: 183189--183213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183179 GCGAAGAAAA
183189 TGTATCGATACAT
1 TGTATCGATACAT
183202 TGTATCGATACA
1 TGTATCGATACA
183214 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:183264 original size:52 final size:52
Alignment explanation
Indices: 183222--183350 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
183212 CACTGATCTT
*
183222 TGTATCGATACATGCAAGCAAATTTACCCAGATGTATCGATACATTATGAAA
1 TGTATCGATACATGCAAGCAAATTTACCCAGATGTATCGATACACTATGAAA
* * *
183274 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAAGCAAATTTACCCAGATGTATCGATACACTATGAAA
*
183326 TGTATCGATATATGCAAGCAAATTT
1 TGTATCGATACATGCAAGCAAATTT
183351 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAAGCAAATTTACCCAGATGTATCGATACACTATGAAA
Found at i:190270 original size:25 final size:26
Alignment explanation
Indices: 190241--190296 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
190231 AAAAATGATG
**
190241 AAAAAGTCAAAAGTAAAC-ACACAAA
1 AAAAAGTCAAAAAAAAACAACACAAA
* *
190266 CAAAAGTTAAAAAAAAACAACACAAA
1 AAAAAGTCAAAAAAAAACAACACAAA
190292 AAAAA
1 AAAAA
190297 AACCAAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.73, C:0.14, G:0.05, T:0.07
Consensus pattern (26 bp):
AAAAAGTCAAAAAAAAACAACACAAA
Found at i:190294 original size:13 final size:12
Alignment explanation
Indices: 190276--190332 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
190266 CAAAAGTTAA
190276 AAAAAAACAACAC
1 AAAAAAA-AACAC
190289 AAAAAAAAA-ACC
1 AAAAAAAAACA-C
190301 AAAAACAAAA-AC
1 AAAAA-AAAACAC
*
190313 AAAAAAATACAC
1 AAAAAAAAACAC
190325 AAAAAAAA
1 AAAAAAAA
190333 GAGAGAGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 4 0.10
12 23 0.59
13 12 0.31
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.02
Consensus pattern (12 bp):
AAAAAAAAACAC
Found at i:191695 original size:30 final size:30
Alignment explanation
Indices: 191628--191922 Score: 285
Period size: 30 Copynumber: 9.7 Consensus size: 30
191618 ATACCTTCTT
**
191628 AAAGTCCACGACTCAGTGGCAATCTCT-TCTT
1 AAAGTCCACGACTCAGTGGC-AT-TCTGTCCC
*
191659 AAAGTCCATGACTCAGTGGCATTCTGTCCC
1 AAAGTCCACGACTCAGTGGCATTCTGTCCC
*
191689 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1 AAAGTCCACGACTCAGTGGC-AT-TCTGTCCC
* * *
191720 AAAGCCCATGACTTAGTGGCATTCTGTCCC
1 AAAGTCCACGACTCAGTGGCATTCTGTCCC
*
191750 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1 AAAGTCCACGACTCAGTGGC-AT-TCTGTCCC
* *
191781 AAAGCCCACGACTCAGTGGCATTTTGTCCC
1 AAAGTCCACGACTCAGTGGCATTCTGTCCC
* * **
191811 AAAGTCCACGACTCAATGGCA-TCTTTTCTT
1 AAAGTCCACGACTCAGTGGCATTC-TGTCCC
* * * *
191841 AAAGCCCACGACTCAATGTCATTTTGTCCC
1 AAAGTCCACGACTCAGTGGCATTCTGTCCC
* *
191871 AAAGTCCACGACTCAGTGGCATCTCT-TTCT
1 AAAGTCCACGACTCAGTGGCAT-TCTGTCCC
* *
191901 AAAGTCTACGACTTAGTGGCAT
1 AAAGTCCACGACTCAGTGGCAT
191923 CTTTTCTTCA
Statistics
Matches: 218, Mismatches: 36, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
29 9 0.04
30 135 0.62
31 68 0.31
32 6 0.03
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATTCTGTCCC
Found at i:191703 original size:61 final size:61
Alignment explanation
Indices: 191628--191922 Score: 425
Period size: 61 Copynumber: 4.9 Consensus size: 61
191618 ATACCTTCTT
* *
191628 AAAGTCCACGACTCAGTGGCAATCTCTTCTTAAAGTCCATGACTCAGTGGCATTCTGTCCC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTTAAAGCCCACGACTCAGTGGCATTCTGTCCC
* * *
191689 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCATGACTTAGTGGCATTCTGTCCC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTTAAAGCCCACGACTCAGTGGCATTCTGTCCC
* *
191750 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCCC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTTAAAGCCCACGACTCAGTGGCATTCTGTCCC
* * * * *
191811 AAAGTCCACGACTCAATGGC-ATCTTTTCTTAAAGCCCACGACTCAATGTCATTTTGTCCC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTTAAAGCCCACGACTCAGTGGCATTCTGTCCC
* * *
191871 AAAGTCCACGACTCAGTGGC-ATCTCTT-TCTAAAGTCTACGACTTAGTGGCAT
1 AAAGTCCACGACTCAGTGGCAATCTCTTCT-TAAAGCCCACGACTCAGTGGCAT
191923 CTTTTCTTCA
Statistics
Matches: 215, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
59 1 0.00
60 79 0.37
61 135 0.63
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTTAAAGCCCACGACTCAGTGGCATTCTGTCCC
Found at i:191979 original size:37 final size:37
Alignment explanation
Indices: 191922--192035 Score: 153
Period size: 37 Copynumber: 3.2 Consensus size: 37
191912 CTTAGTGGCA
*
191922 TCTTTTCTTCAAAGCCCACAACTCTGTGGCACATTTT
1 TCTTTTCTTCAAAGCCCACAACTCTGTGGCACCTTTT
* * *
191959 TCTTTTCTTCAAATCTCACAACTCCGTGGCACCTTTT
1 TCTTTTCTTCAAAGCCCACAACTCTGTGGCACCTTTT
*
191996 TC--TT-TTCAAAGCCCACCACTCTGTGGCACCTTTT
1 TCTTTTCTTCAAAGCCCACAACTCTGTGGCACCTTTT
*
192030 CCTTTT
1 TCTTTT
192036 TAAGTCCATA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
34 27 0.41
35 2 0.03
36 2 0.03
37 35 0.53
ACGTcount: A:0.18, C:0.32, G:0.10, T:0.39
Consensus pattern (37 bp):
TCTTTTCTTCAAAGCCCACAACTCTGTGGCACCTTTT
Found at i:192022 original size:34 final size:34
Alignment explanation
Indices: 191929--192082 Score: 148
Period size: 34 Copynumber: 4.4 Consensus size: 34
191919 GCATCTTTTC
* *
191929 TTCAAAGCCCACAACTCTGTGGCACATTTTTCTTTT
1 TTCAAAGCCCACAACTCTGTGGCAC-CTTTTC-CTT
* * * *
191965 CTTCAAATCTCACAACTCCGTGGCACCTTTTTCTT
1 -TTCAAAGCCCACAACTCTGTGGCACCTTTTCCTT
*
192000 TTCAAAGCCCACCACTCTGTGGCACCTTTTCCTT
1 TTCAAAGCCCACAACTCTGTGGCACCTTTTCCTT
* * * *
192034 TT-TAAGTCCATAACTCTGTGGCATCTTTCTCCTT
1 TTCAAAGCCCACAACTCTGTGGCACCTTT-TCCTT
*
192068 TTCAAAAACCCACAA
1 TTC-AAAGCCCACAA
192083 GTCAATGGCA
Statistics
Matches: 94, Mismatches: 20, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
33 21 0.22
34 38 0.40
35 2 0.02
36 11 0.12
37 22 0.23
ACGTcount: A:0.23, C:0.32, G:0.10, T:0.36
Consensus pattern (34 bp):
TTCAAAGCCCACAACTCTGTGGCACCTTTTCCTT
Found at i:192189 original size:57 final size:56
Alignment explanation
Indices: 192067--192252 Score: 223
Period size: 57 Copynumber: 3.3 Consensus size: 56
192057 TCTTTCTCCT
* * * **
192067 TTTCAAAAACCCACAAGTCAATGGCAACCTTCAAAGCCCACAAATCAGTGGCACCC
1 TTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAGTTGGTGGCACCC
* *
192123 TTATCCAAAGCCCACAAGTCAGTGGCAACCTTCGTAAGCCCACAAGTTGGTGGCACCCC
1 TT-TCAAAAGCCCACAAGTCAGTGGCAACCTTC-AAAGCCCACAAGTTGGTGGCA-CCC
* * *
192182 TTTC-AAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCACACAAGTTGAT-GCAACCC
1 TTTCAAAAGCCCACAAGTCAGTGGCAACCTTC-AAAGCCCACAAGTTGGTGGC-ACCC
192238 TTTCAAAAGCCCACA
1 TTTCAAAAGCCCACA
192253 CAAGTTGGTG
Statistics
Matches: 113, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
56 11 0.10
57 78 0.69
58 19 0.17
59 5 0.04
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (56 bp):
TTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAGTTGGTGGCACCC
Found at i:192227 original size:28 final size:29
Alignment explanation
Indices: 192067--192252 Score: 170
Period size: 28 Copynumber: 6.5 Consensus size: 29
192057 TCTTTCTCCT
* * *
192067 TTTCAAAAACCCACAAGTCAATGGCAACC
1 TTTCAAAAGCCCACAAGTTAGTGGCAACC
* * *
192096 -TTC-AAAGCCCACAAATCAGTGGCACCC
1 TTTCAAAAGCCCACAAGTTAGTGGCAACC
* *
192123 TTATCCAAAGCCCACAAGTCAGTGGCAACC
1 TT-TCAAAAGCCCACAAGTTAGTGGCAACC
** * *
192153 -TTCGTAAGCCCACAAGTTGGTGGCACCCC
1 TTTCAAAAGCCCACAAGTTAGTGGCA-ACC
192182 TTTC-AAAGCCCACAAGTTAGTGGCAACC
1 TTTCAAAAGCCCACAAGTTAGTGGCAACC
*
192210 -TTCAAAAGCACACAAGTT-GAT-GCAACCC
1 TTTCAAAAGCCCACAAGTTAG-TGGCAA-CC
192238 TTTCAAAAGCCCACA
1 TTTCAAAAGCCCACA
192253 CAAGTTGGTG
Statistics
Matches: 132, Mismatches: 16, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
27 28 0.21
28 42 0.32
29 37 0.28
30 25 0.19
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (29 bp):
TTTCAAAAGCCCACAAGTTAGTGGCAACC
Found at i:192433 original size:49 final size:48
Alignment explanation
Indices: 192280--192825 Score: 506
Period size: 49 Copynumber: 11.3 Consensus size: 48
192270 CTTTTAAGTC
* * * *
192280 CAGCATATTGGCACCCTTGA-CTTTAAGACCAATGTCACTGGCCTTGAAT
1 CAGCACATTGGCA-CCTT-ATCTTTAAGTCCAATATCGCTGGCCTTGAAT
*
192329 CAGCACATTAGCA-C----CTTTAAGTCCAATATCGCTGGCCTTGAAT
1 CAGCACATTGGCACCTTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * * * * *
192372 CAGCATATTGGCACCCTTGTCTTGAAGACTAATGTCGTTGGCCTTGAAT
1 CAGCACATTGGCA-CCTTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * *
192421 TAGTACATTGG---C--ATCTTTAAGTCCAATGTCGCTGGCCTTGAAT
1 CAGCACATTGGCACCTTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* *
192464 CAGCACATTGGCATCTTCATC-TTAAGTCCAGTATCGCTGGCCTTGAAT
1 CAGCACATTGGCACCTT-ATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * *
192512 CAGCATATTGGCACCATCATCTTTAAGTCTAATGTCGCTGGCCTTGAAT
1 CAGCACATTGGCACC-TTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
192561 CAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
1 CAGCACATTGGCACC-TTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * *
192610 CAACACATTGGCACCTTCATCTTTAAATCCGATATCGCTGGCCTTGAAT
1 CAGCACATTGGCACCTT-ATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * *
192659 TAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAAT
1 CAGCACATTGGCACC--T-T-ATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * *
192711 TAGTACATTGGCACTTTCATCTTTAAGTCCAATATCGTTGGCCTTGAAT
1 CAGCACATTGGCACCTT-ATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * * *
192760 CAGCATATTGGCGCCTTCGTCATCTTTAA-TACCCAATGTTGTTGGCCTTGAAT
1 CAGCACATTGGCACC-T--T-ATCTTTAAGT--CCAATATCGCTGGCCTTGAAT
192813 CAGCACATTGGCA
1 CAGCACATTGGCA
192826 TTCTTCTCAT
Statistics
Matches: 414, Mismatches: 60, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
43 72 0.17
45 2 0.00
46 1 0.00
47 1 0.00
48 43 0.10
49 210 0.51
50 2 0.00
51 2 0.00
52 51 0.12
53 30 0.07
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (48 bp):
CAGCACATTGGCACCTTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
Found at i:192439 original size:92 final size:93
Alignment explanation
Indices: 192280--192824 Score: 499
Period size: 92 Copynumber: 5.7 Consensus size: 93
192270 CTTTTAAGTC
* * * * *
192280 CAGCATATTGGCACCCTTGACTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAG-CACC
1 CAGCATATTGGCACCCTTGTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCCATC
192344 TTTAAGTCCAATATCGCTGGCCTTGAAT
66 TTTAAGTCCAATATCGCTGGCCTTGAAT
* * * * * *
192372 CAGCATATTGGCACCCTTGTCTTGAAGACTAATGTCGTTGGCCTTGAATTAGTACATTGG-CATC
1 CAGCATATTGGCACCCTTGTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCCATC
*
192436 TTTAAGTCCAATGTCGCTGGCCTTGAAT
66 TTTAAGTCCAATATCGCTGGCCTTGAAT
* * * * * *
192464 CAGCACATTGGCA-TCTTCATC-TTAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCACC
1 CAGCATATTGGCACCCTT-GTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* *
192527 ATCATCTTTAAGTCTAATGTCGCTGGCCTTGAAT
62 --CATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * * *
192561 CAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACCT
1 CAGCATATTGGCACCCTTGTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C-
* *
192626 TCATCTTTAAATCCGATATCGCTGGCCTTGAAT
62 -CATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * * *
192659 TAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGTACATTGGCA
1 CAGCATATTGGCACCCTTG---TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG--
*
192724 CTTTCATCTTTAAGTCCAATATCGTTGGCCTTGAAT
61 C---CATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * *
192760 CAGCATATTGGC-GCCTTCGTCATCTTTAA-TACCCAATGTTGTTGGCCTTGAATCAGCACATTG
1 CAGCATATTGGCACCCTT-G---TCTTTAAGT--CCAATGTCGCTGGCCTTGAATCAGCACATTG
192823 GC
60 GC
192825 ATTCTTCTCA
Statistics
Matches: 384, Mismatches: 53, Indels: 24
0.83 0.11 0.05
Matches are distributed among these distances:
91 32 0.08
92 96 0.25
97 47 0.12
98 85 0.22
100 6 0.02
101 90 0.23
102 28 0.07
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (93 bp):
CAGCATATTGGCACCCTTGTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCCATC
TTTAAGTCCAATATCGCTGGCCTTGAAT
Found at i:192722 original size:101 final size:101
Alignment explanation
Indices: 192280--192825 Score: 559
Period size: 101 Copynumber: 5.6 Consensus size: 101
192270 CTTTTAAGTC
* * * * *
192280 CAGCATATTGGCACCCTTG--A-CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCA
1 CAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
192342 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAAT
66 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * * * * * *
192372 CAGCATATTGGCACCCTTG---TCTTGAAGACTAATGTCGTTGGCCTTGAATTAGTACATTGG--
1 CAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
*
192432 ----CATCTTTAAGTCCAATGTCGCTGGCCTTGAAT
66 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * * * *
192464 CAGCACATT-G-GCATCT-TCATC-TTAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCA
1 CAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* * *
192525 CCATCATCTTTAAGTCTAATGTCGCTGGCCTTGAAT
66 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * *
192561 CAGCACATTGGCACC-TT-T-ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCA
1 CAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* *
192623 CCTTCATCTTTAAATCCGATATCGCTGGCCTTGAAT
66 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * *
192659 TAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGTACATTGGCA
1 CAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* *
192724 CTTTCATCTTTAAGTCCAATATCGTTGGCCTTGAAT
66 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * *
192760 CAGCATATTGGCGCCTTCGTCATCTTTAA-TACCCAATGTTGTTGGCCTTGAATCAGCACATTGG
1 CAGCATATTGGCGCCTTTGTCATCTTTAAGT--CCAATGTCGCTGGCCTTGAATCAGCACATTGG
192824 CA
64 CA
192826 TTCTTCTCAT
Statistics
Matches: 383, Mismatches: 51, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
90 3 0.01
91 30 0.08
92 90 0.23
97 43 0.11
98 83 0.22
99 3 0.01
100 2 0.01
101 99 0.26
102 30 0.08
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (101 bp):
CAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
Found at i:192737 original size:150 final size:148
Alignment explanation
Indices: 192300--192848 Score: 598
Period size: 150 Copynumber: 3.8 Consensus size: 148
192290 GCACCCTTGA
* * * *
192300 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCA----C--CTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC-ATATC
* * *
192359 GCTGGCCTTGAATCAGCATATTGGCACCCTTG---TCTTGAAGACTAATGTCGTTGGCCTTGAAT
65 GCTGGCCTTGAATCAGCATATTGGCA-CCTTGTCATCTTTAAGTCTAATGTCGCTGGCCTTGAAT
192421 TAGTACATTGG------CAT
129 TAGTACATTGGCACTTTCAT
* *
192435 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC-TTAAGTCCAGTATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCA-TATC
* *
192499 GCTGGCCTTGAATCAGCATATTGGCACC--ATCATCTTTAAGTCTAATGTCGCTGGCCTTGAATC
65 GCTGGCCTTGAATCAGCATATTGGCACCTTGTCATCTTTAAGTCTAATGTCGCTGGCCTTGAATT
*
192562 AGCACATTGGCACCTTT-AT
130 AGTACATTGGCA-CTTTCAT
* *
192581 CTTTAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAATCCGATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC-ATATC
* * *
192646 GCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAAT
65 GCTGGCCTTGAATCAGCATATTGGCACC-TTGTCATCTTTAAGTCTAATGTCGCTGGCCTTGAAT
192711 TAGTACATTGGCACTTTCAT
129 TAGTACATTGGCACTTTCAT
* * *
192731 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAA-TACCCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGT--CC-
* * * * * * *
192795 ATGTTGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCTTCAAGTCTAAT
60 ATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTGTCATCTTTAAGTCTAAT
192849 ATTCCTAACT
Statistics
Matches: 351, Mismatches: 34, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
135 39 0.11
139 4 0.01
140 74 0.21
141 1 0.00
146 49 0.14
147 37 0.11
148 1 0.00
149 4 0.01
150 85 0.24
151 1 0.00
152 1 0.00
153 10 0.03
154 44 0.13
155 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (148 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCATATCG
CTGGCCTTGAATCAGCATATTGGCACCTTGTCATCTTTAAGTCTAATGTCGCTGGCCTTGAATTA
GTACATTGGCACTTTCAT
Found at i:193463 original size:52 final size:52
Alignment explanation
Indices: 193405--193533 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
193395 CACTGATCTT
193405 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * * *
193457 TGTATCGACACATACAGGAAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
193509 TGTATCGATATATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
193534 TCATATTTCG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:197042 original size:13 final size:13
Alignment explanation
Indices: 197024--197048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
197014 ACATAAGAGT
197024 TGTATCGATACAA
1 TGTATCGATACAA
197037 TGTATCGATACA
1 TGTATCGATACA
197049 TAAGTTTTGT
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:197050 original size:32 final size:32
Alignment explanation
Indices: 197005--197075 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
196995 AAACTATAAC
197005 TGTATCGACACATAAGAGTTGTATCGATACAA
1 TGTATCGACACATAAGAGTTGTATCGATACAA
* **
197037 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGACACATAAGAGTTGTATCGATACAA
197069 TGTATCG
1 TGTATCG
197076 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCGACACATAAGAGTTGTATCGATACAA
Found at i:197117 original size:13 final size:13
Alignment explanation
Indices: 197099--197126 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
197089 GCCAAGAAAA
197099 TGTATCGATACAT
1 TGTATCGATACAT
197112 TGTATCGATACAT
1 TGTATCGATACAT
197125 TG
1 TG
197127 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:202112 original size:79 final size:79
Alignment explanation
Indices: 201981--202161 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 79
201971 TTTTGGAGAT
** * * * *
201981 AATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGATTACGAAATAAAATCGGGATTGG
1 AATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTACGAAATAAAACCGGGATCGG
202046 AGTATCCCCTTGGA
66 AGTATCCCCTTGGA
* ** * *
202060 AATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTTGGAAATAAAGCCGGGGTCG
1 AATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA-TTACGAAATAAAACCGGGATCG
202124 GAGTATCCCCTTGGA
65 GAGTATCCCCTTGGA
** *
202139 GGTAACAGGGTTGGAGTATCCCC
1 AATAACGGGGTTGGAGTATCCCC
202162 GATGAAATAA
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 1 0.01
79 86 0.99
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
AATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTACGAAATAAAACCGGGATCGG
AGTATCCCCTTGGA
Found at i:202238 original size:107 final size:107
Alignment explanation
Indices: 202042--202240 Score: 231
Period size: 107 Copynumber: 1.9 Consensus size: 107
202032 AAAATCGGGA
* * * *
202042 TTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCATGGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTAG
* * *
202107 AAATAAAGCCGGGGTCGGAGTATCCCCTTGGAGGTAACAGGG
66 AAATAAAACCGGAGTCGGAATATCCCCTTGGAGGTAACAGGG
* * * * * *
202149 TTGGAGTATCCCCGAT-GAAATAATGAGGTTGGAGTATCCTCGATTGTGAAAAA-CTAGTGTTTT
1 TTGGAGTATCCCC-ATGGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATC-AATATTTT
* *
202212 AGAAATAAAATCGGAGTTGGAATATCCCC
64 AGAAATAAAACCGGAGTCGGAATATCCCC
202241 GATTGTGGAG
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
106 1 0.01
107 73 0.97
108 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (107 bp):
TTGGAGTATCCCCATGGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTAG
AAATAAAACCGGAGTCGGAATATCCCCTTGGAGGTAACAGGG
Found at i:202289 original size:51 final size:51
Alignment explanation
Indices: 202173--202291 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
202163 ATGAAATAAT
* *
202173 GAGGTTGGAGTATCCTCGATTGTGAAAAACTAGTGTTTTAGAAATAAAATC
1 GAGGTTGGAGTATCCCCGATTGTGAAAAACTAGTGTTTTAGAAATAAAACC
* * * * *
202224 G-GAGTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACC
1 GAG-GTTGGAGTATCCCCGATTGTGAAAAACTAGTGTTTTAGAAATAAAACC
*
202275 GAGGTTCGAGTATCCCC
1 GAGGTTGGAGTATCCCC
202292 TCGAGAATAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.02
51 55 0.96
52 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GAGGTTGGAGTATCCCCGATTGTGAAAAACTAGTGTTTTAGAAATAAAACC
Found at i:202317 original size:79 final size:80
Alignment explanation
Indices: 202227--202402 Score: 255
Period size: 79 Copynumber: 2.2 Consensus size: 80
202217 TAAAATCGGA
* * * * *
202227 GTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGA-GGTTCGAGTATCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGGTTCGAGTATCCC
* *
202291 CTCGAGAATAATGGG
66 CTCGAAAATAACGGG
*
202306 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGGTTCGAGTATCCC
*
202371 CTTGAAAATAACGGG
66 CTCGAAAATAACGGG
*
202386 GTTGGAGTATCCTCGAT
1 GTTGGAGTATCCCCGAT
202403 GATTAACGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 45 0.52
80 41 0.48
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (80 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGGTTCGAGTATCCC
CTCGAAAATAACGGG
Found at i:202388 original size:28 final size:29
Alignment explanation
Indices: 202356--202426 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 29
202346 ATAAAACCGA
*
202356 GGGTTGGAGTATCCCCTTGA-AAATAACG
1 GGGTTGGAGTATCCCCTCGATAAATAACG
* *
202384 GGGTTGGAGTAT--CCTCGATGATTAACG
1 GGGTTGGAGTATCCCCTCGATAAATAACG
202411 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
202427 GATTGTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.14
27 18 0.49
28 12 0.32
29 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (29 bp):
GGGTTGGAGTATCCCCTCGATAAATAACG
Found at i:202418 original size:237 final size:238
Alignment explanation
Indices: 202027--202482 Score: 623
Period size: 237 Copynumber: 1.9 Consensus size: 238
202017 CGATGATTAC
* * * *
202027 GAAATAAAATCGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAG
1 GAAATAAAACCGGGATTCGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAA
* * * **
202092 AAATCAATATTTTGGAAATAAAGCCGGGGTCGGAGTATCCCCTTGGAGGTAACAGGGTTGGAGTA
66 AAATCAATATTTTAGAAATAAAACCGGGGTCGGAGTATCCCCTTGAAAATAACAGGGTTGGAGTA
* *
202157 TCCCCGATGAAATAATGAGGTTGGAGTATCCTCGATTGTGAAAAACTAGTG-TTTTAGAAATAAA
131 TCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAACTAGTGTTTTTAGAAATAAA
202221 ATCGGAGTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTA
196 ATCGGAGTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTA
* *
202264 GAAATAAAACCGAGG-TTCGAGTATCCCCTC-GAGAATAATGGGGTTGGAGTATCCCCGATTATG
1 GAAATAAAACCG-GGATTCGAGTATCCCCTCGGA-AATAACGGGGTTGGAGTATCCCCAATTATG
** * * *
202327 AAAAATTGATGTTTTAGAAATAAAACCGAGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGA
64 AAAAATCAATATTTTAGAAATAAAACCG-GGGTCGGAGTATCCCCTTGAAAATAACAGGGTTGGA
* * * * * *
202392 GTATCCTCGATG-ATTAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTGGAAAT
128 GTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAACTAGTGTTTTTAGAAAT
* *
202456 AAAATCGGAGTTGGAGTATCCTCGATT
193 AAAATCGGAGTTGGAATATCCCCGATT
202483 ATGAAAAATT
Statistics
Matches: 189, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
236 2 0.01
237 109 0.58
238 78 0.41
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (238 bp):
GAAATAAAACCGGGATTCGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAA
AAATCAATATTTTAGAAATAAAACCGGGGTCGGAGTATCCCCTTGAAAATAACAGGGTTGGAGTA
TCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAACTAGTGTTTTTAGAAATAAA
ATCGGAGTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTA
Found at i:205805 original size:61 final size:60
Alignment explanation
Indices: 205704--206134 Score: 385
Period size: 61 Copynumber: 7.3 Consensus size: 60
205694 TTAAAGTGCA
* * *
205704 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAATATG
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAACA-G
* * *
205765 TCATGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCA-
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAG-GAAA-CAG
* * *
205826 TCCTGCTCTTTGAGGACTAGAAAATGCCGCCAACTTGTGTGGGCTTT-AAGAGG---C-G
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAACAG
* ** * * * **
205881 TCCTGC-CTTTTGAGGATTAGAGGGTGCCAGCAACTCGTGTGGGCTTTGAAAAGAAAAGGTG
1 TCCTGCTC-TTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAA-CAG
* * *
205942 TCCTGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCTAAAA-GAAAGCA-
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTG--AAAAGGAAA-CAG
* *
206003 TCCTACTCTTTGAAGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGC-G
1 TCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGA-AA--CAG
* ***
206064 TCTTGCTCTTTGAGGACT-GAAAGTGCCACCGGGTTGTGTGGGCTTT-AAAAGG---CA-
1 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAACAG
*
206118 TCTTGCTCTTTGAGGAC
1 TCCTGCTCTTTGAGGAC
206135 AAAAAGGTGA
Statistics
Matches: 311, Mismatches: 40, Indels: 45
0.79 0.10 0.11
Matches are distributed among these distances:
54 19 0.06
55 39 0.13
56 4 0.01
58 4 0.01
59 3 0.01
60 36 0.12
61 192 0.62
62 9 0.03
63 5 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAACAG
Found at i:206014 original size:177 final size:177
Alignment explanation
Indices: 205727--206051 Score: 528
Period size: 177 Copynumber: 1.8 Consensus size: 177
205717 GGACTAAAAA
* * *
205727 GTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAATATGTCATGCTCTTTGAGGACTAGAAGGTGC
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGATGTCATGCCCTTTGAGGACTAGAAGGTGC
* * *
205792 CACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTGCTCTTTGAGGACTAGAAAA-TGCCGC
66 CACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTACTCTTTGAAGACT-GAAAAGTGCCAC
205856 CAACTTGTGTGGGCTTTAAGAGGCGTCCTGCCTTTTGAGGATTAGAGG
130 CAACTTGTGTGGGCTTTAAGAGGCGTCCTGCCTTTTGAGGATTAGAGG
* * * *
205904 GTGCCAGCAACTCGTGTGGGCTTTGAAAAGAAAAGGTGTCCTGCCCTTTGAGGACTGGAAGGTGC
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGATGTCATGCCCTTTGAGGACTAGAAGGTGC
205969 CACCAACTTGTGTGGGCTTTGCTAAA-AGAAAGCATCCTACTCTTTGAAGACTGAAAAGTGCCAC
66 CACCAACTTGTGTGGGCTTTGC-AAAGAGAAAGCATCCTACTCTTTGAAGACTGAAAAGTGCCAC
206033 CAACTTGTGTGGGCTTTAA
130 CAACTTGTGTGGGCTTTAA
206052 AAGGAGAAGG
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
176 5 0.04
177 128 0.94
178 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (177 bp):
GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGATGTCATGCCCTTTGAGGACTAGAAGGTGC
CACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCATCCTACTCTTTGAAGACTGAAAAGTGCCACC
AACTTGTGTGGGCTTTAAGAGGCGTCCTGCCTTTTGAGGATTAGAGG
Found at i:206241 original size:55 final size:56
Alignment explanation
Indices: 206157--206403 Score: 243
Period size: 55 Copynumber: 4.4 Consensus size: 56
206147 GGAGAGAGCA
* * *
206157 TCCTGCTCTTTGAGGACT-AGGAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGAGCTTTAAAGAGGCG
* * * * *
206212 TCCTGCTCTTTAAGTACTGAAAAATGCCACCAACCTGTGTGAGCTTTAAAAAGAAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGAGCTTT--AAAG---AGGCG
* ** * *
206273 TCCTGCTCTTTGAGGA-TTAGAAAATGCCACCAACTCATGTGGGCTTTAAA-AGGAG
1 TCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGAGCTTTAAAGAGGCG
* ** *
206328 TCCTGCTCTTTGAGGATTGAAAGTTGCCACCAACTTGTGTGAGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGAGCTTTAAAGAGGCG
206383 TCCTGCTCTTTGAGGACTGAA
1 TCCTGCTCTTTGAGGACTGAA
206404 GGGTGAAAGG
Statistics
Matches: 157, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
55 106 0.68
56 3 0.02
58 3 0.02
59 3 0.02
60 2 0.01
61 40 0.25
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (56 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGAGCTTTAAAGAGGCG
Found at i:206361 original size:116 final size:116
Alignment explanation
Indices: 206157--206374 Score: 319
Period size: 116 Copynumber: 1.9 Consensus size: 116
206147 GGAGAGAGCA
* * ** * *
206157 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCATGTGGGCTTTAAAAGGAGTCCTGCTCTT
*
206222 TAAGTACTGAAAAATGCCACCAACCTGTGTGAGCTTTAAAAAGAAAAAGTG
66 TAAGGACTGAAAAATGCCACCAACCTGTGTGAGCTTTAAAAAGAAAAAGTG
*
206273 TCCTGCTCTTTGAGGATTAGAAAATGCCACCAACTCATGTGGGCTTTAAAAGGAGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCATGTGGGCTTTAAAAGGAGTCCTGCTCTT
* * ** *
206338 TGAGGATTGAAAGTTGCCACCAACTTGTGTGAGCTTT
66 TAAGGACTGAAAAATGCCACCAACCTGTGTGAGCTTT
206375 GAAAGGCGTC
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
116 89 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (116 bp):
TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCATGTGGGCTTTAAAAGGAGTCCTGCTCTT
TAAGGACTGAAAAATGCCACCAACCTGTGTGAGCTTTAAAAAGAAAAAGTG
Found at i:223770 original size:20 final size:20
Alignment explanation
Indices: 223745--223782 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
223735 GTAAAAAGAC
*
223745 AGAATGTATCGATACATTGA
1 AGAATGCATCGATACATTGA
223765 AGAATGCATCGATACATT
1 AGAATGCATCGATACATT
223783 CATATATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
AGAATGCATCGATACATTGA
Found at i:223795 original size:20 final size:20
Alignment explanation
Indices: 223745--223802 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
223735 GTAAAAAGAC
*
223745 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTCA
*
223765 AGAATGCATCGATACATTCA
1 AGAATGTATCGATACATTCA
* *
223785 TA-TATGTATCGTTACATT
1 -AGAATGTATCGATACATT
223803 AAAAAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTCA
Found at i:225078 original size:28 final size:28
Alignment explanation
Indices: 225005--225471 Score: 324
Period size: 28 Copynumber: 16.0 Consensus size: 28
224995 TTTAAAAAAA
*
225005 GGTGCCACTAACATGTGTGGGCTTTGAAAGG
1 GGTGCCACTGAC-T-TGTGGGCTTTGAAA-G
*
225036 GTGTGCCACTAACTTGTGGGCTTTGAAAG
1 G-GTGCCACTGACTTGTGGGCTTTGAAAG
* * *
225065 GGTGCCACTAACTTGTGGGCTTTGGAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
225093 GGTGCTACCGATTTGTGTGGGCTTTGAACAAA
1 GGTGCCACTGA-CT-TGTGGGCTTTG-A-AAG
* * *
225125 GTTGCCACCGACTTGTGTGAACTTTGAAAAG
1 GGTGCCACTGACTTGTG-G-GCTTTG-AAAG
* *
225156 AGTTACCACTGACTTGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
225185 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* ** * * *
225213 GATGCCACCAATTTGTATAGG-TTTCAAAAG
1 GGTGCCACTGACTTG--TGGGCTTT-GAAAG
* * *
225243 GGTGGCACTGACTTGTGTGCTTGGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
225271 AGTGCAACTGACTTGTGGGCTTTGAGAGAG
1 GGTGCCACTGACTTGTGGGCTTTGA-A-AG
* * **
225301 GTTGCCACCGACTTGTGTGGGCTTAAAGAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTGA-AAG
* * *
225332 GATGCCACTAACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
** * * *
225360 TATGCCACTAACTAGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
225388 GATGCCATTGATTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
225416 GATGCCACTGACTTATGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
225445 GATGCAACTGACTTGTGGACTTTGAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAA
225472 AATGACATAT
Statistics
Matches: 355, Mismatches: 64, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
28 171 0.48
29 47 0.13
30 62 0.17
31 19 0.05
32 56 0.16
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:225227 original size:120 final size:116
Alignment explanation
Indices: 225000--225449 Score: 403
Period size: 120 Copynumber: 3.8 Consensus size: 116
224990 GGGCTTTTAA
* * * * * *
225000 AAAAAGGTGCCACTAACATGTGTGGGCTTTGAAAGGGTGTGCCACTAACTTGTGGGCTTTGAAAG
1 AAAAAGTTGCCACTGAC-T-TGTGTGCTTTGAAA-AGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
225065 GGTGCCACTAACTTGTGGGCTTTGGAATGG-TGCTACCGATTTGTGTGGGCTTTG
63 GGTGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACCAATTTGTGTGGGCTTTG
* *
225119 AACAAAGTTGCCACCGACTTGTGTGAACTTTGAAAAGAGTTACCACTGACTTGTGGGCTTTGAAA
1 AA-AAAGTTGCCACTGACTTGTGTG--CTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAA
* * *
225184 GGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAATTTGTATAGG-TTTC
62 GGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAATTTGTGTGGGCTTTG
* * * * *
225238 AAAAGGGTGGCACTGACTTGTGTGC-TTGGAAAGAGTGCAACTGACTTGTGGGCTTTGAGAGAGG
1 AAAAAGTTGCCACTGACTTGTGTGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGA-A-AGG
* * ** * *
225302 TTGCCACCGACTTGTGTGGGCTTAAAGAAGGATGCCACTAA-CT-TGTGGGCTTTG
64 GTGCCACTGAC-T-TGTGGGCTTTGA-AAGGATGCCACCAATTTGTGTGGGCTTTG
* * * * * * *
225356 -AAAA-TATGCCACTAACTAGTGGGCTTTGAAAAGA-TGCCATTGATTTGTGGGCTTTGAAAAGA
1 AAAAAGT-TGCCACTGACTTGTGTGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
*
225418 TGCCACTGACTTATGGGCTTTGAAAAGGATGC
65 TGCCACTGACTTGTGGGCTTTG-AAAGGATGC
225450 AACTGACTTG
Statistics
Matches: 270, Mismatches: 47, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
113 16 0.06
114 23 0.09
115 21 0.08
116 14 0.05
117 42 0.16
118 45 0.17
119 28 0.10
120 81 0.30
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (116 bp):
AAAAAGTTGCCACTGACTTGTGTGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGT
GCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAATTTGTGTGGGCTTTG
Found at i:225346 original size:31 final size:32
Alignment explanation
Indices: 225284--225348 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
225274 GCAACTGACT
** * *
225284 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTG
1 TGTGGGCTTAAAGAGAGGATGCCACCAACTTG
*
225316 TGTGGGCTTAAAGA-AGGATGCCACTAACTTG
1 TGTGGGCTTAAAGAGAGGATGCCACCAACTTG
225347 TG
1 TG
225349 GGCTTTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.28
Consensus pattern (32 bp):
TGTGGGCTTAAAGAGAGGATGCCACCAACTTG
Found at i:225407 original size:56 final size:57
Alignment explanation
Indices: 225001--225472 Score: 240
Period size: 58 Copynumber: 8.1 Consensus size: 57
224991 GGCTTTTAAA
* * * * * *
225001 AAAAGGTGCCACTAACATGTGTGGGCTTTGAAAGGGTGTGCCACTAACTTGTGGGCTTTG
1 AAAAGATGCCACTAAC-T-TATGGGCTTTGAAAAGG-ATGCAACTGACTTGTGGGCTTTG
* * * * * * * *
225061 AAAGGGTGCCACTAACTTGTGGGCTTTGGAATGG-TGCTACCGATTTGTGTGGGCTTTG
1 AAAAGATGCCACTAACTTATGGGCTTTGAAAAGGATGCAACTGA-CT-TGTGGGCTTTG
* ** * * * * *
225119 AACAAAGTTGCCACCGACTTGTGTGAACTTTGAAAAGAGTTACCACTGACTTGTGGGCTTTG
1 -A-AAAGATGCCACTAACTTATG-G-GCTTTGAAAAG-GATGCAACTGACTTGTGGGCTTTG
* * * * * ** * * *
225181 AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACCAATTTGTATAGG-TTTC
1 AAAAGATGCCACTAACTTATGGGCTTTGAAAAGGATGCAACTGACTTG--TGGGCTTTG
* * * * * *
225238 AAAAGGGTGGCACTGACTTGTGTGC-TTGGAAA-GAGTGCAACTGACTTGTGGGCTTTG
1 AAAA-GATGCCACTAACTTATGGGCTTTGAAAAGGA-TGCAACTGACTTGTGGGCTTTG
* * ** * * * *
225295 AGAGAGGTTGCCACCGACTTGTGTGGGC-TTAAAGAAGGATGCCACTAACTTGTGGGCTTTG
1 A-A-AAGATGCCACTAAC-T-TATGGGCTTTGAA-AAGGATGCAACTGACTTGTGGGCTTTG
* * * *
225356 AAAATATGCCACTAAC-TAGTGGGCTTTGAAAA-GATGCCATTGATTTGTGGGCTTTG
1 AAAAGATGCCACTAACTTA-TGGGCTTTGAAAAGGATGCAACTGACTTGTGGGCTTTG
* *
225412 AAAAGATGCCACTGACTTATGGGCTTTGAAAAGGATGCAACTGACTTGTGGACTTTG
1 AAAAGATGCCACTAACTTATGGGCTTTGAAAAGGATGCAACTGACTTGTGGGCTTTG
225469 AAAA
1 AAAA
225473 ATGACATATT
Statistics
Matches: 325, Mismatches: 63, Indels: 51
0.74 0.14 0.12
Matches are distributed among these distances:
56 68 0.21
57 53 0.16
58 78 0.24
59 14 0.04
60 58 0.18
61 25 0.08
62 21 0.06
63 2 0.01
64 6 0.02
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (57 bp):
AAAAGATGCCACTAACTTATGGGCTTTGAAAAGGATGCAACTGACTTGTGGGCTTTG
Found at i:225513 original size:12 final size:13
Alignment explanation
Indices: 225481--225554 Score: 55
Period size: 13 Copynumber: 5.6 Consensus size: 13
225471 AAATGACATA
*
225481 TTGACGAAAATTTC
1 TTGAC-AAAGTTTC
225495 TTGACAAAGTTTC
1 TTGACAAAGTTTC
**
225508 -TGACAAACATTC
1 TTGACAAAGTTTC
*
225520 TCGACAGAAG-TTC
1 TTGACA-AAGTTTC
225533 TTGACGATAA-TTTC
1 TTGAC-A-AAGTTTC
225547 TTGACAAA
1 TTGACAAA
225555 TGGCGAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
12 12 0.24
13 19 0.39
14 18 0.37
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (13 bp):
TTGACAAAGTTTC
Found at i:226757 original size:14 final size:14
Alignment explanation
Indices: 226740--226772 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
226730 GTCTAGACCC
226740 TTTTTTTTTT-GTT
1 TTTTTTTTTTGGTT
226753 TTTTTTTTTTGGTT
1 TTTTTTTTTTGGTT
226767 TTTTTT
1 TTTTTT
226773 GGAACAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (14 bp):
TTTTTTTTTTGGTT
Found at i:230156 original size:19 final size:19
Alignment explanation
Indices: 230132--230194 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
230122 AGCGATACAT
230132 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
230151 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
230164 TGTATCAATACAACACTTA
1 TGTATCGATACAACACTTA
230183 TGTATCGATACA
1 TGTATCGATACA
230195 GTTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 6 0.17
18 1 0.03
19 20 0.56
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:230165 original size:32 final size:32
Alignment explanation
Indices: 230124--230194 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
230114 AGCTTCGTAG
*
230124 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCAATACAACACTTATGTAT
230156 CGATACATTGTATCAATACAACACTTATGTAT
1 CGATACATTGTATCAATACAACACTTATGTAT
230188 CGATACA
1 CGATACA
230195 GTTACTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCAATACAACACTTATGTAT
Found at i:231127 original size:101 final size:99
Alignment explanation
Indices: 230967--231558 Score: 409
Period size: 87 Copynumber: 6.3 Consensus size: 99
230957 GAATGACATG
* * * * * **
230967 TGCTGATTCATGGCCAGCGACATTAGACTTGAAGAAGAA--TGCCAATGTGCTGAGACAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* *
231030 ACGACATTGGGCTTAGGAATGTTAAAGATGCCAATA
66 GCGACATTGGGCTTA-GAATGTCAAAGA-GCCAATA
* * * *
231066 AGCTGATTAAAGGCCAACGATATTGGACTTAAGGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * * * *
231131 GCGACATT-GGTTTGAAAGATGACGAAGACGCCAATG
66 GCGACATTGGGCTT-AGA-ATGTCAAAGA-GCCAATA
* *
231167 TGCTGATTCAAGGCCAGCGATTTTGGACTTAAAGATGAAGGTGCCAATGTGTTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * *
231232 GCGACATTGGACTTAAATATGACAAAGGAGCCAATA
66 GCGACATTGGGCTTAGA-ATGTCAAA-GAGCCAATA
*
231268 TGCTGATTCAAGGCCAGCGATATTGGAC-T-----T----GTGCCAATGTGCTGATTTAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * * * *
231323 GCGACATTGGTCTTA-AA-GACAAGGTGTCAATA
66 GCGACATTGGGCTTAGAATGTCAAAGAGCCAATA
* * * * * *
231355 TGTTGATTAAAGGCCAGCGATATTGGGC-T-----T----GTGCCAATGTGCTAATTCGAGGCAA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * * *
231410 ACGACATTGGTCTTA-AA-GACAAGGTA-CCAATA
66 GCGACATTGGGCTTAGAATGTCAAAG-AGCCAATA
* *
231442 TGCTGATTCAAGGCTAGCGATATTGGAC-T-----T----GTGCCAATGTGCTGATTTAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
* * * * *
231497 ACAACATTGGTCTTA-AA-GACAAAGTGCCAATA
66 GCGACATTGGGCTTAGAATGTCAAAGAGCCAATA
*
231529 TGTTGATTCAAGGCCAGCGATATTGGACTT
1 TGCTGATTCAAGGCCAGCGATATTGGACTT
231559 GTGCCAATGT
Statistics
Matches: 424, Mismatches: 60, Indels: 29
0.83 0.12 0.06
Matches are distributed among these distances:
87 184 0.43
88 6 0.01
89 1 0.00
90 1 0.00
91 37 0.09
95 1 0.00
99 30 0.07
100 6 0.01
101 153 0.36
102 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (99 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGGCTTAGAATGTCAAAGAGCCAATA
Found at i:231128 original size:49 final size:49
Alignment explanation
Indices: 230964--231558 Score: 303
Period size: 52 Copynumber: 12.7 Consensus size: 49
230954 GAAGAATGAC
* * *
230964 ATGTGCTGATTCATGGCCAGCGACATTAGACTTGAA-GAAGAA--TGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AAGGATGAAGGTGCCA
** * * *
231011 ATGTGCTGAGACAAGGCCAACGACATTGGGCTT-AGGAATGTTAAAGATGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGG-ATG---AAGGTGCCA
** * * *
231063 ATAAGCTGATTAAAGGCCAACGATATTGGACTTAAGGATGAAGGTGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
* * **
231112 ATGTGCTGATTCAAGGCCAGCGACATTGG-TTTGAAAGATGACGAAGACGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTT--AAG--GATGAAGGTGCCA
** *
231164 ATGTGCTGATTCAAGGCCAGCGATTTTGGACTTAAAGATGAAGGTGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
* ** *
231213 ATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAATATGACAAAGGAGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATG---AAGGTGCCA
* *
231265 ATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T----GTGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
* * * * *
231304 ATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGTCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
* * * * *
231352 ATATGTTGATTAAAGGCCAGCGATATTGGGC-T-----T----GTGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
* * * * * * * *
231391 ATGTGCTAATTCGAGGCAAACGACATTGGTCTTAAAGA-CAAGGTACCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
* * *
231439 ATATGCTGATTCAAGGCTAGCGATATTGGAC-T-----T----GTGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
* * * * * * *
231478 ATGTGCTGATTTAAGGCCAACAACATTGGTCTTAAAGA-CAAAGTGCCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
* * *
231526 ATATGTTGATTCAAGGCCAGCGATATTGGACTT
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTT
231559 GTGCCAATGT
Statistics
Matches: 417, Mismatches: 83, Indels: 95
0.70 0.14 0.16
Matches are distributed among these distances:
39 88 0.21
40 3 0.01
45 1 0.00
46 2 0.00
47 31 0.07
48 94 0.23
49 78 0.19
50 5 0.01
51 3 0.01
52 107 0.26
53 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGGATGAAGGTGCCA
Found at i:231320 original size:39 final size:39
Alignment explanation
Indices: 231261--231758 Score: 332
Period size: 39 Copynumber: 11.9 Consensus size: 39
231251 TGACAAAGGA
* * *
231261 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGT
*
231300 GCCAATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGACAAGGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT---------GT
* * * * * *
231348 GTCAATATGTTGATTAAAGGCCAGCGATATTGGGCTTGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGT
* * * *
231387 GCCAATGTGCTAATTCGAGGCAAACGACATTGGTCTTAAAGACAAGGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT---------GT
* * * * *
231435 ACCAATATGCTGATTCAAGGCTAGCGATATTGGACTTGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGT
* * *
231474 GCCAATGTGCTGATTTAAGGCCAACAACATTGGTCTTAAAGACAAAGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT---------GT
* * * *
231522 GCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGT
* *
231561 GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTCT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGT
*
231600 GCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT---------GT
* * * * * *
231648 GCCAATATACTAATTCAAGGCCAGTGATATTGGACTTGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGT
* *
231687 GCTAATGTGCTGATTCAAGGCCAACGACATTGGTCTTGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGT
231726 GCCAATGTGCTGA-TCAAGGCCAGCGACATTGGT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGT
231759 TTTAAAGACA
Statistics
Matches: 354, Mismatches: 69, Indels: 73
0.71 0.14 0.15
Matches are distributed among these distances:
38 19 0.05
39 208 0.59
48 127 0.36
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (39 bp):
GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTGT
Found at i:231391 original size:87 final size:87
Alignment explanation
Indices: 231207--231809 Score: 605
Period size: 87 Copynumber: 7.0 Consensus size: 87
231197 AAAGATGAAG
* * * *
231207 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAATATGACAAAGGAGCCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATATGCT
231272 GATTCAAGGCCAGCGATATTGGACTT
62 GATTCAAGGCCAGCGATATTGGACTT
* * * *
231298 GTGCCAATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGTCAATATGTTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* *
231363 AAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGACTT
* * * *
231385 GTGCCAATGTGCTAATTCGAGGCAAACGACATTGGTCTTAAAGACAAGGTACCAATATGCTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
231450 CAAGGCTAGCGATATTGGACTT
66 CAAGGCCAGCGATATTGGACTT
* * * *
231472 GTGCCAATGTGCTGATTTAAGGCCAACAACATTGGTCTTAAAGACAAAGTGCCAATATGTTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
231537 CAAGGCCAGCGATATTGGACTT
66 CAAGGCCAGCGATATTGGACTT
* *
231559 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT-----C----TGCCAATGTGTTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* *
231615 CAAGGCCAGCGACATTGGTCTT
66 CAAGGCCAGCGATATTGGACTT
* * * ** * * *
231637 AAAGACAAGGTGCCAATATACTAATTCAAGGCCAGTGATATTGGACTT---------GTGCTAAT
1 ---------GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAAT
* * * *
231693 GTGCTGATTCAAGGCCAACGACATTGGTCTT
57 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
231724 GTGCCAATGTGCTGA-TCAAGGCCAGCGACATTGGTTTTAAAGACAAGGTGCTAATATACTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
231788 CAAGGCCAGCGATATTGGACTT
66 CAAGGCCAGCGATATTGGACTT
231810 AGAAAAAGAT
Statistics
Matches: 438, Mismatches: 55, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
77 19 0.04
78 47 0.11
82 1 0.00
86 34 0.08
87 295 0.67
88 3 0.01
89 1 0.00
90 2 0.00
91 36 0.08
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (87 bp):
GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTT
Found at i:231620 original size:126 final size:126
Alignment explanation
Indices: 231436--231809 Score: 579
Period size: 126 Copynumber: 3.0 Consensus size: 126
231426 AGACAAGGTA
* * * * * * * *
231436 CCAATATGCTGATTCAAGGCTAGCGATATTGGACTTGTGCCAATGTGCTGATTTAAGGCCAACAA
1 CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTGTGCCAATGTGCTGATTCAAGGCCAGCGA
* **
231501 CATTGGTCTTAAAGACAAAGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTGTG
66 CATTGGTCTTAAAGACAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTGTG
* *
231562 CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTCTGCCAATGTGTTGATTCAAGGCCAGCGA
1 CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTGTGCCAATGTGCTGATTCAAGGCCAGCGA
* *
231627 CATTGGTCTTAAAGACAAGGTGCCAATATACTAATTCAAGGCCAGTGATATTGGACTTGTG
66 CATTGGTCTTAAAGACAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTGTG
*
231688 CTAATGTGCTGATTCAAGGCCAACGACATTGGTCTTGTGCCAATGTGCTGA-TCAAGGCCAGCGA
1 CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTGTGCCAATGTGCTGATTCAAGGCCAGCGA
* *
231752 CATTGGTTTTAAAGACAAGGTGCTAATATACTGATTCAAGGCCAGCGATATTGGACTT
66 CATTGGTCTTAAAGACAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTT
231810 AGAAAAAGAT
Statistics
Matches: 226, Mismatches: 22, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
125 67 0.30
126 159 0.70
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (126 bp):
CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTGTGCCAATGTGCTGATTCAAGGCCAGCGA
CATTGGTCTTAAAGACAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTGTG
Found at i:231775 original size:39 final size:39
Alignment explanation
Indices: 231693--231775 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
231683 TTGTGCTAAT
** * *
231693 GTGCTGATTCAAGGCCAACGACATTGGTCTTGTGCCAAT
1 GTGCTGATTCAAGGCCAACGACATTGGTCTTAAGACAAG
* *
231732 GTGCTGA-TCAAGGCCAGCGACATTGGTTTTAAAGACAAG
1 GTGCTGATTCAAGGCCAACGACATTGGTCTT-AAGACAAG
231771 GTGCT
1 GTGCT
231776 AATATACTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 21 0.57
39 16 0.43
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
GTGCTGATTCAAGGCCAACGACATTGGTCTTAAGACAAG
Found at i:231892 original size:28 final size:30
Alignment explanation
Indices: 231822--231880 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
231812 AAAAAGATGC
231822 CACCAACTTGTGTGGGCTTTTGAAAGGATTG
1 CACCAACTTGTGT-GGCTTTTGAAAGGATTG
231853 CACCAACTTGTGT-GCTTTT-AAAGG-TTG
1 CACCAACTTGTGTGGCTTTTGAAAGGATTG
231880 C
1 C
231881 CACTGACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 4 0.14
28 5 0.18
29 6 0.21
31 13 0.46
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (30 bp):
CACCAACTTGTGTGGCTTTTGAAAGGATTG
Found at i:231943 original size:27 final size:27
Alignment explanation
Indices: 231909--232271 Score: 231
Period size: 27 Copynumber: 12.1 Consensus size: 27
231899 AAAGGAGAAA
231909 GATGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
*
231936 GATGCCACGGAGTTGTGGGCTTTAAAAAG
1 GATGCCACGGAGTTGTGGAC-TT-AAAAG
*
231965 AAAAAGATGCCACGGAGTTATGGACTTAAAAG
1 -----GATGCCACGGAGTTGTGGACTTAAAAG
* * * *
231997 GGTACCACAGAGTTGTGGGCTTTAAAAAGAACAAG
1 GATGCCACGGAGTTGTGGAC-TT------AA-AAG
*
232032 GATGCCATGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
*
232059 GGTGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* *
232086 GGTGCCGCGGAGTTGTGGACTTAAAAGG
1 GATGCCACGGAGTTGTGGACTTAAAA-G
* *
232114 AAAAAGAGTGCGACGGAGTTGTGGGCTTTAAAAAG
1 -----GA-TGCCACGGAGTTGTGGAC-TT-AAAAG
* *
232149 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAACAAG
1 -----GATGCCACGGAGTTGTGGAC-TT------AA-AAG
*
232189 GATGCCATGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
*
232216 GGTGCCACGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
* *
232243 GGTGCCGCGGAGTTGTGGACTTAAAAG
1 GATGCCACGGAGTTGTGGACTTAAAAG
232270 GA
1 GA
232272 AAAAGAGTGC
Statistics
Matches: 276, Mismatches: 30, Indels: 60
0.75 0.08 0.16
Matches are distributed among these distances:
27 142 0.51
28 9 0.03
29 5 0.02
32 5 0.02
33 3 0.01
34 59 0.21
35 44 0.16
36 4 0.01
39 2 0.01
40 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (27 bp):
GATGCCACGGAGTTGTGGACTTAAAAG
Found at i:231975 original size:34 final size:33
Alignment explanation
Indices: 231931--232550 Score: 514
Period size: 34 Copynumber: 19.5 Consensus size: 33
231921 TTGTGGACTT
*
231931 AAAAGGATGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGG-TGCCACGGAGTTGTGGAC-TTAAAAAGA
* *
231966 AAAAGATGCCACGGAGTTATGGACTT-AAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* * *
231997 ----GGTACCACAGAGTTGTGGGCTTTAAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TTAAAAAGA
* *
232027 ACAAGGATGCCATGGAGTTGTGGACTT-AAAAG-
1 AAAAGG-TGCCACGGAGTTGTGGACTTAAAAAGA
232059 ----GGTGCCACGGAGTTGTGGACTT-AAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* *
232086 ----GGTGCCGCGGAGTTGTGGACTTAAAAGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* *
232115 AAAAGAGTGCGACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAG-GTGCCACGGAGTTGTGGAC-TTAAAAAGA
*
232150 AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TTAAAAAGA
* *
232184 ACAAGGATGCCATGGAGTTGTGGACTT-AAAAG-
1 AAAAGG-TGCCACGGAGTTGTGGACTTAAAAAGA
232216 ----GGTGCCACGGAGTTGTGGACTT-AAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* *
232243 ----GGTGCCGCGGAGTTGTGGACTTAAAAGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* *
232272 AAAAGAGTGCGACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAG-GTGCCACGGAGTTGTGGAC-TTAAAAAGA
*
232307 AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TTAAAAAGA
*
232341 AAAAGGTGCCACGGAGTTGTGGACTT-AATAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* * * *
232372 ----GGTGCCACAAAGAGTTGCGGGCTTTGAAAAGA
1 AAAAGGTGCCAC--GGAGTTGTGGAC-TTAAAAAGA
232404 AAAAGGTGCCACGGAGTTGTGGACTT-AAAAG-
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* *
232435 ----GGTGCCACAGAGTTGTGGGCTTTAAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TTAAAAAGA
232465 AAAAGGTGCCACGGAGTTGTGGACTTTAAAAAGA
1 AAAAGGTGCCACGGAGTTGTGGAC-TTAAAAAGA
* * *
232499 AAAATGTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
*
232532 ACAAGGATGCCACGGAGTT
1 AAAAGG-TGCCACGGAGTT
232551 ATTGATTTTG
Statistics
Matches: 493, Mismatches: 50, Indels: 85
0.79 0.08 0.14
Matches are distributed among these distances:
27 131 0.27
28 16 0.03
29 19 0.04
30 2 0.00
31 4 0.01
32 14 0.03
33 30 0.06
34 208 0.42
35 61 0.12
36 8 0.02
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (33 bp):
AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
Found at i:232202 original size:157 final size:156
Alignment explanation
Indices: 231911--232530 Score: 820
Period size: 157 Copynumber: 4.0 Consensus size: 156
231901 AGGAGAAAGA
* * *
231911 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGA-TGC
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGAGTGC
* * * * *
231975 CACGGAGTTATGGAC-TT-AAAAG-----GGTACCACAGAGTTGTGGGCTTTAAAAAGAACAAGG
65 CACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG
*
232033 ATGCCATGGAGTTGTGGACTTAAAAGGG
130 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
232061 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCGCGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCC
*
232126 ACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAACAAGGA
66 ACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGG-
*
232191 TGCCATGGAGTTGTGGACTTAAAAGGG
130 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
232218 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCGCGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCC
232283 ACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGT
66 ACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGT
*
232348 GCCACGGAGTTGTGGACTTAATAGGG
131 GCCACGGAGTTGTGGACTTAAAAGGG
* * *
232374 TGCCACAAAGAGTTGCGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAA-G---
1 TGCCAC--GGAGTTGTGGAC-TT-AAAAG-----GGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* *
232435 --G-GTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAA
57 AAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
* *
232497 GAAAAATGTGCCACAGAGTTGTGGACTTAAAAGG
122 GAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
232531 AACAAGGATG
Statistics
Matches: 431, Mismatches: 22, Indels: 26
0.90 0.05 0.05
Matches are distributed among these distances:
149 14 0.03
150 57 0.13
151 2 0.00
152 5 0.01
156 31 0.07
157 190 0.44
158 98 0.23
159 3 0.01
160 5 0.01
164 1 0.00
165 25 0.06
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (156 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCC
ACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGT
GCCACGGAGTTGTGGACTTAAAAGGG
Found at i:232396 original size:63 final size:61
Alignment explanation
Indices: 232306--232550 Score: 312
Period size: 63 Copynumber: 3.9 Consensus size: 61
232296 CTTTAAAAAG
* *
232306 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
* * *
232367 AATAGGGTGCCACAAAGAGTTGCGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCAC--AGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
232430 AAAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT
* * * *
232492 AAAAAGAAAAATGTGCCACAGAGTTGTGGAC-TTAAAAGGAACAAGGATGCCACGGAGTT
1 -AAAAG-----GGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGG-TGCCACGGAGTT
232551 ATTGATTTTG
Statistics
Matches: 162, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
61 55 0.34
62 2 0.01
63 62 0.38
67 13 0.08
68 30 0.19
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
Found at i:232441 original size:27 final size:28
Alignment explanation
Indices: 232403--232495 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 28
232393 CTTTGAAAAG
*
232403 AAAAAGGTGCCACGGAGTTGTGGAC-TT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
* *
232430 AAAAGGGTGCCACAGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
232458 AAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTTT
232492 AAAA
1 AAAA
232496 AGAAAAATGT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 22 0.41
28 2 0.04
29 5 0.09
33 4 0.07
34 21 0.39
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (28 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTT
Found at i:232634 original size:31 final size:31
Alignment explanation
Indices: 232565--232658 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
232555 ATTTTGGGAC
*
232565 AAGATGCCACTGAATCGTGGAC-TT-GGACA-
1 AAGATGCCACTGAGTCGTGGACTTTAGGA-AG
232594 AGAGATGCCACTGAGTCGTGGACTTTAGGAAG
1 A-AGATGCCACTGAGTCGTGGACTTTAGGAAG
* *
232626 AAGATGCCATTGAGTCGTGGACTTTAGCAAG
1 AAGATGCCACTGAGTCGTGGACTTTAGGAAG
232657 AA
1 AA
232659 TGTTAGGATC
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
29 1 0.02
30 20 0.34
31 33 0.57
32 4 0.07
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (31 bp):
AAGATGCCACTGAGTCGTGGACTTTAGGAAG
Found at i:233070 original size:13 final size:13
Alignment explanation
Indices: 233052--233077 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
233042 TACACAAAGT
233052 ATGTATCGATACA
1 ATGTATCGATACA
233065 ATGTATCGATACA
1 ATGTATCGATACA
233078 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:239284 original size:13 final size:13
Alignment explanation
Indices: 239266--239304 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
239256 ACATTTTTCT
*
239266 TTGTATTGATACA
1 TTGTATCGATACA
239279 TTGTATCGATACA
1 TTGTATCGATACA
* *
239292 CTGTATCCATACA
1 TTGTATCGATACA
239305 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:239459 original size:20 final size:20
Alignment explanation
Indices: 239416--239461 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
239406 AAATCCTTTG
239416 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
239437 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
239457 CAAAA
1 CAAAA
239462 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:242687 original size:31 final size:30
Alignment explanation
Indices: 242647--242833 Score: 171
Period size: 31 Copynumber: 6.0 Consensus size: 30
242637 GCTTTCAAAG
*
242647 AAGATGCCACTGAGTCATGGAATTTGAGAA
1 AAGATGCCACTGAGTCATGGACTTTGAGAA
*
242677 GAGATTGCCACTGAGTCATGGACTTTAGGAAGAA
1 AAGA-TGCCACTGAGTCATGGACTTT--G-AGAA
* * *
242711 AAGGATGCCATTGAGTCGTGGACTTAGA-AA
1 AA-GATGCCACTGAGTCATGGACTTTGAGAA
* *
242741 AAGGATGCCACTAAGTTATGGACTTTGA-AA
1 AA-GATGCCACTGAGTCATGGACTTTGAGAA
* * *
242771 AGATATTGCCACTGGGTCGTGGACTTTGAAGAA
1 A-AGA-TGCCACTGAGTCATGGACTTTG-AGAA
* *
242804 AAGATGCTACTAAGTCATGGACTTTGAGAA
1 AAGATGCCACTGAGTCATGGACTTTGAGAA
242834 GAGAGATGTG
Statistics
Matches: 127, Mismatches: 21, Indels: 18
0.77 0.13 0.11
Matches are distributed among these distances:
30 36 0.28
31 58 0.46
32 4 0.03
33 4 0.03
34 23 0.18
35 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (30 bp):
AAGATGCCACTGAGTCATGGACTTTGAGAA
Found at i:244182 original size:108 final size:107
Alignment explanation
Indices: 243987--244195 Score: 285
Period size: 108 Copynumber: 1.9 Consensus size: 107
243977 TATCCCCTCG
* * * *
243987 GAAATAAGGAGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCAGGGTT
1 GAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAACCAGGGTT
*
244052 GGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCTCCGAT
66 GGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATCTCCGAT
* * *** * *
244094 GAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAATTGGTGCTTTTGGAAATAAAATC-GGAG
1 GAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAAT-ATTTTGGAAATAAAACCAGG-G
244158 TTGGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATC
64 TTGGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATC
244196 CCTGATTATG
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
107 37 0.42
108 51 0.58
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (107 bp):
GAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAACCAGGGTT
GGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATCTCCGAT
Found at i:244206 original size:187 final size:185
Alignment explanation
Indices: 243883--244352 Score: 578
Period size: 187 Copynumber: 2.5 Consensus size: 185
243873 TTTTGGAGAT
* ** * * * *
243883 AATAACGGGGTTGGAGTGTCCCCTTGAAAATAACGAGGCTGGAGTATCCCCGGTTGTGAGAAATC
1 AATAACGGGGTTGGAGTATCCCGATG-AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATT
* *
243948 GATG-ATTAGAAAAAAAATCGG-GATTGGAGTATCCCCTCGGAAATAAGGAGGTTGGAGTATCCC
65 GATGTTTTAGAAATAAAATCGGAG-TTGGAGTATCCCCTCGGAAATAAGGAGGTTGGAGTATCCC
* * *
244011 CAATTATGAGAAATCAATATTTTGGGAATAAAG-CCAGGGTTGGAGTATCCCCTCGGA
129 CAATTATGAGAAATCAATATTTTAGAAATAAAGTCCAGGGTTGGAGTAT-CCCTCGAA
** * *
244068 GGTAACGGGGTTGGAGTATCTCCGATGAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAATT
1 AATAACGGGGTTGGAGTATC-CCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATT
* * *
244133 GGTGCTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAGATAACGG-GGTTGGAGTATCC
65 GATG-TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAA-GGAGGTTGGAGTATCC
** * **
244197 CTGATTATGAGAAATTAATATTTTAGAAATAAAGTCGGGGGTTGGAGTATCCCTCGAA
128 CCAATTATGAGAAATCAATATTTTAGAAATAAAGTCCAGGGTTGGAGTATCCCTCGAA
* *
244255 AATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGA---TGAAAAATT
1 AATAACGGGGTTGGAGTAT-CCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATT
*
244316 GATGTTTTAGAAATAAAATCGGAGTTAGAGTATCCCC
65 GATGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCC
244353 GATTATAGAA
Statistics
Matches: 245, Mismatches: 33, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
182 31 0.13
183 12 0.05
185 52 0.21
186 25 0.10
187 108 0.44
188 17 0.07
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (185 bp):
AATAACGGGGTTGGAGTATCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTG
ATGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAAGGAGGTTGGAGTATCCCCA
ATTATGAGAAATCAATATTTTAGAAATAAAGTCCAGGGTTGGAGTATCCCTCGAA
Found at i:244272 original size:79 final size:80
Alignment explanation
Indices: 244073--244276 Score: 227
Period size: 80 Copynumber: 2.5 Consensus size: 80
244063 TCGGAGGTAA
* * * **
244073 CGGGGTTGGAGTATCTC-CGATGAAATAACGAGGTTGGAGTAT-CCTCAATTGTGAAAAATTGGT
1 CGGGGTTGGAGTATCCCTCGA--AAATAACGGGGTTGGAGTATCCCTCAATTATGAAAAATTAAT
* *
244136 GCTTTTGGAAATAAAAT
64 GATTTTAGAAATAAAAT
* * * * *
244153 CGGAGTTGGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATCCCT-GATTATGAGAAATTAAT-
1 CGGGGTTGGAGTAT-CCCTCGAAAATAACGGGGTTGGAGTATCCCTCAATTATGAAAAATTAATG
*
244216 ATTTTAGAAATAAAGT
65 ATTTTAGAAATAAAAT
244232 CGGGGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCC
1 C-GGGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCC
244277 CGATGATTAA
Statistics
Matches: 104, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
79 42 0.40
80 55 0.53
81 5 0.05
82 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCTCAATTATGAAAAATTAATGA
TTTTAGAAATAAAAT
Found at i:244308 original size:27 final size:27
Alignment explanation
Indices: 244234--244310 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
244224 AATAAAGTCG
*
244234 GGGGTTGGAGTATCCCTCGA-AAATAAC
1 GGGGTTGGAGTATCCC-CGATGAATAAC
*
244261 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATGAATAAC
244288 GGGGTTGGAGTATCCCCGATGAA
1 GGGGTTGGAGTATCCCCGATGAA
244311 AAATTGATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 3 0.07
27 43 0.93
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATGAATAAC
Found at i:244385 original size:50 final size:47
Alignment explanation
Indices: 244295--244406 Score: 120
Period size: 50 Copynumber: 2.3 Consensus size: 47
244285 AACGGGGTTG
* *
244295 GAGTATCCCCGATGAAAAATTGATGTTTTAGAAATAAAATCGGAGTT
1 GAGTATCCCCGATTAAAAATTGATGTTTTAGAAATAAAATCGAAGTT
*
244342 AGAGTATCCCCGATTATAGAAATT-AGTGTTTT-GAAAATGAAATCGAAGTT
1 -GAGTATCCCCGATTA-A-AAATTGA-TGTTTTAG-AAATAAAATCGAAGTT
*
244392 GGGATATCCCCGATT
1 GAG-TATCCCCGATT
244407 GCGGAGAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
48 14 0.25
49 5 0.09
50 36 0.65
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (47 bp):
GAGTATCCCCGATTAAAAATTGATGTTTTAGAAATAAAATCGAAGTT
Found at i:246224 original size:11 final size:11
Alignment explanation
Indices: 246208--246239 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
246198 CAATGGAATA
246208 GTGTTTTTTTT
1 GTGTTTTTTTT
246219 GTG-TTTTTTT
1 GTGTTTTTTTT
246229 G-GTTTTTTTT
1 GTGTTTTTTTT
246239 G
1 G
246240 CTAAAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.05
10 16 0.80
11 3 0.15
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (11 bp):
GTGTTTTTTTT
Found at i:246753 original size:21 final size:21
Alignment explanation
Indices: 246727--246783 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
246717 GTAAACTTCC
246727 TAGATGTATCGATACAAAGAA
1 TAGATGTATCGATACAAAGAA
*
246748 TAGATGTATCGATACACAGAA
1 TAGATGTATCGATACAAAGAA
*
246769 -AAATGTATCGATACA
1 TAGATGTATCGATACA
246784 TTTCCTTGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
TAGATGTATCGATACAAAGAA
Found at i:246825 original size:13 final size:13
Alignment explanation
Indices: 246807--246858 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
246797 AGCTTCCTAG
246807 CGATACATTGTAT
1 CGATACATTGTAT
246820 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
246839 CGATACATTGTAT
1 CGATACATTGTAT
246852 CGATACA
1 CGATACA
246859 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:246839 original size:19 final size:19
Alignment explanation
Indices: 246815--246879 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
246805 AGCGATACAT
246815 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
246834 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
246847 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
246866 TGTATCGATACAAA
1 TGTATCGATACAAA
246880 TCGCTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:246848 original size:32 final size:32
Alignment explanation
Indices: 246807--246877 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
246797 AGCTTCCTAG
246807 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
246839 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
246871 CGATACA
1 CGATACA
246878 AATCGCTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:250843 original size:19 final size:19
Alignment explanation
Indices: 250819--250879 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
250809 AGCGATACAT
250819 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
250838 TGTATCGAT---ACA-TTA
1 TGTATCGATACAACACTTA
250853 --TATCGATACAACACTTA
1 TGTATCGATACAACACTTA
250870 TGTATCGATA
1 TGTATCGATA
250880 TAGTTACTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 7 0.19
15 3 0.08
16 6 0.17
17 3 0.08
19 17 0.47
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:250857 original size:32 final size:32
Alignment explanation
Indices: 250811--250879 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
250801 AGCTTCGTAG
*
250811 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTATATCGATACAACACTTATGTAT
250843 CGATACATTATATCGATACAACACTTATGTAT
1 CGATACATTATATCGATACAACACTTATGTAT
250875 CGATA
1 CGATA
250880 TAGTTACTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTATATCGATACAACACTTATGTAT
Found at i:256400 original size:19 final size:19
Alignment explanation
Indices: 256376--256443 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
256366 AATTCAACAA
256376 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
256395 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
256410 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
256427 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
256444 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:256415 original size:13 final size:13
Alignment explanation
Indices: 256397--256421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
256387 ACATAAGTTT
256397 TGTATCGATACAA
1 TGTATCGATACAA
256410 TGTATCGATACA
1 TGTATCGATACA
256422 TAAGTATTGT
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:256419 original size:32 final size:32
Alignment explanation
Indices: 256378--256440 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
256368 TTCAACAATT
*
256378 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
256410 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
256441 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:256501 original size:13 final size:13
Alignment explanation
Indices: 256483--256508 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
256473 CATTTTTCTG
256483 TGTATCGATACAT
1 TGTATCGATACAT
256496 TGTATCGATACAT
1 TGTATCGATACAT
256509 GGATCTTTGT
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:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:256505 original size:33 final size:33
Alignment explanation
Indices: 256463--256529 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
256453 GCCAAGGAAA
***
256463 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
256496 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
256529 T
1 T
256530 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:258674 original size:323 final size:323
Alignment explanation
Indices: 258047--258692 Score: 1222
Period size: 324 Copynumber: 2.0 Consensus size: 323
258037 TACTCCAGGA
*
258047 TCATGGAATGAACACGTAATGCCCATGTTACCTCCCCTTCTTGATTATAGACGTTCGAATGTCTG
1 TCATGGAATGAACACGTAATGCCCATGTTACCTCCCCTTCTTGATTATAGACATTCGAATGTCTG
258112 TAGCAAGAGCTCGATCTAGTGGAGAAACCAAAAACGATAAACACTTCCTCTGTTTGGTCTGGCAG
66 TAGCAAGAGCTCGATCTAGTGGAGAAACCAAAAACGATAAACACTTCCTCTGTTTGGTCTGGCAG
*
258177 CATGGCAGTATGAGATTGAAAATTATGTAAAAAATTCGAAACGATTTTTCTGAAAATTTTTGATA
131 CACGGCAGTATGAGATTGAAAATTATGTAAAAAATTCGAAACGATTTTTCTGAAAATTTTTGATA
258242 TTTTTTGCTCAAATATCTTTGAATTACCTTTTCAACTGATGTCTTGTTTGTCTCCAGATTCGTCC
196 TTTTTTGCTCAAATATCTTTGAATTACCTTTTCAACTGATGTCTTGTTTGTCTCCAGATTCGTCC
* *
258307 AGACTAGGGAGTTATGATTTTTTGAGTCTAAGCTGTTCAAAAACCCTGGAATCAGTAAAATGC
261 AGACTAGGGAGTTATGATTTTTTGAGTCTAAGCTGTTAAAAAACCCTGGAATCAGGAAAATGC
* *
258370 TCATGGAATGAACACGTGATGCCCATGTTACCTCCCCTATCTTGATTATGGACATTCGAATGTCT
1 TCATGGAATGAACACGTAATGCCCATGTTACCTCCCCT-TCTTGATTATAGACATTCGAATGTCT
258435 GTAGCAAGAGCTCGATCTAGTGGAGAAACCAAAAACGATAAACACTTCCTCTGTTTGGTCTGGCA
65 GTAGCAAGAGCTCGATCTAGTGGAGAAACCAAAAACGATAAACACTTCCTCTGTTTGGTCTGGCA
258500 GCACGGCAGTATGAGATTGAAAATTATGTAAAAAATTCGAAACGATTTTTCTGAAAATTTTTGAT
130 GCACGGCAGTATGAGATTGAAAATTATGTAAAAAATTCGAAACGATTTTTCTGAAAATTTTTGAT
258565 ATTTTTTGCTCAAATATCTTTGAATTACCTTTTCAAC-GATGTCTTGTTTGTCTCCAGATTCGTC
195 ATTTTTTGCTCAAATATCTTTGAATTACCTTTTCAACTGATGTCTTGTTTGTCTCCAGATTCGTC
258629 CAGACTAGGGAGTTATGATTTTTTGAGTCTAAGCTGTTAAAAAACCCTGGAATCAGGAAAATGC
260 CAGACTAGGGAGTTATGATTTTTTGAGTCTAAGCTGTTAAAAAACCCTGGAATCAGGAAAATGC
258693 ATTCTGGTTG
Statistics
Matches: 316, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
323 126 0.40
324 190 0.60
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (323 bp):
TCATGGAATGAACACGTAATGCCCATGTTACCTCCCCTTCTTGATTATAGACATTCGAATGTCTG
TAGCAAGAGCTCGATCTAGTGGAGAAACCAAAAACGATAAACACTTCCTCTGTTTGGTCTGGCAG
CACGGCAGTATGAGATTGAAAATTATGTAAAAAATTCGAAACGATTTTTCTGAAAATTTTTGATA
TTTTTTGCTCAAATATCTTTGAATTACCTTTTCAACTGATGTCTTGTTTGTCTCCAGATTCGTCC
AGACTAGGGAGTTATGATTTTTTGAGTCTAAGCTGTTAAAAAACCCTGGAATCAGGAAAATGC
Found at i:259275 original size:27 final size:28
Alignment explanation
Indices: 259242--259317 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
259232 ATTTTCTATA
259242 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
259269 ATCGGGGATACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
259297 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
259318 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:259376 original size:51 final size:51
Alignment explanation
Indices: 259300--259522 Score: 232
Period size: 52 Copynumber: 4.3 Consensus size: 51
259290 TTATTTCTGA
* * * *
259300 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCATAATC
* * *
259351 GGGGATACTCCAACCCC-AGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGA-TTTTATTTCCAAAACACTAATTTTT-CATAATC
* * * * * *
259403 GGGGATACTCTAACCTCGATTTTATTTTCAAAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTT-TTC-ATAATC
* * * *
259456 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACTAATTTTTCATAATC
*
259508 GAGGATACTCCAACC
1 GGGGATACTCCAACC
259523 TCGTTATTTC
Statistics
Matches: 140, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
50 1 0.01
51 36 0.26
52 57 0.41
53 33 0.24
54 13 0.09
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCATAATC
Found at i:259568 original size:28 final size:27
Alignment explanation
Indices: 259510--259585 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
259500 TCACAATTGA
* *
259510 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCA-CGG
259538 GGATACTCCAACCCCAGTTACTTC-CGAG
1 GGATACTCCAACCCC-GTTACTTCACG-G
*
259566 GGAACACTCCAACCCCGTTA
1 GG-ATACTCCAACCCCGTTA
259586 TTATCTCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.05
28 21 0.50
29 19 0.45
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTACTTCACGG
Found at i:271436 original size:32 final size:33
Alignment explanation
Indices: 271395--271463 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
271385 GGCAGTAGCT
* *
271395 TACATTGTATCGATACAAAAC-TTATGTATTGA
1 TACATTGTATCAATACAAAACTTTATGTATCGA
*
271427 TACATTGTATCAATACAACACTTTATGTATCGA
1 TACATTGTATCAATACAAAACTTTATGTATCGA
271460 TACA
1 TACA
271464 AATCATTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 19 0.58
33 14 0.42
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (33 bp):
TACATTGTATCAATACAAAACTTTATGTATCGA
Found at i:272228 original size:20 final size:20
Alignment explanation
Indices: 272203--272338 Score: 136
Period size: 20 Copynumber: 6.9 Consensus size: 20
272193 GTAAAAAGAT
*
272203 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTCA
*
272223 AGAATGTATCGATGCATTCA
1 AGAATGTATCGATACATTCA
* *
272243 A-CATGTATCGATACATTGA
1 AGAATGTATCGATACATTCA
*
272262 AGAATGTATCGA-GCATTCA
1 AGAATGTATCGATACATTCA
* * *
272281 TA-CAGGTATCGATACATTGA
1 -AGAATGTATCGATACATTCA
*
272301 AGAATGTATCGATGCATTCA
1 AGAATGTATCGATACATTCA
*
272321 TA-CATGTATCGATACATT
1 -AGAATGTATCGATACATT
272339 AAAAAATTTA
Statistics
Matches: 93, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
19 30 0.32
20 62 0.67
21 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTCA
Found at i:272260 original size:39 final size:40
Alignment explanation
Indices: 272206--272338 Score: 243
Period size: 39 Copynumber: 3.4 Consensus size: 40
272196 AAAAGATAGA
272206 ATGTATCGATACATTGAAGAATGTATCGATGCATTCA-AC
1 ATGTATCGATACATTGAAGAATGTATCGATGCATTCATAC
272245 ATGTATCGATACATTGAAGAATGTATCGA-GCATTCATAC
1 ATGTATCGATACATTGAAGAATGTATCGATGCATTCATAC
*
272284 AGGTATCGATACATTGAAGAATGTATCGATGCATTCATAC
1 ATGTATCGATACATTGAAGAATGTATCGATGCATTCATAC
272324 ATGTATCGATACATT
1 ATGTATCGATACATT
272339 AAAAAATTTA
Statistics
Matches: 90, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
38 7 0.08
39 59 0.66
40 24 0.27
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (40 bp):
ATGTATCGATACATTGAAGAATGTATCGATGCATTCATAC
Found at i:277551 original size:28 final size:28
Alignment explanation
Indices: 277509--277581 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 28
277499 TAATTATATG
277509 ATATGAATATAATATAAAAAATAAT-TAAA
1 ATATG-ATATAATATAAAAAATAATAT-AA
* *
277538 ATATGATATGATATATAAAATAATATAA
1 ATATGATATAATATAAAAAATAATATAA
277566 ATATGATATTAATATA
1 ATATGATA-TAATATA
277582 CGAATATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 27 0.69
29 12 0.31
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (28 bp):
ATATGATATAATATAAAAAATAATATAA
Found at i:277587 original size:28 final size:28
Alignment explanation
Indices: 277509--277596 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
277499 TAATTATATG
* *
277509 ATATGAATATAATATAAAAAATAATTAAA
1 ATATG-ATATGATATATAAAATAATTAAA
277538 ATATGATATGATATATAAAATAA-TATAA
1 ATATGATATGATATATAAAATAATTA-AA
* *
277566 ATATGATATTA-ATATACGAATATATTAAA
1 ATATGATATGATATATA-AAATA-ATTAAA
277595 AT
1 AT
277597 TTATATAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
27 7 0.14
28 32 0.63
29 10 0.20
30 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (28 bp):
ATATGATATGATATATAAAATAATTAAA
Found at i:279527 original size:23 final size:23
Alignment explanation
Indices: 279501--279558 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
279491 ACAAATATGA
*
279501 TAGTGTTTTTAAAAATAACTAGG-
1 TAGTGTTTTTAAAAATAAAT-GGC
279524 TA--GTTTTTAAAAATAAATGGC
1 TAGTGTTTTTAAAAATAAATGGC
*
279545 TAGTATTTTTAAAA
1 TAGTGTTTTTAAAA
279559 GAGAGTGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 17 0.57
23 11 0.37
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.41
Consensus pattern (23 bp):
TAGTGTTTTTAAAAATAAATGGC
Found at i:284036 original size:130 final size:130
Alignment explanation
Indices: 283752--284052 Score: 290
Period size: 130 Copynumber: 2.3 Consensus size: 130
283742 GATAATAACG
* * * *
283752 GGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCACCGATTGTGAAAAATCGATGATT
1 GGGTTAGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCACCAATTATGAAAAATCAATGATT
* * *
283817 TAGAAATAAGGCAAGGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAATAGAATCA
66 TAGAAATAAGGCAAGGGTTGAAGTATCCCCGATTATAGAAAATAGATATTTCAAAAATAGAACCA
* * * * * * *
283882 GGATTGGAGTATCCTCGTGAAAATAATGGGGTTGGAGTATC-CTCAATTATGAGAAATTAAT-AT
1 GGGTTAGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCAC-CAATTATGAAAAATCAATGA-
* * * * * *
283945 TTTAGAAATAAGGTC-GGGGTTGAGGTATCCCTGATTGT-GAGAAATCA-ATATTTTAGAAATA-
64 TTTAGAAATAAGG-CAAGGGTTGAAGTATCCCCGATTATAGA-AAAT-AGATATTTCAAAAATAG
284006 AAGCCA
126 AA-CCA
* ***
284012 GGGTTAGAGTATCCCCTTGGAAATAACTATGTTGGAGTATC
1 GGGTTAGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATC
284053 CCCGATGAAA
Statistics
Matches: 136, Mismatches: 29, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
129 6 0.04
130 128 0.94
131 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.29
Consensus pattern (130 bp):
GGGTTAGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCACCAATTATGAAAAATCAATGATT
TAGAAATAAGGCAAGGGTTGAAGTATCCCCGATTATAGAAAATAGATATTTCAAAAATAGAACCA
Found at i:284052 original size:28 final size:28
Alignment explanation
Indices: 284013--284081 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
284003 ATAAAGCCAG
* * *
284013 GGTTAGAGTATCCCC-TTGGAAATAACTA
1 GGTTGGAGTATCCCCGAT-GAAATAACGA
* *
284041 TGTTGGAGTATCCCCGATGAAATAACGG
1 GGTTGGAGTATCCCCGATGAAATAACGA
284069 GGTTGGAGTATCC
1 GGTTGGAGTATCC
284082 TTGATTGTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGA
Found at i:284174 original size:158 final size:159
Alignment explanation
Indices: 283885--284216 Score: 393
Period size: 158 Copynumber: 2.1 Consensus size: 159
283875 AGAATCAGGA
* *
283885 TTGGAGTATCCTCG-TGAAAATAATGGGGTTGGAGTATCCTCAATTATGAGAAATTAATATTTTA
1 TTGGAGTATCCTCGATGAAAATAACGGGGTTGGAGTATCCTCAATTATGAAAAATTAATATTTTA
* * * * *
283949 GAAATAAGGTCGGGGTTGAGGTATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAGCCAGG
66 GAAATAAGATCAGAGTTGAGATATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGG
* * * *
284014 GTTAGAGTATCCCCTTGGAAATAACTATG
131 GTTAGAGTATCCCCTCGAAAATAACGAGG
* ** * * * *
284043 TTGGAGTATCCCCGATG-AAATAACGGGGTTGGAGTATCCTTGATTGTGAAAAATTAGTGTTTTG
1 TTGGAGTATCCTCGATGAAAATAACGGGGTTGGAGTATCCTCAATTATGAAAAATTAATATTTTA
*** * *
284107 GAAATAAGATCAGAGTTG-GAATATCCCTGATTGTG-GAGAATTGGTGTTTTAGAAATAAAACCG
66 GAAATAAGATCAGAGTTGAG-ATATCCCTGATTGTGAGA-AATCAATATTTTAGAAATAAAACCA
* *
284170 GGGTTGGAGTATCCCCTCGAAAATAACGGGG
129 GGGTTAGAGTATCCCCTCGAAAATAACGAGG
284201 TTGGAGTATCCTCGAT
1 TTGGAGTATCCTCGAT
284217 TATGAAAAAT
Statistics
Matches: 145, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
157 3 0.02
158 140 0.97
159 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (159 bp):
TTGGAGTATCCTCGATGAAAATAACGGGGTTGGAGTATCCTCAATTATGAAAAATTAATATTTTA
GAAATAAGATCAGAGTTGAGATATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGG
GTTAGAGTATCCCCTCGAAAATAACGAGG
Found at i:284176 original size:51 final size:51
Alignment explanation
Indices: 284066--284184 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
284056 GATGAAATAA
* * * *
284066 CGGGGTTGGAGTATCCTTGATTGTGAAAAATTAGTGTTTTGGAAATAAGAT
1 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
* * * * * *
284117 CAGAGTTGGAATATCCCTGATTGTGGAGAATTGGTGTTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
284168 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
284185 CTCGAAAATA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
Found at i:284473 original size:75 final size:76
Alignment explanation
Indices: 284145--284570 Score: 595
Period size: 76 Copynumber: 5.5 Consensus size: 76
284135 GATTGTGGAG
284145 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
1 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
*
284210 CCTCGATTATGAAA
66 CCCCG---ATGAAA
* *
284224 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTAT
1 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
284289 CCCCGATGAAA
66 CCCCGATGAAA
* * * *
284300 AATTGGTGTGTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGTTTGGAGTAT
1 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
284365 CCCCGATGAAA
66 CCCCGATGAAA
* * *
284376 AATTGGTGTTTTAGAAATAAAACCAGGGTTGGAGTGTCCCCTCAAAAATAACGGGGTTGGAG-AT
1 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
284440 CCCCGATGAAA
66 CCCCGATGAAA
* * * *
284451 AACTGGTGTTTTAGAAATAAAACCGGGGTTAGAGTGTCCCCTCGAAAATAACGGGGTTGCAGTAT
1 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
*
284516 CCCCAATTGTGAAA
66 CCCCGA---TGAAA
* * * * *
284530 AGTCGATGTTTT-GAAAATAAAATCGGAGTTGGAGTATCCCC
1 AATTGGTGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCC
284571 GATTATGGAA
Statistics
Matches: 312, Mismatches: 30, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
75 70 0.22
76 138 0.44
78 1 0.00
79 103 0.33
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (76 bp):
AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
CCCCGATGAAA
Found at i:284569 original size:51 final size:50
Alignment explanation
Indices: 284506--284682 Score: 189
Period size: 51 Copynumber: 3.5 Consensus size: 50
284496 AAATAACGGG
* * *
284506 GTTGCAGTATCCCCAATTGTGAAAAGTCGATGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAA-TCGATGTTTTGAAAATAAAATCGGA
* *
284557 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTT-AGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATCGATGTTTTGA-AAATAAAATCGGA
* * * * *
284608 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAA-CCGA
1 GTTGGAGTATCCCCGATTATG-AAAATCGATGTTTTGAAAATAAAATCGGA
*
284658 GATTGGAGTATCCCCGA-GATGAAAA
1 G-TTGGAGTATCCCCGATTATGAAAA
284683 ATCTAGAAAT
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
49 4 0.04
50 8 0.07
51 91 0.84
52 5 0.05
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAATCGATGTTTTGAAAATAAAATCGGA
Found at i:286994 original size:20 final size:19
Alignment explanation
Indices: 286969--287055 Score: 69
Period size: 20 Copynumber: 4.7 Consensus size: 19
286959 AAAATGCCTG
286969 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATGA-A
286989 AATGTATCGATACAAT---
1 AATGTATCGATACAATGAA
* *
287005 -A--TATTGATACAATGAGC
1 AATGTATCGATACAATGA-A
* *
287022 CATGTATCTATACAATGCAA
1 AATGTATCGATACAATG-AA
287042 AATGTATCGATACA
1 AATGTATCGATACA
287056 TCTGGGTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
13 11 0.21
15 1 0.02
18 1 0.02
20 39 0.74
21 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:287120 original size:20 final size:20
Alignment explanation
Indices: 287074--287126 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
287064 AACTTCCTAG
*
287074 ATGTATCGATACAAAGATCG
1 ATGTATCGATACAAAGATCA
* *
287094 ATCTATCGATACAATGAAT-A
1 ATGTATCGATACAAAG-ATCA
287114 ATGTATCGATACA
1 ATGTATCGATACA
287127 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACAAAGATCA
Found at i:294395 original size:32 final size:33
Alignment explanation
Indices: 294332--294397 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
294322 TTCAACGATT
*
294332 TGTATCGATACATAAAGTGTTATATCGATACAA
1 TGTATCAATACATAAAGTGTTATATCGATACAA
* *
294365 TGTATCAATACAT-AAGTTTTGTATCGATACAA
1 TGTATCAATACATAAAGTGTTATATCGATACAA
294397 T
1 T
294398 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (33 bp):
TGTATCAATACATAAAGTGTTATATCGATACAA
Found at i:297878 original size:17 final size:17
Alignment explanation
Indices: 297856--297890 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
297846 CTCTTACAAG
*
297856 TGAATTATTGTGCTCTT
1 TGAATTATTGTGCCCTT
*
297873 TGAATTTTTGTGCCCTT
1 TGAATTATTGTGCCCTT
297890 T
1 T
297891 TAAATATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.54
Consensus pattern (17 bp):
TGAATTATTGTGCCCTT
Found at i:303892 original size:88 final size:88
Alignment explanation
Indices: 303790--303967 Score: 322
Period size: 88 Copynumber: 2.0 Consensus size: 88
303780 AAAAATATTA
303790 AATAAAATACGAATTTTAAATTTCATTTTTCATAAAAATAAAGAAAGAAAACAATATTATCTTAT
1 AATAAAATACGAATTTTAAATTTCATTTTTCATAAAAATAAAGAAAGAAAACAATATTATCTTAT
303855 AATTGATAAAC-ATCATTTGAAAC
66 AATTGATAAACAAT-ATTTGAAAC
* *
303878 AATAAAATATGAATTTTAAATTTCATTTTTCATAAAAATAAAGATAGAAAACAATATTATCTTAT
1 AATAAAATACGAATTTTAAATTTCATTTTTCATAAAAATAAAGAAAGAAAACAATATTATCTTAT
303943 AATTGATAAACAATATTTGAAAC
66 AATTGATAAACAATATTTGAAAC
303966 AA
1 AA
303968 ATATCTAACG
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
88 85 0.98
89 2 0.02
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (88 bp):
AATAAAATACGAATTTTAAATTTCATTTTTCATAAAAATAAAGAAAGAAAACAATATTATCTTAT
AATTGATAAACAATATTTGAAAC
Found at i:307916 original size:13 final size:13
Alignment explanation
Indices: 307898--307981 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
307888 AGCTTCGTAG
307898 CGATACATTGTAT
1 CGATACATTGTAT
307911 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
307930 CGATACATTGTAT
1 CGATACATTGTAT
307943 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
307962 CGATACATTGTAT
1 CGATACATTGTAT
307975 CGATACA
1 CGATACA
307982 ATTTCTGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 24 0.41
14 1 0.02
15 2 0.03
16 12 0.20
17 2 0.03
18 1 0.02
19 17 0.29
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:307930 original size:19 final size:19
Alignment explanation
Indices: 307906--307968 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
307896 AGCGATACAT
307906 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
307925 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
307938 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
307957 TGTATCGATACA
1 TGTATCGATACA
307969 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:307939 original size:32 final size:32
Alignment explanation
Indices: 307898--307982 Score: 170
Period size: 32 Copynumber: 2.7 Consensus size: 32
307888 AGCTTCGTAG
307898 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
307930 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
307962 CGATACATTGTATCGATACAA
1 CGATACATTGTATCGATACAA
307983 TTTCTGTTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:309517 original size:50 final size:50
Alignment explanation
Indices: 309459--309558 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
309449 AAATATCAAA
309459 ACAATTCTTTTAAGCCATTATTTAAGTAAATGATTGCAAAATTGAATGGC
1 ACAATTCTTTTAAGCCATTATTTAAGTAAATGATTGCAAAATTGAATGGC
*
309509 ACAATTCTTTTAAGCCATTATTTCAGTAAATGATTGCAAAATTGAATGGC
1 ACAATTCTTTTAAGCCATTATTTAAGTAAATGATTGCAAAATTGAATGGC
309559 CTGGGTTTCG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (50 bp):
ACAATTCTTTTAAGCCATTATTTAAGTAAATGATTGCAAAATTGAATGGC
Found at i:315836 original size:22 final size:22
Alignment explanation
Indices: 315802--315864 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
315792 TCAAAATGAC
* * *
315802 GAAAAAGTCAAAAGCAAAAGCAT
1 GAAAAA-TGAAAAGCAAAAACAA
315825 GAAAAATGAAAAG-AAAAACAA
1 GAAAAATGAAAAGCAAAAACAA
* *
315846 AAAAAATGCAATAGCAAAA
1 GAAAAATG-AAAAGCAAAA
315865 TAAAAAAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 13 0.39
22 10 0.30
23 10 0.30
ACGTcount: A:0.68, C:0.10, G:0.14, T:0.08
Consensus pattern (22 bp):
GAAAAATGAAAAGCAAAAACAA
Found at i:315850 original size:21 final size:22
Alignment explanation
Indices: 315826--315873 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
315816 CAAAAGCATG
315826 AAAAATG-AAAAGAAAAACAAA
1 AAAAATGCAAAAGAAAAACAAA
* * *
315847 AAAAATGCAATAGCAAAATAAA
1 AAAAATGCAAAAGAAAAACAAA
315869 AAAAA
1 AAAAA
315874 CGAGGACATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.77, C:0.06, G:0.08, T:0.08
Consensus pattern (22 bp):
AAAAATGCAAAAGAAAAACAAA
Found at i:317214 original size:27 final size:27
Alignment explanation
Indices: 317184--317825 Score: 347
Period size: 27 Copynumber: 23.3 Consensus size: 27
317174 CACGATTCTA
317184 TGGCATCCTTTTAAGTCCACAACTTCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
*
317211 TGGCATCCTTTTAAGTCCACAACTCCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
* * *
317238 TGGTATCCTTTTAAAGTCAACAACTTTG
1 TGGCATCCTTTT-AAGTCCACAACTTCG
* *
317266 TGGCATTCC-TTTAAGTCCATAACTCCG
1 TGGCA-TCCTTTTAAGTCCACAACTTCG
*
317293 TGGCATCCTTTTAAGTCCACAACTCCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
*
317320 TGGCATCCTTTTAAAGTCCACAACTCCG
1 TGGCATCCTTTT-AAGTCCACAACTTCG
* *
317348 TGGCATCCTTTTAAGTCCATAACTCCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
* * *
317375 TGGCATCCTTTTTAAGCCCACAA-GTCAA
1 TGGCATCC-TTTTAAGTCCACAACTTC-G
* * ** * * *
317403 TGACACCCTTCCAAAGCCCACAAGTTAG
1 TGGCATCCTT-TTAAGTCCACAACTTCG
* * * * * *
317431 TGGTACCCCTTTTTAAGCCCATAA-GTCAA
1 TGGCA-TCC-TTTTAAGTCCACAACTTC-G
* * *
317460 TGGCACCCTTCTAAAG-CTCACAA-GTCAG
1 TGGCATCCTT-TTAAGTC-CACAACTTC-G
* * *
317488 TGGCACCCATTTCAAAG-CCTACAA-GTCAG
1 TGGCATCC-TTT-TAAGTCC-ACAACTTC-G
* * * *
317517 TGGCATCTTTTTTAAGCCCACAA-GTCAA
1 TGGCATC-CTTTTAAGTCCACAACTTC-G
* * *
317545 TGCCATGCCTTTTTAAGCCCACAACTCCG
1 TGGCAT-CC-TTTTAAGTCCACAACTTCG
* * *
317574 TGGCACCCTTTAAAGTCCACAACTCCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
* * *
317601 TGGCA-CCTTTTTAAGTCCATAACTCCA
1 TGGCATCC-TTTTAAGTCCACAACTTCG
* * * *
317628 TGGCACCCTTTTAGGTCCATAACTTCA
1 TGGCATCCTTTTAAGTCCACAACTTCG
* * * * * *
317655 TGCCACCCTTTTAAATTCCATAGCTCCG
1 TGGCATCCTTTT-AAGTCCACAACTTCG
* *
317683 TGGCAGCCTTTTAAGTCAACAAC-TCTG
1 TGGCATCCTTTTAAGTCCACAACTTC-G
* *
317710 TGGCA-CACTTTTAAAGTCCACCACTCCG
1 TGGCATC-CTTTT-AAGTCCACAACTTCG
* * *
317738 TGGCACCCTTTTAGGTCCACAATTTCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
*
317765 TGGCA-CACTTTTAAGTCCACAACTCCG
1 TGGCATC-CTTTTAAGTCCACAACTTCG
* * * *
317792 TGGC-CCCTTTTAAAGTCCATAAGTTCA
1 TGGCATCCTTTT-AAGTCCACAACTTCG
317819 TGGCATC
1 TGGCATC
317826 ATTTCAAAGC
Statistics
Matches: 500, Mismatches: 82, Indels: 65
0.77 0.13 0.10
Matches are distributed among these distances:
26 13 0.03
27 252 0.50
28 164 0.33
29 68 0.14
30 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (27 bp):
TGGCATCCTTTTAAGTCCACAACTTCG
Found at i:317270 original size:55 final size:54
Alignment explanation
Indices: 317184--317810 Score: 440
Period size: 55 Copynumber: 11.4 Consensus size: 54
317174 CACGATTCTA
*
317184 TGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCACAACTCCG
1 TGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCG
* * ** *
317238 TGGTATCCTTTTAAAGTCAACAACTTTGTGGCATTCC-TTTAAGTCCATAACTCCG
1 TGGCATCCTTTT-AAGTCCACAACTCCGTGGCA-TCCTTTTAAGTCCACAACTCCG
317293 TGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCG
1 TGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCG
* * * **
317348 TGGCATCCTTTTAAGTCCATAACTCCGTGGCATCCTTTTTAAGCCCACAAGTCAA
1 TGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCG
* * ** * * ** * * * * * **
317403 TGACACCCTTCCAAAGCCCACAAGTTAGTGGTACCCCTTTTTAAGCCCATAAGTCAA
1 TGGCATCCTT-TTAAGTCCACAACTCCGTGGCA-TCC-TTTTAAGTCCACAACTCCG
* * * * * * * *
317460 TGGCACCCTTCTAAAG-CTCACAAGTCAGTGGCACCCATTTCAAAG-CCTACAAGTCAG
1 TGGCATCCTT-TTAAGTC-CACAACTCCGTGGCATCC-TTT-TAAGTCC-ACAACTCCG
* * * ** * *
317517 TGGCATCTTTTTTAAGCCCACAAGTCAATGCCATGCCTTTTTAAGCCCACAACTCCG
1 TGGCATC-CTTTTAAGTCCACAACTCCGTGGCAT-CC-TTTTAAGTCCACAACTCCG
* * * *
317574 TGGCACCCTTTAAAGTCCACAACTCCGTGGCA-CCTTTTTAAGTCCATAACTCCA
1 TGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCG
* * * * * * * * * *
317628 TGGCACCCTTTTAGGTCCATAACTTCATGCCACCCTTTTAAATTCCATAGCTCCG
1 TGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCG
* * * *
317683 TGGCAGCCTTTTAAGTCAACAACTCTGTGGCA-CACTTTTAAAGTCCACCACTCCG
1 TGGCATCCTTTTAAGTCCACAACTCCGTGGCATC-CTTTT-AAGTCCACAACTCCG
* * * *
317738 TGGCACCCTTTTAGGTCCACAATTTCGTGGCA-CACTTTTAAGTCCACAACTCCG
1 TGGCATCCTTTTAAGTCCACAACTCCGTGGCATC-CTTTTAAGTCCACAACTCCG
*
317792 TGGC-CCCTTTTAAAGTCCA
1 TGGCATCCTTTT-AAGTCCA
317811 TAAGTTCATG
Statistics
Matches: 471, Mismatches: 84, Indels: 36
0.80 0.14 0.06
Matches are distributed among these distances:
53 10 0.02
54 105 0.22
55 201 0.43
56 48 0.10
57 97 0.21
58 10 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (54 bp):
TGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCG
Found at i:317305 original size:82 final size:82
Alignment explanation
Indices: 317184--317810 Score: 442
Period size: 82 Copynumber: 7.6 Consensus size: 82
317174 CACGATTCTA
* * *
317184 TGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCACAACTCCGTGGTATCCTTT
1 TGGCATCCTTTTAAGTCCATAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTT
**
317249 TAAAGTCAACAACTTTG
66 TAAAGTCAACAACTCCG
317266 TGGCATTCC-TTTAAGTCCATAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTT
1 TGGCA-TCCTTTTAAGTCCATAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTT
*
317330 TTAAAGTCCACAACTCCG
65 TTAAAGTCAACAACTCCG
* * ** * *
317348 TGGCATCCTTTTAAGTCCATAACTCCGTGGCATCCTTTTTAAGCCCACAAGTCAATGACACCCTT
1 TGGCATCCTTTTAAGTCCATAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCGTGGCATCCTT
** * * * **
317413 CCAAAGCCCACAAGTTAG
65 TTAAAGTCAACAACTCCG
* * * * ** * * * * *
317431 TGGTACCCCTTTTTAAGCCCATAAGTCAATGGCACCCTTCTAAAG-CTCACAAGTCAGTGGCACC
1 TGGCA-TCC-TTTTAAGTCCATAACTCCGTGGCATCCTT-TTAAGTC-CACAACTCCGTGGCATC
* * * * *
317495 CATTTCAAAGCCTACAAGTCAG
62 C-TTTTAAAGTCAACAACTCCG
* * * * ** * *
317517 TGGCATCTTTTTTAAGCCCACAAGTCAATGCCATGCCTTTTTAAGCCCACAACTCCGTGGCA-CC
1 TGGCATC-CTTTTAAGTCCATAACTCCGTGGCAT-CC-TTTTAAGTCCACAACTCCGTGGCATCC
* *
317581 CTTTAAAGTCCACAACTCCG
63 TTTTAAAGTCAACAACTCCG
* * * * * * * *
317601 TGGCA-CCTTTTTAAGTCCATAACTCCATGGCACCCTTTTAGGTCCATAACTTCATGCCACCCTT
1 TGGCATCC-TTTTAAGTCCATAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTT
* * * *
317665 TTAAATTCCATAGCTCCG
65 TTAAAGTCAACAACTCCG
* * * * * *
317683 TGGCAGCCTTTTAAGTCAACAACTCTGTGGCA-CACTTTTAAAGTCCACCACTCCGTGGCACCCT
1 TGGCATCCTTTTAAGTCCATAACTCCGTGGCATC-CTTTT-AAGTCCACAACTCCGTGGCATCCT
* * * *
317747 TTT-AGGTCCACAATTTCG
64 TTTAAAGTCAACAACTCCG
* *
317765 TGGCA-CACTTTTAAGTCCACAACTCCGTGGC-CCCTTTTAAAGTCCA
1 TGGCATC-CTTTTAAGTCCATAACTCCGTGGCATCCTTTT-AAGTCCA
317811 TAAGTTCATG
Statistics
Matches: 445, Mismatches: 81, Indels: 39
0.79 0.14 0.07
Matches are distributed among these distances:
81 36 0.08
82 190 0.43
83 85 0.19
84 24 0.05
85 67 0.15
86 40 0.09
87 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (82 bp):
TGGCATCCTTTTAAGTCCATAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTT
TAAAGTCAACAACTCCG
Found at i:317443 original size:57 final size:57
Alignment explanation
Indices: 317381--317615 Score: 188
Period size: 57 Copynumber: 4.2 Consensus size: 57
317371 TCCGTGGCAT
* *
317381 CCTTTTTAAGCCCACAAGTCAATGACACCCTTCCAAAGCCCACAAGTTAGTGGTACC
1 CCTTTTTAAGCCCACAAGTCAATGACACCCTTCCAAAGCCCACAAGTCAGTGGCACC
* * * *
317438 CCTTTTTAAGCCCATAAGTCAATGGCACCCTTCTAAAGCTCACAAGTCAGTGGCACC
1 CCTTTTTAAGCCCACAAGTCAATGACACCCTTCCAAAGCCCACAAGTCAGTGGCACC
* ** * * * * * *** * * **
317495 CATTTCAAAGCCTACAAGTCAGTGGCATCTTTTTTAAGCCCACAAGTCAATGCCATG
1 CCTTTTTAAGCCCACAAGTCAATGACACCCTTCCAAAGCCCACAAGTCAGTGGCACC
* ** * * * * *
317552 CCTTTTTAAGCCCACAACTCCGTGGCACCCTT-TAAAGTCCACAACTCCGTGGCA--
1 CCTTTTTAAGCCCACAAGTCAATGACACCCTTCCAAAGCCCACAAGTCAGTGGCACC
317606 CCTTTTTAAG
1 CCTTTTTAAG
317616 TCCATAACTC
Statistics
Matches: 143, Mismatches: 35, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
54 10 0.07
56 16 0.11
57 117 0.82
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (57 bp):
CCTTTTTAAGCCCACAAGTCAATGACACCCTTCCAAAGCCCACAAGTCAGTGGCACC
Found at i:317450 original size:29 final size:29
Alignment explanation
Indices: 317381--317568 Score: 157
Period size: 28 Copynumber: 6.6 Consensus size: 29
317371 TCCGTGGCAT
*
317381 CCTTTTTAAGCCCACAAGTCAATGACA-C
1 CCTTTTTAAGCCCACAAGTCAATGGCACC
*** * * *
317409 CCTTCCAAAGCCCACAAGTTAGTGGTACC
1 CCTTTTTAAGCCCACAAGTCAATGGCACC
*
317438 CCTTTTTAAGCCCATAAGTCAATGGCA-C
1 CCTTTTTAAGCCCACAAGTCAATGGCACC
* * * *
317466 CCTTCTAAAGCTCACAAGTCAGTGGCACC
1 CCTTTTTAAGCCCACAAGTCAATGGCACC
* ** * * *
317495 CATTTCAAAGCCTACAAGTCAGTGGCA-T
1 CCTTTTTAAGCCCACAAGTCAATGGCACC
* * **
317523 CTTTTTTAAGCCCACAAGTCAATGCCATG
1 CCTTTTTAAGCCCACAAGTCAATGGCACC
317552 CCTTTTTAAGCCCACAA
1 CCTTTTTAAGCCCACAA
317569 CTCCGTGGCA
Statistics
Matches: 124, Mismatches: 33, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
28 64 0.52
29 60 0.48
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (29 bp):
CCTTTTTAAGCCCACAAGTCAATGGCACC
Found at i:317850 original size:28 final size:28
Alignment explanation
Indices: 317819--318051 Score: 268
Period size: 28 Copynumber: 8.2 Consensus size: 28
317809 CATAAGTTCA
*
317819 TGGCATCATTTCAAAGCCTACAAGTCAG
1 TGGCATCATTTCAAAGCCCACAAGTCAG
* * * *
317847 TGGCACCATTTCAATGCCCACAAATCCG
1 TGGCATCATTTCAAAGCCCACAAGTCAG
317875 TGGCATCATTTCAAAGCCCACAAGTCAG
1 TGGCATCATTTCAAAGCCCACAAGTCAG
* ** *
317903 TGGCACCATTTTGAATCCCACAAGTCAG
1 TGGCATCATTTCAAAGCCCACAAGTCAG
* * *
317931 TGGCATCATTTCAAAGCCCATAAGTTAA
1 TGGCATCATTTCAAAGCCCACAAGTCAG
* *
317959 TGGCATCCTTTCAAAGCCCACAAGTCTG
1 TGGCATCATTTCAAAGCCCACAAGTCAG
**
317987 TGGCATCATTTCAAAGCCCACAAGTTGG
1 TGGCATCATTTCAAAGCCCACAAGTCAG
* *
318015 TAGCAACTCATTTCAAAGCCTACACAAGTTAG
1 TGGC-A-TCATTTCAAAGCC--CACAAGTCAG
318047 TGGCA
1 TGGCA
318052 ACTAATTTCA
Statistics
Matches: 170, Mismatches: 31, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
28 143 0.84
29 1 0.01
30 13 0.08
31 1 0.01
32 12 0.07
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (28 bp):
TGGCATCATTTCAAAGCCCACAAGTCAG
Found at i:325040 original size:32 final size:33
Alignment explanation
Indices: 324999--325063 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
324989 TAGCCAAACT
*
324999 TGTATCGATACAC-AAAATATGTATTGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
325031 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
325064 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
34 17 0.57
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:327296 original size:21 final size:21
Alignment explanation
Indices: 327263--327312 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
327253 TTGCAAGTTG
*
327263 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
327285 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
327306 AAATAAA
1 AAATAAA
327313 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:329130 original size:15 final size:15
Alignment explanation
Indices: 329110--329140 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
329100 TAAAAATATC
*
329110 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
329125 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
329140 C
1 C
329141 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:331229 original size:20 final size:20
Alignment explanation
Indices: 331158--331235 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
331148 AATGTCCAAA
331158 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACAT-TTTTCT
* *
331178 GTGTATCGATACATTTGGAAATTCA
1 ATGTATCGATACATTT-----TTCT
331203 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
331223 TTGTATCGATACA
1 ATGTATCGATACA
331236 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.04
20 28 0.60
24 2 0.04
25 15 0.32
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Done.