Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold365
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: 1826335
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 11
Found at i:131817 original size:33 final size:33
Alignment explanation
Indices: 131759--131850 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
131749 ATTATGCATT
*
131759 TATCGATACAATG-A-ACATGTATCGATGCAATG
1 TATCGATACAAAGCATA-ATGTATCGATGCAATG
131791 TATCGATACAAAGCATAATGTATCGATGCAATG
1 TATCGATACAAAGCATAATGTATCGATGCAATG
131824 TATCGATACAAAGCATAATGTATCGAT
1 TATCGATACAAAGCATAATGTATCGAT
131851 ACATCTGGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 12 0.21
33 44 0.77
34 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (33 bp):
TATCGATACAAAGCATAATGTATCGATGCAATG
Found at i:133549 original size:13 final size:13
Alignment explanation
Indices: 133530--133569 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
133520 ATAGTAACTC
133530 ATGTATCGATACA
1 ATGTATCGATACA
* *
133543 TTGTATCCATACA
1 ATGTATCGATACA
133556 ATGTATCGATACA
1 ATGTATCGATACA
133569 A
1 A
133570 AGAACATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:137651 original size:19 final size:21
Alignment explanation
Indices: 137607--137658 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
137597 TTCAATAGTT
137607 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAACAGTAAA
* *
137628 TGTATCGATACATA-AGT-GA
1 TGTATCGATACAAACAGTAAA
137647 TGTATCGATACA
1 TGTATCGATACA
137659 GTGTATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAAACAGTAAA
Found at i:137732 original size:33 final size:32
Alignment explanation
Indices: 137690--137755 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
137680 GCCAAGGAAA
*
137690 TGTATCGATACATTATTCAATGTATCCATACAT
1 TGTATCGATACATTACTC-ATGTATCCATACAT
* *
137723 TGTATCGATACATTGCTCATGTATCGATACAT
1 TGTATCGATACATTACTCATGTATCCATACAT
137755 T
1 T
137756 TTACAATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATTACTCATGTATCCATACAT
Found at i:140125 original size:51 final size:50
Alignment explanation
Indices: 140062--140226 Score: 174
Period size: 51 Copynumber: 3.2 Consensus size: 50
140052 ATTTTTCATC
* * *
140062 TCGGGAATACTCCAA-TCCCGGTTTCATTTTCAAAACATCAATTTTTCTCAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACA-CAATTTTTCTCAA
* * *
140113 TCGGGGACACTCCAACTCCGATTTTA-TTTCTAAAACACCCATTTTCCAT-AA
1 TCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACA-CAATTTTTC-TCAA
* * *
140164 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAGAGTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACA-ATTTTTCTCAA
140215 TCGGGGATACTC
1 TCGGGGATACTC
140227 GAACCCTGTT
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
50 5 0.05
51 85 0.89
52 5 0.05
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (50 bp):
TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAATTTTTCTCAA
Found at i:140297 original size:79 final size:79
Alignment explanation
Indices: 140166--140351 Score: 259
Period size: 79 Copynumber: 2.4 Consensus size: 79
140156 TTCCATAATC
* * *
140166 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACAGAGTTTTCACAATCGGGGATACTCGAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACAGAGTTTTCACAATCGGGGATACTCCAAC
*
140231 CCTGTTATTT-TAGA
66 CCCGTTATTTCT-GA
* * * * *
140245 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTA-ATTTTTCATAATCGGGGATAGTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACA-CAGAGTTTTCACAATCGGGGATACTCCAA
140309 CCCCGTTATTTCTGA
65 CCCCGTTATTTCTGA
140324 GGGGATACTCCAACCCCGGTTTTATTTC
1 GGGGATACTCCAACCCCGGTTTTATTTC
140352 ATAATCGGGG
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 94 0.98
80 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACAGAGTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTCTGA
Found at i:140364 original size:34 final size:34
Alignment explanation
Indices: 140286--140385 Score: 104
Period size: 34 Copynumber: 3.1 Consensus size: 34
140276 AACATTAATT
*
140286 TTTCATAATCGGGGATAGTCCAACCCC-G--TTA
1 TTTCATAATCGGGGATACTCCAACCCCGGTTTTA
*
140317 TTTC-TGA--GGGGATACTCCAACCCCGGTTTTA
1 TTTCATAATCGGGGATACTCCAACCCCGGTTTTA
* * * *
140348 TTTCATAATCGGGGATATTCTAACTCCGATTTTA
1 TTTCATAATCGGGGATACTCCAACCCCGGTTTTA
140382 TTTC
1 TTTC
140386 CAAAACACCA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
28 16 0.29
29 1 0.02
30 2 0.04
31 11 0.20
32 2 0.04
34 24 0.43
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (34 bp):
TTTCATAATCGGGGATACTCCAACCCCGGTTTTA
Found at i:140409 original size:113 final size:111
Alignment explanation
Indices: 140245--140462 Score: 283
Period size: 113 Copynumber: 1.9 Consensus size: 111
140235 TTATTTTAGA
* * ** ** * *
140245 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTTCATAATCGGGGATAGTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAACATTTCACAATCGGGGATACTCCAA-
* *
140310 CCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTTCATAATC
65 CCCGTTATTTC-GAGGGGACACTCCAACCCCGGCTTTATTTCATAATC
* * * *
140358 GGGGATATTCTAACTCCGATTTTATTTCCAAAACACCAACATTTCACAATCGGGGATACTCCAAG
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAACATTTCACAATCGGGGATACTCCAAC
*
140423 CCGTTATTTCGAGGGGACACTCCAACCCCGGCTTTCTTTC
66 CCGTTATTTCGAGGGGACACTCCAACCCCGGCTTTATTTC
140463 TAAAACATCA
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
111 27 0.30
112 10 0.11
113 53 0.59
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (111 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAACATTTCACAATCGGGGATACTCCAAC
CCGTTATTTCGAGGGGACACTCCAACCCCGGCTTTATTTCATAATC
Found at i:140674 original size:79 final size:78
Alignment explanation
Indices: 140358--140743 Score: 379
Period size: 79 Copynumber: 5.0 Consensus size: 78
140348 TTTCATAATC
* * * * * **
140358 GGGGATATTCTAACTCCGATTTTATTTCCAAAACACCAACATTTCACAATCGGGGATACTCCAA-
1 GGGGATACTCCAACTCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
140422 GCCGTTATTTCGA
66 CCCGTTATTTCGA
* * * * *
140435 GGGGACACTCCAACCCCGGCTTTCTTTCTAAAACATCAATTTTT--C-ATCGGGGATACTCCAAT
1 GGGGATACTCCAACTCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
140497 CTCGTTATTTTCGA
66 CCCGTTA-TTTCGA
* * * * * * * *
140511 GGGGATACCCCAACCCCTGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTTCAA
1 GGGGATACTCCAACTCC-GGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAA
*
140576 CCCCGCTATTTCGA
65 CCCCGTTATTTCGA
* * * *
140590 GGGGATACTCCAACTCCGGTTTTATTTCTAAAACATCAATTTTTTATAGTCGGGGATGCTCCAAC
1 GGGGATACTCCAACTCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
140655 CCCGTTATTTCCGA
66 CCCGTTATTT-CGA
* * * * * *
140669 GGGGATGA-ACCAA-TCCCGATTTTATTTCCAAATCATCGATTTTTCACAACCGGGGATACTCCA
1 GGGGAT-ACTCCAACT-CCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCA
*
140732 ACCCCATTATTT
64 ACCCCGTTATTT
140744 TCAAAAGGAT
Statistics
Matches: 254, Mismatches: 46, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
74 16 0.06
75 6 0.02
76 21 0.08
77 56 0.22
78 50 0.20
79 84 0.33
80 21 0.08
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACTCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTCGA
Found at i:140761 original size:158 final size:154
Alignment explanation
Indices: 140373--140743 Score: 424
Period size: 155 Copynumber: 2.4 Consensus size: 154
140363 TATTCTAACT
* * ** *
140373 CCGATTTTATTTCCAAAACACCAACATTTCACAATCGGGGATACTCCAA-GCCGTTATTTCGAGG
1 CCGATTTTATTTCCAAATCATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCGAGG
* * * *
140437 GGACACTCCAACCCCGGCTTTCTTTCTAAAACATCAATTTTTCATCGGGGATACTCCAATCTCGT
66 GGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCCGT
* *
140502 TATTTTCGAGGGGATACCCCAACC
131 TATTTCCGAGGGGATACACCAACC
** * * * * * *
140526 CCTGGCTTTATTTCTAAAAT-ATTAATTTCTCATAATCGGGGATACTTCAACCCCGCTATTTCGA
1 CC-GATTTTATTTC-CAAATCATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCGA
* * * *
140590 GGGGATACTCCAACTCCGGTTTTATTTCTAAAACATCAATTTTTTATAGTCGGGGATGCTCCAAC
64 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAA-TTTTT-CA-TCGGGGATACTCCAAC
*
140655 CCCGTTATTTCCGAGGGGATGA-ACCAATC
126 CCCGTTATTTCCGAGGGGAT-ACACCAACC
* * *
140684 CCGATTTTATTTCCAAATCATCGATTTTTCACAACCGGGGATACTCCAACCCCATTATTT
1 CCGATTTTATTTCCAAATCATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTT
140744 TCAAAAGGAT
Statistics
Matches: 175, Mismatches: 35, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
153 2 0.01
154 32 0.18
155 49 0.28
156 9 0.05
157 43 0.25
158 39 0.22
159 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (154 bp):
CCGATTTTATTTCCAAATCATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCGAGG
GGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCCGT
TATTTCCGAGGGGATACACCAACC
Found at i:145541 original size:52 final size:52
Alignment explanation
Indices: 145395--145523 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
145385 CAAAATATGA
* *
145395 AAATTTGCCTACATGTATCTATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* * *
145447 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
145499 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
145524 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:145550 original size:13 final size:13
Alignment explanation
Indices: 145532--145556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
145522 CAAAGATCAG
145532 TGTATCGATACAA
1 TGTATCGATACAA
145545 TGTATCGATACA
1 TGTATCGATACA
145557 TTTGAGTAAT
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:145724 original size:21 final size:20
Alignment explanation
Indices: 145698--145736 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
145688 GTTGGGACCT
145698 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
145719 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
145737 CAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:147931 original size:20 final size:20
Alignment explanation
Indices: 147867--147931 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
147857 TGCCAATTTC
* *
147867 ATGTATCGATACAATTGTGT-
1 ATGTATCGATACAA-AGTATA
147887 ATGTATCGATACAAAG-A-A
1 ATGTATCGATACAAAGTATA
147905 CATGTATCGATACAAAGTATA
1 -ATGTATCGATACAAAGTATA
147926 ATGTAT
1 ATGTAT
147932 GAATACATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 17 0.44
20 21 0.54
21 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAAAGTATA
Found at i:149668 original size:166 final size:164
Alignment explanation
Indices: 149322--149696 Score: 420
Period size: 166 Copynumber: 2.3 Consensus size: 164
149312 GTTTAATGGC
* * *
149322 AATA-TTAGATGAATTATAAAAATATTAAACCGAGAAAAATCTCCCCCAAAAACCTTTATGGAAT
1 AATATTTA-ATGAATTTTAAAAATTTTAAACCGAGAAAAATC-CTCCCAAAAACCTTTATGGAAT
* * * *
149386 AAAAATTCGATTTTTTGAAATCGAAGGCATTTCAAGGAAAAAAAGAAAAACTCAAAAAATTAAAT
64 AAAAACTCAATTTTTTGAAATC-AAGGAATTTCAAGGAAAAAAAGAAAAACTCAAAAAATTAAAA
* * * * *
149451 GAATTTTTTAAAACTGATTTATTATGAATTAAATGAT
128 GAACTTTTCAAAACTAATTTATGATGAATTAAATAAT
* * *
149488 GATATTTTATGAATTTTAAAAATTTTAAACTGAGAAAAATCCTCCCAAAAACCTTTATGGAATGA
1 AATATTTAATGAATTTTAAAAATTTTAAACCGAGAAAAATCCTCCCAAAAACCTTTATGGAAT-A
* * * **
149553 AAACACTCAATTTTTTAGAAAT-AAGGAATTTCAA-GAAAAAAATAAAAATTTGATGAAA-TAAA
65 AAA-ACTCAATTTTTT-GAAATCAAGGAATTTCAAGGAAAAAAAGAAAAA-CTCAAAAAATTAAA
*
149615 AGAAACTTTTCAAAACTAATTTAATGGTGAA-TAAATAAT
127 AG-AACTTTTCAAAACTAATTT-ATGATGAATTAAATAAT
*
149654 AATATTTAATGAATTTTCAAAATTTTAAACCGATG-AAAATCCT
1 AATATTTAATGAATTTTAAAAATTTTAAACCGA-GAAAAATCCT
149697 TCTGAAAAAA
Statistics
Matches: 176, Mismatches: 25, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
165 39 0.22
166 113 0.64
167 19 0.11
168 5 0.03
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (164 bp):
AATATTTAATGAATTTTAAAAATTTTAAACCGAGAAAAATCCTCCCAAAAACCTTTATGGAATAA
AAACTCAATTTTTTGAAATCAAGGAATTTCAAGGAAAAAAAGAAAAACTCAAAAAATTAAAAGAA
CTTTTCAAAACTAATTTATGATGAATTAAATAAT
Found at i:151191 original size:19 final size:20
Alignment explanation
Indices: 151146--151198 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
151136 ATGCCAATTT
*
151146 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATGGAG
*
151166 TATGTATCGATACAA-GGAG
1 CATGTATCGATACAATGGAG
151185 CATGTATCGATACA
1 CATGTATCGATACA
151199 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATGGAG
Found at i:151205 original size:13 final size:13
Alignment explanation
Indices: 151187--151211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
151177 ACAAGGAGCA
151187 TGTATCGATACAT
1 TGTATCGATACAT
151200 TGTATCGATACA
1 TGTATCGATACA
151212 AAGCATAATG
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:151231 original size:33 final size:32
Alignment explanation
Indices: 151168--151232 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
151158 CAATTGAGTA
* * *
151168 TGTATCGATACAAGGAGCATGTATCGATACAT
1 TGTATCGATACAAGCAGAATGTATCAATACAT
*
151200 TGTATCGATACAAAGCATAATGTATCAATACAT
1 TGTATCGATAC-AAGCAGAATGTATCAATACAT
151233 CTGGGTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAAGCAGAATGTATCAATACAT
Found at i:154944 original size:17 final size:16
Alignment explanation
Indices: 154922--154960 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
154912 GAGTTTTATT
154922 AACATTTCCTCTATTAA
1 AACATTT-CTCTATTAA
*
154939 AACATTTTTCTATTAA
1 AACATTTCTCTATTAA
154955 AA-ATTT
1 AACATTT
154961 TGAAAGCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (16 bp):
AACATTTCTCTATTAA
Found at i:158394 original size:33 final size:32
Alignment explanation
Indices: 158352--158419 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
158342 CGTTACAAGC
158352 CAATGTATCGATACAT-TTGGTCATGTATCAATA
1 CAATGTATCGATACATCTT-GT-ATGTATCAATA
*
158385 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCAATA
158417 CAA
1 CAA
158420 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCAATA
Found at i:158517 original size:13 final size:13
Alignment explanation
Indices: 158499--158523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
158489 TACAGTGGTC
158499 ATGTATCGATACA
1 ATGTATCGATACA
158512 ATGTATCGATAC
1 ATGTATCGATAC
158524 TATGCATTAT
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):
ATGTATCGATACA
Found at i:159187 original size:108 final size:109
Alignment explanation
Indices: 158998--159215 Score: 395
Period size: 108 Copynumber: 2.0 Consensus size: 109
158988 AACATATTGC
158998 TTAACCTGTGATCTGATTTCCATAGCTTCAAGAAACACATTAGTAATGTTCAAATATCAAGGTTT
1 TTAACCTGTGATCTGATTTCCATAGCTTCAAGAAACACATTAGTAATGTTCAAATATCAAGGTTT
159063 TTCATTTT-CTTTTTTTTTCTCCC-CTTTAATCAAATAAAAAATT
66 TTCATTTTCCTTTTTTTTTCTCCCTC-TTAATCAAATAAAAAATT
* *
159106 TTAACCTGTGATCTGATTTCCATAGCTTCAAGAAACACATTGGTAATGTTTAAATATCAAGGTTT
1 TTAACCTGTGATCTGATTTCCATAGCTTCAAGAAACACATTAGTAATGTTCAAATATCAAGGTTT
159171 TTCATTTTCCTTTTTTTTTCTCCCTCTTAATCAAATAAAAAATT
66 TTCATTTTCCTTTTTTTTTCTCCCTCTTAATCAAATAAAAAATT
159215 T
1 T
159216 ATGCCCCTTA
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
108 71 0.67
109 34 0.32
110 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (109 bp):
TTAACCTGTGATCTGATTTCCATAGCTTCAAGAAACACATTAGTAATGTTCAAATATCAAGGTTT
TTCATTTTCCTTTTTTTTTCTCCCTCTTAATCAAATAAAAAATT
Found at i:161180 original size:30 final size:27
Alignment explanation
Indices: 161126--161182 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
161116 CAGAGAATGT
*
161126 TGTATCGATACATCTGGGTTTTCCAGA
1 TGTATCGATACATCTGGATTTTCCAGA
161153 TGTATCGATACATTCTGGAAATTTTCCAGA
1 TGTATCGATACA-TCTGG--ATTTTCCAGA
161183 ATTAAGACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 12 0.46
28 5 0.19
30 9 0.35
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (27 bp):
TGTATCGATACATCTGGATTTTCCAGA
Found at i:166487 original size:20 final size:21
Alignment explanation
Indices: 166462--166559 Score: 91
Period size: 20 Copynumber: 4.8 Consensus size: 21
166452 AAAACCCCTA
166462 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACATAATTGC
*
166482 AAAGTATCGATACAT-GTTGC
1 AAAGTATCGATACATAATTGC
* *
166502 AATGTATCGATACATGAA---A
1 AAAGTATCGATACAT-AATTGC
166521 AAGATGTATCGATACAT-ATTGC
1 AA-A-GTATCGATACATAATTGC
*
166543 AATGTATCGATACATAA
1 AAAGTATCGATACATAA
166560 AAAAAGTTGT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
19 5 0.08
20 42 0.68
21 13 0.21
22 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
AAAGTATCGATACATAATTGC
Found at i:166537 original size:41 final size:42
Alignment explanation
Indices: 166485--166579 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 42
166475 ATAATTCAAA
* *
166485 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATAAAAAAAGAT
*
166526 GTATCGATACATATTGCAATGTATCGATACATAAAAAAAGTT
1 GTATCGATACATATTGCAATGTATCGATACATAAAAAAAGAT
166568 GTATCGATACAT
1 GTATCGATACAT
166580 TTCTTGGCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
41 31 0.62
42 19 0.38
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.31
Consensus pattern (42 bp):
GTATCGATACATATTGCAATGTATCGATACATAAAAAAAGAT
Found at i:166636 original size:13 final size:13
Alignment explanation
Indices: 166618--166643 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166608 TACAGCAAGT
166618 ATGTATCGATACA
1 ATGTATCGATACA
166631 ATGTATCGATACA
1 ATGTATCGATACA
166644 CAAAAAATTG
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:167165 original size:34 final size:35
Alignment explanation
Indices: 167102--167168 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
167092 CTAAGTGATT
167102 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
167138 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
167169 TCTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:170297 original size:13 final size:13
Alignment explanation
Indices: 170279--170303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
170269 TTTTCCAAAT
170279 TGTATCGATACAA
1 TGTATCGATACAA
170292 TGTATCGATACA
1 TGTATCGATACA
170304 TTGCTTCAGT
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:172050 original size:20 final size:20
Alignment explanation
Indices: 172027--172099 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
172017 ACAATTCAAA
172027 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
172047 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
172068 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
172088 GTATCGATACAT
1 GTATCGATACAT
172100 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:172078 original size:41 final size:42
Alignment explanation
Indices: 172027--172121 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
172017 ACAATTCAAA
*
172027 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
*
172068 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
172110 GTATCGATACAT
1 GTATCGATACAT
172122 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:172178 original size:13 final size:13
Alignment explanation
Indices: 172160--172185 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
172150 TACAGCAAGT
172160 ATGTATCGATACA
1 ATGTATCGATACA
172173 ATGTATCGATACA
1 ATGTATCGATACA
172186 CAAAAAATTG
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:172707 original size:34 final size:35
Alignment explanation
Indices: 172644--172710 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
172634 CTAAGTGATT
172644 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
172680 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
172711 TCTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:175841 original size:13 final size:13
Alignment explanation
Indices: 175823--175847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175813 TTTTCCAAAT
175823 TGTATCGATACAA
1 TGTATCGATACAA
175836 TGTATCGATACA
1 TGTATCGATACA
175848 TTGCTTCAGT
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:177595 original size:20 final size:20
Alignment explanation
Indices: 177572--177644 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
177562 ACAATTCAAA
177572 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
177592 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
177613 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
177633 GTATCGATACAT
1 GTATCGATACAT
177645 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:177623 original size:41 final size:42
Alignment explanation
Indices: 177572--177666 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
177562 ACAATTCAAA
*
177572 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
*
177613 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
177655 GTATCGATACAT
1 GTATCGATACAT
177667 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:177723 original size:13 final size:13
Alignment explanation
Indices: 177705--177730 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
177695 TACAGCAAGT
177705 ATGTATCGATACA
1 ATGTATCGATACA
177718 ATGTATCGATACA
1 ATGTATCGATACA
177731 CAAAAAATTG
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:178252 original size:34 final size:35
Alignment explanation
Indices: 178189--178255 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
178179 CTAAGTGATT
178189 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
178225 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
178256 TCTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:178589 original size:13 final size:13
Alignment explanation
Indices: 178571--178595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178561 CAAAGATCAG
178571 TGTATCGATACAA
1 TGTATCGATACAA
178584 TGTATCGATACA
1 TGTATCGATACA
178596 TGTGAGTAAT
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:178679 original size:13 final size:13
Alignment explanation
Indices: 178661--178685 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178651 CAAAAAAATA
178661 TGTATCGATACAT
1 TGTATCGATACAT
178674 TGTATCGATACA
1 TGTATCGATACA
178686 ACATTTTATG
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:178681 original size:33 final size:33
Alignment explanation
Indices: 178639--178705 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
178629 AGTAGCTTAA
178639 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
178672 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
178705 A
1 A
178706 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:183206 original size:33 final size:32
Alignment explanation
Indices: 183161--183224 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
183151 GTTACAAGCC
183161 AATGTATCGATACAT-TTGGTCATGTATCGATAT
1 AATGTATCGATACATCTT-GT-ATGTATCGATAT
*
183194 AATGTATTGATACATCTTGTATGTATCGATA
1 AATGTATCGATACATCTTGTATGTATCGATA
183225 CAAACAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.38
33 16 0.55
34 2 0.07
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (32 bp):
AATGTATCGATACATCTTGTATGTATCGATAT
Found at i:183325 original size:13 final size:13
Alignment explanation
Indices: 183307--183331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183297 TACAGTGGTC
183307 ATGTATCGATACA
1 ATGTATCGATACA
183320 ATGTATCGATAC
1 ATGTATCGATAC
183332 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:183863 original size:84 final size:84
Alignment explanation
Indices: 183726--183944 Score: 278
Period size: 84 Copynumber: 2.6 Consensus size: 84
183716 ATTGTTGGGG
* *
183726 AAACTCCATCCCCACTCCTTCGAGGGGATACTCTAACCTCGATCTTAAAAAAAAACTCAAACCTT
1 AAACTCCATCCCCACTCCTCCGAGGGGATACTCTAACCTCGATCTTCAAAAAAAACTCAAA-CTT
* *
183791 TTTTTGTATAA-TTTTTAAA
65 TTTTCGTATAACTTTTGAAA
* * *
183810 AAACTTCATCCCCACTCCCCCGAGGGGATACTCTAACCTCGATCTTCAAAAAAAACTTAAACTTT
1 AAACTCCATCCCCACTCCTCCGAGGGGATACTCTAACCTCGATCTTCAAAAAAAACTCAAACTTT
**
183875 TTTCGTATAACTTTTGGGA
66 TTTCGTATAACTTTTGAAA
* ** * * * *
183894 AAACTCCATCCCCTCTTTTCTGAAGGAATACTCTAACATCGATCTTCAAAA
1 AAACTCCATCCCCACTCCTCCGAGGGGATACTCTAACCTCGATCTTCAAAA
183945 TATTCAAATT
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
83 13 0.11
84 103 0.89
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (84 bp):
AAACTCCATCCCCACTCCTCCGAGGGGATACTCTAACCTCGATCTTCAAAAAAAACTCAAACTTT
TTTCGTATAACTTTTGAAA
Found at i:185645 original size:39 final size:40
Alignment explanation
Indices: 185602--185691 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 40
185592 TTATATGTTT
* * * *
185602 TTTGTTGACTTGTCGATTTTGTCCTGATCAATC-TTCTCA
1 TTTGTTAACTTGTAGATTTTCTCCTGATCAACCTTTCTCA
*
185641 TTTGTTAACTTGTAGGTTTTCTCCTGATCAACCTTTCTCA
1 TTTGTTAACTTGTAGATTTTCTCCTGATCAACCTTTCTCA
185681 TTTGTTAACTT
1 TTTGTTAACTT
185692 ATTAATTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.62
40 17 0.38
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.50
Consensus pattern (40 bp):
TTTGTTAACTTGTAGATTTTCTCCTGATCAACCTTTCTCA
Found at i:186303 original size:103 final size:104
Alignment explanation
Indices: 186139--186370 Score: 238
Period size: 103 Copynumber: 2.2 Consensus size: 104
186129 TGGTTTCACA
* * * * * **
186139 CTAGTCAAC-CATTTCTGATTTATGTTTTACCCTAGTCACCCTTTATTGACTTGTCGGTTTCATC
1 CTAGTCAACTC-TTTTTGACTTAGGTTTTACCCTAGTCACCCTTCATTGACATGTCAATTTCAT-
*
186203 CTAG-TCAACC-CTTAAACTTATTGACTTATCAGTTTTGCC
64 CTAGATCAACCTCTTAAACTTATTAACTTATCAGTTTTGCC
* * * * *
186242 TTGGTCAAC-CTTTTTGGACTTAGGTTTTATCCTAGTCACCCTTCGTTGACATGTCAATTTCATT
1 CTAGTCAACTCTTTTT-GACTTAGGTTTTACCCTAGTCACCCTTCATTGACATGTCAATTTCATC
* * * * * *
186306 TTGATCAACCTTTTTAACTTGTTAACTTATTAGTTTTTCC
65 TAGATCAACCTCTTAAACTTATTAACTTATCAGTTTTGCC
186346 CTAGTCAACTCTTTTTGACTTAGGT
1 CTAGTCAACTCTTTTTGACTTAGGT
186371 CATCCTAAGC
Statistics
Matches: 104, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
102 6 0.06
103 53 0.51
104 39 0.38
105 6 0.06
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (104 bp):
CTAGTCAACTCTTTTTGACTTAGGTTTTACCCTAGTCACCCTTCATTGACATGTCAATTTCATCT
AGATCAACCTCTTAAACTTATTAACTTATCAGTTTTGCC
Found at i:186420 original size:71 final size:73
Alignment explanation
Indices: 186336--186534 Score: 199
Period size: 75 Copynumber: 2.7 Consensus size: 73
186326 GTTAACTTAT
* *
186336 TAGTTTTTCCCTAGTCAACTCTTTTTGACTT-AG-GTCATCCTAAG-CACCCTTTTT-CCCTTAG
1 TAGTTTTACCCTAGTCAAC-CTTTTTGACTTAAGTCTCATCCT-AGTCACCCTTTTTACCCTTAG
186397 TTCACTATTC
64 TTCACTATTC
* ***
186407 TAGTTTTGCCCTAGTCAACCTTTTTTGACTTAAAGTCTCATCCTAGTCATTGTTTTTACCCTTAG
1 TAGTTTTACCCTAGTCAACC-TTTTTGACTT-AAGTCTCATCCTAGTCACCCTTTTTACCCTTAG
*
186472 TTGACTATTC
64 TTCACTATTC
* * * * * * *
186482 TAGTTTCACCTTAGTCAACCCTTTCGAACTTAGGTTTCATCCTAGTCTCCCTT
1 TAGTTTTACCCTAGTCAACCTTTTTG-ACTTAAGTCTCATCCTAGTCACCCTT
186535 AGTTGACTAT
Statistics
Matches: 104, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
70 1 0.01
71 28 0.27
73 4 0.04
74 34 0.33
75 37 0.36
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (73 bp):
TAGTTTTACCCTAGTCAACCTTTTTGACTTAAGTCTCATCCTAGTCACCCTTTTTACCCTTAGTT
CACTATTC
Found at i:188031 original size:6 final size:6
Alignment explanation
Indices: 188020--188085 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
188010 TTATGATGAA
* *
188020 TAATTT TAATTT TAATTT T--TTT TAACTTT TGAACTT CAATTT T-ATTT
1 TAATTT TAATTT TAATTT TAATTT TAA-TTT T-AATTT TAATTT TAATTT
*
188067 T-ATTT T-ATTT TATTTT TAA
1 TAATTT TAATTT TAATTT TAA
188086 CCAATTTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
4 4 0.08
5 15 0.31
6 22 0.45
7 6 0.12
8 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (6 bp):
TAATTT
Found at i:188068 original size:5 final size:5
Alignment explanation
Indices: 188058--188082 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
188048 TTGAACTTCA
188058 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
188083 TAACCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:188915 original size:20 final size:21
Alignment explanation
Indices: 188872--188923 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
188862 TTCTATAATT
* *
188872 TGTATCGATACAATTAGTGAA
1 TGTATCGATACAATCAGAGAA
188893 TGTATCGATAC-ATCAGAGAA
1 TGTATCGATACAATCAGAGAA
188913 TGTATCGATAC
1 TGTATCGATAC
188924 GGGAACATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAATCAGAGAA
Found at i:196548 original size:20 final size:20
Alignment explanation
Indices: 196523--196647 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
196513 AGAATAATAC
196523 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
196543 ATGTATCGATACATCTGGGTAAAAAAACAGA
1 ATGTATCGATACAT-T--G------AA-A-A
* * *
196574 ATGTACCAATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * * * *
196594 ATATATCAATACATTCATAC
1 ATGTATCGATACATTGAAAA
196614 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
196634 ATGTATCGATACAT
1 ATGTATCGATACAT
196648 CTAGGTAAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
20 58 0.73
21 1 0.01
22 2 0.03
23 1 0.01
28 1 0.01
29 2 0.03
30 2 0.03
31 13 0.16
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:196574 original size:78 final size:78
Alignment explanation
Indices: 196445--196596 Score: 234
Period size: 78 Copynumber: 1.9 Consensus size: 78
196435 TTTTAACTAG
* * * *
196445 ATGTATCGATACATTGAAAACTGTATCGATACATTTGGAAAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATTGGGAAAAAAAGACAGAATGTACCAATACAT
196510 TAAAGAATAATAC
66 TAAAGAATAATAC
*
196523 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAA-ACAGAATGTACCAATACA
1 ATGTATCGATACATTGAAAAATGTATCGATACAT-TGGGAAAAAAAGACAGAATGTACCAATACA
*
196587 TTGAAGAATA
65 TTAAAGAATA
196597 TATCAATACA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
78 58 0.87
79 9 0.13
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (78 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATTGGGAAAAAAAGACAGAATGTACCAATACAT
TAAAGAATAATAC
Found at i:198628 original size:21 final size:21
Alignment explanation
Indices: 198587--198630 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
198577 TTCCCCTTTA
* *
198587 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
198608 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
198629 TC
1 TC
198631 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:200438 original size:13 final size:13
Alignment explanation
Indices: 200420--200445 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
200410 ATAATCACCC
200420 TGTATCGATACAA
1 TGTATCGATACAA
200433 TGTATCGATACAA
1 TGTATCGATACAA
200446 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:202540 original size:15 final size:15
Alignment explanation
Indices: 202520--202550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
202510 ATTTCGTTTG
*
202520 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
202535 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
202550 G
1 G
202551 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:204382 original size:21 final size:21
Alignment explanation
Indices: 204353--204397 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
204343 AAGTTTTCAT
*
204353 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
204373 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
204395 TTT
1 TTT
204398 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:206634 original size:13 final size:13
Alignment explanation
Indices: 206616--206641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
206606 CAATTTTTTG
206616 TGTATCGATACAT
1 TGTATCGATACAT
206629 TGTATCGATACAT
1 TGTATCGATACAT
206642 ACTTGCTGTA
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:207649 original size:28 final size:28
Alignment explanation
Indices: 207498--208419 Score: 699
Period size: 28 Copynumber: 31.3 Consensus size: 28
207488 GCTTTTAAAA
*
207498 AAAGG-TGCCACTAACTTATGTGGGCTTTG
1 AAAGGATGCCACTGAC-T-TGTGGGCTTTG
* * *
207527 AAAAGAGTTGCCACCGTCTTGTACGGGCTTTG
1 -AAAG-GATGCCACTGACTTGT--GGGCTTTG
* * **
207559 AAAGGGTGCCGCTGACTTGTAAGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
207587 AAAAAAGAGTTTCCA-TCGACTTGTGTGGGCTTTG
1 ---AAAG-GATGCCACT-GAC-T-TGTGGGCTTTG
* *
207621 AAAGGATGCCACTAACTTGTGGGCATTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
207649 AAAAGGATGTCATTAACTTGTGGGCTTTTG
1 -AAAGGATGCCACTGACTTGTGGGC-TTTG
*
207679 AAAGGATGCCACTGACTTATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
207707 AAAAGATGCCACT-ATCTTGTGGGCTTTAA
1 AAAGGATGCCACTGA-CTTGTGGGCTTT-G
*
207736 AAAGG-TGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
207763 AAAGGGTATGCCACTGACTTGTGGGCTTTG
1 AAA-GG-ATGCCACTGACTTGTGGGCTTTG
* *
207793 AAAGGGTGCCACTGACTTGTGAGCTTTGG
1 AAAGGATGCCACTGACTTGTGGGCTTT-G
* * *
207822 AAAGG-TGTCACTGACTTGTGGGTTTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
207849 AAAGGGTGCCACTGACTTGTGGGCTTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
207877 AAAGGGTGCCA-TGGACTTGTGGGCTTTG
1 AAAGGATGCCACT-GACTTGTGGGCTTTG
* *
207905 AAAGAATGCCACTGACTTGTGAGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* ** *
207933 AAATGGGTTGCCACCAACTTGTGTGGGCTTTAA
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTT-G
* ** *
207966 AATAGGTTGCCACCAACTTGTATGGGCTTTC
1 AA-AGGATGCCACTGACTTG--TGGGCTTTG
* * *
207997 AAATGAGTTGCCACCGACTTGTGTGGACTTCG
1 AAA-G-GATGCCACTGACTTGTG-GG-CTTTG
* * *
208029 AAATGGGTTGCCACCGACTTATGTGGGCTTTT
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
* *
208061 AAATGAGTTGCCACCGACTTGTATGGGCTTTG
1 AAA-G-GATGCCACTGACTTG--TGGGCTTTG
*
208093 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
208121 GAAGGGTACCACTGATTTGTGTGGGCTTTG
1 AAAGGATGCCACTGA-CT-TGTGGGCTTTG
* *
208151 AAAGGGTATGCCACTAACTTCTGGGCTTTG
1 AAA-GG-ATGCCACTGACTTGTGGGCTTTG
*
208181 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * **
208209 AAAGGATGCCACTAACTTATGGTATTTTG
1 AAAGGATGCCACTGACTTGTGG-GCTTTG
*
208238 -AAGAGATGCCATTGACTTGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
*
208266 AAAAGAGTTGCCACTGACTTGTGTGGGCTTTG
1 -AAAG-GATGCCACTGAC-T-TGTGGGCTTTG
* * **
208298 AAAGGGTGCCACAGACTTAAGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
208326 AAAGGGTATACCACTGACTTGTGGGCTTTG
1 AAA-GG-ATGCCACTGACTTGTGGGCTTTG
208356 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
208384 AAAGGATGCCA-TGGAGTTGTGGACTTTA
1 AAAGGATGCCACT-GACTTGTGGGCTTTG
208412 AAAGGATG
1 AAAGGATG
208420 GCACAAAGTT
Statistics
Matches: 740, Mismatches: 97, Indels: 112
0.78 0.10 0.12
Matches are distributed among these distances:
27 11 0.01
28 306 0.41
29 84 0.11
30 153 0.21
31 34 0.05
32 131 0.18
33 7 0.01
34 14 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
AAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:208007 original size:64 final size:64
Alignment explanation
Indices: 207927--208091 Score: 222
Period size: 64 Copynumber: 2.6 Consensus size: 64
207917 TGACTTGTGA
* * * *
207927 GCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTAAAATAGGTTGCCACCAACTTGTATGG
1 GCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTAAAATAGGTTGCCACCAACTTATATGG
* ** * * *
207991 GCTTTCAAATGAGTTGCCACCGACTTGTGTGGACTTCGAAATGGGTTGCCACCGACTTATGTGG
1 GCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTAAAATAGGTTGCCACCAACTTATATGG
* *
208055 GCTTTTAAATGAGTTGCCACCGACTTGTATGGGCTTT
1 GCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTT
208092 GAAAGGGTGC
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 87 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (64 bp):
GCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTAAAATAGGTTGCCACCAACTTATATGG
Found at i:208152 original size:58 final size:56
Alignment explanation
Indices: 207501--208416 Score: 710
Period size: 58 Copynumber: 15.5 Consensus size: 56
207491 TTTAAAAAAA
* * * *
207501 GGTGCCACTAACTTATGTGGGCTTTGAAAAGAGTTGCCACCGTCTTGTACGGGCTTTGAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG-GGTGCCACTGACTTGT--GGGCTTTGAAAG
* ** * *
207563 GGTGCCGCTGACTTGTAAGCTTTGAAAAAAGAGTTTCCA-TCGACTTGTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTG---AAAG-GGTGCCACT-GAC-T-TGTGGGCTTTGAAAG
* * * * * * *
207625 GATGCCACTAACTTGTGGGCATTGAAAAGGATGTCATTAACTTGTGGGCTTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC-TTTGAAAG
* * * * * *
207683 GATGCCACTGACTTATGGGCTTTGAAAAGATGCCACT-ATCTTGTGGGCTTTAAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA-CTTGTGGGCTTTGAAAG
*
207739 GGTGCCACTAACTTGTGGGCTTTGAAAGGGTATGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGG--TGCCACTGACTTGTGGGCTTTGAAAG
* * * *
207797 GGTGCCACTGACTTGTGAGCTTTGGAAA-GGTGTCACTGACTTGTGGGTTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
*
207853 GGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCA-TGGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT-GACTTGTGGGCTTTGAAAG
** * ** *
207909 AATGCCACTGACTTGTGAGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTAAAATAG
1 GGTGCCACTGACTTGTGGGCTTTGAAA-GGG-TGCCACTGAC-T-TGTGGGCTTT-GAA-AG
* ** * * * *
207971 GTTGCCACCAACTTGTATGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGACTTCGAAATG
1 GGTGCCACTGACTTG--TGGGCTTTGAAA-G-GGTGCCACTGACTTGTG-GG-CTTTGAAA-G
* * * *
208034 GGTTGCCACCGACTTATGTGGGCTTTTAAATGAGTTGCCACCGACTTGTATGGGCTTTGAAAG
1 GG-TGCCACTGAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTGACTTG--TGGGCTTTGAAAG
* * *
208097 GGTGCCACTGACTTGTGGGCTTTGGAAGGGTACCACTGATTTGTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA-CT-TGTGGGCTTTGAAAG
* *
208155 GGTATGCCACTAACTTCTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
1 GG--TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
* * * ** * *
208213 GATGCCACTAACTTATGGTATTTTG-AAGAGATGCCATTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGG-GCTTTGAAAG-GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * **
208271 AGTTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACAGACTTAAGGGCTTTGAAAG
1 -GGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
* *
208330 GGTATACCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
1 GG--TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
208388 GATGCCA-TGGAGTTGTGGACTTTAAAAGG
1 GGTGCCACT-GACTTGTGGGCTTTGAAAGG
208417 ATGGCACAAA
Statistics
Matches: 706, Mismatches: 102, Indels: 98
0.78 0.11 0.11
Matches are distributed among these distances:
55 5 0.01
56 162 0.23
57 55 0.08
58 166 0.24
59 30 0.04
60 105 0.15
61 11 0.02
62 81 0.11
63 11 0.02
64 72 0.10
65 4 0.01
66 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (56 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:208416 original size:86 final size:84
Alignment explanation
Indices: 207498--208416 Score: 666
Period size: 86 Copynumber: 10.4 Consensus size: 84
207488 GCTTTTAAAA
* * * *
207498 AAAGG-TGCCACTAACTTATGTGGGCTTTGAAAAGAGTTGCCACCGTCTTGTACGGGCTTTGAAA
1 AAAGGATGCCACTGAC-T-TGTGGGCTTT-AAAAG-GGTGCCACTGACTTGT--GGGCTTTGAAA
* * **
207562 GGGTGCCGCTGACTTGTAAGCTTTG
60 GGATGCCACTGACTTGTGGGCTTTG
* * * * * *
207587 AAAAAAGAGTTTCCA-TCGACTTGTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCATTGAA
1 ---AAAG-GATGCCACT-GAC-T-TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG-A
* * *
207651 AAGGATGTCATTAACTTGTGGGCTTTTG
58 AAGGATGCCACTGACTTGTGGGC-TTTG
* * *
207679 AAAGGATGCCACTGACTTATGGGCTTTGAAAA-GATGCCACT-ATCTTGTGGGCTTTAAAAAGG-
1 AAAGGATGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGA-CTTGTGGGCTTT-GAAAGGA
*
207741 TGCCACTAACTTGTGGGCTTTG
63 TGCCACTGACTTGTGGGCTTTG
* *
207763 AAAGGGTATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGAGCTTTGGAAAGG-
1 AAA-GG-ATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGA
* * *
207827 TGTCACTGACTTGTGGGTTTTA
63 TGCCACTGACTTGTGGGCTTTG
* *
207849 AAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCA-TGGACTTGTGGGCTTTGAAAGAATG
1 AAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACT-GACTTGTGGGCTTTGAAAGGATG
*
207913 CCACTGACTTGTGAGCTTTG
65 CCACTGACTTGTGGGCTTTG
* ** * ** *
207933 AAATGGGTTGCCACCAACTTGTGTGGGCTTTAAAATAGGTTGCCACCAACTTGTATGGGCTTTCA
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTT-AAA-AGGGTGCCACTGACTTG--TGGGCTTTGA
* * *
207998 AATGAGTTGCCACCGACTTGTGTGGACTTCG
58 AA-G-GATGCCACTGACTTGTG-GG-CTTTG
* * * * *
208029 AAATGGGTTGCCACCGACTTATGTGGGCTTTTAAATGAGTTGCCACCGACTTGTATGGGCTTTGA
1 AAA--GGATGCCACTGAC-T-TGTGGGC-TTTAAAAG-GGTGCCACTGACTTG--TGGGCTTTGA
*
208094 AAGGGTGCCACTGACTTGTGGGCTTTG
58 AAGGATGCCACTGACTTGTGGGCTTTG
* * * * * * *
208121 GAAGGGTACCACTGATTTGTGTGGGCTTTGAAAGGGTATGCCACTAACTTCTGGGCTTTGAAAGG
1 AAAGGATGCCACTGA-CT-TGTGGGCTTTAAAAGGG--TGCCACTGACTTGTGGGCTTTGAAAGG
*
208186 GTGCCACTGACTTGTGGGCTTTG
62 ATGCCACTGACTTGTGGGCTTTG
* * ** ** * * *
208209 AAAGGATGCCACTAACTTATGGTATTTTGAAGAGATGCCATTGACTTGTGGGCTTTGAAAAGAGT
1 AAAGGATGCCACTGACTTGTGGGCTTTAAAAG-GGTGCCACTGACTTGTGGGCTTTG-AAAG-GA
208274 TGCCACTGACTTGTGTGGGCTTTG
63 TGCCACTGAC-T-TGTGGGCTTTG
* * ** * *
208298 AAAGGGTGCCACAGACTTAAGGGCTTTGAAAGGGTATACCACTGACTTGTGGGCTTTGAAAGGAT
1 AAAGGATGCCACTGACTTGTGGGCTTTAAAAGGG--TGCCACTGACTTGTGGGCTTTGAAAGGAT
208363 GCCACTGACTTGTGGGCTTTG
64 GCCACTGACTTGTGGGCTTTG
* *
208384 AAAGGATGCCA-TGGAGTTGTGGACTTTAAAAGG
1 AAAGGATGCCACT-GACTTGTGGGCTTTAAAAGG
208417 ATGGCACAAA
Statistics
Matches: 678, Mismatches: 108, Indels: 88
0.78 0.12 0.10
Matches are distributed among these distances:
83 6 0.01
84 73 0.11
85 43 0.06
86 160 0.24
87 20 0.03
88 80 0.12
89 53 0.08
90 67 0.10
91 17 0.03
92 37 0.05
93 9 0.01
94 47 0.07
95 3 0.00
96 60 0.09
97 3 0.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (84 bp):
AAAGGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGC
CACTGACTTGTGGGCTTTG
Found at i:208456 original size:27 final size:27
Alignment explanation
Indices: 208356--208603 Score: 253
Period size: 27 Copynumber: 9.1 Consensus size: 27
208346 GTGGGCTTTG
* * * * *
208356 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGTTGCCACGGAGTTGTGGAC-TTA
* *
208384 AAAGGATGCCATGGAGTTGTGGACTTTA
1 AAAGGTTGCCACGGAGTTGTGGAC-TTA
* * **
208412 AAAGGATGGCACAAAGTTGTGGACTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTA
*
208439 AAAGGTTGCCACGGAGTTATGGACTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTA
* * *
208466 CAAGGGTGCCATGGAGTTGTGGACTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTA
* *
208493 AAAGGTTGCCATGGAGTTATGGACTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTA
* *
208520 AAAGATTGCCACGAAGTTGTGGACTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTA
* * *
208547 AAAGGTTACCACAGAGTTGGGGACTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTA
** *
208574 AAAGGTTGCCATAGAGTTGTGGACATA
1 AAAGGTTGCCACGGAGTTGTGGACTTA
208601 AAA
1 AAA
208604 AGGAATGCCA
Statistics
Matches: 186, Mismatches: 34, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
27 143 0.77
28 43 0.23
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (27 bp):
AAAGGTTGCCACGGAGTTGTGGACTTA
Found at i:210043 original size:21 final size:23
Alignment explanation
Indices: 210019--210079 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
210009 CCTTTCCTTA
210019 TTTTACTTTTGCACTTTTT-TG-
1 TTTTACTTTTGCACTTTTTATGC
* *
210040 TTTTTCTTTT-CATTTTTTATGC
1 TTTTACTTTTGCACTTTTTATGC
*
210062 TTTTGCTTTTG-ACTTTTT
1 TTTTACTTTTGCACTTTTT
210080 CGTAATTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 7 0.21
21 11 0.33
22 15 0.45
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.70
Consensus pattern (23 bp):
TTTTACTTTTGCACTTTTTATGC
Found at i:213512 original size:2 final size:2
Alignment explanation
Indices: 213507--213531 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
213497 GTTTTTTAGA
213507 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
213532 ATTCCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:215371 original size:10 final size:10
Alignment explanation
Indices: 215356--215382 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
215346 CACCATTTAG
215356 AATATTTTGA
1 AATATTTTGA
215366 AATATTTTGA
1 AATATTTTGA
215376 AATATTT
1 AATATTT
215383 CTAGCATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
AATATTTTGA
Found at i:215998 original size:155 final size:151
Alignment explanation
Indices: 215757--216238 Score: 504
Period size: 155 Copynumber: 3.1 Consensus size: 151
215747 TTTGTGTCTT
* * * *
215757 GGTTACTGGATATTTTCATGTCGAAAGTATATCT-TAGGAGTATTTTCATAATTTCTCTA-AATC
1 GGTTACAGGATACTTTCATGTCGAAAGTATA-CTATAGG-GTATTTTCGTAATTT-TTTAGAATC
* * * *
215820 GAGCCTTAGGTTATCACTAAGTTGCTTTTATACCAAAGGTGTGCATTTAGGATAGGTTCGTCCTT
63 GAGTCTTAGGTCATCACT-AGTTGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTTGTCCTT
* *
215885 TTACTGATCTTTTTATATCCTTTAA
127 TTACTAATCTTTTTATGTCCTTTAA
* *
215910 GGTTATCAGGATACTTTCATGTCGAAAGTATACTAGATAGGGCATTTTGGTAATTTTTTAGAATC
1 GGTTA-CAGGATACTTTCATGTCGAAAGTATACT--ATAGGGTATTTTCGTAATTTTTTAGAATC
* * * *
215975 AAGTCTTAGGTCATCATTGAGTTGCTTTTATGCCAAAGGTGTGTATTTAGGATAAGTTTGTCCTT
63 GAGTCTTAGGTCATCACT-AGTTGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTTGTCCTT
* *
216040 TTACTAATCTTTTCATGTTCTTT-A
127 TTACTAATCTTTTTATGTCCTTTAA
* * * * * * *
216064 GGATTACTAAGCTACTTTCACGTCAAAAATATATTCCA-AGGGTATTTTTGTAATTTTTTTAGAA
1 GG-TTAC-AGGATACTTTCATGTCGAAAGTATA--CTATAGGGTATTTTCGTAA-TTTTTTAGAA
* * * * *
216128 TCGAGTCTTAGATCGTCACTAGGTCGCTTTTATGCCAAAGGTATGCATTTGGGATAGGTTTGTCC
61 TCGAGTCTTAGGTCATCACTA-GTTGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTTGTCC
*
216193 TTTTACTAATCTTTTTGTGTCCTTTAA
125 TTTTACTAATCTTTTTATGTCCTTTAA
* *
216220 GATTACCATGATACTTTCA
1 GGTTA-CAGGATACTTTCA
216239 CGTCCAAGAT
Statistics
Matches: 274, Mismatches: 42, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
153 7 0.03
154 45 0.16
155 214 0.78
156 7 0.03
157 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (151 bp):
GGTTACAGGATACTTTCATGTCGAAAGTATACTATAGGGTATTTTCGTAATTTTTTAGAATCGAG
TCTTAGGTCATCACTAGTTGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTTGTCCTTTTAC
TAATCTTTTTATGTCCTTTAA
Found at i:218920 original size:21 final size:21
Alignment explanation
Indices: 218889--218932 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
218879 GTTAAGTATA
218889 AATGTTTTTCAAGCATAAAAAT
1 AATGTTTTTCAAGCA-AAAAAT
*
218911 AATG-TTTTCAAGTAAAAAAT
1 AATGTTTTTCAAGCAAAAAAT
218931 AA
1 AA
218933 CTCAAAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (21 bp):
AATGTTTTTCAAGCAAAAAAT
Found at i:219335 original size:15 final size:15
Alignment explanation
Indices: 219312--219342 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
219302 GCCTATAAAT
219312 ACAACATTCCAAGCA
1 ACAACATTCCAAGCA
*
219327 ACAATATTCCAAGCA
1 ACAACATTCCAAGCA
219342 A
1 A
219343 GAAATTAAAA
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:0.29, G:0.06, T:0.16
Consensus pattern (15 bp):
ACAACATTCCAAGCA
Found at i:220284 original size:33 final size:33
Alignment explanation
Indices: 220247--220310 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
220237 ACAAGCTATG
*
220247 TATCGATACAATT-CATCATGTATCGATACAATA
1 TATCGATAC-ATTGCACCATGTATCGATACAATA
*
220280 TATCGATACATTGTACCATGTATCGATACAA
1 TATCGATACATTGCACCATGTATCGATACAA
220311 ATAGTGGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (33 bp):
TATCGATACATTGCACCATGTATCGATACAATA
Found at i:220378 original size:13 final size:13
Alignment explanation
Indices: 220360--220384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220350 ACAATTAACA
220360 TGTATCGATACAT
1 TGTATCGATACAT
220373 TGTATCGATACA
1 TGTATCGATACA
220385 AAGCATAATG
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:229366 original size:8 final size:8
Alignment explanation
Indices: 229355--229388 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
229345 TACAAAATGC
229355 AAAAAAGA
1 AAAAAAGA
*
229363 AAAAAGGAA
1 AAAAAAG-A
229372 AAAAAAGA
1 AAAAAAGA
229380 AAAAAAGA
1 AAAAAAGA
229388 A
1 A
229389 GAAGAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:230022 original size:36 final size:36
Alignment explanation
Indices: 229998--230069 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 36
229988 TAAATAATTA
229998 ATTAAAATATTTAAATAAACATATAAATAATATATAT
1 ATTAAAA-ATTTAAATAAACATATAAATAATATATAT
*
230035 ATTAAAAATTTAAAT--AC-TATAAA-AATATATTT
1 ATTAAAAATTTAAATAAACATATAAATAATATATAT
230067 ATT
1 ATT
230070 TATCAATACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 11 0.32
33 6 0.18
34 2 0.06
36 8 0.24
37 7 0.21
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (36 bp):
ATTAAAAATTTAAATAAACATATAAATAATATATAT
Found at i:231398 original size:3 final size:3
Alignment explanation
Indices: 231392--231435 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
231382 CTTATTCTTC
* *
231392 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
231436 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:234926 original size:159 final size:159
Alignment explanation
Indices: 234612--234915 Score: 452
Period size: 159 Copynumber: 1.9 Consensus size: 159
234602 GCAATCTAGC
234612 CTTTTCCTCTTCTCTCTTGCCGCAATTTCCCTAAGAAGCAAAAGTTGTCTTCTTGTCTCGTATTC
1 CTTTTCCTCTTCTCTCTTGCCGCAATTTCCCTAAGAAGCAAAAGTTGTCTTCTTGTCTCGTATTC
* ** * *
234677 GGCAAAGGTGAAGGAGGAGACTCAGGAGAGATTCAATTAGGAATCTGAGCTGCTAAAATTGCTCT
66 GACAAAGGTGAAGGAAAAGACTCAGGAGAGATTCAATTAGGAATCTGAGCTGCTAAAATCGCTCC
*
234742 TGGCTAGACAAAGTTCTTGCTTTTGTAGT
131 AGGCTAGACAAAGTTCTTGCTTTTGTAGT
*
234771 CTTTTCCTCTTCTCTCTTGCCGCAATTTCCCTAAGGAGCAAAAGTTGTCTTCTTGTCTCGTATTC
1 CTTTTCCTCTTCTCTCTTGCCGCAATTTCCCTAAGAAGCAAAAGTTGTCTTCTTGTCTCGTATTC
* * **
234836 GACAAAGGTGGAGGAAAAGAC-CGAGGAGAGATTCAATTTGGAATAC-GAGCTG-TCACCATCGC
66 GACAAAGGTGAAGGAAAAGACTC-AGGAGAGATTCAATTAGGAAT-CTGAGCTGCT-AAAATCGC
*
234898 TCCAGGCTAGATAAAGTT
128 TCCAGGCTAGACAAAGTT
234916 GTTATCTTTG
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
158 2 0.02
159 127 0.98
160 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (159 bp):
CTTTTCCTCTTCTCTCTTGCCGCAATTTCCCTAAGAAGCAAAAGTTGTCTTCTTGTCTCGTATTC
GACAAAGGTGAAGGAAAAGACTCAGGAGAGATTCAATTAGGAATCTGAGCTGCTAAAATCGCTCC
AGGCTAGACAAAGTTCTTGCTTTTGTAGT
Found at i:235505 original size:27 final size:27
Alignment explanation
Indices: 235475--235529 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
235465 TCATTGAAGA
*
235475 CTATTAAGGTGAATTTTTAAAATTACT
1 CTATTAAGGTAAATTTTTAAAATTACT
235502 CTATTAAGGTAAATTTTTAAAATTACT
1 CTATTAAGGTAAATTTTTAAAATTACT
235529 C
1 C
235530 CGGACTAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (27 bp):
CTATTAAGGTAAATTTTTAAAATTACT
Found at i:239263 original size:17 final size:15
Alignment explanation
Indices: 239233--239268 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
239223 AATATACATA
239233 TAAATTATAATTTTT
1 TAAATTATAATTTTT
239248 TAAATATATAAATTTTT
1 TAAAT-TAT-AATTTTT
239265 TAAA
1 TAAA
239269 AAAAACTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 3 0.16
17 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATTATAATTTTT
Found at i:241169 original size:2 final size:2
Alignment explanation
Indices: 241158--241202 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
241148 TACAAGAAGC
241158 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
241199 AT AT
1 AT AT
241203 TATTTTACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:246557 original size:24 final size:24
Alignment explanation
Indices: 246525--246577 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
246515 AAAATATATA
*
246525 TTTTTATTTT-TTCACTTCCTTTT-
1 TTTTTATTTTCATC-CTTCCTTTTC
246548 TTTTTAATTTTCATCCTTCCTTTTC
1 TTTTT-ATTTTCATCCTTCCTTTTC
246573 TTTTT
1 TTTTT
246578 TCACCTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 14 0.54
25 7 0.27
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTTATTTTCATCCTTCCTTTTC
Found at i:247092 original size:23 final size:24
Alignment explanation
Indices: 247037--247092 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
247027 ATATAATGAT
*
247037 ATTTAT-ATTATTATAATTTAAAA
1 ATTTATAATTATTATAATTAAAAA
247060 ATTTAAATAATTATT-TAATTAAAAA
1 ATTT--ATAATTATTATAATTAAAAA
247085 ATTTATAA
1 ATTTATAA
247093 ATAAATTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 8 0.28
25 15 0.52
26 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTATAATTATTATAATTAAAAA
Found at i:247642 original size:20 final size:19
Alignment explanation
Indices: 247617--247656 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
247607 GCTCGAATCA
247617 ATTTAAAATTTAAAATTATT
1 ATTTAAAATTTAAAA-TATT
*
247637 ATTTAAATTTTAAAATATT
1 ATTTAAAATTTAAAATATT
247656 A
1 A
247657 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAAAATTTAAAATATT
Found at i:248084 original size:23 final size:23
Alignment explanation
Indices: 248058--248104 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
248048 CACATAGTTA
248058 TAGAGTTCATTAATAGATCATTT
1 TAGAGTTCATTAATAGATCATTT
* *
248081 TAGAGTTCATTGATAGATCCTTT
1 TAGAGTTCATTAATAGATCATTT
248104 T
1 T
248105 TTTATGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (23 bp):
TAGAGTTCATTAATAGATCATTT
Found at i:250750 original size:20 final size:20
Alignment explanation
Indices: 250708--250780 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
250698 ACATGGTCTA
***
250708 GTATCGATACATTTCAAGCAT
1 GTATCGATACA-TTCACTTAT
250729 GTATCGATACATTCACTTAT
1 GTATCGATACATTCACTTAT
* *
250749 GTATTGATACATTAACTTATT
1 GTATCGATACATTCACTTA-T
250770 GTATCGATACA
1 GTATCGATACA
250781 AATTGTAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 23 0.51
21 22 0.49
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (20 bp):
GTATCGATACATTCACTTAT
Found at i:252205 original size:33 final size:33
Alignment explanation
Indices: 252168--252234 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
252158 TTCAATGATT
252168 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
252201 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
252234 T
1 T
252235 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:252206 original size:13 final size:13
Alignment explanation
Indices: 252188--252212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
252178 CATAAAATGT
252188 TGTATCGATACAA
1 TGTATCGATACAA
252201 TGTATCGATACA
1 TGTATCGATACA
252213 TATTTTTTTG
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:252337 original size:52 final size:50
Alignment explanation
Indices: 252274--252414 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
252264 CATTACTCAA
*
252274 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAG
* *
252326 ATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAG
252378 ATGTATCGATACACTATTAAATGTATCGATACATGCA
1 ATGTATCGATACACTATT--ATGTATCGATACATGCA
252415 AACAACTTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:258545 original size:22 final size:24
Alignment explanation
Indices: 258489--258551 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 24
258479 TGTTTTTATC
* *
258489 TTTCTTTTCTTTTG-TT-GTTTTG
1 TTTCTTTTGTTTCGCTTCGTTTTG
* *
258511 TTTCTTTTTTTTCGTTTCGTTTT-
1 TTTCTTTTGTTTCGCTTCGTTTTG
258534 TTT-TTTTGTTTCGCTTCG
1 TTTCTTTTGTTTCGCTTCG
258552 GTGCTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 25 0.71
23 5 0.14
24 5 0.14
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.75
Consensus pattern (24 bp):
TTTCTTTTGTTTCGCTTCGTTTTG
Found at i:258848 original size:70 final size:67
Alignment explanation
Indices: 258774--258944 Score: 191
Period size: 68 Copynumber: 2.5 Consensus size: 67
258764 GTTTTATTAT
*** *
258774 TAGCAGCTTAATTGCTTTTTCTTTCATTTCTTCTTGTTCGTTCATCAGCTGACGTTTCTTTCTTA
1 TAGCAGCTTAATTGCTTTTTCTTTCATTTCTT-GAATT-GTCCATCAGCTGACGTTTCTTTCTT-
258839 ATTGC
63 ATTGC
* * * * *
258844 TAGCAGCTTAATTACTTTTTCTTTCA-TGCATGAATTGTCCATCAGCTGCCGTTTCTTTCTTCTT
1 TAGCAGCTTAATTGCTTTTTCTTTCATTTCTTGAATTGTCCATCAGCTGACGTTTCTTTCTTATT
*
258908 GT
66 GC
*
258910 TGCAGCAGCTTAATTGCTTTCTCTTTCATTTCTTG
1 T--AGCAGCTTAATTGCTTTTTCTTTCATTTCTTG
258945 CTGCCACGTC
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
66 4 0.05
67 23 0.27
68 25 0.30
69 7 0.08
70 25 0.30
ACGTcount: A:0.15, C:0.22, G:0.13, T:0.49
Consensus pattern (67 bp):
TAGCAGCTTAATTGCTTTTTCTTTCATTTCTTGAATTGTCCATCAGCTGACGTTTCTTTCTTATT
GC
Found at i:260800 original size:33 final size:33
Alignment explanation
Indices: 260763--260829 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
260753 TTCAACGATT
260763 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
260796 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
260829 T
1 T
260830 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:260801 original size:13 final size:13
Alignment explanation
Indices: 260783--260807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260773 CATAAAATGT
260783 TGTATCGATACAA
1 TGTATCGATACAA
260796 TGTATCGATACA
1 TGTATCGATACA
260808 TATTTTTTTG
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:260888 original size:13 final size:13
Alignment explanation
Indices: 260870--260894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260860 ATTACTCAAA
260870 TGTATCGATACAT
1 TGTATCGATACAT
260883 TGTATCGATACA
1 TGTATCGATACA
260895 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:269229 original size:31 final size:31
Alignment explanation
Indices: 269188--269812 Score: 334
Period size: 31 Copynumber: 20.2 Consensus size: 31
269178 CTTCAAATAC
* *
269188 CTTCTTAAAGTCCATGACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
*
269219 CTTCTCAAAGTCCACGACTCAGTGGCATCCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCA-CCTT
* *
269251 -TTCTTCAAAGTCCACGACTCAGTGGCA-ATCT
1 CTTC-TCAAAGTCCACGACTCCGTGGCACCT-T
* *
269282 CTGCTCAAAGTCCACGACTCAGTGGCATCCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCA-CCTT
* *
269314 -TTCTTCAAAGTCCACGACTCAGTGGCAATCTT
1 CTTC-TCAAAGTCCACGACTCCGTGGC-ACCTT
*
269346 -TGCTCAAAGTCCACGACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* *
269376 CCTT-TCAAAGCCCACAACTCCGTGGCACTCTT
1 -CTTCTCAAAGTCCACGACTCCGTGGCAC-CTT
* *
269408 TTTCCCTTTTAAAGTCCACGACTCCGTGGCACCTT
1 CTT--C--TCAAAGTCCACGACTCCGTGGCACCTT
* * *
269443 CTTTTCAAAGCCCACAACTCCGTGGCACC--
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * * *
269472 CTT-T-TAAGCCCACAACTCCGTGGCACTTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * *
269501 TTTCATCTTTAAGTCCACAACTCCGTGGCACC--
1 CTTC-TC--AAAGTCCACGACTCCGTGGCACCTT
* * * *
269533 CTT-T-TAAGCCCACAACTCCGTGGCACTTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* ** *
269562 TTTCAGCTTTAAGTCCACAACTCCGTGGCACC--
1 CTT---CTCAAAGTCCACGACTCCGTGGCACCTT
* * * *
269594 CTT-T-TAAGCCCACAACTCCGTGGCACTTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * *
269623 TTTCATCTTTAAGTCCACAACTCCGTGGCACC--
1 CTTC-TC--AAAGTCCACGACTCCGTGGCACCTT
* * *
269655 CTT-T-TAAGCCCACAACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * *
269684 -TTCTTTTAAAGCCCACAACTCCGTGGCACCTT
1 CTTC--TCAAAGTCCACGACTCCGTGGCACCTT
* *
269716 CTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTT
1 CTTC---TCAAAGTCCACGACTCCGTGGCAC-CTT
* *
269751 -TT-T-AAAGCCCACAACTCCGTGGCACTCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCAC-CTT
* *
269780 -TT-T-AAAGCCCACAACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
*
269808 TTTCT
1 CTTCT
269813 TTTTAAAGCC
Statistics
Matches: 502, Mismatches: 44, Indels: 97
0.78 0.07 0.15
Matches are distributed among these distances:
27 85 0.17
28 7 0.01
29 62 0.12
30 9 0.02
31 123 0.25
32 91 0.18
33 6 0.01
34 90 0.18
35 8 0.02
36 21 0.04
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (31 bp):
CTTCTCAAAGTCCACGACTCCGTGGCACCTT
Found at i:269293 original size:63 final size:63
Alignment explanation
Indices: 269189--269402 Score: 292
Period size: 63 Copynumber: 3.4 Consensus size: 63
269179 TTCAAATACC
* * * *
269189 TTCTT-AAAGTCCATGACTCCGTGGC-ACCTTCTTCTCAAAGTCCACGACTCAGTGGCATCCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCAATC-TCTGCTCAAAGTCCACGACTCAGTGGCATCCTT
269251 TTCTTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAAGTCCACGACTCAGTGGCATCCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAAGTCCACGACTCAGTGGCATCCTT
* *
269314 TTCTTCAAAGTCCACGACTCAGTGGCAATCTTTGCTCAAAGTCCACGACTCCGTGGCA-CC-T
1 TTCTTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAAGTCCACGACTCAGTGGCATCCTT
* * * *
269375 TCCTTTCAAAGCCCACAACTCCGTGGCA
1 TTC-TTCAAAGTCCACGACTCAGTGGCA
269403 CTCTTTTTCC
Statistics
Matches: 139, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
61 3 0.02
62 28 0.20
63 106 0.76
64 2 0.01
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (63 bp):
TTCTTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAAGTCCACGACTCAGTGGCATCCTT
Found at i:269384 original size:94 final size:95
Alignment explanation
Indices: 269194--269471 Score: 284
Period size: 94 Copynumber: 2.9 Consensus size: 95
269184 ATACCTTCTT
*
269194 AAAGTCCATGACTCCGTGGCA-CCTTCTTC-TCAAAGTCCACGACTCAGTGGC-ATCCTTTTCTT
1 AAAGTCCACGACTCCGTGGCATCCTT-TTCTTCAAAGTCCACGACTCAGTGGCAAT-C-TTTC-T
*
269256 CAAAGTCCACGACTCAGTGGCA--ATCTCTGCTC
62 CAAAGTCCACGACTCCGTGGCACCATCTCTGCTC
*
269288 AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTTTGCTCAA
1 AAAGTCCACGACTCCGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTTT-CTCAA
* *
269353 AGTCCACGACTCCGTGGCACCTTC-CT-TTC
65 AGTCCACGACTCCGTGGCACCATCTCTGCTC
* * * * * *
269382 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACGACTCCGTGGCACCTTCTTT
1 AAAGTCCACGACTCCGTGGCA-TCCTTTT--C-TTCAAAGTCCACGACTCAGTGGCA--ATCTTT
* *
269447 -TCAAAGCCCACAACTCCGTGGCACC
60 CTCAAAGTCCACGACTCCGTGGCACC
269472 CTTTTAAGCC
Statistics
Matches: 158, Mismatches: 14, Indels: 20
0.82 0.07 0.10
Matches are distributed among these distances:
94 67 0.42
95 36 0.23
96 4 0.03
97 1 0.01
98 45 0.28
100 5 0.03
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (95 bp):
AAAGTCCACGACTCCGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTTTCTCAAA
GTCCACGACTCCGTGGCACCATCTCTGCTC
Found at i:269519 original size:34 final size:33
Alignment explanation
Indices: 269383--269942 Score: 430
Period size: 34 Copynumber: 17.6 Consensus size: 33
269373 CTTCCTTTCA
*
269383 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCACT-TTTTT-CATTTT
* *
269418 AAAGTCCACGACTCCGTGGCACCTTCTTTTCA----
1 -AAGCCCACAACTCCGTGGCA-CTT-TTTTCATTTT
*
269450 AAGCCCACAACTCCGTGGCAC------CCTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
269477 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCAT-TTT
* *
269511 AAGTCCACAACTCCGTGGCAC------CCTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
*
269538 AAGCCCACAACTCCGTGGCACTTTTTTCAGCTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCA-TTTT
* *
269572 AAGTCCACAACTCCGTGGCAC------CCTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
269599 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCAT-TTT
* *
269633 AAGTCCACAACTCCGTGGCAC------CCTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
*
269660 AAGCCCACAACTCCGTGGCAC-CTTTTC-TTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
* *
269691 AAAGCCCACAACTCCGTGGCACCTTCTTC-TTTT
1 -AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
269724 CAAAGCCCACAACTCCGTGGCACTCTTTTT-A----
1 --AAGCCCACAACTCCGTGGCACT-TTTTTCATTTT
269755 AAGCCCACAACTCCGTGGCACTCTTTTT-A----
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATTTT
* *
269784 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
*
269817 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 -AAGCCCACAACTCCGTGGCACT-TTTTT-CATTTT
* *
269853 CAAAGCCCACAACTTCGTGGCACCTTTTT-ATTTT
1 --AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
*
269887 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 -AAGCCCACAACTCCGTGGCACT-TTTTT-CATTTT
* * *
269923 AAGTCCACAAGTCGGTGGCA
1 AAGCCCACAACTCCGTGGCA
269943 ATCACTCTCC
Statistics
Matches: 438, Mismatches: 37, Indels: 99
0.76 0.06 0.17
Matches are distributed among these distances:
23 1 0.00
27 90 0.21
28 10 0.02
29 50 0.11
30 1 0.00
31 22 0.05
32 22 0.05
33 34 0.08
34 121 0.28
35 26 0.06
36 34 0.08
37 27 0.06
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.30
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATTTT
Found at i:269526 original size:61 final size:60
Alignment explanation
Indices: 269411--269914 Score: 546
Period size: 61 Copynumber: 8.1 Consensus size: 60
269401 CACTCTTTTT
* *
269411 CCCTTTTAAAGTCCACGACTCCGTGGCACCTTCTTTTCA----AAGCCCACAACTCCGTGGCA
1 CCCTTTT-AAGCCCACAACTCCGTGGCA-CTT-TTTTCATTTTAAGCCCACAACTCCGTGGCA
*
269470 CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCAT-TTTAAGCCCACAACTCCGTGGCA
* *
269531 CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCAGCTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCA-TTTTAAGCCCACAACTCCGTGGCA
*
269592 CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCAT-TTTAAGCCCACAACTCCGTGGCA
*
269653 CCCTTTTAAGCCCACAACTCCGTGGCAC-CTTTTC-TTTTAAAGCCCACAACTCCGTGGCA
1 CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATTTT-AAGCCCACAACTCCGTGGCA
269712 CCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTT-A----AAGCCCACAACTCCGTG
1 -C--C--CTTTT--AAGCCCACAACTCCGTGGCACT-TTTTTCATTTTAAGCCCACAACTCCGTG
269772 GCA
58 GCA
* * *
269775 CTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCA
1 C-CCTTTT-AAGCCCACAACTCCGTGGCACTTTTTTCATTTT-AAGCCCACAACTCCGTGGCA
* *
269838 CTCTTTTTCCCTTTTCAAAGCCCACAACTTCGTGGCACCTTTTT-ATTTTAAAGCCCACAACTCC
1 --------CCCTTTT--AAGCCCACAACTCCGTGGCACTTTTTTCATTTT-AAGCCCACAACTCC
269902 GTGGCA
55 GTGGCA
*
269908 CTCTTTT
1 CCCTTTT
269915 TCCCTTTTAA
Statistics
Matches: 397, Mismatches: 15, Indels: 63
0.84 0.03 0.13
Matches are distributed among these distances:
56 6 0.02
57 8 0.02
58 43 0.11
59 31 0.08
60 6 0.02
61 167 0.42
62 8 0.02
63 40 0.10
64 5 0.01
66 21 0.05
68 4 0.01
70 30 0.08
71 28 0.07
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.31
Consensus pattern (60 bp):
CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATTTTAAGCCCACAACTCCGTGGCA
Found at i:269561 original size:25 final size:26
Alignment explanation
Indices: 269508--269563 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
269498 TTTTTTCATC
*
269508 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGCCCACAACTCCGTGGCA-CCT
*
269535 TTTAAGCCCACAACTCCGTGGCACTT
1 TTTAAGCCCACAACTCCGTGGCACCT
269561 TTT
1 TTT
269564 TCAGCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.30
Consensus pattern (26 bp):
TTTAAGCCCACAACTCCGTGGCACCT
Found at i:269622 original size:25 final size:26
Alignment explanation
Indices: 269569--269624 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
269559 TTTTTTCAGC
*
269569 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGCCCACAACTCCGTGGCA-CCT
*
269596 TTTAAGCCCACAACTCCGTGGCACTT
1 TTTAAGCCCACAACTCCGTGGCACCT
269622 TTT
1 TTT
269625 TCATCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.30
Consensus pattern (26 bp):
TTTAAGCCCACAACTCCGTGGCACCT
Found at i:269914 original size:70 final size:71
Alignment explanation
Indices: 269777--269922 Score: 258
Period size: 70 Copynumber: 2.1 Consensus size: 71
269767 CCGTGGCACT
* *
269777 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCATTTTAAAGCCCACAACTCCGTGGCACTCT
269842 TTTTCC
66 TTTTCC
*
269848 CTTTTCAAAGCCCACAACTTCGTGGCACCTTTTT-ATTTTAAAGCCCACAACTCCGTGGCACTCT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCATTTTAAAGCCCACAACTCCGTGGCACTCT
269912 TTTTCC
66 TTTTCC
269918 CTTTT
1 CTTTT
269923 AAGTCCACAA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 40 0.56
71 32 0.44
ACGTcount: A:0.20, C:0.33, G:0.11, T:0.36
Consensus pattern (71 bp):
CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCATTTTAAAGCCCACAACTCCGTGGCACTCT
TTTTCC
Found at i:269967 original size:33 final size:33
Alignment explanation
Indices: 269928--270009 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
269918 CTTTTAAGTC
*
269928 CACAAGTCGGTGGCAATCACTCTCCAAAGCCCA
1 CACAAGTCGGTGGCAATCACCCTCCAAAGCCCA
* *
269961 TACAAGTCGGTGGCAATCACCCTCTAAAGCCCA
1 CACAAGTCGGTGGCAATCACCCTCCAAAGCCCA
269994 CACAAGTCGGTGGCAA
1 CACAAGTCGGTGGCAA
270010 CCCTTTTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.16
Consensus pattern (33 bp):
CACAAGTCGGTGGCAATCACCCTCCAAAGCCCA
Found at i:270117 original size:49 final size:49
Alignment explanation
Indices: 270014--270661 Score: 780
Period size: 49 Copynumber: 13.8 Consensus size: 49
270004 TGGCAACCCT
* *
270014 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * *
270057 TTTAAGCCCAATATAGCTGGCCTTGGATCAGCATTTTAGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
270106 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
270149 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
**
270198 TTTAACCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
270247 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
270290 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
**
270339 TTTAACCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
270388 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
270431 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
270480 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * * *
270523 TTTAAGTCCAATATCGCTGGCCTTGACTCAGCACATTGGTACCTTCACC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
* *
270572 TTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACATTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATC
* * *
270624 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
270662 ACATCCTTTT
Statistics
Matches: 519, Mismatches: 53, Indels: 57
0.83 0.08 0.09
Matches are distributed among these distances:
43 190 0.37
45 4 0.01
47 5 0.01
49 281 0.54
51 2 0.00
52 37 0.07
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:270171 original size:92 final size:92
Alignment explanation
Indices: 270014--270613 Score: 825
Period size: 92 Copynumber: 6.5 Consensus size: 92
270004 TGGCAACCCT
*
270014 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
* * *
270079 TTGGATCAGCATTTTAGCACCTTCATC
66 TTGAATCAGCATATTGGCACCTTCATC
*
270106 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
270171 TTGAATCAGCATATTGGCACCTTCATC
66 TTGAATCAGCATATTGGCACCTTCATC
** * * *
270198 TTTAACCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAG
*
270263 CTGGCCTTGAATCAGCACATTGGCA----C--C
60 CTGGCCTTGAATCAGCATATTGGCACCTTCATC
* * * **
270290 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAACCCCAATATAG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAG
270355 CTGGCCTTGAATCAGCATATTGGCACCTTCATC
60 CTGGCCTTGAATCAGCATATTGGCACCTTCATC
*
270388 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
270453 TTGAATCAGCATATTGGCACCTTCATC
66 TTGAATCAGCATATTGGCACCTTCATC
*
270480 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
* * * *
270545 TTGACTCAGCACATTGGTACCTTCACC
66 TTGAATCAGCATATTGGCACCTTCATC
* * *
270572 TTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCAC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
270614 ATTTTCCATC
Statistics
Matches: 464, Mismatches: 32, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
92 382 0.82
94 2 0.00
96 2 0.00
98 78 0.17
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
TTGAATCAGCATATTGGCACCTTCATC
Found at i:270262 original size:141 final size:141
Alignment explanation
Indices: 270014--270661 Score: 942
Period size: 141 Copynumber: 4.6 Consensus size: 141
270004 TGGCAACCCT
* * *
270014 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGCCCAATATAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGCCCAATATAG
* * *
270073 CTGGCCTTGGATCAGCATTTTAGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
270138 ACATTGGCACC
131 ACATTGGCACC
*
270149 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAACCCCAATATAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGCCCAATATAG
270214 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
270279 ACATTGGCACC
131 ACATTGGCACC
*
270290 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAACCCCAATATAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGCCCAATATAG
270355 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
270420 ACATTGGCACC
131 ACATTGGCACC
* *
270431 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGCCCAATATAG
* * * *
270496 CTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGACTCAGC
66 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
270555 ACATTGGTACCTTCACC
131 ACATTGG------CACC
* * * ** *
270572 TTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACATTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTTTAAGCCCAATA
*
270637 TAGCTGGCCTTGAATCAGCACATTG
63 TAGCTGGCCTTGAATCAGCATATTG
270662 ACATCCTTTT
Statistics
Matches: 480, Mismatches: 18, Indels: 21
0.92 0.03 0.04
Matches are distributed among these distances:
135 75 0.16
137 1 0.00
139 1 0.00
141 360 0.75
143 2 0.00
144 41 0.09
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (141 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGCCCAATATAG
CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
ACATTGGCACC
Found at i:270444 original size:233 final size:233
Alignment explanation
Indices: 270014--270670 Score: 984
Period size: 233 Copynumber: 2.8 Consensus size: 233
270004 TGGCAACCCT
* *
270014 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
* * * * *
270079 TTGGATCAGCATTTTAGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
66 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
* * *
270144 GCA---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAC
131 GCACTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---TC--CTTTAAC
270204 CCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
191 CCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
270247 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
**
270312 TTGAATCAGCATATTGGCACCTTCATCTTTAACCCCAATATAGCTGGCCTTGAATCAGCATATTG
66 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
**
270377 GCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTTAAGTCCA
131 GCA-CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCCTTTAACCCCA
*
270441 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
195 ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
270480 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
* * * * *
270545 TTGACTCAGCACATTGGTACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTG
66 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
* *
270610 GCACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
131 GCAC---TT-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCCTTT
270671 TTCTCATCAT
Statistics
Matches: 389, Mismatches: 24, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
232 1 0.00
233 297 0.76
235 3 0.01
236 43 0.11
237 6 0.02
239 39 0.10
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (233 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCC
TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
GCACTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCCTTTAACCCCAA
TATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
Found at i:270644 original size:52 final size:54
Alignment explanation
Indices: 270522--270788 Score: 188
Period size: 52 Copynumber: 4.8 Consensus size: 54
270512 ACATTGGCAC
* * * * * *
270522 CTTTAAGTCCAATATCGCTGGCCTTGACTCAGCACATTGGTACC----T-TCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCATTTTCTCAT
270571 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCATTTTCTCAT
* * * * * *
270623 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCA-CCATTTTCTCAT
* * * * *
270678 CATTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCA-C-----CA--TTT-TC-TC---
270743 AT
53 AT
* *
270745 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACC
270789 TTCATCATCT
Statistics
Matches: 169, Mismatches: 29, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
48 1 0.01
49 37 0.22
52 40 0.24
54 6 0.04
55 37 0.22
60 1 0.01
61 1 0.01
62 3 0.02
63 2 0.01
64 2 0.01
66 1 0.01
67 38 0.22
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCATTTTCTCAT
Found at i:271630 original size:33 final size:33
Alignment explanation
Indices: 271593--271659 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
271583 TTCAACGATT
271593 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
271626 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
271659 T
1 T
271660 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:271631 original size:13 final size:13
Alignment explanation
Indices: 271613--271637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
271603 CATAAAATGT
271613 TGTATCGATACAA
1 TGTATCGATACAA
271626 TGTATCGATACA
1 TGTATCGATACA
271638 TATTTTTTTG
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:271718 original size:13 final size:13
Alignment explanation
Indices: 271700--271724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
271690 ATTACTCAAA
271700 TGTATCGATACAT
1 TGTATCGATACAT
271713 TGTATCGATACA
1 TGTATCGATACA
271725 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:271826 original size:52 final size:52
Alignment explanation
Indices: 271733--271860 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
271723 CACTGATCTT
*
271733 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
271784 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
271836 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
271861 TAATATTTTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:277376 original size:19 final size:20
Alignment explanation
Indices: 277334--277385 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
277324 TACCAGTTTT
* *
277334 ATGTATTGATACAATTGAGT
1 ATGTATCGATACAATTGAGC
277354 ATGTATCGATACAA-TGAGC
1 ATGTATCGATACAATTGAGC
277373 ATGTATCGATACA
1 ATGTATCGATACA
277386 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTGAGC
Found at i:277392 original size:13 final size:13
Alignment explanation
Indices: 277374--277398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277364 ACAATGAGCA
277374 TGTATCGATACAT
1 TGTATCGATACAT
277387 TGTATCGATACA
1 TGTATCGATACA
277399 AAGCATAATG
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:277417 original size:33 final size:32
Alignment explanation
Indices: 277355--277419 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
277345 CAATTGAGTA
* *
277355 TGTATCGATACAATGAGCATGTATCGATACAT
1 TGTATCGATACAAAGAGAATGTATCGATACAT
* *
277387 TGTATCGATACAAAGCATAATGTATTGATACAT
1 TGTATCGATACAAAG-AGAATGTATCGATACAT
277420 CTAGATGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAAAGAGAATGTATCGATACAT
Found at i:285021 original size:8 final size:9
Alignment explanation
Indices: 284999--285039 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
284989 AAAAGCTCTT
284999 GAAAAATGA
1 GAAAAATGA
285008 GAAAAATGA
1 GAAAAATGA
285017 GAAAAATGA
1 GAAAAATGA
285026 GAAAAATGA
1 GAAAAATGA
*
285035 TAAAA
1 GAAAA
285040 CTTTGAATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (9 bp):
GAAAAATGA
Found at i:285375 original size:19 final size:19
Alignment explanation
Indices: 285332--285387 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
285322 CTACTAGTTT
285332 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
285352 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
* *
285371 CATGTATTGATAGAATG
1 CATGTATCGATACAATG
285388 TATCGATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:286236 original size:108 final size:109
Alignment explanation
Indices: 285916--286497 Score: 574
Period size: 110 Copynumber: 5.5 Consensus size: 109
285906 ACTAAACAAG
* * * * * * * *
285916 CCTATTTCAAGGCCAATCTATTGGTGCTTGAGTACTATGTATTTTATGCTAAAATGAATTATCTT
1 CCTATTTCGAGGCCAATCTCTTGGTGCCTGAATACTATGTAATTAATGCAAAAATGAATTATCCT
* * ** * *
285981 ATGTAAAAGGCATTCGTGCGCTACTTTATGACTCTAAACAATGA
66 ATATAAAGGGCATTCGTATGCCACTTTATGACTCTAGACAATGA
* * * *
286025 CCTATTTCGAAGCCACTTTTTTGGTGCCTGAAT-CTATGTAATTAATGCAATTAAATGAATTATC
1 CCTATTTCGAGGCCAATCTCTTGGTGCCTGAATACTATGTAATTAATGCAA--AAATGAATTATC
* *
286089 CTATATAAAGGGCATTCGTATGCCATTTTATGACTCTAGACAGTGA
64 CTATATAAAGGGCATTCGTATGCCACTTTATGACTCTAGACAATGA
* *
286135 CCTATTTCGAGGCCAATCCCTTGGTGCCTGAAT-CTACGTAATTAATGCAAAAATGAATTATCCT
1 CCTATTTCGAGGCCAATCTCTTGGTGCCTGAATACTATGTAATTAATGCAAAAATGAATTATCCT
* *
286199 ATATAAAGGGCATTTGTATGCCACTTTATGGCTCTAGACAATGA
66 ATATAAAGGGCATTCGTATGCCACTTTATGACTCTAGACAATGA
* *
286243 CCTATTTC-AGGGCCAATCTCTTGGTGCCTGAATACTATGTAATTTATACAAAAAATGAATTATC
1 CCTATTTCGA-GGCCAATCTCTTGGTGCCTGAATACTATGTAATTAATGC-AAAAATGAATTATC
* * ** *
286307 CTATATAAAGGGCATCCGTACGCCA--TTACAACTCTAAACAATG-
64 CTATATAAAGGGCATTCGTATGCCACTTTATGACTCTAGACAATGA
* * * *
286350 ---A--T------CTAT-T-TTGGTGCCCGAATACTATGTAATTTATGCGAAAAATTAATTATCC
1 CCTATTTCGAGGCCAATCTCTTGGTGCCTGAATACTATGTAATTAATGC-AAAAATGAATTATCC
* **
286402 TATATAAAGGGCATTTGTATGCCACTTTACAACTCTAGACAATGA
65 TATATAAAGGGCATTCGTATGCCACTTTATGACTCTAGACAATGA
** * ** *
286447 TTTATTTCGAGGCCAGTC-CTTTGGTGCCTGAATACTACATAGTTAATGCAA
1 CCTATTTCGAGGCCAATCTC-TTGGTGCCTGAATACTATGTAATTAATGCAA
286498 TTAAATCCCA
Statistics
Matches: 395, Mismatches: 56, Indels: 44
0.80 0.11 0.09
Matches are distributed among these distances:
94 62 0.16
95 1 0.00
96 20 0.05
100 1 0.00
102 2 0.01
104 1 0.00
107 1 0.00
108 114 0.29
109 40 0.10
110 153 0.39
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (109 bp):
CCTATTTCGAGGCCAATCTCTTGGTGCCTGAATACTATGTAATTAATGCAAAAATGAATTATCCT
ATATAAAGGGCATTCGTATGCCACTTTATGACTCTAGACAATGA
Found at i:286242 original size:218 final size:215
Alignment explanation
Indices: 285907--286503 Score: 625
Period size: 218 Copynumber: 2.8 Consensus size: 215
285897 ACCTTTACGA
* * * *
285907 CTAAACAA-G-CCTATTTCAAGGCCAATCTATTGGTGCTTGAGTACTATGTATTTTATGCTAAAA
1 CTAAACAATGACCTATTTC-AGGCCAATC--TTGGTGCCTGAATACTATGTAATTTATGCAAAAA
* * * * ** * *
285970 TGAATTATCTTATGTAAAAGGCATTCGTGCGCTACTTTATGACTCTAAACAATGACCTATTTCGA
63 TGAATTATCCTATATAAAGGGCATTTGTATGCCACTTTATGACTCTAGACAATGACCTATTTCGA
* * *
286035 AGCCACTTTTTTGGTGCCTGAAT-CTATGTAATTAATGCAATTAAATGAATTATCCTATATAAAG
128 GGCCAATCTTTTGGTGCCTGAATACTATGTAATTAATGCAATTAAATGAATTATCCTATATAAAG
* * **
286099 GGCATTCGTATGCCATTTTATGACT
193 GGCATCCGTACGCCA--TTACAACT
* * * *
286124 CTAGACAGTGACCTATTTCGAGGCCAATCCCTTGGTGCCTGAAT-CTACGTAATTAATGCAAAAA
1 CTAAACAATGACCTATTTC-AGGCCAAT--CTTGGTGCCTGAATACTATGTAATTTATGCAAAAA
*
286188 TGAATTATCCTATATAAAGGGCATTTGTATGCCACTTTATGGCTCTAGACAATGACCTATTTC-A
63 TGAATTATCCTATATAAAGGGCATTTGTATGCCACTTTATGACTCTAGACAATGACCTATTTCGA
* * * *
286252 GGGCCAATCTCTTGGTGCCTGAATACTATGTAATTTATACAA-AAAATGAATTATCCTATATAAA
128 -GGCCAATCTTTTGGTGCCTGAATACTATGTAATTAATGCAATTAAATGAATTATCCTATATAAA
286316 GGGCATCCGTACGCCATTACAACT
192 GGGCATCCGTACGCCATTACAACT
* * *
286340 CTAAACAATGATCTA--T--------T-TTGGTGCCCGAATACTATGTAATTTATGCGAAAAATT
1 CTAAACAATGACCTATTTCAGGCCAATCTTGGTGCCTGAATACTATGTAATTTATGC-AAAAATG
** **
286394 AATTATCCTATATAAAGGGCATTTGTATGCCACTTTACAACTCTAGACAATGATTTATTTCGAGG
65 AATTATCCTATATAAAGGGCATTTGTATGCCACTTTATGACTCTAGACAATGACCTATTTCGAGG
* * ** *
286459 CCAGTCCTTTGGTGCCTGAATACTACATAGTTAATGCAATTAAAT
130 CCAATCTTTTGGTGCCTGAATACTATGTAATTAATGCAATTAAAT
286504 CCCAAAGAGG
Statistics
Matches: 320, Mismatches: 50, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
202 12 0.04
203 13 0.04
204 95 0.30
205 6 0.02
214 1 0.00
216 18 0.06
217 7 0.02
218 125 0.39
219 42 0.13
221 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (215 bp):
CTAAACAATGACCTATTTCAGGCCAATCTTGGTGCCTGAATACTATGTAATTTATGCAAAAATGA
ATTATCCTATATAAAGGGCATTTGTATGCCACTTTATGACTCTAGACAATGACCTATTTCGAGGC
CAATCTTTTGGTGCCTGAATACTATGTAATTAATGCAATTAAATGAATTATCCTATATAAAGGGC
ATCCGTACGCCATTACAACT
Found at i:287042 original size:3 final size:3
Alignment explanation
Indices: 287034--287084 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
287024 AACAAATATT
287034 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
287082 ATA
1 ATA
287085 TCACCTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:287354 original size:8 final size:8
Alignment explanation
Indices: 287341--287413 Score: 53
Period size: 8 Copynumber: 8.9 Consensus size: 8
287331 TAGGCTATCC
287341 TTTTCTTT
1 TTTTCTTT
287349 TTTTC-TT
1 TTTTCTTT
287356 TTTTC--T
1 TTTTCTTT
*
287362 TTTCCTTT
1 TTTTCTTT
287370 TTTTCCTCTT
1 TTTT-CT-TT
287380 TTCTTCTCTT
1 TT-TTCT-TT
*
287390 TTCTTATTT
1 TT-TTCTTT
*
287399 TTTTCTTA
1 TTTTCTTT
287407 TTTTCTT
1 TTTTCTT
287414 CTCTCTTCCT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
6 5 0.09
7 7 0.13
8 20 0.36
9 6 0.11
10 15 0.27
11 2 0.04
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCTTT
Found at i:287371 original size:21 final size:20
Alignment explanation
Indices: 287340--287405 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 20
287330 TTAGGCTATC
287340 CTTTTCTTTTTTTCTTTTTT
1 CTTTTCTTTTTTTCTTTTTT
*
287360 CTTTTCCTTTTTTTCCTCTTTT
1 CTTTT-CTTTTTTT-CTTTTTT
*
287382 CTTCTCTTTTCTTAT-TTTTTT
1 CTTTTCTTTT-TT-TCTTTTTT
287403 CTT
1 CTT
287406 ATTTTCTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 5 0.13
21 21 0.54
22 12 0.31
23 1 0.03
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
CTTTTCTTTTTTTCTTTTTT
Found at i:290782 original size:5 final size:5
Alignment explanation
Indices: 290772--290808 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
290762 TGCTAGATAA
290772 GCATG GCATG GCATG GCATG GCATG GATCATG GCATG
1 GCATG GCATG GCATG GCATG GCATG G--CATG GCATG
290809 AAAATGCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 25 0.83
7 5 0.17
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.22
Consensus pattern (5 bp):
GCATG
Found at i:292474 original size:165 final size:166
Alignment explanation
Indices: 292183--293087 Score: 743
Period size: 167 Copynumber: 5.6 Consensus size: 166
292173 TTCAAGCATC
* * ** * *
292183 AAAATTCTTCAAATATTATCATTTAAATCACATTAAATCAGTTTTGAAAAATTTCTTTCATTTT-
1 AAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTT-AAAAAATTCTTTCATTTTC
* * *
292247 -TTA----TTGACTTTCTT-TTGAAA-TTCTTCATATTTTCAAAATAC-GAGATTTTCTTCT-TC
65 ATTAGTTTTTGAATTTTTTCTTGAAATTTCTT--TATTTTCAAAATACAGAG-TTTTCTACTCT-
* * * *
292303 GTAAATTTTTTCGGGAGGA-TTTTCATGGGTTTAAATTTTT
126 GTAAATTTTTTCGGGAGGATTTTTCTTAGTTTTTAATTTTT
** * *
292343 TTAATTCATCAAATATTATTATTTA-TTCATATTAAATCAGTTTTCAAAAGTTCTTTCATTTTCA
1 AAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTAAAAAATTCTTTCATTTTCA
*
292407 TTAGTTTTTGAATTTTTTCGTTGAAATTTCTTTGTTTTCAAAATACAGAGTTTTCTACTCTGTAA
66 TTAGTTTTTGAATTTTTTC-TTGAAATTTCTTTATTTTCAAAATACAGAGTTTTCTACTCTGTAA
* *
292472 ATTTTTTTGAGGA-GATTTTT-TTTGATTTTTAATTTCTT
130 ATTTTTTCG-GGAGGATTTTTCTTAG-TTTTTAATTT-TT
* *
292510 -AAATTCATCAAATATTATTATTTATTTTATAGTAAATCAGTTTTAAAAAATT-TCTTCATTTTC
1 AAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTAAAAAATTCT-TTCATTTTC
* * * ** *
292573 ATTTGTTTTT-TATTTTTTCTTGAAATTTTCTTGT-TTTT-GAAATATGGAGTTTTGTACTC---
65 ATTAGTTTTTGAATTTTTTCTTGAAA-TTTCTT-TATTTTCAAAATACAGAGTTTTCTACTCTGT
* *
292632 --------CCGAGGA-GATTTTTCTTAATTTTTAATTTTT
128 AAATTTTTTCG-GGAGGATTTTTCTTAGTTTTTAATTTTT
* * * * *
292663 AAAATTCATAAAATATTATTATTTACTTT-ACATTAAATTAGTTTTCAAAAATTCCTTCATTTTC
1 AAAATTCATCAAATATTATTATTTA-TTTCATATTAAATCAGTTTTAAAAAATTCTTTCATTTTC
** * * ** *
292727 ATTA-TTTTTTTATTTTTTCTCTAAAATTT-TCTATTTTTGAAATACGGAGTTTTCTACT-TCGT
65 ATTAGTTTTTGAATTTTTTCT-TGAAATTTCTTTATTTTCAAAATACAGAGTTTTCTACTCT-GT
* * * *
292789 ATATTTTTTTGGGAGGATTTTTCTTGGTTGTTAATTTTT
128 AAATTTTTTCGGGAGGATTTTTCTTAGTTTTTAATTTTT
* * * * * *
292828 AAAATCCATAAAATATTATTATTTATTTTATATTAAATTAGTTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTAAAAAATTCTTTCATTTTCA
* * * * * *
292893 TGAGTTGTTAAATTTTTTCCTTG-AATTT-TTCCTATTTTGAAAGTACAGAGTTTTCTACTCTCT
66 TTAGTTTTTGAATTTTTT-CTTGAAATTTCTT--TATTTTCAAAATACAGAGTTTTCTACTCTGT
* *
292956 AAATTTTTT-TGGAGAAATTTTTCTTAGTTTTTAATTTTT
128 AAATTTTTTCGGGAG-GATTTTTCTTAGTTTTTAATTTTT
* * * * **
292995 AAAATCCATCAAATATTATTATTTATTTCATATGAAATCATTTTTAAAAAATTTCATTCATCATC
1 AAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTAAAAAA-TTCTTTCATTTTC
* *
293060 ATGAGTTTTTGATTTTTTTCTTGAAATT
65 ATTAGTTTTTGAATTTTTTCTTGAAATT
293088 CTCCTTTTGC
Statistics
Matches: 618, Mismatches: 78, Indels: 90
0.79 0.10 0.11
Matches are distributed among these distances:
152 1 0.00
153 12 0.02
154 108 0.17
155 9 0.01
158 16 0.03
159 17 0.03
160 24 0.04
164 15 0.02
165 148 0.24
166 83 0.13
167 153 0.25
168 32 0.05
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (166 bp):
AAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTAAAAAATTCTTTCATTTTCA
TTAGTTTTTGAATTTTTTCTTGAAATTTCTTTATTTTCAAAATACAGAGTTTTCTACTCTGTAAA
TTTTTTCGGGAGGATTTTTCTTAGTTTTTAATTTTT
Found at i:292654 original size:154 final size:154
Alignment explanation
Indices: 292482--293087 Score: 540
Period size: 154 Copynumber: 3.8 Consensus size: 154
292472 ATTTTTTTGA
* * * * *
292482 GGAGATTTTTTTTGATTTTTAATTTCTT-AAATTCATCAAATATTATTATTTATTTTATAGTAAA
1 GGAGATTTTTCTTAATTTTTAATTT-TTAAAATCCATAAAATATTATTATTTATTTTATATTAAA
**
292546 TCAGTTTTAAAAAATTTC-TTCATTTTCATTTGTTTTTTATTTTTTCTTGAAATTTTCTTGTTTT
65 TCAGTTTTAAAAAATTTCATTCATTTTCATGAGTTTTTTATTTTTTCTTGAAATTTTC-T-TTTT
* *
292610 TGAAATATGGAGTTTTGTACTCCCGA-
128 TGAAATACGGAGTTTTCTACTCCCGAT
* * *
292636 GGAGATTTTTCTTAATTTTTAATTTTTAAAATTCATAAAATATTATTATTTACTTTACATTAAAT
1 GGAGATTTTTCTTAATTTTTAATTTTTAAAATCCATAAAATATTATTATTTATTTTATATTAAAT
* * * * * *
292701 TAGTTTTCAAAAA-TTCCTTCATTTTCATTATTTTTTTATTTTTTCTCTAAAATTTTCTATTTTT
66 CAGTTTTAAAAAATTTCATTCATTTTCATGAGTTTTTTATTTTTTCT-TGAAATTTTCT-TTTTT
*
292765 GAAATACGGAGTTTTCTACT-TCGTATATTTTTTT
129 GAAATACGGAGTTTTCTACTCCCG---A------T
** *
292799 GGGAGGATTTTTCTTGGTTGTTAATTTTTAAAATCCATAAAATATTATTATTTATTTTATATTAA
1 -GGA-GATTTTTCTTAATTTTTAATTTTTAAAATCCATAAAATATTATTATTTATTTTATATTAA
* * ** * *
292864 ATTAGTTTTCAAAAA-TTCATTCATTTTCATGAGTTGTTAAATTTTTTCCTTGAATTTTTCCTAT
64 ATCAGTTTTAAAAAATTTCATTCATTTTCATGAGTT-TTTTATTTTTT-CTTGAAATTTT-CTTT
* **
292928 TTTGAAAGTACAGAGTTTTCTACTCTCTAAATTTTTTT
126 TTTGAAA-TACGGAGTTTTCTACTC-C-CGA------T
* * * *
292966 GGAGAAATTTTTCTTAGTTTTTAATTTTTAAAATCCATCAAATATTATTATTTATTTCATATGAA
1 GGAG--ATTTTTCTTAATTTTTAATTTTTAAAATCCATAAAATATTATTATTTATTTTATATTAA
* ** *
293031 ATCATTTTTAAAAAATTTCATTCATCATCATGAGTTTTTGATTTTTTTCTTGAAATT
64 ATCAGTTTTAAAAAATTTCATTCATTTTCATGAGTTTTTTA-TTTTTTCTTGAAATT
293088 CTCCTTTTGC
Statistics
Matches: 380, Mismatches: 46, Indels: 39
0.82 0.10 0.08
Matches are distributed among these distances:
153 7 0.02
154 118 0.31
155 9 0.02
156 1 0.00
164 3 0.01
165 87 0.23
166 27 0.07
167 104 0.27
168 24 0.06
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.53
Consensus pattern (154 bp):
GGAGATTTTTCTTAATTTTTAATTTTTAAAATCCATAAAATATTATTATTTATTTTATATTAAAT
CAGTTTTAAAAAATTTCATTCATTTTCATGAGTTTTTTATTTTTTCTTGAAATTTTCTTTTTTGA
AATACGGAGTTTTCTACTCCCGAT
Done.